DAE tubes imaged in tapping mode

1. The sides of the large tube are 'smooth' with little curvature before opening but afterward they are roughy with shorter wavelength variations.
2. The contours of the large tube appear to follow eachother, as if a single rip meandered back along the length of the tube and that the edges actually bordered this rip. If this is true then we are seeing all the tiles present in the tube and the width measured actually indicated the tiles that were present.
3. At the interface of the open and unopened tube in the image rese033f.gif I measured the apparent width of the tube after opening as 50 nm and the width before opening as 33 nm. Since the final width is less than twice the unopened width, it would seem that tiles were lost during the opening of the tube (which is inconsistent with the previous observation) or perhaps the unopened with is not indicative of the true diameter of the tube. Above unopened tubes the image streaks---the tube is not well fixed in place, perhaps giving an overestimate of its width.
4. The apparent height of the open small tube (and the large tube after opening) is about 2 nm. The height of the unopened large tube was approximately 4.5 nm. This is consistent with the tube being collapsed on the mica surface during imaging.
5. The small tube has at most 5 tiles across at minimum 3 tiles, the large tube, after opening has at most 8 tiles across, at minimum 6.
6. An interesting question is whether the tube width varies (if so this means that there are defects in the tubes.) Even before opening, the apparent width of the large tube seemed to vary slightly---from about 25 nm wide on the top half of the image to 33 nm wide on the bottom.
7. We need to figure out how we are going to consistently measure widths in these images. It is difficult to decide where the edge of a tube is, especially when unopened.

1. The surface is a much more dynamic place than we had assumed. In a sample prepared this way tubes fall to the surface, disappear from the surface, and open long after their initial application.
2. Opened tubes continue to grow (and shrink) after they have opened on the surface. In particular one can watch one tube on the surface grow to 3-4 times its original opened width over the course of the movie. In particular this means that one cannot say anything about tube width based on lattices that occur on the surface unless one has actually seen a tube open leaving a ribbon of lattice behind. That ribbon must be imaged quickly if its width is to be measured before growth occurs. Once could attempt to further dilute the tubes ---this would decrease the growth of tubes after opening.
3. Tube widths appear to vary. Some tubes appear to leave 3 tile (at most) wide ribbons upon opening. Others leave ribbons with what appear to have 4-5 tiles.
4. Some tubes open quickly and others slowly---sometimes there is a single frame between an intact image of a tube and a completely open one. At other times tubes open over the course of several frames.
5. At later times, one can observe obvious faceting of the lattices that have been nucleated by tubes.
6. In many images of tubes there are small lattices in the background. We had previously assumed that these were small lattice fragments that were present in the solution of tubes. The movie clearly shows a tube, in the lower left quadrant, that hits the surface but then is ripped off leaving behind a small lattice fragment. This kind of mechanism could explain many of the small lattice fragments.
7. Small lattice fragments wiggle around---they can move, align and even appear to merge in some instances. It is possible that this is because there is less TAE/Mg (half strength) in this preparation but we do not believe this is the case.
8. In the bottom quarter of the movie, look for a little 'flea' about the size of a few tiles, that dances around, from right to left and then back to the center over the course of the movie. It may be a small salt crystal or a small aggregate of tiles. It is much more loosely bound than the rest of the lattices/tiles.
9. The inter-space striping for 8 tiles appears to be 119 nm rather than 108. It appears that our scanner is currently 8-9% off and needs to be recalibrated.
10. Today, (03/02/11) Nick tried to image some linear nuclei (with no tubes in the preparation) and found a few occasional tubes. We believe these were leftover in the fluid cell since it was not well cleaned after the movie was made on 03/02/07. We should clean the fluid cell better between different types of samples.