Self-consistent ac quantum transport using nonequilibrium Green functions

We develop an approach for self-consistent ac quantum transport in the presence of time-dependent potentials at non-transport terminals. We apply the approach to calculate the high-frequency characteristics of a nanotube transistor with the ac signal applied at the gate terminal. We show that the self-consistent feedback between the ac charge and potential is essential to properly capture the transport properties of the system. In the on-state, this feedback leads to the excitation of plasmons, which appear as pronounced divergent peaks in the dynamic conductance at terahertz frequencies. In the off-state, these collective features vanish, and the conductance exhibits smooth oscillations, a signature of single-particle excitations. The proposed approach is general and will allow the study of the high-frequency characteristics of many other low-dimensional nanoscale materials such as nanowires and graphene-based systems, which are attractive for terahertz devices, including those that exploit plasmonic excitations.Comment: 11 pages, 5 figures, accepted in Physical Review

Refactoring Legacy JavaScript Code to Use Classes: The Good, The Bad and The Ugly

JavaScript systems are becoming increasingly complex and large. To tackle the challenges involved in implementing these systems, the language is evolving to include several constructions for programming- in-the-large. For example, although the language is prototype-based, the latest JavaScript standard, named ECMAScript 6 (ES6), provides native support for implementing classes. Even though most modern web browsers support ES6, only a very few applications use the class syntax. In this paper, we analyze the process of migrating structures that emulate classes in legacy JavaScript code to adopt the new syntax for classes introduced by ES6. We apply a set of migration rules on eight legacy JavaScript systems. In our study, we document: (a) cases that are straightforward to migrate (the good parts); (b) cases that require manual and ad-hoc migration (the bad parts); and (c) cases that cannot be migrated due to limitations and restrictions of ES6 (the ugly parts). Six out of eight systems (75%) contain instances of bad and/or ugly cases. We also collect the perceptions of JavaScript developers about migrating their code to use the new syntax for classes.Comment: Paper accepted at 16th International Conference on Software Reuse (ICSR), 2017; 16 page

On the influence of the magnetic field of the GSI experimental storage ring on the time-modulation of the EC-decay rates of the H-like mother ions

We investigate the influence of the magnetic field of the Experimental storage ring (ESR) at GSI on the periodic time-dependence of the orbital K-shell electron capture decay $(EC$) rates of the H--like heavy ions. We approximate the magnetic field of the ESR by a uniform magnetic field. Unlike the assertion by Lambiase et al., arXiv: 0811.2302 [nucl-th], we show that a motion of the H-like heavy ion in a uniform magnetic field cannot be the origin of the periodic time-dependence of the EC-decay rates of the H-like heavy ions.Comment: 3 pages, 1 figur

Phylogeny of the SNARE vesicle fusion machinery yields insights into the conservation of the secretory pathway in fungi

<p>Abstract</p> <p>Background</p> <p>In eukaryotic cells, directional transport between different compartments of the endomembrane system is mediated by vesicles that bud from a donor organelle and then fuse with an acceptor organelle. A family of integral membrane proteins, termed soluble N-ethylmaleimide-sensitive factor attachment receptor (SNARE) proteins, constitute the key machineries of these different membrane fusion events. Over the past 30 years, the yeast <it>Saccharomyces cerevisiae </it>has served as a powerful model organism for studying the organization of the secretory and endocytic pathways, and a few years ago, its entire set of SNAREs was compiled.</p> <p>Results</p> <p>Here, we make use of the increasing amount of genomic data to investigate the history of the SNARE family during fungi evolution. Moreover, since different SNARE family members are thought to demarcate different organelles and vesicles, this approach allowed us to compare the organization of the endomembrane systems of yeast and animal cells. Our data corroborate the notion that fungi generally encompass a relatively simple set of SNARE proteins, mostly comprising the SNAREs of the proto-eukaryotic cell. However, all fungi contain a novel soluble SNARE protein, Vam7, which carries an N-terminal PX-domain that acts as a phosphoinositide binding module. In addition, the points in fungal evolution, at which lineage-specific duplications and diversifications occurred, could be determined. For instance, the endosomal syntaxins Pep12 and Vam3 arose from a gene duplication that occurred within the Saccharomycotina clade.</p> <p>Conclusion</p> <p>Although the SNARE repertoire of baker's yeast is highly conserved, our analysis reveals that it is more deviated than the ones of basal fungi. This highlights that the trafficking pathways of baker's yeast are not only different to those in animal cells but also are somewhat different to those of many other fungi.</p

An Extended Huckel Theory based Atomistic Model for Graphene Nanoelectronics

An atomistic model based on the spin-restricted extended Huckel theory (EHT) is presented for simulating electronic structure and I-V characteristics of graphene devices. The model is applied to zigzag and armchair graphene nano-ribbons (GNR) with and without hydrogen passivation, as well as for bilayer graphene. Further calculations are presented for electric fields in the nano-ribbon width direction and in the bilayer direction to show electronic structure modification. Finally, the EHT Hamiltonian and NEGF (Nonequilibrium Green's function) formalism are used for a paramagnetic zigzag GNR to show 2e2/h quantum conductance.Comment: 5 pages, 8 figure

Time-Resolved Diffusing Wave Spectroscopy for selected photon paths beyond 300 transport mean free paths

This paper is devoted to the theoretical and experimental demonstration of the possibility to perform time-resolved diffusing wave spectroscopy: we successfully registered field fluctuations for selected photon path lengths that can overpass 300 transport mean free paths. Such a performance opens new possibilities for biomedical optics applications.Comment: 12 pages, 3 figure

Untangling the evolution of Rab G proteins: implications of a comprehensive genomic analysis.

RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are.BACKGROUND: Membrane-bound organelles are a defining feature of eukaryotic cells, and play a central role in most of their fundamental processes. The Rab G proteins are the single largest family of proteins that participate in the traffic between organelles, with 66 Rabs encoded in the human genome. Rabs direct the organelle-specific recruitment of vesicle tethering factors, motor proteins, and regulators of membrane traffic. Each organelle or vesicle class is typically associated with one or more Rab, with the Rabs present in a particular cell reflecting that cell's complement of organelles and trafficking routes. RESULTS: Through iterative use of hidden Markov models and tree building, we classified Rabs across the eukaryotic kingdom to provide the most comprehensive view of Rab evolution obtained to date. A strikingly large repertoire of at least 20 Rabs appears to have been present in the last eukaryotic common ancestor (LECA), consistent with the 'complexity early' view of eukaryotic evolution. We were able to place these Rabs into six supergroups, giving a deep view into eukaryotic prehistory. CONCLUSIONS: Tracing the fate of the LECA Rabs revealed extensive losses with many extant eukaryotes having fewer Rabs, and none having the full complement. We found that other Rabs have expanded and diversified, including a large expansion at the dawn of metazoans, which could be followed to provide an account of the evolutionary history of all human Rabs. Some Rab changes could be correlated with differences in cellular organization, and the relative lack of variation in other families of membrane-traffic proteins suggests that it is the changes in Rabs that primarily underlies the variation in organelles between species and cell types

Incoherent Transport through Molecules on Silicon in the vicinity of a Dangling Bond

We theoretically study the effect of a localized unpaired dangling bond (DB) on occupied molecular orbital conduction through a styrene molecule bonded to a n++ H:Si(001)-(2x1) surface. For molecules relatively far from the DB, we find good agreement with the reported experiment using a model that accounts for the electrostatic contribution of the DB, provided we include some dephasing due to low lying phonon modes. However, for molecules within 10 angstrom to the DB, we have to include electronic contribution as well along with higher dephasing to explain the transport features.Comment: 9 pages, 5 figure