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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 | |