John Fonner

Director, Special Projects

Phone: 512-232-5939 | Email:

John Fonner earned a Ph.D. in Biomedical Engineering at the University of Texas at Austin, where he used a blend of experimental and computational techniques to study binding interactions between peptides and conducting polymers for implant applications in the nervous system. He joined the Life Sciences Computing group at TACC in 2011 and has served on a number of projects that help life sciences researchers leverage advanced computing resources, both through training and through the development of better tools and cyberinfrastructure.

Selected Publications

Leduc R, Vaughn M, Fonner JM, Sullivan M, Williams JG, Blood PD, Taylor J, Barnett W. Leveraging the national cyberinfrastructure for biomedical research. J Am Med Inform Assoc. 2013 Aug 20. doi: 10.1136/amiajnl-2013-002059.

Fonner J. M., Schmidt C.E., Ren P. (2010). A Combined Molecular Dynamics and Experimental Study of Doped Polypyrrole. Polymer, 51: 4985-93.

Fonner J. M., Forciniti L., Nguyen H., Byrne J., Kou Y., Syeda-Nawaz J., and Schmidt C. E. (2008). Biocompatibility Implications of Polypyrrole Synthesis Techniques. Biomedical Materials, 3:034124.

Fonner, J. M. [speaker], Schmidt C.E., Ren P. "Development of a Molecular Mechanics Model for Chloride-Doped Polypyrrole." Society for Biomaterials Annual Meeting, San Antonio, TX, April 22-25, 2009.

Fonner,J. M. [presenter], Schmidt C.E., Ren P. "Selective binding of peptides on conducting polymers." Biomedical Engineering Society Annual Meeting, Austin, TX, October 6-8.

Fonner,J. M. [presenter], Schmidt C.E., Ren P. "Selective binding of peptides on conducting polymers." BioInterface Conference, Atlanta, GA, October 18-20.

Current Projects

  • VDJ Server (co-PI)
  • CyVerse
  • The University of Texas Research Cyberinfrastructure (UTRC) project
  • The Drug Discovery @ TACC Portal

Areas of Research

  • Molecular dynamics simulations of biomolecules and biomaterials
  • Binding free energy calculations
  • Scalability in genomics pipelines and virtual drug screening software


B.S., Biomedical Engineering
Texas A & M University

Ph.D., Biomedical Engineering
University of Texas at Austin