Shawn D. Ryan

Correlation properties of collective motion in bacterial suspensions.

The study of collective motion in bacterial suspensions has been of significant recent interest. To better understand the non-trivial spatio-temporal correlations emerging in the course of collective swimming in suspensions of motile bacteria, a simple model is employed: a bacterium is represented as a force dipole with size, through the use of a short-range repelling potential, and shape. The model emphasizes two fundamental mechanisms: dipolar hydrodynamic interactions and short-range bacterial collisions. Using direct particle simulations validated by a dedicated experiment, we show that changing the swimming speed or concentration alters the time scale of sustained collective motion, consistent with experiment. Also, the correlation length in the collective state is almost constant as concentration and swimming speed change even though increasing each greatly increases the input of energy to the system. We demonstrate that the particle shape is critical for the onset of collective effects. In addition, new experimental results are presented illustrating the onset of collective motion with an ultrasound technique. This work exemplifies the delicate balance between various physical mechanisms governing collective motion in bacterial suspensions and provides important insights into its mesoscopic nature.

A Kinetic Model for Semidilute Bacterial Suspensions

Suspensions of self-propelled microscopic particles, such as swimming bacteria, exhibit collective motion leading to remarkable experimentally observable macroscopic properties. Rigorous mathematical analysis of this emergent behavior can provide significant insight into the mechanisms behind these experimental observations; however, there are many theoretical questions remaining unanswered. In this paper, we study a coupled PDE/ODE system first introduced in the physics literature and used to investigate numerically the effective viscosity of a bacterial suspension. We then examine the kinetic theory associated with the coupled system, which is designed to capture the long-time behavior of a Stokesian suspension of point force dipoles (infinitesimal spheroids representing self-propelled particles) with Lennard-Jones--type repulsion. A planar shear background flow is imposed on the suspension through the novel use of Lees--Edwards quasi-periodic boundary conditions applied to a representative volume. We s...

A model for collective dynamics in ant raids

Ant raiding, the process of identifying and returning food to the nest or bivouac, is a fascinating example of collective motion in nature. During such raids ants lay pheromones to form trails for others to find a food source. In this work a coupled PDE/ODE model is introduced to study ant dynamics and pheromone concentration. The key idea is the introduction of two forms of ant dynamics: foraging and returning, each governed by different environmental and social cues. The model accounts for all aspects of the raiding cycle including local collisional interactions, the laying of pheromone along a trail, and the transition from one class of ants to another. Through analysis of an order parameter measuring the orientational order in the system, the model shows self-organization into a collective state consisting of lanes of ants moving in opposite directions as well as the transition back to the individual state once the food source is depleted matching prior experimental results. This indicates that in the absence of direct communication ants naturally form an efficient method for transporting food to the nest/bivouac. The model exhibits a continuous kinetic phase transition in the order parameter as a function of certain system parameters. The associated critical exponents are found, shedding light on the behavior of the system near the transition.

Curvature-driven foam coarsening on a sphere: A computer simulation.

The von Neumann-Mullins law for the area evolution of a cell in the plane describes how a dry foam coarsens in time. Recent theory and experiment suggest that the dynamics are different on the surface of a three-dimensional object such as a sphere. This work considers the dynamics of dry foams on the surface of a sphere. Starting from first principles, we use computer simulation to show that curvature-driven motion of the cell boundaries leads to exponential growth and decay of the areas of cells, in contrast to the planar case where the growth is linear. We describe the evolution and distribution of cells to the final stationary state.

Anomalous Fluctuations in the Orientation and Velocity of Swarming Bacteria

Simultaneous acquisition of phase-contrast light microscopy and fluorescently labeled bacteria, moving within a dense swarm, reveals the intricate interactions between cells and the collective flow around them. By comparing wild-type and immotile cells embedded in a dense wild-type swarm, the effect of the active thrust generated by the flagella can be singled out. It is shown that while the distribution of angles among cell velocity, cell orientation, and the local flow around it is Gaussian-like for immotile bacteria, wild-type cells exhibit anomalous non-Gaussian deviations and are able to move in trajectories perpendicular to the collective flow. Thus, cells can maneuver or switch between local streams and jets. A minimal model describing bacteria as hydrodynamic force dipoles shows that steric effects, hydrodynamics interactions, and local alignments all have to be taken into account to explain the observed dynamics. These findings shed light on the physical mechanisms underlying bacterial swarming and the balance between individual and collective dynamics.

A finite volume method for computing flow induced orientation of nematic liquid crystals

ABSTRACT In this work, we propose a new method for studying dynamics in a liquid crystal arising from torques due to an externally imposed shear flow or other sources of torque. Here a spatially homogeneous liquid crystal system governed by a Smoluchowski equation for the orientational probability density function is investigated. To analyze the PDE model, we develop a novel direct computational algorithm based on a Voronoi cell-based finite volume scheme. This method has the capability of describing abrupt changes in the density function, using fluxes through cell boundaries. We first validate our approach by capturing prior results from Maier-Saupe theory illustrating a phase transition in the system due to nematic interactions as well as the effects of an externally imposed electric field. We then investigate the coupling of an external flow field with the Smoluchowski equation describing the full orientational dynamics of the system.

Individual based modeling and analysis of pathogen levels in poultry chilling process

Pathogen control during poultry processing critically depends on more enhanced insight into contamination dynamics. In this study we build an individual based model (IBM) of the chilling process. Quantifying the relationships between typical Canadian processing specifications, water chemistry dynamics and pathogen levels both in the chiller water and on individual carcasses, the IBM is shown to provide a useful tool for risk management as it can inform risk assessment models. We apply the IBM to Campylobacter spp. contamination on broiler carcasses, illustrating how free chlorine (FC) sanitization, organic load in the water, and pre-chill carcass pathogen levels affect pathogen levels of post-chill broilers. In particular, given a uniform distribution of Campylobacter levels on incoming poultry we quantify the efficacy of FC control in not only reducing pathogen levels on average, but also the variation of pathogen levels on poultry exiting the chill tank. Furthermore, we demonstrate that the absence/presence of FC input dramatically influences when, during a continuous chilling operation, cross-contamination will be more likely.

Effective Rheological Properties in Semi-dilute Bacterial Suspensions

Interactions between swimming bacteria have led to remarkable experimentally observable macroscopic properties such as the reduction in the effective viscosity, enhanced mixing, and diffusion. In this work, we study an individual-based model for a suspension of interacting point dipoles representing bacteria in order to gain greater insight into the physical mechanisms responsible for the drastic reduction in the effective viscosity. In particular, asymptotic analysis is carried out on the corresponding kinetic equation governing the distribution of bacteria orientations. This allows one to derive an explicit asymptotic formula for the effective viscosity of the bacterial suspension in the limit of bacterium non-sphericity. The results show good qualitative agreement with numerical simulations and previous experimental observations. Finally, we justify our approach by proving existence, uniqueness, and regularity properties for this kinetic PDE model.