Montana State University (MSU) Library in Bozeman Montana State University - Home Montana State University Libraries - Home
    • Login
    View Item 
    •   ScholarWorks Home
    • Scholarship & Research
    • Publications by Colleges and Departments (MSU- Bozeman)
    • College of Letters & Science
    • Mathematical Sciences
    • Scholarly Work - Mathematical Sciences
    • View Item
    •   ScholarWorks Home
    • Scholarship & Research
    • Publications by Colleges and Departments (MSU- Bozeman)
    • College of Letters & Science
    • Mathematical Sciences
    • Scholarly Work - Mathematical Sciences
    • View Item
    JavaScript is disabled for your browser. Some features of this site may not work without it.

    Discontinuous Galerkin calculations for a nonlinear PDE model of DNA transcription with short, transient and frequent pausing

    Thumbnail
    View/Open
    Postprint (8.183Mb)
    Date
    2014-09
    Author
    Davis, Lisa
    Gedeon, Tomáš
    Thorenson, Jennifer
    Metadata
    Show full item record
    Abstract
    A discontinuous Galerkin finite element method is used to approximate solutions to a classical traffic flow PDE. This PDE is used to model the biological process of transcription; the process of transferring genetic information from DNA either to mRNA or to rRNA. The transcription process is punctuated by short, frequent RNAP pauses which are incorporated into the model as traffic lights. These pauses cause a delay in the average transcription process. The DG solution of the nonlinear model is used to calculate the delay and to determine the effect of the pauses on the average transcription time. Numerical error measurements between the DG solution and the true solution (derived by the method of characteristics) are given for a simple model problem. It shows an excellent agreement in a neighborhood away from the shocks as well as O(Δx) convergence for the delay calculation. Preliminary parameter studies indicate that in a system with multiple pauses both the location and time duration of the pauses can significantly affect the average delay experienced by an RNAP.
    URI
    https://scholarworks.montana.edu/xmlui/handle/1/10007
    DOI
    10.4208/jcm.1405-m4370
    Citation
    L. Davis, T. Gedeon and J. Thorenson, Discontinuous Galerkin calculations for a nonlinear PDE model of DNA transcription with short, transient and frequent pausing, Journal of Computational Mathematics vol.32 (6), 2014, 601-629.
    Collections
    • Scholarly Work - Mathematical Sciences

    MSU uses DSpace software, copyright © 2002-2013  Duraspace
    Contact Us | Send Feedback
     

     

    Browse

    All of ScholarWorksCommunities & CollectionsBy Issue DateAuthorsTitlesDepartmentsItem TypeThis CollectionBy Issue DateAuthorsTitlesDepartmentsItem Type

    My Account

    Login

    Guidelines & Policies

    AllFor authorsWhy to submitHow to submit

    Statistics

    View Usage Statistics

    MSU uses DSpace software, copyright © 2002-2013  Duraspace
    Contact Us | Send Feedback