Modelling the growth Rate of Algal in sediment-laden flow

NASA Astrophysics Data System (ADS)

Li, H.

2017-12-01

Phytoplankton plays an important role as a primary producer in aquatic ecosystems. Fluid dynamics can affect the growth of algae in a number of ways and can be divided into two categories. On the one hand the advection and diffusion processes may disrupt the vertical migration of phytoplankton. On the other hand hydrodynamic effects of sediment suspension which can affect algal growth, by releasing nutrients and reducing light intensity. Natural water generally contains sediment. Therefore, when the flow enters the lake, it will cause a change in the phytoplankton community at the junction. Few people have studied the effects of sediment-laden flows to algal growth rates. In this project, Baiyangdian was chosen as the key research area to study the effect of sediment-laden flow on the growth rate of algae. And we conducted a microcosmic experiment in the laboratory to simulate the effect of sediment-laden flow on the growth rate of algae, and constructed a numerical model for the growth rate of algae in sediment-laden flow.

CHITIN TRANSFORMATION AND PESTICIDE INTERACTIONS IN A SIMULATED AQUATIC MICROENVIRONMENTAL SYSTEM

EPA Science Inventory

Interactions between the structural animo-polysaccharide, chitin, and the organophosphate pesticide, azinphosmethyl (Guthion), have been studied in a controlled continuous flow-through microcosm. Pesticide-induced microbial population changes and increases in substrate utilizatio...

Alteration of Rock Fragments from Columbia River Basalt Microcosms

NASA Technical Reports Server (NTRS)

Wentworth, Susan J.; Thomas-Keprta, Kathie L.; Velbel, Michael A.; McKay, David S.; Stevens, Todd O.

1999-01-01

During an earlier study, microorganisms were grown microcosms consisting of sterilized chips of Columbia River Basalt (CRB) and natural CRB ground water with its natural microflora; environmental conditions simulated a deep subsurface, anaerobic, dark environment. Subsequent scanning and transmission electron microscope (SEM and TEM) studies revealed the presence of several types of bacteria and biofilm, some of which were mineralized. Some of these biological features are very similar to possible biogenic features found in two meteorites from Mars, ALH84001 (found in Antarctica) and Nakhla (observed to fall in Egypt). Both ALH84001 and Nakhla contain traces of low-temperature aqueous alteration of silicates, oxides, and sulfides. The goals of this study are to use high-resolution field-emission SEM (FE-SEM) to examine the CRB samples for evidence of alteration features similar to those in the martian meteorites, to determine the extent of alteration during the CRB microcosm experiments, and to determine whether effects of biological activity can be distinguished from inorganic effects.

Biotransformation at 10 C of di-n-butyl phthalate in subsurface microcosms

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chauret, C.; Inniss, W.E.; Mayfield, C.I.

1996-09-01

Di-n-butyl phthalate (DBP) was found to be transformed by microorganisms under aerobic and anaerobic conditions at 10 C in microcosms simulating the Canadian Forces Base (CFB) Borden subsurface environment. Biotransformation of DBP was observed under aerobic, nitrate-reducing, Fe(III)-reducing, and sulfate-reducing conditions. The biotransformation of DBP in the microcosms was significantly decrease3d as the redox potential was lowered, especially under sulfate-reducing conditions. However, other factors such as nutrient depletion and buildup of toxic intermediates could have affected the biotransformation rates. The highest DBP biotransformation rate (0.57 {micro}g DBP{center_dot}g sediment{sup {minus}1}{center_dot}day{sup {minus}1}) was under sulfate-reducing conditions. Biotransformation of DBP at 10 Cmore » was significantly enhanced by the addition of 10 mM NaNO{sub 3} suggesting that both the addition of nitrate and high redox conditions favor its biotransformation in subsurface environments.« less

Impact of oil on bacterial community structure in bioturbated sediments.

PubMed

Stauffert, Magalie; Cravo-Laureau, Cristiana; Jézéquel, Ronan; Barantal, Sandra; Cuny, Philippe; Gilbert, Franck; Cagnon, Christine; Militon, Cécile; Amouroux, David; Mahdaoui, Fatima; Bouyssiere, Brice; Stora, Georges; Merlin, François-Xavier; Duran, Robert

2013-01-01

Oil spills threaten coastlines where biological processes supply essential ecosystem services. Therefore, it is crucial to understand how oil influences the microbial communities in sediments that play key roles in ecosystem functioning. Ecosystems such as sediments are characterized by intensive bioturbation due to burrowing macrofauna that may modify the microbial metabolisms. It is thus essential to consider the bioturbation when determining the impact of oil on microbial communities. In this study, an experimental laboratory device maintaining pristine collected mudflat sediments in microcosms closer to true environmental conditions--with tidal cycles and natural seawater--was used to simulate an oil spill under bioturbation conditions. Different conditions were applied to the microcosms including an addition of: standardized oil (Blend Arabian Light crude oil, 25.6 mg.g⁻¹ wet sediment), the common burrowing organism Hediste (Nereis) diversicolor and both the oil and H. diversicolor. The addition of H. diversicolor and its associated bioturbation did not affect the removal of petroleum hydrocarbons. After 270 days, 60% of hydrocarbons had been removed in all microcosms irrespective of the H. diversicolor addition. However, 16S-rRNA gene and 16S-cDNA T-RFLP and RT-PCR-amplicon libraries analysis showed an effect of the condition on the bacterial community structure, composition, and dynamics, supported by PerMANOVA analysis. The 16S-cDNA libraries from microcosms where H. diversicolor was added (oiled and un-oiled) showed a marked dominance of sequences related to Gammaproteobacteria. However, in the oiled-library sequences associated to Deltaproteobacteria and Bacteroidetes were also highly represented. The 16S-cDNA libraries from oiled-microcosms (with and without H. diversicolor addition) revealed two distinct microbial communities characterized by different phylotypes associated to known hydrocarbonoclastic bacteria and dominated by Gammaproteobacteria and Deltaproteobacteria. In the oiled-microcosms, the addition of H. diversicolor reduced the phylotype-richness, sequences associated to Actinobacteria, Firmicutes and Plantomycetes were not detected. These observations highlight the influence of the bioturbation on the bacterial community structure without affecting the biodegradation capacities.

Short-term changes in the composition of active marine bacterial assemblages in response to diesel oil pollution.

PubMed

Lanfranconi, Mariana P; Bosch, Rafael; Nogales, Balbina

2010-09-01

The changes caused by diesel oil pollution in the metabolically active bacterioplankton from an oligotrophic coastal location were analysed in laboratory microcosms (44 l) using 16S ribosomal RNA (16S rRNA) as molecular marker. The aim was to simulate typical hydrocarbon pollution events in a coastal area exploited for seasonal touristic activities. The experiment consisted in addition of low amounts of diesel oil without nutrients to seawater collected at different times (winter and summer). Bacterial diversity was analysed by terminal-restriction fragment length polymorphism (T-RFLP) profiling of 16S rRNAs after reverse transcription polymerase chain reaction (RT-PCR), and by generation of 16S rRNA clone libraries in control and diesel-polluted microcosms. Diesel addition caused a twofold increase in prokaryotic numbers in comparison with controls at the end of the experiment, both in winter and summer microcosms. Bacterioplankton composition, determined by 16S rRNA T-RFLP data, changed rapidly (within 17 h) in response to treatment. The resulting communities were different in microcosms with water collected in summer and winter. A reduction in diversity (Shannon index, calculated on the basis of T-RFLP data) was observed only in summer microcosms. This was due to the rapid increase of phylotypes affiliated to the Oceanospirillaceae, not observed in winter microcosms. After diesel treatment there was a reduction in the number of phylotypes related to SAR11, SAR86 and picocyanobacteria, while phylotypes of the Roseobacter clade, and the OMG group seemed to be favoured. Our results show that diesel pollution alone caused profound effects on the bacterioplankton of oligotrophic seawater, and explained many of the differences in diversity reported previously in pristine and polluted sites in this coastal area. © 2010 The Authors; Journal compilation © 2010 Society for Applied Microbiology and Blackwell Publishing Ltd.

Impact of surface coating and environmental conditions on the fate and transport of silver nanoparticles in the aquatic environment.

PubMed

Ellis, Laura-Jayne A; Valsami-Jones, Eugenia; Lead, Jamie R; Baalousha, Mohammed

2016-10-15

The role of surface coating (polyvinylpyrrolidone (PVP) and citrate) and water chemistry on the fate and behavior of AgNPs in aquatic microcosms is reported in this study. The migration and transformation of the AgNPs was examined in low (ultrapure water-UPW) and high ionic strength (moderately hard water - MHW) preparations, and in the presence of modeled natural organic matter (NOM) of Suwannee River Fulvic Acid (SRFA). The migration and fate of the AgNPs in the microcosms was validated using a sedimentation-diffusion model and the aggregation behavior was monitored by UV-visible spectrometry (UV-vis). Dissolved and particulate Ag concentrations (% Ag) were analyzed by ultrafiltration methods. Imaging of the AgNPs was captured using transmission electron microscopy (TEM). Results indicate that PVP-coated AgNPs (PVP-AgNPs) remained stable for 28days with similarly distributed concentrations of the PVP-AgNPs throughout the columns in each of the water conditions after approximately 96h (4days). The sedimentation-diffusion model confirmed PVP-AgNP stability in each condition, by showing diffusion dominated transport by using the original unaltered AgNP sizes to fit the parameters. In comparison, citrate AgNPs were largely unstable in the more complex water preparations (MHW). In MHW, aggregation dominated behavior followed by sedimentation/dissolution controlled transport was observed. The addition of SRFA to MHW resulted in small stabilizing effects, to the citrate coated AgNPs, producing smaller sized AgNPs (TEM) and mixed sedimentation and diffusion migration compared the studies absent of SRFA. The results suggest that surface coating and solution chemistry has a major impact on AgNP stability, furthermore the corresponding modeling will support the experimental understanding of the overall fate of AgNPs in the environment. Copyright © 2016 Elsevier B.V. All rights reserved.

Investigating redox processes under diffusive and advective flow conditions using a coupled omics and synchrotron approach

NASA Astrophysics Data System (ADS)

Kemner, K. M.; Boyanov, M.; Flynn, T. M.; O'Loughlin, E. J.; Antonopoulos, D. A.; Kelly, S.; Skinner, K.; Mishra, B.; Brooks, S. C.; Watson, D. B.; Wu, W. M.

2015-12-01

FeIII- and SO42--reducing microorganisms and the mineral phases they produce have profound implications for many processes in aquatic and terrestrial systems. In addition, many of these microbially-catalysed geochemical transformations are highly dependent upon introduction of reactants via advective and diffusive hydrological transport. We have characterized microbial communities from a set of static microcosms to test the effect of ethanol diffusion and sulfate concentration on UVI-contaminated sediment. The spatial distribution, valence states, and speciation of both U and Fe were monitored in situ throughout the experiment by synchrotron x-ray absorption spectroscopy, in parallel with solution measurements of pH and the concentrations of sulfate, ethanol, and organic acids. After reaction initiation, a ~1-cm thick layer of sediment near the sediment-water (S-W) interface became visibly dark. Fe XANES spectra of the layer were consistent with the formation of FeS. Over the 4 year duration of the experiment, U LIII-edge XANES indicated reduction of U, first in the dark layer and then throughout the sediment. Next, the microcosms were disassembled and samples were taken from the overlying water and different sediment regions. We extracted DNA and characterized the microbial community by sequencing 16S rRNA gene amplicons with the Illumina MiSeq platform and found that the community evolved from its originally homogeneous composition, becoming significantly spatially heterogeneous. We have also developed an x-ray accessible column to probe elemental transformations as they occur along the flow path in a porous medium with the purpose of refining reactive transport models (RTMs) that describe coupled physical and biogeochemical processes in environmental systems. The elemental distribution dynamics and the RTMs of the redox driven processes within them will be presented.

PREDICTIVE MODEL OF CONJUGATIVE PLASMID TRANSFER IN THE RHIZOSPHERE AND PHYLLOSPHERE

EPA Science Inventory

A computer simulation model was used to predict the dynamics of survival and conjugation of Pseudomonas cepacia (carrying the transmissible recombinant plasmid R388:Tn1721) with a nonrecombinant recipient strain in simple rhizosphere and phyllosphere microcosms. lasmid transfer r...

Robust Satellite Communications Under Hostile Interference

DTIC Science & Technology

2015-01-08

this analysis , was included in the simulations. Figure 17. STK Simulation Showing SNR Measured During the Uplink Attack (at the Jammer) 4.3...in Decision and Game Theory for Security, pp. 34–43, 2011. 8. Wertz, J. R., and Larson, W. J., Space Mission Analysis and Design, Microcosm, 1999...15  3.2  Analysis of Reactive Jamming Against Satellite Communications ............................... 15  3.2.1

Fungal Denitrification Activity in Vertical Flow Constructed Wetlands as Impacted by Plant Species Richness, Carbon, Nitrogen and pH Amendments.

PubMed

Liu, W L; Zhang, C B; Han, W J; Guan, M; Liu, S Y; Ge, Y; Chang, J

2017-12-01

To control potential fungal denitrification rate (PFDR) in vertical flow simulated wetlands (VFSW) microcosms, thirty VFSW microcosms were established and planted with three plant species richness levels (i.e. unplanted, monoculture, and four-species polyculture treatment), and effects of carbon, nitrogen and pH amendments on the PFDR were investigated using a room-incubating method. Among seven carbon compounds, sodium citrate, glycerol, glucose and sodium succinate were more effective in enhancing PFDRs. These enhanced effects were dependant on a given species richness level. Sodium nitrite mostly stimulated PFDRs to a greater extent than the other three nitrogen compound amendments at any richness level. Treatments with pH 5.6 or 8.4 had significantly greater PFDRs than the treatment with pH 2.8 in the three species richness levels. However, no effect of plant species richness on the PFDR was observed among any carbon, nitrogen and pH amendments. Current results suggest carbon, nitrogen and pH factors should be considered when mediating fungal denitrification in VFSW microcosms.

Factors Influencing TCE Anaerobic Dechlorination Investigated via Simulations of Microcosm Experiments

NASA Astrophysics Data System (ADS)

Mao, X.; Harkness, M.; Lee, M. D.; Mack, E. E.; Dworatzek, S.; Acheson, C.; McCarty, P.; Barry, D. A.; Gerhard, J. I.

2006-12-01

SABRE (Source Area BioREmediation) is a public-private consortium whose charter is to determine if enhanced anaerobic bioremediation can result in effective and quantifiable treatment of chlorinated solvent DNAPL source areas. The focus of this 4-year, $5.7 million research project is a field site in the United Kingdom containing a TCE DNAPL source area. In preparation, a microcosm study was performed to determine the optimal combination of factors to support reductive dechlorination of TCE in site soil and groundwater. The study consisted of 168 bottles distributed between four laboratories (Dupont, GE, SiREM, and Terra Systems) and tested the impact of six carbon substrates (lactate, acetate, methanol, SRS (soybean oil), hexanol, butyl acetate), bioaugmentation with KB-1 bacterial culture, three TCE levels (100 mg/L, 400 mg/L, and 800 mg/L) and two sulphate levels (200 mg/L, >500 mg/L) on TCE dechlorination. This research presents a numerical model designed to simulate the main processes occurring in the microcosms, including substrate fermentation, sequential dechlorination, toxic inhibition, and the influence of sulphate concentration. In calibrating the model to over 60 of the microcosm experiments, lumped parameters were employed to quantify the effect of key factors on the conversion rate of each chlorinated ethene in the TCE degradation sequence. Results quantify the benefit (i.e., increased stepwise dechlorination rate) due to both bioaugmentation and the presence of higher sulphate concentrations. Competitive inhibition is found to increase in significance as TCE concentrations increase; however, inclusion of Haldane inhibition is not supported. Over a wide range of experimental conditions and dechlorination steps, SRS appears to induce relatively little hydrogen limitation, thereby facilitating relatively quick conversion of TCE to ethene. In general, hydrogen limitation is found to increase with increasing TCE concentration and with bioaugmentation, and is most pronounced in the dechlorination of TCE to DCE.

Adaptive radiation of Pseudomonas fluorescens SBW25 in experimental microcosms provides an understanding of the evolutionary ecology and molecular biology of A-L interface biofilm formation.

PubMed

Koza, Anna; Kusmierska, Anna; McLaughlin, Kimberley; Moshynets, Olena; Spiers, Andrew J

2017-07-03

Combined experimental evolutionary and molecular biology approaches have been used to investigate the adaptive radiation of Pseudomonas fluorescens SBW25 in static microcosms leading to the colonisation of the air-liquid interface by biofilm-forming mutants such as the Wrinkly Spreader (WS). In these microcosms, the ecosystem engineering of the early wild-type colonists establishes the niche space for subsequent WS evolution and colonisation. Random WS mutations occurring in the developing population that deregulate diguanylate cyclases and c-di-GMP homeostasis result in cellulose-based biofilms at the air-liquid interface. These structures allow Wrinkly Spreaders to intercept O2 diffusing into the liquid column and limit the growth of competitors lower down. As the biofilm matures, competition increasingly occurs between WS lineages, and niche divergence within the biofilm may support further diversification before system failure when the structure finally sinks. A combination of pleiotropic and epistasis effects, as well as secondary mutations, may explain variations in WS phenotype and fitness. Understanding how mutations subvert regulatory networks to express intrinsic genome potential and key innovations providing a selective advantage in novel environments is key to understanding the versatility of bacteria, and how selection and ecological opportunity can rapidly lead to substantive changes in phenotype and in community structure and function. © FEMS 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

A Semi-Quantitative Study of the Impact of Bacterial Pollutant Uptake Capability on Bioremediation in a Saturated Sand-Packed Two-Dimensional Microcosm: Experiments and Simulation

NASA Astrophysics Data System (ADS)

Zheng, S.; Ford, R.; Van den Berg, B.

2016-12-01

The transport of microorganisms through the saturated porous matrix of soil is critical to the success of bioremediation in polluted groundwater systems. Chemotaxis can direct the movement of microorganisms toward higher concentration of pollutants, which they chemically transform and use as carbon and energy sources, resulting in enhanced bioremediation efficiency. In addition to accessibility and degradation kinetics, bacterial uptake of the pollutants is a critical step in bioremediation. In order to study the impact of bacterial pollutant uptake capability on bioremediation, a two-dimensional microcosm packed with saturated sand was set up to mimic the natural groundwater system where mass transfer limitation poses a barrier (see the figure below). Toluene source was continuously injected into the microcosm from an injection port. Pseudomonas putida F1, either wild-type (WT) or genetic mutants (TodX knockout, TodX and CymD knockout) that exhibited impaired toluene uptake capability, were co-injected with a conservative tracer into the microcosm either above or below the toluene. After each run, samples were collected from a dozen effluent ports to determine the concentration profiles of the bacteria and tracers. Toluene serves as the only carbon source throughout the microcosm. So the percent recovery, which is the ratio of cells collected at the outlet over that at the inlet, can be used as the indicator for bioremediation efficiency. Comparisons were made between the WT and mutant strains, where PpF1 WT showed greater proliferation than the mutants. Comparisons for low and high toluene source concentrations showed that the PpF1 mutant strains exhibited a greater degree of growth inhibition than WT at higher toluene concentration. A mathematical model was applied to evaluate the impact of various parameters on toluene uptake illustrating that with reasonable parameter estimates, the bioremediation efficiency was more sensitive to proliferation than transport. The results show that in a two-dimensional microcosm mimicking features of the natural groundwater system, the toluene uptake capability of bacteria can be the "remediation-rate-liming" step, implying the potential of engineering bacteria for bioremediation efficiency enhancement.

Impact of Oil on Bacterial Community Structure in Bioturbated Sediments

PubMed Central

Stauffert, Magalie; Cravo-Laureau, Cristiana; Jézéquel, Ronan; Barantal, Sandra; Cuny, Philippe; Gilbert, Franck; Cagnon, Christine; Militon, Cécile; Amouroux, David; Mahdaoui, Fatima; Bouyssiere, Brice; Stora, Georges; Merlin, François-Xavier; Duran, Robert

2013-01-01

Oil spills threaten coastlines where biological processes supply essential ecosystem services. Therefore, it is crucial to understand how oil influences the microbial communities in sediments that play key roles in ecosystem functioning. Ecosystems such as sediments are characterized by intensive bioturbation due to burrowing macrofauna that may modify the microbial metabolisms. It is thus essential to consider the bioturbation when determining the impact of oil on microbial communities. In this study, an experimental laboratory device maintaining pristine collected mudflat sediments in microcosms closer to true environmental conditions – with tidal cycles and natural seawater – was used to simulate an oil spill under bioturbation conditions. Different conditions were applied to the microcosms including an addition of: standardized oil (Blend Arabian Light crude oil, 25.6 mg.g−1 wet sediment), the common burrowing organism Hediste (Nereis) diversicolor and both the oil and H. diversicolor. The addition of H. diversicolor and its associated bioturbation did not affect the removal of petroleum hydrocarbons. After 270 days, 60% of hydrocarbons had been removed in all microcosms irrespective of the H. diversicolor addition. However, 16S-rRNA gene and 16S-cDNA T-RFLP and RT-PCR-amplicon libraries analysis showed an effect of the condition on the bacterial community structure, composition, and dynamics, supported by PerMANOVA analysis. The 16S-cDNA libraries from microcosms where H. diversicolor was added (oiled and un-oiled) showed a marked dominance of sequences related to Gammaproteobacteria. However, in the oiled-library sequences associated to Deltaproteobacteria and Bacteroidetes were also highly represented. The 16S-cDNA libraries from oiled-microcosms (with and without H. diversicolor addition) revealed two distinct microbial communities characterized by different phylotypes associated to known hydrocarbonoclastic bacteria and dominated by Gammaproteobacteria and Deltaproteobacteria. In the oiled-microcosms, the addition of H. diversicolor reduced the phylotype-richness, sequences associated to Actinobacteria, Firmicutes and Plantomycetes were not detected. These observations highlight the influence of the bioturbation on the bacterial community structure without affecting the biodegradation capacities. PMID:23762350

Development of Pattern Recognition Techniques for the Evaluation of Toxicant Impacts to Multispecies Systems

DTIC Science & Technology

1993-06-18

the exception. In the Standardized Aquatic Microcosm and the Mixed Flask Culture (MFC) microcosms, multivariate analysis and clustering methods...rule rather than the exception. In the Standardized Aquatic Microcosm and the Mixed Flask Culture (MFC) microcosms, multivariate analysis and...experiments using two microcosm protocols. We use nonmetric clustering, a multivariate pattern recognition technique developed by Matthews and Heame (1991

The University as Microcosm

ERIC Educational Resources Information Center

Kaldis, Byron

2009-01-01

This paper puts forward the model of "microcosm-macrocosm" isomorphism encapsulated in certain philosophical views on the form of university education. The human being as a "microcosm" should reflect internally the external "macrocosm". Higher Education is a socially instituted attempt to guide human beings into forming themselves as microcosms of…

Investigation into ammonia stress on Cyperus alternifolius and its impact on nutrient removal in microcosm experiments.

PubMed

Tao, Wendong; Han, Jianqiu; Li, Hanyan

2015-11-01

Ammonia stress on plants has been investigated at discrete ammonia concentrations in constructed wetlands. This study introduced a Gaussian model to simulate the kinetics of ammonia stress and investigated reversible and irreversible ammonia stress on Cyperus alternifolius in wetland-like microcosms. Ammonia stress on plant weight increase and oxygen release potential started at weekly ammonia concentrations of 27 and 28 mg N/L, reached 50% inhibition at 178 and 158 mg N/L, and resulted in lethal effects at 311 and 303 mg N/L, respectively. The stress of one-time ammonia concentrations up to 400 mg N/L could be reversible. Ammonia concentrations constantly above 219 mg N/L exerted irreversible stress. In the microcosms with ammonia concentrations above the 50% inhibition levels, plants played a minor role in nitrogen removal. Nitrogen removal performance was not affected considerably by ammonia stress. Orthophosphate removal was suppressed by ammonia stress due to less plant uptake. Design and operation of constructed wetlands should consider wastewater ammonia concentration so that the integrity of constructed wetland ecosystems can be maintained. Copyright © 2015 Elsevier Ltd. All rights reserved.

Use of Acetate, Propionate, and Butyrate for Reduction of Nitrate and Sulfate and Methanogenesis in Microcosms and Bioreactors Simulating an Oil Reservoir

PubMed Central

Shen, Yin; An, Dongshan; Voordouw, Gerrit

2017-01-01

ABSTRACT Acetate, propionate, and butyrate (volatile fatty acids [VFA]) occur in oil field waters and are frequently used for microbial growth of oil field consortia. We determined the kinetics of use of these VFA components (3 mM each) by an anaerobic oil field consortium in microcosms containing 2 mM sulfate and 0, 4, 6, 8, or 13 mM nitrate. Nitrate was reduced first, with a preference for acetate and propionate. Sulfate reduction then proceeded with propionate (but not butyrate) as the electron donor, whereas the fermentation of butyrate (but not propionate) was associated with methanogenesis. Microbial community analyses indicated that Paracoccus and Thauera (Paracoccus-Thauera), Desulfobulbus, and Syntrophomonas-Methanobacterium were the dominant taxa whose members catalyzed these three processes. Most-probable-number assays showed the presence of up to 107/ml of propionate-oxidizing sulfate-reducing bacteria (SRB) in waters from the Medicine Hat Glauconitic C field. Bioreactors with the same concentrations of sulfate and VFA responded similarly to increasing concentrations of injected nitrate as observed in the microcosms: sulfide formation was prevented by adding approximately 80% of the nitrate dose needed to completely oxidize VFA to CO2 in both. Thus, this work has demonstrated that simple time-dependent observations of the use of acetate, propionate, and butyrate for nitrate reduction, sulfate reduction, and methanogenesis in microcosms are a good proxy for these processes in bioreactors, monitoring of which is more complex. IMPORTANCE Oil field volatile fatty acids acetate, propionate, and butyrate were specifically used for nitrate reduction, sulfate reduction, and methanogenic fermentation. Time-dependent analyses of microcosms served as a good proxy for these processes in a bioreactor, mimicking a sulfide-producing (souring) oil reservoir: 80% of the nitrate dose required to oxidize volatile fatty acids to CO2 was needed to prevent souring in both. Our data also suggest that propionate is a good substrate to enumerate oil field SRB. PMID:28130297

A multiple testing approach for hazard evaluation of complex mixtures in the aquatic environment: the use of diesel oil as a model

USGS Publications Warehouse

Johnson, B. Thomas

1989-01-01

Traditional single species toxicity tests and multiple component laboratory-scaled microcosm assays were combined to assess the toxicological hazard of diesel oil, a model complex mixture, to a model aquatic environment. The immediate impact of diesel oil dosed on a freshwater community was studied in a model pond microcosm over 14 days: a 7-day dosage and a 7-day recovery period. A multicomponent laboratory microcosm was designed to monitor the biological effects of diesel oil (1·0 mg litre−1) on four components: water, sediment (soil + microbiota), plants (aquatic macrophytes and algae), and animals (zooplanktonic and zoobenthic invertebrates). To determine the sensitivity of each part of the community to diesel oil contamination and how this model community recovered when the oil dissipated, limnological, toxicological, and microbiological variables were considered. Our model revealed these significant occurrences during the spill period: first, a community production and respiration perturbation, characterized in the water column by a decrease in dissolved oxygen and redox potential and a concomitant increase in alkalinity and conductivity; second, marked changes in microbiota of sediments that included bacterial heterotrophic dominance and a high heterotrophic index (0·6), increased bacterial productivity, and the marked increases in numbers of saprophytic bacteria (10 x) and bacterial oil degraders (1000 x); and third, column water acutely toxic (100% mortality) to two model taxa: Selenastrum capricornutum and Daphnia magna. Following the simulated clean-up procedure to remove the oil slick, the recovery period of this freshwater microcosm was characterized by a return to control values. This experimental design emphasized monitoring toxicological responses in aquatic microcosm; hence, we proposed the term ‘toxicosm’ to describe this approach to aquatic toxicological hazard evaluation. The toxicosm as a valuable toxicological tool for screening aquatic contaminants was demonstrated using diesel oil as a model complex mixture.

Identification of active dehalorespiring microbial populations in anoxic river sediment by RNA-based stable isotope probing

NASA Astrophysics Data System (ADS)

Kittelmann, S.; Friedrich, M. W.

2005-12-01

Tetrachloroethene (perchloroethylene, PCE), a persistent contaminant in aquifers, soils and sediments, can be reductively dechlorinated by anaerobic microorganisms in a process referred to as dehalorespiration. However, the biodiversity of dehalorespiring microorganisms and their distribution especially in pristine environments is largely unexplored. Therefore, the aim of this study was to detect potentially novel PCE-dehalorespiring microorganisms by using stable isotope probing (SIP), a technique that allows to directly identify the function of uncultivated microbial populations. We simulated a PCE contamination by incubating pristine river sediment in the presence of PCE at a steady, low aqueous concentration (20 μM). Dehalogenation activity in microcosms (20 nmol cis-dichloroethene per ml slurry per day formed) was detected already after 4 weeks at 20°C with sediment indigenous electron donors. The microbial community in sediment incubations was probed with 13C-labelled acetate (0.5 mM) as electron donor and carbon source at 15°C for 3 days. After RNA extraction, "heavy" 13C-rRNA and light 12C-rRNA were separated by isopycnic centrifugation, and Bacteria-related populations in gradient fractions were characterised by terminal restriction fragment length polymorphism analysis and cloning. In heavy gradient fractions from the microcosm with PCE, we detected a prominent 506-bp terminal restriction fragment (T-RF) and a few minor T-RFs only. In contrast, in the control without PCE, Bacteria-specific rRNA was restricted to light gradient fractions, and the prominent T-RFs found in the PCE-dechlorinating microcosm were of minor importance. Apparently, 13C-acetate was incorporated into bacterial rRNA more effectively in PCE-respiring microcosms. Thus, rRNA-SIP provides strong evidence for the presence of PCE-dehalorespiring, 13C-acetate-utilising populations in river sediment microcosms. Cloning/sequencing analysis identified the prominent members of the heavy gradient fractions as members of the phylum Chloroflexi only distantly related to cultivated dechlorinating Dehalococcides spp.

Population dynamics of transgenic strain Escherichia coli Z905/pPHL7 in freshwater and saline lake water microcosms with differing microbial community structures

NASA Astrophysics Data System (ADS)

Popova, L. Yu.; Kargatova, T. V.; Ganusova, E. E.; Lobova, T. I.; Boyandin, A. N.; Mogilnaya, O. A.; Pechurkin, N. S.

Populations of Escherichia coli Z905/pPHL7, a transgenic microorganism, were heterogenic in the expression of plasmid genes when adapting to the conditions of water microcosms of various mineralization levels and structure of microbial community. This TM has formed two subpopulations (ampicillin-resistant and ampicillin-sensitive) in every microcosm. Irrespective of mineralization level of a microcosm, when E. coli Z905/pPHL7 alone was introduced, the ampicillin-resistant subpopulation prevailed, while introduction of the TM together with indigenous bacteria led to the dominance of the ampicillin-sensitive subpopulation. A high level of lux gene expression maintained longer in the freshwater microcosms than in sterile saline lake water microcosms. A horizontal gene transfer has been revealed between the jointly introduced TM and Micrococcus sp. 9/pSH1 in microcosms with the Lake Shira sterile water.

The influence of environmental conditions on lead transfer from spent gunshot to sediments and water: Other routes for Pb poisoning.

PubMed

Binkowski, Łukasz J

2017-11-01

Lead (Pb) from spent gunshot and fishing sinkers is recognized as the main source of Pb poisoning among waterfowl. It is also suspected to directly pollute water and sediments, but no appropriate, comprehensive evaluation of this issue has so far been carried out. An experiment on Pb pellets in microcosms (n = 160) with two sediment types (mud and gravel), three water pH values (4, 7 and 9) and two wind levels (wind and windless simulation) was therefore run. Substantial differences in Pb transfer (measured with ICP-OES) between sediment types and pH levels of water were observed. Simulated wind conditions were a significant factor only for some variables and circumstances. The strongest Pb deposit to water and sediments occurred in mud microcosms with water of pH value of 4. Median pellet erosion during the experiment differed little between sediment types. The experiment revealed that Pb transfer from spent gunshot to the environment occurs only in specific environmental conditions. Copyright © 2017 Elsevier Ltd. All rights reserved.

Microbial community analysis of switchgrass planted and unplanted soil microcosms displaying PCB dechlorination

PubMed Central

Liang, Yi; Meggo, Richard; Hu, Dingfei; Schnoor, Jerald L.; Mattes, Timothy E.

2015-01-01

Polychlorinated biphenyls (PCBs) pose potential risks to human and environmental health because they are carcinogenic, persistent and bioaccumulative. In this study we investigated bacterial communities in soil microcosms spiked with PCB 52, 77 and 153. Switchgrass (Panicum virgatum) was employed to improve overall PCB removal and redox cycling (i.e. sequential periods of flooding followed by periods of no flooding) was performed in an effort to promote PCB dechlorination. Lesser chlorinated PCB transformation products were detected in all microcosms, indicating the occurrence of PCB dechlorination. Terminal restriction fragment length polymorphism (T-RFLP) and clone library analysis showed that PCB spiking, switchgrass planting and redox cycling affected the microbial community structure. Putative organohalide-respiring Chloroflexi populations, which were not found in unflooded microcosms, were enriched after two weeks of flooding in the redox-cycled microcosms. Sequences classified as Geobacter sp. were detected in all microcosms, and were most abundant in the switchgrass-planted microcosm spiked with PCB congeners. The presence of possible organohalide-respiring bacteria in these soil microcosms suggests they play a role in PCB dechlorination therein. PMID:25820643

Microbial community analysis of switchgrass planted and unplanted soil microcosms displaying PCB dechlorination.

PubMed

Liang, Yi; Meggo, Richard; Hu, Dingfei; Schnoor, Jerald L; Mattes, Timothy E

2015-08-01

Polychlorinated biphenyls (PCBs) pose potential risks to human and environmental health because they are carcinogenic, persistent, and bioaccumulative. In this study, we investigated bacterial communities in soil microcosms spiked with PCB 52, 77, and 153. Switchgrass (Panicum virgatum) was employed to improve overall PCB removal, and redox cycling (i.e., sequential periods of flooding followed by periods of no flooding) was performed in an effort to promote PCB dechlorination. Lesser chlorinated PCB transformation products were detected in all microcosms, indicating the occurrence of PCB dechlorination. Terminal restriction fragment length polymorphism (T-RFLP) and clone library analysis showed that PCB spiking, switchgrass planting, and redox cycling affected the microbial community structure. Putative organohalide-respiring Chloroflexi populations, which were not found in unflooded microcosms, were enriched after 2 weeks of flooding in the redox-cycled microcosms. Sequences classified as Geobacter sp. were detected in all microcosms and were most abundant in the switchgrass-planted microcosm spiked with PCB congeners. The presence of possible organohalide-respiring bacteria in these soil microcosms suggests that they play a role in PCB dechlorination therein.

Bioremediation of diesel and lubricant oil-contaminated soils using enhanced landfarming system.

PubMed

Wang, Sih-Yu; Kuo, Yu-Chia; Hong, Andy; Chang, Yu-Min; Kao, Chih-Ming

2016-12-01

Lubricant and diesel oil-polluted sites are difficult to remediate because they have less volatile and biodegradable characteristics. The goal of this research was to evaluate the potential of applying an enhanced landfarming to bioremediate soils polluted by lubricant and diesel. Microcosm study was performed to evaluate the optimal treatment conditions with the addition of different additives (nutrients, addition of activated sludge from oil-refining wastewater facility, compost, TPH-degrading bacteria, and fern chips) to enhance total petroleum hydrocarbon (TPH) removal. To simulate the aerobic landfarming biosystem, air in the microcosm headspace was replaced once a week. Results demonstrate that the additives of activated sludge and compost could result in the increase in soil microbial populations and raise TPH degradation efficiency (up to 83% of TPH removal with 175 days of incubation) with initial (TPH = 4100 mg/kg). The first-order TPH degradation rate reached 0.01 1/d in microcosms with additive of activated sludge (mass ratio of soil to inocula = 50:1). The soil microbial communities were determined by nucleotide sequence analyses and 16S rRNA-based denatured gradient gel electrophoresis. Thirty-four specific TPH-degrading bacteria were detected in microcosm soils. Chromatograph analyses demonstrate that resolved peaks were more biodegradable than unresolved complex mixture. Results indicate that more aggressive remedial measures are required to enhance the TPH biodegradation, which included the increase of (1) microbial population or TPH-degrading bacteria, (2) biodegradable carbon sources, (3) nutrient content, and (4) soil permeability. Copyright © 2016 Elsevier Ltd. All rights reserved.

From a microcosm to the catchment scale: studying the fate of organic runoff pollutants in aquatic ecosystems

NASA Astrophysics Data System (ADS)

Böttcher, T.; Schroll, R.

2009-04-01

Spray-drift, drainage, erosion and runoff events are the major causes responsible for deportation of agrochemicals as micropollutants to aquatic non-target sites. These processes can lead to the contamination of nearby freshwater ecosystems with considerably high concentrations of xenobiotics. Thus, it is important to unravel the fate of these pollutants and to evaluate their ecological effects. A novel approach to address this goal was established by the development of a microcosm with multiple sampling abilities enabling quantitative assessment of organic volatilisation, mineralization, metabolization and distribution within the aquatic ecosystem. This microcosm system was designed to support modelling approaches of the catchment scale and gain insights into the fate of pesticides simulating a large scale water body. The potential of this microcosm was exemplified for Isoproturon (IPU), a phenylurea derived systemic herbicide, which is frequently found as contaminant in water samples and with the free-floating macrophyte Lemna minor as non-target species, that is common to occur in rural water bodies. During 21 days exposure time, only a small amount of 14C labeled IPU was removed from the aquatic medium. The major portion (about 5%) was accumulated by Lemna minor resulting in a BCF of 15.8. IPU-volatilisation was very low with 0.13% of the initially applied herbicide. Only a minor amount of IPU was completely metabolized, presumably by rhizosphere microorganisms and released as 14CO2. The novel experimental system allowed to quantitatively investigate the fate of IPU and showed a high reproducibility with a mean average 14C-recovery rate of 97.1

Microcosm experiments approach to quantify nitrogen leaching from mineral and organic fertilized soil

NASA Astrophysics Data System (ADS)

Severus Sandor, Mignon; Sandor, Valentina; Mihai Onica, Bogdan; Brad, Traian

2017-04-01

The use of nitrogen inputs to improve agricultural soils fertility is a common practice in arable lands. Depending of nitrogen forms only a part of introduced nitrogen will be effectively used by the crops while another part can be leached from soil with negative impact on the environment. In temperate climate these losses are greater during spring time when rains are frequent and crop plants are in the early growth stage. In a microcosm experiments we simulated this kind of conditions in order to assess nitrogen losses from two different soils (Chernozem, Luvisol) fertilized with mineral (ammonium nitrate) and organic (mustard as green manure, slurry manure and cattle manure) fertilizers. From each microcosms we obtained 100 ml of leachate which was filtered and analyzed from N-NO3 and N-NH4. The leachate was obtained by adding distillate water at the microcosm surface two times during the experiment at a ten days interval. Preliminary results showed that only small quantity of ammonium was leached from fertilized soils, mainly after 20 days of incubation. These amounts were higher in Chernozem soil than in Luvisol and registered the highest amount in cattle manure fertilized soils. In general, the nitrate was leached from soils in high quantities. The highest value was measured in Chernozem soil when cattle manure was used as fertilizer (1200 mg/l) and represents a cumulative amount. For most of the treatments the cumulative loss of nitrate nitrogen was double in Chernozem soil than in Luvisol. The highest quantity of leaching nitrate was measured for both soils in manure fertilized soil.

Site-specific variability in BTEX biodegradation under denitrifying conditions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kao, C.M.; Borden, R.C.

1997-03-01

Laboratory microcosm experiments were conducted to evaluate the feasibility of benzene, toluene, ethylbenzene, m-xylene, and o-xylene (BTEX) biodegradation under denitrifying conditions. Nine different sources of inocula, including contaminated and uncontaminated soil cores from four different sites and activated sludge, were used to establish microcosms. BTEX was not degraded under denitrifying conditions in microcosms inoculated with aquifer material from Rocky Point and Traverse City. However, rapid depletion of glucose under denitrifying conditions was observed in microcosms containing Rocky Point aquifer material. TEX degradation was observed in microcosms containing Rocky Point aquifer material. TEX degradation was observed in microcosms containing aquifer materialmore » from Fort Bragg and Sleeping Bear Dunes and sewage sludge. Benzene was recalcitrant in all microcosms tested. The degradation of o-xylene ceased after toluene, ethylbenzene, and m-xylene were depleted in the Fort Bragg and sludge microcosms, but o-xylene continued to degrade in microcosms with contaminated Sleeping Bear Dunes soil. The most probable number (MPN) of denitrifiers in these nine different inocula were measured using a microtiter technique. There was no correlation between the MPN of denitrifiers and the TEX degradation rate under denitrifying conditions. Experimental results indicate that the degradation sequence and TEX degradation rate under denitrifying conditions may differ among sites. Results also indicate that denitrification alone may not be a suitable bioremediation technology for gasoline-contaminated aquifers because of the inability of denitrifiers to degrade benzene.« less

Metagenome and metatranscriptome data for Rifle CMT-03 laboratory microcosm experiment completed in April 2014

DOE Data Explorer

Jewell, Talia [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Karaoz, Ulas [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Bill, Markus [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Chakraborty, Romy [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Brodie, Eoin L [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Williams, Kenneth Hurst [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Beller, Harry R [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)

2014-04-01

Sediment samples were collected during installation of monitoring borehole CMT-03. Microcosms were constructed and inoculated under anerobic conditions with these sediments and anaerobic Rifle artificial groundwater. Microcosm metagenomes and metatranscriptomes were sampled every 5 days for a period of 20 days. The dataset gives gene-level annotations, binning, metagenomic and metatranscriptomic coverages for these microcosms.

A Reproducible Oral Microcosm Biofilm Model for Testing Dental Materials

PubMed Central

Rudney, J.D.; Chen, R.; Lenton, P.; Li, J.; Li, Y.; Jones, R.S.; Reilly, C.; Fok, A.S.; Aparicio, C.

2012-01-01

Aims Most studies of biofilm effects on dental materials use single-species biofilms, or consortia. Microcosm biofilms grown directly from saliva or plaque are much more diverse, but difficult to characterize. We used the Human Oral Microbial Identification Microarray (HOMIM) to validate a reproducible oral microcosm model. Methods and Results Saliva and dental plaque were collected from adults and children. Hydroxyapatite and dental composite disks were inoculated with either saliva or plaque, and microcosm biofilms were grown in a CDC biofilm reactor. In later experiments, the reactor was pulsed with sucrose. DNA from inoculums and microcosms were analyzed by HOMIM for 272 species. Microcosms included about 60% of species from the original inoculum. Biofilms grown on hydroxyapatite and composites were extremely similar. Sucrose-pulsing decreased diversity and pH, but increased the abundance of Streptococcus and Veilonella. Biofilms from the same donor, grown at different times, clustered together. Conclusions This model produced reproducible microcosm biofilms that were representative of the oral microbiota. Sucrose induced changes associated with dental caries. Significance and Impact of the Study This is the first use of HOMIM to validate an oral microcosm model that can be used to study the effects of complex biofilms on dental materials. PMID:22925110

Population dynamics of transgenic strain Escherichia coli Z905/pPHL7 in freshwater and saline lake water microcosms with differing microbial community structures

NASA Technical Reports Server (NTRS)

Popova, L. Yu; Kargatova, T. V.; Ganusova, E. E.; Lobova, T. I.; Boyandin, A. N.; Mogilnaya, O. A.; Pechurkin, N. S.

2005-01-01

Populations of Escherichia coli Z905/pPHL7, a transgenic microorganism, were heterogenic in the expression of plasmid genes when adapting to the conditions of water microcosms of various mineralization levels and structure of microbial community. This TM has formed two subpopulations (ampicillin-resistant and ampicillin-sensitive) in every microcosm. Irrespective of mineralization level of a microcosm, when E. coli Z905/pPHL7 alone was introduced, the ampicillin-resistant subpopulation prevailed, while introduction of the TM together with indigenous bacteria led to the dominance of the ampicillin-sensitive subpopulation. A high level of lux gene expression maintained longer in the freshwater microcosms than in sterile saline lake water microcosms. A horizontal gene transfer has been revealed between the jointly introduced TM and Micrococcus sp. 9/pSH1 in microcosms with the Lake Shira sterile water. c2005 COSPAR. Published by Elsevier Ltd. All rights reserved.

Impact of municipal wastewater effluent on seed bank response and soils excavated from a wetland impoundment

USGS Publications Warehouse

Finocchiaro, R.G.; Kremer, R.J.; Fredrickson, L.H.

2009-01-01

Intensive management of wetlands to improve wildlife habitat typically includes the manipulation of water depth, duration, and timing to promote desired vegetation communities. Increased societal, industrial, and agricultural demands for water may encourage the use of alternative sources such as wastewater effluents in managed wetlands. However, water quality is commonly overlooked as an influence on wetland soil seed banks and soils. In four separate greenhouse trials conducted over a 2-yr period, we examined the effects of municipal wastewater effluent (WWE) on vegetation of wetland seed banks and soils excavated from a wildlife management area in Missouri, USA. We used microcosms filled with one of two soil materials and irrigated with WWE, Missouri River water, or deionized water to simulate moist-soil conditions. Vegetation that germinated from the soil seed bank was allowed to grow in microcosms for approximately 100 d. Vegetative taxa richness, plant density, and biomass were significantly reduced in WWE-irrigated soil materials compared with other water sources. Salinity and sodicity rapidly increased in WWE-irrigated microcosms and probably was responsible for inhibiting germination or interfering with seedling development. Our results indicate that irrigation with WWE promoted saline-sodic soil conditions, which alters the vegetation community by inhibiting germination or seedling development. ?? 2009, The Society of Wetland Scientists.

Chemical dispersants can suppress the activity of natural oil-degrading microorganisms

PubMed Central

Kleindienst, Sara; Seidel, Michael; Ziervogel, Kai; Grim, Sharon; Loftis, Kathy; Harrison, Sarah; Malkin, Sairah Y.; Perkins, Matthew J.; Field, Jennifer; Sogin, Mitchell L.; Dittmar, Thorsten; Passow, Uta; Medeiros, Patricia M.; Joye, Samantha B.

2015-01-01

During the Deepwater Horizon oil well blowout in the Gulf of Mexico, the application of 7 million liters of chemical dispersants aimed to stimulate microbial crude oil degradation by increasing the bioavailability of oil compounds. However, the effects of dispersants on oil biodegradation rates are debated. In laboratory experiments, we simulated environmental conditions comparable to the hydrocarbon-rich, 1,100 m deep plume that formed during the Deepwater Horizon discharge. The presence of dispersant significantly altered the microbial community composition through selection for potential dispersant-degrading Colwellia, which also bloomed in situ in Gulf deep waters during the discharge. In contrast, oil addition to deepwater samples in the absence of dispersant stimulated growth of natural hydrocarbon-degrading Marinobacter. In these deepwater microcosm experiments, dispersants did not enhance heterotrophic microbial activity or hydrocarbon oxidation rates. An experiment with surface seawater from an anthropogenically derived oil slick corroborated the deepwater microcosm results as inhibition of hydrocarbon turnover was observed in the presence of dispersants, suggesting that the microcosm findings are broadly applicable across marine habitats. Extrapolating this comprehensive dataset to real world scenarios questions whether dispersants stimulate microbial oil degradation in deep ocean waters and instead highlights that dispersants can exert a negative effect on microbial hydrocarbon degradation rates. PMID:26553985

Extending the Marine Microcosm Laboratory

ERIC Educational Resources Information Center

Ryswyk, Hal Van; Hall, Eric W.; Petesch, Steven J.; Wiedeman, Alice E.

2007-01-01

The traditional range of marine microcosm laboratory experiments is presented as an ideal environment to teach the entire analysis process. The microcosm lab provides student-centered approach with opportunities for collaborative learning and to develop critical communication skills.

Stimulation of aerobic degradation of bentazone, mecoprop and dichlorprop by oxygen addition to aquifer sediment.

PubMed

Levi, S; Hybel, A-M; Bjerg, P L; Albrechtsen, H-J

2014-03-01

In order to investigate aerobic degradation potential for the herbicides bentazone, mecoprop and dichlorprop, anaerobic groundwater samples from two monitoring and three drinking water wells near a drinking water abstraction field in Nybølle, Denmark, were screened for their degradation potential for the herbicides. In the presence of oxygen (14)C-labelled bentazone and mecoprop were removed significantly from the two monitoring wells' groundwater samples. Oxygen was added to microcosms in order to investigate whether different oxygen concentrations stimulate the biodegradation of the three herbicides in microcosms using groundwater and sandy aquifer materials. To maintain a certain oxygen concentration this level was measured from the outside of the bottles with a fibre oxygen meter using oxygen-sensitive luminescent sensor foil mounted inside the microcosm, to which supplementary oxygen was added. The highest oxygen concentrations (corresponding to 4-11 mg L(-1)) stimulated degradation (a 14-27% increase for mecoprop, 3-9% for dichlorprop and 15-20% for bentazone) over an experimental period of 200 days. Oxygen was required to biodegrade the herbicides, since no degradation was observed under anaerobic conditions. This is the first time bentazone degradation has been observed in aquifer material at low oxygen concentrations (2 mg L(-1)). The sediment had substantial oxygen consumption (0.92-1.45O2 g(-1)dw over 200 days) and oxygen was depleted rapidly in most incubations soon after its addition, which might be due to the oxidation of organic matter and other reduced species such as Fe(2+), S(2-) and Mn in sediment before the biodegradation of herbicides takes place. This study suggests that oxygen enhancement around a drinking water abstraction field could stimulate the bioremediation of diffuse source contamination. Copyright © 2013. Published by Elsevier B.V.

Use of Acetate, Propionate, and Butyrate for Reduction of Nitrate and Sulfate and Methanogenesis in Microcosms and Bioreactors Simulating an Oil Reservoir.

PubMed

Chen, Chuan; Shen, Yin; An, Dongshan; Voordouw, Gerrit

2017-04-01

Acetate, propionate, and butyrate (volatile fatty acids [VFA]) occur in oil field waters and are frequently used for microbial growth of oil field consortia. We determined the kinetics of use of these VFA components (3 mM each) by an anaerobic oil field consortium in microcosms containing 2 mM sulfate and 0, 4, 6, 8, or 13 mM nitrate. Nitrate was reduced first, with a preference for acetate and propionate. Sulfate reduction then proceeded with propionate (but not butyrate) as the electron donor, whereas the fermentation of butyrate (but not propionate) was associated with methanogenesis. Microbial community analyses indicated that Paracoccus and Thauera ( Paracoccus - Thauera ), Desulfobulbus , and Syntrophomonas - Methanobacterium were the dominant taxa whose members catalyzed these three processes. Most-probable-number assays showed the presence of up to 10 7 /ml of propionate-oxidizing sulfate-reducing bacteria (SRB) in waters from the Medicine Hat Glauconitic C field. Bioreactors with the same concentrations of sulfate and VFA responded similarly to increasing concentrations of injected nitrate as observed in the microcosms: sulfide formation was prevented by adding approximately 80% of the nitrate dose needed to completely oxidize VFA to CO 2 in both. Thus, this work has demonstrated that simple time-dependent observations of the use of acetate, propionate, and butyrate for nitrate reduction, sulfate reduction, and methanogenesis in microcosms are a good proxy for these processes in bioreactors, monitoring of which is more complex. IMPORTANCE Oil field volatile fatty acids acetate, propionate, and butyrate were specifically used for nitrate reduction, sulfate reduction, and methanogenic fermentation. Time-dependent analyses of microcosms served as a good proxy for these processes in a bioreactor, mimicking a sulfide-producing (souring) oil reservoir: 80% of the nitrate dose required to oxidize volatile fatty acids to CO 2 was needed to prevent souring in both. Our data also suggest that propionate is a good substrate to enumerate oil field SRB. Copyright © 2017 American Society for Microbiology.

Erosion characteristics and horizontal variability for small erosion depths in the Sacramento-San Joaquin River Delta, California, USA

NASA Astrophysics Data System (ADS)

Schoellhamer, David H.; Manning, Andrew J.; Work, Paul A.

2017-06-01

Erodibility of cohesive sediment in the Sacramento-San Joaquin River Delta (Delta) was investigated with an erosion microcosm. Erosion depths in the Delta and in the microcosm were estimated to be about one floc diameter over a range of shear stresses and times comparable to half of a typical tidal cycle. Using the conventional assumption of horizontally homogeneous bed sediment, data from 27 of 34 microcosm experiments indicate that the erosion rate coefficient increased as eroded mass increased, contrary to theory. We believe that small erosion depths, erosion rate coefficient deviation from theory, and visual observation of horizontally varying biota and texture at the sediment surface indicate that erosion cannot solely be a function of depth but must also vary horizontally. We test this hypothesis by developing a simple numerical model that includes horizontal heterogeneity, use it to develop an artificial time series of suspended-sediment concentration (SSC) in an erosion microcosm, then analyze that time series assuming horizontal homogeneity. A shear vane was used to estimate that the horizontal standard deviation of critical shear stress was about 30% of the mean value at a site in the Delta. The numerical model of the erosion microcosm included a normal distribution of initial critical shear stress, a linear increase in critical shear stress with eroded mass, an exponential decrease of erosion rate coefficient with eroded mass, and a stepped increase in applied shear stress. The maximum SSC for each step increased gradually, thus confounding identification of a single well-defined critical shear stress as encountered with the empirical data. Analysis of the artificial SSC time series with the assumption of a homogeneous bed reproduced the original profile of critical shear stress, but the erosion rate coefficient increased with eroded mass, similar to the empirical data. Thus, the numerical experiment confirms the small-depth erosion hypothesis. A linear model of critical shear stress and eroded mass is proposed to simulate small-depth erosion, assuming that the applied and critical shear stresses quickly reach equilibrium.

Erosion characteristics and horizontal variability for small erosion depths in the Sacramento-San Joaquin River Delta, California, USA

USGS Publications Warehouse

Schoellhamer, David H.; Manning, Andrew J.; Work, Paul A.

2017-01-01

Erodibility of cohesive sediment in the Sacramento-San Joaquin River Delta (Delta) was investigated with an erosion microcosm. Erosion depths in the Delta and in the microcosm were estimated to be about one floc diameter over a range of shear stresses and times comparable to half of a typical tidal cycle. Using the conventional assumption of horizontally homogeneous bed sediment, data from 27 of 34 microcosm experiments indicate that the erosion rate coefficient increased as eroded mass increased, contrary to theory. We believe that small erosion depths, erosion rate coefficient deviation from theory, and visual observation of horizontally varying biota and texture at the sediment surface indicate that erosion cannot solely be a function of depth but must also vary horizontally. We test this hypothesis by developing a simple numerical model that includes horizontal heterogeneity, use it to develop an artificial time series of suspended-sediment concentration (SSC) in an erosion microcosm, then analyze that time series assuming horizontal homogeneity. A shear vane was used to estimate that the horizontal standard deviation of critical shear stress was about 30% of the mean value at a site in the Delta. The numerical model of the erosion microcosm included a normal distribution of initial critical shear stress, a linear increase in critical shear stress with eroded mass, an exponential decrease of erosion rate coefficient with eroded mass, and a stepped increase in applied shear stress. The maximum SSC for each step increased gradually, thus confounding identification of a single well-defined critical shear stress as encountered with the empirical data. Analysis of the artificial SSC time series with the assumption of a homogeneous bed reproduced the original profile of critical shear stress, but the erosion rate coefficient increased with eroded mass, similar to the empirical data. Thus, the numerical experiment confirms the small-depth erosion hypothesis. A linear model of critical shear stress and eroded mass is proposed to simulate small-depth erosion, assuming that the applied and critical shear stresses quickly reach equilibrium.

NP1EC Degradation Pathways Under Oxic and Microxic Conditions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Montgomery-Brown, John; Li, Yongmei; Ding, Wang-Hsien

2008-03-22

The degradation pathway of nonylphenol ethoxyacetic acid (NP1EC) and the conditions favoring CAP1EC formation were studied in aerobic microcosms constructed with soil from the Mesa soil aquifer treatment (SAT) facility (Arizona, USA) and pristine sediments from Coyote Creek (California, USA). In the Mesa microcosms, para-NP1EC was transformed to para-NP, before being rapidly transformed to nonyl alcohols via ipso-hydroxylation. While the formation of NP from APEMs has been observed by several researchers under anaerobic conditions, this is the first time the transient formation of NP from APEMs has been observed under aerobic conditions. Unlike the Mesa microcosms, large quantities of CAP1ECsmore » were observed in the Coyote Creek microcosms. Initially, CA8P1ECs were the dominant metabolites, but as biodegradation continued, CA6P1ECs became the dominant metabolites. Compared to the CA8P1ECs, the number of CA6P1ECs peaks observed was small (<6) even though their concentrations were high. This suggests that several CA8P1ECs are degraded to only a few CA6P1EC isomers (i.e., the degradation pathway converges) or that some CA6P1EC metabolites are significantly more recalcitrant than others. The different biodegradation pathways observed in the Mesa and Coyote Creek microcosms result from the limited availability of dissolved oxygen in the Coyote Creek microcosms. In both sets of microcosms, the ortho isomers were transformed more slowly than the para isomers and in the Coyote Creek microcosms several ortho-CAP1ECs were observed. In addition, several unknown metabolites were observed in the Coyote Creek microcosms that were not seen in the abiotic or Mesa microcosms; these metabolites appear to be CAP1EC metabolites, have a -CH2-C6H4- fragment, and contain one carboxylic acid. Nitro-nonylphenol was observed in the Mesa microcosms, however, further experimentation illustrated that it was the product of an abiotic reaction between nitrite and nonylphenol under acidic conditions.« less

Do zebra mussels (Dreissena polymorpha) alter lake water chemistry in a way that favours Microcystis growth?

PubMed

Bykova, Olga; Laursen, Andrew; Bostan, Vadim; Bautista, Joseph; McCarthy, Lynda

2006-12-01

This study examined possible relationships between the presence of zebra mussels (Dreissena polymorpha) and Microcystis spp. abundance. Experiments were conducted in 12 microcosms designed to mimic shallow lake ecosystems. Fresh, aerated water with phytoplankton (pseudokirchneriella spp. and Microcystis spp.) was pumped into each microcosm daily to ensure zebra mussels were exposed to oxygen and food. Microcosms containing zebra mussels experienced significantly higher fluxes of nitrate (p=0.019) and lower fluxes of ortho-phosphate (p=0.047) into sediments. In a second experiment, water column nutrient concentrations were compared in microcosms with and without live zebra mussels. Consistent with results of the previous experiment, microcosms with zebra mussels had significantly less nitrate (p=0.023) and organic nitrogen (p=0.003) in the water column, while ammonium (p=0.074), phosphate (p=0.491), and dissolved organic carbon (p=0.820) in the water column were not different between microcosms with or without zebra mussels. Microcosms with zebra mussels also experienced a reduction in green algae (pseudokirchneriella) (p<0.001) and an increase in abundance of Microcystis (p<0.001) relative to microcosms without zebra mussels. In an experiment without zebra mussels, nutrient ratios (N/P) were manipulated to determine potential links between N/P and relative abundance of each phytoplankton. Manipulation of N/P was intended to mimic differences observed in microcosms with and without zebra mussels in the previous experiment. Low N/P (mimicking microcosms with zebra mussels) was related to an increase in Microcystis (p<0.001) and Microcystis/Pseudokirchneriella biovolume (p<0.001). It is this shift in N/P, and possibly some level of selective feeding, that is believed to have driven changes in the relative abundance of Microcystis. In lakes invaded by zebra mussels, alterations in the processing of nitrogen and phosphorus could contribute to the re-emergence of Microcystis blooms.

PERSPECTIVE ON THE ROLE OF MICROCOSMS IN ENVIRONMENTAL FATE AND EFFECTS ASSESSMENTS

EPA Science Inventory

This paper provides a perspective on the possible interfacing of microcosm studies with both waste assimilatory capacity determinations and other less quantitative types of assessment. Some of the problems and inconsistencies in the interpretation and application of microcosm res...

Stability and resilience of oral microcosms toward acidification and Candida outgrowth by arginine supplementation.

PubMed

Koopman, Jessica E; Röling, Wilfred F M; Buijs, Mark J; Sissons, Christopher H; ten Cate, Jacob M; Keijser, Bart J F; Crielaard, Wim; Zaura, Egija

2015-02-01

Dysbiosis induced by low pH in the oral ecosystem can lead to caries, a prevalent bacterial disease in humans. The amino acid arginine is one of the pH-elevating agents in the oral cavity. To obtain insights into the effect of arginine on oral microbial ecology, a multi-plaque "artificial mouth" (MAM) biofilm model was inoculated with saliva from a healthy volunteer and microcosms were grown for 4 weeks with 1.6 % (w/v) arginine supplement (Arginine) or without (Control), samples were taken at several time-points. A cariogenic environment was mimicked by sucrose pulsing. The bacterial composition was determined by 16S rRNA gene amplicon sequencing, the presence and amount of Candida and arginine deiminase system genes arcA and sagP by qPCR. Additionally, ammonium and short-chain fatty acid concentrations were determined. The Arginine microcosms were dominated by Streptococcus, Veillonella, and Neisseria and remained stable in time, while the composition of the Control microcosms diverged significantly in time, partially due to the presence of Megasphaera. The percentage of Candida increased 100-fold in the Control microcosms compared to the Arginine microcosms. The pH-raising effect of arginine was confirmed by the pH and ammonium results. The abundances of sagP and arcA were highest in the Arginine microcosms, while the concentration of butyrate was higher in the Control microcosms. We demonstrate that supplementation with arginine serves a health-promoting function; it enhances microcosm resilience toward acidification and suppresses outgrowth of the opportunistic pathogen Candida. Arginine facilitates stability of oral microbial communities and prevents them from becoming cariogenic.

Assessing microbial responses to iron enrichment in the Subarctic Northeast Pacific: Do microcosms reproduce the in situ condition?

NASA Astrophysics Data System (ADS)

Scarratt, M. G.; Marchetti, A.; Hale, M. S.; Rivkin, R. B.; Michaud, S.; Matthews, P.; Levasseur, M.; Sherry, N.; Merzouk, A.; Li, W. K. W.; Kiyosawa, H.

2006-10-01

A microcosm experiment was conducted in the NE Pacific in July 2002 to compare the microbial response between microcosms and the Subarctic Ecosystem Response to Iron-Enrichment Study (SERIES) in situ iron-enrichment experiment. Seawater microcosms (20 L) were incubated aboard ship under natural light using three treatments: (1) low-iron seawater amended with 4 nmol l -1 FeSO 4 (+Fe); (2) low-iron seawater amended with 4 nmol l -1 FeSO 4 and 86 nmol l -1 GeO 2 (+Fe+Ge); (3) seawater collected from the in situ Fe-enriched patch (PW). The +Fe+Ge treatment used germanium to control diatom growth to assess the role of diatoms in dimethylsulfoniopropionate (DMSP) production. The following variables were measured in the microcosms and in situ: chlorophyll a (chl a), nitrate ( NO3-), silicic acid (Si(OH) 4), phytoplankton abundance and species identification, bacterial abundance (including estimates of low- and high-DNA bacteria), bacterial production, bacterial specific growth rate, particulate and dissolved DMSP and dimethylsulfide (DMS) concentrations. There was little or no significant difference (ANCOVA) in the response of most variables between the +Fe and PW microcosms, but large differences were observed between both these treatments and the in situ data from the enriched patch. Chl a in all microcosms increased from ambient levels (approx. 0.5-1 μg l -1) to approx. 4.5-6.2 μg l -1 after 11 d incubation, when NO3- was fully depleted from all microcosms. During this same period, in situ chl a increased more slowly to a maximum of 2.9 μg l -1 on day 11. Nanophytoplankton and picophytoplankton were more abundant in the microcosms relative to the in situ community, which became dominated by large diatoms. Bacterial abundance was similar in the microcosms and in situ, but bacterial production was significantly higher in the microcosms. While neither DMSP d nor DMS accumulation showed significant differences between the microcosms and in situ , particulate DMSP concentrations increased significantly faster in the +Fe and PW treatments. These differences represent bottle effects resulting from the containment of the microcosms, which suppresses grazing, alters community and food web structure, enhances iron and nutrient regeneration, and isolates the community from physical transport and export processes including sinking. Thus during this experiment, the microcosms were not a good model for the in situ system in terms of the effects of iron on the phytoplankton biomass, nutrient uptake, bacterial dynamics and DMSP p production. In the germanium-amended treatment, the inhibition of diatom growth resulted in enhanced growth of other taxa and a suppression of bacterial production, leading to increased production of DMSP and DMS and strong correlations between DMSP, DMS and non-diatom phytoplankton taxa. Diatoms did not contribute significantly to particulate DMSP concentrations.

Decay of Bacteroidales genetic markers in relation to traditional fecal indicators for water quality modeling of drinking water sources.

PubMed

Sokolova, Ekaterina; Aström, Johan; Pettersson, Thomas J R; Bergstedt, Olof; Hermansson, Malte

2012-01-17

The implementation of microbial fecal source tracking (MST) methods in drinking water management is limited by the lack of knowledge on the transport and decay of host-specific genetic markers in water sources. To address these limitations, the decay and transport of human (BacH) and ruminant (BacR) fecal Bacteroidales 16S rRNA genetic markers in a drinking water source (Lake Rådasjön in Sweden) were simulated using a microbiological model coupled to a three-dimensional hydrodynamic model. The microbiological model was calibrated using data from outdoor microcosm trials performed in March, August, and November 2010 to determine the decay of BacH and BacR markers in relation to traditional fecal indicators. The microcosm trials indicated that the persistence of BacH and BacR in the microcosms was not significantly different from the persistence of traditional fecal indicators. The modeling of BacH and BacR transport within the lake illustrated that the highest levels of genetic markers at the raw water intakes were associated with human fecal sources (on-site sewers and emergency sewer overflow). This novel modeling approach improves the interpretation of MST data, especially when fecal pollution from the same host group is released into the water source from different sites in the catchment.

Assessing the impacts of salinity and nutrient stress to Ruppia ...

EPA Pesticide Factsheets

Healthy seagrass beds were once found throughout the shallow areas of Narragansett Bay, R.I. but have disappeared due to infilling, pollution and disease. In Greenwich Bay, a highly developed embayment within Narragansett Bay, Ruppia maritima has colonized an area on the northern shore historically dominated by Zostera marina. Ruppia is extremely salinity tolerant, and may also be more nutrient tolerant than Zostera. To test this hypothesis 6-week microcosm experiments were conducted in the summers of 2014 and 2015. Microcosms were renewed daily to simulate tidal flushing and the water column was dosed with a 15N tracer for the first week of the experiments. In the 2014 microcosm experiment two salinity (20, 30 ppt) and four nutrient (0, 5, 10, 30 µM inorganic N) levels were used to test the species’ relative tolerance. This experiment yielded structurally significant results for Ruppia but no significant differences were detected for Zostera. In 2015 this experiment was performed for a second time with lower salinity (5, 30 ppt) and higher nutrients (0, 30, 100, 300, 1000 µM inorganic N) in order to determine Zostera’s tolerance to nutrient and salinity stress and confirm the previously observed Ruppia results. Both species had significant structural responses to the nutrient and salinity variables. Isotopic analysis run on above-ground tissue indicated that with increasing nutrient levels δ15N in the seagrass shoots increased, suggesting that nutrients

Phytotoxicity testing of winery wastewater for constructed wetland treatment.

PubMed

Arienzo, Michele; Christen, Evan W; Quayle, Wendy C

2009-09-30

Rapid and inexpensive phytotoxicity bioassays for winery wastewater (WW) are important when designing winery wastewater treatment systems involving constructed wetlands. Three macrophyte wetland species (Phragmites australis, Schoenoplectus validus and Juncus ingens) were tested using a pot experiment simulating a wetland microcosm. The winery wastewater concentration was varied (0.5%, 5%, 10%, 25%, 50%, 75% and 100%) and pH was corrected for some concentrations using lime as an amendment. The tolerance of the three aquatic macrophytes species to winery wastewater was studied through biomass production, total chlorophyll and nitrogen, phosphorous and potassium tissue concentrations. The results showed that at greater than 25% wastewater concentration all the macrophytes died and that Phragmites was the least hardy species. At less than 25% wastewater concentration the wetland microcosms were effective in reducing chemical oxygen demand, phenols and total soluble solids. We also evaluated the performance of two laboratory phytotoxicity assays; (1) Garden Cress (Lepidium sativum), and (2) Onion (Allium coepa). The results of these tests revealed that the effluent was highly toxic with effective concentration, EC(50), inhibition values, as low as 0.25%. Liming the WW increased the EC(50) by 10 fold. Comparing the cress and onion bioassays with the wetland microcosm results indicated that the thresholds for toxicity were of the same order of magnitude. As such we suggest that the onion and cress bioassays could be effectively used in the wine industry for rapid wastewater toxicity assessment.

EFFECTS OF SEDIMENT TYPE ON BENTHIC MACROINFAUNAL COLONIZATION OF LABORATORY MICROCOSMS

EPA Science Inventory

We tested the effects of four different sediment types on macroinfaunal colonization and community development in our laboratory flow-thru microcosm system (all microcosms were 20 cm side-1 and sediment depth was 5 cm) over a period of 41 days. Sediments included Santa Rosa Islan...

MICROCOSM AND IN-SITU FIELD STUDIES OF ENHANCED BIOTRANSFORMATION OF TRICHLOROETHYLENE BY PHENOL-UTILIZING MICROORGANISMS

EPA Science Inventory

The ability of different aerobic groundwater microorganisms to cometabolically degrade trichloroethylene (TCE), 1,2-cis-dichloroethylene (c-DCE), and 1,2-trans-dichloroethylene (t-DCE) was evaluated both in groundwater-fed microcosms and in situ in a shallow aquifer. Microcosms a...

SOME EFFECTS OF CADMIUM ON CONIFEROUS FOREST SOIL AND LITTER MICROCOSMS

EPA Science Inventory

Description and criticism is given of a preliminary design and use of a soil/litter microcosm in which oxygen, temperature, and humidity are kept constant, and oxygen generation and carbon dioxide and heat evolution rates are monitored. Using four microcosms, one acting as a dead...

Effect of Fe(III) on 1,1,2,2-tetrachloroethane degradation and vinyl chloride accumulation in wetland sediments of the Aberdeen proving ground

USGS Publications Warehouse

Jones, E.J.P.; Voytek, M.A.; Lorah, M.M.

2004-01-01

1,1,2,2-Tetrachloroethane (TeCA) contaminated groundwater at the Aberdeen Proving Ground discharges through an anaerobic wetland in West Branch Canal Creek, MD, where dechlorination occurred. Two microbially mediated pathways, dichloroelimination and hydrogenolysis, account for most of the TeCA degradation at this site. The dichloroelimination pathways led to the formation of vinyl chloride (VC), a recalcitrant carcinogen of great concern. The effect of adding Fe(III) to TeCA-amended microcosms of wetland sediment was studied. Differences were identified in the TeCA degradation pathway between microcosms treated with amorphous ferric oxyhydroxide (AFO-treated) and untreated (no AFO) microcosms. TeCA degradation was accompanied by a lower accumulation of VC in AFO-treated microcosms than no AFO microcosms. The microcosm incubations and subsequent experiments with the microcosm materials showed that AFO treatment resulted in lower production of VC by shifting TeCA degradation from dichloroelimination pathways to production of a greater proportion of chlorinated ethane products, and decreasing the microbial capability to produce VC from 1,2-dichloroethylene. VC degradation was not stimulated in the presence of Fe(III). Rather, VC degradation occurred readily under methanogenic conditions and was inhibited under Fe(III)-reducing conditions.

DFN-M field characterization of sandstone for a process-based site conceptual model and numerical simulations of TCE transport with degradation

NASA Astrophysics Data System (ADS)

Pierce, Amanda A.; Chapman, Steven W.; Zimmerman, Laura K.; Hurley, Jennifer C.; Aravena, Ramon; Cherry, John A.; Parker, Beth L.

2018-05-01

Plumes of trichloroethene (TCE) with degradation products occur at a large industrial site in California where TCE as a dense non-aqueous phase liquid (DNAPL) entered the fractured sandstone bedrock at many locations beginning in the late 1940s. Groundwater flows rapidly in closely spaced fractures but plume fronts are strongly retarded relative to groundwater flow velocities owing largely to matrix diffusion in early decades and degradation processes in later decades and going forward. Multiple data types show field evidence for both biotic and abiotic dechlorination of TCE and its degradation products, resulting in non-chlorinated compounds. Analyses were conducted on groundwater samples from hundreds of monitoring wells and on thousands of rock samples from continuous core over depths ranging from 6 to 426 metres below ground surface. Nearly all of the present-day mass of TCE and degradation products resides in the water-saturated, low-permeability rock matrix blocks. Although groundwater and DNAPL flow primarily occur in the fractures, DNAPL dissolution followed by diffusion and sorption readily transfers contaminant mass into the rock matrix. The presence of non-chlorinated degradation products (ethene, ethane, acetylene) and compound specific isotope analysis (CSIA) of TCE and cis-1,2-dichloroethene (cDCE) indicate at least some complete dechlorination by both biotic and abiotic pathways, consistent with the observed mineralogy and hydrogeochemistry and with published results from crushed rock microcosms. The rock matrix contains abundant iron-bearing minerals and solid-phase organic carbon with large surface areas and long contact times, suggesting degradation processes are occurring in the rock matrix. Multiple, high-resolution datasets provide strong evidence for spatially heterogeneous distributions of TCE and degradation products with varying degrees of degradation observed only when using new methods that achieve better detection of dissolved gases (i.e., Snap Sampler™) and contaminant mass stored in the low permeability rock matrix (i.e., CORE-DFN™). Simulations using a discrete fracture-matrix (DFN-M) numerical model capable of rigorously simulating flow and transport in both the fractures and matrix, including interactions, show that even slow, first-order degradation rates (i.e., 5- to 20-year half-lives) informed by site-derived parameters can contribute strongly to natural attenuation, resulting in TCE plumes that become stationary in space and might even retreat after 50 to 100 years, if the DNAPL sources become depleted due to the combination of diffusion and degradation processes.

DFN-M field characterization of sandstone for a process-based site conceptual model and numerical simulations of TCE transport with degradation.

PubMed

Pierce, Amanda A; Chapman, Steven W; Zimmerman, Laura K; Hurley, Jennifer C; Aravena, Ramon; Cherry, John A; Parker, Beth L

2018-05-01

Plumes of trichloroethene (TCE) with degradation products occur at a large industrial site in California where TCE as a dense non-aqueous phase liquid (DNAPL) entered the fractured sandstone bedrock at many locations beginning in the late 1940s. Groundwater flows rapidly in closely spaced fractures but plume fronts are strongly retarded relative to groundwater flow velocities owing largely to matrix diffusion in early decades and degradation processes in later decades and going forward. Multiple data types show field evidence for both biotic and abiotic dechlorination of TCE and its degradation products, resulting in non-chlorinated compounds. Analyses were conducted on groundwater samples from hundreds of monitoring wells and on thousands of rock samples from continuous core over depths ranging from 6 to 426 metres below ground surface. Nearly all of the present-day mass of TCE and degradation products resides in the water-saturated, low-permeability rock matrix blocks. Although groundwater and DNAPL flow primarily occur in the fractures, DNAPL dissolution followed by diffusion and sorption readily transfers contaminant mass into the rock matrix. The presence of non-chlorinated degradation products (ethene, ethane, acetylene) and compound specific isotope analysis (CSIA) of TCE and cis-1,2-dichloroethene (cDCE) indicate at least some complete dechlorination by both biotic and abiotic pathways, consistent with the observed mineralogy and hydrogeochemistry and with published results from crushed rock microcosms. The rock matrix contains abundant iron-bearing minerals and solid-phase organic carbon with large surface areas and long contact times, suggesting degradation processes are occurring in the rock matrix. Multiple, high-resolution datasets provide strong evidence for spatially heterogeneous distributions of TCE and degradation products with varying degrees of degradation observed only when using new methods that achieve better detection of dissolved gases (i.e., Snap Sampler™) and contaminant mass stored in the low permeability rock matrix (i.e., CORE-DFN™). Simulations using a discrete fracture-matrix (DFN-M) numerical model capable of rigorously simulating flow and transport in both the fractures and matrix, including interactions, show that even slow, first-order degradation rates (i.e., 5- to 20-year half-lives) informed by site-derived parameters can contribute strongly to natural attenuation, resulting in TCE plumes that become stationary in space and might even retreat after 50 to 100 years, if the DNAPL sources become depleted due to the combination of diffusion and degradation processes. Copyright © 2018 Elsevier B.V. All rights reserved.

Microcosm Studies to Evaluate Aerobic Cometabolism of Low Concentrations of 1,4-Dioxane by Isobutane-utilizing Microorganisms in the Presence of Chlorinated Solvent Co-contaminants

NASA Astrophysics Data System (ADS)

Rolston, H. M.; Azizian, M.; Hyman, M. R.; Semprini, L.

2015-12-01

Due to its use as a stabilizer for chlorinated solvents, 1,4-dioxane (1,4D), a probable human carcinogen, is a common co-contaminant in solvent spills at industrial and military sites and landfills. Its persistence in large groundwater plumes at low concentrations makes it a relevant candidate for in-situ bioremediation via cometabolism. Microcosm studies are being performed to evaluate the capability of aerobic microorganisms to cometabolize mixtures of 1,4D and chlorinated solvents, such as trichloroethylene (TCE), 1,1,1-trichloroethane (1,1,1TCA), and 1,1-dichloroethene (1,1DCE), with isobutane as the primary substrate. Microcosms were constructed using aquifer solids from Fort Carson, Colorado, a site contaminated with 1,4D and TCE, to assess the isobutane uptake and transformation of 1,4D and chlorinated solvents by microorganisms native to the site. Additional microcosms were augmented with Rhodococcus rhodochrous, a bacterium shown to cometabolize 1,4D and chlorinated solvents. Results indicate that native microcosms cometabolized 1,4D upon stimulation with isobutane after a lag period of about 15 days. TCE was also transformed, but at significantly slower rates. The presence of 1,4D and TCE at 500 and 300 ppb, respectively, did not inhibit the growth of native microorganisms on isobutane, with isobutane uptake and 1,4D transformation occurring simultaneously. Bioaugmented microcosms transformed 1,4D immediately after inoculation with R. rhodochrous. Tests in bioaugmented microorganisms indicated that the presence of TCE at low concentrations inhibits but does not block the transformation of 1,4D. Results from the microcosms will be used to design field tests to be performed at Fort Carson. Additional microcosm studies will compare the stimulation of native and bioaugmented microcosms and the transformation of mixtures of 1,4D, 1,1,1TCA and 1,1DCE. Molecular methods will analyze the monoxygenase enzymes expressed in the native and bioaugmented microcosms.

Bacterial Community Response to Petroleum Hydrocarbon Amendments in Freshwater, Marine, and Hypersaline Water-Containing Microcosms

PubMed Central

Jurelevicius, Diogo; Alvarez, Vanessa Marques; Marques, Joana Montezano; de Sousa Lima, Laryssa Ribeiro Fonseca; Dias, Felipe de Almeida

2013-01-01

Hydrocarbon-degrading bacterial communities from freshwater, marine, and hypersaline Brazilian aquatic ecosystems (with water salinities corresponding to 0.2%, 4%, and 5%, respectively) were enriched with different hydrocarbons (heptadecane, naphthalene, or crude oil). Changes within the different microcosms of bacterial communities were analyzed using cultivation approaches and molecular methods (DNA and RNA extraction, followed by genetic fingerprinting and analyses of clone libraries based on the 16S rRNA-coding gene). A redundancy analysis (RDA) of the genetic fingerprint data and a principal component analysis (PCA) of the clone libraries revealed hydrocarbon-enriched bacterial communities specific for each ecosystem studied. However, within the same ecosystem, different bacterial communities were selected according to the petroleum hydrocarbon used. In general, the results demonstrated that Acinetobacter and Cloacibacterium were the dominant genera in freshwater microcosms; the Oceanospirillales order and the Marinobacter, Pseudomonas, and Cycloclasticus genera predominated in marine microcosms; and the Oceanospirillales order and the Marinobacter genus were selected in the different hydrocarbon-containing microcosms in hypersaline water. Determination of total petroleum hydrocarbons (TPHs) in all microcosms after 32 days of incubation showed a decrease in the hydrocarbon concentration compared to that for the controls. A total of 50 (41.3%) isolates from the different hydrocarbon-contaminated microcosms were associated with the dominant operational taxonomic units (OTUs) obtained from the clone libraries, and their growth in the hydrocarbon contaminating the microcosm from which they were isolated as the sole carbon source was observed. These data provide insight into the general response of bacterial communities from freshwater, marine, and hypersaline aquatic ecosystems to petroleum hydrocarbon contamination. PMID:23872573

Responses of meiofauna and nematode communities to crude oil contamination in a laboratory microcosm experiment

NASA Astrophysics Data System (ADS)

Kang, Teawook; Oh, Je Hyeok; Hong, Jae-Sang; Kim, Dongsung

2016-09-01

We examined the effects of crude oil contamination on community assemblages of meiofauna and nematodes after exposure to total petroleum hydrocarbons in the laboratory. We administered a seawater solution that had been contaminated with total petroleum hydrocarbons to seven treatment groups at different concentrations, while the control group received uncontaminated filtered seawater. The average density of total meiofauna in the experimental microcosms diluted with 0.5%, 1%, 2%, and 4% contaminated seawater was higher than the density in the control. The average density of total meiofauna in the 8%, 15%, and 20% microcosms was lower than the density in the control. The density of nematodes was similar to that of the total meiofauna. Cluster analysis divided the microcosms into group 1 (control, 0.5%, 1%, 2%, and 4% microcosms) and group 2 (8%, 15%, and 20% microcosms). However, SIMPROF analysis showed no significant difference between the two groups ( p > 0.05). Bolbolaimus spp. (37.1%) were dominant among the nematodes. Cluster analysis showed similar results for nematode and meiofaunal communities. The total meiofaunal density, nematode density, and number of Bolbolaimus spp. individuals were significantly negatively associated with the concentration of total petroleum hydrocarbons (Spearman correlation coefficients, p < 0.05). Within the nematodes, epistrate feeders (group 2A: 46%) were the most abundant trophic group. Among the treatment groups, the abundance of group 2A increased in low-concentration microcosms and decreased in high-concentration microcosms. Thus, our findings provide information on the effects of oil pollution on meiofauna in the intertidal zones of sandy beaches.

Modelling the reworking effects of bioturbation on the incorporation of radionuclides into the sediment column: implications for the fate of particle-reactive radionuclides in Irish Sea sediments.

PubMed

Cournane, S; León Vintró, L; Mitchell, P I

2010-11-01

A microcosm laboratory experiment was conducted to determine the impact of biological reworking by the ragworm Nereis diversicolor on the redistribution of particle-bound radionuclides deposited at the sediment-water interface. Over the course of the 40-day experiment, as much as 35% of a (137)Cs-labelled particulate tracer deposited on the sediment surface was redistributed to depths of up to 11 cm by the polychaete. Three different reworking models were employed to model the profiles and quantify the biodiffusion and biotransport coefficients: a gallery-diffuser model, a continuous sub-surface egestion model and a biodiffusion model. Although the biodiffusion coefficients obtained for each model were quite similar, the continuous sub-surface egestion model provided the best fit to the data. The average biodiffusion coefficient, at 1.8 +/- 0.9 cm(2) y(-1), is in good agreement with the values quoted by other workers on the bioturbation effects of this polychaete species. The corresponding value for the biotransport coefficient was found to be 0.9 +/- 0.4 cm y(-1). The effects of non-local mixing were incorporated in a model to describe the temporal evolution of measured (99)Tc and (60)Co radionuclide sediment profiles in the eastern Irish Sea, influenced by radioactive waste discharged from the Sellafield reprocessing plant. Reworking conditions in the sediment column were simulated by considering an upper mixed layer, an exponentially decreasing diffusion coefficient, and appropriate biotransport coefficients to account for non-local mixing. The diffusion coefficients calculated from the (99)Tc and (60)Co cores were in the range 2-14 cm(2) y(-1), which are consistent with the values found by other workers in the same marine area, while the biotransport coefficients were similar to those obtained for a variety of macrobenthic organisms in controlled laboratories and field studies.

Reduction of nitrate in aquifer microcosms by carbon additions

USGS Publications Warehouse

Obenhuber, Donald C.; Lowrance , Richard

1991-01-01

Aquifer microcosms were used to examine the effects of NO−3 and C amendments on groundwater from the Claiborne aquifer. Nitrate concentrations of 12.17 mg L−1 in aquifer microcosms were reduced 0.92%/d to 5.84 mg L−1 by the addition of 10 mg C L−1 for 35 d. Nitrate disappearance correlated with increases in number of denitrifiers and dissolved N2O concentration and decreases in dissolved oxygen, suggesting biological denitrification. Nitrate/chloride ratios decreased in microcosms with 10 mg C L−1 added and then increased when the C addition was removed. Carbon additions of 0.4 mg C L−1 had no effect on the microbial or chemical properties of the microcosms. Nitrous oxide levels in wells sampling the Claiborne aquifer showed an increase with depth, indicating N2O production within the aquifer. Microcosms are useful tools to examine biological transformations of chemical contaminants in unconsolidated aquifer material. The remediation of NO−3 contaminated aquifers by organic infusion is possible and appears to be a function of microbial denitrification.

Atrazine remediation in wetland microcosms.

PubMed

Runes, H B; Bottomley, P J; Lerch, R N; Jenkins, J J

2001-05-01

Laboratory wetland microcosms were used to study treatment of atrazine in irrigation runoff by a field-scale-constructed wetland under controlled conditions. Three experiments, in which 1 ppm atrazine was added to the water column of three wetland, one soil control, and one water control microcosm, were conducted. Atrazine dissipation from the water column and degradate formation (deethylatrazine [DEA]; deisopropylatrazine [DIA]; and hydroxyatrazine [HA]) were monitored. Atrazine dissipation from the water column of wetland microcosms was biphasic. Less than 12% of the atrazine applied to wetland microcosms remained in the water column on day 56. Atrazine degradates were observed in water and sediment, with HA the predominant degradate. Analysis of day 56 sediment samples indicated that a significant portion of the initial application was detected as the parent compound and HA. Most probable number (MPN) assays demonstrated that atrazine degrader populations were small in wetland sediment. Wetland microcosms were able to reduce atrazine concentration in the water column via sorption and degradation. Based on results from this study, it is hypothesized that plant uptake contributed to atrazine dissipation from the water column.

Regulation of pesticide degradation in the detritusphere

NASA Astrophysics Data System (ADS)

Pagel, Holger; Poll, Christian; Ingwersen, Joachim; Ditterich, Franziska; Gebala, Aurelia; Kandeler, Ellen; Streck, Thilo

2015-04-01

The detritusphere is a microbial hot spot of C turnover and degradation of pesticides in soils. We aimed at an improved understanding of the regulation mechanisms, which are responsible for stimulated degradation of the herbicide MCPA (2-Methyl-4-chlorophenoxyacetic acid) in response to increased C availability in the detritusphere. We combined a microcosm experiment with biogeochemical modeling and linked genetic information on abundances of total bacteria, fungi and specific pesticide degraders in soil to the coupled biogeochemical dynamics of C and MCPA. As a result of diffusive and convective C transport from litter into the adjacent soil we found increased dissolved organic C (DOC) in soil up to a 6 mm distance to litter (detritusphere). In the detritusphere, we observed increased microbial C and accelerated MCPA degradation. These dynamics were accurately reproduced by the model. Whereas the observed increase of bacteria and pesticide degrader populations in the detritusphere was simulated satisfactorily, the model could not reproduce the steep increase of fungi indicated by the fungal marker gene. Our simulations suggest that bacterial MCPA degraders mostly benefited from high-quality DOC, whereas fungal activity and growth were specifically stimulated by low-quality DOC. According to the simulations, MCPA was predominantly degraded via fungal co-metabolism. Our study demonstrates that biogeochemical processes in soil hotspots are regulated by the interaction of transport processes and microbial dynamics. It further reveals that mathematical modelling is as powerful tool to gain comprehensive insight into the microbial regulation of matter cycling in soil. Genetic information has a high potential to parameterize and evaluate complex mechanistic models, but model approaches must be improved based on extended information on gene dynamics at the cellular level.

Microbial functional diversity plays an important role in the degradation of polyhydroxybutyrate (PHB) in soil.

PubMed

Dey, Samrat; Tribedi, Prosun

2018-03-01

Towards bioremediation of recalcitrant materials like synthetic polymer, soil has been recognized as a traditional site for disposal and subsequent degradation as some microorganisms in soil can degrade the polymer in a non-toxic, cost-effective, and environment friendly way. Microbial functional diversity is a constituent of biodiversity that includes wide range of metabolic activities that can influence numerous aspects of ecosystem functioning like ecosystem stability, nutrient availability, ecosystem dynamics, etc. Thus, in the current study, we assumed that microbial functional diversity could play an important role in polymer degradation in soil. To verify this hypothesis, we isolated soil from five different sites of landfill and examined several microbiological parameters wherein we observed a significant variation in heterotrophic microbial count as well as microbial activities among the soil microcosms tested. Multivariate analysis (principle component analysis) based on the carbon sources utilization pattern revealed that soil microcosms showed different metabolic patterns suggesting the variable distribution of microorganisms among the soil microcosms tested. Since microbial functional diversity depends on both microbial richness and evenness, Shannon diversity index was determined to measure microbial richness and Gini coefficient was determined to measure microbial evenness. The tested soil microcosms exhibited variation in both microbial richness and evenness suggesting the considerable difference in microbial functional diversity among the tested microcosms. We then measured polyhydroxybutyrate (PHB) degradation in soil microcosms after desired period of incubation of PHB in soil wherein we found that soil microcosms having higher functional diversity showed enhanced PHB degradation and soil microcosms having lower functional diversity showed reduced PHB degradation. We also noticed that all the tested soil microcosms showed similar pattern in both microbial functional diversity and PHB degradation suggesting a strong positive correlation ( r  = 0.95) between microbial functional diversity and PHB degradation. Thus, the results demonstrate that microbial functional diversity plays an important role in PHB degradation in soil by exhibiting versatile microbial metabolic potentials that lead to the enhanced degradation of PHB.

Behavior and Fate of PFOA and PFOS in Sandy Aquifer ...

EPA Pesticide Factsheets

Microcosms were constructed with sediment from beneath a landfill that received waste containing PFOA (perfluorooctanoic acid) and PFOS (perfluorooctane sulfonate). The microcosms were amended with PFOA and PFOS, and sampled after 91, 210, 343, 463, 574, and 740 days of incubation. After 740 days, selected microcosms were extracted to determine the mass of PFOA and PFOS remaining. There was no evidence for degradation of PFOA or PFOS. Over time, the aqueous concentrations of PFOA and PFOS increased in the microcosms, indicating that PFOA and PFOS that had originally sorbed to the sediment was desorbing. At the beginning of the experiment, the adsorption coefficient, Kd, averaged 0.27 L/kg for PFOA and 1.2 L/kg for PFOS. After 740 days of incubation, sorption of PFOA was not detectable and the Kd of PFOS was undetectable in two microcosms and was 0.08 L/kg in a third microcosm. During incubation, the pH of the pore water in the microcosms increased from pH 7.2 to pH ranging from 8.1 to 8.8 and the zeta potential of the sediment decreased with increasing pH. These observations suggest sorption of PFOA and PFOS was controlled by electrostatic sorption on ferric oxide minerals, and not by sorption to organic carbon. These observations suggest sorption of PFOA and PFOS was controlled by electrostatic sorption on ferric oxide minerals, and not by sorption to organic carbon.

U(VI) bioreduction with emulsified vegetable oil as the electron donor--microcosm tests and model development.

PubMed

Tang, Guoping; Wu, Wei-Min; Watson, David B; Parker, Jack C; Schadt, Christopher W; Shi, Xiaoqing; Brooks, Scott C

2013-04-02

We conducted microcosm tests and biogeochemical modeling to study U(VI) reduction in contaminated sediments amended with emulsified vegetable oil (EVO). Indigenous microorganisms in the sediments degraded EVO and stimulated Fe(III), U(VI), and sulfate reduction, and methanogenesis. Acetate concentration peaked in 100-120 days in the EVO microcosms versus 10-20 days in the oleate microcosms, suggesting that triglyceride hydrolysis was a rate-limiting step in EVO degradation and subsequent reactions. Acetate persisted 50 days longer in oleate- and EVO- than in ethanol-amended microcosms, indicating that acetate-utilizing methanogenesis was slower in the oleate and EVO than ethanol microcosms. We developed a comprehensive biogeochemical model to couple EVO hydrolysis, production, and oxidation of long-chain fatty acids (LCFA), glycerol, acetate, and hydrogen, reduction of Fe(III), U(VI) and sulfate, and methanogenesis with growth and decay of multiple functional microbial groups. By estimating EVO, LCFA, and glycerol degradation rate coefficients, and introducing a 100 day lag time for acetoclastic methanogenesis for oleate and EVO microcosms, the model approximately matched observed sulfate, U(VI), and acetate concentrations. Our results confirmed that EVO could stimulate U(VI) bioreduction in sediments and the slow EVO hydrolysis and acetate-utilizing methanogens growth could contribute to longer term bioreduction than simple substrates (e.g., ethanol, acetate, etc.) in the subsurface.

Comparing the impacts of sediment-bound bifenthrin on aquatic macroinvertebrates in laboratory bioassays and field microcosms.

PubMed

Boyle, Rhianna L; Hoak, Molly N; Pettigrove, Vincent J; Hoffmann, Ary A; Long, Sara M

2016-11-01

We conducted two laboratory bioassays and two field microcosm exposures with bifenthrin (a synthetic pyrethroid) in order to evaluate the capacity of single-species laboratory bioassays to predict lethal and sublethal impacts on aquatic invertebrates in microcosms. For the laboratory species, Chironomus tepperi, larval survival was reduced by 24% at 53.66µg/g OC, while adult emergence was reduced at concentrations of 33.33µg/g OC and higher, with a 61% decrease at 77.78µg/g OC and no emergence at 126.67µg/g OC. The abundance of several other microcosm taxa was reduced in the microcosms at a similar concentration range (33.33µg/g OC and above), however there was no impact on the abundance of the congeneric species, Chironomus oppositus. The differences in impacts between test systems were potentially due to both differing species sensitivity and the interaction of ambient temperature with bifenthrin toxicity. Bifenthrin also was associated with early emergence of Chironomus sp. in both test systems, at concentrations of 10µg/g OC and higher (laboratory) and 43.90µg/g OC (microcosm), and with a significant decrease in the proportion of C. oppositus males in a microcosm. These findings indicate that while laboratory bioassays accurately predict many impacts in the field, there are some limitations to the predictive capacity of these tests. Copyright © 2016 Elsevier Inc. All rights reserved.

Fatty acid-oxidizing consortia along a nutrient gradient in the Florida Everglades.

PubMed

Chauhan, Ashvini; Ogram, Andrew

2006-04-01

The Florida Everglades is one of the largest freshwater marshes in North America and has been subject to eutrophication for decades. A gradient in P concentrations extends for several kilometers into the interior of the northern regions of the marsh, and the structure and function of soil microbial communities vary along the gradient. In this study, stable isotope probing was employed to investigate the fate of carbon from the fermentation products propionate and butyrate in soils from three sites along the nutrient gradient. For propionate microcosms, 16S rRNA gene clone libraries from eutrophic and transition sites were dominated by sequences related to previously described propionate oxidizers, such as Pelotomaculum spp. and Syntrophobacter spp. Significant representation was also observed for sequences related to Smithella propionica, which dismutates propionate to butyrate. Sequences of dominant phylotypes from oligotrophic samples did not cluster with known syntrophs but with sulfate-reducing prokaryotes (SRP) and Pelobacter spp. In butyrate microcosms, sequences clustering with Syntrophospora spp. and Syntrophomonas spp. dominated eutrophic microcosms, and sequences related to Pelospora dominated the transition microcosm. Sequences related to Pelospora spp. and SRP dominated clone libraries from oligotrophic microcosms. Sequences from diverse bacterial phyla and primary fermenters were also present in most libraries. Archaeal sequences from eutrophic microcosms included sequences characteristic of Methanomicrobiaceae, Methanospirillaceae, and Methanosaetaceae. Oligotrophic microcosms were dominated by acetotrophs, including sequences related to Methanosarcina, suggesting accumulation of acetate.

U(VI) bioreduction with emulsified vegetable oil as the electron donor--model application to a field test.

PubMed

Tang, Guoping; Watson, David B; Wu, Wei-Min; Schadt, Christopher W; Parker, Jack C; Brooks, Scott C

2013-04-02

We amended a shallow fast-flowing uranium (U) contaminated aquifer with emulsified vegetable oil (EVO) and subsequently monitored the biogeochemical responses for over a year. Using a biogeochemical model developed in a companion article (Tang et al., Environ. Sci. Technol.2013, doi: 10.1021/es304641b) based on microcosm tests, we simulated geochemical and microbial dynamics in the field test during and after the 2-h EVO injection. When the lab-determined parameters were applied in the field-scale simulation, the estimated rate coefficient for EVO hydrolysis in the field was about 1 order of magnitude greater than that in the microcosms. Model results suggested that precipitation of long-chain fatty acids, produced from EVO hydrolysis, with Ca in the aquifer created a secondary long-term electron donor source. The model predicted substantial accumulation of denitrifying and sulfate-reducing bacteria, and U(IV) precipitates. The accumulation was greatest near the injection wells and along the lateral boundaries of the treatment zone where electron donors mixed with electron acceptors in the groundwater. While electron acceptors such as sulfate were generally considered to compete with U(VI) for electrons, this work highlighted their role in providing electron acceptors for microorganisms to degrade complex substrates thereby enhancing U(VI) reduction and immobilization.

Application of molecular simulation to investigate chrome(III)-crosslinked collagen problems

NASA Astrophysics Data System (ADS)

Ding, Yun-Qiao; Chen, Cheng-Lung; Gu, Qi-Rui; Liao, Jun-Min; Chuang, Po-Hsiang

2014-04-01

Molecular dynamics simulation with a modified CHARMM (Chemistry at Harvard Macromolecular Mechanics) force field was carried out to investigate the properties of chrome-tanned collagen in comparison with chrome-free collagen under hydrated and dehydrated conditions. An attempt has been made to explain the microcosmic origins of the various properties of the chromium(III)-crosslinked collagen. The present simulation describes the clear crosslinking topology of polychromiums to peptide chains, identifies the linking site and the capacity of the linkage, explains why the efficiency is not 100% in a practical tanning process and provides a new viewpoint on the crosslinking of the polychromium with the side chains of the collagen.

Fate and Persistence of a Pathogenic NDM-1-Positive Escherichia coli Strain in Anaerobic and Aerobic Sludge Microcosms

PubMed Central

Mantilla-Calderon, David

2017-01-01

ABSTRACT The presence of emerging biological pollutants in treated wastewater effluents has gained attention due to increased interest in water reuse. To evaluate the effectiveness of the removal of such contaminants by the conventional wastewater treatment process, the fate and decay kinetics of NDM-1-positive Escherichia coli strain PI7 and its plasmid-encoded antibiotic resistance genes (ARGs) were assessed in microcosms of anaerobic and aerobic sludge. Results showed that E. coli PI7 decayed at a significantly lower rate under anaerobic conditions. Approximate half-lives were 32.4 ± 1.4 h and 5.9 ± 0.9 h in the anaerobic and aerobic microcosms, respectively. In the aerobic microcosms, after 72 h of operation, E. coli PI7 remained detectable, but no further decay was observed. Instead, 1 in every 10,000 E. coli cells was identified to be recalcitrant to decay and persist indefinitely in the sludge. ARGs associated with the E. coli PI7 strain were detected to have transferred to other native microorganisms in the sludge or were released to the liquid fraction upon host decay. Extracellular DNA quickly degraded in the liquid fraction of the aerobic sludge. In contrast, no DNA decay was detected in the anaerobic sludge water matrix throughout the 24-h sampling period. This study suggests an increased likelihood of environmental dispersion of ARGs associated with anaerobically treated wastewater effluents and highlights the potential importance of persister cells in the dissemination of E. coli in the environment during reuse events of treated wastewater. IMPORTANCE This study examines the decay kinetics of a pathogenic and antibiotic resistant strain of Escherichia coli in microcosms simulating biological treatment units of aerobic and anaerobic sludge. The results of this study point at a significantly prolonged persistence of the E. coli and the associated antibiotic resistance gene in the anaerobic sludge. However, horizontal transfer of the plasmid encoding the antibiotic resistance gene was detected in the aerobic sludge by a cultivation method. A subpopulation of persister E. coli cells was also detected in the aerobic sludge. The findings of this study suggest potential areas of concern arising from pathogenic and antibiotic-resistant E. coli during both anaerobic and aerobic sludge treatment processes. PMID:28411227

Fate and Persistence of a Pathogenic NDM-1-Positive Escherichia coli Strain in Anaerobic and Aerobic Sludge Microcosms.

PubMed

Mantilla-Calderon, David; Hong, Pei-Ying

2017-07-01

The presence of emerging biological pollutants in treated wastewater effluents has gained attention due to increased interest in water reuse. To evaluate the effectiveness of the removal of such contaminants by the conventional wastewater treatment process, the fate and decay kinetics of NDM-1-positive Escherichia coli strain PI7 and its plasmid-encoded antibiotic resistance genes (ARGs) were assessed in microcosms of anaerobic and aerobic sludge. Results showed that E. coli PI7 decayed at a significantly lower rate under anaerobic conditions. Approximate half-lives were 32.4 ± 1.4 h and 5.9 ± 0.9 h in the anaerobic and aerobic microcosms, respectively. In the aerobic microcosms, after 72 h of operation, E. coli PI7 remained detectable, but no further decay was observed. Instead, 1 in every 10,000 E. coli cells was identified to be recalcitrant to decay and persist indefinitely in the sludge. ARGs associated with the E. coli PI7 strain were detected to have transferred to other native microorganisms in the sludge or were released to the liquid fraction upon host decay. Extracellular DNA quickly degraded in the liquid fraction of the aerobic sludge. In contrast, no DNA decay was detected in the anaerobic sludge water matrix throughout the 24-h sampling period. This study suggests an increased likelihood of environmental dispersion of ARGs associated with anaerobically treated wastewater effluents and highlights the potential importance of persister cells in the dissemination of E. coli in the environment during reuse events of treated wastewater. IMPORTANCE This study examines the decay kinetics of a pathogenic and antibiotic resistant strain of Escherichia coli in microcosms simulating biological treatment units of aerobic and anaerobic sludge. The results of this study point at a significantly prolonged persistence of the E. coli and the associated antibiotic resistance gene in the anaerobic sludge. However, horizontal transfer of the plasmid encoding the antibiotic resistance gene was detected in the aerobic sludge by a cultivation method. A subpopulation of persister E. coli cells was also detected in the aerobic sludge. The findings of this study suggest potential areas of concern arising from pathogenic and antibiotic-resistant E. coli during both anaerobic and aerobic sludge treatment processes. Copyright © 2017 Mantilla-Calderon and Hong.

Bench-scale biodegradation tests to assess natural attenuation potential of 1,4-dioxane at three sites in California.

PubMed

Li, Mengyan; Van Orden, E Tess; DeVries, David J; Xiong, Zhong; Hinchee, Rob; Alvarez, Pedro J

2015-02-01

1,4-Dioxane (dioxane) is relatively recalcitrant to biodegradation, and its physicochemical properties preclude effective removal from contaminated groundwater by volatilization or adsorption. Through this microcosm study, we assessed the biodegradation potential of dioxane for three sites in California. Groundwater and sediment samples were collected at various locations at each site, including the presumed source zone, middle and leading edge of the plume. A total of 16 monitoring wells were sampled to prepare the microcosms. Biodegradation of dioxane was observed in 12 of 16 microcosms mimicking natural attenuation within 28 weeks. Rates varied from as high as 3,449 ± 459 µg/L/week in source-zone microcosms to a low of 0.3 ± 0.1 µg/L/week in microcosms with trace level of dioxane (<10 µg/L as initial concentration). The microcosms were spiked with (14)C-labeled dioxane to assess the fate of dioxane. Biological oxidizer-liquid scintillation analysis of bound residue infers that 14C-dioxane was assimilated into cell material only in microcosms exhibiting significant dioxane biodegradation. Mineralization was also observed per (14)CO2 recovery (up to 44% of the amount degraded in 28 weeks of incubation). Degradation and mineralization activity significantly decreased with increasing distance from the contaminant source area (p < 0.05), possibly due to less acclimation. Furthermore, both respiked and repeated microcosms prepared with source-zone samples from Site 1 confirmed relatively rapid dioxane degradation (i.e., 100 % removal by 20 weeks). These results show that indigenous microorganisms capable of degrading dioxane are present at these three sites, and suggest that monitored natural attenuation should be considered as a remedial response.

Erosion Characteristics and Horizontal Variability for Small Erosion Depths in the Sacramento - San Joaquin River Delta, California, USA

NASA Astrophysics Data System (ADS)

Schoellhamer, D. H.; Manning, A. J.; Work, P. A.

2015-12-01

Cohesive sediment in the Sacramento-San Joaquin River Delta affects pelagic fish habitat, contaminant transport, and marsh accretion. Observations of suspended-sediment concentration in the delta indicate that about 0.05 to 0.20 kg/m2 are eroded from the bed during a tidal cycle. If erosion is horizontally uniform, the erosion depth is about 30 to 150 microns, the typical range in diameter of suspended flocs. Application of an erosion microcosm produces similarly small erosion depths. In addition, core erodibility in the microcosm calculated with a horizontally homogeneous model increases with depth, contrary to expectations for a consolidating bed, possibly because the eroding surface area increases as applied shear stress increases. Thus, field observations and microcosm experiments, combined with visual observation of horizontally varying biota and texture at the surface of sediment cores, indicate that a conceptual model of erosion that includes horizontally varying properties may be more appropriate than assuming horizontally homogeneous erosive properties. To test this hypothesis, we collected five cores and measured the horizontal variability of shear strength within each core in the top 5.08 cm with a shear vane. Small tubes built by a freshwater worm and macroalgae were observed on the surface of all cores. The shear vane was inserted into the sediment until the top of the vane was at the top of the sediment, torque was applied to the vane until the sediment failed and the vane rotated, and the corresponding dial reading in Nm was recorded. The dial reading was assumed to be proportional to the surface strength. The horizontal standard deviation of the critical shear stress was about 30% of the mean. Results of the shear vane test provide empirical evidence that surface strength of the bed varies horizontally. A numerical simulation of erosion with an areally heterogeneous bed reproduced erosion characteristics observed in the microcosm.

Impact of glycerin and lignosulfonate on biodegradation of high explosives in soil.

PubMed

Won, Jongho; Borden, Robert C

2016-11-01

Soil microcosms were constructed and monitored to evaluate the impact of substrate addition and transient aerobic and anaerobic conditions on TNT, RDX and HMX biodegradation in grenade range soils. While TNT was rapidly biodegraded under both aerobic and anaerobic conditions with and without organic substrate, substantial biodegradation of RDX, HMX, and RDX daughter products was not observed under aerobic conditions. However, RDX and HMX were significantly biodegraded under anaerobic conditions, without accumulation of TNT or RDX daughter products (2-ADNT, 4-ADNT, MNX, DNX, and TNX). In separate microcosms containing grenade range soil, glycerin and lignosulfonate addition enhanced oxygen consumption, increasing the consumption rate >200% compared to untreated soils. Mathematical model simulations indicate that oxygen consumption rates of 5 to 20g/m 3 /d can be achieved with reasonable amendment loading rates. These results indicate that glycerin and lignosulfonate can be potentially used to stimulate RDX and HMX biodegradation by increasing oxygen consumption rates in soil. Copyright © 2016 Elsevier B.V. All rights reserved.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Piché-Choquette, Sarah; Tremblay, Julien; Tringe, Susannah G.

Soil microbial communities are continuously exposed to H 2 diffusing into the soil from the atmosphere. N 2-fixing nodules represent a peculiar microniche in soil where H 2 can reach concentrations up to 20,000 fold higher than in the global atmosphere (0.530 ppmv). In this study, we investigated the impact of H 2 exposure on soil bacterial community structure using dynamic microcosm chambers simulating soil H 2 exposure from the atmosphere and N 2-fixing nodules. Biphasic kinetic parameters governing H 2 oxidation activity in soil changed drastically upon elevated H 2 exposure, corresponding to a slight but significant decay ofmore » high affinity H 2-oxidizing bacteria population, accompanied by an enrichment or activation of microorganisms displaying low-affinity for H 2. In contrast to previous studies that unveiled limited response by a few species, the relative abundance of 958 bacterial ribotypes distributed among various taxonomic groups, rather than a few distinct taxa, was influenced by H 2 exposure. Furthermore, correlation networks showed important alterations of ribotype covariation in response to H 2 exposure, suggesting that H 2 affects microbe-microbe interactions in soil. Taken together, our results demonstrate that H 2-rich environments exert a direct influence on soil H 2-oxidizing bacteria in addition to indirect effects on other members of the bacterial communities.« less

Microbial degradation of decabromodiphenyl ether (DBDE) in soil slurry microcosms.

PubMed

Chou, Hsi-Ling; Hwa, Mei-Yin; Lee, Yao-Chuan; Chang, Yu-Jie; Chang, Yi-Tang

2016-03-01

Decabromodiphenyl ether (DBDE), which has been identified as an endocrine disrupting compound, is used as brominated flame retardant, and this can result in serious bioaccumulation within ecological systems. The objective of this study was to explore DBDE bioremediation (25 mg/kg) using laboratory scale soil slurry microcosms. It was found that effective biodegradation of DBDE occurred in all microcosms. Various biometabolites were identified, namely polybrominated diphenyl ethers congeners and hydroxylated brominated diphenyl ether. Reductive debrominated products such as tri-BDE to hepta-BDE congeners were also detected, and their total concentrations ranged from 77.83 to 91.07 ng/g. The mechanism of DBDE biodegradation in soil slurry microcosms is proposed to consist of a series of biological reactions involving hydroxylation and debromination. Catechol 2,3-oxygenase genes, which are able to bring about meta-cleavage at specific unbrominated locations in carbon backbones, were identified as present during the DBDE biodegradation. No obvious effect on the ecological functional potential based on community-level physiological profiling was observed during DBDE biodegradation, and one major facultative Pseudomonas sp. (99 % similarity) was identified in the various soil slurry microcosms. These findings provide an important basis that should help environmental engineers to design future DBDE bioremediation systems that use a practical microcosm system. A bacterial-mixed culture can be selected as part of the bioaugmentation process for in situ DBDE bioremediation. A soil/water microcosm system can be successfully applied to carry out ex situ DBDE bioremediation.

Abundance matters: a field experiment testing the more individuals hypothesis for richness–productivity relationships

PubMed Central

Yee, D. A.; Juliano, S. A.

2007-01-01

The more individuals hypothesis (MIH) postulates that productivity increases species richness by increasing mean equilibrium population size, thereby reducing the probability of local extinction. We tested the MIH for invertebrates colonizing microcosms that simulated tree holes by manipulating productivity through additions of leaf or animal detritus and subsequently determining the relationships among richness, total abundance, abundance per species, and measures of productivity. We quantified productivity as the rate of microorganism protein synthesis, microorganism metabolic rate, nutrient ion concentration, and type and amount of detritus. Microcosms with animal detritus attracted more species, more individuals per species, and more total individuals than did microcosms with similar amounts of leaf detritus. Relationships between richness or abundance and productivity varied with date. Richness in June increased as a linear function of productivity, whereas the power function predicted by the MIH fit best in July. Abundance in June and July was best described by a power function of productivity, but the linear function predicted by the MIH fit best in September. Abundance per species was best described by a power function of productivity in June and July. Path analysis showed that the indirect effect of productivity through abundance on richness that is predicted by MIH was important in all months, and that direct links between productivity and richness were unnecessary. Our results support many of the predictions of the MIH, but they also suggest that the effects of abundance on richness may be more complex than expected. PMID:17401581

Hydrogen Limitation, Competition and Syntrophy Among Thermophiles in the Hot Subseafloor

NASA Astrophysics Data System (ADS)

Holden, J. F.; Stewart, L. C.; Topcuoglu, B. D.

2016-02-01

To understand the biogeochemical impact of subseafloor life on surrounding environments and the overlying ocean, the rates of and constraints on growth and metabolite production must be determined for subseafloor microbes. The diversity of thermophiles and hyperthermophiles in the hot subseafloor is low, making them amenable to biogeochemical modeling. At hydrothermal vents, Methanothermococcus and Methanocaldococcus are common thermophilic and hyperthermophilic methanogens; Desulfurobacterium, common thermophilic autotrophic sulfur reducers; and Thermococcus, common hyperthermophilic H2-producing heterotrophs. Diffuse hydrothermal fluids (7-40°C) from Axial Seamount were incubated anaerobically at 55°C and 80°C. Microcosms with 1.2 mM added H2 produced 30-50 times more CH4 than those with 20 µM H2, demonstrating that H2 and heat were the primary constraints on the growth of thermophilic and hyperthermophilic methanogens. For Methanothermococcus thermolithotrophicus and Methanocaldococcus jannaschii, the lower H2 thresholds and half-saturation constants (Ks) for growth in a chemostat were 9-20 µM and 47-69 µM, respectively, near their optimum growth temperatures. The lower H2 threshold and Ks for Desulfurobacterium sp. strain HR11 grown in a batch reactor at 72°C were <3 µM and 29 µM, respectively. Its catalytic efficiency (µmax/Ks) for H2 use was 4 times higher than those of M. thermolithotrophicus and M. jannaschii, but its Ks for thiosulfate was 19 µM, suggesting that it will only outcompete methanogens when sulfur is not growth limiting. Microcosm incubations at 55°C and 80°C supplemented with peptides in lieu of H2 produced the same amount of CH4 as microcosms with 1.2 mM H2. Co-culture incubations showed that H2 production by T. paralvinellae supported the growth of Methanothermococcus sp. strain BW11, Methanocaldococcus bathoardescens, and strain HR11 in H2-free medium, suggesting that syntrophy is a possible alternative H2 source in the subseafloor.

A DNA Origami Mechanical Device for the Regulation of Microcosmic Structural Rigidity.

PubMed

Wan, Neng; Hong, Zhouping; Wang, Huading; Fu, Xin; Zhang, Ziyue; Li, Chao; Xia, Han; Fang, Yan; Li, Maoteng; Zhan, Yi; Yang, Xiangliang

2017-11-01

DNA origami makes it feasible to fabricate a tremendous number of DNA nanostructures with various geometries, dimensions, and functionalities. Moreover, an increasing amount of research on DNA nanostructures is focused on biological and biomedical applications. Here, the reversible regulation of microcosmic structural rigidity is accomplished using a DNA origami device in vitro. The designed DNA origami monomer is composed of an internal central axis and an external sliding tube. Due to the external tube sliding, the device transforms between flexible and rigid states. By transporting the device into the liposome, the conformational change of the origami device induces a structural change in the liposome. The results obtained demonstrate that the programmed DNA origami device can be applied to regulate the microcosmic structural rigidity of liposomes. Because microcosmic structural rigidity is important to cell proliferation and function, the results obtained potentially provide a foundation for the regulation of cell microcosmic structural rigidity using DNA nanostructures. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Microbial response to triepthylphosphate

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hazen, T.C.; Santo Domingo, J.W.; Berry, C.J.

1997-05-01

The effect of triethylphosphate (TEP) on the activity of a landfill aquifer microbial community was evaluated using standard techniques and in situ hybridizations with phylogenetic probes. Benzene was used as an external carbon source to monitor degradation of an aromatic compound in TEP amended microcosms. Microscopical and viable counts were higher in TEP containing microcosms when compared to unamended controls. A significant increase in metabolic activity was also observed for TEP amended samples as determined by the number of cells hybridizing to an eubacterial probe. In addition, the number of beta and gamma Proteobacteria increased from undetectable levels prior tomore » the study to 15-29% of the total bacteria in microcosms containing TEP and benzene. In these microcosms, nearly 40% of the benzene was degraded during the incubation period compared to less than 5% in unamended microcosms. While TEP has previously been used as an alternate phosphate source in the bioremediation of chlorinated aliphatics, this study shows that it can also stimulate the microbial degradation of aromatics in phosphate limited aquifers.« less

Low-cost autonomous orbit control about Mars: Initial simulation results

NASA Astrophysics Data System (ADS)

Dawson, S. D.; Early, L. W.; Potterveld, C. W.; Königsmann, H. J.

1999-11-01

Interest in studying the possibility of extraterrestrial life has led to the re-emergence of the Red Planet as a major target of planetary exploration. Currently proposed missions in the post-2000 period are routinely calling for rendezvous with ascent craft, long-term orbiting of, and sample-return from Mars. Such missions would benefit greatly from autonomous orbit control as a means to reduce operations costs and enable contact with Mars ground stations out of view of the Earth. This paper present results from initial simulations of autonomously controlled orbits around Mars, and points out possible uses of the technology and areas of routine Mars operations where such cost-conscious and robust autonomy could prove most effective. These simulations have validated the approach and control philosophies used in the development of this autonomous orbit controller. Future work will refine the controller, accounting for systematic and random errors in the navigation of the spacecraft from the sensor suite, and will produce prototype flight code for inclusion on future missions. A modified version of Microcosm's commercially available High Precision Orbit Propagator (HPOP) was used in the preparation of these results due to its high accuracy and speed of operation. Control laws were developed to allow an autonomously controlled spacecraft to continuously control to a pre-defined orbit about Mars with near-optimal propellant usage. The control laws were implemented as an adjunct to HPOP. The GSFC-produced 50 × 50 field model of the Martian gravitational potential was used in all simulations. The Martian atmospheric drag was modeled using an exponentially decaying atmosphere based on data from the Mars-GRAM NASA Ames model. It is hoped that the simple atmosphere model that was implemented can be significantly improved in the future so as to approach the fidelity of the Mars-GRAM model in its predictions of atmospheric density at orbital altitudes. Such additional work would take the form of solar flux (F10.7) and diurnal density dependencies. The autonomous controller is a-derivative of the proprietary and patented Microcosm Earth-orbiting control methodology which will be implemented on the upcoming Surrey Satellite Technology (SSTL) UoSAT-12 and the NASA EO-1 spacecraft missions. This work was funded by the NASA Jet Propulsion Laboratory under a Phase I SBIR (96.1 07.02 9444) and by internal Microcosm R&D funds as well as earlier supporting work done under a variety of USAF Research Laboratory-sponsored contracts [1, 2, 4, 12].

Naturally-Derived Microcosms for Estimating Stress Effects in Aquatic Ecosystems

DTIC Science & Technology

1991-05-31

production, respiration, nutrient dynamics, enzyme activities, and species richness. Endpoints can be added or eliminated, depending on the...substrates per microcosm, depending on the experimental design. One to two substrates per microcosm will be placed in a natural ecosystem to accumulate the...water, these substrates should be left to accumulate microbiota for 3-10 d, depending on the flow rate and sediment load. In lentic ecosystems, exposure

Biomineralization of 1,4-dioxane in Pure Culture, Microcosm, and Column Studies Using 13C Labeling

NASA Astrophysics Data System (ADS)

Rolston, H. M.; Azizian, M.; Hyman, M. R.; Semprini, L.

2016-12-01

1,4-dioxane (1,4-D), a probable human carcinogen at low (< 1ppb) concentrations, is a widely occurring groundwater contaminant due to its use as a stabilizer for chlorinated solvents. Aerobic cometabolism, the use of a primary substrate to induce the production of microbial enzymes capable of transforming contaminants into innocuous products, is a promising in-situ treatment strategy for 1,4-D because it has the potential to mineralize trace 1,4-D concentrations to carbon dioxide (CO2). Previous work has confirmed the bacterium Rhodococcus rhodochrous (strain ATCC 21198) will transform 1,4-D when grown on isobutane. In this study, 13C uniformly labeled 1,4-D was used to determine the extent to which strain ATCC 21198 biomineralizes 1,4-D to CO2. Batch experiments have been conducted with pure culture 21198 and in microcosms constructed with aquifer sediments. The rate of resting cell transformation of 1,4-D by ATCC 21198 was over 100 times faster than the rate of CO2 accumulation, indicating the presence of intermediates that were slowly mineralized to CO2 . In microcosms, the use of isobutane as a primary substrate effectively stimulated the native microbial community to transform 1,4-D. Microcosms were also bioaugmented with ATCC 21198. After an initial lag and subsequent additions of isobutane, transformation rates in the native microcosms approached those of the bioaugmented microcosms. Cometabolically active microbes survived several periods of starvation in all microcosms, and nutrient amendment allowed for sustained transformation rates. 13C labeled 1,4-D is currently being used to determine the rates and extents of biomineralization in the microcosms. Column studies are also being conducted to evaluate cometabolism and biominerazation potential of isobutane as a biostimulant and 21198 for bioaugmentation under geochemical and flow conditions more representative of in-situ bioremediation.

Influence of sediment on the fate and toxicity of a polyethoxylated tallowamine surfactant system (MON 0818) in aquatic microcosms

USGS Publications Warehouse

Wang, N.; Besser, J.M.; Buckler, D.R.; Honegger, J.L.; Ingersoll, C.G.; Johnson, B. Thomas; Kurtzweil, M.L.; MacGregor, J.; McKee, M.J.

2005-01-01

The fate and toxicity of a polyethoxylated tallowamine (POEA) surfactant system, MON 0818, was evaluated in water–sediment microcosms during a 4-d laboratory study. A surfactant solution of 8 mg l−1 nominal concentration was added to each of nine 72-l aquaria with or without a 3-cm layer of one of two natural sediments (total organic carbon (TOC) 1.5% or 3.0%). Control well water was added to each of nine additional 72-l aquaria with or without sediment. Water samples were collected from the microcosms after 2, 6, 24, 48, 72, and 96 h of aging to conduct 48-h toxicity tests with Daphnia magna and to determine surfactant concentrations. Elevated mortality of D. magna (43–83%) was observed in overlying water sampled from water-only microcosms throughout the 96-h aging period, whereas elevated mortality (23–97%) was only observed in overlying water sampled from water–sediment microcosms during the first 24 h of aging. Measured concentrations of MON 0818 in water-only microcosms remained relatively constant (4–6 mg l−1) during the 96-h period, whereas the concentrations in overlying water from microcosms containing either of the two types of sediment dissipated rapidly, with half-lives of 13 h in the 3.0% TOC sediment and 18 h in the 1.5% TOC sediment. Both toxicity and the concentration of MON 0818 in overlying water decreased more rapidly in microcosms containing sediment with the higher percent TOC and clay and with a higher microbial biomass. Mortality of D. magna was significantly correlated with surfactant concentrations in the overlying water. These results indicate that the toxicity of the POEA surfactant in water rapidly declines in the presence of sediment due to a reduction in the surfactant concentration in the overlying water above the sediment.

EPA worst case water microcosms for testing phage biocontrol of Salmonella.

PubMed

McLaughlin, Michael R; Brooks, John P

2008-01-01

A microplate method was developed as a tool to test phages for their ability to control Salmonella in aqueous environments. The method used EPA (U.S. Environmental Protection Agency) worst case water (WCW) in 96-well plates. The WCW provided a consistent and relatively simple defined turbid aqueous matrix, high in total organic carbon (TOC) and total dissolved salts (TDS), to simulate swine lagoon effluent, without the inconvenience of malodor and confounding effects from other biological factors. The WCW was originally defined to simulate high turbidity and organic matter in water for testing point-of-use filtration devices. Use of WCW to simulate lagoon effluent for phage testing is a new and innovative application of this matrix. Control of physical and chemical parameters (TOC, TDS, turbidity, temperature, and pH) allowed precise evaluation of microbiological parameters (Salmonella and phages). In a typical application, wells containing WCW were loaded with Salmonella enterica susp. enterica serovar Typhimurium (ATCC14028) and treated with phages alone and in cocktail combinations. Mean Salmonella inactivation rates (k, where the lower the value, the greater the inactivation) of phage treatments ranged from -0.32 to -1.60 versus -0.004 for Salmonella controls. Mean log(10) reductions (the lower the value, the greater the reduction) of Salmonella phage treatments were -1.60 for phage PR04-1, -2.14 for phage PR37-96, and -2.14 for both phages in a sequential cocktail, versus -0.08 for Salmonella controls. The WCW microcosm system was an effective tool for evaluating the biocontrol potential of Salmonella phages.

Enantioselective degradation of amphetamine-like environmental micropollutants (amphetamine, methamphetamine, MDMA and MDA) in urban water.

PubMed

Evans, Sian E; Bagnall, John; Kasprzyk-Hordern, Barbara

2016-08-01

This paper aims to understand enantioselective transformation of amphetamine, methamphetamine, MDMA (3,4-methylenedioxy-methamphetamine) and MDA (3,4-methylenedioxyamphetamine) during wastewater treatment and in receiving waters. In order to undertake a comprehensive evaluation of the processes occurring, stereoselective transformation of amphetamine-like compounds was studied, for the first time, in controlled laboratory experiments: receiving water and activated sludge simulating microcosm systems. The results demonstrated that stereoselective degradation, via microbial metabolic processes favouring S-(+)-enantiomer, occurred in all studied amphetamine-based compounds in activated sludge simulating microcosms. R-(-)-enantiomers were not degraded (or their degradation was limited) which proves their more recalcitrant nature. Out of all four amphetamine-like compounds studied, amphetamine was the most susceptible to biodegradation. It was followed by MDMA and methamphetamine. Photochemical processes facilitated degradation of MDMA and methamphetamine but they were not, as expected, stereoselective. Preferential biodegradation of S-(+)-methamphetamine led to the formation of S-(+)-amphetamine. Racemic MDMA was stereoselectively biodegraded by activated sludge which led to its enrichment with R-(-)-enantiomer and formation of S-(+)-MDA. Interestingly, there was only mild stereoselectivity observed during MDMA degradation in rivers. This might be due to different microbial communities utilised during activated sludge treatment and those present in the environment. Kinetic studies confirmed the recalcitrant nature of MDMA. Copyright © 2016 The Authors. Published by Elsevier Ltd.. All rights reserved.

Biodegradability of HCH in agricultural soils from Guadeloupe (French West Indies): identification of the lin genes involved in the HCH degradation pathway.

PubMed

Laquitaine, L; Durimel, A; de Alencastro, L F; Jean-Marius, C; Gros, O; Gaspard, S

2016-01-01

Banana has been a main agricultural product in the French West Indies (Guadeloupe and Martinique) since the 1960s. This crop requires the intensive use of pesticides to prevent attacks by insect pests. Chlorinated pesticides, such as hexachlorocyclohexane (HCH), chlordecone and dieldrin, were used until the beginning of the 1990s, resulting in a generalized diffuse contamination of the soil and water in the areas of banana production, hence the need to develop solutions for cleanup of the polluted sites. The aims of this work were (i) to assess lindane degradation in soil slurry microcosms treated with lindane at 10 mg/L and (ii) to detect the catabolic genes involved in the HCH degradation pathway. The soil slurry microcosm system showed a 40% lindane degradation efficiency at the end of a 30-day experiment. Lower lindane removal was also detected in the abiotic controls, probably caused by pesticide adsorption to soil particles. Indeed, the lindane concentration decreased from 6000 to 1330 ng/mL and from 800 to 340 ng/mL for the biotic and abiotic soils, respectively. Nevertheless, some of the genes involved in the HCH degradation pathway were amplified by polymerase chain reaction (PCR) from crude deoxyribonucleic acid (DNA) extracted from the Guadeloupe agricultural soil, suggesting that HCH degradation is probably mediated by bacteria closely related to the family Sphingomonadaceae.

Microbial decomposition of dead grassland roots and its influence on the carbon cycle under changing precipitation patterns

NASA Astrophysics Data System (ADS)

Becerra, C.; Schimel, J.

2013-12-01

Soil is the largest reservoir of organic carbon in terrestrial ecosystems and as such, represents a potential sink for carbon dioxide.The decomposition products of dead roots buried in the soil is a contributor to soil organic carbon. However, changing precipitation patterns may affect its fate by influencing the microbial community responsible for decomposing dead roots. To assess the impact of changing precipitation patterns, we constructed microcosms with grassland soil collected from the UCSB Sedgwick Reserve, an active and long-term research site, and dead roots from greenhouse-grown grass, Bromus diandrus. Microcosms were wetted continuously, every seven days, or every twenty days. Sets of microcosms were periodically deconstructed to assess the soil versus the roots-associated microbial community and its function. Differences in respiration rates of microcosms continuously wetted or wetted every 7 days versus microcosms wetted every 20 days existed for the first 70 days. After which, no differences in respiration rates were seen with microcosms containing roots and the no roots control. Relatedly, after a 70% roots mass loss by day 50, there was no difference in the respiration rate of microcosms containing roots and the no roots control. More than half of the roots mass loss had occurred by 30 days. By the end of the incubation period, the roots mass loss in continuously wet and 7-day wetted microcosms were over 80% compared to 67% for the microcosms wetted every 20 days. Microbial biomass in the soil were constant over time and showed no difference in treatment except with the no roots control during the first half of the incubation period. Hydrolytic enzyme activities (β-1,4-glucosidase; α-1,4-glucosidase; β-1,4-xylosidase; β-1,4-cellobiosidase) on the roots versus the soil attached to the roots were over an order greater and decreased faster with the exception of N-acetyl-glucosaminidase and acid phosphatase. Oxidative enzyme activities (phenol oxidase and peroxidase) on the roots versus the soil were also an order of magnitude greater, however the activities were constant over time regardless of the treatment, whereas the activities in the soil increased then decreased after 50 days. Our results suggest that the frequency of precipitation affects early root decomposition and long-term soil carbon storage of dead roots relatively unaffected by changing precipitation patterns.

Impacts of Glutaraldehyde on Microbial Community Structure and Degradation Potential in Streams Impacted by Hydraulic Fracturing.

PubMed

Campa, Maria Fernanda; Techtmann, Stephen M; Gibson, Caleb M; Zhu, Xiaojuan; Patterson, Megan; Garcia de Matos Amaral, Amanda; Ulrich, Nikea; Campagna, Shawn R; Grant, Christopher J; Lamendella, Regina; Hazen, Terry C

2018-05-15

The environmental impacts of hydraulic fracturing, particularly those of surface spills in aquatic ecosystems, are not fully understood. The goals of this study were to (1) understand the effect of previous exposure to hydraulic fracturing fluids on aquatic microbial community structure and (2) examine the impacts exposure has on biodegradation potential of the biocide glutaraldehyde. Microcosms were constructed from hydraulic fracturing-impacted and nonhydraulic fracturing-impacted streamwater within the Marcellus shale region in Pennsylvania. Microcosms were amended with glutaraldehyde and incubated aerobically for 56 days. Microbial community adaptation to glutaraldehyde was monitored using 16S rRNA gene amplicon sequencing and quantification by qPCR. Abiotic and biotic glutaraldehyde degradation was measured using ultra-performance liquid chromatography--high resolution mass spectrometry and total organic carbon. It was found that nonhydraulic fracturing-impacted microcosms biodegraded glutaraldehyde faster than the hydraulic fracturing-impacted microcosms, showing a decrease in degradation potential after exposure to hydraulic fracturing activity. Hydraulic fracturing-impacted microcosms showed higher richness after glutaraldehyde exposure compared to unimpacted streams, indicating an increased tolerance to glutaraldehyde in hydraulic fracturing impacted streams. Beta diversity and differential abundance analysis of sequence count data showed different bacterial enrichment for hydraulic fracturing-impacted and nonhydraulic fracturing-impacted microcosms after glutaraldehyde addition. These findings demonstrated a lasting effect on microbial community structure and glutaraldehyde degradation potential in streams impacted by hydraulic fracturing operations.

Biodegradation of roxarsone by a bacterial community of underground water and its toxic impact.

PubMed

Mafla, S; Moraga, R; León, C G; Guzmán-Fierro, V G; Yañez, J; Smith, C T; Mondaca, M A; Campos, V L

2015-08-01

Roxarsone is included in chicken food as anticoccidial and mainly excreted unchanged in faeces. Microorganisms biotransform roxarsone into toxic compounds that leach and contaminate underground waters used for human consumption. This study evaluated roxarsone biotransformation by underground water microorganisms and the toxicity of the resulting compounds. Underground water from an agricultural field was used to prepare microcosms, containing 0.05 mM roxarsone, and cultured under aerobic or anaerobic conditions. Bacterial communities of microcosms were characterized by PCR-DGGE. Roxarsone degradation was measured by HPLC/HG/AAS. Toxicity was evaluated using HUVEC cells and the Toxi-ChromoTest kit. Roxarsone degradation analysis, after 15 days, showed that microcosms of underground water with nutrients degraded 90 and 83.3% of roxarsone under anaerobic and aerobic conditions, respectively. Microcosms without nutrients degraded 50 and 33.1% under anaerobic and aerobic conditions, respectively. Microcosms including nutrients showed more roxarsone conversion into toxic inorganic arsenic species. DGGE analyses showed the presence of Proteobacteria, Firmicutes, Actinobacteria, Planctomycetes and Spirochaetes. Toxicity assays showed that roxarsone biotransformation by underground water microorganisms in all microcosms generated degradation products toxic for eukaryotic and prokaryotic cells. Furthermore, toxicity increased when roxarsone leached though a soil column and was further transformed by the bacterial community present in underground water. Therefore, using underground water from areas where roxarsone containing manure is used as fertilizer might be a health risk.

Effect of Fe(III) on 1,1,2,2-Tetrachloroethane degradation and vinyl chloride accumulation in wetland sediments of the Aberdeen Proving Ground

USGS Publications Warehouse

Jones, Elizabeth; Voytek, Mary; Lorah, Michelle

2004-01-01

1,1,2,2-Tetrachloroethane (TeCA) contaminated groundwater at the Aberdeen Proving Ground discharges through an anaerobic wetland in West Branch Canal Creek (MD), where dechlorination occurs. Two microbially mediated pathways, dichloroelimination and hydrogenolysis, account for most of the TeCA degradation at this site. The dichloroelimination pathways lead to the formation of vinyl chloride (VC), a recalcitrant carcinogen of great concern. The goal of this investigation was to determine whether microbially-available Fe(III) in the wetland surface sediment influenced the fate of TeCA and its daughter products. Differences were identified in the TeCA degradation pathway between microcosms treated with amorphous ferric oxyhydroxide (AFO-treated) and untreated (no AFO) microcosms. TeCA degradation was accompanied by a lower accumulation of VC in AFO-treated microcosms than untreated microcosms. The microcosm incubations and subsequent experiments with the microcosm materials showed that AFO treatment resulted in lower production of VC by (1) shifting TeCA degradation from dichloroelimination pathways to production of a greater proportion of chlorinated ethane products, and (2) decreasing the microbial capability to produce VC from 1,2-dichloroethene (DCE). VC degradation was not stimulated in the presence of Fe(III). Rather, VC degradation occurred readily under methanogenic conditions and was inhibited under Fe(III)-reducing conditions.

Effect of isobutanol on toluene biodegradation in nitrate amended, sulfate amended and methanogenic enrichment microcosms.

PubMed

Jayamani, Indumathy; Cupples, Alison M

2013-09-01

Isobutanol is an alternate fuel additive that is being considered because of economic and lower emission benefits. However, future gasoline spills could result in co-contamination of isobutanol with gasoline components such as benzene, toluene, ethyl-benzene and xylene. Hence, isobutanol could affect the degradability of gasoline components thereby having an effect on contaminant plume length and half-life. In this study, the effect of isobutanol on the biodegradation of a model gasoline component (toluene) was examined in laboratory microcosms. For this, toluene and isobutanol were added to six different toluene degrading laboratory microcosms under sulfate amended, nitrate amended or methanogenic conditions. While toluene biodegradation was not greatly affected in the presence of isobutanol in five out of the six different experimental sets, toluene degradation was completely inhibited in one set of microcosms. This inhibition occurred in sulfate amended microcosms constructed with inocula from wastewater treatment plant activated sludge. Our data suggest that toluene degrading consortia are affected differently by isobutanol addition. These results indicate that, if co-contamination occurs, in some cases the in situ half-life of toluene could be significantly extended.

Dominant petroleum hydrocarbon-degrading bacteria in the Archipelago Sea in South-West Finland (Baltic Sea) belong to different taxonomic groups than hydrocarbon degraders in the oceans.

PubMed

Reunamo, Anna; Riemann, Lasse; Leskinen, Piia; Jørgensen, Kirsten S

2013-07-15

The natural petroleum hydrocarbon degrading capacity of the Archipelago Sea water in S-W Finland was studied in a microcosm experiment. Pristine and previously oil exposed sites were examined. Bacterial community fingerprinting was performed using terminal restriction fragment length polymorphism (T-RFLP) and samples from selected microcosms were sequenced. The abundance of PAH degradation genes was measured by quantitative PCR. Bacterial communities in diesel exposed microcosms diverged from control microcosms during the experiment. Gram positive PAH degradation genes dominated at both sites in situ, whereas gram negative PAH degrading genes became enriched in diesel microcosms. The dominant bacterial groups after a 14 days of diesel exposure were different depending on the sampling site, belonging to the class Actinobacteria (32%) at a pristine site and Betaproteobacteria (52%) at a previously oil exposed site. The hydrocarbon degrading bacteria in the Baltic Sea differ from those in the oceans, where most hydrocarbon degraders belong to Gammaproteobacteria. Copyright © 2013 Elsevier Ltd. All rights reserved.

Bioaccumulation of polybrominated diphenyl ethers (PBDEs) in sediment aged for 2 years to carps (Cyprinus carpio)

NASA Astrophysics Data System (ADS)

Tian, S. Y.; Li, J. Y.; Jia, X. M.

2017-08-01

In order to understand the risk of polybrominated diphenyl ethers (PBDEs) existing in sediment for years, the accumulation of PBDEs in sediment aged for 2 years to fish was investigated. Simulated aquatic system microcosms were conducted with PBDE contaminated sediment aged for 2 years and carps were cultured in the microcosms for 20 days. PBDE concentrations in carp tissues were analyzed to estimate the bioavailability of aged PBDEs in carps. The main spiked PBDE congeners were detected in sediment even though the contaminated sediment was aged for 2 years. Similarly, the five PBDE (BDE-28, 47, 100, 153 and 154) congeners which probably were bioaccumulated by carp were detected in fish tissues, indicating that PBDEs could be bioaccumulated after aging for 2 years. The PBDEs distribution revealed that the concentrations of polybrominated diphenyl ethers in tissues of Cyprinus carpio is in this order of magnitude: gut > liver > gill > fillet. The PBDEs concentrations in fillet were as high as 67.9 ng/g dry wt, in which BDE-47 contributed almost 50% in profile.

Effects of elevated turbidity and nutrients on the net production of a tropical seagrass community

DOE Office of Scientific and Technical Information (OSTI.GOV)

Caldwell, J.W.

1985-01-01

Dredging effects on seagrass communities in the Florida Keys were examined by (1) comparing impacts on net production resulting from dredging and natural weather events, (2) determining changes in community photosynthetic efficiency, (3) evaluating shading and nutrient effects on net production, and (4) developing a systems dynamics model. Net community production was estimated during numerous meteorological and dredging events using the Odum-Hoskins oxygen technique in flow-through field microcosms. In other experiments, shading and nutrients (phosphorus, nitrate, and ammonia) were manipulated to simulate dredge plume conditions. The greatest depression in net community production resulted from severe thunderstorms and dredging events, respectively.more » In field microcosm experiments, significant interaction occurred between shading and nutrient concentration. The model of seagrass production was most sensitive to changes in nutrient-seagrass relationships, seagrass production estimates, and seagrass-light interactions. Recovery of seagrass biomass following numerous dredging events (3.5 years) was longer than that from the estimated total annual thunderstorms encountered (1 year) but shorter than recovery from hurricane events (4.1 years).« less

Quantitative survival of Leptospira interrogans in soil and water microcosms.

PubMed

Casanovas-Massana, Arnau; Pedra, Gabriel Ghizzi; Wunder, Elsio A; Diggle, Peter J; Begon, Mike; Ko, Albert I

2018-04-27

Leptospira interrogans is the etiological agent of leptospirosis, a globally distributed zoonotic disease. Human infection usually occurs through skin exposure with water and soil contaminated with the urine of chronically infected animals. In this study, we aimed to quantitatively characterize the survival of Leptospira interrogans serovar Copenhageni in environmental matrices. We constructed laboratory microcosms to simulate natural conditions and determined the persistence of DNA markers in soil, mud, spring water and sewage using a qPCR and a PMA-qPCR assay. We found that L. interrogans does not survive at high concentrations in the tested matrices. No net growth was detected in any of the experimental conditions and in all cases the concentration of the DNA markers targeted decreased from the beginning of the experiment following an exponential decay with a decreasing decay rate over time. After 12 and 21 days of incubation the spiked concentration of 10 6 L. interrogans cells/mL or g decreased to approximately 100 cells/mL or g in soil and spring water microcosms, respectively. Furthermore, culturable L. interrogans persisted at concentrations under the limit of detection by PMA-qPCR or qPCR for at least 16 days in soil and 28 days in spring water. Altogether our findings suggest that the environment is not a multiplication reservoir, but a temporary carrier of the L. interrogans Copenhageni, although the observed prolonged persistence at low concentrations may still enable the transmission of the disease. IMPORTANCE Leptospirosis is a zoonotic disease caused by spirochetes of the genus Leptospira that primarily affects impoverished populations worldwide. Although leptospirosis is transmitted by contact with water and soil, little is known about the ability of the pathogen to survive in the environment. In this study, we quantitatively characterized the survival of L. interrogans in environmental microcosms and found that although it cannot multiply in water, soil or sewage, it survives for extended time (days to weeks depending on the matrix). The survival parameters obtained here may help to better understand the distribution of pathogenic Leptospira in the environment and improve the predictions of human infection risks in endemic areas. Copyright © 2018 American Society for Microbiology.

The persistence and ecological impacts of a cyanobacterium genetically engineered to express mosquitocidal Bacillus thuringiensis toxins.

PubMed

Ketseoglou, Irene; Bouwer, Gustav

2016-05-10

The cyanobacterium Anabaena PCC 7120#11 has been genetically engineered to act as a delivery vehicle for Bacillus thuringiensis subspecies israelensis mosquitocidal toxins. To address ecological concerns about releasing this genetically engineered microorganism into the environment for mosquito larva control, the persistence and ecological impacts of PCC 7120#11 was evaluated using multi-species, standardized aquatic microcosms. The microcosms were set up as described in ASTM E1366-02 (Standard Practice for Standardized Aquatic Microcosms: Fresh Water), with a few modifications. The treatment group microcosms were inoculated with PCC 7120#11 and key water quality parameters and non-target effects were compared between the treatment and control groups over a period of 35 days. PCC 7120#11 decreased from a concentration of 4.50 × 10(6) cells/ml (at inoculation) to 1.32 × 10(3) cells/ml after 4 weeks and larvicidal activity against third instar larvae of Anopheles arabiensis was only evident for two weeks after treatment. Both treatment and the interaction of treatment and time had a significant effect on nitrate, phosphate and photosynthetic microorganism concentrations. Treatment with PCC 7120#11 caused a temporary spike in ammonia in the microcosms a week after treatment, but the concentrations were well below acute and chronic criteria values for ammonia in freshwater ecosystems. Cyprinotus vidua concentrations were not significantly different between PCC 7120#11 and control microcosms. In PCC 7120#11 microcosms, Daphnia pulex concentrations were significantly lower than control concentrations between days 18 and 25. By the end of the experiment, none of the measured variables were significantly different between the treatment groups. The standard aquatic microcosm experiments provided more data on the ecological impacts of PCC 7120#11 than single-organism assessments would have. On the basis of the relatively minor, short-term effects that PCC 7120#11 had on water quality parameters and non-target invertebrates, further evaluation of PCC 7120#11 for use in integrated vector management is warranted.

Modelling of Picosatellite Constellation-Based Network and Effects on Quality of Service

DTIC Science & Technology

2015-03-01

the STK -QualNet Interface module. The analysis period for the scenario simulation was chosen as a two-day period from 6 June 2011 to 7 June 2011. This...MIN 0:00:04 0:00:34 AVERAGE 0:58:03 0:21:21 27 THIS PAGE INTENTIONALLY LEFT BLANK 28 VI. DATA ANALYSIS /INTERPRETATION The STK model was... Mission Analysis and Design, 3rd ed. (Space Technology Library, vol. 8). El Segundo, CA: Microcosm, 1999. [5] exactEarth. (2015). ExactView

Penicillium oxalicum reduces the number of cysts and juveniles of potato cyst nematodes.

PubMed

Martinez-Beringola, M L; Salto, T; Vázquez, G; Larena, I; Melgarejo, P; De Cal, A

2013-07-01

To test the biocontrol potential of Penicillium oxalicum, a biocontrol agent against fungal diseases and against the potato cyst nematodes (PCNs), Globodera pallida and Globodera rostochiensis. We tested the effect of P. oxalicum on the nematode cysts under laboratory conditions or in soil microcosms. A reduction in the rate of G. pallida juveniles hatching by P. oxalicum was observed when root diffusates from the 'Monalisa' and the 'Désirée' potato cultivar were used (98·6 and 74·1% reduction, respectively). However, the rate of G. pallida juveniles hatching was not significantly reduced when root diffusates from the 'San Pedro' tomato cultivar were used. Penicillium oxalicum also significantly reduced the ability of the G. rostochiensis juveniles to hatch (30·9% reduction) when root diffusates of the 'Désirée' potato cultivars were used. Penicillium oxalicum treatment of the soil significantly reduced the number of G. pallida cysts that were recovered from the soil of each pot that contained the 'Désirée' potato cultivar. Our results show that P. oxalicum is a potential biocontrol inoculant for protecting potato crops against PCNs. Penicillium oxalicum has potential to be used in order to reduce PCNs. Journal of Applied Microbiology © 2013 The Society for Applied Microbiology.

H 2-saturation of high affinity H 2-oxidizing bacteria alters the ecological niche of soil microorganisms unevenly among taxonomic groups

DOE PAGES

Piché-Choquette, Sarah; Tremblay, Julien; Tringe, Susannah G.; ...

2016-03-10

Soil microbial communities are continuously exposed to H 2 diffusing into the soil from the atmosphere. N 2-fixing nodules represent a peculiar microniche in soil where H 2 can reach concentrations up to 20,000 fold higher than in the global atmosphere (0.530 ppmv). In this study, we investigated the impact of H 2 exposure on soil bacterial community structure using dynamic microcosm chambers simulating soil H 2 exposure from the atmosphere and N 2-fixing nodules. Biphasic kinetic parameters governing H 2 oxidation activity in soil changed drastically upon elevated H 2 exposure, corresponding to a slight but significant decay ofmore » high affinity H 2-oxidizing bacteria population, accompanied by an enrichment or activation of microorganisms displaying low-affinity for H 2. In contrast to previous studies that unveiled limited response by a few species, the relative abundance of 958 bacterial ribotypes distributed among various taxonomic groups, rather than a few distinct taxa, was influenced by H 2 exposure. Furthermore, correlation networks showed important alterations of ribotype covariation in response to H 2 exposure, suggesting that H 2 affects microbe-microbe interactions in soil. Taken together, our results demonstrate that H 2-rich environments exert a direct influence on soil H 2-oxidizing bacteria in addition to indirect effects on other members of the bacterial communities.« less

H2-saturation of high affinity H2-oxidizing bacteria alters the ecological niche of soil microorganisms unevenly among taxonomic groups

PubMed Central

Piché-Choquette, Sarah; Tremblay, Julien; Tringe, Susannah G.

2016-01-01

Soil microbial communities are continuously exposed to H2 diffusing into the soil from the atmosphere. N2-fixing nodules represent a peculiar microniche in soil where H2 can reach concentrations up to 20,000 fold higher than in the global atmosphere (0.530 ppmv). In this study, we investigated the impact of H2 exposure on soil bacterial community structure using dynamic microcosm chambers simulating soil H2 exposure from the atmosphere and N2-fixing nodules. Biphasic kinetic parameters governing H2 oxidation activity in soil changed drastically upon elevated H2 exposure, corresponding to a slight but significant decay of high affinity H2-oxidizing bacteria population, accompanied by an enrichment or activation of microorganisms displaying low-affinity for H2. In contrast to previous studies that unveiled limited response by a few species, the relative abundance of 958 bacterial ribotypes distributed among various taxonomic groups, rather than a few distinct taxa, was influenced by H2 exposure. Furthermore, correlation networks showed important alterations of ribotype covariation in response to H2 exposure, suggesting that H2 affects microbe-microbe interactions in soil. Taken together, our results demonstrate that H2-rich environments exert a direct influence on soil H2-oxidizing bacteria in addition to indirect effects on other members of the bacterial communities. PMID:26989620

Degradation of 1,1,2,2-tetrachloroethane and accumulation of vinyl chloride in wetland sediment microcosms and in situ porewater: biogeochemical controls and associations with microbial communities

NASA Astrophysics Data System (ADS)

Lorah, Michelle M.; Voytek, Mary A.

2004-05-01

The biodegradation pathways of 1,1,2,2-tetrachloroethane (TeCA) and 1,1,2-trichloroethane (112TCA) and the associated microbial communities in anaerobic wetland sediments were evaluated using concurrent geochemical and genetic analyses over time in laboratory microcosm experiments. Experimental results were compared to in situ porewater data in the wetland to better understand the factors controlling daughter product distributions in a chlorinated solvent plume discharging to a freshwater tidal wetland at Aberdeen Proving Ground, Maryland. Microcosms constructed with wetland sediment from two sites showed little difference in the initial degradation steps of TeCA, which included simultaneous hydrogenolysis to 112TCA and dichloroelimination to 1,2-dichloroethene (12DCE). The microcosms from the two sites showed a substantial difference, however, in the relative dominance of subsequent dichloroelimination of 112TCA. A greater dominance of 112TCA dichloroelimination in microcosms constructed with sediment that was initially iron-reducing and subsequently simultaneously iron-reducing and methanogenic caused approximately twice as much vinyl chloride (VC) production as microcosms constructed with sediment that was methanogenic only throughout the incubation. The microcosms with higher VC production also showed substantially more rapid VC degradation. Field measurements of redox-sensitive constituents, TeCA, and its anaerobic degradation products along flowpaths in the wetland porewater also showed greater production and degradation of VC with concurrent methanogenesis and iron reduction. Molecular fingerprinting indicated that bacterial species [represented by a peak at a fragment size of 198 base pairs (bp) by MnlI digest] are associated with VC production from 112TCA dichloroelimination, whereas methanogens (190 and 307 bp) from the Methanococcales or Methanobacteriales family are associated with VC production from 12DCE hydrogenolysis. Acetate-utilizing methanogens (acetotrophs) appear to be involved in the biodegradation of VC. The relative abundance of Methanosarcinaceae, the only methanogen group with acetotrophic members, doubled in microcosms in which degradation of VC was observed. In addition, molecular analyses using primers specific for known dehalorespiring bacteria in the Dehalococcoides and Desulfuromonas groups showed the presence of these bacteria in microcosm slurry from the site that showed the highest VC production and degradation. Determination of biogeochemical controls and microbial consortia involved in TeCA degradation is leading to a better understanding of the heterogeneity in biodegradation rates and daughter product distribution in the wetland, improving capabilities for developing remediation and monitoring plans.

Degradation of 1,1,2,2-tetrachloroethane and accumulation of vinyl chloride in wetland sediment microcosms and in situ porewater: biogeochemical controls and associations with microbial communities

USGS Publications Warehouse

Lorah, Michelle M.; Voytek, Mary A.

2004-01-01

The biodegradation pathways of 1,1,2,2-tetrachloroethane (TeCA) and 1,1,2-trichloroethane (112TCA) and the associated microbial communities in anaerobic wetland sediments were evaluated using concurrent geochemical and genetic analyses over time in laboratory microcosm experiments. Experimental results were compared to in situ porewater data in the wetland to better understand the factors controlling daughter product distributions in a chlorinated solvent plume discharging to a freshwater tidal wetland at Aberdeen Proving Ground, Maryland. Microcosms constructed with wetland sediment from two sites showed little difference in the initial degradation steps of TeCA, which included simultaneous hydrogenolysis to 112TCA and dichloroelimination to 1,2-dichloroethene (12DCE). The microcosms from the two sites showed a substantial difference, however, in the relative dominance of subsequent dichloroelimination of 112TCA. A greater dominance of 112TCA dichloroelimination in microcosms constructed with sediment that was initially iron-reducing and subsequently simultaneously iron-reducing and methanogenic caused approximately twice as much vinyl chloride (VC) production as microcosms constructed with sediment that was methanogenic only throughout the incubation. The microcosms with higher VC production also showed substantially more rapid VC degradation. Field measurements of redox-sensitive constituents, TeCA, and its anaerobic degradation products along flowpaths in the wetland porewater also showed greater production and degradation of VC with concurrent methanogenesis and iron reduction.Molecular fingerprinting indicated that bacterial species [represented by a peak at a fragment size of 198 base pairs (bp) by MnlI digest] are associated with VC production from 112TCA dichloroelimination, whereas methanogens (190 and 307 bp) from the Methanococcales or Methanobacteriales family are associated with VC production from 12DCE hydrogenolysis. Acetate-utilizing methanogens (acetotrophs) appear to be involved in the biodegradation of VC. The relative abundance of Methanosarcinaceae, the only methanogen group with acetotrophic members, doubled in microcosms in which degradation of VC was observed. In addition, molecular analyses using primers specific for known dehalorespiring bacteria in the Dehalococcoides and Desulfuromonas groups showed the presence of these bacteria in microcosm slurry from the site that showed the highest VC production and degradation. Determination of biogeochemical controls and microbial consortia involved in TeCA degradation is leading to a better understanding of the heterogeneity in biodegradation rates and daughter product distribution in the wetland, improving capabilities for developing remediation and monitoring plans.

Degradation of 1,1,2,2-tetrachloroethane and accumulation of vinyl chloride in wetland sediment microcosms and in situ porewater: Biogeochemical controls and associations with microbial communities

USGS Publications Warehouse

Lorah, M.M.; Voytek, M.A.

2004-01-01

The biodegradation pathways of 1,1,2,2-tetrachloroethane (TeCA) and 1,1,2-trichloroethane (112TCA) and the associated microbial communities in anaerobic wetland sediments were evaluated using concurrent geochemical and genetic analyses over time in laboratory microcosm experiments. Experimental results were compared to in situ porewater data in the wetland to better understand the factors controlling daughter product distributions in a chlorinated solvent plume discharging to a freshwater tidal wetland at Aberdeen Proving Ground, Maryland. Microcosms constructed with wetland sediment from two sites showed little difference in the initial degradation steps of TeCA, which included simultaneous hydrogenolysis to 112TCA and dichloroelimination to 1,2-dichloroethene (12DCE). The microcosms from the two sites showed a substantial difference, however, in the relative dominance of subsequent dichloroelimination of 112TCA. A greater dominance of 112TCA dichloroelimination in microcosms constructed with sediment that was initially iron-reducing and subsequently simultaneously iron-reducing and methanogenic caused approximately twice as much vinyl chloride (VC) production as microcosms constructed with sediment that was methanogenic only throughout the incubation. The microcosms with higher VC production also showed substantially more rapid VC degradation. Field measurements of redox-sensitive constituents, TeCA, and its anaerobic degradation products along flowpaths in the wetland porewater also showed greater production and degradation of VC with concurrent methanogenesis and iron reduction. Molecular fingerprinting indicated that bacterial species [represented by a peak at a fragment size of 198 base pairs (bp) by MnlI digest] are associated with VC production from 112TCA dichloroelimination, whereas methanogens (190 and 307 bp) from the Methanococcales or Methanobacteriales family are associated with VC production from 12DCE hydrogenolysis. Acetate-utilizing methanogens (acetotrophs) appear to be involved in the biodegradation of VC. The relative abundance of Methanosarcinaceae, the only methanogen group with acetotrophic members, doubled in microcosms in which degradation of VC was observed. In addition, molecular analyses using primers specific for known dehalorespiring bacteria in the Dehalococcoides and Desulfuromonas groups showed the presence of these bacteria in microcosm slurry from the site that showed the highest VC production and degradation. Determination of biogeochemical controls and microbial consortia involved in TeCA degradation is leading to a better understanding of the heterogeneity in biodegradation rates and daughter product distribution in the wetland, improving capabilities for developing remediation and monitoring plans.

Effect of simulated acid rain on the litter decomposition of Quercus acutissima and Pinus massoniana in forest soil microcosms and the relationship with soil enzyme activities.

PubMed

Wang, Congyan; Guo, Peng; Han, Guomin; Feng, Xiaoguang; Zhang, Peng; Tian, Xingjun

2010-06-01

With the continuing increase in human activities, ecologists are increasingly interested in understanding the effects of acid rain on litter decomposition. Two dominant litters were chosen from Zijin Mountain in China: Quercus acutissima from a broad-leaved forest and Pinus massoniana from a coniferous forest. The litters were incubated in microcosms and treated with simulated acid rain (gradient pH levels). During a six-month incubation, changes in chemical composition (i.e., lignin, total carbohydrate, and nitrogen), litter mass losses, soil pH values, and activities of degradative enzymes were determined. Results showed that litter mass losses were depressed after exposure to acid rain and the effects of acid rain on the litter decomposition rates of needles were higher than on those of leaves. Results also revealed that simulated acid rain restrained the activities of cellulase, invertase, nitrate reductase, acid phosphatase, alkaline phosphatase, polyphenol oxidase, and urease, while it enhanced the activities of catalase in most cases during the six-month decomposition process. Catalase and polyphenol oxidase were primarily responsible for litter decomposition in the broad-leaved forest, while invertase, nitrate reductase, and urease were primarily responsible for litter decomposition in the coniferous forest. The results suggest acid rain-restrained litter decomposition may be due to the depressed enzymatic activities. According to the results of this study, soil carbon in subtropical forests would accumulate as a long-term consequence of continued acid rain. This may presumably alter the balance of ecosystem carbon flux, nutrient cycling, and humus formation, which may, in turn, have multiple effects on forest ecosystems. Copyright (c) 2010 Elsevier B.V. All rights reserved.

Methods for visualising active microbial benzene degraders in in situ microcosms.

PubMed

Schurig, Christian; Mueller, Carsten W; Höschen, Carmen; Prager, Andrea; Kothe, Erika; Beck, Henrike; Miltner, Anja; Kästner, Matthias

2015-01-01

Natural attenuation maybe a cost-efficient option for bioremediation of contaminated sites but requires knowledge about the activity of degrading microbes under in situ conditions. In order to link microbial activity to the spatial distribution of contaminant degraders, we combined the recently improved in situ microcosm approach, so-called 'direct-push bacterial trap' (DP-BACTRAP), with nano-scale secondary ion mass spectrometry (NanoSIMS) analysis on samples from contaminated constructed wetlands. This approach is based on initially sterile microcosms amended with (13)C-labelled benzene as a source of carbon and energy for microorganisms. The microcosms were introduced directly in the constructed wetland, where they were colonised by indigenous microorganisms from the sediment. After incubation in the field, the samples were analysed by NanoSIMS, scanning electron microscopy (SEM) and fluorescence microscopy in order to visualise (13)C-labelled microbial biomass on undisturbed samples from the microcosms. With the approach developed, we successfully visualised benzene-degrading microbes on solid materials with high surface area by means of NanoSIMS. Moreover, we could demonstrate the feasibility of NanoSIMS analysis of unembedded porous media with a highly complex topography, which was frequently reasoned to not lead to sufficient results.

Statistical variances of diffusional properties from ab initio molecular dynamics simulations

NASA Astrophysics Data System (ADS)

He, Xingfeng; Zhu, Yizhou; Epstein, Alexander; Mo, Yifei

2018-12-01

Ab initio molecular dynamics (AIMD) simulation is widely employed in studying diffusion mechanisms and in quantifying diffusional properties of materials. However, AIMD simulations are often limited to a few hundred atoms and a short, sub-nanosecond physical timescale, which leads to models that include only a limited number of diffusion events. As a result, the diffusional properties obtained from AIMD simulations are often plagued by poor statistics. In this paper, we re-examine the process to estimate diffusivity and ionic conductivity from the AIMD simulations and establish the procedure to minimize the fitting errors. In addition, we propose methods for quantifying the statistical variance of the diffusivity and ionic conductivity from the number of diffusion events observed during the AIMD simulation. Since an adequate number of diffusion events must be sampled, AIMD simulations should be sufficiently long and can only be performed on materials with reasonably fast diffusion. We chart the ranges of materials and physical conditions that can be accessible by AIMD simulations in studying diffusional properties. Our work provides the foundation for quantifying the statistical confidence levels of diffusion results from AIMD simulations and for correctly employing this powerful technique.

Dissociative diffusion mechanism in vacancy-rich materials according to mass action kinetics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Biderman, N. J.; Sundaramoorthy, R.; Haldar, Pradeep

We conducted two sets of diffusion-reaction numerical simulations using a finite difference method (FDM) in order to investigate fast impurity diffusion via interstitial sites in vacancy-rich materials such as Cu(In,Ga)Se 2 (CIGS) and Cu 2ZnSn(S, Se) 4 (CZTSSe or CZTS) via the dissociative diffusion mechanism where the interstitial diffuser ultimately reacts with a vacancy to produce a substitutional. The first set of simulations extends the standard interstitial-limited dissociative diffusion theory to vacancy-rich material conditions where vacancies are annihilated in large amounts, introducing non-equilibrium vacancy concentration profiles. The second simulation set explores the vacancy-limited dissociative diffusion where impurity incorporation increases themore » equilibrium vacancy concentration. In addition to diffusion profiles of varying concentrations and shapes that were obtained in all simulations, some of the profiles can be fitted with the constant- and limited-source solutions of Fick’s second law despite the non-equilibrium condition induced by the interstitial-vacancy reaction. The first set of simulations reveals that the dissociative diffusion coefficient in vacancy-rich materials is inversely proportional to the initial vacancy concentration. In the second set of numerical simulations, impurity-induced changes in the vacancy concentration lead to distinctive diffusion profile shapes. The simulation results are also compared with published data of impurity diffusion in CIGS. And according to the characteristic properties of diffusion profiles from the two set of simulations, experimental detection of the dissociative diffusion mechanism in vacancy-rich materials may be possible.« less

Dissociative diffusion mechanism in vacancy-rich materials according to mass action kinetics

DOE PAGES

Biderman, N. J.; Sundaramoorthy, R.; Haldar, Pradeep; ...

2016-05-13

We conducted two sets of diffusion-reaction numerical simulations using a finite difference method (FDM) in order to investigate fast impurity diffusion via interstitial sites in vacancy-rich materials such as Cu(In,Ga)Se 2 (CIGS) and Cu 2ZnSn(S, Se) 4 (CZTSSe or CZTS) via the dissociative diffusion mechanism where the interstitial diffuser ultimately reacts with a vacancy to produce a substitutional. The first set of simulations extends the standard interstitial-limited dissociative diffusion theory to vacancy-rich material conditions where vacancies are annihilated in large amounts, introducing non-equilibrium vacancy concentration profiles. The second simulation set explores the vacancy-limited dissociative diffusion where impurity incorporation increases themore » equilibrium vacancy concentration. In addition to diffusion profiles of varying concentrations and shapes that were obtained in all simulations, some of the profiles can be fitted with the constant- and limited-source solutions of Fick’s second law despite the non-equilibrium condition induced by the interstitial-vacancy reaction. The first set of simulations reveals that the dissociative diffusion coefficient in vacancy-rich materials is inversely proportional to the initial vacancy concentration. In the second set of numerical simulations, impurity-induced changes in the vacancy concentration lead to distinctive diffusion profile shapes. The simulation results are also compared with published data of impurity diffusion in CIGS. And according to the characteristic properties of diffusion profiles from the two set of simulations, experimental detection of the dissociative diffusion mechanism in vacancy-rich materials may be possible.« less

Comparative assessment of fungal augmentation treatments of a fine-textured and historically oil-contaminated soil.

PubMed

Covino, Stefano; Stella, Tatiana; D'Annibale, Alessandro; Lladó, Salvador; Baldrian, Petr; Čvančarová, Monika; Cajthaml, Tomas; Petruccioli, Maurizio

2016-10-01

The removal of aged hydrophobic contaminants from fine-textured soils is a challenging issue in remediation. The objective of this study was to compare the efficacy of augmentation treatments to that of biostimulation in terms of total aliphatic hydrocarbon (TAH) and toxicity removal from a historically contaminated clay soil and to assess their impact on the resident microbial community. To this aim, Pleurotus ostreatus, Botryosphaeria rhodina and a combination of both were used as the inoculants while the addition of a sterilized lignocellulose mixture to soil (1:5, w/w) was used as a biostimulation approach. As opposed to the non-amended control soil, where no changes in TAH concentration and residual toxicity were observed after 60days, the activation of specialized bacteria was found in the biostimulated microcosms resulting in significant TAH removal (79.8%). The bacterial community structure in B. rhodina-augmented microcosms did not differ from the biostimulated microcosms due to the inability of the fungus to be retained within the resident microbiota. Best TAH removals were observed in microcosms inoculated with P. ostreatus alone (Po) and in binary consortium with B. rhodina (BC) (86.8 and 88.2%, respectively). In these microcosms, contaminant degradation exceeded their bioavailability thresholds determined by sequential supercritical CO2 extraction. Illumina metabarcoding of 16S rRNA gene showed that the augmentation with Po and BC led to lower relative abundances of Gram(+) taxa, Actinobacteria in particular, than those in biostimulated microcosms. Best detoxification, with respect to the non-amended incubation control, was found in Po microcosms where a drop in collembola mortality (from 90 to 22%) occurred. At the end of incubation, in both Po and BC, the relative abundances of P. ostreatus sequences were higher than 60% thus showing the suitability of this fungus in bioaugmentation-based remediation applications. Copyright © 2016 Elsevier B.V. All rights reserved.

ENANTIOSELECTIVITY IN THE BIODEGRADATION OF PCB ATROPISOMERS

EPA Science Inventory

Microcosms inoculated with sediment from two locations in a contaminated reservoir, Lake Hartwell, SC, USA, degraded certain PCB atropisomers enantioselectively while other atropisomers were degraded in racemic proportions. The microcosms were spiked with either 234-236 PCB (PCB...

Special Education: A Microcosm of Bureaucracy. Part Two: The Elements of the System

ERIC Educational Resources Information Center

Clark, Ann D.

1971-01-01

Delineates a case study of special education that provides a unique microcosm of the emergence of an educational subsystem with inherent and forceful bureaucratic controls that were present from its inception. (Author)

Combined Effects of Dissolved Nutrients and Oxygen on Plant Litter Decomposition and Associated Fungal Communities.

PubMed

Gomes, Patrícia Pereira; Ferreira, Verónica; Tonin, Alan M; Medeiros, Adriana Oliveira; Júnior, José Francisco Gonçalves

2018-05-01

Aquatic ecosystems worldwide have been substantially altered by human activities, which often induce changes in multiple factors that can interact to produce complex effects. Here, we evaluated the combined effects of dissolved nutrients (nitrogen [N] and phosphorus [P]; three levels: concentration found in oligotrophic streams in the Cerrado biome, 10× and 100× enriched) and oxygen (O 2 ; three levels: hypoxic [4% O 2 ], depleted [55% O 2 ], and saturated [96% O 2 ]) on plant litter decomposition and associated fungal decomposers in laboratory microcosms simulating stream conditions under distinct scenarios of water quality deterioration. Senescent leaves of Maprounea guianensis were incubated for 10 days in an oligotrophic Cerrado stream to allow microbial colonization and subsequently incubated in microcosms for 21 days. Leaves lost 1.1-3.0% of their initial mass after 21 days, and this was not affected either by nutrients or oxygen levels. When considering simultaneous changes in nutrients and oxygen concentrations, simulating increased human pressure, fungal biomass accumulation, and sporulation rates were generally inhibited. Aquatic hyphomycete community structure was also affected by changes in nutrients and oxygen availability, with stronger effects found in hypoxic treatments than in depleted or saturated oxygen treatments. This study showed that the effects of simultaneous changes in the availability of dissolved nutrients and oxygen in aquatic environments can influence the activity and composition of fungal communities, although these effects were not translated into changes in litter decomposition rates.

Stimulation of methane generation from nonproductive coal by addition of nutrients or a microbial consortium

USGS Publications Warehouse

Jones, Elizabeth J.P.; Voytek, Mary A.; Corum, Margo D.; Orem, William H.

2010-01-01

Biogenic formation of methane from coal is of great interest as an underexploited source of clean energy. The goal of some coal bed producers is to extend coal bed methane productivity and to utilize hydrocarbon wastes such as coal slurry to generate new methane. However, the process and factors controlling the process, and thus ways to stimulate it, are poorly understood. Subbituminous coal from a nonproductive well in south Texas was stimulated to produce methane in microcosms when the native population was supplemented with nutrients (biostimulation) or when nutrients and a consortium of bacteria and methanogens enriched from wetland sediment were added (bioaugmentation). The native population enriched by nutrient addition included Pseudomonas spp., Veillonellaceae, and Methanosarcina barkeri. The bioaugmented microcosm generated methane more rapidly and to a higher concentration than the biostimulated microcosm. Dissolved organics, including long-chain fatty acids, single-ring aromatics, and long-chain alkanes accumulated in the first 39 days of the bioaugmented microcosm and were then degraded, accompanied by generation of methane. The bioaugmented microcosm was dominated by Geobacter sp., and most of the methane generation was associated with growth of Methanosaeta concilii. The ability of the bioaugmentation culture to produce methane from coal intermediates was confirmed in incubations of culture with representative organic compounds. This study indicates that methane production could be stimulated at the nonproductive field site and that low microbial biomass may be limiting in situ methane generation. In addition, the microcosm study suggests that the pathway for generating methane from coal involves complex microbial partnerships.

Microbial community characterization and functional gene quantification in RDX-degrading microcosms derived from sediment and groundwater at two naval sites.

PubMed

Wilson, Fernanda Paes; Cupples, Alison M

2016-08-01

The explosive hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) has long been recognized as a problematic environmental pollutant, and efforts to remediate contaminated soils, sediments, and groundwater have been going on for decades. In recent years, much interest has focused on using bioremediation to clean up these sites. The current study investigated the microorganisms (16S rRNA genes, Illumina) and functional genes (xenA, xenB, and xplA) linked to RDX biodegradation in microcosms composed of sediment or groundwater from two Navy sites. For this, experiments included sediment samples from three depths (5 to 30 ft) from two wells located in one Navy site. In addition, the groundwater upstream and downstream of an emulsified oil biobarrier was examined from another Navy site. Further, for the groundwater experiments, the effect of glucose addition was explored. For the sediment experiments, the most enriched phylotypes during RDX degradation varied over time, by depth and well locations. However, several trends were noted, including the enrichment of Pseudomonas, Rhodococcus, Arthrobacter, and Sporolactobacillus in the sediment microcosms. For the groundwater-based experiments, Pseudomonas, unclassified Rhodocyclaceae, Sphingomonas, and Rhodococcus were also highly abundant during RDX degradation. The abundance of both xplA and xenA significantly increased during RDX degradation compared to the control microcosms for many treatments (both groundwater and sediment microcosms). In a limited number of microcosms, the copy number of the xenB gene increased. Phylotype data were correlated with functional gene data to highlight potentially important biomarkers for RDX biodegradation at these two Navy sites.

Evaluation of TCDD biodegradability under different redox conditions.

PubMed

Kao, C M; Chen, S C; Liu, J K; Wu, M J

2001-09-01

Polychlorinated dibenzo-p-dioxins have been generated as unwanted by-products in many industrial processes. Although their widespread distribution in different environmental compartments has been recognized, little is known about their fate in the ultimate environment sinks. The highly stable dioxin isomer 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) has been called the most toxic compound known to man. In this laboratory microcosm study, TCDD bioavailability was evaluated under five reduction/oxidation (redox) conditions including aerobic biodegradation, aerobic cometabolism, methanogenesis, iron reduction, and reductive dechlorination. Activated sludge and aquifer sediments from a TCDD and a pentachlorophenol (PCP) contaminated site were used as the inocula. Acetate, sludge cake, and cane molasses were used as the primary substrates (carbon sources) in cometabolism and reductive dechlorination microcosms. After a 90-day incubation period, microcosms constructed under reductive dechlorination conditions were the only treatment showing promising remediation results. The highest TCDD degradation rate [up to 86% of TCDD removal (with an initial concentration of 96 microg/kg of soil)] was observed in the microcosms with anaerobic activated sludge as the microbial inocula and sludge cakes as the primary substrates. Except for reductive dechlorination microcosms, no significant TCDD removal was observed in the microcosms prepared under other conditions. Thus, application of an effective primary substrate to enhance the reductive dechlorination process is a feasible method for TCDD bioremediation. Bioremediation expense can be significantly reduced by the supplement of some less expensive alternative substrates (e.g., sludge cakes, cane molasses). Results would be useful in designing a scale-up in situ or on-site bioremediation system such as bioslurry reactor for field application.

In-Situ Remediation of MTBE Contaminated Aquifers Using Propane Biosparging. Revision 1

DTIC Science & Technology

2003-01-03

above MTBE’s odor and taste threshold of 40 µg/L. Compared to other gasoline constituents, relatively few studies have been conducted to address the...xii MICROCOSM STUDY RESULTS...16 3.4.2 Microcosm Studies

GALACTIC WINDS DRIVEN BY ISOTROPIC AND ANISOTROPIC COSMIC-RAY DIFFUSION IN DISK GALAXIES

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pakmor, R.; Pfrommer, C.; Simpson, C. M.

2016-06-20

The physics of cosmic rays (CRs) is a promising candidate for explaining the driving of galactic winds and outflows. Recent galaxy formation simulations have demonstrated the need for active CR transport either in the form of diffusion or streaming to successfully launch winds in galaxies. However, due to computational limitations, most previous simulations have modeled CR transport isotropically. Here, we discuss high-resolution simulations of isolated disk galaxies in a 10{sup 11} M {sub ⊙} halo with the moving-mesh code Arepo that include injection of CRs from supernovae, advective transport, CR cooling, and CR transport through isotropic or anisotropic diffusion. Wemore » show that either mode of diffusion leads to the formation of strong bipolar outflows. However, they develop significantly later in the simulation with anisotropic diffusion compared to the simulation with isotropic diffusion. Moreover, we find that isotropic diffusion allows most of the CRs to quickly diffuse out of the disk, while in the simulation with anisotropic diffusion, most CRs remain in the disk once the magnetic field becomes dominated by its azimuthal component, which occurs after ∼300 Myr. This has important consequences for the gas dynamics in the disk. In particular, we show that isotropic diffusion strongly suppresses the amplification of the magnetic field in the disk compared to anisotropic or no diffusion models. We therefore conclude that reliable simulations which include CR transport inevitably need to account for anisotropic diffusion.« less

Anaerobic degradation of 1,1,2,2-tetrachloroethane and association with microbial communities in a freshwater tidal wetland, Aberdeen Proving Ground, Maryland : laboratory experiments and comparisons to field data

USGS Publications Warehouse

Lorah, Michelle M.; Voytek, Mary A.; Kirshtein, Julie D.; Jones, Elizabeth J.

2003-01-01

Defining biodegradation rates and processes is a critical part of assessing the feasibility of monitored natural attenuation as a remediation method for ground water containing organic contaminants. During 1998?2001, the U.S. Geological Survey conducted a microbial study at a freshwater tidal wetland along the West Branch Canal Creek, Aberdeen Proving Ground, Maryland, as part of an investigation of natural attenuation of chlorinated volatile organic compounds (VOCs) in the wetland sediments. Geochemical analyses and molecular biology techniques were used to investigate factors controlling anaerobic degradation of 1,1,2,2-tetrachloroethane (TeCA), and to characterize the microbial communities that potentially are important in its degradation. Rapid TeCA and daughter product degradation observed in laboratory experiments and estimated with field data confirm that natural attenuation is a feasible remediation method at this site. The diverse microbial community that seems to be involved in TeCA degradation in the wetland sediments varies with changing spatial and seasonal conditions, allowing continued effective natural attenuation throughout the year. Rates of TeCA degradation in anaerobic microcosm experiments conducted with wetland sediment collected from two different sites (WB23 and WB30) and during three different seasons (March?April 1999, July?August 1999, and October?November 2000) showed little spatial variability but high seasonal variability. Initial first-order degradation rate constants for TeCA ranged from 0.10?0.01 to 0.16?0.05 per day (half-lives of 4.3 to 6.9 days) for March?April 1999 and October?November 2000 microcosms incubated at 19 degrees Celsius, whereas lower rate constants of 0 ? 0.03 and 0.06 ? 0.03 per day were obtained in July?August 1999 microcosms incubated at 19 degrees Celsius. Microbial community profiles showed that low microbial biomass and microbial diversity in the summer, possibly due to competition for nutrients by the wetland vegetation, could account for these unexpectedly low degradation rates. In microcosms incubated at 5 degrees Celsius, about 50 percent of the initial TeCA in solution was converted to daughter products within a 35-day incubation period, indicating that biodegradation in the wetland sediments can continue during cold winter temperatures. Initial pathways of TeCA degradation were the same in the wetland sediment microcosms regardless of the season or sediment collection site, the reduction-oxidation conditions, and the previous exposure of the sediment to contamination. Immediate and simultaneous dichloroelimination and hydrogenolysis, producing 1,2-dichloro-ethene (12DCE) and 1,1,2-trichloroethane (112TCA), respectively, were the initial TeCA degradation pathways in all live microcosm experiments. The production and degradation of vinyl chloride (VC), which is the most toxic of the TeCA daughter compounds, was affected by spatial and seasonal variability, reduction-oxidation condition, and pre-exposure of the wetland sediment. TeCA-amended microcosms constructed with WB30 sediment showed approximately twice as much VC production as those constructed with WB23 sediment. Results of 112TCA-amended microcosms indicated that the greater production of VC in the WB30 sediment resulted from a greater predominance of the 112TCA dichloro-elimination pathway in these sediments. VC degradation also was substantially higher in microcosms constructed with WB30 sediment than those constructed with WB23 sediment, resulting in lower VC concentrations at the end of WB30 microcosms. Enrichment experiments in which microcosm slurry was amended with high initial VC concentrations showed that the spatial difference in VC degradation was negligible after prolonged incubation under methanogenic conditions. Inhibition of methanogenic activity in microcosms by addition of sulfate or of 2-bromoethanesulfonic acid inhibited production and degradation of VC. Inhibition of methanogenesis b

Molecular simulations of diffusion in electrolytes

NASA Astrophysics Data System (ADS)

Wheeler, Dean Richard

This work demonstrates new methodologies for simulating multicomponent diffusion in concentrated solutions using molecular dynamics (MD). Experimental diffusion data for concentrated multicomponent solutions are often lacking, as are accurate methods of predicting diffusion for nonideal solutions. MD can be a viable means of understanding and predicting multicomponent diffusion. While there have been several prior reports of MD simulations of mutual diffusion, no satisfactory expressions for simulating Stefan-Maxwell diffusivities for an arbitrary number of species exist. The approaches developed here allow for the computation of a full diffusion matrix for any number of species in both nonequilibrium and equilibrium MD ensembles. Our nonequilibrium approach is based on the application of constant external fields to drive species diffusion. Our equilibrium approach uses a newly developed Green-Kubo formula for Stefan-Maxwell diffusivities. In addition, as part of this work, we demonstrate a widely applicable means of increasing the computational efficiency of the Ewald sum, a technique for handling long-range Coulombic interactions in simulations. The theoretical development is applicable to any solution which can be simulated using MD; nevertheless, our primary interest is in electrochemical applications. To this end, the methods are tested by simulations of aqueous salt solutions and lithium-battery electrolytes. KCl and NaCl aqueous solutions were simulated over the concentration range 1 to 4 molal. Intermolecular-potential models were parameterized for these transport-based simulations. This work is the first to simulate all three independent diffusion coefficients for aqueous NaCl and KCl solutions. The results show that the nonequilibrium and equilibrium methods are consistent with each other, and in moderate agreement with experiment. We simulate lithium-battery electrolytes containing LiPF6 in propylene carbonate and mixed ethylene carbonate-dimethyl carbonate solvents. As with the aqueous-solution work, potential parameters were generated for these molecules. These nonaqueous electrolytes demonstrate rich transport behavior, which the simulations are able to reproduce qualitatively. In a mixed-solvent simulation we regress all six independent transport coefficients. The simulations show that strong ion pairing is responsible for the increase in viscosity and maximum in conductivity as ion concentrations are increased.

An accelerated algorithm for discrete stochastic simulation of reaction-diffusion systems using gradient-based diffusion and tau-leaping.

PubMed

Koh, Wonryull; Blackwell, Kim T

2011-04-21

Stochastic simulation of reaction-diffusion systems enables the investigation of stochastic events arising from the small numbers and heterogeneous distribution of molecular species in biological cells. Stochastic variations in intracellular microdomains and in diffusional gradients play a significant part in the spatiotemporal activity and behavior of cells. Although an exact stochastic simulation that simulates every individual reaction and diffusion event gives a most accurate trajectory of the system's state over time, it can be too slow for many practical applications. We present an accelerated algorithm for discrete stochastic simulation of reaction-diffusion systems designed to improve the speed of simulation by reducing the number of time-steps required to complete a simulation run. This method is unique in that it employs two strategies that have not been incorporated in existing spatial stochastic simulation algorithms. First, diffusive transfers between neighboring subvolumes are based on concentration gradients. This treatment necessitates sampling of only the net or observed diffusion events from higher to lower concentration gradients rather than sampling all diffusion events regardless of local concentration gradients. Second, we extend the non-negative Poisson tau-leaping method that was originally developed for speeding up nonspatial or homogeneous stochastic simulation algorithms. This method calculates each leap time in a unified step for both reaction and diffusion processes while satisfying the leap condition that the propensities do not change appreciably during the leap and ensuring that leaping does not cause molecular populations to become negative. Numerical results are presented that illustrate the improvement in simulation speed achieved by incorporating these two new strategies.

The diffusive finite state projection algorithm for efficient simulation of the stochastic reaction-diffusion master equation.

PubMed

Drawert, Brian; Lawson, Michael J; Petzold, Linda; Khammash, Mustafa

2010-02-21

We have developed a computational framework for accurate and efficient simulation of stochastic spatially inhomogeneous biochemical systems. The new computational method employs a fractional step hybrid strategy. A novel formulation of the finite state projection (FSP) method, called the diffusive FSP method, is introduced for the efficient and accurate simulation of diffusive transport. Reactions are handled by the stochastic simulation algorithm.

AEROBIC SOIL MICROCOSMS FOR LONG-TERM BIODEGRADATION OF HYDROCARBON VAPORS

EPA Science Inventory

The aims of this research project included the development of laboratory protocols for the preparation of aerobic soil microcosms using aseptic field soil samples, and for the gas chromatographic analysis of hydrocarbon vapor biodegradation based on vapor samples obtained from th...

METRICS OF PERFORMANCE FOR THE SABRE MICROCOSM STUDY (ABSTRACT ONLY)

EPA Science Inventory

The SABRE (Source Area BioREmediation) project will evaluate accelerated anaerobic bioremediation of chlorinated solvents in areas of high concentration, such as DNAPL source areas. In preparation for a field scale pilot test, a laboratory microcosm study was conducted to provide...

CHARACTERIZING THE MICROBIAL COMMUNITY IN SABRE MICROCOSM STUDIES (ABSTRACT ONLY)

EPA Science Inventory

The SABRE (Source Area BioREmediation) project will evaluate accelerated anaerobic bioremediation of chlorinated solvents in areas of high concentration, such as DNAPL source areas. In preparation for a field scale pilot test, laboratory microcosm and column studies were conducte...

Exposure of Sink Drain Microcosms to Triclosan: Population Dynamics and Antimicrobial Susceptibility

PubMed Central

McBain, Andrew J.; Bartolo, Robert G.; Catrenich, Carl E.; Charbonneau, Duane; Ledder, Ruth G.; Price, Bradford B.; Gilbert, Peter

2003-01-01

Recent concern that the increased use of triclosan (TCS) in consumer products may contribute to the emergence of antibiotic resistance has led us to examine the effects of TCS dosing on domestic-drain biofilm microcosms. TCS-containing domestic detergent (TCSD) markedly lowered biofouling at 50% (wt/vol) but was poorly effective at use levels. Long-term microcosms were established and stabilized for 6 months before one was subjected to successive 3-month exposures to TCSD at sublethal concentrations (0.2 and 0.4% [wt/vol]). Culturable bacteria were identified by 16S rDNA sequence analysis, and their susceptibilities to four biocides and six antibiotics were determined. Microcosms harbored ca. 10 log10 CFU/g of biofilm, representing at least 27 species, mainly gamma proteobacteria, and maintained dynamic stability. Viable cell counts were largely unaffected by TCSD exposure, but species diversity was decreased, as corroborated by denaturing gradient gel electrophoresis analysis. TCS susceptibilities ranged widely within bacterial groups, and TCS-tolerant strains (including aeromonads, pseudomonads, stenotrophomonads, and Alcaligenes spp.) were isolated before and after TCSD exposure. Several TCS-tolerant bacteria related to Achromobacter xylosoxidans became clonally expanded during dosing. TCSD addition did not significantly affect the community profiles of susceptibility to the test biocides or antibiotics. Several microcosm isolates, as well as reference bacteria, caused clearing of particulate TCS in solid media. Incubations of consortia and isolates with particulate TCS in liquid led to putative TCS degradation by the consortia and TCS solubilization by the reference strains. Our results support the view that low-level exposure of environmental microcosms to TCS does not affect antimicrobial susceptibility and that TCS is degradable by common domestic biofilms. PMID:12957932

Influence of phosphate and copper on reductive dechlorination of thiobencarb in California rice field soils.

PubMed

Gunasekara, Amrith S; Tenbrook, Patti L; Palumbo, Amanda J; Johnson, Catherine S; Tjeerdema, Ronald S

2005-12-28

The potential for reductive dechlorination of the herbicide thiobencarb (TB) by microbes and its prevention in saturated anaerobic rice field soils was examined in laboratory microcosms. TB is effective in controlling both annual grasses and broadleaf weeds. In anoxic microcosms, TB was effectively degraded within 30 days to its dechlorinated product, deschlorothiobencarb (DTB), in two Sacramento Valley rice field soils. TB dechlorination, and subsequent degradation, followed pseudo-zero- (lag phase) and first-order (degradation phase) kinetics. Logistic regression analysis (r2 > 0.841) produced a half-life (t(1/2)) in nonsterile soils ranging from 10 to 15 days, which was also observed when microcosms were amended with low concentrations (<3 mg L(-1)) of copper (Cu2+; as the fungicides Cu(OH)2 and CuSO4.5H2O). High Cu2+ concentrations (>40 mg L(-1)) were added to the microcosms to determine if copper toxicity to dechlorinating microbes is concentration dependent within the range used. After 30 days, the low-copper-amended soils closely resembled the nonsterile experiments to which no Cu2+ was added while the high-copper-amended microcosms were similar to the sterile experiment. Microcosms were also separately amended with 5.7 g L(-1) phosphate (PO4(2-); as KH2PO4), a nutrient regularly applied to rice fields. Phosphate-amended experiments also showed TB degradation, but no DTB formation, indicating the phosphate played a role, possibly as a microbial inhibitor or an alternative electron acceptor, in limiting the dechlorination of TB. In summary, TB dechlorination was inhibited at high Cu(OH)2, CuSO4.5H2O, and KH2PO4 concentrations.

Pyrene degradation in forest humus microcosms with or without pine and its mycorrhizal fungus.

PubMed

Koivula, Teija T; Salkinoja-Salonen, Mirja; Peltola, Rainer; Romantschuk, Martin

2004-01-01

The mineralization potential of forest humus and the self-cleaning potential of a boreal coniferous forest environment for polycyclic aromatic hydrocarbon (PAH) compounds was studied using a model ecosystem of acid forest humus (pH = 3.6) and pyrene as the model compound. The matrix was natural humus or humus mixed with oil-polluted soil in the presence and absence of Scots pine (Pinus sylvestris L.) and its mycorrhizal fungus (Paxillus involutus). The rates of pyrene mineralization in the microcosms with humus implants (without pine) were initially insignificant but increased from Day 64 onward to 47 microg kg(-1) d(-1) and further to 144 microg kg(-1) d(-1) after Day 105. In the pine-planted humus microcosms the rate of mineralization also increased, reaching 28 microg kg(-1) d(-1) after Day 105. The 14CO2 emission was already considerable in nonplanted microcosms containing oily soil at Day 21 and the pyrene mineralization continued throughout the study. The pyrene was converted to CO2 at rates of 0.07 and 0.6 microg kg(-1) d(-1) in the oily-soil implanted microcosms with and without pine, respectively. When the probable assimilation of 14CO2 by the pine and ground vegetation was taken into account the most efficient microcosm mineralized 20% of the 91.2 mg kg(-1) pyrene in 180 d. The presence of pine and its mycorrhizal fungus had no statistically significant effect on mineralization yields. The rates of pyrene mineralization observed in this study for forest humus exceeded the total annual deposition rate of PAHs in southern Finland. This indicates that accumulation in forest soil is not to be expected.

Diversity and Dynamics of Microbial Community Structure in Different Mangrove, Marine and Freshwater Sediments During Anaerobic Debromination of PBDEs

PubMed Central

Wang, Ya Fen; Zhu, Hao Wen; Wang, Ying; Zhang, Xiang Ling; Tam, Nora Fung Yee

2018-01-01

Little is known about the diversity and succession of indigenous microbial community during debromination of polybrominated diphenyl ethers (PBDEs). This study examined the diversity and dynamics of microbial community structure in eight saline (mangrove and marine) and freshwater sediment microcosms exhibiting different debrominating capabilities for hexa-BDE 153, a common congener in sediments, using terminal restriction fragment length polymorphism (T-RFLP) and clone library analyses. The results showed that microbial community structure greatly differed between the saline and freshwater microcosms, likely leading to distinct variations in their debrominating capabilities and pathways. Higher relative abundances of Chloroflexi and Deltaproteobacteria succeed by Alphaproteobacteria and Betaproteobacteria were detected in the two mangrove microcosms with the fastest debrominating capabilities mainly via para pathway, respectively; the dominance of Alphaproteobacteria resulted in less accumulation of tetra-BDEs and more complete debromination of lower brominated congeners (from di- to tetra-BDEs). Meanwhile, the shifts in both microbial community structure and PBDE profiles were relatively small in the less efficient freshwater microcosms, with relatively more ortho and meta brominated products of BDE-153 resulted. Coincidently, one of the freshwater microcosms showed sudden increases of Chloroflexi and Deltaproteobacteria by the end of incubation, which synchronized with the increase in the removal rate of BDE-153. The significant relationship between microbial community structure and PBDEs was confirmed by redundancy analysis (18.7% of total variance explained, P = 0.002). However, the relative abundance of the well-known dechlorinator Dehalococcoides showed no clear correlation with the debrominating capability across different microcosms. These findings shed light in the significance of microbial community network in different saline environments on enhancement of PBDE intrinsic debromination. PMID:29867858

Diversity and Dynamics of Microbial Community Structure in Different Mangrove, Marine and Freshwater Sediments During Anaerobic Debromination of PBDEs.

PubMed

Wang, Ya Fen; Zhu, Hao Wen; Wang, Ying; Zhang, Xiang Ling; Tam, Nora Fung Yee

2018-01-01

Little is known about the diversity and succession of indigenous microbial community during debromination of polybrominated diphenyl ethers (PBDEs). This study examined the diversity and dynamics of microbial community structure in eight saline (mangrove and marine) and freshwater sediment microcosms exhibiting different debrominating capabilities for hexa-BDE 153, a common congener in sediments, using terminal restriction fragment length polymorphism (T-RFLP) and clone library analyses. The results showed that microbial community structure greatly differed between the saline and freshwater microcosms, likely leading to distinct variations in their debrominating capabilities and pathways. Higher relative abundances of Chloroflexi and Deltaproteobacteria succeed by Alphaproteobacteria and Betaproteobacteria were detected in the two mangrove microcosms with the fastest debrominating capabilities mainly via para pathway, respectively; the dominance of Alphaproteobacteria resulted in less accumulation of tetra-BDEs and more complete debromination of lower brominated congeners (from di- to tetra-BDEs). Meanwhile, the shifts in both microbial community structure and PBDE profiles were relatively small in the less efficient freshwater microcosms, with relatively more ortho and meta brominated products of BDE-153 resulted. Coincidently, one of the freshwater microcosms showed sudden increases of Chloroflexi and Deltaproteobacteria by the end of incubation, which synchronized with the increase in the removal rate of BDE-153. The significant relationship between microbial community structure and PBDEs was confirmed by redundancy analysis (18.7% of total variance explained, P = 0.002). However, the relative abundance of the well-known dechlorinator Dehalococcoides showed no clear correlation with the debrominating capability across different microcosms. These findings shed light in the significance of microbial community network in different saline environments on enhancement of PBDE intrinsic debromination.

Evaluation of aquatic sediment microcosms and their use in assessing possible effects of introduced microorganisms on ecosystem parameters.

PubMed Central

Wagner-Döbler, I; Pipke, R; Timmis, K N; Dwyer, D F

1992-01-01

In this paper we describe a sediment microcosm system consisting of 20 undisturbed, layered sediment cores with overlying site water which are incubated under identical conditions of temperature, light, stirring rate of overlying water, and water exchange rate. Ecosystem parameters (nutrient level, photosynthetic potential, community structure of heterotrophic bacteria, thymidine incorporation rate, and oxygen microgradients) of the laboratory microcosms and the source ecosystem were compared and shown to be indistinguishable for the first 2 weeks. In weeks 3 and 4, small differences were detectable in the nutrient level, community structure of heterotrophic bacteria, and thymidine incorporation rate. However, the photosynthetic potential, depth profiles of heterotrophic bacterial community structure, and oxygen microgradients were maintained throughout the incubation period and did not differ between laboratory microcosms and the source ecosystem. The microcosm system described here would thus appear to be a valid model of aquatic sediments for up to 4 weeks; the actual period would depend on the sediment source and incubation temperature. The validated systems were used with Rhine river sediment to assess possible effects on ecosystem parameters of Pseudomonas sp. strain B13 FR1(pFRC20P), a genetically engineered microorganism (GEM) that had been constructed to degrade mixtures of halo- and alkylbenzoates and -phenols. The GEM survived in the surface sediment at densities of 5 x 10(4) to 5 x 10(5)/g (dry weight) for 4 weeks and degraded added chloro- and methylaromatics. The GEM did not measurably influence ecosystem parameters such as photosynthesis, densities of selected heterotrophic bacteria, thymidine incorporation rate, and oxygen microgradients. Thus, the microcosm system described here would seem to be useful for the study of the ecology of biodegradation and the fate and effect of microorganisms introduced into the environment. PMID:1599244

Efficiency of surfactant-enhanced bioremediation of aged polycyclic aromatic hydrocarbon-contaminated soil: Link with bioavailability and the dynamics of the bacterial community.

PubMed

Cecotti, Martina; Coppotelli, Bibiana M; Mora, Verónica C; Viera, Marisa; Morelli, Irma S

2018-09-01

Shifts in the bacterial-community dynamics, bioavailability, and biodegradation of polycyclic aromatic hydrocarbons (PAHs) of chronically contaminated soil were analyzed in Triton X-100-treated microcosms at the critical micelle concentration (T-CMC) and at two sub-CMC doses. Only the sub-CMC-dose microcosms reached sorbed-PAH concentrations significantly lower than the control: 166±32 and 135±4mgkg -1 dry soil versus 266±51mgkg -1 ; consequently an increase in high- and low-molecular-weight PAHs biodegradation was observed. After 63days of incubation pyrosequencing data evidenced differences in diversity and composition between the surfactant-modified microcosms and the control, with those with sub-CMC doses containing a predominance of the orders Sphingomonadales, Acidobacteriales, and Gemmatimonadales (groups of known PAHs-degrading capability). The T-CMC microcosm exhibited a lower richness and diversity index with a marked predominance of the order Xanthomonadales, mainly represented by the Stenotrophomonas genus, a PAHs- and Triton X-100-degrading bacterium. In the T-CMC microcosm, whereas the initial surface tension was 35mNm -1 , after 63days of incubation an increase up to 40mNm -1 was registered. The previous observation and the gas-chromatography data indicated that the surfactant may have been degraded at the CMC by a highly selective bacterial community with a consequent negative impact on PAHs biodegradation. This work obtained strong evidence for the involvement of physicochemical and biologic influences determining the different behaviors of the studied microcosms. The results reported here contribute significantly to an optimization of, surfactant-enhanced bioremediation strategies for chronically contaminated soil since the application of doses below the CMC would reduce the overall costs. Copyright © 2018 Elsevier B.V. All rights reserved.

Non-target effects on aquatic decomposer organisms of imidacloprid as a systemic insecticide to control emerald ash borer in riparian trees.

PubMed

Kreutzweiser, David; Good, Kevin; Chartrand, Derek; Scarr, Taylor; Thompson, Dean

2007-11-01

Imidacloprid is effective against emerald ash borer when applied as a systemic insecticide. Following stem or soil injections to trees in riparian areas, imidacloprid residues could be indirectly introduced to aquatic systems via leaf fall or leaching. Either route of exposure may affect non-target, aquatic decomposer organisms. Leaves from ash trees treated with imidacloprid at two field rates and an intentionally-high concentration were added to aquatic microcosms. Leaves from trees treated at the two field rates contained imidacloprid concentrations of 0.8-1.3 ppm, and did not significantly affect leaf-shredding insect survival, microbial respiration or microbial decomposition rates. Insect feeding rates were significantly inhibited at foliar concentrations of 1.3 ppm but not at 0.8 ppm. Leaves from intentionally high-dose trees contained concentrations of about 80 ppm, and resulted in 89-91% mortality of leaf-shredding insects, but no adverse effects on microbial respiration and decomposition rates. Imidacloprid applied directly to aquatic microcosms to simulate leaching from soils was at least 10 times more toxic to aquatic insects than the foliar concentrations, with high mortality at 0.13 ppm and significant feeding inhibition at 0.012 ppm.

Experimental investigation of the effects of aromatic hydrocarbons on a sediment food web. University research initiative. Final draft report

DOE Office of Scientific and Technical Information (OSTI.GOV)

Carman, K.R.; Fleeger, J.W.; Pomarico, S.M.

1994-07-01

The influence of polynuclear aromatic hydrocarbons (PAH) on a sedimentary salt-marsh food web was examined using microcosm and laboratory experiments that simulated natural conditions. Microcosms were dosed with concentrations of PAH-contaminated sediment collected from a produced water site at Pass Fourchon, LA. Bacterial activity and abundance were not influenced by PAH, but microalgal activity and physiological condition were. Grazing by copepods on benthic microalgae was not significantly influenced by PAH concentration, nor was the physiological condition of copepods. Meiofaunal community composition was influenced by PAH, as nematodes became disproportionally abundant, and the nauplius/copepod ratio increased in high-PAH treatments. Overall, sublethalmore » effects of PAH were not pronounced at the concentrations (0.3 to 3.0 ppm) we examined. Fish-predation studies indicated that Leiostomus xanthurus could not detect PAH-contaminated sediments, and continued to feed normally when exposed to them. PAH contamination did not decrease the number of feeding strikes or sediment processing time. This lack of ability to discriminate between contaminated and uncontaminated sediments could have serious implications in terms of bioaccumulation of PAH (or other contaminants) by these bottom-feeding fish.« less

Herbicide mitigation in microcosms simulating stormwater basins subject to polluted water inputs.

PubMed

Bois, P; Huguenot, D; Jézéquel, K; Lollier, M; Cornu, J Y; Lebeau, T

2013-03-01

Non-point source pollution as a result of wine-growing activity is of high concern. Stormwater basins (SWB) found downstream of vineyard watersheds could show a potential for the mitigation of runoff water containing herbicides. In this study, mitigation of vinery-used herbicides was studied in microcosms with a very similar functioning to that recorded in SWB. Mitigation efficiency of glyphosate, diuron and 3,4-dichloroaniline (3,4-DCA) was investigated by taking into account hydraulic flow rate, mitigation duration, bioaugmentation and plant addition. Mitigation efficiency measured in water ranged from 63.0% for diuron to 84.2% for 3,4-DCA and to 99.8% for glyphosate. Water-storage duration in the SWB and time between water supplies were shown to be the most influential factors on the mitigation efficiency. Six hours water-storage duration allowed an efficient sorption of herbicides and their degradation by indigenous microorganisms in 5 weeks. Neither bioaugmentation nor plant addition had a significant effect on herbicide mitigation. Our results show that this type of SWB are potentially relevant for the mitigation of these herbicides stemming from wine-growing activity, providing a long enough hydraulic retention time. Copyright © 2012 Elsevier Ltd. All rights reserved.

Prediction and validation of diffusion coefficients in a model drug delivery system using microsecond atomistic molecular dynamics simulation and vapour sorption analysis.

PubMed

Forrey, Christopher; Saylor, David M; Silverstein, Joshua S; Douglas, Jack F; Davis, Eric M; Elabd, Yossef A

2014-10-14

Diffusion of small to medium sized molecules in polymeric medical device materials underlies a broad range of public health concerns related to unintended leaching from or uptake into implantable medical devices. However, obtaining accurate diffusion coefficients for such systems at physiological temperature represents a formidable challenge, both experimentally and computationally. While molecular dynamics simulation has been used to accurately predict the diffusion coefficients, D, of a handful of gases in various polymers, this success has not been extended to molecules larger than gases, e.g., condensable vapours, liquids, and drugs. We present atomistic molecular dynamics simulation predictions of diffusion in a model drug eluting system that represent a dramatic improvement in accuracy compared to previous simulation predictions for comparable systems. We find that, for simulations of insufficient duration, sub-diffusive dynamics can lead to dramatic over-prediction of D. We present useful metrics for monitoring the extent of sub-diffusive dynamics and explore how these metrics correlate to error in D. We also identify a relationship between diffusion and fast dynamics in our system, which may serve as a means to more rapidly predict diffusion in slowly diffusing systems. Our work provides important precedent and essential insights for utilizing atomistic molecular dynamics simulations to predict diffusion coefficients of small to medium sized molecules in condensed soft matter systems.

Molecular dynamics simulation of metallic impurity diffusion in liquid lead-bismuth eutectic (LBE)

NASA Astrophysics Data System (ADS)

Gao, Yun; Takahashi, Minoru; Cavallotti, Carlo; Raos, Guido

2018-04-01

Corrosion of stainless steels by lead-bismuth eutectic (LBE) is an important problem which depends, amongst other things, on the diffusion of the steel components inside this liquid alloy. Here we present the results of classical molecular dynamics simulations of the diffusion of Fe and Ni within LBE. The simulations complement experimental studies of impurity diffusion by our group and provide an atomic-level understanding of the relevant diffusion phenomena. They are based on the embedded atom method (EAM) to represent many-body interactions among atoms. The EAM potentials employed in our simulations have been validated against ab initio density functional calculations. We show that the experimental and simulation results for the temperature-dependent viscosity of LBE and the impurity diffusion coefficients can be reconciled by assuming that the Ni and Fe diffuse mainly as nanoscopic clusters below 1300 K. The average Fe and Ni cluster sizes decrease with increasing the temperature and there is essentially single-atom diffusion at higher temperatures.

Steady and Unsteady Simulations of the Flow in an Impeller/Diffuser Stage

NASA Technical Reports Server (NTRS)

Canabal, Francisco; Dorney, Daniel J.; Garcia, Roberto; Turner, James E. (Technical Monitor)

2002-01-01

SLI engine designs will require pumps to throttle over a wide flow range while maintaining high performance. Unsteadiness generated by impeller/diffuser interaction is one of the major factors affecting off-design performance. Initial unsteady simulations are completed for impeller/diffuser stage. The Corsair simulations will continue across a wide flow range and for inducer/impeller/diffuser combinations. Results of unsteady simulations are being used to guide and explore new designs.

Behavior and Fate of PFOA and PFOS in Sandy Aquifer Sediment (journal)

EPA Science Inventory

Microcosms were constructed with sediment from beneath a landfill that received waste containing PFOA (perfluorooctanoic acid) and PFOS (perfluorooctane sulfonate). The microcosms were amended with PFOA and PFOS, and sampled after 91, 210, 343, 463, 574, and 740 days of incubat...

BIODEGRADATION OF A PAH MIXTURE BY NATIVE SUBSURFACE MICROBIOTA. (R828770)

EPA Science Inventory

Laboratory microcosm studies were conducted to estimate biodegradation rates for a mixture of five polycyclic aromatic hydrocarbon compounds (PAHs). Static microcosms were assembled using soil samples from two locations collected at a No. 2 fuel oil-contaminated site in the At...

ANAEROBIC BIODEGRADATION OF ALKYLBENZENES IN LABORATORY MICROCOSMS REPRESENTING AMBIENT CONDITIONS

EPA Science Inventory

A microcosm study was performed to document the anaerobic biodegradation of benzene, toluene, ethylbenzene, m- xylene, and/or o-xylene in petroleum-contaminated aquifer sediment from sites in Michigan (MI) and North Carolina (NC) and relate the results to previous field investiga...

Biodegradation of trichloroethylene and its anaerobic daughter products in freshwater wetland sediments

USGS Publications Warehouse

Lorah, M.M.; Olsen, L.D.

2001-01-01

Laboratory microcosms were prepared under methanogenic, sulfate-reducing, and aerobic conditions using sediment and groundwater from a freshwater wetland that is a discharge area for a trichloroethylene (TCE) to evaluate potential biodegradation rates of TCE and its anaerobic daughter products (cis-1,2-dichloroethylene, trans-1,2-dichloroethylene, and vinyl chloride (VC)). Anaerobic degradation of TCE was about an order of magnitude faster under methanogenic conditions than under sulfate-reducing conditions. Both 12DCE and VC were found under sulfate-reducing conditions in the microcosms containing the wetland sediment, but their production, especially for VC, was substantially slower than under methanogenic conditions. Methane concentrations remained approximately constant (when losses in the formalin-amended controls are considered) in the microcosms amended with TCE and increased in the microcosms amended with the 12DCE isomers and VC during the first 18-25 days of incubation. The most rapid decrease in concentrations of TCE, cis-12DCE, trans-12DCE, and VC was found after aerobic methane-oxidizing conditions were definitely established.

Soil metabarcoding identifies season indicators and differentiators of pig and Agrostis/Festuca spp. decomposition.

PubMed

Olakanye, Ayodeji O; Ralebitso-Senior, T Komang

2018-04-15

To gain a better understanding of how environmental microbiota respond to cadaver decomposition, a forensic ecogenomic study was made with soil only control and 4g each of Sus scrofa domesticus and plant litter (Agrostis/Festuca spp.) buried individually in a sandy clay loam (80g) in sealed but perforated triplicate microcosms. The next-generation sequencing (Illumina Miseq) of the soil bacteria (16S rRNA gene) clade revealed seasonal taxomonic shifts at genus-level for the pig and plant litter microcosms compared to the non-burial controls. In particular, numerical abundances of Sphingobacterium (5.9%) and Pedobacter (24.1%) for the pig microcosms, and Rhodanobacter (18.1%) and Shinella (4.6%) for the plant litter microcosms, identified bacterial genera that could be tracked to establish a (seasonal) subsurface postmortem microbial clock. Also, family-level resolution revealed members that were unique to the control, grass and pig soils after 365 days. Copyright © 2018 Elsevier B.V. All rights reserved.

Control of pore geometry in soil microcosms and its effect on the growth and spread of Pseudomonas and Bacillus sp.

NASA Astrophysics Data System (ADS)

Otten, Wilfred; Juyal, Archana; Eickhorst, Thilo; Falconer, Ruth; Spiers, Andrew; Baveye, Philippe

2017-04-01

The way micro-organisms access C and interact with each other in heterogeneous environments is key to our understanding of soil processes. Growth and mobility of bacteria is crucial aspect of these processes in particular how this is affected by complicated pathways of water and air-filled pores. Simplified experimental systems, often referred to with the term microcosms, have played a central role in the development of modern ecological thinking ranging from competitive exclusion to examination of spatial resources and competitive mechanisms, with important model driven insights to the field. However, in the majority of cases these do not include detailed description of the soil physical conditions and hence there is still little insight in how soil structure affects these processes. Recent advances in the use of Xray CT now allow for a different approach to this as we can obtain quantitative insight in to the pathways of interaction and how these are controlled in microcosms. In the current presentation we therefor ask the following questions: - To what extent can we control the pore geometry in microcosm studies through manipulation of common variables such as density and aggregate size? Are replicated microcosms really replicated at the microscale? - What is the effect of pore geometry on the growth dynamics of bacteria following introduction into soil? - What is the effect of pore geometry on the rate and extent of spread of bacteria in soil? We focus on Pseudomonas sp. and Bacillus sp. Both species are abundantly present in the rhizosphere and bulk-soil, frequently studied for their growth promoting ability, yet there is still very little knowledge available on how the growth and spread is affected by soil physical conditions such as pore geometry and wetness. We show how pore geometry, connectivity and interface areas are affected by the way soil is packed into microcosms and how this affects growth and spread of both species. We emphasize that microscopic heterogeneity has significant impact on bacterial dynamics and that soil physical conditions need to be considered in greater detail in microcosm studies to ensure generalisation of results.

Multivariate analysis of the impacts of the turbine fuel JP-4 in a microcosm toxicity test with implications for the evaluation of ecosystem dynamics and risk assessment.

PubMed

Landis, W G; Matthews, R A; Markiewicz, A J; Matthews, G B

1993-12-01

Turbine fuels are often the only aviation fuel available in most of the world. Turbine fuels consist of numerous constituents with varying water solubilities, volatilities and toxicities. This study investigates the toxicity of the water soluble fraction (WSF) of JP-4 using the Standard Aquatic Microcosm (SAM). Multivariate analysis of the complex data, including the relatively new method of nonmetric clustering, was used and compared to more traditional analyses. Particular emphasis is placed on ecosystem dynamics in multivariate space.The WSF is prepared by vigorously mixing the fuel and the SAM microcosm media in a separatory funnel. The water phase, which contains the water-soluble fraction of JP-4 is then collected. The SAM experiment was conducted using concentrations of 0.0, 1.5 and 15% WSF. The WSF is added on day 7 of the experiments by removing 450 ml from each microcosm including the controls, then adding the appropriate amount of toxicant solution and finally bringing the final volume to 3 L with microcosm media. Analysis of the WSF was performed by purge and trap gas chromatography. The organic constituents of the WSF were not recoverable from the water column within several days of the addition of the toxicant. However, the impact of the WSF on the microcosm was apparent. In the highest initial concentration treatment group an algal bloom ensued, generated by the apparent toxicity of the WSF of JP-4 to the daphnids. As the daphnid populations recovered the algal populations decreased to control values. Multivariate methods clearly demonstrated this initial impact along with an additional oscillation seperating the four treatment groups in the latter segment of the experiment. Apparent recovery may be an artifact of the projections used to describe the multivariate data. The variables that were most important in distinguishing the four groups shifted during the course of the 63 day experiment. Even this simple microcosm exhibited a variety of dynamics, with implications for biomonitoring schemes and ecological risk assessments.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Morton, R.D.; Duke, T.W.; Macauley, J.M.

Effects of a used drilling fluid on an experimental seagrass community (Thalassia testudinum) were measured by exposing the community to the suspended particulate phase (SPP) in laboratory microcosms. Structure of the macroinvertebrate assemblage, growth and chlorophyll content of grass and associated epiphytes, and rates of decomposition as indicated by weight loss of grass leaves in treated and untreated microcosms were compared. There were statistically significant differences in community structure and function among untreated microcosms and those receiving the clay and drilling fluid. For example, drilling fluid and clay caused a significant loss in the number of the ten most numericallymore » abundant (dominant) macroinvertebrates, and drilling fluid decreased the rate at which Thalassia leaves decomposed.« less

Predicting the response of soil organic matter microbial decomposition to moisture

NASA Astrophysics Data System (ADS)

Chenu, Claire; Garnier, Patricia; Monga, Olivier; Moyano, Fernando; Pot, Valérie; Nunan, Naoise; Coucheney, Elsa; Otten, Wilfred

2014-05-01

Next to temperature, soil moisture is a main driver of soil C and N transformations in soils, because it affects microbial activity and survival. The moisture sensitivity of soil organic matter decay may be a source of uncertainty of similar magnitude to that of the temperature sensitivity and receives much less attention. The basic concepts and mechanisms relating soil water to microorganisms were identified early (i.e. in steady state conditions : direct effects on microbial physiology, diffusion substrates, nutrients, extracellular enzymes, diffusion of oxygen, movement of microorganisms). However, accounting for how moisture controls soil microbial activity remains essentially empirical and poorly accounts for soil characteristics. Soil microorganisms live in a complex 3-D framework of mineral and organic particles defining pores of various sizes, connections with adjacent pores, and with pore walls of contrasted nature, which result in a variety of microhabitats. The water regime to which microorganisms are exposed can be predicted to depend the size and connectivity of pores in which they are located. Furthermore, the spatial distribution of microorganisms as well as that of organic matter is very heterogeneous, determining the diffusion distances between substrates and decomposers. A new generation of pore scale models of C dynamics in soil may challenge the difficulty of modelling such a complex system. These models are based on an explicit representation of soil structure (i.e. soil particles and voids), microorganisms and organic matter localisation. We tested here the ability of such a model to account for changes in microbial respiration with soil moisture. In the model MOSAIC II, soil pore space is described using a sphere network coming from a geometrical modelling algorithm. MicroCT tomography images were used to implement this representation of soil structure. A biological sub-model describes the hydrolysis of insoluble SOM into dissolved organic matter, its assimilation, respiration and microbial mortality. A recent improvement of the model was the description of the diffusion of soluble organic matter. We tested the model using the results from an experiment where a simple substrate (fructose) was decomposed by bacteria within a simple media (sand). Separate incubations in microcosms were carried out using five different bacterial communities at two different moisture conditions corresponding to water potentials of -0.01 and -0.1 bars. We calibrated the biological parameters using the experimental data obtained at high water content and we tested the model without any parameters change at low water content. Both the experiments and simulations showed a decrease in mineralisation with a decrease of water content, of which pattern depended on the bacterial species and its physiological characteristics. The model was able to correctly simulate the decrease of connectivity between substrate and microorganism due the decrease of water content. The potential and required developments of such models in describing how heterotrophic respiration is affected by micro-scale distribution and processes in soils and in testing scenarios regarding water regimes in a changing climate is discussed.

Freud, Problem Solving, Ethnicity, and Race: Integrating Psychology into the Interdisciplinary Core Curriculum.

ERIC Educational Resources Information Center

Dunn, Dana S.

The new core curriculum at Moravian College, in Pennsylvania, utilizes an interdisciplinary approach, integrating topics of psychology into three of the seven core courses: "Microcosm/Macrocosm"; "Quantitative Problem Solving"; and the seminar "Gender, Ethnicity, and Race." The course "Microcosm/Macrocosm"…

Evolution in a Test Tube: Rise of the Wrinkly Spreaders

ERIC Educational Resources Information Center

Green, Jennifer H.; Koza, Anna; Moshynets, Olena; Pajor, Radoslaw; Ritchie, Margaret R.; Spiers, Andrew J.

2011-01-01

Understanding evolutionary mechanisms is fundamental to a balanced biological education, yet practical demonstrations are rarely considered. In this paper we describe a bacterial liquid microcosm which can be used to demonstrate aspects of evolution, namely adaptive radiation, niche colonisation and competitive fitness. In microcosms inoculated…

BIODEGRADATION OF A PAH MIXTURE BY NATIVE SUBSURFACE MICROBIOTA. (R828770C004)

EPA Science Inventory

Laboratory microcosm studies were conducted to estimate biodegradation rates for a mixture of five polycyclic aromatic hydrocarbon compounds (PAHs). Static microcosms were assembled using soil samples from two locations collected at a No. 2 fuel oil-contaminated site in the At...

EFFECTS OF MICROCOSM PREPARATION ON RATES OF TOLUENE BIODEGRADATION UNDER DENITRIFYING CONDITIONS

EPA Science Inventory

Microcosms were prepared with subsurface material from two aquifers to examine the effects of preparation methods on rates of toluene biodegradation under denitrifying conditions. In both cases, the data fit a zero-order kinetics plot. However, rates of removal were generally pro...

Effect of Biochar on Greenhouse Gas Emissions and Nitrogen Cycling in Laboratory and Field Experiments

NASA Astrophysics Data System (ADS)

Hagemann, Nikolas; Harter, Johannes; Kaldamukova, Radina; Ruser, Reiner; Graeff-Hönninger, Simone; Kappler, Andreas; Behrens, Sebastian

2014-05-01

The extensive use of nitrogen (N) fertilizers in agriculture is a major source of anthropogenic N2O emissions contributing 8% to global greenhouse gas emissions. Soil biochar amendment has been suggested as a means to reduce both CO2 and non-CO2 greenhouse gas emissions. The reduction of N2O emissions by biochar has been demonstrated repeatedly in field and laboratory experiments. However, the mechanisms of the reduction remain unclear. Further it is not known how biochar field-weathering affects GHG emissions and how agro-chemicals, such as the nitrification inhibitor 3,4-dimethylpyrazole phosphate (DMPP), that is often simultaneously applied together with commercial N-fertilizers, impact nitrogen transformation and N2O emissions from biochar amended soils. In order investigate the duration of the biochar effect on soil N2O emissions and its susceptibility to DMPP application we performed a microcosm and field study with a high-temperature (400 ° C) beech wood derived biochar (60 t ha-1 and 5 % (w/w) biochar in the field and microcosms, respectively). While the field site contained the biochar already for three years, soil and biochar were freshly mixed for the laboratory microcosm experiments. In both studies we quantified GHG emissions and soil nitrogen speciation (nitrate, nitrite, ammonium). While the field study was carried out over the whole vegetation period of the sunflower Helianthus annuus L., soil microcosm experiments were performed for up to 9 days at 28° C. In both experiments a N-fertilizer containing DMPP was applied either before planting of the sunflowers or at the beginning of soil microcosms incubation. Laboratory microcosm experiments were performed at 60% water filled pore space reflecting average field conditions. Our results show that biochar effectively reduced soil N2O emissions by up to 60 % in the field and in the soil microcosm experiments. No significant differences in N2O emission mitigation potential between field-aged and fresh biochar were observed for the specific biochar used in this study. N2O emission reduction occurred even in the presence of DMPP in the field and in the laboratory microcosms. Our results suggest that simultaneous measurements of soil samples from the same field site in the laboratory yield similar biochar effects to those quantified in the field and that the mechanisms of N2O mitigation seem to be independent of plant growth and application of the commercial nitrification inhibitor DMPP.

A model for self-diffusion of guanidinium-based ionic liquids: a molecular simulation study.

PubMed

Klähn, Marco; Seduraman, Abirami; Wu, Ping

2008-11-06

We propose a novel self-diffusion model for ionic liquids on an atomic level of detail. The model is derived from molecular dynamics simulations of guanidinium-based ionic liquids (GILs) as a model case. The simulations are based on an empirical molecular mechanical force field, which has been developed in our preceding work, and it relies on the charge distribution in the actual liquid. The simulated GILs consist of acyclic and cyclic cations that were paired with nitrate and perchlorate anions. Self-diffusion coefficients are calculated at different temperatures from which diffusive activation energies between 32-40 kJ/mol are derived. Vaporization enthalpies between 174-212 kJ/mol are calculated, and their strong connection with diffusive activation energies is demonstrated. An observed formation of cavities in GILs of up to 6.5% of the total volume does not facilitate self-diffusion. Instead, the diffusion of ions is found to be determined primarily by interactions with their immediate environment via electrostatic attraction between cation hydrogen and anion oxygen atoms. The calculated average time between single diffusive transitions varies between 58-107 ps and determines the speed of diffusion, in contrast to diffusive displacement distances, which were found to be similar in all simulated GILs. All simulations indicate that ions diffuse by using a brachiation type of movement: a diffusive transition is initiated by cleaving close contacts to a coordinated counterion, after which the ion diffuses only about 2 A until new close contacts are formed with another counterion in its vicinity. The proposed diffusion model links all calculated energetic and dynamic properties of GILs consistently and explains their molecular origin. The validity of the model is confirmed by providing an explanation for the variation of measured ratios of self-diffusion coefficients of cations and paired anions over a wide range of values, encompassing various ionic liquid classes as well as the simulated GILs. The proposed diffusion model facilitates the qualitative a priori prediction of the impact of ion modifications on the diffusive characteristics of new ionic liquids.

Dynamic changes in the structure of microbial communities in Baltic Sea coastal seawater microcosms modified by crude oil, shale oil or diesel fuel.

PubMed

Viggor, Signe; Juhanson, Jaanis; Jõesaar, Merike; Mitt, Mario; Truu, Jaak; Vedler, Eve; Heinaru, Ain

2013-08-25

The coastal waters of the Baltic Sea are constantly threatened by oil spills, due to the extensive transportation of oil products across the sea. To characterise the hydrocarbon-degrading bacterial community of this marine area, microcosm experiments on diesel fuel, crude oil and shale oil were performed. Analysis of these microcosms, using alkane monooxygenase (alkB) and 16S rRNA marker genes in PCR-DGGE experiments, demonstrated that substrate type and concentration strongly influence species composition and the occurrence of alkB genes in respective oil degrading bacterial communities. Gammaproteobacteria (particularly the genus Pseudomonas) and Alphaproteobacteria were dominant in all microcosms treated with oils. All alkB genes carried by bacterial isolates (40 strains), and 8 of the 11 major DGGE bands from the microcosms, had more than 95% sequence identity with the alkB genes of Pseudomonas fluorescens. However, the closest relatives of the majority of sequences (54 sequences from 79) of the alkB gene library from initially collected seawater DNA were Actinobacteria. alkB gene expression, induced by hexadecane, was recorded in isolated bacterial strains. Thus, complementary culture dependent and independent methods provided a more accurate picture about the complex seawater microbial communities of the Baltic Sea. Copyright © 2013 Elsevier GmbH. All rights reserved.

A role for Dehalobacter spp. in the reductive dehalogenation of dichlorobenzenes and monochlorobenzene.

PubMed

Nelson, Jennifer L; Fung, Jennifer M; Cadillo-Quiroz, Hinsby; Cheng, Xu; Zinder, Stephen H

2011-08-15

Previously, we demonstrated the reductive dehalogenation of dichlorobenzene (DCB) isomers to monochlorobenzene (MCB), and MCB to benzene in sediment microcosms derived from a chlorobenzene-contaminated site. In this study, enrichment cultures were established for each DCB isomer and each produced MCB and trace amounts of benzene as end products. MCB dehalogenation activity could only be transferred in sediment microcosms. The 1,2-DCB-dehalogenating culture was studied the most intensively. Whereas Dehalococcoides spp. were not detected in any of the microcosms or cultures, Dehalobacter spp. were detected in 16S rRNA gene clone libraries from 1,2-DCB enrichment cultures, and by PCR using Dehalobacter-specific primers in 1,3-DCB and 1,4-DCB enrichments and MCB-dehalogenating microcosms. Quantitative PCR showed Dehalobacter 16S rRNA gene copies increased up to 3 orders of magnitude upon dehalogenation of DCBs or MCB, and that nearly all of bacterial 16S rRNA genes in a 1,2-DCB-dehalogenating culture belonged to Dehalobacter spp. Dehalobacter 16S rRNA genes from DCB enrichment cultures and MCB-dehalogenating microcosms showed considerable diversity, implying that 16S rRNA sequences do not predict dehalogenation-spectra of Dehalobacter spp. These studies support a role for Dehalobacter spp. in the reductive dehalogenation of DCBs and MCB, and this genus should be considered for its potential impact on chlorobenzene fate at contaminated sites.

The fate of antibiotic resistance genes and class 1 integrons following the application of swine and dairy manure to soils.

PubMed

Sandberg, Kyle D; LaPara, Timothy M

2016-02-01

The goal of this study was to determine the fate of antibiotic resistance genes (ARGs) and class 1 integrons following the application of swine and dairy manure to soil. Soil microcosms were amended with either manure from swine fed subtherapeutic levels of antibiotics or manure from dairy cows that were given antibiotics only rarely and strictly for veterinary purposes. Microcosms were monitored for 6 months using quantitative PCR targeting 16S rRNA genes (a measure of bacterial biomass), intI1, erm(B), tet(A), tet(W) and tet(X). Swine manure had 10- to 100-fold higher levels of ARGs than the dairy manure, all of which decayed over time after being applied to soil. A modified Collins-Selleck model described the decay of ARGs in the soil microcosms well, particularly the characteristic in which the decay rate declined over time. By the completion of the soil microcosm experiments, ARGs in the dairy manure-amended soils returned to background levels, whereas the ARGs in swine manure remained elevated compared to control microcosms. Our research suggests that the use of subtherapeutic use of antibiotics in animal feed could lead to the accumulation of ARGs in soils to which manure is applied. © FEMS 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Effects of the Veterinary Pharmaceutical Ivermectin in Indoor Aquatic Microcosms

PubMed Central

Boonstra, Harry; Reichman, Erik P.

2010-01-01

The effects of the parasiticide ivermectin were assessed in plankton-dominated indoor microcosms. Ivermectin was applied once at concentrations of 30, 100, 300, 1000, 3000, and 10,000 ng/l. The half-life (dissipation time 50%; DT50) of ivermectin in the water phase ranged from 1.1 to 8.3 days. The lowest NOECcommunity that could be derived on an isolated sampling from the microcosm study by means of multivariate techniques was 100 ng/l. The most sensitive species in the microcosm study were the cladocerans Ceriodaphnia sp. (no observed effect concentration, NOEC = 30 ng/l) and Chydorus sphaericus (NOEC = 100 ng/l). The amphipod Gammarus pulex was less sensitive to ivermectin, showing consistent statistically significant reductions at the 1000-ng/l treatment level. Copepoda taxa decreased directly after application of ivermectin in the highest treatment but had already recovered at day 20 posttreatment. Indirect effects (e.g., increase of rotifers, increased primary production) were observed at the highest treatment level starting only on day 13 of the exposure phase. Cladocera showed the highest sensitivity to ivermectin in both standard laboratory toxicity tests as well as in the microcosm study. This study demonstrates that simple plankton-dominated test systems for assessing the effects of ivermectin can produce results similar to those obtained with large complex outdoor systems. PMID:20422169

Change of microbial community structure and functional gene abundance in nonylphenol-degrading sediment.

PubMed

Wang, Zhao; Yang, Yuyin; He, Tao; Xie, Shuguang

2015-04-01

Biodegradation by autochthonous microbial community is an important way to clean up nonylphenol (NP) from contaminated river sediment. Knowledge of sediment microbial community can aid in our understanding of biological processes related to NP degradation. However, the change in sediment microbial community associated with NP biodegradation remains unclear. The present study investigated the shift in bacterial community structure and NP-degrading gene abundance in response to NP attenuation in river sediment. Sediment microcosms with different levels of 4-NP (0, 100, or 300 μg/g) were constructed. A nearly complete attenuation of NP occurred in the microcosm with 100 μg/g NP after 9 days' incubation, while a residual NP rate of 8.1 % was observed in the microcosm with 300 μg/g NP after 22 days' incubation. Illumina MiSeq sequencing analysis indicated that Gammaproteobacteria, Alphaproteobacteria, and Bacteroidetes predominated in NP-degrading river sediment. Sediment bacterial community structure varied significantly during NP biodegradation and subsequent incubation, which was affected by the level of added NP. The n-alkane biodegradation (alkB) gene abundance showed a significant variation in each NP-amended microcosm (100 or 300 μg/g), while a significant increase in the single component monooxygenase (sMO) gene abundance only occurred in the microcosm spiked with 300 μg/g NP. This study can provide some new insights toward NP-degrading microbial ecology in the environment.

Hydrocarbon biodegradation by Arctic sea-ice and sub-ice microbial communities during microcosm experiments, Northwest Passage (Nunavut, Canada).

PubMed

Garneau, Marie-Ève; Michel, Christine; Meisterhans, Guillaume; Fortin, Nathalie; King, Thomas L; Greer, Charles W; Lee, Kenneth

2016-10-01

The increasing accessibility to navigation and offshore oil exploration brings risks of hydrocarbon releases in Arctic waters. Bioremediation of hydrocarbons is a promising mitigation strategy but challenges remain, particularly due to low microbial metabolic rates in cold, ice-covered seas. Hydrocarbon degradation potential of ice-associated microbes collected from the Northwest Passage was investigated. Microcosm incubations were run for 15 days at -1.7°C with and without oil to determine the effects of hydrocarbon exposure on microbial abundance, diversity and activity, and to estimate component-specific hydrocarbon loss. Diversity was assessed with automated ribosomal intergenic spacer analysis and Ion Torrent 16S rRNA gene sequencing. Bacterial activity was measured by (3)H-leucine uptake rates. After incubation, sub-ice and sea-ice communities degraded 94% and 48% of the initial hydrocarbons, respectively. Hydrocarbon exposure changed the composition of sea-ice and sub-ice communities; in sea-ice microcosms, Bacteroidetes (mainly Polaribacter) dominated whereas in sub-ice microcosms, the contribution of Epsilonproteobacteria increased, and that of Alphaproteobacteria and Bacteroidetes decreased. Sequencing data revealed a decline in diversity and increases in Colwellia and Moritella in oil-treated microcosms. Low concentration of dissolved organic matter (DOM) in sub-ice seawater may explain higher hydrocarbon degradation when compared to sea ice, where DOM was abundant and composed of labile exopolysaccharides. © Fisheries and Oceans Canada [2016].

Growth of ammonia-oxidizing archaea in soil microcosms is inhibited by acetylene.

PubMed

Offre, Pierre; Prosser, James I; Nicol, Graeme W

2009-10-01

Autotrophic ammonia-oxidizing bacteria were considered to be responsible for the majority of ammonia oxidation in soil until the recent discovery of the autotrophic ammonia-oxidizing archaea. To assess the relative contributions of bacterial and archaeal ammonia oxidizers to soil ammonia oxidation, their growth was analysed during active nitrification in soil microcosms incubated for 30 days at 30 degrees C, and the effect of an inhibitor of ammonia oxidation (acetylene) on their growth and soil nitrification kinetics was determined. Denaturing gradient gel electrophoresis (DGGE) analysis of bacterial ammonia oxidizer 16S rRNA genes did not detect any change in their community composition during incubation, and quantitative PCR (qPCR) analysis of bacterial amoA genes indicated a small decrease in abundance in control and acetylene-containing microcosms. DGGE fingerprints of archaeal amoA and 16S rRNA genes demonstrated changes in the relative abundance of specific crenarchaeal phylotypes during active nitrification. Growth was also indicated by increases in crenarchaeal amoA gene copy number, determined by qPCR. In microcosms containing acetylene, nitrification and growth of the crenarchaeal phylotypes were suppressed, suggesting that these crenarchaea are ammonia oxidizers. Growth of only archaeal but not bacterial ammonia oxidizers occurred in microcosms with active nitrification, indicating that ammonia oxidation was mostly due to archaea in the conditions of the present study.

Dependence of radiation belt simulations to assumed radial diffusion rates tested for two empirical models of radial transport

NASA Astrophysics Data System (ADS)

Drozdov, Alexander; Shprits, Yuri; Aseev, Nikita; Kellerman, Adam; Reeves, Geoffrey

2017-04-01

Radial diffusion is one of the dominant physical mechanisms that drives acceleration and loss of the radiation belt electrons, which makes it very important for nowcasting and forecasting space weather models. We investigate the sensitivity of the two parameterizations of the radial diffusion of Brautigam and Albert [2000] and Ozeke et al. [2014] on long-term radiation belt modeling using the Versatile Electron Radiation Belt (VERB). Following Brautigam and Albert [2000] and Ozeke et al. [2014], we first perform 1-D radial diffusion simulations. Comparison of the simulation results with observations shows that the difference between simulations with either radial diffusion parameterization is small. To take into account effects of local acceleration and loss, we perform 3-D simulations, including pitch-angle, energy and mixed diffusion. We found that the results of 3-D simulations are even less sensitive to the choice of parameterization of radial diffusion rates than the results of 1-D simulations at various energies (from 0.59 to 1.80 MeV). This result demonstrates that the inclusion of local acceleration and pitch-angle diffusion can provide a negative feedback effect, such that the result is largely indistinguishable simulations conducted with different radial diffusion parameterizations. We also perform a number of sensitivity tests by multiplying radial diffusion rates by constant factors and show that such an approach leads to unrealistic predictions of radiation belt dynamics. References Brautigam, D. H., and J. M. Albert (2000), Radial diffusion analysis of outer radiation belt electrons during the October 9, 1990, magnetic storm, J. Geophys. Res., 105(A1), 291-309, doi:10.1029/1999ja900344. Ozeke, L. G., I. R. Mann, K. R. Murphy, I. Jonathan Rae, and D. K. Milling (2014), Analytic expressions for ULF wave radiation belt radial diffusion coefficients, J. Geophys. Res. [Space Phys.], 119(3), 1587-1605, doi:10.1002/2013JA019204.

Know Thyself: Macrocosm and Microcosm

ERIC Educational Resources Information Center

Tubbs, Nigel

2011-01-01

There was a time when, in the Liberal Arts, philosophy and education enjoyed the most intimate and productive relationship. Drawing together philosophy and nature they sought to understand the greatest of human mysteries. This meant thinking about both the macrocosm and the microcosm and especially the relation between them. In this relation lies…

COMPARISON OF MICROBIAL TRANSFORMATION RATE COEFFICIENTS OF XENOBIOTIC CHEMICALS BETWEEN FIELD-COLLECTED AND LABORATORY MICROCOSM MICROBIOTA

EPA Science Inventory

Two second-order transformation rate coefficients--kb, based on total plate counts, and kA, based on periphyton-colonized surface areas--were used to compare xenobiotic chemical transformation by laboratory-developed (microcosm) and by field-collected microbiota. Similarity of tr...

STIMULATION OF THE REDUCTIVE DECHLORINATION OF TETRACHLOROETHENE IN ANAEROBIC AQUIFER MICROCOSMS BY THE ADDITION OF TOLUENE

EPA Science Inventory

In this study, the biologically mediated interactions of toluene and PCE under anaerobic conditions were investigated by using microcosms constructed with aquifer solids from an area that was exposed to both alkylbenzenes and chlorinated ethenes at the U.S. Coast Guard Air Statio...

Effects Of Nutrient Source And Supply On Crude Oil Biodegradation In Continuous-Flow Beach Microcosms

EPA Science Inventory

Ammonium and nitrate were used as nitrogen sources to support microbial biodegradation of crude oil in continuous-flow beach microcosms to determine whether either nutrient was more effective in open systems, such as intertidal shorelines. No differences in the rate or the exten...

Use Of Statistical Tools To Evaluate The Reductive Dechlorination Of High Levels Of TCE In Microcosm Studies

EPA Science Inventory

A large, multi-laboratory microcosm study was performed to select amendments for supporting reductive dechlorination of high levels of trichloroethylene (TCE) found at an industrial site in the United Kingdom (UK) containing dense non-aqueous phase liquid (DNAPL) TCE. The study ...

Comparison of Rooting Strategies to Explore Rock Fractures for Shallow Soil-Adapted Tree Species with Contrasting Aboveground Growth Rates: A Greenhouse Microcosm Experiment.

PubMed

Nie, Yunpeng; Chen, Hongsong; Ding, Yali; Yang, Jing; Wang, Kelin

2017-01-01

For tree species adapted to shallow soil environments, rooting strategies that efficiently explore rock fractures are important because soil water depletion occurs frequently. However, two questions: (a) to what extent shallow soil-adapted species rely on exploring rock fractures and (b) what outcomes result from drought stress, have rarely been tested. Therefore, based on the expectation that early development of roots into deep soil layers is at the cost of aboveground growth, seedlings of three tree species ( Cyclobalanopsis glauca, Delavaya toxocarpa , and Acer cinnamomifolium ) with distinct aboveground growth rates were selected from a typical shallow soil region. In a greenhouse experiment that mimics the basic features of shallow soil environments, 1-year-old seedlings were transplanted into simulated microcosms of shallow soil overlaying fractured bedrock. Root biomass allocation and leaf physiological activities, as well as leaf δ 13 C values were investigated and compared for two treatments: regular irrigation and repeated cycles of drought stress. Our results show that the three species differed in their rooting strategies in the context of encountering rock fractures, however, these strategies were not closely related to the aboveground growth rate. For the slowest-growing seedling, C. glauca , percentages of root mass in the fractures, as well as in the soil layer between soil and bedrock increased significantly under both treatments, indicating a specialized rooting strategy that facilitated the exploration of rock fractures. Early investment in deep root growth was likely critical to the establishment of this drought-vulnerable species. For the intermediate-growing, A. cinnamomifolium , percentages of root mass in the bedrock and interface soil layers were relatively low and exhibited no obvious change under either treatment. This limited need to explore rock fractures was compensated by a conservative water use strategy. For the fast-growing, D. toxocarpa , percentages of root mass in the bedrock and interface layers increased simultaneously under drought conditions, but not under irrigated conditions. This drought-induced rooting plasticity was associated with drought avoidance by this species. Although, root development might have been affected by the simulated microcosm, contrasting results among the three species indicated that efficient use of rock fractures is not a necessary or specialized strategy of shallow-soil adapted species. The establishment and persistence of these species relied on the mutual complementation between their species-specific rooting strategies and drought adaptations.

Simulation of Helical Flow Hydrodynamics in Meanders and Advection-Turbulent Diffusion Using Smoothed Particle Hydrodynamics

NASA Astrophysics Data System (ADS)

Gusti, T. P.; Hertanti, D. R.; Bahsan, E.; Soeryantono, H.

2013-12-01

Particle-based numerical methods, such as Smoothed Particle Hydrodynamics (SPH), may be able to simulate some hydrodynamic and morphodynamic behaviors better than grid-based numerical methods. This study simulates hydrodynamics in meanders and advection and turbulent diffusion in straight river channels using Microsoft Excel and Visual Basic. The simulators generate three-dimensional data for hydrodynamics and one-dimensional data for advection-turbulent diffusion. Fluid at rest, sloshing, and helical flow are simulated in the river meanders. Spill loading and step loading are done to simulate concentration patterns associated with advection-turbulent diffusion. Results indicate that helical flow is formed due to disturbance in morphology and particle velocity in the stream and the number of particles does not have a significant effect on the pattern of advection-turbulent diffusion concentration.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Morton, R.D.; Duke, T.W.; Macauley, J.M.

Effects of a used drilling fluid on an experimental seagrass community (Thalassia testudinum Konig et Sims) were measured by exposing the community to the suspended particulate phase (SPP) in laboratory microcosms. Structure of the macroinvertebrate assemblage, growth, and chlorophyll content of grass and associated epiphytes, and rates of decomposition as indicated by weight loss of grass leaves in treated and untreated microcosms were compared. There were statistically significant differences in community structure and function among untreated microcosms and those receiving the clay and drilling fluid. For example, drilling fluid and clay caused a significant decrease in the numbers of themore » ten most numerically abundant (dominant) macroinvertebrates, and drilling fluid decreased the rate at which Thalassia leaves decomposed.« less

Quantifying white matter tract diffusion parameters in the presence of increased extra-fiber cellularity and vasogenic edema

PubMed Central

Chiang, Chia-Wen; Wang, Yong; Sun, Peng; Lin, Tsen-Hsuan; Trinkaus, Kathryn; Cross, Anne H.; Song, Sheng-Kwei

2014-01-01

The effect of extra-fiber structural and pathological components confounding diffusion tensor imaging (DTI) computation was quantitatively investigated using data generated by both Monte-Carlo simulations and tissue phantoms. Increased extent of vasogenic edema, by addition of various amount of gel to fixed normal mouse trigeminal nerves or by increasing non-restricted isotropic diffusion tensor components in Monte-Carlo simulations, significantly decreased fractional anisotropy (FA), increased radial diffusivity, while less significantly increased axial diffusivity derived by DTI. Increased cellularity, mimicked by graded increase of the restricted isotropic diffusion tensor component in Monte-Carlo simulations, significantly decreased FA and axial diffusivity with limited impact on radial diffusivity derived by DTI. The MC simulation and tissue phantom data were also analyzed by the recently developed diffusion basis spectrum imaging (DBSI) to simultaneously distinguish and quantify the axon/myelin integrity and extra-fiber diffusion components. Results showed that increased cellularity or vasogenic edema did not affect the DBSI-derived fiber FA, axial or radial diffusivity. Importantly, the extent of extra-fiber cellularity and edema estimated by DBSI correlated with experimentally added gel and Monte-Carlo simulations. We also examined the feasibility of applying 25-direction diffusion encoding scheme for DBSI analysis on coherent white matter tracts. Results from both phantom experiments and simulations suggested that the 25-direction diffusion scheme provided comparable DBSI estimation of both fiber diffusion parameters and extra-fiber cellularity/edema extent as those by 99-direction scheme. An in vivo 25-direction DBSI analysis was performed on experimental autoimmune encephalomyelitis (EAE, an animal model of human multiple sclerosis) optic nerve as an example to examine the validity of derived DBSI parameters with post-imaging immunohistochemistry verification. Results support that in vivo DBSI using 25-direction diffusion scheme correctly reflect the underlying axonal injury, demyelination, and inflammation of optic nerves in EAE mice. PMID:25017446

The Time Dependent Propensity Function for Acceleration of Spatial Stochastic Simulation of Reaction-Diffusion Systems

PubMed Central

Wu, Sheng; Li, Hong; Petzold, Linda R.

2015-01-01

The inhomogeneous stochastic simulation algorithm (ISSA) is a fundamental method for spatial stochastic simulation. However, when diffusion events occur more frequently than reaction events, simulating the diffusion events by ISSA is quite costly. To reduce this cost, we propose to use the time dependent propensity function in each step. In this way we can avoid simulating individual diffusion events, and use the time interval between two adjacent reaction events as the simulation stepsize. We demonstrate that the new algorithm can achieve orders of magnitude efficiency gains over widely-used exact algorithms, scales well with increasing grid resolution, and maintains a high level of accuracy. PMID:26609185

In-situ Subaqueous Capping of Mercury-Contaminated Sediments in a Fresh-Water Aquatic System, Part I-Bench-Scale Microcosm Study to Assess Methylmercury Production

EPA Science Inventory

Bench-scale microcosm experiments were designed to provide a better understanding of the potential for Hg methylation in sediments from an aquatic environment. Experiments were conducted to examine the function of sulfate concentration, lactate concentration, the presence/absenc...

CHANGES IN ENANTIOMERIC FRACTIONS DURING MICROBIAL REDUCTIVE DECHLORINATION OF PCB132, PCB149, AND AROCLOR 1254 IN LAKE HARTWELL SEDIMENT MICROCOSMS

EPA Science Inventory

Enantioselectivity of microbial reductive dechlorination of chiral PCBs in sediments from Lake Hartwell, SC, was determined by microcosm studies and enantiomer-specific GC analysis. Sediments from two locations in the vicinity of the highest levels of PCB contamination were used...

UTILIZATION OF THE CARBON AND HYDROGEN ISOTOPIC COMPOSITION OF INDIVIDUAL COMPOUNDS IN REFINED HYDROCARBON PRODUCTS TO MONITOR THEIR FATE IN THE ENVIRONMENT

EPA Science Inventory

Isotope effects resulting from biodegradation of MTBE
To conduct the microcosm biodegradation study, sediment samples were collected from sites offering high potential of MTBE biodegradation. Sites where sediment samples were collected for the MTBE microcosm c...

Impact of protists on a hydrocarbon-degrading bacterial community from deep-sea Gulf of Mexico sediments: A microcosm study

NASA Astrophysics Data System (ADS)

Beaudoin, David J.; Carmichael, Catherine A.; Nelson, Robert K.; Reddy, Christopher M.; Teske, Andreas P.; Edgcomb, Virginia P.

2016-07-01

In spite of significant advancements towards understanding the dynamics of petroleum hydrocarbon degrading microbial consortia, the impacts (direct or indirect via grazing activities) of bacterivorous protists remain largely unknown. Microcosm experiments were used to examine whether protistan grazing affects the petroleum hydrocarbon degradation capacity of a deep-sea sediment microbial community from an active Gulf of Mexico cold seep. Differences in n-alkane content between native sediment microcosms and those treated with inhibitors of eukaryotes were assessed by comprehensive two-dimensional gas chromatography following 30-90 day incubations and analysis of shifts in microbial community composition using small subunit ribosomal RNA gene clone libraries. More biodegradation was observed in microcosms supplemented with eukaryotic inhibitors. SSU rRNA gene clone libraries from oil-amended treatments revealed an increase in the number of proteobacterial clones (particularly γ-proteobacteria) after spiking sediments with diesel oil. Bacterial community composition shifted, and degradation rates increased, in treatments where protists were inhibited, suggesting protists affect the hydrocarbon degrading capacity of microbial communities in sediments collected at this Gulf of Mexico site.

Influence of macrophyte decomposition on growth rate and community structure of okefenokee swamp bacterioplankton.

PubMed

Murray, R E; Hodson, R E

1986-02-01

Dissolved substances released during decomposition of the white water lily (Nymphaea odorata) can alter the growth rate of Okefenokee Swamp bacterioplankton. In microcosm experiments dissolved compounds released from senescent Nymphaea leaves caused a transient reduction in the abundance and activity of water column bacterioplankton, followed by a period of intense bacterial growth. Rates of [H]thymidine incorporation and turnover of dissolved d-glucose were depressed by over 85%, 3 h after the addition of Nymphaea leachates to microcosms containing Okefenokee Swamp water. Bacterial activity subsequently recovered; after 20 h [H]thymidine incorporation in leachate-treated microcosms was 10-fold greater than that in control microcosms. The recovery of activity was due to a shift in the composition of the bacterial population toward resistance to the inhibitory compounds present in Nymphaea leachates. Inhibitory compounds released during the decomposition of aquatic macrophytes thus act as selective agents which alter the community structure of the bacterial population with respect to leachate resistance. Soluble compounds derived from macrophyte decomposition influence the rate of bacterial secondary production and the availability of microbial biomass to microconsumers.

Influence of macrophyte decomposition on growth rate and community structure of Okefenokee Swamp bacterioplankton

DOE Office of Scientific and Technical Information (OSTI.GOV)

Murray, R.E.; Hodson, R.E.

1986-02-01

Dissolved substances released during decomposition of the white water lily (Nymphaea odorata) can alter the growth rate of Okefenokee Swamp bacterioplankton. In microcosm experiments dissolved compounds released bacterioplankton, followed by a period of intense bacterial growth. Rates of (/sup 3/H)thymidine incorporation and turnover of dissolved D-glucose were depressed by over 85%, 3 h after the addition of Nymphaea leachates to microcosms containing Okefenokee Swamp water. Bacterial activity subsequently recovered; after 20 h (/sup 3/H)thymidine incorporation in leachate-treated microcosms was 10-fold greater than that in control microcosms. The recovery of activity was due to a shift in the composition of themore » bacterial population toward resistance to the inhibitory compounds present in Nymphaea leachates. Inhibitory compounds released during the decomposition of aquatic macrophytes thus act as selective agents which alter the community structure of the bacterial population with respect to leachate resistance. Soluble compounds derived from macrophyte decomposition influence the rate of bacterial secondary production and the availability of microbial biomass to microconsumers.« less

Molecular dynamics simulations of substitutional diffusion

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhou, Xiaowang; Jones, Reese E.; Gruber, Jacob

2016-12-18

In atomistic simulations, diffusion energy barriers are usually calculated for each atomic jump path using a nudged elastic band method. Practical materials often involve thousands of distinct atomic jump paths that are not known a priori. Hence, it is often preferred to determine an overall diffusion energy barrier and an overall pre-exponential factor from the Arrhenius equation constructed through molecular dynamics simulations of mean square displacement of the diffusion species at different temperatures. This approach has been well established for interstitial diffusion, but not for substitutional diffusion at the same confidence. Using In 0.1 Ga 0.9 N as an example,more » we have identified conditions where molecular dynamics simulations can be used to calculate highly converged Arrhenius plots for substitutional alloys. As a result, this may enable many complex diffusion problems to be easily and reliably studied in the future using molecular dynamics, provided that moderate computing resources are available.« less

Methanogenic degradation kinetics of phenolic compounds in aquifer-derived microcosms

USGS Publications Warehouse

Godsy, E.M.; Goerlitz, D.F.; Grbic-Galic, D.

1992-01-01

In this segment of a larger multidisciplinary study of the movement and fate of creosote derived compounds in a sand-and-gravel aquifer, we present evidence that the methanogenic degradation of the major biodegradable phenolic compounds and concomitant microbial growth in batch microcosms derived from contaminated aquifer material can be described using Monod kinetics. Substrate depletion and bacterial growth curves were fitted to the Monod equations using nonlinear regression analysis. The method of Marquardt was used for the determination of parameter values that best fit the experimental data by minimizing the residual sum of squares. The Monod kinetic constants (??max, Ks, Y, and kd) that describe phenol, 2-, 3-, and 4-methylphenol degradation and concomitant microbial growth were determined under conditions that were substantially different from those previously reported for microcosms cultured from sewage sludge. The Ks values obtained in this study are approximately two orders of magnitude lower than values obtained for the anaerobic degradation of phenol in digesting sewage sludge, indicating that the aquifer microorganisms have developed enzyme systems that are adapted to low nutrient conditions. The values for kd are much less than ??max, and can be neglected in the microcosms. The extremely low Y values, approximately 3 orders of magnitude lower than for the sewage sludge derived cultures, and the very low numbers of microorganisms in the aquifer derived microcosms suggest that these organisms use some unique strategies to survive in the subsurface environment. ?? 1992 Kluwer Academic Publishers.

Identification of Anaerobic Aniline-Degrading Bacteria at a Contaminated Industrial Site.

PubMed

Sun, Weimin; Li, Yun; McGuinness, Lora R; Luo, Shuai; Huang, Weilin; Kerkhof, Lee J; Mack, E Erin; Häggblom, Max M; Fennell, Donna E

2015-09-15

Anaerobic aniline biodegradation was investigated under different electron-accepting conditions using contaminated canal and groundwater aquifer sediments from an industrial site. Aniline loss was observed in nitrate- and sulfate-amended microcosms and in microcosms established to promote methanogenic conditions. Lag times of 37 days (sulfate amended) to more than 100 days (methanogenic) were observed prior to activity. Time-series DNA-stable isotope probing (SIP) was used to identify bacteria that incorporated (13)C-labeled aniline in the microcosms established to promote methanogenic conditions. In microcosms from heavily contaminated aquifer sediments, a phylotype with 92.7% sequence similarity to Ignavibacterium album was identified as a dominant aniline degrader as indicated by incorporation of (13)C-aniline into its DNA. In microcosms from contaminated canal sediments, a bacterial phylotype within the family Anaerolineaceae, but without a match to any known genus, demonstrated the assimilation of (13)C-aniline. Acidovorax spp. were also identified as putative aniline degraders in both of these two treatments, indicating that these species were present and active in both the canal and aquifer sediments. There were multiple bacterial phylotypes associated with anaerobic degradation of aniline at this complex industrial site, which suggests that anaerobic transformation of aniline is an important process at the site. Furthermore, the aniline degrading phylotypes identified in the current study are not related to any known aniline-degrading bacteria. The identification of novel putative aniline degraders expands current knowledge regarding the potential fate of aniline under anaerobic conditions.

Bioremediation of oil-based drill cuttings by a halophilic consortium isolated from oil-contaminated saline soil.

PubMed

Rezaei Somee, Maryam; Shavandi, Mahmoud; Dastgheib, Seyed Mohammad Mehdi; Amoozegar, Mohammad Ali

2018-05-01

Oil-based drill cuttings are hazardous wastes containing complex hydrocarbons, heavy metals, and brine. Their remediation is a crucial step before release to the environment. In this work, we enriched a halophilic consortium, from oil-polluted saline soil, which is capable of degrading diesel as the main pollutant of oil-based drill cuttings. The degradation ability of the consortium was evaluated in microcosms using two different diluting agents (fine sand and biologically active soil). During the bioremediation process, the bacterial community dynamics of the microcosms was surveyed using PCR amplification of a fragment of 16S rRNA gene followed by denaturing gradient gel electrophoresis (DGGE). The diesel degradation rates were monitored by total petroleum hydrocarbon (TPH) measurement and the total count of heterotrophic and diesel-degrading bacteria. After 3 months, the microcosm containing fine sand and drill cuttings with the ratio of 1:1 (initial TPH of 36,000 mg/kg) showed the highest TPH removal (40%) and its dominant bacterial isolates belonged to the genera Dietzia, Arthrobacter , and Halomonas . DGGE results also confirmed the role of these genera in drill cuttings remediation. DGGE analysis of the bacterial diversity showed that Propionibacterium, Salinimicrobium, Marinobacter , and Dietzia are dominant in active soil microcosm; whereas Bacillus, Salinibacillus , and Marinobacter are abundant in sand microcosm. Our results suggest that the bioaugmentation strategy would be more successful if the diluting agent does not contain a complex microbial community.

A laboratory study of the biodegradation of an alcohol ethoxylate surfactant by native soil microbes

NASA Astrophysics Data System (ADS)

Ang, Carolina C.; Abdul, Abdul S.

1992-09-01

Laboratory experiments were conducted to study the biodegradation of a nonionic alcohol ethoxylate surfactant by native microbes from a contaminated site. Three sets of experiments consisting of 13 microcosms were carried out to evaluate the rate of biodegradation and the effect of nutrients and supplementary oxygen on the degradation process. The results from these active microcosms were compared with those for controlled microcosms in which a biocide was added to inhibit biological activities. In the presence of ground water and sterilized soil, surfactant solutions with initial concentrations of 1000, 650, 250, and 180 mgl -1 were reduced to less than 5 mgl -1 in 36 days, 20 days, 17 days, and 17 days, respectively. The biodegradation rate in microcosms with added nutrients was more than twice the rate in the reactor without nutrients. The results from experiments in which various nitrogen and phosphorus nutrients were added showed that a ratio of 10 carbon:2 nitrogen:1 phosphorus was the optimum for the biodegradation of surfactant under the microcosm conditions. The addition of 5 mgl -1 of oxygen in the form of hydrogen peroxide increased the degradation rate of surfactant by 30%. The study showed that microbes indigenous to the soil and ground water at a contaminated site rapidly degrade the low levels of the surfactant that may remain at the site after soil washing, and that the degradation rate can be increased by the addition of nutrients and oxygen.

[Dental plaque microcosm biofilm behavior on a resin composite incorporated with nano-antibacterial inorganic filler containing long-chain alkyl quaternary ammonium salt].

PubMed

Junling, Wu; Qiang, Zhang; Ruinan, Sun; Ting, Zhu; Jianhua, Ge; Chuanjian, Zhou

2015-12-01

To develop a resin composite incorporated with nano-antibacterial inorganic filler containing long-chain alkyl quaternary ammonium salt, and to measure its effect on human dental plaque microcosm biofilm. A novel nano-antibacterial inorganic filler containing long-chain alkyl quaternary ammonium salt was synthesized according to methods introduced in previous research. Samples of the novel nano-antibacterial inorganic fillers were modified by a coupling agent and then added into resin composite at 0%, 5%, 10%, 15% or 20% mass fractions; 0% composite was used as control. A flexural test was used to measure resin composite mechanical properties. Results showed that a dental plaque microcosm biofilm model with human saliva as inoculum was formed. Colony-forming unit (CFU) counts, lactic acid production, and live/dead assay of biofilm on the resin composite were calculated to test the effect of the resin composite on human dental plaque microcosm biofilm. The incorporation of nano-antibacterial inorganic fillers with as much as 15% concentration into the resin composite showed no adverse effect on the mechanical properties of the resin composite (P > 0.05). Resin composite containing 5% or more nano-antibacterial inorganic fillers significantly inhibited the metabolic activity of dental plaque microcosm biofilm, suggesting its strong antibacterial potency (P < 0.05). This novel resin composite exhibited a strong antibacterial property upon the addition of up to 5% nano-antibacterial inorganic fillers, thereby leading to effective caries inhibition in dental application.

The multinomial simulation algorithm for discrete stochastic simulation of reaction-diffusion systems.

PubMed

Lampoudi, Sotiria; Gillespie, Dan T; Petzold, Linda R

2009-03-07

The Inhomogeneous Stochastic Simulation Algorithm (ISSA) is a variant of the stochastic simulation algorithm in which the spatially inhomogeneous volume of the system is divided into homogeneous subvolumes, and the chemical reactions in those subvolumes are augmented by diffusive transfers of molecules between adjacent subvolumes. The ISSA can be prohibitively slow when the system is such that diffusive transfers occur much more frequently than chemical reactions. In this paper we present the Multinomial Simulation Algorithm (MSA), which is designed to, on the one hand, outperform the ISSA when diffusive transfer events outnumber reaction events, and on the other, to handle small reactant populations with greater accuracy than deterministic-stochastic hybrid algorithms. The MSA treats reactions in the usual ISSA fashion, but uses appropriately conditioned binomial random variables for representing the net numbers of molecules diffusing from any given subvolume to a neighbor within a prescribed distance. Simulation results illustrate the benefits of the algorithm.

NMR diffusion simulation based on conditional random walk.

PubMed

Gudbjartsson, H; Patz, S

1995-01-01

The authors introduce here a new, very fast, simulation method for free diffusion in a linear magnetic field gradient, which is an extension of the conventional Monte Carlo (MC) method or the convolution method described by Wong et al. (in 12th SMRM, New York, 1993, p.10). In earlier NMR-diffusion simulation methods, such as the finite difference method (FD), the Monte Carlo method, and the deterministic convolution method, the outcome of the calculations depends on the simulation time step. In the authors' method, however, the results are independent of the time step, although, in the convolution method the step size has to be adequate for spins to diffuse to adjacent grid points. By always selecting the largest possible time step the computation time can therefore be reduced. Finally the authors point out that in simple geometric configurations their simulation algorithm can be used to reduce computation time in the simulation of restricted diffusion.

Multi-Algorithm Particle Simulations with Spatiocyte.

PubMed

Arjunan, Satya N V; Takahashi, Koichi

2017-01-01

As quantitative biologists get more measurements of spatially regulated systems such as cell division and polarization, simulation of reaction and diffusion of proteins using the data is becoming increasingly relevant to uncover the mechanisms underlying the systems. Spatiocyte is a lattice-based stochastic particle simulator for biochemical reaction and diffusion processes. Simulations can be performed at single molecule and compartment spatial scales simultaneously. Molecules can diffuse and react in 1D (filament), 2D (membrane), and 3D (cytosol) compartments. The implications of crowded regions in the cell can be investigated because each diffusing molecule has spatial dimensions. Spatiocyte adopts multi-algorithm and multi-timescale frameworks to simulate models that simultaneously employ deterministic, stochastic, and particle reaction-diffusion algorithms. Comparison of light microscopy images to simulation snapshots is supported by Spatiocyte microscopy visualization and molecule tagging features. Spatiocyte is open-source software and is freely available at http://spatiocyte.org .

Effects of the fungicide metiram in outdoor freshwater microcosms: responses of invertebrates, primary producers and microbes.

PubMed

Lin, Ronghua; Buijse, Laura; Dimitrov, Mauricio R; Dohmen, Peter; Kosol, Sujitra; Maltby, Lorraine; Roessink, Ivo; Sinkeldam, Jos A; Smidt, Hauke; Van Wijngaarden, René P A; Brock, Theo C M

2012-07-01

The ecological impact of the dithiocarbamate fungicide metiram was studied in outdoor freshwater microcosms, consisting of 14 enclosures placed in an experimental ditch. The microcosms were treated three times (interval 7 days) with the formulated product BAS 222 28F (Polyram®). Intended metiram concentrations in the overlying water were 0, 4, 12, 36, 108 and 324 μg a.i./L. Responses of zooplankton, macroinvertebrates, phytoplankton, macrophytes, microbes and community metabolism endpoints were investigated. Dissipation half-life (DT₅₀) of metiram was approximately 1-6 h in the water column of the microcosm test system and the metabolites formed were not persistent. Multivariate analysis indicated treatment-related effects on the zooplankton (NOEC(community) = 36 μg a.i./L). Consistent treatment-related effects on the phytoplankton and macroinvertebrate communities and on the sediment microbial community could not be demonstrated or were minor. There was no evidence that metiram affected the biomass, abundance or functioning of aquatic hyphomycetes on decomposing alder leaves. The most sensitive populations in the microcosms comprised representatives of Rotifera with a NOEC of 12 μg a.i./L on isolated sampling days and a NOEC of 36 μg a.i./L on consecutive samplings. At the highest treatment-level populations of Copepoda (zooplankton) and the blue-green alga Anabaena (phytoplankton) also showed a short-term decline on consecutive sampling days (NOEC = 108 μg a.i./L). Indirect effects in the form of short-term increases in the abundance of a few macroinvertebrate and several phytoplankton taxa were also observed. The overall community and population level no-observed-effect concentration (NOEC(microcosm)) was 12-36 μg a.i./L. At higher treatment levels, including the test systems that received the highest dose, ecological recovery of affected measurement endpoints was fast (effect period < 8 weeks).

Transcriptomic responses of a simplified soil microcosm to a plant pathogen and its biocontrol agent reveal a complex reaction to harsh habitat.

PubMed

Perazzolli, Michele; Herrero, Noemí; Sterck, Lieven; Lenzi, Luisa; Pellegrini, Alberto; Puopolo, Gerardo; Van de Peer, Yves; Pertot, Ilaria

2016-10-27

Soil microorganisms are key determinants of soil fertility and plant health. Soil phytopathogenic fungi are one of the most important causes of crop losses worldwide. Microbial biocontrol agents have been extensively studied as alternatives for controlling phytopathogenic soil microorganisms, but molecular interactions between them have mainly been characterised in dual cultures, without taking into account the soil microbial community. We used an RNA sequencing approach to elucidate the molecular interplay of a soil microbial community in response to a plant pathogen and its biocontrol agent, in order to examine the molecular patterns activated by the microorganisms. A simplified soil microcosm containing 11 soil microorganisms was incubated with a plant root pathogen (Armillaria mellea) and its biocontrol agent (Trichoderma atroviride) for 24 h under controlled conditions. More than 46 million paired-end reads were obtained for each replicate and 28,309 differentially expressed genes were identified in total. Pathway analysis revealed complex adaptations of soil microorganisms to the harsh conditions of the soil matrix and to reciprocal microbial competition/cooperation relationships. Both the phytopathogen and its biocontrol agent were specifically recognised by the simplified soil microcosm: defence reaction mechanisms and neutral adaptation processes were activated in response to competitive (T. atroviride) or non-competitive (A. mellea) microorganisms, respectively. Moreover, activation of resistance mechanisms dominated in the simplified soil microcosm in the presence of both A. mellea and T. atroviride. Biocontrol processes of T. atroviride were already activated during incubation in the simplified soil microcosm, possibly to occupy niches in a competitive ecosystem, and they were not further enhanced by the introduction of A. mellea. This work represents an additional step towards understanding molecular interactions between plant pathogens and biocontrol agents within a soil ecosystem. Global transcriptional analysis of the simplified soil microcosm revealed complex metabolic adaptation in the soil environment and specific responses to antagonistic or neutral intruders.

Molecular Analysis of Microbial Community Structures in Pristine and Contaminated Aquifers: Field and Laboratory Microcosm Experiments

PubMed Central

Shi, Y.; Zwolinski, M. D.; Schreiber, M. E.; Bahr, J. M.; Sewell, G. W.; Hickey, W. J.

1999-01-01

This study used phylogenetic probes in hybridization analysis to (i) determine in situ microbial community structures in regions of a shallow sand aquifer that were oxygen depleted and fuel contaminated (FC) or aerobic and noncontaminated (NC) and (ii) examine alterations in microbial community structures resulting from exposure to toluene and/or electron acceptor supplementation (nitrate). The latter objective was addressed by using the NC and FC aquifer materials for anaerobic microcosm studies in which phylogenetic probe analysis was complemented by microbial activity assays. Domain probe analysis of the aquifer samples showed that the communities were predominantly Bacteria; Eucarya and Archaea were not detectable. At the phylum and subclass levels, the FC and NC aquifer material had similar relative abundance distributions of 43 to 65% β- and γ-Proteobacteria (B+G), 31 to 35% α-Proteobacteria (ALF), 15 to 18% sulfate-reducing bacteria, and 5 to 10% high G+C gram positive bacteria. Compared to that of the NC region, the community structure of the FC material differed mainly in an increased abundance of B+G relative to that of ALF. The microcosm communities were like those of the field samples in that they were predominantly Bacteria (83 to 101%) and lacked detectable Archaea but differed in that a small fraction (2 to 8%) of Eucarya was detected regardless of the treatment applied. The latter result was hypothesized to reflect enrichment of anaerobic protozoa. Addition of nitrate and/or toluene stimulated microbial activity in the microcosms, but only supplementation of toluene alone significantly altered community structures. For the NC material, the dominant subclass shifted from B+G to ALF, while in the FC microcosms 55 to 65% of the Bacteria community was no longer identifiable by the phylum or subclass probes used. The latter result suggested that toluene exposure fostered the proliferation of phylotype(s) that were otherwise minor constituents of the FC aquifer community. These studies demonstrated that alterations in aquifer microbial communities resulting from specific anthropogenic perturbances can be inferred from microcosm studies integrating chemical and phylogenetic probe analysis and in the case of hydrocarbon contamination may facilitate the identification of organisms important for in situ biodegradation processes. Further work integrating and coordinating microcosm and field experiments is needed to explore how differences in scale, substrate complexity, and other hydrogeological conditions may affect patterns observed in these systems. PMID:10224013

Molecular dynamics simulation of three plastic additives' diffusion in polyethylene terephthalate.

PubMed

Li, Bo; Wang, Zhi-Wei; Lin, Qin-Bao; Hu, Chang-Ying

2017-06-01

Accurate diffusion coefficient data of additives in a polymer are of paramount importance for estimating the migration of the additives over time. This paper shows how this diffusion coefficient can be estimated for three plastic additives [2-(2'-hydroxy-5'-methylphenyl) (UV-P), 2,6-di-tert-butyl-4-methylphenol (BHT) and di-(2-ethylhexyl) phthalate (DEHP)] in polyethylene terephthalate (PET) using the molecular dynamics (MD) simulation method. MD simulations were performed at temperatures of 293-433 K. The diffusion coefficient was calculated through the Einstein relationship connecting the data of mean-square displacement at different times. Comparison of the diffusion coefficients simulated by the MD simulation technique, predicted by the Piringer model and experiments, showed that, except for a few samples, the MD-simulated values were in agreement with the experimental values within one order of magnitude. Furthermore, the diffusion process for additives is discussed in detail, and four factors - the interaction energy between additive molecules and PET, fractional free volume, molecular shape and size, and self-diffusion of the polymer - are proposed to illustrate the microscopic diffusion mechanism. The movement trajectories of additives in PET cell models suggested that the additive molecules oscillate slowly rather than hopping for a long time. Occasionally, when a sufficiently large hole was created adjacently, the molecule could undergo spatial motion by jumping into the free-volume hole and consequently start a continuous oscillation and hop. The results indicate that MD simulation is a useful approach for predicting the microstructure and diffusion coefficient of plastic additives, and help to estimate the migration level of additives from PET packaging.

Molecular analysis of microbial community structures in pristine and contaminated aquifers--Field and laboratory microcosm experiments

USGS Publications Warehouse

Shi, Y.; Zwolinski, M.D.; Schreiber, M.E.; Bahr, J.M.; Sewell, G.W.; Hickey, W.J.

1999-01-01

Molecular Analysis of Microbial Community Structures in Pristine and Contaminated Aquifers: Field and Laboratory Microcosm Experimentsvar callbackToken='531E8ACDB6C8511'; var subCode='asmjournal_sub'; var OAS_sitepage = 'aem.asm.org'; This study used phylogenetic probes in hybridization analysis to (i) determine in situ microbial community structures in regions of a shallow sand aquifer that were oxygen depleted and fuel contaminated (FC) or aerobic and noncontaminated (NC) and (ii) examine alterations in microbial community structures resulting from exposure to toluene and/or electron acceptor supplementation (nitrate). The latter objective was addressed by using the NC and FC aquifer materials for anaerobic microcosm studies in which phylogenetic probe analysis was complemented by microbial activity assays. Domain probe analysis of the aquifer samples showed that the communities were predominantlyBacteria; Eucarya and Archaea were not detectable. At the phylum and subclass levels, the FC and NC aquifer material had similar relative abundance distributions of 43 to 65% β- and γ-Proteobacteria (B+G), 31 to 35% α-Proteobacteria (ALF), 15 to 18% sulfate-reducing bacteria, and 5 to 10% high G+C gram positive bacteria. Compared to that of the NC region, the community structure of the FC material differed mainly in an increased abundance of B+G relative to that of ALF. The microcosm communities were like those of the field samples in that they were predominantly Bacteria (83 to 101%) and lacked detectable Archaea but differed in that a small fraction (2 to 8%) of Eucarya was detected regardless of the treatment applied. The latter result was hypothesized to reflect enrichment of anaerobic protozoa. Addition of nitrate and/or toluene stimulated microbial activity in the microcosms, but only supplementation of toluene alone significantly altered community structures. For the NC material, the dominant subclass shifted from B+G to ALF, while in the FC microcosms 55 to 65% of theBacteria community was no longer identifiable by the phylum or subclass probes used. The latter result suggested that toluene exposure fostered the proliferation of phylotype(s) that were otherwise minor constituents of the FC aquifer community. These studies demonstrated that alterations in aquifer microbial communities resulting from specific anthropogenic perturbances can be inferred from microcosm studies integrating chemical and phylogenetic probe analysis and in the case of hydrocarbon contamination may facilitate the identification of organisms important for in situ biodegradation processes. Further work integrating and coordinating microcosm and field experiments is needed to explore how differences in scale, substrate complexity, and other hydrogeological conditions may affect patterns observed in these systems.

Model Parameter Variability for Enhanced Anaerobic Bioremediation of DNAPL Source Zones

NASA Astrophysics Data System (ADS)

Mao, X.; Gerhard, J. I.; Barry, D. A.

2005-12-01

The objective of the Source Area Bioremediation (SABRE) project, an international collaboration of twelve companies, two government agencies and three research institutions, is to evaluate the performance of enhanced anaerobic bioremediation for the treatment of chlorinated ethene source areas containing dense, non-aqueous phase liquids (DNAPL). This 4-year, 5.7 million dollars research effort focuses on a pilot-scale demonstration of enhanced bioremediation at a trichloroethene (TCE) DNAPL field site in the United Kingdom, and includes a significant program of laboratory and modelling studies. Prior to field implementation, a large-scale, multi-laboratory microcosm study was performed to determine the optimal system properties to support dehalogenation of TCE in site soil and groundwater. This statistically-based suite of experiments measured the influence of key variables (electron donor, nutrient addition, bioaugmentation, TCE concentration and sulphate concentration) in promoting the reductive dechlorination of TCE to ethene. As well, a comprehensive biogeochemical numerical model was developed for simulating the anaerobic dehalogenation of chlorinated ethenes. An appropriate (reduced) version of this model was combined with a parameter estimation method based on fitting of the experimental results. Each of over 150 individual microcosm calibrations involved matching predicted and observed time-varying concentrations of all chlorinated compounds. This study focuses on an analysis of this suite of fitted model parameter values. This includes determining the statistical correlation between parameters typically employed in standard Michaelis-Menten type rate descriptions (e.g., maximum dechlorination rates, half-saturation constants) and the key experimental variables. The analysis provides insight into the degree to which aqueous phase TCE and cis-DCE inhibit dechlorination of less-chlorinated compounds. Overall, this work provides a database of the numerical modelling parameters typically employed for simulating TCE dechlorination relevant for a range of system conditions (e.g, bioaugmented, high TCE concentrations, etc.). The significance of the obtained variability of parameters is illustrated with one-dimensional simulations of enhanced anaerobic bioremediation of residual TCE DNAPL.

Kinetic Monte Carlo Simulation of Cation Diffusion in Low-K Ceramics

NASA Technical Reports Server (NTRS)

Good, Brian

2013-01-01

Low thermal conductivity (low-K) ceramic materials are of interest to the aerospace community for use as the thermal barrier component of coating systems for turbine engine components. In particular, zirconia-based materials exhibit both low thermal conductivity and structural stability at high temperature, making them suitable for such applications. Because creep is one of the potential failure modes, and because diffusion is a mechanism by which creep takes place, we have performed computer simulations of cation diffusion in a variety of zirconia-based low-K materials. The kinetic Monte Carlo simulation method is an alternative to the more widely known molecular dynamics (MD) method. It is designed to study "infrequent-event" processes, such as diffusion, for which MD simulation can be highly inefficient. We describe the results of kinetic Monte Carlo computer simulations of cation diffusion in several zirconia-based materials, specifically, zirconia doped with Y, Gd, Nb and Yb. Diffusion paths are identified, and migration energy barriers are obtained from density functional calculations and from the literature. We present results on the temperature dependence of the diffusivity, and on the effects of the presence of oxygen vacancies in cation diffusion barrier complexes as well.

Simulations on the Influence of Myelin Water in Diffusion-Weighted Imaging

PubMed Central

Harkins, Kevin D.; Does, Mark D.

2016-01-01

While myelinated axons present an important barrier to water diffusion, many models used to interpret DWI signal neglect other potential influences of myelin. In this work, Monte Carlo simulations were used to test the sensitivity of DWI results to the diffusive properties of water within myelin. Within these simulations, the apparent diffusion coefficient (Dapp) varied slowly over several orders of magnitude of the coefficient of myelin water diffusion (Dm), but exhibited important differences compared to Dapp values simulated that neglect Dm (=0). Compared to Dapp, the apparent diffusion kurtosis (Kapp) was generally more sensitive to Dm. Simulations also tested the sensitivity of Dapp and Kapp to the amount of myelin present. Unique variations in Dapp and Kapp caused by differences in the myelin volume fraction were diminished when myelin water diffusion was included. Also, expected trends in Dapp and Kapp with experimental echo time were reduced or inverted when accounting for myelin water diffusion, and these reduced/inverted trends were seen experimentally in ex vivo rat brain DWI experiments. In general, myelin water has the potential to subtly influence DWI results and bias models of DWI that neglect these components of white matter. PMID:27271991

Conformational dynamics of a crystalline protein from microsecond-scale molecular dynamics simulations and diffuse X-ray scattering.

PubMed

Wall, Michael E; Van Benschoten, Andrew H; Sauter, Nicholas K; Adams, Paul D; Fraser, James S; Terwilliger, Thomas C

2014-12-16

X-ray diffraction from protein crystals includes both sharply peaked Bragg reflections and diffuse intensity between the peaks. The information in Bragg scattering is limited to what is available in the mean electron density. The diffuse scattering arises from correlations in the electron density variations and therefore contains information about collective motions in proteins. Previous studies using molecular-dynamics (MD) simulations to model diffuse scattering have been hindered by insufficient sampling of the conformational ensemble. To overcome this issue, we have performed a 1.1-μs MD simulation of crystalline staphylococcal nuclease, providing 100-fold more sampling than previous studies. This simulation enables reproducible calculations of the diffuse intensity and predicts functionally important motions, including transitions among at least eight metastable states with different active-site geometries. The total diffuse intensity calculated using the MD model is highly correlated with the experimental data. In particular, there is excellent agreement for the isotropic component of the diffuse intensity, and substantial but weaker agreement for the anisotropic component. Decomposition of the MD model into protein and solvent components indicates that protein-solvent interactions contribute substantially to the overall diffuse intensity. We conclude that diffuse scattering can be used to validate predictions from MD simulations and can provide information to improve MD models of protein motions.

Molecular-dynamics simulation of mutual diffusion in nonideal liquid mixtures

NASA Astrophysics Data System (ADS)

Rowley, R. L.; Stoker, J. M.; Giles, N. F.

1991-05-01

The mutual-diffusion coefficients, D 12, of n-hexane, n-heptane, and n-octane in chloroform were modeled using equilibrium molecular-dynamics (MD) simulations of simple Lennard-Jones (LJ) fluids. Pure-component LJ parameters were obtained by comparison of simulations to experimental self-diffusion coefficients. While values of “effective” LJ parameters are not expected to simulate accurately diverse thermophysical properties over a wide range of conditions, it was recently shown that effective parameters obtained from pure self-diffusion coefficients can accurately model mutual diffusion in ideal, liquid mixtures. In this work, similar simulations are used to model diffusion in nonideal mixtures. The same combining rules used in the previous study for the cross-interaction parameters were found to be adequate to represent the composition dependence of D 12. The effect of alkane chain length on D 12 is also correctly predicted by the simulations. A commonly used assumption in empirical correlations of D 12, that its kinetic portion is a simple, compositional average of the intradiffusion coefficients, is inconsistent with the simulation results. In fact, the value of the kinetic portion of D 12 was often outside the range of values bracketed by the two intradiffusion coefficients for the nonideal system modeled here.

Two-dimensional numerical simulation of boron diffusion for pyramidally textured silicon

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ma, Fa-Jun, E-mail: Fajun.Ma@nus.edu.sg; Duttagupta, Shubham; Department of Electrical and Computer Engineering, National University of Singapore, 4 Engineering Drive 3, 117576

2014-11-14

Multidimensional numerical simulation of boron diffusion is of great relevance for the improvement of industrial n-type crystalline silicon wafer solar cells. However, surface passivation of boron diffused area is typically studied in one dimension on planar lifetime samples. This approach neglects the effects of the solar cell pyramidal texture on the boron doping process and resulting doping profile. In this work, we present a theoretical study using a two-dimensional surface morphology for pyramidally textured samples. The boron diffusivity and segregation coefficient between oxide and silicon in simulation are determined by reproducing measured one-dimensional boron depth profiles prepared using different boronmore » diffusion recipes on planar samples. The established parameters are subsequently used to simulate the boron diffusion process on textured samples. The simulated junction depth is found to agree quantitatively well with electron beam induced current measurements. Finally, chemical passivation on planar and textured samples is compared in device simulation. Particularly, a two-dimensional approach is adopted for textured samples to evaluate chemical passivation. The intrinsic emitter saturation current density, which is only related to Auger and radiative recombination, is also simulated for both planar and textured samples. The differences between planar and textured samples are discussed.« less

Near-Complete Genome Sequence of Thalassospira sp. Strain KO164 Isolated from a Lignin-Enriched Marine Sediment Microcosm

PubMed Central

Woo, Hannah L.; O’Dell, Kaela B.; Utturkar, Sagar; McBride, Kathryn R.; Huntemann, Marcel; Clum, Alicia; Pillay, Manoj; Palaniappan, Krishnaveni; Varghese, Neha; Mikhailova, Natalia; Stamatis, Dimitrios; Reddy, T. B. K.; Ngan, Chew Yee; Daum, Chris; Shapiro, Nicole; Markowitz, Victor; Ivanova, Natalia; Kyrpides, Nikos; Woyke, Tanja; Brown, Steven D.

2016-01-01

Thalassospira sp. strain KO164 was isolated from eastern Mediterranean seawater and sediment laboratory microcosms enriched on insoluble organosolv lignin under oxic conditions. The near-complete genome sequence presented here will facilitate analyses into this deep-ocean bacterium’s ability to degrade recalcitrant organics such as lignin. PMID:27881538

ENANTIOSELECTIVE REDUCTIVE TRANSFORMATION OF CHIRAL POLYCHLORINATED BIPHENYLS IN LAKE SEDIMENT MICROCOSMS

EPA Science Inventory

The transformation rates and enantiomeric ratios of two chiral poylchlorinated biphenyls (PCBs), 2,2',3,4',5',6-hexachlorobiphenyl (2,2',3,4',5',6-HCB) and 2,2',3,3',4,4',5,6-octachlorobiphenyl (2,2',3,3',4,4',5,6-OCB), were determined in anaerobic lake sediment microcosms (25oC)...

Near-Complete Genome Sequence of Thalassospira sp. Strain KO164 Isolated from a Lignin-Enriched Marine Sediment Microcosm

DOE PAGES

Woo, Hannah L.; O’Dell, Kaela B.; Utturkar, Sagar; ...

2016-11-23

We isolated Thalassospirasp. strain KO164 from eastern Mediterranean seawater and sediment laboratory microcosms enriched on insoluble organosolv lignin under oxic conditions. Furthermore, an analysis of the deep-ocean bacterium’s ability to degrade recalcitrant organics such as lignin near-complete genome sequence, will be presented here.

Near-Complete Genome Sequence of Thalassospira sp. Strain KO164 Isolated from a Lignin-Enriched Marine Sediment Microcosm

DOE Office of Scientific and Technical Information (OSTI.GOV)

Woo, Hannah L.; O’Dell, Kaela B.; Utturkar, Sagar

We isolated Thalassospirasp. strain KO164 from eastern Mediterranean seawater and sediment laboratory microcosms enriched on insoluble organosolv lignin under oxic conditions. Furthermore, an analysis of the deep-ocean bacterium’s ability to degrade recalcitrant organics such as lignin near-complete genome sequence, will be presented here.

Comparison of an Assay for Dehalococcoides DNA and a Microcosm Study in Predicting Reductive Dechlorination of Chlorinated Ethenes in the field

EPA Science Inventory

The study aims to compare the detection of 16S rRNA gene of Dehalococcoides species and the microcosm study for biotransformation in predicting reductive dechlorination of chlorinated ethylenes in ground water at hazardous waste sites. A total of 72 ground water samples were coll...

Two dimensional finite element modelling for dynamic water diffusion through stratum corneum.

PubMed

Xiao, Perry; Imhof, Robert E

2012-10-01

Solvents penetration through in vivo human stratum corneum (SC) has always been an interesting research area for trans-dermal drug delivery studies, and the importance of intercellular routes (diffuse in between corneocytes) and transcellular routes (diffuse through corneocytes) during diffusion is often debatable. In this paper, we have developed a two dimensional finite element model to simulate the dynamic water diffusion through the SC. It is based on the brick-and-mortar model, with brick represents corneocytes and mortar represents lipids, respectively. It simulates the dynamic water diffusion process through the SC from pre-defined initial conditions and boundary conditions. Although the simulation is based on water diffusions, the principles can also be applied to the diffusions of other topical applied substances. The simulation results show that both intercellular routes and transcellular routes are important for water diffusion. Although intercellular routes have higher flux rates, most of the water still diffuse through transcellular routes because of the high cross area ratio of corneocytes and lipids. The diffusion water flux, or trans-epidermal water loss (TEWL), is reversely proportional to corneocyte size, i.e. the larger the corneocyte size, the lower the TEWL, and vice versa. There is also an effect of the SC thickness, external air conditions and diffusion coefficients on the water diffusion through SC on the resulting TEWL. Copyright © 2012 Elsevier B.V. All rights reserved.

Effect of Ionic Diffusion on Extracellular Potentials in Neural Tissue

PubMed Central

Halnes, Geir; Mäki-Marttunen, Tuomo; Keller, Daniel; Pettersen, Klas H.; Andreassen, Ole A.

2016-01-01

Recorded potentials in the extracellular space (ECS) of the brain is a standard measure of population activity in neural tissue. Computational models that simulate the relationship between the ECS potential and its underlying neurophysiological processes are commonly used in the interpretation of such measurements. Standard methods, such as volume-conductor theory and current-source density theory, assume that diffusion has a negligible effect on the ECS potential, at least in the range of frequencies picked up by most recording systems. This assumption remains to be verified. We here present a hybrid simulation framework that accounts for diffusive effects on the ECS potential. The framework uses (1) the NEURON simulator to compute the activity and ionic output currents from multicompartmental neuron models, and (2) the electrodiffusive Kirchhoff-Nernst-Planck framework to simulate the resulting dynamics of the potential and ion concentrations in the ECS, accounting for the effect of electrical migration as well as diffusion. Using this framework, we explore the effect that ECS diffusion has on the electrical potential surrounding a small population of 10 pyramidal neurons. The neural model was tuned so that simulations over ∼100 seconds of biological time led to shifts in ECS concentrations by a few millimolars, similar to what has been seen in experiments. By comparing simulations where ECS diffusion was absent with simulations where ECS diffusion was included, we made the following key findings: (i) ECS diffusion shifted the local potential by up to ∼0.2 mV. (ii) The power spectral density (PSD) of the diffusion-evoked potential shifts followed a 1/f2 power law. (iii) Diffusion effects dominated the PSD of the ECS potential for frequencies up to several hertz. In scenarios with large, but physiologically realistic ECS concentration gradients, diffusion was thus found to affect the ECS potential well within the frequency range picked up in experimental recordings. PMID:27820827

Effect of Ionic Diffusion on Extracellular Potentials in Neural Tissue.

PubMed

Halnes, Geir; Mäki-Marttunen, Tuomo; Keller, Daniel; Pettersen, Klas H; Andreassen, Ole A; Einevoll, Gaute T

2016-11-01

Recorded potentials in the extracellular space (ECS) of the brain is a standard measure of population activity in neural tissue. Computational models that simulate the relationship between the ECS potential and its underlying neurophysiological processes are commonly used in the interpretation of such measurements. Standard methods, such as volume-conductor theory and current-source density theory, assume that diffusion has a negligible effect on the ECS potential, at least in the range of frequencies picked up by most recording systems. This assumption remains to be verified. We here present a hybrid simulation framework that accounts for diffusive effects on the ECS potential. The framework uses (1) the NEURON simulator to compute the activity and ionic output currents from multicompartmental neuron models, and (2) the electrodiffusive Kirchhoff-Nernst-Planck framework to simulate the resulting dynamics of the potential and ion concentrations in the ECS, accounting for the effect of electrical migration as well as diffusion. Using this framework, we explore the effect that ECS diffusion has on the electrical potential surrounding a small population of 10 pyramidal neurons. The neural model was tuned so that simulations over ∼100 seconds of biological time led to shifts in ECS concentrations by a few millimolars, similar to what has been seen in experiments. By comparing simulations where ECS diffusion was absent with simulations where ECS diffusion was included, we made the following key findings: (i) ECS diffusion shifted the local potential by up to ∼0.2 mV. (ii) The power spectral density (PSD) of the diffusion-evoked potential shifts followed a 1/f2 power law. (iii) Diffusion effects dominated the PSD of the ECS potential for frequencies up to several hertz. In scenarios with large, but physiologically realistic ECS concentration gradients, diffusion was thus found to affect the ECS potential well within the frequency range picked up in experimental recordings.

NMR spin-rotation relaxation and diffusion of methane

NASA Astrophysics Data System (ADS)

Singer, P. M.; Asthagiri, D.; Chapman, W. G.; Hirasaki, G. J.

2018-05-01

The translational diffusion-coefficient and the spin-rotation contribution to the 1H NMR relaxation rate for methane (CH4) are investigated using MD (molecular dynamics) simulations, over a wide range of densities and temperatures, spanning the liquid, supercritical, and gas phases. The simulated diffusion-coefficients agree well with measurements, without any adjustable parameters in the interpretation of the simulations. A minimization technique is developed to compute the angular velocity for non-rigid spherical molecules, which is used to simulate the autocorrelation function for spin-rotation interactions. With increasing diffusivity, the autocorrelation function shows increasing deviations from the single-exponential decay predicted by the Langevin theory for rigid spheres, and the deviations are quantified using inverse Laplace transforms. The 1H spin-rotation relaxation rate derived from the autocorrelation function using the "kinetic model" agrees well with measurements in the supercritical/gas phase, while the relaxation rate derived using the "diffusion model" agrees well with measurements in the liquid phase. 1H spin-rotation relaxation is shown to dominate over the MD-simulated 1H-1H dipole-dipole relaxation at high diffusivity, while the opposite is found at low diffusivity. At high diffusivity, the simulated spin-rotation correlation time agrees with the kinetic collision time for gases, which is used to derive a new expression for 1H spin-rotation relaxation, without any adjustable parameters.

Atomistic models of vacancy-mediated diffusion in silicon

NASA Astrophysics Data System (ADS)

Dunham, Scott T.; Wu, Can Dong

1995-08-01

Vacancy-mediated diffusion of dopants in silicon is investigated using Monte Carlo simulations of hopping diffusion, as well as analytic approximations based on atomistic considerations. Dopant/vacancy interaction potentials are assumed to extend out to third-nearest neighbor distances, as required for pair diffusion theories. Analysis focusing on the third-nearest neighbor sites as bridging configurations for uncorrelated hops leads to an improved analytic model for vacancy-mediated dopant diffusion. The Monte Carlo simulations of vacancy motion on a doped silicon lattice verify the analytic results for moderate doping levels. For very high doping (≳2×1020 cm-3) the simulations show a very rapid increase in pair diffusivity due to interactions of vacancies with more than one dopant atom. This behavior has previously been observed experimentally for group IV and V atoms in silicon [Nylandsted Larsen et al., J. Appl. Phys. 73, 691 (1993)], and the simulations predict both the point of onset and doping dependence of the experimentally observed diffusivity enhancement.

Dependence of radiation belt simulations to assumed radial diffusion rates

NASA Astrophysics Data System (ADS)

Drozdov, A.; Shprits, Y.; Aseev, N.; Kellerman, A. C.; Reeves, G. D.

2017-12-01

Radial diffusion is one of the dominant physical mechanisms that drives acceleration and loss of the radiation belt electrons due to wave-particle interaction with ultra low frequency (ULF) waves, which makes it very important for radiation belt modeling and forecasting. We investigate the sensitivity of several parameterizations of the radial diffusion including Brautigam and Albert [2000], Ozeke et al. [2014] and Ali et al. [2016] on long-term radiation belt modeling using the Versatile Electron Radiation Belt (VERB). Following previous studies, we first perform 1-D radial diffusion simulations. To take into account effects of local acceleration and loss, we perform additional 3-D simulations, including pitch-angle, energy and mixed diffusion. The obtained result demonstrates that the inclusion of local acceleration and pitch-angle diffusion can provide a negative feedback effect, such that the result is largely indistinguishable between simulations conducted with different radial diffusion parameterizations. We also perform a number of sensitivity tests by multiplying radial diffusion rates by constant factors and show that such an approach leads to unrealistic predictions of radiation belt dynamics.

Effective simulations of gas diffusion through kinetically accessible tunnels in multisubunit proteins: O2 pathways and escape routes in T-state deoxyhemoglobin.

PubMed

Shadrina, Maria S; English, Ann M; Peslherbe, Gilles H

2012-07-11

The diffusion of small gases to special binding sites within polypeptide matrices pivotally defines the biochemical specificity and reactivity of proteins. We investigate here explicit O(2) diffusion in adult human hemoglobin (HbA) as a case study employing the recently developed temperature-controlled locally enhanced sampling (TLES) method and vary the parameters to greatly increase the simulation efficiency. The method is carefully validated against standard molecular dynamics (MD) simulations and available experimental structural and kinetic data on ligand diffusion in T-state deoxyHbA. The methodology provides a viable alternative approach to traditional MD simulations and/or potential of mean force calculations for: (i) characterizing kinetically accessible diffusion tunnels and escape routes for light ligands in porous proteins; (ii) very large systems when realistic simulations require the inclusion of multiple subunits of a protein; and (iii) proteins that access short-lived conformations relative to the simulation time. In the case of T-state deoxyHbA, we find distinct ligand diffusion tunnels consistent with the experimentally observed disparate Xe cavities in the α- and β-subunits. We identify two distal barriers including the distal histidine (E7) that control access to the heme. The multiple escape routes uncovered by our simulations call for a review of the current popular hypothesis on ligand escape from hemoglobin. Larger deviations from the crystal structure during simulated diffusion in isolated α- and β-subunits highlight the dampening effects of subunit interactions and the importance of including all subunits of multisubunit proteins to map realistic kinetically accessible diffusion tunnels and escape routes.

Field and microcosm experiments to evaluate the effects of agricultural Cu treatment on the density and genetic structure of microbial communities in two different soils.

PubMed

Ranjard, Lionel; Echairi, Abdelwahad; Nowak, Virginie; Lejon, David P H; Nouaïm, Rachida; Chaussod, Rémi

2006-11-01

The effects of Cu amendment on indigenous soil microorganisms were investigated in two soils, a calcareous silty clay (Ep) and a sandy soil (Au), by means of a 1-year field experiment and a two-month microcosm incubation. Cu was added as 'Bordeaux mixture' [CuSO(4), Ca(OH)(2)] at the standard rate used in viticulture (B1=16 kg Cu kg(-1) soil) and at a higher level of contamination (B3=48 kg Cu ha(-1) soil). More extractable Cu was observed in sandy soil (Au) than in silty soil (Ep). Furthermore, total Cu and Cu-EDTA declined with time in Au soil, whereas they remained stable in Ep soil. Quantitative modifications of the microflora were assessed by C-biomass measurements and qualitative modifications were assessed by the characterization of the genetic structure of bacterial and fungal communities from DNA directly extracted from the soil, using B- and F-ARISA (bacterial and fungal automated ribosomal intergenic spacer analysis). In the field study, no significant modifications were observed in C-biomass whereas microcosm incubation showed a decrease in B3 contamination only. ARISA fingerprinting showed slight but significant modifications of bacterial and fungal communities in field and microcosm incubation. These modifications were transient in all cases, suggesting a short-term effect of Cu stress. Microcosm experiments detected the microbial community modifications with greater precision in the short-term, while field experiments showed that the biological effects of Cu contamination may be overcome or hidden by pedo-climatic variations.

Direct and indirect effects of the fungicide azoxystrobin in outdoor brackish water microcosms.

PubMed

Gustafsson, Kerstin; Blidberg, Eva; Elfgren, Irene Karlsson; Hellström, Anna; Kylin, Henrik; Gorokhova, Elena

2010-02-01

The effects of the strobilurin fungicide azoxystrobin were studied in brackish water microcosms, with natural plankton communities and sediment. Two experiments were conducted: Experiment 1 (nominal conc. 0, 15 and 60 microg/L, 24-L outdoor microcosms for 21 days) and a second, follow-up, Experiment 2 (nominal conc. 0, 3, 7.5, 15 microg/L, 4-L indoor microcosms for 12 days). The microcosms represent a simplified brackish water community found in shallow semi-enclosed coastal areas in agricultural districts in the Baltic Sea region. Measured water concentrations of the fungicide (Experiment 1) were, on average, 83 and 62% of nominal concentrations directly after application, and 25 and 30% after 21 days, for the low and high dose treatments, respectively, corresponding to mean DT50-values of 15.1 and 25.8 days, for low and high dose treatments, respectively. In Experiment 1, direct toxic effects on calanoid copepods at both test concentrations were observed. Similarly, in Experiment 2, the copepod abundance was significantly reduced at all tested concentrations. There were also significant secondary effects on zooplankton and phytoplankton community structure, standing stocks and primary production. Very few ecotoxicological studies have investigated effects of plant protection products on Baltic organisms in general and effects on community structure and function specifically. Our results show that azoxystrobin is toxic to brackish water copepods at considerably lower concentrations than previously reported from single species tests on freshwater crustaceans, and that direct toxic effects on this ecologically important group may lead to cascade effects altering lower food webs and ecosystem functioning.

Impacts of Residual Surfactant on Tetrachloroethene (PCE) Degradation Following Pilot-Scale SEAR Treatment at a Chloroethene-Impacted Site

NASA Astrophysics Data System (ADS)

Ramsburg, C. A.; Abriola, L. M.; Pennell, K. D.; Löffler, F. E.; Gamache, M.; Petrovskis, E. A.

2003-04-01

A pilot-scale surfactant-enhanced aquifer remediation (SEAR) demonstration was completed during the summer of 2000 at the Bachman Road site (Oscoda, MI USA). For this test, an aqueous solution of 60 g/L Tween 80 (polyoxyethylene (20) sorbitan monooleate) was used to recover tetrachloroethene (PCE) from a suspected source zone, located underneath a former dry-cleaning facility. Tween 80 was selected for use based upon its demonstrated capacity to solubilize PCE, “food-grade” status, and biodegradative potential. Hydraulic control was maintained throughout the test, with 95% of the injected surfactant mass recovered by a single extraction well. Source-zone monitoring conducted 15 months after SEAR treatment revealed the presence of previously undetected volatile fatty acids (acetate and formate) and PCE degradation products (trichloroethene, cis-1,2-dichloroethene, trans-1,2-dichlorethene, and vinyl chloride), in conjunction with PCE concentration reductions of approximately two orders-of-magnitude. The detection of volatile fatty acids is relevant, as they are likely fermentation products of residual Tween 80. Microbial reductive dechlorination is limited by available electron donors, and microcosm studies demonstrated that both acetate and formate support reductively dechlorinating populations present at the oligotrophic Bachman Road site aquifer. Surfactant transport simulations, using a regional flow model developed for the site, were employed to determine appropriate down-gradient monitoring locations. Drive point samples taken 15 months post-treatment in the vicinity of the simulated residual surfactant plume, contained elevated concentrations of acetate and PCE daughter products. Ongoing efforts include continued site-monitoring, and microcosm studies to corroborate a causal relationship between Tween 80 fermentation and PCE dechlorination.

Diffusion of a Concentrated Lattice Gas in a Regular Comb Structure

NASA Astrophysics Data System (ADS)

Garcia, Paul; Wentworth, Christopher

2008-10-01

Understanding diffusion in constrained geometries is of interest in a variety of contexts as varied as mass transport in disordered solids, such as a percolation cluster, or intercellular transport of water molecules in biological tissue. In this investigation we explore diffusion in a very simple constrained geometry: a comb-like structure involving a one-dimensional backbone of lattice sites with regularly spaced teeth of fixed length. The model considered assumes a fixed concentration of diffusing particles can hop to nearest-neighbor sites only, and they do not interact with each other except that double occupancy is not allowed. The system is simulated using a Monte Carlo simulation procedure. The mean-square displacement of a tagged particle is calculated from the simulation as a function of time. The simulation shows normal diffusive behavior after a period of anomalous diffusion that increases as the tooth size increases.

Ion radial diffusion in an electrostatic impulse model for stormtime ring current formation

NASA Technical Reports Server (NTRS)

Chen, Margaret W.; Schulz, Michael; Lyons, Larry R.; Gorney, David J.

1992-01-01

Two refinements to the quasi-linear theory of ion radial diffusion are proposed and examined analytically with simulations of particle trajectories. The resonance-broadening correction by Dungey (1965) is applied to the quasi-linear diffusion theory by Faelthammar (1965) for an individual model storm. Quasi-linear theory is then applied to the mean diffusion coefficients resulting from simulations of particle trajectories in 20 model storms. The correction for drift-resonance broadening results in quasi-linear diffusion coefficients with discrepancies from the corresponding simulated values that are reduced by a factor of about 3. Further reductions in the discrepancies are noted following the averaging of the quasi-linear diffusion coefficients, the simulated coefficients, and the resonance-broadened coefficients for the 20 storms. Quasi-linear theory provides good descriptions of particle transport for a single storm but performs even better in conjunction with the present ensemble-averaging.

Conformational dynamics of a crystalline protein from microsecond-scale molecular dynamics simulations and diffuse X-ray scattering

DOE PAGES

Wall, Michael E.; Van Benschoten, Andrew H.; Sauter, Nicholas K.; ...

2014-12-01

X-ray diffraction from protein crystals includes both sharply peaked Bragg reflections and diffuse intensity between the peaks. The information in Bragg scattering is limited to what is available in the mean electron density. The diffuse scattering arises from correlations in the electron density variations and therefore contains information about collective motions in proteins. Previous studies using molecular-dynamics (MD) simulations to model diffuse scattering have been hindered by insufficient sampling of the conformational ensemble. To overcome this issue, we have performed a 1.1-μs MD simulation of crystalline staphylococcal nuclease, providing 100-fold more sampling than previous studies. This simulation enables reproducible calculationsmore » of the diffuse intensity and predicts functionally important motions, including transitions among at least eight metastable states with different active-site geometries. The total diffuse intensity calculated using the MD model is highly correlated with the experimental data. In particular, there is excellent agreement for the isotropic component of the diffuse intensity, and substantial but weaker agreement for the anisotropic component. The decomposition of the MD model into protein and solvent components indicates that protein–solvent interactions contribute substantially to the overall diffuse intensity. In conclusion, diffuse scattering can be used to validate predictions from MD simulations and can provide information to improve MD models of protein motions.« less

Conformational dynamics of a crystalline protein from microsecond-scale molecular dynamics simulations and diffuse X-ray scattering

PubMed Central

Wall, Michael E.; Van Benschoten, Andrew H.; Sauter, Nicholas K.; Adams, Paul D.; Fraser, James S.; Terwilliger, Thomas C.

2014-01-01

X-ray diffraction from protein crystals includes both sharply peaked Bragg reflections and diffuse intensity between the peaks. The information in Bragg scattering is limited to what is available in the mean electron density. The diffuse scattering arises from correlations in the electron density variations and therefore contains information about collective motions in proteins. Previous studies using molecular-dynamics (MD) simulations to model diffuse scattering have been hindered by insufficient sampling of the conformational ensemble. To overcome this issue, we have performed a 1.1-μs MD simulation of crystalline staphylococcal nuclease, providing 100-fold more sampling than previous studies. This simulation enables reproducible calculations of the diffuse intensity and predicts functionally important motions, including transitions among at least eight metastable states with different active-site geometries. The total diffuse intensity calculated using the MD model is highly correlated with the experimental data. In particular, there is excellent agreement for the isotropic component of the diffuse intensity, and substantial but weaker agreement for the anisotropic component. Decomposition of the MD model into protein and solvent components indicates that protein–solvent interactions contribute substantially to the overall diffuse intensity. We conclude that diffuse scattering can be used to validate predictions from MD simulations and can provide information to improve MD models of protein motions. PMID:25453071

Evaluation of Proteins' Rotational Diffusion Coefficients from Simulations of Their Free Brownian Motion in Volume-Occupied Environments.

PubMed

Długosz, Maciej; Antosiewicz, Jan M

2014-01-14

We have investigated the rotational dynamics of hen egg white lysozyme in monodisperse aqueous solutions of concentrations up to 250 mg/mL, using a rigid-body Brownian dynamics method that accurately accounts for anisotropies of diffusing objects. We have examined the validity of the free diffusion concept in the analysis of computer simulations of volume-occupied molecular solutions. We have found that, when as the only intermolecular interaction, the excluded volume effect is considered, rotational diffusion of molecules adheres to the free diffusion model. Further, we present a method based on the exact (in the case of the free diffusion) analytic forms of autocorrelation functions of particular vectors rigidly attached to diffusing objects, which allows one to obtain from results of molecular simulations the three principal rotational diffusion coefficients characterizing rotational Brownian motion of an arbitrarily shaped rigid particle for an arbitrary concentration of crowders. We have applied this approach to trajectories resulting from Brownian dynamics simulations of hen egg white lysozyme solutions. We show that the apparent anisotropy of proteins' rotational motions increases with an increasing degree of crowding. Finally, we demonstrate that even if the hydrodynamic anisotropy of molecules is neglected and molecules are simulated using their average translational and rotational diffusion coefficients, excluded volume effects still lead to their anisotropic rotational dynamics.

Simulations on the influence of myelin water in diffusion-weighted imaging

NASA Astrophysics Data System (ADS)

Harkins, K. D.; Does, M. D.

2016-07-01

While myelinated axons present an important barrier to water diffusion, many models used to interpret DWI signal neglect other potential influences of myelin. In this work, Monte Carlo simulations were used to test the sensitivity of DWI results to the diffusive properties of water within myelin. Within these simulations, the apparent diffusion coefficient (D app) varied slowly over several orders of magnitude of the coefficient of myelin water diffusion (D m), but exhibited important differences compared to D app values simulated that neglect D m (=0). Compared to D app, the apparent diffusion kurtosis (K app) was generally more sensitive to D m. Simulations also tested the sensitivity of D app and K app to the amount of myelin present. Unique variations in D app and K app caused by differences in the myelin volume fraction were diminished when myelin water diffusion was included. Also, expected trends in D app and K app with experimental echo time were reduced or inverted when accounting for myelin water diffusion, and these reduced/inverted trends were seen experimentally in ex vivo rat brain DWI experiments. In general, myelin water has the potential to subtly influence DWI results and bias models of DWI that neglect these components of white matter.

Simulations on the influence of myelin water in diffusion-weighted imaging.

PubMed

Harkins, K D; Does, M D

2016-07-07

While myelinated axons present an important barrier to water diffusion, many models used to interpret DWI signal neglect other potential influences of myelin. In this work, Monte Carlo simulations were used to test the sensitivity of DWI results to the diffusive properties of water within myelin. Within these simulations, the apparent diffusion coefficient (D app) varied slowly over several orders of magnitude of the coefficient of myelin water diffusion (D m), but exhibited important differences compared to D app values simulated that neglect D m (=0). Compared to D app, the apparent diffusion kurtosis (K app) was generally more sensitive to D m. Simulations also tested the sensitivity of D app and K app to the amount of myelin present. Unique variations in D app and K app caused by differences in the myelin volume fraction were diminished when myelin water diffusion was included. Also, expected trends in D app and K app with experimental echo time were reduced or inverted when accounting for myelin water diffusion, and these reduced/inverted trends were seen experimentally in ex vivo rat brain DWI experiments. In general, myelin water has the potential to subtly influence DWI results and bias models of DWI that neglect these components of white matter.

Macromolecular Crowding Studies of Amino Acids Using NMR Diffusion Measurements and Molecular Dynamics Simulations

NASA Astrophysics Data System (ADS)

Virk, Amninder; Stait-Gardner, Timothy; Willis, Scott; Torres, Allan; Price, William

2015-02-01

Molecular crowding occurs when the total concentration of macromolecular species in a solution is so high that a considerable proportion of the volume is physically occupied and therefore not accessible to other molecules. This results in significant changes in the solution properties of the molecules in such systems. Macromolecular crowding is ubiquitous in biological systems due to the generally high intracellular protein concentrations. The major hindrance to understanding crowding is the lack of direct comparison of experimental data with theoretical or simulated data. Self-diffusion is sensitive to changes in the molecular weight and shape of the diffusing species, and the available diffusion space (i.e., diffusive obstruction). Consequently, diffusion measurements are a direct means for probing crowded systems including the self-association of molecules. In this work, nuclear magnetic resonance measurements of the self-diffusion of four amino acids (glycine, alanine, valine and phenylalanine) up to their solubility limit in water were compared directly with molecular dynamics simulations. The experimental data were then analyzed using various models of aggregation and obstruction. Both experimental and simulated data revealed that the diffusion of both water and the amino acids were sensitive to the amino acid concentration. The direct comparison of the simulated and experimental data afforded greater insights into the aggregation and obstruction properties of each amino acid.

Near-Complete Genome Sequence of Thalassospira sp. Strain KO164 Isolated from a Lignin-Enriched Marine Sediment Microcosm.

PubMed

Woo, Hannah L; O'Dell, Kaela B; Utturkar, Sagar; McBride, Kathryn R; Huntemann, Marcel; Clum, Alicia; Pillay, Manoj; Palaniappan, Krishnaveni; Varghese, Neha; Mikhailova, Natalia; Stamatis, Dimitrios; Reddy, T B K; Ngan, Chew Yee; Daum, Chris; Shapiro, Nicole; Markowitz, Victor; Ivanova, Natalia; Kyrpides, Nikos; Woyke, Tanja; Brown, Steven D; Hazen, Terry C

2016-11-23

Thalassospira sp. strain KO164 was isolated from eastern Mediterranean seawater and sediment laboratory microcosms enriched on insoluble organosolv lignin under oxic conditions. The near-complete genome sequence presented here will facilitate analyses into this deep-ocean bacterium's ability to degrade recalcitrant organics such as lignin. Copyright © 2016 Woo et al.

Resuscitation by Ferrioxamine E of Stressed Salmonella enterica Serovar Typhimurium from Soil and Water Microcosms

PubMed Central

Reissbrodt, R.; Heier, H.; Tschäpe, H.; Kingsley, R. A.; Williams, P. H.

2000-01-01

Storage of Salmonella enterica serovar Typhimurium strains in soil and water microcosms resulted in loss of culturability on standard plating media. Prior incubation in buffered peptone water supplemented with ferrioxamine E markedly extended the time that bacteria were recoverable by plating, except in the case of mutants deficient in ferrioxamine E uptake. PMID:10966440

Controlling Culex pipiens: antagonists are more efficient than a neonicotinoid insecticide.

PubMed

Meyabeme Elono, Alvine Larissa; Foit, Kaarina; Duquesne, Sabine; Liess, Matthias

2018-06-01

Species vulnerability to pesticides depends on physiological sensitivity, the potential to recover, and the ecological context. We assessed the vulnerability of the mosquito Culex pipiens to a repeated treatment with thiacloprid in outdoor microcosms with and without antagonists (competitive and predatory invertebrates). Microcosms were treated repeatedly (three times) with thiacloprid at a concentration of 0.1, 1, or 10 µg/liter. In microcosms without antagonists, the abundance of Cx. pipiens larvae decreased moderately after the second and the third exposures to 10 µg/liter thiacloprid. In microcosms with antagonists, the abundance of Cx. pipiens larvae declined to approximately zero in the control group and the low concentration treatments during the five weeks of observation. By contrast, the abundance of Cx. pipiens larvae temporarily increased at 10 µg/liter thiacloprid after the second and third contamination. We explained this positive effect on the development of Cx. pipiens because of the decrease in competition due to the elimination of sensitive antagonists combined with the high recovery potential of Cx. pipiens. Based on these results, natural antagonists must be supported for the sustainable control of mosquitoes. © 2018 The Society for Vector Ecology.

Influence of Macrophyte Decomposition on Growth Rate and Community Structure of Okefenokee Swamp Bacterioplankton †

PubMed Central

Murray, Robert E.; Hodson, Robert E.

1986-01-01

Dissolved substances released during decomposition of the white water lily (Nymphaea odorata) can alter the growth rate of Okefenokee Swamp bacterioplankton. In microcosm experiments dissolved compounds released from senescent Nymphaea leaves caused a transient reduction in the abundance and activity of water column bacterioplankton, followed by a period of intense bacterial growth. Rates of [3H]thymidine incorporation and turnover of dissolved d-glucose were depressed by over 85%, 3 h after the addition of Nymphaea leachates to microcosms containing Okefenokee Swamp water. Bacterial activity subsequently recovered; after 20 h [3H]thymidine incorporation in leachate-treated microcosms was 10-fold greater than that in control microcosms. The recovery of activity was due to a shift in the composition of the bacterial population toward resistance to the inhibitory compounds present in Nymphaea leachates. Inhibitory compounds released during the decomposition of aquatic macrophytes thus act as selective agents which alter the community structure of the bacterial population with respect to leachate resistance. Soluble compounds derived from macrophyte decomposition influence the rate of bacterial secondary production and the availability of microbial biomass to microconsumers. Images PMID:16346986

Inhibitory Effects of Sulfate and Nitrate Reduction on Reductive Dechlorination of PCP in a Flooded Paddy Soil

PubMed Central

Xu, Yan; Xue, Lili; Ye, Qi; Franks, Ashley E.; Zhu, Min; Feng, Xi; Xu, Jianming; He, Yan

2018-01-01

Pentachlorophenol (PCP) is highly toxic and persistent in soils. Bioreduction of PCP often co-occurs with varying concentrations of sulfate and nitrate in flooded paddy soils where each can act as an electron acceptor. Anaerobic soil microcosms were constructed to evaluate the influence of sulfate and nitrate amendments and their redox processes. Microcosms with varying sulfate and nitrate concentrations demonstrated an inhibitory effect on reductive dechlorination of PCP compared to an untreated control. Compared to nitrate, sulfate exhibited a more significant impact on PCP dechlorination, as evidenced by a lower maximum reaction rate and a longer time to reach the maximum reaction rate. Dechlorination of PCP was initiated at the ortho-position, and then at the para- and meta-positions to form 3-CP as the final product in all microcosms. Deep sequencing of microbial communities in the microcosms revealed a strong variation in bacterial taxon among treatments. Specialized microbial groups, such as the genus of Desulfovibrio responding to the addition of sulfate, had a potential to mediate the competitive microbial dechlorination of PCP. Our results provide an insight into the competitive microbial-mediated reductive dechlorination of PCP in natural flooded soil or sediment environments. PMID:29643842

Stimulation of anaerobic biodegradation of DDT and its metabolites in a muck soil: laboratory microcosm and mesocosm studies.

PubMed

Gohil, Hiral; Ogram, Andrew; Thomas, John

2014-09-01

The aim of this study was to evaluate the impact of selected electron donors and electron acceptors on the anaerobic biodegradation of DDT and its major metabolites in a muck soil with a long history of exposure to the pesticide. Loss of DDT was measured in anaerobic microcosms supplemented with H2, lactate, and acetate. The greatest loss of DDT (approximately 87 %) was observed in microcosms amended with lactate and no additional electron acceptor compared to the no additional electron donor or acceptor sets. An increase in measureable concentrations of DDx was observed in un-amended microcosms. In larger scale mesocosms, significant increases in dissolved organic carbon (DOC) corresponded with low redox potentials. Increases in DOC corresponded with sharp increases in measured concentrations of DDx, followed by a decrease in measured DDT concentrations in lactate-amended mesocosms. Our studies indicate that sorbed DDx is released upon anaerobic incubation, and that indigenous microorganisms capable of DDx degradation respond to lactate additions. Both the potential for release of sorbed DDx and the potential for biodegradation of DDx should be considered during remediation of DDx-contaminated organic soils at low redox potentials.

Evaluated fate and effects of atrazine and lambda-cyhalothrin in vegetated and unvegetated microcosms.

PubMed

Bouldin, J L; Farris, J L; Moore, M T; Smith, S; Stephens, W W; Cooper, C M

2005-10-01

Contaminants such as nutrients, metals, and pesticides can interact with constructed wetlands and existing drainage ditches used as agricultural best-management practices. Our research has shown that the presence of macrophytes and a hydrologic regime aid in the transfer and transformation of pesticides associated with agricultural runoff. This study consisted of application of both atrazine (triazine herbicide) and lambda-cyhalothrin (pyrethroid insecticide) to vegetated and unvegetated microcosms in order to measure the fate and effects of pesticides applied at suggested field application rates. Exposures focused on monocultures of Ludwigia peploides (water primrose) and Juncus effusus (soft rush). Pesticide sorption was evident through concentrations of atrazine and lambda-cyhalothrin in plant tissue as high as 2461.4 and 86.50 microg/kg, respectively. Toxicity was measured in water from unvegetated microcosms for 28 days and in Chironomus tentans (midge larvae) exposed to sediment collected from 3 h to 56 days in microcosms receiving the pesticide combination. The comparative survival of test organisms in this study suggests that effective mitigation of pesticides from runoff can depend on the macrophyte contact and vegetative attributes associated with ditches. (c) 2005 Wiley Periodicals, Inc.

Variation of nonylphenol-degrading gene abundance and bacterial community structure in bioaugmented sediment microcosm.

PubMed

Wang, Zhao; Yang, Yuyin; Sun, Weimin; Dai, Yu; Xie, Shuguang

2015-02-01

Nonylphenol (NP) can accumulate in river sediment. Bioaugmentation is an attractive option to dissipate heavy NP pollution in river sediment. In this study, two NP degraders were isolated from crude oil-polluted soil and river sediment. Microcosms were constructed to test their ability to degrade NP in river sediment. The shift in the proportion of NP-degrading genes and bacterial community structure in sediment microcosms were characterized using quantitative PCR assay and terminal restriction fragment length polymorphism analysis, respectively. Phylogenetic analysis indicated that the soil isolate belonged to genus Stenotrophomonas, while the sediment isolate was a Sphingobium species. Both of them could almost completely clean up a high level of NP in river sediment (150 mg/kg NP) in 10 or 14 days after inoculation. An increase in the proportion of alkB and sMO genes was observed in sediment microcosms inoculated with Stenotrophomonas strain Y1 and Sphingobium strain Y2, respectively. Moreover, bioaugmentation using Sphingobium strain Y2 could have a strong impact on sediment bacterial community structure, while inoculation of Stenotrophomonas strain Y1 illustrated a weak impact. This study can provide some new insights towards NP biodegradation and bioremediation.

Emissions of NO and N2O in wetland microcosms for swine wastewater treatment.

PubMed

Zhang, Shunan; Liu, Feng; Xiao, Runlin; Li, Yong; Zhou, Juan; Wu, Jinshui

2015-12-01

Nitric oxide (NO) and nitrous oxide (N2O) emitted from wetland systems contribute an important proportion to the global warming effect. In this study, four wetland microcosms vegetated with Myriophyllum elatinoides (WM), Alternanthera philoxeroides (WA), Eichhornia crassipes (WE), or without vegetation (NW) were compared to investigate the emissions of NO and N2O during nitrogen (N) removal process when treating swine wastewater. After 30-day incubation, TN removal rates of 96.4, 74.2, 97.2, and 47.3 % were observed for the WM, WA, WE, and NW microcosms, respectively. Yet, no significant difference was observed in WM and WE (p > 0.05). The average NO and N2O emissions in WE was significantly higher than those in WM, WA, and NW (p < 0.05). In addition, the emission of N2O in WE accounted for 2.10 % of initial TN load and 2.17 % of the total amount of TN removal, compared with less than 1 % in the other microcosms. These findings indicate that wetland vegetated with M. elatinoides may be an optimal system for swine wastewater treatment, based on its higher removal of N and lower emissions of NO and N2O.

Physics-based agent to simulant correlations for vapor phase mass transport.

PubMed

Willis, Matthew P; Varady, Mark J; Pearl, Thomas P; Fouse, Janet C; Riley, Patrick C; Mantooth, Brent A; Lalain, Teri A

2013-12-15

Chemical warfare agent simulants are often used as an agent surrogate to perform environmental testing, mitigating exposure hazards. This work specifically addresses the assessment of downwind agent vapor concentration resulting from an evaporating simulant droplet. A previously developed methodology was used to estimate the mass diffusivities of the chemical warfare agent simulants methyl salicylate, 2-chloroethyl ethyl sulfide, di-ethyl malonate, and chloroethyl phenyl sulfide. Along with the diffusivity of the chemical warfare agent bis(2-chloroethyl) sulfide, the simulant diffusivities were used in an advection-diffusion model to predict the vapor concentrations downwind from an evaporating droplet of each chemical at various wind velocities and temperatures. The results demonstrate that the simulant-to-agent concentration ratio and the corresponding vapor pressure ratio are equivalent under certain conditions. Specifically, the relationship is valid within ranges of measurement locations relative to the evaporating droplet and observation times. The valid ranges depend on the relative transport properties of the agent and simulant, and whether vapor transport is diffusion or advection dominant. Published by Elsevier B.V.

TrackArt: the user friendly interface for single molecule tracking data analysis and simulation applied to complex diffusion in mica supported lipid bilayers.

PubMed

Matysik, Artur; Kraut, Rachel S

2014-05-01

Single molecule tracking (SMT) analysis of fluorescently tagged lipid and protein probes is an attractive alternative to ensemble averaged methods such as fluorescence correlation spectroscopy (FCS) or fluorescence recovery after photobleaching (FRAP) for measuring diffusion in artificial and plasma membranes. The meaningful estimation of diffusion coefficients and their errors is however not straightforward, and is heavily dependent on sample type, acquisition method, and equipment used. Many approaches require advanced computing and programming skills for their implementation. Here we present TrackArt software, an accessible graphic interface for simulation and complex analysis of multiple particle paths. Imported trajectories can be filtered to eliminate spurious or corrupted tracks, and are then analyzed using several previously described methodologies, to yield single or multiple diffusion coefficients, their population fractions, and estimated errors. We use TrackArt to analyze the single-molecule diffusion behavior of a sphingolipid analog SM-Atto647N, in mica supported DOPC (1,2-dioleoyl-sn-glycero-3-phosphocholine) bilayers. Fitting with a two-component diffusion model confirms the existence of two separate populations of diffusing particles in these bilayers on mica. As a demonstration of the TrackArt workflow, we characterize and discuss the effective activation energies required to increase the diffusion rates of these populations, obtained from Arrhenius plots of temperature-dependent diffusion. Finally, TrackArt provides a simulation module, allowing the user to generate models with multiple particle trajectories, diffusing with different characteristics. Maps of domains, acting as impermeable or permeable obstacles for particles diffusing with given rate constants and diffusion coefficients, can be simulated or imported from an image. Importantly, this allows one to use simulated data with a known diffusion behavior as a comparison for results acquired using particular algorithms on actual, "natural" samples whose diffusion behavior is to be extracted. It can also serve as a tool for demonstrating diffusion principles. TrackArt is an open source, platform-independent, Matlab-based graphical user interface, and is easy to use even for those unfamiliar with the Matlab programming environment. TrackArt can be used for accurate simulation and analysis of complex diffusion data, such as diffusion in lipid bilayers, providing publication-quality formatted results.

Design and Evaluation of a Prompting Instrument to Support Learning within the Diffusion Simulation Game

ERIC Educational Resources Information Center

Kwon, Seolim; Lara, Miguel; Enfield, Jake; Frick, Theodore

2013-01-01

Conducting an iterative usability testing, a set of prompts used as a form of instructional support was developed in order to facilitate the comprehension of the diffusion of innovations theory (Rogers, 2003) in a simulation game called the Diffusion Simulation Game (DSG) (Molenda & Rice, 1979). The six subjects who participated in the study…

Molecular simulations of a CO2/CO mixture in MIL-127

NASA Astrophysics Data System (ADS)

Chokbunpiam, Tatiya; Fritzsche, Siegfried; Parasuk, Vudhichai; Caro, Jürgen; Assabumrungrat, Suttichai

2018-03-01

Adsorption and diffusion of an equimolar feed mixture of CO2 and CO in MIL-127 at three different temperatures and pressures up to 12 bar were investigated by molecular simulations. The adsorption was simulated using Gibbs-Ensemble Monte Carlo (GEMC). The structure of the adsorbed phase and the diffusion in the MIL were investigated using Molecular Dynamics (MD) simulations. The adsorption selectivity of MIL-127 for CO2 over CO at 233 K was about 15. When combining adsorption and diffusion selectivities, a membrane selectivity of about 12 is predicted. For higher temperatures, both adsorption and diffusion selectivity are found to be smaller.

Survival, growth, and body residues of hyalella azteca (Saussure) exposed to fipronil contaminated sediments from non-vegetated and vegetated microcosms.

PubMed

Kröger, Robert; Lizotte, Richard E; Moore, Matthew T

2009-09-01

We assessed chronic effects of fipronil and metabolite contaminated sediments from non-vegetated and Thallia dealbata vegetated wetland microcosms on Hyalella azteca during wet and dry exposures. Mean sediment concentrations (ng g(-1)) ranged from 0.72-1.26, 0.01-0.69, 0.07-0.23, and 0.49-7.87 for fipronil, fipronil-sulfide, fipronil-sulfone, and fipronil-desulfinyl, respectively. No significant differences in animal survival or growth were observed between non-vegetated and vegetated microcosms during wet or dry exposures. Mean animal body residue concentrations (ng g(-1)) ranged from 28.4-77.6, 0-30.7, and 8.3-43.8 for fipronil, fipronil-sulfide, and fipronil-sulfone. Fipronil-desulfinyl was not detected in any animal samples.

Molecular dynamics simulations of propane in slit shaped silica nano-pores: direct comparison with quasielastic neutron scattering experiments.

PubMed

Gautam, Siddharth; Le, Thu; Striolo, Alberto; Cole, David

2017-12-13

Molecular motion under confinement has important implications for a variety of applications including gas recovery and catalysis. Propane confined in mesoporous silica aerogel as studied using quasielastic neutron scattering (QENS) showed anomalous pressure dependence in its diffusion coefficient (J. Phys. Chem. C, 2015, 119, 18188). Molecular dynamics (MD) simulations are often employed to complement the information obtained from QENS experiments. Here, we report an MD simulation study to probe the anomalous pressure dependence of propane diffusion in silica aerogel. Comparison is attempted based on the self-diffusion coefficients and on the time scales of the decay of the simulated intermediate scattering functions. While the self-diffusion coefficients obtained from the simulated mean squared displacement profiles do not exhibit the anomalous pressure dependence observed in the experiments, the time scales of the decay of the intermediate scattering functions calculated from the simulation data match the corresponding quantities obtained in the QENS experiment and thus confirm the anomalous pressure dependence of the diffusion coefficient. The origin of the anomaly in pressure dependence lies in the presence of an adsorbed layer of propane molecules that seems to dominate the confined propane dynamics at low pressure, thereby lowering the diffusion coefficient. Further, time scales for rotational motion obtained from the simulations explain the absence of rotational contribution to the QENS spectra in the experiments. In particular, the rotational motion of the simulated propane molecules is found to exhibit large angular jumps at lower pressure. The present MD simulation work thus reveals important new insights into the origin of anomalous pressure dependence of propane diffusivity in silica mesopores and supplements the information obtained experimentally by QENS data.

Diffusion in confinement: kinetic simulations of self- and collective diffusion behavior of adsorbed gases

DOE Office of Scientific and Technical Information (OSTI.GOV)

Abouelnasr, MKF; Smit, B

2012-01-01

The self- and collective-diffusion behaviors of adsorbed methane, helium, and isobutane in zeolite frameworks LTA, MFI, AFI, and SAS were examined at various concentrations using a range of molecular simulation techniques including Molecular Dynamics (MD), Monte Carlo (MC), Bennett-Chandler (BC), and kinetic Monte Carlo (kMC). This paper has three main results. (1) A novel model for the process of adsorbate movement between two large cages was created, allowing the formulation of a mixing rule for the re-crossing coefficient between two cages of unequal loading. The predictions from this mixing rule were found to agree quantitatively with explicit simulations. (2) Amore » new approach to the dynamically corrected Transition State Theory method to analytically calculate self-diffusion properties was developed, explicitly accounting for nanoscale fluctuations in concentration. This approach was demonstrated to quantitatively agree with previous methods, but is uniquely suited to be adapted to a kMC simulation that can simulate the collective-diffusion behavior. (3) While at low and moderate loadings the self- and collective-diffusion behaviors in LTA are observed to coincide, at higher concentrations they diverge. A change in the adsorbate packing scheme was shown to cause this divergence, a trait which is replicated in a kMC simulation that explicitly models this behavior. These phenomena were further investigated for isobutane in zeolite MFI, where MD results showed a separation in self- and collective-diffusion behavior that was reproduced with kMC simulations.« less

Diffusion in confinement: kinetic simulations of self- and collective diffusion behavior of adsorbed gases.

PubMed

Abouelnasr, Mahmoud K F; Smit, Berend

2012-09-07

The self- and collective-diffusion behaviors of adsorbed methane, helium, and isobutane in zeolite frameworks LTA, MFI, AFI, and SAS were examined at various concentrations using a range of molecular simulation techniques including Molecular Dynamics (MD), Monte Carlo (MC), Bennett-Chandler (BC), and kinetic Monte Carlo (kMC). This paper has three main results. (1) A novel model for the process of adsorbate movement between two large cages was created, allowing the formulation of a mixing rule for the re-crossing coefficient between two cages of unequal loading. The predictions from this mixing rule were found to agree quantitatively with explicit simulations. (2) A new approach to the dynamically corrected Transition State Theory method to analytically calculate self-diffusion properties was developed, explicitly accounting for nanoscale fluctuations in concentration. This approach was demonstrated to quantitatively agree with previous methods, but is uniquely suited to be adapted to a kMC simulation that can simulate the collective-diffusion behavior. (3) While at low and moderate loadings the self- and collective-diffusion behaviors in LTA are observed to coincide, at higher concentrations they diverge. A change in the adsorbate packing scheme was shown to cause this divergence, a trait which is replicated in a kMC simulation that explicitly models this behavior. These phenomena were further investigated for isobutane in zeolite MFI, where MD results showed a separation in self- and collective- diffusion behavior that was reproduced with kMC simulations.

Short-term emissions of ammonia and carbon dioxide from cattle urine contaminated tropical grassland microcosm.

PubMed

Majumdar, Deepanjan; Patel, Manoj; Drabar, Reena; Vyas, Manish

2006-11-01

The study was designed to understand the emissions of ammonia (NH(3)) and carbon dioxide (CO(2)) from a single cattle urination event on a tropical grassland and underline the significance of the emissions in the context of huge animal population grazing on large pasture areas in some countries. Emissions of ammonia (NH(3)) and carbon dioxide (CO(2)) were monitored for three weeks from a tropical grassland (dominated by Cynodon dactylon Pers.) microcosm contaminated with cow and buffalo urine. The grassland microcosms were treated with urine (50 and 100 ml of each) only once and irrigated with water once every week. Ammonia was sampled by an automatic sampling system comprising of a vacuum pump, three-way stopcocks and rubber tubing and an impinger containing suitable absorbing solution (H(2)SO(4)), connected to the tubing suitably. The sampled gas, after sucked by the vacuum pump and absorbed in H(2)SO(4), was allowed to enter the closed microcosm again maintaining internal pressure of the microcosm. Carbon dioxide was sampled by absorption in an alkali (NaOH) trap inside the microcosm. Both NH(3) and CO(2) emissions were highly variable temporally and there was no continuous increasing or decreasing emission trend with time. Respectively, 45 and 46% of total NH(3)-N were emitted within first 48 h from 50 and 100 ml cow urine application while the corresponding values for buffalo urine were 34 and 32%. Total NH(3)-N emissions, integrated for sampling days (i.e. 1, 2, 3, 4, 6, 15, 18 and 21st) were 11 and 6% in cow and 8 and 5% in buffalo urine, of the total-N added through 50 and 100 ml urine samples. Carbon dioxide emissions were standardized at 25 degrees C by using a suitable formula which were lower than actual emissions at actual soil temperature (> 25 degrees C). Carbon dioxide emission rates were classified on the basis of soil repiratory classification and classes ranged from moderately low soil activity up to unusually high soil activity, the latter observed only on very few sampling days. Grasses in the microcosm had shown appreciable growth after urine application. Although variable and somewhat unpredictable, emissions were appreciable and that too only from a patch of single urination, indicating to the huge magnitude of total emissions under the scenario of thousands of cattle grazing on hundreds of acres of grasslands in a tropical country.

Numerical simulation model of hyperacute/acute stage white matter infarction.

PubMed

Sakai, Koji; Yamada, Kei; Oouchi, Hiroyuki; Nishimura, Tsunehiko

2008-01-01

Although previous studies have revealed the mechanisms of changes in diffusivity (apparent diffusion coefficient [ADC]) in acute brain infarction, changes in diffusion anisotropy (fractional anisotropy [FA]) in white matter have not been examined. We hypothesized that membrane permeability as well as axonal swelling play important roles, and we therefore constructed a simulation model using random walk simulation to replicate the diffusion of water molecules. We implemented a numerical diffusion simulation model of normal and infarcted human brains using C++ language. We constructed this 2-pool model using simple tubes aligned in a single direction. Random walk simulation diffused water. Axon diameters and membrane permeability were then altered in step-wise fashion. To estimate the effects of axonal swelling, axon diameters were changed from 6 to 10 microm. Membrane permeability was altered from 0% to 40%. Finally, both elements were combined to explain increasing FA in the hyperacute stage of white matter infarction. The simulation demonstrated that simple water shift into the intracellular space reduces ADC and increases FA, but not to the extent expected from actual human cases (ADC approximately 50%; FA approximately +20%). Similarly, membrane permeability alone was insufficient to explain this phenomenon. However, a combination of both factors successfully replicated changes in diffusivity indices. Both axonal swelling and reduced membrane permeability appear important in explaining changes in ADC and FA based on eigenvalues in hyperacute-stage white matter infarction.

Statistical error in simulations of Poisson processes: Example of diffusion in solids

NASA Astrophysics Data System (ADS)

Nilsson, Johan O.; Leetmaa, Mikael; Vekilova, Olga Yu.; Simak, Sergei I.; Skorodumova, Natalia V.

2016-08-01

Simulations of diffusion in solids often produce poor statistics of diffusion events. We present an analytical expression for the statistical error in ion conductivity obtained in such simulations. The error expression is not restricted to any computational method in particular, but valid in the context of simulation of Poisson processes in general. This analytical error expression is verified numerically for the case of Gd-doped ceria by running a large number of kinetic Monte Carlo calculations.

Visual Representations of Microcosm in Textbooks of Chemistry: Constructing a Systemic Network for Their Main Conceptual Framework

ERIC Educational Resources Information Center

Papageorgiou, George; Amariotakis, Vasilios; Spiliotopoulou, Vasiliki

2017-01-01

The main objective of this work is to analyse the visual representations (VRs) of the microcosm depicted in nine Greek secondary chemistry school textbooks of the last three decades in order to construct a systemic network for their main conceptual framework and to evaluate the contribution of each one of the resulting categories to the network.…

Survival, growth, and body residues of Hyalella azteca (Saussure) exposed to fipronil contaminated sediments from non-vegetated and vegetated microcosms

USDA-ARS?s Scientific Manuscript database

We assessed chronic effects of fipronil and metabolite contaminated sediments from non-vegetated and Thallia dealbata vegetated wetland microcosms on Hyalella azteca during wet and dry exposures. Mean sediment concentrations (ng g-1) ranged from 0.72-1.26, 0.01-0.69, 0.07-0.23, and 0.49-7.87 for fip...

Effects of sediment-spiked lufenuron on benthic macroinvertebrates in outdoor microcosms and single-species toxicity tests.

PubMed

Brock, T C M; Bas, D A; Belgers, J D M; Bibbe, L; Boerwinkel, M-C; Crum, S J H; Diepens, N J; Kraak, M H S; Vonk, J A; Roessink, I

2016-08-01

Sediment ecotoxicity studies were conducted with lufenuron to (i) complement the results of a water-spiked mesocosm experiment with this lipophilic benzoylurea insecticide, (ii) to explore the predictive value of laboratory single-species tests for population and community-level responses of benthic macroinvertebrates, and (iii) to calibrate the tier-1 effect assessment procedure for sediment organisms. For this purpose the concentration-response relationships for macroinvertebrates between sediment-spiked microcosms and those of 28-d sediment-spiked single-species toxicity tests with Chironomus riparius, Hyalella azteca and Lumbriculus variegatus were compared. Lufenuron persisted in the sediment of the microcosms. On average, 87.7% of the initial lufenuron concentration could still be detected in the sediment after 12 weeks. Overall, benthic insects and crustaceans showed treatment-related declines and oligochaetes treatment-related increases. The lowest population-level NOEC in the microcosms was 0.79μg lufenuron/g organic carbon in dry sediment (μg a.s./g OC) for Tanytarsini, Chironomini and Dero sp. Multivariate analysis of the responses of benthic macroinvertebrates revealed a community-level NOEC of 0.79μg a.s./g OC. The treatment-related responses observed in the microcosms are in accordance with the results of the 28-d laboratory toxicity tests. These tests showed that the insect C. riparius and the crustacean H. azteca were approximately two orders of magnitude more sensitive than the oligochaete L. variegatus. In our laboratory tests, using field-collected sediment, the lowest 28-d EC10 (0.49μg a.s./g OC) was observed for C. riparius (endpoint survival), while for the standard OECD test with this species, using artificial sediment, a NOEC of 2.35μg a.s./g OC (endpoint emergence) is reported. In this particular case, the sediment tier-1 effect assessment using the chronic EC10 (field-collected sediment) or chronic NOEC (artificial sediment) of C. riparius and an assessment factor of 10, seems to be protective for the treatment-related responses observed in the sediment-spiked microcosms. Copyright © 2016 Elsevier B.V. All rights reserved.

Estimation of hydrocarbon biodegradation rates in gasoline-contaminated sediment from measured respiration rates

USGS Publications Warehouse

Baker, R.J.; Baehr, A.L.; Lahvis, M.A.

2000-01-01

An open microcosm method for quantifying microbial respiration and estimating biodegradation rates of hydrocarbons in gasoline-contaminated sediment samples has been developed and validated. Stainless-steel bioreactors are filled with soil or sediment samples, and the vapor-phase composition (concentrations of oxygen (O2), nitrogen (N2), carbon dioxide (CO2), and selected hydrocarbons) is monitored over time. Replacement gas is added as the vapor sample is taken, and selection of the replacement gas composition facilitates real-time decision-making regarding environmental conditions within the bioreactor. This capability allows for maintenance of field conditions over time, which is not possible in closed microcosms. Reaction rates of CO2 and O2 are calculated from the vapor-phase composition time series. Rates of hydrocarbon biodegradation are either measured directly from the hydrocarbon mass balance, or estimated from CO2 and O2 reaction rates and assumed reaction stoichiometries. Open microcosm experiments using sediments spiked with toluene and p-xylene were conducted to validate the stoichiometric assumptions. Respiration rates calculated from O2 consumption and from CO2 production provide estimates of toluene and p- xylene degradation rates within about ??50% of measured values when complete mineralization stoichiometry is assumed. Measured values ranged from 851.1 to 965.1 g m-3 year-1 for toluene, and 407.2-942.3 g m-3 year-1 for p- xylene. Contaminated sediment samples from a gasoline-spill site were used in a second set of microcosm experiments. Here, reaction rates of O2 and CO2 were measured and used to estimate hydrocarbon respiration rates. Total hydrocarbon reaction rates ranged from 49.0 g m-3 year-1 in uncontaminated (background) to 1040.4 g m-3 year-1 for highly contaminated sediment, based on CO2 production data. These rate estimates were similar to those obtained independently from in situ CO2 vertical gradient and flux determinations at the field site. In these experiments, aerobic conditions were maintained in the microcosms by using air as the replacement gas, thus preserving the ambient aerobic environment of the subsurface near the capillary zone. This would not be possible with closed microcosms.

Lateral eddy diffusivity estimates from simulated and observed drifter trajectories: a case study for the Agulhas Current system

NASA Astrophysics Data System (ADS)

Rühs, Siren; Zhurbas, Victor; Durgadoo, Jonathan V.; Biastoch, Arne

2017-04-01

The Lagrangian description of fluid motion by sets of individual particle trajectories is extensively used to characterize connectivity between distinct oceanic locations. One important factor influencing the connectivity is the average rate of particle dispersal, generally quantified as Lagrangian diffusivity. In addition to Lagrangian observing programs, Lagrangian analyses are performed by advecting particles with the simulated flow field of ocean general circulation models (OGCMs). However, depending on the spatio-temporal model resolution, not all scale-dependent processes are explicitly resolved in the simulated velocity fields. Consequently, the dispersal of advective Lagrangian trajectories has been assumed not to be sufficiently diffusive compared to observed particle spreading. In this study we present a detailed analysis of the spatially variable lateral eddy diffusivity characteristics of advective drifter trajectories simulated with realistically forced OGCMs and compare them with estimates based on observed drifter trajectories. The extended Agulhas Current system around South Africa, known for its intricate mesoscale dynamics, serves as a test case. We show that a state-of-the-art eddy-resolving OGCM indeed features theoretically derived dispersion characteristics for diffusive regimes and realistically represents Lagrangian eddy diffusivity characteristics obtained from observed surface drifter trajectories. The estimates for the maximum and asymptotic lateral single-particle eddy diffusivities obtained from the observed and simulated drifter trajectories show a good agreement in their spatial pattern and magnitude. We further assess the sensitivity of the simulated lateral eddy diffusivity estimates to the temporal and lateral OGCM output resolution and examine the impact of the different eddy diffusivity characteristics on the Lagrangian connectivity between the Indian Ocean and the South Atlantic.

Comparison of Rooting Strategies to Explore Rock Fractures for Shallow Soil-Adapted Tree Species with Contrasting Aboveground Growth Rates: A Greenhouse Microcosm Experiment

PubMed Central

Nie, Yunpeng; Chen, Hongsong; Ding, Yali; Yang, Jing; Wang, Kelin

2017-01-01

For tree species adapted to shallow soil environments, rooting strategies that efficiently explore rock fractures are important because soil water depletion occurs frequently. However, two questions: (a) to what extent shallow soil-adapted species rely on exploring rock fractures and (b) what outcomes result from drought stress, have rarely been tested. Therefore, based on the expectation that early development of roots into deep soil layers is at the cost of aboveground growth, seedlings of three tree species (Cyclobalanopsis glauca, Delavaya toxocarpa, and Acer cinnamomifolium) with distinct aboveground growth rates were selected from a typical shallow soil region. In a greenhouse experiment that mimics the basic features of shallow soil environments, 1-year-old seedlings were transplanted into simulated microcosms of shallow soil overlaying fractured bedrock. Root biomass allocation and leaf physiological activities, as well as leaf δ13C values were investigated and compared for two treatments: regular irrigation and repeated cycles of drought stress. Our results show that the three species differed in their rooting strategies in the context of encountering rock fractures, however, these strategies were not closely related to the aboveground growth rate. For the slowest-growing seedling, C. glauca, percentages of root mass in the fractures, as well as in the soil layer between soil and bedrock increased significantly under both treatments, indicating a specialized rooting strategy that facilitated the exploration of rock fractures. Early investment in deep root growth was likely critical to the establishment of this drought-vulnerable species. For the intermediate-growing, A. cinnamomifolium, percentages of root mass in the bedrock and interface soil layers were relatively low and exhibited no obvious change under either treatment. This limited need to explore rock fractures was compensated by a conservative water use strategy. For the fast-growing, D. toxocarpa, percentages of root mass in the bedrock and interface layers increased simultaneously under drought conditions, but not under irrigated conditions. This drought-induced rooting plasticity was associated with drought avoidance by this species. Although, root development might have been affected by the simulated microcosm, contrasting results among the three species indicated that efficient use of rock fractures is not a necessary or specialized strategy of shallow-soil adapted species. The establishment and persistence of these species relied on the mutual complementation between their species-specific rooting strategies and drought adaptations. PMID:29018464

Molecular dynamics simulation of framework flexibility effects on noble gas diffusion in HKUST-1 and ZIF-8

DOE PAGES

Parkes, Marie V.; Demir, Hakan; Teich-McGoldrick, Stephanie L.; ...

2014-03-28

Molecular dynamics simulations were used to investigate trends in noble gas (Ar, Kr, Xe) diffusion in the metal-organic frameworks HKUST-1 and ZIF-8. Diffusion occurs primarily through inter-cage jump events, with much greater diffusion of guest atoms in HKUST-1 compared to ZIF-8 due to the larger cage and window sizes in the former. We compare diffusion coefficients calculated for both rigid and flexible frameworks. For rigid framework simulations, in which the framework atoms were held at their crystallographic or geometry optimized coordinates, sometimes dramatic differences in guest diffusion were seen depending on the initial framework structure or the choice of frameworkmore » force field parameters. When framework flexibility effects were included, argon and krypton diffusion increased significantly compared to rigid-framework simulations using general force field parameters. Additionally, for argon and krypton in ZIF-8, guest diffusion increased with loading, demonstrating that guest-guest interactions between cages enhance inter-cage diffusion. No inter-cage jump events were seen for xenon atoms in ZIF-8 regardless of force field or initial structure, and the loading dependence of xenon diffusion in HKUST-1 is different for rigid and flexible frameworks. Diffusion of krypton and xenon in HKUST-1 depends on two competing effects: the steric effect that decreases diffusion as loading increases, and the “small cage effect” that increases diffusion as loading increases. Finally, a detailed analysis of the window size in ZIF-8 reveals that the window increases beyond its normal size to permit passage of a (nominally) larger krypton atom.« less

The effects of high-tannin leaf litter from transgenic poplars on microbial communities in microcosm soils.

PubMed

Winder, Richard S; Lamarche, Josyanne; Constabel, C Peter; Hamelin, Richard C

2013-01-01

The impacts of leaf litter from genetically modified hybrid poplar accumulating high levels of condensed tannins (proanthocyanidins) were examined in soil microcosms consisting of moss growing on sieved soil. Moss preferentially proliferated in microcosms with lower tannin content; DGGE (denaturing gradient gel electrophoresis) detected increased fungal diversity in microcosms with low-tannin litter. The proportion of cloned rDNA sequences from Actinobacteria decreased with litter addition while Bacteroidetes, Chloroflexi, Cyanobacteria, and α-Proteobacteria significantly increased. β-Proteobacteria were proportionally more numerous at high-tannin levels. Tannins had no significant impact on overall diversity of bacterial communities analyzed with various estimators. There was an increased proportion of N-fixing bacteria corresponding to the addition of litter with low-tannin levels. The addition of litter increased the proportion of Ascomycota/Basidiomycota. Dothideomycetes, Pucciniomycetes, and Tremellomycetes also increased and Agaricomycetes decreased. Agaricomycetes and Sordariomycetes were significantly more abundant in controls, whereas Pucciniomycetes increased in soil with litter from transformed trees (P = 0.051). Richness estimators and diversity indices revealed no significant difference in the composition of fungal communities; PCoA (principal coordinate analyses) partitioned the fungal communities into three groups: (i) those with higher amounts of added tannin from both transformed and untransformed treatments, (ii) those corresponding to soils without litter, and (iii) those corresponding to microcosms with litter added from trees transformed only with a β-glucuronidase control vector. While the litter from transformed poplars had significant effects on soil microbe communities, the observed impacts reflected known impacts on soil processes associated with tannins, and were similar to changes that would be expected from natural variation in tannin levels.

Effect of vegetation removal and water table drawdown on the non-methane biogenic volatile organic compound emissions in boreal peatland microcosms

NASA Astrophysics Data System (ADS)

Faubert, Patrick; Tiiva, Päivi; Rinnan, Åsmund; Räty, Sanna; Holopainen, Jarmo K.; Holopainen, Toini; Rinnan, Riikka

2010-11-01

Biogenic volatile organic compound (BVOC) emissions are important in the global atmospheric chemistry and their feedbacks to global warming are uncertain. Global warming is expected to trigger vegetation changes and water table drawdown in boreal peatlands, such changes have only been investigated on isoprene emission but never on other BVOCs. We aimed at distinguishing the BVOCs released from vascular plants, mosses and peat in hummocks (dry microsites) and hollows (wet microsites) of boreal peatland microcosms maintained in growth chambers. We also assessed the effect of water table drawdown (-20 cm) on the BVOC emissions in hollow microcosms. BVOC emissions were measured from peat samples underneath the moss surface after the 7-week-long experiment to investigate whether the potential effects of vegetation and water table drawdown were shown. BVOCs were sampled using a conventional chamber method, collected on adsorbent and analyzed with GC-MS. In hummock microcosms, vascular plants increased the monoterpene emissions compared with the treatment where all above-ground vegetation was removed while no effect was detected on the sesquiterpenes, other reactive VOCs (ORVOCs) and other VOCs. Peat layer from underneath the surface with intact vegetation had the highest sesquiterpene emissions. In hollow microcosms, intact vegetation had the highest sesquiterpene emissions. Water table drawdown decreased monoterpene and other VOC emissions. Specific compounds could be closely associated to the natural/lowered water tables. Peat layer from underneath the surface of hollows with intact vegetation had the highest emissions of monoterpenes, sesquiterpenes and ORVOCs whereas water table drawdown decreased those emissions. The results suggest that global warming would change the BVOC emission mixtures from boreal peatlands following changes in vegetation composition and water table drawdown.

Impact of matric potential and pore size distribution on growth dynamics of filamentous and non-filamentous soil bacteria.

PubMed

Wolf, Alexandra B; Vos, Michiel; de Boer, Wietse; Kowalchuk, George A

2013-01-01

The filamentous growth form is an important strategy for soil microbes to bridge air-filled pores in unsaturated soils. In particular, fungi perform better than bacteria in soils during drought, a property that has been ascribed to the hyphal growth form of fungi. However, it is unknown if, and to what extent, filamentous bacteria may also display similar advantages over non-filamentous bacteria in soils with low hydraulic connectivity. In addition to allowing for microbial interactions and competition across connected micro-sites, water films also facilitate the motility of non-filamentous bacteria. To examine these issues, we constructed and characterized a series of quartz sand microcosms differing in matric potential and pore size distribution and, consequently, in connection of micro-habitats via water films. Our sand microcosms were used to examine the individual and competitive responses of a filamentous bacterium (Streptomyces atratus) and a motile rod-shaped bacterium (Bacillus weihenstephanensis) to differences in pore sizes and matric potential. The Bacillus strain had an initial advantage in all sand microcosms, which could be attributed to its faster growth rate. At later stages of the incubation, Streptomyces became dominant in microcosms with low connectivity (coarse pores and dry conditions). These data, combined with information on bacterial motility (expansion potential) across a range of pore-size and moisture conditions, suggest that, like their much larger fungal counterparts, filamentous bacteria also use this growth form to facilitate growth and expansion under conditions of low hydraulic conductivity. The sand microcosm system developed and used in this study allowed for precise manipulation of hydraulic properties and pore size distribution, thereby providing a useful approach for future examinations of how these properties influence the composition, diversity and function of soil-borne microbial communities.

Trophic structure of amoeba communities near roots of Medicago sativa after contamination with fuel oil no. 6.

PubMed

Cortés-Pérez, Sandra; Rodríguez-Zaragoza, Salvador; Mendoza-López, Ma Remedios

2014-02-01

Root exudation increases microbial activity, selecting bacterial and fungal communities that metabolize organic matter such as hydrocarbons. However, a strong contamination pulse of hydrocarbons around plant roots may reorganize the soil's microbial trophic structure toward amoebae feeding on bacteria. We conducted a microcosm experiment to elucidate the effect of Medicago sativa on the trophic structure of naked amoebae after a strong pulse of pollution (50,000 ppm of fuel oil no. 6, which is a mixture of long chains ranging from C10 to C28). Plants were seeded 24 h after contamination and species of amoebae in the microcosms were identified at 1, 30, and 60 days after pollution. Several species from three trophic groups of naked amoeba were still alive 24 h after the hydrocarbon pulse. Non-planted microcosms harbored three trophic groups after 60 days, while planted ones nourished four groups. The bacterivore group was the most diverse in all microcosms, followed by protist-eaters and omnivores. The quantity of amoebae was significantly higher (3.4×10(3) organisms/g soil) in the planted pots than in the non-planted ones (1.3×10(3) organisms/g soil after 30 days of pollution (P ≤ 0.01). The shortest hydrocarbon chains (C10-C14) disappeared or diminished in all microcosms, and the longest ones increased in the planted ones. M. sativa thus exerted a positive effect on species richness, quantity, and the composition of amoebae trophic groups in contaminated soil. This indirect effect on bacterial predators is another key factor underlying hydrocarbon assimilation by living organisms during phytoremediation.

Dental plaque microcosm response to bonding agents containing quaternary ammonium methacrylates with different chain lengths and charge densities

PubMed Central

Zhou, Han; Li, Fang; Weir, Michael D.; Xu, Hockin H.K.

2013-01-01

Objectives Antibacterial bonding agents are promising to combat bacteria and caries at tooth-restoration margins. The objectives of this study were to incorporate new quaternary ammonium methacrylates (QAMs) to bonding agent and determine the effects of alkyl chain length (CL) and quaternary amine charge density on dental plaque microcosm bacteria response for the first time. Methods Six QAMs were synthesized with CL = 3, 6, 9, 12, 16, 18. Each QAM was incorporated into Scotchbond Multi-purpose (SBMP). To determine the charge density effect, dimethylaminododecyl methacrylate (DMAHDM, CL = 16) was mixed into SBMP at mass fraction = 0%, 2.5%, 5%, 7.5%, 10%. Charge density was measured using a fluorescein dye method. Dental plaque microcosm using saliva from ten donors was tested. Bacteria were inoculated on resins. Early-attachment was tested at 4 hours. Biofilm colony-forming units (CFU) were measured at 2 days. Results Incorporating QAMs into SBMP reduced bacteria early-attachment. Microcosm biofilm CFU for CL = 16 was 4 log lower than SBMP control. Charge density of bonding agent increased with DMAHDM content. Bacteria early-attachment decreased with increasing charge density. Biofilm CFU at 10% DMAHDM was reduced by 4 log. The killing effect was similarly-strong against total microorganisms, total streptococci, and mutans streptococci. Conclusions Increasing alkyl chain length and charge density of bonding agent was shown for the first time to decrease microcosm bacteria attachment and reduce biofilm CFU by 4 orders of magnitude. Novel antibacterial resins with tailored chain length and charge density are promising for wide applications in bonding, cements, sealants and composites to inhibit biofilms and caries. PMID:23948394

Mercury Distribution, Methylation and Volatilization in Microcosms with and without the Sea Anemone Bunodosoma caissarum

NASA Astrophysics Data System (ADS)

Ansari, N. R.; Correia, R. R. S.; Fernandez, M. A. S.; Cordeiro, R. C.; Guimarães, J. R. D.

2014-12-01

Mercury (Hg) can be a dangerous contaminant and has a complex biogeochemical cycling in aquatic environments. The sea anemone Bunodosoma caissarum is an endemic species in Brazil capable of bioaccumulating Hg from the ambient seawater. The radiotracer 203Hg was used in order to investigate mechanisms of Hg uptake and depuration of B. caissarum and the distribution of Hg in laboratory model systems, with and without B. caissarum. A single initial spike of 203Hg was added to each microcosm. Microcosms had continuous air renovation and trapping of Hg volatile forms. Total Hg in different compartments was measured by gamma spectrometry. In the uptake experiment 203Hg activity was determined periodically in seawater and specimens for 6 days. At the end, specimens had an average bioconcentration factor of 70. After the uptake experiment, methylmercury (MeHg) in seawater was extracted and measured by liquid scintillation. In microcosms with and without B. caissarum, respectively 0.05% and 0.32% of the initial spike was found as MeHg. Hg was probably less available for methylation in the first because of bioaccumulation and higher concentrations of suspended particulate matter that could form complexes with Hg. After that, specimens were transferred to unspiked microcosms. After a 48 day depuration specimens still retained 35 - 70% of the previously bioaccumulated Hg and 0.2 - 2.4% of the total Hg was MeHg. The presence of B. caissarum resulted in an unexpected higher volatilization of Hg (58%) compared to controls (17%). This increased volatilization is possibly a result of Hg2+ reduction mediated by microorganisms associated with its tissues and mucus secretions and/or an unknown defense mechanism of this species.

Lability of High Molecular Weight Dissolved Organic Matter Polysaccharides Increases with Mild Acid or Base Treatment.

NASA Astrophysics Data System (ADS)

Pedler Sherwood, B.; Sosa, O.; Nelson, C. E.; Repeta, D.; DeLong, E.

2016-02-01

Approximately 662 Pg of dissolved organic carbon (DOC) has accumulated in the global ocean, yet the biological and chemical constraints on DOC turnover remain poorly understood. High molecular weight dissolved organic matter (HMWDOM) is largely comprised of semi-labile polysaccharides. These polysaccharides resist degradation even in the presence of nutrient amendments, suggesting unknown factors of polysaccharide composition affect microbial degradation. In a series of microcosm incubations conducted at station ALOHA in the North Pacific Subtropical Gyre, we tested the affect of mild base (KOH-DOM) and acid (HCl-DOM) treatments on polysaccharide lability. KOH-DOM, HCl-DOM, and untreated HMWDOM was added to seawater from the deep chlorophyll maximum and 200m. Microcosms amended with KOH-DOM and HCl-DOM yielded higher bacterial abundance and greater carbon drawdown relative to untreated HMWDOM and unamended controls. Microcosms amended with KOH-DOM and HCl-DOM also showed significant production of fluorescent DOM (fDOM), whereas untreated HMWDOM and unamended controls showed a net decrease in fDOM as measured by parallel factor analysis of DOM excitation-emission spectra. Metagenomic analyses revealed that microcosms amended with untreated HMWDOM and controls became dominated by Alteromonas genera ( 60% total sequence reads). In contrast, KOH-DOM and HCl-DOM amended microcosms yielded greater bacterial diversity; Alteromonas genera comprised 25% of sequence reads, with differences primarily accounted for by proportional increases in vibrio, roseobacter, rugeria and marinomonas clades. Transcriptomic analyses identified differential gene expression during growth on each DOM fraction. This study provides new insight into specific chemical moieties that may limit the bacterial degradation rate of semi-labile HMWDOM in the ocean.

Dental plaque microcosm response to bonding agents containing quaternary ammonium methacrylates with different chain lengths and charge densities.

PubMed

Zhou, Han; Li, Fang; Weir, Michael D; Xu, Hockin H K

2013-11-01

Antibacterial bonding agents are promising to combat bacteria and caries at tooth-restoration margins. The objectives of this study were to incorporate new quaternary ammonium methacrylates (QAMs) to bonding agent and determine the effects of alkyl chain length (CL) and quaternary amine charge density on dental plaque microcosm bacteria response for the first time. Six QAMs were synthesized with CL=3, 6, 9, 12, 16, 18. Each QAM was incorporated into Scotchbond multi-purpose (SBMP). To determine the charge density effect, dimethylaminododecyl methacrylate (DMAHDM, CL=16) was mixed into SBMP at mass fraction=0%, 2.5%, 5%, 7.5%, 10%. Charge density was measured using a fluorescein dye method. Dental plaque microcosm using saliva from ten donors was tested. Bacteria were inoculated on resins. Early-attachment was tested at 4h. Biofilm colony-forming units (CFU) were measured at 2 days. Incorporating QAMs into SBMP reduced bacteria early-attachment. Microcosm biofilm CFU for CL=16 was 4 log lower than SBMP control. Charge density of bonding agent increased with DMAHDM content. Bacteria early-attachment decreased with increasing charge density. Biofilm CFU at 10% DMAHDM was reduced by 4 log. The killing effect was similarly-strong against total microorganisms, total streptococci, and mutans streptococci. Increasing alkyl chain length and charge density of bonding agent was shown for the first time to decrease microcosm bacteria attachment and reduce biofilm CFU by 4 orders of magnitude. Novel antibacterial resins with tailored chain length and charge density are promising for wide applications in bonding, cements, sealants and composites to inhibit biofilms and caries. Copyright © 2013 Elsevier Ltd. All rights reserved.

Effect of Flooding and the nosZ Gene in Bradyrhizobia on Bradyrhizobial Community Structure in the Soil.

PubMed

Saeki, Yuichi; Nakamura, Misato; Mason, Maria Luisa T; Yano, Tsubasa; Shiro, Sokichi; Sameshima-Saito, Reiko; Itakura, Manabu; Minamisawa, Kiwamu; Yamamoto, Akihiro

2017-06-24

We investigated the effects of the water status (flooded or non-flooded) and presence of the nosZ gene in bradyrhizobia on the bradyrhizobial community structure in a factorial experiment that examined three temperature levels (20°C, 25°C, and 30°C) and two soil types (andosol and gray lowland soil) using microcosm incubations. All microcosms were inoculated with Bradyrhizobium japonicum USDA6 T , B. japonicum USDA123, and B. elkanii USDA76 T , which do not possess the nosZ gene, and then half received B. diazoefficiens USDA110 T wt (wt for the wild-type) and the other half received B. diazoefficiens USDA110ΔnosZ. USDA110 T wt possesses the nosZ gene, which encodes N 2 O reductase; 110ΔnosZ, a mutant variant, does not. Changes in the community structure after 30- and 60-d incubations were investigated by denaturing-gradient gel electrophoresis and an image analysis. USDA6 T and 76 T strains slightly increased in non-flooded soil regardless of which USDA110 T strain was present. In flooded microcosms with the USDA110 T wt strain, USDA110 T wt became dominant, whereas in microcosms with the USDA110ΔnosZ, a similar change in the community structure occurred to that in non-flooded microcosms. These results suggest that possession of the nosZ gene confers a competitive advantage to B. diazoefficiens USDA110 T in flooded soil. We herein demonstrated that the dominance of B. diazoefficiens USDA110 T wt within the soil bradyrhizobial population may be enhanced by periods of flooding or waterlogging systems such as paddy-soybean rotations because it appears to have the ability to thrive in moderately anaerobic soil.

Soil Communities Promote Temporal Stability and Species Asynchrony in Experimental Grassland Communities

PubMed Central

Pellkofer, Sarah; van der Heijden, Marcel G. A.; Schmid, Bernhard; Wagg, Cameron

2016-01-01

Background Over the past two decades many studies have demonstrated that plant species diversity promotes primary productivity and stability in grassland ecosystems. Additionally, soil community characteristics have also been shown to influence the productivity and composition of plant communities, yet little is known about whether soil communities also play a role in stabilizing the productivity of an ecosystem. Methodology/Principal Findings Here we use microcosms to assess the effects of the presence of soil communities on plant community dynamics and stability over a one-year time span. Microcosms were filled with sterilized soil and inoculated with either unaltered field soil or field soil sterilized to eliminate the naturally occurring soil biota. Eliminating the naturally occurring soil biota not only resulted in lower plant productivity, and reduced plant species diversity, and evenness, but also destabilized the net aboveground productivity of the plant communities over time, which was largely driven by changes in abundance of the dominant grass Lolium perenne. In contrast, the grass and legumes contributed more to net aboveground productivity of the plant communities in microcosms where soil biota had been inoculated. Additionally, the forbs exhibited compensatory dynamics with grasses and legumes, thus lowering temporal variation in productivity in microcosms that received the unaltered soil inocula. Overall, asynchrony among plant species was higher in microcosms where an unaltered soil community had been inoculated, which lead to higher temporal stability in community productivity. Conclusions/Significance Our results suggest that soil communities increase plant species asynchrony and stabilize plant community productivity by equalizing the performance among competing plant species through potential antagonistic and facilitative effects on individual plant species. PMID:26829481

Temporal Stability of the Microbial Community in Sewage-Polluted Seawater Exposed to Natural Sunlight Cycles and Marine Microbiota

PubMed Central

Sassoubre, Lauren M.; Yamahara, Kevan M.

2015-01-01

Billions of gallons of untreated wastewater enter the coastal ocean each year. Once sewage microorganisms are in the marine environment, they are exposed to environmental stressors, such as sunlight and predation. Previous research has investigated the fate of individual sewage microorganisms in seawater but not the entire sewage microbial community. The present study used next-generation sequencing (NGS) to examine how the microbial community in sewage-impacted seawater changes over 48 h when exposed to natural sunlight cycles and marine microbiota. We compared the results from microcosms composed of unfiltered seawater (containing naturally occurring marine microbiota) and filtered seawater (containing no marine microbiota) to investigate the effect of marine microbiota. We also compared the results from microcosms that were exposed to natural sunlight cycles with those from microcosms kept in the dark to investigate the effect of sunlight. The microbial community composition and the relative abundance of operational taxonomic units (OTUs) changed over 48 h in all microcosms. Exposure to sunlight had a significant effect on both community composition and OTU abundance. The effect of marine microbiota, however, was minimal. The proportion of sewage-derived microorganisms present in the microcosms decreased rapidly within 48 h, and the decrease was the most pronounced in the presence of both sunlight and marine microbiota, where the proportion decreased from 85% to 3% of the total microbial community. The results from this study demonstrate the strong effect that sunlight has on microbial community composition, as measured by NGS, and the importance of considering temporal effects in future applications of NGS to identify microbial pollution sources. PMID:25576619

Molecular Dynamics Simulations of Grain Boundary and Bulk Diffusion in Metals.

NASA Astrophysics Data System (ADS)

Plimpton, Steven James

Diffusion is a microscopic mass transport mechanism that underlies many important macroscopic phenomena affecting the structural, electrical, and mechanical properties of metals. This thesis presents results from atomistic simulation studies of diffusion both in bulk and in the fast diffusion paths known as grain boundaries. Using the principles of molecular dynamics single boundaries are studied and their structure and dynamic properties characterized. In particular, tilt boundary bicrystal and bulk models of fcc Al and bcc alpha-Fe are simulated. Diffusion coefficients and activation energies for atomic motion are calculated for both models and compared to experimental data. The influence of the interatomic pair potential on the diffusion is studied in detail. A universal relation between the melting temperature that a pair potential induces in a simulated bulk model and the potential energy barrier height for atomic hopping is derived and used to correlate results for a wide variety of pair potentials. Using these techniques grain boundary and bulk diffusion coefficients for any fcc material can be estimated from simple static calculations without the need to perform more time-consuming dynamic simulations. The influences of two other factors on grain boundary diffusion are also studied because of the interest of the microelectronics industry in the diffusion related reliability problem known as electromigration. The first factor, known to affect the self diffusion rate of Al, is the presence of Cu impurity atoms in Al tilt boundaries. The bicrystal model for Al is seeded randomly with Cu atoms and a simple hybrid Morse potential used to model the Al-Cu interaction. While some effect due to the Cu is noted, it is concluded that pair potentials are likely an inadequate approximation for the alloy system. The second factor studied is the effect of the boundary orientation angle on the diffusion rate. Symmetric bcc Fe boundaries are relaxed to find optimal structures and their diffusion coefficients calculated. Good agreement is found with the dislocation pipe model for tilt boundary diffusion.

A new coarse-grained model for E. coli cytoplasm: accurate calculation of the diffusion coefficient of proteins and observation of anomalous diffusion.

PubMed

Hasnain, Sabeeha; McClendon, Christopher L; Hsu, Monica T; Jacobson, Matthew P; Bandyopadhyay, Pradipta

2014-01-01

A new coarse-grained model of the E. coli cytoplasm is developed by describing the proteins of the cytoplasm as flexible units consisting of one or more spheres that follow Brownian dynamics (BD), with hydrodynamic interactions (HI) accounted for by a mean-field approach. Extensive BD simulations were performed to calculate the diffusion coefficients of three different proteins in the cellular environment. The results are in close agreement with experimental or previously simulated values, where available. Control simulations without HI showed that use of HI is essential to obtain accurate diffusion coefficients. Anomalous diffusion inside the crowded cellular medium was investigated with Fractional Brownian motion analysis, and found to be present in this model. By running a series of control simulations in which various forces were removed systematically, it was found that repulsive interactions (volume exclusion) are the main cause for anomalous diffusion, with a secondary contribution from HI.

An electromechanical based deformable model for soft tissue simulation.

PubMed

Zhong, Yongmin; Shirinzadeh, Bijan; Smith, Julian; Gu, Chengfan

2009-11-01

Soft tissue deformation is of great importance to surgery simulation. Although a significant amount of research efforts have been dedicated to simulating the behaviours of soft tissues, modelling of soft tissue deformation is still a challenging problem. This paper presents a new deformable model for simulation of soft tissue deformation from the electromechanical viewpoint of soft tissues. Soft tissue deformation is formulated as a reaction-diffusion process coupled with a mechanical load. The mechanical load applied to a soft tissue to cause a deformation is incorporated into the reaction-diffusion system, and consequently distributed among mass points of the soft tissue. Reaction-diffusion of mechanical load and non-rigid mechanics of motion are combined to govern the simulation dynamics of soft tissue deformation. An improved reaction-diffusion model is developed to describe the distribution of the mechanical load in soft tissues. A three-layer artificial cellular neural network is constructed to solve the reaction-diffusion model for real-time simulation of soft tissue deformation. A gradient based method is established to derive internal forces from the distribution of the mechanical load. Integration with a haptic device has also been achieved to simulate soft tissue deformation with haptic feedback. The proposed methodology does not only predict the typical behaviours of living tissues, but it also accepts both local and large-range deformations. It also accommodates isotropic, anisotropic and inhomogeneous deformations by simple modification of diffusion coefficients.

Structural and water diffusion of poly(acryl amide)/poly(vinyl alcohol) blend films: Experiment and molecular dynamics simulations.

PubMed

Wang, Yanen; Wei, Qinghua; Wang, Shuzhi; Chai, Weihong; Zhang, Yingfeng

2017-01-01

To study the effects of composition ratios and temperature on the diffusion of water molecules in PVA/PAM blend films, five simulation models of PVA/PAM with ten water molecules at different composition ratios (4/0, 3/1, 2/2, 1/3, 0/4) were constructed and simulated by using a molecular dynamics (MD) simulation. The diffusion behavior of water molecules in blends were investigated from the aspects of the diffusion coefficient, free volume, pair correlation function (PCF) and trajectories of water molecules, respectively. And the hydrophilicity of blend composite was studied based on the contact angle and equilibrium water content (EWC) of the blend films. The simulation results show that the diffusion coefficient of water molecules and fractional free volume (FFV) of blend membranes increase with the addition of PAM, and a higher temperature can also improve the diffusion of water molecules. Additionally, the analysis of PCFs reveals the main reason why the diffusion coefficient of water in blend system increases with the addition of PAM. The measurement results of contact angle and EWC of blend films indicate that the hydrophilicity of blend films decreases with the addition of PAM, but the EWC of blends increases with the addition of PAM. Copyright © 2016 Elsevier Inc. All rights reserved.

Simulations of singlet exciton diffusion in organic semiconductors: a review

DOE PAGES

Bjorgaard, Josiah A.; Kose, Muhammet Erkan

2014-12-22

Our review describes the various aspects of simulation strategies for exciton diffusion in condensed phase thin films of organic semiconductors. Several methods for calculating energy transfer rate constants are discussed along with procedures for how to account for energetic disorder. Exciton diffusion can be modelled by using kinetic Monte-Carlo methods or master equations. Recent literature on simulation efforts for estimating exciton diffusion lengths of various conjugated polymers and small molecules are introduced. Moreover, these studies are discussed in the context of the effects of morphology on exciton diffusion and the necessity of accurate treatment of disorder for comparison of simulationmore » results with those of experiment.« less

Kinetic Monte Carlo (kMC) simulation of carbon co-implant on pre-amorphization process.

PubMed

Park, Soonyeol; Cho, Bumgoo; Yang, Seungsu; Won, Taeyoung

2010-05-01

We report our kinetic Monte Carlo (kMC) study of the effect of carbon co-implant on the pre-amorphization implant (PAL) process. We employed BCA (Binary Collision Approximation) approach for the acquisition of the initial as-implant dopant profile and kMC method for the simulation of diffusion process during the annealing process. The simulation results implied that carbon co-implant suppresses the boron diffusion due to the recombination with interstitials. Also, we could compare the boron diffusion with carbon diffusion by calculating carbon reaction with interstitial. And we can find that boron diffusion is affected from the carbon co-implant energy by enhancing the trapping of interstitial between boron and interstitial.

Hydrogen sulfide production by sulfate-reducing bacteria utilizing additives eluted from plastic resins.

PubMed

Tsuchida, Daisuke; Kajihara, Yusuke; Shimidzu, Nobuhiro; Hamamura, Kengo; Nagase, Makoto

2011-06-01

In the present study it was demonstrated that organic additives eluted from plastic resins could be utilized as substrates by sulfate-reducing bacteria. Two laboratory-scale experiments, a microcosm experiment and a leaching experiment, were conducted using polyvinyl chloride (PVC) as a model plastic resin. In the former experiment, the conversion of sulfate to sulfide was evident in microcosms that received plasticized PVC as the sole carbon source, but not in those that received PVC homopolymer. Additionally, dissolved organic carbon accumulated only in microcosms that received plasticized PVC, indicating that the dissolved organic carbon originated from additives. In the leaching experiment, phenol and bisphenol A were found in the leached solutions. These results suggest that the disposal of waste plastics in inert waste landfills may result in the production of H(2)S.

Numerical simulation of double‐diffusive finger convection

USGS Publications Warehouse

Hughes, Joseph D.; Sanford, Ward E.; Vacher, H. Leonard

2005-01-01

A hybrid finite element, integrated finite difference numerical model is developed for the simulation of double‐diffusive and multicomponent flow in two and three dimensions. The model is based on a multidimensional, density‐dependent, saturated‐unsaturated transport model (SUTRA), which uses one governing equation for fluid flow and another for solute transport. The solute‐transport equation is applied sequentially to each simulated species. Density coupling of the flow and solute‐transport equations is accounted for and handled using a sequential implicit Picard iterative scheme. High‐resolution data from a double‐diffusive Hele‐Shaw experiment, initially in a density‐stable configuration, is used to verify the numerical model. The temporal and spatial evolution of simulated double‐diffusive convection is in good agreement with experimental results. Numerical results are very sensitive to discretization and correspond closest to experimental results when element sizes adequately define the spatial resolution of observed fingering. Numerical results also indicate that differences in the molecular diffusivity of sodium chloride and the dye used to visualize experimental sodium chloride concentrations are significant and cause inaccurate mapping of sodium chloride concentrations by the dye, especially at late times. As a result of reduced diffusion, simulated dye fingers are better defined than simulated sodium chloride fingers and exhibit more vertical mass transfer.

Diffusion Coefficients from Molecular Dynamics Simulations in Binary and Ternary Mixtures

NASA Astrophysics Data System (ADS)

Liu, Xin; Schnell, Sondre K.; Simon, Jean-Marc; Krüger, Peter; Bedeaux, Dick; Kjelstrup, Signe; Bardow, André; Vlugt, Thijs J. H.

2013-07-01

Multicomponent diffusion in liquids is ubiquitous in (bio)chemical processes. It has gained considerable and increasing interest as it is often the rate limiting step in a process. In this paper, we review methods for calculating diffusion coefficients from molecular simulation and predictive engineering models. The main achievements of our research during the past years can be summarized as follows: (1) we introduced a consistent method for computing Fick diffusion coefficients using equilibrium molecular dynamics simulations; (2) we developed a multicomponent Darken equation for the description of the concentration dependence of Maxwell-Stefan diffusivities. In the case of infinite dilution, the multicomponent Darken equation provides an expression for [InlineEquation not available: see fulltext.] which can be used to parametrize the generalized Vignes equation; and (3) a predictive model for self-diffusivities was proposed for the parametrization of the multicomponent Darken equation. This equation accurately describes the concentration dependence of self-diffusivities in weakly associating systems. With these methods, a sound framework for the prediction of mutual diffusion in liquids is achieved.

Methyl t-Butyl Ether Mineralization in Surface-Water Sediment Microcosms under Denitrifying Conditions

USGS Publications Warehouse

Bradley, P.M.; Chapelle, F.H.; Landmeyer, J.E.

2001-01-01

Mineralization of [U-14C] methyl t-butyl ether (MTBE) to 14CO2 without accumulation of t-butyl alcohol (TBA) was observed in surface-water sediment microcosms under denitrifying conditions. Methanogenic activity and limited transformation of MTBE to TBA were observed in the absence of denitrification. Results indicate that bed sediment microorganisms can effectively degrade MTBE to nontoxic products under denitrifying conditions.

Does lead affect microbial metabolism in aquifer sediments under different terminal electron accepting conditions?

USGS Publications Warehouse

Bradley, P.M.; Chapelle, F.H.; Vroblesky, D.A.

1993-01-01

In groundwater from a petroleum hydrocarbon-contaminated aquifer. Substantial accumulation of aliphatic organic acids occurred only in methanogenic microcosms, and only trace amounts of acetic acid were detected in sulfate-reducing microcosms. This pattern parallels field observations in which high organic acid concentrations were detected in methanogenic zones, but only low concentrations of acetic acid were detected in sulfate-reducing zones. -from Authors

Radiation-induced impacts on the degradation of 2,4-D and the microbial population in soil microcosms.

PubMed

Niedrée, Bastian; Vereecken, Harry; Burauel, Peter

2013-01-01

In a soil microcosm experiment, the influence of low-level (137)Cs and (90)Sr contamination on the degradation of (14)C-ring-labeled 2,4-dichlorophenoxyacetic acid (2,4-D) was studied. Two differently treated soils (one native soil and one soil sterilized and reinoculated with a biotic soil aliquot) were artificially contaminated with various concentrations of (137)Cs and (90)Sr as nitrate salts. The cumulative doses increased up to 4 Gy for 30 days of incubation in soil microcosms. Changes in microbial community structure were observed with help of the denaturing gradient gel electrophoresis (DGGE). A radiation-induced impact appeared only in the microcosms treated with 30 times the maximum contamination appearing in the exclusion zone around reactor 4 in Chernobyl. In contrast to the less contaminated soils, the mineralization of 2,4-D was delayed for 4 days before it recovered. Slight shifts in the microbial communities could be traced to radiation effects. However, other parameters had a major impact on mineralization and community structure. Thus the sterilization and reinoculation and, of course, application of the 2,4-D were predominantly reflected in the (14)CO(2) emissions and the DGGE gel patterns. Copyright © 2012 Elsevier Ltd. All rights reserved.

Effects of the phenylurea herbicide diuron on natural riverine microbial communities in an experimental study.

PubMed

Pesce, Stéphane; Fajon, Céline; Bardot, Corinne; Bonnemoy, Frédérique; Portelli, Christophe; Bohatier, Jacques

2006-07-20

The effects of the phenylurea herbicide diuron (10 microgl(-1)) on natural riverine microbial communities were investigated using a three-week laboratory microcosm study. During the first six days, a latency period was observed both in the algal and the bacterial communities despite favorable abiotic conditions and independently of diuron exposure. From the second week, an intense algal bloom (chlorophyll a concentrations and cell abundances) was observed in the uncontaminated microcosms but not in the treated microcosms. The bloom stimulated the bacterial community and led to an increase in heterotrophic bacterial production ([3H]thymidine incorporation), activity (CTC reduction) and cell abundance. In parallel, shifts in bacterial community composition were recorded by polymerase chain reaction (PCR)-temporal temperature gradient gel electrophoresis (TTGE) analysis, whereas no major variation was detected using the fluorescent in situ hybridization (FISH) method. In the treated microcosms, the diuron acted not by damaging the initial communities but by inhibiting the algal bloom and indirectly maintaining constant bacterial conditions throughout the experiment. These inhibitory effects, which were recorded in terms of abundance, activity and diversity, suggest that exposure to diuron can decrease the recovery capacities of microbial communities and delay the resumption of an efficient microbial food web despite favorable environmental conditions.

Accelerated biodegradation of BPA in water-sediment microcosms with Bacillus sp. GZB and the associated bacterial community structure.

PubMed

Xiong, Jukun; An, Taicheng; Li, Guiying; Peng, Ping'an

2017-10-01

Bisphenol A (BPA) is a synthetic chemical primarily used to produce polycarbonate plastics and epoxy resins. Significant industrial and consumer's consumption of BPA-containing products has contributed to extensive contamination in different environmental matrices. In this study, microcosms bioaugmented with Bacillus sp. GZB were constructed to investigate BPA biodegradation, identify the main bacterial community, and evaluate bacterial community responses in the microcosms. Under aerobic conditions, BPA was quickly depleted as a result of bioaugmentation with Bacillus sp. GZB in water-sediment contaminated with pollutants. The pollutants used were generally associated with the electronic wastes (mobile phones, computers, televisions) dismantling process. Adding BPA affected the bacterial community composition in the water-sediment. Furthermore, BPA biodegradation was enhanced by adding electron donors/co-substrates: humic acid, NaCl, glucose, and yeast extract. Metagenomic analysis of the total 16S rRNA genes from the BPA-degrading microcosms with bioaugmentation illustrated that the genera Bacillus, Thiobacillus, Phenylobacterium, and Cloacibacterium were dominant after a 7-week incubation period. A consortium of microorganisms from different bacterial genera may be involved in BPA biodegradation in electronic waste contaminated water-sediment. This study provides new insights about BPA bioaugmentation and bacterial ecology in the BPA-degrading environment. Copyright © 2017 Elsevier Ltd. All rights reserved.

Fate and bioaccumulation of isoproturon in outdoor aquatic microcosms.

PubMed

Merlin, Gerard; Vuillod, Maryline; Lissolo, Thierry; Clement, Bernard

2002-06-01

To gain information concerning the ecotoxicity of isoproturon (IPU) on aquatic ecosystems, six experimental ponds of 5 m3 each were studied. All the experiments were conducted during the summer over two years. Three different types of ecosystems were tested in 1994 and one type of ecosystem was selected and repeated in 1995 with three replicates. In each case, the initial concentration of IPU contamination was set at 10 microg/L. The IPU concentration was determined in the water column and in different species (mainly plants) of the microcosms. A first-order kinetic decrease in IPU concentration was observed in 1994, with half-life ranging from 15 to 35 d, depending on the microcosms. This relatively fast decrease was also confirmed in 1995, but it reached a constant value after two months. A high variability of the IPU concentration was observed in exposed plants, with bioconcentration factors ranging from 100 to 1,200 with large coefficients of variation. The observed plant bioconcentration factors are higher than those predicted by usual numerical models, probably due to the specific binding of IPU on one protein of the photosynthetic apparatus. Our data show that bioconcentration does not occur in mollusks but is important in photosynthetic organisms. Plant bioconcentration and microbial biodegradation are the main processes involved in the IPU decay in our outdoor aquatic microcosms.

Determining the effects of pollutants on soil faunal communities and trophic structure using a refined microcosm system

DOE Office of Scientific and Technical Information (OSTI.GOV)

Parmelee, R.W.; Phillips, C.T.; Checkai, R.T.

1997-06-01

The authors used a refined microcosm technique to investigate the toxicity of copper, cadmium, malathion, and the polychlorinated biphenyl, to trophic groups of soil nematodes and to the microarthropod community. Comparisons of changes in nematode abundance in control soils through time indicated that day 7 was the most appropriate time to sample the microcosms after chemical application. Nematode abundance was reduced after exposure to copper at 100 {micro}g/g, with fungivore, bacterivore, and omnivore-predator nematodes being the most sensitive groups. Cadmium did not affect the nematode or microarthropod communities. Microarthropods were far more sensitive to malathion than were nematodes, and totalmore » microarthropod abundance was lower than controls at 400 {micro}g/g. Prostigmatid mites and other arthropods were the most affected groups. PCB also had a greater negative impact on microarthropods than on nematodes. Total microarthropod abundance declined at 2,500 {micro}g/g, with prostigmatid and oribatid mites exhibiting the highest susceptibility. Strong differential sensitivity between nematode and microarthropod communities indicates that both groups should be examined to fully evaluate the biological impact of chemicals on soils. The authors conclude that microcosms with field-collected soil microfaunal communities offer high resolution of the ecotoxicologic effects of chemicals in complex soil systems.« less

Oligotrophic wetland sediments susceptible to shifts in microbiomes and mercury cycling with dissolved organic matter addition

PubMed Central

Gabor, Rachel S.; Schooler, Shon; McKnight, Diane M.; Knelman, Joseph E.

2018-01-01

Recent advances have allowed for greater investigation into microbial regulation of mercury toxicity in the environment. In wetlands in particular, dissolved organic matter (DOM) may influence methylmercury (MeHg) production both through chemical interactions and through substrate effects on microbiomes. We conducted microcosm experiments in two disparate wetland environments (oligotrophic unvegetated and high-C vegetated sediments) to examine the impacts of plant leachate and inorganic mercury loadings (20 mg/L HgCl2) on microbiomes and MeHg production in the St. Louis River Estuary. Our research reveals the greater relative capacity for mercury methylation in vegetated over unvegetated sediments. Further, our work shows how mercury cycling in oligotrophic unvegetated sediments may be susceptible to DOM inputs in the St. Louis River Estuary: unvegetated microcosms receiving leachate produced substantially more MeHg than unamended microcosms. We also demonstrate (1) changes in microbiome structure towards Clostridia, (2) metagenomic shifts toward fermentation, and (3) degradation of complex DOM; all of which coincide with elevated net MeHg production in unvegetated microcosms receiving leachate. Together, our work shows the influence of wetland vegetation in controlling MeHg production in the Great Lakes region and provides evidence that this may be due to both enhanced microbial activity as well as differences in microbiome composition. PMID:29632744

Screening tests for assessing the anaerobic biodegradation of pollutant chemicals in subsurface environments

USGS Publications Warehouse

Suflita, Joseph M.; Concannon, Frank

1995-01-01

Screening methods were developed to assess the susceptibility of ground water contaminants to anaerobic biodegradation. One method was an extrapolation of a procedure previously used to measure biodegradation activity in dilute sewage sludge. Aquifer solids and ground water with no additional nutritive media were incubated anaerobically in 160-ml serum bottles containing 250 mg·l−1 carbon of the substrate of interest. This method relied on the detection of gas pressure or methane production in substrateamended microcosms relative to background controls. Other screening procedures involved the consumption of stoichiometrically required amounts of sulfate or nitrate from the same type of incubations. Close agreement was obtained between the measured and calculated amounts of substrate bioconversion based on the measured biogas pressure in methanogenic microcosms. Storage of the microcosms for up to 6 months did not adversely influence the onset or rate of benzoic acid mineralization. The lower detection limits of the methanogenic assay were found to be a function of the size of the microcosm headspace, the mean oxidation state of the substrate carbon, and the method used to correct for background temperature fluctuations. Using these simple screening procedures, biodegradation information of regulatory interest could be generated, including, (i) the length of the adaptation period, (ii) the rate of substrate decay and (iii) the completeness of the bioconversion.

Inhibition of Biodegradation of Hydraulic Fracturing Compounds by Glutaraldehyde: Groundwater Column and Microcosm Experiments.

PubMed

Rogers, Jessica D; Ferrer, Imma; Tummings, Shantal S; Bielefeldt, Angela R; Ryan, Joseph N

2017-09-05

The rapid expansion of unconventional oil and gas development has raised concerns about the potential contamination of aquifers; however, the groundwater fate and transport of hydraulic fracturing fluid compounds and mixtures remains a significant data gap. Degradation kinetics of five hydraulic fracturing compounds (2-propanol, ethylene glycol, propargyl alcohol, 2-butoxyethanol, and 2-ethylhexanol) in the absence and presence of the biocide glutaraldehyde were investigated under a range of redox conditions using sediment-groundwater microcosms and flow-through columns. Microcosms were used to elucidate biodegradation inhibition at varying glutaraldehyde concentrations. In the absence of glutaraldehyde, half-lives ranged from 13 d to >93 d. Accurate mass spectrometry indicated that a trimer was the dominant aqueous-phase glutaraldehyde species. Microbial inhibition was observed at glutaraldehyde trimer concentrations as low as 5 mg L -1 , which demonstrated that the trimer retained some biocidal activity. For most of the compounds, biodegradation rates slowed with increasing glutaraldehyde concentrations. For many of the compounds, degradation was faster in the columns than the microcosms. Four compounds (2-propanol, ethylene glycol, propargyl alcohol, and 2-butoxyethanol) were found to be both mobile and persistent in groundwater under a range of redox conditions. The glutaraldehyde trimer and 2-ethylhexanol were more rapidly degraded, particularly under oxic conditions.

Molecular simulation of gas adsorption and diffusion in a breathing MOF using a rigid force field.

PubMed

García-Pérez, E; Serra-Crespo, P; Hamad, S; Kapteijn, F; Gascon, J

2014-08-14

Simulation of gas adsorption in flexible porous materials is still limited by the slow progress in the development of flexible force fields. Moreover, the high computational cost of such flexible force fields may be a drawback even when they are fully developed. In this work, molecular simulations of gas adsorption and diffusion of carbon dioxide and methane in NH2-MIL-53(Al) are carried out using a linear combination of two crystallographic structures with rigid force fields. Once the interactions of carbon dioxide molecules and the bridging hydroxyls groups of the framework are optimized, an excellent match is found for simulations and experimental data for the adsorption of methane and carbon dioxide, including the stepwise uptake due to the breathing effect. In addition, diffusivities of pure components are calculated. The pore expansion by the breathing effect influences the self-diffusion mechanism and much higher diffusivities are observed at relatively high adsorbate loadings. This work demonstrates that using a rigid force field combined with a minimum number of experiments, reproduces adsorption and simulates diffusion of carbon dioxide and methane in the flexible metal-organic framework NH2-MIL-53(Al).

Monte Carlo simulation of the back-diffusion of electrons in nitrogen

NASA Astrophysics Data System (ADS)

Radmilović-Radjenović, M.; Nina, A.; Nikitović, Ž.

2009-01-01

In this paper, the process of back-diffusion in nitrogen is studied by means of Monte Carlo simulations. In particular we analyze the influence of different aspects of back-diffusion in order to simplify the models of plasma displays, low pressure gas breakdown and detectors of high energy particles. The obtained simulation results show that the escape coefficient depends strongly on the reflection coefficient and the initial energy of electrons. It was also found that the back-diffusion range and number of collisions before returning to the cathode in nitrogen are smaller than those in argon for similar conditions.

Coarse-grained hydrodynamics from correlation functions

NASA Astrophysics Data System (ADS)

Palmer, Bruce

2018-02-01

This paper will describe a formalism for using correlation functions between different grid cells as the basis for determining coarse-grained hydrodynamic equations for modeling the behavior of mesoscopic fluid systems. Configurations from a molecular dynamics simulation or other atomistic simulation are projected onto basis functions representing grid cells in a continuum hydrodynamic simulation. Equilibrium correlation functions between different grid cells are evaluated from the molecular simulation and used to determine the evolution operator for the coarse-grained hydrodynamic system. The formalism is demonstrated on a discrete particle simulation of diffusion with a spatially dependent diffusion coefficient. Correlation functions are calculated from the particle simulation and the spatially varying diffusion coefficient is recovered using a fitting procedure.

Influence of acid volatile sulfides and metal concentrations on metal partitioning in contaminated sediments

USGS Publications Warehouse

Lee, J.-S.; Lee, B.-G.; Luoma, S.N.; Choi, H.J.; Koh, C.-H.; Brown, C.L.

2000-01-01

The influence of acid volatile sulfide (AVS) on the partitioning of Cd, Ni, and Zn in porewater (PW) and sediment as reactive metals (SEM, simultaneously extracted metals) was investigated in laboratory microcosms. Two spiking procedures were compared, and the effects of vertical geochemical gradients and infaunal activity were evaluated. Sediments were spiked with a Cd-Ni-Zn mixture (0.06, 3, 7.5 ??mol/g, respectively) containing four levels of AVS (0.5, 7.5, 15, 35 ??mol/g). The results were compared to sediments spiked with four levels of Cd-Ni-Zn mixtures at one AVS concentration (7.5 ??mol/g). A vertical redox gradient was generated in each treatment by an 18-d incubation with an oxidized water column. [AVS] in the surface sediments decreased by 65-95% due to oxidation during incubation; initial [AVS] was maintained at 0.5-7.5 cm depth. PW metal concentrations were correlated with [SEM - AVS] among all data. But PW metal concentrations were variable, causing the distribution coefficient, Kd(pw) (the ratio of [SEM] to PW metal concentrations) to vary by 2-3 orders of magnitude at a given [SEM - AVS]. One reason for the variability was that vertical profiles in PW metal concentrations appeared to be influenced by diffusion as well as [SEM - AVS]. The presence of animals appeared to enhance the diffusion of at least Zn. The generalization that PW metal concentrations are controlled by [SEM - AVS] is subject to some important qualifications if vertical gradients are complicated, metal concentrations vary, or equilibration times differ.The influence of acid volatile sulfide (AVS) on the partitioning of Cd, Ni, and Zn in porewater (PW) and sediment as reactive metals (SEM, simultaneously extracted metals) was investigated in laboratory microcosms. Two spiking procedures were compared, and the effects of vertical geochemical gradients and infaunal activity were evaluated. Sediments were spiked with a Cd-Ni-Zn mixture (0.06, 3, 7.5 ??mol/g, respectively) containing four levels of AVS (0.5, 7.5, 15, 35 ??mol/g). The results were compared to sediments spiked with four levels of Cd-Ni-Zn mixtures at one AVS concentration (7.5 ??mol/g). A vertical redox gradient was generated in each treatment by an 18-d incubation with an oxidized water column. [AVS] in the surface sediments decreased by 65-95% due to oxidation during incubation; initial [AVS] was maintained at 0.5-7.5 cm depth. PW metal concentrations were correlated with [SEM - AVS] among all data. But PW metal concentrations were variable, causing the distribution coefficient, Kdpw (the ratio of [SEM] to PW metal concentrations) to vary by 2-3 orders of magnitude at a given [SEM - AVS]. One reason for the variability was that vertical profiles in PW metal concentrations appeared to be influenced by diffusion as well as [SEM - AVS]. The presence of animals appeared to enhance the diffusion of at least Zn. The generalization that PW metal concentrations are controlled by [SEM - AVS] is subject to some important qualifications if vertical gradients are complicated, metal concentrations vary, or equilibration times differ.

Uncovering stability mechanisms in microbial ecosystems - combining microcosm experiments, computational modelling and ecological theory in a multidisciplinary approach

NASA Astrophysics Data System (ADS)

Worrich, Anja; König, Sara; Banitz, Thomas; Centler, Florian; Frank, Karin; Kästner, Matthias; Miltner, Anja; Thullner, Martin; Wick, Lukas

2015-04-01

Although bacterial degraders in soil are commonly exposed to fluctuating environmental conditions, the functional performance of the biodegradation processes can often be maintained by resistance and resilience mechanisms. However, there is still a gap in the mechanistic understanding of key factors contributing to the stability of such an ecosystem service. Therefore we developed an integrated approach combining microcosm experiments, simulation models and ecological theory to directly make use of the strengths of these disciplines. In a continuous interplay process, data, hypotheses, and central questions are exchanged between disciplines to initiate new experiments and models to ultimately identify buffer mechanisms and factors providing functional stability. We focus on drying and rewetting-cycles in soil ecosystems, which are a major abiotic driver for bacterial activity. Functional recovery of the system was found to depend on different spatial processes in the computational model. In particular, bacterial motility is a prerequisite for biodegradation if either bacteria or substrate are heterogeneously distributed. Hence, laboratory experiments focussing on bacterial dispersal processes were conducted and confirmed this finding also for functional resistance. Obtained results will be incorporated into the model in the next step. Overall, the combination of computational modelling and laboratory experiments identified spatial processes as the main driving force for functional stability in the considered system, and has proved a powerful methodological approach.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bu, Lintao; Nimlos, Mark R.; Robichaud, David J.

Hierarchical mesoporous zeolites exhibit higher catalytic activities and longer lifetime compared to the traditional microporous zeolites due to improved diffusivity of substrate molecules and their enhanced access to the zeolite active sites. Understanding diffusion of biomass pyrolysis vapors and their upgraded products in such materials is fundamentally important during catalytic fast pyrolysis (CFP) of lignocellulosic biomass, since diffusion makes major contribution to determine shape selectivity and product distribution. However, diffusivities of biomass relevant species in hierarchical mesoporous zeolites are poorly characterized, primarily due to the limitations of the available experimental technology. In this work, molecular dynamics (MD) simulations are utilizedmore » to investigate the diffusivities of several selected coke precursor molecules, benzene, naphthalene, and anthracene, in hierarchical mesoporous H-ZSM-5 zeolite. The effects of temperature and size of mesopores on the diffusivity of the chosen model compounds are examined. The simulation results demonstrate that diffusion within the microspores as well as on the external surface of mesoporous H-ZSM-5 dominates only at low temperature. At pyrolysis relevant temperatures, mass transfer is essentially conducted via diffusion along the mesopores. Additionally, the results illustrate the heuristic diffusion model, such as the extensively used Knudsen diffusion, overestimates the diffusion of bulky molecules in the mesopores, thus making MD simulation a powerful and compulsory approach to explore diffusion in zeolites.« less

The heavy ion diffusion region in magnetic reconnection in the Earth's magnetotail

NASA Astrophysics Data System (ADS)

Liu, Y. H.; Mouikis, C. G.; Kistler, L. M.; Wang, S.; Roytershteyn, V.; Karimabadi, H.

2015-05-01

While the plasma in the Earth's magnetotail predominantly consists of protons and electrons, there are times when a significant amount of oxygen is present. When magnetic reconnection occurs, the behavior of these heavy ions can be significantly different from that of the protons, due to their larger gyroradius. In this study, we investigate the heavy ion distribution functions in the reconnection ion diffusion region from a 2.5D three-species particle-in-cell numerical simulation and compare those with Cluster observations from the near-Earth magnetotail. From the simulation results, we find that the heavy ions are demagnetized and accelerated in a larger diffusion region, the heavy ion diffusion region. The ion velocity distribution functions show that, inside the heavy ion diffusion region, heavy ions appear as counterstreaming beams along z in the GSM x-z plane, while drifting in y, carrying cross-tail current. We compare this result with Cluster observations in the vicinity of reconnection regions in the near-Earth magnetotail and find that the simulation predictions are consistent with the observed ion distribution functions in the ion diffusion region, as well as the inflow, exhaust, and separatrix regions. Based on the simulation and observation results, the presence of a multiscale diffusion region model, for O+ abundant reconnection events in the Earth's magnetotail, is demonstrated. A test particle simulation shows that in the diffusion region, the H+ gains energy mainly through Ex, while the O+ energy gain comes equally from Ex and Ey.

Computation of diffuse sky irradiance from multidirectional radiance measurements

NASA Technical Reports Server (NTRS)

Ahmad, Suraiya P.; Middleton, Elizabeth M.; Deering, Donald W.

1987-01-01

Accurate determination of the diffuse solar spectral irradiance directly above the land surface is important in characterizing the reflectance properties of these surfaces, especially vegetation canopies. This determination is also needed to infer the net radiation budget of the earth-atmosphere system above these surfaces. An algorithm is developed here for the computation of hemispheric diffuse irradiance using the measurements from an instrument called PARABOLA, which rapidly measures upwelling and downwelling radiances in three selected wavelength bands. The validity of the algorithm is established from simulations. The standard reference data set of diffuse radiances of Dave (1978), obtained by solving the radiative transfer equation numerically for realistic atmospheric models, is used to simulate PARABOLA radiances. Hemispheric diffuse irradiance is estimated from a subset of simulated radiances by using the algorithm described. The algorithm is validated by comparing the estimated diffuse irradiance with the true diffuse irradiance of the standard data set. The validations include sensitivity studies for two wavelength bands (visible, 0.65-0.67 micron; near infrared, 0.81-0.84 micron), different atmospheric conditions, solar elevations, and surface reflectances. In most cases the hemispheric diffuse irradiance computed from simulated PARABOLA radiances and the true irradiance obtained from radiative transfer calculations agree within 1-2 percent. This technique can be applied to other sampling instruments designed to estimate hemispheric diffuse sky irradiance.

Molecular dynamics simulations of lithium silicate/vanadium pentoxide interfacial lithium ion diffusion in thin film lithium ion-conducting devices

NASA Astrophysics Data System (ADS)

Li, Weiqun

The lithium ion diffusion behavior and mechanism in the glassy electrolyte and the electrolyte/cathode interface during the initial stage of lithium ion diffusing from electrolyte into cathode were investigated using Molecular Dynamics simulation technique. Lithium aluminosilicate glass electrolytes with different R (ratio of the concentration of Al to Li) were simulated. The structural features of the simulated glasses are analyzed using Radial Distribution Function (RDF) and Pair Distribution Function (PDF). The diffusion coefficient and activation energy of lithium ion diffusion in simulated lithium aluminosilicate glasses were calculated and the values are consistent with those in experimental glasses. The behavior of lithium ion diffusion from the glassy electrolyte into a polycrystalline layered intercalation cathode has been studied. The solid electrolyte was a model lithium silicate glass while the cathode was a nanocrystalline vanadia with amorphous V2O5 intergranular films (IGF) between the V2O5 crystals. Two different orientations between the V2O5 crystal planes are presented for lithium ion intercalation via the amorphous vanadia IGF. A series of polycrystalline vanadia cathodes with 1.3, 1.9, 2.9 and 4.4 nm thickness IGFs were simulated to examine the effects of the IGF thickness on lithium ion transport in the polycrystalline vanadia cathodes. The simulated results showed that the lithium ions diffused from the glassy electrolyte into the IGF of the polycrystalline vanadia cathode and then part of those lithium ions diffused into the crystalline V2O5 from the IGF. The simulated results also showed an ordering of the vanadium ion structure in the IGF near the IGF/V2 O5 interface. The ordering structure still existed with glass former silica additive in IGF. Additionally, 2.9 run is suggested to be the optimal thickness of the IGF, which is neither too thick to decrease the capacity of the cathode nor too thin to impede the transport of lithium from glassy electrolyte into the cathode. Parallel molecular dynamic simulation technique was also used for a larger electrolyte/cathode interface system, which include more atoms and more complicated microstructures. Simulation results from larger electrolyte/cathode interface system prove that there is no size effect on simulation of smaller electrolyte/cathode interface system from statistical point of view.

Imaging complex nutrient dynamics in mycelial networks.

PubMed

Fricker, M D; Lee, J A; Bebber, D P; Tlalka, M; Hynes, J; Darrah, P R; Watkinson, S C; Boddy, L

2008-08-01

Transport networks are vital components of multi-cellular organisms, distributing nutrients and removing waste products. Animal cardiovascular and respiratory systems, and plant vasculature, are branching trees whose architecture is thought to determine universal scaling laws in these organisms. In contrast, the transport systems of many multi-cellular fungi do not fit into this conceptual framework, as they have evolved to explore a patchy environment in search of new resources, rather than ramify through a three-dimensional organism. These fungi grow as a foraging mycelium, formed by the branching and fusion of threadlike hyphae, that gives rise to a complex network. To function efficiently, the mycelial network must both transport nutrients between spatially separated source and sink regions and also maintain its integrity in the face of continuous attack by mycophagous insects or random damage. Here we review the development of novel imaging approaches and software tools that we have used to characterise nutrient transport and network formation in foraging mycelia over a range of spatial scales. On a millimetre scale, we have used a combination of time-lapse confocal imaging and fluorescence recovery after photobleaching to quantify the rate of diffusive transport through the unique vacuole system in individual hyphae. These data then form the basis of a simulation model to predict the impact of such diffusion-based movement on a scale of several millimetres. On a centimetre scale, we have used novel photon-counting scintillation imaging techniques to visualize radiolabel movement in small microcosms. This approach has revealed novel N-transport phenomena, including rapid, preferential N-resource allocation to C-rich sinks, induction of simultaneous bi-directional transport, abrupt switching between different pre-existing transport routes, and a strong pulsatile component to transport in some species. Analysis of the pulsatile transport component using Fourier techniques shows that as the colony forms, it self-organizes into well demarcated domains that are identifiable by differences in the phase relationship of the pulses. On the centimetre to metre scale, we have begun to use techniques borrowed from graph theory to characterize the development and dynamics of the network, and used these abstracted network models to predict the transport characteristics, resilience, and cost of the network.

A method for optimizing the cosine response of solar UV diffusers

NASA Astrophysics Data System (ADS)

Pulli, Tomi; Kärhä, Petri; Ikonen, Erkki

2013-07-01

Instruments measuring global solar ultraviolet (UV) irradiance at the surface of the Earth need to collect radiation from the entire hemisphere. Entrance optics with angular response as close as possible to the ideal cosine response are necessary to perform these measurements accurately. Typically, the cosine response is obtained using a transmitting diffuser. We have developed an efficient method based on a Monte Carlo algorithm to simulate radiation transport in the solar UV diffuser assembly. The algorithm takes into account propagation, absorption, and scattering of the radiation inside the diffuser material. The effects of the inner sidewalls of the diffuser housing, the shadow ring, and the protective weather dome are also accounted for. The software implementation of the algorithm is highly optimized: a simulation of 109 photons takes approximately 10 to 15 min to complete on a typical high-end PC. The results of the simulations agree well with the measured angular responses, indicating that the algorithm can be used to guide the diffuser design process. Cost savings can be obtained when simulations are carried out before diffuser fabrication as compared to a purely trial-and-error-based diffuser optimization. The algorithm was used to optimize two types of detectors, one with a planar diffuser and the other with a spherically shaped diffuser. The integrated cosine errors—which indicate the relative measurement error caused by the nonideal angular response under isotropic sky radiance—of these two detectors were calculated to be f2=1.4% and 0.66%, respectively.

Molecular dynamics simulations of hydrogen diffusion in aluminum

DOE PAGES

Zhou, X. W.; El Gabaly, F.; Stavila, V.; ...

2016-03-23

In this study, hydrogen diffusion impacts the performance of solid-state hydrogen storage materials and contributes to the embrittlement of structural materials under hydrogen-containing environments. In atomistic simulations, the diffusion energy barriers are usually calculated using molecular statics simulations where a nudged elastic band method is used to constrain a path connecting the two end points of an atomic jump. This approach requires prior knowledge of the “end points”. For alloy and defective systems, the number of possible atomic jumps with respect to local atomic configurations is tremendous. Even when these jumps can be exhaustively studied, it is still unclear howmore » they can be combined to give an overall diffusion behavior seen in experiments. Here we describe the use of molecular dynamics simulations to determine the overall diffusion energy barrier from the Arrhenius equation. This method does not require information about atomic jumps, and it has additional advantages, such as the ability to incorporate finite temperature effects and to determine the pre-exponential factor. As a test case for a generic method, we focus on hydrogen diffusion in bulk aluminum. We find that the challenge of this method is the statistical variation of the results. However, highly converged energy barriers can be achieved by an appropriate set of temperatures, output time intervals (for tracking hydrogen positions), and a long total simulation time. Our results help elucidate the inconsistencies of the experimental diffusion data published in the literature. The robust approach developed here may also open up future molecular dynamics simulations to rapidly study diffusion properties of complex material systems in multidimensional spaces involving composition and defects.« less

Marine Microcosm Experiments on Effects of Copper and Tributylin-Based Antifouling Paint Leachates

DTIC Science & Technology

1988-06-01

consumers in HliOrg microcosms were probably the thick carpets of green algae ( Cladophora socialis) that developed in those tanks during leachate and...and bottom substrate in the SPG-4 tanks were dominated by a low-diversity community composed primarily of Cladophora socialis, a filamentous green...coverage and diversity of species after 4 weeks of’ exposure. Moderate to thick growths of filamentous green algae ( Cladophora socialis) covered with

Factors affecting microbial 2,4,6-trinitrotoluene mineralization in contaminated soil

USGS Publications Warehouse

Bradley, P.M.; Chapelle, F.H.

1995-01-01

The influence of selected environmental factors on microbial TNT mineralization in soils collected from a TNT-contaminated site at Weldon Spring, MO, was examined using uniformly ring-labeled [14C]TNT. Microbial TNT mineralization was significantly inhibited by the addition of cellobiose and syringate. This response suggests that the indigenous microorganisms are capable of metabolizing TNT but preferentially utilize less recalcitrant substrates when available. The observed inhibition of TNT mineralization by TNT concentrations higher than 100 ??mol/kg of soil and by dry soil conditions suggests that toxic inhibition of microbial activity at high TNT concentrations and the periodic drying of these soils have contributed to the long-term persistence of TNT at Weldon Spring. In comparison to aerobic microcosms, mineralization was inhibited in anaerobic microcosms and in microcosms with a headspace of air amended with oxygen, suggesting that a mosaic of aerobic and anaerobic conditions may optimize TNT degradation at this site.

Monitoring Arthrobacter protophormiae RKJ100 in a 'tag and chase' method during p-nitrophenol bio-remediation in soil microcosms.

PubMed

Pandey, Gunjan; Pandey, Janmejay; Jain, Rakesh K

2006-05-01

Monitoring of micro-organisms released deliberately into the environment is essential to assess their movement during the bio-remediation process. During the last few years, DNA-based genetic methods have emerged as the preferred method for such monitoring; however, their use is restricted in cases where organisms used for bio-remediation are not well characterized or where the public domain databases do not provide sufficient information regarding their sequence. For monitoring of such micro-organisms, alternate approaches have to be undertaken. In this study, we have specifically monitored a p-nitrophenol (PNP)-degrading organism, Arthrobacter protophormiae RKJ100, using molecular methods during PNP degradation in soil microcosm. Cells were tagged with a transposon-based foreign DNA sequence prior to their introduction into PNP-contaminated microcosms. Later, this artificially introduced DNA sequence was PCR-amplified to distinguish the bio-augmented organism from the indigenous microflora during PNP bio-remediation.

SPRUCE Deep Peat Microbial Diversity, CO2 and CH4 Production in Response to Nutrient, Temperature, and pH Treatments during Incubation Studies.

DOE Data Explorer

A., Kluber Laurel [Oak Ridge National Laboratory, U.S. Department of Energy, Oak Ridge, Tennessee, U.S.A.; Allen, Samantha A. [Oak Ridge National Laboratory, U.S. Department of Energy, Oak Ridge, Tennessee, U.S.A.; Hendershot, Nicholas [Oak Ridge National Laboratory, U.S. Department of Energy, Oak Ridge, Tennessee, U.S.A.; Hanson, Paul J. [Oak Ridge National Laboratory, U.S. Department of Energy, Oak Ridge, Tennessee, U.S.A.; Schadt, Christopher W. [Oak Ridge National Laboratory, U.S. Department of Energy, Oak Ridge, Tennessee, U.S.A.

2014-09-01

This data set contains the results of a microcosm incubation study on deep peat collected from the SPRUCE experimental site in the S1 Bog in September 2014. Microcosms were monitored for CO2 and CH4 production, and microbial community dynamics were assessed using qPCR and amplicon sequencing.The experiment was designed with a full factorial design with elevated temperature, nitrogen (N), (P), and pH treatments was used with samples from each transect serving replicates. In all, 96 microcosms were constructed to account for the 16 treatment combinations (N x P x pH x temperature), 2 time points, and 3 replicates. Temperature treatments were 6 °C, to mimic the SPRUCE ambient plot temperatures, and 15 °C to mimic the SPRUCE +9 °C treatment.

RDX (hexahydro-1,3,5-trinitro-1,3,5-triazine) biodegradation in aquifer sediments under manganese-reducing conditions

USGS Publications Warehouse

Bradley, Paul M.; Dinicola, Richard S.

2005-01-01

A shallow, RDX (hexahydro-1,3,5-trinitro-1,3,5-triazine)–contaminated aquifer at Naval Submarine Base Bangor has been characterized as predominantly manganese-reducing, anoxic with local pockets of oxic conditions. The potential contribution of microbial RDX degradation to localized decreases observed in aquifer RDX concentrations was assessed in sediment microcosms amended with [U-14C] RDX. Greater than 85% mineralization of 14C-RDX to 14CO2 was observed in aquifer sediment microcosms under native, manganese-reducing, anoxic conditions. Significant increases in the mineralization of 14C-RDX to 14CO2 were observed in anoxic microcosms under NO3-amended or Mn(IV)-amended conditions. No evidence of 14C-RDX biodegradation was observed under oxic conditions. These results indicate that microbial degradation of RDX may contribute to natural attenuation of RDX in manganese-reducing aquifer systems.

RDX (hexahydro-1,3,5-trinitro-1,3,5-triazine) biodegradation in aquifer sediments under manganese-reducing conditions

USGS Publications Warehouse

Bradley, Paul M.; Dinicola, Richard S.

2005-01-01

A shallow, RDX (hexahydro-1,3,5-trinitro-1,3,5-triazine)–contaminated aquifer at Naval Submarine Base Bangor has been characterized as predominantly manganese-reducing, anoxic with local pockets of oxic conditions. The potential contribution of microbial RDX degradation to localized decreases observed in aquifer RDX concentrations was assessed in sediment microcosms amended with [U-14C] RDX. Greater than 85% mineralization of14C-RDX to 14CO2 was observed in aquifer sediment microcosms under native, manganese-reducing, anoxic conditions. Significant increases in the mineralization of 14C-RDX to 14CO2 were observed in anoxic microcosms under NO3-amended or Mn(IV)-amended conditions. No evidence of 14C-RDX biodegradation was observed under oxic conditions. These results indicate that microbial degradation of RDX may contribute to natural attenuation of RDX in manganese-reducing aquifer systems.

Cometabolic biodegradation of trichloroethylene in microcosms

USGS Publications Warehouse

Kane, Allen C.; Wilson, Timothy P.; Fischer, Jeffrey M.

1997-01-01

Laboratory microcosms were used to determine the concentrations of oxygen (O2) and methane (CH4) that optimize trichloroethylene (TCE) biodegradation in sediment and ground-water samples from a TCE-contaminated aquifer at Picatinny Arsenal, Morris County, New Jersey. The mechanism for degradation is the cometabolic activity of methanotrophic bacteria. The laboratory data will be used to support a field study designed to demonstrate the effectiveness of combining air sparging with cometabolic degradation of TCE for the purpose of aquifer remediation. Microcosms were constructed in autoclaved 250-mL (milliliter) amber glass bottles with valves for repeated headspace sampling. Equal volumes (25 mL) of sediment and ground water, collected from a depth of 40 feet, were added. TCE was added to attain initial aqueous concentrations equal to the field level of 1,400 mu g/L (micrograms per liter). Nine microcosms were constructed with initial headspace O2 concentrations of 5%, 10%, or 14% and CH4 concentrations of 0.5%, 3%, or 5%, with nitrogen making up the balance. Sterile controls, controls without CH4, and controls without sediment were also constructed. A 4-mL gas sample was removed periodically and TCE, O2 , CH4 , and carbon dioxide (CO2) concentrations were measured by using gas chromatography. As biodegradation proceeded, the decrease in O2, CH4 , and TCE concentrations and the production of CO2 were monitored. An initial acclimation period of at least 100 days was observed in those microcosms in which significant microbial activity occurred, as determined from decreases in O2 and CH4 concentrations and an increase in CO2 content. Degradation of TCE occurred with O2 concentrations of 2.7 to 8.7% and CH4 concentrations of 0.5 to 3.5%. Microcosms that initially contained 10% O2 and 3% CH4 showed the greatest microbial activity and the greatest amount of TCE degradation. The greatest rates of TCE degradation occurred when O2 and CH4 headspace concentrations reached levels of 7.7 to 8.7% and 1.7 to 2.7%, respectively, which correspond to aqueous concentrations of 2.9 to 3.5 mg/L and 0.4 to 0.6 mg/L, respectively. Over these ranges, TCE degradation rates ranged from 15 to 20 mu g of TCE per kilogram of sediment per day. Analysis of the control microcosms indicated that these TCE degradation rates are much greater than those attributable to experimental variation. The results indicate that the microbial community of the sediment is capable of TCE degradation and that significant rates of degradation can be achieved with obtainable O2 and CH4 concentrations.

Arctic sea-ice diffusion from observed and simulated Lagrangian trajectories

NASA Astrophysics Data System (ADS)

Rampal, Pierre; Bouillon, Sylvain; Bergh, Jon; Ólason, Einar

2016-07-01

We characterize sea-ice drift by applying a Lagrangian diffusion analysis to buoy trajectories from the International Arctic Buoy Programme (IABP) dataset and from two different models: the standalone Lagrangian sea-ice model neXtSIM and the Eulerian coupled ice-ocean model used for the TOPAZ reanalysis. By applying the diffusion analysis to the IABP buoy trajectories over the period 1979-2011, we confirm that sea-ice diffusion follows two distinct regimes (ballistic and Brownian) and we provide accurate values for the diffusivity and integral timescale that could be used in Eulerian or Lagrangian passive tracers models to simulate the transport and diffusion of particles moving with the ice. We discuss how these values are linked to the evolution of the fluctuating displacements variance and how this information could be used to define the size of the search area around the position predicted by the mean drift. By comparing observed and simulated sea-ice trajectories for three consecutive winter seasons (2007-2011), we show how the characteristics of the simulated motion may differ from or agree well with observations. This comparison illustrates the usefulness of first applying a diffusion analysis to evaluate the output of modeling systems that include a sea-ice model before using these in, e.g., oil spill trajectory models or, more generally, to simulate the transport of passive tracers in sea ice.

Self-learning kinetic Monte Carlo simulations of Al diffusion in Mg

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nandipati, Giridhar; Govind, Niranjan; Andersen, Amity

2016-03-16

Atomistic on-lattice self-learning kinetic Monte Carlo (SLKMC) method was used to examine the vacancy-mediated diffusion of an Al atom in pure hcp Mg. Local atomic environment dependent activation barriers for vacancy-atom exchange processes were calculated on-the-fly using climbing image nudged-elastic band method (CI-NEB) and using a Mg-Al binary modified embedded-atom method (MEAM) interatomic potential. Diffusivities of vacancy and Al atom in pure Mg were obtained from SLKMC simulations and are compared with values available in the literature that are obtained from experiments and first-principle calculations. Al Diffusivities obtained from SLKMC simulations are lower, due to larger activation barriers and lowermore » diffusivity prefactors, than those available in the literature but have same order of magnitude. We present all vacancy-Mg and vacancy-Al atom exchange processes and their activation barriers that were identified in SLKMC simulations. We will describe a simple mapping scheme to map a hcp lattice on to a simple cubic lattice that would enable hcp lattices to be simulated in an on-lattice KMC framework. We also present the pattern recognition scheme used in SLKMC simulations.« less

Diffusion of aromatic hydrocarbons in hierarchical mesoporous H-ZSM-5 zeolite

DOE PAGES

Bu, Lintao; Nimlos, Mark R.; Robichaud, David J.; ...

2018-02-08

Hierarchical mesoporous zeolites exhibit higher catalytic activities and longer lifetime compared to the traditional microporous zeolites due to improved diffusivity of substrate molecules and their enhanced access to the zeolite active sites. Understanding diffusion of biomass pyrolysis vapors and their upgraded products in such materials is fundamentally important during catalytic fast pyrolysis (CFP) of lignocellulosic biomass, since diffusion makes major contribution to determine shape selectivity and product distribution. However, diffusivities of biomass relevant species in hierarchical mesoporous zeolites are poorly characterized, primarily due to the limitations of the available experimental technology. In this work, molecular dynamics (MD) simulations are utilizedmore » to investigate the diffusivities of several selected coke precursor molecules, benzene, naphthalene, and anthracene, in hierarchical mesoporous H-ZSM-5 zeolite. The effects of temperature and size of mesopores on the diffusivity of the chosen model compounds are examined. The simulation results demonstrate that diffusion within the microspores as well as on the external surface of mesoporous H-ZSM-5 dominates only at low temperature. At pyrolysis relevant temperatures, mass transfer is essentially conducted via diffusion along the mesopores. Additionally, the results illustrate the heuristic diffusion model, such as the extensively used Knudsen diffusion, overestimates the diffusion of bulky molecules in the mesopores, thus making MD simulation a powerful and compulsory approach to explore diffusion in zeolites.« less

Modelling and simulating reaction-diffusion systems using coloured Petri nets.

PubMed

Liu, Fei; Blätke, Mary-Ann; Heiner, Monika; Yang, Ming

2014-10-01

Reaction-diffusion systems often play an important role in systems biology when developmental processes are involved. Traditional methods of modelling and simulating such systems require substantial prior knowledge of mathematics and/or simulation algorithms. Such skills may impose a challenge for biologists, when they are not equally well-trained in mathematics and computer science. Coloured Petri nets as a high-level and graphical language offer an attractive alternative, which is easily approachable. In this paper, we investigate a coloured Petri net framework integrating deterministic, stochastic and hybrid modelling formalisms and corresponding simulation algorithms for the modelling and simulation of reaction-diffusion processes that may be closely coupled with signalling pathways, metabolic reactions and/or gene expression. Such systems often manifest multiscaleness in time, space and/or concentration. We introduce our approach by means of some basic diffusion scenarios, and test it against an established case study, the Brusselator model. Copyright © 2014 Elsevier Ltd. All rights reserved.

Stochastic modeling and simulation of reaction-diffusion system with Hill function dynamics.

PubMed

Chen, Minghan; Li, Fei; Wang, Shuo; Cao, Young

2017-03-14

Stochastic simulation of reaction-diffusion systems presents great challenges for spatiotemporal biological modeling and simulation. One widely used framework for stochastic simulation of reaction-diffusion systems is reaction diffusion master equation (RDME). Previous studies have discovered that for the RDME, when discretization size approaches zero, reaction time for bimolecular reactions in high dimensional domains tends to infinity. In this paper, we demonstrate that in the 1D domain, highly nonlinear reaction dynamics given by Hill function may also have dramatic change when discretization size is smaller than a critical value. Moreover, we discuss methods to avoid this problem: smoothing over space, fixed length smoothing over space and a hybrid method. Our analysis reveals that the switch-like Hill dynamics reduces to a linear function of discretization size when the discretization size is small enough. The three proposed methods could correctly (under certain precision) simulate Hill function dynamics in the microscopic RDME system.

Monte Carlo simulations of particle acceleration at oblique shocks: Including cross-field diffusion

NASA Technical Reports Server (NTRS)

Baring, M. G.; Ellison, D. C.; Jones, F. C.

1995-01-01

The Monte Carlo technique of simulating diffusive particle acceleration at shocks has made spectral predictions that compare extremely well with particle distributions observed at the quasi-parallel region of the earth's bow shock. The current extension of this work to compare simulation predictions with particle spectra at oblique interplanetary shocks has required the inclusion of significant cross-field diffusion (strong scattering) in the simulation technique, since oblique shocks are intrinsically inefficient in the limit of weak scattering. In this paper, we present results from the method we have developed for the inclusion of cross-field diffusion in our simulations, namely model predictions of particle spectra downstream of oblique subluminal shocks. While the high-energy spectral index is independent of the shock obliquity and the strength of the scattering, the latter is observed to profoundly influence the efficiency of injection of cosmic rays into the acceleration process.

Internal protein motions in molecular-dynamics simulations of Bragg and diffuse X-ray scattering.

PubMed

Wall, Michael E

2018-03-01

Molecular-dynamics (MD) simulations of Bragg and diffuse X-ray scattering provide a means of obtaining experimentally validated models of protein conformational ensembles. This paper shows that compared with a single periodic unit-cell model, the accuracy of simulating diffuse scattering is increased when the crystal is modeled as a periodic supercell consisting of a 2 × 2 × 2 layout of eight unit cells. The MD simulations capture the general dependence of correlations on the separation of atoms. There is substantial agreement between the simulated Bragg reflections and the crystal structure; there are local deviations, however, indicating both the limitation of using a single structure to model disordered regions of the protein and local deviations of the average structure away from the crystal structure. Although it was anticipated that a simulation of longer duration might be required to achieve maximal agreement of the diffuse scattering calculation with the data using the supercell model, only a microsecond is required, the same as for the unit cell. Rigid protein motions only account for a minority fraction of the variation in atom positions from the simulation. The results indicate that protein crystal dynamics may be dominated by internal motions rather than packing interactions, and that MD simulations can be combined with Bragg and diffuse X-ray scattering to model the protein conformational ensemble.

Internal protein motions in molecular-dynamics simulations of Bragg and diffuse X-ray scattering

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wall, Michael E.

Molecular-dynamics (MD) simulations of Bragg and diffuse X-ray scattering provide a means of obtaining experimentally validated models of protein conformational ensembles. This paper shows that compared with a single periodic unit-cell model, the accuracy of simulating diffuse scattering is increased when the crystal is modeled as a periodic supercell consisting of a 2 × 2 × 2 layout of eight unit cells. The MD simulations capture the general dependence of correlations on the separation of atoms. There is substantial agreement between the simulated Bragg reflections and the crystal structure; there are local deviations, however, indicating both the limitation of using a single structuremore » to model disordered regions of the protein and local deviations of the average structure away from the crystal structure. Although it was anticipated that a simulation of longer duration might be required to achieve maximal agreement of the diffuse scattering calculation with the data using the supercell model, only a microsecond is required, the same as for the unit cell. Rigid protein motions only account for a minority fraction of the variation in atom positions from the simulation. The results indicate that protein crystal dynamics may be dominated by internal motions rather than packing interactions, and that MD simulations can be combined with Bragg and diffuse X-ray scattering to model the protein conformational ensemble.« less

Internal protein motions in molecular-dynamics simulations of Bragg and diffuse X-ray scattering

DOE PAGES

Wall, Michael E.

2018-01-25

Molecular-dynamics (MD) simulations of Bragg and diffuse X-ray scattering provide a means of obtaining experimentally validated models of protein conformational ensembles. This paper shows that compared with a single periodic unit-cell model, the accuracy of simulating diffuse scattering is increased when the crystal is modeled as a periodic supercell consisting of a 2 × 2 × 2 layout of eight unit cells. The MD simulations capture the general dependence of correlations on the separation of atoms. There is substantial agreement between the simulated Bragg reflections and the crystal structure; there are local deviations, however, indicating both the limitation of using a single structuremore » to model disordered regions of the protein and local deviations of the average structure away from the crystal structure. Although it was anticipated that a simulation of longer duration might be required to achieve maximal agreement of the diffuse scattering calculation with the data using the supercell model, only a microsecond is required, the same as for the unit cell. Rigid protein motions only account for a minority fraction of the variation in atom positions from the simulation. The results indicate that protein crystal dynamics may be dominated by internal motions rather than packing interactions, and that MD simulations can be combined with Bragg and diffuse X-ray scattering to model the protein conformational ensemble.« less

Fully Anisotropic Rotational Diffusion Tensor from Molecular Dynamics Simulations.

PubMed

Linke, Max; Köfinger, Jürgen; Hummer, Gerhard

2018-05-31

We present a method to calculate the fully anisotropic rotational diffusion tensor from molecular dynamics simulations. Our approach is based on fitting the time-dependent covariance matrix of the quaternions that describe the rigid-body rotational dynamics. Explicit analytical expressions have been derived for the covariances by Favro, which are valid irrespective of the degree of anisotropy. We use these expressions to determine an optimal rotational diffusion tensor from trajectory data. The molecular structures are aligned against a reference by optimal rigid-body superposition. The quaternion covariances can then be obtained directly from the rotation matrices used in the alignment. The rotational diffusion tensor is determined by a fit to the time-dependent quaternion covariances, or directly by Laplace transformation and matrix diagonalization. To quantify uncertainties in the fit, we derive analytical expressions and compare them with the results of Brownian dynamics simulations of anisotropic rotational diffusion. We apply the method to microsecond long trajectories of the Dickerson-Drew B-DNA dodecamer and of horse heart myoglobin. The anisotropic rotational diffusion tensors calculated from simulations agree well with predictions from hydrodynamics.

Parallel STEPS: Large Scale Stochastic Spatial Reaction-Diffusion Simulation with High Performance Computers

PubMed Central

Chen, Weiliang; De Schutter, Erik

2017-01-01

Stochastic, spatial reaction-diffusion simulations have been widely used in systems biology and computational neuroscience. However, the increasing scale and complexity of models and morphologies have exceeded the capacity of any serial implementation. This led to the development of parallel solutions that benefit from the boost in performance of modern supercomputers. In this paper, we describe an MPI-based, parallel operator-splitting implementation for stochastic spatial reaction-diffusion simulations with irregular tetrahedral meshes. The performance of our implementation is first examined and analyzed with simulations of a simple model. We then demonstrate its application to real-world research by simulating the reaction-diffusion components of a published calcium burst model in both Purkinje neuron sub-branch and full dendrite morphologies. Simulation results indicate that our implementation is capable of achieving super-linear speedup for balanced loading simulations with reasonable molecule density and mesh quality. In the best scenario, a parallel simulation with 2,000 processes runs more than 3,600 times faster than its serial SSA counterpart, and achieves more than 20-fold speedup relative to parallel simulation with 100 processes. In a more realistic scenario with dynamic calcium influx and data recording, the parallel simulation with 1,000 processes and no load balancing is still 500 times faster than the conventional serial SSA simulation. PMID:28239346

Parallel STEPS: Large Scale Stochastic Spatial Reaction-Diffusion Simulation with High Performance Computers.

PubMed

Chen, Weiliang; De Schutter, Erik

2017-01-01

Stochastic, spatial reaction-diffusion simulations have been widely used in systems biology and computational neuroscience. However, the increasing scale and complexity of models and morphologies have exceeded the capacity of any serial implementation. This led to the development of parallel solutions that benefit from the boost in performance of modern supercomputers. In this paper, we describe an MPI-based, parallel operator-splitting implementation for stochastic spatial reaction-diffusion simulations with irregular tetrahedral meshes. The performance of our implementation is first examined and analyzed with simulations of a simple model. We then demonstrate its application to real-world research by simulating the reaction-diffusion components of a published calcium burst model in both Purkinje neuron sub-branch and full dendrite morphologies. Simulation results indicate that our implementation is capable of achieving super-linear speedup for balanced loading simulations with reasonable molecule density and mesh quality. In the best scenario, a parallel simulation with 2,000 processes runs more than 3,600 times faster than its serial SSA counterpart, and achieves more than 20-fold speedup relative to parallel simulation with 100 processes. In a more realistic scenario with dynamic calcium influx and data recording, the parallel simulation with 1,000 processes and no load balancing is still 500 times faster than the conventional serial SSA simulation.

A monte carlo study of restricted diffusion: Implications for diffusion MRI of prostate cancer.

PubMed

Gilani, Nima; Malcolm, Paul; Johnson, Glyn

2017-04-01

Diffusion MRI is used frequently to assess prostate cancer. The prostate consists of cellular tissue surrounding fluid filled ducts. Here, the diffusion properties of the ductal fluid alone were studied. Monte Carlo simulations were used to investigate ductal residence times to determine whether ducts can be regarded as forming a separate compartment and whether ductal radius could determine the Apparent Diffusion Coefficient (ADC) of the ductal fluid. Random walks were simulated in cavities. Average residence times were estimated for permeable cavities. Signal reductions resulting from application of a Stejskal-Tanner pulse sequence were calculated in impermeable cavities. Simulations were repeated for cavities of different radii and different diffusion times. Residence times are at least comparable with diffusion times even in relatively high grade tumors. ADCs asymptotically approach theoretical limiting values. At large radii and short diffusion times, ADCs are similar to free diffusion. At small radii and long diffusion times, ADCs are reduced toward zero, and kurtosis approaches a value of -1.2. Restricted diffusion in cavities of similar sizes to prostate ducts may reduce ductal ADCs. This may contribute to reductions in total ADC seen in prostate cancer. Magn Reson Med 77:1671-1677, 2017. © 2016 International Society for Magnetic Resonance in Medicine. © 2016 International Society for Magnetic Resonance in Medicine.

Molecular dynamics simulation of diffusion and electrical conductivity in montmorillonite interlayers

DOE PAGES

Greathouse, Jeffery A.; Cygan, Randall T.; Fredrich, Joanne T.; ...

2016-01-20

In this study, the diffusion of water and ions in the interlayer region of smectite clay minerals represents a direct probe of the type and strength of clay–fluid interactions. Interlayer diffusion also represents an important link between molecular simulation and macroscopic experiments. Here we use molecular dynamics simulation to investigate trends in cation and water diffusion in montmorillonite interlayers, looking specifically at the effects of layer charge, interlayer cation and cation charge (sodium or calcium), water content, and temperature. For Na-montmorillonite, the largest increase in ion and water diffusion coefficients occurs between the one-layer and two-layer hydrates, corresponding to themore » transition from inner-sphere to outer-sphere surface complexes. Calculated activation energies for ion and water diffusion in Na-montmorillonite are similar to each other and to the water hydrogen bond energy, suggesting the breaking of water–water and water–clay hydrogen bonds as a likely mechanism for interlayer diffusion. A comparison of interlayer diffusion with that of bulk electrolyte solutions reveals a clear trend of decreasing diffusion coefficient with increasing electrolyte concentration, and in most cases the interlayer diffusion results are nearly coincident with the corresponding bulk solutions. Trends in electrical conductivities computed from the ion diffusion coefficients are also compared.« less

Diffusion kinetics of the glucose/glucose oxidase system in swift heavy ion track-based biosensors

NASA Astrophysics Data System (ADS)

Fink, Dietmar; Vacik, Jiri; Hnatowicz, V.; Muñoz Hernandez, G.; Garcia Arrelano, H.; Alfonta, Lital; Kiv, Arik

2017-05-01

For understanding of the diffusion kinetics and their optimization in swift heavy ion track-based biosensors, recently a diffusion simulation was performed. This simulation aimed at yielding the degree of enrichment of the enzymatic reaction products in the highly confined space of the etched ion tracks. A bunch of curves was obtained for the description of such sensors that depend only on the ratio of the diffusion coefficient of the products to that of the analyte within the tracks. As hitherto none of these two diffusion coefficients is accurately known, the present work was undertaken. The results of this paper allow one to quantify the previous simulation and hence yield realistic predictions of glucose-based biosensors. At this occasion, also the influence of the etched track radius on the diffusion coefficients was measured and compared with earlier prediction.

Diffusion in Coulomb crystals.

PubMed

Hughto, J; Schneider, A S; Horowitz, C J; Berry, D K

2011-07-01

Diffusion in Coulomb crystals can be important for the structure of neutron star crusts. We determine diffusion constants D from molecular dynamics simulations. We find that D for Coulomb crystals with relatively soft-core 1/r interactions may be larger than D for Lennard-Jones or other solids with harder-core interactions. Diffusion, for simulations of nearly perfect body-centered-cubic lattices, involves the exchange of ions in ringlike configurations. Here ions "hop" in unison without the formation of long lived vacancies. Diffusion, for imperfect crystals, involves the motion of defects. Finally, we find that diffusion, for an amorphous system rapidly quenched from Coulomb parameter Γ=175 to Coulomb parameters up to Γ=1750, is fast enough that the system starts to crystalize during long simulation runs. These results strongly suggest that Coulomb solids in cold white dwarf stars, and the crust of neutron stars, will be crystalline and not amorphous.

Application of underdamped Langevin dynamics simulations for the study of diffusion from a drug-eluting stent

NASA Astrophysics Data System (ADS)

Regev, Shaked; Farago, Oded

2018-10-01

We use a one-dimensional two layer model with a semi-permeable membrane to study the diffusion of a therapeutic drug delivered from a drug-eluting stent (DES). The rate of drug transfer from the stent coating to the arterial wall is calculated by using underdamped Langevin dynamics simulations. Our results reveal that the membrane has virtually no delay effect on the rate of delivery from the DES. The work demonstrates the great potential of underdamped Langevin dynamics simulations as an easy to implement, efficient, method for solving complicated diffusion problems in systems with a spatially-dependent diffusion coefficient.

Response of radiation belt simulations to different radial diffusion coefficients for relativistic and ultra-relativistic electrons

NASA Astrophysics Data System (ADS)

Drozdov, Alexander; Mann, Ian; Baker, Daniel N.; Subbotin, Dmitriy; Ozeke, Louis; Shprits, Yuri; Kellerman, Adam

Two parameterizations of the resonant wave-particle interactions of electrons with ULF waves in the magnetosphere by Brautigam and Albert [2000] and Ozeke et al. [2012] are evaluated using the Versatile Electron Radiation Belt (VERB) diffusion code to estimate the effect of changing a diffusion coefficient on the radiation belt simulation. The period of investigation includes geomagnetically quiet and active time. The simulations take into account wave-particle interactions represented by radial diffusion transport, local acceleration, losses due to pitch-angle diffusion, and mixed diffusion. 1. Brautigam, D. H., and J. M. Albert (2000), Radial diffusion analysis of outer radiation belt electrons during the October 9, 1990, magnetic storm, J. Geophys. Res., 105(A1), 291-309, doi:10.1029/1999JA900344 2. Ozeke, L. G., I. R. Mann, K. R. Murphy, I. J. Rae, D. K. Milling, S. R. Elkington, A. A. Chan, and H. J. Singer (2012), ULF wave derived radiation belt radial diffusion coefficients, J. Geophys. Res., 117, A04222, doi:10.1029/2011JA017463.

[Effects of naphthalene on soil respiration, nutrients and enzyme activities in the subalpine forest of western Sichuan, China].

PubMed

Yang, Fan; Yang, Wan Qin; Wu, Fu Zhong; Wang, Hui; Lan, Li Ying; Liu, Yu Wei; Guo, Cai Hong; Tan, Bo

2017-06-18

As a biocide to reduce soil and litter faunal populations in field experiments, naphthalene has been widely used in the study of ecological functions of soil fauna, but the non-target effects of naphthalene bring about enormous uncertainty to its application. In order to understand whether there were non-target effects of naphthalene in subalpine forest soil, soil in the subalpine forests of west Qinghai-Tibet Plateau was taken as study object. The short-term responses of soil respiration rate, nutrient content and enzyme activity to naphthalene were studied in microcosms. The results showed that soil respiration rate was significantly suppressed by application of naphthalene within 0-10 days, and then showed a significant promotion effect. Naphthalene significantly affected the dynamics of soil NH 4 + -N and NO 3 - -N contents. With application of naphthalene, the highest contents of NH 4 + -N and NO 3 - -N occurred at the 3rd and 7th day, respectively. But they were observed at the 45th and 52nd day with no-naphthalene, respectively. Moreover, soil dissolved carbon content in the naphthalene microcosms showed a sharp increase and then decrease dynamic at the 3rd day, while small change was detected in the no-naphthalene microcosms. Dissolved nitrogen content in both the naphthalene and no-naphthalene microcosms showed an increase at first and then decreased subsequently during the study period. Similar dynamics were found for the soil enzyme activities in both the naphthalene and no-naphthalene microcosms. The highest activities of urease, nitrate reductase and nitrite reductase in both the naphthalene and no-naphthalene microcosms were at the 45th, 38th and 10th day, respectively. In addition, the interaction of naphthalene treatment and sampling time had significant effects on soil respiration rate, the contents of NH 4 + -N, NO 3 - -N and dissolved nitrogen, but had no significant effects on soil dissolved carbon content, and the activities of invertase, nitrate reductase and nitrite reductase. In a short time, the non-target effect of naphthalene as a biocide to reduce soil fauna abundance might have an important influence on the soil nitrogen cycling in subalpine forest of western Sichuan.

Evaluation of the biodegradation of Alaska North Slope oil in microcosms using the biodegradation model BIOB

PubMed Central

Torlapati, Jagadish; Boufadel, Michel C.

2014-01-01

We present the details of a numerical model, BIOB that is capable of simulating the biodegradation of oil entrapped in the sediment. The model uses Monod kinetics to simulate the growth of bacteria in the presence of nutrients and the subsequent consumption of hydrocarbons. The model was used to simulate experimental results of Exxon Valdez oil biodegradation in laboratory columns (Venosa et al., 2010). In that study, samples were collected from three different islands: Eleanor Island (EL107), Knight Island (KN114A), and Smith Island (SM006B), and placed in laboratory microcosms for a duration of 168 days to investigate oil bioremediation through natural attenuation and nutrient amendment. The kinetic parameters of the BIOB model were estimated by fitting to the experimental data using a parameter estimation tool based on Genetic Algorithms (GA). The parameter values of EL107 and KN114A were similar whereas those of SM006B were different from the two other sites; in particular biomass growth at SM006B was four times slower than at the other two islands. Grain size analysis from each site revealed that the specific surface area per unit mass of sediment was considerably lower at SM006B, which suggest that the surface area of sediments is a key control parameter for microbial growth in sediments. Comparison of the BIOB results with exponential decay curves fitted to the data indicated that BIOB provided better fit for KN114A and SM006B in nutrient amended treatments, and for EL107 and KN114A in natural attenuation. In particular, BIOB was able to capture the initial slow biodegradation due to the lag phase in microbial growth. Sensitivity analyses revealed that oil biodegradation at all three locations were sensitive to nutrient concentration whereas SM006B was sensitive to initial biomass concentration due to its slow growth rate. Analyses were also performed to compare the half-lives of individual compounds with that of the overall polycyclic aromatic hydrocarbons (PAHs). PMID:24860560

Mesoscopic-microscopic spatial stochastic simulation with automatic system partitioning.

PubMed

Hellander, Stefan; Hellander, Andreas; Petzold, Linda

2017-12-21

The reaction-diffusion master equation (RDME) is a model that allows for efficient on-lattice simulation of spatially resolved stochastic chemical kinetics. Compared to off-lattice hard-sphere simulations with Brownian dynamics or Green's function reaction dynamics, the RDME can be orders of magnitude faster if the lattice spacing can be chosen coarse enough. However, strongly diffusion-controlled reactions mandate a very fine mesh resolution for acceptable accuracy. It is common that reactions in the same model differ in their degree of diffusion control and therefore require different degrees of mesh resolution. This renders mesoscopic simulation inefficient for systems with multiscale properties. Mesoscopic-microscopic hybrid methods address this problem by resolving the most challenging reactions with a microscale, off-lattice simulation. However, all methods to date require manual partitioning of a system, effectively limiting their usefulness as "black-box" simulation codes. In this paper, we propose a hybrid simulation algorithm with automatic system partitioning based on indirect a priori error estimates. We demonstrate the accuracy and efficiency of the method on models of diffusion-controlled networks in 3D.

Observed and Simulated Eddy Diffusivity Upstream of the Drake Passage

NASA Astrophysics Data System (ADS)

Tulloch, R.; Ferrari, R. M.; Marshall, J.

2012-12-01

Estimates of eddy diffusivity in the Southern Ocean are poorly constrained due to lack of observations. We compare the first direct estimate of isopycnal eddy diffusivity upstream of the Drake Passage (from Ledwell et al. 2011) with a numerical simulation. The estimate is computed from a point tracer release as part of the Diapycnal and Isopycnal Mixing Experiment in the Southern Ocean (DIMES). We find that the observational diffusivity estimate of about 500m^2/s at 1500m depth is close to that computed in a data-constrained, 1/20th of a degree simulation of the Drake Passage region. This tracer estimate also agrees with Lagrangian float calculations in the model. The role of mean flow suppression of eddy diffusivity at shallower depths will also be discussed.

How a Nanodroplet Diffuses on Smooth Surfaces

NASA Astrophysics Data System (ADS)

Li, Chu; Huang, Jizu; Li, Zhigang

2016-11-01

In this study, we investigate how nanodroplets diffuse on smooth surfaces through molecular dynamics (MD) simulations and theoretical analyses. The simulations results show that the surface diffusion of nanodroplet is different from that of single molecules and solid nanoparticles. The dependence of nanodroplet diffusion coefficient on temperature is surface wettability dependent, which undergoes a transition from linear to nonlinear as the surface wettability is weakened due to the coupling of temperature and surface energy. We also develop a simple relation for the diffusion coefficient by using the contact angle and contact radius of the droplet. It works well for different surface wettabilities and sized nanodroplets, as confirmed by MD simulations. This work was supported by the Research Grants Council of the Hong Kong Special Administrative Region under Grant No. 615312.

Kinetic Monte Carlo Simulation of Oxygen and Cation Diffusion in Yttria-Stabilized Zirconia

NASA Technical Reports Server (NTRS)

Good, Brian

2011-01-01

Yttria-stabilized zirconia (YSZ) is of interest to the aerospace community, notably for its application as a thermal barrier coating for turbine engine components. In such an application, diffusion of both oxygen ions and cations is of concern. Oxygen diffusion can lead to deterioration of a coated part, and often necessitates an environmental barrier coating. Cation diffusion in YSZ is much slower than oxygen diffusion. However, such diffusion is a mechanism by which creep takes place, potentially affecting the mechanical integrity and phase stability of the coating. In other applications, the high oxygen diffusivity of YSZ is useful, and makes the material of interest for use as a solid-state electrolyte in fuel cells. The kinetic Monte Carlo (kMC) method offers a number of advantages compared with the more widely known molecular dynamics simulation method. In particular, kMC is much more efficient for the study of processes, such as diffusion, that involve infrequent events. We describe the results of kinetic Monte Carlo computer simulations of oxygen and cation diffusion in YSZ. Using diffusive energy barriers from ab initio calculations and from the literature, we present results on the temperature dependence of oxygen and cation diffusivity, and on the dependence of the diffusivities on yttria concentration and oxygen sublattice vacancy concentration. We also present results of the effect on diffusivity of oxygen vacancies in the vicinity of the barrier cations that determine the oxygen diffusion energy barriers.

Hybrid stochastic simulation of reaction-diffusion systems with slow and fast dynamics.

PubMed

Strehl, Robert; Ilie, Silvana

2015-12-21

In this paper, we present a novel hybrid method to simulate discrete stochastic reaction-diffusion models arising in biochemical signaling pathways. We study moderately stiff systems, for which we can partition each reaction or diffusion channel into either a slow or fast subset, based on its propensity. Numerical approaches missing this distinction are often limited with respect to computational run time or approximation quality. We design an approximate scheme that remedies these pitfalls by using a new blending strategy of the well-established inhomogeneous stochastic simulation algorithm and the tau-leaping simulation method. The advantages of our hybrid simulation algorithm are demonstrated on three benchmarking systems, with special focus on approximation accuracy and efficiency.

A novel method for computing effective diffusivity: Application to helium implanted α-Fe thin films

NASA Astrophysics Data System (ADS)

Dunn, Aaron; Agudo-Merida, Laura; Martin-Bragado, Ignacio; McPhie, Mathieu; Cherkaoui, Mohammed; Capolungo, Laurent

2014-05-01

The effective diffusivity of helium in thin iron films is quantified using spatially resolved stochastic cluster dynamics and object kinetic Monte Carlo simulations. The roles of total displacement dose (in DPA), damage rate, helium to DPA ratio, layer thickness, and damage type (cascade damage vs Frenkel pair implantation) on effective He diffusivity are investigated. Helium diffusivity is found to decrease with increasing total damage and decreasing damage rate. Arrhenius plots show strongly increased helium diffusivity at high temperatures, high total implantation, and low implantation rates due to decreased vacancy and vacancy cluster concentrations. At low temperatures, effective diffusivity is weakly dependent on foil thickness while at high temperatures, narrower foils prevent defect accumulation by releasing all defects at the free surfaces. Helium to DPA ratio is not shown to strongly change helium diffusivity in the range of irradiation conditions simulated. Frenkel pair implantation is shown to cause higher effective diffusivity and more complex diffusion mechanisms than cascade implantation. The results of these simulations indicate that the differences in damage rates between implantation experiments and fission or fusion environments may result in differences in the final microstructure.

Entry of Yersinia Pestis into the Viable but Nonculturable State in a Low-Temperature Tap Water Microcosm

DTIC Science & Technology

2011-03-16

to enter the VBNC state [17,18,19,20]. In addition, many other bacterial pathogens, including Francisella tularensis, Vibrio cholerae, and Escherichia...sterilized distilled water microcosms at 4uC after 21 days [31]. Likewise, Linder and Oliver reported that Vibrio vulnificus entered the VBNC state... Vibrio cholerae, and Escherichia coli enter the VBNC state [12,21]. In addition, the two closest pathogenic relatives of Y. pestis, namely Y

Morphological Alteration and Survival of Burkholderia pseudomallei in Soil Microcosms

PubMed Central

Kamjumphol, Watcharaporn; Chareonsudjai, Pisit; Taweechaisupapong, Suwimol; Chareonsudjai, Sorujsiri

2015-01-01

The resilience of Burkholderia pseudomallei, the causative agent of melioidosis, was evaluated in control soil microcosms and in soil microcosms containing NaCl or FeSO4 at 30°C. Iron (Fe(II)) promoted the growth of B. pseudomallei during the 30-day observation, contrary to the presence of 1.5% and 3% NaCl. Scanning electron micrographs of B. pseudomallei in soil revealed their morphological alteration from rod to coccoid and the formation of microcolonies. The smallest B. pseudomallei cells were found in soil with 100 μM FeSO4 compared with in the control soil or soil with 0.6% NaCl (P < 0.05). The colony count on Ashdown's agar and bacterial viability assay using the LIVE/DEAD® BacLight™ stain combined with flow cytometry showed that B. pseudomallei remained culturable and viable in the control soil microcosms for at least 120 days. In contrast, soil with 1.5% NaCl affected their culturability at day 90 and their viability at day 120. Our results suggested that a low salinity and iron may influence the survival of B. pseudomallei and its ability to change from a rod-like to coccoid form. The morphological changes of B. pseudomallei cells may be advantageous for their persistence in the environment and may increase the risk of their transmission to humans. PMID:26324731

Oligotrophic wetland sediments susceptible to shifts in microbiomes and mercury cycling with dissolved organic matter addition

DOE Office of Scientific and Technical Information (OSTI.GOV)

Graham, Emily B.; Gabor, Rachel S.; Schooler, Shon

Recent advances have allowed for greater investigation into microbial regulation of mercury toxicity in the environment. In wetlands in particular, dissolved organic matter (DOM) may influence methylmercury (MeHg) production both through chemical interactions and through substrate effects on microbiomes. We conducted microcosm experiments in two disparate wetland environments (oligotrophic unvegetated and high-C vegetated sediments) to examine the impacts of plant leachate and inorganic mercury loadings (20 mg/L HgCl 2) on microbiomes and MeHg production in the St. Louis River Estuary. Our research reveals the greater relative capacity for mercury methylation in vegetated over unvegetated sediments. Further, our work shows howmore » mercury cycling in oligotrophic unvegetated sediments may be susceptible to DOM inputs in the St. Louis River Estuary: unvegetated microcosms receiving leachate produced substantially more MeHg than unamended microcosms. We also demonstrate (1) changes in microbiome structure towards Clostridia, (2) metagenomic shifts toward fermentation, and (3) degradation of complex DOM; all of which coincide with elevated net MeHg production in unvegetated microcosms receiving leachate. Altogether, our work shows the influence of wetland vegetation in controlling MeHg production in the Great Lakes region and provides evidence that this may be due to both enhanced microbial activity as well as differences in microbiome composition.« less

Oligotrophic wetland sediments susceptible to shifts in microbiomes and mercury cycling with dissolved organic matter addition

DOE PAGES

Graham, Emily B.; Gabor, Rachel S.; Schooler, Shon; ...

2018-04-03

Recent advances have allowed for greater investigation into microbial regulation of mercury toxicity in the environment. In wetlands in particular, dissolved organic matter (DOM) may influence methylmercury (MeHg) production both through chemical interactions and through substrate effects on microbiomes. We conducted microcosm experiments in two disparate wetland environments (oligotrophic unvegetated and high-C vegetated sediments) to examine the impacts of plant leachate and inorganic mercury loadings (20 mg/L HgCl 2) on microbiomes and MeHg production in the St. Louis River Estuary. Our research reveals the greater relative capacity for mercury methylation in vegetated over unvegetated sediments. Further, our work shows howmore » mercury cycling in oligotrophic unvegetated sediments may be susceptible to DOM inputs in the St. Louis River Estuary: unvegetated microcosms receiving leachate produced substantially more MeHg than unamended microcosms. We also demonstrate (1) changes in microbiome structure towards Clostridia, (2) metagenomic shifts toward fermentation, and (3) degradation of complex DOM; all of which coincide with elevated net MeHg production in unvegetated microcosms receiving leachate. Altogether, our work shows the influence of wetland vegetation in controlling MeHg production in the Great Lakes region and provides evidence that this may be due to both enhanced microbial activity as well as differences in microbiome composition.« less

The influence of nickel on the bioremediation of multi-component contaminated tropical soil: microcosm and batch bioreactor studies.

PubMed

Taketani, Natália Franco; Taketani, Rodrigo Gouvêa; Leite, Selma Gomes Ferreira; Rizzo, Andrea Camardella de Lima; Tsai, Siu Mui; da Cunha, Cláudia Duarte

2015-07-01

Large petrochemical discharges are responsible for organic and inorganic pollutants in the environment. The purpose of this study was to evaluate the influence of nickel, one of the most abundant inorganic element in crude oil and the main component of hydrogen catalysts for oil refining, on the microbial community structure in artificially petroleum-contaminated microcosms and in solid phase bioreactor studies. In the presence of metals, the oil biodegradation in microcosms was significantly delayed during the first 7 days of operation. Also, increasing amounts of moisture generated a positive influence on the biodegradation processes. The oil concentration, exhibiting the most negative influence at the end of the treatment period. Molecular fingerprinting analyses (denaturing gradient gel electrophoresis--DGGE) indicated that the inclusion of nickel into the contaminated soil promoted direct changes to the microbial community structure. By the end of the experiments, the results of the total petroleum hydrocarbons removal in the bioreactor and the microcosm were similar, but reductions in the treatment times were observed with the bioreactor experiments. An analysis of the microbial community structure by DGGE using various markers showed distinct behaviors between two treatments containing high nickel concentrations. The main conclusion of this study was that Nickel promotes a significant delay in oil biodegradation, despite having only a minor effect over the microbial community.

Developmental thermal plasticity of prey modifies the impact of predation.

PubMed

Seebacher, Frank; Grigaltchik, Veronica S

2015-05-01

Environmental conditions during embryonic development can influence the mean expression of phenotypes as well as phenotypic responses to environmental change later in life. The resulting phenotypes may be better matched to their environment and more resilient to environmental change, including human-induced climate change. However, whether plasticity does improve success in an ecological context is unresolved. In a microcosm experiment, we show that developmental plasticity in embryos of the frog Limnodynastes peronii is beneficial by increasing survivorship of tadpoles in the presence of predators when egg incubation (15 or 25°C) and tadpole acclimation temperature in microcosms (15 or 25°C) coincided at 15°C. Tadpoles that survived predation were smaller, and had faster burst swimming speeds than those kept in no-predator control conditions, but only at high (25°C) egg incubation or subsequent microcosm temperatures. Metabolic rates were determined by a three-way interaction between incubation and microcosm temperatures and predation; maximal glycolytic and mitochondrial metabolic capacities (enzyme activities) were lower in survivors from predation compared with controls, particularly when eggs were incubated at 25°C. We show that thermal conditions experienced during early development are ecologically relevant by modulating survivorship from predation. Importantly, developmental thermal plasticity also impacts population phenotypes indirectly by modifying species interactions and the selection pressure imposed by predation. © 2015. Published by The Company of Biologists Ltd.

The effects of co-contaminants and native wetland sediments on the activity and dominant transformation mechanisms of a 1,1,2,2-tetrachloroethane (TeCA)-degrading enrichment culture

USGS Publications Warehouse

Lorah, Michelle M.; Schiffmacher, Emily N.; Becker, Jennifer G.; Voytek, Mary A.

2016-01-01

Bioremediation strategies, including bioaugmentation with chlorinated ethene-degrading enrichment cultures, have been successfully applied in the cleanup of subsurface environments contaminated with tetrachloroethene (PCE) and/or trichloroethene (TCE). However, these compounds are frequently found in the environment as components of mixtures that may also contain chlorinated ethanes and methanes. Under these conditions, the implementation of bioremediation may be complicated by inhibition effects, particularly when multiple dehalorespirers are present. We investigated the ability of the 1,1,2,2-tetrachloroethane (TeCA)-dechlorinating culture WBC-2 to biotransform TeCA alone, or a mixture of TeCA plus PCE and carbon tetrachloride (CT), in microcosms. The microcosms contained electron donors provided to biostimulate the added culture and sediment collected from a wetland where numerous “hotspots” of contamination with chlorinated solvent mixtures exist. The dominant TeCA biodegradation mechanism mediated by the WBC-2 culture in the microcosms was different in the presence of these wetland sediments than in the sediment-free enrichment culture or in previous WBC-2 bioaugmented microcosms and column tests conducted with wetland sediment collected at nearby sites. The co-contaminants and their daughter products also inhibited TeCA biodegradation by WBC-2. These results highlight the need to conduct biodegradability assays at new sites, particularly when multiple contaminants and dehalorespiring populations are present.

Evaluation of ethyl tert-butyl ether biodegradation in a contaminated aquifer by compound-specific isotope analysis and in situ microcosms.

PubMed

Bombach, Petra; Nägele, Norbert; Rosell, Mònica; Richnow, Hans H; Fischer, Anko

2015-04-09

Ethyl tert-butyl ether (ETBE) is an upcoming groundwater pollutant in Europe whose environmental fate has been less investigated, thus far. In the present study, we investigated the in situ biodegradation of ETBE in a fuel-contaminated aquifer using compound-specific stable isotope analysis (CSIA), and in situ microcosms in combination with total lipid fatty acid (TLFA)-stable isotope probing (SIP). In a first field investigation, CSIA revealed insignificant carbon isotope fractionation, but low hydrogen isotope fractionation of up to +14‰ along the prevailing anoxic ETBE plume suggesting biodegradation of ETBE. Ten months later, oxygen injection was conducted to enhance the biodegradation of petroleum hydrocarbons (PH) at the field site. Within the framework of this remediation measure, in situ microcosms loaded with [(13)C6]-ETBE (BACTRAP(®)s) were exposed for 119 days in selected groundwater wells to assess the biodegradation of ETBE by TLFA-SIP under the following conditions: (i) ETBE as main contaminant; (ii) ETBE as main contaminant subjected to oxygen injection; (iii) ETBE plus other PH; (iv) ETBE plus other PH subjected to oxygen injection. Under all conditions investigated, significant (13)C-incorporation into microbial total lipid fatty acids extracted from the in situ microcosms was found, providing clear evidence of ETBE biodegradation. Copyright © 2014 Elsevier B.V. All rights reserved.

Transfers and transformations of zinc in flow-through wetland microcosms.

PubMed

Gillespie, W B; Hawkins, W B; Rodgers, J H; Cano, M L; Dorn, P B

1999-06-01

Two microcosm-scale wetlands (570-liter containers) were integratively designed and constructed to investigate transfers and transformations of zinc associated with an aqueous matrix, and to provide future design parameters for pilot-scale constructed wetlands. The fundamental design of these wetland microcosms was based on biogeochemical principles regulating fate and transformations of zinc (pH, redox, etc.). Each wetland consisted of a 45-cm hydrosoil depth inundated with 25 cm of water, and planted with Scirpus californicus. Zinc ( approximately 2 mg/liter) as ZnCl2 was amended to each wetland for 62 days. Individual wetland hydraulic retention times (HRT) were approximately 24 h. Total recoverable zinc was measured daily in microcosm inflow and outflows, and zinc concentrations in hydrosoil and S. californicus tissue were measured pre- and post-treatment. Ceriodaphnia dubia and Pimephales promelas7-day aqueous toxicity tests were performed on wetland inflows and outflows, and Hyalella azteca whole sediment toxicity tests (10-day) were performed pre- and post-treatment. Approximately 75% of total recoverable zinc was transferred from the water column. Toxicity decreased from inflow to outflow based on 7-day C. dubia tests, and survival of H. azteca in hydrosoil was >80%. Data illustrate the ability of integratively designed wetlands to transfer and sequester zinc from the water column while concomitantly decreasing associated toxicity. Copyright 1999 Academic Press.

Enhanced and stabilized arsenic retention in microcosms through the microbial oxidation of ferrous iron by nitrate

DOE PAGES

Sun, Jing; Chillrud, Steven N.; Mailloux, Brian J.; ...

2015-10-23

Magnetite strongly retains As, and is relatively stable under Fe(III)-reducing conditions common in aquifers that release As. In this paper, laboratory microcosm experiments were conducted to investigate a potential As remediation method involving magnetite formation, using groundwater and sediments from the Vineland Superfund site. The microcosms were amended with various combinations of nitrate, Fe(II) (aq) (as ferrous sulfate) and lactate, and were incubated for more than 5 weeks. In the microcosms enriched with 10 mM nitrate and 5 mM Fe(II) (aq), black magnetic particles were produced, and As removal from solution was observed even under sustained Fe(III) reduction stimulated bymore » the addition of 10 mM lactate. The enhanced As retention was mainly attributed to co-precipitation within magnetite and adsorption on a mixture of magnetite and ferrihydrite. Sequential chemical extraction, X-ray absorption spectroscopy and magnetic susceptibility measurements showed that these minerals formed at pH 6–7 following nitrate-Fe(II) addition, and As-bearing magnetite was stable under reducing conditions. Scanning electron microscopy and X-ray diffraction indicated that nano-particulate magnetite was produced as coatings on fine sediments, and no aging effect was detected on morphology over the course of incubation. Finally, these results suggest that a magnetite based strategy may be a long-term remedial option for As-contaminated aquifers.« less

Innovation Diffusion: Learner Benefits and Instructor Insights with the DIFFUSION SIMULATION GAME

ERIC Educational Resources Information Center

Kovalik, Cindy L.; Kuo, Chia-Ling

2012-01-01

This research project investigated student reaction to playing the DIFFUSION SIMULATION GAME (DSG) and how an instructor, who is a novice in playing online games, implemented the DSG in an online higher education course. The goal of this research project was to determine whether playing the DSG helps students learn and apply course content. In…

Interstitial and Interlayer Ion Diffusion Geometry Extraction in Graphitic Nanosphere Battery Materials.

PubMed

Gyulassy, Attila; Knoll, Aaron; Lau, Kah Chun; Wang, Bei; Bremer, Peer-Timo; Papka, Michael E; Curtiss, Larry A; Pascucci, Valerio

2016-01-01

Large-scale molecular dynamics (MD) simulations are commonly used for simulating the synthesis and ion diffusion of battery materials. A good battery anode material is determined by its capacity to store ion or other diffusers. However, modeling of ion diffusion dynamics and transport properties at large length and long time scales would be impossible with current MD codes. To analyze the fundamental properties of these materials, therefore, we turn to geometric and topological analysis of their structure. In this paper, we apply a novel technique inspired by discrete Morse theory to the Delaunay triangulation of the simulated geometry of a thermally annealed carbon nanosphere. We utilize our computed structures to drive further geometric analysis to extract the interstitial diffusion structure as a single mesh. Our results provide a new approach to analyze the geometry of the simulated carbon nanosphere, and new insights into the role of carbon defect size and distribution in determining the charge capacity and charge dynamics of these carbon based battery materials.

Liquid-liquid phase transition and anomalous diffusion in simulated liquid GeO 2

NASA Astrophysics Data System (ADS)

Hoang, Vo Van; Anh, Nguyen Huynh Tuan; Zung, Hoang

2007-03-01

We perform molecular dynamics (MD) simulation of diffusion in liquid GeO 2 at the temperatures ranged from 3000 to 5000 K and densities ranged from 3.65 to 7.90 g/cm 3. Simulations were done in a model containing 3000 particles with the new interatomic potentials for liquid and amorphous GeO 2, which have weak Coulomb interaction and Morse-type short-range interaction. We found a liquid-liquid phase transition in simulated liquid GeO 2 from a tetrahedral to an octahedral network structure upon compression. Moreover, such phase transition accompanied with an anomalous diffusion of particles in liquid GeO 2 that the diffusion constant of both Ge and O particles strongly increases with increasing density (e.g. with increasing pressure) and it shows a maximum at the density around 4.95 g/cm 3. The possible relation between anomalous diffusion of particles and structural phase transition in the system has been discussed.

Interstitial and Interlayer Ion Diffusion Geometry Extraction in Graphitic Nanosphere Battery Materials

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gyulassy, Attila; Knoll, Aaron; Lau, Kah Chun

2016-01-01

Large-scale molecular dynamics (MD) simulations are commonly used for simulating the synthesis and ion diffusion of battery materials. A good battery anode material is determined by its capacity to store ion or other diffusers. However, modeling of ion diffusion dynamics and transport properties at large length and long time scales would be impossible with current MD codes. To analyze the fundamental properties of these materials, therefore, we turn to geometric and topological analysis of their structure. In this paper, we apply a novel technique inspired by discrete Morse theory to the Delaunay triangulation of the simulated geometry of a thermallymore » annealed carbon nanosphere. We utilize our computed structures to drive further geometric analysis to extract the interstitial diffusion structure as a single mesh. Our results provide a new approach to analyze the geometry of the simulated carbon nanosphere, and new insights into the role of carbon defect size and distribution in determining the charge capacity and charge dynamics of these carbon based battery materials.« less

Interstitial and interlayer ion diffusion geometry extraction in graphitic nanosphere battery materials

DOE PAGES

Gyulassy, Attila; Knoll, Aaron; Lau, Kah Chun; ...

2016-01-31

Large-scale molecular dynamics (MD) simulations are commonly used for simulating the synthesis and ion diffusion of battery materials. A good battery anode material is determined by its capacity to store ion or other diffusers. However, modeling of ion diffusion dynamics and transport properties at large length and long time scales would be impossible with current MD codes. To analyze the fundamental properties of these materials, therefore, we turn to geometric and topological analysis of their structure. In this paper, we apply a novel technique inspired by discrete Morse theory to the Delaunay triangulation of the simulated geometry of a thermallymore » annealed carbon nanosphere. We utilize our computed structures to drive further geometric analysis to extract the interstitial diffusion structure as a single mesh. Lastly, our results provide a new approach to analyze the geometry of the simulated carbon nanosphere, and new insights into the role of carbon defect size and distribution in determining the charge capacity and charge dynamics of these carbon based battery materials.« less

Effects of microwave electric fields on the translational diffusion of dipolar molecules in surface potential: A simulation study

NASA Astrophysics Data System (ADS)

Kapranov, Sergey V.; Kouzaev, Guennadi A.

2018-01-01

Variations of effective diffusion coefficient of polar molecules exposed to microwave electric fields in a surface potential are studied by solving coupled stochastic differential equations of motion with a deterministic component of the surface force. Being an essential tool for the simulation interpretation, a theoretical approach to effective diffusion in surface potential is first developed. The effective diffusion coefficient is represented as the product of the normal diffusion coefficient and potential-dependent correction function, whose temperature dependence is close to the Arrhenius form. The analytically found zero-diffusion condition defines the state of thermal equilibrium at the surface. The diffusion of a water-like dipole molecule in the potential of graphite surface is simulated in the field-free conditions and in the presence of the alternating electric fields of various magnitude intensities and frequencies. Temperature dependence of the correction function exhibits field-induced variations of the effective Lennard-Jones energy parameter. It demonstrates maximum departure from the zero-field value at certain frequencies and intensities, which is associated with variations in the rotational dynamics. A concept of the amplitude-frequency resonance put forward to interpret the simulation results is explained using a heuristic reasoning and is corroborated by semi-quantitative considerations in terms of the Dissado-Hill cluster theory of dielectric relaxation.

Microbial Activity in Active and Upper Permafrost Layers in Axel Heiberg Island

NASA Astrophysics Data System (ADS)

Vishnivetskaya, T. A.; Allan, J.; Cheng, K.; Chourey, K.; Hettich, R. L.; Layton, A.; Liu, X.; Murphy, J.; Mykytczuk, N. C.; Phelps, T. J.; Pfiffner, S. M.; Saarunya, G.; Stackhouse, B. T.; Whyte, L.; Onstott, T. C.

2011-12-01

Data on microbial communities and their metabolic activity in Arctic wetlands and underlying permafrost sediments is lacking. Samples were collected from different depths of a cryosol (D1, D2) and upper permafrost (D3) at the Axel Heiberg Island in July 2009. Upper cryosol has lower H2O but higher C and N content when compared to deeper horizons including upper permafrost layer. Deep cryosol and upper permafrost contained SO42- (155 and 132 ppm) and NO3- (0.12 and 0.10 ppm), respectively. The phylogenetic analyses of the environmental 16S rRNA genes showed the putative SRB were more abundant in permafrost (8%) than in cryosols, D1 (0.2%) and D2 (1.1%). Putative denitrifying bacteria varied along depth with near 0.1% in D1 and a significant increase in D2 (2.7%) and D3 (2.2%). Methanogens were not detected; methanotrophs were present at low levels in D3 (1%). Two sets of microcosms were set up. Firstly, anaerobic microcosms, amended with 10 mM glucose, sulfate or nitrate, were cultivated at varying temperatures (15o, 6o, and 0o C) for 10 months. Metabolic activity was monitored by measuring CO2 and CH4 every 3 months. A total of 89.5% of the D3-originated microcosms showed higher activity in comparison to cryosols in first 3 months. CH4 was not detected in these microcosms, whereas CO2 production was higher at 15o C or with glucose. Metaproteomics analyses of microcosms with higher levels of CO2 production indicated the presence of stress responsive proteins (e.g. DnaK, GroEL) and proteins essential for energy production and survival under carbon starvation (e.g. F0F1 ATP synthase, acyl-CoA dehydrogenase). These proteins have been previously shown to be up-regulated at low temperatures by permafrost bacteria. Metaproteomics data based on the draft sequences indicated the presence of proteins from the genera Bradyrhizobium, Sphingomonas, Lysinibacillus and Methylophilaceae and these bacteria were also detected by pyrosequencing. Secondly, a duplicate set of anaerobic microcosms inoculated with substrates (80:20 H2/CO2, 30 mM acetate or methanol) were prepared from replicate samples of D2 and D3 and monitored for CH4 and CO2 production during incubation at either 4° or 22o C for 60-80 days. Both CH4 and CO2 production were highest at 22o C and using the CO2/H2 substrate. 16S pyrosequencing analyses of the archaeal diversity indicated Thermoproteales dominated in all microcosms (80-90% of reads) while methanogens belonging to Methanobacteriaceae were also found (0.6 to 11.5%), with the highest amount in the D3 amended with methanol at 22o C. This sample had the highest CH4 production (2.8 nmol g-1 day-1) as well as the only appearance of Methanosarcinaceae (1.4%). Twelve microcosms unresponsive to amendments were transferred to aerobic conditions with a subsequent increase in respiration rate up to 0.4 mmol CO2 g-1 day-1. The current study indicates that increase in temperature, changes in oxygen and nutrition availability enhances metabolic activity in permafrost microbial communities.

Intrinsic bioremediation of MTBE-contaminated groundwater at a petroleum-hydrocarbon spill site

NASA Astrophysics Data System (ADS)

Chen, K. F.; Kao, C. M.; Chen, T. Y.; Weng, C. H.; Tsai, C. T.

2006-06-01

An oil-refining plant site located in southern Taiwan has been identified as a petroleum-hydrocarbon [mainly methyl tert-butyl ether (MTBE) and benzene, toluene, ethylbenzene, and xylenes (BTEX)] spill site. In this study, groundwater samples collected from the site were analyzed to assess the occurrence of intrinsic MTBE biodegradation. Microcosm experiments were conducted to evaluate the feasibility of biodegrading MTBE by indigenous microorganisms under aerobic, cometabolic, iron reducing, and methanogenic conditions. Results from the field investigation and microbial enumeration indicate that the intrinsic biodegradation of MTBE and BTEX is occurring and causing the decrease in MTBE and BTEX concentrations. Microcosm results show that the indigenous microorganisms were able to biodegrade MTBE under aerobic conditions using MTBE as the sole primary substrate. The detected biodegradation byproduct, tri-butyl alcohol (TBA), can also be biodegraded by the indigenous microorganisms. In addition, microcosms with site groundwater as the medium solution show higher MTBE biodegradation rate. This indicates that the site groundwater might contain some trace minerals or organics, which could enhance the MTBE biodegradation. Results show that the addition of BTEX at low levels could also enhance the MTBE removal. No MTBE removal was detected in iron reducing and methanogenic microcosms. This might be due to the effects of low dissolved oxygen (approximately 0.3 mg/L) within the plume. The low iron reducers and methanogens (<1.8×103 cell/g of soil) observed in the aquifer also indicate that the iron reduction and methanogenesis are not the dominant biodegradation patterns in the contaminant plume. Results from the microcosm study reveal that preliminary laboratory study is required to determine the appropriate substrates and oxidation-reduction conditions to enhance the biodegradation of MTBE. Results suggest that in situ or on-site aerobic bioremediation using indigenous microorganisms would be a feasible technology to clean up this MTBE-contaminated site.

Bacterial community shift in the coastal Gulf of Mexico salt-marsh sediment microcosm in vitro following exposure to the Mississippi Canyon Block 252 oil (MC252).

PubMed

Koo, Hyunmin; Mojib, Nazia; Huang, Jonathan P; Donahoe, Rona J; Bej, Asim K

2015-08-01

In this study, we examined the responses by the indigenous bacterial communities in salt-marsh sediment microcosms in vitro following treatment with Mississippi Canyon Block 252 oil (MC252). Microcosms were constructed of sediment and seawater collected from Bayou La Batre located in coastal Alabama on the Gulf of Mexico. We used an amplicon pyrosequencing approach on microcosm sediment metagenome targeting the V3-V5 region of the 16S rRNA gene. Overall, we identified a shift in the bacterial community in three distinct groups. The first group was the early responders (orders Pseudomonadales and Oceanospirillales within class Gammaproteobacteria), which increased their relative abundance within 2 weeks and were maintained 3 weeks after oil treatment. The second group was identified as early, but transient responders (order Rhodobacterales within class Alphaproteobacteria; class Epsilonproteobacteria), which increased their population by 2 weeks, but returned to the basal level 3 weeks after oil treatment. The third group was the late responders (order Clostridiales within phylum Firmicutes; order Methylococcales within class Gammaproteobacteria; and phylum Tenericutes), which only increased 3 weeks after oil treatment. Furthermore, we identified oil-sensitive bacterial taxa (order Chromatiales within class Gammaproteobacteria; order Syntrophobacterales within class Deltaproteobacteria), which decreased in their population after 2 weeks of oil treatment. Detection of alkane (alkB), catechol (C2,3DO) and biphenyl (bph) biodegradation genes by PCR, particularly in oil-treated sediment metacommunity DNA, delineates proliferation of  the hydrocarbon degrading bacterial community. Overall, the indigenous bacterial communities in our salt-marsh sediment in vitro microcosm study responded rapidly and shifted towards members of the taxonomic groups that are capable of surviving in an MC252 oil-contaminated environment.

Local error estimates for adaptive simulation of the Reaction–Diffusion Master Equation via operator splitting

PubMed Central

Hellander, Andreas; Lawson, Michael J; Drawert, Brian; Petzold, Linda

2015-01-01

The efficiency of exact simulation methods for the reaction-diffusion master equation (RDME) is severely limited by the large number of diffusion events if the mesh is fine or if diffusion constants are large. Furthermore, inherent properties of exact kinetic-Monte Carlo simulation methods limit the efficiency of parallel implementations. Several approximate and hybrid methods have appeared that enable more efficient simulation of the RDME. A common feature to most of them is that they rely on splitting the system into its reaction and diffusion parts and updating them sequentially over a discrete timestep. This use of operator splitting enables more efficient simulation but it comes at the price of a temporal discretization error that depends on the size of the timestep. So far, existing methods have not attempted to estimate or control this error in a systematic manner. This makes the solvers hard to use for practitioners since they must guess an appropriate timestep. It also makes the solvers potentially less efficient than if the timesteps are adapted to control the error. Here, we derive estimates of the local error and propose a strategy to adaptively select the timestep when the RDME is simulated via a first order operator splitting. While the strategy is general and applicable to a wide range of approximate and hybrid methods, we exemplify it here by extending a previously published approximate method, the Diffusive Finite-State Projection (DFSP) method, to incorporate temporal adaptivity. PMID:26865735

Two-dimensional Radiative Magnetohydrodynamic Simulations of Partial Ionization in the Chromosphere. II. Dynamics and Energetics of the Low Solar Atmosphere

DOE Office of Scientific and Technical Information (OSTI.GOV)

Martínez-Sykora, Juan; Pontieu, Bart De; Hansteen, Viggo H.

2017-09-20

We investigate the effects of interactions between ions and neutrals on the chromosphere and overlying corona using 2.5D radiative MHD simulations with the Bifrost code. We have extended the code capabilities implementing ion–neutral interaction effects using the generalized Ohm’s law, i.e., we include the Hall term and the ambipolar diffusion (Pedersen dissipation) in the induction equation. Our models span from the upper convection zone to the corona, with the photosphere, chromosphere, and transition region partially ionized. Our simulations reveal that the interactions between ionized particles and neutral particles have important consequences for the magnetothermodynamics of these modeled layers: (1) ambipolarmore » diffusion increases the temperature in the chromosphere; (2) sporadically the horizontal magnetic field in the photosphere is diffused into the chromosphere, due to the large ambipolar diffusion; (3) ambipolar diffusion concentrates electrical currents, leading to more violent jets and reconnection processes, resulting in (3a) the formation of longer and faster spicules, (3b) heating of plasma during the spicule evolution, and (3c) decoupling of the plasma and magnetic field in spicules. Our results indicate that ambipolar diffusion is a critical ingredient for understanding the magnetothermodynamic properties in the chromosphere and transition region. The numerical simulations have been made publicly available, similar to previous Bifrost simulations. This will allow the community to study realistic numerical simulations with a wider range of magnetic field configurations and physics modules than previously possible.« less

Local error estimates for adaptive simulation of the Reaction-Diffusion Master Equation via operator splitting.

PubMed

Hellander, Andreas; Lawson, Michael J; Drawert, Brian; Petzold, Linda

2014-06-01

The efficiency of exact simulation methods for the reaction-diffusion master equation (RDME) is severely limited by the large number of diffusion events if the mesh is fine or if diffusion constants are large. Furthermore, inherent properties of exact kinetic-Monte Carlo simulation methods limit the efficiency of parallel implementations. Several approximate and hybrid methods have appeared that enable more efficient simulation of the RDME. A common feature to most of them is that they rely on splitting the system into its reaction and diffusion parts and updating them sequentially over a discrete timestep. This use of operator splitting enables more efficient simulation but it comes at the price of a temporal discretization error that depends on the size of the timestep. So far, existing methods have not attempted to estimate or control this error in a systematic manner. This makes the solvers hard to use for practitioners since they must guess an appropriate timestep. It also makes the solvers potentially less efficient than if the timesteps are adapted to control the error. Here, we derive estimates of the local error and propose a strategy to adaptively select the timestep when the RDME is simulated via a first order operator splitting. While the strategy is general and applicable to a wide range of approximate and hybrid methods, we exemplify it here by extending a previously published approximate method, the Diffusive Finite-State Projection (DFSP) method, to incorporate temporal adaptivity.

Two-dimensional Radiative Magnetohydrodynamic Simulations of Partial Ionization in the Chromosphere. II. Dynamics and Energetics of the Low Solar Atmosphere

NASA Astrophysics Data System (ADS)

Martínez-Sykora, Juan; De Pontieu, Bart; Carlsson, Mats; Hansteen, Viggo H.; Nóbrega-Siverio, Daniel; Gudiksen, Boris V.

2017-09-01

We investigate the effects of interactions between ions and neutrals on the chromosphere and overlying corona using 2.5D radiative MHD simulations with the Bifrost code. We have extended the code capabilities implementing ion-neutral interaction effects using the generalized Ohm’s law, I.e., we include the Hall term and the ambipolar diffusion (Pedersen dissipation) in the induction equation. Our models span from the upper convection zone to the corona, with the photosphere, chromosphere, and transition region partially ionized. Our simulations reveal that the interactions between ionized particles and neutral particles have important consequences for the magnetothermodynamics of these modeled layers: (1) ambipolar diffusion increases the temperature in the chromosphere; (2) sporadically the horizontal magnetic field in the photosphere is diffused into the chromosphere, due to the large ambipolar diffusion; (3) ambipolar diffusion concentrates electrical currents, leading to more violent jets and reconnection processes, resulting in (3a) the formation of longer and faster spicules, (3b) heating of plasma during the spicule evolution, and (3c) decoupling of the plasma and magnetic field in spicules. Our results indicate that ambipolar diffusion is a critical ingredient for understanding the magnetothermodynamic properties in the chromosphere and transition region. The numerical simulations have been made publicly available, similar to previous Bifrost simulations. This will allow the community to study realistic numerical simulations with a wider range of magnetic field configurations and physics modules than previously possible.

Finite element simulation of crack depth measurements in concrete using diffuse ultrasound

NASA Astrophysics Data System (ADS)

Seher, Matthias; Kim, Jin-Yeon; Jacobs, Laurence J.

2012-05-01

This research simulates the measurements of crack depth in concrete using diffuse ultrasound. The finite element method is employed to simulate the ultrasonic diffusion process around cracks with different geometrical shapes, with the goal of gaining physical insight into the data obtained from experimental measurements. The commercial finite element software Ansys is used to implement the two-dimensional concrete model. The model is validated with an analytical solution and experimental results. It is found from the simulation results that preliminary knowledge of the crack geometry is required to interpret the energy evolution curves from measurements and to correctly determine the crack depth.

Random walk on lattices: Graph-theoretic approach to simulating long-range diffusion-attachment growth models

NASA Astrophysics Data System (ADS)

Limkumnerd, Surachate

2014-03-01

Interest in thin-film fabrication for industrial applications have driven both theoretical and computational aspects of modeling its growth. One of the earliest attempts toward understanding the morphological structure of a film's surface is through a class of solid-on-solid limited-mobility growth models such as the Family, Wolf-Villain, or Das Sarma-Tamborenea models, which have produced fascinating surface roughening behaviors. These models, however, restrict the motion of an incidence atom to be within the neighborhood of its landing site, which renders them inept for simulating long-distance surface diffusion such as that observed in thin-film growth using a molecular-beam epitaxy technique. Naive extension of these models by repeatedly applying the local diffusion rules for each hop to simulate large diffusion length can be computationally very costly when certain statistical aspects are demanded. We present a graph-theoretic approach to simulating a long-range diffusion-attachment growth model. Using the Markovian assumption and given a local diffusion bias, we derive the transition probabilities for a random walker to traverse from one lattice site to the others after a large, possibly infinite, number of steps. Only computation with linear-time complexity is required for the surface morphology calculation without other probabilistic measures. The formalism is applied, as illustrations, to simulate surface growth on a two-dimensional flat substrate and around a screw dislocation under the modified Wolf-Villain diffusion rule. A rectangular spiral ridge is observed in the latter case with a smooth front feature similar to that obtained from simulations using the well-known multiple registration technique. An algorithm for computing the inverse of a class of substochastic matrices is derived as a corollary.

Modeling 2D and 3D diffusion.

PubMed

Saxton, Michael J

2007-01-01

Modeling obstructed diffusion is essential to the understanding of diffusion-mediated processes in the crowded cellular environment. Simple Monte Carlo techniques for modeling obstructed random walks are explained and related to Brownian dynamics and more complicated Monte Carlo methods. Random number generation is reviewed in the context of random walk simulations. Programming techniques and event-driven algorithms are discussed as ways to speed simulations.

Simulations of molecular diffusion in lattices of cells: insights for NMR of red blood cells.

PubMed Central

Regan, David G; Kuchel, Philip W

2002-01-01

The pulsed field-gradient spin-echo (PGSE) nuclear magnetic resonance (NMR) experiment, conducted on a suspension of red blood cells (RBC) in a strong magnetic field yields a q-space plot consisting of a series of maxima and minima. This is mathematically analogous to a classical optical diffraction pattern. The method provides a noninvasive and novel means of characterizing cell suspensions that is sensitive to changes in cell shape and packing density. The positions of the features in a q-space plot characterize the rate of exchange across the membrane, cell dimensions, and packing density. A diffusion tensor, containing information regarding the diffusion anisotropy of the system, can also be derived from the PGSE NMR data. In this study, we carried out Monte Carlo simulations of diffusion in suspensions of "virtual" cells that had either biconcave disc (as in RBC) or oblate spheroid geometry. The simulations were performed in a PGSE NMR context thus enabling predictions of q-space and diffusion tensor data. The simulated data were compared with those from real PGSE NMR diffusion experiments on RBC suspensions that had a range of hematocrit values. Methods that facilitate the processing of q-space data were also developed. PMID:12080109

Effects of superparamagnetic iron oxide nanoparticles on the longitudinal and transverse relaxation of hyperpolarized xenon gas

NASA Astrophysics Data System (ADS)

Burant, Alex; Antonacci, Michael; McCallister, Drew; Zhang, Le; Branca, Rosa Tamara

2018-06-01

SuperParamagnetic Iron Oxide Nanoparticles (SPIONs) are often used in magnetic resonance imaging experiments to enhance Magnetic Resonance (MR) sensitivity and specificity. While the effect of SPIONs on the longitudinal and transverse relaxation time of 1H spins has been well characterized, their effect on highly diffusive spins, like those of hyperpolarized gases, has not. For spins diffusing in linear magnetic field gradients, the behavior of the magnetization is characterized by the relative size of three length scales: the diffusion length, the structural length, and the dephasing length. However, for spins diffusing in non-linear gradients, such as those generated by iron oxide nanoparticles, that is no longer the case, particularly if the diffusing spins experience the non-linearity of the gradient. To this end, 3D Monte Carlo simulations are used to simulate the signal decay and the resulting image contrast of hyperpolarized xenon gas near SPIONs. These simulations reveal that signal loss near SPIONs is dominated by transverse relaxation, with little contribution from T1 relaxation, while simulated image contrast and experiments show that diffusion provides no appreciable sensitivity enhancement to SPIONs.

Simulations of molecular diffusion in lattices of cells: insights for NMR of red blood cells.

PubMed

Regan, David G; Kuchel, Philip W

2002-07-01

The pulsed field-gradient spin-echo (PGSE) nuclear magnetic resonance (NMR) experiment, conducted on a suspension of red blood cells (RBC) in a strong magnetic field yields a q-space plot consisting of a series of maxima and minima. This is mathematically analogous to a classical optical diffraction pattern. The method provides a noninvasive and novel means of characterizing cell suspensions that is sensitive to changes in cell shape and packing density. The positions of the features in a q-space plot characterize the rate of exchange across the membrane, cell dimensions, and packing density. A diffusion tensor, containing information regarding the diffusion anisotropy of the system, can also be derived from the PGSE NMR data. In this study, we carried out Monte Carlo simulations of diffusion in suspensions of "virtual" cells that had either biconcave disc (as in RBC) or oblate spheroid geometry. The simulations were performed in a PGSE NMR context thus enabling predictions of q-space and diffusion tensor data. The simulated data were compared with those from real PGSE NMR diffusion experiments on RBC suspensions that had a range of hematocrit values. Methods that facilitate the processing of q-space data were also developed.

Effect of Hydrodynamic Interactions on Self-Diffusion of Quasi-Two-Dimensional Colloidal Hard Spheres.

PubMed

Thorneywork, Alice L; Rozas, Roberto E; Dullens, Roel P A; Horbach, Jürgen

2015-12-31

We compare experimental results from a quasi-two-dimensional colloidal hard sphere fluid to a Monte Carlo simulation of hard disks with small particle displacements. The experimental short-time self-diffusion coefficient D(S) scaled by the diffusion coefficient at infinite dilution, D(0), strongly depends on the area fraction, pointing to significant hydrodynamic interactions at short times in the experiment, which are absent in the simulation. In contrast, the area fraction dependence of the experimental long-time self-diffusion coefficient D(L)/D(0) is in quantitative agreement with D(L)/D(0) obtained from the simulation. This indicates that the reduction in the particle mobility at short times due to hydrodynamic interactions does not lead to a proportional reduction in the long-time self-diffusion coefficient. Furthermore, the quantitative agreement between experiment and simulation at long times indicates that hydrodynamic interactions effectively do not affect the dependence of D(L)/D(0) on the area fraction. In light of this, we discuss the link between structure and long-time self-diffusion in terms of a configurational excess entropy and do not find a simple exponential relation between these quantities for all fluid area fractions.

Hybrid stochastic simulation of reaction-diffusion systems with slow and fast dynamics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Strehl, Robert; Ilie, Silvana, E-mail: silvana@ryerson.ca

2015-12-21

In this paper, we present a novel hybrid method to simulate discrete stochastic reaction-diffusion models arising in biochemical signaling pathways. We study moderately stiff systems, for which we can partition each reaction or diffusion channel into either a slow or fast subset, based on its propensity. Numerical approaches missing this distinction are often limited with respect to computational run time or approximation quality. We design an approximate scheme that remedies these pitfalls by using a new blending strategy of the well-established inhomogeneous stochastic simulation algorithm and the tau-leaping simulation method. The advantages of our hybrid simulation algorithm are demonstrated onmore » three benchmarking systems, with special focus on approximation accuracy and efficiency.« less

Generating a Simulated Fluid Flow Over an Aircraft Surface Using Anisotropic Diffusion

NASA Technical Reports Server (NTRS)

Rodriguez, David L. (Inventor); Sturdza, Peter (Inventor)

2013-01-01

A fluid-flow simulation over a computer-generated aircraft surface is generated using a diffusion technique. The surface is comprised of a surface mesh of polygons. A boundary-layer fluid property is obtained for a subset of the polygons of the surface mesh. A pressure-gradient vector is determined for a selected polygon, the selected polygon belonging to the surface mesh but not one of the subset of polygons. A maximum and minimum diffusion rate is determined along directions determined using a pressure gradient vector corresponding to the selected polygon. A diffusion-path vector is defined between a point in the selected polygon and a neighboring point in a neighboring polygon. An updated fluid property is determined for the selected polygon using a variable diffusion rate, the variable diffusion rate based on the minimum diffusion rate, maximum diffusion rate, and angular difference between the diffusion-path vector and the pressure-gradient vector.

Simulation studies of chemical erosion on carbon based materials at elevated temperatures

NASA Astrophysics Data System (ADS)

Kenmotsu, T.; Kawamura, T.; Li, Zhijie; Ono, T.; Yamamura, Y.

1999-06-01

We simulated the fluence dependence of methane reaction yield in carbon with hydrogen bombardment using the ACAT-DIFFUSE code. The ACAT-DIFFUSE code is a simulation code based on a Monte Carlo method with a binary collision approximation and on solving diffusion equations. The chemical reaction model in carbon was studied by Roth or other researchers. Roth's model is suitable for the steady state methane reaction. But this model cannot estimate the fluence dependence of the methane reaction. Then, we derived an empirical formula based on Roth's model for methane reaction. In this empirical formula, we assumed the reaction region where chemical sputtering due to methane formation takes place. The reaction region corresponds to the peak range of incident hydrogen distribution in the target material. We adopted this empirical formula to the ACAT-DIFFUSE code. The simulation results indicate the similar fluence dependence compared with the experiment result. But, the fluence to achieve the steady state are different between experiment and simulation results.

A Computational Approach to Increase Time Scales in Brownian Dynamics–Based Reaction-Diffusion Modeling

PubMed Central

Frazier, Zachary

2012-01-01

Abstract Particle-based Brownian dynamics simulations offer the opportunity to not only simulate diffusion of particles but also the reactions between them. They therefore provide an opportunity to integrate varied biological data into spatially explicit models of biological processes, such as signal transduction or mitosis. However, particle based reaction-diffusion methods often are hampered by the relatively small time step needed for accurate description of the reaction-diffusion framework. Such small time steps often prevent simulation times that are relevant for biological processes. It is therefore of great importance to develop reaction-diffusion methods that tolerate larger time steps while maintaining relatively high accuracy. Here, we provide an algorithm, which detects potential particle collisions prior to a BD-based particle displacement and at the same time rigorously obeys the detailed balance rule of equilibrium reactions. We can show that for reaction-diffusion processes of particles mimicking proteins, the method can increase the typical BD time step by an order of magnitude while maintaining similar accuracy in the reaction diffusion modelling. PMID:22697237

Post-processing interstitialcy diffusion from molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Bhardwaj, U.; Bukkuru, S.; Warrier, M.

2016-01-01

An algorithm to rigorously trace the interstitialcy diffusion trajectory in crystals is developed. The algorithm incorporates unsupervised learning and graph optimization which obviate the need to input extra domain specific information depending on crystal or temperature of the simulation. The algorithm is implemented in a flexible framework as a post-processor to molecular dynamics (MD) simulations. We describe in detail the reduction of interstitialcy diffusion into known computational problems of unsupervised clustering and graph optimization. We also discuss the steps, computational efficiency and key components of the algorithm. Using the algorithm, thermal interstitialcy diffusion from low to near-melting point temperatures is studied. We encapsulate the algorithms in a modular framework with functionality to calculate diffusion coefficients, migration energies and other trajectory properties. The study validates the algorithm by establishing the conformity of output parameters with experimental values and provides detailed insights for the interstitialcy diffusion mechanism. The algorithm along with the help of supporting visualizations and analysis gives convincing details and a new approach to quantifying diffusion jumps, jump-lengths, time between jumps and to identify interstitials from lattice atoms.

A scaled-ionic-charge simulation model that reproduces enhanced and suppressed water diffusion in aqueous salt solutions.

PubMed

Kann, Z R; Skinner, J L

2014-09-14

Non-polarizable models for ions and water quantitatively and qualitatively misrepresent the salt concentration dependence of water diffusion in electrolyte solutions. In particular, experiment shows that the water diffusion coefficient increases in the presence of salts of low charge density (e.g., CsI), whereas the results of simulations with non-polarizable models show a decrease of the water diffusion coefficient in all alkali halide solutions. We present a simple charge-scaling method based on the ratio of the solvent dielectric constants from simulation and experiment. Using an ion model that was developed independently of a solvent, i.e., in the crystalline solid, this method improves the water diffusion trends across a range of water models. When used with a good-quality water model, e.g., TIP4P/2005 or E3B, this method recovers the qualitative behaviour of the water diffusion trends. The model and method used were also shown to give good results for other structural and dynamic properties including solution density, radial distribution functions, and ion diffusion coefficients.

Post-processing interstitialcy diffusion from molecular dynamics simulations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bhardwaj, U., E-mail: haptork@gmail.com; Bukkuru, S.; Warrier, M.

2016-01-15

An algorithm to rigorously trace the interstitialcy diffusion trajectory in crystals is developed. The algorithm incorporates unsupervised learning and graph optimization which obviate the need to input extra domain specific information depending on crystal or temperature of the simulation. The algorithm is implemented in a flexible framework as a post-processor to molecular dynamics (MD) simulations. We describe in detail the reduction of interstitialcy diffusion into known computational problems of unsupervised clustering and graph optimization. We also discuss the steps, computational efficiency and key components of the algorithm. Using the algorithm, thermal interstitialcy diffusion from low to near-melting point temperatures ismore » studied. We encapsulate the algorithms in a modular framework with functionality to calculate diffusion coefficients, migration energies and other trajectory properties. The study validates the algorithm by establishing the conformity of output parameters with experimental values and provides detailed insights for the interstitialcy diffusion mechanism. The algorithm along with the help of supporting visualizations and analysis gives convincing details and a new approach to quantifying diffusion jumps, jump-lengths, time between jumps and to identify interstitials from lattice atoms. -- Graphical abstract:.« less

A framework for incorporating DTI Atlas Builder registration into Tract-Based Spatial Statistics and a simulated comparison to standard TBSS.

PubMed

Leming, Matthew; Steiner, Rachel; Styner, Martin

2016-02-27

Tract-based spatial statistics (TBSS) 6 is a software pipeline widely employed in comparative analysis of the white matter integrity from diffusion tensor imaging (DTI) datasets. In this study, we seek to evaluate the relationship between different methods of atlas registration for use with TBSS and different measurements of DTI (fractional anisotropy, FA, axial diffusivity, AD, radial diffusivity, RD, and medial diffusivity, MD). To do so, we have developed a novel tool that builds on existing diffusion atlas building software, integrating it into an adapted version of TBSS called DAB-TBSS (DTI Atlas Builder-Tract-Based Spatial Statistics) by using the advanced registration offered in DTI Atlas Builder 7 . To compare the effectiveness of these two versions of TBSS, we also propose a framework for simulating population differences for diffusion tensor imaging data, providing a more substantive means of empirically comparing DTI group analysis programs such as TBSS. In this study, we used 33 diffusion tensor imaging datasets and simulated group-wise changes in this data by increasing, in three different simulations, the principal eigenvalue (directly altering AD), the second and third eigenvalues (RD), and all three eigenvalues (MD) in the genu, the right uncinate fasciculus, and the left IFO. Additionally, we assessed the benefits of comparing the tensors directly using a functional analysis of diffusion tensor tract statistics (FADTTS 10 ). Our results indicate comparable levels of FA-based detection between DAB-TBSS and TBSS, with standard TBSS registration reporting a higher rate of false positives in other measurements of DTI. Within the simulated changes investigated here, this study suggests that the use of DTI Atlas Builder's registration enhances TBSS group-based studies.

Effects of Potassium Permanganate Oxidation on Subsurface Microbial Activity

NASA Technical Reports Server (NTRS)

Rowland, Martin A.; Brubaker, Gaylen R.; Westray, Mark; Morris, Damon; Kohler, Keisha; McCool, Alex (Technical Monitor)

2001-01-01

In situ chemical oxidation has the potential for degrading large quantities of organic contaminants and can be more effective and timely than traditional ex situ treatment methods. However, there is a need to better characterize the potential effects of this treatment on natural processes. This study focuses on potential inhibition to anaerobic dechlorination of trichloroethene (TCE) in soils from a large manufacturing facility as a result of in situ oxidation using potassium permanganate (KMn04)Previous microcosm studies established that natural attenuation occurs on-site and that it is enhanced by the addition of ethanol to the system. A potential remediation scheme for the site involves the use of potassium permanganate to reduce levels of TCE in heavily contaminated areas, then to inject ethanol into the system to "neutralize" excess oxidant and enhance microbial degradation. However, it is currently unknown whether the exposure of indigenous microbial populations to potassium permanganate may adversely affect biological reductive dechlorination by these microorganisms. Consequently, additional microcosm studies were conducted to evaluate this remediation scheme and assess the effect of potassium permanganate addition on biological reductive dechlorination of TCE. Samples of subsurface soil and groundwater were collected from a TCE-impacted area of the site. A portion of the soil was pretreated with nutrients and ethanol to stimulate microbial activity, while the remainder of the soil was left unamended. Soil/groundwater microcosms were prepared in sealed vials using the nutrient-amended and unamended soils, and the effects of potassium permanganate addition were evaluated using two permanganate concentrations (0.8 and 2.4 percent) and two contact times (1 and 3 weeks). TCE was then re-added to each microcosm and TCE and dichloroethene (DCE) concentrations were monitored to determine the degree to which microbial dechlorination occurred following chemical oxidation. Evidence of microbial degradation was generally detected within four weeks after TCE addition. Increases in DCE concentrations were consistent with decreases in TCE. The concentration of TCE in the nutrient-amended samples exposed to 2.4% KMnO4 for one week degraded somewhat more slowly than the samples exposed to the 0.8% KMnO4. The rates of degradation did not correlate with the length of KMn04 exposure for the nutrient-amended microcosms. Microbial degradation of TCE in the unamended microcosms was generally similar to that observed in the nutrient-amended microcosms. One treatment condition (unamended, one week exposure, 2.4% KMnO4) was exposed to elevated levels of ethanol and showed little evidence of degradation. It is suspected that the high levels of ethanol were toxic to the microorganisms. The results of the study indicate that exposure of indigenous soil and groundwater microbial populations to KMnO4 at concentrations of 0.8 to 2.4% do not impair the ability of the microbial populations to dechlorinate TCE. Consequently, the combination of chemical oxidation followed by enhanced biological reductive dechlorination appears to be a viable remedial strategy for highly-impacted subsurface areas of the site.

Generating a Simulated Fluid Flow over a Surface Using Anisotropic Diffusion

NASA Technical Reports Server (NTRS)

Rodriguez, David L. (Inventor); Sturdza, Peter (Inventor)

2016-01-01

A fluid-flow simulation over a computer-generated surface is generated using a diffusion technique. The surface is comprised of a surface mesh of polygons. A boundary-layer fluid property is obtained for a subset of the polygons of the surface mesh. A gradient vector is determined for a selected polygon, the selected polygon belonging to the surface mesh but not one of the subset of polygons. A maximum and minimum diffusion rate is determined along directions determined using the gradient vector corresponding to the selected polygon. A diffusion-path vector is defined between a point in the selected polygon and a neighboring point in a neighboring polygon. An updated fluid property is determined for the selected polygon using a variable diffusion rate, the variable diffusion rate based on the minimum diffusion rate, maximum diffusion rate, and the gradient vector.

Improving the realism of white matter numerical phantoms: a step towards a better understanding of the influence of structural disorders in diffusion MRI

NASA Astrophysics Data System (ADS)

Ginsburger, Kévin; Poupon, Fabrice; Beaujoin, Justine; Estournet, Delphine; Matuschke, Felix; Mangin, Jean-François; Axer, Markus; Poupon, Cyril

2018-02-01

White matter is composed of irregularly packed axons leading to a structural disorder in the extra-axonal space. Diffusion MRI experiments using oscillating gradient spin echo sequences have shown that the diffusivity transverse to axons in this extra-axonal space is dependent on the frequency of the employed sequence. In this study, we observe the same frequency-dependence using 3D simulations of the diffusion process in disordered media. We design a novel white matter numerical phantom generation algorithm which constructs biomimicking geometric configurations with few design parameters, and enables to control the level of disorder of the generated phantoms. The influence of various geometrical parameters present in white matter, such as global angular dispersion, tortuosity, presence of Ranvier nodes, beading, on the extra-cellular perpendicular diffusivity frequency dependence was investigated by simulating the diffusion process in numerical phantoms of increasing complexity and fitting the resulting simulated diffusion MR signal attenuation with an adequate analytical model designed for trapezoidal OGSE sequences. This work suggests that angular dispersion and especially beading have non-negligible effects on this extracellular diffusion metrics that may be measured using standard OGSE DW-MRI clinical protocols.

Diffusion of biomass pyrolysis products in H-ZSM-5 by molecular dynamics simulations

DOE PAGES

Bu, Lintao; Nimlos, Mark R.; Robichaud, David J.; ...

2016-12-13

Diffusion of biomass pyrolysis vapors and their upgraded products is an essential catalytic property of zeolites during catalytic fast pyrolysis and likely plays a critical role in the selectivity of these catalysts. Characterizing the diffusivities of representative biofuel molecules is critical to understand shape selectivity and interpret product distribution. Yet, experimental measurements on the diffusivities of oxygenated biofuel molecules at pyrolysis temperatures are very limited in the literature. As an alternative approach, we conducted MD simulations to measure the diffusion coefficients of several selected molecules that are representative of biomass pyrolysis vapors, namely water, methanol, glycolaldehyde, and toluene in H-ZSM-5more » zeolite. The results show the diffusion coefficients calculated via MD simulations are consistent with available NMR measurements at room temperature. The effect of molecular weight and molecular critical diameter on the diffusivity among the chosen model compounds is also examined. Furthermore, we have characterized the diffusivities of representative biofuel molecules, namely xylene isomers, in H-ZSM-5. Our calculations determined that the ratio of the diffusion coefficients for xylene isomers is p-xylene: o-xylene: m-xylene ≈ 83:3:1 at 700 K. Furthermore, our results also demonstrate the different diffusivity between p-xylene and toluene is due to the molecular orientations when the molecules diffuse along the channels in H-ZSM-5 and provide deep insight into the effect of molecular orientation on its diffusivity.« less

Interpretation of diffusion coefficients in nanostructured materials from random walk numerical simulation.

PubMed

Anta, Juan A; Mora-Seró, Iván; Dittrich, Thomas; Bisquert, Juan

2008-08-14

We make use of the numerical simulation random walk (RWNS) method to compute the "jump" diffusion coefficient of electrons in nanostructured materials via mean-square displacement. First, a summary of analytical results is given that relates the diffusion coefficient obtained from RWNS to those in the multiple-trapping (MT) and hopping models. Simulations are performed in a three-dimensional lattice of trap sites with energies distributed according to an exponential distribution and with a step-function distribution centered at the Fermi level. It is observed that once the stationary state is reached, the ensemble of particles follow Fermi-Dirac statistics with a well-defined Fermi level. In this stationary situation the diffusion coefficient obeys the theoretical predictions so that RWNS effectively reproduces the MT model. Mobilities can be also computed when an electrical bias is applied and they are observed to comply with the Einstein relation when compared with steady-state diffusion coefficients. The evolution of the system towards the stationary situation is also studied. When the diffusion coefficients are monitored along simulation time a transition from anomalous to trap-limited transport is observed. The nature of this transition is discussed in terms of the evolution of electron distribution and the Fermi level. All these results will facilitate the use of RW simulation and related methods to interpret steady-state as well as transient experimental techniques.

Simulation study of temperature-dependent diffusion behaviors of Ag/Ag(001) at low substrate temperature

NASA Astrophysics Data System (ADS)

Cai, Danyun; Mo, Yunjie; Feng, Xiaofang; He, Yingyou; Jiang, Shaoji

2017-06-01

In this study, a model based on the First Principles calculations and Kinetic Monte Carlo simulation were established to study the growth characteristic of Ag thin film at low substrate temperature. On the basis of the interaction between the adatom and nearest-neighbor atoms, some simplifications and assumptions were made to categorize the diffusion behaviors of Ag adatoms on Ag(001). Then the barriers of all possible diffusion behaviors were calculated using the Climbing Image Nudged Elastic Band method (CI-NEB). Based on the Arrhenius formula, the morphology variation, which is attributed to the surface diffusion behaviors during the growth, was simulated with a temperature-dependent KMC model. With this model, a non-monotonic relation between the surface roughness and the substrate temperature (decreasing from 300 K to 100 K) were discovered. The analysis of the temperature dependence on diffusion behaviors presents a theoretical explanation of diffusion mechanism for the non-monotonic variation of roughness at low substrate temperature.

Summer Work Experience: Determining Methane Combustion Mechanisms and Sub-Scale Diffuser Properties for Space Transporation System Engine Testing

NASA Technical Reports Server (NTRS)

Williams, Powtawche N.

1998-01-01

To assess engine performance during the testing of Space Shuttle Main Engines (SSMEs), the design of an optimal altitude diffuser is studied for future Space Transportation Systems (STS). For other Space Transportation Systems, rocket propellant using kerosene is also studied. Methane and dodecane have similar reaction schemes as kerosene, and are used to simulate kerosene combustion processes at various temperatures. The equations for the methane combustion mechanism at high temperature are given, and engine combustion is simulated on the General Aerodynamic Simulation Program (GASP). The successful design of an altitude diffuser depends on the study of a sub-scaled diffuser model tested through two-dimensional (2-D) flow-techniques. Subroutines given calculate the static temperature and pressure at each Mach number within the diffuser flow. Implementing these subroutines into program code for the properties of 2-D compressible fluid flow determines all fluid characteristics, and will be used in the development of an optimal diffuser design.

Influence of Liquid Structure on Fickian Diffusion in Binary Mixtures of n-Hexane and Carbon Dioxide Probed by Dynamic Light Scattering, Raman Spectroscopy, and Molecular Dynamics Simulations.

PubMed

Klein, Tobias; Wu, Wenchang; Rausch, Michael Heinrich; Giraudet, Cédric; Koller, Thomas M; Fröba, Andreas Paul

2018-06-11

This study contributes to a fundamental understanding how the liquid structure in a model system consisting of weakly associative n-hexane ( n-C 6 H 14 ) and carbon dioxide (CO 2 ) influences the Fickian diffusion process. For this, the benefits of light scattering experiments and molecular dynamics (MD) simulations at macroscopic thermodynamic equilibrium were combined synergistically. Our reference Fickian diffusivities measured by dynamic light scattering (DLS) revealed an unusual trend with increasing CO 2 mole fractions up to a CO 2 concentration of about 70 mol%, which agrees with our simulation results. The molecular impacts on the Fickian diffusion were analyzed by MD simulations, where kinetic contributions related to the Maxwell-Stefan (MS) diffusivity and structural contributions quantified by the thermodynamic factor were studied separately. Both the MS diffusivity and the thermodynamic factor indicate the deceleration of Fickian diffusion compared to an ideal mixture behavior. Computed radial distribution functions as well as a significant blue-shift of the CH-stretching modes of n-C 6 H 14 identified by Raman spectroscopy show that the slowing-down of the diffusion is caused by a structural organization in the binary mixtures over a broad concentration range in the form of self-associated n-C 6 H 14 and CO 2 domains. These networks start to form close to the infinite dilution limits and seem to have their largest extent at a solute-solvent transition point at about 70 mol% of CO 2 . The current results not only improve the general understanding of mass diffusion in liquids, but also serve to develop sound prediction models for Fick diffusivities.

Response of radiation belt simulations to different radial diffusion coefficients

NASA Astrophysics Data System (ADS)

Drozdov, A.; Shprits, Y.; Subbotin, D.; Kellerman, A. C.

2013-12-01

Resonant interactions between Ultra Low Frequency (ULF) waves and relativistic electrons may violate the third adiabatic invariant of motion, which produces radial diffusion in the electron radiation belts. This process plays an important role in the formation and structure of the outer electron radiation belt and is important for electron acceleration and losses in that region. Two parameterizations of the resonant wave-particle interaction of electrons with ULF waves in the magnetosphere by Brautigam and Albert [2000] and Ozeke et al. [2012] are evaluated using the Versatile Electron Radiation Belt (VERB) diffusion code to estimate their relative effect on the radiation belt simulation. The period of investigation includes quiet time and storm time geomagnetic activity and is compared to data based on satellite observations. Our calculations take into account wave-particle interactions represented by radial diffusion transport, local acceleration, losses due to pitch-angle diffusion, and mixed diffusion. We show that the results of the 3D diffusion simulations depend on the assumed parametrization of waves. The differences between the simulations and potential missing physical mechanisms are discussed. References Brautigam, D. H., and J. M. Albert (2000), Radial diffusion analysis of outer radiation belt electrons during the October 9, 1990, magnetic storm, J. Geophys. Res., 105(A1), 291-309, doi:10.1029/1999JA900344 Ozeke, L. G., I. R. Mann, K. R. Murphy, I. J. Rae, D. K. Milling, S. R. Elkington, A. A. Chan, and H. J. Singer (2012), ULF wave derived radiation belt radial diffusion coefficients, J. Geophys. Res., 117, A04222, doi:10.1029/2011JA017463.

Global diffusion of cosmic rays in random magnetic fields

NASA Astrophysics Data System (ADS)

Snodin, A. P.; Shukurov, A.; Sarson, G. R.; Bushby, P. J.; Rodrigues, L. F. S.

2016-04-01

The propagation of charged particles, including cosmic rays, in a partially ordered magnetic field is characterized by a diffusion tensor whose components depend on the particle's Larmor radius RL and the degree of order in the magnetic field. Most studies of the particle diffusion presuppose a scale separation between the mean and random magnetic fields (e.g. there being a pronounced minimum in the magnetic power spectrum at intermediate scales). Scale separation is often a good approximation in laboratory plasmas, but not in most astrophysical environments such as the interstellar medium (ISM). Modern simulations of the ISM have numerical resolution of the order of 1 pc, so the Larmor radius of the cosmic rays that dominate in energy density is at least 106 times smaller than the resolved scales. Large-scale simulations of cosmic ray propagation in the ISM thus rely on oversimplified forms of the diffusion tensor. We take the first steps towards a more realistic description of cosmic ray diffusion for such simulations, obtaining direct estimates of the diffusion tensor from test particle simulations in random magnetic fields (with the Larmor radius scale being fully resolved), for a range of particle energies corresponding to 10-2 ≲ RL/lc ≲ 103, where lc is the magnetic correlation length. We obtain explicit expressions for the cosmic ray diffusion tensor for RL/lc ≪ 1, that might be used in a sub-grid model of cosmic ray diffusion. The diffusion coefficients obtained are closely connected with existing transport theories that include the random walk of magnetic lines.

Drained coastal peatlands: A potential nitrogen source to marine ecosystems under prolonged drought and heavy storm events-A microcosm experiment.

PubMed

Wang, Hongjun; Richardson, Curtis J; Ho, Mengchi; Flanagan, Neal

2016-10-01

Over the past several decades there has been a massive increase in coastal eutrophication, which is often caused by increased runoff input of nitrogen from landscape alterations. Peatlands, covering 3% of land area, have stored about 12-21% of global soil organic nitrogen (12-20Pg N) around rivers, lakes and coasts over millennia and are now often drained and farmed. Their huge nitrogen pools may be released by intensified climate driven hydrologic events-prolonged droughts followed by heavy storms-and later transported to marine ecosystems. In this study, we collected peat monoliths from drained, natural, and restored coastal peatlands in the Southeastern U.S., and conducted a microcosm experiment simulating coupled prolonged-drought and storm events to (1) test whether storms could trigger a pulse of nitrogen export from drought-stressed peatlands and (2) assess how differentially hydrologic managements through shifting plant communities affect nitrogen export by combining an experiment of nitrogen release from litter. During the drought phase, we observed a significant temporal variation in net nitrogen mineralization rate (NMR). NMR spiked in the third month and then decreased rapidly. This pattern indicates that drought duration significantly affects nitrogen mineralization in peat. NMR in the drained site reached up to 490±110kgha(-1)year(-1), about 5 times higher than in the restored site. After the 14-month drought phase, we simulated a heavy storm by bringing peat monoliths to saturation. In the discharge waters, concentrations of total dissolved nitrogen in the monoliths from the drained site (72.7±16.3mgL(-1)) was about ten times as high as from the restored site. Our results indicate that previously drained peatlands under prolonged drought are a potent source of nitrogen export. Moreover, drought-induced plant community shifts to herbaceous plants substantially raise nitrogen release with lasting effects by altering litter quality in peatlands. Copyright © 2016 Elsevier B.V. All rights reserved.

Ecological changes in oral microcosm biofilm during maturation

NASA Astrophysics Data System (ADS)

Kim, Young-Seok; Kang, Si-Mook; Lee, Eun-Song; Lee, Ji Hyun; Kim, Bo-Ra; Kim, Baek-Il

2016-10-01

The aim of this study was to evaluate the ecological changes in the biofilm at different stages of maturation using 16S rDNA gene amplicon sequencing and to identify correlations between red/green (R/G) fluorescence ratio and ecological changes. An oral microcosm biofilm was initiated from the saliva of a single donor and grown anaerobically for up to 10 days in basal medium mucin. Quantitative light-induced fluorescence analysis was shown that the R/G ratio of the biofilm increased consistently, but the slope rapidly decreased after six days. The bacterial compositions of 10 species also consistently changed over time. However, there was no significant correlation between each bacteria and red fluorescence. The monitoring of the maturation process of oral microcosm biofilm over 10 days revealed that the R/G ratio and the bacterial composition within biofilm consistently changed. Therefore, the R/G fluorescence ratio of biofilm may be related with its ecological change rather than specific bacteria.

Local knowledge, environmental politics, and the founding of ecology in the United States. Stephen Forbes and "The Lake as a Microcosm" (1887).

PubMed

Schneider, D W

2000-12-01

Stephen Forbes's "The Lake as a Microcosm" is one of the founding documents of the science of ecology in the United States. By tracing the connections between scientists and local fishermen underlying the research on floodplain lakes presented in "The Lake as a Microcosm," this essay shows how the birth of ecology was tied to local knowledge and the local politics of environmental transformation. Forbes and the other scientists of the Illinois Natural History Survey relied on fishermen for manual labor, expertise in catching fish, and knowledge of the natural history of the fishes. As Forbes and his colleagues worked in close contact with fishermen, they also adopted many of their political concerns over the privatization of the floodplain and became politically active in supporting their interests. The close connection between scientists and local knowledge forced the ecologists to reframe the boundaries of ecology as objective or political, pure or applied, local or scientific.

Effects of acute gamma-irradiation on the aquatic microbial microcosm in comparison with chemicals.

PubMed

Fuma, Shoichi; Ishii, Nobuyoshi; Takeda, Hiroshi; Miyamoto, Kiriko; Yanagisawa, Kei; Doi, Kazutaka; Kawaguchi, Isao; Tanaka, Nobuyuki; Inamori, Yuhei; Polikarpov, Gennady G

2009-12-01

Effects of acute gamma-irradiation were investigated in the aquatic microcosm consisting of green algae (Chlorella sp. and Scenedesmus sp.) and a blue-green alga (Tolypothrix sp.) as producers; an oligochaete (Aeolosoma hemprichi), rotifers (Lecane sp. and Philodina sp.) and a ciliate protozoan (Cyclidium glaucoma) as consumers; and more than four species of bacteria as decomposers. At 100 Gy, populations were not affected in any taxa. At 500-5000 Gy, one or three taxa died out and populations of two or three taxa decreased over time, while that of Tolypothrix sp. increased. This Tolypothrix sp. increase was likely an indirect effect due to interspecies interactions. The principal response curve analysis revealed that the main trend of the effects was a dose-dependent population decrease. For a better understanding of radiation risks in aquatic microbial communities, effect doses of gamma-rays compared with copper, herbicides and detergents were evaluated using the radiochemoecological conceptual model and the effect index for microcosm.

Azolla-anabaena-bacteria system as a natural microcosm

NASA Astrophysics Data System (ADS)

Carrapico, Francisco J.

2002-02-01

Azolla is an aquatic fern that contains a permanent endosymbiotic prokaryotic community (cyanobacteria and bacteria) inside of the cavity in the leaf dorsal lobe of the pteridophyte. This is a unique situation and can be seen as a microcosm inside of an organism and also can be considered a good example of a living model for biological and environmental studies. These symbionts are specific of this symbiosis and lives immobilized in a mucilaginous fibrillar network, which fills part of the cavity. The symbionts works as immobilized organisms in a natural system that can be used as a model for biotechnological research and in biologically based life support systems. The nature and the complexity of this system is simultaneously a reference and a challenge for the research in the communication between the two levels of nature organization (microcosm and mesocosm), and can also be used as a reference for the design of new environmental engineered symbiotic systems that include man as a prelude to life in space.

Anaerobic biodegradation of nonylphenol in river sediment under nitrate- or sulfate-reducing conditions and associated bacterial community.

PubMed

Wang, Zhao; Yang, Yuyin; Dai, Yu; Xie, Shuguang

2015-04-09

Nonylphenol (NP) is a commonly detected pollutant in aquatic ecosystem and can be harmful to aquatic organisms. Anaerobic degradation is of great importance for the clean-up of NP in sediment. However, information on anaerobic NP biodegradation in the environment is still very limited. The present study investigated the shift in bacterial community structure associated with NP degradation in river sediment microcosms under nitrate- or sulfate-reducing conditions. Nearly 80% of NP (100 mg kg(-1)) could be removed under these two anaerobic conditions after 90 or 110 days' incubation. Illumina MiSeq sequencing analysis indicated that Proteobacteria, Firmicutes, Bacteroidetes and Chloroflexi became the dominant phylum groups with NP biodegradation. The proportion of Gammaproteobacteria, Deltaproteobacteria and Choloroflexi showed a marked increase in nitrate-reducing microcosm, while Gammaproteobacteria and Firmicutes in sulfate-reducing microcosm. Moreover, sediment bacterial diversity changed with NP biodegradation, which was dependent on type of electron acceptor. Copyright © 2014 Elsevier B.V. All rights reserved.

A field method using microcosms to evaluate transfer of Cd, Cu, Ni, Pb and Zn from sewage sludge amended forest soils to Helix aspersa snails.

PubMed

Scheifler, R; Ben Brahim, M; Gomot-de Vaufleury, A; Carnus, J-M; Badot, P-M

2003-01-01

Juvenile Helix aspersa snails exposed in field microcosms were used to assess the transfer of Cd, Cu, Ni, Pb and Zn from forest soils amended with liquid and composted sewage sludge. Zn concentrations and contents were significantly higher in snails exposed to liquid and composted sludge after 5 and 7 weeks of exposure, when compared with control. Trends were less clear for the other metals. Present results show that Zn, among the cocktail of metallic trace elements (MTE) coming from sewage sludge disposal, represents the principal concern for food chain transfer and secondary poisoning risks. The microcosm design used in this experiment was well suited for relatively long-term (about 2 months) active biomonitoring with H. aspersa snails. The snails quickly indicated the variations of MTE concentrations in their immediate environment. Therefore, the present study provides a simple but efficient field tool to evaluate MTE bioavailability and transfer.

Functional complexity and ecosystem stability: an experimental approach

DOE Office of Scientific and Technical Information (OSTI.GOV)

Van Voris, P.; O'Neill, R.V.; Shugart, H.H.

1978-01-01

The complexity-stability hypothesis was experimentally tested using intact terrestrial microcosms. Functional complexity was defined as the number and significance of component interactions (i.e., population interactions, physical-chemical reactions, biological turnover rates) influenced by nonlinearities, feedbacks, and time delays. It was postulated that functional complexity could be nondestructively measured through analysis of a signal generated from the system. Power spectral analysis of hourly CO/sub 2/ efflux, from eleven old-field microcosms, was analyzed for the number of low frequency peaks and used to rank the functional complexity of each system. Ranking of ecosystem stability was based on the capacity of the system tomore » retain essential nutrients and was measured by net loss of Ca after the system was stressed. Rank correlation supported the hypothesis that increasing ecosystem functional complexity leads to increasing ecosystem stability. The results indicated that complex functional dynamics can serve to stabilize the system. The results also demonstrated that microcosms are useful tools for system-level investigations.« less

Behavior of pollutant-degrading microorganisms in aquifers: Predictions for genetically engineered organisms

USGS Publications Warehouse

Krumme, M.L.; Smith, R.L.; Egestorff, J.; Thiem, S.M.; Tiedje, J.M.; Timmis, K.N.; Dwyer, D.F.

1994-01-01

Bioremediation via environmental introductions of degradative microorganisms requires that the microbes survive in substantial numbers and effect an increase in the rate and extent of pollutant removal. Combined field and microcosm studies were used to assess these abilities for laboratory-grown bacteria. Following introduction into a contaminated aquifer, viable cells of Pseudomonas sp. B13 were present in the contaminant plume for 447 days; die-off was rapid in pristine areas. In aquifer microcosms, survival of B13 and FR120, a genetically engineered derivative of B13 having enhanced catabolic capabilities for substituted aromatics, was comparable to B13 field results; both bacteria degraded target pollutants in microcosms made with aquifer samples from the aerobic zone of the pollutant plume. Results suggest that field studies with nonrecombinant microorganisms may be coupled to laboratory studies with derivative strains to estimate their bioremediative efficacy. Furthermore, laboratory strains of bacteria can survive for extended periods of time in nature and thus may have important bioremediative applications. ?? 1994 American Chemical Society.

Probing the Interplay between Dendritic Spine Morphology and Membrane-Bound Diffusion.

PubMed

Adrian, Max; Kusters, Remy; Storm, Cornelis; Hoogenraad, Casper C; Kapitein, Lukas C

2017-11-21

Dendritic spines are protrusions along neuronal dendrites that harbor the majority of excitatory postsynapses. Their distinct morphology, often featuring a bulbous head and small neck that connects to the dendritic shaft, has been shown to facilitate compartmentalization of electrical and cytoplasmic signaling stimuli elicited at the synapse. The extent to which spine morphology also forms a barrier for membrane-bound diffusion has remained unclear. Recent simulations suggested that especially the diameter of the spine neck plays a limiting role in this process. Here, we examine the connection between spine morphology and membrane-bound diffusion through a combination of photoconversion, live-cell superresolution experiments, and numerical simulations. Local photoconversion was used to obtain the timescale of diffusive equilibration in spines and followed by global sparse photoconversion to determine spine morphologies with nanoscopic resolution. These morphologies were subsequently used to assess the role of morphology on the diffusive equilibration. From the simulations, we could determine a robust relation between the equilibration timescale and a generalized shape factor calculated using both spine neck width and neck length, as well as spine head size. Experimentally, we found that diffusive equilibration was often slower, but rarely faster than predicted from the simulations, indicating that other biological confounders further reduce membrane-bound diffusion in these spines. This shape-dependent membrane-bound diffusion in mature spines may contribute to spine-specific compartmentalization of neurotransmitter receptors and signaling molecules and thereby support long-term plasticity of synaptic contacts. Copyright © 2017 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Enhanced diffusion on oscillating surfaces through synchronization

NASA Astrophysics Data System (ADS)

Wang, Jin; Cao, Wei; Ma, Ming; Zheng, Quanshui

2018-02-01

The diffusion of molecules and clusters under nanoscale confinement or absorbed on surfaces is the key controlling factor in dynamical processes such as transport, chemical reaction, or filtration. Enhancing diffusion could benefit these processes by increasing their transport efficiency. Using a nonlinear Langevin equation with an extensive number of simulations, we find a large enhancement in diffusion through surface oscillation. For helium confined in a narrow carbon nanotube, the diffusion enhancement is estimated to be over three orders of magnitude. A synchronization mechanism between the kinetics of the particles and the oscillating surface is revealed. Interestingly, a highly nonlinear negative correlation between diffusion coefficient and temperature is predicted based on this mechanism, and further validated by simulations. Our results provide a general and efficient method for enhancing diffusion, especially at low temperatures.

Diffusion-coupled cohesive interface simulations of stress corrosion intergranular cracking in polycrystalline materials

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pu, Chao; Gao, Yanfei; Wang, Yanli

To study the stress corrosion intergranular cracking mechanism, a diffusion-coupled cohesive zone model (CZM) is proposed for the simulation of the stress-assisted diffusional process along grain boundaries and the mechanical response of grain boundary sliding and separation. This simulation methodology considers the synergistic effects of impurity diffusion driven by pressure gradient and degradation of grain boundary strength by impurity concentration. The diffusion-coupled CZM is combined with crystal plasticity finite element model (CPFEM) to simulate intergranular fracture of polycrystalline material under corrosive environment. Significant heterogeneity of the stress field and extensive impurity accumulation is observed at grain boundaries and junction points.more » Deformation mechanism maps are constructed with respect to the grain boundary degradation factor and applied strain rate, which dictate the transition from internal to near-surface intergranular fracture modes under various strain amplitudes and grain sizes.« less

Mesoscale Polymer Dissolution Probed by Raman Spectroscopy and Molecular Simulations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chang, Tsun-Mei; Xantheas, Sotiris S.; Vasdekis, Andreas E.

2016-10-13

The diffusion of various solvents into a polystyrene (PS) matrix was probed experimentally by monitoring the temporal profiles of the Raman spectra and theoretically from molecular dynamics (MD) simulations of the binary system. The simulation results assist in providing a fundamental, molecular level connection between the mixing/dissolution processes and the difference = solvent – PS in the values of the Hildebrand parameter () between the two components of the binary systems: solvents having similar values of with PS (small ) exhibit fast diffusion into the polymer matrix, whereas the diffusion slows down considerably when the ’s are different (large ).more » To this end, the Hildebrand parameter was identified as a useful descriptor that governs the process of mixing in polymer – solvent binary systems. The experiments also provide insight into further refinements of the models specific to non-Fickian diffusion phenomena that need to be used in the simulations.« less

Thermophysical properties of liquid Ni around the melting temperature from molecular dynamics simulation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rozas, R. E.; Department of Physics, University of Bío-Bío, Av. Collao 1202, P.O. Box 5C, Concepción; Demiraǧ, A. D.

Thermophysical properties of liquid nickel (Ni) around the melting temperature are investigated by means of classical molecular dynamics (MD) simulation, using three different embedded atom method potentials to model the interactions between the Ni atoms. Melting temperature, enthalpy, static structure factor, self-diffusion coefficient, shear viscosity, and thermal diffusivity are compared to recent experimental results. Using ab initio MD simulation, we also determine the static structure factor and the mean-squared displacement at the experimental melting point. For most of the properties, excellent agreement is found between experiment and simulation, provided the comparison relative to the corresponding melting temperature. We discuss themore » validity of the Hansen-Verlet criterion for the static structure factor as well as the Stokes-Einstein relation between self-diffusion coefficient and shear viscosity. The thermal diffusivity is extracted from the autocorrelation function of a wavenumber-dependent temperature fluctuation variable.« less

Hydrodynamic theory of diffusion in two-temperature multicomponent plasmas

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ramshaw, J.D.; Chang, C.H.

Detailed numerical simulations of multicomponent plasmas require tractable expressions for species diffusion fluxes, which must be consistent with the given plasma current density J{sub q} to preserve local charge neutrality. The common situation in which J{sub q} = 0 is referred to as ambipolar diffusion. The use of formal kinetic theory in this context leads to results of formidable complexity. We derive simple tractable approximations for the diffusion fluxes in two-temperature multicomponent plasmas by means of a generalization of the hydrodynamical approach used by Maxwell, Stefan, Furry, and Williams. The resulting diffusion fluxes obey generalized Stefan-Maxwell equations that contain drivingmore » forces corresponding to ordinary, forced, pressure, and thermal diffusion. The ordinary diffusion fluxes are driven by gradients in pressure fractions rather than mole fractions. Simplifications due to the small electron mass are systematically exploited and lead to a general expression for the ambipolar electric field in the limit of infinite electrical conductivity. We present a self-consistent effective binary diffusion approximation for the diffusion fluxes. This approximation is well suited to numerical implementation and is currently in use in our LAVA computer code for simulating multicomponent thermal plasmas. Applications to date include a successful simulation of demixing effects in an argon-helium plasma jet, for which selected computational results are presented. Generalizations of the diffusion theory to finite electrical conductivity and nonzero magnetic field are currently in progress.« less

Determination of the effective diffusivity of water in a poly (methyl methacrylate) membrane containing carbon nanotubes using kinetic Monte Carlo simulations.

PubMed

Mermigkis, Panagiotis G; Tsalikis, Dimitrios G; Mavrantzas, Vlasis G

2015-10-28

A kinetic Monte Carlo (kMC) simulation algorithm is developed for computing the effective diffusivity of water molecules in a poly(methyl methacrylate) (PMMA) matrix containing carbon nanotubes (CNTs) at several loadings. The simulations are conducted on a cubic lattice to the bonds of which rate constants are assigned governing the elementary jump events of water molecules from one lattice site to another. Lattice sites belonging to PMMA domains of the membrane are assigned different rates than lattice sites belonging to CNT domains. Values of these two rate constants are extracted from available numerical data for water diffusivity within a PMMA matrix and a CNT pre-computed on the basis of independent atomistic molecular dynamics simulations, which show that water diffusivity in CNTs is 3 orders of magnitude faster than in PMMA. Our discrete-space, continuum-time kMC simulation results for several PMMA-CNT nanocomposite membranes (characterized by different values of CNT length L and diameter D and by different loadings of the matrix in CNTs) demonstrate that the overall or effective diffusivity, D(eff), of water in the entire polymeric membrane is of the same order of magnitude as its diffusivity in PMMA domains and increases only linearly with the concentration C (vol. %) in nanotubes. For a constant value of the concentration C, D(eff) is found to vary practically linearly also with the CNT aspect ratio L/D. The kMC data allow us to propose a simple bilinear expression for D(eff) as a function of C and L/D that can describe the numerical data for water mobility in the membrane extremely accurately. Additional simulations with two different CNT configurations (completely random versus aligned) show that CNT orientation in the polymeric matrix has only a minor effect on D(eff) (as long as CNTs do not fully penetrate the membrane). We have also extensively analyzed and quantified sublinear (anomalous) diffusive phenomena over small to moderate times and correlated them with the time needed for penetrant water molecules to explore the available large, fast-diffusing CNT pores before Fickian diffusion is reached.

Determination of the effective diffusivity of water in a poly (methyl methacrylate) membrane containing carbon nanotubes using kinetic Monte Carlo simulations

NASA Astrophysics Data System (ADS)

Mermigkis, Panagiotis G.; Tsalikis, Dimitrios G.; Mavrantzas, Vlasis G.

2015-10-01

A kinetic Monte Carlo (kMC) simulation algorithm is developed for computing the effective diffusivity of water molecules in a poly(methyl methacrylate) (PMMA) matrix containing carbon nanotubes (CNTs) at several loadings. The simulations are conducted on a cubic lattice to the bonds of which rate constants are assigned governing the elementary jump events of water molecules from one lattice site to another. Lattice sites belonging to PMMA domains of the membrane are assigned different rates than lattice sites belonging to CNT domains. Values of these two rate constants are extracted from available numerical data for water diffusivity within a PMMA matrix and a CNT pre-computed on the basis of independent atomistic molecular dynamics simulations, which show that water diffusivity in CNTs is 3 orders of magnitude faster than in PMMA. Our discrete-space, continuum-time kMC simulation results for several PMMA-CNT nanocomposite membranes (characterized by different values of CNT length L and diameter D and by different loadings of the matrix in CNTs) demonstrate that the overall or effective diffusivity, Deff, of water in the entire polymeric membrane is of the same order of magnitude as its diffusivity in PMMA domains and increases only linearly with the concentration C (vol. %) in nanotubes. For a constant value of the concentration C, Deff is found to vary practically linearly also with the CNT aspect ratio L/D. The kMC data allow us to propose a simple bilinear expression for Deff as a function of C and L/D that can describe the numerical data for water mobility in the membrane extremely accurately. Additional simulations with two different CNT configurations (completely random versus aligned) show that CNT orientation in the polymeric matrix has only a minor effect on Deff (as long as CNTs do not fully penetrate the membrane). We have also extensively analyzed and quantified sublinear (anomalous) diffusive phenomena over small to moderate times and correlated them with the time needed for penetrant water molecules to explore the available large, fast-diffusing CNT pores before Fickian diffusion is reached.

Effects of chlorpyrifos in freshwater model ecosystems: the influence of experimental conditions on ecotoxicological thresholds.

PubMed

van Wijngaarden, René P A; Brock, Theo C M; Douglas, Mark T

2005-10-01

Three experiments were conducted to determine the impact of the insecticide chlorpyrifos (single applications of 0.01 to 10 microg AI litre(-1)) in plankton-dominated nutrient-rich microcosms. The microcosms (water volume approximately 14 litres) were established in the laboratory under temperature, light regimes and nutrient levels that simulated cool 'temperate' and warm 'Mediterranean' environmental conditions. The fate of chlorpyrifos in the water column was monitored and the effects on zooplankton, phytoplankton and community metabolism were followed for 4 or 5 weeks. The mean half-life (t1/2) of chlorpyrifos in the water of the test systems was 45 h under 'temperate' conditions and about 30 h under 'Mediterranean' environmental conditions. Microcrustaceans (cladocerans and copepod nauplii) were amongst the most sensitive organisms. All three experiments yielded community NOEC (no observed effect concentrations) of 0.1 microg AI litre(-1), similar to those derived from more complex outdoor studies. Above this threshold level, responses and effect chains, and time spans for recovery, differed between the experiments. For example, algal blooms as an indirect effect from the impact of exposure on grazing organisms were only observed under the 'Mediterranean' experimental conditions. The relatively simple indoor test system seems to be sufficient to provide estimates of safe threshold levels for the acute insecticidal effects of low-persistence compounds such as chlorpyrifos. The robustness of the community NOEC indicates that this threshold level is likely to be representative for many freshwater systems. Copyright (c) 2005 Society of Chemical Industry.

Ammonia oxidation-dependent growth of group I.1b Thaumarchaeota in acidic red soil microcosms.

PubMed

Wu, Yucheng; Conrad, Ralf

2014-07-01

Accumulating evidence suggests that Thaumarchaeota may control nitrification in acidic soils. However, the composition of the thaumarchaeotal communities and their functioning is not well known. Therefore, we studied nitrification activity in relation to abundance and composition of Thaumarchaeota in an acidic red soil from China, using microcosms incubated with and without cellulose amendment. Cellulose was selected to simulate the input of crop residues used to increase soil fertility by local farming. Accumulation of NO3-(-N) was correlated with the growth of Thaumarchaeota as determined by qPCR of 16S rRNA and ammonia monooxygenase (amoA) genes. Both nitrification activity and thaumarchaeotal growth were inhibited by acetylene. They were also inhibited by cellulose amendment, possibly due to the depletion of ammonium by enhanced heterotrophic assimilation. These results indicated that growth of Thaumarchaeota was dependent on ammonia oxidation. The thaumarchaeotal 16S rRNA gene sequences in the red soil were dominated by a clade related to soil fosmid clone 29i4 within the group I.1b, which is widely distributed but so far uncultured. The archaeal amoA sequences were mainly related to the Nitrososphaera sister cluster. These observations suggest that fosmid clone 29i4 and Nitrososphaera sister cluster represent the same group of Thaumarchaeota and dominate ammonia oxidation in acidic red soil. © 2014 Federation of European Microbiological Societies. Published by John Wiley & Sons Ltd. All rights reserved.

Implementation of jump-diffusion algorithms for understanding FLIR scenes

NASA Astrophysics Data System (ADS)

Lanterman, Aaron D.; Miller, Michael I.; Snyder, Donald L.

1995-07-01

Our pattern theoretic approach to the automated understanding of forward-looking infrared (FLIR) images brings the traditionally separate endeavors of detection, tracking, and recognition together into a unified jump-diffusion process. New objects are detected and object types are recognized through discrete jump moves. Between jumps, the location and orientation of objects are estimated via continuous diffusions. An hypothesized scene, simulated from the emissive characteristics of the hypothesized scene elements, is compared with the collected data by a likelihood function based on sensor statistics. This likelihood is combined with a prior distribution defined over the set of possible scenes to form a posterior distribution. The jump-diffusion process empirically generates the posterior distribution. Both the diffusion and jump operations involve the simulation of a scene produced by a hypothesized configuration. Scene simulation is most effectively accomplished by pipelined rendering engines such as silicon graphics. We demonstrate the execution of our algorithm on a silicon graphics onyx/reality engine.

A Social Diffusion Model with an Application on Election Simulation

PubMed Central

Wang, Fu-Min; Hung, San-Chuan; Kung, Perng-Hwa; Lin, Shou-De

2014-01-01

Issues about opinion diffusion have been studied for decades. It has so far no empirical approach to model the interflow and formation of crowd's opinion in elections due to two reasons. First, unlike the spread of information or flu, individuals have their intrinsic attitudes to election candidates in advance. Second, opinions are generally simply assumed as single values in most diffusion models. However, in this case, an opinion should represent preference toward multiple candidates. Previously done models thus may not intuitively interpret such scenario. This work is to design a diffusion model which is capable of managing the aforementioned scenario. To demonstrate the usefulness of our model, we simulate the diffusion on the network built based on a publicly available bibliography dataset. We compare the proposed model with other well-known models such as independent cascade. It turns out that our model consistently outperforms other models. We additionally investigate electoral issues with our model simulator. PMID:24995351

Modelling algae-duckweed interaction under chemical pressure within a laboratory microcosm.

PubMed

Lamonica, Dominique; Clément, Bernard; Charles, Sandrine; Lopes, Christelle

2016-06-01

Contaminant effects on species are generally assessed with single-species bioassays. As a consequence, interactions between species that occur in ecosystems are not taken into account. To investigate the effects of contaminants on interacting species dynamics, our study describes the functioning of a 2-L laboratory microcosm with two species, the duckweed Lemna minor and the microalgae Pseudokirchneriella subcapitata, exposed to cadmium contamination. We modelled the dynamics of both species and their interactions using a mechanistic model based on coupled ordinary differential equations. The main processes occurring in this two-species microcosm were thus formalised, including growth and settling of algae, growth of duckweeds, interspecific competition between the two species and cadmium effects. We estimated model parameters by Bayesian inference, using simultaneously all the data issued from multiple laboratory experiments specifically conducted for this study. Cadmium concentrations ranged between 0 and 50 μg·L(-1). For all parameters of our model, we obtained biologically realistic values and reasonable uncertainties. Only duckweed dynamics was affected by interspecific competition, while algal dynamics was not impaired. Growth rate of both species decreased with cadmium concentration, as well as competition intensity showing that the interspecific competition pressure on duckweed decreased with cadmium concentration. This innovative combination of mechanistic modelling and model-guided experiments was successful to understand the algae-duckweed microcosm functioning without and with contaminant. This approach appears promising to include interactions between species when studying contaminant effects on ecosystem functioning. Copyright © 2016 Elsevier Inc. All rights reserved.

Impact of a Genetically Engineered Bacterium with Enhanced Alkaline Phosphatase Activity on Marine Phytoplankton Communities

PubMed Central

Sobecky, P. A.; Schell, M. A.; Moran, M. A.; Hodson, R. E.

1996-01-01

An indigenous marine Achromobacter sp. was isolated from coastal Georgia seawater and modified in the laboratory by introduction of a plasmid with a phoA hybrid gene that directed constitutive overproduction of alkaline phosphatase. The effects of this "indigenous" genetically engineered microorganism (GEM) on phosphorus cycling were determined in seawater microcosms following the addition of a model dissolved organic phosphorus compound, glycerol 3-phosphate, at a concentration of 1 or 10 (mu)M. Within 48 h, a 2- to 10-fold increase in the concentration of inorganic phosphate occurred in microcosms containing the GEM (added at an initial density equivalent to 8% of the total bacterial population) relative to controls containing only natural microbial populations, natural populations with the unmodified Achromobacter sp., or natural populations with the Achromobacter sp. containing the plasmid but not the phoA gene. Secondary effects of the GEM on the phytoplankton community were observed after several days, evident as sustained increases in phytoplankton biomass (up to 14-fold) over that in controls. Even in the absence of added glycerol 3-phosphate, a numerically stable GEM population (averaging 3 to 5% of culturable bacteria) was established within 2 to 3 weeks of introduction into seawater. Moreover, alkaline phosphatase activity in microcosms with the GEM was substantially higher than that in controls for up to 25 days, and microcosms containing the GEM maintained the potential for net phosphate accumulation above control levels for longer than 1 month. PMID:16535222

A first approximation kinetic model to predict methane generation from an oil sands tailings settling basin.

PubMed

Siddique, Tariq; Gupta, Rajender; Fedorak, Phillip M; MacKinnon, Michael D; Foght, Julia M

2008-08-01

A small fraction of the naphtha diluent used for oil sands processing escapes with tailings and supports methane (CH(4)) biogenesis in large anaerobic settling basins such as Mildred Lake Settling Basin (MLSB) in northern Alberta, Canada. Based on the rate of naphtha metabolism in tailings incubated in laboratory microcosms, a kinetic model comprising lag phase, rate of hydrocarbon metabolism and conversion to CH(4) was developed to predict CH(4) biogenesis and flux from MLSB. Zero- and first-order kinetic models, respectively predicted generation of 5.4 and 5.1 mmol CH(4) in naphtha-amended microcosms compared to 5.3 (+/-0.2) mmol CH(4) measured in microcosms during 46 weeks of incubation. These kinetic models also predicted well the CH(4) produced by tailings amended with either naphtha-range n-alkanes or BTEX compounds at concentrations similar to those expected in MLSB. Considering 25% of MLSB's 200 million m(3) tailings volume to be methanogenic, the zero- and first-order kinetic models applied over a wide range of naphtha concentrations (0.01-1.0 wt%) predicted production of 8.9-400 million l CH(4) day(-1) from MLSB, which exceeds the estimated production of 3-43 million l CH(4) day(-1). This discrepancy may result from heterogeneity and density of the tailings, presence of nutrients in the microcosms, and/or overestimation of the readily biodegradable fraction of the naphtha in MLSB tailings.

Gonadal development of larval male Xenopus laevis exposed to atrazine in outdoor microcosms

USGS Publications Warehouse

Jooste, A.M.; Du Preez, L.H.; Carr, J.A.; Giesy, J.P.; Gross, T.S.; Kendall, R.J.; Smith, E.E.; Van Der Kraak, G. L.; Solomon, K.R.

2005-01-01

The potential effects of atrazine on gonadal development in metamorphs and subadults of the African clawed frog (Xenopus laevis) were studied under conditions of natural photoperiod and temperatures in outdoor microcosms from August 2002 to June 2003 in South Africa. Triplicate 1100 L microcosms for each nominal concentration of 0.0, 1, 10, and 25 ??g of atrazine/L were used. Measured atrazine concentrations varied <25% throughout the study, and no atrazine was detected in the control microcosms. Tadpoles developed well at all concentrations. On the basis of histological examination of testes of recently metamorphosed stage 66 frogs, 57% of the individuals in the reference group exhibited testicular oocytes as compared with 57, 59, and 39% of the 1, 10, and 25 ??g/L atrazine groups, respectively. The average prevalence of testicular oocytes for all of the treatments including the controls was 54% in a single testis, while, in 35% of individuals, testicular oocytes were observed in both testes. The number of testicular oocytes per individual ranged from 0 to 58 with means of 9.5, 9.8, 8.5, and 11.1 for the 0.0, 1, 10, and 25 ??g of atrazine/L groups, respectively. Ten months after metamorphosis, another subset of juveniles was examined, and the maximum number of testicular oocytes observed was five in one animal. The presence of testicular oocytes was not related to exposure to atrazine and may be a natural phenomenon during ontogeny. ?? 2005 American Chemical Society.

In situ measurements of volatile aromatic hydrocarbon biodegradation rates in groundwater

USGS Publications Warehouse

Cozzarelli, I.M.; Bekins, B.A.; Eganhouse, R.P.; Warren, E.; Essaid, H.I.

2010-01-01

Benzene and alkylbenzene biodegradation rates and patterns were measured using an in situ microcosm in a crude-oil contaminated aquifer near Bemidji, Minnesota. Benzene-D6, toluene, ethylbenzene, o-, m- and p-xylenes and four pairs of C3- and C4-benzenes were added to an in situ microcosm and studied over a 3-year period. The microcosm allowed for a mass-balance approach and quantification of hydrocarbon biodegradation rates within a well-defined iron-reducing zone of the anoxic plume. Among the BTEX compounds, the apparent order of persistence is ethylbenzene > benzene > m,p-xylenes > o-xylene ≥ toluene. Threshold concentrations were observed for several compounds in the in situ microcosm, below which degradation was not observed, even after hundreds of days. In addition, long lag times were observed before the onset of degradation of benzene or ethylbenzene. The isomer-specific degradation patterns were compared to observations from a multi-year study conducted using data collected from monitoring wells along a flowpath in the contaminant plume. The data were fit with both first-order and Michaelis-Menten models. First-order kinetics provided a good fit for hydrocarbons with starting concentrations below 1 mg/L and Michaelis-Menten kinetics were a better fit when starting concentrations were above 1 mg/L, as was the case for benzene. The biodegradation rate data from this study were also compared to rates from other investigations reported in the literature.

Microbial Substrate Use at Sites of Continental Serpentinization: The Tablelands, NL, CAD and the Cedars, CA, USA

NASA Astrophysics Data System (ADS)

Morrill, P. L.; Rietze, A.; Kohl, L.; Miles, S.; Kavanagh, H.; Cox, A.; Brazelton, W. J.; Ishii, S.; Sherwood Lollar, B.; Schrenk, M. O.; Nealson, K. H.; Ziegler, S. E.; Ono, S.; Wang, D. T.; Lang, S. Q.; Cumming, E.

2014-12-01

Ultra-basic reducing springs at continental sites of serpentinization act as portals into the biogeochemistry of a subsurface ultramafic environment rich in hydrogen and methane gases. Field data and results from substrate addition microcosm experiments will be presented from two contrasting continental sites of serpentinization: the Tablelands, NL, CAN and The Cedars, CA, USA both Phanerozoic in age. These continental sites share geochemical characteristics that make these environments challenging for life, such as high pH, low Eh, scarce electron acceptors, and limited dissolved inorganic carbon for autotrophic growth. However, microbiological analyses have demonstrated that life does indeed exist in these environments. While environmental genomic studies indicated the potential metabolic capabilities of microorganisms in the sites, actual microbial metabolic activities in these environments remain unknown. To expand the understanding of biogeochemistry of the sites, we are conducting studies focusing on chemical and isotopic measurements, carbon substrate utilization, energy sources, and metabolic pathways of the microorganisms. Thus far, in situ geochemical data suggests that the methane from the Tablelands is primarily non-microbial, while the methane from The Cedars likely has some microbial contributions. To date, substrate addition microcosm experiments show no microbial production of methane from Tablelands' water and sediments. However, microbial carbon monoxide utilization has been observed in Tableland microcosms, but not in The Cedars microcosms. These results demonstrate how geochemistry and substrate addition experiments can be complementary for the determination of the processes favored at these continental sites of serpentinization.

Effects of diquat and fomesafen applied alone and in combination with a nonylphenol polyethoxylate adjuvant on Lemna minor in aquatic indoor microcosms.

PubMed

Gorzerino, Caroline; Quemeneur, Alphonse; Hillenweck, Anne; Baradat, Maryse; Delous, Georges; Ollitrault, Martine; Azam, Didier; Caquet, Thierry; Lagadic, Laurent

2009-03-01

The influence of tank-mix adjuvants on pesticide toxicity remains largely unknown. Agral 90, a nonylphenol polyethoxylated tank-mix adjuvant, has been used with diquat (bipyridylium herbicide) and fomesafen (diphenyl-ether herbicide) in aquatic indoor microcosms in order to compare the toxicity of the single compounds and of binary herbicide-adjuvant mixtures to Lemna minor. Twenty-four microcosms were used and treatments were performed with substances alone or with herbicide-adjuvant binary mixtures, at two concentrations levels (44.4 and 222.2 microg/L for the herbicides, and 100 and 500 microg/L for Agral 90). Toxicity was assessed weekly for 1 month through growth measurements, as inferred from the relative frond number (RFN) and relative frond area (RFA). Concentrations of diquat and fomesafen in water and sediments were measured weekly. The herbicides showed very different behaviour in microcosms, with a rapid disappearance of diquat from the aqueous phase whereas fomesafen levels remained almost constant over time. Diquat strongly inhibited the growth of L. minor whereas fomesafen had no effect on plant growth. Presence of the adjuvant only slightly reduced the effect of the lowest concentration of diquat, probably as a result of dispersion of the herbicide at the water surface. It is concluded that tank-mix adjuvant designed to improve herbicide efficiency in the terrestrial environment did not have any effect on aquatic plants when applied to the aquatic environment.

Glyceria maxima as new test species for the EU risk assessment for herbicides: a microcosm study.

PubMed

Mohr, S; Schott, J; Hoenemann, L; Feibicke, M

2015-03-01

In its recent guidance document on tiered risk assessment for plant protection products for aquatic organisms, the European Food Safety Authority (EFSA) proposed to use Glyceria maxima as monocotyledonous grass species for the testing of special herbicide groups. However, published toxicity data for this species is very limited and there is no test guideline for Glyceria sp. For this reason a microcosm study was conducted in order to gain experience on the degree of sensitivity of G. maxima to the herbicidal substances clodinafop-propargyl (grass herbicide) and fluroxypyr (auxin) in comparison to the already established test organism water milfoil Myriophyllum spicatum and the duckweed species Landoltia punctata. Five concentrations without replicates were tested for each test substance using 10 microcosms and three microcosms served as controls. The experiment was run for 8 weeks. Morphological endpoints were used to determine growth and EC50 values. The results show that M. spicatum was most sensitive to fluroxypyr (37 days EC50 for roots: 62 µg/L) and G. maxima most sensitive to clodinafop-propargyl (22 days EC50 for total shoot length: 48 µg/L) whereas the duckweed species was considerable less sensitive. Hence, G. maxima turns out to be a good candidate for testing grass specific herbicides, supporting its inclusion as an additional macrophyte test for the risk assessment of herbicides as proposed by the EFSA.

The effect of pH, temperature and plaque thickness on the hydrolysis of monofluorophosphate in experimental dental plaque.

PubMed

Pearce, E I F; Dibdin, G H

2003-01-01

Monofluorophosphate (MFP), an anti-caries agent commonly used in toothpaste, is known to be degraded to fluoride and orthophosphate by bacterial phosphatases in dental plaque. We have examined the effect of pH, temperature, plaque thickness and some ions on this process. Both natural plaque and artificial microcosm plaque incubated with purified MFP at pH 4-10 showed an optimum pH of approximately 8 for hydrolysis. Diffusion and concomitant hydrolysis were examined in an apparatus in which artificial plaque was held between rigid membranes separating two chambers. When MFP diffused through a plaque of 0.51-mm thickness over 4 h it was almost completely hydrolysed at pH 8, but hydrolysis on diffusion decreased as the pH deviated from 8. MFP in toothpaste extract showed a similar pH susceptibility to hydrolysis, according to the inherent pH of the toothpaste. Hydrolysis of MFP in the toothpaste was reduced by no more than 10% when compared with a matched-pH control, suggesting that other toothpaste ingredients had no major influence on hydrolysis. Transport was slower and hydrolysis at pH 6 more complete the thicker the plaque, but hydrolysis was not significantly slower at 23 degrees C than at 37 degrees C. The addition of various potential activating or inhibiting ions at 0.1 and 1.0 mmol/l had small and non-significant effects on hydrolysis. The results suggest that MFP toothpaste should be formulated and used to maximise enzymic hydrolysis of this complex anion, and that plaque pH control is probably the most important factor. Copyright 2003 S. Karger AG, Basel

Reactive transport model of growth and methane production by high-temperature methanogens in hydrothermal regions of the subseafloor

NASA Astrophysics Data System (ADS)

Stewart, L. C.; Algar, C. K.; Topçuoğlu, B. D.; Fortunato, C. S.; Larson, B. I.; Proskurowski, G. K.; Butterfield, D. A.; Vallino, J. J.; Huber, J. A.; Holden, J. F.

2014-12-01

Hydrogenotrophic methanogens are keystone high-temperature autotrophs in deep-sea hydrothermal vents and tracers of habitability and biogeochemical activity in the hydrothermally active subseafloor. At Axial Seamount, nearly all thermophilic methanogens are Methanothermococcus and Methanocaldococcus species, making this site amenable to modeling through pure culture laboratory experiments coupled with field studies. Based on field microcosm incubations with 1.2 mM, 20 μM, or no hydrogen, the growth of methanogens at 55°C and 80°C is limited primarily by temperature and hydrogen availability, with ammonium amendment showing no consistent effect on total methane output. The Arrhenius constants for methane production by Methanocaldococcus jannaschii (optimum 82°C) and Methanothermococcus thermolithotrophicus (optimum 65°C) were determined in pure culture bottle experiments. The Monod constants for hydrogen concentration were measured by growing both organisms in a 2-liter chemostat at two dilution rates; 55°C, 65°C and 82°C; and variable hydrogen concentrations. M. jannaschii showed higher ks and Vmax constants than M. thermolithotrophicus. In the field, hydrogen and methane concentrations in hydrothermal end-member and low-temperature diffuse fluids were measured, and the concentrations of methanogens that grow at 55°C and 80°C in diffuse fluids were determined using most-probable-number estimates. Methane concentration anomalies in diffuse fluids relative to end-member hydrothermal concentrations and methanogen cell concentrations are being used to constrain a 1-D reactive transport model using the laboratory-determined Arrhenius and Monod constants for methane production by these organisms. By varying flow path length and subseafloor cell concentrations in the model, our goal is to determine solutions for the potential depth of the subseafloor biosphere coupled with the amount of methanogenic biomass it contains.

An elemental mercury diffusion coefficient for natural waters determined by molecular dynamics simulation.

PubMed

Kuss, Joachim; Holzmann, Jörg; Ludwig, Ralf

2009-05-01

Mercury is a priority pollutant as its mobility between the hydrosphere and the atmosphere threatens the biosphere globally. The air-water gas transfer of elemental mercury (Hg0) is controlled by its diffusion through the water-side boundary layer and thus by its diffusion coefficient, D(Hg), the value of which, however, has not been established. Here, the diffusion of Hg0 in water was modeled by molecular dynamics (MD) simulation and the diffusion coefficient subsequently determined. Therefore the movement of either Hg(0) or xenon and 1000 model water molecules (TIP4P-Ew) were traced for time spans of 50 ns. The modeled D(Xe) of the monatomic noble gas agreed well with measured data; thus, MD simulation was assumed to be a reliable approach to determine D(Hg) for monatomic Hg(0) as well. Accordingly, Hg(0) diffusion was then simulated for freshwater and seawater, and the data were well-described by the equation of Eyring. The activation energies for the diffusion of Hg0 in freshwater was 17.0 kJ mol(-1) and in seawater 17.8 kJ mol(-1). The newly determined D(Hg) is clearly lower than the one previously used for an oceanic mercury budget. Thus, its incorporation into the model should lead to lower estimates of global ocean mercury emissions.

Linking pore-scale and basin-scale effects on diffusive methane transport in hydrate bearing environments through multi-scale reservoir simulations

NASA Astrophysics Data System (ADS)

Nole, M.; Daigle, H.; Cook, A.; Malinverno, A.; Hillman, J. I. T.

2016-12-01

We explore the gas hydrate-generating capacity of diffusive methane transport induced by solubility gradients due to pore size contrasts in lithologically heterogeneous marine sediments. Through the use of 1D, 2D, and 3D reactive transport simulations, we investigate scale-dependent processes in diffusion-dominated gas hydrate systems. These simulations all track a sand body, or series of sands, surrounded by clays as they are buried through the gas hydrate stability zone. Methane is sourced by microbial methanogenesis in the clays surrounding the sand layers. In 1D, simulations performed in a Lagrangian reference frame demonstrate that gas hydrate in thin sands (3.6 m thick) can occur in high saturations (upward of 70%) at the edges of sand bodies within the upper 400 meters below the seafloor. Diffusion of methane toward the center of the sand layer depends on the concentration gradient within the sand: broader sand pore size distributions with smaller median pore sizes enhance diffusive action toward the sand's center. Incorporating downhole log- and laboratory-derived sand pore size distributions, gas hydrate saturations in the center of the sand can reach 20% of the hydrate saturations at the sand's edges. Furthermore, we show that hydrate-free zones exist immediately above and below the sand and are approximately 5 m thick, depending on the sand-clay solubility contrast. A moving reference frame is also adopted in 2D, and the angle of gravity is rotated relative to the grid system to simulate a dipping sand layer. This is important to minimize diffusive edge effects or numerical diffusion that might be associated with a dipping sand in an Eulerian grid system oriented orthogonal to gravity. Two-dimensional simulations demonstrate the tendency for gas hydrate to accumulate downdip in a sand body because of greater methane transport at depth due to larger sand-clay solubility contrasts. In 3D, basin-scale simulations illuminate how convergent sand layers in a multilayered system can compete for diffusion from clays between them, resulting in relatively low hydrate saturations. All simulations suggest that when hydrate present in clays dissociates with burial, the additional dissolved methane is soaked up by nearby sands preserving high hydrate saturations.

Linking pore-scale and basin-scale effects on diffusive methane transport in hydrate bearing environments through multi-scale reservoir simulations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nole, Michael; Daigle, Hugh; Cook, Ann

We explore the gas hydrate-generating capacity of diffusive methane transport induced by solubility gradients due to pore size contrasts in lithologically heterogeneous marine sediments. Through the use of 1D, 2D, and 3D reactive transport simulations, we investigate scale-dependent processes in diffusion-dominated gas hydrate systems. These simulations all track a sand body, or series of sands, surrounded by clays as they are buried through the gas hydrate stability zone. Methane is sourced by microbial methanogenesis in the clays surrounding the sand layers. In 1D, simulations performed in a Lagrangian reference frame demonstrate that gas hydrate in thin sands (3.6 m thick)more » can occur in high saturations (upward of 70%) at the edges of sand bodies within the upper 400 meters below the seafloor. Diffusion of methane toward the center of the sand layer depends on the concentration gradient within the sand: broader sand pore size distributions with smaller median pore sizes enhance diffusive action toward the sand’s center. Incorporating downhole log- and laboratory-derived sand pore size distributions, gas hydrate saturations in the center of the sand can reach 20% of the hydrate saturations at the sand’s edges. Furthermore, we show that hydrate-free zones exist immediately above and below the sand and are approximately 5 m thick, depending on the sand-clay solubility contrast. A moving reference frame is also adopted in 2D, and the angle of gravity is rotated relative to the grid system to simulate a dipping sand layer. This is important to minimize diffusive edge effects or numerical diffusion that might be associated with a dipping sand in an Eulerian grid system oriented orthogonal to gravity. Two-dimensional simulations demonstrate the tendency for gas hydrate to accumulate downdip in a sand body because of greater methane transport at depth due to larger sand-clay solubility contrasts. In 3D, basin-scale simulations illuminate how convergent sand layers in a multilayered system can compete for diffusion from clays between them, resulting in relatively low hydrate saturations. All simulations suggest that when hydrate present in clays dissociates with burial, the additional dissolved methane is soaked up by nearby sands preserving high hydrate saturations.« less

Metabolic adaptation and in situ attenuation of chlorinated ethenes by naturally occurring microorganisms in a fractured dolomite aquifer near Niagara Falls, New York

USGS Publications Warehouse

Yager, R.M.; Bilotta, S.E.; Mann, C.L.; Madsen, E.L.

1997-01-01

A combination of hydrogeological, geochemical, and microbiological methods was used to document the biotransformation of trichloroethene (TCE) to ethene, a completely dechlorinated and environmentally benign compound, by naturally occurring microorganisms within a fractured dolomite aquifer. Analyses of groundwater samples showed that three microbially produced TCE breakdown products (cis-1,2-dichloroethene, vinyl chloride, and ethene) were present in the contaminant plume. Hydrogen (H2) concentrations in groundwater indicated that iron reduction was the predominant terminal electron-accepting process in the most contaminated geologic zone of the site. Laboratory microcosms prepared with groundwater demonstrated complete sequential dechlorination of TCE to ethene. Microcosm assays also revealed that reductive dechlorination activity was present in waters from the center but not from the periphery of the contaminant plume. This dechlorination activity indicated that naturally occurring microorganisms have adapted to utilize chlorinated ethenes and suggested that dehalorespiring rather than cometabolic, microbial processes were the cause of the dechlorination. The addition of pulverized dolomite to microcosms enhanced the rate of reductive dechlorination, suggesting that hydrocarbons in the dolomite aquifer may serve as electron donors to drive microbially mediated reductive dechlorination reactions. Biodegradation of the chlorinated ethenes appears to contribute significantly to decontamination of the site.A combination of hydrogeological, geochemical, and microbiological methods was used to document the biotransformation of trichloroethene (TCE) to ethene, a completely dechlorinated and environmentally benign compound, by naturally occurring microorganisms within a fractured dolomite aquifer. Analyses of groundwater samples showed that three microbially produced TCE breakdown products (cis-1,2-dichloroethene, vinyl chloride, and ethene) were present in the contaminant plume. Hydrogen (H2) concentrations in groundwater indicated that iron reduction was the predominant terminal electron-accepting process in the most contaminated geologic zone of the site. Laboratory microcosms prepared with groundwater demonstrated complete sequential dechlorination of TCE to ethene. Microcosm assays also revealed that reductive dechlorination activity was present in waters from the center but not from the periphery of the contaminant plume. This dechlorination activity indicated that naturally occurring microorganisms have adapted to utilize chlorinated ethenes and suggested that dehalorespiring rather than cometabolic, microbial processes were the cause of the dechlorination. The addition of pulverized dolomite to microcosms enhanced the rate of reductive dechlorination, suggesting that hydrocarbons in the dolomite aquifer may serve as electron donors to drive microbially mediated reductive dechlorination reactions. Biodegradation of the chlorinated ethenes appears to contribute significantly to decontamination of the site.

Cracking of Clay Due to Contact with Waste Chlorinated Solvents

NASA Astrophysics Data System (ADS)

Otero, M.; Ayral, D.; Shipan, J.; Goltz, M. N.; Huang, J.; Demond, A. H.

2012-12-01

Clays are known to crack upon desiccation. Desiccation cracks of up to 3 cm wide have been reported in natural soils. This raises the question if a similar behavior is seen when a dense non-aqueous phase liquids (DNAPL) waste is in contact with clay. The contact with organic liquids causes the clay structure to shrink, leading to the formation of cracks. Moreover, DNAPL waste not only contains the organic liquid solvent but also includes surface-active solutes or surfactants. Such solutes can enhance the interaction of the organic solvents with the clay. This research will assess whether or not contact with chlorinated organic waste causes cracking. In order to evaluate the possibility of cracking in the clay, microcosms have been constructed that mimic aquifer systems, consisting of a saturated layer of sand, a saturated layer of bentonite clay and a 2.5 cm layer of either pure chlorinated solvents or DNAPL waste. The onset of cracking for the microcosm with tetrachloroethylene (PCE) waste as the DNAPL layer occurred after ten days of contact. Similarly, at eight days, cracks were observed in a microcosm containing trichloroethylene (TCE) waste . Forty-four days later, the length and number of cracks have grown considerably; with a total crack length of 50 cm on a surface of 80 cm2 in the microcosm containing PCE waste. On the other hand it took approximately 161 days for the clay layer in the microcosm containing pure PCE to crack. To quantity the degree of cracking, crack maps were developed using the image software, Image J. Characteristics like crack length, crack aperture, and the percentage of total length for a range of apertures were calculated using this software. For example, for the PCE waste microcosm, it was calculated that 3.7% of the crack length had an aperture of 100-300 microns, 15.1% of the crack length had an aperture of 300-500 microns, 29.7% of the crack length had an aperture of 500-700 microns, 40.1% of the crack length had an aperture of 700-900 microns, 6.3% had an aperture of 900-1,100 microns and 5.1% had an aperture of over 1,100 microns. These data suggest that aquitards in the field might crack when in contact with the DNAPL waste. Moreover, it is apparent that the waste contains solutes that accelerate the cracking of the clay layer. Thus, models examining the impact of storage in low permeability layers need to consider the possible impact of cracking.

Complex Geometric Models of Diffusion and Relaxation in Healthy and Damaged White Matter

PubMed Central

Farrell, Jonathan A.D.; Smith, Seth A.; Reich, Daniel S.; Calabresi, Peter A.; van Zijl, Peter C.M.

2010-01-01

Which aspects of tissue microstructure affect diffusion weighted MRI signals? Prior models, many of which use Monte-Carlo simulations, have focused on relatively simple models of the cellular microenvironment and have not considered important anatomic details. With the advent of higher-order analysis models for diffusion imaging, such as high-angular-resolution diffusion imaging (HARDI), more realistic models are necessary. This paper presents and evaluates the reproducibility of simulations of diffusion in complex geometries. Our framework is quantitative, does not require specialized hardware, is easily implemented with little programming experience, and is freely available as open-source software. Models may include compartments with different diffusivities, permeabilities, and T2 time constants using both parametric (e.g., spheres and cylinders) and arbitrary (e.g., mesh-based) geometries. Three-dimensional diffusion displacement-probability functions are mapped with high reproducibility, and thus can be readily used to assess reproducibility of diffusion-derived contrasts. PMID:19739233

Simulation of Changes in Diffusion Related to Different Pathologies at Cellular Level After Traumatic Brain Injury

PubMed Central

Lin, Mu; He, Hongjian; Schifitto, Giovanni; Zhong, Jianhui

2016-01-01

Purpose The goal of the current study was to investigate tissue pathology at the cellular level in traumatic brain injury (TBI) as revealed by Monte Carlo simulation of diffusion tensor imaging (DTI)-derived parameters and elucidate the possible sources of conflicting findings of DTI abnormalities as reported in the TBI literature. Methods A model with three compartments separated by permeable membranes was employed to represent the diffusion environment of water molecules in brain white matter. The dynamic diffusion process was simulated with a Monte Carlo method using adjustable parameters of intra-axonal diffusivity, axon separation, glial cell volume fraction, and myelin sheath permeability. The effects of tissue pathology on DTI parameters were investigated by adjusting the parameters of the model corresponding to different stages of brain injury. Results The results suggest that the model is appropriate and the DTI-derived parameters simulate the predominant cellular pathology after TBI. Our results further indicate that when edema is not prevalent, axial and radial diffusivity have better sensitivity to axonal injury and demyelination than other DTI parameters. Conclusion DTI is a promising biomarker to detect and stage tissue injury after TBI. The observed inconsistencies among previous studies are likely due to scanning at different stages of tissue injury after TBI. PMID:26256558

CONTRIBUTIONS OF CHEMICAL AND DIFFUSIVE EXCHANGE TO T1ρ DISPERSION

PubMed Central

Cobb, Jared Guthrie; Xie, Jingping; Gore, John C.

2012-01-01

Variations in local magnetic susceptibility may induce magnetic field gradients that affect the signals acquired for MR imaging. Under appropriate diffusion conditions, such fields produce effects similar to slow chemical exchange. These effects may also be found in combination with other chemical exchange processes at multiple time scales. We investigate these effects with simulations and measurements to determine their contributions to rotating frame (R1ρ) relaxation in model systems. Simulations of diffusive and chemical exchange effects on R1ρ dispersion were performed using the Bloch equations. Additionally, R1ρ dispersion was measured in suspensions of Sephadex and latex beads with varying spin locking fields at 9.4T. A novel analysis method was used to iteratively fit for apparent chemical and diffusive exchange rates with a model by Chopra et al. Single- and double-inflection points in R1ρ dispersion profiles were observed, respectively, in simulations of slow diffusive exchange alone and when combined with rapid chemical exchange. These simulations were consistent with measurements of R1ρ in latex bead suspensions and small-diameter Sephadex beads that showed single- and double-inflection points, respectively. These observations, along with measurements following changes in temperature and pH, are consistent with the combined effects of slow diffusion and rapid −OH exchange processes. PMID:22791589

Modeling the rate-controlled sorption of hexavalent chromium

USGS Publications Warehouse

Grove, D.B.; Stollenwerk, K.G.

1985-01-01

Sorption of chromium VI on the iron-oxide- and hydroxide-coated surface of alluvial material was numerically simulated with rate-controlled reactions. Reaction kinetics and diffusional processes, in the form of film, pore, and particle diffusion, were simulated and compared with experimental results. The use of empirically calculated rate coefficients for diffusion through the reacting surface was found to simulate experimental data; pore or particle diffusion is believed to be a possible rate-controlling mechanism. The use of rate equations to predict conservative transport and rate- and local-equilibrium-controlled reactions was shown to be feasible.

Estimating the Diffusion Coefficients of Sugars Using Diffusion Experiments in Agar-Gel and Computer Simulations.

PubMed

Miyamoto, Shuichi; Atsuyama, Kenji; Ekino, Keisuke; Shin, Takashi

2018-01-01

The isolation of useful microbes is one of the traditional approaches for the lead generation in drug discovery. As an effective technique for microbe isolation, we recently developed a multidimensional diffusion-based gradient culture system of microbes. In order to enhance the utility of the system, it is favorable to have diffusion coefficients of nutrients such as sugars in the culture medium beforehand. We have, therefore, built a simple and convenient experimental system that uses agar-gel to observe diffusion. Next, we performed computer simulations-based on random-walk concepts-of the experimental diffusion system and derived correlation formulas that relate observable diffusion data to diffusion coefficients. Finally, we applied these correlation formulas to our experimentally-determined diffusion data to estimate the diffusion coefficients of sugars. Our values for these coefficients agree reasonably well with values published in the literature. The effectiveness of our simple technique, which has elucidated the diffusion coefficients of some molecules which are rarely reported (e.g., galactose, trehalose, and glycerol) is demonstrated by the strong correspondence between the literature values and those obtained in our experiments.

Modeling gas displacement kinetics in coal with Maxwell-Stefan diffusion theory

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wei, X.R.; Wang, G.X.; Massarotto, P.

2007-12-15

The kinetics of binary gas counter-diffusion and Darcy flow in a large coal sample were modeled, and the results compared with data from experimental laboratory investigations. The study aimed for a better understanding of the CO{sub 2}-sequestration enhanced coalbed methane (ECBM) recovery process. The transport model used was based on the bidisperse diffusion mechanism and Maxwell-Stefan (MS) diffusion theory. This provides an alternative approach to simulate multicomponent gas diffusion and flow in bulk coals. A series of high-stress core flush tests were performed on a large coal sample sourced from a Bowen Basin coal mine in Queensland, Australia to investigatemore » the kinetics of one gas displacing another. These experimental results were used to derive gas diffusivities, and to examine the predictive capability of the diffusion model. The simulations show good agreements with the displacement experiments revealing that MS diffusion theory is superior for describing diffusion of mixed gases in coals compared with the constant Fick diffusivity model. The optimized effective micropore and macropore diffusivities are comparable with experimental measurements achieved by other researchers.« less

Niche and neutral processes both shape community structure in parallelized, aerobic, single carbon-source enrichments

DOE Data Explorer

Flynn, Theodore M.; Koval, Jason C.; Greenwald, Stephanie M.; Owens, Sarah M.; Kemner, Kenneth M.; Antonopoulos, Dionysios A.

2017-01-01

We present DNA sequence data in FASTA-formatted files from aerobic environmental microcosms inoculated with a sole carbon source. DNA sequences are of 16S rRNA genes present in DNA extracted from each microcosm along with the environmental samples (soil, water) used to inoculate them. These samples were sequenced using the Illumina MiSeq platform at the Environmental Sample Preparation and Sequencing Facility at Argonne National Laboratory. This data is compatible with standard microbiome analysis pipelines (e.g., QIIME, mothur, etc.).

Finite-Size Effects of Binary Mutual Diffusion Coefficients from Molecular Dynamics

PubMed Central

2018-01-01

Molecular dynamics simulations were performed for the prediction of the finite-size effects of Maxwell-Stefan diffusion coefficients of molecular mixtures and a wide variety of binary Lennard–Jones systems. A strong dependency of computed diffusivities on the system size was observed. Computed diffusivities were found to increase with the number of molecules. We propose a correction for the extrapolation of Maxwell–Stefan diffusion coefficients to the thermodynamic limit, based on the study by Yeh and Hummer (J. Phys. Chem. B, 2004, 108, 15873−15879). The proposed correction is a function of the viscosity of the system, the size of the simulation box, and the thermodynamic factor, which is a measure for the nonideality of the mixture. Verification is carried out for more than 200 distinct binary Lennard–Jones systems, as well as 9 binary systems of methanol, water, ethanol, acetone, methylamine, and carbon tetrachloride. Significant deviations between finite-size Maxwell–Stefan diffusivities and the corresponding diffusivities at the thermodynamic limit were found for mixtures close to demixing. In these cases, the finite-size correction can be even larger than the simulated (finite-size) Maxwell–Stefan diffusivity. Our results show that considering these finite-size effects is crucial and that the suggested correction allows for reliable computations. PMID:29664633

DIFFUSION IN THE VICINITY OF STANDARD-DESIGN NUCLEAR POWER PLANTS-I. WIND-TUNNEL EVALUATION OF DIFFUSIVE CHARACTERISTICS OF A SIMULATED SUBURBAN NEUTRAL ATMOSPHERIC BOUNDARY LAYER

EPA Science Inventory

A large meteorological wind tunnel was used to simulate a suburban atmospheric boundary layer. The model-prototype scale was 1:300 and the roughness length was approximately 1.0 m full scale. The model boundary layer simulated full scale dispersion from ground-level and elevated ...

An exact and efficient first passage time algorithm for reaction-diffusion processes on a 2D-lattice

NASA Astrophysics Data System (ADS)

Bezzola, Andri; Bales, Benjamin B.; Alkire, Richard C.; Petzold, Linda R.

2014-01-01

We present an exact and efficient algorithm for reaction-diffusion-nucleation processes on a 2D-lattice. The algorithm makes use of first passage time (FPT) to replace the computationally intensive simulation of diffusion hops in KMC by larger jumps when particles are far away from step-edges or other particles. Our approach computes exact probability distributions of jump times and target locations in a closed-form formula, based on the eigenvectors and eigenvalues of the corresponding 1D transition matrix, maintaining atomic-scale resolution of resulting shapes of deposit islands. We have applied our method to three different test cases of electrodeposition: pure diffusional aggregation for large ranges of diffusivity rates and for simulation domain sizes of up to 4096×4096 sites, the effect of diffusivity on island shapes and sizes in combination with a KMC edge diffusion, and the calculation of an exclusion zone in front of a step-edge, confirming statistical equivalence to standard KMC simulations. The algorithm achieves significant speedup compared to standard KMC for cases where particles diffuse over long distances before nucleating with other particles or being captured by larger islands.

Anomalous Surface Diffusion of Protons on Lipid Membranes

PubMed Central

Wolf, Maarten G.; Grubmüller, Helmut; Groenhof, Gerrit

2014-01-01

The cellular energy machinery depends on the presence and properties of protons at or in the vicinity of lipid membranes. To asses the energetics and mobility of a proton near a membrane, we simulated an excess proton near a solvated DMPC bilayer at 323 K, using a recently developed method to include the Grotthuss proton shuttling mechanism in classical molecular dynamics simulations. We obtained a proton surface affinity of −13.0 ± 0.5 kJ mol−1. The proton interacted strongly with both lipid headgroup and linker carbonyl oxygens. Furthermore, the surface diffusion of the proton was anomalous, with a subdiffusive regime over the first few nanoseconds, followed by a superdiffusive regime. The time- and distance dependence of the proton surface diffusion coefficient within these regimes may also resolve discrepancies between previously reported diffusion coefficients. Our simulations show that the proton anomalous surface diffusion originates from restricted diffusion in two different surface-bound states, interrupted by the occasional bulk-mediated long-range surface diffusion. Although only a DMPC membrane was considered in this work, we speculate that the restrictive character of the on-surface diffusion is highly sensitive to the specific membrane conditions, which can alter the relative contributions of the surface and bulk pathways to the overall diffusion process. Finally, we discuss the implications of our findings for the energy machinery. PMID:24988343

Anomalous surface diffusion of protons on lipid membranes.

PubMed

Wolf, Maarten G; Grubmüller, Helmut; Groenhof, Gerrit

2014-07-01

The cellular energy machinery depends on the presence and properties of protons at or in the vicinity of lipid membranes. To asses the energetics and mobility of a proton near a membrane, we simulated an excess proton near a solvated DMPC bilayer at 323 K, using a recently developed method to include the Grotthuss proton shuttling mechanism in classical molecular dynamics simulations. We obtained a proton surface affinity of -13.0 ± 0.5 kJ mol(-1). The proton interacted strongly with both lipid headgroup and linker carbonyl oxygens. Furthermore, the surface diffusion of the proton was anomalous, with a subdiffusive regime over the first few nanoseconds, followed by a superdiffusive regime. The time- and distance dependence of the proton surface diffusion coefficient within these regimes may also resolve discrepancies between previously reported diffusion coefficients. Our simulations show that the proton anomalous surface diffusion originates from restricted diffusion in two different surface-bound states, interrupted by the occasional bulk-mediated long-range surface diffusion. Although only a DMPC membrane was considered in this work, we speculate that the restrictive character of the on-surface diffusion is highly sensitive to the specific membrane conditions, which can alter the relative contributions of the surface and bulk pathways to the overall diffusion process. Finally, we discuss the implications of our findings for the energy machinery. Copyright © 2014 Biophysical Society. Published by Elsevier Inc. All rights reserved.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Goltz, M.N.; Carrothers, T.J.; Hopkins, G.D.

A full-scale study of in situ bioremediation is being planned for implementation at a trichloroethylene (TCE) contaminated site at Edwards Air Force Base. To support the demonstration, laboratory studies of sorption and biodegradation were performed. Column studies conducted with TCE and Edwards aquifer material determined the sorption distribution coefficient to be 0.1 millileters per gram, corresponding to a 1.5 retardation factor. Edwards aquifer material from four different depths was used to study cometabolic TCE biodegradation in the presence of toluene under aerobic conditions. The studies showed steady state TCE removal of greater than or equal to 85% in the microcosms.more » A base line simulation was performed using a computer model which incorporated all significant flow and transport processes. The simulation shows how TCE mass declines in both the dissolved and sorbed phases over the four months planned for the demonstration. Based on these preliminary studies, it appears that the planned operation of the bioremediation system can be expected to result in observable decreases in TCE mass and concentration at the Edwards demonstration site.« less

Electron Thermal Transport due to Magnetic Diffusion in the MST RFP

NASA Astrophysics Data System (ADS)

Reusch, J. A.; Anderson, J. K.; den Hartog, D. J.; Forest, C. B.; Kasten, C. P.; Schnack, D. D.; Stephens, H. D.

2011-10-01

Comparison of measurements made in the MST RFP to the results from extensive nonlinear resistive MHD simulations has provided two key observations. First, trapped particles reduce electron thermal diffusion; inclusion of this effect is required for quantitative agreement of simulation to measurement. Second, the structure and evolution of long-wavelength temperature fluctuations measured in MST shows remarkable qualitative similarity to fluctuations appearing in a finite-pressure simulation. These simulations were run at parameters matching those of 400 kA discharges in MST (S ~ 4 ×106). In a zero β simulation, the measured χe is compared to the thermal diffusion due to parallel losses along diffusing magnetic field lines, χst =v∥Dmag . Agreement is only found if the reduction in χst due to trapped particles is taken into account. In a second simulation, the pressure field was evolved self consistently assuming Ohmic heating and anisotropic thermal conduction. Fluctuations in the simulated temperature are very similar in character and time evolution to temperature fluctuations measured in MST. This includes m = 1 , n = 6 fluctuations that flatten the temperature profile as well as m = 1 , n = 5 fluctuations that generate hot island structures near the core shortly after sawtooth crashes. This work supported by the US DOE and NSF.

A3 Subscale Rocket Hot Fire Testing

NASA Technical Reports Server (NTRS)

Saunders, G. P.; Yen, J.

2009-01-01

This paper gives a description of the methodology and results of J2-X Subscale Simulator (JSS) hot fire testing supporting the A3 Subscale Diffuser Test (SDT) project at the E3 test facility at Stennis Space Center, MS (SSC). The A3 subscale diffuser is a geometrically accurate scale model of the A3 altitude simulating rocket test facility. This paper focuses on the methods used to operate the facility and obtain the data to support the aerodynamic verification of the A3 rocket diffuser design and experimental data quantifying the heat flux throughout the facility. The JSS was operated at both 80% and 100% power levels and at gimbal angle from 0 to 7 degrees to verify the simulated altitude produced by the rocket-rocket diffuser combination. This was done with various secondary GN purge loads to quantify the pumping performance of the rocket diffuser. Also, special tests were conducted to obtain detailed heat flux measurements in the rocket diffuser at various gimbal angles and in the facility elbow where the flow turns from vertical to horizontal upstream of the 2nd stage steam ejector.

Kinetics of CO2 diffusion in human carbonic anhydrase: a study using molecular dynamics simulations and the Markov-state model.

PubMed

Chen, Gong; Kong, Xian; Lu, Diannan; Wu, Jianzhong; Liu, Zheng

2017-05-10

Molecular dynamics (MD) simulations, in combination with the Markov-state model (MSM), were applied to probe CO 2 diffusion from an aqueous solution into the active site of human carbonic anhydrase II (hCA-II), an enzyme useful for enhanced CO 2 capture and utilization. The diffusion process in the hydrophobic pocket of hCA-II was illustrated in terms of a two-dimensional free-energy landscape. We found that CO 2 diffusion in hCA-II is a rate-limiting step in the CO 2 diffusion-binding-reaction process. The equilibrium distribution of CO 2 shows its preferential accumulation within a hydrophobic domain in the protein core region. An analysis of the committors and reactive fluxes indicates that the main pathway for CO 2 diffusion into the active site of hCA-II is through a binding pocket where residue Gln 136 contributes to the maximal flux. The simulation results offer a new perspective on the CO 2 hydration kinetics and useful insights toward the development of novel biochemical processes for more efficient CO 2 sequestration and utilization.

Derivation of effective fission gas diffusivities in UO2 from lower length scale simulations and implementation of fission gas diffusion models in BISON

DOE Office of Scientific and Technical Information (OSTI.GOV)

Andersson, Anders David Ragnar; Pastore, Giovanni; Liu, Xiang-Yang

2014-11-07

This report summarizes the development of new fission gas diffusion models from lower length scale simulations and assessment of these models in terms of annealing experiments and fission gas release simulations using the BISON fuel performance code. Based on the mechanisms established from density functional theory (DFT) and empirical potential calculations, continuum models for diffusion of xenon (Xe) in UO 2 were derived for both intrinsic conditions and under irradiation. The importance of the large X eU3O cluster (a Xe atom in a uranium + oxygen vacancy trap site with two bound uranium vacancies) is emphasized, which is a consequencemore » of its high mobility and stability. These models were implemented in the MARMOT phase field code, which is used to calculate effective Xe diffusivities for various irradiation conditions. The effective diffusivities were used in BISON to calculate fission gas release for a number of test cases. The results are assessed against experimental data and future directions for research are outlined based on the conclusions.« less

Simulation of moving flat plate with unsteady translational motion using vortex method

NASA Astrophysics Data System (ADS)

Widodo, A. F.; Zuhal, L. R.

2013-10-01

This paper presents simulation of moving flate plate with unsteady translational motion using Lagrangianmeshless numerical simulation named vortex method. The method solves Navier-Stokes equations in term of vorticity. The solving strategy is splitting the equation into diffusion and convection term to be solved separately. The diffusion term is modeled by particles strength exchange(PSE) which is the most accurate of diffusion modeling in vortex method. The convection term that represents transport of particles is calculated by time step integration of velocity. Velocity of particles is natively calculated using Biot-Savart relation but for acceleration, fastmultiple method(FMM) is employed. The simulation is validated experimentally using digital particle image velocimetry(DPIV) and the results give good agreement.

A computer program for the simulation of heat and moisture flow in soils

NASA Technical Reports Server (NTRS)

Camillo, P.; Schmugge, T. J.

1981-01-01

A computer program that simulates the flow of heat and moisture in soils is described. The space-time dependence of temperature and moisture content is described by a set of diffusion-type partial differential equations. The simulator uses a predictor/corrector to numerically integrate them, giving wetness and temperature profiles as a function of time. The simulator was used to generate solutions to diffusion-type partial differential equations for which analytical solutions are known. These equations include both constant and variable diffusivities, and both flux and constant concentration boundary conditions. In all cases, the simulated and analytic solutions agreed to within the error bounds which were imposed on the integrator. Simulations of heat and moisture flow under actual field conditions were also performed. Ground truth data were used for the boundary conditions and soil transport properties. The qualitative agreement between simulated and measured profiles is an indication that the model equations are reasonably accurate representations of the physical processes involved.

Potential autotrophic metabolisms in ultra-basic reducing springs associated with present-day continental serpentinization

NASA Astrophysics Data System (ADS)

Morrill, P. L.; Miles, S.; Kohl, L.; Kavanagh, H.; Ziegler, S. E.; Brazelton, W. J.; Schrenk, M. O.

2013-12-01

Ultra-basic reducing springs at continental sites of serpentinization act as windows into the biogeochemistry of this subsurface exothermic environment rich in H2 and CH4 gases. Biogeochemical carbon transformations in these systems are of interest because serpentinization creates conditions that are amenable to abiotic and biotic reduction of carbon. However, little is known about the metabolic capabilities of the microorganisms that live in this environment. To determine the potential for autotrophic metabolisms, bicarbonate and CO substrate addition microcosm experiments were performed using water and sediment from an ultra-basic reducing spring in the Tablelands, Newfoundland, Canada, a site of present-day continental serpentinization. CO was consistently observed to be utilized in the Live but not the Killed controlled replicates amended with 10% 13C labelled CO and non-labelled (natural C isotope abundance) CO. In the Live CO microcosms with natural C isotope abundance, the residual CO became enriched in 13C (~10 ‰) consistent with a decrease in the fraction of CO remaining. In the Killed CO controlled replicates with natural C isotope abundance the CO showed little 13C enrichment (~1.3 ‰). The data from the Live CO microcosms were well described by a Rayleigh isotopic distillation model, yielding an isotopic enrichment factor for microbial CO uptake of 15.7 ×0.5 ‰ n=2. These data suggest that there was microbial CO utilization in these experiments. The sediment and water from the 13C-labelled and non-labelled, Live and Killed microcosms were extracted for phospholipid fatty acids (PLFAs) to determine changes in community composition between treatments as well as to determine the microbial uptake of CO. The difference in community composition between the Live and Killed microcosms was not readily resolvable based on PLFA distributions. Additionally, the microbial uptake of 13CO had minimal to no affect on the δ13C of the cellular biomarkers, with the exception of C16 saturated and a C16 monounsaturated PLFAs in one live microcosm which showed >2 ‰ and >10 ‰ enrichment, respectively, compared to the average δ13C values of the same PLFA in the 13C Killed controlled replicates. Therefore the uptake of CO had minimal effect on the overall biomass and community composition in the system. The 13C labelled bicarbonate anaerobic microcosm experiments showed little to no methane production. The methane detected in the 13C labelled Live experiments were not isotopically enriched in 13C compared to the CH4 in the labelled Killed controlled replicates. Therefore bicarbonate was not used as a substrate for microbial methanogenesis via the CO2 reduction pathway. These results are generally consistent with genomic and metagenomic data, which discovered the potential for a carbon fixation pathway involving carbon monoxide, but little evidence for archaea or methanogenesis in the ultra-basic springs in the Tablelands (Brazelton et al., 2012). Reference: Brazelton WJ, Nelson B, & Schrenk MO (2012) Frontiers in Microbiology 2:1-16.

STEPS: efficient simulation of stochastic reaction-diffusion models in realistic morphologies.

PubMed

Hepburn, Iain; Chen, Weiliang; Wils, Stefan; De Schutter, Erik

2012-05-10

Models of cellular molecular systems are built from components such as biochemical reactions (including interactions between ligands and membrane-bound proteins), conformational changes and active and passive transport. A discrete, stochastic description of the kinetics is often essential to capture the behavior of the system accurately. Where spatial effects play a prominent role the complex morphology of cells may have to be represented, along with aspects such as chemical localization and diffusion. This high level of detail makes efficiency a particularly important consideration for software that is designed to simulate such systems. We describe STEPS, a stochastic reaction-diffusion simulator developed with an emphasis on simulating biochemical signaling pathways accurately and efficiently. STEPS supports all the above-mentioned features, and well-validated support for SBML allows many existing biochemical models to be imported reliably. Complex boundaries can be represented accurately in externally generated 3D tetrahedral meshes imported by STEPS. The powerful Python interface facilitates model construction and simulation control. STEPS implements the composition and rejection method, a variation of the Gillespie SSA, supporting diffusion between tetrahedral elements within an efficient search and update engine. Additional support for well-mixed conditions and for deterministic model solution is implemented. Solver accuracy is confirmed with an original and extensive validation set consisting of isolated reaction, diffusion and reaction-diffusion systems. Accuracy imposes upper and lower limits on tetrahedron sizes, which are described in detail. By comparing to Smoldyn, we show how the voxel-based approach in STEPS is often faster than particle-based methods, with increasing advantage in larger systems, and by comparing to MesoRD we show the efficiency of the STEPS implementation. STEPS simulates models of cellular reaction-diffusion systems with complex boundaries with high accuracy and high performance in C/C++, controlled by a powerful and user-friendly Python interface. STEPS is free for use and is available at http://steps.sourceforge.net/

STEPS: efficient simulation of stochastic reaction–diffusion models in realistic morphologies

PubMed Central

2012-01-01

Background Models of cellular molecular systems are built from components such as biochemical reactions (including interactions between ligands and membrane-bound proteins), conformational changes and active and passive transport. A discrete, stochastic description of the kinetics is often essential to capture the behavior of the system accurately. Where spatial effects play a prominent role the complex morphology of cells may have to be represented, along with aspects such as chemical localization and diffusion. This high level of detail makes efficiency a particularly important consideration for software that is designed to simulate such systems. Results We describe STEPS, a stochastic reaction–diffusion simulator developed with an emphasis on simulating biochemical signaling pathways accurately and efficiently. STEPS supports all the above-mentioned features, and well-validated support for SBML allows many existing biochemical models to be imported reliably. Complex boundaries can be represented accurately in externally generated 3D tetrahedral meshes imported by STEPS. The powerful Python interface facilitates model construction and simulation control. STEPS implements the composition and rejection method, a variation of the Gillespie SSA, supporting diffusion between tetrahedral elements within an efficient search and update engine. Additional support for well-mixed conditions and for deterministic model solution is implemented. Solver accuracy is confirmed with an original and extensive validation set consisting of isolated reaction, diffusion and reaction–diffusion systems. Accuracy imposes upper and lower limits on tetrahedron sizes, which are described in detail. By comparing to Smoldyn, we show how the voxel-based approach in STEPS is often faster than particle-based methods, with increasing advantage in larger systems, and by comparing to MesoRD we show the efficiency of the STEPS implementation. Conclusion STEPS simulates models of cellular reaction–diffusion systems with complex boundaries with high accuracy and high performance in C/C++, controlled by a powerful and user-friendly Python interface. STEPS is free for use and is available at http://steps.sourceforge.net/ PMID:22574658

Expanding the calculation of activation volumes: Self-diffusion in liquid water

NASA Astrophysics Data System (ADS)

Piskulich, Zeke A.; Mesele, Oluwaseun O.; Thompson, Ward H.

2018-04-01

A general method for calculating the dependence of dynamical time scales on macroscopic thermodynamic variables from a single set of simulations is presented. The approach is applied to the pressure dependence of the self-diffusion coefficient of liquid water as a particularly useful illustration. It is shown how the activation volume associated with diffusion can be obtained directly from simulations at a single pressure, avoiding approximations that are typically invoked.

A Numerical Method for the Simulation of Skew Brownian Motion and its Application to Diffusive Shock Acceleration of Charged Particles

NASA Astrophysics Data System (ADS)

McEvoy, Erica L.

Stochastic differential equations are becoming a popular tool for modeling the transport and acceleration of cosmic rays in the heliosphere. In diffusive shock acceleration, cosmic rays diffuse across a region of discontinuity where the up- stream diffusion coefficient abruptly changes to the downstream value. Because the method of stochastic integration has not yet been developed to handle these types of discontinuities, I utilize methods and ideas from probability theory to develop a conceptual framework for the treatment of such discontinuities. Using this framework, I then produce some simple numerical algorithms that allow one to incorporate and simulate a variety of discontinuities (or boundary conditions) using stochastic integration. These algorithms were then modified to create a new algorithm which incorporates the discontinuous change in diffusion coefficient found in shock acceleration (known as Skew Brownian Motion). The originality of this algorithm lies in the fact that it is the first of its kind to be statistically exact, so that one obtains accuracy without the use of approximations (other than the machine precision error). I then apply this algorithm to model the problem of diffusive shock acceleration, modifying it to incorporate the additional effect of the discontinuous flow speed profile found at the shock. A steady-state solution is obtained that accurately simulates this phenomenon. This result represents a significant improvement over previous approximation algorithms, and will be useful for the simulation of discontinuous diffusion processes in other fields, such as biology and finance.

A Simulation Tool for Dynamic Contrast Enhanced MRI

PubMed Central

Mauconduit, Franck; Christen, Thomas; Barbier, Emmanuel Luc

2013-01-01

The quantification of bolus-tracking MRI techniques remains challenging. The acquisition usually relies on one contrast and the analysis on a simplified model of the various phenomena that arise within a voxel, leading to inaccurate perfusion estimates. To evaluate how simplifications in the interstitial model impact perfusion estimates, we propose a numerical tool to simulate the MR signal provided by a dynamic contrast enhanced (DCE) MRI experiment. Our model encompasses the intrinsic and relaxations, the magnetic field perturbations induced by susceptibility interfaces (vessels and cells), the diffusion of the water protons, the blood flow, the permeability of the vessel wall to the the contrast agent (CA) and the constrained diffusion of the CA within the voxel. The blood compartment is modeled as a uniform compartment. The different blocks of the simulation are validated and compared to classical models. The impact of the CA diffusivity on the permeability and blood volume estimates is evaluated. Simulations demonstrate that the CA diffusivity slightly impacts the permeability estimates ( for classical blood flow and CA diffusion). The effect of long echo times is investigated. Simulations show that DCE-MRI performed with an echo time may already lead to significant underestimation of the blood volume (up to 30% lower for brain tumor permeability values). The potential and the versatility of the proposed implementation are evaluated by running the simulation with realistic vascular geometry obtained from two photons microscopy and with impermeable cells in the extravascular environment. In conclusion, the proposed simulation tool describes DCE-MRI experiments and may be used to evaluate and optimize acquisition and processing strategies. PMID:23516414

Evidence of polycyclic aromatic hydrocarbon biodegradation in a contaminated aquifer by combined application of in situ and laboratory microcosms using (13)C-labelled target compounds.

PubMed

Bahr, Arne; Fischer, Anko; Vogt, Carsten; Bombach, Petra

2015-02-01

The number of approaches to evaluate the biodegradation of polycyclic aromatic hydrocarbons (PAHs) within contaminated aquifers is limited. Here, we demonstrate the applicability of a novel method based on the combination of in situ and laboratory microcosms using (13)C-labelled PAHs as tracer compounds. The biodegradation of four PAHs (naphthalene, fluorene, phenanthrene, and acenaphthene) was investigated in an oxic aquifer at the site of a former gas plant. In situ biodegradation of naphthalene and fluorene was demonstrated using in situ microcosms (BACTRAP(®)s). BACTRAP(®)s amended with either [(13)C6]-naphthalene or [(13)C5/(13)C6]-fluorene (50:50) were incubated for a period of over two months in two groundwater wells located at the contaminant source and plume fringe, respectively. Amino acids extracted from BACTRAP(®)-grown cells showed significant (13)C-enrichments with (13)C-fractions of up to 30.4% for naphthalene and 3.8% for fluorene, thus providing evidence for the in situ biodegradation and assimilation of those PAHs at the field site. To quantify the mineralisation of PAHs, laboratory microcosms were set up with BACTRAP(®)-grown cells and groundwater. Naphthalene, fluorene, phenanthrene, or acenaphthene were added as (13)C-labelled substrates. (13)C-enrichment of the produced CO2 revealed mineralisation of between 5.9% and 19.7% for fluorene, between 11.1% and 35.1% for acenaphthene, between 14.2% and 33.1% for phenanthrene, and up to 37.0% for naphthalene over a period of 62 days. Observed PAH mineralisation rates ranged between 17 μg L(-1) d(-1) and 1639 μg L(-1) d(-1). The novel approach combining in situ and laboratory microcosms allowed a comprehensive evaluation of PAH biodegradation at the investigated field site, revealing the method's potential for the assessment of PAH degradation within contaminated aquifers. Copyright © 2014 Elsevier Ltd. All rights reserved.

Reductive Dechlorination of 1,2,4-Trichlorobenzene and Its Metabolites at a Contaminated Site in Nanjing, China: Concordance between Field and Microcosm Data

NASA Astrophysics Data System (ADS)

Qiao, W.; Lomheim, L.; Luo, F.; Ye, S.; Wu, J.; Edwards, E.

2016-12-01

Chlorinated benzenes (CBs) are widespread contaminants at many industrial sites, posing a threat to human health and the environment. Bioremediation has the advantage of using natural biological processes to possibly completely destroy target pollutants. A three-year site investigation was conducted from 2012 to 2014 at a former chemical plant in Nanjing, China, which was contaminated by chlorobenzenes (CBs) and benzene. The aquifer was located within a silty clay and clayey silt with extremely low permeability. Soil and groundwater sample analyses revealed that the main contaminants were 1,2,4-tichlorobenzene (TCB) with highest concentration of 7300ug/L, dichlorobenzene (DCB) isomers, monochlorobenzene (MCB) and benzene. The contaminants were mainly located in the vicinity of a former wastewater basin and production facilities of chemical products. TCB was used as a solvent and leaked during the plant manufacturing processes. It is assumed that DCB isomers, MCB and benzene were derived from the anaerobic subsequent dehalogenation of 1,2,4-TCB. A corresponding lab microcosm study was conducted to prove the assumption of indigenous CBs biodegradation. The contaminated soil and groundwater from the site were used to conduct the lab microcosms study to keep the lab experimental conditions the same as the site and to be comparable with the site investigation results. The lab microcosms study results demonstrated that 1,4-DCB, 1,2-DCB and 1,3-DCB were the anaerobic dechlorination product of 1,2,4-TCB, and 1,2-DCB, 1,3-DCB can be transformed to MCB, and benzene can be degraded to CO2 under sulfate reducing condition. The lab microcosms study results were consistent with the site investigation results, which will provide a theoretical proposition on site remediation strategy making. This research method of combing the site investigation with the lab study can be applied and transferable to any other contaminated sites of concern. The site investigation and lab study can authenticate each other, which will make the site remediation strategy much more localized, specific and cost-effective.

Cosmic ray diffusion: Report of the Workshop in Cosmic Ray Diffusion Theory

NASA Technical Reports Server (NTRS)

Birmingham, T. J.; Jones, F. C.

1975-01-01

A workshop in cosmic ray diffusion theory was held at Goddard Space Flight Center on May 16-17, 1974. Topics discussed and summarized are: (1) cosmic ray measurements as related to diffusion theory; (2) quasi-linear theory, nonlinear theory, and computer simulation of cosmic ray pitch-angle diffusion; and (3) magnetic field fluctuation measurements as related to diffusion theory.

A hybrid continuous-discrete method for stochastic reaction-diffusion processes.

PubMed

Lo, Wing-Cheong; Zheng, Likun; Nie, Qing

2016-09-01

Stochastic fluctuations in reaction-diffusion processes often have substantial effect on spatial and temporal dynamics of signal transductions in complex biological systems. One popular approach for simulating these processes is to divide the system into small spatial compartments assuming that molecules react only within the same compartment and jump between adjacent compartments driven by the diffusion. While the approach is convenient in terms of its implementation, its computational cost may become prohibitive when diffusive jumps occur significantly more frequently than reactions, as in the case of rapid diffusion. Here, we present a hybrid continuous-discrete method in which diffusion is simulated using continuous approximation while reactions are based on the Gillespie algorithm. Specifically, the diffusive jumps are approximated as continuous Gaussian random vectors with time-dependent means and covariances, allowing use of a large time step, even for rapid diffusion. By considering the correlation among diffusive jumps, the approximation is accurate for the second moment of the diffusion process. In addition, a criterion is obtained for identifying the region in which such diffusion approximation is required to enable adaptive calculations for better accuracy. Applications to a linear diffusion system and two nonlinear systems of morphogens demonstrate the effectiveness and benefits of the new hybrid method.

Reduce Confusion about Diffusion.

ERIC Educational Resources Information Center

Hebrank, Mary R.

1997-01-01

Presents activities that allow students to explore the fundamental but poorly understood concept of diffusion by appealing to their kinesthetic senses first, then challenging their analytical skills as they try to deduce the mathematical principle involved. Presents a computer simulation of diffusion and discusses diffusion's limitations and…

Computational Analysis on Performance of Thermal Energy Storage (TES) Diffuser

NASA Astrophysics Data System (ADS)

Adib, M. A. H. M.; Adnan, F.; Ismail, A. R.; Kardigama, K.; Salaam, H. A.; Ahmad, Z.; Johari, N. H.; Anuar, Z.; Azmi, N. S. N.

2012-09-01

Application of thermal energy storage (TES) system reduces cost and energy consumption. The performance of the overall operation is affected by diffuser design. In this study, computational analysis is used to determine the thermocline thickness. Three dimensional simulations with different tank height-to-diameter ratio (HD), diffuser opening and the effect of difference number of diffuser holes are investigated. Medium HD tanks simulations with double ring octagonal diffuser show good thermocline behavior and clear distinction between warm and cold water. The result show, the best performance of thermocline thickness during 50% time charging occur in medium tank with height-to-diameter ratio of 4.0 and double ring octagonal diffuser with 48 holes (9mm opening ~ 60%) acceptable compared to diffuser with 6mm ~ 40% and 12mm ~ 80% opening. The conclusion is computational analysis method are very useful in the study on performance of thermal energy storage (TES).

Diffusion control for a tempered anomalous diffusion system using fractional-order PI controllers.

PubMed

Juan Chen; Zhuang, Bo; Chen, YangQuan; Cui, Baotong

2017-05-09

This paper is concerned with diffusion control problem of a tempered anomalous diffusion system based on fractional-order PI controllers. The contribution of this paper is to introduce fractional-order PI controllers into the tempered anomalous diffusion system for mobile actuators motion and spraying control. For the proposed control force, convergence analysis of the system described by mobile actuator dynamical equations is presented based on Lyapunov stability arguments. Moreover, a new Centroidal Voronoi Tessellation (CVT) algorithm based on fractional-order PI controllers, henceforth called FOPI-based CVT algorithm, is provided together with a modified simulation platform called Fractional-Order Diffusion Mobile Actuator-Sensor 2-Dimension Fractional-Order Proportional Integral (FO-Diff-MAS2D-FOPI). Finally, extensive numerical simulations for the tempered anomalous diffusion process are presented to verify the effectiveness of our proposed fractional-order PI controllers. Copyright © 2017 ISA. Published by Elsevier Ltd. All rights reserved.

Micromagnetic simulation of anisotropic grain boundary diffusion for sintered Nd-Fe-B magnets

NASA Astrophysics Data System (ADS)

Li, W.; Zhou, Q.; Zhao, L. Z.; Wang, Q. X.; Zhong, X. C.; Liu, Z. W.

2018-04-01

A systematic investigation on the anisotropic grain boundary diffusion in sintered Nd-Fe-B magnets is carried out by micromagnetic simulation. The results indicate that the critical reason for the anisotropic diffusion effect is not the difference in the amount of Dy diffused along different directions but the macroscopic demagnetizing field. The diffusion parallel to the easy axis from both pole surfaces of the magnet can increase the nucleation fields in the two major regions with large macroscopic demagnetizing fields, where the reverse domains can nucleate easily. As a consequence, the grain boundary diffusion along the directions parallel to the easy axis from two pole surfaces is more effective to improve the coercivity of the magnets than that along other directions. It is also found that, to enhance the coercivity, only a limited diffusion depth is required. The present result is in good agreement with the recent experimental findings.

Exciton diffusion in disordered small molecules for organic photovoltaics: insights from first-principles simulations.

PubMed

Li, Z; Zhang, X; Lu, G

2014-05-07

Exciton diffusion in small molecules 3,6-bis(5-(benzofuran-2-yl)thiophen-2-yl)-2,5-bis(2-ethylhexyl)pyrrolo[3,4-c]pyrrole-1,4-dione [DPP(TBFu)2] is studied using first-principles simulations. We have examined dependence of exciton diffusion on structure disorder, temperature and exciton energy. We find that exciton diffusion length and diffusivity increase with structural order, temperature and the initial exciton energy. Compared to conjugated polymer poly(3-hexylthiophene) (P3HT), DPP(TBFu)2 small molecules exhibit a much higher exciton diffusivity, but a shorter lifetime. The exciton diffusion length in DPP(TBFu)2 is 50% longer than that in P3HT, yielding a higher exciton harvesting efficiency; the physical origin behind these differences is discussed. The time evolutions of exciton energy, electron-hole distance, and exciton localization are explored, and the widely speculated exciton diffusion mechanism is confirmed theoretically. The connection between exciton diffusion and carrier mobilities is also studied. Finally we point out the possibility to estimate exciton diffusivity by measuring carrier mobilities under AC electric fields.

Similarities between principal components of protein dynamics and random diffusion

NASA Astrophysics Data System (ADS)

Hess, Berk

2000-12-01

Principal component analysis, also called essential dynamics, is a powerful tool for finding global, correlated motions in atomic simulations of macromolecules. It has become an established technique for analyzing molecular dynamics simulations of proteins. The first few principal components of simulations of large proteins often resemble cosines. We derive the principal components for high-dimensional random diffusion, which are almost perfect cosines. This resemblance between protein simulations and noise implies that for many proteins the time scales of current simulations are too short to obtain convergence of collective motions.

Reconstructing in-vivo reflectance spectrum of pigmented skin lesion by Monte Carlo simulation

NASA Astrophysics Data System (ADS)

Wang, Shuang; He, Qingli; Zhao, Jianhua; Lui, Harvey; Zeng, Haishan

2012-03-01

In dermatology applications, diffuse reflectance spectroscopy has been extensively investigated as a promising tool for the noninvasive method to distinguish melanoma from benign pigmented skin lesion (nevus), which is concentrated with the skin chromophores like melanin and hemoglobin. We carried out a theoretical study to examine melanin distribution in human skin tissue and establish a practical optical model for further pigmented skin investigation. The theoretical simulation was using junctional nevus as an example. A multiple layer skin optical model was developed on established anatomy structures of skin, the published optical parameters of different skin layers, blood and melanin. Monte Carlo simulation was used to model the interaction between excitation light and skin tissue and rebuild the diffuse reflectance process from skin tissue. A testified methodology was adopted to determine melanin contents in human skin based on in vivo diffuse reflectance spectra. The rebuild diffuse reflectance spectra were investigated by adding melanin into different layers of the theoretical model. One of in vivo reflectance spectra from Junctional nevi and their surrounding normal skin was studied by compare the ratio between nevus and normal skin tissue in both the experimental and simulated diffuse reflectance spectra. The simulation result showed a good agreement with our clinical measurements, which indicated that our research method, including the spectral ratio method, skin optical model and modifying the melanin content in the model, could be applied in further theoretical simulation of pigmented skin lesions.

Simulation of thermally induced processes of diffusion and phase formation in layered binary metallic systems

NASA Astrophysics Data System (ADS)

Rusakov, V. S.; Sukhorukov, I. A.; Zhankadamova, A. M.; Kadyrzhanov, K. K.

2010-05-01

Results of the simulation of thermally induced processes of diffusion and phase formation in model and experimentally investigated layered binary metallic systems are presented. The physical model is based on the Darken phenomenological theory and on the mechanism of interdiffusion of components along the continuous diffusion channels of phases in the two-phase regions of the system. The simulation of processes in the model systems showed that the thermally stabilized concentration profiles in two-layer binary metallic systems are virtually independent of the partial diffusion coefficients; for the systems with the average concentration of components that is the same over the sample depth, the time of the thermal stabilization of the structural and phase state inhomogeneous over the depth grows according to a power law with increasing thickness of the system in such a manner that the thicknesses of the surface layers grow, while the thickness of the intermediate layer approaches a constant value. The results of the simulation of the processes of diffusion and phase formation in experimentally investigated layered binary systems Fe-Ti and Cu-Be upon sequential isothermal and isochronous annealings agree well with the experimental data.

Kinetic Monte Carlo simulation on influence of vacancy on hydrogen diffusivity in tungsten

NASA Astrophysics Data System (ADS)

Oda, Takuji; Zhu, Deqiong; Watanabe, Yoshiyuki

2015-12-01

Kinetic Mote Carlo (KMC) simulations are performed to quantify the influence of trap in hydrogen diffusivity in tungsten. As a typical trap, mono-vacancy is considered in the simulation. Experimental results reported by Frauenfelder are nicely reproduced when hydrogen concentration and trap concentration expected in the experiment are employed in the simulation. The effective diffusivity of hydrogen is evidently decreased by traps even at high temperatures like 1300 K. These results suggest that only high-temperature experimental data, which are not significantly affected by traps, should be fitted to, in order to derive the true hydrogen diffusivity from experiments. Therefore, we recommend D = 1.58 ×10-7exp(- 0.25 eV / kT) m2 s-1 as the equation for hydrogen diffusion coefficient in tungsten, which was obtained by fitting only to experimental data at 1500-2400 K by Heinola and Ahlgren, rather than the most cited equation D = 4.1 ×10-7exp(- 0.39 eV / kT) m2 s-1, which was obtained by fitting to all experimental data at 1100-2400 K including some data that should be affected by traps.

Addition of Rubber to soil damages the functional diversity of soil.

PubMed

Goswami, Madhurankhi; Bhattacharyya, Purnita; Tribedi, Prosun

2017-07-01

Rubber is a polymer of isoprene, consisting mainly of cis-1,4-polyisoprene units. The unmanageable production and its irresponsible disposal pose severe threats to environmental ecology. Therefore, the current study focuses extensively on the ill-effects of Rubber disposal on soil microbial functional diversity as it reflects the health of ecosystem by acting as a key component in ecosystem productivity. To investigate the effect of Rubber on soil microbial functional diversity, soil samples were collected from landfill sites and three different soil microcosms (Rubber treated, untreated, and sterile soil) were prepared. The soil enzymatic activity was determined by fluorescein diacetate hydrolysis followed by the determination of the microbial metabolic potential and functional diversity by average well color development and Shannon-Weaver index (H), respectively. BiOLOG ECO plates were used for determining the microbial functional diversity of the soil microcosms. Higher heterotrophic microbial count as well as higher soil microbial activity was observed in Rubber untreated soil than Rubber treated soil microcosm. The result indicated that the addition of Rubber to soil reduced soil heterotrophic microbial count and soil microbial activity considerably. Similarly, soil microbial metabolic potential as well as microbial functional diversity of soil had been decreased by the addition of Rubber gloves in it. Variation in soil microbial metabolic spectrum between Rubber treated and untreated microcosm was confirmed by multivariate analysis. Collectively, all the results demonstrated that the addition of Rubber to soil reduced the soil microbial functional diversity considerably. Therefore, it is necessary for the commission of serious steps regarding Rubber disposal and protection of the environment from serious environmental issues.

Assessment of factors limiting algal growth in acidic pit lakes--a case study from Western Australia, Australia.

PubMed

Kumar, R Naresh; McCullough, Clint D; Lund, Mark A; Larranaga, Santiago A

2016-03-01

Open-cut mining operations can form pit lakes on mine closure. These new water bodies typically have low nutrient concentrations and may have acidic and metal-contaminated waters from acid mine drainage (AMD) causing low algal biomass and algal biodiversity. A preliminary study was carried out on an acidic coal pit lake, Lake Kepwari, in Western Australia to determine which factors limited algal biomass. Water quality was monitored to obtain baseline data. pH ranged between 3.7 and 4.1, and solute concentrations were slightly elevated to levels of brackish water. Concentrations of N were highly relative to natural lakes, although concentrations of FRP (<0.01 mg/L) and C (total C 0.7-3.7 and DOC 0.7-3.5 mg/L) were very low, and as a result, algal growth was also extremely low. Microcosm experiment was conducted to test the hypothesis that nutrient enrichment will be able to stimulate algal growth regardless of water quality. Microcosms of Lake Kepwari water were amended with N, P and C nutrients with and without sediment. Nutrient amendments under microcosm conditions could not show any significant phytoplankton growth but was able to promote benthic algal growth. P amendments without sediment showed a statistically higher mean algal biomass concentration than controls or microcosms amended with phosphorus but with sediment did. Results indicated that algal biomass in acidic pit lake (Lake Kepwari) may be limited primarily by low nutrient concentrations (especially phosphorus) and not by low pH or elevated metal concentrations. Furthermore, sediment processes may also reduce the nutrient availability.

Response of the Predatory Bacterium, Halobacteriovorax, and Virus to an Influx of a Prey Bacterium in a Natural Water Microcosm and a Three Membered Artificial Sea Water Microcosm.

NASA Astrophysics Data System (ADS)

Williams, H.; Chen, H.; Laws, E. A.; Gulig, P. A.

2016-02-01

Halobacteriovorax (HBx) is a predatory bacterium that preys on Vibrio sp. and many other gram negative bacteria. There is strong evidence that suggest HBx has a role in bacterial mortality in marine and brackish systems. However, its role has not been appropriately explored. In this study the rate of HBx predation on Vibrio vulnificus in comparison to that of viruses has been investigated. Initial experiments compared the responses of HBx and viruses in estuarine water systems to an input of V. vulnificus. Environmental water samples were filtered to remove larger protists and other organisms and debris. The filtered samples were used to establish laboratory microcosms to which was added a suspension of V. vulnificus. To measure the responses of HBx and viruses to the influx of V. vulnificus, samples were removed at intervals over a 40 h incubation period to enumerate HBx and V. vulnificus by culture and viruses by direct microscopic counts. In a subsequent experiment we investigated the responses of a virus and HBx strain when cultured with a suspension of V. vulnificus in a laboratory controlled microcosm of artificial sea water. The results of both experiments revealed that HBx was the first and most rapid responder to the inoculum of V. vulnificus and reduced their numbers significantly. The viruses were relatively non-responsive and did not substantially reduce V. vulnifius numbers. These results show that HBx may be a major contributor to bacterial mortality in conjunction with protists and viruses

Chlorodifluoroacetic acid fate and toxicity to the macrophytes Lemna gibba, Myriophyllum spicatum, and Myriophyllum sibiricum in aquatic microcosms.

PubMed

Hanson, M L; Sibley, P K; Mabury, S A; Muir, D C; Solomon, K R

2001-12-01

Chlorodifluoroacetic acid (CDFA) is a novel haloacetic acid (HAA) and has been recently documented in aquatic systems. It is a suspected degradation product of the refrigerants 1,1,2-trichloro-1,1-difluoroethane (CFC-113) and 1-chloro-1,1-difluoroethane (HCFC-142b). Haloacetic acids can be phytotoxic, putatively acting through inhibition of the citric acid cycle. Replicate (n = 3) 12,000-L model aquatic ecosystems (microcosms) were dosed once at 0.5, 1, 5, and 20 mg/L of neutralized CDFA. Three microcosms served as controls. Each microcosm was stocked with eight individual apical shoots of both Myriophyllum spicatum and Myriophyllum sibiricum and sampled at regular intervals over a 42-d exposure period. The plants were assessed for the somatic endpoints of plant length, root growth, node number, and wet and dry mass and the biochemical endpoints of chlorophyll-a/b and carotenoid content as well as citric acid levels. The duckweed Lemna gibba was also introduced into these systems and monitored over a period of 14 d for wet/dry mass, plant/frond number, chlorophyll content, and growth rate. Concentrations of CDFA remained constant in the water column over the course of the fate investigation (241 d), indicating that this compound undergoes little, if any, degradation in aquatic systems. Results showed few statistically significant differences from controls for all three plant species with exposure to CDFA but no biologically relevant impacts. Overall, CDFA does not appear to pose any risk to these aquatic macrophytes at current environmental concentrations.

Iron oxides alter methanogenic pathways of acetate in production water of high-temperature petroleum reservoir.

PubMed

Pan, Pan; Hong, Bo; Mbadinga, Serge Maurice; Wang, Li-Ying; Liu, Jin-Feng; Yang, Shi-Zhong; Gu, Ji-Dong; Mu, Bo-Zhong

2017-09-01

Acetate is a key intermediate in anaerobic crude oil biodegradation and also a precursor for methanogenesis in petroleum reservoirs. The impact of iron oxides, viz. β-FeOOH (akaganéite) and magnetite (Fe 3 O 4 ), on the methanogenic acetate metabolism in production water of a high-temperature petroleum reservoir was investigated. Methane production was observed in all the treatments amended with acetate. In the microcosms amended with acetate solely about 30% of the acetate utilized was converted to methane, whereas methane production was stimulated in the presence of magnetite (Fe 3 O 4 ) resulting in a 48.34% conversion to methane. Methane production in acetate-amended, β-FeOOH (akaganéite)-supplemented microcosms was much faster and acetate consumption was greatly improved compared to the other conditions in which the stoichiometric expected amounts of methane were not produced. Microbial community analysis showed that Thermacetogenium spp. (known syntrophic acetate oxidizers) and hydrogenotrophic methanogens closely related to Methanothermobacter spp. were enriched in acetate and acetate/magnetite (Fe 3 O 4 ) microcosms suggesting that methanogenic acetate metabolism was through hydrogenotrophic methanogenesis fueled by syntrophic acetate oxidizers. The acetate/β-FeOOH (akaganéite) microcosms, however, differed by the dominance of archaea closely related to the acetoclastic Methanosaeta thermophila. These observations suggest that supplementation of β-FeOOH (akaganéite) accelerated the production of methane further, driven the alteration of the methanogenic community, and changed the pathway of acetate methanogenesis from hydrogenotrophic methanogenesis fueled by syntrophic acetate oxidizers to acetoclastic.

Anaerobic degradation of vinyl chloride in aquifer microcosms.

PubMed

Smits, Theo H M; Assal, Antoine; Hunkeler, Daniel; Holliger, Christof

2011-01-01

The anaerobic degradation potential at a chloroethene-contaminated site was investigated by operating two anoxic column aquifer microcosms enriched in iron(III). One column was fed with vinyl chloride (VC) only (column A) and one with VC and acetate (column B). In column A, after about 600 pore volume exchanges (PVEs), VC started to disappear and reached almost zero VC recovery in the effluent after 1000 PVEs. No formation of ethene was observed. In column B, effluent VC was almost always only a fraction of influent VC. Formation of ethene was observed after 800 PVEs and started to become an important degradation product after 1550 PVEs. However, ethene was never observed in stoichiometric amounts compared with disappeared VC. The average stable isotope enrichment factor for VC disappearance in column A was determined to be -4.3‰. In column B, the isotope enrichment factor shifted from -10.7 to -18.5‰ concurrent with an increase in ethene production. Batch microcosms inoculated with column material showed similar isotope enrichment factors as the column microcosms. These results indicated that two degradation processes occurred, one in column A and two in parallel in column B with increasing importance of reductive dechlorination with time. This study suggests that in addition to reductive dechlorination, other degradation processes such as anaerobic oxidation should be taken into account when evaluating natural attenuation of VC and that isotope analysis can help to differentiate between different pathways of VC removal. American Society of Agronomy, Crop Science Society of America, and Soil Science Society of America.

Wrinkly-Spreader Fitness in the Two-Dimensional Agar Plate Microcosm: Maladaptation, Compensation and Ecological Success

PubMed Central

Spiers, Andrew J.

2007-01-01

Bacterial adaptation to new environments often leads to the establishment of new genotypes with significantly altered phenotypes. In the Wrinkly Spreader (WS), ecological success in static liquid microcosms was through the rapid colonisation of the air-liquid interface by the production of a cellulose-based biofilm. Rapid surface spreading was also seen on agar plates, but in this two-dimensional environment the WS appears maladapted and rapidly reverts to the ancestral smooth (SM)-like colony genotype. In this work, the fitness of WS relative to SM in mixed colonies was found to be low, confirming the WS instability on agar plates. By examining defined WS mutants, the maladaptive characteristic was found to be the expression of cellulose. SM-like revertants had a higher growth rate than WS and no longer expressed significant amounts of cellulose, further confirming that the expression of this high-cost polymer was the basis of maladaptation and the target of compensatory mutation in developing colonies. However, examination of the fate of WS-founded populations in either multiple-colony or single mega-colony agar plate microcosms demonstrated that the loss of WS lineages could be reduced under conditions in which the rapid spreading colony phenotype could dominate nutrient and oxygen access more effectively than competing SM/SM-like genotypes. WS-like isolates recovered from such populations showed increased WS phenotype stability as well as changes in the degree of colony spreading, confirming that the WS was adapting to the two-dimensional agar plate microcosm. PMID:17710140

Test of direct and indirect effects of agrochemicals on the survival of fecal indicator bacteria.

PubMed

Staley, Zachery R; Rohr, Jason R; Harwood, Valerie J

2011-12-01

Water bodies often receive agrochemicals and animal waste carrying fecal indicator bacteria (FIB) and zoonotic pathogens, but we know little about the effects of agrochemicals on these microbes. We assessed the direct effects of the pesticides atrazine, malathion, and chlorothalonil and inorganic fertilizer on Escherichia coli and enterococcal survival in simplified microcosms held in the dark. E. coli strain composition in sediments and water column were positively correlated, but none of the agrochemicals had significant direct effects on E. coli strain composition or on densities of culturable FIBs. In a companion study, microcosms with nondisinfected pond water and sediments were exposed to or shielded from sunlight to examine the potential indirect effects of atrazine and inorganic fertilizer on E. coli. The herbicide atrazine had no effect on E. coli in dark-exposed microcosms containing natural microbial and algal communities. However, in light-exposed microcosms, atrazine significantly lowered E. coli densities in the water column and significantly increased densities in the sediment compared to controls. This effect appears to be mediated by the effects of atrazine on algae, given that atrazine significantly reduced phytoplankton, which was a positive and negative predictor of E. coli densities in the water column and sediment, respectively. These data suggest that atrazine does not directly affect the survival of FIB, rather that it indirectly alters the distribution and abundance of E. coli by altering phytoplankton and periphyton communities. These results improve our understanding of the influence of agricultural practices on FIB densities in water bodies impacted by agricultural runoff.

Test of Direct and Indirect Effects of Agrochemicals on the Survival of Fecal Indicator Bacteria▿

PubMed Central

Staley, Zachery R.; Rohr, Jason R.; Harwood, Valerie J.

2011-01-01

Water bodies often receive agrochemicals and animal waste carrying fecal indicator bacteria (FIB) and zoonotic pathogens, but we know little about the effects of agrochemicals on these microbes. We assessed the direct effects of the pesticides atrazine, malathion, and chlorothalonil and inorganic fertilizer on Escherichia coli and enterococcal survival in simplified microcosms held in the dark. E. coli strain composition in sediments and water column were positively correlated, but none of the agrochemicals had significant direct effects on E. coli strain composition or on densities of culturable FIBs. In a companion study, microcosms with nondisinfected pond water and sediments were exposed to or shielded from sunlight to examine the potential indirect effects of atrazine and inorganic fertilizer on E. coli. The herbicide atrazine had no effect on E. coli in dark-exposed microcosms containing natural microbial and algal communities. However, in light-exposed microcosms, atrazine significantly lowered E. coli densities in the water column and significantly increased densities in the sediment compared to controls. This effect appears to be mediated by the effects of atrazine on algae, given that atrazine significantly reduced phytoplankton, which was a positive and negative predictor of E. coli densities in the water column and sediment, respectively. These data suggest that atrazine does not directly affect the survival of FIB, rather that it indirectly alters the distribution and abundance of E. coli by altering phytoplankton and periphyton communities. These results improve our understanding of the influence of agricultural practices on FIB densities in water bodies impacted by agricultural runoff. PMID:22003017

Trichloroacetic acid fate and toxicity to the macrophytes Myriophyllum spicatum and Myriophyllum sibiricum under field conditions.

PubMed

Hanson, Mark L; Sibley, Paul K; Ellis, David A; Fineberg, Neil A; Mabury, Scott A; Solomon, Keith R; Muir, Derek C

2002-03-01

Trichloroacetic acid (TCA) has been detected in rain, snow, and river samples throughout the world. It may enter into natural water systems via herbicide use, as a by-product of water disinfection, from emissions of spent bleach liquor of kraft pulp mills, and as a natural fungal product. This compound is phytotoxic and likely to accumulate in aquatic environments. A study to assess the fate of TCA in semi-natural aquatic environments and the toxicity of TCA to rooted aquatic macrophytes was conducted. The experiment involved exposing three replicate 12000 l aquatic microcosms at the University of Guelph Microcosm Facility to 0.05, 0.5, 3, and 10 mg/l of TCA for 35 days in a one-way analysis of variance design. Each microcosm was stocked with 14 individual 5 cm apical shoots of Myriophyllum spicatum and M. sibiricum. The plants were sampled at regular intervals and assessed for the somatic endpoints of plant length, root growth, number of nodes and wet and dry mass and the biochemical endpoints of chlorophyll-a and chlorophyll-b, carotenoid content, and citric acid levels. TCA half-lives in the microcosms ranged from 190 to 296 h depending on the initial concentration of TCA. Myriophyllum spp. results indicate that while there were some statistically significant differences from controls, there were no biologically significant effects of TCA for any of the endpoints examined. These data suggest that TCA does not pose a significant risk to these macrophytes up to 10 mg/l, which typically exceeds environmentally relevant concentrations by several orders of magnitude.

Trichloroacetic acid (TCA) and trifluoroacetic acid (TFA) mixture toxicity to the macrophytes Myriophyllum spicatum and Myriophyllum sibiricum in aquatic microcosms.

PubMed

Hanson, Mark L; Sibley, Paul K; Mabury, Scott A; Solomon, Keith R; Muir, Derek C G

2002-02-21

Trichloroacetic acid (TCA) and trifluoroacetic acid (TFA) have been detected together in environmental water samples throughout the world. TCA may enter into aquatic systems via rainout as the degradation product of chlorinated solvents, herbicide use, as a by-product of water disinfection and from emissions of spent bleach liquor of kraft pulp mills. Sources of TFA include degradation of hydrofluorocarbons (HFCs) refrigerants and pesticides. These substances are phytotoxic and widely distributed in aquatic environments. A study to assess the risk of a binary mixture of TCA and TFA to macrophytes in aquatic microcosms was conducted as part of a larger study on haloacetic acids. M. spicatum and M. sibiricum were exposed to 0.1, 1, 3 and 10 mg/l of both TCA and TFA (neutralized with sodium hydroxide) in replicate (n = 3) 12000 l aquatic microcosms for 49 days in an one-way analysis of variance design. Each microcosm was stocked with 14 individual apical shoots per species. The plants were sampled at regular intervals and assessed for the somatic endpoints of plant length, root growth, number of nodes and wet and dry mass and the biochemical endpoints of chlorophyll-a, chlorophyll-b, carotenoid content and citric acid levels. Results indicate that there were statistically significant effects of the TCA/TFA mixture on certain pigment concentrations immediately after the start of exposure (2-7 days), but the plants showed no signs of stress thereafter. These data suggest that TCA/TFA mixtures at environmentally relevant concentrations do not pose a significant risk to these aquatic macrophytes.

Biodegradation of marine oil spill residues using aboriginal bacterial consortium based on Penglai 19-3 oil spill accident, China.

PubMed

Wang, Chuanyuan; Liu, Xing; Guo, Jie; Lv, Yingchun; Li, Yuanwei

2018-09-15

Bioremediation, mainly by indigenous bacteria, has been regarded as an effective way to deal with the petroleum pollution after an oil spill accident. The biodegradation of crude oil by microorganisms co-incubated from sediments collected from the Penglai 19-3 oil platform, Bohai Sea, China, was examined. The relative susceptibility of the isomers of alkylnaphthalenes, alkylphenanthrenes and alkyldibenzothiophene to biodegradation was also discussed. The results showed that the relative degradation values of total petroleum hydrocarbon (TPH) are 43.56% and 51.29% for sediments with untreated microcosms (S-BR1) and surfactant-treated microcosms (S-BR2), respectively. TPH biodegradation results showed an obvious decrease in saturates (biodegradation rate: 67.85-77.29%) and a slight decrease in aromatics (biodegradation rate: 47.13-57.21%), while no significant difference of resins and asphaltenes was detected. The biodegradation efficiency of alkylnaphthalenes, alkylphenanthrenes and alkyldibenzothiophene for S-BR1 and S-BR2 samples reaches 1.28-84.43% and 42.56-86.67%, respectively. The efficiency of crude oil degradation in sediment with surfactant-treated microcosms cultures added Tween 20, was higher than that in sediment with untreated microcosms. The biodegradation and selective depletion is not only controlled by thermodynamics but also related to the stereochemical structure of individual isomer compounds. Information on the biodegradation of oil spill residues by the bacterial community revealed in this study will be useful in developing strategies for bioremediation of crude oil dispersed in the marine ecosystem. Copyright © 2018 Elsevier Inc. All rights reserved.

Viscous diffusion of vorticity in unsteady wall layers using the diffusion velocity concept

DOE Office of Scientific and Technical Information (OSTI.GOV)

Strickland, J.H.; Kempka, S.N.; Wolfe, W.P.

1995-03-01

The primary purpose of this paper is to provide a careful evaluation of the diffusion velocity concept with regard to its ability to predict the diffusion of vorticity near a moving wall. A computer code BDIF has been written which simulates the evolution of the vorticity field near a wall of infinite length which is moving in an arbitrary fashion. The simulations generated by this code are found to give excellent results when compared to several exact solutions. We also outline a two-dimensional unsteady viscous boundary layer model which utilizes the diffusion velocity concept and is compatible with vortex methods.more » A primary goal of this boundary layer model is to minimize the number of vortices generated on the surface at each time step while achieving good resolution of the vorticity field near the wall. Preliminary results have been obtained for simulating a simple two-dimensional laminar boundary layer.« less

Simulation of interdiffusion and voids growth based on cellular automata

NASA Astrophysics Data System (ADS)

Zhang, Fan; Zhang, Boyan; Zhang, Nan; Du, Haishun; Zhang, Xinhong

2017-02-01

In the interdiffusion of two solid-state materials, if the diffusion coefficients of the two materials are not the same, the interface of the two materials will shift to the material with the lower diffusion coefficient. This effect is known as the Kirkendall effect. The Kirkendall effect leads to Kirkendall porosity. The pores act as sinks for vacancies and become voids. In this paper, the movement of the Kirkendall plane at interdiffusion is simulated based on cellular automata. The number of vacancies, the critical radius of voids nucleation and the nucleation rate are analysed. The vacancies diffusion, vacancies aggregation and voids growth are also simulated based on cellular automata.

Bioreduction of U(VI) and stability of immobilized uranium under suboxic conditions.

PubMed

Hu, Nan; Ding, De-xin; Li, Shi-mi; Tan, Xiang; Li, Guang-yue; Wang, Yong-dong; Xu, Fei

2016-04-01

In order to study the bioreduction of U(VI) and stability of immobilized uranium under suboxic conditions, microcosm were amended with ethanol, lactate and glucose, and incubated under suboxic conditions. During the incubation, total dissolved U in amended microcosms decreased from 0.95 mg/L to 0.03 mg/L. Pyrosequencing results showed that, the proportion of anaerobic microorganisms capable of reducing U(VI) under suboxic conditions was small compared with that under anoxic conditions; the proportion of aerobic and facultative anaerobic microorganisms capable of consuming the dissolved oxygen was large; and some of the facultative anaerobic microorganisms could reduce U(VI). These results indicated that different microbial communities were responsible for the bioreduction of U(VI) under suboxic and anoxic conditions. After the electron donors were exhausted, total dissolved U in the amended microcosms remained unchanged, while the U(VI)/U(IV) ratio in the solid phase of sediments increased obviously. This implied that the performance of bioreduction of the U(VI) can be maintained under suboxic condition. Copyright © 2016 Elsevier Ltd. All rights reserved.

Degradation of trichloroethylene by Pseudomonas cepacia G4 and the constitutive mutant strain G4 5223 PR1 in aquifer microcosms

USGS Publications Warehouse

Krumme, M.L.; Timmis, K.N.; Dwyer, D.F.

1993-01-01

Pseudomonas cepacia G4 degrades trichloroethylene (TCE) via a degradation pathway for aromatic compounds which is induced by substrates such as phenol and tryptophan. P. cepacia G4 5223 PR1 (PR1) is a Tn5 insertion mutant which constitutively expresses the toluene ortho-monooxygenase responsible for TCE degradation. In groundwater microcosms, phenol-induced strain G4 and noninduced strain PR1 degraded TCE (20 and 50 microM) to nondetectable levels (< 0.1 microM) within 24 h at densities of 10(8) cells per ml; at lower densities, degradation of TCE was not observed after 48 h. In aquifer sediment microcosms, TCE was reduced from 60 to < 0.1 microM within 24 h at 5 x 10(8) PR1 organisms per g (wet weight) of sediment and from 60 to 26 microM over a period of 10 weeks at 5 x 10(7) PR1 organisms per g. Viable G4 and PR1 cells decreased from approximately 10(7) to 10(4) per g over the 10-week period.

Nitrous oxide emissions from high rate algal ponds treating domestic wastewater.

PubMed

Alcántara, Cynthia; Muñoz, Raúl; Norvill, Zane; Plouviez, Maxence; Guieysse, Benoit

2015-02-01

This study investigated the generation of N2O by microcosms withdrawn from 7-L high rate algal ponds (HRAPs) inoculated with Chlorella vulgaris and treating synthetic wastewater. Although HRAPs microcosms demonstrated the ability to generate algal-mediated N2O when nitrite was externally supplied under darkness in batch assays, negligible N2O emissions rates were consistently recorded in the absence of nitrite during 3.5-month monitoring under 'normal' operation. Thereafter, HRAP A and HRAP B were overloaded with nitrate and ammonium, respectively, in an attempt to stimulate N2O emissions via nitrite in situ accumulation. Significant N2O production (up to 5685±363 nmol N2O/g TSS h) was only recorded from HRAP B microcosms externally supplied with nitrite in darkness. Although confirmation under full-scale outdoors conditions is needed, this study provides the first evidence that the ability of microalgae to synthesize N2O does not affect the environmental performance of wastewater treatment in HRAPs. Copyright © 2014 Elsevier Ltd. All rights reserved.

A flow cytometry-optimized assay using an SOS-green fluorescent protein (SOS-GFP) whole-cell biosensor for the detection of genotoxins in complex environments.

PubMed

Norman, Anders; Hansen, Lars Hestbjerg; Sørensen, Søren J

2006-02-28

Whole-cell biosensors have become popular tools for detection of ecotoxic compounds in environmental samples. We have developed an assay optimized for flow cytometry with detection of genotoxic compounds in mind. The assay features extended pre-incubation and a cell density of only 10(6)-10(7) cells/mL, and proved far more sensitive than a previously published assay using the same biosensor strain. By applying the SOS-green fluorescent protein (GFP) whole-cell biosensor directly to soil microcosms we were also able to evaluate both the applicability and sensitivity of a biosensor based on SOS-induction in whole soil samples. Soil microcosms were spiked with a dilution-series of crude broth extract from the mitomycin C-producing streptomycete Streptomyces caespitosus. Biosensors extracted from these microcosms after 1 day of incubation at 30 degrees C were easily distinguished from extracts of non-contaminated soil particles when using flow cytometry, and induction of the biosensor by mitomycin C was detectable at concentrations as low as 2.5 ng/g of soil.

Performance assessment of aeration and radial oxygen loss assisted cathode based integrated constructed wetland-microbial fuel cell systems.

PubMed

Srivastava, Pratiksha; Dwivedi, Saurabh; Kumar, Naresh; Abbassi, Rouzbeh; Garaniya, Vikram; Yadav, Asheesh Kumar

2017-11-01

The present study explores low-cost cathode development possibility using radial oxygen loss (ROL) of Canna indica plants and intermittent aeration (IA) for wastewater treatment and electricity generation in constructed wetland-microbial fuel cell (CW-MFC) system. Two CW-MFC microcosms were developed. Amongst them, one microcosm was planted with Canna indica plants for evaluating the ROL dependent cathode reaction (CW-MFC dependent on ROL) and another microcosm was equipped with intermittent aeration for evaluating the intermittent aeration dependent cathode reaction (CW-MFC with additional IA). The CW-MFC with additional IA has achieved 78.71% and 53.23%, and CW-MFC dependent on ROL has achieved 72.17% and 46.77% COD removal from synthetic wastewater containing glucose loads of 0.7gL -1 and 2.0gL -1 , respectively. The maximum power density of 31.04mWm -3 and 19.60mWm -3 was achieved in CW-MFC with additional IA and CW-MFC dependent on ROL, respectively. Copyright © 2017 Elsevier Ltd. All rights reserved.

Information diffusion, Facebook clusters, and the simplicial model of social aggregation: a computational simulation of simplicial diffusers for community health interventions.

PubMed

Kee, Kerk F; Sparks, Lisa; Struppa, Daniele C; Mannucci, Mirco A; Damiano, Alberto

2016-01-01

By integrating the simplicial model of social aggregation with existing research on opinion leadership and diffusion networks, this article introduces the constructs of simplicial diffusers (mathematically defined as nodes embedded in simplexes; a simplex is a socially bonded cluster) and simplicial diffusing sets (mathematically defined as minimal covers of a simplicial complex; a simplicial complex is a social aggregation in which socially bonded clusters are embedded) to propose a strategic approach for information diffusion of cancer screenings as a health intervention on Facebook for community cancer prevention and control. This approach is novel in its incorporation of interpersonally bonded clusters, culturally distinct subgroups, and different united social entities that coexist within a larger community into a computational simulation to select sets of simplicial diffusers with the highest degree of information diffusion for health intervention dissemination. The unique contributions of the article also include seven propositions and five algorithmic steps for computationally modeling the simplicial model with Facebook data.

Simulation of radiation driven fission gas diffusion in UO 2, ThO 2 and PuO 2

DOE PAGES

Cooper, Michael William D.; Stanek, Christopher Richard; Turnbull, James Anthony; ...

2016-12-01

Below 1000 K it is thought that fission gas diffusion in nuclear fuel during irradiation occurs through atomic mixing due to radiation damage. Here we present a molecular dynamics (MD) study of Xe, Kr, Th, U, Pu and O diffusion due to irradiation. It is concluded that the ballistic phase does not sufficiently account for the experimentally observed diffusion. Thermal spike simulations are used to confirm that electronic stopping remedies the discrepancy with experiment and the predicted diffusivities lie within the scatter of the experimental data. Here, our results predict that the diffusion coefficients are ordered such that D* 0more » > D* Kr > D* Xe > D* U. For all species >98.5% of diffusivity is accounted for by electronic stopping. Fission gas diffusivity was not predicted to vary significantly between ThO 2, UO 2 and PuO 2, indicating that this process would not change greatly for mixed oxide fuels.« less

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ortoleva, Peter J.

Illustrative embodiments of systems and methods for the deductive multiscale simulation of macromolecules are disclosed. In one illustrative embodiment, a deductive multiscale simulation method may include (i) constructing a set of order parameters that model one or more structural characteristics of a macromolecule, (ii) simulating an ensemble of atomistic configurations for the macromolecule using instantaneous values of the set of order parameters, (iii) simulating thermal-average forces and diffusivities for the ensemble of atomistic configurations, and (iv) evolving the set of order parameters via Langevin dynamics using the thermal-average forces and diffusivities.

Numerical study of centrifugal compressor stage vaneless diffusers

NASA Astrophysics Data System (ADS)

Galerkin, Y.; Soldatova, K.; Solovieva, O.

2015-08-01

The authors analyzed CFD calculations of flow in vaneless diffusers with relative width in range from 0.014 to 0.100 at inlet flow angles in range from 100 to 450 with different inlet velocity coefficients, Reynolds numbers and surface roughness. The aim is to simulate calculated performances by simple algebraic equations. The friction coefficient that represents head losses as friction losses is proposed for simulation. The friction coefficient and loss coefficient are directly connected by simple equation. The advantage is that friction coefficient changes comparatively little in range of studied parameters. Simple equations for this coefficient are proposed by the authors. The simulation accuracy is sufficient for practical calculations. To create the complete algebraic model of the vaneless diffuser the authors plan to widen this method of modeling to diffusers with different relative length and for wider range of Reynolds numbers.

An Urban Diffusion Simulation Model for Carbon Monoxide

ERIC Educational Resources Information Center

Johnson, W. B.; And Others

1973-01-01

A relatively simple Gaussian-type diffusion simulation model for calculating urban carbon (CO) concentrations as a function of local meteorology and the distribution of traffic is described. The model can be used in two ways: in the synoptic mode and in the climatological mode. (Author/BL)

Short- and long-time diffusion and dynamic scaling in suspensions of charged colloidal particles

NASA Astrophysics Data System (ADS)

Banchio, Adolfo J.; Heinen, Marco; Holmqvist, Peter; Nägele, Gerhard

2018-04-01

We report on a comprehensive theory-simulation-experimental study of collective and self-diffusion in concentrated suspensions of charge-stabilized colloidal spheres. In theory and simulation, the spheres are assumed to interact directly by a hard-core plus screened Coulomb effective pair potential. The intermediate scattering function, fc(q, t), is calculated by elaborate accelerated Stokesian dynamics (ASD) simulations for Brownian systems where many-particle hydrodynamic interactions (HIs) are fully accounted for, using a novel extrapolation scheme to a macroscopically large system size valid for all correlation times. The study spans the correlation time range from the colloidal short-time to the long-time regime. Additionally, Brownian Dynamics (BD) simulation and mode-coupling theory (MCT) results of fc(q, t) are generated where HIs are neglected. Using these results, the influence of HIs on collective and self-diffusion and the accuracy of the MCT method are quantified. It is shown that HIs enhance collective and self-diffusion at intermediate and long times. At short times self-diffusion, and for wavenumbers outside the structure factor peak region also collective diffusion, are slowed down by HIs. MCT significantly overestimates the slowing influence of dynamic particle caging. The dynamic scattering functions obtained in the ASD simulations are in overall good agreement with our dynamic light scattering (DLS) results for a concentration series of charged silica spheres in an organic solvent mixture, in the experimental time window and wavenumber range. From the simulation data for the time derivative of the width function associated with fc(q, t), there is indication of long-time exponential decay of fc(q, t), for wavenumbers around the location of the static structure factor principal peak. The experimental scattering functions in the probed time range are consistent with a time-wavenumber factorization scaling behavior of fc(q, t) that was first reported by Segrè and Pusey [Phys. Rev. Lett. 77, 771 (1996)] for suspensions of hard spheres. Our BD simulation and MCT results predict a significant violation of exact factorization scaling which, however, is approximately restored according to the ASD results when HIs are accounted for, consistent with the experimental findings for fc(q, t). Our study of collective diffusion is amended by simulation and theoretical results for the self-intermediate scattering function, fs(q, t), and its non-Gaussian parameter α2(t) and for the particle mean squared displacement W(t) and its time derivative. Since self-diffusion properties are not assessed in standard DLS measurements, a method to deduce W(t) approximately from fc(q, t) is theoretically validated.

Effects of whistler mode hiss waves on the radiation belts structure during quiet times

NASA Astrophysics Data System (ADS)

Ripoll, J. F.; Santolik, O.; Reeves, G. D.; Kurth, W. S.; Denton, M.; Loridan, V.; Thaller, S. A.; Cunningham, G.; Kletzing, C.; Turner, D. L.; Henderson, M. G.; Ukhorskiy, S.; Drozdov, A.; Cervantes Villa, J. S.; Shprits, Y.

2017-12-01

We present dynamic Fokker-Planck simulations of the electron radiation belts and slot formation during the quiet days that can follow a storm. Simulations are made for all energies and L-shells between 2 and 6 in the view of recovering the observations of two particular events. Pitch angle diffusion is essential to energy structure of the belts and slot region. Pitch angle diffusion is computed from data-driven spatially and temporally-resolved whistler mode hiss wave and ambient plasma observations from the Van Allen Probes satellites. The simulations are performed either with a 3D formulation that uses pitch angle diffusion coefficients or with a simpler 1D Fokker-Planck equation based on losses computed from a lifetime. Validation is carried out globally against Magnetic Electron and Ion Spectrometer observations of the belts at all energy. Results are complemented with a sensitivity study involving different radial diffusion coefficients, electron lifetimes, and pitch angle diffusion coefficients. We discuss which models allow to recover the observed "S-shaped" energy-dependent inner boundary to the outer zone that results from the competition between diffusive radial transport and losses. Periods when the plasmasphere extends beyond L 5 favor long-lasting hiss losses from the outer belt. Through these simulations, we explain the full structure in energy and L-shell of the belts and the slot formation by hiss scattering during quiet storm recovery.

Contributions of chemical and diffusive exchange to T1ρ dispersion.

PubMed

Cobb, Jared Guthrie; Xie, Jingping; Gore, John C

2013-05-01

Variations in local magnetic susceptibility may induce magnetic field gradients that affect the signals acquired for MR imaging. Under appropriate diffusion conditions, such fields produce effects similar to slow chemical exchange. These effects may also be found in combination with other chemical exchange processes at multiple time scales. We investigate these effects with simulations and measurements to determine their contributions to rotating frame (R1ρ ) relaxation in model systems. Simulations of diffusive and chemical exchange effects on R1ρ dispersion were performed using the Bloch equations. Additionally, R1ρ dispersion was measured in suspensions of Sephadex and latex beads with varying spin locking fields at 9.4 T. A novel analysis method was used to iteratively fit for apparent chemical and diffusive exchange rates with a model by Chopra et al. Single- and double-inflection points in R1ρ dispersion profiles were observed, respectively, in simulations of slow diffusive exchange alone and when combined with rapid chemical exchange. These simulations were consistent with measurements of R1ρ in latex bead suspensions and small-diameter Sephadex beads that showed single- and double-inflection points, respectively. These observations, along with measurements following changes in temperature and pH, are consistent with the combined effects of slow diffusion and rapid -OH exchange processes. Copyright © 2012 Wiley Periodicals, Inc.

Hybrid modeling and empirical analysis of automobile supply chain network

NASA Astrophysics Data System (ADS)

Sun, Jun-yan; Tang, Jian-ming; Fu, Wei-ping; Wu, Bing-ying

2017-05-01

Based on the connection mechanism of nodes which automatically select upstream and downstream agents, a simulation model for dynamic evolutionary process of consumer-driven automobile supply chain is established by integrating ABM and discrete modeling in the GIS-based map. Firstly, the rationality is proved by analyzing the consistency of sales and changes in various agent parameters between the simulation model and a real automobile supply chain. Second, through complex network theory, hierarchical structures of the model and relationships of networks at different levels are analyzed to calculate various characteristic parameters such as mean distance, mean clustering coefficients, and degree distributions. By doing so, it verifies that the model is a typical scale-free network and small-world network. Finally, the motion law of this model is analyzed from the perspective of complex self-adaptive systems. The chaotic state of the simulation system is verified, which suggests that this system has typical nonlinear characteristics. This model not only macroscopically illustrates the dynamic evolution of complex networks of automobile supply chain but also microcosmically reflects the business process of each agent. Moreover, the model construction and simulation of the system by means of combining CAS theory and complex networks supplies a novel method for supply chain analysis, as well as theory bases and experience for supply chain analysis of auto companies.

Theory and simulation of ion conduction in the pentameric GLIC channel.

PubMed

Zhu, Fangqiang; Hummer, Gerhard

2012-10-09

GLIC is a bacterial member of the large family of pentameric ligand-gated ion channels. To study ion conduction through GLIC and other membrane channels, we combine the one-dimensional potential of mean force for ion passage with a Smoluchowski diffusion model, making it possible to calculate single-channel conductance in the regime of low ion concentrations from all-atom molecular dynamics (MD) simulations. We then perform MD simulations to examine sodium ion conduction through the GLIC transmembrane pore in two systems with different bulk ion concentrations. The ion potentials of mean force, calculated from umbrella sampling simulations with Hamiltonian replica exchange, reveal a major barrier at the hydrophobic constriction of the pore. The relevance of this barrier for ion transport is confirmed by a committor function that rises sharply in the barrier region. From the free evolution of Na(+) ions starting at the barrier top, we estimate the effective diffusion coefficient in the barrier region, and subsequently calculate the conductance of the pore. The resulting diffusivity compares well with the position-dependent ion diffusion coefficient obtained from restrained simulations. The ion conductance obtained from the diffusion model agrees with the value determined via a reactive-flux rate calculation. Our results show that the conformation in the GLIC crystal structure, with an estimated conductance of ~1 picosiemens at 140 mM ion concentration, is consistent with a physiologically open state of the channel.

Two-way coupled SPH and particle level set fluid simulation.

PubMed

Losasso, Frank; Talton, Jerry; Kwatra, Nipun; Fedkiw, Ronald

2008-01-01

Grid-based methods have difficulty resolving features on or below the scale of the underlying grid. Although adaptive methods (e.g. RLE, octrees) can alleviate this to some degree, separate techniques are still required for simulating small-scale phenomena such as spray and foam, especially since these more diffuse materials typically behave quite differently than their denser counterparts. In this paper, we propose a two-way coupled simulation framework that uses the particle level set method to efficiently model dense liquid volumes and a smoothed particle hydrodynamics (SPH) method to simulate diffuse regions such as sprays. Our novel SPH method allows us to simulate both dense and diffuse water volumes, fully incorporates the particles that are automatically generated by the particle level set method in under-resolved regions, and allows for two way mixing between dense SPH volumes and grid-based liquid representations.

Kinetic Monte Carlo Simulation of Oxygen Diffusion in Ytterbium Disilicate

NASA Astrophysics Data System (ADS)

Good, Brian

2015-03-01

Ytterbium disilicate is of interest as a potential environmental barrier coating for aerospace applications, notably for use in next generation jet turbine engines. In such applications, the diffusion of oxygen and water vapor through these coatings is undesirable if high temperature corrosion is to be avoided. In an effort to understand the diffusion process in these materials, we have performed kinetic Monte Carlo simulations of vacancy-mediated oxygen diffusion in Ytterbium Disilicate. Oxygen vacancy site energies and diffusion barrier energies are computed using Density Functional Theory. We find that many potential diffusion paths involve large barrier energies, but some paths have barrier energies smaller than one electron volt. However, computed vacancy formation energies suggest that the intrinsic vacancy concentration is small in the pure material, with the result that the material is unlikely to exhibit significant oxygen permeability.

Diffusion of interacting particles in discrete geometries: Equilibrium and dynamical properties

NASA Astrophysics Data System (ADS)

Becker, T.; Nelissen, K.; Cleuren, B.; Partoens, B.; Van den Broeck, C.

2014-11-01

We expand on a recent study of a lattice model of interacting particles [Phys. Rev. Lett. 111, 110601 (2013), 10.1103/PhysRevLett.111.110601]. The adsorption isotherm and equilibrium fluctuations in particle number are discussed as a function of the interaction. Their behavior is similar to that of interacting particles in porous materials. Different expressions for the particle jump rates are derived from transition-state theory. Which expression should be used depends on the strength of the interparticle interactions. Analytical expressions for the self- and transport diffusion are derived when correlations, caused by memory effects in the environment, are neglected. The diffusive behavior is studied numerically with kinetic Monte Carlo (kMC) simulations, which reproduces the diffusion including correlations. The effect of correlations is studied by comparing the analytical expressions with the kMC simulations. It is found that the Maxwell-Stefan diffusion can exceed the self-diffusion. To our knowledge, this is the first time this is observed. The diffusive behavior in one-dimensional and higher-dimensional systems is qualitatively the same, with the effect of correlations decreasing for increasing dimension. The length dependence of both the self- and transport diffusion is studied for one-dimensional systems. For long lengths the self-diffusion shows a 1 /L dependence. Finally, we discuss when agreement with experiments and simulations can be expected. The assumption that particles in different cavities do not interact is expected to hold quantitatively at low and medium particle concentrations if the particles are not strongly interacting.

Tumor proliferation and diffusion on percolation clusters.

PubMed

Jiang, Chongming; Cui, Chunyan; Zhong, Weirong; Li, Gang; Li, Li; Shao, Yuanzhi

2016-10-01

We study in silico the influence of host tissue inhomogeneity on tumor cell proliferation and diffusion by simulating the mobility of a tumor on percolation clusters with different homogeneities of surrounding tissues. The proliferation and diffusion of a tumor in an inhomogeneous tissue could be characterized in the framework of the percolation theory, which displays similar thresholds (0.54, 0.44, and 0.37, respectively) for tumor proliferation and diffusion in three kinds of lattices with 4, 6, and 8 connecting near neighbors. Our study reveals the existence of a critical transition concerning the survival and diffusion of tumor cells with leaping metastatic diffusion movement in the host tissues. Tumor cells usually flow in the direction of greater pressure variation during their diffusing and infiltrating to a further location in the host tissue. Some specific sites suitable for tumor invasion were observed on the percolation cluster and around these specific sites a tumor can develop into scattered tumors linked by some advantage tunnels that facilitate tumor invasion. We also investigate the manner that tissue inhomogeneity surrounding a tumor may influence the velocity of tumor diffusion and invasion. Our simulation suggested that invasion of a tumor is controlled by the homogeneity of the tumor microenvironment, which is basically consistent with the experimental report by Riching et al. as well as our clinical observation of medical imaging. Both simulation and clinical observation proved that tumor diffusion and invasion into the surrounding host tissue is positively correlated with the homogeneity of the tissue.

Slow-Down in Diffusion in Crowded Protein Solutions Correlates with Transient Cluster Formation.

PubMed

Nawrocki, Grzegorz; Wang, Po-Hung; Yu, Isseki; Sugita, Yuji; Feig, Michael

2017-12-14

For a long time, the effect of a crowded cellular environment on protein dynamics has been largely ignored. Recent experiments indicate that proteins diffuse more slowly in a living cell than in a diluted solution, and further studies suggest that the diffusion depends on the local surroundings. Here, detailed insight into how diffusion depends on protein-protein contacts is presented based on extensive all-atom molecular dynamics simulations of concentrated villin headpiece solutions. After force field adjustments in the form of increased protein-water interactions to reproduce experimental data, translational and rotational diffusion was analyzed in detail. Although internal protein dynamics remained largely unaltered, rotational diffusion was found to slow down more significantly than translational diffusion as the protein concentration increased. The decrease in diffusion is interpreted in terms of a transient formation of protein clusters. These clusters persist on sub-microsecond time scales and follow distributions that increasingly shift toward larger cluster size with increasing protein concentrations. Weighting diffusion coefficients estimated for different clusters extracted from the simulations with the distribution of clusters largely reproduces the overall observed diffusion rates, suggesting that transient cluster formation is a primary cause for a slow-down in diffusion upon crowding with other proteins.

High-grade glioma diffusive modeling using statistical tissue information and diffusion tensors extracted from atlases.

PubMed

Roniotis, Alexandros; Manikis, Georgios C; Sakkalis, Vangelis; Zervakis, Michalis E; Karatzanis, Ioannis; Marias, Kostas

2012-03-01

Glioma, especially glioblastoma, is a leading cause of brain cancer fatality involving highly invasive and neoplastic growth. Diffusive models of glioma growth use variations of the diffusion-reaction equation in order to simulate the invasive patterns of glioma cells by approximating the spatiotemporal change of glioma cell concentration. The most advanced diffusive models take into consideration the heterogeneous velocity of glioma in gray and white matter, by using two different discrete diffusion coefficients in these areas. Moreover, by using diffusion tensor imaging (DTI), they simulate the anisotropic migration of glioma cells, which is facilitated along white fibers, assuming diffusion tensors with different diffusion coefficients along each candidate direction of growth. Our study extends this concept by fully exploiting the proportions of white and gray matter extracted by normal brain atlases, rather than discretizing diffusion coefficients. Moreover, the proportions of white and gray matter, as well as the diffusion tensors, are extracted by the respective atlases; thus, no DTI processing is needed. Finally, we applied this novel glioma growth model on real data and the results indicate that prognostication rates can be improved. © 2012 IEEE

Molecular Dynamic Simulation of Water Vapor and Determination of Diffusion Characteristics in the Pore

NASA Astrophysics Data System (ADS)

Nikonov, Eduard G.; Pavluš, Miron; Popovičová, Mária

2018-02-01

One of the varieties of pores, often found in natural or artificial building materials, are the so-called blind pores of dead-end or saccate type. Three-dimensional model of such kind of pore has been developed in this work. This model has been used for simulation of water vapor interaction with individual pore by molecular dynamics in combination with the diffusion equation method. Special investigations have been done to find dependencies between thermostats implementations and conservation of thermodynamic and statistical values of water vapor - pore system. The two types of evolution of water - pore system have been investigated: drying and wetting of the pore. Full research of diffusion coefficient, diffusion velocity and other diffusion parameters has been made.

Simulation of atomic diffusion in the Fcc NiAl system: A kinetic Monte Carlo study

DOE PAGES

Alfonso, Dominic R.; Tafen, De Nyago

2015-04-28

The atomic diffusion in fcc NiAl binary alloys was studied by kinetic Monte Carlo simulation. The environment dependent hopping barriers were computed using a pair interaction model whose parameters were fitted to relevant data derived from electronic structure calculations. Long time diffusivities were calculated and the effect of composition change on the tracer diffusion coefficients was analyzed. These results indicate that this variation has noticeable impact on the atomic diffusivities. A reduction in the mobility of both Ni and Al is demonstrated with increasing Al content. As a result, examination of the pair interaction between atoms was carried out formore » the purpose of understanding the predicted trends.« less

METAL DIFFUSION IN SMOOTHED PARTICLE HYDRODYNAMICS SIMULATIONS OF DWARF GALAXIES

DOE Office of Scientific and Technical Information (OSTI.GOV)

Williamson, David; Martel, Hugo; Kawata, Daisuke, E-mail: david-john.williamson.1@ulaval.ca

2016-05-10

We perform a series of smoothed particle hydrodynamics simulations of isolated dwarf galaxies to compare different metal mixing models. In particular, we examine the role of diffusion in the production of enriched outflows and in determining the metallicity distributions of gas and stars. We investigate different diffusion strengths by changing the pre-factor of the diffusion coefficient, by varying how the diffusion coefficient is calculated from the local velocity distribution, and by varying whether the speed of sound is included as a velocity term. Stronger diffusion produces a tighter [O/Fe]–[Fe/H] distribution in the gas and cuts off the gas metallicity distributionmore » function at lower metallicities. Diffusion suppresses the formation of low-metallicity stars, even with weak diffusion, and also strips metals from enriched outflows. This produces a remarkably tight correlation between “metal mass-loading” (mean metal outflow rate divided by mean metal production rate) and the strength of diffusion, even when the diffusion coefficient is calculated in different ways. The effectiveness of outflows at removing metals from dwarf galaxies and the metal distribution of the gas is thus dependent on the strength of diffusion. By contrast, we show that the metallicities of stars are not strongly dependent on the strength of diffusion, provided that some diffusion is present.« less