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There is no way to know what the authors of that paper even did. They say they used Python, but mention no libraries. If it is their own implementation of those algorithms in Python, it may tell you next to nothing of the real world performance of optimized implementations those algorithms. Further, they say they encrypted files of 68-235 KB, but do not ...


Rather than using a form of encryption which is slow in one direction, you could use a proof-of-work function instead, as Ricky Demer pointed out in the comments. This allows you to freely tune the slowdown while still using normal, widely accepted encryption and authentication algorithms. For example, you could make the sender look for a partial preimage ...


Perhaps not of relevance if the question is meant in a purely thoretical (i.e. asymptotical) sense, but the CBC encryption mode is inherently sequential, while decryption can easily be performed in parallel.


In lattice-based encryption schemes, the encryption is often slower than the decryption (not artificially, but just as the natural way it works). See this paper Efficient Software Implementation of Ring-LWE Encryption (encryption is 3 times slower than decryption).

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