FIPSDock: A new molecular docking technique driven by fully informed swarm optimization algorithm

The accurate prediction of protein–ligand binding is of great importance for rational drug design. We present herein a novel docking algorithm called as FIPSDock, which implements a variant of the Fully Informed Particle Swarm (FIPS) optimization method and adopts the newly developed energy function of AutoDock 4.20 suite for solving flexible protein–ligand docking problems. The search ability and docking accuracy of FIPSDock were first evaluated by multiple cognate docking experiments. In a benchmarking test for 77 protein/ligand complex structures derived from GOLD benchmark set, FIPSDock has obtained a successful predicting rate of 93.5% and outperformed a few docking programs including particle swarm optimization (PSO)@AutoDock, SODOCK, AutoDock, DOCK, Glide, GOLD, FlexX, Surflex, and MolDock. More importantly, FIPSDock was evaluated against PSO@AutoDock, SODOCK, and AutoDock 4.20 suite by cross‐docking experiments of 74 protein–ligand complexes among eight protein targets (CDK2, ESR1, F2, MAPK14, MMP8, MMP13, PDE4B, and PDE5A) derived from Sutherland‐crossdock‐set. Remarkably, FIPSDock is superior to PSO@AutoDock, SODOCK, and AutoDock in seven out of eight cross‐docking experiments. The results reveal that FIPS algorithm might be more suitable than the conventional genetic algorithm‐based algorithms in dealing with highly flexible docking problems. © 2012 Wiley Periodicals, Inc.     

二阶离散隐马尔科夫模型的严格定义及等价性质

隐马氏模型作为一种具有双重随机过程的统计模型,具有可靠的概率统计理论基础和强有力的数学结构,已被广泛应用于语音识别、生物序列分析、金融数据分析等领域.由于传统的一阶隐马氏模型无法表示更远状态距离间的依赖关系,就可能会忽略很多有用的统计特征,故有人提出二阶隐马氏模型的概念,但此概念并不严格.本文给出二阶离散隐马尔科夫模型的严格定义,并研究了二阶离散隐马尔科夫模型的两个等价性质.     

q value and parent energy optimization using a low-voltage ionization approach increases resolution in linear ion trap mass spectrometry

In this work, the isolation step in the linear ion trap was performed using different “q values” conditions at a low collision-induced dissociation (CID) energy leading to the parent ion resolution improvements, reasonably due to better ion energy distribution. According to the results, we obtained a greater resolution and mass accuracy operating in both traditional electrospray and low voltage ionization near the q value = 0.778 and with a CID energy of 10%. This effect was evaluated with low-molecular-mass compounds (skatole and arginine). The proposed optimization yielded a superior instrument performance without adding technological complexity to mass spectrometry analyses.     

基于改进免疫遗传算法的近红外光谱变量选择方法

该文在免疫遗传算法（IGA）的基础上,提出一种改进免疫遗传算法（iIGA）用于近红外光谱波长变量的选择。该算法舍去了原算法中固定抗体相似度阈值的思想,取而代之的是抗体相似度阈值自适应,同时引入精英保留策略和贪心算法思想,使得算法朝着正确的方向进行局部性探优。将该算法在玉米的淀粉和蛋白质含量数据集上进行实验测试,建立偏最小二乘（PLS）分析模型,并与IGA、遗传算法（GA）以及全谱方法进行了对比。结果表明,在玉米淀粉含量的预测上,iIGA相较于原IGA算法,预测集均方根误差（RMSEP）从0.312 0降至0.298 0,预测集预测精度提升4.5%;在玉米蛋白质含量的预测上,RMSEP从0.124 4降至0.110 3,预测集预测精度提升11.3%。分别对预测淀粉和蛋白质模型的RMSEP值进行显著性检验,F值分别为165.22和182.05,P值分别为9.5 × 10－23和4.5 × 10－24,P值均小于0.05,因此,iIGA能显著提升模型预测精度。     

基于联合分步APIT定位算法的改进

本文研究了无线传感网络( Wireless Sensor Network,WSNs)的节点定位问题,并针对APIT由于锚节点在低密度环境下的节点误判和节点失效等问题给出了改进,在APICT定位算法的基础提出了联合分步定位算法UNION-APICT(Union Approximate Point-In-Circumcircle Test),该算法是结合连通性的测距技术,RSSI测距技术以及质心定位和APICT等技术,来联合解决对未知节点定位问题。通过仿真实验结果表明,改进后的UNION-APICT在APICT算法的基础之上平均定位误差减少了10%-25%,定位性能有了明显的提升;随着通信半径R和最大探测距离rmax的增加,定位误差也在逐渐减小,该算法较APIT和APICT定位算法在锚节点密度、节点覆盖率和定位精度上都有所提高。     

Research on application of polynomial fitting technique in rotary kiln infrared temperature measurement system

Aiming at the linear temperature compensation algorithm’s disadvantage of temperature measurement error in rotary kiln infrared scanning temperature measurement process, this paper proposes a precise nonlinear cubic polynomial fitting temperature compensation algorithm. The proposed algorithm compensates the temperature values of scanning points on rotary kiln surface by following steps: Calculating temperature difference between the real temperature value of rotary kiln and temperature value measured by infrared scanning temperature measurement system; Fitting the temperature difference data with cubic polynomial; Using the obtained function to compensate temperature. Experimental result shows that compared with the usual linear temperature compensation algorithm, the accuracy of proposed algorithm has raised about 2.25 times when cubic polynomial is used.     

基于非同步替代光谱定标的地表下垫面影响分析

对760nm附近的氧气吸收带,选用植被、枯萎植被、人工地物、沙地和雪地五种典型地表类型,基于模拟数据进行非同步替代光谱定标方法的误差分析,比较不同地表类型得到的光谱定标准确度,为高光谱成像仪的非同步替代光谱定标提供定标图像选择策略.结果表明:运用两种光谱匹配方法——光谱角度匹配和欧氏距离法得到的定标误差基本一致;730~800nm的地表反射率曲线标准差在0.05nm以内时,定标误差集中在±0.5nm范围内;人工地物类型中个别地物如橄榄绿光泽涂料和植被大面积覆盖的图像数据不适合用于非同步替代光谱定标.     

HIGH-ORDER-ACCURATE DISCRETIZATION STENCIL FOR AN ELLIPTIC EQUATION

The coefficients for a nine-point high-order-accurate discretization scheme for an elliptic equation ∇²u− γ²u=r₀ (∇² is the two-dimensional Laplacian operator) are derived. Examples with Dirichlet and Neumann boundary condtions are considered. In order to demonstrate the high-order accuracy of the method, numerical results are compared with exact solutions.     

Design and synthesis of interpenetrating polymer networks for second-order nonlinear optics

There has been a tremendous recent interest in the development of second-order nonlinear optical (NLO) polymeric materials for photonic applications. However, a major drawback of second-order NLO polymers that prevents them from being used in device applications is the instability of their electric field induced dipolar alignment. The randomization of the dipole orientation leads to the decay of second-order optical nonlinearities. Numerous efforts have been made to increase the stability of the second-order NLO properties of polymers. The search for new approaches to develop NLO polymers with optimal properties has been an active research area since the past decade. A novel approach, combining the hybrid properties of high glass transition temperatures, extensively extensively crosslinked networks and permanent entanglements, based on interpenetrating polymer networks (IPN) is introduced to develop stable second-order NLO materials. Two types of IPN systems are prepared and their properties are investigated. The designing criteria and the rationale for the selection of polymers are discussed. The IPN samples show excellent temporal stability at elevated temperatures. Long-term stability of the optical nonlinearity at 100°C has been observed in these materials. Temporal stability of the NLO properties of these IPNs is synergistically enhanced. Relaxation behavior of the optical nonlinearity of an IPN system has been studied and compared with that of a typical guest/host system. The improved temporal stability of the second-order NLO properties of this IPN system is a result of the combination of the high rigidity of the polymer backbones, crosslinked matrices and permanent entanglements of the polymer networks. A slight modification of the chemical structure resulted in an improvement of the optical quality of the sample.     

二阶差分方程的奇性边值问题

主要采用上下解方法,研究了一类带有奇性的二阶差分方程的两点边值问题,给出了一系列正解的存在条件.