Phase diagram of nuclear ``pasta' and its uncertainties in supernova cores (2007)
Sonoda, Hidetaka, Watanabe, Gentaro, Sato, Katsuhiko, Yasuoka, Kenji, Ebisuzaki, Toshikazu
We examine the model dependence of the phase diagram of inhomogeneous nulcear matter in supernova cores using the quantum molecular dynamics (QMD). Inhomogeneous matter includes crystallized matter...
Impact of nuclear "pasta" on neutrino transport in collapsing stellar cores (2007)
Sonoda, Hidetaka, Watanabe, Gentaro, Sato, Katsuhiko, Takiwaki, Tomoya, Yasuoka, Kenji, Ebisuzaki, Toshikazu
Nuclear ``pasta'', nonspherical nuclei in dense matter, is predicted to occur in collapsing supernova cores. We show how pasta phases affect the neutrino transport cross section via weak neutral...
Dynamics of two-sign point vortices in positive and negative temperature states (2006)
Yatsuyanagi, Yuichi, Kiwamoto, Yasuhito, Tomita, Hiroyuki, Sano, Mitsusada M., Yoshida, Takeshi, Ebisuzaki, Toshikazu
Growth mechanisms of GaN on the O-terminated ZnO(000-1) surfaces (2006)
Fujiwara, Katsutoshi, Ishii, Akira, Ebisuzaki, Toshikazu, Kobayashi, Atsushi, Kawaguchi, Yuji, Ohta, Jitsuo, ...
We have investigated the stability of the 1ML-GaN on the O-polarity ZnO(000-1) interface structure using the first-principles calculation. We have found in our calculated results that the most stable...
Dynamics of Two-Sign Point Vortices in Positive and Negative Temperature States (2006)
Yatsuyanagi, Yuichi, Kiwamoto, Yasuhito, Tomita, Hiroyuki, Sano, Mitsusada M., Yoshida, Takeshi, Ebisuzaki, Toshikazu
Evolution of Galactic Nuclei. I. orbital evolution of IMBH (2005)
Matsubayashi, Tatsushi, Makino, Junichiro, Ebisuzaki, Toshikazu
Resent observations and theoretical interpretations suggest that IMBHs (intermediate-mass black hole) are formed in the centers of young and compact star clusters born close to the center of their...
Koishi, Takahiro, Yasuoka, Kenji, Ebisuzaki, Toshikazu, Yoo, S., Zeng, Xiao Cheng
We performed large-scale molecular-dynamics simulation of nanoscale hydrophobic interaction manifested by the formation of nanobubble between nanometer-sized hydrophobic clusters at constrained...
Matsubayashi, Tatsushi, Yamazaki, Ryo, Yonetoku, Daisuke, Murakami, Toshio, Ebisuzaki, Toshikazu
Using the luminosity function and the apparent GRB rate inferred from the spectral peak energy-luminosity relation, we investigate the absolute GRB formation rate, taking into account the effects of...
Simulation of Transitions between "Pasta" Phases in Dense Matter (2004)
Watanabe, Gentaro, Maruyama, Toshiki, Sato, Katsuhiko, Yasuoka, Kenji, Ebisuzaki, Toshikazu
Calculations of equilibrium properties of dense matter predict that at subnuclear densities nuclei can be rodlike or slablike. To investigate whether transitions between phases with non-spherical...
Genome Informatics 14: 288--289 (2003) Ecell2d : Distributed E-CELL2 Andrew Stubbings (2004)
Andrew Stubbings, Naota Ishikawa, Takashi Yamazaki, Ariya Fujita, Iriko Kaneko, Yoshinari Fukui, ...
Introduction E-CELL [1, 2, 3] has been developed for whole cell simulation. Although E-CELL1 is run on Linux, E-CELL2 on Windows, and E-CELL3 on Linux and Windows-NT/XP, it is di#cult to port, build,...
Naoki Takada, Noriyuki Futatsugi, Atsushi Suenaga, Tetsu Narumi, Noriaki Okimoto, Hidenori Hirano, ...
Introduction Molecular dynamics (MD) simulation is a very useful technique for studying the structure and dynamics of biologically important molecules such as proteins and DNA/RNA. In MD simulations,...
Genome Informatics 14: 641--642 (2003) 641 SIMDEB-ECS : E-CELL Static Model Debugger (2004)
Naota Ishikawa, Iriko Kaneko, Toshikazu Ebisuzaki
Introduction E-CELL[1, 2, 3] has been developed for whole chemical reaction in a cell simulation. In order to help debugging cell model we developed and E-CELL static model debugger it analyzes the...
Massive Black Holes in Star Clusters. I. Equal-mass clusters (2004)
Baumgardt, Holger, Makino, Junichiro, Ebisuzaki, Toshikazu
In this paper we report results of collisional N-body simulations of the dynamical evolution of equal-mass star clusters containing a massive central black hole. Each cluster is composed of between...
Massive Black Holes in Star Clusters. II. Realistic Cluster Models (2004)
Baumgardt, Holger, Makino, Junichiro, Ebisuzaki, Toshikazu
We have followed the evolution of multi-mass star clusters containing massive central black holes through collisional N-body simulations done on GRAPE6. Each cluster is composed of between 16,384 to...
Dynamics of Intermediate Mass Black Holes in Star Clusters (2004)
Baumgardt, Holger, Zwart, Simon Portegies, McMillan, Steve, Makino, Jun, Ebisuzaki, Toshikazu
We have followed the evolution of multi-mass star clusters containing massive central black holes by N-body simulations on the GRAPE6 computers of Tokyo University. We find a strong cluster expansion...
Random phase vector for calculating the trace of a large matrix (2004)
Iitaka, Toshiaki, Ebisuzaki, Toshikazu
We derive an estimate of statistical error in calculating the trace of a large matrix by using random vector, and show that {\em random phase vector} gives the results with the smallest statistical...
Phases of hot nuclear matter at subnuclear densities (2003)
Watanabe, Gentaro, Sato, Katsuhiko, Yasuoka, Kenji, Ebisuzaki, Toshikazu
Structure of hot dense matter at subnuclear densities is investigated by quantum molecular dynamics (QMD) simulations. We analyze nucleon distributions and nuclear shapes using two-point correlation...
Nuclear pasta structure in hot neutron stars (2003)
Watanabe, Gentaro, Sato, Katsuhiko, Yasuoka, Kenji, Ebisuzaki, Toshikazu
Structure of cold and hot dense matter at subnuclear densities is investigated by quantum molecular dynamics (QMD) simulations. Obtained phase diagrams show that the density of the phase boundaries...
Structure of cold nuclear matter at subnuclear densities by Quantum Molecular Dynamics (2003)
Watanabe, Gentaro, Sato, Katsuhiko, Yasuoka, Kenji, Ebisuzaki, Toshikazu
Structure of cold nuclear matter at subnuclear densities for the proton fraction $x=0.5$, 0.3 and 0.1 is investigated by quantum molecular dynamics (QMD) simulations. We demonstrate that the phases...
Methane Hydrate under High Pressure: Searching for Centering of Hydrogen Bonds (2003)
Iitaka, Toshiaki, Ebisuzaki, Toshikazu
The structural, electronic, and spectroscopic properties of a high-pressure phase of methane hydrate (MH-III) are studied by first principles electronic structure calculations. A detailed analysis of...
Iitaka, Toshiaki, Ebisuzaki, Toshikazu
We introduce an efficient and numerically stable method for calculating linear response functions $\chi(\vec{q},\omega)$ of quantum systems at finite temperatures. The method is a combination of...
Microscopic Study of Slablike and Rodlike Nuclei: Quantum Molecular Dynamics Approach (2002)
Watanabe, Gentaro, Sato, Katsuhiko, Yasuoka, Kenji, Ebisuzaki, Toshikazu
Structure of cold dense matter at subnuclear densities is investigated by quantum molecular dynamics (QMD) simulations. We succeeded in showing that the phases with slab-like and rod-like nuclei etc....
Microscopic Study of Nuclear "Pasta" by Quantum Molecular Dynamics (2001)
Watanabe, Gentaro, Sato, Katsuhiko, Yasuoka, Kenji, Ebisuzaki, Toshikazu
Structure of cold dense stellar matter at subnuclear densities is investigated with quantum molecular dynamics (QMD). We succeeded in showing that the phases with slab-like and rod-like nuclei etc....
First Principles Calculation of Elastic Properties of Solid Argon at High Pressures (2001)
Iitaka, Toshiaki, Ebisuzaki, Toshikazu
The density and the elastic stiffness coefficients of fcc solid argon at high pressures from 1 GPa up to 80 GPa are computed by first-principles pseudopotential method with plane-wave basis set and...
Missing Link Found? --- The ``runaway'' path to supermassive black holes (2001)
Ebisuzaki, Toshikazu, Makino, Junichiro, Tsuru, Takeshi Go, Funato, Yoko, Zwart, Simon Portegies, Hut, Piet, ...
Observations of stellar kinematics, gas dynamics and masers around galactic nuclei have now firmly established that many galaxies host central supermassive black holes (SMBHs) with masses in the...
Calculating response functions in time domain with non-orthonormal basis sets (2000)
Iitaka, Toshiaki, Ebisuzaki, Toshikazu
We extend the recently proposed order-N algorithms (cond-mat/9703224) for calculating linear- and nonlinear-response functions in time domain to the systems described by nonorthonormal basis sets.
Non-degenerate Two Photon Absorption Spectra of Si Nanocrystallites (1999)
Iitaka, Toshiaki, Ebisuzaki, Toshikazu
We propose an efficient linear-scaling time-dependent method for calculating nonlinear response function, and study the size effects in non-degenerate two photon absorption spectra of Si...
Merging of galaxies with central black holes I. Hierarchical mergings of equal-mass galaxies (1995)
Junichiro Makino, Toshikazu Ebisuzaki
We investigated the merging of galaxies with central massive black holes. We performed simulation of hierarchical mergings, in which the merger remnant of one simulation was used as the progenitor...
Merging of galaxies with central black holes I. Hierarchical mergings of equal-mass galaxies (1995)
Junichiro Makino, Toshikazu Ebisuzaki
We investigated the merging of galaxies with central massive black holes. We performed simulation of hierarchical mergings, in which the merger remnant of one simulation was used as the progenitor...
The Effect of Gravitational Scattering on the Anisotropy of the Cosmic Background Radiation (1994)
Fukushige, Toshiyuki, Makino, Junichiro, Ebisuzaki, Toshikazu
The homogeneity of the cosmic microwave background radiation (CBR) is one of the most severe constraint for theories of the structure formation in the universe. We investigated the effect of the...
Matsuyama, Tomoki, Kimura, Makoto T., Koike, Kuniaki, Abe, Tomoko, Nakano, Takeshi, Asami, Tadao, ...
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...
Matsuyama, Tomoki, Kimura, Makoto T., Koike, Kuniaki, Abe, Tomoko, Nakano, Takeshi, Asami, Tadao, ...
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...