On the regularity of iterated hairpin completion of a single word

Lila Kari; Steffen Kopecki; Shinnosuke Seki

Home/Archive/arXiv

arXiv · 1104.2385

On the regularity of iterated hairpin completion of a single word

Lila Kari·Steffen Kopecki·Shinnosuke Seki

View original source ↗Read source document ↗Export metadata ↓

Abstract

Hairpin completion is an abstract operation modeling a DNA bio-operation which receives as input a DNA strand $w = x\alpha y \calpha$, and outputs $w' = x \alpha y \bar{\alpha} \bar{x}$, where $\bar{x}$ denotes the Watson-Crick complement of $x$. In this paper, we focus on the problem of finding conditions under which the iterated hairpin completion of a given word is regular. According to the numbers of words $\alpha$ and $\calpha$ that initiate hairpin completion and how they are scattered, we classify the set of all words $w$. For some basic classes of words $w$ containing small numbers of occurrences of $\alpha$ and $\calpha$, we prove that the iterated hairpin completion of $w$ is regular. For other classes with higher numbers of occurrences of $\alpha$ and $\calpha$, we prove a necessary and sufficient condition for the iterated hairpin completion of a word in these classes to be regular.

Explore related subjects

cs.FL

Keep this discovery

BibTeX RIS

Lila Kari, Steffen Kopecki, Shinnosuke Seki. 2011-04-13. On the regularity of iterated hairpin completion of a single word. https://arxiv.org/abs/1104.2385

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related papers

arXiv2026

Beyond the Turing threshold: Productive grammars generate essentially undecidable languages

Emil Post's productive sets are not even semi-computable, let alone computable, being thus essentially incomputable. Accordingly, formal languages whose set of words is a (completely) productive set are essentially undecidable. In this article, I elaborate on Post productivity from the viewpoint of formal language theory: I design formal grammars that emulate the construction of productive sets of natural numbers and are thus beyond Turing-decidability.

cs.FL↗

arXiv2026

RAGTIMER 1.0: Rapid Rare-Event Partial State Space Construction for Stochastic VAS (extended version)

Transient reachability analysis of rare events in Continuous-Time Stochastic Vector Addition Systems (CTSVAS) such as Chemical Reaction Networks (CRNs) has proven a formidable challenge to cutting-edge tools. Underlying a CTSVAS is a continuous-time Markov chain (CTMC), and CTMC transient reachability analysis calls for Probabilistic Model Checking (PMC). This analysis requires the explicit representation of a model's entire state space. Rare events occur with extremely low probability, compounding the challenge of probabilistic analysis. In CRNs, it is imperative to verify the probability of rare events; even a low concentration of a species can have pathological consequences. This paper presents the RAGTIMER 1.0 tool, which efficiently builds a partial state space for a CTSVAS by enumerating traces to a rare event of interest and expanding them to exploit concurrency and cycles, providing a guaranteed lower bound on the probability of a rare event. Guaranteed lower bounds are particularly useful in synthetic biological applications because they indicate how and when a rare event can be experimentally observed. RAGTIMER is an attractive alternative to existing rare event analysis methods for CTSVAS models. It outperforms existing PMC tools and refutes multiple probability estimates from rare-event stochastic simulation on multiple challenging CRN models. RAGTIMER uses optimized data structures, a simple input format, and memory-safe Rust code to improve the scalability and accessibility of PMC for industry professionals.

cs.FL↗

arXiv2026

Execution-Time Opacity Logic: A Logic for Ensuring ET-Opacity in Timed Systems

Ensuring confidentiality in Cyber-Physical Systems is critical, especially when attackers exploit execution times to infer sensitiveinformation. Traditional opacity models are inadequate for timed systems, as verifying opacity in Timed Automata is undecidable. To address this challenge, we propose Execution-Time Opacity Logic (ETOL), a new formalism that specifies opacity by requiring that for every execution satisfying a secret formula, there exists another execution of the same duration that does not satisfy it. ETOL guarantees that timing observations cannot reveal confidential agent activities. We present a decidable and efficient verification framework based on zone-based model checking, supported by a dedicated algorithm that systematically identifies duration-equivalent executions. Our approach is validated through an ATM case study, showing that ETOL enables efficient verification of execution-time confidentiality under timing attacks. We also developed a prototype tool for the ETOL logic that supports symbolic model checking over timed systems. It allows users to verify ETOL formulas based on clock-constrained execution paths.

cs.FL↗