Approximating Optimal Bounds in Prompt-LTL Realizability in Doubly-exponential Time

We consider the optimization variant of the realizability problem for Prompt Linear Temporal Logic, an extension of Linear Temporal Logic (LTL) by the prompt eventually operator whose scope is bounded by some parameter. In the realizability optimization problem, one is interested in computing the minimal such bound that allows to realize a given specification. It is known that this problem is solvable in triply-exponential time, but not whether it can be done in doubly-exponential time, i.e., whether it is just as hard as solving LTL realizability. We take a step towards resolving this problem by showing that the optimum can be approximated within a factor of two in doubly-exponential time. Also, we report on a proof-of-concept implementation of the algorithm based on bounded LTL synthesis, which computes the smallest implementation of a given specification. In our experiments, we observe a tradeoff between the size of the implementation and the bound it realizes. We investigate this tradeoff in the general case and prove upper bounds, which reduce the search space for the algorithm, and matching lower bounds.Comment: In Proceedings GandALF 2016, arXiv:1609.0364

Protein logic: a statistical mechanical study of signal integration at the single-molecule level

Information processing and decision making is based upon logic operations, which in cellular networks has been well characterized at the level of transcription. In recent years however, both experimentalists and theorists have begun to appreciate that cellular decision making can also be performed at the level of a single protein, giving rise to the notion of protein logic. Here we systematically explore protein logic using a well known statistical mechanical model. As an example system, we focus on receptors which bind either one or two ligands, and their associated dimers. Notably, we find that a single heterodimer can realize any of the 16 possible logic gates, including the XOR gate, by variation of biochemical parameters. We then introduce the novel idea that a set of receptors with fixed parameters can encode functionally unique logic gates simply by forming different dimeric combinations. An exhaustive search reveals that the simplest set of receptors (two single-ligand receptors and one double-ligand receptor) can realize several different groups of three unique gates, a result for which the parametric analysis of single receptors and dimers provides a clear interpretation. Both results underscore the surprising functional freedom readily available to cells at the single-protein level.Comment: 19 pages, 4 figures and 9 pages S