Extension to Multiscale Simulations

[1]  Kaori Fukuzawa,et al.  Folding simulation of small proteins by dissipative particle dynamics (DPD) with non-empirical interaction parameters based on fragment molecular orbital calculations , 2019, Applied Physics Express.

[2]  T. Aminabhavi,et al.  Molecular dynamics simulations to investigate polymer–polymer and polymer–metal oxide interactions ☆ , 2007 .

[3]  Mu-Ping Nieh,et al.  Fluid phase lipid areas and bilayer thicknesses of commonly used phosphatidylcholines as a function of temperature. , 2011, Biochimica et biophysica acta.

[4]  Kurt Kremer,et al.  Hierarchical modeling of polystyrene: From atomistic to coarse-grained simulations , 2006 .

[5]  S. Hyodo,et al.  Dissipative particle dynamics study of spontaneous vesicle formation of amphiphilic molecules , 2002 .

[6]  J. Koelman,et al.  Dynamic simulations of hard-sphere suspensions under steady shear , 1993 .

[7]  Pemra Doruker,et al.  Reverse Mapping of Coarse-Grained Polyethylene Chains from the Second Nearest Neighbor Diamond Lattice to an Atomistic Model in Continuous Space , 1997 .

[8]  Theodora Spyriouni,et al.  Coarse-Grained and Reverse-Mapped United-Atom Simulations of Long-Chain Atactic Polystyrene Melts: Structure, Thermodynamic Properties, Chain Conformation, and Entanglements , 2007 .

[9]  T. Aminabhavi,et al.  Molecular modeling on the binary blend compatibility of poly(vinyl alcohol) and poly(methyl methacrylate): an atomistic simulation and thermodynamic approach. , 2005, The journal of physical chemistry. B.

[10]  W. Goddard,et al.  UFF, a full periodic table force field for molecular mechanics and molecular dynamics simulations , 1992 .

[11]  Martin Hof,et al.  Structure, dynamics, and hydration of POPC/POPS bilayers suspended in NaCl, KCl, and CsCl solutions. , 2012, Biochimica et biophysica acta.

[12]  S. Hyodo,et al.  A Computer Simulation Study of the Mesoscopic Structure of the Polyelectrolyte Membrane Nafion , 2003 .

[13]  Reinhard Lipowsky,et al.  Equilibrium structure and lateral stress distribution of amphiphilic bilayers from dissipative particle dynamics simulations , 2002 .

[14]  Pemra Doruker,et al.  A second generation of mapping/reverse mapping of coarse‐grained and fully atomistic models of polymer melts , 1999 .

[15]  P. Painter,et al.  A practical guide to polymer miscibility , 1990 .

[16]  Joel H. Hildebrand,et al.  A Spectrophotometric Investigation of the Interaction of Iodine with Aromatic Hydrocarbons , 1949 .

[17]  E. Yonemochi,et al.  Self‐Degradable Lipid‐Like Materials Based on “Hydrolysis accelerated by the intra‐Particle Enrichment of Reactant (HyPER)” for Messenger RNA Delivery , 2020, Advanced Functional Materials.

[18]  N. Arai.  Structural analysis of telechelic polymer solution using dissipative particle dynamics simulations , 2015 .

[19]  R. Ueoka,et al.  Molecular dynamics study of lipid bilayers modeling the plasma membranes of normal murine thymocytes and leukemic GRSL cells. , 2013, Biochimica et biophysica acta.

[20]  S. Hyodo,et al.  Nature of water transport and electro-osmosis in nafion: insights from first-principles molecular dynamics simulations under an electric field. , 2008, The journal of physical chemistry. B.

[21]  R. Rousseau,et al.  Atomistic simulation of water percolation and proton hopping in Nafion fuel cell membrane. , 2010, The journal of physical chemistry. B.

[22]  Timothy J. Madden,et al.  Dynamic simulation of diblock copolymer microphase separation , 1998 .

[23]  祐志 望月,et al.  フラグメント分子軌道(FMO)法を用いた散逸粒子動力学シミュレーションのための有効相互作用パラメータ算出の自動化フレームワーク , 2018 .

[24]  N. Maurits,et al.  The dynamic mean-field density functional method and its application to the mesoscopic dynamics of quenched block copolymer melts , 1997 .

[25]  A. G. Schlijper,et al.  Computer simulation of dilute polymer solutions with the dissipative particle dynamics method , 1995 .

[26]  Matt K. Petersen,et al.  Excess proton solvation and delocalization in a hydrophilic pocket of the proton conducting polymer membrane nafion. , 2005, The journal of physical chemistry. B.

[27]  Shigenori Tanaka,et al.  Incorporation of solvation effects into the fragment molecular orbital calculations with the Poisson–Boltzmann equation , 2010 .

[28]  M. Dupuis,et al.  Atomistic simulations of hydrated nafion and temperature effects on hydronium ion mobility. , 2007, The journal of physical chemistry. B.

[29]  Stefan Grimme,et al.  Semiempirical GGA‐type density functional constructed with a long‐range dispersion correction , 2006, J. Comput. Chem..

[30]  Berend Smit,et al.  Phase behavior of monomeric mixtures and polymer solutions with soft interaction potentials , 2001 .

[31]  Roland Faller,et al.  Design Principles for Nanoparticles Enveloped by a Polymer-Tethered Lipid Membrane. , 2014, ACS nano.

[32]  Canan Atilgan,et al.  Mapping and Reverse-Mapping of the Morphologies for a Molecular Understanding of the Self-Assembly of Fluorinated Block Copolymers , 2010 .

[33]  P. B. Warren,et al.  DISSIPATIVE PARTICLE DYNAMICS : BRIDGING THE GAP BETWEEN ATOMISTIC AND MESOSCOPIC SIMULATION , 1997 .

[34]  T. Ikeshoji,et al.  First-principles molecular dynamics study on aqueous sulfuric acid solutions. , 2007, The Journal of chemical physics.

[35]  Yuto Komeiji,et al.  Electron-correlated fragment-molecular-orbital calculations for biomolecular and nano systems. , 2014, Physical chemistry chemical physics : PCCP.

[36]  M. Dupuis,et al.  Atomistic simulation of nafion membrane: I. Effect of hydration on membrane nanostructure. , 2007, The journal of physical chemistry. B.

[37]  John F. Nagle,et al.  Structure of Fully Hydrated Fluid Phase Lipid Bilayers with Monounsaturated Chains , 2006, The Journal of Membrane Biology.

[38]  J. Ávalos,et al.  Dissipative particle dynamics with energy conservation: Modelling of heat flow , 1999 .

[39]  J. Benziger,et al.  Differences in Water Sorption and Proton Conductivity Between Nafion and SPEEK , 2011 .

[40]  S. Paddison,et al.  Dissipative Particle Dynamics interaction parameters from ab initio calculations , 2016 .

[41]  K. Yasuoka,et al.  Dissipative particle dynamics (DPD) simulations with fragment molecular orbital (FMO) based effective parameters for 1-Palmitoyl-2-oleoyl phosphatidyl choline (POPC) membrane , 2017 .

[42]  Y. Mochizuki,et al.  Fragment Molecular Orbital Based Parametrization Procedure for Mesoscopic Structure Prediction of Polymeric Materials. , 2018, The journal of physical chemistry. B.

[43]  Jozef Bicerano,et al.  Prediction of Polymer Properties , 1996 .

[44]  K. Yasuoka,et al.  Theoretical analyses on water cluster structures in polymer electrolyte membrane by using dissipative particle dynamics simulations with fragment molecular orbital based effective parameters , 2018, RSC advances.

[45]  A. Sum,et al.  Molecular characterization of gel and liquid-crystalline structures of fully hydrated POPC and POPE bilayers. , 2007, The journal of physical chemistry. B.

[46]  D. V. Krevelen,et al.  Properties of polymers, their estimation and correlation with chemical structure , 1972 .

[47]  M. Bloom,et al.  Combined influence of cholesterol and synthetic amphiphillic peptides upon bilayer thickness in model membranes. , 1992, Biophysical journal.

[48]  B. D. Olafson,et al.  Application of molecular simulation to derive phase diagrams of binary mixtures , 1992 .

[49]  Matt K. Petersen,et al.  Characterization of the solvation and transport of the hydrated proton in the perfluorosulfonic acid membrane nafion. , 2006, The journal of physical chemistry. B.

[50]  Kazuo Kitaura,et al.  Exploring chemistry with the fragment molecular orbital method. , 2012, Physical chemistry chemical physics : PCCP.

[51]  Masao Doi,et al.  Dynamical Mean Field Calculation of Grafting Reaction of End-Functionalized Polymer , 1997 .

[52]  J. Koelman,et al.  Simulating microscopic hydrodynamic phenomena with dissipative particle dynamics , 1992 .

[53]  G. Voth,et al.  Proton solvation and transport in hydrated nafion. , 2011, The journal of physical chemistry. B.

[54]  Kazuo Kitaura,et al.  The Fragment Molecular Orbital Method: Practical Applications to Large Molecular Systems , 2009 .

[55]  Yoong-Kee Choe,et al.  Nature of proton dynamics in a polymer electrolyte membrane, nafion: a first-principles molecular dynamics study. , 2009, Physical chemistry chemical physics : PCCP.

[56]  I. Vattulainen,et al.  Effect of NaCl and KCl on phosphatidylcholine and phosphatidylethanolamine lipid membranes: insight from atomic-scale simulations for understanding salt-induced effects in the plasma membrane. , 2008, The journal of physical chemistry. B.

[57]  J. H. Zhang,et al.  The effect of POPC acyl chains packing by aromatic amino acid methyl esters investigated by ATR-FTIR combined with QM calculations , 2016 .

[58]  R. D. Groot,et al.  Mesoscopic simulation of cell membrane damage, morphology change and rupture by nonionic surfactants. , 2001, Biophysical journal.

[59]  S. Greenbaum,et al.  High-Pressure Electrical Conductivity and NMR Studies in Variable Equivalent Weight NAFION Membranes , 1996 .

[60]  J. Pozuelo,et al.  Molecular Dynamics Simulations of Proton Conduction in Sulfonated Poly(phenyl sulfone)s , 2006 .