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Got a complete grid but my theory of using letters for atomic numbers isn't working. Any ideas?

I have nothing like a complete grid yet and have not found any rationale for how to identify the thematic clues. It seems as if certain letters have to be removed from one word but the letters do not seem to mean anything. What am I missing?

Prime numbered letters remain. Google "prime number spiral".

I now understand the title, but cannot make the thing work. For instance in 3 down I have to remove 4 letters from marzipan to make the clue work, but two of those are primes, and two of the remaining letters are not primes. The same happens in other clues I have solved.

keep letters 2, 3, 5, 7 = ARIA, plus T, reversed = TAIRA.

I was trying to be too clever, using a=1, b-2.......z=26.

Ready to post entry but having doubts about the initial direction of the spiral. I've opted for right then up from the T but Google images show variants. Am I missing something?

The highlighted letters should spell out a coherent message.

Thanks Jim. What a brilliant, multi-layered crossword!

I'm really struggling with the top right and bottom left corners and would be grateful for some hints, particularly on 6 and 11 across and 9 down; and 32 and 41 across and 28 down. I know that 11 is a thematic clue, but can't be certain of which is the right word - lacquer is suspicious but doesn't produce a word after treatment. 41 across is also thematic but again I can't see which word to treat.