Computational Investigation of Material and Dynamic Properties of Microtubules
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University of Akron / OhioLINK
2018
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ndltd-OhioLink-oai-etd.ohiolink.edu-akron15321083201859372021-08-03T07:07:31Z Computational Investigation of Material and Dynamic Properties of Microtubules Swoger, Maxx Ryan Biophysics Condensed Matter Physics Physics Theoretical Physics microtubule Brownian dynamics simulation hydrodynamic interaction elastic properties slow modes Microtubules are an important component of the cytoskeleton of cells. They provide not only structural support, but also connectivity between different regions of the cell. The motor protein kinesin, for example, transports tethered cargo by walking along microtubules. Microtubules are macromolecules composed of two types of protein subunits, alpha and beta tubulin. Alternating alpha and beta units form long strands called protofilaments that are arranged with a helical pitch to form a hollow tube. This structure is responsible for the unusual mechanic and complex dynamic properties of microtubules in a liquid environment. In this work, we investigate material and dynamic properties of microtubules with computational methods. Since all-atom simulations are restricted to very short (~10 nm) sections of microtubules and very short (~10 ns) time scales, while dynamic processes span a much wider range of length and time scales, we focus on coarse-grained models: an interaction site model for Brownian dynamics simulations, a structural mechanics model for finite element calculations, and a continuum model to analyze normal modes. A comparison of mechanical properties of microtubules under an external force determined from finite element calculations and from Brownian dynamics simulations shows that the structural mechanics model describes a softer microtubule than the interaction site model. To investigate dynamic properties of microtubules in a finite-temperature liquid, we perform Brownian dynamics simulations with and without hydrodynamic interactions. After averaging out the fastest, thermal, motion, we are able to analyze transverse displacement results in terms of eigenmodes of an Euler-Bernoulli cantilever beam. Our results show that, in general, shorter microtubules have faster dynamics and that the inclusion of hydrodynamic interactions affects the slow modes of microtubules. 2018-09-20 English text University of Akron / OhioLINK http://rave.ohiolink.edu/etdc/view?acc_num=akron1532108320185937 http://rave.ohiolink.edu/etdc/view?acc_num=akron1532108320185937 unrestricted This thesis or dissertation is protected by copyright: some rights reserved. It is licensed for use under a Creative Commons license. Specific terms and permissions are available from this document's record in the OhioLINK ETD Center. |
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NDLTD |
| language |
English |
| sources |
NDLTD |
| topic |
Biophysics Condensed Matter Physics Physics Theoretical Physics microtubule Brownian dynamics simulation hydrodynamic interaction elastic properties slow modes |
| spellingShingle |
Biophysics Condensed Matter Physics Physics Theoretical Physics microtubule Brownian dynamics simulation hydrodynamic interaction elastic properties slow modes Swoger, Maxx Ryan Computational Investigation of Material and Dynamic Properties of Microtubules |
| author |
Swoger, Maxx Ryan |
| author_facet |
Swoger, Maxx Ryan |
| author_sort |
Swoger, Maxx Ryan |
| title |
Computational Investigation of Material and Dynamic Properties of Microtubules |
| title_short |
Computational Investigation of Material and Dynamic Properties of Microtubules |
| title_full |
Computational Investigation of Material and Dynamic Properties of Microtubules |
| title_fullStr |
Computational Investigation of Material and Dynamic Properties of Microtubules |
| title_full_unstemmed |
Computational Investigation of Material and Dynamic Properties of Microtubules |
| title_sort |
computational investigation of material and dynamic properties of microtubules |
| publisher |
University of Akron / OhioLINK |
| publishDate |
2018 |
| url |
http://rave.ohiolink.edu/etdc/view?acc_num=akron1532108320185937 |
| work_keys_str_mv |
AT swogermaxxryan computationalinvestigationofmaterialanddynamicpropertiesofmicrotubules |
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1719453847454220288 |