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 …

How water's properties are encoded in its molecular structure and energies

E Brini, CJ Fennell, M Fernandez-Serra… - Chemical …, 2017 - ACS Publications
How are water's material properties encoded within the structure of the water molecule? This
is pertinent to understanding Earth's living systems, its materials, its geochemistry and …

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 review of multiscale computational methods in polymeric materials

A Gooneie, S Schuschnigg, C Holzer - Polymers, 2017 - mdpi.com
Polymeric materials display distinguished characteristics which stem from the interplay of
phenomena at various length and time scales. Further development of polymer systems …

Coarse-graining errors and numerical optimization using a relative entropy framework

A Chaimovich, MS Shell - The Journal of chemical physics, 2011 - pubs.aip.org
The ability to generate accurate coarse-grained models from reference fully atomic (or
otherwise “first-principles”) ones has become an important component in modeling the …

Coarse-grained molecular models of water: a review

KR Hadley, C McCabe - Molecular simulation, 2012 - Taylor & Francis
Coarse-grained (CG) models have proven to be very effective tools in the study of
phenomena or systems involving large time-and length-scales. By decreasing the degrees …

The impact of resolution upon entropy and information in coarse-grained models

TT Foley, MS Shell, WG Noid - The Journal of chemical physics, 2015 - pubs.aip.org
By eliminating unnecessary degrees of freedom, coarse-grained (CG) models tremendously
facilitate numerical calculations and theoretical analyses of complex phenomena. However …

Cooperative multivalent receptor binding promotes exposure of the SARS-CoV-2 fusion machinery core

AJ Pak, A Yu, Z Ke, JAG Briggs, GA Voth - Nature communications, 2022 - nature.com
The molecular events that permit the spike glycoprotein of severe acute respiratory
syndrome coronavirus 2 (SARS-CoV-2) to bind and enter cells are important to understand …

The search for the hydrophobic force law

MU Hammer, TH Anderson, A Chaimovich… - Faraday …, 2010 - pubs.rsc.org
After nearly 30 years of research on the hydrophobic interaction, the search for the
hydrophobic force law is still continuing. Indeed, there are more questions than answers …