Recycling Circuit Simulation Techniques for Mass-Action Biochemical Kinetics

  • Jared E. Toettcher
  • Joshua F. Apgar
  • Anya R. Castillo
  • Bruce Tidor
  • Jacob White


Many numerical techniques developed for analyzing circuits can be “recycled”—that is, they can be used to analyze mass-action kinetics (MAK) models of biological processes. But the recycling must be judicious, as the differences in behavior between typical circuits and typical MAK models can impact a numerical technique’s accuracy and efficiency. In this chapter, we compare circuits and MAK models from this numerical perspective, using illustrative examples, theoretical comparisons of properties such as conservation and invariance of the non-negative orthant, as well as computational results from biological system models.


Circadian Clock Null Space Incidence Matrix Species Concentration Differential Equation System 
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Copyright information

© Springer Science+Business Media B.V. 2011

Authors and Affiliations

  • Jared E. Toettcher
    • 1
  • Joshua F. Apgar
    • 2
  • Anya R. Castillo
    • 3
  • Bruce Tidor
    • 4
  • Jacob White
    • 5
  1. 1.Department of Cellular and Molecular PharmacologyUniversity of CaliforniaSan FranciscoUSA
  2. 2.Systems Biology GroupBoehringer Ingelheim PharmaceuticalsRidgefieldUSA
  3. 3.Engineering Systems DivisionMassachusetts Institute of TechnologyCambridgeUSA
  4. 4.Department of Electrical Engineering and Computer Science and the Department of Biological EngineeringMassachusetts Institute of TechnologyCambridgeUSA
  5. 5.Department of Electrical Engineering and Computer ScienceMassachusetts Institute of TechnologyCambridgeUSA

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