Using metadynamics to explore complex free-energy landscapes

G Bussi, A Laio - Nature Reviews Physics, 2020 - nature.com
Metadynamics is an atomistic simulation technique that allows, within the same framework,
acceleration of rare events and estimation of the free energy of complex molecular systems …

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 …

Data-driven collective variables for enhanced sampling

L Bonati, V Rizzi, M Parrinello - The journal of physical chemistry …, 2020 - ACS Publications
Designing an appropriate set of collective variables is crucial to the success of several
enhanced sampling methods. Here we focus on how to obtain such variables from …

The exploration of chemical reaction networks

JP Unsleber, M Reiher - Annual review of physical chemistry, 2020 - annualreviews.org
Modern computational chemistry has reached a stage at which massive exploration into
chemical reaction space with unprecedented resolution with respect to the number of …

Chemoton 2.0: autonomous exploration of chemical reaction networks

JP Unsleber, SA Grimmel, M Reiher - Journal of Chemical Theory …, 2022 - ACS Publications
Fueled by advances in hardware and algorithm design, large-scale automated explorations
of chemical reaction space have become possible. Here, we present our approach to an …

Deep learning collective variables from transition path ensemble

D Ray, E Trizio, M Parrinello - The Journal of Chemical Physics, 2023 - pubs.aip.org
The study of the rare transitions that take place between long lived metastable states is a
major challenge in molecular dynamics simulations. Many of the methods suggested to …

Autonomous reaction network exploration in homogeneous and heterogeneous catalysis

M Steiner, M Reiher - Topics in Catalysis, 2022 - Springer
Autonomous computations that rely on automated reaction network elucidation algorithms
may pave the way to make computational catalysis on a par with experimental research in …

A human-machine interface for automatic exploration of chemical reaction networks

M Steiner, M Reiher - Nature Communications, 2024 - nature.com
Autonomous reaction network exploration algorithms offer a systematic approach to explore
mechanisms of complex chemical processes. However, the resulting reaction networks are …

From enhanced sampling to reaction profiles

E Trizio, M Parrinello - The Journal of Physical Chemistry Letters, 2021 - ACS Publications
The determination of efficient collective variables is crucial to the success of many enhanced
sampling methods. As inspired by previous discrimination approaches, we first collect a set …

Discover, sample, and refine: Exploring chemistry with enhanced sampling techniques

U Raucci, V Rizzi, M Parrinello - The Journal of Physical Chemistry …, 2022 - ACS Publications
Over the last few decades, enhanced sampling methods have been continuously improved.
Here, we exploit this progress and propose a modular workflow for blind reaction discovery …