Single-molecule microscopy reveals new insights into nucleotide selection by DNA polymerase I.

The mechanism by which DNA polymerases achieve their extraordinary accuracy has been intensely studied because of the linkage between this process and mutagenesis and carcinogenesis. Here, we have used single-molecule fluorescence microscopy to study the process of nucleotide selection and exonuclease action. Our results show that the binding of Escherichia coli DNA polymerase I (Klenow fragment) to a primer-template is stabilized by the presence of the next correct dNTP, even in the presence of a large excess of the other dNTPs and rNTPs. These results are consistent with a model where nucleotide selection occurs in the open complex prior to the formation of a closed ternary complex. Our assay can also distinguish between primer binding to the polymerase or exonuclease domain and, contrary to ensemble-averaged studies, we find that stable exonuclease binding only occurs with a mismatched primer terminus

BCS-Universal Ratios within the Van Hove Scenario

The central result of BCS theory are the Universal Ratios which do not depend on physical parameters of the superconductor under study. Several attempts have been made to introduce the van Hove Scenario within BCS theory but in none of them the Universal Ratios of conventional superconductivity appear to be a number independent of parameters. This fact prevents the precise definition of a deviation from the BCS value for a particular superconductor. This concept is at the basis of several applications of BCS theory in characterizing conventional superconductors. We define a system that constitutes a weak coupling limit that retains the essential features of the high-Tc oxides and which does not differ in any essential way from other models widely used in generalizations of BCS theory to high-Tc superconductors. The difference is that we found a natural way of dealing with the mathematics of the problem so as to get Universal Ratios in the same sense as in conventional superconductivity.Comment: 11 PAGES, NO FIGURES, REVTEX 3.

Crossover from inelastic magnetic scattering of Cooper pairs to spin-wave dispersion produces low-energy kink in cuprates

We present GW based self-energy calculations for the state of coexisting spin-density wave and d-wave superconductivity in a series of cuprate superconductors. In these systems, the spin resonance spectrum exhibits the typical `hour-glass' form, whose upward and downward dispersion branches come from the gapped spin-wave and magnetic scattering of Cooper pairs, respectively. We show that the crossover between these two different dispersion features leads to an abrupt change in slope in the quasiparticle self-energy, and hence the low-energy kink commences in the single-particle quasiparticle spectrum. The calculated electron-bosonic coupling strength agrees well with experimental data as a function of temperature, doping and material. The results demonstrate that the electronic correlations dominate the quasiparticle spectra of cuprates near the low-energy kink, suggesting a relatively smaller role for phonons in this energy range.Comment: 8 pages, 6 figures. revised version submitted to PR

The International Linear Collider beam dumps

The ILC beam dumps are a key part of the accelerator design. At Snowmass 2005, the current status of the beam dump designs were reviewed, and the options for the overall dump layout considered. This paper describes the available dump options for the baseline and the alternatives and considers issues for the dumps that require resolution.Comment: Prepared for 2005 International Linear Collider Physics and Detector Workshop and 2nd ILC Accelerator Workshop, Snowmass, Colorado, 14-27 Aug 200

Bridging k- and q- Space in the Cuprates: Comparing ARPES and STM Results

A critical comparison is made between the ARPES-derived spectral function and STM studies of Friedel-like oscillations in Bi_2Sr_2CaCu_2O_{8+delta} (Bi2212). The data can be made approximately consistent, provided that (a) the elastic scattering seen in ARPES is predominantly small-angle scattering and (b) the `peak' feature seen in ARPES is really a dispersive `bright spot', smeared into a line by limited energy resolution; these are the `bright spots' which control the quasiparticle interferences. However, there is no indication of bilayer splitting in the STM data.Comment: 6 eps figures, revte

Pinned Balseiro-Falicov Model of Tunneling and Photoemission in the Cuprates

The smooth evolution of the tunneling gap of Bi_2Sr_2CaCu_2O_8 with doping from a pseudogap state in the underdoped cuprates to a superconducting state at optimal and overdoping, has been interpreted as evidence that the pseudogap must be due to precursor pairing. We suggest an alternative explanation, that the smoothness reflects a hidden SO(N) symmetry near the (pi,0) points of the Brillouin zone (with N = 3, 4, 5, or 6). Because of this symmetry, the pseudogap could actually be due to any of a number of nesting instabilities, including charge or spin density waves or more exotic phases. We present a detailed analysis of this competition for one particular model: the pinned Balseiro-Falicov model of competing charge density wave and (s-wave) superconductivity. We show that most of the anomalous features of both tunneling and photoemission follow naturally from the model, including the smooth crossover, the general shape of the pseudogap phase diagram, the shrinking Fermi surface of the pseudogap phase, and the asymmetry of the tunneling gap away from optimal doping. Below T_c, the sharp peak at Delta_1 and the dip seen in the tunneling and photoemission near 2Delta_1 cannot be described in detail by this model, but we suggest a simple generalization to account for inhomogeneity, which does provide an adequate description. We show that it should be possible, with a combination of photoemission and tunneling, to demonstrate the extent of pinning of the Fermi level to the Van Hove singularity. A preliminary analysis of the data suggests pinning in the underdoped, but not in the overdoped regime.Comment: 18 pages LaTeX, 26 ps. figure

Limb imaging of the Venus O2 visible nightglow with the Venus Monitoring Camera

We investigated the Venus O2 visible nightglow with imagery from the Venus Monitoring Camera on Venus Express. Drawing from data collected between April 2007 and January 2011, we study the global distribution of this emission, discovered in the late 70s by the Venera 9 and 10 missions. The inferred limb-viewing intensities are on the order of 150 kiloRayleighs at the lower latitudes and seem to drop somewhat towards the poles. The emission is generally stable, although there are episodes when the intensities rise up to 500 kR. We compare a set of Venus Monitoring Camera observations with coincident measurements of the O2 nightglow at 1.27 {\mu}m made with the Visible and Infrared Thermal Imaging Spectrometer, also on Venus Express. From the evidence gathered in this and past works, we suggest a direct correlation between the instantaneous emissions from the two O2 nightglow systems. Possible implications regarding the uncertain origin of the atomic oxygen green line at 557.7 nm are noted.Comment: 7 pages, 3 figure

Carcinogenic adducts induce distinct DNA polymerase binding orientations

DNA polymerases must accurately replicate DNA to maintain genome integrity. Carcinogenic adducts, such as 2-aminofluorene (AF) and N-acetyl-2-aminofluorene (AAF), covalently bind DNA bases and promote mutagenesis near the adduct site. The mechanism by which carcinogenic adducts inhibit DNA synthesis and cause mutagenesis remains unclear. Here, we measure interactions between a DNA polymerase and carcinogenic DNA adducts in real-time by single-molecule fluorescence. We find the degree to which an adduct affects polymerase binding to the DNA depends on the adduct location with respect to the primer terminus, the adduct structure and the nucleotides present in the solution. Not only do the adducts influence the polymerase dwell time on the DNA but also its binding position and orientation. Finally, we have directly observed an adduct- and mismatch-induced intermediate state, which may be an obligatory step in the DNA polymerase proofreading mechanism

Does competition reduce costs? : assessing the impact of regulatory restructuring on U.S. electric generation efficiency

Although the allocative efficiency benefits of competition are a tenet of microeconomic theory, the relation between competition and technical efficiency is less well understood. Neoclassical models of profit-maximization subsume static cost-minimizing behavior regardless of market competitiveness, but agency models of managerial behavior suggest possible scope for competition to influence cost-reducing effort choices. This paper explores the empirical effects of competition on technical efficiency in the context of electricity industry restructuring. Restructuring programs adopted by many U.S. states made utilities residual claimants to cost savings and increased their exposure to competitive markets. We estimate the impact of these changes on annual generating plant-level input demand for non-fuel operating expenses, the number of employees and fuel use. We find that municipally-owned plants, whose owners were for the most part unaffected by restructuring, experienced the smallest efficiency gains over the past decade. Investor-owned utility plants in states that restructured their wholesale electricity markets had the largest reductions in nonfuel operating expenses and employment, while investor-owned plants in nonrestructuring states fell between these extremes. The analysis also highlights the substantive importance of treating the simultaneity of input and output decisions, which we do through an instrumental variables approach