Bottom-up approach to represent dynamic properties in coarse-grained molecular simulations

Memory-induced acceleration and slowdown of barrier crossing

(2018) Julian Kappler et al.   JOURNAL OF CHEMICAL PHYSICS

Coarse-grained simulations of cis- and trans-polybutadiene: A bottom-up approach

(2017) Claire A. Lemarchand et al.   JOURNAL OF CHEMICAL PHYSICS

Microscopic derivation of particle-based coarse-grained dynamics: Exact expression for memory function

(2017) Sergei Izvekov   JOURNAL OF CHEMICAL PHYSICS

Computing the non-Markovian coarse-grained interactions derived from the Mori–Zwanzig formalism in molecular systems: Application to polymer melts

(2017) Zhen Li et al.   JOURNAL OF CHEMICAL PHYSICS

Perspective: Dissipative particle dynamics

(2017) Pep Español et al.   JOURNAL OF CHEMICAL PHYSICS

Iterative Reconstruction of Memory Kernels

(2017) Gerhard Jung et al.   Journal of Chemical Theory and Computation

Bayesian parametrization of coarse-grain dissipative dynamics models

(2015) Alain Dequidt 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

On the importance of shear dissipative forces in coarse-grained dynamics of molecular liquids

(2015) Sergei Izvekov et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Conservative and dissipative force field for simulation of coarse-grained alkane molecules: A bottom-up approach

(2014) Sébastien Trément 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

Multi-scale coarse-graining of non-conservative interactions in molecular liquids

(2014) Sergei Izvekov et al.   JOURNAL OF CHEMICAL PHYSICS

Construction of dissipative particle dynamics models for complex fluids via the Mori–Zwanzig formulation

(2014) Zhen Li et al.   Soft Matter

Microscopic derivation of particle-based coarse-grained dynamics

(2013) Sergei Izvekov   JOURNAL OF CHEMICAL PHYSICS

Perspective: Coarse-grained models for biomolecular systems

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

Bottom-up construction of interaction models of non-Markovian dissipative particle dynamics

(2013) Yuta Yoshimoto et al.   PHYSICAL REVIEW E

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

(2012) Emiliano Brini et al.   Soft Matter

Semi-bottom-up coarse graining of water based on microscopic simulations

(2011) Lianghui Gao et al.   JOURNAL OF CHEMICAL PHYSICS

Conditional reversible work method for molecular coarse graining applications

(2011) Emiliano Brini et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Multiscale modeling of soft matter: scaling of dynamics

(2011) Dominik Fritz et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Colored-Noise Thermostats à la Carte

(2010) Michele Ceriotti et al.   Journal of Chemical Theory and Computation

Direct construction of mesoscopic models from microscopic simulations

(2010) Huan Lei et al.   PHYSICAL REVIEW E

Multiscale simulation of soft matter systems

(2009) Christine Peter et al.   FARADAY DISCUSSIONS

Mori–Zwanzig formalism as a practical computational tool

(2009) Carmen Hijón et al.   FARADAY DISCUSSIONS

Bottom-up derivation of an effective thermostat for united atoms simulations of water

(2009) Anders Eriksson et al.   JOURNAL OF CHEMICAL PHYSICS

A method for estimating the interactions in dissipative particle dynamics from particle trajectories

(2009) Anders Eriksson et al.   JOURNAL OF PHYSICS-CONDENSED MATTER

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

Effective force coarse-graining

(2009) Yanting Wang et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Hierarchical modeling of polymer permeation

(2009) Dominik Fritz et al.   Soft Matter

Effective thermostat induced by coarse graining of simple point charge water

(2008) Anders Eriksson 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

GROMACS 4:  Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation

(2008) Berk Hess et al.   Journal of Chemical Theory and Computation