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检索条件"任意字段=16th International Conference on DNA Computing and Molecular Programming"

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dna computing and molecular programming - 16th international conference, dna 16, Revised Selected Papers

DNA Computing and Molecular Programming - 16th International...

引用

16th international conference on dna computing and molecular programming, dna 16

ISBN: (纸本)9783642183041

the proceedings contain 16 papers. the topics discussed include: improving efficiency of 3-SAT-solving tile systems;optimizing tile concentrations to minimize errors and time for dna tile self-assembly systems;scalable, time-responsive, digital, energy-efficient molecular circuits using dna strand displacement;negative interactions in irreversible self-assembly;search and validation of short genome-wide biomarkers for bacterial biological phylogenies;high-fidelity dna hybridization using programmable molecular dna devices;synthesizing minimal tile sets for patterned dna self-assembly;operation of a dna-based autocatalytic network in serum;triangular tile self-assembly systems;randomized self assembly of rectangular nano structures;design of a functional nanomaterial with recognition ability for constructing light-driven nanodevices;efficient Turing-universal computation with dna polymers;and simple evolution of complex crystal species.

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Analyses on performance of gromacs in hybrid MPI+OpenMP+CUDA Cluster 16

Analyses on performance of gromacs in hybrid MPI+OpenMP+CUDA...

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16th IEEE international conference on High Performance computing and Communications, HPCC 2014, 11th IEEE international conference on Embedded Software and Systems, ICESS 2014 and 6th international Symposium on Cyberspace Safety and Security, CSS 2014

作者： Li, Ce Chen, Wenbo Zhang, Yang Bai, Qifeng School of Information Science and Engineering Lanzhou University Lanzhou730000 China College of Chemistry and Chemical Engineering Lanzhou University Lanzhou730000 China

ISBN: (纸本)9781479961238

the Tri-Level parallel programming pattern of MPI+OpenMP+CUDA, which enables better speedup for applications on popular multi-core architecture cluster, is increasingly admired by research institutions and companies. the interaction of particles of molecular dynamics simulation needs extensive calculation, which will also increases with the extension of system. therefore higher performance for the computing capability and storage ability of current high performance computer is required. As one of main softwares of molecular dynamics simulation, GROMACS can be used for the simulation of hundreds of or even millions of atoms. Based on this kind of hybrid parallel programming pattern, the latest version of GROMACS has higher operation efficiency and shorter simulation time. In this paper, we take advantage of two different sizes of protein simulation system as the data of GROMACS for the molecular simulation of different parallel granularity on mixed cluster which is based on Intel Xeon5650 and NVIDIA C2050. By the result of experiment, we have obtained the best mechanism of hybird CPU-GPU cluster and analyzed the advantage of MPI+OpenMP+CUDA hybrid parallel programming pattern. In the end, we compared GROMACS4.6 with GROMACS4.5. the results of the test also provide a reference for scientists who work on building large-scale molecular dynamics simulation platform and observe the molecular dynamics simulation. © 2014 IEEE.

关键词： molecular dynamics

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programming with chemical reaction networks and dna strand displacement systems

Programming with chemical reaction networks and dna strand d...

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13th international conference on Unconventional Computation and Natural Computation, UCNC 2014

作者： Condon, Anne Department of Computer Science University of British Columbia Vancouver BC V6T 1Z4 Canada

ISBN: (纸本)9783319081229

Chemical reaction networks (CRNs) and dna strand displacement systems (DSDs) are widely-studied and useful models of molecular programming. In this tutorial, we introduce the models, illustrating the expressive power of CRNs as a molecular programming language and how CRNs can be compiled into lower-level, physically realizable dna strand displacement systems. We characterize the power of CRNs in terms of well known complexity classes, describe connections with reversible and distributed computing models, and discuss limits to computing with CRNs. Finally, we discuss directions for future research that could advance our understanding of these models and the possibilities for efficient molecular programs. © 2014 Springer international Publishing Switzerland.

关键词： dna

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Parallel and scalable computation and spatial dynamics with dna-based chemical reaction networks on a surface

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20th international conference on dna computing and molecular programming, dna 2014

作者： Qian, Lulu Winfree, Erik Bioengineering California Institute of Technology PasadenaCA91125 United States Computer Science California Institute of Technology PasadenaCA91125 United States Computation and Neural Systems California Institute of Technology PasadenaCA91125 United States

ISBN: (纸本)9783319112947

We propose a theoretical framework that uses a novel dna strand displacement mechanism to implement abstract chemical reaction networks (CRNs) on the surface of a dna nanostructure, and show that surface CRNs can perform efficient algorithmic computation and create complex spatial dynamics. We argue that programming molecular behaviors with surface CRNs is systematic, parallel and scalable. © Springer international Publishing Switzerland 2014.

关键词： dna

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Prediction Nucleic Acid Secondary Structure with Planar Pseudoknots and Genetic Algorithm 9

Prediction Nucleic Acid Secondary Structure with Planar Pseu...

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9th international conference on Bio-Inspired computing - theories and Applications (BIC-TA)

作者： Zhang, Kai Huang, Xinquan Hu, Wei Liu, Jun Wuhan Univ Sci & Technol Sch Comp Sci Wuhan 430081 Peoples R China

ISBN: (纸本)9783662450482

In recent years, dna and RNA molecules have shown great potential as a design medium for the construction of nanostructures and the programmed assembly of molecular computing. In this paper, we propose a novel genetic algorithm to predict nucleic acid secondary structure with planar pseudoknots. In our algorithm, the free energy and the number of continues base pairs stacking are used as fitness function to evaluate the individuals. We have compared the results obtained by our algorithm with RNAStructure. As will be discussed, our algorithm can efficiently predict the planar pseudoknots with lower free energy and more continues base pairs stacking.

关键词： Secondary structure prediction Genetic algorithm Minimum free energy Dynamic programming Pseudoknots

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High Performance Genomic Sequencing: A Filtered Approach 8

High Performance Genomic Sequencing: A Filtered Approach

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8th international conference on Practical Applications of Computational Biology & Bioinformatics (PACBB)

作者： Retamosa, German de Pedro, Luis Gonzalez, Ivan Tamames, Javier Univ Autonoma Madrid High Performance & Comp Networking Dept E-28049 Madrid Spain CSIC Natl Biotechnol Res Ctr Madrid Spain

ISBN: (纸本)9783319075815;9783319075808

Protein and dna homology detection systems are an essential part in computational biology applications. these algorithms have changed over the time from dynamic programming approaches by finding the optimal local alignment between two sequences to statistical approaches with different kinds of heuristics that minimize former executions times. However, the continuously increasing size of input datasets is being projected into the use of High Performance computing (HPC) hardware and software in order to address this problem. the aim of the research presented in this paper is to propose a new filtering methodology, based on general-purpose graphical processor units (GP-GPUs) and multi-core processors, for removing those sequences considered irrelevant in terms of homology and similarity. the proposed methodology is completely independent from the homology detection algorithm. this approach is very useful for researchers and practitioners because they do not need to understand a new algorithm. this design has been approved by the National Biotechnology Research Center of Spain (CNB).

关键词： Comparison and alignment methods BLAST High Performance computing GP-GPU

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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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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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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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dna computing and molecular programming - 18th international conference, dna 18, Proceedings

DNA Computing and Molecular Programming - 18th International...

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18th international conference on dna computing and molecular programming, dna 18

ISBN: (纸本)9783642322075

the proceedings contain 11 papers. the topics discussed include: Turing universality of step-wise and stage assembly at temperature 1;a type system for dnaQL;deterministic function computation with chemical reaction networks;reachability bounds for chemical reaction networks and strand displacement systems;synthesizing minimal tile sets for complex patterns in the framework of patterned dna self-assembly;a geometric approach to Gibbs energy landscapes and optimal dna codeword design;a dna based molecular logic gate capable of a variety of logical operations;deciding whether a regular language is generated by a splicing system;probabilistic reasoning with a Bayesian dna device based on strand displacement;dna self-assembly and computation studied with a coarse-grained dynamic bonded model;and space and energy efficient computation with dna strand displacement systems.

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