ECS 289 Project Ideas

Theory project

All chemical reactions are reversible, even at some very slow rate. If a CRN is reversible (meaning all of its reactions are reversible), then it cannot have stable configurations, since the last reaction to make the configuration "stable" could always be reversed (hence it cannot really be a stable configuration). Can we design CRNs that compute functions that are "reverse-robust" in the sense that, for any configuration reachable from the initial configuration by either forward or reverse reactions, there is a configuration reachable by only forward reactions that is correct and stable? (where stable is also defined only with respect to forward reactions)

Theory project

The paper The Power of Nondeterminism in Self-Assembly shows that there is an infinite shape S such that some TAS strictly self-assembles S, but no directed TAS strictly self-assembles S. It crucially uses the fact that if a single strength-τ glue connects a tile to the rest of the assembly, then there is no way to guarantee that the tile is attached before some other attachments happen. It could always be the case that arbitrarily many other attachments happen first. However, much of the interesting behavior possible in the temperature-2 aTAM using strength-2 glues can be had using "duples" ( and only strength-1 glues. However, it is not clear how to apply the duple "technology" to the constructions of the paper. It is open whether a similar result can be proved in a TAS that allows duples and forbids strength-τ glues.

Present a paper on chemical reaction networks/population protocols

Present a paper on strand displacement

Present a paper on algorithmic tile self-assembly

Present a paper I didn't list!

Authors of papers I did list have several other papers in the field; check their webpages.