Universität Wien

269019 VO Computational Concepts in Chemistry II (2022S)

3.00 ECTS (2.00 SWS), SPL 26 - Physik
Moodle

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Details

Language: English

Examination dates

Lecturers

Classes

Termine:
Do, 24.03.22
Do, 07.04.22
Do, 05.05.22
Do, 19.05.22
Do, 02.06.22
jeweils 14:00 - 18:00

Institute for Theoretical Chemistry, Währingerstrasse 17, 1090 Vienna, 2nd floor PC pool

Information

Aims, contents and method of the course

Every lecture will have a theoretical part, a practical part, and homework. Practical exercises will be done on a Jupyter server hosted via moodle, so students can use their own laptop to participate.

Graph theoretical approaches:
- Digital representation of chemical compounds and chemical reactions.
- Graph isomorphism problem and canonical labeling.
- Reactions as graph rewrite rules.
- Combinatorial chemistry.

Stochastic methods and reaction kinetics:
- Formal properties of chemical reaction networks
- Stochastic processes, chemical master equation.
- Large reaction networks in homogeneous phase.

Chemical reaction networks as a formal language:
- CRNs as a model of computation.
- Rate-independent computation.
- Steady-state circuits.
- Dual-rail systems.
- CRN equivalence notions.

Implementing chemical reaction networks:
- DNA as a substrate for chemical kinetics.
- DNA strand displacement systems.
- Reaction enumeration and condensation.
- Compilation from CRN to DNA.

Assessment and permitted materials

Preferred: students are graded based on participation, homework and a final presentation. Alternative: an oral exam at the end of the semester.

Minimum requirements and assessment criteria

For a positive grade, a student must develop a basic understanding and the ability to explain the main points of lecture material from 4 of the 5 dates. Active participation and a final presentation of homework solutions can be sufficient for getting the final grade.

A student who takes an oral exam has to explain the covered abstract chemical problems and connect them to appropriate computational concepts. Homework problems will likely be part of the final exam.

Examination topics

A mix of lecture and practical exercises.

Reading list

Literature will be provided after the lectures on the elearning platform.

Association in the course directory

CO-CHE2

Last modified: Th 11.05.2023 11:28