Docente
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DI LEONARDO ROBERTO
(programma)
## Part 1 - What's inside: genetic parts and circuits
1. Introduction
* What is Biophysics?
* What is/means fundamental in biology?
* The beginning of biophysics: Galileo
* Course program: cell biophysics
* Space time and energy scales
2. From genes to proteins
* DNA structure and sequence
* Synthetic biology
* Transcription networks: genes, promoters, transcription factors
* The input function of a gene
* Estimating binding rates
3. Modes of gene regulation
* activators, repressors, inducers, co-repressors
4. Protein dynamics
* Response
* Network motifs
* Autoregulation
* Feed-forward loops
5. Feed forward loops and temporal programs
* Multi input function
* Feed forward loops
* Single input modules (LIFO)
* Multi output FFL (FIFO)
6. Biological oscillators
* Oscillations require autoregulation and delay
* Damped oscillations in a two component negative feedback loop
* Noise sustained oscillations
* Limit cycles oscillations in a synthetic genetic circuit
7. DNA cloning
* BioBrick assembly
* A close look at the Repressilator plasmid
8. Stochastic gene expression
* single molecule microscopy
* the Gillespie algorithm
* stochastic simulation of gene expression
## Part 2 - What's outside: cell motility
9. Introduction to the physics of microswimmers
* the discovery of a microcosmos
* life at low Reynolds number
* flagellar motility
10. Introduction to vector calculus
* scalars, vectors, tensors
* dyadics
* calculus in vector notation
11. Microhydrodynamics
* mass conservation, source doublet
* momentum conservation
* Stokes equation
* Stokeslet
* the drag on an a particle of arbitrary shape
* hydrodynamic interactions
12. Flagellar propulsion
* slender body
* flagellar propulsion
* flow around a microswimmer
* swimming efficiency
13. Watching microswimmers
* from the tracking microscope to holographic microscopy
* flow visualization techniques
* Fourier microscopy
14. Manipulation of microswimmers
* measuring resistance matrix with optical tweezers
* bacteria in microfabricated structures
* biohybrid micromachines
## Part III: Multicellular dynamics
14. Non interacting active particles
* run and tumble in 1D
* chemotaxis in 1D
* photokinesis and painting with bacteria
15. Cell growth and division
* the growth curve
* cell size control
* mother machine
16. Spatio-temporal patterns in colony growth
* Fisher-Kolmogorov, waves, branches, fractals
* quorum sensing: engineering morphogenesis with synthetic biology
17. Tissues
* dynamics of cell monolayers
* vertex models
* self propelled Voronoi
Dispense del corso
Alon, An introduction to systems biology
Alberts, Essential Cell Biology,
Happel, Low Reynolds number hydrodynamics
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