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 …

Combining machine learning and computational chemistry for predictive insights into chemical systems

JA Keith, V Vassilev-Galindo, B Cheng… - Chemical …, 2021 - ACS Publications
Machine learning models are poised to make a transformative impact on chemical sciences
by dramatically accelerating computational algorithms and amplifying insights available from …

Machine learning force fields

OT Unke, S Chmiela, HE Sauceda… - Chemical …, 2021 - ACS Publications
In recent years, the use of machine learning (ML) in computational chemistry has enabled
numerous advances previously out of reach due to the computational complexity of …

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] Perspective on integrating machine learning into computational chemistry and materials science

J Westermayr, M Gastegger, KT Schütt… - The Journal of Chemical …, 2021 - pubs.aip.org
Machine learning (ML) methods are being used in almost every conceivable area of
electronic structure theory and molecular simulation. In particular, ML has become firmly …

[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 …

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 …

Flow-matching: Efficient coarse-graining of molecular dynamics without forces

J Kohler, Y Chen, A Kramer, C Clementi… - Journal of Chemical …, 2023 - ACS Publications
Coarse-grained (CG) molecular simulations have become a standard tool to study molecular
processes on time and length scales inaccessible to all-atom simulations. Parametrizing CG …

Collective variable-based enhanced sampling and machine learning

M Chen - The European Physical Journal B, 2021 - Springer
Collective variable-based enhanced sampling methods have been widely used to study
thermodynamic properties of complex systems. Efficiency and accuracy of these enhanced …