A coarse-graining approach for molecular simulation that retains the dynamics of the all-atom reference system by implementing hydrodynamic interactions

A stochastic optimization approach to coarse-graining using a relative-entropy framework

(2013) Ilias Bilionis et al.   JOURNAL OF CHEMICAL PHYSICS

Coarse-Graining Approach to Infer Mesoscale Interaction Potentials from Atomistic Interactions for Aggregating Systems

(2012) Sergiy Markutsya et al.   INDUSTRIAL & ENGINEERING CHEMISTRY RESEARCH

Time versus temperature rescaling for coarse grain molecular dynamics simulations

(2012) J. B. Accary et al.   JOURNAL OF CHEMICAL PHYSICS

Systematic coarse-graining of potential energy landscapes and dynamics in liquids

(2012) M. Scott Shell   JOURNAL OF CHEMICAL PHYSICS

A coarse-grained model for β-d-glucose based on force matching

(2012) Sergiy Markutsya et al.   THEORETICAL CHEMISTRY ACCOUNTS

A Solvent-Free Coarse Grain Model for Crystalline and Amorphous Cellulose Fibrils

(2011) Goundla Srinivas et al.   Journal of Chemical Theory and Computation

Obtaining fully dynamic coarse-grained models from MD

(2011) Pep Español et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Reintroducing explicit solvent to a solvent-free coarse-grained model

(2011) Seung Ha Kim et al.   PHYSICAL REVIEW E

First-principle approach to rescale the dynamics of simulated coarse-grained macromolecular liquids

(2011) I. Lyubimov et al.   PHYSICAL REVIEW E

Brownian Dynamics Simulation of Nucleocytoplasmic Transport: A Coarse-Grained Model for the Functional State of the Nuclear Pore Complex

(2011) Ruhollah Moussavi-Baygi et al.   PLoS Computational Biology

Concerted Interconversion between Ionic Lock Substates of the β2 Adrenergic Receptor Revealed by Microsecond Timescale Molecular Dynamics

(2010) Tod D. Romo et al.   BIOPHYSICAL JOURNAL

A coarse-grained molecular dynamics model for crystalline solids

(2010) Xiantao Li   INTERNATIONAL JOURNAL FOR NUMERICAL METHODS IN ENGINEERING

A Lipid Pathway for Ligand Binding Is Necessary for a Cannabinoid G Protein-coupled Receptor

(2010) Dow P. Hurst et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

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

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

Atomic-Level Characterization of the Structural Dynamics of Proteins

(2010) D. E. Shaw et al.   SCIENCE

Mori–Zwanzig formalism as a practical computational tool

(2009) Carmen Hijón et al.   FARADAY DISCUSSIONS

An O(N2) approximation for hydrodynamic interactions in Brownian dynamics simulations

(2009) Tihamér Geyer et al.   JOURNAL OF CHEMICAL PHYSICS

Striking Effects of Hydrodynamic Interactions on the Simulated Diffusion and Folding of Proteins

(2009) Tamara Frembgen-Kesner et al.   Journal of Chemical Theory and Computation

CHARMM Additive All-Atom Force Field for Glycosidic Linkages between Hexopyranoses

(2009) Olgun Guvench et al.   Journal of Chemical Theory and Computation

Microsecond Simulations of Spontaneous Methane Hydrate Nucleation and Growth

(2009) M. R. Walsh et al.   SCIENCE

Predicting polymer dynamics at multiple length and time scales

(2009) Vagelis A. Harmandaris et al.   Soft Matter

The multiscale coarse-graining method. II. Numerical implementation for coarse-grained molecular models

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

Modeling diffusive dynamics in adaptive resolution simulation of liquid water

(2008) Silvina Matysiak 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

The MARTINI Coarse-Grained Force Field: Extension to Proteins

(2008) Luca Monticelli et al.   Journal of Chemical Theory and Computation

Computer simulation study of fullerene translocation through lipid membranes

(2008) Jirasak Wong-Ekkabut et al.   Nature Nanotechnology

Coarse-grained single-particle dynamics in two-dimensional solids and liquids

(2008) Jörg R. Silbermann et al.   PHYSICAL REVIEW E

Large-Scale Molecular Dynamics Simulations of Self-Assembling Systems

(2008) M. L. Klein et al.   SCIENCE

Multiscale Simulation of Soft Matter: From Scale Bridging to Adaptive Resolution

(2007) Matej Praprotnik et al.   Annual Review of Physical Chemistry