3.9k citations · 4.8k across the 19 of their papers we have counts for
21 papers
Making PLUMED fly: a tutorial on optimizing performance
Daniele Rapetti, Massimiliano Bonomi, Carlo Camilloni +2
PLUMED is an open-source software package that is widely used for analyzing and enhancing molecular dynamics simulations that works in conjunction with most available molecular dyn…
Using molecular dynamics to investigate the driving force for graphene auto-kirigami
Charlie M. Rawlins, Gareth A. Tribello
Experiments [1] have shown that auto-kirigami structures can grow on the surface of graphene because the graphene-graphene adhesion energy is greater than the graphene-substrate in…
PLUMED Tutorials: a collaborative, community-driven learning ecosystem
Gareth A. Tribello, Massimiliano Bonomi, Giovanni Bussi +60
In computational physics, chemistry, and biology, the implementation of new techniques in a shared and open source software lowers barriers to entry and promotes rapid scientific p…
Measuring friction from simulations of folded graphene sheets
Charlie M. Rawlins, Gareth A. Tribello
We run molecular dynamics simulations of folded graphene sheets and present a procedure to measure the sliding friction in these systems based on the rate of decay of a damped-harm…
Modeling the ferroelectric phase transition in barium titanate with DFT accuracy and converged sampling
Lorenzo Gigli, Alexander Goscinski, Michele Ceriotti +1
The accurate description of the structural and thermodynamic properties of ferroelectrics has been one of the most remarkable achievements of Density Functional Theory (DFT). Howev…
Probing the unfolded configurations of a -hairpin using sketch-map
Albert Ardevol, Gareth A. Tribello, Michele Ceriotti +1
This work examines the conformational ensemble involved in -hairpin folding by means of advanced molecular dynamics simulations and dimensionality reduction. A fully atomistic d…
Can molecular dynamics be used to simulate biomolecular recognition?
Malin Luking, David van der Spoel, Johan Elf +1
There are many problems in biochemistry that are difficult to study experimentally. Simulation methods are appealing due to direct availability of atomic coordinates as a function…
A Fully Quantum-Mechanical Treatment for Kaolinite
Sam Shepherd, Gareth A. Tribello, David M. Wilkins
Neural network potentials for kaolinite minerals have been fitted to data extracted from density functional theory calculation that were performed using the revPBE + D3 and revPBE…
Global free energy landscapes as a smoothly joined collection of local maps
F. Giberti, G. A. Tribello, M. Ceriotti
Enhanced sampling techniques have become an essential tool in computational chemistry and physics, where they are applied to sample activated processes that occur on a time scale t…
Iterative unbiasing of quasi-equilibrium sampling
Federico Giberti, Bingqing Cheng, Gareth Aneurin Tribello +1
Atomistic modelling of phase transitions, chemical reactions, or other rare events that involve overcoming high free energy barriers usually entails prohibitively long simulation t…
Classical nucleation theory predicts the shape of the nucleus in homogeneous solidification
Bingqing Cheng, Michele Ceriotti, Gareth A. Tribello
Macroscopic models of nucleation provide powerful tools for understanding activated phase transition processes. These models do not provide atomistic insights and can thus sometime…
Using data-reduction techniques to analyse biomolecular trajectories
Gareth A. Tribello, Piero Gasparotto
This chapter discusses the way in which dimensionality reduction algorithms such as diffusion maps and sketch-map can be used to analyze molecular dynamics trajectories. The first…
Analyzing and biasing simulations with PLUMED
Giovanni Bussi, Gareth A. Tribello
This chapter discusses how the PLUMED plugin for molecular dynamics can be used to analyze and bias molecular dynamics trajectories. The chapter begins by introducing the notion of…
i-PI 2.0: A Universal Force Engine for Advanced Molecular Simulations
Venkat Kapil, Mariana Rossi, Ondrej Marsalek +23
Progress in the atomic-scale modelling of matter over the past decade has been tremendous. This progress has been brought about by improvements in methods for evaluating interatomi…
Building Maps in Collective Variable Space
Ilaria Gimondi, Gareth A. Tribello, Matteo Salvalaglio
Enhanced sampling techniques such as umbrella sampling and metadynamics are now routinely used to provide information on how the thermodynamic potential, or free energy, depends on…
The Gibbs free energy of homogeneous nucleation: from atomistic nuclei to the planar limit
Bingqing Cheng, Gareth A. Tribello, Michele Ceriotti
In this paper we discuss how the information contained in atomistic simulations of homogeneous nucleation should be used when fitting the parameters in macroscopic nucleation model…
Microscopic Mechanism and Kinetics of Ice Formation at Complex Interfaces: Zooming in on Kaolinite
Gabriele C. Sosso, Tianshu Li, Davide Donadio +2
Most ice in nature forms thanks to impurities which boost the exceedingly low nucleation rate of pure supercooled water. However, the microscopic details of ice nucleation on these…
Ice Formation on Kaolinite: Insights from Molecular Dynamics Simulations
Gabriele C. Sosso, Gareth A. Tribello, Andrea Zen +2
The formation of ice affects many aspects of our everyday life as well as technologies such as cryotherapy and cryopreservation. Foreign substances almost always aid water freezing…
The solid-liquid interfacial free energy out of equilibrium
Bingqing Cheng, Gareth A. Tribello, Michele Ceriotti
The properties of the interface between solid and melt are key to solidification and melting, as the interfacial free energy introduces a kinetic barrier to phase transitions. This…
PLUMED 2: New feathers for an old bird
Gareth A. Tribello, Massimiliano Bonomi, Davide Branduardi +2
Enhancing sampling and analyzing simulations are central issues in molecular simulation. Recently, we introduced PLUMED, an open-source plug-in that provides some of the most popul…
A self-learning algorithm for biased molecular dynamics
Gareth A. Tribello, Michele Ceriotti, Michele Parrinello
A new self-learning algorithm for accelerated dynamics, reconnaissance metadynamics, is proposed that is able to work with a very large number of collective coordinates. Accelerati…