Ideally, self-assembly should rapidly and efficiently produce stable correctly assembled structures. We study the tradeoff between enthalpic and entropic cost in self-assembling systems using RecA-mediated homology search as an example. Earlier work suggested that RecA searches could produce stable final structures with high stringency using a slow testing process that follows an initial rapid search of $\sim 9–15$ bases. In this work, we will show that as a result of entropic and enthalpic barriers, simultaneously testing all $\sim 9–15$ bases as separate individual units results in a longer overall searching time than testing them in groups and stages.

• Received 13 November 2013
• Revised 31 March 2014

DOI:https://doi.org/10.1103/PhysRevE.90.022704