Computer Applications for the classroom -Lecture Material

Biomolecules My Homepage

This page serves to accomodate teaching material from different lectures from the fields of Physical Chemistry, Spectroscopy, Biophysics and Laser.

GRAPH mathematical function scripts

The program GRAPH is an easy to use mathematical function plotting program with a steep learning curve but still including some nice features. Apart from standard functions, the program is capable of parametric functions, polar functions, relations, or determine the derivative of a function just to name a few. In the following some examples are given that were used in class, such as in kinetics, laser mode locking, periodic functions, and the use of Fourier and Taylor expansions. Therefore, the examples are somewhat arbitrary....... .

$exponentials$	$expansion series$	$laser mode locking$
Exponential function	Function Expansion Series	Laser Mode Locking

You can download all the short manuals and scripts here: Graph_Scripts.zip, updated 08th july 2015

VMD scripts

The VMD-based demonstrations and the molecular vibration examples shown during Physical Chemistry, Spectroscopy and Biophysics lectures are included in the zipped script collections 'vmdexamples.zip' and 'viblogfiles.zip'. If you use these resources, I would appreciate getting a notification. The VMD-scripts include button controlled presentations to faciliate use in lectures and talks. Take a look at some screenshots showing VMD with button controlled presentations

Read installation instructions file prior to using the following zipped VMD example script files !

VMDscript Installation and Content

VMDscript_Installation and Content

Further, there is a more thorough manual available, that also describes how to create own scripts of this kind:

VMDscript_Instruction.pdf

The following are the packed script files which are identical in view of content:

vmdexample.tar.gz, updated 04th june 2013
vmdexample.zip, updated 04th june 2013

Vibrational Mode Visualizations

Molecule calculation results for vibrational mode visualisation with molden and molekel as used in the lecture 'Biophysical Chemistry'. Molden was used in the lecture, because it does not only show vibrational mode animation, but also shows the IR and Raman spectra. Take a look at some screenshots.

Download viblogfiles.tar.gz

For questions, please contact:
Peter Schellenberg, phone (+351) 253-604074

Peter Schellenberg 12 july 2015