Splicing Operation Research Articles

Accepting splicing systems

In this paper, we propose a novel approach to splicing systems, namely we consider them as accepting devices. Two ways of iterating the splicing operation and two variants of accepting splicing system are investigated. Altogether, we obtain four models, which are compared with each other as well as with the generating splicing systems from the computational power point of view. Several decision problems concerning the accepting splicing systems are discussed.

Simultaneous measurement of strain and temperature using a reverse index fiber Bragg grating sensor

The simultaneous measurement of strain and temperature is necessary for structural health monitoring of composite structures under diverse temperature environments. The FBG (fiber Bragg grating) sensor head is formed by two FBGs, normal and reverse index FBGs, fabricated by different procedures. The FBG sensor head offers the possibility of multiplexing and embedment, a straightforward measurement system and greater reliability due to the absence of a splicing operation. We evaluated the sensor head analytically and experimentally.

Matrix splicing system

The string splicing system was introduced by Tom Head, which stands as an abstract model for the DNA recombination under the influence of restriction enzymes and ligase enzymes. However, it is observed that strings are not very capable of modelling the complex chemical process. Hence, in this article, matrix splicing system is introduced with a new splicing operation among the matrices. It is shown with an illustration that the DNA recombination process can be simulated by the matrix splicing system, which justifies the suitability of the matrices for modelling the complex processes of the molecules. The properties of the components of the system such as cutting rules and the splicing rules are discussed. Besides some properties of the system, it is shown that this system stands as a theoretical model for splicing strings in parallel. The abstraction of the ligase enzymes is explained which is missing in all the splicing models that have come out so far. The ability of the system in generating new patterns is also outlined.

An Information Transmission Mode for DNA Numerical Calculation

Numerical calculation is an important research direction in DNA computing,which lead to the naissance of the first DNA computer in the world.A prerequisite for designing a computer useful in a wide range of applications is the ability to perform numerical calculations.In this paper,the authors propose a kind of general mode of information transmission in DNA computing,with which we can use splicing operations to implement the N-scale self-assembly addition and subtraction model.The advantage of numerical calculation with DNA molecules computer liken to the traditional electronic computer lie on the great parallelism DNA computing.

IMPACT OF THE SPLICER PARAMETERS ON THE SPLICED OPEN-END DENIM SPUNYARNS PHYSICO-MECHANICAL PERFORMANCES

Abstract In this work, the open end splicer parameters as the compressed air (pressure, P and durations of tearing, Dt), the fibres feeding during splicing operation (1S10 and EII), and the recalling yarn codes (RI, RII and RIII) were investigated. In order to evaluate the contribution of the splicing conditions on the open end splice physicomechanical behaviour, we used the experimental Tagauchi design method. This kind of experimental design allows us, using simplification method, to reduce the amount of the experiments. To evaluate the splice appearance, the subjective (the experts notes) method and the objective (referring to a developed Thickness index value) one are compared. In our experimental field of interest, the results show that the feeding fibres parameter level increase gives the lowest Thickness index value which means good splice appearance. However, the compressed air remains the most important parameter because it represents the influential one on both the strength and the longitudinal characteristics of the spliced open-end spun-yarns (length of splice and the expert judgments).

Constants and label-equivalence: A decision procedure for reflexive regular splicing languages

A structural characterization of reflexive splicing languages has been recently given in [P. Bonizzoni, C. De Felice, R. Zizza, The structure of reflexive regular splicing languages via Schützenberger constants, Theoretical Computer Science 334 (2005) 71–98] and [P. Bonizzoni, G. Mauri, Regular splicing languages and subclasses, Theoretical Computer Science 340 (2005) 349–363] showing surprising connections between long standing notions in formal language theory, the syntactic monoid and Schützenberger constant and the splicing operation. In this paper, we provide a procedure to decide whether a regular language is a reflexive splicing language, based on the above-mentioned characterization that is given in terms of a finite set of constants for the language. The procedure relies on the notion of label-equivalence that induces a finite refinement of the syntactic monoid of a regular language L . A finite set of representatives for label-equivalent classes of constant words in L is defined and it is proved that such a finite set provides the splice sites of splicing rules generating language L .

Network of evolutionary processors with splicing rules and permitting context

In this paper we consider networks of evolutionary processors with splicing rules and permitting context (NEPPS) as language generating and computational devices. Such a network consists of several processors placed on the nodes of a virtual graph and are able to perform splicing (which is a biologically motivated operation) on the words present in that node, according to the splicing rules present there. Before applying the splicing operation on words, we check for the presence of certain symbols (permitting context) in the strings on which the rule is applied. Each node is associated with an input and output filter. When the filters are based on random context conditions, one gets the computational power of Turing machines with networks of size two. We also show how these networks can be used to solve NP-complete problems in linear time.

Regular splicing languages and subclasses

Recent developments in the theory of finite splicing systems have revealed surprising connections between long-standing notions in the formal language theory and splicing operation. More precisely, the syntactic monoid and Schützenberger constant have strong interaction with the investigation of regular splicing languages. This paper surveys results of structural characterization of classes of regular splicing languages based on the above two notions and discusses basic questions that motivate further investigations in this field. In particular, we improve the result in [6] that provides a structural characterization of reflexive symmetric splicing languages by showing that it can be extended to the class of all reflexive splicing languages: this is the larger class for which a characterization is known.

The structure of reflexive regular splicing languages via Schützenberger constants

The splicing operation was introduced in 1987 by Head as a mathematical model of the recombination of DNA molecules under the influence of restriction and ligases enzymes. This operation allows us to define a computing (language generating) device, called a splicing system. Other variants of this original definition were also proposed by Paun and Pixton respectively. The computational power of splicing systems has been thoroughly investigated. Nevertheless, an interesting problem is still open, namely the characterization of the class of regular languages generated by finite splicing systems. In this paper, we will solve the problem for a special class of finite splicing systems, termed reflexive splicing systems, according to each of the definitions of splicing given by Paun and Pixton. This special class of systems contains, in perticular, finite Head splicing systems. The notion of a constant, given by Schützenberger, once again intervenes.

PARALLEL SPLICING ON IMAGES

In this paper, splicing on images of rectangular arrays is introduced as a simple and effective extension of the operation of splicing on strings extensively studied in the context of DNA computing. A comparison of the resulting class of splicing array languages with the local two-dimensional array languages and two-dimensional right linear languages is made. Certain closure properties are obtained. Furthermore, the notion of self cross-over of strings is extended to arrays with respect to the splicing of arrays introduced here.

A continuity method for bridges constructed with precast prestressed concrete girders

A method of making simply supported girders continuous is described for bridges with spans of 30-45 m. The splicing method takes advantage of an induced secondary moment to transform the self-weight stresses in the precast simply supported girders into values representative of a continuous girder. The secondary moment results from prestressing of continuity tendons and detensioning of temporary tendons in the girders. Preliminary sections are selected for spliced U-girder bridges with a range of span lengths. Use of the proposed technique results in girder depth reductions of 500-800 mm when compared to standard simply supported I-girder bridges. The flexural behavior of an example bridge with 40-m spans is examined to illustrate the necessary considerations for determining the optimum sequence of splicing operations.

Separating some splicing models

In this paper we show that the three main definitions of the splicing operation known in the literature, i.e., the Head [Bull. Math. Biology 49 (1987) 737–759], Paun [Theoret. Comput. Sci. 168 (1996) 321–326] and Pixton [Discrete Appl. Math. 69 (1996) 101–124] definitions, give rise to different subclasses of regular languages, when a finite set of rules is iterated on a finite set of axioms. More precisely, we show that the family of regular languages generated by finite splicing, as defined in the early paper by Head, is strictly included in the family defined later by Paun, which is in turn strictly included in the splicing family defined by Pixton. We describe instance languages in the difference sets, and we prove that they cannot be generated by the smaller families.

A Note on Parallel Splicing on Images

The concept of splicing on images which is done in parallel is introduced. This is an extension of the operation of splicing on strings extensively studied in the context of DNA computing. Various properties of splicing on images are examined.

Computing with Membranes

We introduce a new computability model, of a distributed parallel type, based on the notion of a membrane structure. Such a structure consists of several cell-like membranes, recurrently placed inside a unique “skin” membrane. A plane representation is a Venn diagram without intersected sets and with a unique superset. In the regions delimited by the membranes there are placed objects. These objects are assumed to evolve: each object can be transformed in other objects, can pass through a membrane, or can dissolve the membrane in which it is placed. A priority relation between evolution rules can be considered. The evolution is done in parallel for all objects able to evolve. In this way, we obtain a computing device (we call it a P system): start with a certain number of objects in a certain membrane and let the system evolve; if it will halt (no object can further evolve), then the computation is finished, with the result given as the number of objects in a specified membrane. If the development of the system goes forever, then the computation fails to have an output. We prove that the P systems with the possibility of objects to cooperate characterize the recursively enumerable sets of natural numbers; moreover, systems with only two membranes suffice. In fact, we do not need cooperating rules, but we only use catalysts, specified objects which are present in the rules but are not modified by the rule application. One catalyst suffices. A variant is also considered, with the objects being strings over a given alphabet. The evolution rules are now based on string transformations. We investigate the case when either the rewriting operation from Chomsky grammars (with respect to context-free productions) or the splicing operation from H systems investigated in the DNA computing is used. In both cases, characterizations of recursively enumerable languages are obtained by very simple P systems: with three membranes in the rewriting case and four in the splicing case. Several open problems and directions for further research are formulated

Splicing in abstract families of languages

We show that the iterated splicing operation determined by a regular H scheme (with some necessary restrictions) preserves membership in any full abstract family of languages. This involves translation of an H scheme into two alternative forms. The first form, which is closely related to the underlying biochemical operations, uses cutting and pasting rather than splicing. The second form uses matrices of languages, and in this formulation the splicing operation is translated into standard formal language operations (concatenation and quotient). Moreover, in the matrix formulation the splicing language itself may be expressed in terms of standard formal language operations, and this provides an algorithm for calculating the splicing language. As an application we use the cutting and pasting approach to extend the closure result to circular strings.

DNA computing based on splicing: universality results

First, we recall some characterizations of recursively enumerable languages by means of finite H systems with certain regulations on the splicing operation. Then, we consider a variant of the splicing operation where the splicing proceeds always in couples of steps: the two strings obtained after a splicing enter immediately a second splicing (the rules used in the two steps are not prescribed). Somewhat surprising if we take into account the loose control on the performed operations, extended H systems with finite sets of axioms and of splicing rules, using this double splicing operation, can again characterize the recursively enumerable languages. Finally, we consider two types of distributed H systems: communicating distributed H systems and time-varying distributed H systems. For the first type of devices, we give a new proof of the recent result of [25] that (in the extended case) such systems with three components characterize the recursively enumerable languages. In what concerns the second mentioned distributed model, we prove that time-varying H systems with seven components can characterize the recursively enumerable languages. The optimality of these two last-mentioned results is open.

Remarks on Operations Suggested by Mutations in Genomes

In the last years the operation of splicing which models a special type of recombination of genomes has been intensively studied, e.g. the effect of application of splicings to language families of classical formal language theory has been investigated. In this paper we present analogous results with respect to the operations inversion, translocation and duplication which are also descriptions of mutations of genomes.

Controlled H Systems and Chomsky Hierarchy

This paper is an up-to-dated survey of results about the power of controlled extended H systems of various types. Such systems are finite generative devices based on the splicing operation, which, in turn, is a model of the DNA recombination. When no control is imposed on the splicing operation, we get a characterization of regular languages. When a control is considered, we obtain characterizations of recursively enumerable languages. We briefly discuss here H systems with control mechanisms similar to those in regulated rewriting area in formal language theory. We do not present proofs, but only definitions, results, and bibliographical information. Looking for characterizations of families in Chomsky hierarchy other than those of regular and of recursively enumerable languages, we closely investigate the H systems with permitting context conditions. We disprove a conjecture of Chakaravarthy and Krithivasan: such systems of radius one and using only one-sided context conditions can generate all context-free languages (the conjecture was that a characterization of linear languages is obtained). Some open problems are also mentioned.

Natural Computation for Natural Language

Computation not only takes place in provoked contexts of scientific experimentation, but in natural circumstances too. We are going to approach computation in natural contexts. How the nature computes? Turing machines and Chomsky grammars are rewriting systems, and the same is true for Post, Thue, Markov, Lindenmayer and other classes of axiomatic systems. If, among the whole set of natural objects, we focus natural language description, we must say that major trends in contemporary linguistics look at syntax as a rewriting process. Is rewriting unavoidable in this case, does our mind work by rewriting, does the nature compute in this way? We shall attempt to defend that the answer could be negative. The arguments will come from computability theory as well as from linguistics. First we'll formally explain the former ones, then informally the latter ones. With regard to computability theory arguments, we will see that, using the operation of adjoining, a large generative capacity is obtained. This is the case with contextual grammars. It has recently been proved that each recursively enumerable language is the quotient by a regular language of a language generated by a contextual grammar of a particular form. Thus, adjoining (paste) and quotient (cut) lead to computational universality. Recursively enumerable languages can also be characterized as the quotient by a regular language of a language generated by an insertion grammar. The same result is obtained if we take the splicing operation, a formal model of the DNA recombination. This is again a cut-and-paste operation. On the basis of the proof of this result, several further characterizations of recursively enumerable languages have been obtained. Computability theory, then, could be reconstructed without rewriting (and non-terminal symbols) and without any loss in power. Our first aim will be to show some formal aspects of such reconstruction. Later, we'll try to obtain some consequences for the future development of generative theory of natural language.

On the splicing operation

We propose here a systematic formal study of the splicing operation introduced by Head as a model of recombinant behavior of DNA. We consider both simple and iterated splicing, with respect to a finite or an infinite set of splicing rules, in the latter case the whole set of rules constituting a regular language. Relations between these operations and usual operations with languages are investigated, as well as the closure of Chomsky language families under these splicing operations. A series of open problems are formulated too.