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检索条件"任意字段=15th International Conference on DNA Computing and Molecular Programming, DNA 15"

共 143 条记录，以下是11-20 订阅

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Time-Complexity of Multilayered dna Strand Displacement Circuits

Time-Complexity of Multilayered DNA Strand Displacement Circ...

引用

15th international conference on dna computing and molecular programming

作者： Seelig, Georg Soloveichik, David Univ Washington Seattle WA 98195 USA CALTECH Pasadena CA USA

ISBN: (纸本)9783642106033

Recently we have shown how molecular logic circuits with many components arranged in multiple layers can be built using dna strand displacement reactions. the potential applications of this and similar technologies inspire the study of the computation time of multilayered molecular circuits. Using mass action kinetics to model dna strand displacement-based circuits, we discuss how computation time scales with the number of layers. We show that depending on circuit architecture, the time-complexity does not necessarily scale linearly with the depth as is assumed in the usual study of circuit complexity. We compare circuits with catalytic and non-catalytic components, showing that catalysis fundamentally alters asymptotic time-complexity. Our results rely on simple asymptotic arguments that should be applicable to a wide class of chemical circuits. these results may help to improve circuit performance and may be useful for the construction of faster, larger and more reliable molecular circuitry.

关键词： dna

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Survey on dna Encryption Techniques 15

Survey on DNA Encryption Techniques

引用

15th international conference on Advances in computing, Control, and Telecommunication Technologies, ACT 2024

作者： Sowmya, D. Manjula, G.R. Department of CS&E JNNCE Shivamogga India

ISBN: (纸本)9798331300579

the area of dna cryptography is an interdisciplinary field that has emerged recently, focusing on the possible applications of dna (deoxyribonucleic acid) molecules for secure encryption and data storage. It uses dna sequences to create methods for encoding, encrypting, and decoding data by fusing concepts from cryptography and molecular biology. this paper presents various works proposed in dna encoding. © Grenze Scientific Society, 2024.

关键词： Encoding (symbols)

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Renewable, Time-Responsive dna Logic Gates for Scalable Digital Circuits

Renewable, Time-Responsive DNA Logic Gates for Scalable Digi...

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15th international conference on dna computing and molecular programming

作者： Goel, Ashish Ibrahimi, Morteza Stanford Univ Dept Management Sci & Engn Stanford CA 94305 USA Stanford Univ Dept Comp Sci Stanford CA USA Stanford Univ Dept Elect Engn Stanford CA USA

ISBN: (纸本)9783642106033

In this article, we introduce a design of dna logic gates based on enzymatic restriction of dna strands. We present a construction for a set of one and two-input logic gates and argue that our construction can be generalized to implement any Boolean operation. A key feature of our design is its time-responsiveness, in the presence of appropriate fuels these gates can operate continuously and generate a time-dependent output in response to a time-dependant input. they can be interconnected to form digital circuits. Moreover, modulo connectivity information, the strand design and circuit design phases are decoupled.

关键词： Logic gates

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GenAlign - A High Performance Implementation for Aligning the Compressed dna Sequences

GenAlign - A High Performance Implementation for Aligning th...

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15th international conference on Advanced computing Technologies (ICACT)

作者： Satyanvesh, D. Balleda, Kaliuday Baruah, P. K. Sri Sathya Sai Inst Higher Learning Prasanthinilayam India

ISBN: (纸本)9781467328166;9781467328180

In molecular biology, sequence alignment is a way of arranging dna, RNA or protein sequences to identify regions of similarity between the sequences. However, this is a challenging problem since the dna sequences are huge in size and the databases are growing at an exponential rate. It requires tremendous amount of memory and large computational power. For example, the human genome in raw format ranges from 2 to 30 Tera-bytes. the inherent property of dna is that it contains many repeats which makes it highly compressible. this paper presents a new approach of aligning the sequences after compressing them. the alignment consists of both ungapped and gapped alignment. Multi-cores and GPUs can be used to align these huge sequences quickly on the compressed sequences. the focus mainly is on aligning the huge sequences accurately. the ungapped alignment achieves a speedup of upto 56 on K20 Kepler GPUs and the gapped alignment achieves a speedup of upto 15 on multi-cores.

关键词： dna Sequence Bandwidth throughput Compression Ratio Code byte Speedup Gapped alignment Ungapped alignment

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Automatic Design of dna Logic Gates Based on Kinetic Simulation

Automatic Design of DNA Logic Gates Based on Kinetic Simulat...

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15th international conference on dna computing and molecular programming

作者： Kawamata, Ibuki Tanaka, Fumiaki Hagiya, Masami Univ Tokyo Grad Sch Informat Sci & Technol Bunkyo Ku Tokyo 1138656 Japan

ISBN: (纸本)9783642106033

Recently, dna logic gates and dna machines have been developed using only a simple complementary base pairing of dna, that is, hybridization and branch migration. Because such reaction systems have been designed by trial and error, it has been difficult to design a complex system and to correctly verify the reaction. the purpose of this research is to develop a method for automatically searching and designing dna logic gates based on a kinetic simulation. Since the solution space that should be searched is quite large, a simulated-annealing method is used to search for a highly evaluated system from many candidates and find a semi-optimal one. A simulator based on a kinetic model is developed, which calculates the time change of concentrations of abstracted dna molecules. An evaluation function, in which the evaluation value rises when the logic gate works correctly, is also designed. the effectiveness of the proposed method is evaluated experimentally with an AND gate, which is designed automatically.

关键词： dna

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Analysis of dna-dimer frequency in retroviral genomes with a fuzzy itemsets pattern induction strategy

Analysis of DNA-dimer frequency in retroviral genomes with a...

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15th international conference on computing

作者： Garza-Dominguez, R. Bautista-thompson, E. Quiroz-Gutierrez, A. Centro de Tecnologias de Información UNACAR Facultad de Quimica UNACAR

ISBN: (纸本)9780769527086

dSince dna dimer analysis has demonstrated to provide a very conserved pattern that has been suggested as a genome signature, we apply a strategy based on fuzzy sets theory and frequent itemsets pattern induction, for searching hidden structural relations in the dna-dimer frequency patterns of a collection of Retrovirus genomes. We found an interesting differentiation between subsets of retroviruses, as well as some unexpected similarities in the context of the dna-dimer frequency patterns. We believe that identifying basic genomic patterns and connecting this information with other sources of information can give us new and important knowledge about how these patterns are related with the viral structure and its dynamics. the computational methodology presented in this paper has demonstrated to be a robust tool for the study and the analysis of genomic sequences.

关键词： dna

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Optimal design of dna coding based on multi-strategy JAYA algorithm 15

Optimal design of DNA coding based on multi-strategy JAYA al...

引用

15th international conference on Advanced Computational Intelligence (ICACI)

作者： Wang, Siwei Zhu, Donglin Wang, Xiao Zhejiang Normal Univ Sch Math & Comp Sci Jinhua 321000 Zhejiang Peoples R China Zhejiang Normal Univ Xingzhi Coll Jinhua 321000 Peoples R China

ISBN: (纸本)9798350321456

dna computing as a future method of computing, has been widely concerned by many scholars because of its high density, high parallelism and other characteristics, which have led to a significant improvement in the storage capacity and computational speed of dna computing, and the optimization problem of dna computing has remained a popular research area until now. this paper proposes an optimisation design for dna coding based on the improved JAYA algorithm, which incorporates saltation learning, lensing learning and the equalisation of random and Halton sequences to initialise populations, improving the standard JAYA algorithm's shortcomings of strong randomness, uneven population distribution and insufficient inter-population communication, and cleverly balancing the convergence and population diversity of the algorithm, allowing the JAYA algorithm to be able to find better quality in the process of finding the best. the improved JAYA algorithm is proved to be highly practical through ablation study.

关键词： saltation learning lensing learning JAYA Halton sequences dna coding optimization ablation study

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Multi-objective Grasshopper Optimisation Algorithm applied to Design dna Sequences 15

Multi-objective Grasshopper Optimisation Algorithm applied t...

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15th international conference on Advanced Computational Intelligence (ICACI)

作者： Guo, Huaiyu Feng, Zhiyu Wang, Xiao Zhejiang Normal Univ Sch Comp Sci & Math Jinhua 321000 Zhejiang Peoples R China Zhejiang Normal Univ Xingzhi Coll Jinhua 321004 Zhejiang Peoples R China

ISBN: (纸本)9798350321456

High stable and high reliable dna sequences are requisite in dna computing search field. dna sequences can be quantified in an array of thermodynamical and logical constraints which play an important role in process of hybridization. Since designing of dna sequences set regraded as a multi objective optimization problem due to these constraints, epsilon constraint introduced in this paper which is a thought of reduce object dimensions. these constraints can be classified in single squence constraints and multiple sequences constraints, two meta heuristic algorithms tunicate swarm algorithm and grasshopper optimisation algorithm used in different steps according to their features and applicable scenarios. Result of this progress shows that epsilon constraints collaborate with other algorithms may produce advanced dna sequences set compare to previous work.

关键词： dna sequence design dna computing tunicate swarm algorithm grasshopper optimisation algorithm epsilon constraint

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dna Chips for Species Identification and Biological Phylogenies

DNA Chips for Species Identification and Biological Phylogen...

引用

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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Towards Domain-Based Sequence Design for dna Strand Displacement Reactions

Towards Domain-Based Sequence Design for DNA Strand Displace...

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16th international conference on dna computing and molecular programming

作者： Zhang, David Yu CALTECH Pasadena CA 91125 USA

ISBN: (纸本)9783642183041

dna strand displacement has been used to construct a variety of components, devices, and circuits. the sequences of involved nucleic acid molecules can greatly influence the kinetics and function of strand displacement reactions. To facilitate consideration of spurious reactions during the design process, one common strategy is to subdivide dna strands into domains, continuous nucleic acid bases that can be abstracted to act as a unit in hybridization and dissociation. Here, considerations for domain-based sequence design are discussed, and heuristics are presented for the sequence design of domains. Based on these heuristics, a randomized algorithm is implemented for sequence design.

关键词： dna

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