SubjectsSubjects(version: 954)
Course, academic year 2019/2020
Advanced biomolecular modelling - AP143003
Title: Advanced biomolecular modelling
Guaranteed by: Department of Informatics and Chemistry (143)
Faculty: Faculty of Chemical Technology
Actual: from 2019
Semester: both
Points: 0
E-Credits: 0
Examination process:
Hours per week, examination: 3/0, other [HT]
Capacity: winter:unlimited / unknown (unknown)
summer:unknown / unknown (unknown)
Min. number of students: unlimited
State of the course: taught
Language: English
Teaching methods: full-time
Teaching methods: full-time
Note: course is intended for doctoral students only
can be fulfilled in the future
you can enroll for the course in winter and in summer semester
Guarantor: Lankaš Filip doc. Ing. Ph.D.
Interchangeability : P143003
Examination dates   Schedule   
Annotation -
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.
Last update: Pátková Vlasta (08.06.2018)
Aim of the course -

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

Last update: Pátková Vlasta (08.06.2018)
Literature -

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

Last update: Pátková Vlasta (08.06.2018)
Learning resources -

Online course materials

Last update: Pátková Vlasta (08.06.2018)
Syllabus -

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

Last update: Pátková Vlasta (08.06.2018)
Registration requirements -

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

Last update: Pátková Vlasta (08.06.2018)
Course completion requirements -

Oral exam

Last update: Pátková Vlasta (08.06.2018)