Current particle theory, the Standard Model, is faced with very deep problems: quarks, electrons, positrinos and bosons have no physical size and no discrete mass-energy and yet are said to have dynamic energetic properties, and consequently the Model makes no physical connection with spacetime and gravity in the evolving Universe. This book develops a rigorous nonequilibrium thermodynamic theory, and constructs a relativistic particle theory that endows such particles with internal structure and mass-energy. That theory explains the dynamics of evolving systems in the quantum, cosmological and living states, in which the Universe begins in a quiescent quantum state, transforms into a scalar expanding cosmos and accounts for the existence of stereospecific L- amino acids in all living cells. Hamilton develops a rational quantum theory in which photons constitute the most fundamental particles in the Universe, enabling precise description of the dynamics of atomic and molecular systems.