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Thermodynamic Network Analysis of Biological Systems

Author: J. Schnakenberg

Publisher: Springer Science & Business Media

Published: 2012-12-06

Total Pages: 157

ISBN-13: 3642679714

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The first edition of this book was greeted with broad interest from readers en gaged in various disciplines of biophysics. I received many stimulating and en couraging responses, however, some of the book's reviewers wanted to stress the fact that an extensive literature of network theory was not included or reported in the book. But the main aspect of the book is intended to be substantive rather than methodical: networks simply serve as a remedy for doing some first steps in analysing and modelling complex biological systems. For an advanced stage in the investigation of a particular system it may be appropriate to replace the pheno menological network method by more detailed techniques like statistical equations or computer simulations. According to this intention, the second edition of the book has been enlarged by further biological examples for network analysis, not by more network theory. There is a completely new section on a network model for photoreception. For this section I am obliged to J. Tiedge who did most of the detailed calculation and to my colleague Professor Stieve with whom we have had a very fruitful cooperation. Also I would like to mention that this work has been sponsored by the "Deutsche Forschungsgemei nschaft" i n the "Sonderforschungsberei ch 160". Recent results for excitable systems represented by feedback networks have also been included in the second edition, especially for limit cycle networks.

Book Synopsis Thermodynamic Network Analysis of Biological Systems by : J. Schnakenberg

Download or read book Thermodynamic Network Analysis of Biological Systems written by J. Schnakenberg and published by Springer Science & Business Media. This book was released on 2012-12-06 with total page 157 pages. Available in PDF, EPUB and Kindle. Book excerpt: The first edition of this book was greeted with broad interest from readers en gaged in various disciplines of biophysics. I received many stimulating and en couraging responses, however, some of the book's reviewers wanted to stress the fact that an extensive literature of network theory was not included or reported in the book. But the main aspect of the book is intended to be substantive rather than methodical: networks simply serve as a remedy for doing some first steps in analysing and modelling complex biological systems. For an advanced stage in the investigation of a particular system it may be appropriate to replace the pheno menological network method by more detailed techniques like statistical equations or computer simulations. According to this intention, the second edition of the book has been enlarged by further biological examples for network analysis, not by more network theory. There is a completely new section on a network model for photoreception. For this section I am obliged to J. Tiedge who did most of the detailed calculation and to my colleague Professor Stieve with whom we have had a very fruitful cooperation. Also I would like to mention that this work has been sponsored by the "Deutsche Forschungsgemei nschaft" i n the "Sonderforschungsberei ch 160". Recent results for excitable systems represented by feedback networks have also been included in the second edition, especially for limit cycle networks.

Thermodynamics in Biology

Author: Enrico Di Cera

Publisher: Oxford University Press, USA

Published: 2000

Total Pages: 250

ISBN-13: 9780195123272

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Enrico Di Cera, a rising star in biophysics, has organized a superb group of authors to write substantial chapters covering the most exciting and central issues relating to the bioenergetic aspects of proteins, nucleic acids, and their interactions. Topics covered in this book are protein and nucleic acid folding and stability, enzyme-substrate interactions, prediction of the affinity of complexes, electrostatics, and non-equilibrium aspects of protein function. The breadth of the topics covered in this book illustrates the growing importance of thermodynamic approaches in the study of biological phenomena. The book should be of wide interest to biophysicists, biochemists, and structural biologists.

Book Synopsis Thermodynamics in Biology by : Enrico Di Cera

Download or read book Thermodynamics in Biology written by Enrico Di Cera and published by Oxford University Press, USA. This book was released on 2000 with total page 250 pages. Available in PDF, EPUB and Kindle. Book excerpt: Enrico Di Cera, a rising star in biophysics, has organized a superb group of authors to write substantial chapters covering the most exciting and central issues relating to the bioenergetic aspects of proteins, nucleic acids, and their interactions. Topics covered in this book are protein and nucleic acid folding and stability, enzyme-substrate interactions, prediction of the affinity of complexes, electrostatics, and non-equilibrium aspects of protein function. The breadth of the topics covered in this book illustrates the growing importance of thermodynamic approaches in the study of biological phenomena. The book should be of wide interest to biophysicists, biochemists, and structural biologists.

Biological Network Analysis

Author: Pietro Hiram Guzzi

Publisher: Elsevier

Published: 2020-05-11

Total Pages: 212

ISBN-13: 0128193514

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Biological Network Analysis: Trends, Approaches, Graph Theory, and Algorithms considers three major biological networks, including Gene Regulatory Networks (GRN), Protein-Protein Interaction Networks (PPIN), and Human Brain Connectomes. The book's authors discuss various graph theoretic and data analytics approaches used to analyze these networks with respect to available tools, technologies, standards, algorithms and databases for generating, representing and analyzing graphical data. As a wide variety of algorithms have been developed to analyze and compare networks, this book is a timely resource. Presents recent advances in biological network analysis, combining Graph Theory, Graph Analysis, and various network models Discusses three major biological networks, including Gene Regulatory Networks (GRN), Protein-Protein Interaction Networks (PPIN) and Human Brain Connectomes Includes a discussion of various graph theoretic and data analytics approaches

Book Synopsis Biological Network Analysis by : Pietro Hiram Guzzi

Download or read book Biological Network Analysis written by Pietro Hiram Guzzi and published by Elsevier. This book was released on 2020-05-11 with total page 212 pages. Available in PDF, EPUB and Kindle. Book excerpt: Biological Network Analysis: Trends, Approaches, Graph Theory, and Algorithms considers three major biological networks, including Gene Regulatory Networks (GRN), Protein-Protein Interaction Networks (PPIN), and Human Brain Connectomes. The book's authors discuss various graph theoretic and data analytics approaches used to analyze these networks with respect to available tools, technologies, standards, algorithms and databases for generating, representing and analyzing graphical data. As a wide variety of algorithms have been developed to analyze and compare networks, this book is a timely resource. Presents recent advances in biological network analysis, combining Graph Theory, Graph Analysis, and various network models Discusses three major biological networks, including Gene Regulatory Networks (GRN), Protein-Protein Interaction Networks (PPIN) and Human Brain Connectomes Includes a discussion of various graph theoretic and data analytics approaches

Methods in Bioengineering

Author: Arul Jayaraman

Publisher: Artech House

Published: 2009

Total Pages: 329

ISBN-13: 1596934069

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"This cutting-edge volume provides a detailed look at the two main aspects of systems biology: the design of sophisticated experimental methods and the development of complex models to analyze the data. Focusing on methods that are being used to solve current problems in biomedical science and engineering, this comprehensive, richly illustrated resource shows you how to: design of state-of-the art methods for analyzing biological systems Implement experimental approaches for investigating cellular behavior in health and disease; use algorithms and modeling techniques for quantitatively describing biomedical problems; and integrate experimental and computational approaches for a more complete view of biological systems." --Book Jacket.

Book Synopsis Methods in Bioengineering by : Arul Jayaraman

Download or read book Methods in Bioengineering written by Arul Jayaraman and published by Artech House. This book was released on 2009 with total page 329 pages. Available in PDF, EPUB and Kindle. Book excerpt: "This cutting-edge volume provides a detailed look at the two main aspects of systems biology: the design of sophisticated experimental methods and the development of complex models to analyze the data. Focusing on methods that are being used to solve current problems in biomedical science and engineering, this comprehensive, richly illustrated resource shows you how to: design of state-of-the art methods for analyzing biological systems Implement experimental approaches for investigating cellular behavior in health and disease; use algorithms and modeling techniques for quantitatively describing biomedical problems; and integrate experimental and computational approaches for a more complete view of biological systems." --Book Jacket.

Thermodynamics and Regulation of Biological Processes

Author: Ingolf Lamprecht

Publisher: Walter de Gruyter GmbH & Co KG

Published: 2019-07-22

Total Pages: 588

ISBN-13: 3110861194

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No detailed description available for "Thermodynamics and Regulation of Biological Processes".

Book Synopsis Thermodynamics and Regulation of Biological Processes by : Ingolf Lamprecht

Download or read book Thermodynamics and Regulation of Biological Processes written by Ingolf Lamprecht and published by Walter de Gruyter GmbH & Co KG. This book was released on 2019-07-22 with total page 588 pages. Available in PDF, EPUB and Kindle. Book excerpt: No detailed description available for "Thermodynamics and Regulation of Biological Processes".

Thermodynamics and Kinetics of Biological Processes

Author: Ingolf Lamprecht

Publisher: Walter de Gruyter GmbH & Co KG

Published: 2019-07-08

Total Pages: 552

ISBN-13: 3110845911

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No detailed description available for "Thermodynamics and Kinetics of Biological Processes".

Book Synopsis Thermodynamics and Kinetics of Biological Processes by : Ingolf Lamprecht

Download or read book Thermodynamics and Kinetics of Biological Processes written by Ingolf Lamprecht and published by Walter de Gruyter GmbH & Co KG. This book was released on 2019-07-08 with total page 552 pages. Available in PDF, EPUB and Kindle. Book excerpt: No detailed description available for "Thermodynamics and Kinetics of Biological Processes".

Weighted Network Analysis

Author: Steve Horvath

Publisher: Springer Science & Business Media

Published: 2011-04-30

Total Pages: 433

ISBN-13: 144198819X

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High-throughput measurements of gene expression and genetic marker data facilitate systems biologic and systems genetic data analysis strategies. Gene co-expression networks have been used to study a variety of biological systems, bridging the gap from individual genes to biologically or clinically important emergent phenotypes.

Book Synopsis Weighted Network Analysis by : Steve Horvath

Download or read book Weighted Network Analysis written by Steve Horvath and published by Springer Science & Business Media. This book was released on 2011-04-30 with total page 433 pages. Available in PDF, EPUB and Kindle. Book excerpt: High-throughput measurements of gene expression and genetic marker data facilitate systems biologic and systems genetic data analysis strategies. Gene co-expression networks have been used to study a variety of biological systems, bridging the gap from individual genes to biologically or clinically important emergent phenotypes.

Physics of Bioenergetic Processes

Author: L. A. Blumenfeld

Publisher: Springer Science & Business Media

Published: 2012-12-06

Total Pages: 141

ISBN-13: 3642685250

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According to its definition, synergetics is concerned with the cooperation of indi vidual parts of a system that produces macroscopic temporal, spatial or functional structures. A good deal of the volumes published within this series dealt with the formation of truly macroscopic structures which we can s. ee with our eyes. A common scheme could be developed to understand the formation of many patterns through self-organization. In particular, we have to use concepts which go beyond conventio nal thermodynamics. New ideas became crucial. We have to study kinetic processes, and often few highly excited degrees of freedom play the decisive role in the evo lution of structures. Over the past years it has turned out that quite similar lines of approach apply to a world which at first sight would be classified as "microsco pic". That world consists of processes in which biomolecules are involved. An impor tant example for the problems occurring there is provided by Manfred Eigen's theory of evolution of life at the molecular level (cf. his contribution to Volume 17 of this series). Another important example has been provided by Blumenfeld's book on problems of biological physics (Vol. 7 of this series). There it was proposed to treat biological molecules as machines which, in a certain sense, work through "macros copic" degrees of freedom.

Book Synopsis Physics of Bioenergetic Processes by : L. A. Blumenfeld

Download or read book Physics of Bioenergetic Processes written by L. A. Blumenfeld and published by Springer Science & Business Media. This book was released on 2012-12-06 with total page 141 pages. Available in PDF, EPUB and Kindle. Book excerpt: According to its definition, synergetics is concerned with the cooperation of indi vidual parts of a system that produces macroscopic temporal, spatial or functional structures. A good deal of the volumes published within this series dealt with the formation of truly macroscopic structures which we can s. ee with our eyes. A common scheme could be developed to understand the formation of many patterns through self-organization. In particular, we have to use concepts which go beyond conventio nal thermodynamics. New ideas became crucial. We have to study kinetic processes, and often few highly excited degrees of freedom play the decisive role in the evo lution of structures. Over the past years it has turned out that quite similar lines of approach apply to a world which at first sight would be classified as "microsco pic". That world consists of processes in which biomolecules are involved. An impor tant example for the problems occurring there is provided by Manfred Eigen's theory of evolution of life at the molecular level (cf. his contribution to Volume 17 of this series). Another important example has been provided by Blumenfeld's book on problems of biological physics (Vol. 7 of this series). There it was proposed to treat biological molecules as machines which, in a certain sense, work through "macros copic" degrees of freedom.

The Nature of Biological Systems as Revealed by Thermal Methods

Author: D Nes L?rinczy

Publisher: Springer

Published: 2004

Total Pages: 351

ISBN-13: 9786610461677

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The Nature of Biological Systems as Revealed by Thermal Methods is a guide for experiments using thermal methods. The Editor has used his many years of experience to create a unique resource that will enable others with a less mathematical background, to realize the beauty and power of this tool and to gain a better understanding of biological problems. Biological calorimetry (and of course thermal analysis) is of increasing interest and is not covered thoroughly in other resources. The methods presented are macroscopic, for the rather inhomogeneous material (micromethods are often not possible or not pertinent). This book will help beginners in the field of thermal analysis or calorimetry understand the principles of thermodynamics being applied to biological systems. Biological systems are highly organized and very complex. The water and the different types of weak interactions among the macromolecules make the interpretation of thermal events very difficult. This book includes examples how to handle such problems.; The Nature of Biological Systems as Revealed by Thermal Methods is unique in that it: The book is an invaluable resource for anyone interested in thermodynamics, including practising professionals applying thermal methods to biological problems; researchers and graduate students beginning work using thermal methods; and specialists of thermal analysis starting work on biological problems. In addition, this book will be a useful resource for libraries and institutes as the only book covering quantitative thermal analysis of biological systems.

Book Synopsis The Nature of Biological Systems as Revealed by Thermal Methods by : D Nes L?rinczy

Download or read book The Nature of Biological Systems as Revealed by Thermal Methods written by D Nes L?rinczy and published by Springer. This book was released on 2004 with total page 351 pages. Available in PDF, EPUB and Kindle. Book excerpt: The Nature of Biological Systems as Revealed by Thermal Methods is a guide for experiments using thermal methods. The Editor has used his many years of experience to create a unique resource that will enable others with a less mathematical background, to realize the beauty and power of this tool and to gain a better understanding of biological problems. Biological calorimetry (and of course thermal analysis) is of increasing interest and is not covered thoroughly in other resources. The methods presented are macroscopic, for the rather inhomogeneous material (micromethods are often not possible or not pertinent). This book will help beginners in the field of thermal analysis or calorimetry understand the principles of thermodynamics being applied to biological systems. Biological systems are highly organized and very complex. The water and the different types of weak interactions among the macromolecules make the interpretation of thermal events very difficult. This book includes examples how to handle such problems.; The Nature of Biological Systems as Revealed by Thermal Methods is unique in that it: The book is an invaluable resource for anyone interested in thermodynamics, including practising professionals applying thermal methods to biological problems; researchers and graduate students beginning work using thermal methods; and specialists of thermal analysis starting work on biological problems. In addition, this book will be a useful resource for libraries and institutes as the only book covering quantitative thermal analysis of biological systems.

Molecular Collision Dynamics

Author: J.M. Bowman

Publisher: Springer Science & Business Media

Published: 2012-12-06

Total Pages: 167

ISBN-13: 3642819435

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This monograph covers a broad spectrum of topics in the very broad field of gas phase molecular collision dynamics. The Introduction previews each of the four fol lowing topics and attempts to sew them together with a common thread. In addition, a brief review of quantum reactive scattering is given there along with some gen eral remarks which highlight the difficulties in doing quantum reactive scatter ing calculations. The chapters are all written by theoreticians who are, of course, experts in the subjects they have written about. Three chapters, the ones by Secrest, Schatz, and the one by Schinke and Bowman deal with non-reactive atom-molecule scattering. Col lectively, they describe nearly the full breadth of scattering methods in use to day, from fully quantum mechanical to semiclassical and quasiclassical. The chapter by Baer is the only one dealing with quantum reactive scattering with the additional complexity of the coupling of two potential energy surfaces. The one simplifying feature of the treatment is that the reaction is constrained to be collinear. Overall, this monograph is mainly a review of the recent advances in the field of molecular collision dynamics, with, however, a considerable amount of new material. It is hoped that workers and students in the field will find reading the mono graph both enlightening and enjoyable.

Book Synopsis Molecular Collision Dynamics by : J.M. Bowman

Download or read book Molecular Collision Dynamics written by J.M. Bowman and published by Springer Science & Business Media. This book was released on 2012-12-06 with total page 167 pages. Available in PDF, EPUB and Kindle. Book excerpt: This monograph covers a broad spectrum of topics in the very broad field of gas phase molecular collision dynamics. The Introduction previews each of the four fol lowing topics and attempts to sew them together with a common thread. In addition, a brief review of quantum reactive scattering is given there along with some gen eral remarks which highlight the difficulties in doing quantum reactive scatter ing calculations. The chapters are all written by theoreticians who are, of course, experts in the subjects they have written about. Three chapters, the ones by Secrest, Schatz, and the one by Schinke and Bowman deal with non-reactive atom-molecule scattering. Col lectively, they describe nearly the full breadth of scattering methods in use to day, from fully quantum mechanical to semiclassical and quasiclassical. The chapter by Baer is the only one dealing with quantum reactive scattering with the additional complexity of the coupling of two potential energy surfaces. The one simplifying feature of the treatment is that the reaction is constrained to be collinear. Overall, this monograph is mainly a review of the recent advances in the field of molecular collision dynamics, with, however, a considerable amount of new material. It is hoped that workers and students in the field will find reading the mono graph both enlightening and enjoyable.