Verifying polymer reaction networks using bisimulation

Verifying polymer reaction networks using bisimulation

The Chemical Reaction Network model has been proposed as a programming language for molecular programming. Methods to implement arbitrary CRNs using DNA strand displacement circuits have been proposed, as have methods to prove the correctness of those or other implementations. However, the stochastic Chemical Reaction Network model is provably not deterministically Turing-universal, that is, it...

Verifying Chemical Reaction Network Implementations: A Bisimulation Approach

Efforts in programming DNA and other biological molecules have recently focused on general schemes to physically implement arbitrary Chemical Reaction Networks. Errors in some of the proposed schemes have driven a desire for formal verification methods. We show that by interpreting each implementation species as a set of formal species, the concept of weak bisimulation can be adapted to CRNs in...

Syntactic Markovian Bisimulation for Chemical Reaction Networks

In chemical reaction networks (CRNs) with stochastic semantics based on continuous-time Markov chains (CTMCs), the typically large populations of species cause combinatorially large state spaces. This makes the analysis very difficult in practice and represents the major bottleneck for the applicability of minimization techniques based, for instance, on lumpability. In this paper we present syn...

Verifying Concurrent Stacks by Divergence-Sensitive Bisimulation

The verification of linearizability – a key correctness criterion for concurrent objects – is based on trace refinement whose checking is PSPACE-complete. This paper suggests to use branching bisimulation instead. Our approach is based on comparing an abstract specification in which object methods are executed atomically to a real object program. Exploiting divergence sensitivity, this also app...

Bisimulation and Unwinding for Verifying Possibilistic Security Properties