I finished my Ph.D. in Electrical Engineering at Ohio University in the spring of 2008 under the direction of Dr. Savas Kaya and the late Dr. Bob Rakowski. My dissertation research used molecular dynamic simulations investigated ion binding sites and ion transport properties of the Na⁺,K⁺-ATPase.

 

Please take a look at the methodology appendix of the dissertation if you are interested in details of how to set up and run molecular dynamics simulations (with GROMACS) of transmembrane proteins. It covers topics such as homology modelling, membrane insertion, etc. There are many scripts and examples for that as well as permeation pathway (CAVER) and electrostatic analysis using APBS. It's all the information that should be included in the "Methods" sections of papers. Please contact me if you have any questions.

 

I created this image of DNA using VMD for the Fall 2007 issue of Chicago Life magazine.

 

My Master's thesis was a simulation study of the effects of SiO₂ interface roughness in double-gate MOSFETs.