Teaching
- Course #1: "Molecular Dynamics and Monte Carlo methods - the basics" (winter semester) taught at the Faculty of Science & Faculty of Mat. & Phys., Charles University, Prague (course code: MC260P117)
- Course #2: "Methods and applications in computational cell biology and biophysics" (summer semester) taught at the Faculty of Science, Charles University, Prague (course codes: NBCM051 (MFF UK) & MC260P79 (PřF UK))
Lecturs (winter semester 2022/2023): each Wednesday, 10:40am, Ke Karlovu 3, Praha 2, Seminarni mistnost KCHFO (suteren).
First lecture: October 4th, 2023
This course is best suited for master and doctoral students at MFF and PřF UK
It is practically-oriented, topics range from physical chemistry to biophysics with the focus on the latter.
The topics include:
- Physical basis of molecular interactions
- Methods and algorithms used in modern molecular MD simulations
- Practical examples of simulations for various biophysical systems
- Data analysis and visualization, including modern Big Data and machine learning techniques
Applications of MD simulations to biological, pharmaceutical, and medical problems will be discussed.
For example:
- Localization and action of small drug molecules in cellular membranes
- Drug permeability across membranes
- Drug-protein interactions
- Molecular drug delivery systems
- Ageing - lipids under oxidative stress, apoptosis
- Implants biocompatibility
Lecture notes (individual links will become available during the semester):
- Lecture 1, Introduction: link
- Lecture 2, Force fields: link
- Lecture 3, Integrators: link
- Lecture 4, PBC, cutoffs, PME: link
- Lecture 5, Neighbours, constraints: link
- Lecture 6, Ensembles: link
- Lecture 7, Simulation protocol: link
- Lecture 8, Analysis: link
- Lecture 9, Monte Carlo & Docking: link
-
MD Lab materials: link
MD Lab technical info: link
Note! Attending and passing the MD Labs is obligatory in order to pass the course. The MD Labs take place Dec 6 & 13, 10:40-13:40, IOCB, Flamingovo nam. 2, Prague 6 Dejvice
Papers for dicussion (individual links will become available during the semester):
- Paper 1: link
- Paper 2: link
- Paper 3: link
- Paper 4: link
- Paper 5: link
- Paper 6: link
- Paper 7: link
- Paper 8: link
Python examples:
- Google Collab notebooks: link
Course #2: "Methods and applications in computational cell biology and biophysics" (summer semester)
Lecture notes (individual links will become available during the semester):