Publications

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It is necessary to establish confidence in high-consequence codes containing an extensive suite of physics algorithms in the regimes of interest. Verification problems allow code developers to assess numerical accuracy and increase confidence that specific sets of model physics were implemented correctly in the code. The two main verification techniques are code verification and solution verification. In this work, we present verification problems that can be used in other codes to increase confidence in simulations of relativistic beam transport. Specifically, we use the general plasma code EMPIRE to model and compare with the analytical solution to the evolution of the outer radial envelope of a relativistic charged particle beam. We also outline a benchmark test of a relativistic beam propagating through a vacuum and pressurized gas cell, and present the results between EMPIRE and the hybrid code GAZEL. Further, we discuss the subtle errors that were caught with these problems and detail lessons learned.

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Outdoor cultivation is commonly used to produce algal biomass for a variety of bioproducts including food, feed, fuel, pharmaceuticals, and nutraceuticals. Outdoor cultivation ponds are highly susceptible to pest pressures that may lead to periods of low productivity or even entire loss of the algal crop. Therefore, there is a need for rapid, real-time tracking of pests for early intervention to mitigate crop loss. Herein, we describe the development of a field deployable, low-cost qPCR assay for detecting both known and novel pests of a farmed eukaryotic alga species, Nannochloropsis sp. We performed a proximity guided metagenome deconvolution approach (ProxiMeta™) to discover novel pests that temporally correspond to periods of reduced pond productivity. This approach provided high-quality metagenome assemblies that were used to design qPCR probes to detect specific pests of interest. The portable qPCR assay, designed to be deployed at remote field locations, enables low-cost surveillance with a rapid (2 h) turn-around time. Frequent sampling allows for early detection and prompts intervention strategies to remedy infected ponds to minimize crop loss. The qPCR assay was used to successfully detect a known predatory bacterium within the order Bdellovibrionales both in the lab and at a remote field location. Furthermore, we assembled the genome of two novel, site-specific pests in the Saprospiraceae family and successfully designed qPCR probes that differentially detected their presence in two different pond locations. Ultimately, this assay has the potential to monitor multiple pests simultaneously and tailor targets to match likely pest infections that differ across geographical locations, helping to mitigate crop loss on a large scale.