Koordination: D.W. Heermann M. Salmhofer, U. SchwarzDonnerstag 14-16 Uhr
Institut für Theoretische Physik
Seminarraum Philosophenweg 19
- Do 04.11.10 14 Uhr c.t.
Ralf Blossey (Interdisciplinary Research Institute (IRI), Villeneuve d'Ascq, France)
Histone modifications and chromatin remodeling : a kinetic proofreading model for transcription initiation in eukaryotes
In prokaryotes (bacteria), gene transcription is initiated by the diffusion of transcription factors and their binding to regulatory sites. In eukaryotes, this process is hindered: in the nuclei of eukaryotic cells, DNA forms the dynamic structure of chromatin based on nucleosomes, DNA-histone protein complexes. Therefore, chromatin structure must be « remodeled » in order to allow transcription to start. A model is presented which unifies two known key features involved in transcription initiation: histone tail modifications and the ATP-dependent remodeling of chromatin which together allow for a kinetic proofreading scheme (Blossey and Schiessel, HFSP Journal 2008). The recognition of histone tail modifications by recognition domains has been modeled by a protein docking approach, lending quantitative support to the kinetic proofreading model of transcription initiation in eukaryotes. Further steps required to validate the model are discussed.
- Do 18.11.10 14 Uhr c.t.
Klaus Kroy (Leipzig)
Hot Brownian Motion
I will discuss the Markovian description for the non-equilibrium Brownian motion of a heated particle in a simple solvent with a temperature-dependent viscosity. The analytical results for the generalized fluctuation-dissipation and Stokes-Einstein relations compare favorably with measurements of laser-heated gold nano-particles and provide a practical rational basis for emerging photothermal tracer and nano-particle trapping and tracking techniques.
- Do 25.11.10 14 Uhr c.t.
Ulrich Gerland (LMU)
Statistical Physics of Nucleosome Positioning
In organisms ranging from Baker's yeast to Human, the genomic DNA is packaged into chromatin via the formation of nucleosomes. While this packaging renders a genome compact and manageable, the genetic information must also be accessible to proteins for read out and processing. A thorough understanding of this tradeoff has been an important goal in biological and biophysical research ever since the discovery of the nucleosome. Today, experiments ranging from single-molecule studies of nucleosomes to whole-genome mapping of nucleosome positions supply a large knowledge base. This data poses a number of interesting quantitative questions, some of which can be addressed within simple models from statistical physics. For instance, the distribution of nucleosomes along the genome can be described and interpreted using an interacting gas model in one dimension, and fluctuation-induced unwrapping of nucleosomal DNA leads to an interesting stochastic process. I will talk about both of these examples, as well as their connection.
- Do 02.12.10 14 Uhr c.t.
Elmar Bittner (Heidelberg)
Parallel tempering algorithm for computer simulations of critical phenomena
In finite-size scaling analyses of Monte Carlo simulations of second-order phase transitions one often needs an extended temperature range around the critical point. By combining the replica-exchange algorithm with an adaptive routine to find the range of interest, we introduce a flexible and powerful method for systematic investigations of critical phenomena.
- Do 09.12.10 14 Uhr c.t.
Findet zusammen mit BioRegio e.V statt.
- Do 16.12.10 14 Uhr c.t.
Timm Krüger (Max-Planck-Institut für Eisenforschung, Düsseldorf
Mesoscopic Modeling of red blood cell dynamics
Understanding the rheology of blood has been a challenge for many decades. Due to the high volume fraction (45%) of red blood cells, their mechanical properties strongly affect the flow behavior, even on larger scales. A numerical model for particulate blood flow is presented. Some applications are highlighted, e.g., the motion of individual cells in complex geometries and the collective motion of cells in simple shear flow.
- Do 13.01.10 14 Uhr c.t.
Joerg Stelling (ETH Zürich)
Systems approaches to biological complexity
Biological cells are characterized by a high degree of complexity in terms of components and (nonlinear) interactions. Reverse- and forward engineering of biological systems require sufficiently detailed mathematical models. However, incomplete and primarily qualitative biological knowledge and data on parts and interactions, as well as insufficient theoretical methods for analyzing the systems affect the endeavor. Here, we delineate how analysis can proceed from well-characterized systems invariants to complex representations of cellular dynamics, and the associated challenges for systems theory and methods. Specific examples will include (i) methods for structure-based to infer potential network behaviors and how these are controlled, and (ii) ensemble modeling methods to identify and discriminate detailed hypotheses on cellular information processing systems, and (iii) structurally simplified models to approach the impact of space on cellular signaling processes. In perspective, progress towards an understanding of highly integrated dynamic systems in biology could provide valuable blueprints for the analysis (and design) of complex systems in other domains.
- Do 27.01.10 14 Uhr c.t.
Helmut Katzgraber (ETH Zürich and Texas A&M University)
Do spin glasses order in a field?
Spin glasses are paradigmatic models that deliver concepts relevant for a variety of systems. However, despite ongoing research spanning several decades in the area of glassy systems, there remain many fundamental open questions. Rigorous analytical results are difficult to obtain for spin-glass models, in particular for realistic short-range systems. Therefore large-scale numerical simulations are the tool of choice. Concepts from the solution of the mean-field model, such as ergodicity breaking, aging, ultrametricity, and the existence of an instability line at finite magnetic fields known as the Almeida-Thouless line, have been applied to realistic short-range spin-glass models as well as to fields as diverse as structural biology, geology, computer science and even financial analysis. After presenting an overview of the properties of spin glasses, I discuss recent results on the existence of a spin-glass state in an external field. Our results show that the spin-glass state is not stable in a field for short-range systems below the upper critical dimension.
Work done in collaboration with Derek Larson (Natl. Univ. of Taiwan) and A. Peter Young (UC Santa Cruz).