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Concept

Abalone (molecular mechanics)

Publications associées (12)

Hamiltonian-Reservoir Replica Exchange and Machine Learning Potentials for Computational Organic Chemistry

Anne-Clémence Corminboeuf, Alberto Fabrizio, Benjamin André René Meyer, Raimon Fabregat I De Aguilar-Amat, Daniel Hollas

This work combines a machine learning potential energy function with a modular enhanced sampling scheme to obtain statistically converged thermodynamical properties of flexible medium-size organic molecules at high ab initio level. We offer a modular envir ...

AMER CHEMICAL SOC2020

Absolute band alignment at semiconductor-water interfaces using explicit and implicit descriptions for liquid water

Alfredo Pasquarello, Nicola Marzari, Francesco Ambrosio, Oliviero Andreussi, Zhendong Guo

Quantum mechanical simulations that include the effects of the liquid environment are highly relevant for the characterization of solid-liquid interfaces, which is crucial for the design of a wide range of devices. In this work we present a rigorous and sy ...

2019

Dynamic multiple-scattering treatment of X-ray absorption: Parameterization of a new molecular dynamics force field for myoglobin

Majed Chergui

We present a detailed analysis of the X-ray absorption near-edge structure (XANES) data on the Fe K-edge of CO Myoglobin based on a combined procedure of Molecular Dynamics (MD) calculations and MXAN (Minuit XANes) data analysis that we call D-MXAN. The ab ...

AMER INST PHYSICS2018

Molecular dynamics simulations of the intrinsically disordered protein amelogenin

John Christopher Plummer, Matteo Gregorio Modesto Marascio, Alessandra Apicella

Amelogenin refers to a class of intrinsically disordered proteins that are the major constituents of enamel matrix derivative (EMD), an extract of porcine fetal teeth used in regenerative periodontal therapy. Modifications in molecular conformation induced ...

Taylor & Francis Inc2017

Beyond Static Structures: Putting Forth REMD as a Tool to Solve Problems in Computational Organic Chemistry

Michele Ceriotti, Anne-Clémence Corminboeuf, Matthew Wodrich, Riccardo Petraglia, Adrien Georges Nicolai

Computational studies of organic systems are frequently limited to static pictures that closely align with textbook style presentations of reaction mechanisms and isomerization processes. Of course, in reality chemical systems are dynamic entities where a ...

Wiley-Blackwell2016

High order path integrals made easy

Michele Ceriotti, Venkat Kapil

The precise description of quantum nuclear fluctuations in atomistic modelling is possible by employing path integral techniques, which involve a considerable computational overhead due to the need of simulating multiple replicas of the system. Many approa ...

American Institute of Physics2016

Molecular dynamics at constant Cauchy stress

Fabio Pavia

The Parrinello-Rahman algorithm for imposing a general state of stress in periodic molecular dynamics simulations is widely used in the literature and has been implemented in many readily available molecular dynamics codes. However, what is often overlooke ...

American Institute of Physics2016

Assessment of phase-field-crystal concepts using long-time molecular dynamics

William Curtin

The ability of the phase-field-crystal (PFC) model to quantitatively predict atomistic defect structures in crystalline solids is addressed. First, general aspects of the PFC model are discussed within the context of obtaining quantitative results in solid ...

American Physical Society2015

Isobaric first-principles molecular dynamics of liquid water with nonlocal van der Waals interactions

Alfredo Pasquarello, Giacomo Francesco Leonardo Miceli

We investigate the structural properties of liquid water at near ambient conditions using first-principles molecular dynamics simulations based on a semilocal density functional augmented with nonlocal van der Waals interactions. The adopted scheme offers ...

American Institute of Physics2015

Electrostatics of solvated systems in periodic boundary conditions

Nicola Marzari, Oliviero Andreussi

Continuum solvation methods can provide an accurate and inexpensive embedding of quantum simulations in liquid or complex dielectric environments. Notwithstanding a long history and manifold applications to isolated systems in open boundary conditions, the ...

Amer Physical Soc2014

Computation of accommodation coefficients and the use of velocity correlation profiles in molecular dynamics simulations

Peter Spijker

For understanding the behavior of a gas close to a channel wall it is important to model the gas-wall interactions as detailed as possible. When using molecular dynamics simulations these interactions can be modeled explicitly, but the computations are tim ...

2010

Communications: Evaluation of the nondiabaticity of quantum molecular dynamics with the dephasing representation of quantum fidelity

Jiri Vanicek, Tomas Zimmermann

We propose an approximate method for evaluating the importance of non-Born–Oppenheimer effects on the quantum dynamics of nuclei. The method uses a generalization of the dephasing representation (DR) of quantum fidelity to several diabatic potential energy ...

American Institute of Physics2010