Public Methods : Evaporate & Diffuse in Grid Type (Ref: Innate Immune Response Model)

[Rupinder Paul]

Hi ,

I am trying to understand significance of Evaporate & Diffuse methods
in a *biological model* such as in Innate Immune Response.
From the documentation I understand Evaporate function- multiplies all
grid values with a given number, thats about it.
But for diffuse , I am not sure what its doing...doc mentions
diffusion operation on a grid; diffusion of what?

Let me rephrase, I am tinkering with Innate Immune Response Model,
trying to observe different behaviors when varying Evaporate &
diffusion Coeff. - In fact I do observer clear deviations from the
default behavior.And I have three set of questions:

A . I began wondering what the diffusion & evaporate coeff for each
data layer (all the patch variables involved in the model) do to the
BIOLOGY of MODEL . ??

B . I some what understand what "Evaporate" method is doing,
multiplying all values of a given grid with a number, which in turn
effects the calculations of each formula the grid global variable is
involved with. Am I correct?

C . But then I am not so sure about diffuse. ? then I questions how
is it effecting the model behavior

regards
Rupen

[Dutta-Moscato, Joyeeta]

Hi Rupen,

Generally speaking, 'evaporate' and 'diffuse' both operate on diffusible products, such as cytokines and hormones. 'evaporate' simulates the degradation of the product, while 'diffuse' simulates its spread. The function 'diffuse cytokine 0.5' tells each patch to keep 50% of its own cytokine value, and divide the other 50% equally between its neighbors. So, if you were to change the diffusion coefficent of a product, you would change its chemotactic and reactive influence on other substrates, cells or receptors.

Does that help?

Joyeeta Dutta-Moscato, MS
Computational Specialist, Dept. of Surgery
Center for Inflammation and Regenerative Modeling
McGowan Institute
University of Pittsburgh
450 Technology Drive, Suite 300
Pittsburgh, PA 15219
www.mirm.pitt.edu/cirm
________________________________________
From: spark-us...@googlegroups.com [spark-us...@googlegroups.com] On Behalf Of Rupinder Paul [rupen...@gmail.com]
Sent: Monday, March 29, 2010 6:04 PM
To: SPARK Users Group
Subject: Public Methods : Evaporate & Diffuse in Grid Type (Ref: Innate Immune Response Model)

Hi ,

regards
Rupen

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[Rupinder Paul]

okay..thank you Joyeeta

 

regards

Rupen

[Rupinder Paul]

Hi,

I wanted to confirm a particular scenario for diffuse function in
SPARK

If I were to say,

diffuse cytokine 0

then, would it make value of cytokine 0 and provide/diffuse nothing to
neighboring cells
or the value of that cytokine remains the same that is it would keep
100% of itself and give 0% to others

regards
Rupen


On Mar 30, 10:04 am, "Dutta-Moscato, Joyeeta" <duttamosca...@upmc.edu>
wrote:

> Hi Rupen,
>
> Generally speaking, 'evaporate' and 'diffuse' both operate on diffusible products, such as cytokines and hormones.  'evaporate' simulates the degradation of the product, while 'diffuse' simulates its spread.  The function 'diffuse cytokine 0.5' tells each patch to keep 50% of its own cytokine value, and divide the other 50% equally between its neighbors.  So, if you were to change the diffusion coefficent of a product, you would change its chemotactic and reactive influence on other substrates, cells or receptors.
>
> Does that help?
>
> Joyeeta Dutta-Moscato, MS
> Computational Specialist, Dept. of Surgery
> Center for Inflammation and Regenerative Modeling
> McGowan Institute
> University of Pittsburgh
> 450 Technology Drive, Suite 300
> Pittsburgh, PA 15219www.mirm.pitt.edu/cirm
> ________________________________________

> From: spark-us...@googlegroups.com [spark-us...@googlegroups.com] On Behalf Of Rupinder Paul [rupen.p...@gmail.com]

[Alexey]

Hi Rupen,

Everything will be as you described in the second scenario: all values
of cytokine will be unchanged.

Best,
Alexey