News2012-2016

The paper by Dr. Isseki Yu et al. has been published in eLife .

The paper by Drs. Suyong Re and Wataru Nishima has been published in J. Phys. Chem. C.

The paper on the GPU acceleration of GENESIS has been published in J. Chem. Theory Comput..

The paper by Dr. Hiroki Otaki et al. has been published in J. Phys. Chem. B.

The paper by Dr. Kiyoshi Yagi et al. has been publisehd in Biophys. J..

Ms. Masako Ishikawa has left our group.

Ms. Machiko Ishigaki (Assistant) has joined to our group.

Dr. Wataru Nishima moved to Los Alamos National Lab.

GENESIS 1.1.0 has just been released! More

GENESIS website has been renewed! More

Seminar Announcement :Prof. Xuhui Huang（The Hong Kong University of Science and Technology） Jul. 19th, 2016 (Wako)

Seminar Announcement :Luigi D’Ascenzo, Dr. Filip Leonarski, Dr. Pascal Auffinger（IBMC） Jul. 4th, 2016 (Wako)

Seminar Announcement : Prof. Michael Feig (Michigan State University) and Prof. Wonpil Im (University of Kansas) May. 17th, 2016 (Wako)

Seminar Announcement : Prof. Masayoshi Nakasako (Keio University) May. 10th, 2016 (Wako)

Seminar Announcement : Prof. Joanna Trylska (Centre of New Technologies, University of Warsaw, Poland) Apr. 12th, 2016 (Wako)

Dr. Donatas Surblys (Postdoctoral Researcher) has joined to our group.

Dr. Suyong Re moved to the RIKEN QBiC.

RIKEN’s Open Day events Announcement :　Apr. 23rd, 2016 (Wako) More

Dr. Daisuke Matsuoka (Postdoctoral Researcher) has joined to our group.

The paper by Dr. Suyong Re et al. has been published in Biophys. J..

The paper by Dr. Kiyoshi Yagi et al. has been publisehd in Phys. Chem. Chem. Phys..

The paper on the DoME model has been published in J. Phys. Chem. B.

The paper on the data assimilation has been published in J. Chem. Phys..

Seminar Announcement : Prof. James C. Gumbart (Georgia Institute of Technology, USA) Nov. 10th, 2015 (Wako)

Dr. Bo Thomsen received a letter of appreciation from Hiroshi Matsumoto, President of RIKEN, for the Best Poster of Congress Award in the 15th ICQC.

Seminar Announcement : Prof. Naresh Patwari (Indian Institute of Technology Bombay, India) Jul. 22nd, 2015 (Wako)

Dr. Hiroki Otaki moved to the Nagasaki University.

Dr. Bo Thomsen won the best poster of the congress award in the 15th International Congress of Quantum Chemistry (ICQC).

Seminar Announcement : Prof. Sihyun Ham (Sookmyung Women’s University, Korea) Jun. 30th, 2015 (Wako)

The paper on the data assimilation has been published in J. Chem. Phys.

The paper by Dr. Raimondas Galvelis et al. has been published in J. Comput. Chem.

The paper on GENESIS has been published in WIREs Comput. Mol. Sci.

The paper on GENESIS (WIREs Computational Molecular Science) has been press released. More

A new version of GENESIS has been released. More

The paper by Dr. Po-Hung Wang et al. has been published in J. Chem. Theory Comput.

RIKEN’s Open Day events Announcement :　Apr. 18th, 2015 (Wako) More

Dr. Kenta Yamada (Postdoctoral Researcher) has joined to our group.

Dr. Yasuaki Komuro (JSPS Research Fellow) and Dr. Pai-Chi Li (Postdoctoral Researcher) moved.

Seminar Announcement : Dr. Steven Hayward (University of East Anglia, UK) Feb. 26th, 2015 (Wako)

The collaborative research paper with Prof. M. Feig (Michigan State University) has been published in J. Mol. Graph. Model.

Seminar Announcement : Dr. Makoto Taiji（RIKEN Quantitative Biology Center）Feb. 20th, 2015 (Wako)

The paper on a hierarchical domain-motion analysis of conformational changes has been published in Proteins: Struct. Funct. Bioinf.

Dr. Wataru Mizukami moved to the Kyushu University.

Workshop Announcement : “Workshop on Frontier of Biomolecular Quantum Chemistry” Jan. 22-23, 2015 (Wako) (Official Site)

The paper by Dr. S. Re et al. has been published in J. Phys. Chem. Lett.

The paper on replica exchange MD interface (REIN) has been published in Int. J. Quantum Chem.

The paper by Mr. Y. Komuro et al. has been published in J. Chem. Theory Comput.

Workshop Announcement : “Workshop on Computer Modeling and Simulation of Biomolecular Systems” Sep. 22st, 2014 (Wako) (Official Site)

Mr. Y. Komuro won the poster presentation award in the 14th Annual Meeting of the Protein Science Society of Japan.

The collaborative research paper with Prof. O. Nureki (University of Tokyo) has been published in Nature.

The paper on the hybrid parallelization of MD simulations has been published in J. Comput. Chem.

Mr. Bo Thomsen (Technical Staff) has joined to our group.

Dr. W. Mizukami (Special Postdoctoral Researcher) and Dr. R. Galvelis (Postdoctoral Researcher) have joined to our group.

Mr. S. Watabe (Student Trainee) graduated.

Our new MD software GENESIS has been released under GPLv2 license.

Seminar Announcement : Prof. John E. Straub (Boston University, USA), Prof. Wonpil Im (The University of Kansas, USA) Mar. 6th, 2014 (Wako)

Mr. Y. Komuro won the student presentation award in 3rd international conference on molecular simulation (icsm2013).

Seminar Announcement : Dr. Karissa Sanbonmatsu (Los Alamos National Laboratory, USA) Dec. 11th, 2013 (Wako)

The paper on the surface-tension replica-exchange molecular dynamics method has been published in J. Chem. Theory Comput.

The paper on the structure prediction of transmembrane helix dimers has been published in J. Comput. Chem.

The collaborative research paper with Dr. Takao Yoda (Nagahama Institute of Bio-Science and Technology) has been published in PROTEINS: Struct. Funct. Bioinfo.

The paper on the modeling for crowded cellular environment has been published in J. Mol. Graph. Model.

Workshop Announcement : “Molecular Simulations of Biophysics and Biochemistry” Nov. 21st, 2013 (Kobe) (Official Site)

Workshop Announcement : “Modeling Biomolecular Systems in Cellular Environment” Oct. 31st-Nov. 1st, 2013 (Kyoto) (Official Site)

Seminar Announcement : Prof. Kenneth M. Merz Jr. (Michigan State University, USA) Sept. 26th, 2013 (Wako)

The paper on the lookup table for the fast pairwise nonbonded calculations has been published in J. Comput. Chem..

The collaborative research paper with Prof. O. Nureki and R. Ishitani (University of Tokyo) has been published in Proc. Natl. Acad. Sci. USA.

Workshop Announcement : 51st Annual Meeting of the Biophysical Society of Japan “Functional dynamics of Nucleosome and Chromathin in Nuclear Crowding Environment” Oct. 29th, 2013 (Kyoto)

The collaborative research paper with Prof. C. H. Choi (Kyungpook National University, Korea) has been published in J. Phys. Chem. B.

Dr. Po-Hung Wang (Contract Researcher) have joined to our group.

Dr. Andrei Pisliakov moved to the University of Dundee, Scotland.

Workshop Announcement : 13th annual meeting of the protein science society of Japan “Computational protein science in ExaFlops era” Jun 12th, 2013 (Tottori)

Mr. Y. Komuro has been selected for the participant of 2013 International HPC Summer School.

RIKEN’s Open Day events Announcement : Apr. 20th, 2013 (Wako)

Dr. T. Mori (Research Scientist), Dr. H. Otaki (Postdoctoral Fellows for Basic Science), Dr. I. Yu (Contract Researcher) have joined to our group.

Dr. C. Kobayashi (Contract Researcher) and Dr. F. Ogushi (Contract Researcher) moved to Kobe institute and Ochanomizu University, respectively.

The paper by Mr. Y. Komuro et al. has been published in J. Phys. Chem. B.

Mr. Y. Komuro has been selected for the participant of 5th HOPE MEETING.

Workshop Announcement : RIKEN symposium “Theoretical and experimental glycobiology” Mar. 12th, 2013 (Wako)

The paper on the protein stability in crowded cellular environment has been published in J. Am. Chem. Soc.

The paper on the QM/MM reaction path optimization has been published in J. Chem. Phys..

Dr. W. Mizukami (University of Bristol, UK) gave a seminar in Wako.

The collaborative research paper with Prof. C. H. Choi (Kyungpook National University, Korea) has been published in J. Phys. Chem. B.

Dr. K. Yagi (Research Scientist) has joined to our group.

Dr. K. Sanbonmatsu (Los Alamos National Laboratory, USA) gave a seminar in Wako.

A new homepage of Theoretical Molecular Science Laboratory has been opened.

“Confident identification of isomeric N-glycan structures by combined ion mobility mass spectrometry and hydrophilic interaction liquid chromatography.” has been published in Rapid Commun. Mass Spectrom.

Dr. Sugita organizes a symposium at the 50th Annual Meeting of the Biophysical Society of Japan.

“Recent Applications of Replica-Exchange Molecular Dynamics Simulations of Biomolecules” has been published in Curr. Phys. Chem.

“Molecular Dynamics Simulations Reveal Proton Transfer Pathways in Cytochrome C-Dependent Nitric Oxide Reductase” has been published in PLoS Comp. Biol.

“Conformational flexibility of N-glycans in solution studied by REMD simulations” has been published in Biophys. Rev.

“Structural insights into electron transfer in caa3-type cytochrome oxidase” has been published in Nature.

“Quantum mechanical/effective fragment potential molecular dynamics (QM/EFP-MD) study on intra-molecular proton transfer of glycine in water” has been published in Chem. Phys. Lett.

“Effect of Bisecting GlcNAc and Core Fucosylation on Conformational Properties of Biantennary Complex-Type N-Glycans in Solution” has been published in J. Phys. Chem. B

Ms. Yamaji (secretary) moved to Nishina center.

Dr. Sugita was promoted to a Chief Scientist and the laboratory name has been changed to Theoretical Molecular Science Laboratory.

“Crystal structure of alpha 5 beta 1 integrin ectodomain: Atomic details of the fibronectin receptor” has been published in J. Cell. Biol.

“The Intertransmembrane Region of Kaposi’s Sarcoma-Associated Herpesvirus Modulator of Immune Recognition 2 Contributes to B7-2 Downregulation” has been published in J. Virology.

Dr. Karl N. Kirschner（SCAI、Germany）gave a seminar in Wako.

Prof. Sihyun Ham（Sookmyung Women’s University, Korea）gave a seminar in Wako.

The paper on Volonoi analysis of lipid surface area in protein-membrane systems has been published in J. Comp. Chem.

The paper on flip-flop motions of lipid molecules has been published in Chem. Phys. Lett.

The paper on protein-protein interactions under the crowding environment has been published in J. Phys. Chem. B.