Iranian officials were quick to blame Israel and Western intelligence agencies for the explosion that killed Ahmadi Roshan and his driver. The assassination is the fourth since the start of 2010 targeting Iranian physicists and nuclear scientists.
(Click here for pictures of Ahmadi Roshan, including one with his son)
Many analysts believe the terrorist attack -- which comes on the second anniversary of the death of another Iranian scientist, Masoud Ali Mohammadi, by a remote controlled bomb -- is part of a covert war against the Islamic republic, aimed at slowing its nuclear program.
Yet it might have the opposite effect and make Tehran even more determined in pursuing its nuclear program, which Western countries believe is aimed at developing nuclear weapons. Iran maintains all its nuclear activities are peaceful.
Iran's First Vice President Mohammad Reza Rahimi said the attack on Ahmadi Roshan, a deputy director of the Natanz uranium-enrichment facility for commercial affairs, would not stop "progress" in the country's nuclear program.
In a statement, Iran's Revolutionary Guard blamed Israel and "its backers in the White House" for the assassination, adding that it will accelerate Iran's drive to reach the highest scientific peaks.
The hard-line Rajanews, which said the terrorist attacks in Iran are being conducted with the aim of controlling "Iran's technical achievements" and preventing it from consolidating its role "as a regional power," claims many are asking why the Islamic republic is not retaliating.
The website quotes an unnamed "intelligence source" as saying that Iran is in a good position, following information it obtained from the alleged assassin of Alimohammadi, to take retaliatory steps against those behind the killings of the Iranian scientists. Iranian officials have said that Majid Jamali Fashi, who has pleaded guilty to murdering Ali Mohammadi, had received money and training from Israel.
"Iran's reaction will extend beyond the borders and beyond the region, it follows the strategy that none of those who ordered these attacks should feel safe anywhere," the source said, adding that Iran will enter a new era in its "special intelligence operations" against its enemies.
'Can This Not Be Stopped?'
Some Iranians had a very different question than the one raised by Rajanews. They asked in comments to RFE/RL's Radio Farda and also on social-networking site why Iran is not providing its nuclear scientists with better protection.
"In a country where the police's job is to collect people's satellite dishes and arrest women who are badly veiled, and whose security officials are busy harassing young people who send text messages, the security situation cannot be any better than this," a man based in Tehran wrote on Facebook.
Many condemned the assassination of Ahmadi Roshan and other Iranian scientists.
"It's a terrorist act against an innocent civilian and one of the brains of this country," said one young woman from the Iranian capital in an e-mail exchange with "Persian Letters."
-- Golnaz Esfandiari