arXiv subjects

John A. Mackenzie

Publications and source records attributed to John A. Mackenzie.

4 recordsLinked to original sources

arXiv2026

The impact of nonheritable variation in division rates on population growth across environments

Phenotypic heterogeneity is a pervasive feature of biological populations, yet its impact on population growth is often interpreted through changes in mean individual fitness alone. In this paper, we investigate how nonheritable variability in division rates influences the asymptotic growth of a population. Using a class of linear models with phenotypic structure, we show that variability modifies the dominant eigenvalue of the system in a nonlinear manner, leading to an intrinsic tradeoff: while variability reduces population growth under favourable conditions, it mitigates population decline under stress. These results provide a simple mechanistic framework for understanding how heterogeneity influences population-level dynamics. In particular, they suggest that stress-dependent amplification of mutational effects may arise from changes in phenotypic variability, rather than from changes in mean fitness alone. We illustrate this mechanism using mutation accumulation data in Chlamydomonas reinhardtii, where the observed patterns of relative fitness under increasing stress are consistent with increased variability within genotypes. More broadly, our analysis highlights the importance of variability as a determinant of population growth, and shows that some effects commonly attributed to changes in mean fitness may instead reflect the nonlinear consequences of phenotypic heterogeneity.

q-bio.PE↗

arXiv2019

A Moving Mesh Method for Modelling Defects in Nematic Liquid Crystals

The properties of liquid crystals can be modelled using an order parameter which describes the variability of the local orientation of rod-like molecules. Defects in the director field can arise due to external factors such as applied electric or magnetic fields, or the constraining geometry of the cell containing the liquid crystal material. Understanding the formation and dynamics of defects is important in the design and control of liquid crystal devices, and poses significant challenges for numerical modelling. In this paper we consider the numerical solution of a $\bf{Q}$-tensor model of a nematic liquid crystal, where defects arise through rapid changes in the $\bf{Q}$-tensor over a very small physical region in relation to the dimensions of the liquid crystal device. The efficient solution of the resulting six coupled partial differential equations is achieved using a finite element based adaptive moving mesh approach, where an unstructured triangular mesh is adapted towards high activity regions, including those around defects. Spatial convergence studies are presented using a stationary defect as a model test case, and the adaptive method is shown to be optimally convergent using quadratic triangular finite elements. The full effectiveness of the method is then demonstrated using a challenging two-dimensional dynamic Pi-cell problem involving the creation, movement, and annihilation of defects.

math.NA↗

arXiv2019

A Conservative Finite Element ALE Scheme for Mass-Conserving Reaction-Diffusion Equations on Evolving Two-Dimensional Domains

Mass-conservative reaction-diffusion systems have recently been proposed as a general framework to describe intracellular pattern formation. These systems have been used to model the conformational switching of proteins as they cycle from an inactive state in the cell cytoplasm, to an active state at the cell membrane. The active state then acts as input to downstream effectors. The paradigm of activation by recruitment to the membrane underpins a range of biological pathways - including G-protein signalling, growth control through Ras and PI 3-kinase, and cell polarity through Rac and Rho; all activate their targets by recruiting them from the cytoplasm to the membrane. Global mass conservation lies at the heart of these models reflecting the property that the total number of active and inactive forms, and targets, remains constant. Here we present a conservative arbitrary Lagrangian Eulerian (ALE) finite element method for the approximate solution of systems of bulk-surface reaction-diffusion equations on an evolving two-dimensional domain. Fundamental to the success of the method is the robust generation of bulk and surface meshes. For this purpose, we use a moving mesh partial differential equation (MMPDE) approach. Global conservation of the fully discrete finite element solution is established independently of the ALE velocity field and the time step size. The developed method is applied to model problems with known analytical solutions; these experiments indicate that the method is second-order accurate and globally conservative. The method is further applied to a model of a single cell migrating in the presence of an external chemotactic signal.

math.NA↗

arXiv2018

A coupled bulk-surface model for cell polarisation

Several cellular activities, such as directed cell migration, are coordinated by an intricate network of biochemical reactions which lead to a polarised state of the cell, in which cellular symmetry is broken, causing the cell to have a well defined front and back. Recent work on balancing biological complexity with mathematical tractability resulted in the proposal and formulation of a famous minimal model for cell polarisation, known as the wave pinning model. In this study, we present a three-dimensional generalisation of this mathematical framework through the maturing theory of coupled bulk-surface semilinear partial differential equations in which protein compartmentalisation becomes natural. We show how a local perturbation over the surface can trigger propagating reactions, eventually stopped in a stable profile by the interplay with the bulk component. We describe the behavior of the model through asymptotic and local perturbation analysis, in which the role of the geometry is investigated. The bulk-surface finite element method is used to generate numerical simulations over simple and complex geometries, which confirm our analysis, showing pattern formation due to propagation and pinning dynamics. The generality of our mathematical and computational framework allows to study more complex biochemical reactions and biomechanical properties associated with cell polarisation in multi-dimensions.

q-bio.CB↗