Life in lower Manhattan resembled any ordinary day on Wednesday as workers rushed to their jobs in the muggy heat, but time stood still at the World Trade Center site while families wept for loved ones who perished in the Sept. 11 attacks 12 years ago.

For the families, the memories of that day are still vivid, the pain still acute. Some who read the names of a beloved big brother or a cherished daughter could hardly speak through their tears.

"Has it really been 12 years? Or 12 days? Sometimes it feels the same," said Michael Fox, speaking aloud to his brother, Jeffrey, who perished in the south tower. "Sometimes I reach for the phone so I can call you, and we can talk about our kids like we used to do every day."

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A woman pauses along the edge of the Sept. 11 memorial in New York during a ceremony marking the 12th anniversary of the 9/11 attacks. (Justin Lane/Reuters)

On the memorial plaza overlooking two reflecting pools in the imprint of the twin towers, relatives recited the names of the nearly 3,000 people who died when hijacked jets crashed into the towers, the Pentagon and in a field near Shanksville, Pennsylvania. They also recognized the victims of the 1993 trade center bombing.

Bells tolled to mark the planes hitting the towers and the moments when the skyscrapers fell.

In Washington, U.S. President Barack Obama, first lady Michelle Obama, Vice President Joe Biden and wife Jill Biden walked out to the White House's South Lawn for a moment of silence at 8:46 a.m. — the time the first plane struck the north tower in New York. Another jetliner struck the Pentagon at 9:37 a.m.

"Our hearts still ache for the futures snatched away, the lives that might have been," Obama said.

A moment of silence was also held at the U.S. Capitol.

In New York, loved ones milled around the memorial site, making rubbings of names, putting flowers by the names of victims and weeping, arm-in-arm. Former Gov. George Pataki, New Jersey Gov. Chris Christie and others were in attendance. As with last year, no politicians spoke. Mayor Michael Bloomberg watched the ceremony for his final time in office.

Construction at Shanksville Memorial

The anniversary arrived amid changes at the Flight 93 National Memorial in Shanksville, where construction started Tuesday on a new visitor centre. On Wednesday, the families of the passengers and crew aboard United Flight 93 recalled their loved ones as heroes for their unselfish and quick actions. The plane was hijacked with the likely goal of crashing it into the White House or Capitol, but passengers tried to overwhelm the attackers and the plane crashed into the field. All aboard died.

"In a period of 22 minutes, our loved ones made history," said Gordon Felt, president of the Families of Flight 93, whose brother, Edward, was a passenger.

Outside Washington, hundreds of people gathered for a short, simple ceremony at an Arlington County plaza near the Pentagon. First responders from the county were among the first on the scene that day.

Boston airport apologizes for 9/11 fire drill

Officials at Boston's Logan Airport are apologizing for holding a fire drill, complete with smoke and flames, on the 12th anniversary of the Sept. 11 attacks. The two hijacked jets that were flown into the World Trade Center towers that day had taken off from Logan. Gov. Deval Patrick, who did not know in advance about the drill, called the timing of it "dumb." The runway fire drill, announced on the airport's Facebook page, drew harsh condemnation online. The port authority has apologized in a statement and says it "understands that it may have offended many of those touched by the events of Sept. 11."

Bloomberg also spoke at a remembrance service for the 84 Port Authority employees killed on Sept. 11 at St. Peter's Roman Catholic Church, in the shadow of where the World Trade Center once stood.

"On that terrible day, we were united in prayer and compassion for all of you who lost loved ones," the mayor said. "As we woke up this morning, our first thoughts were with you as well."

Dozens of family members and colleagues filled the pews as the Port Authority Police Pipes and Drums played during the posting of colours.

Around the world, thousands of volunteers pledged to do good deeds, honouring an anniversary that was designated a National Day of Service and Remembrance in 2009.

By next year's anniversary, a 9/11 museum is expected to be open beneath the memorial plaza in New York City. While the memorial honours those killed, the museum is intended to present a broader picture, including the experiences of survivors and first responders.

Florida pastor arrested ahead of Qur'an burning

Meanwhile, law enforcement officers arrested a Florida pastor Wednesday as he drove to a park to light nearly 3,000 Qurans on fire to protest the attacks.

Polk County sheriff's deputies arrested pastor Terry Jones, 61, and his associate pastor, Marvin Sapp Jr., 44, each on a felony charge of unlawful conveyance of fuel as they travelled in a pickup truck towing a large barbecue-style grill filled with Qur'ans soaked in kerosene. Jones had said he was heading to a nearby park to burn 2,998 Qur'ans — one for every victim of the Sept. 11 attacks. Sheriff's officials said Wednesday night that Jones was also charged with unlawful open-carry of a firearm, a misdemeanour, and that Sapp faces a charge of having no valid registration for the trailer.

Mulberry's mayor, along with area elected officials, a sheriff's deputy and several Polk County residents have talked about the need to express love and tolerance for all faiths on Sept. 11.

Jones is the pastor of a small evangelical Christian church. He first gained attention in 2010 when he planned to burn a Qur'an on the anniversary of Sept. 11, although he eventually called it off. His congregation did burn the Muslim holy book in March 2011 and last year he promoted an anti-Muslim film. All three incidents sparked violence in the Middle East and Afghanistan.