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rename protein_folding to sub-folder
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applications/chemistry/protein_folding/protein_folding.ipynb renamed to applications/chemistry/protein_folding/protein_folding_with_qaoa/protein_folding.ipynb

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applications/chemistry/protein_folding/protein_folding.metadata.json renamed to applications/chemistry/protein_folding/protein_folding_with_qaoa/protein_folding.metadata.json

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applications/chemistry/protein_folding/protein_folding.qmod renamed to applications/chemistry/protein_folding/protein_folding_with_qaoa/protein_folding.qmod

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applications/chemistry/protein_folding/protein_folding.synthesis_options.json renamed to applications/chemistry/protein_folding/protein_folding_with_qaoa/protein_folding.synthesis_options.json

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