molecular biophysics

J. Heyrovsky Institute of Physical Chemistry, Czech Academy of Sciences, Prague


Course #1: "Molecular Dynamics and Monte Carlo methods - the basics" (winter semester)

Lecturs (winter semester 2019/2020): each Wednesday, 10:40am, Ke Karlovu 3, Praha 2, Seminarni mistnost KCHFO (suteren).
First lecture: October 2nd, 2019

MD Lab exercises: The dates will be announced, Ke Karlovu 3, room M-145 (36) (suteren). For MD lab materials, see below.

Consultations: The dates will be announced, Institute of Organic Chemistry and Biochemistry CAS, Flemingovo nam. 542/6, Prague 6 Dejvice, room A.3.14.

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
    Note! Attending and passing the MD Labs is obligatory in order to pass the course. The MD Labs take place [the dates will be announced] (from 10:40am till 1:40pm ) at Počítačová laboratoř Karlov (link)

Papers for dicussion (individual links will become available during the semester):

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):