Download or read book Topology in Molecular Biology written by Michael I. Monastyrsky and published by Springer Science & Business Media. This book was released on 2006-10-26 with total page 238 pages. Available in PDF, EPUB and Kindle. Book excerpt: Providing a course of modern topology intended for biologists and physicists, this book presents a class of results in molecular biology for which topological methods and ideas are important. These include: the large-scale conformation properties of DNA; computational methods; the structure of proteins; and other problems in molecular biology.
Download or read book Discrete and Topological Models in Molecular Biology written by Nataša Jonoska and published by Springer Science & Business Media. This book was released on 2013-12-23 with total page 522 pages. Available in PDF, EPUB and Kindle. Book excerpt: Theoretical tools and insights from discrete mathematics, theoretical computer science, and topology now play essential roles in our understanding of vital biomolecular processes. The related methods are now employed in various fields of mathematical biology as instruments to "zoom in" on processes at a molecular level. This book contains expository chapters on how contemporary models from discrete mathematics – in domains such as algebra, combinatorics, and graph and knot theories – can provide perspective on biomolecular problems ranging from data analysis, molecular and gene arrangements and structures, and knotted DNA embeddings via spatial graph models to the dynamics and kinetics of molecular interactions. The contributing authors are among the leading scientists in this field and the book is a reference for researchers in mathematics and theoretical computer science who are engaged with modeling molecular and biological phenomena using discrete methods. It may also serve as a guide and supplement for graduate courses in mathematical biology or bioinformatics, introducing nontraditional aspects of mathematical biology.
Download or read book DNA Topology written by Andrew D. Bates and published by Oxford University Press, USA. This book was released on 2005 with total page 224 pages. Available in PDF, EPUB and Kindle. Book excerpt: "A key aspect of DNA is its ability to form a variety of structures, this book explains the origins and importance of such structures"--Provided by publisher.
Download or read book Calculating the Secrets of Life written by National Research Council and published by National Academies Press. This book was released on 1995-04-06 with total page 300 pages. Available in PDF, EPUB and Kindle. Book excerpt: As researchers have pursued biology's secrets to the molecular level, mathematical and computer sciences have played an increasingly important roleâ€"in genome mapping, population genetics, and even the controversial search for "Eve," hypothetical mother of the human race. In this first-ever survey of the partnership between the two fields, leading experts look at how mathematical research and methods have made possible important discoveries in biology. The volume explores how differential geometry, topology, and differential mechanics have allowed researchers to "wind" and "unwind" DNA's double helix to understand the phenomenon of supercoiling. It explains how mathematical tools are revealing the workings of enzymes and proteins. And it describes how mathematicians are detecting echoes from the origin of life by applying stochastic and statistical theory to the study of DNA sequences. This informative and motivational book will be of interest to researchers, research administrators, and educators and students in mathematics, computer sciences, and biology.
Download or read book Topological Data Analysis for Genomics and Evolution written by Raúl Rabadán and published by Cambridge University Press. This book was released on 2019-10-31 with total page 521 pages. Available in PDF, EPUB and Kindle. Book excerpt: Biology has entered the age of Big Data. The technical revolution has transformed the field, and extracting meaningful information from large biological data sets is now a central methodological challenge. Algebraic topology is a well-established branch of pure mathematics that studies qualitative descriptors of the shape of geometric objects. It aims to reduce questions to a comparison of algebraic invariants, such as numbers, which are typically easier to solve. Topological data analysis is a rapidly-developing subfield that leverages the tools of algebraic topology to provide robust multiscale analysis of data sets. This book introduces the central ideas and techniques of topological data analysis and its specific applications to biology, including the evolution of viruses, bacteria and humans, genomics of cancer and single cell characterization of developmental processes. Bridging two disciplines, the book is for researchers and graduate students in genomics and evolutionary biology alongside mathematicians interested in applied topology.
Download or read book Knots Molecules and the Universe written by Erica Flapan and published by American Mathematical Soc.. This book was released on 2015-12-22 with total page 406 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book is an elementary introduction to geometric topology and its applications to chemistry, molecular biology, and cosmology. It does not assume any mathematical or scientific background, sophistication, or even motivation to study mathematics. It is meant to be fun and engaging while drawing students in to learn about fundamental topological and geometric ideas. Though the book can be read and enjoyed by nonmathematicians, college students, or even eager high school students, it is intended to be used as an undergraduate textbook. The book is divided into three parts corresponding to the three areas referred to in the title. Part 1 develops techniques that enable two- and three-dimensional creatures to visualize possible shapes for their universe and to use topological and geometric properties to distinguish one such space from another. Part 2 is an introduction to knot theory with an emphasis on invariants. Part 3 presents applications of topology and geometry to molecular symmetries, DNA, and proteins. Each chapter ends with exercises that allow for better understanding of the material. The style of the book is informal and lively. Though all of the definitions and theorems are explicitly stated, they are given in an intuitive rather than a rigorous form, with several hundreds of figures illustrating the exposition. This allows students to develop intuition about topology and geometry without getting bogged down in technical details.
Download or read book DNA Topology written by Andrew D. Bates and published by Irl Press. This book was released on 1993 with total page 114 pages. Available in PDF, EPUB and Kindle. Book excerpt: The basic structure of the DNA double helix has been recognized for many years, but more recently the existence and biological importance of different conformations of DNA have become known. The most prominent of these are the "topological" deformations such as supercoiling and catenation. Almost all biological processes involving DNA--such as replication, recombination, and transcription--have effects on, and are affected by, the topological state of the DNA. DNA Topology: In Focus provides clear, concise explanations of these concepts in their biological contexts, making it a valuable text for students of molecular biology, biochemistry and related disciplines, and for all researchers in this field.
Download or read book DNA Topoisomerase Protocols written by Mary-Ann Bjornsti and published by Springer Science & Business Media. This book was released on 1999-03-23 with total page 352 pages. Available in PDF, EPUB and Kindle. Book excerpt: DNA Topoisomerase Protocols, I: DNA Topology and Enzymes brings together an unprecedented collection of cutting-edge experimental protocols for investigating DNA structure, topology, and DNA topoisomerase function. Described by expert experimentalists who have perfected the techniques, these unfailingly reproducible methods utilize new approaches to study changes in DNA topology (linking number, knotting, catenation, and relaxation) and DNA structure (bending), as well as to assess chromosome structure through FLP-mediated recombination and to analyze bacterial nucleoid structure. State-of-the-art protocols also detail the expression and purification of bacterial, viral, and eukaryotic DNA topoisomerases from a variety of sources, including baculovirus, and bacterial, yeast and mammalian expression systems. A companion volume, DNA Topoisomerase Protocols, v. 2: Enzymology and Drugs, provides detailed protocols to study the catalytic activities of DNA topoisomerases, as well as their specific interactions with topoisomerase-targeted antitumor and antibacterial drugs. DNA Topoisomerase Protocols, I: DNA Topology and Enzymes will be of immense value to the many basic scientists and clinicians who want better to understand and to exploit proficiently the wealth of recent discoveries about chromatin structure and its relation to gene expression, about DNA topoisomerases as the targets of antitumor and antibacterial agents, and about DNA repair.
Download or read book When Topology Meets Chemistry written by Erica Flapan and published by Cambridge University Press. This book was released on 2000-07-31 with total page 258 pages. Available in PDF, EPUB and Kindle. Book excerpt: The applications of topological techniques for understanding molecular structures have become increasingly important over the past thirty years. In this topology text, the reader will learn about knot theory, 3-dimensional manifolds, and the topology of embedded graphs, while learning the role these play in understanding molecular structures. Most of the results that are described in the text are motivated by questions asked by chemists or molecular biologists, though the results themselves often go beyond answering the original question asked. There is no specific mathematical or chemical prerequisite; all the relevant background is provided. The text is enhanced by nearly 200 illustrations and more than 100 exercises. Reading this fascinating book, undergraduate mathematics students can escape the world of pure abstract theory and enter that of real molecules, while chemists and biologists will find simple, clear but rigorous definitions of mathematical concepts they handle intuitively in their work.
Download or read book Topology and Physics of Circular DNA 1992 written by Alexander Vologodskii and published by CRC Press. This book was released on 2017-11-22 with total page 303 pages. Available in PDF, EPUB and Kindle. Book excerpt: Topology and Physics of Circular DNA presents comprehensive coverage of the physical properties of circular DNA. The author examines how topological constraints arising from cyclization of DNA lead to distinctive properties that make closed molecules radically different from linear DNA. The phenomenon of supercoiling, its geometric and topological analysis, and the formation of noncanonical structures in circular DNA under the influence of supercoiling are emphasized. The combination of consistent theoretical analysis and detailed treatment of major experimental approaches make Topology and Physics of Circular DNA an important reference volume for biophysicists, biochemists, molecular biologists, and researchers and students who want to expand their understanding of circular DNA.
Download or read book Topology in Chemistry written by D H Rouvray and published by Elsevier. This book was released on 2002-04-01 with total page 400 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume addresses a number of topological themes of direct relevance to chemists. Topological concepts are now regularly applied in wide areas of chemistry including molecular engineering and design, chemical toxicology, the study of molecular shape, crystal and surface structures, chemical bonding, macromolecular species such as polymers and DNA, and environmental chemistry. Currently, the design and synthesis of new drugs and agrochemicals are of especial importance. The book's prime focus is on the role played by topological indices in the description and characterisation of molecular species. The Wiener index along with a variety of other major topological indices, are discussed with particular reference to the powerful and much used connectivity indices. In this book an international team of leading experts review their respective fields and present their findings.The considerable benefits offered by topological indices in the investigation of chemical problems in science, medicine, and industry are highlighted. The volume records proceedings of the Harry Wiener Memorial Conference on the Role of Topology in Chemistry, held at the University of Georgia in March 2001, and serves as a fitting tribute to the chemical contributions of the late Harry Wiener. - Focuses on the role played by topological indices in the description and characterisation of molecular species - Records the proceedings of the Harry Weiner Memorial Conference on the Role of Topology in Chemistry, held at the University of Georgia in March 2001 - Along with a variety of other major topological indices, the Wiener index is discussed with particular reference to the powerful and much-used connectivity indices
Download or read book Knots Molecules and the Universe written by Erica Flapan and published by . This book was released on 2012 with total page 406 pages. Available in PDF, EPUB and Kindle. Book excerpt: "This book is an elementary introduction to geometric topology and its applications to chemistry, molecular biology, and cosmology. It does not assume any mathematical or scientific background, sophistication, or even motivation to study mathematics. It is meant to be fun and engaging while drawing students in to learn about fundamental topological and geometric ideas. Though the book can be read and enjoyed by nonmathematicians, college students, or even eager high school students, it is intended to be used as an undergraduate textbook. The book is divided into three parts corresponding to the three areas referred to in the title. Part 1 develops techniques that enable two- and three-dimensional creatures to visualize possible shapes for their universe and to use topological and geometric properties to distinguish one such space from another. Part 2 is an introduction to knot theory with an emphasis on invariants. Part 3 presents applications of topology and geometry to molecular symmetries, DNA, and proteins. Each chapter ends with exercises that allow for better understanding of the material."--Publisher's description.
Download or read book Molecular Biology of the Cell written by and published by . This book was released on 2002 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Algorithms in Structural Molecular Biology written by Bruce R. Donald and published by MIT Press. This book was released on 2023-08-15 with total page 497 pages. Available in PDF, EPUB and Kindle. Book excerpt: An overview of algorithms important to computational structural biology that addresses such topics as NMR and design and analysis of proteins.Using the tools of information technology to understand the molecular machinery of the cell offers both challenges and opportunities to computational scientists. Over the past decade, novel algorithms have been developed both for analyzing biological data and for synthetic biology problems such as protein engineering. This book explains the algorithmic foundations and computational approaches underlying areas of structural biology including NMR (nuclear magnetic resonance); X-ray crystallography; and the design and analysis of proteins, peptides, and small molecules. Each chapter offers a concise overview of important concepts, focusing on a key topic in the field. Four chapters offer a short course in algorithmic and computational issues related to NMR structural biology, giving the reader a useful toolkit with which to approach the fascinating yet thorny computational problems in this area. A recurrent theme is understanding the interplay between biophysical experiments and computational algorithms. The text emphasizes the mathematical foundations of structural biology while maintaining a balance between algorithms and a nuanced understanding of experimental data. Three emerging areas, particularly fertile ground for research students, are highlighted: NMR methodology, design of proteins and other molecules, and the modeling of protein flexibility. The next generation of computational structural biologists will need training in geometric algorithms, provably good approximation algorithms, scientific computation, and an array of techniques for handling noise and uncertainty in combinatorial geometry and computational biophysics. This book is an essential guide for young scientists on their way to research success in this exciting field.
Download or read book Protein Geometry Classification Topology and Symmetry written by William R. Taylor and published by CRC Press. This book was released on 2004-10-01 with total page 349 pages. Available in PDF, EPUB and Kindle. Book excerpt: From a geometric perspective, this book reviews and analyzes the structural principals of proteins with the goal of revealing the underlying regularities in their construction. It also reviews computer methods for structure analysis and the automatic comparison and classification of these structures with an analysis of the statistical significance of comparing different shapes. Following an analysis of the current state of the protein classification, the authors explore more abstract geometric and topological representations, including the occurrence of knotted topologies. The book concludes with a consideration of the origin of higher-level symmetries in protein structure.
Download or read book From Chemical Topology to Three Dimensional Geometry written by Alexandru T. Balaban and published by Springer Science & Business Media. This book was released on 2006-04-11 with total page 436 pages. Available in PDF, EPUB and Kindle. Book excerpt: Even high-speed supercomputers cannot easily convert traditional two-dimensional databases from chemical topology into the three-dimensional ones demanded by today's chemists, particularly those working in drug design. This fascinating volume resolves this problem by positing mathematical and topological models which greatly expand the capabilities of chemical graph theory. The authors examine QSAR and molecular similarity studies, the relationship between the sequence of amino acids and the less familiar secondary and tertiary protein structures, and new topological methods.
Download or read book Molecular Topology written by Mircea V. Diudea and published by Nova Biomedical Books. This book was released on 2001 with total page 350 pages. Available in PDF, EPUB and Kindle. Book excerpt: Most, yet not all, chemical substances consist of molecules. The fact that molecules have a 'structure' is known since the middle of the 19th century. Since then, one of the principal goals of chemistry is to establish the relationships between the chemical and physical properties of substance and the structure of the corresponding molecules. Countless results along these lines have been obtained along these lines and presented in different publications in this field. One group uses so-called topological indices. About 20 years ago, there were dozens of topological indices, but only a few with noteworthy chemical applications. Over time, their numbers have increased enormously. At this moment here is no theory that could serve as a reliable guide for solving this problem. This book is aimed at giving a reasonable comprehensive survey of the present, fin de siècle, state of art theory and practice of topological indices.
