Title: SMT Solving for Vesicle Traffic Systems in Cells,
Abstract: In biology, there are several questions that translate to combinatorial
search. For example, vesicle traffic systems that move cargo within eukaryotic
cells have been proposed to exhibit several graph properties such as three
connectivity. These properties are consequences of underlying biophysical
constraints. A natural question for biologists is: what are the possible
networks for various combinations of those properties? In this paper, we
present novel SMT based encodings of the properties over vesicle traffic
systems and a tool that searches for the networks that satisfies the properties
using SMT solvers. In our experiments, we show that our tool can search for
networks of sizes that are considered to be relevant by biologists.