3,099 research outputs found
Splicing Systems from Past to Future: Old and New Challenges
A splicing system is a formal model of a recombinant behaviour of sets of
double stranded DNA molecules when acted on by restriction enzymes and ligase.
In this survey we will concentrate on a specific behaviour of a type of
splicing systems, introduced by P\u{a}un and subsequently developed by many
researchers in both linear and circular case of splicing definition. In
particular, we will present recent results on this topic and how they stimulate
new challenging investigations.Comment: Appeared in: Discrete Mathematics and Computer Science. Papers in
Memoriam Alexandru Mateescu (1952-2005). The Publishing House of the Romanian
Academy, 2014. arXiv admin note: text overlap with arXiv:1112.4897 by other
author
Drip and Mate Operations Acting in Test Tube Systems and Tissue-like P systems
The operations drip and mate considered in (mem)brane computing resemble the
operations cut and recombination well known from DNA computing. We here
consider sets of vesicles with multisets of objects on their outside membrane
interacting by drip and mate in two different setups: in test tube systems, the
vesicles may pass from one tube to another one provided they fulfill specific
constraints; in tissue-like P systems, the vesicles are immediately passed to
specified cells after having undergone a drip or mate operation. In both
variants, computational completeness can be obtained, yet with different
constraints for the drip and mate operations
Sticker systems over monoids
Molecular computing has gained many interests among researchers since Head introduced the first theoretical model for DNA based computation using the splicing operation in 1987. Another model for DNA computing was proposed by using the sticker operation which Adlemanused in his successful experiment for the computation of Hamiltonian paths in a graph: a double stranded DNA sequence is composed by prolonging to the left and to the right a sequence of (single or double) symbols by using given single stranded strings or even more complex dominoes with sticky ends, gluing these ends together with the sticky ends of the current sequence according to a complementarity relation. According to this sticker operation, a language generative mechanism, called a sticker system, can be defined: a set of (incomplete) double-stranded sequences (axioms) and a set of pairs of single or double-stranded complementary sequences are given. The initial sequences are prolonged to the left and to the right by using sequences from the latter set, respectively. The iterations of these prolongations produce “computations” of possibly arbitrary length. These processes stop when a complete double stranded sequence is obtained. Sticker systems will generate only regular languages without restrictions. Additional restrictions can be imposed on the matching pairs of strands to obtain more powerful languages. Several types of sticker systems are shown to have the same power as regular grammars; one type is found to represent all linear languages whereas another one is proved to be able to represent any recursively enumerable language. The main aim of this research is to introduce and study sticker systems over monoids in which with each sticker operation, an element of a monoid is associated and a complete double stranded sequence is considered to be valid if the computation of the associated elements of the monoid produces the neutral element. Moreover, the sticker system over monoids is defined in this study
Splicing representations of strictly locally testable languages
AbstractThe relationship between the family SH of simple splicing languages, which was recently introduced by Mateescu et al. and the family SLT of strictly locally testable languages is clarified by establishing an ascending hierarchy of families {SiH: i⩾ − 1} of splicing languages for which SH = S1H and the union of the families is the family SLT. A procedure is given which, for an arbitrary regular language L, determines whether L is in SLT and, when L is in SLT, specifies constructively the smallest family in the hierarchy to which L belongs. Examples are given of sets of restriction enzymes for which the action on DNA molecules is naturally represented by splicing systems of the types discussed
Word Blending and Other Formal Models of Bio-operations
As part of ongoing efforts to view biological processes as computations, several formal models of DNA-based processes have been proposed and studied in the formal language literature. In this thesis, we survey some classical formal language word and language operations, as well as several bio-operations, and we propose a new operation inspired by a DNA recombination lab protocol known as Cross-pairing Polymerase Chain Reaction, or XPCR. More precisely, we define and study a word operation called word blending which models a special case of XPCR, where two words x w p and q w y sharing a non-empty overlap part w generate the word x w y. Properties of word blending that we study include closure properties of the Chomsky families of languages under this operation and its iterated version, existence of solution to equations involving this operation, and its state complexity
Shaded Tangles for the Design and Verification of Quantum Programs (Extended Abstract)
We give a scheme for interpreting shaded tangles as quantum programs, with
the property that isotopic tangles yield equivalent programs. We analyze many
known quantum programs in this way -- including entanglement manipulation and
error correction -- and in each case present a fully-topological formal
verification, yielding in several cases substantial new insight into how the
program works. We also use our methods to identify several new or generalized
procedures.Comment: In Proceedings QPL 2017, arXiv:1802.0973
- …