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

Sara Bonella, Fabio Pietrucci, 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