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Modelling with ODEs a complex pathwayHow do the response of an edge change as the input nodes changes?
Metabolism:
A Enzyme B Afdt
dB
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0
1
0
[A]
d[B
]/dt
Michaelis-Menten kinetics
A Enzyme B EBAEEAk
k
k
2
1
1
AK
Av
dt
dB
MM
Max
KMM KMM
vMax
vMax/2
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Michaelis-Menten kinetics
A Enzyme B EBAEEAk
k
k
2
1
1
AK
Av
dt
dB
MM
Max
vMax
1° order kinetics0° order kinetics
Maxvdt
dBA
K
v
dt
dB
MM
Max
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Cooperative kinetics
The enzyme (the DNA) has different binding sites. The affinity to further ligands may change after binding one or more ligands:
Positive the affinity increases after bindingNegative the affinity decreases after binding
Homotropic cooperativity between ligands of the same typeHeterotropic cooperativity between ligands of different types
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Hill kinetics
Hill kinetics allow one to include the
effects of cooperative binding events.
nn
B
n
Max
AK
Av
dt
dB
~
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Hill functions
nn
B
n
AK
AY
n=2 n=5 n=20
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Hill functions
nn
B
n
AK
AY
KB=0.2 KB=0.7 KB=1
n=2 Y=1/2 for A=KB-1/2
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C.Piazza, Università di Udine http://iclp08.dimi.uniud.it/PRESENTAZIONI/Piazza.pdf
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C.Piazza, Università di Udine http://iclp08.dimi.uniud.it/PRESENTAZIONI/Piazza.pdf
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Edges of the network: response function
How do the response of an edge change as the input nodes changes?
Regulation
A X A X
Afdt
dX XAf
dt
dX,
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Ordinary Differential Equations
),,( tpdt
dxf
x
x: variable vector (x1,x2,..,xn)p: parameterst: timef: function vector (f1,f2,..fn)
If f does not depend on time, the ODE is called autonomous
),( pdt
dxf
x
We search for a general solution
or for a particular solution (given some initial condition xo)
),()( ptt Fx
),,()( 0xFx ptt
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Ordinary Differential Equations: Steady state
Consider an autonomous ODE
),( pdt
dxf
x
The steady state, when existing, is the value of x that gives:
0),(0 pdt
d SSxf
x
If x reaches the value xSS at time t0, it will not vary after t0
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Ordinary Differential Equations, 1D
adt
dx The variation rate is constant
The sign of a determines the family of the solution
For all constants C, the solution satisfies the ODE
NO STEADY STATE
Cattx )(
General solution
-20
-15
-10
-5
0
5
10
15
-4 -3 -2 -1 0 1 2 3 4
t
x(t)
a=1, C= 0 a=1, C= -10a=1, C=5 a=-1, C=0a=-1, C=-10 a=-1, C=5
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Ordinary Differential Equations
adt
dx
CCaxx 0)0(0
For determining a particular solution we need some condition on the value of x(t) a some t
Usually the value x(0) = x0
0)( xattx
So
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Ordinary Differential Equations
axdt
dx The variation rate is proportional to x
The sign of a determines the family of the solution
For all constants C, the solution satisfies the ODE
STEADY STATE: xSS=0
atCetx )(General solution
-600
-500
-400
-300
-200
-100
0
100
200
300
400
-4 -3 -2 -1 0 1 2 3 4
t
x(t)
a=1, C= 0
a=1, C= -10
a=1, C=5
a=-1, C=0
a=-1, C=-10
a=-1, C=5
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Ordinary Differential Equations
axdt
dx
CCexx a 0
0 )0(
For determining a particular solution we need some condition on the value of x(t) a some t
Usually the value x(0) = x0
atextx 0)(
So
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Ordinary Differential Equations
2axdt
dx The variation rate is proportional to x2
General solution
Cat
tx
Catx
dtax
dx
1
12
-1.5
-1
-0.5
0
0.5
1
1.5
-44
-38
-32
-26
-20
-14 -8 -2 4 10 16 22 28 34 40
t
x(t)
a=1, C= 0 a=1, C= -10
a=1, C=5 a=-1, C=0
a=-1, C=-10 a=-1, C=5
STEADY STATE: xSS=0
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Ordinary Differential Equations
2axdt
dx
For determining a particular solution we need some condition on the value of x(t) a some t
Usually the value x(0) = x0
So
0
0
11
0
10
xC
CCaxx
tax
x
xat
tx0
0
0
11
1
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Ordinary Differential Equations
x
a
dt
dx The variation rate is inversely proportional to x
General solution
a
CtCattx
Catx
dtadxx
,22
2
2
0
2
4
6
8
10
12
-44
-37
-30
-23
-16 -9 -2 5 12 19 26 33 40
t
x(t)
a=1, C= 0 a=1, C= -10a=1, C=5 a=-1, C=0a=-1, C=-10 a=-1, C=5
NO STEADY STATE
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Ordinary Differential Equations
For determining a particular solution we need some condition on the value of x(t) a some t
Usually the value x(0) = x0
So
x
a
dt
dx
CCaxx 220200
2
00 2)( xatxsigntx
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Linear Ordinary Differential Equations
baxdt
dx
If b≠0 : non-homogeneous case. Find the steady state
a
bx
dt
dx SS 0
Then consider the transformation: SSxxx ˆIt comes that:
xaxxaa
bxabax
dt
dx
dt
xd SS ˆ)(ˆ
So
Homogeneous
a
bCexCex atat ˆ
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Linear Ordinary Differential Equations
baxdt
dx
a
bxCC
a
bCe
a
bxx a
0
0
0 )0(
For determining a particular solution we need some condition on the value of x(t) a some t
Usually the value x(0) = x0
atat ea
bx
a
bCe
a
btx
0)(
So
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-4
-2
0
2
4
6
8
10
12
14
-1 0 1 2 3 4 5 6 7 8
t
x(t)
a=-1, b=1, x0= 0
a=-1, b=1, x0=1
a=-1, b=1, x0=5
0,)(
0,)(
0
0
aexxxtx
aea
bx
a
btx
atSSSS
at
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0
2
4
6
8
10
12
0 5 10 15 20 25 30 35 40 45t
x(t)
a=-1, b=1, x0= 0
a=-1, b=10, x0=0
a=-0.1, b=1, x0=0
0,)( 0
ae
a
bx
a
btx at
The solution converges to the value -b/a; the value a determines the velocity of the response
0,)1()( 0 aexextx atatSS
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0
2
4
6
8
10
12
0 5 10 15 20 25 30 35 40 45t
x(t)
a=-1, b=10, x0=0
a=-0.1, b=1, x0=0
It is the time for reaching xSS/2 starting from 0
ate
xextx ta
SStaSS 2ln
5.02
)1()(
Response time
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-6
-4
-2
0
2
4
6
8
10
12
0 5 10 15 20 25 30 35 40 45
t
x(t)
a=-0.1, b=1, x0=0
a=-0.1, b=1, x0=-4
In general, it is the time for reaching half of the distance between x0 and xSS
a
txx
xxe
xxxexexxtx
SSSSta
SS
tataSS
2ln
21
2)1()(
00
0000
Response time
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Linear systems of autonomous ODEs
nnnnnn
nn
nn
xaxaxadt
dx
xaxaxadt
dx
xaxaxadt
dx
.....
....
.....
.....
2211
22221212
12121111
nx
x
x
...
2
1
x Axx
dt
d
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Linear systems of autonomous ODEs
Axx
dt
d
The general solution can be written as
n
t
b
b
b
et..
where)(2
1
bbx
0 bIAAbbx
tt eedt
d
So:
That is satisfied for all i that are eigenvalues of A and b(i) the corresponding eigenvectors
tn
i
iiect
1
)( ibx
The value of cis are fixed to satisfy initial conditions
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Example in 2 dimensions
2
1
2
1
23
21
x
x
x
x
dt
d
Eigenvalues-Eigenvectors
That is satisfied for all i eigenvalues of A and b(i) the corresponding eigenvectors
023
21det
01)4(0430621 2
1
11
3
24 2
21
)((1)bb
tt ecectx
x
1
1
3
2)( 2
4
1
2
1
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Example in 2 dimensions
2
1
2
1
23
21
x
x
x
x
dt
dWith
1
1
3
2)0(
0
521
2
1cc
x
x
0
50
2
1
x
x
3
1
52
3
2
1
21
12
c
c
cc
cc
tt
tt
eetx
eetx
33
32
4
2
4
1
0
1000
2000
3000
4000
5000
6000
7000
0 0,20,40,60,8 1 1,21,41,61,8
X1 X2
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Linear systems of autonomous ODEs
zAxx
dt
d
The Steady state solution is zAxzAx10 ssss
xAzAxAzAxxx 1 ˆ)(
ˆ
dt
d
dt
d
So
zAbxbx
1ii
t
n
i
i
tn
i
iii ectect
11
)()(ˆ
Define the transformationss
xxx ˆ
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Higher order ODEs
Can be reduced to linear systems, by introducing extra variables
1
22
21
21
2
2
2
,
xkdt
dx
xdt
dx
dt
dxxxx
xkdt
xd
Axx
dt
d
0
102k
A
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Solutions
kk
kk
kk
1,
,1
,
0)(1
detdet
2
1
22
2
(2)
(1)
b
b
IA
ktkt
ktkt
tt
tt
ekcekc
ecec
ebcebc
ebcebc
tx
tx
21
21
2)2(
22)1(
1
1)2(
21)1(
1
2
1
21
21
)(
)(
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Solutions with initial conditions
5.00
1
)0(
)0(21
21
21
2
1
cc
kckc
cc
x
x
)sinh(
)cosh(5.0
)(
)(
2
1
kt
kt
ekek
ee
tx
txktkt
ktkt
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Higher order ODEs
Can be reduced to linear systems, by introducing extra variables
1
22
21
21
2
2
2
,
xkdt
dx
xdt
dx
dt
dxxxx
xkdt
xd
Axx
dt
d
0
102k
A
Harmonic force
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Imaginary solutions
ikik
ikik
kk
1,
,1
,
0)(1
detdet
2
1
22
2
(2)
(1)
b
b
IA
iktikt
iktikt
tt
tt
eikceikc
ecec
ebcebc
ebcebc
tx
tx
21
21
2)2(
22)1(
1
1)2(
21)1(
1
2
1
21
21
)(
)(
1i
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Euler’s formula
)sin()cos( ktikteikt
Proof: the exponential eax function is DEFINED as the function satisfying:
1)0( with xaxdt
dx
Indeed:
1)0( with xikxdt
dx
)cos()sin()cos()sin()sin()cos( ktktiikktikktkktiktdt
d
So we have to proof that the given expression satisfies:
1)0sin()0cos( kik
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Example
2
1
0
121
21
21
cc
ikcikc
cc
With initial condition
0
1
)0(
)0(
dt
dx
x
iktikt
iktikt
tt
tt
eikceikc
ecec
ebcebc
ebcebc
tx
tx
21
21
2)2(
22)1(
1
1)2(
21)1(
1
2
1
21
21
)(
)(
kt
kt
ktii
kt
eikeik
ee
tx
txiktikt
iktikt
sin
cos
sin2
cos2
2
1
2
1
)(
)(
2
1
xkdt
xd 2
2
2
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Time evolution plot
kt
kt
tx
tx
sin
cos
)(
)(
2
1
-1,5
-1
-0,5
0
0,5
1
1,5
00,
81,
62,
43,
2 44,
85,
66,
47,
2 88,
89,
6
t
x1(t
),x2(t
)
x1(t)
x2(t)
X1 and x2 are plotted with respect to time
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Phase space plot
kt
kt
tx
tx
sin
cos
)(
)(
2
1
Relation between x1 and x2 are plotted without reference to time
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Stability of steady states in ODEs
0),( pSSxf
Given an autonomous ODE ),( pdt
dxf
x
The steady state is given by the condition
If x=xss the solution does not varyWe want to analyse the behaviour of the solution when
with small eThe steady state is:STABLE if the system returns to this state upon perturbationUNSTABLE if the system leaves this state upon perturbationMETASTABLE if the system behaviour is indifferent
εxxSS
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Stability of steady states
FORCE
Unstable Stable Metastable
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On phase space
In 1D, linear case 0 , aaxdt
dx
)( axxf
point steady , 0dt
dxx
The phase space is 1D and the f(x) locally defines a vectorial field that represents the rate of change of x in each point
The steady point defines two subspaces with opposite behaviour
The steady state is unstable 0 if
0 if
0
0
0
xx
xxexx(t)
t
tat
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More on phase space
In 1D, linear case 0 , aaxdt
dx
)( axxf
point steady , 0dt
dxx
The steady point divides two subspaces with opposite behaviour
The steady state is stable 0 0, 0
t
at xaexx(t)
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Stability of steady states in 1D linear ODEs
Given an autonomous linear ODE, in 1 dimension
baxdt
dx
The steady state is
The particular solution starting with x0=xss+e is
a
bxss
atatssat ea
be
a
bx
a
be
a
bx
a
btx
ee0)(
The steady state isSTABLE if a<0UNSTABLE if a>0METASTABLE if a=0
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Stability of steady states in 1D linear ODEs
0
0,5
1
1,5
2
2,5
3
3,5
0 1 2 3t
x(t)
a=-1 a=0 a=1
xss
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Non linear equations
In 1D, general case xfdt
dx
)(xf
pointssteady , 0dt
dx
x
The steady point defines five subspaces
The steady states A and C are stable, B and D are not.
A B DC
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Basin of attraction
In 1D, general case xfdt
dx
)(xf
x
Three basins of attraction can be defined:Evolution of points in Basin1 tends to the stable point AEvolution of points in Basin2 tends to the stable point CEvolution of points in Basin3 tends to infinite
A B DC
Basin3Basin2Basin1
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Stability of steady states in 1D non linear ODEs
Given an autonomous linear ODE, in 1 dimension
xfdt
dx
The steady states are the solutions
In proximity of each steady state, the function can be linearized
0ssxf
SSSS x
SS
x
SSSS
dx
df
dt
xd
dx
dfxfxf e
eee
The steady state isSTABLE if df/dx <0UNSTABLE if df/dx >0METASTABLE if df/dx =0
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Logistic model
Population increase with competition on resources
)(xf
x0
0,0 , 1
Kr
K
PrP
dt
dPP:populationr: growth rateK: carrying capacity
0,0 ,with , 1 KrK
Pxxrx
dt
dx
1
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Logistic model: steady states
Steady state stability:x=0: x=1
Unstable Stable
)(xf
x0
0,0 ,with , 1 KrK
Pxxrx
dt
dx
The whole domain x>0 forms a unique basin of attraction converging to the point x=1
1
020
r rrxdx
dfx
021
r rrxdx
dfx
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Logistic model: explicit solution
0,0 ,with , 1 KrK
Pxxrx
dt
dx
tx
x
rdtxx
dxrdt
xx
dx
001
1
11)(
1ln
0
0
0
rt
rtx
xex
extxrt
x
x
x(0)=5
x(0)=1/5
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Stability of steady states in 2D linear ODEs
Given an autonomous linear ODE, in 2 dimension
2222121
1212111
2
1
2
1
2221
1211
2
1
zxaxa
zxaxa
z
z
x
x
aa
aa
x
x
dt
d
1212111 zxaxa
1x
2x
2222121 zxaxa
For each point in the phase space a vector is defined
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Phase space in 2D
2
1
2
1
01
10
x
x
x
x
dt
d
1212
2211
,
,
xxxv
xxxv
Components of the vectors
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Phase space in 2D
2
1
2
1
01
10
x
x
x
x
dt
d
1212
2211
,
,
xxxv
xxxv
Components of the vectors
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Phase space in 2D
2
1
2
1
20
11
x
x
x
x
dt
d
2212
21211
2,
,
xxxv
xxxxv
Components of the vectors
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Stability of steady states in 2D linear ODEs
Given an autonomous linear ODE, in 2 dimension
2222121
1212111
2
1
2
1
2221
1211
2
1
zxaxa
zxaxa
z
z
x
x
aa
aa
x
x
dt
d
Steady state
01212111 zxaxa
02222121 zxaxaNull clines
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Phase space in 2D
2
1
2
1
01
10
x
x
x
x
dt
d
0
0
2
1
x
x
Null clines
Steady state(0,0)
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Phase space in 2D
2
1
2
1
01
10
x
x
x
x
dt
d
0
0
2
1
x
x
Null clines
Steady state(0,0)
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Phase space in 2D
2
1
2
1
20
11
x
x
x
x
dt
d
0
0
2
21
x
xx
Null clines
Steady state(0,0)
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Local stability of a steady point
Stable Unstable Center
Particular directions should be analysed
Saddle
zAxx
dt
d zAbx
1i
t
n
i
iiect
1
)(
with λ, eigenvalues and b, eigenvectors
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Phase space in 2D
2
1
2
1
01
10
x
x
x
x
dt
d
1
1
2
1
Eigenvalues
Eigenvectors
1
1;
1
1
λ=1
λ=-1
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Phase space in 2D
2
1
2
1
20
11
x
x
x
x
dt
d
2
1
2
1
Eigenvalues
Eigenvectors
1
1;
0
1
λ=2
λ=1
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Phase space in 2D
2
1
2
1
01
10
x
x
x
x
dt
d
i
i
2
1
Eigenvalues
ii
1;
1
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Stability of steady states in nD linear ODEs
Given an autonomous linear ODE, in n dimension
zAx
xdt
d
The steady state is
The general solution is
The constant ci for a particular solution starting with x0=x
ss+e are given by:
zAxss 1
zAbx
1i
t
n
i
iiect
1
)(
εbεzAεxzAbx
i1ss1i
n
i
i
n
i
i cc11
)0(
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Stability of steady states in nD linear ODEs
So:
Consider the case in which all the eigenvalues are real.
Considering different e,parallel to the different eigenvectors b(i) we conclude that the system returns to the steady state if i<0 and leaves the steady state if i>0
So the steady state is STABLE if i<0 i (stable node)UNSTABLE if i>0 i (unstable node)UNSTABLE if i>0 for some i (unstable saddle point)
zAbx
1i
t
n
i
iiect
1
)( εb
i
n
i
ic1
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Stability of steady states in 2D linear ODEs
(stable node) (unstable node) (unstable saddle point)
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Stability of steady states in nD linear ODEs
So:
Consider the case in which the eigenvalues are complex.
There are oscillatory parts, but the stability is given by the real part of eigenvalues
So the steady state is STABLE if Re(i)<0 i (stable focus)UNSTABLE if Re(i)>0 i (unstable focus)UNSTABLE if Re(i)=0 i (stable center)
zAbx
1i
t
n
i
iiect
1
)( εb
i
n
i
ic1
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Stability of steady states in 2D linear ODEs
(stable center) (stable focus) (unstable focus)
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General rules of stability in 2D
Given a matrix A (2x2)
We must compute
dc
ba
AAbcaddadc
badetTrdet 22
So:
2
)det(4)(Tr)(Tr 2 AAA
)det(
)(Tr
21
21
A
A
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General rules of stability in 2D
2
)det(4)(Tr)(Tr 2 AAA
If we obtain 2 complex eigenvalues
if Tr(A) > 0: positive real part: UNSTABLE FOCUSif Tr(A) < 0: negative real part: STABLE FOCUSif Tr(A) = 0: null real part: CENTER
If we obtain 2 real eigenvalues
if det(A) < 0: two opposite eigenvevtors: SADDLEif det(A) > 0 and Tr(A) < 0:
two negative eigenvectors: STABLE NODEif det(A) > 0 and Tr(A) > 0:
two positive eigenvectors: UNSTABLE NODE
2)(Tr4
1)det( AA
2)(Tr4
1)det( AA
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=Det (A)
=Tr (A)
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Linear approximation around the steady state
0),( pSSxf
Given an autonomous ODE ),( pdt
dxf
x
The steady state is given by the condition
The stability around the steady state can be analysed considering the linear approximation of the system around it
dt
d
dt
d
dt
dt
dt
d
dt
d εεxεx
xss
ss
εxSS
)(
For each component xi the following condition holds:
n
j
j
j
ik
n
j
n
k
j
kj
in
j
j
j
ii
ii
x
f
xx
f
x
ff
fdt
dx
11 1
2
1
..2
1)(
)(
eeeeSS
SS
εx
x
εxSS
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Linear approximation around the steady state
Jεε
dt
dThen:
with the Jacobian
The eigenvalues of J determine the stability of the system around the steady state
n
nnn
n
n
x
f
x
f
x
f
x
f
x
f
x
f
x
f
x
f
x
f
..
........
..
..
21
2
2
2
1
2
1
2
1
1
1
J
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Lotka-Volterra equations
Non linear system of ODEs that describes the approximation of the prey-predator dynamics
Prey population (x) tends to increase (infinite supply of food) and it decreases only because of the predators
Predator population (y) tends to decrease and it increases only because of the predators
The probability that preys and predators meet is equal to xy
DxyCydt
dy
BxyAxdt
dx
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Lotka-Volterra equations: Steady state
with A, B, C, D > 0Two steady states are present
xSS1=(0;0) xSS2=(C/D;A/B)
The Jacobian matrix is
0
0
DxyCydt
dy
BxyAxdt
dx
0)(
0)(
DxCy
ByAx
DxCDy
BxByAJ
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Lotka-Volterra equations: stability
xSS1=(0;0)
with A, C > 0: saddle point
xSS2=(C/D;A/B)
Tr(J) = 0 ; Det (J) = ACDet (J) > Tr(J)2/4 : Complex solution;Tr(J)=0 : Center
C
AJ
0
0
0
0
B
ADD
BC
J
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Lotka-Volterra equations: stability
xSS1=(0;0)
with A, C > 0: saddle point
xSS2=(C/D;A/B)
The eigenvector are
The system has a center and cyclic orbits around it
C
AJ
0
0
0
0
B
ADD
BC
J
ACi
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Lotka-Volterra equations: Time evolution
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Lotka-Volterra equations: Phase space
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Some other system
1
2
xydt
dy
yxdt
dx
xydt
dy
ydt
dx1)ln(
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Dependence on parameters
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Logistic model with harvesting
Population increase, with competition on resources and constant harvesting
0,0,0 , 1
HKr -H
K
PrP
dt
dPP:populationr: growth rateK: carrying capacityH= Harvesting rate
K
Hh
K
Pxhxrx
dt
dx ,with , 1
Stable points:
r
h
r
rhrrx
hxrx
4112
1
2
4
0 1
2
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Logistic model with harvesting
)(xf
x
0 1
)(xf
x
0
1
r
h
r
rhrrx
hxrx
4112
1
2
4
0 1
2
Stable points:
0,
Stable point: 0
r
hx 411
2
1
4rh 4rh
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Bifurcation
0
0,2
0,4
0,6
0,8
1
1,2
r/4 h
x
Stable node
Unstable node
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Bifurcation in 2D: Saddle-node
ydt
dy
xdt
dx
2 Fixed points )0,();0,(
http://www.egwald.ca/nonlineardynamics/bifurcations.php#hopfbifurcation
y
x
0
y
x
0
Stable Saddle
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Bifurcation in 2D: Saddle-node
ydt
dy
xdt
dx
2Fixed points )0,();0,(
Jacobian
10
02x
http://www.egwald.ca/nonlineardynamics/bifurcations.php#hopfbifurcation
1,2:)0,(
1,2:)0,(
21
21
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Bifurcation in 2D: Pitchfork
ydt
dy
xxdt
dx
3
Fixed points )0,();0,();0,0(
http://www.egwald.ca/nonlineardynamics/bifurcations.php#hopfbifurcation
y
0
y
x
0
Stable StableStable
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Bifurcation in 2D: Pitchfork
ydt
dy
xxdt
dx
3
Fixed points )0,();0,();0,0(
http://www.egwald.ca/nonlineardynamics/bifurcations.php#hopfbifurcation
Jacobian
10
03 2x
1,:)0,0(
1,2:)0,(
21
21
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Bifurcation in 2D: Hopf
22
22
yxyxdt
dy
yxxydt
dx
Analyze fixed point (0,0)
Jacobian
1
1
http://www.egwald.ca/nonlineardynamics/bifurcations.php#hopfbifurcation
i
A limit cycle emerges
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Prey-Predator Holling-Tanner Model
Alexander Panfilov: Introduction to Differential Equations
Prey-Predator Holling-Tanner Model
R: predator with logistic growth competing on preys
P: preys with logistic growth limiting for resources K and with
harvesting depending on predators. When preys increases,
the harvesting saturates to a.
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Prey-Predator Holling-Tanner Model
Alexander Panfilov: Introduction to Differential Equations
Prey-Predator Holling-Tanner Model
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Prey-Predator Holling-Tanner Model
Alexander Panfilov: Introduction to Differential Equations
Prey-Predator Holling-Tanner Model
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Prey-Predator Holling-Tanner Model
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Alternative paradigms for
dynamical modelling of systems
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C.Piazza, Università di Udine http://iclp08.dimi.uniud.it/PRESENTAZIONI/Piazza.pdf
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Prof. Yechiam Yemini (YY) Columbia University
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Prof. Yechiam Yemini (YY) Columbia University
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Prof. Yechiam Yemini (YY) Columbia University
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C.Piazza, Università di Udine http://iclp08.dimi.uniud.it/PRESENTAZIONI/Piazza.pdf
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Biochemical network that controls the cell cycle progression in fission
yeast S.pombe
Davidich, Bornholdt (2008) PLoS ONE 3(2): e1672
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Biochemical network that controls the cell cycle progression in fission
yeast S.pombe
Davidich, Bornholdt (2008) PLoS ONE 3(2): e1672
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Biochemical network that controls the cell cycle progression in fission
yeast S.pombe
Davidich, Bornholdt (2008) PLoS ONE 3(2): e1672
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Biochemical network that controls the cell cycle progression in fission
yeast S.pombe
Davidich, Bornholdt
(2008) PLoS ONE
3(2): e1672
Figure 2. Network state space. State
space of the 1024 possible network
states (green circles) and their
dynamical trajectories, all converging
towards fixed point attractors. Each
circle corresponds to one specific
network state with each of the ten
proteins being in one specific
activation state (active/inactive). The
largest attractor tree corresponds to
all network states flowing to the G1
fixed point (blue node). Arrows
between the network states indicate
the direction of the dynamical flow
from one network state to its
subsequent state. The fission yeast
cell-cycle sequence is shown with
blue arrows.
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Davidich, Bornholdt (2008) PLoS ONE 3(2): e1672
Biochemical network that controls the cell cycle progression in fission
yeast S.pombe
The study indicates that the regulatory robustness of biological chemical
networks may allow for ‘‘robust’’ modeling approaches
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Regulatory network that controls formation and distruction of extra-
cellular matrix
Extracellular matrix (ECM) is the extracellular part of animal tissue that usually
provides structural support to the animal cells in addition to performing various
other important functions. The extracellular matrix is the defining feature of
connective tissue in animals. Extracellular matrix includes the interstitial matrix
and the basement membrane
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Regulatory network that controls formation and distruction of extra-
cellular matrix
Wollbold et al (2009) BMC Systems Biology 3:77
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Regulatory network that controls formation and distruction of extra-
cellular matrix
BMC Systems Biology 2009, 3:77
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Regulatory network that controls formation and distruction of extra-
cellular matrix
BMC Systems Biology 2009, 3:77
TEMPORAL MODELLING
time steps as follows:
Transcription 1 (NFKB1: 2),
Translation: 1,
mRNA lifespan: 1,
protein lifespan: 2.
Since TGFβ1 and TNFα have to be released into the extracellular medium
after translation, they were assumed to take effect three time units after
induction.
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Regulatory network that controls formation and distruction of extra-
cellular matrix
BMC Systems Biology 2009, 3:77
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Regulatory network that controls formation and distruction of extra-
cellular matrix
BMC Systems Biology 2009, 3:77
Literature derived interactions are not in agreement with new experimental
data
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Regulatory network that controls formation and distruction of extra-
cellular matrix
BMC Systems Biology 2009, 3:77
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Regulatory network that controls formation and distruction of extra-
cellular matrix
BMC Systems Biology 2009, 3:77
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Regulatory network that controls formation and distruction of extra-
cellular matrix
BMC Systems Biology 2009, 3:77
Conclusion
The analyses in the present study were based on literature
data valid for healthy human synovial fibroblasts (SFB). These
findings were fine-tuned and adapted to gene expression time course
data triggered by TGFβ1 and TNFα in SFB from RA and OA patients.
Both the assembly of previous knowledge and the adaptation of the
Boolean functions gave detailed insight into disease-related
regulatory processes. To the best of our knowledge, this is the first
dynamical model of ECM formation and degradation by human SFB.
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C.Piazza, Università di Udine http://iclp08.dimi.uniud.it/PRESENTAZIONI/Piazza.pdf
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Wikipedia: Petri net
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Firing example
2H2 + O2 2H2O
H2
O2
H2O
t
2
2
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Firing example
2H2 + O2 2H2O
H2
O2
H2O
t
2
2
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Modeling concurrency
t2
t3
t1 t4
concurrency
In computer science, concurrency is a property of systems in which several
computations are executing simultaneously, and potentially interacting with
each other.
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Simple and intuitive representation of a metabolic network:
stoichiometry of each reaction encoded by the arc weights of its
transition node.
Execution of Petri nets is nondeterministic: when multiple transitions
are enabled at the same time, any one of them may fire. If a transition is
enabled, it may fire, but it doesn't have to.
Petri nets are well suited for modeling the concurrent behavior of
distributed system
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Heiner et al, LNCS 5016, pp. 215-264, 2008.
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ODE description
Heiner et al, LNCS 5016, pp. 215-264, 2008.
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PETRI NET DESCRIPTION
Heiner et al, LNCS 5016, pp. 215-264, 2008.
NOTE that transition states (association
between enzyme and substrate) are
explicitly modeled
Sub+Enz↔ SubEnz Prod+Enz
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Heiner et al, LNCS 5016, pp. 215-264, 2008.
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Heiner et al, LNCS 5016, pp. 215-264, 2008.
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C.Piazza, Università di Udine http://iclp08.dimi.uniud.it/PRESENTAZIONI/Piazza.pdf
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C.Piazza, Università di Udine http://iclp08.dimi.uniud.it/PRESENTAZIONI/Piazza.pdf
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Regev A, Shapiro: The -calculus as an abstraction for biomolecular systems
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Regev A, Shapiro: The -calculus as an abstraction for biomolecular systems
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Regev A, Shapiro: The -calculus as an abstraction for biomolecular systems
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Regev A, Shapiro: The -calculus as an abstraction for biomolecular systems
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Regev A, Shapiro: The -calculus as an abstraction for biomolecular systems
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Stochastic Pi-Calculus
Each channel is associated with a base rate. The channel's
base rate is identical to the mesoscopic rate constant of the
corresponding elementary reaction.
At each state in the pi-calculus system we determine the
actual rate of a channel based on that channel's base rate,
and the number of input and output offers on the channel at
that state (which represent the number of reactant molecules
in the corresponding reaction).
Stochastic selection of communication according to the
probability of a reaction
The resulting state evolution of the -calculus system
corresponds to the state evolution of a (statistically
representative) trajectory of the chemical system.
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C.Piazza, Università di Udine http://iclp08.dimi.uniud.it/PRESENTAZIONI/Piazza.pdf