This action funds an NSF Postdoctoral Research Fellowship in Biology for FY 2020, Integrative Research Investigating the Rules of Life Governing Interactions Between Genomes, Environment and Phenotypes. The fellowship supports research and training of the Fellow that will contribute to the area of Rules of Life in innovative ways. Our daily lives involve biofilms, complex arrangements of beneficial and detrimental bacteria. For example, biofilms affect many forms of wastewater and water treatment. Currently, answering basic ?what-if? questions about controlling biofilms involves intensive, hard to generalize, experimental work. However, improved computing abilities have begun to enable biofilm simulations. Tools such as the Newcastle University Frontiers in Engineering Biology Individual Based Model (NUFEB IbM) of biofilms promise to advance research by enabling rapid design and reducing the number of needed experiments. Right now, the barrier to using these tools is high; expertise is required between many fields and across many ?levels? of biology. The Fellow intends to help the NUFEB model transition from a subject of research into a tool for research not only by improving its predictions, but also by making the tool more useful and usable to a broader range of researchers and educators.

The project goal is to improve the NUFEB IbM through: extension, validation, and facilitation. The Fellow will extend the IbM to simulate antagonistic interactions though type VI secretion systems. Implementing those ecologically relevant systems will also enable modeling the broader class of ?chemically mediated interactions? (e.g., quorum sensing and antimicrobial kin selection). Validation will be performed against biofilms grown in microfluidic reactors incorporating multiple levels of physical and biological complexity. Further, the validation will be model-agnostic, providing a common reference frame for comparisons between biofilm simulations. Facilitation will reduce the barrier to entry and will go beyond ?better documentation?. A domain specific language will be developed which better represents the simulated biology and will be incorporated with a supporting tool-set, similar in spirit to the PyFoam tools used to enhance OpenFOAM computational fluid dynamics usability. The impact will be broadened by using the NUFEB IbM to develop interactive ?play-based? lessons aimed at the secondary school level. Additionally, these goals support the training of the Fellow; they partially overlap with but also significantly extend their skills. The experience will also help the Fellow establish their independence, acquire experience in non-research tasks of a project (e.g., budget management), and establish their professional niche and while growing their existing network.

This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.

National Science Foundation (NSF)
Division of Biological Infrastructure (DBI)
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John Barthell
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Weaver, Joseph Earl
United States
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