84639 - IT Skills for Chemistry

Learning outcomes

By the end of the course, the student will have a basic understanding of operating systems, be able to work on the Unix command line interface, understand the fundamentals of Fortran programming, and be able to create simple flowcharts for programming in any language. Additionally, the student is capable of comprehending and formulating simple algorithms. The student is also proficient in using the most popular chemistry software for data analysis, molecular visualization, and molecular investigation.

Course contents

· Introduction to information technology: scientific and industrial research. Computer Architecture: A brief description of the hardware (CPU, main memory, buses, clocks, and microprocessors). Information coding: representation of information and introduction to the concept of code; binary number system; introduction to basic data types; and floating point representation.

· Overview of operating systems (Windows and Linux). Command line interface in Linux and commands.

· Data processing; amount, export, simple functions (sum, multiplication, average, variance) with Excel and Matlab.

· Algorithms: representation and structure of the main algorithms for numerical calculation and scientific applications. The discussion will focus on the following topics: 1) iteration vs recursion algorithms, 2) sorting algorithms, 3) search algorithms, 4) numerical algorithms and numerical integration, 5) algorithmic strategies.

· Programming languages: Coding of algorithms and basic programming elements: variable declaration, flow control (if-then-else), loops, fundamental data structures (one- and two-dimensional arrays, vectors and matrices, functions); applications in stoichiometry with Matlab.

· Elements of the programming language; execution flow control (if-then/elseif-then/else); make cycles; execute while loops; external functions; formatted input and output; applications in Chemistry with Matlab.

· Design and writing of simple programs oriented towards scientific computing in Matlab.

Representation of chemical structures, introduction to molecular simulations and solving fundamental chemical problems.

Readings/Bibliography

There is enough material in the lessons to get ready for the final exam. At the conclusion of each lesson, a list of any further resources (books, chapters, or papers) that are required for a deeper understanding will be provided.

Teaching methods

· Lessons with multimedia support. The lecture slides contain all the material needed for the final exam and will be available for download before the lecture.
The lectures will be supported by practical exercises, partly carried out in the classroom and partly in the computer laboratory. In the computer lab, students will use the Matlab software and some basics of the Linux operating system.
In consideration of the type of activity and the teaching methods adopted, the attendance of this training activity requires the prior participation of all students in the training on safety in the places of study in e-learning mode.

Assessment methods

The verification of learning takes place through two written exams, which consist of questions and/or exercises concerning all the topics covered in class and during the practical exercises. The first written exam takes place in the lab, and the second one in class. In the second written exam, the use of books, notes, or other electronic media is not permitted; the exception is the use of a personal calculator. All cell phones are turned off. Active cellular devices will result in their respective owners being disqualified from the written test.

Each written test lasts two hours. The first one takes place in the last two hours of the last lab, and the second one in class during the examination period.


Final Mark: If A is the mark of the written test in the lab and B is the mark of the second exam, then two marks can be constructed: FM1=B and FM2=(0.4xA+0.6xB). The final mark is FM=max(FM1,FM2), which means the maximum between FM1 and FM2.

Teaching tools

PC, video projector. The slides projected in class and the laboratory teaching material will be available for download in the institutional repository of the University of Bologna. Laboratory exercises.

Office hours

See the website of Evangelos Bakalis