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User Journal

Journal Journal: Nanoscale programmable molecular assembler

Stayed up till 2:00 AM last night reading the Science article by Liao and Seeman on their artificial DNA programmable nanoassembler. After reading the article carefully enough to understand how the machine worked, I wrote a review of it in the ribosomes news group. Also submitted a Slashdot story about it.

I hope that we are getting close to an exciting new age of creativity and economic innovation involving molecular assemblers, perhaps something akin to the golden years of the microprocessor and the personal computer. It's about time, it's almost 2005 for Pete's sake.

User Journal

Journal Journal: Marching Cubes works

I implemented the marching cubes algorithm, and after correcting a dozen errors in my 256 cases, and writing some hole-patching code, it works beautifully! I can mesh the entire ribosome quickly and easily. For example, I meshed the RNA in 1kpj.pdb at 4 A resolution in 8 seconds! I don't know if that's fast for other implementations, but it's good enough for me.
User Journal

Journal Journal: m-surf

Well, I've given up on l-surf for now because it didn't work. Instead, I've started on m-surf, which is trying to do the same thing (meshing molecules), only it uses the Marching Cubes algorithm which is a whole lot more elegant and simple.
User Journal

Journal Journal: Working on l-Surf

I am currently working on a little project called l-surf when I should be doing something else. l-surf is my attempt to to create a surface mesh around a PDB model of a molecule. It's coming along, but slowly.

I wish I could find other slashdotters who are into molecular modeling to collaborate with.

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Every little picofarad has a nanohenry all its own. -- Don Vonada