谭志杰
1,发展统计力学模型和静电学理论,定量预测生物分子折叠中的静电和离子作用。并结合高分子理论,进行核酸分子设计;2,发展能快速计算分子静电的理论方法:用于计算大分子间的相互作用、DNA/RNA/protein与小分子的相互作用,以及细小体系的静电性质;3,发展和利用计算机模拟方法,理解和预测核酸分子折叠的结构、过程与机制;4,发展聚电解质理论,定量预测高价离子溶液中聚电解质的静电行为;5,软物质系统的自组织和动力学。
个性化签名
- 姓名:谭志杰
- 目前身份:
- 担任导师情况:
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学术头衔:
博士生导师, 教育部“新世纪优秀人才支持计划”入选者
- 职称:-
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学科领域:
凝聚态物理学
- 研究兴趣:1,发展统计力学模型和静电学理论,定量预测生物分子折叠中的静电和离子作用。并结合高分子理论,进行核酸分子设计;2,发展能快速计算分子静电的理论方法:用于计算大分子间的相互作用、DNA/RNA/protein与小分子的相互作用,以及细小体系的静电性质;3,发展和利用计算机模拟方法,理解和预测核酸分子折叠的结构、过程与机制;4,发展聚电解质理论,定量预测高价离子溶液中聚电解质的静电行为;5,软物质系统的自组织和动力学。
谭志杰,教授(博士生导师)
1996年毕业于武汉大学物理系,2001年获武汉大学理学博士学位。攻博期间获中国科学院奖学金,博士学位论文获全国优秀博士论文提名奖和湖北省优秀博士论文。毕业后留武汉大学任教,2001年破格晋升为副教授,后公派赴美国密苏里大学合作研究,并获得该校生命科学博士后奖学金。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。
研究兴趣:
1,发展统计力学模型和静电学理论,定量预测生物分子折叠中的静电和离子作用。并结合高分子理论,进行核酸分子设计;
2,发展能快速计算分子静电的理论方法:用于计算大分子间的相互作用、DNA/RNA/protein与小分子的相互作用,以及细小体系的静电性质;
3,发展和利用计算机模拟方法,理解和预测核酸分子折叠的结构、过程与机制;
4,发展聚电解质理论,定量预测高价离子溶液中聚电解质的静电行为;
5,软物质系统的自组织和动力学。
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【期刊论文】Electrostatic Free Energy Landscapes for DNA Helix Bending
谭志杰, Zhi-Jie Tan and Shi-Jie Chen
Biophysical Journal Volume 94 April 2008 3137-3149,-0001,():
-1年11月30日
Nucleic acids are highly charged polyanionic molecules; thus, the ionic conditions are crucial for nucleic acid structural changes such as bending. We use the tightly bound ion theory, which explicitly accounts for the correlation and ensemble effects for counterions, to calculate the electrostatic free energy landscapes for DNA helix bending. The electrostatic free energy landscapes show that DNA bending energy is strongly dependent on ion concentration, valency, and size. In a Na+ solution, DNA bending is electrostatically unfavorable because of the strong charge repulsion on backbone. With the increase of the Na+ concentration, the electrostatic bending repulsion is reduced and thus the bending becomes less unfavorable. In contrast, in an Mg2+ solution, ion correlation induces a possible attractive force between the different parts of the helical strands, resulting in bending. The electrostatically most favorable and unfavorable bending directions are toward the major and minor grooves, respectively. Decreasing the size of the divalent ions enhances the electrostatic bending attraction, causing an increased bending angle, and shifts the most favorable bending to the direction toward the minor groove. The microscopic analysis on ion-binding distribution reveals that the divalent ion-induced helix bending attraction may come from the correlated distribution of the ions across the grooves in the bending direction.
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谭志杰, Zhi-Jie Tan and Shi-Jie Chen
Biophysical Journal Volume 90 February 2006 1175-1190,-0001,():
-1年11月30日
Metal ions play crucial roles in thermal stability and folding kinetics of nucleic acids. For ions (especially multivalent ions) in the close vicinity of nucleic acid surface, interion correlations and ion-binding mode fluctuations may be important. Poisson-Boltzmann theory ignores these effects whereas the recently developed tightly bound ion (TBI) theory explicitly accounts for these effects. Extensive experimental data demonstrate that the TBI theory gives improved predictions for multivalent ions (e.g., Mg21) than the Poisson-Boltzmann theory. In this study, we use the TBI theory to investigate how the metal ions affect the folding stability of B-DNA helices. We quantitatively evaluate the effects of ion concentration, ion size and valence, and helix length on the helix stability. Moreover, we derive practically useful analytical formulas for the thermodynamic parameters as functions of finite helix length, ion type, and ion concentration. We find that the helix stability is additive for high ion concentration and long helix and nonadditive for low ion concentration and short helix. All these results are tested against and supported by extensive experimental data.
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【期刊论文】Electrostatic correlations and fluctuations for ion binding to a finite length polyelectrolyte
谭志杰, Zhi-Jie Tan and Shi-Jie Chena
J Chem Phys. Author manuscript; available in PMC 2008 July 14.,-0001,():
-1年11月30日
A statistical mechanical model is presented which explicitly accounts for the fluctuations, the electrostatic, and the excluded volume correlations for ions bound to a polyelectrolyte such as DNA. The method can be employed to treat a wide range of ionic conditions including multivalent ions. The microscopic framework of the theory permits the use of realistic finite length and grooved structural model for the polyelectrolyte and modeling of the finite size of the bound ions. Test against Monte Carlo simulations suggests that the theory can give accurate predictions for the ion distribution and the thermodynamic properties. For multivalent ions, the theory makes improved predictions as compared with the mean-field approach. Moreover, for long polyelectrolyte and dilute salt concentration, the theory predicts ion binding properties that agree with the counterion condensation theory.
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谭志杰, Zhi-Jie Tan, Xian-Wu Zou, * Sheng-You Huang, and Zhun-Zhi Jin
,-0001,():
-1年11月30日
Deposition, diffusion, and aggregation (DDA) on percolation substrates were investigated by computer simulations. The nonuniform degree of the substrate is described by the occupied probability p, by which the percolation is generated. p takes values in the range pc<p≤1, where pc is the threshold of percolation. The blocked sites in percolation represent the defects in the substrates. The interactions between defects and deposited particles are involved by introducing the sticking coefficient s. For inert defects (s=0), the defects hinder the deposited particles from diffusing in the substrates. As p decreases from 1 to pc, the morphology of the aggregates varies from the DDA pattern on uniform substrates to the few-and-zigzag-branch pattern. For active defects (s≠0), the defects play a role in absorbing the deposited particles also. With the reduction of p from 1 to pc, the pattern of aggregates changes from DDA on uniform substrates to a site-percolation-like pattern (for s=1) or a dispersed-small-island one (for 0<s<1) on critical percolation substrates. A rapid increase of the fractal dimension Df of aggregates appears in the Df-p curve, which corresponds to the transition of morphologies from a pattern dominated by defects to one controlled by diffusion. Moreover, our simulations show that the Honda-Toyoki-Matsushita relation is reasonable for growth controlled by defecthindering diffusion in fractional spaces.
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【期刊论文】Pattern formation on nonuniform surfaces by correlated random sequential absorptions
谭志杰, Zhi-Jie Tan, Xian-Wu Zou, * Wei Zhang, and Zhun-Zhi Jin
,-0001,():
-1年11月30日
The pattern formation on nonuniform surfaces by correlated-random sequential absorption (CRSA) Process has been investigated by computer simulations. The nonuniform surfaces are represented by percolation clusters with probabilities ps and ps stands for the nonuniform degree of surfaces. The interactions between the particles and the defects in surfaces are involved by introducing a sticking coefficient s. When s-0, the CRSA process is controlled by the absorption of surfaces and the correlation between particles. With the correlation increasing from a weak limit to a strong one, the cluster consisting of absorbed particles changes from the dispersed pattern of site percolation to correlated percolation, and then to Leath percolation clusters. When s-1 and ps-pc, the CRSA process is dominated by the absorption of the defects, where pc is the threshold of percolations. The patterns appear randomly dispersed in spite of the correlation. With the decrease of s and increase of ps, the interaction controlling the CRSA process changes from the absorption of defects to that of surface and the correlation between particles gradually. For the system s-0, the transition correlation exponent ac=ds , where ds is the fractal dimension of the percolation surfaces.
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【期刊论文】Percolation with long-range correlations for epidemic spreading
谭志杰, Zhi-Jie Tan, Xian-Wu Zou, * and Zhun-Zhi Jin
,-0001,():
-1年11月30日
A percolation model with long-range correlations was introduced to investigate the phenomena of epidemic spreading by Monte Carlo simulations. The correlation exponent a and pathogenic ratio s correspond to different spreading methods and pathogenicity of variant epidemics. As the correlation changes from a weak one to a strong one, the patterns change from site percolation to Eden cluster when pathogenic ratio s=1, or Leath percolation cluster when s<1. Corresponding to change of patterns, the fractal dimension increases up to space dimension. The critical behavior in epidemic spreading has been examined based on the model. It is found that correlation has a great influence on the threshold of spreading percolation.
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【期刊论文】Structure transition in cluster-cluster aggregation under external fields
谭志杰, Zhi-Jie Tan, Xian-Wu Zou, * Wen-Bing Zhang, and Zhun-Zhi Jin
,-0001,():
-1年11月30日
The structure transition in cluster-cluster aggregation (CCA) under different external electric fields has been investigated by computer simulations. The aggregates are generated from off-lattice CCA models involving the field-induced dipolar interactions and temperatures by means of a Metropolis algorithm. When the parameter K increases from 0 to ∞, the clusters gradually change from a diffusion-limited CCA to a chainlike pattern, where K stands for the relative strength of the field-induced dipolar interaction with thermal energy. The relation of fractal dimension Df to parameter K can be approximately expressed as Df=DE+(DDLCA-2DE)e-βK with β50.64, where DE and DDLCA stand for the fractal dimensions of the CCA when K-∞ and K-0, respec-tively. This structure transition is a transition between a prototype disorder structure and a relative order one. The transition is attributed to the variation of the dominating interaction of systems from thermal disorder to field-induced dipolar interaction with K rising.
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