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Bioen 599 F, Autumn 2000 Bioengineering Principles of Physiology

Lecture Material and Notes

Week 1, Lecture 3: Rationale for simulation and modeling
Paolo Vicini

Lecture theme and outline: Mathematical models in general: their characteristics and uses. Classes of models: models of data and models of systems. Algebraic and dynamic system models. Purpose of a model. Simulation and estimation. First- and second-order reaction models: a differential equation formulation. The Michaelis-Menten equation. The Hill equation. Principles of MATLAB. Using MATLAB to solve differential equations.

Suggested reading:

  1. Phair RD. Development of kinetic models in the nonlinear world of molecular cell biology. Metabolism. 1997 Dec;46(12):1489-95. Review.
  2. Phair RD, "The Rationale for Kinetic Modeling", in "Integrative Bioinformatics".
  3. Molecular Biology of the Cell P128-135 Fundamentals of binding and enzyme catalysis.
  4. Molecular Biology of the Cell P199-200 Cooperativity in protein binding.
  5. Curran-Everett D, Taylor S, Kafadar K. Fundamental concepts in statistics: elucidation and illustration. J Appl Physiol. 1998 Sep;85(3):775-86. Review.

Software and MATLAB links:

  1. A Matlab Summary and Tutorial from the University of Florida Department of Mathematics
  2. A Matlab tutorial from the Department of Mathematical Sciences at the University of Cincinnati
  3. A Matlab tutorial from the University of Colorado at Boulder
  4. A list of MATLAB Educational Web Sites from the University of California, Riverside, Department of Electrical Engineering

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 Last Updated:
XX/XX/XX

Contact the instructor at: vicini@u.washington.edu