Gillraker analysis and speciation in the thread herring genus Opisthonema

ENGLISH: The thread herrings, genus Opisthonema, family Clupeidae, are marine fishes that occur only in tropical and subtropical waters off both coasts of the American continent. The genus is composed of one Atlantic species and four Pacific species. Opisthonema oglinum (LeSueur), the single species in the western Atlantic Ocean, occurs from Brazil to Massachusetts, at Bermuda, and throughout the West Indies. Opisthonema libertate (Günther), Opisthonema bulleri (Regan), and Opisthonema medirastre, new species, are Pacific coastal species which occur together from Peru to Mexico (with at least one occasionally in California). Opisthonema berlangai, new species, is confined to the vicinity of the Galapagos Islands. SPANISH: Los arenques de hebra, género Opisthonema, familia Clupeidae, son peces marinos que se encuentran sólo en aguas tropicales y subtropicales cerca a ambas costas del continente americano. El género está compuesto de una especie en el Atlántico y de cuatro en el Pacifico. Opisthonema oglinum (LeSueur), única especie que medra el Océano Atlántico occidental, se encuentra del Brasil a Massachusetts, en Bermuda, y las Indias Occidentales. Opisthonema libertate (Günther), Opisthonema bulleri (Regan), y Opisthonema medirastre, especie nueva, son especies costaneras del Pacífico que aparecen entremezcladas del Perú a México (ocasionalmente por lo menos una de ellas en California). Opisthonema berlangai, especie nueva, está confinada a la vecindad de las Islas Galápagos.

Transport Properties And Induced Voltage In The Structure Of Water-Filled Single-Walled Boron-Nitrogen Nanotubes

Density functional theory/molecular dynamics simulations were employed to give insights into the mechanism of voltage generation based on a water-filled single-walled boron-nitrogen nanotube (SWBNNT). Our calculations showed that (1) the transport properties of confined water in a SWBNNT are different from those of bulk water in view of configuration, the diffusion coefficient, the dipole orientation, and the density distribution, and (2) a voltage difference of several millivolts would generate between the two ends of a SWBNNT due to interactions between the water dipole chains and charge carriers in the tube. Therefore, this structure of a water-filled SWBNNT can be a promising candidate for a synthetic nanoscale power cell as well as a practical nanopower harvesting device.

The decline in the commercially important species of fish and predominance of Clarias lazera in Lake Chad

About 86 species of fish have been recorded in the Lake Chad. Most of the species occurring in the lake are widespread including most of the commercially important species. Fish distribution in the lake was adversely affected by the 1972/73 and 1983/84 droughts. The commercially important species before the 1972/73 drought were; Lates, Labeo distichodus, Heterotis, Gymnarchus, Hydrocynus, Citharinus and Bagrus. Other species which had less commercial value at that time include, Clarias, Gnathanemus, Polypterus, Protopterus, Tilapia and Synodontis. Lates niloticus was the most predominant species of commercial importance comprising 50-60% of the total catches of fishermen between 1962 and 1973. Before the 1972/73 drought, occurrence of Clarias lazera was negligible and restricted to long line catches and had little commercial value. As a result of the drought of 1972/73 which resulted in near drying up to the northern sector of the lake, fish populations were confined to isolated pools and were completely scooped out. The remaining fish populations retreated to the southern basin where enough water always remained to hold the surviving representatives of the population. The effects of the drought resulted in occurrence of the little known C. lazera along with other hardy species like Tilapia and Protopterus to dominate the existing fish species composition. In 1976, C. lazera dominated the total catches of fishermen with 85.6%. An overview of the fish population in the lake, their relative abundance, changes in species composition, the effects of drought on the fauna of the lake based on the available data are discussed in this paper

Transport properties and induced voltage in the structure of water-filled single-walled boron-nitrogen nanotubes

Density functional theory/molecular dynamics simulations were employed to give insights into the mechanism of voltage generation based on a water-filled single-walled boron-nitrogen nanotube (SWBNNT). Our calculations showed that (1) the transport properties of confined water in a SWBNNT are different from those of bulk water in view of configuration the diffusion coefficient the dipole orientation and the density distribution and (2) a voltage difference of several millivolts would generate between the two ends of a SWBNNT due to interactions between the water dipole chains and charge carriers in the tube. Therefore this structure of a water-filled SWBNNT can be a promising candidate for a synthetic nanoscale power cell as well as a practical nanopower harvesting device.

The stochastic exit problem for dynamical systems

The problem of "exit against a flow" for dynamical systems subject to small Gaussian white noise excitation is studied. Here the word "flow" refers to the behavior in phase space of the unperturbed system's state variables. "Exit against a flow" occurs if a perturbation causes the phase point to leave a phase space region within which it would normally be confined. In particular, there are two components of the problem of exit against a flow:

i) the mean exit time

ii) the phase-space distribution of exit locations.

When the noise perturbing the dynamical systems is small, the solution of each component of the problem of exit against a flow is, in general, the solution of a singularly perturbed, degenerate elliptic-parabolic boundary value problem.

Singular perturbation techniques are used to express the asymptotic solution in terms of an unknown parameter. The unknown parameter is determined using the solution of the adjoint boundary value problem.

The problem of exit against a flow for several dynamical systems of physical interest is considered, and the mean exit times and distributions of exit positions are calculated. The systems are then simulated numerically, using Monte Carlo techniques, in order to determine the validity of the asymptotic solutions.

Insights into the mechanism of human erythrocyte hexose transport : a transferred NOE study of glucose binding to GLUT1

This study examines binding of α- and β-D-glucose in their equilibrium mixture to the glucose transporter (GLUT1) in human erythrocyte membrane preparations by an ^1H NMR method, the transferred NOE (TRNOE). This method is shown theoretically and experimentally to be a sensitive probe of weak ligand-macromolecule interactions. The TRNOEs observed are shown to arise solely from glucose binding to GLUT1. Sites at both membrane faces contribute to the TRNOEs. Binding curves obtained are consistent with a homogeneous class of sugar sites, with an apparent K_D which varies (from ~30 mM to ~70 mM for both anomers) depending on the membrane preparation examined. Preparations with a higher proportion of the cytoplasmic membrane face exposed to bulk solution yield higher apparent KK_Ds. The glucose transport inhibitor cytochalasin B essentially eliminates the TRNOE. Nonlinearity was found in the dependence on sugar concentration of the apparent inhibition constant for cytochalasin B reversal of the TRNOE observed in the α anomer (and probably the β anomer); such nonlinearity implies the existence of ternary complexes of sugar, inhibitor and transporter. The inhibition results furthermore imply the presence of a class of relatively high-affinity (K_D < 2mM) sugar sites specific for the α anomer which do not contribute to NMR-observable binding. The presence of two classes of sugar-sensitive cytochalasin B sites is also indicated. These results are compared with predictions of the alternating conformer model of glucose transport. Variation of apparent K_D in the NMR-observable sites, the formation of ternary complexes and the presence of an anomer-specific site are shown to be inconsistent with this model. An alternate model is developed which reconciles these results with the known transport behavior of GLUT1. In this model, the transporter possesses (at minimum) three classes of sugar sites: (i) transport sites, which are alternately exposed to the cytoplasmic or the extracellular compartment, but never to both simultaneously, (ii) a class of sites (probably relatively low-affinity) which are confined to one compartment, and (iii) the high-affinity α anomer-specific sites, which are confined to the cytoplasmic compartment.

Interacting single atoms with nanophotonics for chip-integrated quantum networks

Underlying matter and light are their building blocks of tiny atoms and photons. The ability to control and utilize matter-light interactions down to the elementary single atom and photon level at the nano-scale opens up exciting studies at the frontiers of science with applications in medicine, energy, and information technology. Of these, an intriguing front is the development of quantum networks where N >> 1 single-atom nodes are coherently linked by single photons, forming a collective quantum entity potentially capable of performing quantum computations and simulations. Here, a promising approach is to use optical cavities within the setting of cavity quantum electrodynamics (QED). However, since its first realization in 1992 by Kimble et al., current proof-of-principle experiments have involved just one or two conventional cavities. To move beyond to N >> 1 nodes, in this thesis we investigate a platform born from the marriage of cavity QED and nanophotonics, where single atoms at ~100 nm near the surfaces of lithographically fabricated dielectric photonic devices can strongly interact with single photons, on a chip. Particularly, we experimentally investigate three main types of devices: microtoroidal optical cavities, optical nanofibers, and nanophotonic crystal based structures. With a microtoroidal cavity, we realized a robust and efficient photon router where single photons are extracted from an incident coherent state of light and redirected to a separate output with high efficiency. We achieved strong single atom-photon coupling with atoms located ~100 nm near the surface of a microtoroid, which revealed important aspects in the atom dynamics and QED of these systems including atom-surface interaction effects. We present a method to achieve state-insensitive atom trapping near optical nanofibers, critical in nanophotonic systems where electromagnetic fields are tightly confined. We developed a system that fabricates high quality nanofibers with high controllability, with which we experimentally demonstrate a state-insensitive atom trap. We present initial investigations on nanophotonic crystal based structures as a platform for strong atom-photon interactions. The experimental advances and theoretical investigations carried out in this thesis provide a framework for and open the door to strong single atom-photon interactions using nanophotonics for chip-integrated quantum networks.

Ghosts of order on the frontier of chaos

What kinds of motion can occur in classical mechanics? We address this question by looking at the structures traced out by trajectories in phase space; the most orderly, completely integrable systems are characterized by phase trajectories confined to low-dimensional, invariant tori. The KAM theory examines what happens to the tori when an integrable system is subjected to a small perturbation and finds that, for small enough perturbations, most of them survive.

The KAM theory is mute about the disrupted tori, but, for two-dimensional systems, Aubry and Mather discovered an astonishing picture: the broken tori are replaced by "cantori," tattered, Cantor-set remnants of the original invariant curves. We seek to extend Aubry and Mather's picture to higher dimensional systems and report two kinds of studies; both concern perturbations of a completely integrable, four-dimensional symplectic map. In the first study we compute some numerical approximations to Birkhoff periodic orbits; sequences of such orbits should approximate any higher dimensional analogs of the cantori. In the second study we prove converse KAM theorems; that is, we use a combination of analytic arguments and rigorous, machine-assisted computations to find perturbations so large that no KAM tori survive. We are able to show that the last few of our Birkhoff orbits exist in a regime where there are no tori.

Towards conditional RNAi : shape and sequence transduction with small conditional RNAs

RNA interference (RNAi) is a powerful biological pathway allowing for sequence-specific knockdown of any gene of interest. While RNAi is a proven tool for probing gene function in biological circuits, it is limited by being constitutively ON and executes the logical operation: silence gene Y. To provide greater control over post-transcriptional gene silencing, we propose engineering a biological logic gate to implement “conditional RNAi.” Such a logic gate would silence gene Y only upon the expression of gene X, a completely unrelated gene, executing the logic: if gene X is transcribed, silence independent gene Y. Silencing of gene Y could be confined to a specific time and/or tissue by appropriately selecting gene X.

To implement the logic of conditional RNAi, we present the design and experimental validation of three nucleic acid self-assembly mechanisms which detect a sub-sequence of mRNA X and produce a Dicer substrate specific to gene Y. We introduce small conditional RNAs (scRNAs) to execute the signal transduction under isothermal conditions. scRNAs are small RNAs which change conformation, leading to both shape and sequence signal transduction, in response to hybridization to an input nucleic acid target. While all three conditional RNAi mechanisms execute the same logical operation, they explore various design alternatives for nucleic acid self-assembly pathways, including the use of duplex and monomer scRNAs, stable versus metastable reactants, multiple methods of nucleation, and 3-way and 4-way branch migration.

We demonstrate the isothermal execution of the conditional RNAi mechanisms in a test tube with recombinant Dicer. These mechanisms execute the logic: if mRNA X is detected, produce a Dicer substrate targeting independent mRNA Y. Only the final Dicer substrate, not the scRNA reactants or intermediates, is efficiently processed by Dicer. Additional work in human whole-cell extracts and a model tissue-culture system delves into both the promise and challenge of implementing conditional RNAi in vivo.

Guiding and confining fast electrons by transient electric and magnetic fields with a plasma inverse cone

The fast electron propagation in an inverse cone target is investigated computationally and experimentally. Two-dimensional particle-in-cell simulation shows that fast electrons with substantial numbers are generated at the outer tip of an inverse cone target irradiated by a short intense laser pulse. These electrons are guided and confined to propagate along the inverse cone wall, forming a large surface current. The propagation induces strong transient electric and magnetic fields which guide and confine the surface electron current. The experiment qualitatively verifies the guiding and confinement of the strong electron current in the wall surface. The large surface current and induced strong fields are of importance for fast ignition related researches.

Design support for turbomachinery

From the steam turbines which provide most of our electricity to the jet engines which have shrunk our World, turbomachines undoubtedly play a major role in life today. Competition in the turbomachinery industry is fiercely strong [Wisler, 1998], hence good aerodynamic design is vital. However, with efficiency levels already close to their theoretical maxima, companies are increasingly looking to reduce costs and increase reliability through improved design practice. Computational Fluid Dynamics (CFD) can make a strong contribution to assisting this process as it has the potential to increase performance while reducing cost. The situation is, however, complicated by an ever decreasing number of engineers with sufficient design experience to reap the full benefits offered by CFD. With the large risks involved, novice designers of today are increasingly confined to refining old designs rather than gaining experience, like their forebears, through 'clean sheet' exercises. Hence it is desirable to capture the knowledge and experience of older designers, before it is lost, to assist the engineers of tomorrow. It is therefore the aim of this project to produce a design support tool which will not only store the appropriate CFD codes, but also provide a dynamic signpost (based on elicited knowledge and experience) to advise the engineer in their use. The signposting methodology developed for the aerospace industry [Clarkson and Hamilton, 1997] will provide the basic framework for the tool. This paper reviews current turbomachinery design practice (including an examination of the relevant CFD) in order to establish the important issues which a support tool must address. Current design support methodologies and their propriety are then reviewed, followed by a detailed description of the signposting concept. It then sets out a clear statement of the objectives for the research and the methods proposed to meet them. The paper concludes with a timetable of the work.

Magnetohydrodynamic turbulence

We simulate incompressible, MHD turbulence using a pseudo-spectral code. Our major conclusions are as follows.

1) MHD turbulence is most conveniently described in terms of counter propagating shear Alfvén and slow waves. Shear Alfvén waves control the cascade dynamics. Slow waves play a passive role and adopt the spectrum set by the shear Alfvén waves. Cascades composed entirely of shear Alfvén waves do not generate a significant measure of slow waves.

2) MHD turbulence is anisotropic with energy cascading more rapidly along k_⊥ than along k_∥, where k_⊥ and k_∥ refer to wavevector components perpendicular and parallel to the local magnetic field. Anisotropy increases with increasing k_⊥ such that excited modes are confined inside a cone bounded by k_∥ ∝ k^γ_⊥ where γ less than 1. The opening angle of the cone, θ(k_⊥) ∝ k^-(1-γ)_⊥, defines the scale dependent anisotropy.

3) MHD turbulence is generically strong in the sense that the waves which comprise it suffer order unity distortions on timescales comparable to their periods. Nevertheless, turbulent fluctuations are small deep inside the inertial range. Their energy density is less than that of the background field by a factor θ² (k_⊥)≪1.

4) MHD cascades are best understood geometrically. Wave packets suffer distortions as they move along magnetic field lines perturbed by counter propagating waves. Field lines perturbed by unidirectional waves map planes perpendicular to the local field into each other. Shear Alfvén waves are responsible for the mapping's shear and slow waves for its dilatation. The amplitude of the former exceeds that of the latter by 1/θ(k_⊥) which accounts for dominance of the shear Alfvén waves in controlling the cascade dynamics.

5) Passive scalars mixed by MHD turbulence adopt the same power spectrum as the velocity and magnetic field perturbations.

6) Decaying MHD turbulence is unstable to an increase of the imbalance between the flux of waves propagating in opposite directions along the magnetic field. Forced MHD turbulence displays order unity fluctuations with respect to the balanced state if excited at low k by δ(t) correlated forcing. It appears to be statistically stable to the unlimited growth of imbalance.

7) Gradients of the dynamic variables are focused into sheets aligned with the magnetic field whose thickness is comparable to the dissipation scale. Sheets formed by oppositely directed waves are uncorrelated. We suspect that these are vortex sheets which the mean magnetic field prevents from rolling up.

8) Items (1)-(5) lend support to the model of strong MHD turbulence put forth by Goldreich and Sridhar (1995, 1997). Results from our simulations are also consistent with the GS prediction γ = 2/3. The sole not able discrepancy is that the 1D power law spectra, E(k_⊥) ∝ k^-∝_⊥, determined from our simulations exhibit ∝ ≈ 3/2, whereas the GS model predicts ∝ = 5/3.

Microwave absorption and emission from magnetized afterglow plasmas

The microwave scattering properties of an axially magnetized afterglow plasma column in an S-band waveguide have been investigated experimentally. The column axis is perpendicular to the electric field and the direction of wave propagation in the H_(10)-mode waveguide. Strong absorption is found in the range of upper hybrid frequencies, ω_c ≤ ω ≤ [ω^2_c + ω^2_p(r,t)]^(1/2) where ω_c is the electron cyclotron frequency and ω_p is the locally and temporally varying electron plasma frequency. With the high absorption the noise emission approaches the blackbody limit. A microwave radiometer has been used to measure the noise power and with a comparison and null-technique the electron temperature. As emission and absorption are largely confined to a resonant layer, spatially resolved temperature data are obtained. Time resolution is obtained by gating the radiometer. The peak electron density is derived from the emission or absorption onset at the maximum upper hybrid frequency and confirmed by independent measurements. With this diagnostic technique the electron density and temperature decay has been studied under a variety of experimental conditions. Ambipolar diffusion and collisional cooling essentially account for the plasma decay, but impurities and metastable ions play an important role. The diagnostic method is successfully applied in a microwave heating experiment. The existence of absorbing resonant layers is shown by a peak in the radial temperature profile where the local upper hybrid frequency equals the heating frequency. The knowledge of the plasma parameters is important in the study of hot plasma effects. Buchsbaum-Hasegawa modes are investigated in a wide range of magnetic fields (.5 < ω_c/ω < .985).

Study of dynamical behaviour and fermionization of a bosonic gas in funnel potential

This paper presents a funnel external potential model to investigate dynamic properties of ultracold Bose gas. By using variational method, we obtain the ground-state energy and density properties of ultracold Bose atoms. The results show that the ultracold Bose gas confined in a funnel potential experiences the transition from three-dimensional regime to quasi-one-dimensional regime in a small aspect ratio, and undergoes fermionization process as the aspect ratio increases.

Guiding neutral atoms with two current-carrying wires and a vertical bias field on the atom chip

We demonstrate the guiding of neutral atoms with two parallel microfabricated current-carrying wires on the atom chip and a vertical magnetic bias field. The atoms are guided along a magnetic field minimum parallel to the current-carrying wires and confined in the other two directions. We describe in detail how the precooled atoms are efficiently loaded into the two-wire guide. We present a detailed experimental study of the motional properties of the atoms in the guide and the relationship between the location of the guide and the vertical bias field. This two-wire guide with vertical bias field can be used to realize large area atom interferometer.