| 2c4a972 | Lars Hubatsch | 26 October 2021, 13:21:39 UTC | Introduce second reaction rate parameter. | 26 October 2021, 13:21:39 UTC |
| dc9df90 | Lars Hubatsch | 26 October 2021, 12:52:55 UTC | Hacky version of preventing solver getting stuck. Count to ten, abort. | 26 October 2021, 12:52:55 UTC |
| 5fd3f81 | Lars Hubatsch | 20 October 2021, 07:50:52 UTC | Rename params_n to par_n. | 20 October 2021, 07:50:52 UTC |
| c3d0119 | Lars Hubatsch | 19 October 2021, 15:59:34 UTC | Cosmetic changes to plotting and comments. | 19 October 2021, 15:59:34 UTC |
| a9149aa | Lars Hubatsch | 14 October 2021, 19:15:36 UTC | Adapt comparison with Frank/Stefano/Jonathan solution to len(params)==12. | 14 October 2021, 19:15:36 UTC |
| a2137b7 | Lars Hubatsch | 14 October 2021, 19:14:39 UTC | Introduce params_n: now generalized input for more than one species via structure. Reaction diffusion - here we come. | 14 October 2021, 19:14:39 UTC |
| 574a5c3 | Lars Hubatsch | 13 October 2021, 20:26:18 UTC | Update .gitignore. | 13 October 2021, 20:26:18 UTC |
| 927b0c4 | Lars Hubatsch | 13 October 2021, 19:54:06 UTC | Fokker Planck for P~25, eps=0.02. | 13 October 2021, 19:54:06 UTC |
| 162a3ad | Lars Hubatsch | 14 September 2021, 09:25:23 UTC | Ellipsoid .geo file for EMBL application. | 14 September 2021, 09:25:23 UTC |
| 076315b | Lars Hubatsch | 14 September 2021, 09:25:04 UTC | Plots for EMBL application. | 14 September 2021, 09:25:04 UTC |
| 3612889 | Lars Hubatsch | 14 September 2021, 09:18:56 UTC | Introduce half FRAP geometry for initial condition. | 14 September 2021, 09:18:56 UTC |
| 149b4c7 | Lars Hubatsch | 14 September 2021, 09:17:31 UTC | eLife Resubmission. | 14 September 2021, 09:17:31 UTC |
| 734a75e | Lars Hubatsch | 14 September 2021, 09:11:29 UTC | Changed D of product. | 14 September 2021, 09:11:29 UTC |
| f6d018b | Lars Hubatsch | 14 September 2021, 08:24:22 UTC | Change substrate initial condition. | 14 September 2021, 08:24:22 UTC |
| 63bb768 | Lars Hubatsch | 31 August 2021, 07:18:46 UTC | Two different mobilities and space-dependent reaction rate in Hammerhead/Ribozyme system. | 31 August 2021, 07:18:46 UTC |
| 59a93e4 | Lars Hubatsch | 31 August 2021, 07:17:21 UTC | Change substrate initial condition. | 31 August 2021, 07:17:21 UTC |
| 07426b6 | Lars Hubatsch | 31 August 2021, 07:17:05 UTC | Legend and plot for scaffold-substrate system (Hammerhead/Ribozyme). | 31 August 2021, 07:17:05 UTC |
| f14f4d4 | Lars Hubatsch | 27 August 2021, 19:47:42 UTC | Simulate droplet diffusion in ellipsoidal cells-shaped volume. | 27 August 2021, 19:47:42 UTC |
| fb9588a | Lars Hubatsch | 10 August 2021, 09:53:41 UTC | plot_sim can now work with two species. | 10 August 2021, 09:53:41 UTC |
| b047d29 | Lars Hubatsch | 10 August 2021, 09:53:15 UTC | Start working on Hammerhead/Ribozyme reaction. Seems to work in principle. | 10 August 2021, 09:53:15 UTC |
| 6680ed5 | Lars Hubatsch | 09 August 2021, 14:55:35 UTC | Starting work on dip in mobility. Not finished. | 09 August 2021, 19:20:44 UTC |
| a514b11 | Lars Hubatsch | 09 August 2021, 19:19:20 UTC | Merge branch 'master' of https://gitlab.pks.mpg.de/mesoscopic-physics-of-life/frap_theory | 09 August 2021, 19:19:20 UTC |
| 98f21d2 | Lars Hubatsch | 09 August 2021, 19:19:00 UTC | Probably changed D for constant D case to D=1?? | 09 August 2021, 19:19:00 UTC |
| f0dbd45 | Lars Hubatsch | 09 August 2021, 07:01:18 UTC | Merge remote-tracking branch 'origin/master' | 09 August 2021, 07:01:18 UTC |
| 0148575 | Lars Hubatsch | 09 August 2021, 06:47:08 UTC | Update plots for revisions at eLife. New plot for PLYS ATP spatial recovery. New plot for boundary condition PGL New plot for valley in cost function New plot for relative partition coefficient | 09 August 2021, 06:48:54 UTC |
| 3d82759 | Lars Hubatsch | 01 April 2021, 16:48:40 UTC | Equal D across domain still seems to work, Compared visually in Jupyter. | 01 April 2021, 16:48:40 UTC |
| 3b56ab0 | Lars Hubatsch | 30 March 2021, 08:48:10 UTC | Delete remnants of old mean cross jump length. | 30 March 2021, 08:48:10 UTC |
| 53c38f1 | Lars Hubatsch | 30 March 2021, 08:42:33 UTC | run_jump_length now has output values. Mean cross jump length works. | 30 March 2021, 08:42:33 UTC |
| b872172 | Lars Hubatsch | 23 March 2021, 22:54:13 UTC | Test jump length with tanh mobility. Slightly off. | 23 March 2021, 22:54:13 UTC |
| 63b319b | Lars Hubatsch | 19 March 2021, 21:04:27 UTC | Add lb parameter in call of int_prob. | 19 March 2021, 21:04:27 UTC |
| 60c0338 | Lars Hubatsch | 19 March 2021, 20:30:06 UTC | New mobility possible: D=D0*(1-a*phi). Not tested. | 19 March 2021, 20:30:06 UTC |
| 2056a3d | Lars Hubatsch | 14 March 2021, 16:11:49 UTC | Merge remote-tracking branch 'origin/master' | 14 March 2021, 16:11:49 UTC |
| ae8fe0e | Lars Hubatsch | 14 March 2021, 16:11:36 UTC | Introduce constant flux case with Dirichlet BC. Works in principle. | 14 March 2021, 16:11:36 UTC |
| 30ed0fe | Lars Hubatsch | 14 March 2021, 15:39:46 UTC | Merge branch 'master' of https://gitlab.pks.mpg.de/mesoscopic-physics-of-life/frap_theory | 14 March 2021, 15:39:46 UTC |
| 1eb13e1 | Lars Hubatsch | 14 March 2021, 15:39:28 UTC | Trying to combine lb with corrected i->i, o->o. | 14 March 2021, 15:39:28 UTC |
| ba6b4fc | Lars Hubatsch | 14 March 2021, 10:04:47 UTC | Cosmetics and renmaing?? | 14 March 2021, 10:04:47 UTC |
| 5ed22c2 | Lars Hubatsch | 14 March 2021, 09:52:01 UTC | Cosmetic changes. | 14 March 2021, 09:52:01 UTC |
| 5f91647 | Lars Hubatsch | 09 March 2021, 08:54:07 UTC | Merge remote-tracking branch 'origin/master' | 09 March 2021, 08:54:07 UTC |
| b4bb2a7 | Lars Hubatsch | 09 March 2021, 08:53:54 UTC | Figures as per biorxiv submission. | 09 March 2021, 08:53:54 UTC |
| b819c42 | Lars Hubatsch | 22 February 2021, 20:31:03 UTC | Update README.md | 22 February 2021, 20:31:03 UTC |
| 24868c9 | Lars Hubatsch | 20 February 2021, 09:15:29 UTC | Add supplementary plot for D~P and D~P^2. | 20 February 2021, 09:15:29 UTC |
| 094e0c4 | Lars Hubatsch | 14 February 2021, 12:02:45 UTC | Update plots for P vs D_out PGL-3. | 14 February 2021, 12:02:45 UTC |
| abcb1fc | Lars Hubatsch | 13 February 2021, 22:18:43 UTC | Update figure: influence of coverslip and neighbours. | 13 February 2021, 22:18:43 UTC |
| 1f13d18 | Lars Hubatsch | 10 February 2021, 10:06:00 UTC | Make mesh more precise close to zero to have good agreement with Stefano. | 10 February 2021, 10:06:00 UTC |
| 43e91d0 | Lars Hubatsch | 10 February 2021, 09:26:51 UTC | Reducing interval for jump length calcs to save time. | 10 February 2021, 09:26:51 UTC |
| 9df78ee | Lars Hubatsch | 08 February 2021, 16:30:31 UTC | Ignoring interval around boundary works in principle (lb). | 08 February 2021, 16:30:31 UTC |
| f76b43f | Lars Hubatsch | 08 February 2021, 16:27:13 UTC | Implement skipping immediate boundary region for boundary crossing case. | 08 February 2021, 16:27:13 UTC |
| 5b4be0c | Lars Hubatsch | 07 February 2021, 16:31:43 UTC | Adopt multi drop FEM for better accuracy, fix bug in z distance. | 07 February 2021, 16:31:43 UTC |
| 07a0598 | Lars Hubatsch | 07 February 2021, 16:21:12 UTC | nansum for probs in prob_laplace. | 07 February 2021, 16:21:12 UTC |
| e2b75a5 | Lars Hubatsch | 07 February 2021, 16:20:24 UTC | Multi drop meshes updated for compromise between accuracy and runtime. | 07 February 2021, 16:20:24 UTC |
| c1aa0ef | Lars Hubatsch | 05 February 2021, 19:27:28 UTC | Updating multi drop meshes to better accuracy. | 05 February 2021, 19:27:28 UTC |
| e965723 | Lars Hubatsch | 04 February 2021, 21:48:35 UTC | Jump length distros seem to work for boundaries at 3, 5, 7. | 04 February 2021, 21:48:35 UTC |
| 7f3f984 | Lars Hubatsch | 04 February 2021, 21:06:50 UTC | Fix two bugs in calculation of gamma0. | 04 February 2021, 21:06:50 UTC |
| 4153164 | Lars Hubatsch | 04 February 2021, 19:11:50 UTC | .gitignore | 04 February 2021, 19:11:50 UTC |
| 3baadc1 | Lars Hubatsch | 04 February 2021, 19:10:10 UTC | Experiment with moving boundary entropy production. Not finished. | 04 February 2021, 19:10:10 UTC |
| 094a0b0 | Lars Hubatsch | 04 February 2021, 19:04:48 UTC | Cosmetics. | 04 February 2021, 19:04:48 UTC |
| 085b1be | Lars Hubatsch | 04 February 2021, 19:03:30 UTC | Plot Anatol's PGL-3 partitioning data on top of mine. | 04 February 2021, 19:03:30 UTC |
| b5d0290 | Lars Hubatsch | 04 February 2021, 19:02:03 UTC | Try jump length distro for D=const.=0.5. Doesn't work. Old case not working. | 04 February 2021, 19:02:03 UTC |
| 3348fba | Lars Hubatsch | 04 February 2021, 19:01:12 UTC | Introduce new gamma0 parameters to prob_laplace. Not tested. | 04 February 2021, 19:01:12 UTC |
| 20bd2db | Lars Hubatsch | 04 February 2021, 18:58:41 UTC | Better meshing around x0 for Gaussian initial condition. | 04 February 2021, 18:58:41 UTC |
| 0e5cf66 | Lars Hubatsch | 04 February 2021, 18:58:03 UTC | Introduce possibility for constant D across entire domain. Not tested. | 04 February 2021, 18:58:03 UTC |
| 17472f4 | Lars Hubatsch | 03 February 2021, 20:45:13 UTC | Loop for different outputs to Matlab. Toggle eps for long or short profs. | 03 February 2021, 20:45:13 UTC |
| ba22ddc | Lars Hubatsch | 30 January 2021, 21:09:56 UTC | Running finer FEM sims for coverslip with corrected droplet position 0.25. | 30 January 2021, 21:09:56 UTC |
| 88b987c | Lars Hubatsch | 30 January 2021, 15:40:05 UTC | Correct droplet position and mesh resolution in .geo files. | 30 January 2021, 15:40:05 UTC |
| dc58ac5 | Lars Hubatsch | 24 January 2021, 15:48:43 UTC | Minor. | 24 January 2021, 15:48:43 UTC |
| 2568e32 | Lars Hubatsch | 24 January 2021, 10:44:50 UTC | Major update to FRAP paper plotting. | 24 January 2021, 10:44:50 UTC |
| 76aa174 | Lars Hubatsch | 19 January 2021, 13:30:55 UTC | FRAP KL div works except for scaling factor. Normalization? | 19 January 2021, 13:30:55 UTC |
| f630c23 | Lars Hubatsch | 19 January 2021, 13:30:00 UTC | out -> out and in -> in corrected. | 19 January 2021, 13:30:00 UTC |
| 19c9581 | Lars Hubatsch | 18 January 2021, 14:56:10 UTC | KL divergence seems to work in principle, not quite right yet. | 18 January 2021, 14:56:10 UTC |
| 41b55e6 | Lars Hubatsch | 18 January 2021, 14:55:34 UTC | Shorten probability variable name. | 18 January 2021, 14:55:34 UTC |
| 5e1a23c | Lars Hubatsch | 16 January 2021, 18:46:14 UTC | Function for frap distributions, allows calculating all direction quickly. | 16 January 2021, 18:46:14 UTC |
| be7c8af | Lars Hubatsch | 15 January 2021, 10:49:01 UTC | Add lacking (?) boundary position. | 15 January 2021, 10:49:01 UTC |
| 0d3c09b | Lars Hubatsch | 15 January 2021, 10:31:07 UTC | WIP: adapt for jumps in to in, out to out. | 15 January 2021, 10:31:07 UTC |
| 142b034 | Lars Hubatsch | 15 January 2021, 09:30:14 UTC | Change jump direction for distros for plotting. | 15 January 2021, 09:30:14 UTC |
| a4d3368 | Lars Hubatsch | 08 December 2020, 15:49:17 UTC | Introduce defaults parameters for pdepe. | 08 December 2020, 15:49:17 UTC |
| c408643 | Lars Hubatsch | 08 December 2020, 15:48:21 UTC | Merge branch 'master' of https://gitlab.pks.mpg.de/mesoscopic-physics-of-life/frap_theory | 08 December 2020, 15:48:21 UTC |
| 9d48a67 | Lars Hubatsch | 08 December 2020, 15:47:26 UTC | Delete obsolete spacing function. | 08 December 2020, 15:47:26 UTC |
| ebc7c06 | Lars Hubatsch | 02 December 2020, 15:14:32 UTC | Plotting: various visual detail changes. | 02 December 2020, 15:14:32 UTC |
| b8063aa | Lars Hubatsch | 27 November 2020, 08:51:45 UTC | Plotting: Add model sketches to Python. | 27 November 2020, 08:51:45 UTC |
| 4b024eb | Lars Hubatsch | 27 November 2020, 08:48:28 UTC | Plotting: New colors, new markers. | 27 November 2020, 08:48:28 UTC |
| 16cecae | Lars Hubatsch | 27 November 2020, 08:11:00 UTC | WIP: Rearrange plotting notebook, introduce Partitioning instead of phi as titles for artificial data plot. | 27 November 2020, 08:11:00 UTC |
| e3839e8 | Lars Hubatsch | 17 November 2020, 23:35:02 UTC | Initial condition corrected to match proper client profile. | 17 November 2020, 23:35:02 UTC |
| f77666c | Lars Hubatsch | 17 November 2020, 13:32:42 UTC | Reduced difference in normalization to 2.5%. | 17 November 2020, 13:32:42 UTC |
| 6932c1f | Lars Hubatsch | 16 November 2020, 13:58:44 UTC | Finer mesh around x0 also for client. | 16 November 2020, 13:58:44 UTC |
| 17d6965 | Lars Hubatsch | 16 November 2020, 08:05:17 UTC | Reorder prob_labplace | 16 November 2020, 08:05:17 UTC |
| 2ce671c | Lars Hubatsch | 11 November 2020, 14:36:18 UTC | Adding location of output file for mean cross jump length. | 11 November 2020, 14:36:18 UTC |
| 43cf01f | Lars Hubatsch | 11 November 2020, 14:34:38 UTC | Mean cross jump length comparison with Stefano works. | 11 November 2020, 14:34:38 UTC |
| 693a027 | Lars Hubatsch | 11 November 2020, 10:22:05 UTC | Outsourcing jump length calculation to separate function. | 11 November 2020, 10:22:05 UTC |
| 186102d | Lars Hubatsch | 11 November 2020, 10:20:56 UTC | int_prob now lives in its own file. | 11 November 2020, 10:20:56 UTC |
| b6cba63 | Lars Hubatsch | 11 November 2020, 10:19:30 UTC | Real parameters can now be calculated also for square mobility. | 11 November 2020, 10:19:30 UTC |
| b2f0166 | Lars Hubatsch | 09 November 2020, 21:19:39 UTC | Testing several D_i/D_o ratios, generally seems to work. | 09 November 2020, 21:19:39 UTC |
| f433ed8 | Lars Hubatsch | 09 November 2020, 21:18:42 UTC | Enabling Stefanos mobility scaling. Not tested in Matlab. | 09 November 2020, 21:18:42 UTC |
| 788bf59 | Lars Hubatsch | 09 November 2020, 21:16:43 UTC | Generalizing jump lengths distros. | 09 November 2020, 21:16:43 UTC |
| 6bd3292 | Lars Hubatsch | 04 November 2020, 14:29:22 UTC | prob_laplace: changing normalization, not sure if sums to 1 precisely. | 04 November 2020, 14:29:22 UTC |
| 98ee6eb | Lars Hubatsch | 03 November 2020, 14:12:06 UTC | New: comparison between steady state solution and outside numerics. | 03 November 2020, 14:12:06 UTC |
| 0e3e9f0 | Lars Hubatsch | 02 November 2020, 10:06:47 UTC | Plotting: adding figure 4 and 5 for FRAP paper. | 02 November 2020, 10:06:47 UTC |
| 8ea4866 | Lars Hubatsch | 29 October 2020, 15:06:50 UTC | Adding x_scale param to plot_sim, to be able to plot in dimensional space. | 29 October 2020, 15:06:50 UTC |
| 1f5331d | Lars Hubatsch | 26 October 2020, 09:28:48 UTC | Plotting: adding first Fig4 panels. | 26 October 2020, 09:28:48 UTC |
| fce1407 | Lars Hubatsch | 23 October 2020, 11:08:11 UTC | Change signature of int_prob. SS jump lengths work in both directions. | 23 October 2020, 11:08:11 UTC |
| 6e3ece9 | Lars Hubatsch | 22 October 2020, 09:59:43 UTC | prob_laplace: edit saving. | 22 October 2020, 09:59:43 UTC |
