Mathematical concepts and methods in modern biology using modern discrete models
Mathematical Concepts and Methods in Modern Biology offers a quantitative framework for analyzing, predicting, and modulating the behavior of complex biological systems. The book presents important mathematical concepts, methods and tools in the context of essential questions raised in modern biolo...
| Otros Autores: | , , |
|---|---|
| Formato: | Libro electrónico |
| Idioma: | Inglés |
| Publicado: |
Amsterdam ; Boston :
Elsevier/AP
2013.
London : 2013. |
| Edición: | 1st edition |
| Colección: | Gale eBooks
|
| Materias: | |
| Ver en Biblioteca Universitat Ramon Llull: | https://discovery.url.edu/permalink/34CSUC_URL/1im36ta/alma991009628531206719 |
Tabla de Contenidos:
- Half Title; Copyright; Contents; Contributors; Preface; Mechanisms of Gene Regulation: Boolean Network Models of the Lactose Operon in Escherichia coli; 1.1 Introduction; 1.2 E. coli and the lac Operon; 1.3 Boolean Network Models of the lac Operon; 1.3.1 Identifying the Model Variables and Parameters; 1.3.2 Boolean Network Models; 1.3.3 Creating a Boolean Model of the Lac Operon; 1.3.4 Initial Testing of the Boolean Model of the Lac Operon from Eqs. (1.4); 1.3.5 Using Discrete Visualizer of Dynamics (DVD) to Test a Boolean Model; 1.3.6 How to Recognize a Deficient Model
- 1.3.7 A More Refined Boolean Model of the Lac Operon1.4 Determining the Fixed Points of Boolean Networks; 1.5 Conclusions and Discussion; 1.6 Supplementary Materials; References; Bistability in the Lactose Operon of Escherichia coli: A Comparison of Differential Equation and Boolean Network Models; 2.1 Introduction; 2.2 The Lactose Operon of Escherichia coli; 2.3 Modeling Biochemical Reactions with Differential Equations; 2.3.1 Enzymatic Reactions and the Michaelis-Menten Equation; 2.3.2 Multi-Molecule Binding and Hill Equations; 2.4 The Yildirim-Mackey Differential Equation Models
- 2.4.1 Model Justification2.4.2 Numerical Simulation of the Yildirim-Mackey Models and Bistability; 2.5 Boolean Modeling of Biochemical Interactions; 2.6 Boolean Approximations of the Yildirim-Mackey Models; 2.6.1 Boolean Variants of the 3-Variable Model; 2.6.2 Boolean Variants of the 5-Variable Model; 2.7 Conclusions and Discussion; 2.8 Supplementary Materials; References; Inferring the Topology of Gene Regulatory Networks: An Algebraic Approach to Reverse Engineering; 3.1 Introduction; 3.1.1 Gene Regulatory Networks in Molecular Biology; 3.1.2 Reverse Engineering of Gene Regulatory Networks
- 3.2 Polynomial Dynamical Systems (PDSs)3.3 Computational Algebra Preliminaries; 3.4 Construction of the Model Space: A Reverse Engineering Algorithm; 3.5 Model Selection; 3.5.1 Preprocessing: Minimal Sets Algorithm; 3.5.2 Postprocessing: The Gröbner Fan Method; 3.6 Discretization; References; Global Dynamics Emerging from Local Interactions: Agent-Based Modeling for the Life Sciences; 4.1 Introduction; 4.1.1 Agent-Based Modeling and the Biology Mind Set; 4.1.2 A Brief Note About Platforms; 4.1.2.1 ABM Modeling Exercise: Disease Spread; 4.1.3 A Brief History of Agent-Based Modeling
- 4.1.3.1 ABM Modeling Exercises: Segregation4.1.3.2 ABM Modeling Exercises: Flocking; 4.2 Axon Guidance; 4.2.1 Background; 4.2.2 Understanding the Domain: Axon Biology; 4.2.3 Breaking Down the Problem; 4.2.4 Constructing a Model of Axon Development; 4.3 An Agent-Based Model for Cholera; 4.3.1 Model Description; 4.3.2 ABM Modeling Exercises: Cholera and the NetLogo BehaviorSpace; 4.4 Use and Description of ABM in Research: Tick-Borne; 4.4.1 The Model; 4.4.2 Purpose; 4.4.3 State Variables and Scales; 4.4.4 Process Overview and Scheduling; 4.4.5 Design Concepts; 4.4.6 Input
- 4.4.7 Simulation Experiments
