Science is understood by many as discovering and understanding the facts and phenomenons of our universe. However, as seen in past studies these facts are never certainly true. They are widely accepted as the truth but in time new things may be discovered. Given this, it may be possible to eventually know the truth but again given our countless errors maybe we can never be certain about our theories even if they end up being the truth.
Atoms being the smallest building blocks of all matter contribute a lot to our pool of knowledge. By studying these atoms we understand more about the natural world and how things work from the smallest details. We may not necessarily be able to manipulate the atom in more ways than we could ever hope to but in the end we still study these atoms as driven by our natural curiosity. By way of inference we are able to visualize a world invisible to us not perfectly but close enough to feed our brains filled with curiosity and hungry for knowledge.