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

On the power of parallel communicating Watson–Crick automata systems

AbstractParallel communicating Watson–Crick automata systems were introduced in [E. Czeizler, E. Czeizler, Parallel communicating Watson–Crick automata systems, in: Z. Ésik, Z. Fülöp (Eds.), Proc. Automata and Formal Languages, Dobogókő, Hungary, 2005, pp. 83–96] as possible models of DNA computations. This combination of Watson–Crick automata and parallel communicating systems comes as a natural extension due to the new developments in DNA manipulation techniques. It is already known, see [D. Kuske, P. Weigel, The Role of the Complementarity Relation in Watson–Crick Automata and Sticker Systems, DLT 2004, Lecture Notes in Computer Science, Vol. 3340, Auckland, New Zealand, 2004, pp. 272–283], that for Watson–Crick finite automata, the complementarity relation plays no active role. However, this is not the case when considering parallel communicating Watson–Crick automata systems. In this paper we prove that non-injective complementarity relations increase the accepting power of these systems. We also prove that although Watson–Crick automata are equivalent to two-head finite automata, this equivalence is not preserved when comparing parallel communicating Watson–Crick automata systems and multi-head finite automata

Синхронія за К. Г. Юнгом та сплутані квантові стани: кіт Шредінгера «блукає» між хромосомами

Один з найбільш перспективних напрямків дослідження феномену синхронії за К. Г. Юнгом розглядується з позиції останніх досягнень сучасної науки. Увага зосереджена, головним чином, на сплутаних квантових станах та пов'язаних феноменах – квантової когерентності та квантової суперпозиції. Показано що квантова нелокальність, яка здатна розв'язати парадокс Ейнштейна –Подольского-Розена є одним з найбільш адекватних фізичних механізмів у плані відповідності гіпотезі синхронії Юнга. Здійснена спроба психофізіологічного обґрунтування синхронії у контексті молекулярної біології. Запропоновано оригінальну концепцію, згідно якої, біологічні молекули що задіяні при поділу клітини під час мітозу та мейозу, зокрема ДНК, можуть бути матеріальними носіями свідомості. Це припущення може бути сформульовано на основі феноменології аналітичної психології Юнга

DNA computing by blocking

AbstractWe present a method for molecular computing which relies on blocking (inactivating) this part of the total library of molecules that does not contribute to (finding) a solution—this happens essentially in one biostep (after the input has been read). The method is explained by presenting a DNA based algorithm for solving (albeit in the theoretical sense only!) the satisfiability problem

Paradigms for computational nucleic acid design

The design of DNA and RNA sequences is critical for many endeavors, from DNA nanotechnology, to PCR‐based applications, to DNA hybridization arrays. Results in the literature rely on a wide variety of design criteria adapted to the particular requirements of each application. Using an extensively studied thermodynamic model, we perform a detailed study of several criteria for designing sequences intended to adopt a target secondary structure. We conclude that superior design methods should explicitly implement both a positive design paradigm (optimize affinity for the target structure) and a negative design paradigm (optimize specificity for the target structure). The commonly used approaches of sequence symmetry minimization and minimum free‐energy satisfaction primarily implement negative design and can be strengthened by introducing a positive design component. Surprisingly, our findings hold for a wide range of secondary structures and are robust to modest perturbation of the thermodynamic parameters used for evaluating sequence quality, suggesting the feasibility and ongoing utility of a unified approach to nucleic acid design as parameter sets are refined further. Finally, we observe that designing for thermodynamic stability does not determine folding kinetics, emphasizing the opportunity for extending design criteria to target kinetic features of the energy landscape