Journal Articles:

[1] Longcan Mei, Yanping Zhou, Lizhe Zhu, Changlin Liu, Zhuo Wu, Fangkui Wang, Gefei Hao, Di Yu, Hong Yuan*, and Yanfang Cui*. Site-Mutation of Hydrophobic Core Residues Synchronically Poise Super Interleukin 2 for Signaling: Identifying Distant Structural Effects through Affordable Computations. International Journal of Molecular Sciences, 19:916–938, 2018.

[2] Ilona Christy Unarta, Lizhe Zhu, Carmen Ka Man Tse, Peter Pak-Hang Cheung, Jin Yu, and Huang Xuhui. Molecular mechanisms of RNA polymerase II transcription elongation elucidated by kinetic network models. Current Opinion in Structural Biology, 49:54–62, 2018.

[3] Xiangze Zeng, Lizhe Zhu, Xiaoyan Zheng, Marco Cecchini, and Xuhui Huang. Harnessing complexity in molecular self-assembly using computer simulations. Physical Chemistry Chemical Physics, 20:6767–6776, 2018.

[4] Matthew Bratkowski, Ilona C. Unarta, Lizhe Zhu, Xuhui Huang, and Xin Liu*. Structural dissection of the TFIIB-Ssu72 interaction implicated in promotor-terminator crosstalk. Journal of Biological Chemistry, 293:1651–1665, 2018.

[5] Xiangze Zeng, Zhan-Wei Li, Xiaoyan Zheng, Lizhe Zhu, Zhao-Yan Sun, Zhong-Yuan Lu, and Xuhui Huang. Improving the productivity of monodisperse polyhedral cages by the rational design of kinetic self-assembly pathways. Physical Chemistry Chemical Physics, 20:10030–10037, 2018.

[6] Lizhe Zhu, Hanlun Jiang, Fu Kit Sheong, Xuefeng Cui, Yanli Wang, Xin Gao*, and Xuhui Huang*. Understanding the core of RNA interference: The dynamic aspects of Argonaute-mediated processes. Progress in Biophysics and Molecular Biology, 128:39–46, 2017.

[7] Siqin Cao, Lizhe Zhu, and Xuhui Huang*. 3DRISM-HI-D2MSA: An improved analytic theory to compute solvent structure around hydrophobic solutes with proper treatment of solute-solvent electrostatic interactions. Molecular Physics, 102:1–11, 2017.

[8] Wei Wang, Siqin Cao2, Lizhe Zhu2, and Xuhui Huang*. Constructing Markov State Models to elucidate the functional conformational changes of complex biomolecules. Wiley Interdisciplinary Reviews: Computational Molecular Science, page e1343, 2017.

[9] Luming Meng, Fu Kit Sheong, Xiangze Zeng, Lizhe Zhu, and Xuhui Huang*. Path Lumping: an efficient algorithm to identify metastable path channels for conformational dynamics of multi-body systems. The Journal of Chemical Physics, 147(4):044112, 2017.

[10] Xiaoyan Zheng, Lizhe Zhu, Xiangze Zeng, Luming Meng, Lu Zhang, Dong Wang, and Xuhui Huang*. Kinetics-controlled amphiphile self-assembly processes. The Journal of Physical Chemistry Letters, 8(8):1798–1803, 2017.

[11] Song Liu, Lizhe Zhu*, Fu Kit Sheong, Wei Wang, and Xuhui Huang*. Adaptive Partitioning by Local Density peaks (APLoD): an efficient density based clustering algorithm for analyzing molecular dynamics trajectories. Journal of Computational Chemistry, 38(3):152–160, 2017.

[12] Qiushi Zhang, Xiaoyan Zheng, Guowen Kuang, Weihua Wang, Lizhe Zhu, Rui Pang, Xingqiang Shi, Xuesong Shang, Xuhui Huang, Pei Nian Liu*, and Nian Lin*. Singlemolecule investigations of conformation adaptation of porphyrins on surfaces. The Journal of Physical Chemistry Letters, 8(6):1241–1247, 2017.

[13] Xiangze Zeng, Bin Li, Qin Qiao, Lizhe Zhu, Zhong-Yuan Lu*, and Xuhui Huang*. Elucidating dominant pathways of the nano-particle self-assembly process. Physical Chemistry Chemical Physics, 18:23494–23499, 2016.

[14] Lizhe Zhu, Hanlun Jiang, Fu Kit Sheong, Xuefeng Cui, Xin Gao, Yanli Wang, and Xuhui Huang*. A flexible domain-domain hinge promotes an induced-fit dominant mechanism for the loading of guide-DNA into Argonaute protein in Thermus thermophilus. The Journal of Physical Chemistry. B, 120(10):2709–2720, 2016.

[15] Xiaoyan Zheng, Qian Peng*, Lizhe Zhu, Yujun Xie, Xuhui Huang*, and Zhigang Shuai*. Unraveling the aggregation effect on amorphous phase AIE luminogens: a computational study. Nanoscale, 8:15173–15180, 2016.

[16] Lizhe Zhu, Fu Kit Sheong, Xiangze Zeng, and Xuhui Huang*. Elucidation of the conformational dynamics of multi-body systems by construction of Markov state models. Physical Chemistry Chemical Physics, 18:30228–30235, 2016.

[17] Hanlun Jiang, Fu Kit Sheong, Lizhe Zhu, Xin Gao, Julie Bernauer*, and Xuhui Huang*. Markov State Models reveal a two-step mechanism of miRNA loading into the human Argonaute protein: selective binding followed by structural re-arrangement. PLOS Computational Biology, 11(7):e1004404, 2015.

[18] Lizhe Zhu, Peter G. Bolhuis, and Jocelyne Vreede*. The HAMP signal relay domain adopts multiple conformational states through collective piston and tilt motions. PLOS Computational Biology, 9(2):e1002913, 2013.

[19] Lizhe Zhu, Daan Frenkel, and Peter G. Bolhuis*. Role of fluctuations in ligand binding cooperativity of membrane receptors. Physical Review Letters, 106(16):168103, 2011.

[20] Maria Werner, Lizhe Zhu, and Erik Aurell*. Cooperative action in eukaryotic gene regulation: Physical properties of a viral example. Physical Review E, 76:061909, Dec 2007.

Book Chapters:

[1] Hanlun Jiang, Lizhe Zhu, Amélie Héliou, Xin Gao*, Julie Bernauer*, and Xuhui Huang*. Elucidating Mechanisms of Molecular Recognition Between Human Argonaute and miRNA Using Computational Approaches, pages 251–275. Springer New York, New York, NY, 2017.