Author

Toru Niina

RIKEN Center for Biosystems Dynamics ResearchORCID 0000-0003-3025-4418Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

Click to filter author papers

Biophysics· 2

Signature Assays, Organisms & Methods

Click to filter · or open tag

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

Frequent Co-Authors

Shoji TakadaiD· 2 shared Yutaka MurataiD· 2 shared Masataka YamauchiiD· 1 shared

Activity by Year

2025-2026 · peak 1/yr

Co-Author Collaboration Network

3 top collaborators · 3 mutual co-author links

Click any collaborator node to inspect or filter shared papers

Focal author (center)Selected co-authorORCID co-authorUnlinked name

Curved chords = mutual co-authorship

2 shared papersBiophysics

Shoji TakadaORCID

Mutual co-authors in cluster

Author profile →

2 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

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