arXiv subjects

Eamonn A. Gaffney

Publications and source records attributed to Eamonn A. Gaffney.

At least 19 recordsLinked to original sources

arXiv2026

Tunable asymmetric swimming in biflagellate microswimmers

Many biological microswimmers can modulate their swimming gait to achieve directional control of motility, especially when performing steering towards specific directional cues. This can be achieved without the need for obvious morphological or structural asymmetries in the form of the organism, or in the number or organisation of propulsion-generating appendages such as cilia. In this work, we identify and validate a core principle of asymmetric turning in biflagellate microswimmers: propulsive forces interact constructively to drive translation whilst interacting destructively to drive rotation. We explore the ramifications of this tunable biflagellar swimming mechanism across a range of systems, from a simple, back-of-the-envelope model to a detailed computational representation of an exemplar swimmer. This leads to a markedly general quantitative relation between key drivers of asymmetry, such as ciliary beat frequency, and the curvature of emergent trajectories. We discuss how the model green alga Chlamydomonas reinhardtii, which actuates its two cilia in a symmetric breaststroke for forward swimming, may exploit this feature for phototaxis. Finally, we validate our predictions in a Chlamydomonas-inspired robophysical model, implementing closed-loop control to achieve phototactic turning.

physics.bio-ph↗

arXiv2025

Chase-and-Run and Chirality in Nonlocal Models of Pattern Formation

Chase-and-run dynamics, in which one population pursues another that flees from it, are found throughout nature, from predator-prey interactions in ecosystems to the collective motion of cells during development. Intriguingly, in many of these systems, the movement is not straight; instead, 'runners' veer off at an angle from their pursuers. This angled movement often exhibits a consistent left-right asymmetry, known as lateralisation or chirality. Inspired by such phenomena in zebrafish skin patterns and evasive animal motion, we explore how chirality shapes the emergence of patterns in nonlocal (integro-differential) advection-diffusion models. We extend such models to allow movement at arbitrary angles, uncovering a rich landscape of behaviours. We find that chirality can enhance pattern formation, suppress oscillations, and give rise to entirely new dynamical structures, such as rotating pulses of chasers and runners. We also uncover how chase-and-run dynamics can cause populations to mix or separate. Through linear stability analysis, we identify physical mechanisms that drive some of these effects, whilst also exposing striking limitations of this theory in capturing more complex dynamics. Our findings suggest that chirality could have roles in ecological and cellular patterning beyond simply breaking left-right symmetry.

nlin.PS↗

arXiv2025

Modelling the impact of synovial fluid elasticity on tangential stress

The rheological properties of synovial fluid have been observed to substantially impact its lubricating behaviour. While numerous studies have illustrated the importance of its shear-dependent viscosity, the impact of synovial fluid elasticity for oscillatory joint motion is far less characterised. Hence we consider how elasticity impacts the tangential stress, and thus friction, exerted on confining surfaces in rheological models of synovial fluid on the length and time scales of oscillatory joint motion, though in a simplified setting rather than considering the full complexity of a joint. Minor changes in the elastic constitutive equation from a canonical upper convected Oldroyd-B model lead to fundamentally different scalings and predictions for tangential stress compared to either a Newtonian fluid and an Oldroyd-B fluid. In particular, polymer elasticity within physiological fluids is predicted to have a profound effect on friction both within the oscillating joint and more generally, in turn suggesting further examination of synovial fluid elasticity in experimental and modelling studies.

physics.flu-dyn↗

arXiv2025

Pattern Localisation in the Swift-Hohenberg Equation via Slowly Varying Spatial Heterogeneity

Theories of localised pattern formation are important to understand a broad range of natural patterns, but are less well-understood than more established mechanisms of domain-filling pattern formation. Here, we extend recent work on pattern localisation via slow spatial heterogeneity in reaction-diffusion systems to the Swift-Hohenberg equation. We use a WKB asymptotic approach to show that, in the limit of a large domain and slowly varying heterogeneity, conditions for Turing-type linear instability localise in a simple way, with the spatial variable playing the role of a parameter. For nonlinearities locally corresponding to supercritical bifurcations in the spatially homogeneous system, this analysis asymptotically predicts regions where patterned states are confined, which we confirm numerically. We resolve the inner region of this asymptotic approach, finding excellent agreement with the tails of these confined pattern regions. In the locally subcritical case, however, this theory is insufficient to fully predict such confined regions, and so we propose an approach based on numerical continuation of a local homogeneous analog system. Pattern localisation in the heterogeneous system can then be determined based on the Maxwell point of this system, with the spatial variable parameterizing this point. We compare this theory of localisation via spatial heterogeneity to localised patterns arising from homoclinic snaking, and suggest a way to distinguish between different localisation mechanisms in natural systems based on how these structures decay to the background state (i.e. how their tails decay). We also explore cases where both of these local theories of pattern formation fail to capture the interaction between spatial heterogeneity and underlying pattern-forming mechanisms, suggesting that more work needs to be done to fully disentangle exogenous and intrinsic heterogeneity.

nlin.PS↗

arXiv2025

Motility and rotation of multi-timescale microswimmers in linear background flows

Microswimming cells and robots exhibit diverse behaviours due to both their swimming and their environment. One of the core environmental features impacting inertialess swimming is background flows. While the influence of select flows, particularly shear flows, have been extensively investigated, these are special cases. Here, we examine inertialess swimmers in more general flows, specifically general linear planar flows that may also possess rapid oscillations. Relatively weak symmetry constraints are imposed on the swimmer to ensure planarity and to reduce complexity. A further constraint reflecting common observation is imposed, namely that the swimmer is inefficient, which we suitably define. This introduces two separate timescales: a fast timescale associated with swimmer actuation, and a second timescale associated with net swimmer movement, with inefficiency dictating that this latter timescale is much slower, allowing for a multiple timescale simplification of the governing equations. With the exception of mathematically precise edge cases, we find that the behaviour of the swimmer is dictated by two parameter groupings, both of which measure balances between the angular velocity and rate of strain of the background flow. While the measures of flow angular velocity and strain rates that primarily govern the rotational dynamics are modulated by swimmer properties, the primary features of the translational motion are determined solely by a ratio of flow angular velocity to strain rate. Hence, a simple classification of the swimmer dynamics emerges. For example, this illustrates the limited extent to which, and how, microswimmers may control their orientations and trajectories in flows.

physics.flu-dyn↗

arXiv2025

Integral Asymptotics, Coalescing Saddles, and Multiple-scales Analysis of a Generalised Swift-Hohenberg Equation

Integral asymptotics play an important role in the analysis of differential equations and in a variety of other settings. In this work, we apply an integral asymptotics approach to study spatially localized solutions of a heterogeneous generalised Swift-Hohenberg equation. The outer solution is obtained via WKBJ asymptotics, while the inner solution requires the method of coalescing saddles. We modify the classic method of Chester et al. to account for additional technicalities, such as complex branch selection and local transformation to a cubic polynomial. By integrating our results, we construct an approximate global solution to the generalised Swift-Hohenberg problem and validate it against numerical contour integral solutions. We also demonstrate an alternative approach that circumvents the complexity of integral asymptotics by analyzing the original differential equation directly through a multiple-scales analysis and show that this generates the same leading-order inner solution obtained using the coalescing saddles method at least for one of the cases considered via integral asymptotics. Our findings reinforce the significance of integral asymptotics in approximating the fourth order differential equations found in the linear stability analysis for generalisations of the Swift Hohenberg equations. This study has also highlighted a conjecture that, in certain cases, the method of coalescing saddles can be systematically replaced by multiple-scales analysis using an intermediary differential equation, a hypothesis for future investigation.

nlin.PS↗

arXiv2024

Minimal design of a synthetic cilium

We study a slender filament beating in a viscous fluid with novel curvature-dependent bending stiffness. Our numerical and experimental investigations reveal that such differential stiffness can sustain planar bending waves far along flexible filaments, in stark contrast to the uniform-stiffness case which requires more sophisticated control. In particular, we establish basal actuation as a viable, parsimonious mechanism for generating high-amplitude planar bending waves. Moreover, the resulting beat patterns closely resemble the power-and-recovery strokes of propulsive biological filaments such as cilia, suggesting extensive applications in robotic and engineered systems.

cond-mat.soft↗

arXiv2024

Persistent homology classifies parameter dependence of patterns in Turing systems

This paper illustrates a further application of topological data analysis to the study of self-organising models for chemical and biological systems. In particular, we investigate whether topological summaries can capture the parameter dependence of pattern topology in reaction diffusion systems, by examining the homology of sublevel sets of solutions to Turing reaction diffusion systems for a range of parameters. We demonstrate that a topological clustering algorithm can reveal how pattern topology depends on parameters, using the chlorite--iodide--malonic acid system, and the prototypical Schnakenberg system for illustration. In addition, we discuss the prospective application of such clustering, for instance in refining priors for detailed parameter estimation for self-organising systems.

q-bio.QM↗

arXiv2024

A first passage model of intravitreal drug delivery and residence time, in relation to ocular geometry, individual variability, and injection location

Purpose: Standard of care for various retinal diseases involves recurrent intravitreal injections. This motivates mathematical modelling efforts to identify influential factors for drug residence time, aiming to minimise administration frequency. We sought to describe the vitreal diffusion of therapeutics in nonclinical species used during drug development assessments. In human eyes, we investigated the impact of variability in vitreous cavity size and eccentricity, and in injection location, on drug elimination. Methods: Using a first passage time approach, we modelled the transport-controlled distribution of two standard therapeutic protein formats (Fab and IgG) and elimination through anterior and posterior pathways. Detailed anatomical 3D geometries of mouse, rat, rabbit, cynomolgus monkey, and human eyes were constructed using ocular images and biometry datasets. A scaling relationship was derived for comparison with experimental ocular half-lives. Results: Model simulations revealed a dependence of residence time on ocular size and injection location. Delivery to the posterior vitreous resulted in increased vitreal half-life and retinal permeation. Interindividual variability in human eyes had a significant influence on residence time (half-life range of 5-7 days), showing a strong correlation to axial length and vitreal volume. Anterior exit was the predominant route of drug elimination. Contribution of the posterior pathway displayed a small (3%) difference between protein formats, but varied between species (10-30%). Conclusions: The modelling results suggest that experimental variability in ocular half-life is partially attributed to anatomical differences and injection site location. Simulations further suggest a potential role of the posterior pathway permeability in determining species differences in ocular pharmacokinetics.

q-bio.QM↗

arXiv2024

On the speed of propagation in Turing patterns for reaction-diffusion systems

This study investigates transient wave dynamics in Turing pattern formation, focusing on waves emerging from localised disturbances. While the traditional focus of diffusion-driven instability has primarily centred on stationary solutions, considerable attention has also been directed towards understanding spatio-temporal behaviours, particularly the propagation of patterning from localised disturbances. We analyse these waves of patterning using both the well-established marginal stability criterion and weakly nonlinear analysis with envelope equations. Both methods provide estimates for the wave speed but the latter method, in addition, approximates the wave profile and amplitude. We then compare these two approaches analytically near a bifurcation point and reveal that the marginal stability criterion yields exactly the same estimate for the wave speed as the weakly nonlinear analysis. Furthermore, we evaluate these estimates against numerical results for Schnakenberg and CDIMA (chlorine dioxide-iodine-malonic acid) kinetics. In particular, our study emphasises the importance of the characteristic speed of pattern propagation, determined by diffusion dynamics and a complex relation with the reaction kinetics in Turing systems. This speed serves as a vital parameter for comparison with experimental observations, akin to observed pattern length scales. Furthermore, more generally, our findings provide systematic methodologies for analysing transient wave properties in Turing systems, generating insight into the dynamic evolution of pattern formation.

nlin.PS↗

arXiv2023

Turing instabilities are not enough to ensure pattern formation

Symmetry-breaking instabilities play an important role in understanding the mechanisms underlying the diversity of patterns observed in nature, such as in Turing's reaction--diffusion theory, which connects cellular signalling and transport with the development of growth and form. Extensive literature focuses on the linear stability analysis of homogeneous equilibria in these systems, culminating in a set of conditions for transport-driven instabilities that are commonly presumed to initiate self-organisation. We demonstrate that a selection of simple, canonical transport models with only mild multistable non-linearities can satisfy the Turing instability conditions while also robustly exhibiting only transient patterns. Hence, a Turing-like instability is insufficient for the existence of a patterned state. \ak{While it is known that linear theory can fail to predict the formation of patterns, we demonstrate that such failures can appear robustly in systems with multiple stable homogeneous equilibria.} Given that biological systems \ak{such as} gene regulatory networks and spatially distributed ecosystems often exhibit a high degree of multistability and nonlinearity, this raises important questions of how to analyse prospective mechanisms for self-organisation.

nlin.PS↗

arXiv2023

Generalised Jeffery's equations for rapidly spinning particles. Part 2: Helicoidal objects with chirality

In this two-part study, we investigate the motion of rigid, active objects in shear Stokes flow, focusing on bodies that induce rapid rotation as part of their activity. In Part 2, we derive and analyse governing equations for rapidly spinning complex-shaped particles - general helicoidal objects with chirality. Using the multiscale framework we develop in Part 1 (arXiv:2301.11311), we systematically derive emergent equations of motion for the angular and translational dynamics of these chiral spinning objects. We show that the emergent dynamics due to rapid rotation can be described by effective generalised Jeffery's equations, which differ from the classic versions via the inclusion of additional terms that account for chirality and other asymmetries. Furthermore, we use our analytic results to characterise and quantify the explicit effect of rotation on the effective hydrodynamic shape of the chiral objects, significantly expanding the scope of Jeffery's seminal study.

physics.flu-dyn↗

arXiv2023

Generalised Jeffery's equations for rapidly spinning particles. Part 1: Spheroids

The observed behaviour of passive objects in simple flows can be surprisingly intricate, and is complicated further by object activity. Inspired by the motility of bacterial swimmers, in this two-part study we examine the three-dimensional motion of rigid active particles in shear Stokes flow, focusing on bodies that induce rapid rotation as part of their activity. Here, in Part 1, we develop a multiscale framework to investigate these emergent dynamics and apply it to simple spheroidal objects. In Part 2 (arXiv:2301.11032), we apply our framework to understand the emergent dynamics of more complex shapes; helicoidal objects with chirality. Via a multiple-scales asymptotic analysis for nonlinear systems, we systematically derive emergent equations of motion for long-term trajectories that explicitly account for the strong (leading-order) effects of fast spinning. Supported by numerical examples, we constructively link these effective dynamics to the well-known Jeffery's orbits for passive spheroids, deriving an explicit closed-form expression for the effective shape of the active particle, broadening the scope of Jeffery's seminal study to spinning spheroids.

physics.flu-dyn↗

arXiv2023

Patterning of nonlocal transport models in biology: the impact of spatial dimension

Throughout developmental biology and ecology, transport can be driven by nonlocal interactions. Examples include cells that migrate based on contact with pseudopodia extended from other cells, and animals that move based on their vision of other animals. Nonlocal integro-PDE models have been used to investigate contact attraction and repulsion in cell populations in 1D. In this paper, we generalise the analysis of pattern formation in such a model from 1D to higher spatial dimensions. Numerical simulations in 2D demonstrate complex behaviour in the model, including spatio-temporal patterns, multi-stability, and the selection of spots or stripes heavily depending on interactions being attractive or repulsive. Through linear stability analysis in $N$ dimensions, we demonstrate how, unlike in local Turing reaction-diffusion models, the capacity for pattern formation fundamentally changes with dimensionality for this nonlocal model. Most notably, pattern formation is possible only in higher than one spatial dimension for both the single species system with repulsive interactions, and the two species system with `run-and-chase' interactions. The latter case may be relevant to zebrafish stripe formation, which has been shown to be driven by run-and-chase dynamics between melanophore and xanthophore pigment cells.

nlin.PS↗

arXiv2023

Spatial Heterogeneity Localizes Turing Patterns in Reaction-Cross-Diffusion Systems

Motivated by bacterial chemotaxis and multi-species ecological interactions in heterogeneous environments, we study a general one-dimensional reaction-cross-diffusion system in the presence of spatial heterogeneity in both transport and reaction terms. Under a suitable asymptotic assumption that the transport is slow over the domain, while gradients in the reaction heterogeneity are not too sharp, we study the stability of a heterogeneous steady state approximated by the system in the absence of transport. Using a WKB ansatz, we find that this steady state can undergo a Turing-type instability in subsets of the domain, leading to the formation of localized patterns. The boundaries of the pattern-forming regions are given asymptotically by `local' Turing conditions corresponding to a spatially homogeneous analysis parameterized by the spatial variable. We developed a general open-source code which is freely available, and show numerical examples of this localized pattern formation in a Schnakenberg cross-diffusion system, a Keller-Segel chemotaxis model, and the Shigesada-Kawasaki-Teramoto model with heterogeneous parameters. We numerically show that the patterns may undergo secondary instabilities leading to spatiotemporal movement of spikes, though these remain approximately within the asymptotically predicted localized regions. This theory can elegantly differentiate between spatial structure due to background heterogeneity, from spatial patterns emergent from Turing-type instabilities.

nlin.PS↗

arXiv2023

A hydrodynamic slender-body theory for local rotation at zero Reynolds number

Slender objects are commonplace in microscale flow problems, from soft deformable sensors to biological filaments such as flagella and cilia. Whilst much research has focussed on the local translational motion of these slender bodies, relatively little attention has been given to local rotation, even though it can be the dominant component of motion. In this study, we explore a classically motivated ansatz for the Stokes flow around a rotating slender body via superposed rotlet singularities, which leads us to pose an alternative ansatz that accounts for both translation and rotation. Through an asymptotic analysis that is supported by numerical examples, we determine the suitability of these flow ansatzes for capturing the fluid velocity at the surface of a slender body, assuming local axisymmetry of the object but allowing the cross-sectional radius to vary with arclength. In addition to formally justifying the presented slender-body ansatzes, this analysis reveals a markedly simple relation between the local angular velocity and the torque exerted on the body, which we term resistive torque theory. Though reminiscent of classical resistive force theories, this local relation is found to be algebraically accurate in the slender-body aspect ratio, even when translation is present, and is valid and required whenever local rotation contributes to the surface velocity at leading asymptotic order.

physics.flu-dyn↗

arXiv2023

Concentration-Dependent Domain Evolution in Reaction-Diffusion Systems

Pattern formation has been extensively studied in the context of evolving (time-dependent) domains in recent years, with domain growth implicated in ameliorating problems of pattern robustness and selection, in addition to more realistic modelling in developmental biology. Most work to date has considered prescribed domains evolving as given functions of time, but not the scenario of concentration-dependent dynamics, which is also highly relevant in a developmental setting. Here, we study such concentration-dependent domain evolution for reaction-diffusion systems to elucidate fundamental aspects of these more complex models. We pose a general form of one-dimensional domain evolution, and extend this to $N$-dimensional manifolds under mild constitutive assumptions in lieu of developing a full tissue-mechanical model. In the 1D case, we are able to extend linear stability analysis around homogeneous equilibria, though this is of limited utility in understanding complex pattern dynamics in fast growth regimes. We numerically demonstrate a variety of dynamical behaviours in 1D and 2D planar geometries, giving rise to several new phenomena, especially near regimes of critical bifurcation boundaries such as peak-splitting instabilities. For sufficiently fast growth and contraction, concentration-dependence can have an enormous impact on the nonlinear dynamics of the system both qualitatively and quantitatively. We highlight crucial differences between 1D evolution and higher dimensional models, explaining obstructions for linear analysis and underscoring the importance of careful constitutive choices in defining domain evolution in higher dimensions. We raise important questions in the modelling and analysis of biological systems, in addition to numerous mathematical questions that appear tractable in the one-dimensional setting, but are vastly more difficult for higher-dimensional models.

nlin.PS↗

arXiv2022

Cell dynamics in microfluidic devices under heterogeneous chemotaxis and growth conditions: a mathematical study

As motivated by studies of cellular motility driven by spatiotemporal chemotactic gradients in microdevices, we develop a framework for constructing approximate analytical solutions for the location, speed and cellular densities for cell chemotaxis waves in heterogeneous fields of chemoattractant from the underlying partial differential equation models. In particular, such chemotactic waves are not in general translationally invariant travelling waves, but possess a spatial variation that evolves in time, and may even may oscillate back and forth in time, according to the details of the chemotactic gradients. The analytical framework exploits the observation that unbiased cellular diffusive flux is typically small compared to chemotactic fluxes and is first developed and validated for a range of exemplar scenarios. The framework is subsequently applied to more complex models considering the full dynamics of the chemoattractant and how this may be driven and controlled within a microdevice by considering a range of boundary conditions. In particular, even though solutions cannot be constructed in all cases, a wide variety of scenarios can be considered analytically, firstly providing global insight into the important mechanisms and features of cell motility in complex spatiotemporal fields of chemoattractant. Such analytical solutions also provide a means of rapid evaluation of model predictions, with the prospect of application in computationally demanding investigations relating theoretical models and experimental observation, such as Bayesian parameter estimation.

math.AP↗