Does 9/11 simulation 'raise more questions than answers?'

More than five-and-a-half years have passed since terrorists toppled the World Trade Center, and questions still remain about how the buildings came down. Researchers at Purdue University have created a computer model attempting to answer some of those questions.
The simulation found jet engine shafts from airlines flown into the World Trade Center "flew through the building like bullets," according to an Associated Press vide report.
Flaming jet fuel cascaded through the tower stripping away fireproofing material and causing the building to collapse, the AP video reports.
"The weight of the aircraft's fuel, when ignited, acted like a flash flood of flaming liquid," according to the video.
However, the website TRUTHORLIES.ORG believes that the simulation "raises more questions then answers."
Josh Reeves and Mike Swenson write, "The following statement was used in the Purdue simulation: 'The weight of the aircraft's fuel, when ignited, acted like a flash flood of flaming liquid.' This is a direct contradiction of the FEMA report (which can be viewed HERE) which stated: 'despite the huge fireballs caused by the two planes crashing into the WTC towers each with 10,000 gallons of jet fuel, the fireballs did not explode or create a shock wave that would have resulted in structural damage.'"