0

Full Content is available to subscribers

Subscribe/Learn More  >

Brownian Dynamics Simulation of the Dynamics of Stretched DNA

[+] Author Affiliations
Ikenna D. Ivenso, Todd D. Lillian

Texas Tech University, Lubbock, TX

Paper No. DETC2014-35487, pp. V006T10A007; 6 pages
doi:10.1115/DETC2014-35487
From:
  • ASME 2014 International Design Engineering Technical Conferences and Computers and Information in Engineering Conference
  • Volume 6: 10th International Conference on Multibody Systems, Nonlinear Dynamics, and Control
  • Buffalo, New York, USA, August 17–20, 2014
  • Conference Sponsors: Design Engineering Division, Computers and Information in Engineering Division
  • ISBN: 978-0-7918-4639-1
  • Copyright © 2014 by ASME

abstract

DNA is a long flexible polymer and is involved in several fundamental cellular processes such as transcription, replication and chromosome packaging. These processes induce forces and torques in the DNA which deform it. These deformations in turn affect the structure and function of DNA. However, understanding of the dynamic response of DNA to the various forces that act on it is still far from complete. Several experiments have been carried out to study these responses most of which use a micron sized magnetic bead attached to the DNA molecule to both manipulate it and to observe its dynamics. One limitation of this approach is that the dynamics of the DNA molecule has mostly been characterized “indirectly” by observing the dynamics of the magnetic bead. It is also reasonable to expect that, because of the size of the bead relative to that of the DNA, the magnetic bead dynamics will obscure that of the DNA. We adapt existing coarse-grained Brownian dynamics models of DNA to develop a model capable of representing the dynamics of DNA without any of the artifacts inherent to the experiments. This model accounts for bending, torsion, extension, electrostatics, hydrodynamics and the random thermal forces acting on DNA in an electrolyte solution. We then carry out Brownian dynamics simulations with our model to benchmark with well established theoretical results of a stretched polymer in solution. Finally, we employ our model to predict the relaxation time scale for single molecule experiments which sets the framework for future studies in which we plan to further shed light on the dynamics of DNA over long length and time scales.

Copyright © 2014 by ASME

Figures

Tables

Interactive Graphics

Video

Country-Specific Mortality and Growth Failure in Infancy and Yound Children and Association With Material Stature

Use interactive graphics and maps to view and sort country-specific infant and early dhildhood mortality and growth failure data and their association with maternal

NOTE:
Citing articles are presented as examples only. In non-demo SCM6 implementation, integration with CrossRef’s "Cited By" API will populate this tab (http://www.crossref.org/citedby.html).

Some tools below are only available to our subscribers or users with an online account.

Related Content

Customize your page view by dragging and repositioning the boxes below.

Related eBook Content
Topic Collections

Sorry! You do not have access to this content. For assistance or to subscribe, please contact us:

  • TELEPHONE: 1-800-843-2763 (Toll-free in the USA)
  • EMAIL: asmedigitalcollection@asme.org
Sign In