Chemistry 4000: Modelling Biochemical Reaction Networks

Lecture slides

• Introductory lecture
• Lecture 1: Overview of cell biology
• Lecture 2: Overview of biochemistry
• Lecture 3: Overview of chemical kinetics
• Lecture 4: Simplifying biochemical systems
• Lecture 5: Passive transport
• Lecture 6: Coupling uptake and growth
  • xppaut input file for uptake and growth model
• Lecture 7: Numerical integration of ordinary differential equations
  • xppaut input file for the Euler method applied to an exponential decay model
  • xppaut input file for the logistic equation solved by the Euler method
  • xppaut input file for the logistic equation solved by the two-stage Runge-Kutta method
• Lecture 8: Stiff differential equations
  • xppaut input file for the Michaelis-Menten mechanism
• Lecture 9: Glycerol metabolism, part I
• Lecture 10: Glycerol metabolism, part II
  • xppaut input file for the Hynne and Sørensen (2001) model, as extracted from the SBML model database
  • xppaut input file for our glycerol metabolism model
• Lecture 11: Metabolic control analysis of glycerol metabolism
  • xppaut input file for our glycerol metabolism model, with modifications for MCA
• Lecture 12: Stochastic modeling of a single ion channel
• Lecture 13: The chemical master equation for N ion channels
  • xppaut input file for the chemical master equation for a system of N ion channels
• Lecture 14: Stochastic theory of reaction kinetics
  • xppaut input file for the stochastic simulation of a system of N ion channels
• Lecture 15: Analyzing stochastic simulations
  • xppaut input file which generates several simultaneous realizations of the stochastic simulation of a system of N ion channels
• Lecture 16: Gene expression and delay-differential equations
  • xppaut input file for a simple transcription model
• Lecture 17: Modeling the cell cycle, Part I
  • xppaut input file for a two-variable model of the cell cycle
• Lecture 18: Modeling the cell cycle, Part II
  • xppaut input file for a four-variable model of the cell cycle
• Lecture 19: Introduction to bifurcations
• Lecture 20: Genetic toggle switches
  • xppaut input file for the differential equation model
  • xppaut input file for the stochastic model
• Lecture 21: Phase diagrams
• Lecture 22: Somitogenesis and delay-induced oscillations
  • xppaut input file for Lewis's model of the somitogenesis clock