arXiv subjects

Wesley J. M. Ridgway

Publications and source records attributed to Wesley J. M. Ridgway.

3 recordsLinked to original sources

arXiv2026

Coarse-Graining Agent-Based Models of Bacterial Infections

Agent-based models (ABMs) provide a natural framework for representing cell-level rules and spatial heterogeneity in bacterial infections, but their computational cost limits their use for macroscopic tissue-scale simulations and broad parameter exploration. We derive a deterministic coarse-grained description for a class of bacterial-infection ABMs in which immune cells and extracellular bacteria diffuse, immune cells ingest nearby bacteria, and intracellular bacterial loads evolve through prescribed birth and clearance processes. The first coarse-grained model is a semidiscrete reaction--diffusion system that retains a discrete internal state for each immune-cell bacterial load while representing cell and bacterial populations by continuum concentration fields. The key technical step is the derivation of state-dependent effective ingestion rates from the microscopic ABM parameters: these rates are obtained by solving an auxiliary diffusion problem around a single bacterium and computing the flux of immune cells into the interaction region. We then take a continuum limit in the internal state variable, yielding a state-structured reaction--diffusion system in which intracellular dynamics appear as advection and diffusion in state space. Numerical comparisons with ensemble-averaged ABM simulations show close agreement in biologically motivated parameter regimes. The resulting framework preserves the rule-based structure of the ABM while producing PDE models that are substantially more tractable for large-scale simulation and parameter studies.

q-bio.CB↗

arXiv2025

A Weakly Nonlinear Theory for Pattern Formation in Structured Models with Localized Solutions

Structured models, such as PDEs structured by age or phenotype, provide a setting to study pattern formation in heterogeneous populations. Classical tools to quantify the emergence of patterns, such as linear and weakly nonlinear analyses, pose significant mathematical challenges for these models due to sharply peaked or singular steady states. Here, we present a weakly nonlinear framework that extends classical tools to structured PDE models in settings where the base state is spatially uniform, but exponentially localized in the structured variable. Our approach utilizes WKBJ asymptotics and an analysis of the Stokes phenomenon to systematically resolve the solution structure in the limit where the steady state tends to a Dirac-delta function. To demonstrate our method, we consider a chemically structured (nonlocal) model of motile bacteria that interact through quorum sensing. For this example, our analysis yields an amplitude equation that governs the solution dynamics near a linear instability, and predicts a pitchfork bifurcation. From the amplitude equation, we deduce an effective parameter grouping whose sign determines whether the pitchfork bifurcation is subcritical or supercritical. Although we demonstrate our framework for a specific example, our techniques are broadly applicable.

math.AP↗

arXiv2018

Locally and Globally Optimal Configurations of $N$ Particles on the Sphere with Applications in the Narrow Escape and Narrow Capture Problems

Determination of \emph{optimal} arrangements of $N$ particles on a sphere is a well-known problem in physics. A famous example of such is the Thomson problem of finding equilibrium configurations of electrical charges on a sphere. More recently however, similar problems involving other potentials and non-spherical domains have arisen in biophysical systems. Many optimal configurations have previously been computed, especially for the Thomson problem, however few results exist for potentials that correspond to more applied problems. Here we numerically compute optimal configurations corresponding to the \emph{narrow escape} and \emph{narrow capture} problems in biophysics. We provide comprehensive tables of global energy minima for $N\leq120$ and local energy minima for $N\leq65$, and we exclude all saddle points. Local minima up to $N=120$ are available online.

physics.comp-ph↗