XPP model
This model was converted from XPP ode format to SBML using sbmlutils-0.1.5a6
.
# S.A. Hires, L. Pammer, K. Svoboda and D. Golomb
# Tapered whiskers are required for active tactile sensation.
# eLIFE 2:e01350, 2013.
#
# Quasi-static solution of the bending of an isolated whisker.
# File for bifurcation calculation.
#
# For Fig. 2, stable solution, use: theta=-0.174533 rad.
# Use "Bndryval -> Show" in XPPAUT.
#
# p xcen=15.1286239388569 ycen=4.28562676857186
# p xcen=14.8713760611431 ycen=4.71437323142814
p thetap=0.0
p dd=15.6604597633658
# CB: positive rpole, negative theta
p rpole=0.25
# CF: negative rpole, positive theta
##p rpole=-0.25
p g0=0.0 g1=0.0 g2=0.02 g3=0.0 g4=0.0
#
p EE=1.0,rbase=0.03,rtip=0.0015
p LL=20.0
#
gg(vv)=((((g4*vv)+g3)*vv+g2)*vv+g1)*vv+g0
ggp(vv)=(((4.0*g4*vv)+3.0*g3)*vv+2.0*g2)*vv+g1
ggpp(vv)=((12.0*g4*vv)+6.0*g3)*vv+2.0*g2
sqgpxy(vv)=sqrt(1.0+(ggp(vv))^2.0)
#
rr=(1.0-(sobj*sighat/LL)*(1.0-(rtip/rbase)))*rbase
IIarea=0.25*Pi*(rr^4.0)
coefaux=FF/(EE*IIarea)
#
xxaux'=xlen
yyaux'=xlen*(2.0*g2*xxaux)
xlen'=0
xcen'=0
ycen'=0
#
xu'=sobj/sqgpxy(xu)
xx'= sobj*cos(theta)
yy'= sobj*sin(theta)
theta'=(sobj*ggpp(xu)/(sqgpxy(xu)^3))+sobj*coefaux*((xcen-xx-rpole*sin(thobj))*cos(thobj)+(ycen-yy+rpole*cos(thobj))*sin(thobj))
FF'=0
thobj'=0
sobj'=0.0
sighat'=1
#
boundary xxaux
boundary yyaux
boundry xcen'-(xxaux'+rpole*2.0*g2*xxaux'*sqrt(1.0/(1+(4.0*g2*g2*xxaux'*xxaux'))))
boundary ycen'-(yyaux'-rpole*sqrt(1.0/(1+(4.0*g2*g2*xxaux'*xxaux'))))
boundary xxaux'*xxaux'+yyaux'*yyaux'-dd*dd
#
boundary xu
boundary xx
boundary yy
boundary theta-thetap
boundary theta'-thobj'
boundary xx'-xcen+rpole*sin(thobj')
boundary yy'-ycen-rpole*cos(thobj')
boundary sighat
#
xxaux(0)=0.0
yyaux(0)=0.0
xlen(0)=15.0
xcen(0)=15.0
ycen(0)=4.5
#
xu(0)=0.0
xx(0)=0.0
yy(0)=0.0
theta(0)=thetap
sobj(0)=18.0
sighat(0)=0.0
FF(0)=0.0e-8
thobj(0)=0.54042
#
aux kapud=sobj*ggpp(xu)/(sqgpxy(xu)^3)
aux kapd=sobj*coefaux*((xcen-xx-rpole*sin(thobj))*cos(thobj)+(ycen-yy+rpole*cos(thobj))*sin(thobj))
#
@ total=1
@ DT=0.001
@ MAXSTOR=800000
@ BACK=Black
@ XP=xx
@ YP=yy
@ XLO=0.0, XHI=16.0, YLO=-1.0, YHI=5.0
@ NTST=50,NMAX=2000,NPR=50
@ DS=0.002,DSMIN=0.0001,DSMAX=0.05
@ PARMIN=-5.0,PARMAX=5.0,NORMMIN=0.0,NORMMAX=10000.0
@ AUTOVAR=ycen,AUTOXMIN=0.0,AUTOXMAX=5.0,AUTOYMIN=0.0,AUTOYMAX=4.0
done
Terms of use
Copyright © 2017 Matthias Koenig
Redistribution and use of any part of this model, with or without modification, are permitted provided that
the following conditions are met:
Redistributions of this SBML file must retain the above copyright notice, this list of conditions
and the following disclaimer.
Redistributions in a different form must reproduce the above copyright notice, this list of
conditions and the following disclaimer in the documentation and/or other materials provided
with the distribution.
This model is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even
the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
Model :
id
name
time
substance
extent
volume
area
length
L3V1
type
FunctionDefinitions [8]
name
math
sbo
cvterm
FunctionDefinition
max
minimum
x
y
x
x
y
y
FunctionDefinition
min
maximum
x
y
x
x
y
y
FunctionDefinition
heav
heavyside
x
0
x
0
0.5
x
0
1
x
0
0
FunctionDefinition
mod
modulo
x
y
x
y
x
y
x
0
y
0
x
y
x
y
FunctionDefinition
gg
vv
g0
g1
g2
g3
g4
g4
vv
g3
vv
g2
vv
g1
vv
g0
FunctionDefinition
ggp
vv
g1
g2
g3
g4
4
g4
vv
3
g3
vv
2
g2
vv
g1
FunctionDefinition
ggpp
vv
g2
g3
g4
12
g4
vv
6
g3
vv
2
g2
FunctionDefinition
sqgpxy
vv
g1
g2
g3
g4
2
1
ggp
vv
g4
g2
g3
g1
2
type
Parameters [31]
name
constant
value
unit
derived unit
sbo
cvterm
Parameter
thetap
thetap = 0.0
F
0.0
None
Parameter
dd
dd = 15.6604597633658
F
15.6604597633658
None
Parameter
rpole
rpole = 0.25
F
0.25
None
Parameter
g0
g0 = 0.0
F
0.0
None
Parameter
g1
g1 = 0.0
F
0.0
None
Parameter
g2
g2 = 0.02
F
0.02
None
Parameter
g3
g3 = 0.0
F
0.0
None
Parameter
g4
g4 = 0.0
F
0.0
None
Parameter
ee
ee = 1.0
F
1.0
None
Parameter
rbase
rbase = 0.03
F
0.03
None
Parameter
rtip
rtip = 0.0015
F
0.0015
None
Parameter
ll
ll = 20.0
F
20.0
None
Parameter
xxaux
xxaux = 0.0
F
0.0
None
Parameter
yyaux
yyaux = 0.0
F
0.0
None
Parameter
xlen
xlen = 15.0
F
15.0
None
Parameter
xcen
xcen = 15.0
F
15.0
None
Parameter
ycen
ycen = 4.5
F
4.5
None
Parameter
xu
xu = 0.0
F
0.0
None
Parameter
xx
xx = 0.0
F
0.0
None
Parameter
yy
yy = 0.0
F
0.0
None
Parameter
theta
theta
F
0.0
None
Parameter
sobj
sobj = 18.0
F
18.0
None
Parameter
sighat
sighat = 0.0
F
0.0
None
Parameter
ff
ff = 0.0e-8
F
0.0
None
Parameter
thobj
thobj = 0.54042
F
0.54042
None
Parameter
rr
F
0.0
dimensionless
None
Parameter
iiarea
F
0.0
dimensionless
None
Parameter
coefaux
F
0.0
dimensionless
None
Parameter
kapud
F
0.0
dimensionless
None
Parameter
kapd
F
0.0
dimensionless
None
Parameter
t
model time
F
0.0
dimensionless
None
type
InitialAssignments [1]
name
assignment
derived units
sbo
cvterm
InitialAssignment
theta
=
thetap
None
type
Rules [19]
assignment
name
derived units
sbo
cvterm
Rule
d xxaux/dt
=
xlen
None
Rule
d yyaux/dt
=
xlen
2
g2
xxaux
None
Rule
d xlen/dt
=
0
None
Rule
d xcen/dt
=
0
None
Rule
d ycen/dt
=
0
None
Rule
d xu/dt
=
sobj
sqgpxy
xu
g1
g2
g3
g4
None
Rule
d xx/dt
=
sobj
theta
None
Rule
d yy/dt
=
sobj
theta
None
Rule
d theta/dt
=
sobj
ggpp
xu
g2
g3
g4
sqgpxy
xu
g1
g2
g3
g4
3
sobj
coefaux
xcen
xx
rpole
thobj
thobj
ycen
yy
rpole
thobj
thobj
None
Rule
d ff/dt
=
0
None
Rule
d thobj/dt
=
0
None
Rule
d sobj/dt
=
0
None
Rule
d sighat/dt
=
1
None
Rule
rr
=
1
sobj
sighat
ll
1
rtip
rbase
rbase
None
Rule
iiarea
=
0.25
rr
4
None
Rule
coefaux
=
ff
ee
iiarea
None
Rule
kapud
=
sobj
ggpp
xu
g2
g3
g4
sqgpxy
xu
g1
g2
g3
g4
3
None
Rule
kapd
=
sobj
coefaux
xcen
xx
rpole
thobj
thobj
ycen
yy
rpole
thobj
thobj
None
Rule
t
=
time
None