Dresden 2009 – wissenschaftliches Programm
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BP: Fachverband Biologische Physik
BP 20: DNA, RNA and Chromatin
BP 20.7: Vortrag
Donnerstag, 26. März 2009, 16:00–16:15, HÜL 186
An inter-nucleotide potential for DNA: atomistic and coarse-grained simulations — •Maria Fyta1,2, Greg Lakatos1, Simone Melchionna1, and Efthimios Kaxiras1 — 1Department of Physics and School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, USA — 2Present address: Physics Department, Technical University of Munich, Germany
The structural and dynamical properties of double stranded DNA play a critical role in range of fundamental biological and technological processes. Such processes include DNA translocation through both artificial and nuclear nanopores, the wrapping of DNA around histone proteins, and the use of DNA molecules as nanotethers in a variety of nanoscale devices. To understand the behavior of DNA in these contexts, it is desirable to have a computational model capable of treating oligomers with hundreds to thousands of base pairs, on time scales of microseconds or longer. Utilizing accurate density-functional electronic structure techniques, we are developing a coarse-grained molecular model of double stranded DNA (dsDNA) capable of reproducing the molecule’s structural and dynamical properties on these length and time scales. Initial validations of the model indicate that it reproduces a number of experimentally measured structural features of DNA, including the persistence length under physiologic conditions. The model resulting from this study will be used to investigate the behavior of dsDNA during nanopore translocation, and the response of dsDNA to mechanical loads.