Systems Biology: Simulation of Dynamic Network States
Systems Biology: Simulation of Dynamic Network States

Author: Bernhard Ø. Palsson

Publisher: Cambridge University Press

Published: 2011-05-26

Total Pages: 333

ISBN-13: 1139495429

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Biophysical models have been used in biology for decades, but they have been limited in scope and size. In this book, Bernhard Ø. Palsson shows how network reconstructions that are based on genomic and bibliomic data, and take the form of established stoichiometric matrices, can be converted into dynamic models using metabolomic and fluxomic data. The Mass Action Stoichiometric Simulation (MASS) procedure can be used for any cellular process for which data is available and allows a scalable step-by-step approach to the practical construction of network models. Specifically, it can treat integrated processes that need explicit accounting of small molecules and protein, which allows simulation at the molecular level. The material has been class-tested by the author at both the undergraduate and graduate level. All computations in the text are available online in MATLAB® and Mathematica® workbooks, allowing hands-on practice with the material.

Pathway Analysis and Optimization in Metabolic Engineering
Pathway Analysis and Optimization in Metabolic Engineering

Author: Néstor V. Torres

Publisher: Cambridge University Press

Published: 2002-12-19

Total Pages: 328

ISBN-13: 9781139437615

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Facility in the targeted manipulation of the genetic and metabolic composition of organisms, combined with unprecedented computational power, is forging a niche for a new subspecialty of biotechnology called metabolic engineering. First published in 2002, this book introduces researchers and advanced students in biology and engineering to methods of optimizing biochemical systems of biotechnological relevance. It examines the development of strategies for manipulating metabolic pathways, demonstrates the need for effective systems models, and discusses their design and analysis, while placing special emphasis on optimization. The authors propose power-law models and methods of biochemical systems theory toward these ends. All concepts are derived from first principles, and the text is richly illustrated with numerous graphs and examples throughout. Special features include: nontechnical and technical introductions to models of biochemical systems; a review of basic methods of model design and analysis; concepts of optimization; and detailed case studies.

Activation, Metabolism and Perfusion of the Heart
Activation, Metabolism and Perfusion of the Heart

Author: S. Sideman

Publisher: Springer Science & Business Media

Published: 2012-12-06

Total Pages: 735

ISBN-13: 9400933134

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The basic mechanism underlying directional differences in excitability, con duction velocity, andsafetyfactor thatleadtocircusmovementreentry incardiac muscle is generally attributed to a spatial difference in the refractory period as originally described by Mines [1] or to a depressed segment as described by Schmitt and Erlanger [2]. A departure from this depolarization in cardiac muscle involve quantities, such as Vmax' that are not directly descriptive of the underlying mechanisms of propagation.

Systems Biomedicine
Systems Biomedicine

Author: Edison T. Liu

Publisher: Academic Press

Published: 2009-09-17

Total Pages: 450

ISBN-13: 0080919839

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Systems biology is a critical emerging field that quantifies and annotates the complexity of biological systems in order to construct algorithmic models to predict outcomes from component input. Applications in medicine are revolutionizing our understanding of biological processes and systems. Systems Biomedicine is organized around foundations, computational modeling, network biology, and integrative biology, with the extension of examples from human biology and pharmacology, to focus on the applications of systems approaches to medical problems. An integrative approach to the underlying genomic, proteomic, and computational biology principles provides researchers with guidance in the use of qualitative systems and hypothesis generators. To reflect the highly interdisciplinary nature of the field, careful detail has been extended to ensure explanations of complex mathematical and biological principles are clear with minimum technical jargon. - Organized to reflect the important distinguishing characteristics of systems strategies in experimental biology and medicine - Provides precise and comprehensive measurement tools for constructing a model of the system and tools for defining complexity as an experimental dependent variable - Includes a thorough discussion of the applications of quantitative principles to biomedical problems

The Regulation of Cellular Systems
The Regulation of Cellular Systems

Author: Reinhart Heinrich

Publisher: Springer Science & Business Media

Published: 2012-12-06

Total Pages: 387

ISBN-13: 1461311616

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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.

Computational Analysis of Biochemical Systems
Computational Analysis of Biochemical Systems

Author: Eberhard O. Voit

Publisher: Cambridge University Press

Published: 2000-09-04

Total Pages: 556

ISBN-13: 9780521785792

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Teaches the use of modern computational methods for the analysis of biomedical systems using case studies and accompanying software.

Robotics and Factories of the Future ’87
Robotics and Factories of the Future ’87

Author: R. Radharamanan

Publisher: Springer Science & Business Media

Published: 2012-12-06

Total Pages: 868

ISBN-13: 3642738907

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The papers presented at the Second International Conference on Robotics and Factories of the Future held in San Diego, California, USA during July 28-31, 1987 are compiled in this volume. Over two hundred participants attended the conference, made technical presentations and discussed about various aspects of manufacturing, robotics and factories of the future. The number of papers published in this volume and the number of unpublished presentations at the conference indicates the evidance of growing interest in the areas of CAD/CAM, robotics and their role in future factories. The conference consisted of five plenary sessions, twenty three technical sessions, workshops, and exhibits from local industries and educational institutions. I wish to acknowledge with many thanks the contributions of all the authors who presented their work at the conference and submitted the manuscripts for publication. It is also my pleasure to acknowledge the role of keynote, banquet, and plenary sessions speakers whose contributions added greatly to the success of the conference. My sincere thanks to all session chairmen. I wish that the series of the International Conferences on Robotics and Factories of the Future which was initiated in 1984 in Charlotte, North Carolina will have a major impact on the use of robots and computers in the automated factories of the future.

Mathematical Modeling in Systems Biology
Mathematical Modeling in Systems Biology

Author: Brian P. Ingalls

Publisher: MIT Press

Published: 2022-06-07

Total Pages: 423

ISBN-13: 0262545829

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An introduction to the mathematical concepts and techniques needed for the construction and analysis of models in molecular systems biology. Systems techniques are integral to current research in molecular cell biology, and system-level investigations are often accompanied by mathematical models. These models serve as working hypotheses: they help us to understand and predict the behavior of complex systems. This book offers an introduction to mathematical concepts and techniques needed for the construction and interpretation of models in molecular systems biology. It is accessible to upper-level undergraduate or graduate students in life science or engineering who have some familiarity with calculus, and will be a useful reference for researchers at all levels. The first four chapters cover the basics of mathematical modeling in molecular systems biology. The last four chapters address specific biological domains, treating modeling of metabolic networks, of signal transduction pathways, of gene regulatory networks, and of electrophysiology and neuronal action potentials. Chapters 3–8 end with optional sections that address more specialized modeling topics. Exercises, solvable with pen-and-paper calculations, appear throughout the text to encourage interaction with the mathematical techniques. More involved end-of-chapter problem sets require computational software. Appendixes provide a review of basic concepts of molecular biology, additional mathematical background material, and tutorials for two computational software packages (XPPAUT and MATLAB) that can be used for model simulation and analysis.