Full Text Journal Articles by
Author Giovanni Ciccotti

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

Sara Bonella, Alessandro Coretti, Rodolphe Vuilleumier, Giovanni Ciccotti,

In recent work [Coretti et al., J. Chem. Phys., 2018, 149, 191102], a new algorithm to solve numerically the dynamics of the shell model for polarization was presented. The approach, broadly applicable to systems involving adiabatically separated dynamical variables, employs constrained molecular dynamics to strictly enforce the condition that the ... Read more >>

Phys Chem Chem Phys (Physical chemistry chemical physics : PCCP)
[2020, 22(19):10775-10785]

Cited: 0 times

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Quantum Trajectories for the Dynamics in the Exact Factorization Framework: A Proof-of-Principle Test.

Francesco Talotta, Federica Agostini, Giovanni Ciccotti,

In the framework of the exact factorization of the time-dependent electron-nuclear wave function, we investigate the possibility of solving the nuclear time-dependent Schrödinger equation based on trajectories. The nuclear equation is separated in a Hamilton-Jacobi equation for the phase of the wave function, and a continuity equation for its (squared) ... Read more >>

J Phys Chem A (The journal of physical chemistry. A)
[2020, 124(34):6764-6777]

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

Ana Sofia F Oliveira, Christopher J Edsall, Christopher J Woods, Phil Bates, Gerardo Viedma Nunez, Susan Wonnacott, Isabel Bermudez, Giovanni Ciccotti, Timothy Gallagher, Richard B Sessions, Adrian J Mulholland,

Nicotinic acetylcholine receptors (nAChRs) modulate synaptic activity in the central nervous system. The α7 subtype, in particular, has attracted considerable interest in drug discovery as a target for several conditions, including Alzheimer's disease and schizophrenia. Identifying agonist-induced structural changes underlying nAChR activation is fundamentally important for understanding biological function and ... Read more >>

J Am Chem Soc (Journal of the American Chemical Society)
[2019, 141(51):19953-19958]

Cited: 1 time

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Ab initio accelerated molecular dynamics study of the hydride ligands in the ruthenium complex: Ru(H2)2H2(P(C5H9)3)2.

Marco Lauricella, Letizia Chiodo, Giovanni Ciccotti, Alberto Albinati,

The dihydrogen complex Ru(H2)2H2(P(C5H9)3)2 has been investigated, via ab initio accelerated molecular dynamics, to elucidate the H ligands dynamics and possible reaction paths for H2/H exchange. We have characterized the free energy landscape associated with the H atoms positional exchange around the Ru centre. From the free energy landscape, we ... Read more >>

Phys Chem Chem Phys (Physical chemistry chemical physics : PCCP)
[2019, 21(45):25247-25257]

Cited: 0 times

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

Gianpaolo Gobbo, Giovanni Ciccotti, Bernhardt L Trout,

A method to compute solubilities for molecular systems using atomistic simulations, based on an extension of the Einstein crystal method, has recently been presented [Li et al., J. Chem. Phys. 146, 214110 (2017)]. This methodology is particularly appealing to compute solubilities in cases of practical importance including, but not limited ... Read more >>

J Chem Phys (The Journal of chemical physics)
[2019, 150(20):201104]

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

Michael A Bellucci, Gianpaolo Gobbo, Tharanga K Wijethunga, Giovanni Ciccotti, Bernhardt L Trout,

Li and co-workers [Li et al., J. Chem. Phys. 146, 214110 (2017)] have recently proposed a methodology to compute the solubility of molecular compounds from first principles, using molecular dynamics simulations. We revise and further explore their methodology that was originally applied to naphthalene in water at low concentration. In ... Read more >>

J Chem Phys (The Journal of chemical physics)
[2019, 150(9):094107]

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Communication: Constrained molecular dynamics for polarizable models.

Alessandro Coretti, Sara Bonella, Giovanni Ciccotti,

A new algorithm to solve numerically the evolution of empirical shell models of polarizable systems is presented. It employs constrained molecular dynamics to satisfy exactly, at each time step, the crucial condition that the gradient of the potential with respect to the shell degrees of freedom is null. The algorithm ... Read more >>

J Chem Phys (The Journal of chemical physics)
[2018, 149(19):191102]

Cited: 0 times

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Nucleation of Molecular Crystals Driven by Relative Information Entropy.

Gianpaolo Gobbo, Michael A Bellucci, Gareth A Tribello, Giovanni Ciccotti, Bernhardt L Trout,

Simulating nucleation of molecular crystals is extremely challenging for all but the simplest cases. The challenge lies in formulating effective order parameters that are capable of driving the transition process. In recent years, order parameters based on molecular pair-functions have been successfully used in combination with enhanced sampling techniques to ... Read more >>

J Chem Theory Comput (Journal of chemical theory and computation)
[2018, 14(2):959-972]

Cited: 2 times

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

Sara Bonella, Alessandro Coretti, Lamberto Rondoni, Giovanni Ciccotti,

The time-reversal properties of charged systems in a constant external magnetic field are reconsidered in this paper. We show that the evolution equations of the system are invariant under a new symmetry operation that implies a new signature property for time-correlation functions under time reversal. We then show how these ... Read more >>

Phys Rev E (Physical review. E)
[2017, 96(1-1):012160]

Cited: 0 times

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

Sara Bonella, Mauro Ferrario, Giovanni Ciccotti,

Equilibrium and nonequilibrium molecular dynamics simulations are combined to compute the full set of coefficients that appear in the phenomenological equations describing thermal transport in a binary mixture subject to a constant thermal gradient. The Dynamical Non-Equilibrium Molecular Dynamics approach (D-NEMD) is employed to obtain the microscopic time evolution of ... Read more >>

Langmuir (Langmuir : the ACS journal of surfaces and colloids)
[2017, 33(42):11281-11290]

Cited: 1 time

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

Péter Koltai, Giovanni Ciccotti, Christof Schütte,

Unlike for systems in equilibrium, a straightforward definition of a metastable set in the non-stationary, non-equilibrium case may only be given case-by-case-and therefore it is not directly useful any more, in particular in cases where the slowest relaxation time scales are comparable to the time scales at which the external ... Read more >>

J Chem Phys (The Journal of chemical physics)
[2016, 145(17):174103]

Cited: 2 times

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

Alessia Perilli, Carlo Pierleoni, Giovanni Ciccotti, Jean-Paul Ryckaert,

We establish the statistical mechanics framework for a bundle of Nf living and uncrosslinked actin filaments in a supercritical solution of free monomers pressing against a mobile wall. The filaments are anchored normally to a fixed planar surface at one of their ends and, because of their limited flexibility, they ... Read more >>

J Chem Phys (The Journal of chemical physics)
[2016, 144(24):245102]

Cited: 1 time

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Probabilistic Derivation of Spatiotemporal Correlation Functions in the Hydrodynamic Limit.

Giovanni Ciccotti, Sara Bonella, Mauro Ferrario, Carlo Pierleoni,

In this paper, we use probability theory to prove in suitable conditions the equivalence of equilibrium time correlation functions of microscopic density fields with the time correlation functions of local macroscopic density fields evolved by hydrodynamics in (approximate) phenomenological continuum theories of matter. We further discuss a useful and rigorous ... Read more >>

J Phys Chem B (The journal of physical chemistry. B)
[2016, 120(8):1996-2000]

Cited: 0 times

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

Carlo Pierleoni, Giovanni Ciccotti, Jean-Paul Ryckaert,

We consider a single living semi-flexible filament with persistence length ℓp in chemical equilibrium with a solution of free monomers at fixed monomer chemical potential μ1 and fixed temperature T. While one end of the filament is chemically active with single monomer (de)polymerization steps, the other end is grafted normally ... Read more >>

J Chem Phys (The Journal of chemical physics)
[2015, 143(14):145101]

Cited: 3 times

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

Marco Lauricella, Simone Meloni, Shuai Liang, Niall J English, Peter G Kusalik, Giovanni Ciccotti,

For clathrate-hydrate polymorphic structure-type (sI versus sII), geometric recognition criteria have been developed and validated. These are applied to the study of the rich interplay and development of both sI and sII motifs in a variety of hydrate-nucleation events for methane and H2S hydrate studied by direct and enhanced-sampling molecular ... Read more >>

J Chem Phys (The Journal of chemical physics)
[2015, 142(24):244503]

Cited: 4 times

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

Meisam Pourali, Simone Meloni, Francesco Magaletti, Ali Maghari, Carlo Massimo Casciola, Giovanni Ciccotti,

We compare dynamical nonequilibrium molecular dynamics and continuum simulations of the dynamics of relaxation of a fluid system characterized by a non-uniform density profile. Results match quite well as long as the lengthscale of density nonuniformities are greater than the molecular scale (~10 times the molecular size). In presence of ... Read more >>

J Chem Phys (The Journal of chemical physics)
[2014, 141(15):154107]

Cited: 0 times

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Diagnostic and therapeutic utility of transrectal ultrasound in urological office prostatic abscess management: a short report from a single urologic center.

Andrea Fabiani, Alessandra Filosa, Valentina Maurelli, Fabrizio Fioretti, Lucilla Servi, Mara Piergallina, Giovanni Ciccotti, Matteo Tallè, Gabriele Mammana,

Prostatic abscess (PA) is an infrequent condition in the modern antibiotic era. The everyday use of transrectal ultrasound (TRUS) during diagnostic work-up and the widespread recurrence to prostatic biopsies may lead to an increase of PA diagnosis. In this short report we analyze the patients characteristics and the management of ... Read more >>

Arch Ital Urol Androl (Archivio italiano di urologia, andrologia : organo ufficiale [di] Societa italiana di ecografia urologica e nefrologica)
[2014, 86(4):344-348]

Cited: 1 time

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

Andrea Fabiani, Alessandra Filosa, Fabrizio Fioretti, Lucilla Servi, Mara Piergallina, Giovanni Ciccotti, Valentina Maurelli, Matteo Tallè, Gabriele Mammana,

The widespread use of scrotal ultrasound (SUS) has led to a marked increase in the number of incidentally detected testicular lesions. A small incidental nodule (STN) has defined as a non palpable (< 10 mm), asymptomatic solid lesion with normal levels of oncological testicular markers. Nowadays the lack of agreement ... Read more >>

Arch Ital Urol Androl (Archivio italiano di urologia, andrologia : organo ufficiale [di] Societa italiana di ecografia urologica e nefrologica)
[2014, 86(4):373-377]

Cited: 0 times

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

Han Wang, Christof Schütte, Giovanni Ciccotti, Luigi Delle Site,

In this paper, we investigate the conformational dynamics of alanine dipeptide under an external electric field by nonequilibrium molecular dynamics simulation. We consider the case of a constant and of an oscillatory field. In this context, we propose a procedure to implement the temperature control, which removes the irrelevant thermal ... Read more >>

J Chem Theory Comput (Journal of chemical theory and computation)
[2014, 10(4):1376-1386]

Cited: 4 times

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

Zeynab Mohammad Hosseini Naveh, Therese E Malliavin, Luca Maragliano, Grazia Cottone, Giovanni Ciccotti,

Despite the large number of studies available on nicotinic acetylcholine receptors, a complete account of the mechanistic aspects of their gating transition in response to ligand binding still remains elusive. As a first step toward dissecting the transition mechanism by accelerated sampling techniques, we study the ligand-induced conformational changes of ... Read more >>

PLoS ONE (PloS one)
[2014, 9(2):e88555]

Cited: 6 times

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

Edithe Selwa, Tru Huynh, Giovanni Ciccotti, Luca Maragliano, Thérèse E Malliavin,

The catalytic domain of the adenyl cyclase (AC) toxin from Bordetella pertussis is activated by interaction with calmodulin (CaM), resulting in cAMP overproduction in the infected cell. In the X-ray crystallographic structure of the complex between AC and the C terminal lobe of CaM, the toxin displays a markedly elongated ... Read more >>

Proteins (Proteins)
[2014, 82(10):2483-2496]

Cited: 9 times

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

Alin Marin Elena, Simone Meloni, Giovanni Ciccotti,

We perform restrained hybrid Monte Carlo (MC) simulations to compute the equilibrium constant of the dissociation reaction of HF in HF(H2O)7. We find that the HF is a stronger acid in the cluster than in the bulk, and its acidity is higher at lower T. The latter phenomenon has a ... Read more >>

J Phys Chem A (The journal of physical chemistry. A)
[2013, 117(49):13039-13050]

Cited: 3 times

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

Adolfo Poma, Michele Monteferrante, Sara Bonella, Giovanni Ciccotti,

The path integral single sweep method is used to assess quantum effects on the free energy barrier for hydrogen vacancy diffusion in a defective Na(3)AlH(6) crystal. This process has been investigated via experiments and simulations due to its potential relevance in the H release mechanism in sodium alanates, prototypical materials ... Read more >>

Phys Chem Chem Phys (Physical chemistry chemical physics : PCCP)
[2012, 14(44):15458-15463]

Cited: 1 time

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

Michele Monteferrante, Sara Bonella, Giovanni Ciccotti,

We apply the phase integration method for quasiclassical quantum time correlation functions [M. Monteferrante, S. Bonella, and G. Ciccotti, Mol. Phys. 109, 3015 (2011)] to compute the dynamic structure factor of liquid neon. So far the method had been tested only on model systems. By comparing our results for neon ... Read more >>

J Chem Phys (The Journal of chemical physics)
[2013, 138(5):054118]

Cited: 4 times

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

Wojtek Iwo Babiaczyk, Sara Bonella, Giovanni Ciccotti, Maria Laura Coluccio, Francesco Gentile, Enzo Di Fabrizio,

We present a study, via experiments and exploratory molecular dynamics simulations, of self aggregation in cylindrical nanostructures obtained experimentally by combining high resolution electron beam lithography with electroless silver deposition. This process is key to the fabrication of a nanolens device, where a strong surface enhancement can be exploited for ... Read more >>

Nanoscale (Nanoscale)
[2012, 4(7):2362-2371]

Cited: 1 time

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