Summer Semester 2018

Introduction to Molecular Dynamics (MD) simulations of biological systems

Batuhan Kav (MPIKG)

Biological processes, from electron transfer on proteins to cell division, span a broad range of time- and length scales. Rapid processes occurring at short length scales are where molecular level interactions take place. Unfortunately, these processes are not always readily accessible through experiments. Computer simulations, on the other hand, act as a linker between the microscopic and macroscopic world; they can help us to understand the microscopic properties of the system and relate them to the macroscopic observables. This one-week intensive workshop aims to provide an introduction to the molecular dynamics (MD) simulations. No prior knowledge is required as necessary theoretical and technical background will be provided. Two systems, one with a solvated protein and one with a full-hydrated lipid bilayer will be constructed, simulated, and then analyzed. By the end of the workshop the students should be able to grasp how MD simulations work, perform basic simulation and analysis of the biological systems, and proceed to more advanced simulation techniques.

 

Info meeting Monday April 9 at 11 am in the Theory seminar room. Please contact the lecturer if you want to take this course.

Introduction to biology of prokaryotes

Elisa Cerda Donate (MPIKG)

During the course we will deal with the basic aspects of prokaryotic molecular biology, metabolism, evolution and ecology. If any special topic is of interest, we can of course discuss about it during the lecture too.

Please contact the lecturer if you want to take this course.

Concepts of cell biology/membranes

Marzie Karimi, Sunidhi Shetty (MPIKG)

This course will focus on the theoretical principles as well as the practical aspects of molecular organization of cells and membrane biophysics.


The aim of the course is to learn the cellular structure and their processes on a molecular level.


Cell culture, Vesicle preparation with the most common protocols, as well as the basic knowledge of fluorescence and confocal microscopy will be provided.


Course Contents
1. The Evolution of Cell
2. Cell Chemistry and Biosynthesis
3. Macromolecules: Structure, Shape and information
4. How Cells are studied
5. Basic Genetic Mechanisms
6. The Plasma Membrane

 

 
Please contact the lecturers if you plan to take this course.

 

Advanced biophysics

Joachim Heberle (FU, Physics)

This module will present and substantiate biophysical methods and concepts. Selected methods like spectroscopy and diffraction and their application to proteins and biomembranes are of particular relevance. The lecture series will cover a selection of the following methods:

absorption spectroscopy in the UV, visible and IR region;
fluorescence spectroscopy, time-resolved approaches;
spectroscopy with polarized light;
vibrational spectroscopy: Fourier-transform infrared (FTIR), resonance Raman, surfance-enhanced Raman and IR;
diffraction with X-rays, Neutrons and electrons;
crystallization and protein crystallography;
nuclear magnetic resonance (NMR); light scattering; single molecule spectroscopy;
atomic force microscopy (AFM and optical tweezer);
theoretical methods: MD simulations, Poisson-Boltzmann, QM/MM, coarse-grained MD

 

 

Lecture series

N.N.

Lorum ...

Statistical physics and thermodynamics

Roland Netz (FU, Physics)

  • equilibrium ensembles
  • thermodynamics: thermodynamic potentials, laws of thermodynamics, thermodynamic cycles
  • ideal quantum gases
  • phase transitions
  • interacting systems
  • introduction to non-equilibrium statistical mechanics

Please note: There are two appointments per week.

  • Tuesdays from 10 am to 12 pm
  • Fridays from 8 am to 10 am

Cell Biology For Life Scientists

Ralph Graef (UP, Biology)

Statistical physics and thermodynamics

Roland Netz (FU, Physics)

  • equilibrium ensembles
  • thermodynamics: thermodynamic potentials, laws of thermodynamics, thermodynamic cycles
  • ideal quantum gases
  • phase transitions
  • interacting systems
  • introduction to non-equilibrium statistical mechanics

Please note: There are two appointments per week.

  • Tuesdays from 10 am to 12 pm
  • Fridays from 8 am to 10 am