Dissipative particle dynamics simulations in colloid and Interface science: A review

KP Santo, AV Neimark - Advances in colloid and interface science, 2021 - Elsevier
Dissipative particle dynamics (DPD) is one of the most efficient mesoscale coarse-grained
methodologies for modeling soft matter systems. Here, we comprehensively review the …

Perspective: Coarse-grained models for biomolecular systems

WG Noid - The Journal of chemical physics, 2013 - pubs.aip.org
By focusing on essential features, while averaging over less important details, coarse-
grained (CG) models provide significant computational and conceptual advantages with …

[HTML][HTML] Perspective: Dissipative particle dynamics

P Espanol, PB Warren - The Journal of chemical physics, 2017 - pubs.aip.org
Dissipative particle dynamics (DPD) belongs to a class of models and computational
algorithms developed to address mesoscale problems in complex fluids and soft matter in …

[HTML][HTML] 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 …

[HTML][HTML] Constructing many-body dissipative particle dynamics models of fluids from bottom-up coarse-graining

Y Han, J **, GA Voth - The Journal of Chemical Physics, 2021 - pubs.aip.org
Since their emergence in the 1990s, mesoscopic models of fluids have been widely used to
study complex organization and transport phenomena beyond the molecular scale. Even …

[HTML][HTML] Mesoscopic coarse-grained representations of fluids rigorously derived from atomistic models

Y Han, JF Dama, GA Voth - The Journal of Chemical Physics, 2018 - pubs.aip.org
Mesoscopic models are widely used to study complex organization and transport
phenomena in chemical and biological systems. Defining a rigorous procedure by which a …

High-resolution coarse-grained model of hydrated anion-exchange membranes that accounts for hydrophobic and ionic interactions through short-ranged potentials

J Lu, LC Jacobson, YA Perez Sirkin… - Journal of Chemical …, 2017 - ACS Publications
Molecular simulations provide a versatile tool to study the structure, anion conductivity, and
stability of anion-exchange membrane (AEM) materials and can provide a fundamental …

Hierarchical machine learning of low-resolution coarse-grained free energy potentials

S Izvekov, BM Rice - Journal of Chemical Theory and …, 2023 - ACS Publications
A force-matching-based method for supervised machine learning (ML) of coarse-grained
(CG) free energy (FE) potentials─ known as multiscale coarse-graining via force-matching …

Brownian motion of soft particles near a fluctuating lipid bilayer

S Sheikh, B Lonetti, I Touche, A Mohammadi… - The Journal of …, 2023 - pubs.aip.org
The dynamics of a soft particle suspended in a viscous fluid can be changed by the
presence of an elastic boundary. Understanding the mechanisms and dynamics of soft–soft …

Representability and Dynamical Consistency in Coarse-Grained Models

M Palma Banos, AV Popov… - The Journal of Physical …, 2024 - ACS Publications
We address the challenge of representativity and dynamical consistency when unbonded
fine-grained particles are collected together into coarse-grained particles. We implement a …