BIOPHYSICA
COMPUTAZIONALE  

A.A.
2017-2018, 6 ECTS.

A course for the Master Program in Physics is given
in the 1^st semester and is pivotal for the curriculum in biosystems
and part of an integrated syllabus together with courses in BIOCHEMISTRY, MOLECULAR
BIOLOGY, BIOPHYSICS and THEORETICAL BIOPHYSICS.

The class will meet: mon. 12 -14, tue 8-10 and
fri 16-18 in the Careri room (Marconi Building)

Instructor: Andrea Giansanti, room 211 (2^nd
floor, Marconi Building) tel. 0649914367 Andrea.Giansanti@roma1.infn.it

The course
will end on Jan. 12 2018.

Running title: DOING BIOLOGY WITH COMPUTERS AND MODELS: FROM
THE BORN-OPPENHEIMER APPROXIMATION TO THE SPACE OF BIOLOGICAL SEQUENCES AND THE
INTEGRATIVE MODELLING OF SYSTEMS BIOLOGY

Description/Objectives. This course is intended as an introduction
to computational (in silico, as opposed to in vivo/in vitro) Biophysics and
Biology in the evolutionary perspective. The course is conceived as a compact (biased) introduction to: i) ARGUMENTS (A) (principles, ideas); ii) METHODS
(M) (algorithms and techniques);
iii) PERSPECTIVES (What next?) of contemporary computational
biology. As far as the bias is concerned: the course will echo under many
circumstances topics and themes that prof. Anna Tramontano used to teach, until
last year. This 2017-18 course is dedicated to her memory. The style of
teaching will be by illustration not by exhaustive demonstration, and requires
from the students active participation, through questions, statements, and
written essays. Lectures based on detailed demonstration (in the math style)
will be limited in number. On the contrary, 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 made to locate each topic in a
clear scheme to prepare the final exam. The objective of the course is, in a
nutshell, to narrow the gap between the institutional level of training and
that of research. Guest lecturers will 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 mechanics, thermodynamics, chemical equilibrium and quantum mechanics is
required. Basic biological facts will be discussed as needed.

Evaluation: based onwritten essays, written tests and
homeworks and participation to discussions: 40%. Oral exam: 60%.

Topics. The themes of the course
will be partitioned into the three tracks:
A, M, P, mentioned above.

Recommended texts.

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

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

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

NOTE: STUDY MATERIALS CAN BE FOUND IN SEPARATED
FILES AT:

http://server2.phys.uniroma1.it/doc/giansanti/BIOFISICA_COMPUTAZIONALE_2017/

SOME OF THE THEMES THAT WILL BE DISCUSSED

1.     
WHAT IS COMPUTATIONAL
BIOPHYSICS

2.     
BASIC CELL BIOLOGY BY THE
NUMBERS

3.     
PROBABILISTIC REASONING
(BAYES’THEOREM)

4.     
FROM THE SCROEDINGER
EQUATION TO MOLECULAR STRUCTURES AND DYNAMICS

5.     
EVOLUTIONARY
SEQUENCING  OF GENOMES

6.     
METHODS OF SEQUENCE
ANALYSIS/ BASIC BIOINFORMATICS/ PROGRAMMING

7.     
MULTI-VARIATE DATA
ANALYSIS (CLUSTERING)

8.     
PHILOGENETIC METHODS

9.     
MACHINE LEARNING METHODS