The acceleration signal produced by body motion is sampled at a rate of 40 times/second.
Thus, we collected 30 image sequences for each motion; the motions are sampled at 25 frames/s.
Note, that even though naturally these motions are sampled by cyclophilin A at a much slower rate (hundreds of microseconds, corresponding to the time-scale of the reaction), the use of a reaction coordinate with umbrella sampling allows the enzyme to sample these higher energy states more frequently in our simulations.
As discussed previously, it is simply assumed that vectors representing motion primitives are sampled from clusters of data points and that clusters for different primitives are distinct.
It is natural to assume that earthquake ground motions are samples or realizations of a non-stationary random process.
The sample rate for body motion is 40 samples per second.
A wide variety of motions are naturally sampled (over femtosecond to millisecond time-scales) as the enzyme complex moves along the energetic landscape, driven by temperature and dynamical events from the surrounding environment.
Furthermore, for most of the results in Table 1, we simply do not know whether any of the loop motions are readily sampled by free TCRs or whether they are induced by binding and, if they are induced, we do not have estimates of the associated energetic penalties.
Axial sample motion was corrected using the two-step correction algorithm from our previous study [ 22].
In a few samples, where motion was limited, the findings were opposite but within the uncertainty range as illustrated in the muscle data.
