Working with the PhET simulations (pH, membrane channels)

The simulations from PhET

pH Scale

Click to Run


What we did/More information

pH Scale

Note: there is a video primer and more teacher activities here:

There are three parts to this simulation: macro, micro and “My Solution”.

Macro: this is a basically in introduction to pH. There is a list of possible solutions to put into the beaker, after which you can then test the pH by putting the green probe into the solution. Add some water and see how the pH change.

Micro: this is the simulation that introduces the heart of the pH scale. Be sure to work through the questions and do enough problems until you are sure you understand pH: while we are doing biology and not chemistry, pH comes up very often in human biology (we can only survive with our blood being a narrow range of pH) and it is important to understand it.

To begin, what is pH??

The pH value of a solution tells you how many hydronium (H3O+) ions are present in that solution.

The pH scale is centered around 7, because water contains 1 x 107 moles of H3O+ ions per liter. A solution with 100x more H3O+ ions than water has 1 x 105 moles of H3O+ per liter, which gives it a pH of 5. This would be considered a weak acid. A solution with 1,000,000x more H3O+ than water has 1 x 101 moles of H3O+ ions per liter. Any such substance has a pH of 1 and is considered a strong acid. On the other side, a solution with 1/100 the H3O+ ion concentration of water has 1 x 109 moles of H3O+ ions per liter. This solution has a pH of 9 and is considered a weak base.

Is there a preference for using H+ in place of H3O+?
– Both mean the same thing (hydronium ion) although more complex chemistry requires understanding when you would use one or the other. Remember that strictly speaking, an acid cannot act as an acid unless it has something to give its H+ to, so in the absence of (usually water) it’s not an acid at all (e.g., dry, HCl).

Confusing already? Time to play with the simulations!

Use this document to introduce yourself to the pH scale: ph-scale-html-guide_document_1


Once you have played around with the settings, do the following activity:

Create a table in your notebook like the one below… Make enough rows to test 4 chemicals and 4 dilutions:

Chemical pH H3O Count OH- Count Product of [H3O ] x [OH ]
Chem A
Dilute Chem A
  1. Choose 1 chemical (coffee, for example).
  2. Write down the pH, the [H3O+] and the [OH]… Remember: [brackets] represent “concentration.”
  3. Multiply those numbers together. Write down your data.
  4. Make a dilute solution of your chemical. Repeat steps 2 and 3.
  5. Repeat this process for a total of 4 different chemicals and their dilutions. You can do blood (and diluted blood), whichever you like.

Answer these prompts:

  1. Describe the difference between an acid and a base on the molecular level.
  2. What is the product of [H3O+] x [OH]
  3. What happens to pH as [H3O+] increases? Decreases?
  4. What happens to pH as [OH] increases? Decreases?
  5. Add a ninth row to your table… Repeat the process for pure water.


Molecule PolarityMolecule Polarity

Click to Run

Molecule Polarity

I’ve attached three teaching documents from the PhET site to work through (the last one is only if desired – it is very in depth, more appropriate for a chemistry class, but still interesting).




Membrane ChannelsMembrane Channels



Click to Run

Membrane Channels

These are crucial to understand in biology, cell membranes are selectively permeable to  certain molecules in our tissues and bloodstream, or in other words, they only allow particular molecules into the cell. This in turns leads to many vital processes that happen in the cell membrane of our cells: ATP energy processes, mitochondria, nerve impulses, and so on.

But at its heart, we are just talking about tunnels, or channels put into a sea of phospholipids (the membrane). This simulation has you insert channels in a membrane to see what happens. See how different types of channels allow particles to move through the membrane (and not move through the membrane) and how this in turn drives complex and fundamental processes necessary for life.

Simulation work:
— Drag the channels onto the membrane and then investigate what happens.
– – The concentrations graphs are meant to give you qualitative, relative information to
help you understand diffusion.
— In a real cell, leakage channels are always open,  whereas gated channels only open in response to some stimulus.
— Some gated channels respond to the presence of a certain substance (ligand gated), some respond to a change in membrane potential brought about  by changes in ion concentrations (voltage gated), some respond to changes to tension in the cell membrane (mechanically gated), and some respond to light (light gated).
— In real cells, channels do not actively move things through them; they only allow things to diffuse through them. This is true in the simulation too, though in some cases it may appear that an ion is being pulled across a channel. There is no active transport through the channels, it is all passive transport, based on diffusion, and membrane channels do not “pump” anything across the membrane.



Leave a Comment