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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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High-Fidelity dna Hybridization Using Programmable molecular dna Devices

High-Fidelity DNA Hybridization Using Programmable Molecular...

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16th international conference on dna computing and molecular programming

作者： Gopalkrishnan, Nikhil Chandran, Harish Reif, John Duke Univ Dept Comp Sci Durham NC 27708 USA

ISBN: (纸本)9783642183041

the hybridization of complementary nucleic acid strands is the most basic of all reactions involving nucleic acids, but has a major limitation: the specificity of hybridization reactions depends critically on the lengths of the complementary pairs of strands and can drop to very low values for sufficiently long strands. this reduction in specificity occurs especially in the presence of noise in the form of other competing strands that have sequence segments identical to the target. this limits the scale and accuracy of biotechnology and nanotechnology applications which depend on hybridization reactions. Our paper develops techniques for ensuring specific high-fidelity dna hybridization reactions for target strands of arbitrary length. Our protocol is executed autonomously, without external mediation and driven by a series of conversions of single stranded dna into duplex dna that help overcome kinetic energy traps, similar to dna walkers.

关键词： dna hybridization strand displacement

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Optimizing Tile Set Size While Preserving Proofreading with a dna Self-assembly Compiler 1

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24th international conference on dna computing and molecular programming (dna)

作者： Evans, Constantine G. Winfree, Erik Evans Fdn Pasadena CA 91105 USA CALTECH Pasadena CA 91125 USA

ISBN: (数字)9783030000301

ISBN: (纸本)9783030000301;9783030000295

Algorithmic dna tile systems have the potential to allow the construction by self-assembly of large structures with complex nanometer-scale details out of relatively few monomer types, but are constrained by errors in growth and the limited sequence space of orthogonal dna sticky ends that program tile interactions. We present a tile set optimization technique that, through analysis of algorithmic growth equivalence, potentially sensitive error pathways, and potential lattice defects, can significantly reduce the size of tile systems while preserving proofreading behavior that is essential for obtaining low error rates. Applied to systems implementing multiple algorithms that are far beyond the size of currently feasible implementations, the optimization technique results in systems that are comparable in size to already-implemented experimental systems.

关键词： dna

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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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A Content-Addressable dna Database with Learned Sequence Encodings 1

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24th international conference on dna computing and molecular programming (dna)

作者： Stewart, Kendall Chen, Yuan-Jyue Ward, David Liu, Xiaomeng Seelig, Georg Strauss, Karin Ceze, Luis Univ Washington Paul G Allen Sch Comp Sci & Engn Seattle WA 98195 USA Microsoft Res Redmond WA USA

ISBN: (数字)9783030000301

ISBN: (纸本)9783030000301;9783030000295

We present strand and codeword design schemes for a dna database capable of approximate similarity search over a multidimensional dataset of content-rich media. Our strand designs address crosstalk in associative dna databases, and we demonstrate a novel method for learning dna sequence encodings from data, applying it to a dataset of tens of thousands of images. We test our design in the wetlab using one hundred target images and ten query images, and show that our database is capable of performing similarity-based enrichment: on average, visually similar images account for 30% of the sequencing reads for each query, despite making up only 10% of the database.

关键词： Database systems

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Toward molecular programming with dna

Toward molecular programming with DNA

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13th international conference on Architectural Support for programming Languages and Operating Systems, ASPLOS XIII

作者： Winfree, Erik California Institute of Technology Pasadena CA United States Department of Computer Science Computation and Neural Systems and Bioengineering Caltech MIT AI Lab.

ISBN: (纸本)9781595939586

Biological organisms are beautiful examples of programming. the program and data are stored in biological molecules such as dna, RNA, and proteins;the algorithms are carried out by molecular and biochemical processes;and the end result is the creation and function of an organism. If we understood how to program molecular systems, what could we create? Lifelike technologies whose basic operations are chemical reactions? the fields of chemistry, physics, biology, and computer science are converging as we begin to synthesize molecules, molecular machines, and molecular systems of ever increasing complexity, leading to subdisciplines such as dna nanotechnology, dna computing, and synthetic biology. Having demonstrated simple devices and systems - self-assembled structures, molecular motors, chemical logic gates - researchers are now turning to the question of how to create large-scale integrated systems. To do so, we must learn how to manage complexity: how to efficiently specify the structure and behavior of intricate molecular systems, how to compile such specifications down to the design of molecules to be synthesized in the lab, and how to ensure that such systems function robustly. these issues will be illustrated for chemical logic circuits based on cascades of dna hybridization reactions. Copyright © 2008 ACM.

关键词： dna

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Proceedings of the 27th Hawaii international conference on System Sciences (HICSS-27). Part 5 (of 5)

Proceedings of the 27th Hawaii International Conference on S...

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the 27th Hawaii international conference on System Sciences, HICSS-27

ISBN: (纸本)0818650907

the proceedings contains 47 papers on the applications of computing to natural sciences. Topics discussed include dna sequences, proteins, biology, data structures, databases, computer systems, algorithms, molecular structures, genomes, data reduction, drugs, computer programming, computer programming languages, user interfaces, computer graphics and systems analysis.

关键词： Natural sciences computing

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DROM: Read Only Memory Storage in dna computing 4

DROM: Read Only Memory Storage in DNA Computing

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4th international conference on Sustainable Technologies for Industry 4.0, STI 2022

作者： Tabassum, Tamanna Akter, Fatema Uddin, Mohammed Nasir Jagannath University Dept of Computer Science and Engineering Bangladesh Green University Bangladesh Dept of Computer Science and Engineering Bangladesh

ISBN: (纸本)9781665490450

Biomolecular programming performs computing utilizing many sorts of reactions and stores the information in biological macromolecules (proteins and nucleic acids). dna (Deoxyribose Nucleic Acid) exhibits highly predictable molecular behavior, which assists in the construction of logical versions of operating systems and molecular computers. Read Only Memory (ROM), is a form of electronic storage that is built into a device during the manufacturing process. It might be a programmable general-purpose logic device, and a client can customize the storage device as a basic logic gate operation to complex mechanisms on a chip. In this proposed work, a ROM is designed using dna-based gates. the attributes of dna-based computing enable dna-based ROM to execute billions of operations consecutively as well as provide immense storage in a compact space. © 2022 IEEE.

关键词： dna

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dna Sticky End Design and Assignment for Robust Algorithmic Self-assembly

DNA Sticky End Design and Assignment for Robust Algorithmic ...

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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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K Map Reduce: A Scalable Tool for Data-Processing and Search/Ensemble Applications on Large Scale Supercomputers

K Map Reduce: A Scalable Tool for Data-Processing and Search...

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15th IEEE international conference on Cluster computing (CLUSTER)

作者： Matsuda, Motohiko Maruyama, Naoya Takizawa, Shin'ichiro RIKEN AICS Kobe Hyogo Japan

ISBN: (纸本)9781479908981

K MapReduce (KMR) is a high-performance MapReduce system in the MPI environment, targeting large-scale supercomputers such as the K computer. Its objectives are to ease programming for data-processing and to achieve efficiency by utilizing the large amount of memory available in large-scale supercomputers. In KMR, shuffling operation exchanges key-value pairs in a scalable way by collective communication algorithms utilizing the K's interconnect. Mapping and reducing operations are multi-threaded to achieve even greater efficiency in modern multi-core machines. Sorting is optimized using fixed-length packed keys instead of variable-length raw keys, which is extensively used inside of shuffling and reducing operations. Besides the MapReduce operations, KMR provides routines for collective file reading for affinity-aware optimizations. this paper presents the results of experimental performance studies of KMR on the K computer. Affinity-aware file loading improves the performance by about 42% over a non-optimized implementation. We also show how KMR can be used to program real-world scientific applications such as meta-genome search and replica-exchange molecular dynamics.

关键词： multiprocessing systems parallel machines parallel programming search problems sorting

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