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 …

QM/MM methods for biomolecular systems

HM Senn, W Thiel - Angewandte Chemie International Edition, 2009 - Wiley Online Library
Two are better than one: Quantum mechanics/molecular mechanics (QM/MM) methods are
the state‐of‐the‐art computational technique for treating reactive and other “electronic” …

Hydrotropic solubilization of zinc acetates for sustainable aqueous battery electrolytes

D Dong, T Wang, Y Sun, J Fan, YC Lu - Nature Sustainability, 2023 - nature.com
Among the more sustainable battery chemistries, the aqueous zinc system is receiving
renewed interest. To accelerate the practical applications of this promising technology, an …

[PDF][PDF] Amber 10

DA Case, TA Darden, TE Cheatham, CL Simmerling… - 2008 - infoscience.epfl.ch
Amber is the collective name for a suite of programs that allow users to carry out molecular
dynamics simulations, particularly on biomolecules. None of the individual programs carries …

Dynamic multinuclear sites formed by mobilized copper ions in NOx selective catalytic reduction

C Paolucci, I Khurana, AA Parekh, S Li, AJ Shih, H Li… - Science, 2017 - science.org
Copper ions exchanged into zeolites are active for the selective catalytic reduction (SCR) of
nitrogen oxides (NO x) with ammonia (NH3), but the low-temperature rate dependence on …

Oxygen evolution reaction over catalytic single-site Co in a well-defined brookite TiO2 nanorod surface

C Liu, J Qian, Y Ye, H Zhou, CJ Sun, C Sheehan… - Nature Catalysis, 2021 - nature.com
Efficient electrocatalysts for the oxygen evolution reaction (OER) are paramount to the
development of electrochemical devices for clean energy and fuel conversion. However, the …

Metadynamics

A Barducci, M Bonomi… - Wiley Interdisciplinary …, 2011 - Wiley Online Library
Metadynamics is a powerful technique for enhancing sampling in molecular dynamics
simulations and reconstructing the free‐energy surface as a function of few selected …

Metadynamics: a method to simulate rare events and reconstruct the free energy in biophysics, chemistry and material science

A Laio, FL Gervasio - Reports on Progress in Physics, 2008 - iopscience.iop.org
Metadynamics is a powerful algorithm that can be used both for reconstructing the free
energy and for accelerating rare events in systems described by complex Hamiltonians, at …

Using collective variables to drive molecular dynamics simulations

G Fiorin, ML Klein, J Hénin - Molecular Physics, 2013 - Taylor & Francis
A software framework is introduced that facilitates the application of biasing algorithms to
collective variables of the type commonly employed to drive massively parallel molecular …

Full atomistic reaction mechanism with kinetics for CO reduction on Cu (100) from ab initio molecular dynamics free-energy calculations at 298 K

T Cheng, H **ao… - Proceedings of the …, 2017 - National Acad Sciences
A critical step toward the rational design of new catalysts that achieve selective and efficient
reduction of CO2 to specific hydrocarbons and oxygenates is to determine the detailed …