Comparison and visualisation of high-resolution transport modelling with aircraft measurements

This article presents a case study of a comparison of an Eulerian chemical transport model (CTM) and Lagrangian chemical model with measurements taken by aircraft. High-resolution Eulerian integrations produce improved point-by-point comparisons between model results and measurements compared to low resolution. The Lagrangian model requires mixing to be introduced in order to model the measurements.

The use of earth observation techniques to improve catchment-scale pollution predictions

Remote sensing can potentially provide information useful in improving pollution transport modelling in agricultural catchments. Realisation of this potential will depend on the availability of the raw data, development of information extraction techniques, and the impact of the assimilation of the derived information into models. High spatial resolution hyperspectral imagery of a farm near Hereford, UK is analysed. A technique is described to automatically identify the soil and vegetation endmembers within a field, enabling vegetation fractional cover estimation. The aerially-acquired laser altimetry is used to produce digital elevation models of the site. At the subfield scale the hypothesis that higher resolution topography will make a substantial difference to contaminant transport is tested using the AGricultural Non-Point Source (AGNPS) model. Slope aspect and direction information are extracted from the topography at different resolutions to study the effects on soil erosion, deposition, runoff and nutrient losses. Field-scale models are often used to model drainage water, nitrate and runoff/sediment loss, but the demanding input data requirements make scaling up to catchment level difficult. By determining the input range of spatial variables gathered from EO data, and comparing the response of models to the range of variation measured, the critical model inputs can be identified. Response surfaces to variation in these inputs constrain uncertainty in model predictions and are presented. Although optical earth observation analysis can provide fractional vegetation cover, cloud cover and semi-random weather patterns can hinder data acquisition in Northern Europe. A Spring and Autumn cloud cover analysis is carried out over seven UK sites close to agricultural districts, using historic satellite image metadata, climate modelling and historic ground weather observations. Results are assessed in terms of probability of acquisition probability and implications for future earth observation missions. (C) 2003 Elsevier Ltd. All rights reserved.

Towards a nutrient export risk matrix approach to managing agricultural pollution at source

A generic Nutrient Export Risk Matrix (NERM) approach is presented. This provides advice to farmers and policy makers on good practice for reducing nutrient loss and is intended to persuade them to implement such measures. Combined with a range of nutrient transport modelling tools and field experiments, NERMs can play an important role in reducing nutrient export from agricultural land. The Phosphorus Export Risk Matrix (PERM) is presented as an example NERM. The PERM integrates hydrological understanding of runoff with a number of agronomic and policy factors into a clear problem-solving framework. This allows farmers and policy makers to visualise strategies for reducing phosphorus loss through proactive land management. The risk Of Pollution is assessed by a series of informed questions relating to farming intensity and practice. This information is combined with the concept of runoff management to point towards simple, practical remedial strategies which do not compromise farmers' ability to obtain sound economic returns from their crop and livestock.

Transport and distribution of lindane and simazine in a riverine environment: measurements in bed sediments and modelling

Aquatic sediments often remove hydrophobic contaminants from fresh waters. The subsequent distribution and concentration of contaminants in bed sediments determines their effect on benthic organisms and the risk of re-entry into the water and/or leaching to groundwater. This study examines the transport of simazine and lindane in aquatic bed sediments with the aim of understanding the processes that determine their depth distribution. Experiments in flume channels (water flow of 10 cm s(-1)) determined the persistence of the compounds in the absence of sediment with (a) de-ionised water and (b) a solution that had been in contact with river sediment. In further experiments with river bed sediments in light and dark conditions, measurements were made of the concentration of the compounds in the overlying water and the development of bacterial/algal biofilms and bioturbation activity. At the end of the experiments, concentrations in sediments and associated pore waters were determined in sections of the sediment at 1 mm resolution down to 5 mm and then at 10 mm resolution to 50 mm depth and these distributions analysed using a sorption-diffusion-degradation model. The fine resolution in the depth profile permitted the detection of a maximum in the concentration of the compounds in the pore water near the surface, whereas concentrations in the sediment increased to a maximum at the surface itself. Experimental distribution coefficients determined from the pore water and sediment concentrations indicated a gradient with depth that was partly explained by an increase in organic matter content and specific surface area of the solids near the interface. The modelling showed that degradation of lindane within the sediment was necessary to explain the concentration profiles, with the optimum agreement between the measured and theoretical profiles obtained with differential degradation in the oxic and anoxic zones. The compounds penetrated to a depth of 40-50 rum over a period of 42 days. (C) 2004 Society of Chemical Industry.

Nitrate transport in Chalk catchments: monitoring, modelling and policy implications

Rising nitrate levels have been observed in UK Chalk catchments in recent decades, with concentrations now approaching or exceeding legislated maximum values in many areas. In response, strategies seeking to contain concentrations through appropriate land management are now in place. However, there is an increasing consensus that Chalk systems, a predominant landscape type over England and indeed northwest Europe, can retard decades of prior nitrate loading within their deep unsaturated zones. Current levels may not fully reflect the long-term impact of present-day practices, and stringent land management controls may not be enough to avert further medium-term rises. This paper discusses these issues in the context of the EU Water Framework Directive, drawing on data from recent experimental work and a new model (INCA-Chalk) that allows the impacts of different land use management practices to be explored. Results strongly imply that timelines for water quality improvement demanded by the Water Framework directive are not realistic for the Chalk, and give an indication of time-scales over which improvements might be achieved. However, important unresolved scientific issues remain, and further monitoring and targeted data collection is recommended to reduce prediction uncertainties and allow cost effective strategies for mitigation to be designed and implemented. (C) 2007 Elsevier Ltd. All rights reserved.

Catchment-scale modelling of flow and nutrient transport in the Chalk unsaturated zone

The unsaturated zone exerts a major control on the delivery of nutrients to Chalk streams, yet flow and transport processes in this complex, dual-porosity medium have remained controversial. A major challenge arises in characterising these processes, both at the detailed mechanistic level and at an appropriate level for inclusion within catchment-scale models for nutrient management. The lowland catchment research (LOCAR) programme in the UK has provided a unique set of comprehensively instrumented groundwater-dominated catchments. Of these, the Pang and Lambourn, tributaries of the Thames near Reading, have been a particular focus for research into subsurface processes and surface water-groundwater interactions. Data from LOCAR and other sources, along with a new dual permeability numerical model of the Chalk, have been used to explore the relative roles of matrix and fracture flow within the unsaturated zone and resolve conflicting hypotheses of response. From the improved understanding gained through these explorations, a parsimonious conceptualisation of the general response of flow and transport within the Chalk unsaturated zone was formulated. This paper summarises the modelling and data findings of these explorations, and describes the integration of the new simplified unsaturated zone representation with a catchment-scale model of nutrients (INCA), resulting in a new model for catchment-scale flow and transport within Chalk systems: INCA-Chalk. This model is applied to the Lambourn, and results, including hindcast and forecast simulations, are presented. These clearly illustrate the decadal time-scales that need to be considered in the context of nutrient management and the EU Water Framework Directive. (C) 2007 Elsevier B.V. All rights reserved.

Modelling sediment supply and transport in the River Lugg: strategies for controlling sediment loads

The River Lugg has particular problems with high sediment loads that have resulted in detrimental impacts on ecology and fisheries. A new dynamic, process-based model of hydrology and sediments (INCA- SED) has been developed and applied to the River Lugg system using an extensive data set from 1995–2008. The model simulates sediment sources and sinks throughout the catchment and gives a good representation of the sediment response at 22 reaches along the River Lugg. A key question considered in using the model is the management of sediment sources so that concentrations and bed loads can be reduced in the river system. Altogether, five sediment management scenarios were selected for testing on the River Lugg, including land use change, contour tillage, hedging and buffer strips. Running the model with parameters altered to simulate these five scenarios produced some interesting results. All scenarios achieved some reduction in sediment levels, with the 40% land use change achieving the best result with a 19% reduction. The other scenarios also achieved significant reductions of between 7% and 9%. Buffer strips produce the best result at close to 9%. The results suggest that if hedge introduction, contour tillage and buffer strips were all applied, sediment reductions would total 24%, considerably improving the current sediment situation. We present a novel cost-effectiveness analysis of our results where we use percentage of land removed from production as our cost function. Given the minimal loss of land associated with contour tillage, hedges and buffer strips, we suggest that these management practices are the most cost-effective combination to reduce sediment loads.

Wind-tunnel modelling of dispersion from a scalar area source in urban-like roughness

A wind-tunnel study was conducted to investigate ventilation of scalars from urban-like geometries at neighbourhood scale by exploring two different geometries a uniform height roughness and a non-uniform height roughness, both with an equal plan and frontal density of λ p = λ f = 25%. In both configurations a sub-unit of the idealized urban surface was coated with a thin layer of naphthalene to represent area sources. The naphthalene sublimation method was used to measure directly total area-averaged transport of scalars out of the complex geometries. At the same time, naphthalene vapour concentrations controlled by the turbulent fluxes were detected using a fast Flame Ionisation Detection (FID) technique. This paper describes the novel use of a naphthalene coated surface as an area source in dispersion studies. Particular emphasis was also given to testing whether the concentration measurements were independent of Reynolds number. For low wind speeds, transfer from the naphthalene surface is determined by a combination of forced and natural convection. Compared with a propane point source release, a 25% higher free stream velocity was needed for the naphthalene area source to yield Reynolds-number-independent concentration fields. Ventilation transfer coefficients w T /U derived from the naphthalene sublimation method showed that, whilst there was enhanced vertical momentum exchange due to obstacle height variability, advection was reduced and dispersion from the source area was not enhanced. Thus, the height variability of a canopy is an important parameter when generalising urban dispersion. Fine resolution concentration measurements in the canopy showed the effect of height variability on dispersion at street scale. Rapid vertical transport in the wake of individual high-rise obstacles was found to generate elevated point-like sources. A Gaussian plume model was used to analyse differences in the downstream plumes. Intensified lateral and vertical plume spread and plume dilution with height was found for the non-uniform height roughness

Modelling the growth and movement of cyanobacteria in river systems

Bloom-forming and toxin-producing cyanobacteria remain a persistent nuisance across the world. Modelling of cyanobacteria in freshwaters is an important tool for understanding their population dynamics and predicting the location and timing of the bloom events in lakes and rivers. In this article, a new deterministic model is introduced which simulates the growth and movement of cyanobacterial blooms in river systems. The model focuses on the mathematical description of the bloom formation, vertical migration and lateral transport of colonies within river environments by taking into account the four major factors that affect the cyanobacterial bloom formation in freshwaters: light, nutrients, temperature and river flow. The model consists of two sub-models: a vertical migration model with respect to growth of cyanobacteria in relation to light, nutrients and temperature; and a hydraulic model to simulate the horizontal movement of the bloom. This article presents the model algorithms and highlights some important model results. The effects of nutrient limitation, varying illumination and river flow characteristics on cyanobacterial movement are simulated. The results indicate that under high light intensities and in nutrient-rich waters colonies sink further as a result of carbohydrate accumulation in the cells. In turbulent environments, vertical migration is retarded by vertical velocity component generated by turbulent shear stress. (c) 2006 Elsevier B.V. All rights reserved.

Fine sediment delivery and transfer in lowland catchments: modelling suspended sediment concentrations in response to hydrological forcing

Fine sediment delivery to and storage in stream channel reaches can disrupt aquatic habitats, impact river hydromorphology, and transfer adsorbed nutrients and pollutants from catchment slopes to the fluvial system. This paper presents a modelling toot for simulating the time-dependent response of the fine sediment system in catchments, using an integrated approach that incorporates both land phase and in-stream processes of sediment generation, storage and transfer. The performance of the model is demonstrated by applying it to simulate in-stream suspended sediment concentrations in two lowland catchments in southern England, the Enborne and the Lambourn, which exhibit contrasting hydrological and sediment responses due to differences in substrate permeability. The sediment model performs well in the Enborne catchment, where direct runoff events are frequent and peak suspended sediment concentrations can exceed 600 mg l(-1). The general trends in the in-stream concentrations in the Lambourn catchment are also reproduced by the model, although the observed concentrations are low (rarely exceeding 50 mg l(-1)) and the background variability in the concentrations is not fully characterized by the model. Direct runoff events are rare in this highly permeable catchment, resulting in a weak coupling between the sediment delivery system and the catchment hydrology. The generic performance of the model is also assessed using a generalized sensitivity analysis based on the parameter bounds identified in the catchment applications. Results indicate that the hydrological parameters contributing to the sediment response include those controlling (1) the partitioning of runoff between surface and soil zone flows and (2) the fractional loss of direct runoff volume prior to channel delivery. The principal sediment processes controlling model behaviour in the simulations are the transport capacity of direct runoff and the in-stream generation, storage and release of the fine sediment fraction. The in-stream processes appear to be important in maintaining the suspended sediment concentrations during low flows in the River Enborne and throughout much of the year in the River Lambourn. Copyright (c) 2007 John Wiley & Sons, Ltd.

Modelling nitrogen fluxes from the land surface to the coastal zone in European systems: the perspective of the INCA project

This paper describes the results and conclusions of the INCA (Integrated Nitrogen Model for European CAtchments) project and sets the findings in the context of the ELOISE (European Land-Ocean Interaction Studies) programme. The INCA project was concerned with the development of a generic model of the major factors and processes controlling nitrogen dynamics in European river systems, thereby providing a tool (a) to aid the scientific understanding of nitrogen transport and retention in catchments and (b) for river-basin management and policy-making. The findings of the study highlight the heterogeneity of the factors and processes controlling nitrogen dynamics in freshwater systems. Nonetheless, the INCA model was able to simulate the in-stream nitrogen concentrations and fluxes observed at annual and seasonal timescales in Arctic, Continental and Maritime-Temperate regimes. This result suggests that the data requirements and structural complexity of the INCA model are appropriate to simulate nitrogen fluxes across a wide range of European freshwater environments. This is a major requirement for the production of coupled fiver-estuary-coastal shelf models for the management of our aquatic environment. With regard to river-basin management, to achieve an efficient reduction in nutrient fluxes from the land to the estuarine and coastal zone, the model simulations suggest that management options must be adaptable to the prevailing environmental and socio-economic factors in individual catchments: 'Blanket approaches' to environmental policy appear too simple. (c) 2004 Elsevier B.V. All rights reserved.

The cumulus-capped boundary layer. I: Modelling transports in the cloud layer

Scalar-flux budgets have been obtained from large-eddy simulations (LESs) of the cumulus-capped boundary layer. Parametrizations of the terms in the budgets are discussed, and two parametrizations for the transport term in the cloud layer are proposed. It is shown that these lead to two models for scalar transports by shallow cumulus convection. One is equivalent to the subsidence detrainment form of convective tendencies obtained from mass-flux parametrizations of cumulus convection. The second is a flux-gradient relationship that is similar in form to the non-local parametrizations of turbulent transports in the dry-convective boundary layer. Using the fluxes of liquid-water potential temperature and total water content from the LES, it is shown that both models are reasonable diagnostic relations between fluxes and the vertical gradients of the mean fields. The LESs used in this study are for steady-state convection and it is possible to treat the fluxes of conserved thermodynamic variables as independent, and ignore the effects of condensation. It is argued that a parametrization of cumulus transports in a model of the cumulus-capped boundary layer should also include an explicit representation of condensation. A simple parametrization of the liquid-water flux in terms of conserved variables is also derived.

EfeO-cupredoxins: major new members of the cupredoxin superfamily with roles in bacterial iron transport

The EfeUOB system of Escherichia coli is a tripartite, low pH, ferrous iron transporter. It resembles the high-affinity iron transporter (Ftr1p-Fet3p) of yeast in that EfeU is homologous to Ftr1p, an integral-membrane iron-permease. However, EfeUOB lacks an equivalent of the Fet3p component—the multicopper oxidase with three cupredoxin-like domains. EfeO and EfeB are periplasmic but their precise roles are unclear. EfeO consists primarily of a C-terminal peptidase-M75 domain with a conserved ‘HxxE’ motif potentially involved in metal binding. The smaller N-terminal domain (EfeO-N) is predicted to be cupredoxin (Cup) like, suggesting a previously unrecognised similarity between EfeO and Fet3p. Our structural modelling of the E. coli EfeO Cup domain identifies two potential metal-binding sites. Site I is predicted to bind Cu2+ using three conserved residues (C41 and 103, and E66) and M101. Of these, only one (C103) is conserved in classical cupredoxins where it also acts as a Cu ligand. Site II most probably binds Fe3+ and consists of four well conserved surface Glu residues. Phylogenetic analysis indicates that the EfeO-Cup domains form a novel Cup family, designated the ‘EfeO-Cup’ family. Structural modelling of two other representative EfeO-Cup domains indicates that different subfamilies employ distinct ligand sets at their proposed metal-binding sites. The ~100 efeO homologues in the bacterial sequence databases are all associated with various iron-transport related genes indicating a common role for EfeO-Cup proteins in iron transport, supporting a new copper-iron connection in biology.

Modelling disease spread and control in networks: implications for plant sciences

Networks are ubiquitous in natural, technological and social systems. They are of increasing relevance for improved understanding and control of infectious diseases of plants, animals and humans, given the interconnectedness of today's world. Recent modelling work on disease development in complex networks shows: the relative rapidity of pathogen spread in scale-free compared with random networks, unless there is high local clustering; the theoretical absence of an epidemic threshold in scale-free networks of infinite size, which implies that diseases with low infection rates can spread in them, but the emergence of a threshold when realistic features are added to networks (e.g. finite size, household structure or deactivation of links); and the influence on epidemic dynamics of asymmetrical interactions. Models suggest that control of pathogens spreading in scale-free networks should focus on highly connected individuals rather than on mass random immunization. A growing number of empirical applications of network theory in human medicine and animal disease ecology confirm the potential of the approach, and suggest that network thinking could also benefit plant epidemiology and forest pathology, particularly in human-modified pathosystems linked by commercial transport of plant and disease propagules. Potential consequences for the study and management of plant and tree diseases are discussed.

Efficient and cost-effective experimental determination of kinetic constants and data: the success of a Bayesian systematic approach to drug transport, receptor binding, continuous culture and cell transport kinetics

Details about the parameters of kinetic systems are crucial for progress in both medical and industrial research, including drug development, clinical diagnosis and biotechnology applications. Such details must be collected by a series of kinetic experiments and investigations. The correct design of the experiment is essential to collecting data suitable for analysis, modelling and deriving the correct information. We have developed a systematic and iterative Bayesian method and sets of rules for the design of enzyme kinetic experiments. Our method selects the optimum design to collect data suitable for accurate modelling and analysis and minimises the error in the parameters estimated. The rules select features of the design such as the substrate range and the number of measurements. We show here that this method can be directly applied to the study of other important kinetic systems, including drug transport, receptor binding, microbial culture and cell transport kinetics. It is possible to reduce the errors in the estimated parameters and, most importantly, increase the efficiency and cost-effectiveness by reducing the necessary amount of experiments and data points measured. (C) 2003 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.