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PHZ4710 - Introduction to Biological Physics
PHZ4710 - Introduction to Biological Physics
0. What is Biological Physics?
Spatial and temporal scales in Biology
1. Diffusion vs. Navigation
Random walk
Run-and-tumble
2. Probability and Statistics
Counting photons
Fluctuation test
3. Stochastic Processes
Birth-death process
Stochastic gene expression
4. Reaction Kinetics
Protein folding
Protein folding part2
Kinetic proofreading
5. Dynamical Systems
The
lac
Operon
Lotka-Volterra equations
The Lorenz system
6. Neural Networks
Hopfield network
Simple perceptron
Multi-layer networks
7. Data Analyses
Handwritten digits
Eigenworms
Cancer RNA-Seq data
8. Information and Strategy
Bet-hedging
Value of information
Evolutionary games
.md
.pdf
Contents
1. Population growth and extinction
Exercise:
birth-death process
2. Stochastic gene expression
Exercise:
protein production & degradation
3. Chemical reactions and stochastic simulation
Exercise: the Gillespie algorithm
Stochastic Processes
Contents
1. Population growth and extinction
Exercise:
birth-death process
2. Stochastic gene expression
Exercise:
protein production & degradation
3. Chemical reactions and stochastic simulation
Exercise: the Gillespie algorithm
Stochastic Processes
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1. Population growth and extinction
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Exercise:
birth-death process
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2. Stochastic gene expression
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alt text
Exercise:
protein production & degradation
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3. Chemical reactions and stochastic simulation
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alt text
Exercise:
the Gillespie algorithm
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