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 …

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 …

Coarse-graining with equivariant neural networks: A path toward accurate and data-efficient models

TD Loose, PG Sahrmann, TS Qu… - The Journal of Physical …, 2023 - ACS Publications
Machine learning has recently entered into the mainstream of coarse-grained (CG)
molecular modeling and simulation. While a variety of methods for incorporating deep …

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 …

Multibody terms in protein coarse-grained models: A top-down perspective

I Zaporozhets, C Clementi - The Journal of Physical Chemistry B, 2023 - ACS Publications
Coarse-grained models allow computational investigation of biomolecular processes
occurring on long time and length scales, intractable with atomistic simulation. Traditionally …

Prediction rigidities for data-driven chemistry

S Chong, F Bigi, F Grasselli, P Loche, M Kellner… - Faraday …, 2025 - pubs.rsc.org
The widespread application of machine learning (ML) to the chemical sciences is making it
very important to understand how the ML models learn to correlate chemical structures with …

Analogy between Boltzmann machines and Feynman path integrals

SS Iyengar, S Kais - Journal of Chemical Theory and Computation, 2023 - ACS Publications
Machine learning has had a significant impact on multiple areas of science, technology,
health, and computer and information sciences. Through the advent of quantum computing …

On the emergence of machine-learning methods in bottom-up coarse-graining

PG Sahrmann, GA Voth - Current Opinion in Structural Biology, 2025 - Elsevier
Machine-learning methods have gained significant attention in the computational chemistry
community as a viable approach to molecular modeling and analysis. Recent successes in …

Enhancing the Assembly Properties of Bottom-Up Coarse-Grained Phospholipids

PG Sahrmann, GA Voth - Journal of Chemical Theory and …, 2024 - ACS Publications
A plethora of key biological events occur at the cellular membrane where the large
spatiotemporal scales necessitate dimensionality reduction or coarse-graining approaches …

Scaling Graph Neural Networks to Large Proteins

J Airas, B Zhang - Journal of Chemical Theory and Computation, 2024 - ACS Publications
Graph neural network (GNN) architectures have emerged as promising force field models,
exhibiting high accuracy in predicting complex energies and forces based on atomic …