SpinDynamics.org User Support Forum

Hi,

I have a question about simulating ESR transient signals. If I simulate a Davies ENDOR experiment, is it possible for me to extract the net magnetization in the x-direction as a function of time? I'm particularly interested in seeing how the echo shape changes as I change the pulses. Additionally, I'm curious about the unwanted echoes to understand how phase-cycling affects the summed transient.

Part of me thinks that this is simple since I can just modify the davies_endor.m file such that I can extract trajectories from both shaped_pulse_af() and evolution() in the m file. However, I feel like I'm missing something else because of a passage in the examples/tutorials/time_domain_epr.pdf (page 5) that says 'it is not usually possible to predict what the echo is going to look like'.

Any insight is appreciated.

Yes, this is quite easy. Instead of the "final" option in the evolution calls inside endor_davies.m, use "trajectory" option with some suitable time step and an appropriate number of steps. Then put those trajectories into the "answer" variable so that the sequence returns them.

Optionally, in the main script, set parameters.sum_up=0 to tell the powder wrapper that it should not do the powder averaging, but return the trajectory for each individual orientation. Or maybe set the powder grid to 'single_crystal' so that the powder averaging operation des not get in the way.

Essentially, the dynamics you want is being computed anyway, you just need to tell Spinach to return it.

Thank you for the response Prof. Kuprov.

As a follow up, I tried to write a script to predict an echo of a nitroxide from a two-pulse Hahn echo. Attached to this post is the main script that uses the powder wrapper, a script for the Hahn echo pulse sequence, and a the signal as a function of time after the second pulse. I believe I am seeing the expected echo at the 400 ns mark. However, it seems to be smaller than what I expected. I ensured that the pulses provided a correct pi/2 and pi pulse using the holeburn experiment (also included as a section in the main script).

So, I am currently struggling to understand why the echo is small (which I'm assuming is due to a mistake in my implementation of the trajectory).

I do get a better one using standard functionality in Spinach.
The enclosed echo test pulse sequence is a part of Spinach 2.9, the current developer version. It will be released within the next couple of weeks.