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  • Journal article
    Clare MCA, Wallwork JG, Kramer SC, Weller H, Cotter CJ, Piggott MDet al., 2022,

    Multi-scale hydro-morphodynamic modelling using mesh movement methods

    , GEM: International Journal on Geomathematics, Vol: 13, ISSN: 1869-2672

    Hydro-morphodynamic modelling is an important tool that can be used in the protection of coastal zones. The models can be required to resolve spatial scales ranging from sub-metre to hundreds of kilometres and are computationally expensive. In this work, we apply mesh movement methods to a depth-averaged hydro-morphodynamic model for the first time, in order to tackle both these issues. Mesh movement methods are particularly well-suited to coastal problems as they allow the mesh to move in response to evolving flow and morphology structures. This new capability is demonstrated using test cases that exhibit complex evolving bathymetries and have moving wet-dry interfaces. In order to be able to simulate sediment transport in wet-dry domains, a new conservative discretisation approach has been developed as part of this work, as well as a sediment slide mechanism. For all test cases, we demonstrate how mesh movement methods can be used to reduce discretisation error and computational cost. We also show that the optimum parameter choices in the mesh movement monitor functions are fairly predictable based upon the physical characteristics of the test case, facilitating the use of mesh movement methods on further problems.

  • Journal article
    Warder SC, Piggott MD, 2022,

    Optimal experiment design for a bottom friction parameter estimation problem

    , GEM - International Journal on Geomathematics, Vol: 13, ISSN: 1869-2672

    <jats:title>Abstract</jats:title><jats:p>Calibration with respect to a bottom friction parameter is standard practice within numerical coastal ocean modelling. However, when this parameter is assumed to vary spatially, any calibration approach must address the issue of overfitting. In this work, we derive calibration problems in which the control parameters can be directly constrained by available observations, without overfitting. This is achieved by carefully selecting the ‘experiment design’, which in general encompasses both the observation strategy, and the choice of control parameters (i.e. the spatial variation of the friction field). In this work we focus on the latter, utilising existing observations available within our case study regions. We adapt a technique from the optimal experiment design (OED) literature, utilising model sensitivities computed via an adjoint-capable numerical shallow water model, <jats:italic>Thetis</jats:italic>. The OED method uses the model sensitivity to estimate the covariance of the estimated parameters corresponding to a given experiment design, without solving the corresponding parameter estimation problem. This facilitates the exploration of a large number of such experiment designs, to find the design producing the tightest parameter constraints. We take the Bristol Channel as a primary case study, using tide gauge data to estimate friction parameters corresponding to a piecewise-constant field. We first demonstrate that the OED framework produces reliable estimates of the parameter covariance, by comparison with results from a Bayesian inference algorithm. We subsequently demonstrate that solving an ‘optimal’ calibration problem leads to good model performance against both calibration and validation data, thus avoiding overfitting.</jats:p>

  • Journal article
    Brizzi A, Whittaker C, Servo LMS, Hawryluk I, Prete Jr CA, de Souza WM, Aguiar RS, Araujo LJT, Bastos LS, Blenkinsop A, Buss LF, Candido D, Castro M, Costa S, Croda J, de Souza Santos AA, Dye C, Flaxman S, Fonseca PLC, Geddes VEV, Gutierrez B, Lemey P, Levin AS, Mellan T, Bonfim D, Miscoridou X, Mishra S, Monod M, Moreira FRR, Ranzani O, Schnekenberg R, Semenova E, Sonnabend R, Souza RP, Xi X, Sabino E, Faria NR, Bhatt S, Ratmann Oet al., 2022,

    Spatial and temporal fluctuations in COVID-19 fatality rates in Brazilian hospitals

    , Nature Medicine, ISSN: 1078-8956

    The SARS-CoV-2 Gamma variant of concern spread rapidly across Brazil since late 2020, causing substantial infection and death waves. We use individual-level patient records following hospitalisation with suspected or confirmed COVID-19 between 20 January 2020 and 26 July 2021 to document temporary, sweeping shocks in hospital fatality rates that followed Gamma’s spread across 14 state capitals, during which typically more than half of hospitalised patients aged 70 and over died. We show that such extensive shocks in COVID-19 in-hospital fatality rates also existed prior to detection of Gamma. Using a Bayesian fatality rate model, we find that the geographic and temporal fluctuations in Brazil’s COVID-19 in-hospital fatality rates were primarily associated with geographic inequities and shortages in healthcare capacity. We estimate that approximately half of the COVID-19 deaths in hospitals in the 14 cities could have been avoided without pre-pandemic geographic inequities and without pandemic healthcare pressure. Our results suggest that investments in healthcare resources, healthcare optimization, and pandemic preparedness are critical to minimize population wide mortality and morbidity caused by highly transmissible and deadly pathogens such as SARS-CoV-2, especially in low- and middle-income countries.

  • Journal article
    Clare MCA, Piggott MD, Cotter CJ, 2022,

    Assessing erosion and flood risk in the coastal zone through the application of multilevel Monte Carlo methods

    , Coastal Engineering, Vol: 174, ISSN: 0378-3839

    Coastal zones are vulnerable to both erosion and flood risk, which can be assessed using coupled hydro-morphodynamic models. However, the use of such models as decision support tools suffers from a high degreeof uncertainty, due to both incomplete knowledge and natural variability in the system. In this work, we showfor the first time how the multilevel Monte Carlo method (MLMC) can be applied in hydro-morphodynamiccoastal ocean modelling, here using the popular model XBeach, to quantify uncertainty by computing statisticsof key output variables given uncertain input parameters. MLMC accelerates the Monte Carlo approach throughthe use of a hierarchy of models with different levels of resolution. Several theoretical and real-world coastalzone case studies are considered here, for which output variables that are key to the assessment of flood anderosion risk, such as wave run-up height and total eroded volume, are estimated. We show that MLMC cansignificantly reduce computational cost, resulting in speed up factors of 40 or greater compared to a standardMonte Carlo approach, whilst keeping the same level of accuracy. Furthermore, a sophisticated ensemblegenerating technique is used to estimate the cumulative distribution of output variables from the MLMC output.This allows for the probability of a variable exceeding a certain value to be estimated, such as the probabilityof a wave run-up height exceeding the height of a seawall. This is a valuable capability that can be used toinform decision-making under uncertainty

  • Journal article
    Banks-Leite C, Betts MG, Ewers RM, Orme CDL, Pigot ALet al., 2022,

    The macroecology of landscape ecology

    , Trends in Ecology and Evolution, Vol: 37, ISSN: 0169-5347

    One of landscape ecology's main goals is to unveil how biodiversity is impacted by habitat transformation. However, the discipline suffers from significant context dependency in observed spatial and temporal trends, hindering progress towards understanding the mechanisms driving species declines and preventing the development of accurate estimates of future biodiversity change. Here, we discuss recent evidence that populations' and species' responses to habitat change at the landscape scale are modulated by factors and processes occurring at macroecological scales, such as historical disturbance rates, distance to geographic range edges, and climatic suitability. We suggest that placing landscape ecology studies in a macroecological lens will help to explain seemingly inconsistent results and will ultimately create better predictive models to help mitigate the biodiversity crisis.

  • Journal article
    Clare MCA, Kramer SC, Cotter CJ, Piggott MDet al., 2022,

    Calibration, inversion and sensitivity analysis for hydro-morphodynamic models through the application of adjoint methods

    , Computers and Geosciences, Vol: 163, Pages: 1-13, ISSN: 0098-3004

    The development of reliable, sophisticated hydro-morphodynamic models is essential for protecting the coastal environment against hazards such as flooding and erosion. There exists a high degree of uncertainty associated with the application of these models, in part due to incomplete knowledge of various physical, empirical and numerical closure related parameters in both the hydrodynamic and morphodynamic solvers. This uncertainty can be addressed through the application of adjoint methods. These have the notable advantage that the number and/or dimension of the uncertain parameters has almost no effect on the computational cost associated with calculating the model sensitivities. Here, we develop the first freely available and fully flexible adjoint hydro-morphodynamic model framework. This flexibility is achieved through using the pyadjoint library, which allows us to assess the uncertainty of any parameter with respect to any model functional, without further code implementation. The model is developed within the coastal ocean model Thetis constructed using the finite element code-generation library Firedrake. We present examples of how this framework can perform sensitivity analysis, inversion and calibration for a range of uncertain parameters based on the final bedlevel. These results are verified using so-called dual-twin experiments, where the ‘correct’ parameter value is used in the generation of synthetic model test data, but is unknown to the model in subsequent testing. Moreover, we show that inversion and calibration with experimental data using our framework produces physically sensible optimum parameters and that these parameters always lead to more accurate results. In particular, we demonstrate how our adjoint framework can be applied to a tsunami-like event to invert for the tsunami wave from sediment deposits.

  • Journal article
    Phan TD, Verniero JL, Larson D, Lavraud B, Drake JF, Øieroset M, Eastwood JP, Bale SD, Livi R, Halekas JS, Whittlesey PL, Rahmati A, Stansby D, Pulupa M, MacDowall RJ, Szabo PA, Koval A, Desai M, Fuselier SA, Velli M, Hesse M, Pyakurel PS, Maheshwari K, Kasper JC, Stevens JM, Case AW, Raouafi NEet al., 2022,

    Parker Solar Probe Observations of Solar Wind Energetic Proton Beams Produced by Magnetic Reconnection in the Near‐Sun Heliospheric Current Sheet

    , Geophysical Research Letters, Vol: 49, ISSN: 0094-8276
  • Journal article
    Wang S, Toumi R, 2022,

    An analytic model of the tropical cyclone outer size

    , npj Climate and Atmospheric Science, ISSN: 2397-3722
  • Journal article
    Murray-Watson RJ, Gryspeerdt E, 2022,

    Stability-dependent increases in liquid water with droplet number in the Arctic

    , Atmospheric Chemistry and Physics, Vol: 22, Pages: 5743-5756

    <jats:p>Abstract. The effects of aerosols on cloud microphysical properties are a large source of uncertainty when assessing anthropogenic climate change. The aerosol–cloud relationship is particularly unclear in high-latitude polar regions due to a limited number of observations. Cloud liquid water path (LWP) is an important control on cloud radiative properties, particularly in the Arctic, where clouds play a central role in the surface energy budget. Therefore, understanding how aerosols may alter cloud LWP is important, especially as aerosol sources such as industry and shipping move further north in a warming Arctic. Using satellite data, this work investigates the effects of aerosols on liquid Arctic clouds over open ocean by considering the relationship between cloud droplet number concentration (Nd) and LWP, an important component of the aerosol–LWP relationship. The LWP response to Nd varies significantly across the region, with increases in LWP with Nd observed at very high latitudes in multiple satellite datasets, with this positive signal observed most strongly during the summer months. This result is in contrast to the negative response typically seen in global satellite studies and previous work on Arctic clouds showing little LWP response to aerosols. The lower tropospheric stability (LTS) was found to be an important control on the spatial variations in LWP response, strongly influencing the sign and magnitude of the Nd–LWP relationship, with increases in LWP in high-stability environments. The influence of humidity varied depending on the stability, with little impact at low LTS but a strong influence at high LTS. The mean Nd state does not dominate the LWP response, despite the non-linearities in the relationship. As the Nd–LWP sensitivity changed from positive to negative when moving from high- to low-LTS environments, this work shows evidence of a temperature-dependent aerosol indirect effect. Additionally, the LWP&n

  • Journal article
    Johnson JS, Venturelli RA, Balco G, Allen CS, Braddock S, Campbell S, Goehring BM, Hall BL, Neff PD, Nichols KA, Rood DH, Thomas ER, Woodward Jet al., 2022,

    Review article: Existing and potential evidence for Holocene grounding line retreat and readvance in Antarctica

    , The Cryosphere, Vol: 16, Pages: 1543-1562, ISSN: 1994-0416

    Widespread existing geological records from above the modern ice sheet surface and outboard of the current ice margin show that the Antarctic Ice Sheet (AIS) was much more extensive at the Last Glacial Maximum (∼ 20 ka) than at present. However, whether it was ever smaller than present during the last few millennia, and (if so) by how much, is known only for a few locations because direct evidence lies within or beneath the ice sheet, which is challenging to access. Here, we describe how retreat and readvance (henceforth “readvance”) of AIS grounding lines during the Holocene could be detected and quantified using subglacial bedrock, subglacial sediments, marine sediment cores, relative sea-level (RSL) records, geodetic observations, radar data, and ice cores. Of these, only subglacial bedrock and subglacial sediments can provide direct evidence for readvance. Marine archives are of limited utility because readvance commonly covers evidence of earlier retreat. Nevertheless, stratigraphic transitions documenting change in environment may provide support for direct evidence from subglacial records, as can the presence of transgressions in RSL records, and isostatic subsidence. With independent age control, ice structure revealed by radar can be used to infer past changes in ice flow and geometry, and therefore potential readvance. Since ice cores capture changes in surface mass balance, elevation, and atmospheric and oceanic circulation that are known to drive grounding line migration, they also have potential for identifying readvance. A multidisciplinary approach is likely to provide the strongest evidence for or against a smaller-than-present AIS in the Holocene.

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