User:TheLarry/Notebook/Larrys Notebook/2010/08/22

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Bad News

My processivity and run time are fine, but i checked the michaelis menten and that wasn't good. It didn't seem to follow a michaelis menten curve. It seemed to keep the ration of length to time basically constant. Which is not good. so i'm gonna have to go back and check all my rate constants, and see if maybe i made a mistake somewhere.

For clarification i am gonna write down the rules we used to make the rate constants

  1. Stepping and binding is now 1 step that is calculated via a WLC energy landscape with a cusp at the binding site length. this rate constant is calculated via equation 7.73 from Hanngi's 1990 paper
  2. Unbinding rates are calculated from a base value and then an Arrhenius factor is applied to increase or decrease that value. the force is from a wlc again. and the distance is based on 10 aa docking to the head from the 40 (total) aa neck linker.
    • this base value can is mostly from a state of U/D but could be from a monomer or other state
  3. if the kinesin is in a state of D/U (rare) it acts just like U/U since we believe the force is too high for kinesin's neck linker to dock
  4. kinesin head bound while the other head is unbound acts like a kinesin monomer
  5. use rate constants from literature

From this we take away almost all the unknown rate constants in the simulation. But i am just gonna have to double check those rate constants. Most of them i don't need to find but something like ADP binding and the monomer values i want to find again.

I am pretty frustrated at this moment. So i think i'll do this tomorrow.

When i find the rate constants i'll put them on the wiki to keep good track of them this time