On aggregation in multiset-based self-assembly of graphs

We continue the formal study of multiset-based self-assembly. The process of self-assembly of graphs, where iteratively new nodes are attached to a given graph, is guided by rules operating on nodes labelled by multisets. In this way, the multisets and rules model connection points (such as “sticky ends”) and complementarity/affinity between connection points, respectively. We identify three natural ways (individual, free, and collective) to attach (aggregate) new nodes to the graph, and study the generative power of the corresponding self-assembly systems. For example, it turns out that individual aggregation can be simulated by free or collective aggregation. However, we demonstrate that, for a fixed set of connection points, collective aggregation is rather restrictive. We also give a number of results that are independent of the way that aggregation is performed.     

An integrated model for the transshipment yard scheduling problem

A hub-and-spoke railway system is an efficient way of handling freight transport by land. A modern rail–rail train yard consists of huge gantry cranes that move the containers between the trains. In this context, we consider a rail–rail transshipment yard scheduling problem (TYSP) where the containers arrive to the hub and need to be placed on a train that will deliver them to their destination. In the literature, the problem is decomposed hierarchically into five subproblems, which are solved separately. First, the trains have to be grouped into bundles in which they visit the yard. Next, the trains have to be assigned to tracks within these bundles, namely parking positions. Then the final positions for the containers on trains have to be determined. Next, the container moves that need to be performed are assigned to the cranes. Finally, these moves have to be sequenced for each crane for processing. In this paper, an integrated MILP model is proposed, which aims to solve the TYSP as a single optimization problem. The proposed formulation also enables us to define more robust and complex objective functions that include key characteristics from each of the above-mentioned subproblems. The strength of our proposed formulation is demonstrated via computational experiments using the data from the literature. Indeed, the results show that the TYSP can be solved without the use of decomposition techniques and more insight can be obtained from the same input data used to solve particular single decomposed subproblems.     

Effect of Posttranslational Modifications on the Structure and Activity of FTO Demethylase

The FTO protein is involved in a wide range of physiological processes, including adipogenesis and osteogenesis. This two-domain protein belongs to the AlkB family of 2-oxoglutarate (2-OG)- and Fe(II)-dependent dioxygenases, displaying N⁶-methyladenosine (N⁶-meA) demethylase activity. The aim of the study was to characterize the relationships between the structure and activity of FTO. The effect of cofactors (Fe²⁺/Mn²⁺ and 2-OG), Ca²⁺ that do not bind at the catalytic site, and protein concentration on FTO properties expressed in either E. coli (^ECFTO) or baculovirus (^BESFTO) system were determined using biophysical methods (DSF, MST, SAXS) and biochemical techniques (size-exclusion chromatography, enzymatic assay). We found that ^BESFTO carries three phosphoserines (S184, S256, S260), while there were no such modifications in ^ECFTO. The S256D mutation mimicking the S256 phosphorylation moderately decreased FTO catalytic activity. In the presence of Ca²⁺, a slight stabilization of the FTO structure was observed, accompanied by a decrease in catalytic activity. Size exclusion chromatography and MST data confirmed the ability of FTO from both expression systems to form homodimers. The MST-determined dissociation constant of the FTO homodimer was consistent with their in vivo formation in human cells. Finally, a low-resolution structure of the FTO homodimer was built based on SAXS data.     

Bioactive Titanium Surfaces Enriched with Silver Nanoparticles Through an In Situ Reduction: Looking for a Balance Between Cytocompatibility and Antibacterial Activity

This research aims toward an antibacterial and osteoconductive Ti₆Al₄V surface by chemical etching–oxidation treatment and in situ reduction of silver nanoparticles. Starting from a previously developed process, already proved to enhance the osteoinductive ability of titanium, different parameters are changed to tailor the amount of silver and its distribution across the surface oxide layer thickness. The samples are characterized by scanning and transmission electron microscopy, energy-dispersive X-ray spectroscopy, release of silver, biofilm formation (Staphylococcus aureus), and cytocompatibility toward human osteoblasts progenitor cells. The total amount of silver in the surface oxide layer depends only on the concentration of the silver precursor. The time of the addition of the silver precursor, during the oxidation treatment, affects the oxide layer thickness, dimension, and distribution of the nanoparticles across the surface oxide: they are larger and accumulate on the outermost layer, if the addition occurs early. The maximum ion release occurs after 24 h and lasts up to 14 days; the later addition of silver precursors leads to sustaining the silver release for a longer time. The samples prepared with the higher concentration of the silver precursor are bactericide, but highly cytotoxic, whereas the other ones are bacteriostatic and moderately cytotoxic.     

A convenient access to 1,2-diferrocenyl-substituted ethylenes via [3 + 2]-cycloelimination of 2-silylated 4,4,5,5-tetrasubstituted 1,3-dithiolanes

Ferrocenyl thioketones bearing a hetaryl, phenyl or alkyl group as the second substituent react with (trimethylsilyl)diazomethane at ca. ?30°C in THF solution without formation of a stable [3?+?2]-cycloadduct. After the spontaneous evolution of N₂, the corresponding sterically crowded 4,4,5,5-tetrasubstituted 2-silylated 1,3-dithiolanes are formed as products of the second [3?+?2]-cycloaddition of the intermediate thiocarbonyl S-methanide with the starting thioketone. After desilylation by treatment with TBAF, they are converted into the corresponding carbanions, which display different stability depending on the type of substituent. The presence of hetaryl and phenyl groups results in the exclusive formation of 1,2-diferrocenyl ethylenes. In contrast, the presence of methyl groups significantly enhances the stability of the carbanion, which by protonation yields trans-4,5-diferrocenyl-4,5-dimethyl-1,3-dithiolane.     

基于场效应晶体管的太赫兹探测器中天线设计的一种有效方法

在场效应晶体管太赫兹探测器中,合理的天线设计可以增强晶体管和太赫兹波之间的耦合效率,从而提高太赫兹探测器的响应度.提出一种基于晶体管栅极边缘沟道电场的仿真来设计平面天线的方法.这种方法尤其适用于太赫兹波段晶体管输入阻抗不容易得到的情况.通过流片完成的基于氮化镓高电子迁移率晶体管的太赫兹探测器的响应度测试证实了这种方法的有效性.集成碟形天线和双偶极子天线的太赫兹探测器最大响应度分别在170.7 GHz(1568.4 V/W)和124.3 GHz(1047.2 V/W)频点处测得,这个测试结果接近基于晶体管栅极边缘沟道电场的仿真结果.     

Investigations of chromium (VI) ion sorption and reduction on strongly basic anion exchanger

Removal of chromium(VI) ions and their reduction were studied on the anion exchanger Dowex PSR-2 in the pH range from 1.5 to 10. The parameters of Cr(VI) sorption process on the anion exchanger were calculated based on the most popular isotherm models such as: Freundlich, Langmuir, Temkin, and Dubinin–Radushkevich (D-R). The Langmuir isotherm was the most appropriate to describe Cr(VI) sorption. The Cr(VI) uptake by Dowex PSR-2 was found to follow the pseudo-second-order rate kinetics. Reduction of chromium(VI) in the pH range 1.5–10 was observed using the HPLC-ICP-MS (high-performance liquid chromatography–inductively coupled plasma-mass spectrometry) method. Oxidation of tri-n-butyl quaternary ammonium groups during the chromate (VI) removal process was observed.     

Poly(methyl vinyl ether‐alt‐maleic anhydride) functionalized with 3‐aminophenylboronic acid: A new boronic acid polymer for sensing diols in neutral water

Amidation of poly(methyl vinyl ether‐alt‐maleic anhydride) with 3‐aminophenylboronic acid was used to prepare a new boronic acid polymer. The binding of catechol dye, Alizarin Red S to the polymer obtained resulted in getting a stable, colored sensor which was used to establish association constants with different diols in competitive assay. The binding of different diols was readily detected by color change and absorbance values measured at 450 nm were used to calculate the association constants. The polymer obtained formed high‐affinity complexes with ribonucleosides, particularly cytidine and uridine. © 2014 Wiley Periodicals, Inc. J. Appl. Polym. Sci. 2014 , 131, 40778.     

Solvent effects on the rates and mechanisms of reaction of phenols with free radicals

The rates of formal abstraction of phenolic hydrogen atoms by free radicals, Y* + ArOH --> YH + ArO*, are profoundly influenced by the hydrogen-bond-accepting and anion-solvation abilities of solvents, by the electron affinities and reactivities (Y-H bond dissociation enthalpies) of radicals, and by the phenol's ring substituents. These apparently simple reactions can occur by at least three different, nonexclusive mechanisms: hydrogen atom transfer, proton-coupled electron transfer, and sequential proton-loss electron transfer. The delicate balance among these mechanisms depends on both the environment and the reactants. The main features of these mechanisms are described, together with some interesting kinetic consequences.