Fast parallel detection of feline panleukopenia virus DNA by multi‐channel microchip electrophoresis with programmed step electric field strength

A multi‐channel microchip electrophoresis using a programmed step electric field strength (PSEFS) method was investigated for fast parallel detection of feline panleukopenia virus (FPV) DNA. An expanded laser beam, a 10× objective lens, and a charge‐coupled device camera were used to simultaneously detect the separations in three parallel channels using laser‐induced fluorescence detection. The parallel separations of a 100‐bp DNA ladder were demonstrated on the system using a sieving gel matrix of 0.5% poly(ethylene oxide) (M_r = 8 000 000) in the individual channels. In addition, the PSEFS method was also applied for faster DNA separation without loss of resolving power. A DNA size marker, FPV DNA sample, and a negative control were simultaneously analyzed with single‐run and one‐step detection. The FPV DNA was clearly distinguished within 30 s, which was more than 100 times faster than with conventional slab gel electrophoresis. The proposed multi‐channel microchip electrophoresis with PSEFS was demonstrated to be a simple and powerful diagnostic method to analyze multiple disease‐related DNA fragments in parallel with high speed, throughput, and accuracy.     

Continuous development of schemes for parallel computing of the electrostatics in biological systems: Implementation in DelPhi

Due to the enormous importance of electrostatics in molecular biology, calculating the electrostatic potential and corresponding energies has become a standard computational approach for the study of biomolecules and nano‐objects immersed in water and salt phase or other media. However, the electrostatics of large macromolecules and macromolecular complexes, including nano‐objects, may not be obtainable via explicit methods and even the standard continuum electrostatics methods may not be applicable due to high computational time and memory requirements. Here, we report further development of the parallelization scheme reported in our previous work (Li, et al., J. Comput. Chem. 2012, 33, 1960) to include parallelization of the molecular surface and energy calculations components of the algorithm. The parallelization scheme utilizes different approaches such as space domain parallelization, algorithmic parallelization, multithreading, and task scheduling, depending on the quantity being calculated. This allows for efficient use of the computing resources of the corresponding computer cluster. The parallelization scheme is implemented in the popular software DelPhi and results in speedup of several folds. As a demonstration of the efficiency and capability of this methodology, the electrostatic potential, and electric field distributions are calculated for the bovine mitochondrial supercomplex illustrating their complex topology, which cannot be obtained by modeling the supercomplex components alone. © 2013 Wiley Periodicals, Inc.     

VinaMPI: Facilitating multiple receptor high‐throughput virtual docking on high‐performance computers

The program VinaMPI has been developed to enable massively large virtual drug screens on leadership‐class computing resources, using a large number of cores to decrease the time‐to‐completion of the screen. VinaMPI is a massively parallel Message Passing Interface (MPI) program based on the multithreaded virtual docking program AutodockVina, and is used to distribute tasks while multithreading is used to speed‐up individual docking tasks. VinaMPI uses a distribution scheme in which tasks are evenly distributed to the workers based on the complexity of each task, as defined by the number of rotatable bonds in each chemical compound investigated. VinaMPI efficiently handles multiple proteins in a ligand screen, allowing for high‐throughput inverse docking that presents new opportunities for improving the efficiency of the drug discovery pipeline. VinaMPI successfully ran on 84,672 cores with a continual decrease in job completion time with increasing core count. The ratio of the number of tasks in a screening to the number of workers should be at least around 100 in order to have a good load balance and an optimal job completion time. The code is freely available and downloadable. Instructions for downloading and using the code are provided in the Supporting Information. © 2013 Wiley Periodicals, Inc.     

PHI: A powerful new program for the analysis of anisotropic monomeric and exchange‐coupled polynuclear d‐ and f‐block complexes

A new program, PHI, with the ability to calculate the magnetic properties of large spin systems and complex orbitally degenerate systems, such as clusters of d‐block and f‐block ions, is presented. The program can intuitively fit experimental data from multiple sources, such as magnetic and spectroscopic data, simultaneously. PHI is extensively parallelized and can operate under the symmetric multiprocessing, single process multiple data, or GPU paradigms using a threaded, MPI or GPU model, respectively. For a given problem PHI is been shown to be almost 12 times faster than the well‐known program MAGPACK, limited only by available hardware. © 2013 Wiley Periodicals, Inc.     

文化框架下多群智能优化算法的云作业调度

作业调度是一种云计算核心技术,为了获得更优的云计算作业调度方案,提出一种文化框架下多群智能优化算法的云作业调度方法。首先构建云作业调度问题的数学模型,然后借助文化算法模型,粒子群算法组成信仰空间,人工鱼群算法组成群体空间,两者之间并行演化,相互促进,对云计算作业调度数学模型进行求解,最后通过仿真实验测试算法的性能。结果表明,本文加快了算法的收敛速度,获得了更优的云计算作业调度方案,大幅度缩短少云计算作业完成时间,具有一定的实用价值。     

Biocomputing Based on DNA Strand Displacement Reactions

The high sequence specificity and precise base complementary pairing principle of DNA provides a rich orthogonal molecular library for molecular programming, making it one of the most promising materials for developing bio-compatible intelligence. In recent years, DNA has been extensively studied and applied in the field of biological computing. Among them, the toehold-mediated strand displacement reaction (SDR) with properties including enzyme free, flexible design and precise control, have been extensively used to construct biological computing circuits. This review provides a systemic overview of SDR design principles and the applications. Strategies for designing DNA-only, enzymes-assisted, other molecules-involved and external stimuli-controlled SDRs are described. The recently realized computing functions and the application of DNA computing in other fields are introduced. Finally, the advantages and challenges of SDR-based computing are discussed.     

Year Discrimination of Mild Aroma Chinese Liquors Using Three-Dimensional Fluorescence Spectroscopy Combined with Parallel Factor and Neural NetworkSCIEI北大核心CSCD

Three-dimensional fluorescence spectroscopy coupled with parallel factor analysis and neural network was applied to the year discrimination of mild aroma Chinese liquors. The excitation-emission fluorescence matrices (EEMs) of 120 samples with various years were measured by FLS920 fluorescence spectrometer. The trilinear decomposition of the data array was performed and the loading scores of and the excitation-emission profiles of four components were also obtained. The scores were employed as the inputs of the BP neural networks and the PARAFAC-BP identification model was constructed. 10 samples were collected from 10, 20 and 30 years of liquors respectively, and 30 samples were selected as the test sets. The remaining 90 samples were used as the training sets to build the training model. The year prediction of unknown samples was also carried out, and the prediction accuracy was 90%, 100% and 100%, respectively. Meanwhile, the discrimination analysis method and the multi way partial least squares discriminant analysis were compared, namely PARAFAC-BP and NPLS-DA. The results indicated that parallel factor combined with the neural network (PARAFAC-BP) has higher prediction accuracy. The proposed method can effectively extract the spectral characteristics, and also reduce the dimension of the input variables of neural network. A good year discrimination result was finally achieved.     

基于AltiVec技术的PowerPC处理器矢量运算性能测试

基于AltiVec技术的PowerPC处理器,在很多嵌入式信号处理领域已经取代传统的DSP处理器成为信号处理器件的首选。为了评估基于AltiVec技术的PowerPC处理器的矢量运算性能和信号处理能力,选取MPC8641D处理器为硬件测试平台,采用符合VSIPL标准的VSI/Pro Core矢量库和ixlibsav矢量库,通过测试复乘和FFT典型算法不同类型的运算时间,对AltiVec处理单元的矢量运算性能进行了测试评估。通过对测试结果的分析,基于AltiVec技术的PowerPC处理器具备强大的矢量运算处理性能,可以满足嵌入式数字信号处理技术对高性能处理器的需求。     

基于AHP权重和灰色服务器负载预测的云计算On-line迁移策略

为了克服云计算环境下由于实时用户任务的不确定性到来和服务器性能差异而导致的云计算环境的负载不均衡问题,提出了一种AHP权重获取和灰度算法预测服务器负载的云计算on-line虚拟机迁移策略。首先,设计了基于AHP和灰色服务器预测的虚拟机on-line迁移模型,提出了采用AHP获取虚拟机各资源需求权重,然后,采用灰色模型预测下一时刻的服务器负载,采用此权值向量与各无需迁移的服务器的空闲资源向量进行加权得到加权和,将具有最小加权和的物理服务器作为迁移的目标宿主机。最后,定义了基于AHP权重和灰色服务器负载预测的云计算on-line迁移算法。在CloudSim环境下进行实验,结果表明文中的迁移策略使得云计算在响应用户任务时,具有任务失败次数少、SLA违约率低和迁移成功率高的优点,同时与其它方法相比,具有负载均衡程度高的优点,具有较强的可行性。     

基于云环境的分布式软件接口自动化测试

软件测试是保证软件质量,提供可靠服务的重要技术手段。目前基于Web Service的分布式软件越来越多,其测试技术手段也越来越受到关注。Web Service的分布性和多样性使手工测试变得非常低效,因而需要不断提高Web Service测试的自动化程度。另外,云计算因其计算成本低、可伸缩性强的特点为自动化测试提供了新的支持环境。本文结合Web Service的测试需求,首次提出了基于云环境的Web Service接口自动化测试的技术框架,分析了框架内原子Web Service、组合Web Service测试的关键技术,并研发了基于CloudStack云平台的自动化测试的原型系统。实验结果表明,本文所提出的基于云平台的WebService自动化测试方案可行且提高了测试效率。