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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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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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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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Grammar-based immune programming

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NATURAL computing 2011年第1期10卷 209-241页

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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Time-Complexity of Multilayered dna Strand Displacement Circuits

Time-Complexity of Multilayered DNA Strand Displacement Circ...

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15th international conference on dna computing and molecular programming

作者： Seelig, Georg Soloveichik, David Univ Washington Seattle WA 98195 USA CALTECH Pasadena CA USA

ISBN: (纸本)9783642106033

Recently we have shown how molecular logic circuits with many components arranged in multiple layers can be built using dna strand displacement reactions. the potential applications of this and similar technologies inspire the study of the computation time of multilayered molecular circuits. Using mass action kinetics to model dna strand displacement-based circuits, we discuss how computation time scales with the number of layers. We show that depending on circuit architecture, the time-complexity does not necessarily scale linearly with the depth as is assumed in the usual study of circuit complexity. We compare circuits with catalytic and non-catalytic components, showing that catalysis fundamentally alters asymptotic time-complexity. Our results rely on simple asymptotic arguments that should be applicable to a wide class of chemical circuits. these results may help to improve circuit performance and may be useful for the construction of faster, larger and more reliable molecular circuitry.

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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A Domain-Specific Language for programming in the Tile Assembly Model

A Domain-Specific Language for Programming in the Tile Assem...

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15th international conference on dna computing and molecular programming

作者： Doty, David Patitz, Matthew J. Iowa State Univ Dept Comp Sci Ames IA 50011 USA

ISBN: (纸本)9783642106033

We introduce a domain-specific language (DSL) for creating sets of tile types for simulations of the abstract Tile Assembly Model. the language defines objects known as tile templates, which represent related groups of tiles, and a small number of basic operations on tile templates that help to eliminate the error-prone drudgery of enumerating such tile types manually or with low-level constructs of general-purpose programming languages. the language is implemented as a class library in Python (a so-called internal DSL), but is presented independently of Python or object-oriented programming, with emphasis on support for a visual editing tool for creating large sets of complex tile types.

关键词： Problem oriented languages

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