Dresden 2011 – scientific programme
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BP: Fachverband Biologische Physik
BP 4: DNA \& DNA Enzymes
BP 4.6: Talk
Monday, March 14, 2011, 15:45–16:00, ZEU 260
Development of an inter-nucleotide potential for DNA based on Density Functional theory — •Maria Fyta1,2, Greg Lakatos1, Pierfrancesco Rosini3, Amanda Peters1, Simone Melchionna1,4, and Efthimios Kaxiras1 — 1Department of Physics and School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, USA — 2Physics Department, Technical University of Munich, 85748 Garching, Germany — 3Laboratory for Multiscale Modeling of Materials, EPFL, Lausanne, Switzerland — 4Istituto Applicazioni Calcolo, CNR, Rome, Italy
The structural and dynamical properties of double stranded DNA (dsDNA) play a critical role in a range of fundamental biological and technological processes. These include DNA translocation through artificial or biological nanopores, the wrapping of DNA around histone proteins, and the use of DNA molecules as nanotethers in 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 dsDNA capable of reproducing the molecule's structural and dynamical properties on these length and time scales. 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 generated potential model will be capable to investigate the behavior of dsDNA in interesting biophysical processes.