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; the obtained construct is called a super-cell. These objects are assumed to evolve: each object can be transformed in other objects, can pas through a membrane, or can disolve 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 super-cell 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...

Abstract not found

this paper, we present a generalized form of SVG, which supports additional biologically-relevant operations by going beyond homomorphisms, instead uniformly applying substitutions in either a forward or reverse direction (see Definition 2.1) to bindings of logic variables. We give a constructive proof of our conjecture [26] that the languages describable by SVG are contained in the indexed languages, and furthermore show that the containment is proper, thus refining the position of an important class of biological sequences in the hierarchy of languages. We also describe a simple grammar translator, give a number of examples of mathematical and biological languages, discuss the distinctions between SVG, DG, TAG, and RPDAs, and suggest extensions well-suited to the overlapping languages of genes. Finally, we describe a large-scale implementation of a domain-specific parser called GenLang which incorporates a practical version of these ideas, and which has been successful in parsing several types of genes from DNA sequence data [9, 30], in a form of pattern-matching search termed syntactic pattern recognition [10]. 6 2. STRING VARIABLE GRAMMAR

xiv Chapter 1 Introduction 1 Chapter 2 DNA structure and manipulation 6 2.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6 2.2 The structure and manipulation of DNA . . . . . . . . . . . . . . . . 7 2.3 Operations on DNA . . . . . . . . . . . . . . . . . . . . . . . . . . . 9 2.3.1 Synthesis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10 2.3.2 Denaturing, annealing and ligation . . . . . . . . . . . . . . . 10 2.3.3 Hybridisation separation . . . . . . . . . . . . . . . . . . . . . 10 2.3.4 Gel electrophoresis . . . . . . . . . . . . . . . . . . . . . . . . 11 2.3.5 Primer extension and PCR . . . . . . . . . . . . . . . . . . . 13 iii 2.3.6 Restriction enzymes . . . . . . . . . . . . . . . . . . . . . . . 14 2.3.7 Cloning . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15 2.4 Summary . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19 Chapter 3 Models of DNA computation 21 3.1 Introduction . . . . . . . . . . ....

. Motivated by the recombinant behavior of DNA, Tom Head introduced a scheme for the evolution of formal languages called splicing. We give a simpler proof of the fundamental fact that the closure of a regular language under iterated splicing using a finite number of splicing rules is again regular. We then extend this result in two directions, by incorporating circular strings and by using infinite, but regular, sets of splicing rules. Section 1. Introduction In [3] and [4] Tom Head introduced an operation on strings called splicing,. The basic idea is that two strings are cut at specified substrings, called sites, and the first segment of one is reattached to the second segment of the other with the sites suitably modified. The motivation for this operation lies in the study of the recombination of DNA fragments under the effects of restriction enzymes and ligases; we refer the reader to Head's papers for this motivation and for further references. Our basic definition is a general...

In this paper we describe a simulation of Boolean circuits using standard bio-molecular techniques. Previously proposed simulations have been shown to run in time proportional to the size of the circuit. The simulation we present here runs in time proportional to the depth of the circuit. We describe the abstract model and its laboratory implementation, before concluding with a brief analysis.

The aim of this paper is to introduce to the reader the main ideas of computing with membranes, a recent branch of (theoretical) molecular computing. In short, in a cell-like system, multisets of objects evolve according to given rules in the compartments defined by a membrane structure and compute natural numbers as the result of halting sequences of transitions. The model is parallel, nondeterministic. Many variants have already been considered and many problems about them were investigated. We present here some of these variants, focusing on two central classes of results: (1) characterizations of the recursively enumerable sets of numbers and (2) possibilities to solve NP-complete problems in polynomial — even linear — time (of course, by making use of an exponential space). The results are given without proofs. An almost complete bibliography of the domain, at the middle of October 2000, is

From a biological motivation of interactions between linear and circular DNA sequences, we propose a new type of splicing models called circular H systems and show that they have the same computational power as Turing machines. It is also shown that there effectively exists a universal circular H system which can simulate any circular H system with the same terminal alphabet, which strongly suggests a feasible design for a DNA computer based on circular splicing. 1 Introduction Since Adleman's breath-taking paper on molecular (DNA) computing ([1]), there have already been quite a few papers on this challenging topic : [10] shows how to solve NP-complete problems using DNA, while [3] discusses a design method for simulating a Turing machine by molecular biological techniques and shows how to compute PSPACE, and [4]) gives a methodology for breaking the DES using techniques in genetic engineering. In response to the rapid stream of experimental research on this new computation paradigm...

Abstract not found

The paper extends some of the most recently obtained results on the computational universality of specific variants of H systems (e. g. with regular sets of rules) and proves that we can construct universal computers based on various types of H systems with a finite set of splicing rules as well as a finite set of axioms, i. e. we show the theoretical possibility to design programmable universal DNA computers based on the splicing operation. For H systems working in the multiset style (where the numbers of copies of all available strings are counted) we elaborate how a Turing machine computing a partial recursive function can be simulated by an equivalent H system computing the same function; in that way, from a universal Turing machine we obtain a universal H system. Considering H systems as language generating devices we have to add various simple control mechanisms (checking the presence/absence of certain symbols in the spliced strings) to systems with a finite set of splicing ru...