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Merge pull request #48 from jaxleyverse/units
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change units of compute_current
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@huangziwei
huangziwei authored Oct 24, 2024
2 parents 581106d + e53b4a9 commit 1c9fb3c
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Showing 19 changed files with 303 additions and 206 deletions.
32 changes: 18 additions & 14 deletions jaxley_mech/channels/aoyama00.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -25,6 +25,7 @@ class Leak(Channel):
"""Leakage current"""

def __init__(self, name: Optional[str] = None):
self.current_is_in_mA_per_cm2 = True
super().__init__(name)
prefix = self._name
self.channel_params = {
Expand All @@ -46,8 +47,8 @@ def compute_current(
):
"""Given channel states and voltage, return the current through the channel."""
prefix = self._name
gLeak = params[f"{prefix}_gLeak"] * 1000 # mS/cm^2
return gLeak * (v - params[f"{prefix}_eLeak"]) # mS/cm^2 * mV = uA/cm^2
gLeak = params[f"{prefix}_gLeak"] # S/cm^2
return gLeak * (v - params[f"{prefix}_eLeak"]) # S/cm^2 * mV = mA/cm^2

def init_state(self, states, v, params, delta_t):
"""Initialize the state such at fixed point of gate dynamics."""
Expand All @@ -58,6 +59,7 @@ class Na(Channel):
"""Sodium channel"""

def __init__(self, name: Optional[str] = None):
self.current_is_in_mA_per_cm2 = True
super().__init__(name)
prefix = self._name
self.channel_params = {
Expand Down Expand Up @@ -89,11 +91,9 @@ def compute_current(
"""Given channel states and voltage, return the current through the channel."""
prefix = self._name
m, h = states[f"{prefix}_m"], states[f"{prefix}_h"]
gNa = (
params[f"{prefix}_gNa"] * (m**3) * h * 1000
) # mS/cm^2, multiply with 1000 to convert Siemens to milli Siemens.
gNa = params[f"{prefix}_gNa"] * (m**3) * h # S/cm^2

return gNa * (v - params[f"{prefix}_eNa"])
return gNa * (v - params[f"{prefix}_eNa"]) # S/cm^2 * mV = mA/cm^2

def init_state(self, states, v, params, delta_t):
"""Initialize the state such at fixed point of gate dynamics."""
Expand Down Expand Up @@ -124,6 +124,7 @@ class Kdr(Channel):
"""Delayed Rectifying Potassium Channel"""

def __init__(self, name: Optional[str] = None):
self.current_is_in_mA_per_cm2 = True
super().__init__(name)
self.channel_params = {
f"{self._name}_gKdr": 4.5e-3, # S/cm^2
Expand Down Expand Up @@ -154,8 +155,8 @@ def compute_current(
prefix = self._name
m = states[f"{prefix}_m"]
h = states[f"{prefix}_h"]
k_cond = params[f"{prefix}_gKdr"] * m**4 * h * 1000
return k_cond * (v - params["eK"])
k_cond = params[f"{prefix}_gKdr"] * m**4 * h # S/cm^2
return k_cond * (v - params["eK"]) # S/cm^2 * mV = mA/cm^2

def init_state(self, states, v, params, delta_t):
"""Initialize the state such at fixed point of gate dynamics."""
Expand Down Expand Up @@ -187,6 +188,7 @@ class Kto(Channel):
"""Transient Outward Potassium Channel"""

def __init__(self, name: Optional[str] = None):
self.current_is_in_mA_per_cm2 = True
super().__init__(name)
self.channel_params = {
f"{self._name}_gKto": 15e-3, # S/cm^2
Expand Down Expand Up @@ -217,8 +219,8 @@ def compute_current(
prefix = self._name
m = states[f"{prefix}_m"]
h = states[f"{prefix}_h"]
k_cond = params[f"{prefix}_gKto"] * m**3 * h * 1000
return k_cond * (v - params["eK"])
k_cond = params[f"{prefix}_gKto"] * m**3 * h # S/cm^2
return k_cond * (v - params["eK"]) # S/cm^2 * mV = mA/cm^2

def init_state(self, states, v, params, delta_t):
"""Initialize the state such at fixed point of gate dynamics."""
Expand Down Expand Up @@ -250,6 +252,7 @@ class Kar(Channel):
"""Anomalous rectifying Potassium Channel"""

def __init__(self, name: Optional[str] = None):
self.current_is_in_mA_per_cm2 = True
super().__init__(name)
self.channel_params = {
f"{self._name}_gKar": 4.5e-3, # S/cm^2
Expand All @@ -276,8 +279,8 @@ def compute_current(
"""Compute the current through the channel."""
prefix = self._name
m = states[f"{prefix}_m"]
k_cond = params[f"{prefix}_gKar"] * m**5 * 1000
return k_cond * (v - params["eK"])
k_cond = params[f"{prefix}_gKar"] * m**5 # S/cm^2
return k_cond * (v - params["eK"]) # S/cm^2 * mV = mA/cm^2

def init_state(self, states, v, params, delta_t):
"""Initialize the state such at fixed point of gate dynamics."""
Expand All @@ -299,6 +302,7 @@ class Ca(Channel):
"""L-type calcium channel"""

def __init__(self, name: Optional[str] = None):
self.current_is_in_mA_per_cm2 = True
super().__init__(name)
self.channel_params = {
f"{self._name}_gCa": 9e-3, # S/cm^2
Expand Down Expand Up @@ -330,8 +334,8 @@ def compute_current(
"""Compute the current through the channel."""
prefix = self._name
m = states[f"{prefix}_m"]
ca_cond = params[f"{prefix}_gCa"] * m**4 * 1000
current = ca_cond * (v - params["eCa"])
ca_cond = params[f"{prefix}_gCa"] * m**4 # S/cm^2
current = ca_cond * (v - params["eCa"]) # S/cm^2 * mV = mA/cm^2
return current

def init_state(self, states, v, params, delta_t):
Expand Down
52 changes: 24 additions & 28 deletions jaxley_mech/channels/benison01.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -29,6 +29,7 @@ class Leak(Channel):
"""Leakage current"""

def __init__(self, name: Optional[str] = None):
self.current_is_in_mA_per_cm2 = True
super().__init__(name)
prefix = self._name
self.channel_params = {
Expand All @@ -50,10 +51,8 @@ def compute_current(
):
"""""Return the updated states.""" ""
prefix = self._name
gLeak = (
params[f"{prefix}_gLeak"] * 1000
) # mS/cm^2, multiply with 1000 to convert Siemens to milli Siemens.
return gLeak * (v - params[f"{prefix}_eLeak"])
gLeak = params[f"{prefix}_gLeak"] # S/cm^2
return gLeak * (v - params[f"{prefix}_eLeak"]) # S/cm^2 * mV = mA/cm^2

def init_state(self, states, v, params, delta_t):
"""Initialize the state such at fixed point of gate dynamics."""
Expand All @@ -64,6 +63,7 @@ class Na(Channel):
"""Sodium channel"""

def __init__(self, name: Optional[str] = None):
self.current_is_in_mA_per_cm2 = True
super().__init__(name)
prefix = self._name
self.channel_params = {
Expand Down Expand Up @@ -94,10 +94,8 @@ def compute_current(
"""Return the updated states."""
prefix = self._name
m, h = states[f"{prefix}_m"], states[f"{prefix}_h"]
gNa = (
params[f"{prefix}_gNa"] * (m**3) * h * 1000
) # mS/cm^2, multiply with 1000 to convert Siemens to milli Siemens.
return gNa * (v - params[f"{prefix}_eNa"])
gNa = params[f"{prefix}_gNa"] * (m**3) * h # S/cm^2
return gNa * (v - params[f"{prefix}_eNa"]) # S/cm^2 * mV = mA/cm^2

def init_state(self, states, v, params, delta_t):
"""Initialize the state such at fixed point of gate dynamics."""
Expand Down Expand Up @@ -128,6 +126,7 @@ class Kdr(Channel):
"""Delayed Rectifier Potassium channel"""

def __init__(self, name: Optional[str] = None):
self.current_is_in_mA_per_cm2 = True
super().__init__(name)
prefix = self._name
self.channel_params = {
Expand All @@ -145,7 +144,6 @@ def update_states(
prefix = self._name
m = states[f"{prefix}_m"]
new_m = solve_gate_exponential(m, dt, *Kdr.m_gate(v))
# jax.debug.print("new_m={new_m}, v={v}", new_m=new_m, v=v)
return {f"{prefix}_m": new_m}

def compute_current(
Expand All @@ -154,11 +152,9 @@ def compute_current(
"""""Return the updated states.""" ""
prefix = self._name
m = states[f"{prefix}_m"]
gKdr = (
params[f"{prefix}_gKdr"] * (m**4) * 1000
) # mS/cm^2, multiply with 1000 to convert Siemens to milli Siemens.
gKdr = params[f"{prefix}_gKdr"] * m**4 # S/cm^2

return gKdr * (v - params[f"eK"])
return gKdr * (v - params[f"eK"]) # S/cm^2 * mV = mA/cm^2

def init_state(self, states, v, params, delta_t):
"""Initialize the state such at fixed point of gate dynamics."""
Expand Down Expand Up @@ -186,6 +182,7 @@ class KA(Channel):
"""A type Potassium channel"""

def __init__(self, name: Optional[str] = None):
self.current_is_in_mA_per_cm2 = True
super().__init__(name)
prefix = self._name
self.channel_params = {
Expand Down Expand Up @@ -216,10 +213,8 @@ def compute_current(
"""Return the updated states."""
prefix = self._name
m, h = states[f"{prefix}_m"], states[f"{prefix}_h"]
gKA = (
params[f"{prefix}_gKA"] * (m**3) * h * 1000
) # mS/cm^2, multiply with 1000 to convert Siemens to milli Siemens.
return gKA * (v - params[f"eK"])
gKA = params[f"{prefix}_gKA"] * (m**3) * h # S/cm^2
return gKA * (v - params[f"eK"]) # S/cm^2 * mV = mA/cm^2

def init_state(self, states, v, params, delta_t):
"""Initialize the state such at fixed point of gate dynamics."""
Expand Down Expand Up @@ -250,6 +245,7 @@ class CaL(Channel):
"""L-type Calcium channel"""

def __init__(self, name: Optional[str] = None):
self.current_is_in_mA_per_cm2 = True
super().__init__(name)
prefix = self._name
self.channel_params = {
Expand Down Expand Up @@ -280,10 +276,8 @@ def compute_current(
"""Return the updated states."""
prefix = self._name
m = states[f"{prefix}_m"]
gCaL = (
params[f"{prefix}_gCaL"] * (m**2) * 1000
) # mS/cm^2, multiply with 1000 to convert Siemens to milli Siemens.
current = gCaL * (v - states["eCa"])
gCaL = params[f"{prefix}_gCaL"] * (m**2) # S/cm^2
current = gCaL * (v - states["eCa"]) # S/cm^2 * mV = mA/cm^2
return current

def init_state(self, states, v, params, delta_t):
Expand All @@ -306,6 +300,7 @@ class CaN(Channel):
"""N-type Ca channel"""

def __init__(self, name: Optional[str] = None):
self.current_is_in_mA_per_cm2 = True
super().__init__(name)
prefix = self._name
self.channel_params = {
Expand Down Expand Up @@ -335,10 +330,8 @@ def compute_current(
"""Return the updated states."""
prefix = self._name
m, h = states[f"{prefix}_m"], states[f"{prefix}_h"]
gCaN = (
params[f"{prefix}_gCaN"] * (m**2) * h * 1000
) # mS/cm^2, multiply with 1000 to convert Siemens to milli Siemens.
return gCaN * (v - states[f"eCa"])
gCaN = params[f"{prefix}_gCaN"] * (m**2) * h # S/cm^2
return gCaN * (v - states[f"eCa"]) # S/cm^2 * mV = mA/cm^2

def init_state(self, states, v, params, delta_t):
"""Initialize the state such at fixed point of gate dynamics."""
Expand Down Expand Up @@ -369,6 +362,7 @@ class CaPumpNS(Channel):
"""Non-spatial Calcium pump"""

def __init__(self, name: Optional[str] = None):
self.current_is_in_mA_per_cm2 = True
super().__init__(name)
self.channel_constants = {
"F": 96485.3329, # C/mol (Faraday's constant)
Expand Down Expand Up @@ -406,7 +400,7 @@ def update_states(self, states, dt, v, params):
K_pump = params["K_pump"]
j_pump = v_pump * (Cai**4 / (Cai**4 + K_pump**4))

iCa = states["iCa"] / 1_000
iCa = states["iCa"]

driving_channel = -10_000.0 * iCa / (2 * F * V_cell)
driving_channel = select(
Expand All @@ -431,6 +425,7 @@ def init_state(self, states, v, params, delta_t):

class KCa(Channel):
def __init__(self, name: Optional[str] = None):
self.current_is_in_mA_per_cm2 = True
super().__init__(name)
prefix = self._name
self.channel_params = {
Expand Down Expand Up @@ -464,9 +459,9 @@ def compute_current(

# changed to the second-power from fm97
x = (Cai / K_KCa) ** 2
gKCa = params[f"{prefix}_gKCa"] * (x / (1 + x)) * 1000
gKCa = params[f"{prefix}_gKCa"] * (x / (1 + x)) # S/cm^2

return gKCa * (v - params[f"eK"])
return gKCa * (v - params[f"eK"]) # S/cm^2 * mV = mA/cm^2

def init_state(self, states, v, params, delta_t):
"""Initialize the state such at fixed point of gate dynamics."""
Expand All @@ -481,6 +476,7 @@ def __init__(
self,
name: Optional[str] = None,
):
self.current_is_in_mA_per_cm2 = True
super().__init__(name)
self.channel_constants = {
"F": 96485.3329, # C/mol (Faraday's constant)
Expand Down
11 changes: 9 additions & 2 deletions jaxley_mech/channels/chen24.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -15,6 +15,7 @@
"papers": [
"Chen, Q., Ingram, N. T., Baudin, J., Angueyra, J. M., Sinha, R., & Rieke, F. (2024). Light-adaptation clamp: A tool to predictably manipulate photoreceptor light responses. https://doi.org/10.7554/eLife.93795.1",
],
"code": "https://github.com/chrischen2/photoreceptorLinearization",
}


Expand All @@ -29,6 +30,7 @@ def __init__(
atol: float = 1e-8,
max_steps: int = 10,
):
self.current_is_in_mA_per_cm2 = True
super().__init__(name)
SolverExtension.__init__(self, solver, rtol, atol, max_steps)
prefix = self._name
Expand Down Expand Up @@ -151,8 +153,13 @@ def compute_current(
params[f"{prefix}_n"],
params[f"{prefix}_k"],
)
I = -k * G**n # eq(4)
return I
I = -k * G**n # eq(4) #pA

I *= 1e-9
area = 2 * jnp.pi * params["length"] * params["radius"] * 1e-8 # um^2 to cm^2
current_density = I / area

return current_density

def init_state(self, states, v, params, delta_t):
"""Initialize the state at fixed point of gate dynamics."""
Expand Down
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