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Microvi Biotechnologies, Inc.

Superfund Research Program

An Agent-Based Modeling Platform for Environmental Biotechnology

Project Leader: Fatemeh Shirazi
Grant Number: R41ES026541
Funding Period: Phase I: September 2016 - August 2018
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Hazardous compounds in waters and soils are subject to a complex, dynamic web of interactions among physical, chemical, and biological constituents in the natural environment. Computational modeling has been proven indispensable to hazardous substances remediation, particularly integrated modeling of pollutant hydrogeological fate and transport. For the first time, however, advances in molecular-scale characterization have enabled new possibilities for more precise, realistic and truly predictive models for pollutant remediation. Specifically, simulations of complex microbial ecosystems (“microbiomes”) associated with contaminant transformation hold great promise to direct the development of a new generation of more cost effective and reliable bioremediation solutions for a range of compounds and contaminated sites. As part of this project, researchers are developing a new computational platform with the ability to predict key dynamics of natural bioremediation processes, and leveraging that information to better design remedial technologies for environmental restoration. The basis of the platform is an approach called agent-based modeling, where the behavior of individual components within complex ecosystems can calculate systems-level properties. Compared with existing computational modeling approaches, this agent-based modeling approach provides the ability to capture individual heterogeneity within complex environments, balance spatial detail with computational efficiency, and predict non-linear behaviors and kinetics across a range of spatial and temporal dynamics associated with environmental sites. The novelty of this project lies in the ability to leverage molecular and biochemical-scale parameterization to remedy the major deficiencies associated with conventional simulation approaches for pollutant biodegradation, which are often mean-field models and fitted to environmental site data. This multi-scale platform is being built, integrated, and validated in an iterative fashion using microcosm studies of a contaminated environmental site. In this way, this project is designed to both contribute to increased scientific understanding of microbiome functions in natural environments, as well as inform strategies to help further public health and environmental safety. The major outcome of this work will be a proof-of-concept of a novel, integrated and multi-scale agent-based platform for predicting the functional dynamics of environmental bioremediation. The value proposition of this project includes leveraging contemporary bioinformatics tools and databases to develop more precise, reliable and inexpensive approaches for environmental remediation. Compared with existing methods and computational models, the successful outcome of this project stands to provide benefits to a range of stakeholders, including Superfund site managers, government agencies, engineering and consulting firms, and most importantly, populations impacted by the presence of hazardous substances in their communities.

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