详细描述
姓 名： 谭志杰 (Zhi-Jie Tan)
职务/职称：教 授（博士生导师）
电子邮箱：zjtan@whu.edu.cn
招生专业：理论物理、凝聚态物理
本课题组欢迎有志于统计物理与计算生物物理方向的博士生/博士后，也特别欢迎他校保研/考研的同学。
Education & Experience
1996年获武汉大学理学学士，2001年获武汉大学博士学位。1998年留武汉大学任教，2001年破格晋升为副教授，后赴美国密苏里大学合作研究，2008年6月回到武汉大学，晋升为教授，并被遴选为博士生导师。2008年入选教育部新世纪人才计划，2010年获国家自然科学二等奖（第三完成人），2011年获湖北省青年科技奖。主讲弘毅学堂物理班《热力学与统计物理》和研究生通开课《高等固体物理学》。长期担任中国物理学会软物质与生物物理专业委员会委员、中国生物信息学会生物大分子结构预测与模拟常委会委员、全国统计物理与复杂系统会议学术委员会委员等，目前为中国物理学会、美国生物物理学会等学会会员。
Research Interests
课题组主要发展和利用理论与计算模型对核酸结构等性质进行深入研究，所发展模型的共享程序包见https://github.com/Tan-group，具体研究兴趣包括：
1, 发展RNA、RNA-小分子/蛋白质复合体三维结构评估势能函数及其程序包;
2，发展RNA三维结构的理性序列设计模型及其程序包；
3，发展RNA二级结构预测方法与RNA二级结构序列设计方法及其程序包；
4, 发展基于物理的RNA三维结构折叠模型及其程序包;
5，发展RNA三维结构组装模型和RNA三维结构优化模型及其程序包;
6, 利用计算机模拟，预测和理解核酸结构及其动态性与其功能的关系。
Review articles (as a corresponding/1st author)
1, Tan et al. Advances in RNA contact prediction: a benchmark evaluation of computational methods. Commun Theor Phys 77: 125602, 2025.
2, Chen et al. A comprehensive evaluation on RNA secondary structures prediction methods. Chin Phys B 34: 088710, 2025.
3, Wang et al. RNA 3D Structure Prediction: Progress and Perspective. Molecules. 28: 5532, 2023.
4, Tan et al. Statistical potentials for 3D structure evaluation: from proteins to RNAs. Chin Phys B 30: 028705, 2021.
5, Bao et al. Flexibility of nucleic acids: from DNA to RNA. Chin Phys B 25: 018703 (1-11), 2016. (CPB high citation article)
6, Tan et al. RNA folding: structure prediction, folding kinetics and ion electrostatics. Adv Expt Med & Biol 827:143-183, 2015.
7, Shi et al. RNA structure prediction: Progress and perspective. Chin Phys B 23: 078701(1-10), 2014.
8, Tan & Chen. Importance of Diffuse Metal Ion Binding to RNA, 9:101-124. in "Structural and Catalytic Roles of Metal Ions in RNA" (volume of Metal Ions in Life Sciences), edited by Astrid Sigel, Helmut Sigel, and Roland K. O. Sigel. 2011.
9, Tan & Chen. Predicting electrostatic forces in RNA folding, 469:465-487, in "Biophysical Approaches to RNA Structure and Folding" (volume of Methods in Enzymology), edited by Daniel Herschlag. 2009.
Selected Articles (as a corresponding/1st author)
1, Wang et al. TiRNA: a coarse-grained method with temperature and ion effects for RNA structure folding and prediction. Nucleic Acids Res. 54: gkaf1499, 2026.
2, Zheng et al. Low-polar solvent strikingly stiffens double-stranded RNA and reverses its twist-stretch coupling. Biophys J. 125: 982-994, 2026.
3, Zhang et al. Local cation-clamping distorts and softens RNA duplex. Commun Biol 9: 308, 2026.
4, Tang et al. Dual-targeted multifunctional ultrasmall sulfur-AuPt nanocomposite for NIR-II photothermal enhanced chemodynamic therapy. Colloids Surf B Biointerfaces. 258: 115278, 2026.
5, Lou et al. rsRNASP1: A distance- and dihedral-dependent statistical potential for RNA 3D structure evaluation. Biophys J. 2025 124: 2740-2753, 2025.
6, Dong et al. Effect of protein binding on the twist-stretch coupling of double-stranded RNA. J Chem Phys. 162: 145101, 2025.
7, Dong et al. The origin of different bending stiffness between double-stranded RNA and DNA revealed by magnetic tweezers and simulations. Nucleic Acids Res. 52: 2519-2529, 2024.
8, Zheng et al. Effect of ethanol on the elasticities of double-stranded RNA and DNA revealed by magnetic tweezers and simulations. J Chem Phys. 161: 075101, 2024.
9, Wang et al. Predicting 3D structures and stabilities for complex RNA pseudoknots in ion solutions. Biophys J. 122: 1503-1516, 2023.
10, Tan et al. cgRNASP: coarse-grained statistical potentials with residue separation for RNA structure evaluation. NAR Genom Bioinform. 5: lqad016, 2023.
11, Tang et al. Multifunctional AuPt Nanoparticles for Synergistic Photothermal and Radiation Therapy. Int J Nanomedicine. 18: 6869-6882, 2023.
12, Zhao et al. 5-Methyl-cytosine stabilizes DNA but hinders DNA hybridization revealed by magnetic tweezers and simulations. Nucleic Acids Res. 50: 12344-12354, 2022.
13, Zhou et al. FebRNA: An automated fragment-ensemble-based model for building RNA 3D structures. Biophys J. 121: 3381-3392, 2022.
14, Qiang et al. Multivalent cations reverse the twist-stretch coupling of RNA. Phys Rev Lett 128: 108103, 2022.
15, Tan et al. rsRNASP: A residue-separation-based statistical potential for RNA 3D structure evaluation. Biophys J. 121: 142-156, 2022. (New and Notable article)
16, Feng et al. Salt-Dependent RNA pseudoknot stability: effect of spatial confinement. Front Mol Biosci. 8:666369, 2021.
17, Wang et al. An intratumoral injectable nanozyme hydrogel for hypoxia-resistant thermoradiotherapy. Colloids Surf B Biointerfaces. 207: 112026, 2021.
18, Fu et al. Opposite Effects of high-valent cations on the elasticities of DNA and RNA duplexes revealed by magnetic tweezers. Phys Rev Lett 124: 058101, 2020.
19, Wang et al. Salt effect on thermodynamics and kinetics of a single RNA base pair. RNA. 26: 470-480, 2020.
20, Zheng et al. Ion-mediated interactions between like-charged polyelectrolytes with bending flexibility. Sci Rep. 10: 21586, 2020.
21, Jin et al. Structure folding of RNA kissing complexes in salt solutions: predicting 3D structure, stability and folding pathway. RNA. 25: 1532-1548, 2019.
22, Lin et al. Apparent repulsion between equally and oppositely charged spherical polyelectrolytes in symmetrical salt solutions. J Chem Phys 151, 114902, 2019.
23, Liu et al. Structural flexibility of DNA-RNA hybrid duplex: stretching and twist-stretch coupling. Biophys J 117: 74-86, 2019.
24, Tan et al. What is the best reference state for building statistical potentials in RNA 3D structure evaluation? RNA. 25: 793-812, 2019.
25, Jin et al. Modeling structure, stability, and flexibility of double-stranded RNAs in salt solutions. Biophys J 115: 1403-1416, 2018.
26, Shi et al. Predicting 3D structure and stability of RNA pseudoknots in monovalent and divalent ion solutions. PloS Comput Biol 14: e1006222, 2018.
27, Xi et al. Competitive binding of Mg2+ and Na+ ions to nucleic acids: from helices to tertiary structures. Biophys J 114: 1776-1790, 2018.
28, Zhang et al. Potential of mean force between oppositely charged nanoparticles: A comprehensive comparison between Poisson–Boltzmann theory and Monte Carlo simulations. Sci Rep 7: 14145, 2017.
29, Zhang et al. Divalent ion-mediated DNA-DNA interactions: A comparative study of triplex and duplex. Biophys J 113: 517-528, 2017. (Highlighted article).
30, Zhang et al. Radial distribution function of semiflexible oligomers with stretching flexibility. J Chem Phys 147: 054901, 2017. (Featured article).
31, Bao et al. Understanding the relative flexibility of RNA and DNA duplexes: stretching and twist-stretch coupling. Biophys J 112: 1094-1104, 2017.
32, Zhang et al. Potential of mean force between like-charged nanoparticles: many-body effect. Sci Rep 6: 23434 (1-12), 2016.
33, Shi et al. Predicting 3D structure, flexibility and stability of RNA hairpins in monovalent and divalent ion solutions. Biophys J 109: 2654-2665, 2015.
34, Wu et al. Multivalent ion-mediated nucleic acid helix-helix interactions: RNA versus DNA. Nucleic Acids Res 43: 6156-6165, 2015.
35, Wu et al. Flexibility of short DNAs with finite-length effect: from base pairs to tens of base pairs. J Chem Phys 142: 125103(1-13), 2015.
36, Shi et al. A coarse-grained model with implicit salt for RNAs: Predicting 3D structure, stability and salt effect. J Chem Phys 141: 105102(1-13), 2014.
37, Wang et al, Salt contribution to the flexibility of single-stranded nucleic acid of finite length. Biopolymers 99: 370–381, 2013. (Cover story).
38, Tan & Chen. Ion-mediated RNA structural collapse: effect of spatial confinement. Biophys J 103: 827-836, 2012.
39, Tan & Chen. Salt contribution to RNA tertiary structure folding stability. Biophys J 101: 176-187, 2011.
40, Tan & Chen. Predicting ion binding properties for RNA tertiary structures. Biophys J 99: 1565-1576, 2010.
41, Tan & Chen. Salt dependence of nucleic acid hairpin stability. Biophys J 95: 738-752, 2008.
42, Tan & Chen. Electrostatic free energy landscapes for DNA helix bending. Biophys J 94: 3137-3149, 2008.
43, Tan & Chen. RNA helix stability in mixed Na+/Mg2+ solutions. Biophys J 92: 3615-3632, 2007.
44, Tan & Chen. Electrostatic free energy landscapes for nucleic acid helix assembly. Nucleic Acids Res 34:6629-6639, 2006.
45, Tan & Chen. Ion-mediated nucleic acid helix-helix interactions. Biophys J 91: 518-536, 2006.
46, Tan & Chen. Nucleic acid helix stability: effects of salt concentration, cation valency and size, and chain length. Biophys J 90: 1175-1190, 2006.
47, Tan & Chen. Electrostatic correlation and fluctuations for ion binding to finite length polyelectrolyte. J Chem Phys 122:044903(1-16), 2005.
48, Tan et al. Pattern of particle distribution in multi-particle system by random walk with memory enhancement and decay. Phys Rev E 66: 011101, 2002.
49, Tan et al. Deposition, diffusion and aggregation on percolations: A model for nanostructure growth on nonuniform substrates. Phys Rev B 65: 235403, 2002.
50, Tan et al. Pattern formation on nonuniform surfaces by correlated-random sequential adsorption. Phys Rev E 65: 057201, 2002.
51, Tan et al. Random walk with memorial enhancement and decay. Phys Rev E 65: 041101, 2002.
52, Tan et al. Percolation with long-range correlations for epidemic spreading. Phys Rev E 62: 8409-8412, 2000.
53, Tan et al. Structure transition in cluster-cluster aggregation under external fields. Phys Rev E 61: 734-737, 2000.
54, Tan et al. Influence of particle size on diffusion-limited aggregation. Phys Rev E 60: 6202-6205, 1999.
55, Tan et al. Influences of the size and dielectric properties of particles on electrorheological response. Phys Rev E 59: 3177-3181, 1999.
