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15th international conference on dna computing and molecular programming

作者： Bernardino, Heder S. Barbosa, Helio J. C. Lab Nacl Computacao Cient BR-25651075 Petropolis RJ Brazil

this paper describes Grammar-based Immune programming (GIP) for evolving programs in an arbitrary language by immunological inspiration. GIP is based on Grammatical Evolution (GE) in which a grammar is used to define a language and decode candidate solutions to a valid representation (program). However, by default, GE uses a Genetic Algorithm in the search process while GIP uses an artificial immune system. Some modifications are needed of an immune algorithm to use a grammar in order to efficiently decode antibodies into programs. Experiments are performed to analyze algorithm behavior over different aspects and compare it with GEVA, a well known GE implementation. the methods are applied to identify a causal model (an ordinary differential equation) from an observed data set, to symbolically regress an iterated function f(f(x)) = g(x), and to find a symbolic representation of a discontinuous function.

关键词： Artificial immune system Grammatical evolution Immune programming Symbolic regression Model inference

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Reversible Transition of Photonic dna Automaton Using Hairpin-dna Responding to a Single Kind of Photonic Signal

Reversible Transition of Photonic DNA Automaton Using Hairpi...

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16th international conference on dna computing and molecular programming

作者： Sakai, Hiroto Ogura, Yusuke Tanida, Jun Osaka Univ Grad Sch Informat Sci & Technol Dept Informat & Phys Sci Suita Osaka 5650871 Japan

ISBN: (纸本)9783642183041

In this paper, we report a scheme for reversible state-transition of the automaton responding to a single kind of a photonic signal. the state is encoded into the conformation of hairpin-dnas tethered with azobenzene, which is responsive to visible and UV light irradiation. the reversible behavior is realized by carrying out a sequence of conformation-change of the hairpin-dna in a stepwise manner. Experimental results demonstrate that the state can be changed reversibly according to photonic signals.

关键词： dna

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dna-Based Fixed Gain Amplifiers and Linear Classifier Circuits

DNA-Based Fixed Gain Amplifiers and Linear Classifier Circui...

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16th international conference on dna computing and molecular programming

作者： Zhang, David Yu Seelig, Georg CALTECH Pasadena CA 91125 USA Univ Washington Seattle WA 98195 USA

ISBN: (纸本)9783642183041

dna catalysts have been developed as methods of amplifying single-stranded nucleic acid signals. the maximum turnover (gain) of these systems, however, often varies based on strand and complex purities, and has so far not been well-controlled. Here we introduce methods for controlling the asymptotic turnover of strand displacement-based dna catalysts and show how these could be used to construct linear classifier systems.

关键词： dna

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dna walker circuits: computational potential, design, and verification

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NATURAL computing 2015年第2期14卷 195-211页

作者： Dannenberg, Frits Kwiatkowska, Marta thachuk, Chris Turberfield, Andrew J. Univ Oxford Dept Comp Sci Oxford OX1 3QD England Univ Oxford Dept Phys Clarendon Lab Oxford OX1 3PU England

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 and forming composable circuits. We find that systems of multiple walkers have severely limited potential for parallel circuit evaluation. 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. this analysis aids in the design of reliable and efficient dna walker circuits.

关键词： dna computing dna walkers Boolean circuits Probabilistic model checking Computer aided design (CAD)

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Parallel computation using active self-assembly

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NATURAL computing 2015年第2期14卷 225-250页

作者： Chen, Moya Xin, Doris Woods, Damien CALTECH Pasadena CA 91125 USA

We study the computational complexity of the recently proposed nubots model of molecular-scale self-assembly. the model generalises asynchronous cellular automata to have non-local movement where large assemblies of molecules can be moved around, analogous to millions of molecular motors in animal muscle effecting the rapid movement of macroscale arms and legs. We show that nubots is capable of simulating Boolean circuits of polylogarithmic depth and polynomial size, in only polylogarithmic expected time. In computational complexity terms, we show that any problem from the complexity class NC is solved in polylogarithmic expected time on nubots that use a polynomial amount of workspace. Along the way, we give fast parallel algorithms for a number of problems including line growth, sorting, Boolean matrix multiplication and space-bounded Turing machine simulation, all using a constant number of nubot states (monomer types). Circuit depth is a well-studied notion of parallel time, and our result implies that nubots is a highly parallel model of computation in a formal sense. Asynchronous cellular automata are not capable of such parallelism, and our result shows that adding a movement primitive to such a model, to get the nubots model, drastically increases parallel processing abilities.

关键词： molecular robotics Self-assembly Computational complexity

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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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Operation of a dna-Based Autocatalytic Network in Serum

Operation of a DNA-Based Autocatalytic Network in Serum

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16th international conference on dna computing and molecular programming

作者： Graugnard, Elton Cox, Amber Lee, Jeunghoon Jorcyk, Cheryl Yurke, Bernard Hughes, William L. Boise State Univ Boise ID 83725 USA

ISBN: (纸本)9783642183041

the potential for inferring the presence of cancer by the detection of miRNA in human blood has motivated research into the design and operation of dna-based chemical amplifiers that can operate in bodily fluids. As a first step toward this goal, we have tested the operation of a dna-based autocatalytic network in human serum and mouse serum. With the addition of sodium dodecyl sulfate to prevent degradation by nuclease activity, the network was found to operate successfully with both dna and RNA catalysts.

关键词： dna

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Compiling dna strand displacement reactions using a functional programming language

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15th international conference on Verification, Model Checking, and Abstract Interpretation, VMCAI 2014

作者： Lakin, Matthew R. Phillips, Andrew Biological Computation Group Microsoft Research Cambridge CB1 2FB United Kingdom Department of Computer Science University of New Mexico NM 87131 United States

ISBN: (纸本)9783319041315

dna nanotechnology is a rapidly-growing field, with many potential applications in nanoscale manufacturing and autonomous in vivo diagnostic and therapeutic devices. As experimental techniques improve it will become increasingly important to develop software tools and programming abstractions, to enable rapid and correct design of increasingly sophisticated computational circuits. this is analogous to the need for hardware description languages for VLSI. In this paper we discuss our experience implementing a domain-specific language for dna nanotechnology using a functional programming language. the ability to use abstract data types to describe molecular structures and to recurse over these types to derive the various interactions between structures was a major reason for the use of a functional language in this project. © 2014 Springer international Publishing.

关键词： Calculations

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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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programming with chemical reaction networks and dna strand displacement systems

Programming with chemical reaction networks and dna strand d...

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13th international conference on Unconventional Computation and Natural Computation, UCNC 2014

作者： Condon, Anne Department of Computer Science University of British Columbia Vancouver BC V6T 1Z4 Canada

ISBN: (纸本)9783319081229

Chemical reaction networks (CRNs) and dna strand displacement systems (DSDs) are widely-studied and useful models of molecular programming. In this tutorial, we introduce the models, illustrating the expressive power of CRNs as a molecular programming language and how CRNs can be compiled into lower-level, physically realizable dna strand displacement systems. We characterize the power of CRNs in terms of well known complexity classes, describe connections with reversible and distributed computing models, and discuss limits to computing with CRNs. Finally, we discuss directions for future research that could advance our understanding of these models and the possibilities for efficient molecular programs. © 2014 Springer international Publishing Switzerland.

关键词： dna

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