Sara Bonella, Ph.D. - Publications

Affiliations: 
Boston University, Boston, MA, United States 
Area:
theoretical and computational chemistry

57 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2021 Plé T, Huppert S, Finocchi F, Depondt P, Bonella S. Anharmonic spectral features via trajectory-based quantum dynamics: A perturbative analysis of the interplay between dynamics and sampling. The Journal of Chemical Physics. 155: 104108. PMID 34525824 DOI: 10.1063/5.0056824  1
2021 Mauger N, Plé T, Lagardère L, Bonella S, Mangaud É, Piquemal JP, Huppert S. Nuclear Quantum Effects in Liquid Water at Near Classical Computational Cost Using the Adaptive Quantum Thermal Bath. The Journal of Physical Chemistry Letters. 8285-8291. PMID 34427440 DOI: 10.1021/acs.jpclett.1c01722  1
2021 Coretti A, Rondoni L, Bonella S. Erratum: Fluctuation relations for systems in a constant magnetic field [Phys. Rev. E 102, 030101(R) (2020)]. Physical Review. E. 103: 029902. PMID 33736120 DOI: 10.1103/PhysRevE.103.029902  1
2021 Coretti A, Rondoni L, Bonella S. Fluctuation Relations for Dissipative Systems in Constant External Magnetic Field: Theory and Molecular Dynamics Simulations. Entropy (Basel, Switzerland). 23. PMID 33504011 DOI: 10.3390/e23020146  1
2020 Coretti A, Rondoni L, Bonella S. Fluctuation relations for systems in a constant magnetic field. Physical Review. E. 102: 030101. PMID 33075979 DOI: 10.1103/PhysRevE.102.030101  1
2020 Bonella S, Coretti A, Vuilleumier R, Ciccotti G. Adiabatic motion and statistical mechanics via mass-zero constrained dynamics. Physical Chemistry Chemical Physics : Pccp. PMID 32175532 DOI: 10.1039/D0Cp00163E  1
2020 Scalfi L, Limmer DT, Coretti A, Bonella S, Madden PA, Salanne M, Rotenberg B. Charge fluctuations from molecular simulations in the constant-potential ensemble. Physical Chemistry Chemical Physics : Pccp. PMID 31907506 DOI: 10.1039/C9Cp06285H  1
2019 Plé T, Huppert S, Finocchi F, Depondt P, Bonella S. Sampling the thermal Wigner density via a generalized Langevin dynamics. The Journal of Chemical Physics. 151: 114114. PMID 31542021 DOI: 10.1063/1.5099246  1
2019 Mangaud E, Huppert S, Plé T, Depondt P, Bonella S, Finocchi F. The Fluctuation-Dissipation Theorem as a Diagnosis and Cure for Zero-Point Energy Leakage in Quantum Thermal Bath Simulations. Journal of Chemical Theory and Computation. PMID 30939002 DOI: 10.1021/acs.jctc.8b01164  1
2018 Coretti A, Bonella S, Ciccotti G. Communication: Constrained molecular dynamics for polarizable models. The Journal of Chemical Physics. 149: 191102. PMID 30466272 DOI: 10.1063/1.5055704  1
2017 Bonella S, Coretti A, Rondoni L, Ciccotti G. Time-reversal symmetry for systems in a constant external magnetic field. Physical Review. E. 96: 012160. PMID 29347191 DOI: 10.1103/Physreve.96.012160  1
2017 Bonella S, Ferrario M, Ciccotti G. Thermal diffusion in binary mixtures: transient behavior and transport coefficients from equilibrium and non-equilibrium molecular dynamics. Langmuir : the Acs Journal of Surfaces and Colloids. PMID 28915729 DOI: 10.1021/Acs.Langmuir.7B02565  1
2017 Micciarelli M, Curchod BFE, Bonella S, Altucci C, Valadan M, Rothlisberger U, Tavernelli I. Characterization of the Photochemical Properties of 5-Benzyluracil via Time-Dependent Density Functional Theory. The Journal of Physical Chemistry. A. PMID 28467074 DOI: 10.1021/Acs.Jpca.6B12799  1
2017 Basire M, Mouhat F, Fraux G, Bordage A, Hazemann JL, Louvel M, Spezia R, Bonella S, Vuilleumier R. Fermi resonance in CO2: Mode assignment and quantum nuclear effects from first principles molecular dynamics. The Journal of Chemical Physics. 146: 134102. PMID 28390363 DOI: 10.1063/1.4979199  1
2016 Ferrario M, Bonella S, Ciccotti G. On the establishment of thermal diffusion in binary Lennard-Jones liquids European Physical Journal: Special Topics. 1-14. DOI: 10.1140/Epjst/E2016-60137-4  1
2015 Ciccotti G, Bonella S, Ferrario M, Pierleoni C. Probabilistic Derivation of Spatiotemporal Correlation Functions in the Hydrodynamic Limit. The Journal of Physical Chemistry. B. PMID 26720838 DOI: 10.1021/Acs.Jpcb.5B10066  1
2015 Bonella S, Ciccotti G. An introduction to the problem of bridging quantum and classical dynamics European Physical Journal: Special Topics. 224: 2305-2320. DOI: 10.1140/Epjst/E2015-02413-0  1
2015 Beutier J, Vuilleumier R, Bonella S, Ciccotti G. Gas phase infrared spectra from quasi-classical Kubo time correlation functions Molecular Physics. DOI: 10.1080/00268976.2015.1064550  1
2014 Beutier J, Borgis D, Vuilleumier R, Bonella S. Computing thermal Wigner densities with the phase integration method. The Journal of Chemical Physics. 141: 084102. PMID 25173000 DOI: 10.1063/1.4892597  1
2014 Bonella S, Raimondo D, Milanetti E, Tramontano A, Ciccotti G. Mapping the hydropathy of amino acids based on their local solvation structure. The Journal of Physical Chemistry. B. 118: 6604-13. PMID 24845543 DOI: 10.1021/Jp500980X  1
2014 Micciarelli M, Valadan M, Della Ventura B, Di Fabio G, De Napoli L, Bonella S, Röthlisberger U, Tavernelli I, Altucci C, Velotta R. Photophysics and photochemistry of a DNA-protein cross-linking model: a synergistic approach combining experiments and theory. The Journal of Physical Chemistry. B. 118: 4983-92. PMID 24742276 DOI: 10.1021/Jp4115018  1
2014 Bonella S, Ciccotti G. Approximating time-dependent quantum statistical properties Entropy. 16: 86-109. DOI: 10.3390/E16010086  1
2014 Bonella S, Ciccotti G, Rondoni L. Time reversal symmetry in time-dependent correlation functions for systems in a constant magnetic field Epl. 108. DOI: 10.1209/0295-5075/108/60004  1
2014 Beutier J, Monteferrante M, Bonella S, Vuilleumier R, Ciccotti G. Gas phase infrared spectra via the phase integration quasi-classical method Molecular Simulation. 40: 196-207. DOI: 10.1080/08927022.2013.843776  1
2013 Monteferrante M, Bonella S, Ciccotti G. Quantum dynamical structure factor of liquid neon via a quasiclassical symmetrized method. The Journal of Chemical Physics. 138: 054118. PMID 23406109 DOI: 10.1063/1.4789760  1
2013 Rocchia W, Bonella S. A statistical mechanics handbook for protein-ligand binding simulation. Frontiers in Bioscience (Scholar Edition). 5: 478-95. PMID 23277063  1
2013 Mouhat F, Bonella S, Pierleoni C. Charge transport simulations of NaCl in an external magnetic field: The quest for the Hall effect Molecular Physics. 111: 3651-3661. DOI: 10.1080/00268976.2013.846486  1
2012 Poma A, Monteferrante M, Bonella S, Ciccotti G. The quantum free energy barrier for hydrogen vacancy diffusion in Na3AlH6. Physical Chemistry Chemical Physics : Pccp. 14: 15458-63. PMID 23064527 DOI: 10.1039/C2Cp42536J  1
2012 Babiaczyk WI, Bonella S, Ciccotti G, Coluccio ML, Gentile F, Di Fabrizio E. Silver self aggregation in a nanodevice for enhanced Raman spectroscopy: experiments vs. simplified modeling via molecular dynamics. Nanoscale. 4: 2362-71. PMID 22395778 DOI: 10.1039/C2Nr30145H  1
2012 Bonella S, Meloni S, Ciccotti G. Theory and methods for rare events European Physical Journal B. 85. DOI: 10.1140/Epjb/E2012-20366-2  1
2012 Sterpone F, Bonella S, Meloni S. Early stage of the dehydrogenation of NaAlH 4 by ab initio rare event simulations Journal of Physical Chemistry C. 116: 19636-19643. DOI: 10.1021/Jp3019588  1
2011 Monteferrante M, Bonella S, Ciccotti G. Short range hydrogen diffusion in Na3AlH6. Physical Chemistry Chemical Physics : Pccp. 13: 10546-55. PMID 21479327 DOI: 10.1039/C0Cp02852E  1
2011 Monteferrante M, Bonella S, Ciccotti G. Linearized symmetrized quantum time correlation functions calculation via phase pre-averaging Molecular Physics. 109: 3015-3027. DOI: 10.1080/00268976.2011.619506  1
2010 Bonella S, Monteferrante M, Pierleoni C, Ciccotti G. Path integral based calculations of symmetrized time correlation functions. II. The Journal of Chemical Physics. 133: 164105. PMID 21033773 DOI: 10.1063/1.3493449  1
2010 Bonella S, Monteferrante M, Pierleoni C, Ciccotti G. Path integral based calculations of symmetrized time correlation functions. I. The Journal of Chemical Physics. 133: 164104. PMID 21033772 DOI: 10.1063/1.3493448  1
2010 Babiaczyk WI, Bonella S, Guidoni L, Ciccotti G. Hydration structure of the quaternary ammonium cations. The Journal of Physical Chemistry. B. 114: 15018-28. PMID 21028872 DOI: 10.1021/Jp106282W  1
2010 Nassimi A, Bonella S, Kapral R. Analysis of the quantum-classical Liouville equation in the mapping basis. The Journal of Chemical Physics. 133: 134115. PMID 20942531 DOI: 10.1063/1.3480018  1
2010 Bonella S, Ciccotti G, Kapral R. Linearization approximations and Liouville quantum-classical dynamics Chemical Physics Letters. 484: 399-404. DOI: 10.1016/J.Cplett.2009.11.056  1
2010 Huo P, Bonella S, Chen L, Coker DF. Linearized approximations for condensed phase non-adiabatic dynamics: Multi-layered baths and Brownian dynamics implementation Chemical Physics. 370: 87-97. DOI: 10.1016/J.Chemphys.2010.02.021  1
2009 Bonella S, Rocchia W, Amat P, Nifosí R, Tozzini V. SDPhound, a mutual information-based method to investigate specificity-determining positions Algorithms. 2: 764-789. DOI: 10.3390/a2020764  1
2009 Monteferrante M, Bonella S, Meloni S, Ciccotti G. Modified single sweep method for reconstructing free-energy landscapes Molecular Simulation. 35: 1116-1129. DOI: 10.1080/08927020903051598  1
2009 Monteferrante M, Bonella S, Meloni S, Vanden-Eijnden E, Ciccotti G. Calculations of free energy barriers for local mechanisms of hydrogen diffusion in alanates Lecture Notes in Computational Science and Engineering. 68: 187-206. DOI: 10.1007/S10820-008-9097-X  1
2008 Dunkel ER, Bonella S, Coker DF. Iterative linearized approach to nonadiabatic dynamics. The Journal of Chemical Physics. 129: 114106. PMID 19044949 DOI: 10.1063/1.2976441  1
2008 Monteferrante M, Bonella S, Meloni S, Vanden-Eijnden E, Ciccotti G. Calculations of free energy barriers for local mechanisms of hydrogen diffusion in alanates Scientific Modeling and Simulation Smns. 15: 187-206. DOI: 10.1007/s10820-008-9097-x  1
2007 Coker DF, Bonella S. Linearized nonadiabatic dynamics in the adiabatic representation Springer Series in Chemical Physics. 83: 321-340. DOI: 10.1007/978-3-540-34460-5_14  1
2006 Causo MS, Ciccotti G, Bonella S, Vuilleumier R. An adiabatic linearized path integral approach for quantum time-correlation functions II: a cumulant expansion method for improving convergence. The Journal of Physical Chemistry. B. 110: 16026-34. PMID 16898760 DOI: 10.1021/Jp061725D  1
2006 Coker DF, Bonella S. Linearized path integral methods for quantum time correlation functions Lecture Notes in Physics. 703: 553-590. DOI: 10.1007/3-540-35273-2_16  1
2005 Causo MS, Ciccotti G, Montemayor D, Bonella S, Coker DF. An adiabatic linearized path integral approach for quantum time correlation functions: electronic transport in metal-molten salt solutions. The Journal of Physical Chemistry. B. 109: 6855-65. PMID 16851772 DOI: 10.1021/Jp045208B  1
2005 Li Z, Sansom R, Bonella S, Coker DF, Mullin AS. Trajectory study of supercollision relaxation in highly vibrationally excited pyrazine and CO2. The Journal of Physical Chemistry. A. 109: 7657-66. PMID 16834139 DOI: 10.1021/Jp0525336  1
2005 Bonella S, Coker DF. LAND-map, a linearized approach to nonadiabatic dynamics using the mapping formalism. The Journal of Chemical Physics. 122: 194102. PMID 16161558 DOI: 10.1063/1.1896948  1
2005 Bonella S, Montemayor D, Coker DF. Linearized path integral approach for calculating nonadiabatic time correlation functions. Proceedings of the National Academy of Sciences of the United States of America. 102: 6715-9. PMID 15809429 DOI: 10.1073/Pnas.0408326102  1
2005 Bonella S, Coker D. Linearized, time-dependent, non-adiabatic quantum correlation functions Computer Physics Communications. 169: 267-273. DOI: 10.1016/J.Cpc.2005.03.061  1
2003 Bonella S, Coker DF. Semiclassical implementation of the mapping Hamiltonian approach for nonadiabatic dynamics using focused initial distribution sampling Journal of Chemical Physics. 118: 4370-4385. DOI: 10.1063/1.1542883  1
2001 Bonella S, Coker DF. A semiclassical limit for the mapping Hamiltonian approach to electronically nonadiabatic dynamics Journal of Chemical Physics. 114: 7778-7789. DOI: 10.1063/1.1366331  1
2001 Bonella S, Coker DF. Semi-classical implementation of mapping Hamiltonian methods for general non-adiabatic problems Chemical Physics. 268: 189-200. DOI: 10.1016/S0301-0104(01)00329-9  1
1999 Margulis CJ, Horner DA, Bonella S, Coker DF. Vibrational Dynamics of the I3 Radical: A Semiempirical Potential Surface, and Semiclassical Calculation of the Anion Photoelectron Spectrum Journal of Physical Chemistry A. 103: 9552-9563. DOI: 10.1021/Jp992596M  1
1996 Bonella S, Ciccotti G, Coker DF. The semiclassical limit of the intermediate scattering function Molecular Physics. 89: 1203-1207. DOI: 10.1080/00268979609482534  1
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