Modelling the Fluid Mechanics of Cilia and Flagella in Reproduction and Development

Cilia and flagella are actively bending slender organelles, performing functions such as motility, feeding and embryonic symmetry breaking. We review the mechanics of viscous-dominated microscale flow, including time-reversal symmetry, drag anisotropy of slender bodies, and wall effects. We focus on the fundamental force singularity, higher order multipoles, and the method of images, providing physical insight and forming a basis for computational approaches. Two biological problems are then considered in more detail: (1) left-right symmetry breaking flow in the node, a microscopic structure in developing vertebrate embryos, and (2) motility of microswimmers through non-Newtonian fluids. Our model of the embryonic node reveals how particle transport associated with morphogenesis is modulated by the gradual emergence of cilium posterior tilt. Our model of swimming makes use of force distributions within a body-conforming finite element framework, allowing the solution of nonlinear inertialess Carreau flow. We find that a three-sphere model swimmer and a model sperm are similarly affected by shear-thinning; in both cases swimming due to a prescribed beat is enhanced by shear-thinning, with optimal Deborah number around 0.8. The sperm exhibits an almost perfect linear relationship between velocity and the logarithm of the ratio of zero to infinite shear viscosity, with shear-thickening hindering cell progress.Comment: 20 pages, 24 figure

Demonstration of Robust Quantum Gate Tomography via Randomized Benchmarking

Typical quantum gate tomography protocols struggle with a self-consistency problem: the gate operation cannot be reconstructed without knowledge of the initial state and final measurement, but such knowledge cannot be obtained without well-characterized gates. A recently proposed technique, known as randomized benchmarking tomography (RBT), sidesteps this self-consistency problem by designing experiments to be insensitive to preparation and measurement imperfections. We implement this proposal in a superconducting qubit system, using a number of experimental improvements including implementing each of the elements of the Clifford group in single `atomic' pulses and custom control hardware to enable large overhead protocols. We show a robust reconstruction of several single-qubit quantum gates, including a unitary outside the Clifford group. We demonstrate that RBT yields physical gate reconstructions that are consistent with fidelities obtained by randomized benchmarking

Coherence in a transmon qubit with epitaxial tunnel junctions

We developed transmon qubits based on epitaxial tunnel junctions and interdigitated capacitors. This multileveled qubit, patterned by use of all-optical lithography, is a step towards scalable qubits with a high integration density. The relaxation time T1 is .72-.86mu sec and the ensemble dephasing time T2 is slightly larger than T1. The dephasing time T2 (1.36mu sec) is nearly energy-relaxation-limited. Qubit spectroscopy yields weaker level splitting than observed in qubits with amorphous barriers in equivalent-size junctions. The qubit's inferred microwave loss closely matches the weighted losses of the individual elements (junction, wiring dielectric, and interdigitated capacitor), determined by independent resonator measurements

Detection of Water Vapor in the Thermal Spectrum of the Non-Transiting Hot Jupiter upsilon Andromedae b

The upsilon Andromedae system was the first multi-planet system discovered orbiting a main sequence star. We describe the detection of water vapor in the atmosphere of the innermost non-transiting gas giant ups~And~b by treating the star-planet system as a spectroscopic binary with high-resolution, ground-based spectroscopy. We resolve the signal of the planet's motion and break the mass-inclination degeneracy for this non-transiting planet via deep combined flux observations of the star and the planet. In total, seven epochs of Keck NIRSPEC $L$ band observations, three epochs of Keck NIRSPEC short wavelength $K$ band observations, and three epochs of Keck NIRSPEC long wavelength $K$ band observations of the ups~And~system were obtained. We perform a multi-epoch cross correlation of the full data set with an atmospheric model. We measure the radial projection of the Keplerian velocity ($K_P$ = 55 $\pm$ 9 km/s), true mass ($M_b$ = 1.7 $^{+0.33}_{-0.24}$ $M_J$), and orbital inclination \big($i_b$ = 24 $\pm$ 4$^{\circ}$\big), and determine that the planet's opacity structure is dominated by water vapor at the probed wavelengths. Dynamical simulations of the planets in the ups~And~system with these orbital elements for ups~And~b show that stable, long-term (100 Myr) orbital configurations exist. These measurements will inform future studies of the stability and evolution of the ups~And~system, as well as the atmospheric structure and composition of the hot Jupiter.Comment: Accepted to A

Detection of Abrin-Like and Prepropulchellin-Like Toxin Genes and Transcripts Using Whole Genome Sequencing and Full-Length Transcript Sequencing of Abrus precatorius

The sequenced genome and the leaf transcriptome of a near relative of Abrus pulchellus and Abrus precatorius was analyzed to characterize the genetic basis of toxin gene expression. From the high-quality genome assembly, a total of 26 potential coding regions were identified that contain genes with abrin-like, pulchellin-like, and agglutinin-like homology, with full-length transcripts detected in leaf tissue for 9 of the 26 coding regions. All of the toxin-like genes were identified within only five isolated regions of the genome, with each region containing 1 to 16 gene variants within each genomic region (<1 Mbp). The Abrusprecatorius cultivar sequenced here contains genes which encode for proteins that are homologous to certain abrin and prepropulchellin genes previously identified, and we observed substantial diversity of genes and predicted gene products in Abrus precatorius and previously characterized toxins. This suggests diverse toxin repertoires within Abrus, potentially the results of rapid toxin evolution.Open access journalThis item from the UA Faculty Publications collection is made available by the University of Arizona with support from the University of Arizona Libraries. If you have questions, please contact us at [email protected]

Ground- and Space-based Detection of the Thermal Emission Spectrum of the Transiting Hot Jupiter KELT-2Ab

We describe the detection of water vapor in the atmosphere of the transiting hot Jupiter KELT-2Ab by treating the star-planet system as a spectroscopic binary with high-resolution, ground-based spectroscopy. We resolve the signal of the planet's motion with deep combined flux observations of the star and the planet. In total, six epochs of Keck NIRSPEC $L$-band observations were obtained, and the full data set was subjected to a cross correlation analysis with a grid of self-consistent atmospheric models. We measure a radial projection of the Keplerian velocity, $K_P$, of 148 $\pm$ 7 km s$^{-1}$, consistent with transit measurements, and detect water vapor at 3.8$\sigma$. We combine NIRSPEC $L$-band data with $Spitzer$ IRAC secondary eclipse data to further probe the metallicity and carbon-to-oxygen ratio of KELT-2Ab's atmosphere. While the NIRSPEC analysis provides few extra constraints on the $Spitzer$ data, it does provide roughly the same constraints on metallicity and carbon-to-oxygen ratio. This bodes well for future investigations of the atmospheres of non-transiting hot Jupiters.Comment: accepted to A