Archivio della ricerca dell'Università di Modena e Reggio Emiliahttps://iris.unimore.itIl sistema di repository digitale IRIS acquisisce, archivia, indicizza, conserva e rende accessibili prodotti digitali della ricerca.Sun, 25 Aug 2019 09:41:42 GMT2019-08-25T09:41:42Z101161Molecular dynamics study of the plastic-crystalline phase transition of tetraphosphorus triselenidehttp://hdl.handle.net/11380/741387Titolo: Molecular dynamics study of the plastic-crystalline phase transition of tetraphosphorus triselenide
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
Sun, 01 Jan 1995 00:00:00 GMThttp://hdl.handle.net/11380/7413871995-01-01T00:00:00ZStructure of NaCl and KCl concentrated aqueous solutions by ab initio molecular dynamicshttp://hdl.handle.net/11380/307512Titolo: Structure of NaCl and KCl concentrated aqueous solutions by ab initio molecular dynamics
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.
Thu, 01 Jan 2004 00:00:00 GMThttp://hdl.handle.net/11380/3075122004-01-01T00:00:00ZNon-linear effects in rotational dynamics in the liquid statehttp://hdl.handle.net/11380/739853Titolo: Non-linear effects in rotational dynamics in the liquid state
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.
Sun, 01 Jan 1984 00:00:00 GMThttp://hdl.handle.net/11380/7398531984-01-01T00:00:00ZMolecular dynamics simulation of ion association reactions in a polar solventhttp://hdl.handle.net/11380/741084Titolo: Molecular dynamics simulation of ion association reactions in a polar solvent
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
Fri, 01 Jan 1988 00:00:00 GMThttp://hdl.handle.net/11380/7410841988-01-01T00:00:00ZConstrained molecular dynamics and the mean potential for an ion pair in a polar solventhttp://hdl.handle.net/11380/741086Titolo: Constrained molecular dynamics and the mean potential for an ion pair in a polar solvent
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.
Sun, 01 Jan 1989 00:00:00 GMThttp://hdl.handle.net/11380/7410861989-01-01T00:00:00ZDynamical Non-Equilibrium Molecular Dynamicshttp://hdl.handle.net/11380/1010733Titolo: Dynamical Non-Equilibrium Molecular Dynamics
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).
Wed, 01 Jan 2014 00:00:00 GMThttp://hdl.handle.net/11380/10107332014-01-01T00:00:00ZThe mutual interaction of molecular rotation and translationhttp://hdl.handle.net/11380/738350Titolo: The mutual interaction of molecular rotation and translation
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.
Tue, 01 Jan 1980 00:00:00 GMThttp://hdl.handle.net/11380/7383501980-01-01T00:00:00ZConstant pressure-constant temperature molecular dynamics: a correct constrained NPT ensemble using the molecular virialhttp://hdl.handle.net/11380/5324Titolo: Constant pressure-constant temperature molecular dynamics: a correct constrained NPT ensemble using the molecular virial
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.
Wed, 01 Jan 2003 00:00:00 GMThttp://hdl.handle.net/11380/53242003-01-01T00:00:00ZEffective binding force calculation in dimeric proteinshttp://hdl.handle.net/11380/305990Titolo: Effective binding force calculation in dimeric proteins
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.
Thu, 01 Jan 2004 00:00:00 GMThttp://hdl.handle.net/11380/3059902004-01-01T00:00:00ZPartially folded states of HIV-1 protease: Molecular dynamics simulations and ligand bindinghttp://hdl.handle.net/11380/305288Titolo: Partially folded states of HIV-1 protease: Molecular dynamics simulations and ligand binding
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.
Sun, 01 Jan 2006 00:00:00 GMThttp://hdl.handle.net/11380/3052882006-01-01T00:00:00Z