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1 Introduction I: General Remarks
2 Introduction II: Death Process
2.1 Small Population
2.1.1 Survival of one Individual
One individual
Excursion: Probability and Random Variables
Survival Probability
Summary/Conclusion
2.1.2 IBM: Level of small populations
2.1.3 Simulation Techniques
Possibility 1: Transformation
Maximum Likelihood Method
Bayesian Approach
2.2 Deterministic Models
Small population: Expected Values
Large Population: Population Densities
2.3 More than one type of transition
M-Matrices and linear ODE’s
General linear compartmental models
2.4 Examples for compartmental models
2.4.1 Receptor-Ligand Binding
2.4.2 Positron-Emission-Tomography
Compartmental models
Interesting parameters
Estimating parameters: Logan-Plot
2.4.3 Treatment of Hepatitis C
2.5 Summary/Conclusion
2.6 Exercise
Part One: Independent Entities - The Linear Case
3 Discrete Time
3.1 Small Population Size: The Galton-Watson-Process
3.1.1 Example: QPCR
3.1.2 Galton-Watson-Process
Deﬁnition
Analysis
3.1.3 Back To QPCR
3.1.4 Exercise
3.2 Large Population, Discrete State
3.2.1 Example 1: Fibonacci numbers
3.2.2 Linear, discrete dynamical systems
Generic Case / real Jordan normal form
Positive Matrices
Back to Fibonacci
3.2.3 Example 2: Leslie Matrices - Age Structured Population
Lattice Case
3.2.4 Summary/Conclusion
3.2.5 Exercise
3.3 Markov Chains
3.3.1 Socio-Biology: Dunging behavior of pigs
3.3.2 Basic deﬁnitions
3.3.3 A model for common cold in households
Embedded time-discrete Markov process and ﬁnal size distribution
From nonlinear to linear models
Application to data
3.3.4 Exercise
4 Continuous Time
4.1 Small Population Size: The Birth-Death Process
Master equation and Generating Function
Probability of extinction
4.2 Linear Deterministic Dynamics
4.3 Age Structure
The Model
4.4 Spatial Structure
4.4.1 Diﬀusion Equation
Discrete Random Walk
Scaling to the Heat Equation
4.4.2 Excursion: Porous Media Equation
Model and interpretation
Explicite solution of a special example
4.4.3 Correlated Random Walk in one dimension
Model
Parabolic Limit
Cattaneo System
4.4.4 Correlated Random Walk in higher dimensions
Flux and asymptotic velocity
4.5 Exercise
5 Logistic Equation
5.1 Experimental Setup
5.2 Deterministic Logistic Equation: Continuous Time
Real World Data
5.3 Deterministic Logistic Equation: Discrete Time
5.4 Branching Process
5.4.1 The Model
5.4.2 Analysis I: Large population size
5.4.3 Analysis II: Linearization
Application to ecological systems
5.5 Spatially Structured Logistic Equation
5.5.1 Contact Process: Model
5.5.2 Contact Process: Moment Closure Equations
Counting Conﬁgurations
First order dynamics: mean ﬁeld equation
Second order dynamics: pair approximation
Threshold condition, revised
5.5.3 Contact Process: Rapid Stirring Limit
5.5.4 Fisher Equation
5.6 Exercises
Analytic Tools
Analysis of the Model
Experimental Investigation
6.2 Predator-Prey Systems
Lotka-Volterra-Model
Generalizations of the Lotka-Volterra-Model
The Hudson Bay Data
6.3 Chemostat
6.4 Exercise
7 Neuronal Activity
7.1 Hodgkin-Huxley Model
7.2 Fitzhugh-Nagumo Model
Simpliﬁed Model for Neuronal Activity
Analytizing Time Scales: Singular Perturbation Theory
Spikes and periodic Spiking
7.3 Small Networks: Periodic spiking
7.4 Large Networks: Greenberg-Hastings Automata
172 10 PERHAPS: SYSTEM BIOLOGY / REGULATORY NETWORKS????
8 Reaction Kinetics
8.1 Michaelis-Menton
8.2 Belouzov-Zhabotinskii
9 Immunology / Infectious diseases
9.1 Kermack-McKendrick/Standard Model for viral infection
9.2 Age-Structured Model, Vaccination (indirect eﬀect)
10 Perhaps: System Biology / Regulatory Net-
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Mathematical Models in Biology

# Mathematical Models in Biology

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05/02/2012

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