铁尾矿为原料微波法制备介孔分子筛

以鞍山铁尾矿为硅源,CTAB为模板剂,采用微波辐照法合成出全硅介孔分子筛MCM-41。用N2低温吸附、FT-IR、XRD和TEM等表征手段考察了其比表面积、孔径分布、晶体形貌等特性。结果表明:微波辐射法合成的MCM-41分子筛诱导期极短,晶化速度很快,具有典型的按六方对称性排列的孔道结构,FT-IR证明了分子筛具有硅氧四面体骨架。     

聚丙烯酸在硅酸二钙表面吸附的分子动力学模拟

采用分子动力学（MD）方法,模拟研究了聚合物抑制剂聚丙烯酸与β-硅酸二钙（110）晶面的相互作用行为。结果表明:聚丙烯酸与β-硅酸二钙（110）晶面间结合能为负值,在模拟范围内结合能随聚丙烯酸聚合度的增加而增大,聚丙烯酸分子能较好地吸附在β-硅酸二钙（110）表面。通过体系中各种相互作用、径向分布函数以及吸附构象图分析,发现聚丙烯酸主要是通过库仑静电作用吸附在β-硅酸二钙（110）晶面上。聚丙烯酸中不同位置羧基的分子动力学模拟结果差别也很大,链端羧基波动扭转比链中端羧基强度大得多,表明中端羧基与β-2CaO·SiO₂晶体的吸附比链端更牢固因而更能有效地吸附在晶面上,达到抑制熟料二次反应的作用。      

Molecular dynamics simulations of the interaction between OH radicals in plasma with poly-β-1–6-N-acetylglucosamine

Cold atmospheric plasma shows a satisfactory ability to inactivate bacterial biofilms that are difficult to remove using conventional methods in some cases. However, the researches on the inactivation mechanism are not quite sufficient. Poly-β-1–6-N-acetylglucosamine (PNAG), which is one of the important components in some biofilms, was used as the research subject, and the related mechanism of action triggered by different concentrations of the OH in plasma was studied using reactive molecular dynamics simulations. The results showed that OH radicals could not only trigger the hydrogen abstraction reaction leading to cleavage of the PNAG molecular structure, but undergo an OH addition reaction with PNAG molecules. New reaction pathways appeared in the simulations as the OH concentration increased, but the reaction efficiency first increased and then decreased. The simulation study in this paper could, to some extent, help elucidate the microscopic mechanism of the interaction between OH radicals in plasma and bacterial biofilms at the atomic level.     

基于非截断小波有限元的BLT正向问题研究

针对自发荧光断层成像,提出了一种非截断小波有限元算法.该算法采用单元间非截断组合小波基来逼近未知函数,从理论上解决了二维和三维下复杂形状体的剖分,并成功地应用于自发荧光断层成像正向问题中圆柱和圆球仿体的研究.理论分析和数值仿真结果表明,与传统有限元的数值解相比,该算法在获得同样有效解的情况下减少了单元剖分数,降低了计算的复杂度.     

利用C++模拟分子热运动

由于分子太小 ,教学中很难利用现有的技术和仪器直接观察到分子热运动。本文介绍利用C ++语言中的随机函数及描点作图等函数来模拟分子的热运动。本程序所模拟的分子热运动能给人直观、深刻的印象     

GaN中质子辐照损伤的分子动力学模拟研究

本文利用分子动力学方法研究了GaN在质子辐照下的损伤。对不同能量（1~10 keV）初级离位原子（PKA）引起的级联碰撞进行了研究,分析了点缺陷与PKA能量的关系、点缺陷随时间的演化规律、点缺陷的空间分布及点缺陷团簇的尺寸特征。研究结果表明,点缺陷的产生与PKA能量呈线性关系,不同类型的点缺陷随时间演化规律相似,点缺陷多产生在PKA径迹旁,点缺陷团簇多为孤立的点缺陷和小团簇。     

NKChemSQL——针对MySQL的化学信息学扩展

化学数据库是进行化学信息学研究的重要资源,分子属性与指纹计算、分子结构格式转换、分子相似度匹配、精确匹配和子结构匹配以及分子结构图片导出等,都是必需的基本服务内容。应用广泛的数据库系统MySQL却缺乏这些功能,难以满足化学信息处理、网站开发等开发的需求。NKChemSQL是自行编制的MySQL扩展库,通过对开源软件OpenBabel的功能进行包装,以SQL语言的格式完成相应操作。NKChemSQL具有良好的运行表现,经过对含26万余条分子结构信息的NCI数据库进行的测试,全结构匹配只需不到1秒而子结构匹配达300个结构/秒,相似度匹配则达1万个结构/秒。NKChemSQL为开发化学信息学软件和网站提供了非常便利的新方式。     

Effect of postmolding heat treatment on in vitro properties of a polyanhydride implant containing gentamicin sulfate

A polyanhydride implant containing gentamicin sulfate was fabricated using a laboratory-scale injection-molding machine. After injection molding, the implants were subject to heat treatment at 60°C for various time periods with or without nitrogen protection. The impact of this heat treatment on the in vitro properties of the implants including copolymer molecular weights, mechanical properties, and in vitro drug-release profiles was investigated. This heat treatment caused a drastic drop in the molecular weight of the copolymer. Heating without nitrogen protection resulted in the hardening of the implant, but heating in the presence of nitrogen rendered the implant less rigid. It was also found that a faster in vitro drug release profile was shown by implants heated without nitrogen protection and a pronounced slowing down in drug release was exhibited by implants heated with nitrogen protection.     

Nanobody Paratope Ensembles in Solution Characterized by MD Simulations and NMR

Variable domains of camelid antibodies (so-called nanobodies or V_HH) are the smallest antibody fragments that retain complete functionality and therapeutic potential. Understanding of the nanobody-binding interface has become a pre-requisite for rational antibody design and engineering. The nanobody-binding interface consists of up to three hypervariable loops, known as the CDR loops. Here, we structurally and dynamically characterize the conformational diversity of an anti-GFP-binding nanobody by using molecular dynamics simulations in combination with experimentally derived data from nuclear magnetic resonance (NMR) spectroscopy. The NMR data contain both structural and dynamic information resolved at various timescales, which allows an assessment of the quality of protein MD simulations. Thus, in this study, we compared the ensembles for the anti-GFP-binding nanobody obtained from MD simulations with results from NMR. We find excellent agreement of the NOE-derived distance maps obtained from NMR and MD simulations and observe similar conformational spaces for the simulations with and without NOE time-averaged restraints. We also compare the measured and calculated order parameters and find generally good agreement for the motions observed in the ps–ns timescale, in particular for the CDR3 loop. Understanding of the CDR3 loop dynamics is especially critical for nanobodies, as this loop is typically critical for antigen recognition.     

Association Mechanism and Conformational Changes in Trypsin on Its Interaction with Atrazine: A Multi- Spectroscopic and Biochemical Study with Computational Approach

Atrazine (ATR) is a herbicide globally used to eliminate undesired weeds. Herbicide usage leads to various adverse effects on human health and the environment. The primary source of herbicides in humans is the food laced with the herbicides. The ATR binding to trypsin (TYP) was investigated in this study to explore its binding potential and toxicity. In vitro interaction of ATR with TYP was studied using multi-spectroscopic methods, molecular docking, and enzyme kinetics to explore the mechanism of binding for the TYP-ATR system. The TYP-ATR complex revealed binding constants (10³ M⁻¹), suggesting a moderate binding. The free energy for the TYP-ATR complexes was negative, suggesting a spontaneous interaction. Thermodynamic parameters enthalpy (ΔH) and entropy (ΔS) obtained positive values for the TYP-ATR system suggesting hydrophobic interactions in the binding process. Micro-environmental and conformational changes in TYP molecules were induced on interaction with ATR. Reduced catalytic activity of TYP was observed after interaction with ATR owing to the changes in the secondary structure of the TYP.