Experiments

• AG - astrophysics and geophysics
• BK - biophysics and complex systems
• FM - solid state physics and physics of materials
• KT - nuclear physics and particle physics

BK - biophysics and complex systems

• AG.RBK - Rayleigh-Bénard Convection
• BK.ABB - Analysis of Brownian Motion
• BK.CMF - Computational Microfluidics (Digital Lab)
• BK.MDS - Molecular Dynamics Simulations of Proteins
• BK.MIF - Microfluidics
• BK.NLF - Nd:YAG Laser and Second-harmonic generation
• BK.NSE - Nanostructuring by means of Electron Beam Lithography
• BK.OTM - Assembling an optical tweezers microscope
• BK.PKR - Phase Contrast Radiography
• BK.SLM - X-ray reflectivity study of lipid membranes
• BK.STM - STED Microscopy
• BK.TRS - Total Reflection of X-rays and X-ray Reflectivity of Thin Films
• BK.WFS - Wavefront sensor for laser beam and optics characterization

BK.MDS - Molecular Dynamics Simulations of Proteins

Molecular dynamics simulations are a method for describing the dynamics of macromolecules such as proteins, lipids or synthetic polymers. The movements of all the individual atoms of a system are calculated here by computer-based numerical integration. The aim of this experiment is to familiarize you with the basics of this method. For this purpose, simulations of a small protein model system are carried out. By variation of several simulation parameters their effect on the physical behavior of the system can be analyzed. The experiment provides insights into several specific analysis possibilities of the molecular dynamics simulation of proteins and their comparison with respect to conventionally determined quantities.