CAL (Computational Astrophysics Laboratory), Advanced Computing Center

RIKEN (The Institute of Physical and Chemical Research)

Address: 2-1 Hirosawa, Wako, Saitama, 351-0198, JAPAN

Phone: 048-467-9415; Fax: 048-467-4078

Subjects of collaboration

Publications

1. W.Smith and K.Kholmurodov, The Molecular Simulation Package DL_POLY. Newsletter of Molecular Society of Japan (2001).
2. K.Kholmurodov, W.Smith, K.Yasuoka, and T.Ebisuzaki. Tuning DL_POLY for Vector Computers, (This work is part of a UK-Japan agreement to develop applications for high-performance computers.) HPCProfile (The National Publication for High-Performance Computing Applications and Techniques) Eds. R.J.Allan, D.J.Laff and M.F.Guest Issue 24, 12/1999
3. CCP5 Annual Meeting 1999 "Simulating Clusters and Interfaces", Birmingham, 6-8th September 1999, UK.
4. K.Kholmurodov, W.Smith, K.Yasuoka, and T.Ebisuzaki. A highly vectorised "link-cell" FORTRAN code for the DL_POLY molecular dynamics simulation package, RIKEN Review, No.25, November, 1999, pp.87-88.
5. K. Kholmurodov, W. Smith, K. Yasuoka, and T. Ebisuzaki, A Highly Vectorised "Link-Cell" FORTRAN Code for the DL_POLY Molecular Dynamics Simulation Package, Computer Physics Communications, (2000), 125, 167-192.
6. K.Kholmurodov, W.Smith, K.Yasuoka, and T.Ebisuzaki. Some Optimisations of DL_POLY Molecular Dynamics Simulation Code on the Fujitsu VPP700. Proc. High Performance Comput. and Appl., Published by JSPC, Tokyo, Japan, 2000.
7. Kholmurodov, K., Smith, W., Yasuoka, K., Darden, T., and Ebisuzaki, T. A smooth-particle mesh Ewald method for DL_POLY molecular dynamics simulation package on the Fujitsu VPP700. Journal of Computational Chemistry, 21 (13): 1187-1191 , 2000.
8. CFPP - HOKKE'2000 (IPSJ SIGHPC&SIGARC), March 2000, Hokkaido, Japan
9. K.Kholmurodov, W.Smith, K.Yasuoka, T.Narumi, R.Susukita, R.Allan, and T.Ebisuzaki. Fast Forces Calculations on DL_POLY Molecular Simulation Package: Adapting the~Program for a special-purpose computer MDM.
10. K.Kholmurodov, I.Puzynin, K.Yasuoka, T.Ebisuzaki Molecular Dynamics Simulation of Cluster-Beam- Surface Impact Processes for Metallic Phases. Preprint JINR, E11-2000-228, Dubna, 2000.
11. 2nd International Conference on Modern Trends in Computational Physics, "MTCP'2000", Dubna, JINR, 19-24 July, Russia, 2000.
12. 14th Annual Meeting of Molecular Society of Japan, Nagoya University, 16-18 January, Nagoya, Japan, 2001.
13. 14th Annual Workshop on Recent Developments in Computer Simulation Studies in Condensed Matter Physics, Athens, Georgia, February 19-24, 2001.
14. Kholmurodov, K. T.; Yasuoka, K.; Zeng, X. C. MD simulation of heterogeneous vapor nucleation on a solid surface. AIP Conf. Proc. 2000, 534, 253-256.
15. Kholmurodov, K. T.; Yasuoka, K.; Zeng, X. C. Molecular Dynamics simulation of a supersaturated vapor nucleation on a slit pore. II.Atomic wall model. J. Chem. Phys. 2001 (accepted)
16. The Fifteenth International Conference on Nucleation and Atmospheric Aerosols, University of Missouri-Rolla, 6-11 August 2000.
17. Kholmurodov, K. T.; etc. MD simulations of the dynamics and conformational change in the prion proteins. (under preparation)
18. Kholmurodov, K. T.; etc. Computational studies of prion proteins: MD simulations of E200K point mutation in the HuPrP.
19. The effect of Glu200Asp, Glu200Gln, Gln200Ile, and Gln200Val point mutations in the human prion protein using molecular dynamics and quantum chemical calculations.