VAMPIR: Visualization and Analysis of MPI Resources

Performance analysis most often is based on the detailed knowledge of program behavior. One option to get this information is tracing. Based on the research tool PARvis, the visualization environment VAMPIR was developed at KFA which now supports the new message passing standard MPI. VAMPIR translates a given trace file into a variety of graphical views, e.g., state diagrams, activity charts, time-line displays, and statistics. Moreover, it supports an animation mode that can help to locate performance bottlenecks, and it provides flexible filter operations to reduce the amount of information displayed. The most interesting part of VAMPIR is the powerful zooming feature that allows to identify problems at any level of detail

Ramond-Ramond Field Radiation from Rotating Ellipsoidal Membranes

We find a new stable rotator solution in D0-brane matrix mechanics. The solution is interpreted as a D2/D0 brane bound state, constructed as a transversely rotating ellipsoidal membrane with N D0-branes pinned over it. From the membrane point of view the attractive force of tension is exactly cancelled by the repulsive centrifugal force. Dynamical properties of the system are investigated, in particular the emission of spherical waves in the different massless sectors of supergravity. We compute the RR 1-form quadrupole, the RR 3-form dipole and the gravitational quadrupole radiation. Also, we show that our non-singular classical solution is stable against small perturbations in the initial conditions. Furthermore, we comment on a possible fundamental particle interpretation of our system.Comment: 25 pages, 1 eps figure, LaTeX, v2: Minor corrections, refs. adde

Genomes2Drugs: Identifies Target Proteins and Lead Drugs from Proteome Data

Background: Genome sequencing and bioinformatics have provided the full hypothetical proteome of many pathogenic organisms. Advances in microarray and mass spectrometry have also yielded large output datasets of possible target proteins/genes. However, the challenge remains to identify new targets for drug discovery from this wealth of information. Further analysis includes bioinformatics and/or molecular biology tools to validate the findings. This is time consuming and expensive, and could fail to yield novel drugs if protein purification and crystallography is impossible. To pre-empt this, a researcher may want to rapidly filter the output datasets for proteins that show good homology to proteins that have already been structurally characterised or proteins that are already targets for known drugs. Critically, those researchers developing novel antibiotics need to select out the proteins that show close homology to any human proteins, as future inhibitors are likely to cross-react with the host protein, causing off-target toxicity effects later in clinical trials. Methodology/Principal Findings: To solve many of these issues, we have developed a free online resource called Genomes2Drugs which ranks sequences to identify proteins that are (i) homologous to previously crystallized proteins or (ii) targets of known drugs, but are (iii) not homologous to human proteins. When tested using the Plasmodium falciparum malarial genome the program correctly enriched the ranked list of proteins with known drug target proteins. Conclusions/Significance: Genomes2Drugs rapidly identifies proteins that are likely to succeed in drug discovery pipelines

Transcranial Doppler in a Hispanic–Mestizo population with neurological diseases: a study of sonographic window and its determinants

Between 5% and 37% of patients are not suitable for transtemporal insonation with transcranial Doppler (TCD). This unsuitability is particularly frequent in elderly females and non-Caucasians. We aim to evaluate TCD efficiency in a mixed Hispanic population in Santiago, Chile and to determine whether factors associated with the presence of optimal windows depend exclusively on patient-related elements. Seven hundred forty-nine patients were evaluated with power mode TCD. Optimal temporal windows (TWs) included detection of the middle, anterior, posterior cerebral arteries and terminal carotid. The patient's age and sex, the location of the examination, the time of day, whether the test was conducted on weekends and whether mechanical ventilation was used were recorded. Percentages of optimal windows were calculated. Examinations were deemed ideal if both TWs were optimal. TWs were obtained in 82% of cases. In univariate analyses, male sex (P < 0.001), an age below 60 years (P < 0.0001) and mechanical ventilation (P= 0.04) correlated with ideal TWs. Using logistic regression where dependent variable was a non-ideal window only male sex odds ratio (OR) 2.3 (1.51–3.45) and age below 60 OR 13.8 (7.8–24.6) were statistically significant. Our findings indicate that Hispanic populations have detection rates for TWs similar to Europeans and are affected by patient-related elements

Nambu Quantum Mechanics: A Nonlinear Generalization of Geometric Quantum Mechanics

We propose a generalization of the standard geometric formulation of quantum mechanics, based on the classical Nambu dynamics of free Euler tops. This extended quantum mechanics has in lieu of the standard exponential time evolution, a nonlinear temporal evolution given by Jacobi elliptic functions. In the limit where latter's moduli parameters are set to zero, the usual geometric formulation of quantum mechanics, based on the Kahler structure of a complex projective Hilbert space, is recovered. We point out various novel features of this extended quantum mechanics, including its geometric aspects. Our approach sheds a new light on the problem of quantization of Nambu dynamics. Finally, we argue that the structure of this nonlinear quantum mechanics is natural from the point of view of string theory.Comment: 15 pages, LaTeX, typos correcte

Perfect Fluid Theory and its Extensions

We review the canonical theory for perfect fluids, in Eulerian and Lagrangian formulations. The theory is related to a description of extended structures in higher dimensions. Internal symmetry and supersymmetry degrees of freedom are incorporated. Additional miscellaneous subjects that are covered include physical topics concerning quantization, as well as mathematical issues of volume preserving diffeomorphisms and representations of Chern-Simons terms (= vortex or magnetic helicity).Comment: 3 figure

Pointlike structure for super p-branes

We present an efficient method to understand the p-brane dynamics in a unified framework. For this purpose, we reformulate the action for super p-branes in the form appropriate to incorporate the pointlike (parton) structure of higher dimensional p-branes and intend to interpret the p-brane dynamics as the collective dynamics of superparticles. In order to examine such a parton picture of super p-branes, we consider various superparticle configurations that can be reduced from super p-branes, especially, a supermembrane, and study the partonic structure of classical p-brane solutions.Comment: 22 pages, corrected typos, to appear in Phys. Rev. D58, 085018 (1998

Comments on the topological open membrane

Just as non-commutative gauge theories arise from quantising open strings in a large magnetic field, non-Abelian two-form gauge theories may conceivably be constructed by quantising open membranes in a large three-form magnetic background. We make some observations that arise in following this strategy, with an emphasis on the relation to the quantisation of volume-preserving diffeomorphisms (vpd). In particular, we construct consistent non-Abelian interactions of a two-form in 3+1 dimensions, based on gauge invariance under vpd.Comment: 6 pages, latex2e, uses revtex

Imaging Shock Waves in Diamond with Both High Temporal and Spatial Resolution at an XFEL

The advent of hard x-ray free-electron lasers (XFELs) has opened up a variety of scientific opportunities in areas as diverse as atomic physics, plasma physics, nonlinear optics in the x-ray range and protein crystallography. In this article, we access a new field of science by measuring quantitatively the local bulk properties and dynamics of matter under extreme conditions, in this case by using the short XFEL pulse to image an elastic compression wave in diamond. The elastic wave was initiated by an intense optical laser pulse and was imaged at different delay times after the optical pump pulse using magnified x-ray phase-contrast imaging. The temporal evolution of the shock wave can be monitored, yielding detailed information on shock dynamics, such as the shock velocity, the shock front width and the local compression of the material. The method provides a quantitative perspective on the state of matter in extreme conditions