cod. 1006148

Academic year 2022/23
3° year of course - Second semester
Academic discipline
Fisica applicata (a beni culturali, ambientali, biologia e medicina) (FIS/07)
Attività formative affini o integrative
Type of training activity
52 hours
of face-to-face activities
6 credits
hub: PARMA
course unit

Learning objectives

Students, at the end of the course, will have to demonstrate that they are able to:

- know and understand the topics covered by the course, as indicated in the following program
- recall and compare the main features of the experimental techniques introduced in the course
- explain the meaning of the physical quantities and the concepts proper of photophysics, fluorescence microscopy and photoactivatable systems
- exemplify physical systems and molecular mechanisms to which the methodologies studied in the course may be applied
- understand the basic concepts in a recent literature paper
(Knowledge and understanding)

- apply their knowledge to address the study of a biophysical topic
- perform simple calculations to define the experimental conditions in a absorption and fluorescence measurement (e.g. molar concentrations, or dilutions)
- elaborate the general scheme of a mechanistic model describing a molecular process
(Applying knowledge and understanding)

- make a quantitative analysis of relevant biophysical processes both at the theoretical and experimental level
- analyze the structural and functional properties of macromolecules as proteins
- evaluate the elements essential to develop a mechanistic model that describes a molecular process
- evaluate critically the effectiveness limits of the developed models, the advantages / disadvantages of the different methodologies, the analogies and differences between the physical systems.
(Making judgements)

- communicate ideas-problems-solutions on biophysical issues in a clear, concise and effective way
- explain the properties that define the structure, dynamics and function of proteins
- explain the different steps of an absorption and fluorescence measurement and its data analysis
- explain to the group members and the teacher the experimental issues occurred during practical exercises
(Communication skills)

- connect different issues addressed in the course and in others (e.g. Physics of Matter, Quantum Mechanics, Chemistry)
- examine in depth the main biophysical topics discussed in mentioned scientific papers
- understand if Biophysics could represent an own research and study area of interest.
(Learning skills)


Basics of calculus, classical physics and chemistry

Course unit content

This course is intended to give an overview on the modern molecular biophysics.
It introduces in a qualitative manner the modern spectroscopic, microscopy and numerical techniques, applying them to selected and relevant current topics. It is intended to also show how physical methods can become extremely valuable tools for understanding biological processes and that Biopysics is a wide, interdisciplinary topic in Physics, other than Biology.
The theme for all topics in the course is radiation-matter interaction and a photophysical approach to identify molecular mechanisms underlying relevant processes in a cellular contest. The course shows which is the modern molecular Biophysics, and in particular the bio-photonics.

Three macro-subjects can be identified:
1. Short introduction of the fundamentals of molecular biology
2. Radiation-matter interaction
3. Modelling of biophysical processes
Possible practice in lab on steady-state spectroscopic methods (absorption and fluorescence) and data analysis (students divided into small groups)

Full programme

1 Short introduction of the fundamentals of molecular biology, as protein structure and function, protein folding and cellular structure.
2 Radiation-matter interaction: fundamentals of photophysics
Absorption and Fluorescence: from theory (Fermi’s gold rule, transition dipole momentum, radiative and non-radiative transitions) to applications.
Fluorescence microscopy: from confocal microscopy to super-resolution microscopy of the 2014 Nobel Price (spatially patterned excitation and single molecule imaging).
3 Microscopic modeling in order to characterize photophysic processes: from relaxation of excites states to interaction between fluorophores and photoactivable compounds.

Practice in lab on steady-state spectroscopic methods (absorption and fluorescence) and data analysis (students divided into small groups)


Papers from recent literature and slides of the lessons. "Protein structure and function" G.A. Petsko, D. Ringe, Zanichelli; "Biological Physics. Energy, Information, Life. Updated first edition" Philip Nelson, Palgrave Macmillan and WH Freeman ed.; "Principles of fluorescence spectroscopy" J. Lakowicz, Kluver Academic/Plenum Publishers

Teaching methods

The lessons will be held in person. There will be some laboratory practice (24 hours) where students will have to apply theory to very small projects proposed and developed according to the methodological criteria outlined in lectures and in bibliographic and didactic material.
The slides used to support lessons will be uploaded at the end of the lesson on the Elly platform. To download the slides, you need to enroll in the online course.
Slides are considered an integral part of teaching material. It reminds non-attending students to check the available teaching material and information provided by the teacher through the Elly platform.

Assessment methods and criteria

There will be a continuous ongoing but informal training evaluation by discussing with the classroom during the Lessons, or at the beginning of the next lesson to see how much the previously explained concepts have been understood. The exam consists in:
An open written questionnaire to illustrate 3 topics (10 points per response). The duration of the written test is 2 hours. The written test is evaluated on a scale of 0-30. Honors is given in the case of achieving the highest score on each item and the mastery of the disciplinary glossary.
The result of the written test is communicated over the week after the test, via Email. Please note that the on-line application to the exam is MANDATORY.

The student will be evaluated based on the achievement of the objectives previously specified in details:

With a view to verifying whether such knowledge and level of competences have been achieved, the aim of the written examination is to evaluate the ability of the student to re-elaborate, reformulate such knowledge as well as his/her ability to apply the knowledge and skills gained, apply them at a contrastive level, and examine in depth the fundamental topics in biophysics using some of the most recent literature papers in biophysics.
The written evaluation will be considered insufficient if the student is found lacking in any minimum knowledge of topics and specific language; if he/she doesn’t demonstrate skills in analyzing the fundamental properties of (bio)physical systems and formulating independent critical judgements.
A final evaluation of sufficient (18-23/30) is determined if the student is able to show that he/she has mastered the basic notions and contents of the course and is sufficiently able to apply and express them, even simply, to discuss the fundamental properties of (bio)physical systems and formulate independent critical judgements and opinions.
An average mark is awarded to the student who can demonstrate he/she reaches the above learning aims at a more than sufficient (24-25/30) or good (26-27/30) level. The highest marks ( 28-30/30 and merit) are likewise awarded on the basis of a very good to excellent level.

Other information

On Friday, 09:30-11:30 p.m, or in any other day, by appointment (Email).