I became interested in biomolecular simulation when I began undergraduate research in the lab of Dr. David Bevan at Virginia Tech. I had been exposed to computers at a young age, and the thought of combining high-performance computing and biochemistry was a perfect fit. During my time as an undergraduate researcher, I spent time working on a number of projects that involved simulations of proteins, DNA, and membranes.
Broadly speaking, I am interested in applying molecular modeling and simulation methods to systems of biological interest. Simulations can provide insight into many molecular phenomena, such as protein structure-function relationships, catalysis, protein folding/misfolding and aggregation, and drug development. In concert with experimental methods, simulations can provide details necessary for explaining processes that are essential to life and the amelioration of disease.
Alzheimer's Disease and the Amyloid β-Peptide. The project that I worked on during my senior year of undergraduate work became the basis for my Ph.D. dissertation. As an outgrowth of my interest in protein structure-function relationships, I became interested in understanding the pathological misfolding and aggregation of Aβ. This project took me in many new directions, including studying interactions between Aβ and membranes, proteins, and small molecules. My work with Aβ-flavonoid interactions exposed me to the fields of free energy calculations and force field development, an experience that has driven much of my recent work.
Macromolecular Structure-Function Relationships. A central tenet of biology is that function arises from structure. The dynamic nature of macromolecules such as proteins, DNA, and RNA gives rise to cellular processes that are vital to life. Simulations can provide detailed information regarding the folding of these macromolecules and the functionally relevant conformations they sample in vivo. For some time, I have been interested in the connection between macromolecular dynamics and how they relate to (dys)function.
Force Field Development. The quality of a simulation derives from the underlying force field, the potential energy equation and the parameters applied to the molecules in the system. In order to gain useful insight into molecular processes and to further drug design, accurate force fields are required. My current work focuses on refinement and expansion of the Drude polarizable force field, which uses the Drude oscillator model to explicitly account for electronic polarizability of each heavy atom. We hope that this work will further our understanding of biomolecular dynamics and interactions of drug molecules with their target receptors.
Copyright 2013-2016 by Justin Lemkul