Term Paper: Objectives, Instructions and SubjectsThe term paper is a very important component of the course, making up 40% of the total assessment.

I. OBJECTIVES

To provide the opportunity for you to go deeper into a topic of your choice, related to the physical aspects of life science. It may be the topic you have always been interested in and wanted to read up more, or one that may be relevant to your major. A list of suggestions may be found in the final part of this document.

To summarize the knowledge you learned from this module

II. INSTRUCTIONS

A group size of 3 ~ 5 persons is recommended (need not be from the same tutorial group). To form groups would lessen the work for each member, and more importantly, it will allow us to develop a team working spirit, which turns out to be an important element in 21st century education. Apart from this, discussions with friends facilitate learning, and may even lead to some creative brainstorming.

If you can’t find the proper team members yourself, please email the Teaching Assistant Mr. Chin Chee Leong (Email: phyccl@nus.edu.sg ) the topic you prefer. He will help you with the grouping.

When deciding on a topic, your group must try to gain at least a basic understanding /overview of the chosen topic and start looking around for suitable references. Do not leave this until the last minute after approval, as it would be too late to change if you find the topic too hard, or cannot get a hold of suitable books, etc.

To gather your information from one or two main sources, with several ancillary ones. Please do not obtain your information solely from the Internet, as the material found there often lacks scientific depth and rigor. If you do use information from the Internet, you should ensure that your sources are reliable and scientifically sound.

Once your group has finalized a topic, a representative must send an email to Mr. Chin Chee Leong with the following information:

o Selected topico Names and matriculation numbers of every group member o An abstract of less than 100 words

The deadline for this is 18 May 2007, but you are encouraged to do this as early as possible so you can get started on the project.

Your sources should reflect your understanding of the chosen topic. You should give an overview of the topic. It should be pitched at a level that your fellow classmates can understand, and presented in an interesting manner. It should not be a technical report

Please feel free to contact Mr. Chin Chee Leong or myself at any stage during the project, if you encounter any difficulty, have a query, or simply need some suggestions.

The final report o It should be between 25 to 35 pages long. A detailed guide to the

format of the report is given in Appendix 1.o The report will include the following two parts:

Part I (40%)-a comprehensive summary of all lectures given in this module. It should consist of 10 pages for all groups.

Part II (60%)- a topic selected from section III. It should consist of ~ 15 (3 person group), ~ 20 (4 person group), or ~ 25 (5 person group) pages, respectively.

o In total I would expect more materials from a larger group. As a guideline, I expect about 25 pages for a 3-person group, 30 pages for a 4-person group and 35 pages for a 5-person group. In any case, your report should not exceed 35 pages (inclusive of everything: graphs, appendix, etc.).

o A title page consisting of the subject titles, the names and matriculation numbers of all members of your group, should be included at the beginning according to the format given in Appendix 2.

o The report must be properly typed and printed (double-sided). It can be either stapled or bound.

o A soft copy of your report should be submitted together with the hard copy.

o It may contain figures, graphs and equations, if you think that they can help illustrate the points you wish to make. I do recommend more figures and graphs rather than equations. I do not recommend using any equations which you don’t really understand.

All sources of the sections on arguments, facts from the literature or the Internet occurring in the text must be referenced properly. All references should be listed at the end of your report (e.g., author, title, publisher and year, for a book). See Appendix 1 for more details.

The final report must be handed in directly to Mr. Chin Chee Leong by Deadline: 12 June 2007. Reports received after this date will not be considered.

The assessment criteria are as follows: o Content: Does the essay cover the important aspects of the

subject? How much breadth and depth is there? Were figures and illustrations used appropriately? (50%)

o Originality and creativity: Does your essay stand out from the others on the same topic? Is there evidence of trying to rewrite in your own words? Was the topic presented in an interesting or creative way? (30%)

o Overall considerations: Was the essay clearly written? Was it well organized and presented? Has the writing followed the required format of the report (ie. the references)? (20%)

o The difficulty of the chosen topic will also be taken into account. The degree of difficulty will be ranked from 1 (the easiest one) to 5 (the most difficult one).

In certain special cases, I may require you to come for an interview as part of the assessment (e.g., when I cannot be sure whether you understand what you are writing about).

In order to evaluate the contribution from each group member, a short description of the task distribution among the members should be attached at the end of essay.

IMPORTANT WARNING

Everybody is expected to complete and hand in a term paper. If you do not, you will certainly fail the course.

All sources that you use must be properly referenced. Any direct copying of material from your sources must be acknowledged, by placing quotes around the excerpted material and referring to the source in the footnotes or reference section. The direct use of material from any source without such acknowledgement constitutes plagiarism, and, if discovered, would result in your term paper receiving a fail grade.

Direct copying entire paragraphs or sections from a source with only minor paraphrasing is not allowed. If you are unsure about this, I recommend that you first try to read up and understand the subject in question, and then try to rewrite it in your own words without looking at your sources directly.

In view of the preceding warning, it is your responsibility to ensure that your group members do not plagiarize any material.

III. ESSAY TOPICS

Note: the references provided in the following subjects just serve as a starting point for the paper. In order to complete the term paper, you go beyond the provided references to search for more comprehensive info either from Internet or other sources.

Subject 1: Osteoporosis and Microgravity Related Osteoporosis (rank of difficulty: 5).Description: Osteoporosis is a condition in which bones become porous, brittle, and prone to fracture. It was found that over a period of eight months in space, an astronaut loses about as much bone mass as the average person loses between ages 50 and 60. In preparing this essay, you should at least cover the following points:

Basic structure of bones Biomineralization/demineralization during the formation and remodeling

the bones and the relevant physics principles (physics of crystallization, mass transport, etc.) .

Remodeling process and the relation to mass transport and biomineralization/demineralization

Current views on the cause of osteoporosis Space travel and microgravity Microgravity related osteoporosis, and how to avoid it. Your opinions.

References: J.H. Postlethwait & J.L. Hopson, The Nature of Life (the 3d edition), (McGraw-Hill, Inc.). A.R. Ten Cate, Oral Histology: Development, Structure, and Function, (C.V. Mostby

Company). X.Y. Liu, Appl. Phys. Lett. 79, 3539-3542 (2001). X.Y. Liu, J. Chem. Phys. 115, 9970-9974 (DEC 1 2001). Sci. Am 275, 15 (1996).

Subject 2: Dental Caries and the biophysical principles (rank of difficulty: 4). Description: Dental caries is a common disease we encounter in our daily life. To repair dental caries, it costs more than US$15 b in USA. But do you know that dental caries shares a similar physical principle as dissolving sugar in water? You should at least cover the following points in your essay:

What is the structure of tooth? Discuss the biophyical/chemical process of dental caries. Your opinion on how to prevent dental caries based on the above

principles. Current technologies in curing dental caries and the future perspectives.

References:

A.R. Ten Cate, Oral Histology: Development, Structure, and Function, (C.V. Mostby Company).

G. H. Nancollas, Biological Mineralization and Demineralization, (Springer-Verlag: Berlin, 1982).

Subject 3: Freezing and anti freeze protein (rank of difficulty: 4).Description: Freezing is a phenomenon when liquid water turns into solid ice at a temperature lower than 0oC (subzero). When freezing occurs in the cells of a biological system, damage to the cells may be the result. Nevertheless, some plants, fishes and insects can survive in severe winter when the temperature is well below zero. The secret is that these living organisms contain certain proteins, the so-called anti-freeze proteins, which prevent the formation of ice even in strong subzero conditions. These proteins have some important applications in food processing, and life sciences such as the preservation of organs. You should at least cover the following points in your essay:

Why and how does freezing take place? How do anti-freeze proteins stop the formation of ice? How can we produce anti-freeze proteins artificially? Applications of anti-freeze proteins in particular in life sciences. Future perspectives.

References: N. Du and X.Y. Liu, Appl. Phys. Lett. 81, 445-448 (2002). D. Rosenfeld and W. L. Woodley, Nature (London) 405, 440 (2000). P. L. Davies, G. L. Fletcher, and C. L. Hew, in Environmental Stress and Gene

Regulation (BIOS Scientific, Oxford, 1999), p. 61. C. A. Knight, Nature (London) 406, 249 (2000).

Subject 4: Bioelectric signals and Life (rank of difficulty: 5)

Description: In preparing this essay, the following points should be covered Physical principles of bioelectric signals. How are bioelectric signals produced and transmitted in human bodies? Bioelectric signals and our activities Bioelectric signals and our health Imaging of bioelectric signals and disease diagnoses. Bioelectric signals and bio-sensing.

References: J.H. Postlethwait & J.L. Hopson, The Nature of Life (the 3d edition) (McGraw-Hill, Inc.). John D.Cutnell and Kenneth W. Johnson, Physics Wiley, 1998. C. Sybesma, Biophysics, An Introduction (Kluwer Academic Publishers). K. Van Holde , W. Johnson , Pui Shing Ho, Principles of Physical Biochemistry (Prentice-

Hall).

Subject 5: Color and Structure Color of Butterfly (rank of difficulty: 4).

Description: In preparing this essay, you should at least cover the following points

Color-physics origin Explain the optic principles behind structural color. How do different colors occur in wing scales of a butterfly? The implications and applications of structure color.

References:

P. Vukusic, J. R. Sambles, C. R. Lawrence, Nature 404, 457 (2000). Alison Sweeney, Christopher Jiggins ,Sönke Johnsen, Nature 423, 31

(2003).

Subject 6: The structure of protein and protein crystallization (rank of difficulty: 5).Description: In preparing this essay, you should at least cover the following points

Structure and types of proteins Bio functionalities of proteins Methods of determining protein structures Principles and methods of protein crystal growth Protein crystallization and the relationship to our health

References: A. Ducruix, and R.Giege, Crystallization of Nucleic Acid and Proteins, (Oxford Press,

Oxford, 1999). M. Daune, Molecular Biophysics, (Oxford Press, Oxford,1993). C. Sybesma, Biophysics, An Introduction, (Kluwer Academic Publishers).

Subject 10: Silk and our life (rank of difficulty: 5).Description: Spider silk fibers are of practical interest because of their excellent mechanical property. It is strong and tough, and it is optimized by nature to fulfill a wide range of functions using subtle changes in chemical composition and, importantly, in morphological structure at the nanometer scale. Spider dragline silk is a high-performance fiber with mechanical properties rivaling and surpassing the best man-made materials. It is often utilized as a material for making bullet jackets, parachutes and other high performance fabrics, etc. The challenge is that the availability of spider silk is very limited. Worm silk is also an important bio material, and widely used in textile industries and other areas of our

daily life. More importantly, silk worms can be raised and the silk can be obtained easily. The problem is that worm silk is not as strong as spider silk.

You should at least cover the following points in your essay: Importance and applications of both spider silk and worm silk in the high

tech areas and our daily life. What are the key challenges in silk related research? What are the structures of spider and worm silk? What is the correlation between the structure of silk and the mechanical

properties? How to enhance the mechanical properties (ie. strength) of silk? What are the techniques available to “convert” worm silk to spider silk?

And how successful they are? Your comment on the future perspectives in silk related research.

References:

Hinman, M. B., Jones, J. A. & Lewis, R. V. (2000) Trends Biotechnol. 18, 374–379. Hayashi, C. Y., Shipley, N. H. & Lewis, R. V. (1999) Int. J. Biol. Macromol. 24, 271–

275. Tirrell, D. A. (1996) Science 271, 39–40. Cunniff, P. M., Fossey, S. A., Auerbach, M. A., Song, J. W., Kaplan, D. L., Adams, W.

W., Eby, R. K., Mahoney, D. & Vezie, D. L. (1994) Polym. Adv. Technol. 5, 401–410. Vollrath, F. (2000) Strength and structure of spiders’ silks. Reviews in Molecular

Biotechnology 74, 67-83. Kaplan, D. L., Adams, W. W., Viney, C. & Farmer, B. L. (1994) in Silk Polymers-

Material Science and Biotechnology, eds. Kaplan, D., Adams, W. W., Farmer, B.&Viney, C., ACS Symposium Series (Am. Chem. Soc., Washington, DC), Vol. 544, pp. 2–16.

Appendix

Guide for Term Paper

Please read these pages carefully. Meticulous attention to these instructions will not only benefit you but also facilitate the lecturer who reads your report. Careful preparation of the report is the most important single factor enssuring error-free work that precisely reflects your scope.

1. General Instructions ........................................................................................................ 22. Illustrations ...................................................................................................................... 33. Tables ............................................................................................................................... 54. Numbers, Units, Symbols, and Equations ......................................................................... 65. References ........................................................................................................................ 9

1. General Instructions

a. An abstract consisting of 250 words should be given at the beginning.

b. The main body of report, including the references, appendices, should not exceed 35 pages.

c. The original printout of the report including all the necessary references, tables, artwork, photographs, line drawings, etc., must be submitted to the lecturer in charge.

d. The report must be printed in the font size of 11pt, 1.5-SPACE on double sided of good-quality white or near-white A4 paper, with margins of at least one inch on all sides. Illustrations and tables must be prepared as specified in Sections 2 and 3.

e. The first page of the report should give the title of the project and the FULL name(s) and

MATRICULATION NUMBER (s) of the author(s).

f. Figures and tables (detailed, single-spaced) should be inserted in the proper places in the report.

g. Footnotes should be used only if it is not possible to incorporate the thought into the text without disrupting the flow of the argument. The placement of footnotes is indicated in the text by asterisks (or daggers, double daggers, etc., if there is more than one footnote on a page).

2. Illustrations

a. Original inked drawings, high-quality (300 dpi) laser printouts, or high-quality ink jet prints

(minimum 600 dpi on high-quality/photo paper) yield the best results and should be

submitted with the report.

b. The illustrations should be fully lettered, and the lettering must be large enough to remain

legible.

c. ILLUSTRATIONS SHOULD BE FREE OF UNNECESSARY DETAILS. Graphs should be prepared with

ticks on the axes rather than grid lines. Shading should be avoided if it is not essential to the

understanding of the illustration. If screens (dot patterns) or fine patterns are used for

shading, they should be coarse (e.g., big dots). Crosshatching, solid black, solid white, and

(heavy) vertical or horizontal lines should be used instead. (Fine shading arbitrarily drops out

and subtle changes tend to disappear in reproduction/reduction.)

d. Photographs should be used sparingly.

e. Generally, the illustrations should be numbered in a single sequence of arabic numbers

throughout the report, in the order in which they are mentioned in the text. All text references

should employ the word “figure” rather than such varied designations as “diagram,” “chart,”

“photograph,” etc.

3. Tables

a. Each table must be SINGLE-SPACED and should be provided with a brief title. If a table is

a number of pages, the pages should be consecutively numbered, including the table number and

“(cont.).” Descriptive material and lengthy explanations necessary for the understanding of the

table should not be written into the title but typed as footnotes immediately below the table or

discussed at length in the main text.

b. All tables should be numbered consecutively throughout the report, using arabic

numerals. The sequence of table numbers should be independent of those used for figures or other

sequentially numbered elements.

c. Each table should be cited in the text, the reference being made by number and not by

such words as “above” or “below.”

d. Superscript lower-case letters should be used as footnote indices in tables to avoid

confusion with the symbols used for text footnotes that may occur on the same page.

4. Numbers, Units, Symbols, and Equations

a. Numbers up to ten should generally be spelled out, but numerals should be used for numbers

from 11 up, except that numerals are always used in conjunction with symbols and units of

measurement. Commas should separate groups of three digits in numbers of FIVE or more

digits (12,583) but no commas should be used in numbers of four digits (5837) unless they

are aligned in a column with numbers that do contain commas:1,356,789

78,652 5,382

Numbers between zero and one should be written with a digit in front of the decimal point

(0.5—never .5).

b. The International System (SI) of units should be used. Units should be abbreviated when used

with numerals but written out when they occur in the text without numerals. The

abbreviations listed below should be employed. Note that these abbreviations are used

without periods:

ampere A meter mcalorie cal mho spell outcandela cd micrometer mcoulomb C microliter lcubic meter m3 milligram mgcurie Ci milliliter mldecibel db millimeter mmdegree Centigrade C millimeter of mercury mm Hgdegree Kelvin K million electron volts MeVdegree (angle) millivolt mVdyne dyn mole molelectron volt eV nanometer nmerg spell out newton Nfarad F ohm gauss G ohm-centimeter -cmgram g parts per million ppmhenry H percent %hertz Hz radian radhour h roentgen Rjoule J second (time) skiloelectron volt keV second (of arc) "kilogram kg square meter m2kilometer km steradian srkilovolt kV tesla Tkilowatt kW torr Torrlambert L volt Vliter spell out watt Wlumen lm weber Wblux lx

c. The unit abbreviations listed above stand for the plural as well as the singular. Write 5 cm, not

5 cms.

d. The following prefixes may be combined with the basic unit abbreviations:

d deci (10-1) p pico (10-12)

k kilo (103)

c centi (10-2) f femto (10-15)

M mega (106)

m milli (10-3) da deka (10) G giga (109) micro (10-6) h hecto (102) T tera (1012

)n nano (10-9)

e. Displayed equations should be numbered using sequential arabic numerals in parentheses in

the right margin. (Only one sequence should be used for both mathematical and chemical

equations.) In the text, equations should be referred to as Eq. (1), Eqs. (3)–(5); if the word

“Equation” begins a sentence, it should be written out in full. If a parenthetical reference to

an equation is made, the parenthesis around the number should be omitted, e.g., “A

relationship (Eq. 4) is derived….”

f. A displayed equation should be treated grammatically as part of a sentence, and THE TEXT

IMMEDIATELY PRECEDING a displayed equation punctuated according to the position of the

displayed equation in the sentence. (However, please note that PUNCTUATION SHOULD NOT

BE USED WITHIN THE DISPLAYED EQUATION.) Also, please remember, there should be a thin

space on both sides of an equals sign and any other operators.

g. The sequence of signs of aggregation should in general be {[( )]}, with due account taken

of the special meaning of certain types of brackets.

h. Follow customary practice and do not use parentheses around simple arguments of

functions such as the sine, cosine, and logarithm, e.g., use sin 2ax, cos(2x/b), log2 2m.

i. Mathematical and symbolic material in displayed equations and in the body of the text must

be typed (or written) with great care. (If possible, avoid the handwriting of Greek letters and

other special symbols. If you cannot, they must be identified by name at their FIRST

occurrence.) If bold is unavailable, bold letters must be identified by a wavy underline at

EACH occurrence. If it is necessary to use symbols from fonts other than the usual italic or

bold (script, German, etc.), this may be indicated by color-coded underscores, but must

somehow be clearly identified.

j. Particular care must be taken to differentiate clearly between the letter l and the numeral 1,

the italic letter k and the Greek kappa, the italic w and the Greek omega, and also between

the capital and lower-case forms of such letters as c, k, o, p, s, u, v, w, x, and z.

k. Built-up fractions and other notation requiring more than one line of type (this does not

include subscripts and superscripts) should be avoided in the text proper, but if used, should

be displayed. Simple fractions can be converted to one-line form, using the solidus:

Parentheses must be used when ambiguities would otherwise result.

l. In text, the upper and lower limits on, e.g., summation symbols, should be placed to the right of the symbols in the sub-and superscript positions, e.g., i ai; they may be typed in

the customary position in displayed material, e.g., i ai.

m. The form exp (...) rather than e... should be used for complicated exponents, e.g., exponents

with sub-or superscripts; appropriate brackets should be used for the exp form following

point d above.

n. Instead of square root signs, the exponent 1/2 should be used with appropriate brackets.

o. Use forms such as ith rather than ith or ith.

p. The chemical notation selected should avoid ring structures and vertical side chains

whenever possible. Cl OH may without loss of clarity be written as p-C1C6H4OH or CH3

| CH3-CH2-C-CH2-CH2-CH2-CH3 as CH3CH2C(CH3)2(CH2)3CH3 | CH3

Single bones are normally omitted. Indicate where long formulas may be broken.

5. References

a. You are responsible for the accuracy of your references. All names; dates; article, journal,

and volume titles; and volume and page numbers should be checked and double-checked

before the report is submitted.

b. References should be numbered in the order of their first citation in the text. The citation

may be used with or without the author’s name: “…it has been shown by Johnson17 that…”

or “…experiments with calcium,6 potassium,7 and strontium8 have shown….” Several

references may be cited together, the numbers being separated by commas and spaces:

“several recent investigations7, 9, 15 indicate….” If three or more consecutive references

are cited together, an en dash should be used between the lowest and highest reference

numbers: “…while others10–14, 17–19 show that….”

c. The reference list must be printed 1.5-SPACED with one extra line of space between each reference, in the style indicated by the following examples:

1. G. Bhatt, H. Grotch, E. Kazes, and D. A. Owen, Relativistic spin-dependent Compton

scattering from electrons, Phys. Rev. A 28(4), 2195–2200 (1983).

2. R. W. Arnett, K. A. Warren, and L. O. Muller, Optimum Design of Liquid Oxygen Containers,

Wright Air Development Center Technical Report No. 59-62 (August, 1961), pp. 118–120.

3. M. Wellner, Elements of Physics (Plenum Press, New York, 1991).

4. A. J. Duncan and Z. A. Sheikh, in: Polarized Electron/Polarized Photon Physics, edited by H.

Kleinpoppen and W. R. Newell (Plenum Press, New York, 1995), pp. 187–196.

5. Kluwer Academic/Plenum Publishers (New York, January 1, 2000); http://www.wkap.nl.

The examples illustrate the following characteristic cases:

1. A journal article. ALL of the authors are given, initials with a space between, then

surname, followed by a comma. The full title of the article is given. Capitalize only the first

word of the title, the first word of the subtitle (if any), and proper nouns, proper adjectives,

or terms commonly capitalized. The abbreviated name of the journal follows (in the form

listed in Chemical Abstracts - List of Periodicals; names of journals or other periodical

publications not listed there should be spelled out). The volume number is bold and the first

and last page numbers are given (separated by an n-dash), rather than just the first. For

journals with unnumbered volumes, the year takes the place of the volume number: J.

Chem. Soc. 1965, 2516–2522. For journals that start the pagination of each issue with 1, the

issue number must be given in parentheses following the volume number: Pribory i Tekhn.

Eksperim. 7(3), 53–57 (1962).

2. For pamphlets, bulletins, or any publications other than “regular” books or journals, give

all the information available and do not use abbreviations. Do not italicize the title. For

unpublished theses and dissertations, be sure to specify degree and institution (for

unpublished material, “unpublished” “paper,” “essay,” “report,” etc., or “personal

communication,” “in press,” etc., should be the final, PARENTHETICAL element in the

citation).

3. A simple authored book reference.

4. A report in a multiauthored edited volume.

5. A website. The first element would be the individual or registered name (again, give as

much information as possible), then the affiliation/city, and the revision date (THE REVISION

DATE MUST BE GIVEN), the actual address is last.

An online journal would be as the above examples of journal citations with the addition of a

“(Online)” immediately following the journal title.

d. Do not use “ibid.,” “op. cit.,” or “loc. cit.” references, and do not use the abbreviation “et

al.” in the reference list, but list all authors, even when there are very many. However, the

text reference in such a case may take the form “…shown by Jones et al.7….”

APPENDIX 2 THE FORMAT OF TITLE PAGE

GEM1521K: PHYSICS IN LIFE SCIENCES -TERM PAPER

Subject 6:

Optics and vision

By

Tan Yi Lin (Uxx066253)Ng Hoon Hwee (Uxx036250)

Chung Eric (Uxx077263)

June, 2007