Fundamentals of matter physics. Math: analysis, vector and matrix calcolus

Lectures, with the aid of slides. The teacher can show tutorials found on the web;

elearning/teams website: download of ppts and communications between teacher-student;

type of interaction between student and teacher: meeting, email, skype, teams;

language: English

• Introduction to biochemistry
  1. Nature of forces within biomolecules; 
  2. Structure and functions of carbohydrates  
  3. Structure and function of nucleic acids, transcription and translation
  4. Structure and function of proteins, their classification.
  5. Structure and function of lipid membranes, and membrane proteins
  6. Structure of prokaryote and eukaryote cells
  7. Viruses, structure and replication

• Physical chemistry of the cell
  1. Recall of equilibrium thermodynamics; 
  2. Contribution of intramolecular forces to biomolecular stability  
  3. Protein folding, stereospecific recognition
  4. Equilibrium states: protein-ligand binding
  5. Cooperativity, allostery
  6. Molecular crowding
  7. Non-equilibrium thermodynamics: the linear range
  8. Diffusion, Smoluchowski equation and Fick equation
  9. Membrane and diffusion
  10. Electrokinetic potential, Nerst-Planck equation and ion flow
  11. Ion channels and their structure
  12. Goldman-Hodgkin-Katz description of membrane potential
  13. Modeling membrane as a circuit
  14. Action potential
  15. Voltage-gated ion channels
  16. Voltage clamp and Goldman equation
  17. Cable equation and myelination
  18. Ligand-gated ion channels and synapses
  19. Neuron as integrating units
  20. Non-equilibrium thermodynamics
  21. Instability of steady-states and dissipative structures
  22. reaction-diffusion description, linearized systems
  23. Enzymes, allostery and metabolic regulation
  24. Oscillations in glycolysis

• Molecular optical spectroscopy
  1. Electronic absorption
  2. Electronic structure and molecular orbitals
  3. UV absorption of proteins and nucleic acids
  4. π-conjugated systems
  5. Rhodopsin, retinal and vision
  6. Linear and circular dichroism
  7. Spontaneous emission and fluorescence
  8. Non-radiative decay
  9. Intersystem crossing and phosphorescence
  10. Fluorescent Proteins: structure and spectroscopic properties
  11. Absorption and scattering in tissues: near-infrared window
  12. Non linear processes: two photons adsorption and second harmonic generation (SHG) 

• Vibrational spectroscopy
  1. Molecular vibrations
  2. IR spectroscopy (FTIR)
  3. Raman vibrational spectroscopy
  4. Vibrational spectra of proteins
  5. Pre-resonant and resonant Raman spectroscopy
  6. Imaging by Coherent Anti-Stokes Raman Scattering (CARS)

• Structural spectroscopy of biomolecules
  1. Protein Data Bank (PDB)
  2. Protein crystals
  3. X-ray diffraction
  4. Protein models from the electronic density map
  5. Principles of Nuclear Magnetic Resonance
  6. Brief illustration of 2D NMR
  7. Browsing the PDB: visualisation of biomolecules

• Computational modeling of biomolecules
  1. Overview of QM methods
  2. Molecular mechanics
  3. Molecular dynamics: time discretization and integrators of the Newton equation
  4. Applications: protein dynamics and receptor-ligand interactions, protein folding
  5. Overview of methods for protein-structure prediction

• Multi-scale simulations of bio-systems
  1. low-resolution models and multi-scale combinations
  2. Go and network models of biomolecules
  3. Continuum and mechanistic models of biopolymers and membranes
  4. implicit solvent models and surface representations, docking.

• Microscopy
  1. Recall of optics
  2. Bright field microscope
  3. Numeric aperture and resolution
  4. Contrast and sources of contrast
  5. Fluorescence microscope: wide-field
  6. Confocal microscope

Use consultation hours to fill any gap

The final exam is oral. Students have two options 1. they are interviewed directly on the whole program of the course or 2. Students are suggested to focus on a specific topic, by (autonomously or with the teacher help) searching bibliography on it and writing a very short report. The exam starts with the oral presentation of the topic (5-7 mins), and then the candidate is interviewed on other topics of the course. The student is completely free to choose among the two options, although up to now everyone has chosen option 2. In any case, the knowledge of the whole program is tested and the written report is not considered in the final evaluation.