Introducing memory in coarse-grained molecular simulations

V Klippenstein, M Tripathy, G Jung… - The Journal of …, 2021 - ACS Publications
Preserving the correct dynamics at the coarse-grained (CG) level is a pressing problem in
the development of systematic CG models in soft matter simulation. Starting from the seminal …

Coarse-grained modelling out of equilibrium

T Schilling - Physics Reports, 2022 - Elsevier
Abstract Active matter, responsive (“smart”) materials and materials under time-dependent
load are systems out of thermal equilibrium. To construct coarse-grained models for such …

Likelihood-based non-Markovian models from molecular dynamics

H Vroylandt, L Goudenège… - Proceedings of the …, 2022 - National Acad Sciences
We introduce a method to accurately and efficiently estimate the effective dynamics of
collective variables in molecular simulations. Such reduced dynamics play an essential role …

Bottom-up informed and iteratively optimized coarse-grained non-Markovian water models with accurate dynamics

V Klippenstein, NFA van der Vegt - Journal of Chemical Theory …, 2023 - ACS Publications
Molecular dynamics (MD) simulations based on coarse-grained (CG) particle models of
molecular liquids generally predict accelerated dynamics and misrepresent the time scales …

Recent progress towards chemically-specific coarse-grained simulation models with consistent dynamical properties

JF Rudzinski - Computation, 2019 - mdpi.com
Coarse-grained (CG) models can provide computationally efficient and conceptually simple
characterizations of soft matter systems. While generic models probe the underlying physics …

Data-driven coarse-grained modeling of polymers in solution with structural and dynamic properties conserved

S Wang, Z Ma, W Pan - Soft Matter, 2020 - pubs.rsc.org
We present data-driven coarse-grained (CG) modeling for polymers in solution, which
conserves the dynamic as well as structural properties of the underlying atomistic system …

Model reduction techniques for the computation of extended Markov parameterizations for generalized Langevin equations

N Bockius, J Shea, G Jung, F Schmid… - Journal of Physics …, 2021 - iopscience.iop.org
The generalized Langevin equation is a model for the motion of coarse-grained particles
where dissipative forces are represented by a memory term. The numerical realization of …

Transfer learning of memory kernels for transferable coarse-graining of polymer dynamics

Z Ma, S Wang, M Kim, K Liu, CL Chen, W Pan - Soft Matter, 2021 - pubs.rsc.org
The present work concerns the transferability of coarse-grained (CG) modeling in
reproducing the dynamic properties of the reference atomistic systems across a range of …

Accuracy, transferability, and efficiency of coarse-grained models of molecular liquids

MG Guenza, M Dinpajooh, J McCarty… - The Journal of …, 2018 - ACS Publications
Coarse-graining (CG) approaches are becoming essential tools in the study of complex
systems because they can considerably speed up computer simulations, with the promise of …

[HTML][HTML] Dynamical coarse-grained models of molecular liquids and their ideal and non-ideal mixtures

M Tripathy, V Klippenstein… - The Journal of Chemical …, 2023 - pubs.aip.org
Coarse-grained (CG) simulation models of condensed-phase systems can be derived with
well-established methods that perform coarse-graining in space and provide an effective …