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Complex logic circuit of three-input and nine-output by dna strand displacement 13th

Complex logic circuit of three-input and nine-output by DNA ...

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13th international conference on Bio-Inspired computing: theories and Applications, BIC-TA 2018

作者： Wang, Yanfeng Yuan, Guodong Huang, Chun Sun, Junwei Henan Key Lab of Information-Based Electrical Appliances Zhengzhou University of Light Industry Zhengzhou450002 China School of Electrical and Information Engineering Zhengzhou University of Light Industry Zhengzhou450002 China

ISBN: (纸本)9789811328282

In recent years, dna strand displacement technology has developed rapidly with the advantages of high-performance parallel computing and large information capacity. dna strand displacement technology is a dynamic dna nanotechnology developed on the basis of dna self-assembly technology. dna strand displacement technology can realize dynamic connection between input signal and output signal, and it is a method for constructing logic gates and logic circuits. According to the basic principle of dna strand displacement, this paper studies the specific function of the molecular logic circuit model, and constructs a logic circuit with three input and nine output. then a biochemical logic circuit is built based on the dual-rail thought and the construction of seesaw gate. Finally, dna strand displacement simulation platform Visual DSD is used to verify the rationality of the model. It lays the foundation for constructing complex logic circuits. © Springer Nature Singapore Pte Ltd. 2018.

关键词： Timing circuits

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Logic circuit design of sixteen-input encoder by dna strand displacement 1

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13th international conference on Bio-Inspired computing: theories and Applications, BIC-TA 2018

作者： Wang, Yanfeng Lv, Aolong Huang, Chun Sun, Junwei Henan Key Lab of Information-Based Electrical Appliances Zhengzhou University of Light Industry Zhengzhou450002 China School of Electrical Information Engineering Zhengzhou University of Light Industry Zhengzhou450002 China

ISBN: (数字)9789811328299

ISBN: (纸本)9789811328282

As a very powerful tool, dna strand displacement technology is widely used in molecular calculations, which has received more and more attention from people. It has achieved rapid development in recent years. In this paper, a sixteen-input encoder based on dna strand displacement is designed, including dual-rail circuits and seesaw circuits based on dna strand displacement. Visual DSD is a visualization software with compiling and emulation capabilities. All reactions of encoding and simulation are performed in the visualization software Visual DSD. By changing the input signal, the accurate output can be obtained, the function of sixteen-input encoder in digital circuit is realized. With Visual DSD software, more complex logic operations are implemented based on dna strand displacement. this kind of research based on dual-rail circuits by dna strand displacement have great prospects for the development and practical application of biological information processing and molecular computing. © Springer Nature Singapore Pte Ltd. 2018.

关键词： Visualization

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A tool for the design of dna base sequences for molecular circuits 17

A tool for the design of DNA base sequences for molecular ci...

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17th international conference on Control, Automation and Systems (ICCAS)

作者： Yoshida, Yuki Nakakuki, Takashi Kyushu Inst Technol Major Interdisciplinary Informat 680-4 Kawazu Iizuka Fukuoka 8208502 Japan Kyushu Inst Technol Dept Syst Design & Informat 680-4 Kawazu Iizuka Fukuoka 8208502 Japan

ISBN: (纸本)9788993215144

Designing a set of dna base sequences for a large-scale molecular circuit is a difficult problem in the field of dna computing. A dna circuit frequently suffers from unintended dna strand displacements among strands;this problem can ruin the desired function of a dna circuit. In this study, our aim was to develop a computational tool for the design of dna base sequences by means of an original algorithm based on mismatches in a dna base sequence. Validity of the proposed algorithm is confirmed by practical redesign examples.

关键词： dna computing molecular circuit dna base sequence Design tool

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Research on the addition, subtraction, multiplication and division complex logical operations based on the dna strand displacement 1

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13th international conference on Bio-Inspired computing: theories and Applications, BIC-TA 2018

作者： Huang, Chun Wang, Yanfeng Zhou, Qinglei School of Information Engineering Zhengzhou University Zhengzhou450001 China College of Electrical and Electronic Engineering Zhengzhou University of Light Industry Zhengzhou450002 China

ISBN: (数字)9789811328299

ISBN: (纸本)9789811328282

In recent years, the development of biological computers has become faster and faster. In order to adapt to the development of science and technology, some novel logic circuits designs are necessary. In this paper, a complex molecular combinational logic circuit is designed to perform large-scale biological information processing by compound logic operation of addition, subtraction, multiplication and division. the design of compound logic operations of addition, subtraction, multiplication and division based on dna strand has four inputs signals and two output signals, and the dual-track design theory is used to perform the logic circuit operation, and the corresponding output result can be obtained in timely and accurately. the whole reaction progress of logic circuit operations can be programmed and simulated by the Visual DSD software. According to the simulation results of the Visual DSD software, the method of dna strand displacement is feasible to achieve more complex logic computations. this investigation for the addition, subtraction, multiplication and division complex logical operations of a binary number may have a great prospect for the development and application in the biological information processing, medicine diagnosis, molecular computing, and so on. © Springer Nature Singapore Pte Ltd. 2018.

关键词： Logic circuits

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Extracting the Co-occurrences of dna Maximal Repeats in both Human and Viruses 17

Extracting the Co-occurrences of DNA Maximal Repeats in both...

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17th IEEE international conference on Bioinformatics and Bioengineering, BIBE 2017

作者： Wang, Jing-Doo Wang Wang, Yi-Chun Hu, Rouh-Mei Tsai, Jeffrey J.P. Dept. of Computer Science and Information Engineering Asia University Taiwan Dept. of Biomedical Sciences Chung Shan Medical University Taiwan Dept. of Bioinformatics and Medical Engineering Asia University Taiwan

ISBN: (纸本)9781538613245

this paper aims to extract significant dna sequences appearing in both the genomes of human and viruses. To extract the co-occurrences of dna sequences as long as possible, this study adopts a scalable approach that is based on hadoop mapreduce programming model and can extract maximal repeats;meanwhile compute the class frequency distribution of these repeats. the genomes of human and all of 4,388 viruses available in NCBI are downloaded at 2017/1/14. To take the taxonomy of viruses into consideration for further observation, only the 2,712 viruses that had been named with genus are selected from those 4,388 viruses. In this study, the taxonomic level 'genus' is as the units (classes) when comparing viruses and human for experiments. Experimental results show that the longest dna sequence appearing in both human and viruses extracted in this study is 463 base pair (bp), and that sequence, consisting of tandem repeats as '(CTAACC)n', appears in the 5th human chromosome and virus 'Human herpesvirus 6B'. It may be attractive for virologists to have further research why there exists such a long dna fragment existed in both human and that virus. Indeed, this study may provide a new direction for genomic sequences comparison across classesthat can provide clues to inspect the existence of the relationship between these dna maximal repeats (genotypes) with biased class frequency distribution and the features of classes (phenotypes). © 2017 IEEE.

关键词： dna

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On the Use of Binary Trees for dna Hydroxymethylation Analysis 17th

On the Use of Binary Trees for DNA Hydroxymethylation Analys...

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17th international conference on Algorithms and Architectures for Parallel Processing (ICA3PP)

作者： Gonzalez, Cesar Perez, Mariano Orduna, Juan M. Chaves, Javier Garcia, Ana-Barbara Univ Valencia Dept Informat Avda Univ S-N Valencia 46100 Spain CIBERDEM Carlos III Hlth Inst INCLIVA Hlth Res Inst Avda Menendez Pelayo 4 Accesorio Valencia 46010 Spain

ISBN: (纸本)9783319654829;9783319654812

dna methylation (mC) and hydroxymethylation (hmC) can have a significant effect on normal human development, health and disease status. Hydroxymethylation studies require specific treatment of dna, as well as software tools for their analysis. In this paper, we propose a parallel software tool for analyzing the dna hydroxymethylation data obtained by TAB-seq. the software is based on the use of binary trees for searching the different occurrences of methylation and hydroxymethylation in dna samples. the binary trees allow to efficiently store and access the information about the methylation of each methylated/hydroxymethylated cytosines in the samples. Evaluation results shows that the performance of the application is only limited by the computer input/output bandwidth, even for the case of very long samples.

关键词： High performance computing dna hydroxymethylation Parallel pipeline

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Solution to Motif Finding Problem in Membranes 17th

Solution to Motif Finding Problem in Membranes

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17th international conference on Membrane computing (CMC)

作者： Gapuz, Katrina B. Mendoza, Ephraim D. Juayong, Richelle Ann B. Hernandez, Nestine Hope S. Cabarle, Francis George C. Adorna, Henry N. Univ Philippines Diliman Dept Comp Sci Algorithms & Complex Lab Quezon City 1101 Philippines

ISBN: (纸本)9783319540726;9783319540719

the study of genes is an important field of biology. A way to understand genetic composition is through finding regularly occurring nucleotide sequences, or motifs, in a dna sequence. However, finding these motifs is difficult and is shown to be NP-complete. In this paper, we use a variant of P systems called Evolution-Communication P systems with Energy using string objects to solve the Motif Finding Problem in O(lt)-time where l is the length of the motif and t is the number of dna sequences given.

关键词： Membrane computing Evolution-communication P systems with energy Motif finding

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A Shared Memory Method ForEnhancingthe HTNGH AlgorithmPerformance: Proposed Method 17

A Shared Memory Method ForEnhancingThe HTNGH AlgorithmPerfor...

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international conference on Future Networks and Distributed Systems (ICFNDS)

作者： Abu-Hashem, Muhannad A. Uliyan, Diaa M. Abuarqoub, Abdelrahman Middle East Univ Fac Informat Technol Amman Jordan

ISBN: (纸本)9781450348447

In bioinformatics, pair-wise alignment plays a significant role insequence comparison by rating the similarities and distances between protein, DeoxyriboNucleic Acid (dna), and RiboNucleic Acid (RNA)sequences. Sequence comparison considered as a key stone in building distance matrices. Due to the rapid growth of molecular databases, the need for faster sequence comparison and alignment has become anecessity. High performance computing impacthas increased in the last decade through providing many high performance architectures and tools. In this paper we present a parallel shared memory design for a dynamic programming algorithm named Hash Table-N-Gram-Hirschberg (HT-NGH) an extension of Hashing-N-Gram-Hirschberg (HNGH) and N-Gram-Hirschberg (NGH) algorithm, to speed up the sequence alignment construction process. the focus of the proposed method ison the transformation phase of HT-NGH algorithm since it takes10% of HT-NGH overall run time. the experimental evaluation of the proposed parallel designshows an enhancement in the execution time and speedup without sacrificing the accuracy. However,the decomposition method might slightly slowdown the proposed algorithm due to the differences in performance between the processing units.

关键词： Shared-Memory Parallel design High-performance computing Sequence Alignment pair-wise alignment distance matrix construction

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the logic circuit design of fire alarm system device by dna strand displacement 12th

The logic circuit design of fire alarm system device by DNA ...

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12th international conference on Bio-Inspired computing: theories and Applications, BIC-TA 2017

作者： Wang, Yanfeng Li, Jixiang Huang, Chun Sun, Junwei Henan Key Lab of Information-Based Electrical Appliances Zhengzhou University of Light Industry Zhengzhou450002 China College of Electrical and Electronic Engineering Zhengzhou University of Light Industry Zhengzhou450002 China

ISBN: (纸本)9789811071782

dna strand displacement acted as a useful tool is most widely used in the majority computing system. In this paper, a four-input fire alarm system device based on dna strand displacement is designed. the whole reaction course is programmed and simulated in the software visual DSD, which presenting the superb simulation results with inputs and outputs through compiling the procedure for computation device. According to the results of the Visual DSD software, the method of dna strand displacement by dual-rail circuits is feasible to achieve more complex logic computation. this investigation on the basis of dna strand displacement by dual-rail circuits may have a great prospect for the development and application in the biological information processing, molecular computing, and so on. © Springer Nature Singapore Pte Ltd 2017.

关键词： Timing circuits

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Robust directional-diffusive hybrid molecular communication with parity-check erasure coding

Robust directional-diffusive hybrid molecular communication ...

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Joint World Congress of international Fuzzy Systems Association and international conference on Soft computing and Intelligent Systems (IFSA-SCIS)

作者： Hiroaki Egashira Junichi Suzuki Jonathan S. Mitzman Tadashi Nakano Hiroaki Fukuda Department of Information Science and Engineering Shibaura Institute of Technology Tokyo Japan Department of Computer Science University of Massachusetts Boston Boston MA USA Osaka University Institute for Academic Initiatives Osaka Japan

ISBN: (纸本)9781509049189

this paper investigates a robustness enhancement protocols for biologically-enabled machines (or bio-nanomachines) to reliably exchange information by means of molecules in the aqueous, intrabody environment. the proposed protocol performs forward error correction (FEC) for directional-diffusive hybrid transports, in which molecules travel through two different transports: directional and diffusive transports. It allows the transmitter bio-nanomachine to encode molecules in a redundant manner with parity-check erasure codes. the receiver bio-nanomachine can recover the information embedded in lost molecules. Simulation results show that the proposed protocol enhances robustness against molecule losses and in turn improves communication performance. they also reveal the impacts of FEC overhead and molecule redundancy on the communication performance.

关键词： molecular communication dna Protocols Forward error correction Receivers Robustness Transmitters

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