I messed around creating different things, changing settings and re-simulating, and formulating ideas for how I could use it later for other things.
Before I had started using molecular I had been trying to think of a way to implement an idea of using particles to remove parts from another object. When I had reached a roadblock due to either me not knowing enough about blender or blender not being able to support it, I decided to go to the web and found the Molecular add-on.
I had seen it used before in other videos but didn't think I'd take the time to see how to use it until I knew more but molecular allowed you to make solid objects from particles and then you could use collisions to move them away.
I started small, very few particles and no object colliding with the cube, just to get the cube working exactly how I wanted.
simple render:
I really like the look of renders without any colours or shaders, it's so simple yet all the interactions of the shadows and shades of grey give it complexity.
I then increased the resolution (number of particles) used but the way in which it worked at such a simple level doesn't scale to higher levels (following the properties of particles in the universe).
increased resolution with incorrect outcome:

I then changed the tension between particles, Increased the breaking limit and selected another option which allowed me so set properties for when a particles is compressed, where I set the compressed particles breaking limit much lower, giving the effect of only particles in almost direct line of the ball getting removed from the cube.
The finals renders showing the effect working correctly:
I also tried to create a tiny animation but during the night while it was rendering the pc ran out of memory and blender crashed, I will try again with lower settings and fewer frames but until I upgrade my ram and gpu, I doubt I could render an animation.
Edit:
I saw the option before in the collision panel to kill particles, but for some reason I didn't think that would be the best way to create the effect.
Setting the kill particles to on seems to work better than I thought and creates the effect nicely, I most likely didn't have to add the compression settings and tweak the others, all I really needed to do was get the cube to maintain it's shape correctly and it would be done.
Re-render with the change:
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