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Sample records for cfd-based mechanistic deposit

  1. A CFD-Based Study of the Feasibility of Adapting an Erosion Burner Rig for Examining the Effect of CMAS Deposition Corrosion on Environmental Barrier Coatings

    NASA Technical Reports Server (NTRS)

    Miller, Robert A.; Kuczmarski, Maria A.

    2015-01-01

    Thermodynamic and computational fluid dynamics modeling has been conducted to examine the feasibility of adapting the NASA-Glenn erosion burner rigs for use in studies of corrosion of environmental barrier coatings by the deposition of molten CMAS. The effect of burner temperature, Mach number, particle preheat, duct heating, particle size, and particle phase (crystalline vs. glass) were analyzed. Detailed strategies for achieving complete melting of CMAS particles were developed, thereby greatly improving the probability of future successful experimental outcomes.

  2. MECHANISTIC DOSIMETRY MODELS OF NANOMATERIAL DEPOSITION IN THE RESPIRATORY TRACT

    EPA Science Inventory

    Accurate health risk assessments of inhalation exposure to nanomaterials will require dosimetry models that account for interspecies differences in dose delivered to the respiratory tract. Mechanistic models offer the advantage to interspecies extrapolation that physicochemica...

  3. A mechanistic study of phosphinocarboxylic acid for boiler deposit control

    SciTech Connect

    Chang, K.Y.; Patel, S.

    1995-11-01

    A laboratory study has been carried out to identify the key properties of phosphinocarboxylic acid polymers to control boiler water deposits. These multifunctional properties are its ability to: transport iron, disperse boiler water sludge that contains iron oxide, silica and calcium phosphate and dissolution of deposits. The thermal and hydrolytic stability of the phosphinocarboxylic acid polymers was investigated in autoclave studies up to 1,500 psig. The post-autoclave samples were analyzed by Nuclear Magnetic Resonance Spectroscopy and Aqueous Gel Permeation Chromatography to ascertain the polymer integrity. In addition performance tests were carried out for pre- and post-autoclave polymer samples. The performance testing clearly shows that phosphinocarboxylic acid polymers are effective in maintaining deposit control in a boiler due to their inherent thermal stability.

  4. A supportive architecture for CFD-based design optimisation

    NASA Astrophysics Data System (ADS)

    Li, Ni; Su, Zeya; Bi, Zhuming; Tian, Chao; Ren, Zhiming; Gong, Guanghong

    2014-03-01

    Multi-disciplinary design optimisation (MDO) is one of critical methodologies to the implementation of enterprise systems (ES). MDO requiring the analysis of fluid dynamics raises a special challenge due to its extremely intensive computation. The rapid development of computational fluid dynamic (CFD) technique has caused a rise of its applications in various fields. Especially for the exterior designs of vehicles, CFD has become one of the three main design tools comparable to analytical approaches and wind tunnel experiments. CFD-based design optimisation is an effective way to achieve the desired performance under the given constraints. However, due to the complexity of CFD, integrating with CFD analysis in an intelligent optimisation algorithm is not straightforward. It is a challenge to solve a CFD-based design problem, which is usually with high dimensions, and multiple objectives and constraints. It is desirable to have an integrated architecture for CFD-based design optimisation. However, our review on existing works has found that very few researchers have studied on the assistive tools to facilitate CFD-based design optimisation. In the paper, a multi-layer architecture and a general procedure are proposed to integrate different CFD toolsets with intelligent optimisation algorithms, parallel computing technique and other techniques for efficient computation. In the proposed architecture, the integration is performed either at the code level or data level to fully utilise the capabilities of different assistive tools. Two intelligent algorithms are developed and embedded with parallel computing. These algorithms, together with the supportive architecture, lay a solid foundation for various applications of CFD-based design optimisation. To illustrate the effectiveness of the proposed architecture and algorithms, the case studies on aerodynamic shape design of a hypersonic cruising vehicle are provided, and the result has shown that the proposed architecture

  5. Electrophoretic deposition and mechanistic studies of nano-Al/CuO thermites

    NASA Astrophysics Data System (ADS)

    Sullivan, K. T.; Kuntz, J. D.; Gash, A. E.

    2012-07-01

    Electrophoretic deposition was used to deposit thin films (˜10-200 μm) of nano-aluminum/copper oxide thermites, with a density of 29% the theoretical maximum. The reaction propagation velocity was examined using fine-patterned electrodes (0.25 × 20 mm), and the optimum velocity was found to correspond to a fuel-rich equivalence ratio of 1.7. This value did not correlate with the calculated maximum in gas production or temperature, and it is suggested that it is a result of enhanced condensed-phase transport, which is speculated to increase for fuel-rich conditions. A ˜25% drop in propagation velocity occurred above an equivalence ratio of 2.0, where Al2O3 is predicted to undergo a phase change from liquid to solid. This is expected to hinder the kinetics by decreasing the mobility of condensed-phase reacting species. The effect of film thickness on propagation velocity was investigated, using the optimum equivalence ratio. The velocity was seen to exhibit a two-plateau behavior, with one plateau between 13 and 50 μm film thickness, and the other above ˜120 μm. The latter had nearly an order of magnitude faster velocity than the former, 36 m/s vs. 4 m/s, respectively. For film thicknesses in the 50-120 μm range, a linear transitional regime was observed. Images from the combustion studies showed an increase in forward-transported particles as the film thickness increased, along with more turbulent behavior of the flame. It was suggested that the two-plateau behavior indicated a shift in the energy transport mechanism. While nanocomposite thermites have been traditionally thought to exhibit convective energy transport, we find in this work that particle advection may also be important. The velocity of particles ejected through a thin slit mounted above a thermite strip was measured, and was found to be even faster (˜2-3×) than the flame propagation velocity. The morphology of captured particles was examined with an electron microscope, and indicated that

  6. Generalized Mechanistic Model for the Chemical Vapor Deposition of 2D Transition Metal Dichalcogenide Monolayers.

    PubMed

    Govind Rajan, Ananth; Warner, Jamie H; Blankschtein, Daniel; Strano, Michael S

    2016-04-26

    Transition metal dichalcogenides (TMDs) like molybdenum disulfide (MoS2) and tungsten disulfide (WS2) are layered materials capable of growth to one monolayer thickness via chemical vapor deposition (CVD). Such CVD methods, while powerful, are notoriously difficult to extend across different reactor types and conditions, with subtle variations often confounding reproducibility, particularly for 2D TMD growth. In this work, we formulate the first generalized TMD synthetic theory by constructing a thermodynamic and kinetic growth mechanism linked to CVD reactor parameters that is predictive of specific geometric shape, size, and aspect ratio from triangular to hexagonal growth, depending on specific CVD reactor conditions. We validate our model using experimental data from Wang et al. (Chem. Mater. 2014, 26, 6371-6379) that demonstrate the systemic evolution of MoS2 morphology down the length of a flow CVD reactor where variations in gas phase concentrations can be accurately estimated using a transport model (CSulfur = 9-965 μmol/m(3); CMoO3 = 15-16 mmol/m(3)) under otherwise isothermal conditions (700 °C). A stochastic model which utilizes a site-dependent activation energy barrier based on the intrinsic TMD bond energies and a series of Evans-Polanyi relations leads to remarkable, quantitative agreement with both shape and size evolution along the reactor. The model is shown to extend to the growth of WS2 at 800 °C and MoS2 under varied process conditions. Finally, a simplified theory is developed to translate the model into a "kinetic phase diagram" of the growth process. The predictive capability of this model and its extension to other TMD systems promise to significantly increase the controlled synthesis of such materials. PMID:26937889

  7. New Flutter Analysis Technique for CFD-based Unsteady Aeroelasticity

    NASA Technical Reports Server (NTRS)

    Pak, Chan-gi; Jutte, Christine V.

    2009-01-01

    This paper presents a flutter analysis technique for the transonic flight regime. The technique uses an iterative approach to determine the critical dynamic pressure for a given mach number. Unlike other CFD-based flutter analysis methods, each iteration solves for the critical dynamic pressure and uses this value in subsequent iterations until the value converges. This process reduces the iterations required to determine the critical dynamic pressure. To improve the accuracy of the analysis, the technique employs a known structural model, leaving only the aerodynamic model as the unknown. The aerodynamic model is estimated using unsteady aeroelastic CFD analysis combined with a parameter estimation routine. The technique executes as follows. The known structural model is represented as a finite element model. Modal analysis determines the frequencies and mode shapes for the structural model. At a given mach number and dynamic pressure, the unsteady CFD analysis is performed. The output time history of the surface pressure is converted to a nodal aerodynamic force vector. The forces are then normalized by the given dynamic pressure. A multi-input multi-output parameter estimation software, ERA, estimates the aerodynamic model through the use of time histories of nodal aerodynamic forces and structural deformations. The critical dynamic pressure is then calculated using the known structural model and the estimated aerodynamic model. This output is used as the dynamic pressure in subsequent iterations until the critical dynamic pressure is determined. This technique is demonstrated on the Aerostructures Test Wing-2 model at NASA's Dryden Flight Research Center.

  8. A Mechanistic Approach to Predicting Colloid Deposition onto Representative Aquifer Materials and Solution Chemistries in the Presence of an Energy Barrier

    NASA Astrophysics Data System (ADS)

    Trauscht, J. S.; Pazmino, E. F.; Johnson, W. P.

    2014-12-01

    Despite several decades of research we lack a mechanistic theory to predict deposition in porous media in the presence of colloid-collector repulsion (unfavorable conditions). Recently, mechanistic models have been developed that incorporate nanoscale surface heterogeneity in colloid-collector interactions. Comparisons of simulations to experimental data allows backing out a representative heterogeneity for the surface, which to date has been reported only for silica. Colloid deposition onto a variety of representative aquifer materials expected to be unfavorable under environmental conditions (quartz, muscovite and albite) was observed for 0.25, 1.1 and 1.95 μm carboxylate-modified latex microspheres using an impinging jet system. Deposition efficiencies varied in response to changes in collector mineralogy, ionic strength, electrolyte valence and pH. Collector surface charge heterogeneity characteristics (heterodomain size and spatial distribution) were backed out from these experiments via comparison to particle trajectory simulations incorporating discrete nano-scale attractive domains (heterodomains). A bi-modal distribution (1:4, ratio of large to small heterodomains) of 120nm and 60nm heterodomains was found to quantitatively predict retention for all three colloid sizes for a given surface. Varying the surface coverage of heterodomains allowed a characteristic coverage for each observed collector surface to be determined. This developing catalog of surface characteristics will aid prediction of colloid transport and deposition under environmentally relevant conditions (aquifer material composition and groundwater chemistry).

  9. Simultaneous Excitation of Multiple-Input Multiple-Output CFD-Based Unsteady Aerodynamic Systems

    NASA Technical Reports Server (NTRS)

    Silva, Walter A.

    2007-01-01

    A significant improvement to the development of CFD-based unsteady aerodynamic reduced-order models (ROMs) is presented. This improvement involves the simultaneous excitation of the structural modes of the CFD-based unsteady aerodynamic system that enables the computation of the unsteady aerodynamic state-space model using a single CFD execution, independent of the number of structural modes. Four different types of inputs are presented that can be used for the simultaneous excitation of the structural modes. Results are presented for a flexible, supersonic semi-span configuration using the CFL3Dv6.4 code.

  10. Simultaneous Excitation of Multiple-Input Multiple-Output CFD-Based Unsteady Aerodynamic Systems

    NASA Technical Reports Server (NTRS)

    Silva, Walter A.

    2008-01-01

    A significant improvement to the development of CFD-based unsteady aerodynamic reduced-order models (ROMs) is presented. This improvement involves the simultaneous excitation of the structural modes of the CFD-based unsteady aerodynamic system that enables the computation of the unsteady aerodynamic state-space model using a single CFD execution, independent of the number of structural modes. Four different types of inputs are presented that can be used for the simultaneous excitation of the structural modes. Results are presented for a flexible, supersonic semi-span configuration using the CFL3Dv6.4 code.

  11. REVIEW OF EXPERIMENTAL CAPABILITIES AND HYDRODYNAMIC DATA FOR VALIDATION OF CFD-BASED PREDICTIONS FOR SLURRY BUBBLE COLUMN REACTORS

    SciTech Connect

    Donna Post Guillen; Daniel S. Wendt; Steven P. Antal; Michael Z. Podowski

    2007-11-01

    The purpose of this paper is to document the review of several open-literature sources of both experimental capabilities and published hydrodynamic data to aid in the validation of a Computational Fluid Dynamics (CFD) based model of a slurry bubble column (SBC). The review included searching the Web of Science, ISI Proceedings, and Inspec databases, internet searches as well as other open literature sources. The goal of this study was to identify available experimental facilities and relevant data. Integral (i.e., pertaining to the SBC system), as well as fundamental (i.e., separate effects are considered), data are included in the scope of this effort. The fundamental data is needed to validate the individual mechanistic models or closure laws used in a Computational Multiphase Fluid Dynamics (CMFD) simulation of a SBC. The fundamental data is generally focused on simple geometries (i.e., flow between parallel plates or cylindrical pipes) or custom-designed tests to focus on selected interfacial phenomena. Integral data covers the operation of a SBC as a system with coupled effects. This work highlights selected experimental capabilities and data for the purpose of SBC model validation, and is not meant to be an exhaustive summary.

  12. REVIEW OF EXPERIMENTAL CAPABILITIES AND HYDRODYNAMIC DATA FOR VALIDATION OF CFD BASED PREDICTIONS FOR SLURRY BUBBLE COLUMN REACTORS

    SciTech Connect

    Donna Post Guillen; Daniel S. Wendt

    2007-11-01

    The purpose of this paper is to document the review of several open-literature sources of both experimental capabilities and published hydrodynamic data to aid in the validation of a Computational Fluid Dynamics (CFD) based model of a slurry bubble column (SBC). The review included searching the Web of Science, ISI Proceedings, and Inspec databases, internet searches as well as other open literature sources. The goal of this study was to identify available experimental facilities and relevant data. Integral (i.e., pertaining to the SBC system), as well as fundamental (i.e., separate effects are considered), data are included in the scope of this effort. The fundamental data is needed to validate the individual mechanistic models or closure laws used in a Computational Multiphase Fluid Dynamics (CMFD) simulation of a SBC. The fundamental data is generally focused on simple geometries (i.e., flow between parallel plates or cylindrical pipes) or custom-designed tests to focus on selected interfacial phenomena. Integral data covers the operation of a SBC as a system with coupled effects. This work highlights selected experimental capabilities and data for the purpose of SBC model validation, and is not meant to be an exhaustive summary.

  13. Assessment of CFD-based Response Surface Model for Ares I Supersonic Ascent Aerodynamics

    NASA Technical Reports Server (NTRS)

    Hanke, Jeremy L.

    2011-01-01

    The Ascent Force and Moment Aerodynamic (AFMA) Databases (DBs) for the Ares I Crew Launch Vehicle (CLV) were typically based on wind tunnel (WT) data, with increments provided by computational fluid dynamics (CFD) simulations for aspects of the vehicle that could not be tested in the WT tests. During the Design Analysis Cycle 3 analysis for the outer mold line (OML) geometry designated A106, a major tunnel mishap delayed the WT test for supersonic Mach numbers (M) greater than 1.6 in the Unitary Plan Wind Tunnel at NASA Langley Research Center, and the test delay pushed the final delivery of the A106 AFMA DB back by several months. The aero team developed an interim database based entirely on the already completed CFD simulations to mitigate the impact of the delay. This CFD-based database used a response surface methodology based on radial basis functions to predict the aerodynamic coefficients for M > 1.6 based on only the CFD data from both WT and flight Reynolds number conditions. The aero team used extensive knowledge of the previous AFMA DB for the A103 OML to guide the development of the CFD-based A106 AFMA DB. This report details the development of the CFD-based A106 Supersonic AFMA DB, constructs a prediction of the database uncertainty using data available at the time of development, and assesses the overall quality of the CFD-based DB both qualitatively and quantitatively. This assessment confirms that a reasonable aerodynamic database can be constructed for launch vehicles at supersonic conditions using only CFD data if sufficient knowledge of the physics and expected behavior is available. This report also demonstrates the applicability of non-parametric response surface modeling using radial basis functions for development of aerodynamic databases that exhibit both linear and non-linear behavior throughout a large data space.

  14. Directing the deposition of ferromagnetic cobalt onto Pt-tipped CdSe@CdS nanorods: synthetic and mechanistic insights.

    PubMed

    Hill, Lawrence J; Bull, Mathew M; Sung, Younghun; Simmonds, Adam G; Dirlam, Philip T; Richey, Nathaniel E; DeRosa, Sean E; Shim, In-Bo; Guin, Debanjan; Costanzo, Philip J; Pinna, Nicola; Willinger, Marc-Georg; Vogel, Walter; Char, Kookheon; Pyun, Jeffrey

    2012-10-23

    A methodology providing access to dumbbell-tipped, metal-semiconductor and metal oxide-semiconductor heterostructured nanorods has been developed. The synthesis and characterization of CdSe@CdS nanorods incorporating ferromagnetic cobalt nanoinclusions at both nanorod termini (i.e., dumbbell morphology) are presented. The key step in the synthesis of these heterostructured nanorods was the decoration of CdSe@CdS nanorods with platinum nanoparticle tips, which promoted the deposition of metallic CoNPs onto Pt-tipped CdSe@CdS nanorods. Cobalt nanoparticle tips were then selectively oxidized to afford CdSe@CdS nanorods with cobalt oxide domains at both termini. In the case of longer cobalt-tipped nanorods, heterostructured nanorods were observed to self-organize into complex dipolar assemblies, which formed as a consequence of magnetic associations of terminal CoNP tips. Colloidal polymerization of these cobalt-tipped nanorods afforded fused nanorod assemblies from the oxidation of cobalt nanoparticle tips at the ends of nanorods via the nanoscale Kirkendall effect. Wurtzite CdS nanorods survived both the deposition of metallic CoNP tips and conversion into cobalt oxide phases, as confirmed by both XRD and HRTEM analysis. A series of CdSe@CdS nanorods of four different lengths ranging from 40 to 174 nm and comparable diameters (6-7 nm) were prepared and modified with both cobalt and cobalt oxide tips. The total synthesis of these heterostructured nanorods required five steps from commercially available reagents. Key synthetic considerations are discussed, with particular emphasis on reporting isolated yields of all intermediates and products from scale up of intermediate precursors. PMID:22900605

  15. Recent Enhancements to the Development of CFD-Based Aeroelastic Reduced-Order Models

    NASA Technical Reports Server (NTRS)

    Silva, Walter A.

    2007-01-01

    Recent enhancements to the development of CFD-based unsteady aerodynamic and aeroelastic reduced-order models (ROMs) are presented. These enhancements include the simultaneous application of structural modes as CFD input, static aeroelastic analysis using a ROM, and matched-point solutions using a ROM. The simultaneous application of structural modes as CFD input enables the computation of the unsteady aerodynamic state-space matrices with a single CFD execution, independent of the number of structural modes. The responses obtained from a simultaneous excitation of the CFD-based unsteady aerodynamic system are processed using system identification techniques in order to generate an unsteady aerodynamic state-space ROM. Once the unsteady aerodynamic state-space ROM is generated, a method for computing the static aeroelastic response using this unsteady aerodynamic ROM and a state-space model of the structure, is presented. Finally, a method is presented that enables the computation of matchedpoint solutions using a single ROM that is applicable over a range of dynamic pressures and velocities for a given Mach number. These enhancements represent a significant advancement of unsteady aerodynamic and aeroelastic ROM technology.

  16. Mechanistic validation.

    PubMed

    Hartung, Thomas; Hoffmann, Sebastian; Stephens, Martin

    2013-01-01

    Validation of new approaches in regulatory toxicology is commonly defined as the independent assessment of the reproducibility and relevance (the scientific basis and predictive capacity) of a test for a particular purpose. In large ring trials, the emphasis to date has been mainly on reproducibility and predictive capacity (comparison to the traditional test) with less attention given to the scientific or mechanistic basis. Assessing predictive capacity is difficult for novel approaches (which are based on mechanism), such as pathways of toxicity or the complex networks within the organism (systems toxicology). This is highly relevant for implementing Toxicology for the 21st Century, either by high-throughput testing in the ToxCast/Tox21 project or omics-based testing in the Human Toxome Project. This article explores the mostly neglected assessment of a test's scientific basis, which moves mechanism and causality to the foreground when validating/qualifying tests. Such mechanistic validation faces the problem of establishing causality in complex systems. However, pragmatic adaptations of the Bradford Hill criteria, as well as bioinformatic tools, are emerging. As critical infrastructures of the organism are perturbed by a toxic mechanism we argue that by focusing on the target of toxicity and its vulnerability, in addition to the way it is perturbed, we can anchor the identification of the mechanism and its verification. PMID:23665802

  17. Development of Unsteady Aerodynamic State-Space Models from CFD-Based Pulse Responses

    NASA Technical Reports Server (NTRS)

    Silva, Walter A.; Raveh, Daniella E.

    2001-01-01

    A method for computing discrete-time state-space models of linearized unsteady aerodynamic behavior directly from aeroelastic CFD codes is presented. The method involves the treatment of CFD-based pulse responses as Markov parameters for use in a system identification /realization algorithm. Results are presented for the AGARD 445.6 Aeroelastic Wing with four aeroelastic modes at a Mach number of 0.96 using the EZNSS Euler/Navier-Stokes flow solver with aeroelastic capability. The System/Observer/Controller Identification Toolbox (SOCIT) algorithm, based on the Ho-Kalman realization algorithm, is used to generate 15th- and 32nd-order discrete-time state-space models of the unsteady aerodynamic response of the wing over the entire frequency range of interest.

  18. CFD-based method of determining form factor k for different ship types and different drafts

    NASA Astrophysics Data System (ADS)

    Wang, Jinbao; Yu, Hai; Zhang, Yuefeng; Xiong, Xiaoqing

    2016-07-01

    The value of form factor k at different drafts is important in predicting full-scale total resistance and speed for different types of ships. In the ITTC community, most organizations predict form factor k using a low-speed model test. However, this method is problematic for ships with bulbous bows and transom. In this article, a Computational Fluid Dynamics (CFD)-based method is introduced to obtain k for different type of ships at different drafts, and a comparison is made between the CFD method and the model test. The results show that the CFD method produces reasonable k values. A grid generating method and turbulence model are briefly discussed in the context of obtaining a consistent k using CFD.

  19. TADS: A CFD-based turbomachinery and analysis design system with GUI. Volume 2: User's manual

    NASA Technical Reports Server (NTRS)

    Myers, R. A.; Topp, D. A.; Delaney, R. A.

    1995-01-01

    The primary objective of this study was the development of a computational fluid dynamics (CFD) based turbomachinery airfoil analysis and design system, controlled by a graphical user interface (GUI). The computer codes resulting from this effort are referred to as the Turbomachinery Analysis and Design System (TADS). This document is intended to serve as a user's manual for the computer programs which comprise the TADS system. TADS couples a throughflow solver (ADPAC) with a quasi-3D blade-to-blade solver (RVCQ3D) in an interactive package. Throughflow analysis capability was developed in ADPAC through the addition of blade force and blockage terms to the governing equations. A GUI was developed to simplify user input and automate the many tasks required to perform turbomachinery analysis and design. The coupling of various programs was done in a way that alternative solvers or grid generators could be easily incorporated into the TADS framework.

  20. Developing an Accurate CFD Based Gust Model for the Truss Braced Wing Aircraft

    NASA Technical Reports Server (NTRS)

    Bartels, Robert E.

    2013-01-01

    The increased flexibility of long endurance aircraft having high aspect ratio wings necessitates attention to gust response and perhaps the incorporation of gust load alleviation. The design of civil transport aircraft with a strut or truss-braced high aspect ratio wing furthermore requires gust response analysis in the transonic cruise range. This requirement motivates the use of high fidelity nonlinear computational fluid dynamics (CFD) for gust response analysis. This paper presents the development of a CFD based gust model for the truss braced wing aircraft. A sharp-edged gust provides the gust system identification. The result of the system identification is several thousand time steps of instantaneous pressure coefficients over the entire vehicle. This data is filtered and downsampled to provide the snapshot data set from which a reduced order model is developed. A stochastic singular value decomposition algorithm is used to obtain a proper orthogonal decomposition (POD). The POD model is combined with a convolution integral to predict the time varying pressure coefficient distribution due to a novel gust profile. Finally the unsteady surface pressure response of the truss braced wing vehicle to a one-minus-cosine gust, simulated using the reduced order model, is compared with the full CFD.

  1. Multiphase CFD-based models for chemical looping combustion process: Fuel reactor modeling

    SciTech Connect

    Jung, Jonghwun; Gamwo, I.K.

    2008-04-21

    Chemical looping combustion (CLC) is a flameless two-step fuel combustion that produces a pure CO2 stream, ready for compression and sequestration. The process is composed of two interconnected fluidized bed reactors. The air reactor which is a conventional circulating fluidized bed and the fuel reactor which is a bubbling fluidized bed. The basic principle is to avoid the direct contact of air and fuel during the combustion by introducing a highly-reactive metal particle, referred to as oxygen carrier, to transport oxygen from the air to the fuel. In the process, the products from combustion are kept separated from the rest of the flue gases namely nitrogen and excess oxygen. This process eliminates the energy intensive step to separate the CO2 from nitrogen-rich flue gas that reduce the thermal efficiency. Fundamental knowledge of multiphase reactive fluid dynamic behavior of the gas–solid flow is essential for the optimization and operation of a chemical looping combustor. Our recent thorough literature review shows that multiphase CFD-based models have not been adapted to chemical looping combustion processes in the open literature. In this study, we have developed the reaction kinetics model of the fuel reactor and implemented the kinetic model into a multiphase hydrodynamic model, MFIX, developed earlier at the National Energy Technology Laboratory. Simulated fuel reactor flows revealed high weight fraction of unburned methane fuel in the flue gas along with CO2 and H2O. This behavior implies high fuel loss at the exit of the reactor and indicates the necessity to increase the residence time, say by decreasing the fuel flow rate, or to recirculate the unburned methane after condensing and removing CO2.

  2. On the accuracy of CFD-based pressure drop predictions for right-angle ducts

    NASA Astrophysics Data System (ADS)

    Brankovic, Andreja

    1993-07-01

    The predictive capability of computational fluid dynamics (CFD) codes for turbulent flow through curved ducts is of significant importance to the design and performance analysis of modern rocket engine flowpaths. Code calibration and validation studies for this class of flow are desireable to estimate the performance margin and operating range of components designed using Navier-Stokes methods. Parametric experimental studies such as that of Weske (NACA ARR W-39) provided a wealth of performance data for the design of single- and compound elbow configurations with various cross-sections, curvature and aspect ratios at varying Reynolds numbers. In that work, the majority of data is presented in the form of loss coefficients, characterizing pressure losses due to duct curvature, and including losses due to wall friction. Using measured friction coefficients, losses of equivalent straight lengths of duct are subtracted, resulting in performance curves useful for design computations. These data are currently used in a CFD-based parametric study covering a broad range of operating conditions. Of particular interest for the accuracy of CFD predictions are the effects on pressure loss due to inlet boundary layer thickness (dependent on upstream development length), and the wall treatment for the turbulence equations (conventional wall functions vs. wall integration using a two-layer model). The experimental data are reassessed in the form of an error analysis, and are compared with CFD predictions for 18 computational cases. Grid-independence, grid spacing, and convergence requirements of the cases are discussed. Conclusions regarding the relative importance of the parametric variables will be presented.

  3. Mechanistic study of atomic layer deposition of Al{sub x}Si{sub y}O thin film via in-situ FTIR spectroscopy

    SciTech Connect

    Cho, Jea; Kim, Taeseung; Seegmiller, Trevor; Chang, Jane P.

    2015-09-15

    A study of surface reaction mechanism on atomic layer deposition (ALD) of aluminum silicate (Al{sub x}Si{sub y}O) was conducted with trimethylaluminum (TMA) and tetraethoxysilane (TEOS) as precursors and H{sub 2}O as the oxidant. In-situ Fourier transform infrared spectroscopy (FTIR) was utilized to elucidate the underlying surface mechanism that enables the deposition of Al{sub x}Si{sub y}O by ALD. In-situ FTIR study revealed that ineffective hydroxylation of the surface ethoxy (–OCH{sub 2}CH{sub 3}) groups prohibits ALD of SiO{sub 2} by TEOS/H{sub 2}O. In contrast, effective desorption of the surface ethoxy group was observed in TEOS/H{sub 2}O/TMA/H{sub 2}O chemistry. The presence of Al-OH* group in vicinity of partially hydroxylated ethoxy (–OCH{sub 2}CH{sub 3}) group was found to propagate disproportionation reaction, which results in ALD of Al{sub x}Si{sub y}O. The maximum thickness from incorporation of SiO{sub x} from alternating exposures of TEOS/H{sub 2}O chemistry in Al{sub x}Si{sub y}O was found to be ∼2 Å, confirmed by high resolution transmission electron microscopy measurements.

  4. TADS--A CFD-Based Turbomachinery Analysis and Design System with GUI: User's Manual. 2.0

    NASA Technical Reports Server (NTRS)

    Koiro, M. J.; Myers, R. A.; Delaney, R. A.

    1999-01-01

    The primary objective of this study was the development of a Computational Fluid Dynamics (CFD) based turbomachinery airfoil analysis and design system, controlled by a Graphical User Interface (GUI). The computer codes resulting from this effort are referred to as TADS (Turbomachinery Analysis and Design System). This document is intended to serve as a User's Manual for the computer programs which comprise the TADS system, developed under Task 18 of NASA Contract NAS3-27350, ADPAC System Coupling to Blade Analysis & Design System GUI and Task 10 of NASA Contract NAS3-27394, ADPAC System Coupling to Blade Analysis & Design System GUI, Phase II-Loss, Design and, Multi-stage Analysis. TADS couples a throughflow solver (ADPAC) with a quasi-3D blade-to-blade solver (RVCQ3D) in an interactive package. Throughflow analysis and design capability was developed in ADPAC through the addition of blade force and blockage terms to the governing equations. A GUI was developed to simplify user input and automate the many tasks required to perform turbomachinery analysis and design. The coupling of the various programs was done in such a way that alternative solvers or grid generators could be easily incorporated into the TADS framework. Results of aerodynamic calculations using the TADS system are presented for a highly loaded fan, a compressor stator, a low speed turbine blade and a transonic turbine vane.

  5. TADS: A CFD-Based Turbomachinery Analysis and Design System with GUI: Methods and Results. 2.0

    NASA Technical Reports Server (NTRS)

    Koiro, M. J.; Myers, R. A.; Delaney, R. A.

    1999-01-01

    The primary objective of this study was the development of a Computational Fluid Dynamics (CFD) based turbomachinery airfoil analysis and design system, controlled by a Graphical User Interface (GUI). The computer codes resulting from this effort are referred to as TADS (Turbomachinery Analysis and Design System). This document is the Final Report describing the theoretical basis and analytical results from the TADS system developed under Task 10 of NASA Contract NAS3-27394, ADPAC System Coupling to Blade Analysis & Design System GUI, Phase II-Loss, Design and. Multi-stage Analysis. TADS couples a throughflow solver (ADPAC) with a quasi-3D blade-to-blade solver (RVCQ3D) or a 3-D solver with slip condition on the end walls (B2BADPAC) in an interactive package. Throughflow analysis and design capability was developed in ADPAC through the addition of blade force and blockage terms to the governing equations. A GUI was developed to simplify user input and automate the many tasks required to perform turbomachinery analysis and design. The coupling of the various programs was done in such a way that alternative solvers or grid generators could be easily incorporated into the TADS framework. Results of aerodynamic calculations using the TADS system are presented for a multistage compressor, a multistage turbine, two highly loaded fans, and several single stage compressor and turbine example cases.

  6. TADS: A CFD-based turbomachinery and analysis design system with GUI. Volume 1: Method and results

    NASA Technical Reports Server (NTRS)

    Topp, D. A.; Myers, R. A.; Delaney, R. A.

    1995-01-01

    The primary objective of this study was the development of a computational fluid dynamics (CFD) based turbomachinery airfoil analysis and design system, controlled by a graphical user interface (GUI). The computer codes resulting from this effort are referred to as the Turbomachinery Analysis and Design System (TADS). This document describes the theoretical basis and analytical results from the TADS system. TADS couples a throughflow solver (ADPAC) with a quasi-3D blade-to-blade solver (RVCQ3D) in an interactive package. Throughflow analysis capability was developed in ADPAC through the addition of blade force and blockage terms to the governing equations. A GUI was developed to simplify user input and automate the many tasks required to perform turbomachinery analysis and design. The coupling of various programs was done in a way that alternative solvers or grid generators could be easily incorporated into the TADS framework. Results of aerodynamic calculations using the TADS system are presented for a highly loaded fan, a compressor stator, a low-speed turbine blade, and a transonic turbine vane.

  7. Development of CFD-Based Simulation Tools for In-Situ Thermal Processing of Oil Shale/Sands

    SciTech Connect

    None, None

    2012-02-01

    In our research, we are taking the novel approach of developing and applying high performance computing, computational fluid dynamics (CFD)-based simulation tools to a modified in-situ process for production of oil from oil shale. The simulation tools being developed capture the relevant physical processes and data from a large-scale system. The modified in-situ application is a pilot-scale heat transfer process inside Red Leaf Resources EcoShale capsule. We demonstrate the need to understand fluid flow behavior in the convective channels of the rubblized shale bed as convective heating greatly decreases the time required to heat the oil shale to the production temperature when compared with conductive heating alone. We have developed and implemented a geometry creation strategy for a representative section of the EcoShale capsule, developed a meshing approach to deal with the complicated geometry and produce a well-behaved mesh, analyzed the effects of boundary conditions on the simulation results, and devised a new operator splitting solution algorithm that reduces computational costs by taking advantage of the differing convective and conductive time scales occurring in the simulation. These simulation tools can be applied to a wide range of processes involving convective fluid flow heating in rubblized beds.

  8. CFD-based surrogate modeling of liquid rocket engine components via design space refinement and sensitivity assessment

    NASA Astrophysics Data System (ADS)

    Mack, Yolanda

    Computational fluid dynamics (CFD) can be used to improve the design and optimization of rocket engine components that traditionally rely on empirical calculations and limited experimentation. CFD based-design optimization can be made computationally affordable through the use of surrogate modeling which can then facilitate additional parameter sensitivity assessments. The present study investigates surrogate-based adaptive design space refinement (DSR) using estimates of surrogate uncertainty to probe the CFD analyses and to perform sensitivity assessments for complex fluid physics associated with liquid rocket engine components. Three studies were conducted. First, a surrogate-based preliminary design optimization was conducted to improve the efficiency of a compact radial turbine for an expander cycle rocket engine while maintaining low weight. Design space refinement was used to identify function constraints and to obtain a high accuracy surrogate model in the region of interest. A merit function formulation for multi-objective design point selection reduced the number of design points by an order of magnitude while maintaining good surrogate accuracy among the best trade-off points. Second, bluff body-induced flow was investigated to identify the physics and surrogate modeling issues related to the flow's mixing dynamics. Multiple surrogates and DSR were instrumental in identifying designs for which the CFD model was deficient and to help to pinpoint the nature of the deficiency. Next, a three-dimensional computational model was developed to explore the wall heat transfer of a GO2/GH2 shear coaxial single element injector. The interactions between turbulent recirculating flow structures, chemical kinetics, and heat transfer are highlighted. Finally, a simplified computational model of multi-element injector flows was constructed to explore the sensitivity of wall heating and improve combustion efficiency to injector element spacing. Design space refinement

  9. Variability in the Propagation Phase of CFD-Based Noise Prediction: Summary of Results From Category 8 of the BANC-III Workshop

    NASA Technical Reports Server (NTRS)

    Lopes, Leonard; Redonnet, Stephane; Imamura, Taro; Ikeda, Tomoaki; Zawodny, Nikolas; Cunha, Guilherme

    2015-01-01

    The usage of Computational Fluid Dynamics (CFD) in noise prediction typically has been a two part process: accurately predicting the flow conditions in the near-field and then propagating the noise from the near-field to the observer. Due to the increase in computing power and the cost benefit when weighed against wind tunnel testing, the usage of CFD to estimate the local flow field of complex geometrical structures has become more routine. Recently, the Benchmark problems in Airframe Noise Computation (BANC) workshops have provided a community focus on accurately simulating the local flow field near the body with various CFD approaches. However, to date, little effort has been given into assessing the impact of the propagation phase of noise prediction. This paper includes results from the BANC-III workshop which explores variability in the propagation phase of CFD-based noise prediction. This includes two test cases: an analytical solution of a quadrupole source near a sphere and a computational solution around a nose landing gear. Agreement between three codes was very good for the analytic test case, but CFD-based noise predictions indicate that the propagation phase can introduce 3dB or more of variability in noise predictions.

  10. Mechanistic facility safety and source term analysis

    SciTech Connect

    PLYS, M.G.

    1999-06-09

    A PC-based computer program was created for facility safety and source term analysis at Hanford The program has been successfully applied to mechanistic prediction of source terms from chemical reactions in underground storage tanks, hydrogen combustion in double contained receiver tanks, and proccss evaluation including the potential for runaway reactions in spent nuclear fuel processing. Model features include user-defined facility room, flow path geometry, and heat conductors, user-defined non-ideal vapor and aerosol species, pressure- and density-driven gas flows, aerosol transport and deposition, and structure to accommodate facility-specific source terms. Example applications are presented here.

  11. Electron transfer with self-assembled copper ions at Au-deposited biomimetic films: mechanistic ‘anomalies’ disclosed by temperature- and pressure-assisted fast-scan voltammetry

    NASA Astrophysics Data System (ADS)

    Khoshtariya, Dimitri E.; Dolidze, Tinatin D.; Tretyakova, Tatyana; van Eldik, Rudi

    2015-06-01

    It has been suggested that electron transfer (ET) processes occurring in complex environments capable of glass transitions, specifically in biomolecules, under certain conditions may experience the medium’s nonlinear response and nonergodic kinetic patterns. The interiors of self-assembled organic films (SAMs) deposited on solid conducting platforms (electrodes) are known to undergo glassy dynamics as well, hence they may also exhibit the abovementioned ‘irregularities’. We took advantage of Cu2+ ions as redox-active probes trapped in the Au-deposited  -COOH-terminated SAMs, either L-cysteine, or 3-mercaptopropionic acid diluted by the inert 2-mercaptoethanol, to systematically study the impact of glassy dynamics on ET using the fast-scan voltammetry technique and its temperature and high-pressure extensions. We found that respective kinetic data can be rationalized within the extended Marcus theory, taking into account the frictionally controlled (adiabatic) mechanism for short-range ET, and complications due to the medium’s nonlinear response and broken ergodicity. This combination shows up in essential deviations from the conventional energy gap (overpotential) dependence and in essentially nonlinear temperature (Arrhenius) and high-pressure patterns, respectively. Biomimetic aspects for these systems are also discussed in the context of recently published results for interfacial ET involving self-assembled blue copper protein (azurin) placed in contact with a glassy environment.

  12. Mechanistic investigations of shuttle glow

    NASA Technical Reports Server (NTRS)

    Caledonia, G. E.; Holtzclaw, K. W.; Krech, R. H.; Sonnenfroh, D. M.; Leone, A.; Blumberg, W. A. M.

    1993-01-01

    A series of laboratory measurements have been performed in order to provide a mechanistic interpretation for the visible shuttle glow. These studies involved interactions of an 8 km/s oxygen atom beam with both contaminant dosed surfaces and gaseous targets. We conclude that visible shuttle glow arises from surface mediated O + NO recombination via a Langmuir-Hinshelwood mechanism and that the gas-phase exchange reaction O + N2 - NO + N provides a viable source of precursor NO above surfaces oriented in the ram direction.

  13. Mechanistic investigations of shuttle glow

    SciTech Connect

    Caledonia, G.E.; Holtzclaw, K.W.; Krech, R.H.; Sonnenfroh, D.M. ); Leone, A. ); Blumber, W.A.M. )

    1993-03-01

    A series of laboratory measurements have been performed in order to provide a mechanistic interpretation for the visible shuttle glow. These studies involved interactions in an 8 km/s oxygen atom beam with both contaminant dosed surfaces and gaseous targets. The authors conclude that visible shuttle glow arises from surface mediated O + NO recombination via a Langmuir-Hinshelwood mechanism and that the gas-phase exchange reaction O + N[sub 2] [r arrow] NO + N provides a viable source of precursor NO above surfaces oriented in the ram direction. 35 refs., 4 figs.

  14. Food for Thought ... Mechanistic Validation

    PubMed Central

    Hartung, Thomas; Hoffmann, Sebastian; Stephens, Martin

    2013-01-01

    Summary Validation of new approaches in regulatory toxicology is commonly defined as the independent assessment of the reproducibility and relevance (the scientific basis and predictive capacity) of a test for a particular purpose. In large ring trials, the emphasis to date has been mainly on reproducibility and predictive capacity (comparison to the traditional test) with less attention given to the scientific or mechanistic basis. Assessing predictive capacity is difficult for novel approaches (which are based on mechanism), such as pathways of toxicity or the complex networks within the organism (systems toxicology). This is highly relevant for implementing Toxicology for the 21st Century, either by high-throughput testing in the ToxCast/ Tox21 project or omics-based testing in the Human Toxome Project. This article explores the mostly neglected assessment of a test's scientific basis, which moves mechanism and causality to the foreground when validating/qualifying tests. Such mechanistic validation faces the problem of establishing causality in complex systems. However, pragmatic adaptations of the Bradford Hill criteria, as well as bioinformatic tools, are emerging. As critical infrastructures of the organism are perturbed by a toxic mechanism we argue that by focusing on the target of toxicity and its vulnerability, in addition to the way it is perturbed, we can anchor the identification of the mechanism and its verification. PMID:23665802

  15. HTGR Mechanistic Source Terms White Paper

    SciTech Connect

    Wayne Moe

    2010-07-01

    The primary purposes of this white paper are: (1) to describe the proposed approach for developing event specific mechanistic source terms for HTGR design and licensing, (2) to describe the technology development programs required to validate the design methods used to predict these mechanistic source terms and (3) to obtain agreement from the NRC that, subject to appropriate validation through the technology development program, the approach for developing event specific mechanistic source terms is acceptable

  16. Natural selection and mechanistic regularity.

    PubMed

    DesAutels, Lane

    2016-06-01

    In this article, I address the question of whether natural selection operates regularly enough to qualify as a mechanism of the sort characterized by Machamer, Darden, and Craver (2000). Contrary to an influential critique by Skipper and Millstein (2005), I argue that natural selection can be seen to be regular enough to qualify as an MDC mechanism just fine-as long as we pay careful attention to some important distinctions regarding mechanistic regularity and abstraction. Specifically, I suggest that when we distinguish between process vs. product regularity, mechanism-internal vs. mechanism-external sources of irregularity, and abstract vs. concrete regularity, we can see that natural selection is only irregular in senses that are unthreatening to its status as an MDC mechanism. PMID:26921876

  17. Rational and Mechanistic Perspectives on Reinforcement Learning

    ERIC Educational Resources Information Center

    Chater, Nick

    2009-01-01

    This special issue describes important recent developments in applying reinforcement learning models to capture neural and cognitive function. But reinforcement learning, as a theoretical framework, can apply at two very different levels of description: "mechanistic" and "rational." Reinforcement learning is often viewed in mechanistic terms--as…

  18. Data graphs and mechanistic explanation.

    PubMed

    Burnston, Daniel C

    2016-06-01

    It is a widespread assumption in philosophy of science that representations of data are not explanatory-that they are mere stepping stones towards an explanation, such as a representation of a mechanism. I draw on instances of representational and explanatory practice from mammalian chronobiology to suggest that this assumption is unsustainable. In many instances, biologists employ representations of data in explanatory ways that are not reducible to constraints on or evidence for representations of mechanisms. Data graphs are used to represent relationships between quantities across conditions, and often these representations are necessary for explaining particular aspects of the phenomena under study. The benefit of the analysis is two-fold. First, it provides a more accurate account of explanatory practice in broadly mechanistic investigation in biology. Second, it suggests that there is not an explanatorily "fundamental" type of representation in biology. Rather, the practice of explanation consists in the construction of different types of representations and their employment for distinct explanatory purposes. PMID:26871740

  19. Negative mechanistic reasoning in medical intervention assessment.

    PubMed

    Jerkert, Jesper

    2015-12-01

    Traditionally, mechanistic reasoning has been assigned a negligible role in standard EBM (evidence-based medicine) literature, although some recent authors have argued for an upgrade. Even so, the mechanistic reasoning that has received attention has almost exclusively been positive--both in an epistemic sense of claiming that there is a mechanistic chain and in a health-related sense of there being claimed benefits for the patient. Negative mechanistic reasoning has been neglected, both in the epistemic and in the health-related sense. I distinguish three main types of negative mechanistic reasoning and subsume them under a new definition of mechanistic reasoning in the context of assessing medical interventions. This definition is wider than a previous suggestion in the literature. Each negative type corresponds to a range of evidential strengths, and it is argued that there are differences with respect to typical evidential strengths. The variety of negative mechanistic reasoning should be acknowledged in EBM, and it presents a serious challenge to proponents of so-called medical hierarchies of evidence. PMID:26597869

  20. MECHANISTIC INDICATORS OF CHILDHOOD ASTHMA (MICA)

    EPA Science Inventory

    The US Environmental Protection Agency (EPA) is interested in the interplay of environmental and genetic factors on the development and exacerbation of asthma. The Mechanistic Indicators of Childhood Asthma (MICA) study will use exposure measurements and markers of environmental ...

  1. Mechanistic bases for modelling space radiation risk and planning radiation protection of astronauts.

    PubMed

    Ottolenghi, A; Ballarini, F; Biaggi, M

    2001-01-01

    The approaches generally adopted for planning radiation protection in ground-based facilities cannot be applied straightforward for astronaut protection in space. Indeed in such extreme conditions, modelling methods and shielding design must be based on a detailed mechanistic knowledge of the peculiar astronauts irradiation conditions. Great help can derive from mechanistic modelling, generally aimed to better understand the intermediate steps leading from the initial energy depositions to different biological endpoints, up to organ and organism level. In the present work, criteria will be illustrated for using mechanistic approaches in developing practical tools for astronauts radioprotection, once the external field and the interaction cross sections with the spacecraft walls are known; particular attention will be given to the treatment of mixed fields. Techniques for integrating into condensed-history codes stochastic information provided by event-by-event simulations will be presented. PMID:11780618

  2. Mechanistic models in computational social science

    NASA Astrophysics Data System (ADS)

    Holme, Petter; Liljeros, Fredrik

    2015-09-01

    Quantitative social science is not only about regression analysis or, in general, data inference. Computer simulations of social mechanisms have an over 60 years long history. They have been used for many different purposes—to test scenarios, to test the consistency of descriptive theories (proof-of-concept models), to explore emergent phenomena, for forecasting, etc. In this essay, we sketch these historical developments, the role of mechanistic models in the social sciences and the influences from the natural and formal sciences. We argue that mechanistic computational models form a natural common ground for social and natural sciences, and look forward to possible future information flow across the social-natural divide.

  3. Testing mechanistic models of growth in insects.

    PubMed

    Maino, James L; Kearney, Michael R

    2015-11-22

    Insects are typified by their small size, large numbers, impressive reproductive output and rapid growth. However, insect growth is not simply rapid; rather, insects follow a qualitatively distinct trajectory to many other animals. Here we present a mechanistic growth model for insects and show that increasing specific assimilation during the growth phase can explain the near-exponential growth trajectory of insects. The presented model is tested against growth data on 50 insects, and compared against other mechanistic growth models. Unlike the other mechanistic models, our growth model predicts energy reserves per biomass to increase with age, which implies a higher production efficiency and energy density of biomass in later instars. These predictions are tested against data compiled from the literature whereby it is confirmed that insects increase their production efficiency (by 24 percentage points) and energy density (by 4 J mg(-1)) between hatching and the attainment of full size. The model suggests that insects achieve greater production efficiencies and enhanced growth rates by increasing specific assimilation and increasing energy reserves per biomass, which are less costly to maintain than structural biomass. Our findings illustrate how the explanatory and predictive power of mechanistic growth models comes from their grounding in underlying biological processes. PMID:26609084

  4. Exploring Organic Mechanistic Puzzles with Molecular Modeling

    ERIC Educational Resources Information Center

    Horowitz, Gail; Schwartz, Gary

    2004-01-01

    The molecular modeling was used to reinforce more general skills such as deducing and drawing reaction mechanisms, analyzing reaction kinetics and thermodynamics and drawing reaction coordinate energy diagrams. This modeling was done through the design of mechanistic puzzles, involving reactions not familiar to the students.

  5. Mechanistic Indicators of Childhood Asthma (MICA) Study

    EPA Science Inventory

    The Mechanistic Indicators of Childhood Asthma (MICA) Study has been designed to incorporate state-of-the-art technologies to examine the physiological and environmental factors that interact to increase the risk of asthmatic responses. MICA is primarily a clinically-bases obser...

  6. Mechanistic fracture criteria for the failure of human cortical bone

    SciTech Connect

    Nalla, Ravi K.; Kinney, John H.; Ritchie, Robert O.

    2002-12-13

    A mechanistic understanding of fracture in human bone is critical to predicting fracture risk associated with age and disease. Despite extensive work, a mechanistic framework for describing how the underlying microstructure affects the failure mode in bone is lacking.

  7. Mechanistic modeling and correlations for pool-entrainment phenomenon

    SciTech Connect

    Kataoka, I.; Ishii, M.

    1983-04-01

    Entrainment from a liquid pool with boiling or bubbling is of considerable practical importance in safety evaluation of nuclear reactor under off-normal transients or accidents such as loss-of-coolant and loss-of-flow accidents. Droplets which are suspended from a free surface are partly carried away by streaming gas and partly returned back to free surface by the gravity. A correlation is developed for the pool entrainment amount based on simple mechanistic modeling and a number of data. This analysis reveals that there exist three regions of entrainment in the axial direction from a pool surface. In the first region (near surface region), entrainment is independent of height and gas velocity. In the second region (momentum controlled region), the amount of entrainment decreases with increasing height from the free surface and increases with increasing gas velocity. In the third region (deposition controlled region), the entrainment increases with increasing height due to deposition of droplets. The present correlation agrees well with a large number of experimental data over a wide range of pressure for air-water and steam-water systems.

  8. Mechanistic analysis of challenge-response experiments.

    PubMed

    Shotwell, M S; Drake, K J; Sidorov, V Y; Wikswo, J P

    2013-09-01

    We present an application of mechanistic modeling and nonlinear longitudinal regression in the context of biomedical response-to-challenge experiments, a field where these methods are underutilized. In this type of experiment, a system is studied by imposing an experimental challenge, and then observing its response. The combination of mechanistic modeling and nonlinear longitudinal regression has brought new insight, and revealed an unexpected opportunity for optimal design. Specifically, the mechanistic aspect of our approach enables the optimal design of experimental challenge characteristics (e.g., intensity, duration). This article lays some groundwork for this approach. We consider a series of experiments wherein an isolated rabbit heart is challenged with intermittent anoxia. The heart responds to the challenge onset, and recovers when the challenge ends. The mean response is modeled by a system of differential equations that describe a candidate mechanism for cardiac response to anoxia challenge. The cardiac system behaves more variably when challenged than when at rest. Hence, observations arising from this experiment exhibit complex heteroscedasticity and sharp changes in central tendency. We present evidence that an asymptotic statistical inference strategy may fail to adequately account for statistical uncertainty. Two alternative methods are critiqued qualitatively (i.e., for utility in the current context), and quantitatively using an innovative Monte-Carlo method. We conclude with a discussion of the exciting opportunities in optimal design of response-to-challenge experiments. PMID:23859366

  9. Mechanistic studies of carbon monoxide reduction

    SciTech Connect

    Geoffroy, G.L.

    1990-06-12

    The progress made during the current grant period (1 January 1988--1 April 1990) in three different areas of research is summarized. The research areas are: (1) oxidatively-induced double carbonylation reactions to form {alpha}-ketoacyl complexes and studies of the reactivity of the resulting compounds, (2) mechanistic studies of the carbonylation of nitroaromatics to form isocyanates, carbamates, and ureas, and (3) studies of the formation and reactivity of unusual metallacycles and alkylidene ligands supported on binuclear iron carbonyl fragments. 18 refs., 5 figs., 1 tab.

  10. Composite Nanomechanics: A Mechanistic Properties Prediction

    NASA Technical Reports Server (NTRS)

    Chamis, Christos C.; Handler, Louis M.; Manderscheid, Jane M.

    2007-01-01

    A unique mechanistic theory is described to predict the properties of nanocomposites. The theory is based on composite micromechanics with progressive substructuring down to a nanoscale slice of a nanofiber where all the governing equations are formulated. These equations hav e been programmed in a computer code. That computer code is used to predict 25 properties of a mononanofiber laminate. The results are pr esented graphically and discussed with respect to their practical sig nificance. Most of the results show smooth distributions. Results for matrix-dependent properties show bimodal through-the-thickness distr ibution with discontinuous changes from mode to mode.

  11. Composite Nanomechanics: A Mechanistic Properties Prediction

    NASA Technical Reports Server (NTRS)

    Chamis, Christos C.; Handler, Louis M.; Manderscheid, Jane M.

    2007-01-01

    A unique mechanistic theory is described to predict the properties of nanocomposites. The theory is based on composite micromechanics with progressive substructuring down to a nanoscale slice of a nanofiber where all the governing equations are formulated. These equations have been programmed in a computer code. That computer code is used to predict 25 properties of a mononanofiber laminate. The results are presented graphically and discussed with respect to their practical significance. Most of the results show smooth distributions. Results for matrix-dependent properties show bimodal through-the-thickness distribution with discontinuous changes from mode to mode.

  12. Appropriateness of mechanistic and non-mechanistic models for the application of ultrafiltration to mixed waste

    SciTech Connect

    Foust, Henry; Ghosehajra, Malay

    2007-07-01

    This study asks two questions: (1) How appropriate is the use of a basic filtration equation to the application of ultrafiltration of mixed waste, and (2) How appropriate are non-parametric models for permeate rates (volumes)? To answer these questions, mechanistic and non-mechanistic approaches are developed for permeate rates and volumes associated with an ultrafiltration/mixed waste system in dia-filtration mode. The mechanistic approach is based on a filtration equation which states that t/V vs. V is a linear relationship. The coefficients associated with this linear regression are composed of physical/chemical parameters of the system and based the mass balance equation associated with the membrane and associated developing cake layer. For several sets of data, a high correlation is shown that supports the assertion that t/V vs. V is a linear relationship. It is also shown that non-mechanistic approaches, i.e., the use of regression models to are not appropriate. One models considered is Q(p) = a*ln(Cb)+b. Regression models are inappropriate because the scale-up from a bench scale (pilot scale) study to full-scale for permeate rates (volumes) is not simply the ratio of the two membrane surface areas. (authors)

  13. CFD based draft tube hydraulic design optimization

    NASA Astrophysics Data System (ADS)

    McNabb, J.; Devals, C.; Kyriacou, S. A.; Murry, N.; Mullins, B. F.

    2014-03-01

    The draft tube design of a hydraulic turbine, particularly in low to medium head applications, plays an important role in determining the efficiency and power characteristics of the overall machine, since an important proportion of the available energy, being in kinetic form leaving the runner, needs to be recovered by the draft tube into static head. For large units, these efficiency and power characteristics can equate to large sums of money when considering the anticipated selling price of the energy produced over the machine's life-cycle. This same draft tube design is also a key factor in determining the overall civil costs of the powerhouse, primarily in excavation and concreting, which can amount to similar orders of magnitude as the price of the energy produced. Therefore, there is a need to find the optimum compromise between these two conflicting requirements. In this paper, an elaborate approach is described for dealing with this optimization problem. First, the draft tube's detailed geometry is defined as a function of a comprehensive set of design parameters (about 20 of which a subset is allowed to vary during the optimization process) and are then used in a non-uniform rational B-spline based geometric modeller to fully define the wetted surfaces geometry. Since the performance of the draft tube is largely governed by 3D viscous effects, such as boundary layer separation from the walls and swirling flow characteristics, which in turn governs the portion of the available kinetic energy which will be converted into pressure, a full 3D meshing and Navier-Stokes analysis is performed for each design. What makes this even more challenging is the fact that the inlet velocity distribution to the draft tube is governed by the runner at each of the various operating conditions that are of interest for the exploitation of the powerhouse. In order to determine these inlet conditions, a combined steady-state runner and an initial draft tube analysis, using a stage interface between them, must first be performed for each operating condition. Due to the computationally intensive nature of the evaluation process, the efficiency of the optimization algorithm becomes important. Therefore, a state-of-the-art hierarchical-metamodel-assisted evolutionary algorithm is used.

  14. Reaction Coordinates and Mechanistic Hypothesis Tests.

    PubMed

    Peters, Baron

    2016-05-27

    Reaction coordinates are integral to several classic rate theories that can (a) predict kinetic trends across conditions and homologous reactions, (b) extract activation parameters with a clear physical interpretation from experimental rates, and (c) enable efficient calculations of free energy barriers and rates. New trajectory-based rare events methods can provide rates directly from dynamical trajectories without a reaction coordinate. Trajectory-based frameworks can also generate ideal (but abstract) reaction coordinates such as committors and eigenfunctions of the master equation. However, rates and mechanistic insights obtained from trajectory-based methods and abstract coordinates are not readily generalized across simulation conditions or reaction families. We discuss methods for identifying physically meaningful reaction coordinates, including committor analysis, variational transition state theory, Kramers-Langer-Berezhkovskii-Szabo theory, and statistical inference methods that can use path sampling data to screen, mix, and optimize thousands of trial coordinates. Special focus is given to likelihood maximization and inertial likelihood maximization approaches. PMID:27090846

  15. Reaction Coordinates and Mechanistic Hypothesis Tests

    NASA Astrophysics Data System (ADS)

    Peters, Baron

    2016-05-01

    Reaction coordinates are integral to several classic rate theories that can (a) predict kinetic trends across conditions and homologous reactions, (b) extract activation parameters with a clear physical interpretation from experimental rates, and (c) enable efficient calculations of free energy barriers and rates. New trajectory-based rare events methods can provide rates directly from dynamical trajectories without a reaction coordinate. Trajectory-based frameworks can also generate ideal (but abstract) reaction coordinates such as committors and eigenfunctions of the master equation. However, rates and mechanistic insights obtained from trajectory-based methods and abstract coordinates are not readily generalized across simulation conditions or reaction families. We discuss methods for identifying physically meaningful reaction coordinates, including committor analysis, variational transition state theory, Kramers-Langer-Berezhkovskii-Szabo theory, and statistical inference methods that can use path sampling data to screen, mix, and optimize thousands of trial coordinates. Special focus is given to likelihood maximization and inertial likelihood maximization approaches.

  16. Acid Deposition

    EPA Science Inventory

    This indicator presents acid deposition trends in the contiguous U.S. from 1989 to 2007. Data are broken down by wet and dry deposition and deposition of nitrogen and sulfur compounds. Acid deposition is particularly damaging to lakes, streams, and forests and the plants and a...

  17. Mechanistically based mapping of human cardiac fibrillation

    PubMed Central

    Zaman, Junaid A. B.

    2016-01-01

    Abstract The mechanisms underpinning human cardiac fibrillation remain elusive. In his 1913 paper ‘On dynamic equilibrium in the heart’, Mines proposed that an activation wave front could propagate repeatedly in a circle, initiated by a stimulus in the vulnerable period. While the dynamics of activation and recovery are central to cardiac fibrillation, these physiological data are rarely used in clinical mapping. Fibrillation is a rapid irregular rhythm with spatiotemporal disorder resulting from two fundamental mechanisms – sources in preferred cardiac regions or spatially diffuse self‐sustaining activity, i.e. with no preferred source. On close inspection, however, this debate may also reflect mapping technique. Fibrillation is initiated from triggers by regional dispersion in repolarization, slow conduction and wavebreak, then sustained by non‐uniform interactions of these mechanisms. Notably, optical mapping of action potentials in atrial fibrillation (AF) show spiral wave sources (rotors) in nearly all studies including humans, while most traditional electrogram analyses of AF do not. Techniques may diverge in fibrillation because electrograms summate non‐coherent waves within an undefined field whereas optical maps define waves with a visually defined field. Also fibrillation operates at the limits of activation and recovery, which are well represented by action potentials while fibrillatory electrograms poorly represent repolarization. We conclude by suggesting areas for study that may be used, until such time as optical mapping is clinically feasible, to improve mechanistic understanding and therapy of human cardiac fibrillation. PMID:26607671

  18. Mechanistic chemical perspective of hydrogen sulfide signaling.

    PubMed

    Nagy, Péter

    2015-01-01

    Hydrogen sulfide is now a well-appreciated master regulator in a diverse array of physiological processes. However, as a consequence of the rapid growth of the area, sulfide biology suffers from an increasing number of controversial observations and interpretations. A better understanding of the underlying molecular pathways of sulfide's actions is key to reconcile controversial issues, which calls for rigorous chemical/biochemical investigations. Protein sulfhydration and coordination/redox chemical interactions of sulfide with heme proteins are the two most extensively studied pathways in sulfide biochemistry. These pathways are important mediators of protein functions, generate bioactive sulfide metabolites, contribute to sulfide storage/trafficking and carry antioxidant functions. In addition, inorganic polysulfides, which are oxidative sulfide metabolites, are increasingly recognized as important players in sulfide biology. This chapter provides an overview of our mechanistic perspective on the reactions that govern (i) sulfide's bioavailability (including the delicate enzyme machineries that orchestrate sulfide production and consumption and the roles of the large sulfide-storing pools as biological buffers), (ii) biological significance and mechanisms of persulfide formation (including the reduction of disulfides, condensation with sulfenic acids, oxidation of thiols with polysulfides and radical-mediated pathways), (iii) coordination and redox chemical interactions of sulfide with heme proteins (including cytochrome c oxidase, hemoglobins, myoglobins and peroxidases), and (iv) the chemistry of polysulfides. PMID:25725513

  19. Structural and mechanistic insights on nitrate reductases.

    PubMed

    Coelho, Catarina; Romão, Maria João

    2015-12-01

    Nitrate reductases (NR) belong to the DMSO reductase family of Mo-containing enzymes and perform key roles in the metabolism of the nitrogen cycle, reducing nitrate to nitrite. Due to variable cell location, structure and function, they have been divided into periplasmic (Nap), cytoplasmic, and membrane-bound (Nar) nitrate reductases. The first crystal structure obtained for a NR was that of the monomeric NapA from Desulfovibrio desulfuricans in 1999. Since then several new crystal structures were solved providing novel insights that led to the revision of the commonly accepted reaction mechanism for periplasmic nitrate reductases. The two crystal structures available for the NarGHI protein are from the same organism (Escherichia coli) and the combination with electrochemical and spectroscopic studies also lead to the proposal of a reaction mechanism for this group of enzymes. Here we present an overview on the current advances in structural and functional aspects of bacterial nitrate reductases, focusing on the mechanistic implications drawn from the crystallographic data. PMID:26362109

  20. Somatodendritic dopamine release: recent mechanistic insights.

    PubMed

    Rice, Margaret E; Patel, Jyoti C

    2015-07-01

    Dopamine (DA) is a key transmitter in motor, reward and cogitative pathways, with DA dysfunction implicated in disorders including Parkinson's disease and addiction. Located in midbrain, DA neurons of the substantia nigra pars compacta project via the medial forebrain bundle to the dorsal striatum (caudate putamen), and DA neurons in the adjacent ventral tegmental area project to the ventral striatum (nucleus accumbens) and prefrontal cortex. In addition to classical vesicular release from axons, midbrain DA neurons exhibit DA release from their cell bodies and dendrites. Somatodendritic DA release leads to activation of D2 DA autoreceptors on DA neurons that inhibit their firing via G-protein-coupled inwardly rectifying K(+) channels. This helps determine patterns of DA signalling at distant axonal release sites. Somatodendritically released DA also acts via volume transmission to extrasynaptic receptors that modulate local transmitter release and neuronal activity in the midbrain. Thus, somatodendritic release is a pivotal intrinsic feature of DA neurons that must be well defined in order to fully understand the physiology and pathophysiology of DA pathways. Here, we review recent mechanistic aspects of somatodendritic DA release, with particular emphasis on the Ca(2+) dependence of release and the potential role of exocytotic proteins. PMID:26009764

  1. Mechanistically based mapping of human cardiac fibrillation.

    PubMed

    Narayan, Sanjiv M; Zaman, Junaid A B

    2016-05-01

    The mechanisms underpinning human cardiac fibrillation remain elusive. In his 1913 paper 'On dynamic equilibrium in the heart', Mines proposed that an activation wave front could propagate repeatedly in a circle, initiated by a stimulus in the vulnerable period. While the dynamics of activation and recovery are central to cardiac fibrillation, these physiological data are rarely used in clinical mapping. Fibrillation is a rapid irregular rhythm with spatiotemporal disorder resulting from two fundamental mechanisms - sources in preferred cardiac regions or spatially diffuse self-sustaining activity, i.e. with no preferred source. On close inspection, however, this debate may also reflect mapping technique. Fibrillation is initiated from triggers by regional dispersion in repolarization, slow conduction and wavebreak, then sustained by non-uniform interactions of these mechanisms. Notably, optical mapping of action potentials in atrial fibrillation (AF) show spiral wave sources (rotors) in nearly all studies including humans, while most traditional electrogram analyses of AF do not. Techniques may diverge in fibrillation because electrograms summate non-coherent waves within an undefined field whereas optical maps define waves with a visually defined field. Also fibrillation operates at the limits of activation and recovery, which are well represented by action potentials while fibrillatory electrograms poorly represent repolarization. We conclude by suggesting areas for study that may be used, until such time as optical mapping is clinically feasible, to improve mechanistic understanding and therapy of human cardiac fibrillation. PMID:26607671

  2. Black tea polyphenols: a mechanistic treatise.

    PubMed

    Butt, M S; Imran, A; Sharif, M K; Ahmad, Rabia Shabir; Xiao, Hang; Imran, M; Rsool, H A

    2014-01-01

    Dietary interventions are among the emerging trends to curtail physiological malfunctioning like cancer, diabetes, cardiac complications, etc. The essence of phytonutrients has developed the concept of nutraceuticals at the junction of diet health linkages. In this context, theaflavin & thearubigins are the oxidized derivatives of black tea catechins during fermentation having nutraceutical potential owing to esterification of hydroxyl ring with digallate esters. Theaflavin may influence activation of transcription factors such as NFnB or AP-1 that ultimately hinder the formation of nitric oxide expression gene. Likewise, black tea contains a unique amino acid theanine acts as neurotransmitter owing to its ability to cross the blood-brain barrier. Moreover, it boasts immunity by enhancing the disease-fighting ability of gamma delta T cells. Theaflavin & thearubigins act as safeguard against oxidative stress thereby effective in the cardiac functioning. The mechanistic approach of these antioxidants is likely to be associated with inhibition of redox sensitive transcription factors & pro-oxidant enzymes such as xanthine oxidase or nitric oxide synthase. However, their involvement in antioxidative enzyme induction as in glutathione-S-transferases is also well documented. They act as curative agent against numerous pathological disorders by disrupting the electron chain thus inhibiting the progression of certain ailments. Black tea polyphenols established themselves as strong antioxidants due to their standard one-electron potential, and their vitality is dependent on the concentration of polyphenols and pH for their inclusive execution. Present review is an attempt to enrich the readers regarding the health promoting aspects of black tea polyphenols. Concomitantly, it needs core attention of researchers for the exploitations of black tea flavanols as an important dietary constituent for the vulnerable segment. PMID:24499118

  3. Predictive toxicodynamics: Empirical/mechanistic approaches.

    PubMed

    Frazier, J M

    1997-10-01

    A major objective of the toxicological sciences is to predict the in vivo toxicological consequences of human exposure to pure chemicals, complex mixtures and commercial formulations. Historically, the experimental approach to this goal has been to investigate toxicological processes in whole animal models and extrapolate the results obtained to predict human risk using various extrapolation procedures (high-dose/low-dose extrapolation, interspecies extrapolation and route-to-route extrapolation). Can in vitro methods be more widely employed in quantitative risk assessment? One major limitation to the broader application of in vitro toxicity testing methods is the lack of validated techniques for the extrapolation of in vitro-derived toxicodynamic data to the in vivo situation. The objective of this paper is to describe some approaches to the development of techniques to extrapolate in vitro toxicity testing data to predict in vivo toxicological responses. An empirical approach within the context of a mechanistic framework is explored. The basic hypothesis is that the in vivo response can be constructed from a cellular toxicity factor that accounts for the cellular response and a toxicodynamic factor that relates toxicological events at the cellular level to the observable in vivo responses. A predictive paradigm to describe the in vivo acute target organ toxicity (hepatotoxicity) of a model chemical (cadmium) is discussed. The cellular toxicity factor is derived from in vitro toxicity testing studies using isolated rat hepatocytes. The toxicodynamic factor is derived through Biologically-Based Response (BBR) modelling techniques to predict target organ toxicity markers (i.e. plasma hepatic enzyme levels as markers for acute hepatotoxicity). The ultimate goal is to develop validated extrapolation procedures that can be applied to predicting target organ toxicity quantitatively in human populations based on in vitro toxicity studies using human cellular models. PMID

  4. Application of Mechanistic Toxicology Data to Ecological Risk Assessments

    EPA Science Inventory

    The ongoing evolution of knowledge and tools in the areas of molecular biology, bioinformatics, and systems biology holds significant promise for reducing uncertainties associated with ecological risk assessment. As our understanding of the mechanistic basis of responses of organ...

  5. Bridging paradigms: hybrid mechanistic-discriminative predictive models.

    PubMed

    Doyle, Orla M; Tsaneva-Atansaova, Krasimira; Harte, James; Tiffin, Paul A; Tino, Peter; Díaz-Zuccarini, Vanessa

    2013-03-01

    Many disease processes are extremely complex and characterized by multiple stochastic processes interacting simultaneously. Current analytical approaches have included mechanistic models and machine learning (ML), which are often treated as orthogonal viewpoints. However, to facilitate truly personalized medicine, new perspectives may be required. This paper reviews the use of both mechanistic models and ML in healthcare as well as emerging hybrid methods, which are an exciting and promising approach for biologically based, yet data-driven advanced intelligent systems. PMID:23392334

  6. MECHANISTIC STUDIES OF IMPROVED FOAM EOR PROCESSES

    SciTech Connect

    William R. Rossen

    2003-03-31

    . We find that such behavior is consistent with earlier models of foam viscosity in tubes, and a modified model for the low-quality regime can account for this behavior. It is not yet clear why this new regime appears in some cases and not in others. Simple modeling suggests that the answer may have to do with the sensitivity of gas trapping to pressure gradient. Research on Task 3 continued to focus on foam generation at limited pressure gradient in sandpacks. We investigated the effects of permeability, surfactant concentration and liquid injection rates on foam generation. In addition, a careful review of published studies showed that repeated snap-off is not a plausible mechanism of foam generation in homogeneous porous media beyond the stage of initial drainage from a fully liquid-saturated state. Snap-off has been the focus of much research on foam generation and is incorporated into most mechanistic foam simulators. This finding should force a reconsideration of its role in foam generation and properties in porous media.

  7. Mechanistic, kinetic, and processing aspects of tungsten chemical mechanical polishing

    NASA Astrophysics Data System (ADS)

    Stein, David

    This dissertation presents an investigation into tungsten chemical mechanical polishing (CMP). CMP is the industrially predominant unit operation that removes excess tungsten after non-selective chemical vapor deposition (CVD) during sub-micron integrated circuit (IC) manufacture. This work explores the CMP process from process engineering and fundamental mechanistic perspectives. The process engineering study optimized an existing CMP process to address issues of polish pad and wafer carrier life. Polish rates, post-CMP metrology of patterned wafers, electrical test data, and synergy with a thermal endpoint technique were used to determine the optimal process. The oxidation rate of tungsten during CMP is significantly lower than the removal rate under identical conditions. Tungsten polished without inhibition during cathodic potentiostatic control. Hertzian indenter model calculations preclude colloids of the size used in tungsten CMP slurries from indenting the tungsten surface. AFM surface topography maps and TEM images of post-CMP tungsten do not show evidence of plow marks or intergranular fracture. Polish rate is dependent on potassium iodate concentration; process temperature is not. The colloid species significantly affects the polish rate and process temperature. Process temperature is not a predictor of polish rate. A process energy balance indicates that the process temperature is predominantly due to shaft work, and that any heat of reaction evolved during the CMP process is negligible. Friction and adhesion between alumina and tungsten were studied using modified AFM techniques. Friction was constant with potassium iodate concentration, but varied with applied pressure. This corroborates the results from the energy balance. Adhesion between the alumina and the tungsten was proportional to the potassium iodate concentration. A heuristic mechanism, which captures the relationship between polish rate, pressure, velocity, and slurry chemistry, is presented

  8. From formamide to purine: an energetically viable mechanistic reaction pathway.

    PubMed

    Wang, Jing; Gu, Jiande; Nguyen, Minh Tho; Springsteen, Greg; Leszczynski, Jerzy

    2013-02-28

    A step-by-step mechanistic pathway following the transformation of formamide to purine through a five-membered ring intermediate has been explored by density functional theory computations. The highlight of the mechanistic route detailed here is that the proposed pathway represents the simplest reaction pathway. All necessary reactants are generated from a single starting compound, formamide, through energetically viable reactions. Several important reaction steps are involved in this mechanistic route: formylation-dehydration, Leuckart reduction, five- and six-membered ring-closure, and deamination. On the basis of the study of noncatalytic pathways, catalytic water has been found to provide energetically viable step-by-step mechanistic pathways. Among these reaction steps, five-member ring-closure is the rate-determining step. The energy barrier (ca. 42 kcal/mol) of this rate-control step is somewhat lower than the rate-determining step (ca. 44 kcal/mol) for a pyrimidine-based pathway reported previously. The mechanistic pathway reported herein is less energetically demanding than for previously proposed routes to adenine. PMID:23347082

  9. Explanation and inference: mechanistic and functional explanations guide property generalization

    PubMed Central

    Lombrozo, Tania; Gwynne, Nicholas Z.

    2014-01-01

    The ability to generalize from the known to the unknown is central to learning and inference. Two experiments explore the relationship between how a property is explained and how that property is generalized to novel species and artifacts. The experiments contrast the consequences of explaining a property mechanistically, by appeal to parts and processes, with the consequences of explaining the property functionally, by appeal to functions and goals. The findings suggest that properties that are explained functionally are more likely to be generalized on the basis of shared functions, with a weaker relationship between mechanistic explanations and generalization on the basis of shared parts and processes. The influence of explanation type on generalization holds even though all participants are provided with the same mechanistic and functional information, and whether an explanation type is freely generated (Experiment 1), experimentally provided (Experiment 2), or experimentally induced (Experiment 2). The experiments also demonstrate that explanations and generalizations of a particular type (mechanistic or functional) can be experimentally induced by providing sample explanations of that type, with a comparable effect when the sample explanations come from the same domain or from a different domains. These results suggest that explanations serve as a guide to generalization, and contribute to a growing body of work supporting the value of distinguishing mechanistic and functional explanations. PMID:25309384

  10. DEVELOPMENT AND VALIDATION OF A MECHANISTIC GROUND SPRAYER MODEL

    EPA Science Inventory

    In the last ten years the Spray Drift Task Force (SDTF), U.S. Environmental Protection Agency (EPA), USDA Agricultural Research Service, and USDA Forest Service cooperated in the refinement and evaluation of a mechanistically-based aerial spray model (contained within AGDISP and ...

  11. MECHANISTIC AND SOURCE UNDERSTANDING OF PCDD/F FORMATION

    EPA Science Inventory

    The paper discusses mechanistic and source understanding of polychlorinated dibenzo-p-dioxin and dibenzofuran (PCDD/F) formation. (NOTE: Considerable research effort has been expended over the last 15-plus years to understand how combustion sources result in formation of PCDDs/F...

  12. MECHANISTIC-BASED DISINFECTION AND DISINFECTION BYPRODUCT MODELS

    EPA Science Inventory

    We propose developing a mechanistic-based numerical model for chlorine decay and regulated DBP (THM and HAA) formation derived from (free) chlorination; the model framework will allow future modifications for other DBPs and chloramination. Predicted chlorine residual and DBP r...

  13. Does Mechanistic Thinking Improve Student Success in Organic Chemistry?

    ERIC Educational Resources Information Center

    Grove, Nathaniel P.; Cooper, Melanie M.; Cox, Elizabeth L.

    2012-01-01

    The use of the curved-arrow notation to depict electron flow during mechanistic processes is one of the most important representational conventions in the organic chemistry curriculum. Our previous research documented a disturbing trend: when asked to predict the products of a series of reactions, many students do not spontaneously engage in…

  14. Mechanistically Consistent Reduced Models of Synthetic Gene Networks

    PubMed Central

    Mier-y-Terán-Romero, Luis; Silber, Mary; Hatzimanikatis, Vassily

    2013-01-01

    Designing genetic networks with desired functionalities requires an accurate mathematical framework that accounts for the essential mechanistic details of the system. Here, we formulate a time-delay model of protein translation and mRNA degradation by systematically reducing a detailed mechanistic model that explicitly accounts for the ribosomal dynamics and the cleaving of mRNA by endonucleases. We exploit various technical and conceptual advantages that our time-delay model offers over the mechanistic model to probe the behavior of a self-repressing gene over wide regions of parameter space. We show that a heuristic time-delay model of protein synthesis of a commonly used form yields a notably different prediction for the parameter region where sustained oscillations occur. This suggests that such heuristics can lead to erroneous results. The functional forms that arise from our systematic reduction can be used for every system that involves transcription and translation and they could replace the commonly used heuristic time-delay models for these processes. The results from our analysis have important implications for the design of synthetic gene networks and stress that such design must be guided by a combination of heuristic models and mechanistic models that include all relevant details of the process. PMID:23663853

  15. Bridging Mechanistic and Phenomenological Models of Complex Biological Systems

    PubMed Central

    Transtrum, Mark K.; Qiu, Peng

    2016-01-01

    The inherent complexity of biological systems gives rise to complicated mechanistic models with a large number of parameters. On the other hand, the collective behavior of these systems can often be characterized by a relatively small number of phenomenological parameters. We use the Manifold Boundary Approximation Method (MBAM) as a tool for deriving simple phenomenological models from complicated mechanistic models. The resulting models are not black boxes, but remain expressed in terms of the microscopic parameters. In this way, we explicitly connect the macroscopic and microscopic descriptions, characterize the equivalence class of distinct systems exhibiting the same range of collective behavior, and identify the combinations of components that function as tunable control knobs for the behavior. We demonstrate the procedure for adaptation behavior exhibited by the EGFR pathway. From a 48 parameter mechanistic model, the system can be effectively described by a single adaptation parameter τ characterizing the ratio of time scales for the initial response and recovery time of the system which can in turn be expressed as a combination of microscopic reaction rates, Michaelis-Menten constants, and biochemical concentrations. The situation is not unlike modeling in physics in which microscopically complex processes can often be renormalized into simple phenomenological models with only a few effective parameters. The proposed method additionally provides a mechanistic explanation for non-universal features of the behavior. PMID:27187545

  16. THYROID FOLLICULAR CELL CARCINOGENESIS: MECHANISTIC AND SCIENCE POLICY CONSIDERATIONS

    EPA Science Inventory

    EPA's Guidelines for Carcinogen Risk Assessment call for use of mechanistic and other relevant information in making choices about the models to be used in extrapolating hazard estimates from high to low exposures. The Forum report on thyroid neoplasia proposes that, under clearl...

  17. Rearrangements of Allylic Sulfinates to Sulfones: A Mechanistic Study

    ERIC Educational Resources Information Center

    Ball, David B.; Mollard, Paul; Voigtritter, Karl R.; Ball, Jenelle L.

    2010-01-01

    Most current organic chemistry textbooks are organized by functional groups and those of us who teach organic chemistry use functional-group organization in our courses but ask students to learn organic chemistry from a mechanistic approach. To enrich and extend the chemical understanding and knowledge of pericyclic-type reactions for chemistry…

  18. Bridging Mechanistic and Phenomenological Models of Complex Biological Systems.

    PubMed

    Transtrum, Mark K; Qiu, Peng

    2016-05-01

    The inherent complexity of biological systems gives rise to complicated mechanistic models with a large number of parameters. On the other hand, the collective behavior of these systems can often be characterized by a relatively small number of phenomenological parameters. We use the Manifold Boundary Approximation Method (MBAM) as a tool for deriving simple phenomenological models from complicated mechanistic models. The resulting models are not black boxes, but remain expressed in terms of the microscopic parameters. In this way, we explicitly connect the macroscopic and microscopic descriptions, characterize the equivalence class of distinct systems exhibiting the same range of collective behavior, and identify the combinations of components that function as tunable control knobs for the behavior. We demonstrate the procedure for adaptation behavior exhibited by the EGFR pathway. From a 48 parameter mechanistic model, the system can be effectively described by a single adaptation parameter τ characterizing the ratio of time scales for the initial response and recovery time of the system which can in turn be expressed as a combination of microscopic reaction rates, Michaelis-Menten constants, and biochemical concentrations. The situation is not unlike modeling in physics in which microscopically complex processes can often be renormalized into simple phenomenological models with only a few effective parameters. The proposed method additionally provides a mechanistic explanation for non-universal features of the behavior. PMID:27187545

  19. Ferritin Diversity: Mechanistic Studies, Disease Implications, and Materials Chemistry

    NASA Astrophysics Data System (ADS)

    Hilton, Robert J.

    2011-07-01

    The study of ferritin includes a rich history of discoveries and scientific progress. Initially, the composition of ferritin was determined. Soon, it was shown that ferritin is a spherical, hollow protein. Eventually, over several decades of research, the structure and some function of this interesting protein was elucidated. However, the ferritin field was not completely satisfied. Today, for example, researchers are interested in refining the details of ferritin function, in discovering the role of ferritin in a variety of diseases, and in using ferritin for materials chemistry applications. The work presented in this dissertation highlights the progress that we have made in each of these three areas: (1) Mechanistic studies: The buffer used during horse spleen ferritin iron loading significantly influences the mineralization process and the quantity of iron deposited in ferritin. The ferrihydrite core of ferritin is crystalline and ordered when iron is loaded into ferritin in the presence of imidazole buffer. On the other hand, when iron is loaded into ferritin in the presence of MOPS buffer, the ferrihydrite core is less crystalline and less ordered, and a smaller amount of total iron is loaded in ferritin. We also show that iron can be released from the ferritin core in a non-reductive manner. The rate of Fe3+ release from horse spleen ferritin was measured using the Fe3+-specific chelator desferoxamine. We show that iron release occurs by three kinetic events. (2) Disease studies: In order to better understand iron disruption during disease states, we performed in vitro assays that mimicked chronic kidney disease. We tested the hypothesis that elevated levels of serum phosphate interrupted normal iron binding by transferrin and ferritin. Results show that phosphate competes for iron, forming an iron(III)-phosphate complex that is inaccessible to either transferrin or ferritin. Ferritin samples separated from the iron(III)-phosphate complex shows that as the

  20. Recommended Tritium Oxide Deposition Velocity For Use In Savannah River Site Safety Analyses

    SciTech Connect

    Lee, P. L.; Murphy, C. E.; Viner, B. J.; Hunter, C. H.

    2012-07-31

    This report documents the results of examining the deposition velocity of water to forests, the residence time of HTO in forests, and the relation between deposition velocity and residence time with specific consideration given to the topography and experimental work performed at SRS. A simple mechanistic model is used to obtain plausible deposition velocity and residence time values where experimental data are not available and recommendations are made for practical application in a safety analysis model.

  1. A framework for recognizing mechanistic reasoning in student scientific inquiry

    NASA Astrophysics Data System (ADS)

    Russ, Rosemary S.

    A central ambition of science education reform is to help students develop abilities for scientific inquiry. Education research is thus rightly focused on defining what constitutes "inquiry" and developing tools for assessing it. There has been progress with respect to particular aspects of inquiry, namely student abilities for controlled experimentation and scientific argumentation. However, we suggest that in addition to these frameworks for assessing the structure of inquiry we need frameworks for analyzing the substance of that inquiry. In this work we draw attention to and evaluate the substance of student mechanistic reasoning. Both within the history and philosophy of science and within science education research, scientific inquiry is characterized in part as understanding the causal mechanisms that underlie natural phenomena. The challenge for science education, however, is that there has not been the same progress with respect to making explicit what constitutes mechanistic reasoning as there has been in making explicit other aspects of inquiry. This dissertation attempts to address this challenge. We adapt an account of mechanism in professional research science to develop a framework for reliably recognizing mechanistic reasoning in student discourse. The coding scheme articulates seven specific aspects of mechanistic reasoning and can be used to systematically analyze narrative data for patterns in student thinking. It provides a tool for detecting quality reasoning that may be overlooked by more traditional assessments. We apply the mechanism coding scheme to video and written data from a range of student inquiries, from large group discussions among first grade students to the individual problem solving of graduate students. While the primary result of this work is the coding scheme itself and the finding that it provides a reliable means of analyzing transcript data for evidence of mechanistic thinking, the rich descriptions we develop in each case

  2. Mechanistic model for catalytic recombination during aerobraking maneuvers

    NASA Technical Reports Server (NTRS)

    Willey, Ronald J.

    1989-01-01

    Several mechanistic models are developed to predict recombination coefficients for use in heat shield design for reusable surface insulation (RSI) on aerobraking vehicles such as space shuttles. The models are applied over a temperature range of 300 to 1800 K and a stagnation pressure range of 0 to 3,000 Pa. A four parameter model in temperature was found to work best; however, several models (including those with atom concentrations at the surface) were also investigated. Mechanistic models developed with atom concentration terms may be applicable when sufficient data becomes available. The requirement is shown for recombination experiments in the 300 to 1000 K and 1500 to 1850 K temperature range, with deliberate concentration variations.

  3. Answering evolutionary questions: A guide for mechanistic biologists.

    PubMed

    Masel, Joanna; Promislow, Daniel E L

    2016-07-01

    The questions and methods of molecular biology and evolutionary biology are clearly distinct, yet a unified approach can lead to deep insights. Unfortunately, attempts to unify these approaches are fraught with pitfalls. In this informal series of questions and answers, we offer the mechanistically oriented biologist a set of steps to come up with evolutionarily reasonable and meaningful hypotheses. We emphasize the critical power and importance of carefully constructed null hypotheses, and we illustrate our ideas with examples representing a range of topics, from the biology of aging, to protein structure, to speciation, and more. We also stress the importance of mathematics as the lingua franca for biologists of all stripes, and encourage mechanistic biologists to seek out quantitative collaborators to build explicit mathematical models, making their assumptions explicit, and their logic clear and testable. Biologists in all realms of inquiry stand to gain from strong bridges between our disciplines. PMID:27151396

  4. Millifluidics for Chemical Synthesis and Time-resolved Mechanistic Studies

    PubMed Central

    Krishna, Katla Sai; Biswas, Sanchita; Navin, Chelliah V.; Yamane, Dawit G.; Miller, Jeffrey T.; Kumar, Challa S.S.R.

    2013-01-01

    Procedures utilizing millifluidic devices for chemical synthesis and time-resolved mechanistic studies are described by taking three examples. In the first, synthesis of ultra-small copper nanoclusters is described. The second example provides their utility for investigating time resolved kinetics of chemical reactions by analyzing gold nanoparticle formation using in situ X-ray absorption spectroscopy. The final example demonstrates continuous flow catalysis of reactions inside millifluidic channel coated with nanostructured catalyst. PMID:24327099

  5. Millifluidics for chemical synthesis and time-resolved mechanistic studies.

    PubMed

    Krishna, Katla Sai; Biswas, Sanchita; Navin, Chelliah V; Yamane, Dawit G; Miller, Jeffrey T; Kumar, Challa S S R

    2013-01-01

    Procedures utilizing millifluidic devices for chemical synthesis and time-resolved mechanistic studies are described by taking three examples. In the first, synthesis of ultra-small copper nanoclusters is described. The second example provides their utility for investigating time resolved kinetics of chemical reactions by analyzing gold nanoparticle formation using in situ X-ray absorption spectroscopy. The final example demonstrates continuous flow catalysis of reactions inside millifluidic channel coated with nanostructured catalyst. PMID:24327099

  6. Underreliance on mechanistic models: Comment on Ferguson (2015).

    PubMed

    Tryon, Warren W

    2016-09-01

    Ferguson (see record ) proposed that our overreliance on mechanistic models is responsible for the public's negative view of psychology. On the contrary, I claim that our explanations do not actually explain because they lack mechanism information and that is why the public has a negative view of psychology. Some of the mechanism information required to move from interpretations to explanations can be found in parallel distributed processing connectionist neural network models of psychology and behavior. (PsycINFO Database Record PMID:27571530

  7. Mechanistic model and analysis of doxorubicin release from liposomal formulations.

    PubMed

    Fugit, Kyle D; Xiang, Tian-Xiang; Choi, Du H; Kangarlou, Sogol; Csuhai, Eva; Bummer, Paul M; Anderson, Bradley D

    2015-11-10

    Reliable and predictive models of drug release kinetics in vitro and in vivo are still lacking for liposomal formulations. Developing robust, predictive release models requires systematic, quantitative characterization of these complex drug delivery systems with respect to the physicochemical properties governing the driving force for release. These models must also incorporate changes in release due to the dissolution media and methods employed to monitor release. This paper demonstrates the successful development and application of a mathematical mechanistic model capable of predicting doxorubicin (DXR) release kinetics from liposomal formulations resembling the FDA-approved nanoformulation DOXIL® using dynamic dialysis. The model accounts for DXR equilibria (e.g. self-association, precipitation, ionization), the change in intravesicular pH due to ammonia release, and dialysis membrane transport of DXR. The model was tested using a Box-Behnken experimental design in which release conditions including extravesicular pH, ammonia concentration in the release medium, and the dilution of the formulation (i.e. suspension concentration) were varied. Mechanistic model predictions agreed with observed DXR release up to 19h. The predictions were similar to a computer fit of the release data using an empirical model often employed for analyzing data generated from this type of experimental design. Unlike the empirical model, the mechanistic model was also able to provide reasonable predictions of release outside the tested design space. These results illustrate the usefulness of mechanistic modeling to predict drug release from liposomal formulations in vitro and its potential for future development of in vitro - in vivo correlations for complex nanoformulations. PMID:26310713

  8. Home range analysis using a mechanistic home range model

    SciTech Connect

    Moorcroft, P.R. . Dept. of Ecology and Evolutionary Biology); Lewis, M.A. . Dept. of Mathematics) Crabtree, R.L. . Dept. of Fish and Wildlife Resources)

    1999-07-01

    The traditional models used to characterize animal home ranges have no mechanistic basis underlying their descriptions of space use, and as a result, the analysis of animal home ranges has primarily been a descriptive endeavor. In this paper, the authors characterize coyote (Canis latrans) home range patterns using partial differential equations for expected space use that are formally derived from underlying descriptions of individual movement behavior. To the authors' knowledge, this is the first time that mechanistic models have been used to characterize animal home ranges. The results provide empirical support for a model formulation of movement response to scent marks, and suggest that having relocation data for individuals in adjacent groups is necessary to capture the spatial arrangement of home range boundaries. The authors then show how the model fits can be used to obtain predictions for individual movement and scent marking behavior and to predict changes in home range patterns. More generally, the findings illustrate how mechanistic models permit the development of a predictive theory for the relationship between movement behavior and animal spatial distribution.

  9. (Mechanistic examination of organometallic electron transfer reactions: Annual report, 1989)

    SciTech Connect

    Not Available

    1989-01-01

    Our mechanistic examination of electron transfer reactions between organometallic complexes has required data from our stopped-flow infrared spectrophotometer that was constructed in the first year. Our research on organometallic electron transfer reaction mechanisms was recognized by an invitation to the Symposium on Organometallic Reaction Mechanisms at the National ACS meeting in Miami. We have obtained a reasonable understanding of the electron transfer reactions between metal cations and anions and between metal carbonyl anions and metal carbonyl dimers. In addition we have begun to obtain data on the outer sphere electron transfer between metal carbonyl anions and coordination complexes and on reactions involving cluster anions.

  10. Mechanistic systems modeling to guide drug discovery and development

    PubMed Central

    Schmidt, Brian J.; Papin, Jason A.; Musante, Cynthia J.

    2013-01-01

    A crucial question that must be addressed in the drug development process is whether the proposed therapeutic target will yield the desired effect in the clinical population. Pharmaceutical and biotechnology companies place a large investment on research and development, long before confirmatory data are available from human trials. Basic science has greatly expanded the computable knowledge of disease processes, both through the generation of large omics data sets and a compendium of studies assessing cellular and systemic responses to physiologic and pathophysiologic stimuli. Given inherent uncertainties in drug development, mechanistic systems models can better inform target selection and the decision process for advancing compounds through preclinical and clinical research. PMID:22999913

  11. [Mechanistic examination of organometallic electron transfer reactions: Annual report, 1989

    SciTech Connect

    Not Available

    1989-12-31

    Our mechanistic examination of electron transfer reactions between organometallic complexes has required data from our stopped-flow infrared spectrophotometer that was constructed in the first year. Our research on organometallic electron transfer reaction mechanisms was recognized by an invitation to the Symposium on Organometallic Reaction Mechanisms at the National ACS meeting in Miami. We have obtained a reasonable understanding of the electron transfer reactions between metal cations and anions and between metal carbonyl anions and metal carbonyl dimers. In addition we have begun to obtain data on the outer sphere electron transfer between metal carbonyl anions and coordination complexes and on reactions involving cluster anions.

  12. Mechanistic study of a diazo dye degradation by Soybean Peroxidase

    PubMed Central

    2013-01-01

    Background Enzyme based remediation of wastewater is emerging as a novel, efficient and environmentally-friendlier approach. However, studies showing detailed mechanisms of enzyme mediated degradation of organic pollutants are not widely published. Results The present report describes a detailed study on the use of Soybean Peroxidase to efficiently degrade Trypan Blue, a diazo dye. In addition to examining various parameters that can affect the dye degradation ability of the enzyme, such as enzyme and H2O2 concentration, reaction pH and temperature, we carried out a detailed mechanistic study of Trypan Blue degradation. HPLC-DAD and LC-MS/MS studies were carried out to confirm dye degradation and analyze the intermediate metabolites and develop a detailed mechanistic dye degradation pathway. Conclusion We report that Soybean peroxidase causes Trypan Blue degradation via symmetrical azo bond cleavage and subsequent radical-initiated ring opening of the metabolites. Interestingly, our results also show that no high molecular weight polymers were produced during the peroxidase-H2O2 mediated degradation of the phenolic Trypan Blue. PMID:23711110

  13. Surgery for malignant gliomas: mechanistic reasoning and slippery statistics.

    PubMed

    Mitchell, Patrick; Ellison, David W; Mendelow, A David

    2005-07-01

    Current surgical treatment of malignant gliomas largely depends on mechanistic reasoning and data collected in non-randomised studies. Technological advance has enabled more accurate resection of tumours and preservation of eloquent brain areas but ethical considerations have restricted randomised trials on the efficacy of surgery to one small trial that found a 3 month survival advantage for patients over age 65 years who received surgery and interim analysis of a larger trial. There is an argument for surgery as a palliative measure in patients with symptoms caused by mechanisms that are surgically remediable. Whether there is any survival advantage from surgery in patients other than those with immediately life-threatening, surgically remediable complications, such as raised intracranial pressure, is unclear. The available data show that if such an advantage does exist, it is modest at best. Adjuvant treatments given surgically are being studied. Chemotherapy wafers are the most prominent of the adjuvant treatments but the evidence available is insufficient to recommend their use in routine practice. In this review we examine the prevailing mechanistic model and observational data; we assess how these are applied and the priorities they indicate for future research. PMID:15963444

  14. From data patterns to mechanistic models in acute critical illness.

    PubMed

    Aerts, Jean-Marie; Haddad, Wassim M; An, Gary; Vodovotz, Yoram

    2014-08-01

    The complexity of the physiologic and inflammatory response in acute critical illness has stymied the accurate diagnosis and development of therapies. The Society for Complex Acute Illness was formed a decade ago with the goal of leveraging multiple complex systems approaches to address this unmet need. Two main paths of development have characterized the society's approach: (i) data pattern analysis, either defining the diagnostic/prognostic utility of complexity metrics of physiologic signals or multivariate analyses of molecular and genetic data and (ii) mechanistic mathematical and computational modeling, all being performed with an explicit translational goal. Here, we summarize the progress to date on each of these approaches, along with pitfalls inherent in the use of each approach alone. We suggest that the next decade holds the potential to merge these approaches, connecting patient diagnosis to treatment via mechanism-based dynamical system modeling and feedback control and allowing extrapolation from physiologic signals to biomarkers to novel drug candidates. As a predicate example, we focus on the role of data-driven and mechanistic models in neuroscience and the impact that merging these modeling approaches can have on general anesthesia. PMID:24768566

  15. Discerning mechanistically rewired biological pathways by cumulative interaction heterogeneity statistics

    PubMed Central

    Cotton, Travis B.; Nguyen, Hien H.; Said, Joseph I.; Ouyang, Zhengyu; Zhang, Jinfa; Song, Mingzhou

    2015-01-01

    Changes in response of a biological pathway could be a consequence of either pathway rewiring, changed input, or a combination of both. Most pathway analysis methods are not designed for mechanistic rewiring such as regulatory element variations. This limits our understanding of biological pathway evolution. Here we present a Q-method to discern whether changed pathway response is caused by mechanistic rewiring of pathways due to evolution. The main innovation is a cumulative pathway interaction heterogeneity statistic accounting for rewiring-specific effects on the rate of change of each molecular variable across conditions. The Q-method remarkably outperformed differential-correlation based approaches on data from diverse biological processes. Strikingly, it also worked well in differentiating rewired chaotic systems, whose dynamics are notoriously difficult to predict. Applying the Q-method on transcriptome data of four yeasts, we show that pathway interaction heterogeneity for known metabolic and signaling pathways is indeed a predictor of interspecies genetic rewiring due to unbalanced TATA box-containing genes among the yeasts. The demonstrated effectiveness of the Q-method paves the way to understanding network evolution at the resolution of functional biological pathways. PMID:25921728

  16. Trichloroethylene: Mechanistic, Epidemiologic and Other Supporting Evidence of Carcinogenic Hazard

    PubMed Central

    Rusyn, Ivan; Chiu, Weihsueh A.; Lash, Lawrence H.; Kromhout, Hans; Hansen, Johnni; Guyton, Kathryn Z.

    2013-01-01

    The chlorinated solvent trichloroethylene (TCE) is a ubiquitous environmental pollutant. The carcinogenic hazard of TCE was the subject of a 2012 evaluation by a Working Group of the International Agency for Research on Cancer (IARC). Information on exposures, relevant data from epidemiologic studies, bioassays in experimental animals, and toxicity and mechanism of action studies was used to conclude that TCE is carcinogenic to humans (Group 1). This article summarizes the key evidence forming the scientific bases for the IARC classification. Exposure to TCE from environmental sources (including from hazardous waste sites and contaminated water) is common throughout the world. While workplace use of TCE has been declining, occupational exposures remain of concern, especially in developing countries. Strongest human evidence is from studies of occupational TCE exposure and kidney cancer. Positive, although less consistent, associations were reported for liver cancer and non-Hodgkin's lymphoma. TCE is carcinogenic at multiple sites in multiple species and strains of experimental animals. The mechanistic evidence includes extensive data on the toxicokinetics and genotoxicity of TCE and its metabolites. Together, available evidence provided a cohesive database supporting the human cancer hazard of TCE, particularly in the kidney. For other target sites of carcinogenicity, mechanistic and other data were found to be more limited. Important sources of susceptibility to TCE toxicity and carcinogenicity were also reviewed by the Working Group. In all, consideration of the multiple evidence streams presented herein informed the IARC conclusions regarding the carcinogenicity of TCE. PMID:23973663

  17. Discerning mechanistically rewired biological pathways by cumulative interaction heterogeneity statistics.

    PubMed

    Cotton, Travis B; Nguyen, Hien H; Said, Joseph I; Ouyang, Zhengyu; Zhang, Jinfa; Song, Mingzhou

    2015-01-01

    Changes in response of a biological pathway could be a consequence of either pathway rewiring, changed input, or a combination of both. Most pathway analysis methods are not designed for mechanistic rewiring such as regulatory element variations. This limits our understanding of biological pathway evolution. Here we present a Q-method to discern whether changed pathway response is caused by mechanistic rewiring of pathways due to evolution. The main innovation is a cumulative pathway interaction heterogeneity statistic accounting for rewiring-specific effects on the rate of change of each molecular variable across conditions. The Q-method remarkably outperformed differential-correlation based approaches on data from diverse biological processes. Strikingly, it also worked well in differentiating rewired chaotic systems, whose dynamics are notoriously difficult to predict. Applying the Q-method on transcriptome data of four yeasts, we show that pathway interaction heterogeneity for known metabolic and signaling pathways is indeed a predictor of interspecies genetic rewiring due to unbalanced TATA box-containing genes among the yeasts. The demonstrated effectiveness of the Q-method paves the way to understanding network evolution at the resolution of functional biological pathways. PMID:25921728

  18. Myocardial steatosis as a possible mechanistic link between diastolic dysfunction and coronary microvascular dysfunction in women.

    PubMed

    Wei, Janet; Nelson, Michael D; Szczepaniak, Edward W; Smith, Laura; Mehta, Puja K; Thomson, Louise E J; Berman, Daniel S; Li, Debiao; Bairey Merz, C Noel; Szczepaniak, Lidia S

    2016-01-01

    Women with coronary microvascular dysfunction (CMD) and no obstructive coronary artery disease (CAD) have increased rates of heart failure with preserved ejection fraction (HFpEF). The mechanisms of HFpEF are not well understood. Ectopic fat deposition in the myocardium, termed myocardial steatosis, is frequently associated with diastolic dysfunction in other metabolic diseases. We investigated the prevalence of myocardial steatosis and diastolic dysfunction in women with CMD and subclinical HFpEF. In 13 women, including eight reference controls and five women with CMD and evidence of subclinical HFpEF (left ventricular end-diastolic pressure >12 mmHg), we measured myocardial triglyceride content (TG) and diastolic function, by proton magnetic resonance spectroscopy and magnetic resonance tissue tagging, respectively. When compared with reference controls, women with CMD had higher myocardial TG content (0.83 ± 0.12% vs. 0.43 ± 0.06%; P = 0.025) and lower diastolic circumferential strain rate (168 ± 12 vs. 217 ± 15%/s; P = 0.012), with myocardial TG content correlating inversely with diastolic circumferential strain rate (r = -0.779; P = 0.002). This study provides proof-of-concept that myocardial steatosis may play an important mechanistic role in the development of diastolic dysfunction in women with CMD and no obstructive CAD. Detailed longitudinal studies are warranted to explore specific treatment strategies targeting myocardial steatosis and its effect on diastolic function. PMID:26519031

  19. Emerging Mechanistic Targets in Lung Injury Induced by Combustion-Generated Particles

    PubMed Central

    Fariss, Marc W.; Gilmour, M. Ian; Reilly, Christopher A.; Liedtke, Wolfgang; Ghio, Andrew J.

    2013-01-01

    The mechanism for biological effect following exposure to combustion-generated particles is incompletely defined. The identification of pathways regulating the acute toxicological effects of these particles provides specific targets for therapeutic manipulation in an attempt to impact disease following exposures. Transient receptor potential (TRP) cation channels were identified as “particle sensors” in that their activation was coupled with the initiation of protective responses limiting airway deposition and inflammatory responses, which promote degradation and clearance of the particles. TRPA1, V1, V4, and M8 have a capacity to mediate adverse effects after exposure to combustion-generated particulate matter (PM); relative contributions of each depend upon particle composition, dose, and deposition. Exposure of human bronchial epithelial cells to an organic extract of diesel exhaust particle was followed by TRPV4 mediating Ca++ influx, increased RAS expression, mitogen-activated protein kinase signaling, and matrix metalloproteinase-1 activation. These novel pathways of biological effect can be targeted by compounds that specifically inhibit critical signaling reactions. In addition to TRPs and calcium biochemistry, humic-like substances (HLS) and cell/tissue iron equilibrium were identified as potential mechanistic targets in lung injury after particle exposure. In respiratory epithelial cells, iron sequestration by HLS in wood smoke particle (WSP) was associated with oxidant generation, cell signaling, transcription factor activation, and release of inflammatory mediators. Similar to WSP, cytotoxic insoluble nanosized spherical particles composed of HLS were isolated from cigarette smoke condensate. Therapies that promote bioelimination of HLS and prevent the disruption of iron homeostasis could function to reduce the harmful effects of combustion-generated PM exposure. PMID:23322347

  20. Perspectives on the Application of Mechanistic Information in Chemical Hazard and Dose-Response Assessments

    EPA Science Inventory

    This overview summarizes several EPA Assessment publications reviewing approaches for applying mechanistic information in human health risk assessment and exploring opportunities for progress in this area.

  1. A new mechanistic framework to predict OCS fluxes in soils

    NASA Astrophysics Data System (ADS)

    Sauze, Joana; Ogee, Jérôme; Launois, Thomas; Kesselmeier, Jürgen; Van Diest, Heidi; Wingate, Lisa

    2015-04-01

    A better description of the amplitude of photosynthetic and respiratory gross CO2 fluxes at large scales is needed to improve our predictions of the current and future global CO2 cycle. Carbonyl sulfide (COS) is the most abundant sulphur gas in the atmosphere and has been proposed as a new tracer of gross photosynthesis, as the uptake of COS from the atmosphere is dominated by the activity of carbonic anhydrase (CA), an enzyme abundant in leaves that also catalyses CO2 hydration during photosynthesis. However, soils also exchange COS with the atmosphere and there is growing evidence that this flux must also be accounted for in atmospheric budgets. In this context a new mechanistic description of soil-atmosphere COS exchange is clearly needed. Soils can take up COS from the atmosphere as the soil biota also contain CA, and COS emissions from soils have also been reported in agricultural fields or anoxic soils. Previous studies have also shown that soil COS fluxes present an optimum soil water content and soil temperature. Here we propose a new mechanistic framework to predict the fluxes of COS between the soils and the atmosphere. We describe the COS soil budget by a first-order reaction-diffusion-production equation, assuming that the hydrolysis of COS by CA is total and irreversible. To describe COS diffusion through the soil matrix, we use different formulations of soil air-filled pore space and temperature, depending on the turbulence level above the soil surface. Using this model we are able to explain the observed presence of an optimum temperature for soil COS uptake and show how this optimum can shift to cooler temperatures in the presence of soil COS emissions. Our model can also explain the observed optimum with soil moisture content previously described in the literature (e.g. Van Diest & Kesselmeier, 2008) as a result of diffusional constraints on COS hydrolysis. These diffusional constraints are also responsible for the response of COS uptake to soil

  2. Conservative or reactive? Mechanistic chemical perspectives on organic matter stability

    NASA Astrophysics Data System (ADS)

    Koch, Boris

    2016-04-01

    Carbon fixation by terrestrial and marine primary production has a fundamental seasonal effect on the atmospheric carbon content and it profoundly contributes to long-term carbon storage in form of organic matter (OM) in soils, water, and sediments. The efficacy of this sequestration process strongly depends on the degree of OM persistence. Therefore, one of the key issues in dissolved and particulate OM research is to assess the stability of reservoirs and to quantify their contribution to global carbon fluxes. Incubation experiments are helpful to assess OM stability during the first, early diagenetic turnover induced by sunlight or microbes. However, net carbon fluxes within the global carbon cycle also act on much longer time scales, which are not amenable in experiments. It is therefore critical to improve our mechanistic understanding to be able to assess potential future changes in the organic matter cycle. This session contribution highlights some achievements and open questions in the field. An improved mechanistic understanding of OM turnover particularly depends on the molecular characterization of biogeochemical processes and their kinetics: (i) in soils and sediments, aggregation/disaggregation of OM is primarily controlled by its molecular composition. Hence, the chemical composition determines the transfer of organic carbon from the large particulate to the small dissolved organic matter reservoir - an important substrate for microbial metabolism. (ii) In estuaries, dissolved organic carbon gradients usually suggest conservative behavior, whereas molecular-level studies reveal a substantial chemical modification of terrestrial DOM along the land-ocean interface. (iii) In the ocean, previous studies have shown that the recalcitrance of OM depends on bulk concentration and energy yield. However, ultrahigh resolution mass spectrometry in combination with radiocarbon analyses also emphasized that stability is tightly connected to molecular composition

  3. Atrial Fibrillation and Hypertension: Mechanistic, Epidemiologic, and Treatment Parallels

    PubMed Central

    Ogunsua, Adedotun A.; Shaikh, Amir Y.; Ahmed, Mohamed; McManus, David D.

    2015-01-01

    Atrial fibrillation (AF) is an increasingly prevalent condition and the most common sustained arrhythmia encountered in ambulatory and hospital practice. Several clinical risk factors for AF include age, sex, valvular heart disease, obesity, sleep apnea, heart failure, and hypertension (HTN). Of all the risk factors, HTN is the most commonly encountered condition in patients with incident AF. Hypertension is associated with a 1.8-fold increase in the risk of developing new-onset AF and a 1.5-fold increase in the risk of progression to permanent AF. Hypertension predisposes to cardiac structural changes that influence the development of AF such as atrial remodeling. The renin angiotensin aldosterone system has been demonstrated to be a common mechanistic link in the pathogenesis of HTN and AF. Importantly, HTN is one of the few modifiable AF risk factors, and guideline-directed management of HTN may reduce the incidence of AF. PMID:27057292

  4. Atrial Fibrillation and Hypertension: Mechanistic, Epidemiologic, and Treatment Parallels.

    PubMed

    Ogunsua, Adedotun A; Shaikh, Amir Y; Ahmed, Mohamed; McManus, David D

    2015-01-01

    Atrial fibrillation (AF) is an increasingly prevalent condition and the most common sustained arrhythmia encountered in ambulatory and hospital practice. Several clinical risk factors for AF include age, sex, valvular heart disease, obesity, sleep apnea, heart failure, and hypertension (HTN). Of all the risk factors, HTN is the most commonly encountered condition in patients with incident AF. Hypertension is associated with a 1.8-fold increase in the risk of developing new-onset AF and a 1.5-fold increase in the risk of progression to permanent AF. Hypertension predisposes to cardiac structural changes that influence the development of AF such as atrial remodeling. The renin angiotensin aldosterone system has been demonstrated to be a common mechanistic link in the pathogenesis of HTN and AF. Importantly, HTN is one of the few modifiable AF risk factors, and guideline-directed management of HTN may reduce the incidence of AF. PMID:27057292

  5. Mechanistic views on aromatic substitution reactions by gaseous cations.

    PubMed

    Fornarini, S

    1996-01-01

    Recent advances in the understanding of the gas-phase reaction of aromatics with cationic electrophiles in a thermally equilibrated domain are described. The overall substitution reaction is analyzed in terms of its elementary steps. Their contribution to the overall reactivity pattern is dissected by the use of selected systems, which allowed one to highlight the kinetic role of single elementary events. Mechanistic studies have focused on the structure and reactivity of covalent and non-covalent ionic intermediates, which display a rich chemistry and provide benchmark reactivity models. Particular interest has been devoted to proton transfer reactions, which may occur in either an intra- or intermolecular fashion in arenium intermediates. A quantitative study of their rates and associated kinetic isotope effects is reported. © 1997 John Wiley & Sons, Inc. Mass Spectrom Rev 15(6), 365-389, 1997. PMID:27082944

  6. Mechanistic failure mode investigation and resolution of parvovirus retentive filters.

    PubMed

    LaCasse, Daniel; Lute, Scott; Fiadeiro, Marcus; Basha, Jonida; Stork, Matthew; Brorson, Kurt; Godavarti, Ranga; Gallo, Chris

    2016-07-01

    Virus retentive filters are a key product safety measure for biopharmaceuticals. A simplistic perception is that they function solely based on a size-based particle removal mechanism of mechanical sieving and retention of particles based on their hydrodynamic size. Recent observations have revealed a more nuanced picture, indicating that changes in viral particle retention can result from process pressure and/or flow interruptions. In this study, a mechanistic investigation was performed to help identify a potential mechanism leading to the reported reduced particle retention in small virus filters. Permeate flow rate or permeate driving force were varied and analyzed for their impact on particle retention in three commercially available small virus retentive filters. © 2016 American Institute of Chemical Engineers Biotechnol. Prog., 32:959-970, 2016. PMID:27160325

  7. Mechanistic insights into selective autophagy pathways: lessons from yeast.

    PubMed

    Farré, Jean-Claude; Subramani, Suresh

    2016-09-01

    Autophagy has burgeoned rapidly as a field of study because of its evolutionary conservation, the diversity of intracellular cargoes degraded and recycled by this machinery, the mechanisms involved, as well as its physiological relevance to human health and disease. This self-eating process was initially viewed as a non-selective mechanism used by eukaryotic cells to degrade and recycle macromolecules in response to stress; we now know that various cellular constituents, as well as pathogens, can also undergo selective autophagy. In contrast to non-selective autophagy, selective autophagy pathways rely on a plethora of selective autophagy receptors (SARs) that recognize and direct intracellular protein aggregates, organelles and pathogens for specific degradation. Although SARs themselves are not highly conserved, their modes of action and the signalling cascades that activate and regulate them are. Recent yeast studies have provided novel mechanistic insights into selective autophagy pathways, revealing principles of how various cargoes can be marked and targeted for selective degradation. PMID:27381245

  8. Mechanistic Investigations into the Application of Sulfoxides in Carbohydrate Synthesis

    PubMed Central

    Brabham, Robin

    2016-01-01

    Abstract The utility of sulfoxides in a diverse range of transformations in the field of carbohydrate chemistry has seen rapid growth since the first introduction of a sulfoxide as a glycosyl donor in 1989. Sulfoxides have since developed into more than just anomeric leaving groups, and today have multiple roles in glycosylation reactions. These include as activators for thioglycosides, hemiacetals, and glycals, and as precursors to glycosyl triflates, which are essential for stereoselective β‐mannoside synthesis, and bicyclic sulfonium ions that facilitate the stereoselective synthesis of α‐glycosides. In this review we highlight the mechanistic investigations undertaken in this area, often outlining strategies employed to differentiate between multiple proposed reaction pathways, and how the conclusions of these investigations have and continue to inform upon the development of more efficient transformations in sulfoxide‐based carbohydrate synthesis. PMID:26744250

  9. The unique enzymatic and mechanistic properties of plant myosins.

    PubMed

    Henn, Arnon; Sadot, Einat

    2014-12-01

    Myosins are molecular motors that move along actin-filament tracks. Plants express two main classes of myosins, myosin VIII and myosin XI. Along with their relatively conserved sequence and functions, plant myosins have acquired some unique features. Myosin VIII has the enzymatic characteristics of a tension sensor and/or a tension generator, similar to functions found in other eukaryotes. Interestingly, class XI plant myosins have gained a novel function that consists of propelling the exceptionally rapid cytoplasmic streaming. This specific class includes the fastest known translocating molecular motors, which can reach an extremely high velocity of about 60μms(-1). However, the enzymatic properties and mechanistic basis for these remarkable manifestations are not yet fully understood. Here we review recent progress in understanding the uniqueness of plant myosins, while emphasizing the unanswered questions. PMID:25435181

  10. Mechanistic modeling confronts the complexity of molecular cell biology.

    PubMed

    Phair, Robert D

    2014-11-01

    Mechanistic modeling has the potential to transform how cell biologists contend with the inescapable complexity of modern biology. I am a physiologist-electrical engineer-systems biologist who has been working at the level of cell biology for the past 24 years. This perspective aims 1) to convey why we build models, 2) to enumerate the major approaches to modeling and their philosophical differences, 3) to address some recurrent concerns raised by experimentalists, and then 4) to imagine a future in which teams of experimentalists and modelers build-and subject to exhaustive experimental tests-models covering the entire spectrum from molecular cell biology to human pathophysiology. There is, in my view, no technical obstacle to this future, but it will require some plasticity in the biological research mind-set. PMID:25368428

  11. A mechanistic interpretation of the resonant wave-particle interaction

    NASA Astrophysics Data System (ADS)

    Chim, Chi Yung; O'Neil, Thomas M.

    2016-05-01

    This paper provides a simple mechanistic interpretation of the resonant wave-particle interaction of Landau. For the simple case of a Langmuir wave in a Vlasov plasma, the non-resonant electrons satisfy an oscillator equation that is driven resonantly by the bare electric field from the resonant electrons, and in the case of wave damping, this complex driver field is of a phase to reduce the oscillation amplitude. The wave-particle resonant interaction also occurs in waves governed by 2D E × B drift dynamics, such as a diocotron wave. In this case, the bare electric field from the resonant electrons causes E × B drift motion back in the core plasma, reducing the amplitude of the wave.

  12. Mechanistic model for void distribution in flashing flow

    SciTech Connect

    Riznic, J.; Ishii, M.; Afgan, N.

    1987-01-01

    A problem of discharging of an initially subcooled liquid from a high pressure condition into a low pressure environment is quite important in several industrial systems such as nuclear reactors and chemical reactors. A new model for the flashing process is proposed here based on the wall nucleation theory, bubble growth model and drift-flux bubble transport model. In order to calculate the bubble number density, the bubble number transport equation with a distributed source from the wall nucleation sites is used. The model predictions in terms of the void fraction are compared to Moby Dick and BNL experimental data. It shows that satisfactory agreements could be obtained from the present model without any floating parameter to be adjusted with data. This result indicates that, at least for the experimental conditions considered here, the mechanistic prediction of the flashing phenomenon is possible based on the present wall nucleation based model. 43 refs., 4 figs.

  13. Mechanistic model for void distribution in flashing flow

    NASA Astrophysics Data System (ADS)

    Riznic, J.; Ishii, M.; Afgan, N.

    A problem of discharging of an initially subcooled liquid from a high pressure condition into a low pressure environment is quite important in several industrial systems such as nuclear reactors and chemical reactors. A new model for the flashing process is proposed here based on the wall nucleation theory, bubble growth model and drift-flux bubble transport model. In order to calculate the bubble number density, the bubble number transport equation with a distributed source from the wall nucleation sites is used. The model predictions in terms of the void fraction are compared to Moby Dick and BNL experimental data. It shows that satisfactory agreements could be obtained from the present model without any floating parameter to be adjusted with data. This result indicates that, at least for the experimental conditions considered here, the mechanistic prediction of the flashing phenomenon is possible based on the present wall nucleation based model.

  14. Parameter and uncertainty estimation for mechanistic, spatially explicit epidemiological models

    NASA Astrophysics Data System (ADS)

    Finger, Flavio; Schaefli, Bettina; Bertuzzo, Enrico; Mari, Lorenzo; Rinaldo, Andrea

    2014-05-01

    Epidemiological models can be a crucially important tool for decision-making during disease outbreaks. The range of possible applications spans from real-time forecasting and allocation of health-care resources to testing alternative intervention mechanisms such as vaccines, antibiotics or the improvement of sanitary conditions. Our spatially explicit, mechanistic models for cholera epidemics have been successfully applied to several epidemics including, the one that struck Haiti in late 2010 and is still ongoing. Calibration and parameter estimation of such models represents a major challenge because of properties unusual in traditional geoscientific domains such as hydrology. Firstly, the epidemiological data available might be subject to high uncertainties due to error-prone diagnosis as well as manual (and possibly incomplete) data collection. Secondly, long-term time-series of epidemiological data are often unavailable. Finally, the spatially explicit character of the models requires the comparison of several time-series of model outputs with their real-world counterparts, which calls for an appropriate weighting scheme. It follows that the usual assumption of a homoscedastic Gaussian error distribution, used in combination with classical calibration techniques based on Markov chain Monte Carlo algorithms, is likely to be violated, whereas the construction of an appropriate formal likelihood function seems close to impossible. Alternative calibration methods, which allow for accurate estimation of total model uncertainty, particularly regarding the envisaged use of the models for decision-making, are thus needed. Here we present the most recent developments regarding methods for parameter and uncertainty estimation to be used with our mechanistic, spatially explicit models for cholera epidemics, based on informal measures of goodness of fit.

  15. Mechanistic information from analysis of molecular weight distributions of starch.

    PubMed

    Castro, Jeffrey V; Dumas, Céline; Chiou, Herbert; Fitzgerald, Melissa A; Gilbert, Robert G

    2005-01-01

    A methodology is developed for interpreting the molecular weight distributions of debranched amylopectin, based on techniques developed for quantitatively and qualitatively finding mechanistic information from the molecular weight distributions of synthetic polymers. If the only events occurring are random chain growth and stoppage (i.e., the rates are independent of degree of polymerization over the range in question), then the number of chains of degree of polymerization N, P(N), is linear in ln P(N) with a negative slope, where the slope gives the ratio of the stoppage and growth rates. This starting point suggests that mechanistic inferences can be made from a plot of lnP against N. Application to capillary electrophoresis data for the P(N) of debranched starch from across the major taxa, from bacteria (Escherichia coli), green algae (Chlamydomonas reinhardtii), mammals (Bos), and flowering plants (Oryza sativa, rice; Zea mays, maize; Triticum aestivum, wheat; Hordeum vulgare, barley; and Solanum tuberosum, potato), gives insights into the biosynthetic pathways, showing the differences and similarities of the alpha-1,4-glucans produced by the various species. Four characteristic regions for storage starch from the higher plants are revealed: (1) an initial increasing region corresponding to the formation of new branches, (2) a linear ln P region with negative slope, indicating random growth and stoppage, (3) a region corresponding to the formation of the crystalline lamellae and subsequent elongation of chains, and (4) a second linear ln P with negative slope region. Each region can be assigned to specific enzymatic processes in starch synthesis, including determining the ranges of degrees of polymerization which are subject to random and nonrandom processes. PMID:16004469

  16. Mechanistic models of biofilm growth in porous media

    NASA Astrophysics Data System (ADS)

    Jaiswal, Priyank; Al-Hadrami, Fathiya; Atekwana, Estella A.; Atekwana, Eliot A.

    2014-07-01

    Nondestructive acoustics methods can be used to monitor in situ biofilm growth in porous media. In practice, however, acoustic methods remain underutilized due to the lack of models that can translate acoustic data into rock properties in the context of biofilm. In this paper we present mechanistic models of biofilm growth in porous media. The models are used to quantitatively interpret arrival times and amplitudes recorded in the 29 day long Davis et al. (2010) physical scale biostimulation experiment in terms of biofilm morphologies and saturation. The model pivots on addressing the sediment elastic behavior using the lower Hashin-Shtrikman bounds for grain mixing and Gassmann substitution for fluid saturation. The time-lapse P wave velocity (VP; a function of arrival times) is explained by a combination of two rock models (morphologies); "load bearing" which assumes the biofilm as an additional mineral in the rock matrix and "pore filling" which assumes the biofilm as an additional fluid phase in the pores. The time-lapse attenuation (QP-1; a function of amplitudes), on the other hand, can be explained adequately in two ways; first, through squirt flow where energy is lost from relative motion between rock matrix and pore fluid, and second, through an empirical function of porosity (φ), permeability (κ), and grain size. The squirt flow model-fitting results in higher internal φ (7% versus 5%) and more oblate pores (0.33 versus 0.67 aspect ratio) for the load-bearing morphology versus the pore-filling morphology. The empirical model-fitting results in up to 10% increase in κ at the initial stages of the load-bearing morphology. The two morphologies which exhibit distinct mechanical and hydraulic behavior could be a function of pore throat size. The biofilm mechanistic models developed in this study can be used for the interpretation of seismic data critical for the evaluation of biobarriers in bioremediation, microbial enhanced oil recovery, and CO2

  17. Assembly Line Polyketide Synthases: Mechanistic Insights and Unsolved Problems

    PubMed Central

    2015-01-01

    Two hallmarks of assembly line polyketide synthases have motivated an interest in these unusual multienzyme systems, their stereospecificity and their capacity for directional biosynthesis. In this review, we summarize the state of knowledge regarding the mechanistic origins of these two remarkable features, using the 6-deoxyerythronolide B synthase as a prototype. Of the 10 stereocenters in 6-deoxyerythronolide B, the stereochemistry of nine carbon atoms is directly set by ketoreductase domains, which catalyze epimerization and/or diastereospecific reduction reactions. The 10th stereocenter is established by the sequential action of three enzymatic domains. Thus, the problem has been reduced to a challenge in mainstream enzymology, where fundamental gaps remain in our understanding of the structural basis for this exquisite stereochemical control by relatively well-defined active sites. In contrast, testable mechanistic hypotheses for the phenomenon of vectorial biosynthesis are only just beginning to emerge. Starting from an elegant theoretical framework for understanding coupled vectorial processes in biology [Jencks, W. P. (1980) Adv. Enzymol. Relat. Areas Mol. Biol. 51, 75–106], we present a simple model that can explain assembly line polyketide biosynthesis as a coupled vectorial process. Our model, which highlights the important role of domain–domain interactions, not only is consistent with recent observations but also is amenable to further experimental verification and refinement. Ultimately, a definitive view of the coordinated motions within and between polyketide synthase modules will require a combination of structural, kinetic, spectroscopic, and computational tools and could be one of the most exciting frontiers in 21st Century enzymology. PMID:24779441

  18. A Mechanistic Approach for the Prediction of Critical Power in BWR Fuel Bundles

    NASA Astrophysics Data System (ADS)

    Chandraker, Dinesh Kumar; Vijayan, Pallipattu Krishnan; Sinha, Ratan Kumar; Aritomi, Masanori

    The critical power corresponding to the Critical Heat Flux (CHF) or dryout condition is an important design parameter for the evaluation of safety margins in a nuclear fuel bundle. The empirical approaches for the prediction of CHF in a rod bundle are highly geometric specific and proprietary in nature. The critical power experiments are very expensive and technically challenging owing to the stringent simulation requirements for the rod bundle tests involving radial and axial power profiles. In view of this, the mechanistic approach has gained momentum in the thermal hydraulic community. The Liquid Film Dryout (LFD) in an annular flow is the mechanism of CHF under BWR conditions and the dryout modeling has been found to predict the CHF quite accurately for a tubular geometry. The successful extension of the mechanistic model of dryout to the rod bundle application is vital for the evaluation of critical power in the rod bundle. The present work proposes the uniform film flow approach around the rod by analyzing individual film of the subchannel bounded by rods with different heat fluxes resulting in different film flow rates around a rod and subsequently distributing the varying film flow rates of a rod to arrive at the uniform film flow rate as it has been found that the liquid film has a strong tendency to be uniform around the rod. The FIDOM-Rod code developed for the dryout prediction in BWR assemblies provides detailed solution of the multiple liquid films in a subchannel. The approach of uniform film flow rate around the rod simplifies the liquid film cross flow modeling and was found to provide dryout prediction with a good accuracy when compared with the experimental data of 16, 19 and 37 rod bundles under BWR conditions. The critical power has been predicted for a newly designed 54 rod bundle of the Advanced Heavy Water Reactor (AHWR). The selected constitutive models for the droplet entrainment and deposition rates validated for the dryout in tube were

  19. Modeling Bird Migration under Climate Change: A Mechanistic Approach

    NASA Technical Reports Server (NTRS)

    Smith, James A.

    2009-01-01

    How will migrating birds respond to changes in the environment under climate change? What are the implications for migratory success under the various accelerated climate change scenarios as forecast by the Intergovernmental Panel on Climate Change? How will reductions or increased variability in the number or quality of wetland stop-over sites affect migratory bird species? The answers to these questions have important ramifications for conservation biology and wildlife management. Here, we describe the use of continental scale simulation modeling to explore how spatio-temporal changes along migratory flyways affect en-route migration success. We use an individually based, biophysical, mechanistic, bird migration model to simulate the movement of shorebirds in North America as a tool to study how such factors as drought and wetland loss may impact migratory success and modify migration patterns. Our model is driven by remote sensing and climate data and incorporates important landscape variables. The energy budget components of the model include resting, foraging, and flight, but presently predation is ignored. Results/Conclusions We illustrate our model by studying the spring migration of sandpipers through the Great Plains to their Arctic breeding grounds. Why many species of shorebirds have shown significant declines remains a puzzle. Shorebirds are sensitive to stop-over quality and spacing because of their need for frequent refueling stops and their opportunistic feeding patterns. We predict bird "hydrographs that is, stop-over frequency with latitude, that are in agreement with the literature. Mean stop-over durations predicted from our model for nominal cases also are consistent with the limited, but available data. For the shorebird species simulated, our model predicts that shorebirds exhibit significant plasticity and are able to shift their migration patterns in response to changing drought conditions. However, the question remains as to whether this

  20. A new mechanistic framework to predict OCS fluxes from soils

    NASA Astrophysics Data System (ADS)

    Ogée, Jérôme; Sauze, Joana; Kesselmeier, Jürgen; Genty, Bernard; Van Diest, Heidi; Launois, Thomas; Wingate, Lisa

    2016-04-01

    Estimates of photosynthetic and respiratory fluxes at large scales are needed to improve our predictions of the current and future global CO2 cycle. Carbonyl sulfide (OCS) is the most abundant sulfur gas in the atmosphere and has been proposed as a new tracer of photosynthetic gross primary productivity (GPP), as the uptake of OCS from the atmosphere is dominated by the activity of carbonic anhydrase (CA), an enzyme abundant in leaves that also catalyses CO2 hydration during photosynthesis. However soils also exchange OCS with the atmosphere, which complicates the retrieval of GPP from atmospheric budgets. Indeed soils can take up large amounts of OCS from the atmosphere as soil microorganisms also contain CA, and OCS emissions from soils have been reported in agricultural fields or anoxic soils. To date no mechanistic framework exists to describe this exchange of OCS between soils and the atmosphere, but empirical results, once upscaled to the global scale, indicate that OCS consumption by soils dominates OCS emission and its contribution to the atmospheric budget is large, at about one third of the OCS uptake by vegetation, also with a large uncertainty. Here, we propose a new mechanistic model of the exchange of OCS between soils and the atmosphere that builds on our knowledge of soil CA activity from CO2 oxygen isotopes. In this model the OCS soil budget is described by a first-order reaction-diffusion-production equation, assuming that the hydrolysis of OCS by CA is total and irreversible. Using this model we are able to explain the observed presence of an optimum temperature for soil OCS uptake and show how this optimum can shift to cooler temperatures in the presence of soil OCS emission. Our model can also explain the observed optimum with soil moisture content previously described in the literature as a result of diffusional constraints on OCS hydrolysis. These diffusional constraints are also responsible for the response of OCS uptake to soil weight and

  1. Development of a mechanistic model for forced convection subcooled boiling

    NASA Astrophysics Data System (ADS)

    Shaver, Dillon R.

    The focus of this work is on the formulation, implementation, and testing of a mechanistic model of subcooled boiling. Subcooled boiling is the process of vapor generation on a heated wall when the bulk liquid temperature is still below saturation. This is part of a larger effort by the US DoE's CASL project to apply advanced computational tools to the simulation of light water reactors. To support this effort, the formulation of the dispersed field model is described and a complete model of interfacial forces is formulated. The model has been implemented in the NPHASE-CMFD computer code with a K-epsilon model of turbulence. The interfacial force models are built on extensive work by other authors, and include novel formulations of the turbulent dispersion and lift forces. The complete model of interfacial forces is compared to experiments for adiabatic bubbly flows, including both steady-state and unsteady conditions. The same model is then applied to a transient gas/liquid flow in a complex geometry of fuel channels in a sodium fast reactor. Building on the foundation of the interfacial force model, a mechanistic model of forced-convection subcooled boiling is proposed. This model uses the heat flux partitioning concept and accounts for condensation of bubbles attached to the wall. This allows the model to capture the enhanced heat transfer associated with boiling before the point of net generation of vapor, a phenomenon consistent with existing experimental observations. The model is compared to four different experiments encompassing flows of light water, heavy water, and R12 at different pressures, in cylindrical channels, an internally heated annulus, and a rectangular channel. The experimental data includes axial and radial profiles of both liquid temperature and vapor volume fraction, and the agreement can be considered quite good. The complete model is then applied to simulations of subcooled boiling in nuclear reactor subchannels consistent with the

  2. A new mechanistic framework to predict OCS fluxes from soils

    NASA Astrophysics Data System (ADS)

    Ogée, J.; Sauze, J.; Kesselmeier, J.; Genty, B.; Van Diest, H.; Launois, T.; Wingate, L.

    2015-09-01

    Estimates of photosynthetic and respiratory fluxes at large scales is needed to improve our predictions of the current and future global CO2 cycle. Carbonyl sulphide (OCS) is the most abundant sulphur gas in the atmosphere and has been proposed as a new tracer of photosynthesis (GPP), as the uptake of OCS from the atmosphere is dominated by the activity of carbonic anhydrase (CA), an enzyme abundant in leaves that also catalyses CO2 hydration during photosynthesis. But soils also exchange OCS with the atmosphere which complicates the retrieval of GPP from atmospheric budgets. Indeed soils can take up large amounts of OCS from the atmosphere as soil microorganisms also contain CA, and OCS emissions from soils have been reported in agricultural fields or anoxic soils. To date no mechanistic framework exists to describe this exchange of OCS between soils and the atmosphere but empirical results, once upscaled to the global scale, indicate that OCS consumption by soils dominates over production and its contribution to the atmospheric budget is large, at about one third of the OCS uptake by vegetation, with also a large uncertainty. Here, we propose a new mechanistic model of the exchange of OCS between soils and the atmosphere that builds on our knowledge of soil CA activity from CO2 oxygen isotopes. In this model the OCS soil budget is described by a first-order reaction-diffusion-production equation, assuming that the hydrolysis of OCS by CA is total and irreversible. Using this model we are able to explain the observed presence of an optimum temperature for soil OCS uptake and show how this optimum can shift to cooler temperatures in the presence of soil OCS emissions. Our model can also explain the observed optimum with soil moisture content previously described in the literature as a result of diffusional constraints on OCS hydrolysis. These diffusional constraints are also responsible for the response of OCS uptake to soil weight and depth observed previously. In

  3. A new mechanistic framework to predict OCS fluxes from soils

    NASA Astrophysics Data System (ADS)

    Ogee, J.; Sauze, J.; Kesselmeier, J.; Genty, B.; Whelan, M.; Launois, T.; Wingate, L.

    2015-12-01

    A better description of the amplitude of photosynthetic and respiratory gross CO2 fluxes at large scales is needed to improve our predictions of the current and future global CO2 cycle. Carbonyl sulphide (OCS) has been proposed as a new tracer of gross photosynthesis (GPP), as the uptake of OCS from the atmosphere is dominated by the activity of carbonic anhydrase (CA), an enzyme abundant in leaves that also catalyses CO2 hydration during photosynthesis. But soils also exchange OCS with the atmosphere which complicates the retrieval of GPP from atmospheric budgets. Indeed soils can take up large amounts of OCS from the atmosphere as soil microorganisms also contain CA, and OCS emissions from soils have been reported in agricultural or anoxic soils. To date no mechanistic framework exists to describe this exchange of OCS between soils and the atmosphere but empirical results, once up-scaled to the global scale, indicate that OCS consumption by soils dominates over production and its contribution to the atmospheric budget is large, at about one third of the OCS uptake by vegetation, with also a large uncertainty. Here, we propose a new mechanistic model of the exchange of OCS between soils and the atmosphere that builds on our knowledge of soil CA activity from CO2 oxygen isotopes. In this model the OCS soil budget is described by a first-order reaction-diffusion-production equation, assuming that the hydrolysis of OCS by CA is total and irreversible. Using this model we are able to explain the observed presence of an optimum temperature for soil OCS uptake and show how this optimum can shift to cooler temperatures in the presence of soil OCS emissions. Our model can also explain the observed optimum with soil moisture content previously described in the literature as a result of diffusional constraints on OCS hydrolysis. In order to simulate the exact OCS uptake rates and patterns observed on several soils collected from a range of biomes, different CA activities

  4. CFD-based Modeling of Inflight Mercury Capture

    SciTech Connect

    Madsen, J.I.; O'Brien, T.J.

    2007-01-01

    A numerical model of sorbent injection and in-flight mercury capture is presented. There are few existing models of mercury capture, and these typically make gross assumptions of plug gas flow, no velocity slip between particle and gas phase, and uniform sorbent dispersion. All of these assumptions are overcome with the current model, which combines the physics of mass transfer at the microscopic sorbent scale with macroscopic flow conditions provided via Computational Fluid Dynamics (CFD) simulations. The implication is a cost-efficient tool for design of injection systems that maximize capture efficiency. The modeling framework will be presented along with results based on simulation of sites from the DOE/NETL sorbent injection field test program.

  5. CFD-Based Design Optimization for Single Element Rocket Injector

    NASA Technical Reports Server (NTRS)

    Vaidyanathan, Rajkumar; Tucker, Kevin; Papila, Nilay; Shyy, Wei

    2003-01-01

    To develop future Reusable Launch Vehicle concepts, we have conducted design optimization for a single element rocket injector, with overall goals of improving reliability and performance while reducing cost. Computational solutions based on the Navier-Stokes equations, finite rate chemistry, and the k-E turbulence closure are generated with design of experiment techniques, and the response surface method is employed as the optimization tool. The design considerations are guided by four design objectives motivated by the consideration in both performance and life, namely, the maximum temperature on the oxidizer post tip, the maximum temperature on the injector face, the adiabatic wall temperature, and the length of the combustion zone. Four design variables are selected, namely, H2 flow angle, H2 and O2 flow areas with fixed flow rates, and O2 post tip thickness. In addition to establishing optimum designs by varying emphasis on the individual objectives, better insight into the interplay between design variables and their impact on the design objectives is gained. The investigation indicates that improvement in performance or life comes at the cost of the other. Best compromise is obtained when improvements in both performance and life are given equal importance.

  6. CFD-Based Design Optimization Tool Developed for Subsonic Inlet

    NASA Technical Reports Server (NTRS)

    1995-01-01

    The traditional approach to the design of engine inlets for commercial transport aircraft is a tedious process that ends with a less-than-optimum design. With the advent of high-speed computers and the availability of more accurate and reliable computational fluid dynamics (CFD) solvers, numerical optimization processes can effectively be used to design an aerodynamic inlet lip that enhances engine performance. The designers' experience at Boeing Corporation showed that for a peak Mach number on the inlet surface beyond some upper limit, the performance of the engine degrades excessively. Thus, our objective was to optimize efficiency (minimize the peak Mach number) at maximum cruise without compromising performance at other operating conditions. Using a CFD code NPARC, the NASA Lewis Research Center, in collaboration with Boeing, developed an integrated procedure at Lewis to find the optimum shape of a subsonic inlet lip and a numerical optimization code, ADS. We used a GRAPE-based three-dimensional grid generator to help automate the optimization procedure. The inlet lip shape at the crown and the keel was described as a superellipse, and the superellipse exponents and radii ratios were considered as design variables. Three operating conditions: cruise, takeoff, and rolling takeoff, were considered in this study. Three-dimensional Euler computations were carried out to obtain the flow field. At the initial design, the peak Mach numbers for maximum cruise, takeoff, and rolling takeoff conditions were 0.88, 1.772, and 1.61, respectively. The acceptable upper limits on the takeoff and rolling takeoff Mach numbers were 1.55 and 1.45. Since the initial design provided by Boeing was found to be optimum with respect to the maximum cruise condition, the sum of the peak Mach numbers at takeoff and rolling takeoff were minimized in the current study while the maximum cruise Mach number was constrained to be close to that at the existing design. With this objective, the optimum design satisfied the upper limits at takeoff and rolling takeoff while retaining the desirable cruise performance. Further studies are being conducted to include static and cross-wind operating conditions in the design optimization procedure. This work was carried out in collaboration with Dr. E.S. Reddy of NYMA, Inc.

  7. CFD Based Computations of Flexible Helicopter Blades for Stability Analysis

    NASA Technical Reports Server (NTRS)

    Guruswamy, Guru P.

    2011-01-01

    As a collaborative effort among government aerospace research laboratories an advanced version of a widely used computational fluid dynamics code, OVERFLOW, was recently released. This latest version includes additions to model flexible rotating multiple blades. In this paper, the OVERFLOW code is applied to improve the accuracy of airload computations from the linear lifting line theory that uses displacements from beam model. Data transfers required at every revolution are managed through a Unix based script that runs jobs on large super-cluster computers. Results are demonstrated for the 4-bladed UH-60A helicopter. Deviations of computed data from flight data are evaluated. Fourier analysis post-processing that is suitable for aeroelastic stability computations are performed.

  8. Deposition head for laser

    DOEpatents

    Lewis, Gary K.; Less, Richard M.

    1999-01-01

    A deposition head for use as a part of apparatus for forming articles from materials in particulate form in which the materials are melted by a laser beam and deposited at points along a tool path to form an article of the desired shape and dimensions. The deposition head delivers the laser beam and powder to a deposition zone, which is formed at the tip of the deposition head. A controller comprised of a digital computer directs movement of the deposition zone along the tool path and provides control signals to adjust apparatus functions, such as the speed at which the deposition head moves along the tool path.

  9. Quantifying fat, oil, and grease deposit formation kinetics.

    PubMed

    Iasmin, Mahbuba; Dean, Lisa O; Ducoste, Joel J

    2016-01-01

    Fat, oil, and grease (FOG) deposits formed in sanitary sewers are calcium-based saponified solids that are responsible for a significant number of nationwide sanitary sewer overflows (SSOs) across United States. In the current study, the kinetics of lab-based saponified solids were determined to understand the kinetics of FOG deposit formation in sewers for two types of fat (Canola and Beef Tallow) and two types of calcium sources (calcium chloride and calcium sulfate) under three pH (7 ± 0.5, 10 ± 0.5, and ≈14) and two temperature conditions (22 ± 0.5 and 45 ± 0.5 °C). The results of this study displayed quick reactions of a fraction of fats with calcium ions to form calcium based saponified solids. Results further showed that increased palmitic fatty acid content in source fats, the magnitude of the pH, and temperature significantly affect the FOG deposit formation and saponification rates. The experimental data of the kinetics were compared with two empirical models: a) Cotte saponification model and b) Foubert crystallization model and a mass-action based mechanistic model that included alkali driven hydrolysis of triglycerides. Results showed that the mass action based mechanistic model was able to predict changes in the rate of formation of saponified solids under the different experimental conditions compared to both empirical models. The mass-action based saponification model also revealed that the hydrolysis of Beef Tallow was slower compared to liquid Canola fat resulting in smaller quantities of saponified solids. This mechanistic saponification model, with its ability to track the saponified solids chemical precursors, may provide an initial framework to predict the spatial formation of FOG deposits in municipal sewers using system wide sewer collection modeling software. PMID:26599432

  10. Circadian rhythms and addiction: Mechanistic insights and future directions

    PubMed Central

    Logan, Ryan W.; Williams, Wilbur P.; McClung, Colleen A.

    2014-01-01

    Circadian rhythms are prominent in many physiological and behavioral functions. Circadian disruptions either by environmental or molecular perturbation can have profound health consequences, including the development and progression of addiction. Both animal and humans studies indicate extensive bidirectional relationships between the circadian system and drugs of abuse. Addicted individuals display disrupted rhythms, and chronic disruption or particular chronotypes, may increase the risk for substance abuse and relapse. Moreover, polymorphisms in circadian genes and an evening chronotype have been linked to mood and addiction disorders, and recent efforts suggest an association with the function of reward neurocircuitry. Animal studies are beginning to determine how altered circadian gene function results in drug induced neuroplasticity and behaviors. Many studies suggest a critical role for circadian rhythms in reward-related pathways in the brain and indicate that drugs of abuse directly affect the central circadian pacemaker. In this review, we highlight key findings demonstrating the importance of circadian rhythms in addiction, and how future studies will reveal important mechanistic insights into the involvement of circadian rhythms in drug addiction. PMID:24731209

  11. Spectroscopic and Mechanistic Investigations of Dehaloperoxidase B from Amphitrite ornata†

    PubMed Central

    D’Antonio, Jennifer; D’Antonio, Edward L.; Thompson, Matthew K.; Bowden, Edmond F.; Franzen, Stefan; Smirnova, Tatyana; Ghiladi, Reza A.

    2010-01-01

    Dehaloperoxidase (DHP) from the terebellid polychaete Amphitrite ornata is a bifunctional enzyme that possesses both hemoglobin and peroxidase activities. Of the two DHP isoenzymes identified to date, much of the recent focus has been on DHP A, whereas very little is known pertaining to the activity, substrate specificity, mechanism of function, or spectroscopic properties of DHP B. Herein, we report the recombinant expression and purification of DHP B, as well as the details of our investigations into its catalytic cycle using biochemical assays, stopped-flow UV-visible, resonance Raman and rapid-freeze-quench electron paramagnetic resonance spectroscopies, and spectroelectrochemistry. Our experimental design reveals mechanistic insights and kinetic descriptions of the dehaloperoxidase mechanism which have not been previously reported for isoenzyme A. Namely, we demonstrate a novel reaction pathway in which the products of the oxidative dehalogenation of trihalophenols (dihaloquinones) are themselves capable of inducing formation of oxyferrous DHP B, and an updated catalytic cycle for DHP is proposed. We further demonstrate that unlike the traditional monofunctional peroxidases, the oxyferrous state in DHP is a peroxidase competent starting species, which suggests that the ferric oxidation state may not be an obligatory starting point for the enzyme. The data presented herein provide a link between the peroxidase and oxygen transport activities which furthers our understanding of how this bifunctional enzyme is able to unite its two inherent functions in one system. PMID:20545299

  12. Warming will affect phytoplankton differently: evidence through a mechanistic approach

    PubMed Central

    Huertas, I. Emma; Rouco, Mónica; López-Rodas, Victoria; Costas, Eduardo

    2011-01-01

    Although the consequences of global warming in aquatic ecosystems are only beginning to be revealed, a key to forecasting the impact on aquatic communities is an understanding of individual species' vulnerability to increased temperature. Despite their microscopic size, phytoplankton support about half of the global primary production, drive essential biogeochemical cycles and represent the basis of the aquatic food web. At present, it is known that phytoplankton are important targets and, consequently, harbingers of climate change in aquatic systems. Therefore, investigating the capacity of phytoplankton to adapt to the predicted warming has become a relevant issue. However, considering the polyphyletic complexity of the phytoplankton community, different responses to increased temperature are expected. We experimentally tested the effects of warming on 12 species of phytoplankton isolated from a variety of environments by using a mechanistic approach able to assess evolutionary adaptation (the so-called ratchet technique). We found different degrees of tolerance to temperature rises and an interspecific capacity for genetic adaptation. The thermal resistance level reached by each species is discussed in relation to their respective original habitats. Our study additionally provides evidence on the most resistant phytoplankton groups in a future warming scenario. PMID:21508031

  13. A brief review of exercise, bipolar disorder, and mechanistic pathways

    PubMed Central

    Thomson, Daniel; Turner, Alyna; Lauder, Sue; Gigler, Margaret E.; Berk, Lesley; Singh, Ajeet B.; Pasco, Julie A.; Berk, Michael; Sylvia, Louisa

    2015-01-01

    Despite evidence that exercise has been found to be effective in the treatment of depression, it is unclear whether these data can be extrapolated to bipolar disorder. Available evidence for bipolar disorder is scant, with no existing randomized controlled trials having tested the impact of exercise on depressive, manic or hypomanic symptomatology. Although exercise is often recommended in bipolar disorder, this is based on extrapolation from the unipolar literature, theory and clinical expertise and not empirical evidence. In addition, there are currently no available empirical data on program variables, with practical implications on frequency, intensity and type of exercise derived from unipolar depression studies. The aim of the current paper is to explore the relationship between exercise and bipolar disorder and potential mechanistic pathways. Given the high rate of medical co-morbidities experienced by people with bipolar disorder, it is possible that exercise is a potentially useful and important intervention with regard to general health benefits; however, further research is required to elucidate the impact of exercise on mood symptomology. PMID:25788889

  14. Rapid Discrimination Among Putative Mechanistic Models of Biochemical Systems

    PubMed Central

    Lomnitz, Jason G.; Savageau, Michael A.

    2016-01-01

    An overarching goal in molecular biology is to gain an understanding of the mechanistic basis underlying biochemical systems. Success is critical if we are to predict effectively the outcome of drug treatments and the development of abnormal phenotypes. However, data from most experimental studies is typically noisy and sparse. This allows multiple potential mechanisms to account for experimental observations, and often devising experiments to test each is not feasible. Here, we introduce a novel strategy that discriminates among putative models based on their repertoire of qualitatively distinct phenotypes, without relying on knowledge of specific values for rate constants and binding constants. As an illustration, we apply this strategy to two synthetic gene circuits exhibiting anomalous behaviors. Our results show that the conventional models, based on their well-characterized components, cannot account for the experimental observations. We examine a total of 40 alternative hypotheses and show that only 5 have the potential to reproduce the experimental data, and one can do so with biologically relevant parameter values. PMID:27578053

  15. Ultrasound enhanced ethanol production from Parthenium hysterophorus: A mechanistic investigation.

    PubMed

    Singh, Shuchi; Sarma, Shyamali; Agarwal, Mayank; Goyal, Arun; Moholkar, Vijayanand S

    2015-01-01

    This study presents mechanistic investigations in ultrasound-assisted bioethanol fermentation using Parthenium hysterophorus biomass. Ultrasound (35 kHz, 10% duty cycle) has been used for sonication. Experimental results were fitted to mathematical model; the kinetic and physiological parameters in the model were obtained using Genetic Algorithm (GA) based optimization. In control experiments (mechanical shaking), maximum ethanol titer of 10.93 g/L and cell mass concentration of 5.26 g/L was obtained after 18 h. In test experiments (mechanical shaking and intermittent sonication), ethanol titer of 12.14 g/L and cell mass concentration of 5.7 g/L was obtained in 10h. This indicated ∼ 2 × enhanced productivity of ethanol and cell mass with sonication. Trends in model parameters obtained after fitting of model to experimental data essentially revealed that beneficial influence of ultrasound on fermentation is a manifestation of enhanced trans-membrane transportation and dilution of toxic substances due to strong micro-convection induced by ultrasound. PMID:25555927

  16. Mechanistic modeling of destratification in cryogenic storage tanks using ultrasonics.

    PubMed

    Jagannathan, T K; Mohanan, Srijith; Nagarajan, R

    2014-01-01

    Stratification is one of the main causes for vaporization of cryogens and increase of tank pressure during cryogenic storage. This leads subsequent problems such as cavitation in cryo-pumps, reduced length of storage time. Hence, it is vital to prevent stratification to improve the cost efficiency of storage systems. If stratified layers exist inside the tank, they have to be removed by suitable methods without venting the vapor. Sonication is one such method capable of keeping fluid layers mixed. In the present work, a mechanistic model for ultrasonic destratification is proposed and validated with destratification experiments done in water. Then, the same model is used to predict the destratification characteristics of cryogenic liquids such as liquid nitrogen (LN₂), liquid hydrogen (LH₂) and liquid ammonia (LNH₃). The destratification parameters are analysed for different frequencies of ultrasound and storage pressures by considering continuous and pulsed modes of ultrasonic operation. From the results, it is determined that use of high frequency ultrasound (low-power/continuous; high-power/pulsing) or low frequency ultrasound (continuous operation with moderate power) can both be effective in removing stratification. PMID:23810463

  17. Mechanistic studies of malonic acid-mediated in situ acylation.

    PubMed

    Chandra, Koushik; Naoum, Johnny N; Roy, Tapta Kanchan; Gilon, Chaim; Gerber, R Benny; Friedler, Assaf

    2015-09-01

    We have previously introduced an easy to perform, cost-effective and highly efficient acetylation technique for solid phase synthesis (SPPS). Malonic acid is used as a precursor and the reaction proceeds via a reactive ketene that acetylates the target amine. Here we present a detailed mechanistic study of the malonic acid-mediated acylation. The influence of reaction conditions, peptide sequence and reagents was systematically studied. Our results show that the methodology can be successfully applied to different types of peptides and nonpeptidic molecules irrespective of their structure, sequence, or conformation. Using alkyl, phenyl, and benzyl malonic acid, we synthesized various acyl peptides with almost quantitative yields. The ketenes obtained from the different malonic acid derived precursors were characterized by in situ (1) H-NMR. The reaction proceeded in short reaction times and resulted in excellent yields when using uronium-based coupling agents, DIPEA as a base, DMF/DMSO/NMP as solvents, Rink amide/Wang/Merrifield resins, temperature of 20°C, pH 8-12 and 5 min preactivation at inert atmosphere. The reaction was unaffected by Lewis acids, transition metal ions, surfactants, or salt. DFT studies support the kinetically favorable concerted mechanism for CO2 and ketene formation that leads to the thermodynamically stable acylated products. We conclude that the malonic acid-mediated acylation is a general method applicable to various target molecules. PMID:25846609

  18. A mechanistic stochastic framework for regulating bacterial cell division

    PubMed Central

    Ghusinga, Khem Raj; Vargas-Garcia, Cesar A.; Singh, Abhyudai

    2016-01-01

    How exponentially growing cells maintain size homeostasis is an important fundamental problem. Recent single-cell studies in prokaryotes have uncovered the adder principle, where cells add a fixed size (volume) from birth to division, irrespective of their size at birth. To mechanistically explain the adder principle, we consider a timekeeper protein that begins to get stochastically expressed after cell birth at a rate proportional to the volume. Cell-division time is formulated as the first-passage time for protein copy numbers to hit a fixed threshold. Consistent with data, the model predicts that the noise in division timing increases with size at birth. Intriguingly, our results show that the distribution of the volume added between successive cell-division events is independent of the newborn cell size. This was dramatically seen in experimental studies, where histograms of the added volume corresponding to different newborn sizes collapsed on top of each other. The model provides further insights consistent with experimental observations: the distribution of the added volume when scaled by its mean becomes invariant of the growth rate. In summary, our simple yet elegant model explains key experimental findings and suggests a mechanism for regulating both the mean and fluctuations in cell-division timing for controlling size. PMID:27456660

  19. Mechanistic insight into mycobacterial MmpL protein function.

    PubMed

    Székely, R; Cole, S T

    2016-03-01

    Mycobacterial cell walls are complex structures containing a broad range of unusual lipids, glycolipids and other polymers, some of which act as immunomodulators or virulence determinants. Better understanding of the enzymes involved in export processes would enlighten cell wall biogenesis. Bernut et al. () present the findings of a structural and functional investigation of one of the most important transporter families, the MmpL proteins, members of the resistance-nodulation-cell division (RND) superfamily. A Tyr842His missense mutation in the mmpL4a gene was shown to be responsible for the smooth-to-rough morphotype change of the near untreatable opportunistic pathogen Mycobacterium bolletii due to its failure to export a glycopeptidolipid (GPL). This mutation was pleiotropic and markedly increased virulence in infection models. Tyr842 is well conserved in all actinobacterial MmpL proteins suggesting that it is functionally important and this was confirmed by several approaches including replacing the corresponding residue in MmpL3 of Mycobacterium tuberculosis. Structural modelling combined with experimental results showed Tyr842 to be a critical residue for mediating the proton motive force required for GPL export. This mechanistic insight applies to all MmpL proteins and probably to all RND transporters. PMID:26710752

  20. Water in Photosystem II: structural, functional and mechanistic considerations.

    PubMed

    Linke, Katrin; Ho, Felix M

    2014-01-01

    Water is clearly important for the functioning of Photosystem II (PSII). Apart from being the very substrate that needs to be transported in this water oxidation enzyme, water is also vital for the transport of protons to and from the catalytic center as well as other important co-factors and key residues in the enzyme. The latest crystal structural data of PSII have enabled detailed analyses of the location and possible function of water molecules in the enzyme. Significant progress has also been made recently in the investigation of channels and pathways through the protein complex. Through these studies, the mechanistic significance of water for PSII is becoming increasingly clear. An overview and discussion of key aspects of the current research on water in PSII is presented here. The role of water in three other systems (aquaporin, bacteriorhodopsin and cytochrome P450) is also outlined to illustrate further points concerning the central significance that water can have, and potential applications of these ideas for continued research on PSII. It is advocated that water be seen as an integral part of the protein and far from a mere solvent. PMID:23978393

  1. Mechanistic Studies in Friction and Wear of Bulk Materials

    NASA Astrophysics Data System (ADS)

    Sawyer, W. Gregory; Argibay, Nicolas; Burris, David L.; Krick, Brandon A.

    2014-07-01

    From the context of a contemporary understanding of the phenomenological origins of friction and wear of materials, we review insightful contributions from recent experimental investigations of three classes of materials that exhibit uniquely contrasting tribological behaviors: metals, polymers, and ionic solids. We focus on the past decade of research by the community to better understand the correlations between environment parameters, materials properties, and tribological behavior in systems of increasingly greater complexity utilizing novel synthesis and in situ experimental techniques. In addition to such review, and a half-century after seminal publications on the subject, we present recently acquired evidence linking anisotropy in friction response with anisotropy in wear behavior of crystalline ionic solids as a function of crystallographic orientation. Although the tribological behaviors of metals, polymers, and ionic solids differ widely, it is increasingly more evident that the mechanistic origins (such as fatigue, corrosion, abrasion, and adhesion) are essentially the same. However, we hope to present a clear and compelling argument favoring the prominent and irreplaceable role of in situ experimental techniques as a bridge between fundamental atomistic and molecular processes and emergent behaviors governing tribological contacts.

  2. A global scale mechanistic model of the photosynthetic capacity

    NASA Astrophysics Data System (ADS)

    Xu, C.; Ali, A. A.; Fisher, R.; Wullschleger, S. D.; Rogers, A.; McDowell, N. G.; Wilson, C. J.

    2015-12-01

    Although plant photosynthetic capacity as determined by the maximum carboxylation rate (i.e., Vc,max25) and the maximum electron transport rate (i.e., Jmax25) at a reference temperature (generally 25oC) is known to vary substantially in space and time in response to environmental conditions, it is typically parameterized in Earth system models (ESMs) with tabulated values associated to plant functional types. In this study, we developed a mechanistic model of leaf utilization of nitrogen for assimilation (LUNA V1.0) to predict the photosynthetic capacity at the global scale under different environmental conditions, based on the optimization of nitrogen allocated among light capture, electron transport, carboxylation, and respiration. The LUNA model was able to reasonably well capture the observed patterns of photosynthetic capacity in view that it explained approximately 55% of the variation in observed Vc,max25 and 65% of the variation in observed Jmax25 across the globe. Our model simulations under current and future climate conditions indicated that Vc,max25 could be most affected in high-latitude regions under a warming climate and that ESMs using a fixed Vc,max25 or Jmax25 by plant functional types were likely to substantially overestimate future global photosynthesis.

  3. Mechanistic evaluation of virus clearance by depth filtration.

    PubMed

    Venkiteshwaran, Adith; Fogle, Jace; Patnaik, Purbasa; Kowle, Ron; Chen, Dayue

    2015-01-01

    Virus clearance by depth filtration has not been well-understood mechanistically due to lack of quantitative data on filter charge characteristics and absence of systematic studies. It is generally believed that both electrostatic interactions and sized based mechanical entrapment contribute to virus clearance by depth filtration. In order to establish whether the effectiveness of virus clearance correlates with the charge characteristics of a given depth filter, a counter-ion displacement technique was employed to determine the ionic capacity for several depth filters. Two depth filters (Millipore B1HC and X0HC) with significant differences in ionic capacities were selected and evaluated for their ability to eliminate viruses. The high ionic capacity X0HC filter showed complete porcine parvovirus (PPV) clearance (eliminating the spiked viruses to below the limit of detection) under low conductivity conditions (≤2.5 mS/cm), achieving a log10 reduction factor (LRF) of > 4.8. On the other hand, the low ionic capacity B1HC filter achieved only ∼2.1-3.0 LRF of PPV clearance under the same conditions. These results indicate that parvovirus clearance by these two depth filters are mainly achieved via electrostatic interactions between the filters and PPV. When much larger xenotropic murine leukemia virus (XMuLV) was used as the model virus, complete retrovirus clearance was obtained under all conditions evaluated for both depth filters, suggesting the involvement of mechanisms other than just electrostatic interactions in XMuLV clearance. PMID:25683459

  4. Mechanistic Enzymology of the Radical SAM Enzyme DesII

    PubMed Central

    2016-01-01

    DesII is a member of the radical SAM family of enzymes that catalyzes radical-mediated transformations of TDP-4-amino-4,6-didexoy-D-glucose as well as other sugar nucleotide diphosphates. Like nearly all radical SAM enzymes, the reactions begin with the reductive homolysis of SAM to produce a 5′-deoxyadenosyl radical which is followed by regiospecific hydrogen atom abstraction from the substrate. What happens next, however, depends on the nature of the substrate radical so produced. In the case of the biosynthetically relevant substrate, a radical-mediated deamination ensues; however, when this amino group is replaced with a hydroxyl, one instead observes dehydrogenation. The factors that govern the fate of the initially generated substrate radical as well as the mechanistic details underlying these transformations have been a key focus of research into the chemistry of DesII. This review will discuss recent discoveries pertaining to the enzymology of DesII, how it may relate to understanding other radical-mediated lyases and dehydrogenases and the working hypotheses currently being investigated regarding the mechanism of DesII catalysis.

  5. Anti-fibro-hepatocarcinogenic Chinese herbal medicines: A mechanistic overview.

    PubMed

    Boye, Alex; Yang, Yan; Asenso, James; Wei, Wei

    2016-01-01

    Chinese herbal medicine (CHM) is an integral component of complementary/alternative medicine and it is increasingly becoming the preferred therapeutic modality for the treatment of liver fibrosis and hepatocellular carcinoma (HCC) worldwide. Accordingly, the World Health Organization (WHO) has attested to the popularity and efficacy of indigenous herbal therapies including CHM as a first line of treatment for some diseases including liver disorders. However, the WHO and drug discovery experts have always recommended that use of indigenous herbal remedies must go hand-in-hand with the requisite mechanistic elucidation so as to constitute a system of verification of efficacy within the ethnobotanical context of use. Although many CHM experts have advanced knowledge on CHM, nonetheless, more enlightenment is needed, particularly mechanisms of action of CHMs on fibro-hepato-carcinogenesis. We, herein, provide in-depth mechanisms of the action of CHMs which have demonstrated anti-fibro-hepatocarcinogenic effects, in pre-clinical and clinical studies as published in PubMed and other major scientific databases. Specifically, the review brings out the important signaling pathways, and their downstream targets which are modulated at multi-level by various anti-fibro-hepatocarcinogenic CHMs. PMID:27366355

  6. Equation-free mechanistic ecosystem forecasting using empirical dynamic modeling

    PubMed Central

    Ye, Hao; Beamish, Richard J.; Glaser, Sarah M.; Grant, Sue C. H.; Hsieh, Chih-hao; Richards, Laura J.; Schnute, Jon T.; Sugihara, George

    2015-01-01

    It is well known that current equilibrium-based models fall short as predictive descriptions of natural ecosystems, and particularly of fisheries systems that exhibit nonlinear dynamics. For example, model parameters assumed to be fixed constants may actually vary in time, models may fit well to existing data but lack out-of-sample predictive skill, and key driving variables may be misidentified due to transient (mirage) correlations that are common in nonlinear systems. With these frailties, it is somewhat surprising that static equilibrium models continue to be widely used. Here, we examine empirical dynamic modeling (EDM) as an alternative to imposed model equations and that accommodates both nonequilibrium dynamics and nonlinearity. Using time series from nine stocks of sockeye salmon (Oncorhynchus nerka) from the Fraser River system in British Columbia, Canada, we perform, for the the first time to our knowledge, real-data comparison of contemporary fisheries models with equivalent EDM formulations that explicitly use spawning stock and environmental variables to forecast recruitment. We find that EDM models produce more accurate and precise forecasts, and unlike extensions of the classic Ricker spawner–recruit equation, they show significant improvements when environmental factors are included. Our analysis demonstrates the strategic utility of EDM for incorporating environmental influences into fisheries forecasts and, more generally, for providing insight into how environmental factors can operate in forecast models, thus paving the way for equation-free mechanistic forecasting to be applied in management contexts. PMID:25733874

  7. Bioavailability and Pharmacokinetics of Genistein: Mechanistic Studies on its ADME

    PubMed Central

    Yang, Zhen; Kulkarni, Kaustubh; Zhu, Wei; Hu, Ming

    2014-01-01

    Genistein, one of the most active natural flavonoids, exerts various biological effects including chemoprevention, antioxidation, antiproliferation and anticancer. More than 30 clinical trials of genistein with various disease indications have been conducted to evaluate its clinical efficacy. Based on many animals and human pharmacokinetic studies, it is well known that the most challenge issue for developing genistein as a chemoprevention agent is the low oral bioavailability, which may be the major reason relating to its ambiguous therapeutic effects and large interindividual variations in clinical trials. In order to better correlate pharmacokinetic to pharmacodynamics results in animals and clinical studies, an in-depth understanding of pharmacokinetic behavior of genistein and its ADME properties are needed. Numerous in vitro/in vivo ADME studies had been conducted to reveal the main factors contributing to the low oral bioavailability of genistein. Therefore, this review focuses on summarizing the most recent progress on mechanistic studies of genistein ADME and provides a systemic view of these processes to explain genistein pharmacokinetic behaviors in vivo. The better understanding of genistein ADME property may lead to development of proper strategy to improve genistein oral bioavailability via mechanism-based approaches. PMID:22583407

  8. Mechanistic insight into sonochemical biodiesel synthesis using heterogeneous base catalyst.

    PubMed

    Choudhury, Hanif A; Chakma, Sankar; Moholkar, Vijayanand S

    2014-01-01

    The beneficial effect of ultrasound on transesterification reaction is well known. Heterogeneous (or solid) catalysts for biodiesel synthesis have merit that they do not contaminate the byproduct of glycerol. In this paper, we have attempted to identify the mechanistic features of ultrasound-enhanced biodiesel synthesis with the base-catalyst of CaO. A statistical design of experiments (Box-Behnken) was used to identify the influence of temperature, alcohol to oil molar ratio and catalyst loading on transesterification yield. The optimum values of these parameters for the highest yield were identified through Response Surface Method (with a quadratic model) and ANOVA. These values are: temperature=62 °C, molar ratio=10:1 and catalyst loading=6 wt.%. The activation energy was determined as 82.3 kJ/mol, which is higher than that for homogeneous catalyzed system (for both acidic and basic catalyst). The experimental results have been analyzed vis-à-vis simulations of cavitation bubble dynamics. Due to 3-phase heterogeneity of the system, the yield was dominated by intrinsic kinetics, and the optimum temperature for the highest yield was close to boiling point of methanol. At this temperature, the influence of cavitation bubbles (in terms of both sonochemical and sonophysical effect) is negligible, and ultrasonic micro-streaming provided necessary convection in the system. The influence of all parameters on the reaction system was found to be strongly inter-dependent. PMID:23742888

  9. Environmental perception and epigenetic memory: mechanistic insight through FLC

    PubMed Central

    Berry, Scott; Dean, Caroline

    2015-01-01

    Chromatin plays a central role in orchestrating gene regulation at the transcriptional level. However, our understanding of how chromatin states are altered in response to environmental and developmental cues, and then maintained epigenetically over many cell divisions, remains poor. The floral repressor gene FLOWERING LOCUS C (FLC) in Arabidopsis thaliana is a useful system to address these questions. FLC is transcriptionally repressed during exposure to cold temperatures, allowing studies of how environmental conditions alter expression states at the chromatin level. FLC repression is also epigenetically maintained during subsequent development in warm conditions, so that exposure to cold may be remembered. This memory depends on molecular complexes that are highly conserved among eukaryotes, making FLC not only interesting as a paradigm for understanding biological decision-making in plants, but also an important system for elucidating chromatin-based gene regulation more generally. In this review, we summarize our understanding of how cold temperature induces a switch in the FLC chromatin state, and how this state is epigenetically remembered. We also discuss how the epigenetic state of FLC is reprogrammed in the seed to ensure a requirement for cold exposure in the next generation. Significance Statement FLOWERING LOCUS C (FLC) regulation provides a paradigm for understanding how chromatin can be modulated to determine gene expression in a developmental context. This review describes our current mechanistic understanding of how FLC expression is genetically specified and epigenetically regulated throughout the plant life cycle, and how this determines plant life-history strategy. PMID:25929799

  10. A global scale mechanistic model of the photosynthetic capacity

    NASA Astrophysics Data System (ADS)

    Ali, A. A.; Xu, C.; Rogers, A.; Fisher, R. A.; Wullschleger, S. D.; McDowell, N. G.; Massoud, E. C.; Vrugt, J. A.; Muss, J. D.; Fisher, J. B.; Reich, P. B.; Wilson, C. J.

    2015-08-01

    Although plant photosynthetic capacity as determined by the maximum carboxylation rate (i.e., Vc, max25) and the maximum electron transport rate (i.e., Jmax25) at a reference temperature (generally 25 °C) is known to vary substantially in space and time in response to environmental conditions, it is typically parameterized in Earth system models (ESMs) with tabulated values associated to plant functional types. In this study, we developed a mechanistic model of leaf utilization of nitrogen for assimilation (LUNA V1.0) to predict the photosynthetic capacity at the global scale under different environmental conditions, based on the optimization of nitrogen allocated among light capture, electron transport, carboxylation, and respiration. The LUNA model was able to reasonably well capture the observed patterns of photosynthetic capacity in view that it explained approximately 55 % of the variation in observed Vc, max25 and 65 % of the variation in observed Jmax25 across the globe. Our model simulations under current and future climate conditions indicated that Vc, max25 could be most affected in high-latitude regions under a warming climate and that ESMs using a fixed Vc, max25 or Jmax25 by plant functional types were likely to substantially overestimate future global photosynthesis.

  11. Neutron structure and mechanistic studies of diisopropyl fluorophosphatase (DFPase)

    SciTech Connect

    Chen, Julian C.-H.; Mustyakimov, Marat; Schoenborn, Benno P.; Langan, Paul; Blum, Marc-Michael

    2010-11-01

    The structure and mechanism of diisopropyl fluorophosphatase (DFPase) have been studied using a variety of methods, including isotopic labelling, X-ray crystallography and neutron crystallography. The neutron structure of DFPase, mechanistic studies and subsequent rational design efforts are described. Diisopropyl fluorophosphatase (DFPase) is a calcium-dependent phosphotriesterase that acts on a variety of highly toxic organophosphorus compounds that act as inhibitors of acetylcholinesterase. The mechanism of DFPase has been probed using a variety of methods, including isotopic labelling, which demonstrated the presence of a phosphoenzyme intermediate in the reaction mechanism. In order to further elucidate the mechanism of DFPase and to ascertain the protonation states of the residues and solvent molecules in the active site, the neutron structure of DFPase was solved at 2.2 Å resolution. The proposed nucleophile Asp229 is deprotonated, while the active-site solvent molecule W33 was identified as water and not hydroxide. These data support a mechanism involving direct nucleophilic attack by Asp229 on the substrate and rule out a mechanism involving metal-assisted water activation. These data also allowed for the re-engineering of DFPase through rational design to bind and productively orient the more toxic S{sub P} stereoisomers of the nerve agents sarin and cyclosarin, creating a modified enzyme with enhanced overall activity and significantly increased detoxification properties.

  12. Mechanistic modeling of aberrant energy metabolism in human disease

    PubMed Central

    Sangar, Vineet; Eddy, James A.; Simeonidis, Evangelos; Price, Nathan D.

    2012-01-01

    Dysfunction in energy metabolism—including in pathways localized to the mitochondria—has been implicated in the pathogenesis of a wide array of disorders, ranging from cancer to neurodegenerative diseases to type II diabetes. The inherent complexities of energy and mitochondrial metabolism present a significant obstacle in the effort to understand the role that these molecular processes play in the development of disease. To help unravel these complexities, systems biology methods have been applied to develop an array of computational metabolic models, ranging from mitochondria-specific processes to genome-scale cellular networks. These constraint-based (CB) models can efficiently simulate aspects of normal and aberrant metabolism in various genetic and environmental conditions. Development of these models leverages—and also provides a powerful means to integrate and interpret—information from a wide range of sources including genomics, proteomics, metabolomics, and enzyme kinetics. Here, we review a variety of mechanistic modeling studies that explore metabolic functions, deficiency disorders, and aberrant biochemical pathways in mitochondria and related regions in the cell. PMID:23112774

  13. AIR POLLUTION, INFLAMMATION AND PRETERM BIRTH: A POTENTIAL MECHANISTIC LINK

    PubMed Central

    Vadillo-Ortega, Felipe; Osornio-Vargas, Alvaro; Buxton, Miatta A.; Sánchez, Brisa N.; Rojas-Bracho, Leonora; Viveros-Alcaráz, Martin; Castillo-Castrejón, Marisol; Beltrán-Montoya, Jorge; Brown, Daniel G.; O´Neill, Marie S.

    2014-01-01

    Preterm birth is a public health issue of global significance, which may result in mortality during the perinatal period or may lead to major health and financial consequences due to lifelong impacts. Even though several risk factors for preterm birth have been identified, prevention efforts have failed to halt the increasing rates of preterm birth. Epidemiological studies have identified air pollution as an emerging potential risk factor for preterm birth. However, many studies were limited by study design and inadequate exposure assessment. Due to the ubiquitous nature of ambient air pollution and the potential public health significance of any role in causing preterm birth, a novel focus investigating possible causal mechanisms influenced by air pollution is therefore a global health priority. We hypothesize that air pollution may act together with other biological factors to induce systemic inflammation and influence the duration of pregnancy. Evaluation and testing of this hypothesis is currently being conducted in a prospective cohort study in Mexico City and will provide an understanding of the pathways that mediate the effects of air pollution on preterm birth. The important public health implication is that crucial steps in this mechanistic pathway can potentially be acted on early in pregnancy to reduce the risk of preterm birth. PMID:24382337

  14. Physical activity and its mechanistic effects on prostate cancer.

    PubMed

    Wekesa, A; Harrison, M; Watson, R W

    2015-09-01

    Beneficial effects of physical activity have been illustrated in numerous aspects of health. With the increasing incidence of prostate cancer and changes in physical activity of men, understanding the link between the two has important implications for changing this cancer burden. Both positive and negative associations between physical activity and prostate cancer have been previously demonstrated in observational epidemiological studies. Elucidating the biological mechanisms would lead to a better understanding of how physical activity influences the progression of prostate cancer. This review was undertaken to: (1) identify evidence in literature that demonstrates the effects of physical activity on skeletal muscle secretomes, (2) indicate the plausible signaling pathways these proteins might activate, and (3) identify evidence in literature that demonstrates the roles of the signaling pathways in prostate cancer progression and regression. We also discuss proposed biological mechanisms and signaling pathways by which physical activity may prevent the development and progression of prostate cancer. We discuss proteins involved in the normal and aberrant growth and development of the prostate gland that may be affected by physical activity. We further identify future directions for research, including a better understanding of the biological mechanisms, the need to standardize physical activity and identify mechanistic end points of physical activity that can then be correlated with outcomes. PMID:25800589

  15. Thermal hydrogen-atom transfer from methane: A mechanistic exercise

    NASA Astrophysics Data System (ADS)

    Schwarz, Helmut

    2015-06-01

    Hydrogen-atom transfer (HAT) constitutes a key process in a broad range of chemical transformations as it covers heterogeneous, homogeneous, and enzymatic reactions. While open-shell metal oxo species [MO]rad are no longer regarded as being involved in the heterogeneously catalyzed oxidative coupling of methane (2CH4 + → C2H6 + H2O), these reagents are rather versatile in bringing about (gas-phase) hydrogen-atom transfer, even from methane at ambient conditions. In this mini-review, various mechanistic scenarios will be presented, and it will be demonstrated how these are affected by the composition of the metal-oxide cluster ions. Examples will be discussed, how 'doping' the clusters permits the control of the charge and spin situation at the active site and, thus, the course of the reaction. Also, the interplay between supposedly inert support material and the active site - the so-called 'aristocratic atoms' - of the gas-phase catalyst will be addressed. Finally, gas-phase HAT from methane will be analyzed in the broader context of thermal activation of inert Csbnd H bonds by metal-oxo species.

  16. A mechanistic model for permeability evolution in fractured sorbing media

    NASA Astrophysics Data System (ADS)

    Wang, Shugang; Elsworth, Derek; Liu, Jishan

    2012-06-01

    A mechanistic model is presented to represent the evolution of permeability in fractured sorbing media such as coal beds and organic-rich shales. This model accommodates key competing processes of poromechanical dilation and sorption-induced swelling. We show that the significant difference in stiffness between fracture and matrix transforms the composite system from globally unconstrained to locally constrained by the development of a virtual "stiff shell" that envelops the perimeter of a representative elementary volume containing a fracture. It is this transformation that results in swelling-induced permeability reduction at low (sorbing) gas pressures and self consistently allows competitive dilation of the fracture as gas pressures are increased. Importantly, net dilation is shown to require a mismatch in the Biot coefficients of fracture and matrix with the coefficient for the fracture exceeding that for the matrix—a condition that is logically met. Permeability evolution is cast in terms of series and parallel models with the series model better replicating observational data. The model may be cast in terms of nondimensional parameters representing sorptive and poromechanical effects and modulated by the sensitivity of the fracture network to dilation or compaction of the individual fractures. This latter parameter encapsulates the effects of fracture spacing and initial permeability and scale changes in permeability driven by either sorption or poromechanical effects. This model is applied to well-controlled observational data for different ranks of coals and different gases (He, CO2) and satisfactory agreement is obtained.

  17. The road to advanced glycation end products: a mechanistic perspective.

    PubMed

    Cho, S-J; Roman, G; Yeboah, F; Konishi, Y

    2007-01-01

    Protein glycation is a slow natural process involving the chemical modification of the reactive amino and guanidine functions in amino acids by sugars and carbohydrates-derived reactive carbonyls. Its deleterious consequences are obvious in the case of long-lived proteins in aged people and are exacerbated by the high blood concentration of sugars in diabetic patients. The non-enzymatic glycation of proteins occurs through a wide range of concurrent processes comprising condensation, rearrangement, fragmentation, and oxidation reactions. Using a few well established intermediates such as Schiff base, Amadori product and reactive a-dicarbonyls as milestones and the results of in vitro glycation investigations, an overall detailed mechanistic analysis of protein glycation is presented for the first time. The pathways leading to several advanced glycation end products (AGEs) such as (carboxymethyl)lysine, pentosidine, and glucosepane are outlined, whereas other AGEs useful as potential biomarkers of glycation are only briefly mentioned. The current stage of the development of glycation inhibitors has been reviewed with an emphasis on their mechanism of action. PMID:17584071

  18. Equation-free mechanistic ecosystem forecasting using empirical dynamic modeling.

    PubMed

    Ye, Hao; Beamish, Richard J; Glaser, Sarah M; Grant, Sue C H; Hsieh, Chih-Hao; Richards, Laura J; Schnute, Jon T; Sugihara, George

    2015-03-31

    It is well known that current equilibrium-based models fall short as predictive descriptions of natural ecosystems, and particularly of fisheries systems that exhibit nonlinear dynamics. For example, model parameters assumed to be fixed constants may actually vary in time, models may fit well to existing data but lack out-of-sample predictive skill, and key driving variables may be misidentified due to transient (mirage) correlations that are common in nonlinear systems. With these frailties, it is somewhat surprising that static equilibrium models continue to be widely used. Here, we examine empirical dynamic modeling (EDM) as an alternative to imposed model equations and that accommodates both nonequilibrium dynamics and nonlinearity. Using time series from nine stocks of sockeye salmon (Oncorhynchus nerka) from the Fraser River system in British Columbia, Canada, we perform, for the the first time to our knowledge, real-data comparison of contemporary fisheries models with equivalent EDM formulations that explicitly use spawning stock and environmental variables to forecast recruitment. We find that EDM models produce more accurate and precise forecasts, and unlike extensions of the classic Ricker spawner-recruit equation, they show significant improvements when environmental factors are included. Our analysis demonstrates the strategic utility of EDM for incorporating environmental influences into fisheries forecasts and, more generally, for providing insight into how environmental factors can operate in forecast models, thus paving the way for equation-free mechanistic forecasting to be applied in management contexts. PMID:25733874

  19. Anti-fibro-hepatocarcinogenic Chinese herbal medicines: A mechanistic overview

    PubMed Central

    Boye, Alex; Yang, Yan; Asenso, James; Wei, Wei

    2016-01-01

    Chinese herbal medicine (CHM) is an integral component of complementary/alternative medicine and it is increasingly becoming the preferred therapeutic modality for the treatment of liver fibrosis and hepatocellular carcinoma (HCC) worldwide. Accordingly, the World Health Organization (WHO) has attested to the popularity and efficacy of indigenous herbal therapies including CHM as a first line of treatment for some diseases including liver disorders. However, the WHO and drug discovery experts have always recommended that use of indigenous herbal remedies must go hand-in-hand with the requisite mechanistic elucidation so as to constitute a system of verification of efficacy within the ethnobotanical context of use. Although many CHM experts have advanced knowledge on CHM, nonetheless, more enlightenment is needed, particularly mechanisms of action of CHMs on fibro-hepato-carcinogenesis. We, herein, provide in-depth mechanisms of the action of CHMs which have demonstrated anti-fibro-hepatocarcinogenic effects, in pre-clinical and clinical studies as published in PubMed and other major scientific databases. Specifically, the review brings out the important signaling pathways, and their downstream targets which are modulated at multi-level by various anti-fibro-hepatocarcinogenic CHMs. PMID:27366355

  20. Multiscale mechanistic modeling in pharmaceutical research and development.

    PubMed

    Kuepfer, Lars; Lippert, Jörg; Eissing, Thomas

    2012-01-01

    Discontinuation of drug development projects due to lack of efficacy or adverse events is one of the main cost drivers in pharmaceutical research and development (R&D). Investments have to be written-off and contribute to the total costs of a successful drug candidate receiving marketing authorization and allowing return on invest. A vital risk for pharmaceutical innovator companies is late stage clinical failure since costs for individual clinical trials may exceed the one billion Euro threshold. To guide investment decisions and to safeguard maximum medical benefit and safety for patients recruited in clinical trials, it is therefore essential to understand the clinical consequences of all information and data generated. The complexity of the physiological and pathophysiological processes and the sheer amount of information available overcharge the mental capacity of any human being and prevent a prediction of the success in clinical development. A rigorous integration of knowledge, assumption, and experimental data into computational models promises a significant improvement of the rationalization of decision making in pharmaceutical industry. We here give an overview of the current status of modeling and simulation in pharmaceutical R&D and outline the perspectives of more recent developments in mechanistic modeling. Specific modeling approaches for different biological scales ranging from intracellular processes to whole organism physiology are introduced and an example for integrative multiscale modeling of therapeutic efficiency in clinical oncology trials is showcased. PMID:22161351

  1. Stem cell guidance through the mechanistic target of rapamycin

    PubMed Central

    Maiese, Kenneth

    2015-01-01

    Stem cells offer great promise for the treatment of multiple disorders throughout the body. Critical to this premise is the ability to govern stem cell pluripotency, proliferation, and differentiation. The mechanistic target of rapamycin (mTOR), 289-kDa serine/threonine protein kinase, that is a vital component of mTOR Complex 1 and mTOR Complex 2 represents a critical pathway for the oversight of stem cell maintenance. mTOR can control the programmed cell death pathways of autophagy and apoptosis that can yield variable outcomes in stem cell survival and be reliant upon proliferative pathways that include Wnt signaling, Wnt1 inducible signaling pathway protein 1 (WISP1), silent mating type information regulation 2 homolog 1 (Saccharomyces cerevisiae) (SIRT1), and trophic factors. mTOR also is a necessary component for the early development and establishment of stem cells as well as having a significant impact in the regulation of the maturation of specific cell phenotypes. Yet, as a proliferative agent, mTOR can not only foster cancer stem cell development and tumorigenesis, but also mediate cell senescence under certain conditions to limit invasive cancer growth. mTOR offers an exciting target for the oversight of stem cell therapies but requires careful consideration of the diverse clinical outcomes that can be fueled by mTOR signaling pathways. PMID:26328016

  2. A mechanistic compartmental model for total antibody uptake in tumors

    PubMed Central

    Thurber, Greg M.; Dane Wittrup, K.

    2012-01-01

    Antibodies are under development to treat a variety of cancers, such as lymphomas, colon, and breast cancer. A major limitation to greater efficacy for this class of drugs is poor distribution in vivo. Localization of antibodies occurs slowly, often in insufficient therapeutic amounts, and distributes heterogeneously throughout the tumor. While the microdistribution around individual vessels is important for many therapies, the total amount of antibody localized in the tumor is paramount for many applications such as imaging, determining the therapeutic index with antibody drug conjugates, and dosing in radioimmunotherapy. With imaging and pretargeted therapeutic strategies, the time course of uptake is critical in determining when to take an image or deliver a secondary reagent. We present here a simple mechanistic model of antibody uptake and retention that captures the major rates that determine the time course of antibody concentration within a tumor including dose, affinity, plasma clearance, target expression, internalization, permeability, and vascularization. Since many of the parameters are known or can be estimated in vitro, this model can approximate the time course of antibody concentration in tumors to aid in experimental design, data interpretation, and strategies to improve localization. PMID:22974563

  3. Mechanistic Perspectives of Maslinic Acid in Targeting Inflammation

    PubMed Central

    Yap, Wei Hsum; Lim, Yang Mooi

    2015-01-01

    Chronic inflammation drives the development of various pathological diseases such as rheumatoid arthritis, atherosclerosis, multiple sclerosis, and cancer. The arachidonic acid pathway represents one of the major mechanisms for inflammation. Prostaglandins (PGs) are lipid products generated from arachidonic acid by the action of cyclooxygenase (COX) enzymes and their activity is blocked by nonsteroidal anti-inflammatory drugs (NSAIDS). The use of natural compounds in regulation of COX activity/prostaglandins production is receiving increasing attention. In Mediterranean diet, olive oil and table olives contain significant dietary sources of maslinic acid. Maslinic acid is arising as a safe and novel natural pentacyclic triterpene which has protective effects against chronic inflammatory diseases in various in vivo and in vitro experimental models. Understanding the anti-inflammatory mechanism of maslinic acid is crucial for its development as a potential dietary nutraceutical. This review focuses on the mechanistic action of maslinic acid in regulating the inflammation pathways through modulation of the arachidonic acid metabolism including the nuclear factor-kappa B (NF-κB)/COX-2 expression, upstream protein kinase signaling, and phospholipase A2 enzyme activity. Further investigations may provide insight into the mechanism of maslinic acid in regulating the molecular targets and their associated pathways in response to specific inflammatory stimuli. PMID:26491566

  4. A mechanistic stochastic framework for regulating bacterial cell division.

    PubMed

    Ghusinga, Khem Raj; Vargas-Garcia, Cesar A; Singh, Abhyudai

    2016-01-01

    How exponentially growing cells maintain size homeostasis is an important fundamental problem. Recent single-cell studies in prokaryotes have uncovered the adder principle, where cells add a fixed size (volume) from birth to division, irrespective of their size at birth. To mechanistically explain the adder principle, we consider a timekeeper protein that begins to get stochastically expressed after cell birth at a rate proportional to the volume. Cell-division time is formulated as the first-passage time for protein copy numbers to hit a fixed threshold. Consistent with data, the model predicts that the noise in division timing increases with size at birth. Intriguingly, our results show that the distribution of the volume added between successive cell-division events is independent of the newborn cell size. This was dramatically seen in experimental studies, where histograms of the added volume corresponding to different newborn sizes collapsed on top of each other. The model provides further insights consistent with experimental observations: the distribution of the added volume when scaled by its mean becomes invariant of the growth rate. In summary, our simple yet elegant model explains key experimental findings and suggests a mechanism for regulating both the mean and fluctuations in cell-division timing for controlling size. PMID:27456660

  5. Mechanistic biomarkers for clinical decision making in rheumatic diseases

    PubMed Central

    Robinson, William H.; Lindstrom, Tamsin M.; Cheung, Regina K.; Sokolove, Jeremy

    2013-01-01

    The use of biomarkers is becoming increasingly intrinsic to the practice of medicine and holds great promise for transforming the practice of rheumatology. Biomarkers have the potential to aid clinical diagnosis when symptoms are present or to provide a means of detecting early signs of disease when they are not. Some biomarkers can serve as early surrogates of eventual clinical outcomes or guide therapeutic decision making by enabling identification of individuals likely to respond to a specific therapy. Using biomarkers might reduce the costs of drug development by enabling individuals most likely to respond to be enrolled in clinical trials, thereby minimizing the number of participants required. In this Review, we discuss the current use and the potential of biomarkers in rheumatology and in select fields at the forefront of biomarker research. We emphasize the value of different types of biomarkers, addressing the concept of ‘actionable’ biomarkers, which can be used to guide clinical decision making, and ‘mechanistic’ biomarkers, a subtype of actionable biomarker that is embedded in disease pathogenesis and, therefore, represents a superior biomarker. We provide examples of actionable and mechanistic biomarkers currently available, and discuss how development of such biomarkers could revolutionize clinical practice and drug development. PMID:23419428

  6. Mechanistic Differences Leading to Infectious and Sterile Inflammation.

    PubMed

    Behnia, Faranak; Sheller, Samantha; Menon, Ramkumar

    2016-05-01

    Inflammation is a physiologic component of pregnancy and parturition. Overwhelming intrauterine inflammatory load promotes quiescent feto-maternal tissues into a contractile phenotype. Like inflammation, oxidative stress is an inevitable component of both pregnancy and parturition. Pathologic activation of host innate immune response to adverse pregnancy conditions can lead to premature activation of inflammatory and oxidative stress. Inflammation and oxidative stress markers seen with both sterile and infectious inflammation are often similar; therefore, it is difficult to understand causality of conditions like spontaneous preterm birth. This review demonstrates potential mechanistic pathways of activation of sterile and infectious inflammation. We demonstrate the activation of two unique pathways of inflammation by factors that are well-documented proxies for oxidative stress (cigarette smoke extract) and infection (lipopolysaccharide). Sterile inflammation seen after exposure to an oxidative stress inducer is due to cellular elemental damage resulting in p38 mitogen-activated protein kinase (MAPK) induced cellular senescence. Infectious inflammation is through activation of transcription factor NF-κB and independent of oxidative stress-associated damages and p38 MAPK-induced senescence. Understanding the differences in the inflammatory pathway activation by various risk factors is important to design better screening, diagnostic and intervention strategies to reduce the risks of adverse pregnancy outcomes. PMID:26840942

  7. Mechanistic aspects of photooxidation of polyhydroxylated molecules on metal oxides.

    SciTech Connect

    Shkrob, I. A.; Marin, T. M.; Sevilla, M. D.; Chemerisov, S.

    2011-03-24

    Polyhydroxylated molecules, including natural carbohydrates, are known to undergo photooxidation on wide-gap transition-metal oxides irradiated by ultraviolet light. In this study, we examine mechanistic aspects of this photoreaction on aqueous TiO{sub 2}, {alpha}-FeOOH, and {alpha}-Fe{sub 2}O{sub 3} particles using electron paramagnetic resonance (EPR) spectroscopy and site-selective deuteration. We demonstrate that the carbohydrates are oxidized at sites involved in the formation of oxo bridges between the chemisorbed carbohydrate molecule and metal ions at the oxide surface. This bridging inhibits the loss of water (which is the typical reaction of the analogous free radicals in bulk solvent) promoting instead a rearrangement that leads to elimination of the formyl radical. For natural carbohydrates, the latter reaction mainly involves carbon-1, whereas the main radical products of the oxidation are radical arising from H atom loss centered on carbon-1, -2, and -3 sites. Photoexcited TiO{sub 2} oxidizes all of the carbohydrates and polyols, whereas {alpha}-FeOOH oxidizes some of the carbohydrates, and {alpha}-Fe{sub 2}O{sub 3} is unreactive. These results serve as a stepping stone for understanding the photochemistry on mineral surfaces of more complex biomolecules such as nucleic acids.

  8. Microneedle/nanoencapsulation-mediated transdermal delivery: Mechanistic insights

    PubMed Central

    Gomaa, Yasmine A.; Garland, Martin J.; McInnes, Fiona J.; Donnelly, Ryan F.; El-Khordagui, Labiba K.; Wilson, Clive G.

    2014-01-01

    A systematic study was undertaken to gain more insight into the mechanism of transdermal delivery of nanoencapsulated model dyes across microneedle (MN)-treated skin, a complex process not yet explored. Rhodamine B (Rh B) and fluorescein isothiocyanate (FITC) as model hydrophilic and hydrophobic small/medium-size molecules, respectively, were encapsulated in poly lactic-co-glycolic acid (PLGA) nanoparticles (NPs) and delivered through full thickness porcine skin pretreated with MN array. Permeation through MN-treated skin was affected by physicochemical characteristics of NPs and the encapsulated dyes. Dye flux was enhanced by smaller particle size, hydrophilicity, and negative zeta potential of NPs. Regarding encapsulated dyes, solubility at physiological pH and potential interaction with skin proteins proved to outweigh molecular weight as determinants of skin permeation. Data were verified using confocal laser scanning microscopy imaging. Findings coupled with the literature data are supportive of a mechanism involving influx of NPs, particularly of smaller size, deep into MN-created channels, generating depot dye-rich reservoirs. Molecular diffusion of the released dye across viable skin layers proceeds at a rate determined by its molecular characteristics. Data obtained provide mechanistic information of importance to the development of formulation strategies for more effective intradermal and transdermal MN-mediated delivery of nanoencapsulated therapeutic agents. PMID:23461860

  9. A Mechanistic Stochastic Ricker Model: Analytical and Numerical Investigations

    NASA Astrophysics Data System (ADS)

    Gadrich, Tamar; Katriel, Guy

    The Ricker model is one of the simplest and most widely-used ecological models displaying complex nonlinear dynamics. We study a discrete-time population model, which is derived from simple assumptions concerning individual organisms’ behavior, using the “site-based” approach, developed by Brännström, Broomhead, Johansson and Sumpter. In the large-population limit the model converges to the Ricker model, and can thus be considered a mechanistic version of the Ricker model, derived from basic ecological principles, and taking into account the demographic stochasticity inherent to finite populations. We employ several analytical and precise numerical methods to study the model, showing how each approach contributes to understanding the model’s dynamics. Expressing the model as a Markov chain, we employ the concept of quasi-stationary distributions, which are computed numerically, and used to examine the interaction between complex deterministic dynamics and demographic stochasticity, as well as to calculate mean times to extinction. A Gaussian Markov chain approximation is used to obtain quantitative asymptotic approximations for the size of fluctuations of the stochastic model’s time series around the deterministic trajectory, and for the correlations between successive fluctuations. Results of these approximations are compared to results obtained from quasi-stationary distributions and from direct simulations, and are shown to be in good agreement.

  10. Deposit model for volcanogenic uranium deposits

    USGS Publications Warehouse

    Breit, George N.; Hall, Susan M.

    2011-01-01

    The International Atomic Energy Agency's tabulation of volcanogenic uranium deposits lists 100 deposits in 20 countries, with major deposits in Russia, Mongolia, and China. Collectively these deposits are estimated to contain uranium resources of approximately 500,000 tons of uranium, which amounts to 6 percent of the known global resources. Prior to the 1990s, these deposits were considered to be small (less than 10,000 tons of uranium) with relatively low to moderate grades (0.05 to 0.2 weight percent of uranium). Recent availability of information on volcanogenic uranium deposits in Asia highlighted the large resource potential of this deposit type. For example, the Streltsovskoye district in eastern Russia produced more than 100,000 tons of uranium as of 2005; with equivalent resources remaining. Known volcanogenic uranium deposits within the United States are located in Idaho, Nevada, Oregon, and Utah. These deposits produced an estimated total of 800 tons of uranium during mining from the 1950s through the 1970s and have known resources of 30,000 tons of uranium. The most recent estimate of speculative resources proposed an endowment of 200,000 tons of uranium.

  11. DRY DEPOSITION MODULE FOR REGIONAL ACID DEPOSITION

    EPA Science Inventory

    Methods to compute surface dry deposition velocities for sulfur dioxide, sulfate, ozone, NO plus NO2, and nitric acid vapor over much of the North American continent have been developed for use with atmospheric numerical models of long-range transport and deposition. The resultin...

  12. A mechanistic model of global soil nitric oxide emissions: implementation and space based-constraints

    NASA Astrophysics Data System (ADS)

    Hudman, R. C.; Moore, N. E.; Martin, R. V.; Russell, A. R.; Mebust, A. K.; Valin, L. C.; Cohen, R. C.

    2012-02-01

    Soil emissions have been identified as a major source (~15%) of global nitrogen oxide (NOx) emissions. Parameterizations of soil NOx emissions (SNOx) for use in the current generation of chemical transport models were designed to capture mean seasonal behaviour. These parameterizations do not, however, respond quantitatively to the meteorological triggers that result in pulsed SNOx as are widely observed. Here we present a new mechanistic parameterization of SNOx implemented into a global chemical transport model (GEOS-Chem). The parameterization represents available nitrogen (N) in soils using biome specific emission factors, online wet- and dry-deposition of N as well as fertilizer and manure N derived from a spatially explicit dataset distributed using seasonality derived from data obtained by the Moderate Resolution Imaging Spectrometer. Moreover, it represents the functional form of emissions derived from point measurements and ecosystem scale experiments including pulsing following soil wetting by rain or irrigation, and emissions that are a smooth function of soil moisture. This parameterization yields global above-soil SNOx of 10.7 Tg N yr-1, including 1.8 Tg N yr-1 from fertilizer N input (0.68% of applied N) and 0.5 Tg N yr-1 from atmospheric N deposition. Over the United States Great Plains, SNOx are predicted to comprise 15-40% of the tropospheric NO2 column and increase column variability by a factor of 2-4 during the summer months due to chemical fertilizer application and warm temperatures. SNOx enhancements of 50-80% of the simulated NO2 column are predicted over the African Sahel during the monsoon onset (April-June). In this region the day-to-day variability of column NO2 is increased by a factor of 5 due to pulsed-N emissions. We evaluate the model by comparison to observations of the NO2 column from the OMI instrument. We find the model is able to reproduce observations of pulsed-N induced interannual variability over the US Great Plains. We

  13. The ecological impacts of nighttime light pollution: a mechanistic appraisal.

    PubMed

    Gaston, Kevin J; Bennie, Jonathan; Davies, Thomas W; Hopkins, John

    2013-11-01

    The ecological impacts of nighttime light pollution have been a longstanding source of concern, accentuated by realized and projected growth in electrical lighting. As human communities and lighting technologies develop, artificial light increasingly modifies natural light regimes by encroaching on dark refuges in space, in time, and across wavelengths. A wide variety of ecological implications of artificial light have been identified. However, the primary research to date is largely focused on the disruptive influence of nighttime light on higher vertebrates, and while comprehensive reviews have been compiled along taxonomic lines and within specific research domains, the subject is in need of synthesis within a common mechanistic framework. Here we propose such a framework that focuses on the cross-factoring of the ways in which artificial lighting alters natural light regimes (spatially, temporally, and spectrally), and the ways in which light influences biological systems, particularly the distinction between light as a resource and light as an information source. We review the evidence for each of the combinations of this cross-factoring. As artificial lighting alters natural patterns of light in space, time and across wavelengths, natural patterns of resource use and information flows may be disrupted, with downstream effects to the structure and function of ecosystems. This review highlights: (i) the potential influence of nighttime lighting at all levels of biological organisation (from cell to ecosystem); (ii) the significant impact that even low levels of nighttime light pollution can have; and (iii) the existence of major research gaps, particularly in terms of the impacts of light at population and ecosystem levels, identification of intensity thresholds, and the spatial extent of impacts in the vicinity of artificial lights. PMID:23565807

  14. Mechanistic Study of Plasma Damage of Low k Dielectric Surfaces

    SciTech Connect

    Bao Junjing; Shi Hualiang; Huang Huai; Ho, P. S.; Liu Junjun; Goodner, M. D.; Moinpour, M.; Kloster, G. M.

    2007-10-31

    Plasma damage to low k dielectric materials was investigated from a mechanistic point of view. Low k dielectric films were treated by plasma Ar, O{sub 2}, N{sub 2}/H{sub 2}, N{sub 2} and H{sub 2} in a standard RIE chamber and the damage was characterized by Angle Resolved X-ray Photoelectron Spectroscopy (ARXPS), X-Ray Reflectivity (XRR), Fourier Transform Infrared Spectroscopy (FTIR) and Contact Angle measurements. Both carbon depletion and surface densification were observed on the top surface of damaged low k materials while the bulk remained largely unaffected. Plasma damage was found to be a complicated phenomenon involving both chemical and physical effects, depending on chemical reactivity and the energy and mass of the plasma species. A downstream hybrid plasma source with separate ions and atomic radicals was employed to study their respective roles in the plasma damage process. Ions were found to play a more important role in the plasma damage process. The dielectric constant of low k materials can increase up to 20% due to plasma damage and we attributed this to the removal of the methyl group making the low k surface hydrophilic. Annealing was generally effective in mitigating moisture uptake to restore the k value but the recovery was less complete for higher energy plasmas. Quantum chemistry calculation confirmed that physisorbed water in low k materials induces the largest increase of dipole moments in comparison with changes of surface bonding configurations, and is primarily responsible for the dielectric constant increase.

  15. A Mechanistic Link between Olfaction and Autism Spectrum Disorder

    PubMed Central

    Rozenkrantz, Liron; Zachor, Ditza; Heller, Iris; Plotkin, Anton; Weissbrod, Aharon; Snitz, Kobi; Secundo, Lavi; Sobel, Noam

    2015-01-01

    Summary Internal action models (IAMs) are brain templates for sensory-motor coordination underlying diverse behaviors [1]. An emerging theory suggests that impaired IAMs are a common theme in autism spectrum disorder (ASD) [2–4]. However, whether impaired IAMs occur across sensory systems and how they relate to the major phenotype of ASD, namely impaired social communication [5], remains unclear. Olfaction relies on an IAM known as the sniff response, where sniff magnitude is automatically modulated to account for odor valence [6–12]. To test the failed IAM theory in olfaction, we precisely measured the non-verbal non-task-dependent sniff response concurrent with pleasant and unpleasant odors in 36 children—18 with ASD and 18 matched typically developing (TD) controls. We found that whereas TD children generated a typical adult-like sniff response within 305 ms of odor onset, ASD children had a profoundly altered sniff response, sniffing equally regardless of odor valance. This difference persisted despite equal reported odor perception and allowed for 81% correct ASD classification based on the sniff response alone (binomial, p < 0.001). Moreover, increasingly aberrant sniffing was associated with increasingly severe ASD (r = −0.75, p < 0.001), specifically with social (r = −0.72, p < 0.001), but not motor (r < −0.38, p > 0.18), impairment. These results uncover a novel ASD marker implying a mechanistic link between the underpinnings of olfaction and ASD and directly linking an impaired IAM with impaired social abilities. PMID:26144969

  16. Radiation induced base excision repair (BER): a mechanistic mathematical approach.

    PubMed

    Rahmanian, Shirin; Taleei, Reza; Nikjoo, Hooshang

    2014-10-01

    This paper presents a mechanistic model of base excision repair (BER) pathway for the repair of single-stand breaks (SSBs) and oxidized base lesions produced by ionizing radiation (IR). The model is based on law of mass action kinetics to translate the biochemical processes involved, step-by-step, in the BER pathway to translate into mathematical equations. The BER is divided into two subpathways, short-patch repair (SPR) and long-patch repair (LPR). SPR involves in replacement of single nucleotide via Pol β and ligation of the ends via XRCC1 and Ligase III, while LPR involves in replacement of multiple nucleotides via PCNA, Pol δ/ɛ and FEN 1, and ligation via Ligase I. A hallmark of IR is the production of closely spaced lesions within a turn of DNA helix (named complex lesions), which have been attributed to a slower repair process. The model presented considers fast and slow component of BER kinetics by assigning SPR for simple lesions and LPR for complex lesions. In the absence of in vivo reaction rate constants for the BER proteins, we have deduced a set of rate constants based on different published experimental measurements including accumulation kinetics obtained from UVA irradiation, overall SSB repair kinetic experiments, and overall BER kinetics from live-cell imaging experiments. The model was further used to calculate the repair kinetics of complex base lesions via the LPR subpathway and compared to foci kinetic experiments for cells irradiated with γ rays, Si, and Fe ions. The model calculation show good agreement with experimental measurements for both overall repair and repair of complex lesions. Furthermore, using the model we explored different mechanisms responsible for inhibition of repair when higher LET and HZE particles are used and concluded that increasing the damage complexity can inhibit initiation of LPR after the AP site removal step in BER. PMID:25117268

  17. Conceptualising population health: from mechanistic thinking to complexity science

    PubMed Central

    2011-01-01

    The mechanistic interpretation of reality can be traced to the influential work by René Descartes and Sir Isaac Newton. Their theories were able to accurately predict most physical phenomena relating to motion, optics and gravity. This paradigm had at least three principles and approaches: reductionism, linearity and hierarchy. These ideas appear to have influenced social scientists and the discourse on population health. In contrast, Complexity Science takes a more holistic view of systems. It views natural systems as being 'open', with fuzzy borders, constantly adapting to cope with pressures from the environment. These are called Complex Adaptive Systems (CAS). The sub-systems within it lack stable hierarchies, and the roles of agency keep changing. The interactions with the environment and among sub-systems are non-linear interactions and lead to self-organisation and emergent properties. Theoretical frameworks such as epi+demos+cracy and the ecosocial approach to health have implicitly used some of these concepts of interacting dynamic sub-systems. Using Complexity Science we can view population health outcomes as an emergent property of CAS, which has numerous dynamic non-linear interactions among its interconnected sub-systems or agents. In order to appreciate these sub-systems and determinants, one should acquire a basic knowledge of diverse disciplines and interact with experts from different disciplines. Strategies to improve health should be multi-pronged, and take into account the diversity of actors, determinants and contexts. The dynamic nature of the system requires that the interventions are constantly monitored to provide early feedback to a flexible system that takes quick corrections. PMID:21247500

  18. Toward a mechanistic understanding and prediction of biotic homogenization.

    PubMed

    Olden, Julian D; Poff, N LeRoy

    2003-10-01

    The widespread replacement of native species with cosmopolitan, nonnative species is homogenizing the global fauna and flora. While the empirical study of biotic homogenization is substantial and growing, theoretical aspects have yet to be explored. Consequently, the breadth of possible ecological mechanisms that can shape current and future patterns and rates of homogenization remain largely unknown. Here, we develop a conceptual model that describes 14 potential scenarios by which species invasions and/or extinctions can lead to various trajectories of biotic homogenization (increased community similarity) or differentiation (decreased community similarity); we then use a simulation approach to explore the model's predictions. We found changes in community similarity to vary with the type and number of nonnative and native species, the historical degree of similarity among the communities, and, to a lesser degree, the richness of the recipient communities. Homogenization is greatest when similar species invade communities, causing either no extinction or differential extinction of native species. The model predictions are consistent with current empirical data for fish, bird, and plant communities and therefore may represent the dominant mechanisms of contemporary homogenization. We present a unifying model illustrating how the balance between invading and extinct species dictates the outcome of biotic homogenization. We conclude by discussing a number of critical but largely unrecognized issues that bear on the empirical study of biotic homogenization, including the importance of spatial scale, temporal scale, and data resolution. We argue that the study of biotic homogenization needs to be placed in a more mechanistic and predictive framework in order for studies to provide adequate guidance in conservation efforts to maintain regional distinctness of the global biota. PMID:14582007

  19. Toward a mechanistic modeling of nitrogen limitation on vegetation dynamics

    SciTech Connect

    Xu, Chonggang; Fisher, Rosie; Wullschleger, Stan D; Wilson, Cathy; Cai, Michael; McDowell, Nathan

    2012-01-01

    Nitrogen is a dominant regulator of vegetation dynamics, net primary production, and terrestrial carbon cycles; however, most ecosystem models use a rather simplistic relationship between leaf nitrogen content and photosynthetic capacity. Such an approach does not consider how patterns of nitrogen allocation may change with differences in light intensity, growing-season temperature and CO{sub 2} concentration. To account for this known variability in nitrogen-photosynthesis relationships, we develop a mechanistic nitrogen allocation model based on a trade-off of nitrogen allocated between growth and storage, and an optimization of nitrogen allocated among light capture, electron transport, carboxylation, and respiration. The developed model is able to predict the acclimation of photosynthetic capacity to changes in CO{sub 2} concentration, temperature, and radiation when evaluated against published data of V{sub c,max} (maximum carboxylation rate) and J{sub max} (maximum electron transport rate). A sensitivity analysis of the model for herbaceous plants, deciduous and evergreen trees implies that elevated CO{sub 2} concentrations lead to lower allocation of nitrogen to carboxylation but higher allocation to storage. Higher growing-season temperatures cause lower allocation of nitrogen to carboxylation, due to higher nitrogen requirements for light capture pigments and for storage. Lower levels of radiation have a much stronger effect on allocation of nitrogen to carboxylation for herbaceous plants than for trees, resulting from higher nitrogen requirements for light capture for herbaceous plants. As far as we know, this is the first model of complete nitrogen allocation that simultaneously considers nitrogen allocation to light capture, electron transport, carboxylation, respiration and storage, and the responses of each to altered environmental conditions. We expect this model could potentially improve our confidence in simulations of carbon-nitrogen interactions

  20. Mechanistic analysis of cavitation assisted transesterification on biodiesel characteristics.

    PubMed

    Sajjadi, Baharak; Abdul Aziz, A R; Ibrahim, Shaliza

    2015-01-01

    The influence of sonoluminescence transesterification on biodiesel physicochemical properties was investigated and the results were compared to those of traditional mechanical stirring. This study was conducted to identify the mechanistic features of ultrasonication by coupling statistical analysis of the experiments into the simulation of cavitation bubble. Different combinations of operational variables were employed for alkali-catalysis transesterification of palm oil. The experimental results showed that transesterification with ultrasound irradiation could change the biodiesel density by about 0.3kg/m(3); the viscosity by 0.12mm(2)/s; the pour point by about 1-2°C and the flash point by 5°C compared to the traditional method. Furthermore, 93.84% of yield with alcohol to oil molar ratio of 6:1 could be achieved through ultrasound assisted transesterification within only 20min. However, only 89.09% of reaction yield was obtained by traditional macro mixing/heating under the same condition. Based on the simulated oscillation velocity value, the cavitation phenomenon significantly contributed to generation of fine micro emulsion and was able to overcome mass transfer restriction. It was found that the sonoluminescence bubbles reached the temperature of 758-713K, pressure of 235.5-159.55bar, oscillation velocity of 3.5-6.5cm/s, and equilibrium radius of 17.9-13.7 times greater than its initial size under the ambient temperature of 50-64°C at the moment of collapse. This showed that the sonoluminescence bubbles were in the condition in which the decomposition phenomena were activated and the reaction rate was accelerated together with a change in the biodiesel properties. PMID:24981808

  1. Two Mechanistic Pathways for Thienopyridine-Associated Thrombotic Thrombocytopenic Purpura

    PubMed Central

    Bennett, Charles L.; Kim, Benjamin; Zakarija, Anaadriana; Bandarenko, Nicholas; Pandey, Dilip K.; Buffie, Charlie G.; McKoy, June M.; Tevar, Amul D.; Cursio, John F.; Yarnold, Paul R.; Kwaan, Hau C.; De Masi, Davide; Sarode, Ravindra; Raife, Thomas J.; Kiss, Joseph E.; Raisch, Dennis W.; Davidson, Charles; Sadler, J. Evan; Ortel, Thomas L.; Zheng, X. Long; Kato, Seiji; Matsumoto, Masanori; Uemura, Masahito; Fujimura, Yoshihiro

    2011-01-01

    Objectives We sought to describe clinical and laboratory findings for a large cohort of patients with thienopyridine-associated thrombotic thrombocytopenic purpura (TTP). Background The thienopyridine derivatives, ticlopidine and clopidogrel, are the 2 most common drugs associated with TTP in databases maintained by the U.S. Food and Drug Administration (FDA). Methods Clinical reports of TTP associated with clopidogrel and ticlopidine were identified from medical records, published case reports, and FDA case reports (n = 128). Duration of thienopyridine exposure, clinical and laboratory findings, and survival were recorded. ADAMTS13 activity (n = 39) and inhibitor (n = 30) were measured for a subset of individuals. Results Compared with clopidogrel-associated TTP cases (n = 35), ticlopidine-associated TTP cases (n = 93) were more likely to have received more than 2 weeks of drug (90% vs. 26%), to be severely thrombocytopenic (84% vs. 60%), and to have normal renal function (72% vs. 45%) (p < 0.01 for each). Compared with TTP patients with ADAMTS13 activity >15% (n = 13), TTP patients with severely deficient ADAMTS13 activity (n = 26) were more likely to have received ticlopidine (92.3% vs. 46.2%, p < 0.003). Among patients who developed TTP >2 weeks after thienopyridine, therapeutic plasma exchange (TPE) increased likelihood of survival (84% vs. 38%, p < 0.05). Among patients who developed TTP within 2 weeks of starting thienopyridines, survival was 77% with TPE and 78% without. Conclusions Thrombotic thrombocytopenic purpura is a rare complication of thienopyridine treatment. This drug toxicity appears to occur by 2 different mechanistic pathways, characterized primarily by time of onset before versus after 2 weeks of thienopyridine administration. If TTP occurs after 2 weeks of ticlopidine or clopidogrel therapy, therapeutic plasma exchange must be promptly instituted to enhance likelihood of survival. PMID:17868804

  2. A partial mechanistic understanding of the North American monsoon

    NASA Astrophysics Data System (ADS)

    Erfani, Ehsan; Mitchell, David

    2014-12-01

    An understanding of the major governing processes of North American monsoon (NAM) is necessary to guide improvement in global and regional climate modeling of the NAM, as well as NAM's impacts on the summer circulation, precipitation, and drought over North America. A mechanistic understanding of the NAM is suggested by incorporating local- and synoptic-scale processes. The local-scale mechanism describes the effect of the temperature inversion over the Gulf of California (GC) on controlling low-level moisture during the 2004 NAM. The strong low-level inversion inhibits the exchange between the moist air in the marine boundary layer (MBL) and the overlying dry air. This inversion weakens with increasing sea surface temperatures (SSTs) in GC and generally disappears once SSTs exceed 29.5°C, allowing the moist air, trapped in the MBL, to mix with free tropospheric air. This leads to a deep, moist layer that can be transported by across-gulf (along-gulf) flow toward the NAM core region (southwestern U.S.) to form thunderstorms. On the synoptic scale, climatologies from 1983 to 2010 exhibit a temporal correspondence between coastal warm tropical surface water, NAM deep convection, NAM anticyclone center, and NAM-induced strong descent. A hypothesis is proposed to explain this correspondence, based on limited soundings at the GC entrance (suggesting this local mechanism may also be active in that region), the climatologies, and the relevant literature. The warmest SSTs moving up the coast may initiate NAM convection and atmospheric heating, advancing the position of the anticyclone and the region of descent northward.

  3. A mechanistic nitrogen limitation model for CLM(ED)

    NASA Astrophysics Data System (ADS)

    Ali, A. A.; Xu, C.; McDowell, N. G.; Rogers, A.; Wullschleger, S. D.; Fisher, R.; Vrugt, J. A.

    2014-12-01

    Photosynthetic capacity is a key plant trait that determines the rate of photosynthesis; however, in Earth System Models it is either a fixed value or derived from a linear function of leaf nitrogen content. A mechanistic leaf nitrogen allocation model have been developed for a DOE-sponsored Community Land Model coupled to the Ecosystem Demography model (CLM-ED) to predict the photosynthetic capacity [Vc,max25 (μmol CO2 m-2 s-1)] under different environmental conditions at the global scale. We collected more than 800 data points of photosynthetic capacity (Vc,max25) for 124 species from 57 studies with the corresponding leaf nitrogen content and environmental conditions (temperature, radiation, humidity and day length) from literature and the NGEE arctic site (Barrow). Based on the data, we found that environmental control of Vc,max25 is about 4 times stronger than the leaf nitrogen content. Using the Markov-Chain Monte Carlo simulation approach, we fitted the collected data to our newly developed nitrogen allocation model, which predict the leaf nitrogen investment in different components including structure, storage, respiration, light capture, carboxylation and electron transport at different environmental conditions. Our results showed that our nitrogen allocation model explained 52% of variance in observed Vc,max25 and 65% variance in observed Jmax25 using a single set of fitted model parameters for all species. Across the growing season, we found that the modeled Vc,max25 explained 49% of the variability in measured Vc,max25. In the context of future global warming, our model predicts that a temperature increase by 5oC and the doubling of atmospheric carbon dioxide reduced the Vc,max25 by 5%, 11%, respectively.

  4. A mechanistic accounting of SOM speciation and kinetics in soils

    NASA Astrophysics Data System (ADS)

    Maggi, F.; Riley, W. J.; Guerry, N.; Torn, M. S.; Kleber, M.

    2012-12-01

    The nature and dynamics of soil organic matter (SOM) are arguably far from being understood and accurately represented in current site, regional, and global land use and climate models. Whereas consolidated models make use of aggregated pools describing SOM with characteristic turnover times such as inert, passive, slow cycling, and fast cycling, or linking the turnover time to the molecular weight of the compound, recent analyses of SOM below the top soil suggest that those approaches only partially capture SOM dynamics, and that SOM stability may largely be determined by biological and chemical protection as well as other environmental factors rather than the molecular structure of the compound and its molecular weight. We introduce here a new paradigm of SOM speciation and kinetics that explicitly decouples the assumed recalcitrance and turnover time from the SOM molecular density and structure in favour of a mechanistic accounting of microbially mediated processes and chemo-physical interactions among the various SOM species and soil environment. These processes include microbial assimilation, respiration and C recycling; depolymerization of solid litter, root exudates, and dead cells into various decomposed SOM groups; and incorporation of soluble SOM species into a protected phase not available to chemical and biological agents. SOM was described by means of functional compounds including mono- and polysaccharides, lignin, amino compounds, organic acids, nucleic acids, lipids, and phenols, each being accounted for by one or more representative species in the model. Fungal and bacterial microbial functional groups were used to characterize depolymerization and respiration rates. The SOM reaction network and characteristics, its mathematical inclusion within the TOUGHREACT framework, and some preliminary results of modeling grasslands and forested ecosystems are presented here. Biogeochemical reaction network of SOC pathways. Steady state vertical contentration

  5. The attention schema theory: a mechanistic account of subjective awareness

    PubMed Central

    Graziano, Michael S. A.; Webb, Taylor W.

    2015-01-01

    We recently proposed the attention schema theory, a novel way to explain the brain basis of subjective awareness in a mechanistic and scientifically testable manner. The theory begins with attention, the process by which signals compete for the brain’s limited computing resources. This internal signal competition is partly under a bottom–up influence and partly under top–down control. We propose that the top–down control of attention is improved when the brain has access to a simplified model of attention itself. The brain therefore constructs a schematic model of the process of attention, the ‘attention schema,’ in much the same way that it constructs a schematic model of the body, the ‘body schema.’ The content of this internal model leads a brain to conclude that it has a subjective experience. One advantage of this theory is that it explains how awareness and attention can sometimes become dissociated; the brain’s internal models are never perfect, and sometimes a model becomes dissociated from the object being modeled. A second advantage of this theory is that it explains how we can be aware of both internal and external events. The brain can apply attention to many types of information including external sensory information and internal information about emotions and cognitive states. If awareness is a model of attention, then this model should pertain to the same domains of information to which attention pertains. A third advantage of this theory is that it provides testable predictions. If awareness is the internal model of attention, used to help control attention, then without awareness, attention should still be possible but should suffer deficits in control. In this article, we review the existing literature on the relationship between attention and awareness, and suggest that at least some of the predictions of the theory are borne out by the evidence. PMID:25954242

  6. Mechanistic Insights into Homogeneous and Heterogeneous Asymmetric Iron Catalysis

    NASA Astrophysics Data System (ADS)

    Sonnenberg, Jessica

    Our group has been focused on replacing toxic and expensive precious metal catalysts with iron for the synthesis of enantiopure compounds for industrial applications. During an investigation into the mechanism of asymmetric transfer hydrogenation with our first generation iron-(P-N-N-P) catalysts we found substantial evidence for zero-valent iron nanoparticles coated in chiral ligand acting as the active site. Extensive experimental and computational experiments were undertaken which included NMR, DFT, reaction profile analysis, substoichiometric poisoning, electron microscope imaging, XPS and multiphasic analysis, all of which supported the fact that NPs were the active species in catalysis. Reversibility of this asymmetric reaction on the nanoparticle surface was then probed using oxidative kinetic resolution of racemic alcohols, yielding modest enantiopurity and high turnover frequencies (TOF) for a range of aromatic alcohols. Efficient dehydrogenation of ammonia-borane for hydrogen evolution and the formation of B-N oligomers was also shown using the NP system, yielding highly active systems, with a maximum TOF of 3.66 H2/s-1 . We have also begun to focus on the development of iron catalysts for asymmetric direct hydrogenation of ketones using hydrogen gas. New chiral iron-(P-N-P) catalysts were developed and shown to be quite active and selective for a wide range of substrates. Mechanistic investigations primarily using NMR and DFT indicated that a highly active trans-dihydride species was being formed during catalyst activation. Lastly, a new library of chiral P-N-P and P-NH-P ligands were developed, as well as their corresponding iron complexes, some of which show promise for the development of future generations of active asymmetric direct hydrogenation catalysts.

  7. Mechanistic Understanding of Microbial Plugging for Improved Sweep Efficiency

    SciTech Connect

    Steven Bryant; Larry Britton

    2008-09-30

    Microbial plugging has been proposed as an effective low cost method of permeability reduction. Yet there is a dearth of information on the fundamental processes of microbial growth in porous media, and there are no suitable data to model the process of microbial plugging as it relates to sweep efficiency. To optimize the field implementation, better mechanistic and volumetric understanding of biofilm growth within a porous medium is needed. In particular, the engineering design hinges upon a quantitative relationship between amount of nutrient consumption, amount of growth, and degree of permeability reduction. In this project experiments were conducted to obtain new data to elucidate this relationship. Experiments in heterogeneous (layered) beadpacks showed that microbes could grow preferentially in the high permeability layer. Ultimately this caused flow to be equally divided between high and low permeability layers, precisely the behavior needed for MEOR. Remarkably, classical models of microbial nutrient uptake in batch experiments do not explain the nutrient consumption by the same microbes in flow experiments. We propose a simple extension of classical kinetics to account for the self-limiting consumption of nutrient observed in our experiments, and we outline a modeling approach based on architecture and behavior of biofilms. Such a model would account for the changing trend of nutrient consumption by bacteria with the increasing biomass and the onset of biofilm formation. However no existing model can explain the microbial preference for growth in high permeability regions, nor is there any obvious extension of the model for this observation. An attractive conjecture is that quorum sensing is involved in the heterogeneous bead packs.

  8. Vitamins C and E: Beneficial effects from a mechanistic perspective

    PubMed Central

    Traber, Maret G.; Stevens, Jan F.

    2011-01-01

    The mechanistic properties of two dietary antioxidants that are required by humans, vitamins C and E, are discussed relative to their biological effects. Vitamin C (ascorbic acid) is an essential cofactor for α-ketoglutarate-dependent dioxygenases. Examples are prolyl hydroxylases, which play a role in the biosynthesis of collagen and in down-regulation of hypoxia-inducible factor (HIF)-1, a transcription factor that regulates many genes responsible for tumor growth, energy metabolism, and neutrophil function and apoptosis. Vitamin C-dependent inhibition of the HIF pathway may provide alternative or additional approaches for controlling tumor progression, infections and inflammation. Vitamin E (α-tocopherol) functions as an essential lipid soluble antioxidant, scavenging hydroperoxyl radicals in lipid milieu. Human symptoms of vitamin E deficiency suggest that its antioxidant properties play a major role in protecting erythrocyte membranes and nervous tissues. As an antioxidant, vitamin C provides protection against oxidative stress-induced cellular damage by scavenging of reactive oxygen species, vitamin E-dependent neutralization of lipid hydroperoxyl radicals, and by protecting proteins from alkylation by electrophilic lipid peroxidation products. These bioactivities bear relevance to inflammatory disorders. Vitamin C plays also a role in the function of endothelial nitric oxide synthase (eNOS) by recycling the eNOS cofactor, tetrahydrobiopterin, which is relevant to arterial elasticity and blood pressure regulation. Evidence from plants supports a role for vitamin C in the formation of covalent adducts with electrophilic secondary metabolites. Mechanism-based effects of vitamin C and E supplementation on biomarkers and on clinical outcomes from randomized, placebo-controlled trials are emphasized in this review. PMID:21664268

  9. Cascadia Tsunami Deposit Database

    USGS Publications Warehouse

    Peters, Robert; Jaffe, Bruce; Gelfenbaum, Guy; Peterson, Curt

    2003-01-01

    The Cascadia Tsunami Deposit Database contains data on the location and sedimentological properties of tsunami deposits found along the Cascadia margin. Data have been compiled from 52 studies, documenting 59 sites from northern California to Vancouver Island, British Columbia that contain known or potential tsunami deposits. Bibliographical references are provided for all sites included in the database. Cascadia tsunami deposits are usually seen as anomalous sand layers in coastal marsh or lake sediments. The studies cited in the database use numerous criteria based on sedimentary characteristics to distinguish tsunami deposits from sand layers deposited by other processes, such as river flooding and storm surges. Several studies cited in the database contain evidence for more than one tsunami at a site. Data categories include age, thickness, layering, grainsize, and other sedimentological characteristics of Cascadia tsunami deposits. The database documents the variability observed in tsunami deposits found along the Cascadia margin.

  10. UTILITY OF MECHANISTIC MODELS FOR DIRECTING ADVANCED SEPARATIONS RESEARCH & DEVELOPMENT ACTIVITIES: Electrochemically Modulated Separation Example

    SciTech Connect

    Schwantes, Jon M.

    2009-06-01

    The objective for this work was to demonstrate the utility of mechanistic computer models designed to simulate actinide behavior for use in efficiently and effectively directing advanced laboratory R&D activities associated with developing advanced separations methods.

  11. ASSESSING POPULATION EXPOSURES TO MULTIPLE AIR POLLUTANTS USING A MECHANISTIC SOURCE-TO-DOSE MODELING FRAMEWORK

    EPA Science Inventory

    The Modeling Environment for Total Risks studies (MENTOR) system, combined with an extension of the SHEDS (Stochastic Human Exposure and Dose Simulation) methodology, provide a mechanistically consistent framework for conducting source-to-dose exposure assessments of multiple pol...

  12. Dose-response relationships and extrapolation in toxicology - Mechanistic and statistical considerations

    EPA Science Inventory

    Controversy on toxicological dose-response relationships and low-dose extrapolation of respective risks is often the consequence of misleading data presentation, lack of differentiation between types of response variables, and diverging mechanistic interpretation. In this chapter...

  13. Use of Gene Expression Changes in Blood to Elucidate Mechanistic Indicators of Childhood Asthma (MICA)

    EPA Science Inventory

    Risk assessment increasingly relies more heavily on mode of action, thus the identification of human bioindicators of disease becomes all the more important. Genomic methods represent a tool for both mode of action determination and bioindicator identification. The Mechanistic In...

  14. Mechanistic species distribution modelling as a link between physiology and conservation

    PubMed Central

    Evans, Tyler G.; Diamond, Sarah E.; Kelly, Morgan W.

    2015-01-01

    Climate change conservation planning relies heavily on correlative species distribution models that estimate future areas of occupancy based on environmental conditions encountered in present-day ranges. The approach benefits from rapid assessment of vulnerability over a large number of organisms, but can have poor predictive power when transposed to novel environments and reveals little in the way of causal mechanisms that define changes in species distribution or abundance. Having conservation planning rely largely on this single approach also increases the risk of policy failure. Mechanistic models that are parameterized with physiological information are expected to be more robust when extrapolating distributions to future environmental conditions and can identify physiological processes that set range boundaries. Implementation of mechanistic species distribution models requires knowledge of how environmental change influences physiological performance, and because this information is currently restricted to a comparatively small number of well-studied organisms, use of mechanistic modelling in the context of climate change conservation is limited. In this review, we propose that the need to develop mechanistic models that incorporate physiological data presents an opportunity for physiologists to contribute more directly to climate change conservation and advance the field of conservation physiology. We begin by describing the prevalence of species distribution modelling in climate change conservation, highlighting the benefits and drawbacks of both mechanistic and correlative approaches. Next, we emphasize the need to expand mechanistic models and discuss potential metrics of physiological performance suitable for integration into mechanistic models. We conclude by summarizing other factors, such as the need to consider demography, limiting broader application of mechanistic models in climate change conservation. Ideally, modellers, physiologists and

  15. Mechanistic species distribution modelling as a link between physiology and conservation.

    PubMed

    Evans, Tyler G; Diamond, Sarah E; Kelly, Morgan W

    2015-01-01

    Climate change conservation planning relies heavily on correlative species distribution models that estimate future areas of occupancy based on environmental conditions encountered in present-day ranges. The approach benefits from rapid assessment of vulnerability over a large number of organisms, but can have poor predictive power when transposed to novel environments and reveals little in the way of causal mechanisms that define changes in species distribution or abundance. Having conservation planning rely largely on this single approach also increases the risk of policy failure. Mechanistic models that are parameterized with physiological information are expected to be more robust when extrapolating distributions to future environmental conditions and can identify physiological processes that set range boundaries. Implementation of mechanistic species distribution models requires knowledge of how environmental change influences physiological performance, and because this information is currently restricted to a comparatively small number of well-studied organisms, use of mechanistic modelling in the context of climate change conservation is limited. In this review, we propose that the need to develop mechanistic models that incorporate physiological data presents an opportunity for physiologists to contribute more directly to climate change conservation and advance the field of conservation physiology. We begin by describing the prevalence of species distribution modelling in climate change conservation, highlighting the benefits and drawbacks of both mechanistic and correlative approaches. Next, we emphasize the need to expand mechanistic models and discuss potential metrics of physiological performance suitable for integration into mechanistic models. We conclude by summarizing other factors, such as the need to consider demography, limiting broader application of mechanistic models in climate change conservation. Ideally, modellers, physiologists and

  16. A mechanistic model of the cysteine synthase complex.

    PubMed

    Feldman-Salit, Anna; Wirtz, Markus; Hell, Ruediger; Wade, Rebecca C

    2009-02-13

    OAS-TL with E. coli SAT. The proposed models of the enzymes and their complexes provide mechanistic insights into CS complexation. PMID:18801369

  17. Mechanistic, Mutational, and Structural Evaluation of a Taxus Phenylalanine Aminomutase

    SciTech Connect

    Feng, Lei; Wanninayake, Udayanga; Strom, Susan; Geiger, James; Walker, Kevin D.

    2014-10-02

    The structure of a phenylalanine aminomutase (TcPAM) from Taxus canadensis has been determined at 2.4 {angstrom} resolution. The active site of the TcPAM contains the signature 4-methylidene-1H-imidazol-5(4H)-one prosthesis, observed in all catalysts of the class I lyase-like family. This catalyst isomerizes (S)-{alpha}-phenylalanine to the (R)-{beta}-isomer by exchange of the NH{sub 2}/H pair. The stereochemistry of the TcPAM reaction product is opposite of the (S)-{beta}-tyrosine made by the mechanistically related tyrosine aminomutase (SgTAM) from Streptomyces globisporus. Since TcPAM and SgTAM share similar tertiary- and quaternary-structures and have several highly conserved aliphatic residues positioned analogously in their active sites for substrate recognition, the divergent product stereochemistries of these catalysts likely cannot be explained by differences in active site architecture. The active site of the TcPAM structure also is in complex with (E)-cinnamate; the latter functions as both a substrate and an intermediate. To account for the distinct (3R)-{beta}-amino acid stereochemistry catalyzed by TcPAM, the cinnamate skeleton must rotate the C{sub 1}-C{sub {alpha}} and C{sub ipso}-C{sub {beta}} bonds 180{sup o} in the active site prior to exchange and rebinding of the NH{sub 2}/H pair to the cinnamate, an event that is not required for the corresponding acrylate intermediate in the SgTAM reaction. Moreover, the aromatic ring of the intermediate makes only one direct hydrophobic interaction with Leu-104. A L104A mutant of TcPAM demonstrated an 1.5-fold increase in k{sub cat} and a decrease in K{sub M} values for sterically demanding 3'-methyl-{alpha}-phenylalanine and styryl-{alpha}-alanine substrates, compared to the kinetic parameters for TcPAM. These parameters did not change significantly for the mutant with 4'-methyl-{alpha}-phenylalanine compared to those for TcPAM.

  18. Toward a mechanistic modeling of nitrogen limitation for photosynthesis

    NASA Astrophysics Data System (ADS)

    Xu, C.; Fisher, R. A.; Travis, B. J.; Wilson, C. J.; McDowell, N. G.

    2011-12-01

    The nitrogen limitation is an important regulator for vegetation growth and global carbon cycle. Most current ecosystem process models simulate nitrogen effects on photosynthesis based on a prescribed relationship between leaf nitrogen and photosynthesis; however, there is a large amount of variability in this relationship with different light, temperature, nitrogen availability and CO2 conditions, which can affect the reliability of photosynthesis prediction under future climate conditions. To account for the variability in nitrogen-photosynthesis relationship under different environmental conditions, in this study, we developed a mechanistic model of nitrogen limitation for photosynthesis based on nitrogen trade-offs among light absorption, electron transport, carboxylization and carbon sink. Our model shows that strategies of nitrogen storage allocation as determined by tradeoff among growth and persistence is a key factor contributing to the variability in relationship between leaf nitrogen and photosynthesis. Nitrogen fertilization substantially increases the proportion of nitrogen in storage for coniferous trees but much less for deciduous trees, suggesting that coniferous trees allocate more nitrogen toward persistence compared to deciduous trees. The CO2 fertilization will cause lower nitrogen allocation for carboxylization but higher nitrogen allocation for storage, which leads to a weaker relationship between leaf nitrogen and maximum photosynthesis rate. Lower radiation will cause higher nitrogen allocation for light absorption and electron transport but less nitrogen allocation for carboxylyzation and storage, which also leads to weaker relationship between leaf nitrogen and maximum photosynthesis rate. At the same time, lower growing temperature will cause higher nitrogen allocation for carboxylyzation but lower allocation for light absorption, electron transport and storage, which leads to a stronger relationship between leaf nitrogen and maximum

  19. Dry deposition velocities

    SciTech Connect

    Sehmel, G.A.

    1984-03-01

    Dry deposition velocities are very difficult to predict accurately. In this article, reported values of dry deposition velocities are summarized. This summary includes values from the literature on field measurements of gas and particle dry deposition velocities, and the uncertainties inherent in extrapolating field results to predict dry deposition velocities are discussed. A new method is described for predicting dry deposition velocity using a least-squares correlation of surface mass transfer resistances evaluated in wind tunnel experiments. 14 references, 4 figures, 1 table.

  20. Deposition of Atmospheric Pollutants

    NASA Astrophysics Data System (ADS)

    Malet, L. M.

    Deposition of Atmospheric Pollutants, containing the proceedings of a colloquium held at Oberursel/Taunus, FRG, November 9-11, 1981, is divided into three main parts: dry deposition; wet deposition; and deposition on plants and vegetation.The 20 articles in the volume permit a fair survey of present-day knowledge and will be a useful tool to all working on the topic. Pollution by deposition of either the dry or wet sort is very insidious; its importance only appears in the long range, when its effects are or are almost irreversible. That is why concern was so long in emerging from decision makers.

  1. Mechanistic study of silver nanoparticle formation on conducting polymer surfaces.

    PubMed

    Mack, Nathan H; Bailey, James A; Doorn, Stephen K; Chen, Chien-An; Gau, Han-Mou; Xu, Ping; Williams, Darrick J; Akhadov, Elshan A; Wang, Hsing-Lin

    2011-04-19

    Conducting polymer (polyaniline) sheets are shown to be active substrates to promote the growth of nanostructured silver thin films with highly tunable morphologies. Using the spontaneous electroless deposition of silver, we show that a range of nanostructured metallic features can be controllably and reproducibly formed over large surface areas. The structural morphology of the resulting metal-polymer nanocomposite is demonstrated to be sensitive to experimental parameters such as ion concentration, temperature, and polymer processing and can range from densely packed oblate nanosheets to bulk crystalline metals. The deposition mechanisms are explained using a diffusion-limited aggregation (DLA) model to describe the semi-fractal-like growth of the metal nanostructures. We find these composite films to exhibit strong surface-enhanced Raman (SERS) activity, and the nanostructured features are optimized with respect to SERS activity using a self-assembled monolayer of mercapto-benzoic acid as a model Raman reporter. SERS enhancements are estimated to be on the order of 10(7). Through micro-Raman SERS mapping, these materials are shown to exhibit uniform SERS responses over macroscopic areas. These metal-polymer nanocomposites benefit from the underlying polymer's processability to yield SERS-active materials of almost limitless shape and size and show significant promise for future SERS-based sensing and detection schemes. PMID:21434643

  2. Mechanistic Contributions of Biological Cofactors in Islet Amyloid Polypeptide Amyloidogenesis

    PubMed Central

    Nguyen, Phuong Trang; Andraka, Nagore; De Carufel, Carole Anne; Bourgault, Steve

    2015-01-01

    Type II diabetes mellitus is associated with the deposition of fibrillar aggregates in pancreatic islets. The major protein component of islet amyloids is the glucomodulatory hormone islet amyloid polypeptide (IAPP). Islet amyloid fibrils are virtually always associated with several biomolecules, including apolipoprotein E, metals, glycosaminoglycans, and various lipids. IAPP amyloidogenesis has been originally perceived as a self-assembly homogeneous process in which the inherent aggregation propensity of the peptide and its local concentration constitute the major driving forces to fibrillization. However, over the last two decades, numerous studies have shown a prominent role of amyloid cofactors in IAPP fibrillogenesis associated with the etiology of type II diabetes. It is increasingly evident that the biochemical microenvironment in which IAPP amyloid formation occurs and the interactions of the polypeptide with various biomolecules not only modulate the rate and extent of aggregation, but could also remodel the amyloidogenesis process as well as the structure, toxicity, and stability of the resulting fibrils. PMID:26576436

  3. Airfoil deposition model

    NASA Technical Reports Server (NTRS)

    Kohl, F. J.

    1982-01-01

    The methodology to predict deposit evolution (deposition rate and subsequent flow of liquid deposits) as a function of fuel and air impurity content and relevant aerodynamic parameters for turbine airfoils is developed in this research. The spectrum of deposition conditions encountered in gas turbine operations includes the mechanisms of vapor deposition, small particle deposition with thermophoresis, and larger particle deposition with inertial effects. The focus is on using a simplified version of the comprehensive multicomponent vapor diffusion formalism to make deposition predictions for: (1) simple geometry collectors; and (2) gas turbine blade shapes, including both developing laminar and turbulent boundary layers. For the gas turbine blade the insights developed in previous programs are being combined with heat and mass transfer coefficient calculations using the STAN 5 boundary layer code to predict vapor deposition rates and corresponding liquid layer thicknesses on turbine blades. A computer program is being written which utilizes the local values of the calculated deposition rate and skin friction to calculate the increment in liquid condensate layer growth along a collector surface.

  4. Mechanistically Driven Development of Iridium Catalysts for Asymmetric Allylic Substitution

    PubMed Central

    Hartwig, John F.; Stanley, Levi M.

    2010-01-01

    , with high branched-to-linear ratios and high enantioselectivities. Parallel mechanistic studies had revealed the metallacyclic structure of the active catalyst, and subsequent experiments with the purposefully formed metallacycle increased the reaction scope dramatically. Aromatic amines, azoles, ammonia, and amides and carbamates as ammonia equivalents all reacted with high selectivities and yields. Moreover, weakly basic enolates (such as silyl enol ethers) and enolate equivalents (such as enamines) also reacted, and other research groups have used this catalyst to conduct reactions of stabilized carbon nucleophiles in the absence of additional base. One hallmark of the reactions catalyzed by this iridium system is the invariably high enantioselectivity, which reflects a high stereoselectivity for formation of the allyl intermediate. Enantioselectivity typically exceeds 95%, regioselectivity for formation of branched over linear products is usually near 20:1, and yields generally exceed 75% and are often greater than 90%. Thus, the development of iridium catalysts for enantioselective allylic substitution shows how studies of reaction mechanism can lead to a particularly active and a remarkably general system for an enantioselective process. In this case, a readily accessible catalyst effects allylic substitution, with high enantioselectivity and regioselectivity complementary to that of the venerable palladium systems. PMID:20873839

  5. A mechanistic examination of redox cycling activity in carbonaceous particulate matter

    NASA Astrophysics Data System (ADS)

    McWhinney, Robert David

    Mechanistic aspects of carbonaceous aerosol toxicity were examined with respect to the ability of particles to catalyse reactive oxygen species-generating redox cycling reactions. To investigate the role of secondary organic material, we examined two systems. In the first, two-stroke engine exhaust particles were found to increase their ability to catalyse redox cycling in the presence of a reducing agent, dithiothreitol (DTT), when the exhaust was exposed to ozone. This occurred through deposition of redox-active secondary organic aerosol (SOA) onto the particle that was ten times more redox active per microgram than the primary engine particle. In the second system, naphthalene SOA formed highly redox active particles. Activity was strongly correlated to the amount of the 1,4- and 1,2-naphthoquinone measured in the particle phase. However, these species and the newly quantified naphthalene oxidation product 5-hydroxy-1,4-naphthoquinone accounted for only 30% of the observed DTT decay from the particles. Gas-particle partitioning coefficients suggest 1,4- and 1,2- naphthoquinone are not strong contributors to ambient particle redox activity at 25 °C. However, a large number of redox active species are unidentified. Some of these may be highly oxidised products of sufficiently low vapour pressure to be atmospherically relevant. DTT activity of diesel particles was found to be high per unit mass. The activity was found to be associated with the insoluble fraction as filtration of the particles nearly eliminated DTT decay. Neither methanol nor dichloromethane extracts of diesel particles exhibited redox activity, indicating that the redox active species are associated with the black carbon portion of the particles. Examination of particle concentration techniques found that use of water condensation to grow and concentrate particles introduced a large organic artefact to the particles. Experiments with concentrated inorganic particles suggest that the source of this

  6. Mechanistic controls on diverse fates of terrestrial organic components in the East China Sea

    NASA Astrophysics Data System (ADS)

    Zhu, Chun; Wagner, Thomas; Talbot, Helen M.; Weijers, Johan W. H.; Pan, Jian-Ming; Pancost, Richard D.

    2013-09-01

    Terrestrial carbon transferred from the land to sea is a critical component of the global carbon cycle. A range of geochemical proxies has been developed to fingerprint the fate of terrestrial organic matter (TOM) in marine sediments. However, discrepancies among different proxies limit our ability to quantify and interpret the terrestrial signals in marine sediments, with consequences for the investigation of both the modern carbon cycle and past environmental change. To mechanistically understand these discrepancies, we examined the distributions of a range of terrestrial proxies and their aquatic counterparts (i.e. marine proxies) in the Yangtze river-East China Sea (YR-ECS) shelf system, where TOM experiences extensive modification during transport and burial. TOM proxies in the YR-ECS system collectively fit a power-law model but with distinct attenuation rates (the a∗ values) for individual molecular proxy groups. Among a range of TOM proxies, the modeled a∗ values decrease in the order: soil-marker BHPs > triterpenols > lignin > HMW n-alkanols > branched GDGTs > HMW n-alkanes for biomarkers; and Rsoil > BIT > %TOMiso for proxies tracing %TOM. Rapid loss of TOM components through dissociation in the narrow estuary, followed by oxidation over the wide open shelf, are best described by power curves. Inherent chemical reactivity (i.e. the number of functional groups), responses to hydraulic sorting, and in situ production regulate the individual attenuation rates. Of them, chemical reactivity plays the most important role on proxy behavior, supported by a strong correlation between a∗ values and standard molal Gibbs energies. Both, physical protection and chemical reactivity fundamentally control the overall behavior of TOM components, with the relative importance being setting-dependant: The former is relatively important in the estuary, whereas the later is the primary control over the open shelf. Moreover, regional variation of different marine

  7. Using a Mechanistic Reactive Transport Model to Represent Soil Organic Matter Dynamics and Climate Sensitivity

    NASA Astrophysics Data System (ADS)

    Guerry, N.; Riley, W. J.; Maggi, F.; Torn, M. S.; Kleber, M.

    2011-12-01

    The nature of long term Soil Organic Matter (SOM) dynamics is uncertain and the mechanisms involved are crudely represented in site, regional, and global models. Recent work challenging the paradigm that SOM is stabilized because of its sequential transformations to more intrinsically recalcitrant compounds motivated us to develop a mechanistic modeling framework that can be used to test hypotheses of SOM dynamics. We developed our C cycling model in TOUGHREACT, an established 3-dimensional reactive transport solver that accounts for multiple phases (aqueous, gaseous, sorbed), multiple species, advection and diffusion, and multiple microbial populations. Energy and mass exchange through the soil boundaries are accounted for via ground heat flux, rainfall, C sources (e.g., exudation, woody, leaf, root litter) and C losses (e.g., CO2 emissions and DOC deep percolation). SOM is categorized according to the various types of compounds commonly found in the above mentioned C sources and microbial byproducts, including poly- and monosaccharides, lignin, amino compounds, organic acids, nucleic acids, lipids, and phenols. Each of these compounds is accounted for by one or more representative species in the model. A reaction network was developed to describe the microbially-mediated processes and chemical interactions of these species, including depolymerization, microbial assimilation, respiration and deposition of byproducts, and incorporation of dead biomass into SOM stocks. Enzymatic reactions are characterized by Michaelis-Menten kinetics, with maximum reaction rates determined by the species' O/C ratio. Microbial activity is further regulated by soil moisture content, O2 availability, pH, and temperature. For the initial set of simulations, literature values were used to constrain microbial Monod parameters, Michaelis-Menten parameters, sorption parameters, physical protection, partitioning of microbial byproducts, and partitioning of litter inputs, although there is

  8. In Vitro Multitissue Interface Model Supports Rapid Vasculogenesis and Mechanistic Study of Vascularization across Tissue Compartments.

    PubMed

    Buno, Kevin P; Chen, Xuemei; Weibel, Justin A; Thiede, Stephanie N; Garimella, Suresh V; Yoder, Mervin C; Voytik-Harbin, Sherry L

    2016-08-31

    A significant challenge facing tissue engineers is the design and development of complex multitissue systems, including vascularized tissue-tissue interfaces. While conventional in vitro models focus on either vasculogenesis (de novo formation of blood vessels) or angiogenesis (vessels sprouting from existing vessels or endothelial monolayers), successful therapeutic vascularization strategies will likely rely on coordinated integration of both processes. To address this challenge, we developed a novel in vitro multitissue interface model in which human endothelial colony forming cell (ECFC)-encapsulated tissue spheres are embedded within a surrounding tissue microenvironment. This highly reproducible approach exploits biphilic surfaces (nanostructured surfaces with distinct superhydrophobic and hydrophilic regions) to (i) support tissue compartments with user-specified matrix composition and physical properties as well as cell type and density and (ii) introduce boundary conditions that prevent the cell-mediated tissue contraction routinely observed with conventional three-dimensional monodispersion cultures. This multitissue interface model was applied to test the hypothesis that independent control of cell-extracellular matrix (ECM) and cell-cell interactions would affect vascularization within the tissue sphere as well as across the tissue-tissue interface. We found that high-cell-density tissue spheres containing 5 × 10(6) ECFCs/mL exhibit rapid and robust vasculogenesis, forming highly interconnected, stable (as indicated by type IV collagen deposition) vessel networks within only 3 days. Addition of adipose-derived stromal cells (ASCs) in the surrounding tissue further enhanced vasculogenesis within the sphere as well as angiogenic vessel elongation across the tissue-tissue boundary, with both effects being dependent on the ASC density. Overall, results show that the ECFC density and ECFC-ASC crosstalk, in terms of paracrine and mechanophysical signaling

  9. Ionized cluster beam deposition

    NASA Technical Reports Server (NTRS)

    Kirkpatrick, A. R.

    1983-01-01

    Ionized Cluster Beam (ICB) deposition, a new technique originated by Takagi of Kyoto University in Japan, offers a number of unique capabilities for thin film metallization as well as for deposition of active semiconductor materials. ICB allows average energy per deposited atom to be controlled and involves impact kinetics which result in high diffusion energies of atoms on the growth surface. To a greater degree than in other techniques, ICB involves quantitative process parameters which can be utilized to strongly control the characteristics of films being deposited. In the ICB deposition process, material to be deposited is vaporized into a vacuum chamber from a confinement crucible at high temperature. Crucible nozzle configuration and operating temperature are such that emerging vapor undergoes supercondensation following adiabatic expansion through the nozzle.

  10. Performance modeling of the Ballard Mark IV solid polymer electrolyte fuel cell. 1: Mechanistic model development

    SciTech Connect

    Amphlett, J.C.; Baumert, R.M.; Mann, R.F.; Peppley, B.A.; Roberge, P.R. ); Harris, T.J. )

    1995-01-01

    A parametric model predicting the performance of a solid polymer electrolyte, proton exchange membrane (PEM) fuel cell has been developed using a combination of mechanistic and empirical modeling techniques. This paper details the mechanistic model development. Mass transport properties are considered in the mechanistic development via Stefan-Maxwell equations. Thermodynamic equilibrium potentials are defined using the Nernst equation. Activation overvoltages are defined via a Tafel equation, and internal resistance are defined via the Nernst-Planck equation, leading to a definition of ohmic overvoltage via an Ohm's law equation. The mechanistic model cannot adequately model fuel cell performance, since several simplifying approximations have been used in order to facilitate model development. Additionally, certain properties likely to be observed in operational fuel cells, such as thermal gradients, have not been considered. Nonetheless, the insights gained from the mechanistic assessment of fuel cell processes were found to give the resulting empirical model a firmer theoretical basis than many of the models presently available in the literature. Correlation of the empirical model to actual experimental data was very good.

  11. Impact of Surface Chemistry on Copper Deposition in Mesoporous Silicon.

    PubMed

    Darwich, Walid; Garron, Anthony; Bockowski, Piotr; Santini, Catherine; Gaillard, Frédéric; Haumesser, Paul-Henri

    2016-08-01

    An easy, efficient, and safe process is developed to metallize mesoporous silicon (PSi) with Cu from the decomposition of a solution of mesitylcopper (CuMes) in an imidazolium-based ionic liquid (IL), [C1C4Im][NTf2]. The impregnation of a solution of CuMes in IL affords the deposition of metallic islands not only on the surface but also deep within the pores of a mesoporous Si layer with small pores below 10 nm. Therefore, this process is well suited to efficiently and completely metallize PSi layers. An in-depth mechanistic study shows that metal deposition is due to the reduction of CuMes by surface silane groups rather than by Si oxidation as observed in aqueous or water-containing media. This could open a new route to the chemical metallization of PSi by less-noble metals difficult to attain by a conventional displacement reaction. PMID:27368422

  12. 157 nm Pellicles (Thin Films) for Photolithography: Mechanistic Investigation of the VUV and UV-C Photolysis of Fluorocarbons

    SciTech Connect

    Lee, Kwangjoo; Jockusch, Steffen; Turro, Nicholas J.; French, Roger H.; Wheland, Robert C.; Lemon, M F.; Braun, Andre M.; Widerschpan, Tatjana; Dixon, David A.; Li, Jun; Ivan, Marius; Zimmerman, Paul

    2005-06-15

    The use of 157 nm as the next lower wavelength for photolithography for the production of semiconductors has created a need for transparent and radiation-durable polymers for use in soft pellicles, the polymer films which protect the chip from particle deposition. The most promising materials for pellicles are fluorinated polymers, but currently available fluorinated polymers undergo photodegradation and/or photodarkening upon long term exposure to 157 nm irradiation. To understand the mechanism of the photodegradation and photodarkening of fluorinated polymers, mechanistic studies on the photolysis of liquid model fluorocarbons, including perfluorobutylethyl ether and perfluoro-2 H-3-oxa-heptane, were performed employing UV, NMR, FTIR, GC, and GC/MS analyses. All hydrogen-containing compounds showed decreased photostability compared to the fully perfluorinated compounds. Irradiation in the presence of atmospheric oxygen showed reduced photostability compared to deoxygenated samples. Photolysis of the samples was performed at 157, 172, 185, and 254 nm and showed only minor wavelength dependence. Mechanisms for photodegradation of the fluorocarbons are proposed, which involve Rydberg excited states. Time-dependent density functional theory has been used to predict the excitation spectra of model compounds.

  13. Mechanistic similarity and diversity among the guanidine-modifying members of the pentein superfamily

    PubMed Central

    Linsky, Thomas; Fast, Walter

    2014-01-01

    The pentein superfamily is a mechanistically diverse superfamily encompassing both noncatalytic proteins and enzymes that catalyze hydrolase, dihydrolase and amidinotransfer reactions on guanidine substrates. Despite generally low sequence identity, they possess a conserved structural fold and display common mechanistic themes in catalysis. The structurally characterized catalytic penteins possess a conserved core of residues that include a Cys, His and two polar, guanidine-binding residues. All known catalytic penteins use the core Cys to attack the substrate’s guanidine moiety to form a covalent thiouronium adduct and all cleave one or more of the guanidine C–N bonds. The mechanistic information compiled to date supports the hypothesis that this superfamily may have evolved divergently from a catalytically promiscuous ancestor. PMID:20654741

  14. Chemoselective Transformation of Diarylethanones to Arylmethanoic Acids and Diarylmethanones and Mechanistic Insights.

    PubMed

    Wang, Xing; Chen, Rui-Xi; Wei, Zeng-Feng; Zhang, Chen-Yang; Tu, Hai-Yang; Zhang, Ai-Dong

    2016-01-01

    The chemoselective transformation of diarylethanones via either aerobic oxidative cleavage to give arylmethanoic acids or tandem aerobic oxidation/benzilic acid rearrangement/decarboxylation to give diarylmethanones has been developed. The transformation is controllable and applicable to a broad spectrum of substrates and affords the desired products in good to excellent yields. Mechanistic insights with control reactions, (1)H NMR tracking, and single-crystal X-ray diffraction reveal a complex mechanistic network in which two common intermediates, α-ketohydroperoxide and diarylethanedione, and three plausible pathways are proposed and verified. These pathways are interlinked and can be switched reasonably by changing the reaction conditions. This method enables scalable synthesis and access to a number of valuable compounds, including vitamin B3, diphenic acid, and the nonsteroidal anti-inflammatory drug ketoprofen. The present protocol represents a step forward in exploiting complex mechanistic networks to control reaction pathways, achieving divergent syntheses from the same class of starting materials. PMID:26618373

  15. Integrating mechanistic organism--environment interactions into the basic theory of community and evolutionary ecology.

    PubMed

    Baskett, Marissa L

    2012-03-15

    This paper presents an overview of how mechanistic knowledge of organism-environment interactions, including biomechanical interactions of heat, mass and momentum transfer, can be integrated into basic theoretical population biology through mechanistic functional responses that quantitatively describe how organisms respond to their physical environment. Integrating such functional responses into simple community and microevolutionary models allows scaling up of the organism-level understanding from biomechanics both ecologically and temporally. For community models, Holling-type functional responses for predator-prey interactions provide a classic example of the functional response affecting qualitative model dynamics, and recent efforts are expanding analogous models to incorporate environmental influences such as temperature. For evolutionary models, mechanistic functional responses dependent on the environment can serve as fitness functions in both quantitative genetic and game theoretic frameworks, especially those concerning function-valued traits. I present a novel comparison of a mechanistic fitness function based on thermal performance curves to a commonly used generic fitness function, which quantitatively differ in their predictions for response to environmental change. A variety of examples illustrate how mechanistic functional responses enhance model connections to biologically relevant traits and processes as well as environmental conditions and therefore have the potential to link theoretical and empirical studies. Sensitivity analysis of such models can provide biologically relevant insight into which parameters and processes are important to community and evolutionary responses to environmental change such as climate change, which can inform conservation management aimed at protecting response capacity. Overall, the distillation of detailed knowledge or organism-environment interactions into mechanistic functional responses in simple population

  16. Radionuclide deposition control

    DOEpatents

    Brehm, William F.; McGuire, Joseph C.

    1980-01-01

    The deposition of radionuclides manganese-54, cobalt-58 and cobalt-60 from liquid sodium coolant is controlled by providing surfaces of nickel or high nickel alloys to extract the radionuclides from the liquid sodium, and by providing surfaces of tungsten, molybdenum or tantalum to prevent or retard radionuclide deposition.

  17. Deposition patterns with Turbuhaler.

    PubMed

    Borgström, L

    1994-01-01

    The degree of lung deposition is an important factor in the evaluation of different inhalation flow driven dry powder inhalers. A number of studies using radioactive and non-radioactive methods have been performed with Turbuhaler to assess lung deposition under different conditions. Mean total lung deposition of terbutaline sulfate or budesonide via Turbuhaler in healthy volunteers ranged from 21-32% of the dose when a normal inhalation flow (60L/min) was used. At a low flow (30L/min) a mean 15% of the dose was deposited in the lungs, a similar value as for a well-performed inhalation via a pressurized metered dose inhaler. Regional deposition of inhaled drug can be expressed as the ratio between the amount of drug deposited in the more peripheral parts of the lung relative to the more central parts. In a comparative study, budesonide and terbutaline sulfate were given by inhalation via Turbuhaler to healthy volunteers. The ratio of peripheral to central deposition was 2.03 for terbutaline and 1.72 for budesonide. Thus, both the water-soluble terbutaline sulfate and the non-water soluble budesonide seemed to behave in the same way when inhaled via Turbuhaler. In conclusion, Turbuhaler delivers over 20% of a metered dose to the lungs when inhaled at a normal inhalation flow rate. The regional deposition pattern in the lungs was the same for terbutaline sulfate and budesonide, in spite of differences in water solubility. PMID:10147081

  18. Carbamate deposit control additives

    SciTech Connect

    Honnen, L.R.; Lewis, R.A.

    1980-11-25

    Deposit control additives for internal combustion engines are provided which maintain cleanliness of intake systems without contributing to combustion chamber deposits. The additives are poly(oxyalkylene) carbamates comprising a hydrocarbyloxyterminated poly(Oxyalkylene) chain of 2-5 carbon oxyalkylene units bonded through an oxycarbonyl group to a nitrogen atom of ethylenediamine.

  19. Biomimetic thin film deposition

    SciTech Connect

    Rieke, P.R.; Graff, G.E.; Campbell, A.A.; Bunker, B.C.; Baskaran, S.; Song, L.; Tarasevich, B.J.; Fryxell, G.E.

    1995-09-01

    Biological mineral deposition for the formation of bone, mollusk shell and other hard tissues provides materials scientists with illustrative materials processing strategies. This presentation will review the key features of biomineralization and how these features can be of technical importance. We have adapted existing knowledge of biomineralization to develop a unique method of depositing inorganic thin films and coating. Our approach to thin film deposition is to modify substrate surfaces to imitate the proteins found in nature that are responsible for controlling mineral deposition. These biomimetic surfaces control the nucleation and growth of the mineral from a supersaturated aqueous solution. This has many processing advantages including simple processing equipment, environmentally benign reagents, uniform coating of highly complex shapes, and enhanced adherence of coating. Many different types of metal oxide, hydroxide, sulfide and phosphate materials with useful mechanical, optical, electronic and biomedical properties can be deposited.

  20. Solution deposition assembly

    SciTech Connect

    Roussillon, Yann; Scholz, Jeremy H; Shelton, Addison; Green, Geoff T; Utthachoo, Piyaphant

    2014-01-21

    Methods and devices are provided for improved deposition systems. In one embodiment of the present invention, a deposition system is provided for use with a solution and a substrate. The system comprises of a solution deposition apparatus; at least one heating chamber, at least one assembly for holding a solution over the substrate; and a substrate curling apparatus for curling at least one edge of the substrate to define a zone capable of containing a volume of the solution over the substrate. In another embodiment of the present invention, a deposition system for use with a substrate, the system comprising a solution deposition apparatus; at heating chamber; and at least assembly for holding solution over the substrate to allow for a depth of at least about 0.5 microns to 10 mm.

  1. Enantioselective and Regiodivergent Functionalization of N-Allylcarbamates by Mechanistically Divergent Multicatalysis.

    PubMed

    Richmond, Edward; Khan, Ismat Ullah; Moran, Joseph

    2016-08-22

    A pair of mechanistically divergent multicatalytic reaction sequences has been developed consisting of nickel-catalyzed isomerization of N-allylcarbamates and subsequent phosphoric-acid-catalyzed enantioselective functionalization of the resulting intermediates. By appropriate selection of reaction partners, in situ generated imines and ene-carbamates are mechanistically partitioned to yield opposing functionalized products. Formal α-functionalization to give protected α-arylamines is achieved upon enantioselective Friedel-Crafts reaction with arene nucleophiles, whereas formal β-functionalization is achieved upon reaction with diarylimine electrophiles in an enantioselective Povarov-[4+2] cycloaddition. PMID:27461524

  2. Mechanistic Considerations in the Synthesis of 2-Aryl-Indole Analogues under Bischler-Mohlau Conditions

    PubMed Central

    MacDonough, Matthew T.; Shi, Zhe; Pinney, Kevin G.

    2015-01-01

    Mechanistic insight into the pathway of the Bischler-Mohlau indole formation reaction is provided by isotopic labeling utilizing judicious incorporation of a 13C atom within the α-bromoacetophenone analogue reactant. The resulting rearranged 2-aryl indole, isolated as the major product, located the 13C isotope label at the methine carbon of the fused five-membered heterocyclic ring, which suggested that the mechanistic pathway of cyclization, in this specific example, required two equivalents of the aniline analogue reactant partner and proceeded through an imine intermediate rather than by direct formation of the corresponding 3-aryl indole accompanied by a concomitant 1,2-aryl shift rearrangement. PMID:26973358

  3. DEPOSITION AND EMISSION OF GASEOUS MERCURY TO AND FROM LAKE MICHIGAN DURING THE LAKE MICHIGAN MASS BALANCE STUDY (JULY, 1994 - OCTOBER, 1995)

    EPA Science Inventory

    This paper presents measurements of dissolved gaseous mercury (DGM) concentrations in Lake Michigan and the application of a mechanistic approach to estimate deposition and emission fluxes of gaseous mercury (Hg2+ and Hg0) to and from Lake Michigan. Measurements of DGM concentr...

  4. A review of lithium deposition in lithium-ion and lithium metal secondary batteries

    NASA Astrophysics Data System (ADS)

    Li, Zhe; Huang, Jun; Yann Liaw, Bor; Metzler, Viktor; Zhang, Jianbo

    2014-05-01

    Major aspects related to lithium deposition in lithium-ion and lithium metal secondary batteries are reviewed. For lithium-ion batteries with carbonaceous anode, lithium deposition may occur under harsh charging conditions such as overcharging or charging at low temperatures. The major technical solutions include: (1) applying electrochemical models to predict the critical conditions for deposition initiation; (2) preventions by improved battery design and material modification; (3) applying adequate charging protocols to inhibit lithium deposition. For lithium metal secondary batteries, the lithium deposition is the inherent reaction during charging. The major technical solutions include: (1) the use of mechanistic models to elucidate and control dendrite initiation and growth; (2) engineering surface morphology of the lithium deposition to avoid dendrite formation via adjusting the composition and concentration of the electrolyte; (3) controlling battery working conditions. From a survey of the literature, the areas that require further study are proposed; e.g., refining the lithium deposition criteria, developing an effective AC self pre-heating method for low-temperature charging of lithium-ion batteries, and clarifying the role the solid electrolyte interphase (SEI) plays in determining the deposition morphology; to facilitate a refined control of the lithium deposition.

  5. EDITORIAL: Atomic layer deposition Atomic layer deposition

    NASA Astrophysics Data System (ADS)

    Godlewski, Marek

    2012-07-01

    The growth method of atomic layer deposition (ALD) was introduced in Finland by Suntola under the name of atomic layer epitaxy (ALE). The method was originally used for deposition of thin films of sulphides (ZnS, CaS, SrS) activated with manganese or rare-earth ions. Such films were grown for applications in thin-film electroluminescence (TFEL) displays. The ALE mode of growth was also tested in the case of molecular beam epitaxy. Films grown by ALD are commonly polycrystalline or even amorphous. Thus, the name ALE has been replaced by ALD. In the 80s ALD was developed mostly in Finland and neighboring Baltic countries. Deposition of a range of different materials was demonstrated at that time, including II-VI semiconductors (e.g. CdTe, CdS) and III-V (e.g. GaAs, GaN), with possible applications in e.g. photovoltaics. The number of publications on ALD was slowly increasing, approaching about 100 each year. A real boom in interest came with the development of deposition methods of thin films of high-k dielectrics. This research was motivated by a high leakage current in field-effect transistors with SiO2-based gate dielectrics. In 2007 Intel introduced a new generation of integrated circuits (ICs) with thin films of HfO2 used as gate isolating layers. In these and subsequent ICs, films of HfO2 are deposited by the ALD method. This is due to their unique properties. The introduction of ALD to the electronics industry led to a booming interest in the ALD growth method, with the number of publications increasing rapidly to well above 1000 each year. A number of new applications were proposed, as reflected in this special issue of Semiconductor Science and Technology. The included articles cover a wide range of possible applications—in microelectronics, transparent electronics, optoelectronics, photovoltaics and spintronics. Research papers and reviews on the basics of ALD growth are also included, reflecting a growing interest in precursor chemistry and growth

  6. Legitimising data-driven models: exemplification of a new data-driven mechanistic modelling framework

    NASA Astrophysics Data System (ADS)

    Mount, N. J.; Dawson, C. W.; Abrahart, R. J.

    2013-07-01

    In this paper the difficult problem of how to legitimise data-driven hydrological models is addressed using an example of a simple artificial neural network modelling problem. Many data-driven models in hydrology have been criticised for their black-box characteristics, which prohibit adequate understanding of their mechanistic behaviour and restrict their wider heuristic value. In response, presented here is a new generic data-driven mechanistic modelling framework. The framework is significant because it incorporates an evaluation of the legitimacy of a data-driven model's internal modelling mechanism as a core element in the modelling process. The framework's value is demonstrated by two simple artificial neural network river forecasting scenarios. We develop a novel adaptation of first-order partial derivative, relative sensitivity analysis to enable each model's mechanistic legitimacy to be evaluated within the framework. The results demonstrate the limitations of standard, goodness-of-fit validation procedures by highlighting how the internal mechanisms of complex models that produce the best fit scores can have lower mechanistic legitimacy than simpler counterparts whose scores are only slightly inferior. Thus, our study directly tackles one of the key debates in data-driven, hydrological modelling: is it acceptable for our ends (i.e. model fit) to justify our means (i.e. the numerical basis by which that fit is achieved)?

  7. Legitimising neural network river forecasting models: a new data-driven mechanistic modelling framework

    NASA Astrophysics Data System (ADS)

    Mount, N. J.; Dawson, C. W.; Abrahart, R. J.

    2013-01-01

    In this paper we address the difficult problem of gaining an internal, mechanistic understanding of a neural network river forecasting (NNRF) model. Neural network models in hydrology have long been criticised for their black-box character, which prohibits adequate understanding of their modelling mechanisms and has limited their broad acceptance by hydrologists. In response, we here present a new, data-driven mechanistic modelling (DDMM) framework that incorporates an evaluation of the legitimacy of a neural network's internal modelling mechanism as a core element in the model development process. The framework is exemplified for two NNRF modelling scenarios, and uses a novel adaptation of first order, partial derivate, relative sensitivity analysis methods as the means by which each model's mechanistic legitimacy is explored. The results demonstrate the limitations of standard, goodness-of-fit validation procedures applied by NNRF modellers, by highlighting how the internal mechanisms of complex models that produce the best fit scores can have much lower legitimacy than simpler counterparts whose scores are only slightly inferior. The study emphasises the urgent need for better mechanistic understanding of neural network-based hydrological models and the further development of methods for elucidating their mechanisms.

  8. A Mechanistic Study of Arsenic (III) Rejection by Reverse Osmosis and Nanofiltration Membranes

    ERIC Educational Resources Information Center

    Suzuki, Tasuma

    2009-01-01

    Reverse osmosis/nanofiltration (RO/NF) membranes are capable to provide an effective barrier for a wide range of contaminants (including disinfection by-products precursors) in a single treatment step. However, solute rejection mechanisms by RO/NF membranes are not well understood. The lack of mechanistic information arises from experimental…

  9. A mechanistic detachment rate model to predict soil erodibility due to fluvial and seepage forces

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The erosion rate of cohesive soils is typically computed using an excess shear stress model based on the applied fluvial shear stress. However, no mechanistic approaches are available for incorporating additional forces such as localized groundwater seepage forces into the excess shear stress model...

  10. Predictive mechanistic bioenergetics to model habitat suitability of shellfish culture in coastal lakes

    NASA Astrophysics Data System (ADS)

    Rinaldi, A.; Montalto, V.; Manganaro, A.; Mazzola, A.; Mirto, S.; Sanfilippo, M.; Sarà, G.

    2014-05-01

    Quantitative tools based on mechanistic modelling of functional traits able to enhance the sustainability of aquaculture and most other human activities (i.e. reducing the likelihood of detrimental impacts optimising productions), are especially important factors in the decision to site aquaculture facilities in coastal lakes, ponds and lagoons and, in the case of detrimental impact, to adopt mitigation measures. We tested the ability of mechanistic functional trait based models to predict life history traits of cultivable shellfish in shallow coastal lakes. Dynamic Energy Budget (DEB) models were run to generate spatially explicit predictions of Mytilus galloprovincialis life history (LH) traits (e.g. body size and fecundity). Using fortnightly data of food supply and hourly data of body temperatures, and exploiting the power of mechanistic rules, we estimated the amount of faeces ejected by a fixed quantity of organisms cultivated in two shallow Southern Mediterranean (Sicily) lakes. These differed in terms of temperature and food density, implying large differences in life history traits of mussels in the two study areas. This information could help facilitate the selection of sites where environmental conditions are more suitable for aquaculture and contextually compatible with sustainability. The validation exercise obtained by comparing the predicted and observed data was nearly consistent. Therefore, a mechanistic functional traits-based model seems able to capture the link between habitat characteristics and functional traits of organisms, delineating the fundamental portion of an ecological niche, the possibility of predicting LH traits and potential ecological applications in the management of natural coastal resources.

  11. A mechanistic treatment of the dominant soil nitrogen cycling processes: Model development, testing, and application

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The development and initial application of a mechanistic model (TOUGHREACT-N) designed to characterize soil nitrogen (N) cycling and losses are described. The model couples advective and diffusive nutrient transport, multiple microbial biomass dynamics, and equilibrium and kinetic chemical reactions...

  12. CHEMICAL MUTAGENESIS AND CARCINOGENESIS: INCORPORATION OF MECHANISTIC DATA INTO RISK ASSESSMENT

    EPA Science Inventory

    CHEMICAL MUTAGENESIS AND CARCINOGENESIS: INCORPORATION OF MECHANISTIC DATA INTO RISK ASSESSMENT

    The current understanding of cancer as a genetic disease, requiring a specific set of genomic alterations for a normal cell to form a metastatic tumor, has provided the oppor...

  13. Assessing Metal Levels in Children from the Mechanistic Indicators of Childhood Asthma(MICA) study

    EPA Science Inventory

    Toxic and essential metals levels can be used as health indicators. Here, we quantitatively compare and contrast toxic and essential metals levels in vacuum dust, urine, and fingernail samples of 109 children in Detroit, Michigan as part of The Mechanistic Indicators of Childhood...

  14. DEVELOPING MECHANISTIC DATA FOR INCORPORATION INTO CANCER AND GENETIC RISK ASSESSMENTS: OLD PROBLEMS AND NEW APPROACHES

    EPA Science Inventory

    26th Lauriston S. Taylor Lecture
    DEVELOPING MECHANISTIC DATA FOR INCORPORATION INTO CANCER AND
    GENETIC RISK ASSESSMENTS: OLD PROBLEMS AND NEW APPROACHES
    R. Julian Preston, Environmental Carcinogenesis Division, U.S. Environmental Protection
    Agency, NHEERL, Research Tr...

  15. New Simulation Methods to Facilitate Achieving a Mechanistic Understanding of Basic Pharmacology Principles in the Classroom

    ERIC Educational Resources Information Center

    Grover, Anita; Lam, Tai Ning; Hunt, C. Anthony

    2008-01-01

    We present a simulation tool to aid the study of basic pharmacology principles. By taking advantage of the properties of agent-based modeling, the tool facilitates taking a mechanistic approach to learning basic concepts, in contrast to the traditional empirical methods. Pharmacodynamics is a particular aspect of pharmacology that can benefit from…

  16. Territoriality and home-range dynamics in meerkats, Suricata suricatta: a mechanistic modelling approach.

    PubMed

    Bateman, Andrew W; Lewis, Mark A; Gall, Gabriella; Manser, Marta B; Clutton-Brock, Tim H

    2015-01-01

    Multiple approaches exist to model patterns of space use across species, among them resource selection analysis, statistical home-range modelling and mechanistic movement modelling. Mechanistic home-range models combine the benefits of these approaches, describing emergent territorial patterns based on fine-scale individual- or group-movement rules and incorporating interactions with neighbours and the environment. These models have not, to date, been extended to dynamic contexts. Using mechanistic home-range models, we explore meerkat (Suricata suricatta) territorial patterns, considering scent marking, direct group interactions and habitat selection. We also extend the models to accommodate dynamic aspects of meerkat territoriality (territory development and territory shift). We fit models, representing multiple working hypotheses, to data from a long-term meerkat study in South Africa, and we compare models using Akaike's and Bayesian Information Criteria. Our results identify important features of meerkat territorial patterns. Notably, larger groups do not seem to control larger territories, and groups apparently prefer dune edges along a dry river bed. Our model extensions capture instances in which 1) a newly formed group interacts more strongly with its parent groups over time and 2) a group moves its territory core out of aversive habitat. This extends our mechanistic modelling framework in previously unexplored directions. PMID:24995457

  17. From Source to Sink: Mechanistic Reasoning Using the Electron-Pushing Formalism

    ERIC Educational Resources Information Center

    Bhattacharyya, Gautam

    2013-01-01

    Since the introduction of Morrison and Boyd's textbook in organic chemistry over 50 years ago, reaction mechanisms and mechanistic reasoning using the electron-pushing formalism (EPF) have become a mainstay of organic chemistry courses. In recent years there have even been several papers in this Journal and others detailing research on how…

  18. Productivity of "Collisions Generate Heat" for Reconciling an Energy Model with Mechanistic Reasoning: A Case Study

    ERIC Educational Resources Information Center

    Scherr, Rachel E.; Robertson, Amy D.

    2015-01-01

    We observe teachers in professional development courses about energy constructing mechanistic accounts of energy transformations. We analyze a case in which teachers investigating adiabatic compression develop a model of the transformation of kinetic energy to thermal energy. Among their ideas is the idea that thermal energy is generated as a…

  19. REDUCING UNCERTAINTY IN RISK ASSESSMENT USING MECHANISTIC DATA: ENHANCING THE U.S. EPA DEVELOPMENTAL NEUROTOXICITY TESTING GUIDELINES

    EPA Science Inventory

    SUMMARY: Mechanistic data should provide the Agency with a more accurate basis to estimate risk than do the Agency’s default assumptions (10x uncertainty factors, etc.), thereby improving risk assessment decisions. NTD is providing mechanistic data for toxicant effects on two maj...

  20. Chemical vapor deposition growth

    NASA Technical Reports Server (NTRS)

    Ruth, R. P.; Manasevit, H. M.; Kenty, J. L.; Moudy, L. A.; Simpson, W. I.; Yang, J. J.

    1976-01-01

    A chemical vapor deposition (CVD) reactor system with a vertical deposition chamber was used for the growth of Si films on glass, glass-ceramic, and polycrystalline ceramic substrates. Silicon vapor was produced by pyrolysis of SiH4 in a H2 or He carrier gas. Preliminary deposition experiments with two of the available glasses were not encouraging. Moderately encouraging results, however, were obtained with fired polycrystalline alumina substrates, which were used for Si deposition at temperatures above 1,000 C. The surfaces of both the substrates and the films were characterized by X-ray diffraction, reflection electron diffraction, scanning electron microscopy optical microscopy, and surface profilometric techniques. Several experiments were conducted to establish baseline performance data for the reactor system, including temperature distributions on the sample pedestal, effects of carrier gas flow rate on temperature and film thickness, and Si film growth rate as a function of temperature.

  1. World oil shale deposits

    SciTech Connect

    Hook, C.O.; Russell, P.L.

    1982-01-01

    The article estimates resources in-place and their oil equivalent. The major deposits are described in the U.S., Australia, USSR, Peoples Republic of China, Morocco, Israel, Jordan, Syria, Europe and South America. 2 refs.

  2. Automatic Payroll Deposit System.

    ERIC Educational Resources Information Center

    Davidson, D. B.

    1979-01-01

    The Automatic Payroll Deposit System in Yakima, Washington's Public School District No. 7, directly transmits each employee's salary amount for each pay period to a bank or other financial institution. (Author/MLF)

  3. Modeling atmospheric particle deposition

    NASA Astrophysics Data System (ADS)

    Jackson, Msafiri M.

    Experimentally determined dry deposition velocities for atmospheric particles in the size range of 5-80 μm in diameter have been shown to be greater than predictions made with the current state-of-the-art (Sehmel-Hodgson) model which is based on wind tunnel experiment, particularly at higher wind speed. In this research, a model to predict the atmospheric dry deposition velocities of particles has been developed that is similar to a model developed for particle deposition in vertical pipes. The model uses a sigmoid curve to correlate nondimensional inertial deposition velocity (Vdi+) with dimensionless particle relaxation time (/tau+) and flow Reynolds number (Re). Vdi+ obtained from data collected in the atmosphere with particle size classifier system and a flat greased plate, Re, and /tau+ for particles between 1 and 100 μm diameter were fit with a sigmoid curve using the least square procedure to obtain coefficients for the sigmoid curve. Deposition velocities data for particles between 0.06 and 4 μm diameter developed by Sehmel-Hodgson model were used to introduce a Schmidt number (Sc) term to take care of Brownian diffusion. The atmospheric plate deposition velocity model is a function of Vst (Stokes settling velocity), V* (friction velocity), /tau+, Re, and Sc. Model application to 62 atmospheric data set revealed that: generated flux predictions agreed well with atmospheric measurements, and its performance is better than Sehmel-Hodgson model. By comparing the sigmoid curve coefficients developed for vertical pipe data with the coefficients developed for atmospheric data it is concluded that, the two types of deposition are similar when the effects of Re and /tau+ are properly considered. Sensitivity analysis for the model has revealed three distinct regions based on particle size. Of the three physical parameters (/tau+, Re, Sc) in the model, not more than two controls the deposition in any of the identified regions. The plate deposition model which is

  4. The Combined Use of Correlative and Mechanistic Species Distribution Models Benefits Low Conservation Status Species.

    PubMed

    Rougier, Thibaud; Lassalle, Géraldine; Drouineau, Hilaire; Dumoulin, Nicolas; Faure, Thierry; Deffuant, Guillaume; Rochard, Eric; Lambert, Patrick

    2015-01-01

    Species can respond to climate change by tracking appropriate environmental conditions in space, resulting in a range shift. Species Distribution Models (SDMs) can help forecast such range shift responses. For few species, both correlative and mechanistic SDMs were built, but allis shad (Alosa alosa), an endangered anadromous fish species, is one of them. The main purpose of this study was to provide a framework for joint analyses of correlative and mechanistic SDMs projections in order to strengthen conservation measures for species of conservation concern. Guidelines for joint representation and subsequent interpretation of models outputs were defined and applied. The present joint analysis was based on the novel mechanistic model GR3D (Global Repositioning Dynamics of Diadromous fish Distribution) which was parameterized on allis shad and then used to predict its future distribution along the European Atlantic coast under different climate change scenarios (RCP 4.5 and RCP 8.5). We then used a correlative SDM for this species to forecast its distribution across the same geographic area and under the same climate change scenarios. First, projections from correlative and mechanistic models provided congruent trends in probability of habitat suitability and population dynamics. This agreement was preferentially interpreted as referring to the species vulnerability to climate change. Climate change could not be accordingly listed as a major threat for allis shad. The congruence in predicted range limits between SDMs projections was the next point of interest. The difference, when noticed, required to deepen our understanding of the niche modelled by each approach. In this respect, the relative position of the northern range limit between the two methods strongly suggested here that a key biological process related to intraspecific variability was potentially lacking in the mechanistic SDM. Based on our knowledge, we hypothesized that local adaptations to cold

  5. The Combined Use of Correlative and Mechanistic Species Distribution Models Benefits Low Conservation Status Species

    PubMed Central

    Rougier, Thibaud; Lassalle, Géraldine; Drouineau, Hilaire; Dumoulin, Nicolas; Faure, Thierry; Deffuant, Guillaume; Rochard, Eric; Lambert, Patrick

    2015-01-01

    Species can respond to climate change by tracking appropriate environmental conditions in space, resulting in a range shift. Species Distribution Models (SDMs) can help forecast such range shift responses. For few species, both correlative and mechanistic SDMs were built, but allis shad (Alosa alosa), an endangered anadromous fish species, is one of them. The main purpose of this study was to provide a framework for joint analyses of correlative and mechanistic SDMs projections in order to strengthen conservation measures for species of conservation concern. Guidelines for joint representation and subsequent interpretation of models outputs were defined and applied. The present joint analysis was based on the novel mechanistic model GR3D (Global Repositioning Dynamics of Diadromous fish Distribution) which was parameterized on allis shad and then used to predict its future distribution along the European Atlantic coast under different climate change scenarios (RCP 4.5 and RCP 8.5). We then used a correlative SDM for this species to forecast its distribution across the same geographic area and under the same climate change scenarios. First, projections from correlative and mechanistic models provided congruent trends in probability of habitat suitability and population dynamics. This agreement was preferentially interpreted as referring to the species vulnerability to climate change. Climate change could not be accordingly listed as a major threat for allis shad. The congruence in predicted range limits between SDMs projections was the next point of interest. The difference, when noticed, required to deepen our understanding of the niche modelled by each approach. In this respect, the relative position of the northern range limit between the two methods strongly suggested here that a key biological process related to intraspecific variability was potentially lacking in the mechanistic SDM. Based on our knowledge, we hypothesized that local adaptations to cold

  6. Gemstone deposits of Serbia

    NASA Astrophysics Data System (ADS)

    Miladinović, Zoran; Simić, Vladimir; Jelenković, Rade; Ilić, Miloje

    2016-06-01

    Gemstone minerals in Serbia have never been regarded as an interesting and significant resource. Nevertheless, more than 150 deposits and occurrences have been recorded and some of them preliminarily explored in the last 50 years. The majority of deposits and occurrences are located within the Serbo-Macedonian metallogenic province and the most significant metallogenic units at the existing level of knowledge are the Fruska Gora ore district, Cer ore district, Sumadija metallogenic zone, Kopaonik metallogenic zone and Lece-Halkidiki metallogenic zone. The most important genetic type of deposits is hydrothermal, particularly in case of serpentinite/peridotite as host/parent rock. Placer deposits are also economically important. The dominant gemstones are silica minerals: chalcedony (Chrysoprase, carnelian, bluish chalcedony etc.), jasper (picture, landscape, red etc.), common opal (dendritic, green, milky white etc.), silica masses (undivided), and quartz (rock crystal, amethyst etc.). Beside silica minerals significant gemstones in Serbia include also beryl (aquamarine), garnet (almandine and pyrope), tourmaline, fluorite, rhodochrosite, carbonate-silica breccia, carbonate-silica onyx, silicified wood, howlite, serpentinite, marble onyx, and kyanite. This paper aims to present an overview of Serbian gemstone deposits and occurrences and their position based on a simplified gemstone metallogenic map of Serbia, as well as genetic-industrial classification of gemstone deposits and gemstone varieties.

  7. Universal Cluster Deposition System

    NASA Astrophysics Data System (ADS)

    Qiang, You; Sun, Zhiguang; Sellmyer, David J.

    2001-03-01

    We have developed a universal cluster deposition system (UCDS), which combines a new kind of sputtering-gas-aggregation (SGA) cluster beam source with two atom beams from magnetron sputtering. A highly intense, very stable beam of nanoclusters (like Co, Fe, Ni, Si, CoSm or CoPt) are produced. A quadrupole and/or a new high transmission infinite range mass selector have been designed for the cluster beam. The size distribution (Δd/d) is between 0.05+/-0.10, measured in situ by TOF. A range of mean cluster size is 2 to 10 nm. Usually the deposition rate is about 5 deg/s. The cluster concentration in the film is adjusted through the ratio of cluster and atomic beam deposition rates, as measured in situ with a rotatable quartz microbalance. The UCDS can be used to prepare coated clusters. After exiting from the cluster source, the clusters can be coated first with an atomic or molecular species in an evaporation chamber, and deposited alone or co-deposited with another material. This system is used to deposit simultaneously or alternately mesoscopic thin films or multilayers, and offers the possibility to control independently the incident cluster size and concentration, and thereby the interaction between clusters and cluster-matrix material which is of interest for fundamental research and industry applications. Magnetic properties of Co cluster-assembled materials will be discussed. * Research supported by NSF, DARPA through ARO, and CMRA

  8. Modelling airborne concentration and deposition rate of maize pollen

    NASA Astrophysics Data System (ADS)

    Jarosz, Nathalie; Loubet, Benjamin; Huber, Laurent

    2004-10-01

    The introduction of genetically modified (GM) crops has reinforced the need to quantify gene flow from crop to crop. This requires predictive tools which take into account meteorological conditions, canopy structure as well as pollen aerodynamic characteristics. A Lagrangian Stochastic (LS) model, called SMOP-2D (Stochastic Mechanistic model for Pollen dispersion and deposition in 2 Dimensions), is presented. It simulates wind dispersion of pollen by calculating individual pollen trajectories from their emission to their deposition. SMOP-2D was validated using two field experiments where airborne concentration and deposition rate of pollen were measured within and downwind from different sized maize (Zea mays) plots together with micrometeorological measurements. SMOP-2D correctly simulated the shapes of the concentration profiles but generally underestimated the deposition rates in the first 10 m downwind from the source. Potential explanations of this discrepancy are discussed. Incorrect parameterisation of turbulence in the transition from the crop to the surroundings is probably the most likely reason. This demonstrates that LS models for particle transfer need to be coupled with air-flow models under complex terrain conditions.

  9. Becquerel Crater Deposit

    NASA Technical Reports Server (NTRS)

    2002-01-01

    (Released 28 May 2002) The finely layered deposit in Becquerel crater, seen in the center of this THEMIS image, is slowly being eroded away by the action of windblown sand. Dark sand from a source north of the bright deposit is collecting along its northern edge, forming impressive barchan style dunes. These vaguely boomerang-shaped dunes form with their two points extending in the downwind direction, demonstrating that the winds capable of moving sand grains come from the north. Grains that leave the dunes climb the eroding stair-stepped layers, collecting along the cliff faces before reaching the crest of the deposit. Once there, the sand grains are unimpeded and continue down the south side of the deposit without any significant accumulation until they fall off the steep cliffs of the southern margin. The boat-hull shaped mounds and ridges of bright material called yardangs form in response to the scouring action of the migrating sand. To the west, the deposit has thinned enough that the barchan dunes extend well into the deeply eroded north-south trending canyons. Sand that reaches the south side collects and reforms barchan dunes with the same orientation as those on the north side of the deposit. Note the abrupt transition between the bright material and the dark crater floor on the southern margin. Steep cliffs are present with no indication of rubble from the obvious erosion that produced them. The lack of debris at the base of the cliffs is evidence that the bright material is readily broken up into particles that can be transported away by the wind. The geological processes that are destroying the Becquerel crater deposit appear active today. But it is also possible that they are dormant, awaiting a particular set of climatic conditions that produces the right winds and perhaps even temperatures to allow the erosion to continue.

  10. Vacuum arc deposition devices

    SciTech Connect

    Boxman, R.L.; Zhitomirsky, V.N.

    2006-02-15

    The vacuum arc is a high-current, low-voltage electrical discharge which produces a plasma consisting of vaporized and ionized electrode material. In the most common cathodic arc deposition systems, the arc concentrates at minute cathode spots on the cathode surface and the plasma is emitted as a hypersonic jet, with some degree of contamination by molten droplets [known as macroparticles (MPs)] of the cathode material. In vacuum arc deposition systems, the location and motion of the cathode spots are confined to desired surfaces by an applied magnetic field and shields around undesired surfaces. Substrates are mounted on a holder so that they intercept some portion of the plasma jet. The substrate often provides for negative bias to control the energy of depositing ions and heating or cooling to control the substrate temperature. In some systems, a magnetic field is used to guide the plasma around an obstacle which blocks the MPs. These elements are integrated with a deposition chamber, cooling, vacuum gauges and pumps, and power supplies to produce a vacuum arc deposition system.

  11. Pulsed laser deposition: Prospects for commercial deposition of epitaxial films

    SciTech Connect

    Muenchausen, R.E.

    1999-03-01

    Pulsed laser deposition (PLD) is a physical vapor deposition (PVD) technique for the deposition of thin films. The vapor source is induced by the flash evaporation that occurs when a laser pulse of sufficient intensity (about 100 MW/cm{sup 2}) is absorbed by a target. In this paper the author briefly defines pulsed laser deposition, current applications, research directed at gaining a better understanding of the pulsed laser deposition process, and suggests some future directions to enable commercial applications.

  12. An analytical model for particulate deposition on vertical heat transfer surfaces in a boiling environment

    SciTech Connect

    Keefer, R.H.; Rider, J.L.; Waldman, L.A.

    1993-10-01

    A frequent problem in heat exchange equipment is the deposition of particulates entrained in the working fluid onto heat transfer surfaces. These deposits increase the overall heat transfer resistance and can significantly degrade the performance of the heat exchanger. Accurate prediction of the deposition rate is necessary to ensure that the design and specified operating conditions of the heat exchanger adequately address the effects of this deposit layer. Although the deposition process has been studied in considerable detail, much of the work has focused on investigating individual aspects of the deposition process. This paper consolidates this previous research into a mechanistically based analytical prediction model for particulate deposition from a boiling liquid onto vertical heat transfer surfaces. Consistent with the well known Kern-Seaton approach, the model postulates net particulate accumulation to depend on the relative contributions of deposition and reentrainment processes. Mechanisms for deposition include boiling, momentum, and diffusion effects. Reentrainment is presumed to occur via an intermittent erosion process, with the energy for particle removal being supplied by turbulent flow instabilities. The contributions of these individual mechanisms are integrated to obtain a single equation for the deposit thickness versus time. The validity of the resulting model is demonstrated by comparison with data published in the open literature. Model estimates show good agreement with data obtained over a range of thermal-hydraulic conditions in both flow and pool boiling environments. The utility of the model in performing parametric studies (e.g. to determine the effect of flow velocity on net deposition) is also demonstrated. The initial success of the model suggests that it could prove useful in establishing a range of heat exchanger. operating conditions to minimize deposition.

  13. Venus - Landslide Deposits

    NASA Technical Reports Server (NTRS)

    1992-01-01

    The Magellan spacecraft has observed remnant landslide deposits apparently resulting from the collapse of volcanic structures. This image, centered at 45.2 degrees south latitude, 201.4 degrees east longitude, shows a collapse deposit 70 kilometers (43 miles) across. The bright, highly textured deposit near the center of the image probably consists of huge blocks of fractured volcanic rock, many as large as several hundred meters across. A remnant of the volcano itself, about 20 kilometers (12.4 miles) across, is seen at the center of the image. The distorted radar appearance of the volcano is a result of extremely steep slopes on the 'scars' from which the landslide material originated. A field of numerous small volcanic domes can be seen in the northern half of the image. The bright irregular lineaments trending to the north-northwest are ridges caused by regional tectonic deformation of the upper layers of the Venusian crust.

  14. Turbine Airfoil Deposition Models

    NASA Technical Reports Server (NTRS)

    Rosner, D. E.

    1984-01-01

    Gas turbine failures associated with sea-salt ingestion and sulfur-containing fuel impurities have directed attention to alkali sulfate deposition and the associated hot corrosion of gas turbine (GT) blades under some GT operating conditions. These salt deposits form thin, molten films which undermine the protective metal oxide coating normally found on GT blades. The prediction of molten salt deposition, flow and oxide dissolution, and their effects on the lifetime of turbine blades are examined. Goals include rationalizing and helping to predict corrosion patterns on operational GT rotor blades and stators, and ultimately providing some of the tools required to design laboratory simulators and future corrosion-resistant high-performance engines. Necessary background developments are reviewed first, and then recent results and tentative conclusions are presented along with a brief account of the present research plans.

  15. Transcutaneous delivery of leflunomide nanoemulgel: Mechanistic investigation into physicomechanical characteristics, in vitro anti-psoriatic and anti-melanoma activity.

    PubMed

    Pund, Swati; Pawar, Satish; Gangurde, Shashikant; Divate, Deepali

    2015-06-20

    The present study is a mechanistic validation of 'proof of concept' of effective topical delivery of leflunomide (LFD) nanoemulgel for localized efficient treatment of psoriatic lesions as well as melanoma affected skin regions. Hyperproliferation of keratinocytes in psoriasis and symbiotic relationship between keratinocytes and melanocytes, justifies the need of dual acting treatment. LFD is recently introduced significantly effective disease modifying anti-rheumatic drug and has been considered valuable for the treatment of psoriatic arthritis as well as melanoma. Current available treatments for psoriasis and melanoma are inefficient due to systemic side effects, poor transcutaneous permeation and thus present a challenge for development of novel colloidal carriers. We newly reformulated LFD as a nanoemulgel based on self nanoemulsifying technique using Capryol 90, Cremophor EL, Transcutol HP as nanoemulsifying components and Pluronic F127 as a gelling agent. This thermodynamically stable nanoemuslsifying preconcentrate after gelation showed mean globule size, 123.7 nm and viscosity 9620 ± 93 cp. Complete mechanical characterization was carried out using Texture Analyzer and hardness, adhesiveness and springiness index were found to be 523 gms, 431 gms and 1.02, respectively. Ex vivo permeation through rat abdominal skin revealed significant improvement in flux, apparent permeability coefficient, steady state diffusion coefficient and drug deposition in skin due to nanoemulsification of LFD. The in vitro cytoxicity of LFD nanoemulgel in human HaCaT, melanoma A375 and SK-MEL-2 cell lines showed significantly enhanced therapeutic response. In gist, LFD nanoemulgel for trancutaneous delivery will reduce the overall dose and drug consumption, by effectively localizing at the applied target site and will ultimately minimize systemic side effects. PMID:25869452

  16. A Mechanistic study of Plasma Treatment Effects on Demineralized Dentin Surfaces for Improved Adhesive/Dentin Interface Bonding

    PubMed Central

    Dong, Xiaoqing; Chen, Meng; Wang, Yong; Yu, Qingsong

    2014-01-01

    Our previous work has shown that non-thermal plasma treatment of demineralized dentin significantly (p<0.05) improved adhesive/dentin bonding strength for dental composite restoration as compared with the untreated controls. This study is to achieve mechanistic understanding of the plasma treatment effects on dentin surface through investigating the plasma treated dentin surfaces and their interaction with adhesive monomer, 2-Hydroxyethyl methacrylate (HEMA). The plasma treated dentin surfaces from human third molars were evaluated by water contact angle measurements and scanning electron microscopy (SEM). It was found that plasma-treated dentin surface with subsequent HEMA immersion (Plasma/HEMA Treated) had much lower water contact angle compared with only plasma-treated (Plasma Treated) or only HEMA immersed (HEMA Treated) dentin surfaces. With prolong water droplet deposition time, water droplets spread out completely on the Plasma/HEMA Treated dentin surfaces. SEM images of Plasma/HEMA Treated dentin surfaces verified that dentin tubules were opened-up and filled with HEMA monomers. Extracted type I collagen fibrils, which was used as simulation of the exposed dentinal collagen fibrils after acid etching step, were plasma treated and analyzed with Fourier transform infrared spectroscopy (FT-IR) and circular dichroism (CD) spectra. FT-IR spectra of the Plasma/HEMA Treated collage fibrils showed broadened amide I peak at 1660 cm−1 and amide II at 1550 cm−1, which indicate secondary structure changes of the collagen fibrils. CD spectra indicated that 67.4% collagen helix structures were denatured after plasma treatment. These experimental results demonstrate that non-thermal argon plasma treatment was very effective in loosing collagen structure and enhancing adhesive monomer penetration, which are beneficial to thicker hybrid layer and longer resin tag formation, and consequently enhance adhesive/dentin interface bonding. PMID:25267936

  17. Mechanistic Evaluation of LixOy Formation on δ-MnO2 in Nonaqueous Li-Air Batteries.

    PubMed

    Liu, Zhixiao; De Jesus, Luis R; Banerjee, Sarbajit; Mukherjee, Partha P

    2016-09-01

    Transition metal oxides are usually used as catalysts in the air cathode of lithium-air (Li-air) batteries. This study elucidates the mechanistic origin of the oxygen reduction reaction catalyzed by δ-MnO2 monolayers and maps the conditions for Li2O2 growth using a combination of first-principles calculations and mesoscale modeling. The MnO2 monolayer, in the absence of an applied potential, preferentially reacts with a Li atom instead of an O2 molecule to initiate the formation of LiO2. The oxygen reduction products (LiO2, Li2O2, and Li2O molecules) strongly interact with the MnO2 monolayer via the stabilization of Li-O chemical bonds with lattice oxygen atoms. As compared to the disproportionation reaction, direct lithiation reactions are the primary contributors to the stabilization of Li2O2 on the MnO2 monolayer. The energy profiles of (Li2O2)2 and (Li2O)2 nucleation on δ-MnO2 monolayer during the discharge process demonstrate that Li2O2 is the predominant discharge product and that further reduction to Li2O is inhibited by the high overpotential of 1.21 V. Interface structures have been examined to study the interaction between the Li2O2 and MnO2 layers. This study demonstrates that a Li2O2 film can be homogeneously deposited onto δ-MnO2 and that the Li2O2/MnO2 interface acts as an electrical conductor. A mesoscale model, developed based on findings from the first-principles calculations, further shows that Li2O2 is the primary product of electrochemical reactions when the applied potential is smaller than 2.4 V. PMID:27532334

  18. Laser assisted deposition

    NASA Technical Reports Server (NTRS)

    Dutta, S.

    1983-01-01

    Applications of laser-based processing techniques to solar cell metallization are discussed. Laser-assisted thermal or photolytic maskless deposition from organometallic vapors or solutions may provide a viable alternative to photovoltaic metallization systems currently in use. High power, defocused excimer lasers may be used in conjunction with masks as an alternative to direct laser writing to provide higher throughput. Repeated pulsing with excimer lasers may eliminate the need for secondary plating techniques for metal film buildup. A comparison between the thermal and photochemical deposition processes is made.

  19. Mechanistic exploration of a bi-directional PDT-based combination in pancreatic cancer (Conference Presentation)

    NASA Astrophysics Data System (ADS)

    Huang, Huang-Chiao; Mallidi, Srivalleesha; Liu, Joyce; Chiang, Chun-Te; Mai, Zhiming; Goldschmidt, Ruth; Rizvi, Imran; Ebrahim-Zadeh, Neema; Hasan, Tayyaba

    2016-03-01

    It is increasingly evident that the most effective cancer treatments will involve interactive regimens that target multiple non-overlapping pathways, preferably such that each component enhances the others to improve outcomes while minimizing systemic toxicities. Toward this goal, we developed a combination of photodynamic therapy and irinotecan, which mechanistically cooperate with each other, beyond their individual tumor destruction pathways, to cause synergistic reduction in orthotopic pancreatic tumor burden. A three-way mechanistic basis of the observed the synergism will be discussed: (i) PDT downregulates drug efflux transporters to increase intracellular irinotecan levels. (ii) Irinotecan reduces the expression of hypoxia-induced marker, which is upregulated by PDT. (iii) PDT downregulates irinotecan-induced survivin expression to amplify the apoptotic and anti-proliferative effects. The clinical translation potential of the combination will also be highlighted.

  20. Mechanistic determinants of the directionality and energetics of active export by a heterodimeric ABC transporter

    NASA Astrophysics Data System (ADS)

    Grossmann, Nina; Vakkasoglu, Ahmet S.; Hulpke, Sabine; Abele, Rupert; Gaudet, Rachelle; Tampé, Robert

    2014-11-01

    The ATP-binding cassette (ABC) transporter associated with antigen processing (TAP) participates in immune surveillance by moving proteasomal products into the endoplasmic reticulum (ER) lumen for major histocompatibility complex class I loading and cell surface presentation to cytotoxic T cells. Here we delineate the mechanistic basis for antigen translocation. Notably, TAP works as a molecular diode, translocating peptide substrates against the gradient in a strict unidirectional way. We reveal the importance of the D-loop at the dimer interface of the two nucleotide-binding domains (NBDs) in coupling substrate translocation with ATP hydrolysis and defining transport vectoriality. Substitution of the conserved aspartate, which coordinates the ATP-binding site, decreases NBD dimerization affinity and turns the unidirectional primary active pump into a passive bidirectional nucleotide-gated facilitator. Thus, ATP hydrolysis is not required for translocation per se, but is essential for both active and unidirectional transport. Our data provide detailed mechanistic insight into how heterodimeric ABC exporters operate.

  1. A data-intensive approach to mechanistic elucidation applied to chiral anion catalysis

    PubMed Central

    Milo, Anat; Neel, Andrew J.; Toste, F. Dean; Sigman, Matthew S.

    2015-01-01

    Knowledge of chemical reaction mechanisms can facilitate catalyst optimization, but extracting that knowledge from a complex system is often challenging. Here we present a data-intensive method for deriving and then predictively applying a mechanistic model of an enantioselective organic reaction. As a validating case study, we selected an intramolecular dehydrogenative C-N coupling reaction, catalyzed by chiral phosphoric acid derivatives, in which catalyst-substrate association involves weak, non-covalent interactions. Little was previously understood regarding the structural origin of enantioselectivity in this system. Catalyst and substrate substituent effects were probed by systematic physical organic trend analysis. Plausible interactions between the substrate and catalyst that govern enantioselectivity were identified and supported experimentally, indicating that such an approach can afford an efficient means of leveraging mechanistic insight to optimize catalyst design. PMID:25678656

  2. Mechanistic modelling of cancer: some reflections from software engineering and philosophy of science.

    PubMed

    Cañete-Valdeón, José M; Wieringa, Roel; Smallbone, Kieran

    2012-12-01

    There is a growing interest in mathematical mechanistic modelling as a promising strategy for understanding tumour progression. This approach is accompanied by a methodological change of making research, in which models help to actively generate hypotheses instead of waiting for general principles to become apparent once sufficient data are accumulated. This paper applies recent research from philosophy of science to uncover three important problems of mechanistic modelling which may compromise its mainstream application, namely: the dilemma of formal and informal descriptions, the need to express degrees of confidence and the need of an argumentation framework. We report experience and research on similar problems from software engineering and provide evidence that the solutions adopted there can be transferred to the biological domain. We hope this paper can provoke new opportunities for further and profitable interdisciplinary research in the field. PMID:23149931

  3. Mechanistic modelling of cancer: some reflections from software engineering and philosophy of science

    NASA Astrophysics Data System (ADS)

    Cañete-Valdeón, José M.; Wieringa, Roel; Smallbone, Kieran

    2012-12-01

    There is a growing interest in mathematical mechanistic modelling as a promising strategy for understanding tumour progression. This approach is accompanied by a methodological change of making research, in which models help to actively generate hypotheses instead of waiting for general principles to become apparent once sufficient data are accumulated. This paper applies recent research from philosophy of science to uncover three important problems of mechanistic modelling which may compromise its mainstream application, namely: the dilemma of formal and informal descriptions, the need to express degrees of confidence and the need of an argumentation framework. We report experience and research on similar problems from software engineering and provide evidence that the solutions adopted there can be transferred to the biological domain. We hope this paper can provoke new opportunities for further and profitable interdisciplinary research in the field.

  4. Aortic Binding of AZD5248: Mechanistic Insight and Reactivity Assays To Support Lead Optimzation.

    PubMed

    Bragg, Ryan A; Brocklehurst, Simon; Gustafsson, Frida; Goodman, James; Hickling, Kevin; MacFaul, Philip A; Swallow, Steve; Tugwood, Jonathan

    2015-10-19

    The oral dipeptidyl peptidase 1 (DPP1) inhibitor AZD5248 showed aortic binding in a rat quantitative whole-body autoradiography (QWBA) study, and its development was terminated prior to human dosing. A mechanistic hypothesis for this finding was established invoking reactivity with aldehydes involved in the cross-linking of elastin, a major component of aortic tissue. This was tested by developing a simple aldehyde chemical reactivity assay and a novel in vitro competitive covalent binding assay. Results obtained with AZD5248, literature compounds, and close analogues of AZD5248 support the mechanistic hypothesis and provide validation for the use of these assays in a two tier screening approach to support lead optimization. The strengths and limitations of these assays are discussed. PMID:26351880

  5. Synthesis, cytotoxicity and mechanistic evaluation of 4-oxoquinoline-3-carboxamide derivatives: finding new potential anticancer drugs.

    PubMed

    Forezi, Luana da S M; Tolentino, Nathalia M C; de Souza, Alessandra M T; Castro, Helena C; Montenegro, Raquel C; Dantas, Rafael F; Oliveira, Maria E I M; Silva, Floriano P; Barreto, Leilane H; Burbano, Rommel M R; Abrahim-Vieira, Bárbara; de Oliveira, Riethe; Ferreira, Vitor F; Cunha, Anna C; Boechat, Fernanda da C S; de Souza, Maria Cecília B V

    2014-01-01

    As part of a continuing search for new potential anticancer candidates, we describe the synthesis, cytotoxicity and mechanistic evaluation of a series of 4-oxoquinoline-3-carboxamide derivatives as novel anticancer agents. The inhibitory activity of compounds 10-18 was determined against three cancer cell lines using the MTT colorimetric assay. The screening revealed that derivatives 16b and 17b exhibited significant cytotoxic activity against the gastric cancer cell line but was not active against a normal cell line, in contrast to doxorubicin, a standard chemotherapeutic drug in clinical use. Interestingly, no hemolytical activity was observed when the toxicity of 16b and 17b was tested against blood cells. The in silico and in vitro mechanistic evaluation indicated the potential of 16b as a lead for the development of novel anticancer agents against gastric cancer cells. PMID:24858098

  6. Mechanistic basis of resistance to PCBs in Atlantic tomcod from the Hudson River.

    PubMed

    Wirgin, Isaac; Roy, Nirmal K; Loftus, Matthew; Chambers, R Christopher; Franks, Diana G; Hahn, Mark E

    2011-03-11

    The mechanistic basis of resistance of vertebrate populations to contaminants, including Atlantic tomcod from the Hudson River (HR) to polychlorinated biphenyls (PCBs), is unknown. HR tomcod exhibited variants in the aryl hydrocarbon receptor 2 (AHR2) that were nearly absent elsewhere. In ligand-binding assays, AHR2-1 protein (common in the HR) was impaired as compared to widespread AHR2-2 in binding TCDD (2,3,7,8-tetrachlorodibenzo-p-dioxin) and in driving expression in reporter gene assays in AHR-deficient cells treated with TCDD or PCB126. We identified a six-base deletion in AHR2 as the basis of resistance and suggest that the HR population has undergone rapid evolution, probably due to contaminant exposure. This mechanistic basis of resistance in a vertebrate population provides evidence of evolutionary change due to selective pressure at a single locus. PMID:21330491

  7. Formalising a mechanistic linkage between heterotrophic feeding and thermal bleaching resistance

    NASA Astrophysics Data System (ADS)

    Wooldridge, Scott A.

    2014-12-01

    In this paper, I utilise the CO2 (sink) limitation model of coral bleaching to propose a new biochemical framework that explains how certain (well-adapted) coral species can utilise heterotrophic carbon acquisition to combat the damaging algal photoinhibition response sequence that underpins thermal bleaching, thereby increasing thermal bleaching resistance. This mechanistic linkage helps to clarify a number of previously challenging experimental responses arising from feeding (versus starved) temperature stress experiments, and isotope labelling (tracer) experiments with heterotrophic carbon sources (e.g., zooplankton). In an era of rapidly warming surface ocean temperatures, the conferred fitness benefits arising from such a mechanistic linkage are considerable. Yet, various ecological constraints are outlined which caution against the ultimate benefit of the mechanism for raising bleaching thresholds at the coral community (reef) scale. Future experiments are suggested that can strengthen these proposed arguments.

  8. Substrate inhibition in the heterogeneous catalyzed aldol condensation: A mechanistic study of supported organocatalysts

    SciTech Connect

    Kandel, Kapil; Althaus, Stacey M.; Peeraphatdit, Chorthip; Kobayashi, Takeshi; Trewyn, Brian G.; Pruski, Marek; Slowing, Igor I.

    2012-05-23

    In this study, we demonstrate how materials science can be combined with the established methods of organic chemistry to find mechanistic bottlenecks and redesign heterogeneous catalysts for improved performance. By using solid-state NMR, infrared spectroscopy, surface and kinetic analysis, we prove the existence of a substrate inhibition in the aldol condensation catalyzed by heterogeneous amines. We show that modifying the structure of the supported amines according to the proposed mechanism dramatically enhances the activity of the heterogeneous catalyst. We also provide evidence that the reaction benefits significantly from the surface chemistry of the silica support, which plays the role of a co-catalyst, giving activities up to two orders of magnitude larger than those of homogeneous amines. This study confirms that the optimization of a heterogeneous catalyst depends as much on obtaining organic mechanistic information as it does on controlling the structure of the support.

  9. Conceptual models for waste tank mechanistic analysis. Status report, January 1991

    SciTech Connect

    Allemann, R. T.; Antoniak, Z. I.; Eyler, L. L.; Liljegren, L. M.; Roberts, J. S.

    1992-02-01

    Pacific Northwest Laboratory (PNL) is conducting a study for Westinghouse Hanford Company (Westinghouse Hanford), a contractor for the US Department of Energy (DOE). The purpose of the work is to study possible mechanisms and fluid dynamics contributing to the periodic release of gases from double-shell waste storage tanks at the Hanford Site in Richland, Washington. This interim report emphasizing the modeling work follows two other interim reports, Mechanistic Analysis of Double-Shell Tank Gas Release Progress Report -- November 1990 and Collection and Analysis of Existing Data for Waste Tank Mechanistic Analysis Progress Report -- December 1990, that emphasized data correlation and mechanisms. The approach in this study has been to assemble and compile data that are pertinent to the mechanisms, analyze the data, evaluate physical properties and parameters, evaluate hypothetical mechanisms, and develop mathematical models of mechanisms.

  10. Mineral deposit density; an update

    USGS Publications Warehouse

    Singer, Donald A.; Menzie, W. David; Sutphin, David M.; Mosier, Dan L.; Bliss, James D.; contributions to global mineral resource assessment research edited by Schulz, Klaus J.

    2001-01-01

    A robust method to estimate the number of undiscovered deposits is a form of mineral deposit model wherein numbers of deposits per unit area from well-explored regions are counted and the resulting frequency distribution is used either directly for an estimate or indirectly as a guideline in some other method. The 27 mineral deposit density estimates reported here for 13 different deposit types represent a start at compiling the estimates necessary to guide assessments.

  11. Data-driven mechanistic analysis method to reveal dynamically evolving regulatory networks

    PubMed Central

    Intosalmi, Jukka; Nousiainen, Kari; Ahlfors, Helena; Lähdesmäki, Harri

    2016-01-01

    Motivation: Mechanistic models based on ordinary differential equations provide powerful and accurate means to describe the dynamics of molecular machinery which orchestrates gene regulation. When combined with appropriate statistical techniques, mechanistic models can be calibrated using experimental data and, in many cases, also the model structure can be inferred from time–course measurements. However, existing mechanistic models are limited in the sense that they rely on the assumption of static network structure and cannot be applied when transient phenomena affect, or rewire, the network structure. In the context of gene regulatory network inference, network rewiring results from the net impact of possible unobserved transient phenomena such as changes in signaling pathway activities or epigenome, which are generally difficult, but important, to account for. Results: We introduce a novel method that can be used to infer dynamically evolving regulatory networks from time–course data. Our method is based on the notion that all mechanistic ordinary differential equation models can be coupled with a latent process that approximates the network structure rewiring process. We illustrate the performance of the method using simulated data and, further, we apply the method to study the regulatory interactions during T helper 17 (Th17) cell differentiation using time–course RNA sequencing data. The computational experiments with the real data show that our method is capable of capturing the experimentally verified rewiring effects of the core Th17 regulatory network. We predict Th17 lineage specific subnetworks that are activated sequentially and control the differentiation process in an overlapping manner. Availability and Implementation: An implementation of the method is available at http://research.ics.aalto.fi/csb/software/lem/. Contacts: jukka.intosalmi@aalto.fi or harri.lahdesmaki@aalto.fi PMID:27307629

  12. Studies on the interaction of isocyanides with imines: reaction scope and mechanistic variations.

    PubMed

    Ghashghaei, Ouldouz; Manna, Consiglia Annamaria; Vicente-García, Esther; Revés, Marc; Lavilla, Rodolfo

    2014-01-01

    The interaction of imines with isocyanides has been studied. The main product results from a sequential process involving the attack of two units of isocyanide, under Lewis acid catalysis, upon the carbon-nitrogen double bond of the imine to form the 4-membered ring system. The scope of the reaction regarding the imine and isocyanide ranges has been determined, and also some mechanistic variations and structural features have been described. PMID:24454559

  13. Mechanistic interrogation of the asymmetric lithiation-trapping of N-thiopivaloyl azetidine and pyrrolidine.

    PubMed

    Rayner, Peter J; Smith, Joshua C; Denneval, Charline; O'Brien, Peter; Clarke, Paul A; Horan, Richard A J

    2016-01-25

    A fundamental mechanistic study of the s-BuLi/chiral diamine-mediated lithiation-trapping of N-thiopivaloyl azetidine and pyrrolidine is reported. We show that lithiated thiopivalamides are configurationally unstable at -78 °C. Reaction then proceeds via a dynamic resolution of diastereomeric lithiated intermediates and this accounts for the variable sense and degree of asymmetric induction observed compared to N-Boc heterocycles. PMID:26620913

  14. Structural and Mechanistic Aspects of Copper Catalyzed Atom Transfer Radical Polymerization

    NASA Astrophysics Data System (ADS)

    Pintauer, Tomislav; Matyjaszewski, Krzysztof

    During the past decade, atom transfer radical polymerization (ATRP) has had a tremendous impact on the synthesis of macromolecules with well-defined compositions, architectures, and functionalities. Structural features of copper(I) and copper(II) complexes with bidentate, tridentate, tetradentate, and multidentate nitrogen-based ligands commonly utilized in ATRP are reviewed and discussed. Additionally, recent advances in mechanistic understanding of copper-mediated ATRP are outlined.

  15. Quantitative assessment of biological impact using transcriptomic data and mechanistic network models

    SciTech Connect

    Thomson, Ty M.; Sewer, Alain; Martin, Florian; Belcastro, Vincenzo; Frushour, Brian P.; Gebel, Stephan; Park, Jennifer; Schlage, Walter K.; Talikka, Marja; Vasilyev, Dmitry M.; Westra, Jurjen W.; Hoeng, Julia; Peitsch, Manuel C.

    2013-11-01

    Exposure to biologically active substances such as therapeutic drugs or environmental toxicants can impact biological systems at various levels, affecting individual molecules, signaling pathways, and overall cellular processes. The ability to derive mechanistic insights from the resulting system responses requires the integration of experimental measures with a priori knowledge about the system and the interacting molecules therein. We developed a novel systems biology-based methodology that leverages mechanistic network models and transcriptomic data to quantitatively assess the biological impact of exposures to active substances. Hierarchically organized network models were first constructed to provide a coherent framework for investigating the impact of exposures at the molecular, pathway and process levels. We then validated our methodology using novel and previously published experiments. For both in vitro systems with simple exposure and in vivo systems with complex exposures, our methodology was able to recapitulate known biological responses matching expected or measured phenotypes. In addition, the quantitative results were in agreement with experimental endpoint data for many of the mechanistic effects that were assessed, providing further objective confirmation of the approach. We conclude that our methodology evaluates the biological impact of exposures in an objective, systematic, and quantifiable manner, enabling the computation of a systems-wide and pan-mechanistic biological impact measure for a given active substance or mixture. Our results suggest that various fields of human disease research, from drug development to consumer product testing and environmental impact analysis, could benefit from using this methodology. - Highlights: • The impact of biologically active substances is quantified at multiple levels. • The systems-level impact integrates the perturbations of individual networks. • The networks capture the relationships between

  16. Studies on the interaction of isocyanides with imines: reaction scope and mechanistic variations

    PubMed Central

    Ghashghaei, Ouldouz; Manna, Consiglia Annamaria; Vicente-García, Esther; Revés, Marc

    2014-01-01

    Summary The interaction of imines with isocyanides has been studied. The main product results from a sequential process involving the attack of two units of isocyanide, under Lewis acid catalysis, upon the carbon–nitrogen double bond of the imine to form the 4-membered ring system. The scope of the reaction regarding the imine and isocyanide ranges has been determined, and also some mechanistic variations and structural features have been described. PMID:24454559

  17. Mechanistic Studies on Au(I)-Catalyzed [3,3]-Sigmatropic Rearrangements using Cyclopropane Probes

    PubMed Central

    Mauleón, Pablo; Krinsky, Jamin L.

    2009-01-01

    A comparative study of the Au(I)-catalyzed [3,3]-sigmatropic rearrangement of propargylic esters and propargyl vinyl ethers is described. Stereochemically defined cyclopropanes are employed as mechanistic probes to provide new synthetic and theoretical data concerning the reversibility of this type of rearrangement. Factors controlling the structure-reactivity relationship of Au(I)-coordinated allenes have been examined, thereby allowing for controlled access to orthogonal reactivity. PMID:19275228

  18. Mechanistic insights into the potassium tert-butoxide-mediated synthesis of N-heterobiaryls.

    PubMed

    Stephens, David E; Lakey-Beitia, Johant; Burch, Jessica E; Arman, Hadi D; Larionov, Oleg V

    2016-08-01

    We report herein that symmetrical and non-symmetrical N-heterobiaryls are produced by a potassium tert-butoxide-mediated dimerization of heterocyclic N-oxides. The reaction is scalable and transition metal-free, and can be carried out under thermal and microwave conditions. Preliminary mechanistic studies point to the involvement of radical anionic intermediates arising from the N-oxide substrates and potassium tert-butoxide. PMID:27440397

  19. Mechanistic insight into gramicidin-based detection of protein-ligand interactions via sensitized photoinactivation

    NASA Astrophysics Data System (ADS)

    Rokitskaya, Tatyana I.; Macrae, Michael X.; Blake, Steven; Egorova, Natalya S.; Kotova, Elena A.; Yang, Jerry; Antonenko, Yuri N.

    2010-11-01

    Among the many challenges for the development of ion channel-based sensors is the poor understanding of how to engineer modified transmembrane pores with tailored functionality that can respond to external stimuli. Here, we use the method of sensitized photoinactivation of gramicidin A (gA) channels in planar bilayer lipid membranes to help elucidate the underlying mechanistic details for changes in macroscopic transmembrane ionic current observed upon interaction of C-terminally attached gA ligands with specific proteins in solution. Three different systems were studied: (i) carbonic anhydrase (CA) and gA-sulfonamide, (ii) PSD-95 protein (belonging to the 'PDZ domain-containing protein') and a gA analog carrying the KGGHRRSARYLESSV peptide sequence at the C-terminus, and (iii) an anti-biotin antibody and gA-biotin. The results challenge a previously proposed mechanistic hypothesis suggesting that protein-induced current suppression is due to steric blockage of the ion passage through gA channels, while they reveal new insight for consideration in alternative mechanistic models. Additionally, we demonstrate that the length of a linker between the ligand and the gA channel may be less important for gramicidin-based detection of monovalent compared to multivalent protein-ligand interactions. These studies collectively shed new light on the mechanism of protein-induced current alterations in bilayer recordings of gA derivatives, which may be important in the design of new gramicidin-based sensors.

  20. Emergent Global Patterns of Ecosystem Structure and Function from a Mechanistic General Ecosystem Model

    PubMed Central

    Emmott, Stephen; Hutton, Jon; Lyutsarev, Vassily; Smith, Matthew J.; Scharlemann, Jörn P. W.; Purves, Drew W.

    2014-01-01

    Anthropogenic activities are causing widespread degradation of ecosystems worldwide, threatening the ecosystem services upon which all human life depends. Improved understanding of this degradation is urgently needed to improve avoidance and mitigation measures. One tool to assist these efforts is predictive models of ecosystem structure and function that are mechanistic: based on fundamental ecological principles. Here we present the first mechanistic General Ecosystem Model (GEM) of ecosystem structure and function that is both global and applies in all terrestrial and marine environments. Functional forms and parameter values were derived from the theoretical and empirical literature where possible. Simulations of the fate of all organisms with body masses between 10 µg and 150,000 kg (a range of 14 orders of magnitude) across the globe led to emergent properties at individual (e.g., growth rate), community (e.g., biomass turnover rates), ecosystem (e.g., trophic pyramids), and macroecological scales (e.g., global patterns of trophic structure) that are in general agreement with current data and theory. These properties emerged from our encoding of the biology of, and interactions among, individual organisms without any direct constraints on the properties themselves. Our results indicate that ecologists have gathered sufficient information to begin to build realistic, global, and mechanistic models of ecosystems, capable of predicting a diverse range of ecosystem properties and their response to human pressures. PMID:24756001

  1. Life in the balance - a mechanistic view of the crosstalk between autophagy and apoptosis.

    PubMed

    Rubinstein, Assaf D; Kimchi, Adi

    2012-11-15

    Cellular stress triggers a fascinating decision-making process in cells; they can either attempt to survive until the stress is resolved through the activation of cytoprotective pathways, such as autophagy, or can commit suicide by apoptosis in order to prevent further damage to surrounding healthy cells. Although autophagy and apoptosis constitute distinct cellular processes with often opposing outcomes, their signalling pathways are extensively interconnected through various mechanisms of crosstalk. The physiological relevance of the autophagy-apoptosis crosstalk is not well understood, but it is presumed to facilitate a controlled and well-balanced cellular response to a given stress signal. In this Commentary, we explore the various mechanisms by which autophagy and apoptosis regulate each other, and define general paradigms of crosstalk on the basis of mechanistic features. One paradigm relates to physical and functional interactions between pairs of specific apoptotic and autophagic proteins. In a second mechanistic paradigm, the apoptosis or autophagy processes (as opposed to individual proteins) regulate each other through induced caspase and autolysosomal activity, respectively. In a third paradigm unique to autophagy, caspases are recruited and activated on autophagosomal membranes. These mechanistic paradigms are discernible experimentally, and can therefore be used as a practical guide for the interpretation of experimental data. PMID:23377657

  2. Comparative evaluation of statistical and mechanistic models of Escherichia coli at beaches in southern Lake Michigan

    USGS Publications Warehouse

    Safaie, Ammar; Wendzel, Aaron; Ge, Zhongfu; Nevers, Meredith; Whitman, Richard L.; Corsi, Steven R.; Phanikumar, Mantha S.

    2016-01-01

    Statistical and mechanistic models are popular tools for predicting the levels of indicator bacteria at recreational beaches. Researchers tend to use one class of model or the other, and it is difficult to generalize statements about their relative performance due to differences in how the models are developed, tested, and used. We describe a cooperative modeling approach for freshwater beaches impacted by point sources in which insights derived from mechanistic modeling were used to further improve the statistical models and vice versa. The statistical models provided a basis for assessing the mechanistic models which were further improved using probability distributions to generate high-resolution time series data at the source, long-term “tracer” transport modeling based on observed electrical conductivity, better assimilation of meteorological data, and the use of unstructured-grids to better resolve nearshore features. This approach resulted in improved models of comparable performance for both classes including a parsimonious statistical model suitable for real-time predictions based on an easily measurable environmental variable (turbidity). The modeling approach outlined here can be used at other sites impacted by point sources and has the potential to improve water quality predictions resulting in more accurate estimates of beach closures.

  3. Mechanistic models of animal migration behaviour – their diversity, structure and use

    PubMed Central

    Bauer, Silke; Klaassen, Marcel

    2013-01-01

    Migration is a wide-spread phenomenon in the animal kingdom, including many taxonomic groups and modes of locomotion. Developing an understanding of the proximate and ultimate causes for this behaviour not only addresses fundamental ecological questions but has relevance to many other fields, e.g. in relation to the spread of emerging zoonotic diseases, the proliferation of invasive species, aeronautical safety as well as the conservation of migrants.Theoretical methods can make important contributions to our understanding of migration, by allowing us to integrate findings on this complex behaviour, identify caveats in our understanding and guide future empirical research efforts. Various mechanistic models exist to date but their applications seem to be scattered and far from evenly distributed across taxonomic units.Therefore, we provide an overview of the major mechanistic modelling approaches used in the study of migration behaviour and characterise their fundamental features, assumptions and limitations, and discuss their typical data requirements both for model parameterisation and for scrutinizing model predictions.Furthermore, we review 155 studies that have used mechanistic models to study animal migration and analyse them with regard to the approaches used, focal species and also explore their contribution of advancing current knowledge within six broad migration ecology research themes.This identifies important gaps in our present knowledge, which should be tackled in future research using existing and to-be developed theoretical approaches. PMID:23373515

  4. Mechanistic analytical models for long-distance seed dispersal by wind.

    PubMed

    Katul, G G; Porporato, A; Nathan, R; Siqueira, M; Soons, M B; Poggi, D; Horn, H S; Levin, S A

    2005-09-01

    We introduce an analytical model, the Wald analytical long-distance dispersal (WALD) model, for estimating dispersal kernels of wind-dispersed seeds and their escape probability from the canopy. The model is based on simplifications to well-established three-dimensional Lagrangian stochastic approaches for turbulent scalar transport resulting in a two-parameter Wald (or inverse Gaussian) distribution. Unlike commonly used phenomenological models, WALD's parameters can be estimated from the key factors affecting wind dispersal--wind statistics, seed release height, and seed terminal velocity--determined independently of dispersal data. WALD's asymptotic power-law tail has an exponent of -3/2, a limiting value verified by a meta-analysis for a wide variety of measured dispersal kernels and larger than the exponent of the bivariate Student t-test (2Dt). We tested WALD using three dispersal data sets on forest trees, heathland shrubs, and grassland forbs and compared WALD's performance with that of other analytical mechanistic models (revised versions of the tilted Gaussian Plume model and the advection-diffusion equation), revealing fairest agreement between WALD predictions and measurements. Analytical mechanistic models, such as WALD, combine the advantages of simplicity and mechanistic understanding and are valuable tools for modeling large-scale, long-term plant population dynamics. PMID:16224691

  5. Modeling systems-level dynamics: Understanding without mechanistic explanation in integrative systems biology.

    PubMed

    MacLeod, Miles; Nersessian, Nancy J

    2015-02-01

    In this paper we draw upon rich ethnographic data of two systems biology labs to explore the roles of explanation and understanding in large-scale systems modeling. We illustrate practices that depart from the goal of dynamic mechanistic explanation for the sake of more limited modeling goals. These processes use abstract mathematical formulations of bio-molecular interactions and data fitting techniques which we call top-down abstraction to trade away accurate mechanistic accounts of large-scale systems for specific information about aspects of those systems. We characterize these practices as pragmatic responses to the constraints many modelers of large-scale systems face, which in turn generate more limited pragmatic non-mechanistic forms of understanding of systems. These forms aim at knowledge of how to predict system responses in order to manipulate and control some aspects of them. We propose that this analysis of understanding provides a way to interpret what many systems biologists are aiming for in practice when they talk about the objective of a "systems-level understanding." PMID:25462871

  6. Comparative Evaluation of Statistical and Mechanistic Models of Escherichia coli at Beaches in Southern Lake Michigan.

    PubMed

    Safaie, Ammar; Wendzel, Aaron; Ge, Zhongfu; Nevers, Meredith B; Whitman, Richard L; Corsi, Steven R; Phanikumar, Mantha S

    2016-03-01

    Statistical and mechanistic models are popular tools for predicting the levels of indicator bacteria at recreational beaches. Researchers tend to use one class of model or the other, and it is difficult to generalize statements about their relative performance due to differences in how the models are developed, tested, and used. We describe a cooperative modeling approach for freshwater beaches impacted by point sources in which insights derived from mechanistic modeling were used to further improve the statistical models and vice versa. The statistical models provided a basis for assessing the mechanistic models which were further improved using probability distributions to generate high-resolution time series data at the source, long-term "tracer" transport modeling based on observed electrical conductivity, better assimilation of meteorological data, and the use of unstructured-grids to better resolve nearshore features. This approach resulted in improved models of comparable performance for both classes including a parsimonious statistical model suitable for real-time predictions based on an easily measurable environmental variable (turbidity). The modeling approach outlined here can be used at other sites impacted by point sources and has the potential to improve water quality predictions resulting in more accurate estimates of beach closures. PMID:26825142

  7. Mechanistic insight into gramicidin-based detection of protein-ligand interactions via sensitized photoinactivation.

    PubMed

    Rokitskaya, Tatyana I; Macrae, Michael X; Blake, Steven; Egorova, Natalya S; Kotova, Elena A; Yang, Jerry; Antonenko, Yuri N

    2010-11-17

    Among the many challenges for the development of ion channel-based sensors is the poor understanding of how to engineer modified transmembrane pores with tailored functionality that can respond to external stimuli. Here, we use the method of sensitized photoinactivation of gramicidin A (gA) channels in planar bilayer lipid membranes to help elucidate the underlying mechanistic details for changes in macroscopic transmembrane ionic current observed upon interaction of C-terminally attached gA ligands with specific proteins in solution. Three different systems were studied: (i) carbonic anhydrase (CA) and gA-sulfonamide, (ii) PSD-95 protein (belonging to the 'PDZ domain-containing protein') and a gA analog carrying the KGGHRRSARYLESSV peptide sequence at the C-terminus, and (iii) an anti-biotin antibody and gA-biotin. The results challenge a previously proposed mechanistic hypothesis suggesting that protein-induced current suppression is due to steric blockage of the ion passage through gA channels, while they reveal new insight for consideration in alternative mechanistic models. Additionally, we demonstrate that the length of a linker between the ligand and the gA channel may be less important for gramicidin-based detection of monovalent compared to multivalent protein-ligand interactions. These studies collectively shed new light on the mechanism of protein-induced current alterations in bilayer recordings of gA derivatives, which may be important in the design of new gramicidin-based sensors. PMID:21339605

  8. A reconciliation of empirical and mechanistic models of the air-sea gas transfer velocity

    NASA Astrophysics Data System (ADS)

    Goddijn-Murphy, Lonneke; Woolf, David K.; Callaghan, Adrian H.; Nightingale, Philip D.; Shutler, Jamie D.

    2016-01-01

    Models of the air-sea transfer velocity of gases may be either empirical or mechanistic. Extrapolations of empirical models to an unmeasured gas or to another water temperature can be erroneous if the basis of that extrapolation is flawed. This issue is readily demonstrated for the most well-known empirical gas transfer velocity models where the influence of bubble-mediated transfer, which can vary between gases, is not explicitly accounted for. Mechanistic models are hindered by an incomplete knowledge of the mechanisms of air-sea gas transfer. We describe a hybrid model that incorporates a simple mechanistic view—strictly enforcing a distinction between direct and bubble-mediated transfer—but also uses parameterizations based on data from eddy flux measurements of dimethyl sulphide (DMS) to calibrate the model together with dual tracer results to evaluate the model. This model underpins simple algorithms that can be easily applied within schemes to calculate local, regional, or global air-sea fluxes of gases.

  9. Mechanistic Modelling of DNA Repair and Cellular Survival Following Radiation-Induced DNA Damage.

    PubMed

    McMahon, Stephen J; Schuemann, Jan; Paganetti, Harald; Prise, Kevin M

    2016-01-01

    Characterising and predicting the effects of ionising radiation on cells remains challenging, with the lack of robust models of the underlying mechanism of radiation responses providing a significant limitation to the development of personalised radiotherapy. In this paper we present a mechanistic model of cellular response to radiation that incorporates the kinetics of different DNA repair processes, the spatial distribution of double strand breaks and the resulting probability and severity of misrepair. This model enables predictions to be made of a range of key biological endpoints (DNA repair kinetics, chromosome aberration and mutation formation, survival) across a range of cell types based on a set of 11 mechanistic fitting parameters that are common across all cells. Applying this model to cellular survival showed its capacity to stratify the radiosensitivity of cells based on aspects of their phenotype and experimental conditions such as cell cycle phase and plating delay (correlation between modelled and observed Mean Inactivation Doses R(2) > 0.9). By explicitly incorporating underlying mechanistic factors, this model can integrate knowledge from a wide range of biological studies to provide robust predictions and may act as a foundation for future calculations of individualised radiosensitivity. PMID:27624453

  10. Left ventricular partitioning in systolic heart failure subjects: addressing a mechanistic void with current therapies.

    PubMed

    Schäfer, Ulrich

    2016-05-17

    ICD patients with narrow QRS, CRT non-responders, and functional MR patients all have one mechanistic failure mode that is left untreated - the scar left behind following an MI. ICDs, CRTs, and MitraClip implantation are all well-proven therapies, but the Parachute device may address the mechanistic void that remains after each of these therapies has been used and may further improve patients' outcomes. A pooled analysis of 134 subjects was conducted using the first three clinical trials which included subjects with symptomatic ischaemic HF with LV wall motion abnormalities secondary to MI, and an LV ejection fraction less than 40%. The two-year cumulative mortality rate was 12.9%, with 8.7% in the first year and an increment of 4.2% in the second, which is a 53% reduction as compared to the first year. There is a significant proportion of patients with ischaemic heart failure being excluded from cardiac rhythm management (CRT, etc.), leaving a large treatment gap until mechanical support devices (LVAD) or heart transplantation in progressive heart failure are indicated. Along with other heart failure devices, Parachute may be a useful treatment modality, addressing a mechanistic void in the treatment of this disease. Current data support improvements in haemodynamics, functional capacity, six-minute walk distance, quality of life and a promising decline in mortality two years after Parachute implantation. PMID:27174122

  11. Integration of QSAR and SAR methods for the mechanistic interpretation of predictive models for carcinogenicity

    PubMed Central

    Fjodorova, Natalja; Novič, Marjana

    2012-01-01

    The knowledge-based Toxtree expert system (SAR approach) was integrated with the statistically based counter propagation artificial neural network (CP ANN) model (QSAR approach) to contribute to a better mechanistic understanding of a carcinogenicity model for non-congeneric chemicals using Dragon descriptors and carcinogenic potency for rats as a response. The transparency of the CP ANN algorithm was demonstrated using intrinsic mapping technique specifically Kohonen maps. Chemical structures were represented by Dragon descriptors that express the structural and electronic features of molecules such as their shape and electronic surrounding related to reactivity of molecules. It was illustrated how the descriptors are correlated with particular structural alerts (SAs) for carcinogenicity with recognized mechanistic link to carcinogenic activity. Moreover, the Kohonen mapping technique enables one to examine the separation of carcinogens and non-carcinogens (for rats) within a family of chemicals with a particular SA for carcinogenicity. The mechanistic interpretation of models is important for the evaluation of safety of chemicals. PMID:24688639

  12. "Total Deposition (TDEP) Maps"

    EPA Science Inventory

    The presentation provides an update on the use of a hybrid methodology that relies on measured values from national monitoring networks and modeled values from CMAQ to produce of maps of total deposition for use in critical loads and other ecological assessments. Additionally, c...

  13. Mechanistic models

    SciTech Connect

    Curtis, S.B.

    1990-09-01

    Several models and theories are reviewed that incorporate the idea of radiation-induced lesions (repairable and/or irreparable) that can be related to molecular lesions in the DNA molecule. Usually the DNA double-strand or chromatin break is suggested as the critical lesion. In the models, the shoulder on the low-LET survival curve is hypothesized as being due to one (or more) of the following three mechanisms: (1) ``interaction`` of lesions produced by statistically independent particle tracks; (2) nonlinear (i.e., linear-quadratic) increase in the yield of initial lesions, and (3) saturation of repair processes at high dose. Comparisons are made between the various approaches. Several significant advances in model development are discussed; in particular, a description of the matrix formulation of the Markov versions of the RMR and LPL models is given. The more advanced theories have incorporated statistical fluctuations in various aspects of the energy-loss and lesion-formation process. An important direction is the inclusion of physical and chemical processes into the formulations by incorporating relevant track structure theory (Monte Carlo track simulations) and chemical reactions of radiation-induced radicals. At the biological end, identification of repair genes and how they operate as well as a better understanding of how DNA misjoinings lead to lethal chromosome aberrations are needed for appropriate inclusion into the theories. More effort is necessary to model the complex end point of radiation-induced carcinogenesis.

  14. Mechanistic models

    SciTech Connect

    Curtis, S.B.

    1990-09-01

    Several models and theories are reviewed that incorporate the idea of radiation-induced lesions (repairable and/or irreparable) that can be related to molecular lesions in the DNA molecule. Usually the DNA double-strand or chromatin break is suggested as the critical lesion. In the models, the shoulder on the low-LET survival curve is hypothesized as being due to one (or more) of the following three mechanisms: (1) interaction'' of lesions produced by statistically independent particle tracks; (2) nonlinear (i.e., linear-quadratic) increase in the yield of initial lesions, and (3) saturation of repair processes at high dose. Comparisons are made between the various approaches. Several significant advances in model development are discussed; in particular, a description of the matrix formulation of the Markov versions of the RMR and LPL models is given. The more advanced theories have incorporated statistical fluctuations in various aspects of the energy-loss and lesion-formation process. An important direction is the inclusion of physical and chemical processes into the formulations by incorporating relevant track structure theory (Monte Carlo track simulations) and chemical reactions of radiation-induced radicals. At the biological end, identification of repair genes and how they operate as well as a better understanding of how DNA misjoinings lead to lethal chromosome aberrations are needed for appropriate inclusion into the theories. More effort is necessary to model the complex end point of radiation-induced carcinogenesis.

  15. Creep of chemically vapor deposited SiC fibers

    NASA Technical Reports Server (NTRS)

    Dicarlo, J. A.

    1984-01-01

    The creep, thermal expansion, and elastic modulus properties for chemically vapor deposited SiC fibers were measured between 1000 and 1500 C. Creep strain was observed to increase logarithmically with time, monotonically with temperature, and linearly with tensile stress up to 600 MPa. The controlling activation energy was 480 + or - 20 kJ/mole. Thermal pretreatments near 1200 and 1450 C were found to significantly reduce fiber creep. These results coupled with creep recovery observations indicate that below 1400 C fiber creep is anelastic with neglible plastic component. This allowed a simple predictive method to be developed for describing fiber total deformation as a function of time, temperature, and stress. Mechanistic analysis of the property data suggests that fiber creep is the result of beta-SiC grain boundary sliding controlled by a small percent of free silicon in the grain boundaries.

  16. An algorithm for estimating potential deposition of corn pollen for environmental assessment.

    PubMed

    Kawashima, Shigeto; Matsuo, Kazuhito; Du, Mingyuan; Takahashi, Yuichi; Inoue, Satoshi; Yonemura, Seiichiro

    2004-01-01

    The safety and impact on the environment of transgenic crops are important issues, and studies have shown that pollen from transgenic Bt (Bacillus thuringiensis) corn (Zea mays L.) may kill nontarget insects. To develop an algorithm for assessing the environmental effect of transgenic crops, we arranged a field experiment in Tsukuba, Japan. Pollen dispersal and deposition were measured inside and outside a cornfield throughout the flowering period. Weather conditions such as wind speed and direction were measured at the same time. Pollen dispersal peaked 1 week after the start of flowering and continued for 12 days thereafter. The variation in daily pollen dispersal was similar at all observation points. Both pollen dispersal and deposition decreased exponentially with distance from the cornfield on all days. We estimated potential pollen deposition with a quasi-mechanistic model that incorporates the effects of wind direction, wind speed, and flowering intensity. The daily potential deposition was summed over the flowering period, and then the relationship between distance from the cornfield and the integrated potential deposition was estimated. It was possible to show the effective area of the environmental risk zone posed by genetically modified pollen by combining the distance/deposition relationship with the dose/response relationship derived from a laboratory assay. The algorithm described here can be applied to various wind-pollinated plants to estimate both potential and integrated pollen deposition. PMID:16028796

  17. Electrochemically Deposited Ceria Structures for Advanced Solid Oxide Fuel Cells

    NASA Astrophysics Data System (ADS)

    Brown, Evan C.

    As the pursuit towards emissions reduction intensifies with growing interest and nascent technologies, solid oxide fuel cells (SOFCs) remain an illustrious candidate for achieving our goals. Despite myriad advantages, SOFCs are still too costly for widespread deployment, even as unprecedented materials developments have recently emerged. This suggests that, in addition to informed materials selection, the necessary power output--and, thereby, cost-savings--gains must come from the fuel cell architecture. The work presented in this manuscript primarily investigates cathodic electrochemical deposition (CELD) as a scalable micro-/nanoscale fabrication tool for engineering ceria-based components in a SOFC assembly. Also, polymer sphere lithography was utilized to deposit fully connected, yet fully porous anti-dot metal films on yttira-stabilized zirconia (YSZ) with specific and knowable geometries, useful for mechanistic studies. Particular attention was given to anode structures, for which anti-dot metal films on YSZ served as composite substrates for subsequent CELD of doped ceria. By tuning the applied potential, a wide range of microstructures from high surface area coatings to planar, thin films was possible. In addition, definitive deposition was shown to occur on the electronically insulating YSZ surfaces, producing quality YSZ|ceria interfaces. These CELD ceria deposits exhibited promising electrochemical activity, as probed by A.C. Impedance Spectroscopy. In an effort to extend its usefulness as a SOFC fabrication tool, the CELD of ceria directly onto common SOFC cathode materials without a metallic phase was developed, as well as templated deposition schemes producing ceria nanowires and inverse opals.

  18. Electrophoretic deposition of biomaterials

    PubMed Central

    Boccaccini, A. R.; Keim, S.; Ma, R.; Li, Y.; Zhitomirsky, I.

    2010-01-01

    Electrophoretic deposition (EPD) is attracting increasing attention as an effective technique for the processing of biomaterials, specifically bioactive coatings and biomedical nanostructures. The well-known advantages of EPD for the production of a wide range of microstructures and nanostructures as well as unique and complex material combinations are being exploited, starting from well-dispersed suspensions of biomaterials in particulate form (microsized and nanoscale particles, nanotubes, nanoplatelets). EPD of biological entities such as enzymes, bacteria and cells is also being investigated. The review presents a comprehensive summary and discussion of relevant recent work on EPD describing the specific application of the technique in the processing of several biomaterials, focusing on (i) conventional bioactive (inorganic) coatings, e.g. hydroxyapatite or bioactive glass coatings on orthopaedic implants, and (ii) biomedical nanostructures, including biopolymer–ceramic nanocomposites, carbon nanotube coatings, tissue engineering scaffolds, deposition of proteins and other biological entities for sensors and advanced functional coatings. It is the intention to inform the reader on how EPD has become an important tool in advanced biomaterials processing, as a convenient alternative to conventional methods, and to present the potential of the technique to manipulate and control the deposition of a range of nanomaterials of interest in the biomedical and biotechnology fields. PMID:20504802

  19. Intricately Rippled Sand Deposits

    NASA Technical Reports Server (NTRS)

    2006-01-01

    [figure removed for brevity, see original site] Click on the image for Intricately Rippled Sand Deposits (QTVR)

    NASA's Mars Exploration Rover Spirit welcomed the beginning of 2006 on Earth by taking this striking panorama of intricately rippled sand deposits in Gusev Crater on Mars. This is an approximate true-color rendering of the 'El Dorado' ripple field provided by Spirit over the New Year's holiday weekend. The view spans about 160 degrees in azimuth from left to right and consists of images acquired by Spirit's panoramic camera on Spirit's 708th and 710th Martian days, or sols, (Dec. 30, 2005 and Jan. 1, 2006). Spirit used the Pancam's 750-nanometer, 530-nanometer and 430-nanometer filters to capture the colors on Mars. Scientists have eliminated seams between individual frames in the sky portion of the mosaic to better simulate the vista a person standing on Mars would see. Spirit spent several days acquiring images, spectral data, and compositional and mineralogical information about these large sand deposits before continuing downhill toward 'Home Plate.'

  20. Uranium deposits of Brazil

    SciTech Connect

    1991-09-01

    Brazil is a country of vast natural resources, including numerous uranium deposits. In support of the country`s nuclear power program, Brazil has developed the most active uranium industry in South America. Brazil has one operating reactor (Angra 1, a 626-MWe PWR), and two under construction. The country`s economic challenges have slowed the progress of its nuclear program. At present, the Pocos de Caldas district is the only active uranium production. In 1990, the Cercado open-pit mine produced approximately 45 metric tons (MT) U{sub 3}O{sub 8} (100 thousand pounds). Brazil`s state-owned uranium production and processing company, Uranio do Brasil, announced it has decided to begin shifting its production from the high-cost and nearly depleted deposits at Pocos de Caldas, to lower-cost reserves at Lagoa Real. Production at Lagoa Real is schedules to begin by 1993. In addition to these two districts, Brazil has many other known uranium deposits, and as a whole, it is estimated that Brazil has over 275,000 MT U{sub 3}O{sub 8} (600 million pounds U{sub 3}O{sub 8}) in reserves.

  1. Inkjet deposited circuit components

    NASA Astrophysics Data System (ADS)

    Bidoki, S. M.; Nouri, J.; Heidari, A. A.

    2010-05-01

    All-printed electronics as a means of achieving ultra-low-cost electronic circuits has attracted great interest in recent years. Inkjet printing is one of the most promising techniques by which the circuit components can be ultimately drawn (i.e. printed) onto the substrate in one step. Here, the inkjet printing technique was used to chemically deposit silver nanoparticles (10-200 nm) simply by ejection of silver nitrate and reducing solutions onto different substrates such as paper, PET plastic film and textile fabrics. The silver patterns were tested for their functionality to work as circuit components like conductor, resistor, capacitor and inductor. Different levels of conductivity were achieved simply by changing the printing sequence, inks ratio and concentration. The highest level of conductivity achieved by an office thermal inkjet printer (300 dpi) was 5.54 × 105 S m-1 on paper. Inkjet deposited capacitors could exhibit a capacitance of more than 1.5 nF (parallel plate 45 × 45 mm2) and induction coils displayed an inductance of around 400 µH (planar coil 10 cm in diameter). Comparison of electronic performance of inkjet deposited components to the performance of conventionally etched items makes the technique highly promising for fabricating different printed electronic devices.

  2. Pulse plating of nickel deposits

    SciTech Connect

    Stimetz, C.J.; Stevenson, M.F.

    1980-02-01

    Pulse plated and conventional nickel deposits have been compared for differences in morphology, mechanical properties, and microstructure. The deposits were obtained from nickel sulfamate, nickel chloride, and Watts nickel plating solutions. No significant differences were found in the direct and pulse current deposits from the sulfamate and chloride solutions; however, significant differences in microstructure, yield strength, and microhardness were observed in deposits from the Watts nickel solution.

  3. A dynamic and mechanistic model of PCB bioaccumulation in the European hake ( Merluccius merluccius)

    NASA Astrophysics Data System (ADS)

    Bodiguel, Xavier; Maury, Olivier; Mellon-Duval, Capucine; Roupsard, François; Le Guellec, Anne-Marie; Loizeau, Véronique

    2009-08-01

    Bioaccumulation is difficult to document because responses differ among chemical compounds, with environmental conditions, and physiological processes characteristic of each species. We use a mechanistic model, based on the Dynamic Energy Budget (DEB) theory, to take into account this complexity and study factors impacting accumulation of organic pollutants in fish through ontogeny. The bioaccumulation model proposed is a comprehensive approach that relates evolution of hake PCB contamination to physiological information about the fish, such as diet, metabolism, reserve and reproduction status. The species studied is the European hake ( Merluccius merluccius, L. 1758). The model is applied to study the total concentration and the lipid normalised concentration of 4 PCB congeners in male and female hakes from the Gulf of Lions (NW Mediterranean sea) and the Bay of Biscay (NE Atlantic ocean). Outputs of the model compare consistently to measurements over the life span of fish. Simulation results clearly demonstrate the relative effects of food contamination, growth and reproduction on the PCB bioaccumulation in hake. The same species living in different habitats and exposed to different PCB prey concentrations exhibit marked difference in the body accumulation of PCBs. At the adult stage, female hakes have a lower PCB concentration compared to males for a given length. We successfully simulated these sex-specific PCB concentrations by considering two mechanisms: a higher energy allocation to growth for females and a transfer of PCBs from the female to its eggs when allocating lipids from reserve to eggs. Finally, by its mechanistic description of physiological processes, the model is relevant for other species and sets the stage for a mechanistic understanding of toxicity and ecological effects of organic contaminants in marine organisms.

  4. Mechanistic investigation of the endo-alpha-N-acetylgalactosaminidase from Streptococcus pneumoniae R6.

    PubMed

    Willis, Lisa M; Zhang, Ran; Reid, Anne; Withers, Stephen G; Wakarchuk, Warren W

    2009-11-01

    The large (1767-amino acid) endo-alpha-N-acetylgalactosaminidase from Streptococcus pneumoniae (SpGH101) specifically removes an O-linked disaccharide Gal-beta-1,3-GalNAc-alpha from glycoproteins. While the enzyme from natural sources has been used as a reagent for many years, very few mechanistic studies have been performed. Using the recently determined three-dimensional structure of the recombinant protein as a background, we report here a mechanistic investigation of the SpGH101 retaining alpha-glycoside hydrolase using a combination of synthetic and natural substrates. On the basis of a model of the substrate complex of SpGH101, we propose D764 and E796 as the nucleophile and general acid-base residues, respectively. These roles were confirmed by kinetic and mechanistic analysis of mutants at those positions using synthetic substrates and anion rescue experiments. pK(a) values of 5.3 and 7.2 were assigned to D764 and E796 on the basis of the pK(a) values derived from the bell-shaped dependence of k(cat)/K(m) upon pH. The enzyme contains several putative carbohydrate binding modules whose glycan binding specificities were probed using the printed glycan array of the Consortium for Functional Glycomics using the inactive D764A and D764F mutants that had been labeled with Alexafluor 488. These studies revealed binding to galacto-N-biose, consistent with a role for these domains in localizing the enzyme near its substrates. PMID:19788271

  5. A Parsimonious Modular Approach to Building a Mechanistic Belowground C and N Model

    NASA Astrophysics Data System (ADS)

    Abramoff, R. Z.; Davidson, E. A.; Finzi, A.

    2014-12-01

    Ecosystem models simulate belowground processes of element cycling, such as soil carbon dynamics, through numerical representations of our mechanistic understanding of these processes. This poses a great challenge, because many mechanistic models are so highly parameterized and complex that the reasons for their behavior are often difficult to understand, while others are so simplistic that they are unlikely to capture potentially important complexities, such as C-N interactions. Here we propose a mechanistic, but parsimonious modular approach to building a belowground C and N model, with a core processes-level representation of microbial and exoenzymatic activity. We have merged the Dual-Arrhenius Michaelis Menten (DAMM) model of Davidson et al. (2012) with the Microbial Carbon and Nitrogen Physiology (MCNiP) model of Drake et al. (2013). DAMM explicitly simulates the effects of temperature, soil moisture and substrate supply on the kinetics of soil organic matter (SOM) depolymerization. MCNiP is a stoichiometrically constrained model of microbial maintenance and growth respiration, exoenzyme production, and C and N uptake and mineralization. Here we present the results of this model merger, focusing on how temperature, soil moisture, substrate limitation, and the stoichiometry of microbial processes individually and interactively regulate gains or losses of C and N from SOM at the Harvard Forest. We compare model performance running DAMM-MCNiP with and without C-N linkages. We find that substrate limitation is a major constraint over SOM decomposition and that N availability can be a strong regulator of decomposition. The C-only formulation of DAMM-MCNiP generally results in greater losses of SOC than the coupled C-N formulation. Future data-model assimilation and parameter estimation will help determine which aspects of the merged model can be well constrained and which aspects will need further refinement through new data collection or meta-analysis.

  6. Validating Mechanistic Sorption Model Parameters and Processes for Reactive Transport in Alluvium

    SciTech Connect

    Zavarin, M; Roberts, S K; Rose, T P; Phinney, D L

    2002-05-02

    The laboratory batch and flow-through experiments presented in this report provide a basis for validating the mechanistic surface complexation and ion exchange model we use in our hydrologic source term (HST) simulations. Batch sorption experiments were used to examine the effect of solution composition on sorption. Flow-through experiments provided for an analysis of the transport behavior of sorbing elements and tracers which includes dispersion and fluid accessibility effects. Analysis of downstream flow-through column fluids allowed for evaluation of weakly-sorbing element transport. Secondary Ion Mass Spectrometry (SIMS) analysis of the core after completion of the flow-through experiments permitted the evaluation of transport of strongly sorbing elements. A comparison between these data and model predictions provides additional constraints to our model and improves our confidence in near-field HST model parameters. In general, cesium, strontium, samarium, europium, neptunium, and uranium behavior could be accurately predicted using our mechanistic approach but only after some adjustment was made to the model parameters. The required adjustments included a reduction in strontium affinity for smectite, an increase in cesium affinity for smectite and illite, a reduction in iron oxide and calcite reactive surface area, and a change in clinoptilolite reaction constants to reflect a more recently published set of data. In general, these adjustments are justifiable because they fall within a range consistent with our understanding of the parameter uncertainties. These modeling results suggest that the uncertainty in the sorption model parameters must be accounted for to validate the mechanistic approach. The uncertainties in predicting the sorptive behavior of U-1a and UE-5n alluvium also suggest that these uncertainties must be propagated to nearfield HST and large-scale corrective action unit (CAU) models.

  7. A translational preclinical model of interstitial pulmonary fibrosis and pulmonary hypertension: mechanistic pathways driving disease pathophysiology

    PubMed Central

    Jarman, Elizabeth R.; Khambata, Valerie S.; Yun Ye, Li; Cheung, Kenneth; Thomas, Matthew; Duggan, Nicholas; Jarai, Gabor

    2014-01-01

    Abstract Idiopathic pulmonary fibrosis (IPF) is a chronic progressive interstitial lung disease, in which a decline in patient prognosis is frequently associated with the onset of pulmonary hypertension (PH). Animal models exhibiting principle pathophysiological features of IPF and PH could provide greater insight into mechanistic pathways underlying disease progression and a means for evaluating novel therapeutic approaches for intervention. Here, we describe an in vivo disease model, in which animals develop progressive interstitial pulmonary fibrosis and associated PH, as defined by the presence of fibrotic foci adjacent to areas of alveolar injury and remodeling of the pulmonary vasculature. Associated changes in physiological parameters included a decline in lung function and increase in mean pulmonary arterial pressure (mPAP) >25 mmHg. The early fibrotic pathology is associated with a profibrogenic microenvironment, elevated levels of the matrix metalloproteases, MMP‐2, MMP‐7, and MMP‐12, TIMP‐1, the chemoattractant and mitogen, PDGF‐β, and the chemokines CCL2 and CXCL12, that are associated with the recruitment of macrophages, mast cells, and fibrocytes. Principle mechanistic pathways associated with disease pathogenesis are upregulated in the lungs and pulmonary arteries, with sustained increases in gene transcripts for the profibrotic mediator TGF‐β1 and components of the TGF‐β signaling pathway; PAI‐1, Nox‐4, and HIF‐1α. Therapeutic treatment with the ALK‐5/TGF‐β RI inhibitor SB‐525334 reversed established pulmonary fibrosis and associated vascular remodeling, leading to normalization in clinically translatable physiological parameters including lung function and hemodynamic measurements of mPAP. These studies highlight the application of this model in validating potential approaches for targeting common mechanistic pathways driving disease pathogenesis. PMID:25214520

  8. Divergence of mechanistic pathways mediating cardiovascular aging and developmental programming of cardiovascular disease.

    PubMed

    Allison, Beth J; Kaandorp, Joepe J; Kane, Andrew D; Camm, Emily J; Lusby, Ciara; Cross, Christine M; Nevin-Dolan, Rhianon; Thakor, Avnesh S; Derks, Jan B; Tarry-Adkins, Jane L; Ozanne, Susan E; Giussani, Dino A

    2016-05-01

    Aging and developmental programming are both associated with oxidative stress and endothelial dysfunction, suggesting common mechanistic origins. However, their interrelationship has been little explored. In a rodent model of programmed cardiovascular dysfunction we determined endothelial function and vascular telomere length in young (4 mo) and aged (15 mo) adult offspring of normoxic or hypoxic pregnancy with or without maternal antioxidant treatment. We show loss of endothelial function [maximal arterial relaxation to acetylcholine (71 ± 3 vs. 55 ± 3%) and increased vascular short telomere abundance (4.2-1.3 kb) 43.0 ± 1.5 vs. 55.1 ± 3.8%) in aged vs. young offspring of normoxic pregnancy (P < 0.05). Hypoxic pregnancy in young offspring accelerated endothelial dysfunction (maximal arterial relaxation to acetylcholine: 42 ± 1%, P < 0.05) but this was dissociated from increased vascular short telomere length abundance. Maternal allopurinol rescued maximal arterial relaxation to acetylcholine in aged offspring of normoxic or hypoxic pregnancy but not in young offspring of hypoxic pregnancy. Aged offspring of hypoxic allopurinol pregnancy compared with aged offspring of untreated hypoxic pregnancy had lower levels of short telomeres (vascular short telomere length abundance 35.1 ± 2.5 vs. 48.2 ± 2.6%) and of plasma proinflammatory chemokine (24.6 ± 2.8 vs. 36.8 ± 5.5 pg/ml, P < 0.05). These data provide evidence for divergence of mechanistic pathways mediating cardiovascular aging and developmental programming of cardiovascular disease, and aging being decelerated by antioxidants even prior to birth.-Allison, B. J., Kaandorp, J. J., Kane, A. D., Camm, E. J., Lusby, C., Cross, C. M., Nevin-Dolan, R., Thakor, A. S., Derks, J. B., Tarry-Adkins, J. L., Ozanne, S. E., Giussani, D. A. Divergence of mechanistic pathways mediating cardiovascular aging and developmental programming of cardiovascular disease. PMID:26932929

  9. Prediction of Damage in Randomly Oriented Short-Fibre Composites by means of A Mechanistic Approach

    SciTech Connect

    Nguyen, Ba Nghiep; Khaleel, Mohammad A.

    2004-05-01

    A micro-macro mechanistic approach to damage in short-fiber composites is developed in this paper. At the micro-scale, the damage mechanisms such as matrix cracking, fiber/matrix debonding are analyzed to define the associated damage variables. The stiffness reduction law dependent on these variables is then established using micromechanical models and average orientation distributions of fibers and microcracks. The macroscopic response is obtained by means of thermodynamics of continuous media, continuum damage mechanics and a finite element formulation.

  10. Advances in mechanistic understanding of release rate control mechanisms of extended-release hydrophilic matrix tablets.

    PubMed

    Timmins, Peter; Desai, Divyakant; Chen, Wei; Wray, Patrick; Brown, Jonathan; Hanley, Sarah

    2016-08-01

    Approaches to characterizing and developing understanding around the mechanisms that control the release of drugs from hydrophilic matrix tablets are reviewed. While historical context is provided and direct physical characterization methods are described, recent advances including the role of percolation thresholds, the application on magnetic resonance and other spectroscopic imaging techniques are considered. The influence of polymer and dosage form characteristics are reviewed. The utility of mathematical modeling is described. Finally, how all the information derived from applying the developed mechanistic understanding from all of these tools can be brought together to develop a robust and reliable hydrophilic matrix extended-release tablet formulation is proposed. PMID:27444495

  11. A mechanistic model of hydrogen-methanogen dynamics in the rumen.

    PubMed

    Wang, Yuancheng; Janssen, Peter H; Lynch, Tammy A; Brunt, Bruce van; Pacheco, David

    2016-03-21

    Existing mathematical models to estimate methane production in the rumen are based on calculation of hydrogen balances without considering the presence of methanogens. In this study, a mechanistic model of methane production is proposed that depicts the interaction between hydrogen concentration and methanogens in the rumen. Analytical results show that it meets biological expectations, namely increased fractional passage rate leads to a greater growth rate of methanogens, and a greater steady state hydrogen concentration. This model provides a basis on which to develop a more comprehensive model of methane production in the rumen that includes thermodynamics and feed fermentation pathways. PMID:26780651

  12. Mechanistic Studies on Garratt-Braverman Cyclization: The Diradical-Cycloaddition Puzzle.

    PubMed

    Das, Joyee; Bag, Subhendu Sekhar; Basak, Amit

    2016-06-01

    In this work, we present the results of extensive multiprong studies involving the fate of deuterium-labeled substrates, EPR, trapping experiments, and LA-LDI mass spectrometry to sort out the controversies relating to the mechanism of Garratt-Braverman cyclization in two systems, namely bis-propargyl sulfones and ethers. The results are in conformity with a diradical mechamism for the sulfone, while for the ether, the anionic [4 + 2] appears to be the preferred pathway. This shows that the mechanistic pathway toward GB cyclization is dependent upon the nature of heteroatom (O or S in sulfone) bridging the propargyl arms. PMID:27116541

  13. Prediction of Damage in Randomly Oriented Short-Fibre Composites by means of A Mechanistic Approach

    SciTech Connect

    Nguyen, Ba NGHIEP; Khaleel, Mohammad A.

    2004-03-01

    A micro-macro mechanistic approach to damage in short-fiber composites is developed in this paper. At the micro-scale, the damage mechanisms such as matrix cracking, fiber/matrix debonding are analyzed to define the associated damage variables. The stiffness reduction law dependent on these variables is then established using micromechanical models and average orientation distributions of fibers and microcracks. The macroscopic response is obtained by means of thermodynamics of continuous media, continuum damage mechanics and a finite element formulation.

  14. A mechanistic study of the effects of nitrogen on the corrosion properties of stainless steels

    SciTech Connect

    Levey, P.R.; Bennekom, A. van

    1995-12-01

    The effects of nitrogen alloying on the corrosion properties of stainless steels (SS) is a matter of debate. A number of apparently contradictory results have been presented by various researchers. The actual mechanism by which nitrogen alloying influences the corrosion properties of SS has been the topic of even more controversy. The effects of nitrogen on the corrosion and mechanical properties of SS were reviewed. Various proposals relating to the mechanistic effect of nitrogen alloying on the corrosion properties of SS were evaluated critically by comparing the various theories.

  15. GLUT, SGLT, and SWEET: Structural and mechanistic investigations of the glucose transporters.

    PubMed

    Deng, Dong; Yan, Nieng

    2016-03-01

    Glucose is the primary fuel to life on earth. Cellular uptake of glucose is a fundamental process for metabolism, growth, and homeostasis. Three families of secondary glucose transporters have been identified in human, including the major facilitator superfamily glucose facilitators GLUTs, the sodium-driven glucose symporters SGLTs, and the recently identified SWEETs. Structures of representative members or their prokaryotic homologs of all three families were obtained. This review focuses on the recent advances in the structural elucidation of the glucose transporters and the mechanistic insights derived from these structures, including the molecular basis for substrate recognition, alternating access, and stoichiometric coupling of co-transport. PMID:26650681

  16. The Cycloaddition of the Benzimidazolium Ylides with Alkynes: New Mechanistic Insights

    PubMed Central

    Moldoveanu, Costel; Zbancioc, Gheorghita; Mantu, Dorina; Maftei, Dan; Mangalagiu, Ionel

    2016-01-01

    New insights concerning the reaction mechanism in the cycloaddition reaction of benzimidazolium ylides to activated alkynes are presented. The proposed pathway leading both to 2-(1H-pyrrol-1-yl)anilines and to pyrrolo[1,2-a]quinoxalin-4(5H)-ones involves an opening of the imidazole ring from the cycloaddition product, followed by a nucleophilic attack of the aminic nitrogen to a proximal carbonyl group and the elimination of a leaving group. The mechanistic considerations are fully supported by experimental data, including the XRD resolved structure of the key reaction intermediate. PMID:27224656

  17. Copper/TEMPO-Catalyzed Aerobic Alcohol Oxidation: Mechanistic Assessment of Different Catalyst Systems.

    PubMed

    Hoover, Jessica M; Ryland, Bradford L; Stahl, Shannon S

    2013-11-01

    Combinations of homogeneous Cu salts and TEMPO have emerged as practical and efficient catalysts for the aerobic oxidation of alcohols. Several closely related catalyst systems have been reported, which differ in the identity of the solvent, the presence of 2,2'-bipyridine as a ligand, the identity of basic additives, and the oxidation state of the Cu source. These changes have a significant influence on the reaction rates, yields, and substrate scope. In this report, we probe the mechanistic basis for differences among four different Cu/TEMPO catalyst systems and elucidate the features that contribute to efficient oxidation of aliphatic alcohols. PMID:24558634

  18. Parameterization of phosphine ligands reveals mechanistic pathways and predicts reaction outcomes

    NASA Astrophysics Data System (ADS)

    Niemeyer, Zachary L.; Milo, Anat; Hickey, David P.; Sigman, Matthew S.

    2016-06-01

    The mechanistic foundation behind the identity of a phosphine ligand that best promotes a desired reaction outcome is often non-intuitive, and thus has been addressed in numerous experimental and theoretical studies. In this work, multivariate correlations of reaction outcomes using 38 different phosphine ligands were combined with classic potentiometric analyses to study a Suzuki reaction, for which the site selectivity of oxidative addition is highly dependent on the nature of the phosphine. These studies shed light on the generality of hypotheses regarding the structural influence of different classes of phosphine ligands on the reaction mechanism(s), and deliver a methodology that should prove useful in future studies of phosphine ligands.

  19. New mechanistic insights in the NH3-SCR reactions at low temperature

    DOE PAGESBeta

    Ruggeri, Maria Pia; Selleri, Tomasso; Nova, Isabella; Tronconi, Enrico; Pihl, Josh A.; Toops, Todd J.; Partridge, Jr., William P.

    2016-05-06

    The present study is focused on the investigation of the low temperature Standard SCR reaction mechanism over Fe- and Cu-promoted zeolites. Different techniques are employed, including in situ DRIFTS, transient reaction analysis and chemical trapping techniques. The results present strong evidence of nitrite formation in the oxidative activation of NO and of their role in SCR reactions. These elements lead to a deeper understanding of the standard SCR chemistry at low temperature and can potentially improve the consistency of mechanistic mathematical models. Furthermore, comprehension of the mechanism on a fundamental level can contribute to the development of improved SCR catalysts.

  20. Copper/TEMPO-Catalyzed Aerobic Alcohol Oxidation: Mechanistic Assessment of Different Catalyst Systems

    PubMed Central

    Hoover, Jessica M.; Ryland, Bradford L.; Stahl, Shannon S.

    2013-01-01

    Combinations of homogeneous Cu salts and TEMPO have emerged as practical and efficient catalysts for the aerobic oxidation of alcohols. Several closely related catalyst systems have been reported, which differ in the identity of the solvent, the presence of 2,2′-bipyridine as a ligand, the identity of basic additives, and the oxidation state of the Cu source. These changes have a significant influence on the reaction rates, yields, and substrate scope. In this report, we probe the mechanistic basis for differences among four different Cu/TEMPO catalyst systems and elucidate the features that contribute to efficient oxidation of aliphatic alcohols. PMID:24558634

  1. Problems in mechanistic theoretical models for cell transformation by ionizing radiation

    SciTech Connect

    Chatterjee, A.; Holley, W.R.

    1991-10-01

    A mechanistic model based on yields of double strand breaks has been developed to determine the dose response curves for cell transformation frequencies. At its present stage the model is applicable to immortal cell lines and to various qualities (X-rays, Neon and Iron) of ionizing radiation. Presently, we have considered four types of processes which can lead to activation phenomena: (1) point mutation events on a regulatory segment of selected oncogenes, (2) inactivation of suppressor genes, through point mutation, (3) deletion of a suppressor gene by a single track, and (4) deletion of a suppressor gene by two tracks.

  2. Bird Migration Under Climate Change - A Mechanistic Approach Using Remote Sensing

    NASA Technical Reports Server (NTRS)

    Smith, James A.; Blattner, Tim; Messmer, Peter

    2010-01-01

    The broad-scale reductions and shifts that may be expected under climate change in the availability and quality of stopover habitat for long-distance migrants is an area of increasing concern for conservation biologists. Researchers generally have taken two broad approaches to the modeling of migration behaviour to understand the impact of these changes on migratory bird populations. These include models based on causal processes and their response to environmental stimulation, "mechanistic models", or models that primarily are based on observed animal distribution patterns and the correlation of these patterns with environmental variables, i.e. "data driven" models. Investigators have applied the latter technique to forecast changes in migration patterns with changes in the environment, for example, as might be expected under climate change, by forecasting how the underlying environmental data layers upon which the relationships are built will change over time. The learned geostatstical correlations are then applied to the modified data layers.. However, this is problematic. Even if the projections of how the underlying data layers will change are correct, it is not evident that the statistical relationships will remain the same, i.e. that the animal organism may not adapt its' behaviour to the changing conditions. Mechanistic models that explicitly take into account the physical, biological, and behaviour responses of an organism as well as the underlying changes in the landscape offer an alternative to address these shortcomings. The availability of satellite remote sensing observations at multiple spatial and temporal scales, coupled with advances in climate modeling and information technologies enable the application of the mechanistic models to predict how continental bird migration patterns may change in response to environmental change. In earlier work, we simulated the impact of effects of wetland loss and inter-annual variability on the fitness of

  3. Deposition of SOCs in forests

    SciTech Connect

    Horstmann, M.; McLachlan, M.S.

    1995-12-31

    The bulk deposition, wet-only deposition, dry-only deposition and ambient air concentrations of PCDD/Fs, PCBs and PAHs were measured in an 80 year old spruce forest, an 80 year old mixed deciduous (beech and oak) forest, and in an adjacent clearing over a period of 1--2 years. The deposition of the less volatile compounds that are primarily particle bound in the atmosphere was similar at both sites. These compounds were deposited primarily through wet deposition, as shown by the measurements in the clearing. In contrast, the deposition of the more volatile compounds was much higher at the forest sites than in the clearing. For instance, the annual deposition of Cl{sub 4}DF was 5 times higher in the spruce forest and 8 times higher in the deciduous forest. The excess deposition in the deciduous forest was almost completely due to the leaf fall in October--December, while about half of the excess deposition in the spruce forest was the result of needle fall. A further, as yet unexplained deposition mechanism accounted for the remainder of the flux in the spruce forest. Other studies have shown that more volatile SOCs are deposited to vegetation primarily through dry gaseous deposition. Hence, while forests have little influence on the deposition of less volatile compounds like the higher chlorinated PCDD/Fs and the 5--6 ring PAHs, dry deposition to leaves/needles and their subsequent falling to the forest floor make forest soils an extremely important sink for more volatile SOC.

  4. Database of recent tsunami deposits

    USGS Publications Warehouse

    Peters, Robert; Jaffe, Bruce E.

    2010-01-01

    This report describes a database of sedimentary characteristics of tsunami deposits derived from published accounts of tsunami deposit investigations conducted shortly after the occurrence of a tsunami. The database contains 228 entries, each entry containing data from up to 71 categories. It includes data from 51 publications covering 15 tsunamis distributed between 16 countries. The database encompasses a wide range of depositional settings including tropical islands, beaches, coastal plains, river banks, agricultural fields, and urban environments. It includes data from both local tsunamis and teletsunamis. The data are valuable for interpreting prehistorical, historical, and modern tsunami deposits, and for the development of criteria to identify tsunami deposits in the geologic record.

  5. Electrophoretic Deposition for Fabricating Microbatteries

    NASA Technical Reports Server (NTRS)

    West, William; Whitacre, Jay; Bugga, Ratnakumar

    2003-01-01

    An improved method of fabrication of cathodes of microbatteries is based on electrophoretic deposition. Heretofore, sputtering (for deposition) and the use of photoresist and liftoff (for patterning) have been the primary methods of fabricating components of microbatteries. The volume of active electrode material that can be deposited by sputtering is limited, and the discharge capacities of prior microbatteries have been limited accordingly. In addition, sputter deposition is slow. In contrast, electrophoretic deposition is much faster and has shown promise for increasing discharge capacities by a factor of 10, relative to those of microbatteries fabricated by prior methods.

  6. Multi-chamber deposition system

    DOEpatents

    Jacobson, Richard L.; Jeffrey, Frank R.; Westerberg, Roger K.

    1989-10-17

    A system for the simultaneous deposition of different coatings onto a thin web within a large volume vacuum chamber is disclosed which chamber is provided with a plurality of deposition chambers in which the different layers are deposited onto the film as its moves from a supply roll to a finished take-up roll of coated web. The deposition chambers provided within the large vacuum chamber are provided with separate seals which minimize back diffusion of any dopant gas from adjacent deposition chambers.

  7. Multi-chamber deposition system

    DOEpatents

    Jacobson, Richard L.; Jeffrey, Frank R.; Westerberg, Roger K.

    1989-06-27

    A system for the simultaneous deposition of different coatings onto a thin web within a large volume vacuum chamber is disclosed which chamber is provided with a plurality of deposition chambers in which the different layers are deposited onto the film as its moves from a supply roll to a finished take-up roll of coated web. The deposition chambers provided within the large vacuum chamber are provided with separate seals which minimize back diffusion of any dopant gas from adjacent deposition chambers.

  8. Chemical vapor deposition sciences

    SciTech Connect

    1992-12-31

    Chemical vapor deposition (CVD) is a widely used method for depositing thin films of a variety of materials. Applications of CVD range from the fabrication of microelectronic devices to the deposition of protective coatings. New CVD processes are increasingly complex, with stringent requirements that make it more difficult to commercialize them in a timely fashion. However, a clear understanding of the fundamental science underlying a CVD process, as expressed through computer models, can substantially shorten the time required for reactor and process development. Research scientists at Sandia use a wide range of experimental and theoretical techniques for investigating the science of CVD. Experimental tools include optical probes for gas-phase and surface processes, a range of surface analytic techniques, molecular beam methods for gas/surface kinetics, flow visualization techniques and state-of-the-art crystal growth reactors. The theoretical strategy uses a structured approach to describe the coupled gas-phase and gas-surface chemistry, fluid dynamics, heat and mass transfer of a CVD process. The software used to describe chemical reaction mechanisms is easily adapted to codes that model a variety of reactor geometries. Carefully chosen experiments provide critical information on the chemical species, gas temperatures and flows that are necessary for model development and validation. This brochure provides basic information on Sandia`s capabilities in the physical and chemical sciences of CVD and related materials processing technologies. It contains a brief description of the major scientific and technical capabilities of the CVD staff and facilities, and a brief discussion of the approach that the staff uses to advance the scientific understanding of CVD processes.

  9. Thermionic deposition devices (survey)

    SciTech Connect

    Saenko, V.A.

    1985-11-01

    Various devices for the deposition of thin films and coatings from a plasma of solid-phase-material vapor are surveyed. The devices operate by vaporization and ionization of the working material in a vacuum. The classification, parameters, designs and development trends of thermionic devices (plasma vaporizers) are examined. Their characteristics and areas of application in modern high-energy plasma technology are described. The relative simplicity of the design and operation of the devices should allow them to be widely used not only in the laboratory but also in industry. The first manufactured units with thermionic devices and some of the properties of the films they produce are described.

  10. Vacuum deposition system

    SciTech Connect

    Austin, S.; Bark, D.

    1990-05-31

    The Physics Section vacuum deposition system is available for several types of thin film techniques. This vacuum evaporation system operates in the high vacuum range. The evaporation source is a resistive heating element, either a boat or a filament design. Coating is then line of sight from the source. Substrates to be coated can have a maximum diameter of 17 inches. At this time the variations in the thickness of the coatings can be controlled, by monitor, to within about 100 angstroms. The system diagrams follow the Operation Procedures and the Sample Coating Procedures provided in this document. 3 figs.

  11. The Chilean nitrate deposits.

    USGS Publications Warehouse

    Ericksen, G.E.

    1983-01-01

    The nitrate deposits in the arid Atacama desert of northern Chile consist of saline-cemented surficial material, apparently formed in and near a playa lake that formerly covered the area. Many features of their distribution and chemical composition are unique. The author believes the principal sources of the saline constituents were the volcanic rocks of late Tertiary and Quaternary age in the Andes and that the nitrate is of organic origin. Possible sources of the nitrate, iodate, perchlorate and chromate are discussed. -J.J.Robertson

  12. [Triglyceride deposit cardiomyovasculopathy].

    PubMed

    Hirano, Ken-Ichi

    2013-09-01

    Cholesterol is a vital causal factor and focus of research into heart diseases, however the involvement of triglycerides remains unclear. We recently reported a patient suffering from severe congestive heart failure and needing cardiac transplantation. Massive accumulation of triglycerides was noted in coronary atherosclerotic lesions as well as in the myocardium. We named this phenotype"triglyceride deposit cardiomyovasculopathy (TGCV)". The patient was identified as homozygous for a genetic mutation in the adipose triglyceride lipase (ATGL), an essential molecule for hydrolysis of intracellular triglycerides. In this paper, we describe clinical characteristics of ATGL deficiency and discuss what we can learn from this disorder. PMID:24205734

  13. Deposition System Controller

    SciTech Connect

    Conley, Ray; Liu, Chian

    2005-10-01

    This software is a complete thin film deposition controller. The software takes as its input a script file that dictates enablinig/disabling of sputtering power supplies, pause times, velocities and distances to move a substrate. An emulator has been created and built into the software package that can debug in advance any deposition script and decide if there is an overrun condition, accidental infinite look, and can estimate a time for completion. All necessary process variables are data logged and recorded for later inspection. This emulator currently interfaces to a Parker-Compumotor SX6 stepper moror indexer, but the software is written in such a way that it is easily modifiable for interface to othe brand and models of motor drivers. Other process I/O variables may be easily added. The software uses any multifunction DAQ card from National Instruments via their free NIDAQ API package, but again, the software is written such that othe brand DAQ cards may be used.

  14. Deposition System Controller

    Energy Science and Technology Software Center (ESTSC)

    2005-10-01

    This software is a complete thin film deposition controller. The software takes as its input a script file that dictates enablinig/disabling of sputtering power supplies, pause times, velocities and distances to move a substrate. An emulator has been created and built into the software package that can debug in advance any deposition script and decide if there is an overrun condition, accidental infinite look, and can estimate a time for completion. All necessary process variablesmore » are data logged and recorded for later inspection. This emulator currently interfaces to a Parker-Compumotor SX6 stepper moror indexer, but the software is written in such a way that it is easily modifiable for interface to othe brand and models of motor drivers. Other process I/O variables may be easily added. The software uses any multifunction DAQ card from National Instruments via their free NIDAQ API package, but again, the software is written such that othe brand DAQ cards may be used.« less

  15. Mechanistic Study of Manganese-Substituted Glycerol Dehydrogenase Using a Kinetic and Thermodynamic Analysis

    PubMed Central

    Fang, Baishan; Niu, Jin; Ren, Hong; Guo, Yingxia; Wang, Shizhen

    2014-01-01

    Mechanistic insights regarding the activity enhancement of dehydrogenase by metal ion substitution were investigated by a simple method using a kinetic and thermodynamic analysis. By profiling the binding energy of both the substrate and product, the metal ion's role in catalysis enhancement was revealed. Glycerol dehydrogenase (GDH) from Klebsiella pneumoniae sp., which demonstrated an improvement in activity by the substitution of a zinc ion with a manganese ion, was used as a model for the mechanistic study of metal ion substitution. A kinetic model based on an ordered Bi-Bi mechanism was proposed considering the noncompetitive product inhibition of dihydroxyacetone (DHA) and the competitive product inhibition of NADH. By obtaining preliminary kinetic parameters of substrate and product inhibition, the number of estimated parameters was reduced from 10 to 4 for a nonlinear regression-based kinetic parameter estimation. The simulated values of time-concentration curves fit the experimental values well, with an average relative error of 11.5% and 12.7% for Mn-GDH and GDH, respectively. A comparison of the binding energy of enzyme ternary complex for Mn-GDH and GDH derived from kinetic parameters indicated that metal ion substitution accelerated the release of dioxyacetone. The metal ion's role in catalysis enhancement was explicated. PMID:24896258

  16. Induced polarization dependence on pore space geometry: Empirical observations and mechanistic predictions

    NASA Astrophysics Data System (ADS)

    Weller, A.; Slater, L. D.

    2015-12-01

    We use an extensive database to compare empirical observations and previously proposed empirical models against recently developed mechanistic formulations for the induced polarization (IP) response in porous media as a function of pore space geometry and interfacial chemistry. These comparisons support the argument that the pore-volume normalized internal surface (Spor) is the most important geometric parameter influencing the polarization. The specific polarizability derived from the empirical relationship between imaginary conductivity σ″ and Spor is independent of the porosity. By contrast, equivalent specific polarizability terms in recently proposed mechanistic models are found to be significantly correlated with porosity, and thus do not appear to represent an interfacial chemistry factor independent of the pore space geometry. Furthermore, the database shows no evidence for a significant decrease in the counterion mobility of clayey materials relative to clay-free materials, as postulated in recent studies. On the contrary, a single value of cp is consistent with no significant differences in ionic mobility given that all samples were saturated with a NaCl solution close to a common salinity of about 100 mS/m.

  17. Comparison of Two-Phase Pipe Flow in OpenFOAM with a Mechanistic Model

    NASA Astrophysics Data System (ADS)

    Shuard, Adrian M.; Mahmud, Hisham B.; King, Andrew J.

    2016-03-01

    Two-phase pipe flow is a common occurrence in many industrial applications such as power generation and oil and gas transportation. Accurate prediction of liquid holdup and pressure drop is of vast importance to ensure effective design and operation of fluid transport systems. In this paper, a Computational Fluid Dynamics (CFD) study of a two-phase flow of air and water is performed using OpenFOAM. The two-phase solver, interFoam is used to identify flow patterns and generate values of liquid holdup and pressure drop, which are compared to results obtained from a two-phase mechanistic model developed by Petalas and Aziz (2002). A total of 60 simulations have been performed at three separate pipe inclinations of 0°, +10° and -10° respectively. A three dimensional, 0.052m diameter pipe of 4m length is used with the Shear Stress Transport (SST) k - ɷ turbulence model to solve the turbulent mixtures of air and water. Results show that the flow pattern behaviour and numerical values of liquid holdup and pressure drop compare reasonably well to the mechanistic model.

  18. Non-destructive estimation of root pressure using sap flow, stem diameter measurements and mechanistic modelling

    PubMed Central

    De Swaef, Tom; Hanssens, Jochen; Cornelis, Annelies; Steppe, Kathy

    2013-01-01

    Background Upward water movement in plants via the xylem is generally attributed to the cohesion–tension theory, as a response to transpiration. Under certain environmental conditions, root pressure can also contribute to upward xylem water flow. Although the occurrence of root pressure is widely recognized, ambiguity exists about the exact mechanism behind root pressure, the main influencing factors and the consequences of root pressure. In horticultural crops, such as tomato (Solanum lycopersicum), root pressure is thought to cause cells to burst, and to have an important impact on the marketable yield. Despite the challenges of root pressure research, progress in this area is limited, probably because of difficulties with direct measurement of root pressure, prompting the need for indirect and non-destructive measurement techniques. Methods A new approach to allow non-destructive and non-invasive estimation of root pressure is presented, using continuous measurements of sap flow and stem diameter variation in tomato combined with a mechanistic flow and storage model, based on cohesion–tension principles. Key Results Transpiration-driven sap flow rates are typically inversely related to stem diameter changes; however, this inverse relationship was no longer valid under conditions of low transpiration. This decoupling between sap flow rates and stem diameter variations was mathematically related to root pressure. Conclusions Root pressure can be estimated in a non-destructive, repeatable manner, using only external plant sensors and a mechanistic model. PMID:23211757

  19. Using mechanistic Bayesian networks to identify downstream targets of the Sonic Hedgehog pathway

    PubMed Central

    2009-01-01

    Background The topology of a biological pathway provides clues as to how a pathway operates, but rationally using this topology information with observed gene expression data remains a challenge. Results We introduce a new general-purpose analytic method called Mechanistic Bayesian Networks (MBNs) that allows for the integration of gene expression data and known constraints within a signal or regulatory pathway to predict new downstream pathway targets. The MBN framework is implemented in an open-source Bayesian network learning package, the Python Environment for Bayesian Learning (PEBL). We demonstrate how MBNs can be used by modeling the early steps of the sonic hedgehog pathway using gene expression data from different developmental stages and genetic backgrounds in mouse. Using the MBN approach we are able to automatically identify many of the known downstream targets of the hedgehog pathway such as Gas1 and Gli1, along with a short list of likely targets such as Mig12. Conclusions The MBN approach shown here can easily be extended to other pathways and data types to yield a more mechanistic framework for learning genetic regulatory models. PMID:20021670

  20. Life at the Common Denominator: Mechanistic and Quantitative Biology for the Earth and Space Sciences

    NASA Technical Reports Server (NTRS)

    Hoehler, Tori M.

    2010-01-01

    The remarkable challenges and possibilities of the coming few decades will compel the biogeochemical and astrobiological sciences to characterize the interactions between biology and its environment in a fundamental, mechanistic, and quantitative fashion. The clear need for integrative and scalable biology-environment models is exemplified in the Earth sciences by the challenge of effectively addressing anthropogenic global change, and in the space sciences by the challenge of mounting a well-constrained yet sufficiently adaptive and inclusive search for life beyond Earth. Our understanding of the life-planet interaction is still, however, largely empirical. A variety of approaches seek to move from empirical to mechanistic descriptions. One approach focuses on the relationship between biology and energy, which is at once universal (all life requires energy), unique (life manages energy flow in a fashion not seen in abiotic systems), and amenable to characterization and quantification in thermodynamic terms. Simultaneously, a focus on energy flow addresses a critical point of interface between life and its geological, chemical, and physical environment. Characterizing and quantifying this relationship for life on Earth will support the development of integrative and predictive models for biology-environment dynamics. Understanding this relationship at its most fundamental level holds potential for developing concepts of habitability and biosignatures that can optimize astrobiological exploration strategies and are extensible to all life.

  1. Productivity of "collisions generate heat" for reconciling an energy model with mechanistic reasoning: A case study

    NASA Astrophysics Data System (ADS)

    Scherr, Rachel E.; Robertson, Amy D.

    2015-06-01

    We observe teachers in professional development courses about energy constructing mechanistic accounts of energy transformations. We analyze a case in which teachers investigating adiabatic compression develop a model of the transformation of kinetic energy to thermal energy. Among their ideas is the idea that thermal energy is generated as a byproduct of individual particle collisions, which is represented in science education research literature as an obstacle to learning. We demonstrate that in this instructional context, the idea that individual particle collisions generate thermal energy is not an obstacle to learning, but instead is productive: it initiates intellectual progress. Specifically, this idea initiates the reconciliation of the teachers' energy model with mechanistic reasoning about adiabatic compression, and leads to a canonically correct model of the transformation of kinetic energy into thermal energy. We claim that the idea's productivity is influenced by features of our particular instructional context, including the instructional goals of the course, the culture of collaborative sense making, and the use of certain representations of energy.

  2. Ultrasound and Microbubble Guided Drug Delivery: Mechanistic Understanding and Clinical Implications

    PubMed Central

    Wang, Tzu-Yin; Wilson, Katheryne E.; Machtaler, Steven; Willmann, Jürgen K.

    2014-01-01

    Ultrasound mediated drug delivery using microbubbles is a safe and noninvasive approach for spatially localized drug administration. This approach can create temporary and reversible openings on cellular membranes and vessel walls (a process called “sonoporation”), allowing for enhanced transport of therapeutic agents across these natural barriers. It is generally believed that the sonoporation process is highly associated with the energetic cavitation activities (volumetric expansion, contraction, fragmentation, and collapse) of the microbubble. However, a thorough understanding of the process was unavailable until recently. Important progress on the mechanistic understanding of sonoporation and the corresponding physiological responses in vitro and in vivo has been made. Specifically, recent research shed light on the cavitation process of microbubbles and fluid motion during insonation of ultrasound, on the spatio-temporal interactions between microbubbles and cells or vessel walls, as well as on the temporal course of the subsequent biological effects. These findings have significant clinical implications on the development of optimal treatment strategies for effective drug delivery. In this article, current progress in the mechanistic understanding of ultrasound and microbubble mediated drug delivery and its implications for clinical translation is discussed. PMID:24372231

  3. Assessment of mechanistic multiphase methods against independent experiments at large pipe diameter

    SciTech Connect

    Crowley, C.J. )

    1990-02-01

    Previously, the mechanistic multiphase methods for pipelines which have been documented in state of the art reports have been compared extensively with laboratory data from Creare/PRC experiments in pipes at 3.5 and 7 inches diameter. The multiphase methods have also been assessed against field data from 17 pipelines. In order to provide the broadest possible assessment of the methods, this report compares the multiphase methods against independent laboratory data at large pipe diameter from the IFP (Boussens), SINTEF (Trondheim), and Harwell facilities at 6, 8, and 12 inch diameters, respectively. The SINTEF and IFP facilities operate at elevated pressure (high gas density) while the Harwell facility operates at low pressures, near one atmosphere. Selected data from each facility have been published in the open literature. These data are primarily for horizontal pipes, although the IFP data include upward and downward inclinations. The mechanistic multiphase methods are in substantial agreement with most of the data from these facilities (especially at high gas density), including the flow regime maps from each facility, pressure drop and holdup data for the stratified flow regime in the SINTEF facility, and flow characteristics in the slug flow regime for the IFP facility. The agreement with the pressure drop in the Harwell facility is not as good as expected, being a factor of two low. 15 figs.

  4. Toward a Mechanistic Understanding of Environmentally Forced Zoonotic Disease Emergence: Sin Nombre Hantavirus

    PubMed Central

    Carver, Scott; Mills, James N.; Parmenter, Cheryl A.; Parmenter, Robert R.; Richardson, Kyle S.; Harris, Rachel L.; Douglass, Richard J.; Kuenzi, Amy J.; Luis, Angela D.

    2015-01-01

    Understanding the environmental drivers of zoonotic reservoir and human interactions is crucial to understanding disease risk, but these drivers are poorly predicted. We propose a mechanistic understanding of human–reservoir interactions, using hantavirus pulmonary syndrome as a case study. Crucial processes underpinning the disease's incidence remain poorly studied, including the connectivity among natural and peridomestic deer mouse host activity, virus transmission, and human exposure. We found that disease cases were greatest in arid states and declined exponentially with increasing precipitation. Within arid environments, relatively rare climatic conditions (e.g., El Niño) are associated with increased rainfall and reservoir abundance, producing more frequent virus transmission and host dispersal. We suggest that deer mice increase their occupancy of peridomestic structures during spring–summer, amplifying intraspecific transmission and human infection risk. Disease incidence in arid states may increase with predicted climatic changes. Mechanistic approaches incorporating reservoir behavior, reservoir–human interactions, and pathogen spillover could enhance our understanding of global hantavirus ecology, with applications to other directly transmitted zoonoses. PMID:26955081

  5. Stoichiometry of proton translocation by respiratory complex I and its mechanistic implications

    PubMed Central

    Wikström, Mårten; Hummer, Gerhard

    2012-01-01

    Complex I (NADH-ubiquinone oxidoreductase) in the respiratory chain of mitochondria and several bacteria functions as a redox-driven proton pump that contributes to the generation of the protonmotive force across the inner mitochondrial or bacterial membrane and thus to the aerobic synthesis of ATP. The stoichiometry of proton translocation is thought to be 4 H+ per NADH oxidized (2 e-). Here we show that a H+/2 e- ratio of 3 appears more likely on the basis of the recently determined H+/ATP ratio of the mitochondrial F1Fo-ATP synthase of animal mitochondria and of a set of carefully determined ATP/2 e- ratios for different segments of the mitochondrial respiratory chain. This lower H+/2 e- ratio of 3 is independently supported by thermodynamic analyses of experiments with both mitochondria and submitochondrial particles. A reduced H+/2 e- stoichiometry of 3 has important mechanistic implications for this proton pump. In a rough mechanistic model, we suggest a concerted proton translocation mechanism in the three homologous and tightly packed antiporter-like subunits L, M, and N of the proton-translocating membrane domain of complex I. PMID:22392981

  6. Simulating the Risk of Liver Fluke Infection using a Mechanistic Hydro-epidemiological Model

    NASA Astrophysics Data System (ADS)

    Beltrame, Ludovica; Dunne, Toby; Rose, Hannah; Walker, Josephine; Morgan, Eric; Vickerman, Peter; Wagener, Thorsten

    2016-04-01

    Liver Fluke (Fasciola hepatica) is a common parasite found in livestock and responsible for considerable economic losses throughout the world. Risk of infection is strongly influenced by climatic and hydrological conditions, which characterise the host environment for parasite development and transmission. Despite on-going control efforts, increases in fluke outbreaks have been reported in recent years in the UK, and have been often attributed to climate change. Currently used fluke risk models are based on empirical relationships derived between historical climate and incidence data. However, hydro-climate conditions are becoming increasingly non-stationary due to climate change and direct anthropogenic impacts such as land use change, making empirical models unsuitable for simulating future risk. In this study we introduce a mechanistic hydro-epidemiological model for Liver Fluke, which explicitly simulates habitat suitability for disease development in space and time, representing the parasite life cycle in connection with key environmental conditions. The model is used to assess patterns of Liver Fluke risk for two catchments in the UK under current and potential future climate conditions. Comparisons are made with a widely used empirical model employing different datasets, including data from regional veterinary laboratories. Results suggest that mechanistic models can achieve adequate predictive ability and support adaptive fluke control strategies under climate change scenarios.

  7. Ecological Forecasting in Chesapeake Bay: Using a Mechanistic-Empirical Modelling Approach

    SciTech Connect

    Brown, C. W.; Hood, Raleigh R.; Long, Wen; Jacobs, John M.; Ramers, D. L.; Wazniak, C.; Wiggert, J. D.; Wood, R.; Xu, J.

    2013-09-01

    The Chesapeake Bay Ecological Prediction System (CBEPS) automatically generates daily nowcasts and three-day forecasts of several environmental variables, such as sea-surface temperature and salinity, the concentrations of chlorophyll, nitrate, and dissolved oxygen, and the likelihood of encountering several noxious species, including harmful algal blooms and water-borne pathogens, for the purpose of monitoring the Bay's ecosystem. While the physical and biogeochemical variables are forecast mechanistically using the Regional Ocean Modeling System configured for the Chesapeake Bay, the species predictions are generated using a novel mechanistic empirical approach, whereby real-time output from the coupled physical biogeochemical model drives multivariate empirical habitat models of the target species. The predictions, in the form of digital images, are available via the World Wide Web to interested groups to guide recreational, management, and research activities. Though full validation of the integrated forecasts for all species is still a work in progress, we argue that the mechanistic–empirical approach can be used to generate a wide variety of short-term ecological forecasts, and that it can be applied in any marine system where sufficient data exist to develop empirical habitat models. This paper provides an overview of this system, its predictions, and the approach taken.

  8. A tissue-engineered gastric cancer model for mechanistic study of anti-tumor drugs.

    PubMed

    Gao, Ming; Cai, Yiting; Wu, Wei; Shi, Yazhou; Fei, Zhewei

    2013-08-01

    The use of the traditional xenograft subcutaneous tumor model has been contested because of its limitations, such as a slow tumorigenesis, inconsistent chemotherapeutic results, etc. In light of these challenges, we aim to revamp the traditional model by employing an electrospun scaffold composed of polydioxanone, gelatin and elastin to boost the tumorigenesis. The scaffold featured a highly porous microstructure and successfully supported the growth of tumor cells in vitro without provoking apoptosis. In vivo studies showed that in the scaffold model the tumor volume increased by 43.27% and the weight by 75.58%, respectively, within a 12-week period. In addition, the scaffold model saw an increase of CD24(+) and CD44(+) cells in the tumor mass by 42% and 313%, respectively. The scaffolding materials did not lead to phenotypic changes during the tumorigenesis. Thereafter, in the scaffold model, we found that the chemotherapeutic regimen of docetaxel, cisplatin and fluorouracil unleashed a stronger capability than the regimen comprising cisplatin and fluorouracil to deplete the CD44(+) subpopulation. This discovery sheds mechanistic lights on the role of docetaxel for its future chemotherapeutic applications. This revamped model affords cancer scientists a convenient and reliable platform to mechanistically investigate the chemotherapeutic drugs on gastric cancer stem cells. PMID:23715169

  9. Biomimetic and Live Medusae Reveal the Mechanistic Advantages of a Flexible Bell Margin

    PubMed Central

    Colin, Sean P.; Costello, John H.; Dabiri, John O.; Villanueva, Alex; Blottman, John B.; Gemmell, Brad J.; Priya, Shashank

    2012-01-01

    Flexible bell margins are characteristic components of rowing medusan morphologies and are expected to contribute towards their high propulsive efficiency. However, the mechanistic basis of thrust augmentation by flexible propulsors remained unresolved, so the impact of bell margin flexibility on medusan swimming has also remained unresolved. We used biomimetic robotic jellyfish vehicles to elucidate that propulsive thrust enhancement by flexible medusan bell margins relies upon fluid dynamic interactions between entrained flows at the inflexion point of the exumbrella and flows expelled from under the bell. Coalescence of flows from these two regions resulted in enhanced fluid circulation and, therefore, thrust augmentation for flexible margins of both medusan vehicles and living medusae. Using particle image velocimetry (PIV) data we estimated pressure fields to demonstrate a mechanistic basis of enhanced flows associated with the flexible bell margin. Performance of vehicles with flexible margins was further enhanced by vortex interactions that occur during bell expansion. Hydrodynamic and performance similarities between robotic vehicles and live animals demonstrated that the propulsive advantages of flexible margins found in nature can be emulated by human-engineered propulsors. Although medusae are simple animal models for description of this process, these results may contribute towards understanding the performance of flexible margins among other animal lineages. PMID:23145016

  10. The autism puzzle: challenging a mechanistic model on conceptual and historical grounds

    PubMed Central

    2013-01-01

    Although clinicians and researchers working in the field of autism are generally not concerned with philosophical categories of kinds, a model for understanding the nature of autism is important for guiding research and clinical practice. Contemporary research in the field of autism is guided by the depiction of autism as a scientific object that can be identified with systematic neuroscientific investigation. This image of autism is compatible with a permissive account of natural kinds: the mechanistic property cluster (MPC) account of natural kinds, recently proposed as the model for understanding psychiatric disorders. Despite the heterogeneity, multicausality and fuzzy boundaries that complicate autism research, a permissive account of natural kinds (MPC kinds) provides prescriptive guidance for the investigation of objective causal mechanisms that should inform nosologists in their attempt to carve autism’s boundaries at its natural joints. However, this essay will argue that a mechanistic model of autism is limited since it disregards the way in which autism relates to ideas about what kind of behavior is abnormal. As historical studies and definitions of autism show, normative issues concerning disability, impairment and societal needs have been and still are inextricably linked to how we recognize and understand autism. The current search for autism’s unity in neurobiological mechanisms ignores the values, social norms and various perspectives on mental pathology that play a significant role in 'the thing called autism’. Autism research needs to engage with these issues in order to achieve more success in the effort to become clinically valuable. PMID:24207065

  11. Mechismo: predicting the mechanistic impact of mutations and modifications on molecular interactions

    PubMed Central

    Betts, Matthew J.; Lu, Qianhao; Jiang, YingYing; Drusko, Armin; Wichmann, Oliver; Utz, Mathias; Valtierra-Gutiérrez, Ilse A.; Schlesner, Matthias; Jaeger, Natalie; Jones, David T.; Pfister, Stefan; Lichter, Peter; Eils, Roland; Siebert, Reiner; Bork, Peer; Apic, Gordana; Gavin, Anne-Claude; Russell, Robert B.

    2015-01-01

    Systematic interrogation of mutation or protein modification data is important to identify sites with functional consequences and to deduce global consequences from large data sets. Mechismo (mechismo.russellab.org) enables simultaneous consideration of thousands of 3D structures and biomolecular interactions to predict rapidly mechanistic consequences for mutations and modifications. As useful functional information often only comes from homologous proteins, we benchmarked the accuracy of predictions as a function of protein/structure sequence similarity, which permits the use of relatively weak sequence similarities with an appropriate confidence measure. For protein–protein, protein–nucleic acid and a subset of protein–chemical interactions, we also developed and benchmarked a measure of whether modifications are likely to enhance or diminish the interactions, which can assist the detection of modifications with specific effects. Analysis of high-throughput sequencing data shows that the approach can identify interesting differences between cancers, and application to proteomics data finds potential mechanistic insights for how post-translational modifications can alter biomolecular interactions. PMID:25392414

  12. Mechanistic determinants of the directionality and energetics of active export by a heterodimeric ABC transporter

    DOE PAGESBeta

    Grossmann, Nina; Vakkasoglu, Ahmet S.; Hulpke, Sabine; Abele, Rupert; Gaudet, Rachelle; Tampé, Robert

    2014-11-07

    The ATP-binding cassette (ABC) transporter associated with antigen processing (TAP) participates in immune surveillance by moving proteasomal products into the endoplasmic reticulum (ER) lumen for major histocompatibility complex class I loading and cell surface presentation to cytotoxic T cells. Here we delineate the mechanistic basis for antigen translocation. Notably, TAP works as a molecular diode, translocating peptide substrates against the gradient in a strict unidirectional way. We reveal the importance of the D-loop at the dimer interface of the two nucleotide-binding domains (NBDs) in coupling substrate translocation with ATP hydrolysis and defining transport vectoriality. Substitution of the converved aspartate, whichmore » coordinates the ATP-binding site, decreases NBD dimerization affinity and turns the unidirectional primary active pump into a passive bidirectional nucleotide-gated facilitator. Thus, ATP hydrolysis is not required for translocation per se, but is essential for both active and unidirectional transport. As a result, our data provide detailed mechanistic insight into how heterodimeric ABC exporters operate.« less

  13. Mechanistic determinants of the directionality and energetics of active export by a heterodimeric ABC transporter

    SciTech Connect

    Grossmann, Nina; Vakkasoglu, Ahmet S.; Hulpke, Sabine; Abele, Rupert; Gaudet, Rachelle; Tampé, Robert

    2014-11-07

    The ATP-binding cassette (ABC) transporter associated with antigen processing (TAP) participates in immune surveillance by moving proteasomal products into the endoplasmic reticulum (ER) lumen for major histocompatibility complex class I loading and cell surface presentation to cytotoxic T cells. Here we delineate the mechanistic basis for antigen translocation. Notably, TAP works as a molecular diode, translocating peptide substrates against the gradient in a strict unidirectional way. We reveal the importance of the D-loop at the dimer interface of the two nucleotide-binding domains (NBDs) in coupling substrate translocation with ATP hydrolysis and defining transport vectoriality. Substitution of the converved aspartate, which coordinates the ATP-binding site, decreases NBD dimerization affinity and turns the unidirectional primary active pump into a passive bidirectional nucleotide-gated facilitator. Thus, ATP hydrolysis is not required for translocation per se, but is essential for both active and unidirectional transport. As a result, our data provide detailed mechanistic insight into how heterodimeric ABC exporters operate.

  14. Radical Cyclisation of α-Halo Aluminium Acetals: A Mechanistic Study.

    PubMed

    Bénéteau, Romain; Boussonnière, Anne; Rouaud, Jean-Christophe; Lebreton, Jacques; Graton, Jérôme; Jacquemin, Denis; Sebban, Muriel; Oulyadi, Hassan; Hamdoun, Ghanem; Hancock, Amber N; Schiesser, Carl H; Dénès, Fabrice

    2016-03-24

    α-Bromo aluminium acetals are suitable substrates for Ueno-Stork-like radical cyclisations affording γ-lactols and acid-sensitive methylene-γ-lactols in high yields. The mechanistic study herein sets the scope and limitation of this reaction. The influence of the halide (or chalcogenide) atom X (X=Cl, Br, I, SPh, SePh) in the precursors α-haloesters, as well as influence of the solvent and temperature was studied. The structure of the aluminium acetal intermediates resulting from the reduction of the corresponding α-haloesters has been investigated by low-temperature (13) C-INEPT diffusion-ordered NMR spectroscopy (DOSY) experiments and quantum calculations, providing new insights into the structures of these thermally labile intermediates. Oxygen-bridged dimeric structures with a planar Al2 O2 ring are proposed for the least hindered aluminium acetals, while monomeric structures seem to prevail for the most hindered species. A comparison against the radical cyclisation of aluminium acetals derived from allyl and propargyl alcohols with the parent Ueno-Stork has been made at the BHandHLYP/6-311++G(d,p) level of theory, highlighting mechanistic similarities and differences. PMID:26890896

  15. A Mechanistic Model for CO2 Sequestration in Tiffany Coal Bed Methane Field

    SciTech Connect

    Liang, J.; Raterman, K.T.; Robertson, E.P.

    2003-05-01

    The objective of this project is to develop mechanistic models specific to CO2 sequestration in BP's Tiffany coal bed methane (CBM) field. In this study, the original field model was modified to match the field performance of a 5-spot pattern in the northern part of the Tiffany Field where BP plans to perform a micro-pilot test. The modified model consists of one high-permeability fast layer sandwiched between two low-permeability slow layers. In this mechanistic model, the fast layer represents well-cleated and fractured coal from all geological layers while the slow layers represent coal with little or no fracture development from the same geological layers. The model successfully matched the performance of the 5-spot pattern during the enhanced recovery period. However, in order to match nitrogen breakthrough times and nitrogen cut the vertical transmissibility between layers had to be set to zero. During gas injection, nitrogen was allowed to enter all three layers, not just the high-permeability fast layer. However, because the permeabilities of the slow layers were low and there is no communication between the fast and the slow layers, most of the injected nitrogen entered the high-permeability fast layer. This suggests that the future gas injection and CO2 sequestration may be restricted to only one third of the total available pay.

  16. Radioactive deposits in California

    USGS Publications Warehouse

    Walker, George W.; Lovering, Tom G.

    1954-01-01

    Reconnaissance examination by Government geologists of many areas, mine properties, and prospects in California during the period between 1948 and 1953 has confirmed the presence of radioactive materials in place at more than 40 localities. Abnormal radioactivity at these localities is due to concentrations of primary and secondary uranium minerals, to radon gas, radium (?), and to thorium minerals. Of the known occurrences only three were thought to contain uranium oxide (uranitite or pitchblende), 4 contained uranium-bearing columbate, tantalate, or titanate minerals, 12 contained secondary uranium minerals, such as autunite, carnotite, and torbernite, one contained radon gas, 7 contained thorium minerals, and, at the remaining 16 localities, the source of the anomalous radiation was not positively determined. The occurrences in which uranium oxide has been tentatively identified include the Rathgeb mine (Calaveras County), the Yerih group of claims (San Bernardino County), and the Rainbow claim (Madera County). Occurrences of secondary uranium minerals are largely confined to the arid desert regions of south-eastern California including deposits in San Bernardino, Kern, Inyo, and Imperial Counties. Uranium-bearing columbate, tantalate, or titanate minerals have been reported from pegmatite and granitic rock in southeastern and eastern California. Thorium minerals have been found in vein deposits in eastern San Bernardino County and from pegmatites and granitic rocks in various parts of southeastern California; placer concentrations of thorium minerals are known from nearly all areas in the State that are underlain, in part, by plutonic crystalline rocks. The primary uranium minerals occur principally as minute accessory crystals in pegmatite or granitic rock, or with base-metal sulfide minerals in veins. Thorium minerals also occur as accessory crystals in pegmatite or granitic rock, in placer deposits derived from such rock, and, at Mountain Pass, in veins

  17. A Mechanistic Proof-of-concept Clinical Trial With JX-594, a Targeted Multi-mechanistic Oncolytic Poxvirus, in Patients With Metastatic Melanoma

    PubMed Central

    Hwang, Tae-Ho; Moon, Anne; Burke, James; Ribas, Antoni; Stephenson, Joe; Breitbach, Caroline J; Daneshmand, Manijeh; De Silva, Naomi; Parato, Kelley; Diallo, Jean-Simon; Lee, Yeon-Sook; Liu, Ta-Chiang; Bell, John C; Kirn, David H

    2011-01-01

    JX-594 is a targeted and granulocyte macrophage-colony stimulating factor (GM-CSF)-expressing oncolytic poxvirus designed to selectively replicate in and destroy cancer cells through viral oncolysis and tumor-specific immunity. In order to study the mechanisms-of-action (MOA) of JX-594 in humans, a mechanistic proof-of-concept clinical trial was performed at a low dose equivalent to ≤10% of the maximum-tolerated dose (MTD) in other clinical trials. Ten patients with previously treated stage IV melanoma were enrolled. Tumors were injected weekly for up to nine total treatments. Blood samples and tumor biopsies were analyzed for evidence of transgene activity, virus replication, and immune stimulation. The β-galactosidase (β-gal) transgene was expressed in all patients as evidenced by antibody induction. Six patients had significant induction of GM-CSF-responsive white blood cell (WBC) subsets such as neutrophils (25–300% increase). JX-594 replication and subsequent shedding into blood was detectable in five patients after cycles 1–9. Tumor biopsies demonstrated JX-594 replication, perivascular lymphocytic infiltration, and diffuse tumor necrosis. Mild flu-like symptoms were the most common adverse events. In sum, JX-594 replication, oncolysis, and expression of both transgenes were demonstrated; replication was still evident after multiple cycles. These findings have implications for further clinical development of JX-594 and other transgene-armed oncolytic viruses. PMID:21772252

  18. Mechanistic Studies at the Interface Between Organometallic Chemistry and Homogeneous Catalysis

    SciTech Connect

    Casey, Charles P

    2012-11-14

    Mechanistic Studies at the Interface Between Organometallic Chemistry and Homogeneous Catalysis Charles P. Casey, Principal Investigator Department of Chemistry, University of Wisconsin - Madison, Madison, Wisconsin 53706 Phone 608-262-0584 FAX: 608-262-7144 Email: casey@chem.wisc.edu http://www.chem.wisc.edu/main/people/faculty/casey.html Executive Summary. Our goal was to learn the intimate mechanistic details of reactions involved in homogeneous catalysis and to use the insight we gain to develop new and improved catalysts. Our work centered on the hydrogenation of polar functional groups such as aldehydes and ketones and on hydroformylation. Specifically, we concentrated on catalysts capable of simultaneously transferring hydride from a metal center and a proton from an acidic oxygen or nitrogen center to an aldehyde or ketone. An economical iron based catalyst was developed and patented. Better understanding of fundamental organometallic reactions and catalytic processes enabled design of energy and material efficient chemical processes. Our work contributed to the development of catalysts for the selective and mild hydrogenation of ketones and aldehydes; this will provide a modern green alternative to reductions by LiAlH4 and NaBH4, which require extensive work-up procedures and produce waste streams. (C5R4OH)Ru(CO)2H Hydrogenation Catalysts. Youval Shvo described a remarkable catalytic system in which the key intermediate (C5R4OH)Ru(CO)2H (1) has an electronically coupled acidic OH unit and a hydridic RuH unit. Our efforts centered on understanding and improving upon this important catalyst for reduction of aldehydes and ketones. Our mechanistic studies established that the reduction of aldehydes by 1 to produce alcohols and a diruthenium bridging hydride species occurs much more rapidly than regeneration of the ruthenium hydride from the diruthenium bridging hydride species. Our mechanistic studies require simultaneous transfer of hydride from ruthenium to

  19. Electron beam deposition for nanofabrication: Insights from surface science

    NASA Astrophysics Data System (ADS)

    Wnuk, J. D.; Rosenberg, S. G.; Gorham, J. M.; van Dorp, W. F.; Hagen, C. W.; Fairbrother, D. H.

    2011-02-01

    Electron beam induced deposition (EBID) is a direct-write lithographic technique that utilizes the dissociation of volatile precursors by a focused electron beam in a low vacuum environment to create nanostructures. Notable advantages of EBID over competing lithographic techniques are that it is a single step process that allows three-dimensional free-standing structures to be created, including features with single-nanometer scale dimensions. However, despite the inherent advantages of EBID, scientific and technological issues are impeding its development as an industrial nanofabrication tool. Perhaps the greatest single limitation of EBID is that metal-containing nanostructures deposited from organometallic precursors typically possess unacceptable levels of organic contamination which adversely affects the material's properties. In addition to the issue of purity, there is also a lack of understanding and quantitative information on the fundamental surface reactions and reaction cross-sections that are responsible for EBID. In this prospective, we describe how surface analytical techniques have begun to provide mechanistic and kinetic insights into the molecular level processes associated with EBID. This has been achieved by observing the effect of electron irradiation on nanometer thick films of organometallic precursors adsorbed onto solid substrates at low temperatures (< 200 K) under ultra-high vacuum conditions. Experimental observations include probing changes in surface composition, metal oxidation state, and the evolution of volatile species. Insights into surface reactions associated with purification strategies are also detailed. We also discuss unresolved scientific challenges and opportunities for future EBID research.

  20. Experimental reproduction of tsunami deposit

    NASA Astrophysics Data System (ADS)

    Yoshii, T.; Matsuyama, M.; Tanaka, S.

    2015-12-01

    Understanding the process of sediment transport and deposition under a tsunami inundation is essential to provide the credible information about potential tsunamis from tsunami deposits. Detections of tsunami deposit has contributed to reveal centuries-old record of tsunami incursions. However, our knowledge is still not enough for evaluating the scale of past tsunamis using deposits. In this study, a laboratory experiment was conducted to investigate the relationship between the hydraulic condition and sedimentological features of tsunami deposit. The large wave flume in CRIEPI, one of the largest wave flume in the world, which has 205 m length, 3.4 m width and 6 m depth was used. The sandy beach with uniform slope (1/50) were made in the flume. Sand dune of 0.2 high was placed near the shoreline. The tsunami was made by the wave generator which has 2.2 m stroke. The wave at the shore line has 0.6 m depth and the horizontal velocity reached up to 3.5 m/s. The incursion of the wave and its return flow completely washed out the dune and resulted in the deposition especially near the dune. The thickness of deposit shows landward thinning and fining, which has been widely confirmed by field observations. In addition, sedimentary structures of the deposit was investigated using the method similar to that used in geological survey such as core sampling and relief peel sampling. The obtained samples were investigated using a X-ray computed tomography. The obtained CT-images shows that most part of deposition consists two or more subsections divided by horizontal lamination although the deposition near the dune has drastic and complex change thickness and grain size. The subsections shows upward-fining and upward-coarsening which are been reported as common sedimentary structures of tsunami deposit from field surveys. Considering the similarity of sedimentary structures in the deposit reconstructed in this experiment and actual tsunami deposits, this experiment succeeded

  1. Chemical vapor deposition growth

    NASA Technical Reports Server (NTRS)

    Ruth, R. P.; Manasevit, H. M.; Kenty, J. L.; Moudy, L. A.; Simpson, W. I.; Yang, J. J.

    1976-01-01

    The chemical vapor deposition (CVD) method for the growth of Si sheet on inexpensive substrate materials is investigated. The objective is to develop CVD techniques for producing large areas of Si sheet on inexpensive substrate materials, with sheet properties suitable for fabricating solar cells meeting the technical goals of the Low Cost Silicon Solar Array Project. Specific areas covered include: (1) modification and test of existing CVD reactor system; (2) identification and/or development of suitable inexpensive substrate materials; (3) experimental investigation of CVD process parameters using various candidate substrate materials; (4) preparation of Si sheet samples for various special studies, including solar cell fabrication; (5) evaluation of the properties of the Si sheet material produced by the CVD process; and (6) fabrication and evaluation of experimental solar cell structures, using standard and near-standard processing techniques.

  2. Depositing Diamondlike Carbon Films

    NASA Technical Reports Server (NTRS)

    Mirtich, M. J.; Sovey, J. S.; Banks, B. A.

    1986-01-01

    New process demonstrated to make thin films (usually thousands of angstroms to few microns thick) that have properties of diamonds. Various plasma and ion-beam techniques employed to generate films. Films made by radio-frequency plasma decomposition of hydrocarbon gas or other alkanes, by low-energy carbon-ion-beam deposition, or by ion plating and dual ion technique using carbon target. Advantages of new process over others are films produced, though amorphous, are clear, extremely hard, chemically inert, of high resistivity, and have index of refraction of 3.2 properties similar to those of single-crystal diamonds. Films have possible uses in microelectronic applications, high-energy-laser and plastic windows, corrosion protection for metals, and other applications where desired properties of film shaped during the film-formation process.

  3. A Mechanistic Explanation of the Peculiar Amphiphobic Properties of Hybrid Organic-Inorganic Coatings by Combining XPS Characterization and DFT Modeling.

    PubMed

    Motta, Alessandro; Cannelli, Oliviero; Boccia, Alice; Zanoni, Robertino; Raimondo, Mariarosa; Caldarelli, Aurora; Veronesi, Federico

    2015-09-16

    We report a combined X-ray photoelectron spectroscopy and theoretical modeling analysis of hybrid functional coatings constituted by fluorinated alkylsilane monolayers covalently grafted on a nanostructured ceramic oxide (Al2O3) thin film deposited on aluminum alloy substrates. Such engineered surfaces, bearing hybrid coatings obtained via a classic sol-gel route, have been previously shown to possess amphiphobic behavior (superhydrophobicity plus oleophobicity) and excellent durability, even under simulated severe working environments. Starting from XPS, SEM, and contact angle results and analysis, and combining it with DFT results, the present investigation offers a first mechanistic explanation at a molecular level of the peculiar properties of the hybrid organic-inorganic coating in terms of composition and surface structural arrangements. Theoretical modeling shows that the active fluorinated moiety is strongly anchored on the alumina sites with single Si-O-Al bridges and that the residual valence of Si is saturated by Si-O-Si bonds which form a reticulation with two vicinal fluoroalkylsilanes. The resulting hybrid coating consists of stable rows of fluorinated alkyl chains in reciprocal contact, which form well-ordered and packed monolayers. PMID:26308186

  4. Mechanistic aspects of the ethanol steam reforming reaction for hydrogen production on Pt, Ni, and PtNi catalysts supported on gamma-Al2O3.

    PubMed

    Sanchez-Sanchez, Maria Cruz; Navarro Yerga, Rufino M; Kondarides, Dimitris I; Verykios, Xenophon E; Fierro, Jose Luis G

    2010-03-25

    Mechanistic aspects of ethanol steam reforming on Pt, Ni, and PtNi catalysts supported on gamma-Al(2)O(3) are investigated from the analysis of adsorbed species and gas phase products formed on catalysts during temperature-programmed desorption of ethanol and during ethanol steam reforming reaction. DRIFTS-MS analyses of ethanol decomposition and ethanol steam reforming reactions show that PtNi and Ni catalysts are more stable than the Pt monometallic counterpart. Ethanol TPD results on Ni, Pt, and NiPt catalysts point to ethanol dehydrogenation and acetaldehyde decomposition as the first reaction pathways of ethanol steam reforming over the studied catalysts. The active sites responsible for the acetaldehyde decomposition are easily deactivated in the first minutes on-stream by carbon deposits. For Ni and PtNi catalysts, a second reaction pathway, consisting in the decomposition of acetate intermediates formed over the surface of alumina support, becomes the main reaction pathway operating in steam reforming of ethanol once the acetaldehyde decomposition pathway is deactivated. Taking into account the differences observed in the mechanism of ethanol decomposition, the better stability observed for PtNi catalyst is proposed to be related with a cooperative effect between Pt and Ni activities together with the enhanced ability of Ni to gasify the methyl groups formed by decomposition of acetate species. On the contrary, monometallic catalysts are believed to dehydrogenate these methyl groups forming coke that leads to deactivation of metal particles. PMID:19824680

  5. Lunar western limb pyroclastic deposits

    NASA Technical Reports Server (NTRS)

    Coombs, Cassandra R.; Hawke, B. Ray

    1991-01-01

    It has become increasingly evident that the lunar pyroclastic volcanism played an important role in the formation and resurfacing of many areas of the Moon. On-going analysis of lunar Orbiter and Apollo photographs continues to locate and identify pyroclastic deposits and suggests that they just may be more ubiquitous than once thought. Located near mare/highland boundaries, many of these deposits formed contemporaneously with effusive mare volcanism. The mantling deposits formed as products of fire-fountaining. Probable source vents for these deposits include irregular depressions at the head of associated sinuous rilles and/or along irregular fractures in the floors of ancient craters. Here, researchers provide a brief synopsis of the nature of the dark mantling deposits and briefly discuss several newly identified deposits on the western limb.

  6. Global deposition of airborne dioxin.

    PubMed

    Booth, Shawn; Hui, Joe; Alojado, Zoraida; Lam, Vicky; Cheung, William; Zeller, Dirk; Steyn, Douw; Pauly, Daniel

    2013-10-15

    We present a global dioxin model that simulates one year of atmospheric emissions, transport processes, and depositions to the earth's terrestrial and marine habitats. We map starting emission levels for each land area, and we also map the resulting deposits to terrestrial and marine environments. This model confirms that 'hot spots' of deposition are likely to be in northern Europe, eastern North America, and in parts of Asia with the highest marine dioxin depositions being the northeast and northwest Atlantic, western Pacific, northern Indian Ocean and the Mediterranean. It also reveals that approximately 40% of airborne dioxin emissions are deposited to marine environments and that many countries in Africa receive more dioxin than they produce, which results in these countries being disproportionately impacted. Since human exposure to dioxin is largely through diet, this work highlights food producing areas that receive higher atmospheric deposits of dioxin than others. PMID:23962732

  7. Iron Trichloride and Air Mediated Guanylation of Acylthioureas. An Ecological Route to Acylguanidines: Scope and Mechanistic Insights.

    PubMed

    Pape, Simon; Wessig, Pablo; Brunner, Heiko

    2016-06-01

    Recently we introduced iron trichloride as an environmentally benign and cost-efficient reagent for the synthesis of N-benzoylguanidines. This highly attractive synthetic approach grants access to a broad spectrum of N-benzoylguanidines under mild conditions in short reaction times. In this work we present an extended scope of our methodology along with the results obtained from mechanistic studies via in situ IR spectroscopy in combination with LC (liquid chromatography)-MS analyses. On the basis of these new mechanistic insights we were able to optimize the synthetic protocol and to develop an alternative mechanistic proposal. In this context the symbiotic roles of iron trichloride and oxygen in the guanylation process are highlighted. PMID:27181741

  8. Momentum Deposition in Curvilinear Coordinates

    SciTech Connect

    Cleveland, Mathew Allen; Lowrie, Robert Byron; Rockefeller, Gabriel M.; Thompson, Kelly Glen; Wollaber, Allan Benton

    2015-08-03

    The momentum imparted into a material by thermal radiation deposition is an important physical process in astrophysics and inertial confinement fusion (ICF) simulations. In recent work we presented a new method of evaluating momentum deposition that relies on the combination of a time-averaged approximation and a numerical integration scheme. This approach robustly and efficiently evaluates the momentum deposition in spherical geometry. Future work will look to extend this approach to 2D cylindrical geometries.

  9. Determination of the upper and lower limits of the mechanistic stoichiometry of incompletely coupled fluxes. Stoichiometry of incompletely coupled reactions.

    PubMed

    Beavis, A D; Lehninger, A L

    1986-07-15

    A rationale is formulated for the design of experiments to determine the upper and lower limits of the mechanistic stoichiometry of any two incompletely coupled fluxes J1 and J2. Incomplete coupling results when there is a branch at some point in the sequence of reactions or processes coupling the two fluxes. The upper limit of the mechanistic stoichiometry is given by the minimum value of dJ2/dJ1 obtained when the fluxes are systematically varied by changes in steps after the branch point. The lower limit is given by the maximum value of dJ2/dJ1 obtained when the fluxes are varied by changes in steps prior to the branch point. The rationale for determining these limits is developed from both a simple kinetic model and from a linear nonequilibrium thermodynamic treatment of coupled fluxes, using the mechanistic approach [Westerhoff, H. V. & van Dam, K. (1979) Curr. Top. Bioenerg. 9, 1-62]. The phenomenological stoichiometry, the flux ratio at level flow and the affinity ratio at static head of incompletely coupled fluxes are defined in terms of mechanistic conductances and their relationship to the mechanistic stoichiometry is discussed. From the rationale developed, experimental approaches to determine the mechanistic stoichiometry of mitochondrial oxidative phosphorylation are outlined. The principles employed do not require knowledge of the pathway or the rate of transmembrane leaks or slippage and may also be applied to analysis of the stoichiometry of other incompletely coupled systems, including vectorial H+/O and K+/O translocation coupled to mitochondrial electron transport. PMID:3015612

  10. (Acidic deposition and the environment)

    SciTech Connect

    Garten, C.T.; Lindberg, S.E.; Van Miegroet, H.

    1990-10-24

    The travelers presented several papers at the Fourth International Conference on Acidic Deposition. These covered the following topics: atmospheric chemistry and deposition of airborne nitrogen compounds, soil solution chemistry in high-elevation spruce forests, and forest throughfall measurements for estimating total sulfur deposition to ecosystems. In addition, S. E. Lindberg was invited to organize and chair a conference session on Throughfall and Stemflow Experiments, and to present an invited lecture on Atmospheric Deposition and Canopy Interactions of Metals and Nitrogen in Forest Ecosystems: The Influence of Global Change'' at the 110th Anniversary Celebration of the Free University of Amsterdam.

  11. A mechanistic code for intact and defective nuclear fuel element performance

    NASA Astrophysics Data System (ADS)

    Shaheen, Khaled

    During reactor operation, nuclear fuel elements experience an environment featuring high radiation, temperature, and pressure. Predicting in-reactor performance of nuclear fuel elements constitutes a complex multi-physics problem, one that requires numerical codes to be solved. Fuel element performance codes have been developed for different reactor and fuel designs. Most of these codes simulate fuel elements using one-or quasi-two-dimensional geometries, and some codes are only applicable to steady state but not transient behaviour and vice versa. Moreover, while many conceptual and empirical separate-effects models exist for defective fuel behaviour, wherein the sheath is breached allowing coolant ingress and fission gas escape, there have been few attempts to predict defective fuel behaviour in the context of a mechanistic fuel performance code. Therefore, a mechanistic fuel performance code, called FORCE (Fuel Operational peRformance Computations in an Element) is proposed for the time-dependent behaviour of intact and defective CANDU nuclear fuel elements. The code, which is implemented in the COMSOL Multiphysics commercial software package, simulates the fuel, sheath, and fuel-to-sheath gap in a radial-axial geometry. For intact fuel performance, the code couples models for heat transport, fission gas production and diffusion, and structural deformation of the fuel and sheath. The code is extended to defective fuel performance by integrating an adapted version of a previously developed fuel oxidation model, and a model for the release of radioactive fission product gases from the fuel to the coolant. The FORCE code has been verified against the ELESTRES-IST and ELESIM industrial code for its predictions of intact fuel performance. For defective fuel behaviour, the code has been validated against coulometric titration data for oxygen-to-metal ratio in defective fuel elements from commercial reactors, while also being compared to a conceptual oxidation model

  12. A reductionist mechanistic model for bioconcentration of neutral and weakly polar organic compounds in fish.

    PubMed

    Kuo, Dave T F; Di Toro, Dominic M

    2013-09-01

    The bioconcentration factor (BCF) of neutral and weakly polar organic chemicals in fish is modeled using independently calibrated models of chemical partitioning (freely dissolved fraction of chemical in the aqueous phase [φsys ] and wet-weight fish-water partition coefficient [KFW ]), respiratory exchange (respiratory update rate constant [k1 ], and respiratory elimination rate constant [k2  = k1 /KFW ]), and biotransformation (whole-body biotransformation rate constant [kM ]) as BCF = φsys KFW /(1 + kM /k2 ). Existing k1 models tend to overestimate for chemicals with log KOW  < 3.5, which constituted 30% to 50% of the examined chemicals. A revised k1 model covering a wider log KOW range (0-8.5) is presented k1  = (5.46 × 10(-6) MW + 0.261/KOW )(-1) , where MW is the molecular weight. The biotransformation rate constant kM is modeled using biota internal partitioning and Abraham parameters as reactivity descriptors. The reductionist model was tested using 3 different BCF data sets (US Environmental Protection Agency's Estimation Programs Interface [EPI], n = 548; Hertfordshire, n = 210; Arnot-Gobas, n = 1855) and compared with the following 3 state-of-the-art models: 1) the EPI Suite BCFBAF module, 2) the European Commision's Computer Assisted Evaluation of industrial chemical Substances According to Regulations (CAESAR), and 3) the EPI/Arnot mechanistic kinetic model. The reductionist model performed comparably with the alternative models (root mean square errors [RMSEs] = 0.72-0.77), with only 5 fitting parameters and no training against experimental BCFs. Respiratory elimination and biotransformation dominate the total depuration (i.e., [k2  + kM ]/kT  ≥ 0.8) for approximately 98% of the data entries, thus validating the reductionist approximation. Mechanistic models provide greater insights into bioaccumulation and are more sensitive to biological variation. All three BCF data sets and relevant

  13. Bridging the gap between empirical and mechanistic models for nitrate in groundwater

    NASA Astrophysics Data System (ADS)

    Nolan, B. T.; Malone, R. W.; Gronberg, J.; Thorp, K.; Ma, L.

    2011-12-01

    Water-quality models are useful tools for predicting the vulnerability of groundwater to nitrate contamination, and include both empirical and mechanistic approaches. Empirical models commonly are used at regional and national scales. Such models are data-driven and have comparatively few parameters, but their capability to simulate processes is limited. In contrast, mechanistic models are physically based, simulate controlling processes, and can have many parameters. The GroundWAter Vulnerability Assessment model (GWAVA), an example of the first approach, is a national-scale nonlinear regression model (R2=0.80) that predicts areally averaged nitrate concentration in groundwater based on mid-1990s land use. The Root Zone Water Quality Model (RZWQM2) is an example of the second approach and simulates N cycling processes, crop growth, and the fate and transport of agricultural chemicals at the field-scale for daily time steps. Thorough accounting by RZWQM2 of key processes can yield more accurate predictions, but application at large spatial scales is difficult because of the numerous parameters. To bridge the gap between these contrasting scales and approaches, we developed metamodels (MMs) to predict nitrate concentrations and N fluxes in the Corn Belt. Metamodels are simplified representations of mechanistic models which map outputs from the latter onto the inputs. Our MMs consisted of artificial neural networks (ANNs), which are inherently flexible and do not require linearity or normally distributed data. The MMs were based on RZWQM2 models previously calibrated to data from field sites in Nebraska, Iowa, and Maryland. The three sites are in corn-soybean rotation and reflect diverse soil types and climatic conditions as well as different management practices. We calibrated the MMs to RZWQM2 predictions of N in tile drainage and leachate below the root zone of crops. Therefore the MMs represent an integrated approach to vulnerability assessment-nitrate leaching

  14. Intermolecular hydroamination of vinylarenes by iminoanilide alkaline-earth catalysts: a computational scrutiny of mechanistic pathways.

    PubMed

    Tobisch, Sven

    2014-07-14

    A thorough computational exploration of the mechanistic intricacies of the intermolecular hydroamination (HA) of vinylarenes by a recently reported class of kinetically stabilised iminoanilide [{N^N}Ae{N(SiMe3)2}⋅(THF)n] alkaline-earth amido compounds (Ae = Ca, Sr, Ba) is presented. Two distinct mechanistic pathways for catalytic HA mediated by alkaline-earth and rare-earth compounds have emerged over the years that account equally well for the specific features of the process. On one hand, a concerted proton-assisted pathway to deliver the amine product in a single step can be invoked and, on the other, a stepwise σ-insertive pathway that comprises a rapid, reversible migratory olefin insertion step linked to a less facile, irreversible Ae-C alkyl bond aminolysis. The results of the study presented herein, which employed a heavily benchmarked and reliable DFT methodology, supports a stepwise σ-insertive pathway that involves fast and reversible migratory C=C bond insertion into the polar Ae-N pyrrolido σ bond. This proceeds with strict 2,1 regioselectivity via a highly polarised four-centre transition state (TS) structure, linked to irreversible intramolecular Ae-C bond aminolysis of the alkaline-earth alkyl intermediate as the energetically favourable mechanism. Turnover-limiting aminolysis is consistent with the significant KIE measured; the DFT-derived effective barrier matches the Eyring parameter empirically determined for the best-performing {N^N}Ba(NR2) catalyst gratifyingly well. It also predicts the observed trend in reactivity (Ca

  15. Mechanistic models of plant seed dispersal by wind in heterogeneous landscapes

    NASA Astrophysics Data System (ADS)

    Trakhtenbrot, A.; Katul, G. G.; Nathan, R.

    2010-12-01

    Seed dispersal, and especially long-distance dispersal (LDD), is a key process in plant population survival, colonization, and gene flow. Its importance is amplified by the man-induced habitat fragmentation, climate change and invasions of exotic species. Mechanistic seed dispersal models are central to quantitative prediction of dispersal patterns and understanding their underlying mechanisms. For wind dispersal, most current mechanistic models assume homogenous environment. Although both topography and sharp transitions in vegetation stature profoundly affect wind flow, accounting for these effects via simplified models remains a vexing research problem. Such simplified models are needed to inform ecosystem managers about consequences of landscape fragmentation. We modified the Coupled Eulerian-Lagrangian closure (CELC) mechanistic dispersal model to represent scenarios of wind flow over a sharp transition from short to tall vegetation or over forested hilly terrain, and predicted the resulting dispersal distances and direction. We parameterized the wind and vegetation factors using measurements taken on a hill with short height Mediterranean shrubland and pine forest vegetation at Mt. Pithulim, Israel. For the short-to-tall vegetation transition scenario, the main feature of the modeled wind field is an exponential decay of the mean horizontal wind velocity, assuming that the mean momentum equation simplifies to a balance between the advective acceleration and the drag force terms. As a consequence of the incompressibility condition, this exponential decay leads to strong upward mean vertical velocity component. We found that for seed release downwind of the edge, the simulated median (short) and 99-th percentile (long) distances were longer than those for the homogeneous tall vegetation scenario. For seed release upwind of the edge the effect on dispersal distance was more complex and depended on the release height and he seed terminal velocity of the seeds

  16. Mechanistic study of copper-catalyzed aerobic oxidative coupling of arylboronic esters and methanol: insights into an organometallic oxidase reaction.

    PubMed

    King, Amanda E; Brunold, Thomas C; Stahl, Shannon S

    2009-04-15

    Copper-catalyzed aerobic oxidative coupling of arylboronic acid derivatives and heteroatom nucleophiles is a highly useful method for the formation of aryl-heteroatom bonds. Mechanistic studies reveal that this reaction proceeds via an "oxidase"-style mechanism. Kinetic and spectroscopic studies establish that transmetalation of the aryl group from boron to Cu(II) is the turnover-limiting step and reoxidation of the reduced catalyst by O(2) is rapid. Further mechanistic analysis implicates the involvement of an aryl-copper(III) intermediate that undergoes facile C-O bond formation. PMID:19309072

  17. Recent developments in using mechanistic cardiac modelling for drug safety evaluation.

    PubMed

    Davies, Mark R; Wang, Ken; Mirams, Gary R; Caruso, Antonello; Noble, Denis; Walz, Antje; Lavé, Thierry; Schuler, Franz; Singer, Thomas; Polonchuk, Liudmila

    2016-06-01

    On the tenth anniversary of two key International Conference on Harmonisation (ICH) guidelines relating to cardiac proarrhythmic safety, an initiative aims to consider the implementation of a new paradigm that combines in vitro and in silico technologies to improve risk assessment. The Comprehensive In Vitro Proarrhythmia Assay (CiPA) initiative (co-sponsored by the Cardiac Safety Research Consortium, Health and Environmental Sciences Institute, Safety Pharmacology Society and FDA) is a bold and welcome step in using computational tools for regulatory decision making. This review compares and contrasts the state-of-the-art tools from empirical to mechanistic models of cardiac electrophysiology, and how they can and should be used in combination with experimental tests for compound decision making. PMID:26891981

  18. Mechanistic differences between methanol and dimethyl ether carbonylation in side pockets and large channels of mordenite.

    PubMed

    Boronat, Mercedes; Martínez, Cristina; Corma, Avelino

    2011-02-21

    The activity and selectivity towards carbonylation presented by Brønsted acid sites located inside the 8MR pockets or in the main 12MR channels of mordenite is studied by means of quantum-chemical calculations, and the mechanistic differences between methanol and DME carbonylation are investigated. The selectivity towards carbonylation is higher inside the 8MR pockets, where the competitive formation of DME and hydrocarbons that finally leads to catalyst deactivation is sterically impeded. Moreover, inclusion of dispersion interactions in the calculations leads to agreement between the calculated activation barriers for the rate determining step and the experimentally observed higher reactivity of methoxy groups located inside the 8MR channels. PMID:21249237

  19. Dual effect of red wine on liver redox status: a concise and mechanistic review.

    PubMed

    Silva, Paula; Fernandes, Eduarda; Carvalho, Félix

    2015-10-01

    Chronic ethanol consumption is a strong risk factor for the development of liver disease. Multiple mechanisms are involved in ethanol-mediated liver injury; oxidative stress being pointed has an important factor. However, it should be noted that moderate consumption of red wine has been associated with hepatoprotective effects, mainly due to the antioxidant effect of resveratrol, one of its polyphenolic compounds. In this paper, the potential molecular mechanisms through which the protective effects of resveratrol counteract the oxidative effect of ethanol and the way as this dual effect impacts liver oxidative stress are reviewed. Mechanistic evaluation of modulation of oxidative signaling pathways by ethanol and resveratrol may explain the pathogenesis of various liver diseases and ultimately to disclose possible pharmacological therapies. PMID:26026610

  20. Phase Stability of t;#8242;-Zirconia-Based Thermal Barrier Coatings: Mechanistic Insights

    SciTech Connect

    Krogstad, Jessica A.; Krämer, Stephan; Lipkin, Don M.; Johnson, Curtis A.; Mitchell, David R.G.; Cairney, Julie M.; Levi, Carlos G.

    2011-11-07

    The temperature capability of yttria-stabilized zirconia thermal barrier coatings (TBCs) is ultimately tied to the rate of evolution of the 'nontransformable' t' phase into a depleted tetragonal form predisposed to the monoclinic transformation on cooling. The t' phase, however, has been shown to decompose in a small fraction of the time necessary to form the monoclinic phase. Instead, a modulated microstructure consisting of a coherent array of Y-rich and Y-lean lamellar phases develops early in the process, with mechanistic features suggestive of spinodal decomposition. Coarsening of this microstructure leads to loss of coherency and ultimately transformation into the monoclinic form, making the kinetics of this process, and not the initial decomposition, the critical factor in determining the phase stability of TBCs. Transmission electron microscopy is shown to be essential not only for characterizing the microstructure but also for proper interpretation of X-ray diffraction analysis.

  1. Antimalarial benzoheterocyclic 4-aminoquinolines: Structure-activity relationship, in vivo evaluation, mechanistic and bioactivation studies.

    PubMed

    Ongarora, Dennis S B; Strydom, Natasha; Wicht, Kathryn; Njoroge, Mathew; Wiesner, Lubbe; Egan, Timothy J; Wittlin, Sergio; Jurva, Ulrik; Masimirembwa, Collen M; Chibale, Kelly

    2015-09-01

    A novel class of benzoheterocyclic analogues of amodiaquine designed to avoid toxic reactive metabolite formation was synthesized and evaluated for antiplasmodial activity against K1 (multidrug resistant) and NF54 (sensitive) strains of the malaria parasite Plasmodium falciparum. Structure-activity relationship studies led to the identification of highly promising analogues, the most potent of which had IC50s in the nanomolar range against both strains. The compounds further demonstrated good in vitro microsomal metabolic stability while those subjected to in vivo pharmacokinetic studies had desirable pharmacokinetic profiles. In vivo antimalarial efficacy in Plasmodium berghei infected mice was evaluated for four compounds, all of which showed good activity following oral administration. In particular, compound 19 completely cured treated mice at a low multiple dose of 4×10mg/kg. Mechanistic and bioactivation studies suggest hemozoin formation inhibition and a low likelihood of forming quinone-imine reactive metabolites, respectively. PMID:26264839

  2. Helical-Peptide-Catalyzed Enantioselective Michael Addition Reactions and Their Mechanistic Insights.

    PubMed

    Ueda, Atsushi; Umeno, Tomohiro; Doi, Mitsunobu; Akagawa, Kengo; Kudo, Kazuaki; Tanaka, Masakazu

    2016-08-01

    Helical peptide foldamer catalyzed Michael addition reactions of nitroalkane or dialkyl malonate to α,β-unsaturated ketones are reported along with the mechanistic considerations of the enantio-induction. A wide variety of α,β-unsaturated ketones, including β-aryl, β-alkyl enones, and cyclic enones, were found to be catalyzed by the helical peptide to give Michael adducts with high enantioselectivities (up to 99%). On the basis of X-ray crystallographic analysis and depsipeptide study, the amide protons, N(2)-H and N(3)-H, at the N terminus in the α-helical peptide catalyst were crucial for activating Michael donors, while the N-terminal primary amine activated Michael acceptors through the formation of iminium ion intermediates. PMID:27384597

  3. Combating Pathogenic Microorganisms Using Plant-Derived Antimicrobials: A Minireview of the Mechanistic Basis

    PubMed Central

    Upadhyaya, Indu; Kollanoor-Johny, Anup

    2014-01-01

    The emergence of antibiotic resistance in pathogenic bacteria has led to renewed interest in exploring the potential of plant-derived antimicrobials (PDAs) as an alternative therapeutic strategy to combat microbial infections. Historically, plant extracts have been used as a safe, effective, and natural remedy for ailments and diseases in traditional medicine. Extensive research in the last two decades has identified a plethora of PDAs with a wide spectrum of activity against a variety of fungal and bacterial pathogens causing infections in humans and animals. Active components of many plant extracts have been characterized and are commercially available; however, research delineating the mechanistic basis of their antimicrobial action is scanty. This review highlights the potential of various plant-derived compounds to control pathogenic bacteria, especially the diverse effects exerted by plant compounds on various virulence factors that are critical for pathogenicity inside the host. In addition, the potential effect of PDAs on gut microbiota is discussed. PMID:25298964

  4. Pathophysiology of white-nose syndrome in bats: a mechanistic model linking wing damage to mortality.

    PubMed

    Warnecke, Lisa; Turner, James M; Bollinger, Trent K; Misra, Vikram; Cryan, Paul M; Blehert, David S; Wibbelt, Gudrun; Willis, Craig K R

    2013-08-23

    White-nose syndrome is devastating North American bat populations but we lack basic information on disease mechanisms. Altered blood physiology owing to epidermal invasion by the fungal pathogen Geomyces destructans (Gd) has been hypothesized as a cause of disrupted torpor patterns of affected hibernating bats, leading to mortality. Here, we present data on blood electrolyte concentration, haematology and acid-base balance of hibernating little brown bats, Myotis lucifugus, following experimental inoculation with Gd. Compared with controls, infected bats showed electrolyte depletion (i.e. lower plasma sodium), changes in haematology (i.e. increased haematocrit and decreased glucose) and disrupted acid-base balance (i.e. lower CO2 partial pressure and bicarbonate). These findings indicate hypotonic dehydration, hypovolaemia and metabolic acidosis. We propose a mechanistic model linking tissue damage to altered homeostasis and morbidity/mortality. PMID:23720520

  5. Pathophysiology of white-nose syndrome in bats: a mechanistic model linking wing damage to mortality

    USGS Publications Warehouse

    Warnecke, Lisa; Turner, James M.; Bollinger, Trent K.; Misra, Vikram; Cryan, Paul M.; Blehert, David S.; Wibbelt, Gudrun; Willis, Craig K.R.

    2013-01-01

    White-nose syndrome is devastating North American bat populations but we lack basic information on disease mechanisms. Altered blood physiology owing to epidermal invasion by the fungal pathogen Geomyces destructans (Gd) has been hypothesized as a cause of disrupted torpor patterns of affected hibernating bats, leading to mortality. Here, we present data on blood electrolyte concentration, haematology and acid–base balance of hibernating little brown bats, Myotis lucifugus, following experimental inoculation with Gd. Compared with controls, infected bats showed electrolyte depletion (i.e. lower plasma sodium), changes in haematology (i.e. increased haematocrit and decreased glucose) and disrupted acid–base balance (i.e. lower CO2 partial pressure and bicarbonate). These findings indicate hypotonic dehydration, hypovolaemia and metabolic acidosis. We propose a mechanistic model linking tissue damage to altered homeostasis and morbidity/mortality.

  6. Assessing first-order emulator inference for physical parameters in nonlinear mechanistic models

    USGS Publications Warehouse

    Hooten, Mevin B.; Leeds, William B.; Fiechter, Jerome; Wikle, Christopher K.

    2011-01-01

    We present an approach for estimating physical parameters in nonlinear models that relies on an approximation to the mechanistic model itself for computational efficiency. The proposed methodology is validated and applied in two different modeling scenarios: (a) Simulation and (b) lower trophic level ocean ecosystem model. The approach we develop relies on the ability to predict right singular vectors (resulting from a decomposition of computer model experimental output) based on the computer model input and an experimental set of parameters. Critically, we model the right singular vectors in terms of the model parameters via a nonlinear statistical model. Specifically, we focus our attention on first-order models of these right singular vectors rather than the second-order (covariance) structure.

  7. Mechanistic Modeling Reveals the Critical Knowledge Gaps in Bile Acid-Mediated DILI.

    PubMed

    Woodhead, J L; Yang, K; Brouwer, K L R; Siler, S Q; Stahl, S H; Ambroso, J L; Baker, D; Watkins, P B; Howell, B A

    2014-01-01

    Bile salt export pump (BSEP) inhibition has been proposed to be an important mechanism for drug-induced liver injury (DILI). Modeling can prioritize knowledge gaps concerning bile acid (BA) homeostasis and thus help guide experimentation. A submodel of BA homeostasis in rats and humans was constructed within DILIsym, a mechanistic model of DILI. In vivo experiments in rats with glibenclamide were conducted, and data from these experiments were used to validate the model. The behavior of DILIsym was analyzed in the presence of a simulated theoretical BSEP inhibitor. BSEP inhibition in humans is predicted to increase liver concentrations of conjugated chenodeoxycholic acid (CDCA) and sulfate-conjugated lithocholic acid (LCA) while the concentration of other liver BAs remains constant or decreases. On the basis of a sensitivity analysis, the most important unknowns are the level of BSEP expression, the amount of intestinal synthesis of LCA, and the magnitude of farnesoid-X nuclear receptor (FXR)-mediated regulation. PMID:25006780

  8. Mechanistic Target of Rapamycin (Mtor) Is Essential for Murine Embryonic Heart Development and Growth

    PubMed Central

    Zhu, Yi; Pires, Karla M. P.; Whitehead, Kevin J.; Olsen, Curtis D.; Wayment, Benjamin; Zhang, Yi Cheng; Bugger, Heiko; Ilkun, Olesya; Litwin, Sheldon E.; Thomas, George; Kozma, Sara C.; Abel, E. Dale

    2013-01-01

    Mechanistic target of rapamycin (Mtor) is required for embryonic inner cell mass proliferation during early development. However, Mtor expression levels are very low in the mouse heart during embryogenesis. To determine if Mtor plays a role during mouse cardiac development, cardiomyocyte specific Mtor deletion was achieved using α myosin heavy chain (α-MHC) driven Cre recombinase. Initial mosaic expression of Cre between embryonic day (E) 10.5 and E11.5 eliminated a subset of cardiomyocytes with high Cre activity by apoptosis and reduced overall cardiac proliferative capacity. The remaining cardiomyocytes proliferated and expanded normally. However loss of 50% of cardiomyocytes defined a threshold that impairs the ability of the embryonic heart to sustain the embryo’s circulatory requirements. As a result 92% of embryos with cardiomyocyte Mtor deficiency died by the end of gestation. Thus Mtor is required for survival and proliferation of cardiomyocytes in the developing heart. PMID:23342106

  9. Water-soluble NHC-Cu catalysts: applications in click chemistry, bioconjugation and mechanistic analysis.

    PubMed

    Díaz Velázquez, Heriberto; Ruiz García, Yara; Vandichel, Matthias; Madder, Annemieke; Verpoort, Francis

    2014-12-14

    Copper(I)-catalyzed 1,3-dipolar cycloaddition of azides and terminal alkynes (CuAAC), better known as "click" reaction, has triggered the use of 1,2,3-triazoles in bioconjugation, drug discovery, materials science and combinatorial chemistry. Here we report a new series of water-soluble catalysts based on N-heterocyclic carbene (NHC)-Cu complexes which are additionally functionalized with a sulfonate group. The complexes show superior activity towards CuAAC reactions and display a high versatility, enabling the production of triazoles with different substitution patterns. Additionally, successful application of these complexes in bioconjugation using unprotected peptides acting as DNA binding domains was achieved for the first time. Mechanistic insight into the reaction mechanism is obtained by means of state-of-the-art first principles calculations. PMID:25251642

  10. Inhibition of the mechanistic target of rapamycin (mTOR) - Rapamycin and beyond

    PubMed Central

    Lamming, Dudley W.

    2016-01-01

    Rapamycin is an FDA-approved immunosuppressant and anti-cancer agent discovered in the soil of Easter Island in the early 1970s. Rapamycin is a potent and selective inhibitor of the mTOR (mechanistic Target Of Rapamycin) protein kinase, which acts as a central integrator of nutrient signaling pathways. During the last decade, genetic and pharmaceutical inhibition of mTOR pathway signaling has been found to promote longevity in yeast, worms, flies and mice. In this chapter, we will discuss the molecular biology underlying the effects of rapamycin and its physiological effects; evidence for rapamycin as an anti-aging compound; mechanisms by which rapamycin may extend lifespan; and the potential limitations of rapamycin as an anti-aging molecule. Finally, we will discuss possible strategies that may allow us to inhibit mTOR signaling safely while minimizing side effects, and reap the health, social and economic benefits from slowing the aging process. PMID:27048303

  11. Lipids, adiposity and tendinopathy: is there a mechanistic link? Critical review.

    PubMed

    Scott, Alex; Zwerver, Johannes; Grewal, Navi; de Sa, Agnetha; Alktebi, Thuraya; Granville, David J; Hart, David A

    2015-08-01

    Being overweight or obese is associated with an elevated risk of tendon pathology. However, for sportspeople the epidemiological data linking weight or adiposity on one hand, and risk of tendon pathology on the other, are less consistent. Indeed, the mechanistic links between diet, adiposity and tendon pathology remain largely unexamined. Recent studies have begun to examine the effects of dietary interventions on outcomes such as tendon biomechanics or pain. Oxidised low-density lipoprotein has been shown to (A) accumulate in the tendon tissues of mice that eat a fatty diet and (B) induce a pathological phenotype in human tendon cells. This paper addresses the current debate: is excessive body mass index (causing increased load and strain on tendon tissue) per se the underlying mechanism? Or do local or systemic influences of fat on tendons predispose to tendon pathology? This narrative review argues that excessive blood lipids may be an important avenue for clinical investigations. PMID:25488953

  12. Improving Predictive Modeling in Pediatric Drug Development: Pharmacokinetics, Pharmacodynamics, and Mechanistic Modeling

    SciTech Connect

    Slikker, William; Young, John F.; Corley, Rick A.; Dorman, David C.; Conolly, Rory B.; Knudsen, Thomas; Erstad, Brian L.; Luecke, Richard H.; Faustman, Elaine M.; Timchalk, Chuck; Mattison, Donald R.

    2005-07-26

    A workshop was conducted on November 18?19, 2004, to address the issue of improving predictive models for drug delivery to developing humans. Although considerable progress has been made for adult humans, large gaps remain for predicting pharmacokinetic/pharmacodynamic (PK/PD) outcome in children because most adult models have not been tested during development. The goals of the meeting included a description of when, during development, infants/children become adultlike in handling drugs. The issue of incorporating the most recent advances into the predictive models was also addressed: both the use of imaging approaches and genomic information were considered. Disease state, as exemplified by obesity, was addressed as a modifier of drug pharmacokinetics and pharmacodynamics during development. Issues addressed in this workshop should be considered in the development of new predictive and mechanistic models of drug kinetics and dynamics in the developing human.

  13. Activity restriction and the mechanistic basis for extinctions under climate warming.

    PubMed

    R Kearney, Michael

    2013-12-01

    Correlative analyses predict that anthropogenic climate warming will cause widespread extinction but the nature and generality of the underlying mechanisms is unclear. Warming-induced activity restriction has been proposed as a general explanatory mechanism for recent population extinctions in lizards, and has been used to forecast future extinction. Here, I test this hypothesis using globally applied biophysical calculations of the effects of warming and shade reduction on potential activity time and whole-life-cycle energy budgets. These 'thermodynamic niche' analyses show that activity restriction from climate warming is unlikely to provide a general explanation of recent extinctions, and that loss of shade is viable alternative explanation. Climate warming could cause population declines, even under increased activity potential, through joint impacts on fecundity and mortality rates. However, such responses depend strongly on behaviour, habitat (shade, food) and life history, all of which should be explicitly incorporated in mechanistic forecasts of extinction risk under climate change. PMID:24118740

  14. Can mechanistic explanation be reconciled with scale-free constitution and dynamics?

    PubMed

    Bechtel, William

    2015-10-01

    This paper considers two objections to explanations that appeal to mechanisms to explain biological phenomena. Marom argues that the time-scale on which many phenomena occur is scale-free. There is also reason to suspect that the network of interacting entities is scale-free. The result is that mechanisms do not have well-delineated boundaries in nature. I argue that bounded mechanisms should be viewed as entities scientists posit in advancing scientific hypotheses. In positing such entities, scientists idealize. Such idealizations can be highly productive in developing and improving scientific explanations even if the hypothesized mechanisms never precisely correspond to bounded entities in nature. Mechanistic explanations can be reconciled with scale-free constitution and dynamics even if mechanisms as bounded entities don't exist. PMID:25977254

  15. Glucosamine condensation catalyzed by 1-ethyl-3-methylimidazolium acetate: mechanistic insight from NMR spectroscopy.

    PubMed

    Jia, Lingyu; Pedersen, Christian Marcus; Qiao, Yan; Deng, Tiansheng; Zuo, Pingping; Ge, Wenzhi; Qin, Zhangfeng; Hou, Xianglin; Wang, Yingxiong

    2015-09-21

    The basic ionic liquid 1-ethyl-3-methylimidazolium acetate ([C2C1Im][OAc]) could efficiently catalyze the conversion of 2-amino-2-deoxy-d-glucose (GlcNH2) into deoxyfructosazine (DOF) and fructosazine (FZ). Mechanistic investigation by NMR studies disclosed that [C2C1Im][OAc], exhibiting strong hydrogen bonding basicity, could coordinate with the hydroxyl and amino groups of GlcNH2via the promotion of hydrogen bonding in bifunctional activation of substrates and further catalyzing product formation, based on which a plausible reaction pathway involved in this homogeneous base-catalyzed reaction was proposed. Hydrogen bonding as an activation force, therefore, is responsible for the remarkable selectivity and rate enhancement observed. PMID:26278065

  16. Structural and mechanistic aspects of 3C proteases from the Picornavirus family.

    PubMed

    Arad, D; Kreisberg, R; Shokhen, M

    1993-01-01

    Picornavirus 3C proteases are prime targets for rational drug design. This viral protease appears in a large number of viruses from the Picornavirus family that cause serious disease syndromes, and it has an important role in the life cycle of the virus, processing the translation product of the Picornavirus genome by progressive co- and posttranslational cleavages. It is, therefore, important to gain structural and mechanistic information about this family of enzymes. We concentrate in this paper on the specific features of the 3C; particularly, we are trying to show that the 3C constitute a new family to enzymes which is neither a serine- nor a cysteine-type protease. General basic theory on the behavior of sulfur nucleophile vs the behavior of oxygen nucleophile regarding the nucleophilic attack on carbonyl compounds and the possible determinants in the structure of 3C viral proteases of rhinovirus 1A are being discussed. PMID:8320292

  17. Mechanistic Investigation of a Non-Heme Iron Enzyme Catalyzed Epoxidation in (-)-4'-Methoxycyclopenin Biosynthesis.

    PubMed

    Chang, Wei-Chen; Li, Jikun; Lee, Justin L; Cronican, Andrea A; Guo, Yisong

    2016-08-24

    Mechanisms have been proposed for α-KG-dependent non-heme iron enzyme catalyzed oxygen atom insertion into an olefinic moiety in various natural products, but they have not been examined in detail. Using a combination of methods including transient kinetics, Mössbauer spectroscopy, and mass spectrometry, we demonstrate that AsqJ-catalyzed (-)-4'-methoxycyclopenin formation uses a high-spin Fe(IV)-oxo intermediate to carry out epoxidation. Furthermore, product analysis on (16)O/(18)O isotope incorporation from the reactions using the native substrate, 4'-methoxydehydrocyclopeptin, and a mechanistic probe, dehydrocyclopeptin, reveals evidence supporting oxo↔hydroxo tautomerism of the Fe(IV)-oxo species in the non-heme iron enzyme catalysis. PMID:27442345

  18. Synthetic and Mechanistic Studies of Strained Heterocycle Opening Reactions Mediated by Zirconium(IV) Imido Complexes

    PubMed Central

    Blum, Suzanne A.; Rivera, Vicki A.; Ruck, Rebecca T.; Michael, Forrest E.; Bergman, Robert G.

    2005-01-01

    The reactions of the bis(cyclopentadienyl)(tert-butylimido)zirconium complex (Cp2Zr=N-t-Bu)(THF) (1) with epoxides, aziridines, and episulfides were investigated. Heterocycles without accessible β-hydrogens undergo insertion/protonation of the C–X bond to produce 1,2-amino alcohols (X = O) and 1,2-diamines (X = NR), whereas heterocycles with accessible β-hydrogens undergo elimination/protonation to produce allylic alcohols (X = O) and allylic sulfides (X = S). Mechanistic investigations support a stepwise pathway with zwitterionic intermediates for the first reaction class and a concerted pathway for the second reaction class. Additionally, the feasibility of chirality transfer from the planar-chiral ebthi (ebthi = ethylenebis(tetrahydroindenyl)) ligand was demonstrated with a chiral analogue, (ebthi)-Zr=NAr(THF) (Ar = 2,6-dimethylphenyl), 2, through the diastereoselective ring opening of meso epoxides. PMID:16508693

  19. Parameterization of phosphine ligands reveals mechanistic pathways and predicts reaction outcomes.

    PubMed

    Niemeyer, Zachary L; Milo, Anat; Hickey, David P; Sigman, Matthew S

    2016-06-01

    The mechanistic foundation behind the identity of a phosphine ligand that best promotes a desired reaction outcome is often non-intuitive, and thus has been addressed in numerous experimental and theoretical studies. In this work, multivariate correlations of reaction outcomes using 38 different phosphine ligands were combined with classic potentiometric analyses to study a Suzuki reaction, for which the site selectivity of oxidative addition is highly dependent on the nature of the phosphine. These studies shed light on the generality of hypotheses regarding the structural influence of different classes of phosphine ligands on the reaction mechanism(s), and deliver a methodology that should prove useful in future studies of phosphine ligands. PMID:27219707

  20. Mechanistic study of synthesis of gold nanoparticles using multi-functional polymer

    NASA Astrophysics Data System (ADS)

    Yu, Taekyung; Kim, Rayoung; Park, Hoseok; Yi, Jonghyup; Kim, Woo-Sik

    2014-01-01

    This Letter presents a mechanistic study of the large-scale synthesis of Au nanoparticles when using branched polyethyleneimine (BPEI) as a multi-functional reducing agent, capping agent, and stabilizer. During the synthesis, the molar ratio of BPEI/HAuCl4, reaction temperature, and pH of the reacting solution were all found to be important factors in the formation, size control, and stabilization of the Au nanoparticles. The proposed synthetic route provided a highly concentrated product of Au nanoparticles (above 40 g/L), at least 10- to 200-fold more than previous methods, and can be readily applied to a large-scale process due to its simple and mild reaction conditions.

  1. Development of a mechanistic model for predicting corrosion rate in multiphase oil/water/gas flows

    SciTech Connect

    Zhang, R.; Gopal, M.; Jepson, W.P.

    1997-09-01

    A mechanistic model has been developed to predict corrosion rates in multiphase (water/oil/CO{sub 2}) flow conditions. The model takes into account electrochemistry, reaction kinetics, and, mass transport effects. This paper describes the equations used to determine pH and bulk concentrations of various ions, which are then used to calculate the mass transfer rates to the corrosion surface. The result includes the determination of the mass transfer coefficients of various ionic species and corrosion rates. Details of relations used for determination of mass transfer coefficients for multiphase flows, and rates of electrochemical reaction kinetics are discussed and predicted results are compared with experimental observations. Agreement between model results and experimental data is good.

  2. Direct-acting antiviral agents for hepatitis C: structural and mechanistic insights.

    PubMed

    Götte, Matthias; Feld, Jordan J

    2016-06-01

    The treatment of HCV infection has evolved at an extremely rapid pace over the past few years. The development of direct-acting antiviral agents, which potently inhibit different stages in the viral life cycle, has led to the replacement of interferon with well-tolerated oral therapies with cure rates of >90% in most patient populations. Understanding the mechanisms of action of the various agents as well as related issues, including the molecular basis for resistance, helps to guide drug development and clinical use. In this Review, we provide a mechanistic description of NS3/4A protease inhibitors, nucleotide and non-nucleotide inhibitors of the NS5B viral polymerase and inhibitors of the NS5A protein, followed by a summary of clinical data from studies of each drug class alone and in combination. Remaining challenges in drug development efforts are also discussed. PMID:27147491

  3. A Three-Stage Mechanistic Model for Ammonia Borane Dehydrogenation by Shvo's Catalyst.

    PubMed

    Lu, Zhiyao; Conley, Brian L; Williams, Travis J

    2012-10-01

    We propose a mechanistic model for three-stage dehydrogenation of ammonia borane (AB) catalyzed by Shvo's cyclopentadienone-ligated ruthenium complex. We provide evidence for a plausible mechanism for catalyst deactivation, the transition from fast catalysis to slow catalysis, and relate those findings to the invention of a second-generation catalyst that does not suffer from the same deactivation chemistry.The primary mechanism of catalyst deactivation is borazine-mediated hydroboration of the ruthenium species that is the active oxidant in the fast catalysis case. This transition is characterized by a change in the rate law for the reaction and changes in the apparent resting state of the catalyst. Also, in this slow catalysis situation, we see an additional intermediate in the sequence of boron, nitrogen species, aminodiborane. This occurs with concurrent generation of NH(3), which itself does not strongly affect the rate of AB dehydrogenation. PMID:23335832

  4. A Three-Stage Mechanistic Model for Ammonia Borane Dehydrogenation by Shvo’s Catalyst

    PubMed Central

    Lu, Zhiyao; Conley, Brian L.; Williams, Travis J.

    2012-01-01

    We propose a mechanistic model for three-stage dehydrogenation of ammonia borane (AB) catalyzed by Shvo’s cyclopentadienone-ligated ruthenium complex. We provide evidence for a plausible mechanism for catalyst deactivation, the transition from fast catalysis to slow catalysis, and relate those findings to the invention of a second-generation catalyst that does not suffer from the same deactivation chemistry. The primary mechanism of catalyst deactivation is borazine-mediated hydroboration of the ruthenium species that is the active oxidant in the fast catalysis case. This transition is characterized by a change in the rate law for the reaction and changes in the apparent resting state of the catalyst. Also, in this slow catalysis situation, we see an additional intermediate in the sequence of boron, nitrogen species, aminodiborane. This occurs with concurrent generation of NH3, which itself does not strongly affect the rate of AB dehydrogenation. PMID:23335832

  5. Inhibition of the Mechanistic Target of Rapamycin (mTOR)-Rapamycin and Beyond.

    PubMed

    Lamming, Dudley W

    2016-01-01

    Rapamycin is a Food and Drug Administration (FDA)-approved immunosuppressant and anticancer agent discovered in the soil of Easter Island in the early 1970s. Rapamycin is a potent and selective inhibitor of the mechanistic target of rapamycin (mTOR) protein kinase, which acts as a central integrator of nutrient signaling pathways. During the last decade, genetic and pharmaceutical inhibition of mTOR pathway signaling has been found to promote longevity in yeast, worms, flies, and mice. In this article, we will discuss the molecular biology underlying the effects of rapamycin and its physiological effects, evidence for rapamycin as an antiaging compound, mechanisms by which rapamycin may extend life span, and the potential limitations of rapamycin as an antiaging molecule. Finally, we will discuss possible strategies that may allow us to inhibit mTOR signaling safely while minimizing side effects, and reap the health, social, and economic benefits from slowing the aging process. PMID:27048303

  6. Reactions of Co(III)-nitrosyl complexes with superoxide and their mechanistic insights.

    PubMed

    Kumar, Pankaj; Lee, Yong-Min; Park, Young Jun; Siegler, Maxime A; Karlin, Kenneth D; Nam, Wonwoo

    2015-04-01

    New Co(III)-nitrosyl complexes bearing N-tetramethylated cyclam (TMC) ligands, [(12-TMC)Co(III)(NO)](2+) (1) and [(13-TMC)Co(III)(NO)](2+) (2), were synthesized via [(TMC)Co(II)(CH3CN)](2+) + NO(g) reactions. Spectroscopic and structural characterization showed that these compounds bind the nitrosyl moiety in a bent end-on fashion. Complexes 1 and 2 reacted with KO2/2.2.2-cryptand to produce [(12-TMC)Co(II)(NO2)](+) (3) and [(13-TMC)Co(II)(NO2)](+) (4), respectively; these possess O,O'-chelated nitrito ligands. Mechanistic studies using (18)O-labeled superoxide ((18)O2(•-)) showed that one O atom in the nitrito ligand is derived from superoxide and the O2 produced comes from the other superoxide O atom. Evidence supporting the formation of a Co-peroxynitrite intermediate is also presented. PMID:25793706

  7. Mechanistic insights on immunosenescence and chronic immune activation in HIV-tuberculosis co-infection.

    PubMed

    Shankar, Esaki M; Velu, Vijayakumar; Kamarulzaman, Adeeba; Larsson, Marie

    2015-02-12

    Immunosenescence is marked by accelerated degradation of host immune responses leading to the onset of opportunistic infections, where senescent T cells show remarkably higher ontogenic defects as compared to healthy T cells. The mechanistic association between T-cell immunosenescence and human immunodeficiency virus (HIV) disease progression, and functional T-cell responses in HIV-tuberculosis (HIV-TB) co-infection remains to be elaborately discussed. Here, we discussed the association of immunosenescence and chronic immune activation in HIV-TB co-infection and reviewed the role played by mediators of immune deterioration in HIV-TB co-infection necessitating the importance of designing therapeutic strategies against HIV disease progression and pathogenesis. PMID:25674514

  8. Lipids, adiposity and tendinopathy: is there a mechanistic link? Critical review

    PubMed Central

    Scott, Alex; Zwerver, Johannes; Grewal, Navi; de Sa, Agnetha; Alktebi, Thuraya; Granville, David J; Hart, David A

    2015-01-01

    Being overweight or obese is associated with an elevated risk of tendon pathology. However, for sportspeople the epidemiological data linking weight or adiposity on one hand, and risk of tendon pathology on the other, are less consistent. Indeed, the mechanistic links between diet, adiposity and tendon pathology remain largely unexamined. Recent studies have begun to examine the effects of dietary interventions on outcomes such as tendon biomechanics or pain. Oxidised low-density lipoprotein has been shown to (A) accumulate in the tendon tissues of mice that eat a fatty diet and (B) induce a pathological phenotype in human tendon cells. This paper addresses the current debate: is excessive body mass index (causing increased load and strain on tendon tissue) per se the underlying mechanism? Or do local or systemic influences of fat on tendons predispose to tendon pathology? This narrative review argues that excessive blood lipids may be an important avenue for clinical investigations. PMID:25488953

  9. How do animal territories form and change? Lessons from 20 years of mechanistic modelling

    PubMed Central

    Potts, Jonathan R.; Lewis, Mark A.

    2014-01-01

    Territory formation is ubiquitous throughout the animal kingdom. At the individual level, various behaviours attempt to exclude conspecifics from regions of space. At the population level, animals often segregate into distinct territorial areas. Consequently, it should be possible to derive territorial patterns from the underlying behavioural processes of animal movements and interactions. Such derivations are an important element in the development of an ecological theory that can predict the effects of changing conditions on territorial populations. Here, we review the approaches developed over the past 20 years or so, which go under the umbrella of ‘mechanistic territorial models’. We detail the two main strands to this research: partial differential equations and individual-based approaches, showing what each has offered to our understanding of territoriality and how they can be unified. We explain how they are related to other approaches to studying territories and home ranges, and point towards possible future directions. PMID:24741017

  10. Joint modeling of the clinical progression and of the biomarkers' dynamics using a mechanistic model.

    PubMed

    Guedj, Jeremie; Thiébaut, Rodolphe; Commenges, Daniel

    2011-03-01

    Joint models are used to rigorously explore the relationship between the dynamics of biomarkers and clinical events. In the context of HIV infection, where the multivariate dynamics of HIV-RNA and CD4 are complex, a mechanistic approach based on a system of nonlinear differential equations naturally takes into account the correlation between the biomarkers. Using data from a randomized clinical trial comparing dual antiretroviral therapy to a single drug regimen, a full maximum likelihood approach is proposed to explore the relationship between the evolution of the biomarkers and the time to a clinical event. The role of each marker as an independent predictor of disease progression is assessed. We show that the joint dynamics of HIV-RNA and CD4 captures the effect of antiretroviral treatment; the CD4 dynamics alone is found to capture most but not all of the treatment effect. PMID:20377577

  11. Mechanistic Studies on the Copper-Catalyzed N-Arylation of Amides

    PubMed Central

    Strieter, Eric R.; Bhayana, Brijesh; Buchwald, Stephen L.

    2009-01-01

    The copper-catalyzed N-arylation of amides, i.e., the Goldberg reaction, is an efficient method for the construction of products relevant to both industry and academic settings. Herein, we present mechanistic details concerning the catalytic and stoichiometric N-arylation of amides. In the context of the catalytic reaction, our findings reveal the importance of chelating diamine ligands in controlling the concentration of the active catalytic species. The consistency between the catalytic and stoichiometric results suggest that the activation of aryl halides occurs through a 1,2-diamine-ligated copper(I) amidate complex. Kinetic studies on the stoichiometric N-arylation of aryl iodides using 1,2-diamine ligated Cu(I) amidates also provide insights into the mechanism of aryl halide activation. PMID:19072233

  12. Pollution and skin: from epidemiological and mechanistic studies to clinical implications.

    PubMed

    Krutmann, Jean; Liu, Wei; Li, Li; Pan, Xiaochuan; Crawford, Martha; Sore, Gabrielle; Seite, Sophie

    2014-12-01

    In recent years, the health effects associated with air pollution have been intensively studied. Most studies focus on air pollution effects on the lung and the cardiovascular system. More recently, however, epidemiological and mechanistic studies suggest that air pollution is also affecting skin integrity. This state-of-the-art review focuses on this latter aspect; it was developed with the collaboration of European and Chinese board of experts with specific interests in environmental health, clinical and basic research in dermatology and cosmetic dermatology. A literature review limited to pollution and health effects and (sensitive) skin was performed using PubMed. Review and original articles were chosen. We summarize the existing scientific evidence that air pollution exerts detrimental effects on human skin, discuss potential clinical implications and suggest specific and unspecific cosmetic protective measures. PMID:25278222

  13. Mechanistic studies related to the safety of Li/SOCl2 cells

    NASA Technical Reports Server (NTRS)

    Carter, B. J.; Williams, R. M.; Tsay, F. D.; Rodriguez, A.; Kim, S.; Evans, M. M.; Frank, H.

    1985-01-01

    Mechanistic studies of the reactions in Li-SOCl2 cells have been undertaken to improve understanding of the safety problems of these cells. The electrochemical reduction of 1.5M LiAlCl4/SOCl2 has been investigated using gas chromatography, electron spin resonance spectroscopy, and infrared spectroscopy. Cl2 and S2Cl2 have been identified as intermediates in the reduction of SOCl2, along with a radical species (g/xx/ = 2.004, g/yy/ = 2.016, g/zz/ = 2.008) and the proposed triplet ground-state dimer of this radical. SO2 and sulfur have been identified as products. Based upon these findings, a mechanism for the electrochemical reduction of 1.5M LiAlCl4/SOCl2 has been proposed, and its implications for safety of Li-SOCl2 cells during discharge to +0.5V at 25-30 C are discussed.

  14. Enhanced nitrogen deposition over China.

    PubMed

    Liu, Xuejun; Zhang, Ying; Han, Wenxuan; Tang, Aohan; Shen, Jianlin; Cui, Zhenling; Vitousek, Peter; Erisman, Jan Willem; Goulding, Keith; Christie, Peter; Fangmeier, Andreas; Zhang, Fusuo

    2013-02-28

    China is experiencing intense air pollution caused in large part by anthropogenic emissions of reactive nitrogen. These emissions result in the deposition of atmospheric nitrogen (N) in terrestrial and aquatic ecosystems, with implications for human and ecosystem health, greenhouse gas balances and biological diversity. However, information on the magnitude and environmental impact of N deposition in China is limited. Here we use nationwide data sets on bulk N deposition, plant foliar N and crop N uptake (from long-term unfertilized soils) to evaluate N deposition dynamics and their effect on ecosystems across China between 1980 and 2010. We find that the average annual bulk deposition of N increased by approximately 8 kilograms of nitrogen per hectare (P < 0.001) between the 1980s (13.2 kilograms of nitrogen per hectare) and the 2000s (21.1 kilograms of nitrogen per hectare). Nitrogen deposition rates in the industrialized and agriculturally intensified regions of China are as high as the peak levels of deposition in northwestern Europe in the 1980s, before the introduction of mitigation measures. Nitrogen from ammonium (NH4(+)) is the dominant form of N in bulk deposition, but the rate of increase is largest for deposition of N from nitrate (NO3(-)), in agreement with decreased ratios of NH3 to NOx emissions since 1980. We also find that the impact of N deposition on Chinese ecosystems includes significantly increased plant foliar N concentrations in natural and semi-natural (that is, non-agricultural) ecosystems and increased crop N uptake from long-term-unfertilized croplands. China and other economies are facing a continuing challenge to reduce emissions of reactive nitrogen, N deposition and their negative effects on human health and the environment. PMID:23426264

  15. A dynamic, mechanistic model of metabolism in adipose tissue of lactating dairy cattle.

    PubMed

    McNamara, J P; Huber, K; Kenéz, A

    2016-07-01

    Research in dairy cattle biology has resulted in a large body of knowledge on nutrition and metabolism in support of milk production and efficiency. This quantitative knowledge has been compiled in several model systems to balance and evaluate rations and predict requirements. There are also systems models for metabolism and reproduction in the cow that can be used to support research programs. Adipose tissue plays a significant role in the success and efficiency of lactation, and recent research has resulted in several data sets on genomic differences and changes in gene transcription of adipose tissue in dairy cattle. To fully use this knowledge, we need to build and expand mechanistic, dynamic models that integrate control of metabolism and production. Therefore, we constructed a second-generation dynamic, mechanistic model of adipose tissue metabolism of dairy cattle. The model describes the biochemical interconversions of glucose, acetate, β-hydroxybutyrate (BHB), glycerol, C16 fatty acids, and triacylglycerols. Data gathered from our own research and published references were used to set equation forms and parameter values. Acetate, glucose, BHB, and fatty acids are taken up from blood. The fatty acids are activated to the acyl coenzyme A moieties. Enzymatically catalyzed reactions are explicitly described with parameters including maximal velocity and substrate sensitivity. The control of enzyme activity is partially carried out by insulin and norepinephrine, portraying control in the cow. Model behavior was adequate, with sensitive responses to changing substrates and hormones. Increased nutrient uptake and increased insulin stimulate triacylglycerol synthesis, whereas a reduction in nutrient availability or increase in norepinephrine increases triacylglycerol hydrolysis and free fatty acid release to blood. This model can form a basis for more sophisticated integration of existing knowledge and future studies on metabolic efficiency of dairy cattle. PMID

  16. Fetal programming of CVD and renal disease: animal models and mechanistic considerations.

    PubMed

    Langley-Evans, Simon C

    2013-08-01

    The developmental origins of health and disease hypothesis postulates that exposure to a less than optimal maternal environment during fetal development programmes physiological function, and determines risk of disease in adult life. Much evidence of such programming comes from retrospective epidemiological cohorts, which demonstrate associations between birth anthropometry and non-communicable diseases of adulthood. The assertion that variation in maternal nutrition drives these associations is supported by studies using animal models, which demonstrate that maternal under- or over-nutrition during pregnancy can programme offspring development. Typically, the offspring of animals that are undernourished in pregnancy exhibit a relatively narrow range of physiological phenotypes that includes higher blood pressure, glucose intolerance, renal insufficiency and increased adiposity. The observation that common phenotypes arise from very diverse maternal nutritional insults has led to the proposal that programming is driven by a small number of mechanistic processes. The remodelling of tissues during development as a consequence of maternal nutritional status being signalled by endocrine imbalance or key nutrients limiting processes in the fetus may lead to organs having irreversibly altered structures that may limit their function with ageing. It has been proposed that the maternal diet may impact upon epigenetic marks that determine gene expression in fetal tissues, and this may be an important mechanism connecting maternal nutrient intakes to long-term programming of offspring phenotype. The objective for this review is to provide an overview of the mechanistic basis of fetal programming, demonstrating the critical role of animal models as tools for the investigation of programming phenomena. PMID:23312451

  17. Reduction of Carbon Dioxide by a Molybdenum-Containing Formate Dehydrogenase: A Kinetic and Mechanistic Study.

    PubMed

    Maia, Luisa B; Fonseca, Luis; Moura, Isabel; Moura, José J G

    2016-07-20

    Carbon dioxide accumulation is a major concern for the ecosystems, but its abundance and low cost make it an interesting source for the production of chemical feedstocks and fuels. However, the thermodynamic and kinetic stability of the carbon dioxide molecule makes its activation a challenging task. Studying the chemistry used by nature to functionalize carbon dioxide should be helpful for the development of new efficient (bio)catalysts for atmospheric carbon dioxide utilization. In this work, the ability of Desulfovibrio desulfuricans formate dehydrogenase (Dd FDH) to reduce carbon dioxide was kinetically and mechanistically characterized. The Dd FDH is suggested to be purified in an inactive form that has to be activated through a reduction-dependent mechanism. A kinetic model of a hysteretic enzyme is proposed to interpret and predict the progress curves of the Dd FDH-catalyzed reactions (initial lag phase and subsequent faster phase). Once activated, Dd FDH is able to efficiently catalyze, not only the formate oxidation (kcat of 543 s(-1), Km of 57.1 μM), but also the carbon dioxide reduction (kcat of 46.6 s(-1), Km of 15.7 μM), in an overall reaction that is thermodynamically and kinetically reversible. Noteworthy, both Dd FDH-catalyzed formate oxidation and carbon dioxide reduction are completely inactivated by cyanide. Current FDH reaction mechanistic proposals are discussed and a different mechanism is here suggested: formate oxidation and carbon dioxide reduction are proposed to proceed through hydride transfer and the sulfo group of the oxidized and reduced molybdenum center, Mo(6+)═S and Mo(4+)-SH, are suggested to be the direct hydride acceptor and donor, respectively. PMID:27348246

  18. Mechanistic Variants in Gas-Phase Metal-Oxide Mediated Activation of Methane at Ambient Conditions.

    PubMed

    Li, Jilai; Zhou, Shaodong; Zhang, Jun; Schlangen, Maria; Usharani, Dandamudi; Shaik, Sason; Schwarz, Helmut

    2016-09-01

    The C-H bond activation of methane mediated by a prototypical heteronuclear metal-oxide cluster, [Al2Mg2O5](•+), was investigated by using Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR-MS) in conjunction with high-level quantum mechanical calculations. Experimentally, hydrogen-atom abstraction from methane by the cluster ion [Al2Mg2O5](•+) takes place at ambient conditions. As to the mechanism, according to our computational findings, both the proton-coupled electron transfer (PCET) and the conventional hydrogen-atom transfer (HAT) are feasible and compete with each other. This is in distinct contrast to the [XYO2](+) (X, Y = Mg, Al, Si) cluster oxide ions which activate methane exclusively via the PCET route (Li, J.; Zhou, S.; Zhang, J.; Schlangen, M.; Weiske, T.; Usharani, D.; Shaik, S.; Schwarz, H. J. Am. Chem. Soc. 2016, 138, 7973-7981). The electronic origins of the mechanistically rather complex reactivity scenarios of the [Al2Mg2O5](•+)/CH4 couple were elucidated. For the PCET mechanism, in which the Lewis acid-base pair [Al(+)-O(-)] of the cluster acts as the active site, a clear correlation has been established between the nature of the transition state, the corresponding barrier height, the Lewis acidity-basicity of the [M(+)-O(-)] unit, as well as the bond order of the M(+)-O(-) bond. Also addressed is the role of the spin and charge distributions of a terminal oxygen radical site in the direct HAT route. The knowledge of the factors that control the reactivity of PCET and HAT pathways not only deepens our mechanistic understanding of metal-oxide mediated C-H bond activation but may also provide guidance for the rational design of catalysts. PMID:27518766

  19. A mechanistic model for electricity consumption on dairy farms: definition, validation, and demonstration.

    PubMed

    Upton, J; Murphy, M; Shalloo, L; Groot Koerkamp, P W G; De Boer, I J M

    2014-01-01

    Our objective was to define and demonstrate a mechanistic model that enables dairy farmers to explore the impact of a technical or managerial innovation on electricity consumption, associated CO2 emissions, and electricity costs. We, therefore, (1) defined a model for electricity consumption on dairy farms (MECD) capable of simulating total electricity consumption along with related CO2 emissions and electricity costs on dairy farms on a monthly basis; (2) validated the MECD using empirical data of 1yr on commercial spring calving, grass-based dairy farms with 45, 88, and 195 milking cows; and (3) demonstrated the functionality of the model by applying 2 electricity tariffs to the electricity consumption data and examining the effect on total dairy farm electricity costs. The MECD was developed using a mechanistic modeling approach and required the key inputs of milk production, cow number, and details relating to the milk-cooling system, milking machine system, water-heating system, lighting systems, water pump systems, and the winter housing facilities as well as details relating to the management of the farm (e.g., season of calving). Model validation showed an overall relative prediction error (RPE) of less than 10% for total electricity consumption. More than 87% of the mean square prediction error of total electricity consumption was accounted for by random variation. The RPE values of the milk-cooling systems, water-heating systems, and milking machine systems were less than 20%. The RPE values for automatic scraper systems, lighting systems, and water pump systems varied from 18 to 113%, indicating a poor prediction for these metrics. However, automatic scrapers, lighting, and water pumps made up only 14% of total electricity consumption across all farms, reducing the overall impact of these poor predictions. Demonstration of the model showed that total farm electricity costs increased by between 29 and 38% by moving from a day and night tariff to a flat

  20. Exploring BSEP inhibition-mediated toxicity with a mechanistic model of drug-induced liver injury

    PubMed Central

    Woodhead, Jeffrey L.; Yang, Kyunghee; Siler, Scott Q.; Watkins, Paul B.; Brouwer, Kim L. R.; Barton, Hugh A.; Howell, Brett A.

    2014-01-01

    Inhibition of the bile salt export pump (BSEP) has been linked to incidence of drug-induced liver injury (DILI), presumably by the accumulation of toxic bile acids in the liver. We have previously constructed and validated a model of bile acid disposition within DILIsym®, a mechanistic model of DILI. In this paper, we use DILIsym® to simulate the DILI response of the hepatotoxic BSEP inhibitors bosentan and CP-724,714 and the non-hepatotoxic BSEP inhibitor telmisartan in humans in order to explore whether we can predict that hepatotoxic BSEP inhibitors can cause bile acid accumulation to reach toxic levels. We also simulate bosentan in rats in order to illuminate potential reasons behind the lack of toxicity in rats compared to the toxicity observed in humans. DILIsym® predicts that bosentan, but not telmisartan, will cause mild hepatocellular ATP decline and serum ALT elevation in a simulated population of humans. The difference in hepatotoxic potential between bosentan and telmisartan is consistent with clinical observations. However, DILIsym® underpredicts the incidence of bosentan toxicity. DILIsym® also predicts that bosentan will not cause toxicity in a simulated population of rats, and that the difference between the response to bosentan in rats and in humans is primarily due to the less toxic bile acid pool in rats. Our simulations also suggest a potential synergistic role for bile acid accumulation and mitochondrial electron transport chain (ETC) inhibition in producing the observed toxicity in CP-724,714, and suggest that CP-724,714 metabolites may also play a role in the observed toxicity. Our work also compares the impact of competitive and noncompetitive BSEP inhibition for CP-724,714 and demonstrates that noncompetitive inhibition leads to much greater bile acid accumulation and potential toxicity. Our research demonstrates the potential for mechanistic modeling to contribute to the understanding of how bile acid transport inhibitors cause DILI

  1. A Mechanistic Beta-Binomial Probability Model for mRNA Sequencing Data

    PubMed Central

    Smith, Gregory R.; Birtwistle, Marc R.

    2016-01-01

    A main application for mRNA sequencing (mRNAseq) is determining lists of differentially-expressed genes (DEGs) between two or more conditions. Several software packages exist to produce DEGs from mRNAseq data, but they typically yield different DEGs, sometimes markedly so. The underlying probability model used to describe mRNAseq data is central to deriving DEGs, and not surprisingly most softwares use different models and assumptions to analyze mRNAseq data. Here, we propose a mechanistic justification to model mRNAseq as a binomial process, with data from technical replicates given by a binomial distribution, and data from biological replicates well-described by a beta-binomial distribution. We demonstrate good agreement of this model with two large datasets. We show that an emergent feature of the beta-binomial distribution, given parameter regimes typical for mRNAseq experiments, is the well-known quadratic polynomial scaling of variance with the mean. The so-called dispersion parameter controls this scaling, and our analysis suggests that the dispersion parameter is a continually decreasing function of the mean, as opposed to current approaches that impose an asymptotic value to the dispersion parameter at moderate mean read counts. We show how this leads to current approaches overestimating variance for moderately to highly expressed genes, which inflates false negative rates. Describing mRNAseq data with a beta-binomial distribution thus may be preferred since its parameters are relatable to the mechanistic underpinnings of the technique and may improve the consistency of DEG analysis across softwares, particularly for moderately to highly expressed genes. PMID:27326762

  2. Advancements in the mechanistic understanding of the copper-catalyzed azide–alkyne cycloaddition

    PubMed Central

    2013-01-01

    Summary The copper-catalyzed azide–alkyne cycloaddition (CuAAC) is one of the most broadly applicable and easy-to-handle reactions in the arsenal of organic chemistry. However, the mechanistic understanding of this reaction has lagged behind the plethora of its applications for a long time. As reagent mixtures of copper salts and additives are commonly used in CuAAC reactions, the structure of the catalytically active species itself has remained subject to speculation, which can be attributed to the multifaceted aggregation chemistry of copper(I) alkyne and acetylide complexes. Following an introductory section on common catalyst systems in CuAAC reactions, this review will highlight experimental and computational studies from early proposals to very recent and more sophisticated investigations, which deliver more detailed insights into the CuAAC’s catalytic cycle and the species involved. As diverging mechanistic views are presented in articles, books and online resources, we intend to present the research efforts in this field during the past decade and finally give an up-to-date picture of the currently accepted dinuclear mechanism of CuAAC. Additionally, we hope to inspire research efforts on the development of molecularly defined copper(I) catalysts with defined structural characteristics, whose main advantage in contrast to the regularly used precatalyst reagent mixtures is twofold: on the one hand, the characteristics of molecularly defined, well soluble catalysts can be tuned according to the particular requirements of the experiment; on the other hand, the understanding of the CuAAC reaction mechanism can be further advanced by kinetic studies and the isolation and characterization of key intermediates. PMID:24367437

  3. Advancements in the mechanistic understanding of the copper-catalyzed azide-alkyne cycloaddition.

    PubMed

    Berg, Regina; Straub, Bernd F

    2013-01-01

    The copper-catalyzed azide-alkyne cycloaddition (CuAAC) is one of the most broadly applicable and easy-to-handle reactions in the arsenal of organic chemistry. However, the mechanistic understanding of this reaction has lagged behind the plethora of its applications for a long time. As reagent mixtures of copper salts and additives are commonly used in CuAAC reactions, the structure of the catalytically active species itself has remained subject to speculation, which can be attributed to the multifaceted aggregation chemistry of copper(I) alkyne and acetylide complexes. Following an introductory section on common catalyst systems in CuAAC reactions, this review will highlight experimental and computational studies from early proposals to very recent and more sophisticated investigations, which deliver more detailed insights into the CuAAC's catalytic cycle and the species involved. As diverging mechanistic views are presented in articles, books and online resources, we intend to present the research efforts in this field during the past decade and finally give an up-to-date picture of the currently accepted dinuclear mechanism of CuAAC. Additionally, we hope to inspire research efforts on the development of molecularly defined copper(I) catalysts with defined structural characteristics, whose main advantage in contrast to the regularly used precatalyst reagent mixtures is twofold: on the one hand, the characteristics of molecularly defined, well soluble catalysts can be tuned according to the particular requirements of the experiment; on the other hand, the understanding of the CuAAC reaction mechanism can be further advanced by kinetic studies and the isolation and characterization of key intermediates. PMID:24367437

  4. Mechanistic models for the spatial spread of species under climate change.

    PubMed

    Leroux, Shawn J; Larrivée, Maxim; Boucher-Lalonde, Véronique; Hurford, Amy; Zuloaga, Juan; Kerr, Jeremy T; Lutscher, Frithjof

    2013-06-01

    Global climate change is a major threat to biodiversity. The most common methods for predicting the response of biodiversity to changing climate do not explicitly incorporate fundamental evolutionary and ecological processes that determine species responses to changing climate, such as reproduction, dispersal, and adaptation. We provide an overview of an emerging mechanistic spatial theory of species range shifts under climate change. This theoretical framework explicitly defines the ecological processes that contribute to species range shifts via biologically meaningful dispersal, reproductive, and climate envelope parameters. We present methods for estimating the parameters of the model with widely available species occurrence and abundance data and then apply these methods to empirical data for 12 North American butterfly species to illustrate the potential use of the theory for global change biology. The model predicts species persistence in light of current climate change and habitat loss. On average, we estimate that the climate envelopes of our study species are shifting north at a rate of 3.25 +/- 1.36 km/yr (mean +/- SD) and that our study species produce 3.46 +/- 1.39 (mean +/- SD) viable offspring per individual per year. Based on our parameter estimates, we are able to predict the relative risk of our 12 study species for lagging behind changing climate. This theoretical framework improves predictions of global change outcomes by facilitating the development and testing of hypotheses, providing mechanistic predictions of current and future range dynamics, and encouraging the adaptive integration of theory and data. The theory is ripe for future developments such as the incorporation of biotic interactions and evolution of adaptations to novel climatic conditions, and it has the potential to be a catalyst for the development of more effective conservation strategies to mitigate losses of biodiversity from global climate change. PMID:23865232

  5. A minimal mechanistic model for temporal signal processing in the lateral geniculate nucleus.

    PubMed

    Norheim, Eivind S; Wyller, John; Nordlie, Eilen; Einevoll, Gaute T

    2012-06-01

    The receptive fields of cells in the lateral geniculate nucleus (LGN) are shaped by their diverse set of impinging inputs: feedforward synaptic inputs stemming from retina, and feedback inputs stemming from the visual cortex and the thalamic reticular nucleus. To probe the possible roles of these feedforward and feedback inputs in shaping the temporal receptive-field structure of LGN relay cells, we here present and investigate a minimal mechanistic firing-rate model tailored to elucidate their disparate features. The model for LGN relay ON cells includes feedforward excitation and inhibition (via interneurons) from retinal ON cells and excitatory and inhibitory (via thalamic reticular nucleus cells and interneurons) feedback from cortical ON and OFF cells. From a general firing-rate model formulated in terms of Volterra integral equations, we derive a single delay differential equation with absolute delay governing the dynamics of the system. A freely available and easy-to-use GUI-based MATLAB version of this minimal mechanistic LGN circuit model is provided. We particularly investigate the LGN relay-cell impulse response and find through thorough explorations of the model's parameter space that both purely feedforward models and feedback models with feedforward excitation only, can account quantitatively for previously reported experimental results. We find, however, that the purely feedforward model predicts two impulse response measures, the time to first peak and the biphasic index (measuring the relative weight of the rebound phase) to be anticorrelated. In contrast, the models with feedback predict different correlations between these two measures. This suggests an experimental test assessing the relative importance of feedforward and feedback connections in shaping the impulse response of LGN relay cells. PMID:23730357

  6. Explicit kinetic heterogeneity: mechanistic models for interpretation of labeling data in heterogeneous populations

    SciTech Connect

    Ganusov, Vitaly V

    2008-01-01

    Estimation of division and death rates of lymphocytes in different conditions is vital for quantitative understanding of the immune system. Deuterium, in the form of deuterated glucose or heavy water, can be used to measure rates of proliferation and death of lymphocytes in vivo. Inferring these rates from labeling and delabeling curves has been subject to considerable debate with different groups suggesting different mathematical models for that purpose. We show that the three models that are most commonly used are in fact mathematically identical and differ only in their interpretation of the estimated parameters. By extending these previous models, we here propose a more mechanistic approach for the analysis of data from deuterium labeling experiments. We construct a model of 'kinetic heterogeneity' in which the total cell population consists of many sub-populations with different rates of cell turnover. In this model, for a given distribution of the rates of turnover, the predicted fraction of labeled DNA accumulated and lost can be calculated. Our model reproduces several previously made experimental observations, such as a negative correlation between the length of the labeling period and the rate at which labeled DNA is lost after label cessation. We demonstrate the reliability of the new explicit kinetic heterogeneity model by applying it to artificially generated datasets, and illustrate its usefulness by fitting experimental data. In contrast to previous models, the explicit kinetic heterogeneity model (1) provides a mechanistic way of interpreting labeling data; (2) allows for a non-exponential loss of labeled cells during delabeling, and (3) can be used to describe data with variable labeling length.

  7. Mechanistic insights on the Dicer-independent AGO2-mediated processing of AgoshRNAs.

    PubMed

    Liu, Ying Poi; Karg, Margarete; Harwig, Alex; Herrera-Carrillo, Elena; Jongejan, Aldo; van Kampen, Antoine; Berkhout, Ben

    2015-01-01

    Short hairpin RNAs (shRNAs) are widely used for gene knockdown by inducing the RNA interference (RNAi) mechanism, both for research and therapeutic purposes. The shRNA precursor is processed by the RNase III-like enzyme Dicer into biologically active small interfering RNA (siRNA). This effector molecule subsequently targets a complementary mRNA for destruction via the Argonaute 2 (AGO2) complex. The cellular role of Dicer concerns the processing of pre-miRNAs into mature microRNA (miRNA). Recently, a non-canonical pathway was reported for the biogenesis of miR-451, which bypasses Dicer and is processed instead by the slicer activity of AGO2, followed by the regular AGO2-mediated mRNA targeting step. Interestingly, shRNA designs that are characterized by a relatively short basepaired stem also bypass Dicer to be processed by AGO2. We named this design AgoshRNA as these molecules depend on AGO2 both for processing and silencing activity. In this study, we investigated diverse mechanistic aspects of this new class of AgoshRNA molecules. We probed the requirements for AGO2-mediated processing of AgoshRNAs by modification of the proposed cleavage site in the hairpin. We demonstrate by deep sequencing that AGO2-processed AgoshRNAs produce RNA effector molecules with more discrete ends than the products of the regular shRNA design. Furthermore, we tested whether trimming and tailing occurs upon AGO2-mediated processing of AgoshRNAs, similar to what has been described for miR-451. Finally, we tested the prediction that AgoshRNA activity, unlike that of regular shRNAs, is maintained in Dicer-deficient cell types. These mechanistic insights could aid in the design of optimised AgoshRNA tools and therapeutics. PMID:25826416

  8. Descriptive vs. mechanistic network models in plant development in the post-genomic era.

    PubMed

    Davila-Velderrain, J; Martinez-Garcia, J C; Alvarez-Buylla, E R

    2015-01-01

    Network modeling is now a widespread practice in systems biology, as well as in integrative genomics, and it constitutes a rich and diverse scientific research field. A conceptually clear understanding of the reasoning behind the main existing modeling approaches, and their associated technical terminologies, is required to avoid confusions and accelerate the transition towards an undeniable necessary more quantitative, multidisciplinary approach to biology. Herein, we focus on two main network-based modeling approaches that are commonly used depending on the information available and the intended goals: inference-based methods and system dynamics approaches. As far as data-based network inference methods are concerned, they enable the discovery of potential functional influences among molecular components. On the other hand, experimentally grounded network dynamical models have been shown to be perfectly suited for the mechanistic study of developmental processes. How do these two perspectives relate to each other? In this chapter, we describe and compare both approaches and then apply them to a given specific developmental module. Along with the step-by-step practical implementation of each approach, we also focus on discussing their respective goals, utility, assumptions, and associated limitations. We use the gene regulatory network (GRN) involved in Arabidopsis thaliana Root Stem Cell Niche patterning as our illustrative example. We show that descriptive models based on functional genomics data can provide important background information consistent with experimentally supported functional relationships integrated in mechanistic GRN models. The rationale of analysis and modeling can be applied to any other well-characterized functional developmental module in multicellular organisms, like plants and animals. PMID:25757787

  9. Mechanistic modelling of fluidized bed drying processes of wet porous granules: a review.

    PubMed

    Mortier, Séverine Thérèse F C; De Beer, Thomas; Gernaey, Krist V; Remon, Jean Paul; Vervaet, Chris; Nopens, Ingmar

    2011-10-01

    Fluidized bed dryers are frequently used in industrial applications and also in the pharmaceutical industry. The general incentives to develop mechanistic models for pharmaceutical processes are listed, and our vision on how this can particularly be done for fluidized bed drying processes of wet granules is given. This review provides a basis for future mechanistic model development for the drying process of wet granules in pharmaceutical processes. It is intended for a broad audience with a varying level of knowledge on pharmaceutical processes and mathematical modelling. Mathematical models are powerful tools to gain process insight and eventually develop well-controlled processes. The level of detail embedded in such a model depends on the goal of the model. Several models have therefore been proposed in the literature and are reviewed here. The drying behaviour of one single granule, a porous particle, can be described using the continuum approach, the pore network modelling method and the shrinkage of the diameter of the wet core approach. As several granules dry at a drying rate dependent on the gas temperature, gas velocity, porosity, etc., the moisture content of a batch of granules will reside in a certain interval. Population Balance Model (ling) (PBM) offers a tool to describe the distribution of particle properties which can be of interest for the application. PBM formulation and solution methods are therefore reviewed. In a fluidized bed, the granules show a fluidization pattern depending on the geometry of the gas inlet, the gas velocity, characteristics of the particles, the dryer design, etc. Computational Fluid Dynamics (CFD) allows to model this behaviour. Moreover, turbulence can be modelled using several approaches: Reynolds-averaged Navier-Stokes Equations (RANS) or Large Eddy Simulation (LES). Another important aspect of CFD is the choice between the Eulerian-Lagrangian and the Eulerian-Eulerian approach. Finally, the PBM and CFD frameworks

  10. A Mechanistic Beta-Binomial Probability Model for mRNA Sequencing Data.

    PubMed

    Smith, Gregory R; Birtwistle, Marc R

    2016-01-01

    A main application for mRNA sequencing (mRNAseq) is determining lists of differentially-expressed genes (DEGs) between two or more conditions. Several software packages exist to produce DEGs from mRNAseq data, but they typically yield different DEGs, sometimes markedly so. The underlying probability model used to describe mRNAseq data is central to deriving DEGs, and not surprisingly most softwares use different models and assumptions to analyze mRNAseq data. Here, we propose a mechanistic justification to model mRNAseq as a binomial process, with data from technical replicates given by a binomial distribution, and data from biological replicates well-described by a beta-binomial distribution. We demonstrate good agreement of this model with two large datasets. We show that an emergent feature of the beta-binomial distribution, given parameter regimes typical for mRNAseq experiments, is the well-known quadratic polynomial scaling of variance with the mean. The so-called dispersion parameter controls this scaling, and our analysis suggests that the dispersion parameter is a continually decreasing function of the mean, as opposed to current approaches that impose an asymptotic value to the dispersion parameter at moderate mean read counts. We show how this leads to current approaches overestimating variance for moderately to highly expressed genes, which inflates false negative rates. Describing mRNAseq data with a beta-binomial distribution thus may be preferred since its parameters are relatable to the mechanistic underpinnings of the technique and may improve the consistency of DEG analysis across softwares, particularly for moderately to highly expressed genes. PMID:27326762

  11. SOIL REACTION AND ACIDIC DEPOSITION

    EPA Science Inventory

    This chapter discusses the major chemical processes by which acidic deposition interacts with soils. he focus is on forest soils, as the effects of acidic deposition on soils used for production of food and fiber are generally small compared to effects of agricultural practices s...

  12. Variable temperature semiconductor film deposition

    DOEpatents

    Li, X.; Sheldon, P.

    1998-01-27

    A method of depositing a semiconductor material on a substrate is disclosed. The method sequentially comprises (a) providing the semiconductor material in a depositable state such as a vapor for deposition on the substrate; (b) depositing the semiconductor material on the substrate while heating the substrate to a first temperature sufficient to cause the semiconductor material to form a first film layer having a first grain size; (c) continually depositing the semiconductor material on the substrate while cooling the substrate to a second temperature sufficient to cause the semiconductor material to form a second film layer deposited on the first film layer and having a second grain size smaller than the first grain size; and (d) raising the substrate temperature, while either continuing or not continuing to deposit semiconductor material to form a third film layer, to thereby anneal the film layers into a single layer having favorable efficiency characteristics in photovoltaic applications. A preferred semiconductor material is cadmium telluride deposited on a glass/tin oxide substrate already having thereon a film layer of cadmium sulfide.

  13. Variable temperature semiconductor film deposition

    DOEpatents

    Li, Xiaonan; Sheldon, Peter

    1998-01-01

    A method of depositing a semiconductor material on a substrate. The method sequentially comprises (a) providing the semiconductor material in a depositable state such as a vapor for deposition on the substrate; (b) depositing the semiconductor material on the substrate while heating the substrate to a first temperature sufficient to cause the semiconductor material to form a first film layer having a first grain size; (c) continually depositing the semiconductor material on the substrate while cooling the substrate to a second temperature sufficient to cause the semiconductor material to form a second film layer deposited on the first film layer and having a second grain size smaller than the first grain size; and (d) raising the substrate temperature, while either continuing or not continuing to deposit semiconductor material to form a third film layer, to thereby anneal the film layers into a single layer having favorable efficiency characteristics in photovoltaic applications. A preferred semiconductor material is cadmium telluride deposited on a glass/tin oxide substrate already having thereon a film layer of cadmium sulfide.

  14. Deposited films with improved microstructures

    DOEpatents

    Patten, James W.; Moss, Ronald W.; McClanahan, Edwin D.

    1984-01-01

    Methods for improving microstructures of line-of-sight deposited films are described. Columnar growth defects ordinarily produced by geometrical shadowing during deposition of such films are eliminated without resorting to post-deposition thermal or mechanical treatments. The native, as-deposited coating qualities, including homogeneity, fine grain size, and high coating-to-substrate adherence, can thus be retained. The preferred method includes the steps of emitting material from a source toward a substrate to deposit a coating non-uniformly on the substrate surface, removing a portion of the coating uniformly over the surface, again depositing material onto the surface, but from a different direction, and repeating the foregoing steps. The quality of line-of-sight deposited films such as those produced by sputtering, progressively deteriorates as the angle of incidence between the flux and the surface becomes increasingly acute. Depositing non-uniformly, so that the coating becomes progressively thinner as quality deteriorates, followed by uniformly removing some of the coating, such as by resputtering, eliminates the poor quality portions, leaving only high quality portions of the coating. Subsequently sputtering from a different direction applies a high quality coating to other regions of the surface. Such steps can be performed either simultaneously or sequentially to apply coatings of a uniformly high quality, closed microstructure to three-dimensional or large planar surfaces.

  15. MODELING DEPOSITION OF INHALED PARTICLES

    EPA Science Inventory

    Modeling Deposition of Inhaled Particles: ABSTRACT

    The mathematical modeling of the deposition and distribution of inhaled aerosols within human lungs is an invaluable tool in predicting both the health risks associated with inhaled environmental aerosols and the therapeut...

  16. Chemical vapor deposition growth

    NASA Technical Reports Server (NTRS)

    Ruth, R. P.; Manasevit, H. M.; Campbell, A. G.; Johnson, R. E.; Kenty, J. L.; Moudy, L. A.; Shaw, G. L.; Simpson, W. I.; Yang, J. J.

    1978-01-01

    The objective was to investigate and develop chemical vapor deposition (CVD) techniques for the growth of large areas of Si sheet on inexpensive substrate materials, with resulting sheet properties suitable for fabricating solar cells that would meet the technical goals of the Low Cost Silicon Solar Array Project. The program involved six main technical tasks: (1) modification and test of an existing vertical-chamber CVD reactor system; (2) identification and/or development of suitable inexpensive substrate materials; (3) experimental investigation of CVD process parameters using various candidate substrate materials; (4) preparation of Si sheet samples for various special studies, including solar cell fabrication; (5) evaluation of the properties of the Si sheet material produced by the CVD process; and (6) fabrication and evaluation of experimental solar cell structures, using impurity diffusion and other standard and near-standard processing techniques supplemented late in the program by the in situ CVD growth of n(+)/p/p(+) sheet structures subsequently processed into experimental cells.

  17. Chemical vapor deposition growth

    NASA Technical Reports Server (NTRS)

    Ruth, R. P.; Manasevit, H. M.; Johnson, R. E.; Kenty, J. L.; Moudy, L. A.; Simpson, W. I.; Yang, J. J.

    1976-01-01

    A laboratory type CVD reactor system with a vertical deposition chamber and sample pedestal heated by an external RF coil has been extensively modified by installation of mass flow controllers, automatic process sequence timers, and special bellows-sealed air-operated valves for overall improved performance. Various film characterization procedures, including classical metallography, SEM analyses, X ray diffraction analyses, surface profilometry, and electrical measurements (resistivity, carrier concentration, mobility, spreading resistance profiles, and minority-carrier lifetime by the C-V-t method) area used to correlate Si sheet properties with CVD parameters and substrate properties. Evaluation procedures and measurements are given. Experimental solar cell structures were made both in epitaxial Si sheet (on sapphire substrates) and in polycrystalline material on alumina substrates, the former to provide an indication of what might be an upper limit on performance of the latter. Preliminary results are given, as obtained in cell structures not specially designed to allow for the unique properties of the sheet material, and fabricated in material known to be far from optimum for photovoltaic performance. Low power conversion efficiencies have been obtained in the epitaxial as well as the polycrystalline Si sheet.

  18. Radioactive deposits of Nevada

    USGS Publications Warehouse

    Lovering, T.G.

    1953-01-01

    Thirty-five occurrences of radioactive rocks had been reported from Nevada prior to 1952. Twenty-five of these had been investigated by the U. S. Geological Survey and the U. S. Atomic Energy Commission. Of those investigated, uranium minerals were identified in 13; two contained a thorium mineral (monazite); the source of radioactivity on 7 properties was not ascertained; and one showed no abnormal radioactivity. Of the other reported occurrences, one is said to contain uraniferous hydrocarbons and 9 are placers containing thorian monazite. Pitchblende occurs at two localities; the East Walker River area, and the Stalin's Present prospect, where it is sparsely disseminated in tabular bodies cutting granitic rocks. Other uranium minerals found in the state include: carnotite, tyuyamunite, autunite, torbernite, gummite, uranophane, kasolite, and an unidentified mineral which may be dumontit. Monazite is the only thorium mineral of possible economic importance that has been reported. From an economic standpoint 9 only 4 of the properties examined showed reserves of uranium ore in 1952; these are: the Green Monster mine, which shipped 5 tons of ore to Marysvale, Utah, during 1951, the Majuba Hill mine, the Stalin's Present prospect, and the West Willys claim in the Washington district. Reserves of ore grade are small on all of these properties and probably cannot be developed commercially unless an ore-buying station is set up nearby. No estimate has been made of thorium reserves and no commercial deposits of thorium are known.

  19. Vacuum vapor deposition

    NASA Technical Reports Server (NTRS)

    Poorman, Richard M. (Inventor); Weeks, Jack L. (Inventor)

    1995-01-01

    A method and apparatus is described for vapor deposition of a thin metallic film utilizing an ionized gas arc directed onto a source material spaced from a substrate to be coated in a substantial vacuum while providing a pressure differential between the source and the substrate so that, as a portion of the source is vaporized, the vapors are carried to the substrate. The apparatus includes a modified tungsten arc welding torch having a hollow electrode through which a gas, preferably inert, flows and an arc is struck between the electrode and the source. The torch, source, and substrate are confined within a chamber within which a vacuum is drawn. When the arc is struck, a portion of the source is vaporized and the vapors flow rapidly toward the substrate. A reflecting shield is positioned about the torch above the electrode and the source to ensure that the arc is struck between the electrode and the source at startup. The electrode and the source may be confined within a vapor guide housing having a duct opening toward the substrate for directing the vapors onto the substrate.

  20. Ni-Co laterite deposits

    USGS Publications Warehouse

    Marsh, Erin E.; Anderson, Eric D.

    2011-01-01

    Nickel-cobalt (Ni-Co) laterite deposits are an important source of nickel (Ni). Currently, there is a decline in magmatic Ni-bearing sulfide lode deposit resources. New efforts to develop an alternative source of Ni, particularly with improved metallurgy processes, make the Ni-Co laterites an important exploration target in anticipation of the future demand for Ni. This deposit model provides a general description of the geology and mineralogy of Ni-Co laterite deposits, and contains discussion of the influences of climate, geomorphology (relief), drainage, tectonism, structure, and protolith on the development of favorable weathering profiles. This model of Ni-Co laterite deposits represents part of the U.S. Geological Survey Mineral Resources Program's effort to update the existing models to be used for an upcoming national mineral resource assessment.

  1. Experimental and numerical studies on laser-based powder deposition of slurry erosion resistant materials

    NASA Astrophysics Data System (ADS)

    Balu, Prabu

    cracking issue, and 3) the effect of composition and composition gradient of Ni and WC on the slurry erosion resistance over a wide range of erosion conditions. This thesis presents a set of numerical and experimental methods in order to address the challenges mentioned above. A three-dimensional (3-D) computational fluid dynamics (CFD) based powder flow model and three vision based techniques were developed in order to visualize the process of feeding the Ni-WC powder in the LBPD process. The results provide the guidelines for efficiently feeding the Ni-WC composite powder into the laser-formed molten pool. The finite element (FE) based experimentally verified 3-D thermal and thermo-mechanical models are developed in order to understand the thermal and stress evolutions in Ni-WC composite material during the LBPD process. The models address the effect of the process variables, preheating temperature, and different mass fractions of WC in Ni on thermal cycles and stress distributions within the deposited material. The slurry erosion behavior of the single and multilayered deposits of Ni-WC composite material produced by the LBPD process is investigated using an accelerated slurry erosion testing machine and a 3-D FE dynamic model. The verified model is used to identify the appropriate composition and composition gradient of Ni-WC composite material required to achieve erosion resistance over a wide range of erosion conditions.

  2. At the Intersection of Attention and Memory: The Mechanistic Role of the Posterior Parietal Lobe in Working Memory

    ERIC Educational Resources Information Center

    Berryhill, Marian E.; Chein, Jason; Olson, Ingrid R.

    2011-01-01

    Portions of the posterior parietal cortex (PPC) play a role in working memory (WM) yet the precise mechanistic function of this region remains poorly understood. The "pure storage" hypothesis proposes that this region functions as a short-lived modality-specific memory store. Alternatively, the "internal attention" hypothesis proposes that the PPC…

  3. Mechanistic aspects of the gas-phase coupling of thioanisole and chlorobenzene to dibenzothiophene catalyzed by atomic Ho(+).

    PubMed

    Zhou, Shaodong; Schlangen, Maria; Schwarz, Helmut

    2015-04-14

    Mechanistic aspects of the novel gas-phase generation of dibenzothiophene via coupling of thioanisole and chlorobenzene, employing atomic Ho(+) as a catalyst, have been investigated using Fourier-transform ion cyclotron resonance mass spectrometry in conjunction with density functional theory (DFT) calculations. PMID:25765339

  4. Mechanistic Aspects of the Palladium-Catalyzed Isomerization of Allenic Sulfones to 1-Arylsulfonyl 1,3-Dienes.

    PubMed

    Hampton, Carissa S; Harmata, Michael

    2016-06-01

    When an allenic sulfone is treated under palladium catalysis in the presence of a weak acid, isomerization to a 1-arylsulfonyl 1,3-diene occurs. Investigations of the mechanistic aspects of this isomerization were performed, leading to the mechanism proposed herein. Some further studies of reaction parameters are reported. PMID:27127922

  5. A MECHANISTIC MODEL FOR MERCURY CAPTURE WITH IN-SITU GENERATED TITANIA PARTICLES: ROLE OF WATER VAPOR

    EPA Science Inventory

    A mechanistic model to predict the capture of gas phase mercury species using in-situ generated titania nanosize particles activated by UV irradiation is developed. The model is an extension of a recently reported model1 for photochemical reactions that accounts for the rates of...

  6. Mechanistic models as a transferable framework for projecting effects of habitat change on production and delivery of ecosystem services

    EPA Science Inventory

    Drawing a link between habitat change and the production and delivery of ecosystem services is a priority in coastal estuarine ecosystems. Mechanistic modeling tools are highly functional for exploring this link because they allow for the synthesis of multiple ecological and beh...

  7. GENE ARRAYS FOR ELUCIDATING MECHANISTIC DATA FROM MODELS OF MALE INFERTILITY AND CHEMICAL EXPOSURE IN MICE, RATS AND HUMANS

    EPA Science Inventory

    Gene arrays for elucidating mechanistic data from models of male infertility and chemical exposure in mice, rats and humans
    John C. Rockett and David J. Dix
    Gamete and Early Embryo Biology Branch, Reproductive Toxicology Division, National Health and Environmental Effects ...

  8. DEVELOPMENT OF IMMUNOHISTOCHEMICAL METHODS FOR THE VALIDATION OF IN VITRO MECHANISTIC EFFECTS OF ENVIRONMENTAL EXPOSURES IN VIVO

    EPA Science Inventory

    By necessity, most molecular and biochemical toxicology research is conducted using in vitro models which vary in their ability to approximate toxic responses at the organismal level. Validating the relevance of in vitro mechanistic findings in vivo would lead to increased confid...

  9. TULSA UNIVERSITY PARAFFIN DEPOSITION PROJECTS

    SciTech Connect

    Michael Volk; Cem Sarica

    2003-10-01

    As oil and gas production moves to deeper and colder water, subsea multiphase production systems become critical for economic feasibility. It will also become increasingly imperative to adequately identify the conditions for paraffin precipitation and predict paraffin deposition rates to optimize the design and operation of these multiphase production systems. Although several oil companies have paraffin deposition predictive capabilities for single-phase oil flow, these predictive capabilities are not suitable for the multiphase flow conditions encountered in most flowlines and wellbores. For deepwater applications in the Gulf of Mexico, it is likely that multiphase production streams consisting of crude oil, produced water and gas will be transported in a single multiphase pipeline to minimize capital cost and complexity at the mudline. Existing single-phase (crude oil) paraffin deposition predictive tools are clearly inadequate to accurately design these pipelines because they do not account for the second and third phases, namely, produced water and gas. The objective of this program is to utilize the current test facilities at The University of Tulsa, as well as member company expertise, to accomplish the following: enhance our understanding of paraffin deposition in single and two-phase (gas-oil) flows; conduct focused experiments to better understand various aspects of deposition physics; and, utilize knowledge gained from experimental modeling studies to enhance the computer programs developed in the previous JIP for predicting paraffin deposition in single and two-phase flow environments. These refined computer models will then be tested against field data from member company pipelines. The following deliverables are scheduled during the first three projects of the program: (1) Single-Phase Studies, with three different black oils, which will yield an enhanced computer code for predicting paraffin deposition in deepwater and surface pipelines. (2) Two

  10. Glacial atmospheric phosphorus deposition

    NASA Astrophysics Data System (ADS)

    Kjær, Helle Astrid; Dallmayr, Remi; Gabrieli, Jacopo; Goto-Azuma, Kumiko; Hirabayashi, Motohiro; Svensson, Anders; Vallelonga, Paul

    2016-04-01

    Phosphorus in the atmosphere is poorly studied and thus not much is known about atmospheric phosphorus and phosphate transport and deposition changes over time, though it is well known that phosphorus can be a source of long-range nutrient transport, e.g. Saharan dust transported to the tropical forests of Brazil. In glacial times it has been speculated that transport of phosphorus from exposed shelves would increase the ocean productivity by wash out. However whether the exposed shelf would also increase the atmospheric load to more remote places has not been investigated. Polar ice cores offer a unique opportunity to study the atmospheric transport of aerosols on various timescales, from glacial-interglacial periods to recent anthropogenic influences. We have for the first time determined the atmospheric transport of phosphorus to the Arctic by means of ice core analysis. Both total and dissolved reactive phosphorus were measured to investigate current and past atmospheric transport of phosphorus to the Arctic. Results show that glacial cold stadials had increased atmospheric total phosphorus mass loads of 70 times higher than in the past century, while DRP was only increased by a factor of 14. In the recent period we find evidence of a phosphorus increase over the past 50 yrs in ice cores close to human occupation likely correlated to forest fires. References: Kjær, Helle Astrid, et al. "Continuous flow analysis method for determination of dissolved reactive phosphorus in ice cores." Environmental science & technology 47.21 (2013): 12325-12332. Kjær, Helle Astrid, et al. "Greenland ice cores constrain glacial atmospheric fluxes of phosphorus." Journal of Geophysical Research: Atmospheres120.20 (2015).

  11. Deposition + Erosion = Textures

    NASA Technical Reports Server (NTRS)

    2003-01-01

    [figure removed for brevity, see original site]

    Released 7 May 2003

    Toward the westernmost extent of the Medusae Fossae Formation, a 5000+ km long belt of eroding sediments, the interleaving of erosional surfaces produces dramatic textural variations. In the lower third of this image, the cross-hatched MFF layer is being stripped back from a surface that was already heavily eroded before the MFF layer was deposited. Also, note the sinuous and, in places, dendritic ridges that are either linear dunes or inverted channels.

    Image information: VIS instrument. Latitude -3.9, Longitude 154.1East (205.9). 19 meter/pixel resolution.

    Note: this THEMIS visual image has not been radiometrically nor geometrically calibrated for this preliminary release. An empirical correction has been performed to remove instrumental effects. A linear shift has been applied in the cross-track and down-track direction to approximate spacecraft and planetary motion. Fully calibrated and geometrically projected images will be released through the Planetary Data System in accordance with Project policies at a later time.

    NASA's Jet Propulsion Laboratory manages the 2001 Mars Odyssey mission for NASA's Office of Space Science, Washington, D.C. The Thermal Emission Imaging System (THEMIS) was developed by Arizona State University, Tempe, in collaboration with Raytheon Santa Barbara Remote Sensing. The THEMIS investigation is led by Dr. Philip Christensen at Arizona State University. Lockheed Martin Astronautics, Denver, is the prime contractor for the Odyssey project, and developed and built the orbiter. Mission operations are conducted jointly from Lockheed Martin and from JPL, a division of the California Institute of Technology in Pasadena.

  12. Sputter Deposition of Metallic Sponges

    SciTech Connect

    Jankowski, A F; Hayes, J P

    2002-01-18

    Metallic films are grown with a sponge-like morphology in the as-deposited condition using planar magnetron sputtering. The morphology of the deposit is characterized by metallic continuity in three dimensions with continuous porosity on the sub-micron scale. The stabilization of the metallic sponge is directly correlated with a limited range for the sputter deposition parameters of working gas pressure and substrate temperature. This sponge-like morphology augments the features as generally understood in the classic zone models of growth for physical vapor deposits. Nickel coatings are deposited with working gas pressures up to 4 Pa and for substrate temperatures up to 1100 K. The morphology of the deposits is examined in plan and in cross-section with scanning electron microscopy. The parametric range of gas pressure and substrate temperature (relative to absolute melt point) for the deposition processing under which the metallic sponges are produced appear universal for many metals, as for example, including gold, silver, and aluminum.

  13. The upper and lower limits of the mechanistic stoichiometry of mitochondrial oxidative phosphorylation. Stoichiometry of oxidative phosphorylation.

    PubMed

    Beavis, A D; Lehninger, A L

    1986-07-15

    Determination of the intrinsic or mechanistic P/O ratio of oxidative phosphorylation is difficult because of the unknown magnitude of leak fluxes. Applying a new approach developed to overcome this problem (see our preceding paper in this journal), the relationships between the rate of O2 uptake [( Jo)3], the net rate of phosphorylation (Jp), the P/O ratio, and the respiratory control ratio (RCR) have been determined in rat liver mitochondria when the rate of phosphorylation was systematically varied by three specific means. (a) When phosphorylation is titrated with carboxyatractyloside, linear relationships are observed between Jp and (Jo)3. These data indicate that the upper limit of the mechanistic P/O ratio is 1.80 for succinate and 2.90 for 3-hydroxybutyrate oxidation. (b) Titration with malonate or antimycin yields linear relationships between Jp and (Jo)3. These data give the lower limit of the mechanistic P/O ratio of 1.63 for succinate and 2.66 for 3-hydroxybutyrate oxidation. (c) Titration with a protonophore yields linear relationships between Jp, (Jo)3, and (Jo)4 and between P/O and 1/RCR. Extrapolation of the P/O ratio to 1/RCR = 0 yields P/O ratios of 1.75 for succinate and 2.73 for 3-hydroxybutyrate oxidation which must be equal to or greater than the mechanistic stoichiometry. When published values for the H+/O and H+/ATP ejection ratios are taken into consideration, these measurements suggest that the mechanistic P/O ratio is 1.75 for succinate oxidation and 2.75 for NADH oxidation. PMID:3015613

  14. Atmospheric Mercury Deposition Monitoring – National Atmospheric Deposition Program (NADP)

    EPA Science Inventory

    The National Atmospheric Deposition Program (NADP) developed and operates a collaborative network of atmospheric mercury monitoring sites based in North America – the Atmospheric Mercury Network (AMNet). The justification for the network was growing interest and demand from many ...

  15. Tracking colloid transport in porous media using discrete flow fields and sensitivity of simulated colloid deposition to space discretization.

    PubMed

    Li, Zhelong; Zhang, Dongxiao; Li, Xiqing

    2010-02-15

    Advances in pore structure characterization and lattice-Boltzmann (LB) simulations of flow fields in pore spaces are making mechanistic simulations of colloid transport in real porous media a realistic goal. The primary challenge to reach this goal may be the computational demand of LB flow simulations in discretized porous medium domains at an assemblage scale. In this work, flow fields in simple cubic and dense packing systems were simulated at different discretization resolutions using the LB method. The simulated flow fields were incorporated into to a three-dimensional particle tracking model to simulate colloid transport in the two systems. The simulated colloid deposition tended to become asymptotic at a critical discretization resolution (voxel-grain size ratio = 0.01) at groundwater flow regimes for colloids down to submicrometer level under favorable conditions and down to around 1 microm under unfavorable conditions. The average simulated fluid velocities near grain surfaces were extracted to explain the sensitivities of simulated depositions to space discretization under both conditions. At the critical discretization resolution, current computation capacity would allow flow simulations and particle tracking in assemblage porous medium domains. In addition, particle tracking simulations revealed that colloids may be retained in flow vortices under conditions both favorable and unfavorable for deposition. Colloid retention in flow vortices has been proposed only very recently. Here we provide a mechanistic confirmation to this novel retention process. PMID:20088544

  16. Plasma Deposition of Amorphous Silicon

    NASA Technical Reports Server (NTRS)

    Calcote, H. F.

    1982-01-01

    Strongly adhering films of silicon are deposited directly on such materials as Pyrex and Vycor (or equivalent materials) and aluminum by a non-equilibrium plasma jet. Amorphous silicon films are formed by decomposition of silicon tetrachloride or trichlorosilane in the plasma. Plasma-jet technique can also be used to deposit an adherent silicon film on aluminum from silane and to dope such films with phosphorus. Ability to deposit silicon films on such readily available, inexpensive substrates could eventually lead to lower cost photovoltaic cells.

  17. Particle deposition in ventilation ducts

    SciTech Connect

    Sippola, Mark R.

    2002-09-01

    Exposure to airborne particles is detrimental to human health and indoor exposures dominate total exposures for most people. The accidental or intentional release of aerosolized chemical and biological agents within or near a building can lead to exposures of building occupants to hazardous agents and costly building remediation. Particle deposition in heating, ventilation and air-conditioning (HVAC) systems may significantly influence exposures to particles indoors, diminish HVAC performance and lead to secondary pollutant release within buildings. This dissertation advances the understanding of particle behavior in HVAC systems and the fates of indoor particles by means of experiments and modeling. Laboratory experiments were conducted to quantify particle deposition rates in horizontal ventilation ducts using real HVAC materials. Particle deposition experiments were conducted in steel and internally insulated ducts at air speeds typically found in ventilation ducts, 2-9 m/s. Behaviors of monodisperse particles with diameters in the size range 1-16 {micro}m were investigated. Deposition rates were measured in straight ducts with a fully developed turbulent flow profile, straight ducts with a developing turbulent flow profile, in duct bends and at S-connector pieces located at duct junctions. In straight ducts with fully developed turbulence, experiments showed deposition rates to be highest at duct floors, intermediate at duct walls, and lowest at duct ceilings. Deposition rates to a given surface increased with an increase in particle size or air speed. Deposition was much higher in internally insulated ducts than in uninsulated steel ducts. In most cases, deposition in straight ducts with developing turbulence, in duct bends and at S-connectors at duct junctions was higher than in straight ducts with fully developed turbulence. Measured deposition rates were generally higher than predicted by published models. A model incorporating empirical equations based on

  18. Ferroelectric thin films deposited by pulsed laser deposition

    NASA Astrophysics Data System (ADS)

    Dinu, Raluca; Vrejoiu, I.; Verardi, P.; Craciun, F.; Dinescu, Maria

    2001-06-01

    Influence of substrate and electrode on the properties of PbZr0.53Ti0.47O3 (PZT) thin films grown by pulsed laser deposition technique (1060 nm wavelength Nd:YAG laser light, 10 ns pulse duration, 10 Hz repetition rate, 0.35 J/pulse, 25 J/cm2 laser fluence, deposition rate about 1 angstrom/pulse) was studied. The substrate temperatures were in the range 380 degree(s)C-400 degree(s)C. Oriented crystalline PZT layers with 1-3 micrometers thickness were deposited on glass substrates plated with Au/Pt/NiCr electrodes, from a PZT commercial target in oxygen reactive atmosphere. The deposited PZT films with perovskite structure were preferentially oriented along the (111) direction as revealed from XRD spectra. Piezoelectric d33 coefficients up to 30 pC/N were obtained on as deposited films. Ferroelectric hysteresis loops at 100 Hz revealed a remanent polarization of 15 (mu) C/cm2 and a coercive field of 100 kV/cm. A comparison with properties of PZT films deposited using a KrF laser and with SrBi2Ta2O9 (SBT) films is reported.

  19. Impacts of mechanistic changes on HOx formation and recycling in the oxidation of isoprene

    NASA Astrophysics Data System (ADS)

    Archibald, A. T.; Cooke, M. C.; Utembe, S. R.; Shallcross, D. E.; Derwent, R. G.; Jenkin, M. E.

    2010-09-01

    Recently reported model-measurement discrepancies for the concentrations of the HOx radical species (OH and HO2) in locations characterized by high emission rates of isoprene have indicated possible deficiencies in the representation of OH recycling and formation in isoprene mechanisms currently employed in numerical models; particularly at low levels of NOx. Using version 3.1 of the Master Chemical Mechanism (MCM v3.1) as a base mechanism, the sensitivity of the system to a number of detailed mechanistic changes is examined for a wide range of NOx levels, using a simple box model. The studies consider sensitivity tests in relation to three general areas for which experimental and/or theoretical evidence has been reported in the peer-reviewed literature, as follows: (1) implementation of propagating channels for the reactions of HO2 with acyl and β-oxo peroxy radicals with HO2, with support from a number of studies; (2) implementation of the OH-catalysed conversion of isoprene-derived hydroperoxides to isomeric epoxydiols, as characterised by Paulot et al.~(2009a); and (3) implementation of a mechanism involving respective 1,5 and 1,6 H atom shift isomerisation reactions of the β-hydroxyalkenyl and cis-δ-hydroxyalkenyl peroxy radical isomers, formed from the sequential addition of OH and O2 to isoprene, based on the theoretical study of Peeters et al. (2009). All the considered mechanistic changes lead to simulated increases in the concentrations of OH, with (1) and (2) resulting in respective increases of up to about 7% and 16%, depending on the level of NOx. (3) is found to have potentially much greater impacts, with enhancements in OH concentrations of up to a factor of about 3.3, depending on the level of NOx, provided the (crucial) rapid photolysis of the hydroperoxy-methyl-butenal products of the cis-δ-hydroxyalkenyl peroxy radical isomerisation reactions is represented, as also postulated by Peeters et al.~(2009). Additional tests suggest that the

  20. Higher plant modelling for life support applications: first results of a simple mechanistic model

    NASA Astrophysics Data System (ADS)

    Hezard, Pauline; Dussap, Claude-Gilles; Sasidharan L, Swathy

    2012-07-01

    In the case of closed ecological life support systems, the air and water regeneration and food production are performed using microorganisms and higher plants. Wheat, rice, soybean, lettuce, tomato or other types of eatable annual plants produce fresh food while recycling CO2 into breathable oxygen. Additionally, they evaporate a large quantity of water, which can be condensed and used as potable water. This shows that recycling functions of air revitalization and food production are completely linked. Consequently, the control of a growth chamber for higher plant production has to be performed with efficient mechanistic models, in order to ensure a realistic prediction of plant behaviour, water and gas recycling whatever the environmental conditions. Purely mechanistic models of plant production in controlled environments are not available yet. This is the reason why new models must be developed and validated. This work concerns the design and test of a simplified version of a mathematical model coupling plant architecture and mass balance purposes in order to compare its results with available data of lettuce grown in closed and controlled chambers. The carbon exchange rate, water absorption and evaporation rate, biomass fresh weight as well as leaf surface are modelled and compared with available data. The model consists of four modules. The first one evaluates plant architecture, like total leaf surface, leaf area index and stem length data. The second one calculates the rate of matter and energy exchange depending on architectural and environmental data: light absorption in the canopy, CO2 uptake or release, water uptake and evapotranspiration. The third module evaluates which of the previous rates is limiting overall biomass growth; and the last one calculates biomass growth rate depending on matter exchange rates, using a global stoichiometric equation. All these rates are a set of differential equations, which are integrated with time in order to provide

  1. Mechanistic studies of the radical SAM enzyme spore photoproduct lyase (SPL).

    PubMed

    Li, Lei

    2012-11-01

    Spore photoproduct lyase (SPL) repairs a special thymine dimer 5-thyminyl-5,6-dihydrothymine, which is commonly called spore photoproduct or SP at the bacterial early germination phase. SP is the exclusive DNA photo-damage product in bacterial endospores; its generation and swift repair by SPL are responsible for the spores' extremely high UV resistance. The early in vivo studies suggested that SPL utilizes a direct reversal strategy to repair the SP in the absence of light. The research in the past decade further established SPL as a radical SAM enzyme, which utilizes a tri-cysteine CXXXCXXC motif to harbor a [4Fe-4S] cluster. At the 1+ oxidation state, the cluster provides an electron to the S-adenosylmethionine (SAM), which binds to the cluster in a bidentate manner as the fourth and fifth ligands, to reductively cleave the CS bond associated with the sulfonium ion in SAM, generating a reactive 5'-deoxyadenosyl (5'-dA) radical. This 5'-dA radical abstracts the proR hydrogen atom from the C6 carbon of SP to initiate the repair process; the resulting SP radical subsequently fragments to generate a putative thymine methyl radical, which accepts a back-donated H atom to yield the repaired TpT. SAM is suggested to be regenerated at the end of each catalytic cycle; and only a catalytic amount of SAM is needed in the SPL reaction. The H atom source for the back donation step is suggested to be a cysteine residue (C141 in Bacillus subtilis SPL), and the H-atom transfer reaction leaves a thiyl radical behind on the protein. This thiyl radical thus must participate in the SAM regeneration process; however how the thiyl radical abstracts an H atom from the 5'-dA to regenerate SAM is unknown. This paper reviews and discusses the history and the latest progress in the mechanistic elucidation of SPL. Despite some recent breakthroughs, more questions are raised in the mechanistic understanding of this intriguing DNA repair enzyme. This article is part of a Special Issue

  2. Prediction of episodic acidification in North-eastern USA: An empirical/mechanistic approach

    USGS Publications Warehouse

    Davies, T.D.; Tranter, M.; Wigington, P.J., Jr.; Eshleman, K.N.; Peters, N.E.; Van Sickle, J.; DeWalle, David R.; Murdoch, Peter S.

    1999-01-01

    Observations from the US Environmental Protection Agency's Episodic Response Project (ERP) in the North-eastern United States are used to develop an empirical/mechanistic scheme for prediction of the minimum values of acid neutralizing capacity (ANC) during episodes. An acidification episode is defined as a hydrological event during which ANC decreases. The pre-episode ANC is used to index the antecedent condition, and the stream flow increase reflects how much the relative contributions of sources of waters change during the episode. As much as 92% of the total variation in the minimum ANC in individual catchments can be explained (with levels of explanation >70% for nine of the 13 streams) by a multiple linear regression model that includes pre-episode ANC and change in discharge as independent variable. The predictive scheme is demonstrated to be regionally robust, with the regional variance explained ranging from 77 to 83%. The scheme is not successful for each ERP stream, and reasons are suggested for the individual failures. The potential for applying the predictive scheme to other watersheds is demonstrated by testing the model with data from the Panola Mountain Research Watershed in the South-eastern United States, where the variance explained by the model was 74%. The model can also be utilized to assess 'chemically new' and 'chemically old' water sources during acidification episodes.Observations from the US Environmental Protection Agency's Episodic Response Project (ERP) in the Northeastern United States are used to develop an empirical/mechanistic scheme for prediction of the minimum values of acid neutralizing capacity (ANC) during episodes. An acidification episode is defined as a hydrological event during which ANC decreases. The pre-episode ANC is used to index the antecedent condition, and the stream flow increase reflects how much the relative contributions of sources of waters change during the episode. As much as 92% of the total variation in

  3. Mechanistic modeling of ion-exchange process chromatography of charge variants of monoclonal antibody products.

    PubMed

    Kumar, Vijesh; Leweke, Samuel; von Lieres, Eric; Rathore, Anurag S

    2015-12-24

    Ion-exchange chromatography (IEX) is universally accepted as the optimal method for achieving process scale separation of charge variants of a monoclonal antibody (mAb) therapeutic. These variants are closely related to the product and a baseline separation is rarely achieved. The general practice is to fractionate the eluate from the IEX column, analyze the fractions and then pool the desired fractions to obtain the targeted composition of variants. This is, however, a very cumbersome and time consuming exercise. A mechanistic model that is capable of simulating the peak profile will be a much more elegant and effective way to make a decision on the pooling strategy. This paper proposes a mechanistic model, based on the general rate model, to predict elution peak profile for separation of the main product from its variants. The proposed approach uses inverse fit of process scale chromatogram for estimation of model parameters using the initial values that are obtained from theoretical correlations. The packed bed column has been modeled along with the chromatographic system consisting of the mixer, tubing and detectors as a series of dispersed plug flow and continuous stirred tank reactors. The model uses loading ranges starting at 25% to a maximum of 70% of the loading capacity and hence is applicable to process scale separations. Langmuir model has been extended to include the effects of salt concentration and temperature on the model parameters. The extended Langmuir model that has been proposed uses one less parameter than the SMA model and this results in a significant ease of estimating the model parameters from inverse fitting. The proposed model has been validated with experimental data and has been shown to successfully predict peak profile for a range of load capacities (15-28mg/mL), gradient lengths (10-30CV), bed heights (6-20cm), and for three different resins with good accuracy (as measured by estimation of residuals). The model has been also

  4. Computational mechanistic elucidation of the intramolecular aminoalkene hydroamination catalysed by iminoanilide alkaline-earth compounds.

    PubMed

    Tobisch, Sven

    2015-04-27

    A comprehensive computational exploration of plausible alternative mechanistic pathways for the intramolecular hydroamination (HA) of aminoalkenes by a recently reported class of kinetically stabilised iminoanilide alkaline-earth silylamido compounds [{N^N}Ae{N(SiMe3)2}⋅(thf)n] ({N^N} = iminoanilide; Ae = Ca, Sr, Ba) is presented. On the one hand, a proton-assisted concerted N-C/C-H bond-forming pathway to afford the cycloamine in a single step can be invoked and on the other hand, a stepwise σ-insertive pathway that involves a fast, reversible migratory olefin 1,2-insertion step linked to a less rapid, irreversible metal-C azacycle tether σ-bond aminolysis. Notably, these alternative mechanistic avenues are equally consistent with reported key experimental features. The present study, which employs a thoroughly benchmarked and reliable DFT methodology, supports the prevailing mechanism to be a stepwise σ-insertive pathway that sees an initial conversion of the {N^N}Ae silylamido into the catalytically competent {N^N}Ae amidoalkene compound and involves thereafter facile and reversible insertive N-C bond-forming ring closure, linked to irreversible intramolecular Ae-C tether σ-bond aminolysis at the transient {N^N}Ae alkyl intermediate. Turnover-limiting protonolysis accounts for the substantial primary kinetic isotope effect observed; its DFT-derived barrier satisfactorily matches the empirically determined Eyring parameter and predicts the decrease in rate observed across the series Ca>Sr>Ba correctly. Non-competitive kinetic demands militate against the operation of the concerted proton-assisted pathway, which describes N-C bond-forming ring closure triggered by concomitant amino proton delivery at the C=C linkage evolving through a multi-centre TS structure. Valuable insights into the catalytic structure-activity relationships are unveiled by a detailed comparison of [{N^N}Ae(NHR)] catalysts. Moreover, the intriguingly opposite trends in reactivity

  5. Cathodoluminescence in Quaternary carbonate deposits

    NASA Astrophysics Data System (ADS)

    Braithwaite, Colin J. R.

    2016-05-01

    The cathodoluminescent oscillatory and sectoral growth zones common in crystals formed in ancient limestone successions in a variety of putative environments appear to be rare or absent from Recent and Pleistocene marine carbonate sequences. The factors controlling cathodoluminescence and reasons for this disparity are examined. The cathodoluminescent zones in the cements of ancient rocks have been interpreted as responses to variations in the redox potential of formative pore waters during crystal growth; although similar cathodoluminescent behaviour is recorded from some deposits, including travertines and Quaternary speleothems, formed in what are thought to have been strongly oxidizing environments. The apparent absence of cathodoluminescence in the most Recent and Pleistocene marine deposits, that presumably reflect deposition and diagenesis in environments that are also characteristically oxidized, therefore seems anomalous. The controlling influences on cathodoluminescence are reviewed, together with evidence relating to observations of Pleistocene marine deposits and likely conditions of formation but, where it is present, the mechanism(s) for its development remain elusive.

  6. WET DEPOSITION AND SNOWPACK MONITORING

    EPA Science Inventory

    Accurate measurement of snowfall is critical to the assessment of acidic deposition trends, particularly in areas where snow represents 30 percent or more of the annual precipitation. Such areas include the intermountain west, characterized by complex topography and meterology, h...

  7. Modeling Deposition of Inhaled Particles

    EPA Science Inventory

    The mathematical modeling of the deposition and distribution of inhaled aerosols within human lungs is an invaluable tool in predicting both the health risks associated with inhaled environmental aerosols and the therapeutic dose delivered by inhaled pharmacological drugs. Howeve...

  8. The zeolite deposits of Greece

    USGS Publications Warehouse

    Stamatakis, M.G.; Hall, A.; Hein, J.R.

    1996-01-01

    Zeolites are present in altered pyroclastic rocks at many localities in Greece, and large deposits of potential economic interest are present in three areas: (1) the Evros region of the province of Thrace in the north-eastern part of the Greek mainland; (2) the islands of Kimolos and Poliegos in the western Aegean; and (3) the island of Samos in the eastern Aegean Sea. The deposits in Thrace are of Eocene-Oligocene age and are rich in heulandite and/or clinoptilolite. Those of Kimolos and Poliegos are mainly Quaternary and are rich in mordenite. Those of Samos are Miocene, and are rich in clinoptilolite and/or analcime. The deposits in Thrace are believed to have formed in an open hydrological system by the action of meteoric water, and those of the western Aegean islands in a similar way but under conditions of high heat flow, whereas the deposits in Samos were formed in a saline-alkaline lake.

  9. Vapor deposition of hardened niobium

    DOEpatents

    Blocher, Jr., John M.; Veigel, Neil D.; Landrigan, Richard B.

    1983-04-19

    A method of coating ceramic nuclear fuel particles containing a major amount of an actinide ceramic in which the particles are placed in a fluidized bed maintained at ca. 800.degree. to ca. 900.degree. C., and niobium pentachloride vapor and carbon tetrachloride vapor are led into the bed, whereby niobium metal is deposited on the particles and carbon is deposited interstitially within the niobium. Coating apparatus used in the method is also disclosed.

  10. A radon progeny deposition model

    SciTech Connect

    Rielage, Keith; Elliott, Steven R; Hime, Andrew; Guiseppe, Vincente E; Westerdale, S.

    2010-12-01

    The next generation low-background detectors operating underground aim for unprecedented low levels of radioactive backgrounds. Although the radioactive decays of airborne radon (particularly {sup 222}Rn) and its subsequent progeny present in an experiment are potential backgrounds, also problematic is the deposition of radon progeny on detector materials. Exposure to radon at any stage of assembly of an experiment can result in surface contamination by progeny supported by the long half life (22 y) of {sup 210}Pb on sensitive locations of a detector. An understanding of the potential surface contamination from deposition will enable requirements of radon-reduced air and clean room environments for the assembly of low background experiments. It is known that there are a number of environmental factors that govern the deposition of progeny onto surfaces. However, existing models have not explored the impact of some environmental factors important for low background experiments. A test stand has been constructed to deposit radon progeny on various surfaces under a controlled environment in order to develop a deposition model. Results from this test stand and the resulting deposition model are presented.

  11. A Radon Progeny Deposition Model

    SciTech Connect

    Guiseppe, V. E.; Elliott, S. R.; Hime, A.; Rielage, K.; Westerdale, S.

    2011-04-27

    The next generation low-background detectors operating underground aim for unprecedented low levels of radioactive backgrounds. Although the radioactive decays of airborne radon (particularly {sup 222}Rn) and its subsequent progeny present in an experiment are potential backgrounds, also problematic is the deposition of radon progeny on detector materials. Exposure to radon at any stage of assembly of an experiment can result in surface contamination by progeny supported by the long half life (22 y) of {sup 210}Pb on sensitive locations of a detector. An understanding of the potential surface contamination from deposition will enable requirements of radon-reduced air and clean room environments for the assembly of low background experiments. It is known that there are a number of environmental factors that govern the deposition of progeny onto surfaces. However, existing models have not explored the impact of some environmental factors important for low background experiments. A test stand has been constructed to deposit radon progeny on various surfaces under a controlled environment in order to develop a deposition model. Results from this test stand and the resulting deposition model are presented.

  12. Description and evaluation of a mechanistically based conceptual model for spall

    SciTech Connect

    Hansen, F.D.; Knowles, M.K.; Thompson, T.W.

    1997-08-01

    A mechanistically based model for a possible spall event at the WIPP site is developed and evaluated in this report. Release of waste material to the surface during an inadvertent borehole intrusion is possible if future states of the repository include high gas pressure and waste material consisting of fine particulates having low mechanical strength. The conceptual model incorporates the physics of wellbore hydraulics coupled to transient gas flow to the intrusion borehole, and mechanical response of the waste. Degraded waste properties using of the model. The evaluations include both numerical and analytical implementations of the conceptual model. A tensile failure criterion is assumed appropriate for calculation of volumes of waste experiencing fragmentation. Calculations show that for repository gas pressures less than 12 MPa, no tensile failure occurs. Minimal volumes of material experience failure below gas pressure of 14 MPa. Repository conditions dictate that the probability of gas pressures exceeding 14 MPa is approximately 1%. For these conditions, a maximum failed volume of 0.25 m{sup 3} is calculated.

  13. Mechanistic Insights into the Formation of Dodecanethiolate-Stabilized Magnetic Iridium Nanoparticles: Thiosulfate vs Thiol Ligands

    PubMed Central

    2015-01-01

    The synthesis of stable and isolable iridium nanoparticles with an average core size of ∼1.2 ± 0.3 nm was achieved by employing sodium S-dodecylthiosulfate as a ligand precursor during the modified Brust–Schiffrin reaction. Transmission electron microscopy (TEM) of the isolated Ir nanoparticles revealed a high degree of monodispersity. Further characterizations with 1H NMR, FT-IR, UV–vis spectroscopy, thermogravimetric analysis (TGA), and X-ray photoelectron spectroscopy (XPS) confirmed that the synthesized Ir nanoparticles are stabilized by dodecanethiolate ligands produced upon the adsorption/cleavage of S-dodecylthiosulfate on the growing Ir nanoparticle surface. By comparison, synthetic attempts employing dodecanethiol as a stabilizing ligand led to the formation of Ir-thiolate species (Ir(SR)3) as an intermediate and Ir-hydroxide species at the completion of reaction. Mechanistic investigations of these two reactions using S-dodecylthiosulfate and dodecanethiol provided deeper understandings on the novelty of thiosulfate ligands, which allow the successful formation of stable thiolate-capped Ir nanoparticles. Moreover, these Ir nanoparticles were shown to have strong magnetic properties. PMID:25018790

  14. Station Blackout: A case study in the interaction of mechanistic and probabilistic safety analysis

    SciTech Connect

    Curtis Smith; Diego Mandelli; Cristian Rabiti

    2013-11-01

    The ability to better characterize and quantify safety margins is important to improved decision making about nuclear power plant design, operation, and plant life extension. As research and development (R&D) in the light-water reactor (LWR) Sustainability (LWRS) Program and other collaborative efforts yield new data, sensors, and improved scientific understanding of physical processes that govern the aging and degradation of plant SSCs needs and opportunities to better optimize plant safety and performance will become known. The purpose of the Risk Informed Safety Margin Characterization (RISMC) Pathway R&D is to support plant decisions for risk-informed margin management with the aim to improve economics, reliability, and sustain safety of current NPPs. In this paper, we describe the RISMC analysis process illustrating how mechanistic and probabilistic approaches are combined in order to estimate a safety margin. We use the scenario of a “station blackout” wherein offsite power and onsite power is lost, thereby causing a challenge to plant safety systems. We describe the RISMC approach, illustrate the station blackout modeling, and contrast this with traditional risk analysis modeling for this type of accident scenario.

  15. Gridded meteorological data as a resource for mechanistic macroecology in coastal environments.

    PubMed

    Mislan, K A S; Wethey, David S

    2011-10-01

    Gridded weather data were evaluated as sources of forcing variables for biophysical models of intertidal animal body temperature with model results obtained using local weather station data serving as the baseline of comparison. The objective of the study was to determine which gridded data are sufficient to capture observed patterns of thermal stress. Three coastal sites in western North America were included in this analysis: Boiler Bay, Oregon; Bodega Bay, California; and Pacific Grove, California. The gridded data with the highest spatial resolution, the 32-km North American Regional Reanalysis (NARR) and the 38-km Climate Forecasting System Reanalysis (CFSR), predicted daily maximum intertidal animal temperature most similarly to the local weather Station data. Time step size was important for variables that change rapidly throughout the day, such as solar radiation. There were site-based differences in the ability of the model to predict daily maximum intertidal animal temperature, with the gridded data predictions being the closest to local weather station predictions in Boiler Bay, Oregon. In a review of gridded data used as part of ecological studies, there was broad use of the data across subject areas and ecosystems so the recent improvements in the spatial (from 2 degrees to 32 km) and temporal scales (from 6 hours to 1 hour) of gridded data will further add to the applicability within the ecological community particularly for mechanistic studies. PMID:22073652

  16. Mechanistic mathematical model for in vivo aroma release during eating of semiliquid foods.

    PubMed

    Trelea, Ioan Cristian; Atlan, Samuel; Déléris, Isabelle; Saint-Eve, Anne; Marin, Michèle; Souchon, Isabelle

    2008-02-01

    The paper describes a mechanistic mathematical model for aroma release in the oropharynx to the nasal cavity during food consumption. The model is based on the physiology of the swallowing process and is validated with atmospheric pressure chemical ionization coupled with mass spectrometry measurements of aroma concentration in the nasal cavity of subjects eating flavored yogurt. The study is conducted on 3 aroma compounds representative for strawberry flavor (ethyl acetate, ethyl butanoate, and ethyl hexanoate) and 3 panelists. The model provides reasonably accurate time predictions of the relative aroma concentration in the nasal cavity and is able to simulate successive swallowing events as well as imperfect velopharyngeal closure. The most influent parameters are found to be the amount of the residual product in the pharynx and its contact area with the air flux, the volume of the nasal cavity, the equilibrium air/product partition coefficient of the volatile compound, the breath airflow rate, as well as the mass transfer coefficient of the aroma compound in the product, and the amount of product in the mouth. This work constitutes a first step toward computer-aided product formulation by allowing calculation of retronasal aroma intensity as a function of transfer and volatility properties of aroma compounds in food matrices and anatomophysiological characteristics of consumers. PMID:18048371

  17. Structure of the apoptosome: mechanistic insights into activation of an initiator caspase from Drosophila

    PubMed Central

    Pang, Yuxuan; Bai, Xiao-chen; Yan, Chuangye; Hao, Qi; Chen, Zheqin; Wang, Jia-Wei

    2015-01-01

    Apoptosis is executed by a cascade of caspase activation. The autocatalytic activation of an initiator caspase, exemplified by caspase-9 in mammals or its ortholog, Dronc, in fruit flies, is facilitated by a multimeric adaptor complex known as the apoptosome. The underlying mechanism by which caspase-9 or Dronc is activated by the apoptosome remains unknown. Here we report the electron cryomicroscopic (cryo-EM) structure of the intact apoptosome from Drosophila melanogaster at 4.0 Å resolution. Analysis of the Drosophila apoptosome, which comprises 16 molecules of the Dark protein (Apaf-1 ortholog), reveals molecular determinants that support the assembly of the 2.5-MDa complex. In the absence of dATP or ATP, Dronc zymogen potently induces formation of the Dark apoptosome, within which Dronc is efficiently activated. At 4.1 Å resolution, the cryo-EM structure of the Dark apoptosome bound to the caspase recruitment domain (CARD) of Dronc (Dronc-CARD) reveals two stacked rings of Dronc-CARD that are sandwiched between two octameric rings of the Dark protein. The specific interactions between Dronc-CARD and both the CARD and the WD40 repeats of a nearby Dark protomer are indispensable for Dronc activation. These findings reveal important mechanistic insights into the activation of initiator caspase by the apoptosome. PMID:25644603

  18. Sonoenzymatic decolourization of an azo dye employing immobilized horse radish peroxidase (HRP): a mechanistic study.

    PubMed

    Malani, Ritesh S; Khanna, Swati; Moholkar, Vijayanand S

    2013-07-15

    For degradation of biorefractory pollutants, enzymatic treatments and sonochemical treatments have shown high potential. A combined technique of sono-enzymatic treatment is of special interest as it has shown enhancement effect than the individual techniques. This work has attempted to give a mechanistic insight into the interaction of sonochemical and enzymatic treatments using immobilized horseradish peroxidase (HRP) enzyme on the decolourization of acid red dye (an azo dye). In order to segregate the effect of ultrasound and cavitation, experiments were conducted at elevated static pressure. The kinetic parameters of HRP, viz. Vmax and Km were marginally affected by immobilization. There was a minor change in pH optima and temperature optima for immobilized HRP (6.5, 25°C) from free HRP (7.0, 20-25°C). Though the specific activity of free enzyme (0.272U/mg) was found to be higher than the immobilized enzyme (0.104U/mg), immobilized enzyme exhibited higher stability (up to 3 cycles) and degradation potential than free enzyme in all experiments. The results revealed that the coupling of sonication and enzymatic treatment at high pressure in presence of polyethylene glycol (PEG) yielded the highest decolourization of acid red (61.2%). However, the total decolourization achieved with combined technique was lesser than the sum of individual techniques, indicating negative synergy between the sonochemical and enzymatic techniques. PMID:23708258

  19. Toward a mechanistic understanding of animal migration: incorporating physiological measurements in the study of animal movement

    PubMed Central

    Jachowski, David S.; Singh, Navinder J.

    2015-01-01

    Movements are a consequence of an individual's motion and navigational capacity, internal state variables and the influence of external environmental conditions. Although substantial advancements have been made in methods of measuring and quantifying variation in motion capacity, navigational capacity and external environmental parameters in recent decades, the role of internal state in animal migration (and in movement in general) is comparatively little studied. Recent studies of animal movement in the wild illustrate how direct physiological measurements can improve our understanding of the mechanisms underlying movement decisions. In this review, we synthesize and provide examples of how recent technical advances in the physiology-related fields of energetics, nutrition, endocrinology, immunology and ecotoxicology provide opportunities for direct measurements of physiological state in the study of animal movement. We then propose a framework for practitioners to enable better integration of studies of physiological state into animal movement ecology by assessing the mechanistic role played by physiology as both a driver and a modulator of movement. Finally, we highlight the current limitations and research priorities for better integration of direct measurements of animal physiological state into the study of animal movement. PMID:27293720

  20. Disruption of steroidogenesis: Cell models for mechanistic investigations and as screening tools.

    PubMed

    Odermatt, Alex; Strajhar, Petra; Engeli, Roger T

    2016-04-01

    In the modern world, humans are exposed during their whole life to a large number of synthetic chemicals. Some of these chemicals have the potential to disrupt endocrine functions and contribute to the development and/or progression of major diseases. Every year approximately 1000 novel chemicals, used in industrial production, agriculture, consumer products or as pharmaceuticals, are reaching the market, often with limited safety assessment regarding potential endocrine activities. Steroids are essential endocrine hormones, and the importance of the steroidogenesis pathway as a target for endocrine disrupting chemicals (EDCs) has been recognized by leading scientists and authorities. Cell lines have a prominent role in the initial stages of toxicity assessment, i.e. for mechanistic investigations and for the medium to high throughput analysis of chemicals for potential steroidogenesis disrupting activities. Nevertheless, the users have to be aware of the limitations of the existing cell models in order to apply them properly, and there is a great demand for improved cell-based testing systems and protocols. This review intends to provide an overview of the available cell lines for studying effects of chemicals on gonadal and adrenal steroidogenesis, their use and limitations, as well as the need for future improvements of cell-based testing systems and protocols. PMID:26807866

  1. Dynamic Kinetic Resolution Enabled by Intramolecular Benzoin Reaction: Synthetic Applications and Mechanistic Insights.

    PubMed

    Zhang, Guoxiang; Yang, Shuang; Zhang, Xiaoyan; Lin, Qiqiao; Das, Deb K; Liu, Jian; Fang, Xinqiang

    2016-06-29

    The highly enantio-, diastereo-, and regioselective dynamic kinetic resolution of β-ketoesters and 1,3-diketones was achieved via a chiral N-heterocyclic carbene catalyzed intramolecular cross-benzoin reaction. A variety of tetralone derivatives bearing two contiguous stereocenters and multiple functionalities were liberated in moderate to excellent yields and with high levels of stereoselectivity (>95% ee and >20:1 dr in most cases). In addition, the excellent regioselectivity control for aryl/alkyl 1,3-diketones, and the superior electronic differentiation of 1,3-diarylketones were highlighted. Moreover, a set of new mechanistic rationale that differs with the currently widely accepted understanding of intramolecular benzoin reactions was established to demonstrate the superior preference of benzoin over aldol transformation: (1) A coexistence of competitive aldol and benzoin reactions was detected, but a retro-aldol-irreversible benzoin process performs a vital role in the generation of predominant benzoin products. (2) The most essential role of an N-electron-withdrawing substituent in triazolium catalysts was revealed to be accelerating the rate of the benzoin transformation, rather than suppressing the aldol process through reducing the inherent basicity of the catalyst. PMID:27270409

  2. Mechanistic model of radiation-induced cancer after fractionated radiotherapy using the linear-quadratic formula

    SciTech Connect

    Schneider, Uwe

    2009-04-15

    A simple mechanistic model for predicting cancer induction after fractionated radiotherapy is developed. The model is based upon the linear-quadratic model. The inductions of carcinomas and sarcomas are modeled separately. The linear-quadratic model of cell kill is applied to normal tissues which are unintentionally irradiated during a cancer treatment with radiotherapy. Tumor induction is modeled such that each transformation process results in a tumor cell. The microscopic transformation parameter was chosen such that in the limit of low dose and acute exposure, the parameters of the linear-no-threshold model for tumor induction were approached. The differential equations describing carcinoma and sarcoma inductions can be solved analytically. Cancer induction in this model is a function of treatment dose, the cell kill parameters ({alpha},{beta}), the tumor induction variable ({mu}), and the repopulation parameter ({xi}). Carcinoma induction shows a bell shaped behavior as long as cell repopulation is small. Assuming large cell repopulation rates, a plateaulike function is approached. In contrast, sarcoma induction is negligible for low doses and increases with increasing dose up to a constant value. The proposed model describes carcinoma and sarcoma inductions after fractionated radiotherapy as an analytical function of four parameters. In the limit of low dose and for an instant irradiation it reproduces the results of the linear-no-threshold model. The obtained dose-response curves for cancer induction can be implemented with other models such as the organ-equivalent dose model to predict second cancers after radiotherapy.

  3. Mechanistic studies of two-dimensional covalent organic frameworks rapidly polymerized from initially homogenous conditions.

    PubMed

    Smith, Brian J; Dichtel, William R

    2014-06-18

    Covalent organic frameworks (COFs) are periodic two- and three-dimensional (2D and 3D) polymer networks with high surface areas, low densities, and designed structures. Despite intense interest in framework materials, the nucleation and growth processes of COFs, and even of more established metal-organic frameworks (MOFs), are poorly understood. The kinetics of COF growth under varied reaction conditions provides mechanistic insight needed to improve their crystallinity and rationally synthesize new materials. Such kinetic measurements are unprecedented and difficult to perform on typical heterogeneous COF reaction mixtures. Here we synthesize 2D boronate ester-linked COF-5 under conditions in which the monomers are fully soluble. These homogeneous growth conditions provide equal or better material quality compared to any previous report and enable the first rigorous studies of the early stages of COF growth. COF-5 forms within minutes, and the precipitation rate is readily quantified from optical turbidity measurements. COF-5 formation follows an Arrhenius temperature dependence between 60-90 °C with an activation energy of 22-27 kcal/mol. The measured rate law includes a second order in both boronic acid and catechol moieties, and inverse second order in MeOH concentration. A competitive monofunctional catechol slows COF-5 formation but does not redissolve already precipitated COF, indicating both dynamic covalent bond formation and irreversible precipitation. Finally, stoichiometric H2O provides a 4-fold increase in crystallite domain areas, representing the first rational link between reaction conditions and material quality. PMID:24892961

  4. Oxide-ion and proton conducting electrolyte materials for clean energy applications: structural and mechanistic features.

    PubMed

    Malavasi, Lorenzo; Fisher, Craig A J; Islam, M Saiful

    2010-11-01

    This critical review presents an overview of the various classes of oxide materials exhibiting fast oxide-ion or proton conductivity for use as solid electrolytes in clean energy applications such as solid oxide fuel cells. Emphasis is placed on the relationship between structural and mechanistic features of the crystalline materials and their ion conduction properties. After describing well-established classes such as fluorite- and perovskite-based oxides, new materials and structure-types are presented. These include a variety of molybdate, gallate, apatite silicate/germanate and niobate systems, many of which contain flexible structural networks, and exhibit different defect properties and transport mechanisms to the conventional materials. It is concluded that the rich chemistry of these important systems provides diverse possibilities for developing superior ionic conductors for use as solid electrolytes in fuel cells and related applications. In most cases, a greater atomic-level understanding of the structures, defects and conduction mechanisms is achieved through a combination of experimental and computational techniques (217 references). PMID:20848015

  5. Structure-based Mechanistic Insights into Terminal Amide Synthase in Nosiheptide-Represented Thiopeptides Biosynthesis

    PubMed Central

    Liu, Shanshan; Guo, Heng; Zhang, Tianlong; Han, Li; Yao, Pengfei; Zhang, Yan; Rong, Naiyan; Yu, Yi; Lan, Wenxian; Wang, Chunxi; Ding, Jianping; Wang, Renxiao; Liu, Wen; Cao, Chunyang

    2015-01-01

    Nosiheptide is a parent compound of thiopeptide family that exhibit potent activities against various bacterial pathogens. Its C-terminal amide formation is catalyzed by NosA, which is an unusual strategy for maturating certain thiopeptides by processing their precursor peptides featuring a serine extension. We here report the crystal structure of truncated NosA1-111 variant, revealing three key elements, including basic lysine 49 (K49), acidic glutamic acid 101 (E101) and flexible C-terminal loop NosA112-151, are crucial to the catalytic terminal amide formation in nosiheptide biosynthesis. The side-chain of residue K49 and the C-terminal loop fasten the substrate through hydrogen bonds and hydrophobic interactions. The side-chain of residue E101 enhances nucleophilic attack of H2O to the methyl imine intermediate, leading to Cα-N bond cleavage and nosiheptide maturation. The sequence alignment of NosA and its homologs NocA, PbtH, TpdK and BerI, and the enzymatic assay suggest that the mechanistic studies on NosA present an intriguing paradigm about how NosA family members function during thiopeptide biosynthesis. PMID:26244829

  6. Palladium(0)/NHC-Catalyzed Reductive Heck Reaction of Enones: A Detailed Mechanistic Study.

    PubMed

    Raoufmoghaddam, Saeed; Mannathan, Subramaniyan; Minnaard, Adriaan J; de Vries, Johannes G; Reek, Joost N H

    2015-12-14

    We have studied the mechanism of the palladium-catalyzed reductive Heck reaction of para-substituted enones with 4-iodoanisole by using N,N-diisopropylethylamine (DIPEA) as the reductant. Kinetic studies and in situ spectroscopic analysis have provided a detailed insight into the reaction. Progress kinetic analysis demonstrated that neither catalyst decomposition nor product inhibition occurred during the catalysis. The reaction is first order in the palladium and aryl iodide, and zero order in the activated alkene, N-heterocyclic carbene (NHC) ligand, and DIPEA. The experiments with deuterated solvent ([D7]DMF) and deuterated base ([D15]Et3N) supported the role of the amine as a reductant in the reaction. The palladium complex [Pd(0)(NHC)(1)] has been identified as the resting state. The kinetic experiments by stopped-flow UV/Vis also revealed that the presence of the second substrate, benzylideneacetone 1, slows down the oxidative addition of 4-iodoanisole through its competing coordination to the palladium center. The kinetic and mechanistic studies indicated that the oxidative addition of the aryl iodide is the rate-determining step. Various scenarios for the oxidative addition step have been analyzed by using DFT calculations (bp86/def2-TZVP) that supported the inhibiting effect of substrate 1 by formation of resting state [Pd(0)(NHC)(1)] species at the cost of further increase in the energy barrier of the oxidative addition step. PMID:26561034

  7. Dual Lewis Acid/Lewis Base Catalyzed Acylcyanation of Aldehydes: A Mechanistic Study.

    PubMed

    Laurell Nash, Anna; Hertzberg, Robin; Wen, Ye-Qian; Dahlgren, Björn; Brinck, Tore; Moberg, Christina

    2016-03-01

    A mechanistic investigation, which included a Hammett correlation analysis, evaluation of the effect of variation of catalyst composition, and low-temperature NMR spectroscopy studies, of the Lewis acid-Lewis base catalyzed addition of acetyl cyanide to prochiral aldehydes provides support for a reaction route that involves Lewis base activation of the acyl cyanide with formation of a potent acylating agent and cyanide ion. The cyanide ion adds to the carbonyl group of the Lewis acid activated aldehyde. O-Acylation by the acylated Lewis base to form the final cyanohydrin ester occurs prior to decomplexation from titanium. For less reactive aldehydes, the addition of cyanide is the rate-determining step, whereas, for more reactive, electron-deficient aldehydes, cyanide addition is rapid and reversible and is followed by rate-limiting acylation. The resting state of the catalyst lies outside the catalytic cycle and is believed to be a monomeric titanium complex with two alcoholate ligands, which only slowly converts into the product. PMID:26592522

  8. Dynamic, mechanistic, molecular-level modelling of cyanobacteria: Anabaena and nitrogen interaction.

    PubMed

    Hellweger, Ferdi L; Fredrick, Neil D; McCarthy, Mark J; Gardner, Wayne S; Wilhelm, Steven W; Paerl, Hans W

    2016-09-01

    Phytoplankton (eutrophication, biogeochemical) models are important tools for ecosystem research and management, but they generally have not been updated to include modern biology. Here, we present a dynamic, mechanistic, molecular-level (i.e. gene, transcript, protein, metabolite) model of Anabaena - nitrogen interaction. The model was developed using the pattern-oriented approach to model definition and parameterization of complex agent-based models. It simulates individual filaments, each with individual cells, each with genes that are expressed to yield transcripts and proteins. Cells metabolize various forms of N, grow and divide, and differentiate heterocysts when fixed N is depleted. The model is informed by observations from 269 laboratory experiments from 55 papers published from 1942 to 2014. Within this database, we identified 331 emerging patterns, and, excluding inconsistencies in observations, the model reproduces 94% of them. To explore a practical application, we used the model to simulate nutrient reduction scenarios for a hypothetical lake. For a 50% N only loading reduction, the model predicts that N fixation increases, but this fixed N does not compensate for the loading reduction, and the chlorophyll a concentration decreases substantially (by 33%). When N is reduced along with P, the model predicts an additional 8% reduction (compared to P only). PMID:27059435

  9. Performances and mechanistic investigations of a triphosphine trioxide/ionic liquid system for rare earth extraction.

    PubMed

    Turgis, R; Arrachart, G; Dubois, V; Dourdain, S; Virieux, D; Michel, S; Legeai, S; Lejeune, M; Draye, M; Pellet-Rostaing, S

    2016-01-21

    The extraction of rare earth elements (REEs) from nitric acid solution with a triphosphine trioxide (TPO) is presented. Performances of such a ligand in ionic liquids vs. a classical solvent (benzyl ether) are compared. TPO seems to be 10 to 100 times more efficient when it is dissolved in ionic media whatever the concentration of nitric acid involved. Mechanistic investigations reveal that cation exchange classically observed in ionic liquids is not consistent with the experimental data. Moreover, clear differences in the TPO/Ln complexes between classical and ionic media are highlighted. A stable complex of 1 lanthanide for 3 TPO is formed in an ionic liquid whereas a complex of 1 lanthanide for 6 to 9 TPO is formed in benzyl ether. Back extraction is also studied and good recovery of REEs could be obtained. The TPO/ionic liquid system shows remarkable performances i.e. efficiency and selectivity towards lanthanides in a simulated leaching solution of a Nd/Fe/B/Dy magnet. PMID:26673884

  10. A mechanistic model for the prediction of in-use moisture uptake by packaged dosage forms.

    PubMed

    Remmelgas, Johan; Simonutti, Anne-Laure; Ronkvist, Asa; Gradinarsky, Lubomir; Löfgren, Anders

    2013-01-30

    A mechanistic model for the prediction of in-use moisture uptake of solid dosage forms in bottles is developed. The model considers moisture transport into the bottle and moisture uptake by the dosage form both when the bottle is closed and when it is open. Experiments are carried out by placing tablets and desiccant canisters in bottles and monitoring their moisture content. Each bottle is opened once a day to remove one tablet or desiccant canister. Opening the bottle to remove a tablet or canister also causes some exchange of air between the bottle headspace and the environment. In order to ascertain how this air exchange might depend on the customer, tablets and desiccant canisters are removed from the bottles by either carefully removing only one or by pouring all of the tablets or desiccant canisters out of the bottle, removing one, and pouring the remaining ones back into the bottle. The predictions of the model are found to be in good agreement with experimental data for moisture sorption by desiccant canisters. Moreover, it is found experimentally that the manner in which the tablets or desiccant canisters were removed does not appreciably affect their moisture content. PMID:23194882

  11. Genotoxicity of combined exposure to polycyclic aromatic hydrocarbons and UVA--a mechanistic study.

    PubMed

    Douki, Thierry; Ksoury, Zakaria; Marie, Caroline; Favier, Alain; Ravanat, Jean-Luc; Maitre, Anne

    2008-01-01

    Solar UV radiation and benzo[a]pyrene (BaP) are two carcinogenic agents. When combined, their deleterious properties are synergistic. In order to get insights into the underlying processes, we carried out a mechanistic study within isolated DNA photosensitized to UVA radiation by either BaP, its diol epoxide metabolite (BPDE) or the tetraol arising from the hydrolysis of this last molecule. Measurement of the level of the oxidized base 8-oxo-7,8-dihydroguanine revealed that BaP is a poor sensitizer while BPDE and tetraol are more potent ones. None of these compounds was found to photosensitize formation of cyclobutane pyrimidine dimers through triplet energy transfer. On the basis of the distribution of oxidized DNA bases, we could show that photosensitization of DNA by BPDE involves electron abstraction (Type I) while tetraol acts mainly through singlet oxygen production (Type II). Under our experimental conditions, Type I was the major photosensitization process, which shows the lack of involvement of tetraol in the observed photo-oxidation reaction. Finally, we could show that the adducts, resulting from the alkylation of DNA by BPDE, are very potent sensitizers. Indeed, they are located in the close vicinity of the double helix and thus perfectly placed to induce oxidation reactions. PMID:18466204

  12. Mechanistic Insights into the Rate-Limiting Step in Purine-Specific Nucleoside Hydrolase.

    PubMed

    Chen, Nanhao; Zhao, Yuan; Lu, Jianing; Wu, Ruibo; Cao, Zexing

    2015-07-14

    A full enzymatic catalysis cycle in the inosine-adenosine-guanosine specific nucleoside hydrolase (IAG-NH) was assumed to be comprised of four steps: substrate binding, chemical reaction, base release, and ribose release. Nevertheless, the mechanistic details for the rate-limiting step of the entire enzymatic reaction are still unknown, even though the ribose release was likely to be the most difficult stage. Based on state-of-the-art quantum mechanics and molecular mechanics (QM/MM) molecular dynamics (MD) simulations, the ribose release process can be divided into two steps: "ribose dissociation" and "ribose release". The "ribose dissociation" includes "cleavage" and "exchange" stages, in which a metastable 6-fold intermediate will recover to an 8-fold coordination shell of Ca(2+) as observed in apo- IAG-NH. Extensive random acceleration molecular dynamics and MD simulations have been employed to verify plausible release channels, and the estimated barrier for the rate-determining step of the entire reaction is 13.0 kcal/mol, which is comparable to the experimental value of 16.7 kcal/mol. Moreover, the gating mechanism arising from loop1 and loop2, as well as key residues around the active pocket, has been found to play an important role in manipulating the ribose release. PMID:26575755

  13. The effect of zinc on amyloid β-protein assembly and toxicity: A mechanistic investigation

    NASA Astrophysics Data System (ADS)

    Solomonov, Inna; Sagi, Irit

    2014-10-01

    Neurotoxic assemblies of amyloid β-protein (Aβ) are widely believed to be the cause for Alzheimer's disease (AD). Therefore, understanding the factors and mechanisms that control, modulate, and inhibit formation of these assemblies is crucial for the development of therapeutic intervention of AD. This information also can contribute significantly to our understanding of the mechanisms of other amyloidosis diseases, such as Parkinson's disease, Huntington's disease, type 2 diabetes, amyotrophic lateral sclerosis (Lou Gehrig's disease) and prion diseases (e.g. Mad Cow disease). We have developed a multidisciplinary experimental strategy to study structural and dynamic mechanistic aspects that underlie the Aβ assembly process. Utilizing this strategy, we explored the molecular basis leading to the perturbation of the Aβ assembly process by divalent metal ions, mainly Zn2+ ions. Using Zn2+ as reaction physiological relevant probes, it was demonstrated that Zn2+ rapidly (milliseconds) induce self-assembly of Aβ aggregates and stabilize them in a manner that prevents formation of Aβ fibrils. Importantly, the early-formed intermediates are substantially more neurotoxic than fibrils. Our results suggest that relevant Aβ modulators should be targeted against the rapidly evolved intermediate states of Aβ assembly. The design of such modulators is challenging, as they have to compete with different natural mediators (such as Zn2+) of Aβ aggregation, which diverse Aβ assemblies in both specific and nonspecific manners.

  14. Angiotensin receptor neprilysin inhibition in heart failure: mechanistic action and clinical impact.

    PubMed

    Buggey, Jonathan; Mentz, Robert J; DeVore, Adam D; Velazquez, Eric J

    2015-09-01

    Heart failure (HF) is an increasingly common syndrome associated with high mortality and economic burden, and there has been a paucity over the past decade of new pharmacotherapies that improve outcomes. However, recent data from a large randomized controlled trial compared the novel agent LCZ696, a dual-acting angiotensin receptor blocker and neprilysin inhibitor (ARNi), with the well established angiotensin-converting enzyme (ACE) inhibitor enalapril and found significant reduction in mortality among the chronic reduced ejection fraction HF population. Preclinical and clinical data suggest that neprilysin inhibition provides beneficial outcomes in HF patients by preventing the degradation of natriuretic peptides and thereby promoting natriuresis and vasodilatation and counteracting the negative cardiorenal effects of the up-regulated renin-angiotensin-aldosterone system. Agents such as omapatrilat combined neprilysin and ACE inhibition but had increased rates of angioedema. Goals of an improved safety profile provided the rationale for the development of the ARNi LCZ696. Along with significant reductions in mortality and hospitalizations, clinical trials suggest that LCZ696 may improve surrogate markers of HF severity. In this paper, we review the preclinical and clinical data that led to the development of LCZ696, the understanding of the underlying mechanistic action, and the robust clinical impact that LCZ696 may have in the near future. PMID:26209000

  15. Chemopreventive and therapeutic potentials of thymoquinone in HepG2 cells: mechanistic perspectives.

    PubMed

    ElKhoely, Abeer; Hafez, Hafez F; Ashmawy, Abeer M; Badary, Osama; Abdelaziz, Ahmed; Mostafa, Adel; Shouman, Samia A

    2015-07-01

    Liver cancer is the fifth commonest malignancy worldwide and the third leading cause of death. Identifying novel curative and preventive therapy may improve its prognosis. In this study, thymoquinone (TQ), the most active biological ingredient of Nigella sativa Linn, was investigated for its antitumor activity. Mechanistic perspectives underlying this antitumor activity were explored by testing its effect on cell cycle, apoptosis, and angiogenesis. In addition, the chemopreventive effect of TQ was carried out by measuring its effect on phase I CYP1A1 and phase II glutathione S-transferase (GST) drug-metabolizing enzymes. The results of the present study revealed the effectiveness of TQ as an antitumor agent against different types of cancer including brain, colon, cervix and liver at both a time- and concentration-dependent manner. In HepG2 cells, it induced G2/M phase cell cycle arrest and a concentration-dependent increase in the percentage of apoptotic cells with an increase in the ratio of Bax/BCL-2. Moreover, the expression of mRNA and protein level of vascular endothelial growth factor decreased as the concentration of TQ increased. Our data showed a significant inhibition of induced phase I CYP1A1 enzyme, and elevation in the content of glutathione and activity of phase II enzyme GST, in HepG2 cells. Our results provide support for the beneficial use of TQ as a therapeutic and chemopreventive agent against liver cancer. PMID:25796541

  16. Children's developing understanding of the relation between variable causal efficacy and mechanistic complexity.

    PubMed

    Erb, Christopher D; Buchanan, David W; Sobel, David M

    2013-12-01

    Two experiments investigated 3-4-year-olds' ability to infer the causal mechanisms for a pair of lights. In both experiments the exterior of the two lights appeared identical. In Experiment 1, one light displayed a stable activation pattern of a single color while the other light displayed a variable pattern of activation by cycling through a series of different colors (i.e., a more varied effect). Children were asked to judge which light had a more complex internal structure. Four-year-olds were more likely to match the light with the more variable effect with a more complex internal mechanism and the light with the more stable effect with a less complex mechanism. Three-year-olds' responses were at chance. Experiment 2 replicated this finding when the activation patterns of the two lights were described verbally but never demonstrated. Taken together, these results suggest that 4-year-olds appreciate that the variability of an object's causal efficacy is related to the complexity of its internal mechanistic structure. PMID:24041835

  17. Structures of multidrug and toxic compound extrusion transporters and their mechanistic implications.

    PubMed

    Lu, Min

    2016-03-01

    Multidrug resistance poses grand challenges to the effective treatment of infectious diseases and cancers. Integral membrane proteins from the multidrug and toxic compound extrusion (MATE) family contribute to multidrug resistance by exporting a wide variety of therapeutic drugs across cell membranes. MATE proteins are conserved from bacteria to humans and can be categorized into the NorM, DinF and eukaryotic subfamilies. MATE transporters hold great appeal as potential therapeutic targets for curbing multidrug resistance, yet their transport mechanism remains elusive. During the past 5 years, X-ray structures of 4 NorM and DinF transporters have been reported and guided biochemical studies to reveal how MATE transporters extrude different drugs. Such advances, although substantial, have yet to be discussed collectively. Herein I review these structures and the unprecedented mechanistic insights that have been garnered from those structure-inspired studies, as well as lay out the outstanding questions that present exciting opportunities for future work. PMID:26488689

  18. Free radical scavenging reactions of sulfasalazine, 5-aminosalicylic acid and sulfapyridine: mechanistic aspects and antioxidant activity.

    PubMed

    Joshi, Ravi; Kumar, Sudheer; Unnikrishnan, M; Mukherjee, T

    2005-11-01

    Reactions of sulfasalazine (SAZ) and its metabolites, 5-aminosalicylic acid (5-ASA) and sulfapyridine (SP), with various oxidizing and reducing free radicals (hydroxyl, haloperoxyl, one-electron oxidizing, lipid peroxyl, glutathiyl, superoxide, tryptophanyl, etc.) have been studied to understand the mechanistic aspects of its action against free radicals produced during inflammation. Nanosecond pulse radiolysis technique coupled with transient spectrophotometry has been used for in situ generation of free radicals and to follow their reaction pathways. The transients produced in these reactions have been assigned and radical scavenging rate constants have been measured. In addition to scavenging of various primary and secondary free radicals by SAZ, 5-ASA and SP, 5-ASA has also been observed to efficiently scavenge radicals of biomolecules. 5-ASA has been found to be the active moiety of SAZ involved in the scavenging of oxidizing free radicals whereas reduction of SAZ produced molecular radical anion. The study suggests that free radical scavenging activity of 5-ASA may be a major path of pharmacological action of SAZ against inflammatory bowel diseases (IBD). PMID:16298742

  19. Mechanistic insights into the first Lygus-active β-pore forming protein.

    PubMed

    Jerga, Agoston; Chen, Danqi; Zhang, Chunfen; Fu, Jinping; Kouadio, Jean-Louis K; Wang, Yanfei; Duff, Stephen M G; Howard, Jennifer E; Rydel, Timothy J; Evdokimov, Artem G; Ramaseshadri, Parthasarathy; Evans, Adam; Bolognesi, Renata; Park, Yoonseong; Haas, Jeffrey A

    2016-06-15

    The cotton pests Lygus hesperus and Lygus lineolaris can be controlled by expressing Cry51Aa2.834_16 in cotton. Insecticidal activity of pore-forming proteins is generally associated with damage to the midgut epithelium due to pores, and their biological specificity results from a set of key determinants including proteolytic activation and receptor binding. We conducted mechanistic studies to gain insight into how the first Lygus-active β-pore forming protein variant functions. Biophysical characterization revealed that the full-length Cry51Aa2.834_16 was a stable dimer in solution, and when exposed to Lygus saliva or to trypsin, the protein underwent proteolytic cleavage at the C-terminus of each of the subunits, resulting in dissociation of the dimer to two separate monomers. The monomer showed tight binding to a specific protein in Lygus brush border membranes, and also formed a membrane-associated oligomeric complex both in vitro and in vivo. Chemically cross-linking the β-hairpin to the Cry51Aa2.834_16 body rendered the protein inactive, but still competent to compete for binding sites with the native protein in vivo. Our study suggests that disassociation of the Cry51Aa2.834_16 dimer into monomeric units with unoccupied head-region and sterically unhindered β-hairpin is required for brush border membrane binding, oligomerization, and the subsequent steps leading to insect mortality. PMID:27001423

  20. Myricetin arrests human telomeric G-quadruplex structure: a new mechanistic approach as an anticancer agent.

    PubMed

    Mondal, Soma; Jana, Jagannath; Sengupta, Pallabi; Jana, Samarjit; Chatterjee, Subhrangsu

    2016-07-19

    The use of small molecules to arrest G-quadruplex structure has become a potential strategy for the development and design of a new class of anticancer therapeutics. We have studied the interaction of myricetin, a plant flavonoid and a putative anticancer agent, with human telomeric G-quadruplex TTAGGG(TTAGGG)3 DNA. Reverse transcription PCR data revealed significant repression in hTERT expression in MCF-7 breast cancer cells upon increasing the concentration of myricetin. Further, we conducted a telomeric repeat amplification protocol assay to confirm the inhibition of telomerase by myricetin. Optical spectroscopic techniques like circular dichroism, UV spectroscopy and fluorescence spectroscopy revealed the formation of a stable myricetin-G-quadruplex complex. The thermodynamic parameters of myricetin-G-quadruplex complex formation, presented through isothermal titration calorimetry studies, indicate the binding process to be thermodynamically favorable. In addition, high resolution NMR spectroscopy in conjunction with molecular dynamics simulation is employed to provide detailed mechanistic insights into the binding in the myricetin-G-quadruplex complex at the atomic level. Our results thus propose a new mode of action of myricetin as an anticancer agent via arresting telomeric G-quadruplex structure. PMID:27249025