2013 New's Items

During transcription elongation, RNA polymerase has been assumed to attain equilibrium between pre- and post-translocated states rapidly relative to the subsequent catalysis. Under this assumption, recent single-molecule studies proposed a branched Brownian ratchet mechanism that necessitates a putative secondary nucleotide binding site on the enzyme. By challenging individual yeast RNA polymerase II with a nucleosomal barrier, we separately measured the forward and reverse translocation rates. Surprisingly, we found that the forward translocation rate is comparable to the catalysis...

We present time-dependent density functional theory (TDDFT) calculations for single and dimerized Coumarin-343 molecules to investigate the quantum mechanical effects of chromophore aggregation in extended systems designed to function as a new generation of sensors and light-harvesting devices. Using the single-chromophore results, we describe the construction of effective Hamiltonians to predict the excitonic properties of aggregate systems. We compare the electronic coupling properties predicted by such effective Hamiltonians to those obtained from TDDFT calculations of dimers and...

A semiconductor nanocrystal film is a unique class of nanocomposite, whose collective properties are determined by those of its constituents. Colloidal synthetic methods offer precise size control and finely tuned optical properties via quantum confinement, while recent improvements in charge transport through films have led to a variety of optoelectronic applications. However, understanding the role of defects and impurities in doping, crucial for optimizing device performance, has remained more elusive. In this perspective, we review recent progress in understanding and controlling...

At ambient conditions, water sits close to phase coexistence with its crystal. More so than in many other materials, this fact is manifested in the fluctuations that maintain a large degree of local order in the liquid. These fluctuations and how they result in long-ranged order, or its absence, are emergent features of many interacting molecules. Their study therefore requires using the tools of statistical mechanics for their their systematic understanding. In this dissertation we develop such an understanding. In particular, we focus on collective behavior that emerges in liquid...