Eamonn A. Gaffney
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View article: Motility and rotation of multiple-time-scale microswimmers in linear background flows
Motility and rotation of multiple-time-scale microswimmers in linear background flows Open
Microswimming cells and robots exhibit diverse behaviours due to both their swimming and their environment. One key environmental feature is the presence of a background flow. While the influences of select flows, particularly steady shear…
View article: Chase-and-Run and Chirality in Nonlocal Models of Pattern Formation
Chase-and-Run and Chirality in Nonlocal Models of Pattern Formation Open
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 t…
View article: An Asymptotic Analysis of Bivalent Monoclonal Antibody-Antigen Binding
An Asymptotic Analysis of Bivalent Monoclonal Antibody-Antigen Binding Open
View article: An Overview from Physically-Based to Data-Driven Approaches of the Modelling and Simulation of Glioblastoma Progression in Microfluidic Devices
An Overview from Physically-Based to Data-Driven Approaches of the Modelling and Simulation of Glioblastoma Progression in Microfluidic Devices Open
In silico models and computational tools are invaluable instruments that complement experiments to improve our understanding of complex phenomena such as cancer evolution. This work offers a perspective on different approaches that can be …
View article: Understanding antibody–target antigen interactions and the avidity effect using mathematical modelling
Understanding antibody–target antigen interactions and the avidity effect using mathematical modelling Open
Immunotherapies are designed to exploit the immune system to target pathologies such as cancer. Monoclonal antibodies (mAbs) are an important class of immunotherapies that induce anti-tumour effects. Fundamental to the success of mAbs in c…
View article: Modeling the Ocular Pharmacokinetics and Pharmacodynamics of Ranibizumab for Improved Understanding and Data Collection Strategies in Ocular Diseases
Modeling the Ocular Pharmacokinetics and Pharmacodynamics of Ranibizumab for Improved Understanding and Data Collection Strategies in Ocular Diseases Open
This study extends our understanding of the ocular pharmacokinetics and pharmacodynamics of ranibizumab and provides theoretical insights for enhanced data collection schemes to be considered for clinical trials and in the development of n…
View article: An Asymptotic Analysis of Bivalent Monoclonal Antibody-Antigen Binding
An Asymptotic Analysis of Bivalent Monoclonal Antibody-Antigen Binding Open
Ligand-receptor interactions are fundamental to many biological processes. For example in antibody-based immunotherapies, the dynamics of an antibody binding with its target antigen directly influence the potency and efficacy of monoclonal…
View article: Applying population mechanistic modelling to find determinants of chimeric antigen receptor T-cells dynamics in month-one lymphoma patients
Applying population mechanistic modelling to find determinants of chimeric antigen receptor T-cells dynamics in month-one lymphoma patients Open
Background Chimeric antigen receptor (CAR) T-cells have been utilized for the treatment of several malignancies, including Non-Hodgkin lymphomas. A myriad of product- and patient-specific factors determines the extent of patient response, …
View article: Minimal design of a synthetic cilium
Minimal design of a synthetic cilium Open
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 flexi…
View article: RNA editing is a molecular clock in unmodified human cells
RNA editing is a molecular clock in unmodified human cells Open
Despite major advances in spatial RNA sequencing, the ability to extract temporal information in RNA sequencing experiments is still limited. Here, we describe Transcriptome Timestamping (T2), a system which harnesses naturally occurring A…
View article: A First-Passage Model of Intravitreal Drug Delivery and Residence Time—Influence of Ocular Geometry, Individual Variability, and Injection Location
A First-Passage Model of Intravitreal Drug Delivery and Residence Time—Influence of Ocular Geometry, Individual Variability, and Injection Location Open
The modeling 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 permeabilit…
View article: Persistent homology classifies parameter dependence of patterns in Turing systems
Persistent homology classifies parameter dependence of patterns in Turing systems Open
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 dep…
View article: Pattern Localisation in Swift-Hohenberg via Slowly Varying Spatial Heterogeneity
Pattern Localisation in Swift-Hohenberg via Slowly Varying Spatial Heterogeneity Open
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 patter…
View article: On the speed of propagation in Turing patterns for reaction–diffusion systems
On the speed of propagation in Turing patterns for reaction–diffusion systems Open
View article: Understanding Antibody-Target Antigen Interactions and the Avidity Effect Using Mathematical Modelling
Understanding Antibody-Target Antigen Interactions and the Avidity Effect Using Mathematical Modelling Open
Background and Purpose Immunotherapies are designed to exploit the immune system to target pathologies, for instance, but not exclusively, cancer. Monoclonal antibodies (mAbs) are an important class of immunotherapies that induce anti-tumo…
View article: Sensitivity of cartilage mechanical behaviour to spatial variations in material properties
Sensitivity of cartilage mechanical behaviour to spatial variations in material properties Open
Articular cartilage tissue exhibits a spatial dependence in material properties that govern mechanical behaviour. A mathematical model of cartilage tissue under one dimensional confined compression testing is developed for normal tissue th…
View article: A first passage model of intravitreal drug delivery and residence time, in relation to ocular geometry, individual variability, and injection location
A first passage model of intravitreal drug delivery and residence time, in relation to ocular geometry, individual variability, and injection location Open
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 fre…
View article: On the speed of propagation in Turing patterns for reaction-diffusion systems
On the speed of propagation in Turing patterns for reaction-diffusion systems Open
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,…
View article: Minimal design of a synthetic cilium
Minimal design of a synthetic cilium Open
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 flexi…
View article: Turing Instabilities are Not Enough to Ensure Pattern Formation
Turing Instabilities are Not Enough to Ensure Pattern Formation Open
View article: Generalised Jeffery's equations for rapidly spinning particles. Part 1. Spheroids
Generalised Jeffery's equations for rapidly spinning particles. Part 1. Spheroids Open
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…
View article: Generalised Jeffery's equations for rapidly spinning particles. Part 2. Helicoidal objects with chirality
Generalised Jeffery's equations for rapidly spinning particles. Part 2. Helicoidal objects with chirality Open
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 spin…
View article: Turing Pattern Formation in Reaction-Cross-Diffusion Systems with a Bilayer Geometry
Turing Pattern Formation in Reaction-Cross-Diffusion Systems with a Bilayer Geometry Open
Conditions for self-organisation via Turing’s mechanism in biological systems represented by reaction-diffusion or reaction-cross-diffusion models have been extensively studied. Nonetheless, the impact of tissue stratification in such syst…
View article: Mathematical modelling of ocular epithelial transport: a review
Mathematical modelling of ocular epithelial transport: a review Open
Purpose: Ocular epithelial layers are fundamental for the physiology of the eye as they regulate water transport. The purpose of this review is to discuss the existing mathematical models of water transport across these layers. Methods: We…
View article: Patterning of nonlocal transport models in biology: The impact of spatial dimension
Patterning of nonlocal transport models in biology: The impact of spatial dimension Open
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 awareness…
View article: A Mathematical Modelling Study of Chemotactic Dynamics in Cell Cultures: The Impact of Spatio-temporal Heterogeneity
A Mathematical Modelling Study of Chemotactic Dynamics in Cell Cultures: The Impact of Spatio-temporal Heterogeneity Open
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 c…
View article: Turing instabilities are not enough to ensure pattern formation
Turing instabilities are not enough to ensure pattern formation Open
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 transpor…
View article: Patterning of nonlocal transport models in biology: the impact of spatial dimension
Patterning of nonlocal transport models in biology: the impact of spatial dimension Open
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…
View article: Turing pattern formation in reaction-cross-diffusion systems with a bilayer geometry
Turing pattern formation in reaction-cross-diffusion systems with a bilayer geometry Open
Conditions for self-organisation via Turing’s mechanism in biological systems represented by reaction-diffusion or reaction-cross-diffusion models have been extensively studied. Nonetheless, the impact of tissue stratification in such syst…
View article: Squirmer hydrodynamics near a periodic surface topography
Squirmer hydrodynamics near a periodic surface topography Open
The behaviour of microscopic swimmers has previously been explored near large-scale confining geometries and in the presence of very small-scale surface roughness. Here, we consider an intermediate case of how a simple microswimmer, the ta…