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Sonoma Marin-Area Rail Transit may be able to open its doors with commuter-train service between Santa Rosa and San Rafael in the fourth quarter of 2016, but it’s going to be a race. Engineers on the $500 million project are working to solve a slate of engineering puzzles that come with coordinating the new rail, vehicles and signals.

“With a brand new rail vehicle, we have a brand-new state-of-the-art signaling system,” said Bill Gamlen, SMART’s chief engineer. “And we have brand-new grade crossings. We have been focused on each of these components. Now we’re bringing them all together and testing. Various things come up as part of that. ... You have electronics, new vehicles, new wheels. Everything has to wear together and be integrated.”

In August, test trains reached speeds of less than 30 miles an hour. Top speed of the trains will eventually hit 79 miles an hour, Gamlen said, but only in open sections such as north of Santa Rosa or between Petaluma and Novato. Bullet trains in Japan reach 200 miles an hour. The world record for a maglev train was set in April 2015 at 374 miles an hour on an experimental track in Yamanashi.

“We’re not high-speed rail. We’re commuter rail,” said Gamlen, who oversees a team of six engineers. SMART’s big advantage for commuters is avoidance of the Novato narrows section of Highway 101, which jams up every weekday morning and afternoon. When the train opens, SMART commuter fares will typically run $13 a day round-trip, with electronic ticketing through Clipper cards.

“We are bringing all this stuff online,” Gamlen said. “We have been moving at relatively slow speeds on the railroads, not quite up to our design speeds. Grade crossings are timed for a certain speed — a passenger speed of 50 miles per hour. At 30 we’re coming in the system is expecting to pick you up at 50 and operate at that speed. There are those kinds of issues as well.”

“It’s a step process, Gamlen said. “First we focus on the grade crossings. Then we start integrating the vehicles. Then we start integrating the signaling system. Then we start ramping up the speeds.”

The section of track between Santa Rosa and San Rafael is known as “dark territory,” Gamlen said, where previously there was no signaling system. “We have pulled fiber throughout the corridor to support that, to support our communication need,” he said. “The biggest challenge is bringing all this together.”

Santa Rosa-based Sonic installed the fiber-optic cable along the train track in exchange for access to the right-of-way. “We put in the conduits and they pulled all the fiber,” Gamlen said. “It was a good deal for both parties.”

“Sonic is providing fiber-optic communications for their signals and controls,” said Dane Jasper, Sonic’s founder and CEO. “Alongside it, we can send our own traffic as well. We get to use their right-of-way,” serving business parks near the track with broadband access.

Other technical challenges remain for SMART. New continuous welded steel track came in 1,600-foot sections made by Allegheny Rail Products, located in Pueblo, Colo.

The fresh track was covered in mill scale, a flaky surface found on hot-rolled steel composed mostly of magnetite, a blue-gray iron oxide made of three atoms of iron married to four atoms of oxygen. Scale also includes other iron oxides — an inner layer of black wüstite, FeO, and a thin outer layer of hematite, Fe2O3. In recent months, SMART engineers used a grinder to shave off mill scale.

The scale had to be removed because train wheels require clean electrical contact with rails in order to communicate with signals that stop traffic from traversing the track while the train goes by.

“It’s part of the process,” Gamlen said of mill-scale removal, which is ongoing.

There are two types of rail grinding.

Surface grinding takes off scale and imperfections created in milling the steel. It’s to “accelerate that process of getting a nice wheel-wear patch on the rail,” he said.

Then there’s profile rail grinding. “You grind a wheel profile to match the rail head, and the rail head to match,” Gamlen said. The rail head is the top part of the rail profile (cross-section) where wheels of the train roll.

“It’s a little more common in light rail,” Gamlen said, and helps to reduce noise and vibration. “Sometimes freight railroads pursue it as well for longevity,” where trains bear heavy tonnage. “Whatever they can do to not have to replace track — it’s all about making money for them,” he said.

For SMART, profile grinding translates to ride quality, Gamlen said. “We spec’d a particular wheel and the rail to match,” he said. “At this point we’re not trying to get into the science of matching a particular wheel profile. That could come down the road if you had some issues or you want to improve ride quality.”

For a “new starter system with new vehicle, new track, you’re just trying to get that mill scale off,” he said, and “accelerate that process.”

“The rail was rolled in 80-foot sticks,” Gamlen said. “Then they factory-welded it to 1,600-foot lengths — nearly a third of a mile — and brought it here” on special rail cars made for the purpose. “They had these long cars that snake through curves like spaghetti. The rail would snake with it. It’s so long, it starts to turn into a flexible shape,” he said.

“You want to be careful out in the field walking around sticks of rail on the ground,” Gamlen said. “They will expand, and sometimes get a little movement on their own. Rail expansion and contraction is a huge issue, especially in large heat fluctuations” such as in North Dakota. In such cold country, if a rail breaks in the winter, engineers leave a gap appropriate for that temperature then return when the weather warms to cut out another section to allow for expansion.

The new trains run on clean-diesel technology with American-made Cummins engines. “We spec’d a tier-four diesel engine — the highest level — driven by off-highway equipment,” he said.

Tier 4 standards, introduced by the Environmental Protection Agency in 2004 and phased in from 2008 to 2015, require that particulate matter and nitrogen oxides be reduced by about 90 percent. The reductions are achieved by control technologies such as advanced exhaust-gas after-treatment. “We have a urea system,” Gamlen said, similar to that used by diesel cars made by BMW and Mercedes Benz. “They are very low in the diesel world,” he said of the train engines’ emission levels.

Urea — carbamide — is the main nitrogen-containing ingredient in urine excreted by cats, dogs and other mammals. It is colorless, odorless and nearly non-toxic. When misted into hot diesel exhaust, nitrogen oxides are converted to harmless nitrogen gas, water vapor and carbon dioxide.

Another new technology is “positive train control,” according to Gamlen. Recent train crashes drove the technology. A June 2015 Amtrak derailment in Philadelphia where eight passengers died and some 200 were injured led the National Transportation Safety Board to investigate whether the train engineer was using his cell phone just before the crash. An ACE (Altamont Corridor Express) commuter train carrying more than 200 passengers between Fremont and Pleasanton crashed in March 2016 after a mudslide and tree landed on the Union Pacific track, sending a car into a creek and injuring 14 people.

“The federal government mandated that mainline railroads adopt a positive control technology” by 2018, he said. SMART is adopting the technology early. “If a train runs a red signal, it will bring that train to a stop. The technology will kick in and override the operator.”

The system also governs excessive speed. The railroad sets up speed zones. “If an operator is going faster than that zone, he will get an initial warning, and he has a countdown timer in the cabin,” Gamlen said. “If he doesn’t bring his speed down within that zone, it will bring the train to a stop.”

The system also provides for worker safety, defined with speed zones in a particular area for track maintenance, for instance. In April, an Amtrak train south of Philadelphia hit a backhoe, killing two employees and injuring about three dozen passengers.

“We’re starting to move into the testing phase” for positive-control technology, Gamlen said.

Train engineers have no automatic-pilot option the way airline pilots do, according to Gamlen. “He’s operating the train. He’s got speed. He’s got the stop, doors, stations. For pre-recorded announcements, he pushes a button.”

The trains have two braking modes, one for normal deceleration for a “reasonable stop. Then there is full-out emergency braking,” he said. “If you can see the train, assume it can’t stop,” especially a heavy freight train. “It’s eye-opening. You have steel wheels on steel rails. The Kunze-Knorr brakes are from Germany.

So far, SMART has spent roughly $460 million, according to Gamlen, and purchased 14 cars. Operated as two-car sets, the system will have seven sets. The doors and cars were designed in Japan. BART systems cost about $120 million per mile. Light rails costs about $50 million a mile. “We are running about $10 million a mile,” he said, excluding any costs for acquiring right-of-way.

There are four passing sidings, where dual-track sections allow northbound and southbound trains to pass. The longest stretches about two miles; the track so far runs 43 miles. Dispatchers, operating somewhat like air-traffic controllers, line routes and can direct trains onto passing sidings as needed. If schedule changes occurred, a train could be held on a passing siding for another train to go by.

An estimated run time will be just over an hour from Sonoma County’s airport to San Rafael. “We have yet to run a train from end to end at planned speed,” Gamlen said. “All this stuff is still in test mode.”

Gamlen still aims for opening by the end of 2016, and plans to meet all the technical challenges. “We haven’t said the date. We’re still just saying, end of the year,” he said. “It’s going to be a delightful ride, very smooth.”

James Dunn (james.dunn@busjrnl.com, 707-521-4257) covers technology, biotech, law, the food industry, and banking and finance.