Microscopic Derivation of Causal Diffusion Equation using Projection Operator Method

We derive a coarse-grained equation of motion of a number density by applying the projection operator method to a non-relativistic model. The derived equation is an integrodifferential equation and contains the memory effect. The equation is consistent with causality and the sum rule associated with the number conservation in the low momentum limit, in contrast to usual acausal diffusion equations given by using the Fick's law. After employing the Markov approximation, we find that the equation has the similar form to the causal diffusion equation. Our result suggests that current-current correlations are not necessarily adequate as the definition of diffusion constants.Comment: 10 pages, 1 figure, Final version published in Phys. Rev.

Discretization of the velocity space in solution of the Boltzmann equation

We point out an equivalence between the discrete velocity method of solving the Boltzmann equation, of which the lattice Boltzmann equation method is a special example, and the approximations to the Boltzmann equation by a Hermite polynomial expansion. Discretizing the Boltzmann equation with a BGK collision term at the velocities that correspond to the nodes of a Hermite quadrature is shown to be equivalent to truncating the Hermite expansion of the distribution function to the corresponding order. The truncated part of the distribution has no contribution to the moments of low orders and is negligible at small Mach numbers. Higher order approximations to the Boltzmann equation can be achieved by using more velocities in the quadrature

Enhancing e-Infrastructures with Advanced Technical Computing: Parallel MATLAB® on the Grid

MATLAB® is widely used within the engineering and scientific fields as the language and environment for technical computing, while collaborative Grid computing on e-Infrastructures is used by scientific communities to deliver a faster time to solution. MATLAB allows users to express parallelism in their applications, and then execute code on multiprocessor environments such as large-scale e-Infrastructures. This paper demonstrates the integration of MATLAB and Grid technology with a representative implementation that uses gLite middleware to run parallel programs. Experimental results highlight the increases in productivity and performance that users obtain with MATLAB parallel computing on Grids

Identification of hidden population structure in time-scaled phylogenies

Abstract Population structure influences genealogical patterns, however data pertaining to how populations are structured are often unavailable or not directly observable. Inference of population structure is highly important in molecular epidemiology where pathogen phylogenetics is increasingly used to infer transmission patterns and detect outbreaks. Discrepancies between observed and idealised genealogies, such as those generated by the coalescent process, can be quantified, and where significant differences occur, may reveal the action of natural selection, host population structure, or other demographic and epidemiological heterogeneities. We have developed a fast non-parametric statistical test for detection of cryptic population structure in time-scaled phylogenetic trees. The test is based on contrasting estimated phylogenies with the theoretically expected phylodynamic ordering of common ancestors in two clades within a coalescent framework. These statistical tests have also motivated the development of algorithms which can be used to quickly screen a phylogenetic tree for clades which are likely to share a distinct demographic or epidemiological history. Epidemiological applications include identification of outbreaks in vulnerable host populations or rapid expansion of genotypes with a fitness advantage. To demonstrate the utility of these methods for outbreak detection, we applied the new methods to large phylogenies reconstructed from thousands of HIV-1 partial pol sequences. This revealed the presence of clades which had grown rapidly in the recent past, and was significantly concentrated in young men, suggesting recent and rapid transmission in that group. Furthermore, to demonstrate the utility of these methods for the study of antimicrobial resistance, we applied the new methods to a large phylogeny reconstructed from whole genome Neisseria gonorrhoeae sequences. We find that population structure detected using these methods closely overlaps with the appearance and expansion of mutations conferring antimicrobial resistance

A Continuum Description of Rarefied Gas Dynamics (I)--- Derivation From Kinetic Theory

We describe an asymptotic procedure for deriving continuum equations from the kinetic theory of a simple gas. As in the works of Hilbert, of Chapman and of Enskog, we expand in the mean flight time of the constituent particles of the gas, but we do not adopt the Chapman-Enskog device of simplifying the formulae at each order by using results from previous orders. In this way, we are able to derive a new set of fluid dynamical equations from kinetic theory, as we illustrate here for the relaxation model for monatomic gases. We obtain a stress tensor that contains a dynamical pressure term (or bulk viscosity) that is process-dependent and our heat current depends on the gradients of both temperature and density. On account of these features, the equations apply to a greater range of Knudsen number (the ratio of mean free path to macroscopic scale) than do the Navier-Stokes equations, as we see in the accompanying paper. In the limit of vanishing Knudsen number, our equations reduce to the usual Navier-Stokes equations with no bulk viscosity.Comment: 16 page

Closedness type regularity conditions for surjectivity results involving the sum of two maximal monotone operators

In this note we provide regularity conditions of closedness type which guarantee some surjectivity results concerning the sum of two maximal monotone operators by using representative functions. The first regularity condition we give guarantees the surjectivity of the monotone operator $S(\cdot + p)+T(\cdot)$, where $p\in X$ and $S$ and $T$ are maximal monotone operators on the reflexive Banach space $X$. Then, this is used to obtain sufficient conditions for the surjectivity of $S+T$ and for the situation when $0$ belongs to the range of $S+T$. Several special cases are discussed, some of them delivering interesting byproducts.Comment: 11 pages, no figure