About the physics of transmutation in FMA:B
You can find a lot of explanations about the energy in Fma wikia.


  In the 2003 anime, though it is never outright explained from where
  the energy in transmutation comes, alchemists who attempt to create
  objects outside their range of skill are left exhausted, suggesting
  that at least some of the energy comes directly from their bodies. At
  the end of the anime series, it is explained that the energy powering
  transmutation is actually the energy of departed human souls passing
  through The Gate to the alchemical world from our world, negating the
  concept of Equivalent Exchange altogether.


That's one of the reasons some alchemists want the philosopher's stone, since it contains a lot of human souls, it can generate a lot of energy that one alchemist can't generate on his own.