BIOLOGICAL PHYSICS

Second cycle degree in PHYSICS

Campus: PADOVA

Language: English

Teaching period: Second Semester

Lecturer: MARIO BORTOLOZZI

Number of ECTS credits allocated: 6


Syllabus
Prerequisites: Italian knowledge (written and oral).
Examination methods: The final check consists of an oral test in which the solution to some specific problems may be required.
Course unit contents: Nucleic acids, proteins and lipids: the structure of living cells, the central dogma of biology, primary structure of DNA, double helix structure.
Molecular forces in biological structures: electrical nature of interaction energies, interaction between charges and permanent dipoles, induced dipoles, dispersion forces, hydrogen bonds, steric repulsion.
Elementary properties of ions in solutions: random walk, electrodiffusion, the Nernst-Planck equation, hydration shells and diffusion coefficients of small ions.
Elementary properties of channels: the membrane as a capacitor, channel conductance and ion flux limitations by molecular factors. Properties of the K+ channel.
Selective permeability of membranes: the Goldman-Hodgkin-Katz current and voltage equations. Different permeabilities of ions for several types of channels. The nerve action potential as a regenerative wave of Na+ permeability increase.
Selective permeability of channels: the one-ion and multi-ion pore models. Application to Na+ and K+ channels.
Gating mechanisms of channels: kinetic models and single channel recording by patch-clamp. Voltage sensing, fast and slow inactivations. Modification of gating properties and blocking by specific agents.
Atomistic numerical simulations: simulation algorithms, periodic boundary conditions, termostats and barostats.
Energetic configuration: energy minimization, interactions and force fields, Lennard Jones potential, electrostatic interactions, chemical bounds, polarizations.
Protein dynamics: trajectories analysis, fluctuations, deviations, correlations. Salt bridges.
Advanced techniques: Free energy calculations. Potential of mean force.
Membrane channel structure and function: derivation of unitary permeability and conductance of connexin channels.