Magical Particle Accelerator

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The newest Phlebotinum Du Jour - I Love Nuclear Power for The Noughties/The New Tens/Whatever The Hell This Decade Is Called. Presumably thanks to the massive publicity surrounding the Large Hadron Collider (LHC), particle accelerators have become the latest science thingy that can do anything. Note that this usually involves visible beams and massive tunnels that people can stand next to or even inside without suffering unpleasantness such as suffocation, freezing, boiling, electrocution or dying of radiation poisoning shortly after.

Examples of Magical Particle Accelerator include:

Advertising

An advert for the Gillete Fusion razor has scientists making razor blades with some sort of bizarre particle accelerator/fusion reactor thingummybob.

Anime and Manga

"Saturn Ring" system in Darker than Black was an accelerator on the scale of Real Life colliders. It was supposed to destroy Gates along with everything and everyone linked to them. Or at least one quite competent Mad Scientist is quite sure it should, anyway. There was some commotion when the news about this leaked out, of course. Note that the tunnels around the storage ring are evacuated—as far as people on whom "workplace safety" extends are concerned. And that the damaged tube looks like it's under some heavy fire even when no one hits it anymore.
The plot in Steins;Gate is based around the idea that the Large Haldron Collider is going to be used in some way to destroy or take over or something the world.
While the actual LHC and similar devices are nowhere in sight, Tsutomu Nihei's Knights Of Sidonia has most of the Applied Phlebotinum fueled by Higgs Bosons and the Humongous Mecha can perform power boosting combination maneuvers by linking arms together to form a ring, invoking the shape of a toroidal accelerator.

Comic Books

Punisher 2099: the new Punisher uses a sort of Particle Accelerator to "kill" the soul of a criminal that obtained immortality via reincarnation. Possibly the poster definition of "overkilling".
Transformers Generation 2 Redux takes place in the actual Large Hadron Collider, where the Decepticons plan on using it to somehow activate a new energy source they've found and grant themselves new abilities. It works... a little too well.
Watchmen may have been the first example. Dr. Manhattan gains his powers from being caught in a particle physics experiment, even though the terminology used is very different Techno Babble from what you'd get from a modern example.

Film

G.I. Joe: The Rise of Cobra has a No Hadron Colliders Were Harmed version of the LHC, close enough to Paris that the Eiffel Tower is clearly visible. It's also apparently owned and run by a single rich, snooty man and, once he's taken hostage, Cobra is free to use it to activate their stolen nanoweapons.
Iron Man 2 has Tony Stark create a new element by building a particle accelerator in his workshop.
Ghostbusters has portable versions. It's possible to build such a device but they wouldn't act like the ones shown.

Peter Venkman: Why worry? Each of us is wearing an unlicensed nuclear accelerator.

- The producers of the 2016 remake commissioned real particle physicists to produce workable designs for the movie's proton packs using modern technology. Again, they would work, but not as ghost-catching devices.
A particle accelerator firing causes time to repeat in a Groundhog Day Loop for a man in the made-for-TV movie, 12:01. He's aware of the looping of time because he was electrocuted by his alarm clock at exactly the time the particle accelerator fired off the first time, making him able to defeat one Phlebotinum Du Jour with a much older one.

Light Novels

The plot of Volume 19 of A Certain Magical Index kicks off when terrorists steal the controls to a gigantic Particle Accelerator hidden underneath Academy City and threaten to use it to blow up a huge chunk of the city if their demands are not met.

Literature

Angels & Demons features an accelerator at CERN being used to produce enough Antimatter to blow up the Vatican (CERN does really produce antimatter, but only a tiny fraction of that amount).
In the novel Flash Forward, firing the LHC at the exact moment a neutron star erupts starts the plot's Timey Wimequake.

Live-Action TV

This type of device was used in The X-Files episode "Soft Light", giving a guy a literal killer shadow.
Warehouse 13 steals antimatter from the CERN facility to power the Imperceptor vest to break into the Escher Vault and steal cosmetics. Oh, and the plans to a death ray.
Though never actually explained, the brief view on approach to Terra Nova's Hope Plaza include a pair of massive circular structures, probably intended to be particle-accelerator components. Presumably this means that achieving Time Travel requires a Magical Particle Accelerator in that Verse.
The Flash updates the hero's Silver Age Freak Lab Accident+Lightning Can Do Anything to a particle accelerator explosion though given the explosion is intentional and the accelerator was designed by a genius from the future, it is very possible it wasn't actually a particle accelerator and "particle accelerator" was simply a cover. Also doubles as a Mass Super-Empowering Event.

Radio

The Torchwood radio play "Lost Souls", written to celebrate the launch of the LHC, has an alien soul-stealer living in the tunnels of the Collider, let in by a rip in the universe caused by the accelerator. Reversing the polarity of the beams conveniently destroys the beast and reveals the Higgs Boson.
- The monster is a definite case of You Fail Physics Forever. It steals all your neutrons!
- Now we need them to do it at least a few hundred times, to find out whether Higgs Bosons are Random Drops or Organ Drops, and what else these critters can yield.

Video Games

Writing in "LHC" (or "SCIENCE") in Scribblenauts is one of several ways of killing everyone on the screen. Including yourself.
In Another World, Lester gets transported to the titular other world when Lightning Can Do Anything strikes the particle accelerator while he's running an experiment.
In Emperor of The Fading Suns Cyclotron buildings are used to produce singularities for jump drives (the game is very loosely based on the original setting).

Web Comics

In Problem Sleuth, Past-Future Pickle Inspector and Future-Future Pickle Inspector have the Comb Rave power "Large Hadron Anti Part-Pickle Acceleration, where they build a particle accelerator using portals made of traffic lights, destroying DMK's final health bar.

Western Animation

On Futurama, Professor Farnsworth buys a super collider from Pi-kea.

Prof. Farnsworth: Bad news nobody. The Super Collider's Super Exploded. I need you to take it back to trade it in for a wobbly CD rack and some of those rancid meatballs.

Real Life

In what is arguably the closest anyone has ever come to actually being killed by a real-life particle beam, a Russian named Anatoli Bugorsky stuck his head in the proton stream of a particle accelerator while performing some maintenance work. He reportedly saw a flash "brighter than a thousand suns". Amazingly, he survived (though it wasn't pretty). The other wiki has an article about it.
- Good thing he didn't stick his head in the antiproton stream.
Some gems have unusual colors not because of minor chemical contamination — for one, green diamonds. They are either found in places where it was subjected to lots of penetrating radiation over centuries, or made by affecting a normal gem with the same... really quickly.
Another decorative application of high-energy beams: Lichtenberg figures. Like with gems, photo can't show all the beauty of mica-like light reflections in the fine 3D structure, though demonstrates the principle.
Remember those old televisions? They run on cathode tubes, which are technically particle accelerators.
Particle accelerators also have the interesting ability to create elements from other elements. Despite the massive energy requirements, they can be used to transform mundane elements such as Lead into Gold.