With the toll of a bell and a solemn moment of silence, the United States paused Thursday to mark the 13th anniversary of the Sept. 11, 2001, attacks.

Stephen Albert, whose father Jon died during the attacks, kicked off reading the names of the nearly 3,000 people killed in New York, at the Pentagon and near Shanksville, Penn. He said his dad was a dedicated father, husband and respected colleague.

"He will be sorely missed," he said.

The sad roll call was to pause only four times: to mark the times when the first plane struck the World Trade Center, when the second plane struck, when the first tower fell and when the second tower fell.

Thelma Stuart, whose husband Walwyn Wellington Stuart, Jr., 28, was a Port Authority Police Department officer, said the nation should pray for its leaders, "that God will grant them wisdom, knowledge and understanding on directing them on moving forward."

In Washington, a few minutes before 9 a.m. ET, President Barack Obama emerged from the White House with his wife, Michelle, and Vice-President Joe Biden to observe a moment of silence marking the 13th anniversary.

'Thirteen years after small and hateful minds conspired to break us, America stands tall and America stands proud.' - President Barack Obama

Later, in brief remarks at the Pentagon's 9/11 memorial, he offered reasons for optimism about America's situation.

"Thirteen years after small and hateful minds conspired to break us, America stands tall and America stands proud," the president said.

In New York, little about the annual ceremony at ground zero has changed. But so much around it has.

For the first time, the National September 11 Museum — which includes gut-wrenching artifacts and graphic photos of the attacks — is open on the anniversary. Fences around the memorial plaza have come down, integrating the sacred site more fully with the streets of Manhattan while completely opening it up to the public and camera-wielding tourists.

A new mayor is in office, Bill de Blasio, one far less linked to the attacks and their aftermath than his immediate predecessors. And finally, a nearly completed One World Trade Center has risen 541 metres above ground zero and will be filled with office workers by this date in 2015, another sign that a page in the city's history may be turning.

For some who lost loved ones in the attacks, the increasing feel of a return to normalcy in the area threatens to obscure the tragedy that took place there and interfere with their grief.

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A woman places a flower in the inscribed names along the edge of the North Pool during memorial observances held at the site of the World Trade Center in New York, (Justin Lane/Reuters)

"Instead of a quiet place of reflection, it's where kids are running around," said Nancy Nee, whose firefighter brother, George Cain, was killed in the attacks. "Some people forget this is a cemetery. I would never go to the Holocaust museum and take a selfie."

But for others, the changes are an important part of the healing process.

"When I first saw [One World Trade Center], it really made my heart sing," said Debra Burlingame, whose brother Charles Burlingame was the pilot of the plane that crashed into the Pentagon. "It does every time I see it because it's so symbolic of what the country went through."

"I want to see it bustling," she said. "I want to see more housing down there, I want to see it alive and bursting with businesses."

Memorial plaza

The memorial plaza will be closed to the public for most of the day and only available to family members. It will reopen at 6 p.m., at which point thousands of New Yorkers are expected to mark the anniversary at the twin reflecting pools where the towers once stood.

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A rose is placed on a name engraved along the South reflecting pool at the Ground Zero memorial site during the dedication ceremony of the National September 11 Memorial Museum in May. The museum spans seven stories, mostly underground, and contains artifacts from the attack on the World Trade Center Towers on September 11, 2001. (Spencer Platt/Reuters)

On the same day in May when the museum opened in a ceremony attended by President Barack Obama, the fences that had surrounded the plaza for years disappeared, as did the need for visitors to obtain a timed ticket. Now, thousands of people freely visit every day, from cellphone-toting travellers to workers on a lunch break, and those crowds will only swell further this year when One World Trade Center finally opens.

"The memorial and museum is extremely important to those impacted on 9/11," said Mary Fetchet, whose son, died in the attacks. "And surrounding that memorial, Lower Manhattan has been revitalized."

The first ceremony at the site was held six months after the Twin Towers fell and was organized by then-mayor Michael Bloomberg and his aides. Bloomberg, who took office just three months after the attacks, remained in charge, acting as the master of ceremonies for the next decade.

After other elected officials attempted to gain a larger role at the solemn event, in 2012, all politicians — including Bloomberg — were prohibited from speaking at the event. That remains the case now, as de Blasio, who took office in January, agreed to let the National September 11 Memorial & Museum at the World Trade Center Foundation organize the commemoration ceremony. Bloomberg is the foundation's chairman.

The 40 passengers and crew who died when hijacked United Airlines Flight 93 crashed in southwestern Pennsylvania during the attacks were to be honoured in a new way during the 13th anniversary ceremony at the Flight 93 National Memorial.

A Congressional Gold Medal awarded to those who died at the site of the memorial was to be presented as part of the ceremony. Bells were to be rung, and the names of the victims were read starting at 10:03 a.m., the moment the airliner crashed as passengers fought with hijackers for control of the jet.