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Optical Nanofibers for Multiphoton Processes and Selective Mode Interactions with Rubidium
Get PDFOkinawa Institute of Science and Technology Graduate UniversityDoctor of PhilosophyOptical nanofibers (ONFs) interfaced with atoms have found numerous applications for the development of quantum technologies. They feature a strong evanescent held at their waist, thereby providing an intense and tightly focused beam over long distances. This
can be used to achieve strong interactions between light and matter, enabling trapping, probing, and control of atoms along the waist. However, little experimental work has been done with the higher-order fiber guided modes (HOM). These feature inhomogeneous polarization distributions around the waist and some carry more than h of angular momentum (AM). Owing to the intense held gradient in their evanescent held, ONFs make excellent platforms to excite quadrupole-allowed transitions which could be used to store high-density information encoded on the AM of guided light. We predicted a transition probability up to 6 times stronger than for free-space beams using the fundamental mode and up to 4 times stronger using linearly polarized HOMs. We also studied a singlecolor, two-photon transition at 993 nm between the 5SI/2 and 6S1/2 atomic levels in a hot rubidium vapor and showed its suitability as a frequency reference. We experimentally verihed the particular selection rules for this transition and showed that they may be used to characterize the polarization at the waist of an ONF embedded in a cloud of atoms formed by a magneto-optical trap. Finally, we developed a method to generate HOM-like
beams in free-space, inject them into an ONF, and decompose the modal excitation at the output via transfer matrix calculation. This approach combined with absorption of guided-light by cold atoms may be used to infer the mode excitation at the waist and allow us to selectively excite HOMs.doctoral thesi
Forward Genetic Screen for Caenorhabditis elegans Mutants with a Shortened Locomotor Healthspan
Get PDFTwo people with the same lifespan do not necessarily have the same healthspan. One person may retain locomotor and cognitive abilities until the end of life, while another person may lose them during adulthood. Unbiased searches for genes that are required to maintain locomotor ability during adulthood may uncover key regulators of locomotor healthspan. Here, we take advantage of the relatively short lifespan of the nematode Caenorhabditis elegans and develop a novel screening procedure to collect mutants with locomotor deficits that become apparent in adulthood. After ethyl methanesulfonate mutagenesis, we isolated five C. elegans mutant strains that progressively lose adult locomotor ability. In one of the mutant strains, a nonsense mutation in elpc-2, which encodes Elongator Complex Protein Component 2, causes a progressive decline in locomotor ability during adulthood. Mutants and mutations identified in the present screen may provide insights into mechanisms of age-related locomotor impairment and the maintenance of locomotor healthspan.journal articl
Complete mitochondrial genomes from transcriptomes: assessing pros and cons of data mining for assembling new mitogenomes
Get PDFThousands of eukaryotes transcriptomes have been generated, mainly to investigate nuclear genes expression, and the amount of available data is constantly increasing. A neglected but promising use of this large amount of data is to assemble organelle genomes. To assess the reliability of this approach, we attempted to reconstruct complete mitochondrial genomes from RNA-Seq experiments of Reticulitermes termite species, for which transcriptomes and conspecific mitogenomes are available. We successfully assembled complete molecules, although a few gaps corresponding to tRNAs had to be filled manually. We also reconstructed, for the first time, the mitogenome of Reticulitermes banyulensis. The accuracy and completeness of mitogenomes reconstruction appeared independent from transcriptome size, read length and sequencing design (single/paired end), and using reference genomes from congeneric or intra-familial taxa did not significantly affect the assembly. Transcriptome-derived mitogenomes were found highly similar to the conspecific ones obtained from genome sequencing (nucleotide divergence ranging from 0% to 3.5%) and yielded a congruent phylogenetic tree. Reads from contaminants and nuclear transcripts, although slowing down the process, did not result in chimeric sequence reconstruction. We suggest that the described approach has the potential to increase the number of available mitogenomes by exploiting the rapidly increasing number of transcriptomes.journal articl
Optimized Immobilization of Biomolecules on Nonspherical Gold Nanostructures for Efficient Localized Surface Plasmon Resonance Biosensing
Get PDFPlasmonic biosensing techniques employ metal nanostructures, commonly gold (Au), often with biomolecules attached to their surfaces either directly or via other linkers. Various surface chemistry methods based on dispersion and covalent interactions are used to attach biomolecules to Au. As a result, when immobilizing a molecule on a metal surface, quantitative estimates of binding efficiency and stability of these surface chemistry methods are needed. Most prior work to compare such methods deals with bulk/thin film configurations or spherical nanoparticles, and very little is known about immobilization of biomolecules on plasmonic nanostructures of different shapes. Besides, due to rapid advancement of modern nanofabrication techniques, there is a growing need to determine an efficient surface chemistry method for immobilization of biomolecules on nonspherical plasmonic nanostructures. Previous comparison of immobilization methods on spherical Au nanoparticles has shown that physical adsorption resulted in the highest concentration of immobilized antibodies. In our work, we conducted a similar study and compared four representative Au surface functionalization methods as well as estimated how efficient these methods are at attaching biomolecules to nonspherical plasmonic Au nanostructures. We estimated the concentration of immobilized antibody that is specific to human C-reactive protein (anti-hCRP) by measuring the localized surface plasmon resonance (LSPR) shifts after exposing the surface of Au nanostructures to the antibody. Our results differ from the previously reported ones since the highest concentration of anti-hCRP was immobilized using 11-mercaptoundecanoic acid (MUA) chemistry. We demonstrated that immobilized antibodies retained their stability and specificity toward hCRP throughout the immunoassay when diluted hCRP or hCRP-spiked human serum samples were used. These findings have important implications for the fields of biosensing and diagnostics that employ nonspherical plasmonic nanostructures since an overall performance of these devices depends on efficient biomolecule immobilization.journal articl
Coherent impurity transport in an attractive binary Bose–Einstein condensate
Get PDFWe study the dynamics of a soliton-impurity system modeled in terms of a binary Bose–Einstein condensate. This is achieved by 'switching off' one of the two self-interaction scattering lengths, giving a two component system where the second component is trapped entirely by the presence of the first component. It is shown that this system possesses rich dynamics, including the identification of unusual 'weak' dimers that appear close to the zero inter-component scattering length. It is further found that this system supports quasi-stable trimers in regimes where the equivalent single-component gas does not, which is attributed to the presence of the impurity atoms which can dynamically tunnel between the solitons, and maintain the required phase differences that support the trimer state.journal articl
Excitation of whispering gallery modes with a “point-and-play,” fiber-based, optical nano-antenna
Get PDFWe demonstrate the excitation and detection of whispering gallery modes in optical microresonators using a "point-and-play," fiber-based, optical nano-antenna. The coupling mechanism is based on cavity-enhanced Rayleigh scattering. Collected spectra exhibit Lorentzian dips, Fano shapes, or Lorentzian peaks, with a coupling efficiency around 13%. The spectra are characterized by the coupling gap, polarization, and fiber tip position. The coupling method is simple, low-cost and, most importantly, the Q-factor can be maintained at 10(8) over a wide coupling range, thereby making it suitable for metrology, sensing, or cavity quantum electrodynamics experiments.journal articl
Application of spherical substrate to observe bacterial motility machineries by Quick-Freeze-Replica Electron Microscopy
Get PDF3-D Structural information is essential to elucidate the molecular mechanisms of various biological machineries. Quick-Freeze Deep-Etch-Replica Electron Microscopy is a unique technique to give very high-contrast surface profiles of extra- and intra-cellular apparatuses that bear numerous cellular functions. Though the global architecture of those machineries is primarily required to understand their functional features, it is difficult or even impossible to depict side- or highly-oblique views of the same targets by usual goniometry, inasmuch as the objects (e.g. motile microorganisms) are placed on conventional flat substrates. We introduced silica-beads as an alternative substrate to solve such crucial issue. Elongated Flavobacterium and globular Mycoplasmas cells glided regularly along the bead's surface, similarly to those on a flat substrate. Quick-freeze replicas of those cells attached to the beads showed various views; side-, oblique- and frontal-views, enabling us to study not only global but potentially more detailed morphology of complicated architecture. Adhesion of the targets to the convex surface could give surplus merits to visualizing intriguing molecular assemblies within the cells, which is relevant to a variety of motility machinery of microorganisms.journal articl
Gene expression profiles of dicyemid life-cycle stages may explain how dispersing larvae locate new hosts
Get PDFMetazoans have evolved a great variety of life histories in response to environmental conditions. A unique example is encountered in dicyemid mesozoans. In addition to a highly simplified adult body comprising only ~ 30 cells, dicyemids exhibit a parasitic lifestyle that includes nematogens (asexual reproductive adults), rhombogens (sexual reproductive adults), vermiform larvae generated by nematogens, and infusoriform larvae generated by rhombogens. However, due to the difficulties of observing microscopic endoparasites, the complex life cycle and biological functions of life-cycle stages of dicyemids have remained mysterious. Taking advantage of the recently decoded genome of Dicyema japonicum, we examined genes that undergird this lifestyle. Using stage-specific gene expression profiles, we found that biological processes associated with molecular transport, developmental regulation, and sensory response are specified at different stages. Together with the expression of potential neurotransmitters, we further suggest that apical cells in infusoriform larva probably serve sensory functions, although dicyemids have no nervous system. Gene expression profiles show that more genes are expressed in free-living infusoriform larvae than in the other three stages, and that some of these genes are likely involved in locating new hosts. These data provide molecular information about the unique lifestyle of dicyemids and illustrate how an extremely simplified endoparasite adapted and retained gene sets and morphological characters to complete its life cycle. Supplementary information: Supplementary information accompanies this paper at 10.1186/s40851-019-0146-y.journal articl
Control of excitonic absorption by thickness variation in few-layer GaSe
Get PDFWe control the thickness of GaSe on the level of individual layers and study the corresponding optical absorption via highly sensitive differential transmission measurements. Suppression of excitonic transitions is observed when the number of layers is smaller than a critical value of 8. Through ab initio modelling we are able to link this behavior to a fundamental change in the band structure that leads to the formation of a valence band shaped as an inverted Mexican hat in thin GaSe. The thickness-controlled modulation of the optical properties provides attractive resources for the development of functional optoelectronic devices based on a single material.journal articl
A Neurorobotics Approach to Investigating the Emergence of Communication in Robots
Get PDFThis paper introduces our approach to building a robot with communication capability based on the two key features: stochastic neural dynamics and prediction error minimization. A preliminary experiment showed that the humanoid robot was able to imitate other's action by means of those key features. In addition, we found that some sorts of communicative patterns emerged between two robots in which the robots inferred the intention of another agent behind the sensory observation.conference pape