====== Chapter 2: Reaction Kinetics and Biological Dynamics ======


===== Supplementary Material =====


==== Electronic Notebooks ====


    * These all depend on Mathematica(R) and xCellerator. See [[wiki:software_availability|Software availability]]
    * {{:wiki:chapter_2:intro_example.nb|Introductory example: {A->B, B->C}}}
    * {{:wiki:chapter_2:massaction.nb|Mass action kinetics}}
    * {{:wiki:chapter_2:ssa_example.nb|Stochastic simulation algorithm (SSA) example}}
    * {{:wiki:chapter_2:pip3metablismv2.nb|PIP3 metabolism}}
    * Analytic solution of 2×2 master equation for binding/unbinding
    * Analytic solution of trivalent reaction A+B <–> C
    * {{:wiki:chapter_2:huang_ferrell_1996_mapkv2.nb|MAPK cascade model}} of Huang and Ferrell 1996


==== Exercises ====


    * Hill functions
    * Master equation
    * Trivalent mass action


==== Figures - electronic sources ====


    * Hill functions, n=1 and n=2
    * Convergence of bound/unbound probability
    * S-E-P deterministic simulation
    * S-E-P stochastic simulation



==== Bibliography - electronic access - chapter 2 ====


    * [[:wiki:chapter_2:Chapter 2 electronic bibliography|Here]]


===== Text Outline =====


    * 2.1 Example: Growth factor response
    * 2.2 Elementary dynamical models
    * 2.3 Mapping biology to mathematics and computation
    * 2.4 Causal network dynamics
    * 2.5 Summary


===== Missing Topics =====


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