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In this paper we study the a posteriori bounds for a conforming piecewise linear finite element approximation of the Signorini problem. We prove new rigorous a posteriori estimates of residual type in $L^{p}$, for $p \in (4,\infty)$ in two spatial dimensions. This new analysis treats the positive and negative parts of the discretisation error separately, requiring a novel sign- and bound-preserving interpolant, which is shown to have optimal approximation properties. The estimates rely on the sharp dual stability results on the problem in $W^{2,(4 - \varepsilon)/3}$ for any $\varepsilon \ll 1$. We summarise extensive numerical experiments aimed at testing the robustness of the estimator to validate the theory., Comment: 24 pages, 10 figures

In this article we present a numerical method for the Stokes flow of an Oldroyd-B fluid. The viscoelastic stress evolves according to a constitutive law formulated in terms of the upper convected time derivative. A finite difference method is used to discretise along fluid trajectories to approximate the advection and deformation terms of the upper convected derivative in a simple, cheap and cohesive manner, as well as ensuring that the discrete conformation tensor is positive definite. A full implementation with coupling to the fluid flow is presented, along with detailed discussion of the issues that arise with such schemes. We demonstrate the performance of this method with detailed numerical experiments in a lid-driven cavity setup. Numerical results are benchmarked against published data, and the method is shown to perform well in this challenging case., Comment: 26 pages, 8 figures

Mathematical models of infectious disease transmission typically neglect within-host dynamics. Yet within-host dynamics - including pathogen replication, host immune responses, and interactions with microbiota - are crucial not only for determining the progression of disease at the individual level, but also for driving within-host evolution and onwards transmission, and therefore shape dynamics at the population level. Various approaches have been proposed to model both within- and between-host dynamics, but these typically require considerable simplifying assumptions to couple processes at contrasting scales (e.g., the within-host dynamics quickly reach a steady state) or are computationally intensive. Here we propose a novel, readily adaptable and broadly applicable method for modelling both within- and between-host processes which can fully couple dynamics across scales and is both realistic and computationally efficient. By individually tracking the deterministic within-host dynamics of infected individuals, and stochastically coupling these to continuous host state variables at the population-level, we take advantage of fast numerical methods at both scales while still capturing individual transient within-host dynamics and stochasticity in transmission between hosts. Our approach closely agrees with full stochastic individual-based simulations and is especially useful when the within-host dynamics do not rapidly reach a steady state or over longer timescales to track pathogen evolution. By applying our method to different pathogen growth scenarios we show how common simplifying assumptions fundamentally change epidemiological and evolutionary dynamics., Comment: 34 pages, 5 figures

The COVID-19 pandemic, caused by the coronavirus SARS-CoV-2, has led to a wide range of non-pharmaceutical interventions being implemented around the world to curb transmission. However, the economic and social costs of some of these measures, especially lockdowns, has been high. An alternative and widely discussed public health strategy for the COVID-19 pandemic would have been to 'shield' those most vulnerable to COVID-19 (minimising their contacts with others), while allowing infection to spread among lower risk individuals with the aim of reaching herd immunity. Here we retrospectively explore the effectiveness of this strategy using a stochastic SEIR framework, showing that even under the unrealistic assumption of perfect shielding, hospitals would have been rapidly overwhelmed with many avoidable deaths among lower risk individuals. Crucially, even a small (20%) reduction in the effectiveness of shielding would have likely led to a large increase (>150%) in the number of deaths compared to perfect shielding. Our findings demonstrate that shielding the vulnerable while allowing infections to spread among the wider population would not have been a viable public health strategy for COVID-19 and is unlikely to be effective for future pandemics.

In this article we present a goal-oriented adaptive finite element method for a class of subsurface flow problems in porous media, which exhibit seepage faces. We focus on a representative case of the steady state flows governed by a nonlinear Darcy-Buckingham law with physical constraints on subsurface-atmosphere boundaries. This leads to the formulation of the problem as a variational inequality. The solutions to this problem are investigated using an adaptive finite element method based on a dual-weighted a posteriori error estimate, derived with the aim of reducing error in a specific target quantity. The quantity of interest is chosen as volumetric water flux across the seepage face, and therefore depends on an a priori unknown free boundary. We apply our method to challenging numerical examples as well as specific case studies, from which this research originates, illustrating the major difficulties that arise in practical situations. We summarise extensive numerical results that clearly demonstrate the designed method produces rapid error reduction measured against the number of degrees of freedom., Comment: Accepted for publication in The Quarterly Journal of Mechanics and Applied Mathematics Published by Oxford University Press

Combinations of intense non-pharmaceutical interventions ('lockdowns') were introduced in countries worldwide to reduce SARS-CoV-2 transmission. Many governments have begun to implement lockdown exit strategies that allow restrictions to be relaxed while attempting to control the risk of a surge in cases. Mathematical modelling has played a central role in guiding interventions, but the challenge of designing optimal exit strategies in the face of ongoing transmission is unprecedented. Here, we report discussions from the Isaac Newton Institute 'Models for an exit strategy' workshop (11-15 May 2020). A diverse community of modellers who are providing evidence to governments worldwide were asked to identify the main questions that, if answered, will allow for more accurate predictions of the effects of different exit strategies. Based on these questions, we propose a roadmap to facilitate the development of reliable models to guide exit strategies. The roadmap requires a global collaborative effort from the scientific community and policy-makers, and is made up of three parts: i) improve estimation of key epidemiological parameters; ii) understand sources of heterogeneity in populations; iii) focus on requirements for data collection, particularly in Low-to-Middle-Income countries. This will provide important information for planning exit strategies that balance socio-economic benefits with public health.