Synthesis for Vesicle Traffic Systems

TL;DR

This paper introduces a novel method for synthesizing and completing Vesicle Traffic Systems (VTSs) in biological cells by encoding the problem into QBF satisfiability, enabling analysis of known and unknown system components.

Contribution

The paper presents new QBF-based encodings for VTS synthesis, allowing for the completion of partially known systems under specific properties, with an implemented tool demonstrating scalability.

Findings

Method scales to biologically relevant graphs

Successfully applied to natural and synthetic VTSs

Enables systematic completion of incomplete VTS models

Abstract

Vesicle Traffic Systems (VTSs) are the material transport mechanisms among the compartments inside the biological cells. The compartments are viewed as nodes that are labeled with the containing chemicals and the transport channels are similarly viewed as labeled edges between the nodes. Understanding VTSs is an ongoing area of research and for many cells they are partially known. For example, there may be undiscovered edges, nodes, or their labels in a VTS of a cell. It has been speculated that there are properties that the VTSs must satisfy. For example, stability, i.e., every chemical that is leaving a compartment comes back. Many synthesis questions may arise in this scenario, where we want to complete a partially known VTS under a given property. In the paper, we present novel encodings of the above questions into the QBF (quantified Boolean formula) satisfiability problems. We have implemented the encodings in a highly configurable tool and applied to a couple of found-in-nature VTSs and several synthetic graphs. Our results demonstrate that our method can scale up to the graphs of interest.