Giovanni Ciccotti

Giovanni Ciccotti

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Giovanni Ciccotti

Giovanni Ciccotti

Publications by authors named "Giovanni Ciccotti"

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Adiabatic motion and statistical mechanics via mass-zero constrained dynamics.

Phys Chem Chem Phys 2020 Mar 16. Epub 2020 Mar 16.

Institute for Applied Computing "Mauro Picone" (IAC), CNR Via dei Taurini 19, 00185 Rome, Italy and Università di Roma La Sapienza, Ple. A. Moro 5, 00185 Roma, Italy and School of Physics, University College of Dublin UCD-Belfield, Dublin 4, Ireland.

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http://dx.doi.org/10.1039/d0cp00163eDOI Listing
March 2020

Ab initio accelerated molecular dynamics study of the hydride ligands in the ruthenium complex: Ru(H)H(P(CH)).

Phys Chem Chem Phys 2019 Dec 7;21(45):25247-25257. Epub 2019 Nov 7.

Chemistry Department, Milan University, Via C. Golgi 19, 20133, Milan, Italy.

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http://dx.doi.org/10.1039/c9cp03776dDOI Listing
December 2019

A General Mechanism for Signal Propagation in the Nicotinic Acetylcholine Receptor Family.

J Am Chem Soc 2019 Dec 16;141(51):19953-19958. Epub 2019 Dec 16.

Centre for Computational Chemistry, School of Chemistry , University of Bristol , Bristol BS8 1TS , United Kingdom.

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http://dx.doi.org/10.1021/jacs.9b09055DOI Listing
December 2019

On computing the solubility of molecular systems subject to constraints using the extended Einstein crystal method.

J Chem Phys 2019 May;150(20):201104

Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.

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http://dx.doi.org/10.1063/1.5099378DOI Listing
May 2019

The physics of open systems for the simulation of complex molecular environments in soft matter.

Soft Matter 2019 Mar;15(10):2114-2124

Instituto per le Applicazioni del Calcolo, Consiglio Nazionale delle Ricerche, and Universita' La Sapienza, Rome, Italy.

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http://dx.doi.org/10.1039/c8sm02523aDOI Listing
March 2019

Solubility of paracetamol in ethanol by molecular dynamics using the extended Einstein crystal method and experiments.

J Chem Phys 2019 Mar;150(9):094107

Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.

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http://dx.doi.org/10.1063/1.5086706DOI Listing
March 2019

Communication: Constrained molecular dynamics for polarizable models.

J Chem Phys 2018 Nov;149(19):191102

Institute for Applied Computing "Mauro Picone" (IAC), CNR Via dei Taurini 19, 00185 Rome, Italy.

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http://dx.doi.org/10.1063/1.5055704DOI Listing
November 2018

Nucleation of Molecular Crystals Driven by Relative Information Entropy.

J Chem Theory Comput 2018 Feb 10;14(2):959-972. Epub 2018 Jan 10.

Department of Chemical Engineering, Massachusetts Institute of Technology , Cambridge, Massachusetts 02139, United States.

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http://dx.doi.org/10.1021/acs.jctc.7b01027DOI Listing
February 2018

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

Langmuir 2017 10 4;33(42):11281-11290. Epub 2017 Oct 4.

Institute for Applied Mathematics "Mauro Picone" (IAC), CNR , Via dei Taurini 19, 00185 Rome, Italy.

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http://dx.doi.org/10.1021/acs.langmuir.7b02565DOI Listing
October 2017

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

Phys Rev E 2017 Jul 31;96(1-1):012160. Epub 2017 Jul 31.

Institute for Applied Computing "Mauro Picone" (IAC), CNR, Via dei Taurini 19, 00185 Rome, Italy; School of Physics, University College of Dublin UCD-Belfield, Dublin 4, Ireland; and Università di Roma La Sapienza, Ple. A. Moro 5, 00185 Roma, Italy.

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http://dx.doi.org/10.1103/PhysRevE.96.012160DOI Listing
July 2017

On metastability and Markov state models for non-stationary molecular dynamics.

J Chem Phys 2016 Nov;145(17):174103

Institute of Mathematics, Freie Universität Berlin, Berlin, Germany and Zuse Institute Berlin, Berlin, Germany.

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http://dx.doi.org/10.1063/1.4966157DOI Listing
November 2016

Particle-Based Modeling of Living Actin Filaments in an Optical Trap.

Polymers (Basel) 2016 Sep 19;8(9). Epub 2016 Sep 19.

Department of Physics, Université Libre de Bruxelles (ULB), Campus Plaine, CP 223, Brussels B-1050, Belgium.

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http://dx.doi.org/10.3390/polym8090343DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6432230PMC
September 2016

On the properties of a bundle of flexible actin filaments in an optical trap.

J Chem Phys 2016 Jun;144(24):245102

Department of Physical and Chemical Sciences, University of L'Aquila, Via Vetoio 10, 67100 L'Aquila, Italy.

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http://dx.doi.org/10.1063/1.4954186DOI Listing
June 2016

A Structural Model of the Human α7 Nicotinic Receptor in an Open Conformation.

PLoS One 2015 24;10(7):e0133011. Epub 2015 Jul 24.

Department of Physics, University of Roma "La Sapienza", Rome, Italy; School of Physics, University College Dublin, Dublin, Ireland.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0133011PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4514475PMC
May 2016

Probabilistic Derivation of Spatiotemporal Correlation Functions in the Hydrodynamic Limit.

J Phys Chem B 2016 Mar 19;120(8):1996-2000. Epub 2016 Jan 19.

Dipartimento di Scienze Fisiche e Chimiche, University of L'Aquila , 67100 L'Aquila, Italy.

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http://dx.doi.org/10.1021/acs.jpcb.5b10066DOI Listing
March 2016

Spontaneous chiral symmetry breaking in collective active motion.

Phys Rev E 2016 Feb 18;93(2):022410. Epub 2016 Feb 18.

Max Planck Institute for Dynamics and Self-Organization (MPIDS), Am Fassberg 17, 37077 Göttingen, Germany.

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http://dx.doi.org/10.1103/PhysRevE.93.022410DOI Listing
February 2016

A semi-flexible model prediction for the polymerization force exerted by a living F-actin filament on a fixed wall.

J Chem Phys 2015 Oct;143(14):145101

Physics Department, Université Libre de Bruxelles (ULB), Campus Plaine, CP 223, B-1050 Brussels, Belgium.

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http://dx.doi.org/10.1063/1.4932162DOI Listing
October 2015

Clathrate structure-type recognition: Application to hydrate nucleation and crystallisation.

J Chem Phys 2015 Jun;142(24):244503

School of Physics, University College Dublin, Belfield, Dublin 4, Ireland.

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http://dx.doi.org/10.1063/1.4922696DOI Listing
June 2015

Maximum probability domains for the analysis of the microscopic structure of liquids.

J Chem Phys 2015 Feb;142(6):064117

UMR 8640 ENS-CNRS-UPMC, Département de Chimie, 24 rue Lhomond, École Normale Supérieure, 75005 Paris, France.

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http://dx.doi.org/10.1063/1.4907406DOI Listing
February 2015

Diagnostic ultrasound-guided excisional testicular biopsy for small (< 1 cm) incidental nodules. A single institution experience.

Arch Ital Urol Androl 2014 Dec 30;86(4):373-7. Epub 2014 Dec 30.

Surgery Dpt, Section of Urology, ASUR Marche Area Vasta 3, Macerata Hospital, Macerata.

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http://dx.doi.org/10.4081/aiua.2014.4.373DOI Listing
December 2014

Conformational changes in acetylcholine binding protein investigated by temperature accelerated molecular dynamics.

PLoS One 2014 13;9(2):e88555. Epub 2014 Feb 13.

School of Physics, University College Dublin, Dublin, Ireland ; Department of Physics, University of Roma "La Sapienza", Rome, Italy.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0088555PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3923797PMC
October 2014

Temperature-accelerated molecular dynamics gives insights into globular conformations sampled in the free state of the AC catalytic domain.

Proteins 2014 Oct 9;82(10):2483-96. Epub 2014 Jun 9.

Institut Pasteur and CNRS UMR 3528, rue du Dr Roux, Unité de Bioinformatique Structurale, 75015, Paris, France; Université Pierre et Marie Curie, Cellule Pasteur UPMC, rue du Dr Roux, 75015, Paris, France.

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http://dx.doi.org/10.1002/prot.24612DOI Listing
October 2014

Relaxation of a steep density gradient in a simple fluid: comparison between atomistic and continuum modeling.

J Chem Phys 2014 Oct;141(15):154107

Dipartimento di Fisica and CNISM, Università La Sapienza, P.le A. Moro 5, 00185 Rome, Italy.

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http://dx.doi.org/10.1063/1.4897977DOI Listing
October 2014

Exploring the Conformational Dynamics of Alanine Dipeptide in Solution Subjected to an External Electric Field: A Nonequilibrium Molecular Dynamics Simulation.

J Chem Theory Comput 2014 Apr 24;10(4):1376-86. Epub 2014 Mar 24.

Institute for Mathematics, Freie Universität Berlin , 14195 Berlin, Germany.

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http://dx.doi.org/10.1021/ct400993eDOI Listing
April 2014

Equilibrium and rate constants, and reaction mechanism of the HF dissociation in the HF(H2O)7 cluster by ab initio rare event simulations.

J Phys Chem A 2013 Dec 2;117(49):13039-50. Epub 2013 Dec 2.

School of Physics, Room 302 UCD-EMSC, University College Dublin , Belfield, Dublin 4, Dublin, Ireland.

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http://dx.doi.org/10.1021/jp406982hDOI Listing
December 2013

An observable for vacancy characterization and diffusion in crystals.

J Chem Phys 2013 Apr;138(14):144103

School of Physics, University College Dublin, Belfield, Dublin 4, Ireland.

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http://dx.doi.org/10.1063/1.4796322DOI Listing
April 2013

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

J Chem Phys 2013 Feb;138(5):054118

Department of Physics, University of Rome La Sapienza, Ple A. Moro 2, 00185 Rome, Italy.

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http://dx.doi.org/10.1063/1.4789760DOI Listing
February 2013

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

Phys Chem Chem Phys 2012 Nov 15;14(44):15458-63. Epub 2012 Oct 15.

Dipartimento di Fisica Università La Sapienza, P.le A. Moro 5, 00185 Roma, Italy.

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http://dx.doi.org/10.1039/c2cp42536jDOI Listing
November 2012

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

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

Dipartimento di Fisica, Università La Sapienza, Piazzale Aldo Moro 2, 00185 Roma, Italy.

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http://dx.doi.org/10.1039/c2nr30145hDOI Listing
April 2012

Multiphoton absorption of myoglobin-nitric oxide complex: relaxation by D-NEMD of a stationary state.

J Phys Chem B 2012 Mar 6;116(10):3397-410. Epub 2012 Mar 6.

School of Physics, University College Dublin, Dublin, Rep. of Ireland.

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http://dx.doi.org/10.1021/jp212148xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3319090PMC
March 2012

Hydrodynamics from statistical mechanics: combined dynamical-NEMD and conditional sampling to relax an interface between two immiscible liquids.

Phys Chem Chem Phys 2011 Aug 23;13(29):13177-81. Epub 2011 Jun 23.

Consorzio Interuniversitario per le Applicazioni di Supercalcolo Per Università e Ricerca (CASPUR), via dei Tizii 6, 00185 Roma, Italy.

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http://dx.doi.org/10.1039/c1cp20778dDOI Listing
August 2011

Short range hydrogen diffusion in Na3AlH6.

Phys Chem Chem Phys 2011 Jun 11;13(22):10546-55. Epub 2011 Apr 11.

Dipartimento di Fisica Università La Sapienza, P.le A. Moro 5, Roma, Italy.

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http://dx.doi.org/10.1039/c0cp02852eDOI Listing
June 2011

Temperature accelerated Monte Carlo (TAMC): a method for sampling the free energy surface of non-analytical collective variables.

Phys Chem Chem Phys 2011 Apr 21;13(13):5952-9. Epub 2011 Feb 21.

School of Physics, University College Dublin, Belfield, Dublin, Ireland.

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http://dx.doi.org/10.1039/c0cp01335hDOI Listing
April 2011

Infrared spectroscopy of small protonated water clusters at room temperature: an effective modes analysis.

J Chem Phys 2011 Feb;134(8):084302

Département de Chimie, Ecole Normale Supérieure, UMR CNRS-ENS-UPMC, Paris, France.

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http://dx.doi.org/10.1063/1.3533229DOI Listing
February 2011

Infrared spectroscopy and effective modes analysis of the protonated water dimer H+(H2O)2 at room temperature under H/D substitution.

J Chem Phys 2011 Feb;134(8):084303

Département de Chimie, Ecole Normale Supérieure, UMR CNRS-ENS-UPMC, Paris, France.

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http://dx.doi.org/10.1063/1.3521273DOI Listing
February 2011

Direct observation of the substitution effects on the hydrogen bridge dynamics in selected Schiff bases--a comparative molecular dynamics study.

J Chem Phys 2011 Jan;134(3):034308

Faculty of Chemistry, University of Wrocław, F. Joliot-Curie 14, 50-383 Wrocław, Poland.

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http://dx.doi.org/10.1063/1.3528721DOI Listing
January 2011

Hydration structure of the quaternary ammonium cations.

J Phys Chem B 2010 Nov 28;114(46):15018-28. Epub 2010 Oct 28.

Dipartimento di Scienze Biochimiche A. Rossi Fanelli, Università La Sapienza, Piazzale Aldo Moro 5, 00185 Roma, Italy.

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http://dx.doi.org/10.1021/jp106282wDOI Listing
November 2010

Communications: On the linear response of mechanical systems with constraints.

J Chem Phys 2010 Mar;132(11):111103

Institut für Mathematik, Freie Universität Berlin, 14195 Berlin, Germany.

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http://dx.doi.org/10.1063/1.3354126DOI Listing
March 2010

Molecular property investigations of an ortho-hydroxy Schiff base type compound with the first-principle molecular dynamics approach.

J Phys Chem B 2010 Jan;114(1):242-53

University of Wrocław, Faculty of Chemistry, 14 F. Joliot-Curie, 50-383 Wrocław, Poland.

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http://dx.doi.org/10.1021/jp903501mDOI Listing
January 2010

Mapping the network of pathways of CO diffusion in myoglobin.

J Am Chem Soc 2010 Jan;132(3):1010-7

Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois 60637, USA.

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http://dx.doi.org/10.1021/ja905671xDOI Listing
January 2010

Fast simulation of polymer chains.

J Chem Phys 2009 Apr;130(14):144101

Institut für Mathematik, Freie Universität Berlin, Arnimallee 6, 14195 Berlin, Germany.

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http://dx.doi.org/10.1063/1.3110603DOI Listing
April 2009

On the assumptions underlying milestoning.

J Chem Phys 2008 Nov;129(17):174102

Courant Institute of Mathematical Sciences, New York University, New York, New York 10012, USA.

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http://dx.doi.org/10.1063/1.2996509DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2646510PMC
November 2008

Bulk viscosity of the Lennard-Jones system at the triple point by dynamical nonequilibrium molecular dynamics.

Phys Rev E Stat Nonlin Soft Matter Phys 2008 Aug 29;78(2 Pt 1):021204. Epub 2008 Aug 29.

Department of Physics, University of Cagliari, Cittadella Universitaria, I-09042 Monserrato Ca, Italy.

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http://dx.doi.org/10.1103/PhysRevE.78.021204DOI Listing
August 2008

Trotter-based simulation of quantum-classical dynamics.

J Phys Chem B 2008 Jan 22;112(2):424-32. Epub 2007 Dec 22.

School of Physics, Trinity College Dublin, Dublin 2 and School of Physics, University College Dublin, Dublin 4, Ireland.

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http://dx.doi.org/10.1021/jp0761416DOI Listing
January 2008

Computing the acidity of liquids via ab initio molecular dynamics.

Chemphyschem 2007 Oct;8(14):2072-6

Université P. et M. Curie-Paris 6, Laboratoire LI2C-UMR CNRS 7612, case courrier 51, 4 Place Jussieu, 75252 Pariscedex05, France.

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http://dx.doi.org/10.1002/cphc.200700250DOI Listing
October 2007

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

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

Dipartimento di Fisica, Università La Sapienza, Piazzale Aldo Moro 2, 00185 Roma, Italy.

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http://dx.doi.org/10.1021/jp061725dDOI Listing
August 2006

String method in collective variables: minimum free energy paths and isocommittor surfaces.

J Chem Phys 2006 Jul;125(2):24106

Courant Institute of Mathematical Sciences, New York University, New York, NY 10012, USA.

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http://www.cims.nyu.edu/~eve2/string_coll_jcp.pdf
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http://scitation.aip.org/content/aip/journal/jcp/125/2/10.10
Publisher Site
http://dx.doi.org/10.1063/1.2212942DOI Listing
July 2006

The role of loop ZA and Pro371 in the function of yeast Gcn5p bromodomain revealed through molecular dynamics and experiment.

J Mol Recognit 2006 Jan-Feb;19(1):1-9

Commissariat à l'Energie Atomique, DSV-DBJC-SBFM, Centre d'Etudes Saclay, 91191 Gif-sur-Yvette Cedex, France.

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http://dx.doi.org/10.1002/jmr.748DOI Listing
February 2006

Blue moon sampling, vectorial reaction coordinates, and unbiased constrained dynamics.

Chemphyschem 2005 Sep;6(9):1809-14

INFM and Dipartimento di Fisica, Universitá di Roma La Sapienza, P. le A. Moro, 2, 00185 Roma, Italy.

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http://dx.doi.org/10.1002/cphc.200400669DOI Listing
September 2005

The inelastic hard dimer gas: a nonspherical model for granular matter.

J Chem Phys 2005 Apr;122(16):164505

Dipartimento di Fisica, Università di Camerino and Instituto Nazionale per la Fisica della Materia (INFM), Unità di Camerino, Via Madonna delle Carceri, I-62032, Camerino, Italy.

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http://dx.doi.org/10.1063/1.1884999DOI Listing
April 2005

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

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

Dipartimento di Fisica, Università "La Sapienza", Piazzale Aldo Moro, 2, 00185 Roma, Italy.

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http://dx.doi.org/10.1021/jp045208bDOI Listing
April 2005

Deterministic and stochastic algorithms for mechanical systems under constraints.

Philos Trans A Math Phys Eng Sci 2004 Aug;362(1821):1583-94

INFM and Dipartimento di Fisica, Università degli Studi di Roma La Sapienza, Piazzale Aldo Moro 5, 00185 Roma, Italy.

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http://dx.doi.org/10.1098/rsta.2004.1400DOI Listing
August 2004

Atomic mean-square displacements in proteins by molecular dynamics: a case for analysis of variance.

Biophys J 2004 May;86(5):2765-72

National Institute for the Physics of Matter and Physics Department, University of Rome, La Sapienza, 00185 Rome, Italy.

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http://linkinghub.elsevier.com/retrieve/pii/S000634950474330
Publisher Site
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1304147PMC
http://dx.doi.org/10.1016/S0006-3495(04)74330-1DOI Listing
May 2004