Coarse-grained models using local-density potentials optimized with the relative entropy: Application to implicit solvation

Cooperativity in Noncovalent Interactions

(2016) A. Subha Mahadevi et al.   CHEMICAL REVIEWS

A coarse-grain force field for RDX: Density dependent and energy conserving

(2016) Joshua D. Moore et al.   JOURNAL OF CHEMICAL PHYSICS

Parallelization and improvements of the generalized born model with a simple sWitching function for modern graphics processors

(2016) Evan J. Arthur et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Recent advances in molecular simulation: A chemical engineering perspective

(2015) Jeremy C. Palmer et al.   AICHE JOURNAL

A generalized-Yvon-Born-Green method for coarse-grained modeling

(2015) J. F. Rudzinski et al.   European Physical Journal-Special Topics

Bottom-up coarse-grained models that accurately describe the structure, pressure, and compressibility of molecular liquids

(2015) Nicholas J. H. Dunn et al.   JOURNAL OF CHEMICAL PHYSICS

Design and application of implicit solvent models in biomolecular simulations

(2014) Jens Kleinjung et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Coarse-Graining of TIP4P/2005, TIP4P-Ew, SPC/E, and TIP3P to Monatomic Anisotropic Water Models Using Relative Entropy Minimization

(2014) Jibao Lu et al.   Journal of Chemical Theory and Computation

Perspective: Coarse-grained models for biomolecular systems

(2013) W. G. Noid   JOURNAL OF CHEMICAL PHYSICS

The Theory of Ultra-Coarse-Graining. 1. General Principles

(2013) James F. Dama et al.   Journal of Chemical Theory and Computation

Water 16-mers and Hexamers: Assessment of the Three-Body and Electrostatically Embedded Many-Body Approximations of the Correlation Energy or the Nonlocal Energy As Ways to Include Cooperative Effects

(2013) Helena W. Qi et al.   JOURNAL OF PHYSICAL CHEMISTRY A

Dissecting Hydrophobic Hydration and Association

(2013) Richard C. Remsing et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Crowding Induced Collective Hydration of Biological Macromolecules over Extended Distances

(2013) John T. King et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Length-scale crossover of the hydrophobic interaction in a coarse-grained water model

(2013) Aviel Chaimovich et al.   PHYSICAL REVIEW E

Dynamic implicit-solvent coarse-grained models of lipid bilayer membranes: Fluctuating hydrodynamics thermostat

(2013) Yaohong Wang et al.   PHYSICAL REVIEW E

The multiscale coarse-graining method. IX. A general method for construction of three body coarse-grained force fields

(2012) Avisek Das et al.   JOURNAL OF CHEMICAL PHYSICS

A New Multiscale Algorithm and Its Application to Coarse-Grained Peptide Models for Self-Assembly

(2012) Scott P. Carmichael et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Homogeneous Nucleation of Methane Hydrates: Unrealistic under Realistic Conditions

(2012) Brandon C. Knott et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Particle-based multiscale coarse graining with density-dependent potentials: Application to molecular crystals (hexahydro-1,3,5-trinitro-s-triazine)

(2011) Sergei Izvekov et al.   JOURNAL OF CHEMICAL PHYSICS

Coarse-graining entropy, forces, and structures

(2011) Joseph F. Rudzinski et al.   JOURNAL OF CHEMICAL PHYSICS

Towards an understanding of many-particle effects in hydrophobic association in methane solutions

(2011) Sergei Izvekov   JOURNAL OF CHEMICAL PHYSICS

Coarse-graining errors and numerical optimization using a relative entropy framework

(2011) Aviel Chaimovich et al.   JOURNAL OF CHEMICAL PHYSICS

Modeling aqueous solvation with semi-explicit assembly

(2011) C. J. Fennell et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Hydrophobicity of Proteins and Interfaces: Insights from Density Fluctuations

(2011) Sumanth N. Jamadagni et al.   Annual Review of Chemical and Biomolecular Engineering

Hydrophobic interactions in model enclosures from small to large length scales: non-additivity in explicit and implicit solvent models

(2010) Lingle Wang et al.   FARADAY DISCUSSIONS

The search for the hydrophobic force law

(2010) Malte U. Hammer et al.   FARADAY DISCUSSIONS

The multiscale coarse-graining method. VI. Implementation of three-body coarse-grained potentials

(2010) Luca Larini et al.   JOURNAL OF CHEMICAL PHYSICS

The multiscale coarse-graining method. V. Isothermal-isobaric ensemble

(2010) Avisek Das et al.   JOURNAL OF CHEMICAL PHYSICS

Transferability of Nonbonded Interaction Potentials for Coarse-Grained Simulations: Benzene in Water

(2010) Alessandra Villa et al.   Journal of Chemical Theory and Computation

Relative entropy as a universal metric for multiscale errors

(2010) Aviel Chaimovich et al.   PHYSICAL REVIEW E

Evaluating the transferability of coarse-grained, density-dependent implicit solvent models to mixtures and chains

(2009) Erik C. Allen et al.   JOURNAL OF CHEMICAL PHYSICS

The multiscale coarse-graining method. IV. Transferring coarse-grained potentials between temperatures

(2009) Vinod Krishna et al.   JOURNAL OF CHEMICAL PHYSICS

Extended ensemble approach for deriving transferable coarse-grained potentials

(2009) J. W. Mullinax et al.   JOURNAL OF CHEMICAL PHYSICS

Versatile Object-Oriented Toolkit for Coarse-Graining Applications

(2009) Victor Rühle et al.   Journal of Chemical Theory and Computation

CHARMM: The biomolecular simulation program

(2009) B. R. Brooks et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Oil/Water Transfer Is Partly Driven by Molecular Shape, Not Just Size

(2009) Christopher J. Fennell et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

How Surface Wettability Affects the Binding, Folding, and Dynamics of Hydrophobic Polymers at Interfaces

(2009) Sumanth N. Jamadagni et al.   LANGMUIR

Anomalous waterlike behavior in spherically-symmetric water models optimized with the relative entropy

(2009) Aviel Chaimovich et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Quantifying Water Density Fluctuations and Compressibility of Hydration Shells of Hydrophobic Solutes and Proteins

(2009) Sapna Sarupria et al.   PHYSICAL REVIEW LETTERS

Characterizing hydrophobicity of interfaces by using cavity formation, solute binding, and water correlations

(2009) R. Godawat et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Towards temperature-dependent coarse-grained potentials of side-chain interactions for protein folding simulations. I: Molecular dynamics study of a pair of methane molecules in water at various temperatures

(2009) Emil Sobolewski et al.   PROTEIN ENGINEERING DESIGN & SELECTION

The Protein Folding Problem

(2008) Ken A. Dill et al.   Annual Review of Biophysics

A novel algorithm for creating coarse-grained, density dependent implicit solvent models

(2008) Erik C. Allen et al.   JOURNAL OF CHEMICAL PHYSICS

The multiscale coarse-graining method. I. A rigorous bridge between atomistic and coarse-grained models

(2008) W. G. Noid et al.   JOURNAL OF CHEMICAL PHYSICS

The relative entropy is fundamental to multiscale and inverse thermodynamic problems

(2008) M. Scott Shell   JOURNAL OF CHEMICAL PHYSICS

How Interfaces Affect Hydrophobically Driven Polymer Folding†

(2008) Sumanth N. Jamadagni et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Water Modeled As an Intermediate Element between Carbon and Silicon†

(2008) Valeria Molinero et al.   JOURNAL OF PHYSICAL CHEMISTRY B