Mnemonics is a Scala library for generating method bodies in JVM bytecode at run time. Mnemonics supports a large subset of the JVM instructions, for which the static typing of the generator guarantees the well-formedness of the generated bytecode. The library exploits a number of advanced features of Scala's type system (type inference with bounded polymorphism, implicit parameters, and reflection) to guarantee that the compiler only accepts legal combinations of instructions at compile time. Additional instructions can be supported at the price of a check at run time of the generator. In either case, bytecode verification of generated code is guaranteed to succeed.

Protein-protein interactions, which form the basis for most cellular processes, result in the formation of protein interfaces. Believing that the local shape of proteins is crucial, we take a geometric approach and present a definition of an interface surface formed by two or more proteins as a subset of their Voronoi diagram. The definition deals with the difficult and important problem of specifying interface boundaries by invoking methods used in the alpha shape representation of molecules, the discrete flow on Delaunay simplices to define pockets and reconstruct surfaces, and the assessment of the importance of topological features. We present an algorithm to construct the surface and define a hierarchy that distinguishes core and peripheral regions. This hierarchy is shown to have correlation with hot-spots in protein-protein interactions. Finally, we study the geometric and topological properties of interface surfaces and show their high degree of contortion.

Protein-protein interactions, which form the basis for most cellular processes, result in the formation of protein interfaces. Believing that the local shape of proteins is crucial, we take a geometric approach and present a definition of an interface surface formed by two or more proteins. We also present an algorithm and study the geometric and topological properties of these surfaces, thus paving the way for future biochemical studies of protein-protein interactions.