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