Splicing systems using merge and separate operations (original) (raw)
Related papers
A proposal to a generalised splicing with a self assembly approach
arXiv preprint arXiv:0802.0260, 2008
Theory of splicing is an abstract model of the recombinant behaviour of DNAs. In a splicing system, two strings to be spliced are taken from the same set and the splicing rule is from another set. Here we propose a generalised splicing (GS) model with three components, two strings from two languages and a splicing rule from third component. We propose a generalised self assembly (GSA) of strings. Two strings u1xv1 and u2xv2 self assemble over x and generate u1xv2 and u2xv1. We study the relationship between GS and GSA. We study some classes of generalised splicing languages with the help of generalised self assembly.
Locally Evolving Splicing Systems
2017
An extended H system with locally evolving rules is a model of splicing computation with a special feature that the splicing rules evolve at each step. It was originally proved by Paun et al. that all RE languages can be generated by such systems with a finite set of rules of radius at most 4 and with contexts of length at most 7 for the insertion-deletion rules by which the splicing rules evolve. We improve this result by reducing the length of the contexts to at most 2 and we also show that such systems with radius at most 2 and contexts of length at most 3 can generate all RE languages. In both cases, the insertion-deletion rules will insert or delete only one symbol. We also show that if the inserted strings are of length at most 2 and the deleted strings are of length 1, then the system can generate all RE languages with splicing rules of radius 3 and insertion-deletion rules with contexts of length at most 2. Finally, we show that the length of contexts and of the strings inse...
DNA computing based on splicing: The existence of universal computers
1999
Splicing systems are generative mechanisms based on the splicing operation introduced by Tom Head as a model of DNA recombination. We prove that the generative power of finite extended splicing systems equals that of Turing machines, provided we consider multisets or provided a control mechanism is added. We also show that there exist universal splicing systems with the properties above, i. e. there exists a universal splicing system with fixed components which can simulate the behaviour of any given splicing system, when an encoding of the particular splicing system is added to its set of axioms. In this way the possibility of designing programmable DNA computers based on the splicing operation is proved.
{Networks of Uniform Splicing Processors
ArXiv, 2019
In this note we consider a new variant of network of splicing processors which simplifies the general model such that filters remain associated with nodes but the input and output filters of every node coincide. This variant is called {\it network of uniform splicing processors}. Although the communication in the new variant seems less powerful, being based on simpler filters, the new variant is sufficiently powerful to be computationally complete. The main result is that nondeterministic Turing machines can be simulated by networks of uniform splicing processors. Furthermore, the simulation is time efficient.
Networks of Uniform Splicing Processors: Computational Power and Simulation
Mathematics, 2020
We investigated the computational power of a new variant of network of splicing processors, which simplifies the general model such that filters remain associated with nodes but the input and output filters of every node coincide. This variant, called network of uniform splicing processors, might be implemented more easily. Although the communication in the new variant seems less powerful, the new variant is sufficiently powerful to be computationally complete. Thus, nondeterministic Turing machines were simulated by networks of uniform splicing processors whose size depends linearly on the alphabet of the Turing machine. Furthermore, the simulation was time efficient. We argue that the network size can be decreased to a constant, namely six nodes. We further show that networks with only two nodes are able to simulate 2-tag systems. After these theoretical results, we discuss a possible software implementation of this model by proposing a conceptual architecture and describe all its...
Probabilistic Semi–Simple Splicing System and Its Characteristics
Jurnal Teknologi, 2013
The concept of splicing system was first introduced by Head in 1987. This model has been introduced to investigate the recombinant behavior of DNA molecules. Splicing systems with finite sets of axioms only generate regular languages. Hence, different restrictions have been considered to increase the computational power up to the recursively enumerable languages. Recently, probabilistic splicing systems have been introduced where probabilities are initially associated with the axioms, and the probability of a generated string is computed by multiplying the probabilities of all occurrences of the initial strings in the computation of the string. In this paper, some properties of probabilistic semi-simple splicing systems, which are special types of probabilistic splicing systems, are investigated. We prove that probabilistic semi-simple splicing systems can also increase the generative power of the generated languages.
Generalized P-Systems with Splicing and Cutting/Recombination
Grammars, 1999
P-systems recently were introduced by Gheorghe Pa un as a new model for computations based on membrane structures. Using the membranes as a kind of filter for specific objects when transferring them into an inner compartment turned out to be a very powerful mechanism in combination with suitable rules to be applied within the membranes in the model of generalized P-systems, GP-systems for short. In general, GP-systems allow for the simulation of graph controlled grammars of arbitrary type based on productions working on single objects. In this paper we consider GP-systems as computing devices using splicing or cutting and recombination of strings. Various variants of such systems are proved to have universal computational power, e.g., we show how test tube systems based on splicing or cutting and recombination of strings can be simulated by the corresponding GP-systems.
Simulations between Three Types of Networks of Splicing Processors
Mathematics, 2021
Networks of splicing processors (NSP for short) embody a subcategory among the new computational models inspired by natural phenomena with theoretical potential to handle unsolvable problems efficiently. Current literature considers three variants in the context of networks managed by random-context filters. Despite the divergences on system complexity and control degree over the filters, the three variants were proved to hold the same computational power through the simulations of two computationally complete systems: Turing machines and 2-tag systems. However, the conversion between the three models by means of a Turing machine is unattainable because of the huge computational costs incurred. This research paper addresses this issue with the proposal of direct and efficient simulations between the aforementioned paradigms. The information about the nodes and edges (i.e., splicing rules, random-context filters, and connections between nodes) composing any network of splicing proces...
Theoretical Computer Science, 1996
Computing by splicing is a new powerful tool stemming originally from molecular genetics. This new model of computing, splicing systems, is investigated here. Several variants, resulting from the use of the rules in different ways, are considered. The power of such systems with very weak structure imposed on rules turns out to be very large. Characterizations of recursively enumerable languages are obtained for many variants. In this way our study is analogous to the early studies concerning variations of Turing machines. Other classes of such splicing systems generate only regular or context-free languages (giving, in fact, characterizations of these families). With a few exceptions, we are able to obtain precise characterizations for all resulting families. . 0304-3975/96/% 15.00 @ 1996 -Elsevier Science B.V. All rights reserved PIZ SO304-3975(96)00082-S 1. (c)L E EHf,,,(Fl,Fz), for g1 = 1, g2 arbitrary, 2. (c)L E EH,,,f(Fl,Fz), for g2 = 1, g1 arbitrary, 3. L(c) E EHf,,,(Fl,Fz), for g1 = r, g2 arbitrary, 4. L(c) E EH,,,~(FI,F~), for g2 = r, g1 arbitrary, 5. (c)L(c) E EHf,,,(Fl,Fz), for g1 = m, g2 arbitrary, 6. (c)L(c) E EH,,,f(Fl,Fz), for g2 = m, g1 arbitrary. All the corresponding assertions are true also for non-extended families.
Probabilistic simple splicing systems
2014
A splicing system, one of the early theoretical models for DNA computing was introduced by Head in 1987. Splicing systems are based on the splicing operation which, informally, cuts two strings of DNA molecules at the specific recognition sites and attaches the prefix of the first string to the suffix of the second string, and the prefix of the second string to the suffix of the first string, thus yielding the new strings. For a specific type of splicing systems, namely the simple splicing systems, the recognition sites are the same for both strings of DNA molecules. It is known that splicing systems with finite sets of axioms and splicing rules only generate regular languages. Hence, different types of restrictions have been considered for splicing systems in order to increase their computational power. Recently, probabilistic splicing systems have been introduced where the probabilities are initially associated with the axioms, and the probabilities of the generated strings are computed from the probabilities of the initial strings. In this paper, some properties of probabilistic simple splicing systems are investigated. We prove that probabilistic simple splicing systems can also increase the computational power of the splicing languages generated.