Detecting similarities among distant homologous proteins by comparison of domain flexibilities

Aim of this work is to assess the informativeness of protein dynamics in the detection of similarities among distant homologous proteins. To this end, an approach to perform large-scale comparisons of protein domain flexibilities is proposed. CONCOORD is confirmed as a reliable method for fast conformational sampling. The root mean square fluctuation of alpha carbon positions in the essential dynamics subspace is employed as a measure of local flexibility and a synthetic index of similarity is presented. The dynamics of a large collection of protein domains from ASTRAL/SCOP40 is analyzed and the possibility to identify relationships, at both the family and the superfamily levels, on the basis of the dynamical features is discussed. The obtained picture is in agreement with the SCOP classification, and furthermore suggests the presence of a distinguishable familiar trend in the flexibility profiles. The results support the complementarity of the dynamical and the structural information, suggesting that information from dynamics analysis can arise from functional similarities, often partially hidden by a static comparison. On the basis of this first test, flexibility annotation can be expected to help in automatically detecting functional similarities otherwise unrecoverable.     

Broadband light trapping with disordered photonic structures in thin‐film silicon solar cells

We theoretically investigate light trapping with disordered 1D photonic structures in thin‐film crystalline silicon solar cells. The disorder is modelled in a finite‐size supercell, which allows the use of rigorous coupled‐wave analysis to calculate the optical properties of the devices and the short‐circuit current density J_sc. The role of the Fourier transform of the photonic pattern in the light trapping is investigated, and the optimal correlation between size and position disorder is found. This result is used to optimize the disorder in a more effective way, using a single parameter. We find that a Gaussian disorder always enhances the device performance with respect to the best ordered configuration. To properly quantify this improvement, we calculate the Lambertian limit to the absorption enhancement for 1D photonic structures in crystalline silicon, following the previous work for the 2D case [M.A. Green, Progr. Photovolt: Res. Appl. 2002; 10 (4), pp. 235–241]. We find that disorder optimization can give a relevant contribution to approach this limit. Finally, we propose an optimal disordered 2D configuration and estimate the maximum short‐circuit current that can be achieved, potentially leading to efficiencies that are comparable with the values of other thin‐film solar cell technologies. Copyright © 2013 John Wiley & Sons, Ltd.     

Ice crushing tests with variable structural flexibility

To learn more on ice crushing phenomena against a compliant stiffened plate structure, near full-scale ice crushing tests were conducted in Aker Arctic test basin with a 1:3 scaled model. The dimensions of the to be crushed ice sheet and the stiffened plate were chosen to present a full size ship or offshore structure steel plating which are designed to withstand the crushing loads of 60 cm thick level ice. A major difference to the crushing tests published earlier in literature was that the compliance of one stiffener could be adjusted. The instrumentation in the plate included both strain gauges for load paths from the plate to the stiffeners and a large tactile sensor for detailed direct crushing pressure distribution measurement. In order to have repeatable and homogeneous model ice properties the ice blocks were manufactured by snow ice technique with low salinity water impregnation under vacuum in the mould. Altogether 22 ice blocks were crushed with different ice velocities and plate compliancy. The well-known line like contact prevailed in continuous crushing. The test data indicates that the crushing load distribution is independent from the underlying plate stiffness distribution and no higher crushing pressure at the location of stiffeners was found.     

Probing small network differences in sulfur‐cured rubber compounds by combining nuclear magnetic resonance and swelling methods

We studied the network structure of elastomers based on polyisoprene, polybutadiene, and their blends in the narrow range of formulations compatible with actual use in the automotive tyre industry. Cross‐link density (CLD) was quantified comparatively by low‐field ¹H multiple quantum time domain nuclear magnetic resonance (MQ TD‐NMR) and by equilibrium swelling technique. The robustness and agreement of the two methods was demonstrated in measuring minute alterations of unfilled vulcanizates beyond the optimum cure time. Comparison with samples where polysulfidic bonds were selectively cleaved also demonstrates that the length of the sulfur chain constituting the cross‐link does not significantly affect residual dipolar coupling. Kraus, Lorenz, and Parks correction for filler restriction on swelling is validated by MQ TD‐NMR, which also allows extracting information on cross‐link distribution not provided by swelling measurement. Cross‐link distributions in the blends were demonstrated to be significantly different from the weighted average of the pure samples, while average proton–proton residual dipolar coupling values correspond. © 2015 Wiley Periodicals, Inc. J. Appl. Polym. Sci. 2015 , 132, 42700.     

Hierarchically Ordered Supramolecular Protein-Polymer Composites with Thermoresponsive Properties

Synthetic macromolecules that can bind and co-assemble with proteins are important for the future development of biohybrid materials. Active systems are further required to create materials that can respond and change their behavior in response to external stimuli. Here we report that stimuli-responsive linear-branched diblock copolymers consisting of a cationic multivalent dendron with a linear thermoresponsive polymer tail at the focal point, can bind and complex Pyrococcus furiosus ferritin protein cages into crystalline arrays. The multivalent dendron structure utilizes cationic spermine units to bind electrostatically on the surface of the negatively charged ferritin cage and the in situ polymerized poly(di(ethylene glycol) methyl ether methacrylate) linear block enables control with temperature. Cloud point of the final product was determined with dynamic light scattering (DLS), and it was shown to be approximately 31 °C at a concentration of 150 mg/L. Complexation of the polymer binder and apoferritin was studied with DLS, small-angle X-ray scattering, and transmission electron microscopy, which showed the presence of crystalline arrays of ferritin cages with a face-centered cubic (fcc Fm3¯m) Bravais lattice where lattice parameter a = 18.6 nm. The complexation process was not temperature dependent but the final complexes had thermoresponsive characteristics with negative thermal expansion.     

Neurocognitive evidence for test equity in an academic listening assessment

Behaviormetrika - The present study explored the potential of a new neurocognitive approach to test equity which integrates evidence from eye-tracking and functional near-infrared spectroscopy with...     

Occurrence and survival of Campylobacter spp. in dairy matrices investigated by viability qPCR

The aim of this study was to investigate the survival of Campylobacter jejuni in dairy matrices by viability qPCR. Survival in UHT milk was examined first and the cheese outbreak strain, C. jejuni 11 218 showed enhanced tendency to become viable but nonculturable (VBNC). It survived for long at different pH values, in raw and fermented milk and cheese. Viability qPCR was also used to examine the occurrence of viable Campylobacter spp. in raw milk, detecting the bacteria in 40.9% of 25 mL samples negative on culture. Results showed that viability qPCR is valuable in estimating Campylobacter risk in dairy products.