Berlin 2015 – scientific programme

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BP: Fachverband Biologische Physik

BP 17: Posters: Protein structure and dynamics

BP 17.19: Poster

Monday, March 16, 2015, 17:30–19:30, Poster A

CUDA-accelerated FEM-BEM Simulations of Dielectric Relaxation Spectroscopy of solvated Proteins — •Stephan Kramer — Max-Planck-Institut f. biophysikalische Chemie, Am Faßberg 11, 37077 Göttingen

Dielectric relaxation spectroscopy of solvated ubiquitin [1] has shown the sensitivity of the direct current to conformational sampling. Experimentally, this is observed by the appearance of the so-called sub-β peak in the dielectric loss spectrum. A mechanistic explanation of this peak is that different numbers of ions are bound in the hydration shell of the protein, depending on its conformation. This changes the density of mobile ions, thus altering the direct current component. The sub-β peak can be quantified by a stochastic model considering the conformational dynamics as a simple 2-state, ratchet-like process coupled to a Fokker-Planck model for the mobile ions.

We extend the ion dynamics to the Poisson-Nernst-Planck equations in a finite domain with reactive boundaries modeling the setup of a dielectric relaxation spectroscopy experiment. The protein is an excluded volume for the ions. It is converted into a boundary condition for the mobile ions by means of an integral equation. The resulting boundary element problem is solved with CUDA using our SciPAL library [2]. The ion densities are computed from a finite element model. Our results confirm the theory of the origin of the sub-β peak.

[1] Ban et al. Angew. Chem. Int Ed., 50(48):11437-11440, 2011. [2] S. C. Kramer and J. Hagemann, ACM TOPC (to appear), https://code.google.com/p/scipal/