Host-pathogen dynamics and invasion efficiency

Bacteria (Listeria) follow a persistent random walk on top of the gut epithelium (gray), where they try to invade the goblet cells (blue). Bacteria are hunted by phagocytes (purple).

Simulation parameters

Bacteria:

λ_dir

Allows persistent motion of the bacteria; when zero, they only "diffuse".

Speed

Proxy of bacterial "speed"; the number of time steps in the bacterial CPM during one time step of the epidermis/phagocyte models.

k_attach (x1000)

Attachment rate (s^-1). Each second, a fraction k_attach of bacteria currently overlapping a goblet cell will attach to it. Once attached, they can either invade or detach after some time. Note: cumulative chances that a given contact will lead to attachment are different, depending on how many seconds it takes the bacterium to "cross" the goblet.

k_detach (x1000)

Detachment rate (s^-1). Each second, a fraction k_detach of bacteria currently attached to a goblet cell will detach from it, returning to the freely motile population.

k_infect (x1000)

Infection rate (s^-1). Each second, a fraction k_infect of bacteria attached to a goblet cell will infect it. Note: cumulative chances that a given contact will lead to invasion are different, depending on how many seconds the attachment lasts.

Phagocytes:

λ_act

Scales the migration "force" of the protrusion of phagocytes; higher values tend to give both higher speeds and more persistent motion.

max_act

Scales temporal stability of the feedback in the protruding region; higher values tend to yield broader, more persistent cells.

k_φ (x1000)

Phagocytosis rate (step^-1). Each step, bactera overlapping a phagocyte are phagocytosed with p = k_φ. Note: cumulative chances are larger since bacteria "cross" the phagocytes in multiple steps.

Visualization settings (All layers are simulated; this is just for the drawing)

Epithelium/goblet cells
Phagocytes
Phagocytes (protrusion)
Transparent filter
Bacteria
Bacteria (comet trace)
Bacteria (in goblets)

Epithelium:

Color:
Border:
Goblets:

Phagocytes:

Color:
Protrusion min:
Protrusion max:

Bacteria:

Color:
Comet color:
Attached color:
Invaded color:

Simulation controls
These only take effect when you reset ( ). The same settings + parameters + random seed should yield the exact same output every time.

Seed: # Goblets: # Phagocytes: # Bacteria: in circle Runtime:

Record : Tracks (bacteria&phagocytes) Events (infection/phagocytosis)

Epithelial layer with cells, of which goblet cells. Scale bar: 20 pixels = 10 μm
Time: . Phagocytosed :
Infection: bacteria attached and invaded in / goblet cells.

Exports (Save current settings)

Click the button to retrieve current settings, then copy-paste from the text area into a file of your choice.

Model configuration:

Visualization settings:

Outputs (Data from the simulation)

Cell tracks:

Events: