Author

Yutaka Murata

Kyoto UniversityORCID 0000-0001-6636-3320Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Research Focus:chromatin & epigenetic regulation· 2 Approach:deep learning· 2 Approach:statistical model· 2 Approach:biophysical modeling· 1 Assay:DNA methylation· 1 Research Focus:drug response / drug discovery· 1 Assay:Hi-C· 1 Assay:proteomics· 1

Frequent Co-Authors

Shoji TakadaiD· 3 shared Masataka YamauchiiD· 2 shared Toru NiinaiD· 2 shared Fritz NagaeiD· 1 shared Tsuyoshi TerakawaiD· 1 shared

Activity by Year

2025-2026 · peak 2/yr

Co-Author Collaboration Network

5 top collaborators · 8 mutual co-author links

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3 shared papersBiophysics

Shoji TakadaORCID

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3 papers

Recent·Most cited

BiophysicsJournal of Computational ChemistryPeer-reviewedJul 7, 2026

OpenCafeMol with 3SPN.2 DNA model: GPU Acceleration for Long-Time Coarse-Grained Chromatin Simulations

Masataka Yamauchi, Yutaka Murata, Toru Niina, Shoji Takada

The paper extends a GPU-accelerated molecular dynamics simulator to support DNA models and improves efficiency for simulating chromatin interactions over long timescales.

DOI 10.1002/jcc.70460

DNA methylationHi-C

𝕏 PostBluesky

BiophysicsNature CommunicationsPeer-reviewedNov 21, 2025

Mechanistic models of asymmetric hand-over-hand translocation and nucleosome navigation by CMG helicase

Fritz Nagae, Yutaka Murata, Masataka Yamauchi…·Tsuyoshi Terakawa

This study uses molecular dynamics simulations to show how CMG helicase translocates directionally and navigates nucleosomes during DNA replication, with contributions from Csm3/Tof1 and RPA.

4 citations

biophysical modelingchromatin & epigenetic regulation

𝕏 PostBluesky

BiophysicsBiophysical JournalPeer-reviewedJul 15, 2025

OpenCafeMol: A coarse-grained biomolecular simulator on GPU with its application to vesicle fusion

Yutaka Murata, Toru Niina, Shoji Takada

The paper introduces OpenCafeMol, a GPU-accelerated MD simulator for biomolecules, showing speedups over CPU and applying it to vesicle fusion studies.

5 citations

proteomicsdeep learning

𝕏 PostBluesky