The hydraulic description of vegetated river channels: the weaknesses of existing formulations and emerging alternatives

Currently, many of the methods used to predict the effect of vegetation on river flow suffer from one or both of the following problems: (1) a strong dependence on parameters that have a poor physical basis and which are only readily determined using empirical means; and (2) a poor conceptual basis, in terms of the way they represent the effects of vegetation on the flow, especially in higher dimensionality numerical models. This limits their contribution to problems that extend beyond basic hydraulic prediction (e.g., of water levels) to ecosystem understanding. In this study, we show how use of coupled biomechanical–hydraulic models may lead to a much-improved representation of a range of open-channel flow processes. Preliminary experiments over hypothetical vegetation canopies are producing very encouraging results and may provide the means for an improved representation of vegetation in higher dimensionality numerical models that may result in a better justification and more reliable identification of the conveyance parameters needed for both flood identification and the characterization of habitat

High-resolution numerical modelling of flow-vegetation interactions

In this paper, we present and apply a new three-dimensional model for the prediction of canopy-flow and turbulence dynamics in open-channel flow. The approach uses a dynamic immersed boundary technique that is coupled in a sequentially staggered manner to a large eddy simulation. Two different biomechanical models are developed depending on whether the vegetation is dominated by bending or tensile forces. For bending plants, a model structured on the Euler–Bernoulli beam equation has been developed, whilst for tensile plants, an N-pendula model has been developed. Validation against flume data shows good agreement and demonstrates that for a given stem density, the models are able to simulate the extraction of energy from the mean flow at the stem-scale which leads to the drag discontinuity and associated mixing layer

Coherent flow structures in a depth-limited flow over a gravel surface : the role of near-bed turbulance and influence of Reynolds number

In gravel bed rivers, the microtopography of the bed exerts a significant effect on the generation of turbulent flow structures. Although field and laboratory measurements have indicated that flows over gravel beds contain coherent macroturbulent flow structures, the origin of these phenomena, and their relationship to the ensemble of individual roughness elements forming the bed, is not quantitatively well understood. Here we report upon a flume experiment in which flow over a gravel surface is quantified through the application of digital particle imaging velocimetry, which allows study of the downstream and vertical components of velocity over the entire flow field. The results indicate that as the Reynolds number increases (1) the visual distinctiveness of the coherent flow structures becomes more defined, (2) the upstream slope of the structures increases, and (3) the turbulence intensity of the structures increases. Analysis of the mean velocity components, the turbulence intensity, and the flow structure using quadrant analysis demonstrates that these large-scale turbulent structures originate from flow interactions with the bed topography. Detection of the dominant temporal length scales through wavelet analysis enables calculation of mean separation zone lengths associated with the gravel roughness through standard scaling laws. The calculated separation zone lengths demonstrate that wake flapping is a dominant mechanism in the production of large-scale coherent flow structures in gravel bed rivers. Thus, we show that coherent flow structures over gravels owe their origin to bed-generated turbulence and that large-scale outer layer structures are the result of flow-topography interactions in the near-bed region associated with wake flapping

Does the canopy mixing layer model apply to highly flexible aquatic vegetation? Insights from numerical modelling

Vegetation is a characteristic feature of shallow aquatic flows such as rivers, lakes and coastal waters. Flow through and above aquatic vegetation canopies is commonly described using a canopy mixing layer analogy which provides a canonical framework for assessing key hydraulic characteristics such as velocity profiles, large-scale coherent turbulent structures and mixing and transport processes for solutes and sediments. This theory is well developed for the case of semi-rigid terrestrial vegetation and has more recently been applied to the case of aquatic vegetation. However, aquatic vegetation often displays key differences in morphology and biomechanics to terrestrial vegetation due to the different environment it inhabits. Here we investigate the effect of plant morphology and biomechanical properties on flow–vegetation interactions through the application of a coupled LES-biomechanical model. We present results from two simulations of aquatic vegetated flows: one assuming a semi-rigid canopy and the other a highly flexible canopy and provide a comparison of the associated flow regimes. Our results show that while both cases display canopy mixing layers, there are also clear differences in the shear layer characteristics and turbulent processes between the two, suggesting that the semi-rigid approximation may not provide a complete representation of flow–vegetation interactions

Reconstruction of subgrid scale topographic variability and its effect upon the spatial structure of three dimensional river flow

A new approach to describing the associated topography at different scales in computational fluid dynamic applications to gravel bed rivers was developed. Surveyed topographic data were interpolated, using geostatistical methods, into different spatial discretizations, and grain-size data were used with fractal methods to reconstruct the microtopography at scales finer than the measurement (subgrid) scale. The combination of both scales of topography was then used to construct the spatial discretization of a three-dimensional finite volume Computational Fluid Dynamics (CFD) scheme where the topography was included using a mass flux scaling approach. The method was applied and tested on a 15 m stretch of Solfatara Creek, Wyoming, United States, using spatially distributed elevation and grain-size data. Model runs were undertaken for each topography using a steady state solution. This paper evaluates the impact of the model spatial discretization and additional reconstructed-variability upon the spatial structure of predicted three-dimensional flow. The paper shows how microtopography modifies the spatial structure of predicted flow at scales finer than measurement scale in terms of variability whereas the characteristic scale of predicted flow is determined by the CFD scale. Changes in microtopography modify the predicted mean velocity value by 3.6% for a mesh resolution of 5 cm whereas a change in the computational scale modifies model results by 60%. The paper also points out how the spatial variability of predicted velocities is determined by the topographic complexity at different scales of the input topographic model

Antithrombin Budapest 3 An antithrombin variant with reduced heparin affinity resulting from the substitution L99F

AbstractThe molecular basis and functional properties of a variant antithrombin (AT) protein. AT Budapest 3, were studied. A single base substitution was identified in codon 99, CTC→TTC, altering the normal leucine to phenylalanine. The proband presented with a history of venous thrombotic disease and was found to be homozygous for the mutation. The variant protein demonstrated reduced heparin affinity and reduced antiproteinase activity in the presence of either unfractionated heparin or the AT-binding heparin pentasaccharide, when compared to normal AT. A small change in the isoelectric point was also identified. The substituted amino acid residue of AT Budapest 3 is located near to the proposed AT heparin binding site, and it is suggested that reduced heparin affinity of the variant protein may result from substitution-induced distortion of positive charge geometry in the binding site and/or changes in its position relative to the rest of the inhibitor molecule

Large scale numerical investigation of excited states in poly(phenylene)

A density matrix renormalisation group scheme is developed, allowing for the first time essentially exact numerical solutions for the important excited states of a realistic semi-empirical model for oligo-phenylenes. By monitoring the evolution of the energies with chain length and comparing them to the experimental absorption peaks of oligomers and thin films, we assign the four characteristic absorption peaks of phenyl-based polymers. We also determine the position and nature of the nonlinear optical states in this model.Comment: RevTeX, 10 pages, 4 eps figures included using eps

DXA-derived hip shape is related to osteoarthritis:findings from in the MrOS cohort

BF conducted this research whilst on a clinical research primer fellowship awarded by the Elizabeth Blackwell Institute, University of Bristol, UK. This study was funded by Arthritis Research UK project grant ref 20244. CG is funded by Arthritis Research UK grant ref 20000. The Osteoporotic Fractures in Men (MrOS) Study is supported by National Institutes of Health funding. The following institutes provide support: the National Institute on Aging (NIA), the National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS), the National Center for Advancing Translational Sciences (NCATS), and NIH Roadmap for Medical Research under the following grant numbers: R01 AR052000, K24 AR048841, U01 AG027810, U01 AG042124, U01 AG042139, U01 AG042140, U01 AG042143, U01 AG042145, U01 AG042168, U01 AR066160, and UL1 TR000128.Peer reviewedPostprin

Coupled-channel effective field theory and proton-7^7Li scattering

We apply the renormalisation group (RG) to analyse scattering by short-range forces in systems with coupled channels. For two S-wave channels, we find three fixed points, corresponding to systems with zero, one or two bound or virtual states at threshold. We use the RG to determine the power countings for the resulting effective field theories. In the case of a single low-energy state, the resulting theory takes the form of an effective-range expansion in the strongly interacting channel. We also extend the analysis to include the effects of the Coulomb interaction between charged particles. The approach is then applied to the coupled $p+{^7}$Li and $n+{^7}$Be channels which couple to a $J^P=2^-$ state of $^8$Be very close to the $n+{^7}$Be threshold. At next-to-leading order, we are able to get a good description of the $p+{^7}$Li phase shift and the ${^7}$Be(n,p)${^7}$Li cross section using four parameters. Fits at one order higher are similarly good but the available data are not sufficient to determine all five parameters uniquely.Comment: 22 pages, 2 figures, RevTeX4, typos corrected, accepted for publication in European Physical Journal