Jump to main content.


Environmental Modeling and Visualization Laboratory (EMVL) FY2013 Projects

EMVL is managed by the Center for Environmental Computing (CEC), part of the National Computer Center (NCC), Office of Technology Operations and Planning (OTOP), Office of Environmental Information (OEI). These projects reflect the wide variety of science and research being performed at EPA, are supported by EMVL and lead by EPA researchers and scientists. The projects can make use of our High Performance Computing Services, and/or our Visualization and Scientific Computing Services. The majority of these projects are funded through a rigorous application process by the Office of Research and Development.


High Performance Computing

EPA provides HPC computing resources to its researchers and scientists to speed up our ability to make environmental and public health decisions based on sound science. The wide variety of projects described below shows some of the types of research EPA does to help our program offices in their decision making.


Project Title: Computational Support for Analysis of Air Quality Data (AQDSTAT)
Principal Investigator: Dr. Jennifer Richmond-Bryant
Organization: National Center for Environmental Assessment (NCEA)
Project Description: The AQDSTAT project supports the functions of the atmospheric science group within NCEA to provide scientific assessments of the Criteria Air Pollutants (PM, SOx, NO2, CO, O3, Pb) for preparation of Integrated Science Assessments (ISAs) and research priority areas. Statistical analyses of air quality data for detailed assessment of the Criteria Pollutants will be performed under this project.

Project Title: Air Quality Forecasting: Model Development and Data Archive (AQF)
Principal Investigator: Dr. Rohit Mathur
Organization: National Exposure Research Laboratory (NERL) / Atmospheric Modeling and Analysis Division (AMAD)
Project Description: This project uses high-performance computing and data archival resources to leverage the ongoing EPA and National Oceanic and Atmospheric Administration (NOAA) collaboration in air quality forecasting to build a continuous archive of air quality model output from daily forecast applications. The long-term data archive will provide a resource to the States, Regional Planning Organizations (RPOs), and others involved in the State Implementation Plan (SIP) process. It will also provide data for air quality climatology research and linking health and epidemiological data to air quality data.

Project Title: Mitigation of Traffic Emissions Impact by Vegetative and Structural Barriers (BARRIERS)
Principal Investigator: Dr. Gayle Hagler
Organization: National Risk Management Research Laboratory (NRMRL) / Air Pollution Prevention and Control Division (APPCD)
Project Description: The BARRIERS project applies Computational Fluid Dynamics (CFD) modeling to develop a software program supporting measurement activities repeated to characterizing local air pollution impacts in close proximity to transportation sources, also referred to as near-source pollution. The project is developing virtual models of idealized highway and rail yard scenarios, both with and without barriers, and simulating the dispersion of emissions under various meteorological conditions. The project will also develop visualization and interpretation of near-source geospatial air pollution data collected using mobile monitoring approaches.

Project Title: Chesapeake Bay Estuarine Models (CHBAY)
Principal Investigator: Dr. Lewis Linker
Organization: Chesapeake Bay Program Office
Project Description: Researchers are running the Chesapeake Bay Estuary Model Package (CBEMP) to predict the effects of different pollutant control strategies - including air, non-point source, and point-source nutrient and sediment reductions - on the quality of water and living resources in the Bay. The results will be provided to the Chesapeake Executive Council to establish total maximum daily load (TMDL) for ecosystem recovery.

Project Title: CLIMATE: Development and Application of Global and Regional Climate Simulations (CLIMSIM)
Principal Investigator: Dr. Chris Nolte
Organization: National Exposure Research Laboratory (NERL) / Atmospheric Modeling and Analysis Division (AMAD)
Project Description: This project investigates methods to "downscale" global climate models (GCMs) of current and future climate from the global scale to the regional scale over the U.S. and apply those methods to generate regional climate scenarios. These scenarios will be examined to determine the potential impacts of climate change on air quality, and the impacts of adaptation and mitigation strategies on air quality and climate.

Project Title: Computational Atmospheric Chemistry (COMPCHEM)
Principal Investigator: Dr. Edward Edney
Organization: National Exposure Research Laboratory (NERL) / Human Exposure & Atmospheric Sciences Division (HEASD)
Project Description: This project's focus is determining the viability of computational atmospheric chemistry methods for characterizing the chemical reactions that control the formation and fates of gas-phase and aerosol-phase compounds affecting climate change and atmosphere toxicity. Researchers will compare predicted reaction rate constants and chemical pathways to laboratory measurements to assess the computational methods. The methods have the potential to provide EPA with a cost-effective tool for generating data that can supplement lab data and help it meet its regulatory responsibilities in a timely manner.

Project Title: Small Fish Computational Toxicology (FISHTOX)
Principal Investigator: Dr. Rong-Lin Wang
Organization: National Exposure Research Laboratory (NERL) / Ecological Exposure Research Division (EERD)
Project Description: This project uses a combination of whole organism endpoints, genomic, proteomic, and metabonomic approaches, and computational modeling to:
  • Identify new molecular biomarkers of exposure to endocrine disrupting compounds representing several modes/mechanisms of action, and
  • Link those biomarkers to effects that are relevant for both diagnostic and predictive risk assessments using small fish models.

Project Title: Gulf of Mexico Hypoxia Monitoring and Modeling: Linking Satellite Ocean Color Remote Sensing and Hydrodynamic Modeling to Understand the Mechanisms Regulating Hypoxia in the Northern Gulf of Mexico (GULFBREEZE)
Principal Investigators: Dr. John Lehrter (1) and Dr. Russ Kreis (2)
Organization: National Health and Environmental Effects Research Laboratory (NHEERL) /
(1) Gulf Ecology Division (GED) / (2) Mid-Continent Ecology Division (MED)
Project Description: The objective is the development of data analyses, realistic models, and decision support tools to improve understanding and predictive capabilities of nutrients in the environment and their impacts to environmental health. The research and development aspects involve observational and modeling efforts describing how human alterations of nutrient cycles affect nutrient source, transport, fate, and ecosystem impacts at the continental watershed and continental shelf scale. The unique continental scale modeling capacity is being developed within a state-of-the-art modeling framework that links air, land, and freshwater nutrient models to estuarine and coastal ocean models. It is envisioned that the framework could allow simultaneous assessment of air, land, water, and ocean nutrient policy impacts to the environment.

Project Title: Computational Modeling of the Human Respiratory Tract (LUNG)
Principal Investigator: Dr. Jacky Rosati
Organization: National Homeland Security Research Center (NHSRC)
Project Description: NHSRC and EMVL are currently developing a comprehensive computational fluid dynamics (CFD), morphologically-realistic model of the human respiratory tract (from nares to alveoli). The goal of this work is to model the inhalation, deposition, and clearance of contaminants, while making the model adaptable for age, race, sex, and health. The model will be used to predict dose from exposure to hazardous particulate-based contaminants, such as anthrax or ricin. This knowledge will help to better protect the public and EPA’s responders by providing critical information needed on inhaled anthrax or other aerosol-based contaminants. The model will also assist in estimating thresholds and the need for prophylactic measures.

Project Title: Models-3/CMAQ Applications (MOD3APP)
Principal Investigator: Dr. Robin Dennis
Organization: National Exposure Research Laboratory (NERL) / Atmospheric Modeling and Analysis Division (AMAD)
Project Description: Clean air and clean water are among the Administrators seven goals for the Agency. To achieve these goals, scientifically defensible models and decision support tools are needed which will characterize the complete atmospheric deposition budget for ecosystems across the nation and provide the necessary linkages between atmospheric deposition and ecosystem exposure and air quality exposure. This ORD project focuses on addressing adverse effects in both air and water media through model development and application, including connection of multi-media models.

Project Title: Third Generation Modeling System Development (MOD3DEV)
Principal Investigator: Dr. Rohit Mathur
Organization: National Exposure Research Laboratory (NERL) / Atmospheric Modeling and Analysis Division (AMAD)
Project Description: This project actively pursues the ongoing development and improvement of CMAQ simulations to make the models more computationally efficient and accurate. The project seeks to improve the fundamental understanding of atmospheric processes that regulate ambient concentrations and deposition amounts of air pollutants.

Project Title: Models-3/CMAQ Evaluation (MOD3EVAL)
Principal Investigator: Thomas Pierce
Organization: National Exposure Research Laboratory (NERL) / Atmospheric Modeling and Analysis Division (AMAD)
Project Description: The MOD3EVAL group is responsible for developing Community Multiscale Air Quality (CMAQ) simulations to evaluate the current and future releases of the CMAQ modeling system. The objective of the model evaluation is to thoroughly characterize the model performance of CMAQ, with consideration of the meteorology and emission uncertainties and their impacts on the model performance. Emissions-based models are composed of highly complex scientific algorithms concerning natural processes that can be evaluated through comparison with observations. Model evaluation is needed to establish the robustness and credibility of the air quality model simulations. CMAQ is used by the EPA Office of Air Quality Planning and Standards for numerous standard setting and rule making applications as well as by State and local agencies, and they rely on these evaluation studies to ensure the credibility of the model. These evaluation studies are also critical for identifying model improvement needs, understanding the impact of model changes, and for refining EPA's National Emission Inventory (NEI). Several applications are included in MOD3EVAL where new risks are emerging related to air quality.

Project Title: Computational Chemistry Applied to Environmental Analytical Chemistry (PAHLVGOV)
Principal Investigator: Dr. Don Betowski
Organization: National Exposure Research Laboratory (NERL) / National Exposure Research Laboratory Environmental Sciences (ESD)
Project Description: This project provides tools to quantify and predict the chemical behavior of ozone-depletion substitute compounds. It focuses on the Global Warming potentials that are needed to assess over 1,100 chemicals to determine their effect on atmospheric warming. The results from this research will include computer generated infrared spectra for over 1,100 compounds and calculated atmospheric lifetime values for up to 300 chemicals. The results of this research will allow EPA to meet our requirements to examine these compounds and determine their Global Warming potentials and threat to the environment.

Project Title: Statistics and Physiologically-Based PharmacoKinetics (PBPKSTAT)
Principal Investigator: Dr. Woodrow Setzer
Organization: National Center for Computational Toxicology (NCCT)
Project Description: The project is exploring methodology to better estimate parameters for Physiologically-Based Pharmacokinetic (PBPK) models that describe the changes in concentration of a chemical in different parts of the body after the administration of various doses. These models allow one to determine what fraction of the total dose is received by specific tissues after an oral or inhaled dose.

Project Title: Optimize the Performance of Polymeric Membranes under Pervaporation to Improve the Recovery of Biofuels (PERVAPSI)
Principal Investigator: Dr. Paul Harten
Organization: National Risk Management Research Laboratory (NRMRL)
Project Description: The project is using molecular dynamics software to simulate the performance of polymeric membranes under pervaporation. Then, only those determined to be the most promising candidates could be created and tested in the lab for further investigation. Optimizing the search for effective membranes could improve the efficient recovery of biofuels during the fermentation process.

Project Title: Development of Quantitative Structure-Property-Relationship (QSPR) Models to Predict Reactivity/Removal of Organic Chemicals in Drinking Water
Principal Investigator: Dr. Toby Sanan
Organization: National Risk Management Research Laboratory (NRMRL)
Project Description: Molecular modeling techniques, including both ab initio and molecular mechanics/semi-empirical methods, will be used to predict properties of molecules which will be correlated to experimental observables, including formation of disinfection by-products and detoxification. In addition, reaction modeling will be performed to analyze the pathways for formation of specific by-products, including N-nitrosamines, for which the mechanism of formation remains unknown.

This project has implications for several areas of EPA interest. Modeling of disinfection by-product formation and study of the mechanisms of by-product formation are both of interest because of the impact on drinking water quality. In addition, with the proliferation of ever larger numbers of novel organic molecules entering the water supply as pharmaceuticals, personal care products, or other sources, the development of predictive models for the formation of disinfection by-products is an extremely important goal; experimental assessment of risk simply isn't possible given the rapid expansion of potential chemical contaminants. Accordingly, rapid and accurate predictive models are of great importance. In tandem with this goal, improved understandings of the mechanisms of formation of such by-products is of interest both from a pure research standpoint, and because the results will give us greater insight into chemical properties likely to be of relevance to by-product formation. An extension of the above modeling to predictions related to detoxification of aqueous contaminants is of interest to NHSRC, and is also a component of the project.

Project Title: Evaluation of HPC Resources for Exploratory Data Analysis (SYSBIO)
Principal Investigator: Dr. Stephen Edwards and Dr. Holly Mortensen
Organization: National Health and Environmental Effects Research Laboratory (NHEERL)
Project Description: In ORD/NHEERL, sequencing data have been processed and analyzed by the Biostatistics and Bioinformatics Research Core (BBRC). The raw data from next generation sequencers must be aligned to a reference genome (or assembled for novel genomes) before they can be further analyzed. Alignment applications are extremely computationally intense and easily parallelized. Existing infrastructure will not support larger (e.g. genome size) sequencing alignment projects. More computationally intensive processes will be run on the EMVLs HPC machines. All work is being performed in support of the Agency commitment to the evaluation and incorporation of new technologies in molecular biology, bioinformatics, and computational toxicology.

Project Title: UberTool
Principal Investigator: Tom Purucker
Organization: National Exposure Research Laboratory (NERL)
Project Description: This project provides computational support for the Ubertool effort that has Cloud-based environmental models used by EPA for evaluating pesticide risks to ecosystems under the Federal Insecticide, Fungicide, and Rodenticide Act (FIFRA) and the Endangered Species Act (ESA). This will assist in the integration and automation of essential risk assessment functions. These functions estimate exposure and effects for the FIFRA and for listed species under the Endangered Species Act for the EPA's Endangered Species Protection Program.

Visualization and Scientific Computing

EPA provides scientists and researchers with a wide variety of environmental modeling, visualization and scientific computing support through a contract, run by OEI. Most of the projects below are selected through a competitive application process and funded by the Office of Research and Development. Several projects provide their own funding.


Project Title: Aggregated Computational Toxicology Resource (ACToR)
Principal Investigator: Dr. Richard Judson
Organization: National Center for Computational Toxicology (NCCT)
Project Description: Aggregated Computational Toxicology Resource (ACToR) is a very large database of environmental chemicals with a Web interface so that scientists worldwide can browse and search the data by chemical name, other identifiers and by chemical structure. ACToR includes chemical data assembled from over 1000 public data sources regarding over 500,000 chemicals. The ACToR System delivers information on chemical exposure, chemical hazards, and potential risks to human health and the environment. It can be used to query a specific chemical to find all available public hazard, exposure, and risk assessment data as well as previously unpublished studies related to cancer, reproductive, and developmental toxicity.

Project Title: Mitigation of Traffic Emissions Impact by Vegetative and Structural Barriers (BARRIERS)
Principal Investigator: Dr. Gayle Hagler
Organization: National Risk Management Research Laboratory (NRMRL) / Air Pollution Prevention and Control Division (APPCD)
Project Description: The BARRIERS project applies Computational Fluid Dynamics (CFD) modeling to develop a software program supporting measurement activities repeated to characterizing local air pollution impacts in close proximity to transportation sources, also referred to as near-source pollution. The project is developing virtual models of idealized highway and rail yard scenarios, both with and without barriers, and simulating the dispersion of emissions under various meteorological conditions. The project will also develop visualization and interpretation of near-source geospatial air pollution data collected using mobile monitoring approaches.

Project Title: Prediction and Measurement of Pollutant Dispersion from Open Burning and Open Detonation of Military Ordinance (DISPERSE)
Principal Investigator: Dr. Brian Gullet
Organization: National Risk Management Research Laboratory (NRMRL) / Air Pollution Prevention and Control Division (APPCD)
Project Description: EMVL staff is assisting the PI in running the Open Burning Open Detonation Model (OBODM) to simulate actual burning and detonation events at the US Army's disposal at Tooele, Utah. The PI and his research team use a package of air monitoring and measurement instruments held aloft by a balloon positioned in the plumes resulting from the Army's burning and detonation of rocket propellant and munitions. EMVL is also developing scripts to parse OBODM output and Open Source software tools to visualize that parsed model output.

Project Title: Estuary Data Mapper (ESTUARY)
Principal Investigator: Dr. Naomi Detenbeck
Organization: National Health and Environmental Effects Research Laboratory (NHEERL) / Atlantic Ecology Division (AED)
Project Description: The Estuary Data Mapper (EDM) is an application developed in 2009 by EMVL. It is an interactive graphical application that enables scientists to view and select maps of watersheds and estuaries; specify, view, and download data such as tidal measurements, discharge measurements, and water and sediment quality measurements; and save the resulting data subsets for importing into the Analytical Framework for Coastal and Estuarine Systems (ACES). The long-term goal for Estuary Data Mapper is to enable and support a community-of-practice for sharing data from multiple Federal agencies, value-added information products, and decision-support tools for Clean Water Act and related cross-media applications for estuaries and associated coastal watersheds of the United States.

Project Title: Gulf of Mexico Hypoxia Monitoring and Modeling: Linking Satellite Ocean Color Remote Sensing and Hydrodynamic Modeling to Understand the Mechanisms Regulating Hypoxia in the Northern Gulf of Mexico (GULFBREEZE)
Principal Investigators: Dr. John Lehrter (1) and Dr. Russ Kreis (2)
Organization: National Health and Environmental Effects Research Laboratory (NHEERL) /
(1) Gulf Ecology Division (GED) / (2) Mid-Continent Ecology Division (MED)
Project Description: The objective is the development of data analyses, realistic models, and decision support tools to improve understanding and predictive capabilities of nutrients in the environment and their impacts to environmental health. The research and development aspects involve observational and modeling efforts describing how human alterations of nutrient cycles affect nutrient source, transport, fate, and ecosystem impacts at the continental watershed and continental shelf scale. The unique continental scale modeling capacity is being developed within a state-of-the-art modeling framework that links air, land, and freshwater nutrient models to estuarine and coastal ocean models. It is envisioned that the framework could allow simultaneous assessment of air, land, water, and ocean nutrient policy impacts to the environment.

Project Title: Development of a Data Architecture and Modeling Infrastructure for Decision-Focused Life Cycle Assessment (LifeCycle)
Principal Investigator: Dr. Troy Hawkins
Organization: National Risk Management Research Laboratory (NRMRL) / Sustainable Technology Division (STD)
Project Description: Life cycle assessment (LCA) and systems analysis requires bringing together data from a broad array of sources within a common modeling framework. LCA efforts are often hindered by the high cost of data collection. This project furthers the development of a database and modeling suite that can be applied across a wide range of projects. The objective is to set in place the data architecture and modeling infrastructure required to support a wide array of quantitative assessments from a systems-perspective. The work will develop and disseminate models and datasets relevant to environmental decision-support and further the development of an open source, freely distributed software for performing LCA and sustainability analysis studies.

Project Title: Computational Modeling of the Human Respiratory Tract (LUNG)
Principal Investigator: Dr. Jacky Rosati
Organization: National Homeland Security Research Center (NHSRC)
Project Description: NHSRC and EMVL are currently developing a comprehensive computational fluid dynamics (CFD), morphologically-realistic model of the human respiratory tract (from nares to alveoli). The goal of this work is to model the inhalation, deposition, and clearance of contaminants, while making the model adaptable for age, race, sex, and health. The model will be used to predict dose from exposure to hazardous particulate-based contaminants, such as anthrax or ricin. This knowledge will help to better protect the public and EPA's responders by providing critical information needed on inhaled anthrax or other aerosol-based contaminants. The model will also assist in estimating thresholds and the need for prophylactic measures.

Project Title: Pesticide Root Zone Model (PRZM)
Principal Investigator: Dr. Tom Purucker
Organization: Center for Exposure Assessment Modeling (CEAM)
Project Description: PRZM3 is the most recent version of a modeling system that links two subordinate models, PRZM and VADOFT, in order to predict pesticide transport and transformation down through the crop root and unsaturated zone.

PRZM is a one-dimensional, finite-difference model that accounts for pesticide and nitrogen fate in the crop root zone. PRZM3 includes modeling capabilities for such phenomena as soil temperature simulation, volatilization and vapor phase transport in soils, irrigation simulation, microbial transformation, and a method of characteristics (MOC) algorithm to eliminate numerical dispersion. PRZM is capable of simulating transport and transformation of the parent compound and as many as two daughter species. VADOFT is a one-dimensional, finite-element code that solves the Richard's equation for flow in the unsaturated zone. The user may make use of constitutive relationships between pressure, water content, and hydraulic conductivity to solve the flow equations. VADOFT may also simulate the fate of two parent and two daughter products. The PRZM and VADOFT codes are linked together with the aid of a flexible execution supervisor that allows the user to build loading models that are tailored to site-specific situations. In order to perform probability-based exposure assessments, the code is also equipped with a Monte Carlo pre- and post-processor.

Project Title: Remote Sensing Information Gateway (RSIG)
Principal Investigator: Dr. Jim Szykman
Organization: National Exposure Research Laboratory (NERL) / National Exposure Research Laboratory Environmental Sciences (ESD)
Project Description: Advanced Accountability Tools for the Air Program: Remote Sensing Information Gateway. Since 2006 the EMVL staff has worked with EPA scientists to build the Remote Sensing Information Gateway (RSIG). RSIG offers an efficient way for users to get the multi-terabyte environmental datasets they want via an interactive, Web browser-based application. The current focus for RSIG includes 1) increasing (internal and external) access to available 3-dimensional CMAQ output generated within NERL, 2) increasing access to satellite data sets for use in the evaluation of regional chemical transport models such as CMAQ, which a specific focus on evaluation of wildfire emissions 3) continuing development on the application of fused surfaces of CMAQ model predictions and surface observations, along with the prototyping of satellite data for PM surfaces, and 4) development of a new graphical user interface and analyses functions focused on use of data sets available via RSIG for Exceptional Event analysis by state and local agencies and EPA Regions.

Project Title: Streamline Modeling of Subsurface Contamination (SMSC)
Principal Investigator: Dr. Jim Weaver
Organization: National Risk Management Research Laboratory (NRMRL) / Ground Water and Ecosystems Restoration Division (GWERD)
Project Description: To develop an efficient simulator for assessing multiple sources of contamination in watershed-scale aquifers, a combination of approaches will be used to develop a new, extensible and highly efficiency model for solving ground water transport problems. Water supply at the county government level may require balancing a series of decisions where choices for one part of a county might affect water supply in adjacent areas. Large scale simulation of water resources requires consideration of sources of water, contaminated sites, potential receptors and water supply wells. To integrate the effects of all these, efficient simulation models provide the most viable tool. This project seeks to develop an efficient, extensible approach for contaminant transport and water resources assessment at a county or larger scale and to apply the resulting technology in an existing collaborative project.

Project Title: Virtual Embryo (VEMBRYO)
Principal Investigator: Dr. Thomas Knudsen
Organization: National Center for Computational Toxicology (NCCT)
Project Description: The goal of the Virtual Embryo (VEMBRYO) project is to create a computational (in silica) framework for predictive modeling of developmental toxicity in embryos. Diagnostic signatures of prenatal developmental toxicity are being used as inputs to computational models that can extrapolate predictions from cell-level data to the developing embryo. Studies with mice and zebra fish are being used as a basis for the models. The work to date has built a "Morphogenesis Manager" written in Python. Biotapestry is being used as a visualization tool and CompuCell3D as the interactive cell-growth modeler.

Local Navigation


s

Jump to main content.