Distributed and multicore QuBiLS-MIDAS software v2.0: Computing chiral,fuzzy, weighted and truncated geometrical molecular descriptors based on tensor algebra

Advances to the distributed, multi-core and fully cross-platform QuBiLS-MIDAS software v2.0 ( http://tomocomd.com/qubils-midas ) are reported in this article since the v1.0 release. The QuBiLS-MIDAS software is the only one that computes atom-pair and alignment-free geometrical MDs (3D-MDs) from several distance metrics other than the Euclidean distance, as well as alignment-free 3D-MDs that codify structural information regarding the relations among three and four atoms of a molecule. The most recent features added to the QuBiLS-MIDAS software v2.0 are related (a) to the calculation of atomic weightings from indices based on the vertex-degree invariant (e.g., Alikhanidi index); (b) to consider central chirality during the molecular encoding; (c) to use measures based on clustering methods and statistical functions to codify structural information among more than two atoms; (d) to the use of a novel method based on fuzzy membership functions to spherically truncate inter-atomic relations; and (e) to the use of weighted and fuzzy aggregation operators to compute global 3D-MDs according to the importance and/or interrelation of the atoms of a molecule during the molecular encoding. Moreover, a novel module to compute QuBiLS-MIDAS 3D-MDs from their headings was also developed. This module can be used either by the graphical user interface or by means of the software library. By using the library, both the predictive models built with the QuBiLS-MIDAS 3D-MDs and the QuBiLS-MIDAS 3D-MDs calculation can be embedded in other tools. A set of predefined QuBiLS-MIDAS 3D-MDs with high information content and low redundancy on a set comprised of 20,469 compounds is also provided to be employed in further cheminformatics tasks. This set of predefined 3D-MDs evidenced better performance than all the universe of Dragon (v5.5) and PaDEL 0D-to-3D MDs in variability studies, whereas a linear independence study proved that these QuBiLS-MIDAS 3D-MDs codify chemical information orthogonal to the Dragon 0D-to-3D MDs. This set of predefined 3D-MDs would be periodically updated as long as new results be achieved. In general, this report highlights our continued efforts to provide a better tool for a most suitable characterization of compounds, and in this way, to contribute to obtaining better outcomes in future applications.     

An efficient solution for resolving iTRAQ and TMT channel cross‐talk

Isobaric tagging reagents such as isobaric tag for relative and absolute quantitation (iTRAQ) and tandem mass tag (TMT) typically have isotopic impurities that cause significant cross‐talk between channels. Here, we present an efficient solution to compensate for channel cross‐talk using linear algebra and find that it is between 20× and 120× faster than previous methods. We also find that the effects of channel cross‐talk are as important to manage as the effects of ratio compression because of precursor impurities, and we have released an open‐source tool to perform both types of calculations.     

HPLC method transfer study for simultaneous determination of seven angiotensin II receptor blockers

In this study, a sensitive high‐performance liquid chromatography method was developed and validated for the simultaneous determination of seven angiotensin II receptor blockers, namely, hydrochlorothiazide, chlorthalidone, eprosartan mesylate, valsartan, losartan potassium, irbesartan, and candesartan cilexetil. Different chromatographic parameters were tested and fully optimized. Best chromatographic separation was accomplished on a reversed‐phase octadecylsilyl column (250 × 4.6 mm id; 5 μm) under gradient elution using methanol/sodium phosphate monobasic buffer (0.01 M, pH 6.5) as mobile phase. The detection of target analytes was obtained at 254 nm. The pH of the buffer has been selected according to Marvin^® sketch software. The proposed method was validated according to ICH guidelines and showed good precision (relative standard deviation < 1), good linearity (square of correlation coefficient ≥ 0.999), and high accuracy (between 98 and 102%) with detection limit and quantitation limit (40 and 160 ng/mL, respectively) for all the detected analytes.     

菲涅耳衍射的数值计算

利用Mathematica软件分别计算了单缝衍射及双缝衍射的光强分布,成功解决了菲涅耳衍射的计算这一较难问题,并得到了双缝衍射向杨氏双逢干涉过渡的具体条件,完成了实验室内难以完成的任务.     

基于Khimera软件的Se和Sn氧化动力学参数计算

反应速率常数和指前因子、活化能等动力学参数的准确性是研究痕量元素动力学模型的关键,在Se和Sn氧化过程的反应机理研究基础上,借助于量化软件Gaussview和Gaussian及动力学软件Khimera,采用量子化学从头计算理论对Se和Sn氧化过程进行研究,最终得到了在200~2000K温度区间内的反应速率k随温度T变化的关系,进一步计算了Arrhenius参数,得出了活化能随温度变化的关系,弥补了以往只能计算单个温度点的化学反应速率值的不足,为深入研究煤燃烧过程中Se和Sn的生成与排放的动力学模型提供了依据。     

现代教育技术在大学化学实验教学中的应用

多媒体教育技术结合视频录像、微格教学和应用软件等新型教学手段应用于本科实验课教学,不仅能形象地展现抽象的理论概念,揭示复杂的实验原理,而且能活跃课堂气氛,激发学习兴趣,提升创新意识和提高实验效率。这一理念对学生综合素质培养和实验教学方法改革具有重要意义。     

基于MATLAB的GPS软件接收机捕获与跟踪算法实现

研究了GPS软件接收机的捕获和跟踪算法,并基于Matlab软件平台和射频前端在PC上实现了GPS软件接收机样机。介绍了GPS软件接收机的结构和数据采集硬件,讨论了GPSC/A码的特性、产生原理以及捕获过程。针对传统的串行搜索算法慢的缺点以及高动态GPS软件接收机的特点,在该样机中实现了快速的基于循环卷积的并行捕获算法,并联合使用超前滞后环和对相位反转不敏感的科斯塔斯锁相环分别对码相位和多普勒频偏进行跟踪,解调得到导航电文。仿真和测试结果表明,使用GPS软件接收机进行信号处理的思想使用户在算法处理和软件升级等方面具有更大的灵活性,可应用于下一代任何全球导航卫星定位系统(GNSS)和空基增强系统(SBAS)接收机的设计。     

鄱阳湖三维水质模拟软件设计与仿真

随着鄱阳湖生态经济区建设的推进,鄱阳湖水环境保护问题引起了各方高度关注。通过建立水质数学模型,用计算机进行模型求解、模拟和预测,以及设计相应的水质模拟仿真软件来进行水污染扩散仿真,是水污染控制和水环境管理的有效手段。鉴于国外三维水质数据模拟软件价格高、使用受限以及鄱阳湖三维水质数据模拟的特定应用研究需求,利用软件工程的结构化方法和图形可视化技术,设计了一个面向鄱阳湖三维水质数据模拟和分析的软件工具WSAT/H3D-PYH。通过使用该软件进行BOD和DO扩散模拟和趋势预测实验表明,软件具有较好的预测精度,并能以可视化形式直观分析和预测未来一段时间湖区水质浓度的变化趋势。此外,软件还可对局部点污染源扩散进行动态模拟,以便于对突发污染事件可能造成的后果进行提前的估计,为后续治理方案措施的制定提供很好的依据。     

从对比中更好地把握微积分的教学改革

美国微积分教学改革的许多方面值得借鉴.从对比的角度反思微积分教改的不足和差距,以便更好地把握今后的教改工作,明确在点点滴滴的教学过程中,应当实实在在地做些什么、怎么做.