Diffusion and vibrational relaxation of a diatomic molecule in the pore network of a pure silica zeolite: a molecular dynamics study

The vibrational relaxation and the diffusion of diatomic molecules in the zeolite silicalite have been studied through molecular dynamics simulations in the microcanonical statistical ensemble. The adopted model accounts for the vibrations of the framework and sorbed atoms using a harmonic potential for the silicalite and a Morse potential for the diatomic molecule. The results show that the framework favors the relaxation of diatomics oscillating at frequencies near to its characteristic vibrational frequencies, leading in such cases to lower relaxation times and to an increasing in the energy exchanged per collision. The diffusion of a two-site oscillating molecule representing ethane has been also investigated; the diffusion coefficient and the heat of adsorption agree very well with the experimental data. Arrhenius parameters for the diffusion have been calculated, and some insights into the diffusion mechanism have been obtained from log–log plots and by inspection of the distribution of the ethane molecules in the silicalite channels. Therefore the simplified model adopted seems to adequately describe the diffusive motion and the guest–host energy exchanges, and it could be useful in order to study simple bimolecular reactions in zeolites

Fluctuation-Induced Casimir Forces in Granular Fluids

We have numerically investigated the behavior of driven non-cohesive granular media and found that two fixed large intruder particles, immersed in a sea of small particles, experience, in addition to a short range depletion force, a long range repulsive force. The observed long range interaction is fluctuation-induced and we propose a mechanism similar to the Casimir effect that generates it: the hydrodynamic fluctuations are geometrically confined between the intruders, producing an unbalanced renormalized pressure. An estimation based on computing the possible Fourier modes explains the repulsive force and is in qualitative agreement with the simulations.Comment: 4 pages, 3 figures. Accepted in Phys. Rev. Letter

Temperature scaling in a dense vibro-fluidised granular material

The leading order "temperature" of a dense two dimensional granular material fluidised by external vibrations is determined. An asymptotic solution is obtained where the particles are considered to be elastic in the leading approximation. The velocity distribution is a Maxwell-Boltzmann distribution in the leading approximation. The density profile is determined by solving the momentum balance equation in the vertical direction, where the relation between the pressure and density is provided by the virial equation of state. The predictions of the present analysis show good agreement with simulation results at higher densities where theories for a dilute vibrated granular material, with the pressure-density relation provided by the ideal gas law, are in error. The theory also predicts the scaling relations of the total dissipation in the bed reported by McNamara and Luding (PRE v 58, p 813).Comment: ReVTeX (psfrag), 5 pages, 5 figures, Submitted to PR

A Particle-based Multiscale Solver for Compressible Liquid-Vapor Flow

To describe complex flow systems accurately, it is in many cases important to account for the properties of fluid flows on a microscopic scale. In this work, we focus on the description of liquid-vapor flow with a sharp interface between the phases. The local phase dynamics at the interface can be interpreted as a Riemann problem for which we develop a multiscale solver in the spirit of the heterogeneous multiscale method, using a particle-based microscale model to augment the macroscopic two-phase flow system. The application of a microscale model makes it possible to use the intrinsic properties of the fluid at the microscale, instead of formulating (ad-hoc) constitutive relations

Algorithm for numerical integration of the rigid-body equations of motion

A new algorithm for numerical integration of the rigid-body equations of motion is proposed. The algorithm uses the leapfrog scheme and the quantities involved are angular velocities and orientational variables which can be expressed in terms of either principal axes or quaternions. Due to specific features of the algorithm, orthonormality and unit norms of the orientational variables are integrals of motion, despite an approximate character of the produced trajectories. It is shown that the method presented appears to be the most efficient among all known algorithms of such a kind.Comment: 4 pages, 1 figur

Optimized Verlet-like algorithms for molecular dynamics simulations

New explicit velocity- and position-Verlet-like algorithms of the second order are proposed to integrate the equations of motion in many-body systems. The algorithms are derived on the basis of an extended decomposition scheme at the presence of a free parameter. The nonzero value for this parameter is obtained by reducing the influence of truncated terms to a minimum. As a result, the new algorithms appear to be more efficient than the original Verlet versions which correspond to a particular case when the introduced parameter is equal to zero. Like the original versions, the proposed counterparts are symplectic and time reversible, but lead to an improved accuracy in the generated solutions at the same overall computational costs. The advantages of the new algorithms are demonstrated in molecular dynamics simulations of a Lennard-Jones fluid.Comment: 5 pages, 2 figures; submitted to Phys. Rev.

Tackling Exascale Software Challenges in Molecular Dynamics Simulations with GROMACS

GROMACS is a widely used package for biomolecular simulation, and over the last two decades it has evolved from small-scale efficiency to advanced heterogeneous acceleration and multi-level parallelism targeting some of the largest supercomputers in the world. Here, we describe some of the ways we have been able to realize this through the use of parallelization on all levels, combined with a constant focus on absolute performance. Release 4.6 of GROMACS uses SIMD acceleration on a wide range of architectures, GPU offloading acceleration, and both OpenMP and MPI parallelism within and between nodes, respectively. The recent work on acceleration made it necessary to revisit the fundamental algorithms of molecular simulation, including the concept of neighborsearching, and we discuss the present and future challenges we see for exascale simulation - in particular a very fine-grained task parallelism. We also discuss the software management, code peer review and continuous integration testing required for a project of this complexity.Comment: EASC 2014 conference proceedin

Diffusion as mixing mechanism in granular materials

We present several numerical results on granular mixtures. In particular, we examine the efficiency of diffusion as a mixing mechanism in these systems. The collisions are inelastic and to compensate the energy loss, we thermalize the grains by adding a random force. Starting with a segregated system, we show that uniform agitation (heating) leads to a uniform mixture of grains of different sizes. We define a characteristic mixing time, $\tau_{mix}$, and study theoretically and numerically its dependence on other parameters like the density. We examine a model for bidisperse systems for which we can calculate some physical quantities. We also examine the effect of a temperature gradient and demonstrate the appearance of an expected segregation.Comment: 15 eps figures, include

Thermal conductivity of the Toda lattice with conservative noise

We study the thermal conductivity of the one dimensional Toda lattice perturbed by a stochastic dynamics preserving energy and momentum. The strength of the stochastic noise is controlled by a parameter $\gamma$. We show that heat transport is anomalous, and that the thermal conductivity diverges with the length $n$ of the chain according to $\kappa(n) \sim n^\alpha$, with $0 < \alpha \leq 1/2$. In particular, the ballistic heat conduction of the unperturbed Toda chain is destroyed. Besides, the exponent $\alpha$ of the divergence depends on $\gamma$

Quasi Harmonic Lattice Dynamics and Molecular Dynamics calculations for the Lennard-Jones solids

We present Molecular Dynamics (MD), Quasi Harmonic Lattice Dynamics (QHLD) and Energy Minimization (EM) calculations for the crystal structure of Ne, Ar, Kr and Xe as a function of pressure and temperature. New Lennard-Jones (LJ) parameters are obtained for Ne, Kr and Xe to reproduce the experimental pressure dependence of the density. We employ a simple method which combines results of QHLD and MD calculations to achieve densities in good agreement with experiment from 0 K to melting. Melting is discussed in connection with intrinsic instability of the solid as given by the QHLD approximation. (See http://www.fci.unibo.it/~valle for related papers)Comment: 7 pages, 5 figures, REVte