Quantum computers are a topic for theoretical research for nearly 40 years, but only in the last decade advancement in fabrication and design processes resulted in limited but functional processors. One type of promising design is based on superconducting materials used for the fabrication of electrical components called Josephson junctions (JJ). This type of technology is under constant development and research by big enterprises such as Google, Microsoft, IBM, and Intel and smaller companies such as Rigetti, D-Wave, and Honeywell.Unfortunately, this type, and most of other types, suffers from short coherence time which limits dramatically the performance and calculations these computers can execute. The coherence time is limited by an internal phenomenon called Flicker noise. This noise is measurable, and its implications are well understood, but it lacks explanation for its origin at the atomic level.This study aimed to narrow the possible sources for Flicker noise in superconducting JJ by using DFT and quantum dynamics methods to compare the effects of different kinds of defects on the apparent behavior of JJ. The characteristics for evaluating the process included: Structural and electrical properties, Defect formation energies, Phonons vibrations spectrum in the lattice, Charge transport and generated noise.The study was successful in the fact that some of the defects were ruled out as candidates, while others showed good match to measurements, thus increasing the confidence in them being the source for the Flicker noise.