Challenges in protein folding simulations: Timescale, representation, and analysis

Experimental studies of protein folding processes are frequently hampered by the fact that only low resolution structural data can be obtained with sufficient temporal resolution. Molecular dynamics simulations offer a complementary approach, providing extremely high resolution spatial and temporal data on folding processes. The effectiveness of such simulations is currently hampered by continuing questions regarding the ability of molecular dynamics force fields to reproduce the true potential energy surfaces of proteins, and ongoing difficulties with obtaining sufficient sampling to meaningfully comment on folding mechanisms. We review recent progress in the simulation of three common model systems for protein folding, and discuss how recent advances in technology and theory are allowing protein folding simulations to address their current shortcomings.     

Epitope prediction based on random peptide library screening: benchmark dataset and prediction tools evaluation

Epitope prediction based on random peptide library screening has become a focus as a promising method in immunoinformatics research. Some novel software and web-based servers have been proposed in recent years and have succeeded in given test cases. However, since the number of available mimotopes with the relevant structure of template-target complex is limited, a systematic evaluation of these methods is still absent. In this study, a new benchmark dataset was defined. Using this benchmark dataset and a representative dataset, five examples of the most popular epitope prediction software products which are based on random peptide library screening have been evaluated. Using the benchmark dataset, in no method did performance exceed a 0.42 precision and 0.37 sensitivity, and the MCC scores suggest that the epitope prediction results of these software programs are greater than random prediction about 0.09-0.13; while using the representative dataset, most of the values of these performance measures are slightly improved, but the overall performance is still not satisfactory. Many test cases in the benchmark dataset cannot be applied to these pieces of software due to software limitations. Moreover chances are that these software products are overfitted to the small dataset and will fail in other cases. Therefore finding the correlation between mimotopes and genuine epitope residues is still far from resolved and much larger dataset for mimotope-based epitope prediction is desirable.     

理想同心介质球纳米喷流特性

利用有限时域差分方法,对核壳结构进行了模拟研究,得到内核折射率以及内核半径对聚焦光斑纳米喷流特性的影响。研究表明：在内核半径不变的情况下,当内核相对折射率较低时,入射光能量主要集中在内核与外壳层交界区域,此时光波能量有很大一部分处于非聚焦的旁瓣中;当内核折射率超过外层,可以在核壳结构背光面形成双增强点;在内核相对折射率不变的情况下,通过改变内核半径实现了对内、外核聚焦点位置的主动控制。     

Weaving 3D highly conductive hierarchically interconnected nanoporous web by threading MOF crystals onto multi walled carbon nanotubes for high performance Li-Se battery

Lithium-selenium (Li-Se) battery has attracted growing attention.Nevertheless,its practical application is still impeded by the shuttle effect of the formed pol...     

Spin-Free理论与Woodward-Hoffmann规则——丁二烯体系电环合反应的研究

用Spin-Free理论,对丁二烯体系电环合反应进行了研究,得到了基态和各激发态的位能面,解释了加热和加光反应机理和选择定则,对其中的单态和三态光化反应作了初步探讨并求出了有关的活化能。     

Effects of surface-active substances on acid–base indicator reactivity in SiO2 gels

Methyl orange (MO) and phenolphthalein (P) doped SiO₂ gels derived from tetraethyl orthosilicate (TEOS) and modified with cetyltrimethylammonium bromide (CTAB), sodium dodecyl sulfate (SDS) and stearic acid (SA) are prepared. FTIR and TG analyses are used to characterize the gels. The color changes and leaching behavior of MO and P within the gels are investigated and explained on the basis of the gel structures and the reaction mechanism. The experimental results show that surface-active substances have obvious effects on the acid–base response and the leaching behavior of the acid–base indicators within the SiO₂ gels.     

Radioactive contamination of the environment as a result of uranium production: a case study at the abandoned Lincang uranium mine,Yunnan Province,China

The distribution of radioactive pollutants, such as²²²Rn, U, Th and²²⁶Ra in the air, surface waters, soils and crops around the Lincang uranium mine, Yunnan Province, China, is studied. The mechanical, geochemical and biogeochemical processes responsible for the transport and fate of the radioactive elements are discussed based on the monitoring data. The pollutants concentrations of effluents from the mine tunnels were dependent on pH and which were controlled by biochemical oxidation of sulfide in the ore/host rocks. Radon anomalies in air reached 4 km from the tailings pile depending on radon release from the site, topography and climate.²³⁸U and²²⁶Ra abnormities in stream sediments and soil were 40—90 cm deep and 790—800 m away downstream. Anomalies of radioactive contaminants of surface watercourses extended 7.5—13 km from the discharge of effluents of the site mainly depending on mechanical and chemical processes. There were about 2.86 ha rice fields and 1.59 km stream sediments contaminated. Erosion of tailings and mining debris with little or no containment or control accelerated the contamination processes.     

Ni系列催化剂上甲烷直接氧化制合成气

采用固定床流动反应装置，考察负载型Ｎｉ系列催化剂在甲烷直接氧化制合成气反应上的催化活性．空速为５．０×１０５ｈ－１，ＣＨ４／Ｏ２＝２条件下，不同Ｎｉ含量的催化剂中，１５％Ｎｉ／Ａｌ２Ｏ３活性较好．利用ＴＰＤ和ＸＲＤ技术将催化剂引发温度与催化剂组成进行关联，并在７００℃下考察空速对催化性能的影响．随着空速的增加，ＣＨ４的转化率增加，７．０×１０５ｈ－１时达到最大，与此同时，ＣＯ的选择性一直增加．实验结果说明在非平衡体系中，ＣＯ和Ｈ２是由ＣＨ４直接转化而来，ＣＯ２是ＣＯ深度氧化的产物，在此基础上对催化剂过程的机理作了初步的探讨．     

Positively charged covalent organic framework and its application in the dispersive solid-phase extraction of ultraviolet-filters from food packaging material migrants

Abstract

Covalent organic frameworks (COFs) show excellent property, such as high porosity and excellent structure stability and were well applied in fields such as catalysis and adsorption, but most of the COFs showed similar structure and thus similar adsorption performance. Modification of simple COFs to enhance its adsorption performance in separation technique is an important issue. In this study, quaternary ammonium groups with long hydrophobic chain were introduced into a simple COF (TpPa-1) for the first time. The positively charged COF (PC-TpPa-1) can form electrostatic interaction and hydrophobic effect with negatively charged analytes, and showed good adsorption performance for ultraviolet-filters (UV filters). Under the optimum conditions, i.e. adsorbent amount 20?mg, pH?=?7, 1.0?mL acetonitrile as eluent, the obtained recoveries for all UV filters were in the range of 86.4–96.7%.The developed method was successfully applied to the determination of UV filters from food packaging material migrants with the aid of HPLC as a detector.