This is an interesting question. In fact there are two sentences here connected together.
- A particle's energy system jumps about randomly.
- These transitions (with such transitions) are governed by the temperature...
The second sentence has been reduced to join it as a subordinate clause to the first sentence. The with such... actually means [ this kind of transition]. Then the second main verb is reduced by removing are, which appears here because it is a passive voice, leaving only the past participle (governed). So it's a complex sentence with a reduced clause.
Another way to say this could be:
A particle's energy system jumps about randomly and these transitions [meaning random jumps] are governed by....
This is a compound sentence now, connected with and. The first sentence was a complex one using a reduced subordinate clause.
I hope that answers your question.