Selected Publications

The correlation between protein binding to DNA and DNA bending has been observed in many protein-DNA complex structures. These are, however, the correlation in static structures. Due to time and spatial resolutions in experiments, little is known on the dynamic coupling between protein binding and DNA bending. Here, armed with new simulation methods, we investigated the dynamic coupling between protein binding and DNA bending for a bacterial protein HU and 14 other proteins. The sliding of positively-charged HU on negatively-charged DNA is highly coupled with local DNA distortion, which is reminiscent of polaron in physics. In shorter time scale, HU was self-trapped in a locally bent DNA leading to pauses. Spontaneous relaxation in DNA shape resulted in the sliding mode.
J. Am. Chem. Soc., 2016, 138 (27), 8512–8522.

Recent Publications

  • Sequence-dependent nucleosome sliding in rotation-coupled and uncoupled modes revealed by molecular simulations
    PLoS Comp. Biol., 2017, 13 (12), e1005880

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

    Details Full Text

  • Modeling Structural Dynamics of Biomolecular Complexes by Coarse-Grained Molecular Simulations
    Acc. Chem. Res., 2015, 48 (12), 3026–3035.

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  • Atomistic Picture for the Folding Pathway of a Hybrid-1 Type Human Telomeric DNA G-quadruplex
    PLoS Comput. Biol., 2014, 10 (4), e1003562.

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  • Localized Frustration and Binding-Induced Conformational Change in Recognition of 5S RNA by TFIIIA Zinc Finger
    J. Phys. Chem. B, 2013, 117 (50), 15917–15925.

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  • Specific Binding of a Short miRNA Sequence by Zinc Knuckles of Lin28: A Molecular Dynamics Simulation Study
    J. Theor. Comput. Chem., 2013, 12 (8), 1341015.

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  • Low Folding Cooperativity of Hp35 Revealed by Single-Molecule Force Spectroscopy and Molecular Dynamics Simulation
    Biophys J., 2012, 102 (8), 1944-1951.

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Recent & Upcoming Presentations

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At the beginning of 2018, I decided to design a template for my notes in 2018.


Cheat Sheet for LaTeX mathematics.


Build a Chatting bot for Wechat with the wxBot package.


An example of using git-svn to organize code. Specially for git-lovers to use svn.


In this post I present an example of typesetting Japanese Lyrics with Chinese translations using LuaTex.




Yet another dictionary tool written in python. Allow regex.


My snippets for Emacs yasnippet.


A simple tool to plot information content LOGO for PWM. Image format is svg.


This is a package consisting of several small handy tools for analyzing biomolecule structures (protein, RNA, DNA) and CafeMol MD trajectories.


Simple script to perform RESPAC calculations (including APBS) for coarse-grained protein charge distributions.


My spacemacs configurations (init.el) and additional layer settings.


An Emacs major mode for editing CafeMol input file.