6 Commits

Author SHA1 Message Date
  Gaspard Jankowiak 4afaeaeb34 update manifest 11 months ago
  Gaspard Jankowiak 8ad128394e [configs] update omega for recompute 11 months ago
  Gaspard Jankowiak b8a2d6b3f1 [results] save results from before recompute 11 months ago
  Gaspard Jankowiak de7773f942 metrics: typo 11 months ago
  Gaspard Jankowiak a94874ac1d fix config parsing + dir creation 11 months ago
  Gaspard Jankowiak ae34af7599 [nucleus] better compute initial radius 11 months ago
27 changed files with 148 additions and 111 deletions
  1. 80
    75
      Manifest.toml
  2. 2
    3
      configs_metrics/no_nucleus/varia_omega_param.yaml
  3. 1
    2
      configs_metrics/nucleus/varia_omega_param.yaml
  4. 1
    2
      metrics_nonuc_beta.jl
  5. 20
    20
      plot_all_the_plots.jl
  6. 0
    0
      plot_data/before_recompute_nucleus/v_A_KMT_nuc_old.csv
  7. 0
    0
      plot_data/before_recompute_nucleus/v_A_mu_nonuc.csv
  8. 0
    0
      plot_data/before_recompute_nucleus/v_A_mu_nuc_old.csv
  9. 0
    0
      plot_data/before_recompute_nucleus/v_beta_nonuc.csv
  10. 0
    0
      plot_data/before_recompute_nucleus/v_beta_nuc_new.csv
  11. 0
    0
      plot_data/before_recompute_nucleus/v_beta_nuc_old.csv
  12. 0
    0
      plot_data/before_recompute_nucleus/v_kb_nonuc.csv
  13. 0
    0
      plot_data/before_recompute_nucleus/v_kb_nonuc_mun100.csv
  14. 0
    0
      plot_data/before_recompute_nucleus/v_kb_nonuc_mun20.csv
  15. 0
    0
      plot_data/before_recompute_nucleus/v_kb_nuc_new.csv
  16. 0
    0
      plot_data/before_recompute_nucleus/v_kb_nuc_new_mun60.csv
  17. 0
    0
      plot_data/before_recompute_nucleus/v_kb_nuc_old.csv
  18. 0
    0
      plot_data/before_recompute_nucleus/v_kb_nuc_old_mun100.csv
  19. 0
    0
      plot_data/before_recompute_nucleus/v_kb_nuc_old_mun60.csv
  20. 0
    0
      plot_data/before_recompute_nucleus/v_omega_nuc_new.csv
  21. 0
    0
      plot_data/before_recompute_nucleus/v_omega_nuc_old.csv
  22. 0
    0
      plot_data/before_recompute_nucleus/v_width_nonuc.csv
  23. 0
    0
      plot_data/before_recompute_nucleus/v_width_nuc_new.csv
  24. 0
    0
      plot_data/before_recompute_nucleus/v_width_nuc_old.csv
  25. 12
    0
      plot_data/v_omega_nuc.csv
  26. 5
    5
      src/CellSim.jl
  27. 27
    4
      src/Nucleus.jl

+ 80
- 75
Manifest.toml View File

@@ -1,5 +1,11 @@
1 1
 # This file is machine-generated - editing it directly is not advised
2 2
 
3
+[[ArrayInterface]]
4
+deps = ["LinearAlgebra", "Requires", "SparseArrays"]
5
+git-tree-sha1 = "981354dab938901c2b607a213e62d9defa50b698"
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+uuid = "4fba245c-0d91-5ea0-9b3e-6abc04ee57a9"
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+version = "1.2.1"
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+
3 9
 [[AxisAlgorithms]]
4 10
 deps = ["LinearAlgebra", "Random", "SparseArrays", "WoodburyMatrices"]
5 11
 git-tree-sha1 = "a4d07a1c313392a77042855df46c5f534076fab9"
@@ -17,27 +23,21 @@ version = "0.8.10"
17 23
 
18 24
 [[BinaryProvider]]
19 25
 deps = ["Libdl", "SHA"]
20
-git-tree-sha1 = "c7361ce8a2129f20b0e05a89f7070820cfed6648"
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+git-tree-sha1 = "5b08ed6036d9d3f0ee6369410b830f8873d4024c"
21 27
 uuid = "b99e7846-7c00-51b0-8f62-c81ae34c0232"
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-
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-[[CSTParser]]
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+version = "0.5.8"
29 29
 
30 30
 [[Calculus]]
31
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+version = "0.5.8"
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@@ -52,10 +52,10 @@ uuid = "3da002f7-5984-5a60-b8a6-cbb66c0b333f"
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@@ -65,9 +65,9 @@ version = "0.2.0"
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66 66
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71 71
 
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@@ -76,10 +76,10 @@ uuid = "8f4d0f93-b110-5947-807f-2305c1781a2d"
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+deps = ["InteractiveUtils", "OrderedCollections"]
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-version = "0.15.0"
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+version = "0.17.6"
83 83
 
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@@ -90,10 +90,10 @@ deps = ["Mmap"]
90 90
 uuid = "8bb1440f-4735-579b-a4ab-409b98df4dab"
91 91
 
92 92
 [[DiffEqDiffTools]]
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-deps = ["LinearAlgebra"]
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-git-tree-sha1 = "14c4ec4f8796e71ba034f5089b6186876574a49d"
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-version = "0.10.1"
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+version = "1.4.0"
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 deps = ["Compat", "StaticArrays"]
@@ -102,16 +102,16 @@ uuid = "163ba53b-c6d8-5494-b064-1a9d43ac40c5"
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 version = "0.0.4"
103 103
 
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 [[DiffRules]]
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-deps = ["Random", "Test"]
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+version = "0.1.0"
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-deps = ["LinearAlgebra", "Printf", "Random", "Statistics", "Test"]
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-git-tree-sha1 = "a135c7c062023051953141da8437ed74f89d767a"
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@@ -134,10 +134,10 @@ uuid = "53c48c17-4a7d-5ca2-90c5-79b7896eea93"
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135 135
 
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-deps = ["CommonSubexpressions", "DiffResults", "DiffRules", "InteractiveUtils", "LinearAlgebra", "NaNMath", "Random", "SparseArrays", "SpecialFunctions", "StaticArrays", "Test"]
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+deps = ["CommonSubexpressions", "DiffResults", "DiffRules", "NaNMath", "Random", "SpecialFunctions", "StaticArrays"]
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141 141
 
142 142
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@@ -145,15 +145,15 @@ uuid = "b77e0a4c-d291-57a0-90e8-8db25a27a240"
145 145
 
146 146
 [[Interpolations]]
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 deps = ["AxisAlgorithms", "LinearAlgebra", "OffsetArrays", "Random", "Ratios", "SharedArrays", "SparseArrays", "StaticArrays", "WoodburyMatrices"]
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-git-tree-sha1 = "e1bac96b5ef3ea23b50e801b4a988ec21861a47f"
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 uuid = "a98d9a8b-a2ab-59e6-89dd-64a1c18fca59"
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151 151
 
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@@ -165,9 +165,9 @@ version = "0.1.0"
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@@ -196,15 +196,15 @@ uuid = "56ddb016-857b-54e1-b83d-db4d58db5568"
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 deps = ["JuliaInterpreter"]
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@@ -214,28 +214,26 @@ uuid = "d6f4376e-aef5-505a-96c1-9c027394607a"
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 uuid = "a63ad114-7e13-5084-954f-fe012c677804"
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+deps = ["Calculus", "DiffEqDiffTools", "DiffResults", "Distributed", "ForwardDiff"]
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+version = "7.5.0"
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-git-tree-sha1 = "413e54f04a4cbe9804089794eec6b06b2a43bc47"
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+version = "4.2.0"
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-git-tree-sha1 = "ce3b85e484a5d4c71dd5316215069311135fa9f2"
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+version = "0.11.1"
239 237
 
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@@ -244,10 +242,16 @@ uuid = "bac558e1-5e72-5ebc-8fee-abe8a469f55d"
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 version = "1.1.0"
245 243
 
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-deps = ["Markdown", "OrderedCollections", "REPL", "Test"]
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-git-tree-sha1 = "70bdbfb2bceabb15345c0b54be4544813b3444e4"
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+
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+version = "0.3.10"
251 255
 
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 deps = ["Dates", "LibGit2", "Markdown", "Printf", "REPL", "Random", "SHA", "UUIDs"]
@@ -265,9 +269,9 @@ version = "1.91.2"
265 269
 
266 270
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-version = "2.8.1"
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+version = "2.8.2"
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@@ -289,11 +293,17 @@ git-tree-sha1 = "7b1d07f411bc8ddb7977ec7f377b97b158514fe0"
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 uuid = "189a3867-3050-52da-a836-e630ba90ab69"
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 version = "0.2.0"
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+
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-git-tree-sha1 = "0148fc4b3392778e09eb75c4971ce75424acd1d1"
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@@ -313,16 +323,16 @@ deps = ["LinearAlgebra", "Random"]
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 uuid = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
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-deps = ["BinDeps", "BinaryProvider", "Libdl", "Test"]
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-git-tree-sha1 = "0b45dc2e45ed77f445617b99ff2adf0f5b0f23ea"
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+deps = ["BinDeps", "BinaryProvider", "Libdl"]
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 uuid = "276daf66-3868-5448-9aa4-cd146d93841b"
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-version = "0.7.2"
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+version = "0.8.0"
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 deps = ["LinearAlgebra", "Random", "Statistics"]
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-git-tree-sha1 = "db23bbf50064c582b6f2b9b043c8e7e98ea8c0c6"
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+git-tree-sha1 = "5a3bcb6233adabde68ebc97be66e95dcb787424c"
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 uuid = "90137ffa-7385-5640-81b9-e52037218182"
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-version = "0.11.0"
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+version = "0.12.1"
326 336
 
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@@ -332,11 +342,6 @@ uuid = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
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 deps = ["Distributed", "InteractiveUtils", "Logging", "Random"]
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 uuid = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
334 344
 
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-[[Tokenize]]
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-git-tree-sha1 = "0de343efc07da00cd449d5b04e959ebaeeb3305d"
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-version = "0.5.4"
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-
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 deps = ["Test", "Unicode"]
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 git-tree-sha1 = "6ddf8244220dfda2f17539fa8c9de20d6c575b69"

+ 2
- 3
configs_metrics/no_nucleus/varia_omega_param.yaml View File

@@ -44,7 +44,7 @@ params:
44 44
     N_mu: 100 # area constraint relaxation
45 45
     N_target_area: 0.7
46 46
     N_kb: 5e-4 # bending stiffness
47
-    N_ω:  1e-1 # inplane stiffness
47
+    N_ω:  5e1 # inplane stiffness
48 48
     N_W0: 7e-1  # potential offset
49 49
     N_kcont: 5e0 # contact force intensity
50 50
     N_αcont: 1e1 # contact force sharpness
@@ -68,7 +68,7 @@ flags:
68 68
     circular_wall:        false
69 69
     cortex:               true
70 70
     centrosome:           true
71
-    nucleus:              true
71
+    nucleus:              false
72 72
     follow_cam:           false
73 73
     debug:                false
74 74
     force_cortex_area:    true
@@ -94,4 +94,3 @@ config:
94 94
 
95 95
         # shift_nucleus: 0.25 # 3/4 of a period = 3/4 * 2π / f.ω0
96 96
 
97
-   

+ 1
- 2
configs_metrics/nucleus/varia_omega_param.yaml View File

@@ -44,7 +44,7 @@ params:
44 44
     N_mu: 100 # area constraint relaxation
45 45
     N_target_area: 0.7
46 46
     N_kb: 5e-4 # bending stiffness
47
-    N_ω:  1e-1 # inplane stiffness
47
+    N_ω:  5e1 # inplane stiffness
48 48
     N_W0: 7e-1  # potential offset
49 49
     N_kcont: 5e0 # contact force intensity
50 50
     N_αcont: 1e1 # contact force sharpness
@@ -94,4 +94,3 @@ config:
94 94
 
95 95
         # shift_nucleus: 0.25 # 3/4 of a period = 3/4 * 2π / f.ω0
96 96
 
97
-   

+ 1
- 2
metrics_nonuc_beta.jl View File

@@ -4,12 +4,11 @@ import CellSim
4 4
 import Dates
5 5
 
6 6
 # The configuration file from which parameters are taken
7
-base_config = "configs_metrics/no_nucleus/varia_width_param.yaml"
7
+base_config = "configs_metrics/no_nucleus/varia_beta_param.yaml"
8 8
 
9 9
 # The output prefix, this overrides the one set in the configuration file
10 10
 output_prefix = "nonuc_beta"
11 11
 
12
-
13 12
 # Load configuration
14 13
 P, F, config = CellSim.read_config(base_config)
15 14
 

+ 20
- 20
plot_all_the_plots.jl View File

@@ -32,61 +32,61 @@ PyPlot.figure()
32 32
 
33 33
 # kb
34 34
 PyPlot.subplot(241)
35
-plot_csv("plot_data/v_kb_nuc_new.csv", true, label="nuc new μn = 20")
36
-plot_csv("plot_data/v_kb_nuc_new_mun60.csv", true, label="nuc new µn=60")
37
-plot_csv("plot_data/v_kb_nuc_old.csv", true, label="nuc old μn = 20")
38
-plot_csv("plot_data/v_kb_nuc_old_mun60.csv", true, label="nuc old μn=60")
39
-plot_csv("plot_data/v_kb_nuc_old_mun100.csv", true, label="nuc old µn=100")
40
-
41
-plot_csv("plot_data/v_kb_nonuc_mun100.csv", false, label="nonuc μn=100", ls="dotted")
42
-plot_csv("plot_data/v_kb_nonuc_mun20.csv", false, label="nonuc μn=20", ls="dotted")
35
+plot_csv("plot_data/before_recompute_nucleus/v_kb_nuc_new.csv", true, label="nuc new μn = 20")
36
+plot_csv("plot_data/before_recompute_nucleus/v_kb_nuc_new_mun60.csv", true, label="nuc new µn=60")
37
+plot_csv("plot_data/before_recompute_nucleus/v_kb_nuc_old.csv", true, label="nuc old μn = 20")
38
+plot_csv("plot_data/before_recompute_nucleus/v_kb_nuc_old_mun60.csv", true, label="nuc old μn=60")
39
+plot_csv("plot_data/before_recompute_nucleus/v_kb_nuc_old_mun100.csv", true, label="nuc old µn=100")
40
+
41
+plot_csv("plot_data/before_recompute_nucleus/v_kb_nonuc_mun100.csv", false, label="nonuc μn=100", ls="dotted")
42
+plot_csv("plot_data/before_recompute_nucleus/v_kb_nonuc_mun20.csv", false, label="nonuc μn=20", ls="dotted")
43 43
 PyPlot.axhline(0.0, lw=0.5, color="black")
44 44
 PyPlot.legend()
45 45
 PyPlot.title("Velocity vs kb")
46 46
 
47 47
 # mu
48 48
 PyPlot.subplot(242)
49
-plot_csv("plot_data/v_A_mu_nuc_old.csv", true, label="nuc old")
50
-plot_csv("plot_data/v_A_mu_nonuc.csv", true, label="nonuc", ls="dotted")
49
+plot_csv("plot_data/before_recompute_nucleus/v_A_mu_nuc_old.csv", true, label="nuc old")
50
+plot_csv("plot_data/before_recompute_nucleus/v_A_mu_nonuc.csv", true, label="nonuc", ls="dotted")
51 51
 PyPlot.axhline(0.0, lw=0.5, color="black")
52 52
 PyPlot.legend()
53 53
 PyPlot.title("Velocity vs µn")
54 54
 
55 55
 PyPlot.subplot(243)
56
-plot_csv("plot_data/v_A_mu_nuc_old.csv", true, 3, label="nuc old")
56
+plot_csv("plot_data/before_recompute_nucleus/v_A_mu_nuc_old.csv", true, 3, label="nuc old")
57 57
 PyPlot.axhline(0.0, lw=0.5, color="black")
58 58
 PyPlot.legend()
59 59
 PyPlot.title("Area vs µn")
60 60
 
61 61
 # kb
62 62
 PyPlot.subplot(244)
63
-plot_csv("plot_data/v_A_KMT_nuc_old.csv", true, label="nuc old")
63
+plot_csv("plot_data/before_recompute_nucleus/v_A_KMT_nuc_old.csv", true, label="nuc old")
64 64
 PyPlot.axhline(0.0, lw=0.5, color="black")
65 65
 PyPlot.legend()
66 66
 PyPlot.title("Velocity vs kMT")
67 67
 
68 68
 # channel depth
69 69
 PyPlot.subplot(245)
70
-plot_csv("plot_data/v_beta_nuc_old.csv", true, label="nuc old")
71
-plot_csv("plot_data/v_beta_nuc_new.csv", true, label="nuc new")
72
-plot_csv("plot_data/v_beta_nonuc.csv", false, label="nonuc", ls="dotted")
70
+plot_csv("plot_data/before_recompute_nucleus/v_beta_nuc_old.csv", true, label="nuc old")
71
+plot_csv("plot_data/before_recompute_nucleus/v_beta_nuc_new.csv", true, label="nuc new")
72
+plot_csv("plot_data/before_recompute_nucleus/v_beta_nonuc.csv", false, label="nonuc", ls="dotted")
73 73
 PyPlot.axhline(0.0, lw=0.5, color="black")
74 74
 PyPlot.legend()
75 75
 PyPlot.title("Velocity vs f_β")
76 76
 
77 77
 # channel width
78 78
 PyPlot.subplot(246)
79
-plot_csv("plot_data/v_width_nuc_old.csv", true, label="nuc old")
80
-plot_csv("plot_data/v_width_nuc_new.csv", true, label="nuc new")
81
-plot_csv("plot_data/v_width_nonuc.csv", false, label="nonuc", ls="dotted")
79
+plot_csv("plot_data/before_recompute_nucleus/v_width_nuc_old.csv", true, label="nuc old")
80
+plot_csv("plot_data/before_recompute_nucleus/v_width_nuc_new.csv", true, label="nuc new")
81
+plot_csv("plot_data/before_recompute_nucleus/v_width_nonuc.csv", false, label="nonuc", ls="dotted")
82 82
 PyPlot.axhline(0.0, lw=0.5, color="black")
83 83
 PyPlot.legend()
84 84
 PyPlot.title("Velocity vs f_width")
85 85
 
86 86
 # channel pulsation
87 87
 PyPlot.subplot(247)
88
-plot_csv("plot_data/v_omega_nuc_old.csv", true, label="nuc old")
89
-plot_csv("plot_data/v_omega_nuc_new.csv", true, label="nuc new")
88
+plot_csv("plot_data/before_recompute_nucleus/v_omega_nuc_old.csv", true, label="nuc old")
89
+plot_csv("plot_data/v_omega_nuc.csv", true, label="nuc")
90 90
 PyPlot.axhline(0.0, lw=0.5, color="black")
91 91
 PyPlot.legend()
92 92
 PyPlot.title("Velocity vs f_ω")

plot_data/v_A_KMT_nuc_old.csv → plot_data/before_recompute_nucleus/v_A_KMT_nuc_old.csv View File


plot_data/v_A_mu_nonuc.csv → plot_data/before_recompute_nucleus/v_A_mu_nonuc.csv View File


plot_data/v_A_mu_nuc_old.csv → plot_data/before_recompute_nucleus/v_A_mu_nuc_old.csv View File


plot_data/v_beta_nonuc.csv → plot_data/before_recompute_nucleus/v_beta_nonuc.csv View File


plot_data/v_beta_nuc_new.csv → plot_data/before_recompute_nucleus/v_beta_nuc_new.csv View File


plot_data/v_beta_nuc_old.csv → plot_data/before_recompute_nucleus/v_beta_nuc_old.csv View File


plot_data/v_kb_nonuc.csv → plot_data/before_recompute_nucleus/v_kb_nonuc.csv View File


plot_data/v_kb_nonuc_mun100.csv → plot_data/before_recompute_nucleus/v_kb_nonuc_mun100.csv View File


plot_data/v_kb_nonuc_mun20.csv → plot_data/before_recompute_nucleus/v_kb_nonuc_mun20.csv View File


plot_data/v_kb_nuc_new.csv → plot_data/before_recompute_nucleus/v_kb_nuc_new.csv View File


plot_data/v_kb_nuc_new_mun60.csv → plot_data/before_recompute_nucleus/v_kb_nuc_new_mun60.csv View File


plot_data/v_kb_nuc_old.csv → plot_data/before_recompute_nucleus/v_kb_nuc_old.csv View File


plot_data/v_kb_nuc_old_mun100.csv → plot_data/before_recompute_nucleus/v_kb_nuc_old_mun100.csv View File


plot_data/v_kb_nuc_old_mun60.csv → plot_data/before_recompute_nucleus/v_kb_nuc_old_mun60.csv View File


plot_data/v_omega_nuc_new.csv → plot_data/before_recompute_nucleus/v_omega_nuc_new.csv View File


plot_data/v_omega_nuc_old.csv → plot_data/before_recompute_nucleus/v_omega_nuc_old.csv View File


plot_data/v_width_nonuc.csv → plot_data/before_recompute_nucleus/v_width_nonuc.csv View File


plot_data/v_width_nuc_new.csv → plot_data/before_recompute_nucleus/v_width_nuc_new.csv View File


plot_data/v_width_nuc_old.csv → plot_data/before_recompute_nucleus/v_width_nuc_old.csv View File


+ 12
- 0
plot_data/v_omega_nuc.csv View File

@@ -0,0 +1,12 @@
1
+f_β, average_velocity
2
+2.0, 0.0
3
+3.0, 0.0
4
+4.0, 0.0
5
+5.0, 0.0
6
+6.0, 2.7656109789960457
7
+7.0, 2.378292157657167
8
+8.0, 2.7884809265243358
9
+9.0, 3.42454186837457
10
+10.0, 3.4914681640960374
11
+11.0, 3.3714730875781846
12
+12.0, 3.2140518662625457

+ 5
- 5
src/CellSim.jl View File

@@ -195,8 +195,8 @@ function read_config(config_filename::String)
195 195
         config["output_prefix"] = "runs/"
196 196
     end
197 197
 
198
-    if !haskey(config, "recompute_nucleus_coords")
199
-        config["recompute_nucleus_coords"] = 5
198
+    if !haskey(config, "recompute_nucleus_each")
199
+        config["recompute_nucleus_each"] = 5
200 200
     end
201 201
 
202 202
     if (config["metrics"]["start_iteration"] <= 0) && !F.nucleus
@@ -219,9 +219,9 @@ function launch(P::CSC.Params, F::CSC.Flags, config)
219 219
         config["output_prefix"] = "runs/"
220 220
     end
221 221
 
222
-    run(`mkdir -p runs`)
223
-    run(`mkdir -p dumps`)
224
-    run(`mkdir -p $(config["output_prefix"])`)
222
+    mkpath("runs")
223
+    mkpath("dumps")
224
+    mkpath("$(config["output_prefix"])")
225 225
     run(`cp $(config["config_filename"]) $(config["output_prefix"])Run_$(config["date_string"]).yaml`)
226 226
     println("Parameters:")
227 227
     for s in fieldnames(typeof(P))

+ 27
- 4
src/Nucleus.jl View File

@@ -11,6 +11,8 @@ const SA = SparseArrays
11 11
 import LinearAlgebra
12 12
 const LA = LinearAlgebra
13 13
 
14
+import NLsolve
15
+
14 16
 mutable struct NucleusCoords
15 17
     # node coordinates
16 18
     Y::Matrix{Float64}
@@ -417,6 +419,27 @@ function update_Y(c::NucleusCoords, new_c::NucleusCoords,
417 419
     new_c.Y[:] = M\f
418 420
 end
419 421
 
422
+function min_center_to_wall(P::Params)
423
+
424
+    function dist(x)
425
+        return sqrt((x-0.5π/P.f_ω0)^2 + (P.f_width + P.f_β*sin(P.f_ω0*x))^2)
426
+    end
427
+
428
+    function f(x)
429
+        return [x[1] - 0.5π/P.f_ω0 + P.f_ω0*P.f_β*cos(P.f_ω0*x[1])*(P.f_width + P.f_β*sin(P.f_ω0*x[1]))]
430
+    end
431
+
432
+    function fprime(x)
433
+        return [1 + (P.f_ω0*P.f_β)^2*(cos(P.f_ω0*x[1])^2 - sin(P.f_ω0*x[1])^2) - P.f_β*P.f_ω0^2*P.f_width*sin(P.f_ω0*x[1])]
434
+    end
435
+
436
+    res = NLsolve.nlsolve(f, fprime, [π/P.f_ω0])
437
+
438
+    @assert fprime(res.zero)[1] > 0
439
+
440
+    return dist(res.zero[1])
441
+end
442
+
420 443
 function initialize_coords(P::Params, F::Flags, cortex_c::PointCoords; fill_wall::Bool=true)
421 444
     # The nucleus is initialized as a circle centered on the
422 445
     # barycenter of the cell, with radius P.N_r_init
@@ -427,15 +450,15 @@ function initialize_coords(P::Params, F::Flags, cortex_c::PointCoords; fill_wall
427 450
     θ = collect(-0.5*θ0 .+ (0:(P.Nnuc-1))*θ0)
428 451
 
429 452
     if fill_wall
430
-        bc = [0.0 0.5π/P.f_ω0]
431
-        r_init = min(P.f_width + P.f_β - 2/P.f_α, (0.5π + P.f_width)/P.f_ω0)
453
+        nucleus_center = [0.0 0.5π/P.f_ω0]
454
+        r_init = min_center_to_wall(P) - 2/P.f_α
432 455
     else
433
-        bc = sum(cortex_c.x; dims=1) / P.N
456
+        nucleus_center = sum(cortex_c.x; dims=1) / P.N
434 457
         r_init = P.N_r_init
435 458
     end
436 459
 
437 460
     nc = NucleusCoords(
438
-        r_init*[cos.(t) sin.(t)] .+ bc, # Y
461
+        r_init*[cos.(t) sin.(t)] .+ nucleus_center, # Y
439 462
         zeros(P.Nnuc), # α
440 463
         zeros(P.Nnuc), # β
441 464
         1/r_init * ones(P.Nnuc), # k

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