BIOPHYSICS

Course objectives

GENERAL OBJECTIVES The bacterial cell occupies the same special place in biological physics as the hydrogen atom does in condensed matter physics, and for the same reasons. Bacteria are the first "atoms" of life to appear in the known Universe, and everything fundamental in life is found in bacteria, in its simplest forms. The aim of the course is to investigate some fundamental aspects of living systems in a journey that starts from the internal mechanisms by which the bacterial cell "thinks" and acts, passing through how the individual cell moves in the external physical environment and ending with the study of the collective behaviour of bacterial colonies. All topics covered in the course are based on recent literature and discuss both experimental aspects and theoretical modelling. SPECIFIC OBJECTIVES A - Knowledge and understanding OF 1) To know and understand the fundamentals of gene regulation in prokaryotes and the dynamics of transcriptional networks. OF 2) To know and understand the fundamentals of low Reynolds number fluid dynamics. OF 3) To know and understand the main manifestations of the out of equilibrium nature of active matter. B - Application skills OF 4) To be able to discuss the dynamical behaviour of a transcriptional network. OF 5) Tp be able to solve some elementary problems of low Reynolds hydrodynamics. OF 6) Tp be able to model the stochastic dynamics of active particle systems. OF 7) To be able to describe with continuous models the growth of bacterial colonies. C - Autonomy of judgement OF 8) Using the knowledge acquired, the student will be able to formulate new models capable of describing situations not covered in the course. D - Communication skills OF 9) To know how to communicate in written reports an advanced concept. OF 10) To be able to present a recent line of research in biophysics. E - Ability to learn OF 11) To be able to read independently scientific texts and articles in order to elaborate on the topics introduced in the course.

Channel 1
ROBERTO DI LEONARDO Lecturers' profile

Program - Frequency - Exams

Course program
Part 1 - What's inside: genetic parts and circuits From genes to proteins Modes of gene regulation Protein dynamics Feed forward loops and temporal programs Biological oscillators DNA cloning Stochastic gene expression Part 2 - What's outside: cell motility Introduction to the physics of microswimmers Introduction to vector calculus Microhydrodynamics Flagellar propulsion Watching microswimmers Manipulation of microswimmers Part 3: Multicellular dynamics Non equilibrium physics of active particles Non interacting active particles Active matter in nonhomogeneous environments Spatio-temporal patterns in colony growth
Prerequisites
A fundamental prerequisite is that students must have the knowledge requested by the first level University degree in Physics or in Astronomy and Astrophysics. Specific competencies are requested in classical physics, statistical mechanics, optics, mathematical and computational methods for physics. It is useful to have basic knowledge of molecular biology.
Books
R. Di Leonardo, Biophysics lecture notes Alberts, et al. Essential Cell Biology. 3rd Ed., New York: Garland Science (2004). Alon, An Introduction to Systems Biology: Design Principles of Biological Circuits, CRC press (2019).
Teaching mode
The lecture format is through blackboard and slide presentation
Frequency
.Attendance to the lectures is not mandatory but strongly recommended.
Exam mode
The final grading will be based on an oral exam (45 minutes) aimed at assessing the competences acquired by the student during the course. The oral exam consists of an interview on the topics illustrated in the course. To pass the exam the student must be able to present a topic or repeat a calculation discussed during the course and to apply the methods learned to examples and situations similar to those already discussed. The evaluation will take into account: - correctness of the concepts exposed; - clarity and rigor of presentation; - ability to analytically develop the theory
Bibliography
Texts and in-depth material will be indicated in correspondence with the topics covered in the course on the Classroom page
Lesson mode
The lecture format is through blackboard and slide presentation
ROBERTO DI LEONARDO Lecturers' profile

Program - Frequency - Exams

Course program
Part 1 - What's inside: genetic parts and circuits From genes to proteins Modes of gene regulation Protein dynamics Feed forward loops and temporal programs Biological oscillators DNA cloning Stochastic gene expression Part 2 - What's outside: cell motility Introduction to the physics of microswimmers Introduction to vector calculus Microhydrodynamics Flagellar propulsion Watching microswimmers Manipulation of microswimmers Part 3: Multicellular dynamics Non equilibrium physics of active particles Non interacting active particles Active matter in nonhomogeneous environments Spatio-temporal patterns in colony growth
Prerequisites
A fundamental prerequisite is that students must have the knowledge requested by the first level University degree in Physics or in Astronomy and Astrophysics. Specific competencies are requested in classical physics, statistical mechanics, optics, mathematical and computational methods for physics. It is useful to have basic knowledge of molecular biology.
Books
R. Di Leonardo, Biophysics lecture notes Alberts, et al. Essential Cell Biology. 3rd Ed., New York: Garland Science (2004). Alon, An Introduction to Systems Biology: Design Principles of Biological Circuits, CRC press (2019).
Teaching mode
The lecture format is through blackboard and slide presentation
Frequency
.Attendance to the lectures is not mandatory but strongly recommended.
Exam mode
The final grading will be based on an oral exam (45 minutes) aimed at assessing the competences acquired by the student during the course. The oral exam consists of an interview on the topics illustrated in the course. To pass the exam the student must be able to present a topic or repeat a calculation discussed during the course and to apply the methods learned to examples and situations similar to those already discussed. The evaluation will take into account: - correctness of the concepts exposed; - clarity and rigor of presentation; - ability to analytically develop the theory
Bibliography
Texts and in-depth material will be indicated in correspondence with the topics covered in the course on the Classroom page
Lesson mode
The lecture format is through blackboard and slide presentation
  • Lesson code1055361
  • Academic year2025/2026
  • Coursecorso|33602
  • CurriculumPhysics of Biological Systems
  • Year1st year
  • Semester2nd semester
  • SSDFIS/03
  • CFU6
  • Subject areaMicrofisico della materia e delle interazioni fondamentali