Calculation Programs

All of the programs, macros and procedures on this page are available for use without charge, but are copyrighted and can not be resold. For copies of the programs, please email us at rcorn@uci.edu.

Please see our Unicorn Calculations Page for a complete listing of our web-based calculations.

• DNA Web-based Structure and Thermodynamics Calculations

  We use a couple of web-based programs from other groups to calculate the Tm of DNA sequences used in our microarrays, as well as a folding program to check for any unwanted loops or hairpins.

  Click here to go to the DNAmate Server for DNA Thermo and Tm Calculations.

  Click here to go to the Vienna RNA Secondary Structure Prediction Website.

• UBC Group's DNA and RNA Structure Calculations

  We collaborate with Prof. Anne Condon at the University of British Columbia in Vancouver on our projects in the area of DNA computing. As part of this work, Prof. Condon's research group has developed a set of DNA and RNA structure calculations for pairs of DNA and RNA molecules.

  Click here to go to Prof Condon's RNAsoft page for DNA and RNA calculations.

• Two Phase Fresnel Reflectivity Calculation

  2 Phase Web-based Calculation. We have now implemented a web-based two phase Fresnel Calculation that plots both s and p reflectivity plus the electric fields (Es2, Ex2 and Ez2) as a function of incident angle.
  
  To go to our Two Phase Fresnel Calculation Page, please click here.

• Four Phase Fresnel Reflectivity Calculation

  4 Phase Web-based Calculation. We have implemented a web-based version of our 4 Phase Fresnel Calculation. This calculation now plots both s and p reflectivity plus the electric fields (Es2, Ex2 and Ez2) as a function of incident angle.
  
  To go to our 4 Phase Fresnel Reflectivity Calculation Page, please click here.

  Igor Pro Macro Procedure File. We use the application "Igor Pro" (by Wavemetrics) on the Apple Macintosh for many of our calculations. The macros that we use in our four phase Fresnel calculations for the SPR experiment can be viewed as text here.

  These calculations are supported in part by the National Science Foundation (Award No. CHE-0133151).

• N Phase Fresnel Calculation

  For more complex problems, we have developed an N phase calculation program that will calculate Reflectivity, Surface Electric Field Intensity, and Phase Shifts as a function of incident angle for dielectric stacks of up to 10 phases.
  
  Both the Turbo Pascal 6.0 source code and .exe PC files for this program are available in a compressed zip format (Nphase.zip) accessible by clicking here.
  
  This program is now also available as C++ source code in a compressed zip format (Nphase2.zip) accessible by clicking here.

  These calculations are supported in part by the National Science Foundation (Award No. CHE-0133151).

• PM-FTIRRAS Collection and Normalization Macros

  For our polarization-modulation Fourier transform infrared reflection-absorption (PM-FTIRRAS) experiments, we use macros to collect and normalize the data. We use a Mattson FTIR hooked up to a PC to collect the data, and then transfer the spectra over to a Macintosh computer for the normalization and conversion to absorbance units.
  
  The collection macro that works with the Mattson software on a PC can be viewed as text here.
  
  The set of normalization macros that work in Igor Pro on a Macintosh can be viewed as text here.

• PPP (Pople-Pariser-Parr) Calculation

  For our nonlinear susceptibility (beta) calculations, we use PPP wavefunctions for the ground and excited states that are generated by this general PPP program. This program also gives excited state dipole moments and transition dipole moments (extinction coefficients). It comes from IUPUI.
  
  This program is currently available (PPP.zip) accessible by clicking here.