The term vacuum ultraviolet (VUV) ray, as mentioned by Walter, are energetic enough to excite an atom into a higher energy state.
The dark matter detector shown in the episode is based on an actual detector that has been operating since 2016 (construction started ~2012) and as of 2018 is still looking for dark matter: the DEAP-3600 dark matter detector, located at the Sudbury Neutrino Observatory (SNOLAB) in Canada. The actual detector is at 2km depth in a nickel mine. The description they give at the beginning of the episode, about what dark matter is and how the detector works, is accurate, and the detector schematics shown are copied right from the design drawings of DEAP-3600, down to the labels on the components. It is also true that the detector is periodically irradiated with neutrons from a radioactive calibration source to verify that it is working correctly. The signal you obtain if the detector is working as expected is shown on the computer screen while the team explains what they are going to do, and probably taken from one of the publications by the group of scientist operating the detector (though they applied some creative freedom in the TV version of the graphs).
The facsimile of the DEAP detector used in the episode is based on pictures of the incomplete detector, while it was under construction (search for DEAP-300 and National Geographic in a search engine and the pictures come up). The finished detector looks quite different and most notably, is completely immersed in a large water tank.
Most of the remaining 'facts' are a mix-and-match of a number of different experiments in the field of astro-particle physics. There is an underground laboratory in a gold mine in the US (the homestead mine in South Dakota) but it's not as deep and not under the Rocky Mountains. There is an underground lab under a mountain range in Italy (LNGS) but also not that deep. These labs house neutrino and dark matter detectors, but those are separate detectors. The detector shown in the episode is a dark matter detector and incorrectly labelled a neutrino detector. Some neutrino detectors observe neutrinos coming from a particle accelerator beam, but one would never put the accelerator in the underground lab right next to the detectors - this would defeat the point of going deep underground for these sensitive detectors. Particle accelerators of course do not create black holes.
One would, of course, never just carry around a neutron source strong enough to calibrate a dark matter detector, or even keep it in a residential building.
There is no time limit to being underground, and being underground has no significant effects on ones mental capabilities. Miners and scientists do 10 hour shifts underground regularly without any ill effects.
None of the scientists working on the DEAP detector knew that it was featured in this TV show.
The actor Vik Sahay played a supporting role in Chuck (2007), another show with a "geek" cult following. Fellow Chuck co-star Joshua Gomez made an appearance in a previous episode of Scorpion, titled, Queen Scary (2017), playing the character Dave Blakely. In Chuck (2007), they played Lester Patel and Morgan Grimes respectively.
Eddie Kaye Thomas (Toby Curtis) and Vik Sahay (Raja Bhatt) have previously worked together in the 2012 movie American Reunion (2012). They played Finch and Prateek Duraiswamy respectively.