larvaworld.lib.model.deb.gut

Classes

Gut

Gut digestion and absorption model for DEB energetics.

Module Contents

class larvaworld.lib.model.deb.gut.Gut(deb: Any, save_dict: bool = True, **kwargs: Any)

Bases: larvaworld.lib.param.NestedConf

Gut digestion and absorption model for DEB energetics.

Models gut dynamics including ingestion, enzymatic digestion, carrier-mediated absorption, and faecal production. Tracks gut content (food mass M_X, digested product M_P), enzyme dynamics (M_g), and carrier availability (M_c).

Integrates with DEB model to compute assimilation energy flow (p_A) based on gut absorption rather than simplified functional response.

Attributes:

M_gm: Gut capacity per unit volume (C-moles, default: 0.01) k_abs: Absorption rate constant (default: 1.0) k_dig: Digestion rate constant (default: 1.0) k_c: Carrier release rate (default: 1.0) k_g: Enzyme decay rate (default: 1.0) constant_M_c: Keep carrier density constant (default: True) M_X: Current food mass in gut (C-moles) M_P: Current digested product in gut (C-moles) p_A: Assimilation power from gut absorption (J/day)

Example:

>>> gut = Gut(deb=deb_model, save_dict=True)
>>> gut.update(V_X=0.001)  # Ingest food volume
>>> power = gut.p_A  # Get assimilation power

M_gm

r_w2l

r_gut_w

y_P_X

k_abs

f_abs

k_dig

f_dig

k_c

k_g

M_c_per_cm2

J_g_per_cm2

constant_M_c

deb

r_gut_V

r_gut_A

A_g

V_gm

M_c_max

J_g

M_X = 0

M_P = 0

M_Pu = 0

M_g = 0

M_c

mol_not_digested = 0

mol_not_absorbed = 0

mol_faeces = 0

p_A = 0

mol_ingested = 0

V = 0

gut_X = 0

gut_f = 0

Nfeeds = 0

update(V_X: float = 0) → None

resolve_occupancy() → None

digest() → None

property residence_time: float

property M_ingested: float

property M_faeces: float

property M_not_digested: float

property M_not_absorbed: float

property R_absorbed: float

property R_faeces: float

property R_not_digested: float

property R_M_c: float

property R_M_g: float

property R_M_X_M_P: float

property R_M_X: float

property R_M_P: float

property occupancy: float

property M: float

property Vmax: float

property Cmax: float

update_dict() → None

ingested_mass(unit: str = 'g') → float

absorbed_mass(unit: str = 'mg') → float

property ingested_volume: float