Molecular dynamics of flows in the Knudsen regime

Novel technological applications often involve fluid flows in the Knudsen regime in which the mean free path is comparable to the system size. We use molecular dynamics simulations to study the transition between the dilute gas and the dense fluid regimes as the fluid density is increased.Comment: REVTeX, 15 pages, 4 EPS figures, to appear in Physica

Heat conduction in the diatomic Toda lattice revisited

The problem of the diverging thermal conductivity in one-dimensional (1-D) lattices is considered. By numerical simulations, it is confirmed that the thermal conductivity of the diatomic Toda lattice diverges, which is opposite to what one has believed before. Also the diverging exponent is found to be almost the same as the FPU chain. It is reconfirmed that the diverging thermal conductivity is universal in 1-D systems where the total momentum preserves.Comment: 3 pages, 3 figures. To appear in Phys. Rev.

A Symmetry Property of Momentum Distribution Functions in the Nonequilibrium Steady State of Lattice Thermal Conduction

We study a symmetry property of momentum distribution functions in the steady state of heat conduction. When the equation of motion is symmetric under change of signs for all dynamical variables, the distribution function is also symmetric. This symmetry can be broken by introduction of an asymmetric term in the interaction potential or the on-site potential, or employing the thermal walls as heat reservoirs. We numerically find differences of behavior of the models with and without the on-site potential.Comment: 13 pages. submitted to JPS

Effective Interactions and Volume Energies in Charge-Stabilized Colloidal Suspensions

Charge-stabilized colloidal suspensions can be conveniently described by formally reducing the macroion-microion mixture to an equivalent one-component system of pseudo-particles. Within this scheme, the utility of a linear response approximation for deriving effective interparticle interactions has been demonstrated [M. J. Grimson and M. Silbert, Mol. Phys. 74, 397 (1991)]. Here the response approach is extended to suspensions of finite-sized macroions and used to derive explicit expressions for (1) an effective electrostatic pair interaction between pseudo-macroions and (2) an associated volume energy that contributes to the total free energy. The derivation recovers precisely the form of the DLVO screened-Coulomb effective pair interaction for spherical macroions and makes manifest the important influence of the volume energy on thermodynamic properties of deionized suspensions. Excluded volume corrections are implicitly incorporated through a natural modification of the inverse screening length. By including nonlinear response of counterions to macroions, the theory may be generalized to systematically investigate effective many-body interactions.Comment: 13 pages (J. Phys.: Condensed Matter, in press

Granular Collapse as a Percolation Transition

Inelastic collapse is found in a two-dimensional system of inelastic hard disks confined between two walls which act as an energy source. As the coefficient of restitution is lowered, there is a transition between a state containing small collapsed clusters and a state dominated by a large collapsed cluster. The transition is analogous to that of a percolation transition. At the transition the number of clusters n_s of size s scales as $n_s \sim s^{-\tau}$ with $\tau \approx 2.7$.Comment: 10 pages revtex, 5 figures, accepted by Phys Rev E many changes and corrections from previous submissio

Phase behaviour of a model of colloidal particles with a fluctuating internal state

Colloidal particles are not simple rigid particles, in general an isolated particle is a system with many degrees of freedom in its own right, e.g., the counterions around a charged colloidal particle.The behaviour of model colloidal particles, with a simple phenomenological model to account for these degrees of freedom, is studied. It is found that the interaction between the particles is not pairwise additive. It is even possible that the interaction between a triplet of particles is attractive while the pair interaction is repulsive. When this is so the liquid phase is either stable only in a small region of the phase diagram or absent altogether.Comment: 12 pages including 4 figure

Effective Interactions and Volume Energies in Charged Colloids: Linear Response Theory

Interparticle interactions in charge-stabilized colloidal suspensions, of arbitrary salt concentration, are described at the level of effective interactions in an equivalent one-component system. Integrating out from the partition function the degrees of freedom of all microions, and assuming linear response to the macroion charges, general expressions are obtained for both an effective electrostatic pair interaction and an associated microion volume energy. For macroions with hard-sphere cores, the effective interaction is of the DLVO screened-Coulomb form, but with a modified screening constant that incorporates excluded volume effects. The volume energy -- a natural consequence of the one-component reduction -- contributes to the total free energy and can significantly influence thermodynamic properties in the limit of low-salt concentration. As illustrations, the osmotic pressure and bulk modulus are computed and compared with recent experimental measurements for deionized suspensions. For macroions of sufficient charge and concentration, it is shown that the counterions can act to soften or destabilize colloidal crystals.Comment: 14 pages, including 3 figure

Phase Changes in an Inelastic Hard Disk System with a Heat Bath under Weak Gravity for Granular Fluidization

We performed numerical simulations on a two-dimensional inelastic hard disk system under gravity with a heat bath to study the dynamics of granular fluidization. Upon increasing the temperature of the heat bath, we found that three phases, namely, the condensed phase, locally fluidized phase, and granular turbulent phase, can be distinguished using the maximum packing fraction and the excitation ratio, or the ratio of the kinetic energy to the potential energy.It is shown that the system behavior in each phase is very different from that of an ordinary vibrating bed.Comment: 4 pages, including 5 figure

Capturing the essence of folding and functions of biomolecules using Coarse-Grained Models

The distances over which biological molecules and their complexes can function range from a few nanometres, in the case of folded structures, to millimetres, for example during chromosome organization. Describing phenomena that cover such diverse length, and also time scales, requires models that capture the underlying physics for the particular length scale of interest. Theoretical ideas, in particular, concepts from polymer physics, have guided the development of coarse-grained models to study folding of DNA, RNA, and proteins. More recently, such models and their variants have been applied to the functions of biological nanomachines. Simulations using coarse-grained models are now poised to address a wide range of problems in biology.Comment: 37 pages, 8 figure

Nonequilibrium Molecular Dynamics Simulation of Interacting Many Electrons Scattered by Lattice Vibrations

We propose a new model suitable for a nonequilibrium molecular dynamics (MD) simulation of electrical conductors. The model consists of classical electrons and atoms. The atoms compose a lattice vibration system. The electrons are scattered by electron-electron and electron-atom interactions. Since the scattering cross section is physically more important than the functional form of a scattering potential, we propose to devise the electron-atom interaction potential in such a way that its scattering cross section agrees with that of quantum-mechanical one. To demonstrate advantages of the proposed model, we perform a nonequilibrium MD simulation assuming a doped semiconductor at room or higher temperature. In the linear response regime, we confirm Ohm's law, the dispersion relations and the fluctuation-dissipation relation. Furthermore, we obtain reasonable dependence of the electrical conductivity on temperature, despite the fact that our model is a classical model.Comment: 21 pages, 11 figure