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检索条件"任意字段=17th International Conference on DNA Computing and Molecular Programming"

共 163 条记录，以下是71-80 订阅

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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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Construction of AND Gate for RTRACS with the Capacity of Extension to NAND Gate

Construction of AND Gate for RTRACS with the Capacity of Ext...

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15th international conference on dna computing and molecular programming

作者： Sakai, Yoko Mawatari, Yoriko Yamasaki, Kiyonari Shohda, Koh-ichiroh Suyama, Akira Univ Tokyo Grad Sch Arts & Sci Dept Life Sci Meguro Ku 3-8-1 Komaba Tokyo 1538902 Japan Univ Tokyo Grad Sch Arts & Sci Inst Phys Meguro Ku Tokyo 1538902 Japan

ISBN: (纸本)9783642106033

We have succeeded in construction of the AND gate using enzymatic reactions developed for modularized computation elements of the autonomous computing system RTRACS. Experimental results demonstrated that the molecular reaction for the AND gate generated the correct output RNA from input RNAs according to the truth table for the AND gate. the constructed molecular reaction for the AND gate can be extended to the NAND gate by small modifications, because not only a logical 1 but also a logical 0 for inputs and output was associated with the presence of RNA strands.

关键词： logic gate molecular computer

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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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Renewable implementation of rational biomolecular systems design 59

Renewable implementation of rational biomolecular systems de...

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59th Annual conference of the Society-of-Instrument-and-Control-Engineers-of-Japan (SICE)

作者： Tamba, Masaaki Nakakuki, Takashi Kyushu Inst Technol Major Syst Design & Informat Iizuka Fukuoka 8208502 Japan Kyushu Inst Technol Dept Intelligent & Control Syst Iizuka Fukuoka 8208502 Japan

ISBN: (纸本)9781728110899

Recently, a rationally designed method enabling the development of large-scale biomolecular circuits by combining three basic elements (catalysis, degradation, and annihilation mechanisms) like a Lego block was established. Although this method is instrumental in forming a functional biomolecular circuit, the circuit can operate normally only for a limited amount of time, which is a serious limitation in the field of dna computing. In this study, we developed a conventional method of biomolecular implementation to make linear input-to-output systems renewable.

关键词： Biomolecular systems molecular programming Nucleic acid circuits dna strand displacement Renewable

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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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