Wednesday, February 20, 2008

Wednesday, February 6, 2008

breaking 200,000 atoms with pieces of a shaft

I went on something of a quest a few days ago to break one million atoms, that is to model a single structure made of at least 1,000,000 atoms. I started with a shaft section, a little over 50,000 atoms (the above picture is four of these sections), and then just kept extruding and fusing, but ultimately I (or NE1 failed). I did get two long shafts that together were over a half million atoms, but things started to get a little buggy when I tried to fuse them together.

I don't think NE1 has ever been tested out on this side of the envelope, so it's not that much of a surprise this started to get weird. I have a screen shot of the 500,000 atom shafts not quite drawn all the way. I intend to send it to the guy working on improving how NE1 handles those things.

I find this scale interesting, maybe because it is approaching that point were materials can start to be seen at continuous. I can easily transition from my macro-scale machining experience.

and an hour later -or- rough model inspired by Guy's post

Guy just posted a link to an enzyme powered MWNT. I called dibs and produced this from the short article he linked to. I didn't have time to get the full article; that is why I am calling it a rough model.

The upper enzyme is catalase and the lower one is glucose oxidase. Both enzymes are from the PDB.

Atomistic Holliday Junction and RuvA (2)

This atomistic Holliday Junction was created in alpha 9.1 of NE1. The RuvA protein was downloaded from the protein databank and rendered in VMD because QuteMol currently doesn't support the ribbon and tube displays that work so well for proteins. The two images were then combined in PaintShop, but I have an mmp file (NE1's native file format) somewhere with the two structures positioned together.

Sometime this week I intend to bring home Big Red (the tricked out Dell XPS notebook I use at work) to finish the linkages on the Superfullerene.

Friday, February 1, 2008

why artists have apprentices -or- more on the super fullerene

I have been putting this off. It is tedious going, but it's going. There are more finished linkages on the other side. I estimate I'm about 20% done.