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GPU accelerated implementation of density functional theory for hybrid QM/MM simulations
(American Chemical Society, 2014-02)
The hybrid simulation tools (QM/MM) evolved into a fundamental methodology for studying chemical reactivity in complex environments. This paper presents an implementation of electronic structure calculations based on density ...
QM-MM investigation of the reaction products between nitroxyl and O2 in aqueous solution
(Elsevier Science, 2008-09)
By means of combined quantum-classical molecular (QM/MM) dynamics simulations, we investigated the structural properties and the vibrational spectra in aqueous solution of four possible intermediate species of the oxidation ...
Estudo da dinâmica de solvatação de peptídeos por QM/MMStudy of the solvation dynamic of peptides by QM/MM
(Universidade Estadual Paulista (Unesp), 2016)
Docking, qm/mm, and molecular dynamics simulations of the hexose transporter from plasmodium falciparum (pfht)
(Universidade Federal de Minas GeraisBrasilFAR - DEPARTAMENTO DE PRODUTOS FARMACÊUTICOSUFMG, 2016-05)
A silicon laboratory: chemistry without chemicalsUn laboratorio de silicio: química sin reactivos
(Pontificia Universidad Católica del Perú, 2013)
The extraordinary catalytic ability of peroxiredoxins: a combined experimental and QM/MM study on the fast thiol oxidation step
(Royal Society of Chemistry, 2014-07)
Peroxiredoxins (Prxs) catalyze the reduction of peroxides, a process of key relevance in a variety of cellular processes. The first step in the catalytic cycle of all Prxs is the oxidation of a cysteine residue to sulfenic ...
Electron dynamics in complex environments with real-time time dependent density functional theory in a QM-MM framework
(American Institute of Physics, 2014-04)
This article presents a time dependent density functional theory (TDDFT) implementation to propagate the Kohn-Sham equations in real time, including the effects of a molecular environment through a Quantum-Mechanics ...
QM-MM Investigation of the Reaction of Peroxynitrite with Carbon Dioxide in Water
(American Chemical Society, 2007)
A quantum-mechanics molecular-mechanics scheme for extended systems
(IOP Publishing, 2016-06)
We introduce and discuss a hybrid quantum-mechanics molecular-mechanics (QM-MM) approach for Car-Parrinello DFT simulations with pseudopotentials and planewaves basis, designed for the treatment of periodic systems. In ...
Simulating DNA chip design using all-electronic graphene-based substrates
(2019-01-01)
In this paper, we present a theoretical investigation of an all-electronic biochip based on graphene to detect DNA including a full dynamical treatment for the environment. Our proposed device design is based on the changes ...