Systems Biology: Simulation of Dynamic Network States

ISBN-10: 1107001595

ISBN-13: 9781107001596

Edition: 2011

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Book details

List price: $165.00
Copyright year: 2011
Publisher: Cambridge University Press
Publication date: 5/26/2011
Binding: Hardcover
Pages: 332
Size: 7.00" wide x 10.00" long x 1.00" tall
Weight: 1.760
Language: English

Preface
Introduction
Biological networks
Why build and study models?
Characterizing dynamic states
Formulating dynamic network models
The basic information is in a matrix format
Studying dynamic models
Summary
Basic concepts
Properties of dynamic states
Primer on rate laws
More on aggregate variables
Time-scale decomposition
Network structure versus dynamics
Physico-chemical effects
Summary
Simulation of Dynamic States
Dynamic simulation: the basic procedure
Numerical solutions
Graphically displaying the solution
Post-processing the solution
Demonstration of the simulation procedure
Summary
Chemical reactions
Basic properties of reactions
The reversible linear reaction
The reversible bilinear reaction
Connected reversible linear reactions
Connected reversible bilinear reactions
Summary
Enzyme kinetics
Enzyme catalysis
Deriving enzymatic rate laws
Michaelis-Menten kinetics
Hill kinetics for enzyme regulation
The symmetry model
Scaling dynamic descriptions
Summary
Open systems
Basic concepts
Reversible reaction in an open environment
Michaelis-Menten kinetics in an open environment
Summary
Biological Characteristics
Orders of magnitude
Cellular composition and ultra-structure
Metabolism
Macromolecules
Cell growth and phenotypic functions
Summary
Stoichiometric structure
Bilinear biochemical reactions
Bilinearity leads to a tangle of cycles
Trafficking of high-energy phosphate bonds
Charging and recovering high-energy bonds
Summary
Regulation as elementary phenomena
Regulation of enzymes
Regulatory signals: phenomenology
The effects of regulation on dynamic states
Local regulation with Hill kinetics
Feedback inhibition of pathways
Increasing network complexity
Summary
Metabolism
Glycolysis
Glycolysis as a system
The stoichiometric matrix
Defining the steady state
Simulating mass balances: biochemistry
Pooling: towards systems biology
Ratios: towards physiology
Assumptions
Summary
Coupling pathways
The pentose pathway
The combined stoichiometric matrix
Defining the steady state
Simulating the dynamic mass balances
Pooling: towards systems biology
Ratios: towards physiology
Summary
Building networks
AMP metabolism
Network integration
Whole-cell models
Summary
Macromolecules
Hemoglobin
Hemoglobin: the carrier of oxygen
Describing the states of hemoglobin
Integration with glycolysis
Summary
Regulated enzymes
Phosphofructokinase
The steady state
Integration of PFK with glycolysis
Summary
Epilogue
Building dynamic models in the omics era
Going forward
Nomenclature
Homework problems
References
Index
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