Interface-resolved direct numerical simulations of sediment transport in a turbulent oscillatory boundary layer

The flow within an oscillatory boundary layer, which approximates the flow generated by propagating sea waves of small amplitude close to the bottom, is simulated numerically by integrating the Navier-Stokes and continuity equations. The bottom is made up of spherical particles, free to move, which mimic sediment grains. The approach allows one to fully resolve the flow around the particles and to evaluate the forces and torques that the fluid exerts on their surface. Then, the dynamics of sediments is explicitly computed by means of the Newton-Euler equations. For the smallest value of the flow Reynolds number presently simulated, the flow regime turns out to fall in the intermittently turbulent regime such that turbulence appears when the free-stream velocity is close to its largest value but the flow recovers a laminar-like behaviour during the remaining phases of the cycle. For the largest value of the Reynolds number, turbulence is significant during almost the whole flow cycle. The evaluation of the sediment transport rate allows one to estimate the reliability of the empirical predictors commonly used to estimate the amount of sediments transported by sea waves. For large values of the Shields parameter, the sediment flow rate during the accelerating phases does not differ from that observed during the decelerating phases. However, for relatively small values of the Shields parameter, the amount of moving particles depends not only on the bottom shear stress but also on flow acceleration. Moreover, the numerical results provide information on the role that turbulent eddies have on sediment dynamics

Simultaneous determination of eight underivatized biogenic amines in fish by solid phase extraction and liquid chromatography-tandem mass spectrometry

Biogenic amines on fish tissue are formed as a result of bacterial contamination and spoilage during storage. A new method based on liquid chromatography (LC) and tandem mass spectrometry (MS/MS) using a triple quadrupole (QqQ) analyser was developed for the analysis of eight biogenic amines (cadaverine, histamine, phenylethylamine, putrescine, spermine, spermidine, tyramine and tryptamine) in fish tissues. Sample preparation was performed by extraction with trichloroacetic acid 5% and solid phase extraction clean up with STRATA X cartridge. The MS/MS method was validated and compared with a method based on the analysis of dansyl derivatives by LC and fluorescence detector (FD). MS/MS achieved higher sensitivity (from 0.02 mg kg1 for spermidine and phenylethylamine to 0.2 mg kg1 for spermine) when compared to FD (from 1 mg kg1 for putrescine and tyramine to 4 mg kg1 for histamine); MS/MS method showed higher precision too, with intraday relative standard deviations (RSDs) from 1% to 4% with respect to those obtained with FD method (from 3% to 17%). Recovery study was conducted at two different fortification levels and the average ranged from 71% to 93% for all of the studied compounds with RSDs lower than 18%. Matrix-matched standards were used to counteract matrix effect observed in MS/MS determination. The applicability of the method was demonstrated by the analysis of biogenic amines in fish obtained from commercials of Valencia

When the path is never shortest: a reality check on shortest path biocomputation

Shortest path problems are a touchstone for evaluating the computing performance and functional range of novel computing substrates. Much has been published in recent years regarding the use of biocomputers to solve minimal path problems such as route optimisation and labyrinth navigation, but their outputs are typically difficult to reproduce and somewhat abstract in nature, suggesting that both experimental design and analysis in the field require standardising. This chapter details laboratory experimental data which probe the path finding process in two single-celled protistic model organisms, Physarum polycephalum and Paramecium caudatum, comprising a shortest path problem and labyrinth navigation, respectively. The results presented illustrate several of the key difficulties that are encountered in categorising biological behaviours in the language of computing, including biological variability, non-halting operations and adverse reactions to experimental stimuli. It is concluded that neither organism examined are able to efficiently or reproducibly solve shortest path problems in the specific experimental conditions that were tested. Data presented are contextualised with biological theory and design principles for maximising the usefulness of experimental biocomputer prototypes.Comment: To appear in: Adamatzky, A (Ed.) Shortest path solvers. From software to wetware. Springer, 201

Slip distributions on active normal faults measured from LiDAR and field mapping of geomorphic offsets: an example from L\u2019Aquila, Italy, and implications for modelling seismic moment release

Surface slip distributions for an active normal fault in central Italy have been measured using terrestrial laser scanning (TLS), in order to assess the impact of changes in fault orientation and kinematics when modelling subsurface slip distributions that control seismic moment release. The southeastern segment of the surface trace of the Campo Felice active normal fault near the city of L\u2019Aquila was mapped and surveyed using techniques from structural geology and using TLS to define the vertical and horizontal offsets of geomorphic slopes since the last glacial maximum (15 \ub13 ka). The fault geometry and kinematics measured from 43 sites and throw/heave measurements from geomorphic offsets seen on 250 scarp profiles were analysed using a modification of the Kostrov equations to calculate the magnitudes and directions of horizontal principal strain-rates. The map trace of the studied fault is linear, except where a prominent bend has formed to link across a former left-stepping relay-zone. The dip of the fault and slip direction is constant across the bend. Throw-rates since 15 \ub13 ka decrease linearly from the fault centre to the tip, except in the location of the prominent bend where higher throw rates are recorded. Vertical coseismic offsets for two palaeoearthquake ruptures seen as fresh strips of rock at the base of the bedrock scarp also increase within the prominent bend. The principal strain-rate, calculated by combining strike, dip, slip-direction and post 15 \ub13 ka throw, decreases linearly from the fault centre towards the tip; the strain-rate does not increase across the prominent fault bend. The above shows that changes in fault strike, whilst having no effect on the principal horizontal strain-rate, can produce local maxima in throw-rates during single earthquakes that persist over the timescale of multiple earthquakes (15 \ub13 ka). Detailed geomorphological and structural investigation of active faults is therefore a critical input in order to properly define fault activity for the purpose of accurate seismic hazard assessment. We discuss the implications of modelling subsurface slip distributions for earthquake ruptures through inversion of GPS, InSAR and strong motion data using planar fault approximations, referring to recent examples on the nearby Paganica fault that ruptured in the Mw 6.3 2009 L\u2019Aquila Earthquak

Memory effect from spinning unbound binaries

We present a recently developed prescription to obtain ready-to-use gravitational wave (GW) polarization states for spinning compact binaries on hyperbolic orbits. We include leading order spin-orbit interactions, invoking 1.5PN-accurate quasi-Keplerian parametrization for the radial part of the orbital dynamics. We also include radiation reaction effects on $h_+$ and $h_{\times}$ during the interaction. In the GW signals from spinning binaries there is evidence of the memory effect in both polarizations, in contrast to the non-spinning case, where only the cross polarizations exhibits non-vanishing amplitudes at infinite time. We also compute 1PN-accurate GW polarization states for non-spinning compact binaries in unbound orbits in a fully parametric way, and compare them with existing waveforms.Comment: 7 pages, 2 figures. To appear in the Proceedings of the 2014 Sant Cugat Forum on Astrophysics. Astrophysics and Space Science Proceedings, ed. C.Sopuerta (Berlin: Springer-Verlag

Exploring the capability of yeasts isolated from colombian fermented cocoa beans to form and degrade biogenic amines in a lab-scale model system for cocoa fermentation

Yeast starters for cocoa fermentation are usually tested according to their enzymatic activities in terms of mucilage degradation and flavor improvement, disregarding their influence on the production or elimination of toxic compounds as biogenic amines (BAs), important for human health. In this work, we tested 145 strains belonging to 12 different yeast species and isolated from the Colombian fermented cocoa beans (CB) for their capability of producing BAs in vitro. Sixtyfive strains were able to decarboxylate at least one of the amino acids tested. Pichia kudriavzevii ECA33 (Pk) and Saccharomyces cerevisiae 4 (Sc) were selected to evaluate their potential to modulate BAs, organic acids, and volatile organic compounds (VOCs) accumulation during a simulated cocoa fermentation. The growth of Sc or Pk in the presence of CB caused a significant reduction (p < 0.05) of 2-phenylethylamine (84% and 37%) and cadaverine (58% and 51%), and a significant increase of tryptamine and putrescine with a strong influence of temperature in BA formation and degradation. In addition, our findings pointed out that Pk induced a major production of fatty acidand amino acid-derived VOCs, while Sc induced more VOCs derived from fatty acids metabolism. Our results suggest the importance of considering BA production in the choice of yeast starters for cocoa fermentation

Adenosine receptor agonists: Synthesis and binding affinity of 2-(aryl)alkylthioadenosine derivatives

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Dynamical models for sand ripples beneath surface waves

We introduce order parameter models for describing the dynamics of sand ripple patterns under oscillatory flow. A crucial ingredient of these models is the mass transport between adjacent ripples, which we obtain from detailed numerical simulations for a range of ripple sizes. Using this mass transport function, our models predict the existence of a stable band of wavenumbers limited by secondary instabilities. Small ripples coarsen in our models and this process leads to a sharply selected final wavenumber, in agreement with experimental observations.Comment: 9 pages. Shortened version of previous submissio