Plenum - Dynamical Grammar models


The following dynamical grammar models are available as Mathemtica notebooks and can be executed by Plenum. The models are described in detail in the PhD thesis.
  1. Olfactory Epithelium Grammar: OlfactoryEpitheliumGrammar.nb
    • Dynamical grammar model of the development of the olfactory epithelium. The grammar is a 2-dimensional representation of the tissue with 3 cell types: stem cells, progenitor cells, and neurons. The grammar includes a diffusion model for the signaling molecules that control the growth of the tissue. Spring potential functions represent the adhesion forces between neighboring cells.
    • Guy Yosiphon, Kimberly K.Gokoffski, Arthur D.Lander, Anne L.Calof and Eric Mjolsness, Dynamical Grammar Modeling of Growth and Lamination of the Olfactory Epithelium . In preparation, 2009
  2. Complex chemical reactions: ComplexChemicalReactions.nb
    • A dynamical grammar that represents complex chemical reactions - binding and unbinding of molecules according to their association with mutual complexes.
  3. Root growth grammar: rootGrowth.nb
    • Dynamical grammar model for 1-dimensional root growth
    • Mironova, V.and Likhoshvai, V.A.and Omelyanchuk, N.A and Fadeev, S.I.and Yosiphon, G.and Mjolsness, E.and Kolchanov, N.A., Acroptal Auxin Transport Mediates Patterning along the Root Longitudinal Axis . In preparation.
  4. Spiral galaxy grammar: SpiralGalaxy.nb
    • Dynamical grammar model for spiral galaxy formation.
  5. Meta grammar: MetaGrammar.nb
    • Grammar that reverses the direction of rules in an input grammar.