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Chaffing and Winnowing - An interesting paper by Ron Rivest about providing confidentiality without encryption.
 
Foundations of Cryptography - Oded Goldreich. A public domain book available on-line. Only partially completed.
 
Index of Online Crypto Papers - by Bruce Schneier at Counterpane systems, 1300 articles.
 
Paul Garrett's Crypto and Number Theory Lecture Notes - Introduction to cryptology, number-theory, and algorithms. Protocols. Symmetric versus asymmetric systems. Stream, block ciphers. One-way functions, signatures. Key management. (Pseudo-) random number generation. Permutation groups. Primes, Euclidean algorithm. Finite fields. Quadratic reciprocity. Discrete logs, RSA. Pseudoprimes, rho method. Elliptic curve methods.
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