RNAGCN: RNA tertiary structure assessment with a graph convolutional network

RNAs play crucial and versatile roles in cellular biochemical reactions. Since experimental approaches of determining their three-dimensional (3D) structures are costly and less efficient, it is greatly advantageous to develop computational methods to predict RNA 3D structures. For these methods, designing a model or scoring function for structure quality assessment is an essential step but this step poses challenges. In this study, we designed and trained a deep learning model to tackle this problem. The model was based on a graph convolutional network (GCN) and named RNAGCN. The model provided a natural way of representing RNA structures, avoided complex algorithms to preserve atomic rotational equivalence, and was capable of extracting features automatically out of structural patterns. Testing results on two datasets convincingly demonstrated that RNAGCN performs similarly to or better than four leading scoring functions. Our approach provides an alternative way of RNA tertiary structure assessment and may facilitate RNA structure predictions. RNAGCN can be downloaded from https://gitee.com/dcw-RNAGCN/rnagcn.     

Sommerfeld-type integrals for discrete diffraction problems

Three problems for a discrete analog of the Helmholtz equation are studied analytically using the plane wave decomposition and the Sommerfeld integral approach. They are: (1) the problem with a point source on an entire plane; (2) the problem of diffraction by a Dirichlet half-line; (3) the problem of diffraction by a Dirichlet right angle. It is shown that the total field can be represented as an integral of an algebraic function over a contour drawn on some manifold. The latter is a torus. As a result, explicit solutions are obtained in terms of recursive relations (for the Green’s function), algebraic functions (for the half-line problem), or elliptic functions (for the right angle problem).     

基于STEAM理念的高中化学创新实验研究——四氧化三铁磁流体的制备和性质探究

介绍了基于STEAM理念下让学生制备和表征四氧化三铁磁流体的化学实验探究。采用化学共沉淀法制备了磁性Fe3O4纳米颗粒。在外加磁场下磁流体能出现明显凸起。本实验简单、安全、现象明显、试剂用量小、适宜于学生独立实验操作。本研究旨在通过设置科学问题,让学生体验整个科研过程,培养学生的创造力。     

Two-dimension fluorescence correlation spectroscopy to characterize the binding of organic ligands with zinc in eutrophic lake

Metal binding of organic ligands can definitely affect its environmental behavior in waters, while information on the binding heterogeneity with different organic ligands is still lacked till now. In this study, the binding of zinc with organic matters associated with cyanobacterial blooms, including dissolved organic matters (DOM) and attached organic matters (AOM), were studied by using fluorescence quenching titration combined with two-dimensional correlation spectroscopy (2D-COS). Metal-induced fluorescent quenching was obviously observed both for DOM and AOM, indicating the formation of metal-ligand complexes. Compared with the one-dimensional spectra, 2D-COS revealed the sequences of metal-ligand interaction with the following orders: 276 nm > 232 nm for DOM and 232 nm > 276 nm for AOM. Furthermore, the modified Stern-Volmer model showed that the binding constant (log KM) of 276 nm in DOM was higher than that of 232 nm (4.93 vs. 4.51), while AOM was characterized with a high binding affinity for 232 nm (log KM: 4.83). The ranks of log KM values were consistent with the sequential orders derived from 2D-COS results both for the two samples. Fluorescence quenching titration combined with 2D-COS was an effective method to characterize the metal-ligand interaction.     

不同孪晶界密度银纳米线拉伸形变行为的分子动力学模拟

采用分子动力学方法模拟了不同孪晶界密度银纳米线的拉伸形变行为, 分析了孪晶界密度对多晶银纳米线屈服强度、弹性模量和塑性变形机理的影响. 在弹性形变区域, 孪晶界的存在对杨氏模量变化的作用不明显. 在塑性形变阶段, 首先从表面边缘开始产生位错成核, 然后延伸并受阻于孪晶界. 在进一步拉伸载荷作用下, 孪晶界将作为位错源产生新的位错. 模拟结果表明, 银纳米线的强度与孪晶界和晶粒的尺寸有关. 孪晶界密度较小(即晶粒的长径比大于1)时, 此纳米线的屈服应力比单晶纳米线还要小, 只有当孪晶界密度较大时(即晶粒的长径比小于1), 孪晶界使得纳米线得到强化. 综合分析了孪晶界和晶粒尺寸对银纳米线的影响, 为构建高强度金属纳米线打下基础. 最后讨论了温度和拉伸速度对孪晶纳米线屈服应力所产生的影响, 随着温度的升高, 孪晶纳米线与单晶纳米线的屈服应力差先升高后趋于稳定; 当拉伸速度逐渐增大, 孪晶纳米线与单晶纳米线的屈服应力差先稳定后增大.     

A UNIFORMLY CONVERGENT DIFFERENCE SCHEME FOR THE SINGULAR PERTURBATION PROBLEM OF A HIGH ORDER ELLIPTIC DIFFERENTIAL EQUATION

ＡＵＮＩＦＯＲＭＬＹＣＯＮＶＥＲＧＥＮＴＤＩＦＦＥＲＥＮＣＥＳＣＨＥＭＥＦＯＲＴＨＥＳＩＮＧＵＬＡＲＰＥＲＴＵＲＢＡＴＩＯＮＰＲＯＢＬＥＭＯＦＡＨＩＧＨＯＲＤＥＲＥＬＬＩＰＴＩＣＤＩＦＦＥＲＥＮＴＩＡＬＥＱＵＡＴＩＯＮ（刘国庆）（苏煜城）ＡＵＮＩＦＯ...     

Aging properties of styrene-butadiene rubber nanocomposites filled with carbon black and rectorite

To better understand the effect of rectorite and carbon black (CB) on the aging performance of styrene-butadiene rubber (SBR), SBR/CB, SBR/CB/rectorite and SBR/rectorite nanocomposites with the same total filler loading were prepared. The microstructure of the three SBR nanocomposites was characterized by XRD, TEM and SEM. After thermal aging, oxygen-containing molecules were found to be formed in the SBR nanocomposites, as verified by FTIR analysis. The SBR/rectorite nanocomposite showed the highest aging coefficient and the lowest change rate of tensile strength and stress at 100% strain among the three SBR nanocomposites, indicating that the introduction of nano-dispersed rectorite layers can enhance the thermal aging resistance of the nanocomposites. For the SBR/CB/rectorite nanocomposite, the addition of CB helped to improve the interfacial compatibility between the filler and matrix, resulting in the best crack resistance as the aged SBR/CB/rectorite nanocomposite always demonstrated the least cracks on the surface during either stretching or bending experiments.     

Comparison of waveguide properties of curved versus straight planar elastic layers

Dispersion equations are solved for the in-plane and anti-plane wave propagation in planar elastic layer with constant curvature. The classical Lamé formulation of displacements via elastic potentials is applied and appropriate simplifications are employed. The dispersion diagrams in each case are compared with their counterparts for a straight layer, e.g., the classical Rayleigh–Lamb solution. The curvature-induced symmetry-breaking effects are investigated for layers with symmetric boundary conditions. The role of curvature is also investigated in the cases, when the boundary conditions are not symmetrical. The elementary Bernoulli–Euler theory is employed to analyze the wave guide properties of a curved planar elastic beam in its in-plane deformation. The validity range of the Bernoulli–Euler theory is assessed via comparison of dispersion diagrams.     

The epipharyngeal sensilla of the damselfly Ischnura elegans (Odonata,Coenagrionidae)

The knowledge on Odonata adult mouthparts sensilla is scanty and, notwithstanding the epipharynx in the labrum is considered an organ of taste, no ultrastructural investigation has been performed so far on this structure in Odonata. The labrum of the adult of the damselfly Ischnura elegans (Odonata, Coenagrionidae) shows on its ventral side the epipharynx with sensilla represented by articulated hairs and by small pegs located at the apex of slightly raised domes. Under scanning and transmission electron microscope, the articulated hairs, with a well developed socket and tubular body, have the typical structure of bristles, the most common type of insect mechanoreceptors, usually responding to direct touch; the pegs, showing an apical pore together with a variable number of sensory neurons (from two to five), the outer dendritic segments of which show a dendrite sheath stopping along their length, have features typical of contact chemoreceptors.