Publications by Sara Bonella | EPFL Graph Search

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

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 ...

SAGE PUBLICATIONS LTD2025

Giovanni Ciccotti: a Renaissance physicist

Sara Bonella

Taylor & Francis2025

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

Nicola Marzari, Giovanni Pizzi, Sara Bonella, Kristjan Eimre

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. ...

Royal Soc Chemistry2024

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

Giovanni Pizzi, Sara Bonella, Kristjan Eimre, Dou Du

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 ...

2024

OSSCAR, an open platform for collaborative development of computational tools for education in science

Giovanni Pizzi, Sara Bonella, Dou Du

In this paper we present the Open Software Services for Classrooms and Research (OSSCAR) platform. OSSCAR provides an open collaborative environment to develop and access educational resources in the form of web applications, for which various deployment m ...

ELSEVIER2023

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

Sara Bonella

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 ...

2023

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

Simulation of Nuclear Quantum Effects in Condensed Matter Systems via Quantum Baths

Sara Bonella

This paper reviews methods that aim at simulating nuclear quantum effects (NQEs) using generalized thermal baths. Generalized (or quantum) baths simulate statistical quantum features, and in particular zero-point energy effects, through non-Markovian stoch ...

2022

MetalWalls: Simulating electrochemical interfaces between polarizable electrolytes and metallic electrodes

Sara Bonella, Alessandro Coretti

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 ...

2022

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

Sara Bonella

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 ...

2022

Fluctuation Relations for Dissipative Systems in Constant External Magnetic Field: Theory and Molecular Dynamics Simulations

Sara Bonella, Alessandro Coretti

We illustrate how, contrary to common belief, transient Fluctuation Relations (FRs) for systems in constant external magnetic field hold without the inversion of the field. Building on previous work providing generalized time-reversal symmetries for system ...

2021

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

Sara Bonella

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 ...

2021

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

Sara Bonella, David Daniel Girardier, Alessandro Coretti

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 ...

EDP Sciences, Springer2021

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

Sara Bonella

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 ...

2021

Fluctuation relations for systems in a constant magnetic field

Sara Bonella, Alessandro Coretti

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 ...

2020

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

Sara Bonella, Alessandro Coretti

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 ...

2020

Adiabatic motion and statistical mechanics via mass-zero constrained dynamics

Sara Bonella, Alessandro Coretti

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 ...

2020

Charge fluctuations from molecular simulations in the constant-potential ensemble

Sara Bonella, Alessandro Coretti

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 ...

2020

Local control theory for superconducting qubits

Ivano Tavernelli, Sara Bonella

In this work, we develop a method to design control pulses for fixed-frequency superconducting qubits coupled via tunable couplers based on local control theory, an approach commonly employed to steer chemical reactions. Local control theory provides an al ...

AMER PHYSICAL SOC2019

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

Sara Bonella

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 ...

2019