arXiv subjects

Scott W McCue

Publications and source records attributed to Scott W McCue.

At least 19 recordsLinked to original sources

arXiv2026

Self-similar rupture of thin films of power-law fluid

Models that describe Newtonian liquid films evolving due to the competing effects of surface tension and attractive intermolecular or van der Waals forces are known to rupture in finite time in a self-similar manner. We extend the computation of similarity solutions to non-Newtonian power-law liquid films. The resulting bifurcation diagram, indexed by power law exponent $n$, has a highly nontrivial structure with branches merging via a snaking bifurcation around $n=1$. A countably infinite number of solutions are also found in the extreme shear-thinning ($n\to 0$) limit, in which similarity solutions possess an exponentially small inner region. Numerical simulations of the time-dependent model are shown to be attracted to the single primary branch of similarity solutions. The asymptotic structure of solutions in the small $n$ limit is also determined.

cond-mat.soft↗

arXiv2025

Computing sessile droplet shapes on arbitrary surfaces with a new pairwise force smoothed particle hydrodynamics model

The study of the shape of droplets on surfaces is an important problem in the physics of fluids and has applications in multiple industries, from agrichemical spraying to microfluidic devices. Motivated by these real-world applications, computational predictions for droplet shapes on complex substrates -- rough and chemically heterogeneous surfaces -- are desired. Grid-based discretisations in axisymmetric coordinates form the basis of well-established numerical solution methods in this area, but when the problem is not axisymmetric, the shape of the contact line and the distribution of the contact angle around it are unknown. Recently, particle methods, such as pairwise force smoothed particle hydrodynamics (PF-SPH), have been used to conveniently forego explicit enforcement of the contact angle. The pairwise force model, however, is far from mature, and there is no consensus in the literature on the choice of pairwise force profile. We propose a new pair of polynomial force profiles with a simple motivation and validate the PF-SPH model in both static and dynamic tests. We demonstrate its capabilities by computing droplet shapes on a physically structured surface, a surface with a hydrophilic stripe, and a virtual wheat leaf with both micro-scale roughness and variable wettability. We anticipate that this model can be extended to dynamic scenarios, such as droplet spreading or impaction, in the future.

physics.flu-dyn↗

arXiv2024

Long-time emergent dynamics of liquid films undergoing thermocapillary instability

The study of viscous thin film flow has led to the development of highly nonlinear partial differential equations that model how the evolution of the film height is affected by different forces. We investigate a model of interaction between surface tension and the thermocapillary Marangoni effect, with a particular focus on the long-time limit. In this limit, the model predicts the creation of an infinite cascade of successively smaller satellite droplets near points where the film thickness vanishes. Motivated by recent progress on the analysis of discrete self-similarity in thin film equations, we compute solutions in a space- and time-rescaled coordinate system. Using this rescaled system we observe the dynamics much further in time than has previously been achieved. The observed behaviour is close to, but distinct from, previous observations of discretely self-similar thin film flows, in that the rescaled system does not settle down to a periodic solution, but instead has aspects that continue to evolve monotonically in scaled time. This discovery suggests there are as-yet unexplored ways in which discrete self-similarity may be exhibited.

physics.flu-dyn↗

arXiv2024

Two-interface and thin filament approximation in Hele--Shaw channel flow

When a viscous fluid partially fills a Hele--Shaw channel, and is pushed by a pressure difference, the fluid interface is unstable due to the Saffman--Taylor instability. We consider the evolution of a fluid region of finite extent, bounded between two interfaces, in the limit the interfaces are close, that is, when the fluid region is a thin liquid filament separating two gases of different pressure. In this limit, we derive a second-order `thin filament' model that describes the normal velocity of the filament centreline, and evolution of the filament thickness, as functions of the thickness, centreline curvature and their derivatives. We show that the second-order terms in this model, that include the effect of transverse flow along the filament, are necessary to regularise the instability. Numerical simulation of the thin filament model is shown to be in accordance with level-set computations of the complete two-interface model. Solutions ultimately evolve to form a bubble of rapidly increasing radius and decreasing thickness.

physics.flu-dyn↗

arXiv2024

Fisher-KPP-type models of biological invasion: Open source computational tools, key concepts and analysis

This review provides open-access computational tools that support a range of mathematical approaches to analyse three related scalar reaction-diffusion models used to study biological invasion. Starting with the classic Fisher-Kolmogorov (Fisher-KPP) model, we illustrate how computational methods can be used to explore time-dependent partial differential equation (PDE) solutions in parallel with phase plane and regular perturbation techniques to explore invading travelling wave solutions moving with dimensionless speed $c \ge 2$. To overcome the lack of a well-defined sharp front in solutions of the Fisher-KPP model, we also review two alternative modeling approaches. The first is the Porous-Fisher model where the linear diffusion term is replaced with a degenerate nonlinear diffusion term. Using phase plane and regular perturbation methods, we explore the distinction between sharp- and smooth-fronted invading travelling waves that move with dimensionless speed $c \ge 1/\sqrt{2}$. The second alternative approach is to reformulate the Fisher-KPP model as a moving boundary problem on $0 < x < L(t)$, leading to the Fisher-Stefan model with sharp-fronted travelling wave solutions arising from a PDE model with a linear diffusion term. Time-dependent PDE solutions and phase plane methods show that travelling wave solutions of the Fisher-Stefan model can describe both biological invasion $(c > 0)$ and biological recession $(c < 0)$. Open source Julia code to replicate all computational results in this review is available on GitHub; we encourage researchers to use this code directly or to adapt the code as required for more complicated models.

nlin.PS↗

arXiv2024

Discrete and continuous mathematical models of sharp-fronted collective cell migration and invasion

Mathematical models describing the spatial spreading and invasion of populations of biological cells are often developed in a continuum modelling framework using reaction-diffusion equations. While continuum models based on linear diffusion are routinely employed and known to capture key experimental observations, linear diffusion fails to predict well-defined sharp fronts that are often observed experimentally. This observation has motivated the use of nonlinear degenerate diffusion, however these nonlinear models and the associated parameters lack a clear biological motivation and interpretation. Here we take a different approach by developing a stochastic discrete lattice-based model incorporating biologically-inspired mechanisms and then deriving the reaction-diffusion continuum limit. Inspired by experimental observations, agents in the simulation deposit extracellular material, that we call a substrate, locally onto the lattice, and the motility of agents is taken to be proportional to the substrate density. Discrete simulations that mimic a two--dimensional circular barrier assay illustrate how the discrete model supports both smooth and sharp-fronted density profiles depending on the rate of substrate deposition. Coarse-graining the discrete model leads to a novel partial differential equation (PDE) model whose solution accurately approximates averaged data from the discrete model. The new discrete model and PDE approximation provides a simple, biologically motivated framework for modelling the spreading, growth and invasion of cell populations with well-defined sharp fronts

nlin.CG↗

arXiv2023

Survival, extinction, and interface stability in a two--phase moving boundary model of biological invasion

We consider a moving boundary mathematical model of biological invasion. The model describes the spatiotemporal evolution of two adjacent populations: each population undergoes linear diffusion and logistic growth, and the boundary between the two populations evolves according to a two--phase Stefan condition. This mathematical model describes situations where one population invades into regions occupied by the other population, such as the spreading of a malignant tumour into surrounding tissues. Full time--dependent numerical solutions are obtained using a level--set numerical method. We use these numerical solutions to explore several properties of the model including: (i) survival and extinction of one population initially surrounded by the other; and (ii) linear stability of the moving front boundary in the context of a travelling wave solution subjected to transverse perturbations. Overall, we show that many features of the well--studied one--phase single population analogue of this model can be very different in the more realistic two--phase setting. These results are important because realistic examples of biological invasion involve interactions between multiple populations and so great care should be taken when extrapolating predictions from a one--phase single population model to cases for which multiple populations are present. Open source Julia--based software is available on GitHub to replicate all results in this study.

q-bio.PE↗

arXiv2022

Exact time-dependent solutions of a Fisher-KPP-like equation obtained with nonclassical symmetry analysis

We consider a family of exact solutions to a nonlinear reaction-diffusion model, constructed using nonclassical symmetry analysis. In a particular limit, the mathematical model approaches the well-known Fisher-KPP model, which means that it is related to various applications including cancer progression, wound healing and ecological invasion. The exact solution is mathematically interesting since exact solutions of the Fisher-KPP model are rare, and often restricted to long-time travelling wave solutions for special values of the travelling wave speed.

nlin.SI↗

arXiv2022

Non-vanishing sharp-fronted travelling wave solutions of the Fisher-Kolmogorov model

The Fisher-KPP model, and generalisations thereof, is a simple reaction-diffusion models of biological invasion that assumes individuals in the population undergo linear diffusion with diffusivity $D$, and logistic proliferation with rate $λ$. Biologically-relevant initial conditions lead to long-time travelling wave solutions that move with speed $c=2\sqrt{λD}$. Despite these attractive features, there are several biological limitations of travelling wave solutions of the Fisher-KPP model. First, these travelling wave solutions do not predict a well-defined invasion front. Second, biologically-relevant initial conditions lead to travelling waves that move with speed $c=2\sqrt{λD} > 0$. This means that, for biologically-relevant initial data, the Fisher-KPP model can not be used to study invasion with $c \ne 2\sqrt{λD}$, or retreating travelling waves with $c < 0$. Here, we reformulate the Fisher-KPP model as a moving boundary problem on $x < s(t)$, and we show that this reformulated model alleviates the key limitations of the Fisher-KPP model. Travelling wave solutions of the moving boundary problem predict a well-defined front, and can propagate with any wave speed, $-\infty < c < \infty$. Here, we establish these results using a combination of high-accuracy numerical simulations of the time-dependent partial differential equation, phase plane analysis and perturbation methods. All software required to replicate this work is available on GitHub.

nlin.PS↗

arXiv2021

A continuum mathematical model of substrate-mediated tissue growth

We consider a continuum mathematical model of biological tissue formation inspired by recent experiments describing thin tissue growth in 3D-printed bioscaffolds. The continuum model involves a partial differential equation describing the density of tissue, $\hat{u}(\hat{\mathbf{x}},\hat{t})$, that is coupled to the concentration of an immobile extracellular substrate, $\hat{s}(\hat{\mathbf{x}},\hat{t})$. Cell migration is modelled with a nonlinear diffusion term, where the diffusive flux is proportional to $\hat{s}$, while a logistic growth term models cell proliferation. The extracellular substrate $\hat{s}$ is produced by cells, and undergoes linear decay. Preliminary numerical simulations show that this mathematical model, which we call the \textit{substrate model}, is able to recapitulate key features of recent tissue growth experiments, including the formation of sharp fronts. To provide a deeper understanding of the model we then analyse travelling wave solutions of the substrate model, showing that the model supports both sharp-fronted travelling wave solutions that move with a minimum wave speed, $c = c_{\rm{min}}$, as well as smooth-fronted travelling wave solutions that move with a faster travelling wave speed, $c > c_{\rm{min}}$. We provide a geometric interpretation that explains the difference between smooth- and sharp-fronted travelling wave solutions that is based on a slow manifold reduction of the desingularised three-dimensional phase space. In addition to exploring the nature of the smooth- and sharp-fronted travelling waves, we also develop and test a series of useful approximations that describe the shape of the travelling wave solutions in various limits. These approximations apply to both the sharp-fronted travelling wave solutions, and the smooth-fronted travelling wave solutions. Software to implement all calculations is available on GitHub.

q-bio.TO↗

arXiv2021

Spectrogram analysis of surface elevation signals due to accelerating ships

Spectrograms provide an efficient way to analyse surface elevation signals of ship waves taken from a sensor fixed at a single point in space. Recent work based on a simplified model for the ship's disturbance suggests that matching the spectrogram heat-map patterns to a so-called dispersion curve has the potential for estimating of properties of a steadily moving ship, such as the ship's speed and closest distance to the sensor. Here we extend the theory behind the dispersion curve so that it can be applied to ships accelerating along arbitrary paths and demonstrate how acceleration affects the structure of the associated spectrograms. Examples are provided for of a simple model of a ship accelerating/decelerating in a straight line or travelling in a circle with constant angular speed. We highlight a problem with non-uniqueness of the dispersion curve when comparing ships moving along different paths. Finally, we validate the new dispersion curve against experimental results of ship models accelerating in a finite depth basin. Our work will provide a basis for more comprehensive studies that extend the simplified model to take into account the shape of the hull in question.

physics.flu-dyn↗

arXiv2021

Travelling wave analysis of cellular invasion into surrounding tissues

Single-species reaction-diffusion equations, such as the Fisher-KPP and Porous-Fisher equations, support travelling wave solutions that are often interpreted as simple mathematical models of biological invasion. Such travelling wave solutions are thought to play a role in various applications including development, wound healing and malignant invasion. One criticism of these single-species equations is that they do not explicitly describe interactions between the invading population and the surrounding environment. In this work we study a reaction-diffusion equation that describes malignant invasion which has been used to interpret experimental measurements describing the invasion of malignant melanoma cells into surrounding human skin tissues. This model explicitly describes how the population of cancer cells degrade the surrounding tissues, thereby creating free space into which the cancer cells migrate and proliferate to form an invasion wave of malignant tissue that is coupled to a retreating wave of skin tissue. We analyse travelling wave solutions of this model using a combination of numerical simulation, phase plane analysis and perturbation techniques. Our analysis shows that the travelling wave solutions involve a range of very interesting properties that resemble certain well-established features of both the Fisher-KPP and Porous-Fisher equations, as well as a range of novel properties that can be thought of as extensions of these well-studied single-species equations. Of particular interest is that travelling wave solutions of the invasion model are very well approximated by trajectories in the Fisher-KPP phase plane that are normally disregarded. This observation establishes a previously unnoticed link between coupled multi-species reaction diffusion models of invasion and a different class of models of invasion that involve moving boundary problems.

q-bio.TO↗

arXiv2021

Mean exit time for diffusion on irregular domains

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.

physics.bio-ph↗

arXiv2020

Invading and receding sharp-fronted travelling waves

Biological invasion, whereby populations of motile and proliferative individuals lead to moving fronts that invade into vacant regions, are routinely studied using partial differential equation (PDE) models based upon the classical Fisher--KPP model. While the Fisher--KPP model and extensions have been successfully used to model a range of invasive phenomena, including ecological and cellular invasion, an often--overlooked limitation of the Fisher--KPP model is that it cannot be used to model biological recession where the spatial extent of the population decreases with time. In this work we study the \textit{Fisher--Stefan} model, which is a generalisation of the Fisher--KPP model obtained by reformulating the Fisher--KPP model as a moving boundary problem. The nondimensional Fisher--Stefan model involves just one single parameter, $κ$, which relates the shape of the density front at the moving boundary to the speed of the associated travelling wave, $c$. Using numerical simulation, phase plane and perturbation analysis, we construct approximate solutions of the Fisher--Stefan model for both slowly invading and slowly receding travelling waves, as well as for rapidly receding travelling waves. These approximations allow us to determine the relationship between $c$ and $κ$ so that commonly--reported experimental estimates of $c$ can be used to provide estimates of the unknown parameter $κ$. Interestingly, when we reinterpret the Fisher--KPP model as a moving boundary problem, many disregarded features of the classical Fisher--KPP phase plane take on a new interpretation since travelling waves solutions with $c < 2$ are not normally considered. This means that our analysis of the Fisher--Stefan model has both practical value and an inherent mathematical value.

q-bio.TO↗

arXiv2020

Exact sharp-fronted travelling wave solutions of the Fisher-KPP equation

A family of travelling wave solutions to the Fisher-KPP equation with speeds $c=\pm 5/\sqrt{6}$ can be expressed exactly using Weierstrass elliptic functions. The well-known solution for $c=5/\sqrt{6}$, which decays to zero in the far-field, is exceptional in the sense that it can be written simply in terms of an exponential function. This solution has the property that the phase-plane trajectory is a heteroclinic orbit beginning at a saddle point and ends at the origin. For $c=-5/\sqrt{6}$, there is also a trajectory that begins at the saddle point, but this solution is normally disregarded as being unphysical as it blows up for finite $z$. We reinterpret this special trajectory as an exact sharp-fronted travelling solution to a \textit{Fisher-Stefan} type moving boundary problem, where the population is receding from, instead of advancing into, an empty space. By simulating the full moving boundary problem numerically, we demonstrate how time-dependent solutions evolve to this exact travelling solution for large time. The relevance of such receding travelling waves to mathematical models for cell migration and cell proliferation is also discussed.

nlin.PS↗

arXiv2020

A sharp-front moving boundary model for malignant invasion

We analyse a novel mathematical model of malignant invasion which takes the form of a two-phase moving boundary problem describing the invasion of a population of malignant cells into a population of background tissue, such as skin. Cells in both populations undergo diffusive migration and logistic proliferation. The interface between the two populations moves according to a two-phase Stefan condition. Unlike many reaction-diffusion models of malignant invasion, the moving boundary model explicitly describes the motion of the sharp front between the cancer and surrounding tissues without needing to introduce degenerate nonlinear diffusion. Numerical simulations suggest the model gives rise to very interesting travelling wave solutions that move with speed $c$, and the model supports both malignant invasion and malignant retreat, where the travelling wave can move in either the positive or negative $x$-directions. Unlike the well-studied Fisher-Kolmogorov and Porous-Fisher models where travelling waves move with a minimum wave speed $c \ge c^* > 0$, the moving boundary model leads to travelling wave solutions with $|c| < c^{**}$. We interpret these travelling wave solutions in the phase plane and show that they are associated with several features of the classical Fisher-Kolmogorov phase plane that are often disregarded as being nonphysical. We show, numerically, that the phase plane analysis compares well with long time solutions from the full partial differential equation model as well as providing accurate perturbation approximations for the shape of the travelling waves.

nlin.PS↗

arXiv2019

Hole-closing model reveals exponents for nonlinear degenerate diffusivity functions in cell biology

Continuum mathematical models for collective cell motion normally involve reaction-diffusion equations, such as the Fisher-KPP equation, with a linear diffusion term to describe cell motility and a logistic term to describe cell proliferation. While the Fisher-KPP equation and its generalisations are commonplace, a significant drawback for this family of models is that they are not able to capture the moving fronts that arise in cell invasion applications such as wound healing and tumour growth. An alternative, less common, approach is to include nonlinear degenerate diffusion in the models, such as in the Porous-Fisher equation, since solutions to the corresponding equations have compact support and therefore explicitly allow for moving fronts. We consider here a hole-closing problem for the Porous-Fisher equation whereby there is initially a simply connected region (the hole) with a nonzero population outside of the hole and a zero population inside. We outline how self-similar solutions (of the second kind) describe both circular and non-circular fronts in the hole-closing limit. Further, we present new experimental and theoretical evidence to support the use of nonlinear degenerate diffusion in models for collective cell motion. Our methodology involves setting up a 2D wound healing assay that has the geometry of a hole-closing problem, with cells initially seeded outside of a hole that closes as cells migrate and proliferate. For a particular class of fibroblast cells, the aspect ratio of an initially rectangular wound increases in time, so the wound becomes longer and thinner as it closes; our theoretical analysis shows that this behaviour is consistent with nonlinear degenerate diffusion but is not able to be captured with commonly used linear diffusion. This work is important because it provides a clear test for degenerate diffusion over linear diffusion in cell lines.

physics.bio-ph↗

arXiv2017

The role of initial geometry in experimental models of wound closing

Wound healing assays are commonly used to study how populations of cells, initialised on a two-dimensional surface, act to close an artificial wound space. While real wounds have different shapes, standard wound healing assays often deal with just one simple wound shape, and it is unclear whether varying the wound shape might impact how we interpret results from these experiments. In this work, we describe a new kind of wound healing assay, called a sticker assay, that allows us to examine the role of wound shape in a series of wound healing assays performed with fibroblast cells. In particular, we show how to use the sticker assay to examine wound healing with square, circular and triangular shaped wounds. We take a standard approach and report measurements of the size of the wound as a function of time. This shows that the rate of wound closure depends on the initial wound shape. This result is interesting because the only aspect of the assay that we change is the initial wound shape, and the reason for the different rate of wound closure is unclear. To provide more insight into the experimental observations we describe our results quantitatively by calibrating a mathematical model, describing the relevant transport phenomena, to match our experimental data. Overall, our results suggest that the rates of cell motility and cell proliferation from different initial wound shapes are approximately the same, implying that the differences we observe in the wound closure rate are consistent with a fairly typical mathematical model of wound healing. Our results imply that parameter estimates obtained from an experiment performed with one particular wound shape could be used to describe an experiment performed with a different shape. This fundamental result is important because this assumption is often invoked, but never tested.

q-bio.CB↗