We consider graph-controlled insertion-deletion systems and prove that the systems with sizes (i) (3; 1, 1, 1; 1, 0, 1), (ii) (3; 1, 1, 1; 1, 1, 0) and (iii) (2; 2, 0, 0; 1, 1, 1) are computationally complete. Moreover, graph-controlled insertion-deletion systems simulate linear languages with sizes (2; 2, 0, 1, 1, 0, 0), (2; 2, 1, 0; 1, 0, 0), (3; 1, 0, 1; 1, 0, 0), or (3; 1, 1, 0; 1, 0, 0). Simulations of metalinear languages are also studied. The parameters in the size (k; n, i’, i’'; m, j’, j’') of a graph-controlled insertion-deletion system denote (from left to right) the maximum number of components, the maximal length of the insertion string, the maximal length of the left context for insertion, the maximal length of the right context for insertion; a similar list of three parameters concerning deletion follows. © IFIP International Federation for Information Processing 2016.

Lakshmanan K

Department of Analytics

School of Computer Science and Engineering

Vellore Campus

Fernau H

Raman I.

Fulltext

Vellore Institute of Technology (VIT) is a private university located in&nbsp;Tamil Nadu, India. Founded in 1984, as Vellore Engineering College, the institution offers 20 undergraduate, 34 postgraduate, four integrated and four research programs. It has campuses in Vellore, Amravati, Bhopal and Chennai.

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Descriptional Complexity of Graph-Controlled Insertion-Deletion Systems

Descriptional Complexity of Formal Systems Lecture Notes in Computer Science

A graph-controlled insertion–deletion (GCID) system is a regulated extension of an insertion–deletion system. Such a system has several components and each component has some insertion–deletion rules. The transition is performed by any applicable rule in the current component on a string and the resultant string is then moved to the target component specified in the rule. The language of the system is the set of all terminal strings collected in the final component. The parameters in the size (k;n,i′,i″;m,j′,j″) of a GCID system denote (from left to right) the maximum number of components, the maximal length of the insertion string, the maximal length of the left context for insertion, the maximal length of the right context for insertion; the last three parameters follow a similar representation with respect to deletion. In this paper, we discuss the computational completeness of the families of GCID systems of size (k;1,i′,i″;1,j′,j″) with k∈{3,5} and for (nearly) all values of i′,i″j′,j″∈{0,1}. All proofs are based on the simulation of type-0 grammars given in Special Geffert Normal Form (SGNF). The novelty in our proof presentation is that the context-free and the non-context-free rules of the given SGNF grammar are simulated by GCID systems of different sizes and finally we combine them by stitching and overlaying to characterize the recursive enumerable languages. This proof presentation greatly simplifies and unifies the proof of such characterization results. We also connect some of the obtained GCID simulations to the domain of insertion–deletion P systems. © 2017 Elsevier B.V.

Theoretical Computer Science

On the computational completeness of graph-controlled insertion–deletion systems with binary sizes

We study matrix insertion grammars (MIS) towards representation of recursively enumerable languages with small size. We show that pure MIS of size (3; 1, 2, 2) (i.e., having ternary matrices inserting one symbol in two symbol context) can characterize all recursively enumerable languages. This is achieved by either applying an inverse morphism and a weak coding, or a left (right) quotient with a regular language or an intersection with a regular language followed by a weak coding. The obtained results complete known results on insertiondeletion systems from DNA computing area. © Springer International Publishing AG 2017.

Unconventional Computation and Natural Computation Lecture Notes in Computer Science

Universal Matrix Insertion Grammars with Small Size

A regulated extension of an insertion-deletion system known as graph-controlled insertion-deletion (GCID) system has several components and each component contains some insertion-deletion rules. A rule is applied to a string in a component and the resultant string is moved to the target component specified in the rule. When resources are so limited (especially, when deletion is context-free) then GCID systems are not known to describe the class of recursively enumerable languages. Hence, it becomes interesting to find the descriptional complexity of such GCID systems of small sizes with respect to language classes below RE. To this end, we consider closure classes of linear languages. We show that whenever GCID systems describe LIN with t components, we can extend this to GCID systems with just one more component to describe, for instance, 2-LIN and with further addition of one more component, we can extend to GCID systems that describe the rational closure of LIN. © IFIP International Federation for Information Processing 2017.

Graph-Controlled Insertion-Deletion Systems Generating Language Classes Beyond Linearity

Matrix insertion-deletion systems combine the idea of matrix control (as established in regulated rewriting) with that of insertion and deletion (as opposed to replacements). We improve on and complement previous computational completeness results for such systems, showing (for instance) that matrix insertion-deletion systems with matrices of length two, insertion rules of type (1, 1, 1) and context-free deletions are computationally complete. We also show how to simulate (Kleene stars of) metalinear languages with several types of systems with very limited resources. We also generate non-semilinear languages using matrices of length three with context-free insertion and deletion rules. © Springer International Publishing Switzerland 2016.

Generative Power of Matrix Insertion-Deletion Systems with Context-Free Insertion or Deletion

Insertion and deletion are considered to be the basic operations in Biology, more specifically in DNA processing and RNA editing. Based on these evolutionary transformations, a computing model has been formulated in formal language theory known as insertion-deletion systems. Since the biological macromolecules can be viewed as symbols, the gene sequences can be represented as strings. This suggests that the molecular representations can be theoretically analyzed if a biologically inspired computing model recognizes various bio-molecular structures like pseudoknot, hairpin, stem and loop, cloverleaf and dumbbell. In this paper, we introduce a simple grammar system that encompasses many bio-molecular structures including the above mentioned structures. This new grammar system is based on insertion-deletion and matrix grammar systems and is called Matrix insertion-deletion grammars. Finally, we discuss how the ambiguity levels defined for insertion-deletion grammar systems can be realized in bio-molecular structures, thus the ambiguity issues in gene sequences can be studied in terms of grammar systems. © 2011 Springer-Verlag.

Journal	Data powered by TypesetDescriptional Complexity of Formal Systems Lecture Notes in Computer Science
Publisher	Data powered by TypesetSpringer International Publishing
ISSN	0302-9743
Open Access	Yes