topological data analysis of water networks from simulations · topological data analysis of water...

TopologicalDataAnalysisofWaterNetworksfromSimulations

LeeSteinberg&JeremyFreyUniversityofSouthampton,TMCS

ls2m15@soton.ac.ukUnderstandingthestructureofwaternetworkshasmajorimplicationsinthefieldofdrugdiscovery.Forexample,understandinghowthepresenceofasoluteaffectsthenativewaterstructurecouldenableustobuildbettermodelsforthepredictionoffreeenergychangesofsolvation.Investigationofwaternetworkshaspreviouslytakenagraph-theoreticalapproach,definingagraphstructurebasedonameasureofcorrelationbetweenwatermolecules,suchasin[1].Suchmethodshavealsobeenusedinstudyingradiationdamage[2].

However,thesetechniquesrequireauser-input,forexampledefiningavalueofdistancewheretwowatermoleculescanbeconsideredtobecorrelated.Weproposeanalternativeapproachbasedontheuseofpersistenthomology[3],atechniqueinthefieldoftopologicaldataanalysis(TDA),whichdefinesasetofstructuresforthefullrangeofparametervalues,andconsidershowthisseriesevolvestodeterminewhichfeaturesarethemostuseful.Wepresentaninvestigationintothestructureofwaternetworksinvariousmodelsusedinmoleculardynamicssimulations–TIP3P,TIP4P,andSPC.Wediscusstheadaptationofpersistenthomologymethodstotime-seriesdata,suchasthepersistencelandscape[4].Werelatepersistentloopstotheradialdistributionfunctionofthemoleculardynamicsmodel.Wealsodiscussthepresenceofthree-dimensionalvoidsinwaternetworks,andrelateittootherproperties.

Figure1-ThesurfaceofasimulatedTIP3Pwaternetworkat300K.Holesareclearlyvisibleinthesystem.

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