In the paper, we employ a wavefunction approach to investigate the evolution of a two-photon wave packet propagating in a one-dimensional waveguide coupled to the Jaynes-Cummings (JC) system. We derive and solve, both analytically and numerically, a set of equations of motion governing the quantum state of the system. That allows us to provide real-time analysis of the evolution of the wave packet two-photon joint spectrum (2PJS) and the excitation dynamics of the JC system in the course of its interaction with the two-photon pulse. We demonstrate that the 2PJS and the spectrum of the wave packet scattered from the JC system experience transformation for nonzero atom-cavity couplings. Moreover, using Schmidt decomposition, we show that the scattered photons feature frequency entanglement contrary to the incident ones which are not entangled.
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