Recent Publications

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These are the most recent publications of the group (2006-2014). A complete list of the group's publications can be found following the links in the group members webpages.

2014 2013 2012 2011 2010 2009 2008 2007 2006

2014

G. D'Adamo, A. Pelissetto and Carlo Pierleoni, "Accurate coarse-grained models for mixtures of colloids and linear polymers under good-solvent conditions", J. Chem. Phys. 141, 244905 (2014) DOI:10.1063/1.4904392
J. Beutier, R. Vuilleumier, D. Borgis and S. Bonella, "Computing thermal Wigner densities with the phase integration method", J. Chem. Phys., 141, 084102 (2014) DOI: 10.1063/1.4892597
G. D'Adamo, A. Pelissetto and Carlo Pierleoni, "Phase diagram of mixtures of colloids and polymers in the thermal crossover from Good to Theta solvent", J. Chem. Phys. 141, 024902 (2014) DOI:10.1063/1.4885818
S. Bonella, D. Raimondo, E. Milanetti, A. Tramontano, G. Ciccotti, "Mapping the Hydropathy of Amino Acids Based on Their Local Solvation Structure", J. Phys. Chem. B, 118(24), 6604-6613 (2014) DOI:10.1021/jp500980x
M. Micciarelli, S. Bonella et al., "Photophysics and Photochemistry of a DNA-Protein Cross-Linking Model: A Sinergistic Apprach Combining Experiments and Theory", J. Phys. Chem. B, 118(19), 4983-4992 (2014) DOI: 10.1021/jp4115018
C. Violante, L. Chiodo, A. Mosca Conte, F. Bechstedt, O. Pulci, "Si(111) 2x1 surface isomers: DFT investigations on stability and doping effects", Surf. Sci. 621, 123-127 (2014) DOI: 10.1016/j.susc.2013.11.006
S. Bonella, G. Ciccotti "Approximating Time-Dependent Quantum Statistical Properties", Entropy, 16(1), 86-109, (2014) DOI:10.3390/e16010086
F. Gentile, M. Monteferrante, L. Chiodo, A. Toma, M. L. Coluccio, G. Ciccotti, E. Di Fabrizio, "Electroless formation of super-clusters of metal atoms: an experimental and numerical approach", Mol. Phys. 2014 (accepted).

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2013

P. Gargiani, S. Lisi, M. G. Betti, A. T. Ibrahimi, F. Bertran, P. Le Fèvre, L. Chiodo, "Orbital dependent Rashba splitting and electron-phonon coupling of 2D Bi phase on Cu (100) surface", J. Chem. Phys. 139, 184707 (2013) DOI: 10.1063/1.4828865
J. Beutier, M. Monteferrante, S. Bonella, R. Vuilleumier, G. Ciccotti "Gas phase infrared spectra via the phase integration quasi-classical method", Mol. Simulations., 40, 196-207, (2013) DOI: 10.1080/08927022.2013.843776
F. Mouhat, S. Bonella, C. Pierleoni "Charge transport simulations of NaCl in an external magnetic field: the quest for the Hall effect", Mol. Phys. (2013) DOI: http://dx/doi.org.10.1080/00268976.2013.846486
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
W. Rocchia, S. Bonella "A statistical mechanics handbook for protein-ligand binding simulation", Fronteers in bioscience 5, 478-495 (2013) PMID: 23277063
G. Roma, L. Chiodo, "Selenium adsorption on Mo(110): a first principles investigation", Phys. Rev. B 87, 245420 (2013).
A. Tanwar, E. Fabiano, P. E. Trevisanutto, L. Chiodo, F. Della Sala, “Accurate ionization potential of gold anionic clusters from density functional theory and many-body perturbation theory”, Eur. Phys. J. B 86, 161 (2013) DOI: 10.1140/epjb/e2013-40016-5
G. D'Adamo, A. Pelissetto and C. Pierleoni, "Predicting the thermodynamics by using state-dependent interactions", J. Chem. Phys. 138, 234107 (2013)
G. D'Adamo, A. Pelissetto and C. Pierleoni, "Consistent coarse-graining strategy for polymer solutions in the thermal crossover from good to Theta solvent", J. Chem. Phys. 139, 34901 (2013)
G. D'Adamo, A. Pelissetto and C. Pierleoni, "Depletion effecfts in colloid-polymer solutions", Mol. Phys., (2013) DOI:10.1080/00268976.2013.836255

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2012

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
G. D'Adamo, A. Pelissetto, C. Pierleoni "Consistent and transferable coarse-grained model for semidilute polymer solutions in good solvent", J. Chem. Phys. 137, 24901 (2012)
G. D'Adamo, A. Pelissetto, C. Pierleoni "Polymers as compressible soft spheres", J. Chem. Phys. 136,224905 (2012).
G. D'Adamo, A. Pelissetto, C. Pierleoni "Coarse-Graining strategies in polymer solutions",Soft Matter 8, 5151-5167 (2012)
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
G. Cottone, G. Lattanzi, G. Ciccotti and R. Elber "Multiphoton absorption of myoglobin-nitric oxide complex: relaxation by D-NEMD of a stationary state", J. Phys. Chem. B, (2012) DOI: 10.1021/jp21218x
S. Bonella, S. Meloni and G. Ciccotti "Theory and methods for rare events", European Physical Journal B, 85, 97 (2012)

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2011

E. Liberatore, M.A. Morales, D.M. Ceperley, C. Pierleoni "Free-energy methods in Coupled Electron-Ion Monte Carlo", Mol. Phys. 109, 3029 (2011).
M. Monteferrante, S. Bonella and G. Ciccotti "Linearized symmetrized quantum time correlation functions calculation via phase pre-averaging", Mol. Phys. 109, 3015-3027 (2011)
S. Orlandini, S. Meloni and G. Ciccotti "Hydrodynamics from statistical mechanics: combined dynamical-NEMD and conditional sampling to relax an interface between two immiscible liquids", Phys. Chem. Chem. Phys. 13, 13177 (2011).
M. Monteferrante, S. Bonella and G. Ciccotti "Short range hydrogen diffusion in Na3AlH6", Phys. Chem. Chem. Phys. 13, 10546 (2011).
E. Liberatore, C. Pierleoni and D.M. Ceperley "Liquid-Solid transition in fully ionized hydrogen at ultra-high pressure", J. Chem. Phys. 134, 184505 (2011).
G.Ciccotti, and S.Meloni “Temperature Accelerated Monte Carlo (TAMC): a method for sampling the free energy surface of non-analytical collective coordinates” CPPC, 13, 5952 (2011)
F.Agostini, R.Vuilleumier, and G.Ciccotti “Infrared spectroscopy and effective modes analysis of the protonated water dimer H+ (H2O)2 at room temperature under H/D substitution” J.Chem.Phys., 134, 084302 (2011)
F.Agostini, G.Ciccotti, and R.Vuilleumier “Infrared spectroscopy of small protonated water clusters at room temperature: an effective modes analysis”, J.Chem.Phys., 134, 084303 (2011)

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2010

G. D'Adamo, C. Pierleoni, "Crystalline free energy of micelles of diblock copolymer solutions", J. Chem. Phys.,133,204902 (2010)
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)
L.Maragliano, G.Cottone, G.Ciccotti, and E.Vanden-Eijnden, "Mapping the network of pathways of CO diffusion in myoglobin", JACS, 132, 1010 (2010)
S.Bonella, G.Ciccotti, and R.Kapral, "Linearization approximations and Liouville quantum-classical dynamics", Chem.Phys. Letts. 484, 4, 399-404 (2010)
C.Hartmann, C.Schuette, and G.Ciccotti, "On the linear response of mechanical systems with constraints", J.Chem.Phys.,132, 111103 (2010)
A.Jezierska, R.Vuilleumier, J.J.Panek, and G.Ciccotti, "Molecular properties investigations of an ortho- hydroxy Schiff base type compound: a combined DFT, AIM and first-principle molecular dynamics approach", J.Phys.Chem.B, 114, 242-253 (2010)

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2009

M. L. Mugnai, S. Caprara, G. Ciccotti1, C. Pierleoni, and M. Mareschal, "Formation of a compressible Rayleigh-Benard convective cell by dynamical non-equilibrium molecular dynamics", J.Chem.Phys., 131, 064106, (2009)
M.Monteferrante, S.Bonella, S.Meloni, and G.Ciccotti, "Modified single sweep method for reconstructing free energy landscapes", Mol.Sim., 35, 1116-1129, (2009)
M.Mareschal, S.Vantieghem, M.L.Mugnai, S.Caprara, G.Ciccotti, and C.Pierleoni, "Compressible convective instability by Molecular Dynamics", in "Proceedings of Symposium on the 50th Anniversary of the Alder transition", Y. Hiwatari & M. Isobe, Eds, Prog. of Theor.Phys. Suppl., 178, 15, (2009)
C.Hartmann, C.Schuette, G.Kalibaeva, M.Di Pierro, and G.Ciccotti, “Fast simulation of polymer chains”, J.Chem.Phys., 130, 144101 (2009)
M.Venturoli, E.Vanden Eijnden, and G.Ciccotti, “Kinetics of phase transitions in the two-dimensional Ising models studied with the string method”, J.Math.Chem., 45, 188 (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)

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2008

E. Dunkel, S. Bonella, and D.F.Coker "Iterative linearized approach to non adiabatic dynamics", J. Chem. Phys., 129, 114106 (2008)
P.L.Palla, C.Pierleoni, and G.Ciccotti, "Bulk viscosity of the Lennard-Jones system at the triple point by dynamical nonequilibrium molecular dynamics", Phys.Rev.E, 78, 021204 (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)
D.MacKernan, G.Ciccotti, and R.Kapral, "Trotter-Based Simulation of Quantum-Classical Dynamics", J.Phys.Chem., 112, 424-432, (2008)
G.Ciccotti, E.Vanden-Eijnden, and T. Lelievre, "Projection of diffusions on submanifolds: Application to mean force computation", Comm.Pure and Applied Math., 61, 371-408,(2008)

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2007

F.Agostini, S.Caprara, and G.Ciccotti, "Do we have a consistent non adiabatic quantum-classical mechanics?", Europhys. Lett., 78, 30001, (2007)
C.Simon, G.Ciccotti, and M.L.Klein, "Computing the acidity of liquids via ab initio molecular dynamics", Chem.Phys.Chem., 8, 2072, (2007)
V.Marry, and G.Ciccotti, "Trotter derived algorithms for molecular dynamics with constraints : Velocity Verlet revisited", J.Comp.Phys., 222, 428, (2007)

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2006

E.Vanden-Eijnden, and G.Ciccotti, "Second-order integrators for Langevin equations with holonomic constraints", Chem.Phys.Lett., 429, 310, (2006)
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)

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Book Chapters and Conference Proceedings

L. Chiodo, A. Iacomino, M. Palummo, A. Rubio, “Titania nanostructures electronic and optical response by high-level ab-initio computational approaches”, in “Handbook of Functional Nanomaterials”, Nova Science Publishers, Ltd. (New York – USA) (2013).

G.Ciccotti, S.Caprara, and F.Agostini, "Do we have a consistent non-adiabatic quantum-classical statistical mechanics?” in: "Energy Transfer Dynamics in Biomaterial Systems" E.R.Bittner, I.Burghardt, V.May, and D.A.Micha, Eds. CPS, Springer, Berlin (2009)

S.Bonella, D.F.Coker, D.Mac Kernan, R.Kapral, and G.Ciccotti, “Trajectory based simulations of mixed quantum-classical systems” in: "Energy Transfer Dynamics in Biomaterial Systems" E.R.Bittner, I.Burghardt, V.May, and D.A.Micha, Eds. CPS, Springer, Berlin (2009)

D. F. Coker, L. Chen, P. Huo, and S. Bonella "Exploring the linearized approximation for condensed phase non-adiabatic dynamics: multi-layered baths", Multidimensional Quantum Mechanics with trajectories, editors Dmitry Shalashilin and Marcelo Miranda, CCP6 (2009)

M.Mareschal, S.Vantieghem, M.L.Mugnai, S.Caprara, G.Ciccotti, and C.Pierleoni, “Compressible convective instability by Molecular Dynamics” Y.Hiwatari & M.Isobe, Eds Prog. of Theor.Phys.Suppl., 178, 15 (2009)

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