Instructions
1. Choose your mode by clicking the buttons at the top left. Select between 'Basic' mode - which allows you to simulate basic diffusion - and 'Experiment' mode - which lets you explore the effects of membrane thickness, surface area, and fluid flow rate, and then run experiments to collect and record data.
2. Basic Mode:
- Adjust the number of red and blue particles to either side of the dotted line by dragging the sliders, and temperature by dragging the temperature slider.
- Press 'Start' to set the particles in motion, then 'Pause' or 'Cont.' as desired.
- Select 'Initial state' and 'Current state' to toggle between how it started and how it is now, to see the change.
- Select Reset to set the particles back to their initial states.
- The graphs show the numbers of each particle colour on each side of the boundary; the timers stop at the first time there are equal numbers of that colour on each side of the boundary.
3. Experiment Mode:
a) Membrane thickness - choose this from the drop-down menu at the top right. This lets you explore the effect of changing membrane thickness on the rate of diffusion across it.
- Drag the white tab at the top of the right-hand dashed line to change the membrane thickness (see the readout in the right-hand panel for its actual thickness).
- Set the target number of particles by dragging the Target particles slider - the timer will stop once this many particles have crossed the membrane.
- Set the temperature to change particle movement by dragging the Temperature slider.
- Change the proportion of red particles to the left of the left dashed line by dragging the Red concentration slider.
- Click 'Start' to begin the experiment and Pause or Resume as desired; the timer at the bottom will stop once the target number of particles have crossed the right-hand dashed line.
- Toggle the Initial State button to see how it started.
b) Surface area - choose this from the drop-down menu at the top right. This allows you to change the perimeter of a cell whilst keeping its internal area constant, using perimeter/area as an analog for surface area/volume.
- Most options work the same / similar to the membrane thickness experiment.
- Drag the Perimeter slider to increase the perimeter of the cell on the left whilst keeping its area constant, and note the readout of the perimeter, surface area and perimeter: surface area ratio (draw the link between this and the surface area to volume ratio).
- Click Start, the timer will stop once the target number of particles have crossed into the cell.
- Click reset to reset particle positions but not the slider values.
c) Fluid flow - choose this from the drop-down menu at the top right. This is for investigating the effect of fluid flow - such as good blood supply to an alveolus or air movement with transpiration - in terms of maintaining a steep concentration gradient.
- Most options work the same as above.
- The 'Target red decrease' slider sets the end condition for the timer, specifying the percentage of the red particles that need to disappear in order for the timer to stop.
d) Run experiment - toggle this mode on by clicking on the toggle button two-thirds of the way down the options panel.
- Select the independent variable from the drop-down list.
- Select the number of variations of the variable, and the number of repeat measurements for each variation using the sliders.
- Adjust all variables to the desired values - once you start the experiment, you will only be able to change the independent variable.
- Click 'Begin', and when you happy with the value of your independent variable, click 'Start'.
- Once the timer stops, the data will be automatically recorded, click 'Reset' and then 'Start', doing this until you have completed the desired number of repeats, then change the value of the independent variable and repeat the process until you have collected all the desired data.
- You can view your data at any time by clicking the 'Show data' button.
- On the 'Show data' window you can: drag the slider to set the number of decimal places of your data, check the option to show or hide the means, copy the data table as an image, or copy the data table as data (which could be pasted into MS Office an manipulated as desired).
- Click the 'Clear data' button once you are happy to clear the data, this will enable the options to change experiment, select a new independent variable and so on.