TMDIM: an improved algorithm for the structure prediction of transmembrane domains of bitopic dimers

\(\alpha\)-Helical transmembrane proteins are the most important drug targets in rational drug development. However, solving the experimental structures of these proteins remains difficult, therefore computational methods to accurately and efficiently predict the structures are in great demand. We present an improved structure prediction method TMDIM based on Park et al. (Proteins 57:577–585, 2004) for predicting bitopic transmembrane protein dimers. Three major algorithmic improvements are introduction of the packing type classification, the multiple-condition decoy filtering, and the cluster-based candidate selection. In a test of predicting nine known bitopic dimers, approximately 78% of our predictions achieved a successful fit (RMSD <2.0 Å) and 78% of the cases are better predicted than the two other methods compared. Our method provides an alternative for modeling TM bitopic dimers of unknown structures for further computational studies. TMDIM is freely available on the web at https://cbbio.cis.umac.mo/TMDIM. Website is implemented in PHP, MySQL and Apache, with all major browsers supported.     

Investigation of Nutrient Feeding Strategies in a Countercurrent Mixed-Acid Multi-Staged Fermentation: Experimental Data

Nutrients are essential for microbial growth and metabolism in mixed-culture acid fermentations. Understanding the influence of nutrient feeding strategies on fermentation performance is necessary for optimization. For a four-bottle fermentation train, five nutrient contacting patterns (single-point nutrient addition to fermentors F1, F2, F3, and F4 and multi-point parallel addition) were investigated. Compared to the traditional nutrient contacting method (all nutrients fed to F1), the near-optimal feeding strategies improved exit yield, culture yield, process yield, exit acetate-equivalent yield, conversion, and total acid productivity by approximately 31%, 39%, 46%, 31%, 100%, and 19%, respectively. There was no statistical improvement in total acid concentration. The traditional nutrient feeding strategy had the highest selectivity and acetate-equivalent selectivity. Total acid productivity depends on carbon–nitrogen ratio.     

Effect of iridium loading on HZSM-5 for isomerization of n-heptane

The effect of iridium loading on the properties and catalytic isomerization of n-heptane over Ir-HZSM-5 is studied. Ir-HZSM-5 was prepared by impregnation method and subjected to isomerization process in the presence of flowing hydrogen gas. XRD and BET studies show that the presence of iridium stabilizes the crystalline structure of HZSM-5, leading to more ordered framework structure and larger surface area. TGA and FTIR results substantiate that iridium species interacts with OH group on the surface of HZSM-5. Pyridine FT-IR study verifies the interaction between iridium and surface OH group slightly increased the Bro¨nsted and Lewis acid sites without changing the lattice structure of HZSM-5. The presence of iridium and the increase of strong Lewis acid sites on HZSM-5 were found to bring an increase about 4.1%, 33.2% and 11.8% in conversion, selectivity and yield of n-heptane isomerization, respectively.     

Effect of NH4I and I2 concentration on agar gel polymer electrolyte properties for a dye-sensitized solar cell

Gel polymer electrolytes were prepared using agar polymer host, NH₄I, and I₂ salts. The sample of agar paste with 1.0 M of NH₄I and 0.2 μM of I₂ exhibits the highest conductivity and lowest viscosity values at room temperature of (2.64?±?0.19)?×?10^?3?S?cm^?1 and 1.17?±?0.29 Pa?s, respectively. All of the gel polymer electrolytes display Arrhenian behavior, and the optimum agar paste gave the lowest activation energy of 0.25 eV. It also had a good physical appearance compared with the other samples. This gel polymer electrolyte had a good potential and was applicable to a role as electrolyte in ITO-ZnO (N719 dye)/agar paste?+?1.0 M NH₄I?+?0.2 μM I₂/Au-Pd-ITO dye-sensitized solar cell.     

Approximation by Gamma type operators

In this study, we introduce newly defined Gamma operators which preserve constants and e^2μ·, μ>0 functions. In accordance with this purpose, we focus on their approximation properties such as uniform convergence, rate of convergence, asymptotic formula, and saturation results. Superior properties of introduced operators have been tested both theoretically and numerically in certain senses to highlight the performance of the new constructions of Gamma operators.     

Modeling and analysis of system reliability using phase‐type distribution closure properties

Phase‐type distribution closure properties are utilized to devise algorithms for generating reliability functions of systems with basic structures. These structures include series, parallel, K‐out‐of‐N, and standby structures with perfect/imperfect switch. The algorithms form a method for system reliability modeling and analysis based on the relationship between the system lifetime and component lifetimes for general structures. The proposed method is suitable for functional system reliability analysis, which can produce reliability functions of systems with independent components instead of only system reliability values. Once the system reliability function is obtained, other reliability measures such as the system's hazard function and mean time to failure can be obtained efficiently using only matrix algebra. Dimensional and numerical comparisons with computerized symbolic processing are also presented to show the superiority of the proposed method.     

Effect of calcination temperature on the photocatalytic activity of carbon‐doped titanium dioxide revealed by photoluminescence study

Carbon‐doped titania (C‐TiO₂) nanoparticles were synthesized by the sol–gel method at different calcination temperatures (300–600°C) employing titanium tetraisopropoxide (TTIP) as the titanium source and polyoxyethylene sorbitan monooleate (Tween 80) as the carbon source. The physical properties of C‐TiO₂ samples were characterized by X‐ray diffraction (XRD) and scanning electron microscopy (SEM). The photocatalytic activities were checked through the photodegradation of phenolphthalein (PHP) under ultraviolet irradiation. The UV spectrum showed that the carbon doping extends the absorption range of TiO₂ to the visible region. However, the photocatalytic activity is affected by the electron–hole recombination phenomenon, as revealed by the photoluminescence (PL) study. According to the PL spectra, carbon doping reduces the edge‐to‐edge electron–hole recombination. Nevertheless, the number of defect sites is greatly influenced by the calcination temperature of C‐TiO₂. C‐TiO₂ that was calcined at 400°C showed the highest photodegradation percentage of PHP, which was mainly attributed to the synergic effect of the low direct edge‐to‐edge electron–hole recombination, high content of defect sites, and retention of active electrons on the surface hydroxyl group.     

In reply to “A query on the Mg2p of MgO”

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