Molecular Biophysics Class Examples

Visualizing how changing a parameter affects a result can be useful for honing one’s intuition.  Below are simple programs that plot an observable and allow the user to change the input parameters using GUI sliders.  Executables (Mac OS X) for the helix-coil zipper model, the Shottky 2-state model and the Gibbs-Helmholz equation are provided and discussed below.

Helix-coil zipper model

This is a simple demonstration of the Zimm-Bragg zipper model that allows you to see the effect of varying the “s”, “sigma” and number of residues.  For more information consult Cantor and Shimmel Vol 3 Chapter 20.

2-state Shottky model

Below is also a simple Labview program to examine how a change of the energy gap and number of states affects the average energy and heat capacity.  The program will handle more than 2-states.

Shottky 2-state model

Gibbs-Helmholtz Equation
Below is a simple program to graphically display the Gibbs-Helmholtz equation.  Check out what happens when deltaCp is nonzero.

gibbs-helmholtz equation screenshot