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 …

Computational modeling of realistic cell membranes

SJ Marrink, V Corradi, PCT Souza, HI Ingolfsson… - Chemical …, 2019 - ACS Publications
Cell membranes contain a large variety of lipid types and are crowded with proteins,
endowing them with the plasticity needed to fulfill their key roles in cell functioning. The …

Chemically specific coarse‐graining of polymers: Methods and prospects

S Dhamankar, MA Webb - Journal of Polymer Science, 2021 - Wiley Online Library
Coarse‐grained (CG) modeling is an invaluable tool for the study of polymers and other soft
matter systems due to the span of spatiotemporal scales that typify their physics and …

The power of coarse graining in biomolecular simulations

HI Ingólfsson, CA Lopez, JJ Uusitalo… - Wiley …, 2014 - Wiley Online Library
Computational modeling of biological systems is challenging because of the multitude of
spatial and temporal scales involved. Replacing atomistic detail with lower resolution …

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 …

A multiscale coarse-grained model of the SARS-CoV-2 virion

A Yu, AJ Pak, P He, V Monje-Galvan, L Casalino… - Biophysical journal, 2021 - cell.com
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent
of the COVID-19 pandemic. Computer simulations of complete viral particles can provide …

Coarse-graining auto-encoders for molecular dynamics

W Wang, R Gómez-Bombarelli - npj Computational Materials, 2019 - nature.com
Molecular dynamics simulations provide theoretical insight into the microscopic behavior of
condensed-phase materials and, as a predictive tool, enable computational design of new …

OpenMSCG: A software tool for bottom-up coarse-graining

Y Peng, AJ Pak, AEP Durumeric… - The Journal of …, 2023 - ACS Publications
The “bottom-up” approach to coarse-graining, for building accurate and efficient
computational models to simulate large-scale and complex phenomena and processes, is …

Structural basis of membrane bending by the N-BAR protein endophilin

C Mim, H Cui, JA Gawronski-Salerno, A Frost, E Lyman… - Cell, 2012 - cell.com
Functioning as key players in cellular regulation of membrane curvature, BAR domain
proteins bend bilayers and recruit interaction partners through poorly understood …