Computational optimization of electric fields for better catalysis design

VV Welborn, L Ruiz Pestana, T Head-Gordon - Nature Catalysis, 2018 - nature.com
Although the ubiquitous role that long-ranged electric fields play in catalysis has been
recognized, it is seldom used as a primary design parameter in the discovery of new …

QM/AMOEBA description of properties and dynamics of embedded molecules

M Nottoli, M Bondanza, P Mazzeo… - Wiley …, 2023 - Wiley Online Library
We describe the development, implementation, and application of a polarizable QM/MM
strategy, based on the AMOEBA polarizable force field, for calculating molecular properties …

[HTML][HTML] The ONETEP linear-scaling density functional theory program

JCA Prentice, J Aarons, JC Womack… - The Journal of …, 2020 - pubs.aip.org
We present an overview of the onetep program for linear-scaling density functional theory
(DFT) calculations with large basis set (plane-wave) accuracy on parallel computers. The …

Polarizable embedding QM/MM: the future gold standard for complex (bio) systems?

M Bondanza, M Nottoli, L Cupellini… - Physical Chemistry …, 2020 - pubs.rsc.org
Nowadays, hybrid QM/MM approaches are widely used to study (supra) molecular systems
embedded in complex biological matrices. However, in their common formulation, mutual …

Hybrid QM/MM molecular dynamics with AMOEBA polarizable embedding

D Loco, L Lagardère, S Caprasecca… - Journal of chemical …, 2017 - ACS Publications
We present the implementation of a Born–Oppenheimer (BO) hybrid quantum
mechanics/molecular mechanics (QM/MM) molecular dynamics (MD) strategy using density …

Multiscale models for light-driven processes

M Nottoli, L Cupellini, F Lipparini… - Annual Review of …, 2021 - annualreviews.org
Multiscale models combining quantum mechanical and classical descriptions are a very
popular strategy to simulate properties and processes of complex systems. Many alternative …

Quantum-based molecular dynamics simulations using tensor cores

J Finkelstein, JS Smith, SM Mniszewski… - Journal of Chemical …, 2021 - ACS Publications
Tensor cores, along with tensor processing units, represent a new form of hardware
acceleration specifically designed for deep neural network calculations in artificial …

Advanced models for water simulations

O Demerdash, LP Wang… - Wiley Interdisciplinary …, 2018 - Wiley Online Library
Molecular simulations of water using classical, molecular mechanic potential energy
functions have enjoyed a 50‐year history of development, and much has been learned …

A Quasi Time-Reversible Scheme Based on Density Matrix Extrapolation on the Grassmann Manifold for Born–Oppenheimer Molecular Dynamics

F Pes, É Polack, P Mazzeo, G Dusson… - The Journal of …, 2023 - ACS Publications
This Letter introduces the so-called Quasi Time-Reversible scheme based on Grassmann
extrapolation (QTR G-Ext) of density matrices for an accurate calculation of initial guesses in …

Electronic polarization is essential for the stabilization and dynamics of buried ion pairs in staphylococcal nuclease mutants

J Deng, Q Cui - Journal of the American Chemical Society, 2022 - ACS Publications
Buried charged residues play important roles in the modulation of protein stabilities and
conformational dynamics and make crucial contributions to protein functions. Considering …