With the rapidly increasing amount of molecular biological data available, the computer-based analysis of molecular interactions becomes more and more feasible. Methods for computer-aided molecular docking have to inc...
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With the rapidly increasing amount of molecular biological data available, the computer-based analysis of molecular interactions becomes more and more feasible. Methods for computer-aided molecular docking have to include a reasonably accurate model of energy and must be able to deal with the combinatorial complexity incurred by the molecular flexibility of the docking partners. In both respects, recent years have seen substantial progress.
In this paper the numerical and parallel efficiency of the adaptive parallel strategy employed in a multigrid-solver package LiSS, developed in GMD-SCAI, are discussed. Two main aspects in these issues are adaptive cr...
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We consider an industrial cutting problem in textile manufacturing and report on heuristics for computing cutting images and lower bounds on waste for this problem. For the upper bounds we use greedy strategies based ...
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The solution of coupled problems is one of the grand challenges in scientificcomputing. Many problems can only be solved partially. Not all dependencies can be taken into account, e.g. only subproblems can be solved ...
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In the last few years lots of industrial simulation applications were ported onto parallel systems to gain more computational power. Besides other parallelisation techniques message-passing seems to be the most powerf...
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In the last few years lots of industrial simulation applications were ported onto parallel systems to gain more computational power. Besides other parallelisation techniques message-passing seems to be the most powerful and accepted one. Since MPI is the upcoming standard definition for message-passing libraries, portability and adaptation among different hardware- and software-environments becomes more and more realistic. However some problems are still unsolved, if two or more independent parallel MPI-applications are coupled and work together. This article shows some of the problems which might arise in coupling independent parallel codes: e.g. management of separate address spaces, definition of dedicated neighborhoods, integration of dynamic process sets and synchronisation events.
In this paper a rigorous approach to simulate thermal oxidation and diffusion phenomena is presented. Because the numerical problems will increase in future, especially when looking towards three-dimensional process s...
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In this paper a rigorous approach to simulate thermal oxidation and diffusion phenomena is presented. Because the numerical problems will increase in future, especially when looking towards three-dimensional process simulation, special emphasis is laid upon a parallel approach which additionally uses an optimal order solution method. Based on an environment for the parallel solution of elliptic and parabolic PDEs, L/sub i/SS, such a tool was developed.
The protein structure prediction problem is considered as a problem of fitting a sequence into a folding motif, We focus on finding an approximative structure representation providing the best preferences or contact e...
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The protein structure prediction problem is considered as a problem of fitting a sequence into a folding motif, We focus on finding an approximative structure representation providing the best preferences or contact energies. A 2-D structure description in the form of specific contact matrices is used, The main features of our approach are (i) only contacts involved in characteristic interaction patterns are considered, (ii) amino acid pair preferences or contact energies related to these interaction patterns are derived from the structural database and (iii) from the evaluation of individual structure elements, hypotheses on the alignment of a new sequence to a given structure may be derived, Results are demonstrated in particular to examples of the blue copper proteins.
HPC++ is a object-oriented programming environment dedicated to distributed memory parallel computers. It is based on a process model and integrates various parallel programming paradigms. Modularisation, interfaces a...
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ISBN:
(纸本)3540593934
HPC++ is a object-oriented programming environment dedicated to distributed memory parallel computers. It is based on a process model and integrates various parallel programming paradigms. Modularisation, interfaces and dynamic configuration are basic features. Parallel prototypes may be encapsulated in subnets. In the context of an existing commercial CASE tool HPC++ will be used as target language for the translation from graphical design method into code. Within one year, exploitation of HPC++ will be started offering an object-oriented library on top of standard parallel runtime systems.
eNCE (edge label neighborhood controlled) graph grammars belong to the most powerful graph rewriting systems with single-node graphs on the left-hand side of the productions. From an algorithmic point of view, conflue...
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