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Analyzing Photoactivation with Diffusion Models to Study Transport in the Endoplasmic Reticulum Network

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The Plant Endoplasmic Reticulum

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2772))

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Abstract

Photoactivation is a paradigm consisting in local molecular fluorescent activation by laser illumination in a chosen region (source) while measuring the concentration at a target region. Data-driven modeling is concerned with the following questions: how from the measurement in these two regions is it possible to infer the properties of molecular propagation? How is it possible to use such responses to infer motions occurring in networks such as the endoplasmic reticulum? In this book chapter, we shall review the data-driven analysis based on diffusion-transport models and numerical simulations to interpret the photoactivation dynamics and extract biophysical parameters. We will discuss modeling approaches to reconstruct local network properties from photoactivation transients.

Matteo Dora and Frédéric Paquin-Lefebvre equally contributed

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Acknowledgements

We thank Chris Obara for critical feedback on this manuscript. This project has received funding from the European Research Council (ERC) to D.H. under the European Union’s Horizon 2020 research and innovation program (grant agreement No. 882673). D.H. also gratefully acknowledges the support from the Agence Nationale de la Recherche via the grants ANR NEUC 00001 and ANR AstroXcite. F.P.-L. received funding from the Fondation ARC (grant No. ARCPDF12020020001505).

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Authors and Affiliations

  1. Applied Mathematics and Computational Biology, Ecole Normale Supérieure, Paris, France

    Matteo Dora, Frédéric Paquin-Lefebvre & David Holcman

  2. Churchill College, Cambridge University, Cambridge, UK

    David Holcman

Authors
  1. Matteo Dora
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  2. Frédéric Paquin-Lefebvre
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  3. David Holcman
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Editors and Affiliations

  1. Biological and Medical Sciences, Oxford Brookes University, Oxford, UK

    Verena Kriechbaumer

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© 2024 The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature

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Dora, M., Paquin-Lefebvre, F., Holcman, D. (2024). Analyzing Photoactivation with Diffusion Models to Study Transport in the Endoplasmic Reticulum Network. In: Kriechbaumer, V. (eds) The Plant Endoplasmic Reticulum. Methods in Molecular Biology, vol 2772. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-3710-4_31

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  • DOI: https://doi.org/10.1007/978-1-0716-3710-4_31

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-3709-8

  • Online ISBN: 978-1-0716-3710-4

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