The Bay Area Rapid Transit (BART) system will get $2.9 million in federal homeland security funding to address “unique vulnerabilities” in its transit system. The funding comes on the heels of an appeal from San Francisco Mayor Gavin Newsom and Oakland Mayor Jerry Brown, who wrote a letter to Gov. Arnold Schwarzenegger asking for money to tighten BART security. Although specifics regarding how BART will use the money are classified, local officials say that the money will likely be used to minimize the risk to BART’s tunnels, including the Transbay Tube — a 3.6-mile tunnel under the San Francisco Bay. The $2.9 million grant is the largest amount of money BART has received since 9/11 through the Urban Area Security Initiative process, which doles out federal counterterrorism funds to cities and counties.