Fibrils and nanotubes assembled from a modified amyloid-β peptide fragment differ in the packing of the same β-sheet building blocks

The peptide AAKLVFF assembles into fibrils in water and nanotubes in methanol. Solid-state NMR data are consistent with fibrils constructed from β-sheet bilayers and nanotubes bounded by a wall of offset β-sheet monolayers. Remarkably distinct morphologies are thus traced to subtle differences in the arrangement of the same fundamental building blocks.

Control of DNA conformation using 3'-S-phosphorothiolate-modified linkages

An in-depth study into the incorporation of multiple 3'-S-phosphorothiolate modifications into oligodeoxynucleotides (ODNs) and their subsequent effect on ODN/DNA and ODN/RNA duplex stability. 3'-S-Phosphorothiolate linkages increase the stability of ODN/RNA duplexes and decrease the stability of ODN/DNA duplexes.

Plane wave discontinuous Galerkin methods for the 2D Helmholtz equation: analysis of the $p$-version

Plane wave discontinuous Galerkin (PWDG) methods are a class of Trefftz-type methods for the spatial discretization of boundary value problems for the Helmholtz operator $-\Delta-\omega^2$, $\omega>0$. They include the so-called ultra weak variational formulation from [O. Cessenat and B. Després, SIAM J. Numer. Anal., 35 (1998), pp. 255–299]. This paper is concerned with the a priori convergence analysis of PWDG in the case of $p$-refinement, that is, the study of the asymptotic behavior of relevant error norms as the number of plane wave directions in the local trial spaces is increased. For convex domains in two space dimensions, we derive convergence rates, employing mesh skeleton-based norms, duality techniques from [P. Monk and D. Wang, Comput. Methods Appl. Mech. Engrg., 175 (1999), pp. 121–136], and plane wave approximation theory.

Plane wave approximation of homogeneous Helmholtz solutions

In this paper, we study the approximation of solutions of the homogeneous Helmholtz equation Δu + ω 2 u = 0 by linear combinations of plane waves with different directions. We combine approximation estimates for homogeneous Helmholtz solutions by generalized harmonic polynomials, obtained from Vekua’s theory, with estimates for the approximation of generalized harmonic polynomials by plane waves. The latter is the focus of this paper. We establish best approximation error estimates in Sobolev norms, which are explicit in terms of the degree of the generalized polynomial to be approximated, the domain size, and the number of plane waves used in the approximations.

Plane wave approximation in linear elasticity

We consider the approximation of solutions of the time-harmonic linear elastic wave equation by linear combinations of plane waves. We prove algebraic orders of convergence both with respect to the dimension of the approximating space and to the diameter of the domain. The error is measured in Sobolev norms and the constants in the estimates explicitly depend on the problem wavenumber. The obtained estimates can be used in the h- and p-convergence analysis of wave-based finite element schemes.

Comment on “A modified leapfrog scheme for shallow water equations” by Wen-Yih Sun and Oliver M.T. Sun

A recent paper published in this journal considers the numerical integration of the shallow-water equations using the leapfrog time-stepping scheme [Sun Wen-Yih, Sun Oliver MT. A modified leapfrog scheme for shallow water equations. Comput Fluids 2011;52:69–72]. The authors of that paper propose using the time-averaged height in the numerical calculation of the pressure-gradient force, instead of the instantaneous height at the middle time step. The authors show that this modification doubles the maximum Courant number (and hence the maximum time step) at which the integrations are stable, doubling the computational efficiency. Unfortunately, the pressure-averaging technique proposed by the authors is not original. It was devised and published by Shuman [5] and has been widely used in the atmosphere and ocean modelling community for over 40 years.

Toward understanding of differences in current cloud retrievals of ARM ground-based measurements

Accurate observations of cloud microphysical properties are needed for evaluating and improving the representation of cloud processes in climate models and better estimate of the Earth radiative budget. However, large differences are found in current cloud products retrieved from ground-based remote sensing measurements using various retrieval algorithms. Understanding the differences is an important step to address uncertainties in the cloud retrievals. In this study, an in-depth analysis of nine existing ground-based cloud retrievals using ARM remote sensing measurements is carried out. We place emphasis on boundary layer overcast clouds and high level ice clouds, which are the focus of many current retrieval development efforts due to their radiative importance and relatively simple structure. Large systematic discrepancies in cloud microphysical properties are found in these two types of clouds among the nine cloud retrieval products, particularly for the cloud liquid and ice particle effective radius. Note that the differences among some retrieval products are even larger than the prescribed uncertainties reported by the retrieval algorithm developers. It is shown that most of these large differences have their roots in the retrieval theoretical bases, assumptions, as well as input and constraint parameters. This study suggests the need to further validate current retrieval theories and assumptions and even the development of new retrieval algorithms with more observations under different cloud regimes.

Comparison of MODIS broadband albedo over an agricultural site with ground measurements and values derived from Earth observation data at a range of spatial scales

Land surface albedo is dependent on atmospheric state and hence is difficult to validate. Over the UK persistent cloud cover and land cover heterogeneity at moderate (km-scale) spatial resolution can also complicate comparison of field-measured albedo with that derived from instruments such as the Moderate Resolution Imaging Spectrometer (MODIS). A practical method of comparing moderate resolution satellite-derived albedo with ground-based measurements over an agricultural site in the UK is presented. Point measurements of albedo made on the ground are scaled up to the MODIS resolution (1 km) through reflectance data obtained at a range of spatial scales. The point measurements of albedo agreed in magnitude with MODIS values over the test site to within a few per cent, despite problems such as persistent cloud cover and the difficulties of comparing measurements made during different years. Albedo values derived from airborne and field-measured data were generally lower than the corresponding satellite-derived values. This is thought to be due to assumptions made regarding the ratio of direct to diffuse illumination used when calculating albedo from reflectance. Measurements of albedo calculated for specific times fitted closely to the trajectories of temporal albedo derived from both Systeme pour l'Observation de la Terre (SPOT) Vegetation (VGT) and MODIS instruments.

Effects of modified atmosphere packaging on quality of ‘Alphonso’ Mangoes

Postharvest quality of Alphonso mangoes (Mangifera indica L) is vital to ensure proper ripening and good quality. 500 g mature green mangoes, were subjected to three pre- packaging hot water dips (20, 30 & 40°C) for 40 min, two packaging films (OPP unperforated and perforated), using three levels of gas concentrations of 25,50 and 75% v/v CO2 treatments (balance N2) and stored at 10°C for 21 days. During the storage period headspace gas composition, weight loss, ascorbic acid, pulp firmness, external fruit colour and overall quality score were measured to determine optimum storage conditions. The most effective postharvest condition was found to be dipping in water maintained at 40°C for 40 min, followed by packaging under 50% CO2 in bags made of unperforated film when compared to mangoes packed under 25 and 75% CO2 which showed deteriorated quality including spoilage and mould. Good keeping quality of at least 21 days was achieved under these conditions, which was much superior to the control samples that showed deterioration after 12 days of storage.

A modified rapid enzymatic microtiter plate assay for the quantification of intracellular γ-aminobutyric acid and succinate semialdehyde in bacterial cells

The GABase assay is widely used to rapidly and accurately quantify levels of extracellular γ-aminobutyric acid (GABA). Here we demonstrate a modification of this assay that enables quantification of intracellular GABA in bacterial cells. Cells are lysed by boiling and ethanolamine-O-sulphate, a GABA transaminase inhibitor is used to distinguish between GABA and succinate semialdehyde.

Simulation of a domestic ground source heat pump system using a three-dimensional numerical borehole heat exchanger model

Common approaches to the simulation of borehole heat exchangers (BHEs) assume heat transfer in circulating fluid and grout to be in a quasi-steady state and ignore fluctuations in fluid temperature due to transport of the fluid around the loop. However, in domestic ground source heat pump (GSHP) systems, the heat pump and circulating pumps switch on and off during a given hour; therefore, the effect of the thermal mass of the circulating fluid and the dynamics of fluid transport through the loop has important implications for system design. This may also be important in commercial systems that are used intermittently. This article presents transient simulation of a domestic GSHP system with a single BHE using a dynamic three-dimensional (3D) numerical BHE model. The results show that delayed response associated with the transit of fluid along the pipe loop is of some significance in moderating swings in temperature during heat pump operation. In addition, when 3D effects are considered, a lower heat transfer rate is predicted during steady operations. These effects could be important when considering heat exchanger design and system control. The results will be used to develop refined two-dimensional models.

Internal wave drag in stratified flow over mountains on a beta plane

The impact of the variation of the Coriolis parameter f on the drag exerted by internal Rossby-gravity waves on elliptical mountains is evaluated using linear theory, assuming constant wind and static stability and a beta-plane approximation. Previous calculations of inertia-gravity wave drag are thus extended in an attempt to establish a connection with existing studies on planetary wave drag, developed primarily for fluids topped by a rigid lid. It is found that the internal wave drag for zonal westerly flow strongly increases relative to that given by the calculation where f is assumed to be a constant, particularly at high latitudes and for mountains aligned meridionally. Drag increases with mountain width for sufficiently wide mountains, reaching values much larger than those valid in the non-rotating limit. This occurs because the drag receives contributions from a low wavenumber range, controlled by the beta effect, which accounts for the drag amplification found here. This drag amplification is shown to be considerable for idealized analogues of real mountain ranges, such as the Himalayas and the Rocky mountains, and comparable to the barotropic Rossby wave drag addressed in previous studies.

Ground-based aerosol optical depth trends at three high-altitude sites in Switzerland and Southern Germany from 1995–2010

Ground-based aerosol optical depth (AOD) climatologies at three high-altitude sites in Switzerland (Jungfraujoch and Davos) and Southern Germany (Hohenpeissenberg) are updated and re-calibrated for the period 1995 – 2010. In addition, AOD time-series are augmented with previously unreported data, and are homogenized for the first time. Trend analysis revealed weak AOD trends (λ = 500 nm) at Jungfraujoch (JFJ; +0.007 decade-1), Davos (DAV; +0.002 decade-1) and Hohenpeissenberg (HPB; -0.011 decade-1) where the JFJ and HPB trends were statistically significant at the 95% and 90% confidence levels. However, a linear trend for the JFJ 1995 – 2005 period was found to be more appropriate than for 1995 – 2010 due to the influence of stratospheric AOD which gave a trend -0.003 decade-1 (significant at 95% level). When correcting for a recently available stratospheric AOD time-series, accounting for Pinatubo (1991) and more recent volcanic eruptions, the 1995 – 2010 AOD trends decreased slightly at DAV and HPB but remained weak at +0.000 decade-1 and -0.013 decade-1 (significant at 95% level). The JFJ 1995 – 2005 AOD time-series similarly decreased to -0.003 decade-1 (significant at 95% level). We conclude that despite a more detailed re40 analysis of these three time-series, which have been extended by five years to the end of 2010, a significant decrease in AOD at these three high-altitude sites has still not been observed.