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Citing in the Handbook

A lot of effort has been put in elaborating reliable and practical methods of calculating changes in free energies (Christ et al. 2010; Kholmurodov et al. 2003; Meirovitch 2007; Pohorille et al. 2010).
Title of article: Applications of Computational Methods to Simulations of Proteins Dynamics
Editor: Jerzy Leszczynski, Department of Chemistry and Biochemistry, Jackson State University, Jackson, USA


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Book of conference MSSMBS2012

Title: Models in Bioscience and Materials Research: Molecular Dynamics and Related Techniques
Editor: Kh.T. Kholmurodov,
Publisher: Nova Science Publishers, Inc.


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Visiting Scientist of RIKEN:

Dear Dr. Kholmurodov,
It is my pleasure to invite you, to work at RIKEN as a Visiting Scientist
Sincerely yours,
President of RIKEN
Subject: Molecular Modeling in Biosciences and Materials Research
Laboratory: Computational Astrophysics Laboratory
Duration: April 1, 2013 to March 31, 2016



2010 JINR Prize winners:

The prize for applied research is awarded to LRB's scientists
M.A. Ostrovskiy,
Kh.T. Kholmurodov,
T.B. Feldman,

for their work
"Application of the molecular dynamics method to studying the dark-adapted state of the light-sensitive protein rhodopsin of the retinal visual cells"



XVI JINR AYSS'12 Prize winners:

The prize for applied research is awarded to LRB's young scientist
R.A. Eremin
for his work
"Molecular dynamics simulations on pure cis- and trans-decalin solutions and their mixtures"



36th session of the Programme Advisory Committee of the Condensed Matter Physics:

Encouraging Diploma is awarded to
R.A. Eremin
for for the high-quality poster presentation
"Molecular dynamics simulations in modeling of SANS: solutions of mono-carboxilic acids in decalin"




About our Sector:

Head of the Computer Molecular Modeling Sector

Dr. Phys.-Math. Kholmirzo T. Kholmurodov

Kholmirzo T. Kholmurodov graduated with honors from the Tajik State University in 1981. He fulfilled his graduate diploma project at the Joint Institute for Nuclear Research (JINR) in Dubna, Moscow region, Russia.
From JINR, he received his PhD (its russian equivalent called Candidate) degree in 1988 and Doctor's (actually, the second doctoral) degree in 1997 - both in Physical and Mathematical Sciences. Since 2003, he has been holding the position of the Head of the Computer Molecular Modeling Sector at the Laboratory of Radiation Biology, JINR. He was a visiting professor at Nagoya University (1997-1998), worked at RIKEN (The Institute of Physical and Chemical Research, Japan, 1998-2003); and was a member of the Japanese Physical Society (2000-2003) and Computation Collaborative Project 5 (the United Kingdom).
Computational skills: Molecular Dynamics (MD) simulation methods and techniques; Fortran, C programming languages; experience of work with AMBER, DL-POLY, etc. general purpose software; visualization tools for the efficient performing of MD research; networking and OS.
Current research interests: molecular simulations of nano- and biological structures based on parallel-vector and special-purpose architecture computing.

Current position:

Head of the Computer Molecular Modeling Sector
Laboratory of Radiation Biology (LRB), Joint Institute for Nuclear Research (JINR), 141980 Dubna, Moscow Region, Russia.
Phone: (+7-49621) 62-872, Fax: (+7-49621) 65-948, e-mail: mirzo@jinr.ru, mirzo@cv.jinr.ru, http://www.jinr.ru/cmms/

Professor of Dubna International University
Departments of Chemistry and Biophysics, http://www.uni-dubna.ru/, http://chem.uni-dubna.ru/, http://lrb.jinr.ru/kafedra/html/teachers/teachers.shtml, Dubna International University for Nature, Society and Man, University str. 19, 141980 Dubna, Moscow Region.

A Member of the American Chemical Society (ACS)
ACS Division of Biological Chemistry

Previous position:

Scientific Researcher, Advanced Computing Center, RIKEN (The Institute of Physical and Chemical Research), Hirosawa 2-1, Wako, 351-0198, Japan; Phone: +81-(0)48-467-9415, Fax: +81-(0)48-467-4078, mirzo@atlas.riken.go.jp; http://atlas.riken.go.jp/ mirzo/


--- Dr. Sc. in Physics and Mathematics, 1997, Laboratory of Information Technologies (LIT), JINR. Thesis Title: "Mathematical simulations of nonlinear phenomena in condensed matter physics"
--- Ph.D. in Physics and Mathematics, 1988, LIT, JINR; Advisor: Prof. Vladimir G. Makhankov. Thesis Title: "Mathematical simulations of nonlinear effects in Bose-gas models"
--- M.Sc. in Physics, Tajik State University and LIT JINR (1981)
--- B.Sc. in Physics, Tajik State University, Dushanbe, Tajikistan (1979)
--- National Scholarship at Tajik State University, 1976 - 1979
--- Governmental (All-Union) Scholarship, 19801981


--- 2003 - present: Head of the Computer Molecular Modeling Sector, LRB, JINR
--- 1997 - 2003: Scientific Researcher, RIKEN (The Institute of Physical and Chemical Research)
--- 1996 - 1997: Visiting Professor, Department of Mechanical Engineering, Nagoya University (at the Laboratory of Prof. Masao Doi and Associate Prof. Mitsuhiro Matsumoto)

Career research history:

--- Scientific Researcher, JINR, Dubna, Russia (1985-1996);
--- Visiting Professor, Nagoya University, Japan (1996-1997);
--- Scientific Researcher, RIKEN, Wako, Japan (1997-2003);
--- A Member of the Japanese Physical Society (2000-2003);
--- A Member of the IEEE Computer Society (2000-2003);
--- Head of CMM Sector, JINR, Dubna, Russia (2003-now);
--- Professor, Dubna International Univeristy, Russia (2004-now);
--- Visiting Professor, Keio University, Japan (2005-now);
--- Organizing Chairman of the Japan-Russia International Workshop MSSMBS "Molecular Simulation Studies in Material and Biological Sciences" (http://lrb.jinr.ru/cmms/confers/en.shtml);
--- An Editorial Board Member of the Open Nanomedicine Journal
     URL: http://www.benthamscience.com/open/tonmj/index.htm    Logo of TONMJ
--- A Member of the Computational Collaborative Project 5 (the United Kingdom);
--- A Member of the American Chemical Society (ACS); ACS Division of Biological Chemistry (2012-now)
--- Visiting Scientist of RIKEN (April 1, 2013 to March 31, 2016)

The current state of molecular dynamics research

During the last 10 years, we have been performing molecular dynamics (MD) studies in the materials science and on biological problems in close collaboration with advanced research centers of Japan and the United Kingdom. Our research is performed within the activities of the Computer Molecular Modeling Sector of the Laboratory of Radiation Biology (LRB) at the Joint Institute for Nuclear Research (JINR) and Dubna International University. It could be outlined as follows: "COMPUTER MOLECULAR DYNAMICS SIMULATIONS OF NANO- AND BIOSTRUCTURES". We conduct such activities in accordance with JINR's Seven-Year Topical Plan for LRB Research and International Cooperation. We perform MD simulations at different international computing centers, including JINR's Central Information and Computing Complex (CICC), the RIKEN Integrated Cluster of MDGRAPE Clusters (RICC, Japan), Computing Cluster at Yasuoka Laboratory (Keio University, Japan), and develop software in collaboration with the Daresbury Laboratory (UK). Since this July, the LRB has a license for using Amber 11.0 a general-purpose MD package with the support of acceleration on modern GPU/CUDA hardware. Every two years we organize the JapanRussia International workshop "Molecular Simulation Studies in Material and Biological Sciences" (MSSMBS) a unique meeting held in Russia which is specialized in MD modeling.

The aim and scope of MD simulations for bio- and radiobiological research could be outlined as follows:

--- to clarify the difference in protein dynamics and conformation between crystal and relaxed states; native and mutated proteins; liganded and unliganded protein; and so on;
--- to study the system of protein-DNA interactions with the inclusion of substrates, ligands, ions, solvents, and metals;
--- to simulate radiation-induced mutations and perform radiobilogical research concerning mutated proteins;
--- to observe correlations between the native and mutant versions of a protein; to build a the functional property map based on MD structural data.

The protein mutations (single-point amino acid substitutions in the protein structure) could be classified generally as follows:
--- Mutations that have little or no effect on stability;
--- Mutations that disrupt only the local structure;
--- Mutations that cause denaturation (full collapse or destruction of the global structure).

Finding the correlations between the protein mutations and diseases is one of the top targets for the molecular simulation research.

Our collaboration projects

1. Yasuoka Laboratory, Keio University, Japan (Kh. Kholmurodov, K.Yasuoka)

--- MD simulations with Applications in Material & Biological Systems

2. Advanced Center for Computing and Communication, RIKEN, Wako, Japan (Kh.Kholmurodov, T.Ebisuzaki, T.Iitaka)

--- MDGRAPE project, 100 Teraflops (three boards were granted to the LRB JINR; computer time is provided for MD simulations at the RIKEN Super Combined Cluster (RSCC).

3. Computational and Experimental Systems Biology Group, RIKEN, Yokohama, Japan (Kh.Kholmurodov, Y.Ohno, M.Taiji)

--- MDGRAPE-3 project, 1 Petaflop (an MDGRAPE-3 board is granted to LRB JINR; the JINRRIKEN Collaborative Research Agreement was signed).

4. Institute of Biochemical Physics of the Russian Academy of Sciecnes and Photobiology sector LRB (Kh.Kholmurodov, T.Feldman, Acad. M.A.Ostrovsky)

--- MD simulations of wild-type and mutant retinal proteins (rhodopsins)

5. Group of Radiation Genetics and Radiobiology, LRB (Kh.Kholmurodov, E.Krasavin, A.Boreiko)

--- MD simulations of RecA proteins and SOS mutagenesis mechanism

6. Group of Prokaryote Genetics (Kh.Kholmurodov, N.Koltovaya)

--- MD analysis of wild-type and mutant cyclin dependent kinase (CDK) proteins

7. Laboratory of Information Technologies, JINR (Kh.Kholmurodov, E.Dushanov, V.Korenkov, W.Smith (UK))

--- High-performance computing and MD simulations with LIT computer cluster.

MD-simulated snapshots (examples of molecular models).

Organizing Chairman of the Japan-Russia International Workshops "Molecular Simulation Studies in Material and Biological Sciences" MSSMBS'2004, 2006, 2008, 2010

At the Joint Institute for Nuclear Research, we regularly perform every two years the JapanRussia International Workshops "Molecular Simulation Studies in Material and Biological Sciences" (MSSMBS). The participants come from the leading research groups of Japan, Russia, and European countries. The MSSMBS workshops outline the current state and future aspects of computer molecular simulation techniques and methods used in material and life sciences. In MSSMBS'10, for exmaple, the following topics were discussed: Novel MD simulation techniques & methods; Hybrid computational approaches: DFT, QM/MM, MD, MD/CFD; Novel computing & communication architectures; General- & special-purpose MD machines; Video-game computers for accelerating MD; Simulation of biomacromolecules; Protein & DNA modelling; Simulation of radiation-induced mutations; Simulation of crystal & polymer systems; Quantum biophysics, electronic structure of macromolecules, so on.

2010. Visiting Professor at Keio University, Japan (Department of Mechanical Engineering. Yasuoka Laboratory).

Since 1997, our research teams from JINR and Keio University have been performing long-term and very productive joint research on molecular dynamics simulation of nano- and biological systems. We have published several dozens of joint papers in international and domestic scientific journals; presented joint papers at a large number of international meetings and conferences. We have organized and successfully performed several International Workshops "Molecular Simulation Studied in Material and Biological Sciences" (MSSMBS) in 2004, 2006, 2008, and 2010 on methodological and application aspects of the art of molecular dynamics simulation. We have experience of joint MD research on different kinds of computers of parallel or vector architectures, like FujitsuVPP vector supercomputers. During many years, we have been developing simulation techniques, methods, and computer codes under specialized computing architectures, like MDGRAPE-2 and 3 (Tflop and Pflop calculation speed for large biological systems). In recent years, we have been developing codes and methods for GPU computing clusters, which has to be considered as the best target as regards calculation speed and cost for performing large-scale MD simulations on molecular systems.

2010. Teaching a course of MD at the Department of Chemistry, Dubna International University

The course taught at the Department of Chemistry, Dubna International University, to fifth-year Master and graduate students focuses on computer-based design, synthesis, and investigation of chemical systems and materials with advanced properties. The simulation approach and techniques are based on MD methods. The course lasts two semesters, during which the students do research projects and study the fundamentals of the course. During previous years, several Master's and graduate projects have been completed and successfully defended. At the end of the course (after one year of study), several papers were published in international journals by advanced students. This year, we are planning to perform research projects based on MD simulation analysis. The course will be closely correlated with other disciplines of the Chemistry specialty.

2009. Visiting Professor of Keio University, Japan (Department of Mechanical Engineering, Yasuoka Laboratory).

The aims of the visit included molecular dynamics simulations of large biological structures; an analysis of MD simulation data; preparing a joint presentation and a publication; participation in international conferences; exchange and joint analysis of MD simulation data; performing studies on the application of the results of MD simulation data on the structure and energy properties of protein systems for drug design and drug nano-delivery models; correction of models and code optimization; comparison of the obtained results with different model configurations; comparison of MD simulation results with experimental data; and the interpretation of the simulation results for the biomedical application.

2009. Teaching a course of MD at the Department of Chemistry, Dubna International University.

THE following RESEARCH PROJECTS were done by students in the academic year 20092010:

--- Inna Bikmuhammedova and Kirill Ionov. MD simulations of structural and dynamical properties of Cu-Au and Ag-Auusing Gupta potentials.

--- Polina Kolodina and Anna Shurenkova. MD simulations of NaCl in water for different solute/solvent ratios.

--- Evgeniya Solodchenko and Alexandra Kruglova. MD simulations in the O-H-N system (clathrate hydrates: xenon and methane gases in water under high pressure).

--- Elena Alampieva and Alexandr Kristavchuk. MD simulations of a chloroform-lipid system.

2008. Visiting Professor of Keio University, Japan (Department of Mechanical Engineering. Yasuoka Laboratory).

Molecular-dynamics computational algorithm were discussed and developed for the simulation of protein structures. Optimized versions and specialized molecular-dynamics codes (developed by Yasuoka, Narumi, Kholmurodov, 20052009) were tested during the simulation of various mutant protein and protein surrounding models. A seminar and lectures were given to the students and staff of the Faculty of Science and Technology of Keio University.

2008 Teaching a course of MD at the Department of Chemistry, Dubna International University.

THE following RESEARCH PROJECTS were done by students in the academic year 20082009:

--- Alena Chulkova & Kholmirzo Kholmurodov. "Molecular dynamics simulations of the phase behavior of a biphenyl molecule in an active solvent media". Published in International Journal "The Open Physical Chemistry Journal," 2010.

--- Maria Abasheva & Kholmirzo Kholmurodov. "Molecular dynamics simulations of interactions of valinomycin with potassium and sodium ions in water solvent". Published in the International Journal "Advances in Bioscience and Biotechnology", 2010.

--- Viktoria Tuzova & Kholmrzo Kholmurodov. "MD Simulations of SeCd nanocrystals (a prototype of quantum dots systems) with oleic acid".

--- Olga Medvedkina & Kholmirzo Kholmurodov. "Molecular dynamics simulations of interactions of gold nanoparticles with a DNA fragment in hexagonal geometry".

--- Natalia Shastova & Kholmirzo Kholmurodov. "Molecular dynamics simulations of phase transitions of K-Na disilicate glass in an active solvent media".


2005-2010. Visiting RIKEN, Waseda University, and Keio University (Japan); Daresbury Laboratory (United Kingdom), etc.

Collaboration with colleagues from Japan and the United Kingdom has been very productive at this period. The acceleration of MD simulation codes implies both software and hardware development. We developed a molecular-dynamics computational algorithm and regularly exchanged our related experience. Lectures were delivered for students and young researchers as part of the collaboration visits.

Postal address:
LRB, JINR, Joliot-Curie 6,
141980 Dubna, Moscow region, Russia

Phone: +7 (49621) 62688
Telefax: +7 (49621) 65948
E-mail: lrb@jinr.ru

Copyright © LRB, JINR, Oleg Belov