Kateri H. DuBay

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Allosteric regulation is a key component of cellular communication, but the way in which information is passed from one site to another within a folded protein is not often clear. While backbone motions have long been considered essential for long-range information conveyance, side-chain motions have rarely been considered. In this work, we demonstrate(More)
Despite the high density within a typical protein fold, the ensemble of sterically permissible side-chain repackings is vast. Here, we examine the extent of this variability that survives energetic biases due to van der Waals interactions, hydrogen bonding, salt bridges, and solvation. Monte Carlo simulations of an atomistic model exhibit thermal(More)
Folded protein structures are both stable and dynamic. Historically, our clearest window into these structures came from X-ray crystallography, which generally provided a static image of each protein's singular "folded state", highlighting its stability. Deviations away from that crystallographic structure were difficult to quantify, and as a result, their(More)
The Horner method was used to synthesize random copolymers of poly(2-methoxy-5-(2'-ethylhexyloxy)-p-phenylene vinylene) (MEH-PPV) that incorporated different backbone-directing monomers. Single-molecule polarization absorption studies of these new polymers demonstrate that defects that preserve the linear backbone of PPV-type polymers assume the highly(More)
We have measured the single-molecule conductance of a family of bithiophene derivatives terminated with methyl sulfide gold-binding linkers using a scanning tunneling microscope based break-junction technique. We find a broad distribution in the single-molecule conductance of bithiophene compared with that of a methyl sulfide terminated biphenyl. Using a(More)
Raman spectra were recorded experimentally and calculated theoretically for bithiophene, terthiophene, and quaterthiophene samples as a function of excitation polarization. Distinct spectral signatures were assigned and correlated to the molecular/unit cell orientation as determined by X-ray diffraction. The ability to predict molecular/unit cell(More)
The modeling of the conformational properties of conjugated polymers entails a unique challenge for classical force fields. Conjugation imposes strong constraints upon bond rotation. Planar configurations are favored, but the concomitantly shortened bond lengths result in moieties being brought into closer proximity than usual. The ensuing steric repulsions(More)
Previous methods for determining whether a uniform region of a sample is crystalline or isotropic-what we call the "state of internal orientation" S-require a priori knowledge of properties of the purely crystalline and purely isotropic states. In addition, these methods can be ambiguous in their determination of state S for particular materials and, for a(More)
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