Pure Thought? Pure Experiment? Or Both?

This article suggests a possible breakthrough in the understanding of how matter itself is put together. Perhaps this is the beginning of the path that leads to the creation of new, stable, "hyper-elements?"

The interesting thing to me was the idea that the problem was suggested to the theoreticians by an experimental result. But since the experiment left many questions unanswered, the theoreticians decided to do their own experiments, inside a computer. This in silico experiment answered many of the questions the physical experiment could not.

Here you see the pursuit of scientific knowledge on three different levels. On the one level, you have pure theory, the inside-the-human-head conceptualization, and scribbles on the notepad and blackboard. On the second level, you have brute force experiments, using large amounts of energy precisely controlled and analysed. On the third level, you have a type of hybrid. Not exactly experiment, but not exactly human conceptualizing.

Some claim that pure thought is superior to empirical experiment. How do they answer the multiple levels of thought and experiment encountered here?