PyLDM - An open source package for lifetime density analysis of time-resolved spectroscopic data
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Published version
Author(s)
Dorlhiac, GF
Fare, C
van Thor, JJ
Type
Journal Article
Abstract
Ultrafast spectroscopy offers temporal resolution for probing processes in the femto- and picosecond regimes. This has allowed for investigation of energy and charge transfer in numerous photoactive compounds and complexes. However, analysis of the resultant data can be complicated, particularly in more complex biological systems, such as photosystems. Historically, the dual approach of global analysis and target modelling has been used to elucidate kinetic descriptions of the system, and the identity of transient species respectively. With regards to the former, the technique of lifetime density analysis (LDA) offers an appealing alternative. While global analysis approximates the data to the sum of a small number of exponential decays, typically on the order of 2-4, LDA uses a semi-continuous distribution of 100 lifetimes. This allows for the elucidation of lifetime distributions, which may be expected from investigation of complex systems with many chromophores, as opposed to averages. Furthermore, the inherent assumption of linear combinations of decays in global analysis means the technique is unable to describe dynamic motion, a process which is resolvable with LDA. The technique was introduced to the field of photosynthesis over a decade ago by the Holzwarth group. The analysis has been demonstrated to be an important tool to evaluate complex dynamics such as photosynthetic energy transfer, and complements traditional global and target analysis techniques. Although theory has been well described, no open source code has so far been available to perform lifetime density analysis. Therefore, we introduce a python (2.7) based package, PyLDM, to address this need. We furthermore provide a direct comparison of the capabilities of LDA with those of the more familiar global analysis, as well as providing a number of statistical techniques for dealing with the regularization of noisy data.
Date Issued
2017-05-22
Date Acceptance
2017-04-20
Citation
Plos Computational Biology, 2017, 13 (5)
ISSN
1553-7358
Publisher
Public Library of Science
Journal / Book Title
Plos Computational Biology
Volume
13
Issue
5
Copyright Statement
© 2017 Dorlhiac et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Sponsor
The Leverhulme Trust
Engineering & Physical Science Research Council (EPSRC)
Grant Number
RPG-2014-126
EP/M000192/1
Subjects
Science & Technology
Life Sciences & Biomedicine
Biochemical Research Methods
Mathematical & Computational Biology
Biochemistry & Molecular Biology
ULTRAFAST TRANSIENT ABSORPTION
LEAST-SQUARES PROBLEMS
MAXIMUM-ENTROPY
PHOTOSYSTEM-II
CHLAMYDOMONAS-REINHARDTII
ELECTRON-TRANSFER
REACTION CENTERS
ENERGY-TRANSFER
REGULARIZATION
FLUORESCENCE
Publication Status
Published
Article Number
ARTN e1005528