Please don't comment on things you know nothing about. That's a good rule in general. Asking question is GREAT - but refrain from putting out assumptions you clearly know nothing about.

So to clear up the confusion, the particles can range from what they represent but they NEVER represent hydrogen atoms. Except in the case of a molecular simulation, (on scales much much smaller than your finger tip) we will never simulate atoms in a cosmological code. Instead we, sometimes, use particles that represent massive (millions of sun masses) or we don't even use particles and we define a Mesh grided box instead. Sometimes the particles only interacted by gravity (as is the case with Dark Matter) and sometimes they can interact by collisional effects (like shocks and gas heating and thermal injection). Some particles if they are Baryonic, can represent stars of different masses and can model supernova energies going off - but you are NEVER modelling the actual stars or supernova.

The darkmatter is actually the major part. And I this case the only part. The particles are initially set using observations from the cosmic microwave background and the initial power spectrum and then you let gravity work. You output the arrangement of particles at each time step and then at the end you find the oversentenced reigons and define halos. Then you define a model to PUT galaxies into the halos. So... It's a long way off from actually simulating the universe...which we won't do.

As far as the complexity, yeah higher resolution is usually better but for cosmology size and accuracy and modelling observations to maximize statical constraints are more important.