Bottom-up coarse-graining: Principles and perspectives

J **, 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 …

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 …

Advances in coarse-grained modeling of macromolecular complexes

AJ Pak, GA Voth - Current opinion in structural biology, 2018 - Elsevier
Highlights•Coarse-grained models are reduced representations of all-atom models that aim
to retain the essential molecular aspects for the system of interest.•Coarse-grained …

Statistically optimal force aggregation for coarse-graining molecular dynamics

A Krämer, AEP Durumeric, NE Charron… - The Journal of …, 2023 - ACS Publications
Machine-learned coarse-grained (CG) models have the potential for simulating large
molecular complexes beyond what is possible with atomistic molecular dynamics. However …

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 …

Navigating protein landscapes with a machine-learned transferable coarse-grained model

NE Charron, F Musil, A Guljas, Y Chen… - ar**: Coarse-grained electronic property distributions using heteroscedastic Gaussian processes
JC Maier, NE Jackson - The Journal of Chemical Physics, 2022 - pubs.aip.org
We employ deep kernel learning electronic coarse-graining (DKL-ECG) with approximate
Gaussian processes as a flexible and scalable framework for learning heteroscedastic …

Adversarial-residual-coarse-graining: Applying machine learning theory to systematic molecular coarse-graining

AEP Durumeric, GA Voth - The Journal of chemical physics, 2019 - pubs.aip.org
We utilize connections between molecular coarse-graining (CG) approaches and implicit
generative models in machine learning to describe a new framework for systematic …