Question 1

a)
Due to the constant drift velocity, the particle will always drift in a specific direction. The overall motion of the
particle is influenced by both the random walk and the drift. Thus, the mean position of the particle won’t be 0
anymore (which happens when only the random walk is considered.
After time “t”, displacement due to drift: ∆x drift = v d ∆t
After time “t”, overall position (by considering random walk):
x = xo + v d ∆t + ∆x random where:
xo: initial position
v d ∆t: displacement due to drift
∆x random : displacement due to random walk
But we want the mean position:
<x> drift = <xo > + <v d ∆t> + <∆x random > where:
<∆x random > = 0 since the mean displacement of a random walk is 0
Xo and v d ∆t do not change since they are both constant
We have:
<x> drift = xo + v d ∆t
We can set x o = 0 for any initial position, thus we end up with:
<x> drift = v d ∆t

b)
Without drift: <x 2> normal = 2Dt where:
D = L2 / (2∆t) (Nelson)

With Drift: <x2> = (<x> normal + <x> drift)2

= <x>2normal + 2 (<x>normal * <x>drift) + <x>2drift
(We know that <x>normal = 0, thus + 2 (<x>normal * <x>drift) = 0)
= <x> normal + <x>2drift
2

= 2Dt + (v d ∆t)2
c)
When vd = 0, we see that the slope is
constant. Thus, this means that for
vd = 0, there is a linear relationship
between MSD and time. However, as vd
increases, the slope of MSD increases
along with it. This can be explained by
the quadratic factor. Since vd now has a
value, the quadratic second-half of the
equation contributes to the overall
equation. Consequently, this means
that the vesicle will travel a greater
distance with the contribution of the
drift than if it was only relying on
diffusion alone.
 Works Cited

Nelson P. 08/12/2002. Biological Physics: Energy, Information, Life [Internet]. Escola Superior de Agricultura
“Luiz de Queiroz”; [cited 2024 Oct. 4]. Available from:
https://www.esalq.usp.br/lepse/imgs/conteudo_thumb/Biological-Physics-Energy--
Information--Life.pdf
Question 2

For yeast cell;

The average length for a yeast cell is 3.6 µm (Chavez et al).
By diffusion alone:
<𝑥2> (3.6)2
<x2> = 2Dt → t = =
2𝐷 2(5)
t = 1.296s

By diffusion + transported by dynein (this compares to drift as the latter acts as a “motor”):
<x2> = 2Dt + (v d t)2
t2vd2 + 2Dt - <x 2> = 0
−2𝐷 ± √4𝐷2 − 4(𝑣𝑑 2 ∗ − < 𝑥 2 >)
𝑡=
2 (𝑣𝑑 2)
−2(5) ± √4(5)2 − 4(22 ∗ − 3.62 )
𝑡=
2 (22 )
t1 = 0.94s or t2 = -3.44s
Since “t” cannot be negative, t = 0.94s

For eukaryotic fibroblast cell;

Eukaryotic fibroblast cell length varies from10 to 15 µm. Thus, let’s consider the average length as 12.5 µm.
By diffusion alone:
<𝑥2> 12.52
<x2> = 2Dt → t = =
2𝐷 2(5)
t = 15.625s

By diffusion + transported by dynein (this compares to drift as the latter acts as a “motor”):
<x2> = 2Dt + (v d t)2
t vd + 2Dt - <x 2> = 0
2 2

−2𝐷 ± √4𝐷2 − 4(𝑣𝑑 2 ∗ − < 𝑥 2 >)

𝑡=
2 (𝑣𝑑 2)
−2(5) ± √4(5)2 − 4(22 ∗ − 12.52 )
𝑡=
2 (22 )

t1 = 5.12s or t2 = -7.62s
Since “t” cannot be negative, t = 5.12s

Difference for Yeast Cell = 1.296s – 0.94s = 0.356s

Difference for Eukaryotic Fibroblastic Cell = 15.625s – 5.12s = 10.505s

We notice a much greater difference in eukaryotic fibroblastic cell than in yeast cell. This can be explained by
the quadratic part of the previously found formula (<x2> = 2Dt + (v d t)2). Since the yeast cell is so small, the
diffusion component dominates over the drift component because “t” will be relatively small (which reduces
the influence of the quadratic half of the formula). Thus, for the yeast cell, the mean square displacement over
time can be described as linear. However, the eukaryotic fibroblastic cell is bigger than the yeast cell. As a
result, the quadratic half of the formula (drift part) will now dominate over the diffusion part since “t” will now
have a considerable impact when squared. Consequently, mean square displacement will increase
quadratically with time. This explains the great disparity in eukaryotic fibroblastic cells.
 Works Cited

M Chavez, Christina. 2024. The cell morphological diversity of Saccharomycotina yeasts. Oxford Academic
(Internet). [cited 2024 Oct 4]. Available from:
https://academic.oup.com/femsyr/article/doi/10.1093/femsyr/foad055/7492805

A Freitas Jr., Robert. 1999. Nanomedecine [Internet]. Georgetown, Texas; [cited 2024 Oct 4]. Available from:
https://www.nanomedicine.com/NMI/8.5.1.htm#:~:text=Platelets%20are%20~2%20microns%2C%20
red,microns%20long%20and%205%2D10
Question 3:

Description Method:
1) With ImageJ, I traced tangent lines at points x 0 and x i.
2) With Measure tool (under Analyze section), I was able to find the complementary angle of the angle
we are looking at between the vector’s tangent to the polymer. Then, I subtracted this angle from 180
to get the actual target angle.
3) With the hover tool, I found the distance between x 0 and x i using distance formula by marking these
two points on the picture.
Distance formula: √(𝑥1 − 𝑥2 )2 − (𝑦1 − 𝑦2 )2
4) Then, I convert this distance to µm by dividing it by 1x10e6 (because 1 pixel = 100 nm = 0.1 µm)

From original equation, we can isolate Lp:

−𝑠
cos(Ө) = 𝑒 2𝐿𝑝
−𝑠
ln(cos(Ө)) =
2𝐿𝑝
−𝑠
Lp =
2ln(cos(Ө))
Plots:
The Mean and Standard Deviation of Lp:

Actin:

9.09+6.47+17.03+12.79+15.94+10.20+16.20+8.96+9.39+12.88
Mean = = 11.90 µm
10

∑(𝑥𝑖−𝑚𝑒𝑎𝑛)^2
Standard Deviation = √ = 3.63 µm
𝑛−1

Microtubules:
∑ 𝑥𝑖 22.38+19.93+28.00+20.74+23.53+11.54+13.66+38.77+16.02+21.16
Mean = = = 21.53 µm
𝑛 10

∑(𝑥𝑖−𝑚𝑒𝑎𝑛)^2
Standard Deviation = √ = 7.74 µm
𝑛−1

Comparison:

From my reference, actin has a persistence length of 3 to 17 µm (Gittes). The value I found (11.90 µm) is
within this interval.

From my reference, microtubule has a persistence length greater than 1mm (Gittes). The value I found (21.53
µm) is inaccurate considering the scale with which we are working.

Sources of errors:

1) The accuracy of the data itself: the point x o and xi were manually placed by hand in the software which
contributes to error. Furthermore, the computer itself has a “margin of error” meaning that every pixel
has certain dimensions and pinpointing an exact real-life location is near impossible. Furthermore,
since we are working with miniscule scales, it will accentuate our errors even more as misplacing our
points by simply a small margin can result in big differences compared to real life data.

2) The two points x o and x i are not situation on the same line (i.e the polymer isn’t fully stretched out and
doesn’t form a complete straight line). Thus, because of using the distance between two points
formula, we introduced a certain amount of error since this distance doesn’t truly represents the value
of “s”. It would have been much better if we could have used the arc length formula, which calculates
the exacts distance between two points situated on a curve no matter the curvature.

3) Microtubules are very stiff since Lp >> Lc. This indicates that they are generally very rigid and that their
structure doesn’t contain many curves and undulation. As a result, it was hard to traces the tangents
at those two points. Consequently, it was also hard to calculate the angle as the tangents were very
close to one another.

4) Significant figures always contribute to error. It would have been better if we had access to the exact
value of each point of data. However, this would have caused major complications when plotting data
and graphing it. Thus, by using an “approximate” of each real value, we introduced some error.

5) If the two ends of the filament are constrained, then the rigidity of the whole will be affected. Indeed,
if the two ends are, for example, stuck between two physical bodies of any kinds, it will affect how the
entirety of the filament bends. Thus, the Lp value I found would have strayed from the actual value (ie
when it is not constrained).
 Works Cited

Gittes F, Mickey B, Nettleton J, Howard J. Flexural rigidity of microtubules and actin filaments measured from
thermal fluctuations in shape. J Cell Biol. 1993;120:923–34. [PMC free article]
Question 4:

a)
Ovalbumin is unique as it has six cysteine residues. Out of those six, two of them form a disulfide bond while
the others have free sulfhydryl (-SH) groups. Fifty percent of its amino acids are hydrophobic (Guha) which
contributes to hydrophobic bonds. In its native state (in raw eggs), the latter is folded and compact and low in
energy due to the overall stability of the protein. However as soon as ovalbumin is heated, it denatures due to
the increase of temperature. Consequently, further hydrophobic reactions can occur, and exposed free thiol
groups can now create other disulfide bonds, that were not present beforehand, which are in fact irreversible
(Hoffmann et al.). Thus, this increase in temperature changes the secondary structure which also inevitably
leads to changes to its tertiary structure. Broken hydrogen bonds can now form further disulfide bonds which
changes the secondary structure while hydrogen bonds and Van der Waal interactions change the tertiary
structure.

b)
When entropy increases, so does the free energy. Thus, hard-boiled egg will have more free energy than raw
ones. Indeed, due to the denaturation, multiple bonds brake and increase the entropy of the system.
Furthermore, in its denaturized form, ovalbumin will create random disulfide bonds. Even though this decrease
slightly decreases entropy, it doesn’t compare to the native state where everything is “ordered”. Consequently,
the native state has lower free energy since everything is more stable, more compact and has fixed bonds
within its secondary and tertiary structure (Nelson et al.)

c)
The denaturation of RNase A is reversible since it can refold to its original form thanks to its structure. Indeed,
the latter is stabilized greatly by non-covalent interactions and a few disulfide bonds which can all return to
their original state. However, this is not the case for ovalbumin found within hard-boiled eggs. Indeed, like
mentioned before, after denaturation, thiol groups become free. Consequently, the latter can form disulfide
bonds which are irreversible. In addition to these new formed disulfide bonds, other type of bonds such as H-
bonds can be formed since it is denatures. Thus, all these bonds can contribute to the irreversibility of hard -
boiling an egg.
 Works Cited

Gerlsma, S.Y. 1967. Reversible Denaturation of Ribonuclease in Aqueous Solutions as Influenced by

Polyhydric Alchohols and Some Other Additives [Internet]. Netherlands, Laboratory of General and
Technical Biology; [cited 2024 Oct 4].

Guha, Snigdha et al. 2019. Egg Proteins [Internet]. [cited 2024 Oct 4]. Available from:
https://www.sciencedirect.com/science/article/pii/B978008100596521603X

Hoffmann, M.A.M., Roefs, S.P.F.M., Verheul, M., Mil, P.J.J.M.v., and Kruif, K.G.d. 1996. Aggregation of β-
lactoglobulin studied by in situ light scattering. J. Dairy Res. 63 423–440.

Koseki, Taihei, et al. “Irreversible Thermal Denaturation and Formation of Linear Aggregates of Ovalbumin.”
Food Hydrocolloids, vol. 3, no. 2, pp. 123–34, https://doi.org/10.1016/S0268-005X(89)80022-0.

Koshland, Daniel E. and Haurowitz, Felix. "protein". Encyclopedia Britannica, 23 Sep. 2024,
https://www.britannica.com/science/protein.

Nelson, David L., Albert L. Lehninger, and Michael M. Cox. Lehninger principles of biochemistry. Macmillan,
2008.