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 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 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 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 268 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 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 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 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.
Download or read book Nuclear Dynamics written by K. Nagata and published by Springer Science & Business Media. This book was released on 2007-12-03 with total page 285 pages. Available in PDF, EPUB and Kindle. Book excerpt: The dynamics of nuclear structures described in this book furnish the basis for a comprehensive understanding of how the higher-order organization and function of the nucleus is established and how it correlates with the expression of a variety of vital activities such as cell proliferation and differentiation. The resulting volume creates an invaluable source of reference for researchers in the 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 Untangling the Double Helix written by James C. Wang and published by . This book was released on 2009 with total page 252 pages. Available in PDF, EPUB and Kindle. Book excerpt: The problem of unraveling two intertwined strands during the duplication of DNA was recognized shortly after the proposal of the DNA double helix structure in 1953. A group of enzymes called DNA topoisomerases solve this problem by breaking and rejoining DNA molecules in a controlled manner, thereby allowing strands to be passed through each other and thus untangled—not just during DNA replication, but also during many other basic cellular processes. Because of their intimate involvement in the workings of the cell, topoisomerases are also the logical targets of many antibiotics (including Cipro) and anticancer agents. This book, written by James Wang, the discoverer of the first topoisomerase and a leader in the field since, presents ten chapters covering the historical backdrop of the DNA entanglement problem and the discovery of the DNA topoisomerases, how DNA topoisomerases perform their magic in DNA replication, transcription, genetic recombination and chromosome condensation, and how they are targets of therapeutic agents. The book should appeal to readers from undergraduates upwards with interests in the biological and clinical aspects of topoisomerase function, or in the mathematics and physics of topology.
Download or read book Topology for Computing written by Afra J. Zomorodian and published by Cambridge University Press. This book was released on 2005-01-10 with total page 264 pages. Available in PDF, EPUB and Kindle. Book excerpt: The emerging field of computational topology utilizes theory from topology and the power of computing to solve problems in diverse fields. Recent applications include computer graphics, computer-aided design (CAD), and structural biology, all of which involve understanding the intrinsic shape of some real or abstract space. A primary goal of this book is to present basic concepts from topology and Morse theory to enable a non-specialist to grasp and participate in current research in computational topology. The author gives a self-contained presentation of the mathematical concepts from a computer scientist's point of view, combining point set topology, algebraic topology, group theory, differential manifolds, and Morse theory. He also presents some recent advances in the area, including topological persistence and hierarchical Morse complexes. Throughout, the focus is on computational challenges and on presenting algorithms and data structures when appropriate.
Download or read book Knots and Links written by Dale Rolfsen and published by American Mathematical Soc.. This book was released on 2003 with total page 458 pages. Available in PDF, EPUB and Kindle. Book excerpt: Rolfsen's beautiful book on knots and links can be read by anyone, from beginner to expert, who wants to learn about knot theory. Beginners find an inviting introduction to the elements of topology, emphasizing the tools needed for understanding knots, the fundamental group and van Kampen's theorem, for example, which are then applied to concrete problems, such as computing knot groups. For experts, Rolfsen explains advanced topics, such as the connections between knot theory and surgery and how they are useful to understanding three-manifolds. Besides providing a guide to understanding knot theory, the book offers 'practical' training. After reading it, you will be able to do many things: compute presentations of knot groups, Alexander polynomials, and other invariants; perform surgery on three-manifolds; and visualize knots and their complements.It is characterized by its hands-on approach and emphasis on a visual, geometric understanding. Rolfsen offers invaluable insight and strikes a perfect balance between giving technical details and offering informal explanations. The illustrations are superb, and a wealth of examples are included. Now back in print by the AMS, the book is still a standard reference in knot theory. It is written in a remarkable style that makes it useful for both beginners and researchers. Particularly noteworthy is the table of knots and links at the end. This volume is an excellent introduction to the topic and is suitable as a textbook for a course in knot theory or 3-manifolds. Other key books of interest on this topic available from the AMS are ""The Shoelace Book: A Mathematical Guide to the Best (and Worst) Ways to Lace your Shoes"" and ""The Knot Book.""
Download or read book Modern Phylogenetic Comparative Methods and Their Application in Evolutionary Biology written by László Zsolt Garamszegi and published by Springer. This book was released on 2014-07-29 with total page 553 pages. Available in PDF, EPUB and Kindle. Book excerpt: Phylogenetic comparative approaches are powerful analytical tools for making evolutionary inferences from interspecific data and phylogenies. The phylogenetic toolkit available to evolutionary biologists is currently growing at an incredible speed, but most methodological papers are published in the specialized statistical literature and many are incomprehensible for the user community. This textbook provides an overview of several newly developed phylogenetic comparative methods that allow to investigate a broad array of questions on how phenotypic characters evolve along the branches of phylogeny and how such mechanisms shape complex animal communities and interspecific interactions. The individual chapters were written by the leading experts in the field and using a language that is accessible for practicing evolutionary biologists. The authors carefully explain the philosophy behind different methodologies and provide pointers – mostly using a dynamically developing online interface – on how these methods can be implemented in practice. These “conceptual” and “practical” materials are essential for expanding the qualification of both students and scientists, but also offer a valuable resource for educators. Another value of the book are the accompanying online resources (available at: http://www.mpcm-evolution.com), where the authors post and permanently update practical materials to help embed methods into practice.
Download or read book Physics in Molecular Biology written by Kim Sneppen and published by Cambridge University Press. This book was released on 2005-08-25 with total page 328 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book, first published in 2005, is a discussion for advanced physics students of how to use physics to model biological systems.
Download or read book The Nature of the Mechanical Bond written by Carson J. Bruns and published by John Wiley & Sons. This book was released on 2016-10-10 with total page 784 pages. Available in PDF, EPUB and Kindle. Book excerpt: "The story is told by THE inventor-pioneer-master in the field and is accompanied by amazing illustrations... [it] will become an absolute reference and a best seller in chemistry!" —Alberto Credi "... the great opus on the mechanical bond. A most impressive undertaking!" — Jean-Marie Lehn Congratulations to co-author J. Fraser Stoddart, a 2016 Nobel Laureate in Chemistry. In molecules, the mechanical bond is not shared between atoms—it is a bond that arises when molecular entities become entangled in space. Just as supermolecules are held together by supramolecular interactions, mechanomolecules, such as catenanes and rotaxanes, are maintained by mechanical bonds. This emergent bond endows mechanomolecules with a whole suite of novel properties relating to both form and function. They hold unlimited promise for countless applications, ranging from their presence in molecular devices and electronics to their involvement in remarkably advanced functional materials. The Nature of the Mechanical Bond is a comprehensive review of much of the contemporary literature on the mechanical bond, accessible to newcomers and veterans alike. Topics covered include: Supramolecular, covalent, and statistical approaches to the formation of entanglements that underpin mechanical bonds in molecules and macromolecules Kinetically and thermodynamically controlled strategies for synthesizing mechanomolecules Chemical topology, molecular architectures, polymers, crystals, and materials with mechanical bonds The stereochemistry of the mechanical bond (mechanostereochemistry), including the novel types of dynamic and static isomerism and chirality that emerge in mechanomolecules Artificial molecular switches and machines based on the large-amplitude translational and rotational motions expressed by suitably designed catenanes and rotaxanes. This contemporary and highly interdisciplinary field is summarized in a visually appealing, image-driven format, with more than 800 illustrations covering both fundamental and applied research. The Nature of the Mechanical Bond is a must-read for everyone, from students to experienced researchers, with an interest in chemistry’s latest and most non-canonical bond.
