Board Thread:The Reference Desk/@comment-63.143.235.110-20130510130704/@comment-2.96.205.147-20130601230355

consider the fact that the TARDIS is a living being grown on gallifrey which the time lords used as time machines (solving the built or natural conundrum mentioned in various episodes). the matrix is the mind of the TARDIS entity which as a multidimensional lifeform is capable of experiencing all of time simultaneously (explained in "the doctor's wife" - possibly as the timelords develop similar power by exposure to the untempered schism). the vortex energy used by rose is the energy in the heart of the TARDIS, the multidimensional entity itself allowing whoever looks into it to view all of time as the TARDIS can. the eye of harmony is the singularity of a black hole balanced against gallifrey's mass which powers all timelord technology by distributing its energies evenly, even to the TARDIS (see "the three doctors" and "deadly assassin" for alluded confirmation to this) following gallifrey's destruction the eye would no longer exist being tied to the planets mass and rifts were used to refuel. the eye in "journey to the centre of the TARDIS doesnt fit the scientific description of the original and is possibly the doctor's own creation to avoid going back to the rift to refeul and end up running into jack or other people he has moved on from.

this is an interpretation based on available evidence from the show.