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PROGRAMMING AND MOLECULE VISUALIZATION

Degree course: 
Corso di First cycle degree in CHEMICAL AND INDUSTRIAL CHEMISTRY
Academic year when starting the degree: 
2021/2022
Year: 
3
Academic year in which the course will be held: 
2023/2024
Credits: 
6
Period: 
Second semester
Standard lectures hours: 
48
Requirements: 

Knowledge of the basic operation of a computer in a Windows or Linux or Mac environment.

Final Examination: 
Orale

The exam will be a practical computer test. The practical test will consist of a computer exercise on one of the topics and / or applications made during the lessons. The student's ability to perform the exercise correctly will be positively evaluated.

Assessment: 
Voto Finale

The student will learn the basics necessary to address the problems relating to the application of computer / computational / graphical methods to inherently chemical problems.
The course consists of two strongly integrated and interdependent modules. As a result of the strong integration of the two modules, the exam is unique.
In particular, the training objectives of the two modules are:
MODULE A
• To provide the basic concepts of the MATLAB programming language
• Introduce the student to the use of programs for visualizing molecules in 3D
MODULE B
• Apply the basic notions of MATLAB programming in the writing of simple programs for data analysis and function visualization (in 2 and 3 dimensions).
• Application of molecular graphics programs to chemical problems

EXPECTED LEARNING RESULTS
At the end of the course, the student will be able to:
• Carry out the implementation of simple calculation algorithms with MATLAB
• Graphically represent molecular systems in 3D.
• Visualize molecular orbitals
• Carry out a conformational analysis

MODULE A:
• The MATLAB programming environment
• Working with the MATLAB user interface
• Variables and commands
• Data management
• Data interpolation and extrapolation
• Graphical representation of data
• Automate scripted commands
• Working with tabular data
• Adapt models to empirical data
• Introduction to the use of molecular visualization and manipulation programs (AVOGADRO and VMD)
• Preparation of a molecular model

MODULE B:
• Creation, use and analysis of data tables in the MATLAB environment
• Graphical representation of atomic and molecular wave functions using MATLAB
• Visualization and conformational analysis of molecules with AVOGADRO and VMD
• Use of web resources for molecular graphics and for visualization of the electronic structure of molecular systems in 3 dimensions.

Modules