Feature Column from the AMS

http://www.ams.org/samplings/feature-column/fc-2011-10

WhenamonochomaticXraydiractsoacrystalitperformspartofamathematicaloperation:theFouriertransform...
TonyPhillips StonyBrookUniversity EmailTonyPhillips

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Introduction
Xraycrystallographyhasbeenessential,sincethebeginningofthe20thcentury,toourunderstandingofmatter;recently,as knowledgeofthechemicalcompositionofproteinshasprogressed,thedeterminationoftheir3dimensionalstructurehasbecome indispensableforthecorrectinterpretationoftheirfunctions.OurmainaccesstothisinformationisXraycrystallography.(Xraysare usedbecausetheirwavelengthsareontheorderofinteratomicdistancesinmolecules,intherange1100;oneis m). Mathematicsentersintotheprocessattwostages.Thestudyofspacegroupstellswhatperiodiccongurationsarepossibleinthree space;infacttheseareoftencalledcrystallographicgroupsbymathematicians.Theotherconnection,thesubjectofthiscolumn,isthe surprisingandpleasingfactthatwhenamonochomaticXraydiractsoacrystalitperformspartofamathematicaloperation:the Fouriertransform(developedinthe19thcenturyincompletelydierentcontexts);whentheincidenceangleisvaried,thecomplete transformisproduced.Theawinthislovelypictureisthatwecannotmeasureallthedetailsofthediractedwave;otherwisethe entiremolecularstructurecouldbecalculatedbyinvertingtheFouriertransform. TherearemanyonlineresourcesdevotedtoXraycrystallography;IhaveespeciallyprotedfromRandyReadsProtein CrystallographyCourseandfromKevinCowtansInteractiveStructureFactorTutorial.ThanksalsotomyStonyBrookcolleagues PeterStephensandMiguelGarciaDiazforhelpfulcorrespondenceandremarks.

Fourierseries:temperaturedistributioninawire
FourierseriesandtheFouriertransformwereinventedasamethodofdataanalysis.Forexample,letusfollowJeanBaptisteJoseph Fourier(17681830)instudyingthetimeevolutionofthetemperaturedistributioninacircularloopofcircumference ,givenaninitial distributionoftemperature ;(werequire ).WestartbycalculatingwhatarenowknownastheFourier coecientsof :

Itcanbeproved,if issucientlywellbehaved,thatthelinearcombination

(theFourierseriesof ;when

theseformulassimplifypleasantly)convergeseverywhereto

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(Takenasaninitialdistributionseparately,eachofthe

and

functionsdeterminesasimplesolution,asdoesa and ,togive

constantfunction;thelinearityoftheheatequationallowstheseseparatesolutionstobecombined,withcoecients thecompletesolutiontotheproblem.) ItisusefultosimplifytheformulasbyusingEulersidentities toyield ,

andgroupingterms

and

ingeneral,the

arecomplexnumbers.

Electrondensitydistributioninacrystal
Thedualoperationsofintegration: andsummation: canberealizedinothercontexts.Inthiscolumn wewillconsiderthefunction thatgivestheelectrondensitydistributioninthecrystallinestateofsomecompound.Suppose, forsimplicity,thattheunitbuildingblock,correspondingtoamoleculeofthecompound,isarectangularsolid;saywithedgelengths and ;these by by solidsarestackedinthreespacesoastogiveastructurerepeatingevery unitsinthe direction,every unitsinthe andevery unitsinthe .Thenthefunction willbetriplyperiodic,withperiods and ,andconsequently canberepresentedasatripleFourierseries

where

directlygeneralizingourformulasforthecircle.Ifthecoecients areknown,theelectrondensitydistributioncanbecalculated, andthenthestructureofthemoleculecanbedetermined.Itisthereforeremarkablethatthediractionpatternsformedwhenthe crystalisbombardedwithXrayscontainpreciousinformationaboutthe .Roughlyspeaking,wecanimaginethecomplex numbers placedatthevertices ofa3dimensionallattice;eachXraydiractionpatternprojectsthislatticeontotheplane oftheimageplate.Ifwelabelby theprojectionproducedbyabeammeetingthecrystalatageneralizedangle ,avertex whichisgoodpositionwithrespectto (thisconditionalsodependsonthewavelength oftheradiation)willappearontheplateas .Varying willbringanewsetof aspotatlocation andofintensityproportionaltothesquareoftheabsolutevalue verticesintogoodposition;eventuallythelatticecanbereconstructed,alongwiththeabsolutevalueofthecoecientsatthevertices. Thephaseproblem.Theabsolutevalues alone,althoughtheycontainagreatdealofinformationaboutthemoleculein question,donotallow tobecompletelyreconstructed.Asimpleexamplecomesfromtemperaturedistributionslike thosestudiedbyFourier.Consider(withcircumference )thetemperaturedistributions and .Sothecoecentsfor areall ,whilethosefor are .Theabsolutevaluesarethesame,butthedistributionsaredierent,asshownbelow.Xray crystallographershavedevisedmanywaystogetaroundthislimitation,calledthephaseproblem;theyarebeyondthescopeof thiscolumn.

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Thetemperaturedistributions (red)and (blue),onacircularloopof circumference (plottedradially)arequitedierentbuthaveFouriercoecientswiththesameabsolutevalues.

Thereciprocallattice
Xraysinteractwithacrystalthroughinteractionwithparallelfamiliesofplanes.Supposeasbeforethattheunitcellinthecrystalisan rectangularparallelipiped(when and arealldierent,thisstructureiscalledorthorhombic).Everytriple of integersdenesafamilyofplanesthroughthecrystal,denedbytheequation

Letuschangecoordinatesto

.(Wearenowinthereciprocallattice;foranonrectangularcrystalthechangeof

coordinatesisonlyslightlymorecomplicated).Thentheequationdeningtheplanesbecomes

for aninteger.Foreach thisfamilyofparallelplanesllsupthecrystal,inthesensethateachunitcellvertexliesin(exactly) oneofthem,asiseasytocheck.Wecallthesethelatticeplanes.Graphically,itiseasiertorepresenttheanalogousconceptintwo rectangles;inthe coordinatesthese dimensions,sowesuppress and forthemoment.Ourcrystalisthenanarrayof measure .Thepair givesthelines ,for aninteger.Theselinesareparalleltothe axis,andslicethroughthe baseofeachunitcell.Ontheotherhand, givesthelines ,or , gives ,and gives .(Seeimage).

Latticelines:thelinescorrespondingto linesareshown.

areshowninblue,thosefor

inorange,andthosefor

inpurple.Notall

Xraydiraction:howamonochromaticplanewaveperformsFourieranalysisontheelectrondensity

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distribution.

Thisdiagramlabelsthevectorsinvolvedinthecalculationofdiraction.Anincomingplanewave diractsoanelectronat asa wave withtheoppositeincidenceangle ,andalsooanotherelectronatrelativeposition .Thewavevectors and havethe samemagnitude,whichwesetforconveniencetobe ,thereciprocalofthewavelength.Thediractedraystraveldierentlengths: islongerby thanthepaththrough ,asshown. istheprojectionof along andhaslength . isminustheprojectionof along ,andsohaslength .Thisgives,forthedierenceinpath lengths, or .Since isthewavelength,theraytravelingthrough willhaveitsphaseretardedby ; correspondingtoafactor . Thelengthofthevector is ;so ,whichisequaltothecomponentof inthedirectionof timesthe lengthof ,isequalto ;constructiveinterference,whichcorrespondsto ,aninteger,thusalsocorrespondsto .ThisisBraggslaw;itsdiscoveryin1912startedtheeldofXraycrystallography.Thediractioncorrespondingtoa diractionvector andasingleelectronatposition multipliestheamplitudeofthescatteredwavebyaphasefactor .If istheelectrondensityfunctioninthecrystal,theeecton willsumto thepaththrough

Sothestructurefactor appearsastheFouriertransformoftheelectrondensityfunction .(Straightforwarddiraction experimentsonlymeasurethe(squareof)theabsolutevalueof ,whichshowsupastheintensityofthespotcorrespondingto . Ifthephaseswerealsoknown,theFouriertransformcouldbeinvertedtogiveanexactpictureoftheelectrondensity ). Itispossibletorewritethisintegralintermsofthe vectorsinreciprocalspace.Foreachsuchvector wewrite,usingthe reciprocalcoordinates

InthiscasetheinverseFouriertransform

where

isvolumeinreciprocalspace,canbeapproximatedbyaFourierseries

whichcanbecomparedwiththeFourierseriesfor givenatthestartofthiscolumn. Hereisaniceexample,fromKevinCowtansInteractiveStructureFactorTutorial.Theexampleis2dimensional,andshowshow rapidlythestructurefactors,withtheirphases,convergetothetargetstructure.Thetargetelectrondensityfunctionlookslikethis:

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CowtanssimulationleadstotheapproximateFouriersynthesisofthetargetfromjustthesevenlargeststructurefactors:those correspondingto .Hereishowthesynthesisproceeds,stepbystep, eachtimeaddinginthenextstructurefactor.Theseimagesarefromhistutorial,andareusedwithpermission.Theunitcell(not orthorhombic!)isoutlinedindots.

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Comments (2)

Dear Tony: Thank you for a nice article. I have meant to sit down and understand the relationship between wavefronts and Fourier transforms. It is important in radar, the field I work in, and in particular, in antenna theory. All the best. -- Greg Coxson
#1 - Greg Coxson - 10/10/2011 - 13:17

Response to Greg Dear Greg, Thanks for the kind words. It's great to hear from a reader. Best wishes, Tony
#2 - Tony Phillips - 10/18/2011 - 15:58

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