Poster on JHU Biological Physics Labs - ComPADRE · The Biological Physics Labs in the Johns...
Transcript of Poster on JHU Biological Physics Labs - ComPADRE · The Biological Physics Labs in the Johns...
TheBiologicalPhysicsLabsintheJohnsHopkinsUniversity
DepartmentofPhysics&Astronomy
StevenK.Wonnell&DanielH.Reich
DepartmentofPhysicsandAstronomy3400N.CharlesStreet
BalJmore,MD21218E‐Mailcontact:[email protected]
Abstract
• Eightexperimentshavebeendevelopedtoaccompanythetwosemester,junior‐levelcourseinBiologicalPhysicsofferedinJohnsHopkinsUniversity’sDepartmentofPhysicsandAstronomy.
• EachexperimentillustratesafundamentalprincipleofthephysicsunderlyingabiologicalphenomenonoroftheapplicaJonofaphysicaltechniquetobiology,thela[erofwhichisusuallyspectroscopicalinnature.TopicsforwhichwehaveexperimentsincludeFouriersynthesisandanalysis,interference,diffracJonofDNAopJcaltransforms,magneJcresonance,diffusionandmicrofluidics,themicroscope,andBrownianmoJon.
• Inthelecturecourse,importanceisplacedontheexperimentalfundamentalssurroundingdataacquisiJonandanalysis,includingfundamentallimitaJonsandthearJfactsgeneratedbyimproperdataacquisiJon.TheselimitaJonsarearJfactsareexploredinthelabbyourstudents.
• WewilldiscussthechoicesandmoJvaJonsunderlyingthedevelopmentoftheseexperiments;theirintegraJonandsynchronizaJonwiththelecturecourse;funding;andimportantdetailsforeachexperiment.
GeneralInformaJonabouttheExperiments
• Funded($50K)byaporJonofaHowardHughesMedicalInsJtutegranttoJohnsHopkinsUniversity.
• Eachlabexperimentisonetotwohourslongandperformedinoneortwolabsessions
• EnJreclassdoesexperimentsimultaneously(have10‐12copiesofeachexperimentforallbutoneexp.).
• StudentsrecordtheirobservaJons,data,analysis,andconclusions,andsubmitthisrecordfortheirgrade.
• Experimentsarecloselysynchronizedwiththelecturecourse;infactthelecturecourseisneededtoprovidethenecessarybackgroundinformaJon.
FourierAnalysis
• AcJviJes:– Createandobservesoundwaveformsfrommusicalandelectronic
sources– ConstructWaveformsbyspecifyingFouriercomponents
– LearnaboutDataAcquisiJon– MeasureFouriercomponentsfromvariousinstrumentalsounds
Beats,DigiJzaJon,Aliasing
• UsesameapparatusasforFourierAnalysis• AcJviJes– Producebeatsandobservewaveforms
• Tuningforks• Electronically
– ExamineDiscreteness• Inacquiredrawdata• Inprocessed(FourierTransform)data• EffectsofmeasuringJmeandsamplingrate
– Resolvetwocloselyspacedfrequencies– Aliasing:observe(andcalculate)effectofsamplingratebelowNyquistfrequency
Interference&DiffracJonfromSlits
• IntroducJontoInterferenceandDiffracJon• UseCornellslifilm;Pascoslits;CDs,DVDs,graJngs
– Seeeffectsofslitspacing(relatedtolahcespacing)– Seeeffectsofspotintensity(infoaboutslititself)
DiffracJonbyDNAOpJcalTransforms
• UseopJcaldiffracJontosimulateDNAdiffracJon
• SameapparatusasforInterference&DiffracJonlabs;UseDNAOpJcalTransformSlifilmfromICE
• Extractstructureofpa[ernsfrommeasurementsofondiffracJondata– ZigZagslitpa[erns(A‐C):
• Lahceconstant(1‐D)• Widthofindividuallines• Layerlinespacinggiveslahce
constant– SineWavePa[erns(D,E,G,H)
• Lahceconstant• “Amplitude”
– SpacingbetweenHelices(F,I,L)• ModulaJonoflayerlineintensiJes
– Effects(K,J)ofdiscretenessofDNAstructure• ObservaJononlyoftheseeffects
TheMicroscope
• ObservaJonsinconjugatefieldandconjugatebackapertureplanes
• KoehlerIlluminaJon• Effectsofcondenser
diaphragm• ResoluJonof
microscopeanddiffracJoninbackaperture(Abbetheory)
• PhaseContrastobservaJons
• DarkFieldobservaJons
DiffusionandMicrofluidics
• Experimenttomeasurethediffusionofbluefoodcoloringinwaterinamicrofluidiccircuitcard
• AcJviJes:– Observedirectlythelaminarflowofwater– Learnandapplyexperimentaltechniques
• AcquisiJonofdigitalimageswithmicroscope• ExtracJonofquanJtaJveinformaJonfrom
image• FihngofdatatomodelequaJon
– Providelaboratoryexperiencewith• ObservaJonandMeasurementofDiffusion• LaminarFlow• MicrofluidicCircuits
Channel:4.0mmwide,12.1cmlong,100µmdeep
BrownianMoJon• AcJviJes:
– 1micronspheresinwaterphotographedevery2seconds– ImageJusedtoobtainparJclecoordinates– DiffusioncoefficientDcalculatedfromparJcledisplacements;weuse
distribuJonofstepsizes
– DalsocalculatedfromEinsteinrelaJonζD=kBTandviscousdragcoefficientforasphereζ=6πηα(i.e.FfricJon=ζv,Stoke’sequaJon)
– Newexperimentaltechniqueinanalysisofdatafromphotographs
• DirectobservaJonofBrownianmoJon– isaprimarystarJngpointforkineJctheory:probabilitydistribuJons,random
walks,diffusion– IspervasiveenvironmentforBiophysics
• Cellularprocessestakeplaceinanoisyenvironment• InterplaybetweenthermalanddeterminisJcforcesgivesrisetotherichbehaviorofmolecularmachines1
1“TheBiologicalFronJerofPhysics,”byRobPhillipsandStephenR.Quake,inPhysicsToday,May2006,pp38‐4
€
P(Δx) =1
4πDtexp −(Δx)2
4Dt
NuclearMagneJcResonance
• Haveonlyonecopyofthisapparatus(Teachspin’sPulsedNMRApparatus)
• UseEricBlack’swrite‐up(fromCaltech)• Doneasaclass“alltogether”• AcJviJesinclude:– Assemblingandtuningtheapparatus– ObservingfreeinducJondecay– SpinEchoesandmulJplepulsesequences– MeasurementofT1andT2
LectureCourseSyllabus(forwhichthelabsareacomponent)
• SophomoreorJuniorlevel,year‐longphysicscourse.• Intendedforstudentswithaninterestinthebiophysicalorbiologicalsciences.• Three50minutelecturesandone50minuteconferencesecJoneachweek;4credits.• labexperimentssubsJtuteforconferencesecJonson8occasions.• Weeklyhomework;twomidterms;onefinalexam.• Forphysicsmajors,maysubsJtutefor“normal”sophomorewavesandmodernphysicscourses.• Firstsemester:providesanintroducJontowavephenomena,primarilythroughthestudyof
biophysicalprobesthatdependontheinteracJonofelectromagneJcradiaJonwithma[er.– RequiredTextbooks:
• R.K.Hobbie,IntermediatePhysicsforMedicineandBiology• D.B.Murphy,FundamentalsofLightMicroscopyandElectronicImaging• A.P.French,VibraJonsandWaves
– Topicsinclude:• WavesandFourierAnalysis• X‐raydiffracJonandcrystallography• OpJcs‐thephysicsofmodernlightmicroscopy• Quantummechanics• NMRandMRITest
• Secondsemester:coversphysicalprinciplesthatareimportantforunderstandingbiologicalsystemsatthecellularandsub‐cellularlevel.ThecorematerialisclassicalstaJsJcalphysics,buttopicsinfluidmechanicsandelectricityandmagneJsmarealsocovered.– RequiredTextbooks:
• PhilipNelson,BiologicalPhysics:Energy,Informa/on,life.
• CoursestartedbyJHUfacultymemberDanielH.Reich;currentlytaughtbyMarkRobbins.
FirstSemesterSyllabusWeek Topics Notes
1 BasicWaveProperJes;StartFourieranalysis
2 FourierAnalysis
3 Digitalsignalprocessing;PhysicsofHearing Lab1:SoundandFourierSynthesis
4 Intro.toElectromagneJcwaves;InterferenceandDiffracJonin1D
Lab2:Beats,DigitalSignalMeasurement;Aliasing
5 DiffracJonin2Dand3D Midterm
6 X‐rayCrystallography;StructureofDNA Lab3:InterferenceandDiffracJon
7 GeometricalOpJcs;vision;basicmicroscopy Lab4:OpJcalsimulaJonofDNA
8 PhysicsOpJcs;NumericalApertureandallthat
9 Fancymicroscopy;phasecontrast;DIC,imageprocessing Lab5:InsideanopJcalmicroscope
10 QuantumMechanics Midterm2
11 QuantummechanicsapplicaJons;BasicNMR
12 PulsedandFTNMR;MRI Lab6:PulsedNMR
13 MRI
14 Classreview;readingperiod
15 FinalExam
SecondSemesterWeek Readings Topics Notes
1 Nelson1,2,3 Beginnings;probability;IntrotostaJsJcalphysics
2 Nelson3,4 BoltzmanndistribuJon;BrownianmoJon
3 Nelson4 FricJonandDiffusion
4 Nelson5 LifeatlowReynoldsNumber Lab:BrownianMoJon
5 Nelson5 Low‐RapplicaJons‐Microfluidics Midterm
6 Nelson6 StaJsJcalphysics:entropy,temperature,andfreeenergy
Lab:Microfluidics
7 Nelson6 MoreonS,T,andF
8 Nelson7 EntropicForces
9 Nelson7,8 Chemicalforces
10 Nelson8 ChemicalreacJons Midterm2
11 Nelson11 Membranetransport
12 Nelson11‐12 Ionpumping,nerveimpulses
13 Nelson12 NerveconducJon:Hodgkin‐Huxleymodel
14 Classreview;readingperiod
15 FinalExam
ReferencesandFurtherInformaJon
• DNASlifilms– “DNAOpJcalTransformKit,”partno.99‐001,InsJtuteforChemicalEducaJon;UniversityofWisconsin‐
Madison,DepartmentofChemistry,1101UniversityAvenue,Madison,WI53706‐1396.Website:h[p://ice.chem.wisc.edu
• NuclearMagneJcResonance– Wefollow“NuclearMagneJcResonance”byEric.D.Black,inourlab.See
h[p://www.pma.caltech.edu/~ph77/labs/nmr.pdf,accessed21July2009• Microfluidics
– Microfluidiccircuits:AccessT‐SensorcardavailablefromMicronics,Inc.,8463154thAvenue,N.E.,Redmond,WA98052.Website:h[p://www.micronics.net
• BrownianMoJonreferences– “EinsteinandtheexistenceofAtoms,”J.Bernstein,AJP74[10],pp863‐872,October2006.– “Einstein,Perrin,andtherealityofatoms:1905revisited,”R.Newburgh,J.Peidle,andW.Rueckner,AJP
74[6],pp478‐481,June2006.– 3“TheJme,size,viscosity,andtemperaturedependenceoftheBrownianmoJonofpolystyrene
microspheres,”D.Jia,J.Hamilton,L.M.Zaman,andA.Goonewardene,AJP75[2],111‐115,February2007– 4“MeasuringBoltzmann’sconstantusingvideomicroscopyofBrownianmoJon,”P.Nakroshis,M.Amoroso,
J.Legere,andC.Smith,AJP71[6],568‐573,June2003• LabWrite‐ups
– Ourlabwrite‐upsareavailableat:h[p://www.pha.jhu.edu/~wonnell/Biological_Physics_Labs_21Jul09.pdf• ExampleCourseSyllabus
– Firstsemester,“WavePhenomenawithBiophysicalApplicaJons,”h[p://www.pha.jhu.edu/courses/171_210/Syllabus209_06.htm
– Secondsemester,“BiologicalPhysics,”h[p://www.pha.jhu.edu/courses/171_210/Syllabus210_07.htm