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Publications (149)
The need to move toward more sustainable lubricant materials has sparked an ever growing interest on the tribological performances of additives based on environmentally friendly molecules, such as carbon-based compounds, and green liquid media as aqueous solutions. The prediction of the solubility of the additives into the liquid and the tribochemi...
Mechanochemistry and tribochemistry processes involve multiple physical/chemical interactions induced by extreme conditions including molecular confinement, high temperatures and mechanical stress applied. Simulating these processes by molecular dynamics is very challenging. While force fields fall short reproducing the enhanced reactivity arising...
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: Özpinar/TIP3P and Hölzl/(TIP4P/2005)....
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...
Diamond-based coatings are employed in several technological applications, for their outstanding mechanical properties, biocompatibility, and chemical stability. Of significant relevance is the interface with silicon oxide, where phenomena of adhesion, friction, and wear can affect drastically the performance of the coating. Here we monitor such ph...
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...
Diamond-based coatings are employed in several technological applications, for their outstanding mechanical properties, biocompatibility, and chemical stability. Of significant relevance is the interface with silicon oxide, where phenomena of adhesion, friction, and wear can affect drastically the performance of the coating. Here we monitor such ph...
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 ma...
We developed a computational protocol to study solid-solid interfaces with a first principles high throughput approach. Solid interfaces are very relevant systems in materials science, physics and chemistry and central for many applications, ranging from synthetic antiferromagnets and spintronics, battery technology to tribology.
The protocol is ba...
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 extrac...
The potential energy surface (PES) characterizes the mechanical properties of an interface to a large extend. It allows the computation of properties like adhesion, shear strength, static friction, and dislocations, among others [1-4]. In the past we have shown that we are able to apply density functional theory to calculate highly accurate PESs fo...
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...
Tribological phenomena, such as wear and boundary lubrication, are deeply influenced by tribochemical reactions, 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 in...
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, r...
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 general...
Equilibrium and non-equilibrium 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 micros...
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 evolutio...
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 r...
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 Che...
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...
In this paper we reformulate the configurational temperature Nosé-Hoover thermostat of Braga and Travis [J. Chem. Phys. 123, 134101 (2005)] by means of a quasi-Hamiltonian theory in phase space [Phys. Rev. E 64, 056125 (2001)]. The quasi-Hamiltonian structure is exploited to introduce a hybrid configurational-kinetic temperature Nosé-Hoover chain t...
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...
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 sep...
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)] and recently applied to the study of the transient regimes in various fluid...
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 freque...
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 t...
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 c...
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 differen...
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 lu...
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 t...
Progress in the ability of understanding tribological properties in adsorbed film systems is of paramount importance to unravel fundamental issues in the emerging field of nanoscale science and technology. Many extensive studies have used a quartz-crystal microbalance (QCM) to measure the friction between adsorbed rare gas monolayers and metal subs...
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 th...
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...
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.
We present computer simulation results for the spectra of collective quantities of hydrogen bonded systems which present a different degree of hydrogen bond strength. The present analysis allows to clarify which are the features connected with the presence of a structural arrangement of molecules induced by the hydrogen bonding. Localized motion is...
IntroductionLinear One-Dimensional System and the RMTComputer Simulation of a One-Dimensional Lennard-Jones SystemThe Effective Nonlinear PotentialThe Nonlinear Itinerant OscillatorRotation Dynamics: Computer Simulation of Equilibrium and Nonequilibrium PropertiesConcluding Remarks
The basic laws of physics that govern the phenomena on the scales of length and energy relevant for condensed matter systems,
ranging from simple fluids and solids to complex multicomponent materials and even problems of chemical biology, are well
known and understood: one just deals with the Schrödinger equation for the quantum many-body problem o...
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-...
We consider the dissipative nonlinear dynamics of a one-dimensional chain of interacting atoms driven over a substrate potential by an external dc force. The substrate parameters of the model can be tuned in order to introduce disorder effects starting from two geometrically opposite ideal cases: commensurate and incommensurate interfaces. The role...
This extensive and comprehensive collection of lectures by world-leading experts in the field introduces and reviews all relevant computer simulation methods and their applications in condensed matter systems. Volume 1, published as LNP 703 (ISBN 3-540-35270-8) is an in-depth introduction to a vast spectrum of computational techniques for statistic...
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, preventi...
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 observ...
We apply the Blue Moon constrained Molecular Dynamics technique to study a particular case of molecular recognition, one of the main issues of modern 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 w...
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 ξ( r ), a well-defined function in configuration space. By means of holonomic constraints a number of values of ξ( r ) can be prescribed along the releva...
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 positiv...
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 molecul...
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 spa...
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 o...
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 diff...
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 extendi...
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 equatio...
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. To check the role of dynamic processes in this catalytic enhancement...
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 bi...
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"...
Car-Parrinello molecular dynamics calculations have been carried out for phosphorus-selenium mixtures of compositions corresponding to overall stoichiometries PSe and P(2)Se. Comparison of the calculated structure factors with those obtained in neutron scattering experiments suggests that the real materials are characterized by the presence of subs...
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 derive...
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...
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 inelas...
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 d...
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...
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 fi...
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 diffusi...
A seven-site atom-atom potential model has been developed to describe the interactions between tetraphosphorus triselenide (P4Se3) 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 pr...
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...
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 part...
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 differen...
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.
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 simul...
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, T(R), is longer in methanol than in water by a factor of t...
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 i...
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 i...
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 Schrodinger and Newton's equations are solved to determine the proton charge density and solven...
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 ε˙ for a large system (N=2048). The Green-Kubo (GK) value eta(ε˙=0)=3.24+/-0.04 is estimated from a run of 3.6×106 steps (40 nsec). We find no numerical evidence of a t-3/2 lon...
This volume collects the contributions! to the NATO Advanced Study Institute (ASI)
held in Aussois (France) by March 25 - April 5, 1991. This NATO ASI was intended to
present and illustrate recent advances in computer simulation techniques applied to
the study of materials science problems. Introductory lectures have been devoted to
classical simul...
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 coordina...
Order-Disorder phase transition in molecular systems, such as structural phase transformations in molecular solids or nematic-isotropic transitions in liquid crystal, 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 comput...
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...
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 fa...
Recent theoretical and computer simulation work on the dynamics associated with electron transfer processes in polar solvents is described. This includes solvent relaxation subsequent to photo-induced charge transfer, adiabatic electron transfer rates, and the solvent influence on the electronic states relevant to electron transfers.
Molecular dynamics simulation results are presented for model electronically adiabatic electron-transfer reactions in a model polar solvent. Transmission coefficients κ characterizing the departure of the rates from the Marcus theory predictions are determined, and theoretical approaches to predicting κ in terms of solvent dynamics are examined.
