Parallelrechnersystem
Final Report Abstract
M. Emal Alekozai (Computational Molecular Biophysics, Prof. J. C. Smith): Cellulose-Cellulase Interaction Hotspots via MSM - Cellulose holds great potential as a source of biofuel energy. It is a complex carbohydrate that forms the cell walls of plants and gives them rigidity. It consist of several faces with different physical properties. The sugar subunits can be unlocked and fermented to produce ethanol. Plants have developed over time defense mechanism which locks up sugars and makes the fermentation process difficult and not costcompetitive. The cellulase enzyme Cel7A is capable to break up this sugar chains, it consists of two parts, the binding module and the catalytic domain which are hold together by a linker peptide. One of the major research questions is to analyze the mechanical process how the cellulase enzyme accesses the cellulose fiber. There is evidence that the linker peptide shows a high flexibility and could be essential for the understanding of the cellulase dynamic. To guarantee statistical unbiased results multiple independent Brownian dynamics simulations are performed. The huge configuration space is discretized by applying different clustering approaches. A Markov state model (MSM) was used to analyze the dynamics of the system. The MSM description gives a mathematically rigorous approach to combine the statistical information of different independent simulations and to link the biological system with the theory of Markov chains. There is no clear experimental evidence in which order the different enzyme parts access the fiber or which fiber face the enzyme favors to split up the sugar chains. In the context of a MSM the probability for different docking conformations of the fiber are calculated to answer this questions and to identify hotspot regions on the fiber where the interaction with cellulase is favored. Ofir Alon (Physical Chemistry Institute, Prof. Dr. Lorenz S. Cederbaum): Quantum Dynamics of Correlated Bosonic Systems - The dynamics of correlated bosonic systems among which Bose-Einstein condensates in traps and in optical lattices has drawn much attention in the quantum-gas community. Whereas the two basic theoretical methods - Gross-Pitaevskii theory for general traps and Bose-Hubbard model for optical lattices - have gained enormous popularity and are much in use, there are increasingly mounting evidences as well as physical phenomena indicating that one should go beyond these approaches. In this project we employ the essentially-exact many-body propagation theory for interacting bosons developed in Heidelberg - the multiconfigurational time-dependent Hartree for bosons (MCTDHB) - via its parallel implementation to explore the dynamics of bosons in traps and in optical lattices beyond the available in the literature. The MCTDHB has been very successful in unveiling novel physical phenomena of both repulsive and attractive Bose gases and much more is anticipated to come. Michael Bach (Institut für Theoretische Physik, Prof. Dr. Dieter W. Heermann, IWR): Phase Transition of a Polymer System - This project is located in the area of polymer physics. The polymer of interest is a hyaloronan aggrecan complex, which is an essential part ofthe extracellular matrix. One really important task of this molecule is the protection of our cells from mechanical stress. This is the motivation for us to investigate polymer brushes, which consist of simplified hyaloronan aggrecan complexes. Especially we are interested in the different phases of the system, and the coupled phase transition. Robi Banerjee (Institut für Theoretische Astrophysik, Prof. Ralf Klessen) Star Cluster Formation with Mechanical Feedback - Outflows and jets are ubiquitous around young stellar objects. Whether the mechanical feedback from these outflows have a dynamical impact on the star forming region is still unclear. In this project we will study the impact from outflows and jets on the molecular cloud in which the new stars are formed. For this study we will use our modified version of the adaptive mesh refinement code FLASH which already comprises a model description of protostars (sink particles) and their mechanical feedback. Thomas Richter (Institut fuer Angewandte Mathematik, Rannacher, IWR): 3D flow simulations - Simulation of three dimensional fiuid-structure interaction problems with Finite Elements Roland Schulz (ORNL/UT, Jeremy Smith): INM - The Instantaneous Normal Mode (INM) theory predicts, that the diffusion constant is proportional to the number of diffusive modes. The diffusive modes are a subset of all modes with a negative eigenvalue of the Hessian matrix. This subset was computed with good agreement for simple liquids with different filtering methods. We evaluated those methods on a protein over a temperature range from 20-300K. As benchmark for the filtering methods, we compared the so computed diffusion constant with that computed from MSD. For the escape mode method we got a good agreement over two decades. This enables us, to compute temperature dependent dynamical properties of proteins from a few sampled configurations and are able to reproduce the dynamical transition.
Publications
- On the generic parallelisation of iterative solvers for the finite element method. Int. J. Computational Science and Engineering, 4(1):56-69, 2008
P. Bastian and M. Blatt
- C++ components describing parallel domain decomposition and communication. International Journal of Parallel, Emergent and Distributed Systems, 24(6):467-477, 2009
Markus Blatt and Peter Bastian
- The mechanism of photo-energy storage in the halorhodopsin chloride pump. J. Biol. Chem. 284, 13562-13569 (2009)
C. Pfisterer, A. Gruia et al.
- Use of mitochondrial and nuclear genes to infer the origin of two endemic pigeons from the Canary Islands. Journal of Ornithology 150:357-367, 2009
Javier Gonzalez, Guillermo Delgado Castro et al.
- Magnesium-Dependent Active-Site Conformational Selection in the Diels-Alderase Ribozyme. Journal of the American Chemical Society, 132, 12587-12596 (2010)
Berezniak, T. and Zahran, M. and Imhof, P.
- Mechanism of DNA recognition by the restriction enzyme EcoRV. J. Mol. Bio. 401 , 415-432 (2010)
Zahran, M., Daidone, I., Smith, J.C. and Imhof, P.
- The shape and flexibility of tropomyosin coiled-coils: implication for actin filament assembly and regulation. J. Mol. Biol. 395, 327-339 (2010)
X. Li, K.C. Holmes, W. Lehman et al.
