Parameterization of Coarse-Grained Molecular Interactions through Potential of Mean Force Calculations and Cluster Expansion Techniques

Parametrizing coarse grained models for molecular systems at equilibrium

(2016) E. Kalligiannaki et al.   European Physical Journal-Special Topics

Parametric sensitivity analysis for stochastic molecular systems using information theoretic metrics

(2015) Anastasios Tsourtis et al.   JOURNAL OF CHEMICAL PHYSICS

Incorporation of memory effects in coarse-grained modeling via the Mori-Zwanzig formalism

(2015) Zhen Li et al.   JOURNAL OF CHEMICAL PHYSICS

Bottom-up derivation of conservative and dissipative interactions for coarse-grained molecular liquids with the conditional reversible work method

(2014) Gregor Deichmann et al.   JOURNAL OF CHEMICAL PHYSICS

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) J. McCarty et al.   JOURNAL OF CHEMICAL PHYSICS

Quantitative study of equilibrium and non-equilibrium polymer dynamics through systematic hierarchical coarse-graining simulations

(2014) Vagelis A. Harmandaris   KOREA-AUSTRALIA RHEOLOGY JOURNAL

Coarse-graining schemes for stochastic lattice systems with short and long-range interactions

(2014) Markos A. Katsoulakis et al.   MATHEMATICS OF COMPUTATION

Effective potentials for representing polymers in melts as chains of interacting soft particles

(2013) A. J. Clark et al.   JOURNAL OF CHEMICAL PHYSICS

Information-theoretic tools for parametrized coarse-graining of non-equilibrium extended systems

(2013) Markos A. Katsoulakis et al.   JOURNAL OF CHEMICAL PHYSICS

Fitting coarse-grained distribution functions through an iterative force-matching method

(2013) Lanyuan Lu et al.   JOURNAL OF CHEMICAL PHYSICS

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

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

Perspective: Coarse-grained models for biomolecular systems

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

Hierarchical simulations of hybrid polymer–solid materials

(2013) Karen Johnston et al.   Soft Matter

Cluster Expansion in the Canonical Ensemble

(2012) Elena Pulvirenti et al.   COMMUNICATIONS IN MATHEMATICAL PHYSICS

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

Thermodynamic Consistency between Analytic Integral Equation Theory and Coarse-Grained Molecular Dynamics Simulations of Homopolymer Melts

(2012) J. McCarty et al.   MACROMOLECULES

Systematic coarse-graining methods for soft matter simulations – a review

(2012) Emiliano Brini et al.   Soft Matter

Coarse-graining entropy, forces, and structures

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

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

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

Obtaining fully dynamic coarse-grained models from MD

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

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

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

Efficient, Regularized, and Scalable Algorithms for Multiscale Coarse-Graining

(2010) Lanyuan Lu et al.   Journal of Chemical Theory and Computation

From Mesoscale Back to Microscale: Reconstruction Schemes for Coarse-Grained Stochastic Lattice Systems

(2010) José Trashorras et al.   SIAM JOURNAL ON NUMERICAL ANALYSIS

Inversion of radial distribution functions to pair forces by solving the Yvon–Born–Green equation iteratively

(2009) Hyung Min Cho et al.   JOURNAL OF CHEMICAL PHYSICS

A Generalized-Yvon−Born−Green Theory for Determining Coarse-Grained Interaction Potentials

(2009) J. W. Mullinax et al.   Journal of Physical Chemistry C

Dynamics of Polystyrene Melts through Hierarchical Multiscale Simulations

(2009) Vagelis A. Harmandaris et al.   MACROMOLECULES

Coarse-Grained Polymer Melts Based on Isolated Atomistic Chains: Simulation of Polystyrene of Different Tacticities

(2009) Dominik Fritz et al.   MACROMOLECULES

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

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

Generalized Yvon-Born-Green Theory for Molecular Systems

(2009) J. W. Mullinax et al.   PHYSICAL REVIEW LETTERS

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

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

Diffusion Maps, Reduction Coordinates, and Low Dimensional Representation of Stochastic Systems

(2008) R. R. Coifman et al.   MULTISCALE MODELING & SIMULATION

Mathematical strategies in the coarse-graining of extensive systems: Error quantification and adaptivity

(2007) Markos A. Katsoulakis et al.   JOURNAL OF NON-NEWTONIAN FLUID MECHANICS