With a length of 53 feet, 9 inches, a diameter of 10 feet, 3 inches, and a displacement of 74 tons, the Holland VI was John Philip Holland's finest submarine design, incorporating many of the mechanisms and components of modern submarines: dual propulsion, ballast systems, hydrodynamic shape, a fixed center of gravity, and modern weapons systems. The concept of having one propulsion system to operate a submarine on the surface and another while underwater had been proposed before, but Holland developed the first practical system. On the Plunger, with the requirements the U.S. Navy imposed on its design, Holland had to use steam to propel the submarine on the surface, but the steam engine used up an inordinate amount of space and produced high interior temperatures that were intolerable to the crew. The Holland VI, on the other hand, was fitted with a diesel-powered engine that could charge the submarine's electric batteries while operating. When submerged, the submarine used an electric motor powered by batteries. The Holland VI could travel one thousand miles on the surface with its diesel engine and thirty miles underwater on battery power.

The Holland VI was the first submarine to use a main ballast tank to control its descent and surfacing, and a secondary system to adjust for changing loads and torpedoes. The submarine originally had three ballast tanks: a main tank, an aft ballast tank, and a trimming tank in the bow. When the submarine was overhauled in 1899, two additional trim tanks were installed in the aft section of the submarine. With the Holland VI, Holland abandoned his earlier symmetrical ship design for one in which the maximum diameter of the circular superstructure was forward of amidships. He also had his propeller in the centerline of the ship and forward of the rudders, a position that was not adopted by the Navy until the advent of nuclear submarines. Early submarines did not have a fixed center of gravity. With any change of angle of the submarine, the water in the ballast and boiler tanks would slosh in the direction of the lowest end of the vessel, aggravating the angle and making it very difficult to keep the submarine level while underwater. Holland's ballast system included main tanks that were filled completely so the water could not pool at one end or the other. The forward ballast tank was quite small, so allowing water to enter the tank had almost no effect on the longitudinal center of gravity of the submarine.

The Holland VI was fitted with a standard torpedo tube, and the Navy supplied two practice torpedoes for the crew to use during the trials of the submarine in 1898. While the Holland VI 's stability was touchy even with one man loading the torpedoes, the trials were successful and proved that torpedoes could be successfully launched underwater from a submarine.

John Philip Holland has been called the "father of the modern submarine," and rightly so. He was fortunate to live at a time when there was rapid development of mechanization and industrialization. He was quick to see the utility of several of the new inventions and adapted them to his submarines. He used pneumatic power for control operations and to power his guns. He tried to use a steam engine to power a submarine but found that while the engine worked, it generated too much heat and too little power. He finally used diesel power, which was used to power submarines well into the twentieth century, when nuclear-powered submarines were introduced. His propulsion systems, hydrodynamic designs, ballast systems, and weapons systems were all used successfully, and in some cases are still used today.

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