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A new semi-analytical solution to the advection-dispersion-reaction equation for modelling solute transport in layered porous media is derived using the Laplace transform. Our solution approach involves introducing unknown functions representing the dispersive flux at the interfaces between adjacent layers, allowing the multilayer problem to be solved separately on each layer in the Laplace domain before being numerically inverted back to the time domain. The derived solution is applicable to the most general form of linear advection-dispersion-reaction equation, a finite medium comprising an arbitrary number of layers, continuity of concentration and dispersive flux at the interfaces between adjacent layers and transient boundary conditions of arbitrary type at the inlet and outlet. The derived semi-analytical solution extends and addresses deficiencies of existing analytical solutions in a layered medium, which consider analogous processes such as diffusion or reaction-diffusion only and/or require the solution of complicated nonlinear transcendental equations to evaluate the solution expressions. Code implementing our semi-analytical solution is supplied and applied to a selection of test cases, with the reported results in excellent agreement with a standard numerical solution and other analytical results available in the literature., Comment: 13 pages, 3 figures, accepted version of paper published in Transport in Porous Media

Calculating the thermal diffusivity of solid materials is commonly carried out using the laser flash experiment. This classical experiment considers a small (usually thin disc-shaped) sample of the material with parallel front and rear surfaces, applying a heat pulse to the front surface and recording the resulting rise in temperature over time on the rear surface. Recently, Carr and Wood [Int J Heat Mass Transf, 144 (2019) 118609] showed that the thermal diffusivity can be expressed analytically in terms of the heat flux function applied at the front surface and the temperature rise history at the rear surface. In this paper, we generalise this result to radial unidirectional heat flow, developing new analytical formulas for calculating the thermal diffusivity for cylindrical shell and spherical shell shaped samples. Two configurations are considered: (i) heat pulse applied on the inner surface and temperature rise recorded on the outer surface and (ii) heat pulse applied on the outer surface and temperature rise recorded on the inner surface. Code implementing and verifying the thermal diffusivity formulas for both configurations is made available., Comment: 10 pages, 3 figures, accepted version

Australian football goal kicking is vital to team success, but its study is limited. Develop and apply Bayesian models incorporating temporal, spatial and situational variables to predict shot outcomes. The models aim to (i) rank players on their goal kicking and (ii) create clusters of statistically similar players and rank these clusters to provide generalised recommendations about player types.Retrospective longitudinal study with goal kicking data from three seasons, 2018-2020, 576 official Australian Football League matches, containing 26,818 attempts at goal from 778 players.The Bayesian ordinal regression model enables descriptive analysis of goal kicking performance. The models include spatial variables of distance and kick angle, situational variables of shot type and player or cluster with interaction terms. Alternative models included situational variables of weather and player characteristics, spatial variables of stadium location and temporal variables of time and quarter. Approximate leave-one-out cross validation was used to test the model.Overall goal rate of 47% (12,600), behind rate of 35% (9373) with misses the remaining 18% (4845). Accuracy of both player and cluster model achieved 0.51 against an uninformed (predict goal) model result of 0.47. The models allow for analysis of goal kicking accuracy by distance and angle and analysis of player and player-type performance.While credible intervals for all players for set shots and general play were relatively large, some 95% credible intervals excluded zero. Therefore, it may be concluded that some players' goal kicking skill can be quantified and differentiated from other players.

In vitro tumour spheroid experiments have been used to study avascular tumour growth and drug design for the last 50 years. Unlike simpler two-dimensional cell cultures, tumour spheroids exhibit heterogeneity within the growing population of cells that is thought to be related to spatial and temporal differences in nutrient availability. The recent development of real-time fluorescent cell cycle imaging allows us to identify the position and cell cycle status of individual cells within the growing population, giving rise to the notion of a four-dimensional (4D) tumour spheroid. In this work we develop the first stochastic individual-based model (IBM) of a 4D tumour spheroid and show that IBM simulation data qualitatively and quantitatively compare very well with experimental data from a suite of 4D tumour spheroid experiments performed with a primary human melanoma cell line. The IBM provides quantitative information about nutrient availability within the spheroid, which is important because it is very difficult to measure these data in standard tumour spheroid experiments. Software required to implement the IBM is available on GitHub, https://github.com/ProfMJSimpson/4DFUCCI.

Calculating the mean exit time (MET) for models of diffusion is a classical problem in statistical physics, with various applications in biophysics, economics and heat and mass transfer. While many exact results for MET are known for diffusion in simple geometries involving homogeneous materials, calculating MET for diffusion in realistic geometries involving heterogeneous materials is typically limited to repeated stochastic simulations or numerical solutions of the associated boundary value problem (BVP). In this work we derive exact solutions for the MET in irregular annular domains, including some applications where diffusion occurs in heterogenous media. These solutions are obtained by taking the exact results for MET in an annulus, and then constructing various perturbation solutions to account for the irregular geometries involved. These solutions, with a range of boundary conditions, are implemented symbolically and compare very well with averaged data from repeated stochastic simulations and with numerical solutions of the associated BVP. Software to implement the exact solutions is available at https://github.com/ProfMJSimpson/Exit_time., 18 pages, 6 figures, accepted version

The laser flash method for measuring thermal diffusivity of solids involves subjecting the front face of a small sample to a heat pulse of radiant energy and recording the resulting temperature rise on the opposite (rear) surface. For the adiabatic case, the widely-used standard approach estimates the thermal diffusivity from the rear-surface temperature rise history by calculating the half rise time: the time required for the temperature rise to reach one half of its maximum value. In this article, we develop a novel alternative approach by expressing the thermal diffusivity exactly in terms of the area enclosed by the rear-surface temperature rise curve and the steady-state temperature over time. Approximating this integral numerically leads to a simple formula for the thermal diffusivity involving the rear-surface temperature rise history. Using synthetic experimental data we demonstrate that the new formula produces estimates of the thermal diffusivity - for a typical test case - that are more accurate and less variable than the standard approach. The article concludes by briefly commenting on extension of the new method to account for heat losses from the sample., 7 pages, 1 figure, accepted version

Motivated by practical applications in heat conduction and contaminant transport, we consider heat and mass diffusion across a perturbed interface separating two finite regions of distinct diffusivity. Under the assumption of continuity of the solution and diffusive flux at the interface, we use perturbation theory to develop an asymptotic expansion of the solution valid for small perturbations. Each term in the asymptotic expansion satisfies an initial-boundary value problem on the unperturbed domain subject to interface conditions depending on the previously determined terms in the asymptotic expansion. Demonstration of the perturbation solution is carried out for a specific, practically-relevant set of initial and boundary conditions with semi-analytical solutions of the initial-boundary value problems developed using standard Laplace transform and eigenfunction expansion techniques. Results for several choices of the perturbed interface confirm the perturbation solution is in good agreement with a standard numerical solution., 14 pages, 3 figures, accepted version of paper published in Communications in Nonlinear Science and Numerical Simulation

We compute profile likelihoods for a stochastic model of diffusive transport motivated by experimental observations of heat conduction in layered skin tissues. This process is modelled as a random walk in a layered one-dimensional material, where each layer has a distinct particle hopping rate. Particles are released at some location, and the duration of time taken for each particle to reach an absorbing boundary is recorded. To explore whether this data can be used to identify the hopping rates in each layer, we compute various profile likelihoods using two methods: first, an exact likelihood is evaluated using a relatively expensive Markov chain approach; and, second we form an approximate likelihood by assuming the distribution of exit times is given by a Gamma distribution whose first two moments match the expected moments from the continuum limit description of the stochastic model. Using the exact and approximate likelihoods we construct various profile likelihoods for a range of problems. In cases where parameter values are not identifiable, we make progress by re-interpreting those data with a reduced model with a smaller number of layers., 41 pages, 11 figures

The original article was published with an erroneous affiliation details for co-author, David J. Lee. The correct affiliation for the author is Forest Industries Research Centre, University of the Sunshine Coast, Locked Bag 4, Maroochydore DC, QLD, 4558, Australia. The original article has been corrected

Many problems in physics, biology, and economics depend upon the duration of time required for a diffusing particle to cross a boundary. As such, calculations of the distribution of first passage time, and in particular the mean first passage time, is an active area of research relevant to many disciplines. Exact results for the mean first passage time for diffusion on simple geometries, such as lines, discs and spheres, are well--known. In contrast, computational methods are often used to study the first passage time for diffusion on more realistic geometries where closed--form solutions of the governing elliptic boundary value problem are not available. Here, we develop a perturbation solution to calculate the mean first passage time on irregular domains formed by perturbing the boundary of a disc or an ellipse. Classical perturbation expansion solutions are then constructed using the exact solutions available on a disc and an ellipse. We apply the perturbation solutions to compute the mean first exit time on two naturally--occurring irregular domains: a map of Tasmania, an island state of Australia, and a map of Taiwan. Comparing the perturbation solutions with numerical solutions of the elliptic boundary value problem on these irregular domains confirms that we obtain a very accurate solution with a few terms in the series only. Matlab software to implement all calculations is available on GitHub., 31pages, 12 figures

Key message: Increment cores can provide improved predictive capabilities of the modulus of elasticity (MOE) of sawn boards. Multiple increment cores collected at different heights in a tree provide marginally increased accuracy over a single breast-height core, with higher labour costs. Approximately 50% of the variability of the static bending MOE of individual boards is explained by the predicted MOE obtained from a single increment core taken at breast height. Context: Prediction of individual board MOE can lead to accurate optimisation of the value extracted from forest resources, and enhanced decision-making on the management and allocation of the resource to different processors, and improve the processors ability to optimise grade allocation. Aims: The objective of this study is to predict the MOE of individual sawn boards from the MOE measured from cores collected from standing trees. Methods: A five-parameter logistic (5PL) function and radial basis function interpolants are used to obtain a continuous distribution of MOE throughout a log. By developing a “virtual sawing” methodology, we predict the individual board MOE for sixty-eight trees consisting of locally developed F1 and F2 hybrid pines (Pinus caribaea var. hondurensis × Pinuselliottii var. elliottii). Results: Moderate correlations for individual board predictions are observed, with R2 values ranging from 0.47 to 0.53. Good correlations between average predicted board MOE and average measured MOE are also observed, with R2 ≈ 0.83. A pseudo-three-dimensional approach, accounting for variation in height in the tree, affords marginally greater accuracy and predictive capability at the cost of increased data collection and processing. By using a single breast-height core, we can obtain a similar level of prediction of individual board MOE. Conclusion: We have presented a novel non-destructive evaluation approach to predict the MOE of individual boards sawn from trees. This approach can be adapted to other wood properties, and other wood products obtained from trees.

Calculating how long a coupled multi-species reactive-diffusive transport process in a heterogeneous medium takes to effectively reach steady state is important in many applications. In this paper, we show how the time required for such processes to transition to within a small specified tolerance of steady state can be calculated accurately without having to solve the governing time-dependent model equations. Our approach is valid for general first-order reaction networks and an arbitrary number of species. Three numerical examples are presented to confirm the analysis and investigate the efficacy of the approach. A key finding is that for sequential reactions our approach works better provided the two smallest reaction rates are well separated. MATLAB code implementing the methodology and reproducing the results in the paper is made available., 8 pages, 3 figures, accepted version of paper published in Physical Review E

In this work we consider a recent experimental data set describing heat conduction in living porcine tissues. Understanding this novel data set is important because porcine skin is similar to human skin. Improving our understanding of heat conduction in living skin is relevant to understanding burn injuries, which are common, painful and can require prolonged and expensive treatment. A key feature of skin is that it is layered, with different thermal properties in different layers. Since the experimental data set involves heat conduction in thin living tissues of anesthetised animals, an important experimental constraint is that the temperature within the living tissue is measured at one spatial location within the layered structure. Our aim is to determine whether this data is sufficient to reliably infer the heat conduction parameters in layered skin, and we use a simplified two-layer mathematical model of heat conduction to mimic the generation of experimental data. Using synthetic data generated at one location in the two-layer mathematical model, we explore whether it is possible to infer values of the thermal diffusivity in both layers. After this initial exploration, we then examine how our ability to infer the thermal diffusivities changes when we vary the location at which the experimental data is recorded, as well as considering the situation where we are able to monitor the temperature at two locations within the layered structure. Overall, we find that our ability to parameterise a model of heterogeneous heat conduction with limited experimental data is very sensitive to the location where data is collected. Our modelling results provide guidance about optimal experimental design that could be used to guide future experimental studies.NomenclatureA brief description of all variables used in the document are given in Table 1.Table 1:Variable nomenclature and description.

Mathematical models of diffusive transport underpin our understanding of chemical, biochemical and biological transport phenomena. Analysis of such models often focusses on relatively simple geometries and deals with diffusion through highly idealised homogeneous media. In contrast, practical applications of diffusive transport theory inevitably involve dealing with more complicated geometries as well as dealing with heterogeneous media. One of the most fundamental properties of diffusive transport is the concept of mean particle lifetime or mean exit time, which are particular applications of the concept of first passage time, and provide the mean time required for a diffusing particle to reach an absorbing boundary. Most formal analysis of mean particle lifetime applies to relatively simple geometries, often with homogeneous (spatially-invariant) material properties. In this work, we present a general framework that provides exact mathematical insight into the mean particle lifetime, and higher moments of particle lifetime, for point particles diffusing in heterogeneous discs and spheres with radial symmetry. Our analysis applies to geometries with an arbitrary number and arrangement of distinct layers, where transport in each layer is characterised by a distinct diffusivity. We obtain exact closed-form expressions for the mean particle lifetime for a diffusing particle released at an arbitrary location and we generalise these results to give exact, closed-form expressions for any higher-order moment of particle lifetime for a range of different boundary conditions. Finally, using these results we construct new homogenization formulae that provide an accurate simplified description of diffusion through heterogeneous discs and spheres., 19 pages, 3 figures, accepted version of paper published in The Journal of Chemical Physics

Accurately determining the timber properties for products prior to cutting the tree is difficult. In this work we discuss a method for reconstructing a timber billet virtually, including internal features, after it has been peeled into a full veneer (ribbon). This reconstruction process is the first stage in developing a mathematical model for the variation in timber properties within a given tree. The reconstruction of internal timber features is typically achieved through the use of computed tomography (CT) scanning. However, this requires the use of equipment that may be cost-prohibitive. Here we discuss an approach that utilises more readily available equipment for timber processors, including a spindleless lathe and digital SLR camera. In comparison to conventional scanning methods, this reconstruction method based on a destructive process has the key advantage of delivering high-resolution colour images. This reconstruction serves two purposes. Firstly, we are able to generate three-dimensional visualisations of the timber billet, to uncover internal structures such as knots, defects, insect or fungi attack, discoloration, resin etc. Secondly, the reconstruction allows us to map timber properties measured on the veneer to their original location within the billet. This allows us to locally inform the mapping with wood properties and subsequently derive their distribution throughout the billet. From this information it is then possible to extract any part of the billet and obtain the appearance and wood properties of any processed products. To validate our reconstruction process we show that we can obtain reasonable agreement between our predicted billet modulus of elasticity and that measured on the original billet.

We study methods for calculating the thermal diffusivity of solids from laser flash experiments. This experiment involves subjecting the front surface of a small sample of the material to a heat pulse and recording the resulting temperature rise on the opposite (rear) surface. Recently, a method was developed for calculating the thermal diffusivity from the rear-surface temperature rise, which was shown to produce improved estimates compared with the commonly used half-time approach. This so-called rear-surface integral method produced a formula for calculating the thermal diffusivity of homogeneous samples under the assumption that the heat pulse is instantaneously absorbed uniformly into a thin layer at the front surface. In this paper, we show how the rear-surface integral method can be applied to a more physically realistic heat flow model involving the actual heat pulse shape from the laser flash experiment. New thermal diffusivity formulas are derived for handling arbitrary pulse shapes for either a homogeneous sample or a heterogeneous sample comprising two layers of different materials. Presented numerical experiments confirm the accuracy of the new formulas and demonstrate how they can be applied to the kinds of experimental data arising from the laser flash experiment., 10 pages, 3 figures, accepted version

International audience; Numerous problems involving gradient-driven transport processes—e.g., Fourier's and Darcy's law—in heterogeneous materials concern a physical domain that is much larger than the scale at which the coefficients vary spatially. To overcome the prohibitive computational cost associated with such problems, the well-established Distributed Microstructure Model (DMM) provides a two-scale description of the transport process that produces a computationally cheap approximation to the fine-scale solution. This is achieved via the introduction of sparsely distributed micro-cells that together resolve small patches of the fine-scale structure: a macroscopic equation with an effective coefficient describes the global transport and a microscopic equation governs the local transport within each micro-cell. In this paper, we propose a new formulation, the Extended Distributed Microstructure Model (EDMM), where the macroscopic flux is instead defined as the average of the microscopic fluxes within the micro-cells. This avoids the need for any effective parameters and more accurately accounts for a non-equilibrium field in the micro-cells. Another important contribution of the work is the presentation of a new and improved numerical scheme for performing the two-scale computations using control volume, Krylov subspace and parallel computing techniques. Numerical tests are carried out on two challenging test problems: heat conduction in a composite medium and unsaturated water flow in heterogeneous soils. The results indicate that while DMM is more efficient, EDMM is more accurate and is able to capture additional fine-scale features in the solution.

Diffusion in a composite slab consisting of a large number of layers provides an ideal prototype problem for developing and analysing two-scale modelling approaches for heterogeneous media. Numerous analytical techniques have been proposed for solving the transient diffusion equation in a one-dimensional composite slab consisting of an arbitrary number of layers. Most of these approaches, however, require the solution of a complex transcendental equation arising from a matrix determinant for the eigenvalues that is difficult to solve numerically for a large number of layers. To overcome this issue, in this paper, we present a semi-analytical method based on the Laplace transform and an orthogonal eigenfunction expansion. The proposed approach uses eigenvalues local to each layer that can be obtained either explicitly, or by solving simple transcendental equations. The semi-analytical solution is applicable to both perfect and imperfect contact at the interfaces between adjacent layers and either Dirichlet, Neumann or Robin boundary conditions at the ends of the slab. The solution approach is verified for several test cases and is shown to work well for a large number of layers. The work is concluded with an application to macroscopic modelling where the solution of a fine-scale multilayered medium consisting of two hundred layers is compared against an “up-scaled” variant of the same problem involving only ten layers.

Predicting the release performance of a drug delivery device is an important challenge in pharmaceutics and biomedical science. In this paper, we consider a multi-layer diffusion model of drug release from a composite spherical microcapsule into an external surrounding medium. Based on this model, we present two approaches that provide useful indicators of the release time, i.e. the time required for the drug-filled capsule to be depleted. Both approaches make use of temporal moments of the drug concentration versus time curve at the centre of the capsule, which provide useful insight into the timescale of the process and can be computed exactly without explicit calculation of the full transient solution of the multi-layer diffusion model. The first approach, which uses the zeroth and first temporal moments only, provides simple algebraic expressions involving the various parameters in the model (e.g. layer diffusivities, mass transfer coefficients, partition coefficients) to characterize the release time while the second approach yields an asymptotic estimate of the release time that depends on consecutive higher moments. Through several test cases, we show that both approaches provide a computationally-cheap and useful measure to compare \textit{a priori} the release time of different composite microcapsule configurations., 15 pages, 4 figures, submitted

We propose an alternative method for one-dimensional continuum diffusion models with spatially variable (heterogeneous) diffusivity. Our method, which extends recent work on stochastic diffusion, assumes the constant-coefficient homogenized equation takes the form of an advection-diffusion equation with effective (diffusivity and velocity) coefficients. To calculate the effective coefficients, our approach involves solving two uncoupled boundary value problems over the heterogeneous medium and leads to coefficients depending on the spatially-varying diffusivity (as usual) as well as the boundary conditions imposed on the heterogeneous model. Computational experiments comparing our advection-diffusion homogenized model to the standard homogenized model demonstrate that including an advection term in the homogenized equation leads to improved approximations of the solution of the original heterogeneous model., Comment: 7 pages, 2 figures, accepted version of paper published in Physical Review E

The diffusion of molecules in complex intracellular environments can be strongly influenced by spatial heterogeneity and stochasticity. A key challenge when modelling such processes using stochastic random walk frameworks is that negative jump coefficients can arise when transport operators are discretized on heterogeneous domains. Often this is dealt with through homogenization approximations by replacing the heterogeneous medium with an $\textit{effective}$ homogeneous medium. In this work, we present a new class of homogenization approximations by considering a stochastic diffusive transport model on a one-dimensional domain containing an arbitrary number of layers with different jump rates. We derive closed form solutions for the $k$th moment of particle lifetime, carefully explaining how to deal with the internal interfaces between layers. These general tools allow us to derive simple formulae for the effective transport coefficients, leading to significant generalisations of previous homogenization approaches. Here, we find that different jump rates in the layers gives rise to a net bias, leading to a non-zero advection, for the entire homogenized system. Example calculations show that our generalized approach can lead to very different outcomes than traditional approaches, thereby having the potential to significantly affect simulation studies that use homogenization approximations., 9 pages, 2 figures, accepted version of paper published in The Journal of Chemical Physics

We present a general mechanistic model of mass diffusion for a composite sphere placed in a large ambient medium. The multi-layer problem is described by a system of diffusion equations coupled via interlayer boundary conditions such as those imposing a finite mass resistance at the external surface of the sphere. While the work is applicable to the generic problem of heat or mass transfer in a multi-layer sphere, the analysis and results are presented in the context of drug kinetics for desorbing and absorbing spherical microcapsules. We derive an analytical solution for the concentration in the sphere and in the surrounding medium that avoids any artificial truncation at a finite distance. The closed-form solution in each concentric layer is expressed in terms of a suitably-defined inverse Laplace transform that can be evaluated numerically. Concentration profiles and drug mass curves in the spherical layers and in the external environment are presented and the dependency of the solution on the mass transfer coefficient at the surface of the sphere analyzed., Comment: 21 pages, 6 figures, submitted

Diffusion of molecules within biological cells and tissues is strongly influenced by crowding. A key quantity to characterize diffusion is the particle lifetime, which is the time taken for a diffusing particle to exit by hitting an absorbing boundary. Calculating the particle lifetime provides valuable information, for example, by allowing us to compare the timescale of diffusion and the timescale of reaction, thereby helping us to develop appropriate mathematical models. Previous methods to quantify particle lifetimes focus on the mean particle lifetime. Here, we take a different approach and present a simple method for calculating the maximum particle lifetime. This is the time after which only a small specified proportion of particles in an ensemble remain in the system. Our approach produces accurate estimates of the maximum particle lifetime, whereas the mean particle lifetime always underestimates this value compared with data from stochastic simulations. Furthermore, we find that differences between the mean and maximum particle lifetimes become increasingly important when considering diffusion hindered by obstacles., Comment: 10 pages, 1 figure

This paper presents a simple tool for characterising the timescale for continuum diffusion processes through layered heterogeneous media. This mathematical problem is motivated by several practical applications such as heat transport in composite materials, flow in layered aquifers and drug diffusion through the layers of the skin. In such processes, the physical properties of the medium vary across layers and internal boundary conditions apply at the interfaces between adjacent layers. To characterise the timescale, we use the concept of mean action time, which provides the mean timescale at each position in the medium by utilising the fact that the transition of the transient solution of the underlying partial differential equation model, from initial state to steady state, can be represented as a cumulative distribution function of time. Using this concept, we define the characteristic timescale for a multilayer diffusion process as the maximum value of the mean action time across the layered medium. For given initial conditions and internal and external boundary conditions, this approach leads to simple algebraic expressions for characterising the timescale that depend on the physical and geometrical properties of the medium, such as the diffusivities and lengths of the layers. Numerical examples demonstrate that these expressions provide useful insight into explaining how the parameters in the model affect the time it takes for a multilayer diffusion process to reach steady state., Comment: 15 pages, 2 figures, accepted version of paper published in Physical Review E

We study measures of the amount of time required for transient flow in heterogeneous porous media to effectively reach steady state, also known as the response time. Here, we develop a new approach that extends the concept of mean action time. Previous applications of the theory of mean action time to estimate the response time use the first two central moments of the probability density function associated with the transition from the initial condition, at $t=0$, to the steady state condition that arises in the long time limit, as $t \to \infty$. This previous approach leads to a computationally convenient estimation of the response time, but the accuracy can be poor. Here, we outline a powerful extension using the first $k$ raw moments, showing how to produce an extremely accurate estimate by making use of asymptotic properties of the cumulative distribution function. Results are validated using an existing laboratory-scale data set describing flow in a homogeneous porous medium. In addition, we demonstrate how the results also apply to flow in heterogeneous porous media. Overall, the new method is: (i) extremely accurate; and (ii) computationally inexpensive. In fact, the computational cost of the new method is orders of magnitude less than the computational effort required to study the response time by solving the transient flow equation. Furthermore, the approach provides a rigorous mathematical connection with the heuristic argument that the response time for flow in a homogeneous porous medium is proportional to $L^2/D$, where $L$ is a relevant length scale, and $D$ is the aquifer diffusivity. Here, we extend such heuristic arguments by providing a clear mathematical definition of the proportionality constant., 22 pages, 3 figures, accepted version of paper published in Journal of Hydrology

International audience; A robust mathematical model was developed to simulate the heat and mass transfer process that evolves during vacuum-drying of four commercially important Australian native hardwood species. The hardwood species investigated were spotted gum (Corymbia citriodora), blackbutt (Eucalyptus pilularis), jarrah (Eucalyptus marginata), and messmate (Eucalyptus obliqua). These species provide a good test for the model based on their extreme diversity between wood properties and drying characteristics. The model uses boundary condition data from a series of vacuum-drying trials, which were also used to validate predictions. By using measured diffusion coefficient values to calibrate empirical formula, the accuracy of the model was greatly improved. Results of a sensitivity analysis showed that the model outputs provide excellent agreement with experimental observation despite the large range of species behaviour and variation in wood properties. This study confirms that the drying rate is significantly improved as a direct result of the enhanced convective and diffusive transfer along the board thickness. Contrary to softwood, it appears that longitudinal migration provides only a secondary effect. Not only is the model able to predict the heat and mass transfer behaviour of a range of hardwood species, it is also flexible enough to predict the behaviour for both conventional and vacuum-drying scenarios. The outcomes of this work provide the hardwood industry with a well-calibrated predictive drying tool that can be used to optimise drying schedules.

Highlights - We study the boundary conditions (BCs) in a macroscale model of layered diffusion. - A set of corrected macroscale BCs are derived using the method of volume averaging. - For example: a Dirichlet BC at the microscale leads to a Robin BC at the macroscale. - Resulting macroscale field more accurately captures averaged microscale field. - Resulting reconstructed field is in excellent agreement with true microscale field. Abstract This paper investigates the form of the boundary conditions (BCs) used in macroscale models of PDEs with coefficients that vary over a small length-scale (microscale). Specifically, we focus on the one-dimensional multilayer diffusion problem, a simple prototype problem where an analytical solution is available. For a given microscale BC (e.g., Dirichlet, Neumann, Robin, etc.) we derive a corrected macroscale BC using the method of volume averaging. For example, our analysis confirms that a Robin BC should be applied on the macroscale if a Dirichlet BC is specified on the microscale. The macroscale field computed using the corrected BCs more accurately captures the averaged microscale field and leads to a reconstructed microscale field that is in excellent agreement with the true microscale field. While the analysis and results are presented for one-dimensional multilayer diffusion only, the methodology can be extended to and has implications on a broader class of problems.

First aid treatment of burn injuries reduces scarring and improves healing. Here, we quantify the efficacy of various first aid treatments by using a mathematical model to describe a suite of experimental data from a series of in vivo porcine experiments. We study a series of consistent burn injuries that are subject to first aid treatments that vary in both the temperature and duration of the first aid treatment. Calibrating the mathematical model to the experimental data provides estimates of the in vivo thermal diffusivity, the rate at which thermal energy is lost to the blood (perfusion), and the heat transfer coefficient controlling the loss of thermal energy at the interface of the fat and muscle layers. A limitation of working with in vivo animal experiments is the difficulty of resolving spatial variations in temperature across the tissues. Here, we use the solution of the calibrated mathematical model to predict and visualise the temperature distribution across the thickness of the tissue during the creation of the burn injury and the application of various first aid treatments. Using this information we propose, and report values for, a novel measure of the potential for tissue damage. This measure quantifies two important aspects that are thought to be related to thermal injury: (i) the volume of tissue that rises above the threshold temperature associated with the accumulation of tissue damage; and, (ii) the duration of time that the tissue remains above this threshold temperature. We conclude by discussing the clinical relevance of our findings.

The focus of this paper is two-dimensional computational modelling of water flow in unsaturated soils consisting of weakly conductive disconnected inclusions embedded in a highly conductive connected matrix. When the inclusions are small, a two-scale Richards’ equation-based model has been proposed in the literature taking the form of an equation with effective parameters governing the macroscopic flow coupled with a microscopic equation, defined at each point in the macroscopic domain, governing the flow in the inclusions. This paper is devoted to a number of advances in the numerical implementation of this model. Namely, by treating the micro-scale as a two-dimensional problem, our solution approach based on a control volume finite element method can be applied to irregular inclusion geometries, and, if necessary, modified to account for additional phenomena (e.g. imposing the macroscopic gradient on the micro-scale via a linear approximation of the macroscopic variable along the microscopic boundary). This is achieved with the help of an exponential integrator for advancing the solution in time. This time integration method completely avoids generation of the Jacobian matrix of the system and hence eases the computation when solving the two-scale model in a completely coupled manner. Numerical simulations are presented for a two-dimensional infiltration problem.

We develop a new semi-analytical method for solving multilayer diffusion problems with time-varying external boundary conditions and general internal boundary conditions at the interfaces between adjacent layers. The convergence rate of the semi-analytical method, relative to the number of eigenvalues, is investigated and the effect of varying the interface conditions on the solution behaviour is explored. Numerical experiments demonstrate that solutions can be computed using the new semi-analytical method that are more accurate and more efficient than the unified transform method of Sheils [Appl. Math. Model., 46:450-464, 2017]. Furthermore, unlike classical analytical solutions and the unified transform method, only the new semi-analytical method is able to correctly treat problems with both time-varying external boundary conditions and a large number of layers. The paper is concluded by replicating solutions to several important industrial, environmental and biological applications previously reported in the literature, demonstrating the wide applicability of the work., Comment: 24 pages, 8 figures, accepted version of paper published in Applied Mathematics and Computation

Mathematically, it takes an infinite amount of time for the transient solution of a diffusion equation to transition from initial to steady state. Calculating a \textit{finite} transition time, defined as the time required for the transient solution to transition to within a small prescribed tolerance of the steady state solution, is much more useful in practice. In this paper, we study estimates of finite transition times that avoid explicit calculation of the transient solution by using the property that the transition to steady state defines a cumulative distribution function when time is treated as a random variable. In total, three approaches are studied: (i) mean action time (ii) mean plus one standard deviation of action time and (iii) a new approach derived by approximating the large time asymptotic behaviour of the cumulative distribution function. The new approach leads to a simple formula for calculating the finite transition time that depends on the prescribed tolerance $\delta$ and the $(k-1)$th and $k$th moments ($k \geq 1$) of the distribution. Results comparing exact and approximate finite transition times lead to two key findings. Firstly, while the first two approaches are useful at characterising the time scale of the transition, they do not provide accurate estimates for diffusion processes. Secondly, the new approach allows one to calculate finite transition times accurate to effectively any number of significant digits, using only the moments, with the accuracy increasing as the index $k$ is increased., Comment: 17 pages, 2 figures, accepted version of paper published in Physical Review E

International audience; A new dual-scale modeling approach is presented for simulating the drying of a wet hygroscopic porous material that couples the porous medium (macroscale) with the underlying pore structure (microscale). The proposed model is applied to the convective drying of wood at low temperatures and is valid in the so-called hygroscopic range, where hygroscopically held liquid water is present in the solid phase and water exits only as vapor in the pores. Coupling between scales is achieved by imposing the macroscopic gradients of moisture content and temperature on the microscopic field using suitably defined periodic boundary conditions, which allows the macroscopic mass and thermal fluxes to be defined as averages of the microscopic fluxes over the unit cell. This novel formulation accounts for the intricate coupling of heat and mass transfer at the microscopic scale but reduces to a classical homogenization approach if a linear relationship is assumed between the microscopic gradient and flux. Simulation results for a sample of spruce wood highlight the potential and flexibility of the new dual-scale approach. In particular, for a given unit cell configuration it is not necessary to propose the form of the macroscopic fluxes prior to the simulations because these are determined as a direct result of the dual-scale formulation.Read More: http://epubs.siam.org/doi/abs/10.1137/120873005

International audience; An improved mesoscopic model is presented for simulating the drying of porous media. The aim of this model is to account for two scales simultaneously: the scale of the whole product and the scale of the heterogeneities of the porous medium. The innovation of this method is the utilization of a new mass-conservative scheme based on the Control-Volume Finite-Element (CV-FE) method that partitions the moisture content field over the individual sub-control volumes surrounding each node within the mesh. Although the new formulation has potential for application across a wide range of transport processes in heterogeneous porous media, the focus here is on applying the model to the drying of small sections of softwood consisting of several growth rings. The results conclude that, when compared to a previously published scheme, only the new mass-conservative formulation correctly captures the true moisture content evolution in the earlywood and latewood components of the growth rings during drying.

This paper studies time integration methods for large stiff systems of ordinary differential equations (ODEs) of the form u'(t) = g(u(t)). For such problems, implicit methods generally outperform explicit methods, since the time step is usually less restricted by stability constraints. Recently, however, explicit so-called exponential integrators have become popular for stiff problems due to their favourable stability properties. These methods use matrix-vector products involving exponential-like functions of the Jacobian matrix, which can be approximated using Krylov subspace methods that require only matrix-vector products with the Jacobian. In this paper, we implement exponential integrators of second, third and fourth order and demonstrate that they are competitive with well-established approaches based on the backward differentiation formulas and a preconditioned Newton-Krylov solution strategy.

We study Krylov subspace methods for approximating the matrix-function vector product $\varphi(tA)b$ where $\varphi(z) = [\exp(z)-1]/z$. This product arises in the numerical integration of large stiff systems of differential equations by the Exponential Euler Method, where $A$~is the Jacobian matrix of the system. Recently, this method has found application in the simulation of transport phenomena in porous media within mathematical models of wood drying and groundwater flow. We develop an a posteriori upper bound on the Krylov subspace approximation error and provide a new interpretation of a previously published error estimate. This leads to an alternative Krylov approximation to $\varphi(tA)b$, the so-called Harmonic Ritz approximant, which we find does not exhibit oscillatory behaviour of the residual error. References E. J. Carr, T. J. Moroney and I. W. Turner. Efficient simulation of unsaturated flow using exponential time integration. Appl. Math. Comput. , 217(14):6587--6596, 2011. doi:10.1016/j.amc.2011.01.041 E. J. Carr, I. W. Turner and P. Perre. A Jacobian-free exponential integrator for simulating transport in heterogeneous porous media: application to the drying of softwood, submitted for publication. E. J. Carr, I. W. Turner and P. Perre. A new control-volume finite-element scheme for heterogeneous porous media:application to the drying of softwood. Chem. Eng. Technol. , 34(7):1143--1150, 2011. doi:10.1002/ceat.201100060 E. Celledoni and I. Moret. A Krylov projection method for systems of ODEs. Appl. Numer. Math. , 24(2--3):365--378, 1997. doi:10.1016/S0168-9274(97)00033-0 N. J. Higham. Functions of matrices: theory and computation . SIAM, Philadelphia, PA, USA, 2008. M. Hochbruck, M. E. Hochstenbach. Subspace extraction for matrix functions, submitted for publication. http://www.win.tue.nl/ hochsten/pdf/funext.pdf M. Hochbruck, C. Lubich and H. Selhofer. Exponential integrators for large systems of differential equations. SIAM J. Sci. Comput. , 19(5):1552--1574, 1998. doi:10.1137/S1064827595295337 B. V. Minchev and W. M. Wright. A review of exponential integrators for first order semi-linear problems. Numerics No. 2/05, Norwegian University of Science and Technology, Trondheim, Norway, 2005. http://www.math.ntnu.no/preprint/numerics/2005/N2-2005.ps P. Perre and I. Turner. A heterogeneous wood drying computational model that accounts for material property variation across growth rings. Chem. Eng. J. , 86(1--2):117--131, 2002. doi:10.1016/S1385-8947(01)00270-4