8 papers
Reduced-Precision Stochastic Simulation for Mathematical Biology
Tom Kimpson, Mark B. Flegg, Jennifer A. Flegg
The stochastic simulation algorithm (SSA) is widely used to perform exact forward simulation of discrete stochastic processes in biology. However, the computational cost, driven by…
Mathematical modeling of biochemical signal propagation in many-stage enzymatic pathways
Chathranee Jayathilaka, Mark B. Flegg
Biochemical signalling cascades transduce extracellular stimuli into cellular responses through sequences of discrete, node-to-node activations. While signal fidelity depends criti…
Multiscale Modelling of Birth-Death Processes
Tom Kimpson, Domenic P. J. Germano, Jennifer A. Flegg +1
Many biological systems exhibit multiscale dynamics, where some species occur in high copy numbers while others remain rare. This heterogeneity necessitates hybrid modelling approa…
Particle-based simulation of non-elementary bimolecular kinetics
Taylor Kearney, Mark B. Flegg
Particle-based simulations are an essential tool for the study of biochemical systems for scales between molecular/Brownian dynamics and the reaction-diffusion master equation. The…
A hybrid framework for compartmental models enabling simulation-based inference
Domenic P. J. Germano, Alexander E. Zarebski, Sophie Hautphenne +3
Multi-scale systems often exhibit a combination of stochastic and deterministic dynamics. In compartmental models, low occupancy compartments tend to exhibit stochastic dynamics wh…
Evaluating interventions for Plasmodium vivax forest malaria using a three-scale mathematical model
Shoshana Elgart, Mark B. Flegg, Jennifer A. Flegg
The rising proportion of Plasmodium vivax cases concentrated in forest-fringe areas across the Greater Mekong Subregion highlights the importance of pharmaceutical and mosquito con…