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 …

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 …

Bat coronaviruses related to SARS-CoV-2 and infectious for human cells

S Temmam, K Vongphayloth, E Baquero, S Munier… - Nature, 2022 - nature.com
The animal reservoir of SARS-CoV-2 is unknown despite reports of SARS-CoV-2-related
viruses in Asian Rhinolophus bats,,–, including the closest virus from R. affinis, RaTG13 …

Truly combining the advantages of polymeric and zeolite membranes for gas separations

X Tan, S Robijns, R Thür, Q Ke, N De Witte, A Lamaire… - Science, 2022 - science.org
Mixed-matrix membranes (MMMs) have been investigated to render energy-intensive
separations more efficiently by combining the selectivity and permeability performance …

Gas adsorption and framework flexibility of CALF-20 explored via experiments and simulations

R Oktavian, R Goeminne, LT Glasby, P Song… - Nature …, 2024 - nature.com
In 2021, Svante, in collaboration with BASF, reported successful scale up of CALF-20
production, a stable MOF with high capacity for post-combustion CO2 capture which exhibits …

Individual bat virome analysis reveals co-infection and spillover among bats and virus zoonotic potential

J Wang, Y Pan, L Yang, W Yang, K Lv, C Luo… - Nature …, 2023 - nature.com
Bats are reservoir hosts for many zoonotic viruses. Despite this, relatively little is known
about the diversity and abundance of viruses within individual bats, and hence the …

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 …

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 …

Deep learning the slow modes for rare events sampling

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

The role of dynamics in heterogeneous catalysis: Surface diffusivity and N2 decomposition on Fe(111)

L Bonati, D Polino, C Pizzolitto, P Biasi, R Eckert… - Proceedings of the …, 2023 - pnas.org
Dynamics has long been recognized to play an important role in heterogeneous catalytic
processes. However, until recently, it has been impossible to study their dynamical behavior …