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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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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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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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Synthesizing Small and Reliable Tile Sets for Patterned dna Self-assembly

Synthesizing Small and Reliable Tile Sets for Patterned DNA ...

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17th international conference on dna computing and molecular programming

作者： Lempiainen, Tuomo Czeizler, Eugen Orponen, Pekka Aalto Univ Sch Sci HIIT Dept Informat & Comp Sci FI-00076 Aalto Finland

ISBN: (纸本)9783642236372;9783642236389

We consider the problem of finding, for a given 2D pattern of colored tiles, a minimal set of tile types self-assembling to this pattern in the abstract Tile Assembly Model of Winfree (1998). this Patterned self-Assembly Tile set Synthesis (PATS) problem was first introduced by Ma and Lombardi (2008), and subsequently studied by Goos and Orponen (2011), who presented an exhaustive partition-search branch-and-bound algorithm (briefly PS-BB) for it. However, finding the true minimal tile sets is very time consuming, and PS-BB is not well-suited for finding small but not necessarily minimal solutions. In this paper, we modify the basic partition-search framework by using a heuristic to optimize the order in which the algorithm traverses its search space. We find that by running several parallel instances of the modified algorithm PS-H, the search time for small tile sets can be shortened considerably. We also introduce a method for computing the reliability of a tile set, i.e. the probability of its error-free self-assembly to the target tiling, based on Winfree's analysis of the kinetic Tile Assembly Model (1998). We present data on the reliability of tile sets found by the algorithms and find that also here PS-H constitutes a significant improvement over PS-BB.

关键词： Reliability analysis

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ICNCC 2021 - Proceedings of the 2021 10th international conference on Networks, Communication and computing

ICNCC 2021 - Proceedings of the 2021 10th International Conf...

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10th international conference on Networks, Communication and computing, ICNCC 2021

ISBN: (纸本)9781450385848

the proceedings contain 23 papers. the topics discussed include: a convolutional neural network based on self-attention mechanism for molecular property prediction using molecular hidden fingerprints: an efficient molecular property prediction method;co-attention based deep model with domain-adversarial training for spam review detection;fair personalized recommendation through improved matrix factorization by neural networks;an automated approach to domain-specific term extraction for programming language;application-based knowledge capture amongst youth can be a reason for public concern. evidence from the UK;how COVID-19 social restrictions rearranged the pharmaceutical industry financing approach, and how artificial intelligence can help the fight against COVID-19. evidence from a European countries’ perspective;and fingerprint feature extraction method of specific emitter based on correlation of IQ signal.

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Engineering and Verifying Requirements for Programmable Self-Assembling Nanomachines

Engineering and Verifying Requirements for Programmable Self...

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34th international conference on Software Engineering (ICSE)

作者： Lutz, Robyn Lutz, Jack Lathrop, James Klinge, Titus Henderson, Eric Mathur, Divita Sheasha, Dalia Abo Iowa State Univ Dept Comp Sci Ames IA 50011 USA California Inst Technol Jet Prop Lab Pasadena CA 91104 USA Iowa State Univ Dept Genet Dev & Cell Biol Ames IA 50011 USA

ISBN: (纸本)9781467310673

We propose an extension of van Lamsweerde's goal-oriented requirements engineering to the domain of programmable dna nanotechnology. this is a domain in which individual devices (agents) are at most a few dozen nanometers in diameter. these devices are programmed to assemble themselves from molecular components and perform their assigned tasks. the devices carry out their tasks in the probabilistic world of chemical kinetics, so they are individually error-prone. However, the number of devices deployed is roughly on the order of a nanomole (a 6 followed by fourteen 0s), and some goals are achieved when enough of these agents achieve their assigned subgoals. We show that it is useful in this setting to augment the AND/OR goal diagrams to allow goal refinements that are mediated by threshold functions, rather than ANDs or ORs. We illustrate this method by engineering requirements for a system of molecular detectors (dna origami "pliers" that capture target molecules) invented by Kuzuya, Sakai, Yamazaki, Xu, and Komiyama (2011). We model this system in the Prism probabilistic symbolic model checker, and we use Prism to verify that requirements are satisfied, provided that the ratio of target molecules to detectors is neither too high nor too low. this gives prima facie evidence that software engineering methods can be used to make dna nanotechnology more productive, predictable and safe.

关键词： Requirements engineering validation and verification safety dna nanotechnology molecular programming

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