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**PROGRAMMING BIOLOGICAL CELLS
**

by

Jomar F. Rabajante

A master’s thesis submitted to the

Institute of Mathematics

College of Science

University of the Philippines

Diliman, Quezon City

as partial fulfillment of the

requirements for the degree of

Master of Science in Applied Mathematics

(Mathematics in Life and Physical Sciences)

April 2012

This is to certify that this Master’s Thesis entitled “Mathematical Strategies for

Programming Biological Cells”, prepared and submitted by Jomar F. Rabajante

to fulﬁll part of the requirements for the degree of Master of Science in Applied

Mathematics, was successfully defended and approved on March 23, 2012.

Cherryl O. Talaue, Ph.D.

Thesis Co-Adviser

Baltazar D. Aguda, Ph.D.

Thesis Co-Adviser

Carlene P. Arceo, Ph.D.

Thesis Reader

The Institute of Mathematics endorses the acceptance of this Master’s Thesis as partial

fulﬁllment of the requirements for the degree of Master of Science in Applied Mathematics

(Mathematics in Life and Physical Sciences).

Marian P. Roque, Ph.D.

Director

Institute of Mathematics

This Master’s Thesis is hereby oﬃcially accepted as partial fulﬁllment of the requirements

for the degree of Master of Science in Applied Mathematics (Mathematics in Life and

Physical Sciences).

Jose Maria P. Balmaceda, Ph.D.

Dean, College of Science

Brief Curriculum Vitae

09 October 1984 Born, Sta. Cruz, Laguna, Philippines

1997-2001 Don Bosco High School, Sta. Cruz, Laguna

2006 B.S. Applied Mathematics

(Operations Research Option)

University of the Philippines Los Ba˜ nos

2006-2008 Corporate Planning Assistant

Insular Life Assurance Co. Ltd.

2008 Professional Service Staﬀ

International Rice Research Institute

2008-present Instructor, Mathematics Division

Institute of Mathematical Sciences and Physics

University of the Philippines Los Ba˜ nos

PUBLICATIONS

• Rabajante, J.F., Figueroa, R.B. Jr. and Jacildo, A.J. 2009. Modeling the

area restrict searching strategy of stingless bees, Trigona biroi, as a quasi-

random walk process. Journal of Nature Studies, 8(2): 15-21.

• Esteves, R.J.P., Villadelrey, M.C. and Rabajante, J.F. 2010. Determining

the optimal distribution of bee colony locations to avoid overpopulation us-

ing mixed integer programming. Journal of Nature Studies, 9(1): 79-82.

• Castilan, M.G.D., Naanod, G.R.K., Otsuka, Y.T. and Rabajante, J.F. 2011.

From Numbers to Nature. Journal of Nature Studies, 9(2)/10(1): 35-39.

• Tambaoan, R.S., Rabajante, J.F., Esteves, R.J.P. and Villadelrey, M.C. 2011.

Prediction of migration path of a colony of bounded-rational species foraging

on patchily distributed resources. Advanced Studies in Biology, 3(7): 333-345.

iii

Table of Contents

Acknowledgments . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . vii

Abstract . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ix

List of Figures . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . xiv

Chapter 1. Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1

Chapter 2. Preliminaries

Biology of Cellular Programming . . . . . . . . . . . . . . . . . . . . 4

2.1 Stem cells in animals . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4

2.2 Transcription factors and gene expression . . . . . . . . . . . . . . . . . . 8

2.3 Biological noise and stochastic diﬀerentiation . . . . . . . . . . . . . . . . 10

Chapter 3. Preliminaries

Mathematical Models of Gene Networks . . . . . . . . . . . . . . . . 12

3.1 The MacArthur et al. GRN . . . . . . . . . . . . . . . . . . . . . . . . . 13

3.2 ODE models representing GRN dynamics . . . . . . . . . . . . . . . . . . 15

3.2.1 Cinquin and Demongeot ODE formalism . . . . . . . . . . . . . . 16

3.2.2 ODE model by MacArthur et al. . . . . . . . . . . . . . . . . . . 19

3.3 Stochastic Diﬀerential Equations . . . . . . . . . . . . . . . . . . . . . . 20

Chapter 4. Preliminaries

Analysis of Nonlinear Systems . . . . . . . . . . . . . . . . . . . . . . 22

4.1 Stability analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24

4.2 Bifurcation analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27

4.3 Fixed point iteration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28

4.4 Sylvester resultant method . . . . . . . . . . . . . . . . . . . . . . . . . . 30

4.5 Numerical solution to SDEs . . . . . . . . . . . . . . . . . . . . . . . . . 33

Chapter 5. Results and Discussion

Simpliﬁed GRN and ODE Model . . . . . . . . . . . . . . . . . . . . 35

5.1 Simpliﬁed MacArthur et al. model . . . . . . . . . . . . . . . . . . . . . 35

5.2 The generalized Cinquin-Demongeot ODE model . . . . . . . . . . . . . 38

5.3 Geometry of the Hill function . . . . . . . . . . . . . . . . . . . . . . . . 41

5.4 Positive invariance . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 46

5.5 Existence and uniqueness of solution . . . . . . . . . . . . . . . . . . . . 52

iv

Chapter 6. Results and Discussion

Finding the Equilibrium Points . . . . . . . . . . . . . . . . . . . . . 57

6.1 Location of equilibrium points . . . . . . . . . . . . . . . . . . . . . . . . 57

6.2 Cardinality of equilibrium points . . . . . . . . . . . . . . . . . . . . . . 60

6.2.1 Illustration 1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 67

6.2.2 Illustration 2 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 68

Chapter 7. Results and Discussion

Stability of Equilibria and Bifurcation . . . . . . . . . . . . . . . . . . 73

7.1 Stability of equilibrium points . . . . . . . . . . . . . . . . . . . . . . . . 73

7.2 Bifurcation of parameters . . . . . . . . . . . . . . . . . . . . . . . . . . 81

Chapter 8. Results and Discussion

Introduction of Stochastic Noise . . . . . . . . . . . . . . . . . . . . . 85

Chapter 9. Summary and Recommendations . . . . . . . . . . . . . . . . . . . . 100

Appendix A. More on Equilibrium Points: Illustrations . . . . . . . . . . . . . . . 106

A.1 Assume n = 2, c

i

= 1, c

ij

= 1 . . . . . . . . . . . . . . . . . . . . . . . . 107

A.1.1 Illustration 1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 108

A.1.2 Illustration 2 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 109

A.1.3 Illustration 3 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 111

A.1.4 Illustration 4 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 112

A.2 Assume n = 2, c

i

= 2 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 113

A.2.1 Illustration 1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 113

A.2.2 Illustration 2 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 115

A.2.3 Illustration 3 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 116

A.2.4 Illustration 4 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 116

A.2.5 Illustration 5 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 116

A.3 Assume n = 3 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 116

A.3.1 Illustration 1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 116

A.3.2 Illustration 2 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 117

A.3.3 Illustration 3 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 117

A.3.4 Illustration 4 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 117

A.3.5 Illustration 5 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 117

A.3.6 Illustration 6 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 118

A.3.7 Illustration 7 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 118

A.3.8 Illustration 8 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 122

A.4 Ad hoc geometric analysis . . . . . . . . . . . . . . . . . . . . . . . . . . 124

A.5 Phase portrait with inﬁnitely many equilibrium points . . . . . . . . . . 127

Appendix B. Multivariate Fixed Point Algorithm . . . . . . . . . . . . . . . . . . 128

v

Appendix C. More on Bifurcation of Parameters:

Illustrations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 131

C.1 Adding g

i

> 0, Illustration 1 . . . . . . . . . . . . . . . . . . . . . . . . . 131

C.2 Adding g

i

> 0, Illustration 2 . . . . . . . . . . . . . . . . . . . . . . . . . 132

C.3 g

i

as a function of time . . . . . . . . . . . . . . . . . . . . . . . . . . . . 134

C.3.1 As a linear function . . . . . . . . . . . . . . . . . . . . . . . . . . 134

C.3.2 As an exponential function . . . . . . . . . . . . . . . . . . . . . . 137

C.4 The eﬀect of γ

ij

. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 138

C.5 Bifurcation diagrams . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 138

C.5.1 Illustration 1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 139

C.5.2 Illustration 2 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 144

C.5.3 Illustration 3 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 145

Appendix D. Scilab Program for Euler-Maruyama . . . . . . . . . . . . . . . . . . 147

List of References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 149

vi

Acknowledgments

I owe my deepest gratitude to those who made this thesis possible:

To Dr. Baltazar D. Aguda from the National Cancer Institute, USA for providing

the thesis topic, for imparting knowledge about models of cellular regulation, for sim-

plifying the MacArthur et al. (2008) GRN, for giving his valuable time to answer my

questions despite long distance communication, and for his patience, unselﬁsh guidance

and encouragement;

To Dr. Cherryl O. Talaue for her all-out support, for spending time checking my

proofs and editing my manuscript, for granting my requests to write recommendation

letters, for the guidance, for the encouragement, and for always being available;

To Dr. Carlene P. Arceo for doing the proofreading of my thesis manuscript despite

her being on sabbatical leave, and to the members of my thesis panel for the constructive

criticisms;

To Mr. Mark Jayson V. Cortez and Ms. Jenny Lynn B. Carigma for checking my

manuscript for grammatical and style errors as well as for the motivation;

To the University of the Philippines Los Ba˜ nos (UPLB) and to the Math Division,

Institute of Mathematical Sciences and Physics (IMSP), UPLB for allowing me to go on

study leave with pay;

To Dr. Virgilio P. Sison, the Director of IMSP, for all the support and for being the

co-maker in my DOST scholarship contract;

To Prof. Ariel L. Babierra, the Head of the Math Division, IMSP and to Dr. Editha

C. Jose for the invaluable suggestions, help and encouragement;

To the Philippine Council for Industry, Energy and Emerging Technology Research

and Development (PCIEERD), Department of Science and Technology (DOST) for the

generous ﬁnancial support; and

To my family for the inspiration, and to El Elyon for the unwavering strength.

vii

Abstract

Mathematical Strategies for Programming Biological Cells

Jomar F. Rabajante Co-Adviser:

University of the Philippines, 2012 Cherryl O. Talaue, Ph.D.

Co-Adviser:

Baltazar D. Aguda, Ph.D.

In this thesis, we study a phenomenological gene regulatory network (GRN) of a mes-

enchymal cell diﬀerentiation system. The GRN is composed of four nodes consisting of

pluripotency and diﬀerentiation modules. The diﬀerentiation module represents a circuit

of transcription factors (TFs) that activate osteogenesis, chondrogenesis, and adipogen-

esis.

We investigate the dynamics of the GRN using Ordinary Diﬀerential Equations (ODE).

The ODE model is based on a non-binary simultaneous decision model with autocatal-

ysis and mutual inhibition. The simultaneous decision model can represent a cellular

diﬀerentiation process that involves more than two possible cell lineages. We prove some

mathematical properties of the ODE model such as positive invariance and existence-

uniqueness of solutions. We employ geometric techniques to analyze the qualitative

behavior of the ODE model.

We determine the location and the maximum number of equilibrium points given

a set of parameter values. The solutions to the ODE model always converge to a stable

equilibrium point. Under some conditions, the solution may converge to the zero state.

We are able to show that the system can induce multistability that may give rise to

co-expression or to domination by some TFs.

We illustrate cases showing how the behavior of the system changes when we vary

viii

some of the parameter values. Varying the values of some parameters, such as the degra-

dation rate and the amount of exogenous stimulus, can decrease the size of the basin of

attraction of an undesirable equilibrium point as well as increase the size of the basin of

attraction of a desirable equilibrium point. A suﬃcient change in some parameter values

can make a trajectory of the ODE model escape an inactive or a dominated state.

Suﬃcient amounts of exogenous stimuli aﬀect the potency of cells. The introduc-

tion of an exogenous stimulus is a possible strategy for controlling cell fate. A dominated

TF can exceed a dominating TF by adding a corresponding exogenous stimulus. More-

over, increasing the amount of exogenous stimulus can shutdown multistability of the

system such that only one stable equilibrium point remains.

We observe the case where a random noise is present in our system. We add a

Gaussian white noise term to our ODE model making the model a system of stochastic

DEs. Simulations reveal that it is possible for cells to switch lineages when the system is

multistable. We are able to show that a sole attractor can regulate the eﬀect of moderate

stochastic noise in gene expression.

ix

List of Figures

1.1 Analysis of mesenchymal cell diﬀerentiation system. . . . . . . . . . . . 3

2.1 Stem cell self-renewal, diﬀerentiation and programming. This diagram

illustrates the abilities of stem cells to ploriferate through self-renewal,

diﬀerentiate into specialized cells and reprogram towards other cell types. 5

2.2 Priming and diﬀerentiation. Colored circles represent genes or TFs. The

sizes of the circles determine lineage bias. Priming is represented by col-

ored circles having equal sizes. The largest circle governs the possible

phenotype of the cell. [70] . . . . . . . . . . . . . . . . . . . . . . . . . . 7

2.3 The ﬂow of information. The blue solid lines represent general ﬂow and

the blue dashed lines represent special (possible) ﬂow. The red dotted

lines represent the impossible ﬂow as postulated in the Central Dogma of

Molecular Biology [41]. . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9

2.4 C. Waddington’s epigenetic landscape — “creode” [168]. . . . . . . . . . 11

3.1 The coarse-graining of the diﬀerentiation module. The network in (a) is

simpliﬁed into (b), where arrows indicate up-regulation (activation) while

bars indicate down-regulation (repression). [113] . . . . . . . . . . . . . . 13

3.2 The MacArthur et al. [113] mesenchymal gene regulatory network. Arrows

indicate up-regulation (activation) while bars indicate down-regulation (re-

pression). . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14

3.3 Gene expression or the concentration of the TFs can be represented by a

state vector, e.g. ([X

1

], [X

2

], [X

3

], [X

4

]) [70]. For example, TFs of equal

concentration can be represented by a vector with equal components, such

as (2.4, 2.4, 2.4, 2.4). . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15

3.4 Hierarchic decision model and simultaneous decision model. Bars repre-

sent repression or inhibition, while arrows represent activation. [36]. . . . 17

x

4.1 The slope of F(X) at the equilibrium point determines the linear stability.

Positive gradient means instability, negative gradient means stability. If

the gradient is zero, we look at the left and right neighboring gradients.

Refer to the Insect Outbreak Model: Spruce Budworm in [122]. . . . . . 26

4.2 Sample bifurcation diagram showing saddle-node bifurcation. . . . . . . . 28

4.3 An illustration of cobweb diagram. . . . . . . . . . . . . . . . . . . . . . 29

5.1 The original MacArthur et al. [113] mesenchymal gene regulatory network. 35

5.2 Possible paths that result in positive feedback loops. Shaded boxes denote

that the path repeats. . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36

5.3 The simpliﬁed MacArthur et al. GRN . . . . . . . . . . . . . . . . . . . . 37

5.4 Graph of the univariate Hill function when c

i

= 1. . . . . . . . . . . . . . 42

5.5 Possible graphs of the univariate Hill function when c

i

> 1. . . . . . . . . 43

5.6 The graph of Y = H

i

([X

i

]) shrinks as the value of K

i

+

n

j=1,j=i

γ

ij

[X

j

]

c

ij

increases. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 44

5.7 The Hill curve gets steeper as the value of autocatalytic cooperativity c

i

increases. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 44

5.8 The graph of Y = H

i

([X

i

]) is translated upwards by g

i

units. . . . . . . . 45

5.9 The 3-dimensional curve induced by H

i

([X

1

], [X

2

]) + g

i

and the plane in-

duced by ρ

i

[X

i

], an example. . . . . . . . . . . . . . . . . . . . . . . . . . 46

5.10 The intersections of Y = ρ

i

[X

i

] and Y = H

i

([X

i

]) +g

i

with varying values

of K

i

+

n

j=1,j=i

γ

ij

[X

j

]

c

ij

, an example. . . . . . . . . . . . . . . . . . . . 47

5.11 The possible number of intersections of Y = ρ

i

[X

i

] and Y = H

i

([X

i

]) +g

i

where c

i

= 1 and g

i

= 0. The value of K

i

+

n

j=1,j=i

γ

ij

[X

j

]

c

ij

is ﬁxed. . . 49

5.12 The possible number of intersections of Y = ρ

i

[X

i

] and Y = H

i

([X

i

]) +g

i

where c

i

= 1 and g

i

> 0. The value of K

i

+

n

j=1,j=i

γ

ij

[X

j

]

c

ij

is ﬁxed. . . 49

5.13 The possible number of intersections of Y = ρ

i

[X

i

] and Y = H

i

([X

i

]) +g

i

where c

i

> 1 and g

i

= 0. The value of K

i

+

n

j=1,j=i

γ

ij

[X

j

]

c

ij

is ﬁxed. . . 50

5.14 The possible number of intersections of Y = ρ

i

[X

i

] and Y = H

i

([X

i

]) +g

i

where c

i

> 1 and g

i

> 0. The value of K

i

+

n

j=1,j=i

γ

ij

[X

j

]

c

ij

is ﬁxed. . . 50

xi

5.15 Finding the univariate ﬁxed points using cobweb diagram, an example.

We deﬁne the ﬁxed point as [X

i

] satisfying H([X

i

]) +g

i

= ρ

i

[X

i

]. . . . . . 51

5.16 The curves are rotated making the line Y = ρ

i

[X

i

] as the horizontal axis.

Positive gradient means instability, negative gradient means stability. If

the gradient is zero, we look at the left and right neighboring gradients. . 51

5.17 When g

i

= 0, [X

i

] = 0 is a component of a stable equilibrium point. . . . 56

5.18 When g

j

> 0, [X

j

] = 0 will never be a component of an equilibrium point. 56

6.1 Sample numerical solution in time series with the upper bound and lower

bound. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 60

6.2 Y =

[X

i

]

c

i

K+[X

i

]

c

i

will never touch the point (1, 1) for 1 < c

i

< ∞. . . . . . . . 70

6.3 An example where ρ

i

(K

i

1/c

i

) > β

i

; Y = H

i

([X

i

]) and Y = ρ

i

[X

i

] only

intersect at the origin. . . . . . . . . . . . . . . . . . . . . . . . . . . . . 71

7.1 When g

i

= 0, c

i

= 1 and the decay line is tangent to the univariate Hill

curve at the origin, then the origin is a saddle. . . . . . . . . . . . . . . . 76

7.2 Varying the values of parameters may vary the size of the basin of at-

traction of the lower-valued stable intersection of Y = H

i

([X

i

]) + g

i

and

Y = ρ

i

[X

i

]. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 77

7.3 The possible number of intersections of Y = ρ

i

[X

i

] and Y = H

i

([X

i

]) +g

i

where c > 1 and g = 0. The value of K

i

+

n

j=1,j=i

γ

ij

[X

j

]

c

ij

is taken as a

parameter. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 78

7.4 The possible topologies when Y = H

i

([X

i

]) essentially lies below the decay

line Y = ρ

i

[X

i

], g

i

= 0. . . . . . . . . . . . . . . . . . . . . . . . . . . . . 79

7.5 The origin is unstable while the points where [X

i

]

∗

=

β

ρ

−K−

n

j=1,j=i

[X

j

]

∗

are stable. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 81

7.6 Increasing the value of g

i

can result in an increased value of [X

i

] where

Y = H

i

([X

i

]) +g

i

and Y = ρ

i

([X

i

]) intersects. . . . . . . . . . . . . . . . 83

7.7 Increasing the value of g

i

can result in an increased value of [X

i

]

∗

, and

consequently in decreased value of [X

j

] where Y = H

j

([X

j

]) + g

j

and

Y = ρ

j

([X

j

]) intersects, j = i. . . . . . . . . . . . . . . . . . . . . . . . . 84

xii

8.1 For Illustration 1; ODE solution and SDE realization with G(X) = 1. . . 88

8.2 For Illustration 1; ODE solution and SDE realization with G(X) = X. . 88

8.3 For Illustration 1; ODE solution and SDE realization with G(X) =

√

X. 89

8.4 For Illustration 1; ODE solution and SDE realization with G(X) = F(X). 89

8.5 For Illustration 1; ODE solution and SDE realization using the random

population growth model. . . . . . . . . . . . . . . . . . . . . . . . . . . 90

8.6 For Illustration 2; ODE solution and SDE realization with G(X) = 1. . . 92

8.7 For Illustration 2; ODE solution and SDE realization with G(X) = X. . 92

8.8 For Illustration 2; ODE solution and SDE realization with G(X) =

√

X. 93

8.9 For Illustration 2; ODE solution and SDE realization with G(X) = F(X). 93

8.10 For Illustration 2; ODE solution and SDE realization using the random

population growth model. . . . . . . . . . . . . . . . . . . . . . . . . . . 94

8.11 For Illustration 3; ODE solution and SDE realization with G(X) = 1. . . 96

8.12 For Illustration 3; ODE solution and SDE realization with G(X) = X. . 96

8.13 For Illustration 3; ODE solution and SDE realization with G(X) =

√

X. 97

8.14 For Illustration 3; ODE solution and SDE realization with G(X) = F(X). 97

8.15 For Illustration 3; ODE solution and SDE realization using the random

population growth model. . . . . . . . . . . . . . . . . . . . . . . . . . . 98

8.16 Phase portrait of [X

1

] and [X

2

]. . . . . . . . . . . . . . . . . . . . . . . . 98

8.17 Reactivating switched-oﬀ TFs by introducing random noise where G(X) = 1. 99

9.1 The simpliﬁed MacArthur et al. GRN . . . . . . . . . . . . . . . . . . . . 100

A.1 Intersections of F

1

, F

2

and zero-plane, an example. . . . . . . . . . . . . 106

A.2 The intersection of Y = H

1

([X

1

]) + 1 and Y = 10[X

1

] with [X

2

] = 1.001

and [X

3

] = 0. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 125

A.3 The intersection of Y = H

2

([X

2

]) and Y = 10[X

2

] with [X

1

] = 0.10103

and [X

3

] = 0. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 126

A.4 The intersection of Y = H

3

([X

3

]) and Y = 10[X

3

] with [X

1

] = 0.10103

and [X

2

] = 1.001. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 126

A.5 A sample phase portrait of the system with inﬁnitely many non-isolated

equilibrium points. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 127

xiii

C.1 Determining the adequate g

1

> 0 that would give rise to a sole equilibrium

point where [X

1

]

∗

> [X

2

]

∗

. . . . . . . . . . . . . . . . . . . . . . . . . . . 133

C.2 An example where without g

1

, [X

1

]

∗

= 0. . . . . . . . . . . . . . . . . . . 135

C.3 [X

1

]

∗

escaped the zero state because of the introduction of g

1

which is a

decaying linear function. . . . . . . . . . . . . . . . . . . . . . . . . . . . 136

C.4 An example of shifting from a lower stable component to a higher stable

component through adding g

i

(t) = −υ

i

t +g

i

(0). . . . . . . . . . . . . . . 136

C.5 [X

1

]

∗

escaped the zero state because of the introduction of g

1

which is a

decaying exponential function. . . . . . . . . . . . . . . . . . . . . . . . . 137

C.6 Parameter plot of γ, an example. . . . . . . . . . . . . . . . . . . . . . . 138

C.7 Intersections of Y = ρ

i

[X

i

] and Y = H

i

([X

i

]) +g

i

where c > 1 and g = 0;

and an event of bifurcation. . . . . . . . . . . . . . . . . . . . . . . . . . 139

C.8 Saddle node bifurcation; β

1

is varied. . . . . . . . . . . . . . . . . . . . . 140

C.9 Saddle node bifurcation; K

1

is varied. . . . . . . . . . . . . . . . . . . . . 141

C.10 Saddle node bifurcation; ρ

1

is varied. . . . . . . . . . . . . . . . . . . . . 141

C.11 Cusp bifurcation; β

1

and g

1

are varied. . . . . . . . . . . . . . . . . . . . 142

C.12 Cusp bifurcation; K

1

and c are varied. . . . . . . . . . . . . . . . . . . . 142

C.13 Cusp bifurcation; K

1

and g

1

are varied. . . . . . . . . . . . . . . . . . . . 143

C.14 Cusp bifurcation; ρ

1

and g

1

are varied. . . . . . . . . . . . . . . . . . . . 143

C.15 Saddle node bifurcation; ρ

2

is varied. . . . . . . . . . . . . . . . . . . . . 144

C.16 Saddle node bifurcation; g

2

is varied. . . . . . . . . . . . . . . . . . . . . 145

C.17 Saddle node bifurcation; ρ

2

is varied. . . . . . . . . . . . . . . . . . . . . 146

C.18 Saddle node bifurcation; g

2

is varied. . . . . . . . . . . . . . . . . . . . . 146

xiv

Chapter 1

Introduction

The ﬁeld of Biomathematics has proven to be useful and essential for understanding

the behavior and control of dynamic biological interactions. These interactions span a

wide spectrum of spatio-temporal scales — from interacting chemical species in a cell to

individual organisms in a community, and from fast interactions occurring within seconds

to those that slowly progress in years. Mathematical and in silico models enable scientists

to generate quantitative predictions that may serve as initial input for testing biological

hypotheses to minimize trial and error, as well as to investigate complex biological systems

that are impractical or infeasible to study through in situ and in vitro experiments.

One classic question that scientists want to answer is how simple cells generate com-

plex organisms. In this study, we are interested in the analysis of gene interaction net-

works that orchestrate the diﬀerentiation of stem cells to various cell lineages that make

up an organism. We are also motivated by the prospects of utilizing stem cells in regen-

erative medicine (such as through replenishment of damaged tissues as well as treatment

of Parkinson’s disease and diabetes) [1, 50, 107, 151, 171, 180], in revolutionizing drug

discovery [2, 48, 136, 141, 142], and in the control of so-called cancer stem cells that had

been hypothesized to maintain the growth of tumors [57, 65, 110, 171, 172].

The current -omics (genomics, transcriptomics, proteomics, etc.) and systems biol-

ogy revolution [3, 33, 61, 62, 63, 93, 96, 99, 100, 108, 133] are continually providing

details about gene networks. The focus of this study is the mathematical analysis of

a gene network [113] involved in the diﬀerentiation of multipotent stem cells to three

mesenchymal stromal stem cells, namely, cells that form bones (osteoblasts), cartilages

(chondrocytes), and fats (adipocytes). This gene network shows the coupled interaction

among stem-cell-speciﬁc transcription factors and lineage-specifying transcription factors

induced by exogenous stimuli.

1

Chapter 1. Introduction 2

MacArthur et al. [113] proposed a model of this gene network, and we hypothesize

that further and more substantial analytical and computational study of this model would

reveal important insights into the control of the mesenchymal cell diﬀerentiation system.

We refer to the process of controlling the fate of a stem cell towards a chosen lineage as

cellular programming.

We analyze the gene network of MacArthur et al. [113] by simplifying the network

model while preserving the essential qualitative dynamics. In Chapter (5) of this the-

sis, we simplify the MacArthur et al. [113] network model to highlight the essential

components of the mesenchymal cell diﬀerentiation system and for easier analysis.

We translate the simpliﬁed network model into a system of Ordinary Diﬀerential

Equations (ODEs) using the Cinquin-Demongeot formalism [38]. The system of ODEs

formulated by Cinquin-Demongeot [38] is one of the mathematical models appropriate to

represent the dynamics depicted in the simpliﬁed MacArthur et al. [113] gene network.

The state variables of the ODE model represent the concentration of the transcription fac-

tors involved in gene expression. The Cinquin-Demongeot [38] ODE model can represent

various biological interactions, such as molecular interactions during gene transcription,

and it can represent cellular diﬀerentiation with more than two possible outcomes.

Stability and bifurcation analyses of the ODE model are important in understanding

the dynamics of cellular diﬀerentiation. An asymptotically stable equilibrium point is

associated with a certain cell type. In Chapters (6) and (7), we determine the biologically

feasible (nonnegative real-valued) coexisting stable equilibrium points of the ODE model

for a given set of parameters. We also identify if varying the values of some parameters,

such as those associated with the exogenous stimuli, can steer the system toward a desired

state.

Furthermore, in Chapter (8), we numerically investigate the robustness of the gene

network against stochastic noise by adding a noise term to the deterministic ODEs. The

objectives of the study are summarized in the following diagram:

Chapter 1. Introduction 3

Figure 1.1: Analysis of mesenchymal cell diﬀerentiation system.

Chapter 2

Preliminaries

Biology of Cellular Programming

2.1 Stem cells in animals

Stem cells are very important for the development, growth and repair of tissues. These

are cells that can undergo mitosis (cell division) and have two contrasting abilities —

ability for self-renewal and ability to diﬀerentiate into diﬀerent specialized cell types.

Self-renewal is the ability of stem cells to proliferate, that is, one or both daughter cells

remain as stem cells after cell division. When a stem cell undergoes diﬀerentiation,

it develops into a more mature (specialized) cell, losing its abilities to self-renew and to

diﬀerentiate towards other cell types. In addition, scientists have shown that some cells

can dediﬀerentiate and some can be transdiﬀerentiated. Dediﬀerentiation means that

a diﬀerentiated cell is transformed back to an earlier stage, while transdiﬀerentiation

means that a cell is programmed to switch cell lineages.

The maturity of a stem cell is classiﬁed based on the cell’s potency (the cell’s capability

to diﬀerentiate into various types). The three major kinds of stem cell potency are

totipotency, pluripotency and multipotency. Figure (2.1) shows these three types of

potencies and the diﬀerentiation process. Totipotent stem cells have the potential to

generate all cells including extraembryonic tissues, such as the placenta, and they are the

ancestors of all cells of an organism. A zygote is an example of a totipotent stem cell.

Pluripotent stem cells are descendants of totipotent stem cells that have lost their

ability to generate extraembryonic tissues but not their ability to generate all cells of the

embryo. Examples of these stem cells are the cells of the epiblast from the inner cell mass

of the blastocyst embryo. These stem cells can diﬀerentiate into almost all types of cells;

speciﬁcally, they form the endoderm, mesoderm and ectoderm germ layers. Pluripotent

4

Chapter 2. Preliminaries Biology of Cellular Programming 5

Figure 2.1: Stem cell self-renewal, diﬀerentiation and programming. This diagram

illustrates the abilities of stem cells to ploriferate through self-renewal, diﬀerentiate into

specialized cells and reprogram towards other cell types.

stem cells form all cell types found in an adult organism. The stomach, intestines, liver,

pancreas, urinary bladder, lungs and thyroid are formed from the endoderm layer; the

central nervous system, lens of the eye, epidermis, hair, sweat glands, nails, teeth and

mammary glands are formed from the ectoderm layer. The mesoderm layer connects the

endoderm and ectoderm layers, and forms the bones, muscles, connective tissues, heart,

blood cells, kidneys, spleen and middle layer of the skin.

Embryonic stem (ES) cells, epiblast stem cells, embryonic germ cells (derived from

primordial germ cells), spermatogonial male germ stem cells and induced pluripotent

Chapter 2. Preliminaries Biology of Cellular Programming 6

stem cells (iPSCs) are examples of pluripotent stem cells that are cultured in vitro.

ES cells are derived from the inner cell mass of the blastocyst embryo upon explantation

(isolated from the normal embryo).

Some adult stem cells, which can be somatic (related to the body) or germline (related

to the gametes such as ovum and sperm), with embryonic stem cell-like pluripotency have

been found by researchers under certain environments [16, 97, 103, 125, 170, 181]. Um-

bilical cord blood, adipose tissue and bone marrow are found to be sources of pluripotent

stem cells.

The production of iPSCs in 2006 [109, 162] is a major breakthrough for stem cell

research. The iPSCs are cells that are artiﬁcially reprogrammed to dediﬀerentiate from

diﬀerentiated or partially diﬀerentiated cells to become pluripotent again. With only few

ethical issues compared to embryo cloning, iPSCs can be used for possible therapeutic

purposes such as treating degenerative diseases, repairing damaged tissues and repro-

gramming cancer stem cells. However, there are plenty of issues on the use of iPSCs such

as safety and eﬃciency. Currently, there is still no strong proof that generated iPSCs

and natural ES cells are totally identical [158].

Pluripotent stem cells that diﬀerentiate to speciﬁc cell lineages lose their pluripotency,

that is, they lose their ability to generate other kinds of cells. Multipotent stem

cells are descendants of pluripotent stem cells but are already partially diﬀerentiated

— they have the ability to self-renew yet can diﬀerentiate only to speciﬁc cell lineages.

Multipotent stem cells are adult stem cells that are commonly considered as progenitor

cells (cells that are in the stage between being pluripotent and fully diﬀerentiated).

When a multipotent stem cell further diﬀerentiates, it matures to a more specialized

cell lineage. Oligopotent and unipotent stem cells are progenitor cells that have very

limited ability for self-renewal and are less potent. Oligopotent stem cells are descendants

of multipotent stem cells and can only diﬀerentiate into very few cell types. Usually,

stem cells are given special names based on the degree of potency, such as tripotent and

bipotent depending on whether the cell can only diﬀerentiate into three and two cell fates,

respectively. Unipotent stem cells, which are commonly called precursor cells, can only

Chapter 2. Preliminaries Biology of Cellular Programming 7

diﬀerentiate into one cell type but are not the same as fully diﬀerentiated cells. Fully

diﬀerentiated cells are at the determined terminal state, that is, they have completed

the diﬀerentiation process, have exited the cell cycle, and have already lost the ability to

self-renew [23, 123].

Figure 2.2: Priming and diﬀerentiation. Colored circles represent genes or TFs. The

sizes of the circles determine lineage bias. Priming is represented by colored circles having

equal sizes. The largest circle governs the possible phenotype of the cell. [70]

In vitro, ex vivo and in vivo programming have already been done [138, 139, 151,

177]. The idea of programming biological cells indicates that some cells are “plastic”

(i.e., some cells have the ability to change lineages). This plasticity of cells proves that

some cells do not permanently inactivate unexpressed genes but rather retain all genetic

information (see Figure (2.2)). Three in vitro approaches of cellular programming have

been discussed in a review by Yamanaka [177]. These approaches are nuclear transfer,

cell fusion and transcription-factor transduction [19, 44, 51, 58, 106, 177]. The process

of nuclear transfer has been used to successfully clone Dolly the sheep. Transcription-

factor transduction, commonly called direct programming, alters the expression of

Chapter 2. Preliminaries Biology of Cellular Programming 8

transcription factors (TFs) by overexpression or by deletion. Overexpressing one TF

may down-regulate other TFs that would lead to a change in the phenotype of a cell. In

2006, Yamanaka and Takahashi [162] identiﬁed four factors — OCT3/4, SOX2, c-MYC,

and KLF4 — that are enough to reprogram cells from mouse ﬁbroblasts to become

iPSCs (through the use of retrovirus). In 2007, Yamanaka, Takahashi and colleagues

[161] generated iPSCs from adult human ﬁbroblasts by the same deﬁned factors.

The three cellular programming approaches discussed by Yamanaka [177] have re-

vealed common features — demethylation of pluripotency gene promoters and activation

of ES-cell-speciﬁc TFs such as OCT4, SOX2 and NANOG [113, 124, 129]. In this study,

we only consider the TF transduction approach. To understand cellular diﬀerentiation

and TF transduction, we need to look at gene regulatory networks. Gene regulatory

networks (GRNs) establish the interactions of molecules and other signals for the ac-

tivation or inhibition of genes. We consider the key pluripotency transcription factors

OCT4, SOX2 and NANOG as the elements of the core pluripotency module in our GRN.

For a more detailed discussion about stem cells in animals, the following references

may be consulted [1, 12, 20, 22, 25, 34, 39, 42, 59, 74, 78, 80, 84, 103, 117, 148, 151, 159,

169, 177].

2.2 Transcription factors and gene expression

Genes contain hereditary information and are segments of the deoxyribonucleic acid

(DNA). Gene expression is the process in which information from a gene is used to

synthesize functional products such as proteins. Examples of these gene products are

proteins that give the cell its structure and function.

Genes in the DNA direct protein synthesis. Transcription and translation are the two

major processes that transform the information from nucleic acids to proteins (see Figure

(2.3)). In the transcription process, the DNA commands the synthesis of ribonucleic

Chapter 2. Preliminaries Biology of Cellular Programming 9

Figure 2.3: The ﬂow of information. The blue solid lines represent general ﬂow and the

blue dashed lines represent special (possible) ﬂow. The red dotted lines represent the

impossible ﬂow as postulated in the Central Dogma of Molecular Biology [41].

acid (RNA) and the information is transcribed from the DNA template to the RNA. The

RNA, speciﬁcally messenger RNA or mRNA, then carries the information to the part

of the cell where protein synthesis will happen. In the translation process, the cell

translates the information from the mRNA to proteins.

During transcription, the promoter (a DNA sequence where RNA polymerase enzyme

attaches) initiates transcription, while the terminator (also a DNA sequence) marks the

end of transcription. However, the RNA polymerase binds to the promoter only after

some transcription factors (TFs), a collection of proteins, are attached to the pro-

moter.

Gene expression is usually regulated by DNA-binding proteins (such as by TFs) at the

transcription process, sometimes utilizing external signals. TFs play a main role in gene

regulatory networks. A TF that binds to an enhancer (a control element) and stimulates

transcription of a gene is called an activator; a TF that binds to a silencer (also a control

element) and inhibits transcription of a gene is called a repressor. Hundreds of TFs

were discovered in eukaryotes. In highly specialized cells, only a small fraction of their

genes are activated.

Examples of TFs are OCT4, SOX2 and NANOG as well as RUNX2, SOX9 and PPAR-

γ. RUNX2, SOX9 and PPAR-γ stimulate formation of bone cells, cartilage cells and fat

Chapter 2. Preliminaries Biology of Cellular Programming 10

cells, respectively [113].

For a more detailed discussion about the relationship between transcription factors

and gene expression, the following references may be consulted [24, 89, 126].

2.3 Biological noise and stochastic diﬀerentiation

It is believed that stochastic ﬂuctuations in gene expression aﬀect cell fate commitment

in normal development and in in vitro culture of cells. The path that the cell would take

is not absolutely deterministic but is rather aﬀected by two kinds of noise — intrinsic

and extrinsic [128, 130, 160, 174]. Intrinsic noise is the inherent noise produced during

biochemical processes inside the cell, while extrinsic noise is the noise produced from

the external environment (such as from the other cells). In some cases, extrinsic noise

dominates the intrinsic noise and inﬂuences cell-to-cell variation [174] because the internal

environment of a cell is regulated by homeostasis.

Unregulated random ﬂuctuations can cause negative eﬀects to the organism. However,

in most cases, these stochastic ﬂuctuations are naturally regulated enough to maintain

order [30, 111]. Stochastic ﬂuctuations have positive eﬀects to the system such as driving

oscillations and inducing switching in cell fates [71, 111, 174]. The papers [113] and [176]

discuss the importance of random noise in dediﬀerentiation, especially in the production

of iPSCs.

When a stem cell undergoes cell division, the two daughter cells may both still be

identical to the original, may both have already been diﬀerentiated, or may have one cell

identical to the original and the other already diﬀerentiated. Cells that would undergo

diﬀerentiation have plenty of cell lineages to choose from, but their cell fates are based

on some pattern formation [24]. The model “creode” by C. Waddington [168], as shown

in Figure (2.4), illustrates the paths that a cell might take. In Waddington’s model, cell

diﬀerentiation is depicted by a ball rolling down a landscape of hills and valleys. The

parts of the valleys where the ball can stay without rolling can be regarded as attractors

that represent cell types. GRNs determine the topography of the landscape.

Chapter 2. Preliminaries Biology of Cellular Programming 11

Figure 2.4: C. Waddington’s epigenetic landscape — “creode” [168].

For a more detailed discussion about biological noise and stochastic diﬀerentiation,

the following references may be consulted [9, 15, 26, 28, 30, 53, 64, 80, 81, 83, 85, 94,

101, 105, 111, 112, 127, 131, 132, 152, 164, 176].

Chapter 3

Preliminaries

Mathematical Models of Gene Networks

This chapter gives a review of the existing literatures on models of gene regulatory

networks (GRN).

Commonly, to start the mathematical analysis of GRNs, a directed graph is con-

structed to visualize the interaction of the molecules involved. Various network analysis

techniques are available to extract information from the constructed directed graph such

as clustering algorithms and motif analysis [4, 30, 45, 68, 90]. The study of the network

topology is important in understanding the biological system that the network represents.

Gene regulatory systems are commonly modeled as Bayesian networks, Boolean net-

works, generalized logical networks, Petri nets, ordinary diﬀerential equations, partial

diﬀerential equations, chemical master equations, stochastic diﬀerential equations and

rule-based simulations [29, 45]. The choice of mathematical model depends on the as-

sumptions made about the nature of the GRN and on the objectives of the study.

In this thesis, we study the directed graph constructed by MacArthur et al. [113]

and its corresponding Ordinary Diﬀerential Equations (ODEs) formulated by Cinquin-

Demongeot [38] and its corresponding Stochastic Diﬀerential Equations (SDEs). By using

an ODE model, we assume that the time-dependent macroscopic dynamics of the GRN

are continuous in both time and state space. We assume continuous dynamics because the

process of lineage determination involves a temporal extension, that is, cells pass through

intermediate stages [70]. We use ODEs to model the average dynamics of the GRN. ODEs

are primarily used to represent the deterministic dynamics of phenomenological (coarse-

grained) regulatory networks [70, 121]. In addition, we can add a random noise term to

the ODE model to study stochasticity in cellular diﬀerentiation.

12

Chapter 3. Preliminaries Mathematical Models of Gene Networks 13

3.1 The MacArthur et al. GRN

The MacArthur et al. [113] GRN is composed of a pluripotency module (the circuit

consisting of OCT4, SOX2, NANOG and their heterodimer and heterotrimer) and a

diﬀerentiation module (the circuit consisting of RUNX2, SOX9 and PPAR-γ) [113]. The

transcription factors RUNX2, SOX9 and PPAR-γ activate the formation of bone cells,

cartilage cells and fat cells, respectively.

Figure 3.1: The coarse-graining of the diﬀerentiation module. The network in (a) is

simpliﬁed into (b), where arrows indicate up-regulation (activation) while bars indicate

down-regulation (repression). [113]

The derivation of the core diﬀerentiation module is shown in Figure (3.1) where the

interactions through intermediaries are consolidated to create a simpliﬁed network. The

MacArthur et al. [113] GRN that we are going to study is shown in Figure (3.2).

Feedback loops (which are important for the existence of homeostasis) and autoregu-

lation (or autoactivation, which means that a molecule enhances its own expression) are

necessary to attain pluripotency [177]. These feedback loops and autoregulation are also

Chapter 3. Preliminaries Mathematical Models of Gene Networks 14

Figure 3.2: The MacArthur et al. [113] mesenchymal gene regulatory network. Arrows

indicate up-regulation (activation) while bars indicate down-regulation (repression).

present in the MacArthur et al. GRN [113]; however, they are not enough to generate iP-

SCs. Based on the deterministic computational analysis of MacArthur et al. [113], their

pluripotency module cannot be reactivated once silenced, that is, it becomes resistant

to reprogramming. However, they found that introducing stochastic noise to the system

can reactivate the pluripotency module [113].

Chapter 3. Preliminaries Mathematical Models of Gene Networks 15

3.2 ODE models representing GRN dynamics

A state X = ([X

1

], [X

2

], . . . , [X

n

]) represents a temporal stage in the cellular diﬀerentia-

tion or programming process (see Figure (3.3)). We deﬁne [X

i

] as a component (coordi-

nate) of a state. A stable state (stable equilibrium point) X

∗

= ([X

1

]

∗

, [X

2

]

∗

, . . . , [X

n

]

∗

)

represents a certain cell type, e.g., pluripotent, tripotent, bipotent, unipotent or terminal

state.

Figure 3.3: Gene expression or the concentration of the TFs can be represented by a

state vector, e.g. ([X

1

], [X

2

], [X

3

], [X

4

]) [70]. For example, TFs of equal concentration

can be represented by a vector with equal components, such as (2.4, 2.4, 2.4, 2.4).

Modelers of GRN often use the function H

+

(or H

−

) which is bounded monotone

increasing (or decreasing) with values between zero and one. Examples of such functions

are the sigmoidal, hyperbolic and threshold piecewise-linear functions. If we use sigmoidal

H

+

and H

−

called the Hill functions, we deﬁne

H

+

([X], K, c) :=

[X]

c

K

c

+ [X]

c

(3.1)

for activation of gene expression and

H

−

([X], K, c) := 1 −H

+

([X], K, c) =

K

c

K

c

+ [X]

c

(3.2)

for repression, where the variable [X] is the concentration of the molecule involved [69,

73, 96, 121, 144]. The parameter K is the threshold or dissociation constant and is equal

Chapter 3. Preliminaries Mathematical Models of Gene Networks 16

to the value of X at which the Hill function is equal to 1/2. The parameter c is called

the Hill constant or Hill coeﬃcient and describes the steepness of the Hill curve. The Hill

constant often denotes multimerization-induced cooperativity (a multimer is an assembly

of multiple monomers or molecules) and may represent the number of cooperative binding

sites if c is restricted to a positive integer. However, in some cases, the Hill constant can

be a positive real number (usually 1 < c < n where n is the number of equivalent

cooperative binding sites) [73, 174]. If c = 1, then there is no cooperativity [38] and the

Hill function becomes the Michaelis-Menten function which is hyperbolic. If data are

available, we can estimate the value of c by inference.

Various ODE models and formulations are presented in [13, 14, 27, 30, 31, 32, 43,

47, 69, 76, 96, 115, 135, 173]. Examples of these are the neural network [166] model,

the S-systems (power-law) [167] model, the Andrecut [7] model, the Cinquin-Demongeot

2002 [36] model, and the Cinquin-Demongeot 2005 [38] model. The Cinquin-Demongeot

2002 and 2005 models can represent various GRNs and are more amenable to analysis.

3.2.1 Cinquin and Demongeot ODE formalism

According to Waddington’s model [168], cell diﬀerentiation is similar to a ball rolling

down a landscape of hills and valleys. The ridges of the hills can be regarded as the

unstable equilibrium points while the parts of the valleys where the ball can stay without

rolling further (i.e., at relative minima of the landscape) can be regarded as stable equi-

librium points (attractors). Hence, the movement of the ball and its possible location

after some time can be represented by dynamical systems, speciﬁcally ODEs. However,

it should be noted that existing evidence showing the presence of attractors is limited to

some mammalian cells [112].

The theory that some cells can diﬀerentiate into many diﬀerent cell types gives the

idea that the model representing the dynamics of such cells may exhibit multistability

(multiple stable equilibrium points). However, not all GRNs are reducible to binary or

boolean hierarchic decision network (see Figure (3.4)), that is why Cinquin and Demon-

geot formulated models that can represent cellular diﬀerentiation with more than two

Chapter 3. Preliminaries Mathematical Models of Gene Networks 17

Figure 3.4: Hierarchic decision model and simultaneous decision model. Bars represent

repression or inhibition, while arrows represent activation. [36].

possible outcomes (multistability) obtained through diﬀerent developmental pathways

[3, 38, 35]. The simultaneous decision network (see Figure (3.4)) is a near approximation

of the Waddington illustration where there are possibly many cell lineages involved.

In 2002, Cinquin and Demongeot proposed an ODE model representing the simulta-

neous decision network [36]. In 2005, they proposed another ODE model representing

the simultaneous decision network but with autocatalysis (autoactivation) [38]. Both the

Cinquin-Demongeot models are based on the simultaneous decision graph where there is

mutual inhibition. All elements in the Cinquin-Demongeot models are symmetric, that

is, each node has the same relationship with all other nodes, and all equations in the

system of ODEs have equal parameter values.

Chapter 3. Preliminaries Mathematical Models of Gene Networks 18

Equations (3.3) and (3.4) are the Cinquin-Demongeot ODE models without autocatal-

ysis (2002 version, [36]) and with autocatalysis (2005 version, [38]), respectively. Let us

suppose we have n antagonistic transcription factors. The state variable [X

i

] represents

the concentration of the corresponding TF protein such that the TF expression is subject

to a ﬁrst-order degradation (exponential decay). The parameters c, β and g represent the

relative speed of transcription (or strength of the unrepressed TF expression relative to

the ﬁrst-order degradation), cooperativity and “leak”, respectively. The parameter g is a

basal expression of the corresponding TF and a constant production term that enhances

the value of [X

i

], which is possibly aﬀected by an exogenous stimulus. For simpliﬁcation,

only the transcription regulation process is considered in [38]. The models are assumed

to be intracellular and cell-autonomous (i.e., we only consider processes inside a single

cell without the inﬂuence of other cells).

Without autocatalysis :

d[X

i

]

dt

=

β

1 +

n

j=1,j=i

[X

j

]

c

−[X

i

], i = 1, 2, . . . , n (3.3)

With autocatalysis :

d[X

i

]

dt

=

β[X

i

]

c

1 +

n

j=1

[X

j

]

c

−[X

i

] +g, i = 1, 2, . . . , n (3.4)

The terms

β

1 +

n

j=1,j=i

[X

j

]

c

and

β[X

i

]

c

1 +

n

j=1

[X

j

]

c

(3.5)

are Hill-like functions. In this study, we only consider Cinquin-Demongeot (2005 version)

model (3.4) because autocatalysis is a common property of cell fate-determining factors

known as “master” switches [38].

Chapter 3. Preliminaries Mathematical Models of Gene Networks 19

In [38], Cinquin and Demongeot observed that their model (with autocatalysis) can

show the priming behavior of stem cells (i.e., genes are equally expressed) as well as

the up-regulation of one gene and down-regulation of the others. They also proved that

multistability of their model where g = 0 is manipulable by changing the value of c

(cooperativity); however, manipulating the level of cooperativity is of minimal biological

relevance. Also, their model is more sensitive to stochastic noise when the equilibrium

points are near each other.

3.2.2 ODE model by MacArthur et al.

MacArthur et al. [113] proposed an ODE model (Equations (3.6) and (3.7)) to rep-

resent their GRN (refer to Figure (3.2)). Let [P

i

] be the concentration of the TF

protein in the pluripotency module, speciﬁcally, [P

1

] := [OCT4], [P

2

] := [SOX2] and

[P

3

] := [NANOG]. Also, let [L

i

] be the concentration of the TF protein in the diﬀeren-

tiation module where [L

1

] := [RUNX2], [L

2

] := [SOX9] and [L

3

] := [PPAR−γ]. The

parameter s

i

represents the eﬀect of the growth factors stimulating the diﬀerentiation

towards the i-th cell lineage, speciﬁcally, s

1

:= [RA+BMP4], s

2

:= [RA+TGF−β] and

s

3

:= [RA+Insulin]. In mouse ES cells, RUNX2 is stimulated by retinoic acid (RA) and

BMP4; SOX9 by RA and TGF-β; and PPAR-γ by RA and Insulin. The derivation of the

ODE model and the interpretation of the parameters are discussed in the supplementary

materials of [113].

d[P

i

]

dt

=

k

1i

[P

1

][P

2

](1+[P

3

])

(1+k

0

j

s

j)(1+[P

1

][P

2

](1+[P

3

])+k

PL

j

[L

j

])

−b[P

i

] (3.6)

d[L

i

]

dt

=

k

2(s

i

+k

3

j=i

s

j)[L

i

]

2m

1+k

LC

1

[P

1

][P

2

]+k

LC

2

[P

1

][P

2

][P

3

]+[L

i

]

2

+k

LL(s

i

+k

3

j=i

s

j)

j=i

[L

j

]

2

−b[L

i

] (3.7)

However, this system of coupled ODEs is diﬃcult to study using analytic techniques.

MacArthur et al. [113] simply conducted numerical simulations to investigate the behav-

ior of the system. They tried to analytically analyze the system but only for a speciﬁc

Chapter 3. Preliminaries Mathematical Models of Gene Networks 20

case where P

i

= 0, i = 1, 2, 3, that is, when the pluripotency module is switched-oﬀ.

The ODE model (3.8) that they analyzed when the pluripotency module is switched-oﬀ

follows the Cinquin-Demongeot [38] formalism with c = 2, that is,

d[L

i

]

dt

=

[L

i

]

2

1 + [L

i

]

2

+a

j=i

[L

j

]

2

−b[L

i

], i = 1, 2, 3 (3.8)

MacArthur et al. [113] analytically proved that the three cell types (tripotent, bipo-

tent and terminal states) are simultaneously stable for some parameter values in (3.8).

However, as the eﬀect of an exogenous stimulus is increased above some threshold value,

the tripotent state becomes unstable leaving only two stable cell types (bipotent and

terminal state). If the eﬀect of the exogenous stimulus is further increased, the bipotent

state also becomes unstable leaving the terminal state as the sole stable cell type. In

addition, MacArthur et al. [113] showed that dediﬀerentiation is not possible without

the aid of stochastic noise.

3.3 Stochastic Diﬀerential Equations

A time-dependent Gaussian white noise term can be added to the ODE model to inves-

tigate the eﬀect of random ﬂuctuations in gene expression. This Gaussian white noise

term combines and averages multiple heterogeneous sources of temporal noise. Equations

(3.10) to (3.13) show some of the diﬀerent SDE models [71, 72, 113, 174] of the form

dX = F(X)dt +σG(X)dW (3.9)

that we use in this study. We employ diﬀerent G(X) to observe the various eﬀects of

the added Gaussian white noise term. We let F(X) be the right-hand side of our ODE

equations, σ be a diagonal matrix of parameters representing the amplitude of noise, and

Chapter 3. Preliminaries Mathematical Models of Gene Networks 21

W be a Brownian motion (Wiener process). If the genes in a cell are isogenic (essentially

identical) then we can suppose the diagonal entries of the matrix σ are all equal.

dX = F(X)dt +σdW (3.10)

dX = F(X)dt +σXdW (3.11)

dX = F(X)dt +σ

√

XdW (3.12)

dX = F(X)dt +σF(X)dW (3.13)

Notice that in Equations (3.11) and (3.12), the noise term is aﬀected by the value

of X. As the concentration X increases, the eﬀect of the noise term also increases.

Whereas, in Equations (3.13), the noise term is aﬀected by the value of F(X), that is,

as the deterministic change in the concentration X with respect to time

_

dX

dt

= F(X)

_

increases, the eﬀect of the noise term also increases. In Equation (3.10), the noise term

is not dependent on any variable.

For a more detailed discussion about various modeling techniques, the following ref-

erences may be consulted [6, 11, 18, 21, 46, 52, 55, 60, 66, 67, 75, 77, 79, 87, 88, 92, 118,

137, 140, 143, 149, 153, 154, 163, 165, 175, 179, 182].

Chapter 4

Preliminaries

Analysis of Nonlinear Systems

This chapter gives a brief discussion of the theoretical background on the qualitative

analysis of coupled nonlinear dynamical systems.

Consider autonomous system of ODEs

d[X

i

]

dt

= F

i

([X

1

], [X

2

], . . . , [X

n

]), i = 1, 2, . . . , n, (4.1)

with initial condition [X

i

](0) := [X

i

]

0

∀i. We assume that t ≥ 0 and F

i

: B → R

n

,

i = 1, 2, . . . , n where B ⊆ R

n

. If we have a nonautonoumous system of ODEs,

d[X

i

]

dt

=

F

i

([X

1

], [X

2

], . . . , [X

n

], t), i = 1, 2, . . . , n, then we convert it to an autonomous system by

deﬁning t := [X

n+1

] and

d[X

n+1

]

dt

= 1 [134].

For simplicity, let F := (F

i

, i = 1, 2, . . . , n), X := ([X

i

], i = 1, 2, . . . , n) and X

0

:=

([X

i

]

0

, i = 1, 2, . . . , n).

For an ODE model to be useful, it is necessary that it has a solution. Existence of a

unique solution for a given initial condition is important to eﬀectively predict the behavior

of our system. Moreover, we are assured that the solution curves of an autonomous system

do not intersect with each other when existence and uniqueness conditions hold [56].

Suppose X(t) is a diﬀerentiable function. The solution to (4.1) satisﬁes the following

integral equation:

X(t) = X

0

+

_

t

0

F(X(τ))dτ. (4.2)

22

Chapter 4. Preliminaries Analysis of Nonlinear Systems 23

The following are theorems that guarantee local existence and uniqueness of solutions

to ODEs:

Theorem 4.1 Existence theorem (Peano, Cauchy). Consider the autonomous system

(4.1). Suppose that F is continuous on B. Then the system has a solution (not necessarily

unique) on [0, δ] for suﬃciently small δ > 0 given any X

0

∈ B.

Theorem 4.2 Local existence-uniqueness theorem (Picard, Lindel¨ orf, Lipschitz,

Cauchy). Consider the autonomous system (4.1). Suppose that F is locally Lipschitz

continuous on B, that is, F satisﬁes the following condition: For each point X

0

∈ B

there is an -neighborhood of X

0

(denoted as B

(X

0

) where B

(X

0

) ⊆ B) and a positive

constant m

0

such that |F(X) −F(Y )| ≤ m

0

|X −Y | ∀X, Y ∈ B

(X

0

). Then the system

has exactly one solution on [0, δ] for suﬃciently small δ > 0 given any X

0

∈ B.

Theorem (4.2) can be extended to a global case stated as:

Theorem 4.3 Global existence-uniqueness theorem. If there is a positive constant

m such that |F(X) −F(Y )| ≤m|X −Y | ∀X, Y ∈ B (i.e., F is globally Lipschitz

continuous on B) then the system has exactly one solution deﬁned for all t ∈ R

⊕

for

any X

0

∈ B.

If all the partial derivatives

∂F

i

∂[X

j

]

i, j = 1, 2, . . . , n are continuous on B (i.e., F ∈

C

1

(B)) then F is locally Lipschitz continuous on B. If the absolute value of these partial

derivatives are also bounded for all X ∈ B then F is globally Lipschitz continuous on

B. The global condition says that if the growth of F with respect to X is at most linear

then we have a global solution. If F satisﬁes the local Lipschitz condition but not the

global Lipschitz condition, then it is possible that after some ﬁnite time t, the solution

will “blow-up”.

We deﬁne a point X = ([X

1

], [X

2

], . . . , [X

n

]) as a state of the system, and the collec-

tion of these states is called the state space. The solution curve of the system starting

from a ﬁxed initial condition is called a trajectory or orbit. The collection of trajectories

Chapter 4. Preliminaries Analysis of Nonlinear Systems 24

given any initial condition is called the ﬂow of the diﬀerential equation and is denoted by

φ(X

0

). The concept of the ﬂow of the diﬀerential equation indicates the dependence of

the system on initial conditions. The ﬂow of the diﬀerential equation can be represented

geometrically in the phase space R

n

using a phase portrait. There exists a corresponding

vector deﬁned by the ODE that is tangent to each point in every trajectory; and the

collection of all tangent vectors of the system is a vector ﬁeld. A vector ﬁeld is often

helpful in visualizing the phase portrait of the system. Moreover, various methods are

also available to numerically solve the system (4.1) such as the Euler and Runge-Kutta

4 methods.

4.1 Stability analysis

In nonlinear analysis of systems, it is important to ﬁnd points where our system is at rest

and determine whether these points are stable or unstable. In modeling cellular diﬀer-

entiation, an asymptotically stable equilibrium point, which is an attractor, is associated

with a certain cell type. For any initial condition in a neighborhood of the attractor, the

trajectories tend towards the attractor even if slightly perturbed.

Deﬁnition 4.1 Equilibrium point. The point X

∗

:= ([X

1

]

∗

, [X

2

]

∗

, . . . , [X

n

]

∗

) ∈ R

n

is

said to be an equilibrium point (also called as critical point, stationary point or steady

state) of the system (4.1) if and only if F(X

∗

) = 0.

Finding the equilibrium points corresponds to solving for the real-valued solutions to

the system of equations F(X) = 0. It is possible that this system of equations has a

unique solution, several solutions, a continuum of solutions, or no solution.

In order to describe the local behavior of the system (4.1) near a speciﬁc equilibrium

point X

∗

, we linearize the system by getting the Jacobian matrix JF(X), deﬁned as

Chapter 4. Preliminaries Analysis of Nonlinear Systems 25

JF(X) =

_

¸

¸

¸

¸

¸

_

∂F

1

∂[X

1

]

∂F

1

∂[X

2

]

· · ·

∂F

1

∂[Xn]

∂F

2

∂[X

1

]

∂F

2

∂[X

2

]

· · ·

∂F

2

∂[Xn]

.

.

.

.

.

.

.

.

.

.

.

.

∂Fn

∂[X

1

]

∂Fn

∂[X

2

]

· · ·

∂Fn

∂[Xn]

_

¸

¸

¸

¸

¸

_

(4.3)

and then evaluating JF(X

∗

). If none of the eigenvalues of the matrix JF(X

∗

) has zero

real part then X

∗

is called a hyperbolic equilibrium point. In this chapter, we focus

the discussion on hyperbolic equilibrium points; but for details about nonhyperbolic

equilibrium points, refer to [134].

We use the eigenvalues of JF(X

∗

) to determine the stability of equilibrium points.

Deﬁnition 4.2 Asymptotically stable and unstable equilibrium points. The

equilibrium point X

∗

is asymptotically stable when the solutions near X

∗

converge to X

∗

as t → ∞. The equilibrium point X

∗

is unstable when some or all solutions near X

∗

tend away from X

∗

as t →∞.

Theorem 4.4 Stability of equilibrium points. If all the eigenvalues of JF(X

∗

) have

negative real parts then X

∗

is an asymptotically stable equilibrium point. If at least one

of the eigenvalues of JF(X

∗

) has a positive real part then X

∗

is an unstable equilibrium

point.

For simplicity, we will call an asymptotically stable equilibrium point, “stable”. There

are various tests for determining the stability of an equilibrium point such as by using

Theorem (4.4), or by using geometric analysis as shown in Figure (4.1). In addition, we

deﬁne X

∗

as a saddle if it is an unstable equilibrium point but JF(X

∗

) has at least

one eigenvalue with negative real part. For further details regarding the local behavior

of nonlinear systems in the neighborhood of an equilibrium point, refer to the Stable

Manifold Theorem and the Hartman-Grobman Theorem [134].

Chapter 4. Preliminaries Analysis of Nonlinear Systems 26

Figure 4.1: The slope of F(X) at the equilibrium point determines the linear stability.

Positive gradient means instability, negative gradient means stability. If the gradient is

zero, we look at the left and right neighboring gradients. Refer to the Insect Outbreak

Model: Spruce Budworm in [122].

It is also useful to determine the set of initial conditions X

0

with trajectories con-

verging to a speciﬁc stable equilibrium point X

∗

. We call this set of initial conditions

the domain or basin of attraction of X

∗

, denoted by

Ω

X

∗ :=

_

X

0

: lim

t→∞

φ(X

0

) = X

∗

_

. (4.4)

In addition, a set

ˆ

B ⊆ B is called positively invariant with respect to the ﬂow φ(X

0

)

if for any X

0

∈

ˆ

B, φ(X

0

) ⊆

ˆ

B for all t ≥ 0, that is, the ﬂow of the ODE remains in

ˆ

B.

There are other types of attractors, such as ω-limit cycles and strange attractors

[56]. A limit cycle is a periodic orbit (a closed trajectory which is not an equilibrium

point) that is isolated. An asymptotically stable limit cycle is called an ω-limit cycle.

Strange attractors usually occur when the dynamics of the system is chaotic. Moreover,

under some conditions, a trajectory may be contained in a non-attracting but neutrally

stable center (see [56] for discussion about centers). However, the extensive numerical

simulations by MacArthur et al. [113] suggest that their ODE model (Equations (3.6)

and (3.7)) does not have oscillators (periodic orbit) and strange trajectories. Cinquin and

Demongeot [38] also claim that the solutions to their model (refer to Equations (3.4))

always tend towards an equilibrium and never oscillate [38].

Chapter 4. Preliminaries Analysis of Nonlinear Systems 27

The existence of a center, ω-limit cycle or strange attractor that would result to

recurring changes in phenotype is abnormal for a natural fully diﬀerentiated cell. Limit

cycles are associated with the concept of continuous cell proliferation (self-renewal) where

there are recurring biochemical states during cell division cycles [82]. However, cell

division is beyond the scope of this thesis.

Various theorems are available for checking the possible existence or non-existence of

limit cycles (although most are for two-dimensional planar systems only). The Poincar´e-

Bendixson Theorem for planar systems [134] states that if F ∈ C

1

(B) and a trajectory

remains in a compact region of B whose ω-limit set (e.g. attracting set) does not contain

any equilibrium point, then the trajectory approaches a periodic orbit. Furthermore, if

F ∈ C

1

(B) and a trajectory remains in a compact region of B as well as if there are

only a ﬁnite number of equilibrium points, then the ω-limit set of any trajectory of the

planar system can be one of three types — an equilibrium point, a periodic orbit or a

compound separatrix cycle.

Some researches have shown the eﬀect of the presence of positive or negative feedback

loops in GRNs such as possible multistability (existence of multiple stable equilibrium

points) and existence of oscillations [8, 37, 45, 104, 119, 155]. It is also important to note

that a strange (chaotic) attractor will not exist for n < 3 [56].

4.2 Bifurcation analysis

The behavior of the solutions of system (4.1) depends not only on the initial conditions

but also on the values of the parameters. The parameters of the model may be associated

with real-world quantities that can be manipulated to control the solutions. Varying the

value of a parameter (or parameters) may result in dramatic changes in the qualitative

nature of the solutions, such as a change in the number of equilibrium points or a change

in the stability. Here, we now let F be a function of the state variables X and of the

parameter matrix µ (i.e., F(X, µ)). We deﬁne the values of the parameters where such

dramatic change occurs as bifurcation value, denoted by µ

∗

. If we simultaneously vary

the values of p number of parameters then we have a p-parameter bifurcation.

Chapter 4. Preliminaries Analysis of Nonlinear Systems 28

If p-parameter bifurcation is suﬃcient for a bifurcation type to occur then we classify

the bifurcation type as codimension p. Examples of codimension one bifurcation type

are saddle-node (fold), supercritical Poincar´e-Andronov-Hopf and subcritical Poincar´e-

Andronov-Hopf bifurcations. Transcritical, supercritical pitchfork and subcritical pitch-

fork bifurcations are also often regarded as codimension one. Cusp bifurcation is of

codimension two.

Figure 4.2: Sample bifurcation diagram showing saddle-node bifurcation.

In a local bifurcation, the equilibrium point X

∗

is nonhyperbolic at the bifurcation

value. For n ≥ 2, if JF(X

∗

) has a pair of purely imaginary eigenvalues and no other

eigenvalues with zero real part at the bifurcation value then under some assumptions a

Hopf bifurcation may occur and a limit cycle might arise from X

∗

. We can visualize the

bifurcation of equilibria using a bifurcation diagram. For further details about bifurcation

theory, refer to [86, 102, 134]. There are softwares available for numerical bifurcation

analysis such as Oscill8 [40] which uses AUTO (http://indy.cs.concordia.ca/auto/).

4.3 Fixed point iteration

Deﬁnition 4.3 Fixed point. The point X

∗

is a ﬁxed point of the real-valued function

Q if Q(X

∗

) = X

∗

.

Chapter 4. Preliminaries Analysis of Nonlinear Systems 29

We use ﬁxed point iteration (FPI) to ﬁnd approximate stable equilibrium points of

the Cinquin-Demongeot [38] model. If X

∗

is a stable equilibrium point then for initial

conditions X

0

suﬃciently close to X

∗

(where X

0

= X

∗

), the sequences generated by FPI

will converge to X

∗

(i.e., is locally convergent). If X

0

= X

∗

, we can either have a stable

or unstable equilibrium point.

Algorithm 1 Fixed point iteration

Suppose Q is continuous on the region B.

Input initial guess X

(0)

:= X

0

∈ B and acceptable tolerance error ∈ R

⊕

.

While

¸

¸

X

(i+1)

−X

(i)

¸

¸

> do X

(i+1)

:= Q(X

(i)

).

If

¸

¸

X

(i+1)

−X

(i)

¸

¸

≤ is satisﬁed then X

(i+1)

is the approximate ﬁxed point.

Figure 4.3: An illustration of cobweb diagram.

The geometric illustration of FPI is called a cobweb diagram as illustrated in Figure

(4.3).

Chapter 4. Preliminaries Analysis of Nonlinear Systems 30

4.4 Sylvester resultant method

To ﬁnd the equilibrium points, we can rewrite the Cinquin-Demongeot ODE model where

the exponent is a positive integer as a system of polynomial equations. Assume F(X) = 0

can be written as a polynomial system P(X) = 0. The topic of solving multivariate

nonlinear polynomial systems is still in its development stage. However, there are already

various available algebraic and geometric methods for solving P(X) = 0 such as Newton-

like methods, homotopic solvers, subdivision methods, algebraic solvers using Gr¨obner

basis, and geometric solvers using resultant construction [120]. In resultant construction,

we treat the problem of solving P(X) = 0 as a problem of ﬁnding intersections of curves.

All P

i

(X) should have no common factor of degree greater than zero so that P(X)

has a ﬁnite number of complex solutions. The following B´ezout Theorem gives a bound

on the number of complex solutions including the multiplicities.

Theorem 4.5 B´ezout theorem. Consider real-valued polynomials P

1

, P

2

, . . . , P

n

where

P

i

has degree deg

i

. Suppose all the polynomials have no common factor of degree greater

than zero (i.e., they are collectively relatively prime). Then the number of isolated

complex solutions to the system P

1

(X) = P

2

(X) = . . . = P

n

(X) = 0 is at most

(deg

1

)(deg

2

) . . . (deg

n

).

The method of using the Sylvester resultant is a classical algorithm in Algebraic

Geometry used to ﬁnd the complex solutions of a system of two polynomial equations in

two variables. It can also be used for solving a polynomial system of n equations with

n variables where n > 2, by repeated application of the algorithm. The idea of using

Sylvester resultants for solving multivariate polynomial systems is to eliminate all except

for one variable. There are other resultant construction methods for solving multivariate

polynomial systems with n > 2 such as the Dixon resultant, Macaulay resultant and

U-resultant methods, but we will only focus on the Sylvester resultant. The algorithm

for using Sylvester resultants is illustrated in the following paragraphs.

Chapter 4. Preliminaries Analysis of Nonlinear Systems 31

Consider two polynomials P

1

([X

1

], [X

2

]) and P

2

([X

1

], [X

2

]). We eliminate [X

1

] by

constructing the Sylvester matrix associated to the two polynomials with [X

1

] as the

variable (i.e., we take [X

2

] as ﬁxed parameter). The size of the Sylvester matrix is

(deg

1

+ deg

2

) ×(deg

1

+ deg

2

) where deg

1

and deg

2

are the degrees of the polynomial P

1

and P

2

in the variable [X

1

], respectively.

We give an example to show how to construct a Sylvester matrix. Let us suppose

P

1

([X

1

], [X

2

]) = 2[X

1

]

3

+ 4[X

1

]

2

[X

2

] + 7[X

1

][X

2

]

2

+ 10[X

2

]

3

+ 8 (4.5)

P

2

([X

1

], [X

2

]) = 5[X

1

]

2

+ 2[X

1

][X

2

] + [X

2

]

2

+ 6. (4.6)

Since the degree of P

1

in terms of [X

1

] is 3 and the degree of P

2

in terms of [X

1

] is 2, then

the size of the Sylvester matrix (with [X

1

] as variable) is 5 ×5. The Sylvester matrix of

P

1

and P

2

with [X

1

] as variable is

_

¸

¸

¸

¸

¸

¸

¸

¸

_

2 4[X

2

] 7[X

2

]

2

10[X

2

]

3

+ 8 0

0 2 4[X

2

] 7[X

2

]

2

10[X

2

]

3

+ 8

5 2[X

2

] [X

2

]

2

+ 6 0 0

0 5 2[X

2

] [X

2

]

2

+ 6 0

0 0 5 2[X

2

] [X

2

]

2

+ 6

_

¸

¸

¸

¸

¸

¸

¸

¸

_

. (4.7)

The ﬁrst row of the Sylvester matrix contains the coeﬃcients of [X

1

]

3

, [X

1

]

2

, [X

1

]

1

and

[X

1

]

0

in P

1

. We shift each element of the ﬁrst row one column to the right to form the

second row. The third row contains the coeﬃcients of [X

1

]

2

, [X

1

]

1

and [X

1

]

0

in P

2

. We

shift each element of the third row one column to the right to form the fourth row. We

again shift each element of the fourth row one column to the right to form the ﬁfth row.

Generally, we continue the process of shifting each element of the previous row to form

the next row until the coeﬃcient of [X

1

]

0

reaches the last column. All cells of the matrix

without entries coming from the coeﬃcients of the polynomials are assigned the value

zero.

We use the determinant of the Sylvester matrix to ﬁnd the intersection of P

1

and P

2

.

Chapter 4. Preliminaries Analysis of Nonlinear Systems 32

Deﬁnition 4.4 Sylvester resultant. We call the determinant of the Sylvester matrix

of P

1

and P

2

in [X

1

] (where [X

2

] is a ﬁxed parameter) the Sylvester resultant, denoted by

res(P

1

, P

2

; [X

1

]).

Theorem 4.6 Zeroes of the Sylvester resultant. The values where res(P

1

, P

2

; [X

1

]) =

0 are the complex values of [X

2

] where P

1

([X

1

], [X

2

]) = P

2

([X

1

], [X

2

]) = 0.

We denote the complex values of [X

2

] where P

1

([X

1

], [X

2

]) = P

2

([X

1

], [X

2

]) = 0 by

[X

2

]

∗

. To ﬁnd

[X

1

]

∗

, we solve the univariate system P

1

([X

1

],

[X

2

]

∗

) = P

2

([X

1

],

[X

2

]

∗

) = 0

for all possible values of

[X

2

]

∗

.

The following theorem can be used to determine if P

1

and P

2

either do not intersect,

or intersect at inﬁnitely many points.

Theorem 4.7 None and inﬁnitely many solutions. res(P

1

, P

2

; [X

1

]) is nonzero

for any [X

2

] if and only if P

1

([X

1

], [X

2

]) = P

2

([X

1

], [X

2

]) = 0 has no complex solutions.

Furthermore, the following statements are equivalent:

1. res(P

1

, P

2

; [X

1

]) is identically zero (i.e., zero for any values of [X

2

]).

2. P

1

and P

2

have a common factor of degree greater than zero.

3. P

1

= P

2

= 0 has inﬁnitely many complex solutions.

We can extend the Sylvester resultant method to a multivariate case, say with three

polynomials P

1

([X

1

], [X

2

], [X

3

]), P

2

([X

1

], [X

2

], [X

3

]) and P

3

([X

1

], [X

2

], [X

3

]), by getting

R

1

= res(P

1

, P

2

; [X

1

]) and R

2

= res(P

2

, P

3

; [X

1

]). Notice that R

1

and R

2

are both in

terms of [X

2

] and [X

3

]. We then get R

3

= res(R

1

, R

2

; [X

2

]) which is in terms of [X

3

].

We solve the univariate polynomial equation R

3

= 0 by using available solvers to obtain

[X

3

]

∗

. After this, we ﬁnd

[X

2

]

∗

by substituting

[X

3

]

∗

in R

1

and R

2

and solve R

1

=

Chapter 4. Preliminaries Analysis of Nonlinear Systems 33

R

2

= 0. We then ﬁnd

[X

1

]

∗

by solving P

1

([X

1

],

[X

2

]

∗

,

[X

3

]

∗

) = P

2

([X

1

],

[X

2

]

∗

,

[X

3

]

∗

) =

P

3

([X

1

],

[X

2

]

∗

,

[X

3

]

∗

) = 0.

For a more detailed discussion on solving systems of multivariate polynomial equa-

tions, the following references may be consulted [17, 49, 98, 156, 157, 178].

4.5 Numerical solution to SDEs

The solutions to ODEs are functions, while the solutions to SDEs are stochastic processes.

We deﬁne a continuous-time stochastic process X as a set of random variables X

(t)

where the index variable t ≥ 0 takes a continuous set of values. The index variable t may

represent time.

Suppose we have an SDE model of the form dX = F(X)dt + σG(X)dW where W

is a stochastic process called Brownian motion (Wiener process). The diﬀerential dW of

W is called white noise. Brownian motion is the continuous version of “random walk”

and has the following properties:

1. For each t, the random variable W

(t)

is normally distributed with mean zero and

variance t.

2. For each t

i

< t

i+1

, the normal random variable ∆W

(t

i

)

= W

(t

i+1

)

− W

(t

i

)

is in-

dependent of the random variables W

(t

j

)

, 0 ≤ j ≤ t

i

(i.e., W has independent

increments).

3. Brownian motion W can be represented by continuous paths (but is not diﬀeren-

tiable).

Suppose W

(t

0

)

= 0. We can simulate a Brownian motion using computers by dis-

cretizing time as 0 = t

0

< t

1

< . . . and choosing a random number that would represent

∆W

(t

i−1

)

from the normal distribution N(0, t

i

− t

i−1

) =

√

t

i

−t

i−1

N(0, 1). This implies

that we obtain W

(t

i

)

by multiplying

√

t

i

−t

i−1

by a standard normal random number and

then adding the product to W

(t

i−1

)

.

Chapter 4. Preliminaries Analysis of Nonlinear Systems 34

The solution to an SDE model has diﬀerent realizations because it is based on

random numbers. We can approximate a realization of the solution by using numerical

solvers such as the Euler-Maruyama and Milstein methods. In this thesis, we use the

Euler-Maruyama method. The Euler-Maruyama method is similar to the Euler method

for ODEs.

Algorithm 2 Euler-Maruyama method

Discretize the time as 0 < t

1

< t

2

< . . . < t

end

.

Suppose Y

t

i

is the approximate solution to X

(t

i

)

.

Input initial condition X

t

0

. Let Y

t

0

:= X

t

0

.

For i = 0, 1, 2 . . . , end −1 do

∆W

(t

i

)

=

√

t

i+1

−t

i

rand

N(0,1)

, where rand

N(0,1)

is a standard normal random number.

Y

t

i+1

= Y

t

i

+F(Y

t

i

)(t

i+1

−t

i

) +σG(Y

t

i

)(∆W

(t

i

)

).

end

Euler-Maruyama has order 1/2, that is, for any time t the expected value of the error

E {|X

t

−Y

t

|} is an element of O((∆t)

1/2

) as ∆t →0. Note that for easy simulation, we

can suppose that we have equal step sizes ∆t

i

= (t

i+1

−t

i

). For a more detailed discussion

on Brownian motion and SDEs, the following reference may be consulted [95, 147].

For a more detailed discussion on the analysis of nonlinear systems, the following

references may be consulted [3, 56, 134, 146, 147].

Chapter 5

Results and Discussion

Simpliﬁed GRN and ODE Model

In this thesis, we represent the dynamics of the simpliﬁed gene network of MacArthur

et al. [113] using a system of Ordinary Diﬀerential Equations (ODEs) based on the

Cinquin-Demongeot formalism [38]. We prove the existence and uniqueness of solutions

to the ODE model under some assumptions.

5.1 Simpliﬁed MacArthur et al. model

Figure 5.1: The original MacArthur et al. [113] mesenchymal gene regulatory network.

35

Chapter 5. Results and Discussion Simpliﬁed GRN and ODE Model 36

Let us recall the MacArthur et al. [113] GRN in Chapter (3) (see Figure (5.1)). This

GRN represents a multipotent cell that could diﬀerentiate into three cell types — bone,

cartilage and fat.

Figure 5.2: Possible paths that result in positive feedback loops. Shaded boxes denote

that the path repeats.

We refer to the group of OCT4, SOX2, NANOG and their multimers (protein com-

plexes) as the pluripotency module, and the group of SOX9, RUNX2 and PPAR-γ as

the diﬀerentiation module. OCT4, SOX2, NANOG and their multimers in the original

MacArthur et al. GRN [113] do not have autoactivation loops, but notice that the path

NANOG →OCT4-SOX2-NANOG →OCT4 →OCT4-SOX2 →SOX2 →OCT4-SOX2-

NANOG →NANOG is one of the positive feedback loops of the GRN (see Figure (5.2)).

A positive feedback loop that contains OCT4, SOX2, NANOG and their multimers can

be regarded as an autoactivation loop of the pluripotency module.

Both the OCT4-SOX2-NANOG and OCT4-SOX2 multimers inhibit SOX9, RUNX2

and PPAR-γ (as represented by the green bars in Figure (5.1)). On the other hand,

SOX9, RUNX2 and PPAR-γ inhibit OCT4, SOX2 and NANOG (as represented by the

Chapter 5. Results and Discussion Simpliﬁed GRN and ODE Model 37

blue bars in Figure (5.1)). These inhibitions imply that the pluripotency module inhibits

the diﬀerentiation module and vice versa.

Figure 5.3: The simpliﬁed MacArthur et al. GRN

Since the pluripotent module can be represented as a node with autoactivation and

mutual inhibition with the other nodes, then we can simplify the GRN (5.1) by coarse-

graining. We represent the pluripotency module as one node, and we call it the sTF

(stemness transcription factor) node. From eight nodes, we only have four nodes. The

coarse-grained biological network of the MacArthur et al. GRN [113] is shown in Figure

(5.3) and from now on we shall refer to this as our simpliﬁed network. This simpliﬁed

Chapter 5. Results and Discussion Simpliﬁed GRN and ODE Model 38

network represents a phenomenological model of the mesenchymal cell diﬀerentiation

system. Since each node undergoes autocatalysis (autoactivation) and inhibition by

the other nodes (as shown by the arrows and bars) then the simpliﬁed GRN is in the

simultaneous-decision-model form that can be translated into a Cinquin-Demongeot [38]

ODE model (refer to Figure (3.4)).

It is diﬃcult to study the qualitative behavior of the ODE model by MacArthur et

al. [113] (see Equations (3.6) and (3.7)) using analytic methods. This is the reason for

the simpliﬁcation of the MacArthur et al. [113] GRN where the essential qualitative

dynamics are still preserved. We translate the dynamics of the simpliﬁed network into a

Cinquin-Demongeot [38] ODE model for easier analysis.

One limitation of a phenomenological model is that it excludes time-delays that may

arise from the deleted molecular details. However, a phenomenological model is suﬃcient

to address the general principles of cellular diﬀerentiation and cellular programming such

as the temporal behavior of the dynamics of the GRN [70].

5.2 The generalized Cinquin-Demongeot ODE model

In [38], Cinquin and Demongeot suggested to extend their model to include combinato-

rial interactions and non-symmetrical networks (i.e., each node does not have the same

relationship with other nodes and each equation in the system of ODEs does not have

equal parameter values). We include more adjustable parameters to their model to rep-

resent a wider range of situations. In this generalized model, some diﬀerentiation factors

can be stronger than others. We generalize the Cinquin-Demongeot (2005) ODE model

as follows (X = ([X

1

], [X

2

], . . . , [X

n

])):

d[X

i

]

dt

= F

i

(X) =

β

i

[X

i

]

c

i

K

i

c

i

+ [X

i

]

c

i

+

n

j=1,j=i

γ

ij

[X

j

]

c

ij

+α

i

s

i

−ρ

i

[X

i

] (5.1)

where i = 1, 2, ..., n and n is the number of nodes.

Chapter 5. Results and Discussion Simpliﬁed GRN and ODE Model 39

In our simpliﬁed network, we have four nodes and thus, n = 4. Some of our results

are applicable not only to n = 4 but to any dimension. The state variable [X

i

] represents

the concentration of the corresponding TF. Speciﬁcally, let [X

1

] := [RUNX2], [X

2

] :=

[SOX9], [X

3

] := [PPAR−γ] and [X

4

] := [sTF]. To have biological signiﬁcance, we

restrict [X

i

] and the parameters to be nonnegative real numbers.

The parameter β

i

is the relative speed of transcription, ρ

i

is the assumed ﬁrst-order

degradation rate associated with X

i

, and γ

ij

is the diﬀerentiation stimulus that aﬀects

the inhibition of X

i

by X

j

. If γ

ij

= 0 then X

j

does not inhibit the growth of [X

i

]. We

denote the term α

i

s

i

by

g

i

:= α

i

s

i

which represents basal or constitutive expression of the corresponding TF that is aﬀected

by the exogenous stimulus with concentration s

i

. In other words, α

i

s

i

is a constant

production term that enhances the concentration of X

i

. Speciﬁcally, let s

1

:= [RA +

BMP4], s

2

:= [RA +TGF−β], s

3

:= [RA +Insulin] and s

4

:= 0.

We deﬁne the multivariate function H

i

by

H

i

([X

i

], [X

2

], . . . , [X

n

]) =

β

i

[X

i

]

c

i

K

i

c

i

+ [X

i

]

c

i

+

n

j=1,j=i

γ

ij

[X

j

]

c

ij

(5.2)

which comes from the typical Hill equation. The terms

n

j=1,j=i

γ

ij

[X

j

]

c

ij

in the denomi-

nator reﬂects the inhibitory inﬂuence of other TFs on the change of concentration of X

i

.

We denote the parameter K

i

c

i

> 0 by

K

i

:= K

i

c

i

which is related to the threshold or dissociation constant.

The parameter c

i

≥ 1 represents the Hill constant and aﬀects the steepness of the

Hill curve associated with [X

i

], and denotes the homomultimerization-induced positive

cooperativity (for autocatalysis). The parameter c

ij

denotes the heteromultimerization-

induced negative cooperativity (for mutual inhibition). Cooperativity describes the inter-

actions among binding sites where the aﬃnity or relationship of a binding site positively

Chapter 5. Results and Discussion Simpliﬁed GRN and ODE Model 40

or negatively changes depending on itself or on the other binding sites. Note that coop-

erativity requires more than one binding site.

Notice that the lower bound of H

i

(5.2) is zero and its upper bound is β

i

. Thus, the

parameter β

i

can also be interpreted as the maximal expression rate of the corresponding

TF.

Explicitly, two mathematically unequal amounts of concentration can be regarded as

biologically equal if their diﬀerence is not signiﬁcant, that is, [X

i

] ≈ [X

j

] if [X

i

] = [X

j

] ±

where is acceptably small. We say that [X

i

] suﬃciently dominates [X

j

] if [X

i

] >

[X

j

] and [X

i

] ≈ [X

j

]. In addition, scientists compare the concentration of X

i

to the

concentration of X

j

by looking at the ratio of [X

i

] and [X

j

] — for example, [X

i

] ≈ [X

j

],

[X

j

] = 0 if

[X

i

]

[X

j

]

>

1

≥ 1 or if

[X

i

]

[X

j

]

<

2

≤ 1 where

1

and

2

are some acceptable tolerance

constants.

We say that a TF is switched-oﬀ or inactive if [TF] = 0, and switched-on oth-

erwise. However, as an approximation, a TF with suﬃciently low concentration can be

considered to be “switched-oﬀ”.

If no component representing a node from the diﬀerentiation module suﬃciently dom-

inates [sTF] (e.g. [sTF] ≥ [OCT4], [sTF] ≥ [SOX2] and [sTF] ≥ [PPAR−γ]) and sTF

is switched-on, then the state represents a pluripotent cell. If all the components of a

state are (approxmiately) equal and all TFs are switched-on, then the state represents a

primed stem cell.

If at least one component from the diﬀerentiation module suﬃciently dominates

[sTF], then the state represents either a partially diﬀerentiated or a fully diﬀer-

entiated cell. If exactly three components from the diﬀerentiation module are (approx-

imately) equal, then the state represents a tripotent cell. If exactly two components

from the diﬀerentiation module are (approximately) equal and suﬃciently dominate all

other components (possibly including [sTF]), then the state represents a bipotent cell.

If sTF is switched-oﬀ, then the cell had lost its ability to self-renew.

Chapter 5. Results and Discussion Simpliﬁed GRN and ODE Model 41

If exactly one component from the diﬀerentiation module suﬃciently dominates all

other components (possibly including [sTF]) but sTF is still switched-on, then the state

represents a unipotent cell. If exactly one TF from the diﬀerentiation module remains

switched-on and all other TFs including sTF are switched-oﬀ, then the state represents

a fully diﬀerentiated cell.

A trajectory converging to the equilibrium point (0, 0, . . . , 0) is a trivial case because

the zero state neither represents a pluripotent cell nor a cell diﬀerentiating into bone,

cartilage or fat. The trivial case may represent a cell diﬀerentiating towards other cell

types (e.g., towards becoming a neural cell) which are not in the domain of our GRN.

The zero state may also represent a cell that is in quiescent stage.

Deﬁnition 5.1 Stable component and stable equilibrium point. If [X

i

] converges

to [X

i

]

∗

for all initial conditions [X

i

]

0

near [X

i

]

∗

, then we say that the i-th component

[X

i

]

∗

of an equilibrium point X

∗

is stable; otherwise, [X

i

]

∗

is unstable. The equilibrium

point X

∗

= ([X

1

]

∗

, [X

2

]

∗

, . . . , [X

n

]

∗

) of the system (5.1) is stable if and only if all its

components are stable.

5.3 Geometry of the Hill function

The Hill function deﬁned by Equation (5.2) is a multivariate sigmoidal function when

c

i

> 1 and a multivariate hyperbolic-like function when c

i

= 1. If 1 < c

i

< n then X

i

has

autocatalytic cooperativity, and if 1 < c

ij

< n then the aﬃnity of X

j

to X

i

has negative

cooperativity. In addition, the state variable X

i

has no autocatalytic cooperativity if

c

i

= 1, while the aﬃnity of X

j

to X

i

has no negative cooperativity if c

ij

= 1.

We can investigate the multivariate Hill function by looking at the univariate function

deﬁned by

H

i

([X

i

]) =

β

i

[X

i

]

c

i

K

i

+ [X

i

]

c

i

+

n

j=1,j=i

γ

ij

[X

j

]

c

ij

(5.3)

Chapter 5. Results and Discussion Simpliﬁed GRN and ODE Model 42

where [X

j

], j = i is taken as a parameter. This means that we project the high-

dimensional space onto a two-dimensional plane. If c

i

= 1, the graph of the univariate

Hill function in the ﬁrst quadrant of the Cartesian plane is hyperbolic (for any value of

[X

j

], j = i), similar to the topology shown in Figure (5.4). If c

i

> 1, the graph of the

univariate Hill function in the ﬁrst quadrant is sigmoidal or “S”-shaped (for any value of

[X

j

], j = i), similar to one of the topologies shown in Figure (5.5).

When the value of

K

i

+

n

j=1,j=i

γ

ij

[X

j

]

c

ij

(5.4)

in the denominator of H

i

([X

i

]) increases, the graph of the Hill curve (for any c ≥ 1)

shrinks, as illustrated in Figure (5.6). When the value of c

i

increases, the graph of

Y = H

i

([X

i

]) gets steeper, as illustrated in Figure (5.7). If we add a term g

i

to H

i

([X

i

])

then the graph of Y = H

i

([X

i

]) in the Cartesian plane is translated upwards by g

i

units,

as illustrated in Figure (5.8).

We investigate the geometry of the Hill function as a prerequisite to our study of

determining the behavior of equilibrium points of our system (5.1).

Figure 5.4: Graph of the univariate Hill function when c

i

= 1.

Chapter 5. Results and Discussion Simpliﬁed GRN and ODE Model 43

Figure 5.5: Possible graphs of the univariate Hill function when c

i

> 1.

Chapter 5. Results and Discussion Simpliﬁed GRN and ODE Model 44

Figure 5.6: The graph of Y = H

i

([X

i

]) shrinks as the value of K

i

+

n

j=1,j=i

γ

ij

[X

j

]

c

ij

increases.

Figure 5.7: The Hill curve gets steeper as the value of autocatalytic cooperativity c

i

increases.

Chapter 5. Results and Discussion Simpliﬁed GRN and ODE Model 45

Figure 5.8: The graph of Y = H

i

([X

i

]) is translated upwards by g

i

units.

Chapter 5. Results and Discussion Simpliﬁed GRN and ODE Model 46

5.4 Positive invariance

We solve the multivariate equation F

i

(X) = 0 (for a speciﬁc i) by solving the intersections

of the (n+1)-dimensional curve induced by H

i

([X

1

], [X

2

], . . . , [X

n

]) +g

i

and the (n+1)-

dimensional hyperplane induced by ρ

i

[X

i

], as illustrated in Figure (5.9). That is, we ﬁnd

the real solutions to

β

i

[X

i

]

c

i

K

i

+ [X

i

]

c

i

+

n

j=1,j=i

γ

ij

[X

j

]

c

ij

+α

i

s

i

= ρ

i

[X

i

]. (5.5)

For easier analysis, we observe the intersections of the univariate functions deﬁned by

Y = H

i

([X

i

])+g

i

and Y = ρ

i

[X

i

] while varying the value of K

i

+

n

j=1,j=i

γ

ij

[X

j

]

c

ij

in the

denominator of the univariate Hill function H

i

([X

i

]) (see Figure (5.10) for illustration).

In the univariate case, we can look at Y = ρ

i

[X

i

] as a line in the Cartesian plane passing

through the origin with slope equal to ρ.

Figure 5.9: The 3-dimensional curve induced by H

i

([X

1

], [X

2

])+g

i

and the plane induced

by ρ

i

[X

i

], an example.

The following theorem guarantees that the state variables of our ODE model (5.1)

will never take negative values.

Chapter 5. Results and Discussion Simpliﬁed GRN and ODE Model 47

Figure 5.10: The intersections of Y = ρ

i

[X

i

] and Y = H

i

([X

i

]) +g

i

with varying values

of K

i

+

n

j=1,j=i

γ

ij

[X

j

]

c

ij

, an example.

Lemma 5.1 Positive invariance. The ﬂow φ(X

0

) of the generalized (multivariate)

Cinquin-Demongeot ODE model (5.1) (where X

0

= ([X

1

]

0

, [X

2

]

0

, . . . , [X

n

]

0

) ∈ R

⊕

n

can

be any initial condition) is always in R

⊕

n

.

Proof. Suppose ρ

i

> 0 ∀i and we have a nonnegative initial value X

0

. Figures (5.11) to

(5.14) illustrate all possible cases showing the topologies of the intersections of Y = ρ

i

[X

i

]

and Y = H

i

([X

i

]) +g

i

.

We employ the concept of ﬁxed point iteration (where we deﬁne our ﬁxed point as

[X

i

] satisfying H

i

([X

i

]) + g

i

= ρ

i

[X

i

]), or the geometric analysis shown in Figure (4.1)

(where we rotate the graph of the curves, making Y = ρ

i

[X

i

] the horizontal axis) to each

topology of the intersections of Y = ρ

i

[X

i

] and Y = H

i

([X

i

]) + g

i

. Figures (5.15) and

(5.16) illustrate how the ﬁxed point method and the geometric analysis shown in Figure

(4.1) are done.

Given speciﬁc values of [X

j

], j = i, the univariate Hill curve Y = H

i

([X

i

]) and

Y = ρ

i

[X

i

] have the following possible number of intersections (see Figures (5.11) to

(5.14)):

• two intersections (where one is stable);

Chapter 5. Results and Discussion Simpliﬁed GRN and ODE Model 48

• one intersection (which is stable); and

• three intersections (where two are stable).

We can see that there exists a stable intersection located in the ﬁrst quadrant (including

the axes) of the Cartesian plane that always attracts the trajectory of our ODE model

for any initial condition without escaping the ﬁrst quadrant (including the axes). Hence,

the ﬂow of the ODE model (5.1) will stay in R

⊕

n

for ρ

i

> 0 ∀i.

Now, suppose ρ

i

= 0 for at least one i. Then

d[X

i

]

dt

≥ 0 for all ([X

1

], [X

2

], . . . , [X

n

])

given nonnegative initial condition [X

i

]

0

— that is, the change in [X

i

] with respect to

time is always nonnegative implying that the value of [X

i

] will never decrease starting

from the initial condition [X

i

]

0

. Since [X

i

]

0

≥ 0, then [X

i

] ≥ 0 for any time t.

Thus, φ(X

0

) ⊆ R

⊕

n

∀X

0

∈ R

⊕

n

.

Consequently, Lemma (5.1) implies that F

i

is a function F

i

: R

⊕

n

→ R

n

, for i =

1, 2, . . . , n.

The following theorems are consequences of the proof of Theorem (5.1). We use

Lemma (5.2) in proving theorems in the succeeding chapters.

Lemma 5.2 Suppose ρ

i

> 0 for all i. Then the generalized Cinquin-Demongeot ODE

model (5.1) with X

0

∈ R

⊕

n

always has a stable equilibrium point. Moreover, any trajec-

tory of the model will converge to a stable equilibrium point.

Proof. This follows from the proof of Lemma (5.1).

Proposition 5.3 Suppose ρ

i

> 0 for all i. Then F

i

(X) will not “blow-up” and will not

approach inﬁnity given any initial condition X

0

∈ R

⊕

n

.

Proof. Since all trajectories of our system converge to a stable equilibrium point by

Lemma (5.1) and (5.2).

Chapter 5. Results and Discussion Simpliﬁed GRN and ODE Model 49

Figure 5.11: The possible number of intersections of Y = ρ

i

[X

i

] and Y = H

i

([X

i

]) +g

i

where c

i

= 1 and g

i

= 0. The value of K

i

+

n

j=1,j=i

γ

ij

[X

j

]

c

ij

is ﬁxed.

Figure 5.12: The possible number of intersections of Y = ρ

i

[X

i

] and Y = H

i

([X

i

]) +g

i

where c

i

= 1 and g

i

> 0. The value of K

i

+

n

j=1,j=i

γ

ij

[X

j

]

c

ij

is ﬁxed.

Chapter 5. Results and Discussion Simpliﬁed GRN and ODE Model 50

Figure 5.13: The possible number of intersections of Y = ρ

i

[X

i

] and Y = H

i

([X

i

]) +g

i

where c

i

> 1 and g

i

= 0. The value of K

i

+

n

j=1,j=i

γ

ij

[X

j

]

c

ij

is ﬁxed.

Figure 5.14: The possible number of intersections of Y = ρ

i

[X

i

] and Y = H

i

([X

i

]) +g

i

where c

i

> 1 and g

i

> 0. The value of K

i

+

n

j=1,j=i

γ

ij

[X

j

]

c

ij

is ﬁxed.

Chapter 5. Results and Discussion Simpliﬁed GRN and ODE Model 51

Figure 5.15: Finding the univariate ﬁxed points using cobweb diagram, an example.

We deﬁne the ﬁxed point as [X

i

] satisfying H([X

i

]) +g

i

= ρ

i

[X

i

].

Figure 5.16: The curves are rotated making the line Y = ρ

i

[X

i

] as the horizontal axis.

Positive gradient means instability, negative gradient means stability. If the gradient is

zero, we look at the left and right neighboring gradients.

Chapter 5. Results and Discussion Simpliﬁed GRN and ODE Model 52

5.5 Existence and uniqueness of solution

Recall Peano’s Existence Theorem (4.1) stating that if each F

i

is continuous on B then the

system of ODEs has a local solution (not necessarily unique), given any initial condition

X

0

∈ B ⊆ R

⊕

n

.

Also, recall the local and global existence-uniqueness theorems (4.2) and (4.3). If the

partial derivatives

∂F

i

∂[X

j

]

i, j = 1, 2, . . . , n are continuous on B ⊆ R

⊕

n

, then the system of

ODEs has a unique local solution given any initial condition X

0

∈ B. Moreover, if the

absolute value of these partial derivatives are bounded for all X ∈ B, then the system of

ODEs has exactly one solution deﬁned for all t ∈ R

⊕

for any initial condition X

0

∈ B.

Lipschitz continuity is important in proving the existence and uniqueness of solutions.

Observing Figures (5.4) and (5.5), we can see that there are functions H

i

that are not

diﬀerentiable at [X

i

] = 0. Consequently, if H

i

is not diﬀerentiable at [X

i

] = 0 then F

i

is

also not diﬀerentiable at [X

i

] = 0. If we include [X

i

] = 0 in the domain of F

i

, then this

makes F

i

not Lipschitz continuous. We classify F

i

based on the nature of the parameter

c

i

.

We deﬁne two types of c

i

:

Type 1 c

i

≥ 1 and either an integer or a rational of the form c

i

=

p

i

q

i

where p

i

, q

i

are

positive integers and q

i

is odd.

Type 2 c

i

> 1 and either an irrational or a non-integer rational of the form c

i

=

p

i

q

i

where p

i

, q

i

are positive integers and q

i

is even.

The function F

i

, with c

i

of type 1, is diﬀerentiable at [X

i

] = 0; while the function F

i

,

with c

i

of type 2, is not diﬀerentiable at [X

i

] = 0.

Now, we prove several theorems that assure the existence and uniqueness of the

solution to our ODE model (5.1), given an initial condition.

Theorem 5.4 Suppose F

i

: R

⊕

n

→ R

n

, for i = 1, 2, . . . , n. Suppose that for all i, c

i

is

of type 1. Then the generalized Cinquin-Demongeot ODE model (5.1) has exactly one

solution deﬁned for all t ∈ [0, ∞) for any initial condition X

0

∈ R

⊕

n

.

Chapter 5. Results and Discussion Simpliﬁed GRN and ODE Model 53

Proof. Since K

i

> 0, then the denominator of the Hill function H

i

(5.2) is not identically

zero for any X ∈ R

⊕

n

. This implies that each F

i

is deﬁned and continuous on R

⊕

n

. Since

for all i, c

i

is of type 1, then it follows that F

i

is diﬀerentiable on R

⊕

n

.

The partial derivative

∂F

i

∂[X

i

]

is as follows:

∂F

i

∂[X

i

]

=

_

K

i

+ [X

i

]

c

i

+

n

j=1,j=i

γ

ij

[X

j

]

c

ij

_

β

i

c

i

[X

i

]

c

i

−1

−β

i

c

i

[X

i

]

2c

i

−1

_

K

i

+ [X

i

]

c

i

+

n

j=1,j=i

γ

ij

[X

j

]

c

ij

_

2

−ρ

i

. (5.6)

The partial derivative

∂F

i

∂[X

l

]

, i = l is as follows:

∂F

i

∂[X

l

]

=

−β

i

[X

i

]

c

i

(c

il

)γ

il

[X

l

]

c

il

−1

_

K

i

+ [X

i

]

c

i

+

n

j=1,j=i

γ

ij

[X

j

]

c

ij

_

2

. (5.7)

The denominator

_

K

i

+ [X

i

]

c

i

+

n

j=1,j=i

γ

ij

[X

j

]

c

ij

_

2

(5.8)

in the partial derivative

∂F

i

∂[X

l

]

(for l = i and l = i) is not identically zero for all X ∈ R

⊕

n

.

Hence, all the partial derivatives

∂F

i

∂[X

l

]

, i, l = 1, 2, . . . , n are continuous on R

⊕

n

.

Notice that the degree of the denominator (5.8) is greater than the degree of its

corresponding numerator in Equations (5.6) and (5.7). It follows that as the value of

at least one state variable approaches inﬁnity, then the value of

∂F

i

∂[X

i

]

approaches the

constant −ρ

i

and the value of

∂F

i

∂[X

l

]

(l = i) vanishes.

Since

∂F

i

∂[X

l

]

(for l = i and l = i) is continuous on R

⊕

n

(i.e., there are no “asymptotes”

on R

⊕

n

that would make the partial derivatives “blow-up”) and

∂F

i

∂[X

l

]

(l = i and l = i)

approaches a constant as the value of at least one state variable approaches inﬁnity, then

¸

¸

¸

∂F

i

∂[X

l

]

¸

¸

¸, i, l = 1, 2, . . . , n are bounded for all X ∈ R

⊕

n

.

Chapter 5. Results and Discussion Simpliﬁed GRN and ODE Model 54

Therefore, the system has a unique solution deﬁned for all t ∈ R

⊕

for any initial

condition X

0

∈ R

⊕

n

.

Proposition 5.5 Suppose F

i

: R

⊕

n

→ R

n

, for i = 1, 2, . . . , n. Suppose that for at least

one i, c

i

is of type 2. Then the generalized Cinquin-Demongeot ODE model (5.1) has

a local solution (not necessarily unique) given [X

i

]

0

= 0 as an initial value. Moreover,

the generalized Cinquin-Demongeot ODE model (5.1) has a unique local solution given

[X

i

]

0

= 0 as an initial value.

Proof. Since K

i

> 0, then the denominator of the Hill function H

i

(5.2) is not identically

zero for any X ∈ R

⊕

n

. This implies that each F

i

is deﬁned and continuous on R

⊕

n

.

By Peano’s Existence Theorem, the system has a local solution (not necessarily unique)

given [X

i

]

0

= 0 as an initial condition.

Suppose that for at least one i, c

i

is of type 2. Then for such certain i, F

i

is

diﬀerentiable on R

⊕

n

except when [X

i

] = 0. Note that the partial derivatives

∂F

i

∂[X

l

]

,

i, l = 1, 2, . . . , n (see Equation (5.6) and (5.7)) are continuous on R

+

n

(i.e., F

i

is locally

Lipschitz continuous on R

+

n

). Hence, the generalized Cinquin-Demongeot ODE model

(5.1) has a unique local solution given [X

i

]

0

= 0 as an initial value.

Remark: From the preceding proposition, at [X

i

] > 0 the trajectory of our ODE model

(5.1) is unique, but when the trajectory passes through [X

i

] = 0 the ODE model (5.1)

may (i.e., we are not sure) have more than one solution. Nevertheless, this will not aﬀect

our analysis to eﬀectively predict the behavior of our system when g

i

= 0 since [X

i

] = 0

is a component of a stable equilibrium point (i.e., [X

i

] will stay zero as t → ∞). Thus,

assuming g

i

= 0, the ﬂow of our ODE model does not change its qualitative behavior

even if the trajectory passes through [X

i

] = 0. See Figure (5.17) for illustration.

If g

i

> 0, we can show that even with the assumption that c

i

is of type 2 for at least

one i, our ODE model (5.1) can still have a unique solution deﬁned for all t ∈ [0, ∞) by

restricting the domain of F

i

.

Chapter 5. Results and Discussion Simpliﬁed GRN and ODE Model 55

Proposition 5.6 Suppose there are F

j

having g

j

> 0 and c

j

of type 2. Suppose there

are no F

i

, i = j having g

i

= 0 and c

i

of type 2. Then the generalized Cinquin-Demongeot

ODE model (5.1) has exactly one solution deﬁned for all t ∈ [0, ∞) for any initial values

[X

j

]

0

∈ R

+

and [X

i

]

0

∈ R

⊕

, i = j.

Proof. Notice that for g

j

> 0, [X

j

] = 0 will never be a component of a stable equilibrium

point (see Figure (5.18)). This implies that we can reduce the space of positive invariance

associated to [X

j

] (refer to Lemma (5.1)) from R

⊕

to R

+

. Thus, for initial value [X

j

] > 0,

we can restrict the domain of F

j

with respect to the variable [X

j

] to R

+

(i.e., we eliminate

the possibility of making [X

j

] = 0 as an initial value).

We follow the same ﬂow of proof as in Theorem (5.4). Since we only consider [X

j

] ∈

R

+

, then F

j

is now diﬀerentiable everywhere. The absolute value of the partial derivatives

of F

j

are continuous and bounded for all X where [X

j

] ∈ R

+

. Moreover, since there are

no F

i

, i = j having g

i

= 0 and c

i

of type 2, then it means that F

i

must have c

i

of type

1. The absolute value of the partial derivatives of F

i

are continuous and bounded for all

X where [X

i

] ∈ R

⊕

.

Hence, we conclude that the generalized Cinquin-Demongeot ODE model (5.1) has

exactly one solution deﬁned for all t ∈ [0, ∞) for any initial values [X

j

]

0

∈ R

+

and

[X

i

]

0

∈ R

⊕

, i = j.

Suppose g

j

> 0 but [X

j

]

0

= 0 is the j-th component of the initial condition. We

can still do numerical simulations to solve the ODE model (5.1) even when F

j

is not

diﬀerentiable at [X

j

] = 0. However, we need to do the numerical simulation with caution

because we are not sure if multiple solutions will arise. We can use multivariate ﬁxed

point algorithm to investigate the corresponding stable equilibrium point for this kind of

system.

Note that a c

ij

of type 2 does not aﬀect the existence and uniqueness of a solution

because [X

j

]

c

ij

only aﬀects the shrinkage of the graph of H

i

([X

i

]) (see Figure (5.6)).

Chapter 5. Results and Discussion Simpliﬁed GRN and ODE Model 56

Figure 5.17: When g

i

= 0, [X

i

] = 0 is a component of a stable equilibrium point.

Figure 5.18: When g

j

> 0, [X

j

] = 0 will never be a component of an equilibrium point.

Chapter 6

Results and Discussion

Finding the Equilibrium Points

In this chapter, we determine the location and number of equilibrium points of the gen-

eralized Cinquin-Demongeot ODE model (5.1). We only consider the biologically feasible

equilibrium points — those that are real-valued and nonnegative. For the following dis-

cussions, recall that K

i

> 0 ∀i. Appendix A contains illustrations related to this chapter.

6.1 Location of equilibrium points

Lemma 6.1 Given nonnegative state variables and parameters in (5.1), if g

i

> 0 then

ρ

i

> 0 is a necessary and suﬃcient condition for the existence of an equilibrium point.

Proof. Since [X

i

] ≥ 0, g

i

> 0 and all other parameters are nonnegative, then the decay

term −ρ

i

[X

i

] with ρ

i

> 0 is necessary for

F

i

(X) =

β

i

[X

i

]

c

i

K

i

+ [X

i

]

c

i

+

n

j=1,j=i

γ

ij

[X

j

]

c

ij

−ρ

i

[X

i

] +g

i

to be zero. The Hill curve induced by H

i

([X

1

], [X

2

], . . . , [X

n

]) (5.2) translated upwards

by g

i

> 0 and the hyperplane induced by ρ

i

[X

i

] will always intersect when ρ

i

> 0 and

will not intersect if ρ

i

= 0 (see Figures (5.11) to (5.14)).

Remark: If g

i

= 0 and ρ

i

= 0 then we have an equilibrium point with zero i-th component

(i.e.

i

(..., 0, ...)) but this equilibrium point is obviously unstable.

Theorem 6.2 The generalized Cinquin-Demongeot ODE model (5.1) has an equilibrium

point with i-th component equal to zero (i.e., [X

i

]

∗

= 0) if and only if g

i

= 0.

57

Chapter 6. Results and Discussion Finding the Equilibrium Points 58

Proof. If g

i

= 0 then

F

i

(X) =

β

i

[X

i

]

c

i

K

i

+ [X

i

]

c

i

+

n

j=1,j=i

γ

ij

[X

j

]

c

ij

−ρ

i

[X

i

] + 0 = 0,

implying [X

i

] = 0 is a root of F

i

(X) = 0. Furthermore, if [X

i

] = 0 is a root of F

i

(X) = 0

then by substitution,

β

i

[0]

c

i

K

i

+ [0]

c

i

+

n

j=1,j=i

γ

ij

[X

j

]

c

ij

−ρ

i

[0] +g

i

= 0,

g

i

must be zero.

The following corollary is very important because the case where the trajectory con-

verges to the origin is trivial. This zero state neither represents a pluripotent cell nor a

cell diﬀerentiating into bone, cartilage or fat.

Corollary 6.3 The zero state (0, 0, . . . , 0) can only be an equilibrium point if and only

if g

i

= 0 ∀i.

Proposition 6.4 Suppose ρ

i

> 0. If both β

i

> 0 and g

i

> 0 then

g

i

ρ

i

cannot be an i-th

component of an equilibrium point.

Proof. Suppose β

i

> 0, g

i

> 0 and

g

i

ρ

i

is an i-th component of an equilibrium point. Then

F

i

_

[X

1

], . . . ,

g

i

ρ

i

, . . . , [X

n

]

_

=

β

i

_

g

i

ρ

i

_

c

i

K

i

+

_

g

i

ρ

i

_

c

i

+

n

j=1,j=i

γ

ij

[X

j

]

c

ij

−ρ

i

g

i

ρ

i

+g

i

= 0

=

β

i

_

g

i

ρ

i

_

c

i

K

i

+

_

g

i

ρ

i

_

c

i

+

n

j=1,j=i

γ

ij

[X

j

]

c

ij

= 0

implying that β

i

_

g

i

ρ

i

_

c

i

= 0. Thus β

i

= 0 or g

i

= 0, a contradiction.

Chapter 6. Results and Discussion Finding the Equilibrium Points 59

Remark: If g

i

, ρ

i

> 0 then [X

i

] =

g

i

ρ

i

can only be an i-th component of an equilibrium

point if β

i

= 0.

Theorem 6.5 Suppose ρ

i

> 0. The value

g

i

+β

i

ρ

i

is the upper bound of, but will never be

equal to, [X

i

]

∗

(where [X

i

]

∗

is the i-th component of an equilibrium point). The equilibrium

points of our system lie in the hyperspace

_

g

1

ρ

1

,

g

1

+β

1

ρ

1

_

×

_

g

2

ρ

2

,

g

2

+β

2

ρ

2

_

×. . . ×

_

g

n

ρ

n

,

g

n

+β

n

ρ

n

_

. (6.1)

Proof. From Lemma (5.2), our system (5.1) always has an equilibrium point. Note that

[X

i

]

∗

< ∞ ∀i because [X

i

]

∗

= ∞ cannot be a component of an equilibrium point.

The minimum value of H

i

is zero which happens when β

i

= 0 or when [X

i

] = 0.

Hence, if H

i

([X

1

], [X

2

], . . . , [X

n

]) = 0 then F

i

(X) = g

i

−ρ

i

[X

i

] = 0, implying [X

i

] =

g

i

ρ

i

.

The upper bound of H

i

is β

i

which will only happen when [X

i

] = ∞. If H

i

([X

1

], [X

2

],

. . . , [X

n

]) = β

i

then F

i

(X) = β

i

− ρ

i

[X

i

] + g

i

= 0, implying [X

i

] =

g

i

+β

i

ρ

i

(but note that

this is just an upper bound and cannot be a component of an equilibrium point). See

Figure (6.1) for illustration.

Remark: The Hill curve and ρ[X

i

] intersect at inﬁnity when g

i

→∞, β

i

→∞or ρ

i

→0.

Moreover, if we have multiple stable equilibrium points lying on the hyperspace (6.1)

then one strategy for increasing the basin of attraction of a stable equilibrium point is by

increasing the value of β

i

(however, the number of stable equilibrium points may change

by doing this strategy).

In Chapter 5 Section 5.4, we are able to show the existence of an equilibrium point

but we do not know the value of the equilibrium point. Solving the system F

i

(X) = 0,

i = 1, 2, . . . , n can be interpreted as ﬁnding the intersections of the (n + 1)-dimensional

curves induced by each F

i

(X) and the (n + 1)-dimensional zero-hyperplane.

Chapter 6. Results and Discussion Finding the Equilibrium Points 60

Figure 6.1: Sample numerical solution in time series with the upper bound and lower

bound.

6.2 Cardinality of equilibrium points

In this section, we use the B´ezout Theorem (4.5) and Sylvester resultant method to

determine the number and exact values of equilibrium points.

Suppose c

i

and c

ij

are integers for all i and j. The corresponding polynomial equation

to (i = 1, 2, . . . , n)

F

i

(X) =

β

i

[X

i

]

c

i

K

i

+ [X

i

]

c

i

+

n

j=1,j=i

γ

ij

[X

j

]

c

ij

−ρ

i

[X

i

] +g

i

= 0 (6.2)

is

P

i

(X) =β

i

[X

i

]

c

i

+ (g

i

−ρ

i

[X

i

])

_

K

i

+ [X

i

]

c

i

+

n

j=1,j=i

γ

ij

[X

j

]

c

ij

_

= 0

=−ρ

i

[X

i

]

c

i

+1

+ (β

i

+g

i

) [X

i

]

c

i

−

_

K

i

+

n

j=1,j=i

γ

ij

[X

j

]

c

ij

_

(ρ

i

[X

i

])

+g

i

n

j=1,j=i

γ

ij

[X

j

]

c

ij

+g

i

K

i

= 0. (6.3)

Chapter 6. Results and Discussion Finding the Equilibrium Points 61

Theorem 6.6 Assume that all equations in the polynomial system (6.3) have no common

factor of degree greater than zero given a certain set of parameter values. Then the number

of equilibrium points of the generalized Cinquin-Demongeot ODE model (5.1) (where c

i

and c

ij

are integers) is at most

max{c

1

+ 1, c

1j

+ 1 ∀j} ×max{c

2

+ 1, c

2j

+ 1 ∀j} ×. . . ×max{c

n

+ 1, c

nj

+ 1 ∀j}.

Proof. The degree of P

i

is deg

i

= max{c

i

+1, c

ij

+1 ∀j}. Since for some parameter values

we assume that all equations in the polynomial system (6.3) have no common factor of

degree greater than zero then by the B´ezout Theorem (4.5), the number of complex

solutions to the polynomial system is at most max{c

1

+1, c

1j

+1 ∀j}×max{c

2

+1, c

2j

+

1 ∀j} × . . . × max{c

n

+ 1, c

nj

+ 1 ∀j}. It follows that this is the upper bound of the

number of equilibrium points.

The B´ezout Theorem (4.5) does not give the exact number of equilibrium points

but only the upper bound. Also, Theorem (6.6) is dependent on the value of c

i

and

c

ij

as well as on n. According to Cinquin and Demongeot, manipulating the strength

of cooperativity (c

i

and c

ij

) is of minimal biological relevance [38]. Nevertheless, the

possible dependence of the number of equilibrium points on n (dimension of our state

space) has a biological implication. The dependence on n may be due to the potency of

the cell.

It is necessary to check if all equations in the polynomial system have no common

factor of degree greater than zero, because if they do then there will be inﬁnitely many

complex solutions. Recall from Theorem (4.7) that we can determine the existence of

inﬁnitely many complex solutions by checking if res(P

1

, P

2

; X

i

) (the determinant of the

Sylvester matrix) is identically zero, or by checking if P

1

and P

2

have a non-constant

common factor.

However, the inﬁnite number of complex solutions arise if [X

i

] can take any complex

value. There can be solutions with negative (and possibly complex-valued) components

Chapter 6. Results and Discussion Finding the Equilibrium Points 62

that have no biological importance. Consequently, we need to do ad hoc investigation to

remove the solutions with negative or non-real-valued components and to check whether

the inﬁnite number of solutions still arise when [X

i

] ∀i are restricted to be nonnegative

real numbers. It is possible that our polynomial system (6.3) has a ﬁnite number of

nonnegative real solutions even though the system has a non-constant common factor.

In order to determine the exceptions, we determine the set of parameter values (where

the strengths of cooperativity are integer-valued) that would give rise to a system of

equations having a non-constant common factor. We have found one case (and this is

the only case) where such common factor exists.

Theorem 6.7 Suppose c

i

= c

ij

= 1, g

i

= 0, γ

ij

= 1, β

i

= β

j

= β > 0, ρ

i

= ρ

j

= ρ > 0

and K

i

= K

j

= K > 0, for all i and j. Then the ODE model (5.1) has inﬁnitely many

non-isolated equilibrium points if and only if β > ρK. Moreover, if β ≤ ρK then there

is exactly one equilibrium point which is the origin.

Proof. Recall (6.3), from the nonlinear system F

i

(X) = 0 (i = 1, 2, . . . , n),

β

i

[X

i

]

c

i

K

i

+ [X

i

]

c

i

+

n

j=1,j=i

γ

ij

[X

j

]

c

ij

−ρ

i

[X

i

] +g

i

= 0

we have the corresponding polynomial system P

i

(X) = 0 (i = 1, 2, . . . , n),

β

i

[X

i

]

c

i

−ρ

i

K

i

[X

i

] −ρ

i

[X

i

]

c

i

+1

−ρ

i

[X

i

]

n

j=1,j=i

γ

ij

[X

j

]

c

ij

+g

i

K

i

+g

i

[X

i

]

c

i

+g

i

n

j=1,j=i

γ

ij

[X

j

]

c

ij

= 0.

Suppose c

i

= c

ij

= 1, g

i

= 0, γ

ij

= 1, β

i

= β

j

= β > 0, ρ

i

= ρ

j

= ρ > 0 and

K

i

= K

j

= K > 0 (notice that we have a Michaelis-Menten-like symmetric system).

Chapter 6. Results and Discussion Finding the Equilibrium Points 63

Then the polynomial system can be written as (i = 1, 2, . . . , n)

β[X

i

] −ρK[X

i

] −ρ[X

i

]

2

−ρ[X

i

]

n

j=1,j=i

[X

j

] = 0

⇒[X

i

]

_

β −ρK −ρ[X

i

] −ρ

n

j=1,j=i

[X

j

]

_

= 0

⇒[X

i

] = 0 or

_

β −ρK −ρ[X

i

] −ρ

n

j=1,j=i

[X

j

]

_

= 0. (6.4)

Notice that the factor

β −ρK −ρ[X

i

] −ρ

n

j=1,j=i

[X

j

]

= β −ρK −ρ

n

j=1

[X

j

] (6.5)

is common to all equations in the polynomial system given the assumed parameter values.

Thus, by Theorem (4.7), there are inﬁnitely many complex solutions where [X

j

] can be

any complex number. However, note that we have restricted [X

j

] to be nonnegative, so

we do further investigation to determine the conditions for the existence of an inﬁnite

number of solutions given strictly nonnegative [X

j

]. We focus our investigation on real-

valued solutions.

Suppose B = β −ρK.

Case 1: If β = ρK then B = 0 and thus, B−ρ

n

j=1

[X

j

] will never be zero except when

[X

j

] = 0 ∀j (since [X

j

] can take only nonnegative values). Hence, the only equilibrium

point to the system is the origin.

Case 2: If β < ρK then B < 0 and thus, B − ρ

n

j=1

[X

j

] will always be negative and

will not have any zero for any nonnegative value of [X

j

]. Hence, the only equilibrium

point is the origin (which is derived from [X

i

] = 0, i = 1, 2, . . . , n in Equation (6.4)).

Case 3: If β > ρK then B > 0 and thus, there exist solutions to the equation

B − ρ

n

j=1

[X

j

] = 0. Notice that the set of nonnegative real-valued solutions to B −

Chapter 6. Results and Discussion Finding the Equilibrium Points 64

ρ

n

j=1

[X

j

] = 0 is a hyperplane (e.g., it is a line for n = 2 and it is a plane for n = 3).

Hence, there are inﬁnitely many non-isolated equilibrium points when β > ρK.

Conversely, if the generalized Cinquin-Demongeot ODE model (5.1) with c

i

= c

ij

= 1,

g

i

= 0, γ

ij

= 1, β

i

= β

j

= β > 0, ρ

i

= ρ

j

= ρ > 0 and K

i

= K

j

= K > 0 has

inﬁnitely many equilibrium points then the model’s corresponding polynomial system

has a common factor of degree greater than zero. The only possible common factor is

shown in (6.5). The only case where such factor will have inﬁnitely many non-isolated

nonnegative solutions is when β > ρK.

Corollary 6.8 Suppose c

i

= c

ij

= 1, g

i

= 0, γ

ij

= 1, β

i

= β

j

= β > 0, ρ

i

= ρ

j

= ρ > 0

and K

i

= K

j

= K > 0. If β > ρK then the equilibrium points of system (5.1) are the

origin and the non-isolated points lying on the hyperplane with equation

n

j=1

[X

j

] =

β

ρ

−K, [X

j

] ≥ 0 ∀j. (6.6)

Proof. This is a consequence of the proof of Theorem (6.7).

Theorem 6.9 The generalized Cinquin-Demongeot ODE model (5.1) (where c

i

and c

ij

are integers) has a ﬁnite number of equilibrium points except when all of the following

conditions are satisﬁed: c

i

= c

ij

= 1, g

i

= 0, γ

ij

= 1, β

i

= β

j

= β > 0, ρ

i

= ρ

j

= ρ > 0,

K

i

= K

j

= K > 0 and β > ρK, for all i and j.

Proof. When c

i

= c

ij

= 1, g

i

= 0, γ

ij

= 1, β

i

= β

j

= β > 0, ρ

i

= ρ

j

= ρ > 0,

K

i

= K

j

= K > 0 and β > ρK for all i and j then, by Theorem (6.7), the generalized

Cinquin-Demongeot ODE model (5.1) has an inﬁnite number of equilibrium points.

Now, suppose at least one of the following conditions is not satisﬁed: c

i

= c

ij

= 1,

g

i

= 0, γ

ij

= 1, β

i

= β

j

= β > 0, ρ

i

= ρ

j

= ρ > 0, K

i

= K

j

= K > 0 and β > ρK,

for all i and j. Recall the corresponding polynomial system P

i

(X) = 0 (6.3) to our

generalized Cinquin-Demongeot ODE model (5.1) (where c

i

and c

ij

are integers), which

is (for i = 1, 2, . . . , n)

Chapter 6. Results and Discussion Finding the Equilibrium Points 65

β

i

[X

i

]

c

i

−ρ

i

K

i

[X

i

] −ρ

i

[X

i

]

c

i

+1

−ρ

i

[X

i

]

n

j=1,j=i

γ

ij

[X

j

]

c

ij

+g

i

K

i

+g

i

[X

i

]

c

i

+g

i

n

j=1,j=i

γ

ij

[X

j

]

c

ij

= 0. (6.7)

Suppose g

i

= 0. The factorization of the polynomials in the above polynomial system

(6.7) is of the form:

[X

i

]

_

β

i

[X

i

]

c

i

−1

−ρ

i

K

i

−ρ

i

[X

i

]

c

i

−ρ

i

n

j=1,j=i

γ

ij

[X

j

]

c

ij

_

(6.8)

The factor [X

i

] is deﬁnitely not a common factor of our system. Moreover, there will

always be a [X

i

]

c

i

−1

term in the factor β

i

[X

i

]

c

i

−1

−ρ

i

K

i

−ρ

i

[X

i

]

c

i

−ρ

i

n

j=1,j=i

γ

ij

[X

j

]

c

ij

that will make β

i

[X

i

]

c

i

−1

−ρ

i

K

i

−ρ

i

[X

i

]

c

i

−ρ

i

n

j=1,j=i

γ

ij

[X

j

]

c

ij

not a common factor of

our system.

For example, suppose g

i

= 0, γ

ij

= 1, β

i

= β, ρ

i

= ρ, K

i

= K and c

i

= c

ij

for all i

and j, then we have

Factor in equation 1 : [X

1

]

c

1

−1

−ρK −ρ

n

j=1

[X

j

]

c

j

−1

Factor in equation 2 : [X

2

]

c

2

−1

−ρK −ρ

n

j=1

[X

j

]

c

j

−1

(6.9)

.

.

.

Factor in equation 3 : [X

n

]

cn−1

−ρK −ρ

n

j=1

[X

j

]

c

j

−1

.

Notice that the presence of [X

i

]

c

i

−1

in equation i makes at least one factor unique (“at

least one” because at most n − 1 equations may satisfy the restriction: c

i

= c

ij

= 1,

g

i

= 0, γ

ij

= 1, β

i

= β

j

= β > 0, ρ

i

= ρ

j

= ρ > 0, K

i

= K

j

= K > 0 and β > ρK, and

at least one equation does not).

Chapter 6. Results and Discussion Finding the Equilibrium Points 66

Suppose g

i

= 0 for at least one i. By the above proof (for g

j

= 0, j = i) as well as by

the presence of [X

i

]

c

i

(in the ﬁrst term of Equation (6.7)) and [X

i

] (in the second, third

and fourth terms of Equation (6.7)), then the polynomials in the polynomial system (6.7)

are collectively relatively prime.

For example, suppose γ

ij

= 1, β

i

= β, ρ

i

= ρ, K

i

= K, g

i

= g and c

i

= c

ij

for all i

and j, then we have

β[X

1

]

c

1

−ρK[X

1

] −ρ[X

1

]

n

j=1

[X

j

]

c

j

+gK +g

n

j=1

[X

j

]

c

j

β[X

2

]

c

2

−ρK[X

2

] −ρ[X

2

]

n

j=1

[X

j

]

c

j

+gK +g

n

j=1

[X

j

]

c

j

(6.10)

.

.

.

β[X

n

]

cn

−ρK[X

n

] −ρ[X

n

]

n

j=1

[X

j

]

c

j

+gK +g

n

j=1

[X

j

]

c

j

Notice that the presence of [X

i

] in equation i makes at least one equation relatively prime

(“at least one” because at most n −1 equations may satisfy the restriction: c

i

= c

ij

= 1,

g

i

= 0, γ

ij

= 1, β

i

= β

j

= β > 0, ρ

i

= ρ

j

= ρ > 0, K

i

= K

j

= K > 0 and β > ρK, and

at least one equation does not).

Therefore, by Theorem (4.7), there is a ﬁnite number of equilibrium points.

**Now, we prove a theorem showing that the equilibrium points ([X
**

1

]

∗

[X

2

]

∗

, [X

3

]

∗

, 0) of

a system with n = 4 and g

4

= 0 are exactly the equilibrium points of the corresponding

system with n = 3. Generally, we state the following theorem:

Theorem 6.10 Suppose g

n

= 0. Then the n-dimensional system is more general than

the (n − 1)-dimensional system. That is, we can derive the equilibrium points of the

(n−1)-dimensional system by getting the equilibrium points of the n-dimensional system

where [X

n

]

∗

= 0.

Proof. When [X

n

]

∗

= 0 and g

n

= 0, the n-dimensional system reduces to an (n − 1)-

dimensional system.

Chapter 6. Results and Discussion Finding the Equilibrium Points 67

In the following illustrations, we show how to ﬁnd equilibrium points using the

Sylvester resultant. We assign speciﬁc values to some parameters. Let us consider our

simpliﬁed MacArthur et al. GRN where n = 4 (5.3).

6.2.1 Illustration 1

Consider that all parameters are equal to 1 except for g

2

= g

3

= g

4

= 0. We have the

following polynomial system:

P

1

([X

1

], [X

2

], [X

3

], [X

4

]) = [X

1

] −[X

1

](1 + [X

1

] + [X

2

] + [X

3

] + [X

4

])

+ (1 + [X

1

] + [X

2

] + [X

3

] + [X

4

]) = 0

P

2

([X

1

], [X

2

], [X

3

], [X

4

]) = [X

2

] −[X

2

](1 + [X

1

] + [X

2

] + [X

3

] + [X

4

]) = 0 (6.11)

P

3

([X

1

], [X

2

], [X

3

], [X

4

]) = [X

3

] −[X

3

](1 + [X

1

] + [X

2

] + [X

3

] + [X

4

]) = 0

P

4

([X

1

], [X

2

], [X

3

], [X

4

]) = [X

4

] −[X

4

](1 + [X

1

] + [X

2

] + [X

3

] + [X

4

]) = 0.

The Sylvester matrix associated with P

1

and P

2

with [X

1

] as variable is

_

¸

¸

_

−1 1 −[X

2

] −[X

3

] −[X

4

] 1 + [X

2

] + [X

3

] + [X

4

]

−[X

2

] −[X

2

]

2

−[X

2

][X

3

] −[X

2

][X

4

] 0

0 −[X

2

] −[X

2

]

2

−[X

2

][X

3

] −[X

2

][X

4

]

_

¸

¸

_

. (6.12)

Then res(P

1

, P

2

; [X

1

]) = [X

2

]

2

. Therefore, [X

2

]

∗

= 0.

By doing the same procedure as above, res(P

1

, P

3

; [X

1

]) = [X

3

]

2

and res(P

1

, P

4

; [X

1

])

= [X

4

]

2

. Hence, [X

3

]

∗

= [X

4

]

∗

= 0. Note that we cannot use res(P

2

, P

3

; [X

1

]), res(P

3

, P

4

;

[X

1

]) and res(P

2

, P

4

; [X

1

]) because these resultants are identically zero, that is, P

2

, P

3

and P

4

have common factors. So we need to be careful in choosing what combinations

of polynomial equations are to be used in determining the equilibrium points. Note that

P

1

does not share a common factor with the other three polynomial equations.

Chapter 6. Results and Discussion Finding the Equilibrium Points 68

Substituting [X

2

]

∗

= [X

3

]

∗

= [X

4

]

∗

= 0 in P

1

we have −[X

1

]

∗

2

+ 1 + [X

1

]

∗

= 0. This

means that [X

1

]

∗

=

1+

√

5

2

(we disregard

1−

√

5

2

because this is negative).

Therefore, we only have one equilibrium point,

_

1+

√

5

2

, 0, 0, 0

_

.

6.2.2 Illustration 2

Consider that all parameters are equal to 1 except for c

i

= c

ij

= 2, g

i

= 0, i, j = 1, 2, 3, 4.

We have the following polynomial system:

P

1

([X

1

], [X

2

], [X

3

], [X

4

]) = [X

1

]

2

−[X

1

](1 + [X

1

]

2

+ [X

2

]

2

+ [X

3

]

2

+ [X

4

]

2

) = 0

P

2

([X

1

], [X

2

], [X

3

], [X

4

]) = [X

2

]

2

−[X

2

](1 + [X

1

]

2

+ [X

2

]

2

+ [X

3

]

2

+ [X

4

]

2

) = 0 (6.13)

P

3

([X

1

], [X

2

], [X

3

], [X

4

]) = [X

3

]

2

−[X

3

](1 + [X

1

]

2

+ [X

2

]

2

+ [X

3

]

2

+ [X

4

]

2

) = 0

P

4

([X

1

], [X

2

], [X

3

], [X

4

]) = [X

4

]

2

−[X

4

](1 + [X

1

]

2

+ [X

2

]

2

+ [X

3

]

2

+ [X

4

]

2

) = 0.

The Sylvester matrix associated with P

1

and P

2

with [X

1

] as variable is

_

¸

¸

¸

¸

¸

¸

¸

¸

_

a

11

a

12

a

13

a

14

0

0 a

11

a

12

a

13

a

14

a

31

a

32

a

33

0 0

0 a

31

a

32

a

33

0

0 0 a

31

a

32

a

33

_

¸

¸

¸

¸

¸

¸

¸

¸

_

. (6.14)

where a

11

= −1, a

12

= 1, a

13

= −1 −[X

2

]

2

−[X

3

]

2

−[X

4

]

2

, a

14

= 0, a

31

= −[X

2

], a

32

= 0

and a

33

= [X

2

]

2

−[X

2

] −[X

2

]

3

−[X

2

][X

3

]

2

−[X

2

][X

4

]

2

. Then

res(P

1

, P

2

; [X

1

]) =−[X

2

]

3

(−[X

2

] + [X

4

]

2

+ 2[X

2

]

2

+ [X

3

]

2

+ 1) (6.15)

(−[X

2

] + [X

4

]

2

+ [X

2

]

2

+ [X

3

]

2

+ 1).

Chapter 6. Results and Discussion Finding the Equilibrium Points 69

Notice that the factors −[X

2

]+[X

4

]

2

+2[X

2

]

2

+[X

3

]

2

+1 and −[X

2

]+[X

4

]

2

+[X

2

]

2

+[X

3

]

2

+1

in (6.15) do not have real zeros. Therefore, [X

2

]

∗

= 0.

Since the system is symmetric, then it follows that [X

1

]

∗

= [X

3

]

∗

= [X

4

]

∗

= 0, too.

Hence, we only have one equilibrium point which is the origin.

Additional illustrations are presented in Appendix A (for n = 2 and n = 3).

When all parameters are equal to 1 except for c

i

= c

ij

= 2 and g

i

= 0 for all i, j,

then the only equilibrium point is the origin. Actually, this kind of system is the original

Cinquin-Demongeot ODE model [38] without “leak” where β = 1 and c = 2 (refer to

system (3.4)). We state the following proposition:

Proposition 6.11 If c

i

> 1, g

i

= 0, K

i

≥ 1, β

i

= 1 and ρ

i

= 1 for all i, then our system

has only one equilibrium point which is the origin.

Proof. Let us ﬁrst consider the case where [X

j

] = 0 ∀j = i and K

i

= 1. The graphs of

Y = H

i

([X

i

]) (with increasing value of c

i

) and Y = [X

i

] is illustrated in Figure (6.2). If

c

i

→∞then [X

i

]

c

i

→∞for any [X

i

] > 1. As [X

i

]

c

i

→∞(with [X

i

] > 1), the univariate

Hill function H

i

([X

i

]) →β = 1. Hence, the univariate Hill curve Y = H

i

([X

i

]) will never

touch the point (1, 1) lying on Y = [X

i

] for ﬁnite c

i

.

Now, as the values of γ

ij

[X

j

] ∀j = i and K

i

increase then the univariate Hill curve

Y = H

i

([X

i

]) will just shrink and will deﬁnitely not intersect the decay line Y = [X

i

]

except at the origin (see Chapter 5 Section 5.3 for the discussion regarding the geometry

of the Hill curve).

Hence, for any value of [X

i

] and [X

j

] (for all j = i), the univariate Hill curve Y =

H

i

([X

i

]) will only intersect the decay line Y = [X

i

] at the origin. In other words,

[X

i

]

c

i

K + [X

i

]

c

i

+

n

j=1,j=i

γ

ij

[X

j

]

c

i

< [X

i

] (6.16)

except when [X

i

] = 0.

Chapter 6. Results and Discussion Finding the Equilibrium Points 70

Figure 6.2: Y =

[X

i

]

c

i

K+[X

i

]

c

i

will never touch the point (1, 1) for 1 < c

i

< ∞.

Proposition (6.11) implies that the system with c

i

> 1, g

i

= 0, K

i

≥ 1, β

i

= 1 and

ρ

i

= 1 for all i, j represents a trivial case (i.e., the fate of the cell is not in the domain

of our GRN, or the cell is in quiescent stage). This is not the only set of parameters

that gives a trivial case. A generalization of the above Proposition (6.11) is stated in the

following statement:

Proposition 6.12 If c

i

> 1, g

i

= 0 and

ρ

i

(K

i

1/c

i

) ≥ β

i

(6.17)

for all i, then our system has only one equilibrium point which is the origin.

Proof. Let us ﬁrst consider the case where [X

j

] = 0, for all j = i. Recall that the upper

bound of H

i

([X

i

]) is β

i

. Also, recall that when [X

i

] = K

1/c

i

i

then H

i

([X

i

]) = β

i

/2 (see

Section 3.2 in Chapter 3). Note that (K

1/c

i

i

, β

i

/2) is the inﬂection point of our univariate

Hill curve. We substitute [X

i

] = K

1/c

i

i

in the decay function Y = ρ

i

[X

i

], and if the value

of ρ

i

(K

i

1/c

i

) is larger or equal to the value of the upper bound β

i

then Y = H

i

([X

i

]) and

Y = ρ

i

[X

i

] only intersect at the origin. See Figure (6.3) for illustration.

Chapter 6. Results and Discussion Finding the Equilibrium Points 71

Figure 6.3: An example where ρ

i

(K

i

1/c

i

) > β

i

; Y = H

i

([X

i

]) and Y = ρ

i

[X

i

] only

intersect at the origin.

Now, as the values of γ

ij

[X

j

] for all j = i increase then the univariate Hill curve

Y = H

i

([X

i

]) will just shrink and will deﬁnitely not intersect the decay line Y = [X

i

]

except at the origin.

However, note that Proposition (6.12) is a suﬃcient but not a necessary condition.

There are some cases where ρ

i

(K

i

1/c

i

) < β

i

yet Y = H

i

([X

i

]) and Y = ρ

i

[X

i

] only

intersect at the origin.

Corollary 6.13 If c

i

> 1, g

i

= 0, K

i

≥ 1 and ρ

i

≥ β

i

for all i, then our system has only

one equilibrium point which is the origin.

Proof. Since ρ

i

≥ β

i

and K

i

≥ 1, then ρ

i

(K

i

1/c

i

) ≥ β

i

. Then we invoke Theorem

(6.12).

For c

i

= 1 and g

i

= 0, we state the following proposition:

Chapter 6. Results and Discussion Finding the Equilibrium Points 72

Proposition 6.14 Suppose c

i

= 1, g

i

= 0 and

β

i

K

i

≤ ρ

i

for all i. Then our system has

only one equilibrium point which is the origin.

Proof. Let us ﬁrst consider the case where [X

j

] = 0, for all j = i. Recall that Y =

H

i

([X

i

]) where c

i

= 1 is a hyperbolic curve. The partial derivative

∂H

i

∂[X

i

]

=

∂

∂[X

i

]

_

β

i

[X

i

]

K

i

+ [X

i

]

_

=

K

i

β

i

(K

i

+ [X

i

])

2

(6.18)

means that the slope of the hyperbolic curve is monotonically decreasing as [X

i

] increases.

The partial derivative at [X

i

] = 0 is

∂H

i

∂[X

i

]

=

β

i

K

i

≤ ρ

i

, (6.19)

which means that the slope of Y = H

i

([X

i

]) at [X

i

] = 0 is less than the slope of the decay

line Y = ρ

i

[X

i

] at [X

i

] = 0. Hence, the Hill curve Y = H

i

([X

i

]) lies below the decay line

for all [X

i

] > 0.

Suppose c

i

≥ 1 and g

i

= 0 for all i. In general, the origin is the only equilibrium

point of our ODE model (5.1) if and only if the univariate curve Y = H

i

([X

i

]) lies below

the decay line Y = ρ

i

[X

i

] (i.e., H

i

([X

i

]) < ρ

i

[X

i

], ∀[X

i

] > 0) for all i. This statement is

similar to Theorem (7.6) in the next Chapter.

Remark: We have seen the importance of the univariate Hill function H

i

([X

i

]). For

instance, when n = 1, c

1

= 2, ρ

1

> 0 and g

1

= 0, the Hill curve and the decay line

intersect at

[X

1

]

∗

= 0,

β

1

±

_

β

2

1

−4ρ

2

1

K

1

2ρ

1

. (6.20)

Notice that the equilibrium points depend on the parameters β

1

, ρ

1

and K

1

.

According to Cinquin and Demongeot [38], a suﬃciently large c coupled with a suf-

ﬁciently large β are needed for the existence of an equilibrium point with a component

dominating the other components. Moreover, decreasing the value ρ

i

or adding the term

g

i

may result to an increased value of [X

i

]

∗

.

Chapter 7

Results and Discussion

Stability of Equilibria and Bifurcation

We determine the stability of the equilibrium points of the generalized Cinquin-Demongeot

(2005) ODE model (5.1) for a given set of parameters. We also identify if varying the

values of some parameters, such as those associated with the exogenous stimuli, can steer

the system towards a desired state.

7.1 Stability of equilibrium points

Recall Lemma (5.2): Suppose ρ

i

> 0 for all i. Then the generalized Cinquin-Demongeot

ODE model (5.1) with X

0

∈ R

⊕

n

always has a stable equilibrium point. Moreover, any

trajectory of the model will converge to a stable equilibrium point.

Theorem 7.1 Given a set of parameters where ρ

i

> 0 for all i, if the system (5.1) has

only one equilibrium point then this point is stable.

Proof. This is a consequence of Lemma (5.2).

The following theorem assures us that our system (for any dimension n) will never

have an asymptotically stable limit cycle:

Theorem 7.2 Suppose ρ

i

> 0 for all i, then any trajectory of our system (5.1) never

converges to a neutrally stable center, to an ω-limit cycle, or to a strange attractor. This

also implies that (5.1) will never have an asymptotically stable limit cycle.

73

Chapter 7. Results and Discussion Stability of Equilibria and Bifurcation 74

Proof. Since for any nonnegative initial condition, the trajectory of the ODE model

converges to a stable equilibrium point (see Lemma (5.2)), then any trajectory will never

stay orbiting a center, will never converge to an ω-limit cycle, and will never converge to

a strange attractor.

Moreover, suppose an ω-limit cycle exists. Then given some initial condition, the

trajectory of the system converges to this ω-limit cycle. This contradicts Lemma (5.2)

stating that any trajectory always converges to a stable equilibrium point.

Now, the following is the Jacobian of our system.

JF(X) =

_

¸

¸

¸

¸

¸

_

a

11

a

12

· · · a

1n

a

21

a

22

· · · a

2n

.

.

.

.

.

.

.

.

.

.

.

.

a

n1

a

n2

· · · a

nn

_

¸

¸

¸

¸

¸

_

(7.1)

where

a

ii

=

∂F

i

∂[X

i

]

=

_

K

i

+ [X

i

]

c

i

+

n

j=1,j=i

γ

ij

[X

j

]

c

ij

_

β

i

c

i

[X

i

]

c

i

−1

−β

i

c

i

[X

i

]

2c

i

−1

_

K

i

+ [X

i

]

c

i

+

n

j=1,j=i

γ

ij

[X

j

]

c

ij

_

2

−ρ

i

=

_

K

i

+

n

j=1,j=i

γ

ij

[X

j

]

c

ij

_

β

i

c

i

[X

i

]

c

i

−1

_

K

i

+ [X

i

]

c

i

+

n

j=1,j=i

γ

ij

[X

j

]

c

ij

_

2

−ρ

i

(7.2)

a

il

=

∂F

i

∂[X

l

]

=

−β

i

[X

i

]

c

i

(c

il

)γ

il

[X

l

]

c

il

−1

_

K

i

+ [X

i

]

c

i

+

n

j=1,j=i

γ

ij

[X

j

]

c

ij

_

2

, i = l. (7.3)

Chapter 7. Results and Discussion Stability of Equilibria and Bifurcation 75

Notice that

∂F

i

∂[X

i

]

> 0 if

ρ

i

<

_

K

i

+

n

j=1,j=i

γ

ij

[X

j

]

c

ij

_

β

i

c

i

[X

i

]

c

i

−1

_

K

i

+ [X

i

]

c

i

+

n

j=1,j=i

γ

ij

[X

j

]

c

ij

_

2

. (7.4)

Hence, if ρ

i

= 0 then the value of F

i

will always increase as [X

i

] increases. That is why

when ρ

i

= 0 for at least one i, we do not have a stable equilibrium point. Moreover,

∂F

i

∂[X

l

]

, i = l is always non-positive because as [X

l

] increases, the value of F

i

decreases.

Theorem 7.3 In our system (5.1), suppose g

i

= 0 and c

i

= 1 ∀i. Then the origin

is a stable equilibrium point when ρ

i

>

β

i

K

i

∀i, or an unstable equilibrium point when

ρ

i

<

β

i

K

i

for at least one i. When ρ

i

=

β

i

K

i

for at least one i, then we have a nonhyperbolic

equilibrium point, which is an attractor if [X

i

] is restricted to be nonnegative and ρ

j

≥

β

j

K

j

∀j = i.

Proof. The characteristic polynomial associated with the Jacobian of our system when

X = (0, 0, ..., 0) is

|JF(0) −λI| =

¸

¸

¸

¸

¸

¸

¸

¸

¸

¸

¸

β

1

K

1

−ρ

1

−λ 0 · · · 0

0

β

2

K

2

−ρ

2

−λ · · · 0

.

.

.

.

.

.

.

.

.

.

.

.

0 0 · · ·

βn

Kn

−ρ

n

−λ

¸

¸

¸

¸

¸

¸

¸

¸

¸

¸

¸

=

_

β

1

K

1

−ρ

1

−λ

__

β

2

K

2

−ρ

2

−λ

_

. . .

_

β

n

K

n

−ρ

n

−λ

_

. (7.5)

The eigenvalues (λ) are

β

1

K

1

−ρ

1

,

β

2

K

2

−ρ

2

, . . . ,

βn

Kn

−ρ

n

. Therefore, the zero vector is a

stable equilibrium point when

β

i

K

i

−ρ

i

< 0 or ρ

i

>

β

i

K

i

∀i. The zero vector is an unstable

equilibrium point when

β

i

K

i

−ρ

i

> 0 or ρ

i

<

β

i

K

i

for at least one i.

Chapter 7. Results and Discussion Stability of Equilibria and Bifurcation 76

Figure 7.1: When g

i

= 0, c

i

= 1 and the decay line is tangent to the univariate Hill

curve at the origin, then the origin is a saddle.

If

β

i

K

i

−ρ

i

= 0 or ρ

i

=

β

i

K

i

for at least one i then we have a nonhyperbolic equilibrium

point. Geometrically, we can see that this is a saddle — stable at the right and unstable

at the left of [X

i

]

∗

= 0 (see Figure (7.1) for illustration). Hence, if we restrict [X

i

] ≥ 0

and if ρ

j

≥

β

j

K

j

∀j = i, then this nonhyperbolic equilibrium point is stable.

Theorem 7.4 Suppose ρ

i

> 0, g

i

= 0 and c

i

> 1 ∀i, then the origin is a stable equilib-

rium point of the system (5.1).

Proof. By Corollary (6.3), if g

i

= 0 for all i then the origin is an equilibrium point.

The characteristic polynomial associated with the Jacobian of our system when X =

(0, 0, ..., 0) is

|JF(0) −λI| =

¸

¸

¸

¸

¸

¸

¸

¸

¸

¸

¸

−ρ

1

−λ 0 · · · 0

0 −ρ

2

−λ · · · 0

.

.

.

.

.

.

.

.

.

.

.

.

0 0 · · · −ρ

n

−λ

¸

¸

¸

¸

¸

¸

¸

¸

¸

¸

¸

= (−ρ

1

−λ)(−ρ

2

−λ) . . . (−ρ

n

−λ). (7.6)

Chapter 7. Results and Discussion Stability of Equilibria and Bifurcation 77

The eigenvalues (λ) are −ρ

1

, −ρ

2

, . . . , −ρ

n

which are all negative. Therefore, the zero

state is a stable equilibrium point.

We can vary the size of the basin of attraction of the stable zero i-th component (or of

any lower-valued stable component) of an equilibrium point by varying the value of β

i

or

K

i

, or sometimes by varying the value of ρ

i

. Let us consider Figure (7.2) for illustration.

In Figure (7.2), the original basin of attraction of the origin is [0, +∞) but increasing

the value of β

i

decreases the basin of attraction to [0, C). Decreasing the value of K

i

decreases the basin of attraction of the origin to [0, A), and decreasing the value of ρ

i

decreases the basin of attraction of the origin to [0, B).

Figure 7.2: Varying the values of parameters may vary the size of the basin of attraction

of the lower-valued stable intersection of Y = H

i

([X

i

]) +g

i

and Y = ρ

i

[X

i

].

In addition, the size of the basin of attraction of an equilibrium point depends on

the number of existing equilibrium points and on the size of the hyperspace (6.1). Given

speciﬁc parameter values, the hyperspace (6.1) is ﬁxed and the basin of attraction of each

existing equilibrium point is distributed in this hyperspace. If there are multiple stable

Chapter 7. Results and Discussion Stability of Equilibria and Bifurcation 78

equilibrium points then there are multiple basins of attraction that share the size of the

hyperspace.

Now, we propose two additional methods for determining the stability of equilibrium

points other than the usual numerical methods for solving ODEs and other than using

the Jacobian — using a multivariate ﬁxed point algorithm and using ad hoc geometric

analysis. We discuss multivariate ﬁxed point algorithm in Appendix B. We prove the

following theorems using ad hoc geometric analysis.

Theorem 7.5 Suppose c

i

> 1. Then [X

i

]

∗

= 0 (where [X

i

]

∗

is the i-th component of an

equilibrium point) is always a stable component.

Proof. Recall from Theorem (6.2) that our system has an equilibrium point with i-th

component equal to zero if and only if g

i

= 0. The only possible topologies of the

intersections of Y = H

i

([X

i

]) and Y = ρ

i

[X

i

] are shown in Figure (7.3). Notice that zero

i-th component is always stable.

Figure 7.3: The possible number of intersections of Y = ρ

i

[X

i

] and Y = H

i

([X

i

]) + g

i

where c > 1 and g = 0. The value of K

i

+

n

j=1,j=i

γ

ij

[X

j

]

c

ij

is taken as a parameter.

Theorem (7.5) is very important because this proves that when the pluripotency

module (where g

4

= 0, see discussion in Chapter 5 Section 5.2) is switched-oﬀ then it

Chapter 7. Results and Discussion Stability of Equilibria and Bifurcation 79

can never be switched-on again, unless we make g

4

> 0 or introduce some random noise.

This is consistent with the observation of MacArthur et al. in [113].

Theorem 7.6 Suppose c

i

≥ 1 and g

i

= 0 for all i. The only stable equilibrium point

of our ODE model (5.1) is the origin if and only if the univariate curve Y = H

i

([X

i

])

essentially lies below the decay line Y = ρ

i

[X

i

] (i.e., H

i

([X

i

]) ≤ ρ

i

[X

i

], ∀[X

i

] > 0) for all

i.

Proof. Suppose, the curve Y = H

i

([X

i

]) essentially lies below the decay line Y = ρ

i

[X

i

],

then the intersections can be any of the forms shown in Figure (7.4). It is clear that zero

is the only stable intersection.

Figure 7.4: The possible topologies when Y = H

i

([X

i

]) essentially lies below the decay

line Y = ρ

i

[X

i

], g

i

= 0.

Conversely, suppose the only stable equilibrium point is the origin. Hence [X

j

], j = i

must converge to zero. We substitute [X

j

]

∗

= 0, j = i to H

i

([X

1

], [X

2

], . . . , [X

n

]) (5.2).

The intersections of Y = H

i

(0, . . . , [X

i

], . . . , 0) = H([X

i

]) and Y = ρ

i

[X

i

] must contain

the origin (since we assumed that the origin is an equilibrium point). Looking at the

possible topologies of the intersections of Y = H

i

([X

i

]) and Y = ρ

i

[X

i

] (see Figures (5.11)

Chapter 7. Results and Discussion Stability of Equilibria and Bifurcation 80

and (5.13)), zero can only be the sole stable intersection if the intersection is any of the

form shown in Figure(7.4). Therefore, the curve Y = H

i

([X

i

]) essentially lies below the

decay line Y = ρ

i

[X

i

].

Theorem 7.7 Suppose c

i

= c

ij

= 1, g

i

= 0, γ

ij

= 1, β

i

= β

j

= β > 0, ρ

i

= ρ

j

= ρ > 0,

K

i

= K

j

= K > 0 and β > ρK. Then the origin is an unstable equilibrium point of the

system (5.1) while the points lying on the hyperplane

n

j=1

[X

j

] =

β

ρ

−K. (7.7)

are stable equilibrium points.

Proof. From Corollary (6.8), the origin and the points lying on the hyperplane are equi-

librium points of the system (5.1) given the assumed parameter values.

Suppose

n

j=1,j=i

[X

j

] = 0 in the denominator of H

i

(5.2). At [X

i

] = 0, the slope of

the Hill curve Y = H

i

([X

i

]) is

∂H

i

∂[X

i

]

=

β

K

. (7.8)

Since β > ρK then

β

K

> ρ. This implies that the slope of Y = H

i

([X

i

]) at [X

i

] = 0 is

greater than the slope of the decay line Y = ρ[X

i

]. Therefore, when

n

j=1,j=i

[X

j

] = 0

in the denominator of H

i

(5.2), there are two possible intersections of Y = H

i

([X

i

]) and

Y = ρ[X

i

]. The intersection is at the origin (which is unstable) and at [X

i

] =

β

ρ

− K

(which is stable).

Now, suppose

n

j=1,j=i

[X

j

] in the denominator of H

i

varies. Then the intersection

of Y = H

i

([X

i

]) and Y = ρ[X

i

] is at the origin (which is unstable) and at [X

i

] =

β

ρ

−

K−

n

j=1,j=i

[X

j

] (which is stable). Hence, the hyperplane [X

i

] =

β

ρ

−K−

n

j=1,j=i

[X

j

],

where [X

i

] and [X

j

] are nonnegative, is a set of stable equilibrium points. See Figure

(7.5) for illustration.

**Chapter 7. Results and Discussion Stability of Equilibria and Bifurcation 81
**

Figure 7.5: The origin is unstable while the points where [X

i

]

∗

=

β

ρ

−K−

n

j=1,j=i

[X

j

]

∗

are stable.

In GRNs, the existence of inﬁnitely many non-isolated equilibrium points is biolog-

ically volatile. A small perturbation in the initial value of the system may lead the

trajectory of the system to converge to a diﬀerent equilibrium point that may result to a

change in the phenotype of the cell. The basin of attraction of each stable non-isolated

equilibrium point may not be as large compared to the basin of attraction of a stable

isolated equilibrium point. This special phenomenon represents competition where the

co-expression, extinction and domination of the TFs depend on the value of each TF, and

the dependence among TFs is a continuum. The existence of an attracting hyperplane

is also discovered by Cinquin and Demongeot in [38].

7.2 Bifurcation of parameters

We have seen in Chapter 6 and in Section 7.1 (also see Appendix C) the eﬀect of the

parameters β

i

, K

i

, ρ

i

, c

i

, c

ij

and g

i

on the number, size of the basins of attraction and

behavior of equilibrium points. Varying the values of some parameters can decrease the

size of the basin of attraction of an undesirable equilibrium point as well as increase the

size of the basin of attraction of a desirable equilibrium point. We can mathematically

Chapter 7. Results and Discussion Stability of Equilibria and Bifurcation 82

manipulate the parameter values to ensure that the initial condition is in the basin of

attraction of our desired equilibrium point.

Intuitively, we can make the i-th component of an equilibrium point dominate other

components by increasing β

i

or g

i

or, in some instances, by decreasing ρ

i

. Decreasing

the value of K

i

or sometimes increasing the value of c

i

minimizes the size of the basin of

attraction of the lower-valued stable intersection of Y = H

i

([X

i

]) + g

i

and Y = ρ

i

[X

i

],

thus, the chance of converging to an equilibrium point with [X

i

]

∗

> [X

j

]

∗

j = i may

increase. However, the eﬀect of K

i

and c

i

in increasing the value of [X

i

]

∗

is not as drastic

compared to β

i

, g

i

and ρ

i

, since K

i

and c

i

do not aﬀect the upper bound of the hyperspace

(6.1). In addition, increasing the value of c

i

or of c

ij

may result in an increased number

of equilibrium points, and probably in multistability (by Theorem (6.6)).

We show in Appendix C some numerical bifurcation analysis to illustrate possible

bifurcation types that may occur.

In this section, we determine how to obtain an equilibrium point that has an i-th

component suﬃciently dominating other components, especially by introducing an ex-

ogenous stimulus. We focus on the parameter g

i

because the introduction of an exogenous

stimulus is experimentally feasible.

Increasing the eﬀect of exogenous stimuli

If we increase the value of g

i

up to a suﬃcient level, then we can increase the value of [X

i

]

where Y = H

i

([X

i

]) + g

i

and Y = ρ

i

([X

i

]) intersect. We can also make such increased

[X

i

] the only intersection. See Figure (7.6) for illustration.

Moreover, as we increase the value of g

i

up to a suﬃcient level, we increase the possible

value of [X

i

]

∗

. Since [X

i

] inhibits [X

j

], then as we increase the value of [X

i

]

∗

, we can

decrease the value of [X

j

], j = i where Y = H

j

([X

j

]) +g

j

and Y = ρ

j

([X

j

]) intersect. We

can also make such decreased [X

j

] the only intersection. If g

j

= 0, we can make [X

j

] = 0

the only intersection of Y = H

j

([X

j

]) and Y = ρ

j

([X

j

]). See Figure (7.7) for illustration.

Chapter 7. Results and Discussion Stability of Equilibria and Bifurcation 83

Figure 7.6: Increasing the value of g

i

can result in an increased value of [X

i

] where

Y = H

i

([X

i

]) +g

i

and Y = ρ

i

([X

i

]) intersects.

Therefore, by changing the value of g

i

we can have a sole stable equilibrium point

where the i-th component dominates the others. For any initial condition, the trajectory

of the ODE model (5.1) will converge to this sole equilibrium point. By varying the

value of g

i

, we can manipulate the cell fate of a stem cell — controlling the tripotency,

bipotency, unipotency and terminal state of the cell. We present illustrations in Appendix

C showing the eﬀect of increasing the value of g

i

.

Remark: Suppose, given a speciﬁc initial condition, the solution to our system tends

to an equilibrium point with [X

i

]

∗

= 0. If we want our solution to escape [X

i

]

∗

= 0

then one strategy is to add g

i

> 0. The idea of adding a suﬃcient amount of g

i

> 0

is to make the solution of our system escape a certain equilibrium point. However, it

is sometimes impractical or infeasible to continuously introduce a constant amount of

exogenous stimulus to control cell fates, that is why we may rather consider introducing

g

i

that degrades through time.

We can make g

i

a function of time (i.e., g

i

is varying through time). This strategy

means that we are adding another equation and state variable to our system of ODEs.

Chapter 7. Results and Discussion Stability of Equilibria and Bifurcation 84

Figure 7.7: Increasing the value of g

i

can result in an increased value of [X

i

]

∗

, and

consequently in decreased value of [X

j

] where Y = H

j

([X

j

]) + g

j

and Y = ρ

j

([X

j

])

intersects, j = i.

We can think of g

i

as an additional node to our GRN and we call it as the injection

node. In our case, we consider functions that represent a degrading amount of g

i

. Refer

to Appendix C for illustration.

Adding a degrading amount of g

i

aﬀects cell fate but this strategy may not give rise

to a sole equilibrium point. Moreover, this strategy is only applicable to systems with

multiple stable equilibrium points where convergence of trajectories is sensitive to initial

conditions.

Chapter 8

Results and Discussion

Introduction of Stochastic Noise

We numerically investigate the eﬀect of random noise to the cell diﬀerentiation system us-

ing Stochastic Diﬀerential Equations (SDEs). In [38], Cinquin and Demongeot suggested

to extend their model to include stochastic kinetics.

We have written a Scilab [150] program (see Algorithm (5)-(6) in Appendix D) to

simulate the eﬀect of stochastic noise to the dynamics of our GRN. We employ several

functions G (see Section 3.3 in Chapter 3) to observe the various eﬀect of the added

Gaussian white noise term. The diﬀerent functions G are:

G(X) = 1, (8.1)

G(X) = X, (8.2)

G(X) =

√

X, (8.3)

G(X) = F(X), and (8.4)

G(X) =

_

H(X) + ˇ g + ˇ ρX. (8.5)

In function (8.1), the noise term is not dependent on any variable. This function is

used by MacArthur et al. in [113].

The noise term with (8.2) or (8.3) is aﬀected by the value of X. That is, as the

concentration X increases/decreases, the eﬀect of the noise term also increases/decreases.

Function (8.2) is used by Glauche et al. in [71]. However, using (8.2) or (8.3) has

undesirable biological implication — as [X

i

] dominates the other concentration of TFs,

the eﬀect of random noise to [X

i

] intensiﬁes.

85

Chapter 8. Results and Discussion Introduction of Stochastic Noise 86

In (8.4), the noise term is aﬀected by the value of F(X) (the right hand side of our

corresponding ODE model) — that is, as the deterministic change in the concentration

X with respect to time

_

dX

dt

= F(X)

_

increases/decreases, the eﬀect of the noise term

also increases/decreases. In using (8.4), we expect a decreasing amount of noise through

time because our ODE system (5.1) always converges to an equilibrium point. In other

words, as F(X) →0 (since F(X

∗

) = 0), the eﬀect of noise also vanishes.

Function (8.5) is based on the random population growth model [5, 91]. The ˇ g and ˇ ρ

are the matrices containing the parameters g

i

and ρ

i

(i = 1, 2, . . . , n), respectively.

In Algorithm (5)-(6) (see Appendix D), we use Euler Method to numerically solve

the system of ODEs, while we use Euler-Maruyama method to numerically solve the

corresponding system of SDEs. The output of the algorithm is a time-series of the

solutions. The solution of the ODE model is visualized by the thick solid line, while a

realization of the SDE model is visualized by the thin solid line. In the Euler-Maruyama

method, we set [X

i

] < 0 to be [X

i

] = 0.

The SDE models that we have used in this thesis are not exhaustive. We can consider

other types of SDE models, such as

dX = F(X)dt +σ

A

_

H(X)dW

A

−σ

B

_

ˇ ρXdW

B

+σ

C

_

ˇ gdW

C

. (8.6)

In the following examples we suppose n = 4 and σ

ii

= 0.5. Let the simulation step

size be 0.01.

Illustration 1

Suppose our generalized Cinquin-Demongeot ODE model (5.1) has parameters equal to

1 except for β

i

= 5 and g

i

= 0 for all i. This system has inﬁnitely many non-isolated

stable equilibrium points (see Theorem (7.7)).

The corresponding system of SDEs is as follows:

Chapter 8. Results and Discussion Introduction of Stochastic Noise 87

d[X1] =

_

5[X

1

]

1 + [X

1

] + [X

2

] + [X

3

] + [X

4

]

−[X

1

]

_

dt +σ

11

G

1

([X

1

])dW

1

d[X2] =

_

5[X

2

]

1 + [X

1

] + [X

2

] + [X

3

] + [X

4

]

−[X

2

]

_

dt +σ

22

G

2

([X

2

])dW

2

(8.7)

d[X3] =

_

5[X

3

]

1 + [X

1

] + [X

2

] + [X

3

] + [X

4

]

−[X

3

]

_

dt +σ

33

G

3

([X

3

])dW

3

d[X4] =

_

5[X

4

]

1 + [X

1

] + [X

2

] + [X

3

] + [X

4

]

−[X

4

]

_

dt +σ

44

G

4

([X

4

])dW

4

.

We assume G

1

= G

2

= G

3

= G. Suppose the initial condition is [X

i

]

0

= 4 for all i.

Figures (8.1) to (8.5) show diﬀerent realizations of the corresponding SDE model.

In the deterministic case, we expect that the solutions to [X

1

], [X

2

], [X

3

] and [X

4

] will

converge to an equilibrium point with equal components because our system is symmetric

and [X

1

]

0

= [X

2

]

0

= [X

3

]

0

= [X

4

]

0

. However, because of the presence of noise, some TFs

seem to dominate the others. It is possible that the solution to the SDE may approach a

diﬀerent equilibrium point. This biological volatility is due to the presence of inﬁnitely

many stable equilibrium points.

Chapter 8. Results and Discussion Introduction of Stochastic Noise 88

Figure 8.1: For Illustration 1; ODE solution and SDE realization with G(X) = 1.

Figure 8.2: For Illustration 1; ODE solution and SDE realization with G(X) = X.

Chapter 8. Results and Discussion Introduction of Stochastic Noise 89

Figure 8.3: For Illustration 1; ODE solution and SDE realization with G(X) =

√

X.

Figure 8.4: For Illustration 1; ODE solution and SDE realization with G(X) = F(X).

Chapter 8. Results and Discussion Introduction of Stochastic Noise 90

Figure 8.5: For Illustration 1; ODE solution and SDE realization using the random

population growth model.

Chapter 8. Results and Discussion Introduction of Stochastic Noise 91

Illustration 2

Suppose our generalized Cinquin-Demongeot ODE model (5.1) has parameters equal to

1 except for c

i

= c

ij

= 2 (for all i, j), g

1

= 5, g

2

= 3, g

3

= 1 and g

4

= 0. This

system has a sole equilibrium point which is ([X

1

]

∗

≈ 5.72411, [X

2

]

∗

≈ 3.23066, [X

3

]

∗

≈

1.02313, [X

4

]

∗

= 0).

The corresponding system of SDEs is as follows:

d[X1] =

_

[X

1

]

2

1 + [X

1

]

2

+ [X

2

]

2

+ [X

3

]

2

+ [X

4

]

2

−[X

1

] + 5

_

dt +σ

11

G

1

([X

1

])dW

1

d[X2] =

_

[X

2

]

2

1 + [X

1

]

2

+ [X

2

]

2

+ [X

3

]

2

+ [X

4

]

2

−[X

2

] + 3

_

dt +σ

22

G

2

([X

2

])dW

2

(8.8)

d[X3] =

_

[X

3

]

2

1 + [X

1

]

2

+ [X

2

]

2

+ [X

3

]

2

+ [X

4

]

2

−[X

3

] + 1

_

dt +σ

33

G

3

([X

3

])dW

3

d[X4] =

_

[X

4

]

2

1 + [X

1

]

2

+ [X

2

]

2

+ [X

3

]

2

+ [X

4

]

2

−[X

4

]

_

dt +σ

44

G

4

([X

4

])dW

4

.

We assume G

1

= G

2

= G

3

= G. Figures (8.6) to (8.10) show diﬀerent realizations of the

corresponding SDE model with initial condition [X

i

]

0

= 3 for all i.

In the deterministic case, we expect that the solution will converge to the sole equilib-

rium point. From our simulation, it seems that our system is robust against the presence

of moderate noise. The realization of the SDE model nearly follows the deterministic

trajectory. We expect this to happen because for any initial condition, the solution to

our system will tend towards only one attractor.

Recall that one possible strategy for controlling our system to have only one stable

equilibrium point is by introducing adequate amount of exogenous stimuli (see Chapter

7 Section 7.2). In order to have assurance that cells will not change lineages, we need to

make the desired i-th lineage have a corresponding [X

i

]

∗

that suﬃciently dominates the

concentration of the other TFs.

Chapter 8. Results and Discussion Introduction of Stochastic Noise 92

Figure 8.6: For Illustration 2; ODE solution and SDE realization with G(X) = 1.

Figure 8.7: For Illustration 2; ODE solution and SDE realization with G(X) = X.

Chapter 8. Results and Discussion Introduction of Stochastic Noise 93

Figure 8.8: For Illustration 2; ODE solution and SDE realization with G(X) =

√

X.

Figure 8.9: For Illustration 2; ODE solution and SDE realization with G(X) = F(X).

Chapter 8. Results and Discussion Introduction of Stochastic Noise 94

Figure 8.10: For Illustration 2; ODE solution and SDE realization using the random

population growth model.

Chapter 8. Results and Discussion Introduction of Stochastic Noise 95

Illustration 3

Suppose our generalized Cinquin-Demongeot ODE model (5.1) has parameters c

i

= c

ij

=

2, β

i

= 1, K

i

= 1, γ

ij

= 1/8, ρ

i

= 1/21 and g

i

= 0 for all i, j. This system has multiple

stable equilibrium points (see Figure (8.16)).

The corresponding system of SDEs is as follows:

d[X1] =

_

[X

1

]

2

1 + [X

1

]

2

+

1

8

[X

2

]

2

+

1

8

[X

3

]

2

+

1

8

[X

4

]

2

−

1

21

[X

1

]

_

dt +σ

11

G

1

([X

1

])dW

1

d[X2] =

_

[X

2

]

2

1 +

1

8

[X

1

]

2

+ [X

2

]

2

+

1

8

[X

3

]

2

+

1

8

[X

4

]

2

−

1

21

[X

2

]

_

dt +σ

22

G

2

([X

2

])dW

2

(8.9)

d[X3] =

_

[X

3

]

2

1 +

1

8

[X

1

]

2

+

1

8

[X

2

]

2

+ [X

3

]

2

+

1

8

[X

4

]

2

−

1

21

[X

3

]

_

dt +σ

33

G

3

([X

3

])dW

3

d[X4] =

_

[X

4

]

2

1 +

1

8

[X

1

]

2

+

1

8

[X

2

]

2

+

1

8

[X

3

]

2

+ [X

4

]

2

−

1

21

[X

4

]

_

dt +σ

44

G

4

([X

4

])dW

4

.

We assume G

1

= G

2

= G

3

= G. Figures (8.11) to (8.15) show diﬀerent realizations of

the corresponding SDE model with initial condition [X

i

]

0

= 2 for all i.

In the deterministic case, we expect that the solutions to [X

1

], [X

2

], [X

3

] and [X

4

] will

converge to an equilibrium point with equal components because our system is symmetric

and [X

1

]

0

= [X

2

]

0

= [X

3

]

0

= [X

4

]

0

. For a system with regulated noise, the solution to the

SDE may follow the behavior of the trajectory of the ODE. However, it is also possible

that [X

1

]

∗

, [X

2

]

∗

, [X

3

]

∗

and [X

4

]

∗

tend towards diﬀerent values, especially when the eﬀect

of the noise becomes signiﬁcant. Suﬃcient amount of random noise may cause cells to

shift cell types, especially when the initial condition is near the boundary of the basins

of attraction of the equilibrium points. Figure (8.16) shows the possible values of [X

1

]

∗

and [X

2

]

∗

given varying initial condition [X

1

]

0

. To regulate the eﬀect of noise, we can

change the values of some parameters such as degradation rate and eﬀect of exogenous

stimulus to decrease the size of the basin of attraction of an undesirable equilibrium

point. Multistability in the presence of random noise represents stochastic diﬀerentiation

of cells.

Chapter 8. Results and Discussion Introduction of Stochastic Noise 96

Furthermore, the presence of noise may induce abnormal ﬂuctuations in the concen-

tration of the TFs speciﬁcally when using functions (8.2) and (8.3), as shown in Figure

(8.12).

Figure 8.11: For Illustration 3; ODE solution and SDE realization with G(X) = 1.

Figure 8.12: For Illustration 3; ODE solution and SDE realization with G(X) = X.

Chapter 8. Results and Discussion Introduction of Stochastic Noise 97

Figure 8.13: For Illustration 3; ODE solution and SDE realization with G(X) =

√

X.

Figure 8.14: For Illustration 3; ODE solution and SDE realization with G(X) = F(X).

Chapter 8. Results and Discussion Introduction of Stochastic Noise 98

Figure 8.15: For Illustration 3; ODE solution and SDE realization using the random

population growth model.

Figure 8.16: Phase portrait of [X

1

] and [X

2

].

Chapter 8. Results and Discussion Introduction of Stochastic Noise 99

Illustration 4

Suppose our generalized Cinquin-Demongeot ODE model (5.1) has parameters c

i

= c

ij

=

2, β

i

= 1, K

i

= 1, γ

ij

= 1, ρ

i

= 1 and g

i

= 0 for all i, j. Suppose the initial condition

is [X

i

]

0

= 0 for all i, which means that all TFs are switched-oﬀ. Figure (8.17) shows

that with the presence of noise, the TFs can be reactivated again. However, inactive TFs

cannot be activated by using any of the functions (8.2), (8.3), (8.4) or (8.5).

Figure 8.17: Reactivating switched-oﬀ TFs by introducing random noise where

G(X) = 1.

Chapter 9

Summary and Recommendations

We simplify the gene regulatory network (GRN) model of MacArthur et al. [113] to

study the mesenchymal cell diﬀerentiation system. The simpliﬁed MacArthur GRN is

given in the following ﬁgure:

Figure 9.1: The simpliﬁed MacArthur et al. GRN

We translate the simpliﬁed network model into a system of Ordinary Diﬀerential

Equations (ODEs) using a generalized Cinquin-Demongeot model [38]. We generalize

the Cinquin-Demongeot ODE model as:

100

Chapter 9. Summary and Recommendations 101

d[X

i

]

dt

=

β

i

[X

i

]

c

i

K

i

+ [X

i

]

c

i

+

n

j=1,j=i

γ

ij

[X

j

]

c

ij

+g

i

−ρ

i

[X

i

]

where i = 1, 2, ..., n.

The state variables of the ODE model represent the concentration of the transcription

factors (TFs) involved in gene expression. For our simpliﬁed network, [X

1

] := [RUNX2],

[X

2

] := [SOX9], [X

3

] := [PPAR−γ] and [X

4

] := [sTF]. Some of our results are appli-

cable not only to n = 4 but to any dimension.

An asymptotically stable equilibrium point is associated with a certain cell type,

e.g., tripotent, bipotent, unipotent or terminal state. If [X

i

] suﬃciently dominates the

concentrations of the other TFs then the chosen lineage is towards the i-th cell type.

For an ODE model to be useful, it is necessary that it has a solution. It is diﬃcult to

predict the behavior of our system if the solution is not unique. We are able to prove that

there exists a unique solution to our model for some values of c

i

and c

ij

. The exponents

c

i

and c

ij

represent cooperativity among binding sites.

We propose two additional methods for determining the behavior of equilibrium points

other than the usual numerical methods for solving ODEs, and other than using the

Jacobian — (1) using ad hoc geometric analysis; and (2) using multivariate ﬁxed point

algorithm.

The geometry of the Hill function H

i

is essential in understanding the behavior of

the equilibrium points of our ODE system. From the geometric analysis, we are able to

prove that our state variables [X

i

] will never be negative (i.e., R

⊕

n

is positively invariant

with respect to the ﬂow of our ODE model) and that our ODE model always has a stable

equilibrium point. Any trajectory of the model will converge to a stable equilibrium

point.

A stable equilibrium point (0, 0, . . . , 0) is trivial because this state neither represents

a pluripotent cell nor a cell diﬀerentiating into bone, cartilage or fat. In our case, the cell

Chapter 9. Summary and Recommendations 102

may diﬀerentiate to other cell types which are not in the domain of our GRN. The zero

state may also represent a cell that is in quiescent stage. We are able to prove theorems

associated to the existence of a stable zero state, such as

• Our system has an equilibrium point with i-th component equal to zero if and

only if g

i

= 0. Moreover, if ρ

i

> 0 and c

i

> 1 then this zero i-th component

is always stable.

• The zero state (0, 0, . . . , 0) can only be an equilibrium point if and only if

g

i

= 0 ∀i. If ρ

i

> 0 and c

i

> 1 for all i then the zero state is stable.

• Suppose g

i

= 0 for all i. The only stable equilibrium point of our ODE model

is the origin if and only if the univariate Hill curve Y = H

i

([X

i

]) essentially

lies below the decay line Y = ρ

i

[X

i

] for all i.

If converging to the zero state is undesirable, we can decrease the size of the basin

of attraction of the zero state by suﬃciently increasing the value of β

i

or by suﬃciently

decreasing the value of K

i

and ρ

i

. In addition, we can add g

i

> 0 to escape a stable zero

state.

In the case where c

i

> 1 and g

i

= 0, if the TF associated to [X

i

] is switched-oﬀ, then

it can never be switched-on again because the zero i-th component of an equilibrium

point is stable. Two possible strategies for escaping an inactive state is to increase the

value of g

i

or to introduce some random noise.

The following theorems give us ideas regarding the location and number of equilibrium

points ([X

1

]

∗

, [X

2

]

∗

, . . . , [X

n

]

∗

):

• Suppose ρ

i

> 0. The equilibrium points of our system lie in the hyperspace

_

g

1

ρ

1

,

g

1

+β

1

ρ

1

_

×

_

g

2

ρ

2

,

g

2

+β

2

ρ

2

_

×. . . ×

_

gn

ρn

,

gn+βn

ρn

_

.

• The generalized Cinquin-Demongeot ODE model (where c

i

and c

ij

are inte-

gers) has a ﬁnite number of equilibrium points except when all of the follow-

ing conditions are satisﬁed: c

i

= c

ij

= 1, g

i

= 0, γ

ij

= 1, β

i

= β

j

= β > 0,

ρ

i

= ρ

j

= ρ > 0, K

i

= K

j

= K > 0 and β > ρK, for all i and j.

• If the generalized Cinquin-Demongeot ODE model (where c

i

and c

ij

are in-

tegers) has a ﬁnite number of equilibrium points then the possible number

Chapter 9. Summary and Recommendations 103

of equilibrium points is at most max{c

1

+ 1, c

1j

+ 1 ∀j} ×max{c

2

+ 1, c

2j

+

1 ∀j} ×. . . ×max{c

n

+ 1, c

nj

+ 1 ∀j}.

We are able to ﬁnd one case where there are inﬁnitely many stable non-isolated

equilibrium points. This happens in a symmetric Michaelis-Menten-type system. In

GRNs, the existence of inﬁnitely many non-isolated equilibrium points is biologically

volatile. A small perturbation in the initial value of the system may lead the trajectory

of the system to converge to a diﬀerent equilibrium point that may result to a change in

the phenotype of the cell. This special phenomenon represents a competition where the

co-expression, extinction and domination of the TFs continuously depend on the value

of each TF.

If g

n

= 0 then the n-dimensional system is more general than the (n−1)-dimensional

system. That is, we can derive the equilibrium points of the (n −1)-dimensional system

by getting the equilibrium points of the n-dimensional system where [X

n

]

∗

= 0. It is

clear that when [X

n

]

∗

= 0 and g

n

= 0, the n-dimensional system reduces to an (n − 1)-

dimensional system.

Furthermore, we are able to prove an additional theorem related to the behavior of

the solution of our ODE model. The theorem states that if ρ

i

> 0 for all i, then our

system never converges to a center, to an ω-limit cycle or to a strange attractor. The

existence of a center, ω-limit cycle or strange attractor that would result to recurring

changes in phenotype is abnormal for a natural fully diﬀerentiated cell.

The parameters β

i

, K

i

, ρ

i

, γ

ij

, c

i

, c

ij

and g

i

aﬀect the number, size of the basins

of attraction and behavior of equilibrium points. We can make the i-th component of

an equilibrium point dominate other components by increasing β

i

, by increasing g

i

or

sometimes by decreasing ρ

i

. Decreasing the value of K

i

or increasing the value of c

i

may

also increase the chance of having an [X

i

]

∗

dominating the steady-state concentration of

the other TFs. However, the eﬀect of K

i

and c

i

in increasing the value of [X

i

]

∗

is not as

drastic compared to that of β

i

, g

i

and ρ

i

, since K

i

and c

i

do not aﬀect the upper bound

of [X

i

]

∗

. In some instances, varying γ

ij

may also induce the system to have a steady state

Chapter 9. Summary and Recommendations 104

where some TFs dominates the other TFs. Furthermore, increasing the value of c

i

or of

c

ij

may result in multistability.

We focus on manipulating the eﬀect of the exogenous stimulus because this is exper-

imentally feasible. It is possible that changing the value of g

i

can result to a sole stable

equilibrium point where the i-th component dominates the others. That is, we can steer

our system towards a desired state given any initial condition by just introducing an

adequate amount of exogenous stimulus. However, this strategy is not applicable to the

pluripotency module (sTF node) when g

4

= 0. If g

4

= 0, the only possible strategy for a

switched-oﬀ sTF node to be reactivated is to introduce random noise.

We also consider the case where g

i

changes through time. It is sometimes impractical

or infeasible to continuously introduce a constant amount of exogenous stimulus to control

cell fates, that is why we consider an amount of g

i

that degrades through time. We

consider two types of functions to represent g

i

— a linear function with negative slope, and

an exponential function with negative exponent. The idea of initially adding a suﬃcient

amount of g

i

> 0 is to make the solution of our system escape a certain equilibrium point.

However, this strategy is only applicable to systems with multiple stable equilibrium

points where the convergence of the trajectories is sensitive to initial conditions.

Multistability in the presence of random noise represents stochastic diﬀerentiation of

cells. With the presence of random noise, it is possible that the solutions tend towards

diﬀerent attractors. Random noise may cause cells to shift cell types, especially when

equilibrium points are near each other, or when the initial condition is near the boundary

of the basins of attraction of the equilibrium points. However, we can increase the

robustness of our system against the eﬀect of moderate random noise by increasing the

size of the basin of attraction of the desired equilibrium point, or by having only one

stable equilibrium point.

Suppose we only have one stable equilibrium point. Since for any initial condition,

the solution to our ODE system tends toward only one attractor, then we can expect

the realization of the corresponding SDE model to (approximately) follow the determin-

istic trajectory. One possible strategy to ensure that our system has only one stable

Chapter 9. Summary and Recommendations 105

equilibrium point is to introduce an adequate amount of exogenous stimulus.

For validation, we recommend comparing our results with other models of GRN dy-

namics and with existing information gathered in actual experiments. We can extend the

results of this thesis by considering other kinds of GRNs, possibly with more cell lineages

involved. We can also include cell division and intercellular interactions.

Appendix A

More on Equilibrium Points: Illustrations

In our numerical computations, “diﬃcult and computationally expensive” means the

problem is not eﬃciently solvable using Scientiﬁc Workplace [116] run in a laptop with

Intel Pentium P6200 2.13GHz processor and 2GB RAM. In determining the values of

equilibrium points, we need to check if the derived solutions are really solutions of the

system because we may have encountered approximation errors during our numerical

computations.

Solving the system F

i

(X) = 0, i = 1, 2, . . . , n can be interpreted as ﬁnding the

intersections of the (n + 1)-dimensional curves induced by each F

i

(X) and the (n + 1)-

dimensional zero-hyperplane. Figure (A.1) shows an illustration for n = 2.

Figure A.1: Intersections of F

1

, F

2

and zero-plane, an example.

We give some cases where we use Sylvester matrix in ﬁnding equilibrium points.

106

Appendix A. More on Equilibrium Points: Illustrations 107

A.1 Assume n = 2, c

i

= 1, c

ij

= 1

We determine the equilibrium points when c

i

= 1 and c

ij

= 1 for all i and j in a

two-dimensional system. The system of polynomial equations is as follows:

P

1

([X

1

], [X

2

]) =−ρ

1

[X

1

]

2

+ (β

1

+g

1

) [X

1

] −(K

1

+γ

12

[X

2

]) (ρ

1

[X

1

])

+g

1

γ

12

[X

2

] +g

1

K

1

= 0 (A.1)

P

2

([X

1

], [X

2

]) =−ρ

2

[X

2

]

2

+ (β

2

+g

2

) [X

2

] −(K

2

+γ

21

[X

1

]) (ρ

2

[X

2

])

+g

2

γ

21

[X

1

] +g

2

K

2

= 0

If P

1

and P

2

have no common factors then by Theorem (6.6), the number of complex

solutions to the polynomial system (A.1) is at most 4.

The corresponding Sylvester matrix of P

1

and P

2

with X

1

as variable is

_

¸

¸

_

a

11

a

12

a

13

a

21

a

22

0

0 a

21

a

22

_

¸

¸

_

(A.2)

where a

11

= −ρ

1

, a

12

= β

1

+ g

1

− K

1

ρ

1

− γ

12

ρ

1

[X

2

], a

13

= g

1

γ

12

[X

2

] + g

1

K

1

, a

21

=

−γ

21

ρ

2

[X

2

] + g

2

γ

21

and a

22

= −ρ

2

[X

2

]

2

+ (β

2

+ g

2

− K

2

ρ

2

)[X

2

] + g

2

K

2

. The Sylvester

resultant res(P

1

, P

2

; X

1

) is a polynomial in the variable X

2

and is of degree at most 4. By

Fundamental Theorem of Algebra, res(P

1

, P

2

; X

1

) = 0 has at most 4 complex solutions

which is consistent with Theorem (6.6).

It is diﬃcult and computationally expensive to ﬁnd the exact solutions to res(P

1

, P

2

;

X

1

) = 0 in terms of the arbitrary parameters. We investigate speciﬁc cases where we

assign values to some parameters.

Appendix A. More on Equilibrium Points: Illustrations 108

A.1.1 Illustration 1

Suppose all parameters in the system (A.1) are equal to 1, except for arbitrary g

1

and

arbitrary g

2

. Assume g

1

> 0 or g

2

> 0. The Sylvester matrix with [X

1

] as variable is as

follows:

_

¸

¸

_

−1 g

1

−[X

2

] g

1

([X

2

] + 1)

g

2

−[X

2

] −[X

2

]

2

+g

2

[X

2

] +g

2

0

0 g

2

−[X

2

] −[X

2

]

2

+g

2

[X

2

] +g

2

_

¸

¸

_

(A.3)

It follows that

res(P

1

, P

2

; X

1

) = (g

1

+g

2

)[X

2

]

2

−(g

1

g

2

+g

2

2

)[X

2

] −g

2

2

. (A.4)

Then the root of res(P

1

, P

2

; X

1

) = 0 is

[X

2

] =

g

1

g

2

+g

2

2

±

_

(g

1

g

2

+g

2

2

)

2

+ 4(g

1

+g

2

)g

2

2

2(g

1

+g

2

)

. (A.5)

By the same procedure as above, the root of res(P

1

, P

2

; X

2

) = 0 is

[X

1

] =

g

1

g

2

+g

2

1

±

_

(g

1

g

2

+g

2

1

)

2

+ 4(g

1

+g

2

)g

2

1

2(g

1

+g

2

)

. (A.6)

Since g

1

> 0 or g

2

> 0 then g

1

g

2

+g

2

2

≤

_

(g

1

g

2

+g

2

2

)

2

+ 4(g

1

+g

2

)g

2

2

and g

1

g

2

+g

2

1

≤

_

(g

1

g

2

+g

2

1

)

2

+ 4(g

1

+g

2

)g

2

1

. Hence, we have equilibrium point ([X

1

]

∗

, [X

2

]

∗

) equal to

_

g

1

g

2

+g

2

1

+

_

(g

1

g

2

+g

2

1

)

2

+ 4(g

1

+g

2

)g

2

1

2(g

1

+g

2

)

,

g

1

g

2

+g

2

2

+

_

(g

1

g

2

+g

2

2

)

2

+ 4(g

1

+g

2

)g

2

2

2(g

1

+g

2

)

_

.

Therefore, for this example, we have exactly one equilibrium point.

Appendix A. More on Equilibrium Points: Illustrations 109

Now, observe that if g

1

> g

2

then [X

1

]

∗

> [X

2

]

∗

and if if g

2

> g

1

then [X

2

]

∗

> [X

1

]

∗

.

For example, assume g

1

= 2g

2

> 0, that is the ratio of g

1

to g

2

is 1 : 2. Then the

equilibrium point will be

_

2g

2

2

+ 4g

2

2

+

_

(2g

2

2

+ 4g

2

2

)

2

+ 4(2g

2

+g

2

)4g

2

2

2(2g

2

+g

2

)

,

2g

2

2

+g

2

2

+

_

(2g

2

2

+g

2

2

)

2

+ 4(2g

2

+g

2

)g

2

2

2(2g

2

+g

2

)

_

⇒

_

6g

2

2

+

_

36g

4

2

+ 48g

3

2

6g

2

,

3g

2

2

+

_

9g

4

2

+ 12g

3

2

6g

2

_

⇒

_

6g

2

+ 2

_

9g

2

2

+ 12g

2

6

,

3g

2

+

_

9g

2

2

+ 12g

2

6

_

.

Clearly, [X

1

]

∗

=

6g

2

+2

√

9g

2

2

+12g

2

6

> [X

2

]

∗

=

3g

2

+

√

9g

2

2

+12g

2

6

.

In addition, if g

1

= g

2

= g > 0, then [X

1

]

∗

= [X

2

]

∗

=

g+g

√

g

2

+2g

2

.

On the other hand, if g

1

and g

2

are both zero, then, by Theorem (6.7), the only

equilibrium point is (0, 0).

A.1.2 Illustration 2

Suppose all parameters in the system (A.1) are equal to 1, except for arbitrary β

1

= β

2

=

β, arbitrary g

1

and g

2

= 0. The Sylvester matrix with [X

1

] as variable is as follows:

_

¸

¸

_

−1 β +g

1

−1 −[X

2

] g

1

([X

2

] + 1)

−[X

2

] −[X

2

]

2

+ (β −1)[X

2

] 0

0 −[X

2

] −[X

2

]

2

+ (β −1)[X

2

]

_

¸

¸

_

(A.7)

It follows that

res(P

1

, P

2

; X

1

) = βg

1

[X

2

]

2

. (A.8)

Appendix A. More on Equilibrium Points: Illustrations 110

Then the root of res(P

1

, P

2

; X

1

) = 0 is

[X

2

] = 0. (A.9)

Substituting [X

2

] = 0 to the polynomial system (A.1) with the assumed parameter

values, we have

P

1

([X

1

], 0) = −[X

1

]

2

+ (β +g

1

)[X

1

] −[X

1

] +g

1

= 0 (A.10)

P

2

([X

1

], 0) = 0.

Thus,

[X

1

] =

−(β +g

1

−1) ±

_

(β +g

1

−1)

2

+ 4g

1

−2

=

(β +g

1

−1) ∓

_

(β +g

1

−1)

2

+ 4g

1

2

. (A.11)

Suppose g

1

> 0. Since β + g

1

− 1 <

_

(β +g

1

−1)

2

+ 4g

1

then we have equilibrium

point ([X

1

]

∗

, [X

2

]

∗

) equal to

_

(β +g

1

−1) +

_

(β +g

1

−1)

2

+ 4g

1

2

, 0

_

.

Therefore, we have exactly one equilibrium point where [X

1

]

∗

> [X

2

]

∗

when g

1

> 0.

If g

1

= 0 and β > 1 then we have two equilibrium points: (0, 0) and (β − 1, 0). If

g

1

= 0 and β ≤ 1 then the only equilibrium point is (0, 0).

Appendix A. More on Equilibrium Points: Illustrations 111

A.1.3 Illustration 3

Suppose all parameters in the system (A.1) are equal to 1, except for arbitrary K

1

=

K

2

= K, arbitrary g

1

and g

2

= 0. The Sylvester matrix with [X

1

] as variable is as follows:

_

¸

¸

_

−1 1 +g

1

−K −[X

2

] g

1

([X

2

] +K)

−[X

2

] −[X

2

]

2

+ (1 −K)[X

2

] 0

0 −[X

2

] −[X

2

]

2

+ (1 −K)[X

2

]

_

¸

¸

_

(A.12)

It follows that

res(P

1

, P

2

; X

1

) = g

1

[X

2

]

2

. (A.13)

Then the root of res(P

1

, P

2

; X

1

) = 0 is

[X

2

] = 0. (A.14)

Substituting [X

2

] = 0 to the polynomial system (A.1) with the assumed parameter

values, we have

P

1

([X

1

], 0) = −[X

1

]

2

+ (1 +g

1

)[X

1

] −K[X

1

] +g

1

K = 0 (A.15)

P

2

([X

1

], 0) = 0.

Thus,

[X

1

] =

−(1 +g

1

−K) ±

_

(1 +g

1

−K)

2

+ 4g

1

K

−2

=

(1 +g

1

−K) ∓

_

(1 +g

1

−K)

2

+ 4g

1

K

2

. (A.16)

Suppose g

1

> 0. Since 1+g

1

−K <

_

(1 +g

1

−K)

2

+ 4g

1

K then we have equilibrium

point ([X

1

]

∗

, [X

2

]

∗

) equal to

Appendix A. More on Equilibrium Points: Illustrations 112

_

(1 +g

1

−K) +

_

(1 +g

1

−K)

2

+ 4g

1

K

2

, 0

_

.

Therefore, we have exactly one equilibrium point where [X

1

]

∗

> [X

2

]

∗

when g

1

> 0.

If g

1

= 0 and K < 1 then we have two equilibrium points: (0, 0) and (1 − K, 0). If

g

1

= 0 and K ≥ 1 then the only equilibrium point is (0, 0).

A.1.4 Illustration 4

Suppose all parameters in the system (A.1) are equal to 1, except for arbitrary ρ

1

= ρ

2

=

ρ, arbitrary g

1

and g

2

= 0. Assume ρ > 0. The Sylvester matrix with [X

1

] as variable is

as follows:

_

¸

¸

_

−ρ 1 +g

1

−ρ −ρ[X

2

] g

1

([X

2

] + 1)

−ρ[X

2

] −ρ[X

2

]

2

+ (1 −ρ)[X

2

] 0

0 −ρ[X

2

] −ρ[X

2

]

2

+ (1 −ρ)[X

2

]

_

¸

¸

_

(A.17)

It follows that

res(P

1

, P

2

; X

1

) = g

1

ρ[X

2

]

2

. (A.18)

Then the root of res(P

1

, P

2

; X

1

) = 0 is

[X

2

] = 0. (A.19)

Substituting [X

2

] = 0 to the polynomial system (A.1) with the assumed parameter

values, we have

P

1

([X

1

], 0) = −ρ[X

1

]

2

+ (1 +g

1

)[X

1

] −ρ[X

1

] +g

1

= 0 (A.20)

P

2

([X

1

], 0) = 0.

Appendix A. More on Equilibrium Points: Illustrations 113

Thus,

[X

1

] =

−(1 +g

1

−ρ) ±

_

(1 +g

1

−ρ)

2

+ 4ρg

1

−2ρ

=

(1 +g

1

−ρ) ∓

_

(1 +g

1

−ρ)

2

+ 4ρg

1

2ρ

. (A.21)

Suppose g

1

> 0. Since 1 + g

1

−ρ <

_

(1 +g

1

−ρ)

2

+ 4ρg

1

then we have equilibrium

point ([X

1

]

∗

, [X

2

]

∗

) equal to

_

(1 +g

1

−ρ) +

_

(1 +g

1

−ρ)

2

+ 4ρg

1

2ρ

, 0

_

.

Therefore, we have exactly one equilibrium point where [X

1

]

∗

> [X

2

]

∗

when g

1

> 0.

If g

1

= 0 and ρ < 1 then we have two equilibrium points: (0, 0) and (1 − ρ, 0). If

g

1

= 0 and ρ ≥ 1 then the only equilibrium point is (0, 0).

A.2 Assume n = 2, c

i

= 2

A.2.1 Illustration 1

Consider c

i

= 2 and c

ij

= 1 for all i and j. The system of polynomial equations is as

follows:

P

1

([X

1

], [X

2

]) =−ρ

1

[X

1

]

3

+ (β

1

+g

1

) [X

1

]

2

−(K

1

+γ

12

[X

2

]) (ρ

1

[X

1

])

+g

1

γ

12

[X

2

] +g

1

K

1

= 0 (A.22)

P

2

([X

1

], [X

2

]) =−ρ

2

[X

2

]

3

+ (β

2

+g

2

) [X

2

]

2

−(K

2

+γ

21

[X

1

]) (ρ

2

[X

2

])

+g

2

γ

21

[X

1

] +g

2

K

2

= 0

Appendix A. More on Equilibrium Points: Illustrations 114

By Theorem (6.6), the number of complex solutions to the polynomial system (A.22)

is at most 9.

The corresponding Sylvester matrix of P

1

and P

2

with X

1

as variable is

_

¸

¸

¸

¸

¸

_

a

11

a

12

a

13

a

14

a

21

a

22

0 0

0 a

21

a

22

0

0 0 a

21

a

22

_

¸

¸

¸

¸

¸

_

(A.23)

where a

11

= −ρ

1

, a

12

= β

1

+ g

1

, a

13

= −K

1

ρ

1

− γ

12

ρ

1

[X

2

], a

14

= g

1

γ

12

[X

2

] + g

1

K

1

,

a

21

= −γ

21

ρ

2

[X

2

] + g

2

γ

21

and a

22

= −ρ

2

[X

2

]

3

+ (β

2

+ g

2

)[X

2

]

2

− K

2

ρ

2

[X

2

] + g

2

K

2

. The

Sylvester resultant res(P

1

, P

2

; X

1

) is a polynomial with variable X

2

and degree of at most

9. By Fundamental Theorem of Algebra, res(P

1

, P

2

; X

1

) = 0 has at most 9 complex

solutions which is consistent with Theorem (6.6).

It is diﬃcult and computationally expensive to ﬁnd the exact solutions to res(P

1

, P

2

;

X

1

) = 0 in terms of the arbitrary parameters. We investigate speciﬁc cases where we

assign values to some parameters.

Suppose all parameters in the system (A.22) are equal to 1, except for arbitrary g

1

and arbitrary g

2

. The Sylvester matrix is as follows:

_

¸

¸

¸

¸

¸

_

a

11

a

12

a

13

a

14

a

21

a

22

0 0

0 a

21

a

22

0

0 0 a

21

a

22

_

¸

¸

¸

¸

¸

_

(A.24)

where a

11

= −1, a

12

= 1 + g

1

, a

13

= −1 − [X

2

], a

14

= g

1

([X

2

] + 1), a

21

= g

2

− [X

2

]

and a

22

= −[X

2

]

3

+ (1 + g

2

)[X

2

]

2

−[X

2

] + g

2

. The Sylvester resultant res(P

1

, P

2

; X

1

) is

a polynomial with variable X

2

and degree of at most 9. By Fundamental Theorem of

Algebra, res(P

1

, P

2

; X

1

) = 0 has at most 9 complex solutions. But it is still diﬃcult and

computationally expensive to ﬁnd the exact solutions to res(P

1

, P

2

; X

1

) = 0 in terms of

the arbitrary g

1

and g

2

.

Appendix A. More on Equilibrium Points: Illustrations 115

If we add another assumption g

1

= 2g

2

(thus, we only have one arbitrary parameter),

the Sylvester matrix is as follows:

_

¸

¸

¸

¸

¸

_

a

11

a

12

a

13

a

14

a

21

a

22

0 0

0 a

21

a

22

0

0 0 a

21

a

22

_

¸

¸

¸

¸

¸

_

(A.25)

where a

11

= −1, a

12

= 1 +2g

2

, a

13

= −1 −[X

2

], a

14

= 2g

2

([X

2

] +1), a

21

= g

2

−[X

2

] and

a

22

= −[X

2

]

3

+ (1 + g

2

)[X

2

]

2

− [X

2

] + g

2

. The Sylvester resultant res(P

1

, P

2

; X

1

) of the

above matrix is a polynomial with variable X

2

and degree of at most 9. By Fundamental

Theorem of Algebra, res(P

1

, P

2

; X

1

) = 0 has at most 9 complex solutions. Notice that

we only know the upper bound of the number of equilibrium points and not the exact

values. Even with only one arbitrary parameter, it is still diﬃcult and computationally

expensive to ﬁnd the exact solutions to res(P

1

, P

2

; X

1

) = 0.

Hence, we deem not to continue ﬁnding the exact value of all the equilibrium points

using Sylvester resultant method for systems that is more complicated than a system

with n = 2, c

i

= 2, c

ij

= 1 and at least one arbitrary parameter. Notice that for the

above Sylvester matrix, we only have 4 ×4 dimension which means ﬁnding the solution

to res(P

1

, P

2

; X

1

) = 0 for a larger Sylvester matrix with at least one arbitrary parameter

may be more diﬃcult.

Nevertheless, in some instances where we do not have any arbitrary parameter, solving

for res(P

1

, P

2

; X

1

) = 0 is easy. For example, if we further assume that g

1

= 2g

2

where

g

2

= 1 then res(P

1

, P

2

; X

1

) = 0 has only one real nonnegative solution: [X

2

]

∗

≈ 1.3143.

A.2.2 Illustration 2

If c

i

= c

ij

= 2, according to Theorem (6.6), the upper bound of the number of equilibrium

points is 9.

Consider that all parameters are equal to 1 except for c

i

= c

ij

= 2 and g

i

= 0,

i, j = 1, 2. The only equilibrium point is the origin.

Appendix A. More on Equilibrium Points: Illustrations 116

A.2.3 Illustration 3

Consider that all parameters are equal to 1 except for c

i

= c

ij

= 2 (i, j = 1, 2) and g

2

= 0.

The only equilibrium point is ([X

1

]

∗

≈ 1.7549, [X

2

]

∗

= 0).

A.2.4 Illustration 4

Consider that all parameters are equal to 1 except for c

i

= c

ij

= 2, g

i

= 0 and β

i

= 3,

i, j = 1, 2. There are seven equilibrium points (the following values are approximates):

• ([X

1

]

∗

= 2.618, [X

2

]

∗

= 0),

• ([X

1

]

∗

= 0, [X

2

]

∗

= 2.618),

• ([X

1

]

∗

= 0.38197, [X

2

]

∗

= 0),

• ([X

1

]

∗

= 0, [X

2

]

∗

= 0.38197),

• ([X

1

]

∗

= 0.5, [X

2

]

∗

= 0.5),

• ([X

1

]

∗

= 1, [X

2

]

∗

= 1), and

• ([X

1

]

∗

= 0, [X

2

]

∗

= 0).

A.2.5 Illustration 5

Consider that all parameters are equal to 1 except for c

i

= c

ij

= 2, g

2

= 0, β

i

= 20

and ρ

i

= 10, i, j = 1, 2. There are three equilibrium points (the following values are

approximates):

• ([X

1

]

∗

= 1.4633, [X

2

]

∗

= 0),

• ([X

1

]

∗

= 0.5, [X

2

]

∗

= 0), and

• ([X

1

]

∗

= 0.13668, [X

2

]

∗

= 0).

A.3 Assume n = 3

A.3.1 Illustration 1

If c

i

= c

ij

= 1, i, j = 1, 2, 3, then according to Theorem (6.6), the upper bound of the

number of equilibrium points is 8.

Appendix A. More on Equilibrium Points: Illustrations 117

Consider that all parameters are equal to 1 except for g

2

= 0 and g

3

= 0. The only

equilibrium point is ([X

1

]

∗

≈ 1.618, [X

2

]

∗

= 0, [X

3

]

∗

= 0).

A.3.2 Illustration 2

If c

i

= c

ij

= 2, i, j = 1, 2, 3, then according to Theorem (6.6), the upper bound of the

number of equilibrium points is 27.

Consider that all parameters are equal to 1 except for c

i

= c

ij

= 2 (i, j = 1, 2, 3),

g

2

= 0 and g

3

= 0. The only equilibrium point is ([X

1

]

∗

≈ 1.7549, [X

2

]

∗

= 0, [X

3

]

∗

= 0).

A.3.3 Illustration 3

If c

i

= c

ij

= 3, i, j = 1, 2, 3, then according to Theorem (6.6), the upper bound of the

number of equilibrium points is 64.

Consider that all parameters are equal to 1 except for c

i

= c

ij

= 3 and g

i

= 0,

i, j = 1, 2, 3. The only equilibrium point is the origin.

A.3.4 Illustration 4

Consider that all parameters are equal to 1 except for c

i

= c

ij

= 3 (i, j = 1, 2, 3), g

2

= 0

and g

3

= 0. The only equilibrium point is ([X

1

]

∗

≈ 1.8668, [X

2

]

∗

= 0, [X

3

]

∗

= 0).

A.3.5 Illustration 5

Consider that all parameters are equal to 1 except for c

i

= c

ij

= 3, β

i

= 3 and g

i

= 0,

i, j = 1, 2, 3. There are ten equilibrium points (the following values are approximates):

• ([X

1

]

∗

= 1.0097 ×10

−28

≈ 0, [X

2

]

∗

= 0.6527, [X

3

]

∗

= 0),

• ([X

1

]

∗

= 1.5510 ×10

−25

≈ 0, [X

2

]

∗

= 2.8794, [X

3

]

∗

= 0),

• ([X

1

]

∗

= 0.6527, [X

2

]

∗

= 0, [X

3

]

∗

= 0),

• ([X

1

]

∗

= 0, [X

2

]

∗

= 0, [X

3

]

∗

= 0.6527),

Appendix A. More on Equilibrium Points: Illustrations 118

• ([X

1

]

∗

= 2.8794, [X

2

]

∗

= 0, [X

3

]

∗

= 0),

• ([X

1

]

∗

= 0, [X

2

]

∗

= 0, [X

3

]

∗

= 2.8794),

• ([X

1

]

∗

= 1, [X

2

]

∗

= 1, [X

3

]

∗

= 0),

• ([X

1

]

∗

= 1, [X

2

]

∗

= 0, [X

3

]

∗

= 1),

• ([X

1

]

∗

= 0, [X

2

]

∗

= 1, [X

3

]

∗

= 1), and

• ([X

1

]

∗

= 0, [X

2

]

∗

= 0, [X

3

]

∗

= 0).

A.3.6 Illustration 6

Consider that all parameters are equal to 1 except for c

i

= c

ij

= 3, β

i

= 20, ρ

i

= 10,

g

2

= 0 and g

3

= 0, i, j = 1, 2, 3. There are seven equilibrium points (the following values

are approximates):

• ([X

1

]

∗

= 0.10103, [X

2

]

∗

= 1.001, [X

3

]

∗

= 0),

• ([X

1

]

∗

= 0.10103, [X

2

]

∗

= 0, [X

3

]

∗

= 1.001),

• ([X

1

]

∗

= 0.10039, [X

2

]

∗

= 1.6173, [X

3

]

∗

= 0),

• ([X

1

]

∗

= 0.10039, [X

2

]

∗

= 0, [X

3

]

∗

= 1.6173),

• ([X

1

]

∗

= 0.10213, [X

2

]

∗

= 0, [X

3

]

∗

= 0),

• ([X

1

]

∗

= 0.83362, [X

2

]

∗

= 0, [X

3

]

∗

= 0), and

• ([X

1

]

∗

= 1.8123, [X

2

]

∗

= 0, [X

3

]

∗

= 0).

A.3.7 Illustration 7

Consider that all parameters are equal to 1 except for c

i

= c

ij

= 2, γ

ij

= γ, ρ

i

= ρ and

g

i

= 0, i, j = 1, 2, 3. Notice that this system is the system used by MacArthur et al. in

[113] (refer to system (3.8)). The nonlinear system (3.8) is of the form:

[X

1

]

2

1 + [X

1

]

2

+γ[X

2

]

2

+γ[X

3

]

2

−ρ[X

1

] = 0

[X

2

]

2

1 + [X

2

]

2

+γ[X

1

]

2

+γ[X

3

]

2

−ρ[X

2

] = 0 (A.26)

[X

3

]

2

1 + [X

3

]

2

+γ[X

1

]

2

+γ[X

2

]

2

−ρ[X

3

] = 0.

Appendix A. More on Equilibrium Points: Illustrations 119

The corresponding polynomial system is

P

1

([X

1

], [X

2

], [X

3

]) = [X

1

]

2

−ρ[X

1

] −ρ[X

1

]

3

−γρ[X

1

][X

2

]

2

−γρ[X

1

][X

3

]

2

= 0

P

2

([X

1

], [X

2

], [X

3

]) = [X

2

]

2

−ρ[X

2

] −ρ[X

2

]

3

−γρ[X

1

]

2

[X

2

] −γρ[X

2

][X

3

]

2

= 0 (A.27)

P

3

([X

1

], [X

2

], [X

3

]) = [X

3

]

2

−ρ[X

3

] −ρ[X

3

]

3

−γρ[X

1

]

2

[X

3

] −γρ[X

2

]

2

[X

3

] = 0.

The Sylvester matrix associated to P

1

and P

2

with [X

1

] as variable is as follows:

_

¸

¸

¸

¸

¸

¸

¸

¸

_

a

11

a

12

a

13

0 0

0 a

11

a

12

a

13

0

a

31

0 a

33

0 0

0 a

31

0 a

33

0

0 0 a

31

0 a

33

_

¸

¸

¸

¸

¸

¸

¸

¸

_

(A.28)

where a

11

= −ρ, a

12

= 1, a

13

= −ρ − γρ[X

2

]

2

− γρ[X

3

]

2

, a

31

= −γρ[X

2

] and a

33

=

[X

2

]

2

−ρ[X

2

] −ρ[X

2

]

3

−γρ[X

2

][X

3

]

2

.

The Sylvester matrix associated to P

1

and P

3

with [X

1

] as variable is as follows:

_

¸

¸

¸

¸

¸

¸

¸

¸

_

a

11

a

12

a

13

0 0

0 a

11

a

12

a

13

0

a

31

0 a

33

0 0

0 a

31

0 a

33

0

0 0 a

31

0 a

33

_

¸

¸

¸

¸

¸

¸

¸

¸

_

(A.29)

where a

11

= −ρ, a

12

= 1, a

13

= −ρ − γρ[X

2

]

2

− γρ[X

3

]

2

, a

31

= −γρ[X

3

] and a

33

=

[X

3

]

2

−ρ[X

3

] −ρ[X

3

]

3

−γρ[X

2

]

2

[X

3

].

The following are the Sylvester resultants (with [X

1

] as variable) associated to the

polynomial system (A.27):

Appendix A. More on Equilibrium Points: Illustrations 120

• res(P

1

, P

2

; [X

1

]) = −ρ[X

2

]

3

(ρ −[X

2

] +ρ[X

2

]

2

+γρ[X

3

]

2

) (ρ −[X

2

] +ρ[X

2

]

2

+

γρ[X

2

]

2

+ γρ[X

3

]

2

) (γ − 2γρ

2

+ γ

2

ρ

2

+ ρ

2

[X

2

]

2

− ρ[X

2

] + ρ

2

− γ

2

ρ

2

[X

2

]

2

+

γ

3

ρ

2

[X

2

]

2

−2γ

2

ρ

2

[X

3

]

2

+γ

3

ρ

2

[X

3

]

2

+γ

2

ρ[X

2

] −γρ

2

[X

2

]

2

+γρ

2

[X

3

]

2

)

• res(P

1

, P

3

; [X

1

]) = −ρ[X

3

]

3

(ρ −[X

3

] +ρ[X

3

]

2

+γρ[X

2

]

2

) (ρ −[X

3

] +ρ[X

3

]

2

+

γρ[X

3

]

2

+ γρ[X

2

]

2

) (γ − 2γρ

2

+ γ

2

ρ

2

+ ρ

2

[X

3

]

2

− ρ[X

3

] + ρ

2

− γ

2

ρ

2

[X

3

]

2

+

γ

3

ρ

2

[X

3

]

2

−2γ

2

ρ

2

[X

2

]

2

+γ

3

ρ

2

[X

2

]

2

+γ

2

ρ[X

3

] −γρ

2

[X

3

]

2

+γρ

2

[X

2

]

2

).

We investigate all possible combination of the factors of res(P

1

, P

2

; [X

1

]) and res(P

1

,

P

3

; [X

1

]) and their simultaneous nonnegative real zeros. For example, the factors −ρ[X

2

]

3

in res(P

1

, P

2

; [X

1

]) and −ρ[X

3

]

3

in res(P

1

, P

3

; [X

1

]) have a simultaneous nonnegative

real zero which is [X

2

]

∗

= [X

3

]

∗

= 0. However, it is also possible that a factor of

res(P

1

, P

2

; [X

1

]) and a factor of res(P

1

, P

3

; [X

1

]) do not have a simultaneous zero.

Suppose the factors of res(P

1

, P

2

; [X

1

]) and res(P

1

, P

3

; [X

1

]) have a simultaneous non-

negative real zero. An interesting property of such zero is that it satisﬁes one of the

following characteristics:

1. [X

2

]

∗

= [X

3

]

∗

= 0;

2. [X

2

]

∗

= 0 and [X

3

]

∗

> [X

2

]

∗

;

3. [X

3

]

∗

= 0 and [X

2

]

∗

> [X

3

]

∗

;

4. [X

2

]

∗

= [X

3

]

∗

> 0;

5. [X

2

]

∗

> [X

3

]

∗

> 0; and

6. [X

3

]

∗

> [X

2

]

∗

> 0.

Since the structure of each equation in the nonlinear system (A.26) are similar, then

the above enumeration of characteristics of solutions also apply to the relationship be-

tween [X

1

] and [X

2

] as well as to the relationship between [X

1

] and [X

3

].

We can conclude that an equilibrium point satisﬁes one of the following characteristics

(depending on the value of γ and ρ):

Appendix A. More on Equilibrium Points: Illustrations 121

1. [X

1

]

∗

= [X

2

]

∗

= [X

3

]

∗

;

2. [X

1

]

∗

> [X

2

]

∗

= [X

3

]

∗

;

3. [X

2

]

∗

> [X

1

]

∗

= [X

3

]

∗

;

4. [X

3

]

∗

> [X

1

]

∗

= [X

2

]

∗

;

5. [X

1

]

∗

< [X

2

]

∗

= [X

3

]

∗

;

6. [X

2

]

∗

< [X

1

]

∗

= [X

3

]

∗

;

7. [X

3

]

∗

< [X

1

]

∗

= [X

2

]

∗

;

8. [X

1

]

∗

> [X

2

]

∗

> [X

3

]

∗

;

9. [X

2

]

∗

> [X

3

]

∗

> [X

1

]

∗

;

10. [X

3

]

∗

> [X

1

]

∗

> [X

2

]

∗

;

11. [X

1

]

∗

> [X

3

]

∗

> [X

2

]

∗

;

12. [X

2

]

∗

> [X

1

]

∗

> [X

3

]

∗

; and

13. [X

3

]

∗

> [X

2

]

∗

> [X

1

]

∗

.

Each characteristic may represent a cell that is tripotent (primed), bipotent, unipotent

or in terminal state. However, it is also possible to have the origin as the equilibrium

point which is a trivial case. Our observation regarding these possible characteristics of

equilibrium points is also consistent with the ﬁndings of MacArthur et al. [113].

Based from Theorem (6.6), our system may have at most 27 equilibrium points.

Appendix A. More on Equilibrium Points: Illustrations 122

A.3.8 Illustration 8

Consider the system in (A.3.7) (Illustration 7), where γ =

1

8

and ρ =

1

21

. This system has

equilibrium points satisfying all the characteristics enumerated in Illustration 7 (A.3.7).

Moreover, this system has 27 equilibrium points which is equal to the upper bound of the

number of possible equilibrium points. The equilibrium points are (the following values

are approximates):

• ([X

1

]

∗

= 1.3235 ×10

−23

≈ 0, [X

2

]

∗

= 20.952, [X

∗

3

] = 0),

• ([X

1

]

∗

= 18.619, [X

2

] = 0, [X

3

] = 18.619),

• ([X

1

]

∗

= 18.619, [X

2

]

∗

= 18.619, [X

3

]

∗

= 0),

• ([X

1

]

∗

= 0, [X

2

]

∗

= 18.619, [X

3

]

∗

= 18.619),

• ([X

1

]

∗

= 20.832, [X

2

]

∗

= 3.1685, [X

3

]

∗

= 3.1685),

• ([X

1

]

∗

= 3.1685, [X

2

]

∗

= 20.832, [X

3

]

∗

= 3.1685),

• ([X

1

]

∗

= 3.1685, [X

2

]

∗

= 3.1685, [X

3

]

∗

= 20.832),

• ([X

1

]

∗

= 4.7755 ×10

−2

, [X

2

]

∗

= 4.7755 ×10

−2

, [X

3

]

∗

= 4.7755 ×10

−2

),

• ([X

1

]

∗

= 20.894, [X

2

]

∗

= 3.1056, [X

3

]

∗

= 0),

• ([X

1

]

∗

= 20.894, [X

2

]

∗

= 0, [X

3

]

∗

= 3.1056),

• ([X

1

]

∗

= 3.1056, [X

2

]

∗

= 20.894, [X

3

]

∗

= 0),

• ([X

1

]

∗

= 3.1056, [X

2

]

∗

= 0, [X

3

]

∗

= 20.894),

• ([X

1

]

∗

= 0, [X

2

]

∗

= 20.894, [X

3

]

∗

= 3.1056),

• ([X

1

]

∗

= 0, [X

2

]

∗

= 3.1056, [X

3

]

∗

= 20.894),

• ([X

1

]

∗

= 4.7741 ×10

−2

, [X

2

]

∗

= 0, [X

3

]

∗

= 4.7741 ×10

−2

),

• ([X

1

]

∗

= 4.7741 ×10

−2

, [X

2

]

∗

= 4.7741 ×10

−2

, [X

3

]

∗

= 0),

• ([X

1

]

∗

= 0, [X

2

]

∗

= 4.7741 ×10

−2

, [X

3

]

∗

= 4.7741 ×10

−2

),

• ([X

1

]

∗

= 16.752, [X

2

]

∗

= 16.752, [X

3

]

∗

= 16.752),

• ([X

1

]

∗

= 20.952, [X

2

]

∗

= 0, [X

3

]

∗

= 0),

• ([X

1

]

∗

= 0, [X

2

]

∗

= 0, [X

3

]

∗

= 20.952),

• ([X

1

]

∗

= 2.0033 ×10

−25

≈ 0, [X

2

]

∗

= 4.7728 ×10

−2

, [X

3

]

∗

= 0),

• ([X

1

]

∗

= 4.7728 ×10

−2

, [X

2

]

∗

= 0, [X

3

]

∗

= 0),

• ([X

1

]

∗

= 0, [X

2

]

∗

= 0, [X

3

]

∗

= 4.7728 ×10

−2

),

• ([X

1

]

∗

= 18.432, [X

2

]

∗

= 18.432, [X

3

]

∗

= 5.5685),

Appendix A. More on Equilibrium Points: Illustrations 123

• ([X

1

]

∗

= 18.432, [X

2

]

∗

= 5.5685, [X

3

]

∗

= 18.432),

• ([X

1

]

∗

= 5.5685, [X

2

]

∗

= 18.432, [X

3

]

∗

= 18.432), and

• ([X

1

]

∗

= 0, [X

2

]

∗

= 0, [X

3

]

∗

= 0).

The equilibrium points where [X

3

]

∗

= 0 are the equilibrium points of the system when

n = 2. Also, the equilibrium points where [X

2

]

∗

= [X

3

]

∗

= 0 are the equilibrium points

of the system when n = 1.

Remark: Given ﬁxed values of [X

j

], j = i, the univariate Hill curve Y = H

i

([X

i

]) and

Y = ρ

i

[X

i

] have the following possible number of intersections (see Figures (5.11) to

(5.14)):

• two intersections where one is stable;

• one intersection which is stable; and

• three intersections where two are stable.

Notice that the number of stable intersections is greater than or equal to the number of

unstable. However, when we collect all possible equilibrium points of the ODE model

(5.1) (where values of [X

j

], j = i are not ﬁxed), the number of stable equilibrium points

is not necessarily greater than or equal to the number of unstable equilibrium points.

For example, in the previous illustration (A.3.8) (Illustration 8), we have 27 equi-

librium points where only 8 are stable. The following is the list of stable and unstable

equilibrium points:

• ([X

1

]

∗

= 1.3235 × 10

−23

≈ 0, [X

2

]

∗

= 20.952, [X

∗

3

] = 0) — stable (terminal

state),

• ([X

1

]

∗

= 18.619, [X

2

] = 0, [X

3

] = 18.619) — stable (bipotent),

• ([X

1

]

∗

= 18.619, [X

2

]

∗

= 18.619, [X

3

]

∗

= 0) — stable (bipotent),

• ([X

1

]

∗

= 0, [X

2

]

∗

= 18.619, [X

3

]

∗

= 18.619) — stable (bipotent),

• ([X

1

]

∗

= 20.832, [X

2

]

∗

= 3.1685, [X

3

]

∗

= 3.1685) — unstable,

• ([X

1

]

∗

= 3.1685, [X

2

]

∗

= 20.832, [X

3

]

∗

= 3.1685) — unstable,

• ([X

1

]

∗

= 3.1685, [X

2

]

∗

= 3.1685, [X

3

]

∗

= 20.832) — unstable,

• ([X

1

]

∗

= 4.7755 × 10

−2

, [X

2

]

∗

= 4.7755 × 10

−2

, [X

3

]

∗

= 4.7755 × 10

−2

) —

unstable,

Appendix A. More on Equilibrium Points: Illustrations 124

• ([X

1

]

∗

= 20.894, [X

2

]

∗

= 3.1056, [X

3

]

∗

= 0) — unstable,

• ([X

1

]

∗

= 20.894, [X

2

]

∗

= 0, [X

3

]

∗

= 3.1056) — unstable,

• ([X

1

]

∗

= 3.1056, [X

2

]

∗

= 20.894, [X

3

]

∗

= 0) — unstable,

• ([X

1

]

∗

= 3.1056, [X

2

]

∗

= 0, [X

3

]

∗

= 20.894) — unstable,

• ([X

1

]

∗

= 0, [X

2

]

∗

= 20.894, [X

3

]

∗

= 3.1056) — unstable,

• ([X

1

]

∗

= 0, [X

2

]

∗

= 3.1056, [X

3

]

∗

= 20.894) — unstable,

• ([X

1

]

∗

= 4.7741 ×10

−2

, [X

2

]

∗

= 0, [X

3

]

∗

= 4.7741 ×10

−2

) — unstable,

• ([X

1

]

∗

= 4.7741 ×10

−2

, [X

2

]

∗

= 4.7741 ×10

−2

, [X

3

]

∗

= 0) — unstable,

• ([X

1

]

∗

= 0, [X

2

]

∗

= 4.7741 ×10

−2

, [X

3

]

∗

= 4.7741 ×10

−2

) — unstable,

• ([X

1

]

∗

= 16.752, [X

2

]

∗

= 16.752, [X

3

]

∗

= 16.752) — stable (tripotent),

• ([X

1

]

∗

= 20.952, [X

2

]

∗

= 0, [X

3

]

∗

= 0) — stable (terminal state),

• ([X

1

]

∗

= 0, [X

2

]

∗

= 0, [X

3

]

∗

= 20.952) — stable (terminal state)),

• ([X

1

]

∗

= 2.0033 ×10

−25

≈ 0, [X

2

]

∗

= 4.7728 ×10

−2

, [X

3

]

∗

= 0) — unstable,

• ([X

1

]

∗

= 4.7728 ×10

−2

, [X

2

]

∗

= 0, [X

3

]

∗

= 0) — unstable,

• ([X

1

]

∗

= 0, [X

2

]

∗

= 0, [X

3

]

∗

= 4.7728 ×10

−2

) — unstable,

• ([X

1

]

∗

= 18.432, [X

2

]

∗

= 18.432, [X

3

]

∗

= 5.5685) — unstable,

• ([X

1

]

∗

= 18.432, [X

2

]

∗

= 5.5685, [X

3

]

∗

= 18.432) — unstable,

• ([X

1

]

∗

= 5.5685, [X

2

]

∗

= 18.432, [X

3

]

∗

= 18.432) — unstable, and

• ([X

1

]

∗

= 0, [X

2

]

∗

= 0, [X

3

]

∗

= 0) — stable (trivial case).

In the following section, we illustrate how to use ad hoc geometric analysis in deter-

mining the stability of equilibrium points.

A.4 Ad hoc geometric analysis

Consider that all parameters are equal to 1 except for c

i

= c

ij

= 3, β

i

= 20, ρ

i

= 10,

g

2

= 0 and g

3

= 0, i, j = 1, 2, 3 (see Illustration 6 (A.3.6)).

One of the equilibrium points is ([X

1

]

∗

= 0.10103, [X

2

]

∗

= 1.001, [X

3

]

∗

= 0). To

determine the stability of this equilibrium point we use ad hoc geometric analysis. First,

we look at the intersection of Y = H

1

([X

1

]) + 1 and Y = 10[X

1

] with [X

2

] = 1.001 and

Appendix A. More on Equilibrium Points: Illustrations 125

[X

3

] = 0. Then we determine if [X

1

]

∗

= 0.10103 is stable or not. As shown in Figure

(A.2), we conclude that [X

1

]

∗

= 0.10103 is stable.

Now, we test if [X

2

]

∗

= 1.001 is stable or not by looking at the intersection of Y =

H

2

([X

2

]) and Y = 10[X

2

] with [X

1

] = 0.10103 and [X

3

] = 0. Also, we test if [X

3

]

∗

= 0

is stable or not by looking at the intersection of Y = H

3

([X

3

]) and Y = 10[X

3

] with

[X

1

] = 0.10103 and [X

2

] = 1.001. As shown in Figure (A.3) and (A.4), we conclude that

[X

2

]

∗

= 1.001 is unstable and [X

3

] = 0 is stable.

Because of the presence of an unstable component (which is [X

2

]

∗

= 1.001), hence,

the equilibrium point ([X

1

]

∗

= 0.10103, [X

2

]

∗

= 1.001, [X

3

]

∗

= 0) is unstable.

Figure A.2: The intersection of Y = H

1

([X

1

]) + 1 and Y = 10[X

1

] with [X

2

] = 1.001

and [X

3

] = 0.

Appendix A. More on Equilibrium Points: Illustrations 126

Figure A.3: The intersection of Y = H

2

([X

2

]) and Y = 10[X

2

] with [X

1

] = 0.10103 and

[X

3

] = 0.

Figure A.4: The intersection of Y = H

3

([X

3

]) and Y = 10[X

3

] with [X

1

] = 0.10103 and

[X

2

] = 1.001.

Appendix A. More on Equilibrium Points: Illustrations 127

A.5 Phase portrait with inﬁnitely many equilibrium

points

For example, the phase portrait of the system

d[X

1

]

dt

=

5[X

1

]

1 + [X

1

] + [X

2

]

−[X

1

] (A.30)

d[X

2

]

dt

=

5[X

2

]

1 + [X

1

] + [X

2

]

−[X

2

]

is shown in Figure (A.5). The phase portrait was graphed using the Java applet in

http://www.scottsarra.org/applets/dirField2/dirField2.html [145].

Figure A.5: A sample phase portrait of the system with inﬁnitely many non-isolated

equilibrium points.

Appendix B

Multivariate Fixed Point Algorithm

We have written a Scilab [150] program for ﬁnding approximate values of stable equilib-

rium points. This program employs the Fixed Point Iteration method. However, if we

do numerical computations, we need to be cautious about the possible round-oﬀ errors

that we may encounter.

Algorithm 3 Multivariate ﬁxed point algorithm (1st Part)

//input

n=input("Input n=")

for i=1:n

disp(i, "FOR EQUATION")

coeffbeta(i)=input("beta=")

K(i)=input("K=")

rho(i)=input("positive rho=")

g(i)=input("g=")

disp(i, "exponent of x")

c(i)=input("ci=")

for m=1:n

if m~=i then

disp(m, "coefficient of x")

gam(i,m)=input("gamma=")

disp(m, "exponent of x")

z(i,m)=input("cij=")

else

gam(i,m)=1

end

end

end

for i=1:n

disp(i, "initial value for x")

x(i,1)=input("=")

end

128

Appendix B. Multivariate Fixed Point Algorithm 129

Algorithm 4 Multivariate ﬁxed point algorithm (2nd Part)

//fixed point iteration process

tol=input("tolerance error=")

j=1

y(1)=1000

while (y(j)>tol)&(j<500002) then //500,000 max number of steps

for i=1:n

summ(i)=0

for k=1:n

if k~=i then

summ(i)=summ(i)+gam(i,k)*x(k,j)^z(i,k)

end

end

x(i,j+1)=((coeffbeta(i)*x(i,j)^c(i))/(K(i)+x(i,j)^c(i)+summ(i))..

+g(i))/rho(i)

end

j=j+1

y(j)=max(abs(x(:,j)-x(:,j-1)))

end

q=input("q for test of Q-convergence=")

for i=1:j-2

lambda(i)=(norm(x(:,i+2)-x(:,i+1)))/((norm(x(:,i+1)-x(:,i)))^q)

lambdalim=lambda(i)

end

//output

disp(x(:,j), "The approx equilibrium point is ")

disp(j-1, "number of iterations is ")

disp(lambdalim, "when q=1, the approx asymptotic error constant is ")

Appendix B. Multivariate Fixed Point Algorithm 130

We illustrate how to use multivariate ﬁxed point algorithm in determining the stability

of equilibrium points.

Consider the case where all parameters are equal to 1 except for c

i

= c

ij

= 3, β

i

= 20,

ρ

i

= 10, g

2

= 0 and g

3

= 0, i, j = 1, 2, 3.

One of the equilibrium points is ([X

1

]

∗

≈ 0.10039, [X

2

]

∗

≈ 1.6173, [X

3

]

∗

= 0). We

perturb this equilibrium point by adding and subtracting a small positive number per

component (but note that the components should not be negative). Suppose we use

the small positive number 0.00001, then we have ([X

1

] = 0.10039 + 0.00001, [X

2

] =

1.6173 + 0.00001, [X

3

] = 0 + 0.00001) and ([X

1

] = 0.10039 − 0.00001, [X

2

] = 1.6173 −

0.00001, [X

3

] = 0). We use these two perturbed points as the initial conditions in the

multivariate ﬁxed point algorithm.

If both the sequences of points generated by the multivariate ﬁxed point algorithm (us-

ing the two initial conditions) converge to the equilibrium point ([X

1

]

∗

≈ 0.10039, [X

2

]

∗

≈

1.6173, [X

3

]

∗

= 0), then we can conclude that this equilibrium point is stable. If at least

one of the two sequences of points tends away from the equilibrium point then we can

“approximately” conclude that the equilibrium point is unstable. We need to use the

two perturbed points to minimize the probability of converging to a saddle point. We

say “approximately conclude” because a point may seem unstable yet it might be stable

with only very small basin of attraction.

Assuming a tolerance error of 10

−5

, then by the multivariate ﬁxed point algorithm,

the equilibrium point ([X

1

]

∗

= 0.10039, [X

2

]

∗

= 1.6173, [X

3

]

∗

= 0) is stable. Moreover, in

this example, the sequences of points generated by the multivariate ﬁxed point algorithm

converges linearly.

Appendix C

More on Bifurcation of Parameters:

Illustrations

C.1 Adding g

i

> 0, Illustration 1

Consider the following system

d[X

1

]

dt

=

3[X

1

]

3

1 + [X

1

]

3

+ [X

2

]

3

+ [X

3

]

3

−[X

1

]

d[X

2

]

dt

=

3[X

2

]

3

1 + [X

1

]

3

+ [X

2

]

3

+ [X

3

]

3

−[X

2

] (C.1)

d[X

3

]

dt

=

3[X

3

]

3

1 + [X

1

]

3

+ [X

2

]

3

+ [X

3

]

3

−[X

3

].

This system has the following equilibrium points (the following are approximate values):

• ([X

1

]

∗

= 0, [X

2

]

∗

= 0.6527, [X

3

]

∗

= 0) — unstable,

• ([X

1

]

∗

= 0, [X

2

]

∗

= 2.8794, [X

3

]

∗

= 0) — stable (terminal state),

• ([X

1

]

∗

= 0.6527, [X

2

]

∗

= 0, [X

3

]

∗

= 0) — unstable,

• ([X

1

]

∗

= 0, [X

2

]

∗

= 0, [X

3

]

∗

= 0.6527) — unstable,

• ([X

1

]

∗

= 2.8794, [X

2

]

∗

= 0, [X

3

]

∗

= 0) — stable (terminal state),

• ([X

1

]

∗

= 0, [X

2

]

∗

= 0, [X

3

]

∗

= 2.8794) — stable (terminal state),

• ([X

1

]

∗

= 1, [X

2

]

∗

= 1, [X

3

]

∗

= 0) — stable (bipotent),

• ([X

1

]

∗

= 1, [X

2

]

∗

= 0, [X

3

]

∗

= 1) — stable (bipotent),

• ([X

1

]

∗

= 0, [X

2

]

∗

= 1, [X

3

]

∗

= 1) — stable (bipotent), and

• ([X

1

]

∗

= 0, [X

2

]

∗

= 0, [X

3

]

∗

= 0) — stable (trivial case).

131

Appendix C. More on Bifurcation of Parameters: Illustrations 132

Now, let us add g

1

= 1, that is, consider the following system

d[X

1

]

dt

=

3[X

1

]

3

1 + [X

1

]

3

+ [X

2

]

3

+ [X

3

]

3

−[X

1

] + 1

d[X

2

]

dt

=

3[X

2

]

3

1 + [X

1

]

3

+ [X

2

]

3

+ [X

3

]

3

−[X

2

] (C.2)

d[X

3

]

dt

=

3[X

3

]

3

1 + [X

1

]

3

+ [X

2

]

3

+ [X

3

]

3

−[X

3

].

This system has the following sole equilibrium point: ([X

1

]

∗

≈ 3.9522, [X

2

]

∗

= 0, [X

3

]

∗

=

0), which is stable.

If we also add g

2

= 1, that is, consider the following system

d[X

1

]

dt

=

3[X

1

]

3

1 + [X

1

]

3

+ [X

2

]

3

+ [X

3

]

3

−[X

1

] + 1

d[X

2

]

dt

=

3[X

2

]

3

1 + [X

1

]

3

+ [X

2

]

3

+ [X

3

]

3

−[X

2

] + 1 (C.3)

d[X

3

]

dt

=

3[X

3

]

3

1 + [X

1

]

3

+ [X

2

]

3

+ [X

3

]

3

−[X

3

],

then we have the following equilibrium points (the following are approximate values):

• ([X

1

]

∗

= 2.4507, [X

2

]

∗

= 2.4507, [X

3

]

∗

= 0) — stable (bipotent),

• ([X

1

]

∗

= 1.0581, [X

2

]

∗

= 3.8929, [X

3

]

∗

= 0) — stable (unipotent), and

• ([X

1

]

∗

= 3.8929, [X

2

]

∗

= 1.0581, [X

3

]

∗

= 0) — stable (unipotent).

C.2 Adding g

i

> 0, Illustration 2

Consider the following system

d[X

1

]

dt

=

5[X

1

]

2

1 + [X

1

]

2

+ [X

2

]

2

−2[X

1

] (C.4)

d[X

2

]

dt

=

5[X

2

]

2

1 + [X

1

]

2

+ [X

2

]

2

−2[X

2

].

We can add g

1

> 0 to the system if we want [X

1

]

∗

to suﬃciently dominate [X

2

]

∗

. We

can do ad hoc geometric analysis to determine if the value of g

1

is enough to drive the

system to have sole equilibrium point where [X

1

]

∗

> [X

2

]

∗

.

Appendix C. More on Bifurcation of Parameters: Illustrations 133

We ﬁrst graph

Y =

5[X

1

]

2

1 + [X

1

]

2

+g

1

and

Y = 2[X

1

],

then we determine if the two curves have a sole intersection. If they do have more than

one intersection, we increase the value of g

1

. We ﬁnd the value of the sole intersection

and denote it by [X

1

]

(∗)

.

We substitute [X

1

]

(∗)

to [X

1

] in Y =

5[X

2

]

2

1+[X

1

]

2

+[X

2

]

2

. Then we determine if

Y =

5[X

2

]

2

1 + [X

1

]

(∗)

2

+ [X

2

]

2

and

Y = 2[X

2

]

intersect only at one point. If there are more than one intersections, we increase g

1

and

adjust [X

1

]

(∗)

. If there is only one intersection then [X

2

]

∗

= 0.

Figure C.1: Determining the adequate g

1

> 0 that would give rise to a sole equilibrium

point where [X

1

]

∗

> [X

2

]

∗

.

The sole stable equilibrium point of the system with adequate g

i

> 0 is the computed

Appendix C. More on Bifurcation of Parameters: Illustrations 134

([X

1

]

∗

= [X

1

]

(∗)

, [X

2

]

∗

= 0). See Figure (C.1) for illustration. If we suppose g

1

= 1, the

sole equilibrium point is ([X

1

]

∗

≈ 2.698, [X

2

]

∗

= 0).

C.3 g

i

as a function of time

Making g

i

as a function of time (i.e., g

i

changes through time) means that we are adding

another equation and state variable to our system of ODEs. We can think g

i

as an

additional node to our GRN and we call it as the injection node. In this thesis, we

consider two types of functions — linear function with negative slope and exponential

function with negative exponent. Notice that the two functions represent a g

i

that

degrades through time.

Suppose given a speciﬁc initial condition, the solution to our system tends to an

equilibrium point with [X

i

]

∗

= 0. If we want our solution to escape [X

i

]

∗

= 0 then

one strategy is to add g

i

> 0. The idea of adding an enough amount of g

i

> 0 is

to make the solution of our system escape a certain equilibrium point. However, it

is sometimes impractical or infeasible to continuously introduce a constant amount of

exogenous stimulus to control cell fates, that is why we can rather consider introducing

g

i

that degrades through time.

We numerically investigate the case where adding a degrading amount of g

i

aﬀects cell

fate. However, this strategy is only applicable to systems with multiple stable equilibrium

points where convergence of trajectories is sensitive to initial conditions.

C.3.1 As a linear function

Suppose

g

i

(t) = −υ

i

t +g

i

(0) or (C.5)

dg

i

dt

= −υ

i

where the degradation rate υ

i

is positive. We deﬁne g

i

(t) < 0 as g

i

(t) = 0.

Appendix C. More on Bifurcation of Parameters: Illustrations 135

Here is an example where without g

1

, [X

1

]

∗

= 0 (see Figure (C.2)); but by adding

g

1

(t) = −t + 5, the solution converges to a new equilibrium point with [X

1

]

∗

≈ 2.98745

(see Figure (C.3)). Figure (C.2) shows the numerical solution to the system

d[X

1

]

dt

=

3[X

1

]

5

1 + [X

1

]

5

+ [X

2

]

5

−[X

1

] (C.6)

d[X

2

]

dt

=

3[X

2

]

5

1 + [X

1

]

5

+ [X

2

]

5

−[X

2

].

While, Figure (C.3) shows the numerical solution to the system (with g

i

(t))

d[X

1

]

dt

=

3[X

1

]

5

1 + [X

1

]

5

+ [X

2

]

5

−[X

1

] +g

1

d[X

2

]

dt

=

3[X

2

]

5

1 + [X

1

]

5

+ [X

2

]

5

−[X

2

] (C.7)

dg

1

dt

= −1

Limit g

1

≥ 0.

The initial values are [X

1

]

0

= 0.5, [X

2

]

0

= 1 and g

i

(0) = 5.

By looking at Figure (C.4), we can see that [X

1

]

∗

shifted from a lower stable compo-

nent to a higher stable component.

Figure C.2: An example where without g

1

, [X

1

]

∗

= 0.

Appendix C. More on Bifurcation of Parameters: Illustrations 136

Figure C.3: [X

1

]

∗

escaped the zero state because of the introduction of g

1

which is a

decaying linear function.

Figure C.4: An example of shifting from a lower stable component to a higher stable

component through adding g

i

(t) = −υ

i

t +g

i

(0).

Appendix C. More on Bifurcation of Parameters: Illustrations 137

C.3.2 As an exponential function

Suppose

g

i

(t) = (g

i

(0))e

−υ

i

t

or (C.8)

dg

i

dt

= −υ

i

g

i

where the degradation rate υ

i

is positive. We deﬁne g

i

(t) < 0 as g

i

(t) = 0.

Consider the system used in the previous subsection (C.3.1). The time series in Figure

(C.5) has the same behavior as Figure (C.3). Figure (C.5) shows the numerical simulation

to the system

d[X

1

]

dt

=

3[X

1

]

5

1 + [X

1

]

5

+ [X

2

]

5

−[X

1

] +g

1

d[X

2

]

dt

=

3[X

2

]

5

1 + [X

1

]

5

+ [X

2

]

5

−[X

2

] (C.9)

dg

1

dt

= −g

1

Limit g

1

≥ 0

where the initial values are [X

1

]

0

= 0.5, [X

2

]

0

= 1 and g

i

(0) = 5.

Figure C.5: [X

1

]

∗

escaped the zero state because of the introduction of g

1

which is a

decaying exponential function.

Appendix C. More on Bifurcation of Parameters: Illustrations 138

C.4 The eﬀect of γ

ij

The parameter γ

ij

can also aﬀect the equilibrium points. Consider the system

d[X

1

]

dt

=

[X

1

]

2

1 + [X

1

]

2

+γ[X

2

]

2

+γ[X

3

]

2

−

1

21

[X

1

]

d[X

2

]

dt

=

[X

2

]

2

1 +γ[X

1

]

2

+ [X

2

]

2

+γ[X

3

]

2

−

1

21

[X

2

] (C.10)

d[X

3

]

dt

=

[X

3

]

2

1 +γ[X

1

]

2

+γ[X

2

]

2

+ [X

3

]

2

−

1

21

[X

3

].

Figure (C.6) shows a case where varying the value of γ aﬀects the value of the equilibrium

points. Varying γ may induce cell diﬀerentiation (also refer to [113]).

Figure C.6: Parameter plot of γ, an example.

C.5 Bifurcation diagrams

The following are some of the bifurcation types that we have found during our simulation.

We use the software Oscill8 [40] to draw the bifurcation diagrams. Note that the following

bifurcation diagrams are dependent on the given parameter values and initial values.

Appendix C. More on Bifurcation of Parameters: Illustrations 139

For one-parameter bifurcation diagram, the horizontal axis represents the parameter

and the vertical axis represents [X

i

]. Thick lines denote stable equilibrium points and

thin lines denote unstable equilibrium points.

For two-parameter bifurcation diagram, the horizontal axis represents the ﬁrst pa-

rameter and the vertical axis represents the second parameter. The lines in the diagram

indicate the presence of bifurcation.

C.5.1 Illustration 1

Suppose n = 1. Bifurcation may arise due to the sigmoidal shape of the Hill curve (see

Figures (C.7) for illustration). The system initially has a sole equilibrium point which

is stable, then varying a parameter may result to a change in the number of equilibrium

points, e.g. there will be three equilibrium points where one is unstable and the other

two are stable. The bifurcation happens when there are two equilibrium points where

one is stable and the other is unstable.

Figure C.7: Intersections of Y = ρ

i

[X

i

] and Y = H

i

([X

i

]) + g

i

where c > 1 and g = 0;

and an event of bifurcation.

Figures (C.8) to (C.10) illustrate the occurrence of saddle node bifurcations given the

Appendix C. More on Bifurcation of Parameters: Illustrations 140

equation

d[X1]

dt

=

β

1

[X

1

]

c

K

1

+ [X

1

]

c

−ρ

1

[X

1

] +g

1

(C.11)

with initial condition [X

1

]

0

= 5 as well as parameter values c = 2, β

1

= 3, K

1

= 1, ρ

1

= 1

and g

1

= 0. Moreover, ﬁgures (C.11) to (C.14) illustrate that cusp bifurcations may also

arise.

Figure C.8: Saddle node bifurcation; β

1

is varied.

Appendix C. More on Bifurcation of Parameters: Illustrations 141

Figure C.9: Saddle node bifurcation; K

1

is varied.

Figure C.10: Saddle node bifurcation; ρ

1

is varied.

Appendix C. More on Bifurcation of Parameters: Illustrations 142

Figure C.11: Cusp bifurcation; β

1

and g

1

are varied.

Figure C.12: Cusp bifurcation; K

1

and c are varied.

Appendix C. More on Bifurcation of Parameters: Illustrations 143

Figure C.13: Cusp bifurcation; K

1

and g

1

are varied.

Figure C.14: Cusp bifurcation; ρ

1

and g

1

are varied.

Appendix C. More on Bifurcation of Parameters: Illustrations 144

C.5.2 Illustration 2

Suppose we have the system

d[X1]

dt

=

β

1

[X

1

]

c

K

1

+ [X

1

]

c

+γ

12

[X

2

]

c

−ρ

1

[X

1

] +g

1

(C.12)

d[X2]

dt

=

β

2

[X

2

]

c

K

2

+ [X

2

]

c

+γ

21

[X

1

]

c

−ρ

2

[X

2

] +g

2

with initial conditions [X

1

]

0

= 5 and [X

2

]

0

= 5 as well as parameter values c = 2, β

1

= 3,

β

2

= 3, γ

12

= 1, γ

21

= 1, K

1

= 1, K

2

= 1, ρ

1

= 1, ρ

2

= 1, g

1

= 1 and g

2

= 0.

A saddle node bifurcation arises when we vary the parameter ρ

2

— the bifurcation

diagram is shown in Figure (C.15). Also, a saddle node bifurcation arises when we vary

the parameter g

2

— the bifurcation diagram is shown in Figure (C.16).

Figure C.15: Saddle node bifurcation; ρ

2

is varied.

Appendix C. More on Bifurcation of Parameters: Illustrations 145

Figure C.16: Saddle node bifurcation; g

2

is varied.

C.5.3 Illustration 3

Suppose we have the system

d[X

1

]

dt

=

β

1

[X

1

]

c

K

1

+ [X

1

]

c

+γ[X

2

]

c

+γ[X

3

]

c

+γ[X

4

]

c

−ρ

1

[X

1

] +g

1

d[X

2

]

dt

=

β

2

[X

2

]

c

K

2

+ [X

2

]

c

+γ[X

1

]

c

+γ[X

3

]

c

+γ[X

4

]

c

−ρ

2

[X

2

] +g

2

(C.13)

d[X

3

]

dt

=

β

3

[X

3

]

c

K

3

+ [X

3

]

c

+γ[X

1

]

c

+γ[X

2

]

c

+γ[X

4

]

c

−ρ

3

[X

3

] +g

3

d[X

4

]

dt

=

β

4

[X

4

]

c

K

4

+ [X

4

]

c

+γ[X

1

]

c

+γ[X

2

]

c

+γ[X

3

]

c

−ρ

4

[X

4

] +g

4

with initial condition X

0

= (5, 5, 5, 5) as well as parameter values c = 2, β

i

= 3 (i =

1, 2, 3, 4), γ = 1, K

i

= 1 (i = 1, 2, 3, 4), ρ

i

= 1 (i = 1, 2, 3, 4), g

1

= 1, g

2

= 0, g

3

= 0 and

g

4

= 0.

Figures (C.17) and (C.18) illustrate the possible occurrence of saddle node bifurcation.

Appendix C. More on Bifurcation of Parameters: Illustrations 146

Figure C.17: Saddle node bifurcation; ρ

2

is varied.

Figure C.18: Saddle node bifurcation; g

2

is varied.

Appendix D

Scilab Program for Euler-Maruyama

Algorithm 5 Euler-Maruyama with Euler method (1st Part)

//input parameters

n=input("Input n=")

for i=1:n

disp(i, "FOR EQUATION")

coeffbeta(i)=input("beta=")

K(i)=input("K=")

rho(i)=input("rho=")

g(i)=input("g=")

disp(i, "exponent of x")

c(i)=input("ci=")

for m=1:n

if m~=i then

disp(m, "coefficient of x")

gam(i,m)=input("gamma=")

disp(m, "exponent of x")

z(i,m)=input("cij=")

else

gam(i,m)=1

end

end

sig(i)=input("sigma=")

end

for i=1:n

disp(i, "initial value for x")

y(i,1)=input("=")

x(i,1)=y(i,1)

end

147

Appendix D. Scilab Program for Euler-Maruyama 148

Algorithm 6 Euler-Maruyama with Euler method (2nd Part)

//Euler-Maruyama process

tend=input("end time of simulation t_end=")

hstep=input("step size=")

j=1

while (j<tend/hstep+1) then

for i=1:n

summ(i)=0

summx(i)=0

for k=1:n

if k~=i then

summ(i)=summ(i)+gam(i,k)*y(k,j)^z(i,k)

summx(i)=summx(i)+gam(i,k)*x(k,j)^z(i,k)

end

end

G=sqrt(y(i,j)) //You can change G

rand(’normal’)

y(i,j+1)=y(i,j)+((coeffbeta(i)*y(i,j)^c(i))/(K(i)+y(i,j)^c(i)+..

summ(i))+g(i)-rho(i)*y(i,j))*hstep+sig(i)*(G)*..

((sqrt(hstep))*rand())

x(i,j+1)=x(i,j)+((coeffbeta(i)*x(i,j)^c(i))/(K(i)+x(i,j)^c(i)+..

summx(i))+g(i)-rho(i)*x(i,j))*hstep

if y(i,j+1)<0 then

y(i,j+1)=0

end

t(1)=0

t(j+1)=t(j)+hstep

end

j=j+1

end

plot(t,y)

plot(t,x,".")

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