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- Tetsu Narumi, Ryutaro Susukita, +4 authors Toshikazu Ebisuzaki
- SC
- 2000

We performed molecular dynamics (MD) simulation of 9 million pairs of NaCl ions with the Ewald summation and obtained a calculation speed of 1.34 Tflops. In this calculation we used a special-purpose computer, MDM, which we are developing for the calculations of the Coulomb and van der Waals forces. The MDM enabled us to perform large-scale MD simulations… (More)

We describe the GRAPE-4 (Gravity Pipe 4) system, a special-purpose computer for astrophysical N-body simulations. In N-body simulations, most of the computing time is spent to calculate the force between particles, since the number of interactions is proportional to the square of the number of particles. For many problems the accuracy of fast algorithms… (More)

- Kholmirzo Kholmurodov, William Smith, Kenji Yasuoka, Thomas A. Darden, Toshikazu Ebisuzaki
- Journal of Computational Chemistry
- 2000

In this paper, we describe the performance and accuracy of the P 2 M 2 tree code. The P 2 M 2 tree code is a high-accuracy tree code based on the pseudoparticle multipole method (P 2 M 2). P 2 M 2 is a method to express multipole expansion using a small number of pseudoparticles. The potential field of physical particles is approximated by the field… (More)

- Seiji Kawamura, Masaki Ando, +132 authors Taizoh Yoshino
- 2008

- Yousuke Ohno, Eiji Nishibori, +8 authors Makoto Taiji
- SC
- 2007

We have achieved a sustained calculation speed of 281 Tflops for the optimization of the 3-D structures of proteins from the X-ray experimental data by the Genetic Algorithm - Direct Space (GA-DS) method. In this calculation we used MDGRAPE-3, special-purpose computer for molecular simulations, with the peak performance of 752 Tflops. In the GA-DS method, a… (More)

- Tomoki Matsuyama, Makoto T Kimura, +7 authors Hiroki Nagase
- Nucleic acids research
- 2003

Understanding the role of 'epigenetic' changes such as DNA methylation and chromatin remodeling has now become critical in understanding many biological processes. In order to delineate the global methylation pattern in a given genomic DNA, computer software has been developed to create a virtual image of restriction landmark genomic scanning (Vi-RLGS).… (More)

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 2). It is not practically suitable for large-scale simulations on most general-purpose computers. To cut down cost of force calculation one applies… (More)

- Nguyen Hai Chau, Atsushi Kawai, Toshikazu Ebisuzaki
- IJHPCA
- 2008