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  • 2017

  • Funder: National Institutes of Health Project Code: 1R01DK092235-01A1
    Funder Contribution: 526,074 USD
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  • Funder: UK Research and Innovation Project Code: BBS/E/J/000C0645
    Funder Contribution: 951,829 GBP

    The core research focuses on developmental processes through a unique style of multilevel-modelling. By integrating gene regulatory networks and biophysical properties of single cells, through cell deformation, motion and tissue level properties, we study emerging phenomena on the level of multiple cells, organs, as well as the development of whole organisms. To do so, we are coupling the Cellular Potts Model, a model formalism that is very powerful for describing the biophysics of cell dynamics, to gene regulations and metabolics. Mathematical and computational techniques are applied to study the behaviour that emerges from the model at different intermediate levels of organisation, as well as at the level of the whole organism. It provides a framework in which experimental findings related to metabolism and gene regulation can be linked to the observed development, from the cellular level to the level of the whole organism. The focus is towards developmental mechanisms in plants, but with a strong emphasis on the similarities and differences these exhibit to animal development, to overcome the strong segregation that prevails in scientific literature between plant and animal studies that obscures the identification of striking similarities and conserved core mechanisms. Integrated studies of developmental biology requires the cycling between modelling, imaging and experiments. We are developing methods to derive cell shape and time dynamics from (time series of) (3D) images, as well as ways to determine and correct for biases in imaging data, and to extend this by generating through the image analysis substrates for in silico studies. This strategy allows us to test proposed gene regulatory networks, transport mechanisms, etc, using computational techniques and realistic, experimentally measured cells shapes and tissue organisations. To finish the loop, the modelling insights are then used to further steer the experiments.

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  • Funder: National Institutes of Health Project Code: 1R13HD080904-01
    Funder Contribution: 30,000 USD
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  • Funder: National Institutes of Health Project Code: 5R01GM065318-13
    Funder Contribution: 356,449 USD
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  • Funder: Swiss National Science Foundation Project Code: 153217
    Funder Contribution: 329,055
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  • Funder: Swiss National Science Foundation Project Code: 160290
    Funder Contribution: 310,000
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  • Funder: National Institutes of Health Project Code: 5R01CA120409-07
    Funder Contribution: 254,176 USD
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  • Funder: National Science Foundation Project Code: 1406689
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  • Funder: European Commission Project Code: 658437
    Overall Budget: 195,455 EURFunder Contribution: 195,455 EUR

    A moving contact line (MCL) is a moving line of intersection between a fluid/fluid interface and a solid wall. MCLs are central to a wide range of flows in nature and industry, however, their modeling has been a classical difficulty, especially under non-isothermal conditions. The project will tackle this challenge and we will develop a novel computational model enabling simulations of non-isothermal flows involving MCLs with unprecedented efficiency. The model borrows the idea from the large eddy simulation in turbulence modeling; it will resolve the macroscale flows only while model the effect of MCLs using non-isothermal hydrodynamic theories, which will also be developed in the present project. We expect that the model can lead to a reduction of computational effort by nine orders of magnitude for three-dimensional flows, compared with direct numerical simulations using a uniform grid, and it will therefore enable affordable simulations of practical flows in industry.

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  • Funder: National Institutes of Health Project Code: 5T32NR007066-23
    Funder Contribution: 368,323 USD
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85,644 Projects
  • Funder: National Institutes of Health Project Code: 1R01DK092235-01A1
    Funder Contribution: 526,074 USD
    more_vert
  • Funder: UK Research and Innovation Project Code: BBS/E/J/000C0645
    Funder Contribution: 951,829 GBP

    The core research focuses on developmental processes through a unique style of multilevel-modelling. By integrating gene regulatory networks and biophysical properties of single cells, through cell deformation, motion and tissue level properties, we study emerging phenomena on the level of multiple cells, organs, as well as the development of whole organisms. To do so, we are coupling the Cellular Potts Model, a model formalism that is very powerful for describing the biophysics of cell dynamics, to gene regulations and metabolics. Mathematical and computational techniques are applied to study the behaviour that emerges from the model at different intermediate levels of organisation, as well as at the level of the whole organism. It provides a framework in which experimental findings related to metabolism and gene regulation can be linked to the observed development, from the cellular level to the level of the whole organism. The focus is towards developmental mechanisms in plants, but with a strong emphasis on the similarities and differences these exhibit to animal development, to overcome the strong segregation that prevails in scientific literature between plant and animal studies that obscures the identification of striking similarities and conserved core mechanisms. Integrated studies of developmental biology requires the cycling between modelling, imaging and experiments. We are developing methods to derive cell shape and time dynamics from (time series of) (3D) images, as well as ways to determine and correct for biases in imaging data, and to extend this by generating through the image analysis substrates for in silico studies. This strategy allows us to test proposed gene regulatory networks, transport mechanisms, etc, using computational techniques and realistic, experimentally measured cells shapes and tissue organisations. To finish the loop, the modelling insights are then used to further steer the experiments.

    more_vert
  • Funder: National Institutes of Health Project Code: 1R13HD080904-01
    Funder Contribution: 30,000 USD
    more_vert
  • Funder: National Institutes of Health Project Code: 5R01GM065318-13
    Funder Contribution: 356,449 USD
    more_vert
  • Funder: Swiss National Science Foundation Project Code: 153217
    Funder Contribution: 329,055
    more_vert
  • Funder: Swiss National Science Foundation Project Code: 160290
    Funder Contribution: 310,000
    more_vert
  • Funder: National Institutes of Health Project Code: 5R01CA120409-07
    Funder Contribution: 254,176 USD
    more_vert
  • Funder: National Science Foundation Project Code: 1406689
    more_vert
  • Funder: European Commission Project Code: 658437
    Overall Budget: 195,455 EURFunder Contribution: 195,455 EUR

    A moving contact line (MCL) is a moving line of intersection between a fluid/fluid interface and a solid wall. MCLs are central to a wide range of flows in nature and industry, however, their modeling has been a classical difficulty, especially under non-isothermal conditions. The project will tackle this challenge and we will develop a novel computational model enabling simulations of non-isothermal flows involving MCLs with unprecedented efficiency. The model borrows the idea from the large eddy simulation in turbulence modeling; it will resolve the macroscale flows only while model the effect of MCLs using non-isothermal hydrodynamic theories, which will also be developed in the present project. We expect that the model can lead to a reduction of computational effort by nine orders of magnitude for three-dimensional flows, compared with direct numerical simulations using a uniform grid, and it will therefore enable affordable simulations of practical flows in industry.

    more_vert
  • Funder: National Institutes of Health Project Code: 5T32NR007066-23
    Funder Contribution: 368,323 USD
    more_vert