BibTex format

author = {van, Wilderen LJG and Lincoln, CN and van, Thor JJ},
doi = {10.1371/journal.pone.0017373},
journal = {PLoS One},
pages = {1--14},
title = {Modelling multi-pulse population dynamics from ultrafast spectroscopy},
url = {},
volume = {6},
year = {2011}

RIS format (EndNote, RefMan)

AB - Current advanced laser, optics and electronics technology allows sensitive recording of molecular dynamics, from single resonance to multi-colour and multi-pulse experiments. Extracting the occurring (bio-) physical relevant pathways via global analysis of experimental data requires a systematic investigation of connectivity schemes. Here we present a Matlab-based toolbox for this purpose. The toolbox has a graphical user interface which facilitates the application of different reaction models to the data to generate the coupled differential equations. Any time-dependent dataset can be analysed to extract time-independent correlations of the observables by using gradient or direct search methods. Specific capabilities (i.e. chirp and instrument response function) for the analysis of ultrafast pump-probe spectroscopic data are included. The inclusion of an extra pulse that interacts with a transient phase can help to disentangle complex interdependent pathways. The modelling of pathways is therefore extended by new theory (which is included in the toolbox) that describes the finite bleach (orientation) effect of single and multiple intense polarised femtosecond pulses on an ensemble of randomly oriented particles in the presence of population decay. For instance, the generally assumed flat-top multimode beam profile is adapted to a more realistic Gaussian shape, exposing the need for several corrections for accurate anisotropy measurements. In addition, the (selective) excitation (photoselection) and anisotropy of populations that interact with single or multiple intense polarised laser pulses is demonstrated as function of power density and beam profile. Using example values of real world experiments it is calculated to what extent this effectively orients the ensemble of particles. Finally, the implementation includes the interaction with multiple pulses in addition to depth averaging in optically dense samples. In summary, we show that mathematical modelling is es
AU - van,Wilderen LJG
AU - Lincoln,CN
AU - van,Thor JJ
DO - 10.1371/journal.pone.0017373
EP - 14
PY - 2011///
SN - 1932-6203
SP - 1
TI - Modelling multi-pulse population dynamics from ultrafast spectroscopy
T2 - PLoS One
UR -
UR -
UR -
VL - 6
ER -