Thursday, January 1, 2009


Been working all week with Andy, Xi Chen, and Nam on a paper. Using the kinetics from Jongmin Kim's bi-stable switch paper, Nam produced a nice simulation of the amorphous ring oscillator. Happily, these images look much like my earlier, cruder, simulation but now have dimensions. Features are measured in mm and time in hours. I think that's pretty cool -- a molecular scale device producing features at the mm scale. Would be great if it actually works when we try it someday!

Also from this this paper, Andy, Xi Chen, and I came up with a hopefully plausible complementary transcriptional NAND gate. The idea is that all signals are encoded by the sense and anti-sense complements of an RNA sequence. For example, signal "A" is high when some specific RNA sequence is high and it is low when the anti-sense of that sequence is high. The hypothetical gate is made from two complementary promoters on opposite sides of an double stranded DNA. On the left side, two molecular-beacon-like devices sequester half of a promoter that activates only when both inputs are high. On the right side, a single hairpin is folded such that a promoter is normally active but is deactivated when A and B invade (thanks Xi Chen). To work, the kinetics will have to be very delicately balanced so maybe it won't work well but at least it's a conceptual step in the right direction; we've been talking about a CMOS analog for years now and this is the first time we've made any conceptual progress.

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