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DNABased SelfPropagating Algorithm for Solving BoundedFanIn Boolean Circuits
 Genetic Programming 1998: Proceedings of the Third Annual Conference
, 1998
"... This paper proposes a method for simulating Boolean circuits based on primer extension and DNA cleavage. The advantage of the current method is the requirement of little human intervention during the course of simulation. The paper also explores the potential of RecAassisted DNADNA hybridization i ..."
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This paper proposes a method for simulating Boolean circuits based on primer extension and DNA cleavage. The advantage of the current method is the requirement of little human intervention during the course of simulation. The paper also explores the potential of RecAassisted DNADNA hybridization in DNAbased computation. The method could in principle allow simulation of many levels of large Boolean circuits in a single test tube. 1 Introduction DNA computing is an emerging field bridging the gap between computer science and biochemistry. Following seminal work by Adleman (Adleman 1994), the potential of DNA as an alternative device for massively parallel computation has been studied (see (Ogihara et al. 1997) for a survey). Among various topics in this field, exploring methods for simulating abstract parallel computation models seems important. There are two major abstract parallel computation models, the parallel random access machine model (the PRAM model) and the Boolean circuit...
The Inference Based On Molecular Computing
, 2000
"... 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 ..."
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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. 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
Simulating Boolean circuits by finite splicing
, 1999
"... As a computational model to be simulated in a DNA computing context, Boolean circuits are especially interesting because of their parallelism. Simulations in concrete biochemical computing settings have been given by [OR96] and [AD97]. In this paper, we show how to simulate Boolean circuits by finit ..."
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As a computational model to be simulated in a DNA computing context, Boolean circuits are especially interesting because of their parallelism. Simulations in concrete biochemical computing settings have been given by [OR96] and [AD97]. In this paper, we show how to simulate Boolean circuits by finite splicing systems, an abstract model of enzymatic recombination ([Hea87], [Gat94], [P au96a]). We argue that using an abstract model of DNA computation as a basis leads to simulations of greater clarity and generality. In our construction, the running time of the simulating system is proportional to the depth, and the use of material is proportional to the size of the Boolean circuit simulated. However, the rules of the simulating splicing system depend on the size of the Boolean circuit, but not on the connectives used.
Fast Parallel Molecular Algorithms for DNABased Computation: Factoring Integers
"... Abstract—The RSA publickey cryptosystem is an algorithm that converts input data to an unrecognizable encryption and converts the unrecognizable data back into its original decryption form. The security of the RSA publickey cryptosystem is based on the difficulty of factoring the product of two la ..."
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Abstract—The RSA publickey cryptosystem is an algorithm that converts input data to an unrecognizable encryption and converts the unrecognizable data back into its original decryption form. The security of the RSA publickey cryptosystem is based on the difficulty of factoring the product of two large prime numbers. This paper demonstrates to factor the product of two large prime numbers, and is a breakthrough in basic biological operations using a molecular computer. In order to achieve this, we propose three DNAbased algorithms for parallel subtractor, parallel comparator, and parallel modular arithmetic that formally verify our designed molecular solutions for factoring the product of two large prime numbers. Furthermore, this work indicates that the cryptosystems using publickey are perhaps insecure and also presents clear evidence of the ability of molecular computing to perform complicated mathematical operations. Index Terms—Biological parallel computing, DNAbased algorithms, DNAbased computing, factoring integers, RSA publickey cryptosystem. I.
Executing parallel logical operations with DNA
 In Proceedings of the IEEE Congress on Evolutionary Computation
, 1999
"... DNA computation investigates the potential of DNA as a massively parallel computing device. Research is focused on designing parallel computation models executable by DNAbased chemical processes and on developing algorithms in the models. In 1994 Leonard Adleman initiated this area of research by p ..."
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DNA computation investigates the potential of DNA as a massively parallel computing device. Research is focused on designing parallel computation models executable by DNAbased chemical processes and on developing algorithms in the models. In 1994 Leonard Adleman initiated this area of research by presenting a DNAbased method for solving the Hamilton Path Problem. That contribution raised the hope that parallel computation by DNA could be used to tackle NPcomplete problems which are thought of as intractable. The current realization, however, is that NPcomplete problems may not be best suited for DNAbased (more generally, moleculebased) computing. A better subject for DNA computing could be largescale evaluation of parallel computation models. Several proposals have been made in this direction. We overview those methods, discuss technical and theoretical issues involved, and present some possible applications of those methods. 1 Introduction Biomolecular computing is the computi...
DNA computing: implementation of data flow logical operations
, 2001
"... Selfassembly 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 molecu ..."
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Selfassembly 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 DNAbased molecular data flow logic gates. Some experimental results demonstrating implementation of a single logic NAND gate and only in one vessel calculation of a treelike Boolean function with the help of the PCR are provided. These techniques may be utilized in massively parallel computers and on DNA chips. 2001 Elsevier Science B.V. All rights reserved.
Binary arithmetic for DNA computers
 Lect Notes Comput Sci 2568:124–132
, 2003
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Processing DNA tokens in parallel computing
 In Proc. International Parallel and Distributed Processing Symposium
, 2001
"... 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 impl ..."
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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.
Relating the Minimum Model for DNA Computation and Boolean Circuits
 GENETIC AND EVOLUTIONARY COMPUTATION CONFERENCE
, 1999
"... This paper provides a refinement of the minimum DNA computational model by (Ogihara and Ray 1998b), which assumes the smallest set of permissible biochemical operations. The power of the refined model is characterized in terms of standard Boolean circuit complexity classes. ..."
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This paper provides a refinement of the minimum DNA computational model by (Ogihara and Ray 1998b), which assumes the smallest set of permissible biochemical operations. The power of the refined model is characterized in terms of standard Boolean circuit complexity classes.
DNA simulation of nand boolean circuits
 The Electronic International Journal Advanced Modeling and Optimization
"... In this paper we describe a simulation of Boolean circuits using biomolecular techniques. Boolean circuits embody the notion of massively parallel signal processing and are frequently encountered in many parallel algorithms. This model operates on the gates and the inputs by standard molecular tec ..."
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In this paper we describe a simulation of Boolean circuits using biomolecular techniques. Boolean circuits embody the notion of massively parallel signal processing and are frequently encountered in many parallel algorithms. This model operates on the gates and the inputs by standard molecular techniques of sequencespecific annealing, ligation, melting, cleavage, separation and detection by size. It is shown that the simulation is run in the time proportional to the depth of the circuit.