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

共 108 条记录，以下是81-90 订阅

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Experimental and calculated enhancement factor in the SEIRA method

Experimental and calculated enhancement factor in the SEIRA ...

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16th international conference on Spectroscopy of Molecules and Crystals

作者： Dovbeshko, GI Shirshov, YM Chegel, VI Fesenko, OM Natl Acad Sci Ukraine Inst Phys UA-03039 Kiev Ukraine

ISBN: (纸本)0819454443

the use of the method of enhancement of infrared absorption by rough metallic surface (SEIRA) allows one to increase the probability of infrared transitions and to reveal a series of spectral manifestations of structural features of biological molecules. We analyzed various experimental techniques which gives a possibility to achieve enhancement in the infrared (IR) spectra. We studied the applicability of the SEIRA techniques for analysis of nucleic acids, lipids, and membranes. Under the conditions of our experiment and according to literature data, there was observed enhancement factor equal to 320 for vibrations of various molecular groups. Peculiarity of another optical amplifier, namely, colloidal gold that effectively used for enhancement of signal in IR absorption and Raman scattering, have been studied. We made an attempt to model the effect of enhancement of electrical field and their frequency dependence for different metal surfaces and obtained that silver, gold and copper are the best.

关键词： biological molecules dna Fourier transformed infrared (FTIR) spectroscopy surface enhanced infrared absorption (SEIRA) golden substrate gold-colloidal particles surface and local plasmon resonance (SPR)

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A Block-Based Systolic Array on an HBM2 FPGA for dna Sequence Alignment 16th

A Block-Based Systolic Array on an HBM2 FPGA for DNA Sequenc...

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16th international Symposium on Applied Reconfigurable computing

作者： Ben Abdelhamid, Riadh Yamaguchi, Yoshiki Univ Tsukuba Grad Sch Syst & Informat Engn 1-1-1 Ten Ou Dai Tsukuba Ibaraki 3058573 Japan Univ Tsukuba Fac Engn Informat & Syst 1-1-1 Ten Ou Dai Tsukuba Ibaraki 3058573 Japan

ISBN: (纸本)9783030445331;9783030445348

Revealing the optimal local similarity between a pair of genomic sequences is one of the most fundamental issues in bioinformatics. the Smith-Waterman algorithm is a method that was developed for that specific purpose. With the continuous advances in the computer field, this method becomes widely used to an extent where it expanded its reach to cover a broad range of applications, even in areas such as network packet inspections and pattern matching. this algorithm is based on Dynamic programming and is guaranteed to find the optimal local sequence alignment between two base pairs. the computational complexity is O(mn), where m and n are defined as the number of the elements of a query and a database sequence, respectively. Researchers have investigated several manners to accelerate the calculation using CPU, GPU, Cell B.E., and FPGA. Most of them have proposed a data-reuse approach because the Smith-Waterman algorithm has rather high "bytes per operation";in other words, the Smith-Waterman algorithm requires large memory bandwidth. In this paper, we try to minimize the impact of the memory bandwidth bottleneck through the implementation of a block-based systolic array approach that maximizes the usage of memory banks in HBM2 (High Bandwidth Memory). the proposed approach demonstrates a higher performance in terms of GCUPS (Giga Cell Update Per Second) compared to one of the best cases reported in previous works, and also achieves a significant improvement in power efficiency. For example, our implementation could reach 429.39 GCUPS while achieving a power efficiency of 7.68 GCUPS/W. With a different configuration, it could reach 316.73 GCUPS while hitting a peak power efficiency of 8.86 GCUPS/W.

关键词： dna sequence alignment Smith-Waterman algorithm Systolic array HBM2 High Level Synthesis Reconfigurable High Performance computing

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the Co-design of Astrophysical Code for Massively Parallel Supercomputers 16th

The Co-design of Astrophysical Code for Massively Parallel S...

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16th international conference on Algorithms and Architectures for Parallel Processing (ICA3PP)

作者： Glinsky, Boris Kulikov, Igor Chernykh, Igor Weins, Dmitry Snytnikov, Alexey Nenashev, Vladislav Andreev, Andrey Egunov, Vitaly Kharkov, Egor Inst Computat Math & Math Geophys SB RAS Lavrentjeva Ave 6 Novosibirsk 630090 Russia Novosibirsk State Tech Univ Novosibirsk 630073 Russia Volgograd State Tech Univ Volgograd 400005 Russia

ISBN: (纸本)9783319499567;9783319499550

the rapid growth of supercomputer technologies became a driver for the development of natural sciences. Most of the discoveries in astronomy, in physics of elementary particles, in the design of new materials in the dna research are connected with numerical simulation and with supercomputers. Supercomputer simulation became an important tool for the processing of the great volume of the observation and experimental data accumulated by the mankind. Modern scientific challenges put the actuality of the works in computer systems and in the scientific software design to the highest level. the architecture of the future exascale systems is still being discussed. Nevertheless, it is necessary to develop the algorithms and software for such systems right now. It is necessary to develop software that is capable of using tens and hundreds of thousands of processors and of transmitting and storing of large volumes of data. In the present work the technology for the development of such algorithms and software is proposed. As an example of the use of the technology, the process of the software development is considered for some problems of astrophysics.

关键词： Exascale systems Co-design High performance computing Computational astrophysics Physics of plasmas

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the Algebraic computing Structure of Four dna Bases

The Algebraic Computing Structure of Four DNA Bases

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international conference on Artificial Reality and Telexistence (ICAT)

作者： Ping Zhu Xuqing Tang Zhenyuan Xu Weihong Guan School of Science Southern Yangtze University Wuxi China Key Laboratory of Intelligent Computing and Signal Processing of Ministry of Education Anhui University Hefei China

In this paper, we offers a new algebraic point of view for dna molecules and introduce the algebraic system by using the natural operation based on the Sigma = {A, C, G, T} . We characterize its structure by using the algebraic theory. We show that (L, oplus, otimes ) is the distribution lattice of rings with identical element. Furthermore,we generalize this result to the Wrho(V) , a set which elements simulates the dna molecules with sticky ends, the element is called an incomplete double stranded molecules consist of mixed dna molecules with double and single strands.

关键词： dna computing Lattices Laboratories Intelligent structures Signal processing Computational modeling Sequences Biochemistry Biological materials Genetics

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Precise control of dna orientation for improved functionlity in protein binding microarrays

Precise control of DNA orientation for improved functionlity...

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IEEE/LEOS international conference on Optical MEMS

作者： Philipp Spuhler Xirui Zhang Margo Monroe Joseph Greenspun M. Selim Unlu Laura Sola Marcella Chiari Biomedical Engineering Boston University Boston USA Institute for Chemistry of Molecular Recognition Italian National Research Council Milan Italy

We demonstrate controlled orientation of surface anchored dna and utilize spectral self-interference fluorescent microscopy (SSFM) to measure fluorophore height with sub-nm precision to precisely quantify dna orientat... 详细信息

关键词： Polymers Probes dna Proteins Protein engineering Fluorescence

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Functional Interpretation of Gene Sets: Semantic-Based Clustering of Gene Ontology Terms on the BioTest Platform 5th

Functional Interpretation of Gene Sets: Semantic-Based Clust...

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5th international conference on Man-Machine Interactions (ICMMI)

作者： Gruca, Aleksandra Jaksik, Roman Psiuk-Maksymowicz, Krzysztof Silesian Tech Univ Inst Informat Ul Akad 16 PL-44100 Gliwice Poland Silesian Tech Univ Inst Automat Control Ul Akad 16 PL-44100 Gliwice Poland

ISBN: (纸本)9783319677927;9783319677910

Modern high-throughput technologies based on genome, transcriptome or proteome profiling provide abundance of data that needs to be processed, analyzed and, finally, interpreted. Effective and efficient analysis of data coming from molecular profiling is crucial for a detailed diagnosis, prognosis, and prediction of therapy outcome. Meaningful conclusions can be drawn only by the use of sophisticated methods for biomedical and molecular data analysis and interpretation. In this study we present the approach for functional interpretation of gene or protein sets with clusters of Gene Ontology terms. We analyze transcription profiles of human cell line K562 and we show that clustering allows grouping functionally related GO terms and therefore obtaining more concise and comprehensive description. By applying cluster-specific data aggregation tool we are able to calculate statistics for the individual clusters of GO terms and compare the number of differentially expressed genes between two sample pairs. the presented tool is implemented as a part of annotation module available on the BioTest remote platform for hypothesis testing and analysis of biomedical data.

关键词： Gene Ontology Clustering Semantic similarity BioTest platform dna microarrays molecular profiling Functional interpretation

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16th international Symposium on Applied Reconfigurable computing, ARC 2020

16th International Symposium on Applied Reconfigurable Compu...

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16th international Symposium on Applied Reconfigurable computing, ARC 2020

ISBN: (纸本)9783030445331

the proceedings contain 29 papers. the special focus in this conference is on Applied Reconfigurable computing. the topics include: Accelerating a Classic 3D Video Game on Heterogeneous Reconfigurable MPSoCs;Cross-layer CNN Approximations for Hardware Implementation;technique for Vendor and Device Agnostic Hardware Area-Time Estimation;Resource Efficient Dynamic Voltage and Frequency Scaling on Xilinx FPGAs;RISC-V Based MPSoC Design Exploration for FPGAs: Area, Power and Performance;a Modular Software Library for Effective High Level Synthesis of Convolutional Neural Networks;HLS-Based Acceleration Framework for Deep Convolutional Neural Networks;FPGA-Based Computational Fluid Dynamics Simulation Architecture via High-Level Synthesis Design Method;high-Level Synthesis in Implementing and Benchmarking Number theoretic Transform in Lattice-Based Post-Quantum Cryptography Using Software/Hardware Codesign;judiciously Spreading Approximation Among Arithmetic Components with Top-Down Inexact Hardware Design;exploring fpga Optimizations to Compute Sparse Numerical Linear Algebra Kernels;A CGRA Definition Framework for Dataflow Applications;Implementing CNNs Using a Linear Array of Full Mesh CGRAs;A Block-Based Systolic Array on an HBM2 FPGA for dna Sequence Alignment;Comparison of Direct and Indirect Networks for High-Performance FPGA Clusters;A Parameterisable FPGA-Tailored Architecture for YOLOv3-Tiny;Hardware/Algorithm Co-optimization for Fully-Parallelized Compact Decision Tree Ensembles on FPGAs;stocNoC: Accelerating Stochastic Models through Reconfigurable Network on Chip Architectures;Implementation of FM-Index Based Pattern Search on a Multi-FPGA System;Reconfigurable Accelerator for On-Board SAR Imaging Using the Backprojection Algorithm;Optimising Operator Sets for Analytical Database Processing on FPGAs;automated Toolchain for Enhanced Productivity in Reconfigurable Multi-accelerator Systems;Chisel Usecase: Designing General Matrix Multiply for FPGA.

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Central Dogma of molecular Biology - New Paradigm in Evolutionary Computation

Central Dogma of Molecular Biology - New Paradigm in Evoluti...

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international Symposium on Symbolic and Numeric Algorithms for Scientific computing (SYNASC)

作者： Corina Rotar Computer Science Department “1 Decembrie 1918” University Alba Iulia Romania

the aim of this study is to develop a new evolutionary computation paradigm in terms of molecular biology. Standard genetic algorithms are heuristics inspired by the simplified model of natural evolution and genetics. the latest discoveries and innovations from molecular biology, related to the conventional central dogma of molecular biology, generate the necessity of updating the genetic algorithms, although successfully applied in various complex tasks. In this direction, the research in Evolutionary Computation requires a reconsideration of the concepts and theories underlying the development of these popular optimization techniques. Since the emergence of the new features is important in the evolution, the dna code requires progress. Evolutionary Computation which is based on the mutation and the natural selection can be reconsidered in terms of protein synthesis and reverse transcription. From the computational perspective, a biological phenomenon might be interpreted in various forms in order to obtain reliable computational techniques.

关键词： dna Proteins RNA Optimization Evolution (biology)

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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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Simultaneous detection of multiple charged particles using a borosilicate nanopore-based sensor

Simultaneous detection of multiple charged particles using a...

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IEEE conference on Nanotechnology

作者： Yuqian Zhang Leyla Esfandiari Department of electrical and computing system University of Cincinnati Cincinnati OH Department of electrical and computing system University of Cincinnati Cincinnati OH USA

Nanopore sensing has been widely researched owing to its single molecule sensitivity. In this work, we have demonstrated the potential application of a relatively low-cost single borosilicate nanopore-based sensor for... 详细信息

关键词： Nanobioscience Sensors Multiplexing dna Glass Microscopy Proteins

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