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10th international conference on Bio-Inspired computing - theories and Applications (BIC-TA)

作者： Zhang, Xuncai Shen, Chaonan Cui, Guangzhao Wang, Yanfeng Zhengzhou Univ Light Ind Coll Elect & Elect Engn Henan Key Lab Informat Based Elect Appliances Zhengzhou 450002 Henan Peoples R China

ISBN: (纸本)9783662490143;9783662490136

Toehold-mediated strand displacement has great advantage in dna molecular computing. It is widely applied to build the large-scale and complex logic circuits. However, in general, the detection of molecular circuits is achieved by dna double helices with nicked segment. So to some extent it limits the detection method of molecular circuits. Here, we report a strategy implemented by the combinatorial strand displacement technology to control the state of dna nano-tweezer. the distance between the fluorescent dye and the quencher dye is drawn closer because of the closed dna nano-tweezer, inducing the fluorescence signal disappeared in response to the logic gate function. Four logic circuits (AND gate, OR gate, Inhibit gate and XOR gate) are designed in this paper based on the combinatorial strand displacement.

关键词： Combinatorial strand displacement dna nano-tweezer Logic circuits

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Back Translated Peptide K-mer Search and Local Alignment in Large dna Sequence Databases Using BoND-SD-tree Indexing

Back Translated Peptide K-mer Search and Local Alignment in ...

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IEEE international conference on Bioinformatics and Bioengineering

作者： AKM Tauhidul Islam Sakti Pramanik Xinge Ji James R. Cole Qiang Zhu Michigan State University University of Michigan

ISBN: (纸本)9781467379847

In the past, genome sequence databases had used main memory indexing, such as the suffix tree, for fast sequence searches. With next generation sequencing technologies, the amount of sequence data being generated is huge and main memory indexing is limited by the amount of memory available. K-mer based techniques are being more used for various genome sequence database applications such as local alignment. K-mer can also provide an excellent basis for creating efficient disk based indexing. In this paper, we have proposed a k-mer based database searching and local alignment tool using box queries on BoND-SD-tree indexing. BoND-tree is quite efficient for indexing and searching in Non-Ordered Discrete Data Space (NDDS). We have conducted experiments on searching dna sequence databases using back translated protein query sequences and have compared with existing methods. We have also implemented local alignment of back translated protein query sequences with large dna sequence databases using this index based k-mer search. Performances of this local alignment approach have been compared with that of Tblastn of NCBI. the results are quite promising and justify significance of the proposed approach.

关键词： dna Sequence Databases Indexing alignment tool Database searching molecular Sequence Data

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Carcinogenesis Induced by Aflatoxin B1: A Computational Study

Carcinogenesis Induced by Aflatoxin B1: A Computational Stud...

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IEEE international conference on Bioinformatics and Bioengineering

作者： Tibor Kuna Urban Bren Laboratory for Physical Chemistry and Chemical Thermodynamics Faculty of Chemistry and Chemical Technology University of Maribor

ISBN: (纸本)9781467379847

the reported study represents a nice example of how state-of-the-art molecular modeling techniques can be used to study complicated macromolecular complexes, whose structures have not yet been experimentally determined, and to validate these against the available experimental data. the proposed structure will facilitate future studies on the rational design of successful Aflatoxin B1 (AFB1) modulators or on human subpopulations characterized by specific CYP3A4 polymorphisms that are especially sensitive to AFB1 - the most potent natural carcinogen known to men. We also report a series of ab initio and density functional theory simulations of guanine alkylation by aflatoxin B1 exo-8,9-epoxide and predict that the preference of aflatoxin B1 exo-8,9-epoxide over the endo stereoisomer for the reaction with guanine exists in the aqueous solution and is only further amplified in the dna duplex. Finally, through comparison with an analogous reaction between 3a,6a-dihydrofuro[2,3-b]furan exo-4,5-epoxide and guanine, we show that the large planar body of aflatoxin B1 does not enhance its reactivity and related carcinogenicity. this explains why the planar region of related mycotoxins sterigmatocystin and aflatoxin G1 could have been evolutionarily optimized in a different way.

关键词： dna Data models Chemicals Modulation Density functional theory Protocols Kinetic theory

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dna computing and molecular programming - 19th international conference, dna 2013, Proceedings

DNA Computing and Molecular Programming - 19th International...

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19th international conference on dna computing and molecular programming, dna 2013

ISBN: (纸本)9783319019277

the proceedings contain 15 papers. the topics discussed include: extending dna-sticker arithmetic to arbitrary size using staples;parallel computation using active self-assembly;dna walker circuits: computational potential, design, and verification;leaderless deterministic chemical reaction networks;dna sticky end design and assignment for robust algorithmic self-assembly;dna reservoir computing: a novel molecular computing approach;signal transmission across tile assemblies: 3D static tiles simulate active self-assembly by 2D signal-passing tiles;3-color bounded patterned self-assembly;exponential replication of patterns in the signal tile assembly model;modular verification of dna strand displacement networks via serializability analysis;iterative self-assembly with dynamic strength transformation and temperature control;probabilistic reasoning with an enzyme-driven dna device;staged self-assembly and polyomino context-free grammars;and functional analysis of large-scale dna strand displacement circuits.

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Compiling dna strand displacement reactions using a functional programming language

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15th international conference on Verification, Model Checking, and Abstract Interpretation, VMCAI 2014

作者： Lakin, Matthew R. Phillips, Andrew Biological Computation Group Microsoft Research Cambridge CB1 2FB United Kingdom Department of Computer Science University of New Mexico NM 87131 United States

ISBN: (纸本)9783319041315

dna nanotechnology is a rapidly-growing field, with many potential applications in nanoscale manufacturing and autonomous in vivo diagnostic and therapeutic devices. As experimental techniques improve it will become increasingly important to develop software tools and programming abstractions, to enable rapid and correct design of increasingly sophisticated computational circuits. this is analogous to the need for hardware description languages for VLSI. In this paper we discuss our experience implementing a domain-specific language for dna nanotechnology using a functional programming language. the ability to use abstract data types to describe molecular structures and to recurse over these types to derive the various interactions between structures was a major reason for the use of a functional language in this project. © 2014 Springer international Publishing.

关键词： Calculations

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Practical Aspects of Declarative Languages - 16th international Symposium, PADL 2014, Proceedings

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15th international conference on Verification, Model Checking, and Abstract Interpretation, VMCAI 2014

ISBN: (纸本)9783319041315

the proceedings contain 15 papers. the topics discussed include: partial type signatures for Haskell;abstract modular inference systems and solvers;sunroof: a monadic DSL for generating JavaScript;compiling dna strand displacement reactions using a functional programming language;two applications of the ASP-prolog system: decomposable programs and multi-context systems;towards modeling morality computationally with logic programming;a declarative specification of giant number arithmetic;embedding foreign code;on the correctness and efficiency of lock-free expandable tries for tabled logic programs;typelets - a rule-based evaluation model for dynamic, statically typed user interfaces;expand: towards an extensible pandoc system;and generic generic programming.

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Distribution of Wind Power Plants to Reduce Variability of Renewable Generation

Distribution of Wind Power Plants to Reduce Variability of R...

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15th international Scientific conference on Electric Power Engineering (EPE)

作者： Debnath, Dhrupad Musilek, Petr Heckenbergerova, Jana Univ Alberta Elect & Comp Engn Edmonton AB Canada VSB TU Ostrava Comp Sci Ostrava Czech Republic Univ Pardubice Dept Math & Phys Elect Engn & Informat Pardubice Czech Republic

ISBN: (纸本)9781479938070

As the penetration of wind power into generation mix increases, the issue of its integration into the power grid becomes more and more important. the variability of wind power generation is a major concern as wind is highly intermittent. this may result in significant overproduction at times, followed by complete unavailability of wind power at other periods. this intermittency must be compensated for by other, conventional generation sources such as coal and gas fired power plants. this reduces the overall efficiency of the system due to the need of running some generators as spinning reserves, and lowers the overall contribution of renewable generation to the mitigation of greenhouse gas emissions. this paper examines the possibility to optimize the spatial distribution of wind power plants over an extended area to decrease the overall variability of wind power generation in a system. In particular, it considers the integration of spatially distributed wind power generation in the wind-rich province of Alberta, Canada. the distribution of power plants is optimized using simulated annealing and quadratic programming. the results clearly show that the variability of wind power generation can be reduced if the wind resources are integrated over a wide geographic area.

关键词： Wind energy generation Wind power plants Wind energy Greenhouse gas emissions Wind farms Power grids generation mix Power Plants dna Integration integration Geographic Regions

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Fractal dimension of self-assembled 50 bp poly(da)·poly(dt) dna on hopg surface 15

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15th international conference on Biomedical Engineering, ICBME 2013

作者： Nii, R. Takeuchi, H. Doi, K. Kawano, Satoyuki Dept. of Mechanical Science and Bioengineering Graduate School of Engineering Science Osaka University Toyonaka Osaka560-8531 Japan

ISBN: (纸本)9783319029122

Deoxyribonucleic acid (dna) has attracted much attention to be utilized for technological applications of its various cellular functions and possibility to fabricate nanoscaled patterns on various substrate surfaces. Several techniques have also been applied to manipulate biomacromolecules. In our previous studies, self-assembled network patterns of poly(dA)·poly(dT) dna on mica and highly oriented pyrolytic graphite (HOPG) surface could be fabricated and observed by atomic force microscopy (AFM), which is preprocessed by a specific solution concentration of MgCl2. Although negatively charged dna molecules repulsively interact with negatively polarized HOPG surfaces, we built our fabrication techniques to produce self-assembled dna. Focusing on the associated self-assembly mechanism, we develop and perform coarse-grained molecular dynamics simulations, in which 50 base-pairs (bp) long dna fragments are modeled considering both intra- and inter-molecular interactions between the dna and HOPG surface in aqueous solution. Using this model, we carry out Langevin dynamics simulations. As a result, the network pattern formations, in which dna fragments make bonds and bundle structures, are replicated. Our results also indicate that thermal fluctuations in solution work effectively to enhance the assembly process. In this study, characteristics of self-assembly of dna are classified by the fractal dimension, which is associated with various time and spatial scales. © Springer international Publishing Switzerland 2014.

关键词： Self assembly

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Modelling of high-symmetry nanoscale particles by small-angle scattering

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JOURNAL OF APPLIED CRYSTALLOGRAPHY 2014年第1期47卷 84-94页

作者： Alves, Cassio Pedersen, Jan Skov Pinto Oliveira, Cristiano Luis Univ Sao Paulo Inst Phys BR-05314970 Sao Paulo Brazil Univ Aarhus Dept Chem DK-8000 Aarhus C Denmark

A versatile procedure to build high-symmetry objects and to calculate their corresponding small-angle scattering intensity is presented. Starting from a set of vertex positions, available from a large and extensible database, it is possible to build several types of bodies using spherical subunits. A fast implementation, based on the Debye formula using a histogram of distance, is then used to compute the theoretical scattering intensity. Since the model is built from the definition of a small set of parameters, it is possible to perform an optimization of structural parameters against experimental data. Finally, affine size polydispersities can be easily included by the rescaling of the histogram of the positions used in the calculations. Several examples of the calculations are presented, demonstrating the method and its applicability.

关键词： small-angle X-ray scattering modelling self-assembly dna computing high symmetry.

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Arithmetic computation using self-assembly of dna tiles: modular-square over finite field GF(2ⁿ)

Arithmetic computation using self-assembly of DNA tiles: mod...

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15th IEEE international conference on High Performance computing and Communications (HPCC) /11th IEEE/IFIP international conference on Embedded and Ubiquitous computing (EUC)

作者： Li, Yongnan Xiao, Limin Ruan, Li Liang, Aihua Beihang Univ State Key Lab Software Dev Environm Beijing 100191 Peoples R China Beihang Univ Sch Comp Sci & Engn Beijing 100191 Peoples R China

ISBN: (纸本)9780769550886

Tile assembly model is a highly distributed parallel model of dna computing. this paper proposes how the tile assembly process could be used for computing the modularsquare, an operation combining square and reduction, over finite field GF(2(n)). In this molecular computing system, reduction is executed after the completion of square. the time complexity of this molecular computing system is theta(n) and the space complexity is theta(n(2)). this system requires 75 types of computation tiles and 9 types of boundary tiles.

关键词： Modular-square Tile assembly model Finite field GF(2(n)) dna computing

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