Noise and decoherence are major obstacles to the implementation of Josephson
junction qubits in quantum computing. Recent experiments suggest that two level
systems (TLS) in the oxide tunnel barrier are a source of decoherence. We
explore two decoherence mechanisms in which these two level systems lead to the
decay of Rabi oscillations that result when Josephson junction qubits are
subjected to strong microwave driving. (A) We consider a Josephson qubit
coupled resonantly to a two level system, i.e., the qubit and TLS have equal
energy splittings. As a result of this resonant interaction, the occupation
probability of the excited state of the qubit exhibits beating. Decoherence of
the qubit results when the two level system decays from its excited state by
emitting a phonon. (B) Fluctuations of the two level systems in the oxide
barrier produce fluctuations and 1/f noise in the Josephson junction critical
current I_o. This in turn leads to fluctuations in the qubit energy splitting
that degrades the qubit coherence. We compare our results with experiments on
Josephson junction phase qubits.Comment: 23 pages, Latex, 6 encapsulated postscript figure