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3D Visualization of Concentrations from Stochastic Agent-based Signal Transduction Simulations
VISUS - Visualization Research Center, Universität Stuttgart, Germany.ORCID iD: 0000-0003-1511-5006
Institute of Biochemical Engineering and Center Systems Biology, Universität Stuttgart, Germany.
Institute of Biochemical Engineering and Center Systems Biology, Universität Stuttgart, Germany.
VISUS - Visualization Research Center, Universität Stuttgart, Germany.
2010 (English)In: Biomedical Imaging: From Nano to Macro, 2010 IEEE International Symposium on: From Nano to Macro (ISBI 2010), IEEE, 2010, p. 1301-1304Conference paper, Published paper (Refereed)
Abstract [en]

Cellular signal transduction involves a transport step from the plasma membrane towards the nucleus, during which the signaling molecules are partly deactivated in control loops. This leads to a gradient in the concentration of active signaling molecules. The low number of molecules introduces spatio-temporal fluctuations and the asymmetric cellular architecture further increases the complexity. We propose a technique to represent this pattern in a continuous three-dimensional concentration map. The local concentration is computed and visualized with volume rendering techniques at interactive frame rates and is therefore well-suited for time-dependent data. Our approach allows the transition from the nano-scale of single and discrete signaling proteins to a continuous signal on the cell level. In the application context of this paper, we employ an agent-based Monte Carlo simulation to calculate the actual particle positions depending on reaction and transport parameters in the cell. The applicability of the proposed technique is demonstrated by an investigation of the effects of different transport parameters in Mitogen-activated protein kinase (MAPK) signaling.

Place, publisher, year, edition, pages
IEEE, 2010. p. 1301-1304
Series
IEEE International Symposium on Biomedical Imaging, ISSN 1945-7928, E-ISSN 1945-8452
Keywords [en]
3D visualization, active signaling molecule concentration, agent-based Monte Carlo simulation, biochemistry, biology computing, biomembrane transport, Cell SignalTransduction, Nucleus, cellular biophysics, cellular signal transduction, discrete signaling proteins, Mitogen-activated protein kinase signaling, molecular biophysics, Monte Carlo methods, plasma membrane, proteins, spatio-temporal fluctuations, stochastic agent-based signal transduction simulation, stochastic processes
National Category
Media and Communication Technology
Identifiers
URN: urn:nbn:se:liu:diva-143700DOI: 10.1109/ISBI.2010.5490235ISI: 000287997400331ISBN: 978-1-4244-4125-9 (print)ISBN: 978-1-4244-4126-6 (electronic)OAI: oai:DiVA.org:liu-143700DiVA, id: diva2:1166275
Conference
2010 IEEE International Symposium on Biomedical Imaging,14-17 April 2010, Rotterdam, Netherlands
Available from: 2017-12-14 Created: 2017-12-14 Last updated: 2018-01-13

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CiteExportLink to record
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Citation style
  • apa
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