BZ-CA

Platform to physically embody cellular-automaton using Belousov-Zhabotinsky reaction-diffusion chemistry in addressably stirred cells.

Aims of project

• Create working platform of addressable magnetic stirrers
• Use platform to demonstrate control over cell oscillations
• Control patterns of oscillating cell arrays using machine learning

Platform

BZ-CA has a working stirrer array. It is also connected to a series of pump to add/remove liquid.

How to build the platform is explained with detail on the manuscript pre-print.

This document explains how to build the first iteration of the platform, which is what was used to obtain the results obtained there. It used custom-made electronics. The current iteration uses the same hardware and 3D-printed parts, but the electronics are controlled using stacked Adafruit Motor shields.

Software

The software to control this platform is divided into different files:

• bzboard.py controls the motors that actuate the stirrers.
• pumpsctl.py controls the pumps to add and remove liquid from the platform.
• firmware controls the Arduino scripts to control the 2 arduinos that were actuating the stirrers and the pumps.
• image processing is the implementation of the SVM to classify the oscillations between red and blue.

Example Code

An example of how to use the bzboard.py code is provided below and in initBZ.py:

################################################################
# This script should be used before starting the experiments
# to make sure everything is working and tubes are filled
################################################################

import time

from pumpsctl.pumpsctl import PumpsCtl
from bzboard.bzboard import BZBoard
from img_proc.record_cam import RecordVideo
import os, sys
sys.path.append(os.path.abspath('..'))
from tools.volctl import VolCtl 


v = VolCtl()
b = BZBoard("/dev/ttyACM1")
p = PumpsCtl('/dev/ttyACM0', v)

rv = RecordVideo(10)

waste = {'pump':'P0', 'quantity':75, 'speedIn':50, 'speedOut':50}
water = {'pump':'P4', 'quantity':5, 'speedIn':60, 'speedOut':70}
h2so4 = {'pump':'P2', 'quantity':5, 'speedIn':60, 'speedOut':70}
kbro3 = {'pump':'P5', 'quantity':5, 'speedIn':110, 'speedOut':110}
malonic = {'pump':'P3', 'quantity':5, 'speedIn':60, 'speedOut':70}
water_clean = {'pump':'P4', 'quantity':50, 'speedIn':50, 'speedOut':70}
ferroin = {'pump':'P1', 'quantity':2, 'speedIn':50, 'speedOut':50}



# make sure these 4 pumps are filled, I will test ferroin individually 
p.pump_multiple(water, malonic, kbro3, h2so4,ferroin)
# activate all max speed for 30 second to mix
b.activate_all()
time.sleep(30)
b.disable_all()

rv.record_threaded("test")
time.sleep(10)

p.pump_multiple(water_clean, waste)
p.pump_multiple(waste)