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# PES 3950/PHYS 6950: Homework Assignment 3

## Handed out: Friday February 13

Due in: Friday February 20, at the start of class at 3:05 pm sharp
Show all working and reasoning to receive full points.

## Question 1 [10 points]

In this problem you are asked to calculate the effect of position uncertainty in the mean
squared displacement computed from trajectory positions.

Let ri be some observed jump and (xi , yi ) represent the actual points on a trajectory and
∆xi and ∆yi are the errors in the observed position. Assume that the probability P (∆xi ) of
a given ∆xi and P (∆yi ) of a given ∆yi follow a Gaussian probability distribution:
1 ∆x2
i 1 ∆yi2
P (∆xi ) = √ e− 2σ2 and P (∆yi ) = √ e− 2σ2 .
2πσ 2πσ
Here σ is the uncertainty in the position, i.e. σ 2 is the variance of the Gaussian distribution.

## a) Show that the variance in position ∆xi is σ 2 , i.e. show that

Z ∞
2
(∆xi − h∆xi i)2 P (∆xi )d∆xi = σ 2 .

(∆xi − h∆xi i) =
−∞

## Similarly we have (∆yi − h∆yi i)2 = σ 2 .

b) The uncertainty in position must be included when we calculate the mean squared dis-
placement of the ith jump
ri = [(xi + ∆xi ) − (xi−1 + ∆xi−1 )]2 + [(yi + ∆yi ) − (yi−1 + ∆yi−1 )]2

2

## Show that this expression reduces to

ri = (xi − xi−1 )2 + (yi − yi−1 )2 + 4σ 2 .

2

At one point you need to set terms like h∆xi ∆xi−1 i = 0, since errors in position measurement
are not correlated on the trajectory.

Therefore, if we include position uncertainty, we obtain for the mean squared displacement
hr2 i = 4D∆t + 4σ 2 .

## Question 2 [10 points]

The Navier-Stokes equation may be written for fluid flow in a gravitational field ~g = g ĵ
as
∂~v 5P η
+ (~v · 5) ~v = − + 52 ~v − ~g .
∂t ρ ρ
For an airplane and steady air flow, simplify the Navier-Stokes equation and solve it by
integrating both sides over d~y = dy ĵ. The final expression should look familiar to you.
Question 3 [10 points]
Bacteria use swimming to seek out food. Imagine that the bacterium is in a region of low
food concentration. For the bacterium to profit from swimming to a region with more food,
it has to reach there before diffusion of food molecules makes the concentrations in the two
regions the same. In this problem you are asked to find the smallest distance that a bac-
terium needs to swim so it can outrun diffusion. Assume that a bacterium such as E. coli
is swimming at a speed of 50 µm/s. The diffusion constant of a typical food molecule is
roughly 500 µm2 /s.

a) For one dimension, make a plot in which you sketch the distance traveled by a bac-
terium swimming at a constant velocity v as a function of time t, and the distance over
which a food molecule will diffuse in that same time. Indicate on the plot the smallest time
and the smallest distance that the bacterium needs to swim to outrun diffusion.

b) Calculate this minimum time and distance. Check that your answer agrees with your
plot from part a).

c) Estimate the number of ATP molecules the bacterium must consume (hydrolyze) per
second in order to travel at this speed, assuming that all of the energy usage goes into over-
coming fluid drag. The amount of energy released from one ATP molecule is approximately
20 kB T . Note that the bacterial flagella motor is actually powered by a proton gradient and
this estimate focuses on the ATP equivalents associated with overcoming fluid drag. Use
1kB T = 4.1 × 10−21 J.

## Question 4 [20 points] GRADUATE STUDENTS ONLY

In this problem, you will examine the hydrostatic pressure in a fluid at rest.

a) Consider a small fluid element ∆x × ∆y × ∆z at rest. Write down the balance of forces on
the fluid element due to the fluid pressure P and the gravitational pull of the Earth. Show
that this leads to the differential equation
5P = ρ~g ,
where ~g is the acceleration due to gravity and ρ the fluid density. The differential equation
describing fluid at rest can be derived by drawing the forces on a volume element of fluid
and then using reasoning similar to that in book sec. 12.2.3 (Physical Biology of the Cell) or
lecture 10 notes. Note that hydrostatic equilibrium requires that the forces along each axis
sum to zero.

b) Solve the differential equation derived in part a) assuming a uniform fluid density. Show
that the pressure in the fluid is given by
P (z) = P0 − ρgz,
where the z-axis is in the direction opposite to ~g and P0 is the pressure at z = 0.
c) When you raise your arm above your head as the doctor is measuring your blood pressure,
you would expect that the measurement changes compared with when you keep your arm
level with the heart. By how much will the the measurement change compared with when
you keep your arm level with the heart? Derive an expression based on the density of blood
pressure. Blood pressure (BP) is measured in millimeters mercury (mmHg). Use 133.3 Pa
= 1 mmHg.

d) Now, imagine you went to a clinic and put your prediction from part c) to an infor-
mal test with the help of a nurse. The collected data is given in the table below.

Two kinds of pressure were recorded: systolic (sys), when the heart is contracting, and di-
astolic (dias), when the heart is relaxing.

Using this data, plot the change in mean arterial pressure (MAP),
1
M AP = Pdias + (Psys − Pdias )
3
as a function of arm elevation. Fit the data average obtained from the left and right arm
and compare it to your derived expression.

How well does the data agree with you estimate? If the agreement is not good, can you
give a possible reason for the discrepancy between your prediction and measurement?
Question 3

Part a)
distance covered by bacterium: xS = v t
distance covered by food: xD = sqrt(2Dt)

Matlab code:
close all
clear all
clc

t = linspace(0,1,100); %time in s
v = 50; % in um/s
D = 500; % in um^2/s

x_S = v*t; %
x_D = sqrt(2*D*t); % in um

figure(1)
plot(t,x_S,'k','LineWidth',2)
hold on
plot(t,x_D,'r','LineWidth',2)
hold off
ylabel('distance (\mum)','FontSize',16)
xlabel('time (sec)','FontSize',16)
legend('bacterium swimming', 'food diffusing')

50
bacterium swimming
food diffusing
40
distance (µm)

30 at larger distances
than 20 µm
bacterium will
outrun diffusion
20

at longer times
10 than 0.4s
bacterium will
outrun diffusion

0
0 0.2 0.4 0.6 0.8 1
time (sec)
Question 4

d)

Calculated MAP using equation given from average computed from left and right
arm:

## %%%%%%%%% DATA FROM HOSPITAL %%%%%%%%%%%%%%%%%

sys_r = [118,108,88]; % right arm systolic BP in mmHg
dia_r = [62,52,38]; % right arm diastolic BP in mmHg
sys_l = [102,80,62]; % left arm systolic BP in mmHg
dia_l = [68,54,40]; % left arm diastolic BP in mmHg
sys_av = (sys_r+sys_l)/2; %average systolic BP in mmHg
dia_av = (dia_r+dia_l)/2; %average diastolic BP in mmHg
MAP = dia_av+1/3*(sys_av-dia_av); % mean arterial pressure

## %%%%%%%%% PREDICTION FROM PART C %%%%%%%%%%%%%%%%%%%

dP = -0.75*h;

85
hospital data
80 linear fit

75
MAP (mmHg)

yfit = - 1.9*x + 80
70

65

60

55

50

45
0 5 10 15
arm elevation (cm)

## From the prediction, we obtained:

∆P/h = - 0.75 mmHg/cm,
where h can is the arm elevation and ∆P corresponds to the mean arterial pressure
(MAP). Hence, after calculating the mean MAP from the data provided, we can fit the
data and compare the slope of the fit to - 0.75 mmHg/cm.

The fit gives as a slope of -1.9 mmHg/cm. Hence, the observed drop in pressure when
raising an arm is 2.5 times larger! One possible reason for the discrepancy between
prediction and measurement is that raising one's arm changes the resistance in blood
vessels, especially in the shoulder.