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    A recursive body-body formulation for reducing the computational cost of pairwise Coulomb force computation for modeling and simulation of biopolymers

    Author
    Laflin, Jeremy
    View/Open
    177230_Laflin_rpi_0185N_10490.pdf (1.006Mb)
    Other Contributors
    Anderson, Kurt S.; De, Suvranu; Picu, Catalin R.;
    Date Issued
    2016-05
    Subject
    Mechanical engineering
    Degree
    MS;
    Terms of Use
    This electronic version is a licensed copy owned by Rensselaer Polytechnic Institute, Troy, NY. Copyright of original work retained by author.;
    Metadata
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    URI
    https://hdl.handle.net/20.500.13015/1664
    Abstract
    This work presents a method for recursively assembling tensor-like quantities that parameterize the charge distribution of rigid bodies, which result from model reduction of biopolymeric systems using an articulated multibody approach. This is done with the goal of reducing the computational cost associated with the pairwise force determination encountered in molecular dynamics simulations. To achieve a linear computational cost complexity of the force determination, with respect to the number of bodies in the system (N), a recursive assembly and disassembly (evaluation) sweep is proposed. This work proposes assembling these tensor quantities (pseudo-inertia tensors), which are associated with the body's charge distribution, with a method that uses the standard parallel axis theorem to shift these tensors to a common point so they may be summed.; This work presents a preliminary numerical example that examines the accuracy of the force and moment computation using a pseudo-inertia tensor resulting after one level of recursive assembly. The Coulomb force and associated moment on a target body due to the assembled body is computed. The test problem approximates a system that is highly negatively or positively charged. The orientation of the bodies that are assembled is varied, along with the distance between the assembly and the target body. The preliminary results presented herein suggest that this is a viable method of efficiently representing the charge distribution of an assembly. The numerical example presented determines the Coulomb force and the associated moment, as a function of distance and the pseudo-inertia tensor.;
    Description
    May 2016; School of Engineering
    Department
    Dept. of Mechanical, Aerospace, and Nuclear Engineering;
    Publisher
    Rensselaer Polytechnic Institute, Troy, NY
    Relationships
    Rensselaer Theses and Dissertations Online Collection;
    Access
    Restricted to current Rensselaer faculty, staff and students. Access inquiries may be directed to the Rensselaer Libraries.;
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    • RPI Theses Online (Complete)

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