SubjectsSubjects(version: 949)
Course, academic year 2021/2022
Advanced biomolecular modelling - P143003
Title: Pokročilé biomolekulární modelování
Guaranteed by: Department of Informatics and Chemistry (143)
Faculty: Faculty of Chemical Technology
Actual: from 2020
Semester: winter
Points: winter s.:0
E-Credits: winter s.:0
Examination process: winter s.:
Hours per week, examination: winter s.:3/0, other [HT]
Capacity: unknown / unknown (unknown)
Min. number of students: unlimited
Language: Czech
Teaching methods: full-time
Teaching methods: full-time
For type: doctoral
Note: course is intended for doctoral students only
can be fulfilled in the future
Guarantor: Lankaš Filip doc. Ing. Ph.D.
Is interchangeable with: AP143003
Annotation -
Last update: Svozil Daniel prof. Mgr. Ph.D. (23.05.2018)
Processes in molecular biology and genetics take place at different length and time scales. The course deals with modelling at the mesoscopic scale, where the atoms of the biomolecules are united in larger entities. Students will first deepen their knowledge of nucleic acid structure and dynamics, an important application field of the course. Mesoscopic models of biomolecules and the solvent, including the necessary mathematical tools, are then exposed. Biomolecules often behave as stochastic systems, exhibiting transitions between different conformational states. The course therefore also includes an introduction to Markov processes and their algorithmic realization. Case studies will present selected problems based on current journal literature.
Aim of the course -
Last update: Svozil Daniel prof. Mgr. Ph.D. (23.05.2018)

Students will know:

  • They will learn basic approaches to mesoscopic biomolecular modelling
  • They will learn how to model electrostatic and hydrodynamic interactions at the mesoscale
  • They will be able to formulate and implement Markov models of conformational dynamics
  • They will get acquainted with current applications of mesoscopic modelling to molecular biology and genetics

Literature -
Last update: Svozil Daniel prof. Mgr. Ph.D. (23.05.2018)

R: J. N. Israelachvili, Intermolecular and surface forces. Elsevier 2011

R: C. Gardiner, Stochastic methods. Springer 2009

D: L. E. Reichl, A modern course in statistical physics, Wiley 1998

Learning resources -
Last update: Svozil Daniel prof. Mgr. Ph.D. (23.05.2018)

Online course materials

Syllabus -
Last update: Svozil Daniel prof. Mgr. Ph.D. (23.05.2018)

1. Biomolecular modelling in molecular biology and genetics

2. Structure and dynamics of nucleic acids

3. United atom models

4. Rotations and their description

5. Biomolecules represented by systems of rigid bodies

6. Polymer models

7. Vectors and tensors

8. Mesoscopic models of electrostatic interactions

9. Hydrodynamic interactions

10. Markov processes

11. Numerical implementation of random processes

12.–14. Case studies

Registration requirements -
Last update: Svozil Daniel prof. Mgr. Ph.D. (23.05.2018)

Mathematics, physical chemistry, and biochemistry or molecular biology at the level of basic university courses

Course completion requirements -
Last update: Svozil Daniel prof. Mgr. Ph.D. (23.05.2018)

Oral exam