Maximality and Applications of Subword-Closed Languages

Characterizing languages D that are maximal with the property that D* ⊆ S⊗ is an important problem in formal language theory with applications to coding theory and DNA codewords. Given a finite set of words of a fixed length S, the constraint, we consider its subword closure, S⊗, the set of words whose subwords of that fixed length are all in the constraint. We investigate these maximal languages and present characterizations for them. These characterizations use strongly connected components of deterministic finite automata and lead to polynomial time algorithms for generating such languages. We prove that the subword closure S⊗ is strictly locally testable. Finally, we discuss applications to coding theory and encoding arbitrary blocks of information on DNA strands. This leads to very important applications in DNA codewords designed to obtain bond-free languages, which have been experimentally confirmed

Forbidding and enforcing on graphs

We define classes of graphs based on forbidding and enforcing boundary conditions. Forbidding conditions prevent a graph to have certain combinations of subgraphs and enforcing conditions impose certain subgraph structures. We say that a class of graphs is an fe-class if the class can be defined through forbidding and enforcing conditions (fe-system). We investigate properties of fe-systems and characterize familiar classes of graphs such as paths and cycles, trees, bi-partite, complete, Eulerian, and k-regular graphs as fe-classes. © 2012 Elsevier B.V. All rights reserved

Forbidding and enforcing in membrane computing

Motivated by biochemistry and the non-deterministic reactions between molecules, the authors in (Ehrenfeucht and Rozenberg, 2003) introduced the concept of forbidding-enforcing systems (fe-systems) that define families of languages. Using the same concept we propose to study forbidding and enforcing within membrane systems. Two approaches are presented; in the first case the membrane system generates families of languages and in the second case the membrane system generates a single language. We show that by using forbidding-enforcing in membranes, families of languages that cannot be defined by any fe-system can be generated. When a single language is generated, we show that SAT can be solved in a constant time (at price of using an exponential space). Also we show an example of a context-free language that can be generated without any forbidders. © 2003 Kluwer Academic Publishers

Finite language forbidding-enforcing systems

The forbidding and enforcing paradigm was introduced by Ehrenfeucht and Rozenberg as a way to define families of languages based on two sets of boundary conditions. Later, a variant of this paradigm was considered where an fe-system defines a single language. We investigate this variant further by studying fe-systems in which both the forbidding and enforcing sets are finite and show that they define regular languages. We prove that the class of languages defined by finite fe-systems is strictly between the strictly locally testable languages and the class of locally testable languages

Forbidding and enforcing of formal languages, graphs, and partially ordered sets

Forbidding and enforcing systems (fe-systems) provide a new way of defining classes of structures based on boundary conditions. Forbidding and enforcing systems on formal languages were inspired by molecular reactions and DNA computing. Initially, they were used to define new classes of languages (fe-families) based on forbidden subwords and enforced words. This paper considers a metric on languages and proves that the metric space obtained is homeomorphic to the Cantor space. This work studies Chomsky classes of families as subspaces and shows they are neither closed nor open. The paper investigates the fe-families as subspaces and proves the necessary and sufficient conditions for the fe-families to be open. Consequently, this proves that fe-systems define classes of languages different than Chomsky hierarchy. This work shows a characterization of continuous functions through fe-systems and includes results about homomorphic images of fe-families. This paper introduces a new notion of connecting graphs and a new way to study classes of graphs. Forbidding-enforcing systems on graphs define classes of graphs based on forbidden subgraphs and enforced subgraphs. Using fe-systems, the paper characterizes known classes of graphs, such as paths, cycles, trees, complete graphs and k-regular graphs. Several normal forms for forbidding and enforced sets are stated and proved. This work introduces the notion of forbidding and enforcing to posets where fe-systems are used to define families of subsets of a given poset, which in some sense generalizes language fe-systems. Poset fe-systems are, also, used to define a single subset of elements satisfying the forbidding and enforcing constraints. The latter generalizes graph fe-systems to an extent, but defines new classes of structures based on weak enforcing. Some properties of poset fe-systems are investigated. A series of normal forms for forbidding and enforcing sets is presented. This work ends with examples illustrating the computational potential of fe-systems. The process of cutting DNA by an enzyme and ligating is modeled in the setting of language fe-systems. The potential for use of fe-systems in information processing is illustrated by defining the solutions to the k-colorability problem

Generating DNA code words using forbidding and enforcing systems

Research in DNA computing was initiated by Leonard Adleman in 1994 when he solved an instance of an NP-complete problem solely by molecules. DNA code words arose in the attempt to avoid unwanted hybridizations of DNA strands for DNA based computations. Given a set of constraints, generating a large set of DNA strands that satisfy the constraints is an important problem in DNA computing. On the other hand, motivated by the non-determinism of molecular reactions, A. Ehrenfeucht and G. Rozenberg introduced forbidding and enforcing systems (fe-systems) as a model of computation that defines classes of languages based on two sets of constraints. We attempt to establish a connection between these two areas of research in natural computing by characterizing a variety of DNA codes that avoid certain types of cross hybridizations by fe-systems. We show that one fe-system can generate the entire class of DNA codes of a certain property, for example θ-k-codes, and confirm some properties of DNA codes through fe-systems. We generalize by fe-systems some known methods of generating good DNA code words which have been tested experimentally. © 2012 Springer-Verlag

Forbidding - Enforcing Conditions in DNA Self-assembly of Graphs

Starting from a set of strands (or other types of building blocks) a variant of forbidding-enforcing systems for graphs which models DNA self-assembly is proposed. All possible outcomes of the self-assembly process comply with necessary constraints arising from the physical and chemical properties of DNA. A set of forbidding and enforcing rules that describe these constraints are presented