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This paper describes parallelization of the space plasma particle simulation program “KEMPOI” and shows its performance on five different platforms. One of our goals is to solve the Electrostatic Solitary Wave (ESW) problem by intensive computer simulations, which previously took about 1 month for a single experiment (107 particles, 104 time steps). The parallelized version performs the same calculation...
A powerful PDB-data-retrieval system “PDB Diving Booster,” which is a collection of functions/methods for data-retrieval and datatransmission, will enhances high-performance parallel-distributed programming in the field of structural biology. This system provides with 1) functions for reading whatever irregular data in PDB file, 2) methods to access and calculate elementary data in the structured...
Chrysanthemum (Chrysanthemum morifolium Ramat.) is one of the most popular ornamental flowers in the world, and many agronomic traits have recently been introduced to chrysanthemum cultivars by gene transformation. Concerns have been raised, however, regarding transgene flow from transgenic plants to wild plants. In early studies, ethylene receptor genes have been used for genetic modification in...
The ion permeation process, driven by a membrane potential through an outer membrane protein, OmpF porin of Escherichia coli, was simulated by molecular dynamics. A Na+ ion, initially placed in the solvent region at the outer side of the porin channel, moved along the electric field passing through the porin channel in a 1.3 nsec simulation; the permeation rate was consistent with the experimentally...
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