First cycle
degree courses
Second cycle
degree courses
Single cycle
degree courses
School of Science
PHYSICS
Course unit
BIOLOGICAL PHYSICS
SCP7081737, A.A. 2019/20

Information concerning the students who enrolled in A.Y. 2019/20

Information on the course unit
Degree course Second cycle degree in
PHYSICS
SC2382, Degree course structure A.Y. 2017/18, A.Y. 2019/20
N0
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Degree course track PHYSICS OF MATTER [002PD]
Number of ECTS credits allocated 6.0
Type of assessment Mark
Course unit English denomination BIOLOGICAL PHYSICS
Website of the academic structure http://physics.scienze.unipd.it/2019/laurea_magistrale
Department of reference Department of Physics and Astronomy
Mandatory attendance No
Language of instruction English
Branch PADOVA
Single Course unit The Course unit can be attended under the option Single Course unit attendance
Optional Course unit The Course unit can be chosen as Optional Course unit

Lecturers
Teacher in charge MARIO BORTOLOZZI FIS/07

ECTS: details
Type Scientific-Disciplinary Sector Credits allocated
Educational activities in elective or integrative disciplines FIS/03 Material Physics 6.0

Course unit organization
Period Second semester
Year 1st Year
Teaching method frontal

Type of hours Credits Teaching
hours
Hours of
Individual study
Shifts
Lecture 6.0 48 102.0 No turn

Calendar
Start of activities 02/03/2020
End of activities 12/06/2020
Show course schedule 2019/20 Reg.2017 course timetable

Examination board
Board From To Members of the board
2 BIOLOGICAL PHYSICS 01/10/2018 30/11/2019 BORTOLOZZI MARIO (Presidente)
SENO FLAVIO (Membro Effettivo)
STELLA ATTILIO (Supplente)
TROVATO ANTONIO (Supplente)

Syllabus
Prerequisites: The course will be held in English.
Target skills and knowledge: The course aims to illustrate to the students some of the most fascinating cultural and scientific challenges launched by modern biology and to show them how to apply physical methods to answer questions and develop new models and new theories. Together with fundamental notions of biology and classical biophysics, the students will acquire skills of numerical simulation in the Matlab framework.
Examination methods: The final check is composed of a written and an oral part. The written exam consists of writing a report on a biological model solved by the student using a numerical simulation in Matlab. The oral exam consists of presenting by Power Point slides a recent scientific paper related to the course arguments.
Assessment criteria: The exam is intended to ensure the acquisition of the basic knowledge provided by the course using practical tasks which bring the student near the research approach: solving scientific problems and presenting the results by papers and oral presentations.
Course unit contents: Introduction: what is biophysics, top-down and bottom-up approaches.
The living cell: eukariotyc and prokaryotic cells, cell structure and function of its constituents, cell division.
The water: structure and chimical-physical properties, water-protein interaction, optical properties of water, pH and buffering systems, cell incubators.
Membranes and channels: conductance, cell equivalent circuit, Nernst potential, voltage-clamp technique, Hodgkin-Huxley model, neuronal action potential and its simulation, saltatory conduction and Schwann cell, patch-clamp, electrophysiology setup, derivation of cell electrical parameters, single channel current measurement, voltage-activated channel types and blockers, muscle and hair cell synapse, two-state channel model, three- and multi-state models, receptors, activation energies of a channel.
Diffusion: Fick’s laws, diffusion from a point source, random walk and Monte Carlo approach, particle interaction with boundaries, random walk on a grid, numerical simulations of the diffusion process, discretization of the diffusive Laplacian, hydration shells, Kramer equation, electrical mobility, Nernst-Planck equation.
Permeability: partition coefficient, Goldman-Hodgkin-Kats equations, deviation from Ohm’s law, ionic selectivity, single channel permeability, saturation, Eyring’s theory, sodium and potassium channel models.
Chemical reactions: enzymatic reactions, Michaelis-Menten equation, SERCA and PMCA pumps, fluorescent dyes, calcium (Ca2+) dyes, configuration of a fluorescence microscope, relationship between dye fluorescence and Ca2+ concentration, photobleaching, ratiometric dyes, non-equilibrium conditions between Ca2+ and the dye, numerical simulations of Ca2+ dynamics, generation of a reaction-diffusion model and comparison with experiments, Ca2+ dynamics in the inner ear and in cardiac cells, modeling a complex geometry using meshes.
Molecular dynamics: DNA, RNA and proteins, the central dogma of biology, amino acids, folding and protein structures, simulation of protein dynamics, potential energy formula, computational algorithms, boundary conditions and examples of models.
Neural networks: machine learning, learning approaches, artificial neuron and schemes of neural networks, error backpropagation, artificial vision and speech recognition, cerebral organoids, Boltzmann machines.
Planned learning activities and teaching methods: Frontal lessons and exercises in the classroom.
Additional notes about suggested reading: Power Point slides, movies and lecture notes provided by the teacher.
Textbooks (and optional supplementary readings)
  • M. Daune, Molecular Biophysics. --: Oxford University Press, 1999. Cerca nel catalogo
  • Meyer B. Jackson, Molecular and Cellular Biophysics. --: Cambridge University Press, 2006. Cerca nel catalogo

Innovative teaching methods: Teaching and learning strategies
  • Lecturing
  • Interactive lecturing
  • Working in group
  • Problem solving
  • Use of online videos
  • Loading of files and pages (web pages, Moodle, ...)

Innovative teaching methods: Software or applications used
  • Moodle (files, quizzes, workshops, ...)
  • Kaltura (desktop video shooting, file loading on MyMedia Unipd)
  • Top Hat (active quiz, quiz)
  • Matlab