A Soft-Magnetic Slender Body in a Highly Viscous Fluid

Theoretical, numerical, and experimental studies for a rotating soft-magnetic body in low Reynolds number flow which imitates the motion of nodal cilia are considered. This includes a discussion of the torque balance for the coupled magnetic-fluid interaction for a rod rotating in a viscous fluid, and a discussion of experimental results which have suggested alterations to the current slender body theory used to find the flow around a rotating rod. Firstly, the current state of the theory for a slender rod attached to a no-slip plane sweeping out a cone will be discussed in terms of the singularity strength distribution which allows us to calculate the forces and torques on the slender body. This theory has been developed in the works of Terry Jo Leiterman and Longhua Zhao for straight and bent rod geometries respectively. Analogous techniques of the classical fluid slender body theory are then applied for a soft-magnetic rod in free space in order to generate the appropriate strength distribution for the singularities placed along the center line of the rod. A discussion of the magnetic slender body theory is presented for a rod in free space and for a rod held fixed about a point in a uniform background field. Once the appropriate strength distribution is found through asymptotic matching, the magnetic torque on the rod may be calculated. A steady-state problem is considered where the position of the rod relative to the magnetic field may be found by balancing the fluid and magnetic torques. For a straight rod sweeping an upright cone in a uniform background magnetic field, this problem reduces to finding the solution to a polynomial whose arguments are trigonometric functions of the angles involved in describing the position of the rod and magnetic field. From this polynomial, we may construct explicit intervals in which the solution is unique. We also examine various limiting cases that should be seen in the physical experiment as a first-order check to the validity of the magnetic model. The magnetic problem is then extended to bent rod geometries, again using similar techniques derived in the fluid slender body theory. This bent rod geometry creates rather unwieldy expressions for the fluid and magnetic torque, but nonetheless, the torque balance may be solved numerically. This theory is not currently put to use in our experiment since the exact properties of our driving magnet have not been considered. Next, a discussion of the current state of our experiments for a rod rotating in a viscous fluid is presented. It is of great importance to understand the results of our Lagrangian particle tracking which were discussed for both straight and bent pin geometries by Leiterman and Zhao. Progress has been made in the procedure for tracking the rod which ensures that better measurements for the angles which describe the rod position are passed the the theory for comparison. Key differences between the theory and experimental results are presented. In order to corroborate these Lagrangian results and suggest alterations to the current fluid theory, we use a full three-dimensional particle image velocimetry (PIV) to capture an Eulerian view of the fluid flow structure in a horizontal plane slightly above the tip of the rotating rod. A discussion of the experimental setup and parameters is discussed, as well as the metrics we will use to compare the two experimental methods. Results of these experiments are then compared with the theory in various regards. Finally, alterations to the current theory including a consideration of the free surface and lubrication effects are discussed. A comparison is made between particle trajectories for a sphere in a uniform flow over a plane using lubrication theory and singularity theory to establish whether this effect will be non-negligible in our experiment.Doctor of Philosoph

The homeodomain complement of the ctenophore Mnemiopsis leidyi suggests that Ctenophora and Porifera diverged prior to the ParaHoxozoa

<p>Abstract</p> <p>Background</p> <p>The much-debated phylogenetic relationships of the five early branching metazoan lineages (Bilateria, Cnidaria, Ctenophora, Placozoa and Porifera) are of fundamental importance in piecing together events that occurred early in animal evolution. Comparisons of gene content between organismal lineages have been identified as a potentially useful methodology for phylogenetic reconstruction. However, these comparisons require complete genomes that, until now, did not exist for the ctenophore lineage. The homeobox superfamily of genes is particularly suited for these kinds of gene content comparisons, since it is large, diverse, and features a highly conserved domain.</p> <p>Results</p> <p>We have used a next-generation sequencing approach to generate a high-quality rough draft of the genome of the ctenophore <it>Mnemiopsis leidyi </it>and subsequently identified a set of 76 homeobox-containing genes from this draft. We phylogenetically categorized this set into established gene families and classes and then compared this set to the homeodomain repertoire of species from the other four early branching metazoan lineages. We have identified several important classes and subclasses of homeodomains that appear to be absent from <it>Mnemiopsis </it>and from the poriferan <it>Amphimedon queenslandica</it>. We have also determined that, based on lineage-specific paralog retention and average branch lengths, it is unlikely that these missing classes and subclasses are due to extensive gene loss or unusually high rates of evolution in <it>Mnemiopsis</it>.</p> <p>Conclusions</p> <p>This paper provides a first glimpse of the first sequenced ctenophore genome. We have characterized the full complement of <it>Mnemiopsis </it>homeodomains from this species and have compared them to species from other early branching lineages. Our results suggest that Porifera and Ctenophora were the first two extant lineages to diverge from the rest of animals. Based on this analysis, we also propose a new name - ParaHoxozoa - for the remaining group that includes Placozoa, Cnidaria and Bilateria.</p

Rupture in the Hanging Wall of a Basin and Range Normal Fault Revealed by Historical and Geological Analyses

Abstract Analysis of historical accounts of the ϳM 6.3 1884 earthquake in northern Utah reveals that the earthquake had an epicenter near 42.3Њ N, 111.4Њ W, approximately 30 km northwest of the event&apos;s original location. We use detailed reports of damage to structures and the consequences of ground shaking to define a felt area of approximately 70,000 km 2 and estimate the peak ground accelerations as 100-300 cm/sec 2 . Analysis of the geologic structure of the area indicates that the epicentral area is a half-graben bounded on the east by the listric Bear Lake fault and on the west by the steeply dipping West Bear Lake fault. The earthquake epicenter was on the west side of the basin, and we interpret the event to have been the result of slip on the West Bear Lake fault zone at a depth of 4-5 km. This zone consists of steeply dipping antithetic faults in the hanging wall of the East Bear Lake fault. These data suggest that moderate-magnitude earthquakes on antithetic or small-displacement faults pose a significant, if local, seismic hazard in the northeastern Basin and Range province. We also demonstrate the utility of combining geological and historigraphic analyses to examine pre-instrument-era earthquakes

Nuclear receptors from the ctenophore Mnemiopsis leidyi lack a zinc-finger DNA-binding domain: lineage-specific loss or ancestral condition in the emergence of the nuclear receptor superfamily?

<p>Abstract</p> <p>Background</p> <p>Nuclear receptors (NRs) are an ancient superfamily of metazoan transcription factors that play critical roles in regulation of reproduction, development, and energetic homeostasis. Although the evolutionary relationships among NRs are well-described in two prominent clades of animals (deuterostomes and protostomes), comparatively little information has been reported on the diversity of NRs in early diverging metazoans. Here, we identified NRs from the phylum Ctenophora and used a phylogenomic approach to explore the emergence of the NR superfamily in the animal kingdom. In addition, to gain insight into conserved or novel functions, we examined NR expression during ctenophore development.</p> <p>Results</p> <p>We report the first described NRs from the phylum Ctenophora: two from <it>Mnemiopsis leidyi </it>and one from <it>Pleurobrachia pileus</it>. All ctenophore NRs contained a ligand-binding domain and grouped with NRs from the subfamily NR2A (<it>HNF4</it>). Surprisingly, all the ctenophore NRs lacked the highly conserved DNA-binding domain (DBD). NRs from <it>Mnemiopsis </it>were expressed in different regions of developing ctenophores. One was broadly expressed in the endoderm during gastrulation. The second was initially expressed in the ectoderm during gastrulation, in regions corresponding to the future tentacles; subsequent expression was restricted to the apical organ. Phylogenetic analyses of NRs from ctenophores, sponges, cnidarians, and a placozoan support the hypothesis that expansion of the superfamily occurred in a step-wise fashion, with initial radiations in NR family 2, followed by representatives of NR families 3, 6, and 1/4 originating prior to the appearance of the bilaterian ancestor.</p> <p>Conclusions</p> <p>Our study provides the first description of NRs from ctenophores, including the full complement from <it>Mnemiopsis</it>. Ctenophores have the least diverse NR complement of any animal phylum with representatives that cluster with only one subfamily (NR2A). Ctenophores and sponges have a similarly restricted NR complement supporting the hypothesis that the original NR was <it>HNF4</it>-like and that these lineages are the first two branches from the animal tree. The absence of a zinc-finger DNA-binding domain in the two ctenophore species suggests two hypotheses: this domain may have been secondarily lost within the ctenophore lineage or, if ctenophores are the first branch off the animal tree, the original NR may have lacked the canonical DBD. Phylogenomic analyses and categorization of NRs from all four early diverging animal phyla compared with the complement from bilaterians suggest the rate of NR diversification prior to the cnidarian-bilaterian split was relatively modest, with independent radiations of several NR subfamilies within the cnidarian lineage.</p

Angular position of nodes in the superconducting gap of YBCO

The thermal conductivity of a YBCO single crystal has been studied as a function of the relative orientation of the crystal axes and a magnetic field rotating in the Cu-O planes. Measurements were carried out at several temperatures below T_c and at a fixed field of 30 kOe. A four-fold symmetry characteristic of a superconducting gap with nodes at odd multiples of 45 degrees in k-space was resolved. Experiments were performed to exclude a possible macroscopic origin for such a four-fold symmetry such as sample shape or anisotropic pinning. Our results impose an upper limit of 10% on the weight of the s-wave component of the essentially d-wave superconducting order parameter of YBCO.Comment: 10 pages, 4 figure

Reinventing grounded theory: some questions about theory, ground and discovery

Grounded theory’s popularity persists after three decades of broad-ranging critique. In this article three problematic notions are discussed—‘theory,’ ‘ground’ and ‘discovery’—which linger in the continuing use and development of grounded theory procedures. It is argued that far from providing the epistemic security promised by grounded theory, these notions—embodied in continuing reinventions of grounded theory—constrain and distort qualitative inquiry, and that what is contrived is not in fact theory in any meaningful sense, that ‘ground’ is a misnomer when talking about interpretation and that what ultimately materializes following grounded theory procedures is less like discovery and more akin to invention. The procedures admittedly provide signposts for qualitative inquirers, but educational researchers should be wary, for the significance of interpretation, narrative and reflection can be undermined in the procedures of grounded theory

Directing Modernist Spirituality: Evelyn Underhill, the Subliminal Consciousness and Spiritual Direction

Outlining an alternative trajectory for modernist spirituality to that traced in Pericles Lewis’s 'Religious Experience and the Modernist Novel' (2010), I argue that modernist religious thought, far from playing heir to the long march of secularization, was in fact conditioned by a late-nineteenth-century cultural crisis that issued in a range of religious experiments and renewals, one of which was Evelyn Underhill’s 'Mysticism: A Study in the Nature and Development of Man’s Spiritual Consciousness' (1911), a text that not only brought together mystical traditions and scientific discoveries, but also used this interdisciplinary remit to counter existing secularizing perspectives. An important dimension of Underhill’s work was its collaborative nature; it offers, I argue, not access to rarefied enlightenment, but rather a bold attempt to navigate a treacherous religious landscape

Investigating Mercury's Environment with the Two-Spacecraft BepiColombo Mission

The ESA-JAXA BepiColombo mission will provide simultaneous measurements from two spacecraft, offering an unprecedented opportunity to investigate magnetospheric and exospheric dynamics at Mercury as well as their interactions with the solar wind, radiation, and interplanetary dust. Many scientific instruments onboard the two spacecraft will be completely, or partially devoted to study the near-space environment of Mercury as well as the complex processes that govern it. Many issues remain unsolved even after the MESSENGER mission that ended in 2015. The specific orbits of the two spacecraft, MPO and Mio, and the comprehensive scientific payload allow a wider range of scientific questions to be addressed than those that could be achieved by the individual instruments acting alone, or by previous missions. These joint observations are of key importance because many phenomena in Mercury's environment are highly temporally and spatially variable. Examples of possible coordinated observations are described in this article, analysing the required geometrical conditions, pointing, resolutions and operation timing of different BepiColombo instruments sensors.Peer reviewe

The Diversification of the LIM Superclass at the Base of the Metazoa Increased Subcellular Complexity and Promoted Multicellular Specialization

Background: Throughout evolution, the LIM domain has been deployed in many different domain configurations, which has led to the formation of a large and distinct group of proteins. LIM proteins are involved in relaying stimuli received at the cell surface to the nucleus in order to regulate cell structure, motility, and division. Despite their fundamental roles in cellular processes and human disease, little is known about the evolution of the LIM superclass. Results: We have identified and characterized all known LIM domain-containing proteins in six metazoans and three nonmetazoans. In addition, we performed a phylogenetic analysis on all LIM domains and, in the process, have identified a number of novel non-LIM domains and motifs in each of these proteins. Based on these results, we have formalized a classification system for LIM proteins, provided reasonable timing for class and family origin events; and identified lineagespecific loss events. Our analysis is the first detailed description of the full set of LIM proteins from the non-bilaterian species examined in this study. Conclusion: Six of the 14 LIM classes originated in the stem lineage of the Metazoa. The expansion of the LIM superclass at the base of the Metazoa undoubtedly contributed to the increase in subcellular complexity required for the transition from a unicellular to multicellular lifestyle and, as such, was a critically important event in the history of animal multicellularity