Correlated electron transport in molecular electronics

Theoretical and experimental values to date for the resistances of single molecules commonly disagree by orders of magnitude. By reformulating the transport problem using boundary conditions suitable for correlated many-electron systems, we approach electron transport across molecules from a new standpoint. Application of our correlated formalism to benzene-dithiol gives current-voltage characteristics close to experimental observations. The method can solve the open system quantum many-body problem accurately, treats spin exactly, and is valid beyond the linear response regime.

Correlated electron-ion dynamics with open boundaries: formalism

We extend a new formalism, which allows correlated electron-ion dynamics to be applied to the problem of open boundary conditions. We implement this at the first moment level (allowing heating of ions by electrons) and observe the expected cooling in the classical part of the ionic kinetic energy and current-induced heating in the quantum contribution. The formalism for open boundaries should be easily extended to higher moments of the correlated electron-ion fluctuations.

Correlated electron-ion dynamics: the excitation of atomic motion by energetic electrons

Correlated electron-ion dynamics (CEID) is an extension of molecular dynamics that allows us to introduce in a correct manner the exchange of energy between electrons and ions. The formalism is based on a systematic approximation: small amplitude moment expansion. This formalism is extended here to include the explicit quantum spread of the ions and a generalization of the Hartree-Fock approximation for incoherent sums of Slater determinants. We demonstrate that the resultant dynamical equations reproduce analytically the selection rules for inelastic electron-phonon scattering from perturbation theory, which control the mutually driven excitations of the two interacting subsystems. We then use CEID to make direct numerical simulations of inelastic current-voltage spectroscopy in atomic wires, and to exhibit the crossover from ionic cooling to heating as a function of the relative degree of excitation of the electronic and ionic subsystems.

Beyond Ehrenfest: correlated non-adiabatic molecular dynamics

A method for introducing correlations between electrons and ions that is computationally affordable is described. The central assumption is that the ionic wavefunctions are narrow, which makes possible a moment expansion for the full density matrix. To make the problem tractable we reduce the remaining many-electron problem to a single-electron problem by performing a trace over all electronic degrees of freedom except one. This introduces both one- and two-electron quantities into the equations of motion. Quantities depending on more than one electron are removed by making a Hartree-Fock approximation. Using the first-moment approximation, we perform a number of tight binding simulations of the effect of an electric current on a mobile atom. The classical contribution to the ionic kinetic energy exhibits cooling and is independent of the bias. The quantum contribution exhibits strong heating, with the heating rate proportional to the bias. However, increased scattering of electrons with increasing ionic kinetic energy is not observed. This effect requires the introduction of the second moment.

Resting and daily energy expenditures of free-living field voles are positively correlated but reflect extrinsic rather than intrinsic effects

Resting metabolic rates at thermoneutral (RMRts) are unexpectedly variable. One explanation is that high RMRts intrinsically potentiate a greater total daily energy expenditure (DEE), but recent work has suggested that DEE is extrinsically defined by the environment, which independently affects RMRt. This extrinsic effect could occur because expenditure is forced upwards in poor habitats or enabled to rise in good habitats. We provide here an intraspecific test for an association between RMRt and DEE that separates intrinsic from extrinsic effects and forcing from enabling effects. We measured the DEE and RMRt of 75 free-living short-tailed field voles at two time points in late winter. Across all sites, there was a positive link between individual variation in RMRt and DEE. This correlation, however, emerged only because of an effect across sites, rather than because of an intrinsic association within sites. We defined site quality from the survivorship of voles at the sites and the time at which they commenced breeding in spring. The associations between DEE/RMRt and site quality suggested that in February voles in poorer sites had higher energy demands, indicating that DEE was forced upwards, but in March the opposite was true, with higher demands in good sites, indicating that high expenditure was enabled. These data show that daily energy demands are extrinsically defined, with a link to RMRt that is secondary or independent. Both forcing and enabling effects of the environment may pertain at different times of year.

Mutations affecting the Rossman fold of isoleucyl-tRNA synthetase are correlated with low-level mupirocin resistance in Staphylococcus aureus.

The isoleucyl-tRNA synthetase (ileS) gene was sequenced in toto from 9 and in part from 31 Staphylococcus aureus strains with various degrees of susceptibility to mupirocin. All strains for which the mupirocin MIC was greater than 8 µg/ml contained point mutations affecting the Rossman fold via Val-to-Phe changes at either residue 588 (V588F) or residue 631 (V631F). The importance of the V588F mutation was confirmed by an allele-specific PCR survey of 32 additional strains. Additional mutations of uncertain significance were found in residues clustered on the surface of the IleS protein.

Seasonal variations in nitrate reductase activity and internal N pools in intertidal brown algae are correlated with ambient nitrate concentrations.

Nitrogen metabolism was examined in the intertidal seaweeds Fucus vesiculosus, Fucus serratus, Fucus spiralis and Laminaria digitata in a temperate Irish sea lough. Internal NO3- storage, total N content and nitrate reductase activity (NRA) were most affected by ambient NO3-, with highest values in winter, when ambient NO3- was maximum, and declined with NO3- during summer. In all species, NRA was six times higher in winter than in summer, and was markedly higher in Fucus species (e.g. 256 ± 33 nmol NO3- min1 g1 in F. vesiculosus versus 55 ± 17 nmol NO3- min1 g1 in L. digitata). Temperature and light were less important factors for N metabolism, but influenced in situ photosynthesis and respiration rates. NO3- assimilating capacity (calculated from NRA) exceeded N demand (calculated from net photosynthesis rates and C : N ratios) by a factor of 0.7–50.0, yet seaweeds stored significant NO3- (up to 40–86 µmol g1). C : N ratio also increased with height in the intertidal zone (lowest in L. digitata and highest in F. spiralis), indicating that tidal emersion also significantly constrained N metabolism. These results suggest that, in contrast to the tight relationship between N and C metabolism in many microalgae, N and C metabolism could be uncoupled in marine macroalgae, which might be an important adaptation to the intertidal environment.

Spatially Correlated Multiple-Ananna Channel Capacity Distributions

In this paper, we investigate the capacity of multiple-input multiple-output (MIMO) wireless communication systems over spatially correlated Rayleigh distributed flat fading channels with complex Gaussian additive noise. Specifically, we derive the probability density function of the mutual information between transmitted and received complex signals of MIMO systems. Using this density we derive the closed-form ergodic capacity (mean), delay-limited capacity, capacity variance and outage capacity formulas for spatially correlated channels and then evaluate these formulas numerically. Numerical results show how the channel correlation degrades the capacity of MIMO communication systems. We also show that the density of mutual information of correlated/uncorrelated MIMO systems can be approximated by a Gaussian density with derived mean and variance, even for a finite number of inputs and outputs.

Comment on "correlated noise in a logistic growth model"

We argue the results published by Bao-Quan Ai et al [Phys. Rev E 67, 022903 (2003)] on "correlated noise in a logistic growth model " are not correct. Their conclusion that for larger values of the correlation parameter, lambda, the cell population is peaked at x=0, which denotes the high extinction rate is also incorrect. We find the reverse behaviour corresponding to their results, that increasing lambda, promotes the stable growth of tumour cells. In particular, their results for steady-state probability, as a function of cell number, at different correlation strengths, presented in figures 1 and 2 show different behaviour than one would expect from the simple mathematical expression for the steady-state probability. Additionally, their interpretation at small values of cell number that the steady state probability increases as they increase the correlation parameter is also questionable. Another striking feature in their figures (1 and 3) is that for the same values of the parameter lambda and alpha, their simulation produces two different curves both qualitatively and quantitatively.

A complex zinc finger controls the enzymatic activities of nidovirus helicases.

Nidoviruses (Coronaviridae, Arteriviridae, and Roniviridae) encode a nonstructural protein, called nsp10 in arteriviruses and nsp13 in coronaviruses, that is comprised of a C-terminal superfamily 1 helicase domain and an N-terminal, putative zinc-binding domain (ZBD). Previously, mutations in the equine arteritis virus (EAV) nsp10 ZBD were shown to block arterivirus reproduction by disrupting RNA synthesis and possibly virion biogenesis. Here, we characterized the ATPase and helicase activities of bacterially expressed mutant forms of nsp10 and its human coronavirus 229E ortholog, nsp13, and correlated these in vitro activities with specific virus phenotypes. Replacement of conserved Cys or His residues with Ala proved to be more deleterious than Cys-for-His or His-for-Cys replacements. Furthermore, denaturation-renaturation experiments revealed that, during protein refolding, Zn2+ is essential for the rescue of the enzymatic activities of nidovirus helicases. Taken together, the data strongly support the zinc-binding function of the N-terminal domain of nidovirus helicases. nsp10 ATPase/helicase deficiency resulting from single-residue substitutions in the ZBD or deletion of the entire domain could not be complemented in trans by wild-type ZBD, suggesting a critical function of the ZBD in cis. Consistently, no viral RNA synthesis was detected after transfection of EAV full-length RNAs encoding ATPase/helicase-deficient nsp10 into susceptible cells. In contrast, diverse phenotypes were observed for mutants with enzymatically active nsp10, which in a number of cases correlated with the activities measured in vitro. Collectively, our data suggest that the ZBD is critically involved in nidovirus replication and transcription by modulating the enzymatic activities of the helicase domain and other, yet unknown, mechanisms.

WASP-3b: a strongly irradiated transiting gas-giant planet

We report the discovery of WASP-3b, the third transiting exoplanet to be discovered by the WASP and SOPHIE collaboration. WASP-3b transits its host star USNO-B1.01256-0285133 every 1.846834 +/- 0.000002 d. Our high-precision radial velocity measurements present a variation with amplitude characteristic of a planetary-mass companion and in phase with the light curve. Adaptive optics imaging shows no evidence for nearby stellar companions, and line-bisector analysis excludes faint, unresolved binarity and stellar activity as the cause of the radial velocity variations. We make a preliminary spectroscopic analysis of the host star and find it to have Teff = 6400 +/- 100K and log g = 4.25 +/- 0.05 which suggests it is most likely an unevolved main-sequence star of spectral type F7-8V. Our simultaneous modelling of the transit photometry and reflex motion of the host leads us to derive a mass of 1.76+0.08-0.14 MJ and radius 1.31+0.07-0.14 RJ for WASP-3b. The proximity and relative temperature of the host star suggests that WASP-3b is one of the hottest exoplanets known, and thus has the potential to place stringent constraints on exoplanet atmospheric models.