
电子邮件: liming@ucas.ac.cn
通信地址: 北京市石景山区玉泉路19号(甲)
邮政编码: 100049
研究领域
招生信息
招生专业
招生方向
教育背景
1995-09--1999-07 中国科学技术大学 学生
出国学习工作
学历
学位
工作经历
2006.8至今,在国科大物理学院任教,现职为教授。
2009、2011、2013、2014、2016年获评国科大优秀个人。
工作简历
2010-05~2017-11,国科大物理学院, 副教授
2006-08~2010-05,中国科学院研究生院, 讲师
出版信息
1. 黎明、欧阳钟灿,“DNA单分子力学及相关生物学”, 科学(双月刊),2003,55(6): 15-19
2. 黎明、欧阳钟灿, “DNA单分子力学及相关的生物信息学”,《21世纪100个交叉科学难题》(P414-427),科学出版社,2005
3. 黎明,柳飞,周海军,欧阳钟灿,“单分子弹性理论”,《生命科学中的单分子行为及细胞内实时检测》第二十章(p337-357),科学出版社,2005
4. 《软凝聚态物理学》(中国学科发展战略),《绪论》及章节《生物分子马达》,科学出版社,2020
发表论文
[2] Li Ming. Kinetic assays of DNA polymerase fidelity: a new theoretical perspective beyond Michaelis-Menten kinetics. Phy.Rev.E. 2021, [3] Shu, YaoGen, Li, Ming, OuYang, ZhongCan, DeMaria, E, Fred, A, Gamboa, H. Theoretical Study of the Fidelity of Transcription. PROCEEDINGS OF THE 13TH INTERNATIONAL JOINT CONFERENCE ON BIOMEDICAL ENGINEERING SYSTEMS AND TECHNOLOGIES, VOL 3: BIOINFORMATICSnull. 2020, 239-241, http://dx.doi.org/10.5220/0009181002390241.
[4] Li, QiuShi, Zheng, PeiDong, Shu, YaoGen, OuYang, ZhongCan, Li, Ming. Template-specific fidelity of DNA replication with high-order neighbor effects: A first-passage approach. PHYSICAL REVIEW E[J]. 2019, 100(1): https://www.webofscience.com/wos/woscc/full-record/WOS:000476695600004.
[5] ChuanBiao Zhang, FangFu Ye, Ming Li, Xin Zhou. Enhanced sampling based on slow variables of trajectory mapping. 中国科学:物理学、力学、天文学英文版[J]. 2019, 81-86, http://lib.cqvip.com/Qikan/Article/Detail?id=74718871504849574854484948.
[6] Ou Yangzhongcan. Study on the Fidelity of Biodevice T7 DNA Polymerase. Proceedings of the 11th International Joint Conference on Biomedical Engineering Systems and Technologies. 2018, [7] Li, Ming, OuYang, ZhongCan, Shu, YaoGen. Advances in the study of the mechanochemical coupling of kinesin. INTERNATIONAL JOURNAL OF MODERN PHYSICS B[J]. 2018, 32(18): http://ir.itp.ac.cn/handle/311006/22856.
[8] 黎明. DNA超分子水凝胶的粗粒化建模与模拟. 物理学报. 2017, [9] Song, Y, Shu, Y, Zhou, X, Ouyang, Z, Li, M. Proofreading of DNA polymerase: a new kinetic model with higher-order terminal effects. EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERSnull. 2017, 46: S134-S134, [10] 黎明. 驱动马达力学化学耦合机制研究进展. 物理学报[J]. 2016, [11] Shu, YaoGen, Song, YongShun, OuYang, ZhongCan, Li, Ming. A general theory of kinetics and thermodynamics of steady-state copolymerization. JOURNALOFPHYSICSCONDENSEDMATTER[J]. 2015, 27(23): http://www.irgrid.ac.cn/handle/1471x/1114911.
[12] Hat NanNan, Zhou Xin, Li Ming. Influences of the Structure of Lipids on Thermal Stability of Lipid Membranes. COMMUNICATIONS IN THEORETICAL PHYSICS[J]. 2015, 64(2): 249-258, [13] Wu, Fen, Song, Yongshun, Zhao, Zhiyong, Zhang, Shusheng, Yang, Zhongqiang, Li, Zhibo, Li, Ming, Fan, QingHua, Liu, Dongsheng. Preparation and Self-Assembly of Supramolecular Coil-Rod-Coil Triblock Copolymer PPO-dsDNA-PPO. MACROMOLECULES[J]. 2015, 48(20): 7550-7556, http://ir.iccas.ac.cn/handle/121111/29191.
[14] 欧阳钟灿. Formation and dissociation of protonated cytosine-cytosine base pairs in i-motifs by ab initio quantum chemical calculations. CHINESE PHYSICS B[J]. 2014, 23(2): http://www.irgrid.ac.cn/handle/1471x/836553.
[15] 欧阳钟灿. Mechano-chemical selections of two competitive unfolding pathways of a single DNA i-motif. CHINESE PHYSICS B[J]. 2014, 23(6): 625-632, http://www.irgrid.ac.cn/handle/1471x/949156.
[16] Wang ZiQing, Shu YaoGen, Li Ming. A New Cooperation Mechanism of Kinesin Motors when Extracting Membrane Tube. COMMUNICATIONS IN THEORETICAL PHYSICS[J]. 2013, 60(6): 753-760, http://www.irgrid.ac.cn/handle/1471x/836287.
[17] Ou Yangzhongcan. A theoretical study of entropy-driven polymer transport through finite-size nanochannels. Chemical Physics Letters. 2013, [18] Ma, Rui, Li, Ming, OuYang, ZhongCan, Shu, YaoGen. Master equation approach for a cross-bridge power-stroke model with a finite number of motors. PHYSICAL REVIEW E[J]. 2013, 87(5): http://www.irgrid.ac.cn/handle/1471x/836427.
[19] Shu, YaoGen, Zhang, XiaoHu, OuYang, ZhongCan, Li, Ming. The neck linker of kinesin 1 seems optimally designed to approach the largest stepping velocity: a simulation study of an ideal model. JOURNAL OF PHYSICS-CONDENSED MATTER[J]. 2012, 24(3): http://www.irgrid.ac.cn/handle/1471x/836248.
[20] Chen, Chun, Li, Ming, Xing, Yongzheng, Li, Yingmei, Joedecke, CarlChristian, Jin, Juan, Yang, Zhongqiang, Liu, Dongsheng. Study of pH-Induced Folding and Unfolding Kinetics of the DNA i-Motif by Stopped-Flow Circular Dichroism. LANGMUIR[J]. 2012, 28(51): 17743-17748, [21] Shu, YaoGen, Li, Ming. SUBSTEPS OF KINESIN STUDIED WITH A NECK LINKER SWING MODEL. MODERN PHYSICS LETTERS B[J]. 2010, 24(6): 539-548, http://ir.iphy.ac.cn/handle/311004/53928.
[22] Gong, Linchen, Li, Ming, OuYang, Zhongcan. Investigation on Energetic Optimization Problems of Stochastic Thermodynamics with Iterative Dynamic Programming. COMMUNICATIONS IN COMPUTATIONAL PHYSICS[J]. 2010, 7(5): 904-926, https://www.webofscience.com/wos/woscc/full-record/WOS:000277862700002.
[23] Wang, Ziqing, Li, Ming. Force-velocity relations for multiple-molecular-motor transport. PHYSICAL REVIEW E[J]. 2009, 80(4): https://www.webofscience.com/wos/woscc/full-record/WOS:000271350400102.
[24] Mu, Weihua, Li, Ming, Wang, Wei, OuYang, Zhongcan. Study of axial strain-induced torsion of single-wall carbon nanotubes using the 2D continuum anharmonic anisotropic elastic model. NEW JOURNAL OF PHYSICS[J]. 2009, 11: https://www.webofscience.com/wos/woscc/full-record/WOS:000272153200002.
[25] Li Ming, Shu YaoGen, OuYang ZhongCan. Mechanochemical Coupling of Kinesin Studied with a Neck-Linker Swing Model. COMMUNICATIONS IN THEORETICAL PHYSICS[J]. 2009, 51(6): 1143-1148, http://lib.cqvip.com/Qikan/Article/Detail?id=30573168.
[26] Li, Ming, OuYang, Zhongcan. Concentration-induced shape transition of nano-aggregates in solution. THIN SOLID FILMS[J]. 2008, 517(4): 1424-1427, http://dx.doi.org/10.1016/j.tsf.2008.09.048.
[27] Li, Ming, OuYang, ZhongCan. DNA as active polymer: long-range allosteric effect and chromatin loop structure. COMPUTER PHYSICS COMMUNICATIONS[J]. 2007, 177(1-2): 176-179, http://dx.doi.org/10.1016/j.cpc.2007.02.018.
[28] 郭雷. Soft control on collective behavior of a group of autonomous agents by a shill agent. JRL SYST SCI & COMPLEXITY. 2006, 19(1): 54-62, [29] Li, M, OuYang, ZC. An exact numerical method to calculate the base-unpairing probability for any given DNA sequence by Benham model. THIN SOLID FILMS[J]. 2006, 499(1-2): 207-212, http://dx.doi.org/10.1016/j.tsf.2005.07.007.
[30] Li, M, OuYang, ZC. Predicting the function of eukaryotic scaffold/matrix attachment regions via DNA mechanics. JOURNAL OF PHYSICS-CONDENSED MATTER[J]. 2005, 17(31): S2853-S2860, https://www.webofscience.com/wos/woscc/full-record/WOS:000231935000012.
[31] DNA as active polymer: long-range allosteric effect and chromatin loop structure. http://ir.itp.ac.cn/handle/311006/5712.
翻译作品
(2) 《软物质-构筑梦幻的材料》(田珂珂、戴陆如、黎明 译), 上海科技教育出版社, 2013-12, 第 3 作者
(3) 生物物理学:能量,信息与生命(修订版), 上海科技出版社, 2016-11, 第 1 作者
(4) 生命系统的物理建模, 上海科学技术出版社, 2018-08, 第 2 作者
科研活动
1, Oral presentation (Biophysics session): Prediction on Scaffold/Matrix Attachment Regions (S/MARs) by DNA Mechanics, 4th OCPA Joint Meeting of Chinese Physicists World-Wide, June.28-July.1, 2004, Shanghai
2, Poster: Microstructure of Chromosome and Topological Problems in Gene Regulation, 5th International Conference on Biological Physics ICBP 2004, Gothenburg, August 23 - 27, 2004
3, 2006.4-2006.7, visiting KITP at UCSB, the international workshop “New Physical Approaches to Molecular and Cellular Machines”
4, Oral presentation: long-range allosteric effect in gene transcriptional regulation,International Symposium on the Recent Progress in Quantitative and Systems Biology, Dec..9-11, 2006, Chinese University of Hong Kong
5, invited talk: Introduction to Biomolecular nanomachines and related thermodynamics, 2008.7.11, SFI-ITP International Summer School on Complex Systems, Beijing
6, invited talk: DNA as active polymer: long-range allosteric effect and gene transcription, 2009.7.17, CAS Workshop on DNA Nanotechnology, Beijing
7, Two posters at the 7th International Conference on Biological Physics, June 18-25, 2011, UCSD, USA
(1)Kinesin Neck Linker is Optimally Designed to Achieve the largest stepping velocity: a Simulation Study;
(2)A Molecular Simulation Study on the Allosteric Mechanism of Na+ - coupled symporter BetP.
8, “关于步行马达kinesin结构优化的一点思考”,邀请报告,海峡两岸生物学启发的理论科学问题研讨会(BITS8),2012.6.20-25,三峡大学,湖北宜昌
9,“kinetics and thermodynamics of stationary copolymerization processes”,邀请报告,海峡两岸生物学启发的理论科学问题研讨会(BITS9),2014.6.26-28,中原大学,台湾
10, “DNA聚合酶保真度问题的理论研究”,邀请报告,2014年生物物理理论与实验技术进展研讨会,2014.12.6-7, 贵州大学
11, “Flux‐driven information generation: a general theory
of steady-state copolymerization”, 分会场报告,第三届全国统计物理与复杂系统学术会议,2015.7. 22‐24, 兰州
12, “Theoretical models of the steady-state kinetics and
fidelity of DNA/RNA polymerase”, 邀请报告,第十次鼓岭科学会议, 2015.10.23-24, 厦门大学
13,Proofreading of DNA/RNA Polymerase: a new kinetic model with higher-order terminal effects,邀请报告,第十届海峡两岸生物学启发的理论科学问题研讨会(BITS10),2016.6.20-22, 上海-扬州,
14, A general theory of steady-state copolymerization with applications to DNA replication by DNA polymerase, “非平衡统计物理”分会场口头报告(oral presentation), 第26届国际统计物理大会(26th International conference on Statistical Physics of IUPAP), 2016.7.18-22,法国,里昂
15,DNA/RNA复制保真度问题的理论研究,邀请报告,软物质统计动力学研讨会,温州,2018.5.5
16,DNAP复制保真度的动力学理论,邀请报告,第二届统计物理计算方法学术研讨会,大理,2019.1.11-13
17,DNAP/RNAP复制保真度的动力学理论,“软凝聚态物理与生物物理”分会场邀请报告,中国物理学会秋季学术会议,郑州,2019.9.19-22
18,期刊Chinese Physics B 2019年度优秀审稿人(Outstanding Reviewer Awards 2019)
19,参与撰写《软凝聚态物理学》(中国学科发展战略)“绪论”及“生物分子马达”章节
20,The speed-fidelity anti-tradeoff of DNA Polymerase: a theoretical study,邀请报告,第十二届海峡两岸生物学启发的理论科学问题研讨会(BITS12,ZOOM在线会议),主办方:浙江省科学基金委,2021.12.4-6
21,DNA 聚合酶保真度理论及实验数据分析, 分会场邀请报告(“生物物理及医学物理”会场),第十二届全国软物质及生命物质物理学术会议,主办单位:中国物理学会,2022.10.28-31,温州
科研项目
( 2 ) 生物体系信息传递保真度问题的动力学及热力学理论研究, 主持, 国家级, 2012-01--2014-12
( 3 ) DNA杂化体系的多层次可控组装及调控机制研究, 参与, 国家级, 2011-01--2014-12
( 4 ) 分子马达能量利用的经济性问题研究, 参与, 国家级, 2011-01--2013-12
参与会议
(2)DNAP 复制保真度的动力学理论 第二届统计物理计算方法研讨会 2019-01-13
(3)DNA/RNA复制保真度问题的理论研究 软物质统计动力学研讨会 2018-05-05
(4)A general theory of steady-state copolymerization with applications to DNA replication by DNA polymerase 第26届国际统计物理大会 2016-07-18
(5)Proofreading of DNA/RNA Polymerase: a new kinetic model with higher-order terminal effects 第十届海峡两岸生物学启发的理论科学问题研讨会 2016-06-20
(6)Theoretical models of the steady-state kinetics and fidelity of DNA/RNA polymerase 第十次鼓岭科学会议 Ming Li 2015-10-23
(7)Flux‐driven information generation: a general theory of steady-state copolymerization 第三届全国统计物理与复杂系统学术会议 Ming Li 2015-07-22
(8)kinetics and thermodynamics of stationary copolymerization processes 海峡两岸生物学启发的理论科学问题研讨会(BITS9) Ming Li 2014-06-26
(9)关于步行马达kinesin结构优化的一点思考 海峡两岸生物学启发的理论科学问题研讨会(BITS8) Ming Li 2012-06-20
(10)DNA as active polymer: long-range allosteric effect and gene transcription Ming Li 2009-07-17
(11)Introduction to Biomolecular nanomachines and related thermodynamics Ming Li 2008-07-17
(12)long-range allosteric effect in gene transcriptional regulation Ming Li 2006-12-09
合作情况
理论生物物理简介
典型生物分子机器之kinesin
驱动蛋白(kinesin)是细胞中最重要的分子“搬运工”之一。形象地看,它是“两条腿”的步行纳米机器,能利用ATP水解的化学能在微管轨道上产生定向步行,从而运送囊泡。作为自然进化的杰出产物,驱动蛋白在分子结构及相关物理性质方面达到了高度优化,使其能够在热涨落环境中稳定工作,其工作机制、结构设计和优化原理是生物物理学研究的热点。我们对其关键部件neck-linker进行了MD模拟,并建立了简化的马达运动模型,结果表明neck-linker的长度、刚度与马达速度之间存在着匹配关系,意味着驱动马达可能已在速度方面已经达到了进化优化[J. Phys.: Condens. Matter 24 (2012) 035105].

典型生物分子机器之DNA
活细胞中的基因组DNA并非静态的遗传信息载体。对于中温生物,其基因组DNA通常处于负超螺旋态的非平衡态,负超螺旋对DNA分子的结构及功能有显著影响。我们详细研究了处于该状态的DNA的力学性质,计算了真实DNA序列局域解链(local denature)的特征。研究发现,整体拓扑约束会导致DNA不同解链区域之间存在着长程相互作用。通过与基因库数据的比较和分析,进一步发现这种长程相互作用与基因转录调控之间存在着显著的统计关联。本工作首次从理论上提出了DNA负超螺旋参与基因转录调控的一种长程变构机制(long-range allosteric)[ J. Phys.: Condens. Matter, 2005,17:S2853-S2860]。
典型生物分子机器之DNA Polymerase
DNA 聚合酶(DNA polymerase)司职DNA 复制,是细胞中最重要的信息分子机器。它不仅是分子生物学和生物物理学研究的重要对象,并且已经有多种DNAP 广泛应用在DNA 体外扩增(PCR 技术)、单分子测序、生物计算机等方面,具有极大的应用潜力。DNA聚合酶不仅要快速合成新生DNA,而且要确保复制出错率尽可能低(高保真)。为此,DNA聚合酶进化出了专门的“校验”结构域来减小复制差错率。综合最近的实验数据,我们最近对DNA聚合酶提出了一个完整的“聚合-校验”动力学理论模型,进行了详细的模拟和解析计算,结果表明DNA聚合酶可以高效地利用高阶末端近邻效应来完成校验。本工作分为两部分。
第一部分按照生物化学家的惯例,忽略复制模板DNA序列的特异性,将复制过程近似简化为配对(R)-误配(W)的稳态共聚过程,建立相关的动力学主方程并提出了一种解析计算的方法,对复制保真度给出了简明直观的解析表达式。相关文献:J.Phys.: Condens.Matter, 27(23):235105 (2015);J.Phys.: Condens.Matter 29:025101(2017) [本文被该杂志选为2017年年度亮点工作,http://iopscience.iop.org/journal/0953-8984/page/Highlights-2017] 。
第二部分工作则最大程度上考虑了模板序列的特异性以及相应的复制过程的非稳态特性,建立了基于首达过程概念的一种解析计算方法,对任意模板位置处的局域保真度和复制速度都给出近似的解析表达式,与前述稳态分析的结果一致。这个分析方法适用于任意DNA模板序列,且能够推广到RNA合成(基因转录)等其它过程,因此具有极大的普适性。相关文献:Phys. Rev. E, 2019, 100, 012131. 我们的研究也否定了生物学家长期持有的一个观念,即,保真度的提升必须以牺牲速度为代价。我们的解析结论表明,在不减小总体复制速度(甚至速度略有提升)的情况下,保真度可大大提高。这个结论有一定的普适性,也是对高阶模型的一个支持。此外,在这个理论基础上,我们对生物学实验中最常用的保真度表征方法的理论基础进行了质疑和细致的剖析,分析表明两种标准方法(定态方法、瞬态方法)只适用于测量聚合酶聚合域的保真度,而不一定能可靠地测量校验域对保真度的贡献,因此需要设计更可靠的实验方案,我们也同时提出了单分子实验方案。相关文献:Kinetic assays of DNA polymerase fidelity: a new theoretical perspective beyond Michaelis-Menten kinetics, to appear in Phys.Rev.E (2021)
译著
(1) 教材《生物物理学:能量,信息与生命》(第二版),黎明、戴陆如主译,上海科技出版社,2023
(2) 教材《生命系统的物理建模》(第二版),舒咬根、黎明 译,上海科学技术出版社,2023
(3) 教材《从光子到神经元: 光、成像与视觉》(第一版),舒咬根、黎明 译,科学出版社出版,2021
(4) 科普书《软物质-构筑梦幻的材料》, 田珂珂、戴陆如、黎明 译, 上海科技教育出版社, 2013