The film's official novelisation indicates that the plan was to use a particle accelerator to create some manner of high-energy field, illuminating the sand and causing its interatomic bonds to break down. They were then going to use a variety of sensors to monitor what was happening.
The goal of the scientists seems to have been to create a energy beam capable of 'total demolecularization'. They theorise that although they're being told that they're conducting pure research, that the beam will end up being weaponised.
“Well, of…” Donnie looked surprised and pushed his glasses up on the bridge of his nose. “Of course it matters. I mean… total demolecularization… it’s…”
“They’ll weaponize it,” Michel said sourly. “Just you wait.”
“They keep saying it’s going to be just for molecular research,” Donnie protested, but he didn’t sound entirely convinced.
“They can keep saying a Big Mac is filet mignon, but it’s still gonna taste like a Big Mac,” a fourth scientist, Sean O’Shea, commented. He was walking into the lab and heard the tail end of the conversation. Tall and lean, he filled the room with his presence and said with quiet authority, “Gentlemen, ours is not to question why, and so forth and so on, you know the drill. Let’s get our baby up and running, shall we?”
He always referred to the project as “our baby.” Chafin suspected it was because he was more comfortable calling it that than “our future weapon of mass destruction.”
The silicon seems to have been intended as a test material to determine whether the beam and field were performing correctly.
Knowing that the sign screamed DANGER! high energy particle physics test site! keep OUT! would not likely have made him feel any better.
Inside the research facility, the technicians studied the arrays on their computer screens. “Capacitators charged,” Ashley Michel said, satisfied at the results she was getting.
“Right,” said Chafin, confirming it. Then he saw something that didn’t look quite right, and he leaned toward Blaswell. “Donnie, got a little fluctuation on one.”
Adding his own concerns, O’Shea said, “There’s a change in the silicon mass.”
Donnie considered the possibilities and reasonably concluded, “Probably a bird.” It made sense. Stupid birds saw the pile of sand at the base of the particle accelerator gun and didn’t know it was there to measure molecular bonding. They thought it was someplace convenient to build a nest and lay their eggs. “It’ll fly away when we fire it up.”