Members

Research Scientist Cheng Tan

EDUCATION

2007-2014 Ph.D. (physics) Nanjing University, China
2003-2007 B.Sc. (physics) Nanjing University, China

RESEARCH AND TEACHING EXPERIENCES

2024-present Research Scientist, RIKEN Center for Computational Science, Japan
2023-present Associate Professor (Cross-appointment), University of Hyogo, Japan
2019-2024 Postdoctoral researcher, RIKEN Center for Computational Science, Japan
2014-2019 Postdoctoral researcher, Kyoto University, Japan

PROFESSIONAL AFFILIATIONS

The biophysical society of Japan

RESEARCH PROJECTS

PUBLICATIONS

  1. GENESIS CGDYN: large-scale coarse-grained MD simulation with dynamic load balancing for heterogeneous biomolecular systems. Jaewoon Jung*, Cheng Tan*, and Yuji Sugita (*co-first authors) Nat Commun 15, 3370 (2024).
  2. Highly charged proteins and their repulsive interactions antagonize biomolecular condensation. Cheng Tan, Ai Niitsu, and Yuji Suguita
    JACS Au 3, 834-848 (2023).
  3. Micelle-like clusters in phase-separated Nanog condensates: A molecular simulation study. Azuki Mizutani, Cheng Tan, Yuji Sugita, and Shoji Takada PLoS Computat. Biol. 19, 7, e1011321 (2023).
  4. Roe of water-bridged interactions in metal ion coupled protein allostery. Xingye Guan*, Cheng Tan*, Wenfei Li, Wei Wang and D Thirumalai (*co-first authors)
    PLOS Comput. Biol. 18, e1010195 (2022).
  5. Implementation of residue-level coarse-grained models in GENESIS for large-scale molecular dynamics simulations. Cheng Tan, Jaewoon Jung, Chigusa Kobayashi, Diego Ugarte La Torre, Shoji Takada and Yuji Suguita
    PLOS Comput. Biol.18, e1009578 (2022).
  6. Testing mechanisms of DNA sliding by architectural DNA-binding proteins: dynamics of single wild-type and mutant protein molecules in vitro and in vivo. Kiyoto Kamagata, Yuji Itoh, Cheng Tan, Eriko Mano, Yining Wu, Sridhar Mandali, Shoji Takada, and Reid C. Johnson. Nucleic Acids Res. 49, 15, 8642-8664 (2021).
  7. The kinetic landscape of nucleosome assembly: A coarse-grained molecular dynamics study. Giovanni B. Brandani, Cheng Tan, and Shoji Takada. PLoS Computational Biology 17, 7, e1009253 (2021).
  8. A singularity-free torsion angle potential for coarse-grained molecular dynamics simulations. Cheng Tan, Jaewoon Jung, Chigusa Kobayashi, and Yuji Suguita
    J. Chem. Phys. 153, 0441 (2020).
  9. Nucleosome allostery in pioneer transcription factor binding. Cheng Tan and Shoji Takada
    Proc. Natl. Acad. Sci. U.S.A 117, 20586-20596, (2020).
  10. 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, and Yuji Sugita
    J. Comput. Chem. 42, 231-241 (2020)
  11. 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, and Reid C. Johnson.
    Nucleic Acids Res. 48(19) 10820-10831 (2020).
  12. Nucleosomes as allosteric scaffolds for genetic regulatio. Shoji Takada, Giovanni B. Brandani, and Cheng Tan
    Curr. Opin. Struct. Biol. 62 93-101 (2020).
  13. Dynamic and Structural Modeling of the Specificity in Protein–DNA Interactions Guided by Binding Assay and Structure Data. Cheng Tan and Shoji Takada
    J. Chem. Theory. Comput. , 14, 3877-3889 (2018).
  14. DNA sliding in nucleosomes via twist defect propagation revealed by molecular simulations. Giovanni B. Brandani, Toru Niina, Cheng Tan, and Shoji Takada
    Nucleic Acids Res. , 46, 2788-2801 (2018).
  15. Sequence-dependent nucleosome sliding in rotation-coupled and uncoupled modes revealed by molecular simulations. Toru Niina, Giovanni B. Brandani, Cheng Tan, and Shoji Takada
    Plos Comput. Biol. , 13, e1005880 (2017).
  16. Dynamic Coupling among Protein Binding, Sliding, and DNA Bending Revealed by Molecular Dynamics. Cheng Tan, Tsuyoshi Terakawa, and Shoji Takada
    J. Am. Chem. Soc. , 138, 5812-5822 (2016).
  17. Modeling Structural Dynamics of Biomolecular Complexes by Coarse-Grained Molecular Simulations. Shoji Takada, Ryo Kanada, Cheng Tan, Tsuyoshi Terakawa, Wenfei Li, and Hiroo Kenzaki
    Acc. Chem. Res. , 48, 3026-3035 (2015).
  18. Atomistic picture for the folding pathway of a hybrid-1 type human telomeric DNA G-quadruplex. Yunqiang Bian, Cheng Tan, Jun Wang, Yuebiao Sheng, Jian Zhang, and Wei Wang
    Plos Comput. Biol. , 10, e1003562 (2014).
  19. Localized Frustration and Binding-Induced Conformational Change in Recognition of 5S RNA by TFIIIA Zinc Finger. Cheng Tan, Wenfei Li, and Wei Wang
    J. Phys. Chem. B , 117, 15917-15925 (2013).
  20. Specific binding of a short miRNA sequence by zinc knuckles of Lin28: A molecular dynamics simulation study. Cheng Tan, Wenfei Li, and Wei Wang
    J. Theor. Comput. Chem. , 12, 1341015 (2013).
  21. Low Folding Cooperativity of Hp35 Revealed by Single-Molecule Force Spectroscopy and Molecular Dynamics Simulation. Chunmei Lv, Cheng Tan, Meng Qin, Dawei Zou, Yi Cao, and Wei Wang
    Biophys. J. , 102, 1944-1951 (2012).