Results 1  10
of
47
On the Power of Circular Splicing Systems and DNA Computability
 Proc. of IEEE Intern. Conf. on Evol. Comput. (ICEC'97
, 1997
"... 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 sy ..."
Abstract

Cited by 23 (5 self)
 Add to MetaCart
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 breathtaking paper on molecular (DNA) computing ([1]), there have already been quite a few papers on this challenging topic : [10] shows how to solve NPcomplete 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...
Universal Molecular Computation in Ciliates
 Evolution as Computation
, 2002
"... How do cells and nature "compute"? They read and "rewrite" DNA all the time, by processes that modify sequences at the DNA or RNA level. In 1994, Adleman's elegant solution to a sevencity Directed Hamiltonian Path problem using DNA [1] launched the new field of DNA computing, which in a few years h ..."
Abstract

Cited by 21 (3 self)
 Add to MetaCart
How do cells and nature "compute"? They read and "rewrite" DNA all the time, by processes that modify sequences at the DNA or RNA level. In 1994, Adleman's elegant solution to a sevencity Directed Hamiltonian Path problem using DNA [1] launched the new field of DNA computing, which in a few years has grown to international scope. However, unknown to this field, ciliated protozoans of genus Oxytricha and Stylonychia had solved a potentially harder problem using DNA several million years earlier. The solution to this "problem", which occurs during the process of gene unscrambling, represents one of nature's ingenious solutions to the problem of the creation of genes. Here we develop a model for the guided homologous recombinations that take place during gene rearrangement and prove that such a model has the computational power of a Turing machine, the accepted formal model of computation. This indicates that, in principle, these unicellular organisms may have the capacity to perform at ...
Computational Power of Gene Rearrangement
"... In [8] we proposed a model to describe the homologous recombinations that take place during massive gene rearrangements in hypotrichous ciliates. Here we develop the model by introducing the dependency of homologous recombinations on the presence of certain contexts. We then prove that such a model ..."
Abstract

Cited by 20 (4 self)
 Add to MetaCart
In [8] we proposed a model to describe the homologous recombinations that take place during massive gene rearrangements in hypotrichous ciliates. Here we develop the model by introducing the dependency of homologous recombinations on the presence of certain contexts. We then prove that such a model has the computational power of a Turing machine. This indicates that, in principle, some unicellular organisms may have the capacity to perform any computation carried out by an electronic computer.
DNA Computing Based on Splicing: The Existence of Universal Computers
 THEORY OF COMPUTING SYSTEMS
, 1995
"... 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 ..."
Abstract

Cited by 19 (3 self)
 Add to MetaCart
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.
Test Tube Distributed Systems Based on Splicing
 COMPUTERS AND AI
, 1996
"... We define a symbol processing mechanism with the components (test tubes) working as splicing schemes in the sense of T. Head and communicating by redistributing the contents of tubes (in a similar way to the separate operation of LiptonAdleman). (These systems are similar to the distributed generat ..."
Abstract

Cited by 19 (1 self)
 Add to MetaCart
We define a symbol processing mechanism with the components (test tubes) working as splicing schemes in the sense of T. Head and communicating by redistributing the contents of tubes (in a similar way to the separate operation of LiptonAdleman). (These systems are similar to the distributed generative mechanisms called Parallel Communicating Grammar Systems.) Systems with finite initial contents of tubes and finite sets of splicing rules associated to each component are computationally complete, they characterize the family of recursively enumerable languages. The existence of universal test tube distributed systems is obtained on this basis, hence the theoretical proof of the possibility to design universal programmable computers with the structure of such a system.
Paradigms for Biomolecular Computation
 UNCONVENTIONAL MODELS OF COMPUTATION
, 1998
"... Biomolecular Computation (BMC) is computation done at the molecular scale, using Biotechnological techniques. This paper discusses the underlying biotechnology that BMC may utilize, and surveys a number of distinct paradigms for doing BMC. We also identify a number of key future experimental mile ..."
Abstract

Cited by 15 (6 self)
 Add to MetaCart
Biomolecular Computation (BMC) is computation done at the molecular scale, using Biotechnological techniques. This paper discusses the underlying biotechnology that BMC may utilize, and surveys a number of distinct paradigms for doing BMC. We also identify a number of key future experimental milestones for the field of BMC.
Programmability of Chemical Reaction Networks
"... Summary. Motivated by the intriguing complexity of biochemical circuitry within individual cells we study Stochastic Chemical Reaction Networks (SCRNs), a formal model that considers a set of chemical reactions acting on a finite number of molecules in a wellstirred solution according to standard c ..."
Abstract

Cited by 8 (2 self)
 Add to MetaCart
Summary. Motivated by the intriguing complexity of biochemical circuitry within individual cells we study Stochastic Chemical Reaction Networks (SCRNs), a formal model that considers a set of chemical reactions acting on a finite number of molecules in a wellstirred solution according to standard chemical kinetics equations. SCRNs have been widely used for describing naturally occurring (bio)chemical systems, and with the advent of synthetic biology they become a promising language for the design of artificial biochemical circuits. Our interest here is the computational power of SCRNs and how they relate to more conventional models of computation. We survey known connections and give new connections between SCRNs and
Splicing Languages Generated with One Sided Context
 Computing With Biomolecules{Theory and Experiments
, 1997
"... The splicing system concept was created in 1987 to allow the convenient representation in formal language theoretic terms of recombinant actions of certain sets of enzymes on double stranded DNA molecules. Characterizations are given here for those regular languages that are generated by splicing ..."
Abstract

Cited by 7 (1 self)
 Add to MetaCart
The splicing system concept was created in 1987 to allow the convenient representation in formal language theoretic terms of recombinant actions of certain sets of enzymes on double stranded DNA molecules. Characterizations are given here for those regular languages that are generated by splicing systems having splicing rules that test context on only one side. An algorithm is given for deciding whether any arbitrary regular language can be generated by a splicing system in which all splicing rules test context on the same side. Schutzenberger's concept of a constant relative to a language provides the tool for constructing the required splicing rules. To provide a potential biochemical example, the formal generative capacity of the restriction enzyme BpmI in the company of a ligase is discussed. Experimental investigation is invited. Key words: Splicing systems, HSystems, DNAcomputing, biocomputing, bioinformatics, regular languages, finite automata. 1 Introduction The sp...