熔石英中过氧缺陷及中性氧空位缺陷的几何结构、电子结构和吸收光谱的准粒子计算

本文使用密度泛函理论研究了熔石英中peroxy linkage(POL)缺陷和中性氧空位(NOV)缺陷的几何结构,电子结构以及光学性质.采用自洽的准粒子GW计算结合求解Bathe-Salpeter方程的多体理论,研究了缺陷引起的电子结构和光学吸收谱的变化.首先研究了无缺陷非晶结构的电子结构与吸收谱,得到的结果与实验值非常接近.对POL的计算表明,其在基态下的局部结构与过氧化氢分子类似.采用多体理论计算得到的吸收谱表明其最低吸收峰位于6.3 eV处.这一结果不支持实验认为的位于3.8 eV处的吸收峰是由POL缺陷导致的说法.对于NOV缺陷,计算表明其基态的Si—Si键长为2.51?而三重态下的值则为3.56?.相应的GW+BSE计算表明中性氧空位缺陷导致了位于7.4 eV处的吸收峰,与实验测量结果一致.     

Preparing to read the ubiquitin code: top‐down analysis of unanchored ubiquitin tetramers

The characterization of polyubiquitin chains has been an analytical challenge for several decades. It has been shown that anchored and unanchored polyubiquitin chains with different isopeptide linkages and lengths exhibit a wide range of profoundly different cellular functions. However, structure function studies have been hindered by the difficulty of characterizing these complex chain structures. This report presents a broadly applicable workflow to characterize ubiquitin tetramers without the need for genetic mutations or reiterative immunoprecipitations. We use a top‐down proteomic strategy that exploits ETciD activation on an orbitrap Fusion Lumos and manual interpretation aided by graphical interpretation of mass shifts to facilitate characterization of chain topography and lysine linkage sites. Our workflow differentiates all topological features of the numerous isomers of tetraubiquitin, which have molecular masses in excess of 34 000 Da and identifies linkage sites in these branched proteins. Copyright © 2016 John Wiley & Sons, Ltd.     

A note on quasi-Gorenstein rings

In this paper, after giving a criterion for a Noetherian local ring to be quasi-Gorenstein, we obtain some sufficient conditions for a quasi-Gorenstein ring to be Gorenstein. In the course, we provide a slight generalization of a theorem of Evans and Griffith. Received: 16 February 2008     

Application of Deterministic Low-Discrepancy Sequences in Global Optimization

It has been recognized through theory and practice that uniformly distributed deterministic sequences provide more accurate results than purely random sequences. A quasi Monte Carlo (QMC) variant of a multi level single linkage (MLSL) algorithm for global optimization is compared with an original stochastic MLSL algorithm for a number of test problems of various complexities. An emphasis is made on high dimensional problems. Two different low-discrepancy sequences (LDS) are used and their efficiency is analysed. It is shown that application of LDS can significantly increase the efficiency of MLSL. The dependence of the sample size required for locating global minima on the number of variables is examined. It is found that higher confidence in the obtained solution and possibly a reduction in the computational time can be achieved by the increase of the total sample size N. N should also be increased as the dimensionality of problems grows. For high dimensional problems clustering methods become inefficient. For such problems a multistart method can be more computationally expedient.     

Genomic study of ossification of the posterior longitudinal ligament of the spine

Ossification of the posterior longitudinal ligament of the spine (OPLL) is a common disease after the middle age. OPLL frequently causes serious neurological problems due to compression of the spinal cord and/or nerve roots. OPLL occurs in patients with monogenic metabolic diseases including rickets/osteomalacia and hypoparathyroidism; however most of OPLL is idiopathic and is considered as a multi-factorial (polygenic) disease influenced by genetic and environmental factors. Genomic studies for the genetic factors of OPLL have been conducted, mainly in Japan, including linkage and association studies. This paper reviews the recent progress in the genomic study of OPLL and comments on its future direction.     

Palladium‐Assisted Cleavage of Peptides and Proteins Containing a Backbone with Thiazolidine Linkage

The design and synthesis of biomolecules that are responsive to external stimuli is of great interest in various research areas, such as in the preparation of smart biomaterial and chemical biology. Polypeptide backbone disassembly as a response to a particular stimulus is of interest, as it leads to a complete loss of the protein tertiary structure and, as a result, to a loss of function. In this study, a strategy based on palladium‐assisted efficient cleavage of backbone thiazolidine linkage in peptides and proteins was developed. Using a fluorescence‐based assay, encompassing ubiquitinated peptide with a quenching florescence pair, it was possible to optimize the cleavage step after rapid screening of various conditions, such as the type of metal complexes and reaction additives. The optimized conditions prompted fast cleavage of the thiazolidine linkage. The straightforward introduction of a backbone thiazolidine linkage in peptide and proteins coupled with the chemical methods used offers new opportunities in controlling macromolecule function and might, with the aid of cellular protein delivery methods, be applied in cellular settings.     

Antiferroelectric phase in liquid crystalline compounds containing an azo group in their molecular core

Novel lactic acid derivatives containing an azo group in their molecular core have been synthesised and their mesomorphic properties established. Compounds with a short aliphatic non-chiral chain exhibited the SmA* phase and ferroelectric (FE) SmC* phase. The monotropic antiferroelectric (AF) phase was found in the homologues with a longer terminal chain. Spontaneous polarisation and tilt angle were measured for the FE and AF phases. Dielectric spectroscopy in the frequency range 1 Hz–10 MHz was carried out and dielectric properties established within the temperature range of the smectic phases. Two high frequency modes were detected in the AF phase. Small-angle X-ray measurements were conducted, and the temperature dependence of layer spacing values is established and discussed.     

Single Polyelectrolyte Microcapsules Fabricated By Glutaraldehyde‐Mediated Covalent Layer‐By‐Layer Assembly

Summary: Single polyelectrolyte component microcapsules and multilayers, exemplified by poly(allylamine hydrochloride) (PAH), have been prepared using a method of glutaraldehyde (GA)‐mediated covalent layer‐by‐layer (LbL) assembly. The GA cross‐linking of the adsorbed PAH results in surfaces covered by reactive aldehyde groups, which can then react with PAH to result in another layer of covalently linked PAH. The repeated assembly of single polyelectrolyte in an LbL manner can be thus achieved. The PAH multilayers can grow linearly along with the layer number, and their thickness can be controlled at the nanometer scale, as verified by UV‐vis absorption spectrometry and ellipsometry. Single polyelectrolyte microcapsules are obtained after removal of the template cores at low pH. The morphology and integrity are confirmed by scanning force microscopy and confocal laser scanning microscopy.

Schematic illustration of the preparation of a single polyelectrolyte component microcapsule by GA‐mediated covalent LbL assembly.     

Synthesis of an amphiphilic polymer having hydrophobic acetal and hydrophilic pyrrolidone moieties and its application to persisting release of aldehyde as a pro‐fragrance

A polymer having acetal moiety in the side chain was synthesized by a reaction of 1,3‐diol structure of poly(vinyl alcohol‐co‐N‐vinylpyrrolidone) and octanal. The hydrophobicity of the resulting acetal moiety and the hydrophilicity of the pyrrolidone moiety allowed the polymer to exhibit amphiphilicity. The polymer released octanal by hydrolysis of the acetal side chains under acidic conditions. The release of octanal was enhanced by the increased hydrophilicity of the polymer because of the presence of pyrrolidone moiety. © 2010 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 48: 3816–3822, 2010     

RC_Link: Genetic linkage analysis using Bayesian networks

Genetic linkage analysis is a statistical method for mapping genes onto chromosomes, and is useful for detecting and predicting diseases. One of its current limitations is the computational complexity of the problems of interest. This research presents methods for mapping genetic linkage problems as Bayesian networks and then addresses novel techniques for making the problems more tractable. The result is a new tool for solving these problems called RC_Link, which in many cases is orders of magnitude faster than existing tools.