Fig. 7
From: MFsim—an open Java all-in-one rich-client simulation environment for mesoscopic simulation
Definition of compartments for a 30 nm DMPC phospholipid double-layer vesicle and view of the resulting simulation box start configuration of the chemical ensemble described in Fig. 6. Upper left: Modal compartment editor dialog with detailed settings of the bulk phase (with all Kalata B1 cyclotides and the 800.000 bulk water particles) outside any compartment and the 3 sphere compartments for oriented spatial positioning of the inner/outer DMPC phospholipids and the inner vesicle water particles. Upper right: Graphical display of size and spatial position of the 3 overlaid sphere compartments. Lower left: Corresponding Simulation box slicer view of the simulation box start configuration. Lower right: Cross-section through the simulation box for a more detailed view of the DMPC molecule orientation inside the vesicle