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Papers and Presentations

L. Arthurs, 2009, "Natural Organic Matter, Heavy Metals, and Goethite: Towards a quantitative understanding of their complex sorptive interactions," VDMVerlag Dr. Müller Aktiengesellschaft & Co. KG; Saarbrucken, Germany; 248 p.

Stephen E. Cabaniss, Greg Madey, Laura Leff, Patricia A. Maurice and Robert Wetzel, "A stochastic model for the synthesis and degradation of natural organic matter part II: molecular property distributions", Biogeochemistry, Vol. 86, No. 3, December 2007. (pdf)

Stephen E. Cabaniss, Patricia A. Maurice, and Greg Madey, "A stochastic model for the synthesis and degradation of natural organic matter. Part III: Modeling Cu(II) complexation", Applied Geochemistry, Volume 22, Issue 8, August 2007, 1646-1658 (pdf)

Leilani A. Arthurs, "Towards a Quantitative Understanding of the Complex Interactions between Natual Organic Matter, Heavy Metals, and Goethite", unpublished Ph.D. Dissertation, Civil Engineering & Geological Sciences, University of Notre Dame, Notre Dame, IN, July 2007.

R. Kennedy, "Verification and Validation of Agent-Based and Equation-Based Simulations and Bioinformatics Computing: Identifying Transposable Elements in the Aedes aegypti Genome", unpublished masters thesis, Computer Science & Engineering, University of Notre Dame, Notre Dame, IN, April 2006.  (pdf) (slides)

X. Xiang, Y.Huang, G. Madey, S. Cabaniss, L. Arthurs, P. Maurice, "Modeling the Evolution of Natural Organic Matter in the Environment with an Agent-based Stochastic Approach", Natural Resource Modeling Journal, vol. 9, number 1, Spring 2006, pp. 67-90  (pdf)

Ryan C. Kennedy, Xiorong Xiang, Thomas F. Cosimano, Leilani A. Arthurs, Patricia A. Maurice, Greogory R. Madey, Stephen E. Cabaniss, "Verification and Validation of Agent-based and Equation-based Simulations: A Comparison", Agent-Directed Simulation Conference, The Society for Modeling and Simulation International, Huntsville, AL, April 2006.  (pdf)

Cabaniss, S. E., Madey, G., Leff, L., Maurice, P., Wetzel, R., "A Stochastic Model for the Synthesis and Degradation of Natural Organic Matter. Part I. Data Structures and Reaction Kinetics", Biogeochemistry, Springer, Volume 76, Number 2, November 2005, pp. 319 - 347  (paper)

R. C. Kennedy, X. Xiang, G. R. Madey, T. F. Cosimano,  "Verification and Validation of Scientific and Economic Models", Agent2005, Chicago, October 2005. (paper) (slides)

Yingping Huang, Greg Madey, "Autonomic Web-Based Simulation", 38th Annual Simulation Symposium, San Diego, CA, April 2005 (paper)  (slides)

Shillingford, Nadine, Gregory Madey, and Ryan C. Kennedy, Verification and validation of agent-based scientific simulation models, Agent-Directed Simulation Conference, San Diego, CA, April 2005, pp. 27-34.(pdf)

Madey, G.R., Cabaniss, S.E., Maurice, P.A., Xiang, X., Arthurs, L.,  Kennedy, R., Huang, Y., Online Collaboratory for NOM Research: Agent-based Simulations, Data-Mining, and Knowledge-Discovery, ASLO2005 - Aquatic Sciences Meeting, Salt Lake City, February 2005  (abstract) (slides)

Xiaorong Xiang, Ryan Kennedy, Greg Madey, "Verification and Validation of Agent-based Scientific Simulation Models", Agent-Directed Simulation Conference, San Diego, CA, April 2005, pp. 47-55 (paper) (slides)

Yingping Huang, "Autonomic Web-based Simulation", unpublished dissertation, Computer Science & Engineering, University of Notre Dame, Notre Dame, IN, March 2005 (pdf)

Cabaniss, S.E., Madey, G.R., Leff, L.G., Maurice, P.A., Wetzel, R.G., Agent-based Simulation of NOM: Prediciting Ion Binding, Light Adsorption and Microbial Utilization,  ASLO2005 - Aquatic Sciences Meeting, Salt Lake City, February 2005  (abstract) (slides)

Y. Huang, X. Xiang, G. Madey, S. Cabaniss, "Agent-based Scientific Simulation", IEEE Computing in Science & Engineering, Jan-Feb 2005, pp. 22-29. (pdf)

Cabaniss, S.E., Madey, G.R., Maurice, P.A., Huang, Y.,  Leff, L.G., Olapade, O., Wetzel, R., Leenheer, J., Stochastic Synthesis of Natural Organic Matter, Proceedings of the American Chemical Society Meeting, Philadelphia, August 2004  (slides)

Cabaniss, S.E., Madey, G.R., Maurice, P.A., Leff, L.G., "Stochastic Simulation of NOM Formation and Transformation in Surface Waters", ASLO2004 - Aquatic Sciences Meeting, Savannah, GA, June 2004 (abstract)  (slides)

L. Arthurs, P. A. Maurice, X. Xiang, R. Kennedy, G. R. Madey, "Agent-based stochastic simulation of natural organic matter adsorption and mobility in soils", Eleventh International Symposium on Water-Rock Interaction, June 2004 (paper)  (slides)

Y. Huang, X. Xiang, G. Madey, "A Self Manageable Infrastructure for Supporting Web-based Simulations", 37th Annual Simulation Symposium at the Advanced Simulation Technologies Conference 2004 (ASTC'04), Arlington, VA, April 2004  (paper)

Xiaorong Xiang, Greg Madey, Yingping Huang and Steve Cabaniss, "A Web Portal for Environmental Research", ed. Arno Scharl, Environmental Online Communication, Springer, London, 2004. (chapter)

Xiaorong Xiang, Yingping Huang, Greg Madey and Steve Cabaniss, "A Web-based Collaboratory for Supporting Environmental Science Research", Workshop on Applications, Products and Services of Web-based Support Systems at the Joint International Conference on Web Intelligence (2003 IEEE/WIC) and Intelligent Agent Technology, Halifax, Canada, October 2003, pp. 29-36. (paper) (slides)

Leilani Arthurs, Patricia Maurice, Xiaorong Xiang, Greg Madey,and Yingping Huang, "Agent-based simulation of biocomplexity: Effects of adsorption on natural organic mobility through soils", American Chemical Society National Meeting, New York, Sept 2003. (abstract)  (slides)

Xiaorong Xiang, Greg Madey, Yingping Huang and Steve Cabaniss, "A Stochastic Simulation of Natural Organic Matter and Microbes in the Environment", 2003 World Conference on Natural Resource Modeling, (June, 2003) (abstract) (slides)

Xiaorong Xiang, Agent-based Scientific Applications and Collaboration Using JAVA, Master's Thesis, University of Notre Dame, Notre Dame, IN, May 2003 (thesis) (slides.ppt)  (slides.pdf)

Greg Madey and Patricia Maurice, "Agent-Based Simulation of Biocomplexity: Interactions of Natural Organic Matter, Mineral Surfaces, and Microorganisms", Indiana Biocomplexity Symposium, Notre Dame, IN, April 22, 2003. (slides.ppt.)  (slides.pdf)

Yingping Huang, Gregory Madey, Xiaorong Xiang, Eric Chanowich, "Web-based Molecular Modeling using Java/Swarm, J2EE, and RDBMS Technologies", Seventh Annual Swarm Researchers Meeting (Swarm2003), Notre Dame, IN, April 13, 2003. (Also presented at the Indiana Biocomplexity Symposium, Notre Dame, IN, April 22, 2003).(paper)  (slides)

Xiaorong Xiang and Greg Madey, "Exploring performance improvement for Java-based scientific simulations that use the Swarm Toolkit", Seventh Annual Swarm Researchers Meeting (Swarm2003), Notre Dame, IN, April 13, 2003. (Also presented at the Indiana Biocomplexity Symposium, Notre Dame, IN, April 22, 2003). (paper)  (slides)

S. Cabaniss, G. Madey, P. Maurice, L. Leff, Y. Huang, X. Xiang, E. Chanowich, and O. Olapade. "Stochastic synthesis model for the evolution of natural organic matter". 225th American Chemical Society National Meeting. New Orleans, LA: ACS, 2003.

Madey, G., Huang, Y., Xiang, X., Chanowich, E., Cabaniss, S. and Maurice, P., "Simulation of Biocomplexity: Interactions of NOM, Mineral Surfaces, and Microorganisms in Soils". ASLO 2003 - Aquatic Sciences Meeting. Salt Lake City, UT, 2003 (abstract) (slides)

Yingping Huang, Infrastructure, Query Optimization, Data Warehousing and Data Mining for Scientific Simulation, Master's Thesis, University of Notre Dame, Notre Dame, IN, November 2002  (thesis)  (slides)

Madey, G., Huang, Y., Xiang, X., Chanowich, E., Cabaniss, S. and Maurice, P., "Complex system simulation: interactions of NOM molecules, mineral surfaces, and microorganisms in the soil",. Workshop on Modeling Complex Systems. Reno, NV: US Geological Survey, 2002. (abstract)  (slides)

Madey, G., "Using Java and Swarm to Build a Stochastic Simulation of Natural Organic Matter (NOM) and Microbe Interactions in the Soil", Sixth Annual Swarm Researchers Meeting (Swarm2002), Seatle, WA, 2002. (slides)

Poster Presentations

Ryan Kennedy, Xiaorong Xiang, Greg Madey, Yingping Huang, Leilani Authurs, Patricia Maurice, Steve Cabaniss, "Development and Validation of Agent-Based Simulations of Natural Organic Matter", NDEER2004, Notre Dame, IN (pdf)

Yingping Huang and Greg Madey, "Web Data Integration Using Approximate String Join", 13th International World Wide Web Conference (WWW2004), New York, May, 2004 (abstract)  (slides)

Xiaorong Xiang and Greg Madey, "A Semantic Web Services Enabled Web Portal Architecture", IEEE International Conference on Web Services (ICWS 2004), San Diego, July 2004 (abstract)

Leilani Arthurs, "Agent-based simulations of biocomplexity: Effects of adsorption to natural organic mobility through soils", NDEER2003, Notre Dame, IN, November 2003

Ryan Kennedy, Leilani Arthurs, Patricia Maurice, Yingping Huang, Greg Madey "Stochastic Simulation of NOM with RePast:  A Visualization", NDEER2003, Notre Dame, IN, November 2003  (slides)

Xiaorong Xiang, Yingping Huang, Greg Madey, Steve Cabaniss, "An Online Environmental Research Portal", NDEER2003, Notre Dame, IN, November 2003  (slides)

Leilani Arthurs, Patricia Maurice, Gregory Madey, Xiaorong Xiang, and Yingping Huang, "Simulation of natural organic matter adsorption to soils: A preliminary report", Indiana Biocomplexity Symposium, Notre Dame, IN, April 2003  (slides)

Y. Huang, X. Xiang, E. Chanowich, and G. Madey, "A Web-Based Stochastic Simulation of Natural Organic Matter", Notre Dame Environmental Education and Research (NDEER) Symposium, South Bend, IN, November 2002 (slides)
 

Working Papers & Papers Under Review

Nadine Shillingford, Greg Madey and Ryan Kennedy, "Verification and Validation of an Agent-based Simulation Model", working paper, Department of Computer Science & Engineering, University of Notre Dame, Notre Dame, IN, August 2005 (pdf)

Y. Huang, X. Xiang, G. Madey, S. Cabaniss, "Agent-based Scientific Simulation Using Java/Swarm, J2EE, RDBMS and Autonomic Management Technologies", May 2004  (pdf)

X. Xiang, Y. Huang, G. Madey, S. Cabaniss, L. Arthurs, and P. Maurice, "Modeling the Evolution of Natural Organic Matter in the Environment with an Agent-based Stochastic Approach", June 2004.  (paper)

X. Xiang and G. Madey, "A Semantic Web Services Based Framework for Enterprise-Wide Collaborative Engineering Design", April 2004 (paper)

X. Xiang and G. Madey, "End User Oriented Ad Hoc Web Services Composition in a Scientific Application Portal Architecture", Feb 2004. (paper)

L. Arthurs, P. A. Maurice, X. Xiang, R. Kennedy, G. R. Madey, "Agent-based stochastic simulation of natural organic matter adsorption and mobility in soils", Oct 2003 (paper)

Y. Huang, X. Xiang, G. Madey, "A Self Manageable Infrastructure for Supporting Web-based Simulations", Oct 2003  (paper)

X. Xiang, Y. Huang, G. Madey, "Exploring Performance Improvement for Java-based Scientific Simulations", Oct 2003  (paper)

Y. Huang, X. Xiang,  and G. Madey, "Architecture for a Web-based Environmental Research Support Portal", Aug 2003 (paper)

Y. Huang, "Infrastructure, Data Cleansing and Mining for Support of Scientific Simulations", July 2003  (paper)  (slides)

Steve Cabaniss, "Stochastic Synthesis of Natural Organic Matter: Project Overview", Fall 2002,  (slides - pdf) (slides - html)

Steve Cabaniss, "Modeling and Stochastic Simulation of NOM Reactions", working paper, Summer 2002 (paper)

REU Student Papers/Projects

John Korecki, University of Notre Dame (Fall 2004, Spring 2005)

  • A SourceForge.net Project: tMans, an Agent-based Neural Network Simulator, Repast, and SourceForge CVS (pdf)
  • Sourceforge.net CVS ~ Compile Farm (pdf)

Ryan Kennedy, University of Notre Dame (Spring 2004)

  • Generating Oracle Reports for the NOM Project (pdf)

Julio Dovalina, St. Edwards University, Austin, TX (Summer 2003)

  • Exploring new ways of Usability testing for an E-Science/Scientific research application (pdf)
  • NOM Simulator Test Plan (pdf)
  • Simulator_Test PlanOutline (pdf)
  • Simulator Test Cases Specification (pdf)
  • Test Logs (pdf)
  • Test Design Specifications (pdf)

Ryan Kennedy, University of Notre Dame (Summer 2003)

  • Using RePast and JAVA to Enhance the NOM Project: A Report (pdf)
  • Using RePast and JAVA to Enhance the NOM Project: Documentation (pdf)

Eric Chanowich, University of Notre Dame (Summer 2002/ Spring 2003)

  • 3D NOM Simulation: A Design (paper)
  • A Comparison of Probablility Calculations (paper)
  • Digging into Digital Soil: REU Report from Summer 2002  (paper)  (slides)

The material presented at this web site is based in part upon work supported by the National Science Foundation, Information Technology Research/(ITR/AP-DEB), under Grant No. 0112820.

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.

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