Finding finer functions for partially characterized proteins by protein-protein interaction networks

Based on high-throughput data, numerous algorithms have been designed to find functions of novel proteins. However, the effectiveness of such algorithms is currently limited by some fundamental factors, including (1) the low a-priori probability of novel proteins participating in a detailed function; (2) the huge false data present in high-throughput datasets; (3) the incomplete data coverage of functional classes; (4) the abundant but heterogeneous negative samples for training the algorithms; and (5) the lack of detailed functional knowledge for training algorithms. Here, for partially characterized proteins, we suggest an approach to finding their finer functions based on protein interaction sub-networks or gene expression patterns, defined in function-specific subspaces. The proposed approach can lessen the above-mentioned problems by properly defining the prediction range and functionally filtering the noisy data, and thus can efficiently find proteins’ novel functions. For thousands of yeast and human proteins partially characterized, it is able to reliably find their finer functions (e.g., the translational functions) with more than 90% precision. The predicted finer functions are highly valuable both for guiding the follow-up wet-lab validation and for providing the necessary data for training algorithms to learn other proteins.     

A generalized quasi-sum relations for oscillator strengths in transition arrays: theoretical study of the opacity of Ge plasmas

We present a simplified relativistic configuration interaction method (SRCI), by which all the energy levels and oscillator strengths in each transition array can be calculated. There exist generalized quasi-sum relations for the calculated oscillator strengths in the relevant transition arrays by the SRCI and by an unresolved transition array model (UTA). Based on UTA and the detailed configuration accounting (DCA), with a fully relativistic treatment incorporated with the quantum defect theory, the X-ray absorption spectra for any middle- and high-Z plasmas or composite plasmas can be calculated with much less computational efforts. The gross features of calculated spectra by DCA-UTA are in agreement with the relevant experimental measurements, except some detailed structures in some narrow spectral ranges. Such detailed structures can be calculated by SRCI incorporated with DCA-UTA. As an illustrative example, the absorption spectra of Ge plasmas are calculated by DCA-UTA-SRCI and are in agreement with the experimental opacity data. Therefore, the theoretical method (DCA-UTA-SRCI) verified by experimental measurements will not only be a basic tool to provide “precision” opacity data for the inertial confinement fusion research (ICF) and studies in stellar physics but also can be used to analyze the relevant diagnostic measurements for ICF plasmas.     

Au(111)上烷烃硫醇SAMs表面应力的理论研究

应用已建立的关于金属表面吸附层中表面应力的统计热力学理论 ,计算了Au(111)上烷烃硫醇SAMs的表面应力及其与烷烃硫醇链长、吸附覆盖度的定量关系 .计算结果与实验相符 ,较好地解释了Berger等人的实验结果 ,特别是解决了在表面应力符号性质上理论与实验的矛盾 .在表面吸附层应力的多种物理起源中 ,通过底物的分子间作用力有着决定性的贡献 ,揭示了分子的吸附能间接地起着重要作用 .这与阴离子化学吸附体系Cl-/Au(111)的有关研究结果相同 .     

The study of the influence of uniaxial stress on impurity complexes in silicon

The influence of external uniaxial stress on the different indium-donor complexes in silicon has been studied using the perturbed γ –γ angular correlation (PAC) method. Such effect of an applied stress is detected by means of the probe atoms situated at different complexes in the sample. The current results showed that the responses of the probes in an extrinsic silicon samples are found to be dissimilar for the same value of stress. Such change in the local environments of the probe atoms could be associated with the various strain field created by the implantations of varied size of impurities. The phosphorous implantation in silicon has even lead to the complete absence of observable effect of the applied stress suggesting significant lose of the elasticity of the sample.     

Numerical simulations of a filament in a flowing soap film

Experiments concerning the properties of soap films have recently been carried out and these systems have been proposed as experimental versions of theoretical two‐dimensional liquids. A silk filament introduced into a flowing soap film, was seen to demonstrate various stable modes, and these were, namely, a mode in which the filament oscillates and one in which the filament is stationary and aligns with the flow of the liquid. The system could be forced from the oscillatory mode into the non‐ oscillatory mode by varying the length of the filament. In this article we use numerical and computational techniques in order to simulate the strongly coupled behaviour of the filament and the fluid. Preliminary results are presented for the specific case in which the filament is seen to oscillate continuously for the duration of our simulation. We also find that the filament oscillations are strongly suppressed when we reduce the effective length of the filament. We believe that these results are reminiscent of the different oscillatory and non‐oscillatory modes observed in experiment. The numerical solutions show that, in contrast to experiment, vortices are created at the leading edge of the filament and are preferentially grown in the curvature of the filament and are eventually released from the trailing edge of the filament. In a similar manner to oscillating hydrofoils, it seems that the oscillating filaments are in a minimal energy state, extracting sufficient energy from the fluid to oscillate. In comparing numerical and experimental results it is possible that the soap film does have an effect on the fluid flow especially in the boundary layer where surface tension forces are large. Copyright © 2004 John Wiley & Sons, Ltd.     

Classical in-plane negative magnetoresistance and quantum positive magnetoresistance in undoped InSb thin films on GaAs (1 0 0) substrates

Magnetoresistance (MR) effects have been investigated in perpendicular and parallel magnetic fields at 300, 80 K and liquid He temperatures for undoped InSb thin films 0.1–2.3 μm thick grown on GaAs(1 0 0) substrates by MBE. At high temperatures, the intrinsic carriers show the parabolic negative MR observable only in magnetic fields parallel to the film. The skipping-orbit effect due to surface boundary scattering in the classical orbits in the plane vertical to the film has been argued to be responsible for the negative MR. At low temperatures (T=80 K), the transport is dominated by the two-dimensional (2D) electrons in the accumulation layers at the InSb/GaAs(1 0 0) hetero interface; MR is positive and shows a logarithmic increase with anisotropy between parallel and perpendicular field orientation, arising from the 2D weak anti-localization (WAL) that reflects the interplay between the spin-Zeeman effect and strong spin–orbit interaction caused by the asymmetric potential at the interface (Rashba term). The zero-field spin splitting energy of Δ₀13 meV, the electron effective mass of m^*0.10m₀ seven times of the band edge mass in bulk InSb and the effective g-factor of |g^*|15 in the accumulation layer have been inferred from fits of MR for the 0.1 μm thick film to the 2D WL theory.     

Preparation and characterization of acrylic‐based black particles of poly(methyl methacrylate‐co‐ethylene glycol dimethacrylate) by dispersion polymerization for electrophoretic displays

Ultrafine black particles, ranging in diameter from 1 to 3 μm, were prepared by dispersion polymerization in a methanol/water mixture with vinyl monomers, nonpolymerizable Sudan black B dyes, and fluorescein isothiocyanate labeled charge control additives. Both the ratio of the methanol to the water dispersion medium and the polymeric stabilizer concentration had significant effects on the particle size. The important role of the stabilizer concentration lay in the particle formation step, during which it determined the particle stability and final particle size. These could affect the extent of the aggregation of nuclei by changing the adsorption rate of the stabilizer and the viscosity of the dispersion medium, resulting in smaller particles. The fluorescent‐labeled charge control additives strongly affected the electrophoretic mobility. A small concentration of fluorescent‐labeled charge control additives increased the electrophoretic mobility. However, a further addition reduced the electrophoretic mobility of the polymer particles. The concentration dependence of the fluorescent‐labeled charge control additives on the deposition behavior in the polymer particles was successfully imaged and thereafter quantified by image analysis. © 2004 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 42: 5608–5616, 2004     

Cr3+：MgAl2O4晶体EPR参量及其电子精细光谱的研究

考虑了SS(Spin-Spin)作用和SOO(Spin-Other-Orbit)作用，采用完全对角化方法，结合自旋Hamiltonian理论，研究了Cr³⁺∶MgAl₂O₄晶体EPR参量及其吸收光谱，理论与实验符合甚好. 在此基础上，进一步研究了⁴A₂(3d³)离子EPR参量的微观起源. 研究表明，EPR参量起源于四种微观机制：(1) SO(Spin-Orbit) 耦合机制；(2) SS耦合机制；(3)SOO耦合机制；(4) SO～SS～SOO总联合作用机制. 在这些机制中，SO机制是最主要的.     

切伦柯夫相互作用中分段式慢波结构与均匀慢波结构的比较研究

 分析了切伦柯夫束波相互作用中使用单段慢波结构的缺点。指出在分段式慢波结构中，漂移段及其两端的慢波结构组成一Bragg谐振腔，当漂移段长度合适时，根据渡越时间效应理论，这种结构能减小调制束中电子的速度分散，提高束波转化效率。通过粒子模拟方法，比较了均匀慢波结构与分段式慢波结构中束波相互作用的物理图像，验证了理论分析结果，并说明了后者有束密度群聚充分，束电子速度分散小，产生微波功率高、频谱质量好，最佳工作电流大，输入电功率高等优点。     

The long‐time behaviour of the thermoconvective flow in a porous medium

For the Boussinesq approximation of the equations of coupled heat and fluid flow in a porous medium we show that the corresponding system of partial differential equations possesses a global attractor. We give lower and upper bounds of the Hausdorff dimension of the attractor depending on a physical parameter of the system, namely the Rayleigh number of the flow. Numerical experiments confirm the theoretical findings and raise new questions on the structure of the solutions of the system. Copyright © 2004 John Wiley & Sons, Ltd.