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Auxin upstream pumping model

by Michael A. Guravage last modified Sep 13, 2011 02:53 PM

Description:

Plant organ patterning with directed auxin transport.

Detail Description:

This model demonstrates how to implement the traveling-wave hypothesis; a variant of the auxin upstream pumping hypothesis. It assumes a membrane bound matrix protein

Here is the equation which implements the auxin upstream pumping hyphothesis. PIN1 transports auxin actively to adjacent cells; a diffusion term is reponsible for downstream auxin transport. 

 

\frac{dA_i}{dt} = T_{active}\left(\frac{P_{ji} A_j}{k_a + A_j} - \frac{P_{ij} A_y}{k_a + Ai} \right) + T_{diffusive} \sum_j L_y (Aj -Ai)

 

where the sum is over all neighbor cells, A_i is the auxin concentration in cell i. P_{ij} and P_{ji} are the ammount of PIN1 in cell i pumping auxin into cell j and vice versa, and T_{active} and T_{diffusive} are active and passive transport coefficients respectively, and L_{ij} is the length of the wall between cell i and cell j.

For a complete description of the equations involved, and their corresponding implementation in C++ code, please refer to the section entitled 'Polar auxin transport' in 'Building simulation models of developing plant organs using Virtualleaf.'

The protocols are included with the VirtualLeaf framework. Each protocol occupies a unique revision in the mercurial source code repository, and is marked with a  mnemonic tag. Use mercurial's update command to move to the appropriate revision:

> cd virtualleaf
> hg update -r 'auxin upstream pumping'

 

The protocols are not included in the framework build process. To build and install our 'divide over arbitrary axis' model type:

> cd src/protocols
> make

 

 

Language: source code

Source: https://code.google.com/p/virtualleaf : auxin upstream pumping

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