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 …

Unsupervised learning methods for molecular simulation data

A Glielmo, BE Husic, A Rodriguez, C Clementi… - Chemical …, 2021 - ACS Publications
Unsupervised learning is becoming an essential tool to analyze the increasingly large
amounts of data produced by atomistic and molecular simulations, in material science, solid …

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 …

TorchMD: A deep learning framework for molecular simulations

S Doerr, M Majewski, A Pérez, A Kramer… - Journal of chemical …, 2021 - ACS Publications
Molecular dynamics simulations provide a mechanistic description of molecules by relying
on empirical potentials. The quality and transferability of such potentials can be improved …

[HTML][HTML] Coarse graining molecular dynamics with graph neural networks

BE Husic, NE Charron, D Lemm, J Wang… - The Journal of …, 2020 - pubs.aip.org
Coarse graining enables the investigation of molecular dynamics for larger systems and at
longer timescales than is possible at an atomic resolution. However, a coarse graining …

A review on machine learning algorithms for the ionic liquid chemical space

S Koutsoukos, F Philippi, F Malaret, T Welton - Chemical science, 2021 - pubs.rsc.org
There are thousands of papers published every year investigating the properties and
possible applications of ionic liquids. Industrial use of these exceptional fluids requires …

Machine learning coarse-grained potentials of protein thermodynamics

M Majewski, A Pérez, P Thölke, S Doerr… - Nature …, 2023 - nature.com
A generalized understanding of protein dynamics is an unsolved scientific problem, the
solution of which is critical to the interpretation of the structure-function relationships that …

Learning matter: Materials design with machine learning and atomistic simulations

S Axelrod, D Schwalbe-Koda… - Accounts of Materials …, 2022 - ACS Publications
Conspectus Designing new materials is vital for addressing pressing societal challenges in
health, energy, and sustainability. The combination of physicochemical laws and empirical …

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 …

Single-model uncertainty quantification in neural network potentials does not consistently outperform model ensembles

AR Tan, S Urata, S Goldman, JCB Dietschreit… - npj Computational …, 2023 - nature.com
Neural networks (NNs) often assign high confidence to their predictions, even for points far
out of distribution, making uncertainty quantification (UQ) a challenge. When they are …