邱文元
理论化学,结构生物学和计算生物学。
个性化签名
- 姓名:邱文元
- 目前身份:
- 担任导师情况:
- 学位:
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学术头衔:
博士生导师
- 职称:-
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学科领域:
物理化学
- 研究兴趣:理论化学,结构生物学和计算生物学。
邱文元( Wen-Yuan Qiu, Prof. Dr. of Theoretical Chemistry ),1997年7月在中国科技大学(University of Science & Technology of China)化学物理系获得博士学位;1997年9月-1999年9月为中国科技大学博士后,博士后出站被晋升为教授;1999年10月至今在兰州大学化学系( Lanzhou University )物理化学研究所工作,博士生导师;现任物理化学研究所所长,物理化学博士点负责人;2002年起兼任应用数学的硕士生导师;2010年兼任理论物理的博士生导师。在理论化学,DNA和蛋白质纽结理论( DNA and Protein Knot Theory ),拓扑立体化学,结构化学等领域发表90余篇学术论文。
1989年获得甘肃省中青年科学基金;1997年获得中国博士后科学基金;1998年获得中国科学院王宽诚博士后工作奖励基金;2002年获得国家自然科学基金(化学科学部---DNA双螺旋的形成机理);2003-2005年获得国家自然科学基金((“理论物理和生命科学交叉的新研究领域”重大研究计划)--DNA和蛋白质的纽结理论));2003-2005年获得教育部高等学校“博士点基金”。“数学化学”列入兰州大学985工程特色研究方向。参加了国家自然科学基金重点项目(应用图论(2009-2012));承担的“DNA和蛋白质多面体的结构化学研究”获得了国家自然科学基金(面上项目)以及高等学校博士点基金的资助(2010-2012)。
在2000年出版的由美国科学家主编的《数学化学》丛书第6卷《化学拓扑学》中,应邀发表了邱文元撰写的题为“纽结理论和DNA拓扑学及其分子对称性破缺”的长篇研究论文( W.-Y. Qiu, Knot Theory, DNA Topology, and Molecular Symmetry Breaking, in: D. Bonchev and D. H. Rouvray(Eds.), Chemical Topology---Applications and Techniques, Mathematical Chemistry Series Vol. 6, Gordon and Breach Science Publishers, Amsterdam, 2000,pp.175-237(Chapter 3) )。该丛书主编认为邱文元博士是DNA拓扑学领域的前沿工作者之一,对其在DNA纽结理论对称性分析方面的工作给出了评价 (Qiu has been a notable pioneer in the point group analysis of Seifert′s representation in knot theory, … ).
为了应对多面体和多面体链环( polyhedral links )在DNA和蛋白质以及病毒结构的合成和表征方面取得的令人兴奋的的挑战,我们在新颖的DNA和蛋白质多面体链环的理论表征方面做出了重要工作。自2005年以来,本课题在SCI刊物发表14篇学术论文,开创了在DNA和蛋白质多面体上建立多面体链环的新方法,为理解奇特的DNA和蛋白质折叠的新方式探索了理论基础。 最近接受了美国Nova Publishers的邀请,已经和合作者为《数学化学》专著其中一章撰写了题为“DNA多面体的化学和数学”的长篇评述文章(W.-Y.Qiu, Z.Wang and G. Hu, The Chemistry and Mathematics of DNA Polyhedra, In: W.I.Hong (Ed.), Mathematical Chemistry, Chemistry Research and Applications Series, New York: Nova Science Publishers,Inc., 2010(Chapter 4),pp.327-366);同时做为一本书单独出版(W.-Y.Qiu, Z.Wang and G. Hu, The Chemistry and Mathematics of DNA Polyhedra, New York: Nova Science Publishers,Inc., 2010).
最近,A New Euler's Formula for DNA Polyhedra的研究论文已经被PloS One,6(10),e26308(2011)出版发表.(新欧拉公式这个重要的工作研究了DNA多面体的新理论和新方法,揭示了DNA多面体潜在的普适规律,为DNA和病毒多面体的研究打开了新窗口。
研究方向:理论化学,结构生物学和计算生物学。研究工作集中在:(1)探讨用数学和物理,以及立体化学和量子化学的方法揭示生命的基本分子(例如DNA和蛋白质以及多面体病毒结构等)所隐含的数学,物理以及拓扑立体化学的性质;(2)思考标度与生命分子相关的对称性,不对称性和手征性的理论模型以及建立生命分子对称性破缺和对称性守恒的机制等。这一生命科学中的最基本问题在交叉科学领域的探索是我们目前面临的挑战和机遇,旨在探索生物大分子的结构化学和立体化学的理论基础。
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979
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19
【期刊论文】Topological Analysis of Enzymatic Actions on DNA
邱文元, Guang Hu · ZeWang ·Wen-Yuan Qiu
Bull Math Biol (2011) 73:3030–3046,-0001,():
-1年11月30日
Current synthetic biology has witnessed a revolution that natural DNA molecule steps onto a broad scientific area by assembling a large variety of threedimensional structures with the connectivity of polyhedra. A mathematical model of these biomolecules is crucial to clarify the biological self-assembly principle, and unravel a first-step understanding of biological regulation and controlling mechanisms. In this paper, mechanisms of two different enzymatic actions on DNA polyhedra are elucidated through theoretical models of polyhedral links: (1) topoisomerase that untangles DNA polyhedral links produces separated single-stranded DNA circles through the crossing change operation; (2) recombinase generates a class of polyhedral circular paths or polyhedral knots by applying the crossing smoothing operation. Furthermore, we also discuss the possibility of applying two theoretical operations in molecular design of DNA polyhedra. Thus, our research provides a new sight of how geometry and topology of DNA polyhedra can be manipulated and controlled by enzymes, as well as has implications for molecular design and structural analysis of structural genome organization.
Bionanotechnology · Crossing change · Knot theory · DNA polyhedra
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【期刊论文】New Euler’s Formula for DNA Polyhedra
邱文元, Guang Hu, Wen-Yuan Qiu*, Arnout Ceulemans
PLoS ONE 6(10): e26308. doi:10.1371/journal.pone.0026308,-0001,():
-1年11月30日
DNA polyhedra are cage-like architectures based on interlocked and interlinked DNA strands. We propose a formula which unites the basic features of these entangled structures. It is based on the transformation of the DNA polyhedral links into Seifert surfaces, which removes all knots. The numbers of components m, of crossings c, and of Seifert circles s are related by a simple and elegant formula: szm~cz2. This formula connects the topological aspects of the DNA cage to the Euler characteristic of the underlying polyhedron. It implies that Seifert circles can be used as effective topological indices to describe polyhedral links. Our study demonstrates that, the new Euler’s formula provides a theoretical framework for the stereo-chemistry of DNA polyhedra, which can characterize enzymatic transformations of DNA and be used to characterize and design novel cages with higher genus.
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【期刊论文】The architecture of polyhedral links and their HOMFLY polynomials
邱文元, Shu-Ya Liu·Xiao-Sheng Cheng·Heping Zhang·Wen-Yuan Qiu
J Math Chem (2010) 48: 439-456,-0001,():
-1年11月30日
A general approach is proposed to elucidate the topological characteristics ofmolecules with the shape of polyhedral links. For an arbitrary polyhedral graph, four classes of polyhedral links can be obtained by applying the operation of 'X-tangle covering' to the related reduced sets. The relationships between theW-polynomial of a polyhedral graph and the HOMFLY polynomial of each kind of polyhedral links are established. These relationships not only simplify the computation but also provide a method of constructing a general formula for the HOMFLY polynomial of polyhedral links.
Polyhedral links·HOMFLY polynomial·W-polynomial·DNA Polyhedra
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【期刊论文】Molecular design of Goldberg polyhedral links
邱文元, Wen-Yuan Qiu *, Xin-Dong Zhai
Journal of Molecular Structure: THEOCHEM 756 (2005) 163-166,-0001,():
-1年11月30日
A new method for understanding the construction of polyhedral links has been developed on the basis of the novel structure of HK97 capsid and the classification of Goldberg polyhedra. Polyhedral links, the interlinked and interlocked architectures, have been solved by analyzing and characterizing the topological structure of the two types of polyhedral links, which are RnC1ZRnC10(2nC1) and RnC1ZRnC20n. Where, nZ1, 2,., R1Z12 and R represents the number of the interlocked rings. Our results show that these two types of polyhedral links both have I symmetry and therefore are said to possess chirality.
Knot theory, Goldberg polyhedra, Polyhedral links, Symmetry, Chirality, Protein catenane
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【期刊论文】The complexity of Platonic and Archimedean polyhedral links
邱文元, Guang Hu·Wen-Yuan Qiu·Xiao-Sheng Cheng·Shu-Ya Liu
J Math Chem (2010) 48: 401-412,-0001,():
-1年11月30日
A mathematical methodology for understanding the complexity of Platonic and Archimedean polyhedral links has been developed based on some topological invariants from knot theory. Knot invariants discussed here include rossing number, unknotting number, genus and braid index, which are considered significant in viewofDNAnanotechnology. Our results demonstrate that the braid index provides the most structural information; hence, it can be used, among four knot invariants, as the most useful complexity measure. Using such an invariant, it indicates that the complexity of polyhedral links is directed by the number of their building blocks. The research introduces a simple but important concept in the theoretical characterization and analysis of DNA polyhedral catenanes.
Platonic polyhedra·Archimedean polyhedra·Polyhedral links·Knot invariants·Complexity measures·DNA catenanes
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【期刊论文】Two combinatorial operations and a knot theoretical approach forfullerene polyhedra
邱文元, Guang HU and Wen-Yuan QIU*
MATCH Commun. Math. Comput. Chem. 59 (2010) 347-362,-0001,():
-1年11月30日
In this paper, we introduce two combinatorial operations and a knot-theoretical approach forgeneration and description of fullerene architectures. The 'Spherical rotating-vertex bifurcation' operationapplied to original fullerene polyhedra can lead to leapfrog fullerenes. However, the 'Sphericalstretching-vertex bifurcation' operation applied to fullerene generates a family of related polyhedra, whichgo beyond the scope of fullerenes. These related cages, the cubic tessellations containing not only 5-gonsand 6-gons but also 3-gons and 8-gons, are potential candidates in carbon chemistry. By using a simplealgorithm based on knot theory, these two homologous series of molecule graphs can be transformed intovarious polyhedral links. For these interlocked architectures, it is now possible to quantify their propertiesby knot invariants. By means of this application, we show connections (1) between knot polynomials andfullerene isomers determination, (2) between knot genus and fullerene complexity and (3) betweenunknotting numbers and fullerene stability. Our results suggest that techniques coming from knot theoryhave potential applications and offer novel insights in predicting several structural and chemical propertiesof fullerene polyhedra.
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【期刊论文】The keeping and reversal of chirality for dual links
邱文元, Dan Lu and Wen-Yuan Qiu*
MATCH Commun. Math. Comput.Chem. 63(2010)79-90,-0001,():
-1年11月30日
A new method for understanding the construction of dual links has been developed on the basis of medial graph in graph theory and tangle in knot theory. The method defines two types of oriented 4-valent plane graph: Ge and Go, whose vertices are covered by E-tangles and O-tangles, respectively. The result shows that there are two types of dual links: E-dual links and O-dual links, which have many differences in topological properties, especially their chiral rule. In our paper, we show that dual links can be constructed by oriented 4-valent plant graphs and tangles. This research puts forward the definition of dual links and the methodology for the construction of dual links. Dual links open a new approach for the research of links, and the methodology may also be used to direct the synthesis of chiral molecules.
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【期刊论文】Topological transformation of dual polyhedral links
邱文元, Dan Lua, Guang Hua, Yuan-Yuan Qiub, and Wen-Yuan Qiua, *
MATCH Commun. Math. Comput.Chem. 63(2010)67-78,-0001,():
-1年11月30日
In this paper, the novel topology of Platonic polyhedral links is discussed on the basis of the graph theory and topological principles. This interesting problem of the dual polyhedral links has been solved by using our method of the ‘sphere-surface-movement’. There are three classes of dual polyhedral links which can be explored: the tetrahedral link is self-dual, the hexahedral and octahedral link, as well as the dodecahedral and icosahedral link are dual to each other. Our results show that the duality of self-dual tetrahedral link is ‘trivial’, and the duality of hexahedral and octahedral link as well as dodecahedral and icosahedral link are ‘nontrivial’. This study provides further insight into the molecular design and theoretical characterization of the new polyhedral links.
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【期刊论文】A novel molecular design of polyhedral links and their chiral analysis
邱文元, Xiao-Sheng Cheng a, Wen-Yuan Qiu b, He-Ping Zhang a
MATCH Commun.Math.Comput.Chem. 62(2009)115-130,-0001,():
-1年11月30日
Polyhedral links, interlinked and interlocked architectures, have been proposed for the description and analysis of knotted configurations in DNA and proteins. Qiu et al. fabricated cubic polyhedral and carbon nanotube links by the means of three cross curves and double lines covering, and analyzed their chirality by point groups. We present, in this paper, a novel method by replacing three cross curves with branched alternating closed braids to construct a new type of polyhedral links on arbitrary convex polyhedra. We give some conditions to determine the chirality of the polyhedral links in terms of generalized Tutte and Kauffman polynomials. Accordingly, we show that each regular branched closed braid link is chiral. This result shows that the model of bacteriophage HK97 capsid, topologically linked protein catenane, is chiral.
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【期刊论文】The architecture of Platonic polyhedral links
邱文元, Guang Hu, Xin-Dong Zhai, Dan Lu, Wen-Yuan Qiu
J Math Chem (2009) 46: 592-603,-0001,():
-1年11月30日
A new methodology for understanding the construction of polyhedral links has been developed on the basis of the Platonic solids by using our method of the 'n-branched curves and m-twisted double-lines covering'. There are five classes of platonic polyhedral links we can construct: the tetrahedral links; the hexahedral links; the octahedral links; the dodecahedral links; the icosahedral links. The tetrahedral links, hexahedral links, and dodecahedral links are, respectively, assembled by using the method of the '3-branched curves and m-twisted double-lines covering', whereas the octahedral links and dodecahedral links are, respectively, made by using the method of the '4-ranched curves' and '5-branched curves', as well as 'm-twisted double-lines covering'. Moreover, the analysis relating topological properties and link invariants is of considerable importance. Link invariants are powerful tools to classify and measure the complexity of polyhedral catenanes. This study provides further insight into the molecular design, as well as theoretical characterization, of the DNA polyhedral catenanes.
Platonic polyhedra, Polyhedral links, Knot theory, Link invariants, DNA catenanes
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