8.2.7 The Wanderer (Rookie)
The Wanderer (Rookie) is a high-density algorithm operating on a two-dimensional area. It takes the wandering process as a metaphor to optimize the packing of the membrane. The operation differs from the one of the previously discussed random placing algorithms, because it iteratively tries to optimize the placement for each single lipid. There are no additional placement correction and/or annealing processes - it is a greedy algorithm.
The panel shows the options of The Wanderer.
- StepSize: defines the placement step size during the wandering process, higher numbers lead to faster placing process, but precision will be lower
- Possible Missteps: each time a placing process did not succeed - e.g., if there is not enough space at the actual position or the lipid's position is too close to the border - the misstep counter is iterated. If this number is reached, the placing process for the actual membrane side is stopped.
- Wander for Fellow: if this option is activated, each wanderer tries to optimize his position by moving towards it fellow.
- and dance: during approaching the fellow, the lipid dances to optimize its placing position. The following options regulate the resolution of the dancing process, the rotation along the y axis:
- 1,2,3...360: highest dancing resolution
- 0,45,90...315,360: dance in 45 degree steps
- 90,180,270,360: dance in 90 degree steps
- no rotation
A single wandering step
The figure following shows the typical procedure of a wandering run. In this case, the starting point is a membrane which contains two lipids already placed by The Wanderer.
First, a new lipid is generated and placed. Obviously this new lipid is positioned on top of the previously placed lipid - they are intersecting.
Now the wandering process starts. The new lipid moves east for a free position. Next, it would move south if no free position is found. But because the lipid already found a free position, this method is skipped.
Now, the lipid should move west to find a fellow. But again, this procedure is not needed in this case, because the lipid is already positioned directly besides the previously placed lipid (because the lipid did not wander south). Therefore, the next method is invoked, causing the lipid searching for a fellow in the north. The lipid stops when meeting the border in the north.
Now the final process is started: the lipid wanders and dances. The rotation process is associated with a movement to the west and north. The latter cardinal direction does not cause a visual difference, because the lipid already touches the northern border.
The process stops when the new lipid moved very close to the lipid located in the northwestern corner of the layer.
- Written by bjoern
- Category: Cm2help 8. The Lipid Bilayer
- Published: 14 September 2013
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