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Kinesin modeling by Mind Map: Kinesin modeling
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Kinesin modeling



we were thinking to make this paper more of a review of kinesin motility. Showing where all the rate constants came from. something like this

We can paste in most of the stuff from our previous paper writing...especially introduction

References, Definite references, Larry has a bunch already, Probably need to find more prior modeling papers, especially by Fisher, BTW: Astumian is going to be at Santa Fe meeting, Possible refs, Endow spindle modeling paper, Not kinesin modeling (I think), but may show us how to present modeling paper, SJK: Haven't read yet


Poster will be done before paper

Want to have literature very solid for talking with people at poster

Conclusions for poster, Code will be available, Osmotic Pressure slows down velocity, Certain states are blah blah blah

Place code in public; usable

Place code in public; usable, Code must be relatively clean but doesn't have to be too clean, As an example, The cleaning that Larry did for the tracking subVI helped a bunch and is sufficient, Compiled version will require a license to run, Can talk with Malloy to see if his brother (brother in law) can get us some special NI deal so people can run our code for free? Perhaps a license that expires?, 2/2/2010 Steve sent email to Malloy, Virtual machine possiblity (Deepak advice at #scio10), Also possibility of remotely logging in to our own server, Data posted on IR?, Test data (real and simulated), Meeting with Amy next week and will discuss this possibility, Create screen cast to demonstrate how to use, Storyboarding would help, Code to Possibly Make Pulbic, Kinesin simulator, Single run, Multiple runs to do experiments, Rate constant viewer



16 states for a head (Agent)

Multiple rate constants (3 or 4)

Some are modified by other agent (only if strain)

128 states combined

16 states for one head, pi only is not a state, This counts front / back

16x16 is 256, But one head has to be behind the other

Two state energy diagram



This was some way to write the rate constants down, perhaps



Changes to rate constants, Analyze strain through a lens of two state energy diagram. Double check that the constants make sense, Make a that allows for easy change to certain rate constants, right now the user has to look at the code and make changes to the global variables but we want to give the user an interface to change this, Steve thinks we can do something clever to make rate constants easy to view / edit, Search any recent papers for new revelations

Add in references to where all the constants came from

We were thinking that the inorganic phosphate release may be slow because the state it enters is a state with strain. We were looking at Guydosh/Block paper