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RS.mod
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Tue, Nov 19, 20:30
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text/x-Algol68
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Thu, Nov 21, 20:30 (2 d)
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R4670 PySONIC (old)
RS.mod
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TITLE
RS
neuron
:
:
Equations
governing
the
behavior
of
a
regular
spiking
neuron
:
during
ultrasonic
stimulation
,
according
to
the
NICE
model
.
:
:
Written
by
Theo
Lemaire
and
Simon
Narduzzi
,
EPFL
,
2018
:
Contact
:
theo
.
lemaire
@
epfl
.
ch
INDEPENDENT
{
t
FROM
0
TO
1
WITH
1
(
ms
)}
UNITS
{
(
mA
)
=
(
milliamp
)
(
mV
)
=
(
millivolt
)
(
uF
)
=
(
microfarad
)
}
NEURON
{
:
Definition
of
NEURON
mechanism
:
mechanism
name
and
constituting
currents
SUFFIX
RS
NONSPECIFIC_CURRENT
iNa
NONSPECIFIC_CURRENT
iKd
NONSPECIFIC_CURRENT
iM
NONSPECIFIC_CURRENT
iLeak
:
simulation
parameters
(
stimulus
and
dt
)
RANGE
duration
,
PRF
,
DC
,
stimon
:
physiological
variables
RANGE
Q
,
Vmeff
,
gnabar
,
gkdbar
,
gmbar
,
gleak
,
eleak
,
ek
,
ena
}
PARAMETER
{
:
Parameters
set
by
the
user
upon
initialization
:
simulation
parameters
(
stimulus
and
dt
)
duration
=
100
(
ms
)
offset
=
0
(
ms
)
PRF
=
0
(
Hz
)
DC
=
0
dt
=
0.05
(
ms
)
:
membrane
properties
cm
=
1
(
uF
/
cm2
)
ena
=
50
(
mV
)
ek
=
-
90
(
mV
)
eleak
=
-
70.3
(
mV
)
gnabar
=
0.056
(
mho
/
cm2
)
gkdbar
=
0.006
(
mho
/
cm2
)
gmbar
=
7.5
e
-
5
(
mho
/
cm2
)
gleak
=
2.05
e
-
5
(
mho
/
cm2
)
}
STATE
{
:
Differential
variables
other
than
v
,
i
.
e
.
the
ion
channels
gating
states
m
:
iNa
activation
gate
h
:
iNa
inactivation
gate
n
:
iKd
activation
gate
p
:
iM
activation
gate
}
ASSIGNED
{
:
Variables
computed
during
the
simulation
and
whose
value
can
be
retrieved
Q
(
nC
/
cm2
)
Vmeff
(
mV
)
v
(
mV
)
iNa
(
mA
/
cm2
)
iKd
(
mA
/
cm2
)
iM
(
mA
/
cm2
)
iLeak
(
mA
/
cm2
)
alpha_h
(
/
ms
)
beta_h
(
/
ms
)
alpha_m
(
/
ms
)
beta_m
(
/
ms
)
alpha_n
(
/
ms
)
beta_n
(
/
ms
)
alpha_p
(
/
ms
)
beta_p
(
/
ms
)
stimon
tint
(
ms
)
}
BREAKPOINT
{
:
Main
computation
block
:
compute
Q
Q
=
v
*
cm
:
update
stimulation
boolean
stimonoff
()
:
integrate
states
SOLVE
states
METHOD
cnexp
:
compute
Vmeff
if
(
stimon
)
{
Vmeff
=
veff_on
(
Q
)}
else
{
Vmeff
=
veff_off
(
Q
)}
:
compute
ionic
currents
iNa
=
gnabar
*
m
*
m
*
m
*
h
*
(
Vmeff
-
ena
)
iKd
=
gkdbar
*
n
*
n
*
n
*
n
*
(
Vmeff
-
ek
)
iM
=
gmbar
*
p
*
(
Vmeff
-
ek
)
iLeak
=
gleak
*
(
Vmeff
-
eleak
)
}
DERIVATIVE
states
{
:
Compute
states
derivatives
:
compute
ON
or
OFF
rate
constants
accordingly
to
stimon
value
if
(
stimon
)
{
interpolate_on
(
Q
)}
else
{
interpolate_off
(
Q
)}
:
compute
gating
states
derivatives
m
' = alpha_m * (1 - m) - beta_m * m
h'
=
alpha_h
*
(
1
-
h
)
-
beta_h
*
h
n
' = alpha_n * (1 - n) - beta_n * n
p'
=
alpha_p
*
(
1
-
p
)
-
beta_p
*
p
}
UNITSOFF
:
turning
off
units
checking
for
functions
not
working
with
standard
SI
units
INITIAL
{
:
Initialize
variables
and
parameters
:
compute
Q
Q
=
v
*
cm
:
set
initial
states
values
m
=
alpham_off
(
Q
)
/
(
alpham_off
(
Q
)
+
betam_off
(
Q
))
h
=
alphah_off
(
Q
)
/
(
alphah_off
(
Q
)
+
betah_off
(
Q
))
n
=
alphan_off
(
Q
)
/
(
alphan_off
(
Q
)
+
betan_off
(
Q
))
p
=
alphap_off
(
Q
)
/
(
alphap_off
(
Q
)
+
betap_off
(
Q
))
:
initialize
tint
,
set
stimulation
state
and
correct
PRF
tint
=
0
stimon
=
0
PRF
=
PRF
/
2
:
for
some
reason
PRF
must
be
halved
in
order
to
ensure
proper
on
/
off
switch
}
:
Define
function
tables
for
variables
to
be
interpolated
during
ON
and
OFF
periods
FUNCTION_TABLE
veff_on
(
x
)
(
mV
)
FUNCTION_TABLE
veff_off
(
x
)
(
mV
)
FUNCTION_TABLE
alpham_on
(
x
)
(
/
ms
)
FUNCTION_TABLE
alpham_off
(
x
)
(
/
ms
)
FUNCTION_TABLE
betam_on
(
x
)
(
/
ms
)
FUNCTION_TABLE
betam_off
(
x
)
(
/
ms
)
FUNCTION_TABLE
alphah_on
(
x
)
(
/
ms
)
FUNCTION_TABLE
alphah_off
(
x
)
(
/
ms
)
FUNCTION_TABLE
betah_on
(
x
)
(
/
ms
)
FUNCTION_TABLE
betah_off
(
x
)
(
/
ms
)
FUNCTION_TABLE
alphan_on
(
x
)
(
/
ms
)
FUNCTION_TABLE
alphan_off
(
x
)
(
/
ms
)
FUNCTION_TABLE
betan_on
(
x
)
(
/
ms
)
FUNCTION_TABLE
betan_off
(
x
)
(
/
ms
)
FUNCTION_TABLE
alphap_on
(
x
)
(
/
ms
)
FUNCTION_TABLE
alphap_off
(
x
)
(
/
ms
)
FUNCTION_TABLE
betap_on
(
x
)
(
/
ms
)
FUNCTION_TABLE
betap_off
(
x
)
(
/
ms
)
PROCEDURE
interpolate_on
(
Q
){
:
Interpolate
rate
constants
durong
US
-
ON
periods
from
appropriate
tables
alpha_m
=
alpham_on
(
Q
)
beta_m
=
betam_on
(
Q
)
alpha_h
=
alphah_on
(
Q
)
beta_h
=
betah_on
(
Q
)
alpha_n
=
alphan_on
(
Q
)
beta_n
=
betan_on
(
Q
)
alpha_p
=
alphap_on
(
Q
)
beta_p
=
betap_on
(
Q
)
}
PROCEDURE
interpolate_off
(
Q
){
:
Interpolate
rate
constants
durong
US
-
OFF
periods
from
appropriate
tables
alpha_m
=
alpham_off
(
Q
)
beta_m
=
betam_off
(
Q
)
alpha_h
=
alphah_off
(
Q
)
beta_h
=
betah_off
(
Q
)
alpha_n
=
alphan_off
(
Q
)
beta_n
=
betan_off
(
Q
)
alpha_p
=
alphap_off
(
Q
)
beta_p
=
betap_off
(
Q
)
}
UNITSON
:
turn
back
units
checking
PROCEDURE
stimonoff
(){
:
Switch
integration
to
ON
or
OFF
system
according
to
stimulus
if
(
t
<
duration
-
dt
){
if
(
tint
>=
1000
/
PRF
){
:
reset
on
at
pulse
onset
stimon
=
1
tint
=
0
}
else
if
(
tint
<=
DC
*
1000
/
PRF
){
:
ON
during
TON
stimon
=
1
}
else
{
:
OFF
during
TOFF
stimon
=
0
}
tint
=
tint
+
dt
:
increment
by
dt
}
else
{
:
OFF
during
stimulus
offset
stimon
=
0
}
}
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