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Research on the addition, subtraction, multiplication and division complex logical operations based on the dna strand displacement 1

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13th international conference on Bio-Inspired computing: theories and Applications, BIC-TA 2018

作者： Huang, Chun Wang, Yanfeng Zhou, Qinglei School of Information Engineering Zhengzhou University Zhengzhou450001 China College of Electrical and Electronic Engineering Zhengzhou University of Light Industry Zhengzhou450002 China

ISBN: (数字)9789811328299

ISBN: (纸本)9789811328282

In recent years, the development of biological computers has become faster and faster. In order to adapt to the development of science and technology, some novel logic circuits designs are necessary. In this paper, a complex molecular combinational logic circuit is designed to perform large-scale biological information processing by compound logic operation of addition, subtraction, multiplication and division. the design of compound logic operations of addition, subtraction, multiplication and division based on dna strand has four inputs signals and two output signals, and the dual-track design theory is used to perform the logic circuit operation, and the corresponding output result can be obtained in timely and accurately. the whole reaction progress of logic circuit operations can be programmed and simulated by the Visual DSD software. According to the simulation results of the Visual DSD software, the method of dna strand displacement is feasible to achieve more complex logic computations. this investigation for the addition, subtraction, multiplication and division complex logical operations of a binary number may have a great prospect for the development and application in the biological information processing, medicine diagnosis, molecular computing, and so on. © Springer Nature Singapore Pte Ltd. 2018.

关键词： Logic circuits

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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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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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Domain-Based Nucleic-Acid Minimum Free Energy: Algorithmic Hardness and Parameterized Bounds 30

Domain-Based Nucleic-Acid Minimum Free Energy: Algorithmic H...

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30th international conference on dna computing and molecular programming, dna 30 2024

作者： Demaine, Erik D. Gomez, Timothy Grizzell, Elise Hecher, Markus Lynch, Jayson Schweller, Robert Shalaby, Ahmed Woods, Damien Massachusetts Institute of Technology United States University of Texas Rio Grande Valley United States Hamilton Institute Department of Computer Science Maynooth University Ireland

ISBN: (纸本)9783959773447

molecular programmers and nanostructure engineers use domain-level design to abstract away messy dna/RNA sequence, chemical and geometric details. Such domain-level abstractions are enforced by sequence design principles and provide a key principle that allows scaling up of complex multistranded dna/RNA programs and structures. Determining the most favoured secondary structure, or Minimum Free Energy (MFE), of a set of strands, is typically studied at the sequence level but has seen limited domain-level work. We analyse the computational complexity of MFE for multistranded systems in a simple setting were we allow only 1 or 2 domains per strand. On the one hand, with 2-domain strands, we find that the MFE decision problem is NP-complete, even without pseudoknots, and requires exponential time algorithms assuming SAT does. On the other hand, in the simplest case of 1-domain strands there are efficient MFE algorithms for various binding modes. However, even in this single-domain case, MFE is P-hard for promiscuous binding, where one domain may bind to multiple as experimentally used by Nikitin [Nat Chem., 2023], which in turn implies that strands consisting of a single domain efficiently implement arbitrary Boolean circuits. © Erik D. Demaine, Timothy Gomez, Elise Grizzell, Markus Hecher, Jayson Lynch, Robert Schweller, Ahmed Shalaby, and Damien Woods

关键词： Domain-based dna designs efficient algorithms fixed-parameter tractable minimum free energy NC NP-hard P-hard

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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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the Circular dna Model of 0–1 programming Problem Based on dna Strand Displacement

The Circular DNA Model of 0–1 Programming Problem Based on ...

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international conference on Fuzzy Systems and Knowledge Discovery (FSKD)

作者： Zhen Tang Zhixiang Yin Jing Yang Xia Sun Jianzhong Cui School of Mathematics and Big Data AnHui University of Science and Technology Huainan AnHui china School of Electronic and Information Engineering AnHui University of Science and Technology Huainan AnHui china

ISBN: (纸本)9781538680988;9781538680971

dna strand displacement is a new molecular biological technology with strong operability and simple experimental conditions. In this paper, dna strand displacement is applied to solve the 0-1 programming problem, and a model is constructed using the class closed-loop dna structure (known as “circular dna” in this paper). the model fixes the dna strands which represent the variables on the circular dna single strand in counterclockwise order. the dna strand 5' end is attached with the primers which are applied to the displacement of the dna strand. the 3' end is attached with the colored fluorophore. Taking the possible solutions as the input, the results are detected by different fluorescent colors resulting from the dna strand displacement. the dna computing model has better flexibility, realizability and applicability.

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Genalign — A high performance implementation for aligning the compressed dna sequences

Genalign — A high performance implementation for aligning t...

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international conference on Advanced computing Technologies (ICACT)

作者： D Satyanvesh Kaliuday Balleda P K Baruah Sri Sathya Sai Institute of Higher Learning Prasanthi Nilayam India

In molecular biology, sequence alignment is a way of arranging dna, RNA or protein sequences to identify regions of similarity between the sequences. However, this is a challenging problem since the dna sequences are huge in size and the databases are growing at an exponential rate. It requires tremendous amount of memory and large computational power. For example, the human genome in raw format ranges from 2 to 30 Tera-bytes. the inherent property of dna is that it contains many repeats which makes it highly compressible. this paper presents a new approach of aligning the sequences after compressing them. the alignment consists of both ungapped and gapped alignment. Multi-cores and GPUs can be used to align these huge sequences quickly on the compressed sequences. the focus mainly is on aligning the huge sequences accurately. the ungapped alignment achieves a speedup of upto 56 on K20 Kepler GPUs and the gapped alignment achieves a speedup of upto 15 on multi-cores.

关键词： dna Graphics processing units Dynamic programming Heuristic algorithms Instruction sets Random access memory Bioinformatics

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the Biotechnological Method for Constructing Acoustic and Vibration Sequences Based on Genetic dna Sequences

The Biotechnological Method for Constructing Acoustic and Vi...

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4th international conference of Artificial Intelligence, Medical Engineering, Education, AIMEE 2020 held at the Mechanical Engineering Institute of the Russian Academy of Sciences, 2020

作者： Oleynikov, Roman V. Petoukhov, Sergey V. Soshinsky, Ivan S. Mechanical Engineering Research Institute Russian Academy of Sciences M. Kharitonievsky pereulok 4 Moscow Russia Moscow State Tchaikovsky Conservatory Bolshaya Nikitskaya 13/6 Moscow Russia

ISBN: (纸本)9783030671327

the paper is devoted to the usage of binary-oppositional molecular features of dna nucleotides for presentation of dna sequences as interrelated parallel sets of binary-numeric sequences, which can be converted into corresponding sequences of polyphonic incentives of different physical nature: acoustical, vibrational, electrical, magnetic, and optical. Such interrelated sets of binary-numeric sequences reproduce in some degree a complex informational content of genetic sequences and are interesting for their applications in different biotechnologies concerning cell cultures, regenerative medicine and also musical therapy. the binary-numeric representations of eukaryotic and prokaryotic genomes are described, which have universal algebra-harmonic properties, connected with the harmonic progression known long ago in musicology and other scientific fields. these genomic properties were discovered due to a presented method of oligomer sums. © 2021, the Author(s), under exclusive license to Springer Nature Switzerland AG.

关键词： dna sequences

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Toward molecular programming with dna

Toward molecular programming with DNA

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Proceedings of the 13th international conference on Architectural support for programming languages and operating systems

作者： Erik Winfree California Institute of Technology Pasadena CA

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 *** Erik Winfree is an Associate Professor in Computer Science, Computation & Neural Systems, and Bioengineering at Caltech. Winfree is the recipient of the Feynman Prize for Nanotechnology (2006), the NSF PECASE/CAREER Award (2001), the ONR Young Investigators Award (2001), a MacArthur Fellowship (2000), and MIT Technology Review's first TR100 list of "top young innovators" (1999). Prior to joining the faculty at Caltech in 2000, Winfree was a Lewis thomas Postdoctoral Fellow in molecular Biology at Princeton, and a Visiting Scientist at the MIT AI Lab. Winfree received a B.S. in Mathematics w/ Computer Science from the University of Chicago in 1991, and a Ph.D. in Computati

关键词： molecular programming dna

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TBIS:A Web-Based Expert System for Identification of Tephritid Fruit Flies in China Based on dna Barcode

TBIS:A Web-Based Expert System for Identification of Tephrit...

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Computer and computing Technologies in Agriculture IV——4th IFIP TC 12 conference(CCTA2010) Part III

作者： Zhimei Li Zhihong Li Fuxiang Wang Wei Lin Jiajiao Wu Department of Entomology College of Agronomy and BiotechnologyChina Agricultural University National Agricultural Technology Extension Service Center General Administration of Quality Supervision Inspection and Quarantine of the People's Republic of China Guangdong Entry-Exit Inspection and Quarantine Bureau

ISBN: (纸本)9783642183539

Tephritid fruit flies(Diptera:Tephritidae) include serious agricultural insect pests in the *** causing severe damage to fruits and vegetables,this kind of pests could enter countries or regions with international trade *** trade quarantine measures are imposed in many countries or regions in order to prevent their introduction and *** accurate and rapid identification is regarded as an essential component of plant *** expert systems for assistant identification of agricultural insect pests are based on their morphological *** with the morphological identification,however,molecular identification has more advantages especially for the identification of the immature samples which are intercepted more *** the molecular identification methods,dna barcoding is very effective and has been selected by the taxonomists in recent 5 *** view of the above,a network expert system based on the dna barcode,Tephritid Barcode Identification System(TBIS) was developed with *** and C# to improve the molecular identification of fruit fly pests in *** system was supported by Microsoft SQL server 2008 *** functions were provided such as molecular identification based on dna barcode,information browse and *** sequence similarity alignment dynamic programming algorithm served as the inference *** identification knowledge was obtained from the public database on the Internet and Plant Quarantine Laboratory of China Agricultural University,which contained about 400 COI sequences of nearly 150 species of fruit ***,detailed information such as morphological description and pictures of adult,hosts,and geographical distribution are presented in this *** with molecular,morphological and distributional data,the system can be used as an identification tool both for quarantine technicians and for educational purposes in China.

关键词： Expert system Pests identification dna barcode SQL server Tephritidae

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