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Simulations of magnetic materials with MDGRAPE-2

B. G. Elmegreen, R. H. Koch, M. E. Schabes, T. Crawford, T. Ebisuzaki, H. Furusawa, T. Narumi, R. Susukita, K. Yasuoka
2004 IBM Journal of Research and Development  
The use of accelerator hardware for micromagnetics simulations is described, along with some initial results.  ...  Two research programs are highlighted, the simulation of a curved MRAM cell and the simulation of the write head in a computer disk drive.  ...  Osahiko Ohno for his extensive contributions to the MDGRAPE-2 project. *Trademark or registered trademark of International Business Machines Corporation.  ... 
doi:10.1147/rd.482.0199 fatcat:o5mjlb5w4jdz7k75bdoaythzkq

Fast and Accurate P3M Cosmological Simulations Using a Hardware Accelerator

Ryutaro Susukita
2004 Astrophysical Journal Supplement Series  
The results of cosmological N-body simulations using the MDGRAPE-2 P 3 M method agree with those using other P 3 M methods.  ...  We measured calculation times required for the MDGRAPE-2 P 3 M method on the system of a PC and one MDGRAPE-2 board.  ...  (e.g., Yatsuyanagi et al. 2003) , nuclear matter (e.g., Watanabe et al. 2002) , molecular dynamics (e.g., Koishi et al. 2002) , and magnetic materials (Elmegreen et al. 2002) , so that the MDGRAPE  ... 
doi:10.1086/421399 fatcat:juzxepua3jhurbp7kusqbq2hpi

All about RIKEN Integrated Cluster of Clusters (RICC)

Maho Nakata
2012 International Journal of Networking and Computing  
The basic concept of the RICC is to "provide an environment with high power computational resources to facilitate research and development for RIKEN's researchers".  ...  To encourage affirmative participation and proactive initiation, all the services were free of charge; however, access to RICC was limited to researchers and collaborators of RIKEN.  ...  The current the RICC system development would not have been possible without his constructive contribution and devoted management of the RICC and other former super computer systems of RIKEN.  ... 
doi:10.15803/ijnc.2.2_206 fatcat:i7744lphengifbkojz3nzzkj6u

Dynamics of Two-Sign Point Vortices in Positive and Negative Temperature States

Yuichi Yatsuyanagi, Yasuhito Kiwamoto, Hiroyuki Tomita, Mitsusada M. Sano, Takeshi Yoshida, Toshikazu Ebisuzaki
2005 Physical Review Letters  
Dynamics of two-sign point vortices in two-dimensional circular boundary is examined by numerical simulations with MDGRAPE-2.  ...  The massive simulation shows that different configurations appear in the time-asymptotic state depending on the sign of .  ...  computer for molecular dynamics simulations, MDGRAPE-2 [17, 18] .  ... 
doi:10.1103/physrevlett.94.054502 pmid:15783647 fatcat:ulgnlrvdvfapjbv74nuhjo42ii

Improved Recovery and Selectivity of Lanthanide-Ion-Binding Cyclic Peptide Hosts by Changing the Position of Acidic Amino Acids

Yoichi Hosokawa, Ayako Oshima, Takaaki Hatanaka, Nobuhiro Ishida
2022 Minerals  
The insights obtained from this study can be employed for the development of high-performance peptides for the selective recovery of Ln and other metal ions, as well as for the construction of diverse  ...  positions of the acidic amino acids were changed.  ...  ., Inc. for their assistance with the ESI-MS, ICP-OES, and SEM-EDX experiments, respectively. Conflicts of Interest: The authors declare no conflict of interest.  ... 
doi:10.3390/min12020148 fatcat:ojzjzenltfhx3an55ycsgjlbw4

Thermal conductivity and phase separation of the crust of accreting neutron stars

C. J. Horowitz, O. L. Caballero, D. K. Berry
2009 Physical Review E  
Some impurities with low atomic number Z are concentrated in a subregion of the simulation volume. For our composition, the solid crust must separate into regions of different compositions.  ...  We perform molecular dynamics simulations of the structure of the crust of an accreting neutron star using a complex composition that includes many impurities.  ...  Since our simulations have a complex composition, we automatically include the contributions of impurity scattering.  ... 
doi:10.1103/physreve.79.026103 pmid:19391802 fatcat:6swi3dcajfad7odbtyiktvjtzm

Neutron rich matter, neutron stars, and their crusts

C J Horowitz
2011 Journal of Physics, Conference Series  
Moreover, neutron rich matter is being studied with an extraordinary variety of new tools such as Facility for Rare Isotope Beams (FRIB) and the Laser Interferometer Gravitational Wave Observatory (LIGO  ...  Finally, we describe a new equation of state for supernova and neutron star merger simulations based on the Virial expansion at low densities, and large scale relativistic mean field calculations.  ...  Acknowledgments This work was done in collaboration with many people including D. K. Berry, E. F. Brown, K. Kadau, J.  ... 
doi:10.1088/1742-6596/312/4/042003 fatcat:h5cdituxxvdollgmr5ux2zxh3u

Molecular Dynamics Simulation of Iron — A Review

C. P. Chui, Wenqing Liu, Yongbing Xu, Yan Zhou
2015 SPIN  
Molecular dynamics (MD) is a technique of atomistic simulation which has facilitated scienti¯c discovery of interactions among particles since its advent in the late 1950s.  ...  Furthermore, it reveals the current progress of MD in simulating iron by exhibiting some results in the literature.  ...  Recongurable computing and GPUs are common hardware components for MD simulation, yet the former is less employed in simulation of metallic materials.  ... 
doi:10.1142/s201032471540007x fatcat:qbi2ceh2nfhg7dcx2baoztaonu

Phases of hot nuclear matter at subnuclear densities

Gentaro Watanabe, Katsuhiko Sato, Kenji Yasuoka, Toshikazu Ebisuzaki
2004 Physical Review C  
Structure of 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 between the different nuclear structures decreases with increasing temperature due to the thermal expansion of nuclear matter region  ...  The simulations of the 2048-nucleon system are performed using PCs (Pentium III) equipped with MDGRAPE-2, and those of the 16384-nucleon system are done by Fujitsu VPP 5000 equipped with MDGRAPE-2.  ... 
doi:10.1103/physrevc.69.055805 fatcat:seuo2yliqbcj7kbxqt7avnilvy

Structural and Functional Basis of a Role for CRKL in a Fibroblast Growth Factor 8-Induced Feed-Forward Loop

J.-H. Seo, A. Suenaga, M. Hatakeyama, M. Taiji, A. Imamoto
2009 Molecular and Cellular Biology  
By taking advantage of structural simulations, we performed in silico analysis of the interactions of the autophosphorylation sites of FGR receptor 1 (FGFR1) with the SH2 domain of CRKL or a highly related  ...  As predicted by simulations, we confirm the specific physical interaction of phosphorylated Y463 (pY463) in FGFR1 with the CRKL SH2 domain at an affinity ϳ30-fold stronger than that of CRK.  ...  by the Ministry of Education, Culture, Sports, Science and Technology of Japan to M.T.  ... 
doi:10.1128/mcb.01686-08 pmid:19307307 pmcid:PMC2681998 fatcat:bwipltmd4bd3peoyf4oart2roi

Nuclear pasta in supernovae and neutron stars [article]

Gentaro Watanabe, Toshiki Maruyama
2012 arXiv   pre-print
Recently, the formation process of the pasta phases, which has been a long-standing problem, has been unveiled using molecular dynamics simulations.  ...  In supernova cores and neutron star crusts, nuclei with exotic shapes such as rod-like and slab-like nuclei are expected to exist. These nuclei are collectively called nuclear "pasta".  ...  In these studies we used MDGRAPE-2 and -3 of the RIKEN Super Combined Cluster System.  ... 
arXiv:1109.3511v2 fatcat:d54kpgumuzfivglz23oman6lqu