Membranes in 1D : Data Structure¶

Data Structure and Visualization of Membranes in 1D¶

No simulations done here; for diffusion and transport across membranes, please see membranes_2 and other experiments

TAGS : "membranes 1D", "basic", "quick-start"¶

In [1]:

LAST_REVISED = "June 4, 2025"
LIFE123_VERSION = "1.0.0rc6"        # Library version this experiment is based on

In [2]:

#import set_path                    # Using MyBinder?  Uncomment this before running the next cell!

In [3]:

#import sys, os
#os.getcwd()
#sys.path.append("C:/some_path/my_env_or_install")   # CHANGE to the folder containing your venv or libraries installation!
# NOTE: If any of the imports below can't find a module, uncomment the lines above, or try:  import set_path

from life123 import BioSim1D, ChemData, check_version

In [4]:

check_version(LIFE123_VERSION)

OK

In [ ]:

Prepare the initial system¶

with a single non-zero bin concentration of the single chemical A, near the left edge of the system

In [5]:

chem_data = ChemData(names=["A", "B"], plot_colors=["turquoise", "green"])

bio = BioSim1D(n_bins=21, chem_data=chem_data)

In [6]:

bio.inject_gradient(chem_label="A", conc_left = 0., conc_right = 100.)

bio.inject_sine_conc(chem_label="B", number_cycles=2, amplitude=5., bias=10., phase=0)

bio.describe_state()

SYSTEM STATE at Time t = 0:
21 bins and 2 chemical species

Out[6]:

	Species	Diff rate	Bin 0	Bin 1	Bin 2	Bin 3	Bin 4	Bin 5	Bin 6	Bin 7	...	Bin 11	Bin 12	Bin 13	Bin 14	Bin 15	Bin 16	Bin 17	Bin 18	Bin 19	Bin 20
0	A	None	0.0	5.0000	10.000000	15.00000	20.000000	25.000000	30.000000	35.000000	...	55.000000	60.000000	65.000000	70.000000	75.000000	80.000000	85.000000	90.00000	95.000000	100.0000
1	B	None	10.0	12.8166	14.654369	14.87464	13.400864	10.745211	7.830581	5.669873	...	11.473776	13.909157	14.986019	14.330127	12.169419	9.254789	6.599136	5.12536	5.345631	7.1834

2 rows × 23 columns

In [7]:

bio.system_snapshot()

Out[7]:

	A	B
0	0.0	10.000000
1	5.0	12.816600
2	10.0	14.654369
3	15.0	14.874640
4	20.0	13.400864
5	25.0	10.745211
6	30.0	7.830581
7	35.0	5.669873
8	40.0	5.013981
9	45.0	6.090843
10	50.0	8.526224
11	55.0	11.473776
12	60.0	13.909157
13	65.0	14.986019
14	70.0	14.330127
15	75.0	12.169419
16	80.0	9.254789
17	85.0	6.599136
18	90.0	5.125360
19	95.0	5.345631
20	100.0	7.183400

In [8]:

bio.visualize_system()   # Line curve view

In [9]:

bio.system_heatmaps(text_format=".0f")

In [ ]:

Add Membranes¶

In [10]:

bio.membranes().set_membranes(membranes=[ (0, 5) ])

In [11]:

bio.membranes().membrane_list

Out[11]:

[(0, 5)]

In [12]:

bio.system_heatmaps(text_format=".0f")

In [13]:

bio.membranes().set_membranes(membranes=[ (0, 5), (10, 11), (16,21) ])    # Overwrite previous membranes

In [14]:

bio.system_heatmaps(text_format=".0f")

In [ ]: