SC/0092/EN - THEORY AND COMPUTATION IN PHYSICAL CHEMISTRY
Academic Year 2021/2022
Free text for the University
DREW FRANCIS PARSONS (Tit.)
- Teaching style
- Lingua Insegnamento
|[60/69] CHEMICAL SCIENCES||[69/00 - Ord. 2019] PERCORSO COMUNE||6||60|
This course is taught in English. L'insegnamento è condotto in lingua inglese.
KNOWLEDGE AND UNDERSTANDING:
During the course, students will acquire the following knowledge:
Methodologies, theoretical approaches and scattering techniques for the physico-chemical characterization of colloidal and nano-structured systems, and of biological macromolecules.
ABILITY TO APPLY KNOWLEDGE AND UNDERSTANDING:
The course prepares students with both theoretical concepts and practical skills to characterize and understand the evolution of colloidal, nanostructured and macromolecular systems, in order to predict their stability.
AUTONOMY OF JUDGMENT:
The course aims to develop the ability to interpret concepts and data in a critical way, placing each topic in the context of its field of application, thus knowing how to identify the appropriate way to discuss or treat the question.
The course aims to develop the ability to present a scientific topic in a concise and exhaustive way both in written form (open-ended test and scientific report) and oral form (in-depth seminars) also through the use of IT support (PowerPoint presentations) and communicating in English language.
The concepts and notions learned by students give them the ability to apply the knowledge acquired to real systems (colloidal, nanophase and biological) and current scientific topics (nanosciences and nanotechnologies), and develop the curiosity to deepen their understanding through individual study by specialist texts and scientific articles in English.
Students should already possess a good level of preparation in the following areas: a) mathematics and physics; b) general chemistry; c) chemical kinetics; d) chemical physics of interfaces; e) English language
Prior programming experience is not assumed.
This course introduces basic computer programming with an emphasis on the skills used by chemists to prepare lab calculations and analyze
data, together with the skills required to work with theoretical
models in physical and computational chemistry. The Python
programming language is used.
– setting up a working programming environment (Anaconda)
– structuring a computer program
– working with data files
– using scientific library modules
Sample applications include
– calculating buffer solutions
– analyzing reaction kinetics from measured data
– analyzing titration data
– estimating the size of protein molecules
– calculating Debye lengths
– methods used to evaluate ion adsorption layers
(Poisson-Boltzmann model, electrical double layers)
The course is hands-on, students will learn to build programs on their
The course is anticipated to include 30 hours of classroom lessons (lectures and practical tutorials) and 18 hours of practical workshop exercises. The learning experience will involve installation of Python software on students' own computers, use of an Integrated Development Environment, and writing computer programs for analysing chemical data and theory in Python. We will also address mathematical methods used to implement computer programs to develop theory in physical chemistry.
Verification of learning
Assessment is composed of
1. programming assignment in data extraction
2. scientific programming assignment (preparing program to analyse experimental data and writing a formal report of analysis results)
3. theoretical programming assignment (preparing program to implement theory and identify trends in calculations for various conditions)
4. written exam (multiple choice, short-answer questions, debugging errors in sample programs)
Grades will be evaluated based on knowledge of the topics of the course, the ability to link between different topics, the capacity to apply concepts, the use of appropriate terminology.
Final grade. The final mark takes into account several factors:
Quality of knowledge, ability, skills possessed and:
a) appropriateness, accuracy and consistency of knowledge
b) appropriateness, accuracy and consistency of skills
c) appropriateness, accuracy and consistency of competency.
Comprehension and Communication:
a) expressive capacity;
b) Proper use of the specific language of the discipline;
c) logical and consequential capacity in the fitting of the contents;
e) Ability to connect different topics by finding common points and establishing a coherent overall design, giving attention to the structure, organization and logical connections used in communication;
f) capacity to synthesize ideas including through the use of its symbols and nomenclature of the material and the graphic expression of ideas and concepts, for example in the form of formulae, diagrams, equations.
Availability to discuss concepts and interact with the teacher during the course or in assessments.
a) critical spirit;
b) self-assessment ability.
Consequently, the grade can be:
30 cum laude: Implementation of the tasks and themes is correct and presented in detail. Rigorous methods have been applied. The oral presentation was particularly rich and precise and makes use of critical and personal insights. Skills, independent judgment, communication skills and ability to learn are clearly appropriate in every detail.
28-30: Implementation of the tasks and themes is correct and presented in detail. Rigorous methods have been applied. The oral presentation was accurate. Skills, independent judgment, communication skills and ability to learn are appropriate in every detail.
25-27: Implementation of the tasks and themes is correct and described in detail. Skills, their independent judgment, communication skills and learning skills are good though not rich in detail.
22-24: Implementation of the tasks suffers from easily identifiable careless mistakes (wrong signs, incorrect logic). Sometimes exercises and topics are not complete, but still addressing the solution. Skills, their independent judgment, communication skills and learning skills are adequate but some uncertainty.
18-21: Implementation of the tasks suffers from some errors (mostly due to distraction). Sometimes the exercises and topics are not complete, but still addressed adequately. Skills, their independent judgment, communication skills and ability to learn are sufficient.
Insufficient: Serious conceptual errors or conduct. Some exercises or subjects have been done or understood at all.
The main reference book is:
Learning Scientific Programming with Python
Christian Hill, 2nd edition,
Cambridge University Press 2020
Related reference books are available in the Biomedico-Scientific Library at at the Cittadella di Monserrato:
- Computational physics problem solving with Python,
Rubin H. Landau, Manuel J. Páez, Cristian C. Bordeianu, DID 530.15 LAN
- Computational physics, Newman, Mark, DID 530.15 NEW
- Introduction to computational chemistry, Frank Jensen, DID 542.85 JEN
Resources are also available in Italian:
- Pensare in Python, Allen Downey, 2015, Green Tea Press.
- Introduzione a Python, Tony Gaddis (tr. A. Valli), Pearson, 2016, ISBN: 8891900990
In addition to the recommended texts, lecturers will provide:
- pdf files of lecture notes
- simple sample programs
We will use Python via spyder from the Anaconda system. You can install it on your home computer from https://www.anaconda.com/products/individual