公司简介： ThisfreeresourceisdevelopedandmaintainedbytheLaboratoryforComputationalBiology&BiophysicsatMIT,whichisdirectedbyProfessorMarkBathe.PreviousdevelopershaveincludedDo-NyunKim,KeyaoPan,andWilliamBricker.The3DsolutionshapeandflexibilityofprogrammedDNAassembliesarepredictedusingamechanicalmodelofDNAthatassumestheDNAdouble-helixtobeahomogeneouselasticrodwithaxial,twisting,andbendingmodulithathavebeenmeasuredexperimentally[8].Thesemechanicalelementsthatareconstrainedtoneighborsusingdouble-strandedcrossoversprovideinternalconstraintsthatdeformDNAfromitsstraight,rod-likeconformationtocomplexshapesasshownindetailin[4,9-10].ComputationalpredictionofdeformedDNAshapesisperformedusingtheFiniteElementMethodimplementedinthecommercialsoftwareprogramADINA(ADINAR&D,Inc.),whichisawellestablishednumericaltechniquefortheanalysisofcomplexstructuralmechanicsanddynamics[13].Thethermally-inducedfluctuationsofDNAnanostructuresarecomputedusingtheequipartitiontheoremofstatisticalmechanicsandnormalmodeanalysis[14],asshownforproteinsin[15-16].AtomicmodelsofDNAnanostructuresaregeneratedfrom3Dsolutionshapesandthermalfluctuations,asshownforthedesignoflight-harvestingnanodevices[17]andDNAcastingmoldsforinorganicstructures[18].SettinguptheprecedingfiniteelementmodelusingCanDorequiresinputfilesthatspecifythesequencetopologyoftheunderlyingDNAnanostructure,aswellasitsinitialconfiguration(basepaircoordinatesandorientations).OurlabhasdevelopedtheabilitytoreadinthesemodelfeaturesfromeithercaDNAnoorTiamatfiles,whicharetwopopulardrawingprograms,aswellasfromourownfileformatwithextensioncndo.Thesourcecodeneededtogeneratethefiniteelementmodelsareavailableuponrequestbye-mailingDanielDardani(ddardani@mit.edu).TheLaboratoryforComputationalBiology&BiophysicsisgratefultoitssponsorsforfinancialsupportincludingtheOfficeofNavalResearch,theArmyResearchOffice,andtheNationalScienceFoundation.