Simulations and Experiments in Small Scale Bio-Locomotion

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Hoa Nguyen and Orrin Shindell


The most numerous organisms on Earth are also the smallest. Over the past four billion years, single-celled and simple multicellular organisms have evolved motility mechanisms particularly-suited for locomotion in their low Reynolds number environment. Considerable progress has been made to understand biological processes and fluid dynamics at this small scale over the past fifty years. Simulations and experiments have shed light on the complex locomotion strategies spanning from a lone single cell to collective groups of cells in Newtonian and non-Newtonian fluids. In this two-part mini-symposium, researchers studying the locomotion of simple organisms through computer simulations, fluid dynamics theory, and experimental measurements, will present their results. The diversity of these presentations shows the importance of the coordination between modeling and experiments to further our knowledge of the interactions of organisms and their surrounding fluid environment.

Orrin Shindell

Trinity University, United States,
"Rigid Body Dynamics of Motile Bacteria near Surfaces"
Bacteria in their natural environment switch between living as free-swimming individual cells and living as members of surface-aggregated communities. To perform this transition, individual cells must contend with the hydrodynamic force interactions between them and the surface. In our work, we determine these interactions by combining experiments and numerical simulations. Using total internal reflection microscopy, we acquire time lapse images of fluorescent bacteria swimming near a surface. By analyzing the intensity profiles, we reconstruct the three-dimensional trajectories of the bacteria. We then input the measured trajectories into a computational fluid dynamics model – the method of images for regularized Stokeslets – and calculate the force and torque exerted on the bacteria when they swim near the surface. In this talk, we will present the technical details of the experiment, show the resulting measurements, and discuss the computational approach.

Meuriq Galagher

University of Birmingham, United Kingdom,
"FAST: Automated Flagellar Capture as a Research and Clinical Tool"
In an age where huge amounts of imaging data can be readily produced it is increasingly important to be able to accurately and efficiently this information, and to be able to use these analyses as a marker for clinical outcome. However, semen analysis in the human is currently limited to methods such as sperm counting and analysis of fixed cells. To address this, we have developed and released FAST, a free-to-use package for the high-throughput detection and tracking of large numbers of beating flagella in experimental microscopy videos. In this talk we will discuss how the combination of experimental data analysis, integrated with mathematical and numerical modelling of the elastohydrodynamic environment, can be utilised to understand the characteristics of flagellar motility in a semen sample. We will focus on what this means in the context of using clinical data from Birmingham Women’s Hospital, and international partners, in order to improve outcomes from assisted reproductive technologies.

Suzanne Jacobs

UT Austin, United States,
"To Swarm or to Slide? Understanding the Mechanics of Bacterial Colony Expansion"
Whether in our guts or on our skin, on our medical devices or along the roots of our crops, microbes have always been an invisible part of human life. Now, thanks to advances in genomics technology, we can identify which microbes are where and understand how they influence human and environmental health. But to ever effectively manipulate these microbial ecosystems to our benefit, we must understand not only their composition, but also the physics of microbial surface colonization. In this talk, I will describe how colonies of the common soil bacteria Bacillus subtilis swarm and slide along surfaces and what we know about the forces that individual bacteria experience during these processes. Understanding such forces will be crucial to identifying the physical triggers that promote or inhibit various modes of surface colonization.

Bruce Rodenborn

Centre College, United States,
"Life at Low Reynolds Number in a Macroscopic Lab"
The swimming of microorganisms is typically analyzed using biological experiments or numerical simulations because of the difficulty of making microscopic measurements of forces and torques. Our research group uses model macroscopic experiments with typical length scales of ≈ 10 cm, but match the low Reynolds number of microoganisms by using a highly viscous silicone oil that is 105 more viscous than water but with approximately the same density. We can build laboratory scale robotic swimmers and model microorganisms that are typically ≈ 10 µm, while keeping the Reynolds much less than unity. We also explore fundamental theories such as building a laboratory scale three-link swimmer (Purcell 1977). We compare our laboratory experiments of helical flagella with complimentary numerical simulations and find good agreement. We also compare our results with theory from geometric mechanics, which predicts the translation and rotation of a three-link swimmer for a given gate.

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Virtual conference of the Society for Mathematical Biology, 2020.