Function of the hydration layer around an antifreeze protein revealed by atomistic molecular dynamics simulations

Atomistic molecular dynamics simulations are used to investigate the mechanism by which the antifreeze protein from the spruce budworm, Choristoneura fumiferana, binds to ice. Comparison of structural and dynamic properties of the water around the three faces of the triangular prism-shaped protein in aqueous solution reveals that at low temperature the water structure is ordered and the dynamics slowed down around the ice-binding face of the protein, with a disordering effect observed around the other two faces. These results suggest a dual role for the solvation water around the protein. The preconfigured solvation shell around the ice-binding face is involved in the initial recognition and binding of the antifreeze protein to ice by lowering the barrier for binding and consolidation of the protein:ice interaction surface. Thus, the antifreeze protein can bind to the molecularly rough ice surface by becoming actively involved in the formation of its own binding site. Also, the disruption of water structure around the rest of the protein helps prevent the adsorbed protein becoming covered by further ice growth.

Effective e-learning integration with traditional learning in a blended learning environment

E-Learning is an emerging tool that uses advanced technology to provide training and development in higher education and within industry. Its rapid growth has been facilitated by the Internet and the massive opportunities in global education. The aim of this study is to consider how effective and efficient e-learning is when integrated with traditional learning in a blended learning environment. The study will provide a comparison between purist ELearning and Blended learning environment. The paper will also provide directions for the blended learning environment which can be used by all the three main stakeholder student, tutors and institution to make strategic decision about the learning and teaching initiatives. The paper concludes that blended learning approaches offer the most flexible and scalable route to E-Learning.

Acoustic trapped modes in a three-dimensional waveguide of slowly varying cross section

In this paper we develop an asymptotic scheme to approximate the trapped mode solutions to the time harmonic wave equation in a three-dimensional waveguide with a smooth but otherwise arbitrarily shaped cross section and a single, slowly varying `bulge', symmetric in the longitudinal direction. Extending the work in Biggs (2012), we first employ a WKBJ-type ansatz to identify the possible quasi-mode solutions which propagate only in the thicker region, and hence find a finite cut-on region of oscillatory behaviour and asymptotic decay elsewhere. The WKBJ expansions are used to identify a turning point between the cut-on and cut-on regions. We note that the expansions are nonuniform in an interior layer centred on this point, and we use the method of matched asymptotic expansions to connect the cut-on and cut-on regions within this layer. The behaviour of the expansions within the interior layer then motivates the construction of a uniformly valid asymptotic expansion. Finally, we use this expansion and the symmetry of the waveguide around the longitudinal centre, x = 0, to extract trapped mode wavenumbers, which are compared with those found using a numerical scheme and seen to be extremely accurate, even to relatively large values of the small parameter.

A method for estimating the turbulent kinetic energy dissipation rate from a vertically pointing Doppler lidar, and independent evaluation from balloon-borne in situ measurements

A method of estimating dissipation rates from a vertically pointing Doppler lidar with high temporal and spatial resolution has been evaluated by comparison with independent measurements derived from a balloon-borne sonic anemometer. This method utilizes the variance of the mean Doppler velocity from a number of sequential samples and requires an estimate of the horizontal wind speed. The noise contribution to the variance can be estimated from the observed signal-to-noise ratio and removed where appropriate. The relative size of the noise variance to the observed variance provides a measure of the confidence in the retrieval. Comparison with in situ dissipation rates derived from the balloon-borne sonic anemometer reveal that this particular Doppler lidar is capable of retrieving dissipation rates over a range of at least three orders of magnitude. This method is most suitable for retrieval of dissipation rates within the convective well-mixed boundary layer where the scales of motion that the Doppler lidar probes remain well within the inertial subrange. Caution must be applied when estimating dissipation rates in more quiescent conditions. For the particular Doppler lidar described here, the selection of suitably short integration times will permit this method to be applicable in such situations but at the expense of accuracy in the Doppler velocity estimates. The two case studies presented here suggest that, with profiles every 4 s, reliable estimates of ϵ can be derived to within at least an order of magnitude throughout almost all of the lowest 2 km and, in the convective boundary layer, to within 50%. Increasing the integration time for individual profiles to 30 s can improve the accuracy substantially but potentially confines retrievals to within the convective boundary layer. Therefore, optimization of certain instrument parameters may be required for specific implementations.

Numerical modeling of the propagation environment in the atmospheric boundary layer over the Persian Gulf

Strong vertical gradients at the top of the atmospheric boundary layer affect the propagation of electromagnetic waves and can produce radar ducts. A three-dimensional, time-dependent, nonhydrostatic numerical model was used to simulate the propagation environment in the atmosphere over the Persian Gulf when aircraft observations of ducting had been made. A division of the observations into high- and low-wind cases was used as a framework for the simulations. Three sets of simulations were conducted with initial conditions of varying degrees of idealization and were compared with the observations taken in the Ship Antisubmarine Warfare Readiness/Effectiveness Measuring (SHAREM-115) program. The best results occurred with the initialization based on a sounding taken over the coast modified by the inclusion of data on low-level atmospheric conditions over the Gulf waters. The development of moist, cool, stable marine internal boundary layers (MIBL) in air flowing from land over the waters of the Gulf was simulated. The MIBLs were capped by temperature inversions and associated lapses of humidity and refractivity. The low-wind MIBL was shallower and the gradients at its top were sharper than in the high-wind case, in agreement with the observations. Because it is also forced by land–sea contrasts, a sea-breeze circulation frequently occurs in association with the MIBL. The size, location, and internal structure of the sea-breeze circulation were realistically simulated. The gradients of temperature and humidity that bound the MIBL cause perturbations in the refractivity distribution that, in turn, lead to trapping layers and ducts. The existence, location, and surface character of the ducts were well captured. Horizontal variations in duct characteristics due to the sea-breeze circulation were also evident. The simulations successfully distinguished between high- and low-wind occasions, a notable feature of the SHAREM-115 observations. The modeled magnitudes of duct depth and strength, although leaving scope for improvement, were most encouraging.

Reactive Halogens in the Marine Boundary Layer (RHaMBLe): the tropical North Atlantic experiments

The NERC UK SOLAS-funded Reactive Halogens in the Marine Boundary Layer (RHaMBLe) programme comprised three field experiments. This manuscript presents an overview of the measurements made within the two simultaneous remote experiments conducted in the tropical North Atlantic in May and June 2007. Measurements were made from two mobile and one ground-based platforms. The heavily instrumented cruise D319 on the RRS Discovery from Lisbon, Portugal to São Vicente, Cape Verde and back to Falmouth, UK was used to characterise the spatial distribution of boundary layer components likely to play a role in reactive halogen chemistry. Measurements onboard the ARSF Dornier aircraft were used to allow the observations to be interpreted in the context of their vertical distribution and to confirm the interpretation of atmospheric structure in the vicinity of the Cape Verde islands. Long-term ground-based measurements at the Cape Verde Atmospheric Observatory (CVAO) on São Vicente were supplemented by long-term measurements of reactive halogen species and characterisation of additional trace gas and aerosol species during the intensive experimental period. This paper presents a summary of the measurements made within the RHaMBLe remote experiments and discusses them in their meteorological and chemical context as determined from these three platforms and from additional meteorological analyses. Air always arrived at the CVAO from the North East with a range of air mass origins (European, Atlantic and North American continental). Trace gases were present at stable and fairly low concentrations with the exception of a slight increase in some anthropogenic components in air of North American origin, though NOx mixing ratios during this period remained below 20 pptv (note the non-IUPAC adoption in this manuscript of pptv and ppbv, equivalent to pmol mol−1 and nmol mol−1 to reflect common practice). Consistency with these air mass classifications is observed in the time series of soluble gas and aerosol composition measurements, with additional identification of periods of slightly elevated dust concentrations consistent with the trajectories passing over the African continent. The CVAO is shown to be broadly representative of the wider North Atlantic marine boundary layer; measurements of NO, O3 and black carbon from the ship are consistent with a clean Northern Hemisphere marine background. Aerosol composition measurements do not indicate elevated organic material associated with clean marine air. Closer to the African coast, black carbon and NO levels start to increase, indicating greater anthropogenic influence. Lower ozone in this region is possibly associated with the increased levels of measured halocarbons, associated with the nutrient rich waters of the Mauritanian upwelling. Bromide and chloride deficits in coarse mode aerosol at both the CVAO and on D319 and the continuous abundance of inorganic gaseous halogen species at CVAO indicate significant reactive cycling of halogens. Aircraft measurements of O3 and CO show that surface measurements are representative of the entire boundary layer in the vicinity both in diurnal variability and absolute levels. Above the inversion layer similar diurnal behaviour in O3 and CO is observed at lower mixing ratios in the air that had originated from south of Cape Verde, possibly from within the ITCZ. ECMWF calculations on two days indicate very different boundary layer depths and aircraft flights over the ship replicate this, giving confidence in the calculated boundary layer depth.

Think local, act local? Issues of co-ordination and integration in Local Agenda 21

The political response to the complex package of environmental problems which threaten the future of our planet has been to introduce a new agenda of environmental action based on the principles of sustainability and subsidiarity. This has been crystallised in world agreements signed at the Earth Summit in Rio. One of these, Agenda 21, calls for the governments and communities of the world to prepare action plans for their areas which can build consensus between the various stakeholder groups and feed the principles of sustainable development back into their policies and day-to-day practices. This paper explores the experience of Local Agenda 21 type processes at three levels in the South East of England: the regional, county (sub-regional) and local level. In particular it undertakes a critical appraisal of the success of these participatory and consensus-building exercises in developing an integrated and co-ordinated approach to environmental action planning. It concludes that, although much useful work has been done in raising awareness and modifying policy and practice, there are significant cultural and institutional barriers which are hindering progress.

On the numerical integration of a class of singular perturbation problems

A three-point difference scheme recently proposed in Ref. 1 for the numerical solution of a class of linear, singularly perturbed, two-point boundary-value problems is investigated. The scheme is derived from a first-order approximation to the original problem with a small deviating argument. It is shown here that, in the limit, as the deviating argument tends to zero, the difference scheme converges to a one-sided approximation to the original singularly perturbed equation in conservation form. The limiting scheme is shown to be stable on any uniform grid. Therefore, no advantage arises from using the deviating argument, and the most accurate and efficient results are obtained with the deviation at its zero limit.

Boundary-layer friction in midlatitude cyclone

Results from an idealized three-dimensional baroclinic life-cycle model are interpreted in a potential vorticity (PV) framework to identify the physical mechanisms by which frictional processes acting in the atmospheric boundary layer modify and reduce the baroclinic development of a midlatitude storm. Considering a life cycle where the only non-conservative process acting is boundary-layer friction, the rate of change of depth-averaged PV within the boundary layer is governed by frictional generation of PV and the flux of PV into the free troposphere. Frictional generation of PV has two contributions: Ekman generation, which is directly analogous to the well-known Ekman-pumping mechanism for barotropic vortices, and baroclinic generation, which depends on the turning of the wind in the boundary layer and low-level horizontal temperature gradients. It is usually assumed, at least implicitly, that an Ekman process of negative PV generation is the mechanism whereby friction reduces the strength and growth rates of baroclinic systems. Although there is evidence for this mechanism, it is shown that baroclinic generation of PV dominates, producing positive PV anomalies downstream of the low centre, close to developing warm and cold fronts. These PV anomalies are advected by the large-scale warm conveyor belt flow upwards and polewards, fluxed into the troposphere near the warm front, and then advected westwards relative to the system. The result is a thin band of positive PV in the lower troposphere above the surface low centre. This PV is shown to be associated with a positive static stability anomaly, which Rossby edge wave theory suggests reduces the strength of the coupling between the upper- and lower-level PV anomalies, thereby reducing the rate of baroclinic development. This mechanism, which is a result of the baroclinic dynamics in the frontal regions, is in marked contrast with simple barotropic spin-down ideas. Finally we note the implications of these frictionally generated PV anomalies for cyclone forecasting.

Comparison of different boundary layer surface schemes using single point micrometeorological field data

 In the last decade, a vast number of land surface schemes has been designed for use in global climate models, atmospheric weather prediction, mesoscale numerical models, ecological models, and models of global changes. Since land surface schemes are designed for different purposes they have various levels of complexity in the treatment of bare soil processes, vegetation, and soil water movement. This paper is a contribution to a little group of papers dealing with intercomparison of differently designed and oriented land surface schemes. For that purpose we have chosen three schemes for classification: i) global climate models, BATS (Dickinson et al., 1986; Dickinson et al., 1992); ii) mesoscale and ecological models, LEAF (Lee, 1992) and iii) mesoscale models, LAPS (Mihailović, 1996; Mihailović and Kallos, 1997; Mihailović et al., 1999) according to the Shao et al. (1995) classification. These schemes were compared using surface fluxes and leaf temperature outputs obtained by time integrations of data sets derived from the micrometeorological measurements above a maize field at an experimental site in De Sinderhoeve (The Netherlands) for 18 August, 8 September, and 4 October 1988. Finally, comparison of the schemes was supported applying a simple statistical analysis on the surface flux outputs.

Tillage and herbicide treatments with inter-row cultivation influence weed densities and yield of three industrial crops

Field experiments were conducted in northern Greece in 2003 and 2004 to evaluate effects of tillage regimes (moldboard plowing, chisel plowing, and rotary tilling), cropping sequences(continuous cotton, cotton-sugar beet rotation,and continuous tobacco) and herbicide treatments with inter-row hand hoeing on weed population densities. Total weed densities were not affected by tillage treatment except that of barnyardgrass (Echinochloa crus-galli), which increased only in moldboard plowing treated plots during 2003. Redroot pigweed (Amaranthus retroflexus)and black nightshade (Solanum nigrum) densities were reduced in continuous cotton, while purple nutsedge (Cyperus rotundus), E. crus-galli, S. nigrum, and johnsongras(Sorghum halepense) densities were reduced in tobacco. A. retroflexus and S. nigrum were effectively controlled by all herbicide treatments with inter-row hand hoeing,whereas E. crus-galli was effectively reduced by herbicides applied to cotton and tobacco. S. halepense density reduction was a result of herbicide applied to tobacco with inter-row hand hoeing. Yield of all crops was higher under moldboard plowing and herbicide treatments. Pre-sowing and pre-emergence herbicide treatments in cotton and pre-transplant in tobacco integrated with inter-row cultivation resulted in efficient control of annual weed species and good crop yields. These observations are of practical relevance to crop selection by farmers in order to maintain weed populations at economically acceptable densities through the integration of various planting dates, sustainable herbicide use and inter-row cultivation; tools of great importance in integrated weed management systems. Keywords: cropping sequence, herbicide, integrated weed management, inter-row cultivation,tillage.

Measuring significant variability characteristics: An assessment of three UK renewables

The variability of renewable energy is widely recognised as a challenge for integrating high levels of renewable generation into electricity systems. However, to explore its implications effectively, variability itself should first be clearly understood. This is particularly true for national electricity systems with high planned penetration of renewables and limited interconnection such as the UK. Variability cannot be considered as a distinct resource property with a single measurable parameter, but is a multi-faceted concept best described by a range of distinct characteristics. This paper identifies relevant characteristics of variability, and considers their implications for energy research. This is done through analysis of wind, solar and tidal current resources, with a primary focus on the Bristol Channel region in the UK. The relationship with electricity demand is considered, alongside the potential benefits of resource diversity. Analysis is presented in terms of persistence, distribution, frequency and correlation between supply and demand. Marked differences are seen between the behaviours of the individual resources, and these give rise to a range of different implications for system integration. Wind shows strong persistence and a useful seasonal pattern, but also a high spread in energy levels at timescales beyond one or two days. The solar resource is most closely correlated with electricity demand, but is undermined by night-time zero values and an even greater spread of monthly energy delivered than wind. In contrast, the tidal resource exhibits very low persistence, but also much greater consistency in energy values assessed across monthly time scales. Whilst this paper focuses primarily on the behaviour of resources, it is noted that discrete variability characteristics can be related to different system impacts. Persistence and predictability are relevant for system balancing, whereas statistical distribution is more relevant when exploring issues of asset utilisation and energy curtailment. Areas of further research are also identified, including the need to assess the value of predictability in relation to other characteristics.

Comparison of different boundary layer surface schemes using single point micrometeorological field data

 In the last decade, a vast number of land surface schemes has been designed for use in global climate models, atmospheric weather prediction, mesoscale numerical models, ecological models, and models of global changes. Since land surface schemes are designed for different purposes they have various levels of complexity in the treatment of bare soil processes, vegetation, and soil water movement. This paper is a contribution to a little group of papers dealing with intercomparison of differently designed and oriented land surface schemes. For that purpose we have chosen three schemes for classification: i) global climate models, BATS (Dickinson et al., 1986; Dickinson et al., 1992); ii) mesoscale and ecological models, LEAF (Lee, 1992) and iii) mesoscale models, LAPS (Mihailović, 1996; Mihailović and Kallos, 1997; Mihailović et al., 1999) according to the Shao et al. (1995) classification. These schemes were compared using surface fluxes and leaf temperature outputs obtained by time integrations of data sets derived from the micrometeorological measurements above a maize field at an experimental site in De Sinderhoeve (The Netherlands) for 18 August, 8 September, and 4 October 1988. Finally, comparison of the schemes was supported applying a simple statistical analysis on the surface flux outputs.

Some numerical experiments on the effect of the variation of static stability in two-layer quasi-geostrophic models

A method to solve a quasi-geostrophic two-layer model including the variation of static stability is presented. The divergent part of the wind is incorporated by means of an iterative procedure. The procedure is rather fast and the time of computation is only 60–70% longer than for the usual two-layer model. The method of solution is justified by the conservation of the difference between the gross static stability and the kinetic energy. To eliminate the side-boundary conditions the experiments have been performed on a zonal channel model. The investigation falls mainly into three parts: The first part (section 5) contains a discussion of the significance of some physically inconsistent approximations. It is shown that physical inconsistencies are rather serious and for these inconsistent models which were studied the total kinetic energy increased faster than the gross static stability. In the next part (section 6) we are studying the effect of a Jacobian difference operator which conserves the total kinetic energy. The use of this operator in two-layer models will give a slight improvement but probably does not have any practical use in short periodic forecasts. It is also shown that the energy-conservative operator will change the wave-speed in an erroneous way if the wave-number or the grid-length is large in the meridional direction. In the final part (section 7) we investigate the behaviour of baroclinic waves for some different initial states and for two energy-consistent models, one with constant and one with variable static stability. According to the linear theory the waves adjust rather rapidly in such a way that the temperature wave will lag behind the pressure wave independent of the initial configuration. Thus, both models give rise to a baroclinic development even if the initial state is quasi-barotropic. The effect of the variation of static stability is very small, qualitative differences in the development are only observed during the first 12 hours. For an amplifying wave we will get a stabilization over the troughs and an instabilization over the ridges.

A method to diagnose boundary-layer type using Doppler lidar

A new technique for objective classification of boundary layers is applied to ground-based vertically pointing Doppler lidar and sonic anemometer data. The observed boundary layer has been classified into nine different types based on those in the Met Office ‘Lock’ scheme, using vertical velocity variance and skewness, along with attenuated backscatter coefficient and surface sensible heat flux. This new probabilistic method has been applied to three years of data from Chilbolton Observatory in southern England and a climatology of boundary-layer type has been created. A clear diurnal cycle is present in all seasons. The most common boundary-layer type is stable with no cloud (30.0% of the dataset). The most common unstable type is well mixed with no cloud (15.4%). Decoupled stratocumulus is the third most common boundary-layer type (10.3%) and cumulus under stratocumulus occurs 1.0% of the time. The occurrence of stable boundary-layer types is much higher in the winter than the summer and boundary-layer types capped with cumulus cloud are more prevalent in the warm seasons. The most common diurnal evolution of boundary-layer types, occurring on 52 days of our three-year dataset, is that of no cloud with the stability changing from stable to unstable during daylight hours. These results are based on 16393 hours, 62.4% of the three-year dataset, of diagnosed boundary-layer type. This new method is ideally suited to long-term evaluation of boundary-layer type parametrisations in weather forecast and climate models.