A very misunderstood part of bolting stuff together is pre-load, which is the tension placed on the bolt by the nut (as opposed to the load), which doesn’t change whether you’re using heavy hex nuts or regular width ones. A sufficiently high pre-load will protect the bolt from fatigue as the load changes, as the varying load will change the clamping force on the bolted components, rather than the tension on the bolt. As a rule of thumb, the pre-load should exceed the maximum load by 15% or so.
In order for this to work, however, the joint must be stiffer than the bolt. For this reason, the shank of high-tech bolts are often necked down to the same diameter of the root of the thread. As long as it isn’t thinner than the root of the thread, it isn’t any weaker than the thread, and therefore doesn’t effect overall bolt strength, but it is significantly less stiff than the original shank.
A screw thread is a helical groove on a shaft. When used for delivering power, it is called a drive screw. Drive screws aren’t really all that efficient, as they loose a significant amount of power to friction. However, this friction can be put to use in the case of threaded fasteners. You might say that a drive screw is an inclined plane wrapped around a post, while a fastener is a wedge wrapped around a post.
As nuts and bolts are not perfectly rigid, but stretch slightly under load, the distribution of stress on the threads is not uniform. In fact, on a theoretically infinitely long bolt, the first thread takes a third of the load, the first three threads take three-quarters of the load, and the first six threads take essentially the whole load. Beyond the first six threads, the remaining threads are under essentially no load at all. Therefore, a nut or bolt with six threads acts very much like an infinitely long nut or bolt.
Heavy hex nuts come in a wide variety of grades in differing thicknesses and finishes, including stainless steel to go with your stainless steel screws and bolts. Consult a bolt catalog for more.
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