How efficiently can room at the bottom be traded away for speed at the top?

Abstract

Given exponential 2ⁿ space, we know that an Adleman-Lipton computation can decide many hard problems – such as boolean formula and boolean circuit evaluation – in a number of steps that is linear in the problem size n. We wish to better understand the process of designing and comparing bio-molecular algorithms that trade away weakly exponential space to achieve as low a running time as possible, and to analyze the efficiency of their space and time utilization relative to those of their best extant classical/bio-molecular counterparts. We propose a randomized framework which augments that of the sticker model of Roweis et al. to provide an abstract setting for analyzing the space-time efficiency of both deterministic and randomized bio-molecular algorithms. We explore its power by developing and analyzing such algorithms for theCovering Code Creation (CCC) and k-SAT problems. In the process, we uncover new classical algorithms for CCC andk-SAT that, while exploiting the same space-time trade-off as the best previously known classical algorithms, are exponentially more efficient than them in terms of space-time product utilization. This work indicates that the proposed abstract bio-molecular setting for randomized algorithm design provides a logical tool of independent interest.