Some basic number theory and its applications in cryptography: number_theory.md.
Terms like semantic security, chosen-plaintext attack, chosen-ciphertext attack, MACs, collision resistance, random oracle model: security_definitions.md.
Public key security definitions and most known schemes (ElGamal, RSA, DSA): public_key_security.md.
A brief history of provable security: provable_security.md.
Commitment schemes, sigma protocols, zero knowledge proofs: proofs1.md.
Shamir's secret sharing scheme, Paillier's encryption, publicly verifiable encryption: proofs2.md.
Anonymous credential systems: proofs3.md.
Brief descriptions of some of the attacks included in Matasano challenges (length-extension attacks, Bleichenbacher, hash collisions, Wang, RC4 biases ... ): attacks.md.
Briefly about Elliptic Curves Cryptography (ECC) and how to speed up ECC operations: ecc_intro.md.
About math behind Elliptic Curves Cryptography: ecc_math.md.
Some attacks on discrete logarithm (index calculus, Pohlig-Hellman, Pollard's rho): dlog_attacks.md.
About algebraic geometry: algebraic_geometry.md.
About pairing-based crypto: pairing_based_crypto.md.
Some examples related to pairing-based crypto: pairing_examples.md.
Ciphers (only AES for now): ciphers.md.
Some crypto constructs (key derivation functions, Merkle-Damgard paradigm, Davies-Meyer compression function): crypto_constructs.md.
Brief description of some crypto libraries (OpenSSL, scrypt, NaCl, SJCL): crypto_libraries.md.
How some applications use crypto: applications.md.
Some basics about trusted computing: trusted_computing.md.
Some basic info on how to work with bits and bytes in different languages can be found in folder bits_manipulations.