Quantitative Biosciences. Dynamics across Cells, Organisms, and Populations

Cover
Contents
Preface
	Quantitative Biosciences at All Scales of Life
	The Goal
	The Structure of this Book
	You Can Do It
Acknowledgments
I. Molecular and Cellular Biosciences
	1. Fluctuations and the Nature of Mutations
		1.1. Chance Favors the Independent Mutation
		1.2. Cellular Phenotypes
		1.3. Mutations that Depend on Selection
		1.4. Independent Mutations: A Continuous Model
		1.5. Modeling the Growth of (Discrete) Mutants
		1.6. Variance of Mutants When Mutations are Independent of Selection
		1.7. On (In)Direct Inference
		1.8. Take-Home Messages
		1.9. Homework Problems
		1.10. Technical Appendix
	2. Bistability of Genetic Circuits
		2.1. More is Different
		2.2. Molecular Cast and Scene
		2.3. The First Ingredient: Regulation of a Target Gene
		2.4. Feedback and Bistability—Autoregulation
		2.5. The Dynamics of a Genetic Toggle Switch
		2.6. Take-Home Messages
		2.7. Homework Problems
		2.8. Technical Appendix
	3. Stochastic Gene Expression and Cellular Variability
		3.1. Living with Randomness
		3.2. Stochasticity in Gene Regulation
		3.3. Characterizing Dynamics of Individual Cells, Given Stochastic Gene Expression
		3.4. Is Gene Expression Bursty?
		3.5. The Geometry of Bursts
		3.6. Take-Home Messages
		3.7. Homework Problems
		3.8. Technical Appendix
	4. Evolutionary Dynamics: Mutations, Selection, and Diversity
		4.1. Evolution in Action
		4.2. Selection and the Disappearance of Diversity
		4.3. Mechanisms that Restore Diversity
		4.4. Stochasticity in the Evolution of Populations—Baseline Expectations
		4.5. Evolutionary Dynamics with Stochasticity and Selection
		4.6. Sweeps or Hitchhiking or Both?
		4.7. Take-Home Messages
		4.8. Homework Problems
		4.9. Technical Appendix
II. Organismal Behavior and Physiology
	5. Robust Sensing and Chemotaxis
		5.1. On Taxis
		5.2. Why Swim?
		5.3. The Behavior of Swimming E. coli
		5.4. Chemotaxis Machinery
		5.5. Signaling Cascades
		5.6. Fine-Tuned Adaptation
		5.7. Buffering and Robust Cellular Adaptation
		5.8. Take-Home Messages
		5.9. Homework Problems
		5.10. Technical Appendix
	6. Nonlinear Dynamics and Signal Processing in Neurons
		6.1. Walking in the Path of Hodgkin and Huxley
		6.2. The Brain: Memory, Learning, and Behavior
		6.3. Of Ions and Neurons
		6.4. Dynamical Properties of Excitable Neuronal Systems
		6.5. From Neurons to Neural Networks and Information Processing
		6.6. Take-Home Messages
		6.7. Homework Problems
		6.8. Technical Appendix
		Color Plates
	7. Excitations and Signaling from Cells to Tissue
		7.1. From Excitable Cells to Excitable Systems
		7.2. Principles of Oscillatory Dynamics
		7.3. Relaxation Oscillations—a Generalized View
		7.4. Principles of Excitability: From Cardiac Cells to Tissue
		7.5. Take-Home Messages
		7.6. Homework Problems
		7.7. Technical Appendix
	8. Organismal Locomotion through Water, Air, and Earth
		8.1. Movement from Within
		8.2. Movement with Brief Moments in Air
		8.3. Principles of Slow Swimming
		8.4. Terrestrial Locomotion
		8.5. Take-Home Messages
		8.6. Homework Problems
		8.7. Technical Appendix
III. Populations and Ecological Communities
	9. Flocking and Collective Behavior: When Many Become One
		9.1. Life is with Other Organisms
		9.2. Endogenous vs. Exogenous Drivers of Spatial Ordering
		9.3. Vicsek Model: Uniting Static and Dynamic Order
		9.4. Collective Decision Making at the Flock Scale
		9.5. Take-Home Messages
		9.6. Homework Problems
		9.7. Technical Appendix
	10. Conflict and Cooperation Among Individuals and Populations
		10.1. Games, Relatively Speaking
		10.2. Payoffs: A Classic Approach
		10.3. From Payoffs to Populations
		10.4. Games that Real Organisms Play
		10.5. Feedback Between Strategies and the Environment
		10.6. Take-Home Messages
		10.7. Homework problems
		10.8. Technical Appendix
	11. Eco-Evolutionary Dynamics
		11.1. The Power of Exponentials
		11.2. Canonical Models of Population Dynamics
		11.3. Predator-Prey Dynamics
		11.4. Toward Predator-Prey Dynamics with Rapid Evolution
		11.5. Take-Home Messages
		11.6. Homework Problems
		11.7. Technical Appendix
	12. Outbreak Dynamics: From Prediction to Control
		12.1. Modeling in the Age of Pandemics
		12.2. The Core Model of an Outbreak: The SIR Model
		12.3. The Shape of an Outbreak
		12.4. Principles of Control
		12.5. EVD: A Case Study in Control Given Uncertainty
		12.6. On the Ongoing Control of SARS-CoV-2
		12.7. Take-Home Messages
		12.8. Homework Problems
		12.9. Technical Appendix
IV. The Future of Ecosystems
	13. Ecosystems: Chaos, Tipping Points, and Catastrophes
		13.1. Ecosystems—the Integrated Frontier
		13.2. Chaos in Communities
		13.3. Condorcet and Catastrophes
		13.4. Thresholds in Ecosystems and the Earth System
		13.5. The Challenge Continues
References
Index