All questions may be attempted but only marks obtained on the best four solutions will

count.
The use of an electronic calculator is not permitted in this examination.

1. (a) Consider oxygen transport with uniform diffusion constant D = 1/2 and uni-
form absorption rate µ = ν 2 /2 within a thin pipe of constant uniform cross-
section and length L with open ends:

∂C(s, t) 1 ∂ 2 C(s, t) ν 2
= − C(s, t),
∂t 2 ∂s2 2
where s is the distance along the tube, and C(s, t) is the concentration of
oxygen at distance s and time t. The concentrations at the ends are fixed at
C(0, t) = x and C(L, t) = y. Show that, at steady state, the diffusive flux of
oxygen into the end s = 0 is given by
ν ν
f+ = coth(νL)x − cosech(νL)y,
2 2
and find a similar expression for the steady state flux f − into the end s = L.
(b) Twelve pipes of length d with identical cross-sectional areas are connected as
shown below. The oxygen concentration at the open centre of the square is φ.
The diffusion coefficient and absorption rate are the same in all pipes and equal
to D = 1/2 and µ = ν 2 /2 respectively. Using the symmetry of the network
and the expressions found in part (a) and assuming conservation of mass, find
the concentration X of oxygen at the point shown in the figure. There is no
advection.

MATH3307 PLEASE TURN OVER

1
 2. (a) Consider a system of three genes which express proteins A, B, and C (see
the figure). A inhibits B by means of trimer A3 . B activates C by means of
tetramer B4 , and C activates B and inhibits itself by means of dimer C2 . As-
suming gene regulation according to the Hill equations, derive the differential
equations for the concentrations of A, B, and C.

In your derivation assume that:

(i) The expression of A gene occurs with basal rate b.
(ii) The DNA molecule of gene B can be in 4 possible states:
• unbound: OBU ,
• bound with C2 : OBC ,
• bound with A3 : OBA ,
• or bound with A3 and C2 : OBAC .
The expression of gene B occurs with the rate αBU OBU + αBC OBC +
αBA OBA + αBAC OBAC , but can occur only when gene B is bound with
activator C2 , and is not bound with the repressor A3 .
(iii) The DNA molecule of gene C can be in 4 possible states:
• unbound: OCU ,
• bound with C2 : OCC ,
• bound with B4 : OCB ,
• or bound with C2 and B4 : OCCB .
The expression of gene C occurs with the rate αCU OCU + αCB OCB +
αCC OCC + αCCB OCCB , but can occur only when gene C is bound with
its activator B4 .
(iv) The total number of DNA molecules is fixed, i.e., OBU + OBC + OBA +
OBAC = N , and OCU + OCB + OCC + OCCB = N .
(v) All rates for the production of A3 , B4 , and C2 are equal to kd = 1, and they
degrade with the rate k−d = 1. All rates for binding of DNA molecules
with the transcriptional factors are kb = 1 and for unbinding k−b = 1.
(vi) Proteins A, B, and C degrade with rate γ.

MATH3307 CONTINUED

2
 (b) Consider the dynamics of a genetic auto repressor with delay, described by the
following equation:
α
ẋ = − x,
1 + xn (t − τ )
where x is the protein concentration, α > 0 is a constant, t is time, n is
the Hill coefficient (an integer), and τ is the time delay. Find the necessary
condition for genetic oscillations, in terms of n, α, and x0 , where x0 is the
unique equilibrium state of the system.

3. (a) Explain briefly three main manifestations of viscoelasticity. Illustrate your

explanations with plots either for applied force and deformation or with stress-
strain plots as you find appropriate.
(b) Consider the Kelvin model of viscoelasticity shown in the figure:

C K1

F F
X 1T X 2T
K2

X T =XE + X

Find the equation describing the relation between the applied force F (t) and
the response deformation x(t). Here c is the constant of the dashpot, k1 and
k2 are constants of two springs, xT , xT1 , xT2 are the total length of the corre-
sponding parts, xE , xE E
1 , x2 are the length of these parts in equilibrium without
force, and x, x1 , x2 are the deformations of these units (see figure). Use the
notation
x 1 1
τ = , τσ = c( + ).
k1 k1 k2
(c) Suppose that bone described by the Kelvin model is deformed by a force F (t)
defined as
F (t) = F0 (Θ(t) − Θ(t − τ ) + Θ(t − 2τ )) ,
where Θ(t) is the Heaviside step function. Find the analytical expression for
the response deformation x(t) and sketch it. The final expression should be
written using Heaviside functions.

MATH3307 PLEASE TURN OVER

3
 4. (a) Suppose that the temporal activity of the space-clamped nerve axon is mod-
elled with the two–variable FitzHugh-Nagumo model with an external applied
current Ia :
dv dw
= f (v) − w + Ia , = bv − w,
dt dt
where the function f (v) is the piecewise linear function:

 −v, for v ≤ 1
1
f (v) = v − 23 , for 1 ≤ v ≤ 5
 2
6 − v, for v ≥ 5

and Ia is a positive constant.

(i) Find the range of values of the parameters b and Ia for which the model
exhibits periodic behaviour.
(ii) Assume now that b = 1, and Ia = 0, 3.5, or 7. Using the phase plane, show
the equilibrium points and analyse their stability, noting which points are
stable, asymptotically stable or unstable. For each of these three values of
Ia sketch the trajectory in the phase plane (v, w) for the initial conditions
v = 4, w = −2.
(iii) Assume that b = 12 and Ia = 1.5. Using the phase plane show the equi-
librium points and analyse their stability, noting which points are stable,
asymptotically stable or unstable. Sketch a typical trajectory in the phase
plane.
(b) Consider a different model described by the equations:

dv v3 dw
=v− − w, = v + b,
dt 3 dt
where b is a constant. Find the values of b, for which the only attractor is
(i) a stable fixed point;
(ii) a limit cycle.

MATH3307 CONTINUED

4
 5. (a) For one-dimensional fluid flow, derive the equation of continuity. How will it
change if the fluid is incompressible?
(b) If blood is allowed to stand in a container, the red cells will settle out of sus-
pension at a definite rate (velocity), called ESR (the erythrocyte sedimentation
rate). Assuming that the red cells are approximately spherical, use the Stoke’s
law to find ESR and explain why, in illness, ESR always increases dramatically.
(c) Consider the motion of blood (viscous fluid) through a long cylindrical tube of
length L = 0.2m, radius a = 0.5cm and with pressures at the tube’s ends p1
and p2 , p1 > p2 , p1 = p2 = 4.5P a. Assume that blood is incompressible, and
its density ρ = 1060kg/m3 is a constant. Assume also a steady flow. Blood
is allowed to discharge into a weighing tank, and a total of 0.5kg of blood is
collected for a duration of 3min. Derive the expression for a volume flux Q,
and find the viscosity coefficient µ of the blood. You may find the expression
for the Laplace operator in polar coordinates (r, θ) useful:

1 ∂ 2u
 
1 ∂ ∂u
∆u = r + 2 2.
r ∂r ∂r r ∂θ

(d) Derive the Bernoulli equation for incompressible fluids. Using the Bernoulli
equation explain the stability of the Bernoulli ball, for example, a light ball
levitating in the upward flow.

MATH3307 END OF PAPER