I'm interested in doing some research on the ripple system. Is there a whitepaper which explains the underlying fundamentals and how they are realised? I know about the Wiki, but that is not citeable in research publications.
Not that I know of. Opencoin is still playing around with the protocol, so there probably won't be a white paper until they open source it.
Note, that site refers to the original Ripple project and implementations of it such as RipplePay and Villages. Ripple.com is the new distributed implementation of the Ripple project and although not discussed at that site, supported by the original project founder.
Additionally, Ripple released a Consensus Whitepaper in August 2014. They write:
Ripple Labs has just released a whitepaper describing the Ripple network’s consensus algorithm and its properties. The Ripple network combines Ryan Fugger’s original rippling ideas with a p2p transactional database. Consensus is the distributed agreement protocol that the Ripple network uses to irreversibly arbitrate changes to this database in just a few seconds.
Distributed agreement protocols like consensus must operate in the face of unreliable networks and malicious adversaries and must defend against failure modes in which the system might fail to process transactions or fail to agree on current balances. This white paper explains how Ripple’s consensus algorithm operates and how it provides a fast, reliable payment network.
Direct link: Consensus Whitepaper