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A01. Analysis of soft molecular systems
For theoretical calculations, now is the time to challenge problems in soft molecular systems. By using high performance computing resources represented by K computer, behavior of molecular systems comprising 106-107 atoms can now be simulated with femto second increment, and quantum chemistry calculation can incorporate entropy effects.
In A01 project, we analyze functional process of molecular systems by theoretical calculations, focusing on roles of their softness. Theoretical calculations, e.g., molecular simulations at atomic resolution in broad spatiotemporal space are conducted by using quantum mechanics, molecular mechanics and their hybrids, which aim to perform quantitative analysis and prediction of structure change and function in complex molecular systems. Statistical mechanics and other theoretical approaches are also employed to solve the problems in soft molecular systems. As planned research subjects, softness-function relationships in structure formation, molecular recognition and catalytic reaction are elucidated in biomolecular and supramolecular systems. We also investigate soft interface functions in solution, polymer and bio-membrane systems as fields of mass transfer and reaction. Proposed research projects are not limited to these targets and expected to broadly cover studies on a variety of soft molecular systems. More quantitative calculation are planned to be realized by verification and improvement of theoretical/computational methods in collaboration with A02. Molecular design and prediction of structures and functions are performed in collaboration with A03.
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TOPICS |
Penetration of viral proteins into membrane
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Theme
- Development of simulation methods and theories for atomic-resolution analysis in broad spatiotemporal space.
- Elucidating softness-function relationships in structure formation, molecular recognition and catalytic reaction in biomolecular and supramolecular systems.
- Investigation of soft interface functions as fields of mass transfer and reaction.
- Theoretical calculation studies on molecular functions of a variety of soft molecular systems.
- Realization of more quantitative calculation by verification and improvement of theoretical/computational methods.
- Molecular design and prediction of structures and functions.
Keywords
Dynamics of molecular systems, molecular simulation, quantum mechanical calculation, multiscale simulation, molecular theories
Research Area
Theoretical and computational chemistry, computational physics, biophysics
Planned Research Members
Softness-function relationship in large molecules and molecular assemblies investigated at atomic resolution
Leader: |
Akio KITAO |
Department of Life Science and Technology, Tokyo Institute of Technology, Professor |
Theory of Structure and Functions of Liquid and Polymer Interfaces
Leader: |
Akihiro MORITA |
Department of Chemistry, Tohoku University, Professor |
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Tatsuya ISHIYAMA |
Graduate School of Science and Engineering, University of Toyama, Associate Professor |
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Hideaki TAKAHASHI |
Department of Chemistry, Tohoku University, Associate Professor |
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Tatsuya JOUTSUKA |
Department of Chemistry, Tohoku University, Research Scientist |
Theoretical Analysis and Rational Design of Catalytic Activity of Flexible Molecules
Leader: |
Shigehiko HAYASHI |
Graduate School of Science, Kyoto University, Professor |
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Masahiko TAGUCHI |
Graduate School of Science, Kyoto University, Postdoctoral associate |
Proposed Research Subjects (2016-2017)
Fluctuation and response to external fields of soft molecules: Application of non-equilibrium statistical mechanics
Leader: |
Kumiko HAYASHI |
School of Engineering, Tohoku University, Assistant Professor |
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Satoshi P.TSUNODA |
JST, PRESTO Researcher |
Elucidation of the mechanism of multidrug recognition in transporter proteins and the molecular design of their inhibitors
Leader: |
Minoru SAKURAI |
Center for Biological Resources and Informatics, Tokyo Institute of Technology, Professor |
Water like polyamorphism in a monoatomic potential model: liquid-liquid transition and glassy dynamics
Leader: |
Kang KIM |
Graduate School of Engineering Science, Osaka University, Associate Professor |
Structural Formation, Dynamical Behavior, and Spectra of Complex Interaction Systems of Water, Ions, and Biomolecules
Leader: |
Hajime TORII |
Faculty of Education, Shizuoka University, Professor |
Ab initio molecular dynamics simulation of interfaces
Leader: |
Tatsuhiko OHTO |
Graduate School of Engineering Science, Osaka University, Assistant Professor |
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Hirokazu TADA |
Graduate School of Engineering Science, Osaka University, Professor |
Theoretical study of ion transportation of light-driven channel
Leader: |
Norio YOSHIDA |
Department of Chemistry, Graduate University of Science, Kyushu University, Associate Professor |
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Haruyuki NAKANO |
Department of Chemistry, Graduate University of Science, Kyushu University, Professor |
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Yoshihiro WATANABE |
Department of Chemistry, Graduate University of Science, Kyushu University, Assistant Professor |
Mechanism of Stereoselectivity of Flexible Catalytic Reaction Systems
Leader: |
Miho HATANAKA |
Division for Research Strategy, NAIST, Adjunct Associate Professor |
*Until June, 2017
Theoretical analysis of photochemical reactions of transition metal complexes ––the complex processes involving spin symmetry changes––
Leader: |
Yuki KURASHIGE |
Graduate School of Science, Kyoto University, Program-Specific Associate Professor |
Molecular study of the interplay between chemical reactions and protein conformational changes in biomolecular systems
Leader: |
Toshifumi MORI |
Department of Theoretical and Computational Molecular Science, Institute for Molecular Science, Assistant Professor |
Development of vibrational structure theory for biomolecules
Leader: |
Kiyoshi YAGI |
Theoretical Molecular Science Laboratory, RIKEN, Senior Scientist |
Proposed Research Subjects (2014-2015)
Application of non-equilibrium statistical mechanics to intracellular cargo transport by motor proteins
Leader: |
Kumiko HAYASHI |
School of Engineering , Tohoku University, Assistant Profesor |
Theoretical design of new photofunctional molecular devices with a locally flexible helical structure
Leader: |
Yoshiaki AMATATSU |
Graduate School of Engineering and Resource Science, Akita University, Associate Professor |
Hydration Effects and Free Energy Landscapes Determining the Allostery of Flexible Proteins
Leader: |
Minoru SAKURAI |
Center for Biological Resources and Informatics, Tokyo Institute of Technology, Professor |
Theoretical Analysis of the Intensities and Shapes of Vibrational Spectra Arising from Complex Intermolecular Interactions of Biomolecules and Water
Leader: |
Hajime TORII |
School of Education, Shizuoka University, Professor |
Flexibility in protein-DNA molecular recognition studied by multiscale simulations
Leader: |
Shoji TAKADA |
Graduate School of Science, Kyoto University, Professor |
Theoretical study of highly stereoselective aqueous reactions catalyzed by flexible chiral complexes
Leader: |
Miho HATANAKA |
Graduate School of Science and Engineering, Kinki University, Assistant Professor |
Development of Molecular Dynamics Method with the Aid of First-principles Calculations and Application to the Interface
Leader: |
Tatsuhiko OHTO |
Graduate School of Engineering Science, Osaka University, Assistant Professor |
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Hirokazu TADA |
Graduate School of Engineering Science, Osaka University, Professor |
Theoretical study of ion permeation of channel-rhodopsin
Leader: |
Norio YOSHIDA |
Department of Chemistry, Graduate University of Sciences, Kyushu University, Associate Professor |
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Haruyuki NAKANO |
Department of Chemistry, Graduate University of Sciences, Kyushu University, Professor |
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Yoshihiro WATANABE |
Department of Chemistry, Graduate University of Sciences, Kyushu University, Assistant Professor |
Characterization of structural dynamics of flexible histone tails
Leader: |
Sotaro FUCHIGAMI |
Graduate School of Medical Life Science, Yokohama City University, Assistant Professor |
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Satoko AKASHI |
Graduate School of Medical Life Science, Yokohama City University, Associate Professor |
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Kazumi SAIKUSA |
Graduate School of Science, Hiroshima University, Assistant Professor |
Protein functional dynamics investigated by X-ray scattering experiments and molecular dynamics simulations
Leader: |
Tomotaka OROGUCHI |
Department of Physics, Faculty of Science and Technology, Keio University, Assistant Professor |
Entangled quantum states in photochemistry of π-conjugated molecules and complexes with transition metal clusters
Leader: |
Yuki KURASHIGE |
Theoretical and Computational Molecular Science, Institute for Molecular Science, Assistant Professor |
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