0000000001301367
AUTHOR
Jacek Waldmajer
Biomolecular computers with multiple restriction enzymes
Abstract The development of conventional, silicon-based computers has several limitations, including some related to the Heisenberg uncertainty principle and the von Neumann “bottleneck”. Biomolecular computers based on DNA and proteins are largely free of these disadvantages and, along with quantum computers, are reasonable alternatives to their conventional counterparts in some applications. The idea of a DNA computer proposed by Ehud Shapiro’s group at the Weizmann Institute of Science was developed using one restriction enzyme as hardware and DNA fragments (the transition molecules) as software and input/output signals. This computer represented a two-state two-symbol finite automaton t…
Arithmetical Analysis of Biomolecular Finite Automaton
In the paper we present a theoretical analysis of extension of the finite automaton built on DNA (introduced by the Shapiro team) to an arbitrary number of states and symbols. In the implementation we use a new idea of several restriction enzymes instead of one. We give arithmetical conditions for the existence of such extensions in terms of ingredients used in the implementation.
DNA Computing: Concepts for Medical Applications
The branch of informatics that deals with construction and operation of computers built of DNA, is one of the research directions which investigates issues related to the use of DNA as hardware and software. This concept assumes the use of DNA computers due to their biological origin mainly for intelligent, personalized and targeted diagnostics frequently related to therapy. Important elements of this concept are (1) the retrieval of unique DNA sequences using machine learning methods and, based on the results of this process, (2) the construction/design of smart diagnostic biochip projects. The authors of this paper propose a new concept of designing diagnostic biochips, the key elements o…
Theory of tailor automata
Abstract In the paper, a fragment of the new theory of tailor automata is presented, within which a deterministic finite automaton was defined. The proposed automaton provides a theoretical model of an informally characterized biomolecular automaton. The idea of working of which is founded on the concept of alternating cut of some double-stranded fragments of DNA, with the use of a restriction enzyme and ligations of some double-stranded fragments of DNA, with the use of the ligase enzyme.
A detailed experimental study of a DNA computer with two endonucleases
Abstract Great advances in biotechnology have allowed the construction of a computer from DNA. One of the proposed solutions is a biomolecular finite automaton, a simple two-state DNA computer without memory, which was presented by Ehud Shapiro’s group at the Weizmann Institute of Science. The main problem with this computer, in which biomolecules carry out logical operations, is its complexity – increasing the number of states of biomolecular automata. In this study, we constructed (in laboratory conditions) a six-state DNA computer that uses two endonucleases (e.g. AcuI and BbvI) and a ligase. We have presented a detailed experimental verification of its feasibility. We described the effe…
A Representation of Relational Systems
In this paper elements of a theory of multistructures are formulated. The theory of multistructures is used to define a binary representation of relational systems.
A Solution to the Problem of the Maximal Number of Symbols for Biomolecular Computer
The authors present a solution to the problem of generating the maximum possible number of symbols for a biomolecular computer using restriction enzyme BbvI and ligase as the hardware, and transition molecules built of double-stranded DNA as the software. The presented solution offers an answer to the open question, in the algorithm form, of the maximal number of symbols for a biomolecular computer that makes use of the restriction enzyme BbvI.
Biomolecular computers with multiple restriction enzymes
Abstract The development of conventional, silicon-based computers has several limitations, including some related to the Heisenberg uncertainty principle and the von Neumann “bottleneck”. Biomolecular computers based on DNA and proteins are largely free of these disadvantages and, along with quantum computers, are reasonable alternatives to their conventional counterparts in some applications. The idea of a DNA computer proposed by Ehud Shapiro’s group at the Weizmann Institute of Science was developed using one restriction enzyme as hardware and DNA fragments (the transition molecules) as software and input/output signals. This computer represented a two-state two-symbol finite automaton t…