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    Developing A Bitwise Macromolecular Assembly Simulator

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    Xu_ku_0099M_13520_DATA_1.pdf (702.0Kb)
    Issue Date
    2014-08-31
    Author
    Xu, Zaikun
    Publisher
    University of Kansas
    Format
    25 pages
    Type
    Thesis
    Degree Level
    M.A.
    Discipline
    Molecular Biosciences
    Rights
    This item is protected by copyright and unless otherwise specified the copyright of this thesis/dissertation is held by the author.
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    Abstract
    Macromolecular machines play fundamental roles in many cellular tasks, from intracellular transport to protein synthesis and degradation. The majority of these machines must adopt a particular quaternary structure in order to function, and so understanding their assembly represents a critical component of our understanding of overall cellular physiology. Developing a theoretical and conceptual understanding of assembly has been hampered by the lack of general, efficient and scalable computational tools for simulating assembly processes. In this work, we develop a new framework that employs a bitwise representation of assembly intermediates. Using this framework, we have implemented a Bitwise Macromolecular Assembly Simulator (BMAS). This software leverages our binary representation of intermediates to perform most crucial computational steps using bitwise operators. This allows us to perform highly efficient Gillespie-style stochastic simulations of macromolecular assembly, resulting in a general simulation approach that is orders of magnitude faster than existing methods. Our approach is efficient enough to study of a wide variety of macromolecular machines, in addition to providing a tool that should assist in the design of novel self-assembling nanomaterials.
    URI
    http://hdl.handle.net/1808/16809
    Collections
    • Molecular Biosciences Dissertations and Theses [270]
    • Theses [3772]

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    785-864-8983

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    Contact KU ScholarWorks
    785-864-8983
    KU Libraries
    1425 Jayhawk Blvd
    Lawrence, KS 66045
    785-864-8983

    KU Libraries
    1425 Jayhawk Blvd
    Lawrence, KS 66045
    Image Credits
     

     

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