From e2f1d871eb5c2f009bba5fc1be768a6e4cac21b5 Mon Sep 17 00:00:00 2001
From: jessicasyu <15913767+jessicasyu@users.noreply.github.com>
Date: Fri, 7 Jun 2024 18:27:54 -0400
Subject: [PATCH] Add copy of templates and configs from subcell pipeline

---
 configs/free_barbed_end_final.cym             | 122 ++++++++++++++
 configs/linkers_no_compression.cym            | 148 +++++++++++++++++
 configs/no_linkers_no_compression.cym         | 104 ++++++++++++
 templates/vary_compress_rate.cym.tpl          | 149 ++++++++++++++++++
 ...compress_rate_nolinkers_nocompress.cym.tpl | 106 +++++++++++++
 5 files changed, 629 insertions(+)
 create mode 100644 configs/free_barbed_end_final.cym
 create mode 100644 configs/linkers_no_compression.cym
 create mode 100644 configs/no_linkers_no_compression.cym
 create mode 100755 templates/vary_compress_rate.cym.tpl
 create mode 100644 templates/vary_compress_rate_nolinkers_nocompress.cym.tpl

diff --git a/configs/free_barbed_end_final.cym b/configs/free_barbed_end_final.cym
new file mode 100644
index 0000000..950ba41
--- /dev/null
+++ b/configs/free_barbed_end_final.cym
@@ -0,0 +1,122 @@
+% Fiber under compression to measure buckling force
+
+
+% how fast the end gets compressed (µm/s) 150 nm / 10 µs
+
+% fast: 1.5e2, 1.5e3, 1.5e4
+% slow: 0.0015, 0.015, 0.15, 1.5, 15
+
+% the time step (s)
+
+
+% how frequently the compression is applied (time steps)
+
+
+% frequency you save frames (s)
+
+
+% total fiber length
+
+
+% ratio of total length that gets compressed
+
+
+
+% total compression amount
+
+
+% total simulation time (s)
+
+
+% compression_velocity:  150
+% compression_distance:  0.15
+% total_time: 0.001
+% 200 repeats
+% 1 frames saved per repeat
+% translation = 0.00075
+
+set simul system
+{
+    time_step = 5e-07
+    viscosity = 0.01
+}
+
+set space cell
+{
+    shape = sphere
+}
+
+new cell
+{
+    radius = 2
+}
+
+set fiber filament
+{
+    rigidity = 0.041
+    segmentation = 0.001
+    display = ( point=6,1; line=10,2; )
+}
+
+set hand binder
+{
+    % 10 events per second, 0.05 um binding radius
+
+    binding = 10, 0.005
+
+    % 0 events per second, infinite unbinding force
+
+    unbinding = 0, inf
+    bind_also_end = 1
+
+    display = ( width=3; size=12; color=green )
+}
+
+set single linker
+{
+    hand = binder
+    activity = fixed
+    stiffness = 10000000
+}
+
+
+new filament
+{
+    length = 0.5
+    position = 0 0 0
+    orientation = 1 0 0
+    % attach1 = linker, 0, minus_end
+    % attach2 = linker, 0, plus_end
+
+}
+
+new linker
+{
+    position = -0.25 0 0
+    attach = filament, 0, minus_end
+    mark = 1
+}
+
+% make a second linker 5 nm from the first, to keep minus end rotationally fixed
+
+new linker
+{
+    position = -0.24 0 0
+    attach = filament, 0.01, minus_end
+    mark = 2
+}
+
+% make a second linker 5 nm from the first, to keep minus end rotationally fixed
+
+% number of intervals for compression
+repeat 200
+{
+
+% this means you run one step and let it relax 9 time steps
+% and show it for 2 frames
+run 10 system { nb_frames = 1 }
+
+report fiber:points fiber_points.txt
+report single:position singles.txt
+
+}
diff --git a/configs/linkers_no_compression.cym b/configs/linkers_no_compression.cym
new file mode 100644
index 0000000..369d022
--- /dev/null
+++ b/configs/linkers_no_compression.cym
@@ -0,0 +1,148 @@
+% Fiber under compression to measure buckling force
+
+
+% how fast the end gets compressed (µm/s) 150 nm / 10 µs
+
+% fast: 1.5e2, 1.5e3, 1.5e4
+% slow: 0.0015, 0.015, 0.15, 1.5, 15
+
+% the time step (s)
+
+
+% how frequently the compression is applied (time steps)
+
+
+% frequency you save frames (s)
+
+
+% total fiber length
+
+
+% ratio of total length that gets compressed
+
+
+
+% total compression amount
+
+
+% total simulation time (s)
+
+
+% compression_velocity:  150
+% compression_distance:  0.15
+% total_time: 0.001
+% 200 repeats
+% 1 frames saved per repeat
+% translation = 0.00075
+
+set simul system
+{
+    time_step = 5e-07
+    viscosity = 0.01
+}
+
+set space cell
+{
+    shape = sphere
+}
+
+new cell
+{
+    radius = 2
+}
+
+set fiber filament
+{
+    rigidity = 0.041
+    segmentation = 0.001
+    display = ( point=6,1; line=10,2; )
+}
+
+set hand binder
+{
+    % 10 events per second, 0.05 um binding radius
+
+    binding = 10, 0.005
+
+    % 0 events per second, infinite unbinding force
+
+    unbinding = 0, inf
+    bind_also_end = 1
+
+    display = ( width=3; size=12; color=green )
+}
+
+set single linker
+{
+    hand = binder
+    activity = fixed
+    stiffness = 10000000
+}
+
+
+new filament
+{
+    length = 0.5
+    position = 0 0 0
+    orientation = 1 0 0
+    % attach1 = linker, 0, minus_end
+    % attach2 = linker, 0, plus_end
+
+}
+
+new linker
+{
+    position = -0.25 0 0
+    attach = filament, 0, minus_end
+    mark = 1
+}
+
+% make a second linker 5 nm from the first, to keep minus end rotationally fixed
+
+new linker
+{
+    position = -0.24 0 0
+    attach = filament, 0.01, minus_end
+    mark = 2
+}
+
+
+new linker
+{
+    position = 0.25 0 0
+    attach = filament, 0, plus_end
+    mark = 3
+}
+
+% make a second linker 5 nm from the first, to keep minus end rotationally fixed
+
+new linker
+{
+    position = 0.24 0 0
+    attach = filament, 0.01, plus_end
+    mark = 4
+}
+
+% number of intervals for compression
+repeat 200
+{
+
+% this means you run one step and let it relax 9 time steps
+% and show it for 2 frames
+run 10 system { nb_frames = 1 }
+
+report fiber:points fiber_points.txt
+report single:position singles.txt
+
+move linker
+{
+    translation = 0.00075 0 0
+    mark = 1
+}
+move linker
+{
+    translation = 0.00075 0 0
+    mark = 2
+}
+
+}
diff --git a/configs/no_linkers_no_compression.cym b/configs/no_linkers_no_compression.cym
new file mode 100644
index 0000000..77fb1f1
--- /dev/null
+++ b/configs/no_linkers_no_compression.cym
@@ -0,0 +1,104 @@
+% Fiber under compression to measure buckling force
+
+
+% how fast the end gets compressed (µm/s) 150 nm / 10 µs
+
+% fast: 1.5e2, 1.5e3, 1.5e4
+% slow: 0.0015, 0.015, 0.15, 1.5, 15
+
+% the time step (s)
+
+
+% how frequently the compression is applied (time steps)
+
+
+% frequency you save frames (s)
+
+
+% total fiber length
+
+
+% ratio of total length that gets compressed
+
+
+
+% total compression amount
+
+
+% total simulation time (s)
+
+
+% compression_velocity:  150
+% compression_distance:  0.15
+% total_time: 0.001
+% 200 repeats
+% 1 frames saved per repeat
+% translation = 0.00075
+
+set simul system
+{
+    time_step = 5e-07
+    viscosity = 0.01
+}
+
+set space cell
+{
+    shape = sphere
+}
+
+new cell
+{
+    radius = 2
+}
+
+set fiber filament
+{
+    rigidity = 0.041
+    segmentation = 0.001
+    display = ( point=6,1; line=10,2; )
+}
+
+set hand binder
+{
+    % 10 events per second, 0.05 um binding radius
+
+    binding = 10, 0.005
+
+    % 0 events per second, infinite unbinding force
+
+    unbinding = 0, inf
+    bind_also_end = 1
+
+    display = ( width=3; size=12; color=green )
+}
+
+set single linker
+{
+    hand = binder
+    activity = fixed
+    stiffness = 10000000
+}
+
+
+new filament
+{
+    length = 0.5
+    position = 0 0 0
+    orientation = 1 0 0
+    % attach1 = linker, 0, minus_end
+    % attach2 = linker, 0, plus_end
+
+}
+
+% number of intervals for compression
+repeat 200
+{
+
+% this means you run one step and let it relax 9 time steps
+% and show it for 2 frames
+run 10 system { nb_frames = 1 }
+
+report fiber:points fiber_points.txt
+report single:position singles.txt
+
+}
diff --git a/templates/vary_compress_rate.cym.tpl b/templates/vary_compress_rate.cym.tpl
new file mode 100755
index 0000000..10ef77e
--- /dev/null
+++ b/templates/vary_compress_rate.cym.tpl
@@ -0,0 +1,149 @@
+% Fiber under compression to measure buckling force
+
+
+% how fast the end gets compressed (µm/s) 150 nm / 10 µs
+[[compression_velocity = [4.73413649, 15, 47.4341649, 150]]]
+% fast: 1.5e2, 1.5e3, 1.5e4
+% slow: 0.0015, 0.015, 0.15, 1.5, 15
+
+% the time step (s)
+[[timestep = 5e-07]]
+
+% how frequently the compression is applied (time steps)
+[[compression_interval = 10]]
+
+% frequency you save frames (s)
+[[save_time_interval = 5e-07]]
+
+% total fiber length
+[[fiber_length = 0.5]]
+
+% ratio of total length that gets compressed
+[[compression_ratio = 0.3]]
+
+
+% total compression amount
+[[compression_distance = fiber_length*compression_ratio]]
+
+% total simulation time (s)
+[[total_time = round(compression_distance/compression_velocity, 7)]]
+
+% compression_velocity:  [[compression_velocity]]
+% compression_distance:  [[compression_distance]]
+% total_time: [[total_time]]
+% [[round(total_time/timestep/compression_interval)]] repeats
+% [[round(timestep/save_time_interval)]] frames saved per repeat
+% translation = [[round(compression_velocity*timestep*compression_interval,7)]]
+
+set simul system
+{
+    time_step = [[timestep]]
+    viscosity = 0.01
+    random_seed = {{RANDOM_SEED}}
+}
+
+set space cell
+{
+    shape = sphere
+}
+
+new cell
+{
+    radius = 2
+}
+
+set fiber filament
+{
+    rigidity = 0.041
+    segmentation = 0.001
+    display = ( point=6,1; line=10,2; )
+}
+
+set hand binder
+{
+    % 10 events per second, 0.05 um binding radius
+
+    binding = 10, 0.005
+
+    % 0 events per second, infinite unbinding force
+
+    unbinding = 0, inf
+    bind_also_end = 1
+
+    display = ( width=3; size=12; color=green )
+}
+
+set single linker
+{
+    hand = binder
+    activity = fixed
+    stiffness = 10000000
+}
+
+
+new filament
+{
+    length = [[fiber_length]]
+    position = 0 0 0
+    orientation = 1 0 0
+    % attach1 = linker, 0, minus_end
+    % attach2 = linker, 0, plus_end
+
+}
+
+new linker
+{
+    position = -0.25 0 0
+    attach = filament, 0, minus_end
+    mark = 1
+}
+
+% make a second linker 5 nm from the first, to keep minus end rotationally fixed
+
+new linker
+{
+    position = -0.24 0 0
+    attach = filament, 0.01, minus_end
+    mark = 2
+}
+
+
+new linker
+{
+    position = 0.25 0 0
+    attach = filament, 0, plus_end
+    mark = 3
+}
+
+% make a second linker 5 nm from the first, to keep minus end rotationally fixed
+
+new linker
+{
+    position = 0.24 0 0
+    attach = filament, 0.01, plus_end
+    mark = 4
+}
+
+% number of intervals for compression
+repeat [[round(total_time/timestep/compression_interval)]]
+{
+
+% this means you run one step and let it relax 9 time steps
+% and show it for 2 frames
+run [[compression_interval]] system { nb_frames = [[round(timestep/save_time_interval)]] }
+
+report fiber:points fiber_points.txt
+report single:position singles.txt
+
+move linker
+{
+    translation = [[round(compression_velocity*timestep*compression_interval, 7)]] 0 0
+    mark = 1
+}
+move linker
+{
+    translation = [[round(compression_velocity*timestep*compression_interval, 7)]] 0 0
+    mark = 2
+}
+
+}
diff --git a/templates/vary_compress_rate_nolinkers_nocompress.cym.tpl b/templates/vary_compress_rate_nolinkers_nocompress.cym.tpl
new file mode 100644
index 0000000..4312418
--- /dev/null
+++ b/templates/vary_compress_rate_nolinkers_nocompress.cym.tpl
@@ -0,0 +1,106 @@
+% Fiber under compression to measure buckling force
+
+
+% how fast the end gets compressed (µm/s) 150 nm / 10 µs
+[[compression_velocity = [0.15, 0.47434165, 1.5, 4.73413649, 15, 47.4341649, 150]]]
+% fast: 1.5e2, 1.5e3, 1.5e4
+% slow: 0.0015, 0.015, 0.15, 1.5, 15
+
+% the time step (s)
+[[timestep = 5e-07]]
+
+% how frequently the compression is applied (time steps)
+[[compression_interval = 10]]
+
+% frequency you save frames (s)
+[[save_time_interval = 5e-07]]
+
+% total fiber length
+[[fiber_length = 0.5]]
+
+% ratio of total length that gets compressed
+[[compression_ratio = 0.3]]
+
+
+% total compression amount
+[[compression_distance = fiber_length*compression_ratio]]
+
+% total simulation time (s)
+[[total_time = round(compression_distance/compression_velocity, 7)]]
+
+% compression_velocity:  [[compression_velocity]]
+% compression_distance:  [[compression_distance]]
+% total_time: [[total_time]]
+% [[round(total_time/timestep/compression_interval)]] repeats
+% [[round(timestep/save_time_interval)]] frames saved per repeat
+% translation = [[round(compression_velocity*timestep*compression_interval,7)]]
+
+set simul system
+{
+    time_step = [[timestep]]
+    viscosity = 0.01
+}
+
+set space cell
+{
+    shape = sphere
+}
+
+new cell
+{
+    radius = 2
+}
+
+set fiber filament
+{
+    rigidity = 0.041
+    segmentation = 0.001
+    display = ( point=6,1; line=10,2; )
+}
+
+set hand binder
+{
+    % 10 events per second, 0.05 um binding radius
+
+    binding = 10, 0.005
+
+    % 0 events per second, infinite unbinding force
+
+    unbinding = 0, inf
+    bind_also_end = 1
+
+    display = ( width=3; size=12; color=green )
+}
+
+set single linker
+{
+    hand = binder
+    activity = fixed
+    stiffness = 10000000
+}
+
+
+new filament
+{
+    length = [[fiber_length]]
+    position = 0 0 0
+    orientation = 1 0 0
+    % attach1 = linker, 0, minus_end
+    % attach2 = linker, 0, plus_end
+
+}
+
+
+% number of intervals for compression
+repeat [[round(total_time/timestep/compression_interval)]]
+{
+
+% this means you run one step and let it relax 9 time steps
+% and show it for 2 frames
+run [[compression_interval]] system { nb_frames = [[round(timestep/save_time_interval)]] }
+
+report fiber:points fiber_points.txt
+report single:position singles.txt
+
+
+}