Per Aspera ad Astra: On the Way to Parallel Processing

Computational Science and Engineering is being established as a third category of scientific methodology; this innovative discipline supports and supplements the traditional categories: theory and experiment, in order to solve the problems arising from complex systems challenging science and technology. While the successes of the past two decades in scientific computing have been achieved essentially by the technical breakthrough of the vector-supercomputers, today the discussion about the future of supercomputing is focussed on massively parallel computers. The discrepancy, however, between peak performance and sustained performance achievable with algorithmic kernels, software packages, and real applications is still disappointingly high. An important issue are programming models. While Message Passing on parallel computers with distributed memory is the only efficient programming paradigm available today, from a user's point of view it is hard to imagine that this programming model, rather than Shared Virtual Memory, will be capable to serve as the central basis in order to bring computing on massively parallel systems from a sheer computer science trend to the technological breakthrough needed to deal with the large applications of the future; this is especially true for commercial applications where explicit programming the data communication via Message Passing may turn out to be a huge software-technological barrier which nobody might be willing to surmount.KFA Jülich is one of the largest big-science research centres in Europe; its scientific and engineering activities are ranging from fundamental research to applied science and technology. KFA's Central Institute for Applied Mathematics (ZAM) is running the large-scale computing facilities and network systems at KFA and is providing communication services, general-purpose and supercomputer capacity also to the HLRZ ("Höchstleistungsrechenzentrum") established in 1987 in order to further enhance and promote computational science in Germany. Thus, at KFA - and in particular enforced by ZAM - supercomputing has received high priority since more than ten years. What particle accelerators mean to experimental physics, supercomputers mean to Computational Science and Engineering: Supercomputers are the accelerators of theory

On the Super-computational Background of the Research Centre Jülich

KFA Jülich is one of the largest big-science research centres in Europe; its scientific and engineering activities are ranging from fundamental research to applied science and technology. KFA's Central Institute for Applied Mathematics (ZAM) is running the large-scale computing facilities and network systems at KFA and is providing communication services, general-purpose and supercomputer capacity also for the HLRZ ("Höchstleistungsrechenzentrum") established in 1987 in order to further enhance and promote computational science in Germany. Thus, at KFA - and in particular enforced by ZAM - supercomputing has received high priority since more than ten years. What particle accelerators mean to experimental physics, supercomputers mean to Computational Science and Engineering: Supercomputers are the accelerators of theory

Search for Point Sources of High Energy Neutrinos with AMANDA

This paper describes the search for astronomical sources of high-energy neutrinos using the AMANDA-B10 detector, an array of 302 photomultiplier tubes, used for the detection of Cherenkov light from upward traveling neutrino-induced muons, buried deep in ice at the South Pole. The absolute pointing accuracy and angular resolution were studied by using coincident events between the AMANDA detector and two independent telescopes on the surface, the GASP air Cherenkov telescope and the SPASE extensive air shower array. Using data collected from April to October of 1997 (130.1 days of livetime), a general survey of the northern hemisphere revealed no statistically significant excess of events from any direction. The sensitivity for a flux of muon neutrinos is based on the effective detection area for through-going muons. Averaged over the Northern sky, the effective detection area exceeds 10,000 m^2 for E_{mu} ~ 10 TeV. Neutrinos generated in the atmosphere by cosmic ray interactions were used to verify the predicted performance of the detector. For a source with a differential energy spectrum proportional to E_{nu}^{-2} and declination larger than +40 degrees, we obtain E^2(dN_{nu}/dE) <= 10^{-6}GeVcm^{-2}s^{-1} for an energy threshold of 10 GeV.Comment: 46 pages, 22 figures, 4 tables, submitted to Ap.

Implementing Movie Control, Access and Management - from a Formal Description to a Working Multimedia System

In this paper we describe the tool-supported specification and implementation of a multimedia communication protocol on parallel hardware. MCAM is an application layer protocol for movie control, access and management. We specify the full MCAM protocol together with ISO presentation and session layers in Estelle. Using a code generator, we derive parallel C++ code from the specification. The code is compiled and executed on a multiprocessor system under OSF/1 and on UNIX workstations. Measurements show the performance speedup gained by several different configurations of parallel units. We also report on experiences with our methodology

Topological effects in ring polymers: A computer simulation study

Unconcatenated, unknotted polymer rings in the melt are subject to strong interactions with neighboring chains due to the presence of topological constraints. We study this by computer simulation using the bond-fluctuation algorithm for chains with up to N=512 statistical segments at a volume fraction \Phi=0.5 and show that rings in the melt are more compact than gaussian chains. A careful finite size analysis of the average ring size R \propto N^{\nu} yields an exponent \nu \approx 0.39 \pm 0.03 in agreement with a Flory-like argument for the topologica interactions. We show (using the same algorithm) that the dynamics of molten rings is similar to that of linear chains of the same mass, confirming recent experimental findings. The diffusion constant varies effectively as D_{N} \propto N^{-1.22(3) and is slightly higher than that of corresponding linear chains. For the ring sizes considered (up to 256 statistical segments) we find only one characteristic time scale \tau_{ee} \propto N^{2.0(2); this is shown by the collapse of several mean-square displacements and correlation functions onto corresponding master curves. Because of the shrunken state of the chain, this scaling is not compatible with simple Rouse motion. It applies for all sizes of ring studied and no sign of a crossover to any entangled regime is found.Comment: 20 Pages,11 eps figures, Late

On the Suitability of Estelle for Multimedia Systems

Formal Description Techniques have been widely used for the specification of traditional networked applications. They have not been applied to the specification of new applications such as multimedia systems yet. In this paper, we examine the FDT Estelle with respect to its suitability for multimedia system specification and automatic derivation of efficient implementations. We show that it is possible to specify certain aspects of multimedia systems, but that Estelle is not sufficient for others. The derived implementations often perform badly. We show the reasons and propose to use a slightly modified Estelle syntax and semantics to solve the problems. The implemented solution was tested successfully

Identification of novel neutralizing single-chain antibodies against vascular endothelial growth factor receptor 2

Human vascular endothelial growth factor (VEGF) and its receptor (VEGFR-2/kinase domain receptor [KDR]) play a crucial role in angiogenesis, which makes the VEGFR-2 signaling pathway a major target for therapeutic applications. In this study, a single-chain antibody phage display library was constructed from spleen cells of mice immunized with recombinant human soluble extracellular VEGFR-2/KDR consisting of all seven extracellular domains (sKDR D1-7) to obtain antibodies that block VEGF binding to VEGFR-2. Two specific single-chain antibodies (KDR1.3 and KDR2.6) that recognized human VEGFR-2 were selected; diversity analysis of the clones was performed by BstNI fingerprinting and nucleotide sequencing. The single-chain variable fragments (scFvs) were expressed in soluble form and specificity of interactions between affinity purified scFvs and VEGFR-2 was confirmed by ELISA. Binding of the recombinant antibodies for VEGFR-2 receptors was investigated by surface plasmon resonance spectroscopy. In vitro cell culture assays showed that KDR1.3 and KDR2.6 scFvs significantly suppressed the mitogenic response of human umbilical vein endothelial cells to recombinant human VEGF 165 in a dose-dependent manner, and reduced VEGF-dependent cell proliferation by 60% and 40%, respectively. In vivo analysis of these recombinant antibodies in a rat cornea angiogenesis model revealed that both antibodies suppressed the development of new corneal vessels (p &lt; 0.05). Overall, in vitro and in vivo results disclose strong interactions of KDR1.3 and KDR2.6 scFvs with VEGFR-2. These findings indicate that KDR1.3 and KDR2.6 scFvs are promising antiangiogenic therapeutic agents. © 2011 International Union of Biochemistry and Molecular Biology, Inc

Polynomial-Time Algorithms for Prime Factorization and Discrete Logarithms on a Quantum Computer

A digital computer is generally believed to be an efficient universal computing device; that is, it is believed able to simulate any physical computing device with an increase in computation time of at most a polynomial factor. This may not be true when quantum mechanics is taken into consideration. This paper considers factoring integers and finding discrete logarithms, two problems which are generally thought to be hard on a classical computer and have been used as the basis of several proposed cryptosystems. Efficient randomized algorithms are given for these two problems on a hypothetical quantum computer. These algorithms take a number of steps polynomial in the input size, e.g., the number of digits of the integer to be factored.Comment: 28 pages, LaTeX. This is an expanded version of a paper that appeared in the Proceedings of the 35th Annual Symposium on Foundations of Computer Science, Santa Fe, NM, Nov. 20--22, 1994. Minor revisions made January, 199