# User:TheLarry/Notebook/Larrys Notebook/2009/08/01

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## 2nd iteration

I haven't edited this thing for a while but i might as well update what is going on.

I am trying to make a kinetic monte carlo simulation of kinesin walking. For this i'll need to know rate constants and states for this process.

I have read a shit load to find rate constants, and i should rummage through the papers and make a table of the many diff't constants. Later

For now i am gonna write down what I think the states are:

F1 means foot one while F2 means foot two
ATP means that an ATP molecule is bound to the foot
0 means that neither ADP nor ATP is attached b means that the Foot is behind the other foot
f means that the foot is in front of the other foot
and i'll separate the information from each foot with a |

this means that F1 ATP attached (thus is bound to the MT); and is in front. F2 meanwhile is hooked up to an ADP; and is behind

So let's pick a state to start in:

• F2 took a step to the front
• there is a small chance that the foot will diffuse backwards according to Block. I don't know how to deal with this as far as the monte carlo goes
• this is a step of 8.2 nm
• a short amount of time is taken for this step something like 10 microseconds
3. F1-ATP-b | F2-0-f
• ADP has been released from Foot 2
• ATP is turning into ADP
• Released the phosphate group
• ATP has bound

I need to add in the ability for a foot to unbind from the MT and rebind at the same spot--so not diffusing. I wonder if there is anything else i missed.

I read some shit about a pause too. If that really is a state i would have missed that too.

## Questions

1. I don't know when kinesin detaches. i assume it does it while there is no ATP hooked up since ATP causes the kinesin to bind tightly to the MT
• I also haven't seen any rate constants for detachment. All I know is that it usually occurs in 100 steps

## Rate Constants

so right now i have an arrow to and from each of these states except the detachment where it is only a one way street.

also i know that some rate constants are load (force) dependant, but i am gonna ignore this for now.

ok right now the table is in google docs but i'll embed it here soon