A review of advancements in coarse-grained molecular dynamics simulations

SY Joshi, SA Deshmukh - Molecular Simulation, 2021 - Taylor & Francis
Over the last few years, coarse-grained molecular dynamics has emerged as a way to model
large and complex systems in an efficient and inexpensive manner due to its lowered …

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 …

LAMMPS-a flexible simulation tool for particle-based materials modeling at the atomic, meso, and continuum scales

AP Thompson, HM Aktulga, R Berger… - Computer Physics …, 2022 - Elsevier
Since the classical molecular dynamics simulator LAMMPS was released as an open source
code in 2004, it has become a widely-used tool for particle-based modeling of materials at …

Understanding and modeling polymers: The challenge of multiple scales

F Schmid - ACS Polymers Au, 2022 - ACS Publications
Polymer materials are multiscale systems by definition. Already the description of a single
macromolecule involves a multitude of scales, and cooperative processes in polymer …

Coarse‐grained molecular dynamics simulation of polymers: Structures and dynamics

R Shi, HJ Qian, ZY Lu - Wiley Interdisciplinary Reviews …, 2023 - Wiley Online Library
For the simulations of polymeric systems, coarse‐grained (CG) molecular dynamics
simulations are computationally demanding not only because of their high computational …

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

Z Li, HS Lee, E Darve, GE Karniadakis - The Journal of chemical …, 2017 - pubs.aip.org
Memory effects are often introduced during coarse-graining of a complex dynamical system.
In particular, a generalized Langevin equation (GLE) for the coarse-grained (CG) system …

Theory of Disordered Solids

A Zaccone - Cham: Springer, 2023 - Springer
The 1977 Nobel prize in Physics was famously awarded to Sir Neville Mott, Phil W.
Anderson and John H. van Vleck for their pioneering work on the electronic theory of …

[HTML][HTML] Molecular systems with open boundaries: Theory and simulation

L Delle Site, M Praprotnik - Physics Reports, 2017 - Elsevier
Typical experimental setups for molecular systems must deal with a certain coupling to the
external environment, that is, the system is open and exchanges mass, momentum, and …

Utilizing machine learning for efficient parameterization of coarse grained molecular force fields

JL McDonagh, A Shkurti, DJ Bray… - Journal of chemical …, 2019 - ACS Publications
We present a machine learning approach to automated force field development in
dissipative particle dynamics (DPD). The approach employs Bayesian optimization to …

Constructing coarse-grained skyrmion potentials from experimental data with Iterative Boltzmann Inversion

Y Ge, J Rothörl, MA Brems, N Kerber, R Gruber… - Communications …, 2023 - nature.com
In an effort to understand skyrmion behavior on a coarse-grained level, skyrmions are often
described as 2D quasiparticles evolving according to the Thiele equation. Interaction …