Bacteriophage T7 helicase/primase proteins form rings around single-stranded DNA that suggest a general structure for hexameric helicases.

Most helicases studied to date have been characterized as oligomeric, but the relation between their structure and function has not been understood. The bacteriophage T7 gene 4 helicase/primase proteins act in T7 DNA replication. We have used electron microscopy, three-dimensional reconstruction, and protein crosslinking to demonstrate that both proteins form hexameric rings around single-stranded DNA. Each subunit has two lobes, so the hexamer appears to be two-tiered, with a small ring stacked on a large ring. The single-stranded DNA passes through the central hole of the hexamer, and the data exclude substantial wrapping of the DNA about or within the protein ring. Further, the hexamer binds DNA with a defined polarity as the smaller ring of the hexamer points toward the 5' end of the DNA. The similarity in three-dimensional structure of the T7 gene 4 proteins to that of the Escherichia coli RuvB helicase suggests that polar rings assembled around DNA may be a general feature of numerous hexameric helicases involved in DNA replication, transcription, recombination, and repair.

Effective nonlinear model of resonant tunneling nanostructures

We introduce a model of a nonlinear double-barrier structure to describe in a simple way the effects of electron-electron scattering while remaining analytically tractable. The model is based on a generalized effective-mass equation where a nonlinear local field interaction is introduced to account for those inelastic scattering phenomena. Resonance peaks seen in the transmission coefficient spectra for the linear case appear shifted to higher energies depending on the magnitude of the nonlinear coupling. Our results are in good agreement with self-consistent solutions of the Schrodinger and Poisson equations. The calculation procedure is seen to be very fast, which makes our technique a good candidate for a rapid approximate analysis of these structures.

Erratum: Suppression of localization in kronig-penney models with correlated disorder (Vol. 49, PG 147, 1994)

We consider the electron dynamics and transport properties of one-dimensional continuous models with random, short-range correlated impurities. We develop a generalized Poincare map formalism to cast the Schrodinger equation for any potential into a discrete set of equations, illustrating its application by means of a specific example. We then concentrate on the case of a Kronig-Penney model with dimer impurities. The previous technique allows us to show that this model presents infinitely many resonances (zeroes of the reflection coefficient at a single dimer) that give rise to a band of extended states, in contradiction with the general viewpoint that all one-dimensional models with random potentials support only localized states. We report on exact transfer-matrix numerical calculations of the transmission coefFicient, density of states, and localization length for various strengths of disorder. The most important conclusion so obtained is that this kind of system has a very large number of extended states. Multifractal analysis of very long systems clearly demonstrates the extended character of such states in the thermodynamic limit. In closing, we brieBy discuss the relevance of these results in several physical contexts.

Single-exciton spectroscopy of single Mn doped InAs quantum dots

The optical spectroscopy of a single InAs quantum dot doped with a single Mn atom is studied using a model Hamiltonian that includes the exchange interactions between the spins of the quantum dot electron-hole pair, the Mn atom, and the acceptor hole. Our model permits linking the photoluminescence spectra to the Mn spin states after photon emission. We focus on the relation between the charge state of the Mn, A0 or A−, and the different spectra which result through either band-to-band or band-to-acceptor transitions. We consider both neutral and negatively charged dots. Our model is able to account for recent experimental results on single Mn doped InAs photoluminescence spectra and can be used to account for future experiments in GaAs quantum dots. Similarities and differences with the case of single Mn doped CdTe quantum dots are discussed.

Spin dynamics of current-driven single magnetic adatoms and molecules

A scanning tunneling microscope can probe the inelastic spin excitations of a single magnetic atom in a surface via spin-flip assisted tunneling in which transport electrons exchange spin and energy with the atomic spin. If the inelastic transport time, defined as the average time elapsed between two inelastic spin flip events, is shorter than the atom spin-relaxation time, the scanning tunnel microscope (STM) current can drive the spin out of equilibrium. Here we model this process using rate equations and a model Hamiltonian that describes successfully spin-flip-assisted tunneling experiments, including a single Mn atom, a Mn dimer, and Fe Phthalocyanine molecules. When the STM current is not spin polarized, the nonequilibrium spin dynamics of the magnetic atom results in nonmonotonic dI/dV curves. In the case of spin-polarized STM current, the spin orientation of the magnetic atom can be controlled parallel or antiparallel to the magnetic moment of the tip. Thus, spin-polarized STM tips can be used both to probe and to control the magnetic moment of a single atom.

Electrical control of a single Mn atom in a quantum dot

We report on the reversible electrical control of the magnetic properties of a single Mn atom in an individual quantum dot. Our device permits us to prepare the dot in states with three different electric charges, 0, +1e, and -1e which result in dramatically different spin properties, as revealed by photoluminescence. Whereas in the neutral configuration the quantum dot is paramagnetic, the electron-doped dot spin states are spin rotationally invariant and the hole-doped dot spins states are quantized along the growth direction.

Spin-transfer torque on a single magnetic adatom

We theoretically show how the spin orientation of a single magnetic adatom can be controlled by spin polarized electrons in a scanning tunneling microscope configuration. The underlying physical mechanism is spin assisted inelastic tunneling. By changing the direction of the applied current, the orientation of the magnetic adatom can be completely reversed on a time scale that ranges from a few nanoseconds to microseconds, depending on bias and temperature. The changes in the adatom magnetization direction are, in turn, reflected in the tunneling conductance.

Study of dopamine reactivity on platinum single crystal electrode surfaces

Dopamine is the biological molecule responsible, among other functions, of the heart beat and blood pressure regulation. Its loss, in the human body, can result in serious diseases such as Parkinson's, schizophrenia or depression. Structurally, this molecule belongs to the group of catecholamines, together with epinephrine (adrenaline) and norepinephrine (noradrenaline). The hydroquinone moiety of the molecule can be easily oxidized to quinone, rendering the electrochemical methods a convenient approach for the development of dopamine biosensors. The reactivity of similar aromatic molecules, such as catechol and hydroquinone, at well-ordered platinum surfaces, has recently been investigated in our group. In this paper, we extend these studies to the structurally related molecule dopamine. The study has been performed in neutral pH, since this is closer to the natural conditions for these molecules in biological media. Cyclic voltammetry and in situ infra-red spectroscopy have been combined to extract information about the behavior of this molecule on well-defined platinum surfaces. Dopamine appears to be electrochemically active and reveals interesting adsorption phenomena at low potentials (0.15–0.25 V vs RHE), sensitive to the single crystal orientation. The adsorption of dopamine on these surfaces is very strong, taking place at much lower potentials than the electron transfer from solution species. Specifically, the voltammetry of Pt(1 1 1) and Pt(1 0 0) in dopamine solutions shows an oxidation peak at potentials close to the onset of hydrogen evolution, which is related to the desorption of hydrogen and the adsorption of dopamine. On the other hand, adsorption on Pt(1 1 0) is irreversible and the surface appears totally blocked. Spectroscopic results indicate that dopamine is adsorbed flat on the surface. At potentials higher than 0.6 V vs RHE the three basal planes show a common redox process. The initial formation of the quinone moiety is followed by a chemical step resulting in the formation of 5,6-dihydroxyindoline quinone as final product. This oxidation process has also been investigated by vibrational spectroscopy.

Electrochemical behaviour of different redox probes on single wall carbon nanotube buckypaper-modified electrodes

In the present work, the electrochemical properties of single-walled carbon nanotube buckypapers (BPs) were examined in terms of carbon nanotubes nature and preparation conditions. The performance of the different free-standing single wall carbon nanotube sheets was evaluated via cyclic voltammetry of several redox probes in aqueous electrolyte. Significant differences are observed in the electron transfer kinetics of the buckypaper-modified electrodes for both the outer- and inner-sphere redox systems. These differences can be ascribed to the nature of the carbon nanotubes (nanotube diameter, chirality and aspect ratio), surface oxidation degree and type of functionalities. In the case of dopamine, ferrocene/ferrocenium, and quinone/hydroquinone redox systems the voltammetric response should be thought as a complex contribution of different tips and sidewall domains which act as mediators for the electron transfer between the adsorbate species and the molecules in solution. In the other redox systems only nanotube ends are active sites for the electron transfer. It is also interesting to point out that a higher electroactive surface area not always lead to an improvement in the electron transfer rate of various redox systems. In addition, the current densities produced by the redox reactions studied here are high enough to ensure a proper electrochemical signal, which enables the use of BPs in sensing devices.

From community approaches to single-cell genomics: the discovery of ubiquitous hyperhalophilic Bacteroidetes generalists

The microbiota of multi-pond solar salterns around the world has been analyzed using a variety of culture-dependent and molecular techniques. However, studies addressing the dynamic nature of these systems are very scarce. Here we have characterized the temporal variation during 1 year of the microbiota of five ponds with increasing salinity (from 18% to >40%), by means of CARD-FISH and DGGE. Microbial community structure was statistically correlated with several environmental parameters, including ionic composition and meteorological factors, indicating that the microbial community was dynamic as specific phylotypes appeared only at certain times of the year. In addition to total salinity, microbial composition was strongly influenced by temperature and specific ionic composition. Remarkably, DGGE analyses unveiled the presence of most phylotypes previously detected in hypersaline systems using metagenomics and other molecular techniques, such as the very abundant Haloquadratum and Salinibacter representatives or the recently described low GC Actinobacteria and Nanohaloarchaeota. In addition, an uncultured group of Bacteroidetes was present along the whole range of salinity. Database searches indicated a previously unrecognized widespread distribution of this phylotype. Single-cell genome analysis of five members of this group suggested a set of metabolic characteristics that could provide competitive advantages in hypersaline environments, such as polymer degradation capabilities, the presence of retinal-binding light-activated proton pumps and arsenate reduction potential. In addition, the fairly high metagenomic fragment recruitment obtained for these single cells in both the intermediate and hypersaline ponds further confirm the DGGE data and point to the generalist lifestyle of this new Bacteroidetes group.

Controlled Complete Suppression of Single-Atom Inelastic Spin and Orbital Cotunneling

The inelastic portion of the tunnel current through an individual magnetic atom grants unique access to read out and change the atom’s spin state, but it also provides a path for spontaneous relaxation and decoherence. Controlled closure of the inelastic channel would allow for the latter to be switched off at will, paving the way to coherent spin manipulation in single atoms. Here, we demonstrate complete closure of the inelastic channels for both spin and orbital transitions due to a controlled geometric modification of the atom’s environment, using scanning tunneling microscopy (STM). The observed suppression of the excitation signal, which occurs for Co atoms assembled into chains on a Cu2N substrate, indicates a structural transition affecting the dz2 orbital, effectively cutting off the STM tip from the spin-flip cotunneling path.

Tackling barriers to trade in the Single Market. ACES Cases No. 2014.2

This paper focuses on the challenges operating in the single market due to continued persistence of regulatory barriers to trade, despite being considered one of the most integrated and successful areas of market integration. We use a unique data set on infringements to the free movement of goods to assess the types of barriers that firms encounter, their impact and variation across states and sectors, and their resolution method - through Court decisions or the pre-litigation, administrative means available within the infringement proceedings mechanism to restore compliance. We also resort to the Solvit dataset provided to the authors by the Commission to analyse some features and the effectiveness of this informal mechanism in dealing with discriminatory domestic trade and regulatory practices. We examine four key questions: What are the most problematic policy areas in terms of barriers to trade that undermine the single market? What different dispute resolution mechanisms are utilized to address trade barriers and thus improve the functioning of the single market? Under what conditions are different enforcement mechanisms and strategies more likely to be used to resolve barriers for businesses operating in the single market? How important and effective are the more informal strategies in improving market access? In doing so, our goal is to link the research on trade barriers to that of implementation and compliance to assess the diverse strategies undertaken to reduce regulatory barriers to trade.

Petrophysical measurement of ODP Leg 122 and 123 samples (Tables 1, 2)

The capillary-pressure characteristics of 22 samples of lithified post-Paleozoic Indian-Ocean carbonates were compared to published data from older carbonate rocks (lower Paleozoic Hunton Group of Texas and Oklahoma). The Indian-Ocean samples are considerably more porous than are the Paleozoic samples, yet all of the Indian-Ocean samples fit readily into a descriptive petrofacies scheme previously established for the Hunton Group. The Indian-Ocean samples may be assigned to four petrophysical facies (petrofacies) based on the shapes of their capillary-pressure curves, their pore-throat-size distributions, their estimated recovery efficiency values (for nonwetting fluids), and the visual characteristics of their pore systems, as observed with a scanning-electron microscope. Petrofacies assignments for the Indian-Ocean samples are as follows. Petrofacies I includes six samples collected from the coarse basal portions of event deposits (primarily turbidites). These samples have large throats, leptokurtic throat-size distributions, low- to moderate recovery efficiency values, concave cumulative-intrusion capillary-pressure curves, and high porosity values. Petrofacies II includes two sedimentologically dissimilar samples that have medium-size throats, platykurtic throat-size distributions, moderate- to-high recovery efficiency values, gently sloping cumulative-intrusion capillary-pressure curves, and high porosity values. Petrofacies III includes two polymictic sandstones and a skeletal packstone that have small throats, polymodal throat-size distributions, moderate recovery efficiency values, gently sloping cumulative-intrusion capillary-pressure curves, and high porosity values. Petrofacies IV includes 11 samples, mostly recrystallized neritic carbonates, that have small throats, leptokurtic throat-size distributions, high recovery efficiency values, convex cumulative-intrusion capillary-pressure curves, and low porosity values. Comparison of petrofacies assignment to core-, thin-section-, and smear-slide data, and to inferred depositional setting, suggests that pore systems in most samples from Holes 765C and 766A result from primary depositional features, whereas pore systems in samples from Hole 761C and one sample from Hole 765C have been strongly influenced by diagenetic processes. For Hole 761C, prediction of petrophysical parameters should be most successful if based on diagenetic facies patterns. By contrast, the distribution of favorable reservoir facies and of permeability barriers in less highly altered rocks collected from Holes 765C and 766A is related to depositional patterns. Recovery efficiency is inversely related to both porosity and median throat size for the present data set. This relationship is similar to that observed for carbonates of the lower Paleozoic Hunton Group and the Ordovician Ellenburger dolomite, but opposite of that observed for some other ancient carbonates. The coarse deposits of the massive basal units of turbidites are petrophysically distinct and form a coherent petrophysical group (Petrofacies I) with substantial reservoir potential. Two samples assigned to Petrofacies I have extremely large throats (median throat size at least 4 ?m, and at least six times that of any other sample) and therefore high permeability values. These two samples come from thin, coarse turbidites that lack or have poorly developed fine divisions and are interpreted to have been deposited on channeled suprafan lobes in a proximal mid-fan setting. The restriction of extremely high permeability values to a single depositional facies suggests that careful facies mapping of deep-sea fans in a deliberate search for such coarse turbidites could dramatically enhance the success of exploration for aquifers or hydrocarbon reservoirs. Such reservoirs should have substantial vertical heterogeneity. They should have high lateral permeability values but low vertical permeability values, and reservoir sections should include numerous thin units having widely differing petrophysical characteristics.

Statistical Hurdle Models for Single Cell Gene Expression: Differential Expression and Graphical Modeling

Thesis (Ph.D.)--University of Washington, 2016-06

The electric field effect on spin injection in tunneling regime

Using the quantum tunneling theory, we investigate the spin-dependent transport properties of the ferromagnetic metal/Schottky barrier/semiconductor heterojunction under the influence of an external electric field. It is shown that increasing the electric field, similar to increasing the electron density in semiconductor, will result in a slight enhancement of spin injection in tunneling regime, and this enhancement is significantly weakened when the tunneling Schottky barrier becomes stronger. Temperature effect on spin injection is also discussed. (C) 2003 Elsevier B.V. All rights reserved.