Contamination dynamics of active rods in long microchannels
Abstract
Active rods are elongated, self-propelled particles that serve as effective models for motile microorganisms, such as bacteria and sperm cells. When confined to a microfluidic channel, active rods exhibit a distinctive motility pattern: they tend to swim against the fluid flow along channel walls. In pressure-driven channel flow, they alternate between long upstream runs along the walls and short downstream spurts in the bulk. This behavior has practical implications for bacterial contamination of catheters and microfluidic devices against the flow. We study the spreading of a population of active rods along long microchannels using a hierarchy of models. Monte Carlo simulations of a three-dimensional model show that net upstream transport depends non-monotonically on the flow rate, decreases with rotational diffusion, and depends on the shape of the channel cross-section. The simulations also show that upstream and downstream persistence times follow exponentially decaying distributions. This motivates the derivation of a one-dimensional, two-state velocity-jump model. For exponentially distributed persistence times, we derive the evolution equation for the concentration of continuously injected rods and determine its long-time limit in closed form. This analysis reveals a concentration plateau upstream of the source when the mean upstream velocity is positive and exponential decay otherwise. Using parameters measured from the three-dimensional simulations, the one-dimensional model reproduces the concentration profiles from the Monte Carlo simulations, and these results are consistent with recent experimental observations of bacterial contamination in microfluidic devices.
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BibTeX
@misc{palos2026contamination,
title = {{Contamination dynamics of active rods in long microchannels}},
author = {Jason Palos and Chase Brown and Mykhailo Potomkin and Shawn D. Ryan},
howpublished = {arXiv},
year = {2026},
month = oct,
doi = {10.48550/arxiv.2610.09204},
eprint = {2610.09204},
archivePrefix = {arXiv},
url = {https://arxiv.org/abs/2610.09204},
}
RIS
TY - UNPB
TI - Contamination dynamics of active rods in long microchannels
AU - Jason Palos
AU - Chase Brown
AU - Mykhailo Potomkin
AU - Shawn D. Ryan
PY - 2026
DA - 2026/10/06
PB - arXiv
DO - 10.48550/arxiv.2610.09204
UR - https://arxiv.org/abs/2610.09204
AB - Active rods are elongated, self-propelled particles that serve as effective models for motile microorganisms, such as bacteria and sperm cells. When confined to a microfluidic channel, active rods exhibit a distinctive motility pattern: they tend to swim against the fluid flow along channel walls. In pressure-driven channel flow, they alternate between long upstream runs along the walls and short downstream spurts in the bulk. This behavior has practical implications for bacterial contamination of catheters and microfluidic devices against the flow. We study the spreading of a population of active rods along long microchannels using a hierarchy of models. Monte Carlo simulations of a three-dimensional model show that net upstream transport depends non-monotonically on the flow rate, decreases with rotational diffusion, and depends on the shape of the channel cross-section. The simulations also show that upstream and downstream persistence times follow exponentially decaying distributions. This motivates the derivation of a one-dimensional, two-state velocity-jump model. For exponentially distributed persistence times, we derive the evolution equation for the concentration of continuously injected rods and determine its long-time limit in closed form. This analysis reveals a concentration plateau upstream of the source when the mean upstream velocity is positive and exponential decay otherwise. Using parameters measured from the three-dimensional simulations, the one-dimensional model reproduces the concentration profiles from the Monte Carlo simulations, and these results are consistent with recent experimental observations of bacterial contamination in microfluidic devices.
ER -