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Image-based Systems Biology: Modeling and Simulation in Image-derived Geometries

Biological systems differ from engineering systems in a number of ways. Arguably the most evident is the geometric complexity and diversity of biological shapes. These shapes define the environment in which biochemical and biophysical processes take place. Moreover, the complex and dynamic shapes of biological entities often have functional relevance themselves. We model biological systems from images where their shapes are visible. Extracting the true geometries and their dynamics from images allows us to build realistic models that take shape complexity into account. We combine image processing with particle-based simulations in order to simulate dynamic processes such as diffusion, flows, and biochemical reactions directly in the image-derived geometries. Particle methods offer a unique and versatile numerical simulation framework with accuracy and computational cost that are not hampered by shape complexity. We demonstrate this on examples ranging from diffusion in the Endoplasmic Reticulum to brain electromagnetism and Drosophila embryo development.

Type of Seminar:
IfA BISON Seminar
Prof Ivo F. Sbalzarini
MOSAIC Group, ETH Zurich, Switzerland
Oct 18, 2011   13:30

Contact Person:

Elias August
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