The geometry of generalized force matching and related information metrics in coarse-graining of molecular systems

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

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

(2013) Markos A. Katsoulakis 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

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

Multilevel coarse graining and nano-pattern discovery in many particle stochastic systems

(2011) Evangelia Kalligiannaki et al.   JOURNAL OF COMPUTATIONAL PHYSICS

Obtaining fully dynamic coarse-grained models from MD

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

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

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

Quantitative Analysis on the Validity of a Coarse-Grained Model for Nonequilibrium Polymeric Liquids under Flow

(2010) Chunggi Baig et al.   MACROMOLECULES

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

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

Dynamics of Polystyrene Melts through Hierarchical Multiscale Simulations

(2009) Vagelis A. Harmandaris 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

Predicting polymer dynamics at multiple length and time scales

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

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

Numerical and Statistical Methods for the Coarse-Graining of Many-Particle Stochastic Systems

(2008) Markos A. Katsoulakis et al.   JOURNAL OF SCIENTIFIC COMPUTING

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

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