High-throughput Molecular Algorithms
AbstractRecent technological developments allow massive parallel reading (sequencing) and writing (synthesis) of heterogeneous pools of DNA strands. We are no longer limited to circuits built out of a small number of different strands, nor to reading out a few bits of output by fluorescence. While these emerging capabilities are somewhat stochastic and error-prone, new classes of algorithms should feasibly take advantage of them.
We plan to start by investigating new algorithms to record the order in which a series of molecular events occurs, e.g., the appearance of certain chemicals over time in a dynamic chemical soup. A large network of DNA gates acting in parallel records the relationships between the events; the result can be read out by massive DNA sequencing. We plan to study feasible DNA structures to implement this and similar algorithms, simulate them, and investigate their correctness and robustness.
Prerequisites: background in distributed algorithms, verification, and/or synthetic biology.