Working on aerobic fitness so you die less at the end is how virtually all try to do it. Another poster posed a question about 'how to improve sprint endurance' in another thread. Eric DeSanto asked him for more detail in his query. I checked in this morning to see if he had offered that yet. But you ask a very similar question.
When I began coaching the sprinters at West Point, as a group, they'd been underperforming for several years. Without having seen them train or swim, but knowing that West Point cadets are always fit, and that as swim team members they'd been training hard in previous years, I doubted lack of aerobic fitness was to blame.
Just prior to assuming my assistant's position there I'd read an article about the recent Olympic track champion in 100m, Maurice Green. His coach John Smith described the strategy they pursued to win the gold and break the WR as "Delay Deceleration." He said that most sprinters hit peak velocity in mid-race, then began slowing around 65m. He adjusted Mo's training and race approach so he would reach peak velocity more gradually and sustain it longer, aiming to delay deceleration to perhaps 85m.
I was fairly certain that deceleration was at least as common, and possibly more pronounced in an event that took place in water -- and had a duration 4-5x greater than the 100m in track. So I asked the team if they would sign on to a training strategy that focused more on delaying deceleration than on increasing velocity. They did and the results were simply smashing.
In practice we broke down the 100 race as follows:
1st 25 - Groove your stroke. Do not race.
Middle 50 -Build smoothly toward top speed, aiming to feel you're reaching your stride as you approach the 75.
Final 25 - Hold your speed.
I then designed as many practice tasks as I could to mimic the three phases of the race and we rehearsed tirelessly.
I'm also confident in saying that we probably spent more time than most of our rivals on highly exacting work on starts, turns, pushoffs and breakouts.
Conditioning? It happened.
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