A formal methods approach to predicting new features of the eukaryotic vesicle traffic system

Vesicle traffic systems (VTSs) transport cargo among the intracellular compartments of eukaryotic cells. The compartments are viewed as nodes that are labeled by their chemical identity and the transport vesicles are similarly viewed as labeled edges between the nodes. Several interesting questions about VTSs translate to combinatorial search and synthesis problems. We present novel encodings for the problems based on Boolean satisfiability (SAT), satisfiability modulo theories and quantified Boolean formula of the properties over vesicle traffic systems. We have implemented the presented encodings in a tool that searches for the networks that satisfy properties related to transport consistency conditions using these solvers. In our numerical experiments, we show that our tool can search for networks of sizes that are relevant to real cellular systems. Our work illustrates the potential of novel biological applications of SAT solving technology.