Parameter Key

Navigation

To look around: click and drag somewhere other than the menu.
To zoom: use mouse scrollwheel or up/down arrow keys.
To open the menu: click the gray button on the bottom center.

Cycle Diagram

This diagram (left part of menu) shows the 6 possible states for each motor. The transition arrows between states are labeled with the current rate of the transition (units = transitions per simulation second). Each of these rates can be adjusted by clicking and dragging the circular knob within each arrow. The states are defined as follows:

• Mt-KT = ATP bound, bound to tubulin
• Mt-KDP = ADP and Pi bound, bound to tubulin
• KDP = ADP and Pi bound, diffusing freely
• KD = ADP bound, diffusing freely
• Mt-KD = ADP bound, bound to tubulin
• Mt-K = no nucleotide, bound to tubulin

Average Velocity

Calculated by dividing the distance travelled by the time passed since start (or restart).

Time

How much slower the simulation is running compared to real time.

Mean Step Size

The average distance a freely diffusing molecule moves in one step. Each step, this distance is randomly sampled from an exponential distribution with this number as the mean.

Necklink Length

The length of the unstructured necklinker peptide that connects the C-terminal of the motor domain to the bottom of the tropomyosin coiled-coil.

Steer NL

When ATP binds, should the necklinker bind and pull the bottom of the coiled coil to the front of the bound motor?

Snapping Speed

If 'Steer NL' is checked, the necklinker binds with this speed (units = degrees per simulation millisecond)