理論と実験の協奏による柔らかな分子系の機能の科学-文部科学省科学研究費補助金「新学術領域研究」領域代表者 田原太平 (平成25-29年度) やわぶん

   

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.

TOPICS
Penetration of viral proteins into membrane

Penetration of viral proteins into membrane

Theme

  1. Development of simulation methods and theories for atomic-resolution analysis in broad spatiotemporal space.
  2. Elucidating softness-function relationships in structure formation, molecular recognition and catalytic reaction in biomolecular and supramolecular systems.
  3. Investigation of soft interface functions as fields of mass transfer and reaction.
  4. Theoretical calculation studies on molecular functions of a variety of soft molecular systems.
  5. Realization of more quantitative calculation by verification and improvement of theoretical/computational methods.
  6. 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
Tatsuya ISHIYAMA Graduate School of Science and Engineering, University of Toyama, Associate Professor
Hideaki TAKAHASHI Department of Chemistry, Tohoku University, Associate Professor
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
Masahiko TAGUCHI Graduate School of Science, Kyoto University, Postdoctoral associate
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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
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
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
Haruyuki NAKANO Department of Chemistry, Graduate University of Science, Kyushu University, Professor
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
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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
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
Haruyuki NAKANO Department of Chemistry, Graduate University of Sciences, Kyushu University, Professor
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
Satoko AKASHI Graduate School of Medical Life Science, Yokohama City University, Associate Professor
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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