Date of Award

8-2014

Document Type

Thesis

Degree Name

Master of Science (MS)

Legacy Department

Physics and Astronomy

Advisor

Alexov, Emil

Committee Member

Ding , Feng

Committee Member

Sanabria , Hugo

Abstract

As researchers obtain access to greater and greater amounts of computational power, focus has shifted towards modeling macroscopic objects while still maintaining atomic-level details. The Protein Nano-Object Integrator (ProNOI) presented here has been designed to provide a streamlined solution for creating and designing macro-scale objects with atomic-level details to be used in molecular simulations and tools. To accomplish this, two different interfaces were developed: a Protein Data Bank (PDB), PDB-focused interface for generating regularly-shaped three-dimensional atomic objects and a 2D image-based interface for tracing images with irregularly shaped objects and then extracting three-dimensional models from these images. Each interface is dependent upon the C++ backend utility for generating the objects and ensures that the output is consistent across each program. The objects are exported in a standard PDB format which allows for the visualization and manipulation of the objects via standard tools available in Molecular Computational Biophysics.

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