Download or read book Metabolic Networks Elementary Flux Modes and Polyhedral Cones written by Isaac Klapper and published by SIAM. This book was released on 2021-06-15 with total page 133 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book presents a mathematical analysis of the relationship between the cell biology idea of metabolic networks and the mathematical idea of polyhedral cones. Such cones can be used to describe the set of steady state admissible fluxes through metabolic networks, and consequently they have become important constructs in the field of microbiology. Fundamental objects called elementary flux modes (EFMs) can be described mathematically via convex cone concepts; the fundamental algorithm of this relationship is the Double Description method. While this method has an extended history in the field of computational geometry, this monograph addresses its relatively recent use in the context of cellular metabolism, providing an easy-to-read introduction to a central topic of mathematical systems biology. Metabolic Networks, Elementary Flux Modes, and Polyhedral Cones addresses important topics in the mathematical description of metabolic activity that have not previously appeared in unified form and presents a careful study of the Double Description method in the context of metabolic analysis. It makes mathematical aspects of the material readily accessible to bioengineers and system biologists, and biological aspects readily accessible to mathematicians. This book is intended for readers from both mathematical and biological backgrounds, including mathematicians, engineers, and biologists interested in cell metabolism. It will also be helpful to mathematicians interested in applying computational geometry methods in computational biology as well as for systems biologists and modelers interested in the mathematical and algorithmic foundations of metabolic pathway analysis.
Download or read book Multiplicity of Time Scales in Complex Systems written by Bernhelm Booss and published by Springer Nature. This book was released on 2024 with total page 477 pages. Available in PDF, EPUB and Kindle. Book excerpt: Zusammenfassung: This highly interdisciplinary volume brings together a carefully curated set of case studies examining complex systems with multiple time scales (MTS) across a variety of fields: materials science, epidemiology, cell physiology, mathematics, climatology, energy transition planning, ecology, economics, sociology, history, and cultural studies. The book addresses the vast diversity of interacting processes underlying the behaviour of different complex systems, highlighting the multiplicity of characteristic time scales that are a common feature of many and showcases a rich variety of methodologies across disciplinary boundaries. Self-organizing, out-of-equilibrium, ever-evolving systems are ubiquitous in the natural and social world. Examples include the climate, ecosystems, living cells, epidemics, the human brain, and many socio-economic systems across history. Their dynamical behaviour poses great challenges in the pressing context of the climate crisis, since they may involve nonlinearities, feedback loops, and the emergence of spatial-temporal patterns, portrayed by resilience or instability, plasticity or rigidity; bifurcations, thresholds and tipping points; burst-in excitation or slow relaxation, and worlds of other asymptotic behaviour, hysteresis, and resistance to change. Chapters can be read individually by the reader with special interest in such behaviours of particular complex systems or in specific disciplinary perspectives. Read together, however, the case studies, opinion pieces, and meta-studies on MTS systems presented and analysed here combine to give the reader insights that are more than the sum of the book's individual chapters, as surprising similarities become apparent in seemingly disparate and unconnected systems. MTS systems call into question naïve perceptions of time and complexity, moving beyond conventional ways of description, analysis, understanding, modelling, numerical prediction, and prescription of the world around us. This edited collection presents new ways of forecasting, introduces new means of control, and - perhaps as the most demanding task - it singles out a sustainable description of an MTS system under observation, offering a more nuanced interpretation of the floods of quantitative data and images made available by high- and low-frequency measurement tools in our unprecedented era of information flows
Download or read book Foundations of Theoretical Approaches in Systems Biology written by Alberto Marin-Sanguino and published by Frontiers Media SA. This book was released on 2019-01-11 with total page 216 pages. Available in PDF, EPUB and Kindle. Book excerpt: If biology in the 20th century was characterized by an explosion of new technologies and experimental methods, that of the 21st has seen an equally exuberant proliferation of mathematical and computational methods that attempt to systematize and explain the abundance of available data. As we live through the consolidation of a new paradigm where experimental data goes hand in hand with computational analysis, we contemplate the challenge of fusing these two aspects of the new biology into a consistent theoretical framework. Whether systems biology will survive as a field or be washed away by the tides of future fads will ultimately depend on its success to achieve this type of synthesis. The famous quote attributed to Kurt Lewin comes to mind: "there is nothing more practical than a good theory". This book presents a wide assortment of articles on systems biology in an attempt to capture the variety of current methods in systems biology and show how they can help to find answers to the challenges of modern biology.
Download or read book Algorithms in Bioinformatics written by Philipp Bücher and published by Springer Science & Business Media. This book was released on 2006-08-30 with total page 412 pages. Available in PDF, EPUB and Kindle. Book excerpt: Here are the refereed proceedings of the 6th International Workshop on Algorithms in Bioinformatics, WABI 2006, held in the course of the ALGO 2006 conference meetings. The book presents 36 revised full papers addressing all current issues of algorithms in bioinformatics, from mathematical tools to experimental studies of approximation algorithms and reports on significant computational analyses. For the first time, coverage extends to machine-learning approaches along with combinatorial optimization.
Download or read book Large Scale Methods to Enumerate Extreme Rays and Elementary Modes color Print written by Marco Terzer and published by Lulu.com. This book was released on 2009-12-24 with total page 170 pages. Available in PDF, EPUB and Kindle. Book excerpt: A major challenge in systems biology is to improve the understanding of complex metabolic networks. Here, we focus on structural analysis since it requires mainly reaction stoichiometries, in contrary to detailed dynamic methods that are often limited by insufficient knowledge on mechanisms and parameters. Thermodynamic reaction constraints and the steady state assumption reduce the solution space for valid reaction fluxes to a convex polyhedral cone. Pathway analysis methods aim at finding a unique generating set for the flux cone---called extreme rays or elementary modes. We describe critical aspects for an efficient implementation of the double description method for large scale application. The efficiency of introduced techniques is demonstrated with large application examples from combinatorics and systems biology.
Download or read book A Decomposition Approach for Computing Elementary Flux Modes in Genome scale Metabolic Networks written by Siu-hung Joshua Chan and published by . This book was released on 2011 with total page 111 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Models and Algorithms for Metabolic Networks written by Vicente Acuna and published by . This book was released on 2010 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: In this PhD, we present some algorithms and complexity results for two general problems that arise in the analysis of a metabolic network: the search for elementary modes of a network and the search for minimal precursors sets. Elementary modes is a common tool in the study of the cellular characteristic of a metabolic network. An elementary mode can be seen as a minimal set of reactions that can work in steady state independently of the rest of the network. It has therefore served as a mathematical model for the possible metabolic pathways of a cell. Their computation is not trivial and poses computational challenges. We show that some problems, like checking consistency of a network, finding one elementary mode or checking that a set of reactions constitutes a cut are easy problems, giving polynomial algorithms based on LP formulations. We also prove the hardness of central problems like finding a minimum size elementary mode, finding an elementary mode containing two given reactions, counting the number of elementary modes or finding a minimum reaction cut. On the enumeration problem, we show that enumerating all reactions containing one given reaction cannot be done in polynomial total time unless P=NP. This result provides some idea about the complexity of enumerating all the elementary modes. The search for precursor sets is motivated by discovering which external metabolites are sufficient to allow the production of a given set of target metabolites. In contrast with previous proposals, we present a new approach which is the first to formally consider the use of cycles in the way to produce the target. We present a polynomial algorithm to decide whether a set is a precursor set of a given target. We also show that, given a target set, finding a minimal precursor set is easy but finding a precursor set of minimum size is NP-hard. We further show that finding a solution with minimum size internal supply is NP-hard. We give a simple characterisation of precursors sets by the existence of hyperpaths between the solutions and the target. If we consider the enumeration of all the minimal precursor sets of a given target, we find that this problem cannot be solved in polynomial total time unless P=NP. Despite this result, we present two algorithms that have good performance for medium-size networks.
Download or read book Macroscopic Modeling of Metabolic Reaction Networks and Dynamic Identification of Elementary Flux Modes by Column Generation written by and published by . This book was released on 2015 with total page 146 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book The Regulation of Cellular Systems written by Reinhart Heinrich and published by Springer Science & Business Media. This book was released on 2012-12-06 with total page 387 pages. Available in PDF, EPUB and Kindle. Book excerpt: There is no doubt that nowadays, biology benefits greatly from mathematics. In particular, cellular biology is, besides population dynamics, a field where tech niques of mathematical modeling are widely used. This is reflected by the large number of journal articles and congress proceedings published every year on the dynamics of complex cellular processes. This applies, among others, to metabolic control analysis, where the number of articles on theoretical fundamentals and experimental applications has increased for about 15 years. Surprisingly, mono graphs and textbooks dealing with the modeling of metabolic systems are still exceptionally rare. We think that now time is ripe to fill this gap. This monograph covers various aspects of the mathematical description of enzymatic systems, such as stoichiometric analysis, enzyme kinetics, dynamical simulation, metabolic control analysis, and evolutionary optimization. We believe that, at present, these are the main approaches by which metabolic systems can be analyzed in mathematical terms. Although stoichiometric analysis and enzyme kinetics are classical fields tracing back to the beginning of our century, there are intriguing recent developments such as detection of elementary biochemical syn thesis routes and rate laws for the situation of metabolic channeling, which we have considered worth being included. Evolutionary optimization of metabolic systems is a rather new field with promising prospects. Its goal is to elucidate the structure and functions of these systems from an evolutionary viewpoint.
Download or read book Structural Stability And Morphogenesis written by Rene Thom and published by CRC Press. This book was released on 2018-03-05 with total page 404 pages. Available in PDF, EPUB and Kindle. Book excerpt: First Published in 2018. Routledge is an imprint of Taylor & Francis, an Informa company.
Download or read book Expanded Cinema written by Gene Youngblood and published by Fordham University Press. This book was released on 2020-03-03 with total page 464 pages. Available in PDF, EPUB and Kindle. Book excerpt: Fiftieth anniversary reissue of the founding media studies book that helped establish media art as a cultural category. First published in 1970, Gene Youngblood’s influential Expanded Cinema was the first serious treatment of video, computers, and holography as cinematic technologies. Long considered the bible for media artists, Youngblood’s insider account of 1960s counterculture and the birth of cybernetics remains a mainstay reference in today’s hypermediated digital world. This fiftieth anniversary edition includes a new Introduction by the author that offers conceptual tools for understanding the sociocultural and sociopolitical realities of our present world. A unique eyewitness account of burgeoning experimental film and the birth of video art in the late 1960s, this far- ranging study traces the evolution of cinematic language to the end of fiction, drama, and realism. Vast in scope, its prescient formulations include “the paleocybernetic age,” “intermedia,” the “artist as design scientist,” the “artist as ecologist,” “synaesthetics and kinesthetics,” and “the technosphere: man/machine symbiosis.” Outstanding works are analyzed in detail. Methods of production are meticulously described, including interviews with artists and technologists of the period, such as Nam June Paik, Jordan Belson, Andy Warhol, Stan Brakhage, Carolee Schneemann, Stan VanDerBeek, Les Levine, and Frank Gillette. An inspiring Introduction by the celebrated polymath and designer R. Buckminster Fuller—a perfectly cut gem of countercultural thinking in itself—places Youngblood’s radical observations in comprehensive perspective. Providing an unparalleled historical documentation, Expanded Cinema clarifies a chapter of countercultural history that is still not fully represented in the arthistorical record half a century later. The book will also inspire the current generation of artists working in ever-newer expansions of the cinematic environment and will prove invaluable to all who are concerned with the technologies that are reshaping the nature of human communication.
Download or read book Convexity and Optimization in Finite Dimensions I written by Josef Stoer and published by Springer Science & Business Media. This book was released on 2012-12-06 with total page 306 pages. Available in PDF, EPUB and Kindle. Book excerpt: Dantzig's development of linear programming into one of the most applicable optimization techniques has spread interest in the algebra of linear inequalities, the geometry of polyhedra, the topology of convex sets, and the analysis of convex functions. It is the goal of this volume to provide a synopsis of these topics, and thereby the theoretical back ground for the arithmetic of convex optimization to be treated in a sub sequent volume. The exposition of each chapter is essentially independent, and attempts to reflect a specific style of mathematical reasoning. The emphasis lies on linear and convex duality theory, as initiated by Gale, Kuhn and Tucker, Fenchel, and v. Neumann, because it represents the theoretical development whose impact on modern optimi zation techniques has been the most pronounced. Chapters 5 and 6 are devoted to two characteristic aspects of duality theory: conjugate functions or polarity on the one hand, and saddle points on the other. The Farkas lemma on linear inequalities and its generalizations, Motzkin's description of polyhedra, Minkowski's supporting plane theorem are indispensable elementary tools which are contained in chapters 1, 2 and 3, respectively. The treatment of extremal properties of polyhedra as well as of general convex sets is based on the far reaching work of Klee. Chapter 2 terminates with a description of Gale diagrams, a recently developed successful technique for exploring polyhedral structures.
Download or read book Foundations of Computational Mathematics written by Ronald A. DeVore and published by Cambridge University Press. This book was released on 2001-05-17 with total page 418 pages. Available in PDF, EPUB and Kindle. Book excerpt: Collection of papers by leading researchers in computational mathematics, suitable for graduate students and researchers.
Download or read book Color Atlas of Cytology Histology and Microscopic Anatomy written by Wolfgang Kühnel and published by Thieme. This book was released on 2003 with total page 548 pages. Available in PDF, EPUB and Kindle. Book excerpt: This timeless pocket atlas is the ideal visual companion to histology and cytology textbooks. First published in 1950 and translated into eight languages, Kuehnel's Pocket Atlas of Cytology, Histology and Microscopic Anatomy is a proven classic. The fully revised and updated fourth edition contains 745 full-color illustrations - almost 200 more than were included in the third edition. Superb, high-quality microphotographs and pathologic stains are accompanied by legends, informative texts, and numerous cross-references. Key features of the updated fourth edition: More than 700 high-quality illustrations using advanced techniques in histology and electron microscopy Practical, information Concise and focused text Key concepts and ideas illustrated in less than 550 pages Ideal for exam preparation, this world-class book is an indispensable visual study tool for medical, dental and biology students. It can also serve as an outstanding review and refresher text.
Download or read book The Dynamics of Complex Urban Systems written by Sergio Albeverio and published by Springer Science & Business Media. This book was released on 2007-10-16 with total page 489 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book contains the contributions presented at the international workshop "The Dynamics of Complex Urban Systems: an interdisciplinary approach" held in Ascona, Switzerland in November 2004. Experts from several disciplines outline a conceptual framework for modeling and forecasting the dynamics of both growth-limited cities and megacities. Coverage reflects the various interdependencies between structural and social development.
Download or read book The Facts on File Dictionary of Botany written by Jill Bailey and published by Infobase Publishing. This book was released on 2014-05-14 with total page 256 pages. Available in PDF, EPUB and Kindle. Book excerpt: A dictionary containing over 2,000 terms and concepts related to botany.
Download or read book The Expanding Cell written by Jean-Pierre Verbelen and published by Springer Science & Business Media. This book was released on 2006-11-03 with total page 302 pages. Available in PDF, EPUB and Kindle. Book excerpt: The study of plant cell expansion involves many different disciplines and technical approaches, and this book brings this diversity together to present a multifaceted view of the most up-to-date knowledge. Coverage includes data ranging from biophysical measurements and chemical analysis to molecular biological approaches and microscopy.
