In the framework of the stochastic projected Gross-Pitaevskii equation we investigate finite-temperature dynamics of a bosonic Josephson junction (BJJ) formed by a Bose-Einstein condensate of atoms in a two-well trapping potential. We extract the characteristic properties of the BJJ from the stationary finite-temperature solutions and compare the dynamics of the system with the resistively shunted Josephson model. Analyzing the decay dynamics of the relative population imbalance we estimate the effective normal conductance of the junction induced by thermal atoms. The calculated normal conductance at various temperatures is then compared with predictions of the noise-less model and the model of ballistic transport of thermal atoms.

We investigate the low-energy dynamics of two coupled anisotropic Bose-Einstein condensates forming a long Josephson junction. The theoretical study is performed in the framework of the two-dimensional Gross-Pitaevskii equation and the Bogoliubov-de Gennes formalism. We analyze the excitation spectrum of the coupled Bose condensates and show how low-energy excitations of the condensates lead to multiple-frequency oscillations of the atomic populations in the two wells. This analysis generalizes the standard bosnic Josephson euqation approach. We also develop a one-dimensional hydrodynamic model of the coupled condensates, that is capable to reproduce the excitation spectrum and population dynamics of the system.

We present a detailed study of the spectrum and dispersion of Bogoliubov quasiparticles in two coupled elongated Bose-Einstein condensates. We develop an analytically solvable model that approximates two infinite homogeneous condensates and compare its predictions to a numerical simulation of a realistic trapped system. While the comparisons show a reasonable agreement between the two models, they also manifest the existence of several anomalous Bogoliubov modes in the spectrum. These modes show degeneracy in both energy and momentum together with self-localization in the coordinate space.