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19th international conference on dna computing and molecular programming

作者： Evans, Constantine G. Winfree, Erik CALTECH Phys Pasadena CA 91125 USA CALTECH Comp Sci Pasadena CA 91125 USA

ISBN: (纸本)9783319019284;9783319019277

A major challenge in practical dna tile self-assembly is the minimization of errors. Using the kinetic Tile Assembly Model, a theoretical model of self-assembly, it has been shown that errors can be reduced through abstract tile set design. In this paper, we instead investigate the effects of "sticky end" sequence choices in systems using the kinetic model along with the nearest-neighbor model of dna interactions. We show that both the sticky end sequences present in a system and their positions in the system can significantly affect error rates, and propose algorithms for sequence design and assignment.

关键词： Self assembly

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Renewable, Time-Responsive dna Logic Gates for Scalable Digital Circuits

Renewable, Time-Responsive DNA Logic Gates for Scalable Digi...

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15th international conference on dna computing and molecular programming

作者： Goel, Ashish Ibrahimi, Morteza Stanford Univ Dept Management Sci & Engn Stanford CA 94305 USA Stanford Univ Dept Comp Sci Stanford CA USA Stanford Univ Dept Elect Engn Stanford CA USA

ISBN: (纸本)9783642106033

In this article, we introduce a design of dna logic gates based on enzymatic restriction of dna strands. We present a construction for a set of one and two-input logic gates and argue that our construction can be generalized to implement any Boolean operation. A key feature of our design is its time-responsiveness, in the presence of appropriate fuels these gates can operate continuously and generate a time-dependent output in response to a time-dependant input. they can be interconnected to form digital circuits. Moreover, modulo connectivity information, the strand design and circuit design phases are decoupled.

关键词： Logic gates

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Synthesizing Minimal Tile Sets for Patterned dna Self-assembly

Synthesizing Minimal Tile Sets for Patterned DNA Self-assemb...

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16th international conference on dna computing and molecular programming

作者： Goos, Mika Orponen, Pekka Aalto Univ Sch Sci & Technol TKK Dept Informat & Comp Sci FI-00076 Aalto Finland

ISBN: (纸本)9783642183041

the Pattern self-Assembly Tile set Synthesis (PATS) problem is to determine a set of coloured tiles that self-assemble to implement a given rectangular colour pattern. We give an exhaustive branch-and-bound algorithm to find tile sets of minimum cardinality for the PATS problem. Our algorithm makes use of a search tree in the lattice of partitions of the ambient rectangular grid, and an efficient bounding function to prune this search tree. Empirical data on the performance of the algorithm shows that it compares favourably to previously presented heuristic solutions to the problem.

关键词： Self assembly

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Extending dna-Sticker Arithmetic to Arbitrary Size Using Staples

Extending DNA-Sticker Arithmetic to Arbitrary Size Using Sta...

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19th international conference on dna computing and molecular programming

作者： Arnold, Mark G. XLNS Research United States

ISBN: (纸本)9783319019284;9783319019277

the simple-sticker model uses robotic processing of dna strands contained in a fixed number of tubes to implement massively-parallel processing of bit strings. the bits whose value are '1' are recorded by short dna "stickers" that hybridize at specific places on the strand. Other dna models, like folded origami, use "staples" that hybridize to disjoint portions of a single strand. this paper proposes an extended-sticker paradigm that uses staples to hybridize to contiguous portions of two substrands, forming virtual strands. the problem of redundant bits is solved by blotting out old values. As an example of the novel extended-sticker paradigm, a log-time summation algorithm outperforms (with an ideal implementation) any electronic supercomputer conceivable in the near future for large data sets. JavaScript and CUDA simulations validate the theoretical operation of the proposed algorithm.

关键词： dna arithmetic sticker system dna staples addition

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6th international Workshop on dna-Based Computers, dna 2000

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6th international Workshop on dna-Based Computers, dna 2000

ISBN: (纸本)3540420762

the proceedings contain 18 papers. the special focus in this conference is on dna computing. the topics include: Engineered communications for microbial robotics;solution of a satisfiability problem on a gel-based dna computer;Diophantine equations and splicing;a new demonstration of the generative capability of h systems;about time-varying distributed h systems;string tile models for dna computing by self-assembly;from molecular computing to molecular programming;graph replacement chemistry for dna processing;molecular computing with generalized homogeneous p-systems;computationally inspired biotechnologies;improved dna synthesis and associative search using error-correcting codes and vector-quantization;challenges and applications for self-assembled dna nanostructures;a dna-based random walk method for solving k-sat;solving computational learning problems of Boolean formulae on dna computers;the fidelity of annealing-ligation;dna implementation of a royal road fitness evaluation and steady flow micro-reactor module for pipelined dna computations.

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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： Yasubumi Sakakibara Yongli Mi

ISBN: (数字)9783642183058

ISBN: (纸本)9783642183041

this book constitutes the thoroughly refereed post-conference proceedings of the 16th international conference on dna computing and molecular programming, dna16, held in Hong Kong, China, in June 2010. the 16 revised full papers presented were carefully selected during two rounds of reviewing and improvement from 59 submissions. the papers are well balanced between theoretical and experimental work and address all areas that relate to biomolecular computing, including demonstrations of biomolecular computing, theoretical models of biomolecular computing, biomolecular algorithms, computational processes in vitro and in vivo, analysis and theoretical models of laboratory techniques, biotechnological and other applications of dna computing, dna nanostructures, dna devices such as dna motors, dna error evaluation and correction, in vitro evolution, molecular design, self-assembled systems, nucleic acid chemistry, and simulation tools.

关键词： Computation by Abstract Devices Algorithm Analysis and Problem Complexity Computational Biology/Bioinformatics Artificial Intelligence Data Structures

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Functional Analysis of Large-Scale dna Strand Displacement Circuits

Functional Analysis of Large-Scale DNA Strand Displacement C...

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19th international conference on dna computing and molecular programming

作者： Yordanov, Boyan Wintersteiger, Christoph M. Hamadi, Youssef Phillips, Andrew Kugler, Hillel Microsoft Res Cambridge England

ISBN: (纸本)9783319019284;9783319019277

We present a method for the analysis of functional properties of large-scale dna strand displacement (DSD) circuits based on Satisfiability Modulo theories that enables us to prove the functional correctness of dna circuit designs for arbitrary inputs, and provides significantly improved scalability and expressivity over existing methods. We implement this method as an extension to the Visual DSD tool, and use it to formalize the behavior of a 4-bit square root circuit, together with the components used for its construction. We show that our method successfully verifies that certain designs function as required and identifies erroneous computations in others, even when millions of copies of a circuit are interacting with each other in parallel. Our method is also applicable in the verification of properties for more general chemical reaction networks.

关键词： dna

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Probabilistic Reasoning with an Enzyme-Driven dna Device

Probabilistic Reasoning with an Enzyme-Driven DNA Device

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19th international conference on dna computing and molecular programming

作者： Sainz de Murieta, Inaki Rodriguez-Paton, Alfonso UPM Dept Inteligencia Artificial Madrid 28660 Spain

ISBN: (纸本)9783319019284;9783319019277

We present a biomolecular probabilistic model driven by the action of a dna toolbox made of a set of dna templates and enzymes that is able to perform Bayesian inference. the model will take single-stranded dna as input data, representing the presence or absence of a specific molecular signal (the evidence). the program logic uses different dna templates and their relative concentration ratios to encode the prior probability of a disease and the conditional probability of a signal given the disease. When the input and program molecules interact, an enzyme-driven cascade of reactions (dna polymerase extension, nicking and degradation) is triggered, producing a different pair of single-stranded dna species. Once the system reaches equilibrium, the ratio between the output species will represent the application of Bayes' law: the conditional probability of the disease given the signal. In other words, a qualitative diagnosis plus a quantitative degree of belief in that diagnosis. thanks to the inherent amplification capability of this dna toolbox, the resulting system will be able to to scale up (with longer cascades and thus more input signals) a Bayesian biosensor that we designed previously.

关键词： dna

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MULTIPLE SEQUENCE ALIGNMENT A Quick Tour

MULTIPLE SEQUENCE ALIGNMENT A Quick Tour

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15th international conference on Advanced computing Technologies (ICACT)

作者： Chintapalli, Radha Kumar, Amit Parayitam, Laxminarayana Osmania Univ Res & Training Unit Nav Elect Hyderabad 500007 Andhra Pradesh India BIOAXIS DNA Res Ctr Hyderabad Andhra Pradesh India

ISBN: (纸本)9781467328166;9781467328180

Sequence alignment has a lot of significance in the field of bioinformatics. Since multiple sequence alignment (MSA) carries more information than pairwise alignment of the sequences, it has more number of applications. In the past few decades many algorithms and tools have been developed for the computation of multiple sequence alignment. However, accuracy of MSA still remains an open problem for further research. As more and more experimental data is being generated through sequencing technologies of second generation, there is an urgent need to develop tools that make use of integrative methods to derive biologically meaningful information from these immense data and use it to improve the accuracy of MSA. MSA tools that can scale upto the full length genome will also find wide applications in the near future.

关键词： Alignment algorithm dna dynamic programming proteins

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Algorithms for computing variants of the longest common subsequence problem

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thEORETICAL COMPUTER SCIENCE 2008年第2-3期395卷 255-267页

作者： Iliopoulos, Costas S. Rahman, A. Sohel Kings Coll London Dept Comp Sci Algorithm Design Grp London WC2R 2LS England

the longest common subsequence (LCS) problem is one of the classical and well-studied problems in computer science. the computation of the LCS is a frequent task in dna sequence analysis, and has applications to genetics and molecular biology. In this paper we introduce new variants of LCS problem and present efficient algorithms to solve them. In particular we introduce the notion of gap constraints in the LCS problems. For the LCS problem with fixed gap, we first present a naive algorithm runs in O(n(2) + R(K + 1)(2)) time, where R is the total number of ordered pairs of positions at which the two strings match and K is the fixed gap constraint. We then improve the running time to O(n(2) + RK + R log log n) using some novel techniques. Furthermore, we present an algorithm that is independent of K and runs in O(n(2) + R log log n) time. Using these techniques, we also present a new O(n(2)) algorithm to solve the original LCS problem. Additionally, we modify our algorithms to handle elastic and rigid gaps. We also apply the notion of rigidness to the original LCS problem and modify the traditional dynamic programming solution to handle the rigidness presenting a O(n(2)) algorithm to solve the problem. Finally, we also improve the solution to Rigid Fixed Gap LCS to O(n(2)). Notably, in all of the above cases, we assume that the two given strings are of equal length i.e. n. But our results can be easily extended to handle two strings of different length. (c) 2008 Elsevier B.V. All rights reserved.

关键词： algorithm longest common subsequence strings

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