List of Publications

Google Scholar Profile

List of Publications (Updated April 2019):

2019

Etienne Mangaud; Simon Huppert; Thomas Plé; Philippe Depondt; Sara Bonella; Fabio Finocchi

The fluctuation-dissipation theorem as a diagnosis and cure for zero-point energy leakage in quantum thermal bath simulations (Journal Article)

In: Journal of chemical theory and computation, 2019.

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2018

Alessandro Coretti; Sara Bonella; Giovanni Ciccotti

Communication: Constrained molecular dynamics for polarizable models (Journal Article)

In: The Journal of chemical physics, 149 (19), pp. 191102, 2018.

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M Malis; Kl P Barkoutsos; M Ganzhorn; S Filipp; DJ Egger; S Bonella; I Tavernelli

Local control theory for superconducting qubits (Journal Article)

In: arXiv preprint arXiv:1808.10773, 2018.

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Alessandro Coretti; Sara Bonella; Lamberto Rondoni; Giovanni Ciccotti

Time reversal and symmetries of time correlation functions (Journal Article)

In: Molecular Physics, 116 (21-22), pp. 3097–3103, 2018.

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2017

M Micciarelli; BFE Curchod; S Bonella; C Altucci; M Valadan; U Rothlisberger; I Tavernelli

Characterization of the photochemical properties of 5-benzyluracil via time-dependent density functional theory (Journal Article)

In: The Journal of Physical Chemistry A, 121 (20), pp. 3909–3917, 2017.

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Paolo Gregorio; Sara Bonella; Lamberto Rondoni

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

In: Symmetry, 9 (7), pp. 120, 2017.

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Sara Bonella; Mauro Ferrario; Giovanni Ciccotti

Thermal diffusion in binary mixtures: Transient behavior and transport coefficients from equilibrium and nonequilibrium molecular dynamics (Journal Article)

In: Langmuir, 33 (42), pp. 11281–11290, 2017.

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Sara Bonella; Alessandro Coretti; Lamberto Rondoni; Giovanni Ciccotti

Time-reversal symmetry for systems in a constant external magnetic field (Journal Article)

In: Physical Review E, 96 (1), pp. 012160, 2017.

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Marie Basire; Félix Mouhat; Guillaume Fraux; Amélie Bordage; Jean-Louis Hazemann; Marion Louvel; Riccardo Spezia; Sara Bonella; Rodolphe Vuilleumier

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

In: The Journal of chemical physics, 146 (13), pp. 134102, 2017.

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2016

Giovanni Ciccotti; Sara Bonella; Mauro Ferrario; Carlo Pierleoni

Probabilistic derivation of spatiotemporal correlation functions in the hydrodynamic limit (Journal Article)

In: The Journal of Physical Chemistry B, 120 (8), pp. 1996–2000, 2016.

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Mauro Ferrario; S Bonella; G Ciccotti

On the establishment of thermal diffusion in binary Lennard-Jones liquids (Journal Article)

In: The European Physical Journal Special Topics, 225 (8-9), pp. 1629–1642, 2016.

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Luca Gagliardi; Sara Bonella

Charge transport in superionic and melted AgI under a magnetic field studied via molecular dynamics (Journal Article)

In: Physical Review B, 94 (13), pp. 134426, 2016.

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2015

S Bonella; G Ciccotti; L Rondoni

Time reversal symmetry in time-dependent correlation functions for systems in a constant magnetic field (Journal Article)

In: EPL (Europhysics Letters), 108 (6), pp. 60004, 2015.

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S Bonella; G Ciccotti

An introduction to the problem of bridging quantum and classical dynamics (Journal Article)

In: The European Physical Journal Special Topics, 224 (12), pp. 2305–2320, 2015.

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J Beutier; R Vuilleumier; S Bonella; G Ciccotti

Gas phase infrared spectra from quasi-classical Kubo time correlation functions (Journal Article)

In: Molecular Physics, 113 (17-18), pp. 2894–2904, 2015.

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2014

S Bonella; D Raimondo; E Milanetti; A Tramontano; G Ciccotti

Mapping the hydropathy of amino acids based on their local solvation structure (Journal Article)

In: The Journal of Physical Chemistry B, 118 (24), pp. 6604–6613, 2014.

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Marco Micciarelli; Mohammadhassan Valadan; Bartolomeo Della Ventura; Giovanni Di Fabio; Lorenzo De Napoli; Sara Bonella; Ursula Röthlisberger; Ivano Tavernelli; Carlo Altucci; Raffaele Velotta

Photophysics and Photochemistry of a DNA--Protein Cross-Linking Model: A Synergistic Approach Combining Experiments and Theory (Journal Article)

In: The Journal of Physical Chemistry B, 118 (19), pp. 4983–4992, 2014.

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Julien Beutier; D Borgis; R Vuilleumier; Sara Bonella

Computing thermal Wigner densities with the phase integration method (Journal Article)

In: The Journal of chemical physics, 141 (8), pp. 084102, 2014.

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Sara Bonella; Giovanni Ciccotti

Approximating Time-Dependent Quantum Statistical Properties (Journal Article)

In: Entropy, 16 (1), pp. 86–109, 2014.

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Julien Beutier; Michele Monteferrante; Sara Bonella; Rodolphe Vuilleumier; Giovanni Ciccotti

Gas phase infrared spectra via the phase integration quasi-classical method (Journal Article)

In: Molecular Simulation, 40 (1-3), pp. 196–207, 2014.

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2013

Michele Monteferrante; Sara Bonella; Giovanni Ciccotti

Quantum dynamical structure factor of liquid neon via a quasiclassical symmetrized method (Journal Article)

In: The Journal of chemical physics, 138 (5), pp. 054118, 2013.

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F Mouhat; S Bonella; C Pierleoni

Charge transport simulations of NaCl in an external magnetic field: the quest for the Hall effect (Journal Article)

In: Molecular Physics, 111 (22-23), pp. 3651–3661, 2013.

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Walter Rocchia; Sara Bonella

A statistical mechanics handbook for protein-ligand binding simulation. (Journal Article)

In: Frontiers in bioscience (Scholar edition), 5 , pp. 478, 2013.

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2012

Wojtek Iwo Babiaczyk; Sara Bonella; Giovanni Ciccotti; Maria Laura Coluccio; Francesco Gentile; Enzo Di Fabrizio

Silver self aggregation in a nanodevice for enhanced Raman spectroscopy: Experiments vs. simplified modeling via molecular dynamics (Journal Article)

In: Nanoscale, 4 (7), pp. 2362–2371, 2012.

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Fabio Sterpone; Sara Bonella; Simone Meloni

Early stage of the dehydrogenation of NaAlH4 by ab initio rare event simulations (Journal Article)

In: The Journal of Physical Chemistry C, 116 (37), pp. 19636–19643, 2012.

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Sara Bonella; Simone Meloni; Giovanni Ciccotti

Theory and methods for rare events (Journal Article)

In: The European Physical Journal B, 85 (3), pp. 97, 2012.

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Adolfo Poma; Michele Monteferrante; Sara Bonella; Giovanni Ciccotti

The quantum free energy barrier for hydrogen vacancy diffusion in Na 3 AlH 6 (Journal Article)

In: Physical Chemistry Chemical Physics, 14 (44), pp. 15458–15463, 2012.

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2011

Michele Monteferrante; Sara Bonella; Giovanni Ciccotti

Linearized symmetrized quantum time correlation functions calculation via phase pre-averaging (Journal Article)

In: Molecular Physics, 109 (23-24), pp. 3015–3027, 2011.

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Michele Monteferrante; Sara Bonella; Giovanni Ciccotti

Short range hydrogen diffusion in Na 3 AlH 6 (Journal Article)

In: Physical Chemistry Chemical Physics, 13 (22), pp. 10546–10555, 2011.

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2010

S Bonella; M Monteferrante; Carlo Pierleoni; G Ciccotti

Path integral based calculations of symmetrized time correlation functions. II (Journal Article)

In: The Journal of chemical physics, 133 (16), pp. 164105, 2010.

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Ali Nassimi; Sara Bonella; Raymond Kapral

Analysis of the quantum-classical Liouville equation in the mapping basis (Journal Article)

In: The Journal of chemical physics, 133 (13), pp. 134115, 2010.

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Sara Bonella; Giovanni Ciccotti; Raymond Kapral

Linearization approximations and Liouville quantum--classical dynamics (Journal Article)

In: Chemical Physics Letters, 484 (4-6), pp. 399–404, 2010.

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Wojtek Iwo Babiaczyk; Sara Bonella; Leonardo Guidoni; Giovanni Ciccotti

Hydration structure of the quaternary ammonium cations (Journal Article)

In: The Journal of Physical Chemistry B, 114 (46), pp. 15018–15028, 2010.

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P Huo; S Bonella; L Chen; DF Coker

Linearized approximations for condensed phase non-adiabatic dynamics: Multi-layered baths and Brownian dynamics implementation (Journal Article)

In: Chemical Physics, 370 (1-3), pp. 87–97, 2010.

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2009

S Bonella; DF Coker; D Mac Kernan; R Kapral; G Ciccotti

Trajectory based simulations of quantum-classical systems (Incollection)

In: Energy Transfer Dynamics in Biomaterial Systems, pp. 415–436, Springer, 2009.

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Michele Monteferrante; Sara Bonella; Simone Meloni; Giovanni Ciccotti

Modified single sweep method for reconstructing free-energy landscapes (Journal Article)

In: Molecular Simulation, 35 (12-13), pp. 1116–1129, 2009.

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Sara Bonella; Walter Rocchia; Pietro Amat; Riccardo Nifos'i; Valentina Tozzini

SDPhound, a mutual information-based method to investigate specificity-determining positions (Journal Article)

In: Algorithms, 2 (2), pp. 764–789, 2009.

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2008

Michele Monteferrante; Sara Bonella; Simone Meloni; Eric Vanden-Eijnden; Giovanni Ciccotti

Calculations of free energy barriers for local mechanisms of hydrogen diffusion in alanates (Incollection)

In: Scientific Modeling and Simulations, pp. 187–206, Springer, 2008.

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ER Dunkel; S Bonella; DF Coker

Iterative linearized approach to nonadiabatic dynamics (Journal Article)

In: The Journal of chemical physics, 129 (11), pp. 114106, 2008.

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2007

Nikos Doltsinis; Sara Bonella

Ab initio simulations in photochemistry: bringing together nonadiabatic dynamics and electronic structure theory (Journal Article)

In: 2007.

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DF Coker; S Bonella

Linearized nonadiabatic dynamics in the adiabatic representation (Incollection)

In: Quantum Dynamics of Complex Molecular Systems, pp. 321–340, Springer, 2007.

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Lina Chen; Sara Bonella; David F Coker

PHYS 498-LANDmap with re-focusing: A new semi-classical method for extending a short time approximation to compute non-adiabatic dynamics at long times (Inproceedings)

In: ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY, AMER CHEMICAL SOC 1155 16TH ST, NW, WASHINGTON, DC 20036 USA 2007.

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2006

DF Coker; S Bonella

Linearized path integral methods for quantum time correlation functions (Incollection)

In: Computer Simulations in Condensed Matter Systems: From Materials to Chemical Biology Volume 1, pp. 553–590, Springer, 2006.

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Maria Serena Causo; Giovanni Ciccotti; Sara Bonella; Rodolphe Vuilleumier

An adiabatic linearized path integral approach for quantum time-correlation functions II: A cumulant expansion method for improving convergence (Journal Article)

In: The Journal of Physical Chemistry B, 110 (32), pp. 16026–16034, 2006.

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2005

Sara Bonella; Daniel Montemayor; David F Coker

Linearized path integral approach for calculating nonadiabatic time correlation functions (Journal Article)

In: Proceedings of the National Academy of Sciences, 102 (19), pp. 6715–6719, 2005.

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DF Coker; S Bonella

Linearized path integral approach to calculating non-adiabatic time correlation functions. (Inproceedings)

In: ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY, pp. U765–U766, AMER CHEMICAL SOC 1155 16TH ST, NW, WASHINGTON, DC 20036 USA 2005.

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S Bonella; DF Coker

LAND-map, a linearized approach to nonadiabatic dynamics using the mapping formalism (Journal Article)

In: The Journal of chemical physics, 122 (19), pp. 194102, 2005.

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Ziman Li; Rebecca Sansom; Sara Bonella; David F Coker; Amy S Mullin

Trajectory study of supercollision relaxation in highly vibrationally excited pyrazine and CO2 (Journal Article)

In: The Journal of Physical Chemistry A, 109 (34), pp. 7657–7666, 2005.

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Maria Serena Causo; Giovanni Ciccotti; Daniel Montemayor; Sara Bonella; David F Coker

An Adiabatic Linearized Path Integral Approach for Quantum Time Correlation Functions: Electronic Transport in Metal- Molten Salt Solutions (Journal Article)

In: The Journal of Physical Chemistry B, 109 (14), pp. 6855–6865, 2005.

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Sara Bonella; David Coker

Linearized, time-dependent, non-adiabatic quantum correlation functions (Journal Article)

In: Computer physics communications, 169 (1-3), pp. 267–273, 2005.

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