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Using step function in kinetic reaction simulation

Pattamon Teerapanich
Hi

I am trying to simulate the kinetic reaction of biomolecule interaction in fludic channel expecting to have association and dissociation phase (concentration of complex versus time) in the same curve. I knew that it is possible to use step function or smoothed Heaviside step function from COMSOL in order to change the concentration of analyte species at the inlet from C=x mol/m3 to C=0 mol/m3 at a certain time. I have no idea how to find this function and what kind of variables I need to defind. Anyone has any experience on this?

Regards,

Pattamon

5 Replies Last Post Jan 29, 2013, 4:01 AM EST
Posted: 5 years ago Jan 25, 2013, 7:38 PM EST
Hi

in v4 you find these under root-Globa-Definitions, or better: Model-Definitions-Functions, use the dynamic doc and search the HTML or PDF doc

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Good luck
Ivar
Hi in v4 you find these under root-Globa-Definitions, or better: Model-Definitions-Functions, use the dynamic doc and search the HTML or PDF doc -- Good luck Ivar

Pattamon Teerapanich
Posted: 5 years ago Jan 28, 2013, 9:21 AM EST
Hi,

I have tried to put the step function where I want to change the inlet concentration from c0 to 0 at time = 400s.
I defined the step function for concentration in the variables. It didn't not work for now. I guess my function is not correct or I need to add something more. I also attached my short simulation model here.

Thank you for your advice.

Pattamon
Hi, I have tried to put the step function where I want to change the inlet concentration from c0 to 0 at time = 400s. I defined the step function for concentration in the variables. It didn't not work for now. I guess my function is not correct or I need to add something more. I also attached my short simulation model here. Thank you for your advice. Pattamon


Posted: 5 years ago Jan 28, 2013, 3:12 PM EST
Hi

first of all your shape is very thin, with only 1 element across you do not resolve a lot, try to scale the vertical axis by i.e 100 in the mesh advanced tab.

Then your process is over in 4 seconds, your solver steps seem to be far too long, what about cutting your rectangle with a layer (geometry tab) at te half height of 0.3 um, then solve and look at the concentration along this central line in a line plot

--
Good luck
Ivar
Hi first of all your shape is very thin, with only 1 element across you do not resolve a lot, try to scale the vertical axis by i.e 100 in the mesh advanced tab. Then your process is over in 4 seconds, your solver steps seem to be far too long, what about cutting your rectangle with a layer (geometry tab) at te half height of 0.3 um, then solve and look at the concentration along this central line in a line plot -- Good luck Ivar

Magnus Ringh COMSOL Employee
Posted: 5 years ago Jan 29, 2013, 2:57 AM EST
Hi,

The step function uses the concentration as the input argument (the switch), but that should be the time t. Also the step amplitude is the concentration c0, so I don't see why that value is multiplied with the step output in the variable intl: c0*step1((c0-0)[m^3/mol])

I think that you should use:

step1(t[1/s])[mol/m^3]

where "[1/s]" is used to make the argument unitless and the unit of the output is mol/m^3 for a concentration.

Also, perhaps the initial value should be c0 rather than 0? Now the initial value and the boundary condition for the concentration don't match at the start of the simulation.

Best regards,
Magnus Ringh, COMSOL
Hi, The step function uses the concentration as the input argument (the switch), but that should be the time t. Also the step amplitude is the concentration c0, so I don't see why that value is multiplied with the step output in the variable intl: c0*step1((c0-0)[m^3/mol]) I think that you should use: step1(t[1/s])[mol/m^3] where "[1/s]" is used to make the argument unitless and the unit of the output is mol/m^3 for a concentration. Also, perhaps the initial value should be c0 rather than 0? Now the initial value and the boundary condition for the concentration don't match at the start of the simulation. Best regards, Magnus Ringh, COMSOL

Pattamon Teerapanich
Posted: 5 years ago Jan 29, 2013, 4:01 AM EST
Hi

Thank you so much for all advices. It works now :)

Best Regards,

Pattamon
Hi Thank you so much for all advices. It works now :) Best Regards, Pattamon

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