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1、UnbiasedcomputationoftransitiontimesbypathwayrecombinationJ.Kuipers,1G.T.Barkema1,21InstituteforTheoreticalPhysics,UtrechtUniversity,Leuvenlaan4,3584CE,Utrecht,TheNetherlands2Instituut-LorentzforTheoreticalPhysics,LeidenUniversity,NielsBohrweg2,2333CA,Leiden,TheNetherlandsAbstractIn
2、manysystems,thetimescalesofthemicroscopicdynamicsandmacroscopicdynamicsofinterestareseparatedbymanyordersofmagnitude.Examplesabound,forinstancenucle-ation,proteinfolding,andchemicalreactions.Forthesesystems,directsimulationofphasespacetrajectoriesdoesnotefficientlydeterminemostphysica
3、lquantitiesofinterest.Thelastdecadehasseentheadventofmethodscircumventingbruteforcesimulation.Formostdy-namicalquantities,thesemethodsallsharethedrawbackofsystematicalerrors.Wepresentanovelmethodforgeneratingensemblesofphasespacetrajectories.Bysamplingsmallpiecesofthesetrajectoriesi
4、ndifferentphasespacedomainsandpiecingthemtogetherinasmartwayusingequilibriumproperties,weobtainphysicalquantitiessuchastransitiontimes.Thismethoddoesnothaveanysystematicerrorandisveryefficient;thecomputationalefforttocalculatethefirstpassagetimeacrossafreeenergybarrierdoesnotincreasewith
5、theheightofthebarrier.ThestrengthofthemethodisshownintheIsingmodel.Accuratemeasurementsofnucleationtimesspanalmosttenordersofmagnitudeandrevealcorrectionstoclassicalnucleationtheory.1IntroductionTheaveragetimeittakesaproteintofold,anundercooledliquidtocrystallize,orachemicallyactive
6、moleculetoreact,caninprinciplebeobtainedfrombruteforcecomputersimulations,byarXiv:0802.4194v1[cond-mat.other]28Feb2008simplystartingseveraltimesintheunfolded,liquidorpre-reactionstateandthenintegratingthedynamicalequationsintimeuntilfolding,crystallizationorreactiontakesplace.Howeve
7、r,thetypicaltimescalesofthemicroscopicdynamicsandmacroscopicdynamicsofinterestareoftenseparatedbymanyordersofmagnitude;forsuchsystems,directsimulationofrelevantphasespacetrajectoriesisveryinefficient,ifatallpossible.Inthelastdecade,methodshavebeendevelopedthatsampletransitionpathwaysw
8、hilecircumventingbr
