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Easyworm: an open-source software tool to determine the mechanical properties of worm-like chains Lamour, Guillaume; Kirkegaard, Julius B; Li, Hongbin; Knowles, Tuomas P; Gsponer, Jörg

Abstract

Background: A growing spectrum of applications for natural and synthetic polymers, whether in industry or for biomedical research, demands for fast and universally applicable tools to determine the mechanical properties of very diverse polymers. To date, determining these properties is the privilege of a limited circle of biophysicists and engineers with appropriate technical skills. Findings: Easyworm is a user-friendly software suite coded in MATLAB that simplifies the image analysis of individual polymeric chains and the extraction of the mechanical properties of these chains. Easyworm contains a comprehensive set of tools that, amongst others, allow the persistence length of single chains and the Young’s modulus of elasticity to be calculated in multiple ways from images of polymers obtained by a variety of techniques (e.g. atomic force microscopy, electron, contrast-phase, or epifluorescence microscopy). Conclusions: Easyworm thus provides a simple and efficient tool for specialists and non-specialists alike to solve a common problem in (bio)polymer science. Stand-alone executables and shell scripts are provided along with source code for further development.

Item Metadata

Title
Easyworm: an open-source software tool to determine the mechanical properties of worm-like chains
Creator
Lamour, Guillaume; Kirkegaard, Julius B; Li, Hongbin; Knowles, Tuomas P; Gsponer, Jörg
Publisher
BioMed Central
Date Issued
2014-07-10
Description
Background: A growing spectrum of applications for natural and synthetic polymers, whether in industry or for biomedical research, demands for fast and universally applicable tools to determine the mechanical properties of very diverse polymers. To date, determining these properties is the privilege of a limited circle of biophysicists and engineers with appropriate technical skills. Findings: Easyworm is a user-friendly software suite coded in MATLAB that simplifies the image analysis of individual polymeric chains and the extraction of the mechanical properties of these chains. Easyworm contains a comprehensive set of tools that, amongst others, allow the persistence length of single chains and the Young’s modulus of elasticity to be calculated in multiple ways from images of polymers obtained by a variety of techniques (e.g. atomic force microscopy, electron, contrast-phase, or epifluorescence microscopy). Conclusions: Easyworm thus provides a simple and efficient tool for specialists and non-specialists alike to solve a common problem in (bio)polymer science. Stand-alone executables and shell scripts are provided along with source code for further development.
Subject
Matlab; GUI; Polymer; Worm-like chain model; Persistence length; Young’s modulus; AFM
Genre
Article
Type
Text
Language
eng
Date Available
2016-01-08
Provider
Vancouver : University of British Columbia Library
Rights
Attribution 4.0 International (CC BY 4.0)
DOI
10.14288/1.0223216
URI
http://hdl.handle.net/2429/56347
Affiliation
Biochemistry and Molecular Biology, Department of; Chemistry, Department of; Medicine, Faculty of; Science, Faculty of; Other UBC
Citation
Source Code for Biology and Medicine. 2014 Jul 10;9(1):16
Publisher DOI
10.1186/1751-0473-9-16
Peer Review Status
Reviewed
Scholarly Level
Faculty
Copyright Holder
Lamour et al.; licensee BioMed Central Ltd.
Rights URI
http://creativecommons.org/licenses/by/4.0/
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Attribution 4.0 International (CC BY 4.0)