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We present a detailed account of the technical aspects of stochastic quantum molecular dynamics, an approach introduced recently by the authors [H. Appel and M. Di Ventra, Phys. Rev. B 80 212303 (2009)] to describe coupled electron-ion dynamics in open quantum systems. As example applications of the method we consider both finite systems with and without ionic motion, as well as describe its applicability to extended systems in the limit of classical ions. The latter formulation allows the study of important phenomena such as decoherence and energy relaxation in bulk systems and surfaces in the presence of time-dependent fields.

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