On Estimation of a Viral Protein Diffusion Constant on the Curved Intracellular ER Surface

M. M. Knodel (), A. Nägel (), S. Reiter (), M. Rupp (), A. Vogel (), M. Lampe (), P. Targett-Adams (), E. Herrmann () and G. Wittum ()
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M. M. Knodel: Frankfurt University, Goethe-Center for Scientific Computing
M. Lampe: Medivir AB, Department of Biology
P. Targett-Adams: Medivir AB, Department of Biology
E. Herrmann: Goethe University Frankfurt, Department of Medicine

A chapter in High Performance Computing in Science and Engineering ’15, 2016, pp 641-657 from Springer

Abstract: Abstract Advanced simulations within biophysical applications ask for advanced algorithms and implementations which are running efficiently on massively parallel high performance computers. The software framework UG fulfills these preconditions. Therefore, we present insight into the experimental basics, the modelling and simulation details, and the biophysical meaning of the estimation of the diffusion constant of a major player in the replication of the genetic information of the Hepatitis C virus (HCV), namely the NS5A viral protein. NS5A movement is restricted to the surface of the Endoplasmatic Reticulum (ER, a medusa-hair like important cell compartment). Hence, the dynamics of NS5A are described by surface PDEs (sPDE) which mimic experimental FRAP (fluorescence recovery after photobleaching) time series data. The sPDE computations were performed with UG upon large unstructured grids representing realistic reconstructed ER surfaces. We explain the context of the parameter estimations which asked for a substantial amount of single sPDE evaluations which we performed on the HLRS Stuttgart Hermit and Hornet supercomputers for various experimental data sets and for various geometric setups. This enabled us to derive valid final values for the diffusion constant of NS5A on the ER surface. The estimated diffusion constant values are intended to enter spatio-temporal resolved models of HCV replication dynamics at a cellular level.

Keywords: Diffusion Constant; Time Step Size; Newton Step; Yellow Fever Virus; NS5A Protein (search for similar items in EconPapers)
Date: 2016
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Persistent link: https://EconPapers.repec.org/RePEc:spr:sprchp:978-3-319-24633-8_41

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DOI: 10.1007/978-3-319-24633-8_41

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