Modeling inelastic phonon scattering in atomic- and molecular-wire junctions

Computationally inexpensive approximations describing electron-phonon scattering in molecular-scale conductors are derived from the non-equilibrium Green's function method. The accuracy is demonstrated with a first principles calculation on an atomic gold wire. Quantitative agreement between the full non-equilibrium Green's function calculation and the newly derived expressions is obtained while simplifying the computational burden by several orders of magnitude. In addition, analytical models provide intuitive understanding of the conductance including non-equilibrium heating and provide a convenient way of parameterizing the physics. This is exemplified by fitting the expressions to the experimentally observed conductances through both an atomic gold wire and a hydrogen molecule.Comment: 5 pages, 3 figure

Host-Pathogen Interactions in Pseudomonas aeruginosa Invasive and Respiratory Tract Infection

Pseudomonas aeruginosa is an opportunistic bacterium that causes debilitating infections when the immune defence is compromised. It possesses an arsenal of virulence traits to colonize most compartments of the body and is often highly resistant against commonly used antimicrobial drugs.Outer membrane vesicles (OMV) are spheres released from Gram-negative bacteria. They are packed with proteins, including beta-lactamase. By exploring OMV from a pathogen related to P. aeruginosa (Moraxella catarrhalis) we discovered that beta-lactamase inside OMV was protected from neutralization by IgG and could protect bacteria from amoxicillin.Many pathogens avoid killing by the complement system by capturing complement regulators at their bacterial surface. We found that P. aeruginosa from the airways bound more vitronectin than other clinical isolates. By using a proteomic approach, we identified vitronectin-binding adhesins and found that Pseudomonas uses Porin D to capture vitronectin on its surface.To investigate the in vivo importance of vitronectin-binding, we analysed vitronectin concentrations in bronchoalveolar lavage fluid (BALF). Patients with pneumonia had significantly higher concentrations than control subjects. This vitronectin increase was confirmed by pulmonary exposure of endotoxins to healthy volunteers. We also found that bacteria could capture vitronectin from BALF and subsequently survive challenge with serum. Immunocytochemistry indicated that epithelial cells produced vitronectin. This production was confirmed in vitro and was triggered by OMV-dependent stimulation of epithelial cells.Finally, after collecting data on bacteraemic P. aeruginosa episodes, we investigated the effect of comorbidities, treatment, and microbiological characteristics on the outcome of bacteraemia. The choice of treatment was critical, particularly choosing a combination-treatment including ciprofloxacin was beneficial. Moreover, respiratory origin of the infection correlated to high mortality, indicating that compartment-specific factors impacted the outcome.In conclusion, interactions between the host and bacteria are multifaceted and P. aeruginosa utilizes outer membrane proteins and vesicles to protect against the attacks of the human immune system

From tunneling to contact: Inelastic signals in an atomic gold junction

The evolution of electron conductance in the presence of inelastic effects is studied as an atomic gold contact is formed evolving from a low-conductance regime (tunneling) to a high-conductance regime (contact). In order to characterize each regime, we perform density functional theory (DFT) calculations to study the geometric and electronic structures, together with the strength of the atomic bonds and the associated vibrational frequencies. The conductance is calculated by first evaluating the transmission of electrons through the system, and secondly by calculating the conductance change due to the excitation of vibrations. As found in previous studies [Paulsson et al., Phys. Rev. B. 72, 201101(R) (2005)] the change in conductance due to inelastic effects permits to characterize the crossover from tunneling to contact. The most notorious effect being the crossover from an increase in conductance in the tunneling regime to a decrease in conductance in the contact regime when the bias voltage matches a vibrational threshold. Our DFT-based calculations actually show that the effect of vibrational modes in electron conductance is rather complex, in particular when modes localized in the contact region are permitted to extend into the electrodes. As an example, we find that certain modes can give rise to decreases in conductance when in the tunneling regime, opposite to the above mentioned result. Whereas details in the inelastic spectrum depend on the size of the vibrational region, we show that the overall change in conductance is quantitatively well approximated by the simplest calculation where only the apex atoms are allowed to vibrate. Our study is completed by the application of a simplified model where the relevant parameters are obtained from the above DFT-based calculations.Comment: 8 pages, 5 figure

Unified description of inelastic propensity rules for electron transport through nanoscale junctions

We present a method to analyze the results of first-principles based calculations of electronic currents including inelastic electron-phonon effects. This method allows us to determine the electronic and vibrational symmeties in play, and hence to obtain the so-called propensity rules for the studied systems. We show that only a few scattering states -- namely those belonging to the most transmitting eigenchannels -- need to be considered for a complete description of the electron transport. We apply the method on first-principles calculations of four different systems and obtain the propensity rules in each case.Comment: 4 pages, 4 figures, 1 table http://link.aps.org/abstract/PRL/v100/e22660

Inelastic fingerprints of hydrogen contamination in atomic gold wire systems

We present series of first-principles calculations for both pure and hydrogen contaminated gold wire systems in order to investigate how such impurities can be detected. We show how a single H atom or a single H2 molecule in an atomic gold wire will affect forces and Au-Au atom distances under elongation. We further determine the corresponding evolution of the low-bias conductance as well as the inelastic contributions from vibrations. Our results indicate that the conductance of gold wires is only slightly reduced from the conductance quantum G0=2e^2/h by the presence of a single hydrogen impurity, hence making it difficult to use the conductance itself to distinguish between various configurations. On the other hand, our calculations of the inelastic signals predict significant differences between pure and hydrogen contaminated wires, and, importantly, between atomic and molecular forms of the impurity. A detailed characterization of gold wires with a hydrogen impurity should therefore be possible from the strain dependence of the inelastic signals in the conductance.Comment: 5 pages, 3 figures, Contribution to ICN+T2006, Basel, Switzerland, July-August 200

Chemical modification of lignin-rich paper. Part 7, Photostabilizing high-brightness aspen CTMP by combining various classes of additives and acetylation

"April 1998.""Submitted to Nordic Pulp and Paper Research Journal.