mxlmodels 1.0.0__py3-none-any.whl

mxlmodels/pop_dyn.py

@@ -0,0 +1,69 @@
+"""Two-species population dynamics: E. coli and C. glutamicum with fixed affinities."""
+
+from mxlpy import Model
+
+
+def _d_edt(
+    mu_e: float,
+    a_e: float,
+    e_coli: float,
+) -> float:
+    """Net growth rate of E. coli: affinity * population * growth rate."""
+    return a_e * e_coli * mu_e
+
+
+def _d_cdt(
+    mu_c: float,
+    a_c: float,
+    c_gluta: float,
+    theta: float,
+) -> float:
+    """Net growth rate of C. glutamicum minus density-dependent death."""
+    return a_c * c_gluta * mu_c - c_gluta**2.0 * theta
+
+
+def create_model() -> Model:
+    """Build the two-species population dynamics model (E. coli / C. glutamicum)."""
+    return (
+        Model()
+        .add_variable(
+            "e_coli",
+            initial_value=5.0,
+        )
+        .add_variable(
+            "c_gluta",
+            initial_value=5.0,
+        )
+        .add_parameter(
+            "mu_e",
+            value=0.4,
+        )
+        .add_parameter(
+            "mu_c",
+            value=0.3,
+        )
+        .add_parameter(
+            "a_e",
+            value=6.0,
+        )
+        .add_parameter(
+            "a_c",
+            value=4.0,
+        )
+        .add_parameter(
+            "theta",
+            value=0.001,
+        )
+        .add_reaction(
+            "dEdt",
+            fn=_d_edt,
+            args=["mu_e", "a_e", "e_coli"],
+            stoichiometry={"e_coli": 1.0},
+        )
+        .add_reaction(
+            "dCdt",
+            fn=_d_cdt,
+            args=["mu_c", "a_c", "c_gluta", "theta"],
+            stoichiometry={"c_gluta": 1.0},
+        )
+    )