Physics 434, 2014: Scripts

From Ilya Nemenman: Theoretical Biophysics @ Emory
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Back to Physics 434, 2014: Information Processing in Biology.


  • HW1.m -- first homework problem simulation
  • HW2_5.m -- second homework, problem 2 simulation
  • Ecoli.m -- E. coli motion simulation
  • LuriaDelbruck.m -- Luria-Delbruck simulated experiment.
  • LDexpt.mat -- Luria-Delbruck experimental data; courtesy of Phil Nelson
  • gillespie_bd.m -- Birth-death process, Gillespie simulation
  • langevin_bd.m -- Birth-death process, Langevin simulation
  • gillespie_mrna.m -- bursty mRNA expression, Gillespie simulation
  • my_entropy.m -- entropy calculation for a discrete distribution
  • mutual.m -- mutual information calculation for a discrete 2-variable distribution
  • joint_pdf.m -- calculating the joint distribution from the conditional and the marginal
  • CherryAdler.m -- phase portrait of the toggle switch, courtesy of Phil Nelson
  • lac_switch_det.m -- deterministic dynamics of a simplified model of the lac bistable switch
  • lac_switch.m -- Gillespie stochastic dynamics of the same simplified model of the lac bistable switch

Data files: