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Binary Symmetric Matrix Inversion Through Local Complementation

Brijder R., Hoogeboom H.J.

Fundamenta Informaticae

2012

Vol. 116, nr 1-4

15-23

We consider the Schur complement operation for symmetric matrices over GF(2), which we identify with graphs through the adjacency matrix representation. It is known that Schur complementation for such a matrix (i.e., for a graph) can be decomposed into a sequence of two types of elementary Schur complement operations: (1) local complementation on a looped vertex followed by deletion of that vertex and (2) edge complementation on an edge without looped vertices followed by deletion of that edge. We characterize the symmetricmatrices over GF(2) that can be transformed into the empty matrix using only operations of (1). As a consequence, we find that these matrices can be inverted using local complementation. The result is applied to the theory of gene assembly in ciliates.

Multiset-Based Self-Assembly of Graphs

Bernardini F., Brijder R., Rozenberg G., Zandron C.

Fundamenta Informaticae

2007

Vol. 75, nr 1-4

49-75

We present a model for self-assembly of graphs based on multisets and the formalism of membrane systems. The model deals with aggregates of cells which are defined as undirected graphs where a multiset over a fixed alphabet is assigned to each vertex. The evolution of these aggregates is determined by an application of multiset-based aggregation rules to enlarge the current structure as well as an application of membrane-systems-based communication rules to enable cells to exchange objects alongside the edges of the graph. We compare the generative power of self-assembly membrane systems with and without communication rules, and we characterise properties of the sets of graphs generated by these systems. We also introduce two notions of stability for self-assembly processes that capture the idea of having produced a stable structure. Finally, we investigate self-assembly membrane systems where the alphabet is a singleton.