Disorder influence on linear dichroism analyses of smectic phases

Joshua Manor, Ziad Khattari, Tim Salditt, Isaiah T. Arkin*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

7 Scopus citations


Linear dichroism, the unequal absorption of parallel and perpendicular linear polarized light, is often used to determine the anisotropic ordering of rodlike polymers in a smectic phase, such as helices in a lipid bilayer. It is a measure of two properties of the sample: 1), orientation of the chromophore transition dipole moment (TDM) and 2), disorder. Since it is the orientation of the chromophore TDM that is needed for high resolution structural studies, it is imperative to either deconvolve sample disorder, or at a minimum, estimate its effect upon the calculated TDM orientation. Herein, a rigorous analysis of the effects of disorder is undertaken based on the recently developed Gaussian disorder model implemented in linear dichroism data. The calculation of both the rod tilt and rotational pitch angles as a function of the disorder and dichroism, yield the following conclusions: Disorders smaller than 5° have a vanishingly small effect on the calculated polymer orientation, whereas values smaller than 10° have a negligible effect on the calculated parameters. Disorders larger than 10° have an appreciable effect on the calculated orientational parameters and as such must be estimated before any structural characterization. Finally the theory is tested on the HIV vpu transmembrane domain, employing experimental mosaicity measurements from x-ray reflectivity rocking scans and linear dichroism.

Original languageAmerican English
Pages (from-to)563-571
Number of pages9
JournalBiophysical Journal
Issue number1
StatePublished - Jul 2005

Bibliographical note

Funding Information:
This research was supported in part by a grant from the Israel Science Foundation (No. 784/01) to I.T.A., and grants from the Deutsche Forschungsgemeinschaft and from Niedersachsen to I.T.A. and T.S.


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