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17th international conference on dna computing and molecular programming, dna 17

ISBN: (纸本)9783642236372

the proceedings contain 14 papers. the topics discussed include: an autonomous dna nanodevice captures pH maps of living cells in culture and in vivo;the computer science of molecular programming;cooperation in an all-RNA network;designer dna architectures for bionanotechnology;an improved dna-sticker addition algorithm and its application to logarithmic arithmetic;graph-theoretic formalization of hybridization in dna sticker complexes;less haste, less waste: on recycling and its limits in strand displacement systems;computing maximal Kleene closures that are embeddable in a given constrained dna language;modelling, simulating and verifying Turing-powerful strand displacement systems;synthesizing small and reliable tile sets for patterned dna self-assembly;exact shapes and Turing universality at temperature 1 with a single negative glue;and multiple molecular spiders with a single localized source - the one-dimensional case.

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dna computing and molecular programming: 21st international conference, dna 21 Boston and Cambridge, MA, USA, August 17-21, 2015 Proceedings 21st

DNA Computing and Molecular Programming: 21st International ...

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21st international conference on dna computing and molecular programming, 2015

作者： Phillips, Andrew Yin, Peng Microsoft Research Cambridge United Kingdom Wyss Institute BostonMA United States

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computing maximal Kleene closures that are embeddable in a given subword-closed language

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NATURAL computing 2013年第2期12卷 211-222页

作者： Konstantinidis, Stavros Santean, Nicolae St Marys Univ Dept Math & Comp Sci Halifax NS B3H 3C3 Canada

Motivated by certain coding techniques for reliable dna computing, we consider the problem of characterizing nontrivial languages D that are maximal with the property that D (*) is contained in the subword closure of a given set S of words of some fixed length k. this closure is simply the set of all words whose subwords of length k must be in S. We provide a deep structural characterization of these languages D, which leads to polynomial time algorithms for computing such languages.

关键词： Algorithm Automaton Code dna encodings Maximal Regular language Subword closure

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A tool for the design of dna base sequences for molecular circuits 17

A tool for the design of DNA base sequences for molecular ci...

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17th international conference on Control, Automation and Systems (ICCAS)

作者： Yoshida, Yuki Nakakuki, Takashi Kyushu Inst Technol Major Interdisciplinary Informat 680-4 Kawazu Iizuka Fukuoka 8208502 Japan Kyushu Inst Technol Dept Syst Design & Informat 680-4 Kawazu Iizuka Fukuoka 8208502 Japan

ISBN: (纸本)9788993215144

Designing a set of dna base sequences for a large-scale molecular circuit is a difficult problem in the field of dna computing. A dna circuit frequently suffers from unintended dna strand displacements among strands;this problem can ruin the desired function of a dna circuit. In this study, our aim was to develop a computational tool for the design of dna base sequences by means of an original algorithm based on mismatches in a dna base sequence. Validity of the proposed algorithm is confirmed by practical redesign examples.

关键词： dna computing molecular circuit dna base sequence Design tool

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Graph-theoretic formalization of hybridization in dna sticker complexes

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NATURAL computing 2013年第2期12卷 223-234页

作者： Brijder, Robert Gillis, Joris J. M. Van den Bussche, Jan Hasselt Univ Diepenbeek Belgium Transnat Univ Limburg Diepenbeek Belgium

Sticker complexes are a formal graph-based data model for a restricted class of dna complexes, motivated by potential applications to databases. this data model allows for a purely declarative definition of hybridization. We introduce the notion of terminating hybridization, which intuitively means that only a finite number of different products can be generated. We characterize this notion in purely graph-theoretic terms. Under a finite alphabet, each product is shown to be of polynomial size. Yet, terminating hybridization can still produce results of exponential size, in that there may be exponentially many different (nonisomorphic) finished products. We indicate a class of complexes where hybridization is guaranteed to be polynomially bounded.

关键词： dna Hybridization Graph-theory Complexity

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An improved molecular computing model of modular-multiplication over finite field GF(2ⁿ) 17

An improved molecular computing model of modular-multiplicat...

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17th international conference on Parallel and Distributed computing, Applications and Technologies (PDCAT)

作者： Li, Yongan Xiao, Limin Peoples Publ Secur Univ China Sch Invest & Counter Terrorism Beijing 100038 Peoples R China Beihang Univ Sch Comp Sci & Engn Beijing 100191 Peoples R China

ISBN: (纸本)9781509050819

With the rapid development of dna computing, there are some questions worth study that how to implement the arithmetic operations used in cryptosystem based on dna computing models. this paper proposes an improved dna computing model to calculate modular-multiplication over finite field GF(2(n)). Comparing to related works, both assembly time complexity and space complexity are more optimal. the computation tiles performing 4 different functions assemble into the seed configuration with inputs to figure out the result. It is given that how the computation tiles be bitwise coded and how assembly rules work. the assembly time complexity is theta(n) and the space complexity is theta(n(2)). this model requires 148 types of computation tiles and 8 types of boundary tiles.

关键词： Finite field GF(2(n)) dna computing Modular multiplication

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computing Maximal Kleene Closures that Are Embeddable in a Given Constrained dna Language

Computing Maximal Kleene Closures That Are Embeddable in a G...

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17th international conference on dna computing and molecular programming

作者： Konstantinidis, Stavros Santean, Nicolae St Marys Univ Dept Math & Comp Sci Halifax NS B3H 3C3 Canada

ISBN: (纸本)9783642236372

We consider the problem of characterizing nontrivial languages D that are maximal with the property that D*, the Kleene closure of D, is contained in the subword closure of a given set S of words of some fixed length k. the subword closure of S is simply the set of words for which all subwords of length k are in S. We provide a deep structural characterization of these languages D, which leads to polynomial time algorithms for computing such languages. this work is motivated by the problem of encoding arbitrary data into a set of dna molecules such that all blocks of length k in these molecules satisfy the constraint S - eg, they can form no stable bonds between them, or they have a desired g-c ratio.

关键词： algorithm automaton code dna encodings maximal regular language subword closure

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An Autonomous dna Nanodevice Captures pH Maps of Living Cells in Culture and in Vivo

An Autonomous DNA Nanodevice Captures pH Maps of Living Cell...

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17th international conference on dna computing and molecular programming

作者： Surana, Sunaina Modi, Souvik Krishnan, Yamuna Tata Inst Fundamental Res Natl Ctr Biol Sci UAS GKVK Bangalore 560065 Karnataka India

ISBN: (纸本)9783642236372

dna nanomachines are assemblies that rely on molecular inputs that are processed or transduced into measurable outputs. though dna nanotechnology has created a gamut of molecular devices, an outstanding challenge has been the demonstration of functionality and relevance of these devices in living systems. the I-switch is a dna nanodevice that, in response to protons, changes its conformation to produce a fluorescence resonance energy transfer (FRET) signal. We show that this rationally designed molecular device is capable of measuring spatiotemporal pH changes associated with endosomes as they undergo maturation in living cells in culture. Furthermore, we show that the nanomachine retains its autonomous functionality as it maps the same biological process in cells of a living organism like C. elegans. this demonstration of the quantitative functionality of an artificially designed scaffold positions dna nanodevices as powerful tools to interrogate biological phenomena.

关键词： I-switch pH sensor hemocytes coelomocytes

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An Improved dna-Sticker Addition Algorithm and Its Application to Logarithmic Arithmetic

An Improved DNA-Sticker Addition Algorithm and Its Applicati...

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17th international conference on dna computing and molecular programming

作者： Arnold, Mark G. Lehigh Univ Bethlehem PA 18015 USA

ISBN: (纸本)9783642236372;9783642236389

the sticker model of computation, implemented using robotic processing of dna, manipulates in parallel many bitstrings, called strands, that are contained in a limited number of tubes. Prior sticker-addition algorithms are patterned on digital-electronic full-adders that generate carry bits, each of which must be saved in the strand, which involves wasting the strand or using a clear operation (whose biochemical implementation may be problematic). this paper proposes a new sticker-addition algorithm which does not need to record the carry bits. Instead, which tube holds a particular strand implicitly describes whether or not a carry is required. the speed and number of tubes needed are about half that needed by the prior approach. An example is given for real-valued Euclidian norms using the Logarithmic Number System.

关键词： dna arithmetic sticker system addition Logarithmic Number System (LNS)

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computing maximal Kleene closures that are embeddable in a given subword-closed language

Computing maximal Kleene closures that are embeddable in a g...

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17th international conference on dna computing and molecular programming

作者： Konstantinidis, Stavros Santean, Nicolae St Marys Univ Dept Math & Comp Sci Halifax NS B3H 3C3 Canada

关键词： Algorithm Automaton Code dna encodings Maximal Regular language Subword closure

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