Overview of software options for processing,analysis and interpretation of mass spectrometric proteomic data

Recently, the interests in proteomics have been intensively increased, and the proteomic methods have been widely applied to many problems in cell biology. If the age of 1990s is considered to be a decade of genomics, we can claim that the following years of the new century is a decade of proteomics. The rapid evolution of proteomics has continued through these years, with a series of innovations in separation techniques and the core technologies of two‐dimensional gel electrophoresis and MS. Both technologies are fueled by automation and high throughput computation for profiling of proteins from biological systems. As Patterson ever mentioned, ‘data analysis is the Achilles heel of proteomics and our ability to generate data now outstrips our ability to analyze it’. The development of automatic and high throughput technologies for rapid identification of proteins is essential for large‐scale proteome projects and automatic protein identification and characterization is essential for high throughput proteomics. This review provides a snap shot of the tools and applications that are available for mass spectrometric high throughput biocomputation. The review starts with a brief introduction of proteomics and MS. Computational tools that can be employed at various stages of analysis are presented, including that for data processing, identification, quantification, and the understanding of the biological functions of individual proteins and their dynamic interactions. The challenges of computation software development and its future trends in MS‐based proteomics have also been speculated. Copyright © 2014 John Wiley & Sons, Ltd.     

Formation of longitudinal aggregation of inclusions in bulk sapphire and yttrium‐aluminum garnet grown by horizontal directed crystallization method

It is shown that the formation of longitudinal aggregation of inclusions in bulk sapphire and yttrium‐aluminum garnet (YAG) grown by the method of HDC is caused by local accumulation of impurities, disturbance of morphological stability of the crystallization front and capture of inclusions and impurities in the nodal region of the melt two‐vortex convection. Studied is the influence of thermal and geometrical parameters of the melt and the shape of the crystallization front on the conditions of the formation of the capture of inclusions.     

Cooling crystallization of aluminum sulfate in pure water modulated by sodium dodecylbenzenesulfonate

This study investigated the cooling crystallization of aluminum sulfate to explore the basic data for the recovery of aluminum resources from coal spoil. Cooling crystallization process of aluminum sulfate with sodium dodecylbenzenesulfonate (SDBS) was investigated experimentally. The effects of operating conditions, namely rotate speed and cooling rate on the crystal size (Median diameter, D_0.5) were studied. Based on single factor experimental results, the response surface method (RSM) with a Box–Behnken design (BBD) was used to determine the key operating conditions, from which a predictive equation was established to quantitatively describe the relationships of D_0.5 and there relative parameters. The optimum operating conditions for cooling crystallization of aluminum sulfate were as follows: rotate speed of 200–300 rpm, cooling rate of 4–5 °C /min and n (SDBS)/n (Al₂(SO₄)₃) of around 5E‐4. Molecular dynamics (MD) results reveal that SDBS decreases the diffusion coefficient (D) of Al³⁺ molecules, which inhibits nucleation and promotes crystal growth.     

计算机分子模拟在分子印迹技术中的应用

传统的分子印迹技术对模板分子、功能单体、交联剂、致孔剂等的筛选往往依靠经验,常通过反复实验对合成条件进行优化,存在实验周期长、耗材量大等问题。计算机分子模拟技术的应用在实验过程中起到可预见性指导作用,可以实现精准识别位点的裁制、识别驱动力的设计,通过结合能等物化特征参数计算优化识别体系的稳定性,从而合理选择模板分子、功能单体、交联剂、致孔剂,优化聚合条件,以提高聚合物识别特异性和亲和力,缩短实验周期,更符合绿色化学的理念。本文简单介绍了计算机分子模拟技术,重点对其在分子印迹技术中的指导作用进行了综述,并对其在分子印迹技术中的应用进行了展望。     

COMPUTER-ASSISTED TEACHING REFORM FOR THEORETICAL MECHANICS 1)

本文依照四川大学某理论力学教学班实际教学改革的经验,通过具体举例说明计算机技术在理论力学教学中尚未开发的巨大潜力,减小数学运算使学生重点关注理论力学基本原理,批量求解使学生提前接触实际应用案例,普适性求解使学生深化对处理多变量问题的认识。同时本文还探讨了理论力学教学改革的方向和目的,即把教学重点放在普适的教学方法上,借助计算机求解多刚体、多变量问题,以期有助于理论力学教材更好地适应时代发展。     

An Improved Plotting Package Applied to Chemical Graphing Problems

Abstract

A plotting package, written in LINC assembly language, is described. It produces high quality graphs and labels the graphs for direct submission to professional journals. A μ-LINC (Laboratory INstrument (Computer) is used to compute least-squares fitted curves and lines from data entered either on-or off-line and to draw the graphs directly on an incremental plotter. Bar graphs, line graphs, and fitted data can be plotted with options to suppress the lines and/or the points.     

大分子固液界面吸附行为的数字模拟研究方法

介绍了随机数字模拟方法在研究链状大分子吸附行为的一般原理,以立方格子模型的自避行走为例,分析了模型的建立、初始位形的产生以及分子链运动的处理方法.回顾了随机数字模拟方法在研究大分子界面吸附行为方面的发展状况.预测了随机数字模拟方法在大分子吸附行为研究方面的应用前景.     

The Influence of Visual and Spatial Reasoning in Interpreting Simulated 3D Worlds

This paper explores the way in which young children (6 year olds) made sense of screen-based images on the computer. The participants were required to interpret 3D-like representations and relate these images to objects in their environment. Both static and relatively dynamic software programs were used in the investigation. Some of the children could not make links between the screen representation and the intended three-dimensional (3D) objects. It is argued that young children should be exposed to activities that establish explicit links between 2D and 3D objects ``away' from the computer before attempting the more difficult links required to interpret and represent 3D objects in ICT contexts. This revised version was published online in July 2006 with corrections to the Cover Date.     

概率约束规划逼近最优解集的上半收敛性

本文讨论了概率约束规划目标函数的连续收敛性,并利用概率测度弱收敛的特征给出了概率约束规划可行集的收敛性条件,得到了概率约束规划逼近最优解集的上半收敛性.     

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.