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检索条件"任意字段=17th International Conference on DNA Computing and Molecular Programming"

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dna computing Units Based on Fractional Coding 1

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18th international conference on Unconventional Computation and Natural Computation (UCNC)

作者： Salehi, Sayed Ahmad Moore, Peyton Univ Kentucky Lexington KY 40506 USA

ISBN: (数字)9783030193119

ISBN: (纸本)9783030193119;9783030193102

Fractional encoding has been recently proposed as a promising convention to represent information in molecular computing systems. this paper presents new 2-input molecular computing units based on unipolar fractional representation. the units calculate simple computational equations that can be used for the computation of more complex functions. the design of these molecular computing units is inspired by fan-in 2 logic gates in the field of stochastic computing. Each computing unit consists of four chemical reactions with two reactants and one product. We design the dna reactions implementing the chemical reactions of each unit based on the toehold-mediated dna strand-displacement mechanism. Every unit is designed by four input strands and eight fuel gate strands of dna. Since dna molecules related to the input and output of the units have the same form of domain-toehold-domain-toehold, output molecules of each unit can be used as input for other units and this provides the cascading of the units for designing complex circuits. the whole dna pathway for each unit is composed of twenty dna reactions. the simulation results by Visual DSD show that the dna implementations follow the theoretically expected computations of each unit with the maximum of 9.33% error.

关键词： dna computing Fractional coding dna strand-displacement

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dna computing and molecular programming 1

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丛书名： Lecture Notes in Computer Science

1000年

作者： Satoshi Murata Satoshi Kobayashi

ISBN: (数字)9783319112954

ISBN: (纸本)9783319112947

this book constitutes the refereed proceedings of the 20th international conference on dna computing and molecular programming, dna 20, held in Kyoto, Japan, in September 2014. the 10 full papers presented were carefully selected from 55 submissions. the papers are organized in many disciplines (including mathematics, computer science, physics, chemistry, material science and biology) to address the analysis, design, and synthesis of information-based molecular systems.

关键词： Computation by Abstract Devices Algorithm Analysis and Problem Complexity Computational Biology/Bioinformatics Artificial Intelligence Data Structures Discrete Mathematics in Computer Science

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Parallel pairwise operations on data stored in dna: Sorting, shifting, and searching 27

Parallel pairwise operations on data stored in dna: Sorting,...

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27th international conference on dna computing and molecular programming, dna 2021

作者： Chen, Tonglin Solanki, Arnav Riedel, Marc Department of Electrical and Computer Engineering University of Minnesota MinneapolisMN United States

ISBN: (纸本)9783959772051

Prior research has introduced the Single-Instruction-Multiple-Data paradigm for dna computing (SIMD dna). It offers the potential for storing information and performing in-memory computations on dna, with massive parallelism. this paper introduces three new SIMD dna operations: Sorting, shifting, and searching. Each is a fundamental operation in computer science. Our implementations demonstrate the effectiveness of parallel pairwise operations with this new paradigm. © 2021 Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing. All rights reserved.

关键词： Sorting

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dna computing Sequence Design Based on Bacterial Foraging Algorithm 18

DNA Computing Sequence Design Based on Bacterial Foraging Al...

引用

5th international conference on Bioinformatics Research and Applications (ICBRA)

作者： Ren, Jiankang Yao, Yao Dalian Univ Technol Sch Comp Sci & Technol Dalian Peoples R China

ISBN: (纸本)9781450366113

Since the quantity and quality of dna sequence directly affect the accuracy and efficiency of computation, the design of dna sequence is critical to dna computing. In order to improve the reliability of dna computing, there is a rich literature targeting at making dna sequences specifically hybridize at a lower melting temperature, no non-complementary bases pairs or mismatch hybridization in the reformed double helix. However, most of them are not good enough to control the melting temperature, because dna sequence design problem under the constraints of hamming distance, secondary structure, molecular thermodynamic is known to be NP-hard. For the sake of achieving the lower and similar melting temperature for each dna sequence, we proposed a dna sequence coding method based on Bacterial Foraging Algorithm (BFA). An evaluation criterion is particularly proposed to assess the quality of dna sequence in the optimization process. With BFA, high-quality dna strands are replicated to avoid the participation of inferior strands in the operation. Experiments show our proposed approach significantly outperforms existing methods in terms of continuity and melting temperature.

关键词： dna computing dna sequence design BFA

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the circular dna model of 0-1 programming problem based on dna strand displacement 14

The circular DNA model of 0-1 programming problem based on D...

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14th international conference on Natural Computation, Fuzzy Systems and Knowledge Discovery, ICNC-FSKD 2018

作者： Tang, Zhen Yin, Zhixiang Yang, Jing Sun, Xia Cui, Jianzhong School of Mathematics and Big Data AnHui University of Science and Technology Huainan AnHui232001 China School of Electronic and Information Engineering AnHui University of Science and Technology Huainan AnHui232001 China

ISBN: (纸本)9781538680971

dna strand displacement is a new molecular biological technology with strong operability and simple experimental conditions. In this paper, dna strand displacement is applied to solve the 0-1 programming problem, and a model is constructed using the class closed-loop dna structure (known as 'circular dna' in this paper). the model fixes the dna strands which represent the variables on the circular dna single strand in counterclockwise order. the dna strand 5' end is attached with the primers which are applied to the displacement of the dna strand. the 3' end is attached with the colored fluorophore. Taking the possible solutions as the input, the results are detected by different fluorescent colors resulting from the dna strand displacement. the dna computing model has better flexibility, realizability and applicability. © 2018 IEEE.

关键词： dna

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Search and Validation of Short Genome-Wide Biomarkers for Bacterial Biological Phylogenies

Search and Validation of Short Genome-Wide Biomarkers for Ba...

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16th international conference on dna computing and molecular programming

作者： Garzon, Max H. Wong, Tit-Yee Univ Memphis Memphis TN 38152 USA

ISBN: (纸本)9783642183041

We continue the exploration of dna-based indexing as a universal coordinate system in dna spaces to characterize very large groups (families, genera, and even phylla) of organisms on a uniform biomarker reference system, a comprehensive "Atlas of Life", as it is or as it could be on earth. We provide a second confirmation that dna noncrosshybridizing (nxh) sets can be successfully applied to infer ab-alitio phylogenetic trees by providing a method to measure distances among entire genomes indexed by sets of short oligonucleotides selected so as to minimize crosshybridization. these phylogenies are solidly established and well accepted in bacterial biology, albeit done by analyses of relatively small segments of highly conserved rybozomic dna. Second, it is further demonstrated that dna indexing does provide novel and principled genome-wide predictions into the phylogenesis of organisms hitherto inaccessible by current methods, such as a prediction of the origin of the Salmonella plasmid 50 as being acquired horizontally, likely from some bacteria somewhat related to Yesinia. We conclude with some discussion about the scalability and potential of this method to develop a comprehensive tree of life based on genome-wide methods.

关键词： dna codeword design noncrosshybridizing oligonucleotide bases phylogenetic analysis genomic signatures dna chips 16S rRNA tree of life

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dna Chips for Species Identification and Biological Phylogenies

DNA Chips for Species Identification and Biological Phylogen...

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15th international conference on dna computing and molecular programming

作者： Garzon, Max H. Wong, Tit-Yee Phan, Vinhthuy Univ Memphis Memphis TN 38152 USA

ISBN: (纸本)9783642106033

the codeword design problem is an important problem in dna computing and its applications. Several theoretical analyses as well as practical solutions for short oligonucleotides (up to 20-mers) have been generated recently. these solutions have, in turn, suggested new applications to dna-based indexing and natural language processing, in addition to the obvious applications to the problems of reliability and scalability that generated them. Here we continue the exploration of this type of dna-based indexing for biological applications and show that dna noncrosshybridizing (nxh) sets can be successfully applied to infer ab initio phylogenetic trees by providing a way to measure distances among different genomes indexed by sets of short oligonucleotides selected so as to minimize crosshybridization. these phylogenies are solidly established and well accepted in biology. the new technique is much more effective in terms of signal-to-noise ratio, cost and time than current methods. Second, it can be scaled up to newly available universal dna chips readily available both in vitro and in silica. In particular, we show how a recently obtained such set of nxh 16-mers can be used as a universal coordinate system in dna spaces to characterize very large groups (families, genera, and even phylla) of organisms on a uniform reference system, a veritable and comprehensive "Atlas of Life", as it is or as it could be on earth.

关键词： dna codeword design noncrosshybridizing oligonucleotide bases phylogenetic analysis genomic signatures dna chips 16S rRNA tree of life

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Proceedings of the 4th ACM international conference on Nanoscale computing and Communication, NanoCom 2017

Proceedings of the 4th ACM International Conference on Nanos...

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4th ACM international conference on Nanoscale computing and Communication, NanoCom 2017

ISBN: (纸本)9781450349314

the proceedings contain 32 papers. the topics discussed include: received signal strength for randomly distributed molecular nanonodes;event and node identification from a single-pulse transmission in self-powered nanosensor networks;chemical reaction networks for maximum likelihood estimation of the concentration of signalling molecules;ratiometric logic in living cells via competitive binding of synthetic transcription factors;design principles of data converters for building large-scale gene networks in living cells;achieving in-phase synchronization in a diffusion-based nanonetwork with unknown propagation delay;increase detection algorithm for concentration-encoded diffusion-based molecular communication;simulation analysis of inter-symbol interference in diffusion-based molecular communication with non-absorbing receiver;a programming framework for neuromorphic systems with emerging technologies;brain-inspired computing accelerated by memristor technology;towards spiking neuromorphic system-on-a-chip with bio-plausible synapses using emerging devices;molecular communication with dna cellular storage system;prospects for the application of 2-dimensional materials to terahertz-band communications;and a folded wireless network-on-chip using graphene based thz-band antennas.

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Parallel and scalable computation and spatial dynamics with dna-based chemical reaction networks on a surface

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20th international conference on dna computing and molecular programming, dna 2014

作者： Qian, Lulu Winfree, Erik Bioengineering California Institute of Technology PasadenaCA91125 United States Computer Science California Institute of Technology PasadenaCA91125 United States Computation and Neural Systems California Institute of Technology PasadenaCA91125 United States

ISBN: (纸本)9783319112947

We propose a theoretical framework that uses a novel dna strand displacement mechanism to implement abstract chemical reaction networks (CRNs) on the surface of a dna nanostructure, and show that surface CRNs can perform efficient algorithmic computation and create complex spatial dynamics. We argue that programming molecular behaviors with surface CRNs is systematic, parallel and scalable. © Springer international Publishing Switzerland 2014.

关键词： dna

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Space and energy efficient computation with dna strand displacement systems

Space and energy efficient computation with DNA strand displ...

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18th international conference on dna computing and molecular programming, dna 18

作者： thachuk, Chris Condon, Anne Department of Computer Science University of British Columbia Vancouver BC Canada

ISBN: (纸本)9783642322075

Chemical reaction networks (CRN's) are important models of molecular programming that can be realized by logically reversible, and thus energy efficient, dna strand displacement systems (DSD's). Qian et al. [12] showed that energy efficient DSD's are Turing-universal;however their simulation of a computation requires space (or volume) proportional to the number of steps of the computation. Here we show that polynomially space bounded computations can be simulated in both a space and energy efficient manner using logically reversible CRN's and DSD's. A consequence of our proofs is that determining whether a particular molecular species can be produced from an initial pool of molecules of a CRN or DSD is PSPACE-hard, and thus also verifying the correctness of CRN's and DSD's is PSPACE-hard. © 2012 Springer-Verlag.

关键词： Energy efficiency

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