Speaker
Prof.
Anne Condon
(University of British Columbia)
Description
We consider recycling, or reuse of molecules, in chemical
reaction systems and their DNA strand displacement
realizations. Recycling happens when a product of one
reaction is a reactant in a later reaction. Recycling has
the benefits of reducing consumption, or waste, of molecules
and of avoiding fuel depletion. We will describe a binary
counter that recycles molecules efficiently while incurring
just a moderate slowdown compared to alternative counters
that do not recycle strands. This counter is an n-bit
binary reflecting gray code counter; it advances through 2^n
states while consuming just O(n) molecules. In the strand
displacement realization of this counter, the waste---total
number of nucleotides of the DNA strands consumed---is
O(n^3), while alternative counters have waste proportional
to 2^n. We also show limits to the potential for recycling
strands. In particular, our n-bit counter fails to work
correctly when many copies of the species that represent the
state (bits) of the counter are present initially.
Primary author
Prof.
Anne Condon
(University of British Columbia)
