4,573 research outputs found
Mathematical Modelling of Chemical Diffusion through Skin using Grid-based PSEs
A Problem Solving Environment (PSE) with connections to remote distributed Grid processes is developed. The Grid simulation is itself a parallel process and allows steering of individual or multiple runs of the core computation of chemical diffusion through the stratum corneum, the outer layer of the skin. The effectiveness of this Grid-based approach in improving the quality of the simulation is assessed
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Leveraging legacy codes to distributed problem solving environments: A web service approach
This paper describes techniques used to leverage high performance legacy codes as CORBA components to a distributed problem solving environment. It first briefly introduces the software architecture adopted by the environment. Then it presents a CORBA oriented wrapper generator (COWG) which can be used to automatically wrap high performance legacy codes as CORBA components. Two legacy codes have been wrapped with COWG. One is an MPI-based molecular dynamic simulation (MDS) code, the other is a finite element based computational fluid dynamics (CFD) code for simulating incompressible Navier-Stokes flows. Performance comparisons between runs of the MDS CORBA component and the original MDS legacy code on a cluster of workstations and on a parallel computer are also presented. Wrapped as CORBA components, these legacy codes can be reused in a distributed computing environment. The first case shows that high performance can be maintained with the wrapped MDS component. The second case shows that a Web user can submit a task to the wrapped CFD component through a Web page without knowing the exact implementation of the component. In this way, a user’s desktop computing environment can be extended to a high performance computing environment using a cluster of workstations or a parallel computer
A dilating vortex particle method for compressible flow
Vortex methods have become useful tools for the computation of incompressible fluid flow. In this work, a vortex particle method for the simulation of unsteady two-dimensional compressible flow is developed. By decomposing the velocity into irrotational and solenoidal parts, and using particles that are able to change volume and that carry vorticity, dilatation, enthalpy, entropy and density, the equations of motion are satisfied. Spatial derivatives are treated using the method of particle strength exchange with high-order-accurate, non-dissipative kernels. The new vortex method is applied to co-rotating and leapfrogging vortices in compressible flow, with the far acoustic field computed using a two-dimensional Kirchhoff surface
The Density Matrix Renormalization Group for Strongly Correlated Electron Systems: A Generic Implementation
The purpose of this paper is (i) to present a generic and fully functional
implementation of the density-matrix renormalization group (DMRG) algorithm,
and (ii) to describe how to write additional strongly-correlated electron
models and geometries by using templated classes. Besides considering general
models and geometries, the code implements Hamiltonian symmetries in a generic
way and parallelization over symmetry-related matrix blocks.Comment: 2 figures, submitted to Computer Physics Communication
Unified Framework for Finite Element Assembly
At the heart of any finite element simulation is the assembly of matrices and
vectors from discrete variational forms. We propose a general interface between
problem-specific and general-purpose components of finite element programs.
This interface is called Unified Form-assembly Code (UFC). A wide range of
finite element problems is covered, including mixed finite elements and
discontinuous Galerkin methods. We discuss how the UFC interface enables
implementations of variational form evaluation to be independent of mesh and
linear algebra components. UFC does not depend on any external libraries, and
is released into the public domain
Parametric Alignment of Drosophila Genomes
The classic algorithms of Needleman--Wunsch and Smith--Waterman find a
maximum a posteriori probability alignment for a pair hidden Markov model
(PHMM). In order to process large genomes that have undergone complex genome
rearrangements, almost all existing whole genome alignment methods apply fast
heuristics to divide genomes into small pieces which are suitable for
Needleman--Wunsch alignment. In these alignment methods, it is standard
practice to fix the parameters and to produce a single alignment for subsequent
analysis by biologists.
Our main result is the construction of a whole genome parametric alignment of
Drosophila melanogaster and Drosophila pseudoobscura. Parametric alignment
resolves the issue of robustness to changes in parameters by finding all
optimal alignments for all possible parameters in a PHMM. Our alignment draws
on existing heuristics for dividing whole genomes into small pieces for
alignment, and it relies on advances we have made in computing convex polytopes
that allow us to parametrically align non-coding regions using biologically
realistic models. We demonstrate the utility of our parametric alignment for
biological inference by showing that cis-regulatory elements are more conserved
between Drosophila melanogaster and Drosophila pseudoobscura than previously
thought. We also show how whole genome parametric alignment can be used to
quantitatively assess the dependence of branch length estimates on alignment
parameters.
The alignment polytopes, software, and supplementary material can be
downloaded at http://bio.math.berkeley.edu/parametric/.Comment: 19 pages, 3 figure
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