Quality Assurance Model

Jonathan S. Clough Environmental / Computer Consultant

Warren Pinnacle Consulting, Inc. *******@**************.***

P.O. Box 253 http://www.warrenpinnacle.com/

Warren VT 05674 802-***-****; fax 802-***-****

Key Qualifications

Jonathan Clough has been an environmental consultant since 1994 with special emphasis on developing

object-oriented environmental computer models. Since 1995, he has been the primary programmer for the

AQUATOX bioaccumulation, toxicant fate, and effects model. Since 1998, Mr. Clough has been

programming and applying bioaccumulation models for EPA Region 1 in support of the Modeling Study of

PCB Contamination in the Housatonic River including formal reporting of model calibration and validation

and response to peer-reviewer comments. He has been developing and applying the SLAMM (Sea Level

Affecting Marshes Model) since 1998. Mr. Clough founded Warren Pinnacle Consulting, Inc. in 2001.

Education

B.A. Environmental Studies (Honors), Brown University, 1994.

B.A. Economics, Brown University, 1994.

Phillips Academy, Andover MA, Class of 1989.

Relevant Professional Experience

2010-Present Evaluated the AQEA Foodchain Model application for the Grasse River in support of

USEPA Region 2 through AECOM. Work performed includes model benchmarking,

diagnostics, model-to-data comparisons, examination of alternative calibration, and critical

evaluation of the 2010 Analysis of Alternatives document.

1995-Present Produced of AQUATOX 3.1 and performed user support, for U.S. EPA Office of Science

and Technology, through AQUA TERRA Consultants (ATC) and Horsley Witten Group.

Applied the EPA AQUATOX model as part of BASINS Adaptation for Military Facilities,

2009-Present

for U.S. Army (through ATC).

2008-Present Applied SLAMM model (Sea Level Affecting Marshes Model) to 116 USFWS National

Wildlife Refuges in Regions 1, 4, 5, and 8 under contract to USFWS in support of

comprehensive conservation plan production.

2011 Programmed the newest version of the FishRand Migration bioaccumulation model, a

spatially explicit model with a Gobas bioaccumulation engine. Under contract to Exponent.

2010-2011 Evaluated the AQEA Foodchain Model application of the Hudson River for USEPA

Region 2, through Louis Berger. Analysis includes model benchmarking, source code

examination, diagnostics, and sensitivity analysis, and comments on the 2010 Upper Hudson

River Modeling System document.

2009 Produced the SLAMM 6 model including variable accretion feedbacks, improved GUI, and

improved memory management. Performed under contract to the Nature Conservancy.

2007 Implemented and tested Di Toro s Sediment Diagenesis model as a component of

AQUATOX under contract to EPA Office of Science and Technology (via ATC).

2004-2007 Developed and Applied SLAMM under U.S. Environmental Protection Agency STAR grant.

Model predicts the effect of different sea level rise scenarios on the entire Georgia and South

Carolina Coast through the year 2100.

2007 Applied SLAMM model to entire Chesapeake Bay region including Delaware Bay.

Completed application of SLAMM to Puget Sound, WA for National Wildlife Federation.

2006-2007

2006-2007 Applied multi-segment AQUATOX model to Lower Boise River ID and Tenkiller Reservoir

OK. Calibrated model against existing data for use in nutrient studies.

2006 Applied the SLAMM model to Florida with National Wildlife Federation Funding.

2004-2006 Added capabilities for correlated uncertainty and sensitivity analyses to AQUATOX model.

2004-2006 Validated the QEA Foodchain model for EPA Region 1 in support of the Modeling Study of

PCB Contamination in the Housatonic River. Co-authored Final Model Documentation and

Peer Review Responsiveness Summary released in November 2006.

2004-2006 Produced and taught one-day and three-day hands-on workshops on the AQUATOX

model. Produced course materials for AQUATOX training and participated in team teaching

of hands-on, laboratory-based training for the latest AQUATOX models. Three-day course

has been taught in many cities including Seattle WA, Austin TX, Philadelphia PA,

Washington DC, Chicago IL, and Santa Clara CA.

2004 Consolidated the diverse versions of AQUATOX into one general version including the

estuarine version, multi-segmented version, nutrient enhancements, and perfluorinated acid

version. Provided support, documentation, and enhancements to the AQUATOX model.

2001-2005 Calibrated the QEA Foodchain model for EPA Region 1 in support of the Modeling Study of

PCB Contamination in the Housatonic River. Linked model to HSPF hydrology and EFDC

PCB fate models for multiple water segments. Created Windows-based shell around existing

FORTRAN model for use in automated uncertainty and sensitivity analyses. Queried existing

relational databases to filter available empirical data. Performed statistical analyses of empirical

data to determine boundary conditions and calibration datasets. Completed comprehensive

calibration report to undergo peer-review.

2001-2002 Developed the AQUATOX extension for the BASINS GIS modeling system for the EPA

Office of Science and Technology. Output from the GIS interface, HSPF and SWAT

models are automatically linked to AQUATOX through this new interface. AQUATOX

output is made available to the GenScn graphical output processor to allow for additional

graphing capabilities and statistical tests.

1998-2002 Developed and applied the AQUATOX model for the EPA Office of Water in support of

the Modeling Study of PCB Contamination in the Housatonic River. Expanded Model to

simulate multiple organic toxicants simultaneously. Expanded dimensionality of AQUATOX

to allow the simulation of multiple linked river segments simultaneously. Added mass balance

capability to track mass of toxicant through all river segments. Model designed to link with the

EFDC and HSPF models to complete the Housatonic River analysis.

1998-1999 Scientific Programmer: modified the Sea Level Affecting Marshes Model (SLAMM) to create

Version 4 for the EPA Office of Planning and Policy Evaluation. Changes included an upgrade

into a 32-bit operating system, a user-friendly interface, the capability to export to GIS ready

data, and a screen display component.

1996-1999 Scientific Programmer: Developed AQUATOX for the Exposure Assessment Branch of the

EPA Standards and Applied Science Division. Dramatically expanded model capabilities

including the ability to model stratifying systems, and the capability to perform Latin hypercube

uncertainty analyses.

1995-1996 Research Assistant: Abt Associates. Designed and implemented user-friendly GUIs for existing

models, primarily utilizing object Pascal. Started working with AQUATOX model. Converted

model from DOS based model into object-oriented code with Windows GUI. Wrote

significant portions of a Pascal statistics package to be used in sensitivity and uncertainty

analyses and incorporated package into AQUATOX.

1992 Student Programmer: C.S. Draper Laboratory. Programmer within a team environment. Team

modified user interface language (Timeliner) written in Ada as an interface to Space Station

Freedom. Wrote integrated test documents for NASA. Received Employee Recognition

Award for support of project.

Honors and Awards

Brown University: Phi Beta Kappa, University Scholar, Faculty Scholar, Omicron Delta

Epsilon: National Economics Honor Society, Class of 1994

Environmental Studies Award, Honors Thesis, 4.0 GPA

Phillips Academy: Cum Laude Honors Society

Computer Experience

Software Developer, Database Developer, Website Developer, Network Administrator,

Programming Languages: C++, Object Pascal, Ada, FORTRAN

Object Oriented Design: Embarcadero RAD studio XE, Delphi, Microsoft Visual C++

GIS Work: ArcView, Spatial Analyst, MapWindow

Publications:

Clough, Park, Fuller 2010. SLAMM Technical Documentation, Release 6.0 beta, Draft January 2010. Warren

Pinnacle Consulting, Inc.

Carleton, J. N., R. A. Park, and J. S. Clough 2009. Ecosystem Modeling Applied to Nutrient Criteria

Development in Rivers. Environmental Management 44 (3) 485-492.

Park, R. A., and Clough J.S. 2009. AQUATOX (Release 3) Modeling Environmental Fate and Ecological Effects in

Aquatic Ecosystems. Volume 2: Technical Documentation. August 2009, U.S. Environmental Protection Agency,

Office of Science and Technology, Washington, DC.

Craft C, Clough J, Ehman J, Guo H, Joye S, Machmuller M, Park R, and Pennings S., 2009 Effects of

Accelerated Sea Level Rise on Delivery of Ecosystem Services Provided by Tidal Marshes: A Simulation

of the Georgia (USA) Coast. Frontiers in Ecology and the Environment. 2009; 7, doi:10.1890/070219

Park, R. A., J. S. Clough, and M. C. Wellman, 2008. AQUATOX: Modeling environmental fate and ecological

effects in aquatic ecosystems. Ecological Modelling 213:1-15.

Glick, Clough, National Wildlife Fed n et al., 2006. An Unfavorable Tide: Global Warming, Coastal Habitats and

Sportfishing in Florida. http://www.targetglobalwarming.org/files/AnUnfavorableTideReport.pdf

Weston (Weston Solutions, Inc.). 2006a. Responsiveness Summary to the Peer Review of Model Calibration:

Modeling Study of PCB Contamination in the Housatonic River. Prepared for U.S. Army Corps of

Engineers and U.S. Environmental Protection Agency. DCN GE-080105-ACUD. [co-author]

Weston (Weston Solutions, Inc.). 2006b. Model Validation: Modeling Study of PCB Contamination in the

Housatonic River. Prepared for U.S. Army Corps of Engineers and U.S. Environmental Protection Agency.

DCN GE-030706-ADBR. [co-author]

Clough, J. S., and R. A. Park. 2006. AQUATOX (Release 3) Modeling Environmental Fate and Ecological Effects in

Aquatic Ecosystems, Addendum to Release 2 & 2.1 Technical Documentation. U.S. Environmental Protection

Agency, Washington, DC.

Imhoff, Clough, Park, Stoddard, and Hayter, 2005, Comparison of Chemical Bioaccumulation Models to Assist

in Model Selection for Ecological Assessments and TMDL Development Watershed Glenn E. Moglen -

Editor, July 19 22, 2005, Williamsburg, Virginia, USA

Park, R.A., J.S. Clough, and M.C. Wellman. 2004. AQUATOX for Windows: A Modular Fate and Effects Model for

Aquatic Ecosystems-Volume 1: Release 2 User s Manual. EPA-823-R-04-001.

Park, R.A., and J.S. Clough. 2004. AQUATOX for Windows: A Modular Fate and Effects Model for Aquatic

Ecosystems-Volume 2: Release 2 Technical Documentation. EPA-823-R-04-002.

Imhoff, J. C., J.S. Clough, R.A. Park, and A. Stoddard. 2004. Evaluation of Chemical Bioaccumulation Models of Aquatic

Ecosystems: Final Report. Athens GA: U.S. Environmental Protection Agency.

Weston (Weston Solutions, Inc.). 2004a. Modeling Framework Design: Modeling Study of PCB Contamination

in the Housatonic River. Prepared for the U.S. Army Corps of Engineers and U.S. Environmental Protection

Agency. DCN GE-042104-ACDP. [co-author]

Weston (Weston Solutions, Inc.). 2004b. Model Calibration: Modeling Study of PCB Contamination in the

Housatonic River. Prepared for U.S. Army Corps of Engineers and U.S. Environmental Protection Agency.

DCN GE-122304-ACMG. [co-author]

Galbraith, H., R. Jones, R.A. Park, J.S. Clough, S. Herrod-Julius, B. Harrington, and G. Page. 2003. Global

Climate Change and Sea Level Rise: Potential Losses of Intertidal Habitat for Shorebirds. In Ecological

Forecasting: New Tools for Coastal and Marine Ecosystem Management. NOAA Technical Memorandum NOS

NCCOS 1 (Vallette-Silver and Scavia eds). Silver Springs, MD.

Park, R.A., and J.S. Clough. 2003. AQUATOX for Windows: A Modular Fate and Effects Model for Aquatic

Ecosystems: Perfluoroalkylated Surfactant and Estuarine Versions, Addendum to Release 2 Technical Documentation.

EPA Contract 68-C-98-010.

Weston (Weston Solutions, Inc.). 2002. Responsiveness Summary to Peer Review of the Modeling Framework

Design and Quality Assurance Project Plan: Modeling Study of PCB Contamination in the Housatonic River.

Prepared for U.S. Army Corps of Engineers and U.S. Environmental Protection Agency. DCN GE-053102-

ABAQ. [co-author]

Galbraith, H., R. Jones, R.A. Park, J.S. Clough, S. Herrod-Julius, B. Harrington, and G. Page. 2002. Global

Climate Change and Sea Level Rise: Potential Losses of Intertidal Habitat for Shorebirds. Waterbirds

25:173-183.

Beach, R.B., J.S. Clough, P.M. Craig, A.S. Donigian, R.A. McGrath, R.A. Park, A. Stoddard, S.C, Svirsky, and

C.M. Wallen. 2000. Quality Assurance Project Plan--Modeling Study of PCB Contamination in the Housatonic River.

Prepared for U.S. Environmental Protection Agency, Region I, Boston, MA.

Weston (Roy F. Weston, Inc.). 2000. Quality Assurance Project Plan -- Modeling Study of PCB Contamination in

the Housatonic River. Prepared for the U.S. Army Corps of Engineers and U.S. Environmental Protection

Agency. DCN GE-100500-AADY. [co-author]

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