Integrated optical cross strip polarizer concept

Passing across an abrupt junction from a thick vertically bimodal waveguide to a thinner single mode segment, guided light can undergo complete destructive interference, provided that the geometry and the phases of the modes in the initial segment are properly adjusted. We propose to employ this effect to realize a simple polarizer configuration, using a strip that is etched from a planar waveguide. A beam of light is made to pass the strip perpendicularly. The light enters from the single mode waveguide outside the strip into the strip segment, which is configured to support two modes. At the end of the strip, apart from reflections, the amount of power that is guided in the following lower segment depends on the local phases of the two modes. These phases are different for TE and TM light, hence we may expect a polarization dependent power transfer, resulting in polarizer performance for a properly selected geometry. The paper describes in detail the modeling of the device in terms of rigorous mode expansion. Design guidelines and tolerance requirements for geometric and material parameters are discussed. For typical Si₃N₄/SiO₂ materials, our calculations predict a peak performance of 34 dB polarization discrimination and 0.3 dB insertion loss for a device with a total length of about 12 m that selects TE polarization at a wavelength of 1.3 m.     

The Dynamics of Power laws: Fitness and Aging in Preferential Attachment Trees

Continuous-time branching processes describe the evolution of a population whose individuals generate a random number of children according to a birth process. Such branching processes can be used to understand preferential attachment models in which the birth rates are linear functions. We are motivated by citation networks, where power-law citation counts are observed as well as aging in the citation patterns. To model this, we introduce fitness and age-dependence in these birth processes. The multiplicative fitness moderates the rate at which children are born, while the aging is integrable, so that individuals receives a finite number of children in their lifetime. We show the existence of a limiting degree distribution for such processes. In the preferential attachment case, where fitness and aging are absent, this limiting degree distribution is known to have power-law tails. We show that the limiting degree distribution has exponential tails for bounded fitnesses in the presence of integrable aging, while the power-law tail is restored when integrable aging is combined with fitness with unbounded support with at most exponential tails. In the absence of integrable aging, such processes are explosive.     

Critical endpoint and analytical phase diagram of attractive hard-core Yukawa spheres

We analytically calculate the gas-liquid critical endpoint (cep) for hard spheres with a Yukawa attraction. This cep is a boundary condition for the existence of a liquid. We use an analytical Helmholtz energy expression for the attractive Yukawa (hard) spheres based on the first-order mean spherical approximation to the attractive Yukawa potential by Tang and Lu (J. Chem. Phys. 1993, 99, 9828). This theory and our analytical simplification of it predict the gas-liquid and fluid-solid phase behavior, as found from computer simulations, very accurately as long as the range 1/kappa of attraction is not too short. We find that the cep is situated at kappasigma approximately 6 and at a contact potential around 2 kT. It follows that a liquid state is only possible when the attraction range is longer than (1/6) of the particle diameter sigma, and the attraction strength is smaller than 2 kT. The liquid region does not span more than 0.6 kT in strength, and there is also a relatively narrow window for the attraction range.     

Altered Mascot search results by changing the <Emphasis Type="Italic">m</Emphasis>/<Emphasis Type="Italic">z</Emphasis> range of MS/MS spectra: analysis and potential applications

The Mascot search algorithm is one of the most commonly used tools for protein identification. Tandem mass spectrometry data searched against a protein sequence database is utilized for identifying peptides and proteins, each reported with a score. Higher Mascot scores are associated with lower chances of random hits. The process of peak selection performed by the search engine prior to the search is a critical aspect of the process. Here, we show that Mascot divides the MS/MS spectrum into fixed m/z regions for peak selection, starting at the lowest m/z value of the peak list. Therefore, modifying the m/z range of the peak lists by insertion of a dummy peak with low m/z value changes the ensemble of peaks used for searching. As a consequence, Mascot peptide scores and search results are altered significantly and a different subset of the peptides present in the sample is identified after processing. We further show that the effect can be exploited and additional proteins and peptides can be identified by repeating the search with a combined set of differently processed files, even when applying identical false-positive rates.     

A conformationally constrained fused tricyclic nisin AB-ring system mimic toward an improved pyrophosphate binder of lipid II

The bacteria-specific membrane component lipid II is essential for bacterial cell wall synthesis. A tricyclic nisin mimic was designed and synthesized in which both thioether moieties were mimicked by an alkane-bridge, as well as the introduction of a third conformational constraint consisting of a macrocyclic lactam-bridge between the N-terminus and the B-ring. The newly designed tricyclic AB-ring mimic was found to bind lipid II since it was able to inhibit nisin-induced membrane leakage in a dose-dependent manner. These results imply that the tricyclic AB-ring mimic may form a novel class of lead structures for the development of nisin-based peptide antibiotics.     

A Single Thermoresponsive Diblock Copolymer Can Form Spheres,Worms or Vesicles in Aqueous Solution

It is well‐known that the self‐assembly of AB diblock copolymers in solution can produce various morphologies depending on the relative volume fraction of each block. Recently, polymerization‐induced self‐assembly (PISA) has become widely recognized as a powerful platform technology for the rational design and efficient synthesis of a wide range of block copolymer nano‐objects. In this study, PISA is used to prepare a new thermoresponsive poly(N‐(2‐hydroxypropyl) methacrylamide)‐poly(2‐hydroxypropyl methacrylate) [PHPMAC‐PHPMA] diblock copolymer. Remarkably, TEM, rheology and SAXS studies indicate that a single copolymer composition can form well‐defined spheres (4 °C), worms (22 °C) or vesicles (50 °C) in aqueous solution. Given that the two monomer repeat units have almost identical chemical structures, this system is particularly well‐suited to theoretical analysis. Self‐consistent mean field theory suggests this rich self‐assembly behavior is the result of the greater degree of hydration of the PHPMA block at lower temperature, which is in agreement with variable temperature ¹H NMR studies.     

Interstrain Variability of Human Vaginal Lactobacillus crispatus for Metabolism of Biogenic Amines and Antimicrobial Activity against Urogenital Pathogens

Lactobacillus crispatus is the dominant species in the vagina of many women. With the potential for strains of this species to be used as a probiotic to help prevent and treat dysbiosis, we investigated isolates from vaginal swabs with Lactobacillus-dominated and a dysbiotic microbiota. A comparative genome analysis led to the identification of metabolic pathways for synthesis and degradation of three major biogenic amines in most strains. However, targeted metabolomic analysis of the production and degradation of biogenic amines showed that certain strains have either the ability to produce or to degrade these compounds. Notably, six strains produced cadaverine, one produced putrescine, and two produced tyramine. These biogenic amines are known to raise vaginal pH, cause malodour, and make the environment more favourable to vaginal pathogens. In vitro experiments confirmed that strains isolated from women with a dysbiotic vaginal microbiota have higher antimicrobial effects against the common urogenital pathogens Escherichia coli and Enterococcus faecium. The results indicate that not all L. crispatus vaginal strains appear suitable for probiotic application and the basis for selection should not be only the overall composition of the vaginal microbiota of the host from which they came, but specific biochemical and genetic traits.     

Factors affecting gas-phase deuterium scrambling in peptide ions and their implications for protein structure determination

In this report, we evaluate the validity of using hydrogen/deuterium exchange in combination with collision-induced dissociation mass spectrometry (CID MS) for the detailed structural and conformational investigation of peptides and proteins. This methodology, in which partly deuterated peptide ions are subjected to collision-induced dissociation in the vacuum of a mass spectrometer, has emerged as a useful tool in structural biology. It may potentially provide quantitatively the extent of deuterium incorporation per individual amino acid in peptides and proteins, thus providing detailed structural information related to protein structure and folding. We report that this general methodology has limitations caused by the fact that the incorporated deuterium atoms migrate prior or during the CID MS analysis. Our data are focused on a variety of transmembrane peptides, incorporated in a lipid bilayer, in which the near-terminal amino acids that anchor at the lipid-water interface are systematically varied. Our findings suggest that, under the experimental conditions we use, the extent of intramolecular hydrogen scrambling is strongly influenced by experimental factors, such as the exact amino acid sequence of the peptide, the nature of the charge carrier, and therefore most likely by the gas-phase structure of the peptide ion. Moreover, the observed scrambling seems to be independent of the nature of the peptide fragment ions (i.e., protonated B and Y' ' ions, and sodiated A and Y' ions). Our results strongly suggest that scrambling may be reduced by using alkali metal cationization instead of protonation in the ionization process.     

Monotonicity for excited random walk in high dimensions

We prove that the drift θ(d, β) for excited random walk in dimension d is monotone in the excitement parameter ${\beta \in [0,1]}$ , when d is sufficiently large. We give an explicit criterion for monotonicity involving random walk Green’s functions, and use rigorous numerical upper bounds provided by Hara (Private communication, 2007) to verify the criterion for d ≥ 9.     

The Flooding Time in Random Graphs

Based on our analysis of the hopcount of the shortest path between two arbitrary nodes in the class G _p (N) of random graphs, the corresponding flooding time is investigated. The flooding time T _N (p) is the minimum time needed to reach all other nodes from one node. We show that, after scaling, the flooding time T _N (p) converges in distribution to the two-fold convolution ^(2*) of the Gumbel distribution function (z)=exp (–e ^–z ), when the link density p _N satisfies Np _N /(log N)³ if N .