Biological Physics: Selected Projects
Although globular homopolymers are typically highly knotted, less than one in a hundred protein structures contain a knot ( http://knots.mit.edu ). Nevertheless, intriguing counter-examples exist, like the most complicated protein knot, which was discovered recently during a diploma thesis in our group (see figure on the left). Apart from analyzing biological data, we perform Monte Carlo simulations of simplified protein and DNA models to learn more about entanglements in viral DNA, chromatin and proteins. On this topic, we collaborate with theory groups at MIT and an experimental group at the MPI for Polymer Research. If you are interested in interdisciplinary investigations at the frontier of physics, mathematics and molecular biology, please contact Peter Virnau.
All living things depend on membranes. Their basic structure is provided by lipid bilayers, which self-assemble spontaneously in water due to the amphiphilic character of lipid molecules - they contain both hydrophilic and hydrophobic units. In our group, we are interested in generic properties of such amphiphilic bilayers.
We have established a coarse-grained lipid model, which reproduces the main phases and phase transitions of phospholipid membranes at temperatures close to room temperature. As particular highlights, we have (i) recovered and investigated the mysterious modulated "ripple phase" in one-component membranes, which had intrigued researchers for many decades, and (ii) discovered and investigated nanoscale structures, so-called "lipid rafts" in multicomponent membranes. Rafts are small structural entities in biomembranes which are believed to play an important role for many cellular functions. The question whether they can exist in pure lipid membranes had been discussed controversially in the past. We found that ripple states and rafts seem to be stabilized by very similar mechanisms: A propensity for global phase separation, which is suppressed by elastic interactions in the membrane. This is analyzed by computer simulations and elastic theories.
The same approach is used to study lipid-mediated interaction mechanisms membrane proteins. In the past, we have focused on a comparison between analytical predictions and simulation data for "proteins" that can be represented by simple cylindrical inclusions (see Figure). In the future, we also plan to investigate flexible proteins and their interaction with rafts. For more information, please contact Friederike Schmid.
Selective interactions between biomolecules play an essential role in biological systems. Without selective recognition of antigens by corresponding antibodies, for example, the immune system could not work efficiently. One of the most salient features of molecular recognition is the fact that biomolecules often discriminate very accurately between many different but structurally similar interaction partners which are also present in a heterogeneous biological system.
Our studies aim at an understanding of the basic and universal mechanisms of recognition processes between biomolecules in an heterogeneous environment. In order to identify and investigate these basics mechanisms we develop idealised coarse-grained models. These models neglect those details which are particular for a specific system and are thus constructed to represent generic types of recognition processes. The thermostatic and dynamical properties of the models are then analysed with numerical and analytical methods from statistical physics. For more information, please contact Friederike Schmid.