I am trying to model something like the image below and I've made an object like one of those red balls with the two feet attached. Now I need to make thousands more. So my question is, what would use up less memory: duplicating, duplicating linked, or using modifiers. Keep in mind that I may need to change, transform, or animate certain parts of this structure, so I would need to be able to treat these parts separate for the rest while (preferably) keeping everything as a unit (by grouping/parenting?).
A good Idea is to use a Particle system that uses the red object as sourc eobject. If you do you could follow this steps:
create a plane
add the plane a particle system
set the start and end frame to 1 and the lifetime to an high number, for example 20000 (if you plan on doing an animation, the lifetime should be higher than the last frame number, so that the particle won't disappear)
Set emit from Faces, then Grid and set the resolution as high as you need.
Then set the red object as the source
in field weight settings, set the gravity to 0 so the particles won't just fall
in this way you can also create those little "valley" between the proteins (blue object) using a magnetic force field.