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18th international conference on dna computing and molecular programming, dna 18

作者： Kan, Anton Shohda, Koh-Ichiroh Suyama, Akira Department of Life Sciences Institute of Physics University of Tokyo 3-8-1 Komaba Meguro-ku Tokyo 153-8902 Japan

ISBN: (纸本)9783642322075

In this paper we report on a module in the RTRACS molecular computing system, constructed with dna, RNA and enzymes. the module is a 2-input logic gate that receives input and produces output in the form of RNA molecules. Each of the two input molecules is chosen from a set of two, and the logic gate produces an output molecule for each of the four possible input combinations. Two output RNA molecules can be produced by this module, one for only one combination of inputs, whilst the remaining three combinations lead to the production of the other output. Since the RNA strands can be arbitrarily assigned logical values, this module is capable performing multiple logical operations, including AND, NAND, OR and NOR, given the appropriate mapping of RNA molecules to logical values. We performed numerical simulations of the logic gate reaction scheme, revealing the details of the kinetics of the production of output molecules and the theoretical input-output characteristics. We also experimentally demonstrated the proper functioning of the logic gate, showing the correct formation of intermediate steps, the real time production of output molecules as well as the input-output characteristics of the module. We believe this versatile logic gate has significant advantages as a basic module of RTRACS due to the wide variety of possible logical operations. © 2012 Springer-Verlag.

关键词： Logic gates

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One-dimensional staged self-assembly

One-dimensional staged self-assembly

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17th international conference on dna computing and molecular programming

作者： Demaine, Erik D. Eisenstat, Sarah Ishaque, Mashhood Winslow, Andrew MIT Comp Sci & Artificial Intelligence Lab Cambridge MA 02139 USA Tufts Univ Dept Comp Sci Medford MA 02155 USA

ISBN: (纸本)9783642236372

We introduce the problem of staged self-assembly of one-dimensional nanostructures, which becomes interesting when the elements are labeled (e.g., representing functional units that must be placed at specific locations). In a restricted model in which each operation has a single terminal assembly, we prove that assembling a given string of labels with the fewest steps is equivalent, up to constant factors, to compressing the string to be uniquely derived from the smallest possible context-free grammar (a well-studied O(log n)-approximable problem) and that the problem is NP-hard. Without this restriction, we show that the optimal assembly can be substantially smaller than the optimal context-free grammar, by a factor of even for binary strings of length n. Fortunately, we can bound this separation in model power by a quadratic function in the number of distinct glues or tiles allowed in the assembly, which is typically small in practice.

关键词： Context-free grammar Wang tile dna computing Complexity

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Toward a Function-as-a-Service Framework for Genomic Analysis 6

Toward a Function-as-a-Service Framework for Genomic Analysi...

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6th IEEE international conference on Smart computing (SMARTCOMP)

作者： Tricomi, Giuseppe Giosa, Domenico Merlino, Giovanni Romeo, Orazio Longo, Francesco Univ Messina Dipartimento Ingn Messina Italy Univ Messina Dipartimento Med Clin & Sperimentale Messina Italy Univ Messina Dipartimento Sci Chim Biol Farmaceut & Ambientali Messina Italy

ISBN: (数字)9781728169972

ISBN: (纸本)9781728169972

Nowadays, the study of nucleic acids (dna/RNA) has become a digital science thanks to the advent of modern massive parallel sequencing technologies, better known with the acronym NGS standing for next-generation sequencing, and to the availability of a vast amount of genetic data easily accessible from publicly available databases. Due to the quantity and complexity of such data, its processing requires strong computer science knowledge and skills. this background includes topics such as programming and scripting languages, command-line interfaces, low-level data management tools, which are not always part of the toolbox of molecular biologists and geneticists. the need to adapt to entirely new IT tools and workflows slow down even the more experienced researchers, thus dedicated and customizable GUIs would be much more preferable and conducive. In this paper, we tackle this issue by proposing a preliminary architecture for a framework providing the following benefits: i) it supports the post-NGS analysis process definition phase (commonly called pipeline definition) via a graphical dashboard designed with NodeRED;ii) it automatically deploys the workflows on top of a cluster of computational resources, according to the Function-as-a-Service paradigm, i.e., treating each step of the pipeline as a function to be executed within Linux-based containers, pre-configured with all the necessary dependencies;iii) it runs such containers taking care automatically of resource load balancing. Finally, the framework is thought to include human feedback in the loop, thanks to the availability of a smart notification system, allowing the researcher to monitor the workflows and make any decision needed for its continuation.

关键词： FaaS Serverless dna sequence alignment string matching Next Generation Sequencing NodeRED flow editor

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Steady flow micro-reactor module for pipelined dna computations 1

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

作者： McCaskill, John S. Penchovsky, Robert Gohlke, Marlies Ackermann, Jörg Rücker, thomas GMD-National Research Center for Information Technology Schloß Birlinghoven St Augustin53754 Germany

ISBN: (数字)9783540449928

ISBN: (纸本)3540420762

Microflow reactors provide a means of implementing dna computing as a whole, not just individual steps. Contrary to surface based dna Chips[1], microflow reactors with active components in closed flow systems can be used to integrate complete dna computations[2]. Microreactors allow complicated flow topologies to be realized which can implement a dataflowlike architecture for the processing of dna. A technologically feasible scalable approach with many reaction chambers however requires constant hydrodynamic flows. In this work, the experimental construction of a basic constant flow module for dna processing in such a context is addressed. Limited diffusional exchange in parallel flows is used to establish spatio-temporal segregation of reaction conditions which can be crossed by magnetic beads without barriers. As previously outlined[2], linked up with an optical programming technology, this will enable dna selection to be programmed and complex population selection to be performed. the basic first experimental step in the realization of this program is described here: the establishment of a stable hydrodynamic flow pattern which is scalable to many reactors in parallel and the demonstration of a scalable and synchronous clocking of magnetic beadbased processing. First results with fluorescently-labeled dna transfer will also be presented at the conference. the way in which this module may be integrated to solve the maximal clique problem has been proposed elsewhere[2]. © Springer-Verlag Berlin Heidelberg 2001.

关键词： dna

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Improved dna-sticker arithmetic: tube-encoded-carry, Logarithmic Number System and Monte-Carlo methods

Improved DNA-sticker arithmetic: tube-encoded-carry, Logarit...

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17th international conference on dna computing and molecular programming

作者： Arnold, Mark G. POB 605 Laramie WY 82070 USA

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 arithmetic algorithms, patterned on digital-electronics, generate carry bits in the strand, either wasting bits or using a clear operation (with problematic biochemical implementation). the novel addition algorithm here does not need to record the carry. Instead, which tube holds a particular strand implicitly encodes the carry. the speed and number of tubes are half that of prior approaches. Further encoding data in the Logarithmic Number System (LNS) allows such integer operations to perform cost-effective real multiplications, divisions and roots. An example LNS Euclidian norm is more efficient than prior methods, assuming perfect operations. Unfortunately, dna-stickers are unreliable. this paper uses sticker unreliability as a source of randomness to implement Monte-Carlo (MC) arithmetic (previously fabricated in silicon at the cost of pseudo-random generators). With stickers, the randomness is free. MC engineering mimics natural systems using unreliable but redundant components. Here, MC randomness is only useful in low-order bits. Multiple re-testing of the same bit ("refinement") trades improved reliability for slower operation using more tubes. Simulations (with different sizes, probabilities and refinement) show that increasing refinement as a function of bit position allows imperfect implementations to achieve suitable MC strand-error distributions, predicting 1000x speed-mass advantage of sticker-MCLNS over conventional supercomputers.

关键词： dna arithmetic Sticker system Addition Logarithmic Number System (LNS) Monte-Carlo Arithmetic

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Computational design of reaction-diffusion patterns using dna-based chemical reaction networks

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20th international conference on dna computing and molecular programming, dna 2014

作者： Dalchau, Neil Seelig, Georg Phillips, Andrew Microsoft Research CambridgeCB1 2FB United Kingdom University of Washington WA United States

ISBN: (纸本)9783319112947

dna self-assembly is a powerful technology for controlling matter at the nanometre to micron scale, with potential applications in high-precision organisation and positioning of molecular components. However, the ability to program dna-only self-organisation beyond the microscopic scale is currently lacking. In this paper we propose a computational method for programming spatial organisation of dna at the centimetre scale, by means of dna strand displacement reaction diffusion systems. We use this method to analyse the spatiotemporal dynamics of an autocatalytic system, a predator-prey oscillator and a two-species consensus network. We find that both autocatalytic and oscillating systems can support travelling waves across centimetre distances, and that consensus in a spatial context results in the spontaneous formation of distinct spatial domains, in which one species is completely eliminated. Together, our results suggest that programmed spatial self-organisation of dna, through a reaction diffusion mechanism, is achievable with current dna strand displacement technology. © Springer international Publishing Switzerland 2014.

关键词： dna

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Puddle: A Dynamic, Error-Correcting, Full-Stack Microfluidics Platform 19

Puddle: A Dynamic, Error-Correcting, Full-Stack Microfluidic...

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24th international conference on Architectural Support for programming Languages and Operating Systems (ASPLOS)

作者： Willsey, Max Stephenson, Ashley P. Takahashi, Chris Vaid, Pranav Nguyen, Bichlien H. Piszczek, Michal Betts, Christine Newman, Sharon Joshi, Sarang Strauss, Karin Ceze, Luis Univ Washington Seattle WA 98195 USA Microsoft Redmond WA USA Stanford Univ Stanford CA 94305 USA

ISBN: (纸本)9781450362405

Microfluidic devices promise to automate wetlab procedures by manipulating small chemical or biological samples. this technology comes in many varieties, all of which aim to save time, labor, and supplies by performing lab protocol steps typically done by a technician. However, existing microfluidic platforms remain some combination of inflexible, error-prone, prohibitively expensive, and difficult to program. We address these concerns with a full-stack digital microfluidic automation platform. Our main contribution is a runtime system that provides a high-level API for microfluidic manipulations. It manages fluidic resources dynamically, allowing programmers to freely mix regular computation with microfluidics, which results in more expressive programs than previous work. It also provides real-time error correction through a computer vision system, allowing robust execution on cheaper microfluidic hardware. We implement our stack on top of a low-cost droplet microfluidic device that we have developed. We evaluate our system with the fully-automated execution of polymerase chain reaction (PCR) and a dna sequencing preparation protocol. these protocols demonstrate high-level programs that combine computational and fluidic operations such as input/output of reagents, heating of samples, and data analysis. We also evaluate the impact of automatic error correction on our system's reliability.

关键词： runtime systems digital microfluidics molecular computing microfluidics

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Abstract modelling of tethered dna circuits

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20th international conference on dna computing and molecular programming, dna 2014

作者： Lakin, Matthew R. Petersen, Rasmus Gray, Kathryn E. Phillips, Andrew Department of Computer Science University of New Mexico AlbuquerqueNM United States Microsoft Research Cambridge United Kingdom Computer Laboratory University of Cambridge Cambridge United Kingdom

ISBN: (纸本)9783319112947

Sequence-specific dna interactions are a powerful means of programming nanoscale locomotion. these systems typically use a dna track that is tethered to a surface, and molecular interactions enable a signal or cargo to traverse this track. Such low copy number systems are highly amenable to mechanized analyses such as probabilistic model checking, which requires a formal encoding. In this paper we present the first general encoding of tethered dna species into a formal language, which allows the interactions between tethered species to be derived automatically using standard reaction rules. We apply this encoding to a previously published tethered dna circuit architecture based on hairpin assembly reactions. this work enables automated analysis of large-scale tethered dna circuits and, potentially, synthesis of optimized track layouts to implement specific logic functions. © Springer international Publishing Switzerland 2014.

关键词： Encoding (symbols)

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the topology of scaffold routings on non-spherical mesh wireframes 26

The topology of scaffold routings on non-spherical mesh wire...

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26th international conference on dna computing and molecular programming, dna 2020

作者： Mohammed, Abdulmelik Jonoska, Nataa Saito, Masahico Department of Mathematics and Statistics University of South Florida TampaFL United States

ISBN: (纸本)9783959771634

the routing of a dna-origami scaffold strand is often modelled as an Eulerian circuit of an Eulerian graph in combinatorial models of dna origami design. the knot type of the scaffold strand dictates the feasibility of an Eulerian circuit to be used as the scaffold route in the design. Motivated by the topology of scaffold routings in 3D dna origami, we investigate the knottedness of Eulerian circuits on surface-embedded graphs. We show that certain graph embeddings, checkerboard colorable, always admit unknotted Eulerian circuits. On the other hand, we prove that if a graph admits an embedding in a torus that is not checkerboard colorable, then it can be re-embedded so that all its non-intersecting Eulerian circuits are knotted. For surfaces of genus greater than one, we present an infinite family of checkerboard-colorable graph embeddings where there exist knotted Eulerian circuits. © Abdulmelik Mohammed, Nataa Jonoska, and Masahico Saito;licensed under Creative Commons License CC-BY.

关键词： dna

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dna computing and molecular programming: Preface

Lecture Notes in Computer Science (including subseries Lectu...

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Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) 2009年 5877 LNCS卷

作者： Deaton, Russell Suyama, Akira Dept. of Computer Science and Computer Engineering JBHT - CSCE 504 1 University of Arkansas Fayetteville AR 72701 United States Department of Life Science Graduate School of Arts and Sciences University of Tokyo 3-8-1 Komaba Meguro-ku Tokyo 153-8902 Japan

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