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18A Framework for Modeling DNA Based Molecular Systems-3
260S.Sahu,B.Wang,andJ.H.；Reif；Fig.7.Simulationofahybri；8DiscussionandFutureWork；Wepresentedacomprehensiv；Duringthephysicalsimulat；The?rstextensiontoourfra；Webelievethatthemethodsp；
260S.Sahu,B.Wang,andJ.H.ReifFig.7.Simulationofahybridizationevent8DiscussionandFutureWorkWepresentedacomprehensiveframeworkforbuildingasoftwaretoolforsimulatingDNAbasedmolecularsystem,andnottheactualsoftwaretoolitself.Itisimportanttonotethat,asaframework,thephysicalsimulationcomponentandeventsimula-tioncomponentcanbedecoupledasweimproveeachcomponentindividually.Asweimprovetheaccuracyofthephysicalsimulation,i.e.tore?ecttopologicalconstraintsbymodelingmorecomplicatedDNAnano-structuressuchaspseudo-knots[38,13];toprovidemorebiophysicalsoundbehaviorofDNAstrandsbyconsideringstackingenergyanortoachievethemoleculardetailsbyreplacingtheMCsimulationwithaBDsimulationoncecomputationalresourcesareavailable,wecanvalidateitscorrectnessagainstpolymertheoryandexperimentaldata,i.e.averageradiusofgyrationandthediffusionconstant.Wecanconstantlyupdatethephysicalsimulationcomponenttoresultinmorerealisticsimulation.Duringthephysicalsimulationtherandomperturbationsoftenleadtoacon?gurationthatcanbeachievedonlywithalowprobability.Canweoptimizethesimulationsothatwesamplealargerspaceofcon?gurationstoavoidthesewithlowprobability,thereforemakingthesimulationmorecomputationalef?cient?The?rstextensiontoourframeworkistoconsidermorecomplicatedinteractions,i.e.theenzymerestrictioneventandthehairpinformation.Thesecondextensionistoincorporatesequencedesigncapabilities.Wewouldliketodesignandoptimizese-quencesbasedonthegivennano-structureconformations.Furthermore,aconformationchangeofanano-devicecanbedecomposedintounitsoflocaldeformationstoeasethesequencedesign.WebelievethatthemethodspresentedheremakeagoodframeworkfordesigningthesimulatorforDNAbasedmolecularsystems.Thepreliminaryresultsinthispapersupportthefeasibilityoftheapproach.Wedescribethatitispossibletocapturegeo-metricconstraintsofthemoleculeswiththepolymertheoryandMCsimulation.Wealsodescribedtheapproximationsandlimitationsinthisframeworkandthewaysofimprovingthem.References1.L.Adleman.Molecularcomputationofsolutionstocombinatorialproblems.Science,266:94.2.P.AlbertiandJ.L.Mergny.DNAduplex-quadruplexexchangeasthebasisforananomolec-ularmachine.Proc.Natl.Acad.Sci.USA,100:03.3.S.A.AllisonandS.Mazur.Modelingthefreesolutionelectrophoreticmobilityofshortdnafragments.Biopolymers,46:359C373,1998.AFrameworkforModelingDNABasedMolecularSystems2614.S.A.AllisonandJ.A.McCammon.Multistepbrowniandynamics:applicationtoshortwormlikechains.Biopolymers,23:363C375,1984.5.S.R.AragonandR.Pecora.Dynamicsofwormlikechains.Macromolecules,18:.6.R.G.C.Arridge.Anintroductiontopolymermechanics.1985.7.G.A.Arteca,T.Edvinsson,pactionofgraftedwormlikechainsundervariablecon?nement.Phys.Chem.Chem.Phys.,3:01.8.B.MaierB,D.Bensimon,andV.Croquette.Replicationbyasinglednapolymeraseofastretchedsingle-strandeddna.Proc.Natl.Acad.Sci.U.S.A.,97(22):12002C7,October2000.9.Y.Benenson,R.Adar,T.Paz-Elizur,Z.Livneh,andE.Shapiro.DNAmoleculeprovidesacomputingmachinewithbothdataandfuel.Proc.Natl.Acad.Sci.USA,100:03.10.Y.Benenson,B.Gil,U.Ben-Dor,R.Adar,andE.Shapiro.Anautonomousmolecularcomputerforlogicalcontrolofgeneexpression.Nature,429:423C429,2004.11.Y.Benenson,T.Paz-Elizur,R.Adar,E.Keinan,Z.Livneh,andE.Shapiro.Programmableandautonomouscomputingmachinemadeofbiomolecules.Nature,414:430C434,2001.12.I.Biswas,A.Yamamoto,andP.Hsieh.Branchmigrationthroughdnasequenceheterology.J.Mol.Bio,1998.13.JustinS.Bois,SuvirVenkataraman1,HarryM.T.Choi1,AndrewJ.Spakowitz,Zhen-GangWangandNilesA.Pierce1,2,*Topologicalconstraintsinnucleicacidhybridizationkinet-ics.NucleicAcidsResearch,33(13):05.14.C.Bouchiat,M.D.Wang,J.Allemand,T.Strick,S.M.Block,andV.Croquette.Estimatingthepersistencelengthofaworm-likechainmoleculesfromforce-extensionmeasurements.Biophys.J.,76:409,January1999.15.C.Bustamante,J.F.Marko,E.D.Siggia,andS.Smith.Entropicelasticityoflambda-phagednamechanics.Science,265:.16.C.Bustamante,S.Smith,J.Liphardt,andD.Smith.Single-moleculestudiesofdname-chanics.CurrentOpinioninStructuralBiology,10:279,2000.17.J.E.ButlerandE.S.G.Shaqfeh.Browniandynamicssimulationsofa?exiblepolymerchainwhichincludescontinuousresistanceandmulti-bodyhydrodynamicinteraction.JournalofChemicalPhysics,122(05.18.G.A.CarriandM.Marucho.Statisticalmechanicsofworm-likepolymersfromanewgeneratingfunction.J.Chem.Phys.,121(12):04.19.N.Chelyapov,Y.Brun,M.Gopalkrishnan,D.Reishus,B.Shaw,andL.Adleman.DNAtrianglesandself-assembledhexagonaltilings.J.Am.Chem.Soc.,126:,2004.20.Y.ChenandC.Mao.PuttingabrakeonanautonomousDNAnanomotor.J.Am.Chem.Soc.,126:04.21.Y.Chen,M.Wang,andC.Mao.AnautonomousDNAnanomotorpoweredbyaDNAenzyme.Angew.Chem.Int.Ed.,43:04.22.S.Cocco,J.F.Marko,andR.Monasson.Theoreticalmodelsforsingle-moluculednaandrnaexperiments:fromelasticitytounzipping.toappearinCRAS,specialissuededicatedtoSingleMoleculeExperiments,2002.23.C.Desruisseaux,D.Long,G.Drouin,andG.W.Slater.Electrophoresisofcompositemolecularobjects.1.relationbetweenfriction,chargeandionicstrengthinfreesolution.Macromolecules,34:44C59,2001.24.M.N.Dessinges,B.Maier,Y.Zhang,M.Peliti,D.Bensimon,andV.Croquette.Stretchingsinglestrandeddna,amo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Framework for Modeling DNA Based Molecular Systems等内容。　
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