Coupling the PLANKTOM5.0 marine ecosystem model to the OCCAM 1º ocean general circulation model for investigation of the sensitivity of global biogeochemical cycles to variations in ecosystem complexity and physical environment

The earliest marine ecosystem models consisted of a simple representation of the main features of marine ecosystems, including, typically, variables for phytoplankton, zooplankton, nutrient and detritus (NPZD models). These have been incorporated into ocean general circulation models to give a basic representation of ecosystem function, providing predictions of bulk quantities such as global primary production, export and biomass which can be compared with available observations. A recent trend has been to increase the number of phytoplankton and zooplankton groups modelled, as analogues of different plankton groups observed to exist in the ocean, for example diatoms and cocolithophores (the so-called plankton functional type or PFT approach). It is usually assumed that the increase in complexity of the model will result in simulated ecosystems which more faithfully reproduce observations than NPZD models, but this has not been demonstrated systematically. The robustness of the PFT models to changes in model parameters and to changes to the physical environment in which it is embedded, have not been investigated. As a first step towards these goals, we incorporate a state-of-the-art PFT model, PLANKTOM5.0 into the OCCAM ocean general circulation model. A 6 year simulation is performed, covering the years 1989-1994 with identical parameter choices to an existing run of PLANKTOM5.0 coupled to the OPA general circulation model. This document describes the development of the coupled model and the 6 year simulation. Comparison with the OPA model and sensitivity of the solution to parameter choices will be described in a forthcoming journal paper

Transport properties of clean and disordered superconductors in matrix field theory

A comprehensive field theory is developed for superconductors with quenched disorder. We first show that the matrix field theory, used previously to describe a disordered Fermi liquid and a disordered itinerant ferromagnet, also has a saddle-point solution that describes a disordered superconductor. A general gap equation is obtained. We then expand about the saddle point to Gaussian order to explicitly obtain the physical correlation functions. The ultrasonic attenuation, number density susceptibility, spin density susceptibility and the electrical conductivity are used as examples. Results in the clean limit and in the disordered case are discussed respectively. This formalism is expected to be a powerful tool to study the quantum phase transitions between the normal metal state and the superconductor state.Comment: 9 page

EMPOWER-1.0: an Efficient Model of Planktonic ecOsystems WrittEn in R

Modelling marine ecosystems requires insight and judgement when it comes to deciding upon appropriate model structure, equations and parameterisation. Many processes are relatively poorly understood and tough decisions must be made as to how to mathematically simplify the real world. Here, we present an efficient plankton modelling testbed, EMPOWER-1.0 (Efficient Model of Planktonic ecOsystems WrittEn in R), coded in the freely available language R. The testbed uses simple two-layer "slab" physics whereby a seasonally varying mixed layer which contains the planktonic marine ecosystem is positioned above a deep layer that contains only nutrient. As such, EMPOWER-1.0 provides a readily available and easy to use tool for evaluating model structure, formulations and parameterisation. The code is transparent and modular such that modifications and changes to model formulation are easily implemented allowing users to investigate and familiarise themselves with the inner workings of their models. It can be used either for preliminary model testing to set the stage for further work, e.g. coupling the ecosystem model to 1-D or 3-D physics, or for undertaking front line research in its own right. EMPOWER-1.0 also serves as an ideal teaching tool. In order to demonstrate the utility of EMPOWER-1.0, we implemented a simple nutrient–phytoplankton–zooplankton–detritus (NPZD) ecosystem model and carried out both a parameter tuning exercise and structural sensitivity analysis. Parameter tuning was demonstrated for four contrasting ocean sites, focusing on station BIOTRANS in the North Atlantic (47° N, 20° W), highlighting both the utility of undertaking a planned sensitivity analysis for this purpose, yet also the subjectivity which nevertheless surrounds the choice of which parameters to tune. Structural sensitivity tests were then performed comparing different equations for calculating daily depth-integrated photosynthesis, as well as mortality terms for both phytoplankton and zooplankton. Regarding the calculation of daily photosynthesis, for example, results indicated that the model was relatively insensitive to the choice of photosynthesis–irradiance curve, but markedly sensitive to the method of calculating light attenuation in the water column. The work highlights the utility of EMPOWER-1.0 as a means of comprehending, diagnosing and formulating equations for the dynamics of marine ecosystems

Benthic biomass size spectra in shelf and deep-sea sediments

The biomass distributions of marine benthic metazoans (meio- to macro-fauna, 1 ?g–32 mg wet weight) across three contrasting sites were investigated to test the hypothesis that allometry can consistently explain observed trends in biomass spectra. Biomass (and abundance) size spectra were determined from observations made at the Faroe–Shetland Channel (FSC) in the Northeast Atlantic (water depth 1600 m), the Fladen Ground (FG) in the North Sea (150 m), and the hypoxic Oman Margin (OM) in the Arabian Sea (500 m). Observed biomass increased with body size as a power law at FG (scaling exponent, b = 0.16) and FSC (b = 0.32), but less convincingly at OM (b = 0.12 but not significantly different from 0). A simple model was constructed to represent the same 16 metazoan size classes used for the observed spectra, all reliant on a common detrital food pool, and allowing the three key processes of ingestion, respiration and mortality to scale with body size. A micro-genetic algorithm was used to fit the model to observations at the sites. The model accurately reproduces the observed scaling without needing to include the effects of local influences such as hypoxia. Our results suggest that the size-scaling of mortality and ingestion are dominant factors determining the distribution of biomass across the meio- to macrofaunal size range in contrasting marine sediment communities. Both the observations and the model results are broadly in agreement with the "metabolic theory of ecology" in predicting a quarter power scaling of biomass across geometric body size classes

Combination Rules, Charge Symmetry, and Hall Effect in Cuprates

The rule relating the observed Hall coefficient to the spin and charge responses of the uniform doped Mott insulator is derived. It is essential to include the contribution of holon and spinon three-current correlations to the effective action of the gauge field. In the vicinity of the Mott insulating point the Hall coefficient is holon dominated and weakly temperature dependent. In the vicinity of a point of charge conjugation symmetry the holon contribution to the observed Hall coefficient is small: the Hall coefficient follows the temperature dependence of the diamagnetic susceptibility with a sign determined by the Fermi surface shape. NOTE: document prepared using REVTEX. (3 Figs, not included, available on request from: [email protected])Comment: 8 page

Climate change and ocean acidification impacts on lower trophic levels and the export of organic carbon to the deep ocean

Most future projections forecast significant and ongoing climate change during the 21st century, but with the severity of impacts dependent on efforts to restrain or reorganise human activity to limit carbon dioxide (CO2) emissions. A major sink for atmospheric CO2, and a key source of biological resources, the World Ocean is widely anticipated to undergo profound physical and – via ocean acidification – chemical changes as direct and indirect results of these emissions. Given strong biophysical coupling, the marine biota is also expected to experience strong changes in response to this anthropogenic forcing. Here we examine the large-scale response of ocean biogeochemistry to climate and acidification impacts during the 21st century for Representative Concentration Pathways (RCPs) 2.6 and 8.5 using an intermediate complexity global ecosystem model, MEDUSA-2.0. The primary impact of future change lies in stratification-led declines in the availability of key nutrients in surface waters, which in turn leads to a global decrease (1990s vs. 2090s) in ocean productivity (?6.3%). This impact has knock-on consequences for the abundance of the low trophic level biogeochemical actors modelled by MEDUSA-2.0 (?5.8%), and these would be expected to similarly impact higher trophic level elements such as fisheries. Related impacts are found in the flux of organic material to seafloor communities (?40.7% at 1000 m), and in the volume of ocean suboxic zones (+12.5%). A sensitivity analysis removing an acidification feedback on calcification finds that change in this process significantly impacts benthic communities, suggesting that a~better understanding of the OA-sensitivity of calcifying organisms, and their role in ballasting sinking organic carbon, may significantly improve forecasting of these ecosystems. For all processes, there is geographical variability in change – for instance, productivity declines ?21% in the Atlantic and increases +59% in the Arctic – and changes are much more pronounced under RCP 8.5 than the RCP 2.6 scenario

Spectroscopic biomedical imaging with the Medipix2 detector

This study confirms that the Medipix2 x-ray detector enables spectroscopic bio-medical plain radiography. We show that the detector has the potential to provide new, useful information beyond the limited spectroscopic information of modern dual-energy computed tomography (CT) scanners. Full spectroscopic 3D-imaging is likely to be the next major technological advance in computed tomography, moving the modality towards molecular imaging applications. This paper focuses on the enabling technology which allows spectroscopic data collection and why this information is useful. In this preliminary study we acquired the first spectroscopic images of human tissue and other biological samples obtained using the Medipix2 detector. The images presented here include the clear resolution of the 1.4mm long distal phalanx of a 20 week old miscarried foetus, showing clear energy-dependent variations. The opportunities for further research using the forthcoming Medipix3 detector are discussed and a prototype spectroscopic CT scanner (MARS, Medipix All Resolution System) is briefly described

Relaxation rates and collision integrals for Bose-Einstein condensates

Near equilibrium, the rate of relaxation to equilibrium and the transport properties of excitations (bogolons) in a dilute Bose-Einstein condensate (BEC) are determined by three collision integrals, $\mathcal{G}^{12}$, $\mathcal{G}^{22}$, and $\mathcal{G}^{31}$. All three collision integrals conserve momentum and energy during bogolon collisions, but only $\mathcal{G}^{22}$ conserves bogolon number. Previous works have considered the contribution of only two collision integrals, $\mathcal{G}^{22}$ and $\mathcal{G}^{12}$. In this work, we show that the third collision integral $\mathcal{G}^{31}$ makes a significant contribution to the bogolon number relaxation rate and needs to be retained when computing relaxation properties of the BEC. We provide values of relaxation rates in a form that can be applied to a variety of dilute Bose-Einstein condensates.Comment: 18 pages, 4 figures, accepted by Journal of Low Temperature Physics 7/201

Fourier Analysis of Gapped Time Series: Improved Estimates of Solar and Stellar Oscillation Parameters

Quantitative helio- and asteroseismology require very precise measurements of the frequencies, amplitudes, and lifetimes of the global modes of stellar oscillation. It is common knowledge that the precision of these measurements depends on the total length (T), quality, and completeness of the observations. Except in a few simple cases, the effect of gaps in the data on measurement precision is poorly understood, in particular in Fourier space where the convolution of the observable with the observation window introduces correlations between different frequencies. Here we describe and implement a rather general method to retrieve maximum likelihood estimates of the oscillation parameters, taking into account the proper statistics of the observations. Our fitting method applies in complex Fourier space and exploits the phase information. We consider both solar-like stochastic oscillations and long-lived harmonic oscillations, plus random noise. Using numerical simulations, we demonstrate the existence of cases for which our improved fitting method is less biased and has a greater precision than when the frequency correlations are ignored. This is especially true of low signal-to-noise solar-like oscillations. For example, we discuss a case where the precision on the mode frequency estimate is increased by a factor of five, for a duty cycle of 15%. In the case of long-lived sinusoidal oscillations, a proper treatment of the frequency correlations does not provide any significant improvement; nevertheless we confirm that the mode frequency can be measured from gapped data at a much better precision than the 1/T Rayleigh resolution.Comment: Accepted for publication in Solar Physics Topical Issue "Helioseismology, Asteroseismology, and MHD Connections

Properties of spin-triplet, even-parity superconductors

The physical consequences of the spin-triplet, even-parity pairing that has been predicted to exist in disordered two-dimensional electron systems are considered in detail. We show that the presence of an attractive interaction in the particle-particle spin-triplet channel leads to an instability of the normal metal that competes with the localizing effects of the disorder. The instability is characterized by a diverging length scale, and has all of the characteristics of a continuous phase transition. The transition and the properties of the ordered phase are studied in mean-field theory, and by taking into account Gaussian fluctuations. We find that the ordered phase is indeed a superconductor with an ordinary Meissner effect and a free energy that is lower than that of the normal metal. Various technical points that have given rise to confusion in connection with this and other manifestations of odd-gap superconductivity are also discussed.Comment: 15 pp., REVTeX, psfig, 2 ps figs, final version as publishe