Publications by Sara Bonella | EPFL Graph Search

Related publications (34)

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

Sara Bonella, Alessandro Coretti, David Daniel Girardier

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

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

David Daniel Girardier, Fabio Pietrucci, Sara Bonella

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

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

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

Quantum Correlations under Time Reversal and Incomplete Parity Transformations in the Presence of a Constant Magnetic Field

Sara Bonella

We derive the quantum analogues of some recently discovered symmetry relations for time correlation functions in systems subject to a constant magnetic field. The symmetry relations deal with the effect of time reversal and do not requireas in the formulat ...

Mdpi Ag2017

Fermi resonance in CO2: Mode assignment and quantum nuclear effects from first principles molecular dynamics

Sara Bonella, Guillaume André Jean Fraux

Vibrational spectroscopy is a fundamental tool to investigate local atomic arrangements and the effect of the environment, provided that the spectral features can be correctly assigned. This can be challenging in experiments and simulations when double pea ...

Amer Inst Physics2017

Photophysics and Photochemistry of a DNA–Protein Cross-Linking Model: A Synergistic Approach Combining Experiments and Theory

Ursula Röthlisberger, Ivano Tavernelli, Sara Bonella

The photophysical and photochemical properties of 5-benzyluracil and 5,6-benzyluracil, the latter produced by photocyclization of the former through irradiation with femtosecond UV laser pulses, are investigated both experimentally and theoretically. The a ...

2014

Charge transport in superionic and melted AgI under a magnetic field studied via molecular dynamics

Sara Bonella

Charge transport in AgI subject to an external magnetic field is studied via computer simulations. We demonstrate that a recently developed algorithm can effectively complement problematic experiments to detect the ionic Hall effect, and identify previousl ...

Amer Physical Soc2016

Time reversal symmetry in time-dependent correlation functions for systems in a constant magnetic field

Sara Bonella

A generalised time reversal symmetry for systems subject to a constant magnetic field is introduced, based on the analogy between the evolution equations of these systems and those of a system subject to shear. This generalisation makes it possible to deri ...

IOP Publishing - EPL Association2014

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

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

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

Characterization of the Photochemical Properties of 5-Benzyluracil via Time-Dependent Density Functional Theory

Ursula Röthlisberger, Ivano Tavernelli, Basile Curchod, Sara Bonella

We present a detailed study of the excited state properties of 5-benzyluracil (5BU) in the gas phase and in implicit solvent using different electronic structure approaches ranging from time-dependent density functional theory in the linear response regime ...

2017

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

Giovanni Pizzi, Sara Bonella, Dou Du, Kristjan Eimre, Taylor James Baird

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

Time reversal and symmetries of time correlation functions

Sara Bonella, Alessandro Coretti

The time reversal invariance of classical dynamics is reconsidered in this paper with specific focus on its consequences for time correlation functions and associated properties such as transport coefficients. We show that, under fairly common assumptions ...

Taylor & Francis2018

Thermal Diffusion in Binary Mixtures: Transient Behavior and Transport Coefficients from Equilibrium and Nonequilibrium Molecular Dynamics

Sara Bonella

Equilibrium and nonequilibrium molecular dynamics simulations are combined to compute the full set of coefficients that appear in the phenomenological equations describing thermal transport in a binary mixture subject to a constant thermal, gradient The Dy ...

Amer Chemical Soc2017

Gas phase infrared spectra from quasi-classical Kubo time correlation functions

Sara Bonella

We generalise the recently developed phase integration method (PIM) to obtain a computable approximation of the Kubo expression for quantum time correlation functions. Our scheme combines exact sampling of the quantum thermal density with classical dynamic ...

Taylor & Francis2015

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

An introduction to the problem of bridging quantum and classical dynamics

Sara Bonella

Simulating the exact quantum dynamics of realistic interacting systems is presently a task beyond reach but for the smallest of them, as the numerical cost for solving the time-dependent Schrodinger equation scales exponentially with the number of degrees ...

Springer Heidelberg2015

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