
Quantitative Biosciences Companion in R
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Content
- Cover
- Contents
- Preface
- The Goal
- You Can Do It
- Acknowledgments
- I. Molecular and Cellular Biosciences
- 1. Fluctuations and the Nature of Mutations
- 1.1. Hands-On Approach to Mutations and Selection
- 1.2. Sampling from Provided Distributions
- 1.3. Sampling from Custom Distributions
- 1.4. Comparing Binomial and Poisson Distributions
- 1.5. The Start of Dynamics
- 1.6. Inferring Parameters from Data
- Solutions to Challenge Problems
- 2. Bistability of Genetic Circuits
- 2.1. Continuous Models of Cellular Dynamics and Gene Regulation
- 2.2. Simulating Coupled Ordinary Differential Equations
- 2.3. Qualitative Analysis of Nonlinear Dynamical Systems
- 2.4. Evaluating the Local Stability of Equilibria
- 2.5. Bistability and Bifurcation Diagrams
- Solutions to Challenge Problems
- 3. Stochastic Gene Expression and Cellular Variability
- 3.1. Simulating Stochastic Gene Expression
- 3.2. Poisson Processes: Finding the Time of the Next Event
- 3.3. A Theory of Timing Given Multiple Stochastic Processes
- 3.4. Gillespie Algorithm Applied to a Gene Expression Model
- 3.5. Loading and Saving Data
- Solutions to Challenge Problems
- 4. Evolutionary Dynamics: Mutations, Selection, and Diversity
- 4.1. Modeling Evolutionary Dynamics
- 4.2. Transition Matrices in Markov Processes
- 4.3. The Wright-Fisher Model
- Solutions to Challenge Problems
- II. Organismal Behavior and Physiology
- 5. Robust Sensing and Chemotaxis
- 5.1. Toward Chemotaxis in Single-Celled Organisms
- 5.2. Enzyme Kinetics
- 5.3. Time-Dependent Functions in Differential Equations
- 5.4. Probability Distribution Redux
- 5.5. E. Coli Movement
- Solutions to Challenge Problems
- 6. Nonlinear Dynamics and Signal Processing in Neurons
- 6.1. Computational Neuroscience
- 6.2. The Hodgkin-Huxley Model
- 6.3. Firing Without a Current
- 6.4. Neuron Dynamics: Thresholds in Magnitude and Time
- 6.5. Technical Appendix
- Solutions to Challenge Problems
- 7. Excitations and Signaling, from Cells to Tissue
- 7.1. Excitable Media: From Localized to Spatial Dynamics
- 7.2. FitzHugh-Nagumo: The ODE Model
- 7.3. FitzHugh-Nagumo: One-Dimensional PDEs
- Solutions to Challenge Problems
- 8. Organismal Locomotion Through Water, Air, and Earth
- 8.1. Introduction
- 8.2. The Internal Origins of Movement
- 8.3. Orbits in Configuration Space
- 8.4. From Borelli to Newton and Back Again
- 8.5. The Greatest Gait of All
- Solutions to Challenge Problems
- III. Populations and Ecological Communities
- 9. Flocking and Collective Behavior: When Many Become One
- 9.1. Agent-Based Models and Emergence in Flocks
- 9.2. The Vicsek Model
- 9.3. Flocking Dynamics
- 9.4. Bonus: The Power of Leadership
- Solutions to Challenge Problems
- 10. Conflict and Cooperation Among Individuals and Populations
- 10.1. Strategies, Games, and Populations
- 10.2. Mean Field Replicator Dynamics of Microbial Games
- 10.3. Stochastic Versions of Microbial Games
- 10.4. Type VI Secretion-a Killer Game, in Space
- Solutions to Challenge Problems
- 11. Eco-Evolutionary Dynamics
- 11.1. From Predation Events to Population Dynamics
- 11.2. Ecological Dynamics When Evolution is Fast
- 11.3. Functional Responses-a Microscopic Approach
- Solutions to Challenge Problems
- 12. Outbreak Dynamics: From Prediction to Control
- 12.1. Outbreaks: From Deterministic Models to Stochastic Realizations
- 12.2. Epidemic Modeling-Fundamentals
- 12.3. Stochastic Epidemics
- Solutions to Challenge Problems
- IV. The Future of Ecosystems
- 13. Ecosystems: Chaos, Tipping Points, and Catastrophes
- 13.1. Modeling Complexity: An Enabling View
- 13.2. Small Differences, Big Effects
- 13.3. Explosive Growth and Population Catastrophes
- 13.4. Small Models of a Big Climate
- 13.5. Coda
- Solutions to Challenge Problems
- Bibliography
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