The Van Orden Group

The goal of this project is to develop a comprehensive reaction rate model for the formation of secondary and tertiary structure in RNA. We will use fluorescence correlation spectroscopy and related techniques to measure the rate constants and reaction intermediates of RNA hairpin formation. By varying the temperature, solvent conditions, and RNA sequences, we will uncover clues about the rate model governing the reaction. We will then compare our experimental observations with statistical mechanical models developed by our collaborators. Through close cooperation between experimental and theoretical scientists, we will develop refined theoretical models that can predict the folding kinetics of any given RNA sequence. Ultimately these studies will enable quantitative predictions about the myriad roles RNA plays in the biological cell, including chemical modification, gene regulation, and intermolecular interactions.

This project investigates the electronic interactions between quantum dots in closed-packed clusters, films, and solids. Such interactions are important in devices that use quantum dots as light absorbers and emitters, such as solar cells and biological labels. For example, quantum dot-based solar cells have shown promise because the quantum dots can absorb a broad spectrum of sunlight and generate charge carriers that can produce solar electricity. However, gaps in our understanding of the electronic coupling between quantum dots hinder the development of practical solar cells based on these materials. Using spatially correlated single molecule fluorescence spectroscopy and atomic force microscopy, we are studying the fluorescence dynamics of individual quantum dot clusters as a function of cluster size. Electronic coupling between the quantum dots alters the lifetimes, emission spectra, and blinking behavior of the fluorescence. By characterizing these effects at the single species level, we will uncover the kinetics and mechanisms for this coupling. We will also develop the means to control this coupling in the development of third-generation solar cells and new biological sensing devices.

This project investigates the kinetics of chemical and biological reactions under molecularly constrained conditions. One aspect of this project studies fluorescent dye molecules trapped in reverse micelles as model confined systems. Dynamic properties of the dyes, such as isomerization, protonation-deprotonation, and aggregation are characterized in bulk samples and in reverse micelles. It is found that the confined environment of the reverse micelles dramatically alters the dynamics of these processes. By characterizing these changes, we hope to gain basic insight into the role of confinement on a variety of important chemical processes. Another aspect of this project studies the motion and aggregation behavior of cell surface receptors confined to sub-micron regions of a cell surface due to substrate-receptor interactions.