From Biomolecules to Biosystems
1. Physics of biological polymers
2. Entropic effects: macromolecular crowding, depletion interactions
3. Elements of the physics of membranes
4. DNA and RNA
Structure
Basic processes: replication, transcription, translation, recombination
5. Accuracy of biological information processing: proofreading schemes
6. Proteins
Structure
Folding
7. Proteins as molecular machines
Enzymes, Michaelis-Menten description
Cooperative interactions
8. Control of gene expression
Transcription factors, DNA looping
Small RNA in bacteria
RNA interference
6. Physics of molecular motors
Statistical mechanics of barrier crossing by thermal activation
Fokker-Planck formalism
7. Stochastic phenomena in cells
Target search by transcription factors
Signal to noise in signaling pathways
Sensing by receptors
8. Networks
Basics of control theory (feedback, feedforward loops)
Architectures
Noise
Model networks
Regulation of gene expression by RNA
9. Elements of Evolution
The Eigen model
10. Elements of Development
Activator-inhibitor models, Turing instability
11. Photosynthesis
12. Topics in Ecology
Logistic growth (RG analysis of period doubling)
Lotka Volterra
Allee effects
SIR epidemics model
13. Active matter