Realistic Uncertainty Bounds for Complex Dynamic Systems
National Science Foundation, award CTS-0113985
09/01/01 - 06/30/06
Andrew Packard and Michael Frenklach

This material is based upon work supported by the National Science Foundation under Grant No. 0113985.

Any opinions, findings and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation.

Published Papers. These papers were supported by this NSF grant.

• A System Analysis Approach to Atmospheric Observations and Models: the Mesospheric HOx Dilemma, Gregory Smith, Michael Frenklach, Ryan Feeley, Andy Packard and Pete Seiler, appears in Journal of Geophysical Research (Atmospheres), volume 111, 2006.
• Model Discrimination using Data Collaboration, Ryan Feeley, Michael Frenklach, Matt Onsum, Trent Russi, Adam Arkin and Andy Packard, appears in Journal of Physical Chemistry A, vol. 110, no. 21, pp. 6803-6813, 2006.
• Draft of Numerical approaches for collaborative data processing, Pete Seiler, Michael Frenklach, Andrew Packard and Ryan Feeley, appears in Optimization and Engineering, vol. 7, no. 4, pp. 459-479, December 2006.
• "Consistency of a Reaction DataSet", Ryan Feeley, Andrew Packard, Pete Seiler and Michael Frenklach, appears in Journal of Physical Chemistry A, vol. 108, pp. 9573-9583, 2004.
• Draft of Collaborative data processing in developing predictive models of complex reaction systems, Michael Frenklach, Andrew Packard, Pete Seiler and Ryan Feeley, final paper appears in International Journal of Chemical Kinetics, vol. 36, issue. 1, pp. 57-66, 2004.
• Draft of Prediction uncertainty from models and data, Michael Frenklach, Andy Packard and Pete Seiler, appears in 2002 American Control Conference, pp. 4135-4140, May 2002, Anchorage, AK.

Software: The Data Collaboration software has been released. It is available at sourceforge.net. The website is http://collab-sci.sourceforge.net. Follow the link to the code and download it.

Presentations and Slides: these works are licensed under a Creative Commons License.

• Realistic Uncertainty Bounds for Complex Dynamic Systems, project summary, NSF CTS-0113985, August 2006.
• Collaborative Science: Give us your information, not your conclusions, presented at CITRIS/Helios seminar series, Berkeley campus, August 4, 2006.
• Collaborative Science: Give us your information, not your conclusions, project summary slides, August 2006.
• Collaborative Science: Give us your information, not your conclusions, presented at A workshop on the occasion of Keith Glover's 60th birthday, Cambridge University, April 21-22 April 2006.
• Collaborative Science: a case study for chemical kinetics, presented at CITRIS, Berkeley Campus, April 7, 2006.
• Process informatics model (PrIMe)­A customer for ThermoML, M. Frenklach, A. Packard, Z. M. Djurisic, D. M. Golden, C. T. Bowman, W. H. Green, G. J. McRae, T. C. Allison, G. J. Rosasco, M. J. Pilling, Symposium on ThermoML: Purpose, Structure, and Applications, 231st National Meeting of the American Chemical Society, Atlanta, GA, March 26-30, 2006.
• Collaborative Science: a case study for chemical kinetics, presented at CITRIS, Berkeley Campus, October 28, 2005.
• Managing uncertainty when no one's in charge: Uncertainty propagation in distributed projects, presented at "Connections, Foundations and Edges: A celebration to mark John Doyle 50'th Birthday", July 15, 2004.
• Optimization and Consistency of a Reaction Dataset, invited presentation, at Symposium on Molecular Modeling and Reaction Chemistry, 227th National Meeting of the American Chemical Society, Anaheim, CA, March 31-April 1, 2004.
• Predictions from models and data, presented at the 2002 American Control Conference, May 2002.
• Predictions from models and data, presented at the 2002 Mohammed Dahleh Symposium, February 8-9, 2002

Summary Slides: these works are licensed under a Creative Commons License.

• 2004 NSF "Nuggets"
• April 2005 Project Summary (7 slides)
• April 2005 Project Summary (1 slide)

Tutorial Notes: these works are licensed under a Creative Commons License.

• Quadratic Programming with S procedure (Copyright 2002, Pete Seiler)
• E Coli Heat Shock Model Invalidation (Copyright 2002, Pete Seiler)

Original Proposal

• "Realistic uncertainty bounds for complex dynamic models, submitted to NSF, January 2001

Related Links

• GRI-Mech, methane combustion chemistry
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• SOSTOOLS, sum-of-squares optimization toolbox
• PrIMe, combustion community activity for data collection, data evaluation and kinetics model building.
• CMCS, Collaboratory, Multi-Scale Chemical Science
• Pablo Parrilo's publications, polynomial optimization, sum-of-squares, etc.
• Arnold Neumaier Global Optimization page
• Yalmip, a Matlab toolbox for rapid prototyping of optimization problems.