2-D R-matrix propagation: A large scale electron scattering simulation dominated by the multiplication of dynamically changing matrices

We examine the computational aspects of propagating a global R-matrix, R, across sub-regions in a 2-D plane. This problem originates in the large scale simulation of electron collisions with atoms and ions at intermediate energies. The propagation is dominated by matrix multiplications which are complicated because of the dynamic nature of R, which changes the designations of its rows and columns and grows in size as the propagation proceeds. The use of PBLAS to solve this problem on distributed memory HPC machines is the main focus of the paper.

Custom coprocessor based matrix algorithms for image and signal processing

Matrix algorithms are important in many types of applications including image and signal processing. A close examination of the algorithms used in these, and related, applications reveals that many of the fundamental actions involve matrix algorithms such as matrix multiplication. This paper presents an investigation into the design and implementation of different matrix algorithms such as matrix operations, matrix transforms and matrix decompositions using a novel custom coprocessor system for MATrix algorithms based on Reconfigurable Computing (RCMAT). The proposed RCMAT architectures are scalable, modular and require less area and time complexity with reduced latency when compared with existing structures.

Sorption behavior of cationic and anionic dyes from aqueous solution on different types of activated carbons

The effect of dye molecular charges on their adsorption from solution was investigated by using different types of activated carbon adsorbents. Two types of model systems were used representing cationic and anionic dyes. Screening investigations using single point tests were used throughout the study. Cationic dyes, of which Methylene Blue is an example, showed a higher adsorption tendency towards activated carbon over anionic dyes represented by an ate-type reactive compound. Of the number of activated carbons tested, only one of the adsorbents showed an exception to this behavior, and a good relation was observed between Methylene Blue capacity and activated carbon performance. The high capacity of cationic dyes in comparison to anionic dyes was also evident in the results obtained by a preliminary kinetic study carried out on the selected systems. Surface net charge of activated carbon and the nature of attractions between the molecules were suggested to be one of the reasons attributed for this behavior.

Ultrafast Laser-Driven Excitation Dynamics in Ne: An Ab Initio Time-Dependent R-Matrix Approach

An attosecond pump-probe scheme that combines the use of a free-electron laser pulse with an ultrashort pulse is applied in order to explore the ultrafast excitation dynamics in Ne. We describe the multielectron dynamics using a new nonperturbative time-dependent R-matrix theory. This theory enables the interaction of ultrashort light fields with multielectron atoms and atomic ions to be determined from first principles. By probing the emission of an inner 2s electron from Ne we are also able to study the bound state population dynamics during the free-electron laser pulse.

Electron impact excitation collision strengths for neon-like Ni XIX calculated using the relativistic R-matrix method

In a recent paper [Pramana - J. Phys. 64, 129 (2005)] results have been presented for electron impact excitation collision strengths for transitions among the fine-structure levels of the 2s(2)2p(6) and 2s(2)2p(5)3s configurations of Ni XIX. In this paper we demonstrate through an independent calculation with the relativistic R-matrix code that those results are unreliable and the conclusions drawn are invalid.

Time-dependent R -matrix theory for ultrafast atomic processes

We describe an ab initio nonperturbative time-dependent R-matrix theory for ultrafast atomic processes. This theory enables investigations of the interaction of few-femtosecond and -attosecond pulse lasers with complex multielectron atoms and atomic ions. A derivation and analysis of the basic equations are given, which propagate the atomic wave function in the presence of the laser field forward in time in the internal and external R-matrix regions. To verify the accuracy of the approach, we investigate two-photon ionization of Ne irradiated by an intense laser pulse and compare current results with those obtained using the R-matrix Floquet method and an alternative time-dependent method. We also verify the capability of the current approach by applying it to the study of two-dimensional momentum distributions of electrons ejected from Ne due to irradiation by a sequence of 2 as light pulses in the presence of a 780 nm laser field.

2DRMP: A suite of two-dimensional R-matrix propagation codes

The R-matrix method has proved to be a remarkably stable, robust and efficient technique for solving the close-coupling equations that arise in electron and photon collisions with atoms, ions and molecules. During the last thirty-four years a series of related R-matrix program packages have been published periodically in CPC. These packages are primarily concerned with low-energy scattering where the incident energy is insufficient to ionize the target. In this paper we describe previous term2DRMP,next term a suite of two-dimensional R-matrix propagation programs aimed at creating virtual experiments on high performance and grid architectures to enable the study of electron scattering from H-like atoms and ions at intermediate energies.

HBrowse: a GRACE tool for browsing R-matrix H-files

An H-file is used to convey information from the inner-region to the outer-region in R-matrix computations. HBrowse is a workstation tool for displaying a graphical abstraction of a local or remote R-matrix H-file. While it is published as a stand-alone tool for post-processing the output from R-matrix inner-region computations it also forms part of the Graphical R-matrix Atomic Collision Environment (GRACE), HBrowse is written in C and OSF/Motif for the UNIX operating system. (C) 2000 Elsevier Science B.V. All rights reserved.

Sequential extracellular matrix-focused and baited-global cluster analysis of serial transcriptomic profiles identifies candidate modulators of renal tubulointerstitial fibrosis in murine adriamycin-induced nephropathy

Transcriptome analysis using microarray technology represents a powerful unbiased approach for delineating pathogenic mechanisms in disease. Here molecular mechanisms of renal tubulointerstitial fibrosis (TIF) were probed by monitoring changes in the renal transcriptome in a glomerular disease-dependent model of TIF ( adriamycin nephropathy) using Affymetrix (mu74av2) microarray coupled with sequential primary biological function-focused and secondary

Desulfurisation of oils using ionic liquids: selection of cationic and anionic components to enhance extraction efficiency

Extraction of dibenzothiophene from dodecane using ionic liquids as the extracting phase has been investigated for a range of ionic liquids with varying cation classes (imidazolium, pyridinium, and pyrrolidinium) and a range of anion types using liquid-liquid partition studies and QSPR (quantitative structure-activity relationship) analysis. The partition ratio of dibenzothiophene to the ionic liquids showed a clear variation with cation class (dimethylpyridinium > methylpyridinium > pyridinium approximate to imidazolium approximate to pyrrolidinium), with much less significant variation with anion type. Polyaromatic quinolinium-based ionic liquids showed even greater extraction potential, but were compromised by higher melting points. For example, 1-butyl-6-methylquinolinium bis{(trifluoromethyl)sulfonyl} amide (mp 47 degrees C) extracted 90% of the available dibenzothiophene from dodecane at 60 degrees C.

Gelation of ionic liquids using a cross-linked poly(ethylene glycol) gel matrix

Conductive ionic liquid -poly(ethylene glycol) (IL-PEG) gels have been prepared by gelation of the hydrophobic ionic liquid 1-hexyl-3-methylimidazolium bis(trifluoromethanesulfonyl)imide [(C(6)mim] [NTf2]) by the cross-linking reaction of disuccinimidylpropyl PEG monomers with four-arm tetraamine PEG cross-linkers. This is the first time that a crosslinked PEG matrix, such as this, has been used to gel nonaqueous solvents. Initial studies screening other ionic liquids as solvents indicate that the gelation of the ionic liquid is both cation and anion dependent with smaller, coordinating cations disrupting or preventing gel formation.