Radiation pattern of two identical emitters driven by a Laguerre-Gaussian beam: An atom nanoantenna

We study the directional properties of a radiation field emitted by a geometrically small system composed of two identical two-level emitters located at short distances and driven by an optical vortex beam, a Laguerre-Gaussian beam which possesses a structured phase and amplitude. We find that the system may operate as a nanoantenna for controlled and tunable directional emission. Polar diagrams of the radiation intensity are presented showing that a constant phase or amplitude difference at the positions of the emitters plays an essential role in the directivity of the emission. We find that the radiation patterns may differ dramatically for different phase and amplitude differences at the positions of the emitters. As a result the system may operate as a two- or one-sided nanoantenna. In particular, a two-sided highly focused directional emission can be achieved when the emitters experience the same amplitude and a constant phase difference of the driving field. We find a general directional property of the emitted field that when the phase differences at the positions of the emitters equal an even multiple of \pi/4, the system behaves as a two-sided antenna. When the phase difference equals an odd multiple of \pi/4, the system behaves as an one-sided antenna. The case when the emitters experience the same phase but different amplitudes of the driving field is also considered and it is found that the effect of different amplitudes is to cause the system to behave as a uni-directional antenna radiating along the interatomic axis.Comment: published versio

ReformAlign: improved multiple sequence alignments using a profile-based meta-alignment approach

Background: Obtaining an accurate sequence alignment is fundamental for consistently analyzing biological data. Although this problem may be efficiently solved when only two sequences are considered, the exact inference of the optimal alignment easily gets computationally intractable for the multiple sequence alignment case. To cope with the high computational expenses, approximate heuristic methods have been proposed that address the problem indirectly by progressively aligning the sequences in pairs according to their relatedness. These methods however are not flexible to change the alignment of an already aligned group of sequences in the view of new data, resulting thus in compromises on the quality of the deriving alignment. In this paper we present ReformAlign, a novel meta-alignment approach that may significantly improve on the quality of the deriving alignments from popular aligners. We call ReformAlign a meta-aligner as it requires an initial alignment, for which a variety of alignment programs can be used. The main idea behind ReformAlign is quite straightforward: at first, an existing alignment is used to construct a standard profile which summarizes the initial alignment and then all sequences are individually re-aligned against the formed profile. From each sequence-profile comparison, the alignment of each sequence against the profile is recorded and the final alignment is indirectly inferred by merging all the individual sub-alignments into a unified set. The employment of ReformAlign may often result in alignments which are significantly more accurate than the starting alignments. Results: We evaluated the effect of ReformAlign on the generated alignments from ten leading alignment methods using real data of variable size and sequence identity. The experimental results suggest that the proposed meta-aligner approach may often lead to statistically significant more accurate alignments. Furthermore, we show that ReformAlign results in more substantial improvement in cases where the starting alignment is of relatively inferior quality or when the input sequences are harder to align. Conclusions: The proposed profile-based meta-alignment approach seems to be a promising and computationally efficient method that can be combined with practically all popular alignment methods and may lead to significant improvements in the generated alignments

Quantum Hall Physics with Cold Atoms in Cylindrical Optical Lattices

We propose and study various realizations of a Hofstadter-Hubbard model on a cylinder geometry with fermionic cold atoms in optical lattices. The cylindrical optical lattice is created by copropagating Laguerre-Gauss beams, i.e.~light beams carrying orbital angular momentum. By strong focusing of the light beams we create a real space optical lattice in the form of rings, which are offset in energy. A second set of Laguerre-Gauss beams then induces a Raman-hopping between these rings, imprinting phases corresponding to a synthetic magnetic field (artificial gauge field). In addition, by rotating the lattice potential, we achieve a slowly varying flux through the hole of the cylinder, which allows us to probe the Hall response of the system as a realization of Laughlin's thought experiment. We study how in the presence of interactions fractional quantum Hall physics could be observed in this setup.Comment: 10 pages, 9 figure

Arrays of dark optical traps on a toroidal surface

We have theoretically constructed light fields that can generate optical potentials representing rectangular arrays of dark optical traps on the surface of a torus. The arrays are not diffraction-limited, and their period can in principle be deeply sub-wavelength. We discuss the challenges anticipated in realising such potentials which will be of great interest for quantum simulations

Diverse bacterial species contribute to antibiotic-associated diarrhoea and gastrointestinal damage

Objectives: Antibiotic-associated diarrhoea (AAD) caused by C. difficile is one of the most common nosocomial infections, however, little is known about infections related to antimicrobial use for pathogens other than C. difficile. We therefore aimed to provide insight into other bacterial causes of AAD, and how infection with these pathogens causes damage in the dysbiotic gut. Methods: Clinical isolates from C. difficile-negative AAD patients were whole genome sequenced for in silico analysis of potential virulence factors and antimicrobial resistance determinants. A mouse model of infection was developed to assess the capacity of these isolates to cause gastrointestinal damage, which was analysed by studying specific markers in the gastrointestinal mucosa of infected mice. Results: Several bacterial pathogens were isolated from patients with C. difficile-negative AAD. Each isolate showed the potential for virulence based on encoded virulence factors, as well as most showing antimicrobial resistance in vitro. Isolates of Escherichia coli, Pseudomonas aeruginosa, and Klebsiella pneumoniae were tested in the mouse model of infection, inducing damage primarily in the small intestine, affecting adherens junction integrity, cellular polarity, and cellular proliferation. Conclusions: Several pathogens of clinical importance other than C. difficile are able to cause gastrointestinal infection following antimicrobial-mediated dysbiosis. The virulence potential and multidrug resistance identified in these isolates illuminates the importance of further diagnostic screening in cases of C. difficile-negative AAD