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

共 172 条记录，以下是71-80 订阅

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Multiple molecular Spiders with a Single Localized Source-the One-Dimensional Case (Extended Abstract)

Multiple Molecular Spiders with a Single Localized Source-Th...

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17th international conference on dna computing and molecular programming

作者： Semenov, Oleg Olah, Mark J. Stefanovic, Darko Univ New Mexico Dept Comp Sci Albuquerque NM 87131 USA

ISBN: (纸本)9783642236372;9783642236389

molecular spiders are nanoscale walkers made with dna enzyme legs attached to a common body. they move over a surface of dna substrates, cleaving them and leaving behind product dna strands, which they are able to revisit. Simple one-dimensional models of spider motion show significant superdiffusive motion when the leg-substrate bindings are longer-lived than the leg-product bindings. this gives the spiders potential as a faster-than-diffusion transport mechanism. However, analysis shows that single-spider motion eventually decays into an ordinary diffusive motion, owing to the ever increasing size of the region of cleaved products. Inspired by cooperative behavior of natural molecular walkers, we propose a model for multiple walkers moving collectively over a one-dimensional lattice. We show that when walkers are sequentially released from the origin, the collective effect is to prevent the leading walkers from moving too far backwards. Hence there is an effective outward pressure on the leading walkers that keeps them moving superdiffusively for longer times, despite the growth of the product region.

关键词： Substrates

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On Quantitative Modelling and Verification of dna Walker Circuits Using Stochastic Petri Nets 1

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36th international conference on Application and theory of Petri Nets and Concurrency (Petri Nets)

作者： Barbot, Benoit Kwiatkowska, Marta Univ Oxford Dept Comp Sci Oxford OX1 3QD England

ISBN: (数字)9783319194882

ISBN: (纸本)9783319194882;9783319194875

molecular programming is an emerging field concerned with building synthetic biomolecular computing devices at the nanoscale, for example from dna or RNA molecules. Many promising applications have been proposed, ranging from diagnostic biosensors and nanorobots to synthetic biology, but prohibitive complexity and imprecision of experimental observations makes reliability of molecular programs difficult to achieve. this paper advocates the development of design automation methodologies for molecular programming, highlighting the role of quantitative verification in this context. We focus on dna 'walker' circuits, in which molecules can be programmed to traverse tracks placed on a dna origami tile, taking appropriate decisions at junctions and reporting the outcome when reaching the end of the track. the behaviour of molecular walkers is inherently probabilistic and thus probabilistic model checking methods are needed for their analysis. We demonstrate how dna walkers can be modelled using stochastic Petri nets, and apply statistical model checking using the tool Cosmos to analyse the reliability and performance characteristics of the designs. the results are compared and contrasted with those obtained for the PRISM model checker. the paper ends by summarising future research challenges in the field.

关键词： dna

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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： Robert Brijder Lulu Qian

ISBN: (数字)9783319667997

ISBN: (纸本)9783319667980

this book constitutes the refereed proceedings of the 23th international conference on dna computing and molecular programming, dna 23, held Austin, TX, USA, in September 2017. the 16 full papers presented were carefully selected from 23 submissions. Research in dna computing aims to draw together mathematics, computerscience, physics, chemistry, biology, and nanotechnology to address the analysis, design, and synthesis of information-based molecular systems. the papers address all areas related to biomolecular computing such as: algorithms and models for computation with biomolecular systems; computational processes in vitro and in vivo; molecular motors and molecular robotics; studies of fault-tolerance and error correction; software tools for analysis, simulation, and design; synthetic biology and in vitro evolution; applications in engineering, physics, chemistry, biology, and medicine.

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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dna computing and molecular programming 1

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丛书名： Lecture Notes in Computer Science

1000年

作者： Darko Stefanovic Andrew Turberfield

ISBN: (数字)9783642322082

ISBN: (纸本)9783642322075

this book constitutes the refereed proceedings of the 18th international conference on dna computing and molecular programming, dna 18, held in Aarhus, Denmark, in August 2012. the 11 full papers presented were carefully selected from 37 submissions. the papers are organized in topical sections on advancing the engineering and science of biology and chemistry from the point of view of computer science, physics, and mathematics.

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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： David Soloveichik Bernard Yurke

ISBN: (数字)9783319019284

ISBN: (纸本)9783319019277

this book constitutes the refereed proceedings of the 19th international conference on dna computing and molecular programming, dna 19, held in Tempe, AZ, USA, in September 2013. the 14 full papers presented were carefully selected from 29 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.

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computing properties of thermodynamic binding networks: An integer programming approach 27

Computing properties of thermodynamic binding networks: An i...

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

作者： Haley, David Doty, David University of California DavisCA United States

ISBN: (纸本)9783959772051

the thermodynamic binding networks (TBN) model [9] is a tool for studying engineered molecular systems. the TBN model allows one to reason about their behavior through a simplified abstraction that ignores details about molecular composition, focusing on two key determinants of a system's energetics common to any chemical substrate: How many molecular bonds are formed, and how many separate complexes exist in the system. We formulate as an integer program the NP-hard problem of computing stable (a.k.a., minimum energy) configurations of a TBN: those configurations that maximize the number of bonds and complexes. We provide open-source software [13] solving this integer program. We give empirical evidence that this approach enables dramatically faster computation of TBN stable configurations than previous approaches based on SAT solvers [3]. Furthermore, unlike SAT-based approaches, our integer programming formulation can reason about TBNs in which some molecules have unbounded counts. these improvements in turn allow us to efficiently automate verification of desired properties of practical TBNs. Finally, we show that the TBN has a natural representation with a unique Hilbert basis describing the "fundamental components" out of which locally minimal energy configurations are composed. this characterization helps verify correctness of not only stable configurations, but entire "kinetic pathways" in a TBN. © 2021 Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing. All rights reserved.

关键词： thermodynamics

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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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Optimizing Tile Concentrations to Minimize Errors and Time for dna Tile Self-assembly Systems

Optimizing Tile Concentrations to Minimize Errors and Time f...

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16th international conference on dna computing and molecular programming

作者： Chen, Ho-Lin Kao, Ming-Yang CALTECH Ctr Math Informat Pasadena CA 91101 USA Northwestern Univ Dept Elect Engn & Comp Sci Evanston IL USA

ISBN: (纸本)9783642183041

dna tile self-assembly has emerged as a rich and promising primitive for nano-technology. this paper studies the problems of minimizing assembly time and error rate by changing the tile concentrations because changing the tile concentrations is easy to implement in actual lab experiments. We prove that setting the concentration of tile T-i proportional to the square root of N-i where N-i is the number of times T-i appears outside the seed structure in the final assembled shape minimizes the rate of growth errors for rectilinear tile systems. We also show that the same concentrations minimize the expected assembly time for a feasible class of tile systems. Moreover, for general tile systems, given tile concentrations, we can approximate the expected assembly time with high accuracy and probability by running only a polynomial number of simulations in the size of the target shape.

关键词： Self assembly

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Sequence Assembly Validation by Multiple Restriction Digest Fragment Coverage Analysis

Sequence Assembly Validation by Multiple Restriction Digest ...

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6th international conference on Intelligent Systems for molecular Biology, ISMB 1998

作者： Rouchka, Eric C. States, David J. Institute for Biomedical Computing Washington University 700 South Euclid Avenue St. LouisMO63110-1012 United States

ISBN: (纸本)1577350537

dna sequence analysis depends on the accurate assembly of fragment reads for the determination of a consensus sequence. this report examines the possibility of analyzing multiple, independent restriction digests as a method for testing the fidelity of sequence assembly. A dynamic programming algorithm to determine the maximum likelihood alignment of error prone electrophoretic mobility data to the expected fragment mobilities given the consensus sequence and restriction enzymes is derived and used to assess the likelihood of detecting rearrangements in genonúc sequencing projects. the method is shown to reliably detect errors in sequence fragment assembly without the necessity of making reference to an overlying physical map. An html form-based interface is available at http://***/services/***. © 1998, AAAI (***). All rights reserved.

关键词： Dynamic programming

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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.

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