Efficient sampling of atomic configurational spaces.

We describe a method to explore the configurational phase space of chemical systems. It is based on the nested sampling algorithm recently proposed by Skilling (AIP Conf. Proc. 2004, 395; J. Bayesian Anal. 2006, 1, 833) and allows us to explore the entire potential energy surface (PES) efficiently in an unbiased way. The algorithm has two parameters which directly control the trade-off between the resolution with which the space is explored and the computational cost. We demonstrate the use of nested sampling on Lennard-Jones (LJ) clusters. Nested sampling provides a straightforward approximation for the partition function; thus, evaluating expectation values of arbitrary smooth operators at arbitrary temperatures becomes a simple postprocessing step. Access to absolute free energies allows us to determine the temperature-density phase diagram for LJ cluster stability. Even for relatively small clusters, the efficiency gain over parallel tempering in calculating the heat capacity is an order of magnitude or more. Furthermore, by analyzing the topology of the resulting samples, we are able to visualize the PES in a new and illuminating way. We identify a discretely valued order parameter with basins and suprabasins of the PES, allowing a straightforward and unambiguous definition of macroscopic states of an atomistic system and the evaluation of the associated free energies.

Deep-sea benthic footprint of the Deepwater Horizon blowout

The Deepwater Horizon (DWH) accident in the northern Gulf of Mexico occurred on April 20, 2010 at a water depth of 1525 meters, and a deep-sea plume was detected within one month. Oil contacted and persisted in parts of the bottom of the deep-sea in the Gulf of Mexico. As part of the response to the accident, monitoring cruises were deployed in fall 2010 to measure potential impacts on the two main soft-bottom benthic invertebrate groups: macrofauna and meiofauna. Sediment was collected using a multicorer so that samples for chemical, physical and biological analyses could be taken simultaneously and analyzed using multivariate methods. The footprint of the oil spill was identified by creating a new variable with principal components analysis where the first factor was indicative of the oil spill impacts and this new variable mapped in a geographic information system to identify the area of the oil spill footprint. The most severe relative reduction of faunal abundance and diversity extended to 3 km from the wellhead in all directions covering an area about 24 km2. Moderate impacts were observed up to 17 km towards the southwest and 8.5 km towards the northeast of the wellhead, covering an area 148 km2. Benthic effects were correlated to total petroleum hydrocarbon, polycyclic aromatic hydrocarbons and barium concentrations, and distance to the wellhead; but not distance to hydrocarbon seeps. Thus, benthic effects are more likely due to the oil spill, and not natural hydrocarbon seepage. Recovery rates in the deep sea are likely to be slow, on the order of decades or longer.

Accelerating loss of seagrasses across the globe threatens coastal ecosystems

Coastal ecosystems and the services they provide are adversely affected by a wide variety of human activities. In particular, seagrass meadows are negatively affected by impacts accruing from the billion or more people who live within 50 km of them. Seagrass meadows provide important ecosystem services, including an estimated $1.9 trillion per year in the form of nutrient cycling; an order of magnitude enhancement of coral reef fish productivity; a habitat for thousands of fish, bird, and invertebrate species; and a major food source for endangered dugong, manatee, and green turtle. Although individual impacts from coastal development, degraded water quality, and climate change have been documented, there has been no quantitative global assessment of seagrass loss until now. Our comprehensive global assessment of 215 studies found that seagrasses have been disappearing at a rate of 110 square kilometers per year since 1980 and that 29% of the known areal extent has disappeared since seagrass areas were initially recorded in 1879. Furthermore, rates of decline have accelerated from a median of 0.9% per year before 1940 to 7% per year since 1990. Seagrass loss rates are comparable to those reported for mangroves, coral reefs, and tropical rainforests and place seagrass meadows among the most threatened ecosystems on earth.

Small-scale spatial and temporal variability in growth and mortality of fish larvae in the subtropical northcentral Gulf of Mexico: implications for assessing recruitment success

Extensive plankton collections were taken during seven September cruises (1990–93) along the inner continental shelf of the northcentral Gulf of Mexico (GOM). Despite the high productivity and availability of food during these cruises, significant small-scale spatial variability was found in larval growth rates for both Atlantic bumper (Chloroscombrus chrysurus, Carangidae) and vermilion snapper (Rhomboplites aurorubens, Lutjanidae). The observed variability in larval growth rates was not correlated with changes in water temperature or associated with conspicuous hydrographic features and suggested the existence of less-recognizable regions where conditions for growth vary. Cruise estimates of mortality coefficients (Z) for larval Atlantic bumper (n=32,241 larvae from six cruises) and vermilion snapper (n= 2581 larvae from four cruises) ranged from 0.20 to 0.37 and 0.19 to 0.29, respectively. Even in a subtropical climate like the GOM, where larval-stage durations may be as short as two weeks, observed variability in growth rates, particularly when combined with small changes in mortality rates, can cause order-of-magnitude differences in cumulative larval survival. To what extent the observed differences in growth rates at small spatial scales are fine-scale “noise” that ultimately is smoothed by larger-scale processes is not known. Future research is needed to further characterize the small-scale variability in growth rates of larvae, particularly with regard to microzooplankton patchiness and the temporal and spatial pattern of potential predators. Small-scale spatial variability in larval growth rates may in fact be the norm, and understanding the implications of this subtle mosaic may help us to better evaluate our ability to partition the causes of recruitment variability.

Larval and settlement periods of the northern searobin (Prionotus carolinus) and the striped searobin (P. evolans)

This study reports new information about searobin (Prionotus spp.) early life history from samples collected with a Tucker trawl (for planktonic stages) and a beam trawl (for newly settled fish) from the coastal waters of New Jersey. Northern searobin, Prionotus carolinus, were much more numerous than striped searobin, P. evolans, often by an order of magnitude. Larval Prionotus were collected during the period July–October and their densities peaked during September. For both species, notochord flexion was complete at 6–7 mm standard length (SL) and individuals settled at 8–9 mm SL. Flexion occurred as early as 13 days after hatching and settlement occurred as late as 25 days after hatching, according to ages estimated from sagittal microincrements. Both species settled directly in continental shelf habitats without evidence of delayed metamorphosis. Spawning, larval dispersal, or settlement may have occurred within certain estuaries, particularly for P. evolans; thus collections from shelf areas alone do not permit estimates of total larval production or settlement rates. Reproductive seasonality of P. carolinus and P. evolans may vary with respect to latitude and coastal depth. In this study, hatching dates and sizes of age-0 P. carolinus varied with respect to depth or distance from the New Jersey shore. Older and larger age-0 individuals were found in deeper waters. These variations in searobin age and size appear to be the combined result of intraspecific variations in searobin reproductive seasonality and the limited capability of searobin eggs and larvae to disperse.

Preservation of Otolithus argenteus at low temperature

The studies provided data on the spoilage pattern of Otolithus argenteus during low temperature preservation. Changes in the total volatile bases, hypoxanthine, tyrosine, salt soluble nitrogen, non-protein nitrogen, pH, peroxide value, free fatty acids and thiobarbituric acid number along with organoleptic score have been reported. Organoleptically, fish stored at +20 degree C remained in acceptable condition upto 12 days while for those stored at 0 degree C in ice upto 19 days. Of the various indices tested Hypoxanthine, salt soluble nitrogen and total volatile bases nitrogen, in the order of merit can be used as freshness tests for refrigerated fish.

Morphometry, length-weight relationship and food and feeding habits of Otolithoides biauritus (Cantor, 1850) of Bombay waters

Thirteen morphometric and seven meristic characters, length-weight relationship and food and feeding habits of Otolithoides biauritus of Bombay coast (Maharashtra, India) were studied. Compared morphometric characters revealed positive allometric growth and high correlation ("r" ranging 0.898 - 0.996) between each other. Meristic characters were observed to be B sub(vii), D sub(1) 8-10, D sub(2) 27-31, P 17-20, V 5-7 and 7-10. Number of gill rackers on the first left gill arch ranged from 15 to 19. Length-weight relationship for both sexes together worked out to be W = 0.026, L super(2.646). The species is a predator, feeding mainly on motile Acetes, small fish and Loligo in order of preference.

Toxicity of heavy metals to brine shrimp Artemia

Bioassay were carried out on 48h cultured nauplii of brine shrimp Artemia by exposing them to seven trace elements viz. copper (Cu), zinc (Zn), cadmium (Cd), nickel (Ni), lead (Pb), iron (Fe) and manganese (Mn). Synergistic effects of all these elements and additive effects of Cu and Zn, Cd and Pb, and Ni and Fe were also investigated. Comparatively, the degree of toxicity for compound bioassays was higher than individual simple tests. The values were averaged and the expected median lethal concentration [LC sub(50)] of tested heavy metals was obtained by probit analysis on the basis of cumulative numbers of dead organisms after 24 and 48h. The order of toxicity of the metals to Artemia was Pb>Cd>Cu>Ni>Zn>Fe>Mn. Potency ratios of the seven metals were also calculated. The 24 and 48h variations obtained in LC sub(50) values were significantly different and relative implications of these are discussed.

Studies on phenolase enzymes in prawns. Pt. 1. The distribution and physical properties of phenolases in Penaeid prawns

The distribution of phenolases in certain species of Penaeid prawns has been studied. Attempts were made to locate the regions of maximum enzyme activity in the prawns. The relative dopase activity has been examined in extracts from head, tail, shell with cuticles and muscle. The head juice and tail extracts were found to register very high order of enzyme activity. Metapenaeus affinis, Metapenaeus monoceros and Penaeus indicus record comparatively higher enzyme activity than Parapenaeopsis stylifera and Metapenaeus dobsoni, no definite relationship has been found between the relative activity of the enzyme and size grade at least in one species examined. Experiments were done to determine the pH optima of the enzyme and the influence of pH on its deactivation. Exposure to higher temperatures up to 55°c was shown to activate the crude enzyme considerably. The possible implications of the observations have been discussed.

Sulfide binding characteristics of blood serum in Calyptogena pacifica and Vesicomya gigas

The sulfide binding characteristics of blood serum were studied in vitro in two deep-sea vesicomyid clams, Calyptogena pacifica and Vesicomya gigas. Both the C. pacifica and the V. gigas serum concentrated sulfide at least an order of magnitude above ambient levels. V. gigas accumulated sulfide faster than C. pacifica, reaching saturation at 5000 M after an hour. C. pacifica bound sulfide at half the rate of V. gigas, reaching saturation in about two hours at a substantially higher concentration of sulfide. The observed distribution of the animals near cold seeps in the Monterey Submarine Canyon can be explained by their different sulfide binding abilities. The hypothesis that cold seeps are actually much more unstable sources of sulfide than previously assumed is explored.

Influence of particle properties on the erosive wear of sintered boron carbide

Sintered boron carbide is very hard, and can be an attractive material for wear-resistant components in critical applications. Previous studies of the erosion of less hard ceramics have shown that their wear resistance depends on the nature of the abrasive particles. Erosion tests were performed on a sintered boron carbide ceramic with silica, alumina and silicon carbide erodents. The different erodents caused different mechanisms of erosion, either by lateral cracking or small-scale chipping; the relative values of the hardness of the erodent and the target governed the operative mechanism. The small-scale chipping mechanism led to erosion rates typically an order of magnitude lower than the lateral fracture mechanism. The velocity exponents for erosion in the systems tested were similar to those seen in other work, except that measured with the 125 to 150 μm silica erodent. With this erodent the exponent was initially high, then decreased sharply with increasing velocity and became negative. It was proposed that this was due to deformation and fragmentation of the erodent particles. In the erosion testing of ceramics, the operative erosion mechanism is important. Care must be taken to ensure that the same mechanism is observed in laboratory testing as that which would be seen under service conditions, where the most common erodent is silica.

Some aspects of the biology of Tachysurus tenuispinis Day from Veraval

The regression coefficients in length-weight relationship of males and females of Tachysurus tenuispinis differ significantly. The relative condition factor was calculated for females in relation to various lengths and months. The sex ratio in the catch varied widely in the different months. The number of eggs ranged from 72 to 89 for the fish of length 394 to 570 mm. Empty stomachs occurred in a very high percentage (63.5%) of the total stomachs examined. This is a bottom carnivorous feeder. The main food items found in the guts in order of preference were crustaceans, polychaetes, molluscs, fishes and echinoderms.

Bias-dependent recovery time of all-optical resonant nonlinearity in InGaAsP/InGaAsP MQW waveguide

We have investigated a resonant refractive nonlinearity in a semiconductor waveguide by measuring intensity dependent phase shifts and bias-dependent recovery times. The measurements were performed on an optimized 750-μm-long AR coated buried heterostructure MQW p-i-n waveguide with a bandedge at 1.48 μm. Figure 1 shows the experimental arrangement. The mode-locked color center laser was tuned to 50 meV beyond the bandedge and 8 ps pulses with peak incident power up to 57 W were coupled into the waveguide. Some residual bandtail absorption remains at this wavelength and this is sufficient to cause carriers to be photogenerated and these give rise to a refractive nonlinearity, predominantly by plasma and bandfilling effects. A Fabry-Perot interferometer is used to measure the spectrum of the light which exits the waveguide. The nonlinearity within the guide causes self phase modulation (SPM) of the light and a study of the spectrum allows information to be recovered on the magnitude and recovery time of the nonlinear phase shift with a reasonable degree of accuracy. SPM spectra were recorded for a variety of pulse energies coupled into he unbiased waveguide. Figure 2 shows the resultant phase shift measured from the SPM spectra as a function of pulse energy. The relationship is a linear one, indicating that no saturation of the nonlinearity occurs for coupled pulse energies up to 230 pJ. A π phase shift, the minimum necessary for an all-optical switch, is obtained for a coupled pulse energy of 57 pJ while the maximum phase shift, 4 π, was measured for 230 pJ. The SPM spectra were highly asymmetric with pulse energy shifted to higher frequencies. Such spectra are characteristic of a slow, negative nonlinearity. This relatively slow speed is expected for the unbiased guide as the recovery time will be of the order of the recombination time of the photogenerated electrons, about 1 ns for InGaAsP material. In order to reduce the recovery time of the nonlinearity, it is necessary to remove the photogenerated carriers from the waveguide by a process other than recombination. One such technique is to apply a reverse bias to the waveguide in order to sweep the carriers out. Figure 3 shows the effect on the recovery time of the nonlinearity of applying reverse bias to the waveguide for 230 pJ coupled power. The recovery time was reduced from one much longer than the length of the pulse, estimated to be about 1 ns, at zero bias to 18 ± 3 ps for a bias voltage greater than -4 V. This compares with a value of 24 ps obtained in a bulk waveguide.

Gain-switched dynamics of tapered waveguide bow-tie lasers

The use of tapered waveguide lasers and amplifiers for enhanced picosecond pulse generation has led to order-of-magnitude peak power and pulse energy improvements. Monolithic pulse generation schemes have so far relied on a double-tapered bow-tie structure. The modeling of tapered lasers has so far been limited to steady-state operation or has lacked experimental comparison. This paper considers both experimentally and theoretically the gain-switched performance of bow-tie lasers of various taper angles. The role of transverse-mode spatial hole burning in tapered waveguide lasers is thereby investigated.

A Preliminary survey of 21 Ceylon lakes. 3. Parasites and predators, food of fish, and marginal fauna

Three nematodes, two acanthocephalans and three cestodes were collected by dissecting 15 species of fish. Of these parasites only Hedruris sp. a larval nematode is responsible directly for the death of fish, since it is found in predatory species a reduction of these might prove of considerable consequence to fish, production. Bothriocephalus gowleonensis, a cestode probably introduced from China with Chinese carp, was recorded in an indigenous carp Puntius sarana. This parasite causes heavy mortality in grass carp in China and is a potential danger to local species. A single crustacean parasite was recorded. It is likely that they are widespread. No protozoa were recorded but there can be little doubt that they occur in local freshwater species and may be of considerable importance in fisheries. Several predators (insects, fish and other vertebrates) were recorded and are doubtless of considerable importance. However, the role of parasites and of predators (especially fishes) in relation to the productivity of fisheries can hardly be assessed at present and needs further study. A study of the fauna found at the shallow edges of 21 irrigation reservoirs showed an abundance of fauna in the low-country reservoirs whilst the up-country reservoirs had a poor fauna. The fauna showed insects, crustacea and mollusca in this order of abundance. The presence of insect and molluscs feeding fish in our fauna shows that these rich sources of food are being utilised.