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Abstract Many problems in fluid mechanics require single-shot 3D measurements of fluid flows, but are limited by available techniques. Here, we design and build a novel flexible high-speed two-color scanning volumetric laser-induced fluorescence (H2C-SVLIF) technique. The technique is readily adaptable to a range of temporal and spatial resolutions, rendering it easily applicable to a wide spectrum of experiments. The core equipment consists of a single monochrome high-speed camera and a pair of ND: YAG lasers pulsing at different wavelengths. The use of a single camera for direct 3D imaging eliminates the need for complex volume reconstruction algorithms and easily allows for the correction of distortion defects. Motivated by the large data loads that result from high-speed imaging techniques, we develop a custom, open-source, software package, which allows for real time playback with correction of perspective defects while simultaneously overlaying arbitrary 3D data. The technique is capable of simultaneous measurement of 3D velocity fields and a secondary tracer in the flow. To showcase the flexibility and adaptability of our technique, we present a set of experiments: (1) the flow past a sphere, and (2) vortices embedded in laminar pipe flow. In the first experiment, two channel measurements are taken at a resolution of 512 × 512 × 512 with volume rates of 65.1 Hz. In the second experiment, a single-color SVLIF system is integrated on a moving stage, providing imaging at 1280 × 304 × 256 with volume rates of 34.8 Hz. Although this second experiment is only single channel, it uses identical software and much of the same hardware to demonstrate the extraction of multiple information channels from single channel volumetric images. 

Abstract In response to the COVID-19 pandemic, many higher educational institutions moved their courses on-line in hopes of slowing disease spread. The advent of multiple highly-effective vaccines offers the promise of a return to “normal” in-person operations, but it is not clear if—or for how long—campuses should employ non-pharmaceutical interventions such as requiring masks or capping the size of in-person courses. In this study, we develop and fine-tune a model of COVID-19 spread to UC Merced’s student and faculty population. We perform a global sensitivity analysis to consider how both pharmaceutical and non-pharmaceutical interventions impact disease spread. Our work reveals that vaccines alone may not be sufficient to eradicate disease dynamics and that significant contact with an infectious surrounding community will maintain infections on-campus. Our work provides a foundation for higher-education planning allowing campuses to balance the benefits of in-person instruction with the ability to quarantine/isolate infectious individuals. 

Abstract In this paper, we present an open-source software library that can be used to numerically simulate the advection and diffusion of a chemical concentration or heat density in a viscous fluid where a moving, elastic boundary drives the fluid and acts as a source or sink. The fully-coupled fluid-structure interaction problem of an elastic boundary in a viscous fluid is solved using Peskin’s immersed boundary method. The addition or removal of the concentration or heat density from the boundary is solved using an immersed boundary-like approach in which the concentration is spread from the immersed boundary to the fluid using a regularized delta function. The concentration or density over time is then described by the advection-diffusion equation and numerically solved. This functionality has been added to our software library, IB2d , which provides an easy-to-use immersed boundary method in two dimensions with full implementations in MATLAB and Python. We provide four examples that illustrate the usefulness of the method. A simple rubber band that resists stretching and absorbs and releases a chemical concentration is simulated as a first example. Complete convergence results are presented for this benchmark case. Three more biological examples are presented: (1) an oscillating row of cylinders, representative of an idealized appendage used for filter-feeding or sniffing, (2) an oscillating plate in a background flow is considered to study the case of heat dissipation in a vibrating leaf, and (3) a simplified model of a pulsing soft coral where carbon dioxide is taken up and oxygen is released as a byproduct from the moving tentacles. This method is applicable to a broad range of problems in the life sciences, including chemical sensing by antennae, heat dissipation in plants and other structures, the advection-diffusion of morphogens during development, filter-feeding by marine organisms, and the release of waste products from organisms in flows.