Container Subsystem

The container subsystem is responsible for spatial organization of the synthetic cell. In its simplest form, it consists of a biocompatible material that encapsulates the cytoplasm. More complicated container subsystems might include additional internal spatial structure (localization, sub-compartments, etc). In some cases, the boundary of the container subsystem may not be completely distinct from the surrounding environment, as is the case with a condensate or other non-membrane-bound method of spatial organization.

Modeling and Specification

Implementation in BioCRNpyler

BioCRNpyler contains two separate capabilities that are needed for defining containers. The first is the ability to model separate compartments that contain isolated sets of chemical reactions. The second is a set of mechanisms for transport across membranes, including passive diffusion, pores, and transporters. This latter functionality is defined more careful in the Transport Subsystem chapter, and we focus here on the container functionality.