Hello,
I am not making much progress on my own, so I figured that I would ask. I need to simulate the motion of course grain DNA in a 10-20 nm channel. The DNA will be driven my electrophoresis as well as under the influence of 3-4 electrodes in the channel wall, which will be driven with AC voltages. Is this possible with Elmer? I like the program, but I am not able to expend so much effort to realize that what I need to do is impossible.
I am working my way through the example posted here, viewtopic.php?f=3&t=1437&p=4275&hilit=dna#p4275 at the moment.
Thank you
DNA in nanofluidic channel with pads
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brianAshcroft
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raback
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Re: DNA in nanofluidic channel with pads
Hi Brian
So I presume that your EDL so thick that you need to consider that and model the Potential from Poisson-Bolztmann equation coupled with Navier-Stokes. This should be ok.
Additionally you would need to follow the particles. You could do it by solving the advection-diffusion equation but I'm afraid that it may overly diffusive. The alternative is to use particle based method. You can follow particles in the fluid under the influence of electric fields if you can live with the assumption of constant drag coefficient (ParticleDynamics module).
Some things here may require pioneering spirit and testing as the combication of models is somewhat untested but there should be no need for coding, I hope.
-Peter
So I presume that your EDL so thick that you need to consider that and model the Potential from Poisson-Bolztmann equation coupled with Navier-Stokes. This should be ok.
Additionally you would need to follow the particles. You could do it by solving the advection-diffusion equation but I'm afraid that it may overly diffusive. The alternative is to use particle based method. You can follow particles in the fluid under the influence of electric fields if you can live with the assumption of constant drag coefficient (ParticleDynamics module).
Some things here may require pioneering spirit and testing as the combication of models is somewhat untested but there should be no need for coding, I hope.
-Peter
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brianAshcroft
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Re: DNA in nanofluidic channel with pads
is it possible to model the DNA as a chain? I need to model the behavior of the DNA chain in a very, very coarse grained way.
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raback
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Re: DNA in nanofluidic channel with pads
Hi
I know that spherical particles could be modeled as a chain as well. Unfortunately this has not been implemented. It would require some tweaking in the ParticleDynamics module, or a fork of it.
Even that would not solve all the problems. Now there is not much effect of considering the DNA as a chain unless you consider also the drag of the DNA as a chain. Now for spherical objects you can compute the drag coefficient and it will be a constant. For chains there is no such thing. The drag will depend on the shape and orientation of the chain, and also have a nontrivial distribution. To solve the drag of such an object with any precision requires that it is quite accurately meshed. I.e. we have dynamic meshing of problem, or at least some eulerian approach to consider the true shape of the chain. So things become quite difficult...
-Peter
I know that spherical particles could be modeled as a chain as well. Unfortunately this has not been implemented. It would require some tweaking in the ParticleDynamics module, or a fork of it.
Even that would not solve all the problems. Now there is not much effect of considering the DNA as a chain unless you consider also the drag of the DNA as a chain. Now for spherical objects you can compute the drag coefficient and it will be a constant. For chains there is no such thing. The drag will depend on the shape and orientation of the chain, and also have a nontrivial distribution. To solve the drag of such an object with any precision requires that it is quite accurately meshed. I.e. we have dynamic meshing of problem, or at least some eulerian approach to consider the true shape of the chain. So things become quite difficult...
-Peter