We acknowledge the following funding:
SFB 1027: "Physical modeling of non-equilibrium processes in biological systems"
Gene expression in all biological cells is tightly regulated by the binding of transcription factors and by epigenetic modifications of the DNA. Importantly, gene expression and cell differentiation or cell reprogramming are triggered by suitable stimuli in a stochastic manner. Here, atomistic biomolecular simulations and coarse-grained Brownian dynamics simulations will be used to study the binding processes governing gene expression in the E.coli pap operon that is being studied experimentally in project C1. A second part of the project involves stochastic dynamics simulations to model state transitions of the gene-regulatory network centered on the pluripotency factors Oct4, Nanog and Sox2. In collaboration with project C2, we will characterize how dynamic changes of transcription factor concentrations and DNA methylation levels affect cell differentiation during the development of the early mouse embryo until the 32-cell stage.
Graduiertenkolleg 1276: "Strukturbildung und Transport in komplexen Systemen"
Within the post graduate program the research group Helms utilizes computer simulations to study the dynamics and energetics of individual and interacting proteins, as well as their interaction with lipid bilayers. Besides using atomistic molecular dynamics simulations, we study model systems using effective coarse grained potentials where individual beads represent single amino acids or even entire proteins. When stimulating protein-protein interactions or interactions of proteins with membranes, the proteins are typically modelled as rigid bodies and their brownian motion is studied under the influence of external forces.
Pacific Northwest National Laboratory: Grand Challenge Project
William R. Wiley Environmental Molecular Sciences Laboratory (EMSL):
"The Molecular Science Computing Facility annually solicits proposals for allocations of computer time for Computational Grand Challenge Applications (CGCA) projects in environmental molecular science basic and applied research areas that address the environmental problems and research needs facing the U.S. Department of Energy (DOE) and the nation."
The Molecular Science Computing Facility of the Environmental Molecular Sciences Laboratory funds our joint Computational Grand Challenge Project "Complex Enzymatic Reactions"