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--- examples:multiscale [16:23 18.08.2021] – Moved to GitLab Pages Diego Jahn
+++ examples:multiscale [17:19 18.08.2021] (current) – Moved to GitLab Pages Diego Jahn
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-~~NOTOC~~
-===== Multiscale models =====
-==== Dictyostelium ====
-[{{ :examples:example-dicty.png?direct&200|Aggregation of amoebas through chemotaxis towards waves of cAMP.}}]
-{{vimeo>57214708?small }}
-=== Introduction ===
-This model show chemotactic aggregation of Dictyostelium. It was constructed by students attending the [[http://www.math.tu-dresden.de/essim2012/|ECMI modeling week 2012]] in Dresden.
-=== Model description ===
-This model shows an interesting coupling between CPM cells and reaction-diffusion PDE. Cell state depends on the perceived concentration of cAMP, and determines whether a cell produces cAMP and whether it performs chemotaxis. The PDE is governed by a Fitzhugh-Nagumo-like model of an excitable medium, which causes traveling waves upon excitation. Chemotaxis through those waves causes cell aggregation.
-Background colors indicate the cAMP concentration. Cells are color-coded according to their phase: excitable/resting (yellow), excited/chemotactic (green), refractory/resting (red).
-=== Model ===
-<code xml |h Dictyostelium.xml |h>
-extern>
-http://imc.zih.tu-dresden.de/morpheus/examples/Multiscale/Dictyostelium.xml
-</code>
-In Morpheus GUI: ''Examples -> Multiscale -> Dictyostelium.xml''
-=== References ===
-  * Rost F, Quintero A, Myllykoski M, Igolkina A, Rohde O’Sullivan Freltoft A, Dixit N, [[http://www.mafy.lut.fi/EcmiNL/issues.php?action=viewart&ID=280|Morphogenesis and Dynamics of Multicellular Systems]]. //ECMI Newsletter//, 52, 2012.
-  * Savill N and Hogeweg P. [[ http://dx.doi.org/10.1006/jtbi.1996.0237|Modelling morphogenesis: from single cells to crawling slugs]]. //J. Theor. Biol//, 184:229–235, 1997.
-----
-==== MembraneProperties: Cell polarization and chemotaxis ====
-//Note: MembraneProperties are not available in public version of Morpheus.//
-[{{ :examples:cellpolarity0060.png?direct&200|Cell dynamically re-polarizes in response to switching external gradient}}]
-{{vimeo>60636346?small }}
-=== Introduction ===
-This model of cell polarity shows the coupling of three model formalisms:
-  * A cellular Potts model
-  * A PDE model, solved on the membrane of the cell
-  * And an external gradient.
-The cell membrane polarizes in response to the external gradient. Chemotactic cell motility depends on the polarity of the cell and the external gradient.
-=== Description ===
-This example implements two models of cell polarity: Meinhardt's substrate-depletion model and Edelstein-Keshet's wave-pinning model. The user can switch polarity model by ''Disabling''/''Enabling'' the relevant ''System''.
-The model defines a one-dimensional reaction-diffusion system (''MembraneProperty'') representing membrane-bound molecules, and is mapped to a cellular Potts model defining a discrete shaped cell. An external gradient, specified in a ''PDE'', provides a signal for the polarization of the cell. In turn, the polarity of the cell influences its ''chemotaxic'' behavior.
-After a switch in direction of the gradient, the cell re-polarizes in the new direction and starts to move up the gradient, iff the wave pinning model has been selected.
-=== Model ===
-<code xml |h CellPolarity.xml |h>
-extern>
-http://imc.zih.tu-dresden.de/morpheus/examples/Multiscale/CellPolarity.xml
-</code>
-//Note: This model is not available in Morpheus GUI.//