Jonathan O. Allen

Dr. Jonathan Allen has over 20 years of experience in ambient air quality and air quality control research. His current focus is air quality control for coal-fired power plants. He has analyzed the long-term performance of full-scale mercury control equipment using either co-benefit or activated carbon injection.  For these studies he determined the effect of power plant operations on control efficiency, developed empirical process models, and recommended changes to improve mercury control.

In his academic research Dr. Allen used analytical chemistry to understand the sources and fate of aerosols in the atmosphere. He has operated and trained others to use state-of-the-art chemical analysis methods including aerosol mass spectrometry, GC/MS, and HPLC.  His work included extensive data analysis using time series analyses, quantitative inter-comparisons, clustering, and wavelet decomposition.  The YAADA software toolkit which he wrote is used by university research groups worldwide.  He co-authored 29 journal publications that have been cited more than 1000 times (h-index = 15).


  • Massachusetts Institute of Technology, Chemical Engineering Sc.D., 1997
  • Massachusetts Institute of Technology, Chemical Engineering Practice M.S., 1993
  • University of Pennsylvania, Chemical Engineering B.S., 1986
  • University of Pennsylvania, Finance B.S., 1986

Professional Experience

Allen Analytics LLC, Principal, 2009-present

Founded Allen Analytics LLC to provide data-driven discovery in chemical and environmental research.   Clients to date include a large electric utility and associations of electric utilities, including the Utility Air Regulatory Group and Electric Power Research Institute.

Harvard School of Public Health, Visiting Scientist, 2008-2009

Analyzed indoor particulate matter sources and exposure using organic tracer compounds.

Arizona State University, Assistant Professor of Chemical Engineering and Civil & Environmental Engineering, 2001-2008

Developed an interdisciplinary research program on aerosol transport in the environment.
Awarded 17 research grants for total of $8.7M as principal or co-principal investigator.
Mentored 8 undergraduate, 6 masters, and 3 doctoral student researchers.
Taught Numerical Methods, Intermediate Engineering Design, Graduate Chemical Engineering Transport, Air Quality Engineering, and Advanced Atmospheric Chemistry courses; earned “very good” and “excellent” student evaluations.

Aerodyne Research Inc., Senior Research Scientist, 2000

Designed experiments to measure speciated aerosol deposition in the environment.
Co-wrote data acquisition software for rapid measurement of aerosol size and composition.

California Institute of Technology, Postdoctoral Scholar, 1997-2000

Led technical tasks for two field studies on the sources and fate of particulate matter in California.
Wrote open source software (YAADA) to analyze large data sets of single particle mass spectra.
Recommended successful changes to aerosol time-of-flight mass spectrometer.

Massachusetts Institute of Technology, Visiting Lecturer and Visiting Scientist, 1999-2000

Taught Air Quality Engineering class and earned “very good” student evaluations.
Coauthored two successful research proposals to develop aerosol mass spectrometry.

Massachusetts Institute of Technology, Research Assistant, 1991-1997

Conducted three field sampling experiments of organic species in atmospheric particulate matter.
Conducted laboratory experiments on aerosol sampling equipment and aerosol properties.
Co-supervised seven undergraduate researchers.

U. S. Environmental Protection Agency, Enforcement Officer, 1988-1991

Reviewed enforcement actions by Virginia and DC; inspected out-of-compliance facilities.
Inspected chemical research facilities and plants for new chemical and right-to-know rules.
Drafted complaints and negotiated settlements of enforcement actions for PCB rule violations.

TranTech Consultants, Systems Analyst, 1984-1988

Wrote database software for business analysis of chemical manufacturing processes and markets.
Presented to potential customers at sales meetings; trained and supported customers.


  • Awarded fellowship to attend NSF Engineering Education Scholars Workshop in 1999.
  • Awarded fellowship to attend Gordon Conference on Atmospheric Chemistry in 1997.
  • Awarded Bronze Medal in 1997 for resolution of a complex TSCA case for approximately $1.5 M.
  • Awarded MIT Amoco Fellowship in 1991-1992.
  • Awarded Bronze Medal in 1991 for resolution of compliance issues at Federal facilities.
  • Awarded Bronze Medal in 1990 for a complex TSCA inspection with a Federal search warrant.

Professional Affiliations

  • Air & Waste Management Association
  • American Chemical Society
  • American Association for the Advancement of Science
  • Registered Professional Engineer in Pennsylvania · Allen Research Publications