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Dissipative particle dynamics simulations in colloid and Interface science: A review
Dissipative particle dynamics (DPD) is one of the most efficient mesoscale coarse-grained
methodologies for modeling soft matter systems. Here, we comprehensively review the …
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 …
grained (CG) models provide significant computational and conceptual advantages with …
[HTML][HTML] Perspective: Dissipative particle dynamics
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 …
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 …
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
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 …
study complex organization and transport phenomena beyond the molecular scale. Even …
[HTML][HTML] Mesoscopic coarse-grained representations of fluids rigorously derived from atomistic models
Mesoscopic models are widely used to study complex organization and transport
phenomena in chemical and biological systems. Defining a rigorous procedure by which a …
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
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 …
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 …
(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 …
presence of an elastic boundary. Understanding the mechanisms and dynamics of soft–soft …
Representability and Dynamical Consistency in Coarse-Grained Models
We address the challenge of representativity and dynamical consistency when unbonded
fine-grained particles are collected together into coarse-grained particles. We implement a …
fine-grained particles are collected together into coarse-grained particles. We implement a …