UID:
almafu_9959227191202883
Format:
1 online resource (xiii, 317 pages) :
,
digital, PDF file(s).
Edition:
1st ed.
ISBN:
1-107-22024-6
,
1-107-08665-5
,
1-283-29614-4
,
9786613296146
,
1-139-12316-5
,
0-511-73617-7
,
1-139-11741-6
,
1-139-12807-8
,
1-139-11305-4
,
1-139-11524-3
Content:
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.
Note:
Title from publisher's bibliographic system (viewed on 05 Oct 2015).
,
Cover; Title; Copyright; Contents; Preface; 1 Introduction; 1.1 Biological networks; 1.2 Why build and study models?; 1.3 Characterizing dynamic states; 1.4 Formulating dynamic network models; 1.5 The basic information is in a matrix format; 1.6 Studying dynamic models; 1.7 Summary; 2 Basic concepts; 2.1 Properties of dynamic states; 2.2 Primer on rate laws; 2.3 More on aggregate variables; 2.4 Time-scale decomposition; 2.5 Network structure versus dynamics; 2.6 Physico-chemical effects; 2.7 Summary; Part I Simulation of dynamic states; 3 Dynamic simulation: the basic procedure
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3.1 Numerical solutions3.2 Graphically displaying the solution; 3.3 Post-processing the solution; 3.4 Demonstration of the simulation procedure; 3.5 Summary; 4 Chemical reactions; 4.1 Basic properties of reactions; 4.2 The reversible linear reaction; 4.3 The reversible bilinear reaction; 4.4 Connected reversible linear reactions; 4.5 Connected reversible bilinear reactions; 4.6 Summary; 5 Enzyme kinetics; 5.1 Enzyme catalysis; 5.2 Deriving enzymatic rate laws; 5.3 Michaelis-Menten kinetics; 5.4 Hill kinetics for enzyme regulation; 5.5 The symmetry model; 5.6 Scaling dynamic descriptions
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5.7 Summary6 Open systems; 6.1 Basic concepts; 6.2 Reversible reaction in an open environment; 6.3 Michaelis-Menten kinetics in an open environment; 6.4 Summary; Part II Biological characteristics; 7 Orders of magnitude; 7.1 Cellular composition and ultra-structure; 7.2 Metabolism; 7.2.1 What are typical concentrations?; 7.2.2 What are typical metabolic fluxes?; 7.2.3 What are typical turnover times?; 7.2.4 What are typical power densities?; 7.3 Macromolecules; 7.3.1 What are typical characteristics of a genome?; 7.3.2 What are typical protein concentrations?; 7.3.3 What are typical fluxes?
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7.3.4 What are typical turnover times?7.4 Cell growth and phenotypic functions; 7.4.1 What are typical cell-specific production rates?; 7.4.2 Balancing the fluxes and composition in an entire cell; 7.5 Summary; 8 Stoichiometric structure; 8.1 Bilinear biochemical reactions; 8.2 Bilinearity leads to a tangle of cycles; 8.3 Trafficking of high-energy phosphate bonds; 8.3.1 The basic structure of the ``core'' module; 8.3.2 Buffering the energy charge; 8.3.3 Open system: long-term adjustment of the capacity; 8.4 Charging and recovering high-energy bonds; 8.5 Summary
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9 Regulation as elementary phenomena9.1 Regulation of enzymes; 9.2 Regulatory signals: phenomenology; 9.3 The effects of regulation on dynamic states; 9.4 Local regulation with Hill kinetics; 9.4.1 Inhibition; 9.4.2 Activation; 9.5 Feedback inhibition of pathways; 9.6 Increasing network complexity; 9.6.1 Regulation of protein synthesis; 9.6.2 Tight regulation of enzyme activity; 9.7 Summary; Part III Metabolism; 10 Glycolysis; 10.1 Glycolysis as a system; 10.2 The stoichiometric matrix; 10.3 Defining the steady state; 10.4 Simulating mass balances: biochemistry
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10.5 Pooling: towards systems biology
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English
Additional Edition:
ISBN 1-107-00159-5
Language:
English
URL:
https://doi.org/10.1017/CBO9780511736179
