Solution Manual for Chapter 7

7.1 a .
The ODE is stable if 0. The Jacobian must be negative to guarantee against a run-
away solution.
RT = 5 × 105 sites/cell, kf = 7 × 105 M−1min−1, kr = 0.6 min−1
7 10 0.6 0
or
8.57 10 .
Since cannot be negative, it is stable for all positive values of .

7.1 b. The implicit modified Euler method is used to solve the first-order ODE.

The equilibrium concentration of the receptor-ligand complex is

2.69 10

Time taken to reach 99% equilibrium concentration is 3.6 minutes.

7.2 ;
The set of first-order coupled ODEs is

·
The Jacobian is
0 1

The eigenvalues are obtained by solving the equation | | 0

or,
1
0
This gives 0
Solving for ,
√ 4
2
0; 0, so one eigenvalue will be greater than 0 and one will be less than 0. Thus, the
ODE is unstable.

7.3 ; ; .
 1 1
0
1 1
0
1 1
0

The eigenvalues are obtained using the command eig(J).

-0.3333
-0.5716
-0.0215
All three eigenvalues are negative. The solution is stable and not stiff since the eigenvalues are
small. ode45 is used to solve the system of equations.

Initial conditions: 0 100; 0 0; 0 0.

10 years:
CFC loading in troposphere: 75.1 kg
Cl2 loading in stratosphere: 5.0 kg

100 years:
CFC loading in troposphere: 10.8 kg
Cl2 loading in stratosphere: 0.8 kg

7.4 The discretization of an integration scheme can lead to certain variables becoming negative
when this is physically not possible. Within the function program, a control statement must be
added to force S = 0 if S < 0.
Steady state appears to be reached by 3 days. The final total bacterial mass is greater than the
initial total bacterial mass. The concentration of methanol and dissolved oxygen comes back
down to the original values. Initially when the step change in methanol concentration in medium
is introduced, the growth of Pseudomonas bacteria is inhibited strongly and no consumption of
O2 occurs for some time. The hyphomicrobium mass increases due to the abundant food supply.
Soon after, the food supply is depleted, and Psuedomonas growth is no longer inhibited, but the
concentration of hyphomicrobium starts to fall.
function f = popdynamics2(t,y)

% Evaluate f(t, y) for hydrocarbon consuming bacterial population dynamics

% problem.

% Constants

mux1max = 0.185; %1/hr

mux2max = 0.185; %1/hr

Kx1 = 1e-5; % g/L

Kx2 = 5e-6; % g/L

Ki = 1e-4; %g/L

Yx1O2 = 0.2; %g bacteria produced/g O2 consumed

Yx1S = 5.0; % g pseudomonas bacteria produced/g methanol produced

Yx2S = 0.3; % g hyphomicrobium bacteria produced/g methanol consumed

kla = 42.0; % 1/hr

cO2s = 0.008; %g/L

FbyV = 0.08; % 1/hr

 if y(2) < 0

y(2) = 0;

end

% Reaction rates

rx1 = mux1max*y(1)/(Kx1 + y(1))*y(3)/(1 + y(2)/Ki);

rx2 = mux2max*y(2)*y(4)/(Kx2 + y(2));

7.5

1. After 1 second: 18 bound ligand molecules/cell; after 5 seconds: 51 bound ligand molecules
per cell.

2. 4.7 seconds for equilibrium to establish; 62 ligand molecules bind a cell at equilibrium

4 a. After 1 second: 26 bound ligand molecules/cell; after 5 seconds: 124 bound ligand molecules
per cell.

4 b. 337.5 seconds for equilibrium to establish; 1324 ligand molecules bind a cell at equilibrium.

MATLAB Program for solving part 1.

function [R L Ci] = ESHkinetics1(dt, tf)

%ESHkineticsproj1.m uses the Runge-Kutta fourth order method to solve a set of

%coupled first order differential equations and an algebraic equation that

%models the kinetic behavior of the binding of a multivalent ligand in

%solution to the monovalent receptors present on cells in solution. Kinetic

%terms involve the 3-D forward rate constant, the reverse rate constant and

%the 2-D forward crosslinking rate constant. It is assumed that the 2-D reverse

%crosslinking rate constant is equal to the 3-D reverse rate constant.

%Input variables

%dt: increment value for the independent variable time t

%tf: end value of the independent variable time t

%Output variables
 %R: number of unbound receptors/cell at time tf

%L: number of free ligand molecules/cell at time tf

%C: number of ligand molecules bound/cell at time tf, where the

%subscript number indicates the extent of ligation with the surface.

%Constants

v = 18; %total number of binding sites present on the ligand surface

f = 9; % total number of binding sites available for binding to a cell

kf = 3.23e-8; %3-D forward rate constant (#/cell)^-1.s^-1)

kr = 5.47; %Reverse rate constant (s^-1)

k_x = kr; %2-D crosslinking backward rate constant (s^-1)

kx = 0.0003172; %2-D crosslinking forward rate constant ((#/cell)^-1.s^-1)

%given by KX*kr

C0(1) = 4380; %Initial solution concentration of ligand (#/cell)

RT = 10700; %Receptors on a cell surface (#/cell)

%Initial Conditions

t0 = 0; %Starting time (s)

C0(2:f+1) = 0.0; %Starting concentrations of bound ligand on surface (#/cell)

ligation = [0:f]'; % Column vector of the number of ligations by which the ligand can bind a cell

s1 = zeros(f+1,1); s2 = s1; s3 = s1; s4 = s1; %preallocating for improving computation speed

R = RT; %Initially, no receptors are bound to ligand in solution

timesteps = ceil((tf - t0)/dt); %Number of time steps for integration

for repeat = 1:timesteps

s1 = ESHrhsdiffeqns(v,f,kf,kr,kx,k_x,R,C0);

R = RT - (C0+s1*dt/2)*ligation;

s2 = ESHrhsdiffeqns(v,f,kf,kr,kx,k_x,R,C0+s1*dt/2);

R = RT - (C0+s2*dt/2)*ligation;

s3 = ESHrhsdiffeqns(v,f,kf,kr,kx,k_x,R,C0+s2*dt/2);

R = RT - (C0+s3*dt)*ligation;

s4 = ESHrhsdiffeqns(v,f,kf,kr,kx,k_x,R,C0+s3*dt);

C = C0 + dt*((s1+s4)/6 + (s2+s3)/3);

R = RT - C*ligation; %latter term is dot product to determine total receptors bound

C0 = C;

end
Ci = C(2:f+1);

L = C(1);

MATLAB program to solve parts 2 and 4

function [R L Ci Eqtime] = ESHkinetics2(dt)

%ESHkineticsproj2.m uses the Runge-Kutta fourth order method to solve a set of

%coupled first order differential equations and an algebraic equation that

%models the kinetic behavior of the binding of a multivalent ligand in

%solution to the monovalent receptors present on cells in solution. Kinetic

%terms involve the 3-D forward rate constant, the reverse rate constant and

%the 2-D forward crosslinking rate constant. It is assumed that the 2-D reverse

%crosslinking rate constant is equal to the 3-D reverse rate constant.

%Input variables

%dt: increment value for the independent variable time t

%Output variables

%R: number of unbound receptors/cell at time tf

%L: number of free ligand molecules in M at time tf

%C: number of ligand molecules bound/cell at time tf, where the

%subscript number indicates the extent of ligation with the surface.

%Eqtime: time taken for the system to achieve equilibrium conditions

%Constants

v = 18; %total number of binding sites present on the ligand surface

f = 9; % total number of binding sites available for binding to a cell

kf = 3.23e-8; %3-D forward rate constant (#/cell)^-1.s^-1)

kr = 5.47; %Reverse rate constant (s^-1)

k_x = kr; %2-D crosslinking backward rate constant (s^-1)

kx = 0.0003172; %2-D crosslinking forward rate constant ((#/cell)^-1.s^-1)

%given by KX*kr

C0(1) = 4380; %Initial solution concentration of ligand (#/cell)

RT = 10700; %Receptors on a cell surface (#/cell)

%Initial Conditions

t0 = 0; %Starting time (s)

C0(2:f+1) = 0.0; %Starting concentrations of bound ligand on surface (#/cell)

ligation = [0:f]'; % Column vector of the number of ligations by which the ligand can bind a cell

s1 = zeros(f+1,1); s2 = s1; s3 = s1; s4 = s1; %preallocating for improving computation speed

R = RT; %Initially, no receptors are bound to ligand in solution

Rold = 1; time = 0;

while (abs((R-Rold))>0.01*dt) %condition for equilibrium conditions

Rold = R;

s1 = ESHrhsdiffeqns(v,f,kf,kr,kx,k_x,R,C0);

R = RT - (C0+s1*dt/2)*ligation;

s2 = ESHrhsdiffeqns(v,f,kf,kr,kx,k_x,R,C0+s1*dt/2);

R = RT - (C0+s2*dt/2)*ligation;

s3 = ESHrhsdiffeqns(v,f,kf,kr,kx,k_x,R,C0+s2*dt/2);

R = RT - (C0+s3*dt)*ligation;

s4 = ESHrhsdiffeqns(v,f,kf,kr,kx,k_x,R,C0+s3*dt);

C = C0 + dt*((s1+s4)/6 + (s2+s3)/3);

R = RT - C*ligation; %latter term is dot product to determine total receptors bound

C0 = C;

time = time + dt;

end

Ci = C(2:f+1);

L = C0(1);

Eqtime = time;

7.6 The terminal Stokes velocity is 13.44 cm/s. The time taken to attain 99% terminal Stokes
velocity is 63.4 ms. Euler backward method can be used or any ODE solver that handles stiff
equations can be used.