Date of Completion


Embargo Period



Zbigniew M. Bzymek; Horea T. IIies

Field of Study

Mechanical Engineering


Master of Science

Open Access

Open Access


Proteins are the building blocks of many living organisms and to study them is to discover many of nature’s processes. Abnormalities of these superb molecules make them also accountable for a wide range of human diseases. Every sixty seconds an American will be diagnosed with Alzheimer’s disease. The mystery behind this disease and many others might well be revealed by novel protein prediction techniques. This thesis investigates developments of two tools to benefit such techniques.

First, a user-friendly graphical interface (GUI) was developed based on a previously perfected program named ProtoFold. ProtoFold is a protein simulation software that examines the structural and nano-kinematic aspects of protein molecules. Prediction of Hydrogen bonds, mobility and rigidity analysis, and structural energy optimization are some of the capabilities of this graphical interface. The ongoing developments in the area of protein prediction pursued by a diverse community of researchers make modern graphical interfaces such as ProtoFold essential to exchange of information on this phenomenon. We used GUIDE Toolbox provided by MATLAB to design this interface.

Second, we suggested a technique to improve the process of capturing video of transitioning protein structures, which originally appeared chaotic. We used kinematic inversion, coordinate transformation, and displacement techniques to facilitate this process.

Major Advisor

Kazem Kazerounian