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 …

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 …

Forces are not enough: Benchmark and critical evaluation for machine learning force fields with molecular simulations

X Fu, Z Wu, W Wang, T Xie, S Keten… - arXiv preprint arXiv …, 2022 - arxiv.org
Molecular dynamics (MD) simulation techniques are widely used for various natural science
applications. Increasingly, machine learning (ML) force field (FF) models begin to replace ab …

Artificial intelligence for science in quantum, atomistic, and continuum systems

X Zhang, L Wang, J Helwig, Y Luo, C Fu, Y Xie… - arXiv preprint arXiv …, 2023 - arxiv.org
Advances in artificial intelligence (AI) are fueling a new paradigm of discoveries in natural
sciences. Today, AI has started to advance natural sciences by improving, accelerating, and …

Machine learned coarse-grained protein force-fields: Are we there yet?

AEP Durumeric, NE Charron, C Templeton… - Current opinion in …, 2023 - Elsevier
The successful recent application of machine learning methods to scientific problems
includes the learning of flexible and accurate atomic-level force-fields for materials and …

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 …

Slicing and dicing: Optimal coarse-grained representation to preserve molecular kinetics

W Yang, C Templeton, D Rosenberger… - ACS Central …, 2023 - ACS Publications
The aim of molecular coarse-graining approaches is to recover relevant physical properties
of the molecular system via a lower-resolution model that can be more efficiently simulated …

Vendi sampling for molecular simulations: Diversity as a force for faster convergence and better exploration

AP Pasarkar, GM Bencomo, S Olsson… - The Journal of chemical …, 2023 - pubs.aip.org
Molecular dynamics (MD) is the method of choice for understanding the structure, function,
and interactions of molecules. However, MD simulations are limited by the strong …

How to gain atomistic insights on reactions at the water/solid interface?

SN Steinmann, C Michel - ACS Catalysis, 2022 - ACS Publications
Reactions at the water/solid interface are central to the development of sustainable
processes, from biomass upgrading to photo-and electrocatalysis. To gain atomistic insight …