Jan J. Mulawka

Adding numbers with DNA

A novel algorithm based on DNA computing for adding binary integer numbers is presented. It requires the unique representation of bits placed in test tubes treated as registers. Amplification step used for the carry operation allows one, in theory, to add numbers with the same quantity of elementary operations, regardless of the number of bits used for representation. New notation proposed in the paper allows for efficient and abstract description of the technical operations on DNA.

The Inference Based on Molecular Computing

Molecular computing is a new paradigm to perform calculations using nanotechnology. This paper presents the overall research direction from which molecular inference and expert systems are emerging. It introduces the subject matter and a general description of the problems involved. This includes selected methods of knowledge representation by DNA oligonucleotides, strategies of the inference mechanism, concept of the inference engine based on circular DNA molecules, particularly derived from plasmids, practical experience in DNA inference engine implementation, and discussion of the experimental results. The approach allows evaluating logical statements and drawing inferences for generating other statements via DNA computing. A series of experiments have been conducted to confirm practical utility of this approach. In these experiments, parameters of biochemical reactions were varied to determine truth/false recognition accuracy. In addition, we discuss the fundamental issues of inference engine and try to enhance physical insight into the dominating features of the approach proposed.Molecular computing is a new paradigm to perform calculations using nanotechnology. This paper presents the overall research direction from which molecular inference and expert systems are emerging. It introduces the subject matter and a general description of the problems involved. This includes selected methods of knowledge representation by DNA oligonucleotides, strategies of the inference mechanism, concept of the inference engine based on circular DNA molecules, particularly derived from plasmids, practical experience in DNA inference engine implementation, and discussion of the experimental results. The approach allows evaluating logical statements and drawing inferences for generating other statements via DNA computing. A series of experiments have been conducted to confirm practical utility of this approach. In these experiments, parameters of biochemical reactions were varied to determine truth/false recognition accuracy. In addition, we discuss the fundamental issues of inference engine and try ...

DNA computing: implementation of data flow logical operations

Self-assembly of DNA is considered a fundamental operation in realization of molecular logic circuits. We propose a new approach to implementation of data flow logical operations based on manipulating DNA strands. In our method the logic gates, input, and output signals are represented by DNA molecules. Each logical operation is carried out as soon as the operands are ready. This technique employs standard operations of genetic engineering including radioactive labeling as well as digestion by the second class restriction nuclease and polymerase chain reaction (PCR). To check practical utility of the method a series of genetic engineering experiments have been performed. The obtained information confirms interesting properties of the DNA-based molecular data flow logic gates. Some experimental results demonstrating implementation of a single logic NAND gate and only in one vessel calculation of a tree-like Boolean function with the help of the PCR are provided. These techniques may be utilized in massively parallel computers and on DNA chips.

Implementation of the inference engine based on molecular computing technique

Presents a novel application of molecular computing to problems of expert systems. A biochemical reaction on DNA strands is used to realise the backward chaining algorithm. The knowledge base for the expert system is based on the sticker model: memory strands represent rules while stickers represent facts and hypotheses. A series of experiments has been conducted to confirm the practical utility of this approach. In these experiments, the parameters of biochemical reactions were varied to determine true/false recognition accuracy. In addition, we discuss the fundamental issues of inference engines and try to enhance the physical insight into the dominating features of the approach proposed.

Another logical molecular NAND gate system

In this paper we implement a new logic NAND gate using standard operations on DNA strands as well as digestion by the restriction nuclease class II. This concept despite some difficulties looks in general more elegant and can be utilized with fluorescent probes. Some experimental results demonstrating implementation of a single logic NAND gate are provided. The derived logic gates are proposed to be implemented on DNA chips.

Molecular genetic programming

Abstract The paper addresses a new implementation of genetic programming by using molecular approach. Our method is based on dataflow techniques in DNA computing. After description of fundamental operations on DNA molecules and construction of logical functions the genetic programming method is introduced. We propose a way to handle these graph encoding molecules and which can be considered a genetic programming algorithm; a short discussion about experiments in implementing parts of this procedure is added.

The inference via DNA computing

DNA computing is a new paradigm to perform calculations using genetic engineering technology. The paper presents the overall research direction from which molecular inference and expert systems are emerging. It provides an introduction to the subject matter and a general description of the problems involved. This includes selected methods of knowledge representation by DNA strands, strategies of the inference mechanism, concept of the inference engine based on circular DNA molecules, particularly derived from plasmids, practical experience in DNA inference engine implementation, and discussion of the experimental results. The approach allows evaluating logical statements and drawing inferences for generating other statements via DNA computing.

Implementation of Data Flow Logical Operation via Self-Assembly of DNA

Self-assembly of DNA is considered a fundamental operation in realization of molecular logic circuits. We propose a new approach to implementation of data flow logical operations based on manipulating DNA strands. In our method the logic gates, input, and output signals are represented by DNA molecules. Each logical operation is carried out as soon as the operands are ready. This technique employs standard operations of genetic engineering including radioactive labeling. To check practical utility of the method a series of genetic engineering experiments have been performed. The obtained results confirm interesting properties of the DNA-based molecular data flow logic gates. This technique may be utilized in massively parallel computers.

Molecular Inference via Unidirectional Chemical Reactions

Inference process plays an important role in the realisation of expert systems. In this paper it is shown that chemical reactions may by used to perform molecular inference according to the algorithm of forward chaining. This method is accomplished by an adequate interpretation of inorganic chemical compounds and unidirectional reactions. In our approach premise clauses are represented by the reactants while conclusion clauses are represented by the products of reaction. Different inorganic compounds and reactions have been discussed with respect to their utility for the molecular inference. Special attention is focused on qualitative chemistry and a number of reactions has been taken into account. Experimental results demonstrating application of these reactions in expert systems are provided.

Processing DNA tokens in parallel computing

In this paper a new technique of sending data between molecular processors is presented. The molecular processor is a processing data unit. Its computation results have to be sent to other units in the form of addressed messages - tokens. Necessary experiments were performed. All operations were implemented in DNA. DNA processors and tokens were specially designed DNA strings. Results of experiments prove our assumptions.