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Publications associées (13)

Inferring free-energy barriers and kinetic rates from molecular dynamics via underdamped Langevin models

Fabio Pietrucci, Sara Bonella, David Daniel Girardier

Rare events include many of the most interesting transformation processes in condensed matter, from phase transitions to biomolecular conformational changes to chemical reactions. Access to the corresponding mechanisms, free-energy landscapes and kinetic r ...

Aip Publishing2023

Machine Learning Force Fields and Coarse-Grained Variables in Molecular Dynamics: Application to Materials and Biological Systems

Michele Ceriotti, Fabio Pietrucci

Machine learning encompasses tools and algorithms that are now becoming popular in almost all scientific and technological fields. This is true for molecular dynamics as well, where machine learning offers promises of extracting valuable information from t ...

AMER CHEMICAL SOC2020

Microscopic Picture of the Solvent Reorganization During Electron Transfer to Flavin in Water

Murat Kiliç

The redox potential of molecular species is largely modulated by its molecular environment so that a change of the environment will lead to a different redox potential. However, a detailed molecular picture of reorganization of the environment upon reducti ...

AMER CHEMICAL SOC2019

Entropy as a tool for crystal discovery

Pablo Miguel Piaggi

The computational prediction of crystal structures has emerged as an useful alternative to expensive and often cumbersome experiments. We propose an approach to the prediction of crystal structures and polymorphism based on reproducing the crystallization ...

EPFL2019

Predicting polymorphism in molecular crystals using orientational entropy

Pablo Miguel Piaggi

We introduce a computational method to discover polymorphs in molecular crystals at finite temperature. The method is based on reproducing the crystallization process starting from the liquid and letting the system discover the relevant polymorphs. This id ...

National Academy of Sciences2018

Extending the Scope of the Density Overlap Region Indicator

Laurent Alexis Clément Vannay

In this thesis, original applications of the Density Overlap Region Indicator (DORI), a density dependent bonding descriptor capable of simultaneously capturing covalent and noncovalent interactions, are discussed. The use of scalar fields, such as DORI, w ...

EPFL2018

Activated Dissociation of HCl on Au(111)

We report zero-coverage reaction probabilities (S-0) for HCl dissociative adsorption on Au(111) obtained by the seeded molecular beam hot-nozzle method. For measurements at normal incidence with mean translational energies ranging from 0.94 to 2.56 eV (noz ...

Amer Chemical Soc2016

Fate of a Graphene Flake: A New Route toward Fullerenes Disclosed with Ab Initio Simulations

Wanda Andreoni, Fabio Pietrucci

The top-down formation of a fullerene from a graphene flake is investigated via extensive ab initio molecular dynamics simulations in the range 300-3000 K, accelerated by metadynamics. Topological (SPRINT) coordinates are used to ensure a prejudice-free ex ...

Amer Chemical Soc2014

Bridging Static and Dynamical Descriptions of Chemical Reactions: An ab Initio Study of CO2 Interacting with Water Molecules

Wanda Andreoni, Fabio Pietrucci

Extracting reliable thermochemical parameters from molecular dynamics simulations of chemical reactions, although based on ab initio methods, is generally hampered by difficulties in reproducing the results and controlling the statistical errors. This is a ...

Amer Chemical Soc2012

Statistical Analysis of Ion Mobility Spectrometry. II. Adaptively Biased Methods and Shape Correlations

Yury Tsybin

Following a recent effort [J. Am. Soc. Mass Spectrom. 23, 386-396 (2012)], we continue to explore computational methodologies for generating molecular conformations to support collisional cross sections suggested by ion mobility measurements. Here, adaptiv ...

2012

Statistical Study of the Unfolding of Multimodular Proteins and their Energy Landscape by Atomic Force Microscopy

Fabrizio Benedetti

The aim of the present thesis is to investigate several aspects of: the proteins mechanics, interprotein interactions and to study also new techniques, theoretical and technical, to obtain and analyze the force spectroscopy experiments. The first section i ...

EPFL2012

METAGUI. A VMD interface for analyzing metadynamics and molecular dynamics simulations

Fabio Pietrucci

We present a new computational tool, METAGUI, which extends the VMD program with a graphical user interface that allows constructing a thermodynamic and kinetic model of a given process simulated by large-scale molecular dynamics. The tool is specially des ...

2012

Heterogeneous reaction mechanisms of the reduction of nitric oxide on carbon surfaces: a theoretical analysis

Pablo Campomanes Ramos

The mechanism of reaction between NO and two models of carbonaceous materials with active sites was investigated at the UB3LYP/6-31 + G(d) and UM06-2X theory levels. The small model is the anthracene radical and the large one is also a monoradical built wi ...

2010