1. Entropy changes during heat exchange.

Two identical blocks of the same material

with temperature independent heat capacities C
p
are brought together. Their initial
temperatures are T
1
and T
2
. Heat exchange with the surroundings can be neglected. After
some time equilibrium is reached and the temperatures of the blocks become equal. What
is the change of the entropy of the blocks as a result of equilibration?

2
1 2
1 2
1 2
( )
ln( / ) ln( / ) ln
4
p f p f p
T T
S C T T C T T C
TT
! " +
# = + =
$ %
& '



2. Mixing of two ideal gases. n
1
moles of an ideal gas 1 are separated from n
2
moles of
an ideal gas 2 by a partition that does not conduct heat (see Figure below). The volumes
occupied by the gases are V
1
and V
2
, respectively, and their temperatures are T
1
and T
2
.
There is no heat exchange between the entire system (the two gases) and the
surroundings. Assume that both gases have the same, temperature independent molar
heat capacity
V
c




The partition is removed and the gases attain equilibrium. What is the change of the
entropy of the system as a result of this process?


First, we calculate the final temperature T after equilibration by realizing that the total
energy of the system must be conserved:

1 1 2 2 1 2
( )
V V V
n c T n c T n n c T + = +

1 1 2 2 1 2
( ) /( ) T nT n T n n = + +

Then use our result for the entropy of an ideal gas as a function of V and T:

1 2 1 1 2 2 1 2 1 1 2 2
1 2 1 1 2 2
1 1 1 2 2 2 1 2
ln ln ln ln
( ) ( )
V V
V V nT n T V V nT n T
S S S n R n c n R n c
V T n n V T n n
+ + + +
! = ! + ! = + + +
+ +



3. More on thermodynamics of weight lifting. Estimate the change of the entropy of
the surroundings (the room) as a result of the training session described in Problem 2a
from HW1. The temperature inside the room is constant and equal to 300K. Assume that
only 50% of the energy stored in food was used by your body to perform the mechanical
work on the barbell while the remaining 50% were dissipated as heat.


2 100 / 1176 / S mg h T J K ! = " " ! #


4. A simple heat engine. Consider a cylinder containing an ideal gas under a piston, as
shown in Figure below. After a weight m
1
is removed from the piston, the gas expands
and lifts the remaining weight m
2
.

A. Assuming that this process takes place at constant temperature, what is the work W
performed on the weight m
2
as a result of the gas expansion?

To find the final height h
2
for the weight, write down the equation of state for the gas:

2 2 2 2
( / )( ) m g A Ah m gh nRT = =

Similarly, before expansion, we had

2 1 1
( ) m m gh nRT + =

Comparing the above two equations,

1 2
2 1
2
m m
h h
m
+
=

The work done on the weight is equal to the change of its potential energy:

2 2 1 1 1
( ) W m g h h mgh = ! =



B. What is the heat received by the gas in this process?

Since the gas is ideal and its temperature the same before and after the process, its !U is
zero so that
1 1
q W mgh = = (Note the sign: W is the work done by the gas).


C. Think about this contraption as a heat engine that receives heat from the surroundings
and performs work. Does its operation contradict the 2
nd
law? (recall the formulation of
the 2
nd
law that is concerned with heat engines). Explain your answer.
The process is not cyclic (the system does not return to its original state) so all heat
received by the system can be converted into work this does no contradict the 2
nd
law.



D. What is the change of the Helmholtz free energy of the gas !A as a result of the
process?

( ) A U TS T S ! = ! "! = " !


1 2
2 1 2 1 2 1
2
ln( / ) ln( / ) ln( / ) ln
V
m m
S Rn V V C T T Rn h h Rn
m
! " +
# = + = =
$ %
& '


1 2 1 2
1 2 1
2 2
ln ( ) ln
m m m m
A nRT m m gh
m m
! " ! " + +
# = $ = $ +
% & % &
' ( ' (


E. Compare W with !A. Which one is greater? Is your finding consistent with the
equation that we have derived in the class for the maximum work that can be performed
by a system at constant temperature?


Since the process was no reversible, some of the free energy difference must have ben
wasted (not converted into work) so we expect

W A < !"

You can check that the equations derived above satisfy this inequality
[If you set
1 2
/ x m m = then W A < !" is equivalent to /( 1) ln(1 ) x x x + < + . By plotting the
lhs and rhs of this inequality as a function of x you can see that it is satisfied for any x>0].







5. Processes where entropy decreases spontaneously. There are many processes in
which living matter becomes more organized (e.g., a fertilized egg evolving into a bird).
This observation has led certain philosophers to believe that life does not obey the 2
nd

law. Here we analyze a simple process, in which a system becomes more organized
spontaneously, from the 2
nd
law perspective.
Consider a jar of honey inside your fridge, which we will consider to be a
constant temperature and pressure environment. After an appropriate center of
crystallization is placed inside the jar (bread crumbs work well) the honey eventually
becomes crystallized.

A. Did the entropy of honey increase or decrease as a result of this process?

The entropy decreased. Crystalline honey is more ordered.

B. Does the result of part A contradict the 2
nd
law? Explain your answer mathematically
by writing down the 2
nd
law in a form of an inequality and verifying whether or not this
inequality is satisfied. (Hint: does the honey exchange heat with the surroundings? Which
way does the heat flow if it does?)


The 2
nd
law states that / q T S < ! . Since 0 S ! < this requires q<0. The honey gives off
heat.


C. Did the Gibbs free energy G of the honey increase, decrease, or remain constant as a
result of this process? Explain your answer mathematically again by writing the
definition of G and using your results from parts A and B.

Using G=H-TS and q=!H for a constant P process we find that
0 G H T S q T S ! = ! " ! = " ! < . Of course this is what one expects for a spontaneous
process at constant P and T (see Lecture notes)


D. Suppose that immediately after crystallization is initiated, the honey is transferred into
a thermally insulated container. This is done quickly enough that the temperature of the
honey does not change during the transfer. Will the honey continue to crystallize after
that?

Yes, the honey will crystallize (at least partially).

E. Will the entropy of honey increase, decrease or stay the same as a result of the process
it undergoes after being thermally isolated?

Increase (spontaneous process in an isolated system)

F. Do the conclusions you have arrived at in Parts D and E contradict one another?
Explain your answer.

How can the entropy increase as a result of crystallization? This seems to contradict the
conclusion of Part A. What happens is that crystallization of honey is accompanied by a
release of energy (see part B). Since our system is isolated and heat cannot be removed,
this will lead to an overall increase of temperature in the system. As we know, the
entropy of materials tends to go up as their temperature is increased. Because of that, the
reduction of entropy due to crystallization will be offset by the increase in entropy due to
the temperature increase such that the total entropy of the system will be going up

6* (extra credit: 10 points). A bioinformatics problem. As most of you know, a
protein is a chain molecule whose chemical identity (and, consequently, the structure) is
determined by the sequence of its amino acids. There are 20 standard amino acids. In
case you have not taken a biochemistry class, it does not matter for the purpose of this
problem: You may think of a protein as a string of letters taken from an alphabet that
contains a total of 20 letters. If two proteins have similar sequences, they are likely to
have similar structure and/or have an evolutionary relation so there is a lot of interest in
trying to find out how similar sequences of different proteins are. To measure the
similarity between two sequences of the same length N,
1 2
...
N
a a a and
1 2
...
N
bb b , we will
use the following procedure (note that this is not how its really done in bioinformatics):
Align the two sequences against each other
1 2 3
1 2 3
...
...
N
N
a a a a
b b b b

and count the number of times n you see a match between the letters at the respective
positions,
i i
a b = . We then calculate the sequence similarity as the ratio:

/ r n N =

For example, the similarity between VYPTQ and VPYTQ is r = 3/5 = 60% (matches at
positions 1,4, and 5) and the similarity between VYPTQ and QTPYV is r = 1/5 = 20%. If
two sequences are identical, their similarity is 1.

A. Somebody gave you a polypeptide with a sequence A =
1 2
...
N
a a a that is of length
N = 10. Now suppose that you have randomly picked another sequence R of the
same length. What is the probability that the sequence similarity between A and
R is equal to or higher than 20%? (In other words, among all possible sequences
R of length N, what is the fraction of those that have a sequence similarity with A
of 0.2 or higher?)

10
10
2
10 19
1
0.086
20 20
i
i
i
i
!
=
" # " #
" #
$
% & % & % &
' (
' ( ' (
)


B. Answer the question of Part A assuming N=20.




! 0.0159