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List of Projects

TSUBAME Encouragement Program for Young User and Female User FY2020, FY2019, FY2018, FY2017, FY2016
TSUBAME Encouragement Program for Younger User FY2019, FY2018, FY2017, FY2016, FY2015

TSUBAME Encouragement Program for Young User and Female User

FY2020

  • Floris van Eerden (Osaka Univ.)
    Structural Mechanism of T cell activation
  • Tran Phuoc Duy (Tokyo Tech)
    In silico study of hachimoji DNA: toward the new functional biomaterials
  • MOHINI YADAV (Chiba Institute of Technology)
    Theoretical study on the molecular mechanism of subtype-specific drug resistance in influenza A virus
  • Shinji IIDA (N2PC, Next generation Natural Products Chemistry)
    Molecular dynamics simulation for druggable cryptic site on protein surface
  • Takeru Kameda (Hiroshima Univ./RIKEN)
    Analysis of the Unwrapping Dynamics of DNA from Nucleosome Dependent on DNA Methylation
  • Erica Cooper (National Institute of Informatics)
    Transfer Learning for End-to-End Multi-Instrument MIDI-to-Music Synthesis
  • Kota Honda (Univ. of Tsukuba)
    Molecular dynamics study on molecular diffusion coefficient in CO2 hydrate
  • Yi Zhao (National Institute of Informatics)
    Exploring speaker representations and acoustic feature embeddings for VQ-VAE based voice conversion
  • Xiao MA (NMRI, National Maritime Research Institute)
    Quantum chemistry simulation to elucidate the influence of temperature on chemical reaction on marine oxidation catalyst
  • Naohito Okumura (Tokyo Tech)
    Scalable distributed rendering using multiple nodes for various models with clients
  • Yu Komatsu (Astrobiology Center, NINS)
    Search for pigments utilizing NIR and oxidizing H2O
  • Yuko Otani (Univ. of Tokyo)
    Study on dynamics of target proteins and the non-natural ligands

FY2019

  • Large Scale Multi-physics Numerical Simulation of Alkaline Water Electrolysis with GPU
    Kodama Manabu (Tokyo Tech)
  • Membrane Penetrations of Cyclic Peptides Predicted by PaCS-MD
    Ryuhei Harada (Univ. of Tsukuba)
  • Molecular dynamics simulation of early process of amyloid fibril formation
    Tomoko Mizuguchi (Kyoto Institute of Technology)
  • Computational Analysis of the Nucleosome Sliding Dynamics Dependent on DNA Methylation Using Extended Ensemble Methods
    Takeru Kameda (Hiroshima Univ.)
  • Docking simulation between medium molecule drug and Heat Shock Protein
    Matsukura Lisa (Kindai Univ.)
  • Theoretical study on the molecular mechanism of drug resistance of influenza virus
    Mohini Yadav(Chiba Institute of Technology)
  • Atomic-level Characterization for the Entire Transport Cycle of ADP/ATP Carrier Transporter
    Masahiko Taguchi (Kyoto Univ.)
  • Theoretical Analysis of Activation Mechanism of the Membrane Receptors by Lipids
  • Misa SAYAMA (Univ. of Tokyo)
  • Development of calculation method of mutual solubility for long-chain polymer melt using all-atom molecular dynamics simula
    Yamada Kazuo (Osaka Univ.)
  • Molecular dynamics simulation to elucidate the mechanism of attachment/detachment of molecules on catalyst surface
    Xiao MA (NMRI, National Maritime Research Institute)
  • Development of computational code for air-lasing simulator
    ZHANG YOUYUAN(Univ. of Tokyo)

FY2018

  • Development of Flexible Docking Method Based on Parallel Cascade Selection Molecular Dynamics Simulation
    Ryuhei Harada(Univ. of Tsukuba)
  • Investigations on the mechanisms of low salinity EOR by pore scale flow simulation
    Fei Jiang(Yamaguchi Univ.)
  • Finding a drug candidate regulating protein function at an allosteric site
    Yuko Ito(AIST)
  • Rational predictive antibody engineering through molecular simulations
    Daisuke Kuroda(Univ. of Tokyo)
  • DEM-CFD modelling for dehydrogenation of methylcyclohexane on Pt/γ-Al2O3 catalyst.
    Lapizar, Maria Precious Paula Suarnaba(Tokyo Tech)
  • Elucidation of the flow and heat transfer characteristics for the compact and high efficiency electrical rotating machine
    Tomohisa Yuasa(Univ. of Tsukuba)
  • Radiation Hydrodynamic Simulation of First Stars
    Satoshi Tanaka(Univ. of Tsukuba)
  • Rapid design of thermally activated delayed fluorescent molecules with excellent color purity by means of materials informatics based on electronic structures
    Terashima Chieko(Ochanomizu Univ.)
  • Computational Analysis of the Variations of DNA Dynamics and Nucleosome Forming Ability Induced by DNA Methylation.
    Takeru Kameda(Hiroshima Univ.)
  • Molecular dynamics simulation for the elucidation of the molecular transportation behavior in CO2 hydrate
    Rintaro Fujikawa(Univ. of Tsukuba)
  • Theoretical elucidation of intensity anomalies observed in the vibrational spectrum of transition metal noble gas compounds
    Yuriko Ono(Hokkaido Univ.)
  • Analysis of non-equilibrium local heating generated by microwave irradiation
    Ano Taishi(Tokyo Tech)
  • "

  • Interaction Analysis of Extracellular Matrix Protein via All-Atom Molecular Dynamics Simulation
    Shinji Iida(Osaka Univ.)
  • Molecular dynamics simulation for protein-protein interaction using a novel generalized ensemble method without artificial bias potentials
    Tomonori Hayami(Osaka Univ.)
  • Structural analysis of prion protein by using generalized-ensemble simulations
    Hiroki Otaki(Nagasaki Univ.)
  • The Flexible Large-Capacity Memory System for High Performance and High Productivity
    Hiroko Midorikawa(Seijo Univ.)

FY2017

  • Yuko OTANI (Univ. of Tokyo)
    Dynamic control of peptide conformation by using synthetic bridged proline analogs
  • Hiroshi Watanabe (Univ. of Tokyo)
    Development and application of molecular dynamics simulation for hydrogen ion in solution
  • Misa SAYAMA (Univ. of Tokyo)
    Theoretical Analysis of Lipid Binding Pathway to Membrane Receptor Proteins
  • Yohei Miki (Univ. of Tsukuba)
    Hunting wandering intermediate mass black holes in galactic halo
  • Ryuhei Harada (Univ. of Tsukuba)
    Developments of Transition Path Sampling Methods based on Parallel Cascade Selection Molecular Dynamics Simulation
  • Hiroki Otaki (Nagasaki Univ.)
    Molecular dynamics study of aggregation behavior of amyloid fibrils
  • Xiao Ma (Univ. of Tsukuba)
    Molecular dynamics simulation for the elucidation of the molecular diffusion behavior in the CO2 hydrate
  • Azusa MURAOKA (Japan Women's Univ.)
    Solvent effects on the helical inversion reaction pathway of the helical molecules

FY2016

  • Yu YAMAMORI (Osaka Univ.)
    Application of Sparse Structure Learning to Analysis of Molecular Simulation
  • Yuko OTANI (Univ. of Tokyo)
    Generation of protein structure motif based on amino acid sequence involving synthetic bridged proline derivatives
  • Shinji IIDA (Osaka Univ.)
    Functional Analyses of an Intrinsically Disordered Protein by using an Original Extended Ensemble Molecular Dynamics Approach
  • Misa SAYAMA (Univ. of Tokyo)
    Theoretical Analysis of Interactions of Ligands with Membrane Receptor Proteins
  • Kouki KAWAMURA (NMRI)
    Large-Scale Particle Method for Simulation of Ship Behaviour and Safe Ship Design on TSUBAME 2.5
  • Masatoshi TAKAYANAGI (Univ. of Yamanashi)
    An implementation of the communication avoiding QR on GPU clusters
  • Kenji KAWAI (Tokyo Tech & Univ. of Tokyo)
    Numerical research of elastic wave propagation in the porous rock
  • Xiao Ma (Univ. of Tsukuba)
    Molecular dynamics simulation for the elucidation of the molecular diffusion behavior at the growth phase of the CO2 hydrat
  • Azusa MURAOKA (Japan Women's Univ.)
    Theoretical study on the inversion reaction process of high-order helical molecules
  • Chie MOTONO (AIST)
    Protein-ligand binding prediction using Supervised MD simulation

TSUBAME Encouragement Program for Younger User

Apr FY2019

  • Kota HONDA (Univ. of TSUKUBA)
    Molecular dynamics study on molecular diffusion coefficient in CO2 hydrate

Apr FY2018

  • YOSHIMURA Taichi (Osaka Univ.)
    Title of Project: Numerical simulation of crystal growth of Silicon Carbide using the Bottom Seeded Solution Growth method
  • SASAKI Miori (Ochanomizu Univ.)
    Title of Project: A theoretical study on phosphorescence emission from fluorescent molecule embedded in hyper nano-space constructed with organic molecules

Apr FY2017

  • Yohei Cho (Tokyo Tech)
    Title of Project: Improvement of Aerodynamic Property of Human Powered Aircraft by Analyzing Surrounding Fluid Flow (Continuous research)

Jan FY2016

  • Hanaya OKUDA (Univ. of Tokyo)
    Title of Project: Calculations of frictions on (001) plane of brucite (Continuous research)
  • Yohei Cho (Tokyo Tech)
    Title of Project: Improvement of Aerodynamic Property of Human Powered Aircraft by Analyzing Surrounding Fluid Flow
  • Rina YAMAYA (Univ. of Tokyo)
    Title of Project: Waveform inversion for source parameters of deep earthquakes and earth structure (Continuous research)

Oct FY2016

  • Hanaya OKUDA (Univ. of Tokyo)
    Title of Project: Calculations of frictions on (001) plane of brucite

Jul FY2016

  • Rina YAMAYA (Univ. of Tokyo)
    Title of Project: Waveform inversion for source parameters of deep earthquakes and earth structure

Apr FY2016

  • Takeya INOUE (Tokyo Tech)
    Title of Project: Fluid Flow Analysis of a Human Powered Aircraft to improve Design accuracy (Continuous research)

Jan FY2015

  • Takeya INOUE (Tokyo Tech)
    Title of Project: Fluid Flow Analysis of a Human Powered Aircraft to improve Design accuracy
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