International Workshop MSSMBS'2008: Final Program

September 10

Arrival and Registration in "Dubna" hotel

10⁰⁰-10⁴⁵ Mitsuhiro Matsumoto
"Microbubbles: From Mechanical Stability to Hybrid Simulations"
Department of Mechanical Engineering and Science Graduate School of Engineering, Kyoto University, Kyoto 606-8501, Japan
10⁴⁵-11³⁰ Maria G. Khrenova¹, Anastasia V. Bochenkova¹, Alexander V. Nemukhin^1,2
"Computational study of the primary photoproducts of rhodopsin"
¹Department of Chemistry, M.V. Lomonosov Moscow State University, 119991 Moscow, Russian Federation

²N.M Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, 119334 Moscow, Russian Federation
11³⁰-11⁴⁵ Coffee Break

11⁴⁵-12³⁰ Viktor D. Lakhno
"DNA and nanobioelectronics"
Institute of Mathematical Problems of Biology, Russian Academy of Scieces, 142290 Pushchino Scientific Center, Moscow region, Russian Federation
12³⁰-13¹⁵ Alexander V. Nemukhin
"Molecular modeling in chemistry of large molecules"
Department of Chemistry, M.V. Lomonosov Moscow State University, 119991 Moscow, Russian Federation
13¹⁵-14³⁰ Lunch

14³⁰-14⁵⁵ Yoshinori Hirano^1*, Kenji Yasuoka², Makoto Suematsu³, Masato Yasui¹
"Water exclusion mechanism of aquaporin-1 by molecular dynamics simulations"
¹Department of Pharmacology, School of Medicine, Keio University, Japan

²Department of Mechanical Engineering, Keio University, Japan

³Department of Biochemistry & Integrative Medical Biology, School of Medicine, Keio University, Japan

^* 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan
14⁵⁵-15²⁰ Alexey K. Shaytan, Alexei R. Khokhlov
"Solvent Accessibility of Amino Acids Residues in Globular Proteins and its Correlation with Hydrophobicity/Interfacial Activity of Amino Acids"
Department of Physics, M.V. Lomonosov Moscow State University, Moscow 119991, Russia
15²⁰-15⁴⁵ Alexander L. Rabinovich
"Computer simulation studies of conformational properties of hydrocarbon chains of natural lipids: from the unperturbed state to liquid-cristalline membranes"
Institute of Biology, Karelian Research Center, Russian Academy of Sciences, Petrozavodsk, Russia
15⁴⁵-16¹⁰ Mikhail V. Avdeev¹, Irina A. Bodnarchuk², Kholmirzo T. Kholmurodov¹, Viktor I. Petrenko^1,3, Sergei P. Yaradaykin¹
"Limit partial molar volume of mono-carboxylic acids in benzene by molecular dynamics simulations"
¹Joint Institute for Nuclear Research, 141980, Dubna, Moscow region, Russia

²Skobeltsyn Institute of Nuclear Physics, Lomonosov Moscow State University, Russia

³Department of Physics, Kyiv Taras Shevchenko National University, Ukraine

16²⁰-17⁰⁵ Tetsuya Morishita
"First-Principles Molecular-Dinamics Investigation of Polymorphism in Liquids and Amorphous Materials"
RICS, AIST, Umezono 1-1-1, Tsukuba, Ibaraki 305-8568, Japan
17⁰⁵-17⁵⁰ Roman G. Efremov
"Biomembranes as pharmacological targets:insights from computer simulations"
Shemyakin-Ovchinnkov Institute of Bioorganic Chemistry, RAS, ul. Miklukho-Maklaya 16/10, GSP Moscow, 117997 Russia
17⁵⁰-18¹⁵ Olga V. Levtsova, Konstantin V. Shaitan
"Computer simulation of zervamicin IIB action"
Department of Biology, M.V. Lomonosov Moscow State University, Moscow 119991, Russia
18¹⁵-18⁴⁰ Ermuhammad Dushanov^1,2, Kholmirzo Kholmurodov¹, Guzel Aru¹, Vladimir Korenkov¹, William Smith³, Yousuke Ohno⁴, Tetsu Narumi^4,5, Gentaro Morimoto⁴, Makoto Taiji⁴, Kenji Yasuoka⁵
"MD simulations with DL_POLY on computing clusters of different communication architectures"
¹Joint Institute for Nuclear Research, 141980, Dubna, Moscow region, Russia

²Institute of Nuclear Physics, 702132, Ulugbek, Tashkent, Uzbekistan

³Daresbury Laboratory, Warrington, Wa4 4AD, United Kingdom

⁴RIKEN (The Institute of Physical and Chemical Research), Yokohama, Kanagawa 230-0046, Japan

⁵Keio University, 3-14-1 Hiyoshi, Kohoku, Yokohama 223-8522, Japan
19⁰⁰ Welcome party

09⁰⁰-09⁴⁵ Yuichi Masubuchi
"Molecular simulations of polymers with primitive chain network model"
Institute for Chemical Research, Kyoto University, Japan
09⁴⁵-10³⁰ Konstantin V. Shaitan
"Self-organization and rational design of nanobiosystems"
Department of Biology, M.V. Lomonosov Moscow State University, Moscow 119991, Russia
10³⁰-11¹⁵ Testu Narumi, Ryuji Sakamaki, Shun Kameoka, Kenji Yasuoka
"Using Special-Purpose and Video-Game Computers for Accelerating Molecular Dynamics Simulations"
Department of Mechanical Engeneering, Keio University, 3-14-1 Hiyoshi, Kohoku, Yokohama 223-8522, Japan
11¹⁵-11²⁵ Coffee Break

11²⁵-11⁵⁰ Tatyana B. Feldman^ab, Kholmirzo T. Kholmurodov^b, Mikhail A. Ostrovsky^ab
"Molecular simulation of visual pigment rhodopsin with E181K mutation assciated with retinitis pigmentosa"
^aN.M. Emanuel Institute of Biochemical Physics, RAS, Kosygin str. 4, 119334 Moscow, Russia

^bJINR, 141980 Dubna, Moscow region, Russia
11⁵⁰-12¹⁵ Toshihiro Kaneko, Toshiki Mima, Kenji Yasuoka
"Phase transitions of Lennard-Jones fluid confined in slit pores"
Department of Mechanical Engineering, Keio University, 3-14-1 Hiyoshi, Kohoku, Yokohama 223-8522, Japan
12¹⁵-12⁴⁰ Aram A. Shahinyan, L.H. Arsenyan, P.K. Hakobyan, Hrant H. Gharabekyan
"Molecular dynamics study of biological membranes and lyotropic liquid crystals"
Institute of Applied Problems of Physics, National Academy of Sciences, 0014 Yerevan, Republic of Armenia

International Scientific-Educational Centre, National Academy of Sciences of Armenia, 0019 Yerevan, Republic of Armenia
12⁴⁰-13⁴⁵ Lunch

13⁴⁵-14¹⁰ Pavel E. Volynsky, Dmitry E. Nolde, Roman G. Efremov
"Prediction of spatial structure of transmembrane helical dimers using computer simulations"
Shemyakin-Ovchinnkov Institute of Bioorganic Chemistry, RAS, ul. Miklukho-Maklaya 16/10, GSP Moscow, 117997 Russia
14¹⁰-14⁵⁵ Dmitry A. Skladnev^a, S.A. Tyurin^b, A.A. Khodonov^c
"Unfolded bacteriorhodopsin become a phytohormone"
^aState Research Institute of Genetics and Selection of Industrial Microorganisms, Moscow, 1-st Dorozhny pr.,1^A, 117545 Russia

^b"BIOS", Moscow, Bolshoi Drovyanoi per., 21/12, 109004 Russia

^cM.V. Lomonosov Moscow State Academy of Fine Chemical Technology, Moscow, prosp. Vernadskogo, 119571 Russia
14⁵⁵-15²⁰ Abdelouhab Kenoufi
"Minima Hopping: an efficient way to optimize geometry on the Potential Energy Surface and on The Free Energy Surface"
LNEC, Av.do Brasil, 101 1700-066 Lisboa, Portugal
15²⁰-15³⁰ Coffee Break

15³⁰-15⁵⁵ Dmitri A. Shulga¹, Alexander Oliferenko², Sergei Pisarev¹, Vladimir Palyulin^1,2, Nikolay Zefirov^1,2
"A route to molecular electrostatics through atomic charges generated by means of fast and robust empirical schemes"
¹Institute of Physiologically Active Compounds, RAS, 1, Severny Proezd, Chernogolovka, 142432 Moscow, Russia

²Department of Chemistry, Moscow State University, 119992 Moscow, Russia
15⁵⁵-16²⁰ Mikhail V. Altaisky^a, Kholmirzo T. Kholmurodov^a,b, Olga V. Komova^a, Nina L. Shmakova^a,b, Evgenii A. Krasavin^a,b
"On interaction of Au microparticles with pulse microwave radiation aimed to targeted application to tumor cells"
^aJINR (Joint Institute for Nuclear Research), 141980 Dubna, Moscow region, Russia

^b International University "Dubna", 141980 Dubna, Moscow region, Russia
16²⁰-16⁴⁵ Kholmirzo T. Kholmurodov
"MD simulations on mutant protein models (RecA, CDK, Rhodopsin proteins)"
JINR (Joint Institute for Nuclear Research), 141980 Dubna, Moscow region, Russia
16⁴⁵-17⁰⁰ Closing, Round table, Coffee