粒子系生物物理研究チーム

研究概要

主な研究成果

主要論文

• Jung J., Tan C., and Sugita Y.:
  "GENESIS CGDYN: large-scale coarse-grained MD simulation with dynamic load balancing for heterogeneous biomolecular systems"
  Nature Comm. 15, 3370 (2024).
• Jung J., Yagi K., Tan C., Oshima H., Mori T., Yu I., Matsunaga Y., Kobayashi C., Ito S., Ugarte La Torre D., and Sugita Y.:
  "GENESIS 2.1: High-Performance Molecular Dynamics Software for Enhanced Sampling and Free-Energy Calculations for Atomistic, Coarse-Grained, and QM/MM models"
  J. Phys. Chem. B 128, 6028-6048 (2024).
• Ugarte La Torre D., Takada S., and Sugita, Y.;
  "Extension of the iSoLF implicit-solvent coarse-grained model for multicomponent lipid bilayers"
  J. Chem. Phys. 159, 075101 (2023).
• Jung J., Kobayashi C., and Sugita Y.:
  "Acceleration of generalized replica exchange with solute tempering simulations of large biological systems on massively parallel supercomputer"
  J. Comp. Chem, 44, 1740-1749 (2023).
• Mizutani A., Tan C., Sugita Y., and Takada S.:
  "Micelle-like clusters in phase-separated Nanog condensates: A molecular simulation study"
  PLoS Comp. Biol. 19, e1011321 (2023).
• Matsunaga Y., Kamiya M., Oshima H., Jung J., Ito S., and Sugita Y.:
  "Use of multistate Bennett acceptance ratio method for free-energy calculations from enhanced sampling and free-energy perturbation"
  Biophys. Rev.14, 1-10 (2022).
• Zhang Y., Kobayashi C., Cai X., Watanabe S., Tsutsumi A., Kikkawa M., Sugita Y., and Inaba K.:
  "Multiple sub state structures of SERCA2b reveal conformational overlap at transition steps during the catalytic cycle"
  Cell reports 41, 111760 (2022).
• Kobayashi C., Matsunaga Y., Jung J., and Sugita Y.:
  "Structural and energetic analysis of metastable intermediate states in the E1P–E2P transition of Ca2+-ATPase"
  Proc. Natl. Acad. Sci. USA, 118, e2105507118 (2021).
• Jung J., Kasahara K., Kobayashi C., Oshima H., Mori T., and Sugita Y.:
  "Optimized Hydrogen Mass Repartitioning Scheme Combined with Accurate Temperature/Pressure Evaluations for Thermodynamic and Kinetic Properties of Biological Systems"
  J. Chem. Theory Comput. 17, 5312-5321 (2021).
• Mori T., Jung J., Kobayashi C., Dokainish H.M, Re, Yuji Sugita
  "Elucidation of Interactions Regulating Conformational Stability and Dynamics of SARS-CoV-2 S-Protein"
  Biophys. J. 120, 1060-1071 (2021).

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