Kinetics of Vascular Remodeling: Comparison of Solver Approaches

ORAL

Abstract

Results will be presented for kinetics of matrix metalloproteinases (MMP), enzymes that play a significant role in vascular remodeling. Three different computational approaches for well-mixed kinetics processes will be analyzed and compared. The kinetics of one MMP, namely MMP2, were elucidated using a model and rate constants from published literature$^{1}$ and implemented using the \textit{JSim }environment (see nsr.bioeng.washington.edu).$^{ }$Further investigations of this pathway were undertaken using System Biology Workbench (SBW) (see sbw.kgi.edu), where the system of kinetic equations was created using an interactive visual interface. Using SBW the complexity of the kinetics was evaluated using phase space analysis. Finally, we implemented the kinetics model using Discrete Event System Specification (DEVS). Using \textit{adev }(see www.ece.arizona.edu/$\sim $nutaro), an open-source DEVS modeling environment we demonstrate that continuous, well-mixed, enzyme kinetics can be modeled using discrete event simulation. The three computational environments will be compared and their utility and comprehensiveness evaluated. 1. Karagiannis, E. D. and Popel, A. S., J. of Biological Chemistry, \textbf{279} (37):39105--39114, 2004.

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Authors

  • J. Deng

    US Naval Observatory, University of Virginia, Thomas Jefferson National Accelerator Facility, College of William and Mary, US Army Research Office, Brimrose Corporation of America, Hampton University, Department of Physics, University of Rajshahi, Rajshahi, Bangladesh, Department of Physics, Old Dominion University, Norfolk, VA 23529, University of North Carolina at Chapel Hill, Department of Physics, Old Dominion University, Norfolk, Virginia, Department of Physics, Korea University, Seoul, Korea, Department of Physics, University of Virginia, Charlottesville, VA, Department of Physics, Old Dominion University, Norfolk, VA, North Carolina State University and WebAssign, Raleigh, NC, North Carolina State University, Raleigh, NC, Broughton High School, Raleigh, NC, University of Wisconsin at Whitewater, Whitewater, WI, University of North Carolina-Chapel Hill Department of Physics, University of West Virginia - Chemistry Dept., ORNL, Old Dominion University, University of West Virginia Department of Chemistry, Clemson University, South Carolina Governor’s School for Science and Mathematics, College of Charleston, Rice University, Korea Research Institute of Standards and Science, Ohio State University, Wright State University, Yale U, JINR, Dubna, Univ. Fed. do Rio de Janeiro, Vanderbilt Univ./JIHIR(ORNL)/Tsinghua Univ., NSCL(MSU), LLNL, LBNL, Vanderbilt Univ./LBNL/JIHIR(ORNL), Vanderbilt Univ., Jagellonian University, University of Bonn, North Carolina A{\&T} State University, North Carolina Central University, Duke University and TUNL

  • J. Deng

    US Naval Observatory, University of Virginia, Thomas Jefferson National Accelerator Facility, College of William and Mary, US Army Research Office, Brimrose Corporation of America, Hampton University, Department of Physics, University of Rajshahi, Rajshahi, Bangladesh, Department of Physics, Old Dominion University, Norfolk, VA 23529, University of North Carolina at Chapel Hill, Department of Physics, Old Dominion University, Norfolk, Virginia, Department of Physics, Korea University, Seoul, Korea, Department of Physics, University of Virginia, Charlottesville, VA, Department of Physics, Old Dominion University, Norfolk, VA, North Carolina State University and WebAssign, Raleigh, NC, North Carolina State University, Raleigh, NC, Broughton High School, Raleigh, NC, University of Wisconsin at Whitewater, Whitewater, WI, University of North Carolina-Chapel Hill Department of Physics, University of West Virginia - Chemistry Dept., ORNL, Old Dominion University, University of West Virginia Department of Chemistry, Clemson University, South Carolina Governor’s School for Science and Mathematics, College of Charleston, Rice University, Korea Research Institute of Standards and Science, Ohio State University, Wright State University, Yale U, JINR, Dubna, Univ. Fed. do Rio de Janeiro, Vanderbilt Univ./JIHIR(ORNL)/Tsinghua Univ., NSCL(MSU), LLNL, LBNL, Vanderbilt Univ./LBNL/JIHIR(ORNL), Vanderbilt Univ., Jagellonian University, University of Bonn, North Carolina A{\&T} State University, North Carolina Central University, Duke University and TUNL

  • J. Deng

    US Naval Observatory, University of Virginia, Thomas Jefferson National Accelerator Facility, College of William and Mary, US Army Research Office, Brimrose Corporation of America, Hampton University, Department of Physics, University of Rajshahi, Rajshahi, Bangladesh, Department of Physics, Old Dominion University, Norfolk, VA 23529, University of North Carolina at Chapel Hill, Department of Physics, Old Dominion University, Norfolk, Virginia, Department of Physics, Korea University, Seoul, Korea, Department of Physics, University of Virginia, Charlottesville, VA, Department of Physics, Old Dominion University, Norfolk, VA, North Carolina State University and WebAssign, Raleigh, NC, North Carolina State University, Raleigh, NC, Broughton High School, Raleigh, NC, University of Wisconsin at Whitewater, Whitewater, WI, University of North Carolina-Chapel Hill Department of Physics, University of West Virginia - Chemistry Dept., ORNL, Old Dominion University, University of West Virginia Department of Chemistry, Clemson University, South Carolina Governor’s School for Science and Mathematics, College of Charleston, Rice University, Korea Research Institute of Standards and Science, Ohio State University, Wright State University, Yale U, JINR, Dubna, Univ. Fed. do Rio de Janeiro, Vanderbilt Univ./JIHIR(ORNL)/Tsinghua Univ., NSCL(MSU), LLNL, LBNL, Vanderbilt Univ./LBNL/JIHIR(ORNL), Vanderbilt Univ., Jagellonian University, University of Bonn, North Carolina A{\&T} State University, North Carolina Central University, Duke University and TUNL

  • J. Deng

    US Naval Observatory, University of Virginia, Thomas Jefferson National Accelerator Facility, College of William and Mary, US Army Research Office, Brimrose Corporation of America, Hampton University, Department of Physics, University of Rajshahi, Rajshahi, Bangladesh, Department of Physics, Old Dominion University, Norfolk, VA 23529, University of North Carolina at Chapel Hill, Department of Physics, Old Dominion University, Norfolk, Virginia, Department of Physics, Korea University, Seoul, Korea, Department of Physics, University of Virginia, Charlottesville, VA, Department of Physics, Old Dominion University, Norfolk, VA, North Carolina State University and WebAssign, Raleigh, NC, North Carolina State University, Raleigh, NC, Broughton High School, Raleigh, NC, University of Wisconsin at Whitewater, Whitewater, WI, University of North Carolina-Chapel Hill Department of Physics, University of West Virginia - Chemistry Dept., ORNL, Old Dominion University, University of West Virginia Department of Chemistry, Clemson University, South Carolina Governor’s School for Science and Mathematics, College of Charleston, Rice University, Korea Research Institute of Standards and Science, Ohio State University, Wright State University, Yale U, JINR, Dubna, Univ. Fed. do Rio de Janeiro, Vanderbilt Univ./JIHIR(ORNL)/Tsinghua Univ., NSCL(MSU), LLNL, LBNL, Vanderbilt Univ./LBNL/JIHIR(ORNL), Vanderbilt Univ., Jagellonian University, University of Bonn, North Carolina A{\&T} State University, North Carolina Central University, Duke University and TUNL

  • J. Deng

    US Naval Observatory, University of Virginia, Thomas Jefferson National Accelerator Facility, College of William and Mary, US Army Research Office, Brimrose Corporation of America, Hampton University, Department of Physics, University of Rajshahi, Rajshahi, Bangladesh, Department of Physics, Old Dominion University, Norfolk, VA 23529, University of North Carolina at Chapel Hill, Department of Physics, Old Dominion University, Norfolk, Virginia, Department of Physics, Korea University, Seoul, Korea, Department of Physics, University of Virginia, Charlottesville, VA, Department of Physics, Old Dominion University, Norfolk, VA, North Carolina State University and WebAssign, Raleigh, NC, North Carolina State University, Raleigh, NC, Broughton High School, Raleigh, NC, University of Wisconsin at Whitewater, Whitewater, WI, University of North Carolina-Chapel Hill Department of Physics, University of West Virginia - Chemistry Dept., ORNL, Old Dominion University, University of West Virginia Department of Chemistry, Clemson University, South Carolina Governor’s School for Science and Mathematics, College of Charleston, Rice University, Korea Research Institute of Standards and Science, Ohio State University, Wright State University, Yale U, JINR, Dubna, Univ. Fed. do Rio de Janeiro, Vanderbilt Univ./JIHIR(ORNL)/Tsinghua Univ., NSCL(MSU), LLNL, LBNL, Vanderbilt Univ./LBNL/JIHIR(ORNL), Vanderbilt Univ., Jagellonian University, University of Bonn, North Carolina A{\&T} State University, North Carolina Central University, Duke University and TUNL

  • J. Deng

    US Naval Observatory, University of Virginia, Thomas Jefferson National Accelerator Facility, College of William and Mary, US Army Research Office, Brimrose Corporation of America, Hampton University, Department of Physics, University of Rajshahi, Rajshahi, Bangladesh, Department of Physics, Old Dominion University, Norfolk, VA 23529, University of North Carolina at Chapel Hill, Department of Physics, Old Dominion University, Norfolk, Virginia, Department of Physics, Korea University, Seoul, Korea, Department of Physics, University of Virginia, Charlottesville, VA, Department of Physics, Old Dominion University, Norfolk, VA, North Carolina State University and WebAssign, Raleigh, NC, North Carolina State University, Raleigh, NC, Broughton High School, Raleigh, NC, University of Wisconsin at Whitewater, Whitewater, WI, University of North Carolina-Chapel Hill Department of Physics, University of West Virginia - Chemistry Dept., ORNL, Old Dominion University, University of West Virginia Department of Chemistry, Clemson University, South Carolina Governor’s School for Science and Mathematics, College of Charleston, Rice University, Korea Research Institute of Standards and Science, Ohio State University, Wright State University, Yale U, JINR, Dubna, Univ. Fed. do Rio de Janeiro, Vanderbilt Univ./JIHIR(ORNL)/Tsinghua Univ., NSCL(MSU), LLNL, LBNL, Vanderbilt Univ./LBNL/JIHIR(ORNL), Vanderbilt Univ., Jagellonian University, University of Bonn, North Carolina A{\&T} State University, North Carolina Central University, Duke University and TUNL