A QM-MM interface between CHARMM and TURBOMOLE: implementation and application to systems in bulk phase and biologically active systems

The implementation of a hybrid QM-MM approach combining ab initio and density functional methods of TURBOMOLE with the molecular mechanics program package CHARMM is described. An interface has been created to allow data exchange between the two applications. With this method the efficient multiprocessor capabilities of TURBOMOLE can be utilized with CHARMM running as a single processor application. Therefore, features of nonparallel running code in CHARMM like the TRAVEL module for locating saddle points or VIBRAN for the calculation of second derivatives can be exploited by running the CPU intensive QM calculations in parallel. To test the methodology, several small systems are studied with both Hartree-Fock and density functional methods and varying QM-MM boundaries. Also, the computationally efficient RI-J method has been examined for use in QM-MM applications. A B(12) cofactor containing cobalt has been studied, to examine systems with a large QM region and transition metals. All tested methods perform satisfactory in comparison with pure quantum calculations. Additionally, algorithms for the characterization of saddle points have been tested for their potential use in QM-MM problems. The TRAVEL module of CHARMM has been applied to the Menshutkin reaction in the condensed phase, and a saddle point was located. This saddle point was verified by calculation of a steepest descent path connecting educt, transition state, and product, and by calculation of vibrational modes.     

单金纳米棒的光散射分析化学:径向比与分析灵敏度的关系

单纳米颗粒作为信号感应单元在化学与生物传感应用中已引起广泛关注.本文通过暗场显微成像(iDFM)研究了不同径向比金纳米棒的光散射性质.将iDFM与扫描电子显微镜(SEM)结合表征种子生长法制备的金纳米棒,结果发现,因局域表面等离子体共振而展示出的红色散射光随单个金纳米棒的径向比增大逐渐红移,且金纳米棒对其周围介质折光率(RI)变化的敏感程度随径向比增大而增大.这一结果对设计高灵敏的生物纳米传感器、提高分析检测的灵敏度具有很好的指导意义.     

Plant-Derived Molecule 4-Methylumbelliferone Suppresses FcεRI-Mediated Mast Cell Activation and Allergic Inflammation

Mast cells (MCs) are an important treatment target for high-affinity IgE Fc receptor (FcεRI)-mediated allergic diseases. The plant-derived molecule 4-methylumbelliferone (4-MU) has beneficial effects in animal models of inflammation and autoimmunity diseases. The aim of this study was to examine 4-MU effects on MC activation and probe the underlying molecular mechanism(s). We sensitized rat basophilic leukemia cells (RBLs) and mouse bone marrow-derived mast cells (BMMCs) with anti-dinitrophenol (DNP) immunoglobulin (Ig)E antibodies, stimulated them with exposure to DNP-human serum albumin (HSA), and then treated stimulated cells with 4-MU. Signaling-protein expression was determined by immunoblotting. In vivo allergic responses were examined in IgE-mediated passive cutaneous anaphylaxis (PCA) and ovalbumin (OVA)-induced active systemic anaphylaxis (ASA) mouse models. 4-MU inhibited β-hexosaminidase activity and histamine release dose-dependently in FcεRI-activated RBLs and BMMCs. Additionally, 4-MU reduced cytomorphological elongation and F-actin reorganization while down-regulating IgE/Ag-induced phosphorylation of SYK, NF-κB p65, ERK1/2, p38, and JNK. Moreover, 4-MU attenuated the PCA allergic reaction (i.e., less ear thickening and dye extravasation). Similarly, we found that 4-MU decreased body temperature, serum histamine, and IL4 secretion in OVA-challenged ASA model mice. In conclusion, 4-MU had a suppressing effect on MC activation both in vitro and in vivo and thus may represent a new strategy for treating IgE-mediated allergic conditions.     

TD-SCDMA测试仪中Iub接口实现RLC层信令解码

为了更精确地完成TD-SCDMA测试仪中相关信令的解码测试工作,对TD-SCDMA系统的Uu接口RLC 层信令在Iub接口实现的解码进行了深入分析和研究,给出了RLC层的信令消息结构和流程,提出了”RLC解码的 一种算法,并且应用到TD-SCDMA测试仪中,经调试并实际测试后,得到了预期的良好效果。经过再改进,完全可 以满足市场需要。     

气相色谱正构烷烃和直链脂肪酸甲酯两种线性保留指数之间的转换方法

保留指数是气相色谱中用于化合物结构鉴定的重要工具。本研究对基于正构烷烃和直链脂肪酸甲酯的线性保留指数进行线性拟合,发现在所设定的4种不同的升温条件下两种保留指数之间呈现较为固定的线性关系：在弱极性柱（固定液为5%苯基和95%的甲基聚硅氧烷）和极性柱（固定液为聚乙二醇）条件下,正构烷烃保留指数（y）与脂肪酸甲酯保留指数（x）之间的关系分别为y=1.0051x+318.51（r²=1）和y=1.0362x+562.519（r²=1）。采用文献保留指数对所建立的线性关系进行验证,发现通过公式换算得到的保留指数均在其对应文献值的均值加减方差范围内,说明换算公式真实有效。两种保留指数之间关系的建立对于化合物结构鉴定时扩大保留指数搜索范围、减少保留指数测定实验具有重要意义。     

Development of ion transportation, extraction and neutralization systems for atomic beam resonance method

A device that produces a low-energy and largely spin polarized RI beam based on the atomic beam resonance method (RIABR) has been developed. We have performed measurements of stopping and drifting an incoming RI ion beam in a gas chamber, extraction of the ions into a vacuum region, and neutralization of the extracted low-energy ion beam. The drift efficiency of RI ions in a gas and the extraction efficiency at a Laval-type glass nozzle were found to be 0.72±0.04 and 0.033, respectively. The result of the experiment for the neutralization is also discussed.     

Computational analysis for the determination of deleterious nsSNPs in human MTHFD1 gene

Single nucleotide polymorphisms (SNPs) are the most common genetic polymorphisms and play a major role in many inherited diseases. Methylenetetrahydrofolate dehydrogenase 1 (MTHFD1) is one of the enzymes involved in folate metabolism. In the present study, the functional and structural consequences of nsSNPs of human MTHFD1 gene was analyzed using various computational tools like SIFT, PolyPhen2, PANTHER, PROVEAN, SNAP2, nsSNPAnalyzer, PhD-SNP, SNPs&GO, I-Mutant, MuPro, ConSurf, InterPro, NCBI Conserved Domain Search tool, ModPred, SPARKS-X, RAMPAGE, FT Site and PyMol. Out of 327 nsSNPs form human MTHFD1 gene, total 45 SNPs were predicted as functionally most significant SNPs, among which 17 were highly conserved and functional, 17 were highly conserved and structural residues. Among 45 most significant SNPs, 15 were predicted to be involved in post translational modifications. The p.Gly165Arg may interfere in homodimer interface formation. The p.Asn439Lys and p.Asp445Asn may interfere in binding interactions of MTHFD1 protein with cesium cation and potassium. The two SNPs (p.Asp562Gly and p.Gly637Cys) might interfere in interactions of MTHFD1 with ligand.     

Minimizing UV noise in supercritical fluid chromatography. I. Improving back pressure regulator pressure noise

Pressure fluctuations and resulting refractive index changes, induced by the back pressure regulator (BPR) can be a significant source of UV detector noise in supercritical fluid chromatography (SFC). The refractive index (RI) of pure carbon dioxide (CO(2)) changes ≈0.2%/bar at the most commonly used conditions in supercritical fluid chromatography (SFC) (40 °C and 100 bar), compared to 0.0045%/bar for water (CO(2) IS 44× worse). Changes in RI cause changes in the focal length of the detector cell which results in changes in UV intensity entering the detector. The change in RI (ΔRI/bar) of CO(2) decreases 8-fold at 200 bar, compared to 100 bar. A new back pressure regulator (BPR) design representing an order of magnitude improvement in the state of the art is shown to produce peak to peak pressure noise (PN(p-p)) as low as 0.1 bar, at 200 bar, and 20Hz, compared to older equipment that attempted to maintain PN(p-p)<1bar, at <5Hz. With this lower PN(p-p), changes in baseline UV offsets could be measured as a function of very small changes in pressure. A pressure change of ±1 bar at 100 bar, common with some older BPR's, produced a UV baseline offset >0.5 mAU. A pressure change of ±0.5 bar representing the previous state-of-the-art, resulted in a UV offset of 0.3m AU. Baseline noise <0.05 is required to validate methods for trace analysis. The new BPR, with a PN(p-p) of 0.1 bar, demonstrated UV peak to peak noise (N(p-p))<0.02 mAU with a >0.03 min (10Hz) electronic filter under some conditions. This new low noise level makes it possible to validate SFC methods for the first time.     

多复变域R_I(m,n)上Cauchy积分与Poisson-华积分的边界性质

研究多复变域ＲＩ（ｍ,ｎ）上Ｃａｕｃｈｙ积分与Ｐｏｉｓｓｏｎ－华积分,得到边界函数ｆ∈ＬＰ,Ｐ＞１时几乎处处收敛的结果．     

基于SPR原理的葡萄糖浓度折射率特性矩阵测量

设计了一种简洁的角度扫描棱镜SPR传感系统,反射式平行光路设计简化了系统结构。其主要包括光源及光强感知、平行光路结构、电机与温度控制模块构成。通过单电机扫描入射角与温度控制,实现了对葡萄糖的折射率浓度特性有效测量。理论分析存在交叉灵敏度矩阵可同时度量温度及葡萄糖质量浓度共振角度的变化规律,且实验得其灵敏矩阵。为区分温度和质量浓度对共振角度的影响以及校正SPR温度漂移提供参考。