METHODS FOR MOLECULAR DYNAMICS SIMULATION

The course fits into the Master's degree program as it provides the basic concepts for the predictions of the chemical and physical properties of biological molecules by means of molecular dynamics simulations.

KNOWLEDGE AND UNDERSTANDING
At the end of the course students should:
- have acquired a basic knowledge and understanding of both the theoretical concepts used in molecular dynamics simulations and the different formalisms employed;
- have acquired the basic knowledge of some methods for computationally characterizing biological molecules and predicting (some of) their properties.
ABILITY TO APPLY KNOWLEDGE AND UNDERSTANDING
At the end of the course students should be able to apply the different formalisms for investigation biomolecules also using some softwares.
ABILITY TO MAKE JUDGEMENTS
At the end of the course students should be able also to judge and compare the performances, the issues and the applicability of the different simulation techniques in view of the chemical problems to be solved and/or the researches to be carried out.

Basic knowledge in calculus (vectors, matrices, linear algebra, differential and integral calculus) and electromagnetism.
Besides, the students should know (and be able to apply) the basic concepts of quantum chemistry and spectroscopy (to have attained the educational objectives of the corresponding courses, i.e. Quantum Chemistry and Fundamentals of Spectroscopy, possibly but not necessarily having passed the corresponding exams).

BASIC CONCEPTS
Definition of molecular mechanics, molecular dynamics and force fields. Basic concepts on some common molecular representations. Coordinates and some coordinate manipulations. Quantum Chemical and Molecular Mechanics methods and models. The Born Oppenheimer approximation and the potential energy surface. Force fields methods: stretching, bending, out-of-plane bending, umbrella motion, torsion angle and potential, periodicity. Van Der Waals interaction and energy. London Forces. Dispersion terms. Electrostatic energy. Dipole and quadrupole. Polarizable Field Models. Cross terms, torsional parameters. Onion models
MOLECULAR DYNAMICS SIMULATION
Some key concepts on simulation methods. Energy minimization and methods for exploring the potential energy surface. Phase space. Newton’s equations of motion. Time averaged properties. Periodic boundary conditions (PBC). Radial distribution functions. Temperature control. Pressure control. Some algorithm techniques. Examples of molecular dynamics simulations carried out by using some software.
QUANTITATIVE STRUCTURE – ACTIVITY RELATIONSHIPS (QSAR)
Some key concepts on QSAR (Quantitative Structure – Activity Relationships).

Mainly lecture notes.
For insights into the theory, a good starting point is the following book.
Andrew R. Leach, "Molecular Modelling: Principles and Applications", 2nd edition, Pearson Education, 2001.

Oral examination (about 30’).
It consists in the discussion of a simulation project carried out on a molecular system freely chosen by the student itself, together with the presentation of the main results thus obtained. During the presentation the student has to demonstrate both the critical learning of the topics of the entire program and the ability to implement them in the project.

Lectures coupled to examples on the use of some dedicated software packages.
The slides employed during each lecture (and the corresponding supplementary material) will be downloadable from the MOODLE web pages.

English

oral

This subject deals with topics related to the macro-area "Human capital, health, education" and contributes to the achievement of one or more goals of U. N. Agenda for Sustainable Development