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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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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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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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One-dimensional staged self-assembly

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NATURAL computing 2013年第2期12卷 247-258页

作者： Demaine, Erik D. Eisenstat, Sarah Ishaque, Mashhood Winslow, Andrew MIT Comp Sci & Artificial Intelligence Lab Cambridge MA 02139 USA Tufts Univ Dept Comp Sci Medford MA 02155 USA

We introduce the problem of staged self-assembly of one-dimensional nanostructures, which becomes interesting when the elements are labeled (e.g., representing functional units that must be placed at specific locations). In a restricted model in which each operation has a single terminal assembly, we prove that assembling a given string of labels with the fewest steps is equivalent, up to constant factors, to compressing the string to be uniquely derived from the smallest possible context-free grammar (a well-studied O(log n)-approximable problem) and that the problem is NP-hard. Without this restriction, we show that the optimal assembly can be substantially smaller than the optimal context-free grammar, by a factor of even for binary strings of length n. Fortunately, we can bound this separation in model power by a quadratic function in the number of distinct glues or tiles allowed in the assembly, which is typically small in practice.

关键词： Context-free grammar Wang tile dna computing Complexity

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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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dna Walker Circuits: Computational Potential, Design, and Verification

DNA Walker Circuits: Computational Potential, Design, and Ve...

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19th international conference on dna computing and molecular programming

作者： Dannenberg, Fritsw Kwiatkowska, Marta thachuk, Chris Turberfield, Andrew J. Univ Oxford Dept Comp Sci Wolfson BldgPk Rd Oxford OX1 3QD England Univ Oxford Dept Phys Clarendon Lab Oxford OX1 2JD England

ISBN: (纸本)9783319019284;9783319019277

Unlike their traditional, silicon counterparts, dna computers have natural interfaces with both chemical and biological systems. these can be used for a number of applications, including the precise arrangement of matter at the nanoscale and the creation of smart biosensors. Like silicon circuits, dna strand displacement systems (DSD) can evaluate non-trivial functions. However, these systems can be slow and are susceptible to errors. It has been suggested that localised hybridization reactions could overcome some of these challenges. Localised reactions occur in dna 'walker' systems which were recently shown to be capable of navigating a programmable track tethered to an origami tile. We investigate the computational potential of these systems for evaluating Boolean functions. dna walkers, like DSDs, are also susceptible to errors. We develop a discrete stochastic model of dna walker 'circuits' based on experimental data, and demonstrate the merit of using probabilistic model checking techniques to analyse their reliability, performance and correctness.

关键词： dna

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Temporal dna Barcodes: A Time-Based Approach for Single-Molecule Imaging 1

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24th international conference on dna computing and molecular programming (dna)

作者： Shah, Shalin Reif, John Duke Univ Dept Elect & Comp Engn Durham NC 27706 USA Duke Univ Dept Comp Sci Durham NC 27701 USA

ISBN: (数字)9783030000301

ISBN: (纸本)9783030000301;9783030000295

In the past decade, single-molecule imaging has opened new opportunities to understand reaction kinetics of molecular systems. dna-PAINT uses transient binding of dna strands to perform super-resolution fluorescence imaging. An interesting challenge in dna nanoscience and related fields is the unique identification of single-molecules. While wavelength multiplexing (using fluorescent dyes of different colors) can be used to increase the number of distinguishable targets, the resultant total number of targets is still limited by the number of dyes with non-overlapping spectra. In this work, we introduce the use of time-domain to develop a dna-based reporting framework for unique identification of single-molecules. these fluorescent dna devices undergo a series of conformational transformations that result in (unique) time-changing intensity signals. We define this stochastic temporal intensity trace as the device's temporal barcode since it can uniquely identify the corresponding dna device if the collection time is long enough. Our barcodes work with as few as one dye making them easy to design, extremely low-cost, and greatly simplifying the hardware setup. In addition, by adding multiple dyes, we can create a much larger family of uniquely identifiable reporter molecules. Finally, our devices are designed to follow the principle of transient binding and can be imaged using total internal reflection fluorescence (TIRF) microscopes so they are not susceptible to photo-bleaching, allowing us to monitor their activity for extended time periods. We model our devices using continuous-time Markov chains (CTMCs) and simulate their behavior using a stochastic simulation algorithm (SSA). these temporal barcodes are later analyzed and classified in their parameter space. the results obtained from our simulation experiments can provide crucial insights for collecting experimental data.

关键词： molecular reporters dna nanodevices Temporal reporters TIRF Transient binding dna hairpins Single-molecule imaging

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Scalable, Time-Responsive, Digital, Energy-Efficient molecular Circuits Using dna Strand Displacement

Scalable, Time-Responsive, Digital, Energy-Efficient Molecul...

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16th international conference on dna computing and molecular programming

作者： Chiniforooshan, Ehsan Doty, David Kari, Lila Seki, Shinnosuke Univ Western Ontario Dept Comp Sci London ON Canada

ISBN: (纸本)9783642183041

We propose a novel theoretical biomolecular design to implement any Boolean circuit using the mechanism of dna strand displacement. the design is scalable: all species of dna strands can in principle be mixed and prepared in a single test tube, rather than requiring separate purification of each species, which is a barrier to large-scale synthesis. the design is time-responsive: the concentration of output species changes in response to the concentration of input species, so that time-varying inputs may be continuously processed. the design is digital: Boolean values of wires in the circuit are represented as high or low concentrations of certain species, and we show how to construct a single-input, single-output signal restoration gate that amplifies the difference between high and low, which can be distributed to each wire in the circuit to overcome signal degradation. this means we can achieve a digital abstraction of the analog values of concentrations. Finally, the design is energy-efficient: if input species are specified ideally (meaning absolutely 0 concentration of unwanted species), then output species converge to their ideal concentrations at steady-state, and the system at steady-state is in (dynamic) equilibrium, meaning that no energy is consumed by irreversible reactions until the input again changes.

关键词： Timing circuits

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