竺立哲

助理教授

教育背景

博士(阿姆斯特丹大学)

硕士(查尔姆斯理工大学)

学士(华中科技大学)

研究领域
计算化学、计算生物学、生物大分子模拟、分子动力学、增强采样算法、路径搜索、核酸蛋白质相互作用、RNA/DNA干扰机理
电子邮件
zhulizhe@cuhk.edu.cn
个人简介

竺立哲博士毕业于阿姆斯特丹大学化学系,彼时作为玛丽居里初级研究员,通过分子模拟手段研究蛋白质受体别构效应的机理,后于2012年赴香港科技大学从事博士后研究,致力于增强抽样算法同马尔可夫态模型方法的整合。竺博士于2018年8月加入香港中文大学(深圳),现在生命与健康科学学院及瓦谢尔计算生物研究院担任助理教授。

竺博士目前的研究兴趣包括RNA与蛋白质相互作用,RNA/DNA干扰机制,高效自动化路径搜索方法及其他增强采样算法的开发等。竺博士已在国际主流期刊(Physical Review Letters, The Journal of Physical Chemistry Letters, PLOS Computational Biology, Current Opinion in Structural Biology, Journal of Computational Chemistry等)发表论文20篇。

学术著作

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:

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.