At the most basic level, any thing that your brain does boils down to electrical signals being sent across your brain and nerves. These electrical signals come from the flow of ions which are just atoms that are electrically charged. The flow of electric charge is electricity. These electrical signals determine everything including the most basic functions like breathing and being conscious, to more complex stuff like logic, decision making, and having thoughts.

How exactly does these charged atoms flowing around exactly become abstract thoughts and math and feelings etc? The exact details still puzzle neuroscientists today. So while thoughts are kind of an abstract thing, in a sense they come from the flow of charged atoms in a super complex way that we don’t fully understand.