Systems biology : simulation of dynamic network states / Bernhard Ø. Palsson.

Includes bibliographical references (pages 306-313) and index.

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.

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.

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?

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.

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.

10.5 Pooling: towards systems biology.

Master the process of building MASS models with real examples and hands-on practice.

Online resource; title from PDF title page (Cambridge Core, viewed January 22, 2018).

English.

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