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Here's a waveform sampled at its zero crossing points: -

Image from here.

Based on the samples taken, you'd estimate that there was no signal and that ties in with this: -

at the exact Nyquist frequency, 50 kHz, the amplitude is heavily reduced

On the other hand, if the samples happened to be offset by 90° you'd conclude that the amplitude was correct.

there seems to be a DC component

Your image shows virtually nothing (1.6 mV) but, with some waveforms there might be a residual DC offset or, it might just be some small DC value from some signal processing chain.

What is failing in the theoretical Nyquist theorem.

Nothing as far as I can see. The theorem states that the sampling frequency has the be greater than the maximum signal frequency.

Here's a waveform sampled at its zero crossing points: -

Image from here.

Based on the samples taken, you'd estimate that there was no signal and that ties in with this: -

at the exact Nyquist frequency, 50 kHz, the amplitude is heavily reduced

On the other hand, if the samples happened to be offset by 90° you'd conclude that the amplitude was correct.

there seems to be a DC component

Your image shows virtually nothing (1.6 mV) but, with some waveforms there might be a residual DC offset or, it might just be some small DC value from some signal processing chain.

What is failing in the theoretical Nyquist theorem.

Nothing as far as I can see. The theorem states that the sampling frequency has to be greater than the maximum signal frequency.

Here's a waveform sampled at its zero crossing points: -

Image from here.

Based on the samples taken, you'd estimate that there was no signal and that ties in with this: -

at the exact Nyquist frequency, 50 kHz, the amplitude is heavily reduced

On the other hand, if the samples happened to be offset by 90° you'd conclude that the amplitude was correct.

there seems to be a DC component

Your image shows nothing but, with some waveforms there might be or, it might just be a residual DC value.

What is failing in the theoretical Nyquist theorem.

Nothing as far as I can see. The theorem states that the sampling frequency has the be greater than the maximum signal frequency.

Here's a waveform sampled at its zero crossing points: -

Image from here.

Based on the samples taken, you'd estimate that there was no signal and that ties in with this: -

at the exact Nyquist frequency, 50 kHz, the amplitude is heavily reduced

On the other hand, if the samples happened to be offset by 90° you'd conclude that the amplitude was correct.

there seems to be a DC component

Your image shows virtually nothing (1.6 mV) but, with some waveforms there might be a residual DC offset or, it might just be some small DC value from some signal processing chain.

What is failing in the theoretical Nyquist theorem.

Nothing as far as I can see. The theorem states that the sampling frequency has the be greater than the maximum signal frequency.

Here's scenario A (sampling at the zero crossing point): -

Image from here.

Based on the samples taken, you'd estimate that there was no signal and that ties in with this: -

at the exact Nyquist frequency, 50 kHz, the amplitude is heavily reduced

On the other hand, if the samples happened to be offset by 90° you'd conclude that the amplitude was correct.

there seems to be a DC component

Your image shows nothing but, with some waveforms there might be or, it might just be a residual DC value.

What is failing in the theoretical Nyquist theorem.

Nothing as far as I can see. The theorem states that the sampling frequency has the be greater than the maximum signal frequency.

Here's a waveform sampled at its zero crossing points: -

Image from here.

Based on the samples taken, you'd estimate that there was no signal and that ties in with this: -

at the exact Nyquist frequency, 50 kHz, the amplitude is heavily reduced

On the other hand, if the samples happened to be offset by 90° you'd conclude that the amplitude was correct.

there seems to be a DC component

Your image shows nothing but, with some waveforms there might be or, it might just be a residual DC value.

What is failing in the theoretical Nyquist theorem.

Nothing as far as I can see. The theorem states that the sampling frequency has the be greater than the maximum signal frequency.