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9th international conference on Bio-Inspired computing - theories and Applications, BIC-TA 2014

9th International Conference on Bio-Inspired Computing - The...

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9th international conference on Bio-Inspired computing - theories and Applications, BIC-TA 2014

ISBN: (纸本)9783662450482

the proceedings contain 109 papers. the special focus in this conference is on Bio-Inspired computing. the topics include: the application of spiking neural P systems for PLC programming;molecular model for information addressing and transporting based on dna nanotechnology;real-coded genetic algorithm with oriented search towards promising region for parameter optimization;the algorithms and composition of a travel system based on geographical information;using support vector machine to identify imaging biomarkers of major depressive disorder and anxious depression;an adaptive differential evolution algorithm with automatic population resizing for global numerical optimization;an improved method of dna information encryption;an encryption scheme based on dna microdots technology;research on improved locally linear embedding algorithm;an improved evolutionary approach for association rules mining;multiple depots incomplete open vehicle routing problem based on carbon tax;on the convergence of Levenberg Marquardt method for solving nonlinear systems;locate multiple Pareto optima using a species-based multi-objective genetic algorithm;research for performance evaluation of university teachers;an edge detection algorithm based on morphological gradient and the Otsu method;solving the multiobjective multiple traveling salesmen problem using membrane algorithm;a novel method to derive ambulatory blood pressure from the radial pressure waveform;adaptive mutation behavior for quantum particle swarm optimization;bifurcation and global synchronization analysis in diffusively coupled calcium oscillators and uniform solution to partition problem using P systems with membrane division.

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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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Robust digital molecular design of binarized neural networks 27

Robust digital molecular design of binarized neural networks

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27th international conference on dna computing and molecular programming, dna 2021

作者： Linder, Johannes Chen, Yuan-Jyue Wong, David Seelig, Georg Ceze, Luis Strauss, Karin University of Washington Paul G. Allen School of Computer Science and Engineering SeattleWA United States Microsoft Research RedmondWA United States University of Washington Department of Bioengineering SeattleWA United States University of Washington Department of Electrical and Computer Engineering SeattleWA United States

ISBN: (纸本)9783959772051

molecular programming - a paradigm wherein molecules are engineered to perform computation - shows great potential for applications in nanotechnology, disease diagnostics and smart therapeutics. A key challenge is to identify systematic approaches for compiling abstract models of computation to molecules. Due to their wide applicability, one of the most useful abstractions to realize is neural networks. In prior work, real-valued weights were achieved by individually controlling the concentrations of the corresponding "weight" molecules. However, large-scale preparation of reactants with precise concentrations quickly becomes intractable. Here, we propose to bypass this fundamental problem using Binarized Neural Networks (BNNs), a model that is highly scalable in a molecular setting due to the small number of distinct weight values. We devise a noise-tolerant digital molecular circuit that compactly implements a majority voting operation on binary-valued inputs to compute the neuron output. the network is also rate-independent, meaning the speed at which individual reactions occur does not affect the computation, further increasing robustness to noise. We first demonstrate our design on the MNIST classification task by simulating the system as idealized chemical reactions. Next, we map the reactions to dna strand displacement cascades, providing simulation results that demonstrate the practical feasibility of our approach. We perform extensive noise tolerance simulations, showing that digital molecular neurons are notably more robust to noise in the concentrations of chemical reactants compared to their analog counterparts. Finally, we provide initial experimental results of a single binarized neuron. Our work suggests a solid framework for building even more complex neural network computation. © 2021 Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing. All rights reserved.

关键词： Neural networks

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A dna based molecular logic gate capable of a variety of logical operations

A DNA based molecular logic gate capable of a variety of log...

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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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dna implementation of a royal road fitness evaluation 1

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

作者： Goode, Elizabeth Wood, David Harlan Chen, Junghuei University of Delaware NewarkDE19716 United States

ISBN: (数字)9783540449928

ISBN: (纸本)3540420762

A model for dna implementation of Royal Road evolutionary computations is presented. An encoding for a Royal Road problem is presented. Experimental results utilizing 2-d denaturing gradient gel electrophoresis (2-d DGGE) and polyacrylamide gel electrophoresis (PAGE) for separation by fitness in this sample Royal Road problem are shown. Suggestions for possible use of the MutS and MutY proteins as tools for separation by fitness are given. Plans for future experiments and implementation are discussed. © Springer-Verlag Berlin Heidelberg 2001.

关键词： Health

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A dna computing system of modular-multiplication over finite field GF(2n)

A DNA computing system of modular-multiplication over finite...

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13th international conference on Algorithms and Architectures for Parallel Processing, ICA3PP 2013

作者： Li, Yongnan Xiao, Limin Ruan, Li Zhang, Zhenzhong Li, Deguo State Key Laboratory of Software Development Environment Beihang University Beijing 100191 China School of Computer Science and Engineering Beihang University Beijing 100191 China

ISBN: (纸本)9783319038582

the enormous parallel computing ability and high memory density of dna computing bring potential challenges and opportunities to traditional cryptography. Finite field GF(2n) is one of the most commonly used mathematic sets for cryptography. It is an open problem that how to implement the arithmetic operations over finite field GF(2n) based on dna computing. Existing research has the problem that the lengths of parameters in the dna tile assembly process could not match each other strictly. this paper proposes a parallel molecular computing system to compute the modular-multiplication, an operation combining multiplication and reduction over finite field GF(2n). the multiplication and the reduction are executed simultaneously in this system. One concrete example of 1100 · 1001 mod 10011 is proposed to show the details of our tile assembly system. the time complexity of this system is Θ(n) and the space complexity is Θ(n2). this system requires 210 types of computation tiles and 17 types of boundary tiles. © Springer international Publishing Switzerland 2013.

关键词： Cryptography

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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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A Shared Memory Method ForEnhancingthe HTNGH AlgorithmPerformance: Proposed Method 17

A Shared Memory Method ForEnhancingThe HTNGH AlgorithmPerfor...

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international conference on Future Networks and Distributed Systems (ICFNDS)

作者： Abu-Hashem, Muhannad A. Uliyan, Diaa M. Abuarqoub, Abdelrahman Middle East Univ Fac Informat Technol Amman Jordan

ISBN: (纸本)9781450348447

In bioinformatics, pair-wise alignment plays a significant role insequence comparison by rating the similarities and distances between protein, DeoxyriboNucleic Acid (dna), and RiboNucleic Acid (RNA)sequences. Sequence comparison considered as a key stone in building distance matrices. Due to the rapid growth of molecular databases, the need for faster sequence comparison and alignment has become anecessity. High performance computing impacthas increased in the last decade through providing many high performance architectures and tools. In this paper we present a parallel shared memory design for a dynamic programming algorithm named Hash Table-N-Gram-Hirschberg (HT-NGH) an extension of Hashing-N-Gram-Hirschberg (HNGH) and N-Gram-Hirschberg (NGH) algorithm, to speed up the sequence alignment construction process. the focus of the proposed method ison the transformation phase of HT-NGH algorithm since it takes10% of HT-NGH overall run time. the experimental evaluation of the proposed parallel designshows an enhancement in the execution time and speedup without sacrificing the accuracy. However,the decomposition method might slightly slowdown the proposed algorithm due to the differences in performance between the processing units.

关键词： Shared-Memory Parallel design High-performance computing Sequence Alignment pair-wise alignment distance matrix construction

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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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