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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 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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Modular Verification of dna Strand Displacement Networks via Serializability Analysis

Modular Verification of DNA Strand Displacement Networks via...

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19th international conference on dna computing and molecular programming

作者： Lakin, Matthew R. Phillips, Andrew Stefanovic, Darko Univ New Mexico Dept Comp Sci Albuquerque NM 87131 USA Microsoft Res Biol Computat Grp Cambridge CB1 2FB England Univ New Mexico Ctr Biomed Engn Albuquerque NM 87131 USA

ISBN: (纸本)9783319019284;9783319019277

dna strand displacement gates can be used to emulate arbitrary chemical reactions, and a number of different schemes have been proposed to achieve this. Here we develop modular correctness proofs for strand displacement encodings of chemical reaction networks and show how they may be applied to two-domain strand displacement systems. Our notion of correctness is serializability of interleaved reaction encodings, and we infer this global property from the properties of the gates that encode the individual chemical reactions. this allows correctness to be inferred for arbitrary systems constructed using these components, and we illustrate this by applying our results to a two-domain implementation of a well-known approximate majority voting system.

关键词： Encoding (symbols)

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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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Probabilistic reasoning with a Bayesian dna device based on strand displacement

Probabilistic reasoning with a Bayesian DNA device based on ...

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

作者： Sainz De Murieta, Iñaki Rodríguez-Patón, Alfonso Campus de Montegancedo s/n Boadilla del Monte Madrid 28660 Spain

ISBN: (纸本)9783642322075

We present a computing model based on the dna strand displacement technique which performs Bayesian inference. the model will take single stranded dna as input data, representing the presence or absence of a specific molecular signal (evidence). the program logic encodes the prior probability of a disease and the conditional probability of a signal given the disease playing with a set of different dna complexes and their ratios. When the input and program molecules interact, they release a different pair of single stranded dna species whose relative proportion represents the application of Bayes' Law: the conditional probability of the disease given the signal. the models presented in this paper can empower the application of probabilistic reasoning in genetic diagnosis in vitro. © 2012 Springer-Verlag.

关键词： dna

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Reactamole: Functional reactive molecular programming 27

Reactamole: Functional reactive molecular programming

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

作者： Klinge, Titus H. Lathrop, James I. Osera, Peter-Michael Rogers, Allison Drake University Des MoinesIA United States Iowa State University AmesIA United States Grinnell College GrinnellIA United States

ISBN: (纸本)9783959772051

Chemical reaction networks (CRNs) are an important tool for molecular programming, a field that is rapidly expanding our ability to deploy computer programs into biological systems for a variety of applications. However, CRNs are also difficult to work with due to their massively parallel nature, leading to the need for higher-level languages that allow for easier computation with CRNs. Recently, research has been conducted into a variety of higher-level languages for deterministic CRNs but modeling CRN parallelism, managing error accumulation, and finding natural CRN representations are ongoing challenges. We introduce Reactamole, a higher-level language for deterministic CRNs that utilizes the functional reactive programming (FRP) paradigm to represent CRNs as a reactive dataflow network. Reactamole equates a CRN with a functional reactive program, implementing the key primitives of the FRP paradigm directly as CRNs. the functional nature of Reactamole makes reasoning about molecular programs easier, and its strong static typing allows us to ensure that a CRN is well-formed by virtue of being well-typed. In this paper, we describe the design of Reactamole and how we use CRNs to represent the common datatypes and operations found in FRP. We also demonstrate the potential of this functional reactive approach to molecular programming by giving an extended example where a CRN is constructed using FRP to modulate and demodulate an amplitude modulated signal. © 2021 Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing. All rights reserved.

关键词： Application programs

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Modelling and Optimisation of a dna Stack Nano-Device Using Probabilistic Model Checking 28

Modelling and Optimisation of a DNA Stack Nano-Device Using ...

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28th international conference on dna computing and molecular programming, dna 2022

作者： Li, Bowen Mackenzie, Neil Shirt-Ediss, Ben Krasnogor, Natalio Zuliani, Paolo Research Group School of Computing Newcastle University Newcastle upon Tyne United Kingdom

ISBN: (纸本)9783959772532

A dna stack nano-device is a bio-computing system that can read and write molecular signals based on dna-dna hybridisation and strand displacement. In vitro implementation of the dna stack faces a number of challenges affecting the performance of the system. In this work, we apply probabilistic model checking to analyse and optimise the dna stack system. We develop a model framework based on continuous-time Markov chains to quantitatively describe the system behaviour. We use the PRISM probabilistic model checker to answer two important questions: 1) What is the minimum required incubation time to store a signal? And 2) How can we maximise the yield of the system? the results suggest that the incubation time can be reduced from 30 minutes to 5-15 minutes depending on the stack operation stage. In addition, the optimised model shows a 40% increase in the target stack yield. © Bowen Li, Neil Mackenzie, Ben Shirt-Ediss, Natalio Krasnogor, and Paolo Zuliani.

关键词： dna

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molecular machines from topological linkages 27

Molecular machines from topological linkages

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

作者： Breik, Keenan Luchsinger, Austin Soloveichik, David The University of Texas AustinTX United States

ISBN: (纸本)9783959772051

Life is built upon amazingly sophisticated molecular machines whose behavior combines mechanical and chemical action. Engineering of similarly complex nanoscale devices from first principles remains an as yet unrealized goal of bioengineering. In this paper we formalize a simple model of mechanical motion (mechanical linkages) combined with chemical bonding. the model has a natural implementation using dna with double-stranded rigid links, and single-stranded flexible joints and binding sites. Surprisingly, we show that much of the complex behavior is preserved in an idealized topological model which considers solely the graph connectivity of the linkages. We show a number of artifacts including Boolean logic, catalysts, a fueled motor, and chemo-mechanical coupling, all of which can be understood and reasoned about in the topological model. the variety of achieved behaviors supports the use of topological chemical linkages in understanding and engineering complex molecular behaviors. © 2021 Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing. All rights reserved.

关键词： Binding sites

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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： Russell Deaton Akira Suyama

ISBN: (数字)9783642106040

ISBN: (纸本)9783642106033

this book constitutes the thoroughly refereed post-conference proceedings of the 15th international Meeting on dna computing, dna15, held in Fayetteville, AR, USA, in June 2009. the 16 revised full papers presented were carefully selected during two rounds of reviewing and improvement from 38 submissions. the papers feature current interdisciplinary research in molecular-scale manipulation of matter - in particular, implementation of nanoscale computation and programmed assembly of materials are of interest, thus reflecting a broader scope beyond dna-based nanotechnology and computation.

关键词： theory of Computation Biochemistry, general Nanotechnology and Microengineering Computation by Abstract Devices Algorithm Analysis and Problem Complexity Computational Biology/Bioinformatics

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