Sparse sampling of water density fluctuations near liquid-vapor coexistence

Abstract

The free energetics of water density fluctuations in bulk water, at interfaces, and in hydrophobic confinement inform the hydration of hydrophobic solutes as well as their interactions and assembly. The characterisation of such free energetics is typically performed using enhanced sampling techniques such as umbrella sampling. In umbrella sampling, order parameter distributions obtained from adjacent biased simulations must overlap in order to estimate free energy differences between biased ensembles. Many biased simulations are typically required to ensure such overlap, which exacts a steep computational cost. We recently introduced a sparse sampling method, which circumvents the overlap requirement by using thermodynamic integration to estimate free energy differences between biased ensembles. Here we build upon and generalise sparse sampling for characterising the free energetics of water density fluctuations in systems near liquid-vapor coexistence. We also introduce sensible heuristics for choosing the biasing potential parameters and strategies for adaptively refining them, which facilitate the estimation of such free energetics accurately and efficiently. We illustrate the method by characterising the free energetics of cavitation in a large volume in bulk water. We also use sparse sampling to characterise the free energetics of capillary evaporation for water confined between two hydrophobic plates. In both cases, sparse sampling is nearly two orders of magnitude faster than umbrella sampling. Given its efficiency, the sparse sampling method is particularly well suited for characterising free energy landscapes for systems wherein umbrella sampling is prohibitively expensive.     

Species Richness and Invasion Vectors: Sampling Techniques and Biases

During a European Union Concerted Action study on species introductions, an intercalibration workshop on ship ballast water sampling techniques considered various phytoplankton and zooplankton sampling methods. For the first time, all the techniques presently in use worldwide were compared using a plankton tower as a model ballast tank spiked with the brine shrimp and oyster larvae while phytoplankton samples were taken simultaneously in the field (Helgoland Harbour, Germany). Three cone-shaped and 11 non-cone shaped plankton nets of different sizes and designs were employed. Net lengths varied from 50 to 300 cm, diameters 9.7–50 cm, and mesh sizes 10–100 μm. Three pumps, a Ruttner sampler, and a bucket previously used in ballast water sampling studies were also compared. This first assessment indicates that for sampling ballast water a wide range of techniques may be needed. Each method showed different results in efficiency and it is unlikely that any of the methods will sample all taxa. Although several methods proved to be valid elements of a hypothetical `tool box' of effective ship sampling techniques. The Ruttner water sampler and the pump P30 provide suitable means for the quantitative phytoplankton sampling, whereas other pumps prevailed during the qualitative trial. Pump P15 and cone-shaped nets were the best methods used for quantitative zooplankton sampling. It is recommended that a further exercise involving a wider range of taxa be examined in a larger series of mesocosms in conjunction with promising treatment measures for managing ballast water. This revised version was published online in July 2006 with corrections to the Cover Date.     

Inexpensive Device for the Aerobic and Anaerobic Sampling of Microorganisms in Lake and Shallow Ocean Waters

An inexpensive device suitable for sampling microorganisms in water and easily constructed from readily available laboratory equipment is described. The need to transfer subsamples to culturing flasks after collection is eliminated by partly filling the sampling vessels with growth medium prior to sampling. The device is readily adapted for sampling different volumes, is simple and quick to operate, and is suitable for use with prereduced media. Contamination from layers other than that being sampled is insignificant.     

An examination of the factors involved in determining phosphatase activities in estuarine waters. 2: Sampling procedures

Sampling procedures which are significant in the assessment of phosphatase activities in water bodies have been studied. Variations in neutral phosphatase activities among sampling stations and over depth profiles were considered, as well as seasonal and diurnal variations. Large differences were found in neutral phosphatase activities between sampling stations, but the activities in water samples from within a sampling area varied by the less than 3%. Most frequently, phosphatase activity was constant throughout the water column until just above the sediment. Distinct diurnal patterns were always found, but the patterns were not consistent between either sampling stations or sampling dates. Phosphatase activity also varied seasonally. All of the above variations may reflect differences in biomass composition and concentration. The implications of such variations for setting up an adequate sampling program and for assessing data are stressed.     

Temperature dependence on the pesticide sampling rate of polar organic chemical integrative samplers (POCIS)

Laboratory experiments were performed to determine the sampling rates of pesticides for the polar organic chemical integrative samplers (POCIS) used in Japan. The concentrations of pesticides in aquatic environments were estimated from the accumulated amounts of pesticide on POCIS, and the effect of water temperature on the pesticide sampling rates was evaluated. The sampling rates of 48 pesticides at 18, 24, and 30 °C were obtained, and this study confirmed that increasing trend of sampling rates was resulted with increasing water temperature for many pesticides.     

A small dredge for sampling aquatic macrophytes

A small dredge for sampling of aquatic macrophytes in shallow lakes, ponds and rivers is described. The dredge consists of a crown-like stainless steel vessel, disk and legs. The total dredge weight is 550 g. The dredge is useful for sampling higher plants, water ferns, mosses, liverworts and large algae, and for sampling soft sediments.     

Spatial and temporal heterogeneity of trophic variables in a deep lake as reflected by repeated singular samplings

Approaches to compare the strength of pelagic trophic cascades often use singular sampling programs for measuring trophic variables, thus potentially neglecting the spatial and temporal heterogeneity in the distribution of fish, zooplankton and phytoplankton. Here, we compared the composition of six trophic variables from three trophic levels in a deep oligotrophic lake within temporal (diel and seasonal) and spatial (horizontal and vertical) sampling resolutions. Mean values and ratios between the variables were compared between day and night, in three sampling months, four lake basins, and three water depths. Factor analysis was used to determine abiotic variables which may explain the heterogeneous distribution of the trophic variables. All six trophic variables were strongly heterogeneously distributed between the sampling months and the water depths, whereas horizontal and day–night differences were lower. Distribution of fish, zooplankton and phytoplankton correlated with water temperature and nutrient concentrations. Accordingly, for the use in comparative and meta-analyses, singular sampling programs in deep lakes have to integrate the entire water depth and are best repeated over several seasons. Alternatively, mean water temperature and nutrient concentrations may be used as covariates to diminish the unexplained variance between samples from different lakes.     

Convergence of the Chemical Potential in Aqueous simulations

The chemical potential of a sphere in water is calculated using a molecular dynamics simulation. The convergence of a continuous sampling method is examined. Free energy calculations for forming a cavity or methane site in water with a thermodynamic integration are found to be strongly dependent on total simulation time length out to hundreds of picoseconds. The implications of insufficient sampling are given and related to relaxation time scales in the solvent about the solute in an Eisenberg-Kauzmann like analysis. Implications for more complex liquids are discussed.     

On-site filtration of water samples for environmental DNA analysis to avoid DNA degradation during transportation

Environmental DNA (eDNA) analysis is an innovative tool for determining the distribution or abundance of aquatic macroorganisms. However, because eDNA degrades rapidly in water, long delays between sampling and analysis may hinder eDNA quantification. In the present study, we developed a portable filtration system that enables on-site (and on-the-road) filtration of water samples. Degradation rates of eDNA within 6 h were compared using water from an outdoor pond that was subjected to (1) on-site filtration, (2) transportation of water on ice, and (3) transportation of water at ambient temperature. Groups 2 and 3 were filtered in the laboratory 6 h after sampling. The concentration of eDNA was determined as the copy number of the mitochondrial cytochrome b gene of two fish species using real-time polymerase chain reaction. The portable filtration system offers the following benefits: (1) the eDNA concentration is preserved as is at the time of sampling, permitting higher accuracy of eDNA quantification, (2) use of a disposable sealed plastic bag reduces the risk of contamination and ensures on-the-road filtration, (3) time is saved because filtration can be accomplished when driving between sampling sites.     

Water‐borne and plasma corticosterone are not correlated in spotted salamanders

Water‐borne hormone measurement is a noninvasive method suitable for amphibians of all sizes that are otherwise difficult to sample. For this method, containment‐water is assayed for hormones released by the animal. Originally developed in fish, the method has expanded to amphibians, but requires additional species‐specific validations. We wanted to determine physiological relevance of water‐borne corticosterone in spotted salamanders (Ambystoma maculatum) by comparing concentrations to those taken using established corticosterone sampling methods, such as plasma. Using a mixture of field and laboratory studies, we compared water‐borne corticosterone levels to other traditional methods of sampling corticosterone for spotted salamander larvae, metamorphs, and adults. Despite multiple attempts, and detecting differences between age groups, we found no correlations between water‐borne and plasma corticosterone levels in any age group. Water‐borne sampling measures a rate of release; whereas plasma is the concentration circulating in the blood. The unique units of measurement may inherently prevent correlations between the two. These two methods may also require different interpretations of the data and the physiological meaning. We also note caveats with the method, including how to account for differences in body size and life history stages. Collectively, our results illustrate the importance of careful validation of water‐borne hormone levels in each species in order to understand its physiological significance.     

Comet assay and micronucleus test in circulating erythrocytes of Cyprinus carpio specimens exposed in situ to lake waters treated with disinfectants for potabilization

The detection of a possible genotoxic effect of surface water treated with disinfectants for potabilization is the aim of the present work. The Comet assay and the micronucleus test were applied in circulating erythrocytes of Cyprinus carpio. Young specimens (20-30 g) were exposed in experimental basins, built within the potabilization plant of Castiglione del Lago (Perugia, Italy). In this plant the water of the Trasimeno Lake is treated and disinfected for potabilization before it is distributed to the people in the net of drinkable water. A continuous flow of water at a constant rate was supplied to basins; the water was continuously treated at a constant concentration with one of the three tested disinfectants (sodium hypochlorite, peracetic acid and chloride dioxide), one control basin being supplied with untreated water. Three sampling campaigns were performed: October 2000, February 2001 and June 2001. Repeated blood samplings through intracardiac punctures allowed to follow the same fish populations after different exposure times: before introduction of the disinfectant, and 10 or 20 days afterwards. An additional blood sampling was performed 3 h after addition of the disinfectant in other, simultaneously exposed, fish populations. Genotoxic damage was shown in fish exposed to water disinfected with sodium hypochlorite and chloride dioxide. The Comet assay showed an immediate response, i.e. DNA damage that was induced directly in circulating erythrocytes, whereas micronuclei reached their highest frequencies at later sampling times, when a genotoxic damage in stem cells of the cephalic kidney is expressed in circulating erythrocytes. The quality of the untreated surface water seems to be the most important parameter for the long-term DNA damage in circulating erythrocytes.     

The relative merits of open- and closed-path analysers for measurement of eddy fluxes

Theoretical and practical aspects of measuring eddy fluxes of trace gases using open-and closed-path analysers are presented. Trace gas fluxes measured with an open-path analyser require the concurrent measurement of sensible and latent heat fluxes to correct for density fluctuations in trace gas concentration caused by these fluxes. A closed-path analyser eliminates the corrections due to sensible heat flux, but not for water vapour, provided temperature fluctuations are completely removed without significantly reducing fluctuations in the trace gas mixing ratio. Theory for the design of heat exchangers and for the attenuation of concentration fluctuations during air flow through tubes is used to provide design criteria for closed-path systems. Spectral transfer functions are used to estimate flux losses caused by flow through the sampling tube and gas analyser. Other factors considered include cross-sensitivity of infrared CO₂ analysers to water vapour, and deterioration of system performance caused by contaminants on the walls of sampling tubes. Of two open-path, infrared CO₂ analysers tested, one showed a strong interaction between CO₂ and water vapour, while the other showed little sensitivity to the presence of water vapour, other than caused by dilution. A commercial closed-path CO₂ analyser also showed little cross-sensitivity to water vapour. Compared to results for a clean sampling tube, the spectral bandwidth for water vapour fluctuations decreased significantly after several weeks of sampling. No such deterioration in bandwidth was observed for CO₂. These findings are attributed to differential adsorption/desorption of water vapour by dust or salt on the tubing walls. Rain and dust must be removed from open-path analysers to obtain satisfactory measurements. Careful system design and maintenance is required for both open- and closed-path systems to ensure satisfactory long-term measurement of trace gas fluxes. With these precautions, both approaches will provide satisfactory flux measurements.     

Modification and Application of a Leaf Blower-vac for Field Sampling of Arthropods

Rice fields host a large diversity of arthropods, but investigating their population dynamics and interactions is challenging. Here we describe the modification and application of a leaf blower-vac for suction sampling of arthropod populations in rice. When used in combination with an enclosure, application of this sampling device provides absolute estimates of the populations of arthropods as numbers per standardized sampling area. The sampling efficiency depends critically on the sampling duration. In a mature rice crop, a two-minute sampling in an enclosure of 0.13 m² yields more than 90% of the arthropod population. The device also allows sampling of arthropods dwelling on the water surface or the soil in rice paddies, but it is not suitable for sampling fast flying insects, such as predatory Odonata or larger hymenopterous parasitoids. The modified blower-vac is simple to construct, and cheaper and easier to handle than traditional suction sampling devices, such as D-vac. The low cost makes the modified blower-vac also accessible to researchers in developing countries.     

A new transparent handy sampler for collecting water from lakes,rivers and seas

A handy sampler for collecting water from lakes, rivers and seas is described. The sampler consists of an exchangeable sample tube and a new sample-holding system. The system comprises an upper disk, a lower disk, a pair of arms with a guide pin and a semicircular arm guide with a groove. The water sample collected into the acryl tube is held without flow by a tight tube-closing system. Contamination of the sample by chemical and biological materials from the sample tube is minimized by exchanging the tube with a clean one at each sampling station. This new sampler is light, simple and useful for sampling of water from surface to bottom.     

Sampling Plan Optimization: A Data Review and Sampling Frequency Evaluation Process

Lawrence Livermore National Laboratory (LLNL) uses a cost-effective sampling (CES) methodology to evaluate and review ground water contaminant data and optimize the site's ground water monitoring plan. The CES methodology is part of LLNL's regulatory approved compliance monitoring plan (Lamarre et al., 1996). It allows LLNL to adjust the ground water sampling plan every quarter in response to changing conditions at the site. Since the use of the CES methodology has been approved by the appropriate regulatory agencies, such adjustments do not need additional regulatory approval. This permits LLNL to respond more quickly to changing conditions. The CES methodology bases the sampling frequency for each location on trend, variability, and magnitude statistics describing the contaminants at that location, and on the input of the technical staff (hydrologists, chemists, statisticians, and project leaders). After initial setup is complete, each application of CES takes only a few days for as many as 400 wells. Effective use of the CES methodology requires sufficient data, an understanding of contaminant transport at the site, and an adequate number of monitoring wells downgradient of the contamination. The initial implementation of CES at LLNL in 1992 produced a 40% reduction in the required number of annual routine ground water samples at LLNL. This has saved LLNL $390,000 annually in sampling, analysis, and data management costs.     

Access pipes for sampling through thick ice

Access pipes are described which permit water sampling beneath thick ice. The pipes prevent water overflow conditions which are sometimes encountered when sampling arctic lakes. Simple modifications to our design permit broader application to a number of winter sampling conditions.     

长江荆江段的渔业生态环境评价

1997—2002年,对长江荆江段青、草、鲢、鳙产卵场的水环境质量和浮游生物状况进行了调查,并用河流水质综合评价方法和Kolkwitz&Marsson体系法进行了评价。结果表明:在每年5—6月份的青、草、鲢、鳙繁殖季节,仅个别采样点铜或石油类超过渔业水质标准,该江段水质基本符合渔业水质标准和地表水环境质量Ⅱ类标准,能满足青、草、鲢、鳙繁殖对水质质量的要求。浮游生物的指示性表明其水体属于β中污带。       

Monte Carlo Simulation of Pathogen Behavior during the Sprout Production Process

Food-borne disease outbreaks linked to the consumption of raw sprouts have become a concern over the past decade. A Monte Carlo simulation model of the sprout production process was created to determine the most-effective points for pathogen control. Published literature was reviewed, and relevant data were compiled. Appropriate statistical distributions were determined and used to create the Monte Carlo model with Analytica software. Factors modeled included initial pathogen concentration and prevalence, seed disinfection effectiveness, and sampling of seeds prior to sprouting, sampling of irrigation water, or sampling of the finished product. Pathogen concentration and uniformity of seed contamination had a large effect on the fraction of contaminated batches predicted by the simulation. The model predicted that sprout sampling and irrigation water sampling at the end of the sprouting process would be more effective in pathogen detection than seed sampling prior to production. Day of sampling and type of sample (sprout or water) taken had a minimal effect on rate of detection. Seed disinfection reduced the proportion of contaminated batches, but in some cases it also reduced the ability to detect the pathogen when it was present, because cell numbers were reduced below the detection limit. Both the amount sampled and the pathogen detection limit were shown to be important variables in determining sampling effectiveness. This simulation can also be used to guide further research and compare the levels of effectiveness of different risk reduction strategies.     

Biochemical fingerprinting for typing of Aeromonas strains from food and water

The PhenePlate (PhP) system for biochemical fingerprinting is based on analysis of the kinetics of biochemical tests in microplates. This was evaluated for typing Aeromonas spp. isolates from drinking water and food and 78 Aeromonas strains isolated on different occasions over 6 months from three public drinking water systems. The system was highly discriminating and the diversity index, as calculated from 65 unrelated isolates, was 0.993, and 53 different biochemical phenotypes (BPTs) were found. Food isolates were more homogeneous than random Aeromonas strains and identical isolates were sometimes found in food of different origin. Each public drinking water system contained several BPTs but some of these were dominant at several sampling sites and on several sampling occasions in a system. The PhP system is suitable for typing Aeromonas strains from food and water. It is simple to handle and can be used with large numbers of isolates.     

A pedal corer for the quantitative sampling of sediments and benthic organisms in submerged areas accessible on foot

This paper presents a new device to collect quantitative samples of sediment and benthic organisms. The device is specially designed for sampling with the advantages of box-corer or Eckman dredges in submerged areas that are accessible on foot. The pedal corer is a simple, lightweight, user-friendly device that does not disturb the sediment structure and provides easy access to the sample contained inside the core. With this device, sampling in shallow water zones that are constantly submerged is made easy and sampling time is extended in intertidal zones. Handling editor: J. Saros