A new look at the multi-G model for organic carbon degradation in surface marine sediments for coupled benthic-pelagic simulations of the global ocean

NASA Astrophysics Data System (ADS)

Stolpovsky, Konstantin; Dale, Andrew W.; Wallmann, Klaus

2018-06-01

The kinetics of particulate organic carbon (POC) mineralization in marine surface sediments is not well constrained. This creates considerable uncertainties when benthic processes are considered in global biogeochemical or Earth system circulation models to simulate climate-ocean interactions and biogeochemical tracer distributions in the ocean. In an attempt to improve our understanding of the rate and depth distribution of organic carbon mineralization in bioturbated (0-20 cm) sediments at the global scale, we parameterized a 1-D diagenetic model that simulates the mineralization of three discrete POC pools (a multi-G model). The rate constants of the three reactive classes (highly reactive, reactive, refractory) are fixed and determined to be 70, 0.5 and ˜ 0.001 yr-1, respectively, based on the Martin curve model for pelagic POC degradation. In contrast to previous approaches, however, the reactivity of the organic material degraded in the seafloor is continuous with, and set by, the apparent reactivity of material sinking through the water column. Despite the simplifications of describing POC remineralization using G-type approaches, the model is able to simulate a global database (185 stations) of benthic oxygen and nitrate fluxes across the sediment-water interface in addition to porewater oxygen and nitrate distributions and organic carbon burial efficiencies. It is further consistent with degradation experiments using fresh phytoplankton reported in a previous study. We propose that an important yet mostly overlooked consideration in upscaling approaches is the proportion of the reactive POC classes reaching the seafloor in addition to their reactivity. The approach presented is applicable to both steady-state and non-steady state scenarios, and links POC degradation kinetics in sedimentary environments to water depth and the POC rain rate to the seafloor.

Model-Based Analysis of the Role of Biological, Hydrological and Geochemical Factors Affecting Uranium Bioremediation

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

Zhao, Jiao; Scheibe, Timothy D.; Mahadevan, Radhakrishnan

2011-01-24

Uranium contamination is a serious concern at several sites motivating the development of novel treatment strategies such as the Geobacter-mediated reductive immobilization of uranium. However, this bioremediation strategy has not yet been optimized for the sustained uranium removal. While several reactive-transport models have been developed to represent Geobacter-mediated bioremediation of uranium, these models often lack the detailed quantitative description of the microbial process (e.g., biomass build-up in both groundwater and sediments, electron transport system, etc.) and the interaction between biogeochemical and hydrological process. In this study, a novel multi-scale model was developed by integrating our recent model on electron capacitancemore » of Geobacter (Zhao et al., 2010) with a comprehensive simulator of coupled fluid flow, hydrologic transport, heat transfer, and biogeochemical reactions. This mechanistic reactive-transport model accurately reproduces the experimental data for the bioremediation of uranium with acetate amendment. We subsequently performed global sensitivity analysis with the reactive-transport model in order to identify the main sources of prediction uncertainty caused by synergistic effects of biological, geochemical, and hydrological processes. The proposed approach successfully captured significant contributing factors across time and space, thereby improving the structure and parameterization of the comprehensive reactive-transport model. The global sensitivity analysis also provides a potentially useful tool to evaluate uranium bioremediation strategy. The simulations suggest that under difficult environments (e.g., highly contaminated with U(VI) at a high migration rate of solutes), the efficiency of uranium removal can be improved by adding Geobacter species to the contaminated site (bioaugmentation) in conjunction with the addition of electron donor (biostimulation). The simulations also highlight the interactive effect of initial cell concentration and flow rate on U(VI) reduction.« less

Can multi-generational exposure to ocean warming and acidification lead to the adaptation of life history and physiology in a marine metazoan?

PubMed

Gibbin, Emma M; Chakravarti, Leela J; Jarrold, Michael D; Christen, Felix; Turpin, Vincent; Massamba N'Siala, Gloria; Blier, Pierre U; Calosi, Piero

2017-02-15

Ocean warming and acidification are concomitant global drivers that are currently threatening the survival of marine organisms. How species will respond to these changes depends on their capacity for plastic and adaptive responses. Little is known about the mechanisms that govern plasticity and adaptability or how global changes will influence these relationships across multiple generations. Here, we exposed the emerging model marine polychaete Ophryotrocha labronica to conditions simulating ocean warming and acidification, in isolation and in combination over five generations to identify: (i) how multiple versus single global change drivers alter both juvenile and adult life-history traits; (ii) the mechanistic link between adult physiological and fitness-related life-history traits; and (iii) whether the phenotypic changes observed over multiple generations are of plastic and/or adaptive origin. Two juvenile (developmental rate; survival to sexual maturity) and two adult (average reproductive body size; fecundity) life-history traits were measured in each generation, in addition to three physiological (cellular reactive oxygen species content, mitochondrial density, mitochondrial capacity) traits. We found that multi-generational exposure to warming alone caused an increase in juvenile developmental rate, reactive oxygen species production and mitochondrial density, decreases in average reproductive body size and fecundity, and fluctuations in mitochondrial capacity, relative to control conditions. Exposure to ocean acidification alone had only minor effects on juvenile developmental rate. Remarkably, when both drivers of global change were present, only mitochondrial capacity was significantly affected, suggesting that ocean warming and acidification act as opposing vectors of stress across multiple generations. © 2017. Published by The Company of Biologists Ltd.

Toward efficiency in heterogeneous multispecies reactive transport modeling: A particle-tracking solution for first-order network reactions

NASA Astrophysics Data System (ADS)

Henri, Christopher; Fernàndez-Garcia, Daniel

2015-04-01

Modeling multi-species reactive transport in natural systems with strong heterogeneities and complex biochemical reactions is a major challenge for assessing groundwater polluted sites with organic and inorganic contaminants. A large variety of these contaminants react according to serial-parallel reaction networks commonly simplified by a combination of first-order kinetic reactions. In this context, a random-walk particle tracking method is presented. This method is capable of efficiently simulating the motion of particles affected by first-order network reactions in three-dimensional systems, which are represented by spatially variable physical and biochemical coefficients described at high resolution. The approach is based on the development of transition probabilities that describe the likelihood that particles belonging to a given species and location at a given time will be transformed into and moved to another species and location afterwards. These probabilities are derived from the solution matrix of the spatial moments governing equations. The method is fully coupled with reactions, free of numerical dispersion and overcomes the inherent numerical problems stemming from the incorporation of heterogeneities to reactive transport codes. In doing this, we demonstrate that the motion of particles follows a standard random walk with time-dependent effective retardation and dispersion parameters that depend on the initial and final chemical state of the particle. The behavior of effective parameters develops as a result of differential retardation effects among species. Moreover, explicit analytic solutions of the transition probability matrix and related particle motions are provided for serial reactions. An example of the effect of heterogeneity on the dechlorination of organic solvents in a three-dimensional random porous media shows that the power-law behavior typically observed in conservative tracers breakthrough curves can be largely compromised by the effect of biochemical reactions.

A Three-Dimensional Target Depth-Resolution Method with a Single-Vector Sensor

PubMed Central

Zhao, Anbang; Bi, Xuejie; Hui, Juan; Zeng, Caigao; Ma, Lin

2018-01-01

This paper mainly studies and verifies the target number category-resolution method in multi-target cases and the target depth-resolution method of aerial targets. Firstly, target depth resolution is performed by using the sign distribution of the reactive component of the vertical complex acoustic intensity; the target category and the number resolution in multi-target cases is realized with a combination of the bearing-time recording information; and the corresponding simulation verification is carried out. The algorithm proposed in this paper can distinguish between the single-target multi-line spectrum case and the multi-target multi-line spectrum case. This paper presents an improved azimuth-estimation method for multi-target cases, which makes the estimation results more accurate. Using the Monte Carlo simulation, the feasibility of the proposed target number and category-resolution algorithm in multi-target cases is verified. In addition, by studying the field characteristics of the aerial and surface targets, the simulation results verify that there is only amplitude difference between the aerial target field and the surface target field under the same environmental parameters, and an aerial target can be treated as a special case of a surface target; the aerial target category resolution can then be realized based on the sign distribution of the reactive component of the vertical acoustic intensity so as to realize three-dimensional target depth resolution. By processing data from a sea experiment, the feasibility of the proposed aerial target three-dimensional depth-resolution algorithm is verified. PMID:29649173

A Three-Dimensional Target Depth-Resolution Method with a Single-Vector Sensor.

PubMed

Zhao, Anbang; Bi, Xuejie; Hui, Juan; Zeng, Caigao; Ma, Lin

2018-04-12

This paper mainly studies and verifies the target number category-resolution method in multi-target cases and the target depth-resolution method of aerial targets. Firstly, target depth resolution is performed by using the sign distribution of the reactive component of the vertical complex acoustic intensity; the target category and the number resolution in multi-target cases is realized with a combination of the bearing-time recording information; and the corresponding simulation verification is carried out. The algorithm proposed in this paper can distinguish between the single-target multi-line spectrum case and the multi-target multi-line spectrum case. This paper presents an improved azimuth-estimation method for multi-target cases, which makes the estimation results more accurate. Using the Monte Carlo simulation, the feasibility of the proposed target number and category-resolution algorithm in multi-target cases is verified. In addition, by studying the field characteristics of the aerial and surface targets, the simulation results verify that there is only amplitude difference between the aerial target field and the surface target field under the same environmental parameters, and an aerial target can be treated as a special case of a surface target; the aerial target category resolution can then be realized based on the sign distribution of the reactive component of the vertical acoustic intensity so as to realize three-dimensional target depth resolution. By processing data from a sea experiment, the feasibility of the proposed aerial target three-dimensional depth-resolution algorithm is verified.

Reactive Oxygen Species (ROS) generation by lunar simulants

NASA Astrophysics Data System (ADS)

Kaur, Jasmeet; Rickman, Douglas; Schoonen, Martin A.

2016-05-01

The current interest in human exploration of the Moon and past experiences of Apollo astronauts has rekindled interest into the possible harmful effects of lunar dust on human health. In comparison to the Apollo-era explorations, human explorers may be weeks on the Moon, which will raise the risk of inhalation exposure. The mineralogical composition of lunar dust is well documented, but its effects on human health are not fully understood. With the aim of understanding the reactivity of dusts that may be encountered on geologically different lunar terrains, we have studied Reactive Oxygen Species (ROS) generation by a suite of lunar simulants of different mineralogical-chemical composition dispersed in water and Simulated Lung Fluid (SLF). To further explore the reactivity of simulants under lunar environmental conditions, we compared the reactivity of simulants both in air and inert atmosphere. As the impact of micrometeorites with consequent shock-induced stresses is a major environmental factor on the Moon, we also studied the effect of mechanical stress on samples. Mechanical stress was induced by hand crushing the samples both in air and inert atmosphere. The reactivity of samples after crushing was analyzed for a period of up to nine days. Hydrogen peroxide (H2O2) in water and SLF was analyzed by an in situ electrochemical probe and hydroxyl radical (•OH) by Electron Spin Resonance (ESR) spectroscopy and Adenine probe. Out of all simulants, CSM-CL-S was found to be the most reactive simulant followed by OB-1 and then JSC-1A simulant. The overall reactivity of samples in the inert atmosphere was higher than in air. Fresh crushed samples showed a higher level of reactivity than uncrushed samples. Simulant samples treated to create agglutination, including the formation of zero-valent iron, showed less reactivity than untreated simulants. ROS generation in SLF is initially slower than in deionized water (DI), but the ROS formation is sustained for as long as 7.5 h. By contrast ROS is formed rapidly within 30 min when simulants are dispersed in DI, but then the concentration either stabilizes or decreases over time. The results indicate that mechanical stress and the absence of molecular oxygen and water, which are important environmental characteristics of the lunar environment, can lead to enhanced production of ROS in general. However, compositional difference among simulants is the most important factor in governing the production of ROS. Simulants with glass content in excess of 40 wt% appear to produce as much as of order of magnitude more ROS than simulants with lower glass content.

A multi-species exchange model for fully fluctuating polymer field theory simulations.

PubMed

Düchs, Dominik; Delaney, Kris T; Fredrickson, Glenn H

2014-11-07

Field-theoretic models have been used extensively to study the phase behavior of inhomogeneous polymer melts and solutions, both in self-consistent mean-field calculations and in numerical simulations of the full theory capturing composition fluctuations. The models commonly used can be grouped into two categories, namely, species models and exchange models. Species models involve integrations of functionals that explicitly depend on fields originating both from species density operators and their conjugate chemical potential fields. In contrast, exchange models retain only linear combinations of the chemical potential fields. In the two-component case, development of exchange models has been instrumental in enabling stable complex Langevin (CL) simulations of the full complex-valued theory. No comparable stable CL approach has yet been established for field theories of the species type. Here, we introduce an extension of the exchange model to an arbitrary number of components, namely, the multi-species exchange (MSE) model, which greatly expands the classes of soft material systems that can be accessed by the complex Langevin simulation technique. We demonstrate the stability and accuracy of the MSE-CL sampling approach using numerical simulations of triblock and tetrablock terpolymer melts, and tetrablock quaterpolymer melts. This method should enable studies of a wide range of fluctuation phenomena in multiblock/multi-species polymer blends and composites.

Theory of bi-molecular association dynamics in 2D for accurate model and experimental parameterization of binding rates

PubMed Central

Yogurtcu, Osman N.; Johnson, Margaret E.

2015-01-01

The dynamics of association between diffusing and reacting molecular species are routinely quantified using simple rate-equation kinetics that assume both well-mixed concentrations of species and a single rate constant for parameterizing the binding rate. In two-dimensions (2D), however, even when systems are well-mixed, the assumption of a single characteristic rate constant for describing association is not generally accurate, due to the properties of diffusional searching in dimensions d ≤ 2. Establishing rigorous bounds for discriminating between 2D reactive systems that will be accurately described by rate equations with a single rate constant, and those that will not, is critical for both modeling and experimentally parameterizing binding reactions restricted to surfaces such as cellular membranes. We show here that in regimes of intrinsic reaction rate (ka) and diffusion (D) parameters ka/D > 0.05, a single rate constant cannot be fit to the dynamics of concentrations of associating species independently of the initial conditions. Instead, a more sophisticated multi-parametric description than rate-equations is necessary to robustly characterize bimolecular reactions from experiment. Our quantitative bounds derive from our new analysis of 2D rate-behavior predicted from Smoluchowski theory. Using a recently developed single particle reaction-diffusion algorithm we extend here to 2D, we are able to test and validate the predictions of Smoluchowski theory and several other theories of reversible reaction dynamics in 2D for the first time. Finally, our results also mean that simulations of reactive systems in 2D using rate equations must be undertaken with caution when reactions have ka/D > 0.05, regardless of the simulation volume. We introduce here a simple formula for an adaptive concentration dependent rate constant for these chemical kinetics simulations which improves on existing formulas to better capture non-equilibrium reaction dynamics from dilute to dense systems. PMID:26328828

Solute transport with equilibrium aqueous complexation and either sorption or ion exchange: Simulation methodology and applications

USGS Publications Warehouse

Lewis, F.M.; Voss, C.I.; Rubin, J.

1987-01-01

Methodologies that account for specific types of chemical reactions in the simulation of solute transport can be developed so they are compatible with solution algorithms employed in existing transport codes. This enables the simulation of reactive transport in complex multidimensional flow regimes, and provides a means for existing codes to account for some of the fundamental chemical processes that occur among transported solutes. Two equilibrium-controlled reaction systems demonstrate a methodology for accommodating chemical interaction into models of solute transport. One system involves the sorption of a given chemical species, as well as two aqueous complexations in which the sorbing species is a participant. The other reaction set involves binary ion exchange coupled with aqueous complexation involving one of the exchanging species. The methodology accommodates these reaction systems through the addition of nonlinear terms to the transport equations for the sorbing species. Example simulation results show (1) the effect equilibrium chemical parameters have on the spatial distributions of concentration for complexing solutes; (2) that an interrelationship exists between mechanical dispersion and the various reaction processes; (3) that dispersive parameters of the porous media cannot be determined from reactive concentration distributions unless the reaction is accounted for or the influence of the reaction is negligible; (4) how the concentration of a chemical species may be significantly affected by its participation in an aqueous complex with a second species which also sorbs; and (5) that these coupled chemical processes influencing reactive transport can be demonstrated in two-dimensional flow regimes. ?? 1987.

Multi-regulatory network of ROS: the interconnection of ROS, PGC-1 alpha, and AMPK-SIRT1 during exercise.

PubMed

Thirupathi, Anand; de Souza, Claudio Teodoro

2017-11-01

Transcriptional factors are easily susceptible to any stimuli, including exercise. Exercise can significantly influence PGC-1 α and AMPK-SIRT1 pathway, as it is involved in the regulation of energy metabolism and mitochondrial biogenesis. Exercise is a major energy deprivation process by which many of transcription factors get tuned positively. However, how transcription factors help to boost the antioxidant defense system at cellular level is elusive. It is well known that physical exercise can induce reactive oxygen species, but how these reactive oxygen species can help to regulate multiple transcription factors during exercise is an important area to be discussed yet. This review mainly focuses on interconnecting role of PGC-1 α and AMPK-SIRT1 pathway during exercise and how these proteins are getting tuned by reactive oxygen species in exercise condition.

Brief analysis of Jiangsu grid security and stability based on multi-infeed DC index in power system

NASA Astrophysics Data System (ADS)

Zhang, Wenjia; Wang, Quanquan; Ge, Yi; Huang, Junhui; Chen, Zhengfang

2018-02-01

The impact of Multi-infeed HVDC has gradually increased to security and stability operating in Jiangsu power grid. In this paper, an appraisal method of Multi-infeed HVDC power grid security and stability is raised with Multi-Infeed Effective Short Circuit Ratio, Multi-Infeed Interaction Factor and Commutation Failure Immunity Index. These indices are adopted in security and stability simulating calculation of Jiangsu Multi-infeed HVDC system. The simulation results indicate that Jiangsu power grid is operating with a strong DC system. It has high level of power grid security and stability, and meet the safety running requirements. Jinpin-Suzhou DC system is located in the receiving end with huge capacity, which is easily leading to commutation failure of the transmission line. In order to resolve this problem, dynamic reactive power compensation can be applied in power grid near Jinpin-Suzhou DC system. Simulation result shows this method is feasible to commutation failure.

Exposure-time based modeling of nonlinear reactive transport in porous media subject to physical and geochemical heterogeneity.

PubMed

Sanz-Prat, Alicia; Lu, Chuanhe; Amos, Richard T; Finkel, Michael; Blowes, David W; Cirpka, Olaf A

2016-09-01

Transport of reactive solutes in groundwater is affected by physical and chemical heterogeneity of the porous medium, leading to complex spatio-temporal patterns of concentrations and reaction rates. For certain cases of bioreactive transport, it could be shown that the concentrations of reactive constituents in multi-dimensional domains are approximately aligned with isochrones, that is, lines of identical travel time, provided that the chemical properties of the matrix are uniform. We extend this concept to combined physical and chemical heterogeneity by additionally considering the time that a water parcel has been exposed to reactive materials, the so-called exposure time. We simulate bioreactive transport in a one-dimensional domain as function of time and exposure time, rather than space. Subsequently, we map the concentrations to multi-dimensional heterogeneous domains by means of the mean exposure time at each location in the multi-dimensional domain. Differences in travel and exposure time at a given location are accounted for as time difference. This approximation simplifies reactive-transport simulations significantly under conditions of steady-state flow when reactions are restricted to specific locations. It is not expected to be exact in realistic applications because the underlying assumption, such as neglecting transverse mixing altogether, may not hold. We quantify the error introduced by the approximation for the hypothetical case of a two-dimensional, binary aquifer made of highly-permeable, non-reactive and low-permeable, reactive materials releasing dissolved organic matter acting as electron donor for aerobic respiration and denitrification. The kinetically controlled reactions are catalyzed by two non-competitive bacteria populations, enabling microbial growth. Even though the initial biomass concentrations were uniform, the interplay between transport, non-uniform electron-donor supply, and bio-reactions led to distinct spatial patterns of the two types of biomass at late times. Results obtained by mapping the exposure-time based results to the two-dimensional domain are compared with simulations based on the two-dimensional, spatially explicit advection-dispersion-reaction equation. Once quasi-steady state has been reached, we find a good agreement in terms of the chemical-compound concentrations between the two approaches inside the reactive zones, whereas the exposure-time based model is not able to capture reactions occurring in the zones with zero electron-donor release. We conclude that exposure-time models provide good approximations of nonlinear bio-reactive transport when transverse mixing is not the overall controlling process and all reactions are essentially restricted to distinct reactive zones. Copyright © 2016 Elsevier B.V. All rights reserved.

Reactive multi-particle collision dynamics with reactive boundary conditions

NASA Astrophysics Data System (ADS)

Sayyidmousavi, Alireza; Rohlf, Katrin

2018-07-01

In the present study, an off-lattice particle-based method called the reactive multi-particle collision (RMPC) dynamics is extended to model reaction-diffusion systems with reactive boundary conditions in which the a priori diffusion coefficient of the particles needs to be maintained throughout the simulation. To this end, the authors have made use of the so-called bath particles whose purpose is only to ensure proper diffusion of the main particles in the system. In order to model partial adsorption by a reactive boundary in the RMPC, the probability of a particle being adsorbed, once it hits the boundary, is calculated by drawing an analogy between the RMPC and Brownian Dynamics. The main advantages of the RMPC compared to other molecular based methods are less computational cost as well as conservation of mass, energy and momentum in the collision and free streaming steps. The proposed approach is tested on three reaction-diffusion systems and very good agreement with the solutions to their corresponding partial differential equations is observed.

Preliminary Analysis of Pyrite Reactivity Under Venusian Temperature and Atmosphere

NASA Technical Reports Server (NTRS)

Radoman-Shaw, B. G.; Harvey, R. P.; Jacobson, N. S.; Costa, G. C. C.

2015-01-01

Measurements of Venus surface chemistry suggest a basaltic composition with a predominantly CO2 atmosphere. In order to understand the reactivity of certain possible mineral species on the surface, previous simulation chambers conduct experiments at 1 atmosphere with a simplified CO2 atmosphere. Following this procedure, pyrite (FeS2) samples are used to estimate the reactivity of sulfide minerals under a Venusian atmosphere and climate. Sulfurous gas species have been identified and quantified in the Venusian atmosphere, and sulfurous gas and mineral species are known to be created through volcanism, which is suggested to still occur on the surface of Venus. This experimentation is necessary to constrain reactions that could occur between the surface and atmosphere of Venus to understand terrestrial geology in a thick and hot greenhouse atmosphere. Quantifying this reaction can lead to approximations necessary for further experimentation in more complex environments such as those in the GEER chamber at Glenn Research Center that can simulate pressure along with temperature and a more inclusive and representative Venusian atmosphere.

Reactive Transport at the Pore Scale with Applications to the Dissolution of Carbonate Rocks for CO2 Sequestration Operations

NASA Astrophysics Data System (ADS)

Boek, E.; Gray, F.; Welch, N.; Shah, S.; Crawshaw, J.

2014-12-01

In CO2 sequestration operations, CO2 injected into a brine aquifer dissolves in the liquid to create an acidic solution. This may result in dissolution of the mineral grains in the porous medium. Experimentally, it is hard to investigate this process at the pore scale. Therefore we develop a new hybrid particle simulation algorithm to study the dissolution of solid objects in a laminar flow field, as encountered in porous media flow situations. First, we calculate the flow field using a multi-relaxation-time lattice Boltzmann (LB) algorithm implemented on GPUs, which demonstrates a very efficient use of the GPU device and a considerable performance increase over CPU calculations. Second, using a stochastic particle approach, we solve the advection-diffusion equation for a single reactive species and dissolve solid voxels according to our reaction model. To validate our simulation, we first calculate the dissolution of a solid sphere as a function of time under quiescent conditions. We compare with the analytical solution for this problem [1] and find good agreement. Then we consider the dissolution of a solid sphere in a laminar flow field and observe a significant change in the sphericity with time due to the coupled dissolution - flow process. Second, we calculate the dissolution of a cylinder in channel flow in direct comparison with corresponding dissolution experiments. We discuss the evolution of the shape and dissolution rate. Finally, we calculate the dissolution of carbonate rock samples at the pore scale in direct comparison with micro-CT experiments. This work builds on our recent research on calculation of multi-phase flow [2], [3] and hydrodynamic dispersion and molecular propagator distributions for solute transport in homogeneous and heterogeneous porous media using LB simulations [4]. It turns out that the hybrid simulation model is a suitable tool to study reactive flow processes at the pore scale. This is of great importance for CO2 storage and Enhanced Oil Recovery applications. References[1] Rice, R. G. and Do, D.D., Chem. Eng. Sci., 61, 775-778 (2006)[2] Boek, E.S. and Venturoli, M., Comp. and Maths with Appl. 59, 2305-2314 (2010)[3] Yang, J. and Boek, E.S., Comp. and Maths with Appl. 65, 882-890 (2013)[4] Yang, J. Crawshaw, J. and Boek, E.S., Water Resources Research 49, 8531-8538 (2013)

Development of a Regional Structured and Unstructured Grid Methodology for Chemically Reactive Turbulent Flows

NASA Astrophysics Data System (ADS)

Stefanski, Douglas Lawrence

A finite volume method for solving the Reynolds Averaged Navier-Stokes (RANS) equations on unstructured hybrid grids is presented. Capabilities for handling arbitrary mixtures of reactive gas species within the unstructured framework are developed. The modeling of turbulent effects is carried out via the 1998 Wilcox k -- o model. This unstructured solver is incorporated within VULCAN -- a multi-block structured grid code -- as part of a novel patching procedure in which non-matching interfaces between structured blocks are replaced by transitional unstructured grids. This approach provides a fully-conservative alternative to VULCAN's non-conservative patching methods for handling such interfaces. In addition, the further development of the standalone unstructured solver toward large-eddy simulation (LES) applications is also carried out. Dual time-stepping using a Crank-Nicholson formulation is added to recover time-accuracy, and modeling of sub-grid scale effects is incorporated to provide higher fidelity LES solutions for turbulent flows. A switch based on the work of Ducros, et al., is implemented to transition from a monotonicity-preserving flux scheme near shocks to a central-difference method in vorticity-dominated regions in order to better resolve small-scale turbulent structures. The updated unstructured solver is used to carry out large-eddy simulations of a supersonic constrained mixing layer.

Resolving the Multi-scale Behavior of Geochemical Weathering in the Critical Zone Using High Resolution Hydro-geochemical Models

NASA Astrophysics Data System (ADS)

Pandey, S.; Rajaram, H.

2015-12-01

This work investigates hydrologic and geochemical interactions in the Critical Zone (CZ) using high-resolution reactive transport modeling. Reactive transport models can be used to predict the response of geochemical weathering and solute fluxes in the CZ to changes in a dynamic environment, such as those pertaining to human activities and climate change in recent years. The scales of hydrology and geochemistry in the CZ range from days to eons in time and centimeters to kilometers in space. Here, we present results of a multi-dimensional, multi-scale hydro-geochemical model to investigate the role of subsurface heterogeneity on the formation of mineral weathering fronts in the CZ, which requires consideration of many of these spatio-temporal scales. The model is implemented using the reactive transport code PFLOTRAN, an open source subsurface flow and reactive transport code that utilizes parallelization over multiple processing nodes and provides a strong framework for simulating weathering in the CZ. The model is set up to simulate weathering dynamics in the mountainous catchments representative of the Colorado Front Range. Model parameters were constrained based on hydrologic, geochemical, and geophysical observations from the Boulder Creek Critical Zone Observatory (BcCZO). Simulations were performed in fractured rock systems and compared with systems of heterogeneous and homogeneous permeability fields. Tracer simulations revealed that the mean residence time of solutes was drastically accelerated as fracture density increased. In simulations that include mineral reactions, distinct signatures of transport limitations on weathering arose when discrete flow paths were included. This transport limitation was related to both advective and diffusive processes in the highly heterogeneous systems (i.e. fractured media and correlated random permeability fields with σlnk > 3). The well-known time-dependence of mineral weathering rates was found to be the most pronounced in the fractured systems, with a departure from the maximum system-averaged dissolution rate occurring after ~100 kyr followed by a gradual decrease in the reaction rate with time that persists beyond 104 kyr.

Using travel times to simulate multi-dimensional bioreactive transport in time-periodic flows.

PubMed

Sanz-Prat, Alicia; Lu, Chuanhe; Finkel, Michael; Cirpka, Olaf A

2016-04-01

In travel-time models, the spatially explicit description of reactive transport is replaced by associating reactive-species concentrations with the travel time or groundwater age at all locations. These models have been shown adequate for reactive transport in river-bank filtration under steady-state flow conditions. Dynamic hydrological conditions, however, can lead to fluctuations of infiltration velocities, putting the validity of travel-time models into question. In transient flow, the local travel-time distributions change with time. We show that a modified version of travel-time based reactive transport models is valid if only the magnitude of the velocity fluctuates, whereas its spatial orientation remains constant. We simulate nonlinear, one-dimensional, bioreactive transport involving oxygen, nitrate, dissolved organic carbon, aerobic and denitrifying bacteria, considering periodic fluctuations of velocity. These fluctuations make the bioreactive system pulsate: The aerobic zone decreases at times of low velocity and increases at those of high velocity. For the case of diurnal fluctuations, the biomass concentrations cannot follow the hydrological fluctuations and a transition zone containing both aerobic and obligatory denitrifying bacteria is established, whereas a clear separation of the two types of bacteria prevails in the case of seasonal velocity fluctuations. We map the 1-D results to a heterogeneous, two-dimensional domain by means of the mean groundwater age for steady-state flow in both domains. The mapped results are compared to simulation results of spatially explicit, two-dimensional, advective-dispersive-bioreactive transport subject to the same relative fluctuations of velocity as in the one-dimensional model. The agreement between the mapped 1-D and the explicit 2-D results is excellent. We conclude that travel-time models of nonlinear bioreactive transport are adequate in systems of time-periodic flow if the flow direction does not change. Copyright © 2016 Elsevier B.V. All rights reserved.

Reactive Transport Modeling of Induced Calcite Precipitation Reaction Fronts in Porous Media Using A Parallel, Fully Coupled, Fully Implicit Approach

NASA Astrophysics Data System (ADS)

Guo, L.; Huang, H.; Gaston, D.; Redden, G. D.; Fox, D. T.; Fujita, Y.

2010-12-01

Inducing mineral precipitation in the subsurface is one potential strategy for immobilizing trace metal and radionuclide contaminants. Generating mineral precipitates in situ can be achieved by manipulating chemical conditions, typically through injection or in situ generation of reactants. How these reactants transport, mix and react within the medium controls the spatial distribution and composition of the resulting mineral phases. Multiple processes, including fluid flow, dispersive/diffusive transport of reactants, biogeochemical reactions and changes in porosity-permeability, are tightly coupled over a number of scales. Numerical modeling can be used to investigate the nonlinear coupling effects of these processes which are quite challenging to explore experimentally. Many subsurface reactive transport simulators employ a de-coupled or operator-splitting approach where transport equations and batch chemistry reactions are solved sequentially. However, such an approach has limited applicability for biogeochemical systems with fast kinetics and strong coupling between chemical reactions and medium properties. A massively parallel, fully coupled, fully implicit Reactive Transport simulator (referred to as “RAT”) based on a parallel multi-physics object-oriented simulation framework (MOOSE) has been developed at the Idaho National Laboratory. Within this simulator, systems of transport and reaction equations can be solved simultaneously in a fully coupled, fully implicit manner using the Jacobian Free Newton-Krylov (JFNK) method with additional advanced computing capabilities such as (1) physics-based preconditioning for solution convergence acceleration, (2) massively parallel computing and scalability, and (3) adaptive mesh refinements for 2D and 3D structured and unstructured mesh. The simulator was first tested against analytical solutions, then applied to simulating induced calcium carbonate mineral precipitation in 1D columns and 2D flow cells as analogs to homogeneous and heterogeneous porous media, respectively. In 1D columns, calcium carbonate mineral precipitation was driven by urea hydrolysis catalyzed by urease enzyme, and in 2D flow cells, calcium carbonate mineral forming reactants were injected sequentially, forming migrating reaction fronts that are typically highly nonuniform. The RAT simulation results for the spatial and temporal distributions of precipitates, reaction rates and major species in the system, and also for changes in porosity and permeability, were compared to both laboratory experimental data and computational results obtained using other reactive transport simulators. The comparisons demonstrate the ability of RAT to simulate complex nonlinear systems and the advantages of fully coupled approaches, over de-coupled methods, for accurate simulation of complex, dynamic processes such as engineered mineral precipitation in subsurface environments.

Fluid nonlinear frequency shift of nonlinear ion acoustic waves in multi-ion species plasmas in the small wave number region

NASA Astrophysics Data System (ADS)

Feng, Q. S.; Xiao, C. Z.; Wang, Q.; Zheng, C. Y.; Liu, Z. J.; Cao, L. H.; He, X. T.

2016-08-01

The properties of the nonlinear frequency shift (NFS), especially the fluid NFS from the harmonic generation of the ion-acoustic wave (IAW) in multi-ion species plasmas, have been researched by Vlasov simulation. Pictures of the nonlinear frequency shift from harmonic generation and particle trapping are shown to explain the mechanism of NFS qualitatively. The theoretical model of the fluid NFS from harmonic generation in multi-ion species plasmas is given, and the results of Vlasov simulation are consistent with the theoretical result of multi-ion species plasmas. When the wave number k λD e is small, such as k λD e=0.1 , the fluid NFS dominates in the total NFS and will reach as large as nearly 15 % when the wave amplitude |e ϕ / Te|˜0.1 , which indicates that in the condition of small k λD e , the fluid NFS dominates in the saturation of stimulated Brillouin scattering, especially when the nonlinear IAW amplitude is large.

Fluid nonlinear frequency shift of nonlinear ion acoustic waves in multi-ion species plasmas in the small wave number region.

PubMed

Feng, Q S; Xiao, C Z; Wang, Q; Zheng, C Y; Liu, Z J; Cao, L H; He, X T

2016-08-01

The properties of the nonlinear frequency shift (NFS), especially the fluid NFS from the harmonic generation of the ion-acoustic wave (IAW) in multi-ion species plasmas, have been researched by Vlasov simulation. Pictures of the nonlinear frequency shift from harmonic generation and particle trapping are shown to explain the mechanism of NFS qualitatively. The theoretical model of the fluid NFS from harmonic generation in multi-ion species plasmas is given, and the results of Vlasov simulation are consistent with the theoretical result of multi-ion species plasmas. When the wave number kλ_{De} is small, such as kλ_{De}=0.1, the fluid NFS dominates in the total NFS and will reach as large as nearly 15% when the wave amplitude |eϕ/T_{e}|∼0.1, which indicates that in the condition of small kλ_{De}, the fluid NFS dominates in the saturation of stimulated Brillouin scattering, especially when the nonlinear IAW amplitude is large.

Numerical investigation of coupled density-driven flow and hydrogeochemical processes below playas

NASA Astrophysics Data System (ADS)

Hamann, Enrico; Post, Vincent; Kohfahl, Claus; Prommer, Henning; Simmons, Craig T.

2015-11-01

Numerical modeling approaches with varying complexity were explored to investigate coupled groundwater flow and geochemical processes in saline basins. Long-term model simulations of a playa system gain insights into the complex feedback mechanisms between density-driven flow and the spatiotemporal patterns of precipitating evaporites and evolving brines. Using a reactive multicomponent transport model approach, the simulations reproduced, for the first time in a numerical study, the evaporite precipitation sequences frequently observed in saline basins ("bull's eyes"). Playa-specific flow, evapoconcentration, and chemical divides were found to be the primary controls for the location of evaporites formed, and the resulting brine chemistry. Comparative simulations with the computationally far less demanding surrogate single-species transport models showed that these were still able to replicate the major flow patterns obtained by the more complex reactive transport simulations. However, the simulated degree of salinization was clearly lower than in reactive multicomponent transport simulations. For example, in the late stages of the simulations, when the brine becomes halite-saturated, the nonreactive simulation overestimated the solute mass by almost 20%. The simulations highlight the importance of the consideration of reactive transport processes for understanding and quantifying geochemical patterns, concentrations of individual dissolved solutes, and evaporite evolution.

Dissolution Front Instabilities in Reacting Porous Media

NASA Astrophysics Data System (ADS)

Raoof, Amir; Spiers, Chris; Hassanizadeh, Majid

2013-04-01

The main objective of this research is to gain a better understanding of the relation between regime of reaction and dissolution front instability, leading to formation of channels or wormholes. Potential applications are geological sequestration of CO2 and acid-gas injection during enhanced oil recovery. The microscopic pore space is modeled using a multi-directional pore network, allowing for a distribution of pore coordination number, together with distribution of pore sizes. In order to simulate transport of multi-component chemical species, mass balance equations are solved within each element of the network (i.e., pore body and pore throat). We have considered advective and diffusive transport processes within the pore spaces together with multi-component chemical reactions, including both equilibrium and kinetic reactions. Using dimensionless scaling groups (such as Damköhler number and Péclet-Damköhler number) we characterized the dissolution front behavior, and by averaging over the network domain we calculated the evolution of porosity and permeability as well as flux-averaged concentration breakthrough curves. We obtain constitutive relations linking porosity and permeability, under conditions relevant to geological storage of CO2. Effect of distribution of reactive minerals is also evaluated and regime of reaction is shown to play a key role.

Molecular dynamics simulation of sodium aluminosilicate glass structures and glass surface-water reactions using the reactive force field (ReaxFF)

NASA Astrophysics Data System (ADS)

Dongol, R.; Wang, L.; Cormack, A. N.; Sundaram, S. K.

2018-05-01

Reactive potentials are increasingly used to study the properties of glasses and glass water reactions in a reactive molecular dynamics (MD) framework. In this study, we have simulated a ternary sodium aluminosilicate glass and investigated the initial stages of the glass surface-water reactions at 300 K using reactive force field (ReaxFF). On comparison of the simulated glass structures generated using ReaxFF and classical Buckingham potentials, our results show that the atomic density profiles calculated for the surface glass structures indicate a bond-angle distribution dependency. The atomic density profiles also show higher concentrations of non-bridging oxygens (NBOs) and sodium ions at the glass surface. Additionally, we present our results of formation of silanol species and the diffusion of water molecules at the glass surface using ReaxFF.

Analysis of reactive bromine production and ozone depletion in the Arctic boundary layer using 3-D simulations with GEM-AQ: inference from synoptic-scale patterns

NASA Astrophysics Data System (ADS)

Toyota, K.; McConnell, J. C.; Lupu, A.; Neary, L.; McLinden, C. A.; Richter, A.; Kwok, R.; Semeniuk, K.; Kaminski, J. W.; Gong, S.-L.; Jarosz, J.; Chipperfield, M. P.; Sioris, C. E.

2011-04-01

Episodes of high bromine levels and surface ozone depletion in the springtime Arctic are simulated by an online air-quality model, GEM-AQ, with gas-phase and heterogeneous reactions of inorganic bromine species and a simple scheme of air-snowpack chemical interactions implemented for this study. Snowpack on sea ice is assumed to be the only source of bromine to the atmosphere and to be capable of converting relatively stable bromine species to photolabile Br2 via air-snowpack interactions. A set of sensitivity model runs are performed for April 2001 at a horizontal resolution of approximately 100 km×100 km in the Arctic, to provide insights into the effects of temperature and the age (first-year, FY, versus multi-year, MY) of sea ice on the release of reactive bromine to the atmosphere. The model simulations capture much of the temporal variations in surface ozone mixing ratios as observed at stations in the high Arctic and the synoptic-scale evolution of areas with enhanced BrO column amount ("BrO clouds") as estimated from satellite observations. The simulated "BrO clouds" are in modestly better agreement with the satellite measurements when the FY sea ice is assumed to be more efficient at releasing reactive bromine to the atmosphere than on the MY sea ice. Surface ozone data from coastal stations used in this study are not sufficient to evaluate unambiguously the difference between the FY sea ice and the MY sea ice as a source of bromine. The results strongly suggest that reactive bromine is released ubiquitously from the snow on the sea ice during the Arctic spring while the timing and location of the bromine release are largely controlled by meteorological factors. It appears that a rapid advection and an enhanced turbulent diffusion associated with strong boundary-layer winds drive transport and dispersion of ozone to the near-surface air over the sea ice, increasing the oxidation rate of bromide (Br-) in the surface snow. Also, if indeed the surface snowpack does supply most of the reactive bromine in the Arctic boundary layer, it appears to be capable of releasing reactive bromine at temperatures as high as -10 °C, particularly on the sea ice in the central and eastern Arctic Ocean. Dynamically-induced BrO column variability in the lowermost stratosphere appears to interfere with the use of satellite BrO column measurements for interpreting BrO variability in the lower troposphere but probably not to the extent of totally obscuring "BrO clouds" that originate from the surface snow/ice source of bromine in the high Arctic. A budget analysis of the simulated air-surface exchange of bromine compounds suggests that a "bromine explosion" occurs in the interstitial air of the snowpack and/or is accelerated by heterogeneous reactions on the surface of wind-blown snow in ambient air, both of which are not represented explicitly in our simple model but could have been approximated by a parameter adjustment for the yield of Br2 from the trigger.

A single-phase multi-level D-STATCOM inverter using modular multi-level converter (MMC) topology for renewable energy sources

NASA Astrophysics Data System (ADS)

Sotoodeh, Pedram

This dissertation presents the design of a novel multi-level inverter with FACTS capability for small to mid-size (10-20kW) permanent-magnet wind installations using modular multi-level converter (MMC) topology. The aim of the work is to design a new type of inverter with D-STATCOM option to provide utilities with more control on active and reactive power transfer of distribution lines. The inverter is placed between the renewable energy source, specifically a wind turbine, and the distribution grid in order to fix the power factor of the grid at a target value, regardless of wind speed, by regulating active and reactive power required by the grid. The inverter is capable of controlling active and reactive power by controlling the phase angle and modulation index, respectively. The unique contribution of the proposed work is to combine the two concepts of inverter and D-STATCOM using a novel voltage source converter (VSC) multi-level topology in a single unit without additional cost. Simulations of the proposed inverter, with 5 and 11 levels, have been conducted in MATLAB/Simulink for two systems including 20 kW/kVAR and 250 W/VAR. To validate the simulation results, a scaled version (250 kW/kVAR) of the proposed inverter with 5 and 11 levels has been built and tested in the laboratory. Experimental results show that the reduced-scale 5- and 11-level inverter is able to fix PF of the grid as well as being compatible with IEEE standards. Furthermore, total cost of the prototype models, which is one of the major objectives of this research, is comparable with market prices.

Large-Scale Reactive Atomistic Simulation of Shock-induced Initiation Processes in Energetic Materials

NASA Astrophysics Data System (ADS)

Thompson, Aidan

2013-06-01

Initiation in energetic materials is fundamentally dependent on the interaction between a host of complex chemical and mechanical processes, occurring on scales ranging from intramolecular vibrations through molecular crystal plasticity up to hydrodynamic phenomena at the mesoscale. A variety of methods (e.g. quantum electronic structure methods (QM), non-reactive classical molecular dynamics (MD), mesoscopic continuum mechanics) exist to study processes occurring on each of these scales in isolation, but cannot describe how these processes interact with each other. In contrast, the ReaxFF reactive force field, implemented in the LAMMPS parallel MD code, allows us to routinely perform multimillion-atom reactive MD simulations of shock-induced initiation in a variety of energetic materials. This is done either by explicitly driving a shock-wave through the structure (NEMD) or by imposing thermodynamic constraints on the collective dynamics of the simulation cell e.g. using the Multiscale Shock Technique (MSST). These MD simulations allow us to directly observe how energy is transferred from the shockwave into other processes, including intramolecular vibrational modes, plastic deformation of the crystal, and hydrodynamic jetting at interfaces. These processes in turn cause thermal excitation of chemical bonds leading to initial chemical reactions, and ultimately to exothermic formation of product species. Results will be presented on the application of this approach to several important energetic materials, including pentaerythritol tetranitrate (PETN) and ammonium nitrate/fuel oil (ANFO). In both cases, we validate the ReaxFF parameterizations against QM and experimental data. For PETN, we observe initiation occurring via different chemical pathways, depending on the shock direction. For PETN containing spherical voids, we observe enhanced sensitivity due to jetting, void collapse, and hotspot formation, with sensitivity increasing with void size. For ANFO, we examine the effect of reaction rates on shock direction, fuel oil fraction, and crystal/fuel oil/void microstructural arrangement. Sandia National Laboratories is a multi-program laboratory managed and operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Corporation, for the U.S. Dept. of Energy's National Nuclear Security Admin. under contract DEAC0494AL85000.

Multiphase composition changes and reactive oxygen species formation during limonene oxidation in the new Cambridge Atmospheric Simulation Chamber (CASC)

NASA Astrophysics Data System (ADS)

Gallimore, Peter J.; Mahon, Brendan M.; Wragg, Francis P. H.; Fuller, Stephen J.; Giorio, Chiara; Kourtchev, Ivan; Kalberer, Markus

2017-08-01

The chemical composition of organic aerosols influences their impacts on human health and the climate system. Aerosol formation from gas-to-particle conversion and in-particle reaction was studied for the oxidation of limonene in a new facility, the Cambridge Atmospheric Simulation Chamber (CASC). Health-relevant oxidising organic species produced during secondary organic aerosol (SOA) formation were quantified in real time using an Online Particle-bound Reactive Oxygen Species Instrument (OPROSI). Two categories of reactive oxygen species (ROS) were identified based on time series analysis: a short-lived component produced during precursor ozonolysis with a lifetime of the order of minutes, and a stable component that was long-lived on the experiment timescale (˜ 4 h). Individual organic species were monitored continuously over this time using Extractive Electrospray Ionisation (EESI) Mass Spectrometry (MS) for the particle phase and Proton Transfer Reaction (PTR) MS for the gas phase. Many first-generation oxidation products are unsaturated, and we observed multiphase aging via further ozonolysis reactions. Volatile products such as C9H14O (limonaketone) and C10H16O2 (limonaldehyde) were observed in the gas phase early in the experiment, before reacting again with ozone. Loss of C10H16O4 (7-hydroxy limononic acid) from the particle phase was surprisingly slow. A combination of reduced C = C reactivity and viscous particle formation (relative to other SOA systems) may explain this, and both scenarios were tested in the Pretty Good Aerosol Model (PG-AM). A range of characterisation measurements were also carried out to benchmark the chamber against existing facilities. This work demonstrates the utility of CASC, particularly for understanding the reactivity and health-relevant properties of organic aerosols using novel, highly time-resolved techniques.

Multi-fluid Modeling of Magnetosonic Wave Propagation in the Solar Chromosphere: Effects of Impact Ionization and Radiative Recombination

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

Maneva, Yana G.; Laguna, Alejandro Alvarez; Poedts, Stefaan

2017-02-20

In order to study chromospheric magnetosonic wave propagation including, for the first time, the effects of ion–neutral interactions in the partially ionized solar chromosphere, we have developed a new multi-fluid computational model accounting for ionization and recombination reactions in gravitationally stratified magnetized collisional media. The two-fluid model used in our 2D numerical simulations treats neutrals as a separate fluid and considers charged species (electrons and ions) within the resistive MHD approach with Coulomb collisions and anisotropic heat flux determined by Braginskiis transport coefficients. The electromagnetic fields are evolved according to the full Maxwell equations and the solenoidality of the magneticmore » field is enforced with a hyperbolic divergence-cleaning scheme. The initial density and temperature profiles are similar to VAL III chromospheric model in which dynamical, thermal, and chemical equilibrium are considered to ensure comparison to existing MHD models and avoid artificial numerical heating. In this initial setup we include simple homogeneous flux tube magnetic field configuration and an external photospheric velocity driver to simulate the propagation of MHD waves in the partially ionized reactive chromosphere. In particular, we investigate the loss of chemical equilibrium and the plasma heating related to the steepening of fast magnetosonic wave fronts in the gravitationally stratified medium.« less

Kinetic theory and Vlasov simulation of nonlinear ion-acoustic waves in multi-ion species plasmas.

PubMed

Chapman, T; Berger, R L; Brunner, S; Williams, E A

2013-05-10

The theory of damping and nonlinear frequency shifts from particles resonant with ion-acoustic waves (IAWs) is presented for multi-ion species plasma and compared to driven wave Vlasov simulations. Two distinct IAW modes may be supported in multi-ion species plasmas, broadly classified as fast and slow by their phase velocity relative to the constituent ion thermal velocities. In current fusion-relevant long pulse experiments, the ion to electron temperature ratio, T(i)/T(e), is expected to reach a level such that the least damped and thus more readily driven mode is the slow mode, with both linear and nonlinear properties that are shown to differ significantly from the fast mode. The lighter ion species of the slow mode is found to make no significant contribution to the IAW frequency shift despite typically being the dominant contributor to the Landau damping.

Ion-kinetic simulations of D- 3He gas-filled inertial confinement fusion target implosions with moderate to large Knudsen number

DOE PAGES

Larroche, O.; Rinderknecht, H. G.; Rosenberg, M. J.; ...

2016-01-06

Experiments designed to investigate the transition to non-collisional behavior in D 3He-gas inertial confinement fusion target implosions display increasingly large discrepancies with respect to simulations by standard hydrodynamics codes as the expected ion mean-free-paths λ c increase with respect to the target radius R (i.e., when the Knudsen number N K = λ c/R grows). To take properly into account large N K's, multi-ion-species Vlasov-Fokker-Planck computations of the inner gas in the capsules have been performed, for two different values of N K, one moderate and one large. The results, including nuclear yield, reactivity-weighted ion temperatures, nuclear emissivities, and surfacemore » brightness, have been compared with the experimental data and with the results of hydrodynamical simulations, some of which include an ad hocmodeling of kinetic effects. The experimental results are quite accurately rendered by the kinetic calculations in the smaller-N K case, much better than by the hydrodynamical calculations. The kinetic effects at play in this case are thus correctly understood. However, in the higher-N K case, the agreement is much worse. Furthermore, the remaining discrepancies are shown to arise from kinetic phenomena (e.g., inter-species diffusion) occurring at the gas-pusher interface, which should be investigated in the future work.« less

Numerical study of the influence of surface reaction probabilities on reactive species in an rf atmospheric pressure plasma containing humidity

NASA Astrophysics Data System (ADS)

Schröter, Sandra; Gibson, Andrew R.; Kushner, Mark J.; Gans, Timo; O'Connell, Deborah

2018-01-01

The quantification and control of reactive species (RS) in atmospheric pressure plasmas (APPs) is of great interest for their technological applications, in particular in biomedicine. Of key importance in simulating the densities of these species are fundamental data on their production and destruction. In particular, data concerning particle-surface reaction probabilities in APPs are scarce, with most of these probabilities measured in low-pressure systems. In this work, the role of surface reaction probabilities, γ, of reactive neutral species (H, O and OH) on neutral particle densities in a He-H2O radio-frequency micro APP jet (COST-μ APPJ) are investigated using a global model. It is found that the choice of γ, particularly for low-mass species having large diffusivities, such as H, can change computed species densities significantly. The importance of γ even at elevated pressures offers potential for tailoring the RS composition of atmospheric pressure microplasmas by choosing different wall materials or plasma geometries.

Reactive transport modeling of stable carbon isotope fractionation in a multi-phase multi-component system during carbon sequestration

DOE PAGES

Zhang, Shuo; DePaolo, Donald J.; Zheng, Liange; ...

2014-12-31

Carbon stable isotopes can be used in characterization and monitoring of CO 2 sequestration sites to track the migration of the CO 2 plume and identify leakage sources, and to evaluate the chemical reactions that take place in the CO 2-water-rock system. However, there are few tools available to incorporate stable isotope information into flow and transport codes used for CO 2 sequestration problems. We present a numerical tool for modeling the transport of stable carbon isotopes in multiphase reactive systems relevant to geologic carbon sequestration. The code is an extension of the reactive transport code TOUGHREACT. The transport modulemore » of TOUGHREACT was modified to include separate isotopic species of CO 2 gas and dissolved inorganic carbon (CO 2, CO 3 2-, HCO 3 -,…). Any process of transport or reaction influencing a given carbon species also influences its isotopic ratio. Isotopic fractionation is thus fully integrated within the dynamic system. The chemical module and database have been expanded to include isotopic exchange and fractionation between the carbon species in both gas and aqueous phases. The performance of the code is verified by modeling ideal systems and comparing with theoretical results. Efforts are also made to fit field data from the Pembina CO 2 injection project in Canada. We show that the exchange of carbon isotopes between dissolved and gaseous carbon species combined with fluid flow and transport, produce isotopic effects that are significantly different from simple two-component mixing. These effects are important for understanding the isotopic variations observed in field demonstrations.« less

Simulation of reactive polydisperse sprays strongly coupled to unsteady flows in solid rocket motors: Efficient strategy using Eulerian Multi-Fluid methods

NASA Astrophysics Data System (ADS)

Sibra, A.; Dupays, J.; Murrone, A.; Laurent, F.; Massot, M.

2017-06-01

In this paper, we tackle the issue of the accurate simulation of evaporating and reactive polydisperse sprays strongly coupled to unsteady gaseous flows. In solid propulsion, aluminum particles are included in the propellant to improve the global performances but the distributed combustion of these droplets in the chamber is suspected to be a driving mechanism of hydrodynamic and acoustic instabilities. The faithful prediction of two-phase interactions is a determining step for future solid rocket motor optimization. When looking at saving computational ressources as required for industrial applications, performing reliable simulations of two-phase flow instabilities appears as a challenge for both modeling and scientific computing. The size polydispersity, which conditions the droplet dynamics, is a key parameter that has to be accounted for. For moderately dense sprays, a kinetic approach based on a statistical point of view is particularly appropriate. The spray is described by a number density function and its evolution follows a Williams-Boltzmann transport equation. To solve it, we use Eulerian Multi-Fluid methods, based on a continuous discretization of the size phase space into sections, which offer an accurate treatment of the polydispersion. The objective of this paper is threefold: first to derive a new Two Size Moment Multi-Fluid model that is able to tackle evaporating polydisperse sprays at low cost while accurately describing the main driving mechanisms, second to develop a dedicated evaporation scheme to treat simultaneously mass, moment and energy exchanges with the gas and between the sections. Finally, to design a time splitting operator strategy respecting both reactive two-phase flow physics and cost/accuracy ratio required for industrial computations. Using a research code, we provide 0D validations of the new scheme before assessing the splitting technique's ability on a reference two-phase flow acoustic case. Implemented in the industrial-oriented CEDRE code, all developments allow to simulate realistic solid rocket motor configurations featuring the first polydisperse reactive computations with a fully Eulerian method.

Multi-scale modeling of multi-component reactive transport in geothermal aquifers

NASA Astrophysics Data System (ADS)

Nick, Hamidreza M.; Raoof, Amir; Wolf, Karl-Heinz; Bruhn, David

2014-05-01

In deep geothermal systems heat and chemical stresses can cause physical alterations, which may have a significant effect on flow and reaction rates. As a consequence it will lead to changes in permeability and porosity of the formations due to mineral precipitation and dissolution. Large-scale modeling of reactive transport in such systems is still challenging. A large area of uncertainty is the way in which the pore-scale information controlling the flow and reaction will behave at a larger scale. A possible choice is to use constitutive relationships relating, for example the permeability and porosity evolutions to the change in the pore geometry. While determining such relationships through laboratory experiments may be limited, pore-network modeling provides an alternative solution. In this work, we introduce a new workflow in which a hybrid Finite-Element Finite-Volume method [1,2] and a pore network modeling approach [3] are employed. Using the pore-scale model, relevant constitutive relations are developed. These relations are then embedded in the continuum-scale model. This approach enables us to study non-isothermal reactive transport in porous media while accounting for micro-scale features under realistic conditions. The performance and applicability of the proposed model is explored for different flow and reaction regimes. References: 1. Matthäi, S.K., et al.: Simulation of solute transport through fractured rock: a higher-order accurate finite-element finite-volume method permitting large time steps. Transport in porous media 83.2 (2010): 289-318. 2. Nick, H.M., et al.: Reactive dispersive contaminant transport in coastal aquifers: Numerical simulation of a reactive Henry problem. Journal of contaminant hydrology 145 (2012), 90-104. 3. Raoof A., et al.: PoreFlow: A Complex pore-network model for simulation of reactive transport in variably saturated porous media, Computers & Geosciences, 61, (2013), 160-174.

Atomistic Simulations of Chemical Reactivity of TATB Under Thermal and Shock Conditions

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

Manaa, M R; Reed, E J; Fried, L E

2009-09-23

The study of chemical transformations that occur at the reactive shock front of energetic materials provides important information for the development of predictive models at the grain-and continuum scales. A major shortcoming of current high explosives models is the lack of chemical kinetics data of the reacting explosive in the high pressure and temperature regimes. In the absence of experimental data, long-time scale atomistic molecular dynamics simulations with reactive chemistry become a viable recourse to provide an insight into the decomposition mechanism of explosives, and to obtain effective reaction rate laws. These rates can then be incorporated into thermo-chemical-hydro codesmore » (such as Cheetah linked to ALE3D) for accurate description of the grain and macro scales dynamics of reacting explosives. In this talk, I will present quantum simulations of 1,3,5-triamino-2,4,6-trinitrobenzene (TATB) crystals under thermal decomposition (high density and temperature) and shock compression conditions. This is the first time that condensed phase quantum methods have been used to study the chemistry of insensitive high explosives. We used the quantum-based, self-consistent charge density functional tight binding method (SCC{_}DFTB) to calculate the interatomic forces for reliable predictions of chemical reactions, and to examine electronic properties at detonation conditions for a relatively long time-scale on the order of several hundreds of picoseconds. For thermal decomposition of TATB, we conducted constant volume-temperature simulations, ranging from 0.35 to 2 nanoseconds, at {rho} = 2.87 g/cm{sup 3} at T = 3500, 3000, 2500, and 1500 K, and {rho} = 2.9 g/cm{sup 3} and 2.72 g/cm{sup 3}, at T = 3000 K. We also simulated crystal TATB's reactivity under steady overdriven shock compression using the multi-scale shock technique. We conducted shock simulations with specified shock speeds of 8, 9, and 10 km/s for up to 0.43 ns duration, enabling us to track the reactivity of TATB well into the formation of several stable gas products, such as H{sub 2}O, N{sub 2}, and CO{sub 2}. Although complex chemical transformations are occurring continuously in the dynamical, high temperature, reactive environment of our simulations, a simple overall scheme for the decomposition of TATB emerges: Water is the earliest decomposition products to form, followed by a polymerization (or condensation) process in which several TATB remaining fragments are joined together, initiating the early step in the formation of high-nitrogen clusters, along with stable products such as N{sub 2} and CO{sub 2}. Remarkably, these clusters with high concentration of carbon and nitrogen (and little oxygen) remain dynamically stable for the remaining period of the simulations. Our simulations, thus, reveal a hitherto unidentified region of high concentrations of nitrogen-rich heterocyclic clusters in reacting TATB, whose persistence impede further reactivity towards final products of fluid N{sub 2} and solid carbon. These simulations also predict significant populations of charged species such as NCO{sup -}, H{sup +}, OH{sup -}, H{sub 3}O{sup +}, and O{sup -2}, the first such observation in a reacting explosive. Finally, A reduced four steps, global reaction mechanism with Arrhenius kinetic rates for the decomposition of TATB, along with comparative Cheetah decomposition kinetics at various temperatures has been constructed and will be discussed.« less

Multiscale Modeling of Multi-decadal Trends in Ozone and Precursor Species Across the Northern Hemisphere and the United States

EPA Science Inventory

Multi-decadal model calculations for the 1990-2010 period are performed with the coupled WRF-CMAQ modeling system over a domain encompassing the northern hemisphere and a nested domain over the continental U.S. Simulated trends in ozone and precursor species concentrations acros...

Unravelling Darwin's entangled bank: architecture and robustness of mutualistic networks with multiple interaction types.

PubMed

Dáttilo, Wesley; Lara-Rodríguez, Nubia; Jordano, Pedro; Guimarães, Paulo R; Thompson, John N; Marquis, Robert J; Medeiros, Lucas P; Ortiz-Pulido, Raul; Marcos-García, Maria A; Rico-Gray, Victor

2016-11-30

Trying to unravel Darwin's entangled bank further, we describe the architecture of a network involving multiple forms of mutualism (pollination by animals, seed dispersal by birds and plant protection by ants) and evaluate whether this multi-network shows evidence of a structure that promotes robustness. We found that species differed strongly in their contributions to the organization of the multi-interaction network, and that only a few species contributed to the structuring of these patterns. Moreover, we observed that the multi-interaction networks did not enhance community robustness compared with each of the three independent mutualistic networks when analysed across a range of simulated scenarios of species extinction. By simulating the removal of highly interacting species, we observed that, overall, these species enhance network nestedness and robustness, but decrease modularity. We discuss how the organization of interlinked mutualistic networks may be essential for the maintenance of ecological communities, and therefore the long-term ecological and evolutionary dynamics of interactive, species-rich communities. We suggest that conserving these keystone mutualists and their interactions is crucial to the persistence of species-rich mutualistic assemblages, mainly because they support other species and shape the network organization. © 2016 The Author(s).

Phase I and phase II reductive metabolism simulation of nitro aromatic xenobiotics with electrochemistry coupled with high resolution mass spectrometry.

PubMed

Bussy, Ugo; Chung-Davidson, Yu-Wen; Li, Ke; Li, Weiming

2014-11-01

Electrochemistry combined with (liquid chromatography) high resolution mass spectrometry was used to simulate the general reductive metabolism of three biologically important nitro aromatic molecules: 3-trifluoromethyl-4-nitrophenol (TFM), niclosamide, and nilutamide. TFM is a pesticide used in the Laurential Great Lakes while niclosamide and nilutamide are used in cancer therapy. At first, a flow-through electrochemical cell was directly connected to a high resolution mass spectrometer to evaluate the ability of electrochemistry to produce the main reduction metabolites of nitro aromatic, nitroso, hydroxylamine, and amine functional groups. Electrochemical experiments were then carried out at a constant potential of -2.5 V before analysis of the reduction products by LC-HRMS, which confirmed the presence of the nitroso, hydroxylamine, and amine species as well as dimers. Dimer identification illustrates the reactivity of the nitroso species with amine and hydroxylamine species. To investigate xenobiotic metabolism, the reactivity of nitroso species to biomolecules was also examined. Binding of the nitroso metabolite to glutathione was demonstrated by the observation of adducts by LC-ESI(+)-HRMS and the characteristics of their MSMS fragmentation. In conclusion, electrochemistry produces the main reductive metabolites of nitro aromatics and supports the observation of nitroso reactivity through dimer or glutathione adduct formation.

Towards Time Automata and Multi-Agent Systems

NASA Technical Reports Server (NTRS)

Hutzler, G.; Klaudel, H.; Wang, D. Y.

2004-01-01

The design of reactive systems must comply with logical correctness (the system does what it is supposed to do) and timeliness (the system has to satisfy a set of temporal constraints) criteria. In this paper, we propose a global approach for the design of adaptive reactive systems, i.e., systems that dynamically adapt their architecture depending on the context. We use the timed automata formalism for the design of the agents' behavior. This allows evaluating beforehand the properties of the system (regarding logical correctness and timeliness), thanks to model-checking and simulation techniques. This model is enhanced with tools that we developed for the automatic generation of code, allowing to produce very quickly a running multi-agent prototype satisfying the properties of the model.

Benchmarking a Visual-Basic based multi-component one-dimensional reactive transport modeling tool

NASA Astrophysics Data System (ADS)

Torlapati, Jagadish; Prabhakar Clement, T.

2013-01-01

We present the details of a comprehensive numerical modeling tool, RT1D, which can be used for simulating biochemical and geochemical reactive transport problems. The code can be run within the standard Microsoft EXCEL Visual Basic platform, and it does not require any additional software tools. The code can be easily adapted by others for simulating different types of laboratory-scale reactive transport experiments. We illustrate the capabilities of the tool by solving five benchmark problems with varying levels of reaction complexity. These literature-derived benchmarks are used to highlight the versatility of the code for solving a variety of practical reactive transport problems. The benchmarks are described in detail to provide a comprehensive database, which can be used by model developers to test other numerical codes. The VBA code presented in the study is a practical tool that can be used by laboratory researchers for analyzing both batch and column datasets within an EXCEL platform.

Multi-Scale Simulation of Interfacial Phenomena and Nano-Particle Placement in Polymer Matrix Composites

DTIC Science & Technology

2012-08-01

Molecular Dynamics Simulations Coarse-Grain Particle Dynamics Simulations Local structure; Force field parameterization Extended structure...K) C8H18 C12H26 C16H34 Adhesive forces can cause local density gradients and defects " Pronounced layering of polymer near interfaces...reactive end groups (CnH2n+1S) on Cu Gap SubPc on C60 Pentacene on a-SiO2 Cyclopentene on Au Crystalline CuPc on Al Polyimide on Si

Reactive atomistic simulations of shock-induced initiation processes in mixtures of ammonium nitrate and fuel oil

NASA Astrophysics Data System (ADS)

Thompson, Aidan P.; Shan, Tzu-Ray

2014-05-01

Ammonium nitrate mixed with fuel oil (ANFO) is a commonly used blasting agent. In this paper we investigated the shock properties of pure ammonium nitrate (AN) and two different mixtures of ammonium nitrate and n-dodecane by characterizing their Hugoniot states. We simulated shock compression of pure AN and ANFO mixtures using the Multi-scale Shock Technique, and observed differences in chemical reaction. We also performed a large-scale explicit sub-threshold shock of AN crystal with a 10 nm void filled with 4.4 wt% of n-dodecane. We observed the formation of hotspots and enhanced reactivity at the interface region between AN and n-dodecane molecules.

Effects of initial iron corrosion rate on long-term performance of iron permeable reactive barriers: column experiments and numerical simulation.

PubMed

suk O, Jin; Jeen, Sung-Wook; Gillham, Robert W; Gui, Lai

2009-01-26

Column experiments and numerical simulation were conducted to test the hypothesis that iron material having a high corrosion rate is not beneficial for the long-term performance of iron permeable reactive barriers (PRBs) because of faster passivation of iron and greater porosity loss close to the influent face of the PRBs. Four iron materials (Connelly, Gotthart-Maier, Peerless, and ISPAT) were used for the column experiments, and the changes in reactivity toward cis-dichloroethene (cis-DCE) degradation in the presence of dissolved CaCO3 were evaluated. The experimental results showed that the difference in distribution of the accumulated precipitates, resulting from differences in iron corrosion rate, caused a difference in the migration rate of the cis-DCE profiles and a significant difference in the pattern of passivation, indicating a faster passivation in the region close to the influent end for the material having a higher corrosion rate. For the numerical simulation, the accumulation of secondary minerals and reactivity loss of iron were coupled using an empirically-derived relationship that was incorporated into a multi-component reactive transport model. The simulation results provided a reasonable representation of the evolution of iron reactivity toward cis-DCE treatment and the changes in geochemical conditions for each material, consistent with the observed data. The simulations for long-term performance were also conducted to further test the hypothesis and predict the differences in performance over a period of 40 years under typical groundwater conditions. The predictions showed that the cases of higher iron corrosion rates had earlier cis-DCE breakthrough and more reduction in porosity starting from near the influent face, due to more accumulation of carbonate minerals in that region. Therefore, both the experimental and simulation results appear to support the hypothesis and suggest that reactivity changes of iron materials resulting from evolution of geochemical conditions should be considered in the design of iron PRBs.

Numerical simulation of the generation of reactive oxygen and nitrogen species (RONS) in water by atmospheric-pressure plasmas and their effects on Escherichia coli (E. coli)

NASA Astrophysics Data System (ADS)

Ikuse, Kazumasa; Hamaguchi, Satoshi

2016-09-01

We have used two types of numerical simulations to examine biological effects of reactive oxygen and nitrogen species (RONS) generated in water by an atmospheric-pressure plasma (APP) that irradiates the water surface. One is numerical simulation for the generation and transport of RONS in water based on the reaction-diffusion-advection equations coupled with Poisson equation. The rate constants, mobilities, and diffusion coefficients used in the equations are obtained from the literature. The gaseous species are given as boundary conditions and time evolution of the concentrations of chemical species in pure water is solved numerically as functions of the depth in one dimension. Although it is not clear how living organisms respond to such exogenous RONS, we also use numerical simulation for metabolic reactions of Escherichia coli (E. coli) and examine possible effects of such RONS on an in-silico model organism. The computation model is based on the flux balance analysis (FBA), where the fluxes of the metabolites in a biological system are evaluated in steady state, i.e., under the assumption that the fluxes do not change in time. The fluxes are determined with liner programming to maximize the growth rate of the bacteria under the given conditions. Although FBA cannot be directly applied to dynamical responses of metabolic reactions, the simulation still gives insight into the biological reactions to exogenous chemical species generated by an APP. Partially supported by JSPS Grants-in-Aid for Scientific Research.

Novel interactions of mitochondria and reactive oxygen/nitrogen species in alcohol mediated liver disease

PubMed Central

Mantena, Sudheer K; King, Adrienne L; Andringa, Kelly K; Landar, Aimee; Darley-Usmar, Victor; Bailey, Shannon M

2007-01-01

Mitochondrial dysfunction is known to be a contributing factor to a number of diseases including chronic alcohol induced liver injury. While there is a detailed understanding of the metabolic pathways and proteins of the liver mitochondrion, little is known regarding how changes in the mitochondrial proteome may contribute to the development of hepatic pathologies. Emerging evidence indicates that reactive oxygen and nitrogen species disrupt mitochondrial function through post-translational modifications to the mitochondrial proteome. Indeed, various new affinity labeling reagents are available to test the hypothesis that post-translational modification of proteins by reactive species contributes to mitochondrial dysfunction and alcoholic fatty liver disease. Specialized proteomic techniques are also now available, which allow for identification of defects in the assembly of multi-protein complexes in mitochondria and the resolution of the highly hydrophobic proteins of the inner membrane. In this review knowledge gained from the study of changes to the mitochondrial proteome in alcoholic hepatotoxicity will be described and placed into a mechanistic framework to increase understanding of the role of mitochondrial dysfunction in liver disease. PMID:17854139

COUPLED FREE AND DISSOLVED PHASE TRANSPORT: NEW SIMULATION CAPABILITIES AND PARAMETER INVERSION

EPA Science Inventory

The vadose zone free-phase simulation capabilities of the US EPA Hydrocarbon Spill Screening Model (HSSM)have been linked with the 3-D multi-species dissolved-phase contaminant transport simulator MT3DMS.

THC-MP: High performance numerical simulation of reactive transport and multiphase flow in porous media

NASA Astrophysics Data System (ADS)

Wei, Xiaohui; Li, Weishan; Tian, Hailong; Li, Hongliang; Xu, Haixiao; Xu, Tianfu

2015-07-01

The numerical simulation of multiphase flow and reactive transport in the porous media on complex subsurface problem is a computationally intensive application. To meet the increasingly computational requirements, this paper presents a parallel computing method and architecture. Derived from TOUGHREACT that is a well-established code for simulating subsurface multi-phase flow and reactive transport problems, we developed a high performance computing THC-MP based on massive parallel computer, which extends greatly on the computational capability for the original code. The domain decomposition method was applied to the coupled numerical computing procedure in the THC-MP. We designed the distributed data structure, implemented the data initialization and exchange between the computing nodes and the core solving module using the hybrid parallel iterative and direct solver. Numerical accuracy of the THC-MP was verified through a CO2 injection-induced reactive transport problem by comparing the results obtained from the parallel computing and sequential computing (original code). Execution efficiency and code scalability were examined through field scale carbon sequestration applications on the multicore cluster. The results demonstrate successfully the enhanced performance using the THC-MP on parallel computing facilities.

Wind driven saltation: a hitherto overlooked challenge for life on Mars

NASA Astrophysics Data System (ADS)

Bak, Ebbe; Goul, Michael; Rasmussen, Martin; Moeller, Ralf; Nørnberg, Per; Knak Jensen, Svend; Finster, Kai

2017-04-01

The Martian surface is a hostile environment characterized by low water availability, low atmospheric pressure and high UV and ionizing radiation. Furthermore, wind-driven saltation leads to abrasion of silicates with a production of reactive surface sites and, through triboelectric charging, a release of electrical discharges with a concomitant production of reactive oxygen species. While the effects of low water availability, low pressure and radiation have been extensively studied in relation to the habitability of the Martian surface and the preservation of organic biosignatures, the effects of wind-driven saltation have hitherto been ignored. In this study, we have investigated the effect of exposing bacteria to wind-abraded silicates and directly to wind-driven saltation on Mars in controlled laboratory simulation experiments. Wind-driven saltation was simulated by tumbling mineral samples in a Mars-like atmosphere in sealed quartz ampoules. The effects on bacterial survival and structure were evaluated by colony forming unit counts in combination with scanning electron microscopy, quantitative polymerase chain reaction and life/dead-staining with flow cytometry. The viability of vegetative cells of P. putida, B. subtilis and D. radiodurans in aqueous suspensions was reduced by more than 99% by exposure to abraded basalt, while the viability of B. subtilis endospores was unaffected. B. subtilis mutants lacking different spore components were likewise highly resistant to the exposure to abraded basalt, which indicates that the resistance of spores is not associated with any specific spore component. We found a significant but reduced effect of abraded quartz and we suggest that the stress effect of abraded silicates is induced by a production of reactive oxygen species and hydroxyl radicals produced by Fenton-like reactions in the presence of transition metals. Direct exposure to simulated saltation had a dramatic effect on both D. radiodurans cells and B. subtilis spore with a more than 99.9% decrease in survival after 17 days. The high susceptibility of the usually multi-resistant D. radiodurans cells and B. sublitis spores to the effects of wind-driven saltation indicates that wind abraded silicates as well as direct exposure to saltation represent a considerable stress for microorganisms at the Martian surface, which may have limited the chance of indigenous life, could limit the risk of forward contamination and may have degraded potential organic biosignatures.

The global nonmethane reactive organic carbon budget: A modeling perspective

NASA Astrophysics Data System (ADS)

Safieddine, Sarah A.; Heald, Colette L.; Henderson, Barron H.

2017-04-01

The cycling of reactive organic carbon (ROC) is central to tropospheric chemistry. We characterize the global tropospheric ROC budget as simulated with the GEOS-Chem model. We expand the standard simulation by including new emissions and gas-phase chemistry, an expansion of dry and wet removal, and a mass tracking of all ROC species to achieve carbon closure. The resulting global annual mean ROC burden is 16 Tg C, with sources from methane oxidation and direct emissions contributing 415 and 935 Tg C yr-1. ROC is lost from the atmosphere via physical deposition (460 Tg C yr-1), and oxidation to CO/CO2 (875 Tg C yr-1). Ketones, alkanes, alkenes, and aromatic hydrocarbons dominate the ROC burden, whereas aldehydes and isoprene dominate the ROC global mean surface OH reactivity. Simulated OH reactivities are between 0.8-1 s-1, 3-14 s-1, and 12-34 s-1 over selected regions in the remote ocean, continental midlatitudes, and the tropics, respectively, and are consistent with observational constraints.

Multi-species hybrid modeling of plasma interactions at Io and Europa

NASA Astrophysics Data System (ADS)

Sebek, O.; Travnicek, P. M.; Walker, R. J.; Hellinger, P.

2017-12-01

We study the plasma interactions of Galilean satellites, Io and Europa, by means of multi-species global hybrid simulations. For both satellites we consider multi-species background plasma composed of oxygen and sulphur ions and multi-component neutral atmospheres. We consider ionization processes of the neutral atmosphere which is then a source of dense population of pick-up ions. We apply variable background plasma conditions (density, temperature, magnetic field magnitude and orientation) in order to cover the variability in conditions experienced by the satellites when located in different regions of the Jovian plasma torus. We examine global structure of the interactions, formation of Alfvén wings, development of temperature anisotropies and corresponding instabilities, and the fine phenomena caused by the multi-specie nature of the plasma. The results are in good agreement with in situ measurements of magnetic field and plasma density made by the Galileo spacecraft.

Fluid nonlinear frequency shift of nonlinear ion acoustic waves in multi-ion species plasmas in small wave number region

NASA Astrophysics Data System (ADS)

Feng, Qingsong; Xiao, Chengzhuo; Wang, Qing; Zheng, Chunyang; Liu, Zhanjun; Cao, Lihua; He, Xiantu

2016-10-01

The properties of the nonlinear frequency shift (NFS) especially the fluid NFS from the harmonic generation of the ion-acoustic wave (IAW) in multi-ion species plasmas has been researched by Vlasov simulation. The pictures of the nonlinear frequency shift from harmonic generation and particles trapping are shown to explain the mechanism of NFS qualitatively. The theoretical model of the fluid NFS from harmonic generation in multi-ion species plasmas is given and the results of Vlasov simulation are consistent to theoretical result of multi-ion species plasmas. When the wave number kλDe is small, such as kλDe = 0.1 , the fluid NFS dominates in the total NFS and will reach as large as nearly 15% when the wave amplitude | eϕ / Te | 0.1 , which indicates that in the condition of small kλDe , the fluid NFS dominates in the saturation of stimulated Brillouin scattering especially when the nonlinear IAW amplitude is large. National Natural Science Foundation of China (Grant Nos. 11575035, 11475030 and 11435011) and National Basic Research Program of China (Grant No. 2013CB834101).

Reduced description of reactive flows with tabulation of chemistry

NASA Astrophysics Data System (ADS)

Ren, Zhuyin; Goldin, Graham M.; Hiremath, Varun; Pope, Stephen B.

2011-12-01

The direct use of large chemical mechanisms in multi-dimensional Computational Fluid Dynamics (CFD) is computationally expensive due to the large number of chemical species and the wide range of chemical time scales involved. To meet this challenge, a reduced description of reactive flows in combination with chemistry tabulation is proposed to effectively reduce the computational cost. In the reduced description, the species are partitioned into represented species and unrepresented species; the reactive system is described in terms of a smaller number of represented species instead of the full set of chemical species in the mechanism; and the evolution equations are solved only for the represented species. When required, the unrepresented species are reconstructed assuming that they are in constrained chemical equilibrium. In situ adaptive tabulation (ISAT) is employed to speed the chemistry calculation through tabulating information of the reduced system. The proposed dimension-reduction / tabulation methodology determines and tabulates in situ the necessary information of the nr-dimensional reduced system based on the ns-species detailed mechanism. Compared to the full description with ISAT, the reduced descriptions achieve additional computational speed-up by solving fewer transport equations and faster ISAT retrieving. The approach is validated in both a methane/air premixed flame and a methane/air non-premixed flame. With the GRI 1.2 mechanism consisting of 31 species, the reduced descriptions (with 12 to 16 represented species) achieve a speed-up factor of up to three compared to the full description with ISAT, with a relatively moderate decrease in accuracy compared to the full description.

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

Düchs, Dominik; Delaney, Kris T., E-mail: kdelaney@mrl.ucsb.edu; Fredrickson, Glenn H., E-mail: ghf@mrl.ucsb.edu

Field-theoretic models have been used extensively to study the phase behavior of inhomogeneous polymer melts and solutions, both in self-consistent mean-field calculations and in numerical simulations of the full theory capturing composition fluctuations. The models commonly used can be grouped into two categories, namely, species models and exchange models. Species models involve integrations of functionals that explicitly depend on fields originating both from species density operators and their conjugate chemical potential fields. In contrast, exchange models retain only linear combinations of the chemical potential fields. In the two-component case, development of exchange models has been instrumental in enabling stable complexmore » Langevin (CL) simulations of the full complex-valued theory. No comparable stable CL approach has yet been established for field theories of the species type. Here, we introduce an extension of the exchange model to an arbitrary number of components, namely, the multi-species exchange (MSE) model, which greatly expands the classes of soft material systems that can be accessed by the complex Langevin simulation technique. We demonstrate the stability and accuracy of the MSE-CL sampling approach using numerical simulations of triblock and tetrablock terpolymer melts, and tetrablock quaterpolymer melts. This method should enable studies of a wide range of fluctuation phenomena in multiblock/multi-species polymer blends and composites.« less

PHT3D-UZF: A reactive transport model for variably-saturated porous media

USGS Publications Warehouse

Wu, Ming Zhi; Post, Vincent E. A.; Salmon, S. Ursula; Morway, Eric D.; Prommer, H.

2016-01-01

A modified version of the MODFLOW/MT3DMS-based reactive transport model PHT3D was developed to extend current reactive transport capabilities to the variably-saturated component of the subsurface system and incorporate diffusive reactive transport of gaseous species. Referred to as PHT3D-UZF, this code incorporates flux terms calculated by MODFLOW's unsaturated-zone flow (UZF1) package. A volume-averaged approach similar to the method used in UZF-MT3DMS was adopted. The PHREEQC-based computation of chemical processes within PHT3D-UZF in combination with the analytical solution method of UZF1 allows for comprehensive reactive transport investigations (i.e., biogeochemical transformations) that jointly involve saturated and unsaturated zone processes. Intended for regional-scale applications, UZF1 simulates downward-only flux within the unsaturated zone. The model was tested by comparing simulation results with those of existing numerical models. The comparison was performed for several benchmark problems that cover a range of important hydrological and reactive transport processes. A 2D simulation scenario was defined to illustrate the geochemical evolution following dewatering in a sandy acid sulfate soil environment. Other potential applications include the simulation of biogeochemical processes in variably-saturated systems that track the transport and fate of agricultural pollutants, nutrients, natural and xenobiotic organic compounds and micropollutants such as pharmaceuticals, as well as the evolution of isotope patterns.

Multi-Paradigm Multi-Scale Simulations for Fuel Cell Catalysts and Membranes

DTIC Science & Technology

2006-01-01

transfer studies on model systems. . Applying newly developed density functionals QM ( X3LYP ) for estimating the thermodynamics and kinetic energy...Density functional theory methods We have used many QM methods to probe chemical reaction mechanisms and find that the B3LYP and X3LYP [6] flavors of DFT...carried out QM calculations on the surface reactivity of the Pt and PtRu anode catalysts. This QM uses a new ab initio DFT-GGA method ( X3LYP ) [6

The Role of Child Adrenocortical Functioning in Pathways Between Interparental Conflict and Child Maladjustment

PubMed Central

Davies, Patrick T.; Sturge-Apple, Melissa L.; Cicchetti, Dante; Cummings, E. Mark

2012-01-01

This study examined the interplay between interparental conflict and child cortisol reactivity to interparental conflict in predicting child maladjustment in a sample of 178 families and their kindergarten children. Consistent with the allostatic load hypothesis (McEwen & Stellar, 1993), results indicated that interparental conflict was indirectly related to child maladjustment through its association with individual differences in child cortisol reactivity. Analyses indicated that the multi-method assessment of interparental conflict was associated with lower levels of child cortisol reactivity to a simulated phone conflict between parents. Diminished cortisol reactivity, in turn, predicted increases in parental reports of child externalizing symptoms over a two-year period. Associations between interparental conflict, child cortisol reactivity, and child externalizing symptoms remained robust even after taking into account demographic factors and other family processes. PMID:17605525

First Principles Based Reactive Atomistic Simulations to Understand the Effects of Molecular Hypervelocity Impact on Cassini's Ion and Neutral Mass Spectrometer

NASA Technical Reports Server (NTRS)

Jaramillo-Botero, A.; Cheng, M-J; Cvicek, V.; Beegle, Luther W.; Hodyss, R.; Goddard, W. A., III

2011-01-01

We report here on the predicted impact of species such as ice-water, CO2, CH4, and NH3, on oxidized titanium, as well as HC species on diamond surfaces. These simulations provide the dynamics of product distributions during and after a hypervelocity impact event, ionization fractions, and dissociation probabilities for the various species of interest as a function of impact velocity (energy). We are using these results to determine the relevance of the fragmentation process to Cassini INMS results, and to quantify its effects on the observed spectra.

Reactivity of Iron Bearing Minerals and CO 2 Sequestration: A Multi-­Disciplinary and Experimental Approach

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

Schoonen, Martin A.

2014-12-22

The reactivity of sandstones was studied under conditions relevant to the injection of supercritical carbon dioxide in the context of carbon geosequestration. The emphasis of the study was on the reactivity of iron-­bearing minerals when exposed to supercritical CO 2 (scCO 2) and scCO 2 with commingled aqueous solutions containing H 2S and/or SO 2. Flow through and batch experiments were conducted. Results indicate that sandstones, irrespective of their mineralogy, are not reactive when exposed to pure scCO2 or scCO 2 with commingled aqueous solutions containing H 2S and/or SO 2 under conditions simulating the environment near the injection pointmore » (flow through experiments). However, sandstones are reactive under conditions simulating the edge of the injected CO 2 plume or ahead of the plume (batch experiments). Sandstones containing hematite (red sandstone) are particularly reactive. The composition of the reaction products is strongly dependent on the composition of the aqueous phase. The presence of dissolved sulfide leads to the conversion of hematite into pyrite and siderite. The relative amount of the pyrite and siderite is influenced by the ionic strength of the solution. Little reactivity is observed when sulfite is present in the aqueous phase. Sandstones without hematite (grey sandstones) show little reactivity regardless of the solution composition.« less

Automated chemical kinetic modeling via hybrid reactive molecular dynamics and quantum chemistry simulations.

PubMed

Döntgen, Malte; Schmalz, Felix; Kopp, Wassja A; Kröger, Leif C; Leonhard, Kai

2018-06-13

An automated scheme for obtaining chemical kinetic models from scratch using reactive molecular dynamics and quantum chemistry simulations is presented. This methodology combines the phase space sampling of reactive molecular dynamics with the thermochemistry and kinetics prediction capabilities of quantum mechanics. This scheme provides the NASA polynomial and modified Arrhenius equation parameters for all species and reactions that are observed during the simulation and supplies them in the ChemKin format. The ab initio level of theory for predictions is easily exchangeable and the presently used G3MP2 level of theory is found to reliably reproduce hydrogen and methane oxidation thermochemistry and kinetics data. Chemical kinetic models obtained with this approach are ready-to-use for, e.g., ignition delay time simulations, as shown for hydrogen combustion. The presented extension of the ChemTraYzer approach can be used as a basis for methodologically advancing chemical kinetic modeling schemes and as a black-box approach to generate chemical kinetic models.

TiOx deposited by magnetron sputtering: a joint modelling and experimental study

NASA Astrophysics Data System (ADS)

Tonneau, R.; Moskovkin, P.; Pflug, A.; Lucas, S.

2018-05-01

This paper presents a 3D multiscale simulation approach to model magnetron reactive sputter deposition of TiOx⩽2 at various O2 inlets and its validation against experimental results. The simulation first involves the transport of sputtered material in a vacuum chamber by means of a three-dimensional direct simulation Monte Carlo (DSMC) technique. Second, the film growth at different positions on a 3D substrate is simulated using a kinetic Monte Carlo (kMC) method. When simulating the transport of species in the chamber, wall chemistry reactions are taken into account in order to get the proper content of the reactive species in the volume. Angular and energy distributions of particles are extracted from DSMC and used for film growth modelling by kMC. Along with the simulation, experimental deposition of TiOx coatings on silicon samples placed at different positions on a curved sample holder was performed. The experimental results are in agreement with the simulated ones. For a given coater, the plasma phase hysteresis behaviour, film composition and film morphology are predicted. The used methodology can be applied to any coater and any films. This paves the way to the elaboration of a virtual coater allowing a user to predict composition and morphology of films deposited in silico.

Reactive transport modeling of nitrogen in Seine River sediments

NASA Astrophysics Data System (ADS)

Akbarzadeh, Z.; Laverman, A.; Raimonet, M.; Rezanezhad, F.; Van Cappellen, P.

2016-02-01

Biogeochemical processes in sediments have a major impact on the fate and transport of nitrogen (N) in river systems. Organic matter decomposition in bottom sediments releases inorganic N species back to the stream water, while denitrification, anammox and burial of organic matter remove bioavailable N from the aquatic environment. To simulate N cycling in river sediments, a multi-component reactive transport model has been developed in MATLAB®. The model includes 3 pools of particulate organic N, plus pore water nitrate, nitrite, nitrous oxide and ammonium. Special attention is given to the production and consumption of nitrite, a N species often neglected in early diagenetic models. Although nitrite is usually considered to be short-lived, elevated nitrite concentrations have been observed in freshwater streams, raising concerns about possible toxic effects. We applied the model to sediment data sets collected at two locations in the Seine River, one upstream, the other downstream, of the largest wastewater treatment plant (WWTP) of the Paris conurbation. The model is able to reproduce the key features of the observed pore water depth profiles of the different nitrogen species. The modeling results show that the presence of oxygen in the overlying water plays a major role in controlling the exchanges of nitrite between the sediments and the stream water. In August 2012, sediments upstream of the WWTP switch from being a sink to a source of nitrite as the overlying water becomes anoxic. Downstream sediments remain a nitrite sink in oxic and anoxic conditions. Anoxic bottom waters at the upstream location promote denitrification, which produces nitrite, while at the downstream site, anammox and DNRA are important removal processes of nitrite.

Analytical solutions for sequentially coupled one-dimensional reactive transport problems Part I: Mathematical derivations

NASA Astrophysics Data System (ADS)

Srinivasan, V.; Clement, T. P.

2008-02-01

Multi-species reactive transport equations coupled through sorption and sequential first-order reactions are commonly used to model sites contaminated with radioactive wastes, chlorinated solvents and nitrogenous species. Although researchers have been attempting to solve various forms of these reactive transport equations for over 50 years, a general closed-form analytical solution to this problem is not available in the published literature. In Part I of this two-part article, we derive a closed-form analytical solution to this problem for spatially-varying initial conditions. The proposed solution procedure employs a combination of Laplace and linear transform methods to uncouple and solve the system of partial differential equations. Two distinct solutions are derived for Dirichlet and Cauchy boundary conditions each with Bateman-type source terms. We organize and present the final solutions in a common format that represents the solutions to both boundary conditions. In addition, we provide the mathematical concepts for deriving the solution within a generic framework that can be used for solving similar transport problems.

Accounting for the Decreasing Denitrification Potential of Aquifers in Travel-Time Based Reactive-Transport Models of Nitrate

NASA Astrophysics Data System (ADS)

Cirpka, O. A.; Loschko, M.; Wöhling, T.; Rudolph, D. L.

2017-12-01

Excess nitrate concentrations pose a threat to drinking-water production from groundwater in all regions of intensive agriculture worldwide. Natural organic matter, pyrite, and other reduced constituents of the aquifer matrix can be oxidized by aerobic and denitrifying bacteria, leading to self-cleaning of groundwater. Various studies have shown that the heterogeneity of both hydraulic and chemical aquifer properties influence the reactive behavior. Since the exact spatial distributions of these properties are not known, predictions on the temporal evolution of nitrate should be probabilistic. However, the computational effort of pde-based, spatially explicit multi-component reactive-transport simulations are so high that multiple model runs become impossible. Conversely, simplistic models that treat denitrification as first-order decay process miss important controls on denitrification. We have proposed a Lagrangian framework of nonlinear reactive transport, in which the electron-donor supply by the aquifer matrix is parameterized by a relative reactivity, that is the reaction rate relative to a standard reaction rate for identical solute concentrations (Loschko et al., 2016). We could show that reactive transport simplifies to solving a single ordinary dfferential equation in terms of the cumulative relative reactivity for a given combination of inflow concentrations. Simulating 3-D flow and reactive transport are computationally so inexpensive that Monte Carlo simulation become feasible. The original scheme did not consider a change of the relative reactivity over time, implying that the electron-donor pool in the matrix is infinite. We have modified the scheme to address the consumption of the reducing aquifer constituents upon the reactions. We also analyzed how a minimally complex model of aerobic respiration and denitrification could look like. With the revised scheme, we performed Monte Carlo simulations in 3-D domains, confirming that the uncertainty in predicting nitrate breakthrough depends on the scale of observation. Reference: M. Loschko, T. Wöhling, D.L. Rudolph, O.A. Cirpka: Cumulative relative reactivity: a concept for modeling aquifer-scale reactive transport. Water Resour. Res. 52(10): 8117-8137, 2016, doi: 10.1002/2016WR019080.

SEAWAT: A Computer Program for Simulation of Variable-Density Groundwater Flow and Multi-Species Solute and Heat Transport

USGS Publications Warehouse

Langevin, Christian D.

2009-01-01

SEAWAT is a MODFLOW-based computer program designed to simulate variable-density groundwater flow coupled with multi-species solute and heat transport. The program has been used for a wide variety of groundwater studies including saltwater intrusion in coastal aquifers, aquifer storage and recovery in brackish limestone aquifers, and brine migration within continental aquifers. SEAWAT is relatively easy to apply because it uses the familiar MODFLOW structure. Thus, most commonly used pre- and post-processors can be used to create datasets and visualize results. SEAWAT is a public domain computer program distributed free of charge by the U.S. Geological Survey.

The multi-layer multi-configuration time-dependent Hartree method for bosons: theory, implementation, and applications.

PubMed

Cao, Lushuai; Krönke, Sven; Vendrell, Oriol; Schmelcher, Peter

2013-10-07

We develop the multi-layer multi-configuration time-dependent Hartree method for bosons (ML-MCTDHB), a variational numerically exact ab initio method for studying the quantum dynamics and stationary properties of general bosonic systems. ML-MCTDHB takes advantage of the permutation symmetry of identical bosons, which allows for investigations of the quantum dynamics from few to many-body systems. Moreover, the multi-layer feature enables ML-MCTDHB to describe mixed bosonic systems consisting of arbitrary many species. Multi-dimensional as well as mixed-dimensional systems can be accurately and efficiently simulated via the multi-layer expansion scheme. We provide a detailed account of the underlying theory and the corresponding implementation. We also demonstrate the superior performance by applying the method to the tunneling dynamics of bosonic ensembles in a one-dimensional double well potential, where a single-species bosonic ensemble of various correlation strengths and a weakly interacting two-species bosonic ensemble are considered.

Elucidating reactivity regimes in cyclopentane oxidation: Jet stirred reactor experiments, computational chemistry, and kinetic modeling

DOE PAGES

Al Rashidi, Mariam J.; Thion, Sebastien; Togbe, Casimir; ...

2016-06-22

This study is concerned with the identification and quantification of species generated during the combustion of cyclopentane in a jet stirred reactor (JSR). Experiments were carried out for temperatures between 740 and 1250 K, equivalence ratios from 0.5 to 3.0, and at an operating pressure of 10 atm. The fuel concentration was kept at 0.1% and the residence time of the fuel/O 2/N 2 mixture was maintained at 0.7 s. The reactant, product, and intermediate species concentration profiles were measured using gas chromatography and Fourier transform infrared spectroscopy. The concentration profiles of cyclopentane indicate inhibition of reactivity between 850-1000 Kmore » for φ=2.0 and φ=3.0. This behavior is interesting, as it has not been observed previously for other fuel molecules, cyclic or non-cyclic. A kinetic model including both low- and high-temperature reaction pathways was developed and used to simulate the JSR experiments. The pressure-dependent rate coefficients of all relevant reactions lying on the PES of cyclopentyl + O 2, as well as the C-C and C-H scission reactions of the cyclopentyl radical were calculated at the UCCSD(T)-F12b/cc-pVTZ-F12//M06-2X/6-311++G(d,p) level of theory. The simulations reproduced the unique reactivity trend of cyclopentane and the measured concentration profiles of intermediate and product species. Furthermore, sensitivity and reaction path analyses indicate that this reactivity trend may be attributed to differences in the reactivity of allyl radical at different conditions, and it is highly sensitive to the C-C/C-H scission branching ratio of the cyclopentyl radical decomposition.« less

Principles of using Cold Atmospheric Plasma Stimulated Media for Cancer Treatment

PubMed Central

Yan, Dayun; Talbot, Annie; Nourmohammadi, Niki; Cheng, Xiaoqian; Canady, Jerome; Sherman, Jonathan; Keidar, Michael

2015-01-01

To date, the significant anti-cancer capacity of cold atmospheric plasma (CAP) on dozens of cancer cell lines has been demonstrated in vitro and in mice models. Conventionally, CAP was directly applied to irradiate cancer cells or tumor tissue. Over past three years, the CAP irradiated media was also found to kill cancer cells as effectively as the direct CAP treatment. As a novel strategy, using the CAP stimulated (CAPs) media has become a promising anti-cancer tool. In this study, we demonstrated several principles to optimize the anti-cancer capacity of the CAPs media on glioblastoma cells and breast cancer cells. Specifically, using larger wells on a multi-well plate, smaller gaps between the plasma source and the media, and smaller media volume enabled us to obtain a stronger anti-cancer CAPs media composition without increasing the treatment time. Furthermore, cysteine was the main target of effective reactive species in the CAPs media. Glioblastoma cells were more resistant to the CAPs media than breast cancer cells. Glioblastoma cells consumed the effective reactive species faster than breast cancer cells did. In contrast to nitric oxide, hydrogen peroxide was more likely to be the effective reactive species. PMID:26677750

Molecular dynamics simulations of flame propagation along a monopropellant PETN coupled with multi-walled carbon nanotubes

NASA Astrophysics Data System (ADS)

Jain, S.; Mo, G.; Qiao, L.

2017-02-01

Reactive molecular dynamics simulations were conducted to study the flame speed enhancement phenomenon of a solid mono-propellant, Pentaerythritol Tetranitrate (PETN), when coupled to highly conductive multi-walled carbon nanotubes (MWCNTs). The simulations were based on the first-principles derived reactive force field, ReaxFF, which includes both the physical changes such as thermal transport and the chemical changes such as bond breaking and forming. An annular deposition of a PETN layer around the MWCNTs was considered. The thickness of the PETN layer and the diameter of the MWCNT were varied to understand the effect of the MWCNT loading ratio on the flame propagation. Flame speed enhancements up to 3 times the bulk value were observed. An optimal MWCNT loading ratio was determined. The enhancement was attributed to the layering of the PETN molecules around the MWCNT, which increased the heat transport among the PETN molecules near the MWCNT surface, thus causing the flame to travel faster. Furthermore, a stronger ignition source was required for the MWCNT-PETN complex because of the higher thermal transport among the PETN molecules along the MWCNT, which makes the ignition energy dissipate more quickly. Lastly, the MWCNT remained unburned during the PETN combustion process.

Initial Comparison of Direct and Legacy Modeling Approaches for Radial Core Expansion Analysis

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

Shemon, Emily R.

2016-10-10

Radial core expansion in sodium-cooled fast reactors provides an important reactivity feedback effect. As the reactor power increases due to normal start up conditions or accident scenarios, the core and surrounding materials heat up, causing both grid plate expansion and bowing of the assembly ducts. When the core restraint system is designed correctly, the resulting structural deformations introduce negative reactivity which decreases the reactor power. Historically, an indirect procedure has been used to estimate the reactivity feedback due to structural deformation which relies upon perturbation theory and coupling legacy physics codes with limited geometry capabilities. With advancements in modeling andmore » simulation, radial core expansion phenomena can now be modeled directly, providing an assessment of the accuracy of the reactivity feedback coefficients generated by indirect legacy methods. Recently a new capability was added to the PROTEUS-SN unstructured geometry neutron transport solver to analyze deformed meshes quickly and directly. By supplying the deformed mesh in addition to the base configuration input files, PROTEUS-SN automatically processes material adjustments including calculation of region densities to conserve mass, calculation of isotopic densities according to material models (for example, sodium density as a function of temperature), and subsequent re-homogenization of materials. To verify the new capability of directly simulating deformed meshes, PROTEUS-SN was used to compute reactivity feedback for a series of contrived yet representative deformed configurations for the Advanced Burner Test Reactor design. The indirect legacy procedure was also performed to generate reactivity feedback coefficients for the same deformed configurations. Interestingly, the legacy procedure consistently overestimated reactivity feedbacks by 35% compared to direct simulations by PROTEUS-SN. This overestimation indicates that the legacy procedures are in fact not conservative and could be overestimating reactivity feedback effects that are closely tied to reactor safety. We conclude that there is indeed value in performing direct simulation of deformed meshes despite the increased computational expense. PROTEUS-SN is already part of the SHARP multi-physics toolkit where both thermal hydraulics and structural mechanical feedback modeling can be applied but this is the first comparison of direct simulation to legacy techniques for radial core expansion.« less

Identifying functional zones of denitrification in heterogeneous aquifer systems by numerical simulations - a case study

NASA Astrophysics Data System (ADS)

Jang, E.; Kalbacher, T.; He, W.; Shao, H.; Schueth, C.; Kolditz, O.

2014-12-01

Nitrate contamination in shallow groundwater is still one of the common problems in many countries. Because of its high solubility and anionic nature, nitrate can easily leach through soil and persist in groundwater for decades. High nitrate concentration has been suggested as a major cause of accelerated eutrophication, methemoglobinemia and gastric cancer. There are several factors influencing the fate of nitrate in groundwater system, which is e.g. distribution of N- sources to soil and groundwater, distribution and amount of reactive substances maintaining denitrification, rate of nitrate degradation and its kinetics, and geological characteristics of the aquifer. Nitrate transport and redox transformation processes are closely linked to complex and spatially distributed physical and chemical interaction, therefore it is difficult to predict and quantify in the field and laboratory experiment. Models can play a key role in elucidation of nitrate reduction pathway in groundwater system and in the design and evaluation of field tests to investigate in situ remediation technologies as well. The goal of the current study is to predict groundwater vulnerability to nitrate, to identify functional zones of denitrification in heterogeneous aquifer systems and to describe the uncertainty of the predictions due to scale effects. For this aim, we developed a kinetic model using multi-component mass transport code OpenGeoSys coupling with IPhreeqc module of the geochemical solver PHREEQC. The developed model included sequential aerobic and nitrate-based respiration, multi-Monod kinetics, multi-species biogeochemical reactions, and geological characteristics of the groundwater aquifer. Moreover water-rock interaction such as secondary mineral precipitation was also included in this model. In this presentation, we focused on the general modelling approach and present the simulation results of nitrate transport simulation in a hypothetical aquifer systems based on data from Hessian Ried, an important groundwater resource for the densely populated Rhine-Main region in Germany.

Flow effects in a vertical CVD reactor

NASA Technical Reports Server (NTRS)

Young, G. W.; Hariharan, S. I.; Carnahan, R.

1992-01-01

A model is presented to simulate the non-Boussinesq flow in a vertical, two-dimensional, chemical vapor deposition reactor under atmospheric pressure. Temperature-dependent conductivity, mass diffusivity, viscosity models, and reactive species mass transfer to the substrate are incorporated. In the limits of small Mach number and small aspect ratio, asymptotic expressions for the flow, temperature, and species fields are developed. Soret diffusion effects are also investigated. Analytical solutions predict an inverse relationship between temperature field and concentration field due to Soret effects. This finding is consistent with numerical simulations, assisting in the understanding of the complex interactions amongst the flow, thermal, and species fields in a chemically reacting system.

CHARACTERIZATION OF STABLE BENZO(A)PYRENE-7,8-QUINONE-DNA ADDUCTS IN CALF THYMUS DNA

EPA Science Inventory

Benzo[alpyrene-7,8-dione (BPQ) is a reactive aldo-keto reductase-mediated product of B[a]P-7,8-diol, a major P450/epoxide hydrolase metabolite of the multi-species carcinogen, B[a]P. The role of BPQ in B[a]P's genotoxicity and carcinogenesis is evolving. Toxicity pathways involvi...

An alternative to fully coupled reactive transport simulations for long-term prediction of chemical reactions in complex geological systems

NASA Astrophysics Data System (ADS)

De Lucia, Marco; Kempka, Thomas; Kühn, Michael

2014-05-01

Fully-coupled reactive transport simulations involving multiphase hydrodynamics and chemical reactions in heterogeneous settings are extremely challenging from a computational point of view. This often leads to oversimplification of the investigated system: coarse spatial discretization, to keep the number of elements in the order of few thousands; simplified chemistry, disregarding many potentially important reactions. A novel approach for coupling non-reactive hydrodynamic simulations with the outcome of single batch geochemical simulations was therefore introduced to assess the potential long-term mineral trapping at the Ketzin pilot site for underground CO2 storage in Germany [1],[2]. The advantage of the coupling is the ability to use multi-million grid non-reactive hydrodynamics simulations on one side and few batch 0D geochemical simulations on the other, so that the complexity of both systems does not need to be reduced. This contribution shows the approach which was taken to validate this simplified coupling scheme. The procedure involved batch simulations of the reference geochemical model, then performing both non-reactive and fully coupled 1D and 3D reactive transport simulations and finally applying the simplified coupling scheme based on the non-reactive and geochemical batch model. The TOUGHREACT/ECO2N [3] simulator was adopted for the validation. The degree of refinement of the spatial grid and the complexity and velocity of the mineral reactions, along with a cut-off value for the minimum concentration of dissolved CO2 allowed to originate precipitates in the simplified approach were found out to be the governing parameters for the convergence of the two schemes. Systematic discrepancies between the approaches are not reducible, simply because there is no feedback between chemistry and hydrodynamics, and can reach 20 % - 30 % in unfavourable cases. However, even such discrepancy is completely acceptable, in our opinion, given the amount of uncertainty underlying the geochemical models. References [1] Klein, E., De Lucia, M., Kempka, T. Kühn, M. 2013. Evaluation of longterm mineral trapping at the Ketzin pilot site for CO2 storage: an integrative approach using geochemical modelling and reservoir simulation. International Journal of Greenhouse Gas Control 19: 720-730, doi:10.1016/j.ijggc.2013.05.014 [2] Kempka, T., Klein, E., De Lucia, M., Tillner, E. Kühn, M. 2013. Assessment of Long-term CO2 Trapping Mechanisms at the Ketzin Pilot Site (Germany) by Coupled Numerical Modelling. Energy Procedia 37: 5419-5426, doi:10.1016/j.egypro.2013.06.460 [3] Xu, T., Spycher, N., Sonnenthal, E., Zhang, G., Zheng, L., Pruess, K. 2010. TOUGHREACT Version 2.0: A simulator for subsurface reactive transport under non-isothermal multiphase flow conditions, Computers & Geosciences 37(6), doi:10.1016/j.cageo.2010.10.007

Large-eddy simulations of a solid-rocket booster jet

NASA Astrophysics Data System (ADS)

Paoli, Roberto; Poubeau, Adele; Cariolle, Daniel

2014-11-01

Emissions from solid-rocket boosters are responsible for a severe decrease in ozone concentration in the rocket plume during the first hours after a launch. The main source of ozone depletion is due to hydrogen chloride that is converted into chlorine in the high temperature regions of the jet (afterburning). The objective of this study is to evaluate the active chlorine concentration in the plume of a solid-rocket booster using large-eddy simulations. The gas is injected through the entire nozzle of the booster and a local time-stepping method based on coupling multi-instances of a fluid solver is used to extend the computational domain up to 600 nozzle exit diameters. The methodology is validated for a non-reactive case by analyzing the flow characteristics of supersonic co-flowing under expanded jets. Then, the chemistry of chlorine is studied offline using a complex chemistry solver and the LES data extracted from the mean trajectories of sample fluid particles. Finally, the online chemistry is analyzed by means of the multispecies version of the LES solver using a reduced chemistry scheme. The LES are able to capture the mixing of the exhaust with ambient air and the species concentrations, which is also useful to initialize atmospheric simulations on larger domains.

Supercomputing with TOUGH2 family codes for coupled multi-physics simulations of geologic carbon sequestration

NASA Astrophysics Data System (ADS)

Yamamoto, H.; Nakajima, K.; Zhang, K.; Nanai, S.

2015-12-01

Powerful numerical codes that are capable of modeling complex coupled processes of physics and chemistry have been developed for predicting the fate of CO2 in reservoirs as well as its potential impacts on groundwater and subsurface environments. However, they are often computationally demanding for solving highly non-linear models in sufficient spatial and temporal resolutions. Geological heterogeneity and uncertainties further increase the challenges in modeling works. Two-phase flow simulations in heterogeneous media usually require much longer computational time than that in homogeneous media. Uncertainties in reservoir properties may necessitate stochastic simulations with multiple realizations. Recently, massively parallel supercomputers with more than thousands of processors become available in scientific and engineering communities. Such supercomputers may attract attentions from geoscientist and reservoir engineers for solving the large and non-linear models in higher resolutions within a reasonable time. However, for making it a useful tool, it is essential to tackle several practical obstacles to utilize large number of processors effectively for general-purpose reservoir simulators. We have implemented massively-parallel versions of two TOUGH2 family codes (a multi-phase flow simulator TOUGH2 and a chemically reactive transport simulator TOUGHREACT) on two different types (vector- and scalar-type) of supercomputers with a thousand to tens of thousands of processors. After completing implementation and extensive tune-up on the supercomputers, the computational performance was measured for three simulations with multi-million grid models, including a simulation of the dissolution-diffusion-convection process that requires high spatial and temporal resolutions to simulate the growth of small convective fingers of CO2-dissolved water to larger ones in a reservoir scale. The performance measurement confirmed that the both simulators exhibit excellent scalabilities showing almost linear speedup against number of processors up to over ten thousand cores. Generally this allows us to perform coupled multi-physics (THC) simulations on high resolution geologic models with multi-million grid in a practical time (e.g., less than a second per time step).

A multi-species reactive transport model to estimate biogeochemical rates based on single-well push-pull test data

NASA Astrophysics Data System (ADS)

Phanikumar, Mantha S.; McGuire, Jennifer T.

2010-08-01

Push-pull tests are a popular technique to investigate various aquifer properties and microbial reaction kinetics in situ. Most previous studies have interpreted push-pull test data using approximate analytical solutions to estimate (generally first-order) reaction rate coefficients. Though useful, these analytical solutions may not be able to describe important complexities in rate data. This paper reports the development of a multi-species, radial coordinate numerical model (PPTEST) that includes the effects of sorption, reaction lag time and arbitrary reaction order kinetics to estimate rates in the presence of mixing interfaces such as those created between injected "push" water and native aquifer water. The model has the ability to describe an arbitrary number of species and user-defined reaction rate expressions including Monod/Michelis-Menten kinetics. The FORTRAN code uses a finite-difference numerical model based on the advection-dispersion-reaction equation and was developed to describe the radial flow and transport during a push-pull test. The accuracy of the numerical solutions was assessed by comparing numerical results with analytical solutions and field data available in the literature. The model described the observed breakthrough data for tracers (chloride and iodide-131) and reactive components (sulfate and strontium-85) well and was found to be useful for testing hypotheses related to the complex set of processes operating near mixing interfaces.

COUPLED FREE AND DISSOLVED PHASE TRANSPORT: NEW SIMULATION CAPABILITIES AND PARAMETER INVERSION

EPA Science Inventory

The vadose zone free-phase simulation capabilities of the US EPA Hydrocarbon Spill Screening Model (HSSM) (Weaver et al., 1994) have been linked with the 3-D multi-species dissolved-phase contaminant transport simulator MT3DMS (Zheng and Wang, 1999; Zheng, 2005). The linkage pro...

Evaluation of the reactive nitrogen budget of the remote atmosphere in global models using airborne measurements

NASA Astrophysics Data System (ADS)

Murray, L. T.; Strode, S. A.; Fiore, A. M.; Lamarque, J. F.; Prather, M. J.; Thompson, C. R.; Peischl, J.; Ryerson, T. B.; Allen, H.; Blake, D. R.; Crounse, J. D.; Brune, W. H.; Elkins, J. W.; Hall, S. R.; Hintsa, E. J.; Huey, L. G.; Kim, M. J.; Moore, F. L.; Ullmann, K.; Wennberg, P. O.; Wofsy, S. C.

2017-12-01

Nitrogen oxides (NOx ≡ NO + NO2) in the background atmosphere are critical precursors for the formation of tropospheric ozone and OH, thereby exerting strong influence on surface air quality, reactive greenhouse gases, and ecosystem health. The impact of NOx on atmospheric composition and climate is sensitive to the relative partitioning of reactive nitrogen between NOx and longer-lived reservoir species of the total reactive nitrogen family (NOy) such as HNO3, HNO4, PAN and organic nitrates (RONO2). Unfortunately, global chemistry-climate models (CCMs) and chemistry-transport models (CTMs) have historically disagreed in their reactive nitrogen budgets outside of polluted continental regions, and we have lacked in situ observations with which to evaluate them. Here, we compare and evaluate the NOy budget of six global models (GEOS-Chem CTM, GFDL AM3 CCM, GISS E2.1 CCM, GMI CTM, NCAR CAM CCM, and UCI CTM) using new observations of total reactive nitrogen and its member species from the NASA Atmospheric Tomography (ATom) mission. ATom has now completed two of its four planned deployments sampling the remote Pacific and Atlantic basins of both hemispheres with a comprehensive suite of measurements for constraining reactive photochemistry. All six models have simulated conditions climatologically similar to the deployments. The GMI and GEOS-Chem CTMs have in addition performed hindcast simulations using the MERRA-2 reanalysis, and have been sampled along the flight tracks. We evaluate the performance of the models relative to the observations, and identify factors contributing to their disparate behavior using known differences in model oxidation mechanisms, heterogeneous loss pathways, lightning and surface emissions, and physical loss processes.

Time-dependent one-dimensional simulation of atmospheric dielectric barrier discharge in N2/O2/H2O using COMSOL Multiphysics

NASA Astrophysics Data System (ADS)

Sohbatzadeh, F.; Soltani, H.

2018-04-01

The results of time-dependent one-dimensional modelling of a dielectric barrier discharge (DBD) in a nitrogen-oxygen-water vapor mixture at atmospheric pressure are presented. The voltage-current characteristics curves and the production of active species are studied. The discharge is driven by a sinusoidal alternating high voltage-power supply at 30 kV with frequency of 27 kHz. The electrodes and the dielectric are assumed to be copper and quartz, respectively. The current discharge consists of an electrical breakdown that occurs in each half-period. A detailed description of the electron attachment and detachment processes, surface charge accumulation, charged species recombination, conversion of negative and positive ions, ion production and losses, excitations and dissociations of molecules are taken into account. Time-dependent one-dimensional electron density, electric field, electric potential, electron temperature, densities of reactive oxygen species (ROS) and reactive nitrogen species (RNS) such as: O, O-, O+, {O}2^{ - } , {O}2^{ + } , O3, {N}, {N}2^{ + } , N2s and {N}2^{ - } are simulated versus time across the gas gap. The results of this work could be used in plasma-based pollutant degradation devices.

Simulations of the dispersion of reactive pollutants in a street canyon, considering different chemical mechanisms and micromixing

NASA Astrophysics Data System (ADS)

Garmory, A.; Kim, I. S.; Britter, R. E.; Mastorakos, E.

The Stochastic Fields (SF) or Field Monte Carlo method has been used to model the dispersion of reactive scalars in a street canyon, using a simple chemistry and the CBM-IV mechanism. SF is a Probability Density Function (PDF) method which allows both means and variances of the scalars to be calculated as well as considering the effect of segregation on reaction rates. It was found that the variance of reactive scalars such as NO 2 was very high in the mixing region at roof-top level with rms values of the order of the mean values. The effect of segregation on major species such as O 3 was found to be very small using either mechanism, however, some radical species in CBM-IV showed a significant difference. These were found to be the seven species with the fastest chemical timescales. The calculated photostationary state defect was also found to be in error when segregation is neglected.

NABS RESPONSE OF A MULTI-METRIC FISH BIOTIC INDEX TO SPECIES DECLINES

EPA Science Inventory

Multi-metric indices of biotic integrity (IBI) are commonly used to compare fish communities among streams, but ability to monitor trends within streams is largely unknown. We assessed the IBI trend detection ability using simulations which progressively degraded the fish assembl...

Enforcing realizability in explicit multi-component species transport

PubMed Central

McDermott, Randall J.; Floyd, Jason E.

2015-01-01

We propose a strategy to guarantee realizability of species mass fractions in explicit time integration of the partial differential equations governing fire dynamics, which is a multi-component transport problem (realizability requires all mass fractions are greater than or equal to zero and that the sum equals unity). For a mixture of n species, the conventional strategy is to solve for n − 1 species mass fractions and to obtain the nth (or “background”) species mass fraction from one minus the sum of the others. The numerical difficulties inherent in the background species approach are discussed and the potential for realizability violations is illustrated. The new strategy solves all n species transport equations and obtains density from the sum of the species mass densities. To guarantee realizability the species mass densities must remain positive (semidefinite). A scalar boundedness correction is proposed that is based on a minimal diffusion operator. The overall scheme is implemented in a publicly available large-eddy simulation code called the Fire Dynamics Simulator. A set of test cases is presented to verify that the new strategy enforces realizability, does not generate spurious mass, and maintains second-order accuracy for transport. PMID:26692634

Reactive Power Pricing Model Considering the Randomness of Wind Power Output

NASA Astrophysics Data System (ADS)

Dai, Zhong; Wu, Zhou

2018-01-01

With the increase of wind power capacity integrated into grid, the influence of the randomness of wind power output on the reactive power distribution of grid is gradually highlighted. Meanwhile, the power market reform puts forward higher requirements for reasonable pricing of reactive power service. Based on it, the article combined the optimal power flow model considering wind power randomness with integrated cost allocation method to price reactive power. Meanwhile, considering the advantages and disadvantages of the present cost allocation method and marginal cost pricing, an integrated cost allocation method based on optimal power flow tracing is proposed. The model realized the optimal power flow distribution of reactive power with the minimal integrated cost and wind power integration, under the premise of guaranteeing the balance of reactive power pricing. Finally, through the analysis of multi-scenario calculation examples and the stochastic simulation of wind power outputs, the article compared the results of the model pricing and the marginal cost pricing, which proved that the model is accurate and effective.

A novel simulation theory and model system for multi-field coupling pipe-flow system

NASA Astrophysics Data System (ADS)

Chen, Yang; Jiang, Fan; Cai, Guobiao; Xu, Xu

2017-09-01

Due to the lack of a theoretical basis for multi-field coupling in many system-level models, a novel set of system-level basic equations for flow/heat transfer/combustion coupling is put forward. Then a finite volume model of quasi-1D transient flow field for multi-species compressible variable-cross-section pipe flow is established by discretising the basic equations on spatially staggered grids. Combining with the 2D axisymmetric model for pipe-wall temperature field and specific chemical reaction mechanisms, a finite volume model system is established; a set of specific calculation methods suitable for multi-field coupling system-level research is structured for various parameters in this model; specific modularisation simulation models can be further derived in accordance with specific structures of various typical components in a liquid propulsion system. This novel system can also be used to derive two sub-systems: a flow/heat transfer two-field coupling pipe-flow model system without chemical reaction and species diffusion; and a chemical equilibrium thermodynamic calculation-based multi-field coupling system. The applicability and accuracy of two sub-systems have been verified through a series of dynamic modelling and simulations in earlier studies. The validity of this system is verified in an air-hydrogen combustion sample system. The basic equations and the model system provide a unified universal theory and numerical system for modelling and simulation and even virtual testing of various pipeline systems.

Understanding the Reactivity of Lunar Dust for Future Lunar Missions

NASA Technical Reports Server (NTRS)

Wallace, William; Taylor, L. A.; Jeevarajan, Antony

2009-01-01

During the Apollo missions, dust was found to cause numerous problems for various instruments and systems. Additionally, the dust may have caused momentary health issues for some of the astronauts. Therefore, the plan to resume robotic and manned missions to the Moon in the next decade has led to a renewed interest in the properties of lunar dust, ranging from geological to chemical to toxicological. An important property to understand is the reactivity of the dust particles. Due to the lack of an atmosphere on the Moon, there is nothing to protect the lunar soil from ultraviolet radiation, solar wind, and meteorite impacts. These processes could all serve to activate the soil, or produce reactive surface species. On the Moon, these species can be maintained for millennia without oxygen or water vapor present to satisfy the broken bonds. Unfortunately, the Apollo dust samples that were returned to Earth were inadvertently exposed to the atmosphere, causing them to lose their reactive characteristics. In order to aid in the preparation of mitigation techniques prior to returning to the Moon, we measured the ability of lunar dust, lunar dust simulant, and quartz samples to produce hydroxyl radicals in solution[1]. As a first approximation of meteorite impacts on the lunar surface, we ground samples using a mortar and pestle. Our initial studies showed that all three test materials (lunar dust (62241), lunar dust simulant (JSC-1Avf), and quartz) produced hydroxyl radicals after grinding and mixing with water. However, the radical production of the ground lunar dust was approximately 10-fold and 3-fold greater than quartz and JSC-1 Avf, respectively. These reactivity differences between the different samples did not correlate with differences in specific surface area. The increased reactivity produced for the quartz by grinding was attributed to the presence of silicon- or oxygen-based radicals on the surface, as had been seen previously[2]. These radicals may also play a part in the reactivity of the lunar dust and lunar simulant. However, other factors would seem to be required to account for the greatly increased reactivity of the lunar soil. It was proposed that nanometer-size Fe 0 (zero valent) particles in the lunar soil might play a role, as they are not present in quartz or lunar dust simulant. The present work has been performed with the aim of understanding the origin of the considerable reactivity of lunar dust[3]. We have ground 8 lunar soils of varying maturity and source (highland or mare) and measured the hydroxyl-radical production and decay of the reactivity. It was determined that there is a direct correlation between the reactivity and the amount of nanophase metallic iron particles (as a function of soil maturity, I s/FeO, in which Is is the amount of iron present as nanophase iron particles present and FeO is the total iron content) in the samples; thus, the highland soils, with their lesser total FeO content, are less reactive than ground mare soils. Additionally, grinding of nanophase iron simulant [4] showed reactivity in line with the lunar soils and much greater than lunar dust simulant or quartz. Studies aimed at determining the time required to deactivate the reactive soils in a habitable environment showed that the average time to reach 50% of the initial reactivity was approximately 3.5 hours. However, even after one week, none of the soils had returned completely to its unground level of reactivity. In contrast to the reactivity results, there was no obvious correlation between the maturity of the soil and its deactivation time. These results provide the first chemical reactivity and persistence values as an important property of lunar soils, data that is paramount as mankind prepares to return to the Moon.

Total OH reactivity study from VOC photochemical oxidation in the SAPHIR chamber

NASA Astrophysics Data System (ADS)

Yu, Z.; Tillmann, R.; Hohaus, T.; Fuchs, H.; Novelli, A.; Wegener, R.; Kaminski, M.; Schmitt, S. H.; Wahner, A.; Kiendler-Scharr, A.

2015-12-01

It is well known that hydroxyl radicals (OH) act as a dominant reactive species in the degradation of VOCs in the atmosphere. In recent field studies, directly measured total OH reactivity often showed poor agreement with OH reactivity calculated from VOC measurements (e.g. Nölscher et al., 2013; Lu et al., 2012a). This "missing OH reactivity" is attributed to unaccounted biogenic VOC emissions and/or oxidation products. The comparison of total OH reactivity being directly measured and calculated from single component measurements of VOCs and their oxidation products gives us a further understanding on the source of unmeasured reactive species in the atmosphere. This allows also the determination of the magnitude of the contribution of primary VOC emissions and their oxidation products to the missing OH reactivity. A series of experiments was carried out in the atmosphere simulation chamber SAPHIR in Jülich, Germany, to explore in detail the photochemical degradation of VOCs (isoprene, ß-pinene, limonene, and D6-benzene) by OH. The total OH reactivity was determined from the measurement of VOCs and their oxidation products by a Proton Transfer Reaction Time of Flight Mass Spectrometer (PTR-TOF-MS) with a GC/MS/FID system, and directly measured by a laser-induced fluorescence (LIF) at the same time. The comparison between these two total OH reactivity measurements showed an increase of missing OH reactivity in the presence of oxidation products of VOCs, indicating a strong contribution to missing OH reactivity from uncharacterized oxidation products.

An investigation on the effects of air on electron energy in atmospheric pressure helium plasma jets

NASA Astrophysics Data System (ADS)

Liu, Yadi; Tan, Zhenyu; Chen, Xinxian; Li, Xiaotong; Zhang, Huimin; Pan, Jie; Wang, Xiaolong

2018-03-01

In this work, the effects of air on electron energy in the atmospheric pressure helium plasma jet produced by a needle-plane discharge system have been investigated by means of the numerical simulation based on a two-dimensional fluid model, and the air concentration dependences of the reactive species densities have also been calculated. In addition, the synergistic effects of the applied voltage and air concentration on electron energy have been explored. The present work gives the following significant results. For a fixed applied voltage, the averaged electron energy is basically a constant at air concentrations below about 0.5%, but it evidently decreases above the concentration of 0.5%. Furthermore, the averaged densities of four main reactive species O, O(1D), O2(1Δg), and N2(A3Σu+) increase with the increasing air concentration, but the increase becomes slow at air concentrations above 0.5%. The air concentration dependences of the averaged electron energy under different voltage amplitudes are similar, and for a given air concentration, the averaged electron energy increases with the increase in the voltage amplitude. For the four reactive species, the effects of the air concentration on their averaged densities are similar for a given voltage amplitude. In addition, the averaged densities of the four reactive species increase with increasing voltage amplitude for a fixed air concentration. The present work suggests that a combination of high voltage amplitude and the characteristic air concentration, 0.5% in the present discharge system, allows an expected electron energy and also generates abundant reactive species.

Adsorption of Reactive Red M-2BE dye from water solutions by multi-walled carbon nanotubes and activated carbon.

PubMed

Machado, Fernando M; Bergmann, Carlos P; Fernandes, Thais H M; Lima, Eder C; Royer, Betina; Calvete, Tatiana; Fagan, Solange B

2011-09-15

Multi-walled carbon nanotubes and powdered activated carbon were used as adsorbents for the successful removal of Reactive Red M-2BE textile dye from aqueous solutions. The adsorbents were characterised by infrared spectroscopy, N(2) adsorption/desorption isotherms and scanning electron microscopy. The effects of pH, shaking time and temperature on adsorption capacity were studied. In the acidic pH region (pH 2.0), the adsorption of the dye was favourable using both adsorbents. The contact time to obtain equilibrium at 298K was fixed at 1h for both adsorbents. The activation energy of the adsorption process was evaluated from 298 to 323K for both adsorbents. The Avrami fractional-order kinetic model provided the best fit to the experimental data compared with pseudo-first-order or pseudo-second-order kinetic adsorption models. For Reactive Red M-2BE dye, the equilibrium data were best fitted to the Liu isotherm model. Simulated dyehouse effluents were used to check the applicability of the proposed adsorbents for effluent treatment. Copyright © 2011 Elsevier B.V. All rights reserved.

Rate dependent fractionation of sulfur isotopes in through-flowing systems

NASA Astrophysics Data System (ADS)

Giannetta, M.; Sanford, R. A.; Druhan, J. L.

2017-12-01

The fidelity of reactive transport models in quantifying microbial activity in the subsurface is often improved through the use stable isotopes. However, the accuracy of current predictions for microbially mediated isotope fractionations within open through-flowing systems typically depends on nutrient availability. This disparity arises from the common application of a single `effective' fractionation factor assigned to a given system, despite extensive evidence for variability in the fractionation factor between eutrophic environments and many naturally occurring, nutrient-limited environments. Here, we demonstrate a reactive transport model with the capacity to simulate a variable fractionation factor over a range of microbially mediated reduction rates and constrain the model with experimental data for nutrient limited conditions. Two coupled isotope-specific Monod rate laws for 32S and 34S, constructed to quantify microbial sulfate reduction and predict associated S isotope partitioning, were parameterized using a series of batch reactor experiments designed to minimize microbial growth. In the current study, we implement these parameterized isotope-specific rate laws within an open, through-flowing system to predict variable fractionation with distance as a function of sulfate reduction rate. These predictions are tested through a supporting laboratory experiment consisting of a flow-through column packed with homogenous porous media inoculated with the same species of sulfate reducing bacteria used in the previous batch reactors, Desulfovibrio vulgaris. The collective results of batch reactor and flow-through column experiments support a significant improvement for S isotope predictions in isotope-sensitive multi-component reactive transport models through treatment of rate-dependent fractionation. Such an update to the model will better equip reactive transport software for isotope informed characterization of microbial activity within energy and nutrient limited environments.

Feature-Based Statistical Analysis of Combustion Simulation Data

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

Bennett, J; Krishnamoorthy, V; Liu, S

2011-11-18

We present a new framework for feature-based statistical analysis of large-scale scientific data and demonstrate its effectiveness by analyzing features from Direct Numerical Simulations (DNS) of turbulent combustion. Turbulent flows are ubiquitous and account for transport and mixing processes in combustion, astrophysics, fusion, and climate modeling among other disciplines. They are also characterized by coherent structure or organized motion, i.e. nonlocal entities whose geometrical features can directly impact molecular mixing and reactive processes. While traditional multi-point statistics provide correlative information, they lack nonlocal structural information, and hence, fail to provide mechanistic causality information between organized fluid motion and mixing andmore » reactive processes. Hence, it is of great interest to capture and track flow features and their statistics together with their correlation with relevant scalar quantities, e.g. temperature or species concentrations. In our approach we encode the set of all possible flow features by pre-computing merge trees augmented with attributes, such as statistical moments of various scalar fields, e.g. temperature, as well as length-scales computed via spectral analysis. The computation is performed in an efficient streaming manner in a pre-processing step and results in a collection of meta-data that is orders of magnitude smaller than the original simulation data. This meta-data is sufficient to support a fully flexible and interactive analysis of the features, allowing for arbitrary thresholds, providing per-feature statistics, and creating various global diagnostics such as Cumulative Density Functions (CDFs), histograms, or time-series. We combine the analysis with a rendering of the features in a linked-view browser that enables scientists to interactively explore, visualize, and analyze the equivalent of one terabyte of simulation data. We highlight the utility of this new framework for combustion science; however, it is applicable to many other science domains.« less

Light-Duty Drive Cycle Simulations of Diesel Engine-Out Exhaust Properties for an RCCI-Enabled Vehicle

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

Gao, Zhiming; Curran, Scott; Daw, C Stuart

2013-01-01

In-cylinder blending of gasoline and diesel fuels to achieve low-temperature reactivity controlled compression ignition (RCCI) can reduce NOx and PM emissions while maintaining or improving brake thermal efficiency compared to conventional diesel combustion (CDC). Moreover, the dual-fueling RCCI is able to achieve these benefits by tailoring combustion reactivity over a wider range of engine operation than is possible with a single fuel. However, the currently demonstrated range of stable RCCI combustion just covers a portion of the engine speed-load range required in several light-duty drive cycles. This means that engines must switch from RCCI to CDC when speed and loadmore » fall outside of the stable RCCI range. In this study we investigated the impact of RCCI as it has recently been demonstrated on practical engine-out exhaust temperature and emissions by simulating a multi-mode RCCI-enabled vehicle operating over two urban and two highway driving cycles. To implement our simulations, we employed experimental engine maps for a multi-mode RCCI/CDC engine combined with a standard mid-size, automatic transmission, passenger vehicle in the Autonomie vehicle simulation platform. Our results include both detailed transient and cycle-averaged engine exhaust temperature and emissions for each case, and we note the potential implications of the modified exhaust properties on catalytic emissions control and utilization of waste heat recovery on future RCCI-enabled vehicles.« less

Detonation initiation in a model of explosive: Comparative atomistic and hydrodynamics simulations

NASA Astrophysics Data System (ADS)

Murzov, S. A.; Sergeev, O. V.; Dyachkov, S. A.; Egorova, M. S.; Parshikov, A. N.; Zhakhovsky, V. V.

2016-11-01

Here we extend consistent simulations to reactive materials by the example of AB model explosive. The kinetic model of chemical reactions observed in a molecular dynamics (MD) simulation of self-sustained detonation wave can be used in hydrodynamic simulation of detonation initiation. Kinetic coefficients are obtained by minimization of difference between profiles of species calculated from the kinetic model and observed in MD simulations of isochoric thermal decomposition with a help of downhill simplex method combined with random walk in multidimensional space of fitting kinetic model parameters.

Vlasov Simulations of Multi-ion Plasma Turbulence in the Solar Wind

NASA Astrophysics Data System (ADS)

Perrone, D.; Valentini, F.; Servidio, S.; Dalena, S.; Veltri, P.

2013-01-01

Hybrid Vlasov-Maxwell simulations are employed to investigate the role of kinetic effects in a two-dimensional turbulent multi-ion plasma, composed of protons, alpha particles, and fluid electrons. In the typical conditions of the solar-wind environment, and in situations of decaying turbulence, the numerical results show that the velocity distribution functions of both ion species depart from the typical configuration of thermal equilibrium. These non-Maxwellian features are quantified through the statistical analysis of the temperature anisotropy, for both protons and alpha particles, in the reference frame given by the local magnetic field. Anisotropy is found to be higher in regions of high magnetic stress. Both ion species manifest a preferentially perpendicular heating, although the anisotropy is more pronounced for the alpha particles, according to solar wind observations. The anisotropy of the alpha particle, moreover, is correlated to the proton anisotropy and also depends on the local differential flow between the two species. Evident distortions of the particle distribution functions are present, with the production of bumps along the direction of the local magnetic field. The physical phenomenology recovered in these numerical simulations reproduces very common measurements in the turbulent solar wind, suggesting that the multi-ion Vlasov model constitutes a valid approach to understanding the nature of complex kinetic effects in astrophysical plasmas.

CHARACTERIZATION OF STABLE BENZOLALPYRENE-7,8-QUINONE-DNA ADDUCTS IN CALF THYMUS DNA AND POLYDEOXYNUCLEOTIDES

EPA Science Inventory

Bcnzo[a]pyrene-7,8-dione (BPQ) is a reactive aldo-keto reductase-mediated product of B[a]P-7,8-diol, a major P450/epoxide hydrolase metabolite of the multi-species carcinogen, B[a]P. The role of BPQ in B[a]P's genotoxicity and carcinogenesis is evolving. Toxicity pathways involvi...

Comparison of multi-fluid moment models with particle-in-cell simulations of collisionless magnetic reconnection

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

Wang, Liang, E-mail: liang.wang@unh.edu; Germaschewski, K.; Hakim, Ammar H.

2015-01-15

We introduce an extensible multi-fluid moment model in the context of collisionless magnetic reconnection. This model evolves full Maxwell equations and simultaneously moments of the Vlasov-Maxwell equation for each species in the plasma. Effects like electron inertia and pressure gradient are self-consistently embedded in the resulting multi-fluid moment equations, without the need to explicitly solving a generalized Ohm's law. Two limits of the multi-fluid moment model are discussed, namely, the five-moment limit that evolves a scalar pressures for each species and the ten-moment limit that evolves the full anisotropic, non-gyrotropic pressure tensor for each species. We first demonstrate analytically andmore » numerically that the five-moment model reduces to the widely used Hall magnetohydrodynamics (Hall MHD) model under the assumptions of vanishing electron inertia, infinite speed of light, and quasi-neutrality. Then, we compare ten-moment and fully kinetic particle-in-cell (PIC) simulations of a large scale Harris sheet reconnection problem, where the ten-moment equations are closed with a local linear collisionless approximation for the heat flux. The ten-moment simulation gives reasonable agreement with the PIC results regarding the structures and magnitudes of the electron flows, the polarities and magnitudes of elements of the electron pressure tensor, and the decomposition of the generalized Ohm's law. Possible ways to improve the simple local closure towards a nonlocal fully three-dimensional closure are also discussed.« less

Numerical Simulation of High-Speed Combustion Processes in Scramjet Configurations

NASA Astrophysics Data System (ADS)

Potturi, Amarnatha Sarma

Flows through scramjet configurations are simulated using hybrid large-eddy simulation / Reynolds-averaged Navier-Stokes techniques. Present study is performed in three parts: parametric studies to determine the sensitivities of the predictions to modeling and algorithmic variations; formulation, implementation, and testing of several subgrid closures aimed at modeling filtered species production rates, which account for turbulence-chemistry interactions in a finite rate chemistry large-eddy simulation framework; and as a final assessment of the complete methodology, cavity-stabilized ethylene combustion is simulated. Throughout the present study, emphasis is placed on characterizing facility-specific effects, since they can have a significant influence on the numerical solution. In Part One, non-reactive and reactive flows through a model scramjet combustor with a wedge shaped injector are simulated. Different grids, flux reconstruction methods, reaction mechanisms, and inflow boundary conditions are used. To enhance fuel-air mixing, a synthetic eddy method is used to generate turbulence in the injector boundary layers and the hydrogen jets. The results show that in all the cases a lifted flame is predicted with varying standoff distances, heat releases, and shapes. In Part Two, the subgrid closures for modeling the filtered species production rates are tested on two different scramjet configurations with fundamentally different flow patterns and flame structures, one with the wedge shaped injector placed at the center of the combustor section (first, used in Part One), another with a three-dimensional ramp injector located on the upper wall of the combustor section (second). While the impact of these closures on the flow through the first configuration is insignificant, they have a more pronounced effect on the flow through the second configuration. Error analysis and performance quantification of these closures reveal that, relative to a baseline model, two of the closures improve the accuracy of the predictions, but the degree of improvement is quite modest. Also, from a cost-benefit perspective none of the models are a significant improvement over the 'laminar-chemistry' closure (where turbulence-chemistry interactions are ignored), for the configurations tested and the mesh resolutions employed. In Part Three, reactive flow through an ethylene fueled cavity flameholder is simulated using 14- and 22-species ethylene oxidation mechanisms, and the synthetic eddy method (used in Part Two) is used to introduce turbulence at the inflow plane of the flameholder. For an equivalence ratio of 0.15, the 14-species mechanism resulted in a flame blow-out, and the 22-species mechanism predicted a cavity stabilized flame. Results predicted using the 22-species mechanism compare well with the experimental data, especially, water mole-fraction distribution and pressure along the upper wall of the combustor. In general, the predictions show excellent agreement with experimental data within the cavity region; further downstream, experimental results suggest that the heat release is over-predicted in the simulations.

Enhanced reactive oxygen species through direct copper sulfide nanoparticle-doxorubicin complexation

NASA Astrophysics Data System (ADS)

Li, Yajuan; Cupo, Michela; Guo, Liangran; Scott, Julie; Chen, Yi-Tzai; Yan, Bingfang; Lu, Wei

2017-12-01

CuS-based nanostructures loading the chemotherapeutic agent doxorubicin (DOX) exerted excellent cancer photothermal chemotherapy under multi-external stimuli. The DOX loading was generally designed through electrostatic interaction or chemical linkers. However, the interaction between DOX molecules and CuS nanoparticles has not been investigated. In this work, we use PEGylated hollow copper sulfide nanoparticles (HCuSNPs) to directly load DOX through the DOX/Cu2+ chelation process. Distinctively, the synthesized PEG-HCuSNPs-DOX release the DOX/Cu2+ complexes into surrounding environment, which generate significant reactive oxygen species (ROS) in a controlled manner by near-infrared laser. The CuS nanoparticle-mediated photothermal ablation facilitates the ROS-induced cancer cell killing effect. Our current work reveals a DOX/Cu2+-mediated ROS-enhanced cell-killing effect in addition to conventional photothermal chemotherapy through the direct CuS nanoparticle-DOX complexation.

A Multicomponent Blend as a Diesel Fuel Surrogate for Compression Ignition Engine Applications

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

Pei, Yuanjiang; Mehl, Marco; Liu, Wei

A mixture of n-dodecane and m-xylene is investigated as a diesel fuel surrogate for compression ignition engine applications. Compared to neat n-dodecane, this binary mixture is more representative of diesel fuel because it contains an alkyl-benzene which represents an important chemical class present in diesel fuels. A detailed multi-component mechanism for n-dodecane and m-xylene was developed by combining a previously developed n-dodecane mechanism with a recently developed mechanism for xylenes. The xylene mechanism is shown to reproduce experimental ignition data from a rapid compression machine and shock tube, speciation data from the jet stirred reactor and flame speed data. Thismore » combined mechanism was validated by comparing predictions from the model with experimental data for ignition in shock tubes and for reactivity in a flow reactor. The combined mechanism, consisting of 2885 species and 11754 reactions, was reduced to a skeletal mechanism consisting 163 species and 887 reactions for 3D diesel engine simulations. The mechanism reduction was performed using directed relation graph (DRG) with expert knowledge (DRG-X) and DRG-aided sensitivity analysis (DRGASA) at a fixed fuel composition of 77% of n-dodecane and 23% m-xylene by volume. The sample space for the reduction covered pressure of 1 – 80 bar, equivalence ratio of 0.5 – 2.0, and initial temperature of 700 – 1600 K for ignition. The skeletal mechanism was compared with the detailed mechanism for ignition and flow reactor predictions. Finally, the skeletal mechanism was validated against a spray flame dataset under diesel engine conditions documented on the Engine Combustion Network (ECN) website. These multi-dimensional simulations were performed using a Representative Interactive Flame (RIF) turbulent combustion model. Encouraging results were obtained compared to the experiments with regards to the predictions of ignition delay and lift-off length at different ambient temperatures.« less

Methodologies for extracting kinetic constants for multiphase reacting flow simulation

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

Chang, S.L.; Lottes, S.A.; Golchert, B.

1997-03-01

Flows in industrial reactors often involve complex reactions of many species. A computational fluid dynamics (CFD) computer code, ICRKFLO, was developed to simulate multiphase, multi-species reacting flows. The ICRKFLO uses a hybrid technique to calculate species concentration and reaction for a large number of species in a reacting flow. This technique includes a hydrodynamic and reacting flow simulation with a small but sufficient number of lumped reactions to compute flow field properties followed by a calculation of local reaction kinetics and transport of many subspecies (order of 10 to 100). Kinetic rate constants of the numerous subspecies chemical reactions aremore » difficult to determine. A methodology has been developed to extract kinetic constants from experimental data efficiently. A flow simulation of a fluid catalytic cracking (FCC) riser was successfully used to demonstrate this methodology.« less

Kinetic dissolution of carbonates and Mn oxides in acidic water: Measurement of in situ field rates and reactive transport modeling

USGS Publications Warehouse

Brown, J.G.; Glynn, P.D.

2003-01-01

The kinetics of carbonate and Mn oxide dissolution under acidic conditions were examined through the in situ exposure of pure phase samples to acidic ground water in Pinal Creek Basin, Arizona. The average long-term calculated in situ dissolution rates for calcite and dolomite were 1.65??10-7 and 3.64??10-10 mmol/(cm2 s), respectively, which were about 3 orders of magnitude slower than rates derived in laboratory experiments by other investigators. Application of both in situ and lab-derived calcite and dolomite dissolution rates to equilibrium reactive transport simulations of a column experiment did not improve the fit to measured outflow chemistry: at the spatial and temporal scales of the column experiment, the use of an equilibrium model adequately simulated carbonate dissolution in the column. Pyrolusite (MnO2) exposed to acidic ground water for 595 days increased slightly in weight despite thermodynamic conditions that favored dissolution. This result might be related to a recent finding by another investigator that the reductive dissolution of pyrolusite is accompanied by the precipitation of a mixed Mn-Fe oxide species. In PHREEQC reactive transport simulations, the incorporation of Mn kinetics improved the fit between observed and simulated behavior at the column and field scales, although the column-fitted rate for Mn-oxide dissolution was about 4 orders of magnitude greater than the field-fitted rate. Remaining differences between observed and simulated contaminant transport trends at the Pinal Creek site were likely related to factors other than the Mn oxide dissolution rate, such as the concentration of Fe oxide surface sites available for adsorption, the effects of competition among dissolved species for available surface sites, or reactions not included in the model.

Reactive collisions for NO(2Π) + N(4S) at temperatures relevant to the hypersonic flight regime.

PubMed

Denis-Alpizar, Otoniel; Bemish, Raymond J; Meuwly, Markus

2017-01-18

The NO(X 2 Π) + N( 4 S) reaction which occurs entirely in the triplet manifold of N 2 O is investigated using quasiclassical trajectories and quantum simulations. Fully-dimensional potential energy surfaces for the 3 A' and 3 A'' states are computed at the MRCI+Q level of theory and are represented using a reproducing kernel Hilbert space. The N-exchange and N 2 -formation channels are followed by using the multi-state adiabatic reactive molecular dynamics method. Up to 5000 K these reactions occur predominantly on the N 2 O 3 A'' surface. However, for higher temperatures the contributions of the 3 A' and 3 A'' states are comparable and the final state distributions are far from thermal equilibrium. From the trajectory simulations a new set of thermal rate coefficients of up to 20 000 K is determined. Comparison of the quasiclassical trajectory and quantum simulations shows that a classical description is a good approximation as determined from the final state analysis.

Core-Collapse Supernovae Explored by Multi-D Boltzmann Hydrodynamic Simulations

NASA Astrophysics Data System (ADS)

Sumiyoshi, Kohsuke; Nagakura, Hiroki; Iwakami, Wakana; Furusawa, Shun; Matsufuru, Hideo; Imakura, Akira; Yamada, Shoichi

We report the latest results of numerical simulations of core-collapse supernovae by solving multi-D neutrino-radiation hydrodynamics with Boltzmann equations. One of the longstanding issues of the explosion mechanism of supernovae has been uncertainty in the approximations of the neutrino transfer in multi-D such as the diffusion approximation and ray-by-ray method. The neutrino transfer is essential, together with 2D/3D hydrodynamical instabilities, to evaluate the neutrino heating behind the shock wave for successful explosions and to predict the neutrino burst signals. We tackled this difficult problem by utilizing our solver of the 6D Boltzmann equation for neutrinos in 3D space and 3D neutrino momentum space coupled with multi-D hydrodynamics adding special and general relativistic extensions. We have performed a set of 2D core-collapse simulations from 11M ⊙ and 15M ⊙ stars on K-computer in Japan by following long-term evolution over 400 ms after bounce to reveal the outcome from the full Boltzmann hydrodynamic simulations with a sophisticated equation of state with multi-nuclear species and updated rates for electron captures on nuclei.

Multi-Fluid Simulations of a Coupled Ionosphere-Magnetosphere System

NASA Astrophysics Data System (ADS)

Gombosi, T. I.; Glocer, A.; Toth, G.; Ridley, A. J.; Sokolov, I. V.; de Zeeuw, D. L.

2008-05-01

In the last decade we have developed the Space Weather Modeling Framework (SWMF) that efficiently couples together different models describing the interacting regions of the space environment. Many of these domain models (such as the global solar corona, the inner heliosphere or the global magnetosphere) are based on MHD and are represented by our multiphysics code, BATS-R-US. BATS-R-US can solve the equations of "standard" ideal MHD, but it can also go beyond this first approximation. It can solve resistive MHD, Hall MHD, semi-relativistic MHD (that keeps the displacement current), multispecies (different ion species have different continuity equations) and multifluid (all ion species have separate continuity, momentum and energy equations) MHD. Recently we added two-fluid Hall MHD (solving the electron and ion energy equations separately) and are working on an extended magnetohydrodynamics model with anisotropic pressures. Ionosheric outflow can be a significant contributor to the plasma population of the magnetosphere during active geomagnetic conditions. This talk will present preliminary results of our simulations when we couple a new field- aligned multi-fluid polar wind code to the Ionosphere Electrodynamics (IE), and Global Magnetosphere (GM) components of the SWMF. We use multi-species and multi-fluid MHD to track the resulting plasma composition in the magnetosphere.

Long-term Studies of Marine Halogen Release

NASA Astrophysics Data System (ADS)

Tschritter, J.; Holla, R.; Frieß, U.; Platt, U.

2009-04-01

Institute of Enviromental Physics, Heidelberg, Germany. Long term measurements of atmospheric trace gases using multi-axis DOAS instruments are pursued at the new SOLAS observatory on the island of Sao Vicente, (Cape Verde). This research is part of the SOPRAN (Surface Ocean Processes in the ANthropocene) project (Fördernummer:03F0462F). Reactive halogen species (RHS) such as bromine- and iodine- containing species play major roles in the chemistry of ozone in both the troposphere and lower stratosphere and thus possibly influence the ozone budget on a global scale. In addition iodine-species emitted from the ocean surface have been shown to be responsible for the production of new atmospheric particles in the marine boundary layer. This may have an effect on cloud formation and radiation transfer on local and global scales. Long term measurements of RHS abundances will help to identify their key regions and processes for formation. A new long term Multi-MAX-DOAS instrument has been installed at the SOLAS observatory on the island of Sao Vicente, (Cape Verde). The main focus of these unique measurements is the investigation of reactive halogen chemistry in the subtropical marine boundary layer based on measurements of BrO, IO, and possibly OIO. Because of its wide spectral range also the use for O4-retrievals to gain aerosol profiles is possible. IO has been detected with mixing ratios up to 1.3 ppt. For BrO an upper limit of 2 ppt could be determined.

Cell Permeability, Migration, and Reactive Oxygen Species Induced by Multi-Walled Carbon Nanotubes in Human Microvascular Endothelial Cells

PubMed Central

Pacurari, M; Qian, Y; Fu, W; Schwegler-Berry, D; Ding, M; Castranova, V; Guo, NL

2011-01-01

Multi-walled carbon nanotubes (MWCNT) have elicited great interest in biomedical applications due to their extraordinary physical, chemical, and optical properties. Intravenous administration of MWCNT-based medical imaging agents and drugs in animal models was utilized. However, the potential harmful health effects of MWCNT administration in humans have not yet been elucidated. Furthermore, to date, there are no apparent reports regarding the precise mechanisms of translocation of MWCNT into target tissues and organs from blood circulation. This study demonstrates that exposure to MWCNT leads to an increase in cell permeability in human microvascular endothelial cells (HMVEC). The results obtained from this study also showed that the MWCNT-induced rise in endothelial permeability is mediated by reactive oxygen species (ROS) production and actin filament remodeling. In addition, it was found that MWCNT promoted cell migration in HMVEC. Mechanistically, MWCNT exposure elevated the levels of monocyte chemoattractant protein-1 (MCP-1) and intercellular adhesion molecule 1 (ICAM-1) in HMVEC. Taken together, these results provide new insights into the bioreactivity of MWCNT, which may have implications in the biomedical application of MWCNT in vascular targeting, imaging, and drug delivery. The results generated from this study also elucidate the potential adverse effects of MWCNT exposure on humans at the cellular level. PMID:22129238

Modeling variably saturated multispecies reactive groundwater solute transport with MODFLOW-UZF and RT3D

USGS Publications Warehouse

Bailey, Ryan T.; Morway, Eric D.; Niswonger, Richard G.; Gates, Timothy K.

2013-01-01

A numerical model was developed that is capable of simulating multispecies reactive solute transport in variably saturated porous media. This model consists of a modified version of the reactive transport model RT3D (Reactive Transport in 3 Dimensions) that is linked to the Unsaturated-Zone Flow (UZF1) package and MODFLOW. Referred to as UZF-RT3D, the model is tested against published analytical benchmarks as well as other published contaminant transport models, including HYDRUS-1D, VS2DT, and SUTRA, and the coupled flow and transport modeling system of CATHY and TRAN3D. Comparisons in one-dimensional, two-dimensional, and three-dimensional variably saturated systems are explored. While several test cases are included to verify the correct implementation of variably saturated transport in UZF-RT3D, other cases are included to demonstrate the usefulness of the code in terms of model run-time and handling the reaction kinetics of multiple interacting species in variably saturated subsurface systems. As UZF1 relies on a kinematic-wave approximation for unsaturated flow that neglects the diffusive terms in Richards equation, UZF-RT3D can be used for large-scale aquifer systems for which the UZF1 formulation is reasonable, that is, capillary-pressure gradients can be neglected and soil parameters can be treated as homogeneous. Decreased model run-time and the ability to include site-specific chemical species and chemical reactions make UZF-RT3D an attractive model for efficient simulation of multispecies reactive transport in variably saturated large-scale subsurface systems.

VIS/ACT: The next episode

NASA Technical Reports Server (NTRS)

Maney, Tucker; Hamburger, Henry

1993-01-01

VIS/ACT is a multi-media educational system for aircrew coordination training (ACT). Students view video segments, answer questions that are adjusted to individual performance, and engage in related activities. Although the system puts the student in a reactive critiquing role, it has proved effective in improving performance on active targeted ACT skills, in group simulation tasks. VIS/ACT itself is the product of coordination among three Navy agencies.

CHROTRAN: a mathematical and computational model for in situ heavy metal remediation in heterogeneous aquifers

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

Hansen, Scott; Pandey, Sachin; Karra, Satish

Groundwater contamination by heavy metals is a critical environmental problem for which in situ remediation is frequently the only viable treatment option. For such interventions, a three-dimensional reactive transport model of relevant biogeochemical processes is invaluable. To this end, we developed a model, CHROTRAN, for in situ treatment, which includes full dynamics for five species: a heavy metal to be remediated, an electron donor, biomass, a nontoxic conservative bio-inhibitor, and a biocide. Direct abiotic reduction by donor-metal interaction as well as donor-driven biomass growth and bio-reduction are modeled, along with crucial processes such as donor sorption, bio-fouling and biomass death.more » Our software implementation handles heterogeneous flow fields, arbitrarily many chemical species and amendment injection points, and features full coupling between flow and reactive transport. We describe installation and usage and present two example simulations demonstrating its unique capabilities. One simulation suggests an unorthodox approach to remediation of Cr(VI) contamination.« less

CHROTRAN: a mathematical and computational model for in situ heavy metal remediation in heterogeneous aquifers

DOE PAGES

Hansen, Scott; Pandey, Sachin; Karra, Satish; ...

2017-04-25

Groundwater contamination by heavy metals is a critical environmental problem for which in situ remediation is frequently the only viable treatment option. For such interventions, a three-dimensional reactive transport model of relevant biogeochemical processes is invaluable. To this end, we developed a model, CHROTRAN, for in situ treatment, which includes full dynamics for five species: a heavy metal to be remediated, an electron donor, biomass, a nontoxic conservative bio-inhibitor, and a biocide. Direct abiotic reduction by donor-metal interaction as well as donor-driven biomass growth and bio-reduction are modeled, along with crucial processes such as donor sorption, bio-fouling and biomass death.more » Our software implementation handles heterogeneous flow fields, arbitrarily many chemical species and amendment injection points, and features full coupling between flow and reactive transport. We describe installation and usage and present two example simulations demonstrating its unique capabilities. One simulation suggests an unorthodox approach to remediation of Cr(VI) contamination.« less

Simulation of Initiation in Hexanitrostilbene

NASA Astrophysics Data System (ADS)

Thompson, Aidan; Shan, Tzu-Ray; Yarrington, Cole; Wixom, Ryan

We report on the effect of isolated voids and pairs of nearby voids on hot spot formation, growth and chemical reaction initiation in hexanitrostilbene (HNS) crystals subjected to shock loading. Large-scale, reactive molecular dynamics simulations are performed using the reactive force field (ReaxFF) as implemented in the LAMMPS software. The ReaxFF force field description for HNS has been validated previously by comparing the isothermal equation of state to available diamond anvil cell (DAC) measurements and density function theory (DFT) calculations. Micron-scale molecular dynamics simulations of a supported shockwave propagating in HNS crystal along the [010] orientation are performed (up = 1.25 km/s, Us =4.0 km/s, P = 11GPa.) We compare the effect on hot spot formation and growth rate of isolated cylindrical voids up to 0.1 µm in size with that of two 50nm voids set 100nm apart. Results from the micron-scale atomistic simulations are compared with hydrodynamics simulations. Sandia National Laboratories is a multi-program laboratory managed and operated by Sandia Corporation, a wholly owned subsidiary of Lock- heed Martin Corporation, for the U.S. DOE National Nuclear Security Administration under Contract DE-AC04-94AL85000.

Multi-model comparison on the effects of climate change on tree species in the eastern U.S.: results from an enhanced niche model and process-based ecosystem and landscape models

Treesearch

Louis R. Iverson; Frank R. Thompson; Stephen Matthews; Matthew Peters; Anantha Prasad; William D. Dijak; Jacob Fraser; Wen J. Wang; Brice Hanberry; Hong He; Maria Janowiak; Patricia Butler; Leslie Brandt; Chris Swanston

2016-01-01

Context. Species distribution models (SDM) establish statistical relationships between the current distribution of species and key attributes whereas process-based models simulate ecosystem and tree species dynamics based on representations of physical and biological processes. TreeAtlas, which uses DISTRIB SDM, and Linkages and LANDIS PRO, process...

A spectral radius scaling semi-implicit iterative time stepping method for reactive flow simulations with detailed chemistry

NASA Astrophysics Data System (ADS)

Xie, Qing; Xiao, Zhixiang; Ren, Zhuyin

2018-09-01

A spectral radius scaling semi-implicit time stepping scheme has been developed for simulating unsteady compressible reactive flows with detailed chemistry, in which the spectral radius in the LUSGS scheme has been augmented to account for viscous/diffusive and reactive terms and a scalar matrix is proposed to approximate the chemical Jacobian using the minimum species destruction timescale. The performance of the semi-implicit scheme, together with a third-order explicit Runge-Kutta scheme and a Strang splitting scheme, have been investigated in auto-ignition and laminar premixed and nonpremixed flames of three representative fuels, e.g., hydrogen, methane, and n-heptane. Results show that the minimum species destruction time scale can well represent the smallest chemical time scale in reactive flows and the proposed scheme can significantly increase the allowable time steps in simulations. The scheme is stable when the time step is as large as 10 μs, which is about three to five orders of magnitude larger than the smallest time scales in various tests considered. For the test flames considered, the semi-implicit scheme achieves second order of accuracy in time. Moreover, the errors in quantities of interest are smaller than those from the Strang splitting scheme indicating the accuracy gain when the reaction and transport terms are solved coupled. Results also show that the relative efficiency of different schemes depends on fuel mechanisms and test flames. When the minimum time scale in reactive flows is governed by transport processes instead of chemical reactions, the proposed semi-implicit scheme is more efficient than the splitting scheme. Otherwise, the relative efficiency depends on the cost in sub-iterations for convergence within each time step and in the integration for chemistry substep. Then, the capability of the compressible reacting flow solver and the proposed semi-implicit scheme is demonstrated for capturing the hydrogen detonation waves. Finally, the performance of the proposed method is demonstrated in a two-dimensional hydrogen/air diffusion flame.

Multi-level molecular modelling for plasma medicine

NASA Astrophysics Data System (ADS)

Bogaerts, Annemie; Khosravian, Narjes; Van der Paal, Jonas; Verlackt, Christof C. W.; Yusupov, Maksudbek; Kamaraj, Balu; Neyts, Erik C.

2016-02-01

Modelling at the molecular or atomic scale can be very useful for obtaining a better insight in plasma medicine. This paper gives an overview of different atomic/molecular scale modelling approaches that can be used to study the direct interaction of plasma species with biomolecules or the consequences of these interactions for the biomolecules on a somewhat longer time-scale. These approaches include density functional theory (DFT), density functional based tight binding (DFTB), classical reactive and non-reactive molecular dynamics (MD) and united-atom or coarse-grained MD, as well as hybrid quantum mechanics/molecular mechanics (QM/MM) methods. Specific examples will be given for three important types of biomolecules, present in human cells, i.e. proteins, DNA and phospholipids found in the cell membrane. The results show that each of these modelling approaches has its specific strengths and limitations, and is particularly useful for certain applications. A multi-level approach is therefore most suitable for obtaining a global picture of the plasma-biomolecule interactions.

A Comparison of Analytical and Numerical Methods for Modeling Dissolution and Other Reactions in Transport Limited Systems

NASA Astrophysics Data System (ADS)

Hochstetler, D. L.; Kitanidis, P. K.

2009-12-01

Modeling the transport of reactive species is a computationally demanding problem, especially in complex subsurface media, where it is crucial to improve understanding of geochemical processes and the fate of groundwater contaminants. In most of these systems, reactions are inherently fast and actual rates of transformations are limited by the slower physical transport mechanisms. There have been efforts to reformulate multi-component reactive transport problems into systems that are simpler and less demanding to solve. These reformulations include defining conservative species and decoupling of reactive transport equations so that fewer of them must be solved, leaving mostly conservative equations for transport [e.g., De Simoni et al., 2005; De Simoni et al., 2007; Kräutle and Knabner, 2007; Molins et al., 2004]. Complex and computationally cumbersome numerical codes used to solve such problems have also caused De Simoni et al. [2005] to develop more manageable analytical solutions. Furthermore, this work evaluates reaction rates and has reaffirmed that the mixing rate,▽TuD▽u, where u is a solute concentration and D is the dispersion tensor, as defined by Kitanidis [1994], is an important and sometimes dominant factor in determining reaction rates. Thus, mixing of solutions is often reaction-limiting. We will present results from analytical and computational modeling of multi-component reactive-transport problems. The results have applications to dissolution of solid boundaries (e.g., calcite), dissolution of non-aqueous phase liquids (NAPLs) in separate phases, and mixing of saltwater and freshwater (e.g. saltwater intrusion in coastal carbonate aquifers). We quantify reaction rates, compare numerical and analytical results, and analyze under what circumstances which approach is most effective for a given problem. References: DeSimoni, M., et al. (2005), A procedure for the solution of multicomponent reactive transport problems, Water Resources Research, 41(W11410). DeSimoni, M., et al. (2007), A mixing ratios-based formulation for multicomponent reactive transport, Water Resources Research, 43(W07419). Kitanidis, P. (1994), The Concept of the Dilution Index, Water Resources Research, 30(7), 2011-2026. Kräutle, S., and P. Knabner (2007), A reduction scheme for coupled multicomponent transport-reaction problems in porous media: Generalization to problems with heterogeneous equilibrium reactions Water Resources Research, 43. Molins, S., et al. (2004), A formulation for decoupling components in reactive transport porblems, Water Resources Research, 40, 13.

Photoinactivation of bacteria by using Fe-doped TiO2-MWCNTs nanocomposites.

PubMed

Koli, Valmiki B; Delekar, Sagar D; Pawar, Shivaji H

2016-12-01

In this study, nanocomposites of Fe-doped TiO 2 with multi-walled carbon nanotubes (0.1- 0.5 wt. %) were prepared by using sol-gel method. The structural and morphological analysis were carried out with using X-ray diffraction pattern and transmission electron microscopy, which confirm the presence of pure anatase phase and particle sizes in the range 15-20 nm. X-ray photoelectron spectroscopy was used to determine the surface compositions of the nanocomposites. UV-vis diffuse reflectance spectra confirm redshift in the optical absorption edge of nanocomposites with increasing amount of multi-walled carbon nanotubes. Nanocomposites show photoinactivation against gram-positive Bacillus subtilis as well as gram-negative Pseudomonas aeruginosa. Fe-TiO 2 -multi-walled carbon nanotubes (0.5 wt. %) nanocomposites show higher photoinactivation capability as compared with other nanocomposites. The photoluminescence study reveals that the Fe-TiO 2 -multi-walled carbon nanotubes nanocomposites are capable to generate higher rate of reactive oxygen species species than that of other nanocomposites. Our experimental results demonstrated that the Fe-TiO 2 -multi-walled carbon nanotubes nanocomposites act as efficient antibacterial agents against a wide range of microorganisms to prevent and control the persistence and spreading of bacterial infections.

Dynamic adaptive chemistry with operator splitting schemes for reactive flow simulations

NASA Astrophysics Data System (ADS)

Ren, Zhuyin; Xu, Chao; Lu, Tianfeng; Singer, Michael A.

2014-04-01

A numerical technique that uses dynamic adaptive chemistry (DAC) with operator splitting schemes to solve the equations governing reactive flows is developed and demonstrated. Strang-based splitting schemes are used to separate the governing equations into transport fractional substeps and chemical reaction fractional substeps. The DAC method expedites the numerical integration of reaction fractional substeps by using locally valid skeletal mechanisms that are obtained using the directed relation graph (DRG) reduction method to eliminate unimportant species and reactions from the full mechanism. Second-order temporal accuracy of the Strang-based splitting schemes with DAC is demonstrated on one-dimensional, unsteady, freely-propagating, premixed methane/air laminar flames with detailed chemical kinetics and realistic transport. The use of DAC dramatically reduces the CPU time required to perform the simulation, and there is minimal impact on solution accuracy. It is shown that with DAC the starting species and resulting skeletal mechanisms strongly depend on the local composition in the flames. In addition, the number of retained species may be significant only near the flame front region where chemical reactions are significant. For the one-dimensional methane/air flame considered, speed-up factors of three and five are achieved over the entire simulation for GRI-Mech 3.0 and USC-Mech II, respectively. Greater speed-up factors are expected for larger chemical kinetics mechanisms.

Stability of a laminar premixed supersonic free shear layer with chemical reactions

NASA Technical Reports Server (NTRS)

Menon, S.; Anderson, J. D., Jr.; Pai, S. I.

1984-01-01

The stability of a two-dimensional compressible supersonic flow in the wake of a flat plate is discussed. The fluid is a multi-species mixture which is undergoing finite rate chemical reactions. The spatial stability of an infinitesimal disturbance in the fluid is considered. Numerical solutions of the eigenvalue stability equations for both reactive and nonreactive supersonic flows are presented and discussed. The chemical reactions have significant influence on the stability behavior. For instance, a neutral eigenvalue is observed near the freestream Mach number of 2.375 for the nonreactive case, but disappears when the reaction is turned on. For reactive flows, the eigenvalues are not very dependent on the free stream Mach number.

The effect of target materials on the propagation of atmospheric-pressure plasma jets

NASA Astrophysics Data System (ADS)

Ji, Longfei; Yan, Wen; Xia, Yang; Liu, Dongping

2018-05-01

The current study is focused on the effect of target materials (quartz plate, copper sheet, and quartz plate with a grounded copper sheet on the back) on the propagation of atmospheric-pressure helium plasma jets. The dynamics of ionization waves (IWs) and the relative amount of reactive oxygen species (OH and O) in the IW front were compared by using spatial and temporal images and relative optical emission spectroscopy. Our measurements show that the targets can significantly affect the propagation and intensity of the IWs. In addition, strong OH emission lines were detected when the IWs impinged upon the damp surface. Numerical simulations have been carried out to explain the experimental observation. The propagation velocity of IWs predicted by the simulation was in good agreement with the experimental results. Simulation results suggest that the density and velocity of IWs mainly depend on the electric field between the high voltage electrode tip and the target. Analysis indicates that the targets could change the electric field distribution between the high voltage electrode and targets and thus affect the dynamics and the density of the IWs, the generation of reactive oxygen species, and the corresponding sterilization efficiency.

CHROTRAN, 1.0

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

Hansen, Scott K.; Pandey, Sachin; Karra, Satish

2017-04-13

CHROTRAN is a fork of the widely-used PFLOTRAN flow and reactive transport numerical simulation code. It implements custom physics and chemistry appropriate to the design of in-situ reduction of heavy metals such as Cr(VI) in groundwater. CHROTRAN includes full dynamics for five species: the metal to be remediated, an electron donor, biofilm, a nontoxic conservative bio-inhibitor, and a biocide. Direct abiotic reduction by donor-metal interaction as well as donor-driven biomass growth and bio-reduction are modeled, along with crucial processes such as donor sorption, and biofilm inactivation. The software implementation handles heterogeneous flow fields, arbitrarily many chemical species and amendment injectionmore » points, and features full coupling between flow and reactive transport, allowing for assessment of the effect of bio-fouling.« less

Zero dimensional model of atmospheric SMD discharge and afterglow in humid air

NASA Astrophysics Data System (ADS)

Smith, Ryan; Kemaneci, Efe; Offerhaus, Bjoern; Stapelmann, Katharina; Peter Brinkmann, Ralph

2016-09-01

A novel mesh-like Surface Micro Discharge (SMD) device designed for surface wound treatment is simulated by multiple time-scaled zero-dimensional models. The chemical dynamics of the discharge are resolved in time at atmospheric pressure in humid conditions. Simulated are the particle densities of electrons, 26 ionic species, and 26 reactive neutral species including: O3, NO, and HNO3. The total of 53 described species are constrained by 624 reactions within the simulated plasma discharge volume. The neutral species are allowed to diffuse into a diffusive gas regime which is of primary interest. Two interdependent zero-dimensional models separated by nine orders of magnitude in temporal resolution are used to accomplish this; thereby reducing the computational load. Through variation of control parameters such as: ignition frequency, deposited power density, duty cycle, humidity level, and N2 content, the ideal operation conditions for the SMD device can be predicted. The described model has been verified by matching simulation parameters and comparing results to that of previous works. Current operating conditions of the experimental mesh-like SMD were matched and results are compared to the simulations. Work supported by SFB TR 87.

Examination of the nature of lattice matched III V semiconductor interfaces using computer simulated molecular beam epitaxial growth I. AC/BC interfaces

NASA Astrophysics Data System (ADS)

Thomsen, M.; Ghaisas, S. V.; Madhukar, A.

1987-07-01

A previously developed computer simulation of molecular beam epitaxial growth of III-V semiconductors based on the configuration dependent reactive incorporation (CDRI) model is extended to allow for two different cation species. Attention is focussed on examining the nature of interfaces formed in lattice matched quantum well structures of the form AC/BC/AC(100). We consider cation species with substantially different effective diffusion lengths, as is the case with Al and Ga during the growth of their respective As compounds. The degree of intermixing occuring at the interface is seen to be dependent upon, among other growth parameters, the pressure of the group V species during growth. Examination of an intraplanar order parameter at the interfaces reveals the existence of short range clustering of the cation species.

Chemical exposure-response relationship between air pollutants and reactive oxygen species in the human respiratory tract

NASA Astrophysics Data System (ADS)

Lakey, P. S. J.; Berkemeier, T.; Tong, H.; Arangio, A. M.; Lucas, K.; Poeschl, U.; Shiraiwa, M.

2016-12-01

The inhalation of air pollutants such as O3 and particulate matter can lead to the formation of reactive oxygen species (ROS) which can cause damage to biosurfaces such as the lung epithelium unless they are effectively scavenged. Although the chemical processes that lead to ROS formation within the ELF upon inhalation of pollutants are well understood qualitatively, ROS concentrations within the ELF have hardly been quantified so far. The kinetic multi-layer model of surface and bulk chemistry in the epithelial lining fluid (KM-SUB-ELF) has been developed to describe chemical reactions and mass transport and to quantify ROS production rates and concentrations within the epithelial lining fluid. KM-SUB-ELF simulations suggest that O3 will rapidly saturate the ELF whereas antioxidants and surfactant species are effective scavengers of OH. High ambient concentrations of O3 can lead to the depletion of surfactants and antioxidants within the ELF, potentially leading to oxidative stress. KM-SUB-ELF reproduced measurements for the formation of H2O2 and OH due to the presence of iron, copper and quinones in surrogate lung lining fluid. This enabled ROS production rates and concentrations in the ELF to be quantified. We found that in polluted megacities the ROS concentration in the ELF due to inhalation of pollutants was at least as high as the concentrations in the ELF of patients suffering from respiratory diseases. Cu and Fe are found to be the most important redox-active aerosol components for ROS production upon inhalation of PM2.5 in polluted regions. Therefore, a reduction in the emission of Cu and Fe should be major targets of air pollution control. Chemical exposure-response relations provide a quantitative basis for assessing the relative importance of specific air pollutants in different regions of the world, showing that aerosol-induced epithelial ROS levels in polluted megacity air can be several orders of magnitude higher than in pristine rainforest air.

Ecological community integration increases with added trophic complexity

USGS Publications Warehouse

Wright, Christopher K.

2008-01-01

The existence of functional biological organization at the level of multi-species communities has long been contested in ecology and evolutionary biology. I found that adding a trophic level to simulated ecological communities enhanced their ability to compete at the community level, increasing the likelihood of one community forcing all or most species in a second community to extinction. Community-level identity emerged within systems of interacting ecological networks, while competitive ability at the community level was enhanced by intense within-community selection pressure. These results suggest a reassessment of the nature of biological organization above the level of species, indicating that the drive toward biological integration, so prominent throughout the history of life, might extend to multi-species communities.

A low Earth orbit molecular beam space simulation facility

NASA Technical Reports Server (NTRS)

Cross, J. B.

1984-01-01

A brief synopsis of the low Earth orbit (LEO) satellite environment is presented including neutral and ionic species. Two ground based atomic and molecular beam instruments are described which are capable of simulating the interaction of spacecraft surfaces with the LEO environment and detecting the results of these interactions. The first detects mass spectrometrically low level fluxes of reactively and nonreactively surface scattered species as a function of scattering angle and velocity while the second ultrahigh velocity (UHV) molecular beam, laser induced fluorescence apparatus is capable of measuring chemiluminescence produced by either gas phase or gas-surface interactions. A number of proposed experiments are described.

Reactive oxygen species-producing myeloid cells act as a bone marrow niche for sterile inflammation-induced reactive granulopoiesis

PubMed Central

Zhu, Haiyan; Kwak, Hyun-Jeong; Liu, Peng; Bajrami, Besnik; Xu, Yuanfu; Park, Shin-Young; Nombela-Arrieta, Cesar; Mondal, Subhanjan; Kambara, Hiroto; Yu, Hongbo; Chai, Li; Silberstein, Leslie E.; Cheng, Tao; Luo, Hongbo R.

2017-01-01

Summary Both microbial infection and sterile inflammation augment bone marrow (BM) neutrophil production, but whether the induced accelerated granulopoiesis is mediated by a common pathway and the nature of such a pathway are poorly defined. We recently established that BM myeloid cell-derived reactive oxygen species (ROS) externally regulate myeloid progenitor proliferation and differentiation in bacteria-elicited emergency granulopoiesis. Here we show that BM ROS levels are also elevated during sterile inflammation. Similar to in microbial infection, ROS were mainly generated by the phagocytic NADPH oxidase in Gr1+ myeloid cells. The myeloid cells and their ROS were uniformly distributed in the BM when visualized by multi-photon intravital microscopy, and ROS production was both required and sufficient for sterile inflammation-elicited reactive granulopoiesis. Elevated granulopoiesis was mediated by ROS-induced PTEN oxidation and deactivation leading to upregulated PtdIns(3,4,5)P3 signaling and increased progenitor cell proliferation. Collectively, these results demonstrate that although infection-induced emergency granulopoiesis and sterile inflammation-elicited reactive granulopoiesis are triggered by different stimuli and are mediated by distinct upstream signals, the pathways converge to NADPH oxidase-dependent ROS production by BM myeloid cells. Thus, BM Gr1+ myeloid cells represent a key hematopoietic niche that supports accelerated granulopoiesis in both infective and sterile inflammation. This niche may be an excellent target in various immune-mediated pathologies or immune reconstitution after BM transplantation. PMID:28235862

Simulating Salt Movement and Transformation using a Coupled Reactive Transport Model in Variably-Saturated Groundwater Systems

NASA Astrophysics Data System (ADS)

Tavakoli Kivi, S.; Bailey, R. T.; Gates, T.

2016-12-01

Salinization is one of the major concerns in irrigated agricultural landscapes. Increasing salinity concentrations are due principally to evaporative concentration; dissolution of salts from weathered minerals and bedrock; and a high water table that results from excessive irrigation, canal seepage, and a lack of efficient drainage systems; leading to decreasing crop yield. High groundwater salinity loading to nearby river systems also impacts downstream areas, with saline river water diverted for application on irrigated fields. In this study, a solute transport model coupled with equilibrium chemistry reactions has been developed to simulate transport of individual salt ions in regional-scale aquifer systems and thereby investigate strategies for salinity remediation. The physically-based numerical model is based on the UZF-RT3D variably-saturated, multi-species groundwater reactive transport modeling code, and accounts for advection, dispersion, carbon and nitrogen cycling, oxidation-reduction reactions, and salt ion equilibrium chemistry reactions such as complexation, ion exchange, and precipitation/dissolution. Each major salt ion (sulfate, chloride, bicarbonate, calcium, sodium, magnesium, potassium) is included. The model has been tested against measured soil salinity at a small scale (soil profile) and against soil salinity, groundwater salinity, and groundwater salinity loading to surface water at the regional scale (500 km2) in the Lower Arkansas River Valley (LARV) in southeastern Colorado, an area acutely affected by salinization for many decades and greatly influenced by gypsum deposits. Preliminary results of using the model in scenario analysis suggest that increasing irrigation efficiency, sealing earthen canals, and rotational fallowing of land can decrease the groundwater salt load to the Arkansas River by 50 to 70% and substantially lower soil salinity in the root zone.

Mechanisms of electron acceptor utilization: Implications for simulating anaerobic biodegradation

USGS Publications Warehouse

Schreiber, M.E.; Carey, G.R.; Feinstein, D.T.; Bahr, J.M.

2004-01-01

Simulation of biodegradation reactions within a reactive transport framework requires information on mechanisms of terminal electron acceptor processes (TEAPs). In initial modeling efforts, TEAPs were approximated as occurring sequentially, with the highest energy-yielding electron acceptors (e.g. oxygen) consumed before those that yield less energy (e.g., sulfate). Within this framework in a steady state plume, sequential electron acceptor utilization would theoretically produce methane at an organic-rich source and Fe(II) further downgradient, resulting in a limited zone of Fe(II) and methane overlap. However, contaminant plumes often display much more extensive zones of overlapping Fe(II) and methane. The extensive overlap could be caused by several abiotic and biotic processes including vertical mixing of byproducts in long-screened monitoring wells, adsorption of Fe(II) onto aquifer solids, or microscale heterogeneity in Fe(III) concentrations. Alternatively, the overlap could be due to simultaneous utilization of terminal electron acceptors. Because biodegradation rates are controlled by TEAPs, evaluating the mechanisms of electron acceptor utilization is critical for improving prediction of contaminant mass losses due to biodegradation. Using BioRedox-MT3DMS, a three-dimensional, multi-species reactive transport code, we simulated the current configurations of a BTEX plume and TEAP zones at a petroleum- contaminated field site in Wisconsin. Simulation results suggest that BTEX mass loss due to biodegradation is greatest under oxygen-reducing conditions, with smaller but similar contributions to mass loss from biodegradation under Fe(III)-reducing, sulfate-reducing, and methanogenic conditions. Results of sensitivity calculations document that BTEX losses due to biodegradation are most sensitive to the age of the plume, while the shape of the BTEX plume is most sensitive to effective porosity and rate constants for biodegradation under Fe(III)-reducing and methanogenic conditions. Using this transport model, we had limited success in simulating overlap of redox products using reasonable ranges of parameters within a strictly sequential electron acceptor utilization framework. Simulation results indicate that overlap of redox products cannot be accurately simulated using the constructed model, suggesting either that Fe(III) reduction and methanogenesis are occurring simultaneously in the source area, or that heterogeneities in Fe(III) concentration and/or mineral type cause the observed overlap. Additional field, experimental, and modeling studies will be needed to address these questions. ?? 2004 Elsevier B.V. All rights reserved.

Three-Dimensional Multi-fluid Moment Simulation of Ganymede

NASA Astrophysics Data System (ADS)

Wang, L.; Germaschewski, K.; Hakim, A.; Bhattacharjee, A.; Dong, C.

2016-12-01

Plasmas in space environments, such as solar wind and Earth's magnetosphere, are often constituted of multiple species. Conventional MHD-based, single-fluid systems, have additional complications when multiple fluid species are introduced. We suggest space application of an alternative multi-fluid moment approach, treating each species on equal footing using exact evolution equations for moments of their distribution function, and electromagnetic fields through full Maxwell equations. Non-ideal effects like Hall effect, inertia, and even tensorial pressures, are self-consistently embedded without the need to explicitly solve a complicated Ohm's law. Previously, we have benchmarked this approach in classical test problems like the Orszag-Tang vortex and GEM reconnection challenge problem. Recently, we performed three-dimensional two-fluid simulation of the magnetosphere of Ganymede, using both five-moment (scalar pressures) and ten-moment (tensorial pressures) models. In both models, the formation of Alfven wing structure due to subsonic inflow is correctly captured, and the magnetic field data agree well with in-situ measurements from the Galileo flyby G8. The ten-moment simulation also showed the contribution of pressure tensor divergence to the reconnecting electric field. Initial results of coupling to state-of-art global simulation codes like OpenGGCM will also be shown, which will in the future provide a rigorous way for integration of ionospheric physics.

SEAWAT Version 4: A Computer Program for Simulation of Multi-Species Solute and Heat Transport

USGS Publications Warehouse

Langevin, Christian D.; Thorne, Daniel T.; Dausman, Alyssa M.; Sukop, Michael C.; Guo, Weixing

2008-01-01

The SEAWAT program is a coupled version of MODFLOW and MT3DMS designed to simulate three-dimensional, variable-density, saturated ground-water flow. Flexible equations were added to the program to allow fluid density to be calculated as a function of one or more MT3DMS species. Fluid density may also be calculated as a function of fluid pressure. The effect of fluid viscosity variations on ground-water flow was included as an option. Fluid viscosity can be calculated as a function of one or more MT3DMS species, and the program includes additional functions for representing the dependence on temperature. Although MT3DMS and SEAWAT are not explicitly designed to simulate heat transport, temperature can be simulated as one of the species by entering appropriate transport coefficients. For example, the process of heat conduction is mathematically analogous to Fickian diffusion. Heat conduction can be represented in SEAWAT by assigning a thermal diffusivity for the temperature species (instead of a molecular diffusion coefficient for a solute species). Heat exchange with the solid matrix can be treated in a similar manner by using the mathematically equivalent process of solute sorption. By combining flexible equations for fluid density and viscosity with multi-species transport, SEAWAT Version 4 represents variable-density ground-water flow coupled with multi-species solute and heat transport. SEAWAT Version 4 is based on MODFLOW-2000 and MT3DMS and retains all of the functionality of SEAWAT-2000. SEAWAT Version 4 also supports new simulation options for coupling flow and transport, and for representing constant-head boundaries. In previous versions of SEAWAT, the flow equation was solved for every transport timestep, regardless of whether or not there was a large change in fluid density. A new option was implemented in SEAWAT Version 4 that allows users to control how often the flow field is updated. New options were also implemented for representing constant-head boundaries with the Time-Variant Constant-Head (CHD) Package. These options allow for increased flexibility when using CHD flow boundaries with the zero-dispersive flux solute boundaries implemented by MT3DMS at constant-head cells. This report contains revised input instructions for the MT3DMS Dispersion (DSP) Package, Variable-Density Flow (VDF) Package, Viscosity (VSC) Package, and CHD Package. The report concludes with seven cases of an example problem designed to highlight many of the new features.

Interplay between subsurface structural heterogeneity and multi-species reactive transport in human health risk predictions

NASA Astrophysics Data System (ADS)

Henri, C.; Fernandez-Garcia, D.; de Barros, F.

2013-12-01

The increasing presence of toxic chemicals released in the subsurface has led to a rapid growth of social concerns and to the need to develop and employ models that can predict the impact of groundwater contamination in human health under uncertainty. Monitored natural attenuation is a common remediation action in many contamination cases and represents an attractive decontamination method. However, natural attenuation can lead to the production of subspecies of distinct toxicity that may pose challenges in pollution management strategies. The actual threat that these contaminants pose to human health and ecosystems greatly depends on the interplay between the complexity of the geological system and the toxicity of the pollutants and their byproducts. In this work, we examine the interplay between multispecies reactive transport and the heterogeneous structure of the contaminated aquifer on human health risk predictions. The structure and organization of hydraulic properties of the aquifer can lead to preferential flow channels and fast contamination pathways. Early travel times, associated to channeling effects, are intuitively perceived as an indicator for high risk. However, in the case of multi-species systems, early travel times may also lead a limited production of daughter species that may contain higher toxicity as in the case of chlorinated compounds. In this work, we model a Perchloroethylene (PCE) contamination problem followed by the sequential first-order production/biodegradation of its daughter species Trichloroethylene (TCE), Dichloroethylene (DCE) and Vinyl Chlorine (VC). For this specific case, VC is known to be a highly toxic contaminant. By performing numerical experiments, we evaluate transport for two distinct three-dimensional aquifer structures. First, a multi-Gaussian hydraulic conductivity field and secondly, a geostatistically equivalent connected field. These two heterogeneity structures will provide two distinct ranges of mean travel times and other higher order statistics. Uncertainty on the hydraulic conductivity field is considered through a Monte Carlo scheme, and the total risk (TR) for human health related to the mixtures of the four carcinogenic plumes is evaluated. Results show two distinct spatio-temporal behavior of the TR estimation. At a fixed environmentally sensitive location, aquifers with a high degree of connectivity display a lower TR. On the other hand, at the same environmentally sensitive location, the poorly connected aquifer yields higher TR. Our results reflect the interplay between the characteristic reactive time for each component and the characteristic travel time of the plume since the production of VC depends on these factors.

LES study of the impact of moist thermals on the oxidative capacity of the atmosphere in southern West Africa

NASA Astrophysics Data System (ADS)

Brosse, Fabien; Leriche, Maud; Mari, Céline; Couvreux, Fleur

2018-05-01

The hydroxyl radical (OH) is a highly reactive species and plays a key role in the oxidative capacity of the atmosphere. We explore the potential impact of a convective boundary layer on reconciling the calculation-measurement differences for OH reactivity (the inverse of OH lifetime) attributable to the segregation of OH and its reactants by thermals and the resulting modification of averaged reaction rates. The large-eddy simulation version of the Meso-NH model is used, coupled on-line with a detailed chemistry mechanism to simulate two contrasted biogenic and urban chemical regimes. In both environments, the top of the boundary layer is the region with the highest calculated segregation intensities but with the opposite sign. In the biogenic environment, the inhomogeneous mixing of isoprene and OH leads to a maximum decrease of 30 % of the mean reaction rate in this zone. In the anthropogenic case, the effective rate constant for OH reacting with aldehydes is 16 % higher than the averaged value. OH reactivity is always higher by 15 to 40 % inside thermals in comparison to their surroundings as a function of the chemical environment and time of the day. Since thermals occupy a small fraction of the simulated domain, the impact of turbulent motions on domain-averaged total OH reactivity reaches a maximum decrease of 9 % for the biogenic case and a maximum increase of 5 % for the anthropogenic case. Accounting for the segregation of air masses by turbulent motions in regional and global models may increase OH reactivity in urban environments but lower OH reactivity in biogenic environments. In both cases, segregation alone is insufficient for resolving the underestimation between observed and modeled OH reactivity.

An improved AVC strategy applied in distributed wind power system

NASA Astrophysics Data System (ADS)

Zhao, Y. N.; Liu, Q. H.; Song, S. Y.; Mao, W.

2016-08-01

Traditional AVC strategy is mainly used in wind farm and only concerns about grid connection point, which is not suitable for distributed wind power system. Therefore, this paper comes up with an improved AVC strategy applied in distributed wind power system. The strategy takes all nodes of distribution network into consideration and chooses the node having the most serious voltage deviation as control point to calculate the reactive power reference. In addition, distribution principles can be divided into two conditions: when wind generators access to network on single node, the reactive power reference is distributed according to reactive power capacity; when wind generators access to network on multi-node, the reference is distributed according to sensitivity. Simulation results show the correctness and reliability of the strategy. Compared with traditional control strategy, the strategy described in this paper can make full use of generators reactive power output ability according to the distribution network voltage condition and improve the distribution network voltage level effectively.

Numerical simulation of two-dimensional flow over a heated carbon surface with coupled heterogeneous and homogeneous reactions

NASA Astrophysics Data System (ADS)

Johnson, Ryan Federick; Chelliah, Harsha Kumar

2017-01-01

For a range of flow and chemical timescales, numerical simulations of two-dimensional laminar flow over a reacting carbon surface were performed to understand further the complex coupling between heterogeneous and homogeneous reactions. An open-source computational package (OpenFOAM®) was used with previously developed lumped heterogeneous reaction models for carbon surfaces and a detailed homogeneous reaction model for CO oxidation. The influence of finite-rate chemical kinetics was explored by varying the surface temperatures from 1800 to 2600 K, while flow residence time effects were explored by varying the free-stream velocity up to 50 m/s. The reacting boundary layer structure dependence on the residence time was analysed by extracting the ratio of chemical source and species diffusion terms. The important contributions of radical species reactions on overall carbon removal rate, which is often neglected in multi-dimensional simulations, are highlighted. The results provide a framework for future development and validation of lumped heterogeneous reaction models based on multi-dimensional reacting flow configurations.

Microbial respiration and dissolution precipitation reactions of minerals: thermo-kinetics and reactive transport modelling

NASA Astrophysics Data System (ADS)

Azaroual, M. M.; Parmentier, M.; Andre, L.; Croiset, N.; Pettenati, M.; Kremer, S.

2010-12-01

Microbial processes interact closely with abiotic geochemical reactions and mineralogical transformations in several hydrogeochemical systems. Reactive transport models are aimed to analyze these complex mechanisms integrating as well as the degradation of organic matter as the redox reactions involving successive terminal electron acceptors (TEAPs) mediated by microbes through the continuum of unsaturated zone (soil) - saturated zone (aquifer). The involvement of microbial processes in reactive transport in soil and subsurface geologic greatly complicates the mastery of the major mechanisms and the numerical modelling of these systems. The introduction of kinetic constraints of redox reactions in aqueous phase requires the decoupling of equilibrium reactions and the redefinition of mass balance of chemical elements including the concept of basis species and secondary species of thermodynamic databases used in geochemical modelling tools. An integrated methodology for modelling the reactive transport has been developed and implemented to simulate the transfer of arsenic, denitrification processes and the role of metastable aqueous sulfur species with pyrite and organic matter as electron donors entities. A mechanistic rate law of microbial respiration in various geochemical environments was used to simulate reactive transport of arsenic, nitrate and organic matter combined to the generalized rate law of mineral dissolution - precipitation reactions derived from the transition state theory was used for dissolution - precipitation of silica, aluminosilicate, carbonate, oxyhydroxide, and sulphide minerals. The kinetic parameters are compiled from the literature measurements based on laboratory constrained experiments and field observations. Numerical simulations, using the geochemical software PHREEQC, were performed aiming to identify the key reactions mediated by microbes in the framework of in the first hand the concept of the unsaturated - saturated zones of an artificial recharge of deep aquifers system and in a second hand an acid mine drainage system. A large amount of data is available on the old mine site of Cheni (France). This field data on acid mine drainage are compared to a thermokinetic model including biological kinetics, precipitation-dissolution kinetics and surface complexation on ferrihydrite. The kinetic parameters are from literature and from a fitting on batch biological experiments. The integrated approach combining reaction kinetics and biogeochemical thermodynamic constraints is successfully applied to denitrification experiments in the presence of acetate and pyrite conducted in the laboratory for batch and column systems. The powerful of this coupled approach allows a fine description of the different transition species from nitrate to nitrogen. The fitted kinetic parameters established for modelling these laboratory results are thus extended to simulate the denitrification processes in a field case where organic matter and pyrite FeS2 are the electron donors and O2, NO3, Fe(OH)3, SO4 are the electron acceptors in the framework of a continuum UZ - SZ aiming to identify the stabilized redox zones of acid mine drainage. The detailed results obtained on two actual case studies will be presented.

Selective Photocatalytic Disinfection by Coupling StrepMiniSog to the Antibody Catalyzed Water Oxidation Pathway

PubMed Central

2016-01-01

For several decades reactive oxygen species have been applied to water quality engineering and efficient disinfection strategies; however, these methods are limited by disinfection byproduct and catalyst-derived toxicity concerns which could be improved by selectively targeting contaminants of interest. Here we present a targeted photocatalytic system based on the fusion protein StrepMiniSOG that uses light within the visible spectrum to produce reactive oxygen species at a greater efficiency than current photosensitizers, allowing for shorter irradiation times from a fully biodegradable photocatalyst. The StrepMiniSOG photodisinfection system is unable to cross cell membranes and like other consumed proteins, can be degraded by endogenous digestive enzymes in the human gut, thereby reducing the consumption risks typically associated with other disinfection agents. We demonstrate specific, multi-log removal of Listeria monocytogenes from a mixed population of bacteria, establishing the StrepMiniSOG disinfection system as a valuable tool for targeted pathogen removal, while maintaining existing microbial biodiversity. PMID:27617441

Selective Photocatalytic Disinfection by Coupling StrepMiniSog to the Antibody Catalyzed Water Oxidation Pathway.

PubMed

Wurtzler, Elizabeth M; Wendell, David

2016-01-01

For several decades reactive oxygen species have been applied to water quality engineering and efficient disinfection strategies; however, these methods are limited by disinfection byproduct and catalyst-derived toxicity concerns which could be improved by selectively targeting contaminants of interest. Here we present a targeted photocatalytic system based on the fusion protein StrepMiniSOG that uses light within the visible spectrum to produce reactive oxygen species at a greater efficiency than current photosensitizers, allowing for shorter irradiation times from a fully biodegradable photocatalyst. The StrepMiniSOG photodisinfection system is unable to cross cell membranes and like other consumed proteins, can be degraded by endogenous digestive enzymes in the human gut, thereby reducing the consumption risks typically associated with other disinfection agents. We demonstrate specific, multi-log removal of Listeria monocytogenes from a mixed population of bacteria, establishing the StrepMiniSOG disinfection system as a valuable tool for targeted pathogen removal, while maintaining existing microbial biodiversity.

Lipoic acid metabolism and mitochondrial redox regulation.

PubMed

Solmonson, Ashley D; DeBerardinis, Ralph J

2017-11-30

Lipoic acid is an essential cofactor for mitochondrial metabolism and is synthesized de novo using intermediates from mitochondrial fatty acid synthesis type II, S-adenosylmethionine and iron-sulfur clusters. This cofactor is required for catalysis by multiple mitochondrial 2-ketoacid dehydrogenase complexes, including pyruvate dehydrogenase, alpha-ketoglutarate dehydrogenase, and branched-chain ketoacid dehydrogenase. Lipoic acid also plays a critical role in stabilizing and regulating these multi-enzyme complexes.  Many of these dehydrogenases are regulated by reactive oxygen species, mediated through the disulfide bond of the prosthetic lipoyl moiety.  Collectively, its functions explain why lipoic acid is required for cell growth, mitochondrial activity and coordination of fuel metabolism. Lipoic acid is an essential cofactor for mitochondrial metabolism and is synthesized de novo using intermediates from mitochondrial fatty acid synthesis type II, S-adenosylmethionine and iron-sulfur clusters. This cofactor is required for catalysis by multiple mitochondrial 2-ketoacid dehydrogenase complexes, including pyruvate dehydrogenase, alpha-ketoglutarate dehydrogenase, and branched-chain ketoacid dehydrogenase. Lipoic acid also plays a critical role in stabilizing and regulating these multi-enzyme complexes.  Many of these dehydrogenases are regulated by reactive oxygen species, mediated through the disulfide bond of the prosthetic lipoyl moiety.  Collectively, its functions explain why lipoic acid is required for cell growth, mitochondrial activity and coordination of fuel metabolism. Copyright © 2017, The American Society for Biochemistry and Molecular Biology.

Inverse correlation between reactive oxygen species in unwashed semen and sperm motion parameters as measured by a computer-assisted semen analyzer.

PubMed

Takeshima, Teppei; Yumura, Yasushi; Yasuda, Kengo; Sanjo, Hiroyuki; Kuroda, Shinnosuke; Yamanaka, Hiroyuki; Iwasaki, Akira

2017-01-01

This study investigated the correlation between sperm motion parameters obtained by a computer-assisted semen analyzer and levels of reactive oxygen species in unwashed semen. In total, 847 patients, except for azoospermic patients were investigated. At the time of each patient's first consultation, semen parameters were measured using SMAS™ or CellSoft 3000™, and production of reactive oxygen species was measured using a computer-driven LKB Wallac Luminometer 1251 Analyzer. The patients were divided into two groups: reactive oxygen species - positive and negative. The semen parameters within each group were measured using one of the two computer-assisted semen analyzer systems and then compared. Correlations between reactive oxygen species levels and sperm motion parameters in semen from the reactive oxygen species - positive group were also investigated. Reactive oxygen species were detected in semen samples of 282 cases (33.3%). Sperm concentration (P < 0.01; P < 0.01), motility (P < 0.01; P < 0.05), and progressive motility (P < 0.01; P < 0.01) were markedly lower in the reactive oxygen species - positive group than in the reactive oxygen species - negative group. Among the sperm motion parameters in the reactive oxygen species - positive group, sperm concentration (P < 0.01; P < 0.01), motility (P < 0.05; P < 0.01), mALH (P < 0.05; P < 0.01), and progressive motility (P < 0.05; P < 0.01) also showed inverse correlations with the logarithmic transformed reactive oxygen species levels. Therefore, this study demonstrated that excessive reactive oxygen species in semen damage sperm concentration, motility, and other sperm motion parameters.

Preconcentration and Separation of Mixed-Species Samples Near a Nano-Junction in a Convergent Microchannel

PubMed Central

Chiu, Ping-Hsien; Weng, Chen-Hsun; Yang, Ruey-Jen

2015-01-01

A fluidic microchip incorporating a convergent microchannel and a Nafion-nanoporous membrane is proposed for the preconcentration and separation of multi-species samples on a single platform. In the device, sample preconcentration is achieved by means of the ion concentration polarization effect induced at the micro/nano interface under the application of an external electric field, while species separation is achieved by exploiting the different electrophoretic mobilities of the sample components. The experimental results show that the device is capable of detecting C-reactive protein (CRP) with an initial concentration as low as 9.50 × 10−6 mg/L given a sufficient preconcentration time and driving voltage. In addition, it is shown that a mixed-species sample consisting of three negatively-charged components (bovine serum albumin (BSA), tetramethylrhodamine(TAMRA) isothiocyanate-Dextran and fluorescent polymer beads) can be separated and preconcentrated within 20 min given a driving voltage of 100 V across 1 cm microchannel in length. In general, the present results confirm the feasibility of the device for the immunoassay or detection of various multi-species samples under low concentration in the biochemical and biomedical fields. The novel device can therefore improve the detection limit of traditional medical facilities. PMID:26690167

Lattice Boltzmann simulation of CO2 reactive transport in network fractured media

NASA Astrophysics Data System (ADS)

Tian, Zhiwei; Wang, Junye

2017-08-01

Carbon dioxide (CO2) geological sequestration plays an important role in mitigating CO2 emissions for climate change. Understanding interactions of the injected CO2 with network fractures and hydrocarbons is key for optimizing and controlling CO2 geological sequestration and evaluating its risks to ground water. However, there is a well-known, difficult process in simulating the dynamic interaction of fracture-matrix, such as dynamic change of matrix porosity, unsaturated processes in rock matrix, and effect of rock mineral properties. In this paper, we develop an explicit model of the fracture-matrix interactions using multilayer bounce-back treatment as a first attempt to simulate CO2 reactive transport in network fractured media through coupling the Dardis's LBM porous model for a new interface treatment. Two kinds of typical fracture networks in porous media are simulated: straight cross network fractures and interleaving network fractures. The reaction rate and porosity distribution are illustrated and well-matched patterns are found. The species concentration distribution and evolution with time steps are also analyzed and compared with different transport properties. The results demonstrate the capability of this model to investigate the complex processes of CO2 geological injection and reactive transport in network fractured media, such as dynamic change of matrix porosity.

Hybrid Multiscale Finite Volume method for multiresolution simulations of flow and reactive transport in porous media

NASA Astrophysics Data System (ADS)

Barajas-Solano, D. A.; Tartakovsky, A. M.

2017-12-01

We present a multiresolution method for the numerical simulation of flow and reactive transport in porous, heterogeneous media, based on the hybrid Multiscale Finite Volume (h-MsFV) algorithm. The h-MsFV algorithm allows us to couple high-resolution (fine scale) flow and transport models with lower resolution (coarse) models to locally refine both spatial resolution and transport models. The fine scale problem is decomposed into various "local'' problems solved independently in parallel and coordinated via a "global'' problem. This global problem is then coupled with the coarse model to strictly ensure domain-wide coarse-scale mass conservation. The proposed method provides an alternative to adaptive mesh refinement (AMR), due to its capacity to rapidly refine spatial resolution beyond what's possible with state-of-the-art AMR techniques, and the capability to locally swap transport models. We illustrate our method by applying it to groundwater flow and reactive transport of multiple species.

Measurement of Reactive Oxygen Species, Reactive Nitrogen Species, and Redox-Dependent Signaling in the Cardiovascular System

PubMed Central

Griendling, Kathy K.; Touyz, Rhian M.; Zweier, Jay L.; Dikalov, Sergey; Chilian, William; Chen, Yeong-Renn; Harrison, David G.; Bhatnagar, Aruni

2017-01-01

Reactive oxygen species and reactive nitrogen species are biological molecules that play important roles in cardiovascular physiology and contribute to disease initiation, progression, and severity. Because of their ephemeral nature and rapid reactivity, these species are difficult to measure directly with high accuracy and precision. In this statement, we review current methods for measuring these species and the secondary products they generate and suggest approaches for measuring redox status, oxidative stress, and the production of individual reactive oxygen and nitrogen species. We discuss the strengths and limitations of different methods and the relative specificity and suitability of these methods for measuring the concentrations of reactive oxygen and reactive nitrogen species in cells, tissues, and biological fluids. We provide specific guidelines, through expert opinion, for choosing reliable and reproducible assays for different experimental and clinical situations. These guidelines are intended to help investigators and clinical researchers avoid experimental error and ensure high-quality measurements of these important biological species. PMID:27418630

ANTIOXIDANT FUNCTIONS FOR THE HEMOGLOBIN β93 CYSTEINE RESIDUE IN ERYTHROCYTES AND IN THE VASCULAR COMPARTMENT IN VIVO

PubMed Central

Vitturi, Dario A.; Sun, Chiao-Wang; Harper, Victoria M; Thrash-Williams, Bessy; Cantu-Medellin, Nadiezhda; Chacko, Balu K.; Peng, Ning; Dai, Yanying; Michael Wyss, J.; Townes, Tim; Patel, Rakesh P.

2013-01-01

The β93 Cysteine (β93Cys) residue of hemoglobin is conserved in vertebrates but its function in the red blood cell (RBC) remains unclear. Since this residue is present at concentrations more than two orders of magnitude higher than enzymatic components of the RBC antioxidant network, a role in the scavenging of reactive species was hypothesized. Initial studies utilizing mice that express human hemoglobin with either Cys (B93C) or Ala (B93A) at the β93 positions, demonstrated that loss of the β93Cys did not affect activities nor expression of established components of the RBC antioxidant network (catalase, superoxide dismutase, peroxiredoxin-2, glutathione peroxidase, GSH:GSSG ratios). Interestingly, exogenous addition to RBC of reactive species that are involved in vascular inflammation demonstrated a role for the β93Cys in hydrogen peroxide and chloramine consumption. To simulate oxidative stress and inflammation in vivo, mice were challenged with LPS. Notably, LPS induced a greater degree of hypotension and lung injury in B93A versus B93C mice, which was associated with greater formation of RBC reactive species and accumulation of DMPO-reactive epitopes in the lung. These data suggest that the β93Cys is an important effector within the RBC antioxidant network contributing to the modulation of tissue injury during vascular inflammation. PMID:23159546

RECOMMENDED METHODS FOR AMBIENT AIR MONITORING OF NO, NO2, NOY, AND INDIVIDUAL NOZ SPECIES

EPA Science Inventory

The most appropriate monitoring methods for reactive nitrogen oxides are identified subject to the requirements for diagnostic testing of air quality simulation models. Measurements must be made over 1 h or less and with an uncertainty of

Impact of solar UV radiation on toxicity of ZnO nanoparticles through photocatalytic reactive oxygen species (ROS) generation and photo-induced dissolution

EPA Science Inventory

The present study investigated the impact of solar UV radiation on ZnO nanoparticle toxicity through photocatalytic ROS generation and photo-induced dissolution. Toxicity of ZnO nanoparticles to Daphnia magna was examined under laboratory light versus simulated solar UV radiatio...

Potential phototoxicity of aged Al(OH)3-coated Ti02 nanoparticles in retinal pigment epithelial cells

EPA Science Inventory

Titanium dioxide (TiO2) nanoparticles (NPs) exposed to UVA radiation generate reactive oxygen species (ROS). As a component of sunscreen formulations, TiO2 NPs may be coated with Al(OH)3 to prevent ROS from causing oxidative damage to tissues. Simulated swimming pool water (SSPW)...

Photocatalytic ROS production and phototoxicity of titanium dioxide nanoparticles is dependent on solar UV radiation spectrum

EPA Science Inventory

Generation of reactive oxygen species (ROS) by titanium dioxide nanoparticles (nano-TiO2) and its consequent phototoxicity to Daphnia magna were measured under different solar UV radiation spectrum by applying a series of optical filters in a solar simulator. Removing UVB (280-32...

Coupling lattice Boltzmann and continuum equations for flow and reactive transport in porous media.

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

Coon, Ethan; Porter, Mark L.; Kang, Qinjun

2012-06-18

In spatially and temporally localized instances, capturing sub-reservoir scale information is necessary. Capturing sub-reservoir scale information everywhere is neither necessary, nor computationally possible. The lattice Boltzmann Method for solving pore-scale systems. At the pore-scale, LBM provides an extremely scalable, efficient way of solving Navier-Stokes equations on complex geometries. Coupling pore-scale and continuum scale systems via domain decomposition. By leveraging the interpolations implied by pore-scale and continuum scale discretizations, overlapping Schwartz domain decomposition is used to ensure continuity of pressure and flux. This approach is demonstrated on a fractured medium, in which Navier-Stokes equations are solved within the fracture while Darcy'smore » equation is solved away from the fracture Coupling reactive transport to pore-scale flow simulators allows hybrid approaches to be extended to solve multi-scale reactive transport.« less

From conservative to reactive transport under diffusion-controlled conditions

NASA Astrophysics Data System (ADS)

Babey, Tristan; de Dreuzy, Jean-Raynald; Ginn, Timothy R.

2016-05-01

We assess the possibility to use conservative transport information, such as that contained in transit time distributions, breakthrough curves and tracer tests, to predict nonlinear fluid-rock interactions in fracture/matrix or mobile/immobile conditions. Reference simulated data are given by conservative and reactive transport simulations in several diffusive porosity structures differing by their topological organization. Reactions includes nonlinear kinetically controlled dissolution and desorption. Effective Multi-Rate Mass Transfer models (MRMT) are calibrated solely on conservative transport information without pore topology information and provide concentration distributions on which effective reaction rates are estimated. Reference simulated reaction rates and effective reaction rates evaluated by MRMT are compared, as well as characteristic desorption and dissolution times. Although not exactly equal, these indicators remain very close whatever the porous structure, differing at most by 0.6% and 10% for desorption and dissolution. At early times, this close agreement arises from the fine characterization of the diffusive porosity close to the mobile zone that controls fast mobile-diffusive exchanges. At intermediate to late times, concentration gradients are strongly reduced by diffusion, and reactivity can be captured by a very limited number of rates. We conclude that effective models calibrated solely on conservative transport information like MRMT can accurately estimate monocomponent kinetically controlled nonlinear fluid-rock interactions. Their relevance might extend to more advanced biogeochemical reactions because of the good characterization of conservative concentration distributions, even by parsimonious models (e.g., MRMT with 3-5 rates). We propose a methodology to estimate reactive transport from conservative transport in mobile-immobile conditions.

A Quantum Non-Demolition Parity measurement in a mixed-species trapped-ion quantum processor

NASA Astrophysics Data System (ADS)

Marinelli, Matteo; Negnevitsky, Vlad; Lo, Hsiang-Yu; Flühmann, Christa; Mehta, Karan; Home, Jonathan

2017-04-01

Quantum non-demolition measurements of multi-qubit systems are an important tool in quantum information processing, in particular for syndrome extraction in quantum error correction. We have recently demonstrated a protocol for quantum non-demolition measurement of the parity of two beryllium ions by detection of a co-trapped calcium ion. The measurement requires a sequence of quantum gates between the three ions, using mixed-species gates between beryllium hyperfine qubits and a calcium optical qubit. Our work takes place in a multi-zone segmented trap setup in which we have demonstrated high fidelity control of both species and multi-well ion shuttling. The advantage of using two species of ion is that we can individually manipulate and read out the state of each ion species without disturbing the internal state of the other. The methods demonstrated here can be used for quantum error correcting codes as well as quantum metrology and are key ingredients for realizing a hybrid universal quantum computer based on trapped ions. Mixed-species control may also enable the investigation of new avenues in quantum simulation and quantum state control. left the group and working in a company now.

Biogeochemical reactive transport of carbon, nitrogen and iron in the hyporheic zone

NASA Astrophysics Data System (ADS)

Dwivedi, D.; Steefel, C. I.; Newcomer, M. E.; Arora, B.; Spycher, N.; Hammond, G. E.; Moulton, J. D.; Fox, P. M.; Nico, P. S.; Williams, K. H.; Dafflon, B.; Carroll, R. W. H.

2017-12-01

To understand how biogeochemical processes in the hyporheic zone influence carbon and nitrogen cycling as well as stream biogeochemistry, we developed a biotic and abiotic reaction network and integrated it into a reactive transport simulator - PFLOTRAN. Three-dimensional reactive flow and transport simulations were performed to describe the hyporheic exchange of fluxes from and within an intra-meander region encompassing two meanders of East River in the East Taylor watershed, Colorado. The objectives of this study were to quantify (1) the effect of transience on the export of carbon, nitrogen, and iron; and (2) the biogeochemical transformation of nitrogen and carbon species as a function of the residence time. The model was able to capture reasonably well the observed trends of nitrate and dissolved oxygen values that decreased as well as iron (Fe (II)) values that increased along the meander centerline away from the stream. Hyporheic flow paths create lateral redox zonation within intra-meander regions, which considerably impact nitrogen export into the stream system. Simulation results further demonstrated that low water conditions lead to higher levels of dissolved iron in groundwater, which (Fe (II)> 80%) is exported to the stream on the downstream side during high water conditions. An important conclusion from this study is that reactive transport models representing spatial and temporal heterogeneities are required to identify important factors that contribute to the redox gradients at riverine scales.

Mitochondrial reactive oxygen species accelerate gastric cancer cell invasion

PubMed Central

Tamura, Masato; Matsui, Hirofumi; Tomita, Tsutomu; Sadakata, Hisato; Indo, Hiroko P.; Majima, Hideyuki J.; Kaneko, Tsuyoshi; Hyodo, Ichinosuke

2014-01-01

Tumor invasion is the most important factor to decide patient’s prognosis. The relation between reactive oxygen species and tumor invasion is mainly reported that nicotinamide adenine dinucleotide phosphate oxidase in the cell membrane is a reactive oxygen species producer for formulating an invadopodia. On the other hand, mitochondrion was known as one of the most important reactive oxygen species-producer in the cell via an energy transfer system. However, the relation between mitochondrial reactive oxygen species and the tumor invasion was not well clarified. In this study, we evaluated the relation between mitochondrial reactive oxygen species and tumor invasion using a normal gastric mucosal cell-line (RGM-1) and a cancerous mutant RGM-1 cell-line (RGK-1). Manganese superoxide dismutase-expressing RGK-1 cell-lines were used for a scavenging mitochondrial reactive oxygen species. The cells have been evaluated their movement ability as follows; cellular ruffling frequencies, wound healing assay to evaluate horizontal cellular migration, and invasion assay using matrigel to analyze vertical cellular migration. All cellular movement abilities were inhibited by scavenging mitochondrial reactive oxygen species with manganese superoxide dismutase. Therefore mitochondrial reactive oxygen species was one of factors enhancing the tumor invasion in gastric cancer. PMID:24426185

Effect of nanoscale flows on the surface structure of nanoporous catalysts.

PubMed

Montemore, Matthew M; Montessori, Andrea; Succi, Sauro; Barroo, Cédric; Falcucci, Giacomo; Bell, David C; Kaxiras, Efthimios

2017-06-07

The surface structure and composition of a multi-component catalyst are critical factors in determining its catalytic performance. The surface composition can depend on the local pressure of the reacting species, leading to the possibility that the flow through a nanoporous catalyst can affect its structure and reactivity. Here, we explore this possibility for oxidation reactions on nanoporous gold, an AgAu bimetallic catalyst. We use microscopy and digital reconstruction to obtain the morphology of a two-dimensional slice of a nanoporous gold sample. Using lattice Boltzmann fluid dynamics simulations along with thermodynamic models based on first-principles total-energy calculations, we show that some sections of this sample have low local O 2 partial pressures when exposed to reaction conditions, which leads to a pure Au surface in these regions, instead of the active bimetallic AgAu phase. We also explore the effect of temperature on the surface structure and find that moderate temperatures (≈300-450 K) should result in the highest intrinsic catalytic performance, in apparent agreement with experimental results.

Multi-Scale Computational Enzymology: Enhancing Our Understanding of Enzymatic Catalysis

PubMed Central

Gherib, Rami; Dokainish, Hisham M.; Gauld, James W.

2014-01-01

Elucidating the origin of enzymatic catalysis stands as one the great challenges of contemporary biochemistry and biophysics. The recent emergence of computational enzymology has enhanced our atomistic-level description of biocatalysis as well the kinetic and thermodynamic properties of their mechanisms. There exists a diversity of computational methods allowing the investigation of specific enzymatic properties. Small or large density functional theory models allow the comparison of a plethora of mechanistic reactive species and divergent catalytic pathways. Molecular docking can model different substrate conformations embedded within enzyme active sites and determine those with optimal binding affinities. Molecular dynamics simulations provide insights into the dynamics and roles of active site components as well as the interactions between substrate and enzymes. Hybrid quantum mechanical/molecular mechanical (QM/MM) can model reactions in active sites while considering steric and electrostatic contributions provided by the surrounding environment. Using previous studies done within our group, on OvoA, EgtB, ThrRS, LuxS and MsrA enzymatic systems, we will review how these methods can be used either independently or cooperatively to get insights into enzymatic catalysis. PMID:24384841

Non-equilibrium reaction and relaxation dynamics in a strongly interacting explicit solvent: F + CD3CN treated with a parallel multi-state EVB model

NASA Astrophysics Data System (ADS)

Glowacki, David R.; Orr-Ewing, Andrew J.; Harvey, Jeremy N.

2015-07-01

We describe a parallelized linear-scaling computational framework developed to implement arbitrarily large multi-state empirical valence bond (MS-EVB) calculations within CHARMM and TINKER. Forces are obtained using the Hellmann-Feynman relationship, giving continuous gradients, and good energy conservation. Utilizing multi-dimensional Gaussian coupling elements fit to explicitly correlated coupled cluster theory, we built a 64-state MS-EVB model designed to study the F + CD3CN → DF + CD2CN reaction in CD3CN solvent (recently reported in Dunning et al. [Science 347(6221), 530 (2015)]). This approach allows us to build a reactive potential energy surface whose balanced accuracy and efficiency considerably surpass what we could achieve otherwise. We ran molecular dynamics simulations to examine a range of observables which follow in the wake of the reactive event: energy deposition in the nascent reaction products, vibrational relaxation rates of excited DF in CD3CN solvent, equilibrium power spectra of DF in CD3CN, and time dependent spectral shifts associated with relaxation of the nascent DF. Many of our results are in good agreement with time-resolved experimental observations, providing evidence for the accuracy of our MS-EVB framework in treating both the solute and solute/solvent interactions. The simulations provide additional insight into the dynamics at sub-picosecond time scales that are difficult to resolve experimentally. In particular, the simulations show that (immediately following deuterium abstraction) the nascent DF finds itself in a non-equilibrium regime in two different respects: (1) it is highly vibrationally excited, with ˜23 kcal mol-1 localized in the stretch and (2) its post-reaction solvation environment, in which it is not yet hydrogen-bonded to CD3CN solvent molecules, is intermediate between the non-interacting gas-phase limit and the solution-phase equilibrium limit. Vibrational relaxation of the nascent DF results in a spectral blue shift, while relaxation of the post-reaction solvation environment results in a red shift. These two competing effects mean that the post-reaction relaxation profile is distinct from what is observed when Franck-Condon vibrational excitation of DF occurs within a microsolvation environment initially at equilibrium. Our conclusions, along with the theoretical and parallel software framework presented in this paper, should be more broadly applicable to a range of complex reactive systems.

Integration of Advanced Probabilistic Analysis Techniques with Multi-Physics Models

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

Cetiner, Mustafa Sacit; none,; Flanagan, George F.

2014-07-30

An integrated simulation platform that couples probabilistic analysis-based tools with model-based simulation tools can provide valuable insights for reactive and proactive responses to plant operating conditions. The objective of this work is to demonstrate the benefits of a partial implementation of the Small Modular Reactor (SMR) Probabilistic Risk Assessment (PRA) Detailed Framework Specification through the coupling of advanced PRA capabilities and accurate multi-physics plant models. Coupling a probabilistic model with a multi-physics model will aid in design, operations, and safety by providing a more accurate understanding of plant behavior. This represents the first attempt at actually integrating these two typesmore » of analyses for a control system used for operations, on a faster than real-time basis. This report documents the development of the basic communication capability to exchange data with the probabilistic model using Reliability Workbench (RWB) and the multi-physics model using Dymola. The communication pathways from injecting a fault (i.e., failing a component) to the probabilistic and multi-physics models were successfully completed. This first version was tested with prototypic models represented in both RWB and Modelica. First, a simple event tree/fault tree (ET/FT) model was created to develop the software code to implement the communication capabilities between the dynamic-link library (dll) and RWB. A program, written in C#, successfully communicates faults to the probabilistic model through the dll. A systems model of the Advanced Liquid-Metal Reactor–Power Reactor Inherently Safe Module (ALMR-PRISM) design developed under another DOE project was upgraded using Dymola to include proper interfaces to allow data exchange with the control application (ConApp). A program, written in C+, successfully communicates faults to the multi-physics model. The results of the example simulation were successfully plotted.« less

Measurement of Reactive Oxygen Species, Reactive Nitrogen Species, and Redox-Dependent Signaling in the Cardiovascular System: A Scientific Statement From the American Heart Association.

PubMed

Griendling, Kathy K; Touyz, Rhian M; Zweier, Jay L; Dikalov, Sergey; Chilian, William; Chen, Yeong-Renn; Harrison, David G; Bhatnagar, Aruni

2016-08-19

Reactive oxygen species and reactive nitrogen species are biological molecules that play important roles in cardiovascular physiology and contribute to disease initiation, progression, and severity. Because of their ephemeral nature and rapid reactivity, these species are difficult to measure directly with high accuracy and precision. In this statement, we review current methods for measuring these species and the secondary products they generate and suggest approaches for measuring redox status, oxidative stress, and the production of individual reactive oxygen and nitrogen species. We discuss the strengths and limitations of different methods and the relative specificity and suitability of these methods for measuring the concentrations of reactive oxygen and reactive nitrogen species in cells, tissues, and biological fluids. We provide specific guidelines, through expert opinion, for choosing reliable and reproducible assays for different experimental and clinical situations. These guidelines are intended to help investigators and clinical researchers avoid experimental error and ensure high-quality measurements of these important biological species. © 2016 American Heart Association, Inc.

Hybrid finite-volume/transported PDF method for the simulation of turbulent reactive flows

NASA Astrophysics Data System (ADS)

Raman, Venkatramanan

A novel computational scheme is formulated for simulating turbulent reactive flows in complex geometries with detailed chemical kinetics. A Probability Density Function (PDF) based method that handles the scalar transport equation is coupled with an existing Finite Volume (FV) Reynolds-Averaged Navier-Stokes (RANS) flow solver. The PDF formulation leads to closed chemical source terms and facilitates the use of detailed chemical mechanisms without approximations. The particle-based PDF scheme is modified to handle complex geometries and grid structures. Grid-independent particle evolution schemes that scale linearly with the problem size are implemented in the Monte-Carlo PDF solver. A novel algorithm, in situ adaptive tabulation (ISAT) is employed to ensure tractability of complex chemistry involving a multitude of species. Several non-reacting test cases are performed to ascertain the efficiency and accuracy of the method. Simulation results from a turbulent jet-diffusion flame case are compared against experimental data. The effect of micromixing model, turbulence model and reaction scheme on flame predictions are discussed extensively. Finally, the method is used to analyze the Dow Chlorination Reactor. Detailed kinetics involving 37 species and 158 reactions as well as a reduced form with 16 species and 21 reactions are used. The effect of inlet configuration on reactor behavior and product distribution is analyzed. Plant-scale reactors exhibit quenching phenomena that cannot be reproduced by conventional simulation methods. The FV-PDF method predicts quenching accurately and provides insight into the dynamics of the reactor near extinction. The accuracy of the fractional time-stepping technique in discussed in the context of apparent multiple-steady states observed in a non-premixed feed configuration of the chlorination reactor.

Overheating Anomalies during Flight Test Due to the Base Bleeding

NASA Technical Reports Server (NTRS)

Luchinsky, Dmitry; Hafiychuck, Halyna; Osipov, Slava; Ponizhovskaya, Ekaterina; Smelyanskiy, Vadim; Dagostino, Mark; Canabal, Francisco; Mobley, Brandon L.

2012-01-01

In this paper we present the results of the analytical and numerical studies of the plume interaction with the base flow in the presence of base out-gassing. The physics-based analysis and CFD modeling of the base heating for single solid rocket motor performed in this research addressed the following questions: what are the key factors making base flow so different from that in the Shuttle [1]; why CFD analysis of this problem reveals small plume recirculation; what major factors influence base temperature; and why overheating was initiated at a given time in the flight. To answer these questions topological analysis of the base flow was performed and Korst theory was used to estimate relative contributions of radiation, plume recirculation, and chemically reactive out-gassing to the base heating. It was shown that base bleeding and small base volume are the key factors contributing to the overheating, while plume recirculation is effectively suppressed by asymmetric configuration of the flow formed earlier in the flight. These findings are further verified using CFD simulations that include multi-species gas environment both in the plume and in the base. Solid particles in the exhaust plume (Al2O3) and char particles in the base bleeding were also included into the simulations and their relative contributions into the base temperature rise were estimated. The results of simulations are in good agreement with the temperature and pressure in the base measured during the test.

Computational methods for reactive transport modeling: A Gibbs energy minimization approach for multiphase equilibrium calculations

NASA Astrophysics Data System (ADS)

Leal, Allan M. M.; Kulik, Dmitrii A.; Kosakowski, Georg

2016-02-01

We present a numerical method for multiphase chemical equilibrium calculations based on a Gibbs energy minimization approach. The method can accurately and efficiently determine the stable phase assemblage at equilibrium independently of the type of phases and species that constitute the chemical system. We have successfully applied our chemical equilibrium algorithm in reactive transport simulations to demonstrate its effective use in computationally intensive applications. We used FEniCS to solve the governing partial differential equations of mass transport in porous media using finite element methods in unstructured meshes. Our equilibrium calculations were benchmarked with GEMS3K, the numerical kernel of the geochemical package GEMS. This allowed us to compare our results with a well-established Gibbs energy minimization algorithm, as well as their performance on every mesh node, at every time step of the transport simulation. The benchmark shows that our novel chemical equilibrium algorithm is accurate, robust, and efficient for reactive transport applications, and it is an improvement over the Gibbs energy minimization algorithm used in GEMS3K. The proposed chemical equilibrium method has been implemented in Reaktoro, a unified framework for modeling chemically reactive systems, which is now used as an alternative numerical kernel of GEMS.

Towards 100,000 CPU Cycle-Scavenging by Genetic Algorithms

NASA Technical Reports Server (NTRS)

Globus, Al; Biegel, Bryan A. (Technical Monitor)

2001-01-01

We examine a web-centric design using standard tools such as web servers, web browsers, PHP, and mySQL. We also consider the applicability of Information Power Grid tools such as the Globus (no relation to the author) Toolkit. We intend to implement this architecture with JavaGenes running on at least two cycle-scavengers: Condor and United Devices. JavaGenes, a genetic algorithm code written in Java, will be used to evolve multi-species reactive molecular force field parameters.

Global modelling of the total OH reactivity: investigations on the "missing" OH sink and its atmospheric implications

NASA Astrophysics Data System (ADS)

Ferracci, Valerio; Heimann, Ines; Abraham, N. Luke; Pyle, John A.; Archibald, Alexander T.

2018-05-01

The hydroxyl radical (OH) plays a crucial role in the chemistry of the atmosphere as it initiates the removal of most trace gases. A number of field campaigns have observed the presence of a missing OH sink in a variety of regions across the planet. A comparison of direct measurements of the OH loss frequency, also known as total OH reactivity (kOH), with the sum of individual known OH sinks (obtained via the simultaneous detection of species such as volatile organic compounds and nitrogen oxides) indicates that, in some cases, up to 80 % of kOH is unaccounted for. In this work, the UM-UKCA chemistry-climate model was used to investigate the wider implications of the missing reactivity on the oxidising capacity of the atmosphere. Simulations of the present-day atmosphere were performed and the model was evaluated against an array of field measurements to verify that the known OH sinks were reproduced well, with a resulting good agreement found for most species. Following this, an additional sink was introduced to simulate the missing OH reactivity as an emission of a hypothetical molecule, X, which undergoes rapid reaction with OH. The magnitude and spatial distribution of this sink were underpinned by observations of the missing reactivity. Model runs showed that the missing reactivity accounted for on average 6 % of the total OH loss flux at the surface and up to 50 % in regions where emissions of the additional sink were high. The lifetime of the hydroxyl radical was reduced by 3 % in the boundary layer, whilst tropospheric methane lifetime increased by 2 % when the additional OH sink was included. As no OH recycling was introduced following the initial oxidation of X, these results can be interpreted as an upper limit of the effects of the missing reactivity on the oxidising capacity of the troposphere. The UM-UKCA simulations also allowed us to establish the atmospheric implications of the newly characterised reactions of peroxy radicals (RO2) with OH. Whilst the effects of this chemistry on kOH were minor, the reaction of the simplest peroxy radical, CH3O2, with OH was found to be a major sink for CH3O2 and source of HO2 over remote regions at the surface and in the free troposphere. Inclusion of this reaction in the model increased tropospheric methane lifetime by up to 3 %, depending on its product branching. Simulations based on the latest kinetic and product information showed that this reaction cannot reconcile models with observations of atmospheric methanol, in contrast to recent suggestions.

Computational methods for reactive transport modeling: An extended law of mass-action, xLMA, method for multiphase equilibrium calculations

NASA Astrophysics Data System (ADS)

Leal, Allan M. M.; Kulik, Dmitrii A.; Kosakowski, Georg; Saar, Martin O.

2016-10-01

We present an extended law of mass-action (xLMA) method for multiphase equilibrium calculations and apply it in the context of reactive transport modeling. This extended LMA formulation differs from its conventional counterpart in that (i) it is directly derived from the Gibbs energy minimization (GEM) problem (i.e., the fundamental problem that describes the state of equilibrium of a chemical system under constant temperature and pressure); and (ii) it extends the conventional mass-action equations with Lagrange multipliers from the Gibbs energy minimization problem, which can be interpreted as stability indices of the chemical species. Accounting for these multipliers enables the method to determine all stable phases without presuming their types (e.g., aqueous, gaseous) or their presence in the equilibrium state. Therefore, the here proposed xLMA method inherits traits of Gibbs energy minimization algorithms that allow it to naturally detect the phases present in equilibrium, which can be single-component phases (e.g., pure solids or liquids) or non-ideal multi-component phases (e.g., aqueous, melts, gaseous, solid solutions, adsorption, or ion exchange). Moreover, our xLMA method requires no technique that tentatively adds or removes reactions based on phase stability indices (e.g., saturation indices for minerals), since the extended mass-action equations are valid even when their corresponding reactions involve unstable species. We successfully apply the proposed method to a reactive transport modeling problem in which we use PHREEQC and GEMS as alternative backends for the calculation of thermodynamic properties such as equilibrium constants of reactions, standard chemical potentials of species, and activity coefficients. Our tests show that our algorithm is efficient and robust for demanding applications, such as reactive transport modeling, where it converges within 1-3 iterations in most cases. The proposed xLMA method is implemented in Reaktoro, a unified open-source framework for modeling chemically reactive systems.

Reactive composite compositions and mat barriers

DOEpatents

Langton, Christine A.; Narasimhan, Rajendran; Karraker, David G.

2001-01-01

A hazardous material storage area has a reactive multi-layer composite mat which lines an opening into which a reactive backfill and hazardous material are placed. A water-inhibiting cap may cover the hazardous material storage area. The reactive multi-layer composite mat has a backing onto which is placed an active layer which will neutralize or stabilize hazardous waste and a fronting layer so that the active layer is between the fronting and backing layers. The reactive backfill has a reactive agent which can stabilize or neutralize hazardous material and inhibit the movement of the hazardous material through the hazardous material storage area.

Modelling and simulating a crisis management system: an organisational perspective

NASA Astrophysics Data System (ADS)

Chaawa, Mohamed; Thabet, Inès; Hanachi, Chihab; Ben Said, Lamjed

2017-04-01

Crises are complex situations due to the dynamism of the environment, its unpredictability and the complexity of the interactions among several different and autonomous involved organisations. In such a context, establishing an organisational view as well as structuring organisations' communications and their functioning is a crucial requirement. In this article, we propose a multi-agent organisational model (OM) to abstract, simulate and analyse a crisis management system (CMS). The objective is to evaluate the CMS from an organisational view, to assess its strength as well as its weakness and to provide deciders with some recommendations for a more flexible and reactive CMS. The proposed OM is illustrated through a real case study: a snowstorm in a Tunisian region. More precisely, we made the following contribution: firstly, we provide an environmental model that identifies the concepts involved in the crisis. Then, we define a role model that copes with the involved actors. In addition, we specify the organisational structure and the interaction model that rule communications and structure actors' functioning. Those models, built following the GAIA methodology, abstract the CMS from an organisational perspective. Finally, we implemented a customisable multi-agent simulator based on the Janus platform to analyse, through several performed simulations, the organisational model.

Termination Shock Transition in Multi-ion Multi-fluid MHD Models of the Heliosphere

NASA Astrophysics Data System (ADS)

Zieger, B.; Opher, M.; Toth, G.

2013-12-01

As evidenced by Voyager 2 observations, pickup ions (PUIs) play a significant role in the termination shock (TS) transition of the solar wind [Richardson et al., Nature, 2008]. Recent kinetic simulations [Ariad and Gedalin, JGR, 2013] came to the conclusion that the contribution of the high energy tail of PUIs is negligible at the shock transition. The Rankine-Hugoniot (R-H) relations are determined by the low energy body of PUIs. Particle-in-cell simulations by Wu et al. [JGR, 2010] have shown that the sum of the thermal solar wind and non-thermal PUI distributions downstream of the TS can be approximated with a 2-Maxwellian distribution. It is important to note that this 2-Maxwellian distribution neglects the suprathermal tail population that has a characteristic power-law distribution. These results justify the fluid description of PUIs in our large-scale multi-ion multi-fluid MHD simulations of the heliospheric interface [Prested et al., JGR, 2013; Zieger et al., GRL, 2013]. The closure of the multi-ion MHD equations could be implemented with separate momentum and energy equations for the different ion species (thermal solar wind and PUIs) where the transfer rate of momentum and energy between the two ion species are considered as source terms, like in Glocer et al. [JGR, 2009]. Another option is to solve for the total energy equation with an additional equation for the PUI pressure, as suggested by Fahr and Chalov [A&A, 2008]. In this paper, we validate the energy conservation and the R-H relations across the TS in different numerical implementations of our latest multi-ion multi-fluid MHD model. We assume an instantaneous pickup process, where the convection velocity of the two ion fluids are the same, and the so-called strong scattering approximation, where newly born PUIs attain their spherical shell distribution within a short distance on fluid scales (spatial scales much larger than the respective ion gyroradius).

Ultraviolet Radiation: Cellular Antioxidant Response and the Role of Ocular Aldehyde Dehydrogenase Enzymes

PubMed Central

Marchitti, Satori A.; Chen, Ying; Thompson, David C.; Vasiliou, Vasilis

2011-01-01

Solar ultraviolet radiation (UVR) exposes the human eye to near constant oxidative stress. Evidence suggests that UVR is the most important environmental insult leading to the development of a variety of ophthalmoheliosis disorders. UVR-induced reactive oxygen species are highly reactive with DNA, proteins and cellular membranes, resulting in cellular and tissue damage. Antioxidant defense systems present in ocular tissues function to combat reactive oxygen species and protect the eye from oxidative damage. Important enzymatic antioxidants are the superoxide dismutases, catalase, glutathione peroxidases, glutathione reductase and members of the aldehyde dehydrogenase (ALDH) superfamily. Glutathione, ascorbic and uric acids, α-tocopherol, NADPH and ferritin serve as small molecule, nonenzymatic antioxidants. Ocular tissues have high levels of these antioxidants which are essential for the maintenance of redox homeostasis in the eye and protection against oxidative damage. ALDH1A1 and ALDH3A1, present abundantly in the cornea and lens, have been shown to have unique roles in the defense against UVR and the downstream effects of oxidative stress. This review presents the properties and functions of ocular antioxidants that play critical roles in the cellular response to UVR exposure, including a focused discussion of the unique roles that the ALDH1A1 and ALDH3A1 enzymes have as multi-functional ocular antioxidants. PMID:21670692

Dielectric barrier structure with hollow electrodes and its recoil effect

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

Yu, Shuang; Chen, Qunzhi; Liu, Jiahui

2015-06-15

A dielectric barrier structure with hollow electrodes (HEDBS), in which gas flow oriented parallel to the electric field, was proposed. Results showed that with this structure, air can be effectively ignited, forming atmospheric low temperature plasma, and the proposed HEDBS could achieve much higher electron density (5 × 10{sup 15}/cm{sup 3}). It was also found that the flow condition, including outlet diameter and flow rate, played a key role in the evolution of electron density. Optical emission spectroscopy diagnostic results showed that the concentration of reactive species had the same variation trend as the electron density. The simulated distribution of discharge gasmore » flow indicated that the HEDBS had a strong recoil effect on discharge gas, and could efficiently promote generating electron density as well as reactive species.« less

Cellular structure of lean hydrogen flames in microgravity

NASA Technical Reports Server (NTRS)

Patnaik, G.; Kailasanath, K.

1990-01-01

Detailed, time-dependent, two-dimensional numerical simulations of premixed laminar flames have been used to study the initiation and subsequent development of cellular structures in lean hydrogen-air flames. The model includes detailed hydrogen-oxygen combustion with 24 elementary reactions of eight reactive species and a nitrogen diluent, molecular diffusion of all species, thermal conduction, viscosity, and convection. This model has been used to study the nonlinear evolution of cellular flame structure and shows that cell splitting, as observed in experiments, can be predicted numerically for sufficiently reactive mixtures. The structures that evolved also resembled the cellular structures observed in experiments. The present study shows that the 'cell-split limit' postulated from experimental observations is an intrinsic property of the mixture and that external factors such as heat losses are not necessary to cause this limit.

Efficient sampling of reversible cross-linking polymers: Self-assembly of single-chain polymeric nanoparticles

NASA Astrophysics Data System (ADS)

Oyarzún, Bernardo; Mognetti, Bortolo Matteo

2018-03-01

We present a new simulation technique to study systems of polymers functionalized by reactive sites that bind/unbind forming reversible linkages. Functionalized polymers feature self-assembly and responsive properties that are unmatched by the systems lacking selective interactions. The scales at which the functional properties of these materials emerge are difficult to model, especially in the reversible regime where such properties result from many binding/unbinding events. This difficulty is related to large entropic barriers associated with the formation of intra-molecular loops. In this work, we present a simulation scheme that sidesteps configurational costs by dedicated Monte Carlo moves capable of binding/unbinding reactive sites in a single step. Cross-linking reactions are implemented by trial moves that reconstruct chain sections attempting, at the same time, a dimerization reaction between pairs of reactive sites. The model is parametrized by the reaction equilibrium constant of the reactive species free in solution. This quantity can be obtained by means of experiments or atomistic/quantum simulations. We use the proposed methodology to study the self-assembly of single-chain polymeric nanoparticles, starting from flexible precursors carrying regularly or randomly distributed reactive sites. We focus on understanding differences in the morphology of chain nanoparticles when linkages are reversible as compared to the well-studied case of irreversible reactions. Intriguingly, we find that the size of regularly functionalized chains, in good solvent conditions, is non-monotonous as a function of the degree of functionalization. We clarify how this result follows from excluded volume interactions and is peculiar of reversible linkages and regular functionalizations.

Two-Dimensional Self-Consistent Radio Frequency Plasma Simulations Relevant to the Gaseous Electronics Conference RF Reference Cell

PubMed Central

Lymberopoulos, Dimitris P.; Economou, Demetre J.

1995-01-01

Over the past few years multidimensional self-consistent plasma simulations including complex chemistry have been developed which are promising tools for furthering our understanding of reactive gas plasmas and for reactor design and optimization. These simulations must be benchmarked against experimental data obtained in well-characterized systems such as the Gaseous Electronics Conference (GEC) reference cell. Two-dimensional simulations relevant to the GEC Cell are reviewed in this paper with emphasis on fluid simulations. Important features observed experimentally, such as off-axis maxima in the charge density and hot spots of metastable species density near the electrode edges in capacitively-coupled GEC cells, have been captured by these simulations. PMID:29151756

A multi-target caffeine derived rhodium(i) N-heterocyclic carbene complex: evaluation of the mechanism of action.

PubMed

Zhang, Jing-Jing; Muenzner, Julienne K; Abu El Maaty, Mohamed A; Karge, Bianka; Schobert, Rainer; Wölfl, Stefan; Ott, Ingo

2016-08-16

A rhodium(i) and a ruthenium(ii) complex with a caffeine derived N-heterocyclic carbene (NHC) ligand were biologically investigated as organometallic conjugates consisting of a metal center and a naturally occurring moiety. While the ruthenium(ii) complex was largely inactive, the rhodium(i) NHC complex displayed selective cytotoxicity and significant anti-metastatic and in vivo anti-vascular activities and acted as both a mammalian and an E. coli thioredoxin reductase inhibitor. In HCT-116 cells it increased the reactive oxygen species level, leading to DNA damage, and it induced cell cycle arrest, decreased the mitochondrial membrane potential, and triggered apoptosis. This rhodium(i) NHC derivative thus represents a multi-target compound with promising anti-cancer potential.

Moving granular-bed filter development program, Option III: Development of moving granular-bed filter technology for multi-contaminant control. Task 14: Test plan; Topical report

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

Haas, J.C.; Olivo, C.A.; Wilson, K.B.

1994-04-01

An experimental test plan has been prepared for DOE/METC review and approval to develop a filter media suitable for multi-contaminant control in granular-bed filter (GBF) applications. The plan includes identification, development, and demonstration of methods for enhanced media morphology, chemical reactivity, and mechanical strength. The test plan includes media preparation methods, physical and chemical characterization methods for fresh and reacted media, media evaluation criteria, details of test and analytical equipment, and test matrix of the proposed media testing. A filter media composed of agglomerated limestone and clay was determined to be the best candidate for multi-contaminate control in GBF operation.more » The combined limestone/clay agglomerate has the potential to remove sulfur and alkali species, in addition to particulate, and possibly halogens and trace heavy metals from coal process streams.« less

Establishment of a multi-species biofilm model to evaluate chlorhexidine efficacy.

PubMed

Touzel, R E; Sutton, J M; Wand, M E

2016-02-01

Chronic infections, for example, diabetic foot ulcers, have a large impact in terms of patient morbidity and mortality. These wounds are characterized by complex polymicrobial communities of bacteria, which may include a number of difficult-to-eradicate multidrug-resistant pathogens. To establish a multi-species biofilm model to test the efficacy of chlorhexidine and chlorhexidine-containing formulas in eradication of polymicrobial biofilms. A Centers for Disease Control and Prevention bioreactor was used to establish a multi-species biofilm incorporating Klebsiella pneumoniae, Pseudomonas aeruginosa, Staphylococcus aureus and Enterococcus faecalis with equal numbers of each pathogen. This model was used to test the effectiveness of chlorhexidine at controlling the pre-formed biofilm. Chlorhexidine digluconate (CHD) was added to the bioreactor at a range of concentrations. K. pneumoniae and P. aeruginosa survived within multi-species biofilms, up to and including 4% CHD, whereas S. aureus was reduced to below the level of detection at 1%. Wiping the biofilm-containing coupons from the bioreactor with chlorhexidine-containing medical wipes resulted in >3 to <4log10 reduction after 24h, for all species. When the coupons were embedded in a simulated wound bed, formed in an agar plate, CHD-containing medical dressings completely eliminated S. aureus (>8log10 reduction), but had minimal effect (<3log10) against the other species tested. The study demonstrates that the effectiveness of chlorhexidine may be limited in settings where it is required to act on multi-species biofilms. This may compromise the ability of chlorhexidine to control the infection and spread of these pathogens. Crown Copyright © 2016. Published by Elsevier Ltd. All rights reserved.

Yield degradation in inertial-confinement-fusion implosions due to shock-driven kinetic fuel-species stratification and viscous heating

DOE PAGES

Taitano, William T.; Simakov, Andrei N.; Chacon, Luis; ...

2018-04-09

Anomalous thermonuclear yield degradation (i.e., that not describable by single-fluid radiation hydrodynamics) in Inertial Confinement Fusion (ICF) implosions is ubiquitously observed in both Omega and National Ignition experiments. Multiple experimental and theoretical studies have been carried out to investigate the origin of such a degradation. Relative concentration changes of fuel-ion species, as well as kinetically enhanced viscous heating, have been among possible explanations proposed for certain classes of ICF experiments. In this study, we investigate the role of such kinetic plasma effects in detail. To this end, we use the iFP code to perform multi-species ion Vlasov-Fokker-Planck simulations of ICFmore » capsule implosions with the fuel comprising various hydrodynamically equivalent mixtures of deuterium (D) and helium-3 (3He), as in the original. We employ the same computational setup as in O. Larroche, which was the first to simulate the experiments kinetically. However, unlike the Larroche study, and in partial agreement with experimental data, we find a systematic yield degradation in multi-species simulations versus averaged-ion simulations when the D-fuel fraction is decreased. This yield degradation originates in the fuel-ion species stratification induced by plasma shocks, which imprints the imploding system and results in the relocation of the D ions from the core of the capsule to its periphery, thereby reducing the yield relative to a non-separable averaged-ion case. By comparing yields from the averaged-ion kinetic simulations and from the hydrodynamic scaling, we also observe yield variations associated with ion kinetic effects other than fuel-ion stratification, such as ion viscous heating, which is typically neglected in hydrodynamic implosions' simulations. Since our kinetic simulations are driven by hydrodynamic boundary conditions at the fuel-ablator interface, they cannot capture the effects of ion viscosity on the capsule compression, or effects associated with the interface, which are expected to be important. As a result, studies of such effects are left for future work.« less

Yield degradation in inertial-confinement-fusion implosions due to shock-driven kinetic fuel-species stratification and viscous heating

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

Taitano, William T.; Simakov, Andrei N.; Chacon, Luis

Anomalous thermonuclear yield degradation (i.e., that not describable by single-fluid radiation hydrodynamics) in Inertial Confinement Fusion (ICF) implosions is ubiquitously observed in both Omega and National Ignition experiments. Multiple experimental and theoretical studies have been carried out to investigate the origin of such a degradation. Relative concentration changes of fuel-ion species, as well as kinetically enhanced viscous heating, have been among possible explanations proposed for certain classes of ICF experiments. In this study, we investigate the role of such kinetic plasma effects in detail. To this end, we use the iFP code to perform multi-species ion Vlasov-Fokker-Planck simulations of ICFmore » capsule implosions with the fuel comprising various hydrodynamically equivalent mixtures of deuterium (D) and helium-3 (3He), as in the original. We employ the same computational setup as in O. Larroche, which was the first to simulate the experiments kinetically. However, unlike the Larroche study, and in partial agreement with experimental data, we find a systematic yield degradation in multi-species simulations versus averaged-ion simulations when the D-fuel fraction is decreased. This yield degradation originates in the fuel-ion species stratification induced by plasma shocks, which imprints the imploding system and results in the relocation of the D ions from the core of the capsule to its periphery, thereby reducing the yield relative to a non-separable averaged-ion case. By comparing yields from the averaged-ion kinetic simulations and from the hydrodynamic scaling, we also observe yield variations associated with ion kinetic effects other than fuel-ion stratification, such as ion viscous heating, which is typically neglected in hydrodynamic implosions' simulations. Since our kinetic simulations are driven by hydrodynamic boundary conditions at the fuel-ablator interface, they cannot capture the effects of ion viscosity on the capsule compression, or effects associated with the interface, which are expected to be important. As a result, studies of such effects are left for future work.« less

Yield degradation in inertial-confinement-fusion implosions due to shock-driven kinetic fuel-species stratification and viscous heating

NASA Astrophysics Data System (ADS)

Taitano, W. T.; Simakov, A. N.; Chacón, L.; Keenan, B.

2018-05-01

Anomalous thermonuclear yield degradation (i.e., that not describable by single-fluid radiation hydrodynamics) in Inertial Confinement Fusion (ICF) implosions is ubiquitously observed in both Omega and National Ignition experiments. Multiple experimental and theoretical studies have been carried out to investigate the origin of such a degradation. Relative concentration changes of fuel-ion species, as well as kinetically enhanced viscous heating, have been among possible explanations proposed for certain classes of ICF experiments. In this study, we investigate the role of such kinetic plasma effects in detail. To this end, we use the iFP code to perform multi-species ion Vlasov-Fokker-Planck simulations of ICF capsule implosions with the fuel comprising various hydrodynamically equivalent mixtures of deuterium (D) and helium-3 (3He), as in the original Rygg experiments [J. R. Rygg et al., Phys. Plasmas 13, 052702 (2006)]. We employ the same computational setup as in O. Larroche [Phys. Plasmas 19, 122706 (2012)], which was the first to simulate the experiments kinetically. However, unlike the Larroche study, and in partial agreement with experimental data, we find a systematic yield degradation in multi-species simulations versus averaged-ion simulations when the D-fuel fraction is decreased. This yield degradation originates in the fuel-ion species stratification induced by plasma shocks, which imprints the imploding system and results in the relocation of the D ions from the core of the capsule to its periphery, thereby reducing the yield relative to a non-separable averaged-ion case. By comparing yields from the averaged-ion kinetic simulations and from the hydrodynamic scaling, we also observe yield variations associated with ion kinetic effects other than fuel-ion stratification, such as ion viscous heating, which is typically neglected in hydrodynamic implosions' simulations. Since our kinetic simulations are driven by hydrodynamic boundary conditions at the fuel-ablator interface, they cannot capture the effects of ion viscosity on the capsule compression, or effects associated with the interface, which are expected to be important. Studies of such effects are left for future work.

Fully non-linear multi-species Fokker-Planck-Landau collisions for gyrokinetic particle-in-cell simulations of fusion plasma

NASA Astrophysics Data System (ADS)

Hager, Robert; Yoon, E. S.; Ku, S.; D'Azevedo, E. F.; Worley, P. H.; Chang, C. S.

2015-11-01

We describe the implementation, and application of a time-dependent, fully nonlinear multi-species Fokker-Planck-Landau collision operator based on the single-species work of Yoon and Chang [Phys. Plasmas 21, 032503 (2014)] in the full-function gyrokinetic particle-in-cell codes XGC1 [Ku et al., Nucl. Fusion 49, 115021 (2009)] and XGCa. XGC simulations include the pedestal and scrape-off layer, where significant deviations of the particle distribution function from a Maxwellian can occur. Thus, in order to describe collisional effects on neoclassical and turbulence physics accurately, the use of a non-linear collision operator is a necessity. Our collision operator is based on a finite volume method using the velocity-space distribution functions sampled from the marker particles. Since the same fine configuration space mesh is used for collisions and the Poisson solver, the workload due to collisions can be comparable to or larger than the workload due to particle motion. We demonstrate that computing time spent on collisions can be kept affordable by applying advanced parallelization strategies while conserving mass, momentum, and energy to reasonable accuracy. We also show results of production scale XGCa simulations in the H-mode pedestal and compare to conventional theory. Work supported by US DOE OFES and OASCR.

Adsorption Mechanisms of Trivalent Gold onto Iron Oxy-Hydroxides: From the Molecular Scale to the Model

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

Cances, Benjamin; Benedetti, Marc; Farges, Francois

2007-02-02

Gold is a highly valuable metal that can concentrate in iron-rich exogenetic horizons such as laterites. An improved knowledge of the retention mechanisms of gold onto highly reactive soil components such as iron oxy-hydroxides is therefore needed to better understand and predict the geochemical behavior of this element. In this study, we use EXAFS information and titration experiments to provide a realistic thermochemical description of the sorption of trivalent gold onto iron oxy-hydroxides. Analysis of Au LIII-edge XAFS spectra shows that aqueous Au(III) adsorbs from chloride solutions onto goethite surfaces as inner-sphere square-planar complexes (Au(III)(OH,Cl)4), with dominantly OH ligands atmore » pH > 6 and mixed OH/Cl ligands at lower pH values. In combination with these spectroscopic results, Reverse Monte Carlo simulations were used to constraint the possible sorption sites on the surface of goethite. Based on this structural information, we calculated sorption isotherms of Au(III) on Fe oxy-hydroxides surfaces, using the CD-MUSIC (Charge Distribution - MUlti SIte Complexation) model. The various Au(III)-sorbed species were identified as a function of pH, and the results of these EXAFS+CD-MUSIC models are compared with titration experiments. The overall good agreement between the predicted and measured structural models shows the potential of this combined approach to better model sorption processes of transition elements onto highly reactive solid surfaces such as goethite and ferrihydrite.« less

Adsorption Mechanisms of Trivalent Gold onto Iron Oxy-Hydroxides: From the Molecular Scale to the Model

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

Cances, Benjamin; /Marne La Vallee U.; Benedetti, Marc

2006-12-13

Gold is a highly valuable metal that can concentrate in iron-rich exogenetic horizons such as laterites. An improved knowledge of the retention mechanisms of gold onto highly reactive soil components such as iron oxyhydroxides is therefore needed to better understand and predict the geochemical behavior of this element. In this study, we use EXAFS information and titration experiments to provide a realistic thermochemical description of the sorption of trivalent gold onto iron oxy-hydroxides. Analysis of Au L{sub III}-edge XAFS spectra shows that aqueous Au(III) adsorbs from chloride solutions onto goethite surfaces as inner-sphere square-planar complexes (Au(III)(OH,Cl){sub 4}), with dominantly OHmore » ligands at pH > 6 and mixed OH/Cl ligands at lower pH values. In combination with these spectroscopic results, Reverse Monte Carlo simulations were used to constraint the possible sorption sites on the surface of goethite. Based on this structural information, we calculated sorption isotherms of Au(III) on Fe oxy-hydroxides surfaces, using the CD-MUSIC (Charge Distribution--Multi Site Complexation) model. The various Au(III)-sorbed species were identified as a function of pH, and the results of these EXAFS+CD-MUSIC models are compared with titration experiments. The overall good agreement between the predicted and measured structural models shows the potential of this combined approach to better model sorption processes of transition elements onto highly reactive solid surfaces such as goethite and ferrihydrite.« less

The influence of electrohydrodynamic flow on the distribution of chemical species in positive corona

NASA Astrophysics Data System (ADS)

Pontiga, Francisco; Yanallah, Khelifa; Bouazza, R.; Chen, Junhong

2015-09-01

A numerical simulation of positive corona discharge in air, including the effect of electrohydrodynamic (EHD) motion of the gas, has been carried out. Air flow is assumed to be confined between two parallel plates, and corona discharge is produced around a thin wire, midway between the plates. Therefore, fluid dynamics equations, including electrical forces, have been solved together with the continuity equation of each neutral species. The plasma chemical model included 24 chemical reactions and ten neutral species, in addition to electrons and positive ions. The results of the simulation have shown that the influence of EHD flow on the spatial distributions of the species is quite different depending on the species. Hence, reactive species like atomic oxygen and atomic nitrogen are confined to the vicinity of the wire, and they are weakly affected by the EHD gas motion. In contrast, nitrogen oxides and ozone are efficiently dragged outside the active region of the corona discharge by the EHD flow. This work was supported by the Spanish Government Agency ``Ministerio de Ciencia e Innovación'' under Contract No. FIS2011-25161.

Improving Prompt Temperature Feedback by Stimulating Doppler Broadening in Heterogeneous Composite Nuclear Fuel Forms

NASA Astrophysics Data System (ADS)

Morrison, Christopher

Nuclear fuels with similar aggregate material composition, but with different millimeter and micrometer spatial configurations of the component materials can have very different safety and performance characteristics. This research focuses on modeling and attempting to engineer heterogeneous combinations of nuclear fuels to improve negative prompt temperature feedback in response to reactivity insertion accidents. Improvements in negative prompt temperature feedback are proposed by developing a tailored thermal resistance in the nuclear fuel. In the event of a large reactivity insertion, the thermal resistance allows for a faster negative Doppler feedback by temporarily trapping heat in material zones with strong absorption resonances. A multi-physics simulation framework was created that could model large reactivity insertions. The framework was then used to model a comparison of a heterogeneous fuel with a tailored thermal resistance and a homogeneous fuel without the tailored thermal resistance. The results from the analysis confirmed the fundamental premise of prompt temperature feedback and provide insights into the neutron spectrum dynamics throughout the transient process. A trade study was conducted on infinite lattice fuels to help map a design space to study and improve prompt temperature feedback with many results. A multi-scale fuel pin analysis was also completed to study more realistic geometries. The results of this research could someday allow for novel nuclear fuels that would behave differently than current fuels. The idea of having a thermal barrier coating in the fuel is contrary to most current thinking. Inherent resistance to reactivity insertion accidents could enable certain reactor types once considered vulnerable to reactivity insertion accidents to be reevaluated in light of improved negative prompt temperature feedback.

Understanding the Potential Toxic Properties of Lunar Dust

NASA Technical Reports Server (NTRS)

2009-01-01

Lunar dust causes a variety of problems for spacecraft. It can obscure vision, clog equipment, cause seal failures and abrade surfaces. Additionally, lunar dust is potentially toxic and therefore hazardous to astronauts. Lunar dust can be activated by meteorites, UV radiation and elements of solar wind and, if inhaled, could produce reactive species in the lungs (freshly fractured quartz). Methods of lunar dust deactivation must be determined before new lunar missions. This requires knowledge of how to reactivate lunar dust on Earth - thus far crushing/grinding, UV activation and heating have been tested as activation methods. Grinding of lunar dust leads to the production of hydroxyl radicals in solution and increased dissolution of lunar simulant in buffers of different pH. Decreases in pH lead to increased lunar simulant leaching. Additionally, both ground and unground lunar simulant and unground quartz have been shown to promote the production of IL-6 and IL-8, pro-inflammatory cytokines, by alveolar epithelial cells. The results suggest the need for further studies on lunar dust and simulants prior to returning to the lunar surface.

Interaction of single-walled carbon nanotubes and saxitoxin: Ab initio simulations and biological responses in hippocampal cell line HT-22.

PubMed

Ramos, Patrícia; Schmitz, Marcos; Filgueira, Daza; Votto, Ana Paula; Durruthy, Michael; Gelesky, Marcos; Ruas, Caroline; Yunes, João; Tonel, Mariana; Fagan, Solange; Monserrat, José

2017-07-01

Saxitoxins (STXs) are potent neurotoxins that also induce cytotoxicity through the generation of reactive oxygen species. Carbon nanotubes (CNTs) are nanomaterials that can promote a Trojan horse effect, facilitating the entry of toxic molecules to cells when adsorbed to nanomaterials. The interaction of pristine single-walled (SW)CNTs and carboxylated (SWCNT-COOH) nanotubes with STX was evaluated by ab initio simulation and bioassays using the cell line HT-22. Cells (5 × 10 4  cells/mL) were exposed to SWCNT and SWCNT-COOH (5 μg mL -1 ), STX (200 μg L -1 ), SWCNT+STX, and SWCNT-COOH+STX for 30 min or 24 h. Results of ab initio simulation showed that the interaction between SWCNT and SWCNT-COOH with STX occurs in a physisorption. The interaction of SWCNT+STX induced a decrease in cell viability. Cell proliferation was not affected in any treatment after 30 min or 24 h of exposure (p > 0.05). Treatment with SWCNT-COOH induced high reactive oxygen species levels, an effect attenuated in SWCNT-COOH+STX treatment. In terms of cellular oxygen consumption, both CNTs when coexposed with STX antagonize the toxin effect. Based on these results, it can be concluded that the results obtained in vitro corroborate the semiempirical evidence found using density functional theory ab initio simulation. Environ Toxicol Chem 2017;36:1728-1737. © 2016 SETAC. © 2016 SETAC.

Multicale modeling of the detonation of aluminized explosives using SPH-MD-QM method

NASA Astrophysics Data System (ADS)

Peng, Qing; Wang, Guangyu; Liu, Gui-Rong; de, Suvranu

Aluminized explosives have been applied in military industry since decades ago. Compared with ideal explosives, aluminized explosives feature both fast detonation and slow metal combustion chemistry, generating a complex multi-phase reactive flow. Here, we introduce a sequential multiscale model of SPH-MD-QM to simulate the detonation behavior of aluminized explosives. At the bottom level, first-principles quantum mechanics (QM) calculations are employed to obtain the training sets for fitting the ReaxFF potentials, which are used in turn in the reactive molecular dynamics (MD) simulations in the middle level to obtain the chemical reaction rates and equations of states. At the up lever, a smooth particle hydrodynamics (SPH) method incorporated ignition and growth model and afterburning model has been used for the simulation of the detonation and combustion of the aluminized explosive. Simulation is compared with experiment and good agreement is observed. The proposed multiscale method of SPH-MD-QM could be used to optimize the performance of aluminized explosives. The authors would like to acknowledge the generous financial support from the Defense Threat Reduction Agency (DTRA) Grant No. HDTRA1-13-1-0025 and the Office of Naval Research Grants ONR Award No. N00014-08-1-0462 and No. N00014-12-1-0527.

Reactive Oxygen Species, Mitochondria, and Endothelial Cell Death during In Vitro Simulated Dives.

PubMed

Wang, Qiong; Guerrero, François; Mazur, Aleksandra; Lambrechts, Kate; Buzzacott, Peter; Belhomme, Marac; Theron, Michaël

2015-07-01

Excessive reactive oxygen species (ROS) is considered a consequence of hyperoxia and a major contributor to diving-derived vascular endothelial damage and decompression sickness. The aims of this work were: 1) to directly observe endothelial ROS production during simulated air dives as well as its relation with both mitochondrial activity and cell survival; and 2) to determine which ambient factor during air diving (hydrostatic pressure or oxygen and/or nitrogen partial pressure) is responsible for the observed modifications. In vitro diving simulation was performed with bovine arterial endothelial cells under real-time observation. The effects of air diving, hydrostatic, oxygen and nitrogen pressures, and N-acetylcysteine (NAC) treatment on mitochondrial ROS generation, mitochondrial membrane potential and cellular survival during simulation were investigated. Vascular endothelial cells performing air diving simulation suffered excessive mitochondrial ROS, mitochondrial depolarization, and cell death. These effects were prevented by NAC: after NAC treatment, the cells presented no difference in damage from nondiving cells. Oxygen diving showed a higher effect on ROS generation but lower impacts on mitochondrial depolarization and cell death than hydrostatic or nitrogen diving. Nitrogen diving had no effect on the inductions of ROS, mito-depolarization, or cell death. This study is the first direct observation of mitochondrial ROS production, mitochondrial membrane potential and cell survival during diving. Simulated air SCUBA diving induces excessive ROS production, which leads to mitochondrial depolarization and endothelial cell death. Oxygen partial pressure plays a crucial role in the production of ROS. Deleterious effects of hyperoxia-induced ROS are potentiated by hydrostatic pressure. These findings hold new implications for the pathogenesis of diving-derived endothelial dysfunction.

Simulating selenium and nitrogen fate and transport in coupled stream-aquifer systems of irrigated regions

NASA Astrophysics Data System (ADS)

Shultz, Christopher D.; Bailey, Ryan T.; Gates, Timothy K.; Heesemann, Brent E.; Morway, Eric D.

2018-05-01

Elevated levels of selenium (Se) in aqueous environments can harm aquatic life and endanger livestock and human health. Although Se occurs naturally in the rocks and soils of many alluvial aquifers, mining and agricultural activities can increase its rate of mobilization and transport to surface waters. Attention is given here to regions where nonpoint source return flows from irrigated lands carry pollutant loads to aquifers and streams, contributing to concentrations that violate regulatory and performance standards. Of particular concern is the heightened level and mobilization of Se influenced by nitrate (NO3), a harmful pollutant in its own right. We present a numerical model that simulates the reactive transport of Se and nitrogen (N) species in a coupled groundwater-surface water system. Building upon a conceptual model that incorporates the major processes affecting Se and NO3 transport in an irrigated watershed, the model links the finite-difference models MODFLOW, UZF-RT3D, and OTIS, to simulate flow and reactive transport of multiple chemical species in both the aquifer and a stream network, with mass exchange between the two. The capability of the new model is showcased by calibration, testing, and application to a 500 km2 region in Colorado's Lower Arkansas River Valley using a rich data set gathered over a 10-yr period. Simulation of spatial and temporal distributions of Se concentration reveals conditions that exceed standards in groundwater for approximately 20% of the area. For the Arkansas River, standards are exceeded by 290%-450%. Simulation indicates that river concentrations of NO3 alone are near the current interim standard for the total of all dissolved N species. These results indicate the need for future use of the developed model to investigate the prospects for land and water best management practices to decrease pollutant levels.

Simulating selenium and nitrogen fate and transport in coupled stream-aquifer systems of irrigated regions

USGS Publications Warehouse

Shultz, Christopher D.; Bailey, Ryan T.; Gates, Timothy K.; Heesemann, Brent E.; Morway, Eric D.

2018-01-01

Elevated levels of selenium (Se) in aqueous environments can harm aquatic life and endanger livestock and human health. Although Se occurs naturally in the rocks and soils of many alluvial aquifers, mining and agricultural activities can increase its rate of mobilization and transport to surface waters. Attention is given here to regions where nonpoint source return flows from irrigated lands carry pollutant loads to aquifers and streams, contributing to concentrations that violate regulatory and performance standards. Of particular concern is the heightened level and mobilization of Se influenced by nitrate (NO3), a harmful pollutant in its own right. We present a numerical model that simulates the reactive transport of Se and nitrogen (N) species in a coupled groundwater-surface water system. Building upon a conceptual model that incorporates the major processes affecting Se and NO3 transport in an irrigated watershed, the model links the finite-difference models MODFLOW, UZF-RT3D, and OTIS, to simulate flow and reactive transport of multiple chemical species in both the aquifer and a stream network, with mass exchange between the two. The capability of the new model is showcased by calibration, testing, and application to a 500 km2 region in Colorado’s Lower Arkansas River Valley using a rich data set gathered over a 10-yr period. Simulation of spatial and temporal distributions of Se concentration reveals conditions that exceed standards in groundwater for approximately 20% of the area. For the Arkansas River, standards are exceeded by 290%–450%. Simulation indicates that river concentrations of NO3 alone are near the current interim standard for the total of all dissolved N species. These results indicate the need for future use of the developed model to investigate the prospects for land and water best management practices to decrease pollutant levels.

Atomistic Simulation of Initiation in Hexanitrostilbene

NASA Astrophysics Data System (ADS)

Shan, Tzu-Ray; Wixom, Ryan; Yarrington, Cole; Thompson, Aidan

2015-06-01

We report on the effect of cylindrical voids on hot spot formation, growth and chemical reaction initiation in hexanitrostilbene (HNS) crystals subjected to shock. Large-scale, reactive molecular dynamics simulations are performed using the reactive force field (ReaxFF) as implemented in the LAMMPS software. The ReaxFF force field description for HNS has been validated previously by comparing the isothermal equation of state to available diamond anvil cell (DAC) measurements and density function theory (DFT) calculations and by comparing the primary dissociation pathway to ab initio calculations. Micron-scale molecular dynamics simulations of a supported shockwave propagating through the HNS crystal along the [010] orientation are performed with an impact velocity (or particle velocity) of 1.25 km/s, resulting in shockwave propagation at 4.0 km/s in the bulk material and a bulk shock pressure of ~ 11GPa. The effect of cylindrical void sizes varying from 0.02 to 0.1 μm on hot spot formation and growth rate has been studied. Interaction between multiple voids in the HNS crystal and its effect on hot spot formation will also be addressed. Results from the micron-scale atomistic simulations are compared with hydrodynamics simulations. Sandia National Laboratories is a multi-program laboratory managed and operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Corporation, for the U.S. DOE National Nuclear Security Administration under Contract DE-AC04-94AL85000.

Direct coupling of a genome-scale microbial in silico model and a groundwater reactive transport model.

PubMed

Fang, Yilin; Scheibe, Timothy D; Mahadevan, Radhakrishnan; Garg, Srinath; Long, Philip E; Lovley, Derek R

2011-03-25

The activity of microorganisms often plays an important role in dynamic natural attenuation or engineered bioremediation of subsurface contaminants, such as chlorinated solvents, metals, and radionuclides. To evaluate and/or design bioremediated systems, quantitative reactive transport models are needed. State-of-the-art reactive transport models often ignore the microbial effects or simulate the microbial effects with static growth yield and constant reaction rate parameters over simulated conditions, while in reality microorganisms can dynamically modify their functionality (such as utilization of alternative respiratory pathways) in response to spatial and temporal variations in environmental conditions. Constraint-based genome-scale microbial in silico models, using genomic data and multiple-pathway reaction networks, have been shown to be able to simulate transient metabolism of some well studied microorganisms and identify growth rate, substrate uptake rates, and byproduct rates under different growth conditions. These rates can be identified and used to replace specific microbially-mediated reaction rates in a reactive transport model using local geochemical conditions as constraints. We previously demonstrated the potential utility of integrating a constraint-based microbial metabolism model with a reactive transport simulator as applied to bioremediation of uranium in groundwater. However, that work relied on an indirect coupling approach that was effective for initial demonstration but may not be extensible to more complex problems that are of significant interest (e.g., communities of microbial species and multiple constraining variables). Here, we extend that work by presenting and demonstrating a method of directly integrating a reactive transport model (FORTRAN code) with constraint-based in silico models solved with IBM ILOG CPLEX linear optimizer base system (C library). The models were integrated with BABEL, a language interoperability tool. The modeling system is designed in such a way that constraint-based models targeting different microorganisms or competing organism communities can be easily plugged into the system. Constraint-based modeling is very costly given the size of a genome-scale reaction network. To save computation time, a binary tree is traversed to examine the concentration and solution pool generated during the simulation in order to decide whether the constraint-based model should be called. We also show preliminary results from the integrated model including a comparison of the direct and indirect coupling approaches and evaluated the ability of the approach to simulate field experiment. Published by Elsevier B.V.

Carbon storage, timber production, and biodiversity: comparing ecosystem services with multi-criteria decision analysis

USGS Publications Warehouse

Schwenk, W. Scott; Donovan, Therese; Keeton, William S.; Nunery, Jared S.

2012-01-01

Increasingly, land managers seek ways to manage forests for multiple ecosystem services and functions, yet considerable challenges exist in comparing disparate services and balancing trade-offs among them. We applied multi-criteria decision analysis (MCDA) and forest simulation models to simultaneously consider three objectives: (1) storing carbon, (2) producing timber and wood products, and (3) sustaining biodiversity. We used the Forest Vegetation Simulator (FVS) applied to 42 northern hardwood sites to simulate forest development over 100 years and to estimate carbon storage and timber production. We estimated biodiversity implications with occupancy models for 51 terrestrial bird species that were linked to FVS outputs. We simulated four alternative management prescriptions that spanned a range of harvesting intensities and forest structure retention. We found that silvicultural approaches emphasizing less frequent harvesting and greater structural retention could be expected to achieve the greatest net carbon storage but also produce less timber. More intensive prescriptions would enhance biodiversity because positive responses of early successional species exceeded negative responses of late successional species within the heavily forested study area. The combinations of weights assigned to objectives had a large influence on which prescriptions were scored as optimal. Overall, we found that a diversity of silvicultural approaches is likely to be preferable to any single approach, emphasizing the need for landscape-scale management to provide a full range of ecosystem goods and services. Our analytical framework that combined MCDA with forest simulation modeling was a powerful tool in understanding trade-offs among management objectives and how they can be simultaneously accommodated.

The Influences of Airmass Histories on Radical Species During POLARIS

NASA Technical Reports Server (NTRS)

Pierson, James M.; Kawa, S. R.

1998-01-01

The POLARIS mission focused on understanding the processes associated with the decrease of polar stratospheric ozone from spring to fall at high latitudes. This decrease is linked primarily to in situ photochemical destruction by reactive nitrogen species, NO and NO2, which also control other catalytic loss cycles. Steady state models have been used to test photochemistry and radical behavior but are not always adequate in simulating radical species observations. In some cases, air mass history can be important and trajectory models give an improved simulation of the radical species. Trajectory chemistry models, however, still consistently underestimate NO and NO2 abundances compared to measurements along the ER-2 flight track. The Goddard chemistry on trajectory model has been used to test updated rate constants for NO2 + OH, NO2 + O and OH + HNO3, key reactions that affect NO and NO2 abundances. We present comparisons between the modified Goddard chemistry on trajectory model, the JPL steady state model and observations from selected flights.

Measurements of shock-front structure in multi-species plasmas on OMEGA

NASA Astrophysics Data System (ADS)

Rinderknecht, Hans G.; Park, H.-S.; Ross, J. S.; Wilks, S. C.; Amendt, P. A.; Heeter, R. F.; Katz, J.; Hoffman, N. M.; Vold, E.; Taitano, W.; Simakov, A.; Chacon, L.

2016-10-01

The structure of a shock front in a plasma with multiple ion species is measured for the first time in experiments on the OMEGA laser. Thomson scattering of a 263.25 nm probe beam is used to diagnose electron density, electron and ion temperature, ion species concentration, and flow velocity in strong shocks (M 5) propagating through low-density (ρ 0.1 mg/cc) plasmas composed of H(98%)+Ne(2%) and H(98%)+C(2%). Separation of the ion species within the shock front is inferred. Although shocks play an important role in ICF and astrophysical plasmas, the intrinsically kinetic nature of the shock front indicates the need for experiments to benchmark hydrodynamic models. Comparison with PIC, Vlasov-Fokker-Planck, and multi-component hydrodynamic simulations will be presented. This work performed under auspices of U.S. DOE by Lawrence Livermore National Laboratory under Contract DE-AC52-07NA27344.

Modeling of Multi-Tube Pulse Detonation Engine Operation

NASA Technical Reports Server (NTRS)

Ebrahimi, Houshang B.; Mohanraj, Rajendran; Merkle, Charles L.

2001-01-01

The present paper explores some preliminary issues concerning the operational characteristics of multiple-tube pulsed detonation engines (PDEs). The study is based on a two-dimensional analysis of the first-pulse operation of two detonation tubes exhausting through a common nozzle. Computations are first performed to assess isolated tube behavior followed by results for multi-tube flow phenomena. The computations are based on an eight-species, finite-rate transient flow-field model. The results serve as an important precursor to understanding appropriate propellant fill procedures and shock wave propagation in multi-tube, multi-dimensional simulations. Differences in behavior between single and multi-tube PDE models are discussed, The influence of multi-tube geometry and the preferred times for injecting the fresh propellant mixture during multi-tube PDE operation are studied.

Reactive simulation of the chemistry behind the condensed-phase ignition of RDX from hot spots.

PubMed

Joshi, Kaushik L; Chaudhuri, Santanu

2015-07-28

Chemical events that lead to thermal initiation and spontaneous ignition of the high-pressure phase of RDX are presented using reactive molecular dynamics simulations. In order to initiate the chemistry behind thermal ignition, approximately 5% of RDX crystal is subjected to a constant temperature thermal pulse for various time durations to create a hot spot. After application of the thermal pulse, the ensuing chemical evolution of the system is monitored using reactive molecular dynamics under adiabatic conditions. Thermal pulses lasting longer than certain time durations lead to the spontaneous ignition of RDX after an incubation period. For cases where the ignition is observed, the incubation period is dominated by intermolecular and intramolecular hydrogen transfer reactions. Contrary to the widely accepted unimolecular models of initiation chemistry, N-N bond dissociations that produce NO2 species are suppressed in the condensed phase. The gradual temperature and pressure increase in the incubation period is accompanied by the accumulation of short-lived, heavier polyradicals. The polyradicals contain intact triazine rings from the RDX molecules. At certain temperatures and pressures, the polyradicals undergo ring-opening reactions, which fuel a series of rapid exothermic chemical reactions leading to a thermal runaway regime with stable gas-products such as N2, H2O and CO2. The evolution of the RDX crystal throughout the thermal initiation, incubation and thermal runaway phases observed in the reactive simulations contains a rich diversity of condensed-phase chemistry of nitramines under high-temperature/pressure conditions.

A support vector machine based test for incongruence between sets of trees in tree space

PubMed Central

2012-01-01

Background The increased use of multi-locus data sets for phylogenetic reconstruction has increased the need to determine whether a set of gene trees significantly deviate from the phylogenetic patterns of other genes. Such unusual gene trees may have been influenced by other evolutionary processes such as selection, gene duplication, or horizontal gene transfer. Results Motivated by this problem we propose a nonparametric goodness-of-fit test for two empirical distributions of gene trees, and we developed the software GeneOut to estimate a p-value for the test. Our approach maps trees into a multi-dimensional vector space and then applies support vector machines (SVMs) to measure the separation between two sets of pre-defined trees. We use a permutation test to assess the significance of the SVM separation. To demonstrate the performance of GeneOut, we applied it to the comparison of gene trees simulated within different species trees across a range of species tree depths. Applied directly to sets of simulated gene trees with large sample sizes, GeneOut was able to detect very small differences between two set of gene trees generated under different species trees. Our statistical test can also include tree reconstruction into its test framework through a variety of phylogenetic optimality criteria. When applied to DNA sequence data simulated from different sets of gene trees, results in the form of receiver operating characteristic (ROC) curves indicated that GeneOut performed well in the detection of differences between sets of trees with different distributions in a multi-dimensional space. Furthermore, it controlled false positive and false negative rates very well, indicating a high degree of accuracy. Conclusions The non-parametric nature of our statistical test provides fast and efficient analyses, and makes it an applicable test for any scenario where evolutionary or other factors can lead to trees with different multi-dimensional distributions. The software GeneOut is freely available under the GNU public license. PMID:22909268

The oxidative costs of parental care in cooperative and pair-breeding African starlings.

PubMed

Guindre-Parker, Sarah; Rubenstein, Dustin R

2018-06-01

The cost of parental care has long been thought to favor the evolution of cooperative breeding, because breeders can provide reduced parental care when aided by alloparents. Oxidative stress-the imbalance between reactive oxygen species and neutralizing antioxidants-has been proposed to mediate the cost of parental care, though results from empirical studies remain equivocal. We measured changes in oxidative status during reproduction in cooperatively breeding superb starlings (Lamprotornis superbus) to gain insight into the relationships among breeding status, parental care, and oxidative stress. We also compared the oxidative cost of reproduction in the cooperatively breeding superb starling to that in a sympatric non-cooperatively breeding species, the greater blue-eared glossy starling (L. chalybaeus), to determine whether cooperatively breeding individuals face reduced oxidative costs of parental care relative to non-cooperatively breeding individuals. Breeders and alloparents of the cooperative species did not differ in oxidative status throughout a breeding attempt. However, individuals of the non-cooperative species incurred an increase in reactive oxygen metabolites proportionally to an individual's workload during offspring care. These findings suggest that non-cooperative starlings experience an oxidative cost of parental care, whereas cooperatively breeding starlings do not. It is possible that high nest predation risk and multi-brooding in the cooperatively breeding species may have favored reduced physiological costs of parental care more strongly compared to pair-breeding starlings. Reduced physiological costs of caring for young may thus represent a direct benefit that promotes cooperative breeding.

Simulating Bioremediation of Chloroethenes in a Fractured Rock Aquifer.

NASA Astrophysics Data System (ADS)

Curtis, G. P.

2016-12-01

Reactive transport simulations are being conducted to synthesize the results of a field experiment on the enhanced bioremediation of chloroethenes in a heterogeneous fractured-rock aquifer near West Trenton, NJ. The aquifer consists of a sequence of dipping mudstone beds, with water-conducting bedding-plane fractures separated by low-permeability rock where transport is diffusion-limited. The enhanced bioremediation experiment was conducted by injecting emulsified vegetable oil as an electron donor (EOS™) and a microbial consortium (KB1™) that contained dehalococcoides ethenogenes into a fracture zone that had maximum trichloroethene (TCE) concentrations of 84µM. TCE was significantly biodegraded to dichloroethene, chloroethene and ethene or CO2 at the injection well and at a downgradient well. The results also show the concomitant reduction of Fe(III) and S(6) and the production of methane . The results were used to calibrate transport models for quantifying the dominant mass-removal mechanisms. A nonreactive transport model was developed to simulate advection, dispersion and matrix diffusion of bromide and deuterium tracers present in the injection solution. This calibrated model matched tracer concentrations at the injection well and a downgradient observation well and demonstrated that matrix diffusion was a dominant control on tracer transport. A reactive transport model was developed to extend the nonreactive transport model to simulate the microbially mediated sequential dechlorination reactions, reduction of Fe(III) and S(6), and methanogenesis. The reactive transport model was calibrated to concentrations of chloride, chloroethenes, pH, alkalinity, redox-sensitive species and major ions, to estimate key biogeochemical kinetic parameters. The simulation results generally match the diverse set of observations at the injection and observation wells throughout the three year experiment. In addition, the observations and model simulations indicate that a significant pool of TCE that was initially sorbed to either the fracture surfaces or in the matrix was degraded during the field experiment. The calibrated reactive transport model will be used to quantify the extent of chloroethene mass removal from a range of hypothetical aquifers.

Simultaneous leaching of arsenite, arsenate, selenite and selenate, and their migration in tunnel-excavated sedimentary rocks: II. Kinetic and reactive transport modeling.

PubMed

Tabelin, Carlito Baltazar; Sasaki, Ryosuke; Igarashi, Toshifumi; Park, Ilhwan; Tamoto, Shuichi; Arima, Takahiko; Ito, Mayumi; Hiroyoshi, Naoki

2017-12-01

Predicting the fates of arsenic (As) and selenium (Se) in natural geologic media like rocks and soils necessitates the understanding of how their various oxyanionic species behave and migrate under dynamic conditions. In this study, geochemical factors and processes crucial in the leaching and transport of arsenite (As III ), arsenate (As V ), selenite (Se IV ) and selenate (Se VI ) in tunnel-excavated rocks of marine origin were investigated using microscopic/extraction techniques, column experiments, dissolution-precipitation kinetics and one-dimensional reactive transport modeling. The results showed that evaporite salts were important because aside from containing As and Se, they played crucial roles in the evolution of pH and concentrations of coexisting ions, both of which had strong effects on adsorption-desorption reactions of As and Se species with iron oxyhydroxide minerals/phases. The observed leaching trends of As V , As III , Se IV and Se VI were satisfactorily simulated by one-dimensional reactive transport models, which predict that preferential adsorptions of As V and Se IV were magnified by geochemical changes in the columns due to water flow. Moreover, our results showed that migrations of As III , Se IV and Se VI could be predicted adequately by 1D solute transport with simple activity-K' d approach, but surface complexation was more reliable to simulate adsorption-desorption behavior of As V . Copyright © 2017 Elsevier Ltd. All rights reserved.

Optimizing the Performance of Reactive Molecular Dynamics Simulations for Multi-core Architectures

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

Aktulga, Hasan Metin; Coffman, Paul; Shan, Tzu-Ray

2015-12-01

Hybrid parallelism allows high performance computing applications to better leverage the increasing on-node parallelism of modern supercomputers. In this paper, we present a hybrid parallel implementation of the widely used LAMMPS/ReaxC package, where the construction of bonded and nonbonded lists and evaluation of complex ReaxFF interactions are implemented efficiently using OpenMP parallelism. Additionally, the performance of the QEq charge equilibration scheme is examined and a dual-solver is implemented. We present the performance of the resulting ReaxC-OMP package on a state-of-the-art multi-core architecture Mira, an IBM BlueGene/Q supercomputer. For system sizes ranging from 32 thousand to 16.6 million particles, speedups inmore » the range of 1.5-4.5x are observed using the new ReaxC-OMP software. Sustained performance improvements have been observed for up to 262,144 cores (1,048,576 processes) of Mira with a weak scaling efficiency of 91.5% in larger simulations containing 16.6 million particles.« less

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

Keidar, Michael, E-mail: keidar@gwu.edu; Robert, Eric

Intense research effort over last few decades in low-temperature (or cold) atmospheric plasma application in bioengineering led to the foundation of a new scientific field, plasma medicine. Cold atmospheric plasmas (CAP) produce various chemically reactive species including reactive oxygen species (ROS) and reactive nitrogen species (RNS). It has been found that these reactive species play an important role in the interaction of CAP with prokaryotic and eukaryotic cells triggering various signaling pathways in cells.

Inference for finite-sample trajectories in dynamic multi-state site-occupancy models using hidden Markov model smoothing

USGS Publications Warehouse

Fiske, Ian J.; Royle, J. Andrew; Gross, Kevin

2014-01-01

Ecologists and wildlife biologists increasingly use latent variable models to study patterns of species occurrence when detection is imperfect. These models have recently been generalized to accommodate both a more expansive description of state than simple presence or absence, and Markovian dynamics in the latent state over successive sampling seasons. In this paper, we write these multi-season, multi-state models as hidden Markov models to find both maximum likelihood estimates of model parameters and finite-sample estimators of the trajectory of the latent state over time. These estimators are especially useful for characterizing population trends in species of conservation concern. We also develop parametric bootstrap procedures that allow formal inference about latent trend. We examine model behavior through simulation, and we apply the model to data from the North American Amphibian Monitoring Program.

Multi-dimensional multi-species modeling of transient electrodeposition in LIGA microfabrication.

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

Evans, Gregory Herbert; Chen, Ken Shuang

2004-06-01

This report documents the efforts and accomplishments of the LIGA electrodeposition modeling project which was headed by the ASCI Materials and Physics Modeling Program. A multi-dimensional framework based on GOMA was developed for modeling time-dependent diffusion and migration of multiple charged species in a dilute electrolyte solution with reduction electro-chemical reactions on moving deposition surfaces. By combining the species mass conservation equations with the electroneutrality constraint, a Poisson equation that explicitly describes the electrolyte potential was derived. The set of coupled, nonlinear equations governing species transport, electric potential, velocity, hydrodynamic pressure, and mesh motion were solved in GOMA, using themore » finite-element method and a fully-coupled implicit solution scheme via Newton's method. By treating the finite-element mesh as a pseudo solid with an arbitrary Lagrangian-Eulerian formulation and by repeatedly performing re-meshing with CUBIT and re-mapping with MAPVAR, the moving deposition surfaces were tracked explicitly from start of deposition until the trenches were filled with metal, thus enabling the computation of local current densities that potentially influence the microstructure and frictional/mechanical properties of the deposit. The multi-dimensional, multi-species, transient computational framework was demonstrated in case studies of two-dimensional nickel electrodeposition in single and multiple trenches, without and with bath stirring or forced flow. Effects of buoyancy-induced convection on deposition were also investigated. To further illustrate its utility, the framework was employed to simulate deposition in microscreen-based LIGA molds. Lastly, future needs for modeling LIGA electrodeposition are discussed.« less

SUTRA (Saturated-Unsaturated Transport). A Finite-Element Simulation Model for Saturated-Unsaturated, Fluid-Density-Dependent Ground-Water Flow with Energy Transport or Chemically-Reactive Single-Species Solute Transport.

DTIC Science & Technology

1984-12-30

as three dimensional, when the assumption is made that all SUTRA parameters and coefficients have a constant value in the third space direction. A...finite element. The type of element employed by SUTRA for two-dimensional simulation is a quadrilateral which has a finite thickness in the third ... space dimension. This type of a quad- rilateral element and a typical two-dimensional mesh is shown in Figure 3.1. - All twelve edges of the two

The Atmospheric Tomography Mission (ATom): Comparing the Chemical Climatology of Reactive Species and Air Parcels from Measurements and Global Models

NASA Astrophysics Data System (ADS)

Prather, M. J.; Flynn, C.; Wennberg, P. O.; Kim, M. J.; Ryerson, T. B.; Hanisco, T. F.; Diskin, G. S.; Daube, B. C.; Commane, R.; McKain, K.; Apel, E. C.; Blake, N. J.; Blake, D. R.; Elkins, J. W.; Hall, S.; Steenrod, S.; Strahan, S. E.; Lamarque, J. F.; Fiore, A. M.; Horowitz, L. W.; Murray, L. T.; Mao, J.; Shindell, D. T.; Wofsy, S. C.

2017-12-01

The NASA Atmospheric Tomography Mission (ATom) is building a photochemical climatology of the remote troposphere based on objective sampling and profiling transects over the Pacific and Atlantic Oceans. These statistics provide direct tests of chemistry-climate models. The choice of species focuses on those controlling primary reactivity (a.k.a. oxidative state) of the troposphere, specifically chemical tendencies of O3 and CH4. These key species include, inter alia, O3, CH4, CO, C2H6, other alkanes, alkenes, aromatics, NOx, HNO3, HO2NO2, PAN, other organic nitrates, H2O, HCHO, H2O2, CH3OOH. Three of the four ATom deployments are now complete, and data from the first two (ATom-1 & -2) have been released as of this talk (see espoarchive.nasa.gov/archive/browse/atom). The statistical distributions of key species are presented as 1D and 2D probability densities (PDs) and we focus here on the tropical and mid-latitude regions of the Pacific during ATom-1 (Aug) and -2 (Feb). PDs are computed from ATom observations and 6 global chemistry models over the tropospheric depth (0-12 km) and longitudinal extent of the observations. All data are weighted to achieve equal mass-weighting by latitude regimes to account for spatial sampling biases. The models are used to calculate the reactivity in each ATom air parcel. Reweighting parcels with loss of CH4 or production of O3, for example, allows us to identify which air parcels are most influential, including assessment of the importance of fine pollution layers in the most remote troposphere. Another photochemical climatology developed from ATom, and used to test models, includes the effect of clouds on photolysis rates. The PDs and reactivity-weighted PDs reveal important seasonal differences and similarities between the two campaigns and also show which species may be most important in controlling reactivities. They clearly identify some very specific failings in the modeled climatologies and help us evaluate the chemical importance of fine-scale laminae with distinct chemical composition that are beyond model simulations.

Altering CO2 during reperfusion of ischemic cardiomyocytes modifies mitochondrial oxidant injury.

PubMed

Lavani, Romeen; Chang, Wei-Tien; Anderson, Travis; Shao, Zuo-Hui; Wojcik, Kimberly R; Li, Chang-Qing; Pietrowski, Robert; Beiser, David G; Idris, Ahamed H; Hamann, Kimm J; Becker, Lance B; Vanden Hoek, Terry L

2007-07-01

Acute changes in tissue CO2 and pH during reperfusion of the ischemic heart may affect ischemia/reperfusion injury. We tested whether gradual vs. acute decreases in CO2 after cardiomyocyte ischemia affect reperfusion oxidants and injury. Comparative laboratory investigation. Institutional laboratory. Embryonic chick cardiomyocytes. Microscope fields of approximately 500 chick cardiomyocytes were monitored throughout 1 hr of simulated ischemia (PO2 of 3-5 torr, PCO2 of 144 torr, pH 6.8), followed by 3 hrs of reperfusion (PO2 of 149 torr, PCO2 of 36 torr, pH 7.4), and compared with cells reperfused with relative hypercarbia (PCO2 of 71 torr, pH 6.8) or hypocarbia (PCO2 of 7 torr, pH 7.9). The measured outcomes included cell viability (via propidium iodide) and oxidant generation (reactive oxygen species via 2',7'-dichlorofluorescin oxidation and nitric oxide [NO] via 4,5-diaminofluorescein diacetate oxidation). Compared with normocarbic reperfusion, hypercarbia significantly reduced cell death from 54.8% +/- 4.0% to 26.3% +/- 2.8% (p < .001), significantly decreased reperfusion reactive oxygen species (p < .05), and increased NO at a later phase of reperfusion (p < .01). The NO synthase inhibitor N-nitro-L-arginine methyl ester (200 microM) reversed this oxidant attenuation (p < .05), NO increase (p < .05), and the cardioprotection conferred by hypercarbic reperfusion (increasing death to 54.3% +/- 6.0% [p < .05]). Conversely, hypocarbic reperfusion increased cell death to 80.4% +/- 4.5% (p < .01). It also increased reactive oxygen species by almost two-fold (p = .052), without affecting the NO level thereafter. Increased reactive oxygen species was attenuated by the mitochondrial complex III inhibitor stigmatellin (20 nM) when given at reperfusion (p < .05). Cell death also decreased from 85.9% +/- 4.5% to 52.2% +/- 6.5% (p < .01). The nicotinamide adenine dinucleotide phosphate oxidase inhibitor apocynin (300 microM) had no effect on reperfusion reactive oxygen species. Altering CO2 content during reperfusion can significantly affect myocardial postresuscitation injury, in part by modifying mitochondrial oxidants and NO synthase-induced NO production.

Upscaling heterogeneity in aquifer reactivity via exposure-time concept: forward model.

PubMed

Seeboonruang, Uma; Ginn, Timothy R

2006-03-20

Reactive properties of aquifer solid phase materials play an important role in solute fate and transport in the natural subsurface on time scales ranging from years in contaminant remediation to millennia in dynamics of aqueous geochemistry. Quantitative tools for dealing with the impact of natural heterogeneity in solid phase reactivity on solute fate and transport are limited. Here we describe the use of a structural variable to keep track of solute flux exposure to reactive surfaces. With this approach, we develop a non-reactive tracer model that is useful for determining the signature of multi-scale reactive solid heterogeneity in terms of solute flux distributions at the field scale, given realizations of three-dimensional reactive site density fields. First, a governing Eulerian equation for the non-reactive tracer model is determined by an upscaling technique in which it is found that the exposure time of solution to reactive surface areas evolves via both a macroscopic velocity and a macroscopic dispersion in the artificial dimension of exposure time. Second, we focus on the Lagrangian approach in the context of a streamtube ensemble and demonstrate the use of the distribution of solute flux over the exposure time dimension in modeling two-dimensional transport of a solute undergoing simplified linear reversible reactions, in hypothetical conditions following prior laboratory experiments. The distribution of solute flux over exposure time in a given case is a signature of the impact of heterogeneous aquifer reactivity coupled with a particular physical heterogeneity, boundary conditions, and hydraulic gradient. Rigorous application of this approach in a simulation sense is limited here to linear kinetically controlled reactions.

Integrated multi-omic analysis of host-microbiota interactions in acute oak decline.

PubMed

Broberg, Martin; Doonan, James; Mundt, Filip; Denman, Sandra; McDonald, James E

2018-01-30

Britain's native oak species are currently under threat from acute oak decline (AOD), a decline-disease where stem bleeds overlying necrotic lesions in the inner bark and larval galleries of the bark-boring beetle, Agrilus biguttatus, represent the primary symptoms. It is known that complex interactions between the plant host and its microbiome, i.e. the holobiont, significantly influence the health status of the plant. In AOD, necrotic lesions are caused by a microbiome shift to a pathobiome consisting predominantly of Brenneria goodwinii, Gibbsiella quercinecans, Rahnella victoriana and potentially other bacteria. However, the specific mechanistic processes of the microbiota causing tissue necrosis, and the host response, have not been established and represent a barrier to understanding and managing this decline. We profiled the metagenome, metatranscriptome and metaproteome of inner bark tissue from AOD symptomatic and non-symptomatic trees to characterise microbiota-host interactions. Active bacterial virulence factors such as plant cell wall-degrading enzymes, reactive oxygen species defence and flagella in AOD lesions, along with host defence responses including reactive oxygen species, cell wall modification and defence regulators were identified. B. goodwinii dominated the lesion microbiome, with significant expression of virulence factors such as the phytopathogen effector avrE. A smaller proportion of microbiome activity was attributed to G. quercinecans and R. victoriana. In addition, we describe for the first time the potential role of two previously uncharacterised Gram-positive bacteria predicted from metagenomic binning and identified as active in the AOD lesion metatranscriptome and metaproteome, implicating them in lesion formation. This multi-omic study provides novel functional insights into microbiota-host interactions in AOD, a complex arboreal decline disease where polymicrobial-host interactions result in lesion formation on tree stems. We present the first descriptions of holobiont function in oak health and disease, specifically, the relative lesion activity of B. goodwinii, G. quercinecans, Rahnella victoriana and other bacteria. Thus, the research presented here provides evidence of some of the mechanisms used by members of the lesion microbiome and a template for future multi-omic research into holobiont characterisation, plant polymicrobial diseases and pathogen defence in trees.

Ion species stratification within strong shocks in two-ion plasmas

DOE PAGES

Keenan, Brett D.; Simakov, Andrei N.; Taitano, William T.; ...

2018-03-01

We report strong collisional shocks in multi-ion plasmas are featured in many environments, with Inertial Confinement Fusion (ICF) experiments being one prominent example. Recent work [Keenan et al., Phys. Rev. E 96, 053203 (2017)] answered in detail a number of outstanding questions concerning the kinetic structure of steady-state, planar plasma shocks, e.g., the shock width scaling by the Mach number, M. However, it did not discuss shock-driven ion-species stratification (e.g., relative concentration modification and temperature separation). These are important effects since many recent ICF experiments have evaded explanation by standard, single-fluid, radiation-hydrodynamic (rad-hydro) numerical simulations, and shock-driven fuel stratification likelymore » contributes to this discrepancy. Employing the state-of-the-art Vlasov-Fokker-Planck code, iFP, along with multi-ion hydro simulations and semi-analytics, we quantify the ion stratification by planar shocks with the arbitrary Mach number and the relative species concentration for two-ion plasmas in terms of ion mass and charge ratios. In particular, for strong shocks, we find that the structure of the ion temperature separation has a nearly universal character across ion mass and charge ratios. Lastly, we find that the shock fronts are enriched with the lighter ion species and the enrichment scales as M 4 for M»1.« less

Ion species stratification within strong shocks in two-ion plasmas

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

Keenan, Brett D.; Simakov, Andrei N.; Taitano, William T.

We report strong collisional shocks in multi-ion plasmas are featured in many environments, with Inertial Confinement Fusion (ICF) experiments being one prominent example. Recent work [Keenan et al., Phys. Rev. E 96, 053203 (2017)] answered in detail a number of outstanding questions concerning the kinetic structure of steady-state, planar plasma shocks, e.g., the shock width scaling by the Mach number, M. However, it did not discuss shock-driven ion-species stratification (e.g., relative concentration modification and temperature separation). These are important effects since many recent ICF experiments have evaded explanation by standard, single-fluid, radiation-hydrodynamic (rad-hydro) numerical simulations, and shock-driven fuel stratification likelymore » contributes to this discrepancy. Employing the state-of-the-art Vlasov-Fokker-Planck code, iFP, along with multi-ion hydro simulations and semi-analytics, we quantify the ion stratification by planar shocks with the arbitrary Mach number and the relative species concentration for two-ion plasmas in terms of ion mass and charge ratios. In particular, for strong shocks, we find that the structure of the ion temperature separation has a nearly universal character across ion mass and charge ratios. Lastly, we find that the shock fronts are enriched with the lighter ion species and the enrichment scales as M 4 for M»1.« less

Ion species stratification within strong shocks in two-ion plasmas

NASA Astrophysics Data System (ADS)

Keenan, Brett D.; Simakov, Andrei N.; Taitano, William T.; Chacón, Luis

2018-03-01

Strong collisional shocks in multi-ion plasmas are featured in many environments, with Inertial Confinement Fusion (ICF) experiments being one prominent example. Recent work [Keenan et al., Phys. Rev. E 96, 053203 (2017)] answered in detail a number of outstanding questions concerning the kinetic structure of steady-state, planar plasma shocks, e.g., the shock width scaling by the Mach number, M. However, it did not discuss shock-driven ion-species stratification (e.g., relative concentration modification and temperature separation). These are important effects since many recent ICF experiments have evaded explanation by standard, single-fluid, radiation-hydrodynamic (rad-hydro) numerical simulations, and shock-driven fuel stratification likely contributes to this discrepancy. Employing the state-of-the-art Vlasov-Fokker-Planck code, iFP, along with multi-ion hydro simulations and semi-analytics, we quantify the ion stratification by planar shocks with the arbitrary Mach number and the relative species concentration for two-ion plasmas in terms of ion mass and charge ratios. In particular, for strong shocks, we find that the structure of the ion temperature separation has a nearly universal character across ion mass and charge ratios. Additionally, we find that the shock fronts are enriched with the lighter ion species and the enrichment scales as M4 for M ≫ 1.

Reactivity at the Lithium–Metal Anode Surface of Lithium–Sulfur Batteries

DOE PAGES

Camacho-Forero, Luis E.; Smith, Taylor W.; Bertolini, Samuel; ...

2015-11-11

Due to their high energy density and reduced cost, lithium–sulfur batteries are promising alternatives for applications such as electrical vehicles. However, a number of technical challenges need to be overcome in order to make them feasible for commercial uses. These challenges arise from the battery highly interconnected chemistry, which besides the electrochemical reactions includes side reactions at both electrodes and migration of soluble polysulfide (PS) species produced at the cathode to the anode side. The presence of such PS species alters the already complex reactivity of the Li anode. In this paper, interfacial reactions occurring at the surface of Limore » metal anodes due to electrochemical instability of the electrolyte components and PS species are investigated with density functional theory and ab initio molecular dynamics methods. It is found that the bis(trifluoromethane)sulfonimide lithium salt reacts very fast when in contact with the Li surface, and anion decomposition precedes salt dissociation. The anion decomposition mechanisms are fully elucidated. Two of the typical solvents used in Li–S technology, 1,3-dioxolane and 1,2-dimethoxyethane, are found stable during the entire simulation length, in contrast with the case of ethylene carbonate that is rapidly decomposed by sequential 2- or 4-electron mechanisms. Finally, on the other hand, the fast reactivity of the soluble PS species alters the side reactions because the PS totally decomposes before any of the electrolyte components forming Li 2S on the anode surface.« less

Luna: What Did We Learn and What Should We Expect?

NASA Technical Reports Server (NTRS)

Wallace, William T.

2009-01-01

This presentation presents a look at the space program's background prior to lunar exploration and highlights the Apollo program and lessons learned from lunar exploration. The possibilities of exposures and difficulties attributed to lunar dust are described, including obscured vision, clogged equipment, coated surfaces, and inhalation, among others. A lunar dust simulant is proposed to support preliminary studies. Lunar dust is constantly activated by meteorite lunar dust, UV radiation and elements of solar wind - this active dust could produce reactive species. Methods of deactivation must be determined before new lunar missions, but first we must understand how to reactivate dust on Earth. Activation methods tested and described here include crushing/grinding or UV activation. Grinding time has a direct effect on amount of hydroxyl radicals produced upon addition of ground quartz to a solution. An increase in hydroxyl production was also seen for a lunar simulant with increased grinding.

Surface colonized silver nano particles over chitosan poly-electrolyte micro-spheres and their multi-functional behavior

NASA Astrophysics Data System (ADS)

Prakash, B.; Asha, S.; Nimrodh Ananth, A.; Vanithakumari, G.; Okram, G. S.; Jose, Sujin P.; Jothi Rajan, M. A.

2018-02-01

Chitosan/tripolyphosphate polyelectrolyte (TPP) microspheres, decorated and surface functionalized with silver nanoparticles (NPs) of average diameter of 15 nm, were synthesized following a simple two-step procedure. These Ag NP-functionalized polyelectrolyte microspheres (Ag-CSPMs) are found to be biocompatible and enhancing the reactive oxygen species in curcumin with excellent anti-bacterial activity for selected Gram-positive and negative bacterial strains, making them much attractive relative to bare surface counterparts; the well-stabilized silver NPs do not form any agglomerations on the surface of the chitosan microspheres. They also show excellent cytotoxic behavior towards MCF7 cell lines, showing a half-maximal inhibitory concentration (IC50) of 32 μg ml-1. Therefore, Ag-CSPMs exhibit multi-functional ability having potential towards theranostics applications.

Cross-reactivity among antigens of different air-borne fungi detected by ELISA using five monoclonal antibodies against Penicillium notatum.

PubMed

Shen, H D; Lin, W L; Chen, R J; Han, S H

1990-10-01

Cross-reactivity among antigens of 12 genera of air-borne fungi, 13 species of Penicillium, and 5 species of Aspergillus was studied by ELISA using five monoclonal antibodies (MoAbs) against Penicillium notatum. Epitopes recognized by all the five MoAbs were susceptible to treatment of mild periodate oxidation and may therefore be associated with carbohydrates. Furthermore, our results showed that there is cross-reactivity among antigens of Penicillium, Aspergillus, and Eurotium species. By using these MoAbs, cross reactivity was not detected between antigens of Penicillium notatum and antigens of Fusarium solani, Alternaria porri, Cladosporium cladosporoides, Curvularia species, Nigrospora species, Aureobasidium pullulans, Wallemia species, Rhizopus arrhizus, and Candida albicans. Cross-reactivity among antigens of 11 species of Penicillium and 5 species of Aspergillus could be detected by ELISA using one of the five MoAbs (MoAb P15). The fact that there may be cross-reactivity among antigens of closely related fungi species should be considered in the diagnosis and treatment of mold allergic diseases.

HPC Institutional Computing Project: W15_lesreactiveflow KIVA-hpFE Development: A Robust and Accurate Engine Modeling Software

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

Carrington, David Bradley; Waters, Jiajia

KIVA-hpFE is a high performance computer software for solving the physics of multi-species and multiphase turbulent reactive flow in complex geometries having immersed moving parts. The code is written in Fortran 90/95 and can be used on any computer platform with any popular complier. The code is in two versions, a serial version and a parallel version utilizing MPICH2 type Message Passing Interface (MPI or Intel MPI) for solving distributed domains. The parallel version is at least 30x faster than the serial version and much faster than our previous generation of parallel engine modeling software, by many factors. The 5thmore » generation algorithm construction is a Galerkin type Finite Element Method (FEM) solving conservative momentum, species, and energy transport equations along with two-equation turbulent model k-ω Reynolds Averaged Navier-Stokes (RANS) model and a Vreman type dynamic Large Eddy Simulation (LES) method. The LES method is capable modeling transitional flow from laminar to fully turbulent; therefore, this LES method does not require special hybrid or blending to walls. The FEM projection method also uses a Petrov-Galerkin (P-G) stabilization along with pressure stabilization. We employ hierarchical basis sets, constructed on the fly with enrichment in areas associated with relatively larger error as determined by error estimation methods. In addition, when not using the hp-adaptive module, the code employs Lagrangian basis or shape functions. The shape functions are constructed for hexahedral, prismatic and tetrahedral elements. The software is designed to solve many types of reactive flow problems, from burners to internal combustion engines and turbines. In addition, the formulation allows for direct integration of solid bodies (conjugate heat transfer), as in heat transfer through housings, parts, cylinders. It can also easily be extended to stress modeling of solids, used in fluid structure interactions problems, solidification, porous media modeling and magneto hydrodynamics.« less

The Dynamics of the Human Leukocyte Antigen Head Domain Modulates Its Recognition by the T-Cell Receptor.

PubMed

García-Guerrero, Estefanía; Pérez-Simón, José Antonio; Sánchez-Abarca, Luis Ignacio; Díaz-Moreno, Irene; De la Rosa, Miguel A; Díaz-Quintana, Antonio

2016-01-01

Generating the immune response requires the discrimination of peptides presented by the human leukocyte antigen complex (HLA) through the T-cell receptor (TCR). However, how a single amino acid substitution in the antigen bonded to HLA affects the response of T cells remains uncertain. Hence, we used molecular dynamics computations to analyze the molecular interactions between peptides, HLA and TCR. We compared immunologically reactive complexes with non-reactive and weakly reactive complexes. MD trajectories were produced to simulate the behavior of isolated components of the various p-HLA-TCR complexes. Analysis of the fluctuations showed that p-HLA binding barely restrains TCR motions, and mainly affects the CDR3 loops. Conversely, inactive p-HLA complexes displayed significant drop in their dynamics when compared with its free versus ternary forms (p-HLA-TCR). In agreement, the free non-reactive p-HLA complexes showed a lower amount of salt bridges than the responsive ones. This resulted in differences between the electrostatic potentials of reactive and inactive p-HLA species and larger vibrational entropies in non-elicitor complexes. Analysis of the ternary p-HLA-TCR complexes also revealed a larger number of salt bridges in the responsive complexes. To summarize, our computations indicate that the affinity of each p-HLA complex towards TCR is intimately linked to both, the dynamics of its free species and its ability to form specific intermolecular salt-bridges in the ternary complexes. Of outstanding interest is the emerging concept of antigen reactivity involving its interplay with the HLA head sidechain dynamics by rearranging its salt-bridges.

Predicting the impact of combined therapies on myeloma cell growth using a hybrid multi-scale agent-based model.

PubMed

Ji, Zhiwei; Su, Jing; Wu, Dan; Peng, Huiming; Zhao, Weiling; Nlong Zhao, Brian; Zhou, Xiaobo

2017-01-31

Multiple myeloma is a malignant still incurable plasma cell disorder. This is due to refractory disease relapse, immune impairment, and development of multi-drug resistance. The growth of malignant plasma cells is dependent on the bone marrow (BM) microenvironment and evasion of the host's anti-tumor immune response. Hence, we hypothesized that targeting tumor-stromal cell interaction and endogenous immune system in BM will potentially improve the response of multiple myeloma (MM). Therefore, we proposed a computational simulation of the myeloma development in the complicated microenvironment which includes immune cell components and bone marrow stromal cells and predicted the effects of combined treatment with multi-drugs on myeloma cell growth. We constructed a hybrid multi-scale agent-based model (HABM) that combines an ODE system and Agent-based model (ABM). The ODEs was used for modeling the dynamic changes of intracellular signal transductions and ABM for modeling the cell-cell interactions between stromal cells, tumor, and immune components in the BM. This model simulated myeloma growth in the bone marrow microenvironment and revealed the important role of immune system in this process. The predicted outcomes were consistent with the experimental observations from previous studies. Moreover, we applied this model to predict the treatment effects of three key therapeutic drugs used for MM, and found that the combination of these three drugs potentially suppress the growth of myeloma cells and reactivate the immune response. In summary, the proposed model may serve as a novel computational platform for simulating the formation of MM and evaluating the treatment response of MM to multiple drugs.

Impact of multi-component diffusion in turbulent combustion using direct numerical simulations

DOE PAGES

Bruno, Claudio; Sankaran, Vaidyanathan; Kolla, Hemanth; ...

2015-08-28

This study presents the results of DNS of a partially premixed turbulent syngas/air flame at atmospheric pressure. The objective was to assess the importance and possible effects of molecular transport on flame behavior and structure. To this purpose DNS were performed at with two proprietary DNS codes and with three different molecular diffusion transport models: fully multi-component, mixture averaged, and imposing the Lewis number of all species to be unity.

Preface to Special Topic: Plasmas for Medical Applications

NASA Astrophysics Data System (ADS)

Keidar, Michael; Robert, Eric

2015-12-01

Intense research effort over last few decades in low-temperature (or cold) atmospheric plasma application in bioengineering led to the foundation of a new scientific field, plasma medicine. Cold atmospheric plasmas (CAP) produce various chemically reactive species including reactive oxygen species (ROS) and reactive nitrogen species (RNS). It has been found that these reactive species play an important role in the interaction of CAP with prokaryotic and eukaryotic cells triggering various signaling pathways in cells.

Measurements of reactive halogen species as oxidants of mercury over the Gulf of Mexico

NASA Astrophysics Data System (ADS)

Volkamer, R.; Coburn, S.; Dix, B. K.; Sinreich, R.; Terschure, A. F.; Edgerton, E. S.; Wu, Y.; Nair, U. S.

2011-12-01

The gas-phase reaction of bromine and chlorine radicals with gaseous elemental mercury (GEM) is a source for gaseous oxidized mercury (GOM). It has been established that oxidation by bromine is relevant at high latitudes, and can also occur in mid-latitude regions (Peleg et al. 2007), or in the free troposphere. A subject of ongoing debate concerns the role of free tropospheric bromine vs boundary layer bromine in oxidizing mercury. Here we present measurements of reactive halogen species bromine oxide (BrO) and iodine oxide (IO) along with gaseous oxidized mercury (GOM), gaseous elemental mercury (GEM), and particulate mercury (Hgp) at a coastal location in Gulf Breeze, Fl. The University of Colorado has deployed a research grade Multi Axis Differential Optical Absorption Spectroscopy (MAX-DOAS) instrument to measure BrO, IO, as well as formaldehyde (HCHO), glyoxal (CHOCHO), nitrogen dioxide (NO2) and oxygen dimers (O4). Here we present the compilation of the data collected by this instrument over the time period from May 2009 to January 2011, which include the first measurements of BrO, IO, and CHOCHO over the Gulf of Mexico. We also present several case studies for days where significant amounts of reactive halogens were measured, explore the sources and back trajectories of the air masses carrying these compounds, and relate our observations to mercury data collected at a nearby SEARCH network site.

a Transient Semi-Metallic Layer in Detonating Nitromethane

NASA Astrophysics Data System (ADS)

Reed, Evan J.; Manaa, M. Riad; Fried, Laurence E.; Glaesemann, Kurt; Joannopoulos, John D.

2007-12-01

We present the first ever glimpse behind a detonation shock front in a chemically reactive quantum molecular dynamics simulation of the explosive nitromethane (CH3NO2). We discover that the wide-bandgap insulator nitromethane undergoes chemical decomposition and a transformation into a semi-metallic state for a limited distance behind the detonation front. We find this transformation is associated with the production of charged decomposition species.

Aerosol-halogen interaction: Change of physico-chemical properties of SOA by naturally released halogen species

NASA Astrophysics Data System (ADS)

Ofner, J.; Balzer, N.; Buxmann, J.; Grothe, H.; Krüger, H.; Platt, U.; Schmitt-Kopplin, P.; Zetzsch, C.

2011-12-01

Reactive halogen species are released by various sources like photo-activated sea-salt aerosol or salt pans and salt lakes. These heterogeneous release mechanisms have been overlooked so far, although their potential of interaction with organic aerosols like Secondary Organic Aerosol (SOA), Biomass Burning Organic Aerosol (BBOA) or Atmospheric Humic LIke Substances (HULIS) is completely unknown. Such reactions can constitute sources of gaseous organo-halogen compounds or halogenated organic particles in the atmospheric boundary layer. To study the interaction of organic aerosols with reactive halogen species (RHS), SOA was produced from α-pinene, catechol and guaiacol using an aerosol smog-chamber. The model SOAs were characterized in detail using a variety of physico-chemical methods (Ofner et al., 2011). Those aerosols were exposed to molecular halogens in the presence of UV/VIS irradiation and to halogens, released from simulated natural halogen sources like salt pans, in order to study the complex aerosol-halogen interaction. The heterogeneous reaction of RHS with those model aerosols leads to different gaseous species like CO2, CO and small reactive/toxic molecules like phosgene (COCl2). Hydrogen containing groups on the aerosol particles are destroyed to form HCl or HBr, and a significant formation of C-Br bonds could be verified in the particle phase. Carbonyl containing functional groups of the aerosol are strongly affected by the halogenation process. While changes of functional groups and gaseous species were visible using FTIR spectroscopy, optical properties were studied using Diffuse Reflectance UV/VIS spectroscopy. Overall, the optical properties of the processed organic aerosols are significantly changed. While chlorine causes a "bleaching" of the aerosol particles, bromine shifts the maximum of UV/VIS absorption to the red end of the UV/VIS spectrum. Further physico-chemical changes were recognized according to the aerosol size-distributions or the averaged carbon oxidation state (OSc). The heterogeneous reaction of SOA with molecular halogens released from the simulated salt-pan at different simulated environmental conditions leads to changes of several physico-chemical features of the aerosol. However, the halogen release mechanisms are also affected by the presence of organic aerosols. One order of magnitude less BrO was detected by an active Differential Optical Absorption Spectroscopy (DOAS) instrument in the presence of SOA compared to experiments without SOA. This work was supported by the German Research Foundation within the HALOPROC project. Ofner, J., Krüger, H.-U., Grothe, H., Schmitt-Kopplin, P., Whitmore, K., and Zetzsch, C. (2011), Atmos. Chem. Phys., 11, 1-15.

First-principles study of adsorption-desorption kinetics of aqueous V2+/V3+ redox species on graphite in a vanadium redox flow battery.

PubMed

Jiang, Zhen; Klyukin, Konstantin; Alexandrov, Vitaly

2017-06-14

Vanadium redox flow batteries (VRFBs) represent a promising solution to grid-scale energy storage, and understanding the reactivity of electrode materials is crucial for improving the power density of VRFBs. However, atomistic details about the interactions between vanadium ions and electrode surfaces in aqueous electrolytes are still lacking. Here, we examine the reactivity of the basal (0001) and edge (112[combining macron]0) graphite facets with water and aqueous V 2+ /V 3+ redox species at 300 K employing Car-Parrinello molecular dynamics (CPMD) coupled with metadynamics simulations. The results suggest that the edge surface is characterized by the formation of ketonic C[double bond, length as m-dash]O functional groups due to complete water dissociation into the H/O/H configuration with surface O atoms serving as active sites for adsorption of V 2+ /V 3+ species. The formation of V-O bonds at the surface should significantly improve the kinetics of electron transfer at the edge sites, which is not the case for the basal surface, in agreement with the experimentally hypothesized mechanism.

Scaling of plasma-body interactions in low Earth orbit

NASA Astrophysics Data System (ADS)

Capon, C. J.; Brown, M.; Boyce, R. R.

2017-04-01

This paper derives the generalised set of dimensionless parameters that scale the interaction of an unmagnetised multi-species plasma with an arbitrarily charged object - the application in this work being to the interaction of the ionosphere with Low Earth Orbiting (LEO) objects. We find that a plasma with K ion species can be described by 1 + 4 K independent dimensionless parameters. These parameters govern the deflection and coupling of ion species k , the relative electrical shielding of the body, electron energy, and scaling of temporal effects. The general shielding length λ ϕ is introduced, which reduces to the Debye length in the high-temperature (weakly coupled) limit. The ability of the scaling parameters to predict the self-similar transformations of single and multi-species plasma interactions is demonstrated numerically using pdFOAM, an electrostatic Particle-in-Cell—Direct Simulation Monte Carlo code. The presented scaling relationships represent a significant generalisation of past work, linking low and high voltage plasma phenomena. Further, the presented parameters capture the scaling of multi-species plasmas with multiply charged ions, demonstrating previously unreported scaling relationship transformations. The implications of this work are not limited to LEO plasma-body interactions but apply to processes governed by the Vlasov-Maxwell equations and represent a framework upon which to incorporate the scaling of additional phenomena, e.g., magnetism and charging.

A fully coupled 3D transport model in SPH for multi-species reaction-diffusion systems

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

Adami, Stefan; Hu, X. Y.; Adams, N. A.

2011-08-23

Abstract—In this paper we present a fully generalized transport model for multiple species in complex two and threedimensional geometries. Based on previous work [1] we have extended our interfacial reaction-diffusion model to handle arbitrary numbers of species allowing for coupled reaction models. Each species is tracked independently and we consider different physics of a species with respect to the bulk phases in contact. We use our SPH model to simulate the reaction-diffusion problem on a pore-scale level of a solid oxide fuel cell (SOFC) with special emphasize on the effect of surface diffusion.

Understanding DNA under oxidative stress and sensitization: the role of molecular modeling

PubMed Central

Dumont, Elise; Monari, Antonio

2015-01-01

DNA is constantly exposed to damaging threats coming from oxidative stress, i.e., from the presence of free radicals and reactive oxygen species. Sensitization from exogenous and endogenous compounds that strongly enhance the frequency of light-induced lesions also plays an important role. The experimental determination of DNA lesions, though a difficult subject, is somehow well established and allows to elucidate even extremely rare DNA lesions. In parallel, molecular modeling has become fundamental to clearly understand the fine mechanisms related to DNA defects induction. Indeed, it offers an unprecedented possibility to get access to an atomistic or even electronic resolution. Ab initio molecular dynamics may also describe the time-evolution of the molecular system and its reactivity. Yet the modeling of DNA (photo-)reactions does necessitate elaborate multi-scale methodologies to tackle a damage induction reactivity that takes place in a complex environment. The double-stranded DNA environment is first characterized by a very high flexibility, but also a strongly inhomogeneous electrostatic embedding. Additionally, one aims at capturing more subtle effects, such as the sequence selectivity which is of critical important for DNA damage. The structure and dynamics of the DNA/sensitizers complexes, as well as the photo-induced electron- and energy-transfer phenomena taking place upon sensitization, should be carefully modeled. Finally the factors inducing different repair ratios for different lesions should also be rationalized. In this review we will critically analyze the different computational strategies used to model DNA lesions. A clear picture of the complex interplay between reactivity and structural factors will be sketched. The use of proper multi-scale modeling leads to the in-depth comprehension of DNA lesions mechanisms and also to the rational design of new chemo-therapeutic agents. PMID:26236706

Resolving Controversies Concerning the Kinetic Structure of Multi-Ion Plasma Shocks

NASA Astrophysics Data System (ADS)

Keenan, Brett; Simakov, Andrei; Chacon, Luis; Taitano, William

2017-10-01

Strong collisional shocks in multi-ion plasmas are featured in several high-energy-density environments, including Inertial Confinement Fusion (ICF) implosions. Yet, basic structural features of these shocks remain poorly understood (e.g., the shock width's dependence on the Mach number and the plasma ion composition, and temperature decoupling between ion species), causing controversies in the literature; even for stationary shocks in planar geometry [cf., Ref. and Ref.]. Using a LANL-developed, high-fidelity, 1D-2V Vlasov-Fokker-Planck code (iFP), as well as direct comparisons to multi-ion hydrodynamic simulations and semi-analytic predictions, we critically examine steady-state, planar shocks in two-ion species plasmas and put forward resolutions to these controversies. This work was supported by the Los Alamos National Laboratory LDRD Program, Metropolis Postdoctoral Fellowship for W.T.T., and used resources provided by the Los Alamos National Laboratory Institutional Computing Program.

Chemically reactive species in liquids generated by atmospheric-pressure plasmas and their roles in plasma medicine

NASA Astrophysics Data System (ADS)

Hamaguchi, Satoshi

2013-07-01

Plasmas whose gas temperatures are close to room temperature may be generated in ambient air or a gas at atmospheric pressure with the use of low-frequency high voltage or low-power radio-frequency (RF) or microwave power applied to electrodes. Such plasmas can serve as a powerful source of free radicals and/or chemically reactive species that arise from atoms and molecules of the ambient gas. Recently use of such plasmas for medical purposes has attracted much attention as they can be implemented in possible medical devices that can cause blood coagulation, heal wounds, facilitate angiogenesis, sterilize surgical devices as well as living tissues without harming healthy cells, and selectively inactivate cancer cells. Especially of interest among reactive species generated by atmospheric-pressure plasmas (APP) are reactive oxygen species (ROS) and reactive nitrogen species (RNS) that are generated in liquid phase. Since most living tissues and cells are immersed in liquids (such as blood or culture media), reactive species generated by APPs in the gas phase are transported to the liquid phase and possibly converted to different types of reactive species therein before causing some influence on the tissues or cells. In this study, the rate equations are solved to evaluate concentrations of various reactive species in pure water that are originated by plasma reactions in atmosphere and possible effects of such species (including ROS/RNS) on living tissues and cells are discussed.

40 CFR 59.506 - How do I demonstrate compliance if I manufacture multi-component kits?

Code of Federal Regulations, 2011 CFR

2011-07-01

... multi-component kits as defined in § 59.503, then the Kit PWR must not exceed the Total Reactivity Limit. (b) You must calculate the Kit PWR and the Total Reactivity Limit as follows: (1) KIT PWR = (PWR(1) × W1) + (PWR(2) × W2) +. ...+ (PWR(n) × Wn) (2) Total Reactivity Limit = (RL1 × W1) + (RL2 × W2...

40 CFR 59.506 - How do I demonstrate compliance if I manufacture multi-component kits?

Code of Federal Regulations, 2014 CFR

2014-07-01

... multi-component kits as defined in § 59.503, then the Kit PWR must not exceed the Total Reactivity Limit. (b) You must calculate the Kit PWR and the Total Reactivity Limit as follows: (1) KIT PWR = (PWR(1) × W1) + (PWR(2) × W2) +. ...+ (PWR(n) × Wn) (2) Total Reactivity Limit = (RL1 × W1) + (RL2 × W2...

40 CFR 59.506 - How do I demonstrate compliance if I manufacture multi-component kits?

Code of Federal Regulations, 2012 CFR

2012-07-01

... multi-component kits as defined in § 59.503, then the Kit PWR must not exceed the Total Reactivity Limit. (b) You must calculate the Kit PWR and the Total Reactivity Limit as follows: (1) KIT PWR = (PWR(1) × W1) + (PWR(2) × W2) +. ...+ (PWR(n) × Wn) (2) Total Reactivity Limit = (RL1 × W1) + (RL2 × W2...

40 CFR 59.506 - How do I demonstrate compliance if I manufacture multi-component kits?

Code of Federal Regulations, 2013 CFR

2013-07-01

... multi-component kits as defined in § 59.503, then the Kit PWR must not exceed the Total Reactivity Limit. (b) You must calculate the Kit PWR and the Total Reactivity Limit as follows: (1) KIT PWR = (PWR(1) × W1) + (PWR(2) × W2) +. ...+ (PWR(n) × Wn) (2) Total Reactivity Limit = (RL1 × W1) + (RL2 × W2...

2D Lattice Boltzmann Simulation Of Chemical Reactions Within Rayleigh-Bénard And Poiseuille-Bénard Convection Systems

NASA Astrophysics Data System (ADS)

Amaya-Ventura, Gilberto; Rodríguez-Romo, Suemi

2011-09-01

This paper deals with the computational simulation of the reaction-diffusion-advection phenomena emerging in Rayleigh-Bénard (RB) and Poiseuille-Bénard reactive convection systems. We use the Boussinesq's approximation for buoyancy forces and the Lattice Boltzmann method (LBM). The first kinetic mesoscopic model proposed here is based on the discrete Boltzmann equation needed to solve the momentum balance coupled with buoyancy forces. Then, a second lattice Boltzmann algorithm is applied to solve the reaction-diffusion-advection equation to calculate the evolution of the chemical species concentration. We use a reactive system composed by nitrous oxide (so call laughing gas) in air as an example; its spatio-temporal decomposition is calculated. Two cases are considered, a rectangular enclosed cavity and an open channel. The simulations are performed at low Reynolds numbers and in a steady state between the first and second thermo-hydrodynamic instabilities. The results presented here, for the thermo-hydrodynamic behavior, are in good agreement with experimental data; while our| chemical kinetics simulation yields expected results. Some applications of our approach are related to chemical reactors and atmospheric phenomena, among others.

Decontamination of Chemical/Biological Warfare (CBW) Agents Using an Atmospheric Pressure Plasma Jet (APPJ)

NASA Astrophysics Data System (ADS)

Herrmann, Hans W.

1998-11-01

The atmospheric pressure plasma jet (APPJ) is a non-thermal, high pressure, uniform glow discharge that produces a high velocity effluent stream of highly reactive chemical species. The discharge operates on a feedstock gas (e.g. He/O_2/H_2O) which flows between an outer, grounded, cylindrical electrode and an inner, coaxial electrode powered at 13.56 MHz RF. While passing through the plasma, the feedgas becomes excited, dissociated or ionized by electron impact. Once the gas exits the discharge volume, ions and electrons are rapidly lost by recombination, but the fast-flowing effluent still contains metastables (e.g. O2*, He*) and radicals (e.g. O, OH). These reactive species have been shown to be effective neutralizers of surrogates for anthrax spores, mustard blister agent and VX nerve gas. Unlike conventional, wet decontamination methods, the plasma effluent does not cause corrosion of most surfaces and does not damage wiring, electronics, nor most plastics. This makes it highly suitable for decontamination of high value sensitive equipment such as is found in vehicle interiors (i.e. tanks, planes...) for which there is currently no good decontamination technique. Furthermore, the reactive species rapidly degrade into harmless products leaving no lingering residue or harmful byproducts. Physics of the APPJ will be discussed and results of surface decontamination experiments using simulant and actual CBW agents will be presented.

Modelling total OH reactivity: atmospheric implications of the missing OH sink

NASA Astrophysics Data System (ADS)

Ferracci, V.; Archibald, A. T.; Heimann, I.; Pyle, J. A.

2016-12-01

The removal of the majority of reactive trace gases emitted into the atmosphere is initiated by reaction with the hydroxyl radical (OH). Over the last decade, a number of field campaigns have measured the chemical loss rate of OH, also known as total OH reactivity, in a variety of regions across the planet, from urban areas to remote forests. In most cases, comparison of the measured total OH reactivity with that calculated from the sum of the individual OH sinks (obtained via the simultaneous detection of species such as VOCs and NOx) highlighted the presence of "missing" reactivity (up to 80 % of the total measured reactivity), indicating that a significant sink of the hydroxyl radical is currently not accounted for in tropospheric oxidation schemes. Potential candidates for the missing OH reactivity are previously undetected biogenic VOCs, reactive intermediates of the oxidation of known biogenic VOCs (mainly isoprene), or a combination of the two. In this work the Met Office's Unified Model with the United Kingdom Chemistry and Aerosols scheme (UM-UKCA) was used to investigate the potential impacts of a simulated missing OH sink. UM-UKCA is a chemistry-climate model which includes detailed tropospheric chemistry derived from a combination of the JPL-NASA and IUPAC kinetic evaluations as well as the Master Chemical Mechanism database. The missing OH sink was simulated in a number of scenarios: initially, by including in the model chemical reactions that were only recently characterised (e.g., peroxy radicals + OH), then by adding a new chemical tracer, along with its reaction with OH, that would account for most of the missing reactivity observed in the various campaigns across the globe. Sensitivity of the model to the abundance and regional distribution of the new chemical tracer, and to the kinetics and hypothetical products of its reaction with OH are discussed, as well as the impacts of the missing OH sink on the tropospheric ozone budget and methane lifetime, with associated implications for air quality and global warming respectively.

Dehalogenation of persistent halogenated organic compounds: A review of computational studies and quantitative structure-property relationships.

PubMed

Luo, Jin; Hu, Jiwei; Wei, Xionghui; Fu, Liya; Li, Lingyun

2015-07-01

Dehalogenation is one of the highly important degradation reactions for halogenated organic compounds (HOCs) in the environment, which is also being developed as a potential type of the remediation technologies. In combination with the experimental results, intensive efforts have recently been devoted to the development of efficient theoretical methodologies (e.g. multi-scale simulation) to investigate the mechanisms for dehalogenation of HOCs. This review summarizes the structural characteristics of neutral molecules, anionic species and excited states of HOCs as well as their adsorption behavior on the surface of graphene and the Fe cluster. It discusses the key physiochemical properties (e.g. frontier orbital energies and thermodynamic properties) calculated at various levels of theory (e.g. semiempirical, ab initio, density functional theory (DFT) and the periodic DFT) as well as their connections to the reactivity and reaction pathway for the dehalogenation. This paper also reviews the advances in the linear and nonlinear quantitative structure-property relationship models for the dehalogenation kinetics of HOCs and in the mathematical modeling of the dehalogenation processes. Furthermore, prospects of further expansion and exploration of the current research fields are described in this article. Published by Elsevier Ltd.

Identifying the influential aquifer heterogeneity factor on nitrate reduction processes by numerical simulation

NASA Astrophysics Data System (ADS)

Jang, E.; He, W.; Savoy, H.; Dietrich, P.; Kolditz, O.; Rubin, Y.; Schüth, C.; Kalbacher, T.

2017-01-01

Nitrate reduction reactions in groundwater systems are strongly influenced by various aquifer heterogeneity factors that affect the transport of chemical species, spatial distribution of redox reactive substances and, as a result, the overall nitrate reduction efficiency. In this study, we investigated the influence of physical and chemical aquifer heterogeneity, with a focus on nitrate transport and redox transformation processes. A numerical modeling study for simulating coupled hydrological-geochemical aquifer heterogeneity was conducted in order to improve our understanding of the influence of the aquifer heterogeneity on the nitrate reduction reactions and to identify the most influential aquifer heterogeneity factors throughout the simulation. Results show that the most influential aquifer heterogeneity factors could change over time. With abundant presence of electron donors in the high permeable zones (initial stage), physical aquifer heterogeneity significantly influences the nitrate reduction since it enables the preferential transport of nitrate to these zones and enhances mixing of reactive partners. Chemical aquifer heterogeneity plays a comparatively minor role. Increasing the spatial variability of the hydraulic conductivity also increases the nitrate removal efficiency of the system. However, ignoring chemical aquifer heterogeneity can lead to an underestimation of nitrate removals in long-term behavior. With the increase of the spatial variability of the electron donor, i.e. chemical heterogeneity, the number of the ;hot spots; i.e. zones with comparably higher reactivity, should also increase. Hence, nitrate removal efficiencies will also be spatially variable but overall removal efficiency will be sustained if longer time scales are considered and nitrate fronts reach these high reactivity zones.

Optimal line drop compensation parameters under multi-operating conditions

NASA Astrophysics Data System (ADS)

Wan, Yuan; Li, Hang; Wang, Kai; He, Zhe

2017-01-01

Line Drop Compensation (LDC) is a main function of Reactive Current Compensation (RCC) which is developed to improve voltage stability. While LDC has benefit to voltage, it may deteriorate the small-disturbance rotor angle stability of power system. In present paper, an intelligent algorithm which is combined by Genetic Algorithm (GA) and Backpropagation Neural Network (BPNN) is proposed to optimize parameters of LDC. The objective function proposed in present paper takes consideration of voltage deviation and power system oscillation minimal damping ratio under multi-operating conditions. A simulation based on middle area of Jiangxi province power system is used to demonstrate the intelligent algorithm. The optimization result shows that coordinate optimized parameters can meet the multioperating conditions requirement and improve voltage stability as much as possible while guaranteeing enough damping ratio.

An open source platform for multi-scale spatially distributed simulations of microbial ecosystems

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

Segre, Daniel

2014-08-14

The goal of this project was to develop a tool for facilitating simulation, validation and discovery of multiscale dynamical processes in microbial ecosystems. This led to the development of an open-source software platform for Computation Of Microbial Ecosystems in Time and Space (COMETS). COMETS performs spatially distributed time-dependent flux balance based simulations of microbial metabolism. Our plan involved building the software platform itself, calibrating and testing it through comparison with experimental data, and integrating simulations and experiments to address important open questions on the evolution and dynamics of cross-feeding interactions between microbial species.

Modeling Study of the Low-Temperature Oxidation of Large Methyl Esters from C11 to C19

PubMed Central

Herbinet, Olivier; Biet, Joffrey; Hakka, Mohammed Hichem; Warth, Valérie; Glaude, Pierre Alexandre; Nicolle, André; Battin-Leclerc, Frédérique

2013-01-01

The modeling of the low temperature oxidation of large saturated methyl esters really representative of those found in biodiesel fuels has been investigated. Models have been developed for these species and then detailed kinetic mechanisms have been automatically generated using a new extended version of software EXGAS, which includes reactions specific to the chemistry of esters. A model generated for a binary mixture of n-decane and methyl palmitate was used to simulate experimental results obtained in a jet-stirred reactor for this fuel. This model predicts very well the reactivity of the fuel and the mole fraction profiles of most reaction products. This work also shows that a model for a middle size methyl ester such as methyl decanoate predicts fairly well the reactivity and the mole fractions of most species with a substantial decrease in computational time. Large n-alkanes such as n-hexadecane are also good surrogates for reproducing the reactivity of methyl esters, with an important gain in computational time, but they cannot account for the formation of specific products such as unsaturated esters or cyclic ethers with an ester function. PMID:23814504

Self-Assembly of Multi-nanozymes to Mimic an Intracellular Antioxidant Defense System.

PubMed

Huang, Yanyan; Liu, Zhen; Liu, Chaoqun; Ju, Enguo; Zhang, Yan; Ren, Jinsong; Qu, Xiaogang

2016-06-01

In this work, for the first time, we constructed a novel multi-nanozymes cooperative platform to mimic intracellular antioxidant enzyme-based defense system. V2 O5 nanowire served as a glutathione peroxidase (GPx) mimic while MnO2 nanoparticle was used to mimic superoxide dismutase (SOD) and catalase (CAT). Dopamine was used as a linker to achieve the assembling of the nanomaterials. The obtained V2 O5 @pDA@MnO2 nanocomposite could serve as one multi-nanozyme model to mimic intracellular antioxidant enzyme-based defense procedure in which, for example SOD, CAT, and GPx co-participate. In addition, through assembling with dopamine, the hybrid nanocomposites provided synergistic antioxidative effect. Importantly, both in vitro and in vivo experiments demonstrated that our biocompatible system exhibited excellent intracellular reactive oxygen species (ROS) removal ability to protect cell components against oxidative stress, showing its potential application in inflammation therapy. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Structural modification of P-glycoprotein induced by OH radicals: Insights from atomistic simulations

NASA Astrophysics Data System (ADS)

Khosravian, N.; Kamaraj, B.; Neyts, E. C.; Bogaerts, A.

2016-02-01

This study reports on the possible effects of OH radical impact on the transmembrane domain 6 of P-glycoprotein, TM6, which plays a crucial role in drug binding in human cells. For the first time, we employ molecular dynamics (MD) simulations based on the self-consistent charge density functional tight binding (SCC-DFTB) method to elucidate the potential sites of fragmentation and mutation in this domain upon impact of OH radicals, and to obtain fundamental information about the underlying reaction mechanisms. Furthermore, we apply non-reactive MD simulations to investigate the long-term effect of this mutation, with possible implications for drug binding. Our simulations indicate that the interaction of OH radicals with TM6 might lead to the breaking of C-C and C-N peptide bonds, which eventually cause fragmentation of TM6. Moreover, according to our simulations, the OH radicals can yield mutation in the aromatic ring of phenylalanine in TM6, which in turn affects its structure. As TM6 plays an important role in the binding of a range of cytotoxic drugs with P-glycoprotein, any changes in its structure are likely to affect the response of the tumor cell in chemotherapy. This is crucial for cancer therapies based on reactive oxygen species, such as plasma treatment.

Stability of multi-permeable reactive barriers for long term removal of mixed contaminants.

PubMed

Lee, Jai-Young; Lee, Kui-Jae; Youm, Sun Young; Lee, Mi-Ran; Kamala-Kannan, Seralathan; Oh, Byung-Taek

2010-02-01

The Permeable Reactive Barriers (PRBs) are relatively simple, promising technology for groundwater remediation. A PRBs consisting of two reactive barriers (zero valent iron-barrier and bio-barrier) were designed to evaluate the application and feasibility of the barriers for the removal of wide range of pollutants from synthetic water. After 470 days of Multi-PRBs column operation, the pH level in the water sample is increased from 4 to 7, whereas the oxidation reduction potential (ORP) is decreased to -180 mV. Trichloroethylene (TCE), heavy metals, and nitrate were completely removed in the zero valent iron-barrier. Ammonium produced during nitrate reduction is removed in the biologically reactive zone of the column. The results of the present study suggest that Multi-PRBs system is an effective alternate method to confine wide range of pollutants from contaminated groundwater.

Stochastic simulation of uranium migration at the Hanford 300 Area.

PubMed

Hammond, Glenn E; Lichtner, Peter C; Rockhold, Mark L

2011-03-01

This work focuses on the quantification of groundwater flow and subsequent U(VI) transport uncertainty due to heterogeneity in the sediment permeability at the Hanford 300 Area. U(VI) migration at the site is simulated with multiple realizations of stochastically-generated high resolution permeability fields and comparisons are made of cumulative water and U(VI) flux to the Columbia River. The massively parallel reactive flow and transport code PFLOTRAN is employed utilizing 40,960 processor cores on DOE's petascale Jaguar supercomputer to simultaneously execute 10 transient, variably-saturated groundwater flow and U(VI) transport simulations within 3D heterogeneous permeability fields using the code's multi-realization simulation capability. Simulation results demonstrate that the cumulative U(VI) flux to the Columbia River is less responsive to fine scale heterogeneity in permeability and more sensitive to the distribution of permeability within the river hyporheic zone and mean permeability of larger-scale geologic structures at the site. Copyright © 2010 Elsevier B.V. All rights reserved.

Measurements of ion species separation in strong plasma shocks

NASA Astrophysics Data System (ADS)

Rinderknecht, Hans

2017-10-01

Shocks are important dynamic phenomena in inertial confinement fusion (ICF) and astrophysical plasmas. While the relationship between upstream and downstream plasmas far from the shock front is fully determined by conservation equations, the structure of shock fronts is determined by dynamic kinetic processes. Kinetic theory and simulations predict that the width of a strong (M >2) collisional plasma shock front is on the order of tens of ion mean-free-paths. The shock front structure plays an important role for overall dynamics when the shock front width approaches plasma scale lengths, as in the spherically converging shock in the DT-vapor in an ICF implosion. However, there has been no experimental data benchmarking shock front structure in the plasma phase. The structure of a shock front in a plasma with multiple ion species has been directly measured for the first time using a combination of Thomson scattering and proton radiography in experiments on the OMEGA laser. Thomson scattering of a 263.25 nm probe beam is used to diagnose electron density, electron and ion temperature, ion species concentration, and flow velocity in strong shocks (M 5) propagating through low-density (ρ 0.1 mg/cc) plasmas composed of H(98%) +Ne(2%). Within the shock front, velocity separation of the ion species is observed for the first time: the light species (H) accelerates to of order the shocked fluid velocity (450 microns/ns) before the heavy species (Ne) begins to move. This velocity-space separation implies that the separation of ion species occurs at the shock front, a predicted feature of shocks in multi-species plasmas but never observed experimentally until now. Comparison of experimental data with PIC, Vlasov-Fokker-Planck, and multi-component hydrodynamic simulations will be presented.

Multi-level methods and approximating distribution functions

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

Wilson, D., E-mail: daniel.wilson@dtc.ox.ac.uk; Baker, R. E.

2016-07-15

Biochemical reaction networks are often modelled using discrete-state, continuous-time Markov chains. System statistics of these Markov chains usually cannot be calculated analytically and therefore estimates must be generated via simulation techniques. There is a well documented class of simulation techniques known as exact stochastic simulation algorithms, an example of which is Gillespie’s direct method. These algorithms often come with high computational costs, therefore approximate stochastic simulation algorithms such as the tau-leap method are used. However, in order to minimise the bias in the estimates generated using them, a relatively small value of tau is needed, rendering the computational costs comparablemore » to Gillespie’s direct method. The multi-level Monte Carlo method (Anderson and Higham, Multiscale Model. Simul. 10:146–179, 2012) provides a reduction in computational costs whilst minimising or even eliminating the bias in the estimates of system statistics. This is achieved by first crudely approximating required statistics with many sample paths of low accuracy. Then correction terms are added until a required level of accuracy is reached. Recent literature has primarily focussed on implementing the multi-level method efficiently to estimate a single system statistic. However, it is clearly also of interest to be able to approximate entire probability distributions of species counts. We present two novel methods that combine known techniques for distribution reconstruction with the multi-level method. We demonstrate the potential of our methods using a number of examples.« less

Mechanism of superoxide and hydrogen peroxide generation by human electron-transfer flavoprotein and pathological variants.

PubMed

Rodrigues, João V; Gomes, Cláudio M

2012-07-01

Reactive oxygen species production by mitochondrial enzymes plays a fundamental role both in cellular signaling and in the progression of dysfunctional states. However, sources of reactive oxygen species and the mechanisms by which enzymes produce these reactive species still remain elusive. We characterized the generation of reactive oxygen species by purified human electron-transfer flavoprotein (ETF), a mitochondrial enzyme that has a central role in the metabolism of lipids, amino acids, and choline. The results showed that ETF produces significant amounts of both superoxide and hydrogen peroxide in the presence of its partner enzyme medium-chain acyl-CoA dehydrogenase (MCAD). ETF-mediated production of reactive oxygen species is partially inhibited at high MCAD/ETF ratios, whereas it is enhanced at high ionic strength. Determination of the reduction potentials of ETF showed that thermodynamic properties of the FAD cofactor are changed upon formation of a complex between ETF and MCAD, supporting the notion that protein:protein interactions modulate the reactivity of the protein with dioxygen. Two pathogenic ETF variants were also studied to determine which factors modulate the reactivity toward molecular oxygen and promote reactive oxygen species production. The results obtained show that destabilized conformations and defective protein:protein interactions increase the ability of ETF to generate reactive oxygen species. A possible role for these processes in mitochondrial dysfunction in metabolic disorders of fatty acid β-oxidation is discussed. Copyright © 2012 Elsevier Inc. All rights reserved.

Total OH reactivity measurements in ambient air in a southern Rocky Mountain ponderosa pine forest during BEACHON-SRM08 summer campaign

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

Nakashima, Yoshihiro; Kato, Shungo; Greenberg, Jim

2014-03-01

Total OH reactivity was measured during the Bio-hydro-atmosphere interactions of Energy, Aerosols, Carbon, H2O, Organics and Nitrogen-Southern Rocky Mountain 2008 field campaign (BEACHON-SRM08) held at Manitou Experimental Forest (MEF) in Colorado USA during the summer season in August, 2008. The averaged total OH reactivity was 6.8 s-1, smaller than that measured in urban or suburban areas, while sporadically high OH reactivity was also observed during some evenings. The total OH reactivity measurements were accompanied by observations of traces species such as CO, NO, NOy, O3 and SO2 and VOCs. From the calculation of OH reactivity based on the analysis ofmore » these trace species, 35.3-46.3% of OH reactivity for VOCs came from biogenic species that are dominated by 2-methyl-3-butene-2-ol (MBO), and monoterpenes. MBO was the most prominent contribution to OH reactivity of any other trace species. A comparison of observed and calculated OH reactivity shows that the calculated OH reactivity is 29.5-34.8% less than the observed value, implying the existence of missing OH sink. One of the candidates of missing OH was thought to be the oxidation products of biogenic species.« less

Formation of Reactive Br Species by Freezing in Solutions of NaBr-Metal-Hydrogen Peroxide

NASA Astrophysics Data System (ADS)

Kinjo, M.; Arakaki, T.

2005-12-01

The role of reactive halogen species (e.g. BrOH) in the destruction of stratospheric ozone is well known and largely understood. In recent years, it became clear that reactive Br species can also play a significant role in tropospheric ozone destruction, but sources of reactive Br species in the troposphere are not well understood. When an aqueous solution is frozen, solutes in the solution are excluded from the ice phase and the solutes are concentrated in the solution phase. Freezing processes cause red-ox reactions in the solution. We tried to understand the effects of freezing processes of solutions on formation of reactive Br species. Hydrogen peroxide (HOOH) and metallic ions were added to a mixing solution of NaBr and allyl alcohol (AA). If reactive Br species are formed, they react with AA, and free Br ion concentration decreases in the solution. When HOOH and Fe(III) or Cu(II) were added to the NaBr and AA solution and frozen, free Br ion concentration decreased. It is possible that OH radical formation from reaction between HOOH and Fe(II) or Cu(I) was induced by freezing processes and the OH radical probably oxidized Br ion to reactive Br species. Study of the effects of pH showed that decrease of Br ion concentration was the highest at pH = 4.0. Freezing processes could be an important source of reactive Br species in high altitude clouds and Polar Regions.

Thermodynamics and Kinetics of Prenucleation Clusters, Classical and Non-Classical Nucleation

PubMed Central

Zahn, Dirk

2015-01-01

Recent observations of prenucleation species and multi-stage crystal nucleation processes challenge the long-established view on the thermodynamics of crystal formation. Here, we review and generalize extensions to classical nucleation theory. Going beyond the conventional implementation as has been used for more than a century now, nucleation inhibitors, precursor clusters and non-classical nucleation processes are rationalized as well by analogous concepts based on competing interface and bulk energy terms. This is illustrated by recent examples of species formed prior to/instead of crystal nucleation and multi-step nucleation processes. Much of the discussed insights were obtained from molecular simulation using advanced sampling techniques, briefly summarized herein for both nucleation-controlled and diffusion-controlled aggregate formation. PMID:25914369

Grassland Smoke Emission Measurement Supporting Multi-Modeling Framework Simulation of Rangeland Burning Practices for the Kansas Flint Hills Fire Experiment

EPA Science Inventory

Historically, frequent wildfires were essential for the maintenance of native prairie fire adapted ecosystems. Today prescribed fires are used to control invasive woody species and potentially improve forage production in these same prairie ecosystems for the beef-cattle industry...

A Scaffolding Framework to Support Learning of Emergent Phenomena Using Multi-Agent-Based Simulation Environments

ERIC Educational Resources Information Center

Basu, Satabdi; Sengupta, Pratim; Biswas, Gautam

2015-01-01

Students from middle school to college have difficulties in interpreting and understanding complex systems such as ecological phenomena. Researchers have suggested that students experience difficulties in reconciling the relationships between individuals, populations, and species, as well as the interactions between organisms and their environment…

Numerical simulation of physicochemical interactions between oxygen atom and phosphatidylcholine due to direct irradiation of atmospheric pressure nonequilibrium plasma to biological membrane with quantum mechanical molecular dynamics

NASA Astrophysics Data System (ADS)

Uchida, Satoshi; Yoshida, Taketo; Tochikubo, Fumiyoshi

2017-10-01

Plasma medicine is one of the most attractive applications using atmospheric pressure nonequilibrium plasma. With respect to direct contact of the discharge plasma with a biological membrane, reactive oxygen species play an important role in induction of medical effects. However, complicated interactions between the plasma radicals and membrane have not been understood well. In the present work, we simulated elemental processes at the first stage of physicochemical interactions between oxygen atom and phosphatidylcholine using the quantum mechanical molecular dynamics code in a general software AMBER. The change in the above processes was classified according to the incident energy of oxygen atom. At an energy of 1 eV, the abstraction of a hydrogen atom and recombination to phosphatidylcholine were simultaneously occurred in chemical attachment of incident oxygen atom. The exothermal energy of the reaction was about 80% of estimated one based on the bond energies of ethane. An oxygen atom over 10 eV separated phosphatidylcholine partially. The behaviour became increasingly similar to physical sputtering. The reaction probability of oxygen atom was remarkably high in comparison with that of hydrogen peroxide. These results suggest that we can uniformly estimate various physicochemical dynamics of reactive oxygen species against membrane lipids.

Spectrum of antibody profiles in tuberculous elephants, cervids, and cattle.

PubMed

Lyashchenko, Konstantin P; Gortázar, Christian; Miller, Michele A; Waters, W Ray

2018-02-01

Using multi-antigen print immunoassay and DPP ® VetTB Assay approved in the United States for testing captive cervids and elephants, we analyzed antibody recognition of MPB83 and CFP10/ESAT-6 antigens in Asian elephants (Elephas maximus) infected with Mycobacterium tuberculosis and in white-tailed deer (Odocoileus virginianus), fallow deer (Dama dama), elk (Cervus elaphus), and cattle (Bos taurus) infected with Mycobacterium bovis. Serum IgG reactivity to MPB83 was found in the vast majority of tuberculous cattle and cervid species among which white-tailed deer and elk also showed significant CFP10/ESAT-6 recognition rates with added serodiagnostic value. In contrast, the infected elephants developed antibody responses mainly to CFP10/ESAT-6 with MPB83 reactivity being relatively low. The findings demonstrate distinct patterns of predominant antigen recognition by different animal hosts in tuberculosis. Copyright © 2017 Elsevier B.V. All rights reserved.

VERA Core Simulator Methodology for PWR Cycle Depletion

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

Kochunas, Brendan; Collins, Benjamin S; Jabaay, Daniel

2015-01-01

This paper describes the methodology developed and implemented in MPACT for performing high-fidelity pressurized water reactor (PWR) multi-cycle core physics calculations. MPACT is being developed primarily for application within the Consortium for the Advanced Simulation of Light Water Reactors (CASL) as one of the main components of the VERA Core Simulator, the others being COBRA-TF and ORIGEN. The methods summarized in this paper include a methodology for performing resonance self-shielding and computing macroscopic cross sections, 2-D/1-D transport, nuclide depletion, thermal-hydraulic feedback, and other supporting methods. These methods represent a minimal set needed to simulate high-fidelity models of a realistic nuclearmore » reactor. Results demonstrating this are presented from the simulation of a realistic model of the first cycle of Watts Bar Unit 1. The simulation, which approximates the cycle operation, is observed to be within 50 ppm boron (ppmB) reactivity for all simulated points in the cycle and approximately 15 ppmB for a consistent statepoint. The verification and validation of the PWR cycle depletion capability in MPACT is the focus of two companion papers.« less

REDUCING UNCERTAINTIES IN MODEL PREDICTIONS VIA HISTORY MATCHING OF CO2 MIGRATION AND REACTIVE TRANSPORT MODELING OF CO2 FATE AT THE SLEIPNER PROJECT

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

Zhu, Chen

2015-03-31

An important question for the Carbon Capture, Storage, and Utility program is “can we adequately predict the CO2 plume migration?” For tracking CO2 plume development, the Sleipner project in the Norwegian North Sea provides more time-lapse seismic monitoring data than any other sites, but significant uncertainties still exist for some of the reservoir parameters. In Part I, we assessed model uncertainties by applying two multi-phase compositional simulators to the Sleipner Benchmark model for the uppermost layer (Layer 9) of the Utsira Sand and calibrated our model against the time-lapsed seismic monitoring data for the site from 1999 to 2010. Approximatemore » match with the observed plume was achieved by introducing lateral permeability anisotropy, adding CH4 into the CO2 stream, and adjusting the reservoir temperatures. Model-predicted gas saturation, CO2 accumulation thickness, and CO2 solubility in brine—none were used as calibration metrics—were all comparable with the interpretations of the seismic data in the literature. In Part II & III, we evaluated the uncertainties of predicted long-term CO2 fate up to 10,000 years, due to uncertain reaction kinetics. Under four scenarios of the kinetic rate laws, the temporal and spatial evolution of CO2 partitioning into the four trapping mechanisms (hydrodynamic/structural, solubility, residual/capillary, and mineral) was simulated with ToughReact, taking into account the CO2-brine-rock reactions and the multi-phase reactive flow and mass transport. Modeling results show that different rate laws for mineral dissolution and precipitation reactions resulted in different predicted amounts of trapped CO2 by carbonate minerals, with scenarios of the conventional linear rate law for feldspar dissolution having twice as much mineral trapping (21% of the injected CO2) as scenarios with a Burch-type or Alekseyev et al.–type rate law for feldspar dissolution (11%). So far, most reactive transport modeling (RTM) studies for CCUS have used the conventional rate law and therefore simulated the upper bound of mineral trapping. However, neglecting the regional flow after injection, as most previous RTM studies have done, artificially limits the extent of geochemical reactions as if it were in a batch system. By replenishing undersaturated groundwater from upstream, the Utsira Sand is reactive over a time scale of 10,000 years. The results from this project have been communicated via five peer-reviewed journal articles, four conference proceeding papers, and 19 invited and contributed presentations at conferences and seminars.« less

Characterizing low dose and dose rate effects in rodent and human neural stem cells exposed to proton and gamma irradiation.

PubMed

Tseng, Bertrand P; Lan, Mary L; Tran, Katherine K; Acharya, Munjal M; Giedzinski, Erich; Limoli, Charles L

2013-01-01

Past work has shown that exposure to gamma rays and protons elicit a persistent oxidative stress in rodent and human neural stem cells (hNSCs). We have now adapted these studies to more realistic exposure scenarios in space, using lower doses and dose rates of these radiation modalities, to further elucidate the role of radiation-induced oxidative stress in these cells. Rodent neural stem and precursor cells grown as neurospheres and human neural stem cells grown as monolayers were subjected to acute and multi-dosing paradigms at differing dose rates and analyzed for changes in reactive oxygen species (ROS), reactive nitrogen species (RNS), nitric oxide and superoxide for 2 days after irradiation. While acute exposures led to significant changes in both cell types, hNSCs in particular, exhibited marked and significant elevations in radiation-induced oxidative stress. Elevated oxidative stress was more significant in hNSCs as opposed to their rodent counterparts, and hNSCs were significantly more sensitive to low dose exposures in terms of survival. Combinations of protons and γ-rays delivered as lower priming or higher challenge doses elicited radioadaptive changes that were associated with improved survival, but in general, only under conditions where the levels of reactive species were suppressed compared to cells irradiated acutely. Protective radioadaptive effects on survival were eliminated in the presence of the antioxidant N-acetylcysteine, suggesting further that radiation-induced oxidative stress could activate pro-survival signaling pathways that were sensitive to redox state. Data corroborates much of our past work and shows that low dose and dose rate exposures elicit significant changes in oxidative stress that have functional consequences on survival.

A novel compound DT-010 protects against doxorubicin-induced cardiotoxicity in zebrafish and H9c2 cells by inhibiting reactive oxygen species-mediated apoptotic and autophagic pathways.

PubMed

Tang, Fan; Zhou, Xinhua; Wang, Liang; Shan, Luchen; Li, Chuwen; Zhou, Hefeng; Lee, Simon Ming-Yuen; Hoi, Maggie Pui-Man

2018-02-05

Doxorubicin (Dox) is an effective anti-cancer agent but limited by its cardiotoxicity, thus the search for pharmacological agents for enhancing anti-cancer activities and protecting against cardiotoxicity has been a subject of great interest. We have previously reported the synergistic anti-cancer effects of a novel compound DT-010. In the present study, we further investigated the cardioprotective effects of DT-010 in zebrafish embryos in vivo and the molecular underlying mechanisms in H9c2 cardiomyocytes in vitro. We showed that DT-010 prevented the Dox-induced morphological distortions in the zebrafish heart and the associated cardiac impairments, and especially improved ventricular functions. By using H9c2 cells model, we showed that DT-010 directly inhibited the generation of reactive oxygen species by Dox and protected cell death and cellular damage. We further observed that DT-010 protected against Dox-induced myocardiopathy via inhibiting downstream molecular pathways in response to oxidative stress, including reactive oxygen species-mediated MAPK signaling pathways ERK and JNK, and apoptotic pathways involving the activation of caspase 3, caspase 7, and PARP signaling. Recent studies also suggest the importance of alterations in cardiac autophagy in Dox cardiotoxicity. We further showed that DT-010 could inhibit the induction of autophagosomes formation by Dox via regulating the upstream Akt/AMPK/mTOR signaling. Since Dox-induced cardiotoxicity is multifactorial, our results suggest that multi-functional agent such as DT-010 might be an effective therapeutic agent for combating cardiotoxicity associated with chemotherapeutic agents such as Dox. Copyright © 2017 Elsevier B.V. All rights reserved.

A review of direct numerical simulations of astrophysical detonations and their implications

DOE PAGES

Parete-Koon, Suzanne T.; Smith, Christopher R.; Papatheodore, Thomas L.; ...

2013-04-11

Multi-dimensional direct numerical simulations (DNS) of astrophysical detonations in degenerate matter have revealed that the nuclear burning is typically characterized by cellular structure caused by transverse instabilities in the detonation front. Type Ia supernova modelers often use one- dimensional DNS of detonations as inputs or constraints for their whole star simulations. While these one-dimensional studies are useful tools, the true nature of the detonation is multi-dimensional. The multi-dimensional structure of the burning influences the speed, stability, and the composition of the detonation and its burning products, and therefore, could have an impact on the spectra of Type Ia supernovae. Considerablemore » effort has been expended modeling Type Ia supernovae at densities above 1x10 7 g∙cm -3 where the complexities of turbulent burning dominate the flame propagation. However, most full star models turn the nuclear burning schemes off when the density falls below 1x10 7 g∙cm -3 and distributed burning begins. The deflagration to detonation transition (DDT) is believed to occur at just these densities and consequently they are the densities important for studying the properties of the subsequent detonation. In conclusion, this work reviews the status of DNS studies of detonations and their possible implications for Type Ia supernova models. It will cover the development of Detonation theory from the first simple Chapman-Jouguet (CJ) detonation models to the current models based on the time-dependent, compressible, reactive flow Euler equations of fluid dynamics.« less

XPS analysis of PE and EVA samples irradiated at different γ-doses

NASA Astrophysics Data System (ADS)

Dorey, Samuel; Gaston, Fanny; Marque, Sylvain R. A.; Bortolotti, Benjamin; Dupuy, Nathalie

2018-01-01

The principal plastic materials used for the fluid contact and storage in the biopharmaceutical industry are mainly made up of semi-crystalline polymers, polyolefins, PVC, Siloxane and PET. The polyethylene (PE) and the polypropylene (PP) are often used as fluid contact in multi-layer materials like films. As one sterilisation way of single-use plastic devices used in medical and pharmaceutical fields can take place via γ-irradiation, the effect of sterilization on plastics must be investigated. The irradiation process leads to the production of radicals, which can generate changes in the polymer structure and on the polymer surface. It is well known that the presence of oxygen with free radicals precede the generation of peroxide species so called ROS (reactive oxygen species) which are highly reactive. The purpose of this work is to investigate the γ-rays impact on the surface of PE (polyethylene) and EVA (polyethylene vinyl alcohol) based films when ionized at different doses. X-ray Photoelectron Spectroscopy (XPS) was applied to determine the surface compositions of the polymers to highlight the different chemical moieties generated during the γ-irradiation process and to monitor the potential presence of the ROS.

Proteome analysis of Arabidopsis seedlings exposed to bacterial volatiles.

PubMed

Kwon, Young Sang; Ryu, Choong-Min; Lee, Soohyun; Park, Hyo Bee; Han, Ki Soo; Lee, Jung Han; Lee, Kyunghee; Chung, Woo Sik; Jeong, Mi-Jeong; Kim, Hee Kyu; Bae, Dong-Won

2010-11-01

Plant root-associated bacteria (rhizobacteria) elicit plant basal immunity referred to as induced systemic resistance (ISR) against multiple pathogens. Among multi-bacterial determinants involving such ISR, the induction of ISR and promotion of growth by bacterial volatile compounds was previously reported. To exploit global de novo expression of plant proteins by bacterial volatiles, proteomic analysis was performed after exposure of Arabidopsis plants to the rhizobacterium Bacillus subtilis GB03. Ethylene biosynthesis enzymes were significantly up-regulated. Analysis by quantitative reverse transcriptase polymerase chain reaction confirmed that ethylene biosynthesis-related genes SAM-2, ACS4, ACS12, and ACO2 as well as ethylene response genes, ERF1, GST2, and CHIB were up-regulated by the exposure to bacterial volatiles. More interestingly, the emission of bacterial volatiles significantly up-regulated both key defense mechanisms mediated by jasmonic acid and salicylic acid signaling pathways. In addition, high accumulation of antioxidant proteins also provided evidence of decreased sensitivity to reactive oxygen species during the elicitation of ISR by bacterial volatiles. The present results suggest that the proteomic analysis of plant defense responses in bacterial volatile-mediated ISR can reveal the mechanisms of plant basal defenses orchestrated by endogenous ethylene production pathways and the generation of reactive oxygen species.

Endosomal NOX2 oxidase exacerbates virus pathogenicity and is a target for antiviral therapy.

PubMed

To, Eunice E; Vlahos, Ross; Luong, Raymond; Halls, Michelle L; Reading, Patrick C; King, Paul T; Chan, Christopher; Drummond, Grant R; Sobey, Christopher G; Broughton, Brad R S; Starkey, Malcolm R; van der Sluis, Renee; Lewin, Sharon R; Bozinovski, Steven; O'Neill, Luke A J; Quach, Tim; Porter, Christopher J H; Brooks, Doug A; O'Leary, John J; Selemidis, Stavros

2017-07-12

The imminent threat of viral epidemics and pandemics dictates a need for therapeutic approaches that target viral pathology irrespective of the infecting strain. Reactive oxygen species are ancient processes that protect plants, fungi and animals against invading pathogens including bacteria. However, in mammals reactive oxygen species production paradoxically promotes virus pathogenicity by mechanisms not yet defined. Here we identify that the primary enzymatic source of reactive oxygen species, NOX2 oxidase, is activated by single stranded RNA and DNA viruses in endocytic compartments resulting in endosomal hydrogen peroxide generation, which suppresses antiviral and humoral signaling networks via modification of a unique, highly conserved cysteine residue (Cys98) on Toll-like receptor-7. Accordingly, targeted inhibition of endosomal reactive oxygen species production abrogates influenza A virus pathogenicity. We conclude that endosomal reactive oxygen species promote fundamental molecular mechanisms of viral pathogenicity, and the specific targeting of this pathogenic process with endosomal-targeted reactive oxygen species inhibitors has implications for the treatment of viral disease.Production of reactive oxygen species is an ancient antimicrobial mechanism, but its role in antiviral defense in mammals is unclear. Here, To et al. show that virus infection activates endosomal NOX2 oxidase and restricts TLR7 signaling, and that an endosomal NOX2 inhibitor decreases viral pathogenicity.

Reactive trace gas emissions from stressed plants: a poorly characterized major source of atmospheric volatiles

NASA Astrophysics Data System (ADS)

Niinemets, Ülo

2017-04-01

Vegetation constitutes the greatest source of reactive volatile organic compounds in the atmosphere. The current emission estimates primarily rely on constitutive emissions that are present only in some plant species. However, all plant species can be induced to emit reactive volatiles by different abiotic and biotic stresses, but the stress-dependent emissions have been largely neglected in emission measurements and models. This presentation provides an overview of systematic screening of stress-dependent volatile emissions from a broad range of structurally and physiologically divergent plant species from temperate to tropical ecosystems. Ozone, heat, drought and wounding stress were the abiotic stresses considered in the screening, while biotic stress included herbivory, chemical elicitors simulating herbivory and fungal infections. The data suggest that any moderate to severe stress leads to significant emissions of a rich blend of volatiles, including methanol, green leaf volatiles (the lipoxygenase pathway volatiles, dominated by C6 aldehydes, alcohols and derivatives), different mono- and sesquiterpenes and benzenoids. The release of volatiles occurs in stress severity-dependent manner, although the emission responses are often non-linear with more severe stresses resulting in disproportionately greater emissions. Stress volatile release is induced in both non-constitutive and constitutive volatile emitters, whereas the rate of constitutive volatile emissions in constitutive emitters is often reduced under environmental and biotic stresses. Given that plants in natural conditions often experience stress, this analysis suggests that global volatile emissions have been significantly underestimated. Furthermore, in globally changing hotter climates, the frequency and severity of both abiotic and biotic stresses is expected to increase. Thus, the stress-induced volatile emissions are predicted to play a dominant role in plant-atmosphere interactions in near future. Quantitative models that link stress severity, plant volatile emissions and climatic feedbacks are currently being developed, and this presentation argues that incorporating stress-dependent feedbacks in Earth system models in inevitable to simulate future climates.

Reactive Oxygen Species in Cardiovascular Disease

PubMed Central

Sugamura, Koichi; Keaney, John F.

2011-01-01

Based on the ‘free-radical theory’ of disease, researchers have been trying to elucidate the role of oxidative stress from free radicals in cardiovascular disease. Considerable data indicate that ROS and oxidative stress are important features of cardiovascular diseases including atherosclerosis, hypertension, and congestive heart failure. However, blanket strategies with antioxidants to ameliorate cardiovascular disease have not generally yielded favorable results. However, our understanding or reactive oxygen species has evolved to the point that we now realize these species have important roles in physiology as well as pathophysiology. Thus, it is overly simplistic to assume a general antioxidant strategy will yield specific effects on cardiovascular disease. Indeed, there are several sources of reactive oxygen species that are known to be active in the cardiovascular system. This review will address our understanding of reactive oxygen species sources in cardiovascular disease and both animal and human data defining how reactive oxygen species contribute to physiology and pathology. PMID:21627987

Tuning reactivity of diphenylpropynone derivatives with metal-associated amyloid-β species via structural modifications.

PubMed

Liu, Yuzhong; Kochi, Akiko; Pithadia, Amit S; Lee, Sanghyun; Nam, Younwoo; Beck, Michael W; He, Xiaoming; Lee, Dongkuk; Lim, Mi Hee

2013-07-15

A diphenylpropynone derivative, DPP2, has been recently demonstrated to target metal-associated amyloid-β (metal-Aβ) species implicated in Alzheimer's disease (AD). DPP2 was shown to interact with metal-Aβ species and subsequently control Aβ aggregation (reactivity) in vitro; however, its cytotoxicity has limited further biological applications. In order to improve reactivity toward Aβ species and lower cytotoxicity, along with gaining an understanding of a structure-reactivity-cytotoxicity relationship, we designed, prepared, and characterized a series of small molecules (C1/C2, P1/P2, and PA1/PA2) as structurally modified DPP2 analogues. A similar metal binding site to that of DPP2 was contained in these compounds while their structures were varied to afford different interactions and reactivities with metal ions, Aβ species, and metal-Aβ species. Distinct reactivities of our chemical family toward in vitro Aβ aggregation in the absence and presence of metal ions were observed. Among our chemical series, the compound (C2) with a relatively rigid backbone and a dimethylamino group was observed to noticeably regulate both metal-free and metal-mediated Aβ aggregation to different extents. Using our compounds, cell viability was significantly improved, compared to that with DPP2. Lastly, modifications on the DPP framework maintained the structural properties for potential blood-brain barrier (BBB) permeability. Overall, our studies demonstrated that structural variations adjacent to the metal binding site of DPP2 could govern different metal binding properties, interactions with Aβ and metal-Aβ species, reactivity toward metal-free and metal-induced Aβ aggregation, and cytotoxicity of the compounds, establishing a structure-reactivity-cytotoxicity relationship. This information could help gain insight into structural optimization for developing nontoxic chemical reagents toward targeting metal-Aβ species and modulating their reactivity in biological systems.

Accelerating moderately stiff chemical kinetics in reactive-flow simulations using GPUs

NASA Astrophysics Data System (ADS)

Niemeyer, Kyle E.; Sung, Chih-Jen

2014-01-01

The chemical kinetics ODEs arising from operator-split reactive-flow simulations were solved on GPUs using explicit integration algorithms. Nonstiff chemical kinetics of a hydrogen oxidation mechanism (9 species and 38 irreversible reactions) were computed using the explicit fifth-order Runge-Kutta-Cash-Karp method, and the GPU-accelerated version performed faster than single- and six-core CPU versions by factors of 126 and 25, respectively, for 524,288 ODEs. Moderately stiff kinetics, represented with mechanisms for hydrogen/carbon-monoxide (13 species and 54 irreversible reactions) and methane (53 species and 634 irreversible reactions) oxidation, were computed using the stabilized explicit second-order Runge-Kutta-Chebyshev (RKC) algorithm. The GPU-based RKC implementation demonstrated an increase in performance of nearly 59 and 10 times, for problem sizes consisting of 262,144 ODEs and larger, than the single- and six-core CPU-based RKC algorithms using the hydrogen/carbon-monoxide mechanism. With the methane mechanism, RKC-GPU performed more than 65 and 11 times faster, for problem sizes consisting of 131,072 ODEs and larger, than the single- and six-core RKC-CPU versions, and up to 57 times faster than the six-core CPU-based implicit VODE algorithm on 65,536 ODEs. In the presence of more severe stiffness, such as ethylene oxidation (111 species and 1566 irreversible reactions), RKC-GPU performed more than 17 times faster than RKC-CPU on six cores for 32,768 ODEs and larger, and at best 4.5 times faster than VODE on six CPU cores for 65,536 ODEs. With a larger time step size, RKC-GPU performed at best 2.5 times slower than six-core VODE for 8192 ODEs and larger. Therefore, the need for developing new strategies for integrating stiff chemistry on GPUs was discussed.

Detection of bromine monoxide in a volcanic plume.

PubMed

Bobrowski, N; Hönninger, G; Galle, B; Platt, U

2003-05-15

The emission of volcanic gases usually precedes eruptive activity, providing both a warning signal and an indication of the nature of the lava soon to be erupted. Additionally, volcanic emissions are a significant source of gases and particles to the atmosphere, influencing tropospheric and stratospheric trace-gas budgets. Despite some halogen species having been measured in volcanic plumes (mainly HCl and HF), little is known about bromine compounds and, in particular, gas-phase reactive bromine species. Such species are especially important in the stratosphere, as reactive bromine-despite being two orders of magnitude less abundant than chlorine-accounts for about one-third of halogen-catalysed ozone depletion. In the troposphere, bromine-catalysed complete ozone destruction has been observed to occur regularly during spring in the polar boundary layers as well as in the troposphere above the Dead Sea basin. Here we report observations of BrO and SO2 abundances in the plume of the Soufrière Hills volcano (Montserrat) in May 2002 by ground-based multi-axis differential optical absorption spectroscopy. Our estimate of BrO emission leads us to conclude that local ozone depletion and small ozone 'holes' may occur in the vicinity of active volcanoes, and that the amount of bromine emitted from volcanoes might be sufficiently large to play a role not only in the stratosphere, but also in tropospheric chemistry.

Autonomous Decentralized Voltage Profile Control of Super Distributed Energy System using Multi-agent Technology

NASA Astrophysics Data System (ADS)

Tsuji, Takao; Hara, Ryoichi; Oyama, Tsutomu; Yasuda, Keiichiro

A super distributed energy system is a future energy system in which the large part of its demand is fed by a huge number of distributed generators. At one time some nodes in the super distributed energy system behave as load, however, at other times they behave as generator - the characteristic of each node depends on the customers' decision. In such situation, it is very difficult to regulate voltage profile over the system due to the complexity of power flows. This paper proposes a novel control method of distributed generators that can achieve the autonomous decentralized voltage profile regulation by using multi-agent technology. The proposed multi-agent system employs two types of agent; a control agent and a mobile agent. Control agents generate or consume reactive power to regulate the voltage profile of neighboring nodes and mobile agents transmit the information necessary for VQ-control among the control agents. The proposed control method is tested through numerical simulations.

Inactivation of Bacillus atrophaeus by OH radicals

NASA Astrophysics Data System (ADS)

Ono, Ryo; Yonetamari, Kenta; Tokumitsu, Yusuke; Yonemori, Seiya; Yasuda, Hachiro; Mizuno, Akira

2016-08-01

The inactivation of Bacillus atrophaeus by OH radicals is measured. This study aims to evaluate the bactericidal effects of OH radicals produced by atmospheric-pressure nonthermal plasma widely used for plasma medicine; however, in this study, OH radicals are produced by vacuum ultraviolet (VUV) photolysis of water vapor instead of plasma to allow the production of OH radicals with almost no other reactive species. A 172 nm VUV light from a Xe2 excimer lamp irradiates a He-H2O mixture flowing in a quartz tube to photodissociate H2O to produce OH, H, O, HO2, H2O2, and O3. The produced reactive oxygen species (ROS) flow out of the quartz tube nozzle to the bacteria on an agar plate and cause inactivation. The inactivation by OH radicals among the six ROS is observed by properly setting the experimental conditions with the help of simulations calculating the ROS densities. A 30 s treatment with approximately 0.1 ppm OH radicals causes visible inactivation.

The evolution of the temperature field during cavity collapse in liquid nitromethane. Part II: reactive case

NASA Astrophysics Data System (ADS)

Michael, L.; Nikiforakis, N.

2018-02-01

This work is concerned with the effect of cavity collapse in non-ideal explosives as a means of controlling their sensitivity. The main objective is to understand the origin of localised temperature peaks (hot spots) which play a leading order role at the early stages of ignition. To this end, we perform two- and three-dimensional numerical simulations of shock-induced single gas-cavity collapse in liquid nitromethane. Ignition is the result of a complex interplay between fluid dynamics and exothermic chemical reaction. In the first part of this work, we focused on the hydrodynamic effects in the collapse process by switching off the reaction terms in the mathematical formulation. In this part, we reinstate the reactive terms and study the collapse of the cavity in the presence of chemical reactions. By using a multi-phase formulation which overcomes current challenges of cavity collapse modelling in reactive media, we account for the large density difference across the material interface without generating spurious temperature peaks, thus allowing the use of a temperature-based reaction rate law. The mathematical and physical models are validated against experimental and analytic data. In Part I, we demonstrated that, compared to experiments, the generated hot spots have a more complex topological structure and that additional hot spots arise in regions away from the cavity centreline. Here, we extend this by identifying which of the previously determined high-temperature regions in fact lead to ignition and comment on the reactive strength and reaction growth rate in the distinct hot spots. We demonstrate and quantify the sensitisation of nitromethane by the collapse of the isolated cavity by comparing the ignition times of nitromethane due to cavity collapse and the ignition time of the neat material. The ignition in both the centreline hot spots and the hot spots generated by Mach stems occurs in less than half the ignition time of the neat material. We compare two- and three-dimensional simulations to examine the change in topology, temperatures, and reactive strength of the hot spots by the third dimension. It is apparent that belated ignition times can be avoided by the use of three-dimensional simulations. The effect of the chemical reactions on the topology and strength of the hot spots in the timescales considered is also studied, in a comparison between inert and reactive simulations where maximum temperature fields and their growth rates are examined.

[Relationship among the Oxygen Concentration, Reactive Oxygen Species and the Biological Characteristics of Mouse Bone Marrow Hematopoietic Stem Cells].

PubMed

Ren, Si-Hua; He, Yu-Xin; Ma, Yi-Ran; Jin, Jing-Chun; Kang, Dan

2016-02-01

To investigate the effects of oxygen concentration and reactive oxygen species (ROS) on the biological characteristics of hematopoietic stem cells (HSC) and to analyzed the relationship among the oxygen concentration, ROS and the biological characteristics of mouse HSC through simulation of oxygen environment experienced by PB HSC during transplantation. The detection of reactive oxygen species (ROS), in vitro amplification, directional differentiation (BFU-E, CFU-GM, CFU-Mix), homing of adhesion molecules (CXCR4, CD44, VLA4, VLA5, P-selectin), migration rate, CFU-S of NOD/SCID mice irradiated with sublethal dose were performed to study the effect of oxgen concentration and reactive oxygen species on the biological characteristics of mouse BM-HSC and the relationship among them. The oxygen concentrations lower than normal oxygen concentration (especially hypoxic oxygen environment) could reduce ROS level and amplify more Lin(-) c-kit(+) Sca-1(+) BM HSC, which was more helpful to the growth of various colonies (BFU-E, CFU-GM, CFU-Mix) and to maintain the migratory ability of HSC, thus promoting CFU-S growth significantly after the transplantation of HSC in NOD/SCID mice irradiated by a sublethal dose. BM HSC exposed to oxygen environments of normal, inconstant oxygen level and strenuously thanging of oxygen concentration could result in higher level of ROS, at the same time, the above-mentioned features and functional indicators were relatively lower. The ROS levels of BM HSC in PB HSCT are closely related to the concentrations and stability of oxygen surrounding the cells. High oxygen concentration results in an high level of ROS, which is not helpful to maintain the biological characteristics of BM HSC. Before transplantation and in vitro amplification, the application of antioxidancs and constant oxygen level environments may be beneficial for transplantation of BMMSC.

Principles for integrating reactive species into in vivo biological processes: Examples from exercise physiology.

PubMed

Margaritelis, Nikos V; Cobley, James N; Paschalis, Vassilis; Veskoukis, Aristidis S; Theodorou, Anastasios A; Kyparos, Antonios; Nikolaidis, Michalis G

2016-04-01

The equivocal role of reactive species and redox signaling in exercise responses and adaptations is an example clearly showing the inadequacy of current redox biology research to shed light on fundamental biological processes in vivo. Part of the answer probably relies on the extreme complexity of the in vivo redox biology and the limitations of the currently applied methodological and experimental tools. We propose six fundamental principles that should be considered in future studies to mechanistically link reactive species production to exercise responses or adaptations: 1) identify and quantify the reactive species, 2) determine the potential signaling properties of the reactive species, 3) detect the sources of reactive species, 4) locate the domain modified and verify the (ir)reversibility of post-translational modifications, 5) establish causality between redox and physiological measurements, 6) use selective and targeted antioxidants. Fulfilling these principles requires an idealized human experimental setting, which is certainly a utopia. Thus, researchers should choose to satisfy those principles, which, based on scientific evidence, are most critical for their specific research question. Copyright © 2015 Elsevier Inc. All rights reserved.

Generation of reactive species in atmospheric pressure dielectric barrier discharge with liquid water

NASA Astrophysics Data System (ADS)

Zelong, ZHANG; Jie, SHEN; Cheng, CHENG; Zimu, XU; Weidong, XIA

2018-04-01

Atmospheric pressure helium/water dielectric barrier discharge (DBD) plasma is used to investigate the generation of reactive species in a gas-liquid interface and in a liquid. The emission intensity of the reactive species is measured by optical emission spectroscopy (OES) with different discharge powers at the gas-liquid interface. Spectrophotometry is used to analyze the reactive species induced by the plasma in the liquid. The concentration of OH radicals reaches 2.2 μm after 3 min of discharge treatment. In addition, the concentration of primary long-lived reactive species such as H2O2, {{{{NO}}}3}- and O3 are measured based on plasma treatment time. After 5 min of discharge treatment, the concentration of H2O2, {{{{NO}}}3}-, and O3 increased from 0 mg · L-1 to 96 mg · L-1, 19.5 mg · L-1, and 3.5 mg · L-1, respectively. The water treated by plasma still contained a considerable concentration of reactive species after 6 h of storage. The results will contribute to optimizing the DBD plasma system for biological decontamination.

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

Gougar, Hans

This document outlines the development of a high fidelity, best estimate nuclear power plant severe transient simulation capability that will complement or enhance the integral system codes historically used for licensing and analysis of severe accidents. As with other tools in the Risk Informed Safety Margin Characterization (RISMC) Toolkit, the ultimate user of Enhanced Severe Transient Analysis and Prevention (ESTAP) capability is the plant decision-maker; the deliverable to that customer is a modern, simulation-based safety analysis capability, applicable to a much broader class of safety issues than is traditional Light Water Reactor (LWR) licensing analysis. Currently, the RISMC pathway’s majormore » emphasis is placed on developing RELAP-7, a next-generation safety analysis code, and on showing how to use RELAP-7 to analyze margin from a modern point of view: that is, by characterizing margin in terms of the probabilistic spectra of the “loads” applied to systems, structures, and components (SSCs), and the “capacity” of those SSCs to resist those loads without failing. The first objective of the ESTAP task, and the focus of one task of this effort, is to augment RELAP-7 analyses with user-selected multi-dimensional, multi-phase models of specific plant components to simulate complex phenomena that may lead to, or exacerbate, severe transients and core damage. Such phenomena include: coolant crossflow between PWR assemblies during a severe reactivity transient, stratified single or two-phase coolant flow in primary coolant piping, inhomogeneous mixing of emergency coolant water or boric acid with hot primary coolant, and water hammer. These are well-documented phenomena associated with plant transients but that are generally not captured in system codes. They are, however, generally limited to specific components, structures, and operating conditions. The second ESTAP task is to similarly augment a severe (post-core damage) accident integral analyses code with high fidelity simulations that would allow investigation of multi-dimensional, multi-phase containment phenomena that are only treated approximately in established codes.« less

Reactive oxygen species modulator 1, a novel protein, combined with carcinoembryonic antigen in differentiating malignant from benign pleural effusion.

PubMed

Chen, Xianmeng; Zhang, Na; Dong, Jiahui; Sun, Gengyun

2017-05-01

The differential diagnosis of malignant pleural effusion and benign pleural effusion remains a clinical problem. Reactive oxygen species modulator 1 is a novel protein overexpressed in various human tumors. The objective of this study was to evaluate the diagnostic value of joint detection of reactive oxygen species modulator 1 and carcinoembryonic antigen in the differential diagnosis of malignant pleural effusion and benign pleural effusion. One hundred two consecutive patients with pleural effusion (including 52 malignant pleural effusion and 50 benign pleural effusion) were registered in this study. Levels of reactive oxygen species modulator 1 and carcinoembryonic antigen were measured by enzyme-linked immunosorbent assay and radioimmunoassay, respectively. Results showed that the concentrations of reactive oxygen species modulator 1 both in pleural fluid and serum of patients with malignant pleural effusion were significantly higher than those of benign pleural effusion (both p < 0.05). The diagnostic sensitivity and specificity of pleural fluid reactive oxygen species modulator 1 were 61.54% and 82.00%, respectively, with the optimized cutoff value of 589.70 pg/mL. However, the diagnostic sensitivity and specificity of serum reactive oxygen species modulator 1 were only 41.38% and 86.21%, respectively, with the cutoff value of 27.22 ng/mL, indicating that serum reactive oxygen species modulator 1 may not be a good option in the differential diagnosis of malignant pleural effusion and benign pleural effusion. The sensitivity and specificity of pleural fluid carcinoembryonic antigen were 69.23% and 88.00%, respectively, at the cutoff value of 3.05 ng/mL, while serum carcinoembryonic antigen were 80.77% and 72.00% at the cutoff value of 2.60 ng/mL. The sensitivity could be raised to 88.17% in parallel detection of plural fluid reactive oxygen species modulator 1 and carcinoembryonic antigen concentration, and the specificity could be improved to 97.84% in serial detection.

Effect of climate-driven changes in species composition on regional emission capacities of biogenic compounds

NASA Astrophysics Data System (ADS)

Schurgers, G.; Arneth, A.; Hickler, T.

2011-11-01

Regional or global modeling studies of dynamic vegetation often represent vegetation by large functional units (plant functional types (PFTs)). For simulation of biogenic volatile organic compounds (BVOC) in these models, emission capacities, which give the emission under standardized conditions, are provided as an average value for a PFT. These emission capacities thus hide the known heterogeneity in emission characteristics that are not straightforwardly related to functional characteristics of plants. Here we study the effects of the aggregation of species-level information on emission characteristics at PFT level. The roles of temporal and spatial variability are assessed for Europe by comparing simulations that represent vegetation by dominant tree species on the one hand and by plant functional types on the other. We compare a number of time slices between the Last Glacial Maximum (21,000 years ago) and the present day to quantify the effects of dynamically changing vegetation on BVOC emissions. Spatial heterogeneity of emission factors is studied with present-day simulations. We show that isoprene and monoterpene emissions are of similar magnitude in Europe when the simulation represents dominant European tree species, which indicates that simulations applying typical global-scale emission capacities for PFTs tend to overestimate isoprene and underestimate monoterpene emissions. Moreover, both spatial and temporal variability affect emission capacities considerably, and by aggregating these to PFT level averages, one loses the information on local heterogeneity. Given the reactive nature of these compounds, accounting for spatial and temporal heterogeneity can be important for studies of their fate in the atmosphere.

Multi-technique approach to assess the effects of microbial biofilms involved in copper plumbing corrosion.

PubMed

Vargas, Ignacio T; Alsina, Marco A; Pavissich, Juan P; Jeria, Gustavo A; Pastén, Pablo A; Walczak, Magdalena; Pizarro, Gonzalo E

2014-06-01

Microbially influenced corrosion (MIC) is recognized as an unusual and severe type of corrosion that causes costly failures around the world. A microbial biofilm could enhance the copper release from copper plumbing into the water by forming a reactive interface. The biofilm increases the corrosion rate, the mobility of labile copper from its matrix and the detachment of particles enriched with copper under variable shear stress due to flow conditions. MIC is currently considered as a series of interdependent processes occurring at the metal-liquid interface. The presence of a biofilm results in the following effects: (a) the formation of localized microenvironments with distinct pH, dissolved oxygen concentrations, and redox conditions; (b) sorption and desorption of labile copper bonded to organic compounds under changing water chemistry conditions; (c) change in morphology by deposition of solid corrosion by-products; (d) diffusive transport of reactive chemical species from or towards the metal surface; and (e) detachment of scale particles under flow conditions. Using a multi-technique approach that combines pipe and coupon experiments this paper reviews the effects of microbial biofilms on the corrosion of copper plumbing systems, and proposes an integrated conceptual model for this phenomenon supported by new experimental data. Copyright © 2013 Elsevier B.V. All rights reserved.

Modelling the dispersion and transport of reactive pollutants in a deep urban street canyon: using large-eddy simulation.

PubMed

Zhong, Jian; Cai, Xiao-Ming; Bloss, William James

2015-05-01

This study investigates the dispersion and transport of reactive pollutants in a deep urban street canyon with an aspect ratio of 2 under neutral meteorological conditions using large-eddy simulation. The spatial variation of pollutants is significant due to the existence of two unsteady vortices. The deviation of species abundance from chemical equilibrium for the upper vortex is greater than that for the lower vortex. The interplay of dynamics and chemistry is investigated using two metrics: the photostationary state defect, and the inferred ozone production rate. The latter is found to be negative at all locations within the canyon, pointing to a systematic negative offset to ozone production rates inferred by analogous approaches in environments with incomplete mixing of emissions. This study demonstrates an approach to quantify parameters for a simplified two-box model, which could support traffic management and urban planning strategies and personal exposure assessment. Copyright © 2015 Elsevier Ltd. All rights reserved.

Multi-dimensional mesoscale simulations of detonation initiation in energetic materials with density-based kinetics

NASA Astrophysics Data System (ADS)

Jackson, Thomas Luther; Jost, Antoine M. D.; Zhang, Ju; Sridharan, Prashanth; Amadio, Guilherme

2018-03-01

In this work we present multi-dimensional mesoscale simulations of detonation initiation in energetic materials. We solve the reactive Euler equations, with the energy equation augmented by a power deposition term. The reaction rate at the mesoscale is modelled using density-based kinetics, while the deposition term is based on simulations of void collapse at the microscale, modelled at the mesoscale as hot spots. We carry out two- and three-dimensional mesoscale simulations of random packs of HMX crystals in a binder, and show that transition between no-detonation and detonation depends on the number density of the hot spots, the packing fraction, and the post-shock pressure of an imposed shock. In particular, we show that, for a fixed post-shock pressure, there exists a critical value of the number density of hot spots, such that when the number density is below this value a detonation wave will not develop. We highlight the importance of morphology to initiation by comparing with a homogeneous counterpart, and we compare relevant length scales by examining their corresponding power spectra. We also examine the effect of packing fraction and show that at low post-shock pressures there is significant variation in the initiation times, but that this variation disappears as the post-shock pressure is increased. Finally, we compare three-dimensional simulations with the experimental data, and show that the model is capable of qualitatively reproducing the trends shown in the data.

Modeling phosphorus capture by plants growing in a multi-species riparian buffer

USDA-ARS?s Scientific Manuscript database

The NST 3.0 mechanistic nutrient uptake model was used to explore phosphorus (P) uptake to a depth of 120 cm over a 126-d growing season in simulated buffer communities composed of mixtures of cottonwood (Populus deltoids Bartr.), switchgrass (Panicum virgatum L.), and smooth brome (Bromis inermis L...

Surface Modified Particles By Multi-Step Michael-Type Addition And Process For The Preparation Thereof

DOEpatents

Cook, Ronald Lee; Elliott, Brian John; Luebben, Silvia DeVito; Myers, Andrew William; Smith, Bryan Matthew

2005-05-03

A new class of surface modified particles and a multi-step Michael-type addition surface modification process for the preparation of the same is provided. The multi-step Michael-type addition surface modification process involves two or more reactions to compatibilize particles with various host systems and/or to provide the particles with particular chemical reactivities. The initial step comprises the attachment of a small organic compound to the surface of the inorganic particle. The subsequent steps attach additional compounds to the previously attached organic compounds through reactive organic linking groups. Specifically, these reactive groups are activated carbon—carbon pi bonds and carbon and non-carbon nucleophiles that react via Michael or Michael-type additions.

A Hybrid Adaptive Routing Algorithm for Event-Driven Wireless Sensor Networks

PubMed Central

Figueiredo, Carlos M. S.; Nakamura, Eduardo F.; Loureiro, Antonio A. F.

2009-01-01

Routing is a basic function in wireless sensor networks (WSNs). For these networks, routing algorithms depend on the characteristics of the applications and, consequently, there is no self-contained algorithm suitable for every case. In some scenarios, the network behavior (traffic load) may vary a lot, such as an event-driven application, favoring different algorithms at different instants. This work presents a hybrid and adaptive algorithm for routing in WSNs, called Multi-MAF, that adapts its behavior autonomously in response to the variation of network conditions. In particular, the proposed algorithm applies both reactive and proactive strategies for routing infrastructure creation, and uses an event-detection estimation model to change between the strategies and save energy. To show the advantages of the proposed approach, it is evaluated through simulations. Comparisons with independent reactive and proactive algorithms show improvements on energy consumption. PMID:22423207

A hybrid adaptive routing algorithm for event-driven wireless sensor networks.

PubMed

Figueiredo, Carlos M S; Nakamura, Eduardo F; Loureiro, Antonio A F

2009-01-01

Routing is a basic function in wireless sensor networks (WSNs). For these networks, routing algorithms depend on the characteristics of the applications and, consequently, there is no self-contained algorithm suitable for every case. In some scenarios, the network behavior (traffic load) may vary a lot, such as an event-driven application, favoring different algorithms at different instants. This work presents a hybrid and adaptive algorithm for routing in WSNs, called Multi-MAF, that adapts its behavior autonomously in response to the variation of network conditions. In particular, the proposed algorithm applies both reactive and proactive strategies for routing infrastructure creation, and uses an event-detection estimation model to change between the strategies and save energy. To show the advantages of the proposed approach, it is evaluated through simulations. Comparisons with independent reactive and proactive algorithms show improvements on energy consumption.

UV/H2O2 and UV/PDS Treatment of Trimethoprim and Sulfamethoxazole in Synthetic Human Urine: Transformation Products and Toxicity.

PubMed

Zhang, Ruochun; Yang, Yongkui; Huang, Ching-Hua; Li, Na; Liu, Hang; Zhao, Lin; Sun, Peizhe

2016-03-01

Elimination of pharmaceuticals in source-separated human urine is a promising approach to minimize the pharmaceuticals in the environment. Although the degradation kinetics of pharmaceuticals by UV/H2O2 and UV/peroxydisulfate (PDS) processes has been investigated in synthetic fresh and hydrolyzed urine, comprehensive evaluation of the advanced oxidation processes (AOPs), such as product identification and toxicity testing, has not yet been performed. This study identified the transformation products of two commonly used antibiotics, trimethoprim (TMP) and sulfamethoxazole (SMX), by UV/H2O2 and UV/PDS in synthetic urine matrices. The effects of reactive species, including •OH, SO4(•-), CO3(•-), and reactive nitrogen species, on product generation were investigated. Multiple isomeric transformation products of TMP and SMX were observed, especially in the reaction with hydroxyl radical. SO4(•-) and CO3(•-) reacted with pharmaceuticals by electron transfer, thus producing similar major products. The main reactive species deduced on the basis of product generation are in good agreement with kinetic simulation of the advanced oxidation processes. A strain identified as a polyphosphate-accumulating organism was used to investigate the antimicrobial activity of the pharmaceuticals and their products. No antimicrobial property was detected for the transformation products of either TMP or SMX. Acute toxicity employing luminescent bacterium Vibrio qinghaiensis indicated 20-40% higher inhibitory effect of TMP and SMX after treatment. Ecotoxicity was estimated by quantitative structure-activity relationship analysis using ECOSAR.

Chemical fingerprints of cold physical plasmas - an experimental and computational study using cysteine as tracer compound.

PubMed

Lackmann, J-W; Wende, K; Verlackt, C; Golda, J; Volzke, J; Kogelheide, F; Held, J; Bekeschus, S; Bogaerts, A; Schulz-von der Gathen, V; Stapelmann, K

2018-05-16

Reactive oxygen and nitrogen species released by cold physical plasma are being proposed as effectors in various clinical conditions connected to inflammatory processes. As these plasmas can be tailored in a wide range, models to compare and control their biochemical footprint are desired to infer on the molecular mechanisms underlying the observed effects and to enable the discrimination between different plasma sources. Here, an improved model to trace short-lived reactive species is presented. Using FTIR, high-resolution mass spectrometry, and molecular dynamics computational simulation, covalent modifications of cysteine treated with different plasmas were deciphered and the respective product pattern used to generate a fingerprint of each plasma source. Such, our experimental model allows a fast and reliable grading of the chemical potential of plasmas used for medical purposes. Major reaction products were identified to be cysteine sulfonic acid, cystine, and cysteine fragments. Less-abundant products, such as oxidized cystine derivatives or S-nitrosylated cysteines, were unique to different plasma sources or operating conditions. The data collected point at hydroxyl radicals, atomic O, and singlet oxygen as major contributing species that enable an impact on cellular thiol groups when applying cold plasma in vitro or in vivo.

Mechanism of the growth of amorphous and microcrystalline silicon from silicon tetrafluoride and hydrogen

NASA Astrophysics Data System (ADS)

Okada, Y.; Chen, J.; Campbell, I. H.; Fauchet, P. M.; Wagner, S.

1990-02-01

We study the growth of amorphous (a-Si:H,F) and of microcrystalline (μc-Si) silicon over trench patterns in crystalline silicon substrates. We vary the conditions of the SiF4-H2 glow discharge from deposition to etching. All deposited films form lips at the trench mouth and are uniformly thick on the trench walls. Therefore, surface diffusion is not important. The results of a Monte Carlo simulation suggest that film growth is governed by a single growth species with a low (˜0.2) sticking coefficient, in combination with a highly reactive etching species.

Ignition sensitivity study of an energetic train configuration using experiments and simulation

NASA Astrophysics Data System (ADS)

Kim, Bohoon; Yu, Hyeonju; Yoh, Jack J.

2018-06-01

A full scale hydrodynamic simulation intended for the accurate description of shock-induced detonation transition was conducted as a part of an ignition sensitivity analysis of an energetic component system. The system is composed of an exploding foil initiator (EFI), a donor explosive unit, a stainless steel gap, and an acceptor explosive. A series of velocity interferometer system for any reflector measurements were used to validate the hydrodynamic simulations based on the reactive flow model that describes the initiation of energetic materials arranged in a train configuration. A numerical methodology with ignition and growth mechanisms for tracking multi-material boundary interactions as well as severely transient fluid-structure coupling between high explosive charges and metal gap is described. The free surface velocity measurement is used to evaluate the sensitivity of energetic components that are subjected to strong pressure waves. Then, the full scale hydrodynamic simulation is performed on the flyer impacted initiation of an EFI driven pyrotechnical system.

Inferring species trees from incongruent multi-copy gene trees using the Robinson-Foulds distance

PubMed Central

2013-01-01

Background Constructing species trees from multi-copy gene trees remains a challenging problem in phylogenetics. One difficulty is that the underlying genes can be incongruent due to evolutionary processes such as gene duplication and loss, deep coalescence, or lateral gene transfer. Gene tree estimation errors may further exacerbate the difficulties of species tree estimation. Results We present a new approach for inferring species trees from incongruent multi-copy gene trees that is based on a generalization of the Robinson-Foulds (RF) distance measure to multi-labeled trees (mul-trees). We prove that it is NP-hard to compute the RF distance between two mul-trees; however, it is easy to calculate this distance between a mul-tree and a singly-labeled species tree. Motivated by this, we formulate the RF problem for mul-trees (MulRF) as follows: Given a collection of multi-copy gene trees, find a singly-labeled species tree that minimizes the total RF distance from the input mul-trees. We develop and implement a fast SPR-based heuristic algorithm for the NP-hard MulRF problem. We compare the performance of the MulRF method (available at http://genome.cs.iastate.edu/CBL/MulRF/) with several gene tree parsimony approaches using gene tree simulations that incorporate gene tree error, gene duplications and losses, and/or lateral transfer. The MulRF method produces more accurate species trees than gene tree parsimony approaches. We also demonstrate that the MulRF method infers in minutes a credible plant species tree from a collection of nearly 2,000 gene trees. Conclusions Our new phylogenetic inference method, based on a generalized RF distance, makes it possible to quickly estimate species trees from large genomic data sets. Since the MulRF method, unlike gene tree parsimony, is based on a generic tree distance measure, it is appealing for analyses of genomic data sets, in which many processes such as deep coalescence, recombination, gene duplication and losses as well as phylogenetic error may contribute to gene tree discord. In experiments, the MulRF method estimated species trees accurately and quickly, demonstrating MulRF as an efficient alternative approach for phylogenetic inference from large-scale genomic data sets. PMID:24180377

CFD-ACE+: a CAD system for simulation and modeling of MEMS

NASA Astrophysics Data System (ADS)

Stout, Phillip J.; Yang, H. Q.; Dionne, Paul; Leonard, Andy; Tan, Zhiqiang; Przekwas, Andrzej J.; Krishnan, Anantha

1999-03-01

Computer aided design (CAD) systems are a key to designing and manufacturing MEMS with higher performance/reliability, reduced costs, shorter prototyping cycles and improved time- to-market. One such system is CFD-ACE+MEMS, a modeling and simulation environment for MEMS which includes grid generation, data visualization, graphical problem setup, and coupled fluidic, thermal, mechanical, electrostatic, and magnetic physical models. The fluid model is a 3D multi- block, structured/unstructured/hybrid, pressure-based, implicit Navier-Stokes code with capabilities for multi- component diffusion, multi-species transport, multi-step gas phase chemical reactions, surface reactions, and multi-media conjugate heat transfer. The thermal model solves the total enthalpy from of the energy equation. The energy equation includes unsteady, convective, conductive, species energy, viscous dissipation, work, and radiation terms. The electrostatic model solves Poisson's equation. Both the finite volume method and the boundary element method (BEM) are available for solving Poisson's equation. The BEM method is useful for unbounded problems. The magnetic model solves for the vector magnetic potential from Maxwell's equations including eddy currents but neglecting displacement currents. The mechanical model is a finite element stress/deformation solver which has been coupled to the flow, heat, electrostatic, and magnetic calculations to study flow, thermal electrostatically, and magnetically included deformations of structures. The mechanical or structural model can accommodate elastic and plastic materials, can handle large non-linear displacements, and can model isotropic and anisotropic materials. The thermal- mechanical coupling involves the solution of the steady state Navier equation with thermoelastic deformation. The electrostatic-mechanical coupling is a calculation of the pressure force due to surface charge on the mechanical structure. Results of CFD-ACE+MEMS modeling of MEMS such as cantilever beams, accelerometers, and comb drives are discussed.

Simulation of MEMS for the Next Generation Space Telescope

NASA Technical Reports Server (NTRS)

Mott, Brent; Kuhn, Jonathan; Broduer, Steve (Technical Monitor)

2001-01-01

The NASA Goddard Space Flight Center (GSFC) is developing optical micro-electromechanical system (MEMS) components for potential application in Next Generation Space Telescope (NGST) science instruments. In this work, we present an overview of the electro-mechanical simulation of three MEMS components for NGST, which include a reflective micro-mirror array and transmissive microshutter array for aperture control for a near infrared (NIR) multi-object spectrometer and a large aperture MEMS Fabry-Perot tunable filter for a NIR wide field camera. In all cases the device must operate at cryogenic temperatures with low power consumption and low, complementary metal oxide semiconductor (CMOS) compatible, voltages. The goal of our simulation efforts is to adequately predict both the performance and the reliability of the devices during ground handling, launch, and operation to prevent failures late in the development process and during flight. This goal requires detailed modeling and validation of complex electro-thermal-mechanical interactions and very large non-linear deformations, often involving surface contact. Various parameters such as spatial dimensions and device response are often difficult to measure reliably at these small scales. In addition, these devices are fabricated from a wide variety of materials including surface micro-machined aluminum, reactive ion etched (RIE) silicon nitride, and deep reactive ion etched (DRIE) bulk single crystal silicon. The above broad set of conditions combine to be a formidable challenge for space flight qualification analysis. These simulations represent NASA/GSFC's first attempts at implementing a comprehensive strategy to address complex MEMS structures.

Cytotoxic and Antitumor Activity of Sulforaphane: The Role of Reactive Oxygen Species

PubMed Central

Sestili, Piero

2015-01-01

According to recent estimates, cancer continues to remain the second leading cause of death and is becoming the leading one in old age. Failure and high systemic toxicity of conventional cancer therapies have accelerated the identification and development of innovative preventive as well as therapeutic strategies to contrast cancer-associated morbidity and mortality. In recent years, increasing body of in vitro and in vivo studies has underscored the cancer preventive and therapeutic efficacy of the isothiocyanate sulforaphane. In this review article, we highlight that sulforaphane cytotoxicity derives from complex, concurring, and multiple mechanisms, among which the generation of reactive oxygen species has been identified as playing a central role in promoting apoptosis and autophagy of target cells. We also discuss the site and the mechanism of reactive oxygen species' formation by sulforaphane, the toxicological relevance of sulforaphane-formed reactive oxygen species, and the death pathways triggered by sulforaphane-derived reactive oxygen species. PMID:26185755

Equilibrium expert: an add-in to Microsoft Excel for multiple binding equilibrium simulations and parameter estimations.

PubMed

Raguin, Olivier; Gruaz-Guyon, Anne; Barbet, Jacques

2002-11-01

An add-in to Microsoft Excel was developed to simulate multiple binding equilibriums. A partition function, readily written even when the equilibrium is complex, describes the experimental system. It involves the concentrations of the different free molecular species and of the different complexes present in the experiment. As a result, the software is not restricted to a series of predefined experimental setups but can handle a large variety of problems involving up to nine independent molecular species. Binding parameters are estimated by nonlinear least-square fitting of experimental measurements as supplied by the user. The fitting process allows user-defined weighting of the experimental data. The flexibility of the software and the way it may be used to describe common experimental situations and to deal with usual problems such as tracer reactivity or nonspecific binding is demonstrated by a few examples. The software is available free of charge upon request.

Uncertainty of future projections of species distributions in mountainous regions.

PubMed

Tang, Ying; Winkler, Julie A; Viña, Andrés; Liu, Jianguo; Zhang, Yuanbin; Zhang, Xiaofeng; Li, Xiaohong; Wang, Fang; Zhang, Jindong; Zhao, Zhiqiang

2018-01-01

Multiple factors introduce uncertainty into projections of species distributions under climate change. The uncertainty introduced by the choice of baseline climate information used to calibrate a species distribution model and to downscale global climate model (GCM) simulations to a finer spatial resolution is a particular concern for mountainous regions, as the spatial resolution of climate observing networks is often insufficient to detect the steep climatic gradients in these areas. Using the maximum entropy (MaxEnt) modeling framework together with occurrence data on 21 understory bamboo species distributed across the mountainous geographic range of the Giant Panda, we examined the differences in projected species distributions obtained from two contrasting sources of baseline climate information, one derived from spatial interpolation of coarse-scale station observations and the other derived from fine-spatial resolution satellite measurements. For each bamboo species, the MaxEnt model was calibrated separately for the two datasets and applied to 17 GCM simulations downscaled using the delta method. Greater differences in the projected spatial distributions of the bamboo species were observed for the models calibrated using the different baseline datasets than between the different downscaled GCM simulations for the same calibration. In terms of the projected future climatically-suitable area by species, quantification using a multi-factor analysis of variance suggested that the sum of the variance explained by the baseline climate dataset used for model calibration and the interaction between the baseline climate data and the GCM simulation via downscaling accounted for, on average, 40% of the total variation among the future projections. Our analyses illustrate that the combined use of gridded datasets developed from station observations and satellite measurements can help estimate the uncertainty introduced by the choice of baseline climate information to the projected changes in species distribution.

Uncertainty of future projections of species distributions in mountainous regions

PubMed Central

Tang, Ying; Viña, Andrés; Liu, Jianguo; Zhang, Yuanbin; Zhang, Xiaofeng; Li, Xiaohong; Wang, Fang; Zhang, Jindong; Zhao, Zhiqiang

2018-01-01

Multiple factors introduce uncertainty into projections of species distributions under climate change. The uncertainty introduced by the choice of baseline climate information used to calibrate a species distribution model and to downscale global climate model (GCM) simulations to a finer spatial resolution is a particular concern for mountainous regions, as the spatial resolution of climate observing networks is often insufficient to detect the steep climatic gradients in these areas. Using the maximum entropy (MaxEnt) modeling framework together with occurrence data on 21 understory bamboo species distributed across the mountainous geographic range of the Giant Panda, we examined the differences in projected species distributions obtained from two contrasting sources of baseline climate information, one derived from spatial interpolation of coarse-scale station observations and the other derived from fine-spatial resolution satellite measurements. For each bamboo species, the MaxEnt model was calibrated separately for the two datasets and applied to 17 GCM simulations downscaled using the delta method. Greater differences in the projected spatial distributions of the bamboo species were observed for the models calibrated using the different baseline datasets than between the different downscaled GCM simulations for the same calibration. In terms of the projected future climatically-suitable area by species, quantification using a multi-factor analysis of variance suggested that the sum of the variance explained by the baseline climate dataset used for model calibration and the interaction between the baseline climate data and the GCM simulation via downscaling accounted for, on average, 40% of the total variation among the future projections. Our analyses illustrate that the combined use of gridded datasets developed from station observations and satellite measurements can help estimate the uncertainty introduced by the choice of baseline climate information to the projected changes in species distribution. PMID:29320501

Single-walled carbon nanotube, multi-walled carbon nanotube and Fe2O3 nanoparticles induced mitochondria mediated apoptosis in melanoma cells.

PubMed

Naserzadeh, Parvaneh; Ansari Esfeh, Fatemeh; Kaviani, Mahboubeh; Ashtari, Khadijeh; Kheirbakhsh, Raheleh; Salimi, Ahmad; Pourahmad, Jalal

2018-06-01

Nanomaterials (NM) exhibit novel anticancer properties. The toxicity of three nanoparticles that are currently being produced in high tonnage including single-walled carbon nanotube (SWCNT), multi-walled carbon nanotube (MWCNT) and Fe 2 O 3 nanoparticles, were compared with normal and melanoma cells. All tested nanoparticles induced selective toxicity and caspase 3 activation through mitochondria pathway in melanoma cells and mitochondria cause the generating of reactive oxygen species (ROS), mitochondrial membrane potential decline (MMP collapse), mitochondria swelling, and cytochrome c release. The pretreatment of butylated hydroxytoluene (BHT), a cell-permeable antioxidant and cyclosporine A (Cs. A), a mitochondrial permeability transition (MPT), pore sealing agent decreased cytotoxicity, caspase 3 activation, ROS generation, and mitochondrial damages induced by SWCNT, MWCNT, and IONPs. Our promising results provide a potential approach for the future therapeutic use of SWCNT, MWCNT, and IONPs in melanoma through mitochondrial targeting.

Serological cross-reactivity among Sporothrix schenckii, Ceratocystis, Europhium, and Graphium species.

PubMed Central

Ishizaki, H; Wheat, R W; Kiel, D P; Conant, N F

1978-01-01

Ethanol-precipitable culture filtrate antigens of 100 strains of 75 species of the Sporothrix-Ceratocystis-Europhium-Graphium complex and 1 species of Botrytis were examined for neutral sugar components and for serological cross-reactivity with S. schenckii rabbit antiserum and human sporotrichosis sera by capillary precipitin and double immunodiffusion assay. Results revealed that cross-reactive species (60 of 77, ca. 80%) produced exoconidial forms and rhamnose- and mannose-containing polysaccharides and included Ceratocystis, the three known Europhium, and several Graphium-form species. Endoconidial-form Ceratocystis species did not cross-react. Images PMID:99369

Silicates Eroded under Simulated Martian Conditions Effectively Kill Bacteria—A Challenge for Life on Mars

PubMed Central

Bak, Ebbe N.; Larsen, Michael G.; Moeller, Ralf; Nissen, Silas B.; Jensen, Lasse R.; Nørnberg, Per; Jensen, Svend J. K.; Finster, Kai

2017-01-01

The habitability of Mars is determined by the physical and chemical environment. The effect of low water availability, temperature, low atmospheric pressure and strong UV radiation has been extensively studied in relation to the survival of microorganisms. In addition to these stress factors, it was recently found that silicates exposed to simulated saltation in a Mars-like atmosphere can lead to a production of reactive oxygen species. Here, we have investigated the stress effect induced by quartz and basalt abraded in Mars-like atmospheres by examining the survivability of the three microbial model organisms Pseudomonas putida, Bacillus subtilis, and Deinococcus radiodurans upon exposure to the abraded silicates. We found that abraded basalt that had not been in contact with oxygen after abrasion killed more than 99% of the vegetative cells while endospores were largely unaffected. Exposure of the basalt samples to oxygen after abrasion led to a significant reduction in the stress effect. Abraded quartz was generally less toxic than abraded basalt. We suggest that the stress effect of abraded silicates may be caused by a production of reactive oxygen species and enhanced by transition metal ions in the basalt leading to hydroxyl radicals through Fenton-like reactions. The low survivability of the usually highly resistant D. radiodurans indicates that the effect of abraded silicates, as is ubiquitous on the Martian surface, would limit the habitability of Mars as well as the risk of forward contamination. Furthermore, the reactivity of abraded silicates could have implications for future manned missions, although the lower effect of abraded silicates exposed to oxygen suggests that the effects would be reduced in human habitats. PMID:28955310

Silicates Eroded under Simulated Martian Conditions Effectively Kill Bacteria-A Challenge for Life on Mars.

PubMed

Bak, Ebbe N; Larsen, Michael G; Moeller, Ralf; Nissen, Silas B; Jensen, Lasse R; Nørnberg, Per; Jensen, Svend J K; Finster, Kai

2017-01-01

The habitability of Mars is determined by the physical and chemical environment. The effect of low water availability, temperature, low atmospheric pressure and strong UV radiation has been extensively studied in relation to the survival of microorganisms. In addition to these stress factors, it was recently found that silicates exposed to simulated saltation in a Mars-like atmosphere can lead to a production of reactive oxygen species. Here, we have investigated the stress effect induced by quartz and basalt abraded in Mars-like atmospheres by examining the survivability of the three microbial model organisms Pseudomonas putida, Bacillus subtilis , and Deinococcus radiodurans upon exposure to the abraded silicates. We found that abraded basalt that had not been in contact with oxygen after abrasion killed more than 99% of the vegetative cells while endospores were largely unaffected. Exposure of the basalt samples to oxygen after abrasion led to a significant reduction in the stress effect. Abraded quartz was generally less toxic than abraded basalt. We suggest that the stress effect of abraded silicates may be caused by a production of reactive oxygen species and enhanced by transition metal ions in the basalt leading to hydroxyl radicals through Fenton-like reactions. The low survivability of the usually highly resistant D. radiodurans indicates that the effect of abraded silicates, as is ubiquitous on the Martian surface, would limit the habitability of Mars as well as the risk of forward contamination. Furthermore, the reactivity of abraded silicates could have implications for future manned missions, although the lower effect of abraded silicates exposed to oxygen suggests that the effects would be reduced in human habitats.

Assessment of Alternative Conceptual Models Using Reactive Transport Modeling with Monitoring Data

NASA Astrophysics Data System (ADS)

Dai, Z.; Price, V.; Heffner, D.; Hodges, R.; Temples, T.; Nicholson, T.

2005-12-01

Monitoring data proved very useful in evaluating alternative conceptual models, simulating contaminant transport behavior, and reducing uncertainty. A graded approach using three alternative conceptual site models was formulated to simulate a field case of tetrachloroethene (PCE) transport and biodegradation. These models ranged from simple to complex in their representation of subsurface heterogeneities. The simplest model was a single-layer homogeneous aquifer that employed an analytical reactive transport code, BIOCHLOR (Aziz et al., 1999). Due to over-simplification of the aquifer structure, this simulation could not reproduce the monitoring data. The second model consisted of a multi-layer conceptual model, in combination with numerical modules, MODFLOW and RT3D within GMS, to simulate flow and reactive transport. Although the simulation results from the second model were comparatively better than those from the simple model, they still did not adequately reproduce the monitoring well concentrations because the geological structures were still inadequately defined. Finally, a more realistic conceptual model was formulated that incorporated heterogeneities and geologic structures identified from well logs and seismic survey data using the Petra and PetraSeis software. This conceptual model included both a major channel and a younger channel that were detected in the PCE source area. In this model, these channels control the local ground-water flow direction and provide a preferential chemical transport pathway. Simulation results using this conceptual site model proved compatible with the monitoring concentration data. This study demonstrates that the bias and uncertainty from inadequate conceptual models are much larger than those introduced from an inadequate choice of model parameter values (Neuman and Wierenga, 2003; Meyer et al., 2004; Ye et al., 2004). This case study integrated conceptual and numerical models, based on interpreted local hydrogeologic and geochemical data, with detailed monitoring plume data. It provided key insights for confirming alternative conceptual site models and assessing the performance of monitoring networks. A monitoring strategy based on this graded approach for assessing alternative conceptual models can provide the technical bases for identifying critical monitoring locations, adequate monitoring frequency, and performance indicator parameters for performance monitoring involving ground-water levels and PCE concentrations.

Ab initio molecular dynamics simulation of aqueous solution of nitric oxide in different formal oxidation states

NASA Astrophysics Data System (ADS)

Venâncio, Mateus F.; Rocha, Willian R.

2015-10-01

Ab initio molecular dynamics simulations were used to investigate the early chemical events involved in the dynamics of nitric oxide (NOrad), nitrosonium cation (NO+) and nitroxide anion (NO-) in aqueous solution. The NO+ ion is very reactive in aqueous solution having a lifetime of ∼4 × 10-13 s, which is shorter than the value of 3 × 10-10 s predicted experimentally. The NO+ reacts generating the nitrous acid as an intermediate and the NO2- ion as the final product. The dynamics of NOrad revealed the reversibly formation of a transient anion radical species HONOrad -.

Multispecies diffusion models: A study of uranyl species diffusion

NASA Astrophysics Data System (ADS)

Liu, Chongxuan; Shang, Jianying; Zachara, John M.

2011-12-01

Rigorous numerical description of multispecies diffusion requires coupling of species, charge, and aqueous and surface complexation reactions that collectively affect diffusive fluxes. The applicability of a fully coupled diffusion model is, however, often constrained by the availability of species self-diffusion coefficients, as well as by computational complication in imposing charge conservation. In this study, several diffusion models with variable complexity in charge and species coupling were formulated and compared to describe reactive multispecies diffusion in groundwater. Diffusion of uranyl [U(VI)] species was used as an example in demonstrating the effectiveness of the models in describing multispecies diffusion. Numerical simulations found that a diffusion model with a single, common diffusion coefficient for all species was sufficient to describe multispecies U(VI) diffusion under a steady state condition of major chemical composition, but not under transient chemical conditions. Simulations revealed that for multispecies U(VI) diffusion under transient chemical conditions, a fully coupled diffusion model could be well approximated by a component-based diffusion model when the diffusion coefficient for each chemical component was properly selected. The component-based diffusion model considers the difference in diffusion coefficients between chemical components, but not between the species within each chemical component. This treatment significantly enhanced computational efficiency at the expense of minor charge conservation. The charge balance in the component-based diffusion model can be enforced, if necessary, by adding a secondary migration term resulting from model simplification. The effect of ion activity coefficient gradients on multispecies diffusion is also discussed. The diffusion models were applied to describe U(VI) diffusive mass transfer in intragranular domains in two sediments collected from U.S. Department of Energy's Hanford 300A, where intragranular diffusion is a rate-limiting process controlling U(VI) adsorption and desorption. The grain-scale reactive diffusion model was able to describe U(VI) adsorption/desorption kinetics that had been previously described using a semiempirical, multirate model. Compared with the multirate model, the diffusion models have the advantage to provide spatiotemporal speciation evolution within the diffusion domains.

Characterizing Myeloid Cell Activation in NF1 Vasculopathy

DTIC Science & Technology

2017-07-01

stimulation of its receptor (CCR2) and the generation of reactive oxygen species, which are generated in excessive quantities by neurofibromin-deficient...macrophages via monocyte chemotactic peptide-1 (MCP-1) stimulation of its receptor (CCR2) and the generation of reactive oxygen species, which are...neurofibromatosis; stenosis; aneurysm; MCP-1; CCR2; reactive oxygen species; superoxide; macrophages; monocytes; arteries; cardiovascular disease Major

Mitochondria and Reactive Oxygen Species: Physiology and Pathophysiology

PubMed Central

Bolisetty, Subhashini; Jaimes, Edgar A.

2013-01-01

The air that we breathe contains nearly 21% oxygen, most of which is utilized by mitochondria during respiration. While we cannot live without it, it was perceived as a bane to aerobic organisms due to the generation of reactive oxygen and nitrogen metabolites by mitochondria and other cellular compartments. However, this dogma was challenged when these species were demonstrated to modulate cellular responses through altering signaling pathways. In fact, since this discovery of a dichotomous role of reactive species in immune function and signal transduction, research in this field grew at an exponential pace and the pursuit for mechanisms involved began. Due to a significant number of review articles present on the reactive species mediated cell death, we have focused on emerging novel pathways such as autophagy, signaling and maintenance of the mitochondrial network. Despite its role in several processes, increased reactive species generation has been associated with the origin and pathogenesis of a plethora of diseases. While it is tempting to speculate that anti-oxidant therapy would protect against these disorders, growing evidence suggests that this may not be true. This further supports our belief that these reactive species play a fundamental role in maintenance of cellular and tissue homeostasis. PMID:23528859

Equilibrium, kinetic, and reactive transport models for plutonium

NASA Astrophysics Data System (ADS)

Schwantes, Jon Michael

Equilibrium, kinetic, and reactive transport models for plutonium (Pu) have been developed to help meet environmental concerns posed by past war-related and present and future peacetime nuclear technologies. A thorough review of the literature identified several hurdles that needed to be overcome in order to develop capable predictive tools for Pu. These hurdles include: (1) missing or ill-defined chemical equilibrium and kinetic constants for environmentally important Pu species; (2) no adequate conceptual model describing the formation of Pu oxy/hydroxide colloids and solids; and (3) an inability of two-phase reactive transport models to adequately simulate Pu behavior in the presence of colloids. A computer program called INVRS K was developed that integrates the geochemical modeling software of PHREEQC with a nonlinear regression routine. This program provides a tool for estimating equilibrium and kinetic constants from experimental data. INVRS K was used to regress on binding constants for Pu sorbing onto various mineral and humic surfaces. These constants enhance the thermodynamic database for Pu and improve the capability of current predictive tools. Time and temperature studies of the Pu intrinsic colloid were also conducted and results of these studies were presented here. Formation constants for the fresh and aged Pu intrinsic colloid were regressed upon using INVRS K. From these results, it was possible to develop a cohesive diagenetic model that describes the formation of Pu oxy/hydroxide colloids and solids. This model provides for the first time a means of deciphering historically unexplained observations with respect to the Pu intrinsic colloid, as well as a basis for simulating the behavior within systems containing these solids. Discussion of the development and application of reactive transport models is also presented and includes: (1) the general application of a 1-D in flow, three-phase (i.e., dissolved, solid, and colloidal), reactive transport model; (2) a simulation of the effects of dissolution of PuO2 solid and radiolysis on the behavior of Pu diffusing out of a confined pore space; and (3) application of a steady-state three phase reactive transport model to groundwater at the Nevada Test Site.

A Benchmarking Initiative for Reactive Transport Modeling Applied to Subsurface Environmental Applications

NASA Astrophysics Data System (ADS)

Steefel, C. I.

2015-12-01

Over the last 20 years, we have seen the evolution of multicomponent reactive transport modeling and the expanding range and increasing complexity of subsurface environmental applications it is being used to address. Reactive transport modeling is being asked to provide accurate assessments of engineering performance and risk for important issues with far-reaching consequences. As a result, the complexity and detail of subsurface processes, properties, and conditions that can be simulated have significantly expanded. Closed form solutions are necessary and useful, but limited to situations that are far simpler than typical applications that combine many physical and chemical processes, in many cases in coupled form. In the absence of closed form and yet realistic solutions for complex applications, numerical benchmark problems with an accepted set of results will be indispensable to qualifying codes for various environmental applications. The intent of this benchmarking exercise, now underway for more than five years, is to develop and publish a set of well-described benchmark problems that can be used to demonstrate simulator conformance with norms established by the subsurface science and engineering community. The objective is not to verify this or that specific code--the reactive transport codes play a supporting role in this regard—but rather to use the codes to verify that a common solution of the problem can be achieved. Thus, the objective of each of the manuscripts is to present an environmentally-relevant benchmark problem that tests the conceptual model capabilities, numerical implementation, process coupling, and accuracy. The benchmark problems developed to date include 1) microbially-mediated reactions, 2) isotopes, 3) multi-component diffusion, 4) uranium fate and transport, 5) metal mobility in mining affected systems, and 6) waste repositories and related aspects.

Spectroscopy of reactive species produced by low-energy atmospheric-pressure plasma on conductive target material surface

NASA Astrophysics Data System (ADS)

Yamada, Hiromasa; Sakakita, Hajime; Kato, Susumu; Kim, Jaeho; Kiyama, Satoru; Fujiwara, Masanori; Itagaki, Hirotomo; Okazaki, Toshiya; Ikehara, Sanae; Nakanishi, Hayao; Shimizu, Nobuyuki; Ikehara, Yuzuru

2016-10-01

A method for blood coagulation using low-energy atmospheric-pressure plasma (LEAPP) is confirmed as an alternative procedure to reduce tissue damage caused by heat. Blood coagulation using LEAPP behaves differently depending on working gas species; helium is more effective than argon in promoting fast coagulation. To analyse the difference in reactive species produced by helium and argon plasma, spectroscopic measurements were conducted without and with a target material. To compare emissions, blood coagulation experiments using LEAPP for both plasmas were performed under almost identical conditions. Although many kinds of reactive species such as hydroxyl radicals and excited nitrogen molecules were observed with similar intensity in both plasmas, intensities of nitrogen ion molecules and nitric oxide molecules were extremely strong in the helium plasma. It is considered that nitrogen ion molecules were mainly produced by penning ionization by helium metastable. Near the target, a significant increase in the emissions of reactive species is observed. There is a possibility that electron acceleration was induced in a local electric field formed on the surface. However, in argon plasma, emissions from nitrogen ion were not measured even near the target surface. These differences between the two plasmas may be producing the difference in blood coagulation behaviour. To control the surrounding gas of the plasma, a gas-component-controllable chamber was assembled. Filling the chamber with O2/He or N2/He gas mixtures selectively produces either reactive oxygen species or reactive nitrogen species. Through selective treatments, this chamber would be useful in studying the effects of specific reactive species on blood coagulation.

Theoretical study on the reactivity of sulfate species with hydrocarbons

USGS Publications Warehouse

Ma, Q.; Ellis, G.S.; Amrani, A.; Zhang, T.; Tang, Y.

2008-01-01

The abiotic, thermochemically controlled reduction of sulfate to hydrogen sulfide coupled with the oxidation of hydrocarbons, is termed thermochemical sulfate reduction (TSR), and is an important alteration process that affects petroleum accumulations in nature. Although TSR is commonly observed in high-temperature carbonate reservoirs, it has proven difficult to simulate in the laboratory under conditions resembling nature. The present study was designed to evaluate the relative reactivities of various sulfate species in order to provide greater insight into the mechanism of TSR and potentially to fill the gap between laboratory experimental data and geological observations. Accordingly, quantum mechanics density functional theory (DFT) was used to determine the activation energy required to reach a potential transition state for various aqueous systems involving simple hydrocarbons and different sulfate species. The entire reaction process that results in the reduction of sulfate to sulfide is far too complex to be modeled entirely; therefore, we examined what is believed to be the rate limiting step, namely, the reduction of sulfate S(VI) to sulfite S(IV). The results of the study show that water-solvated sulfate anions SO42 - are very stable due to their symmetrical molecular structure and spherical electronic distributions. Consequently, in the absence of catalysis, the reactivity of SO42 - is expected to be extremely low. However, both the protonation of sulfate to form bisulfate anions (HSO4-) and the formation of metal-sulfate contact ion-pairs could effectively destabilize the sulfate molecular structure, thereby making it more reactive. Previous reports of experimental simulations of TSR generally have involved the use of acidic solutions that contain elevated concentrations of HSO4- relative to SO42 -. However, in formation waters typically encountered in petroleum reservoirs, the concentration of HSO4- is likely to be significantly lower than the levels used in the laboratory, with most of the dissolved sulfate occurring as SO42 -, aqueous calcium sulfate ([CaSO4](aq)), and aqueous magnesium sulfate ([MgSO4](aq)). Our calculations indicate that TSR reactions that occur in natural environments are most likely to involve bisulfate ions (HSO4-) and/or magnesium sulfate contact ion-pairs ([MgSO4]CIP) rather than 'free' sulfate ions (SO42 -) or solvated sulfate ion-pairs, and that water chemistry likely plays a significant role in controlling the rate of TSR. ?? 2008 Elsevier Ltd. All rights reserved.

Theoretical study on the reactivity of sulfate species with hydrocarbons

NASA Astrophysics Data System (ADS)

Ma, Qisheng; Ellis, Geoffrey S.; Amrani, Alon; Zhang, Tongwei; Tang, Yongchun

2008-09-01

The abiotic, thermochemically controlled reduction of sulfate to hydrogen sulfide coupled with the oxidation of hydrocarbons, is termed thermochemical sulfate reduction (TSR), and is an important alteration process that affects petroleum accumulations in nature. Although TSR is commonly observed in high-temperature carbonate reservoirs, it has proven difficult to simulate in the laboratory under conditions resembling nature. The present study was designed to evaluate the relative reactivities of various sulfate species in order to provide greater insight into the mechanism of TSR and potentially to fill the gap between laboratory experimental data and geological observations. Accordingly, quantum mechanics density functional theory (DFT) was used to determine the activation energy required to reach a potential transition state for various aqueous systems involving simple hydrocarbons and different sulfate species. The entire reaction process that results in the reduction of sulfate to sulfide is far too complex to be modeled entirely; therefore, we examined what is believed to be the rate limiting step, namely, the reduction of sulfate S(VI) to sulfite S(IV). The results of the study show that water-solvated sulfate anions SO42- are very stable due to their symmetrical molecular structure and spherical electronic distributions. Consequently, in the absence of catalysis, the reactivity of SO42- is expected to be extremely low. However, both the protonation of sulfate to form bisulfate anions ( HSO4-) and the formation of metal-sulfate contact ion-pairs could effectively destabilize the sulfate molecular structure, thereby making it more reactive. Previous reports of experimental simulations of TSR generally have involved the use of acidic solutions that contain elevated concentrations of HSO4- relative to SO42-. However, in formation waters typically encountered in petroleum reservoirs, the concentration of HSO4- is likely to be significantly lower than the levels used in the laboratory, with most of the dissolved sulfate occurring as SO42-, aqueous calcium sulfate ([CaSO 4] (aq)), and aqueous magnesium sulfate ([MgSO 4] (aq)). Our calculations indicate that TSR reactions that occur in natural environments are most likely to involve bisulfate ions ( HSO4-) and/or magnesium sulfate contact ion-pairs ([MgSO 4] CIP) rather than 'free' sulfate ions ( SO42-) or solvated sulfate ion-pairs, and that water chemistry likely plays a significant role in controlling the rate of TSR.

Pore-scale Simulation and Imaging of Multi-phase Flow and Transport in Porous Media (Invited)

NASA Astrophysics Data System (ADS)

Crawshaw, J.; Welch, N.; Daher, I.; Yang, J.; Shah, S.; Grey, F.; Boek, E.

2013-12-01

We combine multi-scale imaging and computer simulation of multi-phase flow and reactive transport in rock samples to enhance our fundamental understanding of long term CO2 storage in rock formations. The imaging techniques include Confocal Laser Scanning Microscopy (CLSM), micro-CT and medical CT scanning, with spatial resolutions ranging from sub-micron to mm respectively. First, we report a new sample preparation technique to study micro-porosity in carbonates using CLSM in 3 dimensions. Second, we use micro-CT scanning to generate high resolution 3D pore space images of carbonate and cap rock samples. In addition, we employ micro-CT to image the processes of evaporation in fractures and cap rock degradation due to exposure to CO2 flow. Third, we use medical CT scanning to image spontaneous imbibition in carbonate rock samples. Our imaging studies are complemented by computer simulations of multi-phase flow and transport, using the 3D pore space images obtained from the scanning experiments. We have developed a massively parallel lattice-Boltzmann (LB) code to calculate the single phase flow field in these pore space images. The resulting flow fields are then used to calculate hydrodynamic dispersion using a novel scheme to predict probability distributions for molecular displacements using the LB method and a streamline algorithm, modified for optimal solid boundary conditions. We calculate solute transport on pore-space images of rock cores with increasing degree of heterogeneity: a bead pack, Bentheimer sandstone and Portland carbonate. We observe that for homogeneous rock samples, such as bead packs, the displacement distribution remains Gaussian with time increasing. In the more heterogeneous rocks, on the other hand, the displacement distribution develops a stagnant part. We observe that the fraction of trapped solute increases from the beadpack (0 %) to Bentheimer sandstone (1.5 %) to Portland carbonate (8.1 %), in excellent agreement with PFG-NMR experiments. We then use our preferred multi-phase model to directly calculate flow in pore space images of two different sandstones and observe excellent agreement with experimental relative permeabilities. Also we calculate cluster size distributions in good agreement with experimental studies. Our analysis shows that the simulations are able to predict both multi-phase flow and transport properties directly on large 3D pore space images of real rocks. Pore space images, left and velocity distributions, right (Yang and Boek, 2013)

A fully non-linear multi-species Fokker–Planck–Landau collision operator for simulation of fusion plasma

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

Hager, Robert, E-mail: rhager@pppl.gov; Yoon, E.S., E-mail: yoone@rpi.edu; Ku, S., E-mail: sku@pppl.gov

2016-06-15

Fusion edge plasmas can be far from thermal equilibrium and require the use of a non-linear collision operator for accurate numerical simulations. In this article, the non-linear single-species Fokker–Planck–Landau collision operator developed by Yoon and Chang (2014) [9] is generalized to include multiple particle species. The finite volume discretization used in this work naturally yields exact conservation of mass, momentum, and energy. The implementation of this new non-linear Fokker–Planck–Landau operator in the gyrokinetic particle-in-cell codes XGC1 and XGCa is described and results of a verification study are discussed. Finally, the numerical techniques that make our non-linear collision operator viable onmore » high-performance computing systems are described, including specialized load balancing algorithms and nested OpenMP parallelization. The collision operator's good weak and strong scaling behavior are shown.« less

Multi-specie isothermal flow calculations of widely-spaced co-axial jets in a confined sudden expansion, with the central jet dominant

NASA Astrophysics Data System (ADS)

Sturgess, G. J.; Syed, S. A.

1982-06-01

A numerical simulation is made of the flow in the Wright Aeronautical Propulsion Laboratory diffusion flame research combustor operating with a strong central jet of carbon dioxide in a weak and removed co-axial jet of air. The simulation is based on a finite difference solution of the time-average, steady-state, elliptic form of the Reynolds equations. Closure for these equations is provided by a two-equation turbulence model. Comparisons between measurements and predictions are made for centerline axial velocities and radial profiles of CO2 concentration. Earlier findings for a single specie, constant density, single jet flow that a large expansion ratio confined jet behaves initially as if it were unconfined, are confirmed for the multiple-specie, variable density, multiple-jet system. The lack of universality in the turbulence model constants and the turbulent Schmidt/Prandtl number is discussed.

A fully non-linear multi-species Fokker–Planck–Landau collision operator for simulation of fusion plasma

DOE PAGES

Hager, Robert; Yoon, E. S.; Ku, S.; ...

2016-04-04

Fusion edge plasmas can be far from thermal equilibrium and require the use of a non-linear collision operator for accurate numerical simulations. The non-linear single-species Fokker–Planck–Landau collision operator developed by Yoon and Chang (2014) [9] is generalized to include multiple particle species. Moreover, the finite volume discretization used in this work naturally yields exact conservation of mass, momentum, and energy. The implementation of this new non-linear Fokker–Planck–Landau operator in the gyrokinetic particle-in-cell codes XGC1 and XGCa is described and results of a verification study are discussed. Finally, the numerical techniques that make our non-linear collision operator viable on high-performance computingmore » systems are described, including specialized load balancing algorithms and nested OpenMP parallelization. As a result, the collision operator's good weak and strong scaling behavior are shown.« less

Validation of chemistry models employed in a particle simulation method

NASA Technical Reports Server (NTRS)

Haas, Brian L.; Mcdonald, Jeffrey D.

1991-01-01

The chemistry models employed in a statistical particle simulation method, as implemented in the Intel iPSC/860 multiprocessor computer, are validated and applied. Chemical relaxation of five-species air in these reservoirs involves 34 simultaneous dissociation, recombination, and atomic-exchange reactions. The reaction rates employed in the analytic solutions are obtained from Arrhenius experimental correlations as functions of temperature for adiabatic gas reservoirs in thermal equilibrium. Favorable agreement with the analytic solutions validates the simulation when applied to relaxation of O2 toward equilibrium in reservoirs dominated by dissociation and recombination, respectively, and when applied to relaxation of air in the temperature range 5000 to 30,000 K. A flow of O2 over a circular cylinder at high Mach number is simulated to demonstrate application of the method to multidimensional reactive flows.

Non-uniform temperature and species concentration measurements in a laminar flame using multi-band infrared absorption spectroscopy

NASA Astrophysics Data System (ADS)

Ma, Liu Hao; Lau, Lok Yin; Ren, Wei

2017-03-01

We report in situ measurements of non-uniform temperature, H2O and CO2 concentration distributions in a premixed methane-air laminar flame using tunable diode laser absorption spectroscopy (TDLAS). A mid-infrared, continuous-wave, room-temperature interband cascade laser (ICL) at 4183 nm was used for the sensitive detection of CO2 at high temperature.The H2O absorption lines were exploited by one distributed feedback (DFB) diode laser at 1343 nm and one ICL at 2482 nm to achieve multi-band absorption measurements with high species concentration sensitivity, high temperature sensitivity, and immunity to variations in ambient conditions. A novel profile-fitting function was proposed to characterize the non-uniform temperature and species concentrations along the line-of-sight in the flame by detecting six absorption lines of CO2 and H2O simultaneously. The flame temperature distribution was measured at different heights above the burner (5-20 mm), and compared with the thermocouple measurement with heat-transfer correction. Our TDLAS measured temperature of the central flame was in excellent agreement (<1.5% difference) with the thermocouple data.The TDLAS results were also compared with the CFD simulations using a detailed chemical kinetics mechanism (GRI 3.0) and considering the heat loss to the surroundings.The current CFD simulation overpredicted the flame temperature in the gradient region, but was in excellent agreement with the measured temperature and species concentration in the core of the flame.

Pressure Monitoring to Detect Fault Rupture Due to CO 2 Injection

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

Keating, Elizabeth; Dempsey, David; Pawar, Rajesh

The capacity for fault systems to be reactivated by fluid injection is well-known. In the context of CO 2 sequestration, however, the consequence of reactivated faults with respect to leakage and monitoring is poorly understood. Using multi-phase fluid flow simulations, this study addresses key questions concerning the likelihood of ruptures, the timing of consequent upward leakage of CO 2, and the effectiveness of pressure monitoring in the reservoir and overlying zones for rupture detection. A range of injection scenarios was simulated using random sampling of uncertain parameters. These include the assumed distance between the injector and the vulnerable fault zone,more » the critical overpressure required for the fault to rupture, reservoir permeability, and the CO 2 injection rate. We assumed a conservative scenario, in which if at any time during the five-year simulations the critical fault overpressure is exceeded, the fault permeability is assumed to instantaneously increase. For the purposes of conservatism we assume that CO 2 injection continues ‘blindly’ after fault rupture. We show that, despite this assumption, in most cases the CO 2 plume does not reach the base of the ruptured fault after 5 years. As a result, one possible implication of this result is that leak mitigation strategies such as pressure management have a reasonable chance of preventing a CO 2 leak.« less

Pressure Monitoring to Detect Fault Rupture Due to CO 2 Injection

DOE PAGES

Keating, Elizabeth; Dempsey, David; Pawar, Rajesh

2017-08-18

The capacity for fault systems to be reactivated by fluid injection is well-known. In the context of CO 2 sequestration, however, the consequence of reactivated faults with respect to leakage and monitoring is poorly understood. Using multi-phase fluid flow simulations, this study addresses key questions concerning the likelihood of ruptures, the timing of consequent upward leakage of CO 2, and the effectiveness of pressure monitoring in the reservoir and overlying zones for rupture detection. A range of injection scenarios was simulated using random sampling of uncertain parameters. These include the assumed distance between the injector and the vulnerable fault zone,more » the critical overpressure required for the fault to rupture, reservoir permeability, and the CO 2 injection rate. We assumed a conservative scenario, in which if at any time during the five-year simulations the critical fault overpressure is exceeded, the fault permeability is assumed to instantaneously increase. For the purposes of conservatism we assume that CO 2 injection continues ‘blindly’ after fault rupture. We show that, despite this assumption, in most cases the CO 2 plume does not reach the base of the ruptured fault after 5 years. As a result, one possible implication of this result is that leak mitigation strategies such as pressure management have a reasonable chance of preventing a CO 2 leak.« less

Exposure to Electrophiles Impairs Reactive Persulfide-Dependent Redox Signaling in Neuronal Cells.

PubMed

Ihara, Hideshi; Kasamatsu, Shingo; Kitamura, Atsushi; Nishimura, Akira; Tsutsuki, Hiroyasu; Ida, Tomoaki; Ishizaki, Kento; Toyama, Takashi; Yoshida, Eiko; Abdul Hamid, Hisyam; Jung, Minkyung; Matsunaga, Tetsuro; Fujii, Shigemoto; Sawa, Tomohiro; Nishida, Motohiro; Kumagai, Yoshito; Akaike, Takaaki

2017-09-18

Electrophiles such as methylmercury (MeHg) affect cellular functions by covalent modification with endogenous thiols. Reactive persulfide species were recently reported to mediate antioxidant responses and redox signaling because of their strong nucleophilicity. In this study, we used MeHg as an environmental electrophile and found that exposure of cells to the exogenous electrophile elevated intracellular concentrations of the endogenous electrophilic molecule 8-nitroguanosine 3',5'-cyclic monophosphate (8-nitro-cGMP), accompanied by depletion of reactive persulfide species and 8-SH-cGMP which is a metabolite of 8-nitro-cGMP. Exposure to MeHg also induced S-guanylation and activation of H-Ras followed by injury to cerebellar granule neurons. The electrophile-induced activation of redox signaling and the consequent cell damage were attenuated by pretreatment with a reactive persulfide species donor. In conclusion, exogenous electrophiles such as MeHg with strong electrophilicity impair the redox signaling regulatory mechanism, particularly of intracellular reactive persulfide species and therefore lead to cellular pathogenesis. Our results suggest that reactive persulfide species may be potential therapeutic targets for attenuating cell injury by electrophiles.

Lunar Dust and Lunar Simulant Activation, Monitoring, Solution and Cellular Toxicity Properties

NASA Technical Reports Server (NTRS)

Jeevarajan, A.S.; Wallace, W.T.

2009-01-01

During the Apollo missions, many undesirable situations were encountered that must be mitigated prior to returning humans to the moon. Lunar dust (that part of the lunar regolith less than 20 m in diameter) was found to produce several problems with astronaut s suits and helmets, mechanical seals and equipment, and could have conceivably produced harmful physiological effects for the astronauts. For instance, the abrasive nature of the dust was found to cause malfunctions of various joints and seals of the spacecraft and suits. Additionally, though efforts were made to exclude lunar dust from the cabin of the lunar module, a significant amount of material nonetheless found its way inside. With the loss of gravity correlated with ascent of the lunar module from the lunar surface to rendezvous with the command module, much of the major portions of the contaminating soil and dust began to float, irritating the astronaut s eyes and being inhaled into their lungs. Our goal has been to understand some of the properties of lunar dust that could lead to possible hazards for humans. Due to the lack of an atmosphere, there is nothing to protect the lunar soil from ultraviolet radiation, solar wind, and meteorite impacts. These processes could all serve to activate the soil, or produce reactive surface species. In order to understand the possible toxic effects of the reactive dust, it is necessary to reactivate the dust, as samples returned during the Apollo missions were exposed to the atmosphere of the Earth. We have used grinding and UV exposure to mimic some of the processes occurring on the Moon. The level of activation has been monitored using two methods: fluorescence spectroscopy and electron paramagnetic resonance spectroscopy (EPR). These techniques allow the monitoring of hydroxyl radical production in solution. We have found that grinding of lunar dust produces 2-3 times the concentration of hydroxyl radicals as lunar simulant and 10 times that of quartz. Exposure of the lunar dust to UV radiation under vacuum was also found to lead to hydroxyl radical production. After grinding, we have also monitored loss of reactivity of the dusts by exposing them to conditions of known humidity and temperature. From these tests, it was found that the reactivity half-life of lunar simulant is approximately 3 hours, while that of quartz is approximately 2 hours. Placing lunar dust in solution could lead to effects on mechanical and physiological systems, as well as other biological systems. For instance, while it is known that lunar dust is highly abrasive and caused a variety of problems with suits and equipment during Apollo, it is unknown as to how these properties might be affected in the presence of water or other liquids. It is possible that the dust may release minerals (e.g., metallic nanophase Fe) into solution that could speed corrosion or rust. Also, as lunar dust produces hydroxyl radicals (and possibly other reactive oxygen species) in solution, these radicals could also lead to the breakdown of suit or habitat materials. In the body (i.e., in lung solution), the effects could be two-fold. First, if the lunar dust dissolves, it may release an excess of elements (such as zero-valence metallic Fe) that are necessary for bodily functions but only in certain concentration ranges. For lunar dust, the presence of nanophase iron being released into the body is a concern. Secondly, the hydroxyl radicals or other reactive oxygen species produced by the dust in solution could conceivably interact with cells, leading to various problems. We have studied the dissolution of both ground and unground lunar simulant in buffer solutions of different pH. The concentration of a number of species was determined using mass spectrometry. These studies showed that lowering the pH of the solution causes a dramatic increase in the amount of each element released into solution and that grinding also produces higher concentrations. Finally, we have perfmed initial tests aimed at understanding the effects of lunar simulant on cellular systems. Alveolar epithelial cells were cultured and exposed to different concentrations of dust suspended in cell culture media. After predetermined amounts of time, the media was removed and the concentrations of important inflammatory cytokines (IL6, IL8, and TNF-alpha ) were measured. The results of these tests are being used to develop the correct protocols for tests to be performed using lunar dust samples.

ARSENIC SPECIES CAUSE RELEASE OF IRON FROM FERRITIN GENERATING REACTIVE OXYGEN SPECIES

EPA Science Inventory

ARSENIC SPECIES CAUSE RELEASE OF IRON FROM FERRITIN GENERATING REACTIVE OXYGEN SPECIES

Arsenic-associated cancer (lung, bladder, skin, liver, kidney) remains a significant world- wide public health problem (e.g., Taiwan, Chile, Bangladesh, India, China and Thailand). Rece...

Modeling and validation of single-chamber microbial fuel cell cathode biofilm growth and response to oxidant gas composition

NASA Astrophysics Data System (ADS)

Ou, Shiqi; Zhao, Yi; Aaron, Douglas S.; Regan, John M.; Mench, Matthew M.

2016-10-01

This work describes experiments and computational simulations to analyze single-chamber, air-cathode microbial fuel cell (MFC) performance and cathodic limitations in terms of current generation, power output, mass transport, biomass competition, and biofilm growth. Steady-state and transient cathode models were developed and experimentally validated. Two cathode gas mixtures were used to explore oxygen transport in the cathode: the MFCs exposed to a helium-oxygen mixture (heliox) produced higher current and power output than the group of MFCs exposed to air or a nitrogen-oxygen mixture (nitrox), indicating a dependence on gas-phase transport in the cathode. Multi-substance transport, biological reactions, and electrochemical reactions in a multi-layer and multi-biomass cathode biofilm were also simulated in a transient model. The transient model described biofilm growth over 15 days while providing insight into mass transport and cathodic dissolved species concentration profiles during biofilm growth. Simulation results predict that the dissolved oxygen content and diffusion in the cathode are key parameters affecting the power output of the air-cathode MFC system, with greater oxygen content in the cathode resulting in increased power output and fully-matured biomass.

Modeling and validation of single-chamber microbial fuel cell cathode biofilm growth and response to oxidant gas composition

DOE PAGES

Ou, Shiqi; Zhao, Yi; Aaron, Douglas S.; ...

2016-08-15

This work describes experiments and computational simulations to analyze single-chamber, air-cathode microbial fuel cell (MFC) performance and cathodic limitations in terms of current generation, power output, mass transport, biomass competition, and biofilm growth. Steady-state and transient cathode models were developed and experimentally validated. Two cathode gas mixtures were used to explore oxygen transport in the cathode: the MFCs exposed to a helium-oxygen mixture (heliox) produced higher current and power output than the group of MFCs exposed to air or a nitrogen-oxygen mixture (nitrox), indicating a dependence on gas-phase transport in the cathode. Multi-substance transport, biological reactions, and electrochemical reactions inmore » a multi-layer and multi-biomass cathode biofilm were also simulated in a transient model. The transient model described biofilm growth over 15 days while providing insight into mass transport and cathodic dissolved species concentration profiles during biofilm growth. Lastly, simulation results predict that the dissolved oxygen content and diffusion in the cathode are key parameters affecting the power output of the air-cathode MFC system, with greater oxygen content in the cathode resulting in increased power output and fully-matured biomass.« less

Quantifying uncertainty and computational complexity for pore-scale simulations

NASA Astrophysics Data System (ADS)

Chen, C.; Yuan, Z.; Wang, P.; Yang, X.; Zhenyan, L.

2016-12-01

Pore-scale simulation is an essential tool to understand the complex physical process in many environmental problems, from multi-phase flow in the subsurface to fuel cells. However, in practice, factors such as sample heterogeneity, data sparsity and in general, our insufficient knowledge of the underlying process, render many simulation parameters and hence the prediction results uncertain. Meanwhile, most pore-scale simulations (in particular, direct numerical simulation) incur high computational cost due to finely-resolved spatio-temporal scales, which further limits our data/samples collection. To address those challenges, we propose a novel framework based on the general polynomial chaos (gPC) and build a surrogate model representing the essential features of the underlying system. To be specific, we apply the novel framework to analyze the uncertainties of the system behavior based on a series of pore-scale numerical experiments, such as flow and reactive transport in 2D heterogeneous porous media and 3D packed beds. Comparing with recent pore-scale uncertainty quantification studies using Monte Carlo techniques, our new framework requires fewer number of realizations and hence considerably reduce the overall computational cost, while maintaining the desired accuracy.

Effects of peptides on generation of reactive oxygen species in subcellular fractions of Drosophila melanogaster.

PubMed

Khavinson, V K; Myl'nikov, S V; Oparina, T I; Arutyunyan, A V

2001-07-01

We studied the effects of Epithalon (Ala-Glu-Asp-Gly) and Vilon (Lys-Glu) on free radical processes in highly inbred HA(+)line of Drosophila melanogaster. Vilon inhibited generation of reactive oxygen species in mitochondria, but stimulated this process in the cytosol. We found sex- and age-related differences in the generation of reactive oxygen species and cytosol antioxidant activity.

Multi-fluid Dynamics for Supersonic Jet-and-Crossflows and Liquid Plug Rupture

NASA Astrophysics Data System (ADS)

Hassan, Ezeldin A.

Multi-fluid dynamics simulations require appropriate numerical treatments based on the main flow characteristics, such as flow speed, turbulence, thermodynamic state, and time and length scales. In this thesis, two distinct problems are investigated: supersonic jet and crossflow interactions; and liquid plug propagation and rupture in an airway. Gaseous non-reactive ethylene jet and air crossflow simulation represents essential physics for fuel injection in SCRAMJET engines. The regime is highly unsteady, involving shocks, turbulent mixing, and large-scale vortical structures. An eddy-viscosity-based multi-scale turbulence model is proposed to resolve turbulent structures consistent with grid resolution and turbulence length scales. Predictions of the time-averaged fuel concentration from the multi-scale model is improved over Reynolds-averaged Navier-Stokes models originally derived from stationary flow. The response to the multi-scale model alone is, however, limited, in cases where the vortical structures are small and scattered thus requiring prohibitively expensive grids in order to resolve the flow field accurately. Statistical information related to turbulent fluctuations is utilized to estimate an effective turbulent Schmidt number, which is shown to be highly varying in space. Accordingly, an adaptive turbulent Schmidt number approach is proposed, by allowing the resolved field to adaptively influence the value of turbulent Schmidt number in the multi-scale turbulence model. The proposed model estimates a time-averaged turbulent Schmidt number adapted to the computed flowfield, instead of the constant value common to the eddy-viscosity-based Navier-Stokes models. This approach is assessed using a grid-refinement study for the normal injection case, and tested with 30 degree injection, showing improved results over the constant turbulent Schmidt model both in mean and variance of fuel concentration predictions. For the incompressible liquid plug propagation and rupture study, numerical simulations are conducted using an Eulerian-Lagrangian approach with a continuous-interface method. A reconstruction scheme is developed to allow topological changes during plug rupture by altering the connectivity information of the interface mesh. Rupture time is shown to be delayed as the initial precursor film thickness increases. During the plug rupture process, a sudden increase of mechanical stresses on the tube wall is recorded, which can cause tissue damage.

Radicals and Reservoirs in the GMI Chemistry and Transport Model: Comparison to Measurements

NASA Technical Reports Server (NTRS)

Douglass, Anne R.; Stolarski, Richard S.; Strahan, Susan E.; Connell, Peter S.

2004-01-01

We have used a three-dimensional chemistry and transport model (CTM), developed under the Global Modeling Initiative (GMI), to carry out two simulations of the composition of the stratosphere under changing halogen loading for 1995 through 2030. The two simulations differ only in that one uses meteorological fields from a general circulation model while the other uses meteorological fields from a data assimilation system. A single year's winds and temperatures are repeated for each 36-year simulation. We compare results from these two simulations with an extensive collection of data from satellite and ground-based measurements for 1993-2000. Comparisons of simulated fields with observations of radical and reservoir species for some of the major ozone-destroying compounds are of similar quality for both simulations. Differences in the upper stratosphere, caused by transport of total reactive nitrogen and methane, impact the balance among the ozone loss processes and the sensitivity of the two simulations to the change in composition.

Axial vs. Equatorial Ligand Rivalry in Controlling the Reactivity of Iron(IV)-Oxo Species: Single-State vs. Two-State Reactivity.

PubMed

Kumar, Ravi; Ansari, Azaj; Rajaraman, Gopalan

2018-05-07

High-valent iron-oxo species are known for their very high reactivity, and this aspect has been studied in detail over the years. The role of axial ligands in fine-tuning the reactivity of the iron(IV)-oxo species has been particularly well studied. The corresponding role of equatorial ligands, however, has rarely been explored, and is of prime importance in the development of non-heme chemistry. Here, we have undertaken detailed DFT calculations on [(L NHC )Fe IV (O)(CH 3 CN)] 2+ (1; L NHC =3,9,14,20-tetraaza1,6,12,17-tetraazoniapenta-cyclohexacosane-1(23),4,6(26),10,12(25),15,17(24),21-octaene) in comparison to compound II of cytochrome P450 [(porphyrin)Fe IV (O)(SH)] - (2) to probe this aspect. The electronic structures of 1 and 2 are found to vary significantly, implying a large variation in their reactivities. In particular, the strong equatorial ligand present in 1 significantly destabilizes the quintet states as compared to species 2. To fully understand the reactivity pattern of these species, we have modelled the hydroxylation of methane by both 1 and 2. Our calculations reveal that 1 reacts via a low-lying S=1 π pathway, and that the generally available S=2 σ pathway is not energetically accessible. In addition to having a significant barrier for C-H bond activation, the -OH rebound step is also computed to have a large barrier height, leading to a marked difference in reactivity between these two species. Of particular relevance here is the observation of pure triplet-state reactivity for 1. We have also attempted to test the role of axial ligands in fine-tuning the reactivity of 1, and our results demonstrate that, in contrast to heme systems, the axial ligands in 1 do not significantly influence the reactivity. This highlights the importance of designing equatorial ligands to fine-tune reactivity of high-valent iron(IV)-oxo species. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Large eddy simulation of reactive pollutants in a deep urban street canyon: Coupling dynamics with O3-NOx-VOC chemistry.

PubMed

Zhong, Jian; Cai, Xiao-Ming; Bloss, William James

2017-05-01

A large eddy simulation (LES) model coupled with O 3 -NO x -VOC chemistry is implemented to simulate the coupled effects of emissions, mixing and chemical pre-processing within an idealised deep (aspect ratio = 2) urban street canyon under a weak wind condition. Reactive pollutants exhibit significant spatial variations in the presence of two vertically aligned unsteady vortices formed in the canyon. Comparison of the LES results from two chemical schemes (simple NO x -O 3 chemistry and a more comprehensive Reduced Chemical Scheme (RCS) chemical mechanism) shows that the concentrations of NO 2 and O x inside the street canyon are enhanced by approximately 30-40% via OH/HO 2 chemistry. NO, NO x , O 3 , OH and HO 2 are chemically consumed, while NO 2 and O x (total oxidant) are chemically produced within the canyon environment. Within-canyon pre-processing increases oxidant fluxes from the canyon to the overlying boundary layer, and this effect is greater for deeper street canyons (as found in many traditional European urban centres) than shallower (lower aspect ratio) streets. There is clear evidence of distinct behaviours for emitted chemical species and entrained chemical species, and positive (or negative) values of intensities of segregations are found between pairs of species with similar (or opposite) behaviour. The simplified two-box model underestimated NO and O 3 levels, but overestimated NO 2 levels for both the lower and upper canyon compared with the more realistic LES-chemistry model. This suggests that the segregation effect due to incomplete mixing reduces the chemical conversion rate of NO to NO 2 . This study reveals the impacts of nonlinear O 3 -NO x -VOC photochemical processes in the incomplete mixing environment and provides a better understanding of the pre-processing of emissions within canyons, prior to their release to the urban boundary layer, through the coupling of street canyon dynamics and chemistry. Copyright © 2017 Elsevier Ltd. All rights reserved.

A dynamic ecosystem growth model for forests at high complexity structure

NASA Astrophysics Data System (ADS)

Collalti, A.; Perugini, L.; Chiti, T.; Matteucci, G.; Oriani, A.; Santini, M.; Papale, D.; Valentini, R.

2012-04-01

Forests ecosystem play an important role in carbon cycle, biodiversity conservation and for other ecosystem services and changes in their structure and status perturb a delicate equilibrium that involves not only vegetation components but also biogeochemical cycles and global climate. The approaches to determine the magnitude of these effects are nowadays various and one of those include the use of models able to simulate structural changes and the variations in forests yield The present work shows the development of a forest dynamic model, on ecosystem spatial scale using the well known light use efficiency to determine Gross Primary Production. The model is predictive and permits to simulate processes that determine forest growth, its dynamic and the effects of forest management using eco-physiological parameters easy to be assessed and to be measured. The model has been designed to consider a tri-dimensional cell structure composed by different vertical layers depending on the forest type that has to be simulated. These features enable the model to work on multi-layer and multi-species forest types, typical of Mediterranean environment, at the resolution of one hectare and at monthly time-step. The model simulates, for each layer, a value of available Photosynthetic Active Radiation (PAR) through Leaf Area Index, Light Extinction Coefficient and cell coverage, the transpiration rate that is closely linked to the intercepted light and the evaporation from soil. Using this model it is possible to evaluate the possible impacts of climate change on forests that may result in decrease or increase of productivity as well as the feedback of one or more dominated layers in terms of CO2 uptake in a forest stand and the effects of forest management activities during the forest harvesting cycle. The model has been parameterised, validated and applied in a multi-layer, multi-age and multi-species Italian turkey oak forest (Q. cerris L., C. betulus L. and C. avellana L.) where the medium-term (10 years) development of forest parameters were simulated. The results obtained for net primary production and for stem, root and foliage compartments as well as for forest structure i.e. Diameter at Breast Height, height and canopy cover are in good accordance with field data (R2>0.95). These results show how the model is able to predict forest yield as well as forest dynamic with good accuracy and encourage testing the model capability on other sites with a more complex forest structure and for long-time period with an higher spatial resolution.

Acetylene-based pathways for prebiotic evolution on Titan

NASA Astrophysics Data System (ADS)

Abbas, O.; Schulze-Makuch, D.

2002-11-01

Due to Titan's reducing atmosphere and lack of an ozone shield, ionizing radiation penetrates the atmosphere creating ions, radicals and electrons that are highly reactive producing versatile chemical species on Titan's surface. We propose that the catalytic hydrogenation of photochemically produced acetylene may be used as simple metabolic pathway by organisms at or near Titan's surface. While the acetylene may undergo this reaction, it can also undertake several other multi-step synthetic schemes that eventually lead to the production of amino acids or other biologically important molecules. Four model synthetic schemes will be described, and their relevance in relation to prebiotic evolution on Earth is discussed.

Boost-phase discrimination research activities

NASA Technical Reports Server (NTRS)

Cooper, David M.; Deiwert, George S.

1989-01-01

Theoretical research in two areas was performed. The aerothermodynamics research focused on the hard-body and rocket plume flows. Analytical real gas models to describe finite rate chemistry were developed and incorporated into the three-dimensional flow codes. New numerical algorithms capable of treating multi-species reacting gas equations and treating flows with large gradients were also developed. The computational chemistry research focused on the determination of spectral radiative intensity factors, transport properties and reaction rates. Ab initio solutions to the Schrodinger equation provided potential energy curves transition moments (radiative probabilities and strengths) and potential energy surfaces. These surfaces were then coupled with classical particle reactive trajectories to compute reaction cross-sections and rates.

Calcium influx through TRP channels induced by short-lived reactive species in plasma-irradiated solution

NASA Astrophysics Data System (ADS)

Sasaki, Shota; Kanzaki, Makoto; Kaneko, Toshiro

2016-05-01

Non-equilibrium helium atmospheric-pressure plasma (He-APP), which allows for a strong non-equilibrium chemical reaction of O2 and N2 in ambient air, uniquely produces multiple extremely reactive products, such as reactive oxygen species (ROS), in plasma-irradiated solution. We herein show that relatively short-lived unclassified reactive species (i.e., deactivated within approximately 10 min) generated by the He-APP irradiation can trigger physiologically relevant Ca2+ influx through ruthenium red- and SKF 96365-sensitive Ca2+-permeable channel(s), possibly transient receptor potential channel family member(s). Our results provide novel insight into understanding of the interactions between cells and plasmas and the mechanism by which cells detect plasma-induced chemically reactive species, in addition to facilitating development of plasma applications in medicine.

Multi-Wave Prospective Examination of the Stress-Reactivity Extension of Response Styles Theory of Depression in High-Risk Children and Early Adolescents

ERIC Educational Resources Information Center

Abela, John R. Z.; Hankin, Benjamin L.; Sheshko, Dana M.; Fishman, Michael B.; Stolow, Darren

2012-01-01

The current study tested the stress-reactivity extension of response styles theory of depression (Nolen-Hoeksema "Journal of Abnormal Psychology" 100:569-582, 1991) in a sample of high-risk children and early adolescents from a vulnerability-stress perspective using a multi-wave longitudinal design. In addition, we examined whether obtained…

Innovative mathematical modeling in environmental remediation.

PubMed

Yeh, Gour-Tsyh; Gwo, Jin-Ping; Siegel, Malcolm D; Li, Ming-Hsu; Fang, Yilin; Zhang, Fan; Luo, Wensui; Yabusaki, Steve B

2013-05-01

There are two different ways to model reactive transport: ad hoc and innovative reaction-based approaches. The former, such as the Kd simplification of adsorption, has been widely employed by practitioners, while the latter has been mainly used in scientific communities for elucidating mechanisms of biogeochemical transport processes. It is believed that innovative mechanistic-based models could serve as protocols for environmental remediation as well. This paper reviews the development of a mechanistically coupled fluid flow, thermal transport, hydrologic transport, and reactive biogeochemical model and example-applications to environmental remediation problems. Theoretical bases are sufficiently described. Four example problems previously carried out are used to demonstrate how numerical experimentation can be used to evaluate the feasibility of different remediation approaches. The first one involved the application of a 56-species uranium tailing problem to the Melton Branch Subwatershed at Oak Ridge National Laboratory (ORNL) using the parallel version of the model. Simulations were made to demonstrate the potential mobilization of uranium and other chelating agents in the proposed waste disposal site. The second problem simulated laboratory-scale system to investigate the role of natural attenuation in potential off-site migration of uranium from uranium mill tailings after restoration. It showed inadequacy of using a single Kd even for a homogeneous medium. The third example simulated laboratory experiments involving extremely high concentrations of uranium, technetium, aluminum, nitrate, and toxic metals (e.g., Ni, Cr, Co). The fourth example modeled microbially-mediated immobilization of uranium in an unconfined aquifer using acetate amendment in a field-scale experiment. The purposes of these modeling studies were to simulate various mechanisms of mobilization and immobilization of radioactive wastes and to illustrate how to apply reactive transport models for environmental remediation. Copyright © 2011 Elsevier Ltd. All rights reserved.

Control of Reactive Species Generated by Low-frequency Biased Nanosecond Pulse Discharge in Atmospheric Pressure Plasma Effluent

NASA Astrophysics Data System (ADS)

Takashima, Keisuke; Kaneko, Toshiro

2016-09-01

The control of hydroxyl radical and the other gas phase species generation in the ejected gas through air plasma (air plasma effluent) has been experimentally studied, which is a key to extend the range of plasma treatment. Nanosecond pulse discharge is known to produce high reduced electric field (E/N) discharge that leads to efficient generation of the reactive species than conventional low frequency discharge, while the charge-voltage cycle in the low frequency discharge is known to be well-controlled. In this study, the nanosecond pulse discharge biased with AC low frequency high voltage is used to take advantages of these discharges, which allows us to modulate the reactive species composition in the air plasma effluent. The utilization of the gas-liquid interface and the liquid phase chemical reactions between the modulated long-lived reactive species delivered from the air plasma effluent could realize efficient liquid phase chemical reactions leading to short-lived reactive species production far from the air plasma, which is crucial for some plasma agricultural applications.

Multi-Fluid Block-Adaptive-Tree Solar Wind Roe-Type Upwind Scheme: Magnetospheric Composition and Dynamics During Geomagnetic Storms, Initial Results

NASA Technical Reports Server (NTRS)

Gkocer, A.; Toth, G.; Ma, Y.; Gombosi, T.; Zhang, J. C.; Kistler, L. M.

2010-01-01

The magnetosphere contains a significant amount of ionospheric O{+}, particularly during geomagnetically active times. The presence of ionospheric plasma in the magnetosphere has a notable impact on magnetospheric composition and processes. We present a new multifluid MHD version of the BATS-R-US model of the magnetosphere to track the fate and consequences of ionospheric outflow. The multi-fluid MHD equations are presented as are the novel techniques for overcoming the formidable challenges associated with solving them. Our new model is then applied to the May 4, 1998 and March 31, 2001 geomagnetic storms. The results are juxtaposed with traditional single- fluid MHD and multispecies MHD simulations from a previous study, thereby allowing us to assess the benefits of using a more complex model with additional physics. We find that our multi-fluid MHD model (with outflow) gives comparable results to the multi-species MHD model (with outflow), including a more strongly negative Dst, reduced CPCP, and a drastically improved magnetic field at geosynchronous orbit, as compared to single-fluid MHD with no outflow. Significant differences in composition and magnetic field are found between the multi-species and multi-fluid approach further away from the Earth. We further demonstrate the ability to explore pressure and bulk velocity differences between H{+} and O(+}, which is not possible when utilizing the other techniques considered.

Defining Tropospheric Chemistry As A Heterogeneous Ensemble Of Reactive Air Parcels

NASA Astrophysics Data System (ADS)

Prather, M. J.; Zhu, X.; Flynn, C.; Mao, J.; Strode, S. A.; Steenrod, S. D.; Strahan, S. E.; Lamarque, J. F.; Fiore, A. M.; Horowitz, L. W.; Shindell, D. T.; Murray, L. T.

2016-12-01

Two major challenges in model-measurement comparisons have been: Which measurements are the most important to match? At what level do models need to simulate the variegated fine structures observed in trace gases and aerosols? This talk presents a novel approach for evaluating high-resolution global chemistry models (1/2 to 1 deg) that is integral to NASA's Atmospheric Tomography (ATom) mission. The approach seeks to develop a chemical climatology for tropospheric regions rather than just event-based testing of specific observations. It enables chemistry-climate models to be readily compared and more severely tested with observations. It uses the reactivity of air parcels (e.g., loss of methane, production and loss of ozone) to weight each parcel in terms of its importance in controlling the two most important chemically reactive greenhouse gases. It looks at the entire statistical distribution of air parcels in terms of a chemical phase space for those species that control the reactivity (e.g., O3, H2O, CH4, CO, NOx, HNO3, HNO4, PAN, CH3NO3, HCHO, HOOH, CH3OOH, C2H6, C3H6O, and other VOCs when present in sufficiently large abundances). It builds statistics of chemically extreme air parcels such as pollution layers to determine if a model failure to match such cases affects the overall reactivity of the region. This approach was designed for the ATom in situ measurements using the DC-8 to slice through the middle of the Pacific and Atlantic Ocean basins each season. The ATom payload will measure the above key trace gases and many other gases and aerosols in every designated air parcel (i.e., 10-sec averages). The first ATom measurements will not be available until mid-2017 and this presentation shows how this climatology looks when sampled with different models. Six global chemistry models have simulated one day in August (no particular year), and we sample all six showing how the 2D probability density plots highlight different regions when weighted by chemical reactivity. These models pre-simulation of ATom provide a target for the ATom measurements. The models also enable us to estimate the representativeness of ATom's single tomographic slice down the ocean basins, and therefore just how well we can observationally determine this chemical climatology of the reactivity of the troposphere.

Global distribution of alkyl nitrates and their impacts on reactive nitrogen in remote regions constrained by aircraft observations and chemical transport modeling

NASA Astrophysics Data System (ADS)

Fisher, J. A.; Atlas, E. L.; Blake, D. R.; Barletta, B.; Thompson, C. R.; Peischl, J.; Tzompa Sosa, Z. A.; Ryerson, T. B.; Murray, L. T.

2017-12-01

Nitrogen oxides (NO + NO­2 = NOx) are precursors in the formation of tropospheric ozone, contribute to the formation of aerosols, and enhance nitrogen deposition to ecosystems. While direct emissions tend to be localised over continental source regions, a significant source of NOx to the remote troposphere comes from degradation of other forms of reactive nitrogen. Long-lived, small chain alkyl nitrates (RONO2) including methyl, ethyl and propyl nitrates may be particularly significant forms of reactive nitrogen in the remote atmosphere as they are emitted directly by the ocean in regions where reactive nitrogen is otherwise very low. They also act as NOx reservoir species, sequestering NO­x in source regions and releasing it far downwind—and through this process may become increasingly important reservoirs as methane, ethane, and propane emissions grow. However, small RONO2 are not consistently included in global atmospheric chemistry models, and their distributions and impacts remain poorly constrained. In this presentation, we will describe a new RONO2 simulation in the GEOS-Chem chemical transport model evaluated using a large ensemble of aircraft observations collected over a 20-year period. The observations are largely concentrated over the Pacific Ocean, beginning with PEM-Tropics in the late 1990s and continuing through the recent HIPPO and ATom campaigns. Both observations and model show enhanced RONO2 in the tropical Pacific boundary layer that is consistent with a photochemical source in seawater. The model reproduces a similarly large enhancement over the southern ocean by assuming a large pool of oceanic RONO2 here, but the source of the seawater enhancement in this environment remains uncertain. We find that including marine RONO2 in the simulation is necessary to correct a large underestimate in simulated reactive nitrogen throughout the Pacific marine boundary layer. We also find that the impacts on NOx export from continental source regions are limited as RONO2 formation competes with other NO­x reservoirs such as PAN, leading to re-partitioning of reactive nitrogen rather than a net reactive nitrogen source. Further implications for NOx and ozone, as well as the impacts of recent changes in the global distribution of methane, ethane, propane, and NOx emissions, will also be discussed.

Renal oncocytoma characterized by the defective complex I of the respiratory chain boosts the synthesis of the ROS scavenger glutathione.

PubMed

Kürschner, Gerrit; Zhang, Qingzhou; Clima, Rosanna; Xiao, Yi; Busch, Jonas Felix; Kilic, Ergin; Jung, Klaus; Berndt, Nikolaus; Bulik, Sascha; Holzhütter, Hermann-Georg; Gasparre, Giuseppe; Attimonelli, Marcella; Babu, Mohan; Meierhofer, David

2017-12-01

Renal oncocytomas are rare benign tumors of the kidney and characterized by a deficient complex I (CI) enzyme activity of the oxidative phosphorylation (OXPHOS) system caused by mitochondrial DNA (mtDNA) mutations. Yet, little is known about the underlying molecular mechanisms and alterations of metabolic pathways in this tumor. We compared renal oncocytomas with adjacent matched normal kidney tissues on a global scale by multi-omics approaches, including whole exome sequencing (WES), proteomics, metabolomics, and metabolic pathway simulation. The abundance of proteins localized to mitochondria increased more than 2-fold, the only exception was a strong decrease in the abundance for CI subunits that revealed several pathogenic heteroplasmic mtDNA mutations by WES. We also observed renal oncocytomas to dysregulate main metabolic pathways, shunting away from gluconeogenesis and lipid metabolism. Nevertheless, the abundance of energy carrier molecules such as NAD + , NADH, NADP, ATP, and ADP were significantly higher in renal oncocytomas. Finally, a substantial 5000-fold increase of the reactive oxygen species scavenger glutathione can be regarded as a new hallmark of renal oncocytoma. Our findings demonstrate that renal oncocytomas undergo a metabolic switch to eliminate ATP consuming processes to ensure a sufficient energy supply for the tumor.

Renal oncocytoma characterized by the defective complex I of the respiratory chain boosts the synthesis of the ROS scavenger glutathione

PubMed Central

Clima, Rosanna; Xiao, Yi; Busch, Jonas Felix; Kilic, Ergin; Jung, Klaus; Berndt, Nikolaus; Bulik, Sascha; Holzhütter, Hermann-Georg; Gasparre, Giuseppe; Attimonelli, Marcella; Babu, Mohan; Meierhofer, David

2017-01-01

Renal oncocytomas are rare benign tumors of the kidney and characterized by a deficient complex I (CI) enzyme activity of the oxidative phosphorylation (OXPHOS) system caused by mitochondrial DNA (mtDNA) mutations. Yet, little is known about the underlying molecular mechanisms and alterations of metabolic pathways in this tumor. We compared renal oncocytomas with adjacent matched normal kidney tissues on a global scale by multi-omics approaches, including whole exome sequencing (WES), proteomics, metabolomics, and metabolic pathway simulation. The abundance of proteins localized to mitochondria increased more than 2-fold, the only exception was a strong decrease in the abundance for CI subunits that revealed several pathogenic heteroplasmic mtDNA mutations by WES. We also observed renal oncocytomas to dysregulate main metabolic pathways, shunting away from gluconeogenesis and lipid metabolism. Nevertheless, the abundance of energy carrier molecules such as NAD+, NADH, NADP, ATP, and ADP were significantly higher in renal oncocytomas. Finally, a substantial 5000-fold increase of the reactive oxygen species scavenger glutathione can be regarded as a new hallmark of renal oncocytoma. Our findings demonstrate that renal oncocytomas undergo a metabolic switch to eliminate ATP consuming processes to ensure a sufficient energy supply for the tumor. PMID:29285300

Formation, characterization, and dynamics of onion-like carbon structures for electrical energy storage from nanodiamonds using reactive force fields

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

Ganesh, P.; Kent, P. R. C.; Mochalin, V.

We simulate the experimentally observed graphitization of nanodiamonds into multi-shell onion-like carbonnanostructures, also called carbon onions, at different temperatures, using reactive force fields. The simulations include long-range Coulomb and van der Waals interactions. Our results suggest that long-range interactions play a crucial role in the phase-stability and the graphitization process. Graphitization is both enthalpically and entropically driven and can hence be controlled with temperature. The outer layers of the nanodiamond have a lower kinetic barrier toward graphitization irrespective of the size of the nanodiamond and graphitize within a few-hundred picoseconds, with a large volume increase. The inner core of themore » nanodiamonds displays a large size-dependent kinetic barrier, and graphitizes much more slowly with abrupt jumps in the internal energy. It eventually graphitizes by releasing pressure and expands once the outer shells have graphitized. The degree of transformation at a particular temperature is thereby determined by a delicate balance between the thermal energy, long-range interactions, and the entropic/enthalpic free energy gained by graphitization. Upon full graphitization, a multi-shell carbonnanostructure appears, with a shell-shell spacing of about ~3.4 Å for all sizes. The shells are highly defective with predominantly five- and seven-membered rings to curve space. Larger nanodiamonds with a diameter of 4 nm can graphitize into spiral structures with a large (~29-atom carbon ring) pore opening on the outermost shell. Such a large one-way channel is most attractive for a controlled insertion of molecules/ions such as Li ions, water, or ionic liquids, for increased electrochemical capacitor or battery electrode applications.« less

Formation, characterization and dynamics of onion like carbon structures from nanodiamonds using reactive force-fields for electrical energy storage

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

Kent, Paul R

We simulate the experimentally observed graphitization of nanodiamonds into multi-shell onion-like carbon nanostructures, also called carbon onions, at different temperatures, using reactive force fields. The simulations include long-range Coulomb and van der Waals interactions. Our results suggest that long-range interactions play a crucial role in the phase-stability and the graphitization process. Graphitization is both enthalpically and entropically driven and can hence be controlled with temperature. The outer layers of the nanodiamond have a lower kinetic barrier toward graphitization irrespective of the size of the nanodiamond and graphitize within a few-hundred picoseconds, with a large volume increase. The inner core ofmore » the nanodiamonds displays a large size-dependent kinetic barrier, and graphitizes much more slowly with abrupt jumps in the internal energy. It eventually graphitizes by releasing pressure and expands once the outer shells have graphitized. The degree of transformation at a particular temperature is thereby determined by a delicate balance between the thermal energy, long-range interactions, and the entropic/enthalpic free energy gained by graphitization. Upon full graphitization, a multi-shell carbon nanostructure appears, with a shell-shell spacing of about {approx}3.4 {angstrom} for all sizes. The shells are highly defective with predominantly five- and seven-membered rings to curve space. Larger nanodiamonds with a diameter of 4 nm can graphitize into spiral structures with a large ({approx}29-atom carbon ring) pore opening on the outermost shell. Such a large one-way channel is most attractive for a controlled insertion of molecules/ions such as Li ions, water, or ionic liquids, for increased electrochemical capacitor or battery electrode applications.« less

Verification of low-Mach number combustion codes using the method of manufactured solutions

NASA Astrophysics Data System (ADS)

Shunn, Lee; Ham, Frank; Knupp, Patrick; Moin, Parviz

2007-11-01

Many computational combustion models rely on tabulated constitutive relations to close the system of equations. As these reactive state-equations are typically multi-dimensional and highly non-linear, their implications on the convergence and accuracy of simulation codes are not well understood. In this presentation, the effects of tabulated state-relationships on the computational performance of low-Mach number combustion codes are explored using the method of manufactured solutions (MMS). Several MMS examples are developed and applied, progressing from simple one-dimensional configurations to problems involving higher dimensionality and solution-complexity. The manufactured solutions are implemented in two multi-physics hydrodynamics codes: CDP developed at Stanford University and FUEGO developed at Sandia National Laboratories. In addition to verifying the order-of-accuracy of the codes, the MMS problems help highlight certain robustness issues in existing variable-density flow-solvers. Strategies to overcome these issues are briefly discussed.

Reacting Multi-Species Gas Capability for USM3D Flow Solver

NASA Technical Reports Server (NTRS)

Frink, Neal T.; Schuster, David M.

2012-01-01

The USM3D Navier-Stokes flow solver contributed heavily to the NASA Constellation Project (CxP) as a highly productive computational tool for generating the aerodynamic databases for the Ares I and V launch vehicles and Orion launch abort vehicle (LAV). USM3D is currently limited to ideal-gas flows, which are not adequate for modeling the chemistry or temperature effects of hot-gas jet flows. This task was initiated to create an efficient implementation of multi-species gas and equilibrium chemistry into the USM3D code to improve its predictive capabilities for hot jet impingement effects. The goal of this NASA Engineering and Safety Center (NESC) assessment was to implement and validate a simulation capability to handle real-gas effects in the USM3D code. This document contains the outcome of the NESC assessment.

The Food Contaminants Nivalenol and Deoxynivalenol Induce Inflammation in Intestinal Epithelial Cells by Regulating Reactive Oxygen Species Release.

PubMed

Adesso, Simona; Autore, Giuseppina; Quaroni, Andrea; Popolo, Ada; Severino, Lorella; Marzocco, Stefania

2017-12-11

Fusarium mycotoxins are fungal metabolites whose ability to affect cereal grains as multi-contaminants is progressively increasing. The trichothecene mycotoxins nivalenol (NIV) and deoxynivalenol (DON) are often found in almost all agricultural commodities worldwide. They are able to affect animal and human health, including at the intestinal level. In this study, NIV, both alone and in combination with DON, induced inflammation and increased the inflammatory response induced by lipopolysaccharide (LPS) plus Interferon-γ (IFN) in the non-tumorigenic intestinal epithelial cell line (IEC-6). The inflammatory response induced by NIV and DON involves tumor necrosis factor-α (TNF-α) production, inducible nitric oxide synthase (iNOS) and cyclooxygenase-2 (COX-2) expression, nitrotyrosine formation, reactive oxygen species (ROS) release, Nuclear Factor-κB (NF-κB), Nuclear factor (erythroid-derived 2)-like 2 (Nrf2) and inflammasome activation. The pro-inflammatory effect was strongly induced by NIV and by the mycotoxin mixture, when compared to DON alone. Mechanistic studies indicate a pivotal role for ROS in the observed pro-inflammatory effects induced by mycotoxins. In this study, the interactions between NIV and DON point out the importance of their food co-contamination, further highlighting the risk assessment process that is of growing concern.

Interactions between plasma-treated carbon nanotubes and electrically neutral materials

NASA Astrophysics Data System (ADS)

Ogawa, Daisuke; Nakamura, Keiji

2014-10-01

A plasma treatment can create dangling bonds on the surface of carbon nanotubes (CNTs). The dangling bonds are so reactive that the bonds possibly interact with other neutral species even out of the plasma if the lifetime of the bonds is effectively long. In order to have good understandings with the interactions, we placed multi-wall CNTs (MWCNTs) in atmospheric dielectric barrier discharge that was created in a closed environment with the voltage at 5 kV. We set 50 W for the operating power and 15 minutes for the process time for this plasma treatment. Our preliminary results showed that the reaction between dangling bonds and neutrals likely occurred in the situation when CNTs were treated with argon plasma, and then exposed in a nitrogen-rich dry box. We did Fourier transform infrared (FTIR) spectroscopy after the treatments. The measurement showed that the spectrum with plasma-treated CNTs was different from pristine CNTs. This is an indication that the plasma-treated CNTs have reactive cites on the surface even after the discharge (~ minutes), and then the CNTs likely reacted with the neutral species that causes the different spectrum. In this poster, we will show more details from our results and further progresses from this research.

Prolonged exposure of resveratrol induces reactive superoxide species-independent apoptosis in murine prostate cells.

PubMed

Kumar, Sanjay; Stokes, James; Singh, Udai P; Scissum-Gunn, Karyn; Singh, Rajesh; Manne, Upender; Mishra, Manoj K

2017-10-01

Nitric oxide, a signaling molecule, inhibits mitochondrial respiration by binding with cytochrome c oxidase, resulting in elevated production of reactive superoxide species (reactive oxygen and nitrogen) in the mitochondria and increased susceptibility to cell death. Generation of mitochondrial superoxide species can be suppressed by natural compounds such as resveratrol, a dietary polyphenol found in the skin of red fruits. In various cancer cells, resveratrol shows anti-oxidant and cancer preventive properties. Since, the effect of resveratrol on reactive superoxide species-independent apoptosis in prostate cancer cells is not well illustrated; therefore, we investigated this phenomenon in TRAMP murine prostate cancer cells. To accomplish this, TRAMP cells were incubated with resveratrol, resveratrol + DETA-NONOate, DETA-NONOate (nitric oxide donor), resveratrol + L-NMMA, or L-NMMA (nitric oxide inhibitor) for 48 h, and reactive superoxide species in the mitochondria and culture supernatant were measured. In addition, the mitochondrial membrane potential, cell viability, expression of apoptotic markers (Bax and Bcl2), γ-H2A.x, p53, and caspase-3 was determined. We found that resveratrol suppressed reactive superoxide species such as reactive oxygen species in the mitochondria and nitric oxide in culture supernatant when compared to the DETA-NONOate treatment and disrupted the mitochondrial membrane potential. Resveratrol also reduced cell viability, altered the expression of apoptotic markers (Bax and Bcl2), and increased expression of γ-H2A.x (indicative marker of DNA fragmentation) and p53 (a critical DNA damage response protein). However, there was no appreciable modulation of the caspase-3. Therefore, our data suggest that resveratrol induces superoxide species-independent apoptosis and may act as a therapeutic agent against prostate cancer.

Multimillion Atom Reactive Simulations of Nanostructured Energetic Materials

DTIC Science & Technology

2007-08-01

code) 2007 Reprint Aug 2006-Aug 2007 Multimillion Atom Reactive Simulations of Nanostructured Energetic Materials W911NF-04-1-0178 sub 2781-USC-DOA...Priya Vashishta 213 821 2663 Reset Multimillion Atom Reactive Simulations of Nanostructured Energetic Materials Priya Vashishta,∗ Rajiv K. Kalia...function of the particle velocity that drives the shock [18]. The MD and experimental data agree very well. Furthermore, the simulation shows a sudden

The Reactive Species Interactome: Evolutionary Emergence, Biological Significance, and Opportunities for Redox Metabolomics and Personalized Medicine.

PubMed

Cortese-Krott, Miriam M; Koning, Anne; Kuhnle, Gunter G C; Nagy, Peter; Bianco, Christopher L; Pasch, Andreas; Wink, David A; Fukuto, Jon M; Jackson, Alan A; van Goor, Harry; Olson, Kenneth R; Feelisch, Martin

2017-10-01

Oxidative stress is thought to account for aberrant redox homeostasis and contribute to aging and disease. However, more often than not, administration of antioxidants is ineffective, suggesting that our current understanding of the underlying regulatory processes is incomplete. Recent Advances: Similar to reactive oxygen species and reactive nitrogen species, reactive sulfur species are now emerging as important signaling molecules, targeting regulatory cysteine redox switches in proteins, affecting gene regulation, ion transport, intermediary metabolism, and mitochondrial function. To rationalize the complexity of chemical interactions of reactive species with themselves and their targets and help define their role in systemic metabolic control, we here introduce a novel integrative concept defined as the reactive species interactome (RSI). The RSI is a primeval multilevel redox regulatory system whose architecture, together with the physicochemical characteristics of its constituents, allows efficient sensing and rapid adaptation to environmental changes and various other stressors to enhance fitness and resilience at the local and whole-organism level. To better characterize the RSI-related processes that determine fluxes through specific pathways and enable integration, it is necessary to disentangle the chemical biology and activity of reactive species (including precursors and reaction products), their targets, communication systems, and effects on cellular, organ, and whole-organism bioenergetics using system-level/network analyses. Understanding the mechanisms through which the RSI operates will enable a better appreciation of the possibilities to modulate the entire biological system; moreover, unveiling molecular signatures that characterize specific environmental challenges or other forms of stress will provide new prevention/intervention opportunities for personalized medicine. Antioxid. Redox Signal. 00, 000-000.

Effect of Heat Processing on IgE Reactivity and Cross-Reactivity of Tropomyosin and Other Allergens of Asia-Pacific Mollusc Species: Identification of Novel Sydney Rock Oyster Tropomyosin Sac g 1.

PubMed

Rolland, Jennifer M; Varese, Nirupama P; Abramovitch, Jodie B; Anania, Jessica; Nugraha, Roni; Kamath, Sandip; Hazard, Anita; Lopata, Andreas L; O'Hehir, Robyn E

2018-05-14

Shellfish allergy is an increasing global health priority, frequently affecting adults. Molluscs are an important shellfish group causing food allergy but knowledge of their allergens and cross-reactivity is limited. Optimal diagnosis of mollusc allergy enabling accurate advice on food avoidance is difficult. We characterized allergens of four frequently ingested Asia-Pacific molluscs: Sydney Rock Oyster (Saccostrea glomerata), Blue Mussel (Mytilus edulis), Saucer Scallop (Amusium balloti) and Southern Calamari (Sepioteuthis australis), examining cross-reactivity between species and with Blue Swimmer Crab tropomyosin, Por p 1. IgE ELISA showed that cooking increased IgE reactivity of mollusc extracts and basophil activation confirmed biologically relevant IgE reactivity. Immunoblotting demonstrated strong IgE reactivity of several proteins including one corresponding to heat-stable tropomyosin in all species (37-40 kDa). IgE-reactive Sydney Rock Oyster proteins were identified by mass spectrometry, and the novel major oyster tropomyosin allergen was cloned, sequenced and designated Sac g 1 by the IUIS. Oyster extracts showed highest IgE cross-reactivity with other molluscs, while mussel cross-reactivity was weakest. Inhibition immunoblotting demonstrated high cross-reactivity between tropomyosins of mollusc and crustacean species. These findings inform novel approaches for reliable diagnosis and improved management of mollusc allergy. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

Characterisation of two-stage ignition in diesel engine-relevant thermochemical conditions using direct numerical simulation

DOE PAGES

Krisman, Alex; Hawkes, Evatt R.; Talei, Mohsen; ...

2016-08-30

With the goal of providing a more detailed fundamental understanding of ignition processes in diesel engines, this study reports analysis of a direct numerical simulation (DNS) database. In the DNS, a pseudo turbulent mixing layer of dimethyl ether (DME) at 400 K and air at 900 K is simulated at a pressure of 40 atmospheres. At these conditions, DME exhibits a two-stage ignition and resides within the negative temperature coefficient (NTC) regime of ignition delay times, similar to diesel fuel. The analysis reveals a complex ignition process with several novel features. Autoignition occurs as a distributed, two-stage event. The high-temperaturemore » stage of ignition establishes edge flames that have a hybrid premixed/autoignition flame structure similar to that previously observed for lifted laminar flames at similar thermochemical conditions. In conclusion, a combustion mode analysis based on key radical species illustrates the multi-stage and multi-mode nature of the ignition process and highlights the substantial modelling challenge presented by diesel combustion.« less

Interactions between multiple filaments and bacterial biofilms on the surface of an apple

NASA Astrophysics Data System (ADS)

He, CHENG; Maoyuan, XU; Shuhui, PAN; Xinpei, LU; Dawei, LIU

2018-04-01

In this paper, the interactions between two dielectric barrier discharge (DBD) filaments and three bacterial biofilms are simulated. The modeling of a DBD streamer is studied by means of 2D finite element calculation. The model is described by the proper governing equations of air DBD at atmospheric pressure and room temperature. The electric field in the computing domain and the self-consistent transportation of reactive species between a cathode and biofilms on the surface of an apple are realized by solving a Poisson equation and continuity equations. The electron temperature is solved by the electron energy conservation equation. The conductivity and permittivity of bacterial biofilms are considered, and the shapes of the bacterial biofilms are irregular in the uncertainty and randomness of colony growth. The distribution of the electrons suggests that two plasma channels divide into three plasma channels when the streamer are 1 mm from the biofilms. The toe-shapes of the biofilms and the simultaneous effect of two streamer heads result in a high electric field around the biofilms, therefore the stronger ionization facilitates the major part of two streamers combined into one streamer and three streamers arise. The distribution of the reactive oxygen species and the reactive nitrogen species captured by time fluences are non-uniform due to the toe-shaped bacterial biofilms. However, the plasma can intrude into the cavities in the adjacent biofilms due to the μm-scale mean free path. The two streamers case has a larger treatment area and realizes the simultaneous treatment of three biofilms compared with one streamer case.

Hormesis enables cells to handle accumulating toxic metabolites during increased energy flux.

PubMed

Zemva, Johanna; Fink, Christoph Andreas; Fleming, Thomas Henry; Schmidt, Leonard; Loft, Anne; Herzig, Stephan; Knieß, Robert André; Mayer, Matthias; Bukau, Bernd; Nawroth, Peter Paul; Tyedmers, Jens

2017-10-01

Energy production is inevitably linked to the generation of toxic metabolites, such as reactive oxygen and carbonyl species, known as major contributors to ageing and degenerative diseases. It remains unclear how cells can adapt to elevated energy flux accompanied by accumulating harmful by-products without taking any damage. Therefore, effects of a sudden rise in glucose concentrations were studied in yeast cells. This revealed a feedback mechanism initiated by the reactive dicarbonyl methylglyoxal, which is formed non-enzymatically during glycolysis. Low levels of methylglyoxal activate a multi-layered defence response against toxic metabolites composed of prevention, detoxification and damage remission. The latter is mediated by the protein quality control system and requires inducible Hsp70 and Btn2, the aggregase that sequesters misfolded proteins. This glycohormetic mechanism enables cells to pre-adapt to rising energy flux and directly links metabolic to proteotoxic stress. Further data suggest the existence of a similar response in endothelial cells. Copyright © 2017 The Authors. Published by Elsevier B.V. All rights reserved.

Shock Waves and Defects in Energetic Materials, a Match Made in MD Heaven

NASA Astrophysics Data System (ADS)

Wood, Mitchell; Kittell, David; Yarrington, Cole; Thompson, Aidan

2017-06-01

Shock wave interactions with defects, such as pores, are known to play a key role in the chemical initiation of energetic materials. In this talk the shock response of Hexanitrostilbene (HNS) is studied through large scale reactive molecular dynamics (RMD) simulations. These RMD simulations provide a unique opportunity to elucidate mechanisms of viscoplastic pore collapse which are often neglected in larger scale hydrodynamic models. A discussion of the macroscopic effects of this viscoplastic material response, such as its role in hot spot formation and eventual initiation, will be provided. Through this work we have been able to map a transition from purely viscoplastic to fluid-like pore collapse that is a function of shock strength, pore size and material strength. In addition, these findings are important reference data for the validation of future multi-scale modeling efforts of the shock response of heterogeneous materials. Examples of how these RMD results are translated into mesoscale models will also be addressed. Sandia National Laboratories is a multi-program laboratory managed and operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Corporation, for the US DOE NNSA under Contract No. DE- AC04-94AL85000.

Hydroxyl radical measurements and oxidation capacity in a boreal forest environment

NASA Astrophysics Data System (ADS)

Hens, K.; Tatum Ernest, C.; Novelli, A.; Paasonen, P.; Sipilä, M.; Petäjä, T.; Nölscher, A.; Taraborrelli, D.; Keronen, P.; Trawny, K.; Kubistin, D.; Oswald, R.; Axinte, R.; Hosaynali Beygi, Z.; Auld, J.; Klüpfel, T.; Mesarchaki, E.; Song, W.; Valverde Canossa, J.; González Orozco, D.; Königstedt, R.; Bohn, B.; Rudolf, M.; Fischer, H.; Williams, J.; Crowley, J.; Martinez, M.; Harder, H. D.; Lelieveld, J.

2012-12-01

Forests cover about one third of the earth's total land surface and are known to be an important global source of biogenic volatile organic compounds (BVOCs) that are partly very reactive towards OH. Different types of forests are known to emit various characteristic BVOCs significantly influencing atmospheric oxidation chemistry. Measurements of OH and HO2 radicals in forest environments, however, reveal a serious lack of understanding of the underlying processes. The HUMPPA-COPEC intensive field campaign took place in summer 2010 at the SMEAR II station, located in Hyytiälä, Southern Finland, as collaboration between the Max Planck Institute for Chemistry and the University of Helsinki. The main goal of the campaign was to investigate the summertime emissions and photochemistry in a boreal forest. Comprehensive measurements including observations of many VOCs, HOx, and total OH reactivity were conducted to increase our understanding of atmospheric self-cleaning processes based on detailed analysis of production and loss mechanisms of the hydroxyl radical. Also the HOx budget in a coniferous forest was examined by using direct calculations from measured species as well as an observationally constrained chemical box model in steady state. For HUMPPA-COPEC chemical reaction schemes considering isoprene as the predominant primary BVOC lead to an over prediction of the measured OH concentration by a factor of up to 4. However, only a minor fraction of the measured total OH reactivity can be explained by measured isoprene. A preliminary terpene mechanism, taking the most abundant terpenes measured during HUMPPA-COPEC-2010 and their oxidation products into account, improves the agreement between simulated and measured OH, but is not sufficient to explain the missing OH reactivity in all cases. HO2 is described reasonably well by the model for conditions where the modeled and measured total OH reactivity agree. For lower than measured reactivity, the HO2 mixing ratios are significantly under predicted indicating that the missing reactivity is an unaccounted source of HO2. An additional α-pinene equivalent is introduced into the model to match the measured total OH reactivity with the simulated one. The modification of the chemical mechanism is analyzed and discussed.

Photodegradation of Paracetamol in Nitrate Solution

NASA Astrophysics Data System (ADS)

Meng, Cui; Qu, Ruijuan; Liang, Jinyan; Yang, Xi

2010-11-01

The photodegradation of paracetamol in nitrate solution under simulated solar irradiation has been investigated. The degradation rates were compared by varying environmental parameters including concentrations of nitrate ion, humic substance and pH values. The quantifications of paracetamol were conducted by HPLC method. The results demonstrate that the photodegradation of paracetamol followed first-order kinetics. The photoproducts and intermediates of paracetamol in the presence of nitrate ions were identified by extensive GC-MS method. The photodegradation pathways involving. OH radicals as reactive species were proposed.

Photodegradation of Paracetamol in Nitrate Solution

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

Meng Cui; Qu Ruijuan; Liang Jinyan

2010-11-24

The photodegradation of paracetamol in nitrate solution under simulated solar irradiation has been investigated. The degradation rates were compared by varying environmental parameters including concentrations of nitrate ion, humic substance and pH values. The quantifications of paracetamol were conducted by HPLC method. The results demonstrate that the photodegradation of paracetamol followed first-order kinetics. The photoproducts and intermediates of paracetamol in the presence of nitrate ions were identified by extensive GC-MS method. The photodegradation pathways involving. OH radicals as reactive species were proposed.

Reactivity-based drug discovery using vitamin B(6)-derived pharmacophores.

PubMed

Wondrak, Georg T

2008-05-01

Endogenous reactive intermediates including photoexcited states of tissue chromophores, reactive oxygen species (ROS), reactive carbonyl species (RCS), transition metal ions, and Schiff bases have been implicated in the initiation and progression of diverse human pathologies including tumorigenesis, atherosclerosis, diabetes, and neurodegenerative disease. In contrast to structure-based approaches that target macromolecules by selective ligands, reactivity-based drug discovery uses chemical reagents as therapeutics that target reactive chemical species involved in human pathology. Reactivity-based design of prototype agents that effectively antagonize, modulate, and potentially even reverse the chemistry underlying tissue damage from oxidative and carbonyl stress therefore holds great promise in delivering significant therapeutic benefit. Apart from its established role as an essential cofactor for numerous enzymes, a large body of evidence suggests that B(6)-vitamers contain reactive pharmacophores that mediate therapeutically useful non-vitamin drug actions as potent antioxidants, metal chelators, carbonyl scavengers, Schiff base forming agents, and photosensitizers. Based on the fascinating chemical versatility of B(6)-derived pharmacophores, B(6)-vitamers are therefore promising lead compounds for reactivity-based drug design.

Water-driven micromotors for rapid photocatalytic degradation of biological and chemical warfare agents.

PubMed

Li, Jinxing; Singh, Virendra V; Sattayasamitsathit, Sirilak; Orozco, Jahir; Kaufmann, Kevin; Dong, Renfeng; Gao, Wei; Jurado-Sanchez, Beatriz; Fedorak, Yuri; Wang, Joseph

2014-11-25

Threats of chemical and biological warfare agents (CBWA) represent a serious global concern and require rapid and efficient neutralization methods. We present a highly effective micromotor strategy for photocatalytic degradation of CBWA based on light-activated TiO2/Au/Mg microspheres that propel autonomously in natural water and obviate the need for external fuel, decontaminating reagent, or mechanical agitation. The activated TiO2/Au/Mg micromotors generate highly reactive oxygen species responsible for the efficient destruction of the cell membranes of the anthrax simulant Bacillus globigii spore, as well as rapid and complete in situ mineralization of the highly persistent organophosphate nerve agents into nonharmful products. The water-driven propulsion of the TiO2/Au/Mg micromotors facilitates efficient fluid transport and dispersion of the photogenerated reactive oxidative species and their interaction with the CBWA. Coupling of the photocatalytic surface of the micromotors and their autonomous water-driven propulsion thus leads to a reagent-free operation which holds a considerable promise for diverse "green" defense and environmental applications.

Photocatalytic reactive oxygen species production and phototoxicity of titanium dioxide nanoparticles are dependent on the solar ultraviolet radiation spectrum.

PubMed

Ma, Hongbo; Brennan, Amanda; Diamond, Stephen A

2012-09-01

Generation of reactive oxygen species (ROS) by titanium dioxide nanoparticles (nano-TiO(2)) and its consequent phototoxicity to Daphnia magna were measured under different solar ultraviolet (UV) spectra by applying a series of optical filters in a solar simulator. Removing UV-B (280-320 nm) from solar radiation had no significant impact on photocatalytic ROS production of nano-TiO(2), whereas removal of UV-A (320-400 nm) decreased ROS production remarkably. Removal of wavelengths below 400 nm resulted in negligible ROS production. A linear correlation between ROS production and D. magna immobilization suggests that photocatalytic ROS production may be a predictor of phototoxicity for nano-TiO(2). Intracellular ROS production within D. magna was consistent with the immobilization of the organism under different solar UV spectra, indicating that oxidative stress was involved in phototoxicity. The dependence of nano-TiO(2) phototoxicity on environmentally realistic variations in solar radiation suggests that risk assessment of these nanomaterials requires careful evaluation of exposure conditions in the environment. Copyright © 2012 SETAC.

Calculation of singlet oxygen formation from one photon absorbing photosensitizers used in PDT

NASA Astrophysics Data System (ADS)

Potasek, M.; Parilov, Evgueni; Beeson, K.

2013-03-01

Advances in biophotonic medicine require new information on photodynamic mechanisms. In photodynamic therapy (PDT), a photosensitizer (PS) is injected into the body and accumulates at higher concentrations in diseased tissue compared to normal tissue. The PS absorbs light from a light source and generates excited-state triplet states of the PS. The excited triplet states of the PS can then react with ground state molecular oxygen to form excited singlet - state oxygen or form other highly reactive species. The reactive species react with living cells, resulting in cel l death. This treatment is used in many forms of cancer including those in the prostrate, head and neck, lungs, bladder, esophagus and certain skin cancers. We developed a novel numerical method to model the photophysical and photochemical processes in the PS and the subsequent energy transfer to O2, improving the understanding of these processes at a molecular level. Our numerical method simulates light propagation and photo-physics in PS using methods that build on techniques previously developed for optical communications and nonlinear optics applications.

Geochemical Reaction Mechanism Discovery from Molecular Simulation

DOE PAGES

Stack, Andrew G.; Kent, Paul R. C.

2014-11-10

Methods to explore reactions using computer simulation are becoming increasingly quantitative, versatile, and robust. In this review, a rationale for how molecular simulation can help build better geochemical kinetics models is first given. We summarize some common methods that geochemists use to simulate reaction mechanisms, specifically classical molecular dynamics and quantum chemical methods and discuss their strengths and weaknesses. Useful tools such as umbrella sampling and metadynamics that enable one to explore reactions are discussed. Several case studies wherein geochemists have used these tools to understand reaction mechanisms are presented, including water exchange and sorption on aqueous species and mineralmore » surfaces, surface charging, crystal growth and dissolution, and electron transfer. The impact that molecular simulation has had on our understanding of geochemical reactivity are highlighted in each case. In the future, it is anticipated that molecular simulation of geochemical reaction mechanisms will become more commonplace as a tool to validate and interpret experimental data, and provide a check on the plausibility of geochemical kinetic models.« less

CO 2 leakage impacts on shallow groundwater. Field-scale reactive-transport simulations informed by observations at a natural analog site

DOE PAGES

Keating, Elizabeth H.; Hakala, J. Alexandra; Viswanathan, Hari; ...

2013-03-01

It is challenging to predict the degree to which shallow groundwater might be affected by leaks from a CO 2 sequestration reservoir, particularly over long time scales and large spatial scales. In this study observations at a CO 2 enriched shallow aquifer natural analog were used to develop a predictive model which is then used to simulate leakage scenarios. This natural analog provides the opportunity to make direct field observations of groundwater chemistry in the presence of elevated CO 2, to collect aquifer samples and expose them to CO 2 under controlled conditions in the laboratory, and to test themore » ability of multiphase reactive transport models to reproduce measured geochemical trends at the field-scale. The field observations suggest that brackish water entrained with the upwelling CO 2 are a more significant source of trace metals than in situ mobilization of metals due to exposure to CO 2. The study focuses on a single trace metal of concern at this site: U. Experimental results indicate that cation exchange/adsorption and dissolution/precipitation of calcite containing trace amounts of U are important reactions controlling U in groundwater at this site, and that the amount of U associated with calcite is fairly well constrained. Simulations incorporating these results into a 3-D multi-phase reactive transport model are able to reproduce the measured ranges and trends between pH, pCO 2, Ca, total C, U and Cl -at the field site. Although the true fluxes at the natural analog site are unknown, the cumulative CO 2 flux inferred from these simulations are approximately equivalent to 37.8E-3 MT, approximately corresponding to a .001% leak rate for injection at a large (750 MW) power plant. The leakage scenario simulations suggest that if the leak only persists for a short time the volume of aquifer contaminated by CO 2-induced mobilization of U will be relatively small, yet persistent over 100 a.« less

Using Paraquat to Generate Anion Free Radicals and Hydrogen Peroxide in "In Vitro": Antioxidant Effect of Vitamin E--A Procedure to Teach Theoretical and Experimental Principles of Reactive Oxygen Species Biochemistry

ERIC Educational Resources Information Center

Jimenez-Del-Rio, Marlene; Suarez-Cedeno, Gerson; Velez-Pardo, Carlos

2010-01-01

The theoretical basis of reactive oxygen species and their impact on health issues are relatively easy to understand by biomedical students. The detection of reactive oxygen species requires expensive equipment, the procedures are time consuming and costly, and the results are hard to interpret. Moreover, cause-and-effect relationships in the…

Evaluating species richness: biased ecological inference results from spatial heterogeneity in species detection probabilities

USGS Publications Warehouse

McNew, Lance B.; Handel, Colleen M.

2015-01-01

Accurate estimates of species richness are necessary to test predictions of ecological theory and evaluate biodiversity for conservation purposes. However, species richness is difficult to measure in the field because some species will almost always be overlooked due to their cryptic nature or the observer's failure to perceive their cues. Common measures of species richness that assume consistent observability across species are inviting because they may require only single counts of species at survey sites. Single-visit estimation methods ignore spatial and temporal variation in species detection probabilities related to survey or site conditions that may confound estimates of species richness. We used simulated and empirical data to evaluate the bias and precision of raw species counts, the limiting forms of jackknife and Chao estimators, and multi-species occupancy models when estimating species richness to evaluate whether the choice of estimator can affect inferences about the relationships between environmental conditions and community size under variable detection processes. Four simulated scenarios with realistic and variable detection processes were considered. Results of simulations indicated that (1) raw species counts were always biased low, (2) single-visit jackknife and Chao estimators were significantly biased regardless of detection process, (3) multispecies occupancy models were more precise and generally less biased than the jackknife and Chao estimators, and (4) spatial heterogeneity resulting from the effects of a site covariate on species detection probabilities had significant impacts on the inferred relationships between species richness and a spatially explicit environmental condition. For a real dataset of bird observations in northwestern Alaska, the four estimation methods produced different estimates of local species richness, which severely affected inferences about the effects of shrubs on local avian richness. Overall, our results indicate that neglecting the effects of site covariates on species detection probabilities may lead to significant bias in estimation of species richness, as well as the inferred relationships between community size and environmental covariates.

Assessing uncertainties in crop and pasture ensemble model simulations of productivity and N2 O emissions.

PubMed

Ehrhardt, Fiona; Soussana, Jean-François; Bellocchi, Gianni; Grace, Peter; McAuliffe, Russel; Recous, Sylvie; Sándor, Renáta; Smith, Pete; Snow, Val; de Antoni Migliorati, Massimiliano; Basso, Bruno; Bhatia, Arti; Brilli, Lorenzo; Doltra, Jordi; Dorich, Christopher D; Doro, Luca; Fitton, Nuala; Giacomini, Sandro J; Grant, Brian; Harrison, Matthew T; Jones, Stephanie K; Kirschbaum, Miko U F; Klumpp, Katja; Laville, Patricia; Léonard, Joël; Liebig, Mark; Lieffering, Mark; Martin, Raphaël; Massad, Raia S; Meier, Elizabeth; Merbold, Lutz; Moore, Andrew D; Myrgiotis, Vasileios; Newton, Paul; Pattey, Elizabeth; Rolinski, Susanne; Sharp, Joanna; Smith, Ward N; Wu, Lianhai; Zhang, Qing

2018-02-01

Simulation models are extensively used to predict agricultural productivity and greenhouse gas emissions. However, the uncertainties of (reduced) model ensemble simulations have not been assessed systematically for variables affecting food security and climate change mitigation, within multi-species agricultural contexts. We report an international model comparison and benchmarking exercise, showing the potential of multi-model ensembles to predict productivity and nitrous oxide (N 2 O) emissions for wheat, maize, rice and temperate grasslands. Using a multi-stage modelling protocol, from blind simulations (stage 1) to partial (stages 2-4) and full calibration (stage 5), 24 process-based biogeochemical models were assessed individually or as an ensemble against long-term experimental data from four temperate grassland and five arable crop rotation sites spanning four continents. Comparisons were performed by reference to the experimental uncertainties of observed yields and N 2 O emissions. Results showed that across sites and crop/grassland types, 23%-40% of the uncalibrated individual models were within two standard deviations (SD) of observed yields, while 42 (rice) to 96% (grasslands) of the models were within 1 SD of observed N 2 O emissions. At stage 1, ensembles formed by the three lowest prediction model errors predicted both yields and N 2 O emissions within experimental uncertainties for 44% and 33% of the crop and grassland growth cycles, respectively. Partial model calibration (stages 2-4) markedly reduced prediction errors of the full model ensemble E-median for crop grain yields (from 36% at stage 1 down to 4% on average) and grassland productivity (from 44% to 27%) and to a lesser and more variable extent for N 2 O emissions. Yield-scaled N 2 O emissions (N 2 O emissions divided by crop yields) were ranked accurately by three-model ensembles across crop species and field sites. The potential of using process-based model ensembles to predict jointly productivity and N 2 O emissions at field scale is discussed. © 2017 John Wiley & Sons Ltd.

Multi-parametric analysis of phagocyte antimicrobial responses using imaging flow cytometry.

PubMed

Havixbeck, Jeffrey J; Wong, Michael E; More Bayona, Juan A; Barreda, Daniel R

2015-08-01

We feature a multi-parametric approach based on an imaging flow cytometry platform for examining phagocyte antimicrobial responses against the gram-negative bacterium Aeromonas veronii. This pathogen is known to induce strong inflammatory responses across a broad range of animal species, including humans. We examined the contribution of A. veronii to the induction of early phagocyte inflammatory processes in RAW 264.7 murine macrophages in vitro. We found that A. veronii, both in live or heat-killed forms, induced similar levels of macrophage activation based on NF-κB translocation. Although these macrophages maintained high levels of viability following heat-killed or live challenges with A. veronii, we identified inhibition of macrophage proliferation as early as 1h post in vitro challenge. The characterization of phagocytic responses showed a time-dependent increase in phagocytosis upon A. veronii challenge, which was paired with a robust induction of intracellular respiratory burst responses. Interestingly, despite the overall increase in the production of reactive oxygen species (ROS) among RAW 264.7 macrophages, we found a significant reduction in the production of ROS among the macrophage subset that had bound A. veronii. Phagocytic uptake of the pathogen further decreased ROS production levels, even beyond those of unstimulated controls. Overall, this multi-parametric imaging flow cytometry-based approach allowed for segregation of unique phagocyte sub-populations and examination of their downstream antimicrobial responses, and should contribute to improved understanding of phagocyte responses against Aeromonas and other pathogens. Copyright © 2015 Elsevier B.V. All rights reserved.

Structure of turbulent non-premixed flames modeled with two-step chemistry

NASA Technical Reports Server (NTRS)

Chen, J. H.; Mahalingam, S.; Puri, I. K.; Vervisch, L.

1992-01-01

Direct numerical simulations of turbulent diffusion flames modeled with finite-rate, two-step chemistry, A + B yields I, A + I yields P, were carried out. A detailed analysis of the turbulent flame structure reveals the complex nature of the penetration of various reactive species across two reaction zones in mixture fraction space. Due to this two zone structure, these flames were found to be robust, resisting extinction over the parameter ranges investigated. As in single-step computations, mixture fraction dissipation rate and the mixture fraction were found to be statistically correlated. Simulations involving unequal molecular diffusivities suggest that the small scale mixing process and, hence, the turbulent flame structure is sensitive to the Schmidt number.

Modeling Analysis of Multi-Decadal Trends in Ozone and Precursor Species across the Northern Hemisphere and the United States

EPA Science Inventory

The WRF-CMAQ modeling system was applied over a domain encompassing the northern hemisphere and a nested domain over the U.S. Model simulations for the 1990-2010 were performed to examine trends in various air pollutant concentrations. Trends in O3 mixing ratios over the U.S. are...

Chemical stability and in chemico reactivity of 24 fragrance ingredients of concern for skin sensitization risk assessment.

PubMed

Avonto, Cristina; Wang, Mei; Chittiboyina, Amar G; Vukmanovic, Stanislav; Khan, Ikhlas A

2018-02-01

Twenty-four pure fragrance ingredients have been identified as potential concern for skin sensitization. Several of these compounds are chemically unstable and convert into reactive species upon exposure to air or light. In the present work, a systematic investigation of the correlation between chemical stability and reactivity has been undertaken. The compounds were subjected to forced photodegradation for three months and the chemical changes were studied with GC-MS. At the end of the stability study, two-thirds of the samples were found to be unstable. The generation of chemically reactive species was investigated using the in chemico HTS-DCYA assay. Eleven and fourteen compounds were chemically reactive before and after three months, respectively. A significant increase in reactivity upon degradation was found for isoeugenol, linalool, limonene, lyral, citronellol and geraniol; in the same conditions, the reactivity of hydroxycitronellal decreased. The non-reactive compounds α-isomethyl ionone, benzyl alcohol, amyl cinnamal and farnesol became reactive after photo-oxidative degradation. Overall, forced degradation resulted in four non-reactive fragrance compounds to display in chemico thiol reactivity, while ten out of 24 compounds remained inactive. Chemical degradation does not necessarily occur with generation of reactive species. Non-chemical activation may be involved for the 10 stable unreactive compounds. Copyright © 2017 Elsevier Ltd. All rights reserved.

3D simulation of polyurethane foam injection and reacting mold flow in a complex geometry

NASA Astrophysics Data System (ADS)

Özdemir, İ. Bedii; Akar, Fırat

2018-05-01

The aim of the present work is to develop a flow model which can be used to determine the paths of the polyurethane foam in the mold filling process of a refrigerator cabinet so that improvements in the distribution and the size of the venting holes can be achieved without the expensive prototyping and experiments. For this purpose, the multi-component, two-phase chemically reacting flow is described by Navier Stokes and 12 scalar transport equations. The air and the multi-component foam zones are separated by an interface, which moves only with advection since the mass diffusion of species are set zero in the air zone. The inverse density, viscosity and other diffusion coefficients are calculated by a mass fraction weighted average of the corresponding temperature-dependent values of all species. Simulations are performed in a real refrigerator geometry, are able to reveal the problematical zones where air bubbles and voids trapped in the solidified foam are expected to occur. Furthermore, the approach proves itself as a reliable design tool to use in deciding the locations of air vents and sizing the channel dimensions.

Accelerated Weathering of Waste Glass at 90°C with the Pressurized Unsaturated Flow (PUF) Apparatus: Implications for Predicting Glass Corrosion with a Reactive Transport Model

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

Pierce, Eric M.; Bacon, Diana H.

2009-09-21

The interest in the long-term durability of waste glass stems from the need to predict radionuclide release rates from the corroding glass over geologic time-scales. Several long-term test methods have been developed to accelerate the glass-water reaction [drip test, vapor hydration test, product consistency test-B, and pressurized unsaturated flow (PUF)]. Currently, the PUF test is the only method that can mimic the unsaturated hydraulic properties expected in a subsurface disposal facility and simultaneously monitor the glass-water reaction. PUF tests are being conducted to accelerate the weathering of glass and validate the model parameters being used to predict long-term glass behavior.more » One dimensional reactive chemical transport simulations of glass dissolution and secondary phase formation during a 1.5-year long PUF experiment was conducted with the subsurface transport over reactive multi-phases (STORM) code. Results show that parameterization of the computer model by combining direct laboratory measurements and thermodynamic data provides an integrated approach to predicting glass behavior over geologic-time scales.« less

An Adaptive Jitter Mechanism for Reactive Route Discovery in Sensor Networks

PubMed Central

Cordero, Juan Antonio; Yi, Jiazi; Clausen, Thomas

2014-01-01

This paper analyses the impact of jitter when applied to route discovery in reactive (on-demand) routing protocols. In multi-hop non-synchronized wireless networks, jitter—a small, random variation in the timing of message emission—is commonly employed, as a means to avoid collisions of simultaneous transmissions by adjacent routers over the same channel. In a reactive routing protocol for sensor and ad hoc networks, jitter is recommended during the route discovery process, specifically, during the network-wide flooding of route request messages, in order to avoid collisions. Commonly, a simple uniform jitter is recommended. Alas, this is not without drawbacks: when applying uniform jitter to the route discovery process, an effect called delay inversion is observed. This paper, first, studies and quantifies this delay inversion effect. Second, this paper proposes an adaptive jitter mechanism, designed to alleviate the delay inversion effect and thereby to reduce the route discovery overhead and (ultimately) allow the routing protocol to find more optimal paths, as compared to uniform jitter. This paper presents both analytical and simulation studies, showing that the proposed adaptive jitter can effectively decrease the cost of route discovery and increase the path quality. PMID:25111238

Systems and methods for forming defects on graphitic materials and curing radiation-damaged graphitic materials

DOEpatents

Ryu, Sunmin; Brus, Louis E.; Steigerwald, Michael L.; Liu, Haitao

2012-09-25

Systems and methods are disclosed herein for forming defects on graphitic materials. The methods for forming defects include applying a radiation reactive material on a graphitic material, irradiating the applied radiation reactive material to produce a reactive species, and permitting the reactive species to react with the graphitic material to form defects. Additionally, disclosed are methods for removing defects on graphitic materials.

Effects of sulfate ligand on uranyl carbonato surface species on ferrihydrite surfaces

USGS Publications Warehouse

Arai, Yuji; Fuller, C.C.

2012-01-01

Understanding uranium (U) sorption processes in permeable reactive barriers (PRB) are critical in modeling reactive transport for evaluating PRB performance at the Fry Canyon demonstration site in Utah, USA. To gain insight into the U sequestration mechanism in the amorphous ferric oxyhydroxide (AFO)-coated gravel PRB, U(VI) sorption processes on ferrihydrite surfaces were studied in 0.01 M Na2SO4 solutions to simulate the major chemical composition of U-contaminatedgroundwater (i.e., [SO42-]~13 mM L-1) at the site. Uranyl sorption was greater at pH 7.5 than that at pH 4 in both air- and 2% pCO2-equilibrated systems. While there were negligible effects of sulfate ligands on the pH-dependent U(VI) sorption (<24 h) in both systems, X-ray absorption spectroscopy (XAS) analysis showed sulfate ligand associated U(VI) surface species at the ferrihydrite–water interface. In air-equilibrated systems, binary and mono-sulfate U(VI) ternary surface species co-existed at pH 5.43. At pH 6.55–7.83, a mixture of mono-sulfate and bis-carbonato U(VI) ternary surface species became more important. At 2% pCO2, there was no contribution of sulfate ligands on the U(VI) ternary surface species. Instead, a mixture of bis-carbonato inner-sphere (38%) and tris-carbonato outer-sphere U(VI) ternary surface species (62%) was found at pH 7.62. The study suggests that the competitive ligand (bicarbonate and sulfate) coordination on U(VI) surface species might be important in evaluating the U solid-state speciation in the AFO PRB at the study site where pCO2 fluctuates between 1 and 2 pCO2%.

Effects of sulfate ligand on uranyl carbonato surface species on ferrihydrite surfaces.

PubMed

Arai, Yuji; Fuller, C C

2012-01-01

Understanding uranium (U) sorption processes in permeable reactive barriers (PRB) are critical in modeling reactive transport for evaluating PRB performance at the Fry Canyon demonstration site in Utah, USA. To gain insight into the U sequestration mechanism in the amorphous ferric oxyhydroxide (AFO)-coated gravel PRB, U(VI) sorption processes on ferrihydrite surfaces were studied in 0.01 M Na(2)SO(4) solutions to simulate the major chemical composition of U-contaminated groundwater (i.e., [SO(4)(2-)] ~13 mM L(-1)) at the site. Uranyl sorption was greater at pH 7.5 than that at pH 4 in both air- and 2% pCO(2)-equilibrated systems. While there were negligible effects of sulfate ligands on the pH-dependent U(VI) sorption (<24 h) in both systems, X-ray absorption spectroscopy (XAS) analysis showed sulfate ligand associated U(VI) surface species at the ferrihydrite-water interface. In air-equilibrated systems, binary and mono-sulfate U(VI) ternary surface species co-existed at pH 5.43. At pH 6.55-7.83, a mixture of mono-sulfate and bis-carbonato U(VI) ternary surface species became more important. At 2% pCO(2), there was no contribution of sulfate ligands on the U(VI) ternary surface species. Instead, a mixture of bis-carbonato inner-sphere (38%) and tris-carbonato outer-sphere U(VI) ternary surface species (62%) was found at pH 7.62. The study suggests that the competitive ligand (bicarbonate and sulfate) coordination on U(VI) surface species might be important in evaluating the U solid-state speciation in the AFO PRB at the study site where pCO(2) fluctuates between 1 and 2 pCO(2)%. Copyright © 2011 Elsevier Inc. All rights reserved.

Serologic Cross-Reactivity of Human IgM and IgG Antibodies to Five Species of Ebola Virus

PubMed Central

MacNeil, Adam; Reed, Zachary; Rollin, Pierre E.

2011-01-01

Five species of Ebola virus (EBOV) have been identified, with nucleotide differences of 30–45% between species. Four of these species have been shown to cause Ebola hemorrhagic fever (EHF) in humans and a fifth species (Reston ebolavirus) is capable of causing a similar disease in non-human primates. While examining potential serologic cross-reactivity between EBOV species is important for diagnostic assays as well as putative vaccines, the nature of cross-reactive antibodies following EBOV infection has not been thoroughly characterized. In order to examine cross-reactivity of human serologic responses to EBOV, we developed antigen preparations for all five EBOV species, and compared serologic responses by IgM capture and IgG enzyme-linked immunosorbent assay (ELISA) in groups of convalescent diagnostic sera from outbreaks in Kikwit, Democratic Republic of Congo (n = 24), Gulu, Uganda (n = 20), Bundibugyo, Uganda (n = 33), and the Philippines (n = 18), which represent outbreaks due to four different EBOV species. For groups of samples from Kikwit, Gulu, and Bundibugyo, some limited IgM cross-reactivity was noted between heterologous sera-antigen pairs, however, IgM responses were largely stronger against autologous antigen. In some instances IgG responses were higher to autologous antigen than heterologous antigen, however, in contrast to IgM responses, we observed strong cross-reactive IgG antibody responses to heterologous antigens among all sets of samples. Finally, we examined autologous IgM and IgG antibody levels, relative to time following EHF onset, and observed early peaking and declining IgM antibody levels (by 80 days) and early development and persistence of IgG antibodies among all samples, implying a consistent pattern of antibody kinetics, regardless of EBOV species. Our findings demonstrate limited cross-reactivity of IgM antibodies to EBOV, however, the stronger tendency for cross-reactive IgG antibody responses can largely circumvent limitations in the utility of heterologous antigen for diagnostic assays and may assist in the development of antibody-mediated vaccines to EBOV. PMID:21666792

Atmospheric Pressure Plasma Jet for Chem/Bio Warfare Decontamination

NASA Astrophysics Data System (ADS)

Herrmann, Hans W.; Henins, Ivars; Park, Jaeyoung; Selwyn, Gary S.

1999-11-01

Atmospheric Pressure Plasma Jet (APPJ) technology may provide a much needed method of CBW decontamination which, unlike traditional decon methods, is dry and nondestructive to sensitive equipment and materials. The APPJ discharge uses a high-flow feedgas consisting primarily of an inert carrier gas, such as He, and a small amount of a reactive additive, such as O2, which flows between capacitively-coupled electrodes powered at 13.56 MHz. The plasma generates highly reactive metastable and atomic species of oxygen which are then directed onto a contaminated surface. The reactive effluent of the APPJ has been shown to effectively neutralize VX nerve agent as well as simulants for anthrax and mustard blister agent. Research efforts are now being directed towards reducing He consumption and increasing the allowable stand-off distance. Recent results demonstrate that by replacing the O2 reactive additive with CO2, ozone formation is greatly reduced. This has the result of extending the lifetime of atomic oxygen by an order of magnitude or more. A recirculating APP Decon Chamber which combines heat, vacuum, forced convection and reactivity is currently being developed for enhanced decontamination of sensitive equipment. Several techniques are also being evaluated for use in an APP Decon Jet for decontamination of items which cannot be placed inside a chamber.

Reactive Nitrogen Distribution and Partitioning in the North American Troposphere and Lowermost Stratosphere

NASA Technical Reports Server (NTRS)

Singh, H. B.; Salas, L.; Herlth, D.; Kolyer, R.; Czech, E.; Crawford, J. H.; Pierce, R. B.; Sachse, G. W.; Blake, D. R.; Cohen, R. C.;

Modeling 3D-CSIA data: Carbon, chlorine, and hydrogen isotope fractionation during reductive dechlorination of TCE to ethene.

PubMed

Van Breukelen, Boris M; Thouement, Héloïse A A; Stack, Philip E; Vanderford, Mindy; Philp, Paul; Kuder, Tomasz

2017-09-01

Reactive transport modeling of multi-element, compound-specific isotope analysis (CSIA) data has great potential to quantify sequential microbial reductive dechlorination (SRD) and alternative pathways such as oxidation, in support of remediation of chlorinated solvents in groundwater. As a key step towards this goal, a model was developed that simulates simultaneous carbon, chlorine, and hydrogen isotope fractionation during SRD of trichloroethene, via cis-1,2-dichloroethene (and trans-DCE as minor pathway), and vinyl chloride to ethene, following Monod kinetics. A simple correction term for individual isotope/isotopologue rates avoided multi-element isotopologue modeling. The model was successfully validated with data from a mixed culture Dehalococcoides microcosm. Simulation of Cl-CSIA required incorporation of secondary kinetic isotope effects (SKIEs). Assuming a limited degree of intramolecular heterogeneity of δ 37 Cl in TCE decreased the magnitudes of SKIEs required at the non-reacting Cl positions, without compromising the goodness of model fit, whereas a good fit of a model involving intramolecular CCl bond competition required an unlikely degree of intramolecular heterogeneity. Simulation of H-CSIA required SKIEs in H atoms originally present in the reacting compounds, especially for TCE, together with imprints of strongly depleted δ 2 H during protonation in the products. Scenario modeling illustrates the potential of H-CSIA for source apportionment. Copyright © 2017 The Authors. Published by Elsevier B.V. All rights reserved.

Reactive Power Compensation Method Considering Minimum Effective Reactive Power Reserve

NASA Astrophysics Data System (ADS)

Gong, Yiyu; Zhang, Kai; Pu, Zhang; Li, Xuenan; Zuo, Xianghong; Zhen, Jiao; Sudan, Teng

2017-05-01

According to the calculation model of minimum generator reactive power reserve of power system voltage stability under the premise of the guarantee, the reactive power management system with reactive power compensation combined generator, the formation of a multi-objective optimization problem, propose a reactive power reserve is considered the minimum generator reactive power compensation optimization method. This method through the improvement of the objective function and constraint conditions, when the system load growth, relying solely on reactive power generation system can not meet the requirement of safe operation, increase the reactive power reserve to solve the problem of minimum generator reactive power compensation in the case of load node.

Hierarchical demographic approaches for assessing invasion dynamics of non-indigenous species: An example using northern snakehead (Channa argus)

USGS Publications Warehouse

Jiao, Y.; Lapointe, N.W.R.; Angermeier, P.L.; Murphy, B.R.

2009-01-01

Models of species' demographic features are commonly used to understand population dynamics and inform management tactics. Hierarchical demographic models are ideal for the assessment of non-indigenous species because our knowledge of non-indigenous populations is usually limited, data on demographic traits often come from a species' native range, these traits vary among populations, and traits are likely to vary considerably over time as species adapt to new environments. Hierarchical models readily incorporate this spatiotemporal variation in species' demographic traits by representing demographic parameters as multi-level hierarchies. As is done for traditional non-hierarchical matrix models, sensitivity and elasticity analyses are used to evaluate the contributions of different life stages and parameters to estimates of population growth rate. We applied a hierarchical model to northern snakehead (Channa argus), a fish currently invading the eastern United States. We used a Monte Carlo approach to simulate uncertainties in the sensitivity and elasticity analyses and to project future population persistence under selected management tactics. We gathered key biological information on northern snakehead natural mortality, maturity and recruitment in its native Asian environment. We compared the model performance with and without hierarchy of parameters. Our results suggest that ignoring the hierarchy of parameters in demographic models may result in poor estimates of population size and growth and may lead to erroneous management advice. In our case, the hierarchy used multi-level distributions to simulate the heterogeneity of demographic parameters across different locations or situations. The probability that the northern snakehead population will increase and harm the native fauna is considerable. Our elasticity and prognostic analyses showed that intensive control efforts immediately prior to spawning and/or juvenile-dispersal periods would be more effective (and probably require less effort) than year-round control efforts. Our study demonstrates the importance of considering the hierarchy of parameters in estimating population growth rate and evaluating different management strategies for non-indigenous invasive species. ?? 2009 Elsevier B.V.

Evolution of Bromoform in a Global Chemistry and Transport Model

NASA Technical Reports Server (NTRS)

Douglass, Anne R.; Pierson, J. M.; Douglass, Anne R.; Einaudi, Franco (Technical Monitor)

2000-01-01

It is well known that many chlorine and bromine compounds that are inert in the troposphere are destroyed in the stratosphere and contribute to the stratospheric burden of reactive chlorine and bromine species. But the contribution from those chlorine and bromine compounds which are reactive in the troposphere is less certain because it is not known whether convection can transport these gases to the upper troposphere rapidly enough to overcome their short tropospheric lifetimes. We examine this issue using a three-dimensional chemistry and transport model to simulate the evolution of three gases which have surface sources, bromoform (CHBr3), methyl chloroform (CH3CCl3), and carbon dioxide (CO2). Our objective is to determine if CHBr3 might enhance the lower stratospheric burden of reactive bromine. The other two gases provide tests of the quality of the simulation. Both CHBr3 and CH3CCl3 are destroyed in the troposphere by reaction with hydroxyl (OH), whose latitudinal and monthly variation is provided by a two-dimensional model and upon which a diurnal variation is imposed. Comparison of the lifetime of CH3CCl3 computed from observations (5 years) with the lifetime computed from the simulation provides an integrated test of the model's transport and photochemistry. Observations also show that CO2 exhibits a strong seasonal cycle in the northern hemisphere troposphere that is not propagated directly across the tropopause into the lower stratosphere. Thus, maintenance of the observed troposphere-stratosphere distinctness of CO2 in the presence of convection is a critical benchmark for meeting our objective.

Reactive Nitrogen Distribution and Partitioning in the North American Troposphere and Lowermost Stratosphere

NASA Technical Reports Server (NTRS)

Singh, H. B.; Salas, L.; Herlth, D.; Kolyer, R.; Czech, E.; Avery, M.; Crawford, J. H.; Pierce, B.; Sachse, G. W.; Blake, D. R.;

Sensitivity analysis of conservative and reactive stream transient storage models applied to field data from multiple-reach experiments

USGS Publications Warehouse

Gooseff, M.N.; Bencala, K.E.; Scott, D.T.; Runkel, R.L.; McKnight, Diane M.

2005-01-01

The transient storage model (TSM) has been widely used in studies of stream solute transport and fate, with an increasing emphasis on reactive solute transport. In this study we perform sensitivity analyses of a conservative TSM and two different reactive solute transport models (RSTM), one that includes first-order decay in the stream and the storage zone, and a second that considers sorption of a reactive solute on streambed sediments. Two previously analyzed data sets are examined with a focus on the reliability of these RSTMs in characterizing stream and storage zone solute reactions. Sensitivities of simulations to parameters within and among reaches, parameter coefficients of variation, and correlation coefficients are computed and analyzed. Our results indicate that (1) simulated values have the greatest sensitivity to parameters within the same reach, (2) simulated values are also sensitive to parameters in reaches immediately upstream and downstream (inter-reach sensitivity), (3) simulated values have decreasing sensitivity to parameters in reaches farther downstream, and (4) in-stream reactive solute data provide adequate data to resolve effective storage zone reaction parameters, given the model formulations. Simulations of reactive solutes are shown to be equally sensitive to transport parameters and effective reaction parameters of the model, evidence of the control of physical transport on reactive solute dynamics. Similar to conservative transport analysis, reactive solute simulations appear to be most sensitive to data collected during the rising and falling limb of the concentration breakthrough curve. ?? 2005 Elsevier Ltd. All rights reserved.

The Reactive Species Interactome: Evolutionary Emergence, Biological Significance, and Opportunities for Redox Metabolomics and Personalized Medicine

PubMed Central

Koning, Anne; Kuhnle, Gunter G.C.; Nagy, Peter; Bianco, Christopher L.; Pasch, Andreas; Wink, David A.; Fukuto, Jon M.; Jackson, Alan A.; van Goor, Harry; Olson, Kenneth R.

2017-01-01

Abstract Significance: Oxidative stress is thought to account for aberrant redox homeostasis and contribute to aging and disease. However, more often than not, administration of antioxidants is ineffective, suggesting that our current understanding of the underlying regulatory processes is incomplete. Recent Advances: Similar to reactive oxygen species and reactive nitrogen species, reactive sulfur species are now emerging as important signaling molecules, targeting regulatory cysteine redox switches in proteins, affecting gene regulation, ion transport, intermediary metabolism, and mitochondrial function. To rationalize the complexity of chemical interactions of reactive species with themselves and their targets and help define their role in systemic metabolic control, we here introduce a novel integrative concept defined as the reactive species interactome (RSI). The RSI is a primeval multilevel redox regulatory system whose architecture, together with the physicochemical characteristics of its constituents, allows efficient sensing and rapid adaptation to environmental changes and various other stressors to enhance fitness and resilience at the local and whole-organism level. Critical Issues: To better characterize the RSI-related processes that determine fluxes through specific pathways and enable integration, it is necessary to disentangle the chemical biology and activity of reactive species (including precursors and reaction products), their targets, communication systems, and effects on cellular, organ, and whole-organism bioenergetics using system-level/network analyses. Future Directions: Understanding the mechanisms through which the RSI operates will enable a better appreciation of the possibilities to modulate the entire biological system; moreover, unveiling molecular signatures that characterize specific environmental challenges or other forms of stress will provide new prevention/intervention opportunities for personalized medicine. Antioxid. Redox Signal. 27, 684–712. PMID:28398072

The Synergistic Effect of Proteins and Reactive Oxygen Species on Electrochemical Behaviour of 316L Stainless Steel for Biomedical Applications

NASA Astrophysics Data System (ADS)

Simionescu, N.; Benea, L.; Dumitrascu, V. M.

2018-06-01

The stainless steels, especially 316L type is the most used metallic biomaterials for biomedical applications due to their good biocompatibility, low price, excellent corrosion resistance, availability, easy processing and high strength. Due to these favorable properties 316L stainless steel has become the most attractive biomaterial for dental implants, stents and orthopedic implants. However an implant material in the human body is exposed to an action effect of other molecules, including proteins (such as albumin) and reactive oxygen species (such as hydrogen peroxide - H2O2 ) produced by bacteria and immune cells. In the literature there are few studies to follow the effect of proteins and reactive oxygen species on 316L stainless steel used as implant material and are still unclear. The degree of corrosion resistance is the first criterion in the use of a metallic biomaterial in the oral or body environment. The aim of this research work is to investigate the influence of proteins (albumin) and reactive oxygen species (H2O2 ) in combination, taking into account the synergistic effect of these two factors on 316L stainless steel. Albumin is present in the body near implants and reactive oxygen species could appear in inflammatory processes as well. The study shows that the presence of albumin and reactive species influences the corrosion resistance of 316L stainless steel in biological solutions. In this research work the corrosion behavior of 316L stainless steel is analyzed by electrochemical methods such as: open circuit potential (OCP), Electrochemical Impedance Spectroscopy (EIS). It was found that, the electrochemical results are in a good agreement with micro photographs taken before and after corrosion assays. The albumin and reactive oxygen species have influence on 316L stainless steel behavior.

Ursodeoxycholic acid inhibits overexpression of P-glycoprotein induced by doxorubicin in HepG2 cells.

PubMed

Komori, Yuki; Arisawa, Sakiko; Takai, Miho; Yokoyama, Kunihiro; Honda, Minako; Hayashi, Kazuhiko; Ishigami, Masatoshi; Katano, Yoshiaki; Goto, Hidemi; Ueyama, Jun; Ishikawa, Tetsuya; Wakusawa, Shinya

2014-02-05

The hepatoprotective action of ursodeoxycholic acid (UDCA) was previously suggested to be partially dependent on its antioxidative effect. Doxorubicin (DOX) and reactive oxygen species have also been implicated in the overexpression of P-glycoprotein (P-gp), which is encoded by the MDR1 gene and causes antitumor multidrug resistance. In the present study, we assessed the effects of UDCA on the expression of MDR1 mRNA, P-gp, and intracellular reactive oxygen species levels in DOX-treated HepG2 cells and compared them to those of other bile acids. DOX-induced increases in reactive oxygen species levels and the expression of MDR1 mRNA were inhibited by N-acetylcysteine, an antioxidant, and the DOX-induced increase in reactive oxygen species levels and DOX-induced overexpression of MDR1 mRNA and P-gp were inhibited by UDCA. Cells treated with UDCA showed improved rhodamine 123 uptake, which was decreased in cells treated with DOX alone. Moreover, cells exposed to DOX for 24h combined with UDCA accumulated more DOX than that of cells treated with DOX alone. Thus, UDCA may have inhibited the overexpression of P-gp by suppressing DOX-induced reactive oxygen species production. Chenodeoxycholic acid (CDCA) also exhibited these effects, whereas deoxycholic acid and litocholic acid were ineffective. In conclusion, UDCA and CDCA had an inhibitory effect on the induction of P-gp expression and reactive oxygen species by DOX in HepG2 cells. The administration of UDCA may be beneficial due to its ability to prevent the overexpression of reactive oxygen species and acquisition of multidrug resistance in hepatocellular carcinoma cells. Copyright © 2013 Elsevier B.V. All rights reserved.

Innovative mathematical modeling in environmental remediation

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

Yeh, Gour T.; National Central Univ.; Univ. of Central Florida

2013-05-01

There are two different ways to model reactive transport: ad hoc and innovative reaction-based approaches. The former, such as the Kd simplification of adsorption, has been widely employed by practitioners, while the latter has been mainly used in scientific communities for elucidating mechanisms of biogeochemical transport processes. It is believed that innovative mechanistic-based models could serve as protocols for environmental remediation as well. This paper reviews the development of a mechanistically coupled fluid flow, thermal transport, hydrologic transport, and reactive biogeochemical model and example-applications to environmental remediation problems. Theoretical bases are sufficiently described. Four example problems previously carried out aremore » used to demonstrate how numerical experimentation can be used to evaluate the feasibility of different remediation approaches. The first one involved the application of a 56-species uranium tailing problem to the Melton Branch Subwatershed at Oak Ridge National Laboratory (ORNL) using the parallel version of the model. Simulations were made to demonstrate the potential mobilization of uranium and other chelating agents in the proposed waste disposal site. The second problem simulated laboratory-scale system to investigate the role of natural attenuation in potential off-site migration of uranium from uranium mill tailings after restoration. It showed inadequacy of using a single Kd even for a homogeneous medium. The third example simulated laboratory experiments involving extremely high concentrations of uranium, technetium, aluminum, nitrate, and toxic metals (e.g.,Ni, Cr, Co).The fourth example modeled microbially-mediated immobilization of uranium in an unconfined aquifer using acetate amendment in a field-scale experiment. The purposes of these modeling studies were to simulate various mechanisms of mobilization and immobilization of radioactive wastes and to illustrate how to apply reactive transport models for environmental remediation.The second problem simulated laboratory-scale system to investigate the role of natural attenuation in potential off-site migration of uranium from uranium mill tailings after restoration. It showed inadequacy of using a single Kd even for a homogeneous medium.« less

Ionophoric polyphenols selectively bind Cu(2+), display potent antioxidant and anti-amyloidogenic properties, and are non-toxic toward Tetrahymena thermophila.

PubMed

Martínez, Alberto; Alcendor, Ralph; Rahman, Tanzeen; Podgorny, Magdalena; Sanogo, Ismaila; McCurdy, Rebecca

2016-08-15

Alzheimer's disease (AD) is the most common form of dementia affecting more than 28million people in the world. Only symptomatic treatments are currently available. Anticipated tri-fold increase of AD incidence in the next 50years has established the need to explore new possible treatments. Accumulation of extracellular amyloid-β (Aβ) plaques, intracellular tangles in the brain, and formation of reactive oxygen species (ROS) are the major hallmarks of the disease. The active role of some metal ions, especially Cu(2+), in promoting both Aβ aggregation and reactive oxygen species formation has rendered ionophoric drugs as a promising treatment strategy. In this work, a series of 5 disease-modifying and multi-target ionophoric polyphenols (1-5), inspired on the structure of natural resveratrol, have been synthesized and characterized. All compounds bind Cu(2+) selectively over other biologically relevant metal ions. They form 2:1 (compound/Cu(2+)) complexes with association constants logKa 12-14 depending on the molecular design. Our results indicate that compounds 1-5 possess excellent antioxidant properties: they inhibit the Cu(2+)-catalyzed reactive oxygen species production between 47% and 100%, and they scavenge DPPH (1,1-diphenyl-2-picryl-hydrazyl) and AAPH (2,2'-azobis(2-amindino-propane)dihydrochloride) free radicals in general better than clioquinol, resveratrol and ascorbic acid. In addition, compounds 1-5 interact with Aβ peptides and inhibit both the Cu(2+)-catalyzed aggregation and the self-assembly of Aβ(1-40) up to a ∼92% extent. Interestingly, 1-5 are also able to disaggregate up to ∼91% of pre-formed Aβ(1-40) aggregates. Furthermore, cytotoxic studies show remarkably low toxicity of 1-5 toward Tetrahymena thermophila with LD50 values higher than 150μM, comparable to non-toxic natural resveratrol. Published by Elsevier Ltd.

Inactivation of Escherichia coli on blueberries using cold plasma with chemical augmentation inside a partial vacuum

USDA-ARS?s Scientific Manuscript database

Justification: The mechanism by which cold plasma inactivates pathogens is through the production of free reactive chemical species. Unfortunately, the most reactive chemical species have the shortest half-life. In a vacuum their half-life is believed to be prolonged. Additionally, these reactive sp...

Cross-reactivity of anti-chicken IgY antibody with immunoglobulins of exotic avian species.

PubMed

Cray, Carolyn; Villar, David

2008-09-01

A major challenge in the serologic diagnosis of infectious diseases in exotic birds is the limited availability of species-specific antibodies. The purpose of the current study was to determine if there is cross reactivity between commercially available anti-chicken IgY antibodies and immunoglobulins of several avian species, with particular emphasis on psittacines. To quantitate the reactivity with anti-chicken IgY, Western blot analysis was performed using plasma samples from many different avian species. Results were compared with gamma globulin fraction quantitation obtained by protein electrophoresis. By Western blot, 2 protein bands corresponding to the heavy and light chains of chicken IgY were identified in species from 21 avian orders using 1 of 2 rabbit anti-chicken IgY antibodies. Densitometric analysis showed that the amount of immunoglobulin estimated from Western blots correlated strongly with data from protein electrophoresis assays. The results demonstrate that some commercially available anti-chicken IgY antibodies exhibit good cross-reactivity with most avian species.

Total OH reactivity in a mediterranean forest of downy oaks

NASA Astrophysics Data System (ADS)

Zannoni, Nora; Gros, Valerie; Sarda, Roland; Lanza, Matteo; Bonsang, Bernard; Kalogridis, Cerise; Preunkert, Suzanne; Legrand, Michel; Jambert, Corinne; Boissard, Christophe; Lathiere, Juliette

2015-04-01

Forests emit large quantities of reactive molecules which can affect the concentration of the most important oxidizing agent in the atmosphere, the hydroxyl radical OH. There are still many unknowns on how biogenic compounds interact with the atmosphere. Among those, we still lack to fully understand the species that can potentially influence the atmospheric oxidative capacity and thus the OH cleansing effect over several forested areas. We conducted total OH reactivity measurements during spring 2014 inside and above the canopy height of a forest dominated at 80% by downy oaks in the Mediterranean basin (Observatoire Haute Provence site, France). Downy oak trees are capable to emit almost exclusively isoprene (~99%), the most abundant volatile organic compound and among the most reactive towards the OH radical. We measured the total OH reactivity with the Comparative Reactivity Method together with atmospheric concentrations of the primary compounds emitted by the forest, main secondary species generated from the oxidation of isoprene, and main atmospheric constituents. We then compared the OH reactivity inferred by measured compounds and their oxidation rate coefficients with the measured total OH reactivity. This approach permits to identify the presence of any primary emitted biogenic compound, unknown before and relevant for OH oxidation; or any secondary generated compound whose associated chemical mechanism is not well established. Our results show higher OH reactivity inside the canopy, with peaks up to 78 s-1, when isoprene concentration reached ~20 ppb due to temperature and PAR increase. Such high level of OH reactivity has only been observed in the tropics so far. Furthermore, our measured total OH reactivity closes the total amount of reactive species present in this specific forest, suggesting that we quantified precisely both the primary emitted species as well as the secondary generated products.

The formation of reactive species having hydroxyl radical-like reactivity from UV photolysis of N-nitrosodimethylamine (NDMA): kinetics and mechanism.

PubMed

Kwon, Bum Gun; Kim, Jong-Oh; Namkung, Kyu Cheol

2012-10-15

This study focuses on the detailed mechanism by which N-nitrosodimethylamine (NDMA) is photolyzed to form oxidized products, i.e., NO(2)(-) and NO(3)(-), and reveals a key reactive species produced during the photolysis of NDMA. Under acidic conditions, NO(2)(-) formed from the photodecomposition of NDMA was more prevalent than NO(3)(-). In this result, key species for the formation of NO(2)(-) are presumably N(2)O(3) and N(2)O(4) as termination products as well as NO and O(2) as reactants. Conversely, under alkaline conditions, NO(3)(-) was more prevalent than NO(2)(-). For this result, a key species for NO(3)(-) formation is presumably peroxynitrite (ONOO(-)). A detailed mechanistic study was performed with a competition reaction (or kinetics) between NDMA and p-nitrosodimethylaniline (PNDA) probe for hydroxyl radical (OH). It is fortuitous that the second-order rate constant for NDMA with an unknown reactive species (URS) was 5.13×10(8) M(-1) s(-1), which was similar to its published value for the reaction of NDMA+OH. Our study results showed that a key reactive species generated during NDMA photo-decomposition had hydroxyl radical-like reactivity and in particular, under alkaline conditions, it is most likely ONOO(-) as a source of nitrate ion. Therefore, for the first time, we experimentally report that an URS having OH-like reactivity can be formed during photochemical NDMA decomposition. This URS could contribute to the formations of NO(2)(-) and NO(3)(-). Copyright © 2012 Elsevier B.V. All rights reserved.

Transient Simulation of the Multi-SERTTA Experiment with MAMMOTH

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

Ortensi, Javier; Baker, Benjamin; Wang, Yaqi

This work details the MAMMOTH reactor physics simulations of the Static Environment Rodlet Transient Test Apparatus (SERTTA) conducted at Idaho National Laboratory in FY-2017. TREAT static-environment experiment vehicles are being developed to enable transient testing of Pressurized Water Reactor (PWR) type fuel specimens, including fuel concepts with enhanced accident tolerance (Accident Tolerant Fuels, ATF). The MAMMOTH simulations include point reactor kinetics as well as spatial dynamics for a temperature-limited transient. The strongly coupled multi-physics solutions of the neutron flux and temperature fields are second order accurate both in the spatial and temporal domains. MAMMOTH produces pellet stack powers that are within 1.5% of the Monte Carlo reference solutions. Some discrepancies between the MCNP model used in the design of the flux collars and the Serpent/MAMMOTH models lead to higher power and energy deposition values in Multi-SERTTA unit 1. The TREAT core results compare well with the safety case computed with point reactor kinetics in RELAP5-3D. The reactor period is 44 msec, which corresponds to a reactivity insertion of 2.685% delta k/kmore » $. The peak core power in the spatial dynamics simulation is 431 MW, which the point kinetics model over-predicts by 12%. The pulse width at half the maximum power is 0.177 sec. Subtle transient effects are apparent at the beginning insertion in the experimental samples due to the control rod removal. Additional difference due to transient effects are observed in the sample powers and enthalpy. The time dependence of the power coupling factor (PCF) is calculated for the various fuel stacks of the Multi-SERTTA vehicle. Sample temperatures in excess of 3100 K, the melting point UO$$_2$$, are computed with the adiabatic heat transfer model. The planned shaped-transient might introduce additional effects that cannot be predicted with PRK models. Future modeling will be focused on the shaped-transient by improving the control rod models in MAMMOTH and adding the BISON thermo-elastic models and thermal-fluids heat transfer.« less

On the potential of GHG emissions estimation by multi-species inverse modeling

NASA Astrophysics Data System (ADS)

Gerbig, Christoph; Boschetti, Fabio; Filges, Annette; Marshall, Julia; Koch, Frank-Thomas; Janssens-Maenhout, Greet; Nedelec, Philippe; Thouret, Valerie; Karstens, Ute

2016-04-01

Reducing anthropogenic emissions of greenhouse gases is one of the most important elements in mitigating climate change. However, as emission reporting is often incomplete or incorrect, there is a need to independently monitor the emissions. Despite this, in the case of CO2 one typically assumes that emissions from fossil fuel burning are well known, and only natural fluxes are constrained by atmospheric measurements via inverse modelling. On the other hand, species such as CO2, CH4, and CO often have common emission patterns, and thus share part of the uncertainties, both related to the prior knowledge of emissions, and to model-data mismatch error. We implemented the Lagrangian transport model STILT driven by ECMWF analysis and short-term forecast meteorological fields together with emission sector and fuel-type specific emissions of CO2, CH4 and CO from EDGARv4.3 at a spatial resolution of 0.1 x 0.1 deg., providing an atmospheric fingerprint of anthropogenic emissions for multiple trace gases. We combine the regional STILT simulations with lateral boundary conditions for CO2 and CO from MACC forecasts and CH4 from TM3 simulations. Here we apply this framework to airborne in-situ measurements made in the context of IAGOS (In-service Aircraft for a Global Observing System) and in the context of a HALO mission conducted for testing the active remote sensing system CHARM-F during April/May 2015 over central Europe. Simulated tracer distributions are compared to observed profiles of CO2, CH4, and CO, and the potential for a multi-species inversion using synergies between different tracers is assessed with respect to the uncertainty reduction in retrieved emission fluxes. Implications for inversions solving for anthropogenic emissions using atmospheric observations from ICOS (Integrated Carbon Observing System) are discussed.

Hierarchical calibration and validation of computational fluid dynamics models for solid sorbent-based carbon capture

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

Lai, Canhai; Xu, Zhijie; Pan, Wenxiao

2016-01-01

To quantify the predictive confidence of a solid sorbent-based carbon capture design, a hierarchical validation methodology—consisting of basic unit problems with increasing physical complexity coupled with filtered model-based geometric upscaling has been developed and implemented. This paper describes the computational fluid dynamics (CFD) multi-phase reactive flow simulations and the associated data flows among different unit problems performed within the said hierarchical validation approach. The bench-top experiments used in this calibration and validation effort were carefully designed to follow the desired simple-to-complex unit problem hierarchy, with corresponding data acquisition to support model parameters calibrations at each unit problem level. A Bayesianmore » calibration procedure is employed and the posterior model parameter distributions obtained at one unit-problem level are used as prior distributions for the same parameters in the next-tier simulations. Overall, the results have demonstrated that the multiphase reactive flow models within MFIX can be used to capture the bed pressure, temperature, CO2 capture capacity, and kinetics with quantitative accuracy. The CFD modeling methodology and associated uncertainty quantification techniques presented herein offer a solid framework for estimating the predictive confidence in the virtual scale up of a larger carbon capture device.« less

The nuclear question: rethinking species importance in multi-species animal groups.

PubMed

Srinivasan, Umesh; Raza, Rashid Hasnain; Quader, Suhel

2010-09-01

1. Animals group for various benefits, and may form either simple single-species groups, or more complex multi-species associations. Multi-species groups are thought to provide anti-predator and foraging benefits to participant individuals. 2. Despite detailed studies on multi-species animal groups, the importance of species in group initiation and maintenance is still rated qualitatively as 'nuclear' (maintaining groups) or 'attendant' (species following nuclear species) based on species-specific traits. This overly simplifies and limits understanding of inherently complex associations, and is biologically unrealistic, because species roles in multi-species groups are: (i) likely to be context-specific and not simply a fixed species property, and (ii) much more variable than this dichotomy indicates. 3. We propose a new view of species importance (measured as number of inter-species associations), along a continuum from 'most nuclear' to 'least nuclear'. Using mixed-species bird flocks from a tropical rainforest in India as an example, we derive inter-species association measures from randomizations on bird species abundance data (which takes into account species 'availability') and data on 86 mixed-species flocks from two different flock types. Our results show that the number and average strength of inter-species associations covary positively, and we argue that species with many, strong associations are the most nuclear. 4. From our data, group size and foraging method are ecological and behavioural traits of species that best explain nuclearity in mixed-species bird flocks. Parallels have been observed in multi-species fish shoals, in which group size and foraging method, as well as diet, have been shown to correlate with nuclearity. Further, the context in which multi-species groups occur, in conjunction with species-specific traits, influences the role played by a species in a multi-species group, and this highlights the importance of extrinsic factors in shaping species importance. 5. Our view of nuclearity provides predictive power in examining species roles in a variety of situations (e.g. predicting leadership in differently composed communities), and can be applied to examine a broad range of ecological and evolutionary questions pertinent to multi-species groups in general.

Nonenzymatic Reactions above Phospholipid Surfaces of Biological Membranes: Reactivity of Phospholipids and Their Oxidation Derivatives

PubMed Central

Solís-Calero, Christian; Ortega-Castro, Joaquín; Frau, Juan; Muñoz, Francisco

2015-01-01

Phospholipids play multiple and essential roles in cells, as components of biological membranes. Although phospholipid bilayers provide the supporting matrix and surface for many enzymatic reactions, their inherent reactivity and possible catalytic role have not been highlighted. As other biomolecules, phospholipids are frequent targets of nonenzymatic modifications by reactive substances including oxidants and glycating agents which conduct to the formation of advanced lipoxidation end products (ALEs) and advanced glycation end products (AGEs). There are some theoretical studies about the mechanisms of reactions related to these processes on phosphatidylethanolamine surfaces, which hypothesize that cell membrane phospholipids surface environment could enhance some reactions through a catalyst effect. On the other hand, the phospholipid bilayers are susceptible to oxidative damage by oxidant agents as reactive oxygen species (ROS). Molecular dynamics simulations performed on phospholipid bilayers models, which include modified phospholipids by these reactions and subsequent reactions that conduct to formation of ALEs and AGEs, have revealed changes in the molecular interactions and biophysical properties of these bilayers as consequence of these reactions. Then, more studies are desirable which could correlate the biophysics of modified phospholipids with metabolism in processes such as aging and diseases such as diabetes, atherosclerosis, and Alzheimer's disease. PMID:25977746

Reactive pathways of hydrogen and carbon removal from organosilicate glass low- κ films by F atoms

NASA Astrophysics Data System (ADS)

Voronina, Ekaterina N.; Mankelevich, Yuri A.; Rakhimova, Tatyana V.

2017-07-01

Direct molecular dynamic simulation on the base of the density functional theory (DFT) method is used to study some critical reactions of F atoms with organosilicate glass (OSG) low-κ films. Here static and dynamic DFT-based approaches are applied for a variety of reactive pathways of hydrogen and carbon removal in the form of volatile products (HF, CF2 and CF3 molecules) from initial SiCH3 surface groups. These reactions constitute an important part of the proposed multi-step mechanism of OSG films damage and etching by thermal F atoms. Two models (POSS and TMCTS macromolecules and their modifications) are used to illustrate the peculiarities and dynamics of the successive reactions of F atoms with the initial SiCH3 and appeared SiCHxFy (x + y ≤ 3) surface groups. Contribution to the Topical Issue "Dynamics of Molecular Systems (MOLEC 2016)", edited by Alberto Garcia-Vela, Luis Banares and Maria Luisa Senent.

Lattice Boltzmann simulation of dissolution-induced changes in permeability and porosity in 3D CO2 reactive transport

NASA Astrophysics Data System (ADS)

Tian, Zhiwei; Wang, Junye

2018-02-01

Dissolution and precipitation of rock matrix are one of the most important processes of geological CO2 sequestration in reservoirs. They change connections of pore channels and properties of matrix, such as bulk density, microporosity and hydraulic conductivity. This study builds on a recently developed multi-layer model to account for dynamic changes of microporous matrix that can accurately predict variations in hydraulic properties and reaction rates due to dynamic changes in matrix porosity and pore connectivity. We apply the model to simulate the dissolution and precipitation processes of rock matrix in heterogeneous porous media to quantify (1) the effect of the reaction rate on dissolution and matrix porosity, (2) the effect of microporous matrix diffusion on the overall effective diffusion and (3) the effect of heterogeneity on hydraulic conductivity. The results show the CO2 storage influenced by factors including the matrix porosity change, reaction front movement, velocity and initial properties. We also simulated dissolution-induced permeability enhancement as well as effects of initial porosity heterogeneity. The matrix with very low permeability, which can be unresolved on X-ray CT, do contribute to flow patterns and dispersion. The concentration of reactant H+ increases along the main fracture paths where the flow velocity increases. The product Ca++ shows the inversed distribution pattern against the H+ concentration. This demonstrates the capability of this model to investigate the complex CO2 reactive transport in real 3D heterogeneous porous media.

Comparison of OH reactivity instruments in the atmosphere simulation chamber SAPHIR

NASA Astrophysics Data System (ADS)

Fuchs, Hendrik

2016-04-01

OH reactivity measurement has become an important measurement to constrain the total OH loss frequency in field experiments. Different techniques have been developed by various groups. They can be based on flow-tube or pump and probe techniques, which include direct OH detection by fluorescence, or on a comparative method, in which the OH loss of a reference species competes with the OH loss of trace gases in the sampled air. In order to ensure that these techniques deliver equivalent results, a comparison exercise was performed under controlled conditions. Nine OH reactivity instruments measured together in the atmosphere simulation chamber SAPHIR (volume 270 m3) during ten daylong experiments in October 2015 at ambient temperature (5 to 10° C) and pressure (990-1010 hPa). The chemical complexity of air mixtures in these experiments varied from CO in pure synthetic air to emissions from real plants and VOC/NOx mixtures representative of urban atmospheres. Potential differences between measurements were systematically investigated by changing the amount of reactants (including isoprene, monoterpenes and sesquiterpenes), water vapour, and nitrogen oxides. Some of the experiments also included the oxidation of reactants with ozone or hydroxyl radicals, in order to elaborate, if the presence of oxidation products leads to systematic differences between measurements of different instruments. Here we present first results of this comparison exercise.

Comparison of two strategies for detection of reactive oxygen species

NASA Astrophysics Data System (ADS)

Gao, Weidong; Zhou, Yuanshu; Gu, Yueqing

2014-09-01

Photodynamic therapy (PDT) is a clinically approved treatment that was applied to oncology , dermatology, and ophthalmology. Reactive oxygen species (ROS) play a important role in the efficacy of PDT. Online monitoring of reactive oxygen species is the key to understand effect of PDT treatment. We used Fluorescence probes DPBF and luminescent probe luminal to measure the ROS in cells. And we revaluate the relationship between the amount of light and cell survival. There is strongly correlated between the amount of light and cell kill.

Final Technical Report

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

Alexander Pigarov

2012-06-05

This is the final report for the Research Grant DE-FG02-08ER54989 'Edge Plasma Simulations in NSTX and CTF: Synergy of Lithium Coating, Non-Diffusive Anomalous Transport and Drifts'. The UCSD group including: A.Yu. Pigarov (PI), S.I. Krasheninnikov and R.D. Smirnov, was working on modeling of the impact of lithium coatings on edge plasma parameters in NSTX with the multi-species multi-fluid code UEDGE. The work was conducted in the following main areas: (i) improvements of UEDGE model for plasma-lithium interactions, (ii) understanding the physics of low-recycling divertor regime in NSTX caused by lithium pumping, (iii) study of synergistic effects with lithium coatings andmore » non-diffusive ballooning-like cross-field transport, (iv) simulation of experimental multi-diagnostic data on edge plasma with lithium pumping in NSTX via self-consistent modeling of D-Li-C plasma with UEDGE, and (v) working-gas balance analysis. The accomplishments in these areas are given in the corresponding subsections in Section 2. Publications and presentations made under the Grant are listed in Section 3.« less

Multi-variable mathematical models for the air-cathode microbial fuel cell system

NASA Astrophysics Data System (ADS)

Ou, Shiqi; Kashima, Hiroyuki; Aaron, Douglas S.; Regan, John M.; Mench, Matthew M.

2016-05-01

This research adopted the version control system into the model construction for the single chamber air-cathode microbial fuel cell (MFC) system, to understand the interrelation of biological, chemical, and electrochemical reactions. The anodic steady state model was used to consider the chemical species diffusion and electric migration influence to the MFC performance. In the cathodic steady state model, the mass transport and reactions in a multi-layer, abiotic cathode and multi-bacteria cathode biofilm were simulated. Transport of hydroxide was assumed for cathodic pH change. This assumption is an alternative to the typical notion of proton consumption during oxygen reduction to explain elevated cathode pH. The cathodic steady state model provided the power density and polarization curve performance results that can be compared to an experimental MFC system. Another aspect considered was the relative contributions of platinum catalyst and microbes on the cathode to the oxygen reduction reaction (ORR). Simulation results showed that the biocatalyst in a cathode that includes a Pt/C catalyst likely plays a minor role in ORR, contributing up to 8% of the total power calculated by the models.

Effects of Langmuir Turbulence on Reactive Tracers in the Upper Ocean

NASA Astrophysics Data System (ADS)

Smith, K.; Hamlington, P.; Niemeyer, K.; Fox-Kemper, B.; Lovenduski, N. S.

2017-12-01

Reactive tracers such as carbonate chemical species play important roles in the oceanic carbon cycle, allowing the ocean to hold 60 times more carbon than the atmosphere. However, uncertainties in regional ocean sinks for anthropogenic CO2 are still relatively high. Many carbonate species are non-conserved, flux across the air-sea interface, and react on time scales similar to those of ocean turbulent processes, such as small-scale wave-driven Langmuir turbulence. All of this complexity gives rise to heterogeneous tracer distributions that are not fully understood and can greatly affect the rate at which CO2 fluxes across the air-sea interface. In order to more accurately model the biogeochemistry of the ocean in Earth system models (ESMs), a better understanding of the fundamental interactions between these reactive tracers and relevant turbulent processes is required. Research on reacting flows in other contexts has shown that the most significant tracer-flow couplings occur when coherent structures in the flow have timescales that rival reaction time scales. Langmuir turbulence, a 3D, small-scale, wave-driven process, has length and time scales on the order of O(1-100m) and O(1-10min), respectively. Once CO2 transfers across the air-sea interface, it reacts with seawater in a series of reactions whose rate limiting steps have time scales of 10-25s. This similarity in scales warrants further examination into interactions between these small-scale physical and chemical processes. In this presentation, large eddy simulations are used to examine the evolution of reactive tracers in the presence of realistic upper ocean wave- and shear-driven turbulence. The reactive tracers examined are those specifically involved in non-biological carbonate chemistry. The strength of Langmuir turbulence is varied in order to determine a relationship between the degree of enhancement (or reduction) of carbon that is fluxed across the air-sea interface due to the presence of Langmuir turbulence. By examining different reaction chemistry and surface forcing scenarios, the coupled turbulence-reactive tracer dynamics are connected with spatial and statistical properties of the resulting tracer fields. These results, along with implications for development of reduced order reactive tracer models, are discussed.

Comprehensive measurements of atmospheric OH reactivity and trace species within a suburban forest near Tokyo during AQUAS-TAMA campaign

NASA Astrophysics Data System (ADS)

Ramasamy, Sathiyamurthi; Nagai, Yoshihide; Takeuchi, Nobuhiro; Yamasaki, Shohei; Shoji, Koki; Ida, Akira; Jones, Charlotte; Tsurumaru, Hiroshi; Suzuki, Yuhi; Yoshino, Ayako; Shimada, Kojiro; Nakashima, Yoshihiro; Kato, Shungo; Hatakeyama, Shiro; Matsuda, Kazuhide; Kajii, Yoshizumi

2018-07-01

Total OH reactivity, which gives the instantaneous loss rate of OH radicals due to reactive species, is an invaluable technique to understand regional air quality, as it gives the overall reactivity of the air mass, the fraction of each trace species reactive to OH, the fraction of missing sinks, O3 formation potential, etc. Total OH reactivity measurement was conducted in a small suburban forest located ∼30 km from Tokyo during the air quality study at field museum TAMA (AQUAS-TAMA) campaign in early autumn 2012 and summer 2013. The average measured OH reactivities during that autumn and summer were 7.4 s-1 and 11.4 s-1, respectively. In summer, isoprene was the major contributor, accounting for 28.2% of the OH reactivity, as a result of enhanced light-dependent biogenic emission, whereas NO2 was major contributor in autumn, accounting for 19.6%, due to the diminished contribution from isoprene as a result of lower solar strength. Higher missing OH reactivity 34% was determined in summer, and linear regression analysis showed that oxygenated VOCs could be the potential candidates for missing OH reactivity. Lower missing OH reactivity 25% was determined in autumn and it was significantly reduced (11%) if the interference of peroxy radicals to the measured OH reactivity were considered.

Surrogate model approach for improving the performance of reactive transport simulations

NASA Astrophysics Data System (ADS)

Jatnieks, Janis; De Lucia, Marco; Sips, Mike; Dransch, Doris

2016-04-01

Reactive transport models can serve a large number of important geoscientific applications involving underground resources in industry and scientific research. It is common for simulation of reactive transport to consist of at least two coupled simulation models. First is a hydrodynamics simulator that is responsible for simulating the flow of groundwaters and transport of solutes. Hydrodynamics simulators are well established technology and can be very efficient. When hydrodynamics simulations are performed without coupled geochemistry, their spatial geometries can span millions of elements even when running on desktop workstations. Second is a geochemical simulation model that is coupled to the hydrodynamics simulator. Geochemical simulation models are much more computationally costly. This is a problem that makes reactive transport simulations spanning millions of spatial elements very difficult to achieve. To address this problem we propose to replace the coupled geochemical simulation model with a surrogate model. A surrogate is a statistical model created to include only the necessary subset of simulator complexity for a particular scenario. To demonstrate the viability of such an approach we tested it on a popular reactive transport benchmark problem that involves 1D Calcite transport. This is a published benchmark problem (Kolditz, 2012) for simulation models and for this reason we use it to test the surrogate model approach. To do this we tried a number of statistical models available through the caret and DiceEval packages for R, to be used as surrogate models. These were trained on randomly sampled subset of the input-output data from the geochemical simulation model used in the original reactive transport simulation. For validation we use the surrogate model to predict the simulator output using the part of sampled input data that was not used for training the statistical model. For this scenario we find that the multivariate adaptive regression splines (MARS) method provides the best trade-off between speed and accuracy. This proof-of-concept forms an essential step towards building an interactive visual analytics system to enable user-driven systematic creation of geochemical surrogate models. Such a system shall enable reactive transport simulations with unprecedented spatial and temporal detail to become possible. References: Kolditz, O., Görke, U.J., Shao, H. and Wang, W., 2012. Thermo-hydro-mechanical-chemical processes in porous media: benchmarks and examples (Vol. 86). Springer Science & Business Media.

Method of conditional moments (MCM) for the Chemical Master Equation: a unified framework for the method of moments and hybrid stochastic-deterministic models.

PubMed

Hasenauer, J; Wolf, V; Kazeroonian, A; Theis, F J

2014-09-01

The time-evolution of continuous-time discrete-state biochemical processes is governed by the Chemical Master Equation (CME), which describes the probability of the molecular counts of each chemical species. As the corresponding number of discrete states is, for most processes, large, a direct numerical simulation of the CME is in general infeasible. In this paper we introduce the method of conditional moments (MCM), a novel approximation method for the solution of the CME. The MCM employs a discrete stochastic description for low-copy number species and a moment-based description for medium/high-copy number species. The moments of the medium/high-copy number species are conditioned on the state of the low abundance species, which allows us to capture complex correlation structures arising, e.g., for multi-attractor and oscillatory systems. We prove that the MCM provides a generalization of previous approximations of the CME based on hybrid modeling and moment-based methods. Furthermore, it improves upon these existing methods, as we illustrate using a model for the dynamics of stochastic single-gene expression. This application example shows that due to the more general structure, the MCM allows for the approximation of multi-modal distributions.

PhreeqcRM: A reaction module for transport simulators based on the geochemical model PHREEQC

USGS Publications Warehouse

Parkhurst, David L.; Wissmeier, Laurin

2015-01-01

PhreeqcRM is a geochemical reaction module designed specifically to perform equilibrium and kinetic reaction calculations for reactive transport simulators that use an operator-splitting approach. The basic function of the reaction module is to take component concentrations from the model cells of the transport simulator, run geochemical reactions, and return updated component concentrations to the transport simulator. If multicomponent diffusion is modeled (e.g., Nernst–Planck equation), then aqueous species concentrations can be used instead of component concentrations. The reaction capabilities are a complete implementation of the reaction capabilities of PHREEQC. In each cell, the reaction module maintains the composition of all of the reactants, which may include minerals, exchangers, surface complexers, gas phases, solid solutions, and user-defined kinetic reactants.PhreeqcRM assigns initial and boundary conditions for model cells based on standard PHREEQC input definitions (files or strings) of chemical compositions of solutions and reactants. Additional PhreeqcRM capabilities include methods to eliminate reaction calculations for inactive parts of a model domain, transfer concentrations and other model properties, and retrieve selected results. The module demonstrates good scalability for parallel processing by using multiprocessing with MPI (message passing interface) on distributed memory systems, and limited scalability using multithreading with OpenMP on shared memory systems. PhreeqcRM is written in C++, but interfaces allow methods to be called from C or Fortran. By using the PhreeqcRM reaction module, an existing multicomponent transport simulator can be extended to simulate a wide range of geochemical reactions. Results of the implementation of PhreeqcRM as the reaction engine for transport simulators PHAST and FEFLOW are shown by using an analytical solution and the reactive transport benchmark of MoMaS.

Multi-species ion transport in ICF relevant conditions

NASA Astrophysics Data System (ADS)

Vold, Erik; Kagan, Grigory; Simakov, Andrei; Molvig, Kim; Yin, Lin; Albright, Brian

2017-10-01

Classical transport theory based on Chapman-Enskog methods provides self consistent approximations for kinetic fluxes of mass, heat and momentum for each ion species in a multi-ion plasma characterized with a small Knudsen number. A numerical method for solving the classic forms of multi-ion transport, self-consistently including heat and species mass fluxes relative to the center of mass, is given in [Kagan-Baalrud, arXiv '16] and similar transport coefficients result from recent derivations [Simakov-Molvig, PoP, '16]. We have implemented a combination of these methods in a standalone test code and in xRage, an adaptive-mesh radiation hydrodynamics code, at LANL. Transport mixing is examined between a DT fuel and a CH capsule shell in ICF conditions. The four ion species develop individual self-similar density profiles under the assumption of P-T equilibrium in 1D and show interesting early time transient pressure and center of mass velocity behavior when P-T equilibrium is not enforced. Some 2D results are explored to better understand the transport mix in combination with convective flow driven by macroscopic fluid instabilities at the fuel-capsule interface. Early transient and some 2D behaviors from the fluid transport are compared to kinetic code results. Work performed under the auspices of the U.S. DOE by the LANS, LLC, Los Alamos National Laboratory under Contract No. DE-AC52-06NA25396. Funding provided by the Advanced Simulation and Computing (ASC) Program.

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

Krasheninnikov, Sergei I.; Angus, Justin; Lee, Wonjae

The goal of the Edge Simulation Laboratory (ESL) multi-institutional project is to advance scientific understanding of the edge plasma region of magnetic fusion devices via a coordinated effort utilizing modern computing resources, advanced algorithms, and ongoing theoretical development. The UCSD team was involved in the development of the COGENT code for kinetic studies across a magnetic separatrix. This work included a kinetic treatment of electrons and multiple ion species (impurities) and accurate collision operators.

Assessing multi-taxa sensitivity to the human footprint, habitat fragmentation and loss by exploring alternative scenarios of dispersal ability and population size: A simulation approach

Treesearch

Brian K. Hand; Samuel A. Cushman; Erin L. Landguth; John Lucotch

2014-01-01

Quantifying the effects of landscape change on population connectivity is compounded by uncertainties about population size and distribution and a limited understanding of dispersal ability for most species. In addition, the effects of anthropogenic landscape change and sensitivity to regional climatic conditions interact to strongly affect habitat...

Designing optimized multi-species monitoring networks to detect range shifts driven by climate change: a case study with bats in the North of Portugal.

PubMed

Amorim, Francisco; Carvalho, Sílvia B; Honrado, João; Rebelo, Hugo

2014-01-01

Here we develop a framework to design multi-species monitoring networks using species distribution models and conservation planning tools to optimize the location of monitoring stations to detect potential range shifts driven by climate change. For this study, we focused on seven bat species in Northern Portugal (Western Europe). Maximum entropy modelling was used to predict the likely occurrence of those species under present and future climatic conditions. By comparing present and future predicted distributions, we identified areas where each species is likely to gain, lose or maintain suitable climatic space. We then used a decision support tool (the Marxan software) to design three optimized monitoring networks considering: a) changes in species likely occurrence, b) species conservation status, and c) level of volunteer commitment. For present climatic conditions, species distribution models revealed that areas suitable for most species occur in the north-eastern part of the region. However, areas predicted to become climatically suitable in the future shifted towards west. The three simulated monitoring networks, adaptable for an unpredictable volunteer commitment, included 28, 54 and 110 sampling locations respectively, distributed across the study area and covering the potential full range of conditions where species range shifts may occur. Our results show that our framework outperforms the traditional approach that only considers current species ranges, in allocating monitoring stations distributed across different categories of predicted shifts in species distributions. This study presents a straightforward framework to design monitoring schemes aimed specifically at testing hypotheses about where and when species ranges may shift with climatic changes, while also ensuring surveillance of general population trends.

Developmental origins of infant stress reactivity profiles: A multi-system approach.

PubMed

Rash, Joshua A; Thomas, Jenna C; Campbell, Tavis S; Letourneau, Nicole; Granger, Douglas A; Giesbrecht, Gerald F

2016-07-01

This study tested the hypothesis that maternal physiological and psychological variables during pregnancy discriminate between theoretically informed infant stress reactivity profiles. The sample comprised 254 women and their infants. Maternal mood, salivary cortisol, respiratory sinus arrhythmia (RSA), and salivary α-amylase (sAA) were assessed at 15 and 32 weeks gestational age. Infant salivary cortisol, RSA, and sAA reactivity were assessed in response to a structured laboratory frustration task at 6 months of age. Infant responses were used to classify them into stress reactivity profiles using three different classification schemes: hypothalamic-pituitary-adrenal (HPA)-axis, autonomic, and multi-system. Discriminant function analyses evaluated the prenatal variables that best discriminated infant reactivity profiles within each classification scheme. Maternal stress biomarkers, along with self-reported psychological distress during pregnancy, discriminated between infant stress reactivity profiles. These results suggest that maternal psychological and physiological states during pregnancy have broad effects on the development of the infant stress response systems. © 2016 Wiley Periodicals, Inc. Dev Psychobiol 58: 578-599, 2016. © 2016 Wiley Periodicals, Inc.

Comparison of cellular toxicity between multi-walled carbon nanotubes and onion-like shell-shaped carbon nanoparticles

NASA Astrophysics Data System (ADS)

Kang, Seunghyon; Kim, Ji-Eun; Kim, Daegyu; Woo, Chang Gyu; Pikhitsa, Peter V.; Cho, Myung-Haing; Choi, Mansoo

2015-09-01

The cellular toxicity of multi-walled carbon nanotubes (MWCNTs) and onion-like shell-shaped carbon nanoparticles (SCNPs) was investigated by analyzing the comparative cell viability. For the reasonable comparison, physicochemical characteristics were controlled thoroughly such as crystallinity, carbon bonding characteristic, hydrodynamic diameter, and metal contents of the particles. To understand relation between cellular toxicity of the particles and generation of reactive oxygen species (ROS), we measured unpaired singlet electrons of the particles and intracellular ROS, and analyzed cellular toxicity with/without the antioxidant N-acetylcysteine (NAC). Regardless of the presence of NAC, the cellular toxicity of SCNPs was found to be lower than that of MWCNTs. Since both particles show similar crystallinity, hydrodynamic size, and Raman signal with negligible contribution of remnant metal particles, the difference in cell viability would be ascribed to the difference in morphology, i.e., spherical shape (aspect ratio of one) for SCNP and elongated shape (high aspect ratio) for MWCNT.

Multi-walled carbon nanotubes suppress potassium channel activities in PC12 cells

NASA Astrophysics Data System (ADS)

Xu, Haifei; Bai, Juan; Meng, Jie; Hao, Wei; Xu, Haiyan; Cao, Ji-Min

2009-07-01

The advancement in nanotechnology has produced technological and conceptual breakthroughs but the effects nanomaterials have on organisms at the cellular level are poorly understood. Here we report that carboxyl-terminated multi-walled carbon nanotubes (MWCNTs) act as antagonists of three types of potassium channels as assessed by whole-cell patch clamp electrophysiology on undifferentiated pheochromocytoma (PC12) cells. Our results showed that carboxyl-terminated MWCNTs suppress the current densities of Ito, IK and IK1 in a time-dependent and irreversible manner. The suppressions were most distinct 24 h after incubation with MWCNTs. However, MWCNTs did not significantly change the expression levels of reactive oxygen species (ROS) or intracellular free calcium and also did not alter the mitochondrial membrane potential (ΔΨm) in PC12 cells. These results suggest that oxidative stress was not involved in the MWCNTs suppression of Ito, IK and IK1 current densities. Nonetheless, the suppression of potassium currents by MWCNTs will impact on electrical signaling of excitable cells such as neurons and muscles.

Cellular cytotoxic response induced by highly purified multi-wall carbon nanotube in human lung cells.

PubMed

Tsukahara, Tamotsu; Haniu, Hisao

2011-06-01

Carbon nanotubes, a promising nanomaterial with unique characteristics, have applications in a variety of fields. The cytotoxic effects of carbon nanotubes are partially due to the induction of oxidative stress; however, the detailed mechanisms of nanotube cytotoxicity and their interaction with cells remain unclear. In this study, the authors focus on the acute toxicity of vapor-grown carbon fiber, HTT2800, which is one of the most highly purified multi-wall carbon nanotubes (MWCNT) by high-temperature thermal treatment. The authors exposed human bronchial epithelial cells (BEAS-2B) to HTT2800 and measured the cellular uptake, mitochondrial function, cellular LDH release, apoptotic signaling, reactive oxygen species (ROS) generation and pro-inflammatory cytokine release. The HTT2800-exposed cells showed cellular uptake of the carbon nanotube, increased cell death, enhanced DNA damage, and induced cytokine release. However, the exposed cells showed no obvious intracellular ROS generation. These cellular and molecular findings suggest that HTT2800 could cause a potentially adverse inflammatory response in BEAS-2B cells.

Damaging Effects of Multi-walled Carbon Nanotubes on Pregnant Mice with Different Pregnancy Times

NASA Astrophysics Data System (ADS)

Qi, Wei; Bi, Juanjuan; Zhang, Xiaoyong; Wang, Jing; Wang, Jianjun; Liu, Peng; Li, Zhan; Wu, Wangsuo

2014-03-01

The mechanism by which nanoparticles cross the placental barrier was studied by using isotopic tracers. The abortion rates and other related data were counted and analysed in pregnant mice with different pregnancy times. Results showed that oxidised multi-walled carbon nanotubes (oMWCNTs) crossed the placental barrier and entered the foetus body. The abortion rates in the pregnant mice depended on pregnancy times. The abortion rates in the first-time, second-time and fourth-time pregnant mice were 70%, 40% and 50%, respectively. The maternal body weight gain was inhibited until gestational ages of 13, 10 and 11 d. oMWCNTs decreased the serum progesterone level and increased the serum oestradiol level in a dose- and time-dependent manner. However, this effect decreased with gestational age. The histology and vascular endothelial growth factor/reactive oxygen species content in the placenta showed that oMWCNTs narrowed the blood vessel and decreased the number of blood vessels in the placenta.

Simulations of multi-component explosives using simplified geometric arrangements of their constituents

NASA Astrophysics Data System (ADS)

Butler, George; Pemberton, Steven

2017-06-01

Modeling and simulation is extremely important in the design and formulation of new explosives and explosive devices due to the high cost of experiment-based development. However, the efficacy of simulations depends on the accuracy of the equations of state (EOS) and reactive burn models used to characterize the energetic materials. We investigate the possibility of using the components of an explosive fill as discrete elements in a simulation, based on the relative amounts of the constituents. This is accomplished by assembling a mosaic, or ``checkerboard'', in which each cell comprises the relative amounts of the constituents as in the mixture; it is assumed that each constituent has a well-defined set of simulation parameters. We do not consider the underlying microstructure, and recognize there will be limitations to the usefulness of this technique. We are interested in determining whether there are applications for this technique that might prove useful. As a test of the concept, two binary explosives were considered. We considered shapes for a periodic cellular structure and compared results from the checkerboards with those of the baseline explosives; detonation rates, cylinder expansion, and gap test predictions were compared.

A tomographic technique for the simultaneous imaging of temperature, chemical species, and pressure in reactive flows using absorption spectroscopy with frequency-agile lasers

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

Cai, Weiwei; Kaminski, Clemens F., E-mail: cfk23@cam.ac.uk

2014-01-20

This paper proposes a technique that can simultaneously retrieve distributions of temperature, concentration of chemical species, and pressure based on broad bandwidth, frequency-agile tomographic absorption spectroscopy. The technique holds particular promise for the study of dynamic combusting flows. A proof-of-concept numerical demonstration is presented, using representative phantoms to model conditions typically prevailing in near-atmospheric or high pressure flames. The simulations reveal both the feasibility of the proposed technique and its robustness. Our calculations indicate precisions of ∼70 K at flame temperatures and ∼0.05 bars at high pressure from reconstructions featuring as much as 5% Gaussian noise in the projections.

The impact of (n, γ) reaction rate uncertainties of unstable isotopes near N = 50 on the i-process nucleosynthesis in He-shell flash white dwarfs

NASA Astrophysics Data System (ADS)

Denissenkov, Pavel; Perdikakis, Georgios; Herwig, Falk; Schatz, Hendrik; Ritter, Christian; Pignatari, Marco; Jones, Samuel; Nikas, Stylianos; Spyrou, Artemis

2018-05-01

The first-peak s-process elements Rb, Sr, Y and Zr in the post-AGB star Sakurai's object (V4334 Sagittarii) have been proposed to be the result of i-process nucleosynthesis in a post-AGB very-late thermal pulse event. We estimate the nuclear physics uncertainties in the i-process model predictions to determine whether the remaining discrepancies with observations are significant and point to potential issues with the underlying astrophysical model. We find that the dominant source in the nuclear physics uncertainties are predictions of neutron capture rates on unstable neutron rich nuclei, which can have uncertainties of more than a factor 20 in the band of the i-process. We use a Monte Carlo variation of 52 neutron capture rates and a 1D multi-zone post-processing model for the i-process in Sakurai's object to determine the cumulative effect of these uncertainties on the final elemental abundance predictions. We find that the nuclear physics uncertainties are large and comparable to observational errors. Within these uncertainties the model predictions are consistent with observations. A correlation analysis of the results of our MC simulations reveals that the strongest impact on the predicted abundances of Rb, Sr, Y and Zr is made by the uncertainties in the (n, γ) reaction rates of 85Br, 86Br, 87Kr, 88Kr, 89Kr, 89Rb, 89Sr, and 92Sr. This conclusion is supported by a series of multi-zone simulations in which we increased and decreased to their maximum and minimum limits one or two reaction rates per run. We also show that simple and fast one-zone simulations should not be used instead of more realistic multi-zone stellar simulations for nuclear sensitivity and uncertainty studies of convective–reactive processes. Our findings apply more generally to any i-process site with similar neutron exposure, such as rapidly accreting white dwarfs with near-solar metallicities.

Up-regulation of A1M/α1-microglobulin in skin by heme and reactive oxygen species gives protection from oxidative damage.

PubMed

Olsson, Magnus G; Allhorn, Maria; Larsson, Jörgen; Cederlund, Martin; Lundqvist, Katarina; Schmidtchen, Artur; Sørensen, Ole E; Mörgelin, Matthias; Akerström, Bo

2011-01-01

During bleeding the skin is subjected to oxidative insults from free heme and radicals, generated from extracellular hemoglobin. The lipocalin α(1)-microglobulin (A1M) was recently shown to have reductase properties, reducing heme-proteins and other substrates, and to scavenge heme and radicals. We investigated the expression and localization of A1M in skin and the possible role of A1M in the protection of skin tissue from damage induced by heme and reactive oxygen species. Skin explants, keratinocyte cultures and purified collagen I were exposed to heme, reactive oxygen species, and/or A1M and investigated by biochemical methods and electron microscopy. The results demonstrate that A1M is localized ubiquitously in the dermal and epidermal layers, and that the A1M-gene is expressed in keratinocytes and up-regulated after exposure to heme and reactive oxygen species. A1M inhibited the heme- and reactive oxygen species-induced ultrastructural damage, up-regulation of antioxidation and cell cycle regulatory genes, and protein carbonyl formation in skin and keratinocytes. Finally, A1M bound to purified collagen I (K(d) = 0.96×10(-6) M) and could inhibit and repair the destruction of collagen fibrils by heme and reactive oxygen species. The results suggest that A1M may have a physiological role in protection of skin cells and matrix against oxidative damage following bleeding.

Multi-phenology WorldView-2 imagery improves remote sensing of savannah tree species

NASA Astrophysics Data System (ADS)

Madonsela, Sabelo; Cho, Moses Azong; Mathieu, Renaud; Mutanga, Onisimo; Ramoelo, Abel; Kaszta, Żaneta; Kerchove, Ruben Van De; Wolff, Eléonore

2017-06-01

Biodiversity mapping in African savannah is important for monitoring changes and ensuring sustainable use of ecosystem resources. Biodiversity mapping can benefit from multi-spectral instruments such as WorldView-2 with very high spatial resolution and a spectral configuration encompassing important spectral regions not previously available for vegetation mapping. This study investigated i) the benefits of the eight-band WorldView-2 (WV-2) spectral configuration for discriminating tree species in Southern African savannah and ii) if multiple-images acquired at key points of the typical phenological development of savannahs (peak productivity, transition to senescence) improve on tree species classifications. We first assessed the discriminatory power of WV-2 bands using interspecies-Spectral Angle Mapper (SAM) via Band Add-On procedure and tested the spectral capability of WorldView-2 against simulated IKONOS for tree species classification. The results from interspecies-SAM procedure identified the yellow and red bands as the most statistically significant bands (p = 0.000251 and p = 0.000039 respectively) in the discriminatory power of WV-2 during the transition from wet to dry season (April). Using Random Forest classifier, the classification scenarios investigated showed that i) the 8-bands of the WV-2 sensor achieved higher classification accuracy for the April date (transition from wet to dry season, senescence) compared to the March date (peak productivity season) ii) the WV-2 spectral configuration systematically outperformed the IKONOS sensor spectral configuration and iii) the multi-temporal approach (March and April combined) improved the discrimination of tress species and produced the highest overall accuracy results at 80.4%. Consistent with the interspecies-SAM procedure, the yellow (605 nm) band also showed a statistically significant contribution in the improved classification accuracy from WV-2. These results highlight the mapping opportunities presented by WV-2 data for monitoring the distribution status of e.g. species often harvested by local communities (e.g. Sclerocharya birrea), encroaching species, or species-specific tree losses induced by elephants.

Toward efficiency in heterogeneous multispecies reactive transport modeling: A particle-tracking solution for first-order network reactions

NASA Astrophysics Data System (ADS)

Henri, Christopher V.; Fernàndez-Garcia, Daniel

2014-09-01

Modeling multispecies reactive transport in natural systems with strong heterogeneities and complex biochemical reactions is a major challenge for assessing groundwater polluted sites with organic and inorganic contaminants. A large variety of these contaminants react according to serial-parallel reaction networks commonly simplified by a combination of first-order kinetic reactions. In this context, a random-walk particle tracking method is presented. This method is capable of efficiently simulating the motion of particles affected by first-order network reactions in three-dimensional systems, which are represented by spatially variable physical and biochemical coefficients described at high resolution. The approach is based on the development of transition probabilities that describe the likelihood that particles belonging to a given species and location at a given time will be transformed into and moved to another species and location afterward. These probabilities are derived from the solution matrix of the spatial moments governing equations. The method is fully coupled with reactions, free of numerical dispersion and overcomes the inherent numerical problems stemming from the incorporation of heterogeneities to reactive transport codes. In doing this, we demonstrate that the motion of particles follows a standard random walk with time-dependent effective retardation and dispersion parameters that depend on the initial and final chemical state of the particle. The behavior of effective parameters develops as a result of differential retardation effects among species. Moreover, explicit analytic solutions of the transition probability matrix and related particle motions are provided for serial reactions. An example of the effect of heterogeneity on the dechlorination of organic solvents in a three-dimensional random porous media shows that the power-law behavior typically observed in conservative tracers breakthrough curves can be largely compromised by the effect of biochemical reactions.

Glutathionylation and Reduction of Methacrolein in Tomato Plants Account for Its Absorption from the Vapor Phase1[OPEN

PubMed Central

Muramoto, Shoko; Matsubara, Yayoi; Mwenda, Cynthia Mugo; Koeduka, Takao; Sakami, Takuya; Tani, Akira; Matsui, Kenji

2015-01-01

A large portion of the volatile organic compounds emitted by plants are oxygenated to yield reactive carbonyl species, which have a big impact on atmospheric chemistry. Deposition to vegetation driven by the absorption of reactive carbonyl species into plants plays a major role in cleansing the atmosphere, but the mechanisms supporting this absorption have been little examined. Here, we performed model experiments using methacrolein (MACR), one of the major reactive carbonyl species formed from isoprene, and tomato (Solanum lycopersicum) plants. Tomato shoots enclosed in a jar with MACR vapor efficiently absorbed MACR. The absorption efficiency was much higher than expected from the gas/liquid partition coefficient of MACR, indicating that MACR was likely metabolized in leaf tissues. Isobutyraldehyde, isobutyl alcohol, and methallyl alcohol (MAA) were detected in the headspace and inside tomato tissues treated with MACR vapor, suggesting that MACR was enzymatically reduced. Glutathione (GSH) conjugates of MACR (MACR-GSH) and MAA (MAA-GSH) were also detected. MACR-GSH was essentially formed through spontaneous conjugation between endogenous GSH and exogenous MACR, and reduction of MACR-GSH to MAA-GSH was likely catalyzed by an NADPH-dependent enzyme in tomato leaves. Glutathionylation was the metabolic pathway most responsible for the absorption of MACR, but when the amount of MACR exceeded the available GSH, MACR that accumulated reduced photosynthetic capacity. In an experiment simulating the natural environment using gas flow, MACR-GSH and MAA-GSH accumulation accounted for 30% to 40% of the MACR supplied. These results suggest that MACR metabolism, especially spontaneous glutathionylation, is an essential factor supporting MACR absorption from the atmosphere by tomato plants. PMID:26169680

Direct Numerical Simulation of a Cavity-Stabilized Ethylene/Air Premixed Flame

NASA Astrophysics Data System (ADS)

Chen, Jacqueline; Konduri, Aditya; Kolla, Hemanth; Rauch, Andreas; Chelliah, Harsha

2016-11-01

Cavity flame holders have been shown to be important for flame stabilization in scramjet combustors. In the present study the stabilization of a lean premixed ethylene/air flame in a rectangular cavity at thermo-chemical conditions relevant to scramjet combustors is simulated using a compressible reacting multi-block direct numerical simulation solver, S3D, incorporating a 22 species ethylene-air reduced chemical model. The fuel is premixed with air to an equivalence ratio of 0.4 and enters the computational domain at Mach numbers between 0.3 and 0.6. An auxiliary inert channel flow simulation is used to provide the turbulent velocity profile at the inlet for the reacting flow simulation. The detailed interaction between intense turbulence, nonequilibrium concentrations of radical species formed in the cavity and mixing with the premixed main stream under density variations due to heat release rate and compressibility effects is quantified. The mechanism for flame stabilization is quantified in terms of relevant non-dimensional parameters, and detailed analysis of the flame and turbulence structure will be presented. We acknowledge the sponsorship of the AFOSR-NSF Joint Effort on Turbulent Combustion Model Assumptions and the DOE Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences, and Biosciences.

Cross-Reactivity between Immunoglobulin G Antibodies of Whales and Dolphins Correlates with Evolutionary Distance▿

PubMed Central

Nollens, Hendrik H.; Ruiz, Carolina; Walsh, Michael T.; Gulland, Frances M. D.; Bossart, Gregory; Jensen, Eric D.; McBain, James F.; Wellehan, James F. X.

2008-01-01

Growing morphological and molecular evidence indicates that the porpoises, dolphins, and whales evolved within the even-toed ungulates, formerly known as Artiodactyla. These animals are now grouped in the Cetartiodactyla. We evaluated the antigenic similarity of the immunoglobulin G (IgG) molecules of 15 cetacean species and the domestic cow. The similarity was scored using three distinct antibodies raised against bottlenose dolphin (Tursiops truncatus) IgG in a Western blot, an indirect enzyme-linked immunosorbent assay (ELISA), and a competitive ELISA format. A score was generated for the genetic distance between each species and T. truncatus using the cytochrome b sequence. Each antibody displayed a distinct pattern of reactivity with the IgG antibodies of the various species. The monoclonal antibody (MAb) specific for the γ heavy chain of T. truncatus was reactive with all monodontids, delphinids, and phocoenids. The light-chain-specific MAb reacted with IgG of delphinoid and phocoenid species and one of the two mysticete species tested. The polyclonal antibody was broadly cross-reactive across all cetaceans and the domestic cow. Using the MAb specific for the γ heavy chain, the degree of IgG cross-reactivity ranged from less than 17% for the mysticetes to 106% for killer whale Orcinus orca. The IgG in beaked whale and baleen whale sera was significantly less cross-reactive with bottlenose dolphin IgG than sera from other toothed whales. A strong negative correlation was demonstrated between antigenic cross-reactivity of IgG molecules and the genetic distance of their hosts. The data generated will be useful for the development of clinical serodiagnostics in diverse cetacean species. PMID:18768672

Cross-reactivity between immunoglobulin G antibodies of whales and dolphins correlates with evolutionary distance.

PubMed

Nollens, Hendrik H; Ruiz, Carolina; Walsh, Michael T; Gulland, Frances M D; Bossart, Gregory; Jensen, Eric D; McBain, James F; Wellehan, James F X

2008-10-01

Growing morphological and molecular evidence indicates that the porpoises, dolphins, and whales evolved within the even-toed ungulates, formerly known as Artiodactyla. These animals are now grouped in the Cetartiodactyla. We evaluated the antigenic similarity of the immunoglobulin G (IgG) molecules of 15 cetacean species and the domestic cow. The similarity was scored using three distinct antibodies raised against bottlenose dolphin (Tursiops truncatus) IgG in a Western blot, an indirect enzyme-linked immunosorbent assay (ELISA), and a competitive ELISA format. A score was generated for the genetic distance between each species and T. truncatus using the cytochrome b sequence. Each antibody displayed a distinct pattern of reactivity with the IgG antibodies of the various species. The monoclonal antibody (MAb) specific for the gamma heavy chain of T. truncatus was reactive with all monodontids, delphinids, and phocoenids. The light-chain-specific MAb reacted with IgG of delphinoid and phocoenid species and one of the two mysticete species tested. The polyclonal antibody was broadly cross-reactive across all cetaceans and the domestic cow. Using the MAb specific for the gamma heavy chain, the degree of IgG cross-reactivity ranged from less than 17% for the mysticetes to 106% for killer whale Orcinus orca. The IgG in beaked whale and baleen whale sera was significantly less cross-reactive with bottlenose dolphin IgG than sera from other toothed whales. A strong negative correlation was demonstrated between antigenic cross-reactivity of IgG molecules and the genetic distance of their hosts. The data generated will be useful for the development of clinical serodiagnostics in diverse cetacean species.

Convective Dynamics and Disequilibrium Chemistry in the Atmospheres of Giant Planets and Brown Dwarfs

NASA Astrophysics Data System (ADS)

Bordwell, Baylee; Brown, Benjamin P.; Oishi, Jeffrey S.

2018-02-01

Disequilibrium chemical processes significantly affect the spectra of substellar objects. To study these effects, dynamical disequilibrium has been parameterized using the quench and eddy diffusion approximations, but little work has been done to explore how these approximations perform under realistic planetary conditions in different dynamical regimes. As a first step toward addressing this problem, we study the localized, small-scale convective dynamics of planetary atmospheres by direct numerical simulation of fully compressible hydrodynamics with reactive tracers using the Dedalus code. Using polytropically stratified, plane-parallel atmospheres in 2D and 3D, we explore the quenching behavior of different abstract chemical species as a function of the dynamical conditions of the atmosphere as parameterized by the Rayleigh number. We find that in both 2D and 3D, chemical species quench deeper than would be predicted based on simple mixing-length arguments. Instead, it is necessary to employ length scales based on the chemical equilibrium profile of the reacting species in order to predict quench points and perform chemical kinetics modeling in 1D. Based on the results of our simulations, we provide a new length scale, derived from the chemical scale height, that can be used to perform these calculations. This length scale is simple to calculate from known chemical data and makes reasonable predictions for our dynamical simulations.

Oxidants, Antioxidants, and the Beneficial Roles of Exercise-Induced Production of Reactive Species

PubMed Central

Gomes, Elisa Couto; Silva, Albená Nunes; de Oliveira, Marta Rubino

2012-01-01

This review offers an overview of the influence of reactive species produced during exercise and their effect on exercise adaptation. Reactive species and free radicals are unstable molecules that oxidize other molecules in order to become stable. Although they play important roles in our body, they can also lead to oxidative stress impairing diverse cellular functions. During exercise, reactive species can be produced mainly, but not exclusively, by the following mechanisms: electron leak at the mitochondrial electron transport chain, ischemia/reperfusion and activation of endothelial xanthine oxidase, inflammatory response, and autooxidation of catecholamines. Chronic exercise also leads to the upregulation of the body's antioxidant defence mechanism, which helps minimize the oxidative stress that may occur after an acute bout of exercise. Recent studies show a beneficial role of the reactive species, produced during a bout of exercise, that lead to important training adaptations: angiogenesis, mitochondria biogenesis, and muscle hypertrophy. The adaptations occur depending on the mechanic, and consequently biochemical, stimulus within the muscle. This is a new area of study that promises important findings in the sphere of molecular and cellular mechanisms involved in the relationship between oxidative stress and exercise. PMID:22701757

Human Survivors of Disease Outbreaks Caused by Ebola or Marburg Virus Exhibit Cross-Reactive and Long-Lived Antibody Responses.

PubMed

Natesan, Mohan; Jensen, Stig M; Keasey, Sarah L; Kamata, Teddy; Kuehne, Ana I; Stonier, Spencer W; Lutwama, Julius Julian; Lobel, Leslie; Dye, John M; Ulrich, Robert G

2016-08-01

A detailed understanding of serological immune responses to Ebola and Marburg virus infections will facilitate the development of effective diagnostic methods, therapeutics, and vaccines. We examined antibodies from Ebola or Marburg survivors 1 to 14 years after recovery from disease, by using a microarray that displayed recombinant nucleoprotein (NP), viral protein 40 (VP40), envelope glycoprotein (GP), and inactivated whole virions from six species of filoviruses. All three outbreak cohorts exhibited significant antibody responses to antigens from the original infecting species and a pattern of additional filoviruses that varied by outbreak. NP was the most cross-reactive antigen, while GP was the most specific. Antibodies from survivors of infections by Marburg marburgvirus (MARV) species were least cross-reactive, while those from survivors of infections by Sudan virus (SUDV) species exhibited the highest cross-reactivity. Based on results revealed by the protein microarray, persistent levels of antibodies to GP, NP, and VP40 were maintained for up to 14 years after infection, and survival of infection caused by one species imparted cross-reactive antibody responses to other filoviruses. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

Comparison between the water activation effects by pulsed and sinusoidal helium plasma jets

NASA Astrophysics Data System (ADS)

Xu, Han; Liu, Dingxin; Xia, Wenjie; Chen, Chen; Wang, Weitao; Liu, Zhijie; Wang, Xiaohua; Kong, Michael G.

2018-01-01

Comparisons between pulsed and sinusoidal plasma jets have been extensively reported for the discharge characteristics and gaseous reactive species, but rarely for the aqueous reactive species in water solutions treated by the two types of plasma jets. This motivates us to compare the concentrations of aqueous reactive species induced by a pulsed and a sinusoidal plasma jet, since it is widely reported that these aqueous reactive species play a crucial role in various plasma biomedical applications. Experimental results show that the aqueous H2O2, OH/O2-, and O2-/ONOO- induced by the pulsed plasma jet have higher concentrations, and the proportional difference increases with the discharge power. However, the emission intensities of OH(A) and O(3p5P) are higher for the sinusoidal plasma jet, which may be attributed to its higher gas temperature since more water vapor could participate in the plasma. In addition, the efficiency of bacterial inactivation induced by the pulsed plasma jet is higher than that for the sinusoidal plasma jet, in accordance with the concentration relation of aqueous reactive species for the two types of plasma jets.

Acoustic classification of multiple simultaneous bird species: a multi-instance multi-label approach

Treesearch

F. Briggs; B. Lakshminarayanan; L. Neal; X.Z. Fern; R. Raich; S.F. Hadley; A.S. Hadley; M.G. Betts

2012-01-01

Although field-collected recordings typically contain multiple simultaneously vocalizing birds of different species, acoustic species classification in this setting has received little study so far. This work formulates the problem of classifying the set of species present in an audio recording using the multi-instance multi-label (MIML) framework for machine learning...

[Modulating Effect of Extracellular HSP70 on Generation of Reactive Oxigen Species in Populations of Phagocytes].

PubMed

Troyanova, N I; Shevchenko, M A; Boyko, A A; Mirzoyev, R R; Pertseva, M A; Kovalenko, E I; Sapozhnikov, A M

2015-01-01

Reactive oxygen species (ROS) produced by phagocytic cells of the innate immune system play an important role in the first line of defense protecting the host from pathogens. The NADPH oxidase multi-subunit complex is the main source of ROS in all types of the phagocytes. Formation of the membrane-associated enzyme complex and its activity are dependent on many different factors controlling both intensification and suppression of the ROS production rate. However, the evidences are emerging in recent years indicating existence of poorly studied mechanisms of restriction of ROS generation level in phagocytes directed at protection of host tissues in the sites of inflammation from destruction caused by the oxygen free radicals. Our previous data and results of other authors demonstrate that a mechanism of the limitation of ROS production by phagocytes may by connected with immunomodulating activity of extracellular pool. of HSP70. In the present work, we used inhibitors of NADPH oxidase and in vitro cultures of different phagocytes to study a possible relationship between down-regulating effect of exogenous HSP70 on ROS generation and the interaction of the protein with the enzyme subunits. Our results confirmed the literature data concerning the ability of extracellular HSP70 to modulate NADPH oxidase activity and demonstrated for the first time an inhibitory effect of the protein on intracellular ROS generation in phagocytes.

Examining the effects of microstructure and loading on the shock initiation of HMX with mesoscale simulations

NASA Astrophysics Data System (ADS)

Springer, H. Keo; Tarver, Craig; Bastea, Sorin

2015-06-01

We perform reactive mesoscale simulations to study shock initiation in HMX over a range of pore morphologies and sizes, porosities, and loading conditions in order to improve our understanding of structure-performance relationships. These relationships are important because they guide the development of advanced macroscale models incorporating hot spot mechanisms and the optimization of novel energetic material microstructures. Mesoscale simulations are performed using the multiphysics hydrocode, ALE3D. Spherical, elliptical, polygonal, and crack-like pore geometries 0.1, 1, 10, and 100 microns in size and 2, 5, 10, and 14% porosity are explored. Loading conditions are realized with shock pressures of 6, 10, 20, 38, and 50 GPa. A Cheetah-based tabular model, including temperature-dependent heat capacity, is used for the unreacted and the product equation-of-state. Also, in-line Cheetah is used to probe chemical species evolution. The influence of microstructure and shock loading on shock-to-detonation-transition run distance, reaction rate and product gas species evolution are discussed. This work performed under the auspices of the U.S. DOE by LLNL under Contract DE-AC52-07NA27344. This work is funded by the Joint DoD-DOE Munitions Program.

Collaborative Project: Building improved optimized parameter estimation algorithms to improve methane and nitrogen fluxes in a climate model

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

Mahowald, Natalie

Soils in natural and managed ecosystems and wetlands are well known sources of methane, nitrous oxides, and reactive nitrogen gases, but the magnitudes of gas flux to the atmosphere are still poorly constrained. Thus, the reasons for the large increases in atmospheric concentrations of methane and nitrous oxide since the preindustrial time period are not well understood. The low atmospheric concentrations of methane and nitrous oxide, despite being more potent greenhouse gases than carbon dioxide, complicate empirical studies to provide explanations. In addition to climate concerns, the emissions of reactive nitrogen gases from soils are important to the changing nitrogenmore » balance in the earth system, subject to human management, and may change substantially in the future. Thus improved modeling of the emission fluxes of these species from the land surface is important. Currently, there are emission modules for methane and some nitrogen species in the Community Earth System Model’s Community Land Model (CLM-ME/N); however, there are large uncertainties and problems in the simulations, resulting in coarse estimates. In this proposal, we seek to improve these emission modules by combining state-of-the-art process modules for emissions, available data, and new optimization methods. In earth science problems, we often have substantial data and knowledge of processes in disparate systems, and thus we need to combine data and a general process level understanding into a model for projections of future climate that are as accurate as possible. The best methodologies for optimization of parameters in earth system models are still being developed. In this proposal we will develop and apply surrogate algorithms that a) were especially developed for computationally expensive simulations like CLM-ME/N models; b) were (in the earlier surrogate optimization Stochastic RBF) demonstrated to perform very well on computationally expensive complex partial differential equations in earth science with limited numbers of simulations; and, c) will be (as part of the proposed research) significantly improved both by adding asynchronous parallelism, early truncation of unsuccessful simulations, and the improvement of both serial and parallel performance by the use of derivative and sensitivity information from global and local surrogate approximations S(x). The algorithm development and testing will be focused on the CLM-ME/N model application, but the methods are general and are expected to also perform well on optimization for parameter estimation of other climate models and other classes of continuous multimodal optimization problems arising from complex simulation models. In addition, this proposal will compile available datasets of emissions of methane, nitrous oxides and reactive nitrogen species and develop protocols for site level comparisons with the CLM-ME/N. Once the model parameters are optimized against site level data, the model will be simulated at the global level and compared to atmospheric concentration measurements for the current climate, and future emissions will be estimated using climate change as simulated by the CESM. This proposal combines experts in earth system modeling, optimization, computer science, and process level understanding of soil gas emissions in an interdisciplinary team in order to improve the modeling of methane and nitrogen gas emissions. This proposal thus meets the requirements of the SciDAC RFP, by integrating state-of-the-art computer science and earth system to build an improved earth system model.« less

Apple polyphenols, phloretin and phloridzin: new trapping agents of reactive dicarbonyl species.

PubMed

Shao, Xi; Bai, Naisheng; He, Kan; Ho, Chi-Tang; Yang, Chung S; Sang, Shengmin

2008-10-01

Reactive dicarbonyl species, such as methylglyoxal (MGO) and glyoxal (GO), have received extensive attention recently due to their high reactivity and ability to form advanced glycation end products (AGEs) with biological substances such as proteins, phospholipids, and DNA. In the present study, we found that both phloretin and its glucoside, phloridzin, the major bioactive apple polyphenols, could efficiently trap reactive MGO or GO to form mono- and di-MGO or GO adducts under physiological conditions (pH 7.4, 37 degrees C). More than 80% MGO was trapped within 10 min, and 68% GO was trapped within 24 h by phloretin. Phloridzin also had strong trapping efficiency by quenching more than 70% MGO and 60% GO within 24 h. The glucosylation of the hydroxyl group at position 2 could significantly slow down the trapping rate and the formation of MGO or GO adducts. The products formed from phloretin (or phloridzin) and MGO (or GO), combined at different ratios, were analyzed using LC/MS. We successfully purified the major mono-MGO adduct of phloridzin and found that it was a mixture of tautomers based on the one- and two-dimensional NMR spectra. Our LC/MS and NMR data showed that positions 3 and 5 of the phloretin or phloridzin A ring were the major active sites for trapping reactive dicarbonyl species. We also found that phloretin was more reactive than lysine and arginine in terms of trapping reactive dicarbonyl species, MGO or GO. Our results suggest that dietary flavonoids that have the same A ring structure as phloretin may have the potential to trap reactive dicarbonyl species and therefore inhibit the formation of AGEs.

Rosacea, Reactive Oxygen Species, and Azelaic Acid

PubMed Central

2009-01-01

Rosacea is a common skin condition thought to be primarily an inflammatory disorder. Neutrophils, in particular, have been implicated in the inflammation associated with rosacea and mediate many of their effects through the release of reactive oxygen species. Recently, the role of reactive oxygen species in the pathophysiology of rosacea has been recognized. Many effective agents for rosacea, including topical azelaic acid and topical metronidazole, have anti-inflammatory properties. in-vitro models have demonstrated the potent antioxidant effects of azelaic acid, providing a potential mechanistic explanation for its efficacy in the treatment of rosacea. PMID:20967185

Rosacea, reactive oxygen species, and azelaic Acid.

PubMed

Jones, David A

2009-01-01

Rosacea is a common skin condition thought to be primarily an inflammatory disorder. Neutrophils, in particular, have been implicated in the inflammation associated with rosacea and mediate many of their effects through the release of reactive oxygen species. Recently, the role of reactive oxygen species in the pathophysiology of rosacea has been recognized. Many effective agents for rosacea, including topical azelaic acid and topical metronidazole, have anti-inflammatory properties. in-vitro models have demonstrated the potent antioxidant effects of azelaic acid, providing a potential mechanistic explanation for its efficacy in the treatment of rosacea.

[Development and application of a multi-species water quality model for water distribution systems with EPANET-MSX].

PubMed

Sun, Fu; Chen, Ji-ning; Zeng, Si-yu

2008-12-01

A conceptual multi-species water quality model for water distribution systems was developed on the basis of the toolkit of the EPANET-MSX software. The model divided the pipe segment into four compartments including pipe wall, biofilm, boundary layer and bulk liquid. The involved processes were substrate utilization and microbial growth, decay and inactivation of microorganisms, mass transfer of soluble components through the boundary layer, adsorption and desorption of particular components between bulk liquid and biofilm, oxidation and halogenation of organic matter by residual chlorine, and chlorine consumption by pipe wall. The fifteen simulated variables included the seven common variables both in the biofilm and in the bulk liquid, i.e. soluble organic matter, particular organic matter, ammonia nitrogen, residual chlorine, heterotrophic bacteria, autotrophic bacteria and inert solids, as well as biofilm thickness on the pipe wall. The model was validated against the data from a series of pilot experiments, and the simulation accuracy for residual chlorine and turbidity were 0.1 mg/L and 0.3 NTU respectively. A case study showed that the model could reasonably reflect the dynamic variation of residual chlorine and turbidity in the studied water distribution system, while Monte Carlo simulation, taking into account both the variability of finished water from the waterworks and the uncertainties of model parameters, could be performed to assess the violation risk of water quality in the water distribution system.

How can model comparison help improving species distribution models?

PubMed

Gritti, Emmanuel Stephan; Gaucherel, Cédric; Crespo-Perez, Maria-Veronica; Chuine, Isabelle

2013-01-01

Today, more than ever, robust projections of potential species range shifts are needed to anticipate and mitigate the impacts of climate change on biodiversity and ecosystem services. Such projections are so far provided almost exclusively by correlative species distribution models (correlative SDMs). However, concerns regarding the reliability of their predictive power are growing and several authors call for the development of process-based SDMs. Still, each of these methods presents strengths and weakness which have to be estimated if they are to be reliably used by decision makers. In this study we compare projections of three different SDMs (STASH, LPJ and PHENOFIT) that lie in the continuum between correlative models and process-based models for the current distribution of three major European tree species, Fagussylvatica L., Quercusrobur L. and Pinussylvestris L. We compare the consistency of the model simulations using an innovative comparison map profile method, integrating local and multi-scale comparisons. The three models simulate relatively accurately the current distribution of the three species. The process-based model performs almost as well as the correlative model, although parameters of the former are not fitted to the observed species distributions. According to our simulations, species range limits are triggered, at the European scale, by establishment and survival through processes primarily related to phenology and resistance to abiotic stress rather than to growth efficiency. The accuracy of projections of the hybrid and process-based model could however be improved by integrating a more realistic representation of the species resistance to water stress for instance, advocating for pursuing efforts to understand and formulate explicitly the impact of climatic conditions and variations on these processes.

How Can Model Comparison Help Improving Species Distribution Models?

PubMed Central

Gritti, Emmanuel Stephan; Gaucherel, Cédric; Crespo-Perez, Maria-Veronica; Chuine, Isabelle

2013-01-01

Today, more than ever, robust projections of potential species range shifts are needed to anticipate and mitigate the impacts of climate change on biodiversity and ecosystem services. Such projections are so far provided almost exclusively by correlative species distribution models (correlative SDMs). However, concerns regarding the reliability of their predictive power are growing and several authors call for the development of process-based SDMs. Still, each of these methods presents strengths and weakness which have to be estimated if they are to be reliably used by decision makers. In this study we compare projections of three different SDMs (STASH, LPJ and PHENOFIT) that lie in the continuum between correlative models and process-based models for the current distribution of three major European tree species, Fagus sylvatica L., Quercus robur L. and Pinus sylvestris L. We compare the consistency of the model simulations using an innovative comparison map profile method, integrating local and multi-scale comparisons. The three models simulate relatively accurately the current distribution of the three species. The process-based model performs almost as well as the correlative model, although parameters of the former are not fitted to the observed species distributions. According to our simulations, species range limits are triggered, at the European scale, by establishment and survival through processes primarily related to phenology and resistance to abiotic stress rather than to growth efficiency. The accuracy of projections of the hybrid and process-based model could however be improved by integrating a more realistic representation of the species resistance to water stress for instance, advocating for pursuing efforts to understand and formulate explicitly the impact of climatic conditions and variations on these processes. PMID:23874779

Final Report: Ionization chemistry of high temperature molecular fluids

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

Fried, L E

2007-02-26

With the advent of coupled chemical/hydrodynamic reactive flow models for high explosives, understanding detonation chemistry is of increasing importance to DNT. The accuracy of first principles detonation codes, such as CHEETAH, are dependent on an accurate representation of the species present under detonation conditions. Ionic species and non-molecular phases are not currently included coupled chemistry/hydrodynamic simulations. This LDRD will determine the prevalence of such species during high explosive detonations, by carrying out experimental and computational investigation of common detonation products under extreme conditions. We are studying the phase diagram of detonation products such as H{sub 2}O, or NH{sub 3} andmore » mixtures under conditions of extreme pressure (P > 1 GPa) and temperature (T > 1000K). Under these conditions, the neutral molecular form of matter transforms to a phase dominated by ions. The phase boundaries of such a region are unknown.« less

High-resolution modeling of indirectly driven high-convergence layered inertial confinement fusion capsule implosions

DOE PAGES

Haines, Brian M.; Aldrich, C. H.; Campbell, J. M.; ...

2017-04-24

In this study, we present the results of high-resolution simulations of the implosion of high-convergence layered indirect-drive inertial confinement fusion capsules of the type fielded on the National Ignition Facility using the xRAGE radiation-hydrodynamics code. In order to evaluate the suitability of xRAGE to model such experiments, we benchmark simulation results against available experimental data, including shock-timing, shock-velocity, and shell trajectory data, as well as hydrodynamic instability growth rates. We discuss the code improvements that were necessary in order to achieve favorable comparisons with these data. Due to its use of adaptive mesh refinement and Eulerian hydrodynamics, xRAGE is particularlymore » well suited for high-resolution study of multi-scale engineering features such as the capsule support tent and fill tube, which are known to impact the performance of high-convergence capsule implosions. High-resolution two-dimensional (2D) simulations including accurate and well-resolved models for the capsule fill tube, support tent, drive asymmetry, and capsule surface roughness are presented. These asymmetry seeds are isolated in order to study their relative importance and the resolution of the simulations enables the observation of details that have not been previously reported. We analyze simulation results to determine how the different asymmetries affect hotspot reactivity, confinement, and confinement time and how these combine to degrade yield. Yield degradation associated with the tent occurs largely through decreased reactivity due to the escape of hot fuel mass from the hotspot. Drive asymmetries and the fill tube, however, degrade yield primarily via burn truncation, as associated instability growth accelerates the disassembly of the hotspot. Finally, modeling all of these asymmetries together in 2D leads to improved agreement with experiment but falls short of explaining the experimentally observed yield degradation, consistent with previous 2D simulations of such capsules.« less

Superconductivity in human body; myth or necessity.

PubMed

Alexiou, Athanasios; Rekkas, John

2015-01-01

During the last years there is an increasing trend on the study of mitochondrial populations mainly in neural cells, due to their association with neurological disorders like Alzheimer's disease, Parkinson's disease, Autism, and CMT2A. Several studies concerning modeling of mitochondrial protein pathways, simulation of mitochondrial dynamics, biomarkers associated with Reactive Oxygen Species and many other related topics are already published. In this study we establish the idea of natural superconductivity in mitochondrial level as a necessary theoretical framework for the normal production of ATP and the avoidance of adverse reactions in Central Neural System.

Small unilamellar liposomes as a membrane model for cell inactivation by cold atmospheric plasma treatment

NASA Astrophysics Data System (ADS)

Maheux, S.; Frache, G.; Thomann, J. S.; Clément, F.; Penny, C.; Belmonte, T.; Duday, D.

2016-09-01

Cold atmospheric plasma is thought to be a promising tool for numerous biomedical applications due to its ability to generate a large diversity of reactive species in a controlled way. In some cases, it can also generate pulsed electric fields at the zone of treatment, which can induce processes such as electroporation in cell membranes. However, the interaction of these reactive species and the pulse electric field with cells in a physiological medium is very complex, and we still need a better understanding in order to be useful for future applications. A way to reach this goal is to work with model cell membranes such as liposomes, with the simplest physiological liquid and in a controlled atmosphere in order to limit the number of parallel reactions and processes. In this paper, where this approach has been chosen, 1,2-Dioleoyl-sn-glycero-3-phosphocholine (DOPC) small unilamellar vesicles (SUV) have been synthesized in a phosphate buffered aqueous solution, and this solution has been treated by a nanosecond pulsed plasma jet under a pure nitrogen atmosphere. It is only the composition of the plasma gas that has been changed in order to generate different cocktails of reactive species. After the quantification of the main plasma reactive species in the phosphate buffered saline (PBS) solution, structural, surface charge state, and chemical modifications generated on the plasma treated liposomes, due to the interaction with the plasma reactive species, have been carefully characterized. These results allow us to further understand the effect of plasma reactive species on model cell membranes in physiological liquids. The permeation through the liposomal membrane and the reaction of plasma reactive species with molecules encapsulated inside the liposomes have also been evaluated. New processes of degradation are finally presented and discussed, which come from the specific conditions of plasma treatment under the pure nitrogen atmosphere.

Communication: Reactivity borrowing in the mode selective chemistry of H + CHD3 → H2 + CD3

NASA Astrophysics Data System (ADS)

Ellerbrock, Roman; Manthe, Uwe

2017-12-01

Quantum state-resolved reaction probabilities for the H + CHD3 → H2 + CD3 reaction are calculated by accurate full-dimensional quantum dynamics calculations using the multi-layer multi-configurational time-dependent Hartree approach and the quantum transition state concept. Reaction probabilities of various ro-vibrational states of the CHD3 reactant are investigated for vanishing total angular momentum. While the reactivity of the different vibrational states of CHD3 mostly follows intuitive patterns, an unusually large reaction probability is found for CHD3 molecules triply excited in the CD3 umbrella-bending vibration. This surprising reactivity can be explained by a Fermi resonance-type mixing of the single CH-stretch excited and the triple CD3 umbrella-bend excited vibrational states of CHD3. These findings show that resonant energy transfer can significantly affect the mode-selective chemistry of CHD3 and result in counter-intuitive reactivity patterns.

Cold atmospheric-pressure air plasma treatment of C6 glioma cells: effects of reactive oxygen species in the medium produced by the plasma on cell death

NASA Astrophysics Data System (ADS)

Wang, Yuyang; Cheng, Cheng; Gao, Peng; Li, Shaopeng; Shen, Jie; Lan, Yan; Yu, Yongqiang; Chu, Paul K.

2017-02-01

An atmospheric-pressure air plasma is employed to treat C6 glioma cells in vitro. To elucidate on the mechanism causing cell death and role of reactive species (RS) in the medium produced by the plasma, the concentration of the long-lived RS such as hydrogen peroxide, nitrate, and ozone in the plasma-treated liquid (phosphate-buffered saline solution) is measured. When vitamin C is added to the medium as a ROS quencher, the viability of C6 glioma cells after the plasma treatment is different from that without vitamin C. The results demonstrate that reactive oxygen species (ROS) such as H2O2, and O3 constitute the main factors for inactivation of C6 glioma cells and the reactive nitrogen species (RNS) may only play an auxiliary role in cell death.

Oxidative stress and mitochondrial dysfunction-linked neurodegenerative disorders.

PubMed

Islam, Md Torequl

2017-01-01

Reactive species play an important role in physiological functions. Overproduction of reactive species, notably reactive oxygen (ROS) and nitrogen (RNS) species along with the failure of balance by the body's antioxidant enzyme systems results in destruction of cellular structures, lipids, proteins, and genetic materials such as DNA and RNA. Moreover, the effects of reactive species on mitochondria and their metabolic processes eventually cause a rise in ROS/RNS levels, leading to oxidation of mitochondrial proteins, lipids, and DNA. Oxidative stress has been considered to be linked to the etiology of many diseases, including neurodegenerative diseases (NDDs) such as Alzheimer diseases, Amyotrophic lateral sclerosis, Friedreich's ataxia, Huntington's disease, Multiple sclerosis, and Parkinson's diseases. In addition, oxidative stress causing protein misfold may turn to other NDDs include Creutzfeldt-Jakob disease, Bovine Spongiform Encephalopathy, Kuru, Gerstmann-Straussler-Scheinker syndrome, and Fatal Familial Insomnia. An overview of the oxidative stress and mitochondrial dysfunction-linked NDDs has been summarized in this review.

Reagents that block neuronal death from Huntington's disease also curb oxidative stress.

PubMed

Valencia, Antonio; Sapp, Ellen; Reeves, Patrick B; Alexander, Jonathan; Masso, Nicholas; Li, Xueyi; Kegel, Kimberly B; DiFiglia, Marian

2012-01-04

Patients with Huntington's disease suffer severe neuronal loss and signs of oxidative damage in the brain. Previously we found that primary neurons from embryonic cortex of mice bearing the Huntington's disease mutation (140 glutamines inserted into exon 1 of huntingtin) showed higher levels of reactive oxygen species before cell death. Here, we treated mutant neurons with known neuroprotective agents and determined the effects on neuronal survival and levels of reactive oxygen species. Primary neurons were exposed to the neurotrophin, brain derived neurotrophic factor, the antioxidant N-acetyl-cysteine or a specific inhibitor of glycogen synthase kinase 3-β, SB216763. Each reagent increased the survival of the mutant neurons compared with untreated mutant neurons and also reduced the levels of reactive oxygen species to levels of wild-type neurons. These results suggest that reducing the levels of reactive oxygen species may be necessary to protect neurons with the Huntington's disease mutation from cell death.

Inactivation of myeloma cancer cells by helium and argon plasma jets: The effect comparison and the key reactive species

NASA Astrophysics Data System (ADS)

Chen, Zeyu; Cui, Qingjie; Chen, Chen; Xu, Dehui; Liu, Dingxin; Chen, H. L.; Kong, Michael G.

2018-02-01

In plasma cancer therapy, the inactivation of cancer cells under plasma treatment is closely related to the reactive oxygen and nitrogen species (RONS) induced by plasmas. Quantitative study on the plasma-induced RONS that related to cancer cells apoptosis is critical for advancing the research of plasma cancer therapy. In this paper, the effects of several reactive species on the inactivation of LP-1 myeloma cancer cells are comparatively studied with variable working gas composition, surrounding gas composition, and discharge power. The results show that helium plasma jet has a higher cell inactivation efficiency than argon plasma jet under the same discharge power. By comparing the concentration of aqueous phase reactive species and the cell inactivation efficiency under different working gases and discharge powers, it is demonstrated that the inactivation efficiency of LP-1 myeloma cancer cells is strongly correlated with the concentration of peroxynitrite (ONOOH/ONOO-).

Characterizing 3-D flow velocity in evolving pore networks driven by CaCO3 precipitation and dissolution

NASA Astrophysics Data System (ADS)

Chojnicki, K. N.; Yoon, H.; Martinez, M. J.

2015-12-01

Understanding reactive flow in geomaterials is important for optimizing geologic carbon storage practices, such as using pore space efficiently. Flow paths can be complex in large degrees of geologic heterogeneities across scales. In addition, local heterogeneity can evolve as reactive transport processes alter the pore-scale morphology. For example, dissolved carbon dioxide may react with minerals in fractured rocks, confined aquifers, or faults, resulting in heterogeneous cementation (and/or dissolution) and evolving flow conditions. Both path and flow complexities are important and poorly characterized, making it difficult to determine their evolution with traditional 2-D transport models. Here we characterize the development of 3-D pore-scale flow with an evolving pore configuration due to calcium carbonate (CaCO3) precipitation and dissolution. A simple pattern of a microfluidic pore network is used initially and pore structures will become more complex due to precipitation and dissolution processes. At several stages of precipitation and dissolution, we directly visualize 3-D velocity vectors using micro particle image velocimetry and a laser scanning confocal microscope. Measured 3-D velocity vectors are then compared to 3-D simulated flow fields which will be used to simulate reactive transport. Our findings will highlight the importance of the 3-D flow dynamics and its impact on estimating reactive surface area over time. Sandia National Laboratories is a multi-program laboratory managed and operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Corporation, for the U.S. Department of Energy's National Nuclear Security Administration under contract DE-AC04-94AL85000. This material is based upon work supported as part of the Center for Frontiers of Subsurface Energy Security, an Energy Frontier Research Center funded by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences under Award Number DE-SC0001114.

Computer simulation of wolf-removal strategies for animal-damage control

USGS Publications Warehouse

Haight, R.G.; Travis, L.E.; Nimerfro, K.; Mech, L.D.

2002-01-01

Because of the sustained growth of the gray wolf (Canis lupus) population in the western Great Lakes region of the United States, management agencies are anticipating gray wolf removal from the federal endangered species list and are proposing strategies for wolf management. Strategies are needed that would balance public demand for wolf conservation with demand for protection against wolf depredation on livestock, poultry, and pets. We used a stochastic, spatially structured, individually based simulation model of a hypothetical wolf population, representing a small subset of the western Great Lakes wolves, to predict the relative performance of 3 wolf-removal strategies. Those strategies included reactive management (wolf removal occurred in summer after depredation), preventive management (wolves removed in winter from territories with occasional depredation), and population-size management (wolves removed annually in winter from all territories near farms). Performance measures included number of depredating packs and wolves removed, cost, and population size after 20 years. We evaluated various scenarios about immigration, trapping success, and likelihood of packs engaging in depredation. Four robust results emerged from the simulations: 1) each strategy reduced depredation by at least 40% compared with no action, 2) preventive and population-size management removed fewer wolves than reactive management because wolves were removed in winter before pups were born, 3)population-size management was least expensive because repeated annual removal kept most territories near farms free of wolves, and 4) none of the strategies threatened wolf populations unless they were isolated because wolf removal took place near farms and not in wild areas. For isolated populations, reactive management alone ensured conservation and reduced depredation. Such results can assist decision makers in managing gray wolves in the western Great Lakes states.

Contrasting characteristics of aqueous reactive species induced by cross-field and linear-field plasma jets

NASA Astrophysics Data System (ADS)

Xu, Han; Chen, Chen; Liu, Dingxin; Xu, Dehui; Liu, Zhijie; Wang, Xiaohua; Kong, Michael G.

2017-06-01

A comparative study on aqueous reactive species in deionized water treated by two types of plasma jets is presented. Classified by the direction of the electric field in the jet device, a linear-field jet and cross-field jet have been set up. Concentrations of several aqueous reactive species are measured quantitatively by chemical fluorescent assays and electron spin resonance spectrometer. Results show that these two-type plasma jets would generate approximately the same gaseous reactive species under the same discharge power, but the linear-field plasma jet is much more efficient at delivering those species to the remote deionized water. This leads to a much more aqueous short-lived species including OH and \\text{O}2- produced in water, which are mainly correlated to the solvation of gaseous short-lived species such as ions and electrons. Regarding the long-lived species of aqueous H2O2, the concentration grows faster when treated by the linear-field plasma jet in the initial stage, but after 10 min it is similar to that treated by the cross-field counterpart due to the vapor-liquid equilibrium. The aqueous peroxynitrite is also predicted to be produced as a result of the air inclusion in the feeding gas.

Arrhythmic risk biomarkers for the assessment of drug cardiotoxicity: from experiments to computer simulations

PubMed Central

Corrias, A.; Jie, X.; Romero, L.; Bishop, M. J.; Bernabeu, M.; Pueyo, E.; Rodriguez, B.

2010-01-01

In this paper, we illustrate how advanced computational modelling and simulation can be used to investigate drug-induced effects on cardiac electrophysiology and on specific biomarkers of pro-arrhythmic risk. To do so, we first perform a thorough literature review of proposed arrhythmic risk biomarkers from the ionic to the electrocardiogram levels. The review highlights the variety of proposed biomarkers, the complexity of the mechanisms of drug-induced pro-arrhythmia and the existence of significant animal species differences in drug-induced effects on cardiac electrophysiology. Predicting drug-induced pro-arrhythmic risk solely using experiments is challenging both preclinically and clinically, as attested by the rise in the cost of releasing new compounds to the market. Computational modelling and simulation has significantly contributed to the understanding of cardiac electrophysiology and arrhythmias over the last 40 years. In the second part of this paper, we illustrate how state-of-the-art open source computational modelling and simulation tools can be used to simulate multi-scale effects of drug-induced ion channel block in ventricular electrophysiology at the cellular, tissue and whole ventricular levels for different animal species. We believe that the use of computational modelling and simulation in combination with experimental techniques could be a powerful tool for the assessment of drug safety pharmacology. PMID:20478918

Modifying ceria (111) with a TiO2 nanocluster for enhanced reactivity.

PubMed

Nolan, Michael

2013-11-14

Modification of ceria catalysts is of great interest for oxidation reactions such as oxidative dehydrogenation of alcohols. Improving the reactivity of ceria based catalysts for these reactions means that they can be run at lower temperatures and density functional theory (DFT) simulations of new structures and compositions are proving valuable in the development of these catalysts. In this paper, we have used DFT+U (DFT corrected for on-site Coulomb interactions) to examine the reactivity of a novel modification of ceria, namely, modifying with TiO2, using the example of a Ti2O4 species adsorbed on the ceria (111) surface. The oxygen vacancy formation energy in the Ti2O4-CeO2 system is significantly reduced over the bare ceria surfaces, which together with previous work on ceria-titania indicates that the presence of the interface favours oxygen vacancy formation. The energy gain upon hydrogenation of the catalyst, which is the rate determining step in oxidative dehydrogenation, further points to the improved oxidation power of this catalyst structure.

Emergence of chaos in a spatially confined reactive system

NASA Astrophysics Data System (ADS)

Voorsluijs, Valérie; De Decker, Yannick

2016-11-01

In spatially restricted media, interactions between particles and local fluctuations of density can lead to important deviations of the dynamics from the unconfined, deterministic picture. In this context, we investigated how molecular crowding can affect the emergence of chaos in small reactive systems. We developed to this end an amended version of the Willamowski-Rössler model, where we account for the impenetrability of the reactive species. We analyzed the deterministic kinetics of this model and studied it with spatially-extended stochastic simulations in which the mobility of particles is included explicitly. We show that homogeneous fluctuations can lead to a destruction of chaos through a fluctuation-induced collision between chaotic trajectories and absorbing states. However, an interplay between the size of the system and the mobility of particles can counterbalance this effect so that chaos can indeed be found when particles diffuse slowly. This unexpected effect can be traced back to the emergence of spatial correlations which strongly affect the dynamics. The mobility of particles effectively acts as a new bifurcation parameter, enabling the system to switch from stationary states to absorbing states, oscillations or chaos.

Multi-objective Operation Chart Optimization for Aquatic Species Habitat Conservation of Cascaded Hydropower System on Yuan River, Southwestern China

NASA Astrophysics Data System (ADS)

Wen, X.; Lei, X.; Fang, G.; Huang, X.

2017-12-01

Extensive cascading hydropower exploitation in southwestern China has been the subject of debate and conflict in recent years. Introducing limited ecological curves, a novel approach for derivation of hydropower-ecological joint operation chart of cascaded hydropower system was proposed, aiming to optimize the general hydropower and ecological benefits, and to alleviate the ecological deterioration in specific flood/dry conditions. The physical habitat simulation model is proposed initially to simulate the relationship between streamflow and physical habitat of target fish species and to determine the optimal ecological flow range of representative reach. The ecological—hydropower joint optimization model is established to produce the multi-objective operation chart of cascaded hydropower system. Finally, the limited ecological guiding curves were generated and added into the operation chart. The JS-MDS cascaded hydropower system on the Yuan River in southwestern China is employed as the research area. As the result, the proposed guiding curves could increase the hydropower production amount by 1.72% and 5.99% and optimize ecological conservation degree by 0.27% and 1.13% for JS and MDS Reservoir, respectively. Meanwhile, the ecological deterioration rate also sees a decrease from 6.11% to 1.11% for JS Reservoir and 26.67% to 3.89% for MDS Reservoir.

TOUGHREACT: a new code of the TOUGH Family for Non-Isothermal multiphase reactive geochemical transport in variably saturated geologic media

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

Xu, Tianfu; Sonnenthal, Eric; Spycher, Nicolas

Coupled modeling of subsurface multiphase fluid and heat flow, solute transport and chemical reactions can be used for the assessment of acid mine drainage remediation, waste disposal sites, hydrothermal convection, contaminant transport, and groundwater quality. We have developed a comprehensive numerical simulator, TOUGHREACT, which considers non-isothermal multi-component chemical transport in both liquid and gas phases. A wide range of subsurface thermo-physical-chemical processes is considered under various thermohydrological and geochemical conditions of pressure, temperature, water saturation, and ionic strength. The code can be applied to one-, two- or three-dimensional porous and fractured media with physical and chemical heterogeneity.

Activation of nuclear transcription factor-kappaB in mouse brain induced by a simulated microgravity environment

NASA Technical Reports Server (NTRS)

Wise, Kimberly C.; Manna, Sunil K.; Yamauchi, Keiko; Ramesh, Vani; Wilson, Bobby L.; Thomas, Renard L.; Sarkar, Shubhashish; Kulkarni, Anil D.; Pellis, Neil R.; Ramesh, Govindarajan T.

2005-01-01

Microgravity induces inflammatory responses and modulates immune functions that may increase oxidative stress. Exposure to a microgravity environment induces adverse neurological effects; however, there is little research exploring the etiology of these effects resulting from exposure to such an environment. It is also known that spaceflight is associated with increase in oxidative stress; however, this phenomenon has not been reproduced in land-based simulated microgravity models. In this study, an attempt has been made to show the induction of reactive oxygen species (ROS) in mice brain, using ground-based microgravity simulator. Increased ROS was observed in brain stem and frontal cortex with concomitant decrease in glutathione, on exposing mice to simulated microgravity for 7 d. Oxidative stress-induced activation of nuclear factor-kappaB was observed in all the regions of the brain. Moreover, mitogen-activated protein kinase kinase was phosphorylated equally in all regions of the brain exposed to simulated microgravity. These results suggest that exposure of brain to simulated microgravity can induce expression of certain transcription factors, and these have been earlier argued to be oxidative stress dependent.

Redox signaling regulated by an electrophilic cyclic nucleotide and reactive cysteine persulfides.

PubMed

Fujii, Shigemoto; Sawa, Tomohiro; Nishida, Motohiro; Ihara, Hideshi; Ida, Tomoaki; Motohashi, Hozumi; Akaike, Takaaki

2016-04-01

Reactive oxygen (oxidant) and free radical species are known to cause nonspecific damage of various biological molecules. The oxidant toxicology is developing an emerging concept of the physiological functions of reactive oxygen species in cell signaling regulation. Redox signaling is precisely modulated by endogenous electrophilic substances that are generated from reactive oxygen species during cellular oxidative stress responses. Among diverse electrophilic molecular species that are endogenously generated, 8-nitroguanosine 3',5'-cyclic monophosphate (8-nitro-cGMP) is a unique second messenger whose formation, signaling, and metabolism in cells was recently clarified. Most important, our current studies revealed that reactive cysteine persulfides that are formed abundantly in cells are critically involved in the metabolism of 8-nitro-cGMP. Modern redox biology involves frontiers of cell research and stem cell research; medical and clinical investigations of infections, cancer, metabolic syndrome, aging, and neurodegenerative diseases; and other fields. 8-Nitro-cGMP-mediated signaling and metabolism in cells may therefore be potential targets for drug development, which may lead to discovery of new therapeutic agents for many diseases. Copyright © 2015 Elsevier Inc. All rights reserved.

Bromine Explosions In Smog Chamber Experiments: A comparison of Cavity-Enhanced (CE) and White-cell DOAS

NASA Astrophysics Data System (ADS)

Buxmann, J.; Hoch, D. J.; Sihler, H.; Pöhler, D.; Platt, U.; Bleicher, S.; Balzer, N.; Zetzsch, C.

2011-12-01

Reactive halogen species (RHS), such as Cl, Br or BrO, can significantly influence chemical processes in the troposphere, including the destruction of ozone, change in the chemical balance of hydrogen radicals (OH, HO2), increased deposition of toxic compounds (like mercury) with potential consequences for the global climate. Previous studies have shown that salt lakes can be significant sources for gaseous RHS. Environmental conditions such as salt composition, relative humidity (RH), pH, and temperature (T) can strongly influence reactive bromine levels, but are difficult to quantify in the field. Therefore, we conducted laboratory experiments by exposing NaCl salt containing 0.33% (by weight) NaBr to simulated sunlight in a Teflon smog-chamber under various conditions of RH and ozone concentrations. BrO levels were observed by a Differential-Optical-Absorption-Spectrometer (DOAS) in combination with a multi-reflection cell (White-cell). The concentrations of OH- and Cl- radicals were quantified by the radical clock method. We present the first direct observation of BrO from the "Bromine Explosion" (auto catalytic release of reactive bromine from salt surfaces - key to ozone destruction) in the laboratory above a simulated salt pan. The maximum BrO mixing ratio of 6419±71 ppt at 60% RH was observed to be one order of magnitude higher than at 37% RH and 2% RH. The release of RHS from the salt pan is possibly controlled by the thickness of the quasi liquid layer, covering the reactive surface of the halide crystals, as the layer thickness strongly depends on RH. Furthermore, a new cavity enhanced DOAS (CE-DOAS) instrument was designed and successfully used in chamber experiments. For the first time, such an instrument uses a spectral interval in the UV - wavelength range (325-365 nm) to identify BrO. We show a comparison of the CE-DOAS and White-cell DOAS instrument in a series of experiments, where e.g. a peak BrO mixing ratio up to 380 ppt within the first minutes was observed by both instruments (relative humidity 29%, 20°C, initial [O3]=300ppb). The detection limits with a time resolution of less than five minutes per measurement were found for BrO at 25 ppt, for HCHO at 5.5 ppb, for O3 at 55 ppb for the CE-DOAS. The White-cell has a higher detection limit at a better minimal time resolution of one minute per measurement with BrO at 40 ppt, for HCHO at 10 ppb and for O3 at 300 ppb, respectively. The new BrO-CE DOAS instruments with high spatial resolution also looks very promising for future field measurement campaigns aimed at a better understanding of atmospheric processes, such as halogen activation.

Preliminary Results for the OECD/NEA Time Dependent Benchmark using Rattlesnake, Rattlesnake-IQS and TDKENO

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

DeHart, Mark D.; Mausolff, Zander; Weems, Zach

2016-08-01

One goal of the MAMMOTH M&S project is to validate the analysis capabilities within MAMMOTH. Historical data has shown limited value for validation of full three-dimensional (3D) multi-physics methods. Initial analysis considered the TREAT startup minimum critical core and one of the startup transient tests. At present, validation is focusing on measurements taken during the M8CAL test calibration series. These exercises will valuable in preliminary assessment of the ability of MAMMOTH to perform coupled multi-physics calculations; calculations performed to date are being used to validate the neutron transport solver Rattlesnake\\cite{Rattlesnake} and the fuels performance code BISON. Other validation projects outsidemore » of TREAT are available for single-physics benchmarking. Because the transient solution capability of Rattlesnake is one of the key attributes that makes it unique for TREAT transient simulations, validation of the transient solution of Rattlesnake using other time dependent kinetics benchmarks has considerable value. The Nuclear Energy Agency (NEA) of the Organization for Economic Cooperation and Development (OECD) has recently developed a computational benchmark for transient simulations. This benchmark considered both two-dimensional (2D) and 3D configurations for a total number of 26 different transients. All are negative reactivity insertions, typically returning to the critical state after some time.« less

Kinetic Modeling of the Mitochondrial Energy Metabolism of Neuronal Cells: The Impact of Reduced α-Ketoglutarate Dehydrogenase Activities on ATP Production and Generation of Reactive Oxygen Species

PubMed Central

Berndt, Nikolaus; Bulik, Sascha; Holzhütter, Hermann-Georg

2012-01-01

Reduced activity of brain α-ketoglutarate dehydrogenase complex (KGDHC) occurs in a number of neurodegenerative diseases like Parkinson's disease and Alzheimer's disease. In order to quantify the relation between diminished KGDHC activity and the mitochondrial ATP generation, redox state, transmembrane potential, and generation of reactive oxygen species (ROS) by the respiratory chain (RC), we developed a detailed kinetic model. Model simulations revealed a threshold-like decline of the ATP production rate at about 60% inhibition of KGDHC accompanied by a significant increase of the mitochondrial membrane potential. By contrast, progressive inhibition of the enzyme aconitase had only little impact on these mitochondrial parameters. As KGDHC is susceptible to ROS-dependent inactivation, we also investigated the reduction state of those sites of the RC proposed to be involved in ROS production. The reduction state of all sites except one decreased with increasing degree of KGDHC inhibition suggesting an ROS-reducing effect of KGDHC inhibition. Our model underpins the important role of reduced KGDHC activity in the energetic breakdown of neuronal cells during development of neurodegenerative diseases. PMID:22719765

Variation in structure of proteins by adjusting reactive oxygen and nitrogen species generated from dielectric barrier discharge jet

NASA Astrophysics Data System (ADS)

Park, Ji Hoon; Kim, Minsup; Shiratani, Masaharu; Cho, Art. E.; Choi, Eun Ha; Attri, Pankaj

2016-10-01

Over the last few years, the variation in liquid chemistry due to the development of radicals generated by cold atmospheric plasma (CAP) has played an important role in plasma medicine. CAP direct treatment or CAP activated media treatment in cancer cells shows promising anticancer activity for both in vivo and in vitro studies. However, the anticancer activity or antimicrobial activity varies between plasma devices due to the different abilities among plasma devices to generate the reactive oxygen and nitrogen species (RONS) at different ratios and in different concentrations. While the generation of RONS depends on many factors, the feeding gas plays the most important role among the factors. Hence, in this study we used different compositions of feeding gas while fixing all other plasma characteristics. We used Ar, Ar-O2 (at different ratios), and Ar-N2 (at different ratios) as the working gases for CAP and investigated the structural changes in proteins (Hemoglobin (Hb) and Myoglobin (Mb)). We then analyzed the influence of RONS generated in liquid on the conformations of proteins. Additionally, to determine the influence of H2O2 on the Hb and Mb structures, we used molecular dynamic simulation.

Production and Consumption of Reactive Oxygen Species by Fullerenes

EPA Science Inventory

Reactive oxygen species (ROS) are one of the most important intermediates in chemical, photochemical, and biological processes. To understand the environmental exposure and toxicity of fullerenes better, the production and consumption of ROS (singlet oxygen, superoxide, hydrogen ...

Endocellular regulation by free radicals and hydrogen peroxide: key determinants of the inflammatory response.

PubMed

Vitetta, Luis; Linnane, Anthony W

2014-04-01

The formations of reactive oxygen species (ROS) and reactive nitrogen species (RNS) have long been considered as major contributors to the dysregulation of the inflammatory response. Reactive oxygen species and RNS productions often are reported to be associated with the development of chronic diseases and acceleration of the aging process. Mechanistically, this association has linked the phenomena of oxidative stress with the occurrence of random deleterious modifications of macromolecules with progressive development of pro-inflammatory conditions promoting age-associated systemic diseases. On the contrary the so-called random modification of macromolecules is incorrect rather ROS and RNS are molecular regulators (second messengers) and not universal toxins whose overproduction should be annulled by antioxidants. We have previously reviewed the physiological role of superoxide anion (and hydrogen peroxide) and nitric oxide (and peroxynitrite) and concluded that these reactive molecular species behave as pro-oxidant second messengers. Reactive oxygen species and RNS are produced at specific cellular locations and are essential for both the normal physiological function of the metabolome and the regulated inflammatory response. This brings into question the whole concept of the orally administering of antioxidant molecular species to down-regulate or abrogate an overproduction of free radical activity. There are no human clinical trials that demonstrate that small molecules, the so-called antioxidants (e.g., vitamins C, vitamin E and beta-carotene), confer a favorable clinical outcome of long-lasting control of inflammation.

Solutions to a reduced Poisson–Nernst–Planck system and determination of reaction rates

PubMed Central

Li, Bo; Lu, Benzhuo; Wang, Zhongming; McCammon, J. Andrew

2010-01-01

We study a reduced Poisson–Nernst–Planck (PNP) system for a charged spherical solute immersed in a solvent with multiple ionic or molecular species that are electrostatically neutralized in the far field. Some of these species are assumed to be in equilibrium. The concentrations of such species are described by the Boltzmann distributions that are further linearized. Others are assumed to be reactive, meaning that their concentrations vanish when in contact with the charged solute. We present both semi-analytical solutions and numerical iterative solutions to the underlying reduced PNP system, and calculate the reaction rate for the reactive species. We give a rigorous analysis on the convergence of our simple iteration algorithm. Our numerical results show the strong dependence of the reaction rates of the reactive species on the magnitude of its far field concentration as well as on the ionic strength of all the chemical species. We also find non-monotonicity of electrostatic potential in certain parameter regimes. The results for the reactive system and those for the non-reactive system are compared to show the significant differences between the two cases. Our approach provides a means of solving a PNP system which in general does not have a closed-form solution even with a special geometrical symmetry. Our findings can also be used to test other numerical methods in large-scale computational modeling of electro-diffusion in biological systems. PMID:20228879

Hugoniot curve calculation of nitromethane decomposition mixtures: A reactive force field molecular dynamics approach

NASA Astrophysics Data System (ADS)

Guo, Feng; Zhang, Hong; Hu, Hai-Quan; Cheng, Xin-Lu; Zhang, Li-Yan

2015-11-01

We investigate the Hugoniot curve, shock-particle velocity relations, and Chapman-Jouguet conditions of the hot dense system through molecular dynamics (MD) simulations. The detailed pathways from crystal nitromethane to reacted state by shock compression are simulated. The phase transition of N2 and CO mixture is found at about 10 GPa, and the main reason is that the dissociation of the C-O bond and the formation of C-C bond start at 10.0-11.0 GPa. The unreacted state simulations of nitromethane are consistent with shock Hugoniot data. The complete pathway from unreacted to reacted state is discussed. Through chemical species analysis, we find that the C-N bond breaking is the main event of the shock-induced nitromethane decomposition. Project supported by the National Natural Science Foundation of China (Grant No. 11374217) and the Shandong Provincial Natural Science Foundation, China (Grant No. ZR2014BQ008).

A Microfabricated 8-40 GHz Dual-Polarized Reflector Feed

NASA Technical Reports Server (NTRS)

Vanhille, Kenneth; Durham, Tim; Stacy, William; Karasiewicz, David; Caba, Aaron; Trent, Christopher; Lambert, Kevin; Miranda, Felix

2014-01-01

Planar antennas based on tightly coupled dipole arrays (also known as a current sheet antenna or CSA) are amenable for use as electronically scanned phased arrays. They are capable of performance nearing a decade of bandwidth. These antennas have been demonstrated in many implementations at frequencies below 18 GHz. This paper describes the implementation using a relatively new multi-layer microfabrication process resulting in a small, 6x6 element, dual-linear polarized array with beamformer that operates from 8 to 40 GHz. The beamformer includes baluns that feed the dual-polarized differential antenna elements and reactive splitter networks that also cover the full frequency range of operation. This antenna array serves as a reflector feed for a multi-band instrument designed to measure snow water equivalent (SWE) from airborne platforms. The instrument has both radar and radiome try capability at multiple frequencies. Scattering-parameter and time-domain measurements have been used to characterize the array feed. Radiation patterns of the antenna have been measured and are compared to simulation. To the best of the authors' knowledge, this work represents the most integrated multi-octave millimeter-wave antenna feed fabricated to date.

Modeling of Alkane Oxidation Using Constituents and Species

NASA Technical Reports Server (NTRS)

Bellan, Jasette; Harstad, Kenneth G.

2010-01-01

It is currently not possible to perform simulations of turbulent reactive flows due in particular to complex chemistry, which may contain thousands of reactions and hundreds of species. This complex chemistry results in additional differential equations, making the numerical solution of the equation set computationally prohibitive. Reducing the chemical kinetics mathematical description is one of several important goals in turbulent reactive flow modeling. A chemical kinetics reduction model is proposed for alkane oxidation in air that is based on a parallel methodology to that used in turbulence modeling in the context of the Large Eddy Simulation. The objective of kinetic modeling is to predict the heat release and temperature evolution. This kinetic mechanism is valid over a pressure range from atmospheric to 60 bar, temperatures from 600 K to 2,500 K, and equivalence ratios from 0.125 to 8. This range encompasses diesel, HCCI, and gas-turbine engines, including cold ignition. A computationally efficient kinetic reduction has been proposed for alkanes that has been illustrated for n-heptane using the LLNL heptane mechanism. This model is consistent with turbulence modeling in that scales were first categorized into either those modeled or those computed as progress variables. Species were identified as being either light or heavy. The heavy species were decomposed into defined 13 constituents, and their total molar density was shown to evolve in a quasi-steady manner. The light species behave either in a quasi-steady or unsteady manner. The modeled scales are the total constituent molar density, Nc, and the molar density of the quasi-steady light species. The progress variables are the total constituent molar density rate evolution and the molar densities of the unsteady light species. The unsteady equations for the light species contain contributions of the type gain/loss rates from the heavy species that are modeled consistent with the developed mathematical forms for the total constituent molar density rate evolution; indeed, examination of these gain/loss rates shows that they also have a good quasi-steady behavior with a functional form resembling that of the constituent rate. This finding highlights the fact that the fitting technique provides a methodology that can be repeatedly used to obtain an accurate representation of full or skeletal kinetic models. Assuming success with the modified reduced model, the advantage of the modeling approach is clear. Because this model is based on the Nc rate rather than on that of individual heavy species, even if the number of species increases with increased carbon number in the alkane group, providing that the quasi-steady rate aspect persists, then extension of this model to higher alkanes should be conceptually straightforward, although it remains to be seen if the functional fits would remain valid or would require reconstruction.

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

Stagg, Alan K; Yoon, Su-Jong

This report describes the Consortium for Advanced Simulation of Light Water Reactors (CASL) work conducted for completion of the Thermal Hydraulics Methods (THM) Level 3 Milestone THM.CFD.P11.02: Hydra-TH Extensions for Multispecies and Thermosolutal Convection. A critical requirement for modeling reactor thermal hydraulics is to account for species transport within the fluid. In particular, this capability is needed for modeling transport and diffusion of boric acid within water for emergency, reactivity-control scenarios. To support this need, a species transport capability has been implemented in Hydra-TH for binary systems (for example, solute within a solvent). A species transport equation is solved formore » the species (solute) mass fraction, and both thermal and solutal buoyancy effects are handled with specification of a Boussinesq body force. Species boundary conditions can be specified with a Dirichlet condition on mass fraction or a Neumann condition on diffusion flux. To enable enhanced species/fluid mixing in turbulent flow, the molecular diffusivity for the binary system is augmented with a turbulent diffusivity in the species transport calculation. The new capabilities are demonstrated by comparison of Hydra-TH calculations to the analytic solution for a thermosolutal convection problem, and excellent agreement is obtained.« less

Radical Chemistry and Structural Relationships of PPCP Degradation by UV/Chlorine Treatment in Simulated Drinking Water.

PubMed

Guo, Kaiheng; Wu, Zihao; Shang, Chii; Yao, Bo; Hou, Shaodong; Yang, Xin; Song, Weihua; Fang, Jingyun

2017-09-19

The UV/chlorine process is an emerging advanced oxidation process (AOP) used for the degradation of micropollutants. However, the radical chemistry of this AOP is largely unknown for the degradation of numerous structurally diverse micropollutants in water matrices of varying quality. These issues were addressed by grouping 34 pharmaceuticals and personal care products (PPCPs) according to the radical chemistry of their degradation in the UV/chlorine process at practical PPCP concentrations (1 μg L -1 ) and in different water matrices. The contributions of HO • and reactive chlorine species (RCS), including Cl • , Cl 2 •- , and ClO • , to the degradation of different PPCPs were compound specific. RCS showed considerable reactivity with olefins and benzene derivatives, such as phenols, anilines, and alkyl-/alkoxybenzenes. A good linear relationship was found between the RCS reactivity and negative values of the Hammett ∑σ p + constant for aromatic PPCPs, indicating that electron-donating groups promote the attack of benzene derivatives by RCS. The contribution of HO • , but not necessarily RCS, to PPCP removal decreased with increasing pH. ClO • showed high reactivity with some PPCPs, such as carbamazepine, caffeine, and gemfibrozil, with second-order rate constants of 9.2 × 10 7 , 1.03 × 10 8 , and 4.16 × 10 8 M -1 s -1 , respectively, which contributed to their degradation. Natural organic matter (NOM) induced significant scavenging of ClO • and greatly decreased the degradation of PPCPs that was attributable to ClO • , with a second-order rate constant of 4.5 × 10 4 (mg L -1 ) -1 s -1 . Alkalinity inhibited the degradation of PPCPs that was primarily attacked by HO • and Cl • but had negligible effects on the degradation of PPCPs by ClO • . This is the first study on the reactivity of RCS, particularly ClO • , with structurally diverse PPCPs under simulated drinking water condition.

Multi-disciplinary coupling effects for integrated design of propulsion systems

NASA Technical Reports Server (NTRS)

Chamis, C. C.; Singhal, S. N.

1993-01-01

Effective computational simulation procedures are described for modeling the inherent multi-disciplinary interactions which govern the accurate response of propulsion systems. Results are presented for propulsion system responses including multi-disciplinary coupling effects using coupled multi-discipline thermal, structural, and acoustic tailoring; an integrated system of multi-disciplinary simulators; coupled material behavior/fabrication process tailoring; sensitivities using a probabilistic simulator; and coupled materials, structures, fracture, and probabilistic behavior simulator. The results demonstrate that superior designs can be achieved if the analysis/tailoring methods account for the multi-disciplinary coupling effects. The coupling across disciplines can be used to develop an integrated coupled multi-discipline numerical propulsion system simulator.

Comprehensive Peptide Ion Structure Studies Using Ion Mobility Techniques: Part 3. Relating Solution-Phase to Gas-Phase Structures.

PubMed

Kondalaji, Samaneh Ghassabi; Khakinejad, Mahdiar; Valentine, Stephen J

2018-06-01

Molecular dynamics (MD) simulations have been utilized to study peptide ion conformer establishment during the electrospray process. An explicit water model is used for nanodroplets containing a model peptide and hydronium ions. Simulations are conducted at 300 K for two different peptide ion charge configurations and for droplets containing varying numbers of hydronium ions. For all conditions, modeling has been performed until production of the gas-phase ions and the resultant conformers have been compared to proposed gas-phase structures. The latter species were obtained from previous studies in which in silico candidate structures were filtered according to ion mobility and hydrogen-deuterium exchange (HDX) reactivity matches. Results from the present study present three key findings namely (1) the evidence from ion production modeling supports previous structure refinement studies based on mobility and HDX reactivity matching, (2) the modeling of the electrospray process is significantly improved by utilizing initial droplets existing below but close to the calculated Rayleigh limit, and (3) peptide ions in the nanodroplets sample significantly different conformers than those in the bulk solution due to altered physicochemical properties of the solvent. Graphical Abstract ᅟ.

Mass transfer in thin films under counter-current gas: experiments and numerical study

NASA Astrophysics Data System (ADS)

Lucquiaud, Mathieu; Lavalle, Gianluca; Schmidt, Patrick; Ausner, Ilja; Wehrli, Marc; O Naraigh, Lennon; Valluri, Prashant

2016-11-01

Mass transfer in liquid-gas stratified flows is strongly affected by the waviness of the interface. For reactive flows, the chemical reactions occurring at the liquid-gas interface also influence the mass transfer rate. This is encountered in several technological applications, such as absorption units for carbon capture. We investigate the absorption rate of carbon dioxide in a liquid solution. The experimental set-up consists of a vertical channel where a falling film is sheared by a counter-current gas flow. We measure the absorption occurring at different flow conditions, by changing the liquid solution, the liquid flow rate and the gas composition. With the aim to support the experimental results with numerical simulations, we implement in our level-set flow solver a novel module for mass transfer taking into account a variant of the ghost-fluid formalism. We firstly validate the pure mass transfer case with and without hydrodynamics by comparing the species concentration in the bulk flow to the analytical solution. In a final stage, we analyse the absorption rate in reactive flows, and try to reproduce the experimental results by means of numerical simulations to explore the active role of the waves at the interface.

Kinetic Effects in Parametric Instabilities of Finite Amplitude Alfven Waves in a Drifting Multi-Species Plasma

NASA Astrophysics Data System (ADS)

Maneva, Y. G.; Araneda, J. A.; Poedts, S.

2014-12-01

We consider parametric instabilities of finite-amplitude large-scale Alfven waves in a low-beta collisionless multi-species plasma, consisting of fluid electrons, kinetic protons and a drifting population of minor ions. Complementary to many theoretical studies, relying on fluid or multi-fluid approach, in this work we present the solutions of the parametric instability dispersion relation, including kinetic effects in the parallel direction, along the ambient magnetic field. This provides us with the opportunity to predict the importance of some wave-particle interactions like Landau damping of the daughter ion-acoustic waves for the given pump wave and plasma conditions. We apply the dispersion relation to plasma parameters, typical for low-beta collisionless solar wind close to the Sun. We compare the analytical solutions to the linear stage of hybrid numerical simulations and discuss the application of the model to the problems of preferential heating and differential acceleration of minor ions in the solar corona and the fast solar wind. The results of this study provide tools for prediction and interpretation of the magnetic field and particles data as expected from the future Solar Orbiter and Solar Probe Plus missions.