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1、AlgorithmicSelf-AssemblyofDNAThesisbyErikWinfreeInPartialFulfillmentoftheRequirementsfortheDegreeofDoctorofPhilosophyTETITUOFSNTIECAIHNNROO1891LFOILGAYCCaliforniaInstituteofTechnologyPasadena,California1998(SubmittedMay19,1998)iic1998ErikWinfreeAllRight
2、sReservediiiAcknowledgementsThisthesisreportsanunusualandunexpectedjourneythroughintellectualterritoryentirelynewtome.Whoispreparedforsuchjourneys?Iwasnot.Thusmydebtisgreattothosewhohavehelpedmealongtheway,withoutwhosehelpIwouldhavebeencompletelylostan
3、duninspired.Thereisnowaytogivesufficientthankstomyadvisor,JohnHopfield.Hisencouragementformetogetmyfeetwet,andhisadvicecuttingtotheboneofeachissue,havebeeninvaluable.John’spolicyhasbeen,inhisownwords,togivehisstudents“enoughropetohangthemselveswith.”Buth
4、eknowsfullwellthatalotofropeisneededtoweavemacrame.Perhapstheonlypossiblerepaymentisinkind:tomaintainahighstandardofintegrity,andwhenmyturncomes,toprovideanurturingenvironmentforotheryoungminds.LenAdlemanandNedSeemanhaveeachbeenmentorsduringmythesiswor
5、k.Inmanyways,myresearchcanbeseenasthedirectoffspringoftheirwork,combiningthenotionofusingDNAforcomputationwiththeabilitytodesignDNAstructureswithartificialtopology.BothLenandNedhaveprovidedencouragement,support,andvaluablefeedbackthroughoutthisproject.I
6、wouldlikeadditionallytothankNedSeemanandXiaopingYangforteachingmehowtodolaboratoryexperimentswithDNA.Xiaoping’spatientandcarefultutoringprovidedmewithasolidfirststeptowardbecomingacompetentexperimenter.JohnAbelsongenerouslymademewelcometocontinuemyexper
7、imentingatCaltechinafriendlyandexpertenvironment;IamdeeplygratefultohimandtoallthemembersofhislaboratorywithoutwhosehelpIcouldhavedonelittle.Forteachingmetousetheatomicforcemicroscope,IthankAncaSegall,BobMoision,andElyRabani;withtheirencouragementandhe
8、lpIsawthefirstexcitingimagesofDNAlattices.Likewise,RobRossi’sfriendlyandspiritedmanagementoftheCaltechSPMroommadedoingsciencethereabreeze.Iamgratefulfortheencouragementandfeedbackofmythesiscommittee:JohnAbelson,YaserAbu-Mostafa,LenAdlema