{"id":145,"date":"2022-06-07T18:02:36","date_gmt":"2022-06-07T18:02:36","guid":{"rendered":"https:\/\/xiakunchu.people.ust.hk\/?page_id=145"},"modified":"2026-01-12T11:39:40","modified_gmt":"2026-01-12T11:39:40","slug":"publications","status":"publish","type":"page","link":"https:\/\/xiakunchu.people.ust.hk\/?page_id=145","title":{"rendered":"Publications"},"content":{"rendered":"\n
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Full list at Google Scholar<\/a> and Publon<\/a>.<\/p>\n<\/div>\n<\/div>\n\n\n\n

Selected articles in recent years<\/strong><\/p>\n\n\n\n

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  1. Jinyu Chen<\/strong>, Cibo Feng<\/strong>, Yong Wang, and Xiakun Chu<\/strong>*. DNA actively regulates the \u201csafety-belt\u201d dynamics of condensin during loop extrusion.\u00a0Nature Communications<\/em>, 2026.<\/li>\n\n\n\n
  2. Cibo Feng<\/strong> and Xiakun Chu<\/strong>*. (A)symmetry in the Allele-Specific Chromosomal Structural Dynamics during Embryogenesis.\u00a0International Journal of Biological Macromolecules<\/em>, 334(Part 1), 149067, 2025.<\/li>\n\n\n\n
  3. Chengzhen Xu<\/strong> and Xiakun Chu<\/strong>*. Contact networks encode the ATP-induced dynamic structural asymmetry of condensin head domains.\u00a0The Journal of Chemical Physics<\/em>,\u00a0163(23), 2025.<\/li>\n\n\n\n
  4. Tao Zhu<\/strong>, Chunhe Li*, and Xiakun Chu<\/strong>*. Transcriptional condensates encode a \u201cgolden mean\u201d to optimize enhancer\u2013promoter communication across genomic distances. Proceedings of the National Academy of Sciences<\/em>, 122(43), e2513371122, 2025.<\/li>\n\n\n\n
  5. Guoqing Zhang<\/strong>, Cibo Feng<\/strong>, and Xiakun Chu<\/strong>*. Repulsive vs Attractive Crowding Distinctly Regulate TDP-43 Condensates through Region-specific Structural Dynamics. JACS Au<\/em>, 2025.<\/li>\n\n\n\n
  6. Shuai Wang<\/strong>, Jun Gao*, and Xiakun Chu<\/strong>*. Residue-Specific Structural and Dynamical Coupling of Protein and Hydration Water Revealed by Molecular Dynamics Simulations. Biomolecules<\/em>, 15<\/em>(5), 660, 2025.<\/li>\n\n\n\n
  7. Yuxiang Luo, Zhaoyue Yan, Xiakun Chu<\/strong>, Ying Zhang, Yufan Qiu, and Huilin Li*. Binding mechanism and distant regulation of histone deacetylase 8 by PCI-34051. Communications Biology<\/em>, 8<\/em>(1), 221, 2025.<\/li>\n\n\n\n
  8. Chen Wang, Cheng Ma, Yuanyou Xu, Shenghai Chang, Hangjun Wu, Chunlan Yan, Jinghua Chen, Yongping Wu, Shaoya An, Jiaqi Xu, Qin Han, Yujie Jiang, Zhinong Jiang, Xiakun Chu<\/strong>, Haichun Gao*, Xing Zhang*, and Yunjie Chang*. Dynamics of the mammalian pyruvate dehydrogenase complex revealed by in-situ structural analysis. Nature Communications<\/em>, 16<\/em>(1), 917, 2025.<\/li>\n\n\n\n
  9. Chengzhen Xu<\/strong> and Xiakun Chu<\/strong>*. Dissecting the Roles of Electrostatic Interactions in Modulating the Folding Stability and Cooperativity of Engrailed Homeodomain. Biochemistry<\/em>, 63<\/em>(24), 3261-3272, 2024.<\/li>\n\n\n\n
  10. Tao Zhu<\/strong>, Chunhe Li, and Xiakun Chu<\/strong>*. Fluctuating Chromatin Facilitates Enhancer\u2013Promoter Communication by Regulating Transcriptional Clustering Dynamics. The Journal of Physical Chemistry Letters<\/em>, 15<\/em>(45), 11428-11436, 2024.<\/li>\n\n\n\n
  11. Shiqinrui Xu<\/strong>, Chengze Huo<\/strong>, and Xiakun Chu<\/strong>*. Unraveling the Interplay between Stability and Flexibility in the Design of Polyethylene Terephthalate (PET) Hydrolases. Journal of Chemical Information and Modeling<\/em>, 64<\/em>(19), 7576-7589, 2024.<\/li>\n\n\n\n
  12. Guoqing Zhang<\/strong> and Xiakun Chu<\/strong>*. Balancing thermodynamic stability, dynamics, and kinetics in phase separation of intrinsically disordered proteins. The Journal of Chemical Physics<\/em>, 161<\/em>(9), 2024.<\/li>\n\n\n\n
  13. Yongqiang He, Shuai Wang<\/strong>, Junping Wen, Niu Feng, Ruxiang Ma, Hetong Zhang, Guoxun Chen, Xiakun Chu<\/strong>, Yiping Chen*. Redesigned Guide DNA Enhanced Clostridium butyricum Argonaute Activity for Amplification-Free and Multiplexed Detection of Pathogens. Nano Letters<\/em>, 24<\/em>(31), 9750-9759, 2024.<\/li>\n\n\n\n
  14. Xiakun Chu<\/strong>, Cibo Feng<\/strong>, and Jin Wang*. Deciphering the dynamical chromosome structural reorganizations in human neural development. Physical Review Research<\/em>, 6<\/em>(2), 023309, 2024.<\/li>\n\n\n\n
  15. Qiang Zhu, Didi Geng, Jingchao Li, Jinqiu Zhang, Haofan Sun, Zhiya Fan, Jiahui He, Ninghui Hao, Yinping Tian, Liuqing Wen, Tiehai Li, Weijie Qin, Xiakun Chu<\/strong>, Yong Wang*, Wen Yi*. Computational and Chemical Design Strategy for Manipulating Glycan\u2010Protein Recognition. Advanced Science<\/em>, 11<\/em>(24), 2308522, 2024.<\/li>\n\n\n\n
  16. Xiakun Chu<\/strong> and Jin Wang*. Quantifying the large-scale chromosome structural dynamics during the mitosis-to-G1 phase transition of cell cycle. Open Biology, <\/em>13(11), 230175, 2023<\/li>\n\n\n\n
  17. Cibo Feng,<\/strong> Jin Wang* and Xiakun Chu<\/strong>*. Large-scale data-driven and physics-based models offer insights into the relationships among the structures, dynamics, and functions of the chromosomes. Journal of Molecular Cell Biology, 15<\/em>(6), mjad042, 2023<\/li>\n\n\n\n
  18. Xiakun Chu<\/strong> and Jin Wang*. Insights into the cell fate decision-making processes from chromosome structural reorganizations. Biophysics Reviews, <\/em>3(4), 041402, 2022<\/li>\n\n\n\n
  19. Xiakun Chu<\/strong> and Jin Wang*. Quantifying chromosome structural reorganizations during the differentiation, reprogramming and transdifferentiation. Physical Review Letters<\/em>, 129(6), 068102, 2022<\/li>\n\n\n\n
  20. Jing Huang+, Xiakun Chu+ (co-first)<\/strong>, Yuxiang Luo+, Yong Wang, Ying Zhang, Yu Zhang, and Huilin Li*. Insights into phosphorylation induced protein allostery and conformational dynamics of Glycogen Phosphorylase via integrative structural mass spectrometry and in silico modeling. ACS Chemical Biology<\/em>, 17(7), 1951-1962, 2022<\/li>\n\n\n\n
  21. Wenting Chu, Xiakun Chu<\/strong>, and Jin Wang*. Uncovering the quantitative relationships among chromosome fluctuations, epigenetics, and gene expressions of transdifferentiation on Waddington landscape. Advanced Science<\/em>, 9<\/em>(10), 2103617, 2022.<\/li>\n\n\n\n
  22. Xiakun Chu<\/strong>, Zucai Suo and Jin Wang*. Investigating the conformational dynamics of a Y-family DNA polymerase during its folding and binding to DNA and a nucleotide. JACS Au<\/em>, 2(2), 341-356, 2022.<\/li>\n\n\n\n
  23. Xiakun Chu <\/strong>and Jin Wang*. Dynamics and pathways of chromosome structural organizations during cell transdifferentiation. JACS Au<\/em>, 2(1), 116-127, 2022.<\/li>\n\n\n\n
  24. Xiakun Chu<\/strong>, Suhani Nagpal, Victor Mu\u00f1oz*. Molecular Simulations of Intrinsically Disordered Proteins and Their Binding Mechanisms. In Protein Folding: Methods and Protocols<\/em> (pp. 343-362). New York, NY: Springer US, 2021.<\/li>\n\n\n\n
  25. Xiakun Chu<\/strong>, Yong Wang, Pengfei Tian, Wenfei Li, Davide Mercadante. Advanced Sampling and Modeling in Molecular Simulations for Slow and Large-Scale Biomolecular Dynamics. Frontiers in Molecular Biosciences<\/em>, 8<\/em>, 795991, 2021.<\/li>\n\n\n\n
  26. Wenting Chu, Zhiqiang Yan, Xiakun Chu<\/strong>, Xiliang Zheng, Zuojia Liu, Li Xu, Kun Zhang and Jin Wang*. Physics of biomolecular recognition and conformational dynamics. Reports on Progress in Physics<\/em>, 84<\/em>(12), 126601, 2021.<\/li>\n\n\n\n
  27. Xiakun Chu <\/strong>and Jin Wang*. Deciphering the molecular mechanism of the cancer formation by chromosome structural dynamics. PLoS Computational Biology<\/em>, 17(11), e1009596, 2021.<\/li>\n\n\n\n
  28. Qing-Miao Nie, Li-Zhen Sun, Hai-Bin Li, Xiakun Chu\u2217 (co-corr)<\/strong> and Jin Wang*. Effects of electrostatic interactions on global folding and local conformational dynamics of a multidomain Y-family DNA polymerase. Physical Chemistry Chemical Physics<\/em>, 23(37), 20841-20847, 2021.<\/li>\n\n\n\n
  29. Xiakun Chu<\/strong>, Zucai Suo and Jin Wang*. Investigating the trade-off between folding and function in a multidomain Y-family DNA polymerase. eLife<\/em>, 9, e60434, 2020.<\/li>\n\n\n\n
  30. Xiakun Chu <\/strong>and Jin Wang*. Microscopic chromosomal structural and dynamical origin of cell differentiation and reprogramming. Advanced Science<\/em>, 7(20) 2001572, 2020.<\/li>\n\n\n\n
  31. Xiakun Chu <\/strong>and Jin Wang*. Conformational state switching and pathways of chromosome dynamics in cell cycle. Applied Physics Reviews<\/em>, 7(3), 031403, 2020.<\/li>\n\n\n\n
  32. Wenting Chu, Xiakun Chu<\/strong>, and Jin Wang*. Investigations of the underlying mechanisms of HIF-1\u03b1 and CITED2 binding to TAZ1. Proceedings of the National Academy of Sciences<\/em>, 117<\/em>(11), 5595-5603, 2020.<\/li>\n\n\n\n
  33. Xiakun Chu<\/strong> and Jin Wang*. Theoretical investigations of a multi-domain protein folding under confinements and crowders. Biophysical Journal<\/em>, 118<\/em>(3), 510a, 2020.<\/li>\n\n\n\n
  34. Xiakun Chu<\/strong>, Zucai Suo and Jin Wang*. Confinement and crowding effects on folding of a multidomain Y-Family DNA polymerase. Journal of Chemical Theory and Computation<\/em>, 16(2), 1319\u20131332, 2020.<\/li>\n<\/ol>\n","protected":false},"excerpt":{"rendered":"

    Full list at Google Scholar and Publon. Selected articles in recent years<\/p>\n","protected":false},"author":1,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"footnotes":""},"_links":{"self":[{"href":"https:\/\/xiakunchu.people.ust.hk\/index.php?rest_route=\/wp\/v2\/pages\/145"}],"collection":[{"href":"https:\/\/xiakunchu.people.ust.hk\/index.php?rest_route=\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/xiakunchu.people.ust.hk\/index.php?rest_route=\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/xiakunchu.people.ust.hk\/index.php?rest_route=\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/xiakunchu.people.ust.hk\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=145"}],"version-history":[{"count":49,"href":"https:\/\/xiakunchu.people.ust.hk\/index.php?rest_route=\/wp\/v2\/pages\/145\/revisions"}],"predecessor-version":[{"id":1307,"href":"https:\/\/xiakunchu.people.ust.hk\/index.php?rest_route=\/wp\/v2\/pages\/145\/revisions\/1307"}],"wp:attachment":[{"href":"https:\/\/xiakunchu.people.ust.hk\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=145"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}