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。     

Facile preparation of MgAl2O4/CeO2/Mn3O4 heterojunction photocatalyst and enhanced photocatalytic activity

Novel Mn₃O₄-promoted double p?n junction MgAl₂O₄/CeO₂/Mn₃O₄ heterojunction photocatalyst was constructed by one-step synthesis method and two-step synthesis method. The X-ray powder diffraction, Fourier transform infrared spectrum, X-ray photoelectron spectroscopy, optical and photoluminescence demonstrated that the MgAl₂O₄/CeO₂/Mn₃O₄ heterojunction photocatalyst was synthesized by the two-step synthesis method comprehends a high crystallinity, charge carrier migration and separation efficiency, and relatively low optical absorption coefficient. The MgAl₂O₄/CeO₂/Mn₃O₄ heterojunction photocatalysts were efficiently used as simulated sunlight-driven n-n and p-n double junction photocatalyst for the simultaneous degradation of methylene blue (MB) dye. The continuous double p?n junction MgAl₂O₄/CeO₂/Mn₃O₄ heterojunctions strengthened the function of single n-n or p-n junction and guided the charge carrier migration and separation direction; thus, the oxidation and reduction reactions occur at the active site of spatial separation and prevent the recombination of electrons and holes. The results suggest that the continuous double p?n junction MgAl₂O₄/CeO₂/Mn₃O₄ heterojunctions are very promising candidate material for enhancing the photocatalytic activity in the photocatalytic degradation of MB dye.     

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.     

Steering spatially separated dual sites on nano-TiO2 through SMSI and lattice matching for robust photocatalytic hydrogen evolution

Spatial isolation of different functional sites at the nanoscale in multifunctional catalysts for steering reaction sequence and paths remains a major challenge. Herein, we reported the spatial separation of dual-site Au and RuO₂ on the nanosurface of TiO₂ (Au/TiO₂/RuO₂) through the strong metal-support interaction (SMSI) and the lattice matching (LM) for robust photocatalytic hydrogen evolution. The SMSI between Au and TiO₂ induced the encapsulation of Au nanoparticles by an impermeable TiO_x overlayer, which can function as a physical separation barrier to the permeation of the second precursor. The LM between RuO₂ and rutile-TiO₂ can increase the stability of RuO₂/TiO₂ interface and thus prevent the aggregation of dual-site Au and RuO₂ in the calcination process of removing TiO_x overlayer of Au. The photocatalytic hydrogen production is used as a model reaction to evaluate the performance of spatially separated dual-site Au/TiO₂/RuO₂ catalysts. The rate of hydrogen production of the Au/TiO₂/RuO₂ is as high as 84 μmol h⁻¹ g⁻¹ under solar light irradiation without sacrificial agents, which is 2.5 times higher than the reference Au/TiO₂ and non-separated Au/RuO₂/TiO₂ samples. Systematic characterizations verify that the spatially separated dual-site Au and RuO₂ on the nanosurface of TiO₂ can effectively separate the photo-generated carriers and lower the height of the Schottky barrier, respectively, under UV and visible light irradiation. This study provides new inspiration for the precise construction of different sites in multifunctional catalysts.     

CORSICA: correction of structured noise in fMRI by automatic identification of ICA components

When applied to functional magnetic resonance imaging (fMRI) data, spatial independent component analysis (sICA), a data-driven technique that addresses the blind source separation problem, seems able to extract components specifically related to physiological noise and brain movements. These components should be removed from the data to achieve structured noise reduction and improve any subsequent detection and analysis of signal fluctuations related to neural activity. We propose a new automatic method called CORSICA (CORrection of Structured noise using spatial Independent Component Analysis) to identify the components related to physiological noise, using prior information on the spatial localization of the main physiological fluctuations in fMRI data. As opposed to existing spectral priors, which may be subject to aliasing effects for long-TR data sets (typically acquired with TR >1 s), such spatial priors can be applied to fMRI data, regardless of the TR of the acquisitions. By comparing the proposed automatic selection to a manual selection performed visually by a human operator, we first show that CORSICA is able to identify the noise-related components for long-TR data with a high sensitivity and a specificity of 1. On short-TR data sets, we validate that the proposed method of noise reduction allows a substantial improvement of the signal-to-noise ratio evaluated at the cardiac and respiratory frequencies, even in the gray matter, while preserving the main fluctuations related to neural activity.     

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。