Babi Baruani

Graduate Student

Chemistry Graduate Program

Major Professor: Dr. Wei Yang


Title: Uncovering the link between the motion of enzymes and their chemical transformations


Multiscale modeling in the simulation of macromolecules is a promising approach to tackle many of the remaining mysteries in the realm of enzyme kinetics. The fields of chemical kinetics and biochemistry have provided an array of tools for quantifying the rate and equilibrium constants for the processes that govern life. Unfortunately, the missing link between the structure and dynamic properties of biological macromolecules and their corresponding kinetic and thermodynamic parameters has yet to be unearthed. Quantum Mechanical / Molecular Mechanical Molecular Dynamics (QM/MM MD) simulations provide a detailed picture of chemical transformation, but with commonly accessible computing resources, it is challenging to achieve enzymatic timescales and capture the coupling between the chemical process and the enzymes’ slower conformational transitions. This work aims to extend the Orthogonal Space tempering scheme for GPU accelerated QM/MM simulations enable long timescale characterization of the chemical transformations mediated by CypA, KSI, and DHFR.


Malcolm McCray

Graduate Student

Chemistry Graduate Program

Major Professor: Dr. Brian Miller


Title: Polymerization as a form of Enzyme Regulation


Enzyme regulation in cells has been a large topic of interest throughout the biochemical community. It has been found that mutations in some enzymes can cause disease states and understanding these enzymes and their functions can lead to the creation of drugs inhibiting or activating them based on necessity; and hopefully relieving the aforementioned state. Recently, discoveries have been made that indicate the formation of multi-enzyme complexes and the use of aggregation into filaments or higher order structures as mechanisms for regulation of many different proteins. We have found evidence that eludes to Glucokinase (hexokinase IV) possessing the ability to form these filaments as a method of regulation and hence have conducted experiments in order to understand the size of these filaments and method by which these filaments form.