N -body simulation is a time consuming task in which force calculation part is most dominant part. The simplest and most accurate algorithm for force calculation is direct summation which has time complexity O(N). It is not practically suitable for large-scale simulations on most general-purpose computers. To cut down cost of force calculation one applies fast algorithms or performs force calcu...

In order to investigate the contribution of individual amino acids to protein and peptide solubility, we carried out 100 ns molecular dynamics (MD) simulations of 10(6) Å(3) cubic boxes containing ~3 × 10(4) water molecules and 27 tetra-peptides regularly positioned at 23 Å from each other and composed of a single amino acid type for all natural amino acids but cysteine and glycine. The calcula...

Recent experimental and theoretical developments have motivated interest in a more detailed exploration of heavy ion collisions in the range √ s NN =5–15 GeV. In contrast to interactions at the full RHIC energy of √ s NN =200 GeV, such collisions result in systems characterized by much higher baryon chemical potential, μB. Extensions of lattice QCD calculations to non-zero values of μB suggest ...

Due to the biological importance of long chain fatty acyl-CoA synthetase (ACSL), ACSL has been studied extensively in the past quarter century. ACSL is a ubiquitous enzyme from bacteria to mammal, and its product, long chain fatty acyl-CoA, is well known to be utilized for the energy metabolism. Furthermore ACSL participates in the cellular uptake of the exogenous Correspondence/Reprint request...

Two ATP-binding cassette transporters involved in (S)-2-aminoethyl-cysteine uptake in 1 Thermus thermophilus 2 3 Running title: AEC transporters of T. thermophilus 4 5 Yuko Kanemaru, Fumihito Hasebe, Takeo Tomita, Tomohisa Kuzuyama, and 6 Makoto Nishiyama 7 8 Biotechnology Research Center, The University of Tokyo, Tokyo 113-8657, Japan 9 RIKEN SPring-8 Center, Hyogo 679-5148, Japan 10 11 Corres...

In this paper, we present our XcalableMP implementation of the HPCC HPL, RandomAccess, FFT, and the Himeno benchmark [1] which is a typical stencil application. The highlights of this submission are as follows: • We implemented three HPCC benchmarks; HPL, RandomAccess, and FFT. In addition, we implemented the Himeno benchmark. • The SLOC (Source lines of code) of the benchmarks is shown in Tabl...

BRIKEN is a complex detection system to be installed at the RIB-facility of the RIKEN Nishina Center. It is aimed at the detection of heavy-ion implants, β-particles, γ-rays and β-delayed neutrons. The whole detection setup involves the Advanced Implantation Detection Array (AIDA), two HPGe Clover detectors and a large set of 166 counters of 3He embedded in a high-density polyethylene matrix. T...

The understanding of aqueous solution properties is recognized as being important in many areas of physical chemistry and molecular biophysics. Computer simulation has become an important tool in understanding the structure and dynamics of aqueous electrolyte solutions at the atomic or molecular level. Many works of molecular dynamics (MD) simulations have been carried out to investigate hydrat...

Akira SAITO, Junpei MARUYAMA, Ken MANABE, Katsuyuki KITAMOTO, Koji TAKAHASHI, Kazuhiro TAKAMI, Shinji HIROTSUNE, Yasumasa TAKAGI, Yoshihito TANAKA, Daigo MIWA, Makina YABASHI, Masahi ISHII, Megumi AKAI-KASAYA, Shik SHIN, Tetsuya ISHIKAWA, Yuji KUWAHARA and Masakazu AONO Department of Material and Life Science, Graduate School of Engineering, Osaka University, 2-1 Yamada-oka, Suita, Osaka 565-08...

A 3-D position determining mean is an indispensable function in the industrial automation system to obtain the spatial information. Optical methods have been used widely for this purpose. Semiconductor position sensitive device (PSD) is used widely because of its simplisity in instrumentation. A new type of PSD called R-IIPSD has invented to realize high precision detection. Relative resolution...