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Agent Base Modeling
After talking with Koch yesterday it seems like taking an agent based modeling approach will be more interesting. We'll treat each head as a different object and watch as their interact.
To do this i'll need a sub.vi that figures out the rate constants for each situation which is encountered. I thought about making a giant matrix and just looking up terms but this would be difficult and i want to see it work before i make it more complicated.
So each head can be in a state of |position; state; nucleotide> which means it is defined with where it is right now, bound/unbound to MT, and if it has a nucleotide currently bound to it.
So i'll need to calculate each rate constant for each state that comes across for both heads. There seems to be 12 rate constants. + means that it is moving forward, and - is backwards.
So there it is 12 different rate constants. I think i have to calculate each one for each time the state changes. Most of these will be zero of course.
I forgot the kinesin coming off the MT in general, but that should happen if the other foot disassociates while the other is in the air.
So there are 16 different states possible (2 positions * 2 states * 4 nucleotide = 16 possible). This is why i thought about a matrix. But the elements in the matrix would have to be arrays of the 12 k's? I don't know and am not gonna think about it now.
So let's get started
not sure what else have to get back to this
There needs to be another state. like this needs to be behind or something but i can't find anything that states that explicitly
Unbind from MT
Bind to MT
I have completed what Koch suggested, and a base program is now completed. I am gonna put in some fake values to see if it is actually working tomorrow. I'll try to make it fit the flow. it should be fun. and by fun i mean crazy annoying to put in numbers in like 20 3 element arrays. but i am curious to see it work.
Kinesin Motors: No Strain, No Gain: this article is a quick review of some work Yildiz did. It basically is a good review of how strain affects processivity.