Enhanced sampling methods for molecular dynamics simulations

J Hénin, T Lelièvre, MR Shirts, O Valsson… - arxiv preprint arxiv …, 2022 - arxiv.org
Enhanced sampling algorithms have emerged as powerful methods to extend the utility of
molecular dynamics simulations and allow the sampling of larger portions of the …

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 …

Machine-guided path sampling to discover mechanisms of molecular self-organization

H Jung, R Covino, A Arjun, C Leitold… - Nature Computational …, 2023 - nature.com
Molecular self-organization driven by concerted many-body interactions produces the
ordered structures that define both inanimate and living matter. Here we present an …

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

X Fu, Z Wu, W Wang, T **e, 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 …

Deep learning the slow modes for rare events sampling

L Bonati, GM Piccini… - Proceedings of the …, 2021 - National Acad Sciences
The development of enhanced sampling methods has greatly extended the scope of
atomistic simulations, allowing long-time phenomena to be studied with accessible …

Enhanced sampling with machine learning

S Mehdi, Z Smith, L Herron, Z Zou… - Annual Review of …, 2024 - annualreviews.org
Molecular dynamics (MD) enables the study of physical systems with excellent
spatiotemporal resolution but suffers from severe timescale limitations. To address this …

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

X Zhang, L Wang, J Helwig, Y Luo, C Fu, Y **e… - 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 …

Kinetics from metadynamics: Principles, applications, and outlook

D Ray, M Parrinello - Journal of Chemical Theory and …, 2023 - ACS Publications
Metadynamics is a popular enhanced sampling algorithm for computing the free energy
landscape of rare events by using molecular dynamics simulation. Ten years ago, Tiwary …

Hierarchical materials from high information content macromolecular building blocks: construction, dynamic interventions, and prediction

L Shao, J Ma, JL Prelesnik, Y Zhou, M Nguyen… - Chemical …, 2022 - ACS Publications
Hierarchical materials that exhibit order over multiple length scales are ubiquitous in nature.
Because hierarchy gives rise to unique properties and functions, many have sought …

A unified framework for machine learning collective variables for enhanced sampling simulations: mlcolvar

L Bonati, E Trizio, A Rizzi, M Parrinello - The Journal of Chemical …, 2023 - pubs.aip.org
Identifying a reduced set of collective variables is critical for understanding atomistic
simulations and accelerating them through enhanced sampling techniques. Recently …