Professional Documents
Culture Documents
Article history: Received 5 January 2014, Accepted 3 March 2014, Published 10 March 2014.
Abstract: In this paper the analytical solution of steady state non-linear boundary value
problem in phosphoinositide dynamics is discussed. The analytical expression of the
receptor desensitization and the reaction-diffusion process of the phosphoinositide can be
obtained using Homotopy perturbation method (HPM) for various values of the relevant
parameters. In this study, the analytical results have been compared with perturbation
method and which showed that, the present approach has less computational aspect and are
applicable for solving other non-linear boundary value problem.
1. Introduction
Cellular migration is a coordinated process that resultsfrom the interaction of specific cell
surface receptorswith ligands of the extracellular matrix ~ECM. Usingwell-controlled, stable, ligand
substrates, a number ofligand properties have been shown to affect activation ofcellmotility, including,
for example, ligand surface concentration, strength of ligand–receptor adhesion, degreeof receptor
occupancy by the ligand, and ligand affinity[1].The general consensus that, the synthesis of PtdIns is
constitutive and which is the centre of major regulatory mechanisms on the subsequent generationof
the polyphosphoinositides[2]. Actin reorganization is a bidirectional process that orchestratescomplex
cellular events such as, cell migration, neurite extension and bud growth in yeast.The WASP family of
scaffoldingproteins, WASP, N-WASP and WAVE, participate in theseprocesses by relaying signals
from Rho-family GTPases to the actin remodeling machinery [3].Precise regulation of protein-protein
interaction is criticalfor determining the wiring of cellular signaling pathways [4].
Receptors are responsible for transmitting information about theexternal environment to the
cell internum, and therefore theirmechanism of activation and action must be well characterizedbefore
the details of the intracellular networks can be analyzedand modeled mathematically (signaling
network).Two-dimensional molecular gradients in cell membranesare also relevant in signal
transduction. Most signalingpathways involve specific membrane-associated intermediatesthat are
produced or activated through recruitment ofsignaling enzymes to the plasma membrane. Gradients in
thedensity of specific membrane lipids or activated lipidanchoredproteins may form on the nanometer
scale if therates of the reactions that produce them are rapid enough tobe limited by lateral diffusion
and gradients on longer length scales can form whenthe extracellular stimulus is spatially confined or
otherwiseorganized [5].
A fundamental problem of directional sensingis its exquisite sensitivity. Even in the presence
of relativelyshallow chemoattractant gradients, cell projections are extendedprecisely in the region
exposed to the highest chemoattractant concentration. This reflects the existence of a mechanism
foramplifying the external signal.A key problem in directional sensing is the elucidationof the
mechanism underlying the formation of ahighly polarized distribution of actin polymers in responseto
a mild gradient. Indeed, chemoattractant gradients imposed in the extracellular space are often
quitesmall ~1%–2% concentration change over the length of the cell.If a chemo-attractant gradient is
imposed on the cells,GFP–PH migrates within 5–10 s to the leading edge ofthe cell, and persistently
maintains this polarized distribution.This stands in sharp contrast to the results obtainedin response to a
uniform chemo-attractant concentration profile [6].Systems biology modeling of signal transduction
pathwaystraditionally employs ordinary differential equations,deterministic models based on the
assumptions of spatial homogeneity. Cell signaling is an essential, ubiquitous process thatliving
systems use to respond to the environment [7]. Distinguishing modes of Eukaryotic gradient sensing is
developed by Skupsky et.al. [8]. During directional gradient sensing, eukaryotic cells suchas
Dictyostelium and neutrophils exhibit extraordinarysensitivity to external chemical gradients.Shannon
K Hughes-Alford et.al. discussed quantitative analysis of gradient sensing [9]. Noritaka Masaki et.al.
proposed single cell level analysis of PDE expression in Dictyostelium [10].
To simulate the experiments, it is assumed that before the cell is subjected to a chemoattractant
perturbation ( t 0), it is in a homogeneous steady state, ( r10 , p , ps , i 0), corresponding to a
r10 D 2 r10
1
t 1 K l l ed K10
k 01 ea,t k10 ed K10 r10 2r (1)
R 2
p Dp 2 p
k f r10 p 2 p s k r p i c p k p p 2 (2)
t R 2
ps D p 2 ps
k f r10 p 2 p s k r p i c p k p p 2s (3)
t R 2
i
t
D 2i
s k f r10 p 2 p s k r p i ci k i i 2i
R 2
(4)
Here, Dr , D p , D ps and Di denote the lateral diffusivities of R10, P , Ps and I , and R denotes the cell
radius. The factor s , denoting membrane length per unit cell area, is required since synthesis and
removal rates of P are based on the length of the plasma membrane. Since the cell is circular,
concentrations and fluxes must be equal at 0 and 2 . Thus, we require the periodic boundary
conditions
x(0, t ) x(2 , t )
x (0, t ) x(2 , t ), ,t 0 (5)
where x r10 , p, p s , i. The initial conditions for the reduced equations are
1 K l l ed K10
t 0 ; r10 r , p p , p s pt p , i i (6)
1 K l l ed K10
10
l , is transmitted to the receptors instantaneously. Thus, r10 changes during this rapid
k f r10 pt2 c p pt kp Dp C 2
f , p , p , p (9)
k r spt kr spt k r spt k r spt
Dp s C 2 ci spt k D C2 l
p , i , i i , i i , (10)
s
k r spt k r spt k r spt k r spt Kl
p p s - i
, s
, ι (11)
pt pt spt
Where C denotes the circumference of the cell. Thus we get the dimensionless equations of (1)-(6) are
as follows:
X1 2 X1
k1 (1 X 1 ) r (12)
2
X2 2 X 2
k 2 X 1 X 2 X 3 X 2 X 4 k3 k 4 X 2 p
2
(13)
2
X3 2 X3
k 2 X 1 X 22 X 3 X 2 X 4 k 3 k 4 X 2 ps (14)
2
X4 2 X 4
k 2 X 1 X 22 X 3 X 2 X 4 k 5 k 6 X 4 r (15)
2
with initial conditions
0 , X 1 u1 , X 2 u 2 , X 3 1 u 2 and X 4 u3 (16)
01 a ,t
k1 , k 2 f , k3 p , k 4 p , k5 i , k6 i (20)
1 1 / d
u1
1 1 / d
, u 2 , u 3 ι- (21)
1 1 / ( ) d
2 X1 2 X 2 2 X 3 2 X 4
By considering 0 (22)
2 2 2 2
Then the equations (12)-(15) becomes
X1
k1 (1 X 1 ) (23)
X2
k 2 X 1 X 22 X 3 X 2 X 4 k 3 k 4 X 2 (24)
X3
k 2 X 1 X 22 X 3 X 2 X 4 k 3 k 4 X 2 (25)
X4
k 2 X 1 X 22 X 3 X 2 X 4 k 5 k 6 X 4 (26)
with the initial conditions
0 , X 1 u1 , X 2 u 2 , X 3 1 u 2 and X 4 u3 (27)
Linear and non-linear phenomena are of fundamental importance in various fields of science
and engineering. Most models of real – life problems are still very difficult to solve. Therefore,
approximate analytical solutions such as Homotopy perturbation method (HPM) [11-24] were
introduced. This method is the most effective and convenient ones for both linear and non-linear
equations. Perturbation method is based on assuming a small parameter. The majority of non-linear
problems, especially those having strong non-linearity, have no small parameters at all and the
approximate solutions obtained by the perturbation methods, in most cases, are valid only for small
values of the small parameter. Generally, the perturbation solutions are uniformly valid as long as a
scientific system parameter is small. However, we cannot rely fully on the approximations, because
there is no criterion on which the small parameter should exists. Thus, it is essential to check the
validity of the approximations numerically and/or experimentally. To overcome these difficulties,
HPM have been proposed recently.
Recently, many authors have applied the Homotopy perturbation method (HPM) to solve the
non-linear problem in physics and engineering sciences [11-14]. This method is also used to solve
some of the non-linear problem in physical sciences [15-17]. This method is a combination of
Homotopy in topology and classic perturbation techniques. Ji-Huan He used to solve the Lighthill
equation [15], the Duffing equation [16] and the Blasius equation [17-18]. The HPM is unique in its
applicability, accuracy and efficiency. The HPM uses the imbedding parameter p as a small parameter,
and only a few iterations are needed to search for an asymptotic solution. Using this method [19-24],
we can obtain solution of the eqns. (23) - (27) are as follows:
X1 (t ) (u1 1) e 1 (28)
k k
(u 3 5 ) k 3 e 6
k k k (1 u 2 ) k k k
2
32 5
k6
X 2 (t ) u 2 3 e k4 3 d1 e k4 2 3
3 k 4 (k 4 k 6 )
k4 k4 k4 k4 k6
k k
2 k 2 k 3 (1 u 2 ) (u 3 5 ) k 2 (1 u 2 ) (u 2 3 ) 2 e 2 k4
e k4 2 5
v k k6 k4
k k4 k4
6
k ( k 2 k )
2 k 1 k 2 (1 u 2 ) (u1 1) (u 2 3 ) 2 e 1 4
k (1 u 2 ) (u1 1) k 3 e k4
2
2
k 4 ( k 4 k 1 ) ( k 1 k 4 )
k k (k k ) k ( k k )
(u 2 3 ) (u 3 4 ) e 4 6 2 k 2 k 3 (1 u 2 ) (u1 1) (u 2 3 ) e 4 6
k4 k6 k4
k6 k1
(29)
k k
(u 3 5 ) k 3 e 6
u 2 k 3 e k 4 k 3 d 1 e k 4 k 2 (1 u 2 ) k 3 k 3 k 5
2
k6
k4 3 2 k (k k )
4
k k 4 k 4 k 6
4 4 6
k k
2 k 2 k 3 (1 u 2 ) (u 3 5 ) k 2 (1 u 2 ) (u 2 3 ) 2 e 2 k 4
e k4 v 2 k 5 k6
k4
k k4 k4
6
X 3 (t ) 1
k 3 2 ( k1 2 k 4 )
k (1 u 2 ) (u1 1) (u 2 ) e
k 2 (1 u 2 ) (u1 1) k 32 e k 1 2 k4
k 42 (k 4 k1 ) ( k1 k 4 )
k3 k 4 ( k 4 k6 ) k 3 ( k4 k6 )
(u 2 ) (u 3 ) e 2 k 2 k 3 (1 u 2 ) (u1 1) (u 2 ) e
k4 k6 k4
k6 k1
(30)
k k k (1 u ) k 2 k k
X 4 (t ) u 3 5 e k6 5 d 2 e k6 2 2 2 3 3 25
k6 k6 k4 k6 k4k6
k k k k ( k k )
(u 2 3 ) k 5 2 k 2 k 3 (1 u 2 ) (u 3 5 ) (u 2 3 ) (u 3 5 ) e 6 6
e k4
k4 k6 k4 k6
6
k k 4
k 6 k 4
k 4
k 2k k k
k 2 (1 u 2 ) (u 2 3 ) 2 e 4 2 k1
(u 3 5 ) k 3 t e 6
k4 k 2 (1 u 2 ) (u1 1) k 3 e
k6
( k 6 2k 4 ) k 4 ( k 6 k1 )
2
k4
(31)
k ( k 2 k 41 ) k ( k k )
k 2 (1 u 2 )(u1 1) (u 2 3 ) 2 e 2 k 2 k 3 (1 u 2 ) (u1 1) (u 2 3 ) e 1 4
k4 k4
( k 6 k1 2 k 4 ) k 4 ( k 6 k1 k 4 )
Fig. 1: Illustration of experiment for identifying the firstpolarized component in the signal transduction
pathway.
4. Numerical Simulation
The non-linear differential eqns. (23) - (27) are also solved by numerical methods using Scilab
software. Its numerical solution is compared with Homotopy perturbation method in Figs (3) – (6) and
it gives satisfactory result for all small values of the dimensionless parameters. The Scilab program is
also given in Appendix (C).
Fig. 2: The phosphoinositide cycle (a) and the model scheme (b). In the model scheme, R10 denotes
active receptors; P, I, and Ps denote the pools of membrane phosphoinositicides, cytosolic inosilol and
its phosphates, and phosphoinositicides in the endoplasmic reticulum, respectively.
Eqns.(28-31) are the new approximate analytical expressions for the ligand –bound sensitive
receptors, membrane phosphoinositicides, stored phosphoinositicides and cytosolic inosilol
phosphates. Figs 3,4 shows the evolution of the solutions when the chemoattractant concentration is
The observation from the Fig. 3, it is evident that when the dimensionless ligand concentrations
increases, the corresponding concentrations X 1 and X 2 increases. Whereas, the dimensionless
concentration stored phosphoinositicides X 3 and the dimensionless inositol phosphates X 4 versus the
dimensionless time were represented in Fig. 4.
From the Fig. 4, it is inferred that, when the dimensionless ligand concentration increases,
there was a correspond decrease in the concentration of X 3 , and the concentrations of X 4 increases
observed that the concentration of membrane phosphoinositicides and cytosolic inosilol phosphates are
coinciding with respect to the ligand concentration.
phosphoinositides X 2 , the stored phosphoinositicides X 3 and the inositol phosphates X 4 versus the
dimensionless time . The curve is plotted for the various values of dimensionless ligand
concentration , when 200 and 1000.
6. Conclusions
It has been observed and concluded that, a reaction-diffusion model based on the kinetics of the
phosphoinositicides cycle captures and explains many of the phosphoinositicides dynamics associated
with directional sensing in cell migration. The analytical expressions of the dimensionless
concentrations of ligand-bound sensitive receptors, membrane phosphoinositicides, stored
phosphoinositicides in endoplasmic reticulum and inosilol phosphates for all the small values of the
corresponding dimensionless parameters. The analytical results are compared to the numerical
simulations. The HPM is an extremely simple compared to other method and it is also a promising
method to solve other non-linear equations. This method can be easily extended to find the solution of
all other non-linear equations.
Acknowledgement
The authors are thankful to Shri. S. Natanagopal, Secretary, Madura College Board, Madurai
and Dr. R. Murali, The Principal for their constant encouragement.
References
[1] JanesS. Tjia and Prabhas V. Moghe, Cell Migration on Cell-Internalizable Ligand Microdepots:
A Phenomenological Model, Annals of Biomedical Engineering, 30(2002):851–866.
[2] Samer J. Nuwayhid, Martha Vega, Paul D. Walden, Marie E. Monaco1,Regulation of de novo
phosphatidylinositol synthesisThe WRP component of the WAVE-1complex attenuates Rac-
mediated signaling, Journal of lipid research, 47 (2006): 1449-1456.
[3] Scott H. Soderling, Kathleen L. Binns, Gary A. Wayman, Stephen M. Davee, Siew Hwa Ong,
Tony Pawson, John D. ScottThe WRP component of the WAVE-1complex attenuates Rac-
mediated signaling, Nature cell Biology,4 (2003): 970-975.
[4] Nathan A. Sallee, Brian J. Yeh, and Wendell A. Lim, Engineering Modular ProteinInteraction
Switches bySequence Overlap, Biophysical Journal, 86 (2004): 589–598.
[5] Jason M. Haugh and Ian C. Schneider, Spatial Analysis of 39 Phosphoinositide Signaling in
Living Fibroblasts: I. Uniform Stimulation Model and Bounds on Dimensionless Groups,Bio
Physical Journal, 86 (2004): 589-598.
[6] Atulnarang, K. K. Subramanian,and D. A. Lauffenburger, A Mathematical Model for
Chemoattractant Gradient Sensing Based on Receptor-Regulated Membrane
PhospholipidSignaling Dynamics, Annals of Biomedical Engineering, 29 (2001): 677-691.
Appendix A
Basic concept of Homotopy perturbation method [11-24]
To explain this method, let us consider the following function:
Do (u) f (r ) 0, r (A. 1)
with the boundary conditions of
u
Bo (u, ) 0, r (A. 2)
n
where Do is a general differential operator, Bo is a boundary operator, f (r ) is a known analytical
function and is the boundary of the domain . In general, the operator Do can be divided into a
linear part L and a non-linear part N . Eq. (A.1) can therefore be written as
L(u) N (u) f (r ) 0 (A. 3)
By the Homotopy technique, we construct a Homotopy v(r, p) : [0,1] that satisfies
H (v, p) (1 p)[ L(v) L(u0 )] p[ Do (v) f (r )] 0. (A. 4)
wherep [0, 1] is an embedding parameter, and u 0 is an initial approximation of Eq. (A. 1) that
satisfies the boundary conditions. From Eq. (A.4) and Eq. (A.5), we have
H (v,0) L(v) L(u0 ) 0 (A. 6)
We first use the embedding parameter p as a “small parameter” and assume that the solutions of Eq.
(A.4) and Eq. (A.5) can be written as a power series in p :
Appendix B
Solution of the boundary value problem eqns. (23) - (27) using Homotopy perturbation method.
In this Appendix, we indicate how eqns. (28) - (31) are derived in this paper. Solving eqns. (23) and
(27) we get the solution is
X 1 (u1 1) e 1 (B.1)
To find the solution of the eqns. (24) – (27), we construct the Homotopy as follows:
dX dx
(1 p) 2 k 4 X 2 k 3 p 2 k 4 X 2 k 2 X 1 X 22 X 3 X 2 X 4 k 3 0 (B.2)
dt dt
dX dX
(1 p) 3 k 4 X 2 k 3 p 3 k 4 X 2 k 2 X 1 X 22 X 3 X 2 X 4 k 3 0 (B.3)
dt dt
dX dX
(1 p) 4 k 6 X 4 k 5 p 4 k 6 X 4 k 2 X 1 X 22 X 3 X 2 X 4 k 5 0 (B.4)
dt dt
The analytical solutions of (B.2), (B.3) and (B.4) is
X 2 X 200 p X 211 p 2 X 222 .......... (B.5)
Substituting the eqns. (B.5), (B.6) and (B.7) in (B.2), (B.3) and (B.4) respectively we get
d ( X 200 p X 211 p 2 X 222 .....)
(1 p ) k 4 ( X 200 p X 211 p 2 X 222 .....) k 3
dt
d ( X 200 p X 211 p 2 X 222 .....)
k 4 ( X 200 p X 211 p 2 X 222 .....)
dt
(B.8)
p k 2 X 1 ( X 200 p X 211 p X 222 .....) ( X 300 p X 311 p X 322 .....) 0
2 2 2
( X 200 p X 211 p 2 X 222 .....)( X 400 p X 411 p 2 X 422 .....) k 3
d X 20
p0 : k 40 X 20 k 3 0 (B.11)
dt
d X 30
p0 : k3 0 (B.12)
dt
dX 40
p0 : k 60 X 40 k 5 0 (B.13)
dt
dX 21
p1 : k 4 X 21 k 2 X 1 X 220 X 30 X 20 X 40 (B.14)
dt
dX 31
p1 : k 4 X 21 k 2 X 1 x220 X 30 X 20 X 40 (B.15)
dt
dx41
p1 : k 6 x21 k 2 x1 x220 x30 x20 x40 (B.16)
dt
The initial approximations are as follows
X 10 (0) u1 , X 20 (0) u 2 , X 30 (0) 1 u 2 and X 40 (0) u3 (B.17)
k k
X 20 u 2 3 e k 4 3 (B.19)
k4 k4
k5
2 k k (1 u ) (u )
2 2 3 2 3
32 5 t e k4 2 5 6
k (1 u ) k k k v k k
X 21 d1 e k4 2 2 3
3 k k
k4 k4 k6
6 4
k 2 2 k k k
k 2 (1 u 2 ) (u 2 3 ) e 4 (u3 5 ) k 3 e 6
k 2 (1 u 2 ) (u1 1) k 3 e
2 k
1 k6
k4
k4 k 4 (k 4 k1 )
2 k (k k )
4 4 6
k 2 ( k 2 k ) k k ( k k )
k 2 (1 u 2 ) (u1 1) (u 2 3 ) e 1 4 (u 2 3 ) (u 3 4 ) e 4 6
k4 k4 k6
(k1 k 4 ) k6
k ( k k )
2 k 2 k 3 (1 u 2 ) (u1 1) (u 2 3 ) e 4 6
k4
k1
(B.20)
Where
k
k 2 (1 u 2 ) (u 2 3 ) 2
k k
k 2 (1 u 2 ) k 32 k 4 k 2 (1 u 2 ) (u1 1) k 32
d1 32 5
k 43 k 2
4 6
k k 4
k 4 ( k 4 k1 )
k k k k
(u 3 5 ) k 3 k 2 (1 u 2 ) (u1 1) (u 2 3 ) 2 (u 2 3 ) (u 3 4 )
k6 k4 k4 k6
k (k k ) (k1 k 4 ) k6
4 4 6
k
2 k 2 k 3 (1 u 2 ) (u1 1) (u 2 3 )
k4
k1
(B.21)
dX 2 dX 3
Since 0, we get
d d
X 3 1 X 2 (B.22)
k k
X 40 u3 5 e k6 5 (B.23)
k6 k6
k3 k5
(u ) k 2 k k (1 u ) ( u )
k 2 (1 u 2 ) k 32 k 3 k 5 e k4
2 5 2 3 2 3
k6 k4 k6
X 41 d 2 e
2
k 42 k 6
k 4 6 6
k k k 4 k6 k4
k 2k k5 k6
k 2 (1 u 2 ) (u 2 3 ) 2 e 4 (u ) k e
k4 k 2 (1 u 2 ) (u1 1) k 3 e 1
2 k 3
k6
3
( k 6 2k 4 ) k 4 (k 6 k1 )
2 k4
k ( k 2 k 41 )
k 2 (1 u 2 )(u1 1) (u 2 3 ) 2 e
k4
(k 6 k1 2 k 4 )
k ( k k ) k k ( k k )
2 k 2 k 3 (1 u 2 ) (u1 1) (u 2 3 ) e 1 4 (u 2 3 ) (u 3 5 ) e 6 6
k4 k4 k6 (B.24)
k 4 (k 6 k1 k 4 ) k4
where
k k
(u 2 3 ) k 5 2 k 2 k 3 (1 u 2 ) (u 3 5 )
k k 1
k 2 (1 u 2 ) k 32 k4 k6
d 2 3 25
k4k6 k 42 k 6 k6 k4 k6 k4
k k k t
k 2 (1 u 2 ) (u 2 3 ) 2 (u 3 5 ) k 3 t e 6
k 4 k 2 (1 u 2 ) (u1 1) k 3
2
k6
( k 6 2k 4 ) k 4 (k 6 k1 )
2 k4
k k
k 2 (1 u 2 )(u1 1) (u 2 3 ) 2 2 k 2 k 3 (1 u 2 ) (u1 1) (u 2 3 )
k4 k4
(k 6 k1 2 k 4 ) k 4 (k 6 k1 k 4 )
k k
(u 2 3 ) (u 3 5 )
k4 k6
k4
(B.25)
According to the HPM, we can conclude that
X 2 lim X 2 (t ) X 20 0 X 211 (B.26)
p1
X3 1 X 2 (B.27)
Appendix C
Scilab program to find the solutions of the Equations (23)-(27)
function
options= odeset('RelTol',1e-6,'Stats','on');
%initial conditions
x0 = [10.08174387; .1; .9; .1];
tspan = [0,200];
tic
[t,x] = ode45(@TestFunction,tspan,x0,options);
toc
figure
hold on
%plot(t, x(:,1))
%plot(t, x(:,2))
plot(t, x(:,3))
%plot(t, x(:,4))
legend('x','y','z')
ylabel('x')
xlabel('t')
return
function [dx_dt]= TestFunction(t,x)
k1=.09523809524;k2=1.1;k3=.01;k4=.1;k5=.01;k6=.11;
dx_dt(1)=k1*(1-x(1));
dx_dt(2)=k2*x(1)*x(2)^2*x(3)-x(2)*x(4)+k3-k4*x(2);
dx_dt(3)=-(k2*x(1)*x(2)^2*x(3)-x(2)*x(4)+k3-k4*x(2));
dx_dt(4)=k2*x(1)*x(2)^2*x(3)-x(2)*x(4)+k5-k6*x(4);
dx_dt = dx_dt';
return
Appendix D
Nomenclature
Symbols Meaning
aij Rate constants for association of E a or E d with Rij
al Rate constants for association of Rij with L
ci Basal synthesis rate of synthesis of inosital phosphates
c Circumference of the cell
Di Lateral diffusivity of inosital phosphates
Dp Lateral diffusivity of phoshoinositides in plasma membrane