On the iterated hairpin completion

The hairpin completion is a natural operation on formal languages which has been inspired by biochemistry and DNA-computing. In this paper we solve two problems which were posed first in 2008 and 2009, respectively, and still left open: 1.) It is known that the iterated hairpin completion of a regular language is not context-free in general, but it was open whether the iterated hairpin completion of a singleton or finite language is regular or at least context-free. We will show that it can be non-context-free. (It is of course context-sensitive.) 2.) A restricted but also very natural variant of the hairpin completion is the bounded hairpin completion. It was unknown whether the iterated bounded hairpin completion of a regular language remains regular. We prove that this is indeed the case. Actually we derive a more general result. We will present a general representation of the iterated bounded hairpin completion for any language using basic operations. Thus, each language class closed under these basic operations is also closed under iterated bounded hairpin completion

Two-Sided Derivatives for Regular Expressions and for Hairpin Expressions

The aim of this paper is to design the polynomial construction of a finite recognizer for hairpin completions of regular languages. This is achieved by considering completions as new expression operators and by applying derivation techniques to the associated extended expressions called hairpin expressions. More precisely, we extend partial derivation of regular expressions to two-sided partial derivation of hairpin expressions and we show how to deduce a recognizer for a hairpin expression from its two-sided derived term automaton, providing an alternative proof of the fact that hairpin completions of regular languages are linear context-free.Comment: 28 page

It Is NL-complete to Decide Whether a Hairpin Completion of Regular Languages Is Regular

The hairpin completion is an operation on formal languages which is inspired by the hairpin formation in biochemistry. Hairpin formations occur naturally within DNA-computing. It has been known that the hairpin completion of a regular language is linear context-free, but not regular, in general. However, for some time it is was open whether the regularity of the hairpin completion of a regular language is is decidable. In 2009 this decidability problem has been solved positively by providing a polynomial time algorithm. In this paper we improve the complexity bound by showing that the decision problem is actually NL-complete. This complexity bound holds for both, the one-sided and the two-sided hairpin completions

Dagstuhl Reports : Volume 1, Issue 2, February 2011

Online Privacy: Towards Informational Self-Determination on the Internet (Dagstuhl Perspectives Workshop 11061) : Simone Fischer-Hübner, Chris Hoofnagle, Kai Rannenberg, Michael Waidner, Ioannis Krontiris and Michael Marhöfer Self-Repairing Programs (Dagstuhl Seminar 11062) : Mauro Pezzé, Martin C. Rinard, Westley Weimer and Andreas Zeller Theory and Applications of Graph Searching Problems (Dagstuhl Seminar 11071) : Fedor V. Fomin, Pierre Fraigniaud, Stephan Kreutzer and Dimitrios M. Thilikos Combinatorial and Algorithmic Aspects of Sequence Processing (Dagstuhl Seminar 11081) : Maxime Crochemore, Lila Kari, Mehryar Mohri and Dirk Nowotka Packing and Scheduling Algorithms for Information and Communication Services (Dagstuhl Seminar 11091) Klaus Jansen, Claire Mathieu, Hadas Shachnai and Neal E. Youn

生化学反応による計算能力の研究

早大学位記番号:新6514早稲田大

Holographic Duals of Long Open Strings

We study the holographic map between long open strings, which stretch between D-branes separated in the bulk space-time, and operators in the dual boundary theory. We focus on a generalization of the Sakai-Sugimoto holographic model of QCD, where the simplest chiral condensate involves an operator of this type. Its expectation value is dominated by a semi-classical string worldsheet, as for Wilson loops. We also discuss the deformation of the model by this operator, and in particular its effect on the meson spectrum. This deformation can be thought of as a generalization of a quark mass term to strong coupling. It leads to the first top-down holographic model of QCD with a non-Abelian chiral symmetry which is both spontaneously and explicitly broken, as in QCD. Other examples we study include half-supersymmetric open Wilson lines, and systems of D-branes ending on NS5-branes, which can be analyzed using worldsheet methods.Comment: 35 pages, 4 figures, harvmac. v2: added reference

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

Comparison of free energy estimators and their dependence on dissipated work

The estimate of free energy changes based on Bennett's acceptance ratio method is examined in several limiting cases and compared with other estimates based on the Jarzynski equality and on the Crooks relation. While the absolute amount of dissipated work, defined as the surplus of average work over the free energy difference, limits the practical applicability of Jarzynski's and Crooks' methods, the reliability of Bennett's approach is restricted by the difference of the dissipated works in the forward and the backward process. We illustrate these points by considering a Gaussian chain and a hairpin chain which both are extended during the forward and accordingly compressed during the backward protocol. The reliability of the Crooks relation predominantly depends on the sample size; for the Jarzynski estimator the slowness of the work protocol is crucial, and the Bennett method is shown to give precise estimates irrespective of the pulling speed and sample size as long as the dissipated works are the same for the forward and the backward process as it is the case for Gaussian work distributions. With an increasing dissipated work difference the Bennett estimator also acquires a bias which increases roughly in proportion to this difference. A substantial simplification of the Bennett estimator is provided by the 1/2-formula which expresses the free energy difference by the algebraic average of the Jarzynski estimates for the forward and the backward processes. It agrees with the Bennett estimate in all cases when the Jarzynski and the Crooks estimates fail to give reliable results

Deciding Regularity of Hairpin Completions of Regular Languages in Polynomial Time

The hairpin completion is an operation on formal languages that has been inspired by the hairpin formation in DNA biochemistry and by DNA computing. In this paper we investigate the hairpin completion of regular languages. It is well known that hairpin completions of regular languages are linear context-free and not necessarily regular. As regularity of a (linear) context-free language is not decidable, the question arose whether regularity of a hairpin completion of regular languages is decidable. We prove that this problem is decidable and we provide a polynomial time algorithm. Furthermore, we prove that the hairpin completion of regular languages is an unambiguous linear context-free language and, as such, it has an effectively computable growth function. Moreover, we show that the growth of the hairpin completion is exponential if and only if the growth of the underlying languages is exponential and, in case the hairpin completion is regular, then the hairpin completion and the underlying languages have the same growth indicator