Computer Simulations

B. Strodel (Structural Biochemistry)
R. G. Winkler (Theoretical Soft Matter and Biophysics)
(building 15.1X, room 249)

The lecture series consists of two parts. The first part on computational biology is given by Birgit Strodel, the second part on computational soft matter by Roland Winkler. The soft matter part of the course requires basic knowledge on molecular dynamics simulations that is tought in the computational biology lectures.

• B. Strodel (Structural Biochemistry)
  Simulation Techniques in Computational Biology

  The focus of the lecture series is on molecular dynamics (MD) simulations for biomolecules. The outline for the three lectures is as following:

  • Lecture 1: Force Fields (room change: building 04.8, room 337/338)
    - Bonded and nonbonded interactions in biomolecular force fields
    - Calculation of nonbonded interactions
     
    
  • Lecture 2: Molecular Dynamics
    - Introduction to MD simulations
    - Thermostats and barostats in MD simulations
    - Langevin and Brownian dynamics
     
    
  • Lecture 3: Advanced Simulation Techniques
    - Introduction to Monte-Carlo simulations
    - Replica exchange MD
    - Umbrella sampling MD
     
    
  In the hands-on course in July, the students will be taught to setup and run MD simulations with GROMACS and how to analyze the resulting MD trajectories.

  Wednesday, March 30, 3:00-4:30 (room change: building 04.8, room 337/338)
  Wednesday, April 27, 3:00-4:30
  Wednesday, May 18, 3:00-4:30
  

• R. G. Winkler (Theoretical Soft Matter and Biophysics)
  Computational Soft Matter

  Studies of large-scale dynamical properties of biological systems such as (bio-) macromolecules (e.g., proteins, DNA) or self-propelled systems (e.g. bacteria) require coarse-grained simulation techniques for both the mesoscopic object as well as the solvent. In the lectures, these aspects will be addressed; specifically:

  • Coarse-grained molecular dynamics simulations for (bio-)macromolecules
  • Hydrodynamic interactions in solutions
  • Mesoscale hydrodynamic simulations of soft-matter and biological systems

  Wednesday, June 8, 3:00-4:30
  Wednesday, June 29, 3:00-4:30