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检索条件"任意字段=28th International Conference on DNA Computing and Molecular Programming, DNA 2022"

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28th international conference on dna computing and molecular programming, dna 2022

28th International Conference on DNA Computing and Molecular...

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28th international conference on dna computing and molecular programming, dna 2022

ISBN: (纸本)9783959772532

the proceedings contain 9 papers. the topics discussed include: fast and robust strand displacement cascades via systematic design strategies;universal shape replication via self-assembly with signal-passing tiles;a coupled reconfiguration mechanism for single-stranded dna strand displacement systems;exploring material design space with a deep-learning guided genetic algorithm;modelling and optimization of a dna stack nano-device using probabilistic model checking;on Turedo hierarchies and intrinsic universality;computing real numbers with large-population protocols having a continuum of equilibria;the structural power of reconfigurable circuits in the Amoebot model;and fault-tolerant shape formation in the Amoebot model.

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Modelling and Optimisation of a dna Stack Nano-Device Using Probabilistic Model Checking 28

Modelling and Optimisation of a DNA Stack Nano-Device Using ...

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28th international conference on dna computing and molecular programming, dna 2022

作者： Li, Bowen Mackenzie, Neil Shirt-Ediss, Ben Krasnogor, Natalio Zuliani, Paolo Research Group School of Computing Newcastle University Newcastle upon Tyne United Kingdom

ISBN: (纸本)9783959772532

A dna stack nano-device is a bio-computing system that can read and write molecular signals based on dna-dna hybridisation and strand displacement. In vitro implementation of the dna stack faces a number of challenges affecting the performance of the system. In this work, we apply probabilistic model checking to analyse and optimise the dna stack system. We develop a model framework based on continuous-time Markov chains to quantitatively describe the system behaviour. We use the PRISM probabilistic model checker to answer two important questions: 1) What is the minimum required incubation time to store a signal? And 2) How can we maximise the yield of the system? the results suggest that the incubation time can be reduced from 30 minutes to 5-15 minutes depending on the stack operation stage. In addition, the optimised model shows a 40% increase in the target stack yield. © Bowen Li, Neil Mackenzie, Ben Shirt-Ediss, Natalio Krasnogor, and Paolo Zuliani.

关键词： dna

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RF-dna: Large-Scale Physical-layer Identifications of RFIDs via Dual Natural Attributes 22

RF-DNA: Large-Scale Physical-layer Identifications of RFIDs ...

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28th Annual international conference on Mobile computing and Networking (ACM MobiCom)

作者： Pan, Qingrui An, Zhenlin Yang, Xueyuan Zhao, Xiaopeng Yang, Lei Hong Kong Polytech Univ Dept Comp Hong Kong Peoples R China

ISBN: (纸本)9781450391818

Physical-layer identification aims to identify wireless devices during RF communication by exploiting the imperfections of their radio circuitry, i.e., hardware fingerprint. Previous work proposed several hardware fingerprints for RFIDs (e.g., TIE, ABD, PSD, etc). However, these proposed fingerprints suffer from either unscalability or acquisition inefficiency. this work presents RF-dna, a new hardware fingerprint composed of millions of Dual Natural Attributes (dna) organized in a helical structure, where a pair of dna represents a tag's intrinsic response at some frequency. We take advantage of the frequency agnostic phenomenon that a commercial RFID tag can respond within a wider band than the regulated, to acquire 10x more features than previous fingerprints. At the heart of this work are the context-free acquisition approach to extracting dna from backscatter signals;and the accurate dna matching algorithm for verifying a tag's identity. A total of 160,000 RF-dna instances were collected from 16,000 tags using a customized automatic acquisition system. We subsequently carried out large-scale experiments to test the identification accuracy of RF-dna and previously proposed fingerprints. Our comprehensive evaluation reveals that RF-dna can achieve a mean accuracy of 95.98%. In contrast, those of previous fingerprints fall to 60% below when in face of thousands of tags.

关键词： Security RFID Physical-layer Identification

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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 Coupled Reconfiguration Mechanism for Single-Stranded dna Strand Displacement Systems 28

A Coupled Reconfiguration Mechanism for Single-Stranded DNA ...

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28th international conference on dna computing and molecular programming, dna 2022

作者： Johnson, Hope Amber Condon, Anne The University of British Columbia Vancouver Canada

ISBN: (纸本)9783959772532

dna Strand Displacement (DSD) systems model basic reaction rules, such as toehold-mediated strand displacement and 4-way branch migration, that modify complexes of bound dna strands. DSD systems have been widely used to design and reason about the correctness of molecular programs, including implementations of logic circuits, neural networks, and Chemical Reaction Networks. Such implementations employ a valuable toolkit of mechanisms – sequences of basic reaction rules – that achieve catalysis, reduce errors (e.g., due to leak), or simulate simple computational units such as logic gates, both in solution and on surfaces. Expanding the DSD toolkit of DSD mechanisms can lead to new and better ways of programming with dna. Here we introduce a new mechanism, which we call controlled reconfiguration. We describe one example where two single-stranded DSD complexes interact, changing the bonds in both complexes in a way that would not be possible for each independently on its own via the basic reaction rules allowed by the model. We use coupled reconfiguration to refer to instances of controlled reconfiguration in which two reactants change each other in this way. We note that our DSD model disallows pseudoknots and that properties of our coupled reconfiguration construction rely on this restriction of the model. A key feature of our coupled reconfiguration example, which distinguishes it from mechanisms (such as 3-way strand displacement or 4-way branch migration) that are typically used to implement molecular programs, is that the reactants are single-stranded. Leveraging this feature, we show how to use coupled reconfiguration to implement Chemical Reaction Networks (CRNs), with a DSD system that has both single-stranded signals (which represent the species of the CRN) and single-stranded fuels (which drive the CRN reactions). Our implementation also has other desirable properties;for example it is capable of implementing reversible CRNs and uses just two distinct toeho

关键词： dna

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Proceedings - 2020 28th Euromicro international conference on Parallel, Distributed and Network-Based Processing, PDP 2020

Proceedings - 2020 28th Euromicro International Conference o...

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28th Euromicro international conference on Parallel, Distributed and Network-Based Processing, PDP 2020

ISBN: (纸本)9781728165820

the proceedings contain 67 papers. the topics discussed include: windsurfing with APPA: automating computational fluid dynamics simulations of wind flow using cloud computing;parallel comparison of huge dna sequences in multiple GPUs with block pruning;accelerating deep learning using multiple GPUs and FPGA-based 10GbE switch;adaptive load balancing based on machine learning for iterative parallel applications;switching at flit level: a congestion efficient flow control strategy for network-on-chip;robustness and energy-elasticity of crown schedules for sets of parallelizable tasks on many-core systems with DVFS;and scalable parallel genetic algorithm for solving large integer linear programming models derived from behavioral synthesis.

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computing Real Numbers with Large-Population Protocols Having a Continuum of Equilibria 28

Computing Real Numbers with Large-Population Protocols Havin...

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28th international conference on dna computing and molecular programming, dna 2022

作者： Huang, Xiang Huls, Rachel N. Department of Computer Science University of Illinois Springfield United States Department of Mathematics University of Illinois Springfield United States

ISBN: (纸本)9783959772532

Bournez, Fraigniaud, and Koegler [6] defined a number in [0,1] as computable by their Large-Population Protocol (LPP) model, if the proportion of agents in a set of marked states converges to said number over time as the population grows to infinity. the notion, however, restricts the ordinary differential equations (ODEs) associated with an LPP to have only finitely many equilibria. this restriction places an intrinsic limitation on the model. As a result, a number is computable by an LPP if and only if it is algebraic, namely, not a single transcendental number can be computed under this notion. In this paper, we lift the finitary requirement on equilibria. that is, we consider systems with a continuum of equilibria. We show that essentially all numbers in [0,1] that are computable by bounded general-purpose analog computers (GPACs) or chemical reaction networks (CRNs) can also be computed by LPPs under this new definition. this implies a rich series of numbers (e.g., the reciprocal of Euler’s constant, π/4, Euler’s γ, Catalan’s constant, and Dottie number) are all computable by LPPs. Our proof is constructive: We develop an algorithm that transfers bounded GPACs/CRNs into LPPs. Our algorithm also fixes a gap in Bournez et al.’s construction of LPPs designed to compute any arbitrary algebraic number in [0,1]. © Xiang Huang and Rachel N. Huls.

关键词： Analog computers

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FindeR: Accelerating FM-Index-based Exact Pattern Matching in Genomic Sequences through ReRAM technology 28

FindeR: Accelerating FM-Index-based Exact Pattern Matching i...

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28th international conference on Parallel Architectures and Compilation Techniques (PACT)

作者： Zokaee, Farzaneh Zhang, Mingzhe Jiang, Lei Indiana Univ Bloomington Bloomington IN 47405 USA Chinese Acad Sci ICT Beijing Peoples R China

ISBN: (纸本)9781728136134

Genomics is the critical key to enabling precision medicine, ensuring global food security and enforcing wildlife conservation. the massive genomic data produced by various genome sequencing technologies presents a significant challenge for genome analysis. Because of errors from sequencing machines and genetic variations, approximate pattern matching (APM) is a must for practical genome analysis. Recent work proposes FPGA, ASIC and even process-in-memory-based accelerators to boost the APM throughput by accelerating dynamic-programming based algorithms (e.g., Smith-Waterman). However, existing accelerators lack the efficient hardware acceleration for the exact pattern matching (EPM) that is an even more critical and essential function widely used in almost every step of genome analysis including assembly, alignment, annotation and compression. State-of-the-art genome analysis adopts the FM-Index that augments the space-efficient BWT with additional data structures permitting fast EPM operations. But the FM-Index is notorious for poor spatial locality and massive random memory accesses. In this paper, we propose a ReRAM-based process-in-memory architecture, FindeR, to enhance the FM-Index EPM search throughput in genomic sequences. We build a reliable and energy efficient Hamming distance unit to accelerate the computing kernel of FM-Index search using commodity ReRAM chips without introducing extra CMOS logic. We further architect a full-fledged FM-Index search pipeline and improve its search throughput by lightweight scheduling on the NVDIMM. We also create a system library for programmers to invoke FindeR to perform EPMs in genome analysis. Compared to state-of-the-art accelerators, FindeR improves the FM-Index search throughput by 83% similar to 30K x and throughput per Watt by 3.5 x similar to 42.5K x.

关键词： short dna alignment ReRAM

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DROM: Read Only Memory Storage in dna computing

DROM: Read Only Memory Storage in DNA Computing

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Sustainable Technologies for Industry 4.0 (STI), international conference on

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

关键词： Proteins Sequential analysis Operating systems dna molecular biophysics Logic gates programming

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Accelerating Self-Assembly of Crisscross Slat Systems 29

Accelerating Self-Assembly of Crisscross Slat Systems

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29th international conference on dna computing and molecular programming, dna 2023

作者： Doty, David Fleming, Hunter Hader, Daniel Patitz, Matthew J. Vaughan, Lukas A. University of California DavisCA United States University of Arkansas FayettevilleAR United States

ISBN: (纸本)9783959772976

We present an abstract model of self-assembly of systems composed of "crisscross slats", which have been experimentally implemented as a single-stranded piece of dna [21] or as a complete dna origami structure [28]. We then introduce a more physically realistic "kinetic" model and show how important constants in the model were derived and tuned, and compare simulation-based results to experimental results [21,28]. Using these models, we show how we can apply optimizations to designs of slat systems in order to lower the numbers of unique slat types required to build target structures. In general, we apply two types of techniques to achieve greatly reduced numbers of slat types. Similar to the experimental work implementing dna origami-based slats, in our designs the slats oriented in horizontal and vertical directions are each restricted to their own plane and sets of them overlap each other in square regions which we refer to as macrotiles. Our first technique extends their previous work of reusing slat types within macrotiles and requires analyses of binding domain patterns to determine the potential for errors consisting of incorrect slat types attaching at undesired translations and reflections. the second technique leverages the power of algorithmic self-assembly to efficiently reuse entire macrotiles which self-assemble in patterns following designed algorithms that dictate the dimensions and patterns of growth. Using these designs, we demonstrate that in kinetic simulations the systems with reduced numbers of slat types self-assemble more quickly than those with greater numbers. this provides evidence that such optimizations will also result in greater assembly speeds in experimental systems. Furthermore, the reduced numbers of slat types required have the potential to vastly reduce the cost and number of lab steps for crisscross assembly experiments. © David Doty, Hunter Fleming, Daniel Hader, Matthew J. Patitz, and Lukas A. Vaughan;licensed under Creative C

关键词： dna

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