Molecular Simulations in Macromolecular Science

Duo Xu; Hai-Xiao Wan; Xue-Rong Yao; Juan Li; Li-Tang Yan

doi:10.1007/s10118-023-2968-5

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Molecular Simulations in Macromolecular Science

TUTORIAL | Updated：2023-08-24

- Molecular Simulations in Macromolecular Science
- Molecular Simulations in Macromolecular Science
- 高分子科学（英文版） 2023年41卷第9期页码：1361-1370
- Affiliations：
  
  a.State Key Laboratory of Chemical Engineering, Department of Chemical Engineering, Tsinghua University, Beijing 100084, China
  b.Beijing Research Institute of Chemical Industry, SINOPEC, Beijing 100013, China
- Author bio：
  
  ltyan@mail.tsinghua.edu.cn
- Funds：
  
  This work was financially supported by the National Natural Science Foundation of China (Nos. 22025302 and 21873053).;Li-Tang Yan received his Ph.D. in polymer physics and chemistry at Tsinghua University in 2007. Then he went to Bayreuth University in Germany as a Humboldt Research Fellow. In 2010, he joined Prof. Anna Balazs’ group at University of Pittsburgh in USA as a Postdoctoral Research Fellow. He returned to Tsinghua University as a faculty from May 2011, and now is a full professor with tenure. He leads a polymer theory and physics group working on polymer theory and simulation, soft condense matter physics, biophysics and nonequilibrium physics.
- DOI：10.1007/s10118-023-2968-5
  中图分类号：
- 收稿：2022-12-18，
  
  修回：2023-1-30，
  
  录用：2023-2-9，
  
  网络首发：2023-03-22，
  
  纸质出版：2023-09-01
- Accepted：
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Xu, D.; Wan, H. X.; Yao, X. R.; Li, J.; Yan, L. T. Molecular simulations in macromolecular science. Chinese J. Polym. Sci. 2023, 41, 1361–1370

Duo Xu, Hai-Xiao Wan, Xue-Rong Yao, et al. Molecular Simulations in Macromolecular Science[J]. Chinese Journal of Polymer Science, 2023, 41(9): 1361-1370.
Xu, D.; Wan, H. X.; Yao, X. R.; Li, J.; Yan, L. T. Molecular simulations in macromolecular science. Chinese J. Polym. Sci. 2023, 41, 1361–1370 DOI： 10.1007/s10118-023-2968-5.

Duo Xu, Hai-Xiao Wan, Xue-Rong Yao, et al. Molecular Simulations in Macromolecular Science[J]. Chinese Journal of Polymer Science, 2023, 41(9): 1361-1370. DOI： 10.1007/s10118-023-2968-5.

摘要

This tutorial provides an overview of molecular simulations in the rapid progress of macromolecular science and suggests guidance for researchers who start exploiting molecular simulations in their study

by featuring several prominent and classical simulation methods and software

as well as the applications in various directions of macromolecular science.

Abstract

Molecular simulations are now an essential part of modern chemistry and physics

especially for the investigation of macromolecules. They have evolved into mature approaches that can be used effectively to understand the structure-to-property relationships of diverse macromolecular systems. In this article

we provide a tutorial on molecular simulations

focusing on the technical and practical aspects. Several prominent and classical simulation methods and software are introduced. The applications of molecular simulations in various directions of macromolecular science are then featured by representative systems

including self-assembly

crystallization

chemical reaction

and some typical non-equilibrium systems. This tutorial paper provides a useful overview of molecular simulations in the rapid progress of macromolecular science

and suggests guidance for researchers who start exploiting molecular simulations in their study.

关键词

Keywords

references

Frenkel,D.;Smit,B. Understanding Molecular Simulation: from Algorithms to Applications .Elsevier: 2001 ,Vol.1..

Allen,M.P.;Tildesley,D.J. Computer Simulation of Liquids .OxfordUniversityPress: 2017 ..

Levine,B.G.;LeBard,D.N.;DeVane,R.;Shinoda,W.;Kohlmeyer,A.;Klein,M.L.MicellizationstudiedbyGPU-acceleratedcoarse-grainedmoleculardynamics. J. Chem. Theory. Comput. 2011 , 7 ,4135−45..

Pall,S.;Zhmurov,A.;Bauer,P.;Abraham,M.;Lundborg,M.;Gray,A.;Hess,B.;Lindahl,E.HeterogeneousparallelizationandaccelerationofmoleculardynamicssimulationsinGROMACS. J. Chem. Phys. 2020 , 153 ,134110..

Smith,W.;Forester,T.R.DL_POLY_2.0:ageneral-purposeparallelmoleculardynamicssimulationpackage. J. Mol. Graphics 1996 , 14 ,136−141..

Gotz,A.W.;Williamson,M.J.;Xu,D.;Poole,D.;LeGrand,S.;Walker,R.C.RoutinemicrosecondmoleculardynamicssimulationswithAMBERonGPUs.1.Generalizedborn. J. Chem. Theory Comput. 2012 , 8 ,1542−1555..

Plimpton,S.Fastparallelalgorithmsforshrot-rangemoleculardynamics. J. Comput. Phys. 1995 , 117 ,1−19..

Phillips,J.C.;Braun,R.;Wang,W.;Gumbart,J.;Tajkhorshid,E.;Villa,E.;Chipot,C.;Skeel,R.D.;Kale,L.;Schulten,K.ScalablemoleculardynamicswithNAMD. J. Comput. Chem. 2005 , 26 ,1781−1802..

Anderson,J.A.;Glaser,J.;Glotzer,S.C.HOOMD-blue:APythonpackageforhigh-performancemoleculardynamicsandhardparticleMonteCarlosimulations. Comp. Mater. Sci. 2020 , 173 ,109363..

Zhu,Y.L.;Liu,H.;Li,Z.W.;Qian,H.J.;Milano,G.;Lu,Z.Y.GALAMOST:GPU-acceleratedlarge-scalemolecularsimulationtoolkit. J. Comput. Chem. 2013 , 34 ,2197−2211..

Berendsen,H.J.C.;Spoel,D.V.D.;Drunen,R.V.GROMACS:amessage-passingparallelmoleculardynamicsimplementation. Comput. Phys. Commun. 1995 , 91 ,43−56..

Rapaport,D.C. The Art of Molecular Dynamics Simulation .CambridgeUniversityPress: 2004 ..

Hu,W.B.Computersimulationofpolymers:bridgingthegapbetweentheoryandexperiment. Chinese J. Polym. Sci. 2022 , 40 ,709−710..

Xu,Z.;Gao,L.;Chen,P.;Yan,L.T.Diffusivetransportofnanoscaleobjectsthroughcellmembranes:acomputationalperspective. Soft Matter 2020 , 16 ,3869−3881..

Laurien,M.;Demir,B.;Büttemeyer,H.;Herrmann,A.S.;Walsh,T.R.;Ciacchi,L.C.Atomisticmodelingoftheformationofathermoset/thermoplasticinterphaseduringco-curing. Macromolecules 2018 , 51 ,3983−3993..

Li,C.;Strachan,A.Molecularscalesimulationsonthermosetpolymers:areview. J. Polym. Sci., Part B: Polym. Phys. 2015 , 53 ,103−122..

Nielsen,O.H.;Martin,R.M.First-principlescalculationofstress. Phys. Rev. Lett. 1983 , 50 ,697−700..

Cohen,A.J.;Mori-Sanchez,P.;Yang,W.Challengesfordensityfunctionaltheory. Chem. Rev. 2012 , 112 ,289−320..

Kmiecik,S.;Gront,D.;Kolinski,M.;Wieteska,L.;Dawid,A.E.;Kolinski,A.Coarse-grainedproteinmodelsandtheirapplications. Chem. Rev. 2016 , 116 ,7898−7936..

Vendruscolo,M.;Dobson,C.M.Proteindynamics:Moore'slawinmolecularbiology. Curr. Biol. 2011 , 21 ,R68−70..

Dai,X.B.;Zhang,Y.X.;Gao,L.J.;Yan,L.T.Superentropyeffectandmacromolecularentropycontrolstrategy. Acta Polymerica Sinica (inChinese) 2021 , 52 ,1076−1099..

Xu,Z.;Liu,G.;Gao,L.;Xu,D.;Wan,H.;Dai,X.;Zhang,X.;Tao,L.;Yan,L.T.Configurationalentropy-enabledthermostabilityofcellmembranesinextremophiles:frommolecularmechanismtobioinspireddesign. Nano Lett. 2023 , 23 ,1109−1118..

Weiner,S.J.;Kollman,P.A.;Case,D.A.;Singh,U.C.;Ghio,C.;Alagona,G.;SalvatoreProfeta,J.;Weiner,P.ANewforcefieldformolecularmechanicalsimulationofnucleicacidsandproteins. J. Am. Chem. Soc. 1984 , 106 ,765−784..

Brooks,B.R.;Bruccoleri,R.E.;Olafson,B.D.;States,D.J.;Swaminathan,S.;Karplus,M.CHARMM:aprogramformacromolecularenergy,minimization,anddynamicscalculations. J. Comput. Chem. 1983 , 4 ,187−217..

Jorgensen,W.L.;Tirado-Rives,J.TheOPLSpotentialfunctionsforproteins.energyminimizationsforcrystalsofcyclicpeptidesandcrambin. J. Am. Chem. Soc. 1988 , 110 ,1657−1666..

Dauber-Osguthorpe,P.;Roberts,V.A.;Osguthorpe,D.J.;Wolff,J.;Genest,M.;Hagler,A.T.Structureandenergeticsofligandbindingtoproteins: Escherichia Coli dihydrofolatereductase-trimethoprim,adrug-receptorsystem. Proteins 1988 , 4 ,31−47..

Leonard,A.N.;Wang,E.;Monje-Galvan,V.;Klauda,J.B.Developingandtestingoflipidforcefieldswithapplicationstomodelingcellularmembranes. Chem. Rev. 2019 , 119 ,6227−6269..

Cellmer,T.;Fawzi,N.L.Coarse-grainedsimulationsofproteinaggregation. Methods Mol. Biol. 2012 , 899 ,453−470..

Ulam,S.M.;VonNeumann,J.Randomergodictheorems. Bull. Amer. Math. Soc. 1945 , 51 ,660..

Groot,R.D.;Warren,P.B.Dissipativeparticledynamics:bridgingthegapbetweenatomisticandmesoscopicsimulation. J. Chem. Phys. 1997 , 107 ,4423−4435..

Español,P.;Warren,P.Statisticalmechanicsofdissipativeparticledynamics. Europhys. Lett. 1995 , 30 ,191−196..

Flory,P.J. Principles of Polymer Chemistry .CornellUniversityPress: 1953 ..

Ermak,D.L.;McCammon,J.A.Browniandynamicswithhydrodynamicinteractions. J. Chem. Phys. 1978 , 69 ,1352..

Hao,Q.-H.;Zheng,Z.;Xia,G.;Tan,H.G.Browniandynamicssimulationsofrigidpolyelectrolytechainsgraftingtosphericalcolloid. Chinese J. Polym. Sci. 2018 , 36 ,791−798..

Akcora,P.;Liu,H.;Kumar,S.K.;Moll,J.;Li,Y.;Benicewicz,B.C.;Schadler,L.S.;Acehan,D.;Panagiotopoulos,A.Z.;VictorPryamitsyn;Ganesan,V.;Ilavsky,J.;Thiyagarajan,P.;Colby,R.H.;Douglas,J.F.Anisotropicself-assemblyofsphericalpolymer-graftednanoparticles. Nat. Mater. 2009 , 8 ,354−359..

Harmat,A.L.;JavanNikkhah,S.;Sammalkorpi,M.DissipativeparticledynamicssimulationsofH-shapeddiblockcopolymerself-assemblyinsolvent. Polymer 2021 , 233 ,124198..

Carlson,J.C.T.;Jena,S.S.;Flenniken,M.;Chou,T.F.;Siegel,R.A.;Wagner,C.R.Chemicallycontrolledself-assemblyofproteinnanorings. J. Am. Chem. Soc. 2006 , 128 ,7630−7638..

Bai,Y.;Luo,Q.;Liu,J.Proteinself-assembly via supramolecularstrategies. Chem. Soc. Rev. 2016 , 45 ,2756−2767..

Fu,I.W.;Markegard,C.B.;Nguyen,H.D.Solventeffectsonkineticmechanismsofself-assemblybypeptideamphiphiles via moleculardynamicssimulations. Langmuir 2015 , 31 ,315−324..

Whitesides,G.M.;Grzybowski,B.Self-assemblyatallscales. Science 2002 , 295 ,2418−2421..

Whitesides,G.M.;Boncheva,M.Beyondmolecules:self-assemblyofmesoscopicandmacroscopiccomponents. Proc. Natl. Acad. Sci. USA 2002 , 99 ,4769−4774..

Zhu,G.;Huang,Z.;Xu,Z.;Yan,L.T.Tailoringinterfacialnanoparticleorganizationthroughentropy. Acc. Chem. Res. 2018 , 51 ,900−909..

Yamamoto,T.Moleculardynamicsmodelingofpolymercrystallizationfromthemelt. Polymer 2004 , 45 ,1357−1364..

Yamamoto,T.Moleculardynamicsofpolymercrystallizationrevisited:crystallizationfromthemeltandtheglassinlongerpolyethylene. J. Chem. Phys. 2013 , 139 ,054903..

Xu,D.;Lu,Y.Y.;Luo,C.F.Shapeaccuracyandresidualstressdistributionofnano-moldedsemicrystallinepolymer:asimulationstudy. Chinese J. Polym. Sci. 2022 , 40 ,642−650..

Muthukumar,M.,ModelingPolymerCrystallization.In Interphases and Mesophases in Polymer Crystallization III , 2005 ;Vol.191,pp.241−274..

Gee,R.H.;Lacevic,N.;Fried,L.E.Atomisticsimulationsofspinodalphaseseparationprecedingpolymercrystallization. Nat. Mater. 2006 , 5 ,39−43..

Nie,Y.;Zhao,Y.;Matsuba,G.;Hu,W.Shish-Kebabcrystallitesinitiatedbyshearfractureinbulkpolymers. Macromolecules 2018 , 51 ,480−487..

Luo,C.;Kröger,M.;Sommer,J.U.Moleculardynamicssimulationsofpolymercrystallizationunderconfinement:entanglementeffect. Polymer 2017 , 109 ,71−84..

Najafi,M.;Roghani-Mamaqani,H.;Salami-Kalajahi,M.;Haddadi-Asl,V.Acomprehensivemontecarlosimulationofstyreneatomtransferradicalpolymerization. Chinese J. Polym. Sci. 2010 , 28 ,483−497..

Rienstra-Kiracofe,J.C.;Allen,W.D.;III,H.F.S.TheC 2 H 5 +O 2 reactionmechanism:high-levelabinitiocharacterizations. J. Phys. Chem. A 2000 , 104 ,9823−9840..

Strachan,A.;vanDuin,A.C.;Chakraborty,D.;Dasgupta,S.;Goddard,W.A.3rd.Shockwavesinhigh-energymaterials:theinitialchemicaleventsinnitramineRDX. Phys. Rev. Lett. 2003 , 91 ,098301..

Ludwig,J.;Vlachos,D.G.DynamicsofthedissociationofhydrogenonsteppedplatinumsurfacesusingtheReaxFFreactiveforcefield. J. Phys. Chem. B 2006 , 110 ,4274−4282..

Chenoweth,K.;Duin,A.C.T.V.;Goddard,W.A.ReaxFFreactiveforcefieldformoleculardynamicssimulationsofhydrocarbonoxidation. J. Phys. Chem. A 2008 , 112 ,1040−1053..

Chenoweth,K.;Cheung,S.;Duin,A.C.T.V.;III,W.A.G.;Kober,E.M.Simulationsonthethermaldecompositionofapoly(dimethylsiloxane)polymerusingthereaxffreactiveforcefiel. J. Am. Chem. Soc. 2005 , 127 ,7192−7202..

Yan,Y.D.;Xue,Y.H.;Zhao,H.Y.;Liu,H.;Lu,Z.Y.;Gu,F.L.Insightintothepolymerization-inducedself-assembly via arealisticcomputersimulationstrategy. Macromolecules 2019 , 52 ,6169−6180..

Nagayama,G.;Takematsu,M.;Mizuguchi,H.;Tsuruta,T.Moleculardynamicsstudyoncondensation/evaporationcoefficientsofchainmoleculesatliquid-vaporinterface. J. Chem. Phys. 2015 , 143 ,014706..

Katiyar,P.;Singh,J.K.Evaporationinducedself-assemblyofdifferentshapesandsizesofnanoparticles:amoleculardynamicsstudy. J. Chem. Phys. 2019 , 150 ,044708..

Sherman,Z.M.;Swan,J.W.Transmutablecolloidalcrystalsandactivephaseseparation via dynamic,directedself-assemblywithtoggledexternalfields. ACS Nano 2019 , 13 ,764−771..

Mallory,S.A.;Valeriani,C.;Cacciuto,A.Anactiveapproachtocolloidalself-assembly. Annu. Rev. Phys. Chem. 2018 , 69 ,59−79..

Tung,C.;Harder,J.;Valeriani,C.;Cacciuto,A.Micro-phaseseparationintwodimensionalsuspensionsofself-propelledspheresanddumbbells. Soft Matter 2016 , 12 ,555−561..

Lu,H.;Isralewitz,B.;Krammer,A.;Vogel,V.;Schulten,K.Unfoldingoftitinimmunoglobulindomainsbysteeredmoleculardynamicssimulation. Biophys. J. 1998 , 75 ,662−671..

Yan,L.T.;Xie,X.M.Computationalmodelingandsimulationofnanoparticleself-assemblyinpolymericsystems:structures,propertiesandexternalfieldeffects. Prog. Polym. Sci. 2013 , 38 ,369−405..

Yan,J.;Han,M.;Zhang,J.;Xu,C.;Luijten,E.;Granick,S.Reconfiguringactiveparticlesbyelectrostaticimbalance. Nat. Mater. 2016 , 15 ,1095−1099..

Joseph,A.;Contini,C.;Cecchin,D.;Nyberg,S.;Ruiz-Perez,L.;Gaitzsch,J.;Fullstone,G.;Tian,X.;Azizi,J.;Preston,J.;Volpe,G.;Battaglia,G.Chemotacticsyntheticvesicles:designandapplicationsinblood-brainbarriercrossing. Sci. Adv. 2017 , 3 ,e1700362..

Do,P.C.;Lee,E.H.;Le,L.Steeredmoleculardynamicssimulationinrationaldrugdesign. J. Chem. Inf. Model. 2018 , 58 ,1473−1482..

Izrailev,S.;Stepaniants,S.;Isralewitz,B.;Kosztin,D.;Lu,H.;Molnar,F.;Wriggers,W.;Schulten,K.Computationalmoleculardynamics:challenges,methods. Lect. Notes Comput. Sci. Eng. 1999 , 4 ,39−65..

Zhang,X.;Wang,Y.;Xia,R.;Wu,B.;Chen,P.;Qian,J.S.;Liang,H.J.Effectofchainconfigurationonthermalconductivityofpolyethylene—amoleculardynamicsimulationstudy. Chinese J. Polym. Sci. 2020 , 38 ,1418−1425..

Yang,Y.I.;Shao,Q.;Zhang,J.;Yang,L.;Gao,Y.Q.Enhancedsamplinginmoleculardynamics. J. Chem. Phys. 2019 , 151 ,070902..

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