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Items: 18

1.

The Fluctuation-Dissipation Theorem as a Diagnosis and Cure for Zero-Point Energy Leakage in Quantum Thermal Bath Simulations.

Mangaud E, Huppert S, Plé T, Depondt P, Bonella S, Finocchi F.

J Chem Theory Comput. 2019 May 14;15(5):2863-2880. doi: 10.1021/acs.jctc.8b01164. Epub 2019 Apr 17.

PMID:
30939002
2.

Communication: Constrained molecular dynamics for polarizable models.

Coretti A, Bonella S, Ciccotti G.

J Chem Phys. 2018 Nov 21;149(19):191102. doi: 10.1063/1.5055704.

PMID:
30466272
3.

Time-reversal symmetry for systems in a constant external magnetic field.

Bonella S, Coretti A, Rondoni L, Ciccotti G.

Phys Rev E. 2017 Jul;96(1-1):012160. doi: 10.1103/PhysRevE.96.012160. Epub 2017 Jul 31.

PMID:
29347191
4.

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

Bonella S, Ferrario M, Ciccotti G.

Langmuir. 2017 Oct 24;33(42):11281-11290. doi: 10.1021/acs.langmuir.7b02565. Epub 2017 Oct 4.

PMID:
28915729
5.

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

Basire M, Mouhat F, Fraux G, Bordage A, Hazemann JL, Louvel M, Spezia R, Bonella S, Vuilleumier R.

J Chem Phys. 2017 Apr 7;146(13):134102. doi: 10.1063/1.4979199.

PMID:
28390363
6.

Probabilistic Derivation of Spatiotemporal Correlation Functions in the Hydrodynamic Limit.

Ciccotti G, Bonella S, Ferrario M, Pierleoni C.

J Phys Chem B. 2016 Mar 3;120(8):1996-2000. doi: 10.1021/acs.jpcb.5b10066. Epub 2016 Jan 19.

PMID:
26720838
7.

Photophysics and photochemistry of a DNA-protein cross-linking model: a synergistic approach combining experiments and theory.

Micciarelli M, Valadan M, Della Ventura B, Di Fabio G, De Napoli L, Bonella S, Röthlisberger U, Tavernelli I, Altucci C, Velotta R.

J Phys Chem B. 2014 May 15;118(19):4983-92. doi: 10.1021/jp4115018. Epub 2014 May 2.

PMID:
24742276
8.

Quantum dynamical structure factor of liquid neon via a quasiclassical symmetrized method.

Monteferrante M, Bonella S, Ciccotti G.

J Chem Phys. 2013 Feb 7;138(5):054118. doi: 10.1063/1.4789760.

PMID:
23406109
9.

A statistical mechanics handbook for protein-ligand binding simulation.

Rocchia W, Bonella S.

Front Biosci (Schol Ed). 2013 Jan 1;5:478-95. Review.

PMID:
23277063
10.

The quantum free energy barrier for hydrogen vacancy diffusion in Na3AlH6.

Poma A, Monteferrante M, Bonella S, Ciccotti G.

Phys Chem Chem Phys. 2012 Nov 28;14(44):15458-63. doi: 10.1039/c2cp42536j. Epub 2012 Oct 15.

PMID:
23064527
11.

Silver self aggregation in a nanodevice for enhanced Raman spectroscopy: experiments vs. simplified modeling via molecular dynamics.

Babiaczyk WI, Bonella S, Ciccotti G, Coluccio ML, Gentile F, Di Fabrizio E.

Nanoscale. 2012 Apr 7;4(7):2362-71. doi: 10.1039/c2nr30145h. Epub 2012 Mar 6.

PMID:
22395778
12.

Short range hydrogen diffusion in Na3AlH6.

Monteferrante M, Bonella S, Ciccotti G.

Phys Chem Chem Phys. 2011 Jun 14;13(22):10546-55. doi: 10.1039/c0cp02852e. Epub 2011 Apr 11.

PMID:
21479327
13.

Hydration structure of the quaternary ammonium cations.

Babiaczyk WI, Bonella S, Guidoni L, Ciccotti G.

J Phys Chem B. 2010 Nov 25;114(46):15018-28. doi: 10.1021/jp106282w. Epub 2010 Oct 28.

PMID:
21028872
14.

Analysis of the quantum-classical Liouville equation in the mapping basis.

Nassimi A, Bonella S, Kapral R.

J Chem Phys. 2010 Oct 7;133(13):134115. doi: 10.1063/1.3480018.

PMID:
20942531
15.

An adiabatic linearized path integral approach for quantum time-correlation functions II: a cumulant expansion method for improving convergence.

Causo MS, Ciccotti G, Bonella S, Vuilleumier R.

J Phys Chem B. 2006 Aug 17;110(32):16026-34.

PMID:
16898760
16.

An adiabatic linearized path integral approach for quantum time correlation functions: electronic transport in metal-molten salt solutions.

Causo MS, Ciccotti G, Montemayor D, Bonella S, Coker DF.

J Phys Chem B. 2005 Apr 14;109(14):6855-65.

PMID:
16851772
17.

Trajectory study of supercollision relaxation in highly vibrationally excited pyrazine and CO2.

Li Z, Sansom R, Bonella S, Coker DF, Mullin AS.

J Phys Chem A. 2005 Sep 1;109(34):7657-66.

PMID:
16834139
18.

Linearized path integral approach for calculating nonadiabatic time correlation functions.

Bonella S, Montemayor D, Coker DF.

Proc Natl Acad Sci U S A. 2005 May 10;102(19):6715-9. Epub 2005 Apr 4.

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