The ion is trapped in an electromagnetic field within the small cube at the centre and cooled with lasers to just a fraction above absolute zero. The lasers are fired through three of the glass shafts emanating from the cube, but must be carefully directed out of the other side to prevent them scattering within the clock, which is why there are six shafts in total.
Once the ion is cooled, another laser makes it resonate between two energy states with an incredible regularity governed by quantum mechanics. It gives off a regular pulse of optical radiation exactly 444,779,044,095,485 times per second.
Strange how something created with nothing but function in mind has such incredible form.