Sara Bonella's Publications

• M. Monteferrante, S. Bonella, G. Ciccotti "Quantum dynamical structure factor of liquid neon via a quasiclassical symmetrized method", J. Chem. Phys. 138, 054118 (2013) DOI: 10.1063/1.4789760
• Rocchia W. and S. Bonella “A Statistical Mechanics handbook for protein-ligand binding simulation” Frontiers in Bioscience, Scholar, 5, 478-495 (2013) DOI: 10.2741/S384
• F. Sterpone, S. Bonella, S. Meloni "Early stage of the dehydrogenation of NaAlH4 by ab initio rare events simulations", J. Phys. Chem. C, 19636-19643 (2012) DOI: 10.1021/jp3019588
• A. Poma, M. Monteferrante, S. Bonella, G. Ciccotti " The quantum free energy barrier for hydrogen vacancy diffusion in Na3AlH6", Phys. Chem. Chem. Phys., 14, 15458-15463 (2012) DOI: 10.1039/C2CP42536J
• W. Babiaczyk, S. Bonella, G. Ciccotti, M. L. Coluccio, F. Gentile and E. Di Fabrizio "Silver self aggregation in a nanodevice for enhanced Raman spectroscopy: experiments vs simplified modeling via molecular dynamics", Nanoscale, 4, 2362-2371 (2012), DOI: 10.1039/c2nr30145h
• S. Bonella, S. Meloni and G. Ciccotti "Theory and methods for rare events", European Physical Journal B, 85, 97 (2012)
• M. Monteferrante, S. Bonella and G. Ciccotti "Linearized symmetrized quantum time correlation functions calculation via phase pre-averaging", Mol. Phys. 109, 3015-3027 (2011)
• M. Monteferrante, S. Bonella and G. Ciccotti "Short range hydrogen diffusion in Na3AlH6", Phys. Chem. Chem. Phys. 13, 10546 (2011)
• W.I.Babiaczyk, S.Bonella, L.Guidoni, and G.Ciccotti "Hydration structure of the quaternary ammonium cations", J.Phys.Chem. B, 114, 15018-15028 (2010)
• S.Bonella, M.Monteferrante, C.Pierleoni, and G.Ciccotti "Path integral based calculations of symmetrized time correlation functions, I" J.Chem.Phys., 133, 164104 (2010)
• S.Bonella, M.Monteferrante, C.Pierleoni, and G.Ciccotti "Path integral based calculations of symmetrized time correlation functions, II" J.Chem.Phys., 133, 164105 (2010)
• A. Nassimi, S. Bonella, and R. Kapral, "Analysis of the quantum-classical Liouville equation in the mapping basis", J. Chem. Phys, 133, 134115-134126 (2010)
• P. Huo, S.Bonella, L. Chen, and D.F. Coker, "Linearization approximations for condensed phase non-adiabatic dynamics: multi-layered baths and brownian dynamics implementation", Chem.Phys., 370, 87-97 (2010)
• S.Bonella, G.Ciccotti, and R.Kapral, "Linearization approximations and Liouville quantum-classical dynamics", Chem.Phys. Letts. 484, 4, 399-404 (2010)
• M.Monteferrante, S.Bonella, S.Meloni, and G.Ciccotti, "Modified single sweep method for reconstructing free energy landscapes", Mol.Sim., 35, 1116-1129, (2009)
• S. Bonella, W. Rocchia, P. Amat, R. Nifosi and V. Tozzini, "SDPhound, a mutual information-based method to investigate specificity-determining positions", Algorithms, 2, 764-789 (2009)
• E. Dunkel, S. Bonella, and D.F.Coker "Iterative linearized approach to non adiabatic dynamics", J. Chem. Phys., 129, 114106 (2008)
• M.Monteferrante, S.Bonella, S.Meloni, E.Vanden Eijnden, and G.Ciccotti, "Calculations of free energy barriers for local mechanisms of hydrogen diffusion in alanates", Scientific Modeling & Simulation SMNS, vol. 15, 187 (2008)

•  M. .S. Causo, G. Ciccotti, S. Bonella, and R. Vuilleumier "An Adiabatic Linearized Path Integral Approach for Quantum Time Correlation Functions II: A cumulant expansion method for improving convergence", J. Phys. Chem. B, 110, 3638 (2006)
• G. Ciccotti, and S. Bonella "Quantum-classical statistical dynamics with trajectories", Dynamics of Open Quantum Systems, editor K.H. Hughes, CCP6 (2006)
• D.F.Coker, and S. Bonella "Linearized non-adiabatic dynamics in the adiabatic representation", "Quantum Dynamics of Complex Systems" editors I. Burghardt and D. A. Micha, Springer-Verlag, Berlin (2006)
• D.F.Coker, and S. Bonella "Linearized path integral methods for quantum time correlation functions", Springer Lecture Notes in Physics, "Computer Simulations in Condensed Matter: from Materials to Chemical Biology" editors Ferrario, K. Binder, G. Ciccotti, (2006)
• S. Bonella, D. Montemayor, and D. F. Coker "Linearized path integral approach for calculating nonadiabatic time correlation functions" Proc. Natl. Ac. Sci. USA, 102, 6715-6719 (2005) Δ
• M.S. Causo, G. Ciccotti, D. Montemayor, S. Bonella, and D.F. Coker "An adiabatic linearized path integral approach for quantum Time correlation functions: Electronic transport in metal-molten salt solutions", J. Phys. Chem. B, 109, 6855-6865 (2005)
• S. Bonella and D.F. Coker "LAND-Map, a linearized approach to non-adiabatic dynamics using the mapping formalism", J. Chem. Phys., 122, 194102 (2005)
• Z. Li, R. Sansom, S. Bonella, D.F.Coker, and A.S. Mullin "Theoretical study of supercollision relaxation in highly vibrationally excited pyrazine and CO₂", J. Phys. Chem. A, 109, 7657-7666 (2005)
• S. Bonella, and D.F.Coker "Linearized, time-dependent, non-adiabatic quantum correlation functions", in Proceedings of the Europhysics Conference on Computational Physics CCP2004, Comp. Phys. Comm. (2004)
• S. Bonella, and D.F. Coker, "Semiclassical implementation of the mapping Hamiltonian approach for non-adiabatic dynamics: Focused initial distribution sampling'', J. Chem. Phys., 118, 4370-4385 (2003)
• S. Bonella, and D.F. Coker, "Semiclassical implementation of the mapping Hamiltonian methods for general non-adiabatic problems'', Chem. Phys., 268, 323-334 (2001)
• S. Bonella, and D.F. Coker, "A semiclassical limit for the mapping Hamiltonian approach to electronically non-adiabatic dynamics'', J. Chem. Phys., 114, 7778-7789 (2001)
• Margulis CJ, Horner DA, Bonella S, et al. "Vibrational dynamics of the I-3 radical: A semiempirical potential surface, and semiclassical calculation of the anion photoelectron spectrum", J Phys. Chem A 103 (47), 9552-9563 (1999)
• V. Filinov, S. Bonella et al, "Quantum molecular dynamics using Wigner representation''}, Proceedings of the International School of Physics ", Computer Simulation of Rare Events and the Dynamics of Classical and Quantum Condensed-Phase Systems", Lerici (1997)
• S. Bonella, G. Ciccotti, and D.F. Coker "The semiclassical limit of the intermediate scattering function", Mol. Phys. 89 (4), 1203-1207 (1996)