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.
COMMUNICATION SKILLS
At the end the students should be able to communicate the knowledge learned, and to describe the results obtained from the application of a given simulation techniques, with appropriate language, to specialists and non-specialists interlocutors.

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 (by using slides in PPT and/or PDF format, 8 min max) of the main results thus obtained, followed by some open questions. During the discussion, the presentation and the open questions 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, and that he/she is able to communicate the knowledge learned, and to describe the results obtained from the application of a simulation technique with appropriate language.

Classroom lectures (both traditional whiteboard and PPT or PDF slides will be used) coupled to the use of some dedicated software packages, and problems/exercises; besides, scientific articles, will be used during the lectures.
During the classroom lectures the students will use also softwares for the simulation (and analysis) of molecular systems of increasing complexity; it is recomended to bring a laptop during the lectures.
After each lecture, the slides employed (and the corresponding supplementary material) will be downloadable from the MOODLE web pages.

English

Accessibility, Disability and Inclusion
Accommodation and support services for students with disabilities and students with specific learning impairments:
Ca’ Foscari abides by Italian Law (Law 17/1999; Law 170/2010) regarding support services and accommodation available to students with disabilities. This includes students with mobility, visual, hearing and other disabilities (Law 17/1999), and specific learning impairments (Law 170/2010). In the case of disability or impairment that requires accommodations (i.e., alternate testing, readers, note takers or interpreters) please contact the Disability and Accessibility Offices in Student Services: disabilita@unive.it.

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