An American-trained Pakistani neuroscientist with ties to operatives of Al Qaeda has been charged with trying to kill American soldiers and FBI agents in a police station in Afghanistan last month, the Justice Department said Monday night. The scientist, Aafia Siddiqui, who studied at Brandeis University and the Massachusetts Institute of Technology, was transferred to New York on Monday, and is to be arraigned Tuesday in the United States District Court for the Southern District of New York, the department said in a statement. Ms. Siddiqui, 36, disappeared with her three children while visiting her parents’ home in Karachi, Pakistan, in March 2003, leading human rights groups and her family to believe she had been secretly detained. But in interviews Monday and in a criminal complaint made public later Monday, American officials said they had no knowledge of Ms. Siddiqui’s location for the past five years until July 17, when Ms. Siddiqui and a teenage boy were detained in Ghazni, Afghanistan.