Determination of total arsenic and arsenic (III) in phosphate fertilizers and phosphate rocks by HG-AAS after multivariate optimization based on Box-Behnken design

In the present paper, a procedure for the determination of total arsenic and arsenic (III) in phosphate fertilizers and phosphate rocks by slurry sampling (SS) with hydride generation atomic absorption spectrometry (HG-AAS) is proposed. Arsenic (III) is determinated directly and total arsenic is determinated after reduction reaction. The procedure was optimized for the flow rate of NaBH₄, NaBH₄ and hydrochloric acid concentrations using a full two-level factorial and also a Box-Behnken design. Slurry preparation with hydrochloric acid in an ultrasonic bath allowed the determination of arsenic (III) with limits of detection and quantification of 0.1 and 0.3 μg L⁻¹, respectively. The precision of results, expressed as relative standard deviation (RSD), was always lower than 3%. The accuracy of this method was confirmed by analysis of certified sediment reference materials, while the procedure also allows for calibration using aqueous external standards. This method (SS/HG-AAS) was used to determine total arsenic and arsenic (III) in two phosphate rock samples and two phosphate fertilizer samples. In these samples, total arsenic concentrations varied from 5.2 to 20.0 mg kg⁻¹, while As (III) concentrations varied from 2.1 to 5.5 mg kg⁻¹, in agreement with published values. All samples were also analyzed using acid digestion/HG-AAS. Both, a paired t-test and a linear regression model demonstrated no significant difference (95% CL) between the results obtained using these two sample preparation procedures.     

Determination of heteronuclear coupling constants from 3D HSQC-TOCSY experiment with optimized random sampling of evolution time space

An application of 3D version of HSQC-TOCSY experiment for the measurement of heteronuclear coupling constants of organic compounds yielding complex spectra is proposed. The approach presented here is based on the optimized random sampling of the evolution time space followed by Multidimensional Fourier Transform (MFT). In this study, we show that the interpretation of omega(3)-(13)C coupled (1)H-(13)C 3D HSQC-TOCSY spectra with E.COSY-type multiplets allows one to evaluate heteronuclear coupling constants of strychnine with high accuracy, whereas the employment of 2D methods is associated with signal overlap and use of conventionally recorded 3D NMR spectra cannot provide accurate results in an overnight experiment.     

Closing the side-chain gap in protein loop modeling

The success of structure-based drug design relies on accurate protein modeling where one of the key issues is the modeling and refinement of loops. This study takes a critical look at modeled loops, determining the effect of re-sampling side-chains after the loop conformation has been generated. The results are evaluated in terms of backbone and side-chain conformations with respect to the native loop. While models can contain loops with high quality backbone conformations, the side-chain orientations could be poor, and therefore unsuitable for ligand docking and structure-based design. In this study, we report on the ability to model loop side-chains accurately using a variety of commercially available algorithms that include rotamer libraries, systematic torsion scans and knowledge-based methods. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

基于抽样理论的改进型星座覆盖分析方法

针对传统网格点方法在分析星座对目标区域的覆盖性能时,存在着计算效率不高的问题,利用抽样理论中借助样本统计量对总体参数进行估计的思想,对传统网格点方法加以了改进;通过分析星座对目标区域内所有网格点的覆盖情况与网格点经纬度之间的关系,确立了对所有网格点构成的总体采用先分层后随机的抽样方式,并分析了层的划分和样本量在各层的分配;根据不同指标的统计特征,给出了不同星座覆盖性能指标的估计方法和不同精度条件下总样本量的计算过程,并建立了改进网格点法的实施流程;最后利用改进方法计算了仿真时段内北斗卫星导航系统对某一地面区域的平均PDOP值,通过与传统网格点方法的仿真结果进行比较并对仿真数据进行分析,证明了该改进方法在保证计算精度的同时,有效地提升了计算效率。     

抽样法与灵敏度法k_(eff)不确定度量化

核反应堆的中子学模拟计算中,核数据的不确定度导致的积分量计算结果的不确定度,通常采用基于微扰理论的灵敏度与不确定度分析方法 (简称灵敏度法)量化.灵敏度分析法原则上只适用于线性模型,且一般输运计算程序难以直接进行灵敏度分析.而抽样法直接抽样核数据输入中子学计算程序进行计算,通过对计算结果的统计分析评估计算量的不确定度.抽样法易于实现、计算精确、且适用性强.在灵敏度分析与不确定度量化程序SURE中,增加了抽样法不确定度的量化功能.为将抽样法不确定度量化应用于复杂问题的模拟计算,需对其进行细致的考核.为此,选取简单的临界基准实验模型,分别采用灵敏度分析法和抽样法进行不确定度量化,得到了各核素各反应道核数据导致的k_(eff)计算不确定度.对比显示,两种方法的不确定度计算结果有很好的符合,验证了SURE程序抽样法功能的正确性.抽样法计算的k_(eff)符合正态分布,说明在一般核数据的不确定度范围内,k_(eff)与核数据近似成线性关系,利用灵敏度分析法评估k_(eff)计算值的不确定度是适用的.     

基于Hough变换的椭圆检测算法

为了实现光电仪器对椭圆形目标的准确识别与跟踪,基于Hough变换提出了一种新的椭圆检测算法。该算法随机采样2点,再利用椭圆极和极弦的性质来搜索第3点并筛除大量无效采样;然后,以这3点为中心作正方形窗口,用窗口内的所有点来拟合椭圆方程。在验证候选椭圆时,提出了一种新方法来判断边缘点是否在椭圆上,并且给出了确定真实椭圆的自适应阈值。实验显示,该算法的平均长度误差为0．5pixel,平均角度误差为0．6°,平均耗时为79ms,表明该算法精度高,速度快,检测性能较好。     

An Original Monomer Sampling from a Ready-Made Aβ42 NMR Fibril Suggests a Turn-β-Strand Synergetic Seeding Mechanism

Aggregation of amyloid beta (Aβ) is a central step of Alzheimer's disease. Aβ42 monomers are building blocks in the formation of both “on pathway” intermediate structures and “off pathway” oligomers. How to sample an Aβ monomer becomes a problem however due to the instinct of Aβ high flexibility and diversity as well as aggregation propensity. Currently, (1) most samplings focus on either the ready-made helix-rich 1Z0Q/1IYT NMR structure, or the completely extended conformation, but (2) few on a ready-made Aβ NMR fibril (i. e., 2BEG). Here we compare the simulation results from sampling in scheme (1) with that in scheme (2), and find that the coil and β-sheet contents in the 1Z0Q-sampled system are comparable to the counterparts in the 2BEG-sampled system, but with a large difference in simulation time and dynamics character. 1Z0Q-sampled system not only takes several times longer than the 2BEG-sampled one, and only β1-seeding dynamics characteristic is observed probably due to far insufficient conformation transition in the limited simulation time. Two dynamics characteristics of Aβ42 folding observed experimentally, that either β1 region or β2 region aggregates first, reproduce in the present simulations for 2BEG-sampled system however, suggesting a preferential sampling in the future simulation. In addition, a turn-β-strand synergetic seeding mechanism of aggregation is first proposed based on the trajectory analyses on the four regions of Aβ42 chain.     

Advances in Enhanced Sampling Molecular Dynamics Simulations for Biomolecules

Molecular dynamics simulation has emerged as a powerful computational tool for studying biomolecules as it can provide atomic insights into the conformational transitions involved in biological functions. However, when applied to complex biological macromolecules, the conformational sampling ability of conventional molecular dynamics is limited by the rugged free energy landscapes, leading to inherent timescale gaps between molecular dynamics simulations and real biological processes. To address this issue, several advanced enhanced sampling methods have been proposed to improve the sampling efficiency in molecular dynamics. In this review, the theoretical basis, practical applications, and recent improvements of both constraint and unconstrained enhanced sampling methods are summarized. Furthermore, the combined utilizations of different enhanced sampling methods that take advantage of both approaches are also briefly discussed.