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; G. Wittum

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

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, G. Wittum

^*Corresponding author for this work

Research output: Chapter in Book/Report/Conference proceeding › Chapter › peer-review

5 Scopus citations

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.

Original language	English (US)
Title of host publication	High Performance Computing in Science and Engineering '15
Subtitle of host publication	Transactions of the High Performance Computing Center, Stuttgart (HLRS) 2015
Publisher	Springer International Publishing
Pages	641-657
Number of pages	17
ISBN (Electronic)	9783319246338
ISBN (Print)	9783319246314
DOIs	https://doi.org/10.1007/978-3-319-24633-8_41
State	Published - Jan 1 2016
Externally published	Yes

ASJC Scopus subject areas

General Computer Science
General Physics and Astronomy
General Mathematics
General Chemistry

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

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

Cite this

Knodel, M. M., Nägel, A., Reiter, S., Rupp, M., Vogel, A., Lampe, M., Targett-Adams, P., Herrmann, E., & Wittum, G. (2016). On estimation of a viral protein diffusion constant on the curved intracellular ER surface. In High Performance Computing in Science and Engineering '15: Transactions of the High Performance Computing Center, Stuttgart (HLRS) 2015 (pp. 641-657). Springer International Publishing. https://doi.org/10.1007/978-3-319-24633-8_41

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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.",

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Knodel, MM, Nägel, A, Reiter, S, Rupp, M, Vogel, A, Lampe, M, Targett-Adams, P, Herrmann, E & Wittum, G 2016, On estimation of a viral protein diffusion constant on the curved intracellular ER surface. in High Performance Computing in Science and Engineering '15: Transactions of the High Performance Computing Center, Stuttgart (HLRS) 2015. Springer International Publishing, pp. 641-657. https://doi.org/10.1007/978-3-319-24633-8_41

On estimation of a viral protein diffusion constant on the curved intracellular ER surface. / Knodel, M. M.; Nägel, A.; Reiter, S. et al.
High Performance Computing in Science and Engineering '15: Transactions of the High Performance Computing Center, Stuttgart (HLRS) 2015. Springer International Publishing, 2016. p. 641-657.

Research output: Chapter in Book/Report/Conference proceeding › Chapter › peer-review

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AU - Nägel, A.

AU - Reiter, S.

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AU - Lampe, M.

AU - Targett-Adams, P.

AU - Herrmann, E.

AU - Wittum, G.

PY - 2016/1/1

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AB - 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.

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Knodel MM, Nägel A, Reiter S, Rupp M, Vogel A, Lampe M et al. On estimation of a viral protein diffusion constant on the curved intracellular ER surface. In High Performance Computing in Science and Engineering '15: Transactions of the High Performance Computing Center, Stuttgart (HLRS) 2015. Springer International Publishing. 2016. p. 641-657 doi: 10.1007/978-3-319-24633-8_41

On estimation of a viral protein diffusion constant on the curved intracellular ER surface

Abstract

ASJC Scopus subject areas

UN SDGs

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