TheBiologicalPhysicsLabsintheJohnsHopkinsUniversity

DepartmentofPhysics&Astronomy

StevenK.Wonnell&DanielH.Reich

DepartmentofPhysicsandAstronomy3400N.CharlesStreet

BalJmore,MD21218E‐Mailcontact:wonnell@pha.jhu.edu

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

MicrofluidicsCircuitCartonMicroscopeStage

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