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Created with Raphaël 2.2.014Mar832122Feb212015Jan24Nov26Oct2019141314Sep31Aug271091Apr30Mar231914922Feb201413108754330Jan24191816158Dec227Nov18171611943229Oct2623222120191413729Sep2825242221181716159875331Aug302726252418121065431Jul30292221201918171614131279Jun22May2015121110328Apr272220161412118762127Mar26252423201917151412109625Feb241716141312111031Jan2015146330Dec1918328Nov2726251918Add .mov to .gitignore.Add Ribozyme figure (with data and Sim from Matlab).Changing ellipsoid (probably for plotting).Playing with interfacial resistance by changing gamma at boundary (Matlab).Playing with interfacial resistance at boundary, not working.Change plotting presets.analytical solution workinganalytical solution wiplength(x) substituted with size(x)[1] because of type(collect(LinRange))included cut_ghost function, independent internal and external grid spacing commented out: first check solution and solve ghost pointsDin, Dout added to the model in separate file, added function compute alphaGraphs working!commit cleaned notebookAnalyse half times:partitioning corrected.Analyse half times. WIP: partitioning.Works!Functions apparently run much faster in Julia than scripts!Fixed Normalization (I). Cosmetics.First time step roughly works.Starting work on effective droplet model in Julia.Introduced a dip in phi_tot close to boundary. Commented out.New attempt at effective droplet model in Matlab. Still not working, butIntroduce second reaction rate parameter.Hacky version of preventing solver getting stuck. Count to ten, abort.Rename params_n to par_n.Cosmetic changes to plotting and comments.Adapt comparison with Frank/Stefano/Jonathan solution to len(params)==12.Introduce params_n: now generalized input for more than one species viaUpdate .gitignore.Fokker Planck for P~25, eps=0.02.Ellipsoid .geo file for EMBL application.Plots for EMBL application.Introduce half FRAP geometry for initial condition.eLife Resubmission.Changed D of product.Change substrate initial condition.Two different mobilities and space-dependent reaction rate inChange substrate initial condition.Legend and plot for scaffold-substrate system (Hammerhead/Ribozyme).Simulate droplet diffusion in ellipsoidal cells-shaped volume.