Bottom-up coarse-graining: Principles and perspectives

J Jin, AJ Pak, AEP Durumeric, TD Loose… - Journal of chemical …, 2022 - ACS Publications
Large-scale computational molecular models provide scientists a means to investigate the
effect of microscopic details on emergent mesoscopic behavior. Elucidating the relationship …

Perspective: Advances, challenges, and insight for predictive coarse-grained models

WG Noid - The Journal of Physical Chemistry B, 2023 - ACS Publications
By averaging over atomic details, coarse-grained (CG) models provide profound
computational and conceptual advantages for studying soft materials. In particular, bottom …

Flow-matching: Efficient coarse-graining of molecular dynamics without forces

J Kohler, Y Chen, A Kramer, C Clementi… - Journal of Chemical …, 2023 - ACS Publications
Coarse-grained (CG) molecular simulations have become a standard tool to study molecular
processes on time and length scales inaccessible to all-atom simulations. Parametrizing CG …

Utilizing machine learning to greatly expand the range and accuracy of bottom-up coarse-grained models through virtual particles

PG Sahrmann, TD Loose… - Journal of Chemical …, 2023 - ACS Publications
Coarse-grained (CG) models parametrized using atomistic reference data, ie,“bottom up”
CG models, have proven useful in the study of biomolecules and other soft matter. However …

Temperature and phase transferable bottom-up coarse-grained models

J Jin, A Yu, GA Voth - Journal of chemical theory and computation, 2020 - ACS Publications
Despite the high fidelity of bottom-up coarse-grained (CG) approaches to recapitulate the
structural correlations in atomistic simulations, the general use of bottom-up CG methods is …

From system modeling to system analysis: The impact of resolution level and resolution distribution in the computer-aided investigation of biomolecules

M Giulini, M Rigoli, G Mattiotti, R Menichetti… - Frontiers in Molecular …, 2021 - frontiersin.org
The ever increasing computer power, together with the improved accuracy of atomistic force
fields, enables researchers to investigate biological systems at the molecular level with …

Rigorous Progress in Coarse-Graining

WG Noid, RJ Szukalo, KM Kidder… - Annual Review of …, 2024 - annualreviews.org
Low-resolution coarse-grained (CG) models provide remarkable computational and
conceptual advantages for simulating soft materials. In principle, bottom-up CG models can …

A temperature-dependent length-scale for transferable local density potentials

RJ Szukalo, WG Noid - The Journal of Chemical Physics, 2023 - pubs.aip.org
Recent coarse-grained (CG) models have often supplemented conventional pair potentials
with potentials that depend upon the local density around each particle. In this work, we …

[HTML][HTML] A new one-site coarse-grained model for water: Bottom-up many-body projected water (BUMPer). II. Temperature transferability and structural properties at …

J Jin, AJ Pak, Y Han, GA Voth - The Journal of Chemical Physics, 2021 - pubs.aip.org
A number of studies have constructed coarse-grained (CG) models of water to understand
its anomalous properties. Most of these properties emerge at low temperatures, and an …

Energetic and entropic considerations for coarse-graining

KM Kidder, RJ Szukalo, WG Noid - The European Physical Journal B, 2021 - Springer
Molecular dynamics simulations often adopt coarse-grained (CG) models to investigate
length-and time-scales that cannot be effectively addressed with atomically detailed models …