Parametrizing coarse grained models for molecular systems at equilibrium

Path-space variational inference for non-equilibrium coarse-grained systems

(2016) Vagelis Harmandaris et al.   JOURNAL OF COMPUTATIONAL PHYSICS

Path-Space Information Bounds for Uncertainty Quantification and Sensitivity Analysis of Stochastic Dynamics

(2016) Paul Dupuis et al.   SIAM-ASA Journal on Uncertainty Quantification

Solid-liquid work of adhesion of coarse-grained models of n-hexane on graphene layers derived from the conditional reversible work method

(2015) Vikram Reddy Ardham et al.   JOURNAL OF CHEMICAL PHYSICS

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

Wavelets as basis functions to represent the coarse-graining potential in multiscale coarse graining approach

(2015) M. Maiolo et al.   JOURNAL OF COMPUTATIONAL PHYSICS

Computer Simulations of Soft Matter: Linking the Scales

(2014) Raffaello Potestio et al.   Entropy

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

Multiscale modeling of polyisoprene on graphite

(2014) Yogendra Narayan Pandey 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

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

Perspective: Coarse-grained models for biomolecular systems

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

Hierarchical Multiscale Modeling of Polymer–Solid Interfaces: Atomistic to Coarse-Grained Description and Structural and Conformational Properties of Polystyrene–Gold Systems

(2013) Karen Johnston et al.   MACROMOLECULES

Hierarchical simulations of hybrid polymer–solid materials

(2013) Karen Johnston et al.   Soft Matter

The multiscale coarse-graining method. X. Improved algorithms for constructing coarse-grained potentials for molecular systems

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

The Role of Many-Body Correlations in Determining Potentials for Coarse-Grained Models of Equilibrium Structure

(2012) Joseph F. Rudzinski et al.   JOURNAL OF PHYSICAL CHEMISTRY B

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

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

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

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

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

(2010) Chunggi Baig et al.   MACROMOLECULES

Gaussian Approximation Potentials: The Accuracy of Quantum Mechanics, without the Electrons

(2010) Albert P. Bartók et al.   PHYSICAL REVIEW LETTERS

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

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

Comparative atomistic and coarse-grained study of water: What do we lose by coarse-graining?

(2009) Han Wang et al.   EUROPEAN PHYSICAL JOURNAL E

Mori–Zwanzig formalism as a practical computational tool

(2009) Carmen Hijón et al.   FARADAY DISCUSSIONS

Systematic coarse-graining of molecular models by the Newton inversion method

(2009) Alexander Lyubartsev et al.   FARADAY DISCUSSIONS

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

Systematic coarse graining from structure using internal states: Application to phospholipid/cholesterol bilayer

(2009) Teemu Murtola 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

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

Multiscale modeling of emergent materials: biological and soft matter

(2009) Teemu Murtola 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

Multiscale simulation of soft matter systems – from the atomistic to the coarse-grained level and back

(2009) Christine Peter et al.   Soft Matter

Maximum likelihood drift estimation for multiscale diffusions

(2009) A. Papavasiliou et al.   STOCHASTIC PROCESSES AND THEIR APPLICATIONS

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

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

Transferability of coarse-grained force fields: The polymer case

(2008) Paola Carbone 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

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

Multibody Interactions in Coarse-Graining Schemes for Extended Systems

(2008) Sasanka Are et al.   SIAM JOURNAL ON SCIENTIFIC COMPUTING