The theory of superconducting phase qubits---also known as current-biased Josephson junctions---is presented. In the first part of this thesis, I introduce quantum computation, quantum simulation, and their deep connection with symplectic integration. I then consider the fundamental many-body theory of superconductivity and Josephson junctions and show how the quantum dynamics of a single macroscopic degree of freedom, the gauge invariant phase difference, emerges. A complete study of the Hilbert space structure of such a variable is performed for the current-biased junction. The resulting resonance structure is studied in detail, using various formalisms including the WKB approximation, instanton methods, the complex scaling transformation, basis set stabilization, numerical integration, and dynamical simulation using Lie algebraic wave-packet propagation.

The second part of this thesis explores how the current-biased junction can be used as an element of a quantum computer---a quantum bit (qubit). Single qubit operations are studied, followed by the presentation of the theory of coupled qubit devices. My key result is the design and optimization of quantum logic gates with high fidelity (F ~ 0.9999) for capacitively coupled phase qubits with short gate times (~ 10 ns). Finally, I examine an advanced qubit-coupling scheme, a resonant coupling method utilizing a harmonic oscillator as the auxiliary degree of freedom. The models and methods presented here have been developed in direct collaboration with an experimental program. These experiments are the first to show spectroscopic evidence for entanglement between two and three macroscopic degrees of freedom in a superconducting circuit.