COMPUTATIONAL BIOPHYSICS SYLLABUS

doing biology with models and computers: from the Born-Oppenheimer approximation to the space of biological sequences, artificial intelligence, integrative approaches of systems biology and medicine

Academic Year 2021-2022, 6 ECTS.

LOCATION/TIME:  Room 5, Fermi Building: mondays, 8am-9am; tuesdays 2pm-4pm; thursdays 8am-20am

This is a course for the Master Program in Physics, given in the 2^nd semesterand, in perspective,  is quite strictly related to other courses in the BIOSYSTEMS program, namely: BIOCHEMISTRY, MOLECULAR BIOLOGY, BIOPHYSICS, THEORETICAL BIOPHYSICS AND SOFT&BIOLOGICAL MATTER.

Description/Objectives. This course is intended as an introduction to computational (in silico, as opposed to in vivo/in vitro) biophysics/biology, in an evolutionary perspective. The style of teaching is by active illustration not by exhaustive passive demonstration. It will require from the students an active participation through: questions, statements, and written essays. Extensive reference and critical introductions to the literature and to many specialized texts will be offered as a thread for personal study. An effort will be done to locate each topic in a clear scheme of references, useful to prepare the final exam. The objective of this course is, in a nutshell, to narrow the gap between the institutional level of training and that of research. Guest lecturers will occasionally present specialized views and lines of contemporary research of impact and interest to an audience of students enrolled in the biosystems and theoretical curricula.

Requirements.Enrolled students should have taken the basic courses of the BA program. In particular, basic competence in classical mechanics, thermodynamics, chemical equilibrium and quantum mechanics is required together with basic programming skills. Biological facts will be discussed as needed. 

Evaluation:based onwritten essays, written tests, home-works and participation to discussions: 40%. Final oral exam: 60%.

Recommended texts. 

For a quantitative assessment of modern biology

[MP] Ron Milo and Rob Phillips, Cell Biology by the numbers, Garland, New York, 2016.

Reference textbook for the entire course

[HA] PG Higgs, TK Attwood, Bioinformatics and Molecular Evolution, Blackwell, 2006.

Mathematical backbone and proofs

[DU] R Durbin, Eddy, Krogh, Michison. Biological Sequence Analysis. CUP, 1999.

 Further reading and extra materials for individual study will be suggested along the course. 

 OUTLINE OF THE PROGRAM

• BASIC CELL BIOLOGY BY THE NUMBERS
  
• WHAT IS COMPUTATIONAL BIOPHYSICS 
• PROBABILISTIC REASONING (BAYESIAN MODEL SELECTION) 
  
• FROM THE B.O. APPROXIMATION TO (PROTEIN) MOLECULAR DYNAMICS
• SEQUENCING
• ELEMENTS OF PROTEIN STRUCTURES AND DATABASES
• DIRECT COUPLING ANALYSIS AND CONTACT PREDICTIONS
  
• THE PROTEIN FOLDING PROBLEM
  
• MODELS OF SEQUENCE EVOLUTION
• SEQUENCE ALIGNMENT ALGORITHMS
• SEARCHING DATABASES OF BIOLOGICAL SEQUENCES
• MACHINE LEARNING METHODS AND AI
• SYSTEMS BIOLOGY