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01/02 Catalog

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OGI School of Science &

Engineering

www.ogi.edu/catalog

20000 N.W. Walker Road • Beaverton, OR • 97006-8921phone (503) 748-1027 toll free (800) 685-2423 fax (503) 748-1285

e-mail [email protected] URL www.ogi.edu

www.ogi.edu/catalog

01/02Catalog

OGI School of Science &

Engineering

TA B L E O F C O N T E N T S | O G I

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W E L C O M E T O T H E O G I S C H O O L O F S C I E N C E & E N G I N E E R I N G

H I S T O R I C A L B A C K G R O U N D A N D R E C E N T M E R G E R . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4

A C A D E M I C C A L E N D A R . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4

L E T T E R F R O M T H E D E A N . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5

S C H O O L M I S S I O N . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5

E Q U A L O P P O R T U N I T Y . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5

A B O U T T H I S C ATA L O G . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5

O V E R V I E W

A C A D E M I C D E P A R T M E N T S . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6

D E G R E E P R O G R A M S . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6

C E R T I F I C AT E P R O G R A M S . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6

S T U D E N T S N O T S E E K I N G D E G R E E S . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6

C O L L A B O R AT I V E / J O I N T P R O G R A M S . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6

A C C R E D I TAT I O N . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6

A D M I S S I O N S P R O C E D U R E S . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6

T U I T I O N / F I N A N C E S . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7

A C A D E M I C P O L I C I E S . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7

S C H O O L C A M P U S

G E O G R A P H I C S E T T I N G . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9

L I B R A R Y . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9

C O M P U T E R FA C I L I T I E S . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9

H O U S I N G . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9

S T U D E N T C O U N C I L . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9

A C A D E M I C D E P A R T M E N T S / P R O G R A M S / R E S E A R C H / FA C U LT Y

B I O C H E M I S T R Y A N D M O L E C U L A R B I O L O G Y . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1 1

C O M P U T E R S C I E N C E A N D E N G I N E E R I N G . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2 3

E L E C T R I C A L A N D C O M P U T E R E N G I N E E R I N G . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4 5

E N V I R O N M E N TA L S C I E N C E A N D E N G I N E E R I N G . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6 7

M A N A G E M E N T I N S C I E N C E A N D T E C H N O L O G Y . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7 9

O G I | AC A D E M I C C A L E N DA R

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WELCOME

H I S T O R I C A L B A C K G R O U N D

The OGI School of Science & Engineering’sroots go back to the early 1960s whenOregon Governor Mark Hatfield and anadvisory committee of industrial andeducational leaders recommended creatingan independent institution for graduateeducation and research in the Portlandmetropolitan area. In 1963 they establishedthe Oregon Graduate Center for Study andResearch, which changed its name toOregon Graduate Institute of Science andTechnology in 1989.

By the 1990s OGI had emerged as a matureinstitution, and over the course of thedecade it awarded more than 1,000graduate degrees, offered hundreds ofcontinuing education classes andworkshops, and pursued more than $100million in largely federally funded research.Then, in July 2001, laying the groundworkfor the next phase of the institution’sgrowth, OGI merged with Oregon Health& Science University, becoming OHSU’sfourth school alongside the Schools ofDentistry, Medicine and Nursing.

The merger was particularly timely becauseof the growing need for collaborationbetween the health sciences, theinformation sciences and the environmentalsciences. The resulting benefits will includethe design of new medical instrumentation,the development of bioinformaticsdatabases, a better understanding of therelationship between the environment andhuman health, and the cross-fertilizationthat takes place whenever interdisciplinaryinvestigations occur. The merger is alsohelping OGI expand its programs incomputer science, computer engineeringand environmental science.

2 0 0 1 | 2 0 0 2 A C A D E M I C C A L E N D A R

FALL QUARTER 2001

August 6 Registration begins for fall quarter

September 20 Last day to register without late fees

September 21 New student orientation (Dept of Grad.Ed closed 1-5 p.m.)

September 24 Fall quarter instruction begins

November 12 Registration begins for winter quarter

November 22-23 Thanksgiving holiday (no classes, OGI offices closed)

December 3-7 Final exams

December 25 Christmas holiday (OGI offices closed)

WINTER QUARTER 2002

November 12 Registration begins for winter quarter

January 1 New Year’s holiday (OGI offices closed)

January 3 Last day to register without late fees

January 7 Winter quarter instruction begins

January 21 Martin Luther King, Jr.’s Birthday

(no classes, OGI offices closed)

February 11 Registration begins for spring quarter

February 18 Presidents’ Day (no classes, OGI offices closed)

March 18-22 Final exams

SPRING QUARTER 2002

February 11 Registration begins for spring quarter

March 28 Last day to register without late fees

April 1 Spring quarter instruction begins

May 6 Registration begins for summer quarter

May 27 Memorial Day holiday (no classes, OGI offices closed)

June 10-14 Final exams

June 15 Commencement

SUMMER QUARTER 2002

May 6 Registration begins for summer quarter

June 20 Last day to register without late fees

June 24 Summer quarter instruction begins

July 4 Independence Day holiday (no classes, OGI offices closed)

September 2 Labor Day holiday (OGI offices closed)

September 3-6 Final exams

L E T T E R F R O M T H E D E A N | O G I

MISSIONThe mission of the OGI School of Science& Engineering is to provide outstandinggraduate and professional education andconduct internationally acclaimed researchin science and engineering to meet regionaland national needs.

T O A C C O M P L I S H T H I S M I S S I O N , T H E S C H O O L :• provides students with the necessary

knowledge, skills and breadth for leadership in a technological society;

• supports, through research, educationand training, the people, industries andorganizations that drive the economicgrowth of the Pacific Northwest;

• attracts and develops high-qualityfaculty, students and staff.

EQUAL OPPORTUNITYThe OGI School of Science & Engineeringat Oregon Health & Science University iscommitted to providing equal opportunityand access to all school facilities andacademic programs to everyone withoutregard to race, color, religion, gender,national origin, age, sexual orientation,disability or veteran’s status.

ABOUT THIS CATALOGThis catalog is as accurate as possible as ofOct. 1, 2001. Information contained in thecatalog may be changed during the courseof any academic year, including but notlimited to changes in policies, fees, courseofferings and requirements. This documentshould not be construed as forming thebasis of a contract.

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A L E T T E R F R O M T H E D E A N

The OGI School of Science & Engineering at Oregon Health & ScienceUniversity is one of the most innovative, exciting and productive schools ofits size anywhere in the world.

Indeed the school’s modest size has long been one of its attractions. Studentshave close access, for instance, to top-notch faculty in both the classroomand the research lab, plus we pride ourselves on our flexibility in meetingstudents’ academic needs. And our recent merger with OHSU further raisesour stature as one component of a highly regarded institution that sharesour dedication to education and research.

We have long been extremely successful in competing for limited researchfunding. A wide variety of public- and private-sector funding organizationsbelieve in us so firmly, in fact, that they support nearly $20 million inresearch annually at OGI. Students can thus be assured that OGI faculty areproviding instruction grounded on leading-edge research in their discipline.Such research-informed education has always been the cornerstone of ourapproach to graduate education in disciplines such as computer science,environmental science, electrical engineering and molecular biology. Andour merger with OHSU will bring added growth in those disciplines as wellas more interdisciplinary activities, including a major new initiative inbiomedical engineering.

OGI’s close relationship with the high-tech industry is also very important.Many of our part-time students, for instance, are full-time employees ofcompanies both large and small. As a result, these students acquirepragmatic knowledge and skills that will enhance their careers, plus our full-time students establish valuable contacts within industry. And classroominteractions benefit from a healthy measure of real-world experience.

Classroom and research interactions are further enhanced by the diversebackgrounds of our faculty and students, who represent a cross section ofcultures and sub-disciplines.

All of which taken together helps explain why our alumni find great successin a variety of career paths — whether their inclinations lead them towardacademia, entrepreneurship or advancement with established companies.We pride ourselves on their achievements.

O G I | O G I S C H O O L O F S C I E N C E & E N G I N E E R I N G

OVERVIEW

A C A D E M I C D E P A R T M E N T S

The OGI School of Science & Engineering hasfive academic departments: Biochemistry andMolecular Biology (BMB), Computer Scienceand Engineering (CSE), Electrical andComputer Engineering (ECE), EnvironmentalScience and Engineering (ESE), andManagement in Science and Technology(MST). Research and educational interactionamong these departments is ensured in partby research programs that utilize facultymembers from multiple departments. Thisencourages the exchange of ideas betweenpersons working in related research areasand enables the fullest use of the wide rangeof instrumentation available at the School.

D E G R E E P R O G R A M S

The OGI School of Science & Engineeringoffers Master of Science degrees and Ph.D.degrees in Biochemistry and MolecularBiology, Computer Science and Engineering,Electrical Engineering, and EnvironmentalScience and Engineering. The school offersMaster of Science degrees in Managementin Science and Technology and inComputational Finance. OGI also offersa professional degree, the Oregon Master ofSoftware Engineering.

C E R T I F I C AT E P R O G R A M S

Three certificate programs are offered inApplied Computing, Computational Finance,and Management in Science and Technology.

S T U D E N T S N O T S E E K I N G D E G R E E S

Any qualified student may take courses at OGIin a part-time capacity without enrolling in adegree program. Students may take a full-timecourse load for only one quarter while waitingfor a decision regarding admission to a degreeprogram. Up to 21 credits taken at OGI priorto matriculation (enrollment in a degreeprogram) may be accepted toward degreerequirements. Individual departments’regulations may be more restrictive.

C O L L A B O R AT I V E / J O I N T P R O G R A M S

Full-time students in the school’s ComputerScience and Engineering (CSE) and Electricaland Computer Engineering (ECE)departments may take certain courses atPortland State University at no additionalcost. Similar arrangements are beingexplored for other OGI departments.

Contact the Department of GraduateEducation for details.

The OGI School also participates in theOregon Master of Software Engineering(OMSE) program, a joint program withPortland State University, Oregon StateUniversity and the University of Oregon.Students apply for this master’s degreethrough one of the participating schools.Please direct inquiries to (503) 725-2900 [email protected].

A C C R E D I TAT I O N

Oregon Health & Science University isaccredited by the Commission on Colleges ofthe Northwest Association of Schools andColleges, an institutional accrediting bodyrecognized by the Council for HigherEducation Accreditation and the U.S.Department of Education. The commission’saddress is 11130 NE 33rd Place, Suite 120,Bellevue, WA 98004.

ADMISSIONS PROCEDURESPrinted application forms are available fromthe school’s Department of GraduateEducation. Completed applications,transcripts and other application materialsshould be sent to:

Department of Graduate EducationOGI School of Science & Engineering20000 NW Walker RoadBeaverton, OR 97006-8921Phone: (503) 748-1027Toll-free: (800) 685-2423Fax: (503) 748-1285E-mail: [email protected]

You may also apply for admission on-line atwww.ogi.edu/forms/application.html

Students may become matriculated (enrolledin a degree program) only after completingthe requirements for a bachelor’s degree orits equivalent, although students may beprovisionally admitted prior to that time.

D E G R E E P R O G R A M S

The following items must be submitted:

• Complete OGI School of Science & Engineeringapplication form or Oregon Master of SoftwareEngineering (OMSE) degree program applicationform, if applicable.

• $50 nonrefundable application fee, whichis valid for one year and cannot be waivedor deferred.

• Official transcripts from each college oruniversity attended.

• Three letters of recommendation.

• Official GRE scores.

The GRE general test is required for M.S.applicants in Computational Finance (GMATcould be substituted); Computer Science andEngineering; Environmental Science andEngineering; Environmental SystemsManagement, and the Oregon Master ofSoftware Engineering.

The GRE general test is required for PhDapplicants in Biochemistry and MolecularBiology (subject test is also required);Computer Science and Engineering; Electricaland Computer Engineering, andEnvironmental Science and Engineering.

Applications may be submitted as early asone year before the proposed date ofenrollment.

Applications received by March 1 (Feb. 15 forthe Environmental Science and EngineeringDepartment) will receive priority review foradmission and financial support.

C E R T I F I C AT E P R O G R A M S

The following items must be submitted:

• Completed OGI certificate program application form.

• $20 nonrefundable application fee, whichis valid for one year and cannot be waivedor deferred.

A D D I T I O N A L R E Q U I R E M E N T S F O R

I N T E R N AT I O N A L S T U D E N T S

To be considered for admission to OGI for afull course of study, international studentsmust also provide documents to show thatthey meet the requirements described below.

• Evidence of adequate financial resources to payfor their OGI education and their cost of living.

• Written TOEFL scores are required of all M.S.and Ph.D. applicants whose native language isnot English. Students who have earned a degreein the United States are exempt from thisrequirement. Minimum required TOEFL scoresvary by department: BMB 550; CSE 600; ECE575; ESE 600; MST 625. The minimum desiredTOEFL score for admission is 575, but a lowerscore may be offset by excellent GRE scores.

Please note: the minimum TOEFL scores aboveare for the paper-based test only. The computer-based TOEFL uses a different score scale. Formore information on the computer-based scorescale, please visit www.toefl.org.

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O G I S C H O O L O F S C I E N C E & E N G I N E E R I N G | O G I

TUITION AND FINANCES

T U I T I O N

For the 2001-2002 academic year, tuition forfull-time matriculated students (defined as 9or more credit hours per quarter) is $4,905per quarter. Part-time tuition for regular OGISchool of Science & Engineering courses is$545 per credit hour or audit unit. Pleasenote that there is no full-time tuition rate fornon-matriculated students, except when anadmission decision is pending. There are nostudent fees.

• Tuition for Computational Finance core coursesis $695 per credit hour or audit unit. Studentsmatriculated in the Computational Financedegree pay only for credits required to fulfilldegree requirements. Credits taken during the12-month program beyond the 45 required tofulfill degree requirements will not incur charges(up to a limit of 54 credits). Full-time quarterlytuition for students not matriculated in theComputational Finance program who take oneComputational Finance course is $5,355; withtwo Computational Finance courses it is $5,805.Full-time Ph.D students do not incur additionalcost for registering for ComputationalFinance courses.

• ESE students pay tuition on an annual basis.That tuition may be paid in full at the beginningof the year or in quarterly installments.

• Courses in the Oregon Master of SoftwareEngineering program are $495 per credit hour. Full-time matriculated students may register forOMSE courses when paying full-time tuition.

Note: Payment or arrangement for deferredpayment for all courses must be made beforeyour place in a class is confirmed. The schooloffers students the option of deferring most ofthe payment through no-interest promissorynotes. Students who are reimbursed for theircourses must make payment arrangements withtheir employer, but those students still incurfinancial responsibility for courses. Coursessponsored by the Oregon Center for AdvancedTechnological Education (OCATE), whether takenfor credit or audit, must be paid in full at thetime of registration.

F I N A N C I A L A I D

Entering full-time Ph.D. students can obtainfinancial support though a combination oftuition scholarships, OGI fellowships, namedfellowships, graduate research assistantshipsand (for U.S. citizens only) low-intereststudent loans. Part-time Ph.D. students maybe eligible for some of the above. Partial-tuition scholarships may be awarded toentering full-time M.S. students, and full- and

part-time M.S. students who are U.S. citizensmay apply for low-interest student loans.

Fellowships, scholarships and assistantshipsare awarded by individual departments.

Title IV Federal Student Loan programs areadministered through the OHSU Financial Aidoffice. These loans are available to U.S.citizens and eligible non-citizens. Forapplication materials and additional infor-mation, contact Cherie Honnell, Director ofFinancial Aid & Registrar, at (503) 494-5117or [email protected]. Applications forfederal student loans (FAFSA) are availablefrom OGI’s Department of GraduateEducation, or www.ogi.edu/students/fin.html.

ACADEMIC POLICIESThe following is a summary of select OGISchool of Science & Engineering academicpolicies. A more comprehensive listing can befound in the school’s Student Handbook atwww.ogi.edu/students/studenthandbook.pdf.

O N S I T E ( R E S I D E N C Y ) R E Q U I R E M E N T S

The school has a two-year Ph.D. residencyrequirement. For full-time students, thisrequirement is normally met by an on-sitedissertation project. In exceptionalcircumstances (e.g., dissertation topicsrequiring access to special facilities onlyavailable elsewhere), other arrangementsmay be proposed to the Educational PolicyCommittee (EPC). In such cases, a writtenplan of the research, with a schedule anddescription of the special circumstances andunderstandings between the student, thesisadvisor and Student Program Committee(SPC), must be included. Approval of thisplan by the EPC is required before a studentis granted candidacy status for Ph.D. workunder such an arrangement. For part-timePh.D. students, the first year of the residencyrequirement can be satisfied by attendance inclasses on the OGI campus. The second yearof residency, however, must be spent full-timeon campus under the advisement of an OGIfaculty member.

There is no residency requirement for M.S. orcertificate programs at OGI.

T I M E L I M I T S T O C O M P L E T E T H E D E G R E E

Ph.D.: Six years of full-time study or eightyears of part-time study.

M.S.: Three years of full-time study or fouryears of part-time study.

Petitions for extensions must be approved bythe department and submitted to theEducational Policy Committee for approval.

C O N T I N U O U S E N R O L L M E N T

A Ph.D. or Master’s student who has begunwork on the dissertation or thesis mustregister and pay for at least one credit hourof research per quarter in order to maintainmatriculated status. If all requirements havenot been satisfied at the end of fourconsecutive academic quarters of registeringfor only one credit per quarter, or if analternate plan of completion has not beenapproved by the department and theEducational Policy Committee, matriculatedstatus will be terminated. If the studentwishes to return to his or her program at alater date, it will be necessary to reapply foradmission. Continuous enrollment is notrequired of Master’s students not pursuing athesis, nor of Master’s or Ph.D. students whohave not yet begun working on the thesis ordissertation. However, all matriculatedstudents are required to register for classesOR to indicate temporary inactive status byfiling a Temporary Inactive Status form withthe Department of Graduate Education.

L E A V E O F A B S E N C E

In special circumstances, leaves of absencefrom a graduate program may be allowed. Astudent considering a leave should firstdiscuss the issue with his or her advisor oranother faculty member. If the departmentsupports the leave of absence, the studentthen submits a petition to the school’sEducational Policy Committee for approval.

S T U D E N T S TAT U S

A matriculated student is one enrolled in adegree program. A non-matriculated studentis not working toward completing a degree.Full-time matriculated students carry aminimum of nine credits per quarter. (Auditunits do not count toward this minimumexcept in special circumstances.) Academicdepartments may require students to carrymore than nine credits per quarter as acondition of eligibility for a stipend and/ortuition scholarship. Part-time matriculatedstudents are admitted to a degree program,carry fewer than nine credits per quarter andpay tuition at the appropriate per credit rate.

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Non-matriculated students have not beenadmitted into a degree program, typicallycarry fewer than nine credits per quarter,and pay tuition at the appropriatehourly rate.

A U D I T I N G A C O U R S E

OGI courses are offered for graded graduatecredit hours or ungraded audit units.Students may register to audit an OGI courseon a space-available basis. Students taking acourse for credit have priority over studentstaking a course for audit. Audits are recordedon the student’s transcript at the discretion ofthe instructor, based upon a reasonableexpectation of attendance and minimalparticipation. Audits are charged at thestandard tuition rate. Audit units do not counttoward a student’s full-time status.Instructors have final discretion over allowingaudits of their classes and defining theacademic expectations of audits.

C R E D I T L O A D P E R Q U A R T E R

Twelve credits per quarter is considered anormal course load for full-time students,although nine or more is also considered full-time. Up to 18 credits/audits may be takenwith the approval of the department.Registering for more than 18 credits requiresEducational Policy Committee permission; 18credits plus up to 4 audit units does notrequire EPC permission and does not incuradditional cost. Students in the Electrical andComputer Engineering Department arelimited to 12 credits per quarter, but maytake up to16 with their advisor’s and homedepartment’s written approval.

T R A N S F E R C R E D I T

OGI accepts transfer credit from accreditedinstitutions provided that such prioracademic work has not been previouslyapplied toward another degree. A maximumof 21 credits earned prior to matriculation atOGI may be applied. This may include up to12 credits transferred from anotherinstitution (up to 18 from Portland StateUniversity, University of Oregon and OregonState University) and/or up to 21 creditstaken at OGI prior to matriculation. Contacteach academic department for specificpolicies and procedures. Transfer creditgrades, other than those from OGI, arenot calculated in the OGI grade-pointaverage (GPA).

G R A D I N G / S AT I S FA C T O R Y A C A D E M I C P R O G R E S S

All OGI courses are graded with a lettergrade; an exception is that Ph.D. studentsmay receive P/NP for work in a seminar.In addition, faculty may assign P/NP orletter grades to research work, but gradesfor research cannot be counted in astudent’s GPA.

The following scale is employed at the school:

A = 4.0 B- = 2.67 C = 2.0

A- = 3.67 B = 3.0 C- = 1.67

B+ = 3.33 C+ = 2.33 F = 0.0

The grading system is defined as:

A = Excellent

B = Satisfactory

C = Below graduate standard

F = Failure

The following marks are also used:

AU = Audit, no credit

P = Satisfactory completion

NP = No credit, unsatisfactory

I = Incomplete

PI = Permanent Incomplete

W = Withdrawn (after the add/drop period)Matriculated students must maintain acumulative GPA of 3.0 on all work taken atOGI. Failure to do so may result in probationor dismissal.

I N C O M P L E T E S

The school’s policy is that an Incomplete mustbe completed by the end of the quarterfollowing that in which the Incomplete wasawarded. In cases where the Incomplete isnot completed, the instructor has the choiceof assigning a grade or converting theIncomplete into a Permanent Incomplete. Thegrade may be an F if the course work was notcompleted, but instructors have the option ofassigning another grade if they feel qualityand quantity of work that was accomplishedwarrants it. If an extension of this one-quarter deadline is desired, the student maypetition the Educational Policy Committee,showing the instructor’s support of theextension (a separate letter or signature onthe petition will suffice). Normally an

extension will be granted, as long as the planis specific, includes a date by which the gradewill be assigned, and is submitted to theGraduate Education manager in writing.

4 0 0 - L E V E L C O U R S E S

Courses offered and designated by 400-seriesnumbers within academic departments at theschool are not considered to satisfy anydegree requirements. These courses do notcarry graduate credit at the school, but areentered on the transcript.

C O N F I D E N T I A L I T Y O F S T U D E N T R E C O R D S

With the passage of the Federal FamilyEducational Rights and Privacy Act (FERPA)of 1974, OGI adopted rules to govern thecollection, use and disclosure of studentrecords with the goal of ensuring theirprivacy. Students have the right to inspecttheir educational records that are maintainedby OGI; the right to a hearing to challenge thecontents of those records when they allegethe records contain misleading or inaccurateinformation; and the right to give theirwritten consent prior to the release of theirrecords to any person, agency or organizationother than OGI officials and certainauthorized federal and state authorities.

D I R E C T O R Y I N F O R M AT I O N

Certain public domain information, known asdirectory information, can be released by theschool unless a student files a writtenrequest in the Graduate EducationDepartment. The school limits thisinformation to the student’s name, homeaddress, e-mail address, dates of attendance,degrees and awards received, number ofcredits earned and the fact of enrollment,including whether the student is enrolled full-or part-time. The school does not make thisinformation available to vendors.

T R A N S C R I P T S

Your transcript is a formal, written record ofyour educational experience at the OGISchool of Science & Engineering. All coursesyou take at the school are recorded on it, asare all grades and degrees you earn while atOGI. If you have transferred credits fromanother institution, they will be recorded onyour transcript as well. By law, requests fortranscripts must be in writing and submittedby fax, mail or in person to the Department of Graduate Education. Official transcripts

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are on special paper and have the officialschool seal; unofficial transcripts are printed on regular paper without the seal.There is no charge for unofficial transcripts;official transcripts cost $4 per copy. Requestsare usually processed immediately, but weask that you allow three days. Your requestmust have your name, signature and socialsecurity number (if applicable); indicatewhether you will pick up the transcript(s) orinclude the address(es) to which thetranscript(s) should be mailed; and includepayment information, if relevant. You cansend a check, submit a credit card number orpay cash. Sending cash through the mail isnot recommended.

THE CAMPUS

G E O G R A P H I C S E T T I N G

The greater-Portland metropolitan area has apopulation of about 1.5 million, nearly halfthe population of Oregon. It provides diversecultural activities, including art, music,entertainment and sports. Portland has anextensive park system, including the largestwilderness park within the limits of any cityin the United States. The OGI School ofScience & Engineering is located 10 mileswest of downtown. We are the newest schoolwithin Oregon Health & Science University(OHSU), joining the Schools of Medicine,Dentistry and Nursing, which are located onthe main campus on Marquam Hilloverlooking downtown Portland. OGI is nowpart of OHSU’s newly named West Campus,which also includes the NeurologicalSciences Institute, the Oregon RegionalPrimate Research Center, and the Vaccineand Gene Therapy Institute. OGI’s campusconsists of modern, attractive buildings,providing spacious laboratories, offices anda research library.

L I B R A R Y

The Samuel L. Diack Memorial Library’scollection includes more than 18,000monographic titles and 400 print journalsubscriptions. These support the teaching andresearch efforts at OGI by providing texts,conference proceedings, reference materials,journals and research monographs in thesubject areas of computer science, electricalengineering, environmental sciences,

biochemistry, molecular biology, andmanagement as related to science andtechnology. In addition, the OHSU Libraryholds more than 74,000 monographs and1,200 journal subscriptions. These printcollections are available for use when visitingthe libraries. Materials unavailable at OGIare obtained on interlibrary loan for faculty,staff and students. An on-line catalog,acquisitions and circulation system is inplace. Access to other college and universitycollections is provided by access todatabases, library catalogs and grantscirculation privileges to OGI students at 13other area institutions, including PortlandState University and Reed College.

OGI library workstations not only enablestudents and faculty to search the catalogand the library’s databases but also provideentry to Web resources, telnetting and ftpoptions for faculty, staff and students. TheOGI librarians will perform searches on thesystems and databases that are not directlyavailable to students. Library orientation ispart of the introduction to OGI for newstudents, and classes on library researchmethods are offered throughout the year.

Most of OGI’s electronic library resources willbe integrated with those of the other OHSUschools and institutes by 2003.

C O M P U T E R FA C I L I T I E S

The OGI School of Science and Engineering’scomputing environment gives members of thecommunity access to a rich array oftechnologies and information resources.Many of these resources, including networksand telecommunications, are theresponsibility of OHSU’s central InformationTechnology Group (ITG). In addition, manyschool departments and laboratories maintaintheir own computing facilities. Most of OGI’scomputers connect to a school-wide local-area network and to the Internet, providingconvenient access to the World Wide Web.The local-area network is connected to theInternet through two high-speed data paths.In addition, it is also connected to Internet 2(Internet2.edu) resources. The Internet 2connection was made possible through analliance of local academic institutions.

H O U S I N G

While OGI has no on-campus housing, it is located in the midst of a very largeresidential area. There are numerousapartment complexes, rental houses, buand light rail lines, and shopping areasnear the school. The Office of StudentServices in the Graduate EducationDepartment maintains a list of localapartment buildings for students toreference. In addition, the Student Councilhas a Web site for current, new andprospective OGI students who are lookingfor housing information, roommates,etc. This service is found atcslu.cse.ogi.edu/council/st_forum.html.

S T U D E N T C O U N C I L

The Student Council serves as the liaisonbetween the student body and the faculty andadministration, and it strives to improve OGIstudents’ quality of life. Studentrepresentatives make themselves available tostudents in their department in order toforward their comments, ideas and concernsto the Student Council and to promote theirinvolvement in student body activities.Representatives also serve to disseminate allpertinent information to the students in theirdepartments. As liaisons, members of theStudent Council represent the student bodyand student interests on a wide variety of OGItask forces and committees, including theFaculty Senate, the Educational PolicyCommittee and the Safety Committee. Eachquarter the Student Council also sponsorsand coordinates at least one major socialevent, which is open to everyone at OGI.These events have included a coffeehousewith live music performed by people fromthroughout the school, an annualinternational food and cultural fair, and aneducational forum. There are also monthlyand weekly events, including movie nightsand bagel breakfasts in the student lounge.More information on the Student Council isavailable on its Web site atcslu.cse.ogi.edu/council/ or by e-mail [email protected].

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Department of Biochemistry andMolecular Biology

www.bmb.ogi.edu

D E P A R T M E N T H E A D

Nin ian J . B lackburn

(503) 748-1384 E-mail: [email protected]

D E P A R T M E N T A D M I N I S T R A T O R

Nancy Chr ist ie

(503) 748-1070E-mail: [email protected]

A D M I N I S T R A T I V E C O O R D I N A T O R

Terr ie Hadf ie ld


B M B G E N E R A L I N Q U I R I E S

E-mail: [email protected](503) 748-1070

THE DEPARTMENT OF BIOCHEMISTRY AND

MOLECULAR BIOLOGY offers graduatestudy leading to M.S. and Ph.D.degrees. Participation in researchbegins immediately upon enteringour program. This early exposure toresearch allows each student tobecome familiar with the variety ofactivities represented in thedepartment and aids the student inthesis research selection.

R E S E A R C H A R E A S I N C L U D E :• Metallobiochemistry (with an emphasis on the

structure and function of metal ions in proteinsand the mechanisms of metal trafficking in cells)

• Fungal and yeast biochemistry and molecularbiology (with an emphasis on gene regulationand enzyme characterization)

• Ion transport across biological membranes (withan emphasis on molecular biology andreconstitution of cation or anion carriers)

The research experience at OGI is extensive.Much of the research is interdisciplinary,covering basic and applied aspects. Studentsare involved in all aspects of thedepartmental research program and haveready access to modern researchinstrumentation. As a result, our graduatesare well qualified for research careers inacademia, government and industry.

ADMISSION REQUIREMENTSAdmission requirements are the same as thegeneral requirements of the institution. Inaddition, Ph.D. applicants must submitgeneral GRE scores and a GRE subject scorefor one of the following tests: (a) biology, (b)chemistry or (c) biochemistry, cell andmolecular biology. M.S. applicants are notrequired to submit GRE scores. Prospectivestudents should carefully examine the facultyresearch interests and departmentalresearch programs to determine whethertheir specific professional needs can befulfilled at OGI. Communication withindividual faculty members is encouragedprior to applying or enrolling.

DEGREE REQUIREMENTS

M . S . P R O G R A M S

Two options are offered for the M.S. inbiochemistry and molecular biology.

N O N - T H E S I S O P T I O N

The non-thesis M.S. requires satisfactorycompletion of 44 credits, 28 of which are ingraded courses and 16 of which are derivedfrom an experimental research project(BMB610); and a written report on theresearch. Graded courses include 12 creditsin BMB527-528-529, and 16 or more creditsin advanced courses (BMB532-542), studentseminars (BMB594 or 596) and SpecialTopics (BMB580). The research for the non-thesis degree is typically a specificcontribution to a larger project, providing thestudent with extensive hands-on experiencein biochemical and molecular biologicaltechniques. The non-thesis M.S. degree canbe completed in one year of full-time study.

T H E S I S O P T I O N

The thesis M.S. is a research degree thatrequires satisfactory completion of 44credits, 20 of which are in graded courses(12 credits in BMB 527-528-529 and eight ormore credits in advanced courses), and awritten thesis based on independent research(BMB700). The thesis M.S. degree can becompleted in 18 months of full-time study.

P H . D . P R O G R A M

The department offers a Ph.D. inbiochemistry and molecular biology. Ph.D.candidates are required to take the BMB527-528-529 biochemistry sequence andthree of the following core courses:

BMB532 Bioenergetics and Membrane Transport, 4 credits

BMB533 Enzyme Structure, Function and Mechanisms, 4 credits

BMB534 Instrumental Methods in Biophysics I, 4 credits

BMB540 Advanced Molecular Biology, 4 credits

BMB542 Molecular Cell Biology, 4 credits

Students must register for 12 credits perquarter. These credits typically includestudent seminars (BMB594 or BMB596),Department Seminar (BMB 591) andResearch (BMB600 or BMB800).

The qualifying examination for the Ph.D. is acomprehensive examination. The qualifyingexam must be completed within two years ofentering OGI. An oral defense of the Ph.D.dissertation is required. Cheng Wu is a doctora l

student in Matt Sachs ’s lab.

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COURSE DESCRIPTIONSBMB527 Biochemistry I: Proteins and EnzymesPrimary, secondary and tertiary structure of proteins;enzyme mechanisms; enzyme kinetics. 4 credits

BMB528 Biochemistry II: Introduction toMolecular BiologyDNA replication, RNA synthesis and protein synthe-sis; genetic code; gene regulation. 4 credits

BMB529 Biochemistry III: Metabolismand BioenergeticsMetabolism of carbohydrates, lipids and aminoacids; bioenergetics; photosynthesis; oxidativephosphorylation. 4 credits

BMB532 Bioenergetics and Membrane TransportCritical evaluation of the chemiosmotic theory withspecific reference to oxidative phosphorylation,photophosphorylation and metabolite transport.Biochemical mechanisms of energy transductioncommon to bacterial and mitochondrial respiration,and bacterial and plant photosynthesis are reviewed.

4 credits

BMB533 Enzyme Structure, Function and MechanismsProvides an in-depth analysis of the structural ori-gins of protein interactions and catalysis that are thebasis for biological function. The course develops thebasic principles of structural biology through anoverview of X-ray crystal structures and foldingprocesses, acquainting students with computationalresources for protein structure analysis. The struc-tural foundation is expanded into a detailedinvestigation of enzyme active sites, including theapplication of kinetic approaches to understandingenzymatic reaction mechanisms. 4 credits

BMB534 Instrumental Methods in Biophysics ITheory and application of physical techniques toproblems in biochemistry. Optical, fluorescence, cir-cular dichroism, infrared and Raman spectroscopyof chromophoric groups. Magnetic susceptibility andnuclear magnetic resonance of metalloproteins.

4 credits

BMB535 Instrumental Methods in Biophysics IIInvestigation of physical techniques particularlyuseful for studying metalloproteins. Electron para-magnetic resonance, electron spin echo, magneticcircular dichroism, and X-ray absorption spec-troscopy. The course has significant “hands-on”exposure to instrumentation and computer simula-tion techniques. 4 credits

BMB537 Metals in BiochemistryComprehensive study of the chemistry and biochem-istry of metal ions in biological molecules and livingsystems. Topics include metalloprotein structure,metal ion specificity, biological oxidation mecha-nisms, metal ion catalysis in enzymes, metal iontransport and gene regulation. 4 credits

BMB538 Coordination ChemistryStructures and stabilities of transition metal coordi-nation compounds with mono- and multi-dentateligands; coordination compounds as models for bio-logical metal centers; strategies for synthesis oftransition metal complexes. 4 credits

BMB539 Chemical Group TheoryProperties of mathematical groups; symmetry proper-ties of molecules; symmetry groups, representationsand character tables. Applications of group theory tothe study of structure and spectroscopy of organic andinorganic molecules; Hückel molecular orbital theory;ligand field theory; electronic spectroscopy and vibra-tional spectroscopy. 4 credits

BMB540 Advanced Molecular BiologyAn in-depth study of the molecular mechanisms gov-erning the replication, recombination, transcriptionand translation of genetic material. Emphasis isplaced on experimental approaches that have led toour understanding of these fundamental processes.

4 credits

BMB541 Molecular Genetics of DevelopmentA focused study of selected topics examining theregulation of gene expression during cellular differ-entiation. Emphasis is placed on the molecularnature of cell-cell interactions and the genetic con-trol of complex cellular responses to developmentaland environmental stimuli. 4 credits

BMB542 Molecular Cell BiologyThe techniques of molecular biology have created anexplosion in knowledge of cell structure and func-tion. This course examines the following topics:cellular organization; cell signaling; cell differentia-tion; cell evolution. Knowledge of the cell is obtainedthrough combining core readings and lectures withstudent-led discussions of primary research papers.

4 credits

BMB543 Current Topics in ProteomicsProteomics is a new area of molecular biology thataims to identify and map the total protein comple-ment of a genome. It expands the scope of biologicalinvestigation from studying single proteins to sys-tematically studying all proteins. Proteomics hasbroad applications in disease diagnosis, drug dis-covery and agriculture. The key technologies used inproteomics are two-dimensional gel electrophore-sis, mass spectrometry (ESI-MS, MALDI-TOF),imaging and database software. This course will uselectures, student seminars and literature readingsto focus on electrophoresis, mass spectrometry andapplications. 3 credits

BMB544 Introduction to BioinformaticsPrimary literature of computational biology andhands-on experience in data manipulation fromlocal and remote databases. 3 credits

BMB580 Special Topics in BiotechnologyExamination of current and past research papers ina specific area of biotechnology that is of mutualinterest to the student and the faculty member.Requires a written review paper or seminar presen-tation in one of the Student Seminar series.

Variable and repetitive credit

BMB591 Department Seminar: Biochemistry/Molecular Biology

1 credit, repetitive

BMB594 Metallobiochemistry Student SeminarPresentations and discussions of selected topicsfrom the recent literature and of ongoing researchprojects in the department. 2 credits, repetitive

BMB596 Molecular Biology/BiochemistryStudent SeminarPresentation and discussion of journal articles fromthe recent literature in molecular biology, geneticsand biochemistry. 2 credits, repetitive

BMB600 ResearchSupervised research participation.


BMB610 Nonthesis ResearchSupervised research as a component of the nonthe-sis M.S. degree. Variable and repetitive credit

BMB620 Professional InternshipThese courses provide the student with an opportu-nity to earn credit for relevant work experience inindustry. Students gain valuable industrial experi-ence that allows them to both apply the knowledgegained in the classroom and prepare for their futurecareers. Enrollment requires a faculty advisorand is limited by the number of internship opportu-nities available. Variable credit

BMB700 M.S. Thesis ResearchResearch toward the thesis for the M.S. degree.


BMB800 Ph.D. Dissertation ResearchResearch toward the dissertation for the Ph.D. degree.


RESEARCH PROGRAMSTranslational Control in Fungal Amino Acid Biosynthesis

A greater understanding of many human healthissues relies on increased knowledge of how cellsexpress genetic information. Gene expression canbe controlled by regulating the synthesis andstability of functional RNA and protein. The goal ofour research is to obtain a greater understandingof how these mechanisms work using theNeurospora crassa arg-2 and Saccharomycescerevisiae CPA1 genes as models. Thesehomologous genes encode the first enzyme inarginine biosynthesis, and they are negativelyregulated at transcriptional and translational levelsin response to the availability of arginine. Anevolutionarily conserved upstream open readingframe (uORF) present in the 5’-leader regions ofthese transcripts is responsible for translationalcontrol. Synthesis of the uORF-encoded peptidecauses ribosomes to stall when the level of arginineis high, blocking access of ribosomes to thetranslation initiation site for the polypeptideencoding the arginine biosynthetic enzyme. Ourcurrent work is focused on developing a molecularunderstanding of how synthesis of this uORF-encoded peptide causes ribosomes to stall, sincethis will provide important insights into thefundamental cellular process of protein synthesis.Sachs

Translational Control of Human Proto-Oncogenes

The transcripts specified by many genes involved inhuman cancers contain uORFs; these include theher-2 and bcl-2 proto-oncogenes. Using methodssimilar to those developed for understanding theroles of the uORFs of N. crassa arg-2 and S.cerevisiae CPA1 gene expression, we are examining

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the functions of these mammalian uORFs, to betterunderstand their role in controlling the expressionof these critically important genes. Sachs

The Neurospora Genome

We are part of a team that is sequencing andannotating the genome of Neurospora crassa(see www.genome.wi.mit.edu/annotation/fungi/neurospora/), and are gearing up to apply thisinformation to large-scale community-wide effortsin functional genomics. This is the first genome of afilamentous fungus that has been sequenced withpublic funds; the annotation of this sequence isproving invaluable for understanding fungal genomeevolution; many fungi important for agriculture andmedicine are closely related to N. crassa. Werecently began experiments aimed at cloning andanalyzing the telomeric regions of N. crassa andthe closely related pathogenic rice blast fungusMagnaporthe grisea because mounting evidenceindicates that genes near telomeres evolve morequickly and are frequently involved in pathogenicinteractions with hosts. Sachs

Mechanisms of Mammalian Chemical Communication andVomeronasal Olfaction

Chemical communication plays a significant role inlife strategies for many mammals. Our researchfocuses on chemical identification of pheromonesfunctioning during reproductive events in theAsian elephant, Elephas maximus. A female-to-male preovulatory urinary sex pheromone,(Z)-7-dodecen-1-yl acetate, has been identified anddemonstrated to be robust in its synthetic form.This compound is also bioactive in manyLepidoptera, making it a good example ofconvergent evolution of structure and function.Biochemical studies have established the presenceof the pheromone in the serum, and future studieswill investigate its biosynthetic pathways.Considerable progress has been made onestablishing the proteins functioning as pheromonetransporters prior to signal transduction in theneuroreceptive cells of the vomeronasal organ.Radiolabeled analogs, competition experiments andmolecular biological studies have establishedunusual roles for elephant albumin and olfactorybinding protein. A second pheromonal system isactively being investigated. The facial temporalgland, breath and urine exude unusual chemicalcompounds during musth in Asian male elephants.These signals have a role in mate choice by femaleelephants, spatial distribution by male elephantsand other reactions by conspecifics. Utilizingseveral state-of-the-art gas chromatographic/massspectrometric techniques, we are identifyingspecific compounds that have a chemicalcommunication function, i.e., elicit behavioralresponses, and correlating the release of suchcompounds with serum androgen levels.Rasmussen

Chemistry of Copper-Containing Enzymes

Increasing numbers of important enzymes areknown to contain copper at their active sites. Ofparticular interest are enzymes involved in biogenicamine biosynthesis and metabolism (includingimportant neuroactive amines such as nor-

adrenaline and amphetamine); enzymes protectingagainst oxidative cellular damage caused byreduced oxygen metabolites; and enzymescatalyzing the biosynthesis of neuropeptidehormones. A major goal is to understand thecatalytic role of copper and the molecularmechanism of oxygen binding and utilization bythese oxidase and oxygenase enzymes. Blackburn

Spectroscopy of Copper Proteins

Spectroscopic techniques are used to probe thestructures of the copper sites in the native proteinsand their complexes with substrates and inhibitors.Since the chemistry of the catalytic processes isgenerally centered on the Cu(I) forms of theenzymes, we are concentrating on the challengingtask of developing spectroscopic probes of the Cu(I)oxidation state, which is transparent to mostcommon spectroscopic techniques. Our work thusincludes Fourier transform infrared, X-rayabsorption edge and EXAFS spectroscopies, andemphasizes the use of computer simulation ofspectra on our Alpha work station. Data for thelatter two techniques are collected at national andinternational synchrotron radiation facilities.Proteins under investigation include dopamine-betahydroxylase, cytochrome c oxidase, hemocyanin,peptide amidating enzyme, Menkes and Wilson’sdisease proteins, and copper chaperones. Blackburn

Radical Copper Oxidases

Radical copper oxidases are a new class of redoxmetalloenzymes (including the fungal enzymesgalactose oxidase and glyoxal oxidase) containing aprotein free radical directly coordinated to acopper center. This free radical-coupled Cucomplex catalyzes the two-electron oxidation ofsimple alcohols and aldehydes and the reduction ofO2 to hydrogen peroxide, fueling extracellularperoxidases involved in lignin degradation. In theseproteins, the free radical is localized on a tyrosineresidue covalently crosslinked to a cysteinyl sidechain (a Tyr-Cys dimer). The catalytically activeenzyme is an intense green color, a result ofunusual optical spectra arising from electronictransitions within the copper radical complex. Lowenergy transitions in the near IR result frominterligand redox in this metal complex, ligand-to-ligand charge transfer (LLCT) processes that areclosely related to the electron transfer coordinatefor substrate oxidation. The active site metalcomplex is surprisingly flexible, twisting through apseudorotation distortion when exogenous ligandsbind, thereby modulating the basicity of a secondtyrosine ligand that serves as a general base incatalysis. Many of these aspects of electronicstructure and dynamics of the radical copperoxidases are the focus of active research. Whittaker

Manganese Metalloenzymes

Manganese is an essential element for life, formingthe active site for a large number ofmetalloenzymes catalyzing hydrolytic or redoxreactions, including the photosynthetic oxygenevolving complex. We are interested in the Mnredox sites in Mn superoxide dismutase (MnSD,mononuclear Mn) and Mn catalase (MnC, dinuclearMn), enzymes that provide protection from toxic

oxygen metabolites. The key question is: How dointeractions between the protein, metal ion andexogenous ligands tune the redox potential andchemistry of these complexes? We are combiningthe powerful tools of molecular biology withadvanced spectroscopic and computationalapproaches to explore the structure and dynamicsof Mn active sites. For MnSD, we find anunexpected temperature dependence for thestructures of anion complexes, which changecoordination as the temperature is raised. Thisthermal transition implies that the stability of theactive site structure is determined by dynamicalfeatures of the complex and that dynamicalexcitation may play an important role in controllingthe energetics of ligand binding and redox. A widerange of projects relating to the chemistry andbiology of Mn are in progress. Whittaker

Electronic Spectroscopy of Biological Metal Complexes

Electronic spectroscopy extends structural studiesof biomolecules beyond the atomic resolution ofX-ray crystallography to a level of structural detailthat directly relates to chemistry. The techniquesused in these studies span five decades of theelectromagnetic spectrum, from microwaves tothe ultraviolet and beyond. At the lowest energy,electron paramagnetic resonance (EPR)spectroscopy gives information on the electronicground state, defining the molecular orbital thatcontains the unpaired electron in a paramagneticcomplex. At higher energy, UV-visible absorptionspectroscopy excites orbital transitions betweenelectronic states, giving information oncharacteristic metal-ligand interaction energiesthat can be understood in terms of a ligand field ormolecular orbital analysis. Polarizationspectroscopy (linear dichroism, circular dichroismand magnetic circular dichroism) can give moredetailed information on ground and excited stateelectronic wave functions using geometric featuresof light to probe the active site. These experimentalapproaches can be complemented by spectroscopicmodeling and computational biology methods toprovide a detailed description of a metalloproteincomplex and its interactions. Whittaker

Vibrational Spectroscopy of Metalloprotein Active Sites

Many spectroscopic methods are available for theinvestigation of structural and functional propertiesof metal ions in enzymes and proteins. We useelectronic, vibrational (especially resonanceRaman) and EPR spectroscopy to characterizemetal-ion active sites. Our laboratory has asensitive, state-of-the-art Raman instrument: a fastspectrograph with a liquid N2-cooled CCD detector.We also use a combined FT-IR/FT-Ramaninstrument for protein and model compoundstudies. Our research focuses on the description ofthe molecular and electronic structures of heme(iron porphyrin), nonheme-iron and copperenzymes to gain an understanding of the role of themetal ion in enzymatic catalysis. Of particularinterest is the biochemistry of O2. Metalloproteinsare involved in O2 binding (hemoglobin orhemocyanin) and in oxidative chemistry wherebyO2 is reduced and substrates are oxygenated oroxidized. Trapped reaction intermediates and model

14


compounds help us unravel these complexprocesses and define reaction mechanisms. In allprojects, modern molecular biology techniquesprovide site-directed mutants that permitalterations in structures and reactivities. Loehr

Heme Oxygenase

Heme oxygenase is a fascinating system that usesthe O2-binding affinity of its heme substrate in thecellular degradation of heme to open-chainbiliverdin. These studies are carried out with PaulR. Ortiz de Montellano’s group at U.C. SanFrancisco. The resting heme-heme oxygenaseenzyme substrate complex is much like myoglobin:The heme is linked to the enzyme by an iron-histidine bond, and the iron exists mainly in a six-coordinate, high-spin state with an additional waterligand. The Fe-N(His) bond was identified from itsresonance Raman vibration at 216 cm-1 in theFe(II)-heme complex. The absence of thisfingerprint frequency in the H25A mutant clearlyidentified His25 as the axial ligand. Remarkably,when imidazole was added to the inactive H25Apreparation, activity was fully restored. Ourcurrent efforts, in collaboration with Angela Wilksat the University of Maryland, examine thestructure and activity of several bacterial hemeoxygenases. Loehr and Moënne-Loccoz

Oxygen Activation by Iron Proteins

Several diiron enzymes react with molecularoxygen to form powerful oxidizing agents importantin biology. Examples include (i) ribonucleotidereductase protein R2, which oxidizes its tyrosine122 to its catalytically important neutral radicalform; (ii) methane monooxygenase, whosehydroxylase component oxidizes hydrocarbons toalcohols; (iii) plant desaturases, which oxidize fattyacids to olefins, e.g., stearoyl to oleoyl; and (iv)ferroxidase reactions, in which Fe2+ is oxidized toFe3+. A common feature of these enzymes appearsto be the formation of an initial peroxointermediate from the reduced enzyme. However, inthe respiratory protein, hemerythrin, binding ofdioxygen is accomplished by reduction to peroxidein a reaction that is readily reversible. Inribonucleotide reductase, peroxide is similarlyformed but decomposes irreversibly to a ferrylintermediate that is capable of carrying outoxidative chemistry. This dichotomy of behavior isreminiscent of the respiratory vs. peroxidasefunctions of different heme-containing proteins. Weare interested in determining common principlesthat influence the pathways of oxygen utilization.This problem is being approached by structuralelucidation of the iron sites in the proteinsthemselves and in model complexes, as well as bystudying mechanisms of their reactions with oxygen-containing substrates. Loehr and Moënne-Loccoz

Interaction of Nitric Oxide with Metalloproteins

Nitric oxide (NO) is of intense interest due to itsrole in a diverse range of biological processes. Theimportance of NO in mammalian physiology isindicated by the award of the 1998 Nobel Prize forMedicine for the discovery of its role as a signalingmolecule in the cardiovascular system. In bacteria,NO is produced as an intermediate during

denitrification — the process by which certainorganisms convert nitrate to N2 or N2O. Theproduction of NO is the first opportunity for fixednitrogen to be lost from the soil to the atmosphere,with implications ranging from fertilizer loss toatmospheric pollution. Throughout biological NOchemistry, proteins with Fe- or Cu-containingactive sites play a central role in generating andreleasing NO as well as in sensing and initiatingchemistry in response to changes in NO levels. Ourresearch is aimed at investigating the structuresand mechanisms of these metalloproteins throughthe use of a variety of spectroscopic, biochemicaland kinetic techniques. Andrew

Regulation of Long Chain Fatty Acid Transport andOxidation in Mammalian Heart and Liver

The rate-limiting step in ß-oxidation is theconversion of long-chain acyl-CoA to acylcarnitine,a reaction catalyzed by the outer mitochondrialmembrane enzyme carnitine palmitoyltransferase I(CPTI) and inhibited by malonyl-CoA. Theacylcarnitine is then translocated across the innermitochondrial membrane by thecarnitine/acylcarnitine translocase and convertedback to acyl-CoA by CPTII. This reaction in intactmitochondria is inhibited by malonyl-CoA, the firstintermediate in fatty acid synthesis, suggestingcoordinated regulation of fatty acid oxidation andsynthesis. Although CPTII has been examined indetail, studies on CPTI have been hampered by aninability to purify CPTI in an active form fromCPTII. In particular, it has not been conclusivelydemonstrated that CPTI is even catalytically active,or whether sensitivity of CPTI to malonyl-CoA is anintrinsic property of the enzyme or is contained ina separate regulatory subunit that interacts withCPTI. To address these questions, the genes forhuman heart muscle M-CPTI and rat liver LCPTIand CPTII were separately expressed in Pichiapastoris, a yeast with no endogenous CPT activity.High levels of CPT activity were present in purifiedmitochondrial preparations from both CPTI- andCPTII-expressing strains. Furthermore, CPTIactivity was highly sensitive to inhibition bymalonyl-CoA while CPTII was not. Thus, CPTcatalytic activity and malonyl-CoA sensitivity arecontained within a single CPTI-polypeptide inmammalian mitochondrial membranes. Mylaboratory is the first to describe the kineticcharacteristics for the yeast-expressed CPTIs, thefirst such report for a CPTI enzyme in the absenceof CPTII. Both yeast-expressed M-CPTI and L-CPTIare inactivated by detergent solubilization.However, removal of the detergent in the presenceof phospholipids resulted in the recovery ofmalonyl-CoA-sensitive CPTI activity, suggesting thatCPTI requires a membranous environment. CPTI isthus reversibly inactivated by detergents. We haveisolated and sequenced the promoter region of thegene for the human heart M-CPTI. We have mappedthe malonyl-CoA and substrate binding sites inhuman heart M-CPTI and liverL-CPTI by deletion, site-directed mutagenesis andchemical modification studies using residue-specific reagents. Our deletion and point mutationanalyses have demonstrated that glutamate-3 andhistidine-5 are necessary for malonyl-CoA

inhibition and binding of CPTI but not for catalysis.We will determine the structural basis for the highmalonyl-CoA sensitivity of M-CPTI by constructingchimeras between M-CPTI and L-CPTI and by site-directed mutagenesis. We will prepare milligramquantities of the expressed highly purified humanheart M-CPTI and liver L-CPTI for structuralcharacterization studies. Finally, we plan to studythe regulation of human heart M-CPTI geneexpression by hormonal, developmental and dietaryfactors. Our goal is to elucidate the molecularmechanism of the regulation of fatty acid transportand oxidation in mammalian cells. Woldegiorgis

The Mitochondrial ATP-sensitive K+ Channel (mitoKATP)

MitoKATP resides in the inner membrane ofmitochondria, where it serves to regulate thevolume of mitochondrial compartments and also totrigger cell signaling leading to cardioprotectionand gene transcription. We showed that mitoKATP

mediates the actions of potassium channel openersand ischemic preconditioning to protect the heartagainst ischemia-reperfusion injury. We are nowworking to understand the mechanisms of thiseffect and the normal physiological role of mitoKATP

in heart and brain. We introduced techniques forpurification and reconstitution of mitoKATP in lipidvesicles and use this preparation to study thetransport kinetics of the channel. We havepurified the mitoKATP subunits to homogeneityand will use these to obtain the molecularstructure of mitoKATP. Garlid

Mitochondrial Uncoupling Proteins

Our laboratory was the first to demonstratereconstitutive activity of the new uncouplingproteins, UCP2 and UCP3, and we have long beenactive in the study of UCP1. Flux studies inproteoliposomes containing UCP have led to a newmechanism of UCP-mediated uncoupling in whichthe fatty acid anion is transported by UCP and theprotonated fatty acid cycles spontaneously backacross the bilayer to deliver protons. Garlid

Mitochondrial Bioenergetics

Progress in understanding mitochondrialbioenergetics has not kept pace with the enormousprogress in structure-function of the enzymes ofoxidative phosphorylation. This occurs at a timewhen understanding bioenergetics at thephysiological level is most needed, in view of theincreased recognition of the roles played bymitochondria in cell physiology andpathophysiology. A number of unresolved questionsrelating to the mechanism of energy conservationin mitochondria are being addressed by theoreticaland experimental approaches. Subjects beinginvestigated include the question of redox slip;volume activation of electron transport; and therole of the intermembrane space in regulatingenergy transfers between matrix and cytosol. Garlid

Anaerobiosis of Bacillus subtilis

A gram-positive soil bacterium, B. subtilis, ishighly amenable to genetic analysis and has beenused as a model system to study fundamentalmicrobiological research. In addition, B. subtilis ismedically and industrially important since itproduces a variety of antibiotics and extracellular

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B I O C H E M I S T R Y A N D M O L E C U L A R B I O L O G Y | B M B

enzymes. Although the organism has been widelyused, it has been mistakenly referred to as a strictaerobe until recently. Our studies, together withothers, have shown that B. subtilis is able to growunder anaerobic conditions by utilizing nitrate ornitrite as an alternative electron acceptor. In theabsence of terminal electron acceptors, itundergoes fermentative growth. Our research aimsinclude elucidation of the regulatory mechanismsthrough which the cells adapt to oxygen limitation.Molecular genetic and biochemical approaches areapplied. Nakano

Two Physiological Roles of Nitrate and Nitrite Reductases

Nitrate and nitrite reductases have two roles inmetabolism of B. subtilis: assimilation ofnitrate/nitrite and anaerobic respiration. Twogenetically and biochemically distinct nitratereductases are present to fulfill the dual roles; incontrast, a single nitrite reductase functions inboth assimilation and respiration. The functionaldifferences of the enzymes correspond to thedifference in gene regulation. We have studied howthese nitrate and nitrite reductase genes areregulated in response to nitrogen and oxygenlimitation by promoter analysis of these genes andidentification of trans-acting factors. Themechanisms of transcriptional activation of thenitrate/nitrite reductase genes are beinginvestigated. Nakano

ResD-ResE Two-Component Signal Transduction System

Bacteria often encounter sudden environmentalchanges. Cells cope with such changes by anelaborate network of adaptive responses. The two-component signal transduction system senses andthen processes information derived fromenvironmental changes so that the cell can choosethe appropriate adaptive response. This simplesignal transduction system is widespread inbacteria and also found in plants and lowereukaryotes. ResE is a histidine kinase and ResD isa response regulator of this large protein family.We have shown that ResD and ResE areindispensable for anaerobic respiration inB. subtilis. A specific signal derived by oxygenlimitation is recognized by the N-terminal inputdomain of the ResE kinase leading toautophosphorylation of a conserved histidineresidue in the C-terminal transmitter domain. Thisphosphoryl group is then transferred to aspartatein the conserved N-terminal domain of ResD,altering the activity of its C-terminal domain as atranscriptional activator. The ResD-ResE signaltransduction system is activated by oxygenlimitation or by addition of nitric oxide generators.The objectives of our studies are to determine howResE senses oxygen limitation or nitric oxide andhow anaerobically induced genes are activated byResD. Nakano

Flavohemoglobin (Hmp)

Flavohemoglobin is a ubiquitous protein present inorganisms ranging from Escherichia coli toSaccharomyces cerevisiae. The N-terminal part ofthe protein has similarity to hemoglobin, and theC-terminus is homologous to reductase with aflavin-binding domain. Recent studies showed that

flavohemoglobin is involved in detoxification ofnitric oxide. B. subtilis hmp was identified amonggenes, expression of which is induced by oxygenlimitation. The anaerobic induction of hmp requiresthe ResD-ResE signal transduction pairs andnitrite. The expression is also induced byexogenous nitric oxide through ResDE-dependentand -independent mechanisms. The detailedregulatory mechanism of hmp expression and itsfunctional role in anaerobiosis are underinvestigation. Nakano

Peptide Antibiotic Biosynthesis

Our research is aimed at understanding themechanism of antimicrobial peptide biosynthesis.Peptide antibiotics are synthesized either by thenon-ribosomal thiotemplate mechanism or arebacteriocins that are gene-encoded and synthesizedon ribosomes. Both classes are used as bio-controlagents in medicine, agriculture and the foodindustry. Non-ribosomally synthesized peptides alsoinclude iron-scavenging siderophores which arerequired for virulence by some bacterial pathogensand toxins produced by a variety of bacterial andfungal species that infect plants. A knowledge ofhow peptide and bacteriocin biosyntheses arecarried out at the molecular level may provideinformation that can ultimately be used to designways to control the virulence of pathogenicmicroorganisms and to synthesize peptides with adefined structure and bioactivity. The spore-forming bacterium Bacillus subtilis will produce anabundance of peptide antibiotics and bacteriocinsunder conditions of nutritional stress and oxygenlimitation. The genes encoding the enzymes thatcatalyze peptide biosynthesis have been cloned,and we are engaged in genetic engineering of theenzymes to understand the mechanism ofantimicrobial peptide biosynthesis. Zuber

Prokaryotic Signal Transduction/Gene Regulation

Bacteria can respond in a variety of ways to agrowth-restricting environment. Prolongedexposure to a nutritionally poor environmentresults in the induction of antibiotic biosynthesis,functions required for cell motility and processes ofcellular differentiation that give rise to highlyresistant cell types. How cells respond tonutritional stress is profoundly influenced by celldensity. Extracellular signal molecules accumulatein the local environment of densely populated cellcultures and trigger antibiotic production anddevelopmental processes such as sporulation andgenetic competence. The objective of our researchis to understand, in molecular terms, theregulatory networks that cells utilize to choose themost appropriate response to harsh conditions. Inthe spore-forming bacterium Bacillus subtilis,establishment of genetic competence is co-regulated with peptide antibiotic biosynthesis by acomplex network of signal transduction pathwaysthat utilize protein components common to allprokaryotic and most eukaryotic organisms. Zuber

Biochemistry of Lignin Degradation

Lignin is the most abundant renewable aromaticpolymer, constituting approximately 25 percent ofwoody plant cell walls. Our multidisciplinary

RESEARCH FACILIT IESThe department is well equipped to carry on a vigorous research program. Instruments andequipment available in the department include:

• Gas chromatograph/mass spectrometer

w i th computer data system

• High-reso lut ion mass spectrometer

• Capi l lary co lumn gas chromatographs with f lame

ion izat ion detectors

• Four ier t ransform infrared spectrometers

• Four ier t ransform Raman

spectrometer w i th CW Nd:YAG laser

• X-band e lectron paramagnet ic

resonance spectrometer

• Ultrav io let/v is ib le/near- in f rared spectrophotometers

• Scanning f luorescence spectrophotometers

• Magnet ic c i rcu lar d ichro ism (MCD) spectrometer

• Diode array UV/VIS spectrophotometer

• Laser Raman spectrophotometer

• Raman spectrograph with CCD detector

• Ar, Kr, He-Cd, He-Ne, and dye lasers

• High-vacuum l ines

• Phosphor imager

• Contro l led atmosphere react ion chamber

• Super speed centr i fuges

• Ultracentr i fuges

• HPLCs

• FPLCs

• Fract ion co l lectors

• Liqu id sc int i l lat ion systems

• Gel e lectrophores is systems

• Laminar f low hoods for ster i le cu l ture

• Growth chambers

• Constant temperature rooms

• Light and e lectron microscopes

• Ultraf i l t rat ion systems

• Autoc laves

• Photographic fac i l i t ies

• Probe type son icators and extruder

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research program aims to understand and exploitthe fungal degradation of this underutilizedresource. The metabolic pathways and enzymaticcomponents of the lignin degradative system areexamined using biochemical, enzymological andmolecular biological methods. Two novelextracellular heme peroxidases (lignin peroxidaseand manganese peroxidase) involved in thedegradation of lignin were discovered in ourlaboratory. Lignin peroxidase oxidizes a variety ofnonphenolic lignin model compounds and prioritypollutants. Manganese peroxidase oxidizes MnII toMnIII, which in turn oxidizes phenolic andnonphenolic substrates. The structures, activesites, mechanisms, catalytic cycles and regulationof these enzymes are being characterized in ourlaboratory and via collaborations usingspectroscopy, stopped-flow kinetics, proteinchemistry, enzymology, X-ray crystallography andbio-organic and molecular genetic methods.Recently, we developed a homologous expressionsystem for these peroxidases. This system allowsstructure/function studies by site-directedmutagenesis. Applications for lignin-degradingsystems include the more efficient utilization ofbiomass, nonpolluting forest products technologiesand toxic waste cleanup. We also are studyingseveral intracellular enzymes such as quinonereductases, ring-cleaving dioxygenases andreductive dehalogenases that are involved in ligninand pollutant degradation. Gold

Molecular Biology and Genetics of Phanerochaetechrysosporium and Its Lignin-Degrading System

We are isolating and sequencing the genesencoding components of the P. chrysosporiumlignin-degrading system. These include genesencoding lignin and manganese peroxidases, anovel quinone reductase and several other genes.We are analyzing the coding and promoter regionsof these genes and studying the regulation of theirtranscription. We have discovered that Mnperoxidase is regulated by Mn ion, the substratefor the enzyme, as well as by nutrient nitrogen,heat shock and oxidative stress. Using reportergenes and RT-PCR, we are elucidating themolecular mechanisms involved in Mn peroxidasegene regulation. Recently we developed atranscriptional reporter system based on the geneencoding green fluorescent protein from jellyfish.We also are undertaking molecular biology studieson the manganese peroxidase gene of Dichomitussqualens and on its heterologous expression inP. chrysosporium. Gold

Biodegradation of Aromatic Pollutants

The nonspecific and oxidative nature of the lignindegradation system of the fungus Phanerochaetechrysosporium enables this organism to degrade avariety of toxic aromatic pollutants, includingpolychlorinated phenols, polychlorinated dioxins,chlorophenoxyacetic acid and nitrotoluenes. We areexamining the biochemical pathways, enzymes andregulatory mechanisms involved in the totaldegradation of these compounds. We have shownthat the fungus utilizes extracellular peroxidases aswell as intracellular quinone reductases, reductivedehalogenases and dioxygenases to carry out these

processes. We are attempting to characterize theseenzymes and their encoding genes to more fullyunderstand the mechanisms involved in thedegradation of these pollutants. Recently wediscovered a novel reductive dechlorination systemin white-rot fungi that removes chlorines fromchlorinated hydroquinones. This system is beingexamined by biochemical and molecular biologicalmethods. Gold

Oxidative Enzymes Involved in FungalCellulose Degradation

Cellulose constitutes 40 percent to 60 percent ofplant cell wall material; its biotechnologicalconversion, initially to glucose and then to ethanol,can provide an alternative source of energy. Thisapplication requires a complete understanding ofthe various enzymes involved in fungal cellulosedegradation. The cellulose-degrading cultures ofPhanerochaete chrysosporium produce a uniquehemoflavoenzyme, cellobiose dehydrogenase (CDH),which oxidizes cellobiose to cellobionolactone. Wehave purified CDH to homogeneity in high yields.Cellulases bind to crystalline cellulose using aspecific cellulose-binding domain. CDH appears tohave a similar domain for cellulose binding. Theamino acid sequence responsible for cellulosebinding and the binding mechanism are underinvestigation. Our recent research suggests that apossible physiological role of CDH is to enhancecrystalline cellulose degradation by cellulases, therate-limiting step in the bioconversion of celluloseto glucose. A detailed study of the structure,function and mechanism of CDH usingspectroscopic, biochemical and molecularbiological methods is in progress. Gold

N I N I A N J . B L A C K B U R NProfessor and Department HeadPh.D., Inorganic ChemistryUniversity of Dundee, Scotland, U.K., [email protected]

R E S E A R C H I N T E R E S T S

Structure and function of oxidaseand oxygenase metalloenzymes;spectroscopy of metal sites inproteins with emphasis on EPR,EXAFS, absorption edge, and FTIRspectroscopies; coordinationchemistry and biochemistry ofcopper. Biochemistry of metaltrafficking in cells.

R E P R E S E N TAT I V E P U B L I C AT I O N SF.C. Rhames, N.N. Murthy, K.D. Karlin

and N.J. Blackburn, “Isocyanide Bindingto the Copper(I) Centers of theCatalytic Core of PeptidylglycineMonooxygenase (PHMcc).” J. Biol.Inorg. Chem. 2001, 6, 567-577.

S. Jaron and N.J. Blackburn,“Characterization of a Half-ApoDerivative of PeptidylglycineMonooxygenase. Insight into theReactivity of Each Active Site Copper.”Biochemistry 2001, 40, 6867-6875.

N.J. Blackburn, F.C. Rhames, M.Ralle and S. Jaron, “Major Changesin Copper Coordination AccompanyReduction of PeptidylglycineMonooxygenase: Implications forElectron Transfer and the CatalyticMechanism.” J. Biol. Inorg. Chem.2000, 5, 341-353.

J.F. Eisses, J.P. Stasser, M. Ralle,J.H. Kaplan and N.J. Blackburn,“Domains I and III of Human CopperChaperone for Superoxide DismutaseInteract via a Cysteine-BridgedDicopper(I) Cluster.” Biochemistry2000, 38, 7337-7342.

N.J. Blackburn, M. Ralle, R. Hassettand D.J. Kosman, “SpectroscopicAnalysis of the Trinuclear Cluster in theFet3 Protein from Yeast, a MultinuclearCopper Oxidase.” Biochemistry 2000,39, 2316-2324.

C O L I N A N D R E WResearch Assistant ProfessorPh.D., Chemistry, University of NewcastleUpon Tyne, [email protected]


Bioinorganic chemistry; structure,function and spectroscopy ofmetalloenzymes; generation,mobilization and sensing of nitricoxide by metalloproteins;redox-active copper proteins.

R E P R E S E N TAT I V E P U B L I C AT I O N SC.R. Andrew, E.L. Green, D.M. Lawson

and R.R. Eady, “Resonance RamanStudies of Cytochrome c Support theBinding of NO and CO to Opposite Sidesof the Heme: Implications for LigandDiscrimination in Heme-Based Sensor.”Biochemistry 2001, 40, 4115-4122.

D.M. Lawson, C.E.M. Stevenson, C.R.Andrew and R.R. Eady, “UnprecedentedProximal Binding of Nitric Oxide to Heme:Implications for Guanylate Cyclase.”EMBO J. 2000, 19, 5661-5671.

J.P. Hannan, S.L. Davy, G.R. Moore,R.R. Eady and C.R. Andrew “Effect ofNickel(II) Substitution on theResonance Raman and NMR Spectraof Alcaligenes xylosoxidans Azurin II:Implications for Axial-Ligand BondingInteractions in Cupredoxin ActiveSites.” Biol. Inorg. Chem. 1998, 3,282-291.

C.R. Andrew, J. Han, T. den Blauuwen,G. van Pouderoyen, E. Vijgenboom,G.W. Canters and J. Sanders-Loehr,“Cysteine Ligand Vibrations areResponsible for the Complex ResonanceRaman Spectrum of Azurin.” Biol.Inorg. Chem. 1997, 2, 98-107.

C.R. Andrew and J. Sanders-Loehr,“Copper-Sulfur Proteins: Using RamanSpectroscopy to Predict CoordinationGeometry” [Review]. Acc. Chem. Res.1996, 29, 365-372.

K E I T H D . G A R L I DProfessorM.D., The Johns HopkinsUniversity School of Medicine, 1961Dr. technicae norwegiensis,Physical ChemistryNorwegian Institute of Technology, [email protected]


The structure-function of themitochondrial ATP-sensitive K+

channel (mitoKATP) and its role incardioprotection and cardiacphysiology; the structure-functionof uncoupling proteins;mitochondrial and cellularbioenergetics.

R E P R E S E N TAT I V E P U B L I C AT I O N SR. Bajgar, S. Seetharaman, A.J.

Kowaltowski, K.D. Garlid and P. Paucek,“The ATP-Sensitive Potassium Channelof Brain Mitochondria.” J. Biol. Chem.2001, 276, 33369-33374.

A.J. Kowaltowski, S. Seetharaman, P.Paucek and K.D. Garlid, “BioenergeticConsequences of Opening theATP-Sensitive K+ Channel of HeartMitochondria.” Am. J. Physiol. HeartCirc. Physiol. 2001, 280, H649-H657.

K.D. Garlid, M. Jaburek, P. Jezekand M. Varecha, “How Do UncouplingProteins Uncouple?” Biochim. Biophys.Acta 2000, 1459, 383-389.

G.J. Grover and K.D. Garlid,“ATP-Sensitive Potassium Channels:A Review of Their CardioprotectivePharmacology.” J. Mol. Cell. Cardiol.2000, 32, 677-695.

K.D. Garlid, P. Paucek, V. Yarov-Yarovoy, H.N. Murray, R.B. Darbenzio,A.J. D’Alonzo, N.J. Lodge, M.A. Smithand G.J. Grover, “CardioprotectiveEffect of Diazoxide and its Interactionwith Mitochondrial ATP-Sensitive K+

Channels. Possible Mechanism ofCardioprotection.” Circ. Res. 1997, 81,1072-1082.

M I C H A E L H . G O L DInstitute ProfessorPh.D., BiochemistryState University of N.Y. at Buffalo, [email protected]


Biochemistry; molecular biology;genetics of fungi; fungaldegradation of lignin andenvironmental pollutants;structure and function of novelperoxidases; structure expressionand regulation of fungal genes;biotechnology.

R E P R E S E N TAT I V E P U B L I C AT I O N SG.V.B. Reddy and M.H. Gold,

“Purification and Characterizationof Glutathione Conjugate Reductase:A Component of theTetrachlorohydroquinone ReductiveDehalogenase System fromPhanerochaete chrysosporium.” Arch.Biochem. Biophys. 2001, 391, 271-277.

F.A.J. Rotsaert, B. Li, V. Renganathanand M.H. Gold, “Site-directedMutagenesis of the Heme Axial Ligandsin the Hemoflavoenzyme, CellobioseDehydrogenase.” Arch. Biochem.Biophys. 2001, 390, 206-214.

H.L. Youngs, M.D. Sollewijn Gelpke,D. Li, M. Sundaramoorthy and M.H.Gold, “The Role of E39 in MnII Bindingand Oxidation by ManganesePeroxidase from Phanerochaetechrysosporium.” Biochemistry 2001,40, 2243-2250.

D. Li, H.L. Youngs and M.H. Gold,“Heterologous Expression of aThermostable Manganese Peroxidasefrom Dichomitus squalens inPhanerochaete chrysosporium.” Arch.Biochem. Biophys. 2001, 385, 348-356.

B. Ma, M.B. Mayfield and M.H. Gold,“The Green Fluorescent Protein GeneFunctions as a Reporter of GeneExpression in Phanerochaetechrysosporium.” Appl. Environ.Microbiol. 2001, 67, 948-955.

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F A C U L T Y | B I O C H E M I S T R Y A N D M O L E C U L A R B I O L O G Y | B M B

T H O M A S M . L O E H RProfessorPh.D., Inorganic ChemistryCornell University, [email protected]


Metallobiochemistry; biologicalrole of transition metals;molecular and electronicstructures of metalloenzyme activesites; chemistry of O2 metabolism;metal-oxo intermediates;resonance and FT Raman, FT-IR, and EPR spectroscopy.

R E P R E S E N TAT I V E P U B L I C AT I O N S J. Hirst, S.K. Wilcox, J. Ai, P. Moënne-

Loccoz, T.M. Loehr and D.B. Goodin,“Replacement of the Axial HistidineLigand with Imidazole in Cytochromec Peroxidase. 2. Effects on HemeCoordination and Function.”Biochemistry 2001, 40, 1274-1283.

J. Baldwin, W.C. Voegtli, N. Khidekel,P. Moënne-Loccoz, C. Krebs, B.A. Ley,B.H. Huynh, T.M. Loehr, A. C.Rosenzweig and J.M. Bollinger, Jr.,“Rational Reprogramming of the R2Subunit of Escherichia coliRibonucleotide Reductase into a Self-Hydroxylating Monooxygenase.” J. Am.Chem. Soc. 2001, 123, 7017-7030.

E.L. Green, S. Taoka, R. Banerjee andT.M. Loehr, “Resonance RamanCharacterization of the Heme Cofactorin Cystathionine Beta-Synthase.Identification of the Fe-S(Cys) Vibrationin the Six-Coordinate Low-Spin Heme.”Biochemistry 2001, 40, 459-463.

Y. Liu, L. Koenigs Lightning, H.-w.Huang, P. Moënne-Loccoz, D.J.Schuller, T.L. Poulos, T.M. Loehr andP.R. Ortiz de Montellano, “Replacementof the Distal Glycine 139 TransformsHuman Heme Oxygenase-1 into aPeroxidase.” J. Biol. Chem. 2000, 275,34501-34507.

L.S. Koo, R.A. Tschirret-Guth, W.E.Straub, P. Moënne-Loccoz, T.M. Loehrand P.R. Ortiz de Montellano, “TheActive Site of the Thermophillic cyp119from Sulfolobus solfataricus.” J. Biol.Chem. 2000, 275, 14112-14123.

P I E R R E M O Ë N N E - L O C C O ZAssistant ProfessorPh.D., BiophysicsUniversity of Pierre & Marie Curie,Paris VI, [email protected]


Structure-function relationshipswithin proteins. Metallo- andheme-proteins. Spectroscopicstudies of enzyme-active sites and their cofactors. Reactionintermediates within catalysts.

R E P R E S E N TAT I V E P U B L I C AT I O N SR.A. Ghiladi, K.R. Hatwell, K.D. Karlin,

H.-w. Huang, P. Moënne-Loccoz,C. Krebs, B.H. Huynh, L.A. Marzilli,R.J. Cotter, S. Kaderli and A.D.Zuberbuhler, “Dioxygen Reactivity ofMononuclear Heme and CopperComponents Yielding a High-SpinHeme-Peroxo-Cu Complex.”J. Am. Chem. Soc. 2001, 123,6183-6184.

K. Auclair, P. Moënne-Loccoz andP.R. Ortiz de Montellano, “Roles of theProximal Heme Thiolate Ligand inCytochrome P450cam.” J. Am. Chem.Soc. 2001, 123, 4877-4885.

P. Moënne-Loccoz, O.-M.H. Richter,H.-w. Huang, I. Wasser, R.A. Ghiladi,K.D. Karlin and S. de Vries, “NitricOxide Reductase from Paracoccusdenitrificans Contains an Oxo-BridgedHeme/Non-Heme Diiron Center.” J. Am.Chem. Soc. 2000, 122, 9344-9345.

A. Wilks and P. Moënne-Loccoz,“Identification of the Proximal LigandHis-20 in Heme Oxygenase (HmuO)from Corynebacterium diphtheriae.Oxidative Cleavage of the HemeMacrocycle Does Not Require theProximal Histidine.” J. Biol. Chem.2000, 275, 11686-11692.

P. Moënne-Loccoz, C. Krebs,K. Herlihy, D.E. Edmondson, E.C. Theil,B.H. Huynh and T.M. Loehr, “TheFerroxidase Reaction of FerritinReveals a Diferric mu-1,2 BridgingPeroxide Intermediate in Common withOther O2 - Activating Non-Heme DiironProteins.” Biochemistry 1999, 38,5290-5295.

M I C H I K O N A K A N OResearch Associate ProfessorPh.D., Cell BiologyUniversity of Tokyo, [email protected]


Anaerobiosis of Bacillus subtilis;oxygen-controlled gene regulation;two-component signal transductionsystem; transcriptional activation;nitrate/nitrite reductases;flavohemoglobin; anaerobicelectron transport; nitricoxide signaling.

R E P R E S E N TAT I V E P U B L I C AT I O N SM.M. Nakano and Y. Zhu, “Involvement

of the ResE Phosphatase Activity inDown-Regulation of ResD-ControlledGenes in Bacillus subtilis DuringAerobic Growth.” J. Bacteriol. 2001,183, 1938-1944.

M.M. Nakano, Y. Zhu, M. LaCelle,X. Zhang and F.M. Hulett, “Interactionof ResD with Regulatory Regions ofAnaerobically Induced Genes inBacillus subtilis.” Mol. Microbiol. 2000,37, 1198-1207.

M.M. Nakano, Y. Zhu, J. Liu, D.Y.Reyes, H. Yoshikawa and P. Zuber,“Mutations Conferring Amino AcidResidue Substitutions in the Carboxy-Terminal Domain of RNA Polymerasealpha Can Suppress clpX and clpP withRespect to Developmentally RegulatedTranscription in Bacillus subtilis.” Mol. Microbiol. 2000, 37, 869-884.

M.M. Nakano, G. Zheng and P. Zuber,“Dual Control of sbo-alb OperonExpression by the Spo0 and ResDESystems of Signal Transduction UnderAnaerobic Conditions in Bacillussubtilis.” J. Bacteriol. 2000, 182,3274-3277.

C. Jourlin-Castelli, N. Mani, M.M.Nakano and A.L. Sonenshein, “CcpC,a Novel Regulator of the LysR FamilyRequired for Glucose Repression of thecitB Gene in Bacillus subtilis.” J. Mol.Biol. 1999, 295, 865-878.

P E T R P A U C E KResearch Assistant ProfessorDr.Rer.Nat., Biophysics and Chemical PhysicsPalacky University (CZ), 1988Ph.D., Biological ScienceThe Academy of Sciences of the Czech Republic, [email protected]


Molecular biophysics ofmitochondrial cation transportersand channels, with emphasis onthe ATP-dependent K+ channel incardiac and brain mitochondria;receptor properties and their rolesin cellular signaling, bioenergeticsand pharmacology.

R E P R E S E N TAT I V E P U B L I C AT I O N SR. Bajgar, S. Seetharaman, A.J.

Kowaltowski, K.D. Garlid and P. Paucek,“Identification and Properties of aNovel Intracellular (Mitochondrial)ATP-Sensitive Potassium Channel inBrain.” J. Biol. Chem. 2001, 276,3369-33374.

G.J. Grover, A.J. D’Alonzo, K.D.Garlid, N.J. Lodge, P.G. Sleph, R.B.Darbenzio, T.A. Hess, M.A. Smith, P.Paucek and K.S. Atwal, “PharmacologicCharacterization of BMS-101-05, aMitochondrial KATP Opener with NoPeripheral Vasodilator or CardiacAction Potential Shortening Activity.”J. Pharmacol. Exp. Ther. 2001, 297,1184-1192.

A.J. Kowaltowski, S. Seetharaman,P. Paucek and K.D. Garlid, “Bioener-getic Consequences of Opening theATP-Sensitive K+ Channel of HeartMitochondria.” Am. J. Physiol. HeartCirc. Physiol. 2001, 280, H649-H657.

M. Jaburek, V. Yarov-Yarovoy,P. Paucek, W. Li and K.D. Garlid“State-Dependent Inhibition of theMitochondrial KATP Channel byGlyburide and 5-Hydroxydecanoate.”J. Biol. Chem. 1998, 273, 13578.

K.D. Garlid, P. Paucek, V. Yarov-Yarovoy, H.N. Murray, R.B. Darbenzio,A.J. D’Alonzo, N.J. Lodge, M.A. Smithand G.J. Grover. “CardioprotectiveEffect of Diazoxide and Its Interactionwith Mitochondrial ATP-Sensitive K+

Channels: Possible Mechanism ofCardioprotection.” Circ. Res. 1997, 81, 1072.

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M A R T I N A R A L L EResearch ScientistPh.D., Chemistry University of Bonn, Germany, [email protected]


Metallobiochemistry; structure-function analysis ofmetalloenzymes. Spectroscopiccharacterization of coppertransporters such as Wilson’s andMenkes disease protein, usingextended X-ray absorption finestructure spectroscopy (EXAFS).Cloning, overexpression andcharacterization of proteinsinvolved in copper transport in themammalian cell.

R E P R E S E N TAT I V E P U B L I C AT I O N SJ.F. Eisses, J.P. Stasser, M. Ralle, J.H.

Kaplan and N.J. Blackburn, “Domains Iand III of Human Copper Chaperone forSuperoxide Dismutase Interact via aCysteine-Bridged Dicopper(I) Cluster.”Biochemistry 2000, 38, 7337-7342.

N.J. Blackburn, M. Ralle, R. Hassettand D.J. Kosman, “SpectroscopicAnalysis of the Trinuclear Cluster in theFet3 Protein from Yeast, a MultinuclearCopper Oxidase.” Biochemistry 2000,39, 2316-2324.

M. Ralle, M.L. Verkhovskaya,J.E. Morgan, M.I. Verkhovsky, M.Wikstrom and N.J. Blackburn,“Coordination of CuB in Reduced andCO-liganded States of Cytochrome bo3from Escherichia coli. Is Chloride Ion aCofactor?” Biochemistry, 1999, 38,7185-7194.

N.J. Blackburn, M. Ralle, E. Gomez,M.G. Hill, A. Pastuszyn, D. Sanders andJ.A. Fee, “Selenomethionine-substitutedThermus thermophilus Cytochrome ba3:Characterization of the CuA Site by Seand Cu K-EXAFS.” Biochemistry, 1999,38, 7075-7084.

M. Ralle, M.J. Cooper, S. Lutsenkoand N.J. Blackburn, “The MenkesDisease Protein Binds Copper via Novel2-Coordinate Cu(I)-Cysteinates in theN-Terminal Domain.” J. Am. Chem.Soc. 1998, 120, 13525-13526.

L . E . L . ( B E T S ) R A S M U S S E NResearch ProfessorPh.D., NeurochemistryWashington University (St. Louis), [email protected]


Mammalian chemocommunication:the transport, olfactory andvomeronasal organ reception of(Z)-7-dodecenyl acetate, the sexpheromone of the Asian elephant;the origin and synthesis of (Z)-7-dodecenyl acetate; identificationand function of pheromones andchemical signals of the elephant-unique temporal gland.

R E P R E S E N TAT I V E P U B L I C AT I O N SL.E.L. Rasmussen, “Source

and Cyclic Release Pattern of (Z)-7-Dodecenyl Acetate, the PreovulatoryPheromone of the Female AsianElephant.” Chem. Senses 2001, 26,611-623.

L.E.L. Rasmussen and V.Krishnamurthy, “How Chemical SignalsIntegrate Asian Elephant Society: TheKnown and the Unknown.” Zoo Biol.2000, 19, 405-423.

L.E.L. Rasmussen, “ElephantOlfaction.” ChemoSenses, 1999, 2, 4-5.

L.E.L. Rasmussen and T.E. Perrin,“Physiological Correlates of Musth:Lipid Metabolites and ChemosignalComposition.” Physiol. Behav. 1999, 67,539-549.

L.E.L. Rasmussen, “ChemicalCommunication: An Integral Part ofFunctional Asian Elephant (Elephasmaximus) Society.” Ecoscience 1998,5, 410-426.

M AT T H E W S . S A C H SAssociate ProfessorPh.D., BiologyMassachusetts Institute ofTechnology, [email protected]


Mechanisms of translational andtranscriptional control thatregulate the expression of theNeurospora crassa arg-2 andSaccharomyces cerevisiaeCPA1 genes; translationalcontrol of human proto-oncogenes;fungal genomes.

R E P R E S E N TAT I V E P U B L I C AT I O N SD.D. Perkins, A. Radford and M.S.

Sachs, The Neurospora Compendium:Chromosomal Loci. Academic Press,2001.

H.S. Kelkar, J. Griffiths, M.E. Case,S.F. Covert, D.A. Hall, C. Keith,J.S. Oliver, M.J. Orbach, M.S. Sachs,J.R. Wagner, M.J. Weise,J.K. Wunderlich and J. Arnold, “TheNeurospora Crassa Genome: LibrariesSorted by Chromosome.” Genetics2001, 157, 979-990.

P. Fang, Z. Wang and M.S. Sachs,“Evolutionarily Conserved Features ofthe Arginine Attenuator Peptide Providethe Necessary Requirements for itsFunction in Translational Regulation.”J. Biol. Chem. 2000, 275, 26710-26719.

A.P. Geballe and M.S. Sachs,“Translational Control by UpstreamOpen Reading Frames,” inTranslational Control of GeneExpression (N. Sonenberg, J.W. B.Hershey and M.B. Mathews, eds.),Cold Spring Harbor Laboratory Press,New York, 2000, pp. 595-614.

Z. Wang, A. Gaba and M.S. Sachs, “A Highly Conserved Mechanism ofRegulated Ribosome Stalling Mediatedby Fungal Arginine Attenuator PeptidesThat Appears Independent of theCharging Status of Arginyl-tRNAs.” J. Biol. Chem. 1999, 274,37565-37574.

J A M E S W. W H I T TA K E RAssociate ProfessorPh.D., BiochemistryUniversity of Minnesota, [email protected]


Electronic structures anddynamics of metalloenzymeactive sites; spectroscopic andcomputational approaches tobiomolecular structure;metalloenzyme mechanisms;enzyme engineering; biologyof metal ions.

R E P R E S E N TAT I V E P U B L I C AT I O N SM.M. Whittaker and J.W. Whittaker,

“Catalytic Reaction Profile for AlcoholOxidation by Galactose Oxidase.”Biochemistry 2001, 40, 7140-7148.

R.A. Edwards, M.M. Whittaker, J.W.Whittaker, E.N. Baker and G.B.Jameson, “Outer Sphere MutationsPerturb Metal Reactivity in ManganeseSuperoxide Dismutase.” Biochemistry2001, 40, 15-27.

M.M. Whittaker and J.W. Whittaker,“Expression of Recombinant GalactoseOxidase by Pichia pastoris.” ProteinExpr. Purif. 2000, 20, 105-111.

M.M. Whittaker and J.W. Whittaker,“Recombinant Superoxide Dismutasefrom a Hyperthermophilic Archaeon,Pyrobaculum aerophilium.” J. Biol.Inorg. Chem. 2000, 5, 402-408.

M.M. Whittaker, V.V. Barynin, S.V.Antonyuk and J.W. Whittaker, “TheOxidized (3,3) State of ManganeseCatalase. Comparison of Enzymes fromThermus thermophilus andLactobacillus plantarum.”Biochemistry 1999, 38, 9126-9136.

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F A C U L T Y | B I O C H E M I S T R Y A N D M O L E C U L A R B I O L O G Y | B M B

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G E B R E TAT E O S W O L D E G I O R G I SAssociate ProfessorPh.D., Nutritional BiochemistryUniversity of Wisconsin-Madison, [email protected]


Regulation of carnitinepalmitoyltransferase I; regulationof long-chain fatty acid transportand oxidation in mammalian cells;regulation of cell metabolism andsignaling by long-chain acyl CoAesters; mitochondrial ion transportand bioenergetics.

R E P R E S E N TAT I V E P U B L I C AT I O N S C. Nicot, F.G. Hegardt, G. Woldegiorgis,

D. Haro and P.F. Marrero, “Pig LiverCarnitine Palmitoyltransferase I,with low Km for Carnitine and HighSensitivity to Malonyl-CoA Inhibition,is a Natural Chimera of Rat Liver andMuscle Enzymes.” Biochemistry 2001,40, 2260-2266.

J. Dai, H. Zhu, J. Shi and G.Woldegiorgis, “Identification byMutagenesis of Conserved Arginineand Tryptophan Residues in Rat LiverCarnitine Palmitoyltransferase IImportant for Catalytic Activity.” J. Biol. Chem. 2000, 275,22020-22024.

J. Shi, H. Zhu, D.N. Arvidson and G.Woldegiorgis, “The First 28 N-TerminalAmino Acid Residues of Human HeartMuscle Carnitine Palmitoyltransferase Iare Essential for Malonyl CoASensitivity and High-Affinity Binding.”Biochemistry 2000, 39, 712-717.

G. Woldegiorgis, J. Shi, H. Zhuand D.N. Arvidson, “FunctionalCharacterization of MammalianMitochondrial Palmitoyltransferases Iand II Expressed in the Yeast Pichiapastoris.” J. Nutr. 2000, 130, 310S-314S.

L. Abu-Elheiga, W.R. Brinkley,L. Zhong, S.S. Chirala, G. Woldegiorgisand S.J. Wakil, “The SubcellularLocalization of Acetyl-CoA Carboxylase2.” Proc. Natl. Acad. Sci. USA 2000,97, 1444-1449.

P E T E R Z U B E RProfessorPh.D., MicrobiologyUniversity of [email protected]


Regulation of prokaryotic geneexpression and development inresponse to stress; signaltransduction; regulation andmechanism of peptide antibioticbiosynthesis; regulation of geneticcompetence in Bacillus subtilis.

R E P R E S E N TAT I V E P U B L I C AT I O N SP. Zuber, “Specificity Through

Flexibility.” Nat. Struct. Biol. 2000,7, 1079-1081.

J. Liu and P. Zuber, “The ClpXProtein of Bacillus subtilus IndirectlyInfluences RNA PolymeraseHoloenzyme Composition and DirectlyStimulates SigmaH-DependentTranscription In Vitro.” Mol. Microbiol.2000, 37, 885-897.

G. Zheng, R. Hehn and P. Zuber,“Mutational Analysis of thesbo-alb Locus of Bacillus subtilis:Identification of Genes Required forSubtilosin Production and Immunity.”J. Bacteriol. 2000, 182, 3266-3273.

M.M. Nakano, Y. Zhu, J. Liu, D.Y.Reyes, H. Yoshikawa and P. Zuber,“Mutations Conferring Amino AcidResidue Substitutions in the Carboxy-Terminal Domain of RNA PolymeraseAlpha Can Suppress clpX and clpP withRespect to Developmentally RegulatedTranscription in Bacillus subtilis.” Mol. Microbiol. 2000, 37, 869-884.

M.M. Nakano, G. Zheng and P. Zuber,“Dual Control of sbo-alb OperonExpression by the Spo0 and ResDESystems of Signal Transduction UnderAnaerobic Conditions in Bacillussubtilis.” J. Bacteriol. 2000, 182,3274-3277.

JOINT FACULTY

D A V I D R . B O O N E

Environmental BiologyPortland State University

J A M E S M . G R E G G

Keck Graduate Instituteof Applied Life Sciences

B E R N A R D A . F O X

Earle A. Chiles Research InstituteProvidence Medical Center

S T E P H E N B . H A L L

Pulmonary and Critical Care MedicineOregon Health & Science University

J A M E S F. P A N K O W

Environmental Science and EngineeringOGI School of Science& Engineering at OHSU

P A U L G . T R AT N Y E K

Environmental Science and EngineeringOGI School of Science& Engineering at OHSU

ADJUNCT FACULTY

G . D O Y L E D A V E S

Consultant

K E N T H E R M S M E Y E R

Oregon Regional Primate Research Center

J A M E S K . H U R S T

Washington State University

G E O R G E D . O L S E N

Oregon Health & Science University

V. R E N G A N AT H A N

Consultant

C A R L C . W A M S E R

Portland State University

RESEARCH ASSOCIATES

E L E N A C R U C E R E S C U

Ph.D., Microbiologyand ParasitologyUniversity of Medicineand Pharmacy, Iassy, Romania.

H O N G - W E I H U A N G

Ph.D., Pharmaceutical ScienceKanazawa University, Japan

M A R T I N J A B Ü R E K

Ph.D., Molecular Biology and BiochemistryOGI School of Science& Engineering at OHSU

S U B R A M A N I A M S E E T H A R A N

M.D., Stanley Medical CollegeUniversity of MadrasMadras, India

M A L AYA L A M S R I D H A R

Ph.D., Organic Chemistry Indian Institute of ScienceBangalore, India

M E I M . W H I T TA K E R

Ph.D., BiochemistryUniversity of Minnesota

G U O L U Z H E N G

Ph.D., Food MicrobiologyUniversity of Arkansas

SENIOR STAFF

D E E P A L I D AT TA

M.Sc., ZoologyDelhi University, India

K A I T L I N G R A M M E R

B.S., GeologyUniversity of Alaska-Fairbanks

M A R Y M AY F I E L D - G A M B I L L

B.S., MicrobiologyOregon State University

S H U N J I N A K A N O

B.S., Molecular BiologyNagoya University, Japan

J A R M I L A P A U C K O VA

M.D., Palacky UniversityCzech Republic

C R A I G S E M R A D

B.S., PhysicsStanford University

M I C H E L L E T R E B E R

B.S., Biological SciencesCalifornia PolytechnicState University

THE DEPARTMENT OF COMPUTER SCIENCE

AND ENGINEERING has an internationallyacclaimed research program. Thebreadth and depth of the researchprogram is evidenced by theresearch projects and researchcenters listed below, and by theeducational program.Four degrees are offered: Master of Sciencein Computer Science and Engineering, Masterof Science in Computational Finance, OregonMaster of Software Engineering, and Doctorof Philosophy in Computer Science andEngineering. In addition to these degrees, weoffer a Certificate in Computational Finance,Applied Computing, and Oregon Master ofSoftware Engineering.

ADMISSION REQUIREMENTSAdmission requirements are the same as thegeneral requirements of the institution.General aptitude GRE scores are required,except in cases of advanced placementadmission for M.S. students (see below). Acandidate must hold a bachelor’s degree incomputer science, mathematics, engineering,one of the biological or physical sciences, orone of the quantitative social sciences.Candidates with a degree in a field other thancomputer science must have completedcourses in the following subject areas:

• An introduction to programming ina high-level language

• Data structures*

• Discrete mathematics*

• Logic design and computer organization

• Calculus or other college-level mathematics

*APC515 Data Structures and Discrete Mathematics may be taken to meetthe prerequisite.

A D VA N C E D P L A C E M E N T A D M I S S I O N S

F O R M S S T U D E N T S

Students who are currently studying at OGIand have earned 12 credits in computerscience classes are exempt from the GRE andTOEFL requirements. Only two letters ofrecommendation are required; all otheradmissions requirements remain the same.The CSE courses must include at least two,

preferably three, courses from the MS Core(list follows). Students must earn an overallGrade Point Average of 3.0 and a B or betterin each MS Core class to be eligible to applythrough Advanced Placement:

CSE500 Introduction to Software Engineering

CSE511 Principles of Compiler Design

CSE513 Introduction to Operating Systems

CSE514 Introduction to Database Systems

CSE521 Introduction to Computer Architecture

CSE532 Analysis and Design of Algorithms

CSE533 Automata and Formal Languages

If a student applies to the ComputationalFinance program through advanced placement,the 12 credits earned may be from CSE, ECE APCor FIN courses.

DEGREE REQUIREMENTSA Student Program Committee (SPC) thatprovides academic advising is assigned foreach matriculating student. The student’s SPCalso approves the application of coursestoward the degree requirements.

A maximum of 21 credits earned prior tomatriculation at OGI may be applied towardthe master’s degree. This may include up to12 credits transferred from other institutions(up to 18 from Portland State University, theUniversity of Oregon or Oregon StateUniversity) and credits taken at OGI prior tomatriculation.

The program of study for each master’sstudent may be tailored to meet individualneeds by the SPC. Students are particularlyencouraged to include special-topic courses(CSE 58X) relevant to their interests.

CSE MS PROFESSIONAL INTERNSHIP OPTION

Participation is limited by available industrialinternships. Students declaring this option mustcomplete 45 credits of course work and up to anadditional 3 credits of a professional internship.(CSE620)

MASTER OF SCIENCE IN COMPUTER SCIENCE AND ENGINEERING

All M.S. students must complete the M.S. core of21 credits.

M.S. CSE CORE

The following courses are required of all M.S. CSE students:

CSE500 Introduction to Software Engineering 3 credits

CSE511 Principles of Compiler Design 3 credits

CSE513 Introduction to Operating Systems 3 credits

CSE514 Introduction to Database Systems 3 credits

CSE521 Introduction to Computer Architecture 3 credits

Department of Computer Science

and Engineeringwww.cse.ogi.edu


J im Hook



Dana Director


A C A D E M I C C O O R D I N A T O R

Shir ley Kapsch


D E P A R T M E N T S E C R E T A R Y

Barbara Mosher


C S E G E N E R A L I N Q U I R I E S


Doctoral student Francis Chang ( left) and facultymember Wu-chang Feng are working on networksupport for streaming dig ita l media.

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C S E | C O M P U T E R S C I E N C E A N D E N G I N E E R I N G

CSE532 Analysis and Design of Algorithms 3 credits

CSE533 Automata and Formal Languages 3 credits

M . S . T H E S I S O P T I O N

Students choosing the thesis option mustsubmit and defend a master’s thesis and mayapply up to 12 credits of thesis research(CSE 700) toward the 45 credit requirement.

1. M.S. CSE CORE (listed above)

2. CSE 700 M.S. THESIS (maximum 12 credits)

3. ELECTIVES (12 credits), as directed by the thesis advisor or SPC

Please note: Students may not receive credit forboth CSE504 and OMSE533.

M . S . N O N T H E S I S O P T I O N S

Students choosing the nonthesis M.S. optionmust complete 15 courses and a minimum of45 credits; up to six credits of nonthesisresearch (CSE 610) may be included, withthe approval of the student’s SPC. Studentsmatriculated prior to Winter Quarter 2002are exempt from the 15 course requirement.Students pursuing the non-thesis option maychoose one of the nine areas of emphasisdefined below or consult their SPC to definea custom program.

ADAPTIVE SYSTEMS AREA OF EMPHASIS NONTHESIS M.S. CSE DEGREE


2. ADAPTIVE SYSTEMS CORE (12 credits):

Required:

CSE547 Statistical Pattern Recognition 3 credits

CSE560 Artificial Intelligence 3 credits

Choose two of:

CSE540 Neural Network Algorithms & Architecture 3 credits

CSE545 Advanced Neural and Adaptive Algorithms 3 credits

CSE546 Data and Signal Compression 3 credits

CSE548 Statistical Computing 3 credits

CSE550 Spoken Language Systems 3 credits

CSE562 Natural Language Processing 3 credits

CSE564 Human-Computer Interaction 3 credits

CSE568 Empirical Research Methods 3 credits

ECE554 Adaptive Signal Processing 4 credits

3. SUGGESTED ELECTIVES (12 credits)

CSE563 Multi-Agent Systems 3 credits

CSE569 Scholarship Skills 3 credits

CSE58X appropriate special topics course (or)any CSE class not already taken


COMPUTATIONAL FINANCE AREA OF EMPHASISNONTHESIS M.S. CSE DEGREE

1. M.S. CSE Core (listed above)

2. COMPUTATIONAL FINANCE CORE (18 credits):

Required: (Choose 6 of the following:)

FIN541 Principles of Modern Finance 3 credits

FIN544 Investment and Portfolio Management 3 credits

FIN547 Global Markets and Foreign Exchange 3 credits

FIN551 Options and Futures 3 credits

FIN552 Options and Futures II 3 credits

FIN558 Advanced Numerical Computing in Finance3 credits

FIN561 Risk Management 3 credits

FIN573 Financial Time-Series Analysis 3 credits

FIN576 Financial Markets and Trading 3 credits

FIN585 Topics in Computational Finance 3 credits


CSE509 Object-Oriented Programming 3 credits

CSE540 Neural Network Algorithms & Architecture 3 credits

CSE544 Introduction to Probability andStatistical Inference 3 credits




CSE548 Statistical Computing 3 credits

CSE549 Applied Business Forecasting 3 credits

CSE555 Mathematical Methods for Engineering & Finance 3 credits



CSE58X Special Topics

ECE525 Analytical Techniques in Process& Communication 4 credits

ECE555 Engineering Optimization 4 credits(or) any CSE class not already taken

Please note: Students may not receive credit forboth CSE504 and OMSE533

COMPUTER SECURITY AREA OF EMPHASISNONTHESIS M.S. CSE DEGREE


2. COMPUTER SECURITY CORE (15 credits)

Required:

CSE503 Software Engineering Processes 3 credits

CSE524 TCP/IP Internetworking Protocols 3 credits

CSE527 Principles and Practices of System Security 3 credits

CSE58X Cryptography 3 credits

CSE58X Security Assurance 3 credits


CSE515 Distributed Computing Systems 3 credits(or) any CSE class not already taken.

Please note: Students may not receive credit forboth CSE504 and OMSE533

DATA-INTENSIVE SYSTEMS AREA OF EMPHASISNONTHESIS M.S. CSE DEGREE

1. M.S. CSE Core (listed above)

2. DATA-INTENSIVE SYSTEMS CORE (12 credits)

Four of:

CSE515 Distributed Computing Systems 3 credits

CSE526 Modern Operating System Design 3 credits

CSE541 Database Implementation 3 credits

CSE542 Object Data Management 3 credits

CSE58X Informational Retrieval and the Internet 3 credits

CSE58X Any special topics course in the database area

One course from the System Software Core

One course from the Software Engineering Core or theSoftware Engineering for Industry Professionals Core


Any CSE class not already taken.


HUMAN-COMPUTER INTERFACES AREA OF EMPHASIS NONTHESIS M.S. CSE DEGREE


2. HUMAN-COMPUTER INTERFACES CORE (18 credits)

Required:



Choose four of:


CSE551 Structure of Spoken Language 3 credits

CSE552 Hidden Markov Models for Speech Recognition 3 credits

CSE561 Dialogue 3 credits


CSE563 Multi Agent Systems 3 credits

CSE567 Developing User-Oriented Systems 3 credits


CSE58X Any special topics course appropriate to this area


CSE507 Logic Programming 3 credits


CSE540 Neural Network Algorithms & Architecture3 credits


(or) any CSE class not already taken.

Please note: Students may not receive credit forboth CSE 04 and OMSE533.

SOFTWARE ENGINEERING AREA OF EMPHASISNONTHESIS M.S. CSE DEGREE


2. SOFTWARE ENGINEERING CORE (15 credits)

Required:


CSE504 Object-Oriented Analysis and Design 3 credits


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C O M P U T E R S C I E N C E A N D E N G I N E E R I N G | C S E

MST512 Project Management 3 credits

Choose one of:




Any CSE class not already taken


SOFTWARE ENGINEERING FOR INDUSTRY PROFESSIONALS AREAOF EMPHASIS NONTHESIS M.S. CSE DEGREE


2. SOFTWARE ENGINEERING FOR INDUSTRY PROFESSIONALS CORE (15 credits)

Required:

OMSE511 Managing Software Development 3 credits

OMSE521 Using Metrics & Models 3 credits

OMSE531 Software Requirements Engineering 3 credits

OMSE533 Software Design Techniques 3 credits

Choose one of:




Any CSE course not already taken.


SPOKEN LANGUAGE SYSTEMS AREA OF EMPHASISNONTHESIS M.S. CSE DEGREE

1 M.S. CSE CORE (listed above)

2. SPOKEN LANGUAGE SYSTEMS CORE (12-16 credits)

Three of:






ECE541 Speech Processing 3 credits

ECE545 Speech Systems 4 credits

ECE58X Speech Synthesis 4 credits

Choose one of the following or one more from theabove list:

CSE540 Neural Network Algorithms & Architectures (S)3 credits

CSE545 Advanced Neural & Adaptive Algorithms 3 credits

CSE547 Statistical Pattern Recognititon 3 credits


CSE564 Human Computer Interaction 3 credits


ECE540 Auditory & Visual Proc. by Human & Machine 4 credits

ECE544 Intro to Signals, Systems and Info. Processing 4 credits

ECE551 Introduction to Digital Signal Processing4 credits

ECE552 Digital Signal Processing II 4 credits


3. SUGGESTED ELECTIVES (8-12 credits)

Courses in the Spoken Language Systems core, or any CSE classes not already taken.

Please note: Students may not receive credit forboth CSE 504 and OMSE 533.

SYSTEMS SOFTWARE AREA OF EMPHASISNONTHESIS M.S. CSE DEGREE


2. SYSTEMS SOFTWARE CORE (12 credits)

Choose four of:




CSE527 Principles and Practices of System Security 3 credits


CSE58X Internet Technology 3 credits

CSE58X Multi-Media Networking 3 credits

CSE58X plus any special topics courses appropriate to this area


Any course in the Systems Software area coreor any CSE class not already taken.

Please note: Students may not receive credit forboth CSE 504 and OMSE 533.

M A S T E R O F S C I E N C E I N C O M P U TAT I O N A L F I N A N C E

The Master of Science in ComputationalFinance is an interdisciplinary programoffering students the flexibility to learntechnical skills directly relevant toquantitative or computational work in thefinancial securities industry. A professionalinternship track is also available. (see below)

1. M.S. IN COMPUTATIONAL FINANCE CORE (24 credits)

Choose eight of:




FIN551 Options and Futures I 3 credits


FIN558 Advanced Numerical Computing in Finance 3 credits


FIN573 Financial Time Series Analysis 3 credits


FIN585 Topics in Computational Finance

2. BREADTH REQUIREMENT (21 credits)

Breadth requirement courses must come from atleast two of the following tracks. The course lists

for each track are representative, not exhaustive.Students with strong backgrounds or specialinterests may request approval to substitute otherOGI courses in place of those listed below:

A. APPLIED COMPUTING

APC500 Development with Visual Basic for Applications 3 credits

APC501 Accelerated Development with Visual Basic 3 credits

APC503 Web Development with Perl 5 3 credits

APC505 Applications Programming in C++ 3 credits

APC506 Advanced Applications Programming in C++ 3 credits

APC508 Web Development with Java 2 3 credits

APC511 Computational Tools for Engineering and Finance 3 credits

APC515 Data Structures and Discrete Math 3 credits

B. COMPUTER SCIENCE

CSE500 Principles of Software Engineering 3 credits






C. APPLIED MATHEMATICS, STATISTICS, AND MACHINE LEARNING

CSE540 Neural Network Algorithms and Architectures 3 credits

CSE544 Introduction to Probability and Statistical Inference 3 credits



CSE548 Modern Applied Statistics 3 credits


CSE555 Mathematical Methods for Science and Engineering 3 credits

CSE556 Simulation and Optimization 3 credits

D. ENGINEERING

ECE525 Analytical Techniques in Statistical Signal Processing 4 credits

ECE544 Introduction to Signals, Systems andInformation Processing 4 credits

ECE550 Linear Systems 4 credits

ECE551 Introduction to Digital Signal Processing 4 credits


ECE555 Engineering Optimization 3 credits

E. MANAGEMENT SCIENCE

MST501 Managerial & Financial Accounting 4 credits

MST502 Financial Management 4 credits

MST512 Project Management 3 credits

MST520 Managing in Science and Technology 4 credits

MST540 International Management in Science & Technology 3 credits

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F. FINANCE

Finance core courses beyond the 8-course core requirement.

M A S T E R O F S C I E N C E , C O M P U TAT I O N A L

F I N A N C E P R O F E S S I O N A L I N T E R N S H I P P R O G R A M

Participation in this program option is limitedby available industrial internships. Forstudents declaring this option, the breadthrequirement courses must come from at leastone of the tracks previously listed, plusFIN620 Professional Internship in Finance.

O R E G O N M A S T E R O F S O F T W A R E

E N G I N E E R I N G ( O M S E )

OGI School of Science and Engineering,Portland State University, Oregon StateUniversity, and the University of Oregonjointly offer the Oregon Master of SoftwareEngineering (OMSE) degree to meet theneeds of software professionals. Thecurriculum emphasizes the technical andleadership aspects of software engineering,teamwork and communication skills, and thebusiness aspects of developing industrial-strength software. Admission requirementsinclude a B.S. with pre-foundation courses inprogramming, discrete mathematics, datastructures, operating systems, and computerarchitecture as well as two years of workingexperience. Courses may be taken on non-admitted basis. For additional information,see www.omse.org.

Oregon Master of Software Engineering studentswill take the following courses:

OMSE500 Principles of Software Engineering 3 credits

OMSE511 Managing Software Development 3 credits

OMSE512 Understanding the Software Business 3 credits

OMSE513 Professional Communication Skills for Software Engineers 3 credits

OMSE521 Using Metrics and Models to Support QuantitativeDecision Making 3 credits

OMSE522 Modeling and Analysis of Software Systems 3 credits

OMSE525 Software Quality Analysis 3 credits

OMSE531 Software Requirements Engineering 3 credits

OMSE532 Software Architecture and Domain Analysis 3 credits

OMSE533 Software Design Techniques 3 credits

OMSE535 Software Implementation and Testing 3 credits

OMSE551 Strategic Software Engineering 3 credits

OMSE555 Software Development Practicum I 3 credits

OMSE556 Software Development Practicum II 3 credits

Any two CSE or OMSE classes not already taken. 6 credits

The courses on software development in contextprovide instruction in the basic areas of softwaredevelopment: requirements, architecture, design,implementation, and testing. The course material ineach of these areas provides instruction inunderlying principles, development methods andtools, and analytic methods and tools with a focuson applying principles, techniques and tools.Course material focuses on applying techniquesand skills from the foundation courses to realisticexamples of the products of each developmentphase. Course emphasis is on understanding theapplication and effect of the techniques covered inthe context of real software development.

OMSE 531 Software Requirements Engineering 3 credits

OMSE 532 Software Architecture and Domain Analysis3 credits

OMSE 533 Software Design Techniques 3 credits

OMSE 535 Software Implementation and Testing 3 credits

PART 3: PROGRAM INTEGRATION AND STRATEGICDEVELOPMENT SKILLS (9 Credits)

Courses in this area focus on integrating the skillstaught in the OMSE program and on the ability tothink abstractly about the processes and productsof software engineering. Students must havecompleted Part 1 and Part 2 of the OMSE programbefore beginning Part 3. (Exception: A student maybegin taking courses in Part 3 in the same term astaking any remaining courses in the first twoparts.) In OMSE 551, Strategic SoftwareEngineering students learn the skills necessary tounderstand, model, and adapt their softwareengineering processes to meet emerging needs. InOMSE 555/556, the Software DevelopmentPracticum, students participate in the end-to-enddevelopment of a significant software product andapply the personal competencies and developmentskills learned throughout the program in adevelopment context that includes the essentialcharacteristics of real commercial softwaredevelopment.

OMSE 551 Strategic Software Engineering 3 credits

OMSE 555 Software Development Practicum I 3 credits

OMSE 556 Software Development Practicum II 3 credits

PART 4: ELECTIVES (6 credits)

Any CSE or OMSE class not already taken.

O R E G O N G R A D U AT E E N G I N E E R I N G

I N T E R N S H I P P R O G R A M

For information and availability regarding the OGI School’s Department of ComputerScience Internships, please contactthe department.

C O O P E R AT I V E C O M P U T E R S C I E N C E P R O G R A M S

OGI has established undergraduate/graduatecooperative programs with Lewis & ClarkCollege, Pacific University, Reed College, andWillamette University. These programs allowselected undergraduate students to enter the

master’s program in computer science andengineering at the beginning of their senioryear. In two years of residence at OGI, the student can simultaneously fulfillrequirements for the bachelor’s degree at theundergraduate institution and the master’sdegree at OGI.

PH.D. PROGRAMThe Ph.D. program is strongly orientedtoward preparation for research. Eachstudent has the opportunity to work closelywith a faculty research advisor throughouthis or her residency at OGI. A student mustsatisfy the institutional requirements for the Ph.D.

Candidacy is satisfied in three parts:

FOUNDATION REQUIREMENTS: Students are required totake six foundation courses. Particularly well-prepared students can waive some of these coursesby passing an examination on the course material.

AREA REQUIREMENTS: Students choose three courseswithin one area and three courses out of that area,as outlined below.

RESEARCH SKILLS ASSESSMENT: Students are requiredto take CSE 569 Scholarship Skills and to pass theresearch proficiency examination (RPE), whichrequires a written and oral presentation of aresearch paper. The RPE normally takes place inthe spring quarter of the second year of residence.

Ph.D. students must obtain a grade of ‘B’ orbetter on each required course. Requiredcourses should be completed by the end ofthe second year. The doctoral dissertationwill document a significant, original researchcontribution and must be of publishablequality, both in content and presentation.

The faculty strongly recommends thatstudents prepare a formal thesis proposalbetween 9 and 18 months before the Ph.D.defense. The proposal is not a candidatescreening tool, but instead a means to ensurean acceptable level of intellectual vigor andmaturity. Starting in the second year, thefaculty strongly recommends that studentsdeliver yearly research talks. The RPE,presentation at the student researchsymposium, the thesis proposal, and talks atrefereed conferences satisfy thisrequirement. Practice talks for conferencepapers should be open for commentary.

The program of study for each Ph.D. studentis tailored to meet individual needs andinterests. Each student’s Student Program

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Committee provides academic advisementand is in direct control of each student’sprogram of study. The SPC will work with the student to set and review goals on atwice-yearly basis. Students must write aprogress report for all SPC meetings exceptthe first one.

FOUNDATION REQUIREMENTS (18 credits)

Required:

CSE513 Introduction to Operating Systems 3 credits



CSE533 Automata and Formal Languages 3 credits

Choose one programming language course:

CSE502 Functional Programming 3 credits



CSE531 Foundations of Semantics 3 credits

Choose one interactive and adaptive systems course:




DISTRIBUTION REQUIREMENTS (18 credits)

Three courses from one of the following six areas,and three other courses not from that area notalready taken:

Adaptive Systems and Applications






FIN573 Financial Time Series Analysis 3 credits

ECE540 Auditory and Visual Processing by Human and Machine 4 credits

ECE553 Control Systems: Classical, Neural and Fuzzy 4 credits


Human-Computer Interactive Systems







CSE563 Multi-Agent Systems 3 credits




CSE58X Special Topics: Computer Graphics variable

ECE540 Auditory and Visual Processing by Human and Machine 4 credits

Programming Languages and Software Engineering


CSE502 Functional Programming 3 credits





CSE511 Principles of Compiler Design 3 credits

CSE512 Compiling Functional Languages 3 credits

CSE518 Software Design and Development 3 credits

CSE530 Introduction to Mathematical Logic 3 credits



Systems Software


CSE510 Software Tools 3 credits





CSE527 Principles and Practices of System Security3 credits


CSE542 Object Data Management 3 credits

Theory

CSE530 Introduction to Mathematical Logic 3 credits


CSE534 Computability and Intractability 3 credits

CSE535 Categories in Computer Science 3 credits

RESEARCH SKILLS REQUIREMENT (3 credits)


Research Proficiency Exam

COURSE DESCRIPTIONSCSE500 Introduction to Software EngineeringSoftware engineering is concerned with the ways inwhich people conduct their work activities and apply technology to produce and maintain softwareproducts and software-intensive systems. Issues of concern include specification, design, implemen-tation, verification, validation, and evolution ofsoftware artifacts. Related topics include softwaremetrics, project management, configuration management, quality assurance, peer reviews, risk management, and process improvement. This course presents an integrated view ofthese topics and related issues. It is an essentialcourse for anyone working in development, mainte-nance, management, or related areas in a softwareorganization. 3 credits

CSE502 Functional ProgrammingIn functional programming, we shift our focus from

data objects and their representations to functionsthat act on data. Programs are formulated as com-positions of functions, rather than as sequences ofstatements. This leads to a programming methodol-ogy that is quite different from that learned in usingstatement-oriented languages. This course intro-duces the student to functional notation, recursion,higher-order functions, reasoning about functions,and polymorphic type systems. Functional program-ming languages are known for their increasedproductivity and reliability, due in part to the higherlevels of abstraction provided by functional lan-guages. Course is taught by lecture with smallweekly programming assignments. Experience isgained by programming in the functional languageHaskell or one of its close derivatives. Recentadvances in functional programming languagesallow them to use updatable state in a safe mannerand to cause effects on the real world. Students gainexperience by writing programs using these featuresto program interactive window-based programsusing an embedded “widget” library. 3 credits

CSE503 Software Engineering ProcessesThis course is concerned with examining andimproving the software development processes,including the technical, managerial, and culturalprocesses, used by organizations to develop andmaintain high quality software systems in a timelyand economical manner. Various process models,including the SEI Capability Maturity Models, theISO SPICE model, the Team Software Process, andthe Personal Software Process are studied and con-trasted. Tailoring of process models to fit localsituations and various approaches to softwareprocess improvement are presented. Studentsselect and complete term projects that address top-ics in software process improvement. 3 credits

CSE504 Object-Oriented Analysis and DesignThis course presents an integrated set of techniquesfor software analysis and design based on object-oriented concepts. The techniques focus onproducing the artifacts and work products,expressed in UML, appropriate for the analysis anddesign phases of the software development lifecycle.We adopt a use case model for requirements and aresponsibility-driven approach for the developmentof object models. Design patterns and frameworksare also emphasized. Note that CSE 509 Object-Oriented Programming is intended as a follow-oncourse for CSE 504. 3 credits

CSE507 Logic ProgrammingLogic programming is an attempt to construct com-puter languages with completely declarativesemantics: The programmer only states “what”should be done; the interpreter or compiler mustdecide “how.” This course examines existing logicprogramming languages, notably Prolog; providesthe foundations in logic and theorem proving forsuch languages; and covers implementation of logic programming languages. Other topics mayinclude an introduction to modal logic and intuition-istic logic. 3 credits

CSE509 Object-Oriented ProgrammingThis course provides a rigorous introduction to theconcepts behind object-oriented programming. It is

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for students who are already familiar with the con-cept of object-orientation and with object-orientedanalysis and design techniques. One way to learnthis background material is by taking CSE 504Object-Oriented Analysis and Design. In CSE 509,students gain a thorough understanding of incre-mental programming, type-safety, polymorphism,encapsulation, and set-based abstraction, and applythese concepts through a variety of programmingprojects. We study several programming languages,including Java and Smalltalk, so students areexposed to different realizations of these conceptsand gain an appreciation for the programming lan-guage design space. We also look at publishedobject-oriented design patterns and see how theycan be implemented in different object-oriented pro-gramming languages. Students are required to readappropriate research papers, complete severalshort programming assignments, complete a sub-stantial programming project, and write some shortessays. Prerequisite: CSE 504 or equivalent.

3 credits

CSE511 Principles of Compiler DesignThis course introduces the student to the basics ofbuilding a compiler using a multi-phase translationprocess. It covers lexical analysis, parsing, andtranslation to abstract syntax using modern parsergenerator technology. It discusses binding of identi-fiers and symbol table organization, and a variety ofintermediate representations that are suitable forback end analysis. It investigates back end transfor-mations and optimizations for a number oflanguages. Other topics include type checking, stat-ic analysis, and basic runtime support. Compiling isessentially a process of symbolically manipulatingprogram representations represented by tree andgraph-like data structures. Because of this, we willuse tools that facilitate symbolic manipulation anddefinition of such structures as parser and lexicalgenerators, and tools for generating code from pat-tern-based descriptions. Prerequisite: CSE 533.

3 credits

CSE512 Compiling Functional LanguagesA project-oriented course on the theory and designof a compiler for a typed, functional programminglanguage. Topics include understanding a formaldefinition of programming language semantics, com-piling pattern analysis, lifting abstractions,continuation-passing style of implementation,abstract machines, code generation and addressassignment, register allocation and assignment ongeneral-register machines, run-time storage admin-istration, data-flow analysis, and code improvement.Prerequisite: CSE 511. 3 credits

CSE513 Introduction to Operating SystemsA study of the design and implementation of modernoperating systems. The course concentrates onoperating system kernel design, and includes thefollowing topics: concurrent processes, interprocesscommunication, synchronization, scheduling,resource allocation, memory management, the con-cept of virtual memory and the required underlyinghardware support, secondary storage management,file systems, and security. We will use the Linuxoperating system to ground the discussion ofabstract concepts. Interested students will be

encouraged to read the Linux source code for dis-cussions in class. 3 credits

CSE514 Introduction to Database SystemsA survey of database fundamentals emphasizing theuse of database systems. Topics include databasedesign, data dependencies and normalization, sec-ondary storage structures, query languages, queryprocessing, query optimization, transactions, recov-ery, and embedded SQL. This course focuses onrelational database systems and the SQL query lan-guage. Students participate in a project to design,populate, and query a database. Prerequisites: Data structures, discrete mathematics, and mathe-matical logic. 3 credits

CSE515 Distributed Computing SystemsThis course concentrates on distributed computingfrom a systems software perspective. Major topicsinclude communications middleware (remote proce-dure call, remote method invocation and causalbroadcast), operating system support, distributedfile systems, distributed transaction processing,load balancing, distributed programming languagesand systems, fault-tolerance and replication algo-rithms, distributed timing issues, and distributedalgorithms. Prerequisites: CSE513 Introduction toOperating Systems. (Also a basic understanding ofcomputer communications problems and protocols.)

3 credits

CSE518 Software Design and DevelopmentContemporary, object-oriented software design,using the Java programming language. An introduc-tion to the eXtreme Programming softwaredevelopment methodology, which is based upon theprinciple that change is inevitable and successfulsoftware designs undergo continual evolution.Techniques that will be taught in the course includeprogram refactoring, automated unit testing, pairprogramming, participatory design and managingshort product development cycles. These principlesand techniques will be illustrated in a term-lengthproject that provides members of the class withdesign and implementation experience. 3 credits

CSE521 Introduction to Computer ArchitectureThis course provides a broad introduction to com-puter architecture. The course covers a largeamount of material in moderate depth, giving thestudent a good understanding of the basic issues incomputer system design. Specifically, the coursecovers instruction set design, pipelining, the memo-ry heirarchy, I/O systems, networking issues, andmultiprocessors. Example systems include the Intelx86, MIPS, and DEC Alpha processors.Prerequisites: Experience writing software, prefer-ably with some C or assembler programming. NOTE:Computer architecture has become a quantitativescience, so there will be considerable algebraicmanipulation involved in the performance analysiscomponent of the course. 3 credits

CSE522 Advanced Computer ArchitectureThis course covers new architectural trends indesigning high-performance clusters with examples.Topics to be covered include I/O & IPC interconnects(routing, switch designs, virtual lanes, etc.); singlesystem image and scheduling; lightweight messagingand use-level networking; suitable I/O architectures;

commercial cluster interfaces and systems; andpresence of clusters in data centers. Commercialand academic examples will be covered for each ofthe above topics, such as InfiniBandTM, VirtualInterface Architecture (VIA), ServerNet, Beowulf,Memory Channel, etc. Prerequisite: CSE 521.

3 credits

CSE524 TCP/IP Internetworking ProtocolsThis course provides an overview of the structureand algorithms used in the TCP/IP networking pro-tocols that make up the foundation of the Internet.Protocols and technologies covered will include anintroduction to the link layer, ARP, IP, ICMP, UDP,TCP, routing protocols, and application protocolsand systems like the DNS, NFS, SMTP, FTP, HTTP,and multicasting protocols and applications. To pro-vide architectural insight into protocol design issuesand operating system implementation techniques,typically in terms of the Berkeley UNIX socket pro-gramming model. To provide socket programmingexperience with the client/server model. To provideexperience reading Internet RFC’s and/or drafts.Prerequisites: familiarity with the functions of amodern multiuser operating system such as is cov-ered in CSE 513 or in PSU’s CS 533; familiarity withC programming on modern UNIX computers.

3 credits

CSE526 Modern Operating System DesignThis course includes an in-depth study of modernoperating system design. The course is based on acollection of recent research papers, and includesan emphasis on evaluating the papers in addition tounderstanding the systems they describe. Topicsinclude micro-kernel operating systems, lightweightinterprocess communication, extensible operatingsystems, file systems, mobile computing, worksta-tion clusters, adaptive resource manage-ment, andOS support for multimedia systems. Prerequisites:CSE 513 and CSE 521. 3 credits

CSE527 Principles and Practices of System SecurityIn the Internet age, host system security is essentialand difficult. This course will educate students inthe principles and practices of securing host sys-tems. Students learn the principles of how to buildsecure systems and how various real systems suc-ceed and fail in living up to these principles. We willstudy various security enhancing technologies, ineach case relating the security enhancement to theprinciples of secure systems. Prerequisite:CSE 513. 3 credits

CSE530 Introduction to Mathematical LogicProvides a theoretical foundation for the logic ofcomputation. Propositional and first-order predicatecalculi, soundness and completeness, incomplete-ness and incomputability, the Church-Turing thesis,term-rewriting systems, and application to programverification. 3 credits

CSE531 Foundations of SemanticsFormal semantics aims to answer two importantquestions: 1) when are two programs equal? And 2) when does a program faithfully implement amathematical specification? The course exploresdenotational semantics, operational semantics, andprogram logic, studying how they are related andhow they can answer the motivating questions.

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Programming language concepts, such as impera-tive programming, functional programming,call-by-name, call-by-value, and continuations, arecontrasted and explained in terms of their semanticfoundations. Key concepts include full abstractionand the use of least fixed point constructions tosolve recursive equations. The course is designedfor students interested in the mathematical founda-tions of programming languages and programminglogics. Prerequisite: Discrete mathematics. 3 credits

CSE532 Analysis and Design of AlgorithmsAn introduction to the design and analysis of algo-rithms. The course covers design techniques, suchas dynamic programming and greedy methods, aswell as fundamentals of analyzing algorithms forcorrectness and time and space bounds. Topicsinclude advanced sorting and searching methods,graph algorithms and geometric algorithms. Other areas vary from year to year, and may includecomputational geometry, matrix manipulations,string and pattern matching, set algorithms, polynomial computations, and the fast Fouriertransform. Prerequisite: Data structures and dis-crete mathematics. 3 credits

CSE533 Automata and Formal LanguagesAutomata theory introduces fundamental modelsthat are used over and over again in computer sci-ence for programming languages, in compilerconstruction, and in algorithms. These models are avaluable part of the repertoire of any computer sci-entist or engineer. This course introducesprogressively more powerful models of computation,starting with finite automata and moving throughcounter, stack, and Turing machines. It also pres-ents the regular, context-free, recursive, andrecursively enumerable languages, and shows howthey correspond to the various models of computa-tion and to generation mechanisms such as regularexpressions and grammars. The emphasis is onunderstanding the properties of these models, therelationships among them, and how modificationssuch as nondeterminism and resource bounds affectthem. The course includes application of these con-cepts to problems arising in other parts of computerscience. Prerequisite: Discrete mathematics.

3 credits

CSE534 Computability and IntractabilityComputability and complexity theory identify class-es of languages based on characteristics ofmachines that recognize them. The course presentselementary results from recursive function theory,including recursive and recursively enumerablesets, and degrees of undecidability. Using recursiontheory as a model, it develops the classical resultsof complexity theory, including time and space com-plexity classes, hierarchy theorems, and elementaryresults from parallel complexity. The course con-cludes by studying classes of problems that areprovably intractable, with a particular emphasis onNP-complete problems. Prerequisites: CSE 532 orCSE 533. 3 credits

CSE535 Categories in Computer ScienceCategory theory provides a powerful and concisenotation for abstract properties of functions.Originally developed for algebraic topology, it has

found widespread application in computer science.This course introduces the basic notions of category theory, including functors, natural trans-formations, products, sums, limits, colimits,monads, and adjunctions. These concepts are illus-trated with examples from computer science andmathematics, including the relationship betweencartesian closed categories and the lambda-calcu-lus. Familiarity with discrete mathematics is anessential prerequisite. 3 credits

CSE540 Neural Network Algorithms and ArchitecturesThis course introduces the fundamentals of connec-tionist and neural network models. Paradigms forboth unsupervised and supervised learning are cov-ered. Topics include introduction to neuralprocessing elements, Hebbian learning, LMS andback propagation algorithms, competitive learning,computational capability, and elements of statisticalpattern recognition. Specific architectures coveredinclude Hopfield nets, single and multilayerPerceptrons, and Kohonen maps. Programmingprojects involve network simulations and applica-tion problems. Prerequisites: Some knowledge oflinear algebra and calculus is required.Programming experience is necessary. 3 credits

CSE541 Database ImplementationThis course provides hands-on experience imple-menting high-performance database managementsystems. The goal of the course is to implementdatabase software and to understand techniquesused to provide maximum performance and func-tionality on modern architectures. Typical topicsdiscussed include benchmarking, transaction pro-cessing, file and index implementation, buffermanagement, concurrency control, recovery, queryoptimization, and a variety of query processing algo-rithms. The data model to be implemented, and thecomputer architecture to be used, will changebetween offerings. Prerequisite: CSE 514. Thiscourse is offered at Portland State University as CS 545. 3 credits

CSE542 Object Data ManagementA variety of products for managing object data haveemerged in the marketplace. Object-oriented data-base systems and persistent programminglanguages have been joined by object-relationaldatabases and middleware component technologies,such as Enterprise Java Beans. Other storageengines, such as LDAP and XML servers, have anobject flavor. This course begins with the conceptsin types, data models, and languages that underlieobject data management. It then looks at exampleprototype and commercial systems, and examinesdesign dimensions such as data model, persistence,encapsulation, hierarchies, query languages, andtransactions. It touches on application developmentand data management issues and concludes withtreatment of software architecture and implementa-tion techniques. Students will do a project using acommercial product. 3 credits

CSE544 Introduction to Probability and Statistical InferenceThis course provides a comprehensive introduction toprobability, statistical inference and stochasticprocesses. The topics include the elements of

exploratory data analysis, sampling distribution theo-ry, confidence intervals, hypothesis testing, linearregression, goodness-of-fit, ANOVA, maximum likeli-hood estimation, Bayesian inference, cross-validation,nonparametric tests, random walks, martingales, sto-chastic processes and stochastic differentialequations. The goal of the course is to provide a com-prehensive review of essential concepts in probabilityand statistics. The primary analysis tools for thiscourse are S-PLUS and MATLAB. 3 credits

CSE545 Advanced Neural and Adaptive AlgorithmsAn advanced treatment of architectures and algo-rithms for pattern recognition, regression,timeseries prediction, and datamining. Typical top-ics include convergence, effects of noise,optimization methods, probabilistic framework(including Bayesian estimation), generalization abil-ity and regularization and pruning, Hebbianlearning, and clustering and density modeling.Prerequisites: CSE 540 or instructor permission.

3 credits

CSE546 Data and Signal CompressionThe need for signal and data compression is ubiqui-tous in image, video, and speech processing,finance, and computational science. Where datastores become very large (e.g. video, finance, earthscience), the need is not met by simple lossless filecompression schemes, and we must turn to sophis-ticated coding techniques.This course addressesboth the theoretical basis and practical algorithmsfor data and signal compression. Topics include loss-less entropy based coding including Huffman andLempel-Ziv, and lossy compression techniquesincluding: scalar quantizers, transform coding(Karhunen-Loeve, DCT, and nonlinear transformcodes), predictive coding, vector quantization, adap-tive codes, and wavelets. The relation betweencompression schemes and probabilistic data model-ing is emphasized in conjunction with eachtechnique. Application to speech, image, and videocoding are discussed. Students will have the oppor-tunity to design compression schemes for suchdiverse applications as earth science data, finance,speech, or video depending on their specific inter-ests. Prerequisites: Undergraduate calculus,introductory probability and statistics, some pro-gramming experience. 3 credits

CSE547 Statistical Pattern RecognitionTheory and practice of statistical pattern recogni-tion. Students will learn fundamental theory andpractices that are common to a broad range of pat-tern recognition applications and technologies, andapply principles to real-world examples.The empha-sis is on developing tools, both theoretical andpractical, that provide grounding in pattern recogni-tion problems and methods; rather than onshowcasing particular technologies. The course willbenefit those whose work may use any of a variety ofrecognition technologies in broad-ranging applica-tions such as speech and image processing, datamining, finance. Topics include: random vectors,detection problems (binary decision problems), like-lihood ratio tests, ROC curves, parametric andnon-parametric density estimation, classificationmodels, theoretical error bounds and practical error

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estimation through cross-validation. Maximum likeli-hood and Bayesian parameter estimation. Featureextraction for dimensionality reduction, and for clas-sification. Prerequisites: The course is designed to beself-contained. Familiarity with undergraduate prob-ability and statistics is useful. 3 credits

CSE548 Statistical ComputingThis course provides an introduction to modernapplied statistics. The topics include distributionsand data summaries, density estimation, general-ized linear models, modern nonlinear regression,robust statistics, factor analysis, linear and nonlin-ear classifiers, Bayesian classifiers, clusteranalysis, decision trees, ensemble learning meth-ods, validation techniques and Bootstrap and MonteCarlo methods. The goal of the course is to providea solid understanding of practical statistical infer-ence methods and proficiency in using modernstatistical tools. The primary analysis tool for thiscourse is S-PLUS. Prerequisite: CSE544Introduction to Probability and Statistical Inferenceor equivalent. 3 credits

CSE549 Applied Business ForecastingThis course is taught over the World Wide Web usingWebCT; enrollment limitations may apply. An appliedcourse in business forecasting, the course empha-sizes generating and implementing businessforecasts. Designed for those wishing to understandthe basics of modern forecasting, the course empha-sizes modern statistical methods widely used togenerate business forecasts. Specific applications tobusiness include forecasting sales, production,inventory, macroeconomic variables such as inter-est rates and exchange rates, and other applicationsrelated to business planning, both short- and long-term. Topics include data considerations and modelselection, applied statistics, moving averages andexponential smoothing, regression analysis, time-series decomposition, Box-Jenkins (ARIMA) models,bootstrapping, optimal forecast combination, andforecast implementation. The course is based uponthe FORECASTXTM integrated econometric and sta-tistical analysis language for Windows 95 and NT,which accompanies Wilson and Keating’s BusinessForecasting, McGraw Hill-Irwin, 4th Edition.Knowledge of basic statistics and regression analy-sis is highly recommended, but not required.

3 credits

CSE550 Spoken Language SystemsIn the not too distant future, spoken language sys-tems will revolutionize human-computer interactionby enabling natural conversations between peopleand machines. In addition to telephony applications,such as voice browsing of the web, these systemsalso will support face-to-face communication withintelligent animated agents. These animated human-like agents will combine acoustic information withthe speaker’s facial cues and gestures to understandspeech, and produce natural and expressive speechwith accurate facial movements and expressions.This course reviews the state of the art in humanlanguage technology, and explains how key tech-nologies are combined to produce spoken languagesystems. The course combines lectures by experts inthe field with hands-on experience using and building spoken language systems using the CSLU

Toolkit. The course materials are included inhttp://www.cse.ogi.edu/ CSLU/hltsurvey/hltsurvey.html.

3 credits

CSE551 Structure of Spoken LanguageThis course provides a foundation for subsequentlearning and research in computer speech recogni-tion. We examine the structure of spoken Englishthrough selected readings in speech perception andacoustic phonetics and examination of visual dis-plays of speech. The goals are to understand theacoustic cues for each major phonetic category,understand how these cues are affected by context,understand the perceptual strategies that listenersuse to understand speech, and evaluate the assump-tion that speech can be described as anorderedsequence of phonetic segments. 3 credits

CSE552 Hidden Markov Models for Speech RecognitionHidden Markov Model-based technology is usedwidely in today’s speech recognition systems. Thiscourse is an introduction to speech recognitionusing HMM technology. Topics include the theory ofHidden Markov Models (discrete, semi-continuous,and continuous) and their applications to speechrecognition, along with the basic mathematics(probability theory, statistics, stochastic process,information theory, and signal processing) that arenecessary for speech recognition. The course isfocused on understanding the theory behind thesefundamental technologies, and applying the technol-ogy to develop speech recognition systems.Prerequisite: Some knowledge of engineering math-ematics (calculus and linear algebra) is required;C programming experience is necessary. 3 credits

CSE555 Mathematical Methods for Engineering and FinanceThis course explores the essential mathematicalmethods required for quantitative analysis in engi-neering and finance. The course examines aselection of topics from multivariate calculus, dif-ferential equations, stochastic calculus andmathematical optimization. Advanced topics includepartial differential equations, Ito calculus, martin-gales, stochastic control and constrainedoptimization. The focus is on explaining the keyMathematical results and, by means of examplesand assignments, showing how they may be appliedin engineering and finance. Prerequisites: Knowledgeof calculus, linear algebra and basic differentialequations. 3 credits

CSE556 Simulation and OptimizationThis course introduces modern, advanced numericalmethods for quantitative work in engineering,finance and operations research, focusing on MonteCarlo Simulation and Optimization techniques. InMonte-Carlo simulation we will cover pseudo-ran-dom and quasi-random number generators,generation of stochastic processes, variance reduc-tion techniques, bootstrapping and other statisticaltechniques. In Optimization we will briefly reviewclassical methods, and study in detail new tech-niques such as genetic algorithms, differentialevolution, simulated annealing and ant colony opti-mization. Students will be introduced tomathematical modeling, and learn the science andart of effectively applying these techniques. Grading

will be based on assignments and a group project,and these will involve programming in Matlab. Theassignments, project and examples in class will bedrawn from practical problems in engineering andfinance. Prerequisites: Programming experience,linear algebra, calculus, CSE544 Introduction toProbability and Statistical Inference (or equivalent).

3 credits

CSE560 Artificial IntelligenceThis course surveys the foundations and applica-tions of symbolic approaches to artificialintelligence. The approach emphasizes the formalbasis of automated reasoning and includes an intro-duction to programming in Prolog. Fundamentalscovered include search, knowledge representation,automated inference, planning, nonmonotonic rea-soning, and reasoning about belief. Applicationsinclude expert systems, natural language processingand agent architectures. 3 credits

CSE561 DialogueThis course provides an in-depth treatment of themajor theories of dialogue, including finite-state,plan-based, and joint action theories. Dialogue isexamined at a level general enough to encompassconversations between humans, between humanand computer, and among computers, while at thesame time being precise enough to support imple-mentations. The course introduces basic speech acttheory, planning, and reasoning through a number ofclassic papers. Plan-based theories are examined indetail, including their incorporation into spoken dia-logue systems, and their potential effects uponspeech recognition components. Students will devel-op dialogue components and integrate them intoworking systems. Prerequisite: CSE 560.

3 credits

CSE562 Natural Language ProcessingAn introduction to artificial intelligence techniquesfor machine understanding of human language. Thecourse introduces key aspects of natural language,along with the analyses, data structures and algo-rithms developed for computers to understand it.Computational approaches to phonology, morpholo-gy, syntax, semantics, and discourse are covered.Programming assignments are written in Prolog.Prerequisite: CSE 560 or equivalent. 3 credits

CSE563 Multi-Agent SystemsThis course covers the emerging theory and practiceof multi-agent systems: semi-autonomous, semi-intelligent distributed computing systems that canbe organized ad hoc to meet the immediate needs ofa user. The course covers a variety of individual andmulti-agent architectures, including the ContractNet protocol, distributed blackboard systems, andmobile agents. Also discussed are principles forbuilding networks of heterogeneous agents, rangingfrom simple rule-based systems to databases andhumans. In order to collaborate to solve a user’sproblem, agents need to communicate. We examineagent communication languages, including KQMLand FIPA, as well as the underlying general speechact theories. Students learn how to model these sys-tems formally, and will develop and programindividual agents that can participate in a multi-agent system. 3 credits

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CSE564 Human-Computer InteractionThis course emphasizes the experience of comput-ing, which centers on an understanding of real usersand the specific tasks they need to accomplish whencomputing. In the pursuit of optimal user support,an interdisciplinary approach to system design andevaluation is stressed. The course reviews currentresearch viewpoints and activities in the field ofhuman-computer interaction, surveys key researchchallenges that exist, and discusses trends in next-generation system design. Students gain hands-onexperience by critiquing existing interfaces, as wellas hearing reports from experts in industry on thestate of the field. An introduction to this topic isessential for everyone working in the field of com-puter science. 3 credits

CSE567 Developing User-Oriented SystemsThis course explores a range of issues and methodsneeded to design and evaluate user-oriented soft-ware applications. Topics focus on field andethnographically based design studies, participatorydesign methods, user laboratory studies, and usabil-ity testing. The purpose is to have access to a rangeof methods that help uncover opportunities, break-downs, and interactions that affect the design anduse of developing systems. Students are challengedto evaluate the underlying perspectives of theapproaches and decide which approach or combina-tion of approaches works best for particularproblems. They apply the methods in field and class-room exercises and produce a real-world project orpaper using course methods. The intended result isto make students more effective not only at gatheringrelevant user-based information, but also at inte-grating it into the development process. 3 credits

CSE568 Empirical Research MethodsThis course introduces principles of experimentaldesign and data analysis for empirical research.Topics include the goals and logic of experimentaldesign, hypothesis formation and testing, probabili-ty and sampling theory, descriptive statistics,correlation and regression, basic parametric andnonparametric tests of statistical significance (e.g.,Binomial, t-test, chi-square, analysis of variance),standard designs for single- and multi-factor exper-iments, and strategies of scientific investigation(e.g., Exploratory vs. Directed). The course is fun-damental for anyone who plans to conductindependent research in the future or needs to crit-ically evaluate the research of others. Studentsparticipate in designing and analyzing data in orderto answer scientific questions and present theresults of these activities both orally and in writing.

3 credits

CSE569 Scholarship SkillsScientific results have little value if they are notcommunicated clearly or are disconnected fromprior work in a field. This course teaches students toresearch, write, present, and review effectively forthe computer sciences. It emphasizes learning bydoing, and students have frequent writing and pres-entation assignments. Students learn how to locateand organize background materials, how to writeclearly about technical topics, organizing web con-tent, the structure and stylistic conventions of

scientific documents (such as conference abstracts,journal papers, theses, and proposals), how to pre-pare and deliver short and long presentations, therefereeing process, and how to prepare and respondto a review. This course is required for Ph.D. stu-dents and strongly recommended for master’sstudents, especially those pursuing the thesisoption. It also is useful for professionals who mustwrite or speak to a technical audience. 3 credits

CSE58X Special TopicsUnder this number, we offer courses of particularrelevance to the research interests of faculty or instate-of-the-art subjects of interest to the community.

CSE600 ResearchSupervised research activity.

Variable and repetitive credit.

CSE610 Nonthesis ResearchSupervised research for up to six credits as a com-ponent of the nonthesis master’s degree. Studentsare required to produce concrete research deliver-ables, including a final report equivalent to a CSEtechnical report.

CSE620 Professional InternshipThese courses provide the student with an opportu-nity to earn credit for relevant work experience inindustry. Students gain valuable industrial experi-ence that allows them to both apply the knowledgegained in the classroom and prepare for their futurecareers in computer science. A written report mustbe submitted to the CSE faculty advisor at the end ofthe experience.

Enrollment requires a faculty advisor and is limitedby the number of internship opportunities available.

1 to 3 credits per quarter

CSE700 M.S. Thesis ResearchResearch toward the thesis for the M.S. degree.


CSE800 Ph.D. Dissertation ResearchResearch toward the dissertation for the Ph.D. degree.


FIN541 Principles of Modern FinanceThis course examines the theory and practice ofmodern corporate finance stressing the six centralconcepts in finance: Net Present Value, CapitalAsset Pricing Model, Efficient Capital Markets,Value Additivity (Capital Structure Theory), OptionTheory and Agency Theory.

Topics include discounted cash flow analysis, capitalbudgeting, capital structure theory, mean-varianceportfolio theory, arbitrage-pricing theory, Black-Scholes option pricing, and real options theory. Inaddition, students will learn the nuances of evaluat-ing an Ebusiness. The principal goal of the course isto provide students with an intuitive foundation ofmodern finance upon which the student can applyadvanced computational techniques. This will beaccomplished through interaction between the text,instructor, case studies, MATLAB assignments, andstudent presentations/discussions. This course ful-fills all or part of the prerequisite requirements forFIN576 Financial Markets and Trading. 3 credits

FIN544 Investment and Portfolio ManagementThis course provides students with an overall intro-duction to practical and theoretical aspects ofinvestment analysis and portfolio management.Specifically, the course surveys various models ofasset valuation and their use in constructing effec-tive investment portfolios. Topics include investmentvehicles and asset classes, market structure andmarket efficiency, security valuation models, finan-cial statement analysis, setting investment goalsand policies, designing investment portfolios, equityand fixed-income portfolio strategies, measuringinvestment performance, and managing investmentrisk. To help students integrate the course knowl-edge into their actual investment practice, thecourse includes team projects to analyze actualinvestment securities and design investment portfo-lios. Students have access to investment data andanalytics provided by Barra and Standard and Poor’s Micropal. 3 credits

FIN547 Global Markets and Foreign ExchangeThis course surveys the modern paradigms in inter-national finance. Specifically, the course examinesthe theory linking the world’s various foreignexchange, money, and securities markets, empha-sizing global investment and risk management.Topics include spot and forward FX markets, FXoptions, interest rate parity, purchasing power par-ity, exchange rate theory, global investing, global FXrisk management, and emerging markets and cur-rency crises. Course assignments make use ofMATLAB’s-Plus and Barra on campus. 3 credits

FIN551 Options and Futures IThis course introduces the trading, pricing and risk-management applications of financial derivativesincluding futures, swaps, and option contracts.Emphasis is given to pricing models including arbi-trage pricing theory, risk-neutral valuation, andBlack-Scholes analysis. Topics covered includefutures and swap pricing, methods for pricingAmerican style options, hedging and speculationusing derivatives, Ito calculus, portfolio insurance,option trading strategies, dynamic hedging strate-gies, and numerical models. Course assignmentsrequire use of MATLAB. 3 credits

FIN552 Options and Futures IIA continuation of FIN551 Options and Futures I, thiscourse examines derivative pricing models sinceBlack-Scholes, models for the term structure ofinterest rates and relevant numerical methods. Thecourse begins with a review of stochastic calculusand stochastic differential equations. Specific topicsinclude arbitrage pricing, equivalent martingalemeasures, risk neutrality, and optimal stoppingtimes as applied to American options. Equilibriumand no-arbitrage term structure models are pre-sented, from Vasicek through Heath-Jarrow-Morton.In addition, emphasis is given to pricing fixed-income derivatives, credit derivatives, and exoticsusing numerical solution methods such as theCrank-Nicholson, finite difference methods, andMonte Carlo search. Prerequisite: FIN551 Optionsand Futures I or permission from instructor.

3 credits

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FIN558 Advanced Numerical Computing in FinanceThis course introduces the major numerical meth-ods needed for quantitative work in finance, focusingon derivatives pricing and fixed income applications.Topics include binomial and trinomial methods,finite difference solution of partial differential equa-tions, Crank-Nicholson methods for various exoticoptions, treatment of discrete dividends, projected-SOR method for American options, numerical meth-ods for stochastic differential equations, randomnumber generators, Monte-Carlo methods forEuropean and least-squared Monte-Carlomethodsfor American options. The course is lab oriented.Prerequisite: FIN552 Options and Futures II or per-mission from instructor. 3 credits

FIN561 Risk ManagementThis course explores various aspects of manage-ment of risk associated with operating amultinational enterprise. Emphasis is on evaluatingand hedging financial risks (fixed-income, equity,commodity, and foreign exchange risk exposures),with emphasis on value-at-risk (VAR) models. Topicsinclude sources and measurement of risk and expo-sure, value at risk, hedging linear and nonlinearderivatives risk, delta-normal VAR, historical simu-lation VAR, Monte Carlo approaches to VAR, andimplementation and evaluation of risk managementsystems. Course assignments make use of MATLABand BARRA On Campus. 3 credits

FIN573 Financial Time-Series AnalysisThis course reviews advanced time-series tech-niques and their application to the analysis andforecasting of financial time-series. Emphasis isgiven to multivariate and nonlinear methods appliedto high-frequency financial data. Topics coveredinclude ARIMA models, GARCH models, martingalesand random walks, stochastic trends, co-integrationand error-corrections models. The primary analysistool for this course is S-PLUS. Prerequisite: CSE548Modern Applied Statistics. 3 credits

FIN576 Financial Markets and TradingThis course provides a survey of the structure anddynamics of financial markets, the behavior of finan-cial price series, and trading techniques. Topicsinclude market microstructure, market efficiencyand documented anomalies, noise traders andbounded rationality, properties of high frequencydata, nonlinear price behavior, speculative bubblesand crashes, market psychology, and technical trad-ing systems. The course draws upon the academicliterature and the practitioners’ lore. Students useMATLAB, S-PLUS, and extensive data resources toanalyze price behavior and build and test simpletechnical trading systems. Prerequisites: FIN541Principles of Modern Finance and FIN573 FinancialTime-Series Analysis. 3 credits

FIN620 Professional Internship in FinanceThis course provides the student with an opportuni-ty to earn credit for relevant work experience infinance and related industries. It enables studentsto enhance their understanding of the practical real-ities of modern finance, including such areas ascorporate treasury operations, investment analysis,portfolio management, risk management, deriva-tives pricing, forecasting and trading. Students gain

valuable industrial experience that both allows themto learn to apply their knowledge gained in theclassroom and to better prepare for their futurecareers in finance. Enrollment requires the permis-sion of the instructor and is limited by the number ofinternship opportunities available. 1-3 credits

A P P L I E D C O M P U T I N G C O U R S E S

These courses may be applicable to theMaster in Computational Finance or as aprerequisite for the Master in ComputerScience and Engineering or the OregonMaster of Software Engineering.

APC500 Development with Visual Basic for ApplicationsThis course introduces Visual Basic for Applicationsas a tool for rapid application development, cus-tomization and system integration in Windowsenvironments. The course focuses on combining VBAwith Microsoft Office. Topics covered include thestructure of the VBA programming language andbuilt-in functions, enhancing recorded macros usingVBA code, applying the MS Office object models andaccessing relational databases using ActiveX DataObjects (ADO). Students will gain expertise inadvanced analysis and data manipulation, develop-ing and customizing applications, and integratingthem with existing systems. Prerequisites: experi-ence with MS Excel and Access, and knowledge of aprogramming language. 3 credits

APC501 Accelerated Development with Visual BasicThis course uses Visual Basic 6.0 and Visual Basicfor Applications as tools to introduce the concepts ofrapid application development, systems integrationand customization on Windows platforms. Whilestudying Visual Basic, students will gain an under-standing of the architecture of Windows applicationsand create COM components, ActiveX controls andexecutable programs. Students will also learn howto apply basic analysis and design techniques, andhow to make their user interfaces friendly and effi-cient. Assignments involve practical work with thesesoftware tools, using applications fromindustry/business as case studies. This fast-pacedcourse is intended for experienced programmerswishing to augment their skills with knowledge ofVisual Basic. Prerequisites are programming experi-ence with C, C++ or Java. APC500 is not aprerequisite for this course. 3 credits

APC503 Web Development with Perl 5This course uses “Perl 5” technology to introducethe essential concepts needed to develop web appli-cations with server side scripting. Topics include thestructure and elements of the Perl 5 language (vari-ables, control structures, file I/O, regularexpressions, objects and built-in functions), impor-tant Perl libraries, writing CGI scripts, buildingdynamic web pages and extracting data from data-bases using basic SQL queries. Important issues,such as the security of web applications, will beaddressed and additional topics, such as XML, maybe introduced, time permitting. On completion, stu-dents will understand the conceptual architecture ofweb applications with server side automation and bein a position to contribute to their design and devel-

opment. Assignments include writing programs anda project to develop a web application.Prerequisites: knowledge of a programming lan-guage and basic HTML. 3 credits

APC505 — Applications Programming in C++ This course provides an introduction to program-ming in C++, which is used widely for developingengineering and business applications. This courseintroduces students to C++ language constructs,data structures and classes. The student will also beshown how access class and template libraries,including the standard template library (STL). Thecourse is suitable for students in engineering, man-agement and finance who wish to gain anunderstanding of the language. On completion, stu-dents will be in a position to contribute to the designand development of systems using C++.Assignments include writing programs and a pro-gramming project. Prerequisites are knowledge of aprogramming language. 3 credits

APC506 Advanced Applications Programming in C++This course explores advanced topics concerningapplications programming in C++. The course willfocus on writing efficient, extensible and reusableprograms, and introduce concepts in software engi-neering, program analysis and design, and datamodeling. Students will develop class libraries, andlearn how to apply design patterns. The course issuitable for students in science, engineering andfinance who wish to further their understanding ofthe language. On completion, students will be in aposition to the design and develop systems usingC++. Assignments include writing programs and aprogramming project. Prerequisites: APC 505 orequivalent knowledge of C++. 3 credits

APC508 Web Development with Java 2This course uses “Java 2” technology to introducethe essential concepts needed to develop web appli-cations with client side scripting. Topics include thestructure and elements of Java, Java FoundationClasses (JFC), Java applets and servlets, JavaBeans and Remote Method Invocation (RMI). Othertopics, such as JDBC and XML may be introduced,time permitting. On completion, students will under-stand the conceptual architecture of webapplications with client side automation and be in aposition to contribute to their design and develop-ment. Assignments include writing programs and aproject to develop a web application. Prerequisites:knowledge of a programming language. 3 credits

APC511 Computational Tools for Engineering and FinanceThis course provides an introduction to essentialprogramming skills needed for engineering andfinance. The course reviews key topics in linearalgebra, explores basic numerical methods, andprovides a comprehensive introduction to computingin Matlab. Mathematical topics include vectorspaces, matrix computation, solution of linear sys-tems, interpolation, regression, approximation,numerical precision, convergence and algorithmcomplexity. Matlab topics include language features,handling vectors, matrices and cells, programmingin Matlab (functions and script files), 2D and 3Dgraphics, using key toolboxes, developing a graphi-cal user interface, and other advanced features.

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Programming assignments focus on the practicaluse of Matlab. Prerequisites: knowledge of a pro-gramming language. 3 credits

APC515 Data Structures and Discrete MathThis course covers fundamental topics in data struc-tures and discrete mathematics. The topics arepresented in an integrated manner that provides thediscrete math foundations for data structures andcomputing applications of discrete mathematicsconcepts. Topics covered include stacks, queues,linked lists, trees, algorithms for searching and sort-ing, finite state automata, and concepts ofcomputability and decidability. Topics from discretemath include sets and various types of relations(functions, graphs, trees, lattices), recursion andinductive proofs, boolean logic, relational algebra,predicate calculus, series and limits, and asymptot-ic behavior of searching and sorting algorithms.Programming exercises are assigned throughout thecourse. Prerequisites: APC505 or equivalent knowl-edge of C or C++. 3 credits

O R E G O N M A S T E R O F S O F T W A R E E N G I N E E R I N G

C O U R S E O F F E R I N G S

OMSE500 Principles of Software EngineeringThis course serves as an introduction to softwareengineering. The course’s focus is on understandingthe software engineering process and its attendantproblems as manifest in real development projects.The course compares and contrasts different modelsof the software engineering process and approachesto process improvement. It includes the analysis ofwhere and how things go wrong motivated by casestudies. This course is intended as a leveling coursefor entering students who have not had priorinstruction in software engineering and may bewaived for students with an equivalent senior-levelor master’s-level course or equivalent work experi-ence. Prerequisite: Knowledge of programming.Relevant work experience recommended but notrequired. 3 credits

OMSE 511 Managing Software DevelopmentThis course provides the knowledge and skills need-ed to plan, organize, lead, and control softwareprojects. Topics include planning and estimating,measuring and controlling, and achieving results inenvironments that include a great deal of ambiguityand contradictory information. Quantitative meas-ures and risk management will be emphasizedthroughout the course. Students will prepare projectplans for real or hypothetical software projects, toinclude effort, cost, and schedule estimates and riskmanagement plans. Prerequisite: OMSE 500.

3 credits

OMSE512 Understanding the Software BusinessThis course provides a familiarity with the businessand economic aspects of software companies andother high-technology companies that develop soft-ware. Topics include fundamental macro-economicconcepts, basic accounting and financial principlesand methods, basic business law, and the functionsand role of marketing in enterprises that developsoftware products or products that include soft-ware. Prerequisite: OMSE 500. 3 credits

OMSE513 Professional Communication Skills forSoftware EngineersThis course covers the skills necessary for appro-priate professional conduct and effectivecommunication in a professional setting. It includestechnical writing, making effective presentations,conducting effective meetings, conflict resolution,team and decision-making skills, and professionalethics. Prerequisite: OMSE 500. 3 credits

OMSE521 Using Metrics and Models to SupportQuantitative Decision MakingThis course provides the knowledge and skills need-ed to apply quantitative tools based on metrics andmodels of the software product and developmentprocess to make decisions under uncertainty. Topicscovered will include measurement concepts, deci-sion-making under uncertainty, and model andmetric development for the software developmententerprise. Prerequisite: OMSE 500. 3 credits

OMSE522 Modeling and Analysis of Software SystemsAbstract models are used to formalize specificationsof software systems. Formalized reference specifi-cations serve as a basis for the design of softwareimplementations and for validating critical proper-ties of software systems. This course provides thefundamental mathematical concepts needed tounderstand abstract models of software and to rea-son about them as well as examples showing howthey are applied. Prerequisite: OMSE 500. 3 credits

OMSE525 Software Quality AnalysisThis course covers processes, methods, and tech-niques for developing quality software, for assessingsoftware quality, and for maintaining the quality ofsoftware. Course material emphasizes the tradeoffsbetween software cost, schedule time, and quality;the integration of quality into the software develop-ment process; formal review and inspectionmethods; principles of testing and test planning;module design for testability; and maintaining qual-ity while supporting existing software. Prerequisite:OMSE 500. 3 credits

OMSE531 Software Requirements EngineeringThis course covers the principles, tools, and tech-niques for requirements elicitation, specification,and analysis. The course focus is on understandingthe role of requirements in system development andmaintenance, goals of the requirements phase,essential difficulties of specifying requirements forreal systems, and effective methods tools and tech-niques. The course covers techniques for formallymodeling and specifying software requirements withhands-on experience as well as the role of prototyp-ing in validating requirements. Prerequisites: OMSE500, OMSE 522, and the Formal Inspections partofQuality Analysis. 3 credits

OMSE532 Software Architecture and Domain AnalysisThis course covers the principles and methods of thearchitectural design of complex software systems. Itincludes a survey of the major architectural styles,strengths and weaknesses of each style, and trade-offs among them; application of domain analysis toidentifying and capturing common architecture insoftware domains (e.g., Product lines); the impact ofplatform dependence and independence on architec-tural decisions; and the relation of software

architecture to requirements and its effects ondownstream design. Students will examine domainanalysis and the architectural design process andproducts in context including the effect of decisionson function, quality, cost, and schedule.Prerequisites: OMSE 500, OMSE 522. 3 credits

OMSE533 Software Design TechniquesThis course covers the principles of software designand a survey of design methods, techniques, andtools. In-depth and hands-on study of at least onemethod such as object-oriented design as applied toa realistic industrial problem. It examines theeffects ofdesign decisions on the functional and non-functional properties of the software (e.g., Ease ofunderstanding, maintainability, reuse) and how soft-ware engineering principles are applied to makeappropriate trade-offs. Students also examine thedesign process and products in context including theeffect of design decisions on function, quality, cost,and schedule. Prerequisites: OMSE 500, OMSE 522.CSE students may not receive credit for both CSE504 and OMSE 533 because there is significantoverlap in content. 3 credits

OMSE535 Software Implementation and TestingThis course covers the principles of implementingand verifying computer software. Implementationtopics include coding style, packaging principles,reuse, testability, and maintainability. Verificationtopics include structural (white box) testing andtechniques for code verification. Also included willbe verification and integration of foreign code, test-ing techniques and how to apply them, includingcode-based and specification-based testing, hands-on application of the testing process, including testcase generation, and test adequacy, test validation,test execution, and automation. Prerequisites:OMSE 500, OMSE 522, OMSE 525. 3 credits

OMSE551 Strategic Software EngineeringWhere traditional software engineering focuses onthe development and maintenance of individual sys-tems strategic software engineering addresses thedevelopment of multiple systems over time. Recentwork has shown that significant gains in productivi-ty, cost, and schedule can result from systematicimprovement of a company’s overall software devel-opment process and systematic reuse of life-cycleproducts over multiple developments. This coursecovers the principles, methods, and tools for suchstrategic software development including long-termprocess modeling and improvement, developing pro-grams as instances of families of systems, andsystematic approaches to code generation and thereuse of non-code products including requirementsand design. Prerequisites: OMSE Foundation andContext courses. 3 credits

OMSE555 Software Development Practicum I 3 credits

OMSE556 Software Development Practicum IIThe development practicum provides an opportunityfor students to apply the knowledge and skills gainedin other courses as they synthesize a solution to asignificant, realistic, and practical problem.Students work in teams to analyze a problem, devel-op a software concept, plan a software developmenteffort, define requirements, and implement a solu-

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tion. Each offering of the practicum will include atleast one hour of lecture per week. Students willwork closely with OMSE program faculty and, wherepossible, reviewers from industry to apply advancedsoftware engineering techniques to a disciplineddevelopment of a realistic product and evaluate theresults. Software development artifacts created aspart of the practicum will become part of the stu-dent’s professional portfolio. Contents of theportfolio include such products as the concept defi-nition, cost estimate, project plan and schedule,formal requirements specification, test plan, soft-ware quality assurance plan, software architecture,software design, implementation artifacts, testresults, and metrics collected. The portfolio contents provide examples of the student’s profes-sional capabilities. 3 credits

RESEARCH PROGRAMSThe specific research projects under way at anygiven time depend upon current interests and obli-gations of faculty, students, and research sponsors.

Agent-Based Systems

This project will design a new agentcommunication language (AGENTTALK) andmultiagent architecture. Unlike DARPA’s currentlanguage (KQML), the language offers a truesemantics, and provably correct dialogue protocols,based on joint intention theory. The Adaptive AgentArchitecture, a successor to our earlier OpenAgent Architecture, offers platform and applicationinteroperability, facilitated communication, properconcurrent operation, dynamic reconfigurability offacilitators, and separation of data and control.Quickset has been reimplemented to use this archi-tecture, gaining a more robust capability forsupporting human-human collaboration, multime-dia, and dynamic adaptation to processingenvironments. Cohen

Autonomix: Component, Network, and System Autonomy

Autonomix pragmatically seeks to provideautonomic defenses for commodity informationsystems. Our contribution is in three complementa-ry areas: Component Autonomy, to make existingindividual components more robust to attack,Network Autonomy, to allow existing componentsto access CIDF capabilities via current Internetstandard protocols, and Systemic Autonomy, tomodel, analyze and implement coordinated, adap-tive responses of multiple components. Componentautonomy is developing a family of tools(StackGuard, PointGuard, FormatGuard, andRaceGuard) that make applications vulnerabilitytolerant by making broad classes of vulnerabilities(buffer overflows, printf format string bugs, andtemporary file races) unexploitable. Network andSystemic Autonomy are providing a family of toolsto enable large-loop intrusion tolerant responses,where in a distributed network of machines canadaptively respond to intrusions. ComponentAutonomy work is being done at WireXCommunications, Inc., and Network and SystemicAutonomy work is being done at OGI. Cowan,Maier, Delcambre

Constructing Software from Specifications

Research in formal methods for software engineer-ing has been concerned primarily with softwarespecification. This research explores the nextstep: given a declarative specification, to generatepractical and efficient software by the technologiesof program transformation and specialization.

We have demonstrated a new softwaredevelopment method in which software componentsare constructed from executable specifications bytyped, staged functional programs and atranslation directed by an interface specificationthat determines data representations. Systematictechniques for proving the semantic validity of rep-resentations for data types are explored. Kieburtz,Hook, Sheard, Launchbury

Digital Government

DOT is collaborating with the US Forest Service,Bureau of Land Management, Fish and WildlifeService and other government agencies to build aforest information portal for the AdaptiveManagement Area (AMA) program. The AMAsdevelop and test innovative approaches to forestmanagement. We are developing an informationmodel called Metadata++ to locate documents anddocument fragments along several dimensions andto search for documents based on ìsimilaritysearch between locations. The Forest project alsoincludes participants from the MST and ESEdepartments at OGI, from UNLV and from the pri-vate sector. Delcambre, Maier, Toccalino, Phillips,Steckler, Tolle, Landis, Palmer

Domain Specific Languages

A domain-specific language can provide a declara-tive programming interface for specialists in anapplication domain who are not primarily softwareengineers. A well-designed domain-specificlanguage improves productivity, reduces the inci-dence of programming errors and furnishes aneasily understood medium for documentation of asoftware artifact. A barrier to the widespreadadoption of domain specific languages is the inher-ent difficulty of language design andimplementation. We are developing semantics com-binators to allow rapid implementation ofdeclarative, domain-specific languages. We are alsopursuing staged implementations as a means ofefficiently embedding a domain specific languageinto a broad-spectrum functional language frame-work. Sheard, Hook, Kieburtz, Launchbury

Functional Programming Languages

Functional programming languages are based uponthe idea that programs can be designed as mathe-matical functions with logical properties.Functional abstraction is a powerful and flexiblemeans of constructing concise programs. PacSoftfaculty have a continuing interest in techniques foranalysis and efficient implementation of functionalprogramming languages including ML and Haskell.These techniques include staged programming, par-tial evaluation, effects encapsulation with monads,automatic program transformation, and advancedtype systems. Black, Hook, Jones, Kieburtz,Launchbury, Sheard

Machine Learning and Adaptive Systems

Machine learning, neural computation andadaptive systems are studied from both theoreticaland practical standpoints. Research in theory,architectures, and algorithm design includeslearning algorithms (supervised, unsupervised,and reinforcement), generalization theory(including model selection and pruning, invariantlearning), deterministic and stochastic optimiza-tion, context-sensitive learning, signal processing,time series analysis, and control. Practical appli-cation domains include adaptive signal processing,pattern recognition, speech recognition, imageprocessing, medical screening technology, controlsystems, macroeconomics, and finance.Hermansky, Leen, Moody, Pavel, Song, Wan

Multimodal Systems

Multimodal interfaces enable more natural andefficient interaction between humans and machinesby supporting multiple coordinated channelsthrough which input and output can pass. TheCenter for Human-Computer Communication isengaged in empirical investigation of multimodalinteraction. This informs our research and develop-ment of architectures for multimodal languageprocessing, work which draws on a range of fieldssuch as cognitive science, natural languageprocessing, multimedia, user interface design,speech recognition, gesture recognition, and visualparsing. The Quickset system developed at CHCCsupports multimodal pen/voice interaction withcomplex visual/spatial displays such as maps.Cohen, Oviatt

Natural Language Dialogue

The performance of speech recognition systemsimproves significantly when the spoken languageunderstanding system can predict the next utter-ance. Accordingly, we are performing perceptualstudies of dialogue and building models of human-human and human-computer dialogue in order todevelop computational models of conversation thatcan be used to track and predict spoken language.This work is based on speech-act theory, multi-agent architectures, and models of spontaneousspeech. Cohen, Heeman, Oviatt

Net Data Management

We believe that data management systems of thefuture must stress data movement over data storage.NIAGARA is an initial effort, conducted with theUniversity of Wisconsin, to move beyond disk-centric data management to net-centric systems.Current work includes algebras and special opera-tors for XML, exploiting stream semantics forefficient processing, and data-query hybrids for dis-tributed query evaluation. Maier, DeWitt, Naughton

Operating SystemsOur operating systems-related research focusesprimarily on adaptive systems software and itsapplication in distributed, mobile, and multimediacomputing environments. Several large projectsare currently under way in the areas of quality ofservice control, adaptive resource managementand dynamic specialization for enhanced perform-ance, survivability and evolvability of largesoftware systems. Black, Steere, Walpole

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Query Optimization

Our work on query optimization and evaluationdeals with both general frameworks and specifictechniques for different data model and querylanguage features. Columbia is a C++-based, top-down framework for construction of cost-basedquery optimizers. We are currently examiningpruning techniques for searching, transforms forcollection-valued attributes and nested queries,and ìmultiplex query optimization for efficientlyoptimizing groups of queries. Columbia is a jointproject with Portland State University. Maier,Shapiro

Speech Recognition

The goal of Large Vocabulary Continuous SpeechRecognition research is to enable normal humanspeech as an input device in next generation com-puters alongside today’s keyboard and mouse input.This technology can be used for dictation andcommand control applications when used by itself.It can also form part of a powerful informationprocessing system when used together with infor-mation retrieval and natural languageunderstanding systems. The research focusesinclude accurate acoustic modeling, speaker adap-tation, confidence measure and rejection, andmodeling spontaneous speech. Yan, Heeman

Spoken Language Systems

Spoken language systems make it possible forpeople to interact with computers using speech,the most natural mode of communication. A spokenlanguage system combines speech recognition,natural language understanding and humaninterface technology. It functions by recognizing theperson’s words, interpreting the words in terms ofthe context and goals of the task, and providing anappropriate response to the user. We are involvedin the analysis and development of various compo-nents of such systems, ranging from empiricalstudies of human dialogues through the construc-tion of interactive systems to the development ofabstract models of behavior. Cohen, Oviatt,Heeman, van Santen

Superimposed Information and Superimposed Applications

We are interested in providing typical databasesystem capabilities in an environment where wedo not own or manage the underlying, baseinformation. We seek to develop a superimposedlayer of information that can reference selectedinformation from the base layer and can also addnew information to highlight, interconnect, elabo-rate, or annotate the selected information. We havedefined an architecture for building superimposedapplications and have implemented our first tool:SLIMPad, a scratchpad application that allowsusers to easily create “scraps” that referenceselected items from the base layer and organizescraps into bundles. The tendency to use scrapsand bundles to organize our thoughts is commonpractice, as confirmed by our observationalresearch team that is studying how clinicians seekand use information in a hospital intensive careunit. Observational team: Gorman, Ash,Lavelle;computer science team: Delcambre, Maier

Tracking Footprints through an Information Space:Leveraging the Document Selections of Experts

The goal of this project is to help expert problemsolvers find needed information in a large, complexinformation space. The focus is on one example ofexpert problem solving; the physician seeking todiagnose and treat a patient while using the med-ical record. Sorting through a heterogeneouscollection of electronic and other media materialsto find needed information, sometimes under timepressures, can be formidable. This project propos-es to capture the trace of information used byexperts-to monitor the paths taken and collectionresources used by physicians, in moving fromobservation, to information gathering, to solutionof a given health care problem. By capturing thetrace information artifacts associated withinformation seeking and selection, it ishypothesized that greater insight can be gainedinto behaviors of users and patterns of usage.This knowledge can then be fed-back into thedesign and development of new information envi-ronments. The work is conducted by a cross-disciplinary team comprised of an MD focusing oninformation seeking behaviors of physicians, and agroup of computer scientists focusing on extractingand using regularly structured information. Theusefulness of the approaches will be tested indomains other than health care, in particular theaircraft design industry through the active supportof the Boeing Corp. Delcambre, Maier, and Dr.Paul Gorman, Oregon Health & Science University

RESEARCH CENTERS

C E N T E R F O R H U M A N - C O M P U T E R C O M M U N I C AT I O N

Kimberly Tice, Center Administrator(503) [email protected]

The Center for Human-Computer Communication isdedicated to realizing a vision of transparentinformation and service access. Research projectsare broadly interdisciplinary, and includecollaborations with numerous universities, federalresearch laboratories, and the Data-IntensiveSystems Center at OGI.

Research activities focus on:

• Multimodal human-computer interaction thatallows people to state their needs using speech,writing, and gestures, and that providesmultimedia output.

• User-centered design of next-generationinterface technology, including spoken languageand multimodal interfaces, and interfaces formobile and multimedia technology.

• Intelligent agent technologies - software systemsthat assist users in accomplishing tasks and canreason about how and where to carry out theusers’ requests in a worldwide distributedinformation environment.

• Collaboration technologies to support human-human communication, and collaborativedecision making among groups of people.

CHCC organizes an annual Distinguished LectureSeries on the Future of Human-ComputerInteraction. World-class researchers are invited toshare current topics.

Dr. Philip Cohen and Dr. Sharon Oviatt are co-directors of the center. Other center faculty includeDr. Peter Heeman, and Dr. Misha Pavel. For moreinformation, visit CHCC’s web pages atwww.cse.ogi.edu/CHCC/.

P A C I F I C S O F T W A R E R E S E A R C H C E N T E R

Kelly Atkinson, Center [email protected]

Sheri Dhuyvetter, Center [email protected]

The Pacific Software Research Center (PacSoft) isa team of faculty, students and professionalresearch staff who study mathematically basedtechniques for the specification, development andvalidation of complex computer software. Our goalsare to explore and test new techniques that cansupport the development of software products inwhich clients can have high confidence.

PacSoft’s approach to software specification anddevelopment is grounded in functionalprogramming, type theory, and formal semantics ofprogramming languages. Our research methodsextend from theoretical investigation throughprototype software tool development toexperimental validation.

Much of our work during the past decade hasfocused on techniques for the design andimplementation of domain-specific languages. A domain-specific language is able to express theabstractions and operations used in a particularengineering domain, in terms familiar to domainexperts. One domain in which this work hasdemonstrated considerable success is the design of complex microarchitectures for high-performance microprocessors.

The Hawk project has exploited abstraction andequational specification techniques from functionalprogramming languages to produce a new kind ofhardware specification language. Amicroarchitecture specification written in Hawkcan be directly executed as a simulation,symbolically manipulated as a hardware algebra, orsubmitted to formal verification of its properties bymodel checking or by a theorem prover.

Among current PacSoft projects is Programatica,an exploration of computer-supported techniquesfor developing property-certified programs(ìprogramming as if properties matteredî). ProjectTimber is developing new means of programmingembedded applications that involve both time-critical and critical-rate tasks.

Dr. Tim Sheard is the current Director of theCenter. Dr Richard Kieburtz is the foundingDirector. Other faculty members of PacSoft are Dr.James Hook, Dr. Mark Jones and Dr. John

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Launchbury of OHSU/OGI and Dr. Andrew Tolmachof Portland State University. The Center employssix postdoctoral researchers and has numerousvisitors each year.

Research by PacSoft scientists is supported bygrants and contracts from the National ScienceFoundation, DARPA, the National Security Agency,Intel Corp. and Compaq.

For additional information, visit the PacSoft website, http://www.cse.ogi.edu/PacSoft/.

T H E S Y S T E M S G R O U P

Database and Object Technology LaboratoryJo Ann Binkerd, Center [email protected]

Systems Software LaboratoryCynthia Pfaltzgraff, Center [email protected]

The Systems Group consists of two researchlaboratories — the Systems Software Laboratoryand the Database and Object TechnologyLaboratory.

The Database and Object Technology Lab (DOT)conducts theoretical and applied research relatedto database management and object-orientedsystems. Query processing is a long-term focus,particularly query optimization frameworks as wellas design, optimization and evaluation of object-oriented query languages. Another area of interestis scientific data management, most recently insupport of multi-disciplinary studies in forestcanopy science.

DOT research includes conceptual modeling,including semantic and object-oriented databasemodels, models for object-oriented analysis anddesign, and models for superimposed information.Other topics include data dissemination, focusingparticularly on information utility andsuperimposed information management.Superimposed information enhances the utility and value of existing data sources by layering small amounts of information over them. We areexamining superimposed information in connectionwith improving accessibility of medical records.Finally, we are investigating architectures foradaptable software and middleware support for application building, especially object-oriented approaches.

Dr. Dave Maier of OGI is the director of DOT.Additional DOT-affiliated faculty members areDr.Crispin Cowan, Dr. Lois Delcambre, and Dr.Dylan McNamee of OGI, and Dr. Leonard Shapiro ofPortland State University.

The Software Systems Lab (SySL) is a center forresearch spanning the areas of distributed andmobile computing, operating systems, networking,and wide-area-network based informationmanagement systems. SySL focuses on thedevelopment of adaptive systems that utilizetechniques such as feedback-control, specialization,

domain-specific languages, and quality of servicemanagement to enable them to operate effectivelyin today’s rapidly evolving and widelyheterogeneous distributed environments. Weemphasize the real-world applicability of ourresearch results and we continue to builddistributed and scalable prototype systems forapplication areas such as multimedia computingand communications, active networks, Internet-based information management, and survivabledistributed systems. We collaborate closely withindustry sponsors such as Intel and IBM, and havestrong federal funding from DARPA and NSF. Dr.Jonathan Walpole is the director of SySL.Additional SySL-affiliated faculty are Drs. Wu-chiFeng, Wu-chang Feng, Andrew Black and DavidSteere of OGI, and Dr. Molly Shor of OSU.

FACILIT IESOGI’s Department of Computer Science andEngineering provides a state-of-the-art computingenvironment designed to support the needs ofresearch and education. The computing facilitiesstaff has a wide range of skills that allows thecomputing environment at CSE to be flexible and responsive in meeting the changing needs ofthe department.

Support for central services such as mail, dial-upaccess, video conferencing, database access, andfile and printer sharing as well as access toInternet and Internet2 services are distributedacross a group of Sun computers and a NetworkAppliance file server that comprise the coresupport environment.

While Sun computers are highly visible at CSE,both Intel and Alpha based machines runningWindows or Linux are mainstays of our researchactivities. The generous support of our industry andgovernment research partners allows CSE tomaintain a high-quality computing infrastructurecapable of supporting a high degree ofheterogeneity as required for high-quality research.

In all, a facilities staff of nine supports almost400 computer systems, X terminals, and peripheral devices spanning multiple networksusing a variety of automated techniques, manydeveloped internally, to cope with the high degree of complexity inherent in such aheterogeneous environment.

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F A C U L T Y | C O M P U T E R S C I E N C E A N D E N G I N E E R I N G | C S E

J A M E S H O O KAssociate Professor andDepartment Head Ph.D., Computer ScienceCornell University, [email protected]


Domain-specific languages, formal methods, and functional programming.

R E P R E S E N TAT I V E P U B L I C AT I O N SJ. Hook, E. Meijer, & D. Leijen,

“Client-side web scripting in Haskell”,in proceedings of Practical Applicationsof Declarative Languages, January 1999.

J. Hook, E. Meijer, & D. Leijen,“Haskell as an Automation Controller”,in “Advanced Functional Programming”,Swierstra, Henriques and Oliveira(Eds.), Springer Verlgan, LNCS Vol. 1608.

T. Widen &J. Hook, “Software DesignAutomation: Language Design in theContext of Domain Engineering,” Sere98, June 1998.

J. Bell, F. Bellegarde & J. Hook,“Type-driven Defunctionalization,” ICFP ‘97, June 1997.

R. Kieburtz, F. Bellegarde, et al.,“Calculating Software Generators fromSolution Specifications,” TAPSOFT ‘95,Springer-Verlag, LNCS, May 1995.

F. Bellegarde & J. Hook, “Substitution:A Formal Methods Case Study usingMonads and Transformations,” Scienceof Computer Programming, 22(2-3),287, 1994.

J. Bell, J. Hook, et al., “SoftwareDesign for Reliability and Reuse: AProof-of-Concept Demonstration,”TRI-Ada ‘94 Proceedings, ACM Press,November 1994.

F. Bellegarde & J. Hook, “Monads,Indexes, and Transformations,”Proceedings of the Colloquium onFormal Approaches to SoftwareEngineering (TAPSOFT ‘93), LNCS,April 1993.

D A V I D B A S T E R F I E L DAssistant ProfessorPh.D., Decision TheoryUniversity of Manchester, [email protected]


Numerical computing, simulation, optimization, genetic algorithms, informationsystems, time series analysis and computational finance.

R E P R E S E N TAT I V E P U B L I C AT I O N SD. Basterfield, “Error bounds on

Tree methods for CalculatingOptions Prices”, Paper Presented at Computational Finance 2000, June 2000.

D. Basterfield, T. Bundt andG.Murphy, “The Stable ParetianHypothesis and the Asian CurrencyCrisis”, Paper Presented atComputational Finance 2000, June 2000.

A N D R E W P. B L A C KProfessorD. Phil, University of Oxford,(Balliol College) [email protected]


Programming languages;distributed systems; streaminginfrastructure for wide-areanetworks; object-orientedlanguages and systems;programming environments; andthe ways in which all of theseareas interrelate.

R E P R E S E N TAT I V E P U B L I C AT I O N SA. P. Black, J. Huang and J. Walpole,

“Reifying Communication at theApplication Level”. Oregon GraduateInstitute, Department of ComputerScience & Engineering, Beaverton, OR,Technical Report CSE-01-006, May 2001.

C. Pu, A. Black, C. Cowan, J. Walpole,& C. Consel, “Microlanguages forOperating System Specialization,” Proc. First ACM SIGPLAN Workshop on Domain-Specific Languages, Paris,France, p. 49-57, January 1997.

C. Pu, T. Autrey, A.P. Black, C. Consel,C. Cowan, J. Inouye, L. Kethana, J. Walpole & K. Zhang, “OptimisticIncremental Specialization:Streamlining in a CommercialOperating System,” Proceedings of the15th ACM Symposium on OperatingSystems Principles, December 1995.

A.P. Black & M.P. Immel,“Encapsulating Plurality,” Proceedingsof European Conference on Object-Oriented Programming, July 1993.

R.K. Raj, E.D. Tempero, H.M. Levy,A.P. Black, N.C. Hutchinson & E. Jul,“Emerald, A GeneralPurposeProgramming Language,” SoftwarePractice & Experience, 21(1), 91,January 1991.

A.P. Black & Y. Artsy, DigitalEquipment Corp., “ImplementingLocation Independent Invocation,” IEEE Trans. On Parallel and DistributedSystems, 1(1), 107, January 1990.

T H O M A S B U N D TAssociate ProfessorPh.D., EconomicsMichigan State University, [email protected]


International monetary theory andempirical models of exchange ratedetermination, time series analysisand forecasting and pedagogicaltools in finance. Professor Bundthas also written instructionalmanuals (distance learningcourses) in Managerial Economics,Business Forecasting andEbusiness Valuations.

R E P R E S E N TAT I V E P U B L I C AT I O N ST. Bundt, T.F. Cosimano &

J.A. Halloran, “DIDMCA and BankMarket Risk: Theory and Evidence,”Journal of Banking and Finance, 16,1179-1193, 1992.

T. Bundt & J.H. Bergstrand, “Currency Substitution and MonetaryAutonomy: The Foreign Demand forU.S. Demand Deposits,” Journal ofInternational Money and Finance, 9, 325-334, 1990.

T. Bundt & R. Schweitzer,“Deregulation, Deposit Markets, andBanks’ Costs of Funds,” The FinancialReview, 24(3), 417-430, August 1989.

T. Bundt, J.S. Chiesa & B.P. Keating,“Common Bond Type and Credit UnionBehavior,” Review of Social Economy,47(1), 27-42, Spring 1989.

T. Bundt & A. Solocha, “Debt, Deficits and the Dollar,” Journal of Policy Modeling, 10(4), 581-600,October 1988.

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P H I L C O H E NProfessor and Co-Director, Center for Human-ComputerCommunicationPh.D., Computer ScienceUniversity of Toronto, [email protected]


Multimodal interfaces, human-computer interaction, naturallanguage processing, dialogue,delegation technology, cooperatingagents, communicative action,applications to mobile computing,information management, networkmanagement, manufacturing.

R E P R E S E N TAT I V E P U B L I C AT I O N SOviatt, Sharon & Cohen, Philip.

“Multimodal Interfaces ThatProcess What Comes Naturally”,Communications of the ACM, Vol. 43,No. 3, pp. 45-53, March 2000.

D. McGee, P. Cohen, & L. Wu, (2000)“Something from nothing: Augmenting a paper-based work practice with multimodal interaction,” in Proceedingsof the Designing Augmented RealityEnvironments Conference, ACM Press,pp. 71-80, Copenhagen, Denmark, April 12-14, 2000.

S. Kumar, & P. Cohen, “Towards aFault-Tolerant Multi-Agent SystemArchitecture.” To appear in TheFourth International Conference onAutonomous Agents (Agents 2000),Barcelona, Spain, June 3-7, 2000.

L. Wu, S.L. Oviatt, & P. Cohen,“Multimodal Integration — A Statistical View,” IEEE Transactionson Multimedia, Vol. 1, No. 4,pp. 334-341, December 1999.

P. Cohen, D. McGee, S.L. Oviatt,L. Wu, J. Clow, R. King, S. Julier, &L. Rosenblum, “Multimodal Interactionsfor 2D and 3D Environments,” IEEEComputer Graphics and Applications,pp.10-13, July/August 1999.

S. Kumar, P. Cohen, & H. Levesque,“The Adaptive Agent Architecture:Achieving Fault-Tolerance UsingPersistent Broker Teams.” To appear in The Fourth International Conferenceon Multi-Agent Systems (ICMAS 2000),Boston, MA, USA, (Acceptance rate20%), July 7-12, 2000.

C R I S P I N C O W A NAssistant Research ProfessorPh.D., Computer ScienceUniversity of Western Ontario,[email protected]


System security and survivability,operating systems, distributedsystems, computer architecture,optimism, programming languages.

R E P R E S E N TAT I V E P U B L I C AT I O N SC. Cowan, S. Beattie, C. Wrigth, &

G. Kroah-Hartman, “RaceGuard:Automatic Adaptive Detection andPrevention of Buffer-Overflow Attacks,”Tenth USENIX Security Conference2001.

C. Cowan, M. Barringer, S. Beattie,G. Kroah-Hartman, M. Frantzen, & J. Lokier, “FormatGuard: AutomaticAdaptive Detection and Prevention ofBuffer-Overflow Attacks,” Tenth USENIX Security Conference 2001.

D. McNamee, J. Walpole, C. Cowan, C. Pu, C. Krasic, P. Wagle, C. Consel, G. Muller & R.Marlet, “SpecializationTools and Techniques for SystematicOptimization of Systems Software,”ACM Transactions on ComputerSystems, Volume 19, No. 2, May 2001.

C. Cowan, C. Pu, D. Maier, H. Hinton,J. Walpole, P. Bakke, S. Beattie, A. Grier, P. Wagle, & Q. Zhang,“Stackguard: Automatic AdaptiveDetection and Prevention of Buffer-Overflow Attacks,” Seventh USENIXSecurity Conference, 1998.

C. Cowan & H. Lutfiyya, “A Wait-FreeAlgorithm for Optimistic Programming:HOPE Realized,” 16th InternationalConference on Distributed ComputingSystems (ICDCS’96), Hong Kong, 1996.

C. Cowan, T. Autrey, C. Krasic,C. Pu, & J. Walpole, “Fast ConcurrentDynamic Linking for an AdaptiveOperating System,” in The InternationalConference on Configurable DistributedSystems (ICCDS’96), Annapolis, MD,1996.

C. Pu, T. Autrey, A. Black, C. Consel,C. Cowan, J. Inouye, L. Kethana, J.Walpole, & K. Zhang, “OptimisticIncremental Specialization:Streamlining a Commercial OperatingSystem,” in Proceedings of the 15thACM Symposium on Operating SystemsPrinciples (SOSP’95), CopperMountain, Colorado, 1995.

L O I S D E L C A M B R EProfessorPh.D., Computer ScienceUniversity of SouthwesternLouisiana, [email protected]


Superimposed information,database system data models,scientific data management.

R E P R E S E N TAT I V E P U B L I C AT I O N SS. Bowers and L. Delcambre.

A generic representation for exploitingmodel-based information. To appear,ETAI Journal, 2001.

L. Delcambre, D. Maier, S. Bowers, L. Deng, M. Weaver, P. Gorman, J. Ash, M. Lavelle, and J. Lyman.Bundles in captivity: An applicationof superimposed information.“Proceedings of the IEEE InternationalConference on Data Engineering,Heidelberg, Germany, April 2001.

S. Bowers and L. Delcambre.Representing and transforming model-based information. In Proceedings ofthe International Workshop on theSemantic Web, in conjunction withECDL 2000, Lisbon, Portugal,September 2000.

P. Gorman, J. Ash, M. Lavelle, J. Lyman, L. Delcambre, D. Maier, S. Bowers and M. Weaver. Bundles inthe wild: Tools for managing informa-tion to solve problems and maintainsituation awareness. Library Trends49(2), Fall 2000.

D. Maier and L. Delcambre,ìSuperimposed information for theInternetî, in Proc. of the ACM SIGMODWorkshop on The Web and Databases(WebDB ‘99), pages 1-9, June 1999.

L. Delcambre and D. Maier, “Models for superimposed information,”in Advances in Conceptual Modeling(ER ‘99), Volume 1727, Lecture Notesin Computer Science, pages 264-280,November 1999.

L. Delcambre & E. Ecklund, “ABehaviorally Driven Approach toObject-Oriented Analysis and Designwith Object-Oriented Data Modeling,”in Object-Oriented Data Modeling,M. Papazouglu, S. Spaccateria, & Z.Tari (Eds), MIT Press, 1999.

R I C H A R D E . ( D I C K ) FA I R L E YProfessor and Director of Software EngineeringPh.D., Computer ScienceUCLA, [email protected]


All aspects of softwareengineering, including but notlimited to systems engineering ofsoftware-intensive systems,software process modeling andprocess improvement, softwarerequirements engineering,software design, software qualityengineering, software metrics,software project management,software cost and scheduleestimation, software riskmanagement, and softwareengineering policies, procedures,standards, and guidelines.

R E P R E S E N TAT I V E P U B L I C AT I O N SSoftware Project Management,

Encyclopedia of Computer Science,Groves Dictionaries, 2001.

“Software Estimation Risk,”Encyclopedia of Software Engineering,Volume 2, John Wiley and Sons, 2000.

R. Fairley, “A Process-OrientedApproach to Software ProductImprovement,” PROFES’99 ConferenceProceedings, Oulu, Finland, June 1999.

R. Fairley, “The Concept ofOperations-The Bridge fromOperational Requirements to TechnicalSpecifications,” Annals of SoftwareEngineering, Vol. 3, Baltzer Publishers,Amsterdam, The Netherlands,September 1997.

R. Fairley, “Standard for Conceptof Operations Documents,” IEEE

Standard Vol. 1362, IEEE ComputerSociety, 1997.

R. Fairley, “Standard for SoftwareProject Management Plans,” IEEEStandard, Vol. 1058, IEEE ComputerSociety, 1997.

R. Fairley, “Risk-Based CostEstimation,” Proceedings of the 11thCOCOMO Users Group, Los Angeles,CA, November 1996.

R. Fairley, “Some Hard Questions for Software Engineering Educators,”keynote presentation, CSEE 95Proceedings, ACM Conference onSoftware Engineering Education, NewOrleans, March 1995.

C S E | C O M P U T E R S C I E N C E A N D E N G I N E E R I N G | F A C U L T Y

W U - C H A N G F E N GAssistant ProfessorPh.D., Computer ScienceUniversity of Michigan, [email protected]


Scalable Internet systems, Internetcongestion control and queuemanagement, wireless networking,programmable networkinfrastructure.

R E P R E S E N TAT I V E P U B L I C AT I O N SW. Feng, D. Kandlur, D. Saha, K. Shin,

“Blue: An Alternative Approach toActive Queue Management,” NOSSDAV2001, June 2001.

W. Feng, D. Kandlur, D. Saha, K. Shin,“Stochastic Fair Blue: A QueueManagement Algorithm for EnforcingFairness,” INFOCOM 2001, April 2001.

W. Feng, D. Kandlur, D. Saha, K. Shin,“A Self-Configuring RED Gateway,”INFOCOM 1999, May 1999.

W. Feng, D. Kandlur, D. Saha, K. Shin,“Adaptive Packet Marking forMaintaining End-to-End Throughput ina Differentiated Services Internet,”IEEE/ACM Transactions on Networking,v. 7, n. 5, October 2001.

W. Feng, D. Kandlur, D. Saha, K. Shin,“Understanding and Improving TCPPerformance over Networks withMinimum Rate Guarantees,” IEEE/ACMTransactions on Networking, Vol. 7, No.2, pp. 173-187, April 1999.

W U - C H I F E N GAssociate Professor Ph.D., Computer ScienceUniversity of Michigan, [email protected]


Networking, multimedia systems,multimedia networking, videocoding, middleware services, andmassively scalable streaminginfrastructures.

R E P R E S E N TAT I V E P U B L I C AT I O N SGuohong Cao, Wu-chi Feng,

Mukesh Singhal, Online VBR VideoTraffic Smoothing, to appear ComputerCommunications.

Wu-chi Feng, Ming Liu, ExtendingCritical Bandwidth AllocationTechniques for Stored Video DeliveryAcross Best-Effort Networks, toappear International Journal ofCommunication Systems.

Ali Saman Tosun, Wu-chi Feng,Lightweight Security Mechanisms forWireless Video Transmission, inProceedings of the IEEE InternationalConference on Information Technology:Coding and Computing 2001, Las Vegas,Nevada, April 2001.

Ali Saman Tosun, Wu-ch Feng, OnImproving Quality of Video for H.263over Wireless CDMA Networks, inProceedings of the IEEE WirelessCommunications and NetworkingConference, Chicago, Illinois,September 2000.

Amit Agarwal, Wu-chi Feng, ChristineWolfe, A Multi-Differential Video CodingAlgorithm for Robust VideoConferencing, in Proceedings of theSPIE Voice, Video, and DataCommunications Conference, Boston,Massachusetts, November 2000.

Ali Saman Tosun, Amit Agarwal, Wu-chi Feng, Providing Efficient Supportfor Lossless Video Transmission andPlayback, in 10th InternationalWorkshop on Network and OperatingSystems Support for Digital Audio andVideo, Chapel Hill, North Carolina, June 2000.

P E T E R A . H E E M A NAssistant Professor and Ph.D., Computer ScienceUniversity of Rochester, [email protected]


Spontaneous speech recognition,modeling disfluencies andintonation, dialogue management,collaboration, spoken dialoguesystems, natural languageprocessing.

R E P R E S E N TAT I V E P U B L I C AT I O N SP. Heeman & J. Allen, “Improving

Robustness by Modeling SpontaneousSpeech Events,” in J. Junqua and G. van Noord (Ds.), Robustness in lan-guage and speech technology, KluwerAcademic Publishers, 2000.

K. Ward & P. Heeman, “Acknowledgmentsin Human-Computer Interaction,” inProceedings of the 1st Conference ofthe North American Chapter of theAssociation for ComputationalLinguistics, Seattle, May 2000.

P. Heeman, “Modeling Speech Repairsand Intonational Phrasing to ImproveSpeech Recognition,” in IEEE Workshopon Automatic Speech Recognition andUnderstanding, Keystone, Colorado,December 1999.

P. Heeman & J. Allen, “SpeechRepairs, Intonational Phrases andDiscourse Markers: Modeling Speakers’ Utterances in SpokenDialog,” Computational Linguistics, Vol. 25-4, 1999.

P. Heeman, “POS Tags and DecisionTrees for Language Modeling,” inProceedings of the Joint SIGDATConference on Empirical Methods inNatural Language Processing and VeryLarge Corpora, College Park, Maryland,June 1999.

P. Heeman, M. Johnston, J. Denney & E. Kaiser, “Beyond StructuredDialogues: Factoring Out Grounding,” in Proceedings of the InternatialConference on Spoken LanguageProcessing (ICSLP-98), Sydney,Australia, December 1998.

P. Heeman & G. Damnati, “DerivingPhrase-based Language Models,” IEEEWorkshop on Speech Recognition andUnderstanding, Santa Barbara,California, December 1997.

M I C H A E L J O H N S T O N ( o n l e a v e 2 0 0 1 - 0 2 )Assistant Research ProfessorPh.D., Linguistics, University ofCalifornia at Santa Cruz, [email protected]


Natural language processing,human-computer interaction,multimodal interfaces, spokendialogue systems, syntax,semantics, and pragmatics ofhuman language, computationalmodels of phonology, morphology,and the lexicon, natural language understanding andcomputational semantics.

R E P R E S E N TAT I V E P U B L I C AT I O N SM. Johnston, P. Cohen, D. Mcgee,

S.L. Oviatt, J.A. Pittman, I. Smith,“Unification-based MultimodalIntegration,” Proceedings of the 35thAnnual Meeting of the Association forComputational Linguistics, Madrid,Spain, 281-288, 1997.

P. Cohen, M. Johnston, D. Mcgee, S.L. Oviatt, J.A. Pittman, I. Smith, L.Chen, & J. Clow, “quickset: Multimodalinteraction for distributedapplications,” Proceedings of the FifthACM International MultimediaConference, CM Press, New York, 1997.

M. Johnston, “The Telic/AtelicDistinction and the Individuation ofQuantificational Domains,” in EmpiricalIssues in Formal Syntax and Semantics:Selected Papers from the Colloque deSyntaxe et de Sémantique de Paris(CSSP 95), Daniéle Godard and FrancisCorblin (Eds.). Peter Lang, Bern, 269-290, 1997.

J. Pustejovsky, B. Boguraev, M.Verhagen, P. Buitelaar & M. Johnston,“Semantic Indexing and TypedHyperlinking,” in Proceedings of theAAAI Spring Symposium on NaturalLanguage Processing for the WorldWide Web, American Association forArtificial Intelligence, 1997.

M. Johnston & F. Busa, “QualiaStructure and the CompositionalInterpretation of Compounds,” inProceedings of ACL SIGLEX Workshop1996: Breadth and Depth of SemanticLexicons, Association for ComputationalLinguistics, 1996.

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M A R K P. J O N E SAssociate ProfessorD.Phil., ComputationUniversity of Oxford, [email protected]


Programming language design and implementation; programmingparadigms; module and componentsystems; type theory; semantics;program transformation and analysis.

R E P R E S E N TAT I V E P U B L I C AT I O N SMark P. Jones , Type Classes with

Functional Dependencies, inProceedings of the 9th EuropeanSymposium on Programming, ESOP2000, Berlin, Germany, March 2000,Springer-Verlag LNCS 1782.

M.P. Jones, “First-class Polymorphismwith Type Inference,” in Proceedings ofthe Twenty Fourth Annual ACMSIGPLAN-SIGACT Symposium onPrinciples of Programming Languages,Paris, France, Jan. 15-17, 1997.

M.P. Jones, “Using ParameterizedSignatures to Express ModularStructure,” in Proceedings of the Twenty Third Annual ACMSIGPLAN-SIGACT Symposium onPrinciples of Programming Languages,St. Petersburg Beach, Florida, Jan. 21-24, 1996.

M.P. Jones, “Simplifying andImproving Qualified Types,” in proceedings of FPCA ‘95: Conferenceon Functional Programming Languagesand Computer Architecture, La Jolla,CA, June 1995.

M.P. Jones, “A system of constructorclasses: overloading and implicit higher-order

polymorphism,” Journal of FunctionalProgramming, 5, 1, CambridgeUniversity Press, January 1995.

S. Liang, P. Hudak, & M.P. Jones,“Monad Transformers and ModularInterpreters,” in Conference Record ofPOPL’95: 22nd ACM SIGPLAN-SIGACTSymposium on Principles ofProgramming Languages, SanFrancisco, CA, January 1995.

M.P. Jones, Qualified Types: Theoryand Practice, Cambridge UniversityPress, November 1994.

R I C H A R D B . K I E B U R T ZProfessor Ph.D., Electrical EngineeringUniversity of Washington, [email protected]


Functional programming, programtransformation, domain-specificlanguages, program verification,high-confidence software

R E P R E S E N TAT I V E P U B L I C AT I O N SR. B. Kieburtz, Real-time Reactive

Programming for EmbeddedControllers, (QAPL 2001)September 2001.

R. B. Kieburtz, A Logic for Rewriting Strategies, (Strategies ë01)June 2001.

R. B. Kieburtz, Defining andImplementing Closed Domain-SpecificLanguages, (SAIG 00),September 2000.

R. B. Kieburtz, Taming Effects withMonadic Typing, Richard Kieburtz, inProc.3rd International Conf. onFunctional Programming, ACM Press,April 1998.

R. B. Kieburtz, Reactive FunctionalProgramming, in PROCOMET’98, pp. 263-284, Chapman and Hall, June 1998.

R.B. Kieburtz, L. McKinney, J. Bell, J. Hook, A. Kotov, J. Lewis, D. Oliva, T. Sheard, I. Smith & L.Walton, “ASoftware Engineering Experiment inSoftware Component Generation,” inProceedings of the 18th InternationalConference on Software Engineering,Berlin, March 1996.

R.B. Kieburtz, F. Bellegarde, J. Bell, J. Hook, J. Lewis, D. Oliva, T. Sheard,L. Walton & T. Zhou,” CalculatingSoftware Generators from SolutionSpecifications,” TAPSOFT ‘95, Springer-Verlag, series LNCS, 915, 546, 1995.

R.B. Kieburtz, “Programming withAlgebras,” Advanced FunctionalProgramming, E. Meijer & J.Jeuring(Eds.), Springer-Verlag, Series LNCS,Vol. 925, 1995.

R.B. Kieburtz, “Results of the SDRRValidation Experiment,” PacificSoftware Research Center SoftwareDesign for Reliability and Reuse: Phase I Final Scientific and TechnicalReport, Vol. VI, CDRL No. 0002.11,February 1995.

J O H N L A U N C H B U R YProfessorPh.D., Computing ScienceUniversity of Glasgow, [email protected]


Functional programming languages,semantics-based program analysis,program transformation, andpartial evaluation.

R E P R E S E N TAT I V E P U B L I C AT I O N SJ. Lewis, M. Shields, E. Maijer,

& J.Launchbury, “Implicit Parameters,”Implicit Parameters, ACM Principles ofProgramming Languages, 2000.

J. Matthews & J. Launchbury, “Elementary Microarchitecture Algebra,”Computer Aided Verification, 1999.

J. Launchbury, J. Lewis, & B. Cook. “On embedding a microarchitecturedesign language within Haskell,”International Conference on FunctionalProgramming. ACM, 1999.

J. Launchbury & A. Sabry,“Axiomatization and Type Safety of Monadic State,” Proc. ACMInternational Conference on FunctionalProgramming, 1997.

J. Launchbury & R. Paterson,“Parametricity and Unboxing withUnpointed Types,” Proc. EuropeanSymposium on Programming,Linkoping, 1996.

J. Launchbury & S.P. Jones, “State in Haskell,” J. Of Lisp and SymbolicComputation, December 1995.

J. Launchbury & S.P. Jones, “LazyFunctional State Threads,” in Proc. SIG-PLAN Programming Languages Designand Implementation, Orlando, FL, 1994.

A. Gill, J. Launchbury & S.P. Jones, “A Short Cut to Deforestation,” in Proc. SIGPLAN/SIGARCH FunctionalProgramming and Computer Architecture,Copenhagen, Denmark, 1993.

J. Launchbury, “A Natural Semanticsfor Lazy Evaluation,” in Proc. SIGPLANPrinciples of Programming Languages,Charleston, SC, 1993.

J. Hughes & J. Launchbury,“Projections for Polymorphic First-Order Strictness Analysis,” inMathematical Structures in ComputerScience, 2, 301, C.U.P., 1992.

J. Hughes & J. Launchbury,“Relational Reversal of AbstractInterpretation,” in Journal of Logic andComputation, 2(4), 465, O.U.P., 1992.

T O D D K . L E E NProfessorPh.D., PhysicsUniversity of Wisconsin, [email protected]


Machine learning including: neural networks, local and mixture models, stochasticlearning, model complexity, andinvariance; applications to signalcompression, sensor fusion, andanomaly detection, adaptation inbiological systems.

R E P R E S E N TAT I V E P U B L I C AT I O N SR. Sharma, T.K. Leen, and M. Pavel,

“Bayesian Image Sensor Fusion UsingLocal Generative Models,” OpticalEngineering, 2001, in press.

C. Archer and Todd K. Leen, “TheCoding Optimal Transform,” in DataCompression Conference 2001, IEEEComputer Society Press, 2001.

C. Archer and T.K. Leen, “FromMixtures of Mixtures to AdaptiveTransform Coding,” in T. Leen, T. Dietterich, and V. Tresp (eds.),Advances in Neural InformationProcessing Systems 13, The MIT Press, 2001.

R. Sharma, T.K. Leen & M. Pavel,“Probabilistic Image Sensor Fusion,” in Advances in Neural InformationProcessing Systems 11, Kearn, Solla,Cohn (Eds.), The MIT Press, 1999.

W. Wei, T. Leen & E. Barnard, “A Fast Histogram-Based Post-proces-sor that Improves Posterior ProbabilityEstimates,” Neural Computation, Vol. 11, No. 5, 1999.

T.K. Leen, B. Schottky, & D. Saad,“Optimal Asymptotic Learning Rates:Macroscopic Versus MicroscopicDynamics,” Physical Review, E-59,985-991, 1999.

T.K. Leen, “Exact and PerturbationSolutions for the Ensemble Dynamics,”in Online Learning in Neural Networks,The Newton Institute Series, D. Saad(Ed.), Cambridge University Press,Cambridge, 1998.

T.K. Leen, B. Schottky & D. Saad, “Two Approaches to OptimalAnnealing,” in Advances in NeuralInformation Processing Systems 10,The MIT Press, 1998.

D A V I D M A I E RProfessorPh.D., Electrical Engineering and Computer SciencePrinceton University, [email protected]


Database systems (includingobject-oriented databasemanagement systems, queryprocessing, scientific informationmanagement, superimposedinformation and net datamanagement), object-oriented andlogic programming languages,algorithms, survivability ofinformation systems, and healthinformation technology.

R E P R E S E N TAT I V E P U B L I C AT I O N SJ. Shanmugasundaram, K. Tufte,

D. DeWitt, J. Naughton, D. Maier.Architecting a Network Query Enginefor Producing Partial Results. In TheWorld Wide Web and Databases (ThirdInternational Workshop WebDB 2000),Lecture Notes in Computer Science,Vol. 1997, Springer-Verlag, 2001.

L. Delcambre, D. Maier, S. Bowers, L. Deng, M. Weaver, P. Gorman, J. Ash,M. Lavelle, and J. Lyman. Bundles incaptivity: An application ofsuperimposed information. Proceedingsof the IEEE International Conferenceon Data Engineering, Heidelberg,Germany, April 2001.

Gorman, J. Ash, M. Lavelle, J. Lyman,L. Delcambre, D. Maier, S. Bowers andM. Weaver. ìBundles in the wild: Toolsfor managing information to solve problems and maintain situation aware-ness. Library Trends 49(2), Fall 2000.

L. Fegaras and D. Maier. Optimizingobject queries using an effective calcu-lus. ACM Transactions on DatabaseSystems 25(4), December 2000.

Q. Wang, D. Maier and L. Shapiro. Thehybrid technique for reference materi-alization in object query processing.Proceedings of the 4th InternationalConference on Database Engineeringand Applications (IDEAS2000), Tokyo,Japan, September 2000.

J O H N E . M O O D YProfessorPh.D., Theoretical PhysicsPrinceton University, [email protected]


Computational finance,time series analysis,analysis of financial markets,forecasting, and statisticallearning theory and algorithms.Applications of machinelearning to problemsin finance, economics andthe sciences.

R E P R E S E N TAT I V E P U B L I C AT I O N SLearning to Trade via Direct

Reinforcement, John Moody andMatthew Saffell, IEEE Transactionson Neural Networks, Vol. 12, No. 4,July 2001.

Term Structure of Interactions ofForeign Exchange Rates, John Moodyand Howard Yang, in ComputationalFinance 1999, edited by Y. S. Abu-Mostafa, B. LeBaron, A. W. Lo, andA. S. Weigend, Cambridge, MA:MIT Press, 2000.

Predicting Blood Glucose Metabolismin Diabetics -- A Machine LearningSolution, Volker Tresp and John Moody,IEEE Transactions on BioMedicalEngineering, 1999.

Performance Functions andReinforcement Learning for TradingSystems and Portfolios, John Moody,Lizhong Wu, Yuansong Liao andMatthew Saffell, Journal of Forecasting,vol. 17, pp. 441-470, 1998.

High Frequency Foreign ExchangeRates: Price Behavior Analysis and`True Price' Models, John Moody andLizhong Wu, Chapter 2 of NonlinearModelling of High Frequency FinancialData, Christian Dunis and Bin Zhou,editors, Wiley Financial Publishing,London, 1998.

Stochastic Manhattan Learning: Time-evolution Operator for the EnsembleDynamics, Todd Leen and John Moody,Physical Review E, 1997.

Smoothing Regularizers for ProjectiveBasis Function Networks, John Moodyand Thorsteinn Rognvaldsson, inAdvances in Neural InformationProcessing Systems 9, M.C. Mozer,M.I. Jordan and T. Petsche, eds, MITPress, Cambridge, 1997.

S H A R O N L . O V I AT TProfessorCo-Director for Center for Human-Computer CommunicationPh.D., Experimental PsychologyUniversity of Toronto, [email protected]


Multimodal and spoken languagesystems, modality effects incommunication (speech, writing,keyboard, etc.), communicationmodels, telecommunications and technology-mediatedcommunication, mobile andinteractive systems, human-computer interaction, empirically based design andevaluation of human-computerinterfaces, cognitive science, and research methodology.

R E P R E S E N TAT I V E P U B L I C AT I O N SS. L. Oviatt, ìMultimodal Input and

Output, Handbook of Human-ComputerInteraction, (ed. By J. Jacko & A.Sears), Lawrence Erlbaum Assoc:Mahwah, New Jersey, invited bookchapter to appear in 2002.

S. L. Oviatt, P. R. Cohen, L. Wu, J.Vergo, L. Duncan, B. Suhm, J. Bers, T.Holzman, T. Winograd, J. Landay, J.Larson, & D. Ferro. ìDesigning the userinterface for multimodal speech andgesture applications: State-of-the-artsystems and research directions.Human Computer Interaction, 15(4),263-322, 2000. (to be reprinted in J.Carroll (Ed.) Human-ComputerInteraction in the New Millennium,Addison-Wesley Press: Boston, 2001).

S. L. Oviatt, ìMultimodal SystemProcessing in Mobile Environments,Proceedings of the Thirteenth AnnualACM Symposium on User InterfaceSoftware Technology (UIST’2000), 21-30, ACM: New York, N.Y., 2000.

S. L. Oviatt, ì Multimodal SignalProcessing in Naturalistic NoisyEnvironments. In B. Yuan, T. Huang &X. Tang (Eds.), Proceedings of theInternational Conference on SpokenLanguage Processing (ICSLP’2000), Vol.2, (pp. 696-699). Beijing, China:Chinese Friendship Publishers.

S. L. Oviatt, ìTaming RecognitionErrors with a Multimodal Architecture,Communications of the ACM, 43 (9),45-51, September 2000 (special issueon “Conversational Interfaces”).

C A LT O N P UProfessorPh.D., Computer ScienceUniversity of Washington, [email protected]


Transaction processing, distributed databases, scientificdatabases, parallel and distributedoperating systems.

R E P R E S E N TAT I V E P U B L I C AT I O N SL. Liu & C. Pu, “An Adaptive Object-

Oriented Approach to Integration andAccess of Heterogeneous InformationSources,” International Journal onDistributed and Parallel Databases,5(2), April 1997.

K.L. Wu, P.S. Yu & C. Pu, “DivergenceControl for Epsilon-Serializability,”IEEE Transactions on Knowledge and Data Engineering, 9(2),March/April 1997.

J. Biggs, C. Pu, A. Groeninger & P.E. Bourne, “pdbtool: An InteractiveBrowser and Geometry Checker forProtein Structures,” Journal of AppliedCrystallography, 29(4), 1996.

L. Liu, C. Pu, R. Barga & T. Zhou,“Differential Evaluation of ContinualQueries,” Proceedings of the 16thInternational Conference on DistributedComputing Systems, Hong Kong, May 1996.

K. Ramamrithan & C. Pu, “A FormalCharacterization of EpsilonSerializability,” IEEE Transactions onKnowledge and Data Engineering, 7(6),December 1995.

C. Pu, T. Autrey, A.P. Black, C. Consel,C. Cowan, J. Inouye, L. Kethana, J. Walpole & K. Zhang, “OptimisticIncremental Specialization:Streamlining a Commercial OperatingSystem,” Proceedings of the FifteenthSymposium on Operating SystemsPrinciples, December 1995.

R. Barga & C. Pu, “A Practical andModular Implementation Technique ofExtended Transaction Models,”Proceedings of the 21st InternationalConference on Very Large Data Bases,Zurich, Switzerland, September 1995.

K. Ramamrithan & C. Pu, “A FormalCharacterization of EpsilonSerializability,” IEEE Transactions onKnowledge and Data Engineering, 7(3),June 1995.

41


T I M S H E A R DAssociate Professor, DirectorPacific Software Research CenterPh.D., Computer and Information ScienceUniversity of Massachusetts at Amherst, [email protected]


Functional programming, softwarespecification, program generation,meta-programming and staging.

R E P R E S E N TAT I V E P U B L I C AT I O N ST. Sheard. “Accomplishments

and Research Challenges in Meta-Programming.” Invited talk, SecondInternational Workshop on Semantics,Applications, and Implementation ofProgram Generation (SAIG 2001).LNCS 2196. Florence, Italy, September 2001.

T. Sheard. “Generic Unification viaTwo-Level Types and ParameterizedModules.” Sixth ACM SIGPLANInternational Conference on FunctionalProgramming (ICFP’01). ACM Press.Florence, Italy, September 3-5, 2001.

T. Sheard, Z. Benaissa, & E. Pasalic.“DSL Implementation Using Staging andMonads,” Usenix, Second Conference onDomain Specific Languages. Austin,Texas. October 3-5, 1999.

W. Taha, Z. Benaissa, & T. Sheard.“Multi-Stage Programming:Axiomatization and Type Safety,” 25th International Colloquium onAutomata, Languages andProgramming, July 1998.

M. Shields, T. Sheard, & S. PeytonJones, “Dynamic Typing as Staged TypeInference,” ACM-SIGPLAN-SIGACTSymposium on Principles of Program-ming Languages (POPL ‘98), San Diego,CA, January 1998.

T. Sheard, “A Type-Directed, On-Line,Partial Evaluator for a PolymorphicLanguage,” ACM-SIGPLAN Conferenceon Partial Evaluation and Semantics-Based Program Manipulation,Amsterdam, June 1997.

W. Taha & T. Sheard, “Multi-StageProgramming with ExplicitAnnotations,” ACM-SIGPLANConference on Partial Evaluation andSemantics-Based ProgramManipulation, Amsterdam, June 1997.

D A V I D C . S T E E R EAssistant ProfessorPh.D., Computer ScienceCarnegie Mellon University, [email protected]


Operating systems, mobilecomputing, distributedinformation systems.

R E P R E S E N TAT I V E P U B L I C AT I O N SD.C. Steere, A. Goel, J. Gruenberg, D.

McNamee, C. Pu, & J. Walpole, “AFeedback-driven Proportion Allocatorfor Real-Rate Scheduling,” OperatingSystems Design and Implementation,February 1999.

J. Walpole, C. Krasic, L. Liu, D. Maier,C. Pu, D. McNamee, & D.C. Steere,“Quality of Service Semantics forMultimedia Database Systems,” toappear in Proceedings Data Semantics8: Semantic Issues in MultimediaSystems IFIP TC-2 Working Conference,Rotorua, New Zealand, January 1999.

D. McNamee, D. Revel, D.C. Steere, &J. Walpole, “Adaptive Prefetching forDevice Independent File I/O,” inProceedings of Multimedia Computingand Networking 1998 (MMCN98),January 1998.

D.C. Steere, “Exploiting the Non-Determinism and Asynchrony of SetIterators to Reduce Aggregate File I/OLatency,” in Proceedings of the 16thacmsymposium on Operating SystemsPrinciples, October 1997.

D.C. Steere & J. Wing, “SpecifyingWeak Sets,” in Proceedings of the 15thInternational Conference on DistributedComputing Systems, 414-421,Vancouver, BC, June 1995.

M. Satyanarayanan, H.H. Mashburn,P. Kumar, D.C. Steere & J.J. Kistler,“Lightweight Recoverable VirtualMemory,” ACM Transactions onComputer Systems, 12(1), 33-57,February 1994. Corrigendum: ACMTransactions on Computer Systems,12(2), 165-172, May 1994.

M. R. Ebling, L.B. Mummert & D.C.Steere, “Overcoming the NetworkBottleneck in Mobile Computing,” inProceedings of the First Workshop onMobile Computing Systems andApplications, 34-36, Santa Cruz, CA,December 1994.

J O N AT H A N W A L P O L EProfessorPh.D., Computer ScienceUniversity of Lancaster, [email protected]


Adaptive systems software and itsapplication in distributed, mobile,and multimedia computingenvironments and environmentalobservation and forecastingsystems. Quality of servicespecification, adaptive resourcemanagement and dynamicspecialization for enhancedperformance, survivability andevolvability of large softwaresystems.

R E P R E S E N TAT I V E P U B L I C AT I O N SK. Li, C. Krasic, J. Walpole,

M. Shor, C.Pu, The Minimal BufferingRequirements of Congestion ControlledInteractive Multimedia Applications, inProceedings of the 8th InternationalWorkshop on Interactive DistributedMultimedia Systems, iDMS 2001,Lancaster, UK, September 2001. Alsopublished in Springer Verlag’s LectureNotes in Computer Science Series.

Black, J. Huang, J. Walpole, ReifyingCommunication at the ApplicationLevel, in Proceedings of theInternational Workshop on MultimediaMiddleware, Ottawa, Canada, October2001. Also available as OGI TechnicalReport CSE-01-006, June 2001.

C. Krasic, J. Walpole, Priority-Progress Streaming for Quality-Adaptive Multimedia, in Proceedings of the ACM Multimedia DoctoralSymposium, Ottawa, Canada, October 2001.

R. Koster, A. Black, J. Huang, J. Walpole, C. Pu, Thread Transparencyin Information Flow Middleware,Middleware 2001-IFIP/AcMInternational Conference on DistributedSystems Platforms, Heidelberg,Germany, November 2001. Also available as OGI Technical Report CSE-01-004.

J. Huang, A. Black, J. Walpole, C. Pu, ìInfopipes ñ An Abstraction forInformation Flow, in proceedings of theECOOP Workshop on the Next 700Distributed Object Systems, Budapest,Hungary, June 2001.

42


JOINT FACULTY

D R . A N T O N I O B A P T I S TA

Environmental Scienceand EngineeringOGI School of Scienceand Engineering

D R . F R A N C O I S E B E L L E G A R D E

University of FrancheComte, France

D R . D A N H A M M E R S T R O M

Electrical andComputer EngineeringOGI School of Scienceand Engineering

D R . H Y N E K H E R M A N S K Y


D R . J O D Y H O U S E


D R . M I S H A P A V E L


D R . L E O N A R D S H A P I R O

Department of Computer SciencePortland State University

D R . X U B O S O N G


D R . A N D R E W T O L M A C H

Department of Computer SciencePortland State University

D R . J A N P. H . VA N S A N T E N


D R . E R I C W A N


D R . Y O N G H O N G YA N


PART-TIME FACULTY

D R . F R A N C O I S E B E L L E G A R D E

University of Franche Comte, France

D R . C H A R L E S C O N S E L

University of Bordeaux

D R . D A V I D G . N O V I C K

University of Texas, El Paso

ADJUNCT FACULTY

D R . L O U G I E A N D E R S O N

Gemstone Systems Inc.

M R . J O N B AT C H E L L E R

Synopsys, Inc.

M R . R O B E R T B A U E R

Rational Software Corp.

D R . C . M I C B O W M A N

Intel Corporation

D R . T E D B R U N N E R

Tektronix Inc.

D R . S H A N W E I C E N

Tektronix Inc.

D R . C H R I S T O P H E R D U B AY

Oregon Health &Science University

D R . E A R L E C K L U N D

Objective Technology Group

M S . A N N I E G R O E N I N G E R

Performance Logic, Inc.

M R . R O Y H A L L

Crisis in Perspective

D R . D A V I D H A N S E N

George Fox University

D R . S E B A S T I E N H I LY

Intel Corporation

D R . H O L LY J I M I S O N

Oregon Health &Science University

D R . J A M E S L A R S O N

Intel Corporation

M R . S C O T T LY M A N

Merix Corporation

D R . E R I C M E I J E R

Microsoft

M R . M A R K M O R R I S S E Y


D R . G I L N E I G E R

Intel Corporation

D R . H A R R Y P O R T E R

Consultant

M R . S A N J E E V Q A Z I

Intel Corporation

M R . D A N S A W Y E R

M R . B R U C E S C H A F E R

Oregon College of Engineeringand Computer Science

M R . R A N D A L S C H W A R T Z

Stonehenge Consulting

D R . R I C H A R D S P R O AT

AT&T Labs, New Jersey

M S . E L I S A B E T H S U L L I VA N

TruSec Solutions

D R . A N D R E W T O L M A C H


M R . P E R R Y W A G L E

Computer Scienceand EngineeringOGI School of Science& Engineering

D R . M A Z I N Y O U S I F

Intel Corporation


43

The primary mission of theDEPARTMENT OF ELECTRICAL AND

COMPUTER ENGINEERING is to providequality graduate education, researchand technology transfer in the areasof Intelligent Signal Processing,Semiconductor Materials andDevices, Computer and SystemsEngineering, and BiomedicalEngineering.We currently have a very successful andwell-focused program in Intelligent SignalProcessing, which includes speechrecognition and synthesis, image processing,adaptive filtering and control, andanthropomorphic signal processing. Thedepartment has two centers in this area, theCenter for Information Technology (CIT) andthe Center for Spoken LanguageUnderstanding (CSLU). Close interaction withthe high-tech industry is a critical element ofthe activities reflected in numerouscollaborative projects funded by industrialorganizations including Intel, Qualcomm, andmany others.

The Semiconductor Materials and Devicesprogram has many new people and is in themiddle of a rebuilding process. We have anexcellent group, and investment includes a 5-year, $1 million Intel grant. We are creatinga number of new laboratories. Although somesemiconductor processing will be done, mostof the effort and laboratory space will bedevoted to education and to semiconductormaterials and device characterization,including high-speed devices. These, plus ourexisting electron microscopy facility, are ofvalue to local industry.

Computer and Systems Engineering isfocused primarily on research into hardwareand systems for implementing intelligentsignal processing and robotic control. Thisprocess also includes the VLSI design ofspecialized devices for computation andintelligent sensing. Computationalneuroscience plays an important part of thiswork. A new laboratory with 8 stations forDSP and FPGA programming is available,with help from Intel and Altera, to supporteducation and research in this area. Thisarea has several adjunct faculty fromcompanies such as Intel, RadiSys, IDT,

Cypress, Maxim and Triquint. There is onecenter in this area, the Center for BiologicallyInspired Information Engineering (CBIIE).

The Biomedical Engineering (BME) programconcentrates on Biomedical Optics, TissueEngineering, and Medical Informatics.Biomedical Optics develops opticaltechnologies for imaging and characterizingtissues and laser-tissue interactions formachining tissues and surgical techniques.Faculty are emphasizing tissue engineeringwith research at the affiliated OregonMedical Laser Center (OMLC). Severalpeople are also faculty at Oregon Health &Science University (OHSU) with a laboratoryat OGI where students conduct research thatinterfaces with medical clinicians andinvestigators.

The department offers a wide variety offormal courses in core areas as well as inspecific research areas. The curriculum foreach student is determined in part by his orher academic background and interest, and isset after discussion with a faculty advisor.

The major fields of research activity in thedepartment are:

• Advanced Lithography

• Atmospheric Optics

• Biomedical Engineering

• Biosensors

• Digital Signal Processing

• Display Technology including Thin FilmTransistors and Phosphors

• Electro-Optic Systems

• Human Information Processing

• Image and Video Processing

• Man-Machine Interfaces

• MEMS

• Neural Networks

• Optical Remote Sensing

• Pattern Recognition

• Processing for Ultra Shallow Device Technology

• Semiconductor Electronic Devices

• Semiconductor Materials and Processing

• Speech Recognition, Enhancement,and Synthesis

• Systems Dynamics

• Technology Transfer

Department of Electrical

and Computer Engineering

www.ece.ogi.edu


Dan Hammerstrom



Don Johansen


A C A D E M I C C O O R D I N A T O R

Barbara O lsen


A D M I N I S T R A T I V E C O O R D I N A T O R

Joan S ims


G E N E R A L I N Q U I R I E S


Jinshan Huo is a Ph.D. student and Intelintern whose interests involve copperinterconnects for microelectronic deviceand materials characterization.

46

E C E | E L E C T R I C A L A N D C O M P U T E R E N G I N E E R I N G

• Transient Thermal Processing

• VLSI/FPGA Design

• VLSI Architecture for Intelligent Computing

Students may become involved in relativelyfundamental investigations (such asatmospheric effects on laser beams, andsemiconductor materials characterization andprocessing) or in advanced engineeringapplications (such as video displaytechnology or signal/image processing). In allcases, the emphasis is on scientific andengineering investigations having well-definedgoals and real utility in an atmosphereresembling that of a working research anddevelopment laboratory. The academicprogram, while rigorous, is innovative andindividually planned to meet each student’sneeds. The limited number of students inresidence assures close attention to eachstudent and progress at a rate determined bythe student’s ability and effort.

D E P A R T M E N T S E M I N A R S

The department and other local educationaland corporate organizations host invited talksand seminars on topics of interest in the fieldof electrical engineering. M.S. students arerequired to obtain at least three credits ofseminar to graduate. Seminar schedules areposted each quarter. Additionally, the ECEDepartment in conjunction with PortlandState University’s Department of Electricaland Computer Engineering sponsor thePortland Area Semiconductor Seminar Series(PASSS). These seminars offer an opportunityto meet leading local and nationallyrecognized EE professionals and learn aboutthe latest technical advancements in thehigh-technology industry.

ADMISSIONS REQUIREMENTSAdmission requirements are the same as thegeneral requirements of the institution. TheGRE is not required for the part-timeprogram or the twelve-month M.S. program.It is recommended for M.S. students who maywant to apply for the Ph.D. at a later date.The GRE is required for all applicants to thePh.D. program. The TOEFL is required of allinternational student applicants for both theM.S. and Ph.D. programs.

Prerequisite: B.S. or M.S. in physics, appliedphysics, engineering physics, electricalengineering, or equivalent. Since modern

electrical engineering programs are broadand diverse, students with undergraduatedegrees in applied mathematics as well asother branches of engineering are encouragedto apply.

OGI offers the Ph.D. in ElectricalEngineering. Students must have a Master ofScience degree acceptable to the ECEDepartment to be considered for the Ph.D.program. The M.S. degree may be from OGIor another institution of higher education.

DEGREE REQUIREMENTS

M A S T E R O F S C I E N C E ( M . S . ) P R O G R A M

The M.S. program in Electrical Engineering isdesigned to enable professionals or recentgraduates to adapt quickly to the changingneeds of their fields. ECE’s M.S. programoffers three degree options for full-time andpart-time students. The M.S. degree requiressuccessful completion of 48 credits and maybe obtained with a non-thesis option, a non-thesis project option, or a thesis option. Allcourses, non-thesis research, and thesisresearch must be taken for graded credit tobe counted towards the ECE M.S. degree.Courses taken outside of the ECE Departmentmust also be taken for graded credit; Pass/NoPass is not acceptable. A minimum gradepoint average of 3.0 must be maintainedthroughout the degree program. Students’course of study should be reviewed andapproved by a faculty advisor. Students arelimited to 12 credits per quarter unless awaiver is obtained from their advisor.

N O N - T H E S I S O P T I O N

The non-thesis option requires completion ofa minimum of 48 credits of graded coursework. While students are strongly encouragedto focus on courses in ECE, students maytake up to 24 credits of course work in otherOGI academic departments provided thecourses fall within the curriculum standardsset by the ECE Department. For studentsseeking an M.S. degree in ElectricalEngineering, a minimum of 24 credits mustbe taken from the OGI’s ECE departmentcurriculum. All courses, regardless of OGIdepartment, must be taken for graded credit.

N O N - T H E S I S P R O J E C T O P T I O N

The non-thesis project option requirescompletion of a minimum of 48 gradedcredits, comprising 40 credits of course work

and a minimum of 8 credits of research(ECE610). The research project is morelimited in scope than a thesis and mayinclude experimental work, a criticalliterature review, or a specific contribution toa larger project. Completion of the non-thesisproject requires the submission of a writtenreport to satisfy the research graderequirements. The student is encouraged towork with a faculty advisor in formulating anappropriate project.

T H E S I S O P T I O N

The M.S. thesis option requires successfulcompletion of a minimum of 32 credits ofgraded course work and a minimum of 16credits of graded research (ECE700). Thethesis is an original independent workresulting in publication. The student will workwith a faculty member to select courses anddesign an appropriate thesis researchprogram. A thesis committee is assigned toguide and advise the research program.Completion of the M.S. thesis requires thesubmission of the written thesis and asuccessful oral defense. Thesis researchcredits earned towards an M.S. degree mustbe graded.

S U M M E R P R O J E C T S

Although not required, students shouldseriously consider taking at least one projectcourse for the M.S. degree. Because mostfaculty use the summer to do research, it isan ideal time to do a project. In addition,there are often summer internships availableat local companies, which also qualify. Thedepartment is not required to provideprojects for students, but usually there aremany opportunities. Projects can involve realimplementation and often are done in a teamsetting, which make them an idealpreparation for a career in engineering.Projects are done as Special Topics courses,ECE 580, and they are graded. The specificsof a project are the responsibility of thesponsoring faculty member. Industrial adjunctfaculty may also advise projects.

T R A N S F E R C R E D I T S

Up to 12 credits from accredited institutionsmay be transferred to OGI. Students maypetition for transfer of up to 18 credits fromthe following institutions: Portland StateUniversity, Oregon State University, andUniversity of Oregon. Students petitioning foracceptance of transfer credits should provide

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E L E C T R I C A L A N D C O M P U T E R E N G I N E E R I N G | E C E

(1) written request, (2) detailed coursedescriptions from institution catalogs and/orwebsite, and (3) original transcript verifyingcredit hours and grades earned.

Upon approval from the department head,students may apply to their ECE degree amaximum of 21 credits from other OGIdepartments towards their ECE degree.Acceptance of all transfer credits will besubject to review and approval by the ECEdepartment’s Curriculum Committee. Transfercredits will not replace the degree/creditrequirement of 24 credits from OGI’s ECEdepartment curriculum. Cross-listed coursesmay not be used as part of these 24 credits.

P H . D . P R O G R A M

OGI offers a PhD degree program inElectrical Engineering. Admission to the PhDprogram generally requires a prior M.S. inElectrical Engineering, Computer Engineeringor related field, whether from OGI or fromanother institution. Upon entry into theprogram a Student Program Committee (SPC)of three faculty members is formed. Thestudent discusses feasible research areas andeventual research directions with thecommittee and together they chart anindividualized course of study to prepare thestudent for the Qualifying Exam.

The Qualifying Exam may be written or oralor both, at the discretion of the SPC, and mayadditionally involve a formal researchproposal. It is normally taken within 12months of enrolling in the program, and isscheduled at any time during the year. Theamount of course work to be completed beforetaking the Qualifying Exam is dependent onthe individual’s level of preparation at entry.At minimum, 3 graded courses from OGI’sECE department must be successfullycompleted before taking the exam.

After the Qualifying Exam is passed, studentand Committee then work closely together todevelop a research plan specifically for thedissertation. Ph.D. students are required tomake annual reports to the SPC on the statusof their research, and may be called upon todeliver timely research presentations as thework progresses. The dissertation itself mustconstitute a significant research contributionand must be of publishable quality. The Ph.D.degree is granted following the presentationof an acceptable dissertation and successfuloral defense.

ECE CURRICULUM FOCUS AREASStudents can elect to focus exclusively withinone area of specialization or may combinetwo or more of these focus areas into abroader course of study.

• Biomedical Engineering

• Communications & Networking

• Computer Engineering & Design

• Materials, Semiconductors & Devices

• Signal Processing, Speech & Imaging

Students should refer to the ECE Department’s12-month Curriculum Plan for the scheduledoffering of courses in the 2001/2002academic year.

BIOMEDICAL ENGINEERING

Biomedical engineering is a rapidly developingbroad field of study comprising basic biology andmedicine, bioinformatics, biomedical signalprocessing, imaging, biomaterials, informationtechnology and many other areas. Within thebiomedical engineering program the ECEDepartment, in conjunction with other departmentsin the OGI School of Science and Engineering aswell as departments at the OHSU Schools ofMedicine, Dentistry, and Nursing, offers students avariety of opportunities to acquire breadth anddepth of knowledge and expertise in this field. Theresearch efforts are expanding to cover anincreasing number of areas, including biomedicalsensors and instrumentation, biomechanics(including laser-tissue interaction and tissueengineering), intelligent biomedical signalprocessing and analysis, computationalneuroscience, biomedical image analysis, data-mining, and technology in healthcare delivery.Current research topics also include intelligentrehabilitation and assistive technologies for futurehealthcare delivery in smart homes (home health)using wearable sensors and networked devices,exploiting intelligent data fusion and incorporatingthe latest results in functional genomics.

Because of the diversity of the field, each student isencouraged to devise a program tailored to his orher specific career objectives. The availablecourses include introductory courses in biology andmedicine, biomedical sensors and instrumentation,laser-tissue interactions, biomaterials,biomechanics, neuroscience, molecularengineering, audio and video processing by humansand machines, biomedical signal processing,biological pattern recognition and datamining,bioinformatics, and medical informatics. To beprepared for the challenge, students are expectedto take, in addition to specific biomedicalengineering courses, a number of basic engineeringcourses in statistical signal analysis andrecognition, digital signal processing, imageprocessing, pattern recognition, databases, andinformation retrieval.

ECE500 Introduction to Electronics and Instrumentation

ECE525 Analytical Techniques in Statistical Signal Processing & Communications

ECE529* Optical Fibers

ECE532* Biomedical Optics I: Tissue Optics

ECE533* Biomedical Optics II: Laser Tissue Interactions

ECE534* Biomedical Optics III: Engineering Design

ECE551 Introduction to Digital Signal Processing

ECE552 Digital Signal Processing II

ECE554 Adaptive Signal Processing

ECE540 Auditory and Visual Processing by Human and Machine

ECE541 Speech Processing

ECE542 Introduction to Image Processing

ECE580-PGO Physical and Geometric Optics

ECE580-CLT Computational Approaches to LightTransport in Biological Tissues

ECE580-CLI Computational Approaches to LaserInteraction with Biological Tissues

ECE580 Optical Non-Destructive Evaluation-ONDE

Other OGI School Courses

CSE514 Introduction to Database Systems

CSE540 Neural Network Algorithms and Architectures

CSE544 Probability and Statistical Inference

CSE547 Statistical Pattern Recognition

CSE548 Statistical Computing

CSE564 Human-Computer Interaction

BMB534 Instrumental Methods in Biophysics I & II

BMB540 Advanced Molecular Biology

BMB541 Molecular Genetics of Development

ESE500 Numerical Methods

ESE506 Environmental Systems Analysis

ESE550 Environmental Microbiology

ESE570 Principles of Toxicology and Risk Assessment

Oregon Health & Science University School of Medicine Courses

CON621 Molecular and Cell Biology I: Topicsin Biochemistry

CON622 Molecular and Cell Biology II: Molecular Genetics

CON627 Systems Neurophysiology

BMB610 Medical Biochemistry

BCH611/612 Biochemistry

BCH511 Advanced Biochemistry

BMB618 Biochemical Properties of Proteins andProtein Engineering

BMB620 Biochemical & Biophyiscal Propertiesof Membranes

CBA610 Gross Anatomy

AN611 Gross Anatomy

CBA611 Histology

AN613 General Histology

CBA607 Seminar: Cancer Biology

PHC610 Pharmacology

PHY610 Human Physiology

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PHY611 Physiology - Nervous and Cardiovascular Systems

PHY612 Physiology Respiratory, Renal, andAlimentary Systems

PHY615 Physiological Instrumentation and Techniques

PHY607 Seminar: Biophysical Physiology

PHY617 Advanced Cardiovascular Physiology

MED791 Electrocardiology

NEU792 Experimental Neurology

PTH610 General Pathology

* May be offered in alternating years,beginning FY03

COMMUNICATIONS AND NETWORKING

Job opportunities in communications and computernetworking are exploding. This field is enjoying arenaissance due to the rapid progress of opticalfiber technology and digital signal processingtechniques, and the need to move larger and largeramounts of information on a global basis.


ECE526 Analog and Binary DigitalCommunications Systems




ECE543 Introduction to Digital Video Processing

ECE544 Introduction to Signals, Systems and Information Processing

ECE550 Linear Systems




ECE557* Computer-Aided Analysis of Circuits(alternating years, FY03)

ECE580-DDC Design of Digital Communication Circuits

ECE580-CN Introduction to Computer Networks

ECE580-DCS Digital Fiber-Optic Communication Systems

ECE580-IE Internet Engineering

ECE580-IVC Information Visualization and Computer Graphics

ECE580 Wireless Communications Systems-WCSI

ECE580-MC Multimedia Communications

ECE580-SSY Speech Synthesis


COMPUTER ENGINEERING AND DESIGN

Computer engineering is a hybrid program utilizingelectrical engineering and computer sciencecourses. It involves the engineering aspects ofhardware, including logic design, integrated circuitdesign, and computer architecture.

ECE500 Introduction to Electronics and Instrumentation


ECE557* Computer-Aided Analysis of Circuits(alternating years-FY03)

ECE558 High Speed Interconnect Design

ECE559 Design with Programmable Logic

ECE571 Analog Integrated Circuit Design

ECE572 Digital Integrated Circuit Design

ECE573 Introduction to Computer Logic Design

ECE574 CMOS Digital VLSI Design I

ECE575 CMOS Digital VLSI Design II

ECE580 Introduction to Computer Organization-COD and Design

ECE580-AIC Analog CMOS IC Design

ECE580-ACD Special Topics in Analog IC Design4 credits

Other OGI School courses


CSE522 Advanced Computer Architecture 3 credits


PSU ECE510 Design for Test

PSU ECE672 Advanced Logic Synthesis

Oregon State University

OSU ECE619 Low Power IC Design

OSU ECE527 VLSI System Design


MATERIALS, SEMICONDUCTORS & DEVICES

ECE offers a broad spectrum of courses insemiconductor synthesis, processing, devicephysics, and integrated circuits. Courses aredesigned to prepare the student for growth areas insemiconductor-based technology. Specific groups ofcourses are designed to provide a strong, cohesive,and marketable body of knowledge in deviceprocessing, device physics and design, andintegrated circuit design. Course selections can betailored to create unique specializations that willprepare students for careers in this importanttechnology field.

ECE507 Introduction to Electromagnetics for Modern Applications

ECE508 Electromagnetics for Modern Applications II

ECE509 Electromagnetics for Modern Applications III

ECE510* Introduction to Quantum Mechanics for Electrical and Computer Engineers

ECE511* Advanced Quantum Mechanics for Electrical and Computer Engineers

ECE512 Operation of Semiconductor Devices: Diodesand Bipolar Transistors

ECE513 Operation of Semiconductor Devices: MOS Transistors

ECE514 MOSFET Modeling for VLSI Circuit Design

ECE515 Introduction to Semiconductors

ECE516 Fundamental Semiconductor Device Structures

ECE517 Advanced Semiconductor Devices: Structures & Materials

ECE520* Transmission Line Theory

ECE521* Microwave Engineering Concepts

ECE535* Thin Film Deposition and Applications in Semiconductor Fabrication

ECE558 High Speed Interconnect Design

ECE560 Microelectronic Device Fabrication I

ECE561 Microelectronic Device Fabrication II

ECE562 Microelectronic Device Fabrication III

ECE563 Plasma Processing of Semiconductors I

ECE565 Analytical Scanning Electron Microscopy

ECE566 Focused Ion Beam Technology

ECE567 Transmission Electron Microscopy

ECE568 Failure and Reliability in Microelectronics

ECE569 Electronic Materials and Device Characterization

ECE571 Analog Integrated Circuit Design

ECE572 Digital Integrated Circuit Design

ECE580-FSM Fundamentals of Sensors & MEMS Fabrication

ECE580-ISM Introduction to Sensor Microfabrication (Lab Only)

ECE580-MPE Modern Photolithographic Engineering

ECE580Simulation & Modeling of VLSI Interconnect-SMVI

ECE580-SSE Semiconductor Sensors

ECE580-TP Technology of Photoresists

ECE580-CP Copper Plating

ECE580 Microelectromechanical Systems (MEMS)-MEM

ECE580-RFD Reliability and Failure of Device Packaging

ECE580-CCM Capstone Course: MEMS & Microsensors Project

ECE580-MTF Mechanics and Thin Films


SIGNAL PROCESSING, SPEECH & IMAGING

With rapid advances in technology, we areexperiencing a paradigm shift toward information-intensive systems for sophisticated multimediatelecommunication and human-machineinteraction. This master-level program represents aunique combination of traditional engineeringsignal processing with human informationprocessing that prepares students for theinformation-intensive society of the coming century.Multimodal communication is an emergingengineering area that comprises multipledisciplines extending from human factors andalgorithm development to network protocols anddesigning electronic devices. Existing and futuremultimedia applications combine audio and video(and other possible modalities) to extend thecapabilities of a human operator. Students benefitfrom exposure to real problems throughpartnerships with industry and government.





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ECE543 Introduction to Digital Video Processing

ECE544 Introduction to Signals, Systems and Information Processing

ECE545 Speech Systems



ECE553* Control Systems: Classical, Neural and Fuzzy


ECE555 Engineering Optimization


ECE580-SSL Structure of Spoken Language

Other OGI School courses

CSE540 Neural Network Algorithms and Architectures3 credits





CSE552 Hidden Markov Models 3 credits


COURSE DESCRIPTIONSECE500 Introduction to Electronics and InstrumentationReview of fundamental electronics components anddesign: passive components, transistor circuits, opamps, RC circuits, frequency domain, and timedomain response. Feedback theory, op amp limita-tions, precision op amp circuits. Noise, interference,grounding, and shielding. Phase-locked loops, lock-in amplifiers. Practical advice on componentselection and circuit design. Equipment and circuitdemonstrations in class. Homework includes Pspicecircuit simulation problems. 4 credits

ECE507 Introduction to Electromagnetics for Modern ApplicationsThis series (ECE507-509) cover essentials of elec-tromagnetic theory for modern practitioners in suchareas of engineering and applied science as semi-conductor devices; IC design; optics, lasers, andoptoelectronics; wireless and optical communica-tions; electronic displays; electron and ion beamtechnology; vacuum electronic devices; and variousbiomedical applications. The course is practicallyoriented, and presents both analytical and numeri-cal methods. The first course introduces basicexperimental laws and theoretical concepts.Laplace and Poisson equations for static electricand magnetic potentials. Basic properties of elec-tromagnetic materials. Maxwell equations for staticand time-varying fields. Wave equations andPoynting theorem. Finite-difference numerical solu-tion of boundary-value problems. Prerequisite:Some undergraduate electromagnetism, calculusthrough ordinary and partial differential equations,some vector calculus, or consent of instructor.

4 credits

ECE508 Electromagnetics for Modern Applications IIThis course introduces additional mathematicaltools and covers topics basic to circuit design, semi-

conductor device operation, IC design, optics, trans-mission lines, and antenna design. Covered arewaves in conductors and skin effect.Retarded poten-tials for time-varying fields. Electromagnetics oflumped-element circuit theory. Plane wave propaga-tion, reflection, and refraction. Polarization statesand Stokes parameters. Analytical methods forboundary-value problems and numerical solution byboundary-element method. Introductory (TEM) fieldtheory of transmission lines, and its relation to cir-cuit model. Prerequisite: ECE507 and some linearalgebra or consent of instructor. 4 credits

ECE509 Electromagnetics for Modern Applications IIIThis course covers advanced transmission line andwaveguide field theory for high speed interconnects,microwave and optical waveguides; resonant cavi-ties for frequency control and lasers; and radiationbasics for communications and optics. Topicsinclude TE and TM transmission-line and wave-guide modes. Field theory of multiple-conductortransmission lines: Modes, coupling, crosstalk, andtermination. Dielectric waveguides. Resonant cavi-ties. Radiation from antennas and apertures.Additional topics as time permits, chosen from:electromagnetic properties of materials; variationalformulation of field problems and finite elementnumerical solution; analytical and numerical calcu-lation of charged-particle motion in electromagneticfields; suggestions of students. Prerequisite:ECE508 and some linear algebra or consent ofinstructor. 4 credits

ECE510 Introduction to Quantum Mechanics forElectrical and Computer EngineersCourses ECE510-511 present basic quantum theoryfor understanding practical applications such assolid state devices, lasers and other optoelectronicdevices, properties of electronic materials, band-gap engineering, quantum effects due to shrinking ICfeature sizes, quantum-dot and quantum-welldevices, and quantum computing. The first courseintroduces basic concepts and results essential tounderstanding solid-state band structure, devicesbased on tunnelling, and quantum-well devices.Topics include a review of classical mechanics. TheSchroedinger equation, postulates of QuantumMechanics, and basic Hilbert-Dirac formalism. Thefree particle. One-dimensional quantum-well boundstates and tunneling through potential barriers.Bloch functions in periodic potentials and the originof solid-state band structure. Prerequisite: Calculusthrough ordinary and partial differential equations,or consent of instructor. 4 credits

ECE511 Advanced Quantum Mechanics for Electrical andComputer EngineersThis course covers two- and three-dimensionalapplications, and introduces new physical phenom-ena, mathematical formulations, and tools essentialfor understanding materials science, lasers, solidstate devices, quantum optics, and quantum com-puting. Covered are two- and three-dimensionalquantum wells. The simple harmonic oscillator andalgebraic methods. Angular momentum and spin.Matrix formulation of Quantum Mechanics. Atomicstructure. Approximation methods, including per-turbation theory. Interaction of matter andelectromagnetic waves. Prerequisite: ECE510 plus

some linear algebra, or consent of instructor.4 credits

ECE 512 Operation of Semiconductor Devices: Diodesand Bipolar Transistors.Short review of semiconductor basics; metal-semi-conductor contacts and Schottky diodes; pn junctiondiodes: Depletion approximation, capacitance/volt-age behavior and current/voltage characteristics,role of minority carrier diffusion and storage, idealand nonideal behavior, Shockley-Hall-Read recombi-nation. Fundamentals of bipolar transistors: IdealShockley model, current gain, low- and high-levelinjection effects, transit-time concepts. Ebers-Molland Gummel-Poon models. Device parameterextraction for SPICE models. 4 credits

ECE 513 Operation of Semiconductor Devices:MOS Transistors.Fundamentals: Contact potentials and semiconduc-tor surfaces, analysis of the MOS capacitor, the roleof oxide charge. MOSFET modeling, one-dimensionalapproaches based on depletion and charge sheetapproximations: Threshold voltage and body effect,sub-threshold behavior based on concepts of weak,moderate, and strong inversion; ion implanted chan-nels; short and narrow channel effects, such aschannel length modulation, velocity saturation, effec-tive threshold variations, series resistance effects,breakdown and punch-through; device parameterextraction for SPICE models, device scaling.4 credits

ECE 514 MOSFET modeling for VLSI circuit designA comprehensive study of compact models used incircuit simulators for VLSI design. Topics coveredinclude modeling of small geometry effects, highspeed and frequency (non-quasistatic) models,quantum effects, substrate and gate current modelsfor reliability simulation and device scaling issues.In-depth study of parameter extraction, optimizationand device characterization techniques required fordeveloping compact models. Development of statis-tical, mismatch and noise models for analog circuitdesign. Review of state of the art models used inindustry. Implementation algorithms for MOSFETmodels in circuit simulators. 4 credits

ECE515 Introduction to SemiconductorsThe fundamental properties and concepts needed tounderstand semiconductors are introduced in thiscourse. We begin with semiconductor crystals, theirstructure and bonding, and thermal properties. Wethen examine electron interactions in semiconduc-tor crystals. The physics behind the energy bandgapin semiconductors are examined, and used to ulti-mately derive the energy band structure, effectivemass, and equilibrium carrier statistics. Next, weuse these statistics to define carrier transport insemiconducting materials. Finally, we study andunderstand the dielectric and optical response ofsemiconductors.. This course is recommended if youhave never taken a semiconductor device course (orif you need a refresher). The materials covered willprovide you with background for other semiconduc-tor device, processing, and characterization coursesoffered at OGI. Although not required, you willachieve a more advanced understanding of the con-cepts discussed in this class if you have takenquantum mechanics. 4 credits

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ECE516 Fundamental Semiconductor Device StructuresSemiconductor bulk, junction and surface proper-ties. We develop the fundamentals of semiconductorstructures; bulk defects; mechanisms affecting elec-tron/hole transport at low and high electric fields;junction formation/stability (p-n, metal-semiconductor,and metal-insulator); and relationships betweensemiconductor properties and device performance.The underlying concepts of minority carrier andmajority carrier devices are expounded and clarified.

4 credits

ECE517 Advanced Semiconductor Devices:Structures and Materials The complex interplay between materials proper-ties, fabrication technologies, and deviceperformance will be examined in the context of elu-cidating such current technology developments assilicon on insulator (SOI), high-K dielectrics, SiGeheterojunctions, heterojunction bipolar transistors(HBT), pseudomorphic high electron mobility tran-sistors (PHEMT), Vertical Cavity Surface EmittingLasers (VCSEL), quantum dots, single electron tran-sistors, and organic semiconductors. 4 credits

ECE520 Transmission-Line TheoryMaxwell’s equations; Field analysis of transmission-lines; Circuit analysis of transmission-lines(telegrapher’s equations, equivalent circuit models);Microstrip; Stripline; Signal integrity (transientresponse, impedance mismatch, reflections, bouncediagrams); Skin effect; Dispersion; Discontinuities(bends, vias); Multi-conductor transmission-lines inmulti-layered dielectric systems ([L] and [C] matri-ces). Numerical analysis of multi-conductortransmission-line networks (method of momentstechnique); Crosstalk. 4 credits

ECE521 Microwave Engineering ConceptsTraveling waves and transmission-line concepts;Time harmonic transmission-line equations; Smithchart (construction and applications); Impedancematching networks; Impedance transformation;Matrix representation of multi-port transmission-line networks ([S], [Z], [Y], and chain matrices); [S]parameters properties; Matrix conversions ([Z] to[S] and vice-versa); Numerical analysis of transmis-sion-line discontinuities at microwave engineeringfrequencies (Finite Difference Time Domain, FDTDtechnique). 4 credits

ECE525 Analytical Techniques in Statistical SignalProcessing and CommunicationsDevelopment of the mathematical techniques need-ed to analyze systems involving random variablesand/or stochastic processes with particular applica-tion to communications and instrumentation. Topicsinclude Bayes Theorem (discrete and continuousforms), Tchebycheff inequality, Chernoff Bound,Central Limit Theorem, stationary processes andlinear systems, mean square estimation, Poissonprocess, Gaussian process, Markoff process, andseries representations. MATLAB and the MATLABStatistics Tool Box are used in this course. 4 credits

ECE526 Analog and Binary DigitalCommunications SystemsMathematical descriptions of signals and noise,bandwidth requirements, sampling theorem, inter-symbol interference, digital multiplexing, line

encoding, pulse code modulation, quantizing, quanti-zation and noise error in PCM, bandpass randomprocesses, quadrature representation, Wiener-Hopffilter, amplitude modulation systems (AM, DSB,SSB, VSB), angle modulated systems (PM, FM) pre-emphasis/de-emphasis. MATLAB and the MATLABStatistics Tool Box are used in this course. 4 credits

ECE527 M-ary Communication Systems,Information Theory, and CodingOften times in communication systems, the band-width available for the system is fixed. Thisconstrains the communication rate to a maximum oftwice the bandwidth if a binary digital system isused. However, in many modern systems such aswireless communications and computer communi-cations, communication rates in excess of twice thebandwidth are needed. This problem has beensolved by using M-ary communication systemswhere the digital system has M distinct statesrather than just two. Using M-ary communication inconjunction with long sequences for communicationefficiency and coding for error correction allows formodern communication systems that meet therequirements of such systems. This course coverstopics that relate to modern communication sys-tems, including Optimum threshold detection,geometrical representation of signals, optimum M-ary Communication (MASK, MPSK, MFSK) systems,Gram-Schmidt orthogonalization procedure, meas-ure of information, source encoding, channelcapacity, error-correcting codes (linear block,cyclic, burst-error detecting and correcting, inter-laced, convolutional), Viterbi’s Algorithm. MATLABand the MATLAB Statistics Tool Box are used in thiscourse. 4 credits

ECE529 Fiber OpticsAn introductory course in fiber optics aimed at sci-entists and engineers from widely varyingbackgrounds. Topics include light propagation indielectric media, attenuation in optical fibers, step-and index-graded fibers, photon generation anddetection devices used in fiber optics, and integra-tion of fiber optics with the photon devices.4 credits

ECE532 Biomedical Optics I: Tissue OpticsLight propagation in tissue: This course treats lighttransport in scattering and absorbing media such asbiological tissue. Light transport is modeled using avariety of theories and computational techniques,including Monte Carlo simulations and approximatesolutions of the radiative transport equation.Steady-state and time-dependent problems aretreated. Spectroscopy and fluorescence measure-ments are introduced. Optical imaging techniquesAre presented. Students learn the basics requiredfor design of optical devices for therapy and diag-nostics. 4 creditsCourse offered every other year; next session,Fall 02/03

ECE533 Biomedical Optics II: Laser-Tissue InteractionsPhysics of laser-tissue interactions: The coursetreats the immediate physical processes thataccompany the absorption of light by biological tis-sues, including photochemical reactions, heatingand tissue coagulation, vaporization, creation ofplasmas, and production of stress waves in tissue.Such processes are modeled using finite-difference

techniques. Applications in medicine and biology arediscussed. Prerequisites: ECE 532 or permission ofinstructor. 4 creditsCourse offered every other year; next session,Winter 02/03

ECE534 Biomedical Optics III: Engineering DesignThe students work as a team in preparing five busi-ness plans throughout the quarter. Each businessplan is devoted to a potential medical device or pro-tocol using optical technologies. The team is dividedinto a CEO, scientific officer, marketing manager,regulatory affairs manager, and manufacturing man-ager. The roles are rotated amongst the students foreach business plan. Feasibility studies are conduct-ed in a laboratory exercise designed by the students.The team formally presents a business plan everytwo weeks. Prerequisites: ECE 532 and ECE 533, orpermission of instructor. 4 credits Course offered every other year; next session,Spring 02/03

ECE535 Thin Film Deposition and Applications inSemiconductor FabricationCovers thin film deposition topics, such as thermalevaporation, plasma deposition, chemical vapordeposition (CVD and MOCVD), molecular beam epi-taxy (MBE), atomic layer epitaxy (ALE),electrochemical deposition, and electroless deposi-tion. Thin film deposition forms the basis formanufacture of modern integrated circuits; a knowl-edge of methods available for thin film deposition isessential for IC process engineers. Course isdesigned to cover the theory and applications ofmain deposition techniques in use or being consid-ered for future IC fabrication processes. 4 credits

ECE536 Surface Science for Semiconductor TechnologyThe study of gas-solid surface science with empha-sis on understanding semiconductor systems andthe mechanisms of epitaxial growth of semiconduc-tor films by molecular beam epitaxy (MBE),metal-organic molecular beam epitaxy (MOMBE),atomic layer epitaxy (ALE), etc. The study of ther-mal desorption, surface diffusion. Surface electronicproperties such as work function. Physical absorp-tion, the growth of multilayer films and theapplication of this phenomena to the study of theBET equation as a tool for the determination of sur-face area. 4 credits

ECE537 Characterization of Thin Films forSemiconductor TechnologyAn introduction to the techniques of surface analy-sis, such as Auger analysis, X-ray photoelectronspectroscopy, energy dispersive X-ray analysis, X-ray wavelength dispersive spectroscopy, secondaryion mass spectroscopy, Rutherford Back scatteringSpectroscopy, together with their interpretations.Particular emphasis on semiconductor technologyapplications. 4 credits

ECE540 Auditory and Visual Processing by Human and MachineInteraction between humans and machines could begreatly enhanced by machines that could communi-cate using human sensory signals such as speechand gestures. Knowledge of human information pro-cessing including audition, vision, and theircombination is, therefore, critical in the design of

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effective human-machine interfaces. The courseintroduces selected phenomena in auditory andvisual perception, and motor control. Students learnhow to interpret empirical data, how to incorporatethese data in models, and how to apply these mod-els to engineering problems. The anthropomorphic(human-like) signal processing approach is illustrat-ed on engineering models of perceptual phenomena.

4 credits

ECE541 Speech ProcessingSpeech is one of the most important means of com-munication. This course teaches theory of humanspeech production, properties of speech signal andtechniques for its processing in speech coding, andautomatic speech and speaker recognition.Emphasis is on active research in auditory modelingthat exploits special properties of speech to improveperformance of speech technology in practicalapplications. Prerequisites: ECE 540, ECE 551, orconsent of instructor. 4 credits

ECE542 Introduction to Image ProcessingCourse covers basic image processing principlesand techniques with a brief introduction to machinevision. Students acquire theoretical and workingknowledge of image processing approaches includ-ing image representation, transform methods, imagefiltering, multi-resolution representation, edgedetection, texture characterization, and motionanalysis. Course demonstrates application of thesemethods to image enhancement, image restoration,and image compression, with emphasis on imagequality metrics based on human visual perception.Selected areas in machine vision include image seg-mentation, elementary techniques in patternrecognition, and object representation. Applicationof these techniques is illustrated in numerous exam-ples. Prerequisite: ECE 551. 4 credits

ECE543 Introduction to Digital Video ProcessingCourse provides introduction to digital video pro-cessing for multimedia systems. The course firstintroduces video capture, image formation, analogand digital video signal and standards, and spatio-temporal sampling. Subsequent topics includemotion estimation, segmentation and tracking,videofiltering, and video standards conversion. Studentsare familiarized with video compression techniquesand standards (JPEG, MPEG2, H.261, H.263), andmodel-based video quality estimation. Students gainworking knowledge of these video techniquesthrough class projects. Familiarity with digital sig-nal processing and transform methods is desirable.

4 credits

ECE544 Introduction to Signals, Systems andInformation ProcessingThis course provides the essential mathematicaltools and analytical techniques needed for theanalysis of continuous-time and discrete-time sys-tems. Basic signal and system characteristics —linearity, time-invariance, convolution and correla-tion — are first examined from the time domainperspective. We then proceed to study a family of Transforms - Fourier Series, Fourier IntegralTransform, Laplace Transform, Discrete Time FourierTransform (DTFT), Discrete Fourier Transform (DFT)and z-Transform — which take the study of these

systems to a deeper level and introduce a host ofuseful properties which the time perspective alonedoes not reveal. Basic applications taken from theareas of information processing, communication andcontrol will serve to fill out the mathematicallyderived results.

A greater portion of the syllabus in ECE 544 is allot-ted to continuous time signals/systems than todiscrete time signals/systems, for reason that thelatter are taken up in detail in other informationprocessing courses, particularly ECE 551. A goal ofthe presentation in ECE 544 is to impart the essen-tial unity of all the Transforms and the almostperfect correspondence of approach in continuous-time and discrete-time contexts. You then become awell equipped practitioner who knows the wayaround the entire territory. This course is a usefulprerequisite or co-requisite to ECE 551 and allother courses in the information processing area.

4 credits

ECE545 Speech SystemsSpeech is one of the most natural means for com-munication and carries information from manysources. The explosive growth of communicationsand computer technologies puts new demands ontechniques for machine extraction of informationcontent of speech signals, for its storage or trans-mission, and for reconstruction of the speech signalfrom its parametric representation. Course coverstechniques for processing of speech signal used forspeech coding and synthesis, enhancement ofdegraded speech, speech recognition, speakerrecognition, and language identification. 4 credits

ECE547 Signals for Multimedia EngineeringThe course discusses concept of signal as a carrierof information, basic principles of signal analysis inengineering, and fundamentals of human auditoryand visual perception. It is intended for those whohave a good undergraduate-level of basic knowledgein mathematics and physics but who need an intro-duction to or refreshing of fundamental concepts ofsignals, systems, and human information process-ing, necessary for further mastering specializedmulti-media topics in speech and image processing,classification, and transmission. 4 credits

ECE550 Linear SystemsThis course introduces the State Variable represen-tation of linear dynamical systems and studies alarge body of State Space techniques to reveal bothinner structure and external behavior of the systemsmodeled in this way. A general framework for treat-ing time-varying linear systems is developed andutilized. Major emphasis is placed, however, on thetime-invariant systems, whose structure anddynamics are investigable and knowable to the veryutmost detail. Both continuous-time and discrete-time linear systems are explicitly studied. Thecourse provides a strong body of foundational mate-rial, which is utilized either explicitly or implicitly invirtually all applications-specific areas pertaining tosystem analysis/design and signal/information pro-cessing. The major topics covered are: canonicalrealizations, equivalent systems, canonical transfor-mations, canonical decompositions, solution of stateequations, stability, controllability and observability,

design of asymptotic observers, state-feedback com-pensation schemes. Linear Quadratic Regulator andKalman Filter are also introduced. The LinearAlgebra material required for this study — matricesas linear operators , solutions of sets of linear equa-tions, eigenvalues and eigenvectors, eigenstructurefactorizations and spectral decompositions — willbe presented and developed concurrently, as need-ed. The relevant Differential Equations material willalso be concurrently reviewed. 4 credits

ECE 551 Introduction to Digital Signal ProcessingThe representation and processing of signals andsystems in the discrete or digital domain is the pre-ferred mode in todayís computer and informationdriven technologies. DSP provides the core buildingblock from cell phones to modems, HDTV to videoconferencing, or from speech recognition to MP3audio.This classes covers the fundamental conceptsand mathematics including representation andanalysis of discrete time signals and systems, Z-Transforms, Discrete-Time Fourier Transform(DTFT), and the Discrete Fourier Transform (DFT),sampling and windowing techniques pertaining todiscrete time processing of continuous signals,analysis and design of recursive (IIR) and nonrecur-sive (FIR) digital filters, signal flow graphrealizations of finite word-length implemented dis-crete time linear systems, and applications of theFast Fourier Transform (FFT) to convolution, spec-tral analysis, and audio processing. 4 credits

ECE552 Digital Signal Processing IIThis follow-up course to ECE 551 examines severalwidely used advanced signal processing. Topicsinclude computational complexity considerations inDSP algorithm development; multirate signal pro-cessing; filterbanks and wavelets, and theirapplication in audio and image processing (e.g.MPEG standards). Topic coverage is weightedtoward the interests of the students enrolled.

4 credits

ECE553 Control Systems: Classical, Neural, and FuzzyApplications of modern control systems range fromadvanced fighter aircraft to processes control inintegrated circuit manufacturing, to fuzzy washingmachines. The aim of this class is to integrate dif-ferent trends in control theory. Background andperspective are provided through the study of basicclassical techniques in feedback control (root locus,bode, etc.), as well as state-space approaches (lin-ear quadratic regulators, Kalman estimators, andintroduction to optimal control). The course coversrecent movements at the forefront of control tech-nology. Neural network control is presented withemphasis on nonlinear dynamics, back-propagation-through-time, model reference control, andreinforcement learning. The course also coversfuzzy logic and fuzzy systems as a simple heuristic-based, yet often effective, alter-native for manycontrol problems. Prerequisite: ECE 551, ECE 554,or equivalent. 4 credits

ECE 554 Adaptive Signal ProcessingThe field of adaptive filters and systems constitutesan important part of statistical signal processing. Anadaptive system alters or adjusts its definingparameters in such a way that it improves perform-

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ance through contact with the environment.Adaptive filters are currently applied in suchdiverse fields as communications, control, radar,seismology, and biomedical electronics. This coursewill cover the theory and applications of adaptivelinear systems. Topics include Wiener filters, leastsquares, steepest descent, LMS, RLS, Newton’smethod, FIR and IIR adaptive structures, andKalman filters. Applications covered include noisecanceling, signal enhancement, adaptive control,adaptive beam-forming, system identification, andadaptive equalization. The theory also lays the foun-dation for study in nonlinear signal processing withneural networks and will be introduced in the laterhalf of the class. This course should be of interest toelectrical and computer engineers specializing insignal processing and the information sciences. Thiscourse should also be taken as background for addi-tional classes offered in artificial neural networks,connectionist models, and machine learning.

4 credits

ECE555 Engineering OptimizationIssues of Optimization appear in virtually every areaof Engineering and Applied Research. Most practi-tioners tend merely to rely on “canned” routineswhen optimization needs to be performed. But suc-cessful Optimization entails both a lot of science anda lot of art — deep mathematical derivations andformal convergence proofs on the one hand, conven-tional engineering “folklore and experiential “rulesof thumb on the other. Through this course you willbe able to choose intelligently among the very widerange of available optimization strategies, customizegiven algorithms; to your own specific applications,and even write your own routines entirely fromscratch when this approach is needed or preferred.After reviewing some necessary mathematical fun-damentals from Linear Algebra and MultivariableCalculus, including Lagrange Multipliers and Kuhn-Tucker conditions, the following topics will becovered. Unconstrained and Constrained nonlinearMultivariable Optimization, via direct-search andgradient-based methods, including: Pattern Search,Simplex Search, Conjugate Gradient, VariableMetric, Feasible Directions, Cutting Plane, GradientProjection and Penalty Function methods.Algorithms for specially structured problems, suchas: Linear Programming, Quadratic Programming,Integer Programming, Geometric Programming.Methods which utilize random heuristics, including:Genetic Algorithm, Dynamic Evolution andSimulated Annealing. Time permitting, an introduc-tion to Dynamic Programming and the OptimalControl problem will also be included. 4 credits

ECE556 Principles of Electronic PackagingThis course introduces the principles and tradeoffsinvolved in the design of electronic packaging forintegrated circuits. Topics include packaging archi-tecture, electrical design concepts in electronicpackaging design, thermal management, mechanicdesign, electrical contacts, reliability and testing,material selection and fabrication, plated through-hole technology, etching by wet processes, joiningmaterials, stress issues, diffusion problems, chemi-cal and physical methods of analysis, and trends inelectronic packaging. 4 credits

ECE557 Computer-Aided Analysis of CircuitsCourse covers the algorithms and techniques for for-mulation and solution of circuit equations forlarge-scale VLSI circuits. Topics include Equationformulation, linear AC and DC networks, linear tran-sient networks, and stability analysis. Solution ofnonlinear DC and transient problems. Frequencydomain (AWE) techniques for VLSI interconnections,Sensitivity analysis, harmonic balance, circuit opti-mization, and statistical design.The implementationof device models in circuit simulators and conver-gence issues is covered. Assignments stresscomputer-aided implementation techniques and useof simulators such as PSPICE. 4 credits

ECE558 High Speed Interconnect DesignElectrical analysis, design, and validation of inter-connect for digital buses operating at speeds greaterthan 1 GHz. Key topics include: transmission lineanalysis and tools, digital signals and timing analy-sis, measurement equipment and techniques, lossyand coupled transmission lines, advanced signalingtechniques, design tools and methodology. A designproject is used to give students practical insight intohigh speed bus design problems. 4 credits

ECE559 Design with Programmable LogicProgrammable logic, such as FPGA and PLDdevices, has become a major component of digitaldesign. This course will discuss design tools andtechniques for creating logic designs using program-mable logic. A design is first created in Verilog, ahigh-level Register Transfer Level (RTL) language,and simulated. Synthesis to a programmable logicdevice is then performed. In addition, common prob-lems of poor routing and placement are discussedwhile presenting the student with a comprehensiveunderstanding of the operation of synthesis tools.The course has a strong project orientation.Students will take several designs from concept to RTL verification and synthesis, then to program-mable device implementation. A commercial set of software tools will be used. PREREQUISITES:ECE573 Intro to Computer Logic Design or consentof instructor. 4 credits.

ECE560 Microelectronic Device Fabrication IThis course is the first in a full year, three termsequence that treats both the science and practiceof modern microelectronic fabrication. The princi-ples of crystal growth and wafer preparation, ionimplantation, doping and diffusion, and oxidationare all covered. Emphasis is placed on understand-ing the basic chemistry, physics, and materialscience of wafer processing. This includes crystalstructure and defects, heterogeneous chemicalreactions, the thermodynamics and kinetics of diffu-sion, etc. In addition, the practical implementationof these processes is also discussed. This includesrealistic process flows, physical metrology, devicestructure and electrical behavior, trade-offs, etc.The course is intended to serve a wide communityincluding both working process engineers andmatriculating graduate students. 4 credits

ECE561 Microelectronic Device Fabrication IIIn the second class of this series emphasis is onmetallization and dielectrics. Metallization issuesexamined include silicides, barrier layers, intercon-

nects (e.g., Cu), multilevel metallization, and low kdielectrics. This followed by discussion of depositionand properties of different dielectric films. Finally,processing issues of epitaxial growth and propertiesof SOI devices are covered. Class assignmentsinclude computer simulation of device fabrication.

4 credits

ECE562 Microelectronic Device Fabrication IIIThis class starts with electron beam, x-ray, and pho-tolithography, including discussion of resisttechnology (e.g., chemically amplified resists). Thisfollowed by fundamentals and applications of plas-mas for etching and deposition (e.g., high densityplasmas), including plasma damage. Other topicsconsidered are process integration that includesseveral devices such as BiCMOS and memories.Finally yield and reliability statistics as related tomicroelectronic device fabrication is discussed.Class assignments include computer simulation ofdevice fabrication and testing. 4 credits

ECE563 Plasma Processing of Semiconductors IFundamental plasma properties. Plasma produc-tion, properties, and characterization. DC and RF plasmas. Sputtering as a deposition process forthe growth of thin films. Multicomponent films.Plasma etching. 4 credits

ECE564 Plasma Processing of Semiconductors IIThis course, a continuation of ECE 563, covers spe-cific applications of plasmas for processingsemiconductor materials. Topics include etching anddeposition and the dependence of these processeson plasma parameters. Materials based on both sil-icon and III-V technology are examined. 4 credits

ECE565 Analytical Scanning Electron MicroscopyThis course introduces the operation and theory ofSEM and covers sources, lenses, accelerating volt-age, detectors, image formation, beam-specimeninteractions, beam-produced signals, the combinedeffects of signal-to-noise ratio and spot size in deter-mining resolution, and stereo imaging SEM. Theprocess of specimen preparation, metallo-graphicgrinding and focused ion beam-produced transversecross sections, planar sections, coating techniquesfor nonconductors, sampling of powders, and isola-tion of contaminants are some of the topics covered.Students are encouraged to work on materials theyprovide. The course covers the operation of energydispersive X-ray detectors, qualitative analysis,quantitative analysis, elemental mapping, spectrumartifacts, and contaminant and compound identifica-tion. The lecture portion of this course can bepresented on site at companies in a 6 week period.Corresponding lab sessions are done at OGI. A proj-ect requiring operation of the SEM at the studentsíconvenience during the remainder of the quarterand a written report is the basis for a grade.

4 credits

ECE566 Focused Ion Beam TechnologyThis course covers operation and theory of a FIBworkstation, including ion sources, acceleratingvoltage, electrostatic lenses, beam-material interac-tions, resolution, beam intensity distribution, beamproduced signals, detectors, metal and oxide depo-sition, and enhanced etch. FIB-produced site-

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specific SEM transverse cross sections, the locationand sectioning of micron and sub-micron scalestructures on the surface and buried in multilayeredstacks or bulk materials, cross sections in metals,semiconductors, ceramics, and composites are cov-ered. The location and sectioning of micron andsubmicron surface and buried structures to createelectron transparent foils with little or no damage inmetals, semiconductors, ceramics, and composites,and artifacts of specimen preparation are present-ed.† Ion beam lithography and microfabrication ofstructures on the micron and sub-micron scales arealso covered.† This course uses a combination oflectures and hands-on practice to cover these top-ics. The lecture portion of this course can bepresented on site at companies in a 6 week period.Corresponding lab sessions are done at OGI. A proj-ect requiring operation of the FIB at the studentsconvenience during the remainder of the quarterand a written report is the basis for a grade.

4 credits

ECE567 Transmission Electron MicroscopyElectron microscopy is a continually evolving disci-pline, which, has developed a wide range oftechniques to solve specific problems. This course isdesigned to help the student develop a broad appre-ciation and knowledge of the important techniquesfor the analysis of crystalline and amorphous mate-rials. Modern transmission electron microscopescan give the investigator detailed information ofcrystal structure, crystal defects and quantitativelocal chemistries on a nanometer scale. This infor-mation is often critical to the understanding ofmaterial properties. Principles, methods and appli-cation of transmission electron microscopy tocrystalline materials. The construction and design ofelectron microscopes, electron diffraction, recipro-cal lattice and Ewald Sphere construction will becovered. Kinematic and dynamic theories of imageformation will be introduced. Combining lectureswith hands-on laboratory practice, students will beinstructed in the use of sample preparation equip-ment and an analytical transmission electronmicroscope. Students will be expected to carry outbasic experiments on selected materials which illus-trate fundamental concepts covered in the lecture.The lecture portion of this course can be presentedon site at companies in a 6 week period.Corresponding lab sessions are done at OGI. A proj-ect requiring operation of the SEM at the studentsconvenience during the remainder of the quarterand a written report is the basis for a grade.

4 credits

ECE568 Failure and Reliability in MicroelectronicsThe failure and reliability of microelectronicsdepends on the stability of thin films and the purityof the bulk semiconductors. Contamination, filmthickness, diffusion and phase changes all drivemechanisms of failure. Characterization of a faileddevice depends on analysis of thin film structure,crystalline structures, contaminant identificationand microchemistry. This requires a variety ofmicroanalytical techniques involving the SEM, TEM,and FIB. This course covers the potential defects,failure mechanisms and the methodology used toanalyze them. Case studies also are discussed. The

lecture portion of this course can be presented onsite at companies in a 6 week period. Correspondinglab sessions are done at OGI. A project requiringoperation of the SEM at the students convenienceduring the remainder of the quarter and a writtenreport is the basis for a grade. 4 credits

ECE569 Electronic Materials and Device CharacterizationThis class is designed for engineers and scientistswho wish to understand the basic principals behindthe electrical and optical techniques used to char-acterize semiconductor materials and devices.These techniques are crucial in determining thecauses of failure in semiconductor devices. Amongthe parameters to be covered include contact resist-ance, carrier mobility and lifetime, defects, oxideand interface trapped charges, as well as seriesresistance, channel length /width, threshold voltageand hot carriers in MOSFETs. This class will includesome lab time. 4 credits

ECE570 Gallium Arsenide MESFET Integrated Circuit DesignTechnology overview, device structures, SPICE mod-els, limitations, regions of MESFET operation.Transconductance, output resistance, biasing.Single-stage, high-gain, and feedback amplifiers,current sources, compensation. Buffered FET logic,enhancement/depletion technology,data conversion,comparators, digital-to-analog converters. 4 credits

ECE571 Analog Integrated Circuit DesignDesign techniques for analog integrated circuits.Silicon bipolar and JFET analog integrated circuitdesign. Technology overview, device structures,Ebers-Moll equations, hybrid-pi model. Single-stageamplifiers, current sources, active loads, outputstages. Operational amplifiers, frequency response,feedback, stability. Design project. 4 credits

ECE572 Digital Integrated Circuit DesignDesign techniques for digital integrated circuits.Silicon bipolar and MOS digital integrated circuitdesign. Technology overview, device structures,modeling. Standard logic families. NMOS and CMOSlogic design. Regenerative circuits and memory.Design project. 4 credits

ECE573 Introduction to Computer Logic DesignThis course constitutes a basic introduction to thedesign and implementation of computer logic. Basicprinciples of discrete logic will be presented, includ-ing boolean algebra, finite-state machine theory,minimization, and optimization. Students will applylogic design theory to actual PLD (ProgrammableLogic Devices) and FPGA (Field Programmable GateArray) devices. In addition, students will learn thebasics of the hardware design languages, Verilogand VHDL. This course or its equivalent is a prereq-uisite to all other ECE Electronics DesignAutomation courses. 4 credits

ECE574 CMOS Digital VLSI Design IAn introduction to CMOS digital IC design. Coursecovers basic MOS transistor theory; operation ofbasic CMOS inverter; noise margins; switch levelmodeling of MOS devices; capacitive characteristicsof MOS devices; introduction to device fabrication,design rules and layout issues; power consumption;

gate design/transistor sizing; pass transistors andcomplimentary pass transistor logic; dynamic domi-no and precharge/discharge circuits; memoryelement design (RAM/ROM/flip-flops) and subsystemdesign (adders, multipliers, etc.). An understandingof basic digital design concepts is assumed. Labexercises use industry standard design tools.Laboratories include circuit validation and charac-terization. Prerequisite: ECE 573. 4 credits

ECE575 CMOS Digital VLSI Design IIConcentration on advanced digital VLSI circuitdesign techniques. Architecture and micro-architec-ture of VLSI components, clocking schemes,input/output circuits, and special functional blockssuch as random access memories, read only memo-ries and programmable logic arrays. The coursecovers design tradeoffs, especially considering cost,power and performance. The course devotes a con-siderable amount of time to layout, parasitics andperformance verification. Introduction to design andverification tools with hands-on experience.Prerequisites: ECE 574, familiarity with MOS tran-sistor operation; computer architecture andorganization; logic design. 4 credits

ECE577 Principles for Technology Development andIntroduction to ManufacturingA project-oriented course on management proce-dures and key underlying concepts for effectivemanufacturing technology planning and develop-ment; an introduction to commercial production in acompetitive environment. While emphasis is onsemiconductor technology, most principles andmethodology are generally applicable to both hard-ware and software technology management. Issuesof technology strategic planning, process definitionand characterization, decision making, technologytransfer, product definition, yield and reliabilityimprovement, and concurrent engineering areexplored to identify effective managementapproaches to shorten time-to-volume production,reduce risk, and minimize engineering effort.

4 credits

ECE578 Embedded and Real Time Operating SystemsA study of concepts, techniques, and standards inembedded operating systems including real timeembedded operating systems. Topics include kerneldesign, device driver and interface techniques,scheduling, robustness and industry standards suchas Windows-CE and Tornado (VxWorks). This is ahands-on lab course where students will experiencereal-world real time embedded systems using com-mercial software tools. Prerequisites: CSE 521Introduction to Computer Architecture or a demon-strable understanding of computer architecture.

4 credits

ECE579 Embedded Computer SystemsA study of concepts, techniques, and standards inembedded systems from design through deploymentto retirement. Topics include programmable logic,interfacing, power supply, packaging, robustness,certification, and maintenance. This is a hands-onlab course based on a student project, where stu-dents will experience real-world embedded systemsusing commercial software and hardware tools.Prerequisites: CSE581 Introduction to Computer

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Architecture, ECE 578 Embedded and Real TimeOperating Systems, or permission from instructor.

4 credits

ECE580-XXX Special Topics Under this number, we offer courses of particularrelevance to the research interests of faculty or instate-of-the-art subjects of interest to the communi-ty. Individual course descriptions are listed asfollows. Special Topic courses are subject to changeand are offered intermittently. For Special Topicsoffered during the current term, please viewwww.ogi.edu/schedule.

ECE580-ACD Selected Topics in Analog IC Design

ECE580-ACS Advanced Control Systems: Nonlinear,Neural & Fuzzy

ECE580-AFA Applied Functional Analysis

ECE580-AIC Analog CMOS Integrated Circuit Design

ECE580-CLI Computational Approaches to Laser Interactionwith Biological Tissues

ECE580-CLT Computational Approaches to Light Transportin Biological Tissues

ECE580-CMP Chemical Mechanical Planarization

ECE580-CN Introduction to Computer Networks

ECE580-COD Introduction to Computer Organizationand Design

ECE580-CP The New Millenium in Copper Plating:Faster Chips with Slower Plating

ECE580-DDC Design of digital Communication Circuits

ECE580-FLC Fabrication Lab Class

ECE580-FSM Fundamentals of Sensors and MEMS Fabrication

ECE580-GAP Introduction to Genetic Algorithmsand Programming

ECE580- IB Introduction to Biomaterials (formerlyMSE589)

ECE580-IE Internet Engineering

ECE580-ISM Introduction to Sensor Microfabrication

ECE580-IVC Information Visualization and Computer Graphics

ECE580-LCD Introduction to Liquid Crystal Displays

ECE580-MBD Introduction to Modeling of Business Dynamics

ECE580-MC Multimedia Communications

ECE580-MEM Microelectromechanical Systems

ECE580-MPE Modern Photolithographic Engineering

ECE580-MTF Mechanics and Thin Films

ECE580-ONE Optical Non-destructive Evaluation

ECE580-PEM Phase Equilibria in Microelectronics (offered Fall 2001)

ECE580-PGO Physical and Geometric Optics,

ECE580-QM Quantitative Microscopy

ECE580-RFD Reliability and Failure of Electronic Devices, Packages, and Assemblies

ECE580-SJM Soldering and Joining in Microelectronics

ECE580-SLD Statistical Learning and Data Mining

ECE580-SMVI Simulation & Modeling of VLSI Interconnect

ECE580-SSE Semiconductor Sensors

ECE580-SSL Structure of Spoken Language


ECE580-TP Technology of Photoresists

ECE580-WCS Wireless Communication Systems

ECE580-UOS Understanding Operation ofSemiconductor Devices

ECE591 Independent StudyStudent works with professor on selected topic(s).Requires pre-approval of professor, ECE Depart-ment, as well as formal agreement between studentand professor outlining objectives and expectationsof independent study topic. May only be taken onceduring a student’s graduate program at OGI for amaximum of 3 credits.

ECE600 Prequalifying Ph.D. ResearchSupervised research participation. Pre-qualifyingPh.D. research prior to passing ECE departmentqualifying examination.


ECE610 M.S. Nonthesis Project ResearchSupervised research for up to eight credits as acomponent of the nonthesis M.S. degree. Studentsare required to produce cogent research deliver-able(s) including, but not limited to, a final reportequivalent to an EE project paper. This researchclassification requires the approval of the depart-ment head and the student’s SPC.

Variable and repetititive credit

ECE620 Professional InternshipThis course provides the student with an opportuni-ty to earn credit for relevant work experience inindustry. Students gain valuable industrial experi-ence that allows them to both apply the knowledgegained in the classroom and prepare for their futurecareers.U.S. citizens, permanent residents, studentson F-1 visas enrolled in Curricular PracticalTraining take ECE620 and must obtain additionalpermission from OGI personnel department.Enrollment requires a faculty advisor and is limitedby the number of internship opportunities available.


ECE700 M.S. ThesisResearch toward the thesis for the M.S. degree.


ECE800 Ph.D. DissertationResearch toward the dissertation for the Ph.D.degree. Variable and repetitive credit.

RESEARCH CENTERS

CENTER FOR BIOLOGICALLY INSPIRED INFORMATION

ENGINEERING (CBI IE)

Science and engineering have achieved greatadvances in automating and creating informationprocessing and analysis tools. Microelectronics,programming, signal processing and informationtheory underpin these achievements. Modernmicroprocessors and those that will be producedover the next decade will provide hugecomputational power, enabling new informationprocessing applications. In fact, it will soon bepossible to place one billion transistors on a singlepiece of silicon.

Many information-processing applications involvehuge amounts of real world data that have to beprocessed and analyzed for making decisions. Thecomplexity of the analysis is often beyond currentscience and engineering’s techniques andmethodologies. Yet, natural evolution has evolvedvery sophisticated information processing systems,and the information analysis performed by thehuman brain, or even by the brain of simpleanimals, is far superior to what current state-of-the-art human-developed techniques can achieve.

A new research area is now coalescing which isdevoted to consolidating and refining existingsolutions, and finding better solutions to thesetransformation problems. The term IntelligentSignal Processing (ISP) is being used to describealgorithms and techniques that involve thecreation, efficient representation, and effectiveutilization of complex models of semantic andsyntactic relationships. Even the most primitivebiological systems perform complex ISP. Inaddition, biological computing is robust in thepresence of faulty and failing hardware, and isfundamentally asynchronous. Biological computingis energy efficient, consists of networks of sparsely connected and sparsely activated nodes,and requires only moderate levels of computational precision.

We believe that the merging of neuroscience andsemiconductor engineering is creating what AndyGrove, ex-CEO of Intel, refers to as a strategicinflection point. Therefore, the mission of theCenter for Biologically Inspired InformationEngineering is to harvest biology for solutions toreal-world information engineering and IntelligentSignal Processing problems, and leverage theincredible functional density of GSI (Giga-ScaleIntegrated) Silicon. The Center was established in2001 and currently consists of two professors -Dan Hammerstrom and Marwan Jabri - and theirstaff and graduate students. The Center currentlyreceives funding from NASA, NSF, SRC, ONR and Intel.

Current projects focus on:

• Computational models of sensorimotor control;

• High-level visual feature extraction usingunsupervised learning techniques;

• Top-down/bottom up sensory fusion andsensorimotor control;

• Simulation of large-scale networks on PC clusters;

• Mapping computational neurobiology to FPGAs and eventually custom silicon; and

• Understanding the issues involved in scalingneural models to very large configurations.

CENTER FOR INFORMATION TECHNOLOGY (CIT)

Digital signal processing has made a significantimpact on human lives since its introductionseveral decades ago. The broad field of informationtechnologies has become a vital driving force in the


United States economy, both regionally andnationally. Industries are in the process of shiftingemphasis from instrumentation and manufacturingto multimedia and communications services. Widearrays of technologies, ranging from digitaltelephones to the ability to accurately predict thebehavior of complex systems, rely on elegantmathematical concepts and on the power of digitalcomputers. Even the most advanced techniques,however, fail to carry out many tasks that areeffortlessly performed by humans.

The mission of the Center for InformationTechnology (CIT) is to support the development anddeployment of signal-processing systems thatwould emulate and surpass human informationprocessing capabilities. CIT activities focus on the“human-like,” or anthropic, processing side ofinformation systems. The anthropic signalprocessing is the synthesis of robust signal-processing techniques that exceed the performanceof standard classical signal-processing methods byappealing to human-like processing strategies andcapabilities. This unique combination ofengineering and human information processingstrategies is strengthened by recent incorporationof OGI into Oregon Health & Sciences Universitythat allows for close collaboration betweenengineering and humanistic sciences.

The center’s efforts focus on several target-engineering systems, including robust featureextraction for speech recognition systems, speechquality enhancement in cellular communications,automatic target detection and identification, and a forward visibility system for aviation. These projects are supported by basic research on several key-supporting technologies, including neural networks, prediction, image and speech representation, information fusion and the incorporation of prior knowledge inadaptive systems.

Within the OGI School, CIT provides a naturalcomplement to other centers, including the Centerfor Spoken Language Understanding and its Centerfor Human-Computer Communication. CITcompliments CSLU by developing advanced signalprocessing techniques used in speech processing.In a similar way, CIT is developing solutions to avariety of signal-processing problems in naturalcommunication using images, sound and gestures.CIT is an important component in the ECEdepartment’s focus on intelligent signal processing.

CENTER FOR SPOKEN LANGUAGE UNDERSTANDING

The research program of the Center for SpokenLanguage Understanding (CSLU) encompasses abroad range of technologies critical to advances inthe development of interactive conversationalsystems. Such research is inherentlymultidisciplinary, and the center brings together ateam with expertise in signal processing, speechrecognition, speech synthesis, dialogue modeling,natural language processing, multimodal systems,linguistics and human-computer interaction.

Within CSLU there are five collaboratingresearch groups:

• Neural Speech Enhancement Lab

• Anthropic Signal Processing Group

• Speech Recognition Group

• Speech Synthesis Research Group

• Natural Dialog Group

These groups focus on specific problem areas suchas: robust methods for enhancing speech in noisyenvironments; large vocabulary recognition ofcontinuous speech, as in broadcast news; unitselection and voice conversion for more realisticspeech synthesis; robust parsing and interpretationof spoken and multimodal input; modeling ofdisfluencies in spontaneous speech; and effectivemethods for dialog management. CSLU researchprojects incorporate and evaluate these researchadvances. For example, one project involves thedevelopment of an animated conversational agentfor learning and language training with profoundlydeaf children. The center is also highly active in thedevelopment and distribution of a wide variety oflanguage resources, including corpora oftranscribed telephone and cellular speech data forover 20 languages.

Professor Jan van Santen is the director of OGI’sCenter for Spoken Language Understanding. Thecenter is co-directed by Professors Peter Heeman,John-Paul Hosom, Yonghong Yan, and Eric Wan.Other center faculty includes Professors Todd Leen,Hynek Hermansky, and Xubo Song. The centerreceives support from government agenciesincluding NSF, DARPA, and ONR, as well asindustrial sources. For additional information, visit the CSLU web site: www.cslu.ogi.edu.

RESEARCH PROGRAMSAdvanced LithographyLithography is the key technology pacing the evolu-tion of microelectronics. Research is ongoing indeveloping a viable patterning technology for usein large scale manufacturing of semiconductordevices. By using either semiconductor technologyor new cathode materials, it should be possible togenerate arrays with significantly enhanced speedand improved pattern fidelity. Berglund, Freeouf,McCarthy

Atmospheric OpticsThe use of laser systems to transmit signalsthrough the atmosphere for purposes of communi-cation, radar, recognition, and designation isseverely limited by scattering due to turbulenceand particulates such as water droplets or dust.Turbulence, which causes shimmer on a hot dayand makes stars seem to twinkle, results in therandom steering, spreading and breaking-up (scin-tillation) of a laser beam. Particulate scatteringthat severely attenuates the received signal alsocauses depolarization and multiple path effectssuch as pulse stretching and scrambling of the sig-nal. Experimental studies, which in conjunction

with concurrent theoretical work, are contributingsignificantly to fundamental understanding of theeffects of atmospheric turbulence on laser beam,speckle propagation and its application to opticalremote sensing. Holmes

Biomedical OpticsThe program in Biomedical Optics prepares thestudent to use lasers and light to measure, image,modify and machine materials, with emphasis onbiological materials but with broad application to avariety of materials. The program offers a series ofcourses and labs on tissue optics, laser-tissueinteractions, and engineering design, with electivecourses in optics, spectroscopy, optical fibers, bio-mechanics, imaging and image analysis, opticalmeasurement techniques, and computational meth-ods for simulating light transport through andinteraction with biological materials. Students havethe opportunity to work in the hospital-basedresearch laboratories at the Oregon Medical LaserCenter at Providence St. Vincent Medical Centerand the Biomedical Optics Laboratory on the OHSUMedical Center campus. Jacques, Kirkpatrick,Prahl, Song

Electronic Materials An active research program in the area ofelectronic materials growth and characterization isfocused on demands of the ever shrinkingmicroelectronic devices. The main materialsgrowth technique investigated is atomic layer depo-sition which allows growth of highly conformal thinfilms, one atomic layer at a time. Materials investi-gated using this approach include thin gatedielectrics, including nanolaminates and metallicfilms which include copper seed layers and barriermetals. Another area of research involveselectrodeposition of copper films for microelectron-ic device interconnect applications. The focus ofthis investigation is to determine the correlationbetween the bath chemistry to the physical proper-ties of the films and their electromigrationlifetimes. Solanki, Freeouf, McCarthy

Flat Panel DisplaysThe video screen is becoming an indispensable linkbetween information processing electronicssystems and human beings. Although the cathoderay tube (CRT) remains the dominant display tech-nology, its size, weight, and power requirementsbecome unsuitable for many applications. As areplacement for CRTs, several flat panel displaytechnologies are being explored due to their com-pactness, light weight and low power consumption.A flat panel display research group has been estab-lished to develop research capabilities and to workclosely with the emerging display companies toassist them in overcoming technological hurdles. Atpresent, research is directed towards electrolumi-nescent, field emission, and liquid crystal displays.Berglund, Solanki, Rananavare, McCarthy

Image Processing and AnalysisThe main research interests of our group aretwofold. One thrust is image processing and imagerecognition. One of the techniques we are investi-gating is incorporating contextual information intorecognition. Context incorporation is a mechanism

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that ensures accurate perception and appropriateinterpretation of ambiguities. Ambiguities ariseeitherbecause information is missing or becauseinformation is partially or completely obscured bynoise. Probabilistic or statistical models can bedeveloped for context incorporation, and it hasbeen demonstrated that utilizing contextual infor-mation is crucial for improving recognitionaccuracy. Another research thrust is on machinelearning and data mining. We are interested in afundamental understanding of learning, and in thedevelopment of learning systems that achieve stateof the art performance. Song

Modification of Semiconductor MaterialsResearch is under way on the processing and char-acterization of semiconductor materials as affectedby localized transient heating, plasma passivation,and thermal annealing. The recrystallization ofpolysilicon is studied using various laser sourcesand rapid thermal annealing. Solanki, Freeouf,McCarthy

Neural Networks and Adaptive Systems Neural computation and adaptive systems are stud-ied from both theoretical and practical standpoints.Current research in theory, architecture, and algo-rithm design includes deterministic and stochasticnetwork dynamics, learning algorithms(supervised, unsupervised, and reinforcement),generalization theory (including model selectionand pruning, invariant learning), context-sensitivelearning, signal processing, time series analysis,and control. Practical application domains includeadaptive signal processing, pattern recognition,speech recognition, image processing, control sys-tems, macroeconomics, and finance. Leen, Moody,Pavel, Song, Wan

Optical Remote SensingAnalytical and experimental studies are beingmade on the use of the interaction of electromag-netic radiation and turbulence to measure windsand turbulence. Recent efforts include analytical,numerical and experimental work on a CO2,optical heterodyne system for remote measurementof atmospheric cross winds and strength ofturbulence. Holmes

Organizational EvolutionIn recent years an increased understanding ofevolutionary processes has emerged from work inmolecular biology, computer science and complexsystems analysis. This new understanding poten-tially can be harnessed by managers to createhuman organizations which evolve rapidly indesired directions. Our objective is to develop aconceptual toolkit for “evolutionary management”.In our research, we draw analogies betweenpolicies and genes, between mutations and policyinnovations, and between recombination andlearning. We present a theoretical frameworkdrawing on a computer simulation environmentcombining system dynamics modeling with geneticalgorithms. Currently, we use this framework toexplore the evolutionary implications ofmanagement hierarchy and team learning. House

Speech and Speaker Recognition in AdverseCommunication EnvironmentsBiological signals such as speech carry largeamounts of information from different informationsources. Typical engineering applications such asautomatic speech recognition, speaker verification,or low bit-rate coding of speech may require infor-mation from only one particular source, and allother information introduces undesirable andharmful variability into the signal. Humans appearto be able to partially separate the various infor-mation sources in the speech signal. This abilityspurred interest in modeling human-like processingof speech by modern discrete signal processingtechniques. The anthropomorphic signal processingtechniques could, in principle, yield improved per-formance of man/machine I/O technologies in realpractical environments. Our research project onspeech analysis, carried on jointly with theInternational Computer Science Institute, Berkeley,Calif., focuses on human-like processing of speechin realistic telecommunications environments toensure reliable recognition of speech in adverseconditions such as the current mobile cellulartelephone. Hermansky

Speech SynthesisSpeech is the most natural and efficient means bywhich individuals may access most information,and the need for speech-based interfaces is grow-ing as computing gradually moves off of thedesktop and into mobile devices. Since most on-lineinformation is represented as ASCII text, the auto-matic conversion of text to speech provides acritical component in voice-based systems. Text-to-speech synthesis (TTS) has the further advantageof providing textual information to people who arevisually impaired or functionally illiterate. The cur-rent trend in TTS research is to develop algorithmsthat rely on automatic training of models fromlabeled data, rather than hand-tuned rules as usedhistorically. This strategy leads to systems that canbe “trained” rapidly to speak in a new language orspeaking style. Our work has been focused on sig-nal processing models of the human voice and theiruse in data-driven speech synthesis algorithms.This is an interdisciplinary field that drawselements from linguistics, computer science,machine learning, human perception, and digitalsignal processing. van Santen, Hosom

VLSI Architecture for Intelligent ComputingSome of the most fundamental problems incomputing involve teaching computers to act ina more intelligent manner. Key to this is theefficient representation of knowledge or contextualinformation. In this project a variety of highlyparallel algorithms are studied, includingneuromorphic structures, with the intent ofimplementing knowledge representation andmanipulation in silicon. Hammerstrom

MEMS and Micro-sensorsMicroelectromechanical systems (MEMS) andmicro-sensors are rapidly becoming ubiquitous intechnological society. Research applications rangefrom micro-cilia, micro-turbines, and chips that

R E S E A R C H FA C I L I T I E S

The department has a completecomplement of electronic measuring,recording, amplifying, signal generating,data processing, and servicing gearwith associated power supplies andcomponent stocks. Additional facilitiesand equipment include:

• Access to FT-IR, fluorescence, diode array UV/VIS,scanning UV/VI Snear IR spectrophotometers

• NT/PC Computer Lab

• Solaris Servers with X-terminal access

• DTV Lab

• Intel Semiconductor Educational Lab

• Embedded Computer Lab

• High-end PCs & workstations

• Far-infrared Fourier spectrometer

• Parallel f ield-vibrating sample magnetometer

• Mossbauer spectrometer

• Field electron and ion microscopes

• Ultra-high vacuum systems

• Thin-fi lm evaporation equipment

• Electron energy analyzers for Auger and field electron spectroscopy

• Micromachining capabil ities

• Scanning electron microscope and transmissionelectron microscope

• High-resolution electron and ion microprobes

• Work function analysis instrumentation

• Quadrupole mass spectrometers for surfacedesorption studies

• Arc zone refinement system for single crystalspecimen preparation

• Wire bonder

• Die attach system

• X-ray diffraction generator and cameras

• Facil ity for electronic transport and luminescencemeasurements as a function of temperature

• Visible, ultraviolet, and infrared gas, solid state,and dye lasers

• MOCVD crystal growth reactors

• 1.25 meter visible and IR spectrometer

• High-performance optical microscope

• Depth profil ing ell ipsometer

• Photolithography and semiconductor metall ization

• Sputter etching

• Device interconnect and packaging

• C-V, I-V measurement facil ities

• Pulsed uv-laser processing system

• Electrical characterization (Hall)

• Sputtering machine

• Atomic layer epitaxy

• Liquid crystal display lab with pretilt rubbing, andsingle-cell electro-optic characterization facil ities

• Scanning Auger Microprobe

• Spectroscopic Ell ipsometers

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walk to MEMS & micro-sensors that have beencommercialized in diverse applications such asairbag accelerometers and ‘electronic noses’ usedto detect gases and chemicals. While VLSI fabrica-tion techniques are exploited to produce MEMSand micro-sensor devices economically, thesedevices can be fabricated by an even greaterrange of processes and with a far wider variety ofmaterials. The MEM/micro-sensor microfabrica-tion laboratory in ECE is building glucose sensors,pressure sensors, and even micro-peristalticpumps with a multidisciplinary exposure tomechanics, electronics, physics and fluid dynam-ics. Research and courses on MEMS andmicro-sensors are focused on developingunderstanding of a large toolbox of processes andmaterials to design and fabricate these devices.Scholl, House, McCarthy

MicroanalysisThe characterization, failure studies and in-situtesting of materials and structures used in micro-electronics, opto-electronics, micro electro-mechanical systems(MEMS), sensors and biotech-nology require a range of techniques that allow themeasurement of properties on an ever decreasingscale. Probing materials on the sub-micron andnanometer scales was first necessary in the fabri-cation of sub-micron transistors to providefeedback on the thin film fabrication processes.These same thin film processes are now beingemployed by the budding biotechnology, MEMSand sensor industries. The probing isaccomplished by scanned atomic force microscopetips, light, electron and ion beams. The signalsproduced by the probes are used to create highresolution images of surfaces and internal struc-tures, measure compositions, thickness, roughnessand identify crystal structures. The geometries,crystal structures, elements present and composi-tions revealed can then be correlated withelectrical, mechanical, thermal and optical proper-ties or more generally the performance of amicroelctronic device, MEMS or sensor. The devel-opment of microanalysis techniques andapplication to research and development projectsat OGI-ECE has a long history and continues to bea major portion of efforts here. Optical, atomicforce, scanning electron, scanning Auger electronand transmission electron microscopes are used tocharacterize materials following tests, changes inprocesses or failures in service. The recent addi-tion of a heating straining stage to the SEM and aheating stage with electrical feed-through’s to theTEM will permit the complete evolution ofmicrostructures during thermal processing ormechanical failures to be recorded digitally givinga more complete and accurate picture of mecha-nisms of change in materials on the micron andnanometer scales. McCarthy, House, Freeouf

Focused Ion Beam TechnologyThe use of focused ion beam workstations(FIB) inthe microelectronics industry as development andproduction tools is widespread. The first researchand development steps in producing practical FIBworkstations in collaboration with local microelec-

tronics companies were taken here at OGI.Focused ion beams are used to locate micron andsub-micron structures and produce cross-sectionsof these structures for examination in scanningand transmission electron microscopes. The deepsub-micron development efforts now in progressrequire the nano- and atomic scale characteriza-tion feedback on fabrication processes provided bythese FIB produced cross-sections for the develop-ment efforts to be successful. The FIB is also usedto modify existing microelectronic devices byadding or removing components by the removal oraddition of conductors and insulators. This permitsdesigners to test a change in a device quickly andinexpensively before making a costly change to afabrication line or a mask. More generally the FIBprovides the ability to micro-machine and micro-form on the micron and sub-micron scale in threedimensions. This has applications in the MEMS,sensor and biotechnology fields as a micron andsub-micron prototype fabrication tool. The FIB isalso a lithography tool that does not requireresists. A region is made chemically more activeby careful control of the area of beam scan, beamenergy and dwell to produce a volume of materialthat reacts when subjected to wet or dry etches.There is active research at OGI-ECE on the devel-opment of sub-micron cantilevers as highfrequency electromechanical switches using ionlithography. McCarthy

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D A N H A M M E R S T R O MDoug Strain Professorand Department HeadPh.D., Electrical Engineering1977, University of [email protected]


Neuromorphic computing.Application of FPGAs to imageprocessing, digital video,intelligent and neuromorphiccomputing. VLSI design. Highlyparallel computer architecture and microarchitecture.Technology transfer.

R E P R E S E N TAT I V E P U B L I C AT I O N SD. Hammerstrom, “Computational

Neurobiology Meets SemiconductorEngineering,” Invited Paper MultiValuedLogic 2000, May 2000.

S. Rehfuss & D. Hammerstrom,“Comparing SFMD and SPMDComputation for On-ChipMultiprocessing of Intermediate LevelImage Understanding Algorithms,”Proceedings of the conference forComputer Architectures for MachinePerception 1997, Boston, MA, October 1997.

D. Hammerstrom & D. Lulich, “ImageProcessing Using One-DimensionalProcessor Arrays,” The Proceedings ofthe IEEE, 84(7), 27-43, July 1996.

S. Rehfuss & D. Hammerstrom,“Model Matching and Single FunctionMultiple Data Computation (SFMD),”NIPS Proceedings, November 1995.

D. Hammerstrom, “Digital VLSI forNeural Networks,” Handbook of BrainTheory and Neural Networks, M. Arbib(Ed.), Bradford Books/MIT Press, 1995.

D. Hammerstrom, “A Digital VLSIArchitecture for Real WorldApplications,” An Introduction to Neural and Electronic Networks, S.F. Zornetzer, J.L. Davis, C. Lau & T.McKenna (Eds.), Academic Press, 1995.

A N T H O N Y E . B E L LAssociate ProfessorPh.D., Physical ChemistryUniversity of London, [email protected]


Development of liquid metal fieldion sources; field ionization,surface physics, and chemistry;field emission microscopy andenergy distribution measurements.Selected area processing formicrocircuit fabrication usingfocused electron beams. Direct-write electron-beam lithographyfor both mask making and ICfabrication using multiple photo-emitted electron beams. Plasmaprocessing for thin film depositionand etching.

R E P R E S E N TAT I V E P U B L I C AT I O N SA.E. Bell & D.F. Barofsky, “Field

Emission and Field Ionization,” inEncyclopedia of Applied Physics, 6, 379, 1993.

A.E. Bell, K. Jousten & L.W. Swanson,“High Field Ion Sources,” Rev. Sci. Intr.,61(1) Part II, 363, 1990.

S. Rao, A.E. Bell, G.A. Schwind & L.W. Swanson, “Angular Distribution of Ions from a AuSi Liquid MetalSource,” J. Vac. Sci. Technol., A8(3),2258, 1990.

S. Rao, A.E. Bell, G.A. Schwind & L.W. Swanson, “A CombinationElectron/Ion Field Emission Source,” J. Vac. Sci. Technol., B7, 1793, 1989.

L.W. Swanson & A.E. Bell, “LiquidMetal Ion Sources,” I.G. Brown (Ed.),The Physics and Technology of IonSources, John Wiley & Co., 313, 1989.

C . N E I L B E R G L U N DProfessorPh.D., Electrical EngineeringStanford University, [email protected]


Management of technology, andadvanced lithography forsemiconductor fabrication.

R E P R E S E N TAT I V E P U B L I C AT I O N SJ. Ye, M. Takac, C.N. Berglund,

G. Owen & R.F.W. Pease, “An ExactAlgorithm for the Self-Calibration ofPrecision X-Y Stages,” Conference onElectron, Ion & Photon BeamTechnology and Nanofabrication, May 1996.

M.T. Takac, J. Ye, M.R. Raugh, R.F.W.Pease, C.N. Berglund & G. Owen, “Self-Calibration in Two Dimensions:The Experiment,” 1996 SPIEInternational Symposium onMicrolithography, March 1996.

W. Wang, J. Ye, A.B. Owen, C.N.Berglund & R.F.W. Pease, “AdaptiveMetrology: An Economical Strategy forJudging the Acceptability of a MaskPattern,” J. Vac. Sci. Technol., B13(6),November/December 1995.

J. Ye, C.N. Berglund & R.F.W. Pease,“Field Distortion Characterization UsingLinewidth or Pitch Measurement,” J. Vac. Sci. Technol. B13(6),November/December 1995.

J. Ye, C.N. Berglund, J. Robinson &R.F.W. Pease, “A Review of Mask Errorson a Variety of Pattern Generators,”IEEE Transactions on SemiconductorManufacturing, 8(3), 319-325, August 1995.

J. Ingino, G. Owen, C.N. Berglund, R. Browning & R.F.W. Pease,“Workpiece Charging in Electron BeamLithography,” J. Vac. Sci. Technol.,B12(3), 1367-1371, May/June 1994.

J O H N L . F R E E O U FProfessorPh.D., Physics,University of Chicago, [email protected]


The large and growingsemiconductor industry has clearlyestablished that to controlsomething you must be able tomeasure it. A major thrust of myresearch efforts is to determinehow to measure the specificparameters required to bestunderstand and improve oursemiconductor materials anddevices. Typically, thesemeasurements will involveincident photons; the output maybe either photons or someelectrical response.

R E P R E S E N TAT I V E P U B L I C AT I O N SSeung-Gu Lim, Thomas N. Jackson,

W.C. Mitchel, R. Bertke and J.L.Freeouf, Optical Characterization of4H-SiC by Far Ultraviolet SpectroscopicEllipsometry, Applied Physics Letters,vol. 79, No. 2, 2001.

Todd Holden, P. Ram, Fred H. Pollak,J. L. Freeouf, B. X. Yang and M. C.Tomargo, Spectral EllipsometryInvestigation of Zn Cd Se LatticeMatched to InP, Physical Review B56,4037, 1997.

M. Leibovitch, P. Ram, L. Malikova,Fred H. Pollak, J. L. Freeouf, L. Kronik,B. Mishon, Yoram Shapira, A. R.Clawson, and C. M. Hanson, ReflectionAnisotropy Spectroscopy, SurfacePhotovoltage Spectroscopy, andContactless ElectroreflectanceInvestigation of the InP/In0.53Ga0.47As(001) Heterojunction System, J. Vac.Sci. Technol. B14, 3089, 1996.

J. L. Freeouf, N. Braslau, and M.Wittmer, Lifetime Measurements onSilicon on Insulator Wafers, Appl. Phys.Lett. 63, 198, 1993.

M. Wittmer and J. L. Freeouf, IdealSchottky Diodes on Passivated Silicon,Phys. Rev. Lett. 69, 2701, 1992.

J. L. Freeouf, D. A. Buchanan, S. L. Wright, T. N. Jackson, and B.Robinson, Accumulation Capacitancefor GaAs SiO2 Interfaces With SiInterlayers, Appl. Phys. Lett. 57, 1919, 1990.

K E N T O N G R E G O R YAssociate ProfessorM.D. School of MedicineUniversity of Southern California,1980


Application of laser energy for thetreatment of altheroscleroticvascular disease, laserthrombolysis in acute myocardialinfarction and stroke, vascularsmooth muscle response to light,Elastin biomaterials for tissuereplacement and repair, and dye-targeted laser-tissue fusion.

R E P R E S E N TAT I V E P U B L I C AT I O N SM.J. Girsky, K.W. Gregory, A. Shearin

& S.A. Prahl, “Photoacoustic DrugDelivery to Arterial Thrombus: A NewMethod for Local Drug Delivery,”American Heart Association, 69thAnnual Scientific Session, New Orleans,LA, November 1996.

K.W. Gregory, “Laser Thrombolysis in Acute Myocardial Infarction,”Current Review of InterventionalCardiology (D. Holmes Jr. & P.Serruys), 3rd Edition, August 1996.

E.N. LaJoie, A.D. Barofsky, K.W.Gregory & S.A. Prahl, “Welding ArtificalBiomaterial with a Pulsed Diode Laserand Indocyanine Green,” SPIE, LaserTissue Interaction VI (S.L. Jacques,Ed.), San Jose, CA, 1995.

H. Shangguan, L.W. Casperson, A. Shearin, K.W. Gregory & S.A. Prahl,“Photoacoustic Drug Delivery: TheEffect of Laser Parameters on SpatialDistribution of Delivered Drug,” SPIE,Laser Tissue Interaction VI (S.L.Jacques, Ed.), San Jose, CA, 1995.

K.W. Gregory & J.M. Grunkemeier,“Arterial Reconstruction using anElastin-based Biopolymer with DyeTargeted Diode Laser Fusion,”American Society for Laser Medicineand Surgery, 15th Annual Meeting, San Diego, CA, April 1995.

H Y N E K H E R M A N S K YProfessorDr. Eng., Electrical EngineeringUniversity of Tokyo, [email protected]


Communication between humanand machine; human perceptionand its computer simulation;speech production and perception;automatic recognition of speech,speech coding, synthesis andenhancement; identification and extraction of linguisticinformation in realisticcommunication environments.

R E P R E S E N TAT I V E P U B L I C AT I O N SH. Hermansky, “Should Recognizers

Have Ears?” Speech Communication,Publishers, Holland, June 1998.

H. Hermansky, “Modulation Spectrumin Speech Processing, in SignalAnalysis and Prediction,” Prochazka,Uhlir, Rayner, Kingsbury, Eds., 1998.

H. Hermansky & N Malayath,“Speaker Verification using Speaker-Specific Mappings,” Proceedings of Speaker Recognition and itsCommercial and Forensic Application,France, 1998.

C. Avendano & H. Hermansky, “On the Properties of Temporal Processingfor Speech in Adverse Environments,”Proceedings of 1997 Workshop onApplication of Signal Processing toAudio and Acoustics, Mohonk MountainHouse, New Paltz, New York, October 1997.

S. Tibrewala & H. Hermansky, “Multi-band and Adaptation Approaches toRobust Speech Recognition,” to appearin Proceedings of EUROSPEECH ‘97,Rhodos, Greece, September 1997.

S. van Vuuren & H. Hermansky, “Data-driven Design of RASTA-likeFilters,” Proceedings of EUROSPEECH97, Rhodos, Greece, September 1997.

H. Hermansky, C. Avendano, S. vanVuuren, & S. Tibrewala, “RecentAdvances in Addressing Sources ofNon-Linguistic Information,”Proceedings of ESCA-NATO Tutorial and Research Workshop on RobustSpeech Recognition for UnknownCommunication Channels, 103-106,Pont-a-Mousson, France, April 1997.

J . F R E D H O L M E SProfessor EmeritusPh.D., Electrical EngineeringUniversity of Washington, [email protected]


Speckle propagation throughturbulence, optical remote sensing of wind and turbulence,electro-optic systems,instrumentation signal processing,and biomedical optics.

R E P R E S E N TAT I V E P U B L I C AT I O N SJ. Fred Holmes, Steven L. Jacques,

and John M. Hunt, “Adaptingatmospheric lidar techniques to imag-ing biological tissue”, SPIE, Bios 2000Conference, San Jose, California,January 22 - 28, 2000.

M. Becker, J.F. Holmes, & L. Meekisho,“Interdisciplinary CurriculumDevelopment in Electronics PackagingUsing Course Segmentation,” ASEE1998 Frontiers in EducationConference, Tempe, Arizona, November 4-7, 1998.

J.F. Homes & B. J. Rask, “RangeResolved, 3-D Optical Remote Sensingof Atmospheric Winds Using a CWLidar,” Advances in AtmosphericRemote Sensing with Lidar, A.Amsmann, R. Neuber, P. Rairoux, andU. Wandinger (eds.), Springer-Verlag,Berlin, 1997.

J. F. Holmes & C. Zhou, “PathResolved, Optical Remote Sensing ofthe Strength of Turbulence Using aPseudo Random Code Modulated CWLidar and Coherent OpticalProcessing,” 9th Conference onCoherent Laser Radar, Linkoping,Sweden, June, 1997.

J.F. Holmes & B.J. Rask, “The Effectof Aerosol Speckle Phase Decorrelationon the Allowable Signal Averaging Timefor Coherent Optical Receivers,” SPIEAnnual Meeting, August 1996.

J.F. Holmes & B.J. Rask, “RangeResolved, 3-D, Optical Remote Sensing of Atmospheric Winds Using aCW Lidar,” 18th International LaserRadar Conference, Berlin, Germany,July 1996.

J.F. Holmes & B.J. Rask, “Optimum,Optical Local Oscillator Levels forCoherent Detection Using Photodiodes,”Appl. Opt., 34, February 1995.

J O D Y H O U S EAssistant ProfessorSc.D., Electrical Engineering 1998. Massachusetts Instituteof [email protected]


Electronic and photonic devicedesign for microsensorapplications with a currentconcentration on materials.Applications in genetic algorithmsand programs as applied toelectronic materials and devicesas well as human organizations.System dynamics modeling ofhuman organizations for publicpolicy development. The role earlyengineering education processeshave in retention and attraction offemale engineering students.

R E P R E S E N TAT I V E P U B L I C AT I O N SHines, J. and House, The Source of

Poor Policy: Controlling Learning Driftand Premature Consensus in HumanOrganization. System Dynamics Review,17(1); p. 3-32, 2001.

Hines, J.H. and J.L. House.Management fads & poor policies: Ayear of organization evolution research.In 2001 NSF Design and ManufacuringResearch Conference. Tampa, FL, 2001

House, J.A. Kain and J. Hines.Evolutionary Algorithm: Metaphor forLearning. In Genetic and EvolutionaryComputation Conference. Las Vegas,NV: Morgan Kaufmann, 2000.

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R O B E R T S . J A F F EInstructorPh.D., in Electrical andComputer EngineeringPortland State University in 1988 [email protected]


Robert S. Jaffe is a full-timeinstructor in ECE. He teaches inthe areas of signals and systems,applied mathematics andmathematical systems theory. Hisarea of specialization is linearsystems and robust control. Hereceived a Ph.D. in Electrical andComputer Engineering fromPortland State University in 1988.During an earlier career phase hewas a Professor of Philosophy anda researcher in the philosophy ofeducation.

M A R W A N J A B R IGordon and Bettie MooreProfessor of MicroelectronicsPh.D., Electrical EngineeringUniversity of Sydney 1988 [email protected]


Artificial intelligence, computerarchitecture. The understanding of the principles by which humans and/or other organismsperceive the environment, process sensory signals, reason,make decisions and learn. Thedesign and engineering ofhumanoids that exhibit facultiessimilar to humans.

R E P R E S E N TAT I V E P U B L I C AT I O N SO. Coenen, M. Arnold, T. Sejnowski

and M. Jabri, Bayesian analysis of parallel fiber coding in the Cerebellum,ICONIPí2000, pp 1301-1306, Korea, 2000.

M.A. Jabri and R. Coggins, “MicroPower Adaptive Circuits forImplantable Devices,” Low Power –Low Voltage Circuits and System,E. Sanchez-Sinencio & AndreasAndreou Editors, IEEE Press, USA, pp. 500-518, 1999.

Raymond J. W. Wang and MarwanJabri, “A Computational Model of the Auditory Pathway to the SuperiorColliculus,” in Brain-like computationand Intelligent Information Systems,Shun-ichi Amari and Nikola Kasabov(Eds.), Springer Verlag, pp. 81-104,1998.

R. Coggins, R. Wang and M.A. Jabri,“A micropower adaptive linear trans-form vector quantiser,” to appear inAnalog integrated circuits and signalprocessing, Kluwer, February 1999.

R. Coggins, M.A. Jabri, A LowComplexity Intracardiac ElectrogramCompression Algorithm, IEEETransactions on BiomedicalEngineering, Vol. 46, No. 1, pp. 82-91,January 1999.

X.Q. Li and M.A. Jabri, “Machinelearning based VLSI Cells ShapeFunction Estimation,” IEEETransactions on CAD for IntegratedCircuits and Systems, Vol 17, No. 7,pp. 613-623, 1998.

M. Schenkel and M.A. Jabri,† “Lowresolution degraded document recogni-tion using neural networks and hiddenMarkov models,” Pattern RecognitionLetters, V19 N3-4 pp. 365-371, 1998.

M. Partridge and M.A. Jabri,“Template Decision Trees,” Journal ofApplied Intelligence, 1997.

M.A. Jabri and E. Tinker, “Classifierarchitectures for Single ChamberArrhythmia Recognition,” Journal ofApplied Intelligence, Kluwer AcademicPress, 6:3, pp. 215-224, July 1996.

M.A. Jabri, R. Coggins and B. Flower,“Adaptive Analog Neural Systems,”Chapman and Hall, UK, 1996.

M.A. Jabri, “Neural Networks for ECG Signal Interpretation,” Handbookof Neural Computation, Institute ofPhysics Publishing and OxfordUniversity Press, G2.5, 1996.

S T E V E N L . J A C Q U E SProfessorPh.D., Biophysics and Medical PhysicsUniversity of California, Berkeley, [email protected]


Biomedical optics and laser-tissueinteractions. Development ofdiagnostic and therapeutic devicesfor medicine and biology usingoptical technologies.

R E P R E S E N TAT I V E P U B L I C AT I O N SS. L. Jacques, J. R. Roman, K. Lee,

“Imaging superficial tissues with polar-ized light,” Lasers Surg. Med.26:119-129, 2000.

L. V. Wang, S. L. Jacques, “Source oferror in calculation of optical diffusereflectance from turbid media using dif-fusion theory,” Comput MethodsPrograms Biomed. 61(3):163-170,2000.

S. L. Jacques, “Modeling photontransport in transabdominal fetaloximetry,” J Biomed. Optics, in press,2000.

S. L. Jacques, “Light distributionsfrom point, line, and plane sources forphotochemical reactions and fluores-cence in turbid biological tissues,”Photochem. Photobiol. 67:23-32, 1998.

S. L. Jacques, S. J. Kirkpatrick,“Acoustically modulated speckle imag-ing of biological tissues,” OpticsLetters, 23:879-881, 1998.

S. L. Jacques, “Path integral descrip-tion of light transport in tissue,” Ann NY Acad Sci. 9;838:1-13, 1998.


J O H N - P A U L H O S O MAssistant ProfessorPh.D., Computer Scienceand Engineering2000, Oregon GraduateInstitute of Science and [email protected]


Automatic speech recognition(ASR). Time alignment ofphonemes. Acoustic-phoneticanalysis of speech. Assistive technology.

R E P R E S E N TAT I V E P U B L I C AT I O N SHosom, J.P., “Automatic Speech

Recognition,” in H. Bidgoli, S. B. Eom,A. Prestage (Eds.), Encyclopedia ofInformation Systems. San Francisco:Academic Press, 2001.

Hosom, J.P. and Cole, R.A., “BurstDetection Based on Measurements ofIntensity Discrimination,” Proceedingsof ICSLP 2000, Beijing, vol. IV, pp. 564-567, October 2000.

Cosi, P. and Hosom, J. P., “HighPerformance General Purpose PhoneticRecognition for Italian,” Proceedings ofICSLP 2000, Beijing, vol. II, pp. 527-530, October 2000.

Hosom, J.P., Cole, R.A, and Cosi, P.,“Improvements in Neural-NetworkTraining and Search Techniques forContinuous Digit Recognition,”Australian Journal of IntelligentInformation Processing Systems (AJI-IPS), vol. 5, no. 4, pp. 277-284,Summer 1999, (invited paper).

Cole, R.A., Serridge, B., Hosom, J.P.,Cronk, A., and Kaiser, E., “A Platformfor Multilingual Research in SpokenDialogue Systems,” Proceedings of theWorkshop on Multi-LingualInteroperability in Speech Technology(MIST), Leusden, The Netherlands,September 1999.

Hosom, J. P. and Yamaguchi. M.,“Proposal and Evaluation of a Methodfor Accurate Analysis of Glottal SourceParameters,” The Institute ofElectronics, Information andCommunication Engineers (IEICE)Transactions on Information andSystems, vol. E77-D, no. 10, pp. 1130-1141, October 1994.

S E A N J . K I R K P AT R I C KAssociate ProfessorPh.D., Biomechanics University of Miami, [email protected]


Development and application ofcoherent light techniques toaddress issues in biomaterialsscience and tissue mechanics.Laser speckle techniques are ofparticular interest. Recentinvestigations have focused on theevaluation of the micromechanicalbehavior of vascular,dermatological, and skeletaltissues using novel laser specklestrain measurement methods. We envision that theseinvestigations will lead not only to an expansion of our basicscience understanding of tissuemechanics and laser-tissueinteraction, but will also result in optical instrumentation to assist in the diagnosis andtreatment of disease. Otherinterests include experimentalinvestigations into themicromechanics of syntheticbiomaterials used to replace or augment damaged orpathological tissue.

R E P R E S E N TAT I V E P U B L I C AT I O N SKirkpatrick, S.J. and Duncan,

D.D., Processing techniques for laser speckle data derived from biological tissues, J. Biomed. Optics (in press), 2001.

Kirkpatrick, S.J. and Duncan, D.D. Acousto-optic elastography,Proceedings SPIE 4257, 2001.

Patrickeyev, I., Kirkpatrick, S.J., andDuncan, D.D., Tracking speckle motionwith directional wavelets, ProceedingsSPIE 4257, 2001.

Kirkpatrick, S.J. and Cipolla, M.J., High resolution images laserspeckle strain gauge for vascular applications, J. Biomed Optics, 5(1):62-71, 2000.

Kirkpatrick, S.J. and Jacques, S.L.,Acoustically modulated speckle imagingof soft tissue, ASME BED vol. 43, 1999Advances in Bioengineering, Wayne,J.S. (Ed.), American Society ofMechanical Engineers, N.Y., 1999.

Kirkpatrick, S. J. Transform methodfor laser speckle strain rate measure-ments in biological tissues andbiomaterials. In “Light ScatteringTechnologies in Biomedicine andMaterials Science”, SPIE Press,Bellingham, WA, 1998.

Kirkpatrick, S.J. and Cipolla, M.J.High resolution imaged laser specklestrain gauge for vascular applications.J. Biomed. Optics (accepted), 1998.

Jacques, S.L. and Kirkpatrick, S.J. Acoustically modulated speckleimaging of biological tissue. Opt.Letters 23:879-881, 1998.

Kirkpatrick, S.J. and Brooks, B.W. Micromechanical behavior of cortical bone as inferred from laserspeckle data. J. Biomed. Mater. Res.3:373-379, 1998.

J A C K M c C A R T H YAssistant ProfessorPh.D., Materials Science and EngineeringOregon Graduate Institute ofScience and Technology, [email protected]


Mechanisms of change inmetallization and insulator thinfilms used in microelectronicapplications, in-situ testing ofthese films in transmission andscanning electron microscopes todevelop better processingtechniques and more reliable thinfilms. The development of focusedion beam processes for thefabrication of structures on themicron and sub-micron scales toproduce sensors and electro-mechanical devices for testing thephysical properties of sub-micronthin films. Thin film transmissivephotocatodes for use in multi-beam electron lithography andsurface reactions at the emissionsite. Materials characterizationtechniques using analyticalelectron microscopy and focusedion beam technology.

R E P R E S E N TAT I V E P U B L I C AT I O N SF. Radulescu, J.M.McCarthy, “The

Effect of Stress in the PdGe MediatedSolid Phase Epitaxial Growth of Ge onGaAs,” MRS Symposium Proceedings,Substrate Engineering for Epitaxy, 587, 1999.

F. Radulescu, J.M.McCarthy, E.Stach“In-Situ Annealing TransmissionElectron Microscopy of Pd/Ge/Pd/GaAsInterfacial Reactions,” MRS SymposiumProceedings, Advances in MaterialsProblem Solving with the ElectronMicroscope, 589, 1999.

J.McCarthy, Z. Pei, M.Becker,D.Atteridge “FIB MicromachinedSubmicron Thickness Cantilevers forthe Study of Thin Film Properties,” Thin Solid Films 358 (2000) p146-151.Accepted 8/31/99.

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S. Gosavi, J.M.McCarthy, C.N.Berglund, W.A.Mackie, L.A.Southall“Practical Gold Thin FilmPhotocathodes for Advanced ElectronBeam Lithography,” BACUS Symposiumon Photomask Technology, SPIEVol.3873, September 1999.

Z. ei, J.McCarthy, C.N.Berglund,T.H.P.Chang, M.Mankos, K.Y.LEE and M.L.Yu, “Thin Film GatedPhotocathode for e-Beam Lithography,”J.VAC.Sci.Technol.B 17(6), p2814, 1999.

J.M. McCarthy, SEM and TEMCharacterization of Materials Using a Focused Ion Beam MillingWorkstation, IMS ConferenceProceedings in MaterialsCharacterization.Accepted 1997.

M I S H A P A V E LProfessorPh.D., Experimental PsychologyNew York University, [email protected]


Analysis and modeling of complexbehaviors of biological systems,including visual and auditoryprocessing, pattern recognition,information fusion and decisionmaking. Development ofengineering systems mimickingthese abilities to supportmultimodal communicationbetween humans and machines(speech and video), machinevision, visually guided vehicularcontrol, and virtual reality.Applications of these techniques to the development of future biomedical andhealthcare systems.

R E P R E S E N TAT I V E P U B L I C AT I O N SJ. Palmer, P. Verghese, and M. Pavel,

The psychophysics of visual search,Vision Research, 40, 1227-1268, 2000.

Arai, T., Pavel, M., Hermansky, H.,and Avendano, C. Syllable intelligibilityfor temporally filtered LPC cepstraltrajectories, The Journal of theAcoustical Society of America, 105,2783-2791, 1999.

Sharma, R.K., Leen, T.K., and Pavel,M. Probabilistic image sensor fusion. InM.S. Kearns, S.A. Solla, and D.A. Cohn(Eds.), Advances in Neural InformationProcessing Systems 11. Cambridge,MA: MIT Press, 1999.

M. Pavel and H. Hermansky:“Information Fusion by Human andMachine,” in Proccedings of the FirstEuropean Conference on SignalAnalysis and Prediction, pp. 350-353,Prague, Czech Republic, June 1997.

M. Pavel & H.A. Cunningham, “Eye Movements and the Complexity of Visual Processing,” in M.S. Landy,L.T. Maloney and M. Pavel (Eds.),Exploratory Vision: The Active Eye,101-120 New York, NY, Springer-Verlag,1996.

H. Hermansky & M. Pavel,“Psychophysics of Speech EngineeringSystems,” invited paper, Proceedings of the 13th International Congress onPhonetic Science, Stockholm, Sweden,August 1995.

P. Suppes, M. Pavel & J. Falmagne,“C. Representations and Models inPsychology,” Annu. Rev. Psycho., 45, 517, 1994.

M. Pavel, “Predictive Control of Eye Movement,” in E. Kowler (Eds.),Eye Movement and Their Role in Visual and Cognitive Processes, 71-114, Amsterdam, Elsvier, 1990.

S C O T T A . P R A H LAssistant ProfessorPh.D., Biomedical EngineeringUniversity of Texas at Austin, [email protected]


Diagnostic and therapeuticapplications of light in medicine:laser thrombolysis, non-invasiveoptical diagnostics, hemostasisand tissue repair.

R E P R E S E N TAT I V E P U B L I C AT I O N SWadia Y, Xie H, Kajitani M, and Prahl

SA, Liver repair and hemorrhage con-trol using laser soldering of liquidalbumin in a porcine model, in SPIEProceedings of Lasers in Surgery, vol.3907, 74-81, 2000.

Viator JA, Jacques SL, and Prahl SA,Depth profiling of absorbing soft mate-rials using photoacoustic methods,IEEE Journal of Selected Topics inQuantum Electronics 5:989-996, 1999.

Viator JA and Prahl SA, Laserthrombolysis using long pulse frequen-cy-doubled Nd:YAG lasers, Lasers inSurgery and Medicine 25:379-388,1999.

Prahl SA, Denison T, and La Joie EN,Laser repair of liver, in Malek RS, ed.,SPIE Proceedings of Lasers in Surgery:Advanced Characterization,Therapeutics and Systems XI, vol. 4244, 2001.

Paltaulf G, Viator JA, Prahl SA,and Jacques SL, Iterative reconstruc-tion method for three-dimensionaloptoacoustic imaging, Journal of Acoustic Society of America (submitted).

Janis AD, Nyara AN, Prahl SA,Gregory KW, and Buckley LA, A reconstituted in vitro clot model forevaluating laser thrombolysis, Lasers in Surgery and Medicine, (submitted).

Moffitt TP and Prahl SA, Dual-sizedfiber reflectometry for measuring localoptical properties, IEEE Journal ofSelected Topics in QuantumElectronics, (submitted).

S H A N K A R R A N A N A VA R EAssociate Research ProfessorPh.D., Physical ChemistryUniversity of Missouri, St. Louis, [email protected]


Nanotechnology: Nanoparticlesand Photoresists, Dynamics ofcomplex systems, Ferroelectric,Antiferroelectric and AmphitropicLiquid Crystals, Flat PanelDisplays, Phase Transitions andCritical Phenomena.

R E P R E S E N TAT I V E P U B L I C AT I O N S

Ciro Di Meglio, S. B. Rananavare, S. Sorenson, D. H. Thompson, “Bolaamphiphilic Phosphocholines:Structure and Phase Behavior inAqueous Media,” Langmuir, 16, 128,2000.

V.G.K.M. Pisipati & S.B. Rananavare,“X-Ray Diffraction Studies of 10O.14and 10O.8,” Mol. Cryst. Liq.Cryst.,238,, 207-214, 1994.

J.H. Freed, A. Naveem & S.B.Rananavare, “ESR and Liquid Crystals:Statistical Mechanics and GeneralizedSmoluchowski Equations,” Chapter 4,71-84, “ESR and Molecular Motions inLiquid Crystals,” “Thermodynamics ofLiquid Crystals and the Relation toMolecular Dynamics: ESR Studies,”“ESR Studies of Molecular Dynamics atPhase Transitions in Liquid Crystals,”“ESR and Slow Motions in LiquidCrystals,” Chapters 12-15, 271-402,The Molecular Dynamics of LiquidCrystals, (G. R. Luckhurst and C. A. Veracini eds.), NATO ASI Series,Kluwer Academic Publishers,Netherlands, 1994.

S.B. Rananavare, V.G.K.M. Pisipati &E.W. Wong, “The ACC Multicritical Pointin Ferroelectric Liquid Crystals,” Phys.Rev. Lett, 72, 3558, 1994.

S.B. Rananavare, V.G.K.M. Pisipati & E.W. Wong, “A Lifshitz Point inFerroelectric Liquid Crystals,” LiquidCrystal Materials, Devices andApplications III, (R. Shashidhar, ed.),2175, 108-119, SPIE-94, San Jose, CA,Feb. 8-10, 1994.

V. G. K. M. Pisipati and S. B.Rananavare, “Interdigitated Smectic Aand B Mesophases in HigherHomologues of 50.m Series,” LiquidCrystals, 13,757-764, 1993.

M I LT O N R . S C H O L LAssociate ProfessorPh.D., Materials Science and EngineeringOGI School of Science and Engineering, [email protected]


Micro-mechanical systems andtheir design and use, particularlythe mechanics, the materials, andinteraction of contacting surfaces,i.e. tribology of microsystems.Tribological systems ranging fromchemical mechanical polishing, tofiber-plate interactions in chiprefining and woodcutting, towheel-rail interactions.Tribological performance ofmaterials including abrasive anderosive wear, sliding behavior,rolling / sliding conditions and theinteractions of the phenomenawith the working environment,focusing on surface response toexternal stimuli and mitigationtechniques to reduce or eliminatesurface damage.

R E P R E S E N TAT I V E P U B L I C AT I O N SM. Scholl, “Abrasive wear of titanium

nitride coatings,” Wear, Vol. 203-204,57- 64, 1997.

M. Scholl, “Unique Thermal SprayCoatings by High Energy PlasmaSpraying,” Proceedings of theInternational Conference on Advancesin Welding Technology: Joining of HighPerformance Materials, Columbus,Ohio, Nov. 6-8, 1996.

D. Christensen, Y. Jia, M. Scholl, P. Clayton, & S. Abubakr, “SurfaceDeterioration of Refiner Plates forThermo-Mechanical Pulping,”Proceedings of the 1994 PulpingConference, Nov. 6-10, 1994, SanDiego, California, pub. by TAPPI Press,Atlanta, 1994, pp. 193-203.

M. Scholl, “Plasma Spraying with WireFeedstock,” Proceedings of the 1994National Thermal Spray Conference,Boston, MA, June 1994.

M. Scholl, C. Steinkamp & W.E. Wood,“Acoustic Emission Monitoring ofPlasma Sprayed Tubes,” EWI ResearchReport, 1994.

M. Scholl & P. Clayton, “SurfaceTexture and Abrasive Wear Resistanceof Some High Velocity Air PlasmaSprayed Coatings,” Proceedings of the1991 National Thermal SprayConference, Pittsburgh, PA, May 1991.

R A J S O L A N K IProfessorPh.D., PhysicsColorado State University, [email protected]


Atomic Layer Deposition, copperelectrodeposition andelectromigration, multilevelmetallization, high k gatedielectrics, inorganic and organicelectroluminescent devices,polysilicon thin film transistors.

R E P R E S E N TAT I V E P U B L I C AT I O N SH. Zhang and R. Solanki, Atomic Layer

Deposition of High Dielectric ConstantNanolaminates, J. Electrochem. Soc.63, 148, 2001.

(Invited paper) B. Pathangey and R. Solanki, Atomic layer deposition fornanoscale thin film coatings, VacuumTech. and Coatings, 1 , 32, 2000.

R. Solanki and B. Pathangey, AtomicLayer Deposition of Copper SeedLayers, Electrochem and Solid-StateLetters, 3 , 479, 2000.

H. Zhang, R. Solanki, B. Roberds, G. Bai, and I. Banerjee, HighPermittivity Thin Film Nanolaminates, J. Appl. Phys. 87, 1921, 2000.

A.T. Voutsas, M.A. Marmorstein, and R. Solanki, The Effect of LaserAnnealing Ambient on the Performanceof Excimer Laser Annealed Thin FilmTransistors,î J. Electrochemical Soc.146 , 3500, 1999.

R. Engelmann, J. Ferguson, andR.Solanki, “Quantum Well ActivatedPhosphors-A New Concept forElectroluminescent Displays,” Appl.Phys. Lett. 70, 411, 1997.

J. Fogarty, W. Kong, and R.Solanki,”Monte Carlo Simulation ofHigh Field Electron Transport in ZnS,”Solid-State Electronics, 38, 653, 1995.

W. Kong and R. Solanki, “The Effect of Ultraviolet Radiation on a ZnS:TbThin Film Electroluminescent Device,”J. of Appl. Phys.75, 3311, 1994.

T. Dosluoglu and R. Solanki, “Self-Consistent Calculations of CarrierDistribution and Energy Bands inInGaAs/InP PIN Diodes,” Solid StateComm., 85, 243, 1993.


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X U B O S O N GAssistant ProfessorPh.D., Electrical EngineeringCalifornia Institute of Technology, [email protected]

R E S E A R C H I N T E R E S T S :

Digital Image/Video Processing;Sensor Fusion; Computer Vision;Pattern Recognition; MachineLearning; Information Theory andCoding; Biomedical Engineering.

R E P R E S E N TAT I V E P U B L I C AT I O N SXubo Song, Yaser Abu-Mostafa, Joseph

Sill, Harvey Kasdan, “Image Recognitionin Context: Application to MicroscopicUrinalysis,” in Advances in NeuralInformation Processing Systems, S.A. Solla, T.K. Leen and K.-R.Muller,Editors, MIT Press, pp. 963-969, 2000.

Xubo Song, Yaser Abu-Mostafa, Joseph Sill, Harvey Kasdan,“Incorporating Contextual Informationinto White Blood Cell ImageRecognition,” in Advances in NeuralInformation Processing Systems, M.I.Jordan, M.J. Kearns and S.A. Solla,Editors, MIT Press, pp. 950-956, 1998.

Yaser Abu-Mostafa, Xubo Song, “Bin Model for Neural Networks,” in Proceedings of the InternationalConference on Neural InformationProcessing, S. Amari, L. Xu, L. Chan, I. King and K. Leung, Editors, Springer,pp. 169-173, 1996.

Xubo Song, “Contextual PatternRecognition with Applications toBiomedical Image Identification,” PhD Thesis, California Institute ofTechnology, 1999.

Yaser Abu-Mostafa, Xubo Song,Alexander Nicholson, Malik Magdon-Ismail, “The Bin Model,” under revisionfor IEEE Transactions on InformationTheory, 2001.

Xubo Song, “Pattern Recognition inContext,” to be submitted to IEEETransactions on Pattern Analysis andMachine Intelligence, 2001.

Xubo Song, “Contextual BiomedicalImage Recognition,” to be submitted to IEEE Transactions on BiomedicalEngineering, 2001.

Malik Magdon-Ismail, Xubo Song,“Effective Choice of Weight DecayParameters,” to be submitted to NeuralComputation, 2001.

J A N P. H . VA N S A N T E NProfessor and Center Directorof CSLUPh.D., Mathematical PsychologyUniversity of Michigan, [email protected]


Speech timing, intonation, signalprocessing, statistical analysis oftext and speech corpora, and text-to-speech (TTS) system evaluation.

R E P R E S E N TAT I V E P U B L I C AT I O N SGu W., Shih C., and van Santen J.

“An Efficient Speaker AdaptationMethod for TTS Duration Model”.Proceedings of EUROSPEECH 99,Budapest, Hungary, 1999.

van Santen J., and Sproat R., “High-accuracy automatic segmentation”.Proceedings of EUROSPEECH 99,Budapest, Hungary, 1999.

Sproat R., van Santen J., “AutomaticAmbiguity Detection.” Proceedings ofICSLP 98. Sydney, Australia, 1998.

van Santen J. “Evaluation.” InMultilingual Text-to-Speech Synthesis:The Bell Labs Approach Kluwer,Dordrecht, 1998.

van Santen J., Sproat R.W., Olive J.,and Hirschberg J. (Eds.). Progress inspeech synthesis. Springer Verlag, New York, 1996.

E R I C A . W A NAssociate ProfessorPh.D., Electrical EngineeringStanford University, [email protected]


Learning algorithms andarchitectures for neural networks and adaptive signalprocessing; applications to time-series prediction, speechenhancement, adaptive control,and telecommunications.

R E P R E S E N TAT I V E P U B L I C AT I O N SE. A. Wan and R. van der Merwe,

The Unscented Kalman Filter. InKalman Filtering and Neural Networks,chap. Chapter 7, Wiley Publishing, Eds.S. Haykin, 2001.

E. Wan & A. Nelson, “Networks forSpeech Enhancement,” in Handbook of Neural Networks for SpeechProcessing, Edited by Shigeru Katagiri,Artech House, Boston, USA, 1999.

E. Wan & F. Beaufays, “DiagrammaticMethods for Deriving and RelatingTemporal Neural Networks Algorithms,In Adaptive Processing of Sequencesand Data Structures,” Lecture Notes in Artificial Intelligence, M. Gori & C.L. Giles (eds.), Springer Verlag,1998.

E. Wan and A. Nelson, “Neural Dual Extended Kalman Filtering:Applications in Speech Enhancementand Monaural Blind Signal Separation,”IEEE Workshop on Neural Networksand Signal Processing, 1997.

E. Wan, “Adjoint LMS: An Alternativeto Filtered-X LMS and Multiple ErrorLMS,” ICASSP96, 3, 1842-1845, 1996.

E. Wan, “Time Series Prediction Usinga Neural Network with EmbeddedTapped Delay-Lines,” in Predicting theFuture and Understanding the Past, A.Weigend and N. Gershenfeld (eds.), SFIStudies in the Science of Complexity,Proc., 17, Addison-Wesley, 1993.

E. Wan, “Discrete Time NeuralNetworks,” Journal of AppliedIntelligence, 3(1), 91-105, 1993.

E. Wan, “Neural NetworkClassification: A BayesianInterpretation,” IEEE Transactions on Neural Networks, 1(4), 303-305,December 1990.

Y O N G H O N G YA NAssociate Professor Ph.D.,Computer Science& Engineering, [email protected]


Human computer interface design, spoken language system,large vocabulary speechrecognition, computer vision, real time embedded system,speech signal processing.

R E P R E S E N TAT I V E P U B L I C AT I O N SX. Wu & Y. Yan. Linear regression

under maximum a posteriori criterionwith markov random field prior. In proceedings IEEE ICASSP2000, June 2000.

C. Liu and Y. Yan. Speaker changedetection using minimum messagelength criterion. In proceedings 6thInternational Conference on SpokenLanguage Processing, vol 3. pp 514-515, October 2000.

C. Zheng, Y. Yan. Efficiently UsingSpeaker Adaptation Data. In proceed-ings ICSLP, 2000.

Y. Yan. Speech Recognition using cor-relation generated neural networktarget. IEEE Trans. on Speech andAudio Processing, May 1999.

E. Barnard,Y. Yan. Toward new language adaptation for language identification. Speech Communication,21(4):245-254, May 1997.

Y. Yan, E. Barnard, R.A. Cole.Development of an Approach toAutomatic Language Identificationbased on Phone Recognition. InComputer, Speech Language, Volume10(1), pp. 37-54, January 1996.

JOINT FACULTYAPPOINTMENTS

R O B D A A S C H

Electrical EngineeringPortland State University

J A C K F E R R A C A N E

School of DentistryOregon Health & Science University

A N D R E W F R A S E R


T O D D L E A N

Computer Science and EngineeringOGI School of Science & Engineering

S H I H - L I E N L U

Computer ScienceOregon State University

J O H N E . M O O D Y

Computer Science and EngineeringOGI School of Science & Engineering

N E L S O N M O R G A N

Electrican Engineering &Computer SciencesUniversity of California

M I N G D E YA N

ChemistryPortland State University

ADJUNCT FACULTY

J O H N C . A B E L E

Lewis and Clark College

S H A R I A R S . A H M E D

Intel Corp.

C H E D L E Y A O U R I R I

Intel Corp.

A H M E D R A H H A L - A R A B I

Intel Corp.

S H E K H A R B O R K A R

Intel Corp.

S T E V E B R A I N E R D

Integrated Device Technology, Inc.

R O B C O N T O L I N I

Novellus

A L A N C O P P O L A

Cypress Semiconductor, Inc.

D O U G L A S C . D R A P E R

Portland Community College

S T E P H E N R . E A R LY

Consultant

Y O U S S E F A . E L - M A N S Y

Intel Corp.

R E I N H A R T E N G L E M A N N

Consultant

D A V I D E VA N S

Sharp MicroelectronicsTechnology Inc.

W AY N E K . F O R D

Intel Corp.

M A R K F R A N K

Conexant

R . T H O M A S H A W K I N S I I

Consultant

H O W A R D H E C K

Intel Corp.

D A E M A N N K I M

Pohang Institute of Science & Tech., Korea

R I C H A R D Y. K O YA M A

TriQuint Semiconductor Inc.

R O Y K R A V I T Z

Radisys Corporation

W I L L I A M A . M A C K I E

Linfield College

V. D A K S H I N A M U R T Y

University of Portland

H A M I D R A B I E E

Intel Corp.

K A R T I K R A O L

Intel Corp.

E D W A R D F. R I T Z , J R .

Consultant

L A W R E N C E R U B Y

University of California, Berkeley

LY N W O O D W. S W A N S O N

FEI Co.

S T E W A R T S . TAY L O R

Maxim

T H O M A S T H O M A S

Intel Corp.

T R A N T H O N G

Microsystems Engineering, Inc.

J A M E S A . VA N V E C H T E N

Transient Thermal Processing


65

Global pos i t ion ing system (GPS) technology isan important component of f ie ld- invest igat ionac i t iv i t ies in the department ’s curr icu lum.

Department ofEnvironmental Science

and Engineeringwww.ese.ogi.edu


A n t ó n i o M . B a p t i s t a



Therese Young


E S E G E N E R A L I N Q U I R I E S

E-mail: [email protected]

THE DEPARTMENT OF ENVIRONMENTAL

SCIENCE AND ENGINEERING is one of theoldest stand-alone environmental andengineering programs in the country.Founded more than 25 years ago, weare known for our research andgraduate education programs thatbalance practical applications withfundamental investigations of thephysical, chemical, and biologicalprocesses underlying environmentalphenomena. The curriculum is highlyinterdisciplinary and is built on asolid foundation of fundamentalscience and engineering.The department offers graduate study leadingto the degrees of Doctor of Philosophy (Ph.D.)and Master of Science (M.S.). M.S. programsare offered with both thesis and non-thesisoptions. All programs may be pursued on afull-time or part-time basis. Ph.D. studentsand M.S. thesis students participate in aprogram that includes both formal coursework and research. The research experienceis intensive and consists of laboratory,computational, theoretical and/or fieldstudies. Thesis students are involved in allaspects of departmental research and haveready access to modern analyticalinstrumentation and computers.

The Ph.D. program can be completed in 4 to5 years, and the M.S. thesis option takesapproximately 2 years to complete. Thesisstudents can concentrate their studies in thefollowing areas:

• Environmental Science and Engineering (ESE)(traditional program)

• Environmental Information Technology (EIT)

The non-thesis M.S. program can becompleted in 12 months. Students in the non-thesis M.S. program can concentrate theirstudies in the following areas:

• Environmental Science and Engineering (ESE)(traditional program)

• Ecosystem Management and Restoration (EMR)

• Environmental Information Technology (EIT)(beginning Fall 2002)

ADMISSION REQUIREMENTS Applications for admission to full-time and

part-time degree programs are invited frompersons with bachelor’s degrees in thephysical or biological sciences, mathematics,or engineering. Previous course work inchemistry, biology, and mathematics (throughat least one year of calculus) is expected.

Requirements for admission to theDepartment of Environmental Science andEngineering are the same as the OGI Schoolof Science and Engineering’s admissionrequirements, except for the minimumTOEFL score. The department requiresTOEFL scores of all applicants whose nativelanguage is not English. The minimumacceptable TOEFL score is 600 for thewritten test or 250 for the computer-basedtest. Students who earned undergraduatedegrees in the United States are not requiredto submit TOEFL scores. GRE generalaptitude scores are required for admission toall of the department’s M.S. and Ph.D.programs. A GRE subject examination scoreis not required.

Completed Ph.D. applications should bereceived by February 15 for matriculationin the fall of the same year. M.S. applicationsare accepted year-round, although mostnew M.S. students apply by July formatriculation in the fall. Prospectiveapplicants for the Ph.D. program shouldexamine the faculty research programs athttp://www.ese.ogi.edu/people.html todetermine whether their professional goalscan be fulfilled in the department.Communication with individual facultymembers prior to applying is encouraged.

DEGREE REQUIREMENTSDISTRIBUTION REQUIREMENTS

To achieve the necessary breadth in training,students in all programs take courses that cover arange of scientific disciplines and environmentalmedia. Five courses must be taken that satisfy thefollowing distribution requirements. No course cansatisfy more than one requirement.

At least one course must be taken from three of thefollowing four discipline groups:

Applied Mathematics ESE500; ESE504; ESE506; ESE508

Chemistry ESE510; ESE511; ESE514; ESE516

Fluid Dynamics ESE520; ESE530; ESE537; ESE539

Biology ESE550; ESE554

And, at least one course must be taken from eachof the following environmental media groups:

Surface Waters ESE520; ESE530; ESE537; ESE539

Ground Water ESE540; ESE541; ESE542; ESE543

E S E | E N V I R O N M E N TA L S C I E N C E A N D E N G I N E E R I N G

68

All full-time students are required to takeEnvironmental Science Seminar (ESE599)during the Fall, Winter, and Spring quarters.However, this course does not count towarddegree credit requirements.

For all ESE educational programs, up to 8credits may be granted for courses taken inother OHSU departments. Up to 12 quartercredits may be transferable from otheraccredited institutions for graduate coursescomparable in content and level to coursesoffered in the department. The StudentProgram Committee (SPC) decides onthe appropriateness of internship andtransfer credits.

Transfer credits do not reduce the annualtuition, but may allow for greater flexibilityin scheduling.

P H . D . I N E N V I R O N M E N TA L S C I E N C E

A N D E N G I N E E R I N G

Students may complete the Ph.D. programin Environmental Science and Engineering(ESE) or Environmental InformationTechnology (EIT). The EIT program is a trackwithin the ESE Department. Students whocomplete the EIT program receive theirdegree in Environmental Science andEngineering with a concentration in EIT.

Ph.D. students must complete 5 distributioncourses as outlined above. Students mustalso complete additional courses for a totalof at least 52 credit hours of course work,selected with the approval of their SPC.

Ph.D. candidates must also pass a two-partcomprehensive exam. The first part is awritten examination covering four subjectareas selected by the department. The second part is the preparation and oraldefense of a proposal that defines thestudent’s Ph.D. dissertation research. Awritten Ph.D. dissertation with an oraldefense is also required.

M . S . I N E N V I R O N M E N TA L S C I E N C E

A N D E N G I N E E R I N G

M . S . T H E S I S O P T I O N S

Students may pursue M.S. thesis optionsin Environmental Science and Engineering(ESE) or, beginning Fall 2002, EnvironmentalInformation Technology (EIT). The EITprogram is a track within the ESEDepartment. Students who complete the

EIT program receive their degree inEnvironmental Science and Engineering witha concentration in EIT.

Students pursuing the M.S. thesis optionmust complete at least 45 credits. Thesecredits include the distribution requirementsoutlined above, additional courses selectedwith the approval of the SPC, and researchcredits. Master’s thesis research (ESE 700)is usually no more than 9 credits.Comprehensive examinations are notrequired of M.S. thesis students. However, awritten M.S. dissertation with an oral defenseis required.

M . S . N O N - T H E S I S O P T I O N S

Students may pursue the M.S. non-thesisoptions in Environmental Science andEngineering (ESE), Ecosystem Managementand Restoration (EMR) or, beginning Fall2002, Environmental Information Technology(EIT). The EMR and EIT programs are trackswithin the ESE Department. Students whocomplete the EMR or EIT programs receivetheir degree in Environmental Science andEngineering with a concentration in EMRor EIT.

For the non-thesis M.S. degree, 5 distributioncourses must be taken as outlined above.Students must complete additional coursesfor a total of at least 45 credit hours. Upto 8 credits may be granted for approvedparticipation in non-thesis research orapproved work as an intern with a localcompany or government agency. Nocomprehensive examinations are requiredfor the non-thesis M.S. options.

DEGREE PROGRAMS

ENVIRONMENTAL SCIENCE AND ENGINEERING (ESE)

( T R A D I T I O N A L P R O G R A M )

The department offers Ph.D., M.S. thesis, andM.S. non-thesis options in EnvironmentalScience and Engineering (ESE). The ESEprogram is known for its research andeducation programs that balance practicalapplications with fundamental investigationsof the physical, chemical, and biologicalprocesses underlying environmentalphenomena. The curriculum is highlyinterdisciplinary and is built on a solidfoundation of fundamental science andengineering. For more information, pleasesee http://www.ese.ogi.edu/curriculum.html.

E C O S Y S T E M M A N A G E M E N T

A N D R E S T O R AT I O N ( E M R )

The Ecosystem Management and Restoration(EMR) program is a 12-month, non-thesisM.S. track offered within the Department ofEnvironmental Science and Engineering. Theobjective of the EMR program is to integraterigorous environmental principles, field andlaboratory applications, modeling, projectmanagement, and policy/regulation into acohesive curriculum. The program emphasisis on timely issues, including nonpointsource pollution, water quality, andecological and human risk assessments.For more information, please seehttp://www.ese.ogi.edu/EMR/. Requirementsfor the EMR program are the same as for thenon-thesis M.S. option described above,except that students must include ESE570and ESE589 in their elective course work.

E N V I R O N M E N TA L I N F O R M AT I O N

T E C H N O L O G Y ( E I T )

The Environmental Information Technology(EIT) program is the newest program offeredwithin the Department of EnvironmentalScience and Engineering. The Ph.D. option inEIT began Fall 2001, and the M.S. thesis andnon-thesis options in EIT will begin Fall2002. The EIT program combines theexpertise and coursework found in ESE andin the Computer Science and Engineering(CSE) and Electrical and ComputerEngineering (ECE) Departments at the OGISchool of Science and Engineering. The goalof the EIT program is to combine a deepunderstanding of environmental processeswith mastery of sensing, modeling, andinformation technology. Requirements for theEIT program are the same as the thesis andnon-thesis options described above, exceptthat students in the EIT program completeapproximately 20% of their coursework in theCSE and ECE Departments. The EITcurriculum includes fundamental courses,science courses, technology courses, electivecourses, and capstone integrative courses.Elective courses may include classes offeredthrough OHSU’s Medical Informaticsprogram. For more information on the EITprogram and its curriculum, please seehttp://www.ese.ogi.edu/EIT/.

A N O T E A B O U T T U I T I O N

Tuition for the full-time non-thesis M.S.program is $19,620 for the 2001-2002

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E N V I R O N M E N TA L S C I E N C E A N D E N G I N E E R I N G | E S E

academic year, which is typically spreadequally over the first four quarters. Uponadmission to the department, a $100 depositis required with the return of a student’sacceptance to reserve a place in thedepartment. This deposit will be appliedtoward tuition and is non-refundable.

COURSE OFFERINGSESE500 Introduction to Discrete MethodsThis course is an introduction to discrete methodsfor environmental fluid dynamics. Lectures coverthe theory and application of the numerical solutionof boundary-value and mixed initial-boundary valueproblems. Emphasis is on finite differences, finiteelements and finite volumes. Prerequisites: Calculus.new for 2002/2003 4 credits

ESE504 Uncertainty AnalysisA survey of basic probability concepts followed byintroductions to several statistical advanced tech-niques that play an important role in environmentaldata analysis. Topics may include distribution func-tions, propagation of error, hypothesis testing,analysis of variance, experimental design, samplingtheory, regression analysis, time-series analysis,and spatial statistics techniques. The course pro-vides a balance of theory and application usingenvironmental data sets.not offered 2001/2002 4 credits

ESE506 Environmental Systems AnalysisIntroduction to techniques of systems analysisapplied to environmental quality management.Emphasis is placed on development and applicationof mathematical models with computer simulationand optimization. Analysis is efficient computationalalgorithms and search techniques. Linear and sepa-rable programming applied to evaluate managementalternatives. Applications to air, water, solid, andhazardous waste management. Prerequisites:Computer programming and calculus. not offered 2001/2002 4 credits

ESE508 Computational Fluid DynamicsThis course describes advanced topics in computa-tional fluid dynamics, including specialized discretemethods (e.g., for advection-dominated problems),formal analysis of stability and accuracy, and select-ed simulations of complex environmental andbiological systems. Prerequisites: Advanced calcu-lus and ESE 500. new for 2003/2004 4 credits

ESE510 Aquatic Chemistry General acid/base concepts (mono- and polyproticsystems); activity corrections; numerical calcula-tions; titration concepts as applied to naturalsystems; buffer intensity; dissolved CO2 chemistry;pH, acidity, and alkalinity in open CO2 systems;minerals and their role in controlling natural waterchemistry; solubility characteristics of oxide andhydroxides; redox chemistry in natural systems;pe-pH diagram. 4 credits

ESE514 Distribution and Fate of Organic PollutantsDiscussion of the physico-chemical processes thatcontrol the behavior and fate of organic chemicals inthe environment. Introduction considers all environ-mental compartments, water, soil, and air, andpartitioning between those phases. Recommendedprerequisite: ESE 510. 4 credits

ESE516 Chemical Degradation and RemediationA thorough introduction to the transformation reac-tions that contribute to the fate of organicsubstances in the environment. The course coverspathways, mechanisms and kinetics of hydrolysis,oxidation, reduction, elimination, conjugation, etc.Treatment is balanced to reflect the importance ofthese processes in all types of environmental watersranging from engineered systems to groundwater,surface water, rain, and fog. Recommended prepa-ration: ESE 510 and ESE 514. 4 credits

ESE519 Air Pollution: Origins, Chemistry, and ControlThis course will focus on tropospheric air pollutionwith particular emphasis on the urban and regionalscales. It will discuss the following items: basicstructure of the atmosphere and relevant meteoro-logical considerations; sources of tropospheric airpollutants; atmospheric photochemistry; the ozone,oxide of nitrogen, and hydrocarbon chemical cycles;chemistry of toxic organic compounds in the atmos-phere; gas and aqueous phase chemistry of sulfurdioxide; size distributions, lifetimes, origins and for-mation mechanisms of aerosols; and control ofatmospheric emissions. 3 credits

ESE520 Introduction to Environmental Observation andForecasting SystemsThis course introduces environmental observationand forecasting systems and their applicationtowards the enhanced understanding and manage-ment of natural resources. Emphasis is on estuariesand coasts. Students are exposed to a novel, cross-disciplinary culture for understanding andinteracting with environmental systems. This cul-ture relies heavily on “real-time” generation ofmodeling and observational data, which are inte-grated and distributed through informationnetworks designed to bring the right environmentalinformation at the right time to the right user.Prerequisite: Instructor permission. 4 credits

ESE522 Introduction to Spatial SciencesStudents will learn theoretical and practical appli-cations of geospatial sciences within the context ofEnvironmental Sciences and Engineering. Theory ofsatellite-based Geographic Positioning Systems(GPS) will be studied while performing practical,hands-on laboratory experiments using the latest inGPS equipment. Classroom discussions will thenfocus on relating location on the Earth’s surface to acommon mapping grid. Non-projected and projectedmaps, ellipsoids and spheroids, and geoids will bediscussed. Spatial relationships, or analysis, of con-tinuous and categorical data will be addressedthrough the application of standard statistics andprobability. ARCVIEW, a popular GeographicInformation System (GIS) software tool willbe stressed. 4 credits

ESE523 Introduction to Remote Sensing ofthe EnvironmentThis course will explore the acquisition, analysisand visualization of remotely sensed data. Thephysics behind the collection of remotely senseddata will be introduced as will both airborne-plat-form and satellite-platform sensors. Data from theLight Detection and Ranging (LIDAR) sensor as itpertains to Airborne Topographic Mapping will beused. Single band, multi-spectral and hyper-spectraldata sets will be used to discuss such concepts asimage statistics, radiometric and geometric correc-tions, spatial filtering and special transformationslike the Normalized Difference Vegetation Index.Supervised and Unsupervised classificationschemes will be discussed as will change detection.The course pedagogy is designed to address theneeds of the advanced level Environmental Scienceand Engineering graduate student. While there is noprerequisite for this course, many topics fromESE522, Introduction to Spatial Science are incor-porated into this course. It is thereforerecommended that students unfamiliar with classifi-cation methods and the fundamental concepts ofGeographic Information Systems complete ESE522or equivalent. 4 credits

ESE530 Transport ProcessesAn introductory course in the physics of transportprocesses in the natural environment. The courseexamines heat, mass, and momentum transport viaconservation principles and the Reynolds TransportTheorem, but strongly emphasizes the environmen-tal applications of these processes. Example studiesinclude atmospheric and oceanic circulation, flowand dispersion in rivers, and heat budgets for lakesand reservoirs. 4 credits

ESE532 Modeling Coastal Circulation and Transport I This course introduces the students to the processof modeling coastal circulation and transport. Topicsinclude governing equations, review of state-of-the-art models, in-depth description of selected models,and solution of benchmark problems. Prerequisites:ESE500 or ESE508, and ESE530.new for 2001/2002 4 credits

ESE533 Modeling Coastal Circulation and Transport IIThis course provides an advanced treatment ofcoastal circulation and transport modeling. Studentsare introduced to the detailed modeling of complexestuarine, plume, and continental shelf processes,through a combination of lectures and labs focusedon specific sites and processes. Prerequisites:ESE532.new for 2002/2003 4 credits

ESE534 Modeling Coastal Flow and TransportDescription of state-of-the-art modeling principlesand techniques for simulation of flow and of conser-vative and nonconservative transport in coasts andestuaries. Students have the opportunity to modelan actual coastal system through a hands-on termproject that includes a realistic sequence ofmodeling steps: data analysis, grid generation,flow modeling, modeling of conservative transport,and modeling of nonconservative transport.Prerequisites: ESE 500, ESE 532.not offered 2001/2002 4 credits

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ESE537 Methods in OceanographyThis course covers the fundamentals of processingestuarine and coastal oceanographic data, includingtime series (e.g., surface elevation, currents, andwinds) and data obtained from vessels (e.g., profileand bathymetric data).not offered 2001/2002 2 credits

ESE539 Methods in Estuarine Oceanography:Field ObservationThis course covers the fundamentals of estuarineand coastal oceanographic data collection using ves-sels and remotely moored equipment. Topics includevessel logistics and sampling, navigation systems,interfacing of instruments with personal computers,types of moorings and their deployment and recov-ery, and telemetry.not offered 2001/2002 2 credits

ESE540 Subsurface HydrologyHydrologic cycle infiltration theory; principles ofunsaturated and saturated flow in the subsurface;well hydraulics; analytical models of drawdown,capture zones and velocity plots; porous mediacharacterization methods and tools. 4 credits

ESE541 Groundwater ModelingApplied groundwater modeling using finite differ-ence and finite element methods. Introduction tonumerical methods for solving the partial differen-tial equations for saturated and unsaturatedsubsurface flow. Model execution and calibration.Prerequisite: ESE 540.not offered 2001/2002 4 credits

ESE542 Contaminant HydrologyProcesses controlling subsurface contaminantmovement in porous and fractured media, includinggroundwater flow, dispersion, diffusion, sorption,and degradation. Parameter estimation, math-ematical and laboratory modeling of aquifers isalso covered. 4 credits

ESE543 Modeling in Contaminant HydrogeologyThis course is designed to be taken concurrentlywith ESE 542. It emphasizes the hands-on use ofcommon mathematical models for groundwater flowand transport (e.g., MODFLOW, RANDOMWALK,SUMATRA) to examine real groundwater contamina-tion problems. Prerequisite: ESE 542.not offered 2001/2002 4 credits

ESE550 Environmental MicrobiologyIntroduction to environmental microbiology, withemphasis on the role of microbes in the environmentand in remediation processes. Microbes and theirinteraction and activities in soil and aquatic envi-ronments will be discussed, as well as elementalcycling as influenced by microbes. Microbially-mediated transformation of organic pollutants,transformation kinetics, and remediation technolo-gies will be considered. 4 credits offered in combination with ESE554 in 2001/2002

ESE554 Biodegradation and BioremediationA process-oriented survey of microbially mediatedtransformations of organic pollutants.Transformations occurring in the natural environ-ment as well as in remediation technologies areconsidered. Emphasis is on the pollutant properties,

micro-biological factors, and medium propertiesthat determine the pathways and kinetics of bio-degradation. Recommended preparation: ESE 550.

4 creditsoffered in combination with ESE 550 in 2001/2002

ESE560 Environmental Soil ScienceSoil physics, chemistry, and microbiology; soildevelopment, soil description and mapping, soilsand land use, agricultural and urban forestry; soil-plant relationships for environmental restoration;soil process modeling. Prerequisites: ESE 510 andESE 550. not offered 2001/2002 4 credits

ESE562 Ecosystem EcologyPrinciples of ecology and of ecosystem process,description, and measurement, with emphasis on ecosystem health assessment. Simulation modeling of ecosystem processes; transport and transformation.not offered 2001/2002 4 credits

ESE570 Principles of Toxicology and Risk AssessmentThis course applies toxicological principles to bothhuman and ecological risk assessments. The princi-ples and methodologies for risk assessments arepresented within a regulatory context. Topicsinclude hazard identification, exposure assessment,LD50, dose-response relationships, deterministicand probabilistic risk assessments, responses ofvarious receptors to different contaminants, andenvironmental management decisions. 3 credits

ESE58X Special TopicsTypically involves a scholarly and critical review ofan advanced scientific topic by one or more studentstogether with one or more faculty members.Requirements of the student typically include a writ-ten review paper and/or a seminar to be given aspart of ESE 599. Selection of this course for creditand the topic to be investigated must be approved bythe Student’s Program Committee.


ESE580 Ecosystem Management and RestorationThis course will provide an overview of ecosystemmanagement and restoration at the local and region-al scale. It will follow the hydrologic cycle fromupland watersheds through streams, rivers andestuaries to the ocean and will track important sys-tem parameters such as water flow andtemperature. 4 credits

ESE586 Environmental Law and RegulationA survey of environmental law and regulation con-cepts essential to practicing scientists andengineers. Topics covered include the theory andpractice of environmental regulation, environmentallitigation, and legislation including Superfund(CERCLA), the Clean Water Act, the ResourceConservation and Recovery Act (RCRA), the CleanAir Act, and the Toxic Substances Control Act(TSCA). 3 credits

ESE587 Clean Air Act Laws and RegulationsA thorough introduction to the Clean Air Act in itsfederal and state permutations, as well as thedetailed regulations guiding the Act’s implementa-tion. The course focuses on the practical aspects of

statutory and regulatory interpretation, applicationto specific facilities, and negotiation of Clean Air Actissues with EPA and the states not offered 2001/2002 2 credits

ESE589 Special Topics: Advanced Topics in FieldSampling and AnalysisAn intensive capstone course that integrates fieldprocesses with theory from previous lecture materi-al. Approximately 1 week is spent at site locationswhere students critically examine current tech-niques for collecting surface water, groundwater,and soil samples to characterize chemical, biologi-cal, and physical properties. Laboratory methodsfor analyzing organic and inorganic chemicals areincluded. Students work in teams on projects to col-lect and evaluate data, write reports, and makerecommendations for future management of thesites. Anticipate overnight travel. Variable credit

ESE598 Organization of Environmental Science andEngineering SeminarThis course is for the Ph.D. student responsible formanaging the weekly Environmental Science andEngineering Seminar series (ESE599). Studentsenroll for this course with their advisor’s approval.

1 credit

ESE599 Environmental Science SeminarWeekly seminars by invited guests on all aspects ofenvironmental science, and by ESE faculty and stu-dents on their research. Visitors are welcome.Schedules are available on the World Wide Web athttp://www.ese.ogi.edu/seminars/, or by request [email protected]. 1 credit

ESE600 ResearchResearch toward the dissertation for the Ph.D.degree before completing the comprehensive exam-inations. Variable and repetitive credit

ESE610 Non-Thesis ResearchSupervised research as a component of the non-the-sis M.S. degree. The plan of research and finaldeliverables must be approved by the research advi-sor and the Student Program Committee.Deliverables include a written report and/or semi-nar given as part of ESE 599. A maximum of 8credits from ESE 610 and ESE 620 can be appliedto a degree. Variable and repetitive credit

ESE620 Professional InternshipThis course provides the student with an opportuni-ty to earn credit for relevant work experience inindustry. Students gain valuable experience thatallows them to both apply the knowledge gained inthe classroom and prepare for their future careers.

Enrollment requires a faculty advisor and is limitedby the number of internship opportunities available.International students need to submit appropriatepaperwork for the Immigration and NaturalizationService. A maximum of 8 credits from ESE 610 andESE 620 can be applied to a degree.


ESE700 M.S. Thesis ResearchResearch toward the M.S. thesis degree. Variable and repetitive credit

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ESE800 Ph.D. Dissertation ResearchResearch toward the dissertation for the Ph.D.degree after completing the comprehensive exami-nations. Variable and repetitive credit

RESEARCH PROGRAMSContaminant Diffusion in ClayClay liners are often used in waste disposalfacilities to prevent the advective transport ofcontaminants into the surrounding groundwater.Even when advective transport is small, however,contaminant transport through liners may be sig-nificant as the result of molecular diffusion. Thisphenomenon has been studied in the laboratoryand at actual waste disposal facilities to evaluateits roles in mass transport and groundwater con-tamination. Johnson

Processes Controlling the Subsurface Transportof Dense Chlorinated SolventsThe uncontrolled release of chlorinated solvents isa common cause of serious groundwater contami-nation in many parts of the world. It is in thiscontext that it is important to understand thephysical and chemical principles that govern themovement of these dense nonaqueous phase liquids(DNAPLs). Experiments under way at OGI and inconjunction with the University of Waterloo areexamining the behavior and remediation of chlori-nated solvents in the saturated and unsaturatedzones. Johnson

Simulation of Subsurface Processes Using Very LargeScale Experimental AquifersMany important chemical, physical, and biologicalprocesses are difficult to study in the laboratorybecause of problems of scaling. Many of theseprocesses are also difficult to characterize in thefield, because of the complex and uncontrollednature of environmental systems. For thesereasons, OGI has established the LargeExperimental Aquifer Program (OGI/LEAP). Atpresent, the facility consists of five large aquifersused to examine the movements of organic solventsand petroleum compounds in the unsaturated andsaturated porous media. Future LEAP aquifers willexamine inorganic geochemistry and the interac-tions between chemical, biological, and physicalprocesses in contaminated aquifers. Johnson andother faculty

Gas-Phase Transport in Unsaturated Porous MediaGas-phase transport is important in controllingmany subsurface processes including respiration,pesticide behavior, and contaminant volatilizationand movement. Laboratory experiments have beenconducted to determine diffusion rates of a varietyof organic compounds in porous media and thekinetics of adsorption and desorption for a varietyof soil types and a range of water contents.Johnson

Multi-Phase Monitoring of Gasoline Movement Usinga Very Large Physical Model (OGI/LEAP) Leaks from underground storage tanks (UST) rep-resent a major ongoing source of groundwatercontamination. The rapid detection of leaks is,therefore, a major goal of UST legislation. The

OGI/LEAP facility is used to study the movement ofgasoline components in the vapor, aqueous, andpure-product phases. This work will help establishwhich of a variety of leak-detection technologies isbest suited to detect leaks under a range of envi-ronmental conditions. Johnson

Remediation of Halocarbon-Contaminated GroundwaterThere is enormous demand for improved ways toclean up aquifers that have been contaminatedwith halogenated hydrocarbon solvents like carbontetrachloride and TCE. Recent field-scale testshave shown that technologies based on dechlorina-tion with granular iron may have substantialvalue. The goal of our research in this area is toprovide a sound scientific basis for designing andoperating such technologies by determining themechanisms of dechlorination by iron and thegeochemical and microbiological processes thataffect the performance of this technique in thefield. For more information on this work, seehttp://cgr.ese.ogi.edu/iron. Tratnyek

Reduction Reactions of Organic Pollutants inAnaerobic EnvironmentsSome organic pollutants undergo rapid reduction inanaerobic sediments, soils, and groundwaters.Despite the potential importance of this process,little is known about the natural reducing agentsthat are responsible for these reactions. In thisproject, assays are being developed that will iden-tify and quantify environmental reducing agents insitu. These assays will be used in kinetic studies ofimportant pollutant reduction reactions. Tratnyek

Oxidation Reactions of Organic PollutantsSome organic pollutants undergo rapid oxidation innatural waters, when catalyzed by sunlight, and intechnological systems, when chemical oxidants areadded to effect remediation. These reactions areusually mediated by “activated oxygen species”such as hydroxyl radical. We are studying thekinetics, mechanisms, and products of these reac-tions with a wide variety of contaminants. The aimof this work is help assess the suitability of variousadvanced oxidation technologies (AOTs) for remedi-ation of groundwater, as well as to betterunderstand the fate of contaminants in naturalwaters that are exposed to sunlight. Tratnyek

Correlation Analysis of Contaminant ReactivityQuantitative Structure-Activity Relationships(QSARs) are of enormous importance in environ-mental chemistry and toxicology because of theirpredictive power, but they also reveal a great dealabout reaction mechanisms and the nature of sub-stituent effects. We are involved in thedevelopment of QSARs for a wide range of redoxreactions involving organic contaminants. Thiswork involves the use of computational chemistrymethods as well as advanced statistical techniquesin exploratory data analysis. Tratnyek

Fate and Effects of Fuel OxygenatesThe recent realization that oxygenated fueladditives such as MTBE are becoming widely dis-tributed groundwater contaminants has created asudden and pressing demand for data on theprocesses that control their environmental fate.

On-going work in this area includes modeling ofMTBE infiltration to the groundwater, laboratorystudies of MTBE biodegradation, and field studiesof several contaminated sites for MTBE and itspossible breakdown products. For more informa-tion on this work, see http://cgr.ese.ogi.edu/mtbe/. Pankow, Tratnyek, Johnson

Hydrocarbon Biodegradation in SoilPetroleum hydrocarbon contamination is prevalentin soils and groundwater. Efforts to clean up thisextensive petroleum contamination have promptedresearch into in-situ bioremediation. Dependingon site characteristics, in-situ hydrocarbonbiodegradation is a cost effective and environmen-tally sound remediation alternative or partner topump-and-treat and vacuum extraction technolo-gies. We have studied the processes by which thebiodegradation rates of organic compounds can beoptimized. Toccalino

Human-Health Assessment of Water QualityA national effort is underway with the U.S.Geological Survey’s National Water-QualityAssessment (NAWQA) program, in collaborationwith the U.S. Environmental Protection Agency(USEPA) and State agencies to conduct a piloteffort to develop, test, and refine concepts to moreeffectively communicate water-quality informationin a human-health context. The study includesdetermining how to effectively communicate thedata from this study in a human-health context toCongress, the media, the public, etc. Toccalino

Distribution of Organic Compounds Between the Gasand Urban Aerosol Particulate PhasesThe behavior of organic compounds in the atmos-phere depends in large part on the extent to whichthey partition from the gas phase to aerosol partic-ulate matter. Processes that are affected by thispartitioning process include precipitation scaveng-ing of gases and particles as well as dry depositionof gases and particles. Fundamental gas/solid sorp-tion theory is being used to investigate importantaspects of atmospheric gas/particle partitioning.The study involves the investigation of basic parti-tioning behavior of a wide range of representativeatmospheric compounds (including alkanes andpolycyclic aromatic hydrocarbons) on a variety ofrepresentative model particulate substrates,including elemental carbon, organic carbon, silica,and clay. Pankow

Thermodynamics of Inorganic Solid SolutionsThe manner in which inorganic solid solutionsbehave is one of the last major research frontiersin ambient temperature aqueous geochemistry.Coprecipitation of metal ions is well known innature, e.g., Sr2+ can form a solid solution in calci-um carbonate (CaCO3(s)). Unfortunately, little isknown about the thermodynamics of such solidsolutions. That is, little is known about how theactivity coefficients of metal ions vary as a functionof composition in solid solutions of various types.The values of the activity coefficients are of inter-est because they control the extent to which theconstituents in the solid solutions will be soluble inwater, e.g., the extent to which a toxic metal ionlike Cd2+ that is present in calcium carbonate will

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be soluble in water. In this work, activitycoefficient values for a variety of environmentallyimportant divalent metal ions are being sought asa function of composition in calcium carbonate.Pankow

Global Distributions and Mass Balances of Halocarbons,Nitrous Oxide, and Other Trace GasesGases such as CCl3F (F-11), CCl2F2 (F-12) CHClF2

(F-22), CF4 (F-14), C2Cl3F2 (F-113), CH3CCl3,CH3Cl and N2O are being added to the atmosphereby various industrial processes and the use ofhigh-technology products by the public. Such chlo-rine-containing compounds are believed to threatenthe earth’s natural ozone layer high in the atmos-phere (stratosphere). This research willsystematically obtain a long-time series of concen-tration measurements by a flask sampling system.The results are then interpreted with global massbalance models and sophisticated statistical tech-niques to quantify the sources and lifetimes ofthese gases in the environment. Such data are nowobtained from sites all over the world extendingfrom the Arctic Circle to the South Pole.Rasmussen

Studies of Past AtmospheresAtmospheric gases such as N2O, CO2, CO, CH3Cl,carbonyl sulfide (OCS), and CH4 are primarily pro-duced by natural processes, but over the pastcentury human activities have been adding growingamounts to their natural abundance. This processcan upset the cycles of these gases and lead topossibly adverse environmental effects such as thewarming of the earth’s surface (N2O, CO2, CH4).When both natural and anthropogenic processescontribute to the current atmospheric abundanceof a trace gas, it is of interest to determine theamount which existed before human activities hadany effect. Perhaps the only realistic method todetermine the composition of the ancientatmosphere is to analyze the air in bubbles burieddeep in polar ice. The depth of the ice indicates theage of the air in the bubbles. By going far enoughback in time, the relationship between past atmos-pheric composition and climate might be found.The novel and simple method of studying the oldatmosphere of the earth is beset by many problemsthat complicate the relationship between the gasesin the bubbles and the composition of the oldatmosphere. Theoretical and experimentalresearch for resolving these problems as well asthe measurement of trace gases are the majorgoals of this project. Rasmussen

Ocean-Air Exchange of GasesSome atmospheric gases are greatly influenced bythe earth’s oceans. For instance, a large amount ofthe atmospheric methyl chloride (CH3Cl) andmethyl iodide (CH3I) are produced in the oceans,possibly by biogenic processes. It has also beenshown recently that carbonyl sulfide (OCS) is pro-duced in the oceans and subsequently emitted tothe atmosphere. On the other hand, man-madegases such as CCl3F (F-11) can dissolve in theoceans and thus be removed from the atmosphere.This research project is devoted to determining thesolubility of such gases in water and to modelingthe flux of gases into or out of the oceans. The

results obtained are essential ingredients in deter-mining the sources and fates of atmospheric tracegases and in estimating the effects of human activi-ties on the future warming of the earth or depletionof the ozone layer. Rasmussen

Studies of Atmospheric MethaneConsiderable evidence has been accumulatedshowing that methane (CH4) is increasing in theatmosphere, most likely as an indirect result ofgrowing human population. In the future, such anincrease of CH4 can lead to a global warming byenhancing the earth’s natural greenhouse effectand create more ozone and carbon monoxide in theatmosphere. However, it might also prevent someof the destruction of the stratospheric ozone layerby the man-made fluorocarbons 11 and 12. In thisproject, experimental and theoretical research isfocused on statistical trend analyses for the globalincrease of CH4, its seasonal variation, sources andsinks, models of its effect on the CO, O3, and OHcycles and its role in the future of the environment.Rasmussen

Development of Experimental Methods for Trace|Gas MeasurementsAt present, some 50 atmospheric gases can bemeasured at the Trace Gas Laboratory. Still, newmethods are needed to improve the accuracy andprecision of measurements and to satisfy the strin-gent demands of ultra-clean background airsampling. New methods are also being developedfor automated real-time analysis of many tracegases. Research programs include development ofgas chromatographic and mass spectrometricmethods for the analysis of trace gases. At present,GC/MS systems in the laboratory are being used toroutinely measure C2-C12 nonmethane hydrocar-bons at tens of parts per trillion levels. Techniquesfor collecting and storing air and water samplesalso are being developed. Rasmussen

Biogenic Sources of Atmospheric Gases

Living organisms produce and consume a variety ofgases and may therefore form an integral part ofthe global cycle of a trace gas. Selected plants andanimals, living in the sea or on land, are beingstudied to determine their role in the cycles of CH4,N2O, CH3CI, CH3I, isoprene and other hydrocarbons.Rasmussen

The Global Cycle of Carbon Monoxide (CO)Based on 15 years of global sampling and the application of modern trend analysis techniques,our data have shown that CO increased in theatmosphere until around 1987 and has sincedeclined. These changes in CO have major implica-tions for atmospheric chemistry and the role ofbiomass burning in causing global increases oftrace gases. Present research includes modeling ofthe global budgets, seasonal cycles, and potentialenvironmental effects. Rasmussen

Methane Emissions from Rice FieldsMethane concentrations have nearly tripled com-pared to the natural atmosphere of 300 years ago(based on ice core analyses). The increase of riceagriculture to sustain an increasing population maybe a major contributor to the increase of methane

during the last century. This research program isdesigned to determine the role of rice agriculturein the global methane cycle. Field experiments arebeing conducted in China, Indonesia and the U.S.Laboratory experiments and theoretical researchare being done at the Global Change ResearchCenter (Portland State University) in a comprehen-sive research program. This work includesmodeling the production, oxidation and transport ofmethane in the rice paddy ecosystem and measur-ing the controlling parameters. Rasmussen

Land-Margin Ecosystem Research in the ColumbiaRiver EstuaryThe Columbia River Estuary Land-MarginEcosystem Research (LMER) Program funded bythe National Science Foundation focuses on theestuarine turbidity maximum, which is the heart ofthe estuarine ecosystem. Long-term funding allowsanalysis of seasonal and interannual variability inestuarine processes and evaluation of the impactsof flow regulation on the system. The extensivedata sets collected by this program provide a basisfor studies of estuarine circulation, hydraulic con-trol processes at the estuary mouth, nonstationarytidal processes, suspended sediment transport,turbulence and mixing, and biological processes.Jay, Baptista, and external collaborators

Internal Circulation in Tidal Channels and StraitsThis project, funded by the Office of NavalResearch, seeks to use wavelet data analysis tech-niques and novel modeling strategies to improveour conceptual understanding of estuarine circula-tion and scalar transport. Continuous wavelettransforms allow resolution of time variation intidal processes in each frequency band. Dr. Jay’sgroup is using this technique to understand estuar-ine internal circulation and shelf internal tides inbuoyant plumes. Modeling efforts use symbolicmathematics software to provide a balancebetween the intuitive understanding and compactnature of analytical solutions and the superior flex-ibility and accuracy of full-numerical solutions. Jay

CORMIX Graphic User Interface and GISDatabase IntegrationThis project develops computer informationsystems for the CORMIX mixing zone water qualitymodel. A fully interactive Windows-based applica-tion is proposed, designed to give CORMIXadditional functionality, flexibility, and power usingobject-oriented rule-base technology for forms-based interactive data entry, flow classification,simulation logic description, and GIS database inte-gration. Doneker

D-CORMIX Decision Support SystemThis project involves development, validation, andscientific review of the D-CORMIX decision supportsystem. D-CORMIX is a physically-based simulationmodel linked to a knowledge-based classificationsystem for predicting of water quality and sedimentdeposition impacts resulting from dredging opera-tions. The purpose of the project is to assist waterquality managers in performing waste load alloca-tions for continuous dredge discharges. Themethodologies developed in this project are alsonecessary for long term pollutant fate and trans-

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port studies by providing information on initialboundary conditions. This project also developsvalidation studies and documentation for USEPAScience Advisory Board (SAB) review ofD-CORMIX. Doneker

CORMIX Documentation Development, WorkshopInstruction, and Technical SupportOGI has a 3-year cooperative agreement to main-tain, update and distribute the CORMIX usermanual, conduct technical training workshops onmixing zone models, and to provide technical assis-tance to CORMIX model users. The CORMIX waterquality model has approximately 1000 users world-wide, feedback from them through technicalsupport and training workshops directly supportscurrent model development activities. Doneker

C O R I E : A P I L O T E S T U A R I N E N O W C A S T- F O R E C A S T S Y S T E M (http://www.ccalmr.ogi.edu/CORIE)

Since 1996, we have been developing CORIE,an observation and forecasting system for theColumbia River estuary. The motivation is two fold.First, the Columbia River and its near-shore plumeare a dominant oceanographic feature of thenortheastern Pacific Ocean and the focus of con-troversial ecosystem management issues. CORIErepresents a novel, promising, and much neededinfrastructure for physical and ecological researchin this system. Second, we envision that multi-purpose nowcast-forecast systems will becomecentral to the management of coasts and estuariesworldwide. The Columbia River estuary is a chal-lenging natural laboratory to test concepts andtools, and CORIE is a pilot system developed toanchor our observation and forecasting research.

CORIE has three main components. The first com-ponent is a real-time data acquisition system,including an array of 12 permanent stations, avariable number of temporary stations, and onemobile station. We currently monitor, in variouscombinations at each station: temperature, conduc-tivity, water pressure, water velocities, acousticbackscatter, wind speed and direction, air temper-ature, and atmospheric pressure. “Real-time” isdefined by latencies of typically a few seconds, andis achieved through a telemetry network based onspread-spectrum radio technology. The secondcomponent of CORIE is a suite of circulation andtransport models currently extending from theBonneville dam to the coastal vicinity of the CRestuary, and including parts of the Willamette andCowlitz rivers. Hindcast model runs are being usedto benchmark systematically all models, individual-ly and in their contrasting features. The thirdcomponent of CORIE is a data management anddistribution system, with real-time and archivalaccess through the web to script-generated graphi-cal displays and actual data. Baptista

C O U P L E D P H Y S I C A L A N D B I O G E O C H E M I C A L P R O C E S S E S AT S E D I M E N T- W AT E R I N T E R FA C E S

The overall goal of this project is to advance ourquantitative understanding of the fate and bioavail-ability of chemical elements in estuaries bycoupling meso-scale experimentation with diagnos-tic numerical modeling and field observations. In a

preparatory phase, we designed, constructed andinstrumented a meso-scale biogechemical rotatingannular flume (RALF). We are beginning theprocess-based research phase on the project, inwhich we will focus on elements important for bothwater quality and ecosystem dynamics, namely thecycling of Fe, Mn, and other divalent metals atsediment-water interfaces (SWI). We are especiallyinterested in quantifying the effect of episodic sedi-ment disruptions on the speciation and phase(dissolved, particulate, and colloidal) of these met-als. We are also interested in the effect of shearupon particle desegregation, differential settling,sorption, precipitation, and dissolution. We willplace the chemical reactions in a controlled, yetrealistic, shear-driven physical environment byconducting primary experiments in the controlledenvironment of RALF. For more information onthis work, see http:www.ccalmr.ogi.edu/ralf/. Baptista, Tratnyek, external collaborators

O C E A N S U R V I VA L O F S A L M O N I D SWe are initiating an integrated observational/ mod-eling study of the physical variability of theColumbia River plume and estuary, to provideoceanographic context for research on the role ofthe coastal ocean on the life cycle of salmon. Baptista, Jay, external collaborators

C A S C A D I A S U B D U C T I O N Z O N E T S U N A M I SLarge tsunamis are believed to be locally generat-ed in the Cascadia Subduction Zone (CSZ) every200 to 600 years, based on geological records. Thelast large tsunami dates back about 300 years,raising concerns about the protection of coastalcommunities in Oregon, Washington, California,and British Columbia. The coastal impact of poten-tial CSZ tsunamis is being investigated throughnumerical modeling. The need to use geological evi-dence on paleotsunamis as the sole, loosereference for model validation makes this anunusually interesting and challenging problem. TheOregon Department of Geology and MineralIndustry (DOGAMI) has incorporated our jointresearch results into the development of tsunamiinundation maps for the Oregon and Washingtoncoasts. Baptista, external collaborators

RESEARCH CENTERS

C E N T E R F O R G R O U N D W AT E R R E S E A R C HThe principal mission of the Center forGroundwater Research (CGR) is to conduct state-of-the-art research in areas relating to thetransport and fate of contaminants in the subsur-face. This is accomplished through a combinationof research grants and contracts, support fromCenter corporate sponsors, and through collabora-tion with other universities, industries, andgovernment agencies.

The Center coordinates a range of projects relatingto the transport and fate of contaminants in soilsand groundwater. The scope of the Center includes,among other things, the development of: 1) newsampling and site characterization techniques; 2)new analytical techniques; and 3) improved ground-

water remediation methods.

The Center operates the Large ExperimentalAquifer Program (LEAP) which contains the experi-mental cells outlined below. The LEAP facilityprovides staff with the capability to conduct bothbench-scale experiments and pilot-scaledemonstrations. Current projects include transportthrough fractured clay, air sparging of sourcepetroleum zones containing MTBE, and a pilotscale demonstration of zeolite as an in-situ perme-able barrier material.

Students involved in LEAP research graduate witha rare combination of experience in full-scaleremediation engineering and a process-level under-standing of contaminant hydrology and chemistry.

Additional information about CGR may be obtained from:

DR. RICHARD JOHNSONphone: (503) 748-1193 e-mail: [email protected] Web site: cgr.ese.ogi.edu.

C G R FA C U LT YRichard Johnson, Associate Professor Paul Tratnyek, Associate ProfessorJames F. Pankow, ProfessorPatricia L. Toccalino, Assistant Professor

L E A P E Q U I P M E N T• Five tanks: one 10 m x 10 m x 3 m, two 10 m x 10 m x 5 m,

one 10 m x 2.5 m x 0.5 m, and one 8 m x 2.5 m x 0.5 m

• In situ instrumentation, including: automatedtemperature, pressure, and water level monitoring;multi level samplers; down hole video camera; andautomated vapor and product sensing equipment

• Remediation equipment, including soil vapor extractionand air sparging capabil ities

• Automated on-site analytical equipment, includingcapil lary GC-MS instrumentation

C E N T E R F O R C O A S TA L A N D L A N DM A R G I N R E S E A R C H ( C C A L M R )

The Center for Coastal and Land-Margin Research(CCALMR) is an interdisciplinary research centeraffiliated with the Department of EnvironmentalScience and Engineering. CCALMR conductsresearch, graduate education and advanced tech-nology development that directly address the needfor better scientific understanding of coasts, landmargins and estuaries. Improved knowledge ofthese complex systems is necessary to preserveand enhance their environmental integrity, main-tain the economic viability of communitiesdependent on them and protect human populationsfrom natural and man-made hazards.

Real-world natural resource management issuesmotivate CCALMR research and education activi-ties. Insights drawn from the experience of scienceand engineering professionals in the public andprivate sectors influence the identification of emerging research challenges, the design ofresearch projects, the development of supportingtools and applications and the transfer of knowledgeand technology.

Additional information about CCALMR may beobtained from:

74


D R . A N T Ó N I O M . B A P T I S TAphone (503) 748-1147 e-mail [email protected] Web site: www.ccalmr.ogi.edu/

C C A L M R F E AT U R E D P R O J E C T S

• Cascadia Subduction Zone tsunamis

• CORIE: a pilot estuarine nowcast-forecast system

• CORMIX: mixing zone decision support system

• Coupled physical and biogeochemical processes atsediment-water interfaces

• Internal circulation in tidal channels and straits

• Land-margin ecosystem research in the Columbia River estuary

• Ocean survival of salmonids

• Reduction reactions of organic pollutants in anaerobic environments

• Trace element distributions

• Watershed analysis

C C A L M R FA C I L I T YThe Center is well equipped to conduct state-of-the-art scientific research. The following isa list of facilities and instruments available in addi-tion to those available through the Department ofEnvironmental Science and Engineering.

O C E A N O G R A P H I C E Q U I P M E N T

• 300, 600 and 1200 kHz Acoustic doppler currentprofilers (RD)

• 500 and 1500 kHz Acoustic doppler profi lers (Sontek)

• Conductivity and temperature pairs (Seabird)

• Conductivity, temperature and pressure sensors (CoastalLeasing and Ocean Sensors)

• Echosounder and digitizer (Ross)

• Optical backscatter sensors (Downing Associates)

• Wind gauges (Coastal Leasing)

• High-density thermistor chains (CCALMR)

• Differential GPS (Trimble)

• Spread spectrum radio data modems (FreeWave)

R E A L - T I M E D ATA A C Q U I S I T I O N N E T W O R K ( C O R I E )

The pilot nowcast-forecast system CORIE includesa real-time data acquisition network with twelvemulti-sensor oceanographic stations in theColumbia River estuary. Field operations are con-ducted from the Marine Environmental Researchand Training Station (MERTS). MERTS is a facilitydeveloped in partnership with and operated by the Clatsop Community College (CCC). CCC operatestwo training and research vessels: the 50-foot M/VForerunner and the 21-foot R/V Tansy Point.

B I O G E O C H E M I C A L R O TAT I N G A N N U L A R F L U M E ( R A L F )

RALF, a 2-meter biogeochemical rotating annularflume, supports research on coupled physical andbiogeochemical processes at sediment-water inter-faces. Instrumentation providing real-time orpseudo real-time data include:

• 3-dimensional Acoustic Doppler Velocimeter (Sontek)

• DO (Orion) and pH/ISE (Orion)

• DLK-100 Potentiostat (AIS)

• Solid State Au/Hg amalgam microelectrodes

• Bipotentiostat equipped with rotating disk electrode (Pine)

RESEARCH FACILIT IESThe department is well equipped to carry on avigorous research program Instruments and equip-ment available, in addition to those listed for thecenters, include:

G E N E R A L A N D A N A LY T I C A L E Q U I P M E N T• Carbon/nitrogen/sulfur analyzer• Several high-performance l iquid chromatographs

with UV-absorbance, fluorescence, refraction index,and conductivity detectors.

• Ion chromatograph• Graphite furnace atomic absorption

spectrophotometer• Access to FT-IR, fluorescence, diode array UV/VIS,

scanning UV/VI Snear IR spectrophotometers• Access to scanning electron microscopes• Access to a complete Raman spectroscopy facil ity• Purge and trap concentrator and thermal

desorption apparatus• Rain and air sampling equipment• Groundwater and soil sampling equipment• Groundwater monitoring equipment, including

water table, ambient, and ground temperaturemeasurement, and pressure transducers allintegrated into a data logging system

• Equipment for supercritical f luid extraction andsupercritical f luid chromatography

• Several rapid flow injection analysis systems• Sediment samplers• Two-dimensional polyacrylamide| gel densitometer• Aerosol samplers• Trace reduction-gas analyzer• Liquid nitrogen freezer

C O M P U T E R E Q U I P M E N T• Computer lab with numerous Pentium

and Pentium Pro PCs running Windows NT• SPARC workstations• Network access via X-terminals and

personal computers• Numerous IBM compatible and Apple Macintosh

computers with HP LaserJet printers, digitizingtablets, plotters and a fi lm image recorder

S U P P O R T FA C I L I T I E S• Fully equipped machine shop• Toxic chemicals handling laboratory• Electronics support personnel• Greenhouse facil ity and growth chambers

A N T Ó N I O M . B A P T I S TAProfessor and Department HeadDirector, Center for Coastal and Land-Margin Research

Ph.D., Civil EngineeringMassachusetts Institute of Technology, [email protected]


Integrated understanding andprediction of hydrodynamicand environmental processesin estuaries and coasts.Development of associatedconcepts and technologies:environmental observation andforecasting systems, numericalmethods and models, physically-based ecological indicators.

R E P R E S E N TAT I V E P U B L I C AT I O N S

Baptista, A.M, “EnvironmentalObservation and Forecasting Systems,”Encyclopedia of Physical Science andTechnology, 3rd Edition, Volume 5,Academic Press, in press.

Myers, E.P. and A.M. Baptista,“Inversion for Tides in the EasternNorth Pacific Ocean”, Advances inWater Resources, Vol. 24(5),|pp. 505-519, 2001.

Myers E.P. and A.M. Baptista,“Analysis of Factors InfluencingSimulations of the 1993 HokkaidoNansei-Oki and 1964 Alaska Tsunamis,”Natural Hazards, 23(1):1-28, 2001.

Oliveira A., A.B. Fortunato, and A.M.Baptista “Mass Balance in Eulerian-Lagrangian Transport Simulations inEstuaries,” ASCE Journal of HydraulicEngineering, 126(8):605-614, 2000.

Yang Z., A.M. Baptista, and J.Darland, “Numerical Modeling of FlowCharacteristics in a Rotating AnnularFlume,” Dynamics of Atmospheres andOceans, 31:271-294, 2000.

Baptista, A.M., M. Wilkin, P. Pearson,P. Turner, C. McCandlish, and P.Barrett, “Coastal And EstuarineForecast Systems: A Multi-PurposeInfrastructure for the Columbia River,”Earth System Monitor, 9(3), NationalOceanic and AtmosphericAdministration, Washington, D.C, 1999.

Oliveira A. and A.M. Baptista, “On theRole of Tracking on Eulerian-Lagrangian Solutions of the TransportEquation,” Advances in WaterResources, 21(7), 539-554, 1998.

R O B E R T L . D O N E K E R , P. E .Assistant ProfessorPh.D., Environmental EngineeringCornell University, [email protected]


Development of decision supportsystems for environmentalsimulation modeling, engineeringdesign optimization, and naturalresource management. Currentresearch areas focus ondevelopment of technology transfersystems with emphasis on waterquality modeling and control ofpoint and nonpoint sourcepollutant transport.

R E P R E S E N TAT I V E P U B L I C AT I O N SDoneker, R. L. And G. H. Jirka, 1999.

Discussion of “Mixing In Inclined DenseJets” by P.W. Roberts, A. Ferrier, andG. Daviero, Journal of HydraulicEngineering, ASCE, vol. 125 No.3pp.317-318.

Ford D.A., A.P. Kruzic, and R.L.Doneker, “Using GLEAMS to Evaluatethe Agricultural Waste ApplicationRule-Based Decision Support System(AWARDS) Computer Program”, WaterScience and Technology, Vol. 28, No-35,pp.625-634, 1993.

Doneker, R.L., and G.H. Jirka “ExpertSystems for Mixing Zone Analysis andDesign Aqueous Pollutant Discharges,”Journal of Water Resources Planningand Management, ASCE, Vol. 117,No. 6, November/December 1991.

Jirka, G.H. and R.L. Doneker“Hydrodynamic Classification ofSubmerged Single Port Discharges”,Journal of Hydraulics Division, ASCE,Vol. 117, No. 9, September 1991.

Jirka G.H., R.L. Doneker, and T.O.Barnwell, “CORMIX: A ComprehensiveExpert System for Mixing Zone Analysisof Aqueous Pollutant Discharges,”Water Science and Technology, 24,No. 6, 267-274, 1991.

Doneker R.L., and G.H. Jirka,“Schematization in Regulatory MixingZone Analysis”, Journal of WaterResources Planning and Management,ASCE, Vol 128, No. 1, Jan./Feb. 2002.

Doneker, R.L., and G.H. Jirka,“CORMIX-GI Systms for Mixing ZoneAnalysis of Brine WastewaterDisposal,” Desalination, 139, 2001.

D A V I D A . J AYAssociate ProfessorPh.D., Physical OceanographyUniversity of Washington, [email protected]


River basin, estuarine, andcontinental shelf processes,turbulent mixing, tides and tidalanalysis. A unifying theme is theinfluence of hydrodynamicprocesses on ecosystems.

R E P R E S E N TAT I V E P U B L I C AT I O N SCudaback, Cynthia N. and D. A. Jay,

2001, “Tidal asymmetry in an estuarinepycnocline, 2”, Transport J. Geophys.Res. 106: 2639-2652.

Cudaback, C. N., and D. A. Jay, 2000,“Tidal asymmetry in an estuarine pycn-ocline: Depth and thickness”, J.Geophys. Res. 105: 26,237-26,252.

Jay, D. A., W. R. Geyer andD. R. Montgomery, 2000, “An ecologicalperspective on estuarine classification:Estuarine Science, A SyntheticApproach to Research and Practice”,J. E. Hobbie (ed.), Island Press,pp. 149-175.

Flinchem, E. P. and D. A. Jay, 2000,“An introduction to wavelet transformtidal analysis methods”, Coast. Estuar.Shelf Sci. 51: 177-200.

Jay, D. A. and Flinchem, E. P., 1997,“Interaction of fluctuating river flowwith a barotropic tide: A test of wavelettidal analysis methods”, J. Geophys.Res. 102: 5705-5720.

B.M. Hickey, L.J. Pietrafesa, D.A. Jay&W.C. Boicourt, 1996, “The ColumbiaRiver Plume Study:subtidal variabilityin the velocity and salinity field,”J. Geophysical Research, 103(10),229-368.

D.A. Jay & J.D. Musiak, 1996,“Internal Tidal Asymmetry in ChannelFlows: Origins and Consequences”,C. Pattiaratchi (Ed.), “Mixing Processesin Estuaries and Coastal Seas, anAmerican Geophysical Union,” Coastaland Estuarine Sciences, 53, 219-258.

D.A. Jay & J.D. Musiak, 1994,“Particle trapping in estuarine turbiditymaxima,” J. of Geophysical Research,99(20), 446-461.

R I C H A R D L . J O H N S O NAssociate Professor and Director,Center for Groundwater ResearchPh.D., Environmental ScienceOregon Graduate Center, [email protected]


Physical and chemical behaviorof organic contaminants in theair, soil, and water; analyticalorganic chemistry; groundwatertransport, fate, and modeling ofcontaminants in porous andfractured porous media.

R E P R E S E N TAT I V E P U B L I C AT I O N SThomson, N.R. and R.L. Johnson.

“Air Distribution During In Situ AirSparging: An Overview of MathematicalModeling”, J. Hazardous Materials72(2-3), 265-282 (2000).

Johnson, R.L., J.F. Pankow D. Bender,C. Price and J. Zogorski. “To WhatExtent Will Past MTBE ReleasesContaminate Community Water SupplyWells?” Environ. Science and Technol.34, 2A-7A, (2000).

Slater, L., A.M. Binley, W. Daily andR.L. Johnson. “Cross-hole electricalimaging of a controlled saline tracerinjection.” J. Applied Geophysics,44, 85-102 (2000).

Johnson, P. C.; M. W. Kemblowski,R. L. Johnson. “Assessing the signifi-cance of subsurface contaminant vapormigration to enclosed spaces: site-spe-cific alternatives to generic estimates.”J. Soil Contam. 8(3), 389-421 (1999).

Daily, W., A. Ramirez and R.L.Johnson. “Electrical ImpedanceTomography of a PerchloroethyleneRelease”, J. Explor. Eng. Geology,2, 189-201 (1998).

Johnson, P.C., R.L. Johnson,C. Neaville, E.E. Hansen, S.M. Stearns,and I.J. Dortch. “An Assessment ofConventional In situ Air SpargingTests.” Ground Water, 35(5),765-774, (1997).

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F A C U L T Y | E N V I R O N M E N TA L S C I E N C E A N D E N G I N E E R I N G | E S E

J A M E S F. P A N K O WProfessor Ph.D., EnvironmentalEngineering ScienceCalifornia Institute of Technology, [email protected]


Physical and analytical chemistryof organic compounds and metalsin natural waters and in theatmosphere; the formation andchemistry of atmospheric aerosols;the chemistry of nicotine intobacco smoke.

R E P R E S E N TAT I V E P U B L I C AT I O N SPankow, J.F., J.H. Seinfeld,

W.E. Asher, G.B. Erdakos, “Modelingthe Formation of Secondary OrganicAerosols. 1. Theory andMeasurements for the (-Pinene-, (-Pinene-, Sabinene-, (3-Carene, and Cyclohexene-Ozone Systems,” Env. Sci. Technol., 35, 1164-1172(2001). See also Errata, Env. Sci.Technol., 35, 3272 (2001).

Seinfeld, J.H., W.E. Asher,G.B. Erdakos, J. F. Pankow, “Modelingthe Formation of Secondary OrganicAerosols. 2. The Predicted Effects ofRelative Humidity on Aerosol Formationin the (-Pinene-, (-Pinene-, Sabinene-,(3-Carene, and Cyclohexene-OzoneSystems,” Env. Sci. Technol., 35, 1806-1817 (2001).

Johnson, R.L., J. Pankow, D. Bender,C. Price, J. Zogorski, “MTBE, To WhatExtent will Past Releases ContaminateCommunity Water Supply Wells?”Environmental Science & Technology,210A-217A (2000).

J.F. Pankow, B.T. Mader, L.M. Isabelle, W. Luo, A. Pavlick, C. Liang, “Conversion of Nicotine inTobacco Smoke to its Volatile andAvailable Free-Base Form through the Action of Gaseous Ammonia,”Environmental Science and Technology,31, 2428-2433 (1997).

C. Liang & J.F. Pankow, “Gas/ParticlePartitioning of Organic Compounds to Environmental Tobacco Smoke:Partition Coefficient Measurements byDesorption,” Environ. Sci. Technol.30(9), 2800-2805 (1996).

J.F. Pankow, “An Absorption Model of Gas/Particle Partitioning in theAtmosphere,” Atmos. Environ., 28, 189 (1994).

R E I N H O L D A . R A S M U S S E NProfessorPh.D., Botany Plant PhysiologyWashington University, St. Louis, [email protected]


Atmospheric chemistry of tracegases; biogenic and anthropogenicemissions of trace gases and theirroles in stratospheric ozonedestruction and troposphericozone formation; measurements of trace gases at parts per trillionto parts per quadrillion levels;sources and sinks of isoprene and other hydrocarbons.

R E P R E S E N TAT I V E P U B L I C AT I O N SC. Geron, R.A. Rasmussen, R.R. Arnts,

A. Guenther, “A review and synthesis ofmonoterpene speciation from forests inthe United States,” Atmos. Environ,34(11), 1761-1781 (2000).

J. Zhang, K.R. Smith, R. Uma, Y. Ma,V.V.N. Kishore, K. Lata, M.A.K. Khalil,R.A. Rasmussen, S.T. Thorneloe,“Carbon monoxide from cookstoves indeveloping countries: 2. Exposurepotentials,” Chemosphere: GlobalChange Sci., 1(1-3), 367-375 (1999).

J. Zhang, K.R. Smith, R. Uma, Y. Ma,V.V.N. Kishore, K. Lata, M.A.K. Khalil,R.A. Rasmussen, S.T. Thorneloe,“Carbon monoxide from cookstoves in developing countries: 1. Emissionfactors,” Chemosphere: Global ChangeSci., 1(1-3), 353-366 (1999).

E. Grosjean, R.A. Rasmussen, D. Grosjean, “Toxic air contaminants inPorto Alegre, Brazil,” Environ. Sci.Technol., 33(12) 1970-1978 (1999)

R.A. Rasmussen, M.A.K. Khalil & F. Moraes, “Permafrost MethaneContent: 1. Experimental Data fromSites in Northern Alaska,”Chemosphere, 26:591 (1993).

M.A.K. Khalil, R.A. Rasmussen, J.R. French & J. Holt, “The Influence of Termites on Atmospheric TraceGases: CH4, CO2, CHCl3, N2O, CO, H2 and Light Hydrocarbons,”J. Geophys. Res., 95:3619 (1990).

D.A. Hegg, L.F. Radke, P.V. Hobbs, R.A. Rasmussen & P.J. Riggan,“Emissions of some trace gases frombiomass fires,” J. Geophys. Res.,95:5669 (1990).

P AT R I C I A L . T O C C A L I N OAssistant Professor and Director of EducationPh.D., Environmental Science and EngineeringOregon Graduate Institute ofScience and Technology, 1992 [email protected]


Human and ecological riskassessments, water-qualityassessments, optimization ofhydrocarbon biodegradation in soil and subsurface systems,contaminant fate and transport in various environmental media.

R E P R E S E N TAT I V E P U B L I C AT I O N SA N D T E C H N I C A L R E P O R T S

Toccalino, P. L., L. Nowell, and R. Phillips. 2001. “Recommendationsfor the development of health-basedscreening levels.” Report to U.S.Geological Survey, U.S. EnvironmentalProtection Agency, and N.J. Departmentof Environmental Protection.

Toccalino, P. L. and R. Binder.2000. “Methodologies for presentingcontaminant concentration data fromthe Glassboro, New Jersey study areain a human-health risk context.”Report to U.S. Geological Survey, U.S. Environmental Protection Agency,and N.J. Department of EnvironmentalProtection.

Toccalino, P. L., K. M. Auer, D. A. Mervyn, and B. Stirling. 1997.Phase II Remedial Investigation/RiskAssessment Report for Westside LightRail Transit (LRT) Construction Spoilsat the Port of Portland’s PortlandInternational Center, Portland, OR.

Toccalino, P. L. 1997. Evaluation ofthe Contained Burn of Two M88 NIKERocket Motors for Environmental Safety& Health Implications, Nevada Test SiteX-Tunnel Facility (U25X), Las Vegas, NV.

Toccalino, P. L., R. L. Johnson, and D. R. Boone. 1993. “Nitrogen limita-tion and nitrogen fixation during alkanebiodegradation in a sandy soil.” Appl.Environ. Microbiol. 59:2977-2983.

Toccalino, P. L., K. M. Harmon, and J. Harmon. 1988. “Hydrogenbonding. Part 26. Thermodynamicsof dissociation and infrared spectra-crystal structure correlationsfor betaine monohydrate and trimethy-lamine oxide dihydrate.” J. Mol. Struct.189:373-382.

P A U L G . T R AT N Y E KAssociate ProfessorPh.D., ChemistryColorado School of Mines, [email protected]


Mechanistic and kinetic aspects ofthe fate of organic pollutants inthe environment; degradationreactions involving pesticides,phenols, munitions, dyestuffs andchlorinated hydrocarbon solvents;chemical and microbiologicalprocesses in sediments, soils andgroundwaters as well asphotochemical processes insurface waters; natural andengineered remediation systems.

R E P R E S E N TAT I V E P U B L I C AT I O N STratnyek, P. G.; Scherer, M. M.;

Deng, B.; Hu, S. (2001) “Effects of natural organic matter, anthropogenicsurfactants, and model quinones on the reduction of contaminants by zero-valent iron.” Wat. Res., in press.

Scherer, M. M.; Johnson, K.; Westall,J. C.; Tratnyek, P. G. (2001) “Masstransport effects on the kinetics ofnitrobenzene reduction by iron metal.”Environ. Sci. Technol., 35(13), 2804-2811.

Tratnyek, P. G.; Reilkoff, T. E.; Lemon,A.; Scherer, M. M.; Balko, B. A.; Feik,L. M.; Henegar, B. (2001) “Visualizingredox chemistry: Probing environmentaloxidation-reduction reactions with indi-cator dyes.” The Chemical Educator,6(3), 172-179.

Nam, S.; Tratnyek, P. G. (2000)“Reduction of azo dyes with zero-valentiron.” Wat. Res., 34(6), 1837-1845.

Tratnyek, P. G.; Macalady, D. L.(2000) “Oxidation-reduction reactionsin the aquatic environment.” In:Handbook of Property EstimationMethods for Chemicals: Environmentaland Health Sciences; Mackay, D.;Boethling, R. S., Eds.; Lewis: BocaRaton, FL; pp. 383-415.

Church, C. D.; Pankow, J. F.;Tratnyek, P. G. (1999) “Hydrolysis oftert-butyl formate: Kinetics, products,and implications for the environmentalimpact of MTBE.” Environ. Toxicol.Chem., 18(12), 2789-2796.

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E S E | E N V I R O N M E N TA L S C I E N C E A N D E N G I N E E R I N G | F A C U L T Y

JOINT APPOINTMENTS

D R . J . F R E D H O L M E S

Electrical and ComputerEngineering OGI School of Science and Engineering

D R . J A M E S H U N T Z I C K E R

Center for Professional DevelopmentOGI School of Science and Engineering

ADJUNCT FACULTY

D R . M A R Y A B R A M S

DEQ Laboratory DivisionOregon Department ofEnvironmental Quality

D R . D A V I D B O O N E

Department of Environmental Biology,Portland State University

D R . N O R M A N E D E R

Conkling Fiskum & McCormick, Inc.

D R . W I L L I A M F I S H

Department of EnvironmentalSciences and Resources,Portland State University

D R . B R U C E H O P E

Environmental Toxicologist, Oregon Department ofEnvironmental Quality

D R . A S L A M K H A L I L

Department of PhysicsPortland State University

K E N N E T H R O S E N B A U M , J . D .

Environmental Law Institute(Visiting Scholar), Washington, D.C.

D R . J O H N C . W E S TA L L

Department of Chemistry,Oregon State University

RESEARCH SCIENTISTS

A R U N C H A W L A

Research ScientistPh.D., Civil Engineering,University of Delaware

W E N TA I L U O

Research ScientistPh.D., Environmental Science and Engineering, Oregon Graduate Institute

T O D D S A N D E R S

Research ScientistPh.D., Physical Oceanography,University of Delaware

D O U G W I L S O N

Research ScientistPh.D., Physical Oceanography, Memorial University ofNewfoundland

Y I N G L O N G ( J O S E P H ) Z H A N G

Research ScientistPh.D., Applied Mathematics and Fluid Mechanics,University of Wollongong, Australia

M I C H A E L Z U L A U F

Research ScientistPh.D., Meteorology,University of Utah

SENIOR STAFF

B O B D A L L U G E

Research AssociateB.S., Psychology, Washington State University

A N N A FA R R E N K O P F

Research AssociatePh.D., Marine Studies, University of Delaware at Lewes

L O R N E M . I S A B E L L E

Senior Research AssociateM.S., Chemistry,San Francisco State University

C O L E M C C A N D L I S H

Scientific ProgrammerM.S., Atmospheric Sciences, Oregon State University

R O S E M A R I E M I E H R

Research AssociatePh.D., Chemistry, Technical University, Munich, Germany

J I M M O H A N

Systems ManagerM.S., Management in Science and Technology, Oregon Graduate Institute

I N G A O ’ B R I E N

Research AssociateM.A., Health Communication& Development,Ohio University

P H I L I P O R T O N

Research AssociateB.S., Physical Oceanography,University of Michigan

R O B Y N P H I L L I P S

Research AssociateM.S., EnvironmentalManagement/Toxicology,Duke University

C H A R L E S S E AT O N

Research AssistantM.S. Environmental Science& EngineeringOregon Graduate Institute

B O B W AT K I N S

Research TechnicianB.S., Chemical Engineering, Washington State University

M I C H A E L W I L K I N

Research AssociateB.S., Oceanography and Geology, University of Southampton, U.K. 77

F A C U L T Y | E N V I R O N M E N TA L S C I E N C E A N D E N G I N E E R I N G | E S E

THE DEPARTMENT OF MANAGEMENT

IN SCIENCE AND TECHNOLOGY

provides the rigorouseducational preparationnecessary for highly effectivemanagerial- and professional-level work in industries,organizations and departments that have a strong technical,engineering, manufacturingor scientific orientation.Our courses, certificate and master’s degreeprograms focus on managing people andprocesses and building effective andcompetitive organizations in the specificcontexts of technology and science. Managingchange and competing in the globalmarketplace are prominent themes in theMST program.

L E A R N O N - L I N E , A N Y T I M E , A N Y W H E R E

MST delivers challenging and engagingversions of its courses over the Internet.This is an excellent option for studentsfacing time pressures or working inlocations where travel to the OGI campus isnot feasible. The course delivery system isbased on interactive multimedia lecturesand lessons, faculty-managed chat, and on-line discussions, all in a seamless browser-centric environment. Students can takeindividual courses, enroll in the Certificatein Management in Science and Technologyprogram, or apply for the full Master ofScience degree (currently only the Managingthe Technology Company degree option isoffered on-line). Courses offered on-line willhave a “D” designation following the coursenumber. For further information dial tollfree in the U.S. 1-877-GO TO OGI (1-877-468-6644) or visit the MST on-line learningWeb site: http://elearning.cenquest.com/

I N D I V I D U A L C O U R S E S I N M S T

Each MST course has been designed as avaluable professional developmentexperience for working professionals.Project Management, Quality Management,Building Effective Organizations in Scienceand Technology, for example, may be takenas stand-alone courses. We encourage non-matriculated students to join our courses

for their own career development inspecific areas.

CERTIF ICATE OPTIONSThe MST department offers certificatesin Management Studies and Technology,Building the General Manager, andIndustrial Design.

M A N A G E M E N T S T U D I E S

MST offers a six-course certificate inManagement Studies. The following fivecourses, plus an additional MST electivecourse chosen in consultation with a facultyadvisor, are required:

MST501/501D Managerial and Financial Accountingfor Science and Technology 4 credits

MST503/503D Marketing in Science and Technology 4 credits

MST510/510D Principles and Trends inTechnology Management 3 credits

MST512/512D Project Management 3 credits

MST520/520D Managing in Science and Technology 4 credits

Elective to be chosen after consultationwith faculty advisor 3-4 credits

B U I L D I N G T H E G E N E R A L M A N A G E R ( B G M )

A C E R T I F I C AT E P R O G R A M F O R S E N I O R M A N A G E R S

I N T E C H N O L O G Y- I N T E N S I V E C O M P A N I E S

The program focuses on building generalmanagement skills needed to successfullymanage the established but still-growinghigh-tech business, and can be completed ina series of long weekends over the course ofone year.

The ideal BGM participant does not need anadditional degree for career advancement,can spare the time only for a concentratedprogram, and wishes to leverage the learningexperience to build a network of peers inother technology companies.

The three key areas of the BGM Certificateare: Business Management Foundations,which selectively draws on MST courses; andExecutive Assessment and Coaching, which isincorporated into the program with pre- andpost-assessment and jointly undertaken withincumbent companies; and Building ExecutiveLeadership Skills, which serves as the core ofthe program.

B U I L D I N G E X E C U T I V E L E A D E R S H I P S K I L L S C O R E

( 6 C R E D I T S )

MST541/541D Seminar in Leadership Development 3 credits

MST522/522D Building Effective Organizations 3 credits

Department of Management in Science

and Technologywww.ogi.edu/MST/


Fred Ph i l l ips



Victor ia Ty ler


P R O G R A M A S S I S T A N T S

Stac i Sutton


Maryann Burn ingham


G E N E R A L I N Q U I R I E S


MST student Dave Kennedy presents a bus iness p lan for h is Capstone Pro ject .

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In addition, four workshops, chosen inconsultation with the firms employing eachBGM participant, help build executive skills.Workshops conclude with a team project-ahigh-impact business project for thecompany. Nationally recognized instructorsjoin the OGI faculty to teach these executiveworkshops. Titles include: Leading theStrategy Process; Mindset and Skills forManaging Globally; Managing DevelopmentProjects for Profits, Growth and Renewal; andManaging for Innovation and Leading Change.

I N D U S T R I A L D E S I G N

This certificate program introducesparticipants to the full range of activitiesinvolved in the design of products for industryand the marketplace. The role of the IDprocess within the organization is addressed,as are the key elements of an effective designproject from conceptualization to productmanufacturing, product launch andmarketing program.

Topics taught include new productdevelopment and design managementstrategy, application of CAD in productdevelopment (including CAD/CAE/CAMintegration), and an overview of futuredevelopment in technology for ID andmanufacturing. During the previous year,certificate requirements included 40 contact-hours in Industrial Design, 40 contact-hoursin Modeling Computer Aided Development, 20contact-hours in management seminars, plusa number of site visits.

ADMISSION REQUIREMENTSAdmission requirements are the same as thegeneral requirements for the institution. Inaddition, the MST department requires:

• A bachelor, master or doctoral degree from anaccredited institution

• A recommended cumulative undergraduategrade point average of 3.0

• A minimum of two years of full-time workexperience-preferably at the professional,supervisory or managerial level-in a technical,scientific, business, or related area

• Three letters of recommendation, one of whichshould come from an employer or supervisor

• Recommended TOEFFL score of 625 if Englishis not the applicant’s first language. Scores arenot required for students who earned an under-graduate degree in the United States, or who haveworked for a business for at least two years andwhere the primary business language is English

• GMAT or GRE scores are not required, exceptunder certain circumstances

Part-time students may apply for admissionto the M.S. program during any quarter. Full-time students must begin in the fall quarter.

DEGREE REQUIREMENTSMST offers a non-thesis M.S. in Managementin Science and Technology. Students elect oneof three areas of concentration within thedegree program: Managing the TechnologyCompany, Computational Finance orManaging in the Software Industries.Students must complete a minimum of 53credits with an average of ‘B’ or better; up tofour courses or twelve credits taken in thedepartment prior to matriculation may beused toward the degree requirements.

MST CORE SEQUENCE

All M.S. students must take the MST coresequence, consisting of the following courses ortheir equivalent (38 credits). The courses listedbelow are offered both on-campus and on-line.Either is acceptable for the M.S. in Management inScience and Technology degree. If you intend totake ONLY on-line courses, please see the DistanceDegree Requirements after this section.

MST501/501D Managerial and Financial Accountingfor Science & Technology 4 credits

MST502/502D Financial Management 4 credits

MST503/503D Marketing: Planning for Market 4 credits

MST510/510D Principles and Trends inTechnology Management 3 credits

MST512/512D Project Management 4 credits

MST513/513D Manufacturing Practicesand Management 3 credits

MST520/520D Managing in Science and Technology 4 credits

MST530/530D Strategic Management and Planning 4 credits

MST550/550D Capstone Project: Business Plan 4 credits

MST590/590D Effective Business Writingfor Management OR 1 credit

MST591/590D Professional Writing forNon-native Speakers 1 credit

A R E A O F E M P H A S I SAll emphasis areas require the completion of the34-credit M.S. core sequence. Specific coursesrequired for each emphasis area are as follows:

MANAGING THE TECHNOLOGY COMPANY SEQUENCE

Core Sequence plus three of the following MST Core Sequence plus three of the following fivecourses are required (9 credits):

MST511/511D Quality Management 3 credits

MST514/514D Issues in R&D Management 3 credits

MST522/522D Building Effective Organizations inScience and Technology 3 credits

MST540/540D International Management in Scienceand Technology 3 credits

MST541/541D Seminar in Leadership Development 3 credits

ELECTIVES: Any course in the above list notalready taken and/or any of the following(6-7 credits):

ECE555 Engineering Optimization 4 credits

ECE577 Principles for Technology Developmentand Introduction to Manufacturing 3 credits

ESE504 Uncertainty Analysis 4 credits

ESE586 Environmental Law and Regulation 3 credits

CSE503 Software Process Processes 3 credits





FIN547 Global Markets &Foreign Exchange 3 credits

FIN551 Options and Futures I 3 credits


FIN558 Advanced Numerical Computingin Finance 3 credits




MST504 Marketing: Going to Market 3 credits

MST515 Supply Chain Management 3 credits

MST517 Global Logistics andFinancial Management 3 credits

MST521/ Human Resource Management in521D Science and Technology 3 credits

MST523 New Products Development 4 credits

MST524 Digital Economy: Strategy for Success 4 credits

MST531 Software Commercialization 3 credits

MST542 Seminar in Social Issues in Management 3 credits

MST543 Commercialization Practicum 3 credits

MST544/MST544D Strategic Alliances 3 credits

MST58X Special Topics (special electives offeredon a one-time only basis)

Students may petition the MST department forelective credit for other OGI School academiccourses relevant to the theory or practice ofmanagement.

COMPUTATIONAL FINANCE SEQUENCE

MST Core Sequence plus the following threecourses are required (9 credits):


FIN551 Options and Futures 1 3 credits


Electives: three of the following courses arerequired (9 credits)




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FIN558 Advanced Numerical Computingin Finance 3 credits



Students should note that tuition for the CSEComputational Finance courses listed above(FINxxx) is higher than for other OGI courses.

MANAGING IN THE SOFTWARE INDUSTRIES SEQUENCE

MST Core Sequence plus the following two coursesare required (6 credits):

MST531 Software Commercialization 3 credits


Electives: Four of the following courses arerequired (12-13 credits):

CSE503 Software Process Practicum 4 credits



CSE518 Software Design and Development 3 credits


CSE564+ Human-Computer Interaction 3 credits

CSE567+ Developing User-Oriented Systems 3 credits

MST504 Marketing: Going to Market 3 credits

MST511/511D Quality Management 3 credits

MST522/ Building Effective Organizations in522D Science and Technology 3 credits

MST540/ International Management in Science540D and Technology 3 credits

MST541 Seminar in Leadership Development 3 credits

+Credit will be given for no more than one of theindicated courses.

Students may petition the MST department headfor elective credits for other OGI academic coursesrelevant to the theory or practice of management.

YOU CAN COMPLETE YOUR ENTIRE DEGREE ON LINE!

MST DISTANCE DEGREE REQUIREMENTSThe department of Management in Scienceand Technology recommends that studentstake at least two on-campus courses. Aproctored comprehensive exam may berequired at or near the completion of the MSTDistance degree requirements. Students mustcomplete a minimum of 52 credits with anaverage of B or better.

MST DISTANCE CORE SEQUENCE

All M.S. student must take the MST core sequence,consisting of the following courses or theirequivalent (34 credits):

MST501D Managerial and Financial Accountingfor Science and Technology 4 credits

MST502D Financial Management 4 credits

MST503D Marketing in Science and Technology 4 credits

MST510D Principles and Trends inTechnology Management 3 credits

MST512D Project Management 4 credits

MST513D Manufacturing Practicesand Management 3 credits

MST520D Managing in Science and Technology 4 credits

MST530D Strategic Management and Planning 4 credits

MST550D Capstone Project: Business Plan 4 credits

MST590D Effective Business Writing(4 workshops at .25 credits each) OR 1 credit

MST 591D Professional Writing for Non-native Speakers (with dept. approval; 4 workshops at .25 credits each) 1 credit

AREA OF EMPHASIS —DISTANCE DEGREEMST currently offers only the Managing theTechnology Company emphasis to studentswho take only online classes.

MANAGING THE TECHNOLOGY COMPANY DISTANCE SEQUENCE

MST Distance Core Sequence plus three of thefollowing four courses are required (9 credits)

MST511D Quality Management 3 credits

MST514D Issues in R&D Management 3 credits

MST522D Building Effective Organizations inScience and Technology 3 credits

MST540D International Management in Scienceand Technology 3 credits

Electives: any course in the above list not alreadytaken and/or any of the following (9 credits)

MST521D Human Resource Management inScience and Technology 3 credits

MST544D Strategic Alliances 3 credits

MST58XD Special Topics Variable credits

Students may petition the MST department headfor elective credits for other OGI School academiccourses relevant to the theory or practice ofmanagement.

COURSE DESCRIPTIONSMST 501, MST 501D Managerial and FinancialAccounting for Science and TechnologyThe course focuses on understanding and evaluatingfinancial reports and information for use in makingdecisions, particularly as they pertain to managing inscience, technology, engineering, and manufacturing.

4 credits

MST 502, MST 502D Financial Managementfor Science and TechnologyThe course combines a survey of the relevantaspects of micro- and macroeconomics with in-depth study of key concepts in financialmanagement of a firm, financial structure and finan-cial analysis of the firm, working capitalmanagement and short- and long-term financing.Particular attention is paid to valuation of invest-ment alternatives through study of risk and rates ofreturn, bond and stock valuation, and capital budg-eting. The course is designed to achieve balancebetween understanding theoretical foundations and

techniques of practical application. Prerequisite:MST 501. 4 credits

MST 503, MST 503D Marketing in Scienceand TechnologyThe course introduces the graduate student to thefull range of issues and activities involved in themarketing of technology-based products. The role ofmarketing within the organization is addressed, asare the key elements of an effective marketing pro-gram. The course is organized to cover the fullproduct introduction process, from market identifi-cation to product conception and definition, tomarket research, to competitive analysis, and ulti-mately, to product launch. Topics include pricing,sales and distribution alternatives, and marketingcommunications. To the extent possible, assign-ments utilize or draw from students’ workexperiences in technology, engineering, manufactur-ing, and science. 4 credits

MST 504, Marketing: Going to MarketThe overall goal of this course is to teach studentsto write a marketing plan that develops a productor service’s business model and persuasively makesthe business case. This goal is achieved by usingtwo strategies: by helping students understand andapply the critical concepts and principles drivingthe implementation of a high technology-orientedmarketing plan; and by helping students acquireand develop the language, methodologies, models,processes, standards, tools, and skills for analyzingand dealing with the high technology opportunitiesand challenges facing marketing at the dawn of thisnew century. 3 credits

MST 510, MST 510D Principles and Trendsin Technology ManagementThis course is about how companies choose,acquire, and develop the technologies that they useto develop, manufacture, deliver and support theirproducts. We look at these practices both from thevendor and buyer points of view, and also considerinternal technology development for internal use.Other topics addressed include profitably managingtechnology cycles; standards; technology forecast-ing; and the technology startup company. Relatedtopics such as competitive analysis, managingresearchers, and maintaining an innovative organi-zational atmosphere are dealt with in MST 503 andMST 514. The format includes lectures, discussions,guest speakers, and team and homework projects.

3 credits

MST 511, MST 511D Quality Management

The course covers total quality management (TQM)from the managerial vantage point-that is, both thebehavioral and operations management aspects,excluding sophisticated statistical analysis, of TQMare addressed. Classroom discussion, based on theparticipants’ experiences and the assigned read-ings from the text and cases, is the primary sourceof learning for many students. Lectures are usedbut generally as a basis for a facilitated discussionled by the instructor. The limitations of TQM alsoare discussed, given the inherent risks of excessiveoptimism associated with any social trend or per-ceived panacea. 3 credits

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MST 512, MST 512D Project ManagementThe course focuses on the managerial aspects ofproject selection and management. Topics addressedinclude planning, design, scheduling, implementa-tion, control, evaluation, and termination. 4 credits

MST 513, MST 513D Manufacturing Practicesand ManagementTopics covered include practices and trends in theoverall design, analysis, organization, and control ofmanufacturing operations, as well as relationshipswith vendors, suppliers, and customers. 3 credits

MST 514, MST 514D Issues in R & D ManagementParticipants examine issues in managing R&D andtechnological innovation in an environment ofincreasing time- and competence-based competi-tion, a competition that is simultaneously globaland local in both markets and technology, wherecompetitors draw on an existing technology basethat supports incremental innovation through radi-cal innovation, and where quality is a given.Particular attention is given to R&D managementissues in integrating technology into business strat-egy and operations, managing internal developmentand external sourcing of technology, seeking com-petitive advantage through collaborative advantage,and building new technical competence as a part ofevery project. Key trends, new conceptual frame-works, management tools and techniques, and bestpractices in R&D management are examinedthrough presentation, interactive class discussions,selected readings, case studies, and a numberof invited speakers from both small and largecompanies. 3 credits

MST 515 Supply Chain ManagementThis is a course in Supply Chain Management, aterm which denotes a total system approach to themanagement of all of those activities involved inphysically moving raw materials, inventory, and fin-ished goods inventory from point of origin to point ofconsumption. Supply Chain Management (SCM) is asystem approach to managing the entire flow ofinformation, materials, products, and financialfunds to and from suppliers and end-customers.

3 credits

MST 516 SCM – Advanced ModelingThis course will introduce the use of mathematicalprogramming in supply chain modeling. The empha-sis will be mainly on large-scale optimization ofreal-world supply chain distribution networks. Themajor skills taught are problem definition, modelformulation, and solution analysis. We will teachthe use of commercial software, which include theMAPLE algebraic modeling system for planningproblems, What’s BEST for decision-making, andGSCM for large mixed-integer programming net-work design. 3 credits

MST 517 Global Logistics and Financial ManagementThe global environment that characterizes the busi-ness world of today has pointed out the importanceof developing strategies that go beyond the geo-graphical boundaries of one country. Nowadays, it isnot uncommon to see a company that develops anew product in the US manufactures it in Asia and

sells it in Europe. Wage-rate differentials, expand-ing foreign markets, and improved transportationare breaking down barriers of time and spacebetween countries forcing the logistics function totake a global dimension. Global logistics is theresponse to the increasing integration of interna-tional markets as firms try to remain competitive.

The emphasis of the course is the operations andlogistics function in firms that source, produce, dis-tribute and market in multiple nations. Themanagement of logistics in such firms differs fromits domestic counterpart along several key dimen-sions. First, there is the need to be able to identifyand analyze factors that differ across nations, whichinfluence the effectiveness of this function. Theseinclude worker productivity, process adaptability,governmental concerns, transportation availability,culture and soon. In addition, because of the dis-tances involved, transportation and distribution areof greater significance. Finally, these geographicallydispersed set of facilities and markets must be inte-grated and manage to enhance the strategy of thebusiness unit. Therefore, some of the sessions of thecourse will focus on cross-national decisions andothers will focus on managing across nations.

3 credits

MST 520, MST 520D Managing in Scienceand TechnologyThis course focuses on developing participants’ abil-ity to understand and influence human behavior.Four theory-based frames are elaborated and usedfor understanding human behavior. Using the struc-tural frame, we examine work design and redesignfor individuals and groups, and consider the impactof restructuring. Using the human resource frame,we examine interpersonal and group dynamics,communication and creativity. Using the politicalframe, we consider power, conflict, and differencesin the workplace. Using the symbolic frame, weexamine the impact of individual leadership and cor-porate culture on organizational outcomes.

The course also examines the influence processesand network of relationships required for managingresearch scientists, engineers, and other profes-sionals, as individuals and in teams, in a fast-changing environment. Self-assessment, network-ing, and developmental relationships are exploredas means of developing influence and having impactwithin a technologically driven organization.

4 credits

MST 521, MST 521D Human Resource Managementin Science and TechnologyThis course focuses on the development, implemen-tation, and evaluation of human resourcemanagement (HRM) systems, and the relationshipbetween an organization’s HRM practices and theorganization’s effectiveness and competitive suc-cess. Specifically, the course addresses the choicesan organization must make in three HRM policyareas: organization of work and employee influence;personnel flows and development; and measurementand rewards. We consider the perspectives of boththe line manager and the HRM specialist in examin-ing these three policy areas. The course also

includes a limited overview of employment law, witha particular focus on recent cases and changes inemployment legislation. 3 credits

MST 522, MST 522D Building Effective Organizationsin Science and TechnologyThis course focuses on designing effective organiza-tions and managing change in organizations in whichengineering, manufacturing, and/or scientific tech-nologies are critical. Tools for assessing the need forreorganization and implementing structural changesare emphasized. The course pays special attentionto organizing for lateral coordination and integra-tion, as this is a required capability in technology-intensive organizations. Students are invited to con-sider the relationship between organizational theoryand practice. A range of theoretical perspectives isreviewed, and students are encouraged to compiletheir own approach by combining those presented.Extensive use is made of cases and actual examplesdrawn from the readings and from course partici-pants’ experiences. Taking MST 520 first isrecommended. 3 credits

MST 523 New Product DevelopmentSuccessful product development has been key tosurvival in today’s competitive markets. This coursewas designed to address professionals who are inproduct development organizations or support suchorganizations. It has been seen that technology inte-gration and creating innovative environments havebeen critical to developing profitable products intoday’s technology oriented companies. The coursewill review cases and published articles addressingkey issues in new product development. Topics suchas Disruptive Technologies, Technology Integration,Concurrent Engineering, and Managing TechnologicalInnovation will be covered. 4 credits

MST 524 Digital Economy: Strategy for SuccessThe purpose of this course is to equip the studentwith a practical and conceptual understanding ofwhat it takes to develop and maintain a competitiveadvantage in the new economy. We will look at it fromseveral perspectives. We will start by investigatingthe fundamental changes that the Internet and othertechnologies introduce in the economy and how thiscompletely changes the rules of the competitivegame. We will then look at how entire industries andactivities are being transformed and why.

In the second part of the course we will look atstrategy from several angles. The first one willaddress the question of what a company shouldconsider to develop its competitive advantage andits competitive strategy. The second angle willaddress the Internet marketing side or how to go tomarket and rise to the top. The third angle isaddressing the question of how successful compa-nies organize and what they do to operate at the“speed of change.” Students will use the learningthey acquire to develop a business concept to bepresented at the last session. The course will besupported by a Web site, where course materialsand resources will be made available. We will alsocarry discussions off-line. Several executives fromlocal companies have been invited to share theirexperience in the dot-com world. 4 credits

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MST 530, MST 530D Strategic Managementand PlanningThis course focuses on the analysis of the competi-tive environment and on the decision-makingprocess leading to the formulation and implementa-tion of strategy. Other topics include using time,knowledge, and technologies as competitive advan-tages, managing strategic change, and developingstrategic plans. Prerequisites: MST 502, MST 503,MST 520. 4 credits

MST 531 Software CommercializationThis course examines the structure of the softwareindustry, and problems of marketing privately devel-oped software and commercializing software fromthe government and nonprofit sector. Because thebusiness models for hardware and software compa-nies are quite different, the course focuses on thespecial problems of marketing, entrepreneurship,globalization, and alliances experienced by softwarefirms. Relationships between marketing strategyand development strategy also are examined.

3 credits

MST 540, MST 540D International Managementin Science and TechnologyTopics in this course include trends in the conduct ofinternational business, the international businessenvironment, the operation of multinational enter-prises, international technology transfer, and thespecial considerations associated with managing onthe international level. 3 credits

MST 541 Leadership and NegotiationThis course focuses on the negotiation and interper-sonal communication skills required to exerciseeffective leadership. Topics include creating clarityabout one’s own values and mission, exercisinginfluence through both formal and informal authori-ty channels, and being a catalyst for change.

3 credits

MST 542 Seminar in Social Issues in ManagementThis course focuses on ethical dilemmas, socialissues and responsibilities, and government regula-tions and influences. First, the course examinesdifferent frameworks for individual decision makingin an organizational setting. Next, the impact oforganizational policies and practices, and the wordsand actions of managers, on the behavior of individ-uals within those organizations is examined. Finally,the course focuses on the relationship betweenorganizations and the societies in which they oper-ate. We consider the perspectives of keystakeholders, including government regulators,community representatives, customers, employees,managers, and stockholders, and examine differentviews on corporate social responsibility. 3 credits

MST 543 Commercialization PracticumStudents will have the opportunity to work in teamswith real technologies. Student teams will produceassessments and plans for bringing new technolo-gies to market using Vijay Jolly’s Mind to MarketTechnology Commercialization and other frame-works such as a Total Life Cycle Planning approach.Wherever possible, industry advisors will mentorstudents in their area of expertise within the design,management and product manufacturing process.

Each team adopts a real technology held by Batelle-Pacific Northwest Laboratories, OHSU, OGI,Oregon Medical Laser Center, or others. Studentswill make one or more field trips to these institu-tions. The technologies may be in the areas ofenvironmental, health, genetics, multimedia, com-puters or other fields.

Each team’s final paper - which may include marketresearch, a design for a manufacturable product,profiles of desired management teams, licensingplans, tech-marketing feasibility, and/or preliminarystartup business plan, will be submitted to the insti-tution that originated the technology. MST studentsmay choose to use their 581 project as a prelimi-nary exercise for the capstone project. 3 credits

MST 544, MST 544D Strategic AlliancesThis course explores a model of implementingstrategic alliances, business partnering and jointventures originally outlined by Robert Lynch, seniorpartner of The Warren Company, in his bookBusiness Alliances Guide (John Wiley and Sons,1993). The book is a compilation of best practices instrategic alliance formation and implementation dis-tilled from approximately 40 different highperformance international and domestic strategicalliances. It offers a well-articulated framework,which is applicable across a broad range of alliancetypes. The objective of this course is to provide eachstudent with an opportunity to learn practical, effec-tive methods for forming, implementing andexecuting high-performance strategic alliances.

3 credits

MST 550 Capstone Project: Business PlanIn the program’s capstone course, students com-plete major integrative projects as members ofteams. Prerequisites: MST 530 and approval ofinstructor. 4 credits

MST 58X, MST 58XD – Special TopicsUnder this number, courses of particular relevanceand interest to students and faculty are offered.

Variable credits.

MST590, MST 590D Effective Business Writingfor ManagementThis course will review several aspects of conven-tional punctuation and grammar that address theneeds of the participants. In addition, attention isgiven to stylistics for clear, concise communicationnecessary in business writing. Class size is limitedto ten students. 1 credit

MST 591, MST 591D Professional Writing forNon-native SpeakersAn intensive review of English grammar and sen-tence structure with a focus on formal English forprofessional purposes. Some attention to the aca-demic essay as well as business writing. Class sizeis limited to ten students. No prerequisite. 1 credit

Note: descriptions for Computational Finance courses,designated FINxxx, are found in the catalog under theDepartment of Computer Science and EngineeringCourse Description section.

F R E D Y O U N G P H I L L I P SProfessor and Department HeadPh.D., ManagementScience/Business AdministrationThe University of Texasat Austin, [email protected]


Market research, marketinginnovation and high-technologyproducts, managing the newproduct development process,incubation and commercializationof new technologies, strategic andinnovative use of computers

R E P R E S E N TAT I V E P U B L I C AT I O N SF. Phillips, “Market-Oriented

Technology Management: Innovatingfor Profit in Entrepreneurial Times.”Springer-Verlag, Heidelberg, 2001.

F. Phillips and M. Burningham, “WTO vs. WTA? Exploring the WorldTrade Organization’s Impact onTechnopolis.” Presented at 4thInternational Conference On TechnologyPolicy & Innovation, Curitiba, Brazil,August, 2000.

F. Phillips and S. Tuladhar, “Measuresof Organizational Flexibility.”Technological Forecasting & SocialChange 64/1, May, 2000.

F. Phillips, L. Ochs, and M. Schrock,“The Product is Dead; Long Live theProduct-Service.” Research TechnologyManagement, vol. 42, no. 4, July-August, 51-56, 1999.

F. Phillips, A. Donoho, W. Keep, W. Mayberry, J.M. McCann, K. Shapiroand D. Smith, “ElectronicallyConnecting Retailers and Customers:Summary of an Expert Roundtable,”Journal of Shopping Center Research,4(2), 63-94, 1997.

F. Phillips and N. Kim, “Implicationsof Chaos Research for New ProductForecasting.” Technological Forecastingand Social Change, Vol. 54, No. 1,1996.

P. Brockett, A. Charnes, W.W. Cooper,D.B. Learner and F. Phillips,“Marketing Research Unification byInformation Theoretic Methods,”European Journal of OperationsResearch, 84, pp. 310-329,1995.

S. Thore, G. Kozmetsky and F. Phillips,“DEA of Financial Statements Data:The U.S. Computer Industry,” Journal ofProductivity Analysis, 5(3), 229, 1994.

F. Phillips, “Conditional InformationCharacterization of Brand Shifting in aHierarchical Market Structure,”Journal of the Operational ResearchSociety, 45(8), 901, 1994.

F. Phillips, R.K. Srivastava andR.S. Springer, “Project Valuation andScheduling with Recourse,” Proceedingsof PICMET 91, the PortlandInternational Conference onManagement of Engineering andTechnology. IEEE EngineeringManagement Society, 1991.

F. Phillips and B. Golany, “A Heuristicfor Estimating Densities from Data inHistogram Form,” Decision Sciences,24(4), 862-881, 1990.

C . N E I L B E R G L U N DProfessor/Joint Appointmentwith Department of Electricaland Computer EngineeringPh.D., Electrical EngineeringStanford University, [email protected]


Management of technology, andadvanced lithography forsemiconductor fabrication.

R E P R E S E N TAT I V E P U B L I C AT I O N SJ. Ye, M. Takac, C.N. Berglund,

G. Owen & R.F.W. Pease, “An ExactAlgorithm for the Self- Calibration ofPrecision X-Y Stages,” Conference onElectron, Ion & Photon BeamTechnology & Nanofabrication(May 1996).

M.T. Takac, J. Ye, M.R. Raugh, R.F.W.Pease, C.N. Berglund & G. Owen, “Self-Calibration in Two Dimensions:The Experiment,” 1996 SPIEInternational Symposium onMicrolithography (March 1996).

W. Wang, J. Ye, A.B. Owen, C.N.Berglund & R.F.W. Pease, “AdaptiveMetrology: An Economical Strategy forJudging the Acceptability of a MaskPattern,” J. Vac. Sci. Technol., B13(6)(November/December 1995).

J. Ye, C.N. Berglund & R.F.W. Pease,“Field Distortion Characterization UsingLinewidth or Pitch Measurement,” J. Vac. Sci. Technol. B13(6)(November/December 1995).

J. Ye, C.N. Berglund, J. Robinson &R.F.W. Pease, “A Review of Mask Errorson a Variety of Pattern Generators,”IEEE Transactions on SemiconductorManufacturing, 8(3), pp. 319-325(August 1995).

J. Ingino, G. Owen, C.N. Berglund,R. Browning & R.F.W. Pease,“Workpiece Charging in ElectronBeam Lithography,” J. Vac. Sci.Technol., B12(3), pp. 1367-1371(May/June 1994).

M A R I A N N E K O C HVisiting Associate ProfessorPh.D., Human ResourceManagement andIndustrial RelationsColumbia University, 1989 [email protected]


The human side of technologytransfer; work/family policies andpractices; coaching faculty in thedevelopment and teaching ofe-learnings courses.

R E P R E S E N TAT I V E P U B L I C AT I O N S :M. Koch & D Moshavi, “The Adoption

of Family-Friendly Policies in Family-Owned Firms: Paragon or Paradox,Proceedings of the 2001 SouthernManagement Association AnnualMeeting, New Orleans, LA, 2001.

M. Koch, L. Long, & A. Meyer,“Adoption of Innovations in Hospitals:Exploring the Validity of a Multi-StageModel,” forthcoming, InternationalJournal of Technology Management;alsoin Academy of Management BestPapers Proceedings, August, 1996.

M. Koch & G. Hundley, “The Effects ofUnionism on Recruitment and SelectionPractices,”Industrial Relations, Vol.36,No.3, pp.349-370, 1997.

M. Koch & R. McGrath, “ImprovingLabor Productivity: Human ResourceManagement Policies Do Matter,” 1996,Strategic Management Journal, Vol.17,pp.335-354, 1996. Awarded an AnbarElectronic Intelligence Citation ofExcellence Award for 1997.

M. Koch. “Hiring Practices andLabor Productivity”, 1995. GarlandPublishing, Inc., New York, N.Y., 1995.

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J A C K R A I T O NSenior FellowMBA, Finance & StatisticsUniversity of Washington, [email protected]

Jack Raiton has been VP and CFOat Planar Systems for the last fouryears, and also served as VP andCFO at Smith’s Home Furnishings.His prior experience includesworking at Tektronix for about 22years, the last 12 as the CorporateController and serving as PlantController for Fairchild Cameraand Instruments. Jack earned hisBS in Mathematics from OregonState University in 1966 and hisMBA in Finance and Statisticsfrom the University of Washingtonin 1967. He attended HarvardUniversity’s three-month AdvancedManagement Program, and passedthe CPA exam in 1979.

A R E A S O F E X P E R T I S E

Performance Measurement,Capital Structure, Stock Optionsand Incentive Plans, ForensicAccounting

A D R I A N R O B E R T SSenior AdvisorPh.D., MetallurgyUniversity of Manchester, England

Adrian Roberts is a consultant ontechnology management,specializing in R&D managementand technology commercialization.Acting as advisor to BattelleMemorial Institute and otherclients on technology projects andnew business creation, Adrian wasrecently appointed InterimDirector of Battelle-PacificNorthwest National Laboratories.This past year, he has contributedto the Center for EntrepreneurialGrowth and has taught the MSTcourse on TechnologyManagement, as well as workingwith Brookhaven, Oak Ridge andPacific Northwest NationalLaboratories on programs for theUS Department of Energy.

A R E A S O F E X P E R T I S E

Technology management,commercialization of technologies,R&D management, strategicplanning.

N I C O L E S T E C K L E RAssociate ProfessorPh.D., Organizational BehaviorHarvard University, [email protected]


Tools for diagnosing andimproving leadershipeffectiveness, roles inimplementing (and resisting)organizational change,interpersonal communicationand influence in organizations,and lateral coordinationin organizations.

R E P R E S E N TAT I V E P U B L I C AT I O N SN.A. Steckler & N. Fondas,

“Building Team Leader Effectiveness:A Diagnostic Tool,” OrganizationalDynamics, Vol. 23, 20-35,Winter/Spring 1995.

J. White, S. Jacobson, R. Jacques,N. Fondas & N.A. Steckler, “YouJust Don’t Understand: GenderedInteraction and the Process of ‘Doing’Organizational Scholarship,” Journal of Management Inquiry, 4(4), p. 370-379, December 1995.

N.A. Steckler & A. Donnellon,“Review of Peter K. Manning’s‘Organizational Communication’,”Academy of Management Review,Vol. 18, 374-377, 1993.

N.A. Steckler & R. Rosenthal, “SexDifferences in Nonverbal and VerbalCommunication with Bosses, Peers,and Subordinates,” Journal of AppliedPsychology, Vol. 70, 157-163, 1985.

N.C. Ware, N.A. Steckler &J. Leserman, “Undergraduate women:Who chooses a science major?”Journal of Higher Education,Vol. 56, 73-84, 1985.

A LV I N H . T O N GProfessor of ManagementPh.D., Electrical EngineeringUniversity of Minnesota, [email protected]


Alvin Tong teaches ProjectManagement and theCapstoneProject (Business Plan)course, and has been with MSTsince 1996. Alvin served as amentor for the 1999 student team,ArtCentral that won first place inthe New Venture Championship2000, a national/internationalbusiness plan competition held inBeaverton, Oregon. Alvin hasthirty years of working experiencein the computer and relatedindustry, which includes serving aschief operating officer of Acer,Inc., a Taiwan-based manufacturerof personal computers. While withAcer, he also served as Presidentof their venture capital arm. Priorto Acer, he worked for fourteenyears at IBM. In addition, he alsohad a significant role as the firstdeputy director-general of theHsin-chu Science-Based IndustrialPark (SBIP) in Taiwan. Alvinhas conducted numerousmanagement-training seminarsand is frequently invited to speakand lecture on the subject ofGlobalization and Hi-Tech Science-Based Industrial Parks.

R E P R E S E N TAT I V E P U B L I C AT I O N SP. Schumann, D. Prestwood, A. Tong,

& J. Vanston, “Innovate!”, McGraw-Hill,Inc., 1994.

F A C U L T Y | M A N AG E M E N T I N S C I E N C E A N D T E C H N O L O G Y | M S T

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M S T | M A N AG E M E N T I N S C I E N C E A N D T E C H N O L O G Y | F A C U L T Y

ADJUNCT FACULTY

K E N A N T H O N Y

Rapid Innovations

J E A N C L A U D E B A L L A N D

JCB Associates

T U G R U L D A I M

Intel Corporation

D E A N D E R R A H

Infocus Systems

R I C H A R D D O R F

University of California at Davis

D A V I D D R A K E

Catalyst Communications, Inc.

W I L L I A M D R E S S E L H O U S

Dresselhaus Design Group

R I C H A R D F O U R N I E R


R I C H A R D G O L D G A R

Covasoft

S T E P H E N G O M E S

Oregon Health & ScienceUnversity

J U L I A N G R E S S E R

LogosNet

J I L L B . K E L LY


K E I T H L A R S O N

Intel Corporation

R I TA L A X T O N - B E N Z A N

IMMEDIAD’s ChildRomProductions

K AT H Y M A N G E L - D A V I S

Professionally Speaking

M I C H A E L M C L E A N

AC Transit

D E I R D R E M E N D E Z

University of Texas at Austin

M I G U E L M E N D E Z


P A U L N E W M A N

Cooper Mountain Research, Inc.

LY L E O C H S

Technology & InnovationManagement Inc.

R I C H A R D P R I N S

Group 3

J E S S E R E E D E R

Leadership Dynamics

Y O N G - I N S H I N

Intel Corporation

J AY S H U T T E R

Momentum Research Group

L E S L I E S M I D

IBM

T H O I T R U O N G

Emery Worldwide

H A R V E Y U T E C H


J O H N W A L L N E R

Tektronix, Inc.

E U G E N E Y. W E I S S M A N

Weissman Associates

OHSU is an equal opportunity, affirmative action institution.

OHSU includes four schools, two hospitals, numerous primary care and specialty clinics,multiple research institutes, and several public service and outreach units.

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OGISchool of Science & Engineering Catalog

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