Analytical study of an exclusive genetic switch

The nonequilibrium stationary state of an exclusive genetic switch is considered. The model comprises two competing species and a single binding site which, when bound to by a protein of one species, causes the other species to be repressed. The model may be thought of as a minimal model of the power struggle between two competing parties. Exact solutions are given for the limits of vanishing binding/unbinding rates and infinite binding/unbinding rates. A mean field theory is introduced which is exact in the limit of vanishing binding/unbinding rates. The mean field theory and numerical simulations reveal that generically bistability occurs and the system is in a symmetry broken state. An exact perturbative solution which in principle allows the nonequilibrium stationary state to be computed is also developed and computed to first and second order.Comment: 28 pages, 6 figure

Asymptotic entanglement in a two-dimensional quantum walk

The evolution operator of a discrete-time quantum walk involves a conditional shift in position space which entangles the coin and position degrees of freedom of the walker. After several steps, the coin-position entanglement (CPE) converges to a well defined value which depends on the initial state. In this work we provide an analytical method which allows for the exact calculation of the asymptotic reduced density operator and the corresponding CPE for a discrete-time quantum walk on a two-dimensional lattice. We use the von Neumann entropy of the reduced density operator as an entanglement measure. The method is applied to the case of a Hadamard walk for which the dependence of the resulting CPE on initial conditions is obtained. Initial states leading to maximum or minimum CPE are identified and the relation between the coin or position entanglement present in the initial state of the walker and the final level of CPE is discussed. The CPE obtained from separable initial states satisfies an additivity property in terms of CPE of the corresponding one-dimensional cases. Non-local initial conditions are also considered and we find that the extreme case of an initial uniform position distribution leads to the largest CPE variation.Comment: Major revision. Improved structure. Theoretical results are now separated from specific examples. Most figures have been replaced by new versions. The paper is now significantly reduced in size: 11 pages, 7 figure

Toward the Ultrasonic Sensing of Organic Carbon in Seagrass-Bearing Sediments

Ten percent of all organic carbon (Corg) absorbed by the ocean each year is stored in seagrass-bearing sediments. The preservation of these carbon stores is considered a vital method to mitigate climate change. Seagrass-bearing sediments have been correlated with sediment geophysical properties yet have not been related to sediment acoustic properties. For this purpose, sediment cores were collected from a Thalassia testudinum seagrass meadow in South Texas, USA, where geophysical, acoustical, and Corg properties were measured. It is hypothesized that when deposits of Corg adsorb onto mineral surfaces and are stored in pore spaces, compliant layers between grain contacts and the formation of an organic-rich suspension reduce sediment stiffness. Results from this seagrass meadow demonstrated a strong correlation between sediment P wave modulus and Corg and show promise toward the development of an in situ ultrasonic sediment probe to more rapidly quantify and monitor seagrass carbon stores

Matching fields of a long superconducting film

We obtain the vortex configurations, the matching fields and the magnetization of a superconducting film with a finite cross section. The applied magnetic field is normal to this cross section, and we use London theory to calculate many of its properties, such as the local magnetic field, the free energy and the induction for the mixed state. Thus previous similar theoretical works, done for an infinitely long superconducting film, are recovered here, in the special limit of a very long cross section.Comment: Contains a REVTeX file and 4 figure

Registration of Great Northern Common Bean Cultivar ‘Coyne’ with Enhanced Disease Resistance to Common Bacterial Blight and Bean Rust

Great northern common bean (Phaseolus vulgaris L.) ‘Coyne’ (Reg. No. CV-287, PI 655574) was developed by the dry bean breeding program at the University of Nebraska Agricultural Research Division and released in 2008. It was bred specifically for adaptation to Nebraska growing conditions and for enhanced resistance to common bacterial blight (CBB), a major disease of common bean caused by the seed-borne bacterium Xanthomonas campestris pv. phaseoli (Smith) Dye, and bean common rust Uromyces appendiculatus (Pers.:Pers) Unger. Coyne is a great northern F7:8 line derived from a three-way cross (G95023/Weihing//BelMiNeb-RMR-11). The first cross was made in winter 2003. The F7:8 was tested in advanced yield trials at Scottsbluff and Mitchell, NE, and in growers’ fields in Nebraska. Yield of Coyne was only 47 kg ha–1 lower than ‘Marquis’ in Morrill and Scotts Bluff, NE, counties. Reaction of Coyne to CBB under field conditions was consistent across 3 yr at the West Central Research and Extension Center, North Platte, NE, where fi eld disease ratings of 3.2, 3.5, and 4.4 were recorded in 2005, 2006, and 2007, respectively. Coyne has the Ur-3 and Ur-6 genes for resistance to common bean rust and carries the single dominant hypersensitive I gene that provides resistance to all non-necrotic strains of Bean common mosaic virus. Coyne has bright white seed, blooms 44 d after planting, and is a midseason bean, maturing 91 d after planting

Application of acoustical remote sensing techniques for ecosystem monitoring of a seagrass meadow

Seagrasses provide a multitude of ecosystem services and serve as important organic carbon stores. However, seagrass habitats are declining worldwide, threatened by global climate change and regional shifts in water quality. Acoustical methods have been applied to assess changes in oxygen production of seagrass meadows since sound propagation is sensitive to the presence of bubbles, which exist both within the plant tissue and freely floating the water as byproducts of photosynthesis. This work applies acoustic remote sensing techniques to characterize two different regions of a seagrass meadow: a densely vegetated meadow of Thalassia testudinum and a sandy region sparsely populated by isolated stands of T. testudinum. A Bayesian approach is applied to estimate the posterior probability distributions of the unknown model parameters. The sensitivity of sound to the void fraction of gas present in the seagrass meadow was established by the narrow marginal probability distributions that provided distinct estimates of the void fraction between the two sites. The absolute values of the estimated void fractions are biased by limitations in the forward model, which does not capture the full complexity of the seagrass environment. Nevertheless, the results demonstrate the potential use of acoustical methods to remotely sense seagrass health and density

Inter-seasonal comparison of acoustic propagation in a Thalassia testudinum seagrass meadow in a shallow sub-tropical lagoon

Acoustic propagation measurements were collected in a seagrass meadow in a shallow lagoon for periods of over 65 h in winter and 93 h in summer. A bottom-deployed sound source transmitted chirps (0.1–100 kHz) every 10 min that were received on a four-receiver horizontal hydrophone array. Oceanographic probes measured various environmental parameters. Daytime broadband acoustic attenuation was 2.4 dB greater in summer than winter, and the median received acoustic energy levels were 8.4 dB lower in summer compared to winter. These differences were attributed in part to seasonal changes in photosynthesis bubble production and above-ground seagrass biomass

Inter-seasonal comparison of acoustic propagation in a Thalassia testudinum seagrass meadow in a shallow sub-tropical lagoon

Acoustic propagation measurements were collected in a seagrass meadow in a shallow lagoon for periods of over 65 h in winter and 93 h in summer. A bottom-deployed sound source transmitted chirps (0.1–100 kHz) every 10 min that were received on a four-receiver horizontal hydrophone array. Oceanographic probes measured various environmental parameters. Daytime broadband acoustic attenuation was 2.4 dB greater in summer than winter, and the median received acoustic energy levels were 8.4 dB lower in summer compared to winter. These differences were attributed in part to seasonal changes in photosynthesis bubble production and above-ground seagrass biomass

Broadband sound propagation in a seagrass meadow throughout a diurnal cycle

Acoustic propagation measurements were conducted in a Thalassia testudinum meadow in the Lower Laguna Madre, a shallow bay on the Texas Gulf of Mexico coast. A piezoelectric source transmitted frequency-modulated chirps (0.1 to 100 kHz) over a 24-h period during which oceanographic probes measured environmental parameters including dissolved oxygen and solar irradiance. Compared to a nearby less vegetated area, the received level was lower by as much as 30 dB during the early morning hours. At the peak of photosynthesis-driven bubble production in the late afternoon, an additional decrease in level of 11 dB was observed

Satellite-Derived Variability in Chlorophyll, Wind Stress, Sea Surface Height, and Temperature in the Northern California Current System

Satellite-derived data provide the temporal means and seasonal and nonseasonal variability of four physical and biological parameters off Oregon and Washington ( 41 degrees - 48.5 degrees N). Eight years of data ( 1998 - 2005) are available for surface chlorophyll concentrations, sea surface temperature ( SST), and sea surface height, while six years of data ( 2000 - 2005) are available for surface wind stress. Strong cross-shelf and alongshore variability is apparent in the temporal mean and seasonal climatology of all four variables. Two latitudinal regions are identified and separated at 44 degrees - 46 degrees N, where the coastal ocean experiences a change in the direction of the mean alongshore wind stress, is influenced by topographic features, and has differing exposure to the Columbia River Plume. All these factors may play a part in defining the distinct regimes in the northern and southern regions. Nonseasonal signals account for similar to 60 - 75% of the dynamical variables. An empirical orthogonal function analysis shows stronger intra-annual variability for alongshore wind, coastal SST, and surface chlorophyll, with stronger interannual variability for surface height. Interannual variability can be caused by distant forcing from equatorial and basin-scale changes in circulation, or by more localized changes in regional winds, all of which can be found in the time series. Correlations are mostly as expected for upwelling systems on intra-annual timescales. Correlations of the interannual timescales are complicated by residual quasi-annual signals created by changes in the timing and strength of the seasonal cycles. Examination of the interannual time series, however, provides a convincing picture of the covariability of chlorophyll, surface temperature, and surface height, with some evidence of regional wind forcing