  The microscopic structure of ultra-thin oxide barriers often plays a major
role in modern nano-electronic devices. In the case of superconducting
electronic circuits, their operation depends on the electrical non-linearity
provided by one or more such oxide layers in the form of ultra-thin tunnel
barriers (also known as Josephson junctions). Currently available fabrication
techniques manufacture an amorphous oxide barrier, which is attributed as a
major noise source within the device. The nature of this noise is currently an
open question and requires both experimental and theoretical investigation.
Here, we present a methodology for constructing atomic scale computational
models of Josephson junctions using a combination of molecular mechanics,
empirical and ab initio methods. These junctions consist of ultra-thin
amorphous aluminium-oxide layers sandwiched between crystalline aluminium. The
stability and structure of these barriers as a function of density and
stoichiometry are investigated, which we compare to experimentally observed
parameters
