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 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 …
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
Machine learning has recently entered into the mainstream of coarse-grained (CG)
molecular modeling and simulation. While a variety of methods for incorporating deep …
molecular modeling and simulation. While a variety of methods for incorporating deep …
Statistically optimal force aggregation for coarse-graining molecular dynamics
Machine-learned coarse-grained (CG) models have the potential for simulating large
molecular complexes beyond what is possible with atomistic molecular dynamics. However …
molecular complexes beyond what is possible with atomistic molecular dynamics. However …
Multibody terms in protein coarse-grained models: A top-down perspective
Coarse-grained models allow computational investigation of biomolecular processes
occurring on long time and length scales, intractable with atomistic simulation. Traditionally …
occurring on long time and length scales, intractable with atomistic simulation. Traditionally …
Prediction rigidities for data-driven chemistry
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 …
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 …
health, and computer and information sciences. Through the advent of quantum computing …
On the emergence of machine-learning methods in bottom-up coarse-graining
Machine-learning methods have gained significant attention in the computational chemistry
community as a viable approach to molecular modeling and analysis. Recent successes in …
community as a viable approach to molecular modeling and analysis. Recent successes in …
Enhancing the Assembly Properties of Bottom-Up Coarse-Grained Phospholipids
A plethora of key biological events occur at the cellular membrane where the large
spatiotemporal scales necessitate dimensionality reduction or coarse-graining approaches …
spatiotemporal scales necessitate dimensionality reduction or coarse-graining approaches …
Scaling Graph Neural Networks to Large Proteins
Graph neural network (GNN) architectures have emerged as promising force field models,
exhibiting high accuracy in predicting complex energies and forces based on atomic …
exhibiting high accuracy in predicting complex energies and forces based on atomic …