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Mathematical Biology
Features
• Uses complex systems, complex networks, and dynamics to derive models
and computer simulations of various biological systems
• Presents a wide range of models, from ECG signal processing to pandemic
modelling to population dynamics
• Requires no advanced knowledge of mathematics
• Includes exercises as well as computational and research projects at the
end of each chapter
K12463
Series Editors
N. F. Britton
Department of Mathematical Sciences
University of Bath
Xihong Lin
Department of Biostatistics
Harvard University
Hershel M. Safer
Mona Singh
Department of Computer Science
Princeton University
Anna Tramontano
Department of Biochemical Sciences
University of Rome La Sapienza
Proposals for the series should be submitted to one of the series editors above or directly to:
CRC Press, Taylor & Francis Group
4th, Floor, Albert House
1-4 Singer Street
London EC2A 4BQ
UK
Michael Small
CRC Press
Taylor & Francis Group
6000 Broken Sound Parkway NW, Suite 300
Boca Raton, FL 33487-2742
This book contains information obtained from authentic and highly regarded sources. Reasonable efforts
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Preface xiii
ix
x
11 Conclusion 251
11.1 Models Are a Reflection of Reality . . . . . . . . . . . . . . . 251
Bibliography 255
Index 259
Preface
Biological systems exhibit rich dynamic behaviour over a vast range of time
and space scales: from the spontaneous rapid firing of cortical neurons to
the spatial diffusion of disease epidemics and evolutionary speciation. This
text unifies many of these diverse phenomena and provides the computational
and mathematical platform to understand the underlying processes. Through
an extensive tour of various biological systems, we introduce computational
methods for simulating spatial diffusion processes in excitable media (such as
the human heart), and mathematical tools for dealing with systems of nonlin-
ear ordinary and partial differential equations (necessary to describe neuronal
activation and disease diffusion). We show that even relatively simple math-
ematical descriptions are capable of capturing a wide range of observed bio-
logical behaviour and offering insight into the dynamic system hidden within.
We present mathematical models and computer simulations that can provide
insight into cardiac pacemakers and artificial electrical defibrillation, and can
suggest appropriate control strategies to mediate the effects of past and future
pandemics.
The key concept of this text is the idea of the model: a computational
or mathematical abstraction of a more concrete description. At various lay-
ers, the models we use to describe specific biological systems become more
abstract and hence more manageable. At the same time, the scope of the
model becomes broader. The same basic mathematical description can de-
scribe very different biological phenomena. There is a natural convergence
between models of hormone secretion, respiratory carbon dioxide uptake and
ecological population fluctuations. Starting from each separate biological sys-
tem, we can obtain models that at various levels of abstraction are equivalent.
Consequently, when the models exhibit gradual loss of stability and onset of
chaotic dynamics through a sequence of period doublings, we can begin to
understand the origin of the same characteristic pattern in each of the diverse
biological systems.
Via a range of models, we observe a host of different bifurcations and dy-
namic structures in a wide range of both temporal and spatial systems. Con-
sideration is also given to emerging research areas in complex biological sys-
tems: pattern formation and flocking behaviour, interaction of autonomous
agents, hierarchical and structured network topologies in a range of systems
(from neuronal aggregations in the nematode worm to synchronous behaviour
in herd animals and disease transmission dynamics). Tools from complex sys-
tems and complex networks are introduced and demonstrated to be useful for
xiii
xiv Preface
Acknowledgements
During the writing of this book I was provided with financial support from
the Hong Kong Polytechnic University (Internal grant G-YG35 and G-U867)
and funding from the General Research Fund of the Hong Kong University
Grants Council (PolyU 5279/08E and PolyU 5300/09E).
MATLAB® is a registered trademark of The MathWorks, Inc. For product
information, please contact:
The MathWorks, Inc.
3 Apple Hill Drive
Natick, MA 01760-2098 USA
Tel: 508-647-7000
Fax: 508-647-7001
E-mail: [email protected]
Web: www.mathworks.com
Finally, the cover illustration is the work of Henry Small (aged 7).
Preface xv
Feedback
Although the best way to really understand how these techniques work is
to create your own implementation of the necessary computer code, this is
not always possible. Therefore, I have made MATLAB® implementations of
many of the key algorithms and the various case studies, available from my
website (http://small.eie.polyu.edu.hk/). You are most welcome to send me
your comments and feedback ([email protected]).
Michael Small
Hong Kong
Chapter 1
Biological Systems and Dynamics
1
2 Dynamics of Biological Systems
4 6
10
6
4
5
t t
20 40 60 80 100 20 40 60 80 100
!2
!5
!4
!6
12 18
20
15
20
10
10
5
t t
20 40 60 80 100 20 40 60 80 100
!5
!10
!10
!20
!15
2
0 5 10 15 20 25 30 35 40 45 50
t
Figure 1.1: Dynamics of systems. The top four plots show the stable
dy
dynamic behaviour for the theoretical Rössler system ( dxdt = −y − z, dt =
x + 0.1y, and dz
dt = 0.1 + z(x − c)). The horizontal axis is time and in each
case the system changes continuously. For a parameter (c) value of 4, the
system is periodic. However, as we change the value of the parameter, the
behaviour of the system changes. For c = 6 the system is now bi-periodic and
for c = 12 the system becomes period three. Of course, for all intermediate
values of c the system behaviour changes gradually. But for any fixed value
of c, the system will oscillate — changing continuously. Finally, for c =
18, the system behaviour is bounded and not periodic — it exhibits what is
mathematically defined as chaos. The lower panel illustrates a real recording
of the electrocardiogram of a human and shows a second example of the
change in dynamics between (in this case, at least) three states: from a stable
(almost periodic) regular heartbeat on the left, to ventricular tachycardia in
the middle and ventricular fibrillation on the right. This trace illustrates
the progression of onset of a heart attack and in this case the patient (in a
coronary care unit) only recovered after medical intervention. Within each
window, past behaviour provides (some) guide to the future. But when the
system parameter changes, this is not possible because it is not possible to
predict how the system parameter changes.
Biological Systems and Dynamics 3
the precise values of the system (we will see later why such precise numeri-
cal predictions, quantitative predictions, cannot be made). However, as your
attention shifts from this text to the activities of last Friday night (what-
ever they were), delicate chemical signals in your brain change the balance
between different neurotransmitters (the family of chemicals responsible for
the transmission of information between different brain regions, and between
individual neurons) within different regions of the brain and this causes the
activity of these individual neurons to change. The parameters of the mathe-
matical description of each neuron needs to change, and hence the qualitative
behaviour changes.
This book is about both sorts of change: the way in which a biological
system in a stable equilibrium changes, and the way in which systems can
4 Dynamics of Biological Systems
Left Right
Atrium Atrium
Pulmonary circulation
Systemic circulation
Left Ventricle Right Ventricle
Arteries
at the centre. Both oxygenated blood from the lungs on its way to the body
and deoxygenated blood from the body returning to the lungs pass through
the heart. The deoxygenated blood passes through the right chambers of the
heart on the return trip to the lungs and the fresh oxygenated blood passes
through the left chambers. On each side there are two chambers: an atrium
and a ventricle. The left atrium receives the blood from the lungs and passes
it to the left ventricle and then onto the body. The right atrium receives
blood from the body and passes it to the right ventricle before returning to
the lungs. The circulatory system is divided into two sections, one side of the
figure eight, dealing with blood flow to and from the lungs is the pulmonary
circulatory system. The other side of the figure eight is connected to the body
and is known as the systemic circulatory system.
The heart acts as a pump and essentially drives the blood through the body.
Hence, the blood leaving the heart through blood vessels known as arteries
is at high pressure, while the blood returning to the heart through veins is
at low pressure. Within the heart itself, the atria are relatively small upper
chambers of the heart and connected via a valve to the much larger lower
chambers. It is these lower chambers, the ventricles (and in particular the
left ventricle) that do most of the work of the heart. In a healthy human at
rest, the left ventricle pumps about 72 beats/minute and about 70 mL/beat.
In doing so, the left ventricle generates about 1.7 W of mechanical power.
During vigorous exercise, the body’s demand for oxygen increases and the
heart rate can increase to over 160 beats/minute.
indexcirculatory system!heart
Figure 1.3 depicts a simple model of the human circulatory system with
the various nomenclature described previously. In Fig. 1.4 we simplify that
model to another model in which the circulatory system is represented as a
pipe in a figure-eight configuration with a pump at the central crossing point.
Now consider a section of that pipe. Or, consider a major artery leaving the
heart. How is the physical force exerted by the heart to pump blood related
to the physical flow realised in the pipe?
We start our description of this system with another model — represented
in Fig. 1.5. Here we focus on a single cylindrical section of pipe and we apply
the standard mathematical model of fluid flow to describe the movement of
blood in that pipe. The Navier–Stokes equation1 is a second-order partial
differential equation describing the spatial-temporal relationship between the
flow of a fluid u(x, y, z, t), pressure P , fluid density ρ and viscosity ν. Note
that the function u describes the instantaneous velocity as a function of time
and space, and this function satisfies the following differential equation,
∂u ∇P
+ u · ∇u = − + ν∇2 u. (1.1)
∂t ρ
Lungs
Heart
Body
Q R Z
C
Figure 1.5: An even more simplified model. Now we consider only one
part of the human circulatory system — the flow of blood in a cylindrical,
permeable and elastic walled pipe. The flow Q is driven by the forcing pressure
P , subject to an end load resistance Z. The pipe itself has some flow resistance
R and the elasticity of the pipe leads to deformation governed by a parameter
C. The meaning of the three parameters R, Z and C and the model variables
P and Q is explained in detail in the text. We see that these five quantities are
sufficient to explain the basic features of cardiovascular dynamics. Moreover,
this system can be represented both as a differential equation model in Eqn.
(1.4) and by an equivalent electronic circuit, Fig. 1.6.
∂uy ∂u ∂u
= ux ∂x + uy ∂yy + uz ∂zy ,
∂uz ∂uz ∂uz
ux ∂x + uy ∂y + uz ∂z
Language: English
BY
NEW YORK
DODD, MEAD & COMPANY
1924
Printed in U. S. A.
THE PRICELESS PEARL
CONTENTS
PAGE
CHAPTER I 1
CHAPTER TWO 53
CHAPTER THREE 94
CHAPTER FOUR 141
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