• Blended Learning & Flipped Classroom

Molecular simulations are the theoretician’s tools to understanding the fundamentals behind many physical and chemical phenomena. This course is designed to introduce the student to the theory and methodology behind these tools, and to expose the student to the power of molecular level simulations and modeling through practical applications. Topics will span two core techniques: molecular  mechanics and molecular dynamics. 

In the laboratory activity students will be divided in groups and for each group a different project will be assigned.

To complement the project activities and to stimulate active learning, the structuring skills of thinking and knowledge and the assessment among colleagues, each group of students is responsible for examining a specific topic that will be presented and discussed with other students in flipped/blended classroom modality.

At the end of the course, the student is able to:
1. use different MD software to study biomolecules;
2. explain the origin of intermolecular interactions and calculate Boltzmann- and orientationally averaged interaction energies between molecules represented by charge distributions as a function of distance;
3. explain the molecular driving forces energy  and their implications for molecular assembly and shape (folding);
4. reproduce a number of molecular descriptors and be able to perform regression analysis leading to such relationships;
5. reproduce the general ideas behind molecular modeling techniques and be able to generate and analyze data using modeling software;
6. collect primary scientific literature pertaining to the self-assembly or folding behavior of a class of molecules and summarize this material in an essay written in English;
7. point out the assumptions made in the derivations of the equations and their limitations in relation to the techniques used in rational molecular design.

Students are expected to acquire competences following the Dublin Descriptors reported below:

A: KNOWLEDGE AND UNDERSTANDING.

Knowledge and ability to discuss and present the main theoretical aspects presented in the course. Knowledge of the structure/function correlation in proteins.

B: APPLYING KNOWLEDGE AND UNDERSTANDING

Resolving problems and exercises in molecular modelling applying the correct mathematical models. Setting virtual experiments for charaterisation of proteins. 

C: INDIPENDENCE IN JUDGEMENT

Critically analysing the recent literature on molecular modeling and discussing results.

D: COMUNICATION SKILLS

Abilty to present a paper of the most recent literature, the course is in english and students are encouraged to ask questions and discuss in english.

- From quantum to classical mechanics: Brief review of the basic principles of quantum mechanics of atoms and molecules.

-Definition and terms of FORCE FIELD (FF), bonded and non-bonded terms. Treatment of long range interactions

-Introduction to Statistical Mechanics

- Energy minimization , the Potential Energy Surface and minimization algorithm

-Molecular Dynamics, ergodic Hypothesis and simulations in different ensambles

-Coarse Grain Models

PRACTICALS

Velocity distribution and Maxwell-Boltzman distribution

Verlet algorithm for the integration of the equation of motion

PRACTICALS IN LABORATORY

Utilization of visualization software packages: VMD

Energy Minimization

How to build a new force field

Molecular dynamics simulation and analysis of MD trayectories

Steered Molecular dynamics

In the second part of the course a project will be assigned and in the remaining part of the course it will be accomplished. The project will end with a report that will be presented and discussed in classroom.

The exam consists of an written exam in which the students have to answer questions based on the material/theory taught during the lectures.

The evaluation of the written part accounts for 60% of the final grade.

40% of the grade is based on the evaluation of the presentation given by each student in English on the report describing the project results obtained in the second part of the course.