Introduction:
ATPase is a molecular motor that carries protons across the mitochondrial membrane from a low-pH (acidic) medium to a high pH (basic) medium as it produces ATP from ADP and phosphate molecules. In this problem, we model the F0 portion of the ATPase rotor to observe the state of the protonation sites on the basic (high pH) side of the membrane over time. The motor is modeled as a Markov process and the Crank-Nicolsen method is used to solve for the probability density function. We also measure the volocity of the rotor as a function of the load force to evaluate the stall force. Finally, we also performed our simulation at three different pH values of the “basic” side of the membrane to see how the stall force changes.
Modeling F0 ATPase
A final project by Ned Cameron, Stephen Soukasene, March 15, 2005, for ME 389 Molecular Machines in Biology
Link to ME 389 Molecular Machines in Biology class page.
Probability vs. Distance vs. Time
From the Report [PDF]:
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