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The Department of Transportation received a $41 million federal grant to replace signaling infrastructure at South Station in an effort to ensure that the trains will run on time, state transportation officials said.

The money, awarded by the US Department of Transportation, will go toward updating South Station’s Tower 1, which houses a control system for the Massachusetts Bay Transportation Authority and Amtrak, Patrick Marvin, a Department of Transportation spokesman, said.

The existing signal infrastructure will be modernized, and the high-tech computers will be elevated to prevent water damage from any future flooding, Marvin said. These improvements will help MBTA and Amtrak trains to become more reliable, consistently getting riders where they need to go on time, officials said..

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The existing signaling system in Tower 1 is “outdated and hinders service,” the Department of Transportation said in a statement Tuesday.

In February 2016, signaling problems in Tower 1 resulted in major interruptions to Amtrak and commuter rail service for two days. The problems caused the signaling system to have to be operated manually, limiting how many trains come in and out of the station, the Globe reported.

Updating and maintaining the infrastructure is essential because almost 60,000 passengers pass through South Station daily, and due to the amount of trains that depend on Tower 1, a five-minute shutdown can create delays that affect thousands of them. It will also allow for future expansion of South Station, the Department of Transportation said.

The full Tower 1 project is expected to cost $82 million. The other $41 million will come from the MBTA and Amtrak, the MBTA said.

“South Station is an essential hub for transportation in Massachusetts and along the North East Corridor,” Senator Edward J. Markey said in the statement. “With this grant, the Massachusetts Department of Transportation can begin to make critical improvements to South Station that will enhance the reliability and efficiency of travel for passengers on both Amtrak and the MBTA. The federal investment will benefit Boston, surrounding communities, and the North East region as a whole.”

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Maria Lovato can be reached at maria.lovato@globe.com. Follow her on Twitter @maria_lovato99.