Operando modeling of zeolite-catalyzed reactions using first-principles molecular dynamics simulations

V Van Speybroeck, M Bocus, P Cnudde… - ACS …, 2023 - ACS Publications
Within this Perspective, we critically reflect on the role of first-principles molecular dynamics
(MD) simulations in unraveling the catalytic function within zeolites under operating …

Forward flux sampling for rare event simulations

RJ Allen, C Valeriani… - Journal of physics …, 2009 - iopscience.iop.org
Rare events are ubiquitous in many different fields, yet they are notoriously difficult to
simulate because few, if any, events are observed in a conventional simulation run. Over the …

Partial differential equations and stochastic methods in molecular dynamics

T Lelievre, G Stoltz - Acta Numerica, 2016 - cambridge.org
The objective of molecular dynamics computations is to infer macroscopic properties of
matter from atomistic models via averages with respect to probability measures dictated by …

Simulating rare events in equilibrium or nonequilibrium stochastic systems

RJ Allen, D Frenkel, PR ten Wolde - The Journal of chemical physics, 2006 - pubs.aip.org
We present three algorithms for calculating rate constants and sampling transition paths for
rare events in simulations with stochastic dynamics. The methods do not require a priori …

[HTML][HTML] Strategies for the exploration of free energy landscapes: Unity in diversity and challenges ahead

F Pietrucci - Reviews in Physics, 2017 - Elsevier
Computer simulations play an important role in the study of transformation processes of
condensed matter, including phase transitions, chemical reactions, and conformational …

Temperature and loading-dependent diffusion of light hydrocarbons in ZIF-8 as predicted through fully flexible molecular simulations

RJ Verploegh, S Nair, DS Sholl - Journal of the American …, 2015 - ACS Publications
Accurate and efficient predictions of hydrocarbon diffusivities in zeolitic imidazolate
frameworks (ZIFs) are challenging, due to the small pore size of materials such as ZIF-8 and …

Atomistic simulations of membrane ion channel conduction, gating, and modulation

E Flood, C Boiteux, B Lev, I Vorobyov… - Chemical …, 2019 - ACS Publications
Membrane ion channels are the fundamental electrical components in the nervous system.
Recent developments in X-ray crystallography and cryo-EM microscopy have revealed what …

Reaction coordinates and mechanistic hypothesis tests

B Peters - Annual review of physical chemistry, 2016 - annualreviews.org
Reaction coordinates are integral to several classic rate theories that can (a) predict kinetic
trends across conditions and homologous reactions,(b) extract activation parameters with a …

Discovering mountain passes via torchlight: methods for the definition of reaction coordinates and pathways in complex macromolecular reactions

MA Rohrdanz, W Zheng… - Annual review of physical …, 2013 - annualreviews.org
The long-timescale dynamics of macromolecular systems can be oftentimes viewed as a
reaction connecting metastable states of the system. In the past decade, various approaches …

Molecular free energies, rates, and mechanisms from data-efficient path sampling simulations

G Lazzeri, H Jung, PG Bolhuis… - Journal of Chemical …, 2023 - ACS Publications
Molecular dynamics is a powerful tool for studying the thermodynamics and kinetics of
complex molecular events. However, these simulations can rarely sample the required time …