PHY332 Assignment #3 Tim Henley 1000234506

Problem 3

I decided it was simplest to do a basic linear regression in python:

from matplotlib.pyplot import plot,title,show

from numpy import arange,array,ones,sin
from scipy import stats

y = [76.,73.,70.,66.]
theta = [1.41,2,2.54,3]
x = [(sin(i*0.0005))*(sin(i*0.0005)) for i in theta]
slope, intercept, r_value, p_value, std_err = stats.linregress(x,y)
lamb = 0.154 #nm
RG = sqrt((-3.*(lamb**2)*slope)/(16.*(pi**4)))
SR = RG/(sqrt(3./5.))

print 'r value =', r_value

print 'p_value =', p_value
print 'standard deviation =', std_err
print 'slope =', slope
print 'intercept =', intercept
print 'Radius of Gyration =', RG,'nm'
print 'Spherical Radius =', SR,'nm'

y2=[intercept, 76.,73.,70.,66.]
theta2 = [0, 1.41,2,2.54,3]
x2 = [(sin(i*0.0005))*(sin(i*0.0005)) for i in theta2]
line = [slope*i+intercept for i in x2]

plot(x2,y2,'o')
plot(x2, line, 'r')
title('Guinier plot - Linear Fit for low-angle X-ray scattering data')
show()

The results returned were:

r value = -0.99885837479
p_value = 0.0011416252101
standard deviation = 190090.418851
slope = -5621165.25725
intercept = 78.7822518737
Radius of Gyration = 16.018977381 nm
Spherical Diameter = 41.3608217467 nm

The linear regression in the plot in figure 1 is theoretically represented by the equation:
16 4 2 2
ln(()) ln((0)) = sin ( 2)
32

Using the values from the linear regression the radius of gyration was found by:

32
=
16 4
PHY332 Assignment #3 Tim Henley 1000234506

The value of = 16 nm seems a bit small but the right order of magnitude but I checked the
math several times and could not spot any bugs. From the radius of gyration for a spherical
particle the approximate diameter is given by:

= 2 53
Again, based on our radius of gyration, the spherical diameter of 41 nm seems a bit small but the
right order of magnitude. Our values for suggest the particle could be measured by light
scattering. Generally small particles are poor scatterers, but from lecture 5, angular
measurements are useful for > 50. For visible light that means greater than about 9 to 14
nm, thus our value just fits this criteria. On the other hand, our value suggest small angle
X-ray scattering would be better for revealing structural details, (below 10 nm).

The data points and regression were also used to make a rudimentary Guinier plot.

Figure 1. Guinier plot from linear regression based on low-angle X-ray scattering data for 50S ribosomal
subunits from E. coli.