Mauro FERRARIO - personale UniMoRe

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Mauro FERRARIO

Professore Ordinario
Dipartimento di Scienze Fisiche, Informatiche e Matematiche sede ex-Fisica

Pubblicazioni

2023 - Continuum mechanics from molecular dynamics via adiabatic time and length scale separation [Articolo su rivista]
Dicarlo, A; Bonella, S; Ferrario, M; Ciccotti, G
abstract

We show how to construct, by exploiting adiabatic time and length scale separation between atomistic and continuum mechanics, a multiscale scheme for continuum dynamics free from macroscopic constitutive modeling. To do so, we introduce a new set of degrees of freedom that simultaneously represent the macroscopic and the microscopic dynamics, based on a space tessellation. In this new formulation, the dynamics of the macroscopic fields steers the microscopic particle dynamics by producing the conditions under which they evolve and, concurrently, the particle dynamics drives the evolution of the macroscopic fields by providing them with atomistically based constitutive information. Under conditions of adiabatic separation both in time and length scales, it is possible to decimate the tessellating cells and let the macroscopic equations of motion be driven by the time average of the terms coupling them with the microscopic degrees of freedom.

2023 - Interaction of Water and Oxygen Molecules with Phosphorene: An Ab Initio Study [Articolo su rivista]
Benini, F.; Bassoli, N.; Restuccia, P.; Ferrario, M.; Righi, M. C.
abstract

Phosphorene, the 2D form of black phosphorus, has recently attracted interest for optoelectronic and tribological applications. However, its promising properties are affected by the strong tendency of the layers to oxidize in ambient conditions. A significant effort has been made to identify the role of oxygen and water in the oxidation process. In this work, we introduce a first-principles study of the phosphorene phase diagram and provide a quantitative estimate of the interaction of pristine and fully oxidized phosphorene layers with oxygen and water molecules. Specifically, we study oxidized layers with oxygen coverages of 25% and 50% that keep the typical anisotropic structure of the layers. We found that hydroxilated and hydrogenated phosphorene layers are both energetically unfavorable, leading to structural distortions. We also studied the water physisorption on both pristine and oxidized layers, finding that the adsorption energy gain doubled on the oxidized layers, whereas dissociative chemisorption was always energetically unfavorable. At the same time, further oxidation (i.e., the dissociative chemisorption of O (Formula presented.)) was always favorable, even on oxidized layers. Ab initio molecular dynamics simulations of water intercalated between sliding phosphorene layers showed that even under harsh tribological conditions water dissociation was not activated, thus further strengthening the results obtained from our static calculations. Overall, our results provide a quantitative description of the interaction of phosphorene with chemical species that are commonly found in ambient conditions at different concentrations. The phase diagram that we introduced confirms the tendency of phosphorene layers to fully oxidize due to the presence of O (Formula presented.), resulting in a material with improved hydrophilicity, a piece of information that is relevant for the application of phosphorene, e.g., as a solid lubricant. At the same time, the structural deformations found for the H- and OH- terminated layers undermine their electrical, mechanical, and tribological anisotropic properties and, therefore, the usage of phosphorene.

2023 - Prediction of aqueous solubility of a strongly soluble solute from molecular simulation [Articolo su rivista]
Carruthers, J.; Ferrario, M.; Anwar, J.
abstract

The prediction of solubilities of compounds by means of molecular simulation has been receiving increasing attention due to the key role played by solubility in countless applications. We have predicted the aqueous solubility of urea at 300 K from chemical potential calculations for two urea model combinations: ozpinar/TIP3P and Holzl/(TIP4P/2005). The methodology assumes that the intramolecular contribution of the urea molecule to the chemical potentials is identical in the crystal and in solution and, hence, cancels out. In parallel to the chemical potential calculations, we also performed direct coexistence simulations of a urea crystal slab in contact with urea-water solutions with the aim to identify upper and lower bounds to the solubility value using an independent route. The chemical potential approach yielded similar solubilities for both urea models, despite the actual chemical potential values showing a significant dependence on the force field. The predicted solubilities for the two models were 0.013-0.018 (ozpinar) and 0.008-0.012 (Holzl) mole fraction, which are an order of magnitude lower than the experimental solubility that lies in a range of 0.125-0.216 mole fraction. The direct coexistence solubility bounds were relatively wide and did not encompass the chemical potential based solubilities, although the latter were close to the lower bound values.

2022 - Adhesion, Friction and Tribochemical Reactions at the Diamond-Silica Interface [Articolo su rivista]
Cutini, M.; Forghieri, G.; Ferrario, M.; Righi, M. C.
abstract

2022 - Correction to: Molecular simulations: past, present, and future (a Topical Issue in EPJB) (The European Physical Journal B, (2022), 95, 1, (3), 10.1140/epjb/s10051-021-00249-x) [Articolo su rivista]
Ciccotti, G.; Dellago, C.; Ferrario, M.; Hernandez, E. R.; Tuckerman, M. E.
abstract

2022 - High-throughput generation of potential energy surfaces for solid interfaces [Articolo su rivista]
Wolloch, M.; Losi, G.; Chehaimi, O.; Yalcin, F.; Ferrario, M.; Righi, M. C.
abstract

A robust, modular, and ab initio high-throughput workflow is presented to automatically match and characterize solid–solid interfaces using density functional theory calculations with automatic error corrections. The potential energy surface of the interface is computed in a highly efficient manner, exploiting the high-symmetry points of the two mated surfaces. A database is automatically populated with results to ensure that already available data are not unnecessarily recomputed. Computational parameters and slab thicknesses are converged automatically to minimize computational cost while ensuring accurate results. The surfaces are matched according to user-specified maximal cross-section area and mismatches. Example results are presented as a proof of concept and to show the capabilities of our approach that will serve as the basis for many more interface studies.

2022 - Molecular simulations: past, present, and future (a Topical Issue in EPJB) [Articolo su rivista]
Ciccotti, G.; Dellago, C.; Ferrario, M.; Hernandez, E. R.; Tuckerman, M. E.
abstract

2021 - A new boundary driven NEMD scheme for heat and particle diffusion in binary mixtures [Articolo su rivista]
Templeton, C.; Elber, R.; Ferrario, M.; Ciccotti, G.
abstract

A new method for Boundary Driven Non-Equilibrium Molecular Dynamics (BD-NEMD) simulation is presented. It allows the simultaneous imposition of both a constant temperature and concentration gradient. By varying the strength of the imposed gradients and obtaining stationary values of the mass and energy flux, this new technique can be used to extract the Onsager transport coefficients directly. We demonstrate the setup and measure explicitly the Soret and Dufour effects for a binary mixture of Argon and Krypton. We compare the Soret coefficient computed using this new scheme against the experimentally inspired protocol where the system has no mass current. However, this method is limited to only an estimate of the Soret coefficient rendered inefficient due to the poor signal-to-noise ratio and cannot give the transport coefficients explicitly. The new technique allows for accurate measurements of non-zero flux values and, if run in the linear response domain, the full set of transport coefficients can be extracted directly. We also speculate about how this scheme could be applied to more complex systems with applications for polymer separations and biological activities.

2020 - Monitoring water and oxygen splitting at graphene edges and folds: Insights into the lubricity of graphitic materials [Articolo su rivista]
Restuccia, P.; Ferrario, M.; Righi, M. C.
abstract

The functionality of graphene as lubricant material is affected by extrinsic factors, such as the film thickness and the environmental conditions. Graphite lubricating capability depends as well on air humidity. To accurately describe the tribochemistry mechanisms underlying these behaviours we adopt a Quantum Mechanics/Molecular Mechanics approach. We show that reactive edges are able to cause a huge friction increase, which is quantified for graphene flakes between sliding diamond surfaces. Moreover, folds spontaneously formed in single layer graphene under tribological conditions are shown to be highly reactive due to carbon re-hybridization. This observation offers a new hint for interpreting the dependence of graphene friction on the number of layers. Both water and oxygen molecules are found to be effective in quenching the reactivity of defects by dissociative chemisorption. However, peculiar mechanisms of water molecules makes humidity more effective than oxygen for enabling the lubricity of graphitic media. They include collective processes as Grotthus-like proton diffusion enhanced by confinement, and the strong change in hydrophilic character of the passivated media. This comprehensive study sheds a new light on debated issues of graphene and graphite tribology, and highlights the potentiality of these materials for metal-free catalysis, e.g., for H production by water splitting.

2020 - Quantum Mechanics/Molecular Mechanics (QM/MM) applied to tribology: Real-time monitoring of tribochemical reactions of water at graphene edges [Articolo su rivista]
Restuccia, Paolo; Ferrario, Mauro; Righi, Maria Clelia
abstract

Tribological phenomena, such as wear and boundary lubrication, are deeply influenced by tribochemical re- actions, i.e., chemical reactions occurring in the presence of mechanical stresses. Atomistic descriptions of these processes are still in their infancies because of the high computational costs required to properly describe the buried sliding interface by theoretical methods. In this paper we outline the application of the Quantum Mechanics/Molecular Mechanics approach to simulate tribochemical reactions during sliding and show that it can accurately describe the tribochemistry of graphene interacting with water molecules, a system which is of relevance for technological applications. Comparison with ab initio (Car-Parrinello) and classical (using the ReaxFF force field) molecular dynamics calculations highlights the advantages of this hybrid approach both in terms of computational costs and accuracy of the results.

2019 - High-throughput screening of the static friction and ideal cleavage strength of solid interfaces [Articolo su rivista]
Wolloch, M.; Losi, G.; Ferrario, M.; Righi, M. C.
abstract

We present a comprehensive ab initio, high-throughput study of the frictional and cleavage strengths of interfaces of elemental crystals with different orientations. It is based on the detailed analysis of the adhesion energy as a function of lateral, γ(x, y), and perpendicular displacements, γ(z), with respect to the considered interface plane. We use the large amount of computed data to derive fundamental insight into the relation of the ideal strength of an interface plane with its adhesion. Moreover, the ratio between the frictional and cleavage strengths is provided as good indicator for the material failure mode – dislocation propagation versus crack nucleation. All raw and curated data are made available to be used as input parameters for continuum mechanic models, benchmarks, or further analysis.

2019 - Il metodo Monte Carlo di Metropolis (The Metropolis Monte Carlo method) [Articolo su rivista]
Ciccotti, Giovanni; Ferrario, Mauro
abstract

Monte Carlo method refers to a set of computational methods of ve- ry wide application in physics and in all disciplines needing intensive computa- tion. In this paper we present the Metropolis algorithm, introduced in 1953 by Rosenbluth and collaborators. It is the most powerful tool of Computational Theoretical Physics

2018 - Holonomic Constraints: A Case for Statistical Mechanics of Non-Hamiltonian Systems [Articolo su rivista]
Ciccotti, Giovanni; Ferrario, Mauro
abstract

A dynamical system submitted to holonomic constraints is Hamiltonian only if considered in the reduced phase space of its generalized coordinates and momenta, which need to be defined ad hoc in each particular case. However, specially in molecular simulations, where the number of degrees of freedom is exceedingly high, the representation in generalized coordinates is completely unsuitable, although conceptually unavoidable, to provide a rigorous description of its evolution and statistical properties. In this paper, we first review the state of the art of the numerical approach that defines the way to conserve exactly the constraint conditions (by an algorithm universally known as SHAKE) and permits integrating the equations of motion directly in the phase space of the natural Cartesian coordinates and momenta of the system. We then discuss in detail SHAKE numerical implementations in the notable cases of Verlet and velocity-Verlet algorithms. After discussing in the same framework how constraints modify the properties of the equilibrium ensemble, we show how, at the price of moving to a dynamical system no more (directly) Hamiltonian, it is possible to provide a direct interpretation of the dynamical system and so derive its Statistical Mechanics both at equilibrium and in non-equilibrium conditions. To achieve that, we generalize the statistical treatment to systems no longer conserving the phase space volume (equivalently, we introduce a non-Euclidean invariant measure in phase space) and derive a generalized Liouville equation describing the ensemble even out of equilibrium. As a result, we can extend the response theory of Kubo (linear and nonlinear) to systems subjected to constraints.

2018 - Ideal adhesive and shear strengths of solid interfaces: A high throughput ab initio approach [Articolo su rivista]
Restuccia, Paolo; Levita, Giacomo; Wolloch, Michael; Losi, Gabriele; Fatti, Giulio; Ferrario, Mauro; Righi, M. C.
abstract

We release a computational protocol to calculate two intrinsic tribological properties of solid interfaces from first principles, namely the adhesion energy, γ and the ideal interfacial shear strength, τ. These properties, which correspond to the energy required to separate two surfaces from contact and to the static friction force per unit area, respectively, are ruled by physical/chemical interactions between the surfaces in contact. First principles calculations based on Density Functional Theory (DFT) can accurately describe surface-surface interactions, offering the possibility to characterize the adhesive and shear strengths of materials in silico. We implemented the computational protocol as an AiiDA workflow (WF) that allows to obtain the γ and τ figures of merits in a high throughput manner. The software we produced uses a simple input file and most computational parameters determined automatically. To our best knowledge, this is the first time a high throughput approach has been used in tribology.

2018 - Molecular Dynamics vs. Stochastic Processes: Are We Heading Anywhere? [Articolo su rivista]
Ciccotti, Giovanni; Ferrario, Mauro; Schütte, Christof
abstract

Introduction for the Special Issue "Understanding Molecular Dynamics via Stochastic Processes"

2017 - Thermal Diffusion in Binary Mixtures: Transient Behavior and Transport Coefficients from Equilibrium and Nonequilibrium Molecular Dynamics [Articolo su rivista]
Bonella, Sara; Ferrario, Mauro; Ciccotti, Giovanni
abstract

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 the density and temperature fields, together with that of the mass and energy fluxes. D-NEMD enables one to study not only the steady state, but also the evolution of the fields during the transient that follows the onset of the thermal gradient, up to the establishment of the steady state. This makes it possible to ensure that the system has indeed reached a stationary condition, and to analyze the transient mechanisms and time scales of the mass and energy transport. A local time averaging procedure is applied to each trajectory contributing to the calculation to improve the signal-to-noise ratio in the estimation of the fluxes and to obtain a clear signal with the, relatively limited, statistics available.

2016 - First-Principle Molecular Dynamics of Sliding Diamond Surfaces: Tribochemical Reactions with Water and Load Effects [Articolo su rivista]
Righi, Maria Clelia; Zilibotti, Giovanna; Corni, Stefano; Ferrario, Mauro; Bertoni, Carlo Maria
abstract

Ab initio molecular dynamics offers an unexpected tool to understand many aspects of complex and macroscopic phenomena, like friction, lubrication, and surface passivation through chemical reactions induced by load and confinement, as found in recent works (Zilibotti et al., in Phys. Rev. Lett. 111:146101, 2013; De Barros Bouchet et al., J Phys Chem C 116:6966, 2012). Here we review the results of first-principle molecular dynamics simulations of diamond interfaces interacting with water molecules, at different concentrations. We found that the molecular confinement induced by the applied load promotes water dissociation. The consequent surface passivation prevents the formation of carbon bonds across the interface, reducing adhesion and friction. The possibility to extend the use of an atomistic approach to understand the kinetics of tribochemical reactions and their effects on friction will also be discussed.

2016 - Non-equilibrium by molecular dynamics: a dynamical approach [Articolo su rivista]
Ciccotti, Giovanni; Ferrario, Mauro
abstract

Some time ago, Ciccotti and Jacucci [Phys. Rev. Lett. 1975;35:789-792] – on the basis of Onsager regression hypothesis as explained by Kubo – suggested and implemented an original approach to study both stationary and time-dependent situations in non-equilibrium systems. The key idea of their approach was to tackle separately the dynamical evolution from the problem of sampling the initial condition. In this review, we discuss the evolution of this approach dubbed D-NEMD, the dynamical approach to non-equilibrium molecular dynamics, to differentiate it from the stationary NEMD methods. We will go through the D-NEMD theoretical framework and illustrate how it allows to compute time-dependent macroscopic dynamical behaviours by averaging on a large sample of non-equilibrium trajectories starting from an ensemble of initial conditions associated to a suitable distribution (either equilibrium or non-equilibrium) at time zero. We discuss a few case studies where the D-NEMD method is illustrated: first for ‘historical’ applications, like the study of transport properties in the linear and non-linear regimes, including a divertissement on the calculation of time correlation functions in the Gran Canonical ensemble. We finally briefly illustrate D-NEMD applications to the study of problems arising in key hydrodynamic processes such as the formation of convective cells and the relaxation of a non-uniform density profile in a fluid, giving attention to the problem of sampling the conditional probability density ensemble associated with the initial states.

2016 - On the configurational temperature Nosè-Hoover thermostat [Articolo su rivista]
Beckedahl, Derrick; Obaga, Emmanuel O.; Uken, Daniel A.; Sergi, Alessandro; Ferrario, Mauro
abstract

In this paper we reformulate the configurational temperature Nosé-Hoover thermostat of Braga and Travis (2005) by means of a quasi-Hamiltonian theory in phase space Sergi and Ferrario (2001). The quasi-Hamiltonian structure is exploited to introduce a hybrid configurational-kinetic temperature Nosé-Hoover chain thermostat that can achieve a uniform sampling of phase space (also for stiff harmonic systems), as illustrated by simulating the dynamics of one-dimensional harmonic and quartic oscillators. An integration algorithm, based on the symmetric Trotter decomposition of the propagator, is presented and tested against implicit geometric algorithms with a structure similar to the velocity and position Verlet. In order to obtain an explicit form for the symmetric Trotter propagator algorithm, in the case of non-harmonic and non-linear interaction potentials, a position-dependent harmonically approximated propagator is introduced. Such a propagator approximates the dynamics of the configurational degrees of freedom as if they were locally moving in a harmonic potential. The resulting approximated locally harmonic dynamics is tested with good results in the case of a one-dimensional quartic oscillator: The integration is stable and locally time-reversible. Instead, the implicit geometric integrator is stable and time-reversible globally (when convergence is achieved). We also verify the stability of the approximated explicit integrator for a three-dimensional N-particle system interacting through a soft Weeks-Chandler-Andersen potential.

2016 - On the establishment of thermal diffusion in binary Lennard-Jones liquids [Articolo su rivista]
Ferrario, Mauro; Bonella, S.; Ciccotti, G.
abstract

The establishment of thermal diffusion in an Ar-Kr Lennard-Jones mixture is investigated via dynamical non equilibrium molecular dynamics [G. Ciccotti, G. Jacucci, Phys. Rev. Lett. 35, 789 (1975)]. We observe, in particular, the evolution of the density and temperature fields of the system following the onset of the thermal gradient. In stationary conditions, we also compute the Soret coefficient of the mixture. This study confirms that dynamical non equilibrium molecular dynamics is an effective tool to gather information on transient phenomena, even though the full evolution of the mass and energy fluxes associated to the temperature and density fields requires, in this case, a more substantial numerical effort than the one employed here.

2016 - Probabilistic Derivation of Spatiotemporal Correlation Functions in the Hydrodynamic Limit [Articolo su rivista]
Ciccotti, Giovanni; Bonella, Sara; Ferrario, Mauro; Pierleoni, Carlo
abstract

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 numerical algorithm, derived from this framework, to compute macroscopic space- and time-dependent behaviors (such as the hydrodynamical one) via molecular dynamics simulations.

2016 - Size-dependent commensurability and its possible role in determining the frictional behavior of adsorbed systems [Articolo su rivista]
Restuccia, Paolo; Ferrario, Mauro; Sivestrelli, Pier Luigi; Mistura, Giampaolo; Righi, Maria Clelia
abstract

Recent nanofriction experiments of xenon on graphene revealed that the slip onset can be induced by increasing the adsorbate coverage above a critical value, which depends on temperature. Moreover, the xenon slippage on gold is much higher than on graphene in spite of the same physical nature of the interactions. To shed light on these intriguing results we have performed molecular dynamics simulations relying on ab initio derived potentials. By monitoring the interfacial structure factor as a function of coverage and temperature, we show that the key mechanism to interpret the observed frictional phenomena is the size-dependence of the island commensurability. The latter quantity is deeply affected also by the lattice misfit, which explains the different frictional behavior of Xe on graphene and gold.

2014 - Dynamical Non-Equilibrium Molecular Dynamics [Articolo su rivista]
Giovanni, Ciccotti; Ferrario, Mauro
abstract

In this review, we discuss the Dynamical approach to Non-Equilibrium Molecular Dynamics (D-NEMD), which extends stationary NEMD to time-dependent situations, be they responses or relaxations. Based on the original Onsager regression hypothesis, implemented in the nineteen-seventies by Ciccotti, Jacucci and MacDonald, the approach permits one to separate the problem of dynamical evolution from the problem of sampling the initial condition. D-NEMD provides the theoretical framework to compute time-dependent macroscopic dynamical behaviors by averaging on a large sample of non-equilibrium trajectories starting from an ensemble of initial conditions generated from a suitable (equilibrium or non-equilibrium) distribution at time zero. We also discuss how to generate a large class of initial distributions. The same approach applies also to the calculation of the rate constants of activated processes. The range of problems treatable by this method is illustrated by discussing applications to a few key hydrodynamic processes (the “classical” flow under shear, the formation of convective cells and the relaxation of an interface between two immiscible liquids).

2014 - Molecular Dynamics Simulation [Curatela]
Ciccotti, Giovanni; Ferrario, Mauro; Schuette, Christof
abstract

The contributions collected in this book move from the quantum-statistical description to the validity of classical modeling; they present some perspectives in the algorithmic and in the enhanced sampling approaches, tackling some longstanding challenges to simulation in the area of non-equilibrium, rare events, mesoscale and quantum-classical simulation. Initially, the book deals with the validity of molecular dynamics modeling, starting from the adiabatic hypothesis for the electronic ground state; the first contribution explores different descriptions of the potential energy surfaces one can use in a molecular dynamics simulation; the second analyzes in detail the Born-Oppenheimer schemes for ab initio MD within Kohn– Sham density functional theory, while the third one tackles the problem from the alternative perspective of a quantum Monte Carlo approach. The next contribution dwells on how to improve the statistical ensemble properties of time integrators for Langevin dynamics by including an acceptance–rejection scheme. The subject of free energy calculations by molecular dynamics is illustrated in the next two contributions, first with a presentation of alternative dynamical approaches for performing enhanced sampling by force biasing and temperature acceleration, then using non-equilibrium path sampling within the framework of Jarzynski identity and Crooks fluctuation theorem. The general ideas behind non-equilibrium molecular dynamics are the focus of the next two contributions, regarding calculation of dynamical responses and the application of Malliavin weight sampling to dynamical trajectories. Many of the same ideas are at the core of the study of rare, reactive, events by molecular dynamics as discussed in the next two contributions, more in general in the first and then with specific reference to the Markov state models approach. The last four invited contributions are dedicated to the problem of dealing with well separated space and time scales. First, the general philosophy of multiscale approaches and the related computational strategies within molecular dynamics are discussed in a concept paper, while the other three deals with specific non-adiabatic dynamical approaches for systems with a mixed quantum- classical description, based upon alternative approaches borrowing either from the Wigner transform representation or from the Bohmian formulation of quantum dynamics. The book is completed by the contributed papers to the molecular dynamics special issue.

2013 - Transient behavior of a model fluid under applied shear [Articolo su rivista]
D., Costa; A., Sergi; Ferrario, Mauro
abstract

We study the transient behavior of a model fluid composed by soft repulsive spheres subjected to a planar uniform shear. To this aim, we use a dynamical non-equilibrium molecular dynamics method originally developed by Ciccotti and Jacucci [Phys. Rev. Lett. 35, 789 (1975)10.1103/PhysRevLett.35.789] and recently applied to the study of the transient regimes in various fluid systems. We show that the dynamical method allows one to study the transient behavior of the viscous time-dependent response over a wide range of applied shear rates, provided that a temperature control is enforced on the system. In this study, we adopt in particular the configurational thermostat of Braga and Travis [J. Chem. Phys. 123, 134101 (2005)10.1063/1.2013227]. The initial behavior of the dynamical response to a θ-like perturbation is characterized by a rapid increase, culminating in a pronounced peak, later relaxing to a plateau value. The latter positively reproduces the values of the viscosity observed in standard steady-state non-equilibrium molecular dynamics.

2011 - Ab initio calculation of adhesion and potential corrugation of diamond (001) interfaces [Articolo su rivista]
Zilibotti, Giovanna; Ferrario, Mauro; Bertoni, Carlo Maria; Righi, Maria Clelia
abstract

The system consisting of two diamond (001) surfaces in contact was studied by means of plane-wave/pseudopotential density functional calculations. Different hydrogen coverages, ranging from fully hydrogenation to bare surfaces, were considered. The adhesion energy was calculated as a function of both the separation and the lateral displacement of the two surfaces. The effects of dangling carbon bonds on the adhesion and potential corrugation are quantitatively discussed.

2011 - Coarse-graining stiff bonds [Articolo su rivista]
P., Español; J. A., de la Torre; Ferrario, Mauro; G., Ciccotti
abstract

The method of constraints in molecular dynamics is useful because it avoids the resolution of high frequency motions with very small time steps. However, the price to pay is that both the dynamics and the statistics of a constrained system differ from those of the unconstrained one. Instead of using constraints, we propose to dispose of high frequency motions by a coarse-graining procedure in which fast variables are eliminated. These fast variables are thus modeled as friction and thermal fluctuations. We illustrate the methodology with a simple model case, a diatomic molecule in a monoatomic solvent, in which the bond between the atoms of a diatomic molecule is stiff. Although the example is very simple and does not display the interesting effects of “wrong” statistics of the constrained system (i.e. the well-known issue connected to the Fixman potential), it is well suited to give the proof of concept of the whole procedure.

2010 - Correction for Reguzzoni et al., Onset of frictional slip by domain nucleation in adsorbed monolayers [Abstract in Rivista]
Reguzzoni, M.; Ferrario, M.; Zapperi, S.; Righi, M. C.
abstract

2010 - Onset of frictional slip by domain nucleation in adsorbed monolayers [Articolo su rivista]
Reguzzoni, Marco; Ferrario, Mauro; Zapperi, Stefano; Righi, Maria Clelia
abstract

It has been known for centuries that a body in contact with a substrate will start to slide when the lateral force exceeds the static friction force. Yet the microscopic mechanisms ruling the crossover from static to dynamic friction are still the object of active research. Here, we analyze the onset of slip of a xenon (Xe) monolayer sliding on a copper (Cu) substrate. We consider thermal-activated creep under a small external lateral force, and observe that slip proceeds by the nucleation and growth of domains in the commensurate interface between the film and the substrate. We measure the activation energy for the nucleation process considering its dependence on the external force, the substrate corrugation, and particle interactions in the film. To understand the results, we use the classical theory of nucleation and compute analytically the activation energy which turns out to be in excellent agreement with numerical results. We discuss the relevance of our results to understand experiments on the sliding of adsorbed monolayers.

2009 - Ab initio study on the surface chemistry and nanotribological properties of passivated diamond surfaces [Articolo su rivista]
Zilibotti, G; Righi, Maria Clelia; Ferrario, Mauro
abstract

Experimental findings indicate that the impressively low friction and wear of diamond in humid environments are determined by the surface passivation. In this paper, we investigate the relationship between the surface chemistry and the nanotribological properties of diamond surfaces. We consider the (2x1)-C(001) surface taking into account different terminations constituted of hydrogen, oxygen, and hydroxyl groups. We analyze the adsorbate geometry and the polarization of the surface bonds. We discuss the stability of the different surface terminations in different conditions, which account for the presence in the environment of H-2, O-2, and H2O molecules in different concentrations and we present the surface phase diagram. Finally, we report the calculated adhesion energy between the passivated surfaces and analyze its variation as a function both of the surface separation and of the surface relative lateral position. In this way, we provide information on the effect of the different adsorbates on the interaction between diamond surfaces and on the magnitude and anisotropy of friction forces.

2008 - Boundary-lubricated friction in presence of a nano-well [Articolo su rivista]
Capozza, R; Fasolino, A; Vanossi, A; Ferrario, Mauro
abstract

The advantage of surface macro- and micro-scopic patterning has been recently proved for improving tribological performances of mechanical sliding contacts. The effects of scaling down the texturing dimensions to the nanoscale have not yet been investigated to a comparable extent. By means of classical Molecular Dynamics simulations, we show that the frictional behavior of a thin film in boundary-lubricated regime is significantly affected by the presence of nanoscale superficial patterning of the moving confining walls, leading to a significant suppression of the high dissipative stick-slip dynamics and a consequent friction reduction. We believe these findings to be relevant for nanotechnology applications.

2008 - Lubricated friction on nanopatterned surfaces via molecular dynamics simulations [Articolo su rivista]
Capozza, R; Fasolino, A; Ferrario, Mauro; Vanossi, A.
abstract

Recent studies have proved the usefulness of macroscopic surface patterning for the improvement of tribological performances of sliding contacts. Here we investigate the effects of scaling down the texturing dimensions to the nanoscale. By means of classical molecular dynamics simulations, we show that the sliding frictional properties of a thin lubricant film are significantly affected by the presence of nanoscale superficial patterning of the moving confining walls, leading to a "mitigation" of the so-called stick-slip regime and to a consequent reduction of friction. We believe these findings to be relevant for nanotechnology applications.

2007 - Condensed matter theory by computer simulation: from materials to chemical biology [Articolo su rivista]
Ferrario, Mauro; Ciccotti, G; Binder, K.
abstract

The role of computer simulation as the central and basic method of approach of condensed matter theory will become ever more important. An exciting challenge for many years to come is the goal is to develop simulation approaches for complex materials and biological matter that successfully bridge the gap from the small scales of electronic structure calculations to the mesoscopic scales of pattern formation in soft matter (where one uses coarse-grained simulation techniques such as dissipative particle dynamics, multiscale collision dynamics, etc.).

2007 - Nonlinear mobility of a driven system: Temperature and disorder effects [Articolo su rivista]
Guerra, R; Vanossi, A; Ferrario, Mauro
abstract

We consider the dissipative nonlinear dynamics of a model of interacting atoms driven over a substrate potential. The substrate parameters can be suitably tuned in order to introduce disorder effects starting from two geometrically opposed ideal cases: commensurate and incommensurate interfaces. The role of temperature is also investigated through the inclusion of a stochastic force via a Langevin molecular dynamics approach. Here, we focus on the most interesting tribological case of underdamped sliding dynamics. For different values of the chain stiffness, we evaluate the static friction threshold and consider the depinning transition mechanisms as a function of the applied driving force. As experimentally observed in QCM frictional measurements of adsorbed layers, we find that disorder operates differently depending on the starting geometrical configuration. For commensurate interfaces, randomness lowers considerably the chain depinning threshold. On the contrary, for incommensurate mating contacts, disorder favors static pinning destroying the possible frictionless (superlubric) sliding states. Interestingly, thermal and disorder effects strongly influence also the occurrence of parametric resonances inside the chain, capable of converting the kinetic energy of the center-of-mass motion into internal vibrational excitations. We comment on the nature of the different dynamical states and hysteresis (due to system bi-stability) observed at different increasing and decreasing strengths of the external force.

2007 - Potential energy surface for rare gases adsorbed on Cu(111): Parameterization of the gas/metal interaction potential [Articolo su rivista]
Righi, Maria Clelia; Ferrario, Mauro
abstract

We propose a model potential function to describe the interaction between rare-gas atoms and a metal surface with parameters derived on the basis of ab initio calculations. We discuss the merits of the proposed functional form for applications in molecular dynamics studies of nanotribology. © IOP Publishing Ltd.

2007 - Pressure Induced Friction Collapse of Rare Gas Boundary Layers Sliding over Metal Surfaces [Articolo su rivista]
Righi, Maria Clelia; Ferrario, Mauro
abstract

In this Letter we show that friction of anticorrugating systems can be dramatically decreased by applying an external load. The counterintuitive behavior that deviates from the macroscopic Amonton law is dictated by quantum mechanical effects that induce a transformation from anticorrugation to corrugation in the near-surface region. We describe the load-driven modifications occurring in the potential energy surface of different rare gas-metal adsorbate systems, namely, Ar, Kr, Xe on Cu(111), and Xe on Ag(111), and we calculate the consequent friction drop for the commensurate Xe/Cu system by means of combined ab initio and classical molecular dynamics simulations.

2006 - Computer Simulation in Condensed Matter: From Materials to Chemical Biology. Vol. 1 [Curatela]
Ferrario, Mauro; Ciccotti, G; Binder, K.
abstract

The school that was held at the Ettore Majorana Foundation and Center for Scientific Culture (EMFCSC), Erice (Sicily), in July 2005, aimed to provide an up-to-date overview of almost all technical advances of computer simulation in statistical mechanics, giving a fair glimpse of the domains of interesting appli- cations. Full details on the school programme and participants, plus some ad- ditional material, are available at its Web site, http://cscm2005.unimore.itComputer simulation is now a very well established and active field, and its applications are far too numerous and widespread to be covered in a single school lasting less than 2 weeks. Thus, a selection of topics was required, and it was decided to focus on perspectives in the celebration of the 65th birthday of Mike Klein, whose research has significantly pushed forward the frontiers of computer simulation applications in a broad range, from materials science to chemical biology. Prof. M. L. Klein (Dept. Chem., Univ. Pennsylvania, Philadelphia, USA) is internationally recognized as a pioneer in this field; he is the winner of both the prestigious Aneesur Rahman Prize for Computa- tional Physics awarded by the American Physical Society, and its European counterpart, the Berni J. Alder CECAM Prize, given jointly with the Euro- pean Physical Society. The festive session held on July 23rd, 2005, highlighting these achievements, has been a particular focus in this school. In the frame- work of the EMFCSC International School of Solid State Physics Series, the present school was the 34th course of its kind.However, this school can be considered as being the third (and perhaps last?) event in a series of comprehensive schools on computer simulation, 10 years after the COMO Euroconference on “Monte Carlo and Molecular Dy- namics of Condensed Matter systems,” and 20 years after the VARENNA Enrico Fermi Summer School on “Molecular Dynamics of Statistical Mechan- ical Systems.” Comparing the topics emphasized upon in these schools, both the progress in achieving pioneering applications to problems of increasing complexity, and the impressive number of new methodological developments are evident. While the focus of the Varenna School was mostly on Molecular Dynamics (MD) and its applications from simple to complex fluids, the Como school included both Monte Carlo (MC) simulations of lattice systems (from quantum problems to the advanced analysis of critical phenomena in classi- cal systems like the simple Ising model), and the density functional theory of electronic structure up to the Car-Parrinello ab initio Molecular Dynamics techniques (CPMD). At the Erice school, a new focus was put on the para- digma of “Multiscale Simulation”, i.e. the idea to combine different methods of simulation on different scales of length and time in a coherent fashion. This method allow us to clarify the properties of complex materials or biosystems where a single technique (like CPMD or MD or MC etc.) due to excessive needs of computer resources is bound to fail. Good examples presented at this school for such multiscale simulation approaches included MD studies of polymers coupled with a solvent, which is described only in a coarse-grained fashion by the lattice Boltzmann technique and hybrid quantum mechanical/molecular mechanics (QM/MM) methods for CPMD simulations of biomolecules, etc.As a second “leitmotif,” emphasis has been put on rapidly emerging novel simulation techniques. Techniques that have been dealt with at this school in- clude the methods of “transition path sampling” (i.e. a Monte Carlo sampling not intending to clarify the properties of a state in the space of thermodynamic variables, but the properties of the dominating paths that lead “in the course of a transition” from one stable state to another), density of state methods (like Wang-Landau sampling and multicanonical Monte Carlo, allowing an elegant assessment of free ener

2006 - Computer Simulation in Condensed Matter: From Materials to Chemical Biology. Vol. 2 [Curatela]
Ferrario, Mauro; Ciccotti, G; Binder, K.
abstract

.The school that was held at the Ettore Majorana Foundation and Center for Scientific Culture (EMFCSC), Erice (Sicily), in July 2005, aimed to provide an up-to-date overview of almost all technical advances of computer simulation in statistical mechanics, giving a fair glimpse of the domains of interesting appli- cations. Full details on the school programme and participants, plus some ad- ditional material, are available at its Web site, http://cscm2005.unimore.it Computer simulation is now a very well established and active field, and its applications are far too numerous and widespread to be covered in a single school lasting less than 2 weeks. Thus, a selection of topics was required, and it was decided to focus on perspectives in the celebration of the 65th birthday of Mike Klein, whose research has significantly pushed forward the frontiers of computer simulation applications in a broad range, from materials science to chemical biology. Prof. M. L. Klein (Dept. Chem., Univ. Pennsylvania, Philadelphia, USA) is internationally recognized as a pioneer in this field; he is the winner of both the prestigious Aneesur Rahman Prize for Computa- tional Physics awarded by the American Physical Society, and its European counterpart, the Berni J. Alder CECAM Prize, given jointly with the Euro- pean Physical Society. The festive session held on July 23rd, 2005, highlighting these achievements, has been a particular focus in this school. In the frame- work of the EMFCSC International School of Solid State Physics Series, the present school was the 34th course of its kind. However, this school can be considered as being the third (and perhaps last?) event in a series of comprehensive schools on computer simulation, 10 years after the COMO Euroconference on “Monte Carlo and Molecular Dy- namics of Condensed Matter systems,” and 20 years after the VARENNA Enrico Fermi Summer School on “Molecular Dynamics of Statistical Mechan- ical Systems.” Comparing the topics emphasized upon in these schools, both the progress in achieving pioneering applications to problems of increasing complexity, and the impressive number of new methodological developments are evident. While the focus of the Varenna School was mostly on Molecular Dynamics (MD) and its applications from simple to complex fluids, the Como school included both Monte Carlo (MC) simulations of lattice systems (from quantum problems to the advanced analysis of critical phenomena in classi- cal systems like the simple Ising model), and the density functional theory of electronic structure up to the Car-Parrinello ab initio Molecular Dynamics techniques (CPMD). At the Erice school, a new focus was put on the para- digma of “Multiscale Simulation”, i.e. the idea to combine different methods of simulation on different scales of length and time in a coherent fashion. This method allow us to clarify the properties of complex materials or biosystems where a single technique (like CPMD or MD or MC etc.) due to excessive needs of computer resources is bound to fail. Good examples presented at this school for such multiscale simulation approaches included MD studies of polymers coupled with a solvent, which is described only in a coarse-grained fashion by the lattice Boltzmann technique and hybrid quantum mechanical/molecular mechanics (QM/MM) methods for CPMD simulations of biomolecules, etc. As a second “leitmotif,” emphasis has been put on rapidly emerging novel simulation techniques. Techniques that have been dealt with at this school in- clude the methods of “transition path sampling” (i.e. a Monte Carlo sampling not intending to clarify the properties of a state in the space of thermodynamic variables, but the properties of the dominating paths that lead “in the course of a transition” from one stable state to another), density of state methods (like Wang-Landau sampling and multicanonical Monte Carlo, allowing an elegant assessment of free

2006 - Introduction: Condensed Matter Theory by Computer Simulation [Relazione in Atti di Convegno]
Ciccotti, G; Ferrario, Mauro; Binder, K.
abstract

Until about 50 years ago, condensed matter theory was in a very unsatisfactory status: although a formal framework for the theoretical description of the problems in terms of quantum and classical statistical mechanics did exist, a reliable set of tools, which would allow to make valuable predictions for static and dynamic properties and phenomena of most condensed-matter systems, was missing. This situation has changed fundamentally through the invention of computer simulation, which provides a different paradigm towards all these problems.

2006 - Partially folded states of HIV-1 protease: Molecular dynamics simulations and ligand binding [Articolo su rivista]
Cavallari, Manuela; C., Ghio; S., Monti; Ferrario, Mauro; A., Maritan; P., Carloni
abstract

All-atom molecular dynamics simulations were performed on partially folded states (with different secondary structure content) of the dimeric enzyme HIV-1 protease in aqueous solution. The calculations were based on previous simulations of the folding process of the protein based on a Go-model. The structures turn out to be stable, and the subunit-subunit contact surface is smaller than that of the native state. Interestingly, the flexibility of the partially folded states is similar to that observed for the monomer in the native state. The intersubunit contacts are formed by conserved residues, suggesting that these residues may play a role for the folding process. Docking a large set of molecules suggests that several ligands not yet associated to HIV-1 protease may bind to these partially unfolded structures. (c) 2006 Elsevier B.V. All rights reserved.

2005 - COMPUTER PHYSICS COMMUNICATIONS Proceedings of the Europhysics Conference on Computational Physics 2004 (CCP 2004) [Curatela]
Ferrario, Mauro; Melchionna, S; Pierleoni, C.
abstract

This volume contains the Proceedings of the Europhysics Conference on Computational Physics 2004, held in Genova, Italy, 1–4 September 2004.

2005 - Experimental and simulative dissociation of dimeric Cu, Zn superoxide dismutase doubly mutated at the intersubunit surface [Articolo su rivista]
L., Maragliano; M., Falconi; A., Sergi; P., Cioni; S., Castelli; A., Lania; M. E., Stroppolo; G., Strambini; Ferrario, Mauro; A., Desideri
abstract

The equilibrium properties of dimeric Photobacterium leiognathi Cu, Zn superoxide dismutase mutant bearing two negative charges in the amino acid clusters at the association interface has been studied, experimentally and computationally, and compared to those of the native enzyme. Pressure-dependent dissociation is observed for the mutant, as observed by the fluorescence shift of the unique tryptophan residue located at the intersubunit surface. The spectral shift occurs slowly, reaching a plateau after 15 - 20 min, and is fully reversible. Measurement of the degree of dissociation allows us to calculate the standard volume variation upon association and the dissociation constant at atmospheric pressure. On the other hand the native protein is undissociable at any pressure. In the simulative approach, the dissociation free energy has been calculated through the blue moon calculation method for the case of a multidimensional reaction coordinate, corrected for the rotational contribution within the semiclassical approximation for a free rigid-body rotor. The scheme permits to define a definite path for the rupture of the dimer and to calculate the effective force involved in the process. The calculated free energy difference is close to the experimental one, and the value obtained for the mutant is well below that obtained for the native protein, indicating that the theoretical reaction scheme is able to reproduce the experimental trend. Moreover, we find that, when the separation distance increases, the protein structure of the monomer is stable in line with the fast recovery of the original fluorescence properties after decompression, which excludes the presence of partly unfolded intermediates during the dimer-monomer transition.

2005 - Molecular dynamics simulations of the Trp repressor-DNA complex and the AV77 mutant [Articolo su rivista]
M., Cavallari; A., Desideri; M., Falconi; Ferrario, Mauro
abstract

Molecular dynamics simulations were performed on E. coli wild type (WT) Trp repressor and the AV77 mutant in interaction with DNA. Alanine to valine mutation at position 77 results in a repressor with enhanced activity at low concentrations of the L-Trp co-repressor. However, WT and AV77 mutant show an identical crystallographic structure, preventing to devise a clear structure-function correlation and suggesting that the different activity could be ascribed to a varied dynamical behavior. Root mean square deviations, dynamical cross correlation and hydrogen bond analysis have been performed to detect specific differences between the two repressor forms, showing that both ligand and DNA binding is different in the two complexes.

2005 - Proceedings of the Europhysics Conference on Computational Physics 2004 - CCP 2004 - Genova, Italy - September 1-4, 2004 - Preface [Relazione in Atti di Convegno]
Ferrario, Mauro; Melchionna, S; Pierleoni, C.
abstract

Preface to the Conference Proceedings

2004 - Blue moon approach to rare events [Articolo su rivista]
G., Ciccotti; Ferrario, Mauro
abstract

The Blue Moon ensemble is a computationally efficient molecular dynamics method to estimate the rate constants of rare activated events when the process can be described by a reaction coordinate xi(r), a well-defined function in configuration space. By means of holonomic constraints a number of values of (r) can be prescribed along the relevant path to identify the bottleneck region first and to sample an ensemble of starting conditions to generate activated trajectories. These MD trajectories sample phase space according to a biased configurational distribution. With a suitable re-weighting of averages from such ensemble of trajectories one can characterize completely rare events.

2004 - Effective binding force calculation in dimeric proteins [Articolo su rivista]
L., Maragliano; Ferrario, Mauro; G., Ciccotti
abstract

We apply the Blue Moon constrained Molecular Dynamics technique to study a particular case of molecular recognition, one of the main issues of modem molecular biology. We investigate the effects of mutation of interface residues on the binding strength of the dimeric protein superoxide dismutase from Photobacterium leiognathi. With our technique we produce a specific path describing the separation of the dimers and we calculate the effective mean force involved in the process. We apply the method to two mutants and compare the results with those obtained in an earlier calculation on the native enzyme. The method is sensitive to the mutations and allows us to establish a semi-quantitative hierarchy for the association strengths of the three enzymes.

2004 - Structure of NaCl and KCl concentrated aqueous solutions by ab initio molecular dynamics [Articolo su rivista]
M., Cavallari; C., Cavazzoni; Ferrario, Mauro
abstract

We compare the microscopic structure of concentrated aqueous solutions of sodium and potassium chloride obtained using different, rigid charge, intermolecular potentials with those calculated in ab initio simulations. We see that pair correlation functions provide a more severe test than simpler averages like thermodynamic properties, where positive and negative contributions can cancel out even large deviations. The potential models investigated here, in particular, do not provide a consistent picture of the structure of the solution, shedding some doubts on their use within simulation of biological systems.

2003 - A microscopic description of concentrated potassium fluoride aqueous solutions by molecular dynamics simulation [Articolo su rivista]
Y., Laudernet; T., Cartailler; P., Turq; Ferrario, Mauro
abstract

We describe the microscopic structure and dynamical properties of potassium fluoride aqueous solutions at T = 298 K as a function of concentration up to 11.9 M. All calculations are made using constant temperature and pressure as well as microcanonical molecular dynamics simulations on the basis of an optimized pair potential model which is a mix of Coulomb plus standard Lennard-Jones short-range terms for water and ion-water interactions and Tosi-Fumi potential for ion-ion interactions. In particular we propose a modified ion-water interaction that successfully reproduces the experimental behavior of the density and water self-diffusion of the solutions as a function of concentration. Finally, we analyze hydrogen-bonding in solutions looking at pair distribution energies and residence times. We find strong evidence for K+-F- pairing in solutions at the higher concentrations.

2003 - Constant pressure-constant temperature molecular dynamics: a correct constrained NPT ensemble using the molecular virial [Articolo su rivista]
Kalibaeva, G; Ferrario, Mauro; Ciccotti, G.
abstract

In the present work we introduce a simple, Nose-Hoover style isothermal-isobaric molecular dynamics method for systems with holonomic molecular constraints and the molecular representation of the virial. We prove, using the non-Hamiltonian dynamics approach, recently developed by Tuckerman et al. [1999, Europhys. Lett., 45, 149], that the phase space distribution, generated by our equations, samples the desired ensemble under all circumstances. We also write down the explicit reversible integrator for our equations. This integrator has been implemented in the last version of the DLProtein program.

2003 - Static and dynamic water molecules in Cu,Zn superoxide dismutase [Articolo su rivista]
M., Falconi; M., Brunelli; A., Pesce; Ferrario, Mauro; M., Bolognesi; A., Desideri
abstract

Understanding protein hydration is a crucial, and often underestimated issue, in unraveling protein function. Molecular dynamics (MD) computer simulation can provide a microscopic description of the water behavior. We have applied such a simulative approach to dimeric Photobacterium leiognathi Cu,Zn superoxide dismutase, comparing the water molecule sites determined using 1.0 ns MD simulation with those detected by X-ray crystallography. Of the water molecules detected by the two techniques, 20% fall at common sites. These are evenly distributed over the protein surface and located around crevices, which represent the preferred hydration sites. The water mean residence time, estimated by means of a survival probability function on a given protein hydration shell, is relatively short and increases for low accessibility sites constituted by polar atoms. Water molecules trapped in the dimeric protein intersubunit cavity, as identified in the crystal structure, display a trajectory mainly confined within the cavity. The simulation shows that these water molecules are characterized by relatively short residence times, because they continuously change from one site to another within the cavity, thus hinting at the absence of any relationship between spatial and temporal order for solvent molecules in proximity of protein surface.

2002 - Effective binding force calculation in a dimeric protein by molecular dynamics simulation [Articolo su rivista]
A., Sergi; G., Ciccotti; M., Falconi; A., Desideri; Ferrario, Mauro
abstract

A good example of macromolecular recognition is found in the interaction of the two monomers of the dimeric superoxide dismutase protein found in Photobacterium leiognathi. We have produced, by molecular dynamics simulation techniques, a specific path for the rupture of the dimer and calculated the effective force involved in the process by extending a well established free energy calculation scheme, the molecular dynamics blue moon approach to rare events. Within this picture we have generalized the approach to a vectorial reaction coordinate and performed a number of different simulations in function of the monomer-momomer separation, at fixed relative orientation. We find a deep minimum and we compute the height of the free energy barrier to break the dimer. As for the system characterization we have found that, when the separation distance increases, the protein structure is stable and the monomer-monomer interface is uniformly hydrated. Moreover, identifying the crucial contacts for the stabilization of the dimer, we have found the sequence of the different microscopic events in the monomer-monomer recognition and we have developed a view of the process which requires a merging of standard explanations, in agreement with the recent picture of recognition as a dynamical process mixing the various mechanisms previously considered [Kimura , Biophys. J. 80 635 (2001)].

2002 - Solubility of KF in water by molecular dynamics using the Kirkwood integration method [Articolo su rivista]
Ferrario, Mauro; G., Ciccotti; E., Spohr; T., Cartailler; P., Turq
abstract

We have studied the solubility of potassium fluoride in aqueous solution at near ambient condition, using a simple modeling for the ion and water interactions and computing the values of the chemical potential by molecular dynamics within the framework of Kirkwood generalized thermodynamic integration approach for the evaluation of free energy differences. We report the details of the procedure we used, which is based-at variance with previous attempts-on the individual determination of the chemical potential for the ions in solution. We explore a wide range of salt concentrations up to more than 25 M and determine the solubility. The agreement with the experimental value is reasonable, taking account of the rather crude model used.

2002 - Static and dynamic waters in Cu, Zn superoxide dismutase: Molecular dynamics simulation and x-ray experiment [Articolo su rivista]
Falconi, M; Brunelli, M; Pesce, A; Ferrario, M; Bolognesi, M; Desideri, A
abstract

2001 - Density Functional study of the photoactive yellow protein's chromophore [Articolo su rivista]
A., Sergi; M., Gruning; Ferrario, Mauro; F., Buda
abstract

We have investigated the structural and electronic properties of p-coumaric acid, the chromophore of the photoactive yellow protein (PYP), by means of first-principles molecular dynamics based on density functional theory (DFT). We have studied the chromophore both in the vacuum and in an extended model which includes the nearest residues in the binding pocket of PYP, as derived from crystallographic data. We have characterized the ground state of the isolated chromophore in its protonated and deprotonated forms and computed the energy barrier involved in the trans to cis isomerization process around the carbon-carbon double bond. A comparison of the optimized structures of the chromophore in the vacuum and in the extended protein model, both in the trans (ground state of PYP in the dark) and cis (first light-activated intermediate) configuration, shows how the protein environment affects the chromophore in the first step of the photocycle. Our model gives an energy storage of 25 kcal/mol associated with the trans-to-cia photoisomerization. Finally, we have elucidated the nature of the electronic excitation relevant for the photochemistry of PYP by means of time-dependent DFT calculations.

2001 - Dynamics-function correlation in Cu, Zn superoxide dismutase: A spectroscopic and molecular dynamics simulation study [Articolo su rivista]
M., Falconi; M. E., Stroppolo; P., Cioni; G., Strambini; A., Sergi; Ferrario, Mauro; A., Desideri
abstract

A single mutation (Val29 --> Gly) at the subunit interface of a Cu, Zn superoxide dismutase dimer leads to a twofold increase in the second order catalytic rate, when compared to the native enzyme, without causing any modification of the structure or the electric field distribution (Stroppolo et al., 2000). To check the role of dynamic processes in this catalytic enhancement, the flexibility of the dimeric protein at the subunit interface region has been probed by the phosphorescence and fluorescence properties of the unique tryptophan residue. Multiple spectroscopic data indicate that Trp83 experiences a very similar, and relatively hydrophobic, environment in both wild-type and mutant protein, whereas its mobility is distinctly more restrained in the latter. Molecular dynamics simulation confirms this result, and provides, at the molecular level, details of the dynamic change felt by tryptophan. Moreover, the simulation shows that the loops surrounding the active site are more flexible in the mutant than in the native enzyme, making the copper more accessible to the incoming substrate, and being thus responsible for the catalytic rate enhancement. Evidence for increased, dynamic copper accessibility also comes from faster copper removal in the mutant by a metal chelator, These results indicate that differences in dynamic, rather than structural, features of the two enzymes are responsible for the observed functional change.

2001 - Non-Hamiltonian equations of motion with a conserved energy [Articolo su rivista]
Sergi, A; FERRARIO, Mauro
abstract

In 1980 Andersen introduced the use of extended system as a means of exploring by molecular dynamics simulation the phase space of a physical model according to a desired ensemble distribution different from the standard microcanonical function. Following his original work on constant pressure-constant enthalpy a large number of different equations of motion, not directly derivable from a Hamiltonian, have been proposed in recent years, the most notable of which is the so-called Nose-Hoover formulation for canonical molecular dynamics simulation. Using a generalization of the symplectic form of the Hamilton equations of motion we show here that there is a unique general structure that underlies most, if not all the equations of motion for.,extended systems. We establish a unifying formalism that allows one to identify and separately control the conserved quantity, usually known as the total energy of the system, and the phase-space compressibility. Moreover, we define a standard procedure to construct conservative non-Hamiltonian flows that sample the phase space according to a chosen distribution function [Tuckerman et al., Europhys. Lett. 45, 149 (1999)]. To illustrate the formalism we derive new equations of motion for two example cases. First we modify the equations of motion of the Nose-Hoover thermostat applied to a one-dimensional harmonic oscillator, and we show how to overcome the ergodicity problem and obtain a canonical sampling of phase space without making recourse to additional degrees of freedom. Finally we recast an idea recently put forward by Marchi and Ballone [J, Chem. Phys. 110, 3697 (1999)] and derive a dynamical scheme for sampling phase space with arbitrary statistical biases, showing as an explicit application a demixing transition in a simple Lennard-Jones binary mixture.

2000 - Rare events by constrained molecular dynamics [Articolo su rivista]
G., Ciccotti; Ferrario, Mauro
abstract

We present a computationally efficient molecular dynamics method, based on holonomic constraints, devised to estimate the rate constants of rare activated events of short duration. We assume that the process is described by a reaction coordinate xi (r), a well-defined function in configuration space, and we constrain the system at the bottleneck region by prescribing the value of xi (r) MD trajectories sample phase space according to a biased configurational distribution and averages can be taken from such a new Blue Moon. ensemble, with suitable reweighting, to study rare events. (C) 2000 Elsevier Science B.V. All rights reserved.

2000 - Structure of phosphorus-selenium glasses: results from ab initio molecular dynamics simulations [Articolo su rivista]
A., Sergi; Ferrario, Mauro; F., Buda; Ir, Mcdonald
abstract

Car-Parrinello molecular dynamics calculations have been carried out for phosphorus-selenium mixtures of compositions corresponding to overall stoichiometries PSe and P2Se. Comparison of the calculated structure factors with those obtained in neutron scattering experiments suggests that the real materials are characterized by the presence of substantial numbers of well defined molecular units.

1999 - Reversible integrators for basic extended system molecular dynamics [Articolo su rivista]
A., Sergi; Ferrario, Mauro; D., Costa
abstract

Starting from a family of equations of motion for the dynamics of extended systems whose trajectories sample constant pressure and temperature ensemble distributions (Ferrario, M., 1993, in Computer Simulation in Chemical Physics, edited by M. P. Alien and D. J. Tildesley (Dordrecht: Kluwer)), explicit time reversible integration schemes are derived through a straightforward Trotter factorization of the dynamic Liouville propagator, along the lines first described by Tuckerman, M., Martyna, G. J., and Berne, B. J., 1992, J. chem. Phys., 97, 1990. The original Andersen's constant-pressure dynamics are recovered in the limit of zero coupling with the Nose thermostat. Reversible integration schemes are derived as a generalization of the velocity Verlet algorithm, with direct handling of the velocity dependent forces in such a way that both predictions and relative iterative corrections are not required. For the sake of clarity both the, equations of motion and the Trotter factorization are kept to the basic level. The proposed structure can accommodate easily, when needed, complications such as multiple timesteps and more effective thermostats (Nose-Hoover-chain). Finally, an application is made to a model molecular system subjected to holonomic constraints by means of the SHAKE algorithm. In the constant pressure case it is no longer possible to avoid using a prediction for the constraint contribution to the volume acceleration; however, recourse to a minimal iteration scheme still achieves excellent overall behaviour for the proposed integration algorithm, with no perceptible difference from the unconstrained case.

1998 - Interaction of Cl-2 molecules with GaAs(110) surface [Articolo su rivista]
A., Marcellini; C. A., Pignedoli; Ferrario, Mauro; Bertoni, Carlo Maria
abstract

We present ab-initio molecular dynamics calculations for the chemisorption of Cl on GaAs(110), to study the adsorption sites and the presentation of surface order at the early stages of adsorption. We simulated the impact of a single Cl-2 molecule on the surface using a (2 x 2) surface cell and the repeated slab geometry. Along the dynamical path dissociation occurs, bonds are created between Cl and the atoms of Ga and As and local quenching of the buckling relaxation is found. The dynamical results are compared with the optimization geometries obtained by allowing the two Cl atoms to adsorb on Ga and As. The adsorption on both sites is the most stable arrangement. Disorder effects are seen in the dynamics. (C) 1998 Elsevier Science B.V. All rights reserved.

1997 - Long-time tails in two-dimensional fluids by molecular dynamics [Articolo su rivista]
Ferrario, Mauro; A., Fiorino; G., Ciccotti
abstract

We report on molecular dynamics simulation of long-time tails in the velocity and stress autocorrelation functions of a dense two-dimensional fluid. Large systems of the order of hundred thousand particles have been investigated, performing canonical averages over an ensemble of trajectories generated on a parallel computer. We find the well-known t(-1) decay for the velocity autocorrelation function at two different densities of the;fluid, together with a faster than linear time dependence for the mean-square displacement at long times. Although there are indications of an asymptotically faster decay, the data are not precise enough to discriminate whether the decay is in agreement with the (t root 1n t)(-1) prediction of consistent mode-coupling theory or it is due to finite size effects. No evidence, within the statistical errors, is found for a long-time tail in the stress autocorrelation function. This finding is in agreement with recent NEMD results [Hoover et al., Phys. Rev. E 51 (1995) 273; Gravina et al., Phys. Rev. E 52 (1995) 6123], who find an analytical dependence of the shear viscosity upon the shear rate with no evidence for divergence in the Green-Kubo value.

1996 - First-principles simulation of phosphorus-selenium systems [Articolo su rivista]
A., Sergi; Ferrario, Mauro; F., Buda; Ir, Mcdonald
abstract

Car-Parrinello molecular dynamics calculations have been carried out for a single P4Se3 molecule and for an amorphous system of 72 atoms of overall stoichiometry P2Se. A systematic study has been made of the effects of variation in the basis set energy cutoff on the calculated bond lengths and vibrational frequencies of the isolated molecule. We find that when a sufficiently large cutoff is used the calculated values are in good agreement with experiment. The simulation of the amorphous system was initiated from a configuration consisting of eight P4Se3 molecules and 16 added phosphorus atoms, prepared by a classical molecular dynamics calculation. After a total of approximately 10 ps Car-Parrinello simulation, only two molecules remained intact, but a variety of other partly ordered local structures were generated, including rings of phosphorus atoms and distorted versions of the P4Se3 molecule in which bonds between basal phosphorus atoms had broken.

1996 - Molecular dynamics simulation of rare events: Calculation of rate constants [Relazione in Atti di Convegno]
G., Ciccotti; Ferrario, Mauro
abstract

We present a computationally efficient molecular dynamics method based on holonomic constraints devised to estimate the rate constants of rare activated events of short duration.We assume that the process is described by a reaction coordinate $ \xi(r)$, a well-defined function in configuration space, and we constrain the system at the ``bottleneck" region by prescribing the value of $ \xi(r)$. MD trajectories sample now phase space according to a biased configurational distribution and averages can be taken from such a new, {\it Blue Moon }, ensemble with suitable reweighting to study rare events. Applications are not restricted to classical processes and ways to extend the method to quantum activated processes in condensed phases are also outlined.

1995 - Cation Transport in Lithium Sulphate Based Crystals [Articolo su rivista]
Ferrario, Mauro; Klein, M. L.; Mcdonald, I. R.
abstract

Molecular dynamics simulations have been carried out of the fast-ion-conducting solid phases of lithium sulphate (Li2SO4), sodium-doped Li2SO4 and lithium sodium sulphate (LiNaSO4). An interionic potential model has been developed which provides a good fit to the experimental pressures, sound velocities, neutron structure factors and cation diffusion coefficients. The static distribution of the mobile cations is discussed in terms of the occupancy of interstitial sites and of anion-cation coordination. It is shown that the cations are almost invariably bonded to one and often to two oxygen atoms of neighbouring sulphate groups. The latter therefore play an essential role in the cation diffusion mechanism. The diffusion coefficients are partitioned in a way that makes it possible to identify separately the contributions from centre-of-mass displacements and rotations of the sulphate groups. It is concluded that the diffusion coefficient of Li+ is enhanced by up to approximately 50% by anion reorientation and that of Na+ by approximately 30%. The near equality of the diffusion coefficients of Li+ and Na+ in both doped Li2SO4 and LiNaSO4 is shown to arise as a balance between mass and size effects; the implications of this for related systems are noted.

1995 - Molecular dynamics study of the plastic-crystalline phase transition of tetraphosphorus triselenide [Articolo su rivista]
Alessandro, Sergi; Ferrario, Mauro; Stephen, Elliott; Ian, Mcdonald
abstract

A seven-site atom-atom potential model has been developed to describe the interactions between tetraphosphorus triselenide (P 4 Se 3 ) molecules. When used in molecular dynamics calculations the model predicts a transition to an orientationally disordered phase at a temperature close to that of the experimentally observed disordering transition. The predicted melting temperature of the model also is in good agreement with experiment. Below the transition, reorientation of the P 4 Se 3 molecules is of purely librational character. Above the transition, the molecules rotate about all three principal axes, but end-over-end rotation of the molecule is favoured relative to spinning motion around the threefold axis; the rotation becomes more isotropic as the temperature increases. Orientational disordering is shown to be accompanied by a transition to a hexagonal-close-packed structure. The positions and intensities of lines in the X-ray scattering pattern of the model system suggest that the structure of the disordered phase is the same as that of a previously uncharacterized plastic-crystalline modification already studied experimentally by Blachnik and Wickel. The work points to the need for further X-ray or neutron scattering studies of the high-temperature solid phases

1994 - Activation free energy for proton transfer in solution [Articolo su rivista]
Daniel, Laria; Giovanni, Ciccotti; Ferrario, Mauro; Raymond, Kapral
abstract

Path integral molecular dynamics methods are employed to compute the free energy for proton transfer reactions for strongly hydrogen bonded systems in a polar solvent. The free energy profile is calculated using several different techniques, including: integration of the mean force acting on the proton path with its centroid constrained at different values, the integral form of the free energy calculation in the constrained-reaction-coordinate-dynamics ensemble and direct simulation of the unconstrained dynamics. The results show that estimates of the free energy barrier obtained by harmonic extrapolation are likely to be in error. Both quantum and classical results for the free energy are obtained and compared with simulations using adiabatic quantum dynamics. Comparison of the quantum and classical results show that there are quantum corrections to the solvent contributions to the free energy.

1994 - Quantum effects on the solvent contribution to the activation free energy [Articolo su rivista]
Ferrario, Mauro; Daniel, Laria; Giovanni, Ciccotti; Raymond, Kapral
abstract

Quantum effects on the activation free energy for the transfer of a quantum particle between two ions immersed in a classical dipolar solvent are investigated. The bare potential for the quantum particle-ion complex has an intrinsic barrier that is negligible compared to k(B)T and corresponds to a strongly hydrogen bonded system if the quantum particle is a proton. In this circumstance the activation free energy is dominated by solvent contributions. We compare the solvent free energies along the reaction coordinate for a classical particle with charge +1, a proton and a muon. The quantum calculations are carried out using Feynman's path integral methods. The smaller mass of the muon gives rise to enhanced quantum effects and allows one to probe the effects of the dispersion of the charge density of the particle undergoing transfer on the solvent contribution to the free energy.

1994 - Simulation of superoxide-superoxide dismutase association rate for six natural variants. Comparison with the experimental catalytic rate [Articolo su rivista]
Alessandro, Sergi; Ferrario, Mauro; Fabio, Polticelli; Peter, O'Neill; Alessandro, Desideri
abstract

A Brownian dynamics simulation method has been implemented to study the superoxide-superoxide dismutase association reaction. Electrostatic potential and forces are calculated solving the linearized finite difference Poisson-Boltzmann equation. The accuracy of the algorithm has been tested carrying out simulations at different ionic strength values on bovine Cu,Zn superoxide dismutase (SOD), whose three-dimensional structure is known at 2 Angstrom resolution, and comparing the calculated association rates with the experimentally determined catalytic rates. Application of the algorithm to six Cu,Zn SOD variants shows that simulations well reproduce the experimental catalytic rate and demonstrates that the diffusion of the superoxide anion to the active site copper is the rate-Limiting step in the catalytic process of Cu,Zn superoxide dismutase.

1994 - Structural fluctuations and the order-disorder phase transition in calcite [Articolo su rivista]
Ferrario, Mauro; R. M., Lynden Bell; I. R., Mcdonald
abstract

Molecular-dynamics calculations have been carried out on the ordered (low-temperature) and orientationally disordered (high-temperature) phases of calcite. The potential model used is shown to reproduce the main features of the experimentally observed order-disorder transition. The significance of the results for the interpretation of recent inelastic neutron-scattering experiments is discussed with particular reference to a possible competition between different ordering processes. Comparison is made with previously reported simulations of the corresponding phase transition in sodium nitrate and differences in behaviour between the two systems are noted.

1993 - Dynamical behavior of the azide ion in protic solvents [Articolo su rivista]
Ferrario, Mauro; Michael L., Klein; Ian R., Mcdonald
abstract

Molecular dynamics calculations based on rigid molecules have been used to study the solvation structure and dynamics of an azide ion in methanol and water. The ion is found to have either five to six methanols or six to seven waters in its solvation cage. The calculated reorientation time, TR, is longer in methanol than in water by a factor of two to three and is sensitive to the assumed charge distribution of the ion. The results of the simulations are discussed in the light of recent measurement of TR and of the energy relaxation and dephasing times for the asymmetric stretching vibration of N−3 in protic solvents.

1993 - SCIENTIFIC VISUALIZATION, A USER VIEW [Relazione in Atti di Convegno]
Ferrario, Mauro
abstract

Virtually all comprehension in science, technology, and even art,calls on our ability to visualize. The ability to visualize is almost synonymous with understanding. Modern science goes beyond isolated theories, and demands computer simulation to understand real-world situations. Scientific Visualization - a set of software tools coupled with a powerful 3D graphical computer environment -is the eyes through which simulations are viewed. From today post-processing of data to future tracking and steering of simulations,Scientific Visualization has become an essential part of the research process for the computational scientist.

1993 - Simulation of site-site soft-core liquid crystal models [Articolo su rivista]
Gaia, Paolini; Giovanni, Ciccotti; Ferrario, Mauro
abstract

Suggested mechanisms responsible for liquid-crystalline ordering include non-spherical excluded volume effects, anisotropic attraction forces and flexibility. It has been shown using hard-core models that non-spherical excluded volume effects are the essential factor and can qualitatively explain the phenomenology of the problem. However, the simulation of hard-core models is technically demanding. A simpler and more direct alternative is to use a model with a soft-core site-site potential. We employ here a system of molecules composed of a few (11) atoms, constrained to form a multilinear molecule, and in mutual interaction via a continuous repulsive site-site potential of the form r -12 . Our results show that such a model is capable of exhibiting nematic and smectic liquid-crystal phases.

1993 - Statistical geometry of hard particles on a sphere: analysis of defects at high density [Articolo su rivista]
S., Prestipino Giarritta; Ferrario, Mauro; P. V., Giaquinta
abstract

We analyse the geometry of the solid phase shaped by densely packed hard calottes on a sphere. We show that in this phase topological defects are not distributed at random over the surface but segregate into clusters that give rise to an upper level of organization in the form of a superstructure with icosahedral symmetry.

1993 - THERMODYNAMIC CONSTRAINTS [Relazione in Atti di Convegno]
Ferrario, Mauro
abstract

In theoretical developments, thermodynamic constraints are introduced by putting the system of interest in contact with some other virtually infinite system, the `reservoir', with a coupling vanishingly small in the thermodynamic limit. Neither ofthese `infinite' conditions can be reproduced in molecular dynamics simulations where the time evolution of an isolated system with a finite number of degrees of freedom is numerically integrated, producing trajectories representative of the microcanonical ensemble. Several ways have been proposed to overcome this limitation. Here the case of MD simulations at constant temperature and/or pressure will be treated within the extended system framework introduced by Andersen in his1980 seminal paper, and later generalised mainly by Nos\'e.The $N$-particle physical system of interest is put in contact with externalreservoirs, which are, in contrast to theoretical infinite ones, represented just bya few degrees of freedom. The equations of motion for the extended system are chosenin such a way that the dynamical trajectory in the phase space of the system ofinterest is representative of the desired ensemble. Moreover the coupling isnon-linear yielding good ergodic properties and can be chosen to be weak enough to leavethe dynamical properties of the system of interest unaltered.

1992 - Molecular-dynamics study of adiabatic proton-transfer reactions in solution [Articolo su rivista]
Laria, D.; Ciccotti, G.; Ferrario, M.; Kapral, R.
abstract

A molecular-dynamics study of adiabatic proton transfer between two ions in a polar solvent is presented. The proton is treated as a quantum particle in three dimensions and the polar solvent is composed of classical rigid, dipolar molecules. The coupled Schrödinger and Newton's equations are solved to determine the proton charge density and solvent configuration. The rate coefficient for the proton transfer is computed from correlation function expressions and corrections to transition-state theory due to recrossing of a free-energy barrier are determined. The simulation results are compared with a simple two-state model. © 1992 American Institute of Physics.

1992 - Solvent-solute hydrogen bonding in dilute solutions of CN - and CH 3 CN in water and methanol [Articolo su rivista]
Ferrario, Mauro; Ian, Mcdonald; Martyn C. R., Symons
abstract

Molecular-dynamics calculations have been carried out for dilute solutions of CN- and CH3CN in water and methanol at a temperature of 300 K. Results are reported for the numbers, energy distributions and lifetimes of hydrogen-bonded solute-solvent pairs. The numbers of bonds formed to methanol (c. 5.2 for CN-, 0.5 for CH3CN) are found to be fewer in number than those formed to water (c. 6.3 for CN-, 1.8 for CH3CN), but the lifetimes of the bonds in methanol are longer by factors of approximately three (for CN-) or eight (for CH3CN) than those in water. In the case of CN-, bonding to the nitrogen atom is favoured both in water and in methanol, and there is also evidence for the formation of short-lived, bifurcated structures. The results for CN- in solution present a more consistent pattern than those for CH3CN, and it is concluded that the description in terms of hydrogen bonding is less appropriate for the molecule than for the ion. However, the results for both solute species are in satisfactory overall agreement with those obtained experimentally by spectroscopic methods.

1992 - Statistical geometry of hard particles on a sphere [Articolo su rivista]
S., Prestipino Giarritta; Ferrario, Mauro; P. V., Giaquinta
abstract

We present a Monte Carlo study of a two-dimensional system of hard particles embedded on the surface of a sphere. Thermodynamic and structural evidence of an ordering phase transition is found at high densities in spite of the frustration induced on the hexagonal covering by the peculiar topology of the host surface. The nature of this transition is analyzed and contrasted with the fluid-solid transition occuring in a flat geometry.

1991 - Activation energies by molecular dynamics with constraints [Articolo su rivista]
Emanuele, Paci; Giovanni, Ciccotti; Ferrario, Mauro; Raymond, Kapral
abstract

Recently Tobias and Broods introduced a method to compute by molecular dynamics with constraints the probability density P(≈r) = < δ(r − ≈r) &>; associated with rate values≈r of a spatial coordinate r. In this Letter we extend their approach to the case of a general reaction coordinate ξ(r), an arbitrary function of the configuration-space coordinates. The generalized version is shown to be the integral form of the free energy calculation in the constrained-reaction-coordinate ensemble where the mean force is computed as an average in a ξ-constrained ensemble. The two approaches are shown to be of equal computational efficiency for a very simple Lennard-Jones test case.

1991 - ORIENTATIONAL DISORDER AND STRUCTURAL PHASE-TRANSITIONS IN PLASTIC MOLECULAR-CRYSTALS [Relazione in Atti di Convegno]
Ferrario, Mauro
abstract

Order-Disorder phase transition in molecular systems, such as structural phase transformations in molecular solids or nematic-isotropic transitions in liquid crystals, can be studied in details by means of constant pressure-constant temperature molecular dynamics computer simulation. A number of microscopically defined order parameters can be computed in order to describe the transitions within the framework of Landau theory. Simulation allows to study in details the orientational motion and the diffuse scattering observed in neutron and X-ray scattering experiments in the high temperature orientationally disordered solid phases, and to quantify the role of the translation-rotation coupling in the ordering process. Strong coupling, when present, may be held responsible for the appearance of metastable phases on cooling of the disordered system. In these cases it is possible to show that the mechanism of phase transition can be completely controlled by pre-ordering processes in the disordered phase.

1991 - Shear-rate dependence of the viscosity of the Lennard-Jones liquid at the triple point [Articolo su rivista]
Ferrario, Mauro; Ciccotti, G.; Holian, B. L.; Ryckaert, J. P.
abstract

High-precision molecular-dynamics (MD) data are reported for the shear viscosity eta of the Lennard-Jones liquid at its triple point, as a function of the shear rate epsilon for a large system (N = 2048). The Green-Kubo (GK) value eta(epsilon = 0) = 3.24 +/- 0.04 is estimated from a run of 3.6 x 10(6) steps (40 nsec). We find no numerical evidence of a t-3/2 long-time tail for the GK integrand (stress-stress time-correlation function). From our nonequilibrium MD results, obtained both at small and large values of epsilon, a consistent picture emerges that supports an analytical (quadratic at low shear rate) dependence of the viscosity on epsilon.

1990 - Dynamics of ion pair interconversion in a polar solvent [Articolo su rivista]
Ciccotti, G.; Ferrario, Mauro; Hynes, J. T.; Kapral, R.
abstract

The reaction rate and mechanism of the interconversion between a contact ion pair and solvent separated ion pair in model polar solvents is investigated by molecular dynamics (MD) simulation. The full rate constant for the model reaction is estimated from the product of the transition state theory (TST) rate constant, determined from the potential of mean force between the ions in an equilibrium solvent, and the transmission coefficient, which depends on the details of the dynamics. The collective character of the solvent motion in the reaction barrier crossing is examined in some detail, and the important role of solvent dynamics in causing the reaction rate to markedly deviate from the TST rate is discussed. The MD results are compared with the predictions of Kramers and Grote–Hynes theories.

1990 - Molecular Dynamics simulation of aqueous mixtures: Methanol, acetone and ammonia [Articolo su rivista]
Ferrario, Mauro; Haughney, M.; Mcdonald, I. R.; Klein, M. L.
abstract

Effective pair‐potential models, parametrized to the properties of the pure liquids, have been used in molecular‐dynamics simulations of aqueous (binary) mixtures containing methanol, ammonia, or acetone. Results are reported for thermodynamic and structural properties, self‐diffusion coefficients, and reorientational correlation times. There is fair agreement with a wide variety of experimental data. The pattern of hydrogen bonding and the distribution of hydrogen‐bond lifetimes in the simulated mixtures have been investigated. The observed anomalous behavior of methanol and acetone solutions appears to be related to specific features of the hydrogen bonding—namely, the ability of these molecules to exhibit enhanced acceptor character. As a consequence of the assumed intermolecular potentials, the balance between the competing effects of hydrophobic hydration of methyl groups and hydrogen bonding to oxygen atoms is tipped towards the latter. A number of interesting structural effects have been noted. In particular, the distribution function g(R) for water oxygen atoms sharpens appreciably on addition of the second component. The structure of the water–ammonia system is discussed in detail. There is good accord with available x‐ray data at low concentration, but there are no measurements available to test the predictions at high concentration.

1989 - A molecular dynamics study of orientational disordering in crystalline sodium nitrate [Articolo su rivista]
R. M., Lynden Bell; Ferrario, Mauro; I. R., Mcdonald; E., Salje
abstract

Molecular dynamics computer simulations have been made of the ordered low-temperature and orientationally disordered high-temperature phases of crystalline sodium nitrate. The interionic force model used in the simulations is based on a rigid-ion representation of the electrostatic interactions, supplemented by a set of atom-atom potentials of the Buckingham type. Five simulations have been carried out, covering the temperature range from 293 to 570 K. Where possible, detailed comparison is made with experiment, and generally satisfactory agreement is found. Anion disorder is shown to consist primarily in reorientation about an axis parallel to the crystallographic c direction, but only at the highest temperature studied can the motion be described as that of a free, quasi-two-dimensional rotor. The spectra of translational and librational lattice modes have been compared and the way in which these change with temperature is discussed in terms of translational-rotation coupling. Numerical estimates are presented of the degree of correlation between translations and rotations at different points in the Brillouin zone, and possible ordering processes are identified. The diffuse scattering predicted by the model is analysed in detail and related to the results of X-ray and neutron scattering experiments. It is suggested that in the high-temperature phase there exist two major ordering processes and that the competition between the two results in the experimentally observed critical exponent for the macroscopic order parameter being significantly less than its classical value. The same argument is formulated on the basis of a Landau-type expression for the free energy. Although the simulation have been limited to the specific case of sodium nitrate, the results should also be helpful in understanding the nature of the corresponding phase transition in calcite.

1989 - Constrained molecular dynamics and the mean potential for an ion pair in a polar solvent [Articolo su rivista]
Giovanni, Ciccotti; Ferrario, Mauro; James T., Hynes; Raymond, Kapral
abstract

A constrained molecular dynamics (MD) method for the calculation of the potential of mean force is described, and applied to study the solvent-separated and contact ion pair equilibrium in a polar solvent. The method uses holonomic constraints on the MD to fix ion pair internuclear separation. The average force exerted on the ions by the solvent is computed as a function of ion separation, and the potential of mean force follows from an integration of the mean force. The ion pair mean potential, the reaction equilibrium constant and the solvent structure in the vicinity of the ions are examined for two model solvents with differing molecular dipole moments. The relevance of this study for the dynamics of the contact ion pair-solvent separated ion pair reaction is pointed out.

1989 - Diffusion effects of hydrogen bond fluctuations. I. The long time regime of the translational and rotational diffusion of water [Articolo su rivista]
Davide, Bertolini; Mario, Cassettari; Ferrario, Mauro; Paolo, Grigolini; Giuseppe, Salvetti; Alessandro, Tani
abstract

A theoretical scheme to evaluate the long‐time effects of hydrogen bond fluctuations on water dynamics is carefully reexamined in the light of recent experimental results of quasi-elastic neutron scattering (QENS). A molecular dynamics computer simulation is also carried out on a fairly large (343 TIP4P molecules) sample and for a total time of ≈100 ps. at three temperatures. The length of the runs has allowed to obtain good results for a number of properties. Also the temperature dependence of the static dielectric constant agrees with the experimental data. Further, some crucial predictions of our theoretical model have been carefully checked. The prediction on the deviation from Fick’s law is found to be in a satisfactory accord with the results of our computer simulation. The reasons for the less satisfactory agreement with the low‐temperature results of QENS are discussed.

1989 - Molecular dynamics simulation of electron-transfer reactions in solution [Articolo su rivista]
Dominic A., Zichi; Giovanni, Ciccotti; James T., Hynes; Ferrario, Mauro
abstract

Molecular dynamics simulation results are presented for model electronically adiabatic electron-transfer reactions in a model polar solvent. Transmission coefficients K characterizing the departure of the rates from the Marcus theory predictions are determined, and theoretical approaches to predicting K in terms of solvent dynamics are examined.

1988 - Molecular dynamics simulation of ion association reactions in a polar solvent [Articolo su rivista]
Giovanni, Ciccotti; Ferrario, Mauro; James T., Hynes; Raymond, Kapral
abstract

Ion-pair association reactions in solution are studied by molecular dynamics with a simple model of dipolar solvent. The results are analyzed in terms of potential energy barriers, reactive trajectories and solvent dynamics

1988 - Molecular dynamics study of a sodium octanoate micelle in aqueous solution [Articolo su rivista]
Kyoko, Watanabe; Ferrario, Mauro; Michael L., Klein
abstract

The structure of a sodium octanoate micelle, consisting of 15 monomers in aqueous solution, has been studied by molecular dynamics calculations. The micelle was found to be stable over the length of the simulation (0.2 ns). The overall size and net charge of the micelle are both in excellent accord with experimental deductions. Micellization yields an increased proportion of trans conformations in the alkyl chains. The results of our simulation of the micelle and solvent appear to offer support for studies based on more simplified models.

1988 - Spectroscopic and molecular dynamics studies of solvation of cyanomethane and cyanide ions [Capitolo/Saggio]
Graham, Eaton; Anthony S., Pena Nuñez; Martyn C. R., Symons; Ferrario, Mauro; Ian R., Mcdonald
abstract

Infrared (C—N stretch) and n.m.r (13^C,14^N) methods have been used to probe the solvation of MeCN molecules and CN– ions in water,methanol and a range of mixed protic-aprotic media. For MeCN,the i.r. results are unusual in that protic solvents induce a high-frequency shift in νmax(CN),whereas dipolar aprotic solvents give a low-frequency shift. The interpretation given of this is that both σ- and π-electron interactions play an important role in hydrogen-bond formation,whereas π interactions are dominant for dipolar solvents such as Me2SO. The 13^C(CN) shifts are too small to give useful information,but the 14^N shifts correlate well with the i.r. results. It is argued that in methanolic solution MeCN forms only one hydrogen bond and that ca. 50% of the molecules are not hydrogen bonded. In water,all MeCN molecules are hydrogen bonded. The results do not distinguish between mono- and di-bonding,but other evidence suggests that di-bonding is likely to occur. Similar experiments on CN– ions show again that protic solvents induce a high-frequency shift. Mixed-solvent studies suggest that at least four methanol or water molecules are normally hydrogen bonded to the ions; this is in accord with other spectroscopic results on the same solvents. The experiments have been complemented by a series of molecular dynamics simulations on dilute solutions of MeCN and CN– in water and methanol. The predicted solvation numbers from the simulations are in good agreement with those derived from the experimental data,particularly for MeCN. There are some discrepancies for CN–,but these may in part be attributable to difficulties involved in finding an acceptable definition of solvation number in cases where this quantity is large.

1987 - A molecular dynamics study of the rotator phase of t-butyl bromide [Articolo su rivista]
Ferrario, Mauro; Michael L., Klein; Ruth M., Lynden Bell; Ian R., Mcdonald
abstract

Molecular dynamics calculations are reported for the cubic plastic-crystal phase of t-butyl bromide. An intermolecular potential model has been constructed that yields a stable rotator phase, reasonable thermodynamic properties and a neutron structure factor in fair accord with experimental observations. The calculated orientational distribution functions show that the C—Br and C—Me bonds align preferentially along the (110) crystal axes and avoid the (111) directions; there is only a small difference between these two distributions. The fluctuations in collective orientational parameters and their relation to the transition to an ordered phase are discussed in terms of a generalised Landau model. We find that the primary order parameters are probably certain L= 3 variables, suggesting that the ordering process is analogous to that in carbon tetrabromide, rather than to that found in t-butyl cyanide.

1987 - Molecular-dynamics simulation of liquid methanol [Articolo su rivista]
Michael, Haughney; Ferrario, Mauro; Ian R., Mcdonald
abstract

Four recently proposed intermolecular-potential models have been used in molecular-dynamics simulations of liquid methanol over a temperature range of approximately70K. Results are reported for thermodynamic and structural properties, self-diffusion coefficients, and reorientational correlation times. Two of the models are shown to give results in fair agreement with a wide variety of experimental data. The pattern of hydrogen bonding and the distribution of hydrogen-bond lifetimes in the simulated liquids have been investigated. The structure in each case is found to be dominated by winding chains, in agreement with earlier work. For the more realistic models, the mean hydrogen-bond lifetime at room temperature is approximately 1 to 2 ps, which is several times larger than the corresponding time for liquid water.

1987 - Structural Transition on Cooling of Plastic Adamantane: A Molecular-Dynamics Study [Articolo su rivista]
Giovanni, Ciccotti; Ferrario, Mauro; Elisabetta, Memeo; Madeleine, Meyer
abstract

The new molecular-dynamics methods of Andersen and others have been used to study the structural phase transition that occurs in solid adamantane. While the transition between ordered and plastic-crystal phases is spontaneous on heating, cooling leads to metastable structures. The transition to the ordered phase can, however, be induced by extension to the complete molecular-dynamics sample of the short-range orientational correlations characteristic of the high-temperature phase.

1987 - Structure of solid t-butyl cyanide: a study by means of constant-temperature, constant-pressure, molecular dynamics simulation [Articolo su rivista]
Ferrario, Mauro; Klein, M. L.; Mcdonald, I. R.
abstract

The structural phase transition that occurs in solid t‐butyl cyanide just before melting has been studied by constant‐temperature, constant‐pressure, molecular‐dynamics simulations. The simulations were based on a six‐site potential model with parameters obtained from static‐energy calculations for the observed, low‐temperature, monoclinic structure. Changes in the lattice constants and in order parameters for the molecular orientations show that an apparently first‐order transition to a tetragonal, orientationally disordered phase occurs at a temperature in the range between 250 and 275 K; experimentally, a similar transition is observed at 233 K. Comparison is made with neutron‐scattering results for the tetragonal phase, and deficiencies in the potential model and in the model used to parametrize it are discussed.

1986 - Anion ordering in alkali cyanide crystals [Articolo su rivista]
Ferrario, Mauro; Ian R., Mcdonald; Michael L., Klein
abstract

Further molecular dynamics calculations have been carried out on sodium, potassium, and rubidium cyanides in their orientationally disordered cubic (Fm3m) phase. Simple, computationally efficient, rigid ion potentials are found to account for the overall range of static and dynamic properties. However, minor but systematic variations are required in the anion charge distribution. These changes mean that the charge distribution becomes more spherical as the size of the cation increases.

1985 - A molecular dynamics study of the TIP4P model of water [Articolo su rivista]
Ferrario, Mauro; A., Tani
abstract

Molecular dynamics calculations with a simple of 343 molecules are reported for the TIP4P model of water at the three temperatures −30.25 and 75°C. Structural and dynamical properties of this model are discussed in relation to experiment and other simulation results.

1985 - Constant pressure-constant temperature molecular dynamics for rigid and partially rigid molecular systems [Articolo su rivista]
Ferrario, Mauro; J. P., Ryckaert
abstract

The method of molecular dynamics at fixed pressure and/or temperature is adapted to rigid or partly rigid molecular systems with geometrical constraints using the cartesian coordinate approach. Both isotropic and anisotropic volume fluctuations, allowing for shape variation, are considered. The simulation of a benzene crystal at zero pressure and various temperatures is given as an illustration.

1985 - Pair interactions and hydrogen-bond networks in models of liquid methanol [Articolo su rivista]
Michael, Haughney; Ferrario, Mauro; Ian R., Mcdonald
abstract

A simple pair potential is developed for use in molecular-dynamics simulations of liquid methanol and shown to give results in good agreement with experiment for a variety of properties. The calculations suggest that the degree of hydrogen bonding in the liquid is greater than has previously been supposed. The bonds persist for times that are an order of magnitude longer than those recorded in simulations of liquid water.

1985 - Structure of solid t‐butyl cyanide: Interpretation of experimental data by means of molecular dynamics simulation [Articolo su rivista]
Ferrario, Mauro; Ian R., Mcdonald; Michael L., Klein
abstract

Molecular dynamics calculations have been carried out on the disordered phase I of solid t‐butyl cyanide. The nature of the orientational disorder has been investigated using a variety of intermolecular potentials based on site–site interactions between rigid molecules. The potentials were parametrized, in part, to the properties of the low‐temperature, monoclinic phase II. In phase I, rotation around the C–C≡N axis is found to occur on a picosecond time scale, in good agreement with deductions based on neutron scattering data. No evidence has been obtained for preferred orientations for the molecular symmetry axis. The intensities of Bragg and diffuse scattering have been calculated and compare favorably with neutron scattering results. The lattice vibrations have been investigated and it is found that the transverse acoustic phonons are heavily damped, at least for those wave vectors accessible in the simulations.

1984 - Hydrogen bond statistics and dynamics in water: Self‐diffusion and dielectric relaxation [Articolo su rivista]
Davide, Bertolini; Mario, Cassettari; Ferrario, Mauro; Giuseppe, Salvetti; Paolo, Grigolini
abstract

Dynamical properties of water up to the supercooled region are analyzed by explicitly taking into account the dynamics of the hydrogen bonds. The H‐bond dynamics is described by means of a stochastic variable η exploring different states according to the number of H bonds established by the tagged molecule with its neighbors. Application of the ‘‘reduced’’ model theory leads to a master equation for the long‐time diffusional properties of water, depending only on meaningful physical quantities that are obtained either from experiments and computer simulations or on the ground of physical considerations. Dielectric relaxation and self‐diffusion behaviors are successfully reproduced and also recent results from incoherent neutron scattering can be rationalized.

1984 - Non-linear effects in rotational dynamics in the liquid state [Articolo su rivista]
Ferrario, Mauro; Paolo, Grigolini; Marco, Leoncini; Lucio, Pardi; Alessandro, Tani
abstract

Through general theoretical considerations, based only on the Markoffian assumption, it is shown that equilibrium non-gaussian properties can be used to predict how the decay of excited states deviates from a linear response theory behaviour. To check this prediction, a computer experiment on a ‘two-dimensional liquid’ of discs interacting via a Lennard-Jones plus electric dipole potential is carried out. The results obtained for both equilibrium and excited correlation functions confirm completely the intimate relation between equilibrium non-gaussian properties and excitation behaviour.Via approximate analytical expressions and exact solutions, it is also shown that a non-linear version of the popular itinerant oscillator provides the same equilibrium non-gaussian properties and, in consequence of that, the same kind of deviation from linear response as the two-dimensional system.

1983 - A “microscopic” model for the dynamics of water [Articolo su rivista]
Davide, Bertolini; Mario, Cassettari; Ferrario, Mauro; Giuseppe, Salvetti; Paolo, Grigolini
abstract

A “reduced” model for the dipolar relaxation of water taking hydrogen-bond dynamics into account is built up. Via proper diffusional assumptions this leads us to study dielectric relaxation in terms of some relevant statistical properties of the hydrogen bond. The resulting relationship is shown to fit well with experiment. This approach is argued to be especially suitable for effectively using information from computer simulation so as to make it possible to explore the short-time region.

1983 - Non-Gaussian effects in the computer simulation of dichloro methane [Articolo su rivista]
Ferrario, Mauro; P., Marin; P., Grigolini; M. W., Evans
abstract

It has recently been suggested that non-linearity implies that the statistics governing the transient behaviour of translational correlation functions of the motion cannot be Gaussian. A computer simulation of CH2Cl2 under EMLG pilot project conditions shows that rotational as well as translational motion exhibits strong dynamical non-Gaussian features. It is shown that these effects cannot be ascribed to the non-linear drift appearing in the Markoffian version of the Euler-Langevin equation. This strongly supports an investigation line based on the research of a hidden non-linear dissipation coupling.

1983 - The structure of liquid benzene [Articolo su rivista]
M., Claessens; Ferrario, Mauro; J. P., Ryckaert
abstract

Molecular dynamics simulation of liquid benzene is exploited to test the degree of sensitivity of the local structure to the intermolecular potential. Three effective potential models (based on a six Lennard-Jones centres potential) are investigated. The usually admitted picture of a liquid with quasi-crystalline short range molecular arrangement is shown to be very doubtful.Analysis of the crystalline structure predicted by the different interaction potentials indicates a manifest superiority of the only model including a point quadrupole at the centre of the benzene ring.

1982 - Computer simulation of dichloromethane. II. Molecular dynamics [Articolo su rivista]
Ferrario, Mauro; Myron W., Evans
abstract

The technique of computer simulation is used to compute some molecular dynamical properties of liquid CH2CL2. The results are compared with experimental data from a variety of spectral sources, and emphasize the importance of keeping to an accurate representation of the shape of CH2 CL2 through a five-atom Lennard-Jones potential. The nature of the interaction between a tagged molecule and its thermal bath gives rise to non -gaussian statistics in the interval t = O to a few picoseconds. The same source is responsible for rotation-translation coupling, clearly observable in the moving frame of reference defined by the three principal moment of inertia axes of the asymmetric top CH2CL2

1982 - Computer simulation of the generalized brownian motion. II. An argon particle in argon fluid [Articolo su rivista]
Giovanni, Ciccotti; Ferrario, Mauro; Jean Paul, Ryckaert
abstract

We introduce a new method, based on the theory of stationary stochastic processes, to represent by an analytical reference model a large class of autocorrelation functions known numerically.The analytical reference model is then used to give a very accurate representation of the velocity autocorrelation function of argon near the triple point by a Mori continued fraction truncated at very high order (up to 25 Mori coefficients). Under some restrictive hypothesis, the results of this analysis together with an appropriate numerical algorithm, permit the simulation of generalized brownian dynamics of an argon particle in argon fluid in a realistic way.

1982 - Computer simulation of the molecular dynamics of liquid dichloro methane [Articolo su rivista]
M. W., Evans; Ferrario, Mauro
abstract

The molecular dynamics of CH2Cl2 in the liquid state have been simulated with two model representations of the intermolecular potential. These consist of a 3 × 3 and 5 × 5 atom-atom simulation with or without fractional charges at the atomic sites. A variety of thermodynamical and spectroscopic results show that the 5 × 5 potential is the more accurate. The effect of adding charges is significant but not pronounced. For example the simulated far infra-red spectrum looks 15% more like the real thing after an attempt has been made to include charge-charge electrodynamics. It is clear, however, that a better representation of the intermolecular pair potential of CH2Cl2 is needed to match the far infra-red results, and this can probably be obtained by measurements of the second virial of CH2Cl2 over a sufficient temperature range. A coordinated experimental effort is needed to test the wide-range of simulated spectra now available for the asymmetric top CH2Cl2.

1982 - Correlation times for liquid CH2Cl2 [Articolo su rivista]
M. W., Evans; Ferrario, Mauro
abstract

The overall consistency of experimentally available correlation times for liquid CH2Cl2 is tested with the aid of a new computer simulation at 293K lbar, using a 5 × 5 Lennard-Jones atom-atom potential with charges situated at the atomic sites. The various N.M.R. correlation times and the dielectric relaxation time are satisfactorily in line with the computer simulation. The infra-red correlation time reported by van Konynenberg and Steele is consistent with the simulation, but those reported by Rothschild are over 100 too short. The correlation time from depolarised Rayleigh scattering is over 3 times longer than the simulation result, and the neutron-scattering correlation time of Brier and Perry is about 100. shorter. The computer simulation reproduces the far infra-red spectrum of liquid CH2Cl2 fairly well and is therefore considered to be reliable.A coordinated project, such as the EMLG Delta Project is needed to improve the overall consistency of these basic features of liquid phase molecular dynamics, exemplified by liquid CH2Cl2.

1982 - Cybernetic spectroscopy of molecular rototranslation in the liquid state [Articolo su rivista]
M. W., Evans; Ferrario, Mauro
abstract

We introduce (following Ciccotti et al.) the subject of cybernetic spectroscopy with reference to the computer simulation of rototranslational mixed a.c.f.'s in the molecule-fixed frame of CH2Cl2 in the liquid state (E.M.L.G. pilot project). The detailed acquisition of such “signatures” is possible only via numerical methods using fast computers and provides a corroborative challenge both in the fields of experimental spectroscopy and phenomenological theory. Up to nine elements each of the mixed a.c.f. matrices are observable depending on molecular symmetry. The properties of these elements are basically important in the interpretation of molecular diffusion and broad-band spectroscopy of liquids and mesophases.

1982 - Dielectric relaxation as a multiplicative stochastic process: I. General theory [Articolo su rivista]
M. W., Evans; Ferrario, Mauro; P., Grigolini
abstract

A rigorous and general approach is developed to the relaxation of molecular dipoles on the microscopic scale, embodied in the orientational time-autocorrelation function. The usual difficulties of using the stochastic Liouville equation (SLE) are bypassed by replacing the cumulant expansion with a continued fraction. This reduces to that of Sack or Gross in the appropriate limit.The autocorrelation function is formed from approximants of this continued fraction, which is ideally suited for numerical computation, and as a basis for the newly developed technique of semi-stochastic molecular dynamics simulation. The numerical solution automatically produces the spectral moments of interest to order of truncation, so that the number of unknowns is reduced to one at each and every stage of approximation. This concerns the rate of energy dissipation, denoted by β, a scalar, tensor or super-tensor according to the nature of the diffusion process under consideration.The new continued fraction can be used to describe spatial rotational diffusion of the asymmetric top using the appropriate Fokker-Planck diffusion operator. It is a considerable improvement therefore on a model such as the planar itinerant librator, an approximant of the Mori continued fraction.

1982 - Molecular dynamics computer simulation of liquid dichloromethane. I. Equilibrium properties [Articolo su rivista]
Ferrario, Mauro; Myron W., Evans
abstract

The molecular dynamics of CH2C2 in the liquid state have been simulated with two model representations of the intermolecular potential. These consist of a three-interaction site model and a five-interaction site one with or without fractional electrical charges at the atomic sites. The MD algorithms used in the simulation are described in detail. Equilibrium thermodynamic properties are calculated and compared with experimental data. In part two some dynamical properties are presented and some attention is given to the reproduction of the experimental far infrared spectra.

1982 - Molecular dynamics of CH2Cl2: temperature dependences of the far infra-red spectrum. Part 1: experimental and simulation [Articolo su rivista]
J. K., Vij; C. J., Reid; G. J., Evans; Ferrario, Mauro; M. W., Evans
abstract

The temperature dependence of the rotational diffusion in liquid CH2Cl2 has been measured in the far infrared from 10 to 220 cm−1 and 177K to 313K (f.p. to b.p. at 1bar). The results are interpreted at 177K and 293K with a molecular dynamics simulation using a 5 × 5 atom-atom potential with charge-charge electrodynamics. The simulation reproduces the basic features of the spectra but some experimental detail of the dependency of f_max,the far infrared peak frequency,on temperature is not followed by the simulation. The situation can be improved by accurately measuring the second dielectric virial coefficient βϵ of CH2Cl2 vapour in order to improve our knowledge of the intermolecular pair potential.

1982 - Molecular dynamics of rigid systems in cartesian coordinates A general formulation [Articolo su rivista]
G., Ciccotti; Ferrario, Mauro; J. P., Ryckaert
abstract

The dynamics of rigid polyatomic systems, either molecules or rigid portions of large molecules, is described by cartesian equations of motion for its atoms. In comparison with the original version of the method of constraints

1982 - Molecular dynamics simulation of liquid CH2Cl2 with 3×3 and 5×5 site-site interactions [Articolo su rivista]
Ferrario, Mauro; M. W., Evans
abstract

A molecular dynamics simulation of liquid CH2Cl2 is compared with the far infrared spectrum at the same state point (293K, 1 bar). Two representations of the force field are used, a 3×3 and 5×5 site-site interaction consisting of Lennard-Jones and charge terms. The far infra-red spectrum shows unambiguously that the 5×5 representation is more realistic in the sense that it reproduces the observed spectrum more closely.

1982 - Numerical solution of fokker/planck/kramers equations [Articolo su rivista]
Ferrario, Mauro; M. W., Evans; W. T., Coffey
abstract

Some Fokker/Planck/Kramers equations of current interest are solved numerically for autocorrelation functions and spectra. It is demonstrated that uncritical use of these equations should be avoided because of the neglect of memory effects inherent in their make-up. Only in the case discussed by Evans (1976) does this type of equation produce realistic spectra, and then only over a limited range of temperature and viscosity. The way to proceed in problems involving molecular diffusion of this type is to use molecular dynamics simulation

1982 - The correlation of molecular rotational and translational kinetic energy in liquid CH2Cl2 and CHCl3 [Articolo su rivista]
M. W., Evans; Ferrario, Mauro
abstract

A “molecular dynamics” computer simulation of liquid CH2Cl2 and CHCl3 has revealed a time dependence of the simple kinetic energy correlation function 〈v^2(O)J^2(t)〉/(〈v^2(O)〉〈J^2(O)〉) where is the c. of m. linear velocity and the molecular momentum. This is constant at unity for all t in conventional analytical theory, which is therefore in need of development. The variates and are not Gaussian during the approach to equilibrium.

1981 - A spectrometer for far i.r. hot broad band fluorescence in gases [Articolo su rivista]
G. J., Evans; C. J., Reid; Ferrario, Mauro; M. W., Evans
abstract

An apparatus is described for detecting broad band far i.r. fluorescence in gases pumped by a variety of C02 laser lines. It consists of three major components: (i) an Apollo Instruments tunable CO2 laser, pumping (ii) a specially designed sample cell which collimates the emitted radiation for subsequent analysis in (iii) an N.P.L./Grubb-Parson ‘Cube Interferometer’, incorporating the Fellgett and Jaquinot advantages. As shown by Roodhardt and Wegdam [1] in HCl pumped via SF6, the induced far i.r. fluorescence is rotationally very ‘hot’, i.e. the distribution of the rotational absorption envelope peaks at an equivalent temperature of some thousands of Kelvin, and is no longer describable by Blotzmann statistics. We present experimental evidence for broad band, far i.r., CO2-induced fluorescence in the asymmetric top CH2CF2 for different CO2 laser lines. The results are discussed in terms of a model of the collisional dynamics involved in the transfer of vibrational to rotational energy.

1981 - A theory of the dielectric loss in the aligned nematic mesophase [Articolo su rivista]
Ferrario, Mauro; Myron, Evans
abstract

A theory of dielectric absorption and dispersion in the nematic phase is developed which does not rely on the use of a nematic “director”. The major features of the spectrum are reproduced by using the fact that the autocorrelation functions 〈μ(0) · υ(t)〉 and 〈υ(t) · μ(0)〉 are no longer symmetry disallowed when the overall sample is anisotropic, as in the aligned nematic. Here μ is the dipole vector of the diffusing molecule and υ the centre of mass linear velocity.

1981 - Brownian motion with superimposed interaction: cosine potential and molecular dynamics simulation [Articolo su rivista]
Myron W., Evans; Ferrario, Mauro; William T., Coffey
abstract

A molecular dynamics simulation of 108 C2v triatomics is used to evaluate a model of the molecular liquid based on the Evans and Calderwood/Coffey itinerant oscillator concepts. Several weaknesses of the original models are investigated using Pn Legendre a.c.f.'s of orientation and the related angular momentum a.c.f. The harmonic binding between cage and encaged molecule is clearly shown to be an oversimplification. Replacement by a cosine potential gives a better result after a numerical analysis due to Ferrario.

1981 - Cumulant expansion of the orientational auto-correlation function [Articolo su rivista]
Ferrario, Mauro; M. W., Evans
abstract

A general method is developed to relate the orientational and angular momentum auto-correlation functions of a vector embedded in the rotating asymmetric top. It is shown that a previous attempt along these lines by Nee and Zwanzig contains an error which is rectified in this paper. The reduction to the free rotor limit is discussed carefully. The continuity equation, whose solution is a time-ordered exponential does not produce an orientational a.c.f. valid at the free rotor limit. This is because in this limit the kinematic relation between orientation and angular velocity is no longer a multiplicative stochastic process.

1981 - Intermolecular pair and trimer potentials for methyl fluoride [Articolo su rivista]
Ahmed A., Hasanein; Ferrario, Mauro; Myron, Evans
abstract

Ab initio calculations of the pair and trimer interaction energy of methyl fluoride are reported in various approach configurations. These are based on the 6 - 31G and 4 - 31G basis sets of the Gaussian 76 program of Pople and co-workers. The potential energy surface of pair interaction is compared with that of Copeland and Cole, based on gas viscosity, second pressure virial and second dielectric virial data, and with an unoptimised 5 × 5 atom-atom potential. The “experimental” Copeland/Cole potential and the ab initio calculations are more often in better agreement for different dimer configurations than with the atom-atom potential. Non-pair-additivity energy in the minimised cyclic trimer of CH3F is of the order of 10% of the total trimer interaction energy and is expected to become more important in bigger (multimer) clusters.The results indicate that a parameterisation of the ab initio results or alternatively a straightforward use of the Copeland/Cole form is more likely to be realistic in a molecular dynamics simulation of CH3F when using the assumption of pair interaction. However it is best to avoid this assumption in the manner of Finney et al.

1981 - Itinerant oscillation with a cosine potential [Articolo su rivista]
Ferrario, Mauro; M. W., Evans; W. T., Coffey
abstract

The equations of motion of the planar itinerant librator are extended to involve a cosine potential rather than a harmonic form for interaction, and are solved numerically to produce the angular velocity autocorrelation function and its Fourier transform (real and imaginary parts). The behaviour of the cosine potential is matched with that of the harmonic potential through these functions and in general conforms more closely to the indication of zero-THz spectroscopy and computer simulation.

1981 - Probability diffusion in non-Markhovian, non-Gaussian molecular ensembles: A theoretical analysis and computer simulation [Articolo su rivista]
P., Grigolini; Ferrario, Mauro; M. W., Evans
abstract

A theoretical generalisation of the Fokker/Planck equation for atomic and molecular diffusion is compared with the results of a molecular dynamics simulation of a triatomic molecule of C_2v symmetry. The molecular dynamics results are non-Markhovian and non-Gaussian in nature, markedly so in the case of the centre of mass linear velocity V. This may be ascertained by simulating the long-time limit of the three dimensional kinetic energy autocorrelation function <V^2(t)V^2(0)>/<V^2(0)V^2(0)>, which falls well below the theoretical Gaussian value of 3/5. By expressing the Mori continued fraction as a multidimensional Markhovian chain of differential equations and expressing this in turn as a non-Gaussian probability-diffusion equation of the Kramers/Moyal type it is possible to account for the simulation results in a qualitative fashion.

1981 - Role of rotational thermal bath excitation on the EPR transient regime: A theoretical discussion [Articolo su rivista]
Ferrario, Mauro; Paolo, Grigolini
abstract

The excitation of rotational thermal baths can result in long‐lived effects on spin relaxation in the slow motional region. An attempt at obtaining their quantitative evaluation is successfully made by enriching the Mori–Kivelson–Ogan (MKO) theory through comparison with the Kubo–Freed (KF) one and vice versa. This comparison, in turn, is allowed by suitably extending the MKO theory so as to deal with spin excitation by external radiation fields. The MKO, furthermore, is limited to the second‐order Mori truncation while the KF one is related to the two‐jump case. It is shown, then, that in the usual kind of steady‐state experiments, the MKO theory provides the same result as the KF one. In contrast, when spin relaxation is monitored in the presence of a fluctuating force whose time average intensity is not vanishing, the two theories can result in quite different physical effects.

1981 - The intermolecular dimer potential of non-dipolar linear molecules [Articolo su rivista]
A. A., Hasanein; Ferrario, Mauro; M., Evans
abstract

The intermolecular potentials of H2, D2, F2, 02, N2 and C02 are examined using three independent estimates:1. The Kihara/Koide method, involving core anisotropy, van den Waals dispersion, quadrupolar interaction and octopolar induction terms.2. The ab initio calculation for dimers of these molecules, using 4 - 31G and 6 - 31G basis sets.3. The atom-atom (R.I.S.M.) method.While some consistent features emerge, there is qualitative disagreement in the majority of approach configurations which implies that the Kihara/Koide potential is overestimating the attractive part of the potential energy surface and underestimating the anisotropy of this surface in comparison with the ab initio method.The atom-atom and Kihara/Koide potentials agree almost quantitatively in the majority of approach configurations, so that the extra electrostatic features considered by Kihara et al seem generally to have little effect on the atom-atom results.

1980 - Non-gaussian distributions in computer triatomics [Articolo su rivista]
M. W., Evans; Ferrario, Mauro; P., Grigolini
abstract

A molecular dynamics simulation of 108 triatomic molecules of C2v symmetry reveals markedly non-gaussian statistical distributions of vectors such as the centre-of-mass linear velocity, molecular angular momentum, positional and orientational coordinates. The results are reproduced qualitatively in the case of linear velocity by a straightforward extension of the Fokker-Planck equation.

1980 - The mutual interaction of molecular rotation and translation [Articolo su rivista]
M. W., Evans; Ferrario, Mauro; P., Grigolini
abstract

The dynamics of molecular rototranslation are treated with an equation of motion with a non-Markovian, stochastic force/torque. It is shown that this Mori/Kubo/Zwanzig representation is equivalent to a multidimensional Markov equation which may be identified with analytical models of the molecular motion. Langevin and Fokker-Planck equations for two such models are derived from the general equations of motion. The analytical results are compared with a computer simulation of the velocity/angular velocity mixed autocorrelation function, C vω ( t ) = v (0) . ω( t )> for a triatomic of C 2 v symmetry.

1980 - Theory of transient response for arbitrarily strong driving fields [Articolo su rivista]
M. W., Evans; Ferrario, Mauro; P., Grigolini
abstract

A theory of the dynamical Kerr effect is developed for arbitrarily strong driving fields using a modification of the Mori equation of motion due to Grigolini et al. Using the multidimensional expansion of Grigolini and Ferrario the non-Markovian Mori equation may be written in Markov form. It is possible then to derive a macro–micro correlation theorem for the system by applying the method of Kivelson et al. In this way it is possible to bypass the linear response approximation of classical dielectric theory.

1979 - A generalization of the kubo—freed relaxation theory [Articolo su rivista]
Ferrario, Mauro; P., Grigolini
abstract

The Kubo—Freed relaxation theory is suitably extended in such a way as to include any type of non-markovian diffusion. It is shown how the appearance of new absorption peaks may easily be explained by using simple mechanical models of molecular relaxation.

1979 - The non‐Markovian relaxation process as a ‘‘contraction’’ of a multidimensional one of Markovian type [Articolo su rivista]
Ferrario, Mauro; P., Grigolini
abstract

A new approach for obtaining the Fokker–Planck equation to be associated with the generalized Langevin equation is discussed. By using the Mori expansion of the ’’memory kernel,’’ it is shown that any information of interest may be provided by a suitable multidimensional Fokker–Planck equation of Markovian type. A suitable ’’contraction’’ process, furthermore, enables us to find the same two‐point conditional probability as the one recently obtained by Fox. This approach may be useful to overcome the Markov approximation which is present in the stochastic Liouville equation theory.

Università degli studi di Modena e Reggio Emilia

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