title: Multi-platform compatible software for analysis of polymer bending mechanics.
abstract: Cytoskeletal polymers play a fundamental role in the responses of cells to both external and internal stresses. Quantitative knowledge of the mechanical properties of those polymers is essential for developing predictive models of cell mechanics and mechano-sensing. Linear cytoskeletal polymers, such as actin filaments and microtubules, can grow to cellular length scales at which they behave as semiflexible polymers that undergo thermally-driven shape deformations. Bending deformations are often modeled using the wormlike chain model. A quantitative metric of a polymer's resistance to bending is the persistence length, the fundamental parameter of that model. A polymer's bending persistence length is extracted from its shape as visualized using various imaging techniques. However, the analysis methodologies required for determining the persistence length are often not readily within reach of most biological researchers or educators. Motivated by that limitation, we developed user-friendly, multi-platform compatible software to determine the bending persistence length from images of surface-adsorbed or freely fluctuating polymers. Three different types of analysis are available (cosine correlation, end-to-end and bending-mode analyses), allowing for rigorous cross-checking of analysis results. The software is freely available and we provide sample data of adsorbed and fluctuating filaments and expected analysis results for educational and tutorial purposes.
authors.affiliation: Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, United States of America.
authors.forename: John S
authors.initials: JS
authors.lastname: Graham
authors.affiliation: Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, United States of America.
authors.forename: Brannon R
authors.initials: BR
authors.lastname: McCullough
authors.affiliation: Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, United States of America.
authors.forename: Hyeran
authors.initials: H
authors.lastname: Kang
authors.affiliation: Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, United States of America.
authors.forename: W Austin
authors.initials: WA
authors.lastname: Elam
authors.affiliation: Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, United States of America.
authors.forename: Wenxiang
authors.initials: W
authors.lastname: Cao
authors.affiliation: Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, United States of America.
authors.forename: Enrique M
authors.initials: EM
authors.lastname: De La Cruz
mesh_terms: D008841:Actin Cytoskeleton / Q000737:chemistry / Q000378:metabolism*; D001696:Biomechanical Phenomena; D019295:Computational Biology / Q000379:methods*; D004548:Elasticity; D008954:Models, Biological; D008958:Models, Molecular; D015203:Reproducibility of Results; D012984:Software; D013314:Stress, Mechanical
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