Splicing Systems from Past to Future: Old and New Challenges

A splicing system is a formal model of a recombinant behaviour of sets of double stranded DNA molecules when acted on by restriction enzymes and ligase. In this survey we will concentrate on a specific behaviour of a type of splicing systems, introduced by P\u{a}un and subsequently developed by many researchers in both linear and circular case of splicing definition. In particular, we will present recent results on this topic and how they stimulate new challenging investigations.Comment: Appeared in: Discrete Mathematics and Computer Science. Papers in Memoriam Alexandru Mateescu (1952-2005). The Publishing House of the Romanian Academy, 2014. arXiv admin note: text overlap with arXiv:1112.4897 by other author

Information flow analysis for a dynamically typed language with staged metaprogramming

Web applications written in JavaScript are regularly used for dealing with sensitive or personal data. Consequently, reasoning about their security properties has become an important problem, which is made very difficult by the highly dynamic nature of the language, particularly its support for runtime code generation via eval. In order to deal with this, we propose to investigate security analyses for languages with more principled forms of dynamic code generation. To this end, we present a static information flow analysis for a dynamically typed functional language with prototype-based inheritance and staged metaprogramming. We prove its soundness, implement it and test it on various examples designed to show its relevance to proving security properties, such as noninterference, in JavaScript. To demonstrate the applicability of the analysis, we also present a general method for transforming a program using eval into one using staged metaprogramming. To our knowledge, this is the first fully static information flow analysis for a language with staged metaprogramming, and the first formal soundness proof of a CFA-based information flow analysis for a functional programming language

Shaded Tangles for the Design and Verification of Quantum Programs (Extended Abstract)

We give a scheme for interpreting shaded tangles as quantum programs, with the property that isotopic tangles yield equivalent programs. We analyze many known quantum programs in this way -- including entanglement manipulation and error correction -- and in each case present a fully-topological formal verification, yielding in several cases substantial new insight into how the program works. We also use our methods to identify several new or generalized procedures.Comment: In Proceedings QPL 2017, arXiv:1802.0973

On Special forms of Splicing on Arrays and Graphs

Tom Head (1987), in his pioneering work on formal language theory applied to DNA computing, introduced a new operation of splicing on strings, while proposing a model of certain recombination behaviour of DNA molecules under the action of restriction enzymes and ligases. Since then this operation has been studied in great depth giving rise to a number of theoretical results of great interest in formal language theory. Extension of this operation of splicing to higher dimensional structures such as circular words, arrays, trees and graphs have been proposed in the literature. Here we examine the effect of certain specific forms of the splicing operation applied to arrays and graphs

Networks of Bio-inspired Processors

The goal of this work is twofold. Firstly, we propose a uniform view of three types of accepting networks of bio-inspired processors: networks of evolutionary processors, networks of splicing processors and networks of genetic processors. And, secondly, we survey some features of these networks: computational power, computational and descriptional complexity, the existence of universal networks, eciency as problem solvers and the relationships among them

Splitting Line Patterns in Free Groups

We construct a boundary of a finite rank free group relative to a finite list of conjugacy classes of maximal cyclic subgroups. From the cut points and uncrossed cut pairs of this boundary we construct a simplicial tree on which the group acts cocompactly. We show that the quotient graph of groups is the JSJ decomposition of the group relative to the given collection of conjugacy classes. This provides a characterization of virtually geometric multiwords: they are the multiwords that are built from geometric pieces. In particular, a multiword is virtually geometric if and only if the relative boundary is planar.Comment: 22 pages, 6 figures; v2 fixed a few typos; v3 38 pages, 21 figures; v4 30 pages, 11 figures 'Preliminaries' section expanded to make paper self-contained and split into two sections. Some arguments refactored and simplified. Paper streamlined; v5 56 pages, 21 figures Added examples and improved exposition according to referee comments. To appear in Algebraic & Geometric Topolog