Molecular Model Development for Implantable Artificial Kidney Design
Advisor:Conlisk, A. Terrence
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Publisher:The Ohio State University
Series/Report no.:The Ohio State University. Department of Mechanical Engineering Honors Theses; 2009
An artificially implantable renal assistive device (RAD) is under development as an in vivo clinical solution to end stage renal disease, a condition which affects millions of people worldwide. The RAD, employing a synthetic silica membrane with slit-shaped nanopores, will be designed to partially replace the functions of a native biological kidney. This study is principally concerned with the design of the RAD’s nanopore ultrafiltration membrane. The width of the nanopores in question is in the range of 10 nanometers. This length scale is below the resolution of current experimental fluid flow measurement techniques, and theoretical continuum approximations, which hold in macroscale fluid mechanics models, cannot resolve the detailed structure of biomolecules which is useful for ultrafiltration design. Therefore, this study focuses on the development of computational molecular dynamics (MD) models, which are valid at this length scale, using GROMACS. This thesis presents the development of computational a MD model in several levels. First, the albumin structure was derived from an experimental result taken from the Protein Data Bank and simulated without flow. This MD model is currently being developed to model the transport of albumin through a rectangular silica nanopore. Electrostatic calculations are performed to determine the preliminary interaction between albumin and the silica walls of the RAD. Because MD models require excessive computational time, their primary function is to discover and understand new molecular-scale phenomena and parameters which can be incorporated into less computationally intensive continuum models to complete the RAD design. MD is a new technique to my engineering lab, and thus one aspect of this study is the creation of a working manual which can serve as an internal teaching tool in the future.
1st Place in Engineering at 2009 Denman Undergraduate Research Forum
The Ohio State University College of Engineering Honors Undergraduate Scholarship.