APS USAXS/SAXS/WAXS facility

Ultra-Small-Angle X-ray Scattering Facility

Clementine

Clementine — Modeling decay kinetics using MEM and least-squares fitting

NOTE: This package has not been actively maintained for at least 10 years. It is provided as-is; it may still work in current Igor Pro versions, but no updates or support should be expected. If you find it useful and encounter problems, contact the author.

Clementine is a package for Igor Pro developed to model decay kinetics processes using either the maximum entropy method (MEM, included) or least-squares fitting. The project is hosted on the Wavemetrics Igor site: https://www.wavemetrics.com/project/Clementine.

What it does

The math of the analysis (decay times are "tau"):

  • MEM: signal(time) = FlatOffset + sum( P(tau) · exp(−time/tau) )
  • LSQF: signal(time) = FlatOffset + sum( P(tau) · exp(−(time+TimeShift)/tau) )

The package will:

  • MEM — generate the distribution of P(tau) values using the Maximum Entropy method over a user-defined number of bins in tau (log-spaced).
  • LSQF — model (and least-squares fit) a sum of up to 5 different P(tau), TimeShift, and tau combinations. Both P(tau) and tau can be fitted.

The code loosely follows these manuscripts:

  • Zs. Ablonczy, A. Lukacs, E. Papp, "Application of the maximum entropy method to absorption kinetic rate processes," Biophysical Chemistry 104 (2003) 249–258.
  • A. K. Livesey and J. C. Brochon, "Analyzing the distribution of decay constants in pulse-fluorimetry using the maximum entropy method," Biophysical Journal 52 (1987) 693–706.

Data input

Clementine can use various data types:

  1. One signal wave with x-scaling in seconds — with or without an errors wave. This is raw data from an instrument that measures the signal at fixed intervals. Such data are not properly spaced for MEM analysis and need to be rebinned to log-time scaling — check the "Rebin the data" checkbox. With this data type you can also use an instrument response function.
  2. Two waves (signal/time) — signal and associated time for each point. You can still rebin the data on a log scale if needed, but you cannot use an instrument response function.
  3. Three waves (signal/time/errors) — signal, error for signal, and times. You cannot use an instrument response function, but you can rebin the data if necessary.

Installation and loading

The package consists of:

  • Load_Clementine.ipf — should be in (or linked to) "Igor Procedures"
  • DecayModeling_Load.ipf — should be in (or linked to) "User Procedures/Clementine"
  • DecayModeling_GUI.ipf — should be in (or linked to) "User Procedures/Clementine"
  • DecayModeling_1.ipf — should be in (or linked to) "User Procedures/Clementine"
  • DecayModeling_2.ipf — should be in (or linked to) "User Procedures/Clementine"
  • DecayModeling.ifh — the help file, should be in (or linked to) "Igor Help Files"

You also need:

  • MaxEntPackage.ipf — should be in (or linked to) "User Procedures/Maximum Entropy"

Loading the package: select "Load Clementine MEM modeling" in the Macros menu. This loads and compiles the necessary procedure files and adds the command "MEM Decay fitting" to the Macros menu, which opens the main control window. For more details, please read the included help file (accessible via a button in the main control window).