BioEc112/c215 MEc115/c216

Molecular Biomechanics and Mechanobiology of the Cell

Homework3
Due: 3/4/19 (2:59PM) Electronically on course website


EXERCISE 1. Read the article “Mechanical LINCs of the nuclear envelope: Where
SUN meets KASH” by Jahed et al. 2018
(https://www.sciencedirect.com/science/article/pii/S2352431617301876) and
answer the following questions:
a. Describe the load-bearing components across the nuclear envelop.
b. Describe the type(s) of forces that can be transmitted between the
cytoskeleton and nucleoskeleton. Use schematics to augment your
arguments.
c. Comment on what cellular processes that may be influenced by or rely on
these transmitted mechanical forces.


EXERCISE 2. Find the crystal structure of human SUN2 protein from protein data
bank (PBD ID: 4DXT). Use VMD to visualize it. Describe different structural features
of this protein, and speculate on how you think they may contribute to the
mechanics of this molecule. Feel free to use schematics to support your conjectures.


EXERCISE 3 (Entropy). Imagine we have two types of gases in two separate
containers, separated by a wall. There are 4 atoms in 4 slots in each side. The wall is
then removed and the gases start mixing. Draw different macroscopic states that
might happen during the mixing process and find the multiplicity for all of them.
Indicate the state with the highest entropy and explain why this state is the most
statistically expected state. How does that relate to the disorderedness of the
system?

EXERCISE 4 (Entropy). Derive the probability form of Boltzmann’s equation from
the multiplicity form of it.
EXERCISE 5 (Entropy). Imagine we are rolling a dice 6 times. We can add weights
to the sides of the dice so that we get biased results. Find the entropy for each of the
following cases, find the maximum entropy, and explain why the entropy is different
in each case.
• Case1: Equal weights have been added to sides 1,2,3 so that probability of
each of these sides is half of the probability of other sides.
• Case2: The same weight above has been added to sides 1 and 6.
• Case 3: No weight has been added.