Single-Cell Biophysics: Measurement, Modulation, and Modeling

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Single-Cell Biophysics: Measurement, Modulation, and Modeling Poster Abstracts
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1-POS Board 1
Modelling Intracellular Transport in Realistic Environments
Vesa Aho1, Markko Myllys 1, Thomas Kühn2,3 , Jussi Timonen1, Keijo Mattila1,4, Carolyn A.
Larabell5,6, Maija Vihinen-Ranta1.
1University of Jyväskylä, Jyväskylä, Finland, 4Tampere University of Technology, Tampere,
Finland, 2University of Eastern Finland, Kuopio, Finland, 5University of California, San
Francisco, CA, USA, 6Lawrence Berkeley National Laboratory, Berkeley, CA, USA.3Finnish
Meteorological Institute, Kuopio, Finland,
The environment inside a cell is highly complex including, e.g., the chromatin network and
membrane structures. In order to realistically model intracellular transport, the essential features
of this environment must be captured and incorporated into a model. Here we describe our recent
studies in computational modelling of intracellular transport utilizing realistic environments
reconstructed from images obtained with microscopy methods. We first present our research of
modelling diffusion through the nuclear envelope [1]. In this study the permeability of the
nuclear envelope to a fluorescent molecule is determined by comparing simulated changes in
fluorophore distribution to changes measured in a fluorescence microscopy experiment.
Secondly, we present our modelling results for the diffusive motion of herpes simplex virus 1
capsids towards the nuclear envelope through the chromatin network that is characterized using
soft x-ray tomography imaging [2,3]. In conclusion, we show that simulating the motion of
particles in the reconstructions of their actual environments allows us to gain new insights into
intracellular transport phenomena.
[1] Aho, V., K. Mattila, T. Kühn, P. Kekäläinen, O. Pulkkinen, R. Brondani Minussi, M.
Vihinen-Ranta, and J. Timonen. 2016. Diffusion through thin membranes: Modeling across
scales. Phys. Rev. E. 93: 043309
[2] Myllys, M., V. Ruokolainen, V. Aho, E. A. Smith, S. Hakanen, P. Peri, A. Salvetti, J.
Timonen, V. Hukkanen, C. A. Larabell, and M. Vihinen-Ranta. 2016. Herpes simplex virus 1
induces egress channels through marginalized host chromatin. Sci. Rep. 6:28844
[3] Aho, V., M. Myllys, V. Ruokolainen, S. Hakanen, E. Mäntylä, J. Virtanen, V. Hukkanen, T.
Kühn, J. Timonen, K. Mattila, C. A. Larabell, and M. Vihinen-Ranta. 2017. Chromatin
organization regulates viral egress dynamics. Submitted for publication in Scientific Reports.