Incorporating the effect of ionic strength in free energy calculations using explicit ions

The incorporation of explicit ions to mimic the effect of ionic strength or to neutralize the overall charge on a system in free energy calculations using molecular dynamics simulations is investigated. The difference in the free energy of hydration between two triosephosphate isomerase inhibitors calculated at five different ion concentrations is used as an example. We show that the free energy difference can be highly sensitive to the presence of explicit ions even in cases where the mutation itself does not involve a change in the overall charge. The effect is most significant if the molecule carries a net charge close to the site mutated. Furthermore, it is shown that the introduction of a small number of ions can lead to very severe sampling problems suggesting that in practical calculations convergence can best be achieved by incorporating either no counterions or by simulating at high ionic strength to ensure sufficient sampling of the ion distribution.     

Aspects of thermal conductivity relative to heat flow

Summary The various techniques and methodologies of thermal conductivity measurement have been conventionally based on the determination of the rate of directional heat flow through a material having a unit temperature differential between its opposing faces. The constancy of this rate depends on the material density, its thermal resistance and the heat flow path itself. The last of these variables contributes most significantly to the true value of steady-state axial and radial heat dissipation depending on the magnitude of transient thermal diffusivity along these directions. The purpose of this paper is to exemplify the above features by defined parameters of heat flow measurement by existing methodologies. No new method is proposed here. Importantly, the relationship between the rate of heat transfer, total heat transferred and thermal conductivity at a given temperature under steady-state conditions for a fixed heat flow path will be illustrated.     

无脂链磺化酞菁铜多层膜体系：电子非弹性平均自由程的研究

磺化酞菁铜多层膜体系是利用Langmuir-Blodgett技术制备的有序有机分子膜,它对于XPS测试有很好的稳定性,本文在固定电子出射角的条件下利用XPS方法研究了不同厚度的膜样品中Cu_((2(?))_(3/2))、Ni_(1(?))、S_(2p)峰强度的变化规律,讨论了膜内分子有序排列引起的散射效应对电子平均自由程的影响。     

predForm-Site: Formylation site prediction by incorporating multiple features and resolving data imbalance

Formylation is one of the newly discovered post-translational modifications in lysine residue which is responsible for different kinds of diseases. In this work, a novel predictor, named predForm-Site, has been developed to predict formylation sites with higher accuracy. We have integrated multiple sequence features for developing a more informative representation of formylation sites. Moreover, decision function of the underlying classifier have been optimized on skewed formylation dataset during prediction model training for prediction quality improvement. On the dataset used by LFPred and Formator predictor, predForm-Site achieved 99.5% sensitivity, 99.8% specificity and 99.8% overall accuracy with AUC of 0.999 in the jackknife test. In the independent test, it has also achieved more than 97% sensitivity and 99% specificity. Similarly, in benchmarking with recent method CKSAAP_FormSite, the proposed predictor significantly outperformed in all the measures, particularly sensitivity by around 20%, specificity by nearly 30% and overall accuracy by more than 22%. These experimental results show that the proposed predForm-Site can be used as a complementary tool for the fast exploration of formylation sites. For convenience of the scientific community, predForm-Site has been deployed as an online tool, accessible at http://103.99.176.239:8080/predForm-Site.     

Molecular vibrations in a gradient extremal path

Summary The calculation of vibrational states using a gradient extremal path is discussed. Gradient extremal paths are defined by local criteria, which lead to stable solutions. This has certain advantages in comparison with a steepest-descent path, which is often difficult to determine accurately. For cases where a reaction path formalism is applicable, a path based on the gradient extremal concept gives results in close agreement with those obtained using traditional steepest-descent methods. We present algorithms for carrying out such calculations and also give some numerical results.     

Variational transition state theory without the minimum-energy path

In this paper we propose a method for carrying out variational transition state theory calculations without first obtaining a converged minimum-energy path (MEP). We illustrate the method in two ways, first of all by employing an unconverged MEP and secondly by using a dynamically optimized distinguished reaction path. Preliminary tests of the algorithm for the reactions OH+H₂→H₂O+H and C₂H₅→C₂H₄+H are very encouraging. Received: 22 January 1997 / Accepted: 11 March 1997     

集成滤波器在谱图信号除噪中的应用

本文提出了一种由神经元网络与线性自适应滤波器组成的集成滤波器的实现方法，用于谱图信号除噪处理。     

基于知识体系整合的元素无机化学教学改革

元素无机化学是大学化学及相关专业无机化学课程的核心内容。如何教好、学好元素无机化学的知识一直是教学工作者研究的课题。为改变教学现状，提高教学效果，培养学生的逻辑思维和科学创新能力，提出一种整合元素无机化学知识的思路，即：以化合物类型为主线对元素无机化学知识进行系统化整合，并以氧化物部分为例加以说明。     

基于国际化产科教融合实训平台的教学模式改革与实践

在分析当前省属工科院校教育以能力为导向培养目标完成实施过程中遇到国际化困难问题的基础上，以青岛大学材料学科为例，提出了基于国际化产科教融合实训平台的教学模式改革举措，并经过实践验证证实其切实可行。包括：充分整合校内外材料学科整体资源，建立了国际化的产科教深度融合实训平台，构建了高效的国际化产科教深度融合协同育人实训平台动态管理运行机制；以实训平台为依托实现师资队伍、教学内容、教学模式、科研等全方位的国际化改革；基于国际化产教研融合实训平台的教学模式改革的实践收到显著成效，对全国省属高等院校理工学科专业建设国际化改革的推广有较好的示范作用。     

Simple algorithm for isothermal-isobaric molecular dynamics

We review principles of non-Hamiltonian statistical mechanics and present a new set of equations and integration algorithm for isothermal-isobaric dynamics. The chief advantage of the present scheme is that it is somewhat simpler than previous methods. We perform numerical simulations to test the accuracy of the algorithm and compare its stability to that of a "gold standard," a symplectic integrator for Hamiltonian dynamics of the same system. The stability of the isothermal-isobaric algorithm is comparable to the stability of the symplectic integrator.