RAFFS: Model Checking a Robust Abstract Flash File Store

Accepted for publication in the Proceedings of the 11th International Conference on Formal Engineering Methods, ICFEM 2009. This paper presents a case study in modeling and verifying a POSIX-like file store for Flash memory. This work fits in the context of Hoare’s verification challenge and, in particular, Joshi and Holzmann’s mini-challenge to build a verifiable file store. We have designed a simple robust file store and implemented it in the form of a Promela model. A test harness is used to exercise the file store in a number of ways. Model checking technology has been extensively used to verify the correctness of our implementation. A distinguishing feature of our approach is the (bounded) exhaustive verification of power loss recovery

Linkage-specific ubiquitin chain formation depends on a lysine hydrocarbon ruler.

Virtually all aspects of cell biology are regulated by a ubiquitin code where distinct ubiquitin chain architectures guide the binding events and itineraries of modified substrates. Various combinations of E2 and E3 enzymes accomplish chain formation by forging isopeptide bonds between the C terminus of their transiently linked donor ubiquitin and a specific nucleophilic amino acid on the acceptor ubiquitin, yet it is unknown whether the fundamental feature of most acceptors—the lysine side chain—affects catalysis. Here, use of synthetic ubiquitins with non-natural acceptor site replacements reveals that the aliphatic side chain specifying reactive amine geometry is a determinant of the ubiquitin code, through unanticipated and complex reliance of many distinct ubiquitin-carrying enzymes on a canonical acceptor lysine. [Figure not available: see fulltext.