Dimethyl isotope labeling assisted de novo peptide sequencing

Here, we explore a de novo sequencing strategy in which we combine Lys-N protein digestion with differential isotopic dimethyl labeling to facilitate the (de novo) identification of multiply charged peptides in ESI-MS, both under CID and ETD conditions. For a large fraction of the Lys-N generated peptides, all primary amines are present at the N-terminal lysine, enabling specific labeling of the N-terminus. Differential derivatization of only the peptide N-terminus in combination with the simultaneous fragmentation of the corresponding isotopologues allows the straightforward distinction of N-terminal fragments from C-terminal and internal fragments. Furthermore, also singly and multiply charged N-terminal fragments can easily be distinguished due to the mass differences of the isotope labeled fragment pairs. As a proof of concept, we applied this approach to proteins isolated from an avocado fruit, and were able to partially de novo sequence and correctly align, with green plant homologues, a previously uncharacterized avocado ascorbate peroxidase.     

Polynuclear Cu(II), Ni(II) and Cd(II) coordination compounds with bis(pyrimidin-2-yl)amine and dicyanamide

In this study the synthesis, crystal structure and characterization of three new transition metal polynuclear compounds with formula [Cu(dipm)(μ-dca)₂]_n(H₂O) (1), [Ni(dipm)(μ-dca)₂]_n(C₂H₆O)_1/2 (2) and [Cd(dipm)(μ-dca)₂]_n (3) (in which dipm = bis(pyrimidin-2-yl)amine and dca = dicyanamide) are reported. The isostructural compounds 1 and 2 contain a double-bridging end-to-end dca unit connecting two metal ions and a single bridging end-to-end dca unit between subsequent metals. Compound 3 exhibits only single bridging end-to-end dca units, oriented in three directions, giving rise to a 3D framework.     

Trends in aircraft noise annoyance: the role of study and sample characteristics

Recently, it has been suggested that the annoyance of residents at a given aircraft noise exposure level increases over the years. The objective of the present study was to verify the hypothesized trend and to identify its possible causes. To this end, the large database used to establish earlier exposure-response relationships on aircraft noise was updated with original data from several recent surveys, yielding a database with data from 34 separate airports. Multilevel grouped regression was used to determine the annoyance response per airport, after which meta-regression was used to investigate whether study characteristics could explain the heterogeneity in annoyance response between airports. A significant increase over the years was observed in annoyance at a given level of aircraft noise exposure. Furthermore, the type of annoyance scale, the type of contact, and the response percentage were found to be sources of heterogeneity. Of these, only the scale factor could statistically account for the trend, although other findings rule it out as a satisfactory explanation. No evidence was found for increased self-reported noise sensitivity. The results are of importance to the applicability of current exposure-annoyance relationships for aircraft noise and provide a basis for decisions on whether these need to be updated.     

Inhibited spontaneous emission of quantum dots observed in a 3D photonic band gap

We present time-resolved emission experiments of semiconductor quantum dots in silicon 3D inverse-woodpile photonic band gap crystals. A systematic study is made of crystals with a range of pore radii to tune the band gap relative to the emission frequency. The decay rates averaged over all dipole orientations are inhibited by a factor of 10 in the photonic band gap and enhanced up to 2× outside the gap, in agreement with theory. We discuss the effects of spatial inhomogeneity, nonradiative decay, and transition dipole orientations on the observed inhibition in the band gap.     

Probing the out-of-plane distortion of single point defects in atomically thin hexagonal boron nitride at the picometer scale

Crystalline systems often lower their energy by atom displacements from regular high-symmetry lattice sites. We demonstrate that such symmetry lowering distortions can be visualized by ultrahigh resolution transmission electron microscopy even at single point defects. Experimental investigation of structural distortions at the monovacancy defects in suspended bilayers of hexagonal boron nitride (h-BN) accompanied by first-principles calculations reveals a characteristic charge-induced pm symmetry configuration of boron vacancies. This symmetry breaking is caused by interlayer bond reconstruction across the bilayer h-BN at the negatively charged boron vacancy defects and results in local membrane bending at the defect site. This study confirms that boron vacancies are dominantly present in the h-BN membrane.     

Varieties of wonder:: John Wilkins' mathematical magic and the perpetuity of invention

Akin to the mathematical recreations, John Wilkins' Mathematicall Magick ( 1648) elaborates the pleasant, useful and wondrous part of practical mathematics, dealing in particular with its material culture of machines and instruments. We contextualize the Mathematicall Magick by studying its institutional setting and its place within changing conceptions of art, nature, religion and mathematics. We devote special attention to the way Wilkins inscribes mechanical innovations within a discourse of wonder. Instead of treating ‘wonder’ as a monolithic category, we present a typology, showing that wonders were not only recreative, but were meant to inspire Wilkins' readers to new mathematical inventions.     

Largest bounding box,smallest diameter,and related problems on imprecise points

Imprecision of input data is one of the main obstacles that prevent geometric algorithms from being used in practice. We model an imprecise point by a region in which the point must lie. Given a set of imprecise points, we study computing the largest and smallest possible values of various basic geometric measures on point sets, such as the diameter, width, closest pair, smallest enclosing circle, and smallest enclosing bounding box. We give efficient algorithms for most of these problems, and identify the hardness of others.     

Wave propagation with tunneling in a highly discontinuous layered medium

An impulsive plane wave traverses a stratified medium consisting of a large number N of homogeneous isotropic perfectly elastic layers. The directly transmitted wave is greatly reduced by the cumulative effect of scattering loss at each of the many interfaces. However, close to the arrival of the direct wave is a broad pulse, arising from multiple scattering; this pulse does not decay as rapidly as the direct wave and ultimately appears to diffuse about a moving center. The latter process, which is determined by the medium statistics, leads to time delays, effective anisotropy, and apparent attenuation.

The present work may be regarded as an extension of that described by Burridge, White and Papanicolaou (1988) and Burridge and Chang (1989) to allow for tunneling P waves for S-wave incidence beyond the critical angle.

When the reflection coefficients at the interfaces are scaled as 1/√N while N → ∞, and when time is measured in units of vertical travel time across an average layer, numerical solutions of the exact problem show that the shape of the broad transmitted pulse approaches the limiting form given as the solution of a certain integrodifferential equation in accordance with our asymptotic theory.