Van der Waals Perspective on Coarse-Graining: Progress toward Solving Representability and Transferability Problems.
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[1] Florian Müller-Plathe,et al. Temperature dependence of coarse-grained potentials for liquid hexane. , 2011, Physical chemistry chemical physics : PCCP.
[2] David Chandler,et al. Roles of Repulsive and Attractive Forces in Liquids : The Equilibrium Theory of Classical Fluids , 2007 .
[3] A. Louis. Beware of density dependent pair potentials , 2002, cond-mat/0205110.
[4] Valeria Molinero,et al. Water-Driven Cavity-Ligand Binding: Comparison of Thermodynamic Signatures from Coarse-Grained and Atomic-Level Simulations. , 2012, Journal of chemical theory and computation.
[5] Marcus Mueller,et al. Biological and synthetic membranes: What can be learned from a coarse-grained description? , 2006 .
[6] Aleksander E. P. Durumeric,et al. On the representability problem and the physical meaning of coarse-grained models. , 2016, The Journal of chemical physics.
[7] M. Guenza,et al. An analytical coarse-graining method which preserves the free energy, structural correlations, and thermodynamic state of polymer melts from the atomistic to the mesoscale. , 2014, The Journal of chemical physics.
[8] W G Noid,et al. Systematic methods for structurally consistent coarse-grained models. , 2013, Methods in molecular biology.
[9] M Scott Shell,et al. Anomalous waterlike behavior in spherically-symmetric water models optimized with the relative entropy. , 2009, Physical chemistry chemical physics : PCCP.
[10] W G Noid,et al. Bottom-up coarse-grained models that accurately describe the structure, pressure, and compressibility of molecular liquids. , 2015, The Journal of chemical physics.
[11] Alexander Lyubartsev,et al. Systematic coarse-graining of molecular models by the Newton inversion method. , 2010, Faraday discussions.
[12] Hansen,et al. Can polymer coils Be modeled as "Soft colloids"? , 2000, Physical review letters.
[13] Kurt Kremer,et al. Multiscale simulation of soft matter systems. , 2010, Faraday discussions.
[14] W. L. Jorgensen,et al. Development and Testing of the OPLS All-Atom Force Field on Conformational Energetics and Properties of Organic Liquids , 1996 .
[15] Hendrik Meyer,et al. Coarse Graining of Short Polythylene Chains for Studying Polymer Crystallization. , 2006, Journal of chemical theory and computation.
[16] William R. Smith,et al. Pair and triplet interactions in argon , 1969 .
[17] R. Baron,et al. Configurational entropies of lipids in pure and mixed bilayers from atomic-level and coarse-grained molecular dynamics simulations. , 2006, The journal of physical chemistry. B.
[18] W. Noid,et al. Bottom-up coarse-grained models with predictive accuracy and transferability for both structural and thermodynamic properties of heptane-toluene mixtures. , 2016, The Journal of chemical physics.
[19] Carlo Pierleoni,et al. Predicting the thermodynamics by using state-dependent interactions. , 2012, The Journal of chemical physics.
[20] M. Guenza. Thermodynamic consistency and other challenges in coarse-graining models , 2015 .
[21] Sergei Izvekov,et al. Towards an understanding of many-particle effects in hydrophobic association in methane solutions. , 2011, The Journal of chemical physics.
[22] Alexander P. Lyubartsev,et al. OSMOTIC AND ACTIVITY COEFFICIENTS FROM EFFECTIVE POTENTIALS FOR HYDRATED IONS , 1997 .
[23] Christos N. Likos,et al. EFFECTIVE INTERACTIONS IN SOFT CONDENSED MATTER PHYSICS , 2001 .
[24] Salvatore Torquato,et al. Statistical mechanical models with effective potentials: Definitions, applications, and thermodynamic consequences , 2002 .
[25] M Scott Shell,et al. The relative entropy is fundamental to multiscale and inverse thermodynamic problems. , 2008, The Journal of chemical physics.
[26] Connecting local structure to interface formation: a molecular scale van der Waals theory of nonuniform liquids. , 2001, Annual review of physical chemistry.
[27] Marissa G. Saunders,et al. Coarse-graining methods for computational biology. , 2013, Annual review of biophysics.
[28] Pritam Ganguly,et al. Systematic coarse-graining methods for soft matter simulations - a review , 2013 .
[29] Gregory A Voth,et al. The multiscale coarse-graining method. VII. Free energy decomposition of coarse-grained effective potentials. , 2011, The Journal of chemical physics.
[30] Gregory C Rutledge,et al. A novel algorithm for creating coarse-grained, density dependent implicit solvent models. , 2008, The Journal of chemical physics.
[31] Markus Deserno,et al. Mesoscopic membrane physics: concepts, simulations, and selected applications. , 2009, Macromolecular rapid communications.
[32] Gregory A Voth,et al. The multiscale coarse-graining method. IV. Transferring coarse-grained potentials between temperatures. , 2009, The Journal of chemical physics.
[33] Margaret E. Johnson,et al. Representability problems for coarse-grained water potentials. , 2007, The Journal of chemical physics.
[34] Kurt Kremer,et al. Comparative atomistic and coarse-grained study of water: What do we lose by coarse-graining? , 2009, The European physical journal. E, Soft matter.
[35] M. Guenza,et al. Thermodynamic Consistency between Analytic Integral Equation Theory and Coarse-Grained Molecular Dynamics Simulations of Homopolymer Melts , 2012 .
[36] Roland Faller,et al. State point dependence of systematically coarse–grained potentials , 2007 .
[37] I. Bahar,et al. Normal mode analysis of biomolecular structures: functional mechanisms of membrane proteins. , 2010, Chemical reviews.
[38] Yuqing Qiu,et al. Coarse-Graining of TIP4P/2005, TIP4P-Ew, SPC/E, and TIP3P to Monatomic Anisotropic Water Models Using Relative Entropy Minimization. , 2014, Journal of chemical theory and computation.
[39] M. Guenza,et al. Thermodynamic consistency in variable-level coarse graining of polymeric liquids. , 2012, Physical review letters.
[40] A. Lyubartsev,et al. Effective solvent mediated potentials of Na+ and Cl- ions in aqueous solution: temperature dependence. , 2011, Physical chemistry chemical physics : PCCP.
[41] Changbong Hyeon,et al. Capturing the essence of folding and functions of biomolecules using coarse-grained models. , 2011, Nature communications.
[42] William George Noid,et al. Extended ensemble approach for deriving transferable coarse-grained potentials , 2009 .
[43] Gregory A Voth,et al. Multiscale coarse graining of liquid-state systems. , 2005, The Journal of chemical physics.
[44] M. Tuckerman. Statistical Mechanics: Theory and Molecular Simulation , 2010 .
[45] Gregory A Voth,et al. A multiscale coarse-graining method for biomolecular systems. , 2005, The journal of physical chemistry. B.
[46] M. Scott Shell,et al. The impact of resolution upon entropy and information in coarse-grained models. , 2015, The Journal of chemical physics.
[47] P. Madden,et al. Three-body dispersion contributions to the thermodynamic properties and effective pair interactions in liquid argon , 1999 .
[48] Gregory A. Voth,et al. The multiscale coarse-graining method. I. A rigorous bridge between atomistic and coarse-grained models. , 2008, The Journal of chemical physics.
[49] Reinier L. C. Akkermans,et al. A structure-based coarse-grained model for polymer melts , 2001 .
[50] J. Kirkwood. Statistical Mechanics of Fluid Mixtures , 1935 .
[51] Wataru Shinoda,et al. Multi-property fitting and parameterization of a coarse grained model for aqueous surfactants , 2007 .
[52] Avisek Das,et al. The multiscale coarse-graining method. V. Isothermal-isobaric ensemble. , 2010, The Journal of chemical physics.
[53] Joseph F Rudzinski,et al. Coarse-graining entropy, forces, and structures. , 2011, The Journal of chemical physics.
[54] W G Noid,et al. Perspective: Coarse-grained models for biomolecular systems. , 2013, The Journal of chemical physics.