I attended the Clarion science fiction writing workshop at Michigan State University in 1992, and we were privileged to tour the university's Cyclotron. Of course, the first thing we asked was, "How do you kill someone with one of these?" (we'd been working on plotting). The scientist's answer was very disappointing -- he insisted that it was all very safe, with too many checks and balances to be a useful murder weapon. As I recall, he suggested that you could pry loose a brick from the wall and hit someone in the head with it.
As you can see from the picture, the beam entered the back of Bugorski's head and came out around his nose. Shortly after this happened, Bugorski's left half of his face swelled up beyond recognition. He was taken to the hospital and studied as this was something that had never been seen before and so they closely monitored him thereafter, fully expecting him to die within a few days at most.What Happens When You Stick Your Head Into a Particle Accelerator (via Warren Ellis)
Although the skin on the part of his face and back of his head where the beam hit eventually peeled off over the next few days, Bugorski did not die as they thought he would. The beam also burned through his skull and brain tissue along with the afore mentioned skin. However, ultimately he came through it all surprisingly well.
Despite the beam going through his brain, his intellectual capacity remained the same as before. The few negative health drawbacks he did experience were not life threatening either. He lost the hearing in his left ear and experienced a constant unpleasant noise in that ear from then on. The left half of his face slowly became paralyzed over the course of the next two years. He also gets significantly more fatigued with mental work, though he did go on to get his PhD after this incident. The remaining side effects were occasional absence seizures and later tonic-clonic seizures, though these didn't show up right away.
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