Relationships Between Bounded Languages, Counter Machines, Finite-Index Grammars, Ambiguity, and Commutative Equivalence

It is shown that for every language family that is a trio containing only semilinear languages, all bounded languages in it can be accepted by one-way deterministic reversal-bounded multicounter machines (DCM). This implies that for every semilinear trio (where these properties are effective), it is possible to decide containment, equivalence, and disjointness concerning its bounded languages. A condition is also provided for when the bounded languages in a semilinear trio coincide exactly with those accepted by DCM machines, and it is used to show that many grammar systems of finite index — such as finite-index matrix grammars (Mfin) and finite-index ET0L (ET0Lfin) — have identical bounded languages as DCM. Then connections between ambiguity, counting regularity, and commutative regularity are made, as many machines and grammars that are unambiguous can only generate/accept counting regular or com- mutatively regular languages. Thus, such a system that can generate/accept a non-counting regular or non-commutatively regular language implies the existence of inherently ambiguous languages over that system. In addition, it is shown that every language generated by an unambiguous Mfin has a rational char- acteristic series in commutative variables, and is counting regular. This result plus the connections are used to demonstrate that the grammar systems Mfin and ET0Lfin can generate inherently ambiguous languages (over their grammars), as do several machine models. It is also shown that all bounded languages generated by these two grammar systems (those in any semilinear trio) can be generated unambiguously within the systems. Finally, conditions on Mfin and ET0Lfin languages implying commutative regularity are obtained. In particular, it is shown that every finite-index ED0L language is commutatively regular

Formal models of the extension activity of DNA polymerase enzymes

The study of formal language operations inspired by enzymatic actions on DNA is part of ongoing efforts to provide a formal framework and rigorous treatment of DNA-based information and DNA-based computation. Other studies along these lines include theoretical explorations of splicing systems, insertion-deletion systems, substitution, hairpin extension, hairpin reduction, superposition, overlapping concatenation, conditional concatenation, contextual intra- and intermolecular recombinations, as well as template-guided recombination. First, a formal language operation is proposed and investigated, inspired by the naturally occurring phenomenon of DNA primer extension by a DNA-template-directed DNA polymerase enzyme. Given two DNA strings u and v, where the shorter string v (called the primer) is Watson-Crick complementary and can thus bind to a substring of the longer string u (called the template) the result of the primer extension is a DNA string that is complementary to a suffix of the template which starts at the binding position of the primer. The operation of DNA primer extension can be abstracted as a binary operation on two formal languages: a template language L1 and a primer language L2. This language operation is called L1-directed extension of L2 and the closure properties of various language classes, including the classes in the Chomsky hierarchy, are studied under directed extension. Furthermore, the question of finding necessary and sufficient conditions for a given language of target strings to be generated from a given template language when the primer language is unknown is answered. The canonic inverse of directed extension is used in order to obtain the optimal solution (the minimal primer language) to this question. The second research project investigates properties of the binary string and language operation overlap assembly as defined by Csuhaj-Varju, Petre and Vaszil as a formal model of the linear self-assembly of DNA strands: The overlap assembly of two strings, xy and yz, which share an overlap y, results in the string xyz. In this context, we investigate overlap assembly and its properties: closure properties of various language families under this operation, and related decision problems. A theoretical analysis of the possible use of iterated overlap assembly to generate combinatorial DNA libraries is also given. The third research project continues the exploration of the properties of the overlap assembly operation by investigating closure properties of various language classes under iterated overlap assembly, and the decidability of the completeness of a language. The problem of deciding whether a given string is terminal with respect to a language, and the problem of deciding if a given language can be generated by an overlap assembly operation of two other given languages are also investigated