Knowledge of basic concepts of the physics of matter. A short description of fundamental thermodynamics concepts for biology will be presented during the course

Lectures, with the aid of slides. The teacher can show tutorials found on the web; elearning website: download of ppts and communications between teacher-student; type of interaction between student and teacher: meeting, email, skype; language: English

Cell Biophysics (36 hours)

A – The biological world (10 hours)

1. A short excursus in biology and biochemistry
   1. Biophysics and the natural selection
   2. The cell
   3. The biological macromolecules
   4. The cycle of biological information: replication, transcription, and translation
   5. What is epigenetics?
   6. A short introduction to energy metabolism
   7. Compartmentalization, membranes
   8. Receptors and signaling
   9. Parasites: the universe of SARS-CoV-2
2. Fluorescence microscopy to investigate cells (and parasites)
   1. Seeing is believing how to look at cell’s machinery
   2. The revolution of fluorescent protein
   3. Nanoscale details by super-resolution and single-molecule microscopy

B – Thermodynamics and kinetics in biology (6 hours)

1. Equilibrium thermodynamics
   1. Introduction to equilibrium thermodynamics. The Gibbs equation.
   2. Equilibrium chemistry. Bistable systems.
   3. Membrane assembly and hydrophobic effect
   4. Protein folding, protein binding, allostery, light-driven conformational changes
   5. Molecular crowding, confinement
2. Kinetics
   1. Reaction kinetics and physicochemical parameters
   2. Michaelis-Menten mechanism, allosteric enzymes
3. Non-equilibrium thermodynamics
   1. Local formulation of thermodynamics
   2. Processes close to equilibrium. Steady-states. Diffusion.
   3. Processes far from equilibrium. Stability of steady-states and dissipative structures
   4. Fluorescence relaxation microscopy and dluorescence correlation spectroscopy: windows to cell’s dynamics

C – Cell dynamics (8 hours)

1. Plasma membrane transport
   1. Passive and active processes
   2. Ion channels: structure
   3. Nerst equation. Donnan potential.
   4. Planck-Nernst equation. Goldman-Hodgkin-Katz equation
   5. Voltage-gated and ligand-gated ion channels
   6. Membrane as a circuit
   7. Transmission of action potential
2. Nucleocytoplasmic transport of proteins
   1. Passive and active processes. Karyopherins
   2. Energy gradient
3. Dynamics of molecular motors
   1. Rectified Brownian motor
   2. Polymerization and translocation as motor action

C – When biology is far from equilibrium (6 hours)

1. Oscillations and chaos in metabolic pathways
   1. Enzyme non-linearity and feedback cycles
   2. Oscillation in glycolysis

D – Molecular evolution (6 hours)

1. Natural selection applied to molecules
   1. The first molecules
   2. Hypercycles and molecular transitions
2. Other interesting phenomena: how virus diffuse and mutate?
3. When the cell becomes selfish: the birth of tumors

Beside the slides of the course (that will be made available to all students following each lesson), some topics are covered by the following books:

• R. Phillips et al. "Physical Biology of the Cell", Garland Science-Taylor and Francis Group, 2nd edition, 2012
• M. B. Jackson "Molecular and Cellular Biophysics", Cambridge University Press, 2006
• M. A. Nowak "Evolutionary Dynamics", Harvard University Press, 2006

The oral examination consists of an interview between the candidate and the teachers. During the oral examination the candidate may also be asked to solve "think as a scientist" or to try to approach an experimental problem with the right scientific plan. The duration of the interview is about 40 minutes, the number of questions is generally 4.