At the level that you're talking about, you'll start running into the unresolved questions of modern physics. One of the best ways to look at this is through t

At the level that you're talking about, you'll start running into the unresolved questions of modern physics. One of the best ways to look at this is through the Standard Model of particle physics, which essentially defines how the fundamental particles of the universe are related. Between the number of observations and large-scale experiments dealing with high-energy collision products, astrophysics, neutrino detectors, etc., some people consider the Standard Model to be the most thoroughly-tested and verified framework in all of science. That's a pretty grand claim, but hey. But it still falls short in some ways--for one, it starts breaking down past a certain scale. Classical field theory as defined by general relativity (another model that has had enormous success under test both theoretically and experimentally) and particle physics don't get along. Neither one fully explains reality, and the interface between those two models of reality hasn't been found. That's why people research things like string theory--they're attempting to find a mathematical framework that can resolve those two frameworks, among other things. So while each of them describes the universe extremely accurately in their own domain (check the sigma values and number of observations of experiments run on the LHC), they're not 100% right, since they can't be correctly extended to cover all scales and frames. The models remain just that--models which provide a useful framework to interpret reality, but don't fully describe the physical reality itself.