Biography

I am currently a postdoctoral researcher in the Computational Biophysics Research Team at RIKEN. I have started my current job since May, 2019. My research interests include functional mechanisms of DNA-protein binding, multi-scale organization of the genome, liquid-liquid phase separation in gene expression, and modeling of biomolecules in molecular dynamics (MD) simulations. Besides, I write code for MD softwares GENESIS and CafeMol.

I used to be a free software fanatic (FSF), with up to 10+ years of using various Linux distributions. But now I prefer to use many paid softwares, if available, to save my time and to focus more on truely interesting things.

In order to participate in a sport without any physical contact, I started practicing the Rubik’s cube from 2009, and I broke the national record for the $2\times 2$ cube in a game in 2010. Unfortunately, I stopped practicing since then.

• New parallel computing algorithm of molecular dynamics for extremely huge scale biological systems
  Jaewoon Jung, Chigusa Kobayashi, Kento Kasahara, Cheng Tan, Akiyoshi Kuroda, Kazuo Minami, Shigeru Ishiduki, Tatsuo Nishiki, Hikaru Inoue, Yutaka Ishikawa, Michael Feig, Yuji Sugita
  J. Comput. Chem., 2020.

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• The HMGB chromatin protein Nhp6A can bypass obstacles when traveling on DNA
  Kiyoto Kamagata, Kana Ouchi, Cheng Tan, Eriko Mano, Sridhar Mandali, Yining Wu, Shoji Takada, Satoshi Takahashi, Reid C Johnson
  Nucleic Acids Research, 2020, 48 (19), 10820-10831.

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• Nucleosome allostery in pioneer transcription factor binding
  Cheng Tan, Shoji Takada
  Proc. Natl. Acad. Sci., 2020, 117 (34), 20586-20596.

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• A singularity-free torsion angle potential for coarse-grained molecular dynamics simulations
  Cheng Tan, Jaewoon Jung, Chigusa Kobayashi, Yuji Sugita
  J. Chem. Phys., 2020, 153, 044110.

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• Nucleosomes as allosteric scaffolds for genetic regulation
  Shoji Takada, Giovanni B Brandani, Cheng Tan
  Curr. Opin. Struct. Biol., 2020, 62, 93-101.

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• Dynamic and Structural Modeling of the Specificity in Protein-DNA Interactions Guided by Binding Assay and Structure Data
  Cheng Tan, Shoji Takada
  J. Chem. Theory Comput., 2018, 14 (7), 3877-3889.

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• DNA sliding in nucleosomes via twist defect propagation revealed by molecular simulations
  Giovanni B. Brandani, Toru Niina, Cheng Tan, Shoji Takada
  Nucl. Acids Res., 2018, 46 (6), 2788-2801

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• Sequence-dependent nucleosome sliding in rotation-coupled and uncoupled modes revealed by molecular simulations
  Toru Niina, Giovanni B. Brandani, Cheng Tan, Shoji Takada
  PLoS Comp. Biol., 2017, 13 (12), e1005880

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• Dynamic Coupling among Protein Binding, Sliding, and DNA Bending Revealed by Molecular Dynamics
  Cheng Tan, Tsuyoshi Terakawa, Shoji Takada
  J. Am. Chem. Soc., 2016, 138 (27), 8512–8522.

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• Modeling Structural Dynamics of Biomolecular Complexes by Coarse-Grained Molecular Simulations
  Shoji Takada, Ryo Kanada, Cheng Tan, Tsuyoshi Terakawa, Wenfei Li, Hiroo Kenzaki
  Acc. Chem. Res., 2015, 48 (12), 3026–3035.

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• A singularity-free torsion angle potential for coarse-grained molecular dynamics simulations

  Wed, Sep 16, 2020, The 58th Annual Meeting of the Biophysical Society of Japan

• Allostery of Nucleosomal DNA for Transcription Factor Binding

  Tue, Sep 24, 2019, The 57th Annual Meeting of the Biophysical Society of Japan (Symposium: Integrative approaches towards understanding of gene expression)

• Binding and Diffusion of HMG Proteins on DNA Studied by Molecular Dynamics Simulations

  Fri, Dec 21, 2018, Visit to Prof. Kamagata’s group in Tohoku Univ.

• ctan@c-tan.com
• 81-78-304-5323
• @C_Tan
• Integrated Innovation Building (IIB) N702, 6-7-1 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo, Japan
• Workday 10:00 to 20:00