Control of Light-Atom Solitons and Atomic Transport by Optical Vortex Beams Propagating through a Bose-Einstein Condensate.

We model propagation of far-red-detuned optical vortex beams through a Bose-Einstein condensate using nonlinear Schrödinger and Gross-Pitaevskii equations. We show the formation of coupled light-atomic solitons that rotate azimuthally before moving off tangentially, carrying angular momentum. The number, and velocity, of solitons, depends on the orbital angular momentum of the optical field. Using a Bessel-Gauss beam increases radial confinement so that solitons can rotate with fixed azimuthal velocity. Our model provides a highly controllable method of channeling a BEC and atomic transport.

Multiple Self-Organized Phases and Spatial Solitons in Cold Atoms Mediated by Optical Feedback.

We study the transverse self-structuring of cold atomic clouds with effective atomic interactions mediated by a coherent driving beam retroreflected by means of a single mirror. The resulting self-structuring due to optomechanical forces is much richer than that of an effective-Kerr medium, displaying hexagonal, stripe and honeycomb phases depending on the interaction strength parametrized by the linear susceptibility. Phase domains are described by Ginzburg-Landau amplitude equations with real coefficients. In the stripe phase the system recovers inversion symmetry. Moreover, the subcritical character of the honeycomb phase allows for light-density feedback solitons functioning as self-sustained dark atomic traps with motion controlled by phase gradients in the driving beam.

Control of spatially rotating structures in diffractive Kerr cavities.

Turing patterns in self-focussing nonlinear optical cavities pumped by beams carrying orbital angular momentum (OAM) m are shown to rotate with an angular velocity ω=2m/R 2 on rings of radii R. We verify this prediction in 1D models on a ring and for 2D Laguerre-Gaussian and top-hat pumps with OAM. Full control over the angular velocity of the pattern in the range -2m/R 2≤ω≤2m/R 2 is obtained by using cylindrical vector beam pumps that consist of orthogonally polarized eigenmodes with equal and opposite OAM. Using Poincaré beams that consist of orthogonally polarized eigenmodes with different magnitudes of OAM, the resultant angular velocity is ω=(m L+m R)/R 2, where m L,m R are the OAMs of the eigenmodes, assuming good overlap between the eigenmodes. If there is no, or very little, overlap between the modes then concentric Turing pattern rings, each with angular velocity ω=2m L,R /R 2 will result. This can lead to, for example, concentric, counter-rotating Turing patterns creating an optical peppermill-type structure. Full control over the speeds of multiple rings has potential applications in particle manipulation and stretching, atom trapping, and circular transport of cold atoms and BEC wavepackets.

Optical Rogue Waves in Vortex Turbulence.

We present a spatiotemporal mechanism for producing 2D optical rogue waves in the presence of a turbulent state with creation, interaction, and annihilation of optical vortices. Spatially periodic structures with bound phase lose stability to phase unbound turbulent states in complex Ginzburg-Landau and Swift-Hohenberg models with external driving. When the pumping is high and the external driving is low, synchronized oscillations are unstable and lead to spatiotemporal vortex-mediated turbulence with high excursions in amplitude. Nonlinear amplification leads to rogue waves close to turbulent optical vortices, where the amplitude tends to zero, and to probability density functions (PDFs) with long tails typical of extreme optical events.

Polarization Shaping for Control of Nonlinear Propagation.

We study the nonlinear optical propagation of two different classes of light beams with space-varying polarization-radially symmetric vector beams and Poincaré beams with lemon and star topologies-in a rubidium vapor cell. Unlike Laguerre-Gauss and other types of beams that quickly experience instabilities, we observe that their propagation is not marked by beam breakup while still exhibiting traits such as nonlinear confinement and self-focusing. Our results suggest that, by tailoring the spatial structure of the polarization, the effects of nonlinear propagation can be effectively controlled. These findings provide a novel approach to transport high-power light beams in nonlinear media with controllable distortions to their spatial structure and polarization properties.

Diffraction gratings for chiral molecules and their applications.

We suggest the use of certain readily producible types of light to exert a force that points in opposite directions for the enantiomers of a chiral molecule and propose multiple devices based upon this novel manifestation of optical activity: in particular, our discriminatory chiral diffraction grating; a device that could be employed, for example, to measure the enantiomeric excess of a sample of chiral molecules simply and to high precision. Our work is relevant for many types of molecules and our proposed devices may be realizable using currently existing technology.

Microrheology with optical tweezers.

Microrheology is the study of the flow of materials over small scales. It is of particular interest to those involved with investigations of fluid properties within Lab-on-a-Chip structures or within other micron-scale environments. The article briefly reviews existing active and passive methods used in the study of fluids. It then explores in greater detail the use of optical tweezers as an emerging method to investigate rheological phenomena, including, for example, viscosity and viscoelasticity, as well as the related topic of flow. The article also describes, briefly, potential future applications of this topic, in the fields of biological measurement, in general, and Lab-on-a-Chip, in particular.

Multipoint viscosity measurements in microfluidic channels using optical tweezers.

We demonstrate the technique of multipoint viscosity measurements incorporating the accurate calibration of micron sized particles. We describe the use of a high-speed camera to measure the residual motion of particles trapped in holographic optical tweezers, enabling us to calculate the fluid viscosity at multiple points across the field-of-view of the microscope within a microfluidic system.

Systematic identification of pseudogenes through whole genome expression evidence profiling.

The identification of pseudogenes is an integral and significant part of the genome annotation because of their abundance and their impact on the experimental analysis of functional genes. Most of the computational annotation systems are not optimized for systematic pseudogene recognition, often annotating pseudogenes as functional genes, and users then propagate these errors to subsequent analyses and interpretations. In order to validate gene annotations and to identify pseudogenes that are potentially mis-annotated, we developed a novel approach based on whole genome profiling of existing transcript and protein sequences. This method has two important features: (i) equally detects both processed and non-processed pseudogenes and (ii) can identify transcribed pseudogenes. Applying this method to the human Ensembl gene predictions, we discovered that 2011 (9% of total) Ensembl genes in the categories of known and novel might be pseudogenes based on expression evidence. Of these, 1200 genes are found to have no existing evidence of transcription, and 811 genes are found with transcription evidence but contain significant translation disruption. Approximately 40% of the 2011 identified pseudogenes presented a multi-exon structure, representing non-processed pseudogenes. We have demonstrated the power of whole genome profiling of expression sequences to improve the accuracy of gene annotations.

Chirality and the angular momentum of light.

Chirality is exhibited by objects that cannot be rotated into their mirror images. It is far from obvious that this has anything to do with the angular momentum of light, which owes its existence to rotational symmetries. There is nevertheless a subtle connection between chirality and the angular momentum of light. We demonstrate this connection and, in particular, its significance in the context of chiral light-matter interactions.This article is part of the themed issue 'Optical orbital angular momentum'.

Standardized metadata for human pathogen/vector genomic sequences.

High throughput sequencing has accelerated the determination of genome sequences for thousands of human infectious disease pathogens and dozens of their vectors. The scale and scope of these data are enabling genotype-phenotype association studies to identify genetic determinants of pathogen virulence and drug/insecticide resistance, and phylogenetic studies to track the origin and spread of disease outbreaks. To maximize the utility of genomic sequences for these purposes, it is essential that metadata about the pathogen/vector isolate characteristics be collected and made available in organized, clear, and consistent formats. Here we report the development of the GSCID/BRC Project and Sample Application Standard, developed by representatives of the Genome Sequencing Centers for Infectious Diseases (GSCIDs), the Bioinformatics Resource Centers (BRCs) for Infectious Diseases, and the U.S. National Institute of Allergy and Infectious Diseases (NIAID), part of the National Institutes of Health (NIH), informed by interactions with numerous collaborating scientists. It includes mapping to terms from other data standards initiatives, including the Genomic Standards Consortium's minimal information (MIxS) and NCBI's BioSample/BioProjects checklists and the Ontology for Biomedical Investigations (OBI). The standard includes data fields about characteristics of the organism or environmental source of the specimen, spatial-temporal information about the specimen isolation event, phenotypic characteristics of the pathogen/vector isolated, and project leadership and support. By modeling metadata fields into an ontology-based semantic framework and reusing existing ontologies and minimum information checklists, the application standard can be extended to support additional project-specific data fields and integrated with other data represented with comparable standards. The use of this metadata standard by all ongoing and future GSCID sequencing projects will provide a consistent representation of these data in the BRC resources and other repositories that leverage these data, allowing investigators to identify relevant genomic sequences and perform comparative genomics analyses that are both statistically meaningful and biologically relevant.

Real time characterization of hydrodynamics in optically trapped networks of micro-particles.

The hydrodynamic interactions of micro-silica spheres trapped in a variety of networks using holographic optical tweezers are measured and characterized in terms of their predicted eigenmodes. The characteristic eigenmodes of the networks are distinguishable within 20-40 seconds of acquisition time. Three different multi-particle networks are considered; an eight-particle linear chain, a nine-particle square grid and, finally, an eight-particle ring. The eigenmodes and their decay rates are shown to behave as predicted by the Oseen tensor and the Langevin equation, respectively. Finally, we demonstrate the potential of using our micro-ring as a non-invasive sensor to the local environmental viscosity, by showing the distortion of the eigenmode spectrum due to the proximity of a planar boundary.

Measuring storage and loss moduli using optical tweezers: broadband microrheology.

We present an experimental procedure to perform broadband microrheological measurements with optical tweezers. A generalized Langevin equation is adopted to relate the time-dependent trajectory of a particle in an imposed flow to the frequency-dependent moduli of the complex fluid. This procedure allows us to measure the material linear viscoelastic properties across the widest frequency range achievable with optical tweezers.

Quantum correlations in optical angle-orbital angular momentum variables.

Entanglement of the properties of two separated particles constitutes a fundamental signature of quantum mechanics and is a key resource for quantum information science. We demonstrate strong Einstein, Podolsky, and Rosen correlations between the angular position and orbital angular momentum of two photons created by the nonlinear optical process of spontaneous parametric down-conversion. The discrete nature of orbital angular momentum and the continuous but periodic nature of angular position give rise to a special sort of entanglement between these two variables. The resulting correlations are found to be an order of magnitude stronger than those allowed by the uncertainty principle for independent (nonentangled) particles. Our results suggest that angular position and orbital angular momentum may find important applications in quantum information science.

Giant excess noise and transient gain in misaligned laser cavities.

The excess noise factor is calculated analytically for a very general class of optical cavities, and is shown to have a superexponential dependence on cavity misalignment, easily attaining values of order 10(10). The physical basis is shown to be "ransient gain" associated with amplified spontaneous emission. Similarly dramatic effects of symmetry breaking can be expected in other physical systems with non-normal modes.

Gene and alternative splicing annotation with AIR.

Designing effective and accurate tools for identifying the functional and structural elements in a genome remains at the frontier of genome annotation owing to incompleteness and inaccuracy of the data, limitations in the computational models, and shifting paradigms in genomics, such as alternative splicing. We present a methodology for the automated annotation of genes and their alternatively spliced mRNA transcripts based on existing cDNA and protein sequence evidence from the same species or projected from a related species using syntenic mapping information. At the core of the method is the splice graph, a compact representation of a gene, its exons, introns, and alternatively spliced isoforms. The putative transcripts are enumerated from the graph and assigned confidence scores based on the strength of sequence evidence, and a subset of the high-scoring candidates are selected and promoted into the annotation. The method is highly selective, eliminating the unlikely candidates while retaining 98% of the high-quality mRNA evidence in well-formed transcripts, and produces annotation that is measurably more accurate than some evidence-based gene sets. The process is fast, accurate, and fully automated, and combines the traditionally distinct gene annotation and alternative splicing detection processes in a comprehensive and systematic way, thus considerably aiding in the ensuing manual curation efforts.