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Dynamic systems biology modeling and simulation

Author: Joseph J DiStefano, III
Publisher: London, UK : Academic Press, [2015?] ©2014
Edition/Format:   eBook : Document : EnglishView all editions and formats
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Material Type: Document
Document Type: Book, Computer File
All Authors / Contributors: Joseph J DiStefano, III
ISBN: 9780124104938 0124104932
OCLC Number: 932054811
Notes: Issued in print: 2014.
Description: 1 online resource : illustrations
Contents: Computation & Scale in Biology; ; Overview of the Modeling Process & Biomodeling Goals; ; Looking Ahead: A Top-Down Model of the Chapters; ; References; ; 2 Math Models of Systems: Biomodeling 101; ; Some Basics & a Little Philosophy; ; Algebraic or Differential Equation Models; ; Differential & Difference Equation Models; ; Different Kinds of Differential & Difference Equation Models; ; Linear & Nonlinear Mathematical Models; ; Piecewise-Linearized Models: Mild/Soft Nonlinearities; ; Solution of Ordinary Differential (ODE) & Difference Equation (DE) Models; ; Special Input Forcing Functions (Signals) & Their Model Responses: Steps & Impulses; ; State Variable Models of Continuous-Time Systems; ; Linear Time-Invariant (TI) Discrete-Time Difference Equations (DEs) & Their Solution; ; Linearity & Superposition. Laplace Transform Solution of ODEs; ; Transfer Functions of Linear TI ODE Models; ; More on System Stability; ; Looking Ahead; ; Exercises; ; References; ; 3 Computer Simulation Methods; ; Overview; ; Initial-Value Problems; ; Graphical Programming of ODEs; ; Time-Delay Simulations; ; Multiscale Simulation and Time-Delays; ; Normalization of ODEs: Magnitude- & Time-Scaling; ; Numerical Integration Algorithms: Overview; ; The Taylor Series; ; Taylor Series Algorithms for Solving Ordinary Differential Equations; ; Computational/Numerical Stability; ; Self-Starting ODE Solution Methods; ; Algorithms for Estimating and Controlling Stepwise Precision; ; Taylor Series-Based Method Comparisons; ; Stiff ODE Problems; ; How to Choose a Solver?; ; Solving. Difference Equations (DEs) Using an ODE Solver; ; Other Simulation Languages & Software Packages; ; Two Population Interaction Dynamics Simulation Model Examples; ; Taking Stock & Looking Ahead; ; Exercises; ; References; ; 4 Structural Biomodeling from Theory & Data: Compartmentalizations; ; Introduction; ; Compartmentalization: A First-Level Formalism for Structural Biomodeling; ; Mathematics of Multicompartmental Modeling from the Biophysics; ; Nonlinear Multicompartmental Biomodels: Special Properties & Solutions; ; Dynamic System Nonlinear Epidemiological Models; ; Compartment Sizes, Concentrations & the Concept of Equivalent Distribution Volumes; ; General n-Compartment Models with Multiple Inputs & Outputs; ; Data-Driven Modeling of Indirect & Time-Delayed Inputs; ; Pools & Pool Models: Accommodating Inhomogeneities; ; Recap & Looking Ahead; ; Exercises; ; References; ; 5 Structural Biomodeling from Theory & Data: Sizing, Distinguishing & Simplifying Multicompartmental Models; ; Introduction; ; Output Data (Dynamical Signatures) Reveal Dynamical Structure; ; Multicompartmental Model Dimensionality, Modal Analysis & Dynamical Signatures; ; Model Simplification: Hidden Modes & Additional Insights; ; Biomodel Structure Ambiguities: Model Discrimination, Distinguishability & Input-Output Equivalence; ; Algebra and Geometry of MC Model Distinguishability; ; Reducible, Cyclic & Other MC Model Properties; ; Tracers, Tracees & Linearizing Perturbation Experiments; ; Recap and Looking Ahead; ; Exercises; ; References; ; 6 Nonlinear Mass Action & Biochemical Kinetic Interaction Modeling; ; Overview; ; Kinetic Interaction Models; ; Law of Mass Action; ; Reaction Dynamics in Open Biosystems; ; Enzymes & Enzyme Kinetics; ; Enzymes & Introduction to Metabolic and Cellular Regulation; ; Exercises; ; Extensions: Quasi-Steady State Assumption Theory; ; References; ; 7 Cellular Systems Biology Modeling: Deterministic & Stochastic; ; Overview; ; Enzyme-Kinetics Submodels Extrapolated to Other Biomolecular Systems; ; Coupled-Enzymatic Reactions & Protein Interaction Network (PIN) Models; ; Production, Elimination & Regulation Combined: Modeling Source, Sink & Control Components; ; The Stoichiometric Matrix N; ; Special Purpose Modeling Packages in Biochemistry, Cell Biology & Related Fields; ; Stochastic Dynamic Molecular Biosystem Modeling; ; When a Stochastic Model is Preferred; ; Stochastic Process Models & the Gillespie Algorithm; ; Exercises; ; References; ; 8 Physiologically Based, Whole-Organism Kinetics & Noncompartmental Modeling; ; Overview; ; Physiologically Based (PB) Modeling; ; Experiment Design Issues in Kinetic Analysis (Caveats); ; Whole-Organism Parameters: Kinetic Indices of Overall Production, Distribution & Elimination; ; Noncompartmental (NC) Biomodeling & Analysis (NCA); ; Recap & Looking Ahead; ; Exercises; ; References; ; 9 Biosystem Stability & Oscillations; ; Overview/Introduction; ; Stability of NL Biosystem Models; ; Stability of Linear System Models; ; Local Nonlinear Stability via Linearization; ; Bifurcation Analysis; ; Oscillations in Biology; ; Other Complex Dynamical Behaviors; ; Nonlinear Modes; ; Recap & Looking Ahead; ; Exercises; ; References; ; 10 Structural Identifiability; ; Introduction; ; Basic Concepts; ; Formal Definitions: Constrained Structures, Optimization Methods 101: Analytical and Numerical; ; Parameter Estimation Quality Assessments; ; Other Biomodel Quality Assessments; ; Recap and Looking Ahead; ; Exercises; ; References; ; 13 Parameter Estimation Methods II: Fa.
Responsibility: Joseph DiStefano III.

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