Publications by Sara Bonella | EPFL Graph Search

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In several domains of physics, including first principle simulations and classical models for polarizable systems, the minimization of an energy function with respect to a set of auxiliary variables must be performed to define the dynamics of physical degr ...

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 ...

A new algorithm for efficient and fully time-reversible integration of first-principles molecular dynamics based on orbital-free density functional theory (OFDFT) is presented. The algorithm adapts to this nontrivial case, the recently introduced Mass-Zero ...

We revisit the statistical mechanics of charge fluctuations in capacitors. In constant-potential classical molecular simulations, the atomic charges of electrode atoms are treated as additional degrees of freedom which evolve in time so as to satisfy the c ...

We demonstrate the accuracy and efficiency of a recently introduced approach to account for nuclear quantum effects (NQEs) in molecular simulations: the adaptive quantum thermal bath (adQTB). In this method, zero-point energy is introduced through a genera ...

Classical molecular dynamics simulations have recently become a standard tool for the study of electrochemical systems. State-of-the-art approaches represent the electrodes as perfect conductors, modeling their responses to the charge distribution of elect ...

Interactive notebooks are a precious tool for creating graphical user interfaces and teaching materials. Python and Jupyter are becoming increasingly popular in this context, with Jupyter widgets at the core of the interactive functionalities. However, whi ...

Electrochemistry is central to many applications, ranging from biology to energy science. Studies now involve a wide range of techniques, both experimental and theoretical. Modeling and simulations methods, such as density functional theory or molecular dy ...

Quantum thermal bath (QTB) simulations reproduce statistical nuclear quantum effects via a Langevin equation with a colored random force. Although this approach has proven efficient for a variety of chemical and condensed-matter problems, the QTB, as many ...

In recent work [Coretti et al., J. Chem. Phys., 2018, 149, 191102], a new algorithm to solve numerically the dynamics of the shell model for polarization was presented. The approach, broadly applicable to systems involving adiabatically separated dynamical ...

The performance of different approximate algorithms for computing anharmonic features in vibrational spectra is analyzed and compared on model and more realistic systems that present relevant nuclear quantum effects. The methods considered combine approxim ...

We show how to construct, by exploiting adiabatic time and length scale separation between atomistic and continuum mechanics, a multiscale scheme for continuum dynamics free from macroscopic constitutive modeling. To do so, we introduce a new set of degree ...

The Open Databases Integration for Materials Design (OPTIMADE) application programming interface (API) empowers users with holistic access to a growing federation of databases, enhancing the accessibility and discoverability of materials and chemical data. ...

The validity of the fluctuation relations (FRs) for systems in a constant magnetic field is investigated. Recently introduced time-reversal symmetries that hold in the presence of static electric and magnetic fields and of deterministic thermostats are use ...

Speed and efficiency of codes for atomistic simulations can be improved through refactoring and tailoring for GPU architectures. This activity, however, comes with associated, often overlooked, costs, namely a reduced readability and flexibility upon optim ...

Sara Bonella

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Mass-Zero constrained dynamics and statistics for the shell model in magnetic field

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

Mass-zero constrained dynamics for simulations based on orbital-free density functional theory

Charge fluctuations from molecular simulations in the constant-potential ensemble

Nuclear Quantum Effects in Liquid Water at Near Classical Computational Cost Using the Adaptive Quantum Thermal Bath

Mass-zero constrained molecular dynamics for electrode charges in simulations of electrochemical systems

Jupyter widgets and extensions for education and research in computational physics and chemistry

MetalWalls: Simulating electrochemical interfaces between polarizable electrolytes and metallic electrodes

The Fluctuation Dissipation Theorem as a Diagnosis and Cure for Zero-Point Energy Leakage in Quantum Thermal Bath Simulations

Adiabatic motion and statistical mechanics via mass-zero constrained dynamics

Anharmonic spectral features via trajectory-based quantum dynamics: A perturbative analysis of the interplay between dynamics and sampling

Continuum mechanics from molecular dynamics via adiabatic time and length scale separation

Developments and applications of the OPTIMADE API for materials discovery, design, and data exchange

Fluctuation relations for systems in a constant magnetic field

A tale of two codes: CUDA vs OpenACC for mass-zero constrained dynamics

Giovanni Ciccotti: a Renaissance physicist