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检索条件"任意字段=25th International Conference on DNA Computing and Molecular Programming, DNA 2019"

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25th international conference on dna computing and molecular programming, dna 2019

25th International Conference on DNA Computing and Molecular...

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25th international conference on dna computing and molecular programming, dna 2019

ISBN: (纸本)9783030268060

the proceedings contain 12 papers. the special focus in this conference is on dna computing and molecular programming. the topics include: Error-Free Stable Computation with Polymer-Supplemented Chemical Reaction Networks;SIMD||dna: Single Instruction, Multiple Data Computation with dna Strand Displacement Cascades;Implementing Arbitrary CRNs Using Strand Displacing Polymerase;real-Time Equivalence of Chemical Reaction Networks and Analog Computers;a Reaction Network Scheme Which Implements Inference and Learning for Hidden Markov Models;Efficient Parameter Estimation for dna Kinetics Modeled as Continuous-Time Markov Chains;new Bounds on the Tile Complexity of thin Rectangles at Temperature-1;non-cooperatively Assembling Large Structures;simulation of Programmable Matter Systems Using Active Tile-Based Self-Assembly;combined Amplification and molecular Classification for Gene Expression Diagnostics.

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SIMD||dna: Single Instruction, Multiple Data Computation with dna Strand Displacement Cascades 1

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25th international conference on dna computing and molecular programming, dna 2019

作者： Wang, Boya Chalk, Cameron Soloveichik, David The University of Texas at Austin Austin United States

ISBN: (数字)9783030268077

ISBN: (纸本)9783030268060

Typical dna storage schemes do not allow in-memory computation, and instead transformation of the stored data requires dna sequencing, electronic computation of the transformation, followed by synthesizing new dna. In contrast we propose a model of in-memory computation that avoids the time consuming and expensive sequencing and synthesis steps, with computation carried out by dna strand displacement. We demonstrate the flexibility of our approach by developing schemes for massively parallel binary counting and elementary cellular automaton Rule 110 computation. © 2019, Springer Nature Switzerland AG.

关键词： dna

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A MICROFLUIDIC GENERATOR OF RANDOM DISTRIBUTIONS OF dna 25

A MICROFLUIDIC GENERATOR OF RANDOM DISTRIBUTIONS OF DNA

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25th international conference on Miniaturized Systems for Chemistry and Life Sciences, MicroTAS 2021

作者： Okumura, Shu Hapsianto, Benediktus N. Lobato-Dauzier, Nicolas Kim, Soo Hyeon Genot, Anthony Fujii, Teruo The University of Tokyo Japan LIMMS CNRS-Institute of Industrial Science UMI 2820 University of Tokyo Japan

ISBN: (纸本)9781733419031

Understanding stochasticity at the molecular level is a challenge for biology and chemistry. Here we use droplet microfluidics and dna computing to generate random distributions of dna strands. A miRNA is Poisson-encapsulated, and programmed to trigger one of two dna amplifiers with equal probability. this creates a Bernoulli distribution of two dna species, confirmed by fluorescence microscopy. this system, which can synthesize a variety of dnas from a single solution, is expected to enable a bottom-up approach to studying the response of chemical reactions to large numbers of random numbers. © 2021 MicroTAS 2021 - 25th international conference on Miniaturized Systems for Chemistry and Life Sciences. All rights reserved.

关键词： dna

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Efficient Parameter Estimation for dna Kinetics Modeled as Continuous-Time Markov Chains 1

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25th international conference on dna computing and molecular programming, dna 2019

作者： Zolaktaf, Sedigheh Dannenberg, Frits Winfree, Erik Bouchard-CÃ´tÃ©, Alexandre Schmidt, Mark Condon, Anne University of British Columbia VancouverBC Canada California Institute of Technology PasadenaCA United States

ISBN: (数字)9783030268077

ISBN: (纸本)9783030268060

Nucleic acid kinetic simulators aim to predict the kinetics of interacting nucleic acid strands. Many simulators model the kinetics of interacting nucleic acid strands as continuous-time Markov chains (CTMCs). States of the CTMCs represent a collection of secondary structures, and transitions between the states correspond to the forming or breaking of base pairs and are determined by a nucleic acid kinetic model. the number of states these CTMCs can form may be exponentially large in the length of the strands, making two important tasks challenging, namely, mean first passage time (MFPT) estimation and parameter estimation for kinetic models based on MFPTs. Gillespieâ€™s stochastic simulation algorithm (SSA) is widely used to analyze nucleic acid folding kinetics, but could be computationally expensive for reactions whose CTMC has a large state space or for slow reactions. It could also be expensive for arbitrary parameter sets that occur in parameter estimation. Our work addresses these two challenging tasks, in the full state space of all non-pseudoknotted secondary structures of each reaction. In the first task, we show how to use a reduced variance stochastic simulation algorithm (RVSSA), which is adapted from SSA, to estimate the MFPT of a reactionâ€™s CTMC. In the second task, we estimate model parameters based on MFPTs. To this end, first, we show how to use a generalized method of moments (GMM) approach, where we minimize a squared norm of moment functions that we formulate based on experimental and estimated MFPTs. Second, to speed up parameter estimation, we introduce a fixed path ensemble inference (FPEI) approach, that we adapt from RVSSA. We implement and evaluate RVSSA and FPEI using the Multistrand kinetic simulator. In our experiments on a dataset of dna reactions, FPEI speeds up parameter estimation compared to inference using SSA, by more than a factor of three for slow reactions. Also, for reactions with large state spaces, it speeds up parameter

关键词： Stochastic systems

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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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12th international conference on Practical Applications of Computational Biology and Bioinformatics, PACBB 2018

12th International Conference on Practical Applications of C...

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12th international conference on Practical Applications of Computational Biology and Bioinformatics, PACBB 2018

ISBN: (纸本)9783319987019

the proceedings contain 26 papers. the special focus in this conference is on Practical Applications of Computational Biology and Bioinformatics. the topics include: A bioinformatics protocol for quickly creating large-scale phylogenetic trees;Deep learning analysis of binding behavior of virus displayed peptides to AuNPs;compression of amino acid sequences;NET-ASAR: A tool for dna sequence search based on data compression;Can an integrative SNP approach substitute standard identification in comprehensive case/control analyses?;simple pattern-only heuristics lead to fast subgraph matching strategies on very large networks;in silico predictions for fucoxanthin production by the diatom phaeodactylum tricornutum;EvoPPI: A web application to compare protein-protein interactions (PPIs) from different databases and species;a review on metabolomics data analysis for cancer applications;parameter estimation of essential amino acids in Arabidopsis thaliana using hybrid of bees algorithm and harmony search;a framework for the automatic combination and evaluation of gene selection methods;parallel cellular automaton tumor growth model;MOSCA: An automated pipeline for integrated metagenomics and metatranscriptomics data analysis;metabolite integration pipeline for the improvement of human metabolic models;a genetic programming approach applied to feature selection from medical data;A dna sequence corpus for compression benchmark;17α-ethinylestradiol analysis of endo- and exometabolome of ulva lactuca (chlorophyta) by 1H-NMR spectroscopy and bioinformatics tools;in silico modeling and simulation approach for apoptosis caspase pathways;molecular dynamic simulations suggest that P152R mutation within MeCP2 can lead to higher dna binding affinity and loss of selective binding to methylated 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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dna Tile Self-Assembly for 3D-Surfaces: Towards Genus Identification 29

DNA Tile Self-Assembly for 3D-Surfaces: Towards Genus Identi...

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

作者： Becker, Florent Heydarshahi, Shahrzad Univ. Orléans INSA Centre Val de Loire LIFO EA 4022 OrléansF-45067 France

ISBN: (纸本)9783959772976

We introduce a new dna tile self-assembly model: the Surface Flexible Tile Assembly Model (SFTAM), where 2D tiles are placed on host 3D surfaces made of axis-parallel unit cubes glued together by their faces, called polycubes. the bonds are flexible, so that the assembly can bind on the edges of the polycube. We are interested in the study of SFTAM self-assemblies on 3D surfaces which are not always embeddable in the Euclidean plane, in order to compare their different behaviors and to compute the topological properties of the host surfaces. We focus on a family of polycubes called order-1 cuboids. Order-0 cuboids are polycubes that have six rectangular faces, and order-1 cuboids are made from two order-0 cuboids by substracting one from the other. thus, order-1 cuboids can be of genus 0 or of genus 1 (then they contain a tunnel). We are interested in the genus of these structures, and we present a SFTAM tile assembly system that determines the genus of a given order-1 cuboid. the SFTAM tile assembly system which we design, contains a specific set Y of tile types with the following properties. If the assembly is made on a host order-1 cuboid C of genus 0, no tile of Y appears in any producible assembly, but if C has genus 1, every terminal assembly contains at least one tile of Y. thus, for order-1 cuboids our system is able to distinguish the host surfaces according to their genus, by the tiles used in the assembly. this system is specific to order-1 cuboids but we can expect the techniques we use to be generalizable to other families of shapes. © Florent Becker and Shahrzad Heydarshahi;licensed under Creative Commons License CC-BY 4.0.

关键词： Assembly

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High Accuracy Multi-input dna Logic Gate Using the Spatially Localized dna Structures

High Accuracy Multi-input DNA Logic Gate Using The Spatially...

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international CSI Computer conference, CSICC

作者： Ehsan Jamalzadeh Ali Jahanian Faculty of Computer Science and Engineering Shahid Beheshti University G. C. Tehran Iran

ISBN: (数字)9781728159379

ISBN: (纸本)9781728159386

A combination of engineering and biology, using the dna for computation, is an interesting and hopeful area. the future of this area looks very promising for diagnosis and treatment of diseases. Various dna-based logic sensors are proposed in the past years. Recent attempts have shown that localized dna strand displacement circuits, wherein dna components are physically attached to a dna surface, can improve the quality and speed of the reactions. Whereby, simultaneously run multiple instances of circuits on spatially separated locations that will be increased the speed of computation, scalability, and modularity. In this paper, we proposed a scalable method to design multiinput logic gates with spatially localized dna hairpins that has fewer materials and speed up the desired concentration. Experimental results show that the response time and the number of required strands (fuels and anchored hairpins) are reduced more than 27% and 14%, respectively and these improvements will be more considerable in large fan-in and complex circuits.

关键词： biocomputing logic design logic gates Logic gates biology computing Logic design dna Computational molecular Biology circuit complexity Reaction Time Electric circuits hair clasp multi-input Modularity

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Integration of UAV and Fog-Enabled Vehicle: Application in Post-Disaster Relief

Integration of UAV and Fog-Enabled Vehicle: Application in P...

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international conference on Parallel and Distributed Systems (ICPADS)

作者： Chaogang Tang Chunsheng Zhu Xianglin Wei Hao Peng Yi Wang School of Computer Science and Technology China University of Mining and Technology Xuzhou China SUSTech Institute of Future Networks Southern University of Science and Technology Shenzhen China PCL Research Center of Networks and Communications Peng Cheng Laboratory Shenzhen China Naniing Telecommunication Technology Research Institute Nanjing China College of Mathematics and Computer Sciences Zhejiang Normal University

ISBN: (纸本)9781728125848

In addition to military applications, Unmanned Aerial Vehicles (UAVs) have attracted more and more attention in civilian applications such as the post-disaster relief assistance. Indeed, advantages including better line-of-sight (LOS), wider communication range and more flexible on-demand deployment make UAVs play a unique role in rescue and disaster scenarios. Emergency tasks assigned to UAVs such as people search and rescue usually require real-time responses, since it is a life-and-death matter regarding the post-disaster relief. Considering the limited computing resources and harsh energy supply replenishment for UAVs in the post-disaster relief operations, we in this paper propose a hybrid fog computing paradigm called H-FVFC that integrates UAVs and vehicular fog computing (VFC) to run the highly demanding tasks with strict latency requirements. An architecture of H-FVFC consisting of three layers is proposed and investigated in this paper, with hope to explore the possibilities of applying this computing paradigm to post-disaster relief operations. Experiments are carried out to evaluate the task offloading in H-FVFC compared to UAV-to-Cloud scheduling strategy. the results show that task offloading in the UAV-to-Vehicle way can significantly reduce the response latency. Issues not addressed in this paper are also discussed with purpose of providing some insights to the application of integration of UAV and fog-enabled vehicle in the post-disaster relief.

关键词： UAV VFC Task offloading Architecture Post-disaster Unmanned Aerial Vehicle voltage frequency conversion drone honey bees Disaster relief Building construction ARCHITECTURE relief operations dna Integration integration relief Rescue

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