SimuLab 4: The Homopolymer Collapse

                        

You will be able to: a) Understand the thermodynamics of the homopolymer collapse transition; b) Determine the critical q-point.; c) Compare the process with the condensation of liquid near the critical density.

1. Open Universal Application. Press on Play Movie and select Collapse.mov. Press Forward.


~ You see a protein of 256 monomers in the fully unfolded state at high temperature. We will slowly cool down the system taking away the energy. Watch the movie from the beginning to the end. The protein gradually changes its shape from the unfolded irregular coil to a collapsed globule of roughly spherical shape.
~ Copy the table below: 

time	temperature	Radius of Gyration	Potential Energy
1000
2000
3000
4000
5000
6000
7000
8000
9000
10000
11000
12000
13000
14000
15000
16000
17000
18000
19000
20000
21000


2. Rewind the movie till beginning. Reset the Averaging for Movies window and record the values of temperature, Radius of Gyration and potential energy into the table each 1000 units time till time 21000. Press Forward.





                        


Q2.29: Construct the Temperature, Radius of Gyration and Potential Energy vs. time graphs. Does the temperature vs. time graph have a plateau like in freezing?

Answers to the question

Simulab 4

A2.29: The temperature vs. time graph does not have a plateau like in freezing instead it have an inflexion point at the critical point named the q-point. The graphs of potential energy and radius of gyration has the maximal local slope in the vicinity of this point. The slope of this graph is the heat capacity C_V that has is maximum near the q-point. For very long polymer chain the heat capacity will have infinitely sharp and high peak at the q-point.