Science.gov

Sample records for accurate transport models

  1. Accurate Characterization of Ion Transport Properties in Binary Symmetric Electrolytes Using In Situ NMR Imaging and Inverse Modeling.

    PubMed

    Sethurajan, Athinthra Krishnaswamy; Krachkovskiy, Sergey A; Halalay, Ion C; Goward, Gillian R; Protas, Bartosz

    2015-09-17

    We used NMR imaging (MRI) combined with data analysis based on inverse modeling of the mass transport problem to determine ionic diffusion coefficients and transference numbers in electrolyte solutions of interest for Li-ion batteries. Sensitivity analyses have shown that accurate estimates of these parameters (as a function of concentration) are critical to the reliability of the predictions provided by models of porous electrodes. The inverse modeling (IM) solution was generated with an extension of the Planck-Nernst model for the transport of ionic species in electrolyte solutions. Concentration-dependent diffusion coefficients and transference numbers were derived using concentration profiles obtained from in situ (19)F MRI measurements. Material properties were reconstructed under minimal assumptions using methods of variational optimization to minimize the least-squares deviation between experimental and simulated concentration values with uncertainty of the reconstructions quantified using a Monte Carlo analysis. The diffusion coefficients obtained by pulsed field gradient NMR (PFG-NMR) fall within the 95% confidence bounds for the diffusion coefficient values obtained by the MRI+IM method. The MRI+IM method also yields the concentration dependence of the Li(+) transference number in agreement with trends obtained by electrochemical methods for similar systems and with predictions of theoretical models for concentrated electrolyte solutions, in marked contrast to the salt concentration dependence of transport numbers determined from PFG-NMR data.

  2. Pre-Modeling Ensures Accurate Solid Models

    ERIC Educational Resources Information Center

    Gow, George

    2010-01-01

    Successful solid modeling requires a well-organized design tree. The design tree is a list of all the object's features and the sequential order in which they are modeled. The solid-modeling process is faster and less prone to modeling errors when the design tree is a simple and geometrically logical definition of the modeled object. Few high…

  3. New model accurately predicts reformate composition

    SciTech Connect

    Ancheyta-Juarez, J.; Aguilar-Rodriguez, E. )

    1994-01-31

    Although naphtha reforming is a well-known process, the evolution of catalyst formulation, as well as new trends in gasoline specifications, have led to rapid evolution of the process, including: reactor design, regeneration mode, and operating conditions. Mathematical modeling of the reforming process is an increasingly important tool. It is fundamental to the proper design of new reactors and revamp of existing ones. Modeling can be used to optimize operating conditions, analyze the effects of process variables, and enhance unit performance. Instituto Mexicano del Petroleo has developed a model of the catalytic reforming process that accurately predicts reformate composition at the higher-severity conditions at which new reformers are being designed. The new AA model is more accurate than previous proposals because it takes into account the effects of temperature and pressure on the rate constants of each chemical reaction.

  4. Accurate Prediction of Ligand Affinities for a Proton-Dependent Oligopeptide Transporter

    PubMed Central

    Samsudin, Firdaus; Parker, Joanne L.; Sansom, Mark S.P.; Newstead, Simon; Fowler, Philip W.

    2016-01-01

    Summary Membrane transporters are critical modulators of drug pharmacokinetics, efficacy, and safety. One example is the proton-dependent oligopeptide transporter PepT1, also known as SLC15A1, which is responsible for the uptake of the β-lactam antibiotics and various peptide-based prodrugs. In this study, we modeled the binding of various peptides to a bacterial homolog, PepTSt, and evaluated a range of computational methods for predicting the free energy of binding. Our results show that a hybrid approach (endpoint methods to classify peptides into good and poor binders and a theoretically exact method for refinement) is able to accurately predict affinities, which we validated using proteoliposome transport assays. Applying the method to a homology model of PepT1 suggests that the approach requires a high-quality structure to be accurate. Our study provides a blueprint for extending these computational methodologies to other pharmaceutically important transporter families. PMID:27028887

  5. An Accurate, Simplified Model Intrabeam Scattering

    SciTech Connect

    Bane, Karl LF

    2002-05-23

    Beginning with the general Bjorken-Mtingwa solution for intrabeam scattering (IBS) we derive an accurate, greatly simplified model of IBS, valid for high energy beams in normal storage ring lattices. In addition, we show that, under the same conditions, a modified version of Piwinski's IBS formulation (where {eta}{sub x,y}{sup 2}/{beta}{sub x,y} has been replaced by {Eta}{sub x,y}) asymptotically approaches the result of Bjorken-Mtingwa.

  6. Accurate measurement of liquid transport through nanoscale conduits

    PubMed Central

    Alibakhshi, Mohammad Amin; Xie, Quan; Li, Yinxiao; Duan, Chuanhua

    2016-01-01

    Nanoscale liquid transport governs the behaviour of a wide range of nanofluidic systems, yet remains poorly characterized and understood due to the enormous hydraulic resistance associated with the nanoconfinement and the resulting minuscule flow rates in such systems. To overcome this problem, here we present a new measurement technique based on capillary flow and a novel hybrid nanochannel design and use it to measure water transport through single 2-D hydrophilic silica nanochannels with heights down to 7 nm. Our results show that silica nanochannels exhibit increased mass flow resistance compared to the classical hydrodynamics prediction. This difference increases with decreasing channel height and reaches 45% in the case of 7 nm nanochannels. This resistance increase is attributed to the formation of a 7-angstrom-thick stagnant hydration layer on the hydrophilic surfaces. By avoiding use of any pressure and flow sensors or any theoretical estimations the hybrid nanochannel scheme enables facile and precise flow measurement through single nanochannels, nanotubes, or nanoporous media and opens the prospect for accurate characterization of both hydrophilic and hydrophobic nanofluidic systems. PMID:27112404

  7. Fast Monte Carlo Electron-Photon Transport Method and Application in Accurate Radiotherapy

    NASA Astrophysics Data System (ADS)

    Hao, Lijuan; Sun, Guangyao; Zheng, Huaqing; Song, Jing; Chen, Zhenping; Li, Gui

    2014-06-01

    Monte Carlo (MC) method is the most accurate computational method for dose calculation, but its wide application on clinical accurate radiotherapy is hindered due to its poor speed of converging and long computation time. In the MC dose calculation research, the main task is to speed up computation while high precision is maintained. The purpose of this paper is to enhance the calculation speed of MC method for electron-photon transport with high precision and ultimately to reduce the accurate radiotherapy dose calculation time based on normal computer to the level of several hours, which meets the requirement of clinical dose verification. Based on the existing Super Monte Carlo Simulation Program (SuperMC), developed by FDS Team, a fast MC method for electron-photon coupled transport was presented with focus on two aspects: firstly, through simplifying and optimizing the physical model of the electron-photon transport, the calculation speed was increased with slightly reduction of calculation accuracy; secondly, using a variety of MC calculation acceleration methods, for example, taking use of obtained information in previous calculations to avoid repeat simulation of particles with identical history; applying proper variance reduction techniques to accelerate MC method convergence rate, etc. The fast MC method was tested by a lot of simple physical models and clinical cases included nasopharyngeal carcinoma, peripheral lung tumor, cervical carcinoma, etc. The result shows that the fast MC method for electron-photon transport was fast enough to meet the requirement of clinical accurate radiotherapy dose verification. Later, the method will be applied to the Accurate/Advanced Radiation Therapy System ARTS as a MC dose verification module.

  8. Mitigating the Erratic Behavior of the Transportation Working Capital Fund Through Accurate Forecasting

    DTIC Science & Technology

    2015-06-19

    MITIGATING THE ERRATIC BEHAVIOR OF THE TRANSPORTATION WORKING CAPITAL FUND THROUGH ACCURATE FORECASTING...MITIGATING THE ERRATIC BEHAVIOR OF THE TRANSPORTATION WORKING ...DISTRIBUTION UNLIMITED. AFIT-ENS-GRP-15-J-028 MITIGATING THE ERRATIC BEHAVIOR OF THE TRANSPORTATION WORKING CAPITAL FUND THROUGH ACCURATE

  9. Faster and more accurate transport procedures for HZETRN

    SciTech Connect

    Slaba, T.C.; Blattnig, S.R.; Badavi, F.F.

    2010-12-10

    The deterministic transport code HZETRN was developed for research scientists and design engineers studying the effects of space radiation on astronauts and instrumentation protected by various shielding materials and structures. In this work, several aspects of code verification are examined. First, a detailed derivation of the light particle (A {<=} 4) and heavy ion (A > 4) numerical marching algorithms used in HZETRN is given. References are given for components of the derivation that already exist in the literature, and discussions are given for details that may have been absent in the past. The present paper provides a complete description of the numerical methods currently used in the code and is identified as a key component of the verification process. Next, a new numerical method for light particle transport is presented, and improvements to the heavy ion transport algorithm are discussed. A summary of round-off error is also given, and the impact of this error on previously predicted exposure quantities is shown. Finally, a coupled convergence study is conducted by refining the discretization parameters (step-size and energy grid-size). From this study, it is shown that past efforts in quantifying the numerical error in HZETRN were hindered by single precision calculations and computational resources. It is determined that almost all of the discretization error in HZETRN is caused by the use of discretization parameters that violate a numerical convergence criterion related to charged target fragments below 50 AMeV. Total discretization errors are given for the old and new algorithms to 100 g/cm{sup 2} in aluminum and water, and the improved accuracy of the new numerical methods is demonstrated. Run time comparisons between the old and new algorithms are given for one, two, and three layer slabs of 100 g/cm{sup 2} of aluminum, polyethylene, and water. The new algorithms are found to be almost 100 times faster for solar particle event simulations and

  10. Faster and More Accurate Transport Procedures for HZETRN

    NASA Technical Reports Server (NTRS)

    Slaba, Tony C.; Blattnig, Steve R.; Badavi, Francis F.

    2010-01-01

    Several aspects of code verification are examined for HZETRN. First, a detailed derivation of the numerical marching algorithms is given. Next, a new numerical method for light particle transport is presented, and improvements to the heavy ion transport algorithm are discussed. A summary of various coding errors is also given, and the impact of these errors on exposure quantities is shown. Finally, a coupled convergence study is conducted. From this study, it is shown that past efforts in quantifying the numerical error in HZETRN were hindered by single precision calculations and computational resources. It is also determined that almost all of the discretization error in HZETRN is caused by charged target fragments below 50 AMeV. Total discretization errors are given for the old and new algorithms, and the improved accuracy of the new numerical methods is demonstrated. Run time comparisons are given for three applications in which HZETRN is commonly used. The new algorithms are found to be almost 100 times faster for solar particle event simulations and almost 10 times faster for galactic cosmic ray simulations.

  11. Turbulence Models for Accurate Aerothermal Prediction in Hypersonic Flows

    NASA Astrophysics Data System (ADS)

    Zhang, Xiang-Hong; Wu, Yi-Zao; Wang, Jiang-Feng

    Accurate description of the aerodynamic and aerothermal environment is crucial to the integrated design and optimization for high performance hypersonic vehicles. In the simulation of aerothermal environment, the effect of viscosity is crucial. The turbulence modeling remains a major source of uncertainty in the computational prediction of aerodynamic forces and heating. In this paper, three turbulent models were studied: the one-equation eddy viscosity transport model of Spalart-Allmaras, the Wilcox k-ω model and the Menter SST model. For the k-ω model and SST model, the compressibility correction, press dilatation and low Reynolds number correction were considered. The influence of these corrections for flow properties were discussed by comparing with the results without corrections. In this paper the emphasis is on the assessment and evaluation of the turbulence models in prediction of heat transfer as applied to a range of hypersonic flows with comparison to experimental data. This will enable establishing factor of safety for the design of thermal protection systems of hypersonic vehicle.

  12. A quick accurate model of nozzle backflow

    NASA Technical Reports Server (NTRS)

    Kuharski, R. A.

    1991-01-01

    Backflow from nozzles is a major source of contamination on spacecraft. If the craft contains any exposed high voltages, the neutral density produced by the nozzles in the vicinity of the craft needs to be known in order to assess the possibility of Paschen breakdown or the probability of sheath ionization around a region of the craft that collects electrons for the plasma. A model for backflow has been developed for incorporation into the Environment-Power System Analysis Tool (EPSAT) which quickly estimates both the magnitude of the backflow and the species makeup of the flow. By combining the backflow model with the Simons (1972) model for continuum flow it is possible to quickly estimate the density of each species from a nozzle at any position in space. The model requires only a few physical parameters of the nozzle and the gas as inputs and is therefore ideal for engineering applications.

  13. UZ Colloid Transport Model

    SciTech Connect

    M. McGraw

    2000-04-13

    The UZ Colloid Transport model development plan states that the objective of this Analysis/Model Report (AMR) is to document the development of a model for simulating unsaturated colloid transport. This objective includes the following: (1) use of a process level model to evaluate the potential mechanisms for colloid transport at Yucca Mountain; (2) Provide ranges of parameters for significant colloid transport processes to Performance Assessment (PA) for the unsaturated zone (UZ); (3) Provide a basis for development of an abstracted model for use in PA calculations.

  14. Accurate spectral modeling for infrared radiation

    NASA Technical Reports Server (NTRS)

    Tiwari, S. N.; Gupta, S. K.

    1977-01-01

    Direct line-by-line integration and quasi-random band model techniques are employed to calculate the spectral transmittance and total band absorptance of 4.7 micron CO, 4.3 micron CO2, 15 micron CO2, and 5.35 micron NO bands. Results are obtained for different pressures, temperatures, and path lengths. These are compared with available theoretical and experimental investigations. For each gas, extensive tabulations of results are presented for comparative purposes. In almost all cases, line-by-line results are found to be in excellent agreement with the experimental values. The range of validity of other models and correlations are discussed.

  15. In-Band Asymmetry Compensation for Accurate Time/Phase Transport over Optical Transport Network

    PubMed Central

    Siu, Sammy; Hu, Hsiu-fang; Lin, Shinn-Yan; Liao, Chia-Shu; Lai, Yi-Liang

    2014-01-01

    The demands of precise time/phase synchronization have been increasing recently due to the next generation of telecommunication synchronization. This paper studies the issues that are relevant to distributing accurate time/phase over optical transport network (OTN). Each node and link can introduce asymmetry, which affects the adequate time/phase accuracy over the networks. In order to achieve better accuracy, protocol level full timing support is used (e.g., Telecom-Boundary clock). Due to chromatic dispersion, the use of different wavelengths consequently causes fiber link delay asymmetry. The analytical result indicates that it introduces significant time error (i.e., phase offset) within 0.3397 ns/km in C-band or 0.3943 ns/km in L-band depending on the wavelength spacing. With the proposed scheme in this paper, the fiber link delay asymmetry can be compensated relying on the estimated mean fiber link delay by the Telecom-Boundary clock, while the OTN control plane is responsible for processing the fiber link delay asymmetry to determine the asymmetry compensation in the timing chain. PMID:24982948

  16. Railway switch transport model.

    PubMed

    Horvat, Martin; Prosen, Tomaž; Benenti, Giuliano; Casati, Giulio

    2012-11-01

    We propose a simple model of coupled heat and particle transport based on zero-dimensional classical deterministic dynamics, which is reminiscent of a railway switch whose action is a function only of the particle's energy. It is shown that already in the minimal three-terminal model, where the second terminal is considered as a probe with zero net particle and heat currents, one can find extremely asymmetric Onsager matrices as a consequence of time-reversal symmetry breaking of the model. This minimalistic transport model provides a better understanding of thermoelectric heat engines in the presence of time-reversal symmetry breaking.

  17. Lagrangian Sediment Transport Model

    NASA Astrophysics Data System (ADS)

    Maderych, V.; Brovchenko, I.; Fenical, S.; Shepsis, V.

    2004-12-01

    A new two-dimensional Lagrangian sediment transport model was developed to simulate a wide-range of sediment transport processes, including sediment mobility under combined current and wave action, sediment transport and bed change under wave and currents effects, sediment transport patterns at nearshore coastal and offshore structures, and turbidity and sediment motion during dredging and dredged material placement. The Lagrangian technique was used to simulate transport of sediments, deposition, and re-suspension. The model can be applied to cohesive, non-cohesive, or mixed sediments. The sediment transport is simulated using bathymetry data, bed resistance characteristics, wave height and period, depth-averaged current velocity and bed material type, size and gradation, which vary throughout the model domain.The non-cohesive sediment transport model is based on a solution of two-dimensional mass conservation equations for the bed layer material and 2D equations for movement of sediment fractions either bed load or suspended load. The water column and bottom are divided into a set of layers: water layer, active layer, several active bed layers, and the bed layer. The model also takes into account the effects of armoring and changes in the bed composition. Cohesive sediments move entirely as suspended load in the water layer and sediment transport computations are based on a solution of the two-dimensional mass conservation equations for the bed layer material and two-dimensional equations for movement of sediment as suspended load. The water column and bed, as for non-cohesive sediments, was divided into a set of layers. Following the approach of Van Ledden (2002), the erosion of sediments made up of mud and sand mixtures is non-cohesive if the mud content is below a critical level. Above a critical mud content, the bed behaves cohesively. Deposition fluxes of mud and sand are independent. The sediment concentration in the water and active layer is represented by

  18. Modeling axisymmetric flow and transport

    USGS Publications Warehouse

    Langevin, C.D.

    2008-01-01

    Unmodified versions of common computer programs such as MODFLOW, MT3DMS, and SEAWAT that use Cartesian geometry can accurately simulate axially symmetric ground water flow and solute transport. Axisymmetric flow and transport are simulated by adjusting several input parameters to account for the increase in flow area with radial distance from the injection or extraction well. Logarithmic weighting of interblock transmissivity, a standard option in MODFLOW, can be used for axisymmetric models to represent the linear change in hydraulic conductance within a single finite-difference cell. Results from three test problems (ground water extraction, an aquifer push-pull test, and upconing of saline water into an extraction well) show good agreement with analytical solutions or with results from other numerical models designed specifically to simulate the axisymmetric geometry. Axisymmetric models are not commonly used but can offer an efficient alternative to full three-dimensional models, provided the assumption of axial symmetry can be justified. For the upconing problem, the axisymmetric model was more than 1000 times faster than an equivalent three-dimensional model. Computational gains with the axisymmetric models may be useful for quickly determining appropriate levels of grid resolution for three-dimensional models and for estimating aquifer parameters from field tests.

  19. Modeling axisymmetric flow and transport.

    PubMed

    Langevin, Christian D

    2008-01-01

    Unmodified versions of common computer programs such as MODFLOW, MT3DMS, and SEAWAT that use Cartesian geometry can accurately simulate axially symmetric ground water flow and solute transport. Axisymmetric flow and transport are simulated by adjusting several input parameters to account for the increase in flow area with radial distance from the injection or extraction well. Logarithmic weighting of interblock transmissivity, a standard option in MODFLOW, can be used for axisymmetric models to represent the linear change in hydraulic conductance within a single finite-difference cell. Results from three test problems (ground water extraction, an aquifer push-pull test, and upconing of saline water into an extraction well) show good agreement with analytical solutions or with results from other numerical models designed specifically to simulate the axisymmetric geometry. Axisymmetric models are not commonly used but can offer an efficient alternative to full three-dimensional models, provided the assumption of axial symmetry can be justified. For the upconing problem, the axisymmetric model was more than 1000 times faster than an equivalent three-dimensional model. Computational gains with the axisymmetric models may be useful for quickly determining appropriate levels of grid resolution for three-dimensional models and for estimating aquifer parameters from field tests.

  20. Reactive transport modeling

    Technology Transfer Automated Retrieval System (TEKTRAN)

    This special section in the Vadose Zone Journal focusing on reactive transport modeling was developed from a special symposium jointly sponsored by the Soil Physics and Soil Chemistry Divisions of the Soil Science Society of America at the 2010 annual meetings held in Long Beach, CA. It contains eig...

  1. An Accurate and Dynamic Computer Graphics Muscle Model

    NASA Technical Reports Server (NTRS)

    Levine, David Asher

    1997-01-01

    A computer based musculo-skeletal model was developed at the University in the departments of Mechanical and Biomedical Engineering. This model accurately represents human shoulder kinematics. The result of this model is the graphical display of bones moving through an appropriate range of motion based on inputs of EMGs and external forces. The need existed to incorporate a geometric muscle model in the larger musculo-skeletal model. Previous muscle models did not accurately represent muscle geometries, nor did they account for the kinematics of tendons. This thesis covers the creation of a new muscle model for use in the above musculo-skeletal model. This muscle model was based on anatomical data from the Visible Human Project (VHP) cadaver study. Two-dimensional digital images from the VHP were analyzed and reconstructed to recreate the three-dimensional muscle geometries. The recreated geometries were smoothed, reduced, and sliced to form data files defining the surfaces of each muscle. The muscle modeling function opened these files during run-time and recreated the muscle surface. The modeling function applied constant volume limitations to the muscle and constant geometry limitations to the tendons.

  2. Accurate transport properties for H–CO and H–CO{sub 2}

    SciTech Connect

    Dagdigian, Paul J.

    2015-08-07

    Transport properties for collisions of hydrogen atoms with CO and CO{sub 2} have been computed by means of quantum scattering calculations. The carbon oxides are important species in hydrocarbon combustion. The following potential energy surfaces (PES’s) for the interaction of the molecule fixed in its equilibrium geometry were employed: for H–CO, the PES was taken from the work of Song et al. [J. Phys. Chem. A 117, 7571 (2013)], while the PES for H–CO{sub 2} was computed in this study by a restricted coupled cluster method that included single, double, and (perturbatively) triple excitations. The computed transport properties were found to be significantly different from those computed by the conventional approach that employs isotropic Lennard-Jones (12-6) potentials. The effect of using the presently computed accurate transport properties in 1-dimensional combustion simulations of methane-air flames was investigated.

  3. Accurate modelling of unsteady flows in collapsible tubes.

    PubMed

    Marchandise, Emilie; Flaud, Patrice

    2010-01-01

    The context of this paper is the development of a general and efficient numerical haemodynamic tool to help clinicians and researchers in understanding of physiological flow phenomena. We propose an accurate one-dimensional Runge-Kutta discontinuous Galerkin (RK-DG) method coupled with lumped parameter models for the boundary conditions. The suggested model has already been successfully applied to haemodynamics in arteries and is now extended for the flow in collapsible tubes such as veins. The main difference with cardiovascular simulations is that the flow may become supercritical and elastic jumps may appear with the numerical consequence that scheme may not remain monotone if no limiting procedure is introduced. We show that our second-order RK-DG method equipped with an approximate Roe's Riemann solver and a slope-limiting procedure allows us to capture elastic jumps accurately. Moreover, this paper demonstrates that the complex physics associated with such flows is more accurately modelled than with traditional methods such as finite difference methods or finite volumes. We present various benchmark problems that show the flexibility and applicability of the numerical method. Our solutions are compared with analytical solutions when they are available and with solutions obtained using other numerical methods. Finally, to illustrate the clinical interest, we study the emptying process in a calf vein squeezed by contracting skeletal muscle in a normal and pathological subject. We compare our results with experimental simulations and discuss the sensitivity to parameters of our model.

  4. Local Debonding and Fiber Breakage in Composite Materials Modeled Accurately

    NASA Technical Reports Server (NTRS)

    Bednarcyk, Brett A.; Arnold, Steven M.

    2001-01-01

    A prerequisite for full utilization of composite materials in aerospace components is accurate design and life prediction tools that enable the assessment of component performance and reliability. Such tools assist both structural analysts, who design and optimize structures composed of composite materials, and materials scientists who design and optimize the composite materials themselves. NASA Glenn Research Center's Micromechanics Analysis Code with Generalized Method of Cells (MAC/GMC) software package (http://www.grc.nasa.gov/WWW/LPB/mac) addresses this need for composite design and life prediction tools by providing a widely applicable and accurate approach to modeling composite materials. Furthermore, MAC/GMC serves as a platform for incorporating new local models and capabilities that are under development at NASA, thus enabling these new capabilities to progress rapidly to a stage in which they can be employed by the code's end users.

  5. Transport Properties for Combustion Modeling

    SciTech Connect

    Brown, N.J.; Bastein, L.; Price, P.N.

    2010-02-19

    This review examines current approximations and approaches that underlie the evaluation of transport properties for combustion modeling applications. Discussed in the review are: the intermolecular potential and its descriptive molecular parameters; various approaches to evaluating collision integrals; supporting data required for the evaluation of transport properties; commonly used computer programs for predicting transport properties; the quality of experimental measurements and their importance for validating or rejecting approximations to property estimation; the interpretation of corresponding states; combination rules that yield pair molecular potential parameters for unlike species from like species parameters; and mixture approximations. The insensitivity of transport properties to intermolecular forces is noted, especially the non-uniqueness of the supporting potential parameters. Viscosity experiments of pure substances and binary mixtures measured post 1970 are used to evaluate a number of approximations; the intermediate temperature range 1 < T* < 10, where T* is kT/{var_epsilon}, is emphasized since this is where rich data sets are available. When suitable potential parameters are used, errors in transport property predictions for pure substances and binary mixtures are less than 5 %, when they are calculated using the approaches of Kee et al.; Mason, Kestin, and Uribe; Paul and Warnatz; or Ern and Giovangigli. Recommendations stemming from the review include (1) revisiting the supporting data required by the various computational approaches, and updating the data sets with accurate potential parameters, dipole moments, and polarizabilities; (2) characterizing the range of parameter space over which the fit to experimental data is good, rather than the current practice of reporting only the parameter set that best fits the data; (3) looking for improved combining rules, since existing rules were found to under-predict the viscosity in most cases; (4

  6. An Accurate Temperature Correction Model for Thermocouple Hygrometers 1

    PubMed Central

    Savage, Michael J.; Cass, Alfred; de Jager, James M.

    1982-01-01

    Numerous water relation studies have used thermocouple hygrometers routinely. However, the accurate temperature correction of hygrometer calibration curve slopes seems to have been largely neglected in both psychrometric and dewpoint techniques. In the case of thermocouple psychrometers, two temperature correction models are proposed, each based on measurement of the thermojunction radius and calculation of the theoretical voltage sensitivity to changes in water potential. The first model relies on calibration at a single temperature and the second at two temperatures. Both these models were more accurate than the temperature correction models currently in use for four psychrometers calibrated over a range of temperatures (15-38°C). The model based on calibration at two temperatures is superior to that based on only one calibration. The model proposed for dewpoint hygrometers is similar to that for psychrometers. It is based on the theoretical voltage sensitivity to changes in water potential. Comparison with empirical data from three dewpoint hygrometers calibrated at four different temperatures indicates that these instruments need only be calibrated at, e.g. 25°C, if the calibration slopes are corrected for temperature. PMID:16662241

  7. An accurate temperature correction model for thermocouple hygrometers.

    PubMed

    Savage, M J; Cass, A; de Jager, J M

    1982-02-01

    Numerous water relation studies have used thermocouple hygrometers routinely. However, the accurate temperature correction of hygrometer calibration curve slopes seems to have been largely neglected in both psychrometric and dewpoint techniques.In the case of thermocouple psychrometers, two temperature correction models are proposed, each based on measurement of the thermojunction radius and calculation of the theoretical voltage sensitivity to changes in water potential. The first model relies on calibration at a single temperature and the second at two temperatures. Both these models were more accurate than the temperature correction models currently in use for four psychrometers calibrated over a range of temperatures (15-38 degrees C). The model based on calibration at two temperatures is superior to that based on only one calibration.The model proposed for dewpoint hygrometers is similar to that for psychrometers. It is based on the theoretical voltage sensitivity to changes in water potential. Comparison with empirical data from three dewpoint hygrometers calibrated at four different temperatures indicates that these instruments need only be calibrated at, e.g. 25 degrees C, if the calibration slopes are corrected for temperature.

  8. More-Accurate Model of Flows in Rocket Injectors

    NASA Technical Reports Server (NTRS)

    Hosangadi, Ashvin; Chenoweth, James; Brinckman, Kevin; Dash, Sanford

    2011-01-01

    An improved computational model for simulating flows in liquid-propellant injectors in rocket engines has been developed. Models like this one are needed for predicting fluxes of heat in, and performances of, the engines. An important part of predicting performance is predicting fluctuations of temperature, fluctuations of concentrations of chemical species, and effects of turbulence on diffusion of heat and chemical species. Customarily, diffusion effects are represented by parameters known in the art as the Prandtl and Schmidt numbers. Prior formulations include ad hoc assumptions of constant values of these parameters, but these assumptions and, hence, the formulations, are inaccurate for complex flows. In the improved model, these parameters are neither constant nor specified in advance: instead, they are variables obtained as part of the solution. Consequently, this model represents the effects of turbulence on diffusion of heat and chemical species more accurately than prior formulations do, and may enable more-accurate prediction of mixing and flows of heat in rocket-engine combustion chambers. The model has been implemented within CRUNCH CFD, a proprietary computational fluid dynamics (CFD) computer program, and has been tested within that program. The model could also be implemented within other CFD programs.

  9. A streamline splitting pore-network approach for computationally inexpensive and accurate simulation of transport in porous media

    SciTech Connect

    Mehmani, Yashar; Oostrom, Martinus; Balhoff, Matthew

    2014-03-20

    Several approaches have been developed in the literature for solving flow and transport at the pore-scale. Some authors use a direct modeling approach where the fundamental flow and transport equations are solved on the actual pore-space geometry. Such direct modeling, while very accurate, comes at a great computational cost. Network models are computationally more efficient because the pore-space morphology is approximated. Typically, a mixed cell method (MCM) is employed for solving the flow and transport system which assumes pore-level perfect mixing. This assumption is invalid at moderate to high Peclet regimes. In this work, a novel Eulerian perspective on modeling flow and transport at the pore-scale is developed. The new streamline splitting method (SSM) allows for circumventing the pore-level perfect mixing assumption, while maintaining the computational efficiency of pore-network models. SSM was verified with direct simulations and excellent matches were obtained against micromodel experiments across a wide range of pore-structure and fluid-flow parameters. The increase in the computational cost from MCM to SSM is shown to be minimal, while the accuracy of SSM is much higher than that of MCM and comparable to direct modeling approaches. Therefore, SSM can be regarded as an appropriate balance between incorporating detailed physics and controlling computational cost. The truly predictive capability of the model allows for the study of pore-level interactions of fluid flow and transport in different porous materials. In this paper, we apply SSM and MCM to study the effects of pore-level mixing on transverse dispersion in 3D disordered granular media.

  10. Fast and Accurate Circuit Design Automation through Hierarchical Model Switching.

    PubMed

    Huynh, Linh; Tagkopoulos, Ilias

    2015-08-21

    In computer-aided biological design, the trifecta of characterized part libraries, accurate models and optimal design parameters is crucial for producing reliable designs. As the number of parts and model complexity increase, however, it becomes exponentially more difficult for any optimization method to search the solution space, hence creating a trade-off that hampers efficient design. To address this issue, we present a hierarchical computer-aided design architecture that uses a two-step approach for biological design. First, a simple model of low computational complexity is used to predict circuit behavior and assess candidate circuit branches through branch-and-bound methods. Then, a complex, nonlinear circuit model is used for a fine-grained search of the reduced solution space, thus achieving more accurate results. Evaluation with a benchmark of 11 circuits and a library of 102 experimental designs with known characterization parameters demonstrates a speed-up of 3 orders of magnitude when compared to other design methods that provide optimality guarantees.

  11. Gravel transport by ice in a subarctic river from accurate laser scanning

    NASA Astrophysics Data System (ADS)

    Lotsari, Eliisa; Wang, Yunsheng; Kaartinen, Harri; Jaakkola, Anttoni; Kukko, Antero; Vaaja, Matti; Hyyppä, Hannu; Hyyppä, Juha; Alho, Petteri

    2015-10-01

    For decades the importance of ice and the effects of cold-region processes on river channel morphology have been discussed, with a general consensus as to their importance emerging only recently. River ice cover, anchor ice, frazil ice, and ice jams may not only scour the channel bed and banks but also pick up, transport, and deposit fine sediments and gravels during winter, especially during the spring ice breakup period. However, knowledge of the interactions between coarse sediment transport and ice processes remains insufficient, particularly in rockier river reaches, with a lack of accurate and sufficiently extensive data hindering their quantification. The aim of this study was to quantify and analyse the impact of river ice on gravel transport in a subarctic river during one winter via the acquisition of laser scanning data for the river channel and ice surface. Terrestrial and mobile laser scanning were performed in 2012-2013 on the Tana River in northern Finland. Both of these techniques are considered accurate and applicable for detecting elevation and volumetric changes in river bed, defining gravel clast sizes, and detecting the movement of individual clasts. More importantly, ice surface, thickness, and decay during spring were also captured via laser scanning. In the winter of 2012-2013, a period characterised by an absence of ice jams and mid-winter ice-decay periods, with spring ice breakup discharges close to average yearly conditions, ice had the most significant role, greater than that of flowing water, in erosion and transport of coarse sediment from the channel bed and gently sloping banks. Changes in river bed elevation and volume were recorded throughout the study site, and erosion predominated. In addition to broader scale erosion, the movement of single clasts up to 2 m in size occurred. However, the observed overall channel change patterns did not coincide with the areas of fastest ice decay. The obtained results could also be applied to

  12. Accurate pressure gradient calculations in hydrostatic atmospheric models

    NASA Technical Reports Server (NTRS)

    Carroll, John J.; Mendez-Nunez, Luis R.; Tanrikulu, Saffet

    1987-01-01

    A method for the accurate calculation of the horizontal pressure gradient acceleration in hydrostatic atmospheric models is presented which is especially useful in situations where the isothermal surfaces are not parallel to the vertical coordinate surfaces. The present method is shown to be exact if the potential temperature lapse rate is constant between the vertical pressure integration limits. The technique is applied to both the integration of the hydrostatic equation and the computation of the slope correction term in the horizontal pressure gradient. A fixed vertical grid and a dynamic grid defined by the significant levels in the vertical temperature distribution are employed.

  13. Mouse models of human AML accurately predict chemotherapy response

    PubMed Central

    Zuber, Johannes; Radtke, Ina; Pardee, Timothy S.; Zhao, Zhen; Rappaport, Amy R.; Luo, Weijun; McCurrach, Mila E.; Yang, Miao-Miao; Dolan, M. Eileen; Kogan, Scott C.; Downing, James R.; Lowe, Scott W.

    2009-01-01

    The genetic heterogeneity of cancer influences the trajectory of tumor progression and may underlie clinical variation in therapy response. To model such heterogeneity, we produced genetically and pathologically accurate mouse models of common forms of human acute myeloid leukemia (AML) and developed methods to mimic standard induction chemotherapy and efficiently monitor therapy response. We see that murine AMLs harboring two common human AML genotypes show remarkably diverse responses to conventional therapy that mirror clinical experience. Specifically, murine leukemias expressing the AML1/ETO fusion oncoprotein, associated with a favorable prognosis in patients, show a dramatic response to induction chemotherapy owing to robust activation of the p53 tumor suppressor network. Conversely, murine leukemias expressing MLL fusion proteins, associated with a dismal prognosis in patients, are drug-resistant due to an attenuated p53 response. Our studies highlight the importance of genetic information in guiding the treatment of human AML, functionally establish the p53 network as a central determinant of chemotherapy response in AML, and demonstrate that genetically engineered mouse models of human cancer can accurately predict therapy response in patients. PMID:19339691

  14. Mouse models of human AML accurately predict chemotherapy response.

    PubMed

    Zuber, Johannes; Radtke, Ina; Pardee, Timothy S; Zhao, Zhen; Rappaport, Amy R; Luo, Weijun; McCurrach, Mila E; Yang, Miao-Miao; Dolan, M Eileen; Kogan, Scott C; Downing, James R; Lowe, Scott W

    2009-04-01

    The genetic heterogeneity of cancer influences the trajectory of tumor progression and may underlie clinical variation in therapy response. To model such heterogeneity, we produced genetically and pathologically accurate mouse models of common forms of human acute myeloid leukemia (AML) and developed methods to mimic standard induction chemotherapy and efficiently monitor therapy response. We see that murine AMLs harboring two common human AML genotypes show remarkably diverse responses to conventional therapy that mirror clinical experience. Specifically, murine leukemias expressing the AML1/ETO fusion oncoprotein, associated with a favorable prognosis in patients, show a dramatic response to induction chemotherapy owing to robust activation of the p53 tumor suppressor network. Conversely, murine leukemias expressing MLL fusion proteins, associated with a dismal prognosis in patients, are drug-resistant due to an attenuated p53 response. Our studies highlight the importance of genetic information in guiding the treatment of human AML, functionally establish the p53 network as a central determinant of chemotherapy response in AML, and demonstrate that genetically engineered mouse models of human cancer can accurately predict therapy response in patients.

  15. Simple Mathematical Models Do Not Accurately Predict Early SIV Dynamics

    PubMed Central

    Noecker, Cecilia; Schaefer, Krista; Zaccheo, Kelly; Yang, Yiding; Day, Judy; Ganusov, Vitaly V.

    2015-01-01

    Upon infection of a new host, human immunodeficiency virus (HIV) replicates in the mucosal tissues and is generally undetectable in circulation for 1–2 weeks post-infection. Several interventions against HIV including vaccines and antiretroviral prophylaxis target virus replication at this earliest stage of infection. Mathematical models have been used to understand how HIV spreads from mucosal tissues systemically and what impact vaccination and/or antiretroviral prophylaxis has on viral eradication. Because predictions of such models have been rarely compared to experimental data, it remains unclear which processes included in these models are critical for predicting early HIV dynamics. Here we modified the “standard” mathematical model of HIV infection to include two populations of infected cells: cells that are actively producing the virus and cells that are transitioning into virus production mode. We evaluated the effects of several poorly known parameters on infection outcomes in this model and compared model predictions to experimental data on infection of non-human primates with variable doses of simian immunodifficiency virus (SIV). First, we found that the mode of virus production by infected cells (budding vs. bursting) has a minimal impact on the early virus dynamics for a wide range of model parameters, as long as the parameters are constrained to provide the observed rate of SIV load increase in the blood of infected animals. Interestingly and in contrast with previous results, we found that the bursting mode of virus production generally results in a higher probability of viral extinction than the budding mode of virus production. Second, this mathematical model was not able to accurately describe the change in experimentally determined probability of host infection with increasing viral doses. Third and finally, the model was also unable to accurately explain the decline in the time to virus detection with increasing viral dose. These results

  16. How Accurate Is A Hydraulic Model? | Science Inventory | US ...

    EPA Pesticide Factsheets

    Symposium paper Network hydraulic models are widely used, but their overall accuracy is often unknown. Models are developed to give utilities better insight into system hydraulic behavior, and increasingly the ability to predict the fate and transport of chemicals. Without an accessible and consistent means of validating a given model against the system it is meant to represent, the value of those supposed benefits should be questioned. Supervisory Control And Data Acquisition (SCADA) databases, though ubiquitous, are underused data sources for this type of task. Integrating a network model with a measurement database would offer professionals the ability to assess the model’s assumptions in an automated fashion by leveraging enormous amounts of data.

  17. Generating Facial Expressions Using an Anatomically Accurate Biomechanical Model.

    PubMed

    Wu, Tim; Hung, Alice; Mithraratne, Kumar

    2014-11-01

    This paper presents a computational framework for modelling the biomechanics of human facial expressions. A detailed high-order (Cubic-Hermite) finite element model of the human head was constructed using anatomical data segmented from magnetic resonance images. The model includes a superficial soft-tissue continuum consisting of skin, the subcutaneous layer and the superficial Musculo-Aponeurotic system. Embedded within this continuum mesh, are 20 pairs of facial muscles which drive facial expressions. These muscles were treated as transversely-isotropic and their anatomical geometries and fibre orientations were accurately depicted. In order to capture the relative composition of muscles and fat, material heterogeneity was also introduced into the model. Complex contact interactions between the lips, eyelids, and between superficial soft tissue continuum and deep rigid skeletal bones were also computed. In addition, this paper investigates the impact of incorporating material heterogeneity and contact interactions, which are often neglected in similar studies. Four facial expressions were simulated using the developed model and the results were compared with surface data obtained from a 3D structured-light scanner. Predicted expressions showed good agreement with the experimental data.

  18. Inverter Modeling For Accurate Energy Predictions Of Tracking HCPV Installations

    NASA Astrophysics Data System (ADS)

    Bowman, J.; Jensen, S.; McDonald, Mark

    2010-10-01

    High efficiency high concentration photovoltaic (HCPV) solar plants of megawatt scale are now operational, and opportunities for expanded adoption are plentiful. However, effective bidding for sites requires reliable prediction of energy production. HCPV module nameplate power is rated for specific test conditions; however, instantaneous HCPV power varies due to site specific irradiance and operating temperature, and is degraded by soiling, protective stowing, shading, and electrical connectivity. These factors interact with the selection of equipment typically supplied by third parties, e.g., wire gauge and inverters. We describe a time sequence model accurately accounting for these effects that predicts annual energy production, with specific reference to the impact of the inverter on energy output and interactions between system-level design decisions and the inverter. We will also show two examples, based on an actual field design, of inverter efficiency calculations and the interaction between string arrangements and inverter selection.

  19. Quantifying errors in trace species transport modeling

    PubMed Central

    Prather, Michael J.; Zhu, Xin; Strahan, Susan E.; Steenrod, Stephen D.; Rodriguez, Jose M.

    2008-01-01

    One expectation when computationally solving an Earth system model is that a correct answer exists, that with adequate physical approximations and numerical methods our solutions will converge to that single answer. With such hubris, we performed a controlled numerical test of the atmospheric transport of CO2 using 2 models known for accurate transport of trace species. Resulting differences were unexpectedly large, indicating that in some cases, scientific conclusions may err because of lack of knowledge of the numerical errors in tracer transport models. By doubling the resolution, thereby reducing numerical error, both models show some convergence to the same answer. Now, under realistic conditions, we identify a practical approach for finding the correct answer and thus quantifying the advection error. PMID:19066224

  20. Accurate SHAPE-directed RNA secondary structure modeling, including pseudoknots

    PubMed Central

    Hajdin, Christine E.; Bellaousov, Stanislav; Huggins, Wayne; Leonard, Christopher W.; Mathews, David H.; Weeks, Kevin M.

    2013-01-01

    A pseudoknot forms in an RNA when nucleotides in a loop pair with a region outside the helices that close the loop. Pseudoknots occur relatively rarely in RNA but are highly overrepresented in functionally critical motifs in large catalytic RNAs, in riboswitches, and in regulatory elements of viruses. Pseudoknots are usually excluded from RNA structure prediction algorithms. When included, these pairings are difficult to model accurately, especially in large RNAs, because allowing this structure dramatically increases the number of possible incorrect folds and because it is difficult to search the fold space for an optimal structure. We have developed a concise secondary structure modeling approach that combines SHAPE (selective 2′-hydroxyl acylation analyzed by primer extension) experimental chemical probing information and a simple, but robust, energy model for the entropic cost of single pseudoknot formation. Structures are predicted with iterative refinement, using a dynamic programming algorithm. This melded experimental and thermodynamic energy function predicted the secondary structures and the pseudoknots for a set of 21 challenging RNAs of known structure ranging in size from 34 to 530 nt. On average, 93% of known base pairs were predicted, and all pseudoknots in well-folded RNAs were identified. PMID:23503844

  1. Towards Accurate Molecular Modeling of Plastic Bonded Explosives

    NASA Astrophysics Data System (ADS)

    Chantawansri, T. L.; Andzelm, J.; Taylor, D.; Byrd, E.; Rice, B.

    2010-03-01

    There is substantial interest in identifying the controlling factors that influence the susceptibility of polymer bonded explosives (PBXs) to accidental initiation. Numerous Molecular Dynamics (MD) simulations of PBXs using the COMPASS force field have been reported in recent years, where the validity of the force field in modeling the solid EM fill has been judged solely on its ability to reproduce lattice parameters, which is an insufficient metric. Performance of the COMPASS force field in modeling EMs and the polymeric binder has been assessed by calculating structural, thermal, and mechanical properties, where only fair agreement with experimental data is obtained. We performed MD simulations using the COMPASS force field for the polymer binder hydroxyl-terminated polybutadiene and five EMs: cyclotrimethylenetrinitramine, 1,3,5,7-tetranitro-1,3,5,7-tetra-azacyclo-octane, 2,4,6,8,10,12-hexantirohexaazazisowurzitane, 2,4,6-trinitro-1,3,5-benzenetriamine, and pentaerythritol tetranitate. Predicted EM crystallographic and molecular structural parameters, as well as calculated properties for the binder will be compared with experimental results for different simulation conditions. We also present novel simulation protocols, which improve agreement between experimental and computation results thus leading to the accurate modeling of PBXs.

  2. k-Space Image Correlation Spectroscopy: A Method for Accurate Transport Measurements Independent of Fluorophore Photophysics

    PubMed Central

    Kolin, David L.; Ronis, David; Wiseman, Paul W.

    2006-01-01

    We present the theory and application of reciprocal space image correlation spectroscopy (kICS). This technique measures the number density, diffusion coefficient, and velocity of fluorescently labeled macromolecules in a cell membrane imaged on a confocal, two-photon, or total internal reflection fluorescence microscope. In contrast to r-space correlation techniques, we show kICS can recover accurate dynamics even in the presence of complex fluorophore photobleaching and/or “blinking”. Furthermore, these quantities can be calculated without nonlinear curve fitting, or any knowledge of the beam radius of the exciting laser. The number densities calculated by kICS are less sensitive to spatial inhomogeneity of the fluorophore distribution than densities measured using image correlation spectroscopy. We use simulations as a proof-of-principle to show that number densities and transport coefficients can be extracted using this technique. We present calibration measurements with fluorescent microspheres imaged on a confocal microscope, which recover Stokes-Einstein diffusion coefficients, and flow velocities that agree with single particle tracking measurements. We also show the application of kICS to measurements of the transport dynamics of α5-integrin/enhanced green fluorescent protein constructs in a transfected CHO cell imaged on a total internal reflection fluorescence microscope using charge-coupled device area detection. PMID:16861272

  3. Personalized Orthodontic Accurate Tooth Arrangement System with Complete Teeth Model.

    PubMed

    Cheng, Cheng; Cheng, Xiaosheng; Dai, Ning; Liu, Yi; Fan, Qilei; Hou, Yulin; Jiang, Xiaotong

    2015-09-01

    The accuracy, validity and lack of relation information between dental root and jaw in tooth arrangement are key problems in tooth arrangement technology. This paper aims to describe a newly developed virtual, personalized and accurate tooth arrangement system based on complete information about dental root and skull. Firstly, a feature constraint database of a 3D teeth model is established. Secondly, for computed simulation of tooth movement, the reference planes and lines are defined by the anatomical reference points. The matching mathematical model of teeth pattern and the principle of the specific pose transformation of rigid body are fully utilized. The relation of position between dental root and alveolar bone is considered during the design process. Finally, the relative pose relationships among various teeth are optimized using the object mover, and a personalized therapeutic schedule is formulated. Experimental results show that the virtual tooth arrangement system can arrange abnormal teeth very well and is sufficiently flexible. The relation of position between root and jaw is favorable. This newly developed system is characterized by high-speed processing and quantitative evaluation of the amount of 3D movement of an individual tooth.

  4. A conservative finite volume scheme with time-accurate local time stepping for scalar transport on unstructured grids

    NASA Astrophysics Data System (ADS)

    Cavalcanti, José Rafael; Dumbser, Michael; Motta-Marques, David da; Fragoso Junior, Carlos Ruberto

    2015-12-01

    In this article we propose a new conservative high resolution TVD (total variation diminishing) finite volume scheme with time-accurate local time stepping (LTS) on unstructured grids for the solution of scalar transport problems, which are typical in the context of water quality simulations. To keep the presentation of the new method as simple as possible, the algorithm is only derived in two space dimensions and for purely convective transport problems, hence neglecting diffusion and reaction terms. The new numerical method for the solution of the scalar transport is directly coupled to the hydrodynamic model of Casulli and Walters (2000) that provides the dynamics of the free surface and the velocity vector field based on a semi-implicit discretization of the shallow water equations. Wetting and drying is handled rigorously by the nonlinear algorithm proposed by Casulli (2009). The new time-accurate LTS algorithm allows a different time step size for each element of the unstructured grid, based on an element-local Courant-Friedrichs-Lewy (CFL) stability condition. The proposed method does not need any synchronization between different time steps of different elements and is by construction locally and globally conservative. The LTS scheme is based on a piecewise linear polynomial reconstruction in space-time using the MUSCL-Hancock method, to obtain second order of accuracy in both space and time. The new algorithm is first validated on some classical test cases for pure advection problems, for which exact solutions are known. In all cases we obtain a very good level of accuracy, showing also numerical convergence results; we furthermore confirm mass conservation up to machine precision and observe an improved computational efficiency compared to a standard second order TVD scheme for scalar transport with global time stepping (GTS). Then, the new LTS method is applied to some more complex problems, where the new scalar transport scheme has also been coupled to

  5. Minority Transportation Expenditure Allocation Model

    SciTech Connect

    Vyas, Anant D.; Santini, Danilo J.; Marik, Sheri K.

    1993-04-12

    MITRAM (Minority TRansportation expenditure Allocation Model) can project various transportation related attributes of minority (Black and Hispanic) and majority (white) populations. The model projects vehicle ownership, vehicle miles of travel, workers, new car and on-road fleet fuel economy, amount and share of household income spent on gasoline, and household expenditures on public transportation and taxis. MITRAM predicts reactions to sustained fuel price changes for up to 10 years after the change.

  6. Stochastic models of intracellular transport

    NASA Astrophysics Data System (ADS)

    Bressloff, Paul C.; Newby, Jay M.

    2013-01-01

    The interior of a living cell is a crowded, heterogenuous, fluctuating environment. Hence, a major challenge in modeling intracellular transport is to analyze stochastic processes within complex environments. Broadly speaking, there are two basic mechanisms for intracellular transport: passive diffusion and motor-driven active transport. Diffusive transport can be formulated in terms of the motion of an overdamped Brownian particle. On the other hand, active transport requires chemical energy, usually in the form of adenosine triphosphate hydrolysis, and can be direction specific, allowing biomolecules to be transported long distances; this is particularly important in neurons due to their complex geometry. In this review a wide range of analytical methods and models of intracellular transport is presented. In the case of diffusive transport, narrow escape problems, diffusion to a small target, confined and single-file diffusion, homogenization theory, and fractional diffusion are considered. In the case of active transport, Brownian ratchets, random walk models, exclusion processes, random intermittent search processes, quasi-steady-state reduction methods, and mean-field approximations are considered. Applications include receptor trafficking, axonal transport, membrane diffusion, nuclear transport, protein-DNA interactions, virus trafficking, and the self-organization of subcellular structures.

  7. Modeling electronic quantum transport with machine learning

    NASA Astrophysics Data System (ADS)

    Lopez-Bezanilla, Alejandro; von Lilienfeld, O. Anatole

    2014-06-01

    We present a machine learning approach to solve electronic quantum transport equations of one-dimensional nanostructures. The transmission coefficients of disordered systems were computed to provide training and test data sets to the machine. The system's representation encodes energetic as well as geometrical information to characterize similarities between disordered configurations, while the Euclidean norm is used as a measure of similarity. Errors for out-of-sample predictions systematically decrease with training set size, enabling the accurate and fast prediction of new transmission coefficients. The remarkable performance of our model to capture the complexity of interference phenomena lends further support to its viability in dealing with transport problems of undulatory nature.

  8. Modeling energy transport in nanostructures

    NASA Astrophysics Data System (ADS)

    Pattamatta, Arvind

    Heat transfer in nanostructures differ significantly from that in the bulk materials since the characteristic length scales associated with heat carriers, i.e., the mean free path and the wavelength, are comparable to the characteristic length of the nanostructures. Nanostructure materials hold the promise of novel phenomena, properties, and functions in the areas of thermal management and energy conversion. Example of thermal management in micro/nano electronic devices is the use of efficient nanostructured materials to alleviate 'hot spots' in integrated circuits. Examples in the manipulation of heat flow and energy conversion include nanostructures for thermoelectric energy conversion, thermophotovoltaic power generation, and data storage. One of the major challenges in Metal-Oxide Field Effect Transistor (MOSFET) devices is to study the 'hot spot' generation by accurately modeling the carrier-optical phonon-acoustic phonon interactions. Prediction of hotspot temperature and position in MOSFET devices is necessary for improving thermal design and reliability of micro/nano electronic devices. Thermoelectric properties are among the properties that may drastically change at nanoscale. The efficiency of thermoelectric energy conversion in a material is measured by a non-dimensional figure of merit (ZT) defined as, ZT = sigmaS2T/k where sigma is the electrical conductivity, S is the Seebeck coefficient, T is the temperature, and k is the thermal conductivity. During the last decade, advances have been made in increasing ZT using nanostructures. Three important topics are studied with respect to energy transport in nanostructure materials for micro/nano electronic and thermoelectric applications; (1) the role of nanocomposites in improving the thermal efficiency of thermoelectric devices, (2) the interfacial thermal resistance for the semiconductor/metal contacts in thermoelectric devices and for metallic interconnects in micro/nano electronic devices, (3) the

  9. Describing and compensating gas transport dynamics for accurate instantaneous emission measurement

    NASA Astrophysics Data System (ADS)

    Weilenmann, Martin; Soltic, Patrik; Ajtay, Delia

    Instantaneous emission measurements on chassis dynamometers and engine test benches are becoming increasingly usual for car-makers and for environmental emission factor measurement and calculation, since much more information about the formation conditions can be extracted than from the regulated bag measurements (integral values). The common exhaust gas analysers for the "regulated pollutants" (carbon monoxide, total hydrocarbons, nitrogen oxide, carbon dioxide) allow measurement at a rate of one to ten samples per second. This gives the impression of having after-the-catalyst emission information with that chronological precision. It has been shown in recent years, however, that beside the reaction time of the analysers, the dynamics of gas transport in both the exhaust system of the car and the measurement system last significantly longer than 1 s. This paper focuses on the compensation of all these dynamics convoluting the emission signals. Most analysers show linear and time-invariant reaction dynamics. Transport dynamics can basically be split into two phenomena: a pure time delay accounting for the transport of the gas downstream and a dynamic signal deformation since the gas is mixed by turbulence along the way. This causes emission peaks to occur which are smaller in height and longer in time at the sensors than they are after the catalyst. These dynamics can be modelled using differential equations. Both mixing dynamics and time delay are constant for modelling a raw gas analyser system, since the flow in that system is constant. In the exhaust system of the car, however, the parameters depend on the exhaust volume flow. For gasoline cars, the variation in overall transport time may be more than 6 s. It is shown in this paper how all these processes can be described by invertible mathematical models with the focus on the more complex case of the car's exhaust system. Inversion means that the sharp emission signal at the catalyst out location can be

  10. Theoretical Transport Model for Tokamaks

    NASA Astrophysics Data System (ADS)

    Ghanem, Elsayed Mohammad

    In the present thesis work a theoretical transport model is suggested to study the anomalous transport of plasma particles and energy across the axisymmetric equilibrium toroidal magnetic flux surfaces in tokamaks. The model suggests a linear combination of two transport mechanisms; drift waves, which dominate the transport in the core region, and resistive ballooning modes, which dominate the transport in the edge region. The resulting unified model has been used in a predictive transport code to simulate the plasma transport in different tokamak experiments operating in both the ohmic heating phase and the low confinement mode (L-mode). For ohmic plasma, the model was used to study the saturation of energy confinement time at high plasma density. The effect of the resistive ballooning mode as a possible cause of the saturation phenomena has been investigated together with the effect of the ion temperature gradient mode. For the low confinement mode plasmas, the study has emphasized on using the model to obtain a scaling law for the energy confinement time with the various plasma parameters compared to the scaling laws that are derived based on fitting the experimental data.

  11. Groundwater flow and transport modeling

    USGS Publications Warehouse

    Konikow, L.F.; Mercer, J.W.

    1988-01-01

    Deterministic, distributed-parameter, numerical simulation models for analyzing groundwater flow and transport problems have come to be used almost routinely during the past decade. A review of the theoretical basis and practical use of groundwater flow and solute transport models is used to illustrate the state-of-the-art. Because of errors and uncertainty in defining model parameters, models must be calibrated to obtain a best estimate of the parameters. For flow modeling, data generally are sufficient to allow calibration. For solute-transport modeling, lack of data not only limits calibration, but also causes uncertainty in process description. Where data are available, model reliability should be assessed on the basis of sensitivity tests and measures of goodness-of-fit. Some of these concepts are demonstrated by using two case histories. ?? 1988.

  12. Heterogeneous processes affecting metal ion transport in the presence of organic ligands: Reactive transport modeling

    NASA Astrophysics Data System (ADS)

    Kantar, Cetin

    2007-04-01

    The development of models to accurately simulate metal ion transport through saturated systems under variable chemical conditions, e.g., in systems containing organic ligands (L) such as natural organic matter (NOM), has two essential aspects: (1) establishing the ability to simulate metal ion sorption to aquifer solids over a range of metal/ligand ratios; and (2) to incorporate this ability to simulate metal speciation over a range in chemical conditions (e.g., pH, ligand activity) into mass transport models. Modeling approaches to evaluate metal ion sorption and transport in the presence of NOM include: (1) isotherm-based transport models, and (2) multicomponent (MC) transport models. The accuracy of transport models depends on how well the chemical interactions affecting metal ion transport in the presence of organic ligands (e.g., metal/ligand complexation) are described in transport equations. The isotherm-based transport models often fail to accurately describe metal ion transport in the presence of NOM since these models treat NOM as a single solute despite the fact that NOM is a multicomponent mixture of subcomponents with different chemical and polyfunctional behavior. On the other hand, the calculations presented in this study suggest that a multicomponent reactive transport model, in conjunction with a mechanistic modeling approach for the description of metal ion binding by NOM in a manner conducive to the application of surface complexation modeling (SCM), can effectively be used as an important predictive tool in simulating metal ion sorption and transport under variable chemical conditions in the presence of NOM.

  13. BRYNTRN: A baryon transport model

    NASA Technical Reports Server (NTRS)

    Wilson, John W.; Townsend, Lawrence W.; Nealy, John E.; Chun, Sang Y.; Hong, B. S.; Buck, Warren W.; Lamkin, S. L.; Ganapol, Barry D.; Khan, Ferdous; Cucinotta, Francis A.

    1989-01-01

    The development of an interaction data base and a numerical solution to the transport of baryons through an arbitrary shield material based on a straight ahead approximation of the Boltzmann equation are described. The code is most accurate for continuous energy boundary values, but gives reasonable results for discrete spectra at the boundary using even a relatively coarse energy grid (30 points) and large spatial increments (1 cm in H2O). The resulting computer code is self-contained, efficient and ready to use. The code requires only a very small fraction of the computer resources required for Monte Carlo codes.

  14. Next Generation Transport Phenomenology Model

    NASA Technical Reports Server (NTRS)

    Strickland, Douglas J.; Knight, Harold; Evans, J. Scott

    2004-01-01

    This report describes the progress made in Quarter 3 of Contract Year 3 on the development of Aeronomy Phenomenology Modeling Tool (APMT), an open-source, component-based, client-server architecture for distributed modeling, analysis, and simulation activities focused on electron and photon transport for general atmospheres. In the past quarter, column emission rate computations were implemented in Java, preexisting Fortran programs for computing synthetic spectra were embedded into APMT through Java wrappers, and work began on a web-based user interface for setting input parameters and running the photoelectron and auroral electron transport models.

  15. Particle Image Velocimetry Measurements in Anatomically-Accurate Models of the Mammalian Nasal Cavity

    NASA Astrophysics Data System (ADS)

    Rumple, C.; Richter, J.; Craven, B. A.; Krane, M.

    2012-11-01

    A summary of the research being carried out by our multidisciplinary team to better understand the form and function of the nose in different mammalian species that include humans, carnivores, ungulates, rodents, and marine animals will be presented. The mammalian nose houses a convoluted airway labyrinth, where two hallmark features of mammals occur, endothermy and olfaction. Because of the complexity of the nasal cavity, the anatomy and function of these upper airways remain poorly understood in most mammals. However, recent advances in high-resolution medical imaging, computational modeling, and experimental flow measurement techniques are now permitting the study of airflow and respiratory and olfactory transport phenomena in anatomically-accurate reconstructions of the nasal cavity. Here, we focus on efforts to manufacture transparent, anatomically-accurate models for stereo particle image velocimetry (SPIV) measurements of nasal airflow. Challenges in the design and manufacture of index-matched anatomical models are addressed and preliminary SPIV measurements are presented. Such measurements will constitute a validation database for concurrent computational fluid dynamics (CFD) simulations of mammalian respiration and olfaction. Supported by the National Science Foundation.

  16. Clarifying types of uncertainty: when are models accurate, and uncertainties small?

    PubMed

    Cox, Louis Anthony Tony

    2011-10-01

    Professor Aven has recently noted the importance of clarifying the meaning of terms such as "scientific uncertainty" for use in risk management and policy decisions, such as when to trigger application of the precautionary principle. This comment examines some fundamental conceptual challenges for efforts to define "accurate" models and "small" input uncertainties by showing that increasing uncertainty in model inputs may reduce uncertainty in model outputs; that even correct models with "small" input uncertainties need not yield accurate or useful predictions for quantities of interest in risk management (such as the duration of an epidemic); and that accurate predictive models need not be accurate causal models.

  17. Accurate Modeling of Scaffold Hopping Transformations in Drug Discovery.

    PubMed

    Wang, Lingle; Deng, Yuqing; Wu, Yujie; Kim, Byungchan; LeBard, David N; Wandschneider, Dan; Beachy, Mike; Friesner, Richard A; Abel, Robert

    2017-01-10

    The accurate prediction of protein-ligand binding free energies remains a significant challenge of central importance in computational biophysics and structure-based drug design. Multiple recent advances including the development of greatly improved protein and ligand molecular mechanics force fields, more efficient enhanced sampling methods, and low-cost powerful GPU computing clusters have enabled accurate and reliable predictions of relative protein-ligand binding free energies through the free energy perturbation (FEP) methods. However, the existing FEP methods can only be used to calculate the relative binding free energies for R-group modifications or single-atom modifications and cannot be used to efficiently evaluate scaffold hopping modifications to a lead molecule. Scaffold hopping or core hopping, a very common design strategy in drug discovery projects, is critical not only in the early stages of a discovery campaign where novel active matter must be identified but also in lead optimization where the resolution of a variety of ADME/Tox problems may require identification of a novel core structure. In this paper, we introduce a method that enables theoretically rigorous, yet computationally tractable, relative protein-ligand binding free energy calculations to be pursued for scaffold hopping modifications. We apply the method to six pharmaceutically interesting cases where diverse types of scaffold hopping modifications were required to identify the drug molecules ultimately sent into the clinic. For these six diverse cases, the predicted binding affinities were in close agreement with experiment, demonstrating the wide applicability and the significant impact Core Hopping FEP may provide in drug discovery projects.

  18. New process model proves accurate in tests on catalytic reformer

    SciTech Connect

    Aguilar-Rodriguez, E.; Ancheyta-Juarez, J. )

    1994-07-25

    A mathematical model has been devised to represent the process that takes place in a fixed-bed, tubular, adiabatic catalytic reforming reactor. Since its development, the model has been applied to the simulation of a commercial semiregenerative reformer. The development of mass and energy balances for this reformer led to a model that predicts both concentration and temperature profiles along the reactor. A comparison of the model's results with experimental data illustrates its accuracy at predicting product profiles. Simple steps show how the model can be applied to simulate any fixed-bed catalytic reformer.

  19. Etch modeling for accurate full-chip process proximity correction

    NASA Astrophysics Data System (ADS)

    Beale, Daniel F.; Shiely, James P.

    2005-05-01

    The challenges of the 65 nm node and beyond require new formulations of the compact convolution models used in OPC. In addition to simulating more optical and resist effects, these models must accommodate pattern distortions due to etch which can no longer be treated as small perturbations on photo-lithographic effects. (Methods for combining optical and process modules while optimizing the speed/accuracy tradeoff were described in "Advanced Model Formulations for Optical and Process Proximity Correction", D. Beale et al, SPIE 2004.) In this paper, we evaluate new physics-based etch model formulations that differ from the convolution-based process models used previously. The new models are expressed within the compact modeling framework described by J. Stirniman et al. in SPIE, vol. 3051, p469, 1997, and thus can be used for high-speed process simulation during full-chip OPC.

  20. Mathematical Modeling of Kidney Transport

    PubMed Central

    Layton, Anita T.

    2013-01-01

    In addition to metabolic waste and toxin excretion, the kidney also plays an indispensable role in regulating the balance of water, electrolytes, nitrogen, and acid-base. In this review, we describe representative mathematical models that have been developed to better understand kidney physiology and pathophysiology, including the regulation of glomerular filtration, the regulation of renal blood flow by means of the tubuloglomerular feedback mechanisms and of the myogenic mechanism, the urine concentrating mechanism, epithelial transport, and regulation of renal oxygen transport. We discuss the extent to which these modeling efforts have expanded our understanding of renal function in both health and disease. PMID:23852667

  1. Towards an Accurate Performance Modeling of Parallel SparseFactorization

    SciTech Connect

    Grigori, Laura; Li, Xiaoye S.

    2006-05-26

    We present a performance model to analyze a parallel sparseLU factorization algorithm on modern cached-based, high-end parallelarchitectures. Our model characterizes the algorithmic behavior bytakingaccount the underlying processor speed, memory system performance, aswell as the interconnect speed. The model is validated using theSuperLU_DIST linear system solver, the sparse matrices from realapplications, and an IBM POWER3 parallel machine. Our modelingmethodology can be easily adapted to study performance of other types ofsparse factorizations, such as Cholesky or QR.

  2. Accurate testing of aspheric surfaces using the transport of intensity equation by properly selecting the defocusing distance.

    PubMed

    Soltani, Peyman; Darudi, Ahmad; Nehmetallah, George; Moradi, Ali Reza; Amiri, Javad

    2016-12-10

    In the last decade, the transport of intensity has been increasingly used in microscopy, wavefront sensing, and metrology. In this study, we verify by simulation and experiment the use of the transport of intensity equation (TIE) in the accurate testing of optical aspheric surfaces. Guided by simulation results and assuming that the experimental setup parameters and the conic constants are known, one can estimate an appropriate defocusing distance Δz that leads to an accurate solution of the TIE. In this paper, this method is verified through the construction of a non-nulled experiment for testing the 2D profile of an aspheric surface. The theoretical method and experimental results are compared to validate the results. Finally, to validate the TIE methodology, the phase distribution obtained by TIE is compared with the phase distribution obtained by a Shack-Hartmann sensor.

  3. Modeling for accurate dimensional scanning electron microscope metrology: then and now.

    PubMed

    Postek, Michael T; Vladár, András E

    2011-01-01

    A review of the evolution of modeling for accurate dimensional scanning electron microscopy is presented with an emphasis on developments in the Monte Carlo technique for modeling the generation of the electrons used for imaging and measurement. The progress of modeling for accurate metrology is discussed through a schematic technology timeline. In addition, a discussion of a future vision for accurate SEM dimensional metrology and the requirements to achieve it are presented.

  4. How Accurate is Land/Ocean Moisture Transport Variability in Reanalyses?

    NASA Technical Reports Server (NTRS)

    Robertson, F. R.; Bosilovich, M. G.

    2014-01-01

    Quantifying the global hydrological cycle and its variability across various time scales remains a challenge to the climate community. Direct measurements of evaporation (E), evapotranspiration (ET), and precipitation (P) are not feasible on a global scale, nor is the transport of water vapor over the global oceans and sparsely populated land areas. Expanding satellite data streams have enabled development of various water (and energy) flux products, complementing reanalyses and facilitating observationally constrained modeling. But the evolution of the global observing system has produced additional complications--improvements in satellite sensor resolution and accuracy have resulted in "epochs" of observational quasi-uniformity that can adversely affect reanalysis trends. In this work we focus on vertically integrated moisture flux convergence (VMFC) variations within the period 1979 - present integrated over global land. We show that VMFC in recent reanalyses (e.g. ERA-I, NASA MERRA, NOAA CFSR and JRA55) suffers from observing system changes, though differently in each product. Land Surface Models (LSMs) forced with observations-based precipitation, radiation and near-surface meteorology share closely the interannual P-ET variations of the reanalyses associated with ENSO events. (VMFC over land and P-ET estimates are equivalent quantities since atmospheric storage changes are small on these scales.) But the long-term LSM trend over the period since 1979 is approximately one-fourth that of the reanalyses. Additional reduced observation reanalyses assimilating only surface pressure and /or specifying seasurface temperature also have a much smaller trend in P-ET like the LSMs. We explore the regional manifestation of the reanalysis P-ET / VMFC problems, particularly over land. Both principal component analysis and a simple time series changepoint analysis highlight problems associated with data poor regions such as Equatorial Africa and, for one reanalysis, the

  5. ACCURATE LOW-MASS STELLAR MODELS OF KOI-126

    SciTech Connect

    Feiden, Gregory A.; Chaboyer, Brian; Dotter, Aaron

    2011-10-10

    The recent discovery of an eclipsing hierarchical triple system with two low-mass stars in a close orbit (KOI-126) by Carter et al. appeared to reinforce the evidence that theoretical stellar evolution models are not able to reproduce the observational mass-radius relation for low-mass stars. We present a set of stellar models for the three stars in the KOI-126 system that show excellent agreement with the observed radii. This agreement appears to be due to the equation of state implemented by our code. A significant dispersion in the observed mass-radius relation for fully convective stars is demonstrated; indicative of the influence of physics currently not incorporated in standard stellar evolution models. We also predict apsidal motion constants for the two M dwarf companions. These values should be observationally determined to within 1% by the end of the Kepler mission.

  6. Accurate two-equation modelling of falling film flows

    NASA Astrophysics Data System (ADS)

    Ruyer-Quil, Christian

    2015-11-01

    The low-dimensional modeling of the wave dynamics of a falling liquid film on an inclined plane is revisited. The advantages and shortcomings of existing modelling approaches: weighted residual method, center-manifold analysis, consistent Saint-Venant approach are discussed and contrasted. A novel formulation of a two-equation consistent model is proposed. The proposed formulation cures the principal limitations of previous approaches: (i) apart from surface tension terms, it admits a conservative form which enables to make use of efficient numerical schemes, (ii) it recovers with less than 1 percent of error the asymptotic speed of solitary waves in the inertial regime found by DNS, (iii) it adequately captures the velocity field under the waves and in particular the wall drag. Research supported by Insitut Universitaire de France.

  7. Building accurate geometric models from abundant range imaging information

    SciTech Connect

    Diegert, C.; Sackos, J.; Nellums, R.

    1997-05-01

    The authors define two simple metrics for accuracy of models built from range imaging information. They apply the metric to a model built from a recent range image taken at the Laser Radar Development and Evaluation Facility (LDERF), Eglin AFB, using a Scannerless Range Imager (SRI) from Sandia National Laboratories. They also present graphical displays of the residual information produced as a byproduct of this measurement, and discuss mechanisms that these data suggest for further improvement in the performance of this already impressive SRI.

  8. Magnetic field models of nine CP stars from "accurate" measurements

    NASA Astrophysics Data System (ADS)

    Glagolevskij, Yu. V.

    2013-01-01

    The dipole models of magnetic fields in nine CP stars are constructed based on the measurements of metal lines taken from the literature, and performed by the LSD method with an accuracy of 10-80 G. The model parameters are compared with the parameters obtained for the same stars from the hydrogen line measurements. For six out of nine stars the same type of structure was obtained. Some parameters, such as the field strength at the poles B p and the average surface magnetic field B s differ considerably in some stars due to differences in the amplitudes of phase dependences B e (Φ) and B s (Φ), obtained by different authors. It is noted that a significant increase in the measurement accuracy has little effect on the modelling of the large-scale structures of the field. By contrast, it is more important to construct the shape of the phase dependence based on a fairly large number of field measurements, evenly distributed by the rotation period phases. It is concluded that the Zeeman component measurement methods have a strong effect on the shape of the phase dependence, and that the measurements of the magnetic field based on the lines of hydrogen are more preferable for modelling the large-scale structures of the field.

  9. Accurate first principles model potentials for intermolecular interactions.

    PubMed

    Gordon, Mark S; Smith, Quentin A; Xu, Peng; Slipchenko, Lyudmila V

    2013-01-01

    The general effective fragment potential (EFP) method provides model potentials for any molecule that is derived from first principles, with no empirically fitted parameters. The EFP method has been interfaced with most currently used ab initio single-reference and multireference quantum mechanics (QM) methods, ranging from Hartree-Fock and coupled cluster theory to multireference perturbation theory. The most recent innovations in the EFP model have been to make the computationally expensive charge transfer term much more efficient and to interface the general EFP dispersion and exchange repulsion interactions with QM methods. Following a summary of the method and its implementation in generally available computer programs, these most recent new developments are discussed.

  10. Can contaminant transport models predict breakthrough?

    USGS Publications Warehouse

    Peng, Wei-Shyuan; Hampton, Duane R.; Konikow, Leonard F.; Kambham, Kiran; Benegar, Jeffery J.

    2000-01-01

    A solute breakthrough curve measured during a two-well tracer test was successfully predicted in 1986 using specialized contaminant transport models. Water was injected into a confined, unconsolidated sand aquifer and pumped out 125 feet (38.3 m) away at the same steady rate. The injected water was spiked with bromide for over three days; the outflow concentration was monitored for a month. Based on previous tests, the horizontal hydraulic conductivity of the thick aquifer varied by a factor of seven among 12 layers. Assuming stratified flow with small dispersivities, two research groups accurately predicted breakthrough with three-dimensional (12-layer) models using curvilinear elements following the arc-shaped flowlines in this test. Can contaminant transport models commonly used in industry, that use rectangular blocks, also reproduce this breakthrough curve? The two-well test was simulated with four MODFLOW-based models, MT3D (FD and HMOC options), MODFLOWT, MOC3D, and MODFLOW-SURFACT. Using the same 12 layers and small dispersivity used in the successful 1986 simulations, these models fit almost as accurately as the models using curvilinear blocks. Subtle variations in the curves illustrate differences among the codes. Sensitivities of the results to number and size of grid blocks, number of layers, boundary conditions, and values of dispersivity and porosity are briefly presented. The fit between calculated and measured breakthrough curves degenerated as the number of layers and/or grid blocks decreased, reflecting a loss of model predictive power as the level of characterization lessened. Therefore, the breakthrough curve for most field sites can be predicted only qualitatively due to limited characterization of the hydrogeology and contaminant source strength.

  11. WASP TRANSPORT MODELING AND WASP ECOLOGICAL MODELING

    EPA Science Inventory

    A combination of lectures, demonstrations, and hands-on excercises will be used to introduce pollutant transport modeling with the U.S. EPA's general water quality model, WASP (Water Quality Analysis Simulation Program). WASP features include a user-friendly Windows-based interfa...

  12. Accurate numerical solutions for elastic-plastic models. [LMFBR

    SciTech Connect

    Schreyer, H. L.; Kulak, R. F.; Kramer, J. M.

    1980-03-01

    The accuracy of two integration algorithms is studied for the common engineering condition of a von Mises, isotropic hardening model under plane stress. Errors in stress predictions for given total strain increments are expressed with contour plots of two parameters: an angle in the pi plane and the difference between the exact and computed yield-surface radii. The two methods are the tangent-predictor/radial-return approach and the elastic-predictor/radial-corrector algorithm originally developed by Mendelson. The accuracy of a combined tangent-predictor/radial-corrector algorithm is also investigated.

  13. Accurate Force Field Development for Modeling Conjugated Polymers.

    PubMed

    DuBay, Kateri H; Hall, Michelle Lynn; Hughes, Thomas F; Wu, Chuanjie; Reichman, David R; Friesner, Richard A

    2012-11-13

    The modeling of the conformational properties of conjugated polymers entails a unique challenge for classical force fields. Conjugation imposes strong constraints upon bond rotation. Planar configurations are favored, but the concomitantly shortened bond lengths result in moieties being brought into closer proximity than usual. The ensuing steric repulsions are particularly severe in the presence of side chains, straining angles, and stretching bonds to a degree infrequently found in nonconjugated systems. We herein demonstrate the resulting inaccuracies by comparing the LMP2-calculated inter-ring torsion potentials for a series of substituted stilbenes and bithiophenes to those calculated using standard classical force fields. We then implement adjustments to the OPLS-2005 force field in order to improve its ability to model such systems. Finally, we show the impact of these changes on the dihedral angle distributions, persistence lengths, and conjugation length distributions observed during molecular dynamics simulations of poly[2-methoxy-5-(2'-ethylhexyloxy)-p-phenylene vinylene] (MEH-PPV) and poly 3-hexylthiophene (P3HT), two of the most widely used conjugated polymers.

  14. Delft Mass Transport model DMT-2

    NASA Astrophysics Data System (ADS)

    Ditmar, Pavel; Hashemi Farahani, Hassan; Inacio, Pedro; Klees, Roland; Zhao, Qile; Guo, Jing; Liu, Xianglin; Sun, Yu; Riva, Ricardo; Ran, Jiangjun

    2013-04-01

    Gravity Recovery And Climate Experiment (GRACE) satellite mission has enormously extended our knowledge of the Earth's system by allowing natural mass transport of various origin to be quantified. This concerns, in particular, the depletion and replenishment of continental water stocks; shrinking of polar ice sheets; deformation of the Earth's crust triggered by large earthquakes, and isostatic adjustment processes. A number of research centers compute models of temporal gravity field variations and mass transport, using GRACE data as input. One of such models - Delft Mass Transport model - is being produced at the Delft University of Technology in collaboration with the GNSS Research Center of Wuhan University. A new release of this model, DMT-2, has been produced on the basis of a new (second) release of GRACE level-1b data. This model consists of a time-series of monthly solutions spanning a time interval of more than 8 years, starting from Feb. 2003. Each solution consists of spherical harmonic coefficients up to degree 120. Both unconstrained and optimally filtered solutions are obtained. The most essential improvements of the DMT-2 model, as compared to its predecessors (DMT-1 and DMT-1b), are as follows: (i) improved estimation and elimination of low-frequency noise in GRACE data, so that strong mass transport signals are not damped; (ii) computation of accurate stochastic models of data noise for each month individually with a subsequent application of frequency-dependent data weighting, which allows statistically optimal solutions to be compiled even if data noise is colored and gradually changes in time; (iii) optimized estimation of accelerometer calibration parameters; (iv) incorporation of degree 1 coefficients estimated with independent techniques; (v) usage of state-of-the-art background models to de-alias GRACE data from rapid mass transport signals (this includes the EOT11a model of ocean tides and the latest release of the AOD1B product describing

  15. An accurate halo model for fitting non-linear cosmological power spectra and baryonic feedback models

    NASA Astrophysics Data System (ADS)

    Mead, A. J.; Peacock, J. A.; Heymans, C.; Joudaki, S.; Heavens, A. F.

    2015-12-01

    We present an optimized variant of the halo model, designed to produce accurate matter power spectra well into the non-linear regime for a wide range of cosmological models. To do this, we introduce physically motivated free parameters into the halo-model formalism and fit these to data from high-resolution N-body simulations. For a variety of Λ cold dark matter (ΛCDM) and wCDM models, the halo-model power is accurate to ≃ 5 per cent for k ≤ 10h Mpc-1 and z ≤ 2. An advantage of our new halo model is that it can be adapted to account for the effects of baryonic feedback on the power spectrum. We demonstrate this by fitting the halo model to power spectra from the OWLS (OverWhelmingly Large Simulations) hydrodynamical simulation suite via parameters that govern halo internal structure. We are able to fit all feedback models investigated at the 5 per cent level using only two free parameters, and we place limits on the range of these halo parameters for feedback models investigated by the OWLS simulations. Accurate predictions to high k are vital for weak-lensing surveys, and these halo parameters could be considered nuisance parameters to marginalize over in future analyses to mitigate uncertainty regarding the details of feedback. Finally, we investigate how lensing observables predicted by our model compare to those from simulations and from HALOFIT for a range of k-cuts and feedback models and quantify the angular scales at which these effects become important. Code to calculate power spectra from the model presented in this paper can be found at https://github.com/alexander-mead/hmcode.

  16. Modeling Radionuclide Transport in Clays

    SciTech Connect

    Zheng, Liange; Li, Lianchong; Rutqvist, Jonny; Liu, Hui -Hai; Birkholzer, Jens

    2012-05-01

    tests (e.g. Garcia-Gutierrez et al. 2006, Soler et al. 2008, van Loon et al. 2004, Wu et al. 2009) and numerical modeling (de Windt et al. 2003; 2006), the effects of THMC processes on radionuclide transport are not fully investigated. The objectives of the research activity documented in this report are to improve a modeling capability for coupled THMC processes and to use it to evaluate the THMC impacts on radionuclide transport. This research activity addresses several key Features, Events and Processes (FEPs), including FEP 2.2.08, Hydrologic Processes, FEP 2.2.07, Mechanical Processes and FEP 2.2.09, Chemical Process— Transport, by studying near-field coupled THMC processes in clay/shale repositories and their impacts on radionuclide transport. This report documents the progress that has been made in FY12. Section 2 discusses the development of THMC modeling capability. Section 3 reports modeling results of THMC impacts on radionuclide transport. Planned work for the remaining months of FY12 and proposed work for FY13 are presented in Section 4.

  17. Accurate transport properties for O(3P)-H and O(3P)-H2

    NASA Astrophysics Data System (ADS)

    Dagdigian, Paul J.; Kłos, Jacek; Warehime, Mick; Alexander, Millard H.

    2016-10-01

    Transport properties for collisions of oxygen atoms with hydrogen atoms and hydrogen molecules have been computed by means of time-independent quantum scattering calculations. For the O(3P)-H(2S) interaction, potential energy curves for the four OH electronic states emanating from this asymptote were computed by the internally-contracted multi-reference configuration interaction method, and the R-dependent spin-orbit matrix elements were taken from Parlant and Yarkony [J. Chem. Phys. 110, 363 (1999)]. For the O(3P)-H2 interaction, diabatic potential energy surfaces were derived from internally contracted multi-reference configuration interaction calculations. Transport properties were computed for these two collision pairs and compared with those obtained with the conventional approach that employs isotropic Lennard-Jones (12-6) potentials.

  18. Modeling Tokamak Transport with Neural-Network Based Models

    NASA Astrophysics Data System (ADS)

    Meneghini, O.; Luna, C.; Penna, J.; Smith, S. P.; Lao, L. L.

    2014-10-01

    This work uses neural networks (NNs) as a means to extract information from the massive volume of aggregated data that are available either from experiments or from simulation databases, and distill an accurate transport model for the heat, particle, and momentum transport fluxes as a function of local dimensionless plasma parameters. The resulting model has been benchmarked with over 4000 DIII-D plasmas in different regimes, and it is able to capture the experimental behavior inside of ρ < 0 . 95 with average error <20% for all transport channels. The NN model was embedded into the ONETWO transport code and is now being used to develop time-dependent scenarios in support of DIII-D operations. The simulated temperature, density and rotation profiles closely match the experimental measurements, and a stiff response of the heat fluxes has been observed in the model for increasing source power. The numerical efficiency of the NN approach makes it ideal for real time plasma control and scenario preparation for current experiments and for ITER. Work supported in part by the US DOE under DE-FG02-95ER54309 and DE-FC02-04ER54698.

  19. Multiscale Models for Reactive Transport in Porous Media

    NASA Astrophysics Data System (ADS)

    Tartakovsky, A. M.

    2012-12-01

    Under certain conditions, Darcy-scale reactive transport equations cannot provide sufficiently accurate predictions of multiphase flow and reactive transport. Pore-scale models are based on fundamental conservation laws and, in general, are more accurate than the Darcy-scale models. But, for domains of practical importance, number of unknowns in the pore-sale models may be on the order of billions or trillions and a direct solution of the pore-scale equations is often unfeasible even on modern super-computes. Several novel multiscale methods including a Langevin approach and a dimension reduction method based on a computational closure will be presented. The purpose of these methods is to provide an accurate description of the system averages while retaining critical pore-scale information. The advantages, range of applicability and limitations of the mentioned above multiscale methods will be discussed.

  20. A guide to properly select the defocusing distance for accurate solution of transport of intensity equation while testing aspheric surfaces

    NASA Astrophysics Data System (ADS)

    Soltani, Peyman; Darudi, Ahmad; Moradi, Ali Reza; Amiri, Javad; Nehmetallah, Georges

    2016-05-01

    In this paper, the Transport of Intensity Equation (TIE) for testing of an aspheric surface is verified experimentally. Using simulation, a proper defocus distance Δ𝑧 that leads to an accurate solution of TIE is estimated whenever the conic constant and configuration of the experiment are known. To verify this procedure a non-nulled experiment for testing an aspheric is used. For verification of the solution, the results are compared with the Shack-Hartmann sensor. The theoretical method and experimental results are compared to validate the results.

  1. An accurate theoretical description for electronic transport properties of single molecular junctions

    NASA Astrophysics Data System (ADS)

    Luo, Yi

    2002-03-01

    We have developed a new theoretical approach to characterize the electron transport process in molecular devices based on the elastic-scattering Green's function theory in connection with the hybrid density functional theory without using any fitting parameters. Two molecular devices with benzene-1,4-dithiol and octanedithiol molecules embedded between two gold electrodes have been studied. The calculated current-voltage characteristics are in very good agreement with existing experimental results reported by Reed et. al for benzene-1,4-dithiol [Science, 278(1997) 252] and by Cui et al. for octanedithiol [Science, 294(2001) 571]. Our approach is very straightforward and can apply to quite large systems. Most importantly, it provides a reliable way to design and optimize molecular devices theoretically, thereby avoiding extremely difficult, time consuming laboratory tests.

  2. Accurate dose assessment system for an exposed person utilising radiation transport calculation codes in emergency response to a radiological accident.

    PubMed

    Takahashi, F; Shigemori, Y; Seki, A

    2009-01-01

    A system has been developed to assess radiation dose distribution inside the body of exposed persons in a radiological accident by utilising radiation transport calculation codes-MCNP and MCNPX. The system consists mainly of two parts, pre-processor and post-processor of the radiation transport calculation. Programs for the pre-processor are used to set up a 'problem-dependent' input file, which defines the accident condition and dosimetric quantities to be estimated. The program developed for the post-processor part can effectively indicate dose information based upon the output file of the code. All of the programs in the dosimetry system can be executed with a generally used personal computer and accurately give the dose profile to an exposed person in a radiological accident without complicated procedures. An experiment using a physical phantom was carried out to verify the availability of the dosimetry system with the developed programs in a gamma ray irradiation field.

  3. Accurate ab initio potential for the krypton dimer and transport properties of the low-density krypton gas.

    PubMed

    Waldrop, Jonathan M; Song, Bo; Patkowski, Konrad; Wang, Xiaopo

    2015-05-28

    A new highly accurate potential energy curve for the krypton dimer was constructed using coupled-cluster calculations up to the singles, doubles, triples, and perturbative quadruples level, including corrections for core-core and core-valence correlation and for relativistic effects. The ab initio data points were fitted to an analytic potential which was used to compute the most important transport properties of the krypton gas. The viscosity, thermal conductivity, self-diffusion coefficient, and thermal diffusion factor were calculated by the kinetic theory at low density and temperatures from 116 to 5000 K. The comparisons with literature experimental data as well as with values from other pair potentials indicate that our new potential is superior to all previous ones. The transport property values computed in this work are recommended as standard values over the complete temperature range.

  4. Comparisons of Accurate Electronic, Transport, and Bulk Properties of XP (X = B, Al, Ga, In)

    NASA Astrophysics Data System (ADS)

    Malozovsky, Yuriy; Ejembi, John; Saliev, Azizjon; Franklin, Lashounda; Bagayoko, Diola

    We present comparisons of results from ab-initio,self-consistent local density approximation (LDA) calculations of accurate, electronic and related properties of zinc blende XP (X =B, Al, Ga, In) phosphides. We implemented the linear combination of atomic orbitals following the Bagayoko, Zhao, and Williams (BZW) method as enhanced by Ekuma and Franklin (BZW-EF). Consequently, our results have the full physical content of DFT and agree very well with corresponding experimental ones [AIP Advances, 4, 127104 (2014)]. Our calculated, indirect band gap of 2.02 eV for BP, 2.56 eV for AlP, and of 2.29 eV for GaP, from Γ to X-point, are in excellent agreement with experimental values. Our calculated direct band gap of 1.43 eV, at Γ, for InP is also in an excellent agreement with experimental value. We discuss calculated electron and hole effective masses, total (DOS) and partial (pDOS) densities of states, and the bulk modulus of these phosphides. Acknowledgments: NSF and the Louisiana Board of Regents, LASiGMA [Award Nos. EPS- 1003897, NSF (2010-15)-RII-SUBR] and NSF HRD-1002541, DOE - National, Nuclear Security Administration (NNSA) (Award Nos. DE-NA0001861 and DE- NA0002630), LaSPACE, and LONI-SUBR.

  5. Risk management model in road transport systems

    NASA Astrophysics Data System (ADS)

    Sakhapov, R. L.; Nikolaeva, R. V.; Gatiyatullin, M. H.; Makhmutov, M. M.

    2016-08-01

    The article presents the results of a study of road safety indicators that influence the development and operation of the transport system. Road safety is considered as a continuous process of risk management. Authors constructed a model that relates the social risks of a major road safety indicator - the level of motorization. The model gives a fairly accurate assessment of the level of social risk for any given level of motorization. Authors calculated the dependence of the level of socio-economic costs of accidents and injured people in them. The applicability of the concept of socio-economic damage is caused by the presence of a linear relationship between the natural and economic indicators damage from accidents. The optimization of social risk is reduced to finding the extremum of the objective function that characterizes the economic effect of the implementation of measures to improve safety. The calculations make it possible to maximize the net present value, depending on the costs of improving road safety, taking into account socio-economic damage caused by accidents. The proposed econometric models make it possible to quantify the efficiency of the transportation system, allow to simulate the change in road safety indicators.

  6. Coupled transport in rotor models

    NASA Astrophysics Data System (ADS)

    Iubini, S.; Lepri, S.; Livi, R.; Politi, A.

    2016-08-01

    Steady nonequilibrium states are investigated in a one-dimensional setup in the presence of two thermodynamic currents. Two paradigmatic nonlinear oscillators models are investigated: an XY chain and the discrete nonlinear Schrödinger equation. Their distinctive feature is that the relevant variable is an angle in both cases. We point out the importance of clearly distinguishing between energy and heat flux. In fact, even in the presence of a vanishing Seebeck coefficient, a coupling between (angular) momentum and energy arises, mediated by the unavoidable presence of a coherent energy flux. Such a contribution is the result of the ‘advection’ induced by the position-dependent angular velocity. As a result, in the XY model, the knowledge of the two diagonal elements of the Onsager matrix suffices to reconstruct its transport properties. The analysis of the nonequilibrium steady states finally allows to strengthen the connection between the two models.

  7. Accurate Electronic, Transport, and Bulk Properties of Wurtzite Beryllium Oxide (BeO)

    NASA Astrophysics Data System (ADS)

    Bamba, Cheick Oumar; Malozovsky, Yuriy; Franklin, Lashounda; Bagayoko, Diola

    We present ab-initio, self-consistent density functional theory (DFT) description of electronic, transport, and bulk properties of wurtzite Beryllium oxide (w-BeO). We used a local density approximation potential (LDA) and the linear combination of atomic orbitals (LCOA) formalism. Our implementation of the Bagayoko, Zhao, and Williams (BZW) method, as enhanced by Ekuma and Franklin (BZW-EF), ensures the full, physical content of our local density approximation (LDA) calculations - as per the derivation of DFT [AIP Advances, 4, 127104 (2014) We report the band gap, density of states, partial density of state, effective masses, and the bulk modulus. Our calculated band gap of 10.29 eV, using an experimental, room temperature lattice constant of 2.6979 A at room temperature is in agreement with the experimental value of 10.6 eV. Acknowledgments:This work was funded in part the US National Science Foundation [NSF, Award Nos. EPS-1003897, NSF (2010-2015)-RII-SUBR, and HRD-1002541], the US Department of Energy, National Nuclear Security Administration (NNSA, Award No. DE-NA0002630), LaSPACE, and LONI-SUBR.

  8. Modeling Biodegradation and Reactive Transport: Analytical and Numerical Models

    SciTech Connect

    Sun, Y; Glascoe, L

    2005-06-09

    The computational modeling of the biodegradation of contaminated groundwater systems accounting for biochemical reactions coupled to contaminant transport is a valuable tool for both the field engineer/planner with limited computational resources and the expert computational researcher less constrained by time and computer power. There exists several analytical and numerical computer models that have been and are being developed to cover the practical needs put forth by users to fulfill this spectrum of computational demands. Generally, analytical models provide rapid and convenient screening tools running on very limited computational power, while numerical models can provide more detailed information with consequent requirements of greater computational time and effort. While these analytical and numerical computer models can provide accurate and adequate information to produce defensible remediation strategies, decisions based on inadequate modeling output or on over-analysis can have costly and risky consequences. In this chapter we consider both analytical and numerical modeling approaches to biodegradation and reactive transport. Both approaches are discussed and analyzed in terms of achieving bioremediation goals, recognizing that there is always a tradeoff between computational cost and the resolution of simulated systems.

  9. Creation of Anatomically Accurate Computer-Aided Design (CAD) Solid Models from Medical Images

    NASA Technical Reports Server (NTRS)

    Stewart, John E.; Graham, R. Scott; Samareh, Jamshid A.; Oberlander, Eric J.; Broaddus, William C.

    1999-01-01

    Most surgical instrumentation and implants used in the world today are designed with sophisticated Computer-Aided Design (CAD)/Computer-Aided Manufacturing (CAM) software. This software automates the mechanical development of a product from its conceptual design through manufacturing. CAD software also provides a means of manipulating solid models prior to Finite Element Modeling (FEM). Few surgical products are designed in conjunction with accurate CAD models of human anatomy because of the difficulty with which these models are created. We have developed a novel technique that creates anatomically accurate, patient specific CAD solids from medical images in a matter of minutes.

  10. Model transport directional solidification apparatus

    SciTech Connect

    Mason, J.T.; Eshelman, M.A.

    1986-07-01

    A model transport directional solidification apparatus is described. It has three functional components, each of which are described: the temperature gradient stage, the motor and drive mechanism, and the measuring systems. A small amount of sample is held between two glass slides on the temperature gradient stage so that the portion of sample in the hot chamber is molten and the portion in the cold chamber is solidified. Conditions are set so that the solid-liquid interface occurs in the gap between the chambers and can be observed through the microscope system. In-situ directional solidification is observed by driving the sample from the hot chamber to the cold chamber and observing the solidification process as it occurs. (LEW)

  11. Modeling Transport Through Synthetic Nanopores

    PubMed Central

    Aksimentiev, Aleksei; Brunner, Robert K.; Cruz-Chú, Eduardo; Comer, Jeffrey; Schulten, Klaus

    2011-01-01

    Nanopores in thin synthetic membranes have emerged as convenient tools for high-throughput single-molecule manipulation and analysis. Because of their small sizes and their ability to selectively transport solutes through otherwise impermeable membranes, nanopores have numerous potential applications in nanobiotechnology. For most applications, properties of the nanopore systems have to be characterize at the atomic level, which is currently beyond the limit of experimental methods. Molecular dynamics (MD) simulations can provide the desired information, however several technical challenges have to be met before this method can be applied to synthetic nanopore systems. Here, we highlight our recent work on modeling synthetic nanopores of the most common types. First, we describe a novel graphical tool for setting up all-atom systems incorporating inorganic materials and biomolecules. Next, we illustrate the application of the MD method for silica, silicon nitride, and polyethylene terephthalate nanopores. Following that, we describe a method for modeling synthetic surfaces using a bias potential. Future directions for tool development and nanopore modeling are briefly discussed at the end of this article. PMID:21909347

  12. Continuous Modeling of Calcium Transport Through Biological Membranes

    NASA Astrophysics Data System (ADS)

    Jasielec, J. J.; Filipek, R.; Szyszkiewicz, K.; Sokalski, T.; Lewenstam, A.

    2016-08-01

    In this work an approach to the modeling of the biological membranes where a membrane is treated as a continuous medium is presented. The Nernst-Planck-Poisson model including Poisson equation for electric potential is used to describe transport of ions in the mitochondrial membrane—the interface which joins mitochondrial matrix with cellular cytosis. The transport of calcium ions is considered. Concentration of calcium inside the mitochondrion is not known accurately because different analytical methods give dramatically different results. We explain mathematically these differences assuming the complexing reaction inside mitochondrion and the existence of the calcium set-point (concentration of calcium in cytosis below which calcium stops entering the mitochondrion).

  13. Fast and accurate calculation of dilute quantum gas using Uehling-Uhlenbeck model equation

    NASA Astrophysics Data System (ADS)

    Yano, Ryosuke

    2017-02-01

    The Uehling-Uhlenbeck (U-U) model equation is studied for the fast and accurate calculation of a dilute quantum gas. In particular, the direct simulation Monte Carlo (DSMC) method is used to solve the U-U model equation. DSMC analysis based on the U-U model equation is expected to enable the thermalization to be accurately obtained using a small number of sample particles and the dilute quantum gas dynamics to be calculated in a practical time. Finally, the applicability of DSMC analysis based on the U-U model equation to the fast and accurate calculation of a dilute quantum gas is confirmed by calculating the viscosity coefficient of a Bose gas on the basis of the Green-Kubo expression and the shock layer of a dilute Bose gas around a cylinder.

  14. An efficient and accurate model of the coax cable feeding structure for FEM simulations

    NASA Technical Reports Server (NTRS)

    Gong, Jian; Volakis, John L.

    1995-01-01

    An efficient and accurate coax cable feed model is proposed for microstrip or cavity-backed patch antennas in the context of a hybrid finite element method (FEM). A TEM mode at the cavity-cable junction is assumed for the FEM truncation and system excitation. Of importance in this implementation is that the cavity unknowns are related to the model fields by enforcing an equipotential condition rather than field continuity. This scheme proved quite accurate and may be applied to other decomposed systems as a connectivity constraint. Comparisons of our predictions with input impedance measurements are presented and demonstrate the substantially improved accuracy of the proposed model.

  15. Bayesian parameter estimation of a k-ε model for accurate jet-in-crossflow simulations

    SciTech Connect

    Ray, Jaideep; Lefantzi, Sophia; Arunajatesan, Srinivasan; Dechant, Lawrence

    2016-05-31

    Reynolds-averaged Navier–Stokes models are not very accurate for high-Reynolds-number compressible jet-in-crossflow interactions. The inaccuracy arises from the use of inappropriate model parameters and model-form errors in the Reynolds-averaged Navier–Stokes model. In this study, the hypothesis is pursued that Reynolds-averaged Navier–Stokes predictions can be significantly improved by using parameters inferred from experimental measurements of a supersonic jet interacting with a transonic crossflow.

  16. RADIONUCLIDE TRANSPORT MODELS UNDER AMBIENT CONDITIONS

    SciTech Connect

    S. Magnuson

    2004-11-01

    The purpose of this model report is to document the unsaturated zone (UZ) radionuclide transport model, which evaluates, by means of three-dimensional numerical models, the transport of radioactive solutes and colloids in the UZ, under ambient conditions, from the repository horizon to the water table at Yucca Mountain, Nevada.

  17. Langevin model for reactive transport in porous media

    NASA Astrophysics Data System (ADS)

    Tartakovsky, Alexandre M.

    2010-08-01

    Existing continuum models for reactive transport in porous media tend to overestimate the extent of solute mixing and mixing-controlled reactions because the continuum models treat both the mechanical and diffusive mixings as an effective Fickian process. Recently, we have proposed a phenomenological Langevin model for flow and transport in porous media [A. M. Tartakovsky, D. M. Tartakovsky, and P. Meakin, Phys. Rev. Lett. 101, 044502 (2008)10.1103/PhysRevLett.101.044502]. In the Langevin model, the fluid flow in a porous continuum is governed by a combination of a Langevin equation and a continuity equation. Pore-scale velocity fluctuations, the source of mechanical dispersion, are represented by the white noise. The advective velocity (the solution of the Langevin flow equation) causes the mechanical dispersion of a solute. Molecular diffusion and sub-pore-scale Taylor-type dispersion are modeled by an effective stochastic advection-diffusion equation. Here, we propose a method for parameterization of the model for a synthetic porous medium, and we use the model to simulate multicomponent reactive transport in the porous medium. The detailed comparison of the results of the Langevin model with pore-scale and continuum (Darcy) simulations shows that: (1) for a wide range of Peclet numbers the Langevin model predicts the mass of reaction product more accurately than the Darcy model; (2) for small Peclet numbers predictions of both the Langevin and the Darcy models agree well with a prediction of the pore-scale model; and (3) the accuracy of the Langevin and Darcy model deteriorates with the increasing Peclet number but the accuracy of the Langevin model decreases more slowly than the accuracy of the Darcy model. These results show that the separate treatment of advective and diffusive mixing in the stochastic transport model is more accurate than the classical advection-dispersion theory, which uses a single effective diffusion coefficient (the dispersion

  18. RESEARCH ACTIVITIES AT U.S. GOVERNMENT AGENCIES IN SUBSURFACE REACTIVE TRANSPORT MODELING

    EPA Science Inventory

    The fate of contaminants in the environment is controlled by both chemical reactions and transport phenomena in the subsurface. Our ability to understand the significance of these processes over time requires an accurate conceptual model that incorporates the various mechanisms ...

  19. Improving light propagation Monte Carlo simulations with accurate 3D modeling of skin tissue

    SciTech Connect

    Paquit, Vincent C; Price, Jeffery R; Meriaudeau, Fabrice; Tobin Jr, Kenneth William

    2008-01-01

    In this paper, we present a 3D light propagation model to simulate multispectral reflectance images of large skin surface areas. In particular, we aim to simulate more accurately the effects of various physiological properties of the skin in the case of subcutaneous vein imaging compared to existing models. Our method combines a Monte Carlo light propagation model, a realistic three-dimensional model of the skin using parametric surfaces and a vision system for data acquisition. We describe our model in detail, present results from the Monte Carlo modeling and compare our results with those obtained with a well established Monte Carlo model and with real skin reflectance images.

  20. Accurate determination of electronic transport properties of silicon wafers by nonlinear photocarrier radiometry with multiple pump beam sizes

    SciTech Connect

    Wang, Qian; Li, Bincheng

    2015-12-07

    In this paper, photocarrier radiometry (PCR) technique with multiple pump beam sizes is employed to determine simultaneously the electronic transport parameters (the carrier lifetime, the carrier diffusion coefficient, and the front surface recombination velocity) of silicon wafers. By employing the multiple pump beam sizes, the influence of instrumental frequency response on the multi-parameter estimation is totally eliminated. A nonlinear PCR model is developed to interpret the PCR signal. Theoretical simulations are performed to investigate the uncertainties of the estimated parameter values by investigating the dependence of a mean square variance on the corresponding transport parameters and compared to that obtained by the conventional frequency-scan method, in which only the frequency dependences of the PCR amplitude and phase are recorded at single pump beam size. Simulation results show that the proposed multiple-pump-beam-size method can improve significantly the accuracy of the determination of the electronic transport parameters. Comparative experiments with a p-type silicon wafer with resistivity 0.1–0.2 Ω·cm are performed, and the electronic transport properties are determined simultaneously. The estimated uncertainties of the carrier lifetime, diffusion coefficient, and front surface recombination velocity are approximately ±10.7%, ±8.6%, and ±35.4% by the proposed multiple-pump-beam-size method, which is much improved than ±15.9%, ±29.1%, and >±50% by the conventional frequency-scan method. The transport parameters determined by the proposed multiple-pump-beam-size PCR method are in good agreement with that obtained by a steady-state PCR imaging technique.

  1. Accurate modeling of high-repetition rate ultrashort pulse amplification in optical fibers

    PubMed Central

    Lindberg, Robert; Zeil, Peter; Malmström, Mikael; Laurell, Fredrik; Pasiskevicius, Valdas

    2016-01-01

    A numerical model for amplification of ultrashort pulses with high repetition rates in fiber amplifiers is presented. The pulse propagation is modeled by jointly solving the steady-state rate equations and the generalized nonlinear Schrödinger equation, which allows accurate treatment of nonlinear and dispersive effects whilst considering arbitrary spatial and spectral gain dependencies. Comparison of data acquired by using the developed model and experimental results prove to be in good agreement. PMID:27713496

  2. Towards more accurate wind and solar power prediction by improving NWP model physics

    NASA Astrophysics Data System (ADS)

    Steiner, Andrea; Köhler, Carmen; von Schumann, Jonas; Ritter, Bodo

    2014-05-01

    nighttime to well mixed conditions during the day presents a big challenge to NWP models. Fast decrease and successive increase in hub-height wind speed after sunrise, and the formation of nocturnal low level jets will be discussed. For PV, the life cycle of low stratus clouds and fog is crucial. Capturing these processes correctly depends on the accurate simulation of diffusion or vertical momentum transport and the interaction with other atmospheric and soil processes within the numerical weather model. Results from Single Column Model simulations and 3d case studies will be presented. Emphasis is placed on wind forecasts; however, some references to highlights concerning the PV-developments will also be given. *) ORKA: Optimierung von Ensembleprognosen regenerativer Einspeisung für den Kürzestfristbereich am Anwendungsbeispiel der Netzsicherheitsrechnungen **) EWeLiNE: Erstellung innovativer Wetter- und Leistungsprognosemodelle für die Netzintegration wetterabhängiger Energieträger, www.projekt-eweline.de

  3. Modelling aeolian sand transport using a dynamic mass balancing approach

    NASA Astrophysics Data System (ADS)

    Mayaud, Jerome R.; Bailey, Richard M.; Wiggs, Giles F. S.; Weaver, Corinne M.

    2017-03-01

    Knowledge of the changing rate of sediment flux in space and time is essential for quantifying surface erosion and deposition in desert landscapes. Whilst many aeolian studies have relied on time-averaged parameters such as wind velocity (U) and wind shear velocity (u*) to determine sediment flux, there is increasing field evidence that high-frequency turbulence is an important driving force behind the entrainment and transport of sand. At this scale of analysis, inertia in the saltation system causes changes in sediment transport to lag behind de/accelerations in flow. However, saltation inertia has yet to be incorporated into a functional sand transport model that can be used for predictive purposes. In this study, we present a new transport model that dynamically balances the sand mass being transported in the wind flow. The 'dynamic mass balance' (DMB) model we present accounts for high-frequency variations in the horizontal (u) component of wind flow, as saltation is most strongly associated with the positive u component of the wind. The performance of the DMB model is tested by fitting it to two field-derived (Namibia's Skeleton Coast) datasets of wind velocity and sediment transport: (i) a 10-min (10 Hz measurement resolution) dataset; (ii) a 2-h (1 Hz measurement resolution) dataset. The DMB model is shown to outperform two existing models that rely on time-averaged wind velocity data (e.g. Radok, 1977; Dong et al., 2003), when predicting sand transport over the two experiments. For all measurement averaging intervals presented in this study (10 Hz-10 min), the DMB model predicted total saltation count to within at least 0.48%, whereas the Radok and Dong models over- or underestimated total count by up to 5.50% and 20.53% respectively. The DMB model also produced more realistic (less 'peaky') time series of sand flux than the other two models, and a more accurate distribution of sand flux data. The best predictions of total sand transport are achieved using

  4. Whole muscle length-tension relationships are accurately modeled as scaled sarcomeres in rabbit hindlimb muscles.

    PubMed

    Winters, Taylor M; Takahashi, Mitsuhiko; Lieber, Richard L; Ward, Samuel R

    2011-01-04

    An a priori model of the whole active muscle length-tension relationship was constructed utilizing only myofilament length and serial sarcomere number for rabbit tibialis anterior (TA), extensor digitorum longus (EDL), and extensor digitorum II (EDII) muscles. Passive tension was modeled with a two-element Hill-type model. Experimental length-tension relations were then measured for each of these muscles and compared to predictions. The model was able to accurately capture the active-tension characteristics of experimentally-measured data for all muscles (ICC=0.88 ± 0.03). Despite their varied architecture, no differences in predicted versus experimental correlations were observed among muscles. In addition, the model demonstrated that excursion, quantified by full-width-at-half-maximum (FWHM) of the active length-tension relationship, scaled linearly (slope=0.68) with normalized muscle fiber length. Experimental and theoretical FWHM values agreed well with an intraclass correlation coefficient of 0.99 (p<0.001). In contrast to active tension, the passive tension model deviated from experimentally-measured values and thus, was not an accurate predictor of passive tension (ICC=0.70 ± 0.07). These data demonstrate that modeling muscle as a scaled sarcomere provides accurate active functional but not passive functional predictions for rabbit TA, EDL, and EDII muscles and call into question the need for more complex modeling assumptions often proposed.

  5. Neutron Transport Models and Methods for HZETRN and Coupling to Low Energy Light Ion Transport

    NASA Technical Reports Server (NTRS)

    Blattnig, S.R.; Slaba, T.C.; Heinbockel, J.H.

    2008-01-01

    Exposure estimates inside space vehicles, surface habitats, and high altitude aircraft exposed to space radiation are highly influenced by secondary neutron production. The deterministic transport code HZETRN has been identified as a reliable and efficient tool for such studies, but improvements to the underlying transport models and numerical methods are still necessary. In this paper, the forward-backward (FB) and directionally coupled forward-backward (DC) neutron transport models are derived, numerical methods for the FB model are reviewed, and a computationally efficient numerical solution is presented for the DC model. Both models are compared to the Monte Carlo codes HETCHEDS and FLUKA, and the DC model is shown to agree closely with the Monte Carlo results. Finally, it is found in the development of either model that the decoupling of low energy neutrons from the light ion (A<4) transport procedure adversely affects low energy light ion fluence spectra and exposure quantities. A first order correction is presented to resolve the problem, and it is shown to be both accurate and efficient.

  6. Two-point model for divertor transport

    SciTech Connect

    Galambos, J.D.; Peng, Y.K.M.

    1984-04-01

    Plasma transport along divertor field lines was investigated using a two-point model. This treatment requires considerably less effort to find solutions to the transport equations than previously used one-dimensional (1-D) models and is useful for studying general trends. It also can be a valuable tool for benchmarking more sophisticated models. The model was used to investigate the possibility of operating in the so-called high density, low temperature regime.

  7. Accurate protein structure modeling using sparse NMR data and homologous structure information.

    PubMed

    Thompson, James M; Sgourakis, Nikolaos G; Liu, Gaohua; Rossi, Paolo; Tang, Yuefeng; Mills, Jeffrey L; Szyperski, Thomas; Montelione, Gaetano T; Baker, David

    2012-06-19

    While information from homologous structures plays a central role in X-ray structure determination by molecular replacement, such information is rarely used in NMR structure determination because it can be incorrect, both locally and globally, when evolutionary relationships are inferred incorrectly or there has been considerable evolutionary structural divergence. Here we describe a method that allows robust modeling of protein structures of up to 225 residues by combining (1)H(N), (13)C, and (15)N backbone and (13)Cβ chemical shift data, distance restraints derived from homologous structures, and a physically realistic all-atom energy function. Accurate models are distinguished from inaccurate models generated using incorrect sequence alignments by requiring that (i) the all-atom energies of models generated using the restraints are lower than models generated in unrestrained calculations and (ii) the low-energy structures converge to within 2.0 Å backbone rmsd over 75% of the protein. Benchmark calculations on known structures and blind targets show that the method can accurately model protein structures, even with very remote homology information, to a backbone rmsd of 1.2-1.9 Å relative to the conventional determined NMR ensembles and of 0.9-1.6 Å relative to X-ray structures for well-defined regions of the protein structures. This approach facilitates the accurate modeling of protein structures using backbone chemical shift data without need for side-chain resonance assignments and extensive analysis of NOESY cross-peak assignments.

  8. Uncertainty in tsunami sediment transport modeling

    USGS Publications Warehouse

    Jaffe, Bruce E.; Goto, Kazuhisa; Sugawara, Daisuke; Gelfenbaum, Guy R.; La Selle, SeanPaul M.

    2016-01-01

    Erosion and deposition from tsunamis record information about tsunami hydrodynamics and size that can be interpreted to improve tsunami hazard assessment. We explore sources and methods for quantifying uncertainty in tsunami sediment transport modeling. Uncertainty varies with tsunami, study site, available input data, sediment grain size, and model. Although uncertainty has the potential to be large, published case studies indicate that both forward and inverse tsunami sediment transport models perform well enough to be useful for deciphering tsunami characteristics, including size, from deposits. New techniques for quantifying uncertainty, such as Ensemble Kalman Filtering inversion, and more rigorous reporting of uncertainties will advance the science of tsunami sediment transport modeling. Uncertainty may be decreased with additional laboratory studies that increase our understanding of the semi-empirical parameters and physics of tsunami sediment transport, standardized benchmark tests to assess model performance, and development of hybrid modeling approaches to exploit the strengths of forward and inverse models.

  9. Charge-transport model for conducting polymers

    NASA Astrophysics Data System (ADS)

    Dongmin Kang, Stephen; Jeffrey Snyder, G.

    2016-11-01

    The growing technological importance of conducting polymers makes the fundamental understanding of their charge transport extremely important for materials and process design. Various hopping and mobility edge transport mechanisms have been proposed, but their experimental verification is limited to poor conductors. Now that advanced organic and polymer semiconductors have shown high conductivity approaching that of metals, the transport mechanism should be discernible by modelling the transport like a semiconductor with a transport edge and a transport parameter s. Here we analyse the electrical conductivity and Seebeck coefficient together and determine that most polymers (except possibly PEDOT:tosylate) have s = 3 and thermally activated conductivity, whereas s = 1 and itinerant conductivity is typically found in crystalline semiconductors and metals. The different transport in polymers may result from the percolation of charge carriers from conducting ordered regions through poorly conducting disordered regions, consistent with what has been expected from structural studies.

  10. Fast and accurate focusing analysis of large photon sieve using pinhole ring diffraction model.

    PubMed

    Liu, Tao; Zhang, Xin; Wang, Lingjie; Wu, Yanxiong; Zhang, Jizhen; Qu, Hemeng

    2015-06-10

    In this paper, we developed a pinhole ring diffraction model for the focusing analysis of a large photon sieve. Instead of analyzing individual pinholes, we discuss the focusing of all of the pinholes in a single ring. An explicit equation for the diffracted field of individual pinhole ring has been proposed. We investigated the validity range of this generalized model and analytically describe the sufficient conditions for the validity of this pinhole ring diffraction model. A practical example and investigation reveals the high accuracy of the pinhole ring diffraction model. This simulation method could be used for fast and accurate focusing analysis of a large photon sieve.

  11. Dissipative particle dynamics model for colloid transport in porous media

    SciTech Connect

    Pan, W.; Tartakovsky, A. M.

    2013-08-01

    We present that the transport of colloidal particles in porous media can be effectively modeled with a new formulation of dissipative particle dynamics, which augments standard DPD with non-central dissipative shear forces between particles while preserving angular momentum. Our previous studies have demonstrated that the new formulation is able to capture accurately the drag forces as well as the drag torques on colloidal particles that result from the hydrodynamic retardation effect. In the present work, we use the new formulation to study the contact efficiency in colloid filtration in saturated porous media. Note that the present model include all transport mechanisms simultaneously, including gravitational sedimentation, interception and Brownian diffusion. Our results of contact efficiency show a good agreement with the predictions of the correlation equation proposed by Tufenkji and EliMelech, which also incorporate all transport mechanisms simultaneously without the additivity assumption.

  12. Development of modified cable models to simulate accurate neuronal active behaviors

    PubMed Central

    2014-01-01

    In large network and single three-dimensional (3-D) neuron simulations, high computing speed dictates using reduced cable models to simulate neuronal firing behaviors. However, these models are unwarranted under active conditions and lack accurate representation of dendritic active conductances that greatly shape neuronal firing. Here, realistic 3-D (R3D) models (which contain full anatomical details of dendrites) of spinal motoneurons were systematically compared with their reduced single unbranched cable (SUC, which reduces the dendrites to a single electrically equivalent cable) counterpart under passive and active conditions. The SUC models matched the R3D model's passive properties but failed to match key active properties, especially active behaviors originating from dendrites. For instance, persistent inward currents (PIC) hysteresis, frequency-current (FI) relationship secondary range slope, firing hysteresis, plateau potential partial deactivation, staircase currents, synaptic current transfer ratio, and regional FI relationships were not accurately reproduced by the SUC models. The dendritic morphology oversimplification and lack of dendritic active conductances spatial segregation in the SUC models caused significant underestimation of those behaviors. Next, SUC models were modified by adding key branching features in an attempt to restore their active behaviors. The addition of primary dendritic branching only partially restored some active behaviors, whereas the addition of secondary dendritic branching restored most behaviors. Importantly, the proposed modified models successfully replicated the active properties without sacrificing model simplicity, making them attractive candidates for running R3D single neuron and network simulations with accurate firing behaviors. The present results indicate that using reduced models to examine PIC behaviors in spinal motoneurons is unwarranted. PMID:25277743

  13. Anomalous transport modelling of tokamak plasmas

    SciTech Connect

    Kinsey, J.; Singer, C.; Malone, G.; Tiouririne, N.

    1992-12-31

    Theory based transport simulations of DIII-D, JET, ITER are compared to experimental data using a combination of anamolous transport models. The Multiple-mode Transport Model is calibrated to a give set of L-mode and H-mode discharges with an emphasis on testing the adequacy of anomalous flux contributions from drift/{eta}{sub i} and resistive ballooning mode theories. A survey of possible additions and/or alternatives to the model from recent theories on neoclassical MHD effects, hot ion modes, circulating electron modes, and high-m tearing modes is also included.

  14. Anomalous transport modelling of tokamak plasmas

    SciTech Connect

    Kinsey, J.; Singer, C.; Malone, G.; Tiouririne, N.

    1992-01-01

    Theory based transport simulations of DIII-D, JET, ITER are compared to experimental data using a combination of anamolous transport models. The Multiple-mode Transport Model is calibrated to a give set of L-mode and H-mode discharges with an emphasis on testing the adequacy of anomalous flux contributions from drift/[eta][sub i] and resistive ballooning mode theories. A survey of possible additions and/or alternatives to the model from recent theories on neoclassical MHD effects, hot ion modes, circulating electron modes, and high-m tearing modes is also included.

  15. VIRTUS, a model of virus transport in unsaturated soils.

    PubMed Central

    Yates, M V; Ouyang, Y

    1992-01-01

    As a result of the recently proposed mandatory groundwater disinfection requirements to inactivate viruses in potable water supplies, there has been increasing interest in virus fate and transport in the subsurface. Several models have been developed to predict the fate of viruses in groundwater, but few include transport in the unsaturated zone and all require a constant virus inactivation rate. These are serious limitations in the models, as it has been well documented that considerable virus removal occurs in the unsaturated zone and that the inactivation rate of viruses is dependent on environmental conditions. The purpose of this research was to develop a predictive model of virus fate and transport in unsaturated soils that allows the virus inactivation rate to vary on the basis of changes in soil temperature. The model was developed on the basis of the law of mass conservation of a contaminant in porous media and couples the flows of water, viruses, and heat through the soil. Model predictions were compared with measured data of virus transport in laboratory column studies and, with the exception of one point, were within the 95% confidence limits of the measured concentrations. The model should be a useful tool for anyone wishing to estimate the number of viruses entering groundwater after traveling through the soil from a contamination source. In addition, model simulations were performed to identify parameters that have a large effect on the results. This information can be used to help design experiments so that important variables are measured accurately. PMID:1622230

  16. Accurate path integration in continuous attractor network models of grid cells.

    PubMed

    Burak, Yoram; Fiete, Ila R

    2009-02-01

    Grid cells in the rat entorhinal cortex display strikingly regular firing responses to the animal's position in 2-D space and have been hypothesized to form the neural substrate for dead-reckoning. However, errors accumulate rapidly when velocity inputs are integrated in existing models of grid cell activity. To produce grid-cell-like responses, these models would require frequent resets triggered by external sensory cues. Such inadequacies, shared by various models, cast doubt on the dead-reckoning potential of the grid cell system. Here we focus on the question of accurate path integration, specifically in continuous attractor models of grid cell activity. We show, in contrast to previous models, that continuous attractor models can generate regular triangular grid responses, based on inputs that encode only the rat's velocity and heading direction. We consider the role of the network boundary in the integration performance of the network and show that both periodic and aperiodic networks are capable of accurate path integration, despite important differences in their attractor manifolds. We quantify the rate at which errors in the velocity integration accumulate as a function of network size and intrinsic noise within the network. With a plausible range of parameters and the inclusion of spike variability, our model networks can accurately integrate velocity inputs over a maximum of approximately 10-100 meters and approximately 1-10 minutes. These findings form a proof-of-concept that continuous attractor dynamics may underlie velocity integration in the dorsolateral medial entorhinal cortex. The simulations also generate pertinent upper bounds on the accuracy of integration that may be achieved by continuous attractor dynamics in the grid cell network. We suggest experiments to test the continuous attractor model and differentiate it from models in which single cells establish their responses independently of each other.

  17. Can phenological models predict tree phenology accurately under climate change conditions?

    NASA Astrophysics Data System (ADS)

    Chuine, Isabelle; Bonhomme, Marc; Legave, Jean Michel; García de Cortázar-Atauri, Inaki; Charrier, Guillaume; Lacointe, André; Améglio, Thierry

    2014-05-01

    The onset of the growing season of trees has been globally earlier by 2.3 days/decade during the last 50 years because of global warming and this trend is predicted to continue according to climate forecast. The effect of temperature on plant phenology is however not linear because temperature has a dual effect on bud development. On one hand, low temperatures are necessary to break bud dormancy, and on the other hand higher temperatures are necessary to promote bud cells growth afterwards. Increasing phenological changes in temperate woody species have strong impacts on forest trees distribution and productivity, as well as crops cultivation areas. Accurate predictions of trees phenology are therefore a prerequisite to understand and foresee the impacts of climate change on forests and agrosystems. Different process-based models have been developed in the last two decades to predict the date of budburst or flowering of woody species. They are two main families: (1) one-phase models which consider only the ecodormancy phase and make the assumption that endodormancy is always broken before adequate climatic conditions for cell growth occur; and (2) two-phase models which consider both the endodormancy and ecodormancy phases and predict a date of dormancy break which varies from year to year. So far, one-phase models have been able to predict accurately tree bud break and flowering under historical climate. However, because they do not consider what happens prior to ecodormancy, and especially the possible negative effect of winter temperature warming on dormancy break, it seems unlikely that they can provide accurate predictions in future climate conditions. It is indeed well known that a lack of low temperature results in abnormal pattern of bud break and development in temperate fruit trees. An accurate modelling of the dormancy break date has thus become a major issue in phenology modelling. Two-phases phenological models predict that global warming should delay

  18. Final Report for "Accurate Numerical Models of the Secondary Electron Yield from Grazing-incidence Collisions".

    SciTech Connect

    Seth A Veitzer

    2008-10-21

    Effects of stray electrons are a main factor limiting performance of many accelerators. Because heavy-ion fusion (HIF) accelerators will operate in regimes of higher current and with walls much closer to the beam than accelerators operating today, stray electrons might have a large, detrimental effect on the performance of an HIF accelerator. A primary source of stray electrons is electrons generated when halo ions strike the beam pipe walls. There is some research on these types of secondary electrons for the HIF community to draw upon, but this work is missing one crucial ingredient: the effect of grazing incidence. The overall goal of this project was to develop the numerical tools necessary to accurately model the effect of grazing incidence on the behavior of halo ions in a HIF accelerator, and further, to provide accurate models of heavy ion stopping powers with applications to ICF, WDM, and HEDP experiments.

  19. Polar auxin transport: models and mechanisms.

    PubMed

    van Berkel, Klaartje; de Boer, Rob J; Scheres, Ben; ten Tusscher, Kirsten

    2013-06-01

    Spatial patterns of the hormone auxin are important drivers of plant development. The observed feedback between the active, directed transport that generates auxin patterns and the auxin distribution that influences transport orientation has rendered this a popular subject for modelling studies. Here we propose a new mathematical framework for the analysis of polar auxin transport and present a detailed mathematical analysis of published models. We show that most models allow for self-organised patterning for similar biological assumptions, and find that the pattern generated is typically unidirectional, unless additional assumptions or mechanisms are incorporated. Our analysis thus suggests that current models cannot explain the bidirectional fountain-type patterns found in plant meristems in a fully self-organised manner, and we discuss future research directions to address the gaps in our understanding of auxin transport mechanisms.

  20. Highway and interline transportation routing models

    SciTech Connect

    Joy, D.S.; Johnson, P.E.

    1994-06-01

    The potential impacts associated with the transportation of hazardous materials are important issues to shippers, carriers, and the general public. Since transportation routes are a central characteristic in most of these issues, the prediction of likely routes is the first step toward the resolution of these issues. In addition, US Department of Transportation requirements (HM-164) mandate specific routes for shipments of highway controlled quantities of radioactive materials. In response to these needs, two routing models have been developed at Oak Ridge National Laboratory under the sponsorship of the U.S. Department of Energy (DOE). These models have been designated by DOE`s Office of Environmental Restoration and Waste Management, Transportation Management Division (DOE/EM) as the official DOE routing models. Both models, HIGHWAY and INTERLINE, are described.

  1. NODA for EPA's Updated Ozone Transport Modeling

    EPA Pesticide Factsheets

    Find EPA's NODA for the Updated Ozone Transport Modeling Data for the 2008 Ozone National Ambient Air Quality Standard (NAAQS) along with the ExitExtension of Public Comment Period on CSAPR for the 2008 NAAQS.

  2. Accurate and efficient halo-based galaxy clustering modelling with simulations

    NASA Astrophysics Data System (ADS)

    Zheng, Zheng; Guo, Hong

    2016-06-01

    Small- and intermediate-scale galaxy clustering can be used to establish the galaxy-halo connection to study galaxy formation and evolution and to tighten constraints on cosmological parameters. With the increasing precision of galaxy clustering measurements from ongoing and forthcoming large galaxy surveys, accurate models are required to interpret the data and extract relevant information. We introduce a method based on high-resolution N-body simulations to accurately and efficiently model the galaxy two-point correlation functions (2PCFs) in projected and redshift spaces. The basic idea is to tabulate all information of haloes in the simulations necessary for computing the galaxy 2PCFs within the framework of halo occupation distribution or conditional luminosity function. It is equivalent to populating galaxies to dark matter haloes and using the mock 2PCF measurements as the model predictions. Besides the accurate 2PCF calculations, the method is also fast and therefore enables an efficient exploration of the parameter space. As an example of the method, we decompose the redshift-space galaxy 2PCF into different components based on the type of galaxy pairs and show the redshift-space distortion effect in each component. The generalizations and limitations of the method are discussed.

  3. An analytic model for accurate spring constant calibration of rectangular atomic force microscope cantilevers.

    PubMed

    Li, Rui; Ye, Hongfei; Zhang, Weisheng; Ma, Guojun; Su, Yewang

    2015-10-29

    Spring constant calibration of the atomic force microscope (AFM) cantilever is of fundamental importance for quantifying the force between the AFM cantilever tip and the sample. The calibration within the framework of thin plate theory undoubtedly has a higher accuracy and broader scope than that within the well-established beam theory. However, thin plate theory-based accurate analytic determination of the constant has been perceived as an extremely difficult issue. In this paper, we implement the thin plate theory-based analytic modeling for the static behavior of rectangular AFM cantilevers, which reveals that the three-dimensional effect and Poisson effect play important roles in accurate determination of the spring constants. A quantitative scaling law is found that the normalized spring constant depends only on the Poisson's ratio, normalized dimension and normalized load coordinate. Both the literature and our refined finite element model validate the present results. The developed model is expected to serve as the benchmark for accurate calibration of rectangular AFM cantilevers.

  4. 5D model for accurate representation and visualization of dynamic cardiac structures

    NASA Astrophysics Data System (ADS)

    Lin, Wei-te; Robb, Richard A.

    2000-05-01

    Accurate cardiac modeling is challenging due to the intricate structure and complex contraction patterns of myocardial tissues. Fast imaging techniques can provide 4D structural information acquired as a sequence of 3D images throughout the cardiac cycle. To mode. The beating heart, we created a physics-based surface model that deforms between successive time point in the cardiac cycle. 3D images of canine hearts were acquired during one complete cardiac cycle using the DSR and the EBCT. The left ventricle of the first time point is reconstructed as a triangular mesh. A mass-spring physics-based deformable mode,, which can expand and shrink with local contraction and stretching forces distributed in an anatomically accurate simulation of cardiac motion, is applied to the initial mesh and allows the initial mesh to deform to fit the left ventricle in successive time increments of the sequence. The resulting 4D model can be interactively transformed and displayed with associated regional electrical activity mapped onto anatomic surfaces, producing a 5D model, which faithfully exhibits regional cardiac contraction and relaxation patterns over the entire heart. The model faithfully represents structural changes throughout the cardiac cycle. Such models provide the framework for minimizing the number of time points required to usefully depict regional motion of myocardium and allow quantitative assessment of regional myocardial motion. The electrical activation mapping provides spatial and temporal correlation within the cardiac cycle. In procedures which as intra-cardiac catheter ablation, visualization of the dynamic model can be used to accurately localize the foci of myocardial arrhythmias and guide positioning of catheters for optimal ablation.

  5. Monte Carlo modeling provides accurate calibration factors for radionuclide activity meters.

    PubMed

    Zagni, F; Cicoria, G; Lucconi, G; Infantino, A; Lodi, F; Marengo, M

    2014-12-01

    Accurate determination of calibration factors for radionuclide activity meters is crucial for quantitative studies and in the optimization step of radiation protection, as these detectors are widespread in radiopharmacy and nuclear medicine facilities. In this work we developed the Monte Carlo model of a widely used activity meter, using the Geant4 simulation toolkit. More precisely the "PENELOPE" EM physics models were employed. The model was validated by means of several certified sources, traceable to primary activity standards, and other sources locally standardized with spectrometry measurements, plus other experimental tests. Great care was taken in order to accurately reproduce the geometrical details of the gas chamber and the activity sources, each of which is different in shape and enclosed in a unique container. Both relative calibration factors and ionization current obtained with simulations were compared against experimental measurements; further tests were carried out, such as the comparison of the relative response of the chamber for a source placed at different positions. The results showed a satisfactory level of accuracy in the energy range of interest, with the discrepancies lower than 4% for all the tested parameters. This shows that an accurate Monte Carlo modeling of this type of detector is feasible using the low-energy physics models embedded in Geant4. The obtained Monte Carlo model establishes a powerful tool for first instance determination of new calibration factors for non-standard radionuclides, for custom containers, when a reference source is not available. Moreover, the model provides an experimental setup for further research and optimization with regards to materials and geometrical details of the measuring setup, such as the ionization chamber itself or the containers configuration.

  6. Mathematical modeling plasma transport in tokamaks

    SciTech Connect

    Quiang, Ji

    1997-01-01

    In this work, the author applied a systematic calibration, validation and application procedure based on the methodology of mathematical modeling to international thermonuclear experimental reactor (ITER) ignition studies. The multi-mode plasma transport model used here includes a linear combination of drift wave branch and ballooning branch instabilities with two a priori uncertain constants to account for anomalous plasma transport in tokamaks. A Bayesian parameter estimation method is used including experimental calibration error/model offsets and error bar rescaling factors to determine the two uncertain constants in the transport model with quantitative confidence level estimates for the calibrated parameters, which gives two saturation levels of instabilities. This method is first tested using a gyroBohm multi-mode transport model with a pair of DIII-D discharge experimental data, and then applied to calibrating a nominal multi-mode transport model against a broad database using twelve discharges from seven different tokamaks. The calibrated transport model is then validated on five discharges from JT-60 with no adjustable constants. The results are in a good agreement with experimental data. Finally, the resulting class of multi-mode tokamak plasma transport models is applied to the transport analysis of the ignition probability in a next generation machine, ITER. A reference simulation of basic ITER engineering design activity (EDA) parameters shows that a self-sustained thermonuclear burn with 1.5 GW output power can be achieved provided that impurity control makes radiative losses sufficiently small at an average plasma density of 1.2 X 1020/m3 with 50 MW auxiliary heating. The ignition probability of ITER for the EDA parameters, can be formally as high as 99.9% in the present context. The same probability for concept design activity (CDA) parameters of ITER, which has smaller size and lower current, is only 62.6%.

  7. Using a highly accurate self-stop Cu-CMP model in the design flow

    NASA Astrophysics Data System (ADS)

    Izuha, Kyoko; Sakairi, Takashi; Shibuki, Shunichi; Bora, Monalisa; Hatem, Osama; Ghulghazaryan, Ruben; Strecker, Norbert; Wilson, Jeff; Takeshita, Noritsugu

    2010-03-01

    An accurate model for the self-stop copper chemical mechanical polishing (Cu-CMP) process has been developed using CMP modeling technology from Mentor Graphics. This technology was applied on data from Sony to create and optimize copper electroplating (ECD), Cu-CMP, and barrier metal polishing (BM-CMP) process models. These models take into account layout pattern dependency, long range diffusion and planarization effects, as well as microloading from local pattern density. The developed ECD model accurately predicted erosion and dishing over the entire range of width and space combinations present on the test chip. Then, the results of the ECD model were used as an initial structure to model the Cu-CMP step. Subsequently, the result of Cu-CMP was used for the BM-CMP model creation. The created model was successful in reproducing the measured data, including trends for a broad range of metal width and densities. Its robustness is demonstrated by the fact that it gives acceptable prediction of final copper thickness data although the calibration data included noise from line scan measurements. Accuracy of the Cu-CMP model has a great impact on the prediction results for BM-CMP. This is a critical feature for the modeling of high precision CMP such as self-stop Cu-CMP. Finally, the developed model could successfully extract planarity hotspots that helped identify potential problems in production chips before they were manufactured. The output thickness values of metal and dielectric can be used to drive layout enhancement tools and improve the accuracy of timing analysis.

  8. Coarse-grained red blood cell model with accurate mechanical properties, rheology and dynamics.

    PubMed

    Fedosov, Dmitry A; Caswell, Bruce; Karniadakis, George E

    2009-01-01

    We present a coarse-grained red blood cell (RBC) model with accurate and realistic mechanical properties, rheology and dynamics. The modeled membrane is represented by a triangular mesh which incorporates shear inplane energy, bending energy, and area and volume conservation constraints. The macroscopic membrane elastic properties are imposed through semi-analytic theory, and are matched with those obtained in optical tweezers stretching experiments. Rheological measurements characterized by time-dependent complex modulus are extracted from the membrane thermal fluctuations, and compared with those obtained from the optical magnetic twisting cytometry results. The results allow us to define a meaningful characteristic time of the membrane. The dynamics of RBCs observed in shear flow suggests that a purely elastic model for the RBC membrane is not appropriate, and therefore a viscoelastic model is required. The set of proposed analyses and numerical tests can be used as a complete model testbed in order to calibrate the modeled viscoelastic membranes to accurately represent RBCs in health and disease.

  9. Stochastic model of radioiodine transport

    SciTech Connect

    Schwarz, G.; Hoffman, F.O.

    1980-01-01

    A research project has been underway at the Oak Ridge National Laboratory with the objective to evaluate dose assessment models and to determine the uncertainty associated with the model predictions. This has resulted in the application of methods to propagate uncertainties through models. Some techniques and results related to this problem are discussed.

  10. Yield-Ensuring DAC-Embedded Opamp Design Based on Accurate Behavioral Model Development

    NASA Astrophysics Data System (ADS)

    Jang, Yeong-Shin; Nguyen, Hoai-Nam; Ryu, Seung-Tak; Lee, Sang-Gug

    An accurate behavioral model of a DAC-embedded opamp (DAC-opamp) is developed for a yield-ensuring LCD column driver design. A lookup table for the V-I curve of the unit differential pair in the DAC-opamp is extracted from a circuit simulation and is later manipulated through a random error insertion. Virtual ground assumption simplifies the output voltage estimation algorithm. The developed behavioral model of a 5-bit DAC-opamp shows good agreement with the circuit level simulation with less than 5% INL difference.

  11. Time resolved diffuse optical spectroscopy with geometrically accurate models for bulk parameter recovery

    PubMed Central

    Guggenheim, James A.; Bargigia, Ilaria; Farina, Andrea; Pifferi, Antonio; Dehghani, Hamid

    2016-01-01

    A novel straightforward, accessible and efficient approach is presented for performing hyperspectral time-domain diffuse optical spectroscopy to determine the optical properties of samples accurately using geometry specific models. To allow bulk parameter recovery from measured spectra, a set of libraries based on a numerical model of the domain being investigated is developed as opposed to the conventional approach of using an analytical semi-infinite slab approximation, which is known and shown to introduce boundary effects. Results demonstrate that the method improves the accuracy of derived spectrally varying optical properties over the use of the semi-infinite approximation. PMID:27699137

  12. Body charge modelling for accurate simulation of small-signal behaviour in floating body SOI

    NASA Astrophysics Data System (ADS)

    Benson, James; Redman-White, William; D'Halleweyn, Nele V.; Easson, Craig A.; Uren, Michael J.

    2002-04-01

    We show that careful modelling of body node elements in floating body PD-SOI MOSFET compact models is required in order to obtain accurate small-signal simulation results in the saturation region. The body network modifies the saturation output conductance of the device via the body-source transconductance, resulting in a pole/zero pair being introduced in the conductance-frequency response. We show that neglecting the presence of body charge in the saturation region can often yield inaccurate values for the body capacitances, which in turn can adversely affect the modelling of the output conductance above the pole/zero frequency. We conclude that the underlying cause of this problem is the use of separate models for the intrinsic and extrinsic capacitances. Finally, we present a simple saturation body charge model which can greatly improve small-signal simulation accuracy for floating body devices.

  13. Molecular model of the neural dopamine transporter

    NASA Astrophysics Data System (ADS)

    Ravna, Aina Westrheim; Sylte, Ingebrigt; Dahl, Svein G.

    2003-05-01

    The dopamine transporter (DAT) regulates the action of dopamine by reuptake of the neurotransmitter into presynaptic neurons, and is the main molecular target of amphetamines and cocaine. DAT and the Na+/H+ antiporter (NhaA) are secondary transporter proteins that carry small molecules across a cell membrane against a concentration gradient, using ion gradients as energy source. A 3-dimensional projection map of the E. coli NhaA has confirmed a topology of 12 membrane spanning domains, and was previously used to construct a 3-dimensional NhaA model with 12 trans-membrane α-helices (TMHs). The NhaA model, and site directed mutagenesis data on DAT, were used to construct a detailed 3-dimensional DAT model using interactive molecular graphics and empiric force field calculations. The model proposes a dopamine transport mechanism involving TMHs 1, 3, 4, 5, 7 and 11. Asp79, Tyr252 and Tyr274 were the primary cocaine binding residues. Binding of cocaine or its analogue, (-)-2β-carbomethoxy-3β-(4-fluorophenyl)tropane (CFT), seemed to lock the transporter in an inactive state, and thus inhibit dopamine transport. The present model may be used to design further experimental studies of the molecular structure and mechanisms of DAT and other secondary transporter proteins.

  14. Reduced Dynamic Models in Epithelial Transport

    PubMed Central

    Hernández, Julio A.

    2013-01-01

    Most models developed to represent transport across epithelia assume that the cell interior constitutes a homogeneous compartment, characterized by a single concentration value of the transported species. This conception differs significantly from the current view, in which the cellular compartment is regarded as a highly crowded media of marked structural heterogeneity. Can the finding of relatively simple dynamic properties of transport processes in epithelia be compatible with this complex structural conception of the cell interior? The purpose of this work is to contribute with one simple theoretical approach to answer this question. For this, the techniques of model reduction are utilized to obtain a two-state reduced model from more complex linear models of transcellular transport with a larger number of intermediate states. In these complex models, each state corresponds to the solute concentration in an intermediate intracellular compartment. In addition, the numerical studies reveal that it is possible to approximate a general two-state model under conditions where strict reduction of the complex models cannot be performed. These results contribute with arguments to reconcile the current conception of the cell interior as a highly complex medium with the finding of relatively simple dynamic properties of transport across epithelial cells. PMID:23533397

  15. Accurate prediction of wall shear stress in a stented artery: newtonian versus non-newtonian models.

    PubMed

    Mejia, Juan; Mongrain, Rosaire; Bertrand, Olivier F

    2011-07-01

    A significant amount of evidence linking wall shear stress to neointimal hyperplasia has been reported in the literature. As a result, numerical and experimental models have been created to study the influence of stent design on wall shear stress. Traditionally, blood has been assumed to behave as a Newtonian fluid, but recently that assumption has been challenged. The use of a linear model; however, can reduce computational cost, and allow the use of Newtonian fluids (e.g., glycerine and water) instead of a blood analog fluid in an experimental setup. Therefore, it is of interest whether a linear model can be used to accurately predict the wall shear stress caused by a non-Newtonian fluid such as blood within a stented arterial segment. The present work compares the resulting wall shear stress obtained using two linear and one nonlinear model under the same flow waveform. All numerical models are fully three-dimensional, transient, and incorporate a realistic stent geometry. It is shown that traditional linear models (based on blood's lowest viscosity limit, 3.5 Pa s) underestimate the wall shear stress within a stented arterial segment, which can lead to an overestimation of the risk of restenosis. The second linear model, which uses a characteristic viscosity (based on an average strain rate, 4.7 Pa s), results in higher wall shear stress levels, but which are still substantially below those of the nonlinear model. It is therefore shown that nonlinear models result in more accurate predictions of wall shear stress within a stented arterial segment.

  16. Accurate halo-model matter power spectra with dark energy, massive neutrinos and modified gravitational forces

    NASA Astrophysics Data System (ADS)

    Mead, A. J.; Heymans, C.; Lombriser, L.; Peacock, J. A.; Steele, O. I.; Winther, H. A.

    2016-06-01

    We present an accurate non-linear matter power spectrum prediction scheme for a variety of extensions to the standard cosmological paradigm, which uses the tuned halo model previously developed in Mead et al. We consider dark energy models that are both minimally and non-minimally coupled, massive neutrinos and modified gravitational forces with chameleon and Vainshtein screening mechanisms. In all cases, we compare halo-model power spectra to measurements from high-resolution simulations. We show that the tuned halo-model method can predict the non-linear matter power spectrum measured from simulations of parametrized w(a) dark energy models at the few per cent level for k < 10 h Mpc-1, and we present theoretically motivated extensions to cover non-minimally coupled scalar fields, massive neutrinos and Vainshtein screened modified gravity models that result in few per cent accurate power spectra for k < 10 h Mpc-1. For chameleon screened models, we achieve only 10 per cent accuracy for the same range of scales. Finally, we use our halo model to investigate degeneracies between different extensions to the standard cosmological model, finding that the impact of baryonic feedback on the non-linear matter power spectrum can be considered independently of modified gravity or massive neutrino extensions. In contrast, considering the impact of modified gravity and massive neutrinos independently results in biased estimates of power at the level of 5 per cent at scales k > 0.5 h Mpc-1. An updated version of our publicly available HMCODE can be found at https://github.com/alexander-mead/hmcode.

  17. Model aids cuttings transport prediction

    SciTech Connect

    Gavignet, A.A. ); Sobey, I.J. )

    1989-09-01

    Drilling of highly deviated wells can be complicated by the formation of a thick bed of cuttings at low flow rates. The model proposed in this paper shows what mechanisms control the thickness of such a bed, and the model predictions are compared with experimental results.

  18. Accurate modeling of switched reluctance machine based on hybrid trained WNN

    NASA Astrophysics Data System (ADS)

    Song, Shoujun; Ge, Lefei; Ma, Shaojie; Zhang, Man

    2014-04-01

    According to the strong nonlinear electromagnetic characteristics of switched reluctance machine (SRM), a novel accurate modeling method is proposed based on hybrid trained wavelet neural network (WNN) which combines improved genetic algorithm (GA) with gradient descent (GD) method to train the network. In the novel method, WNN is trained by GD method based on the initial weights obtained per improved GA optimization, and the global parallel searching capability of stochastic algorithm and local convergence speed of deterministic algorithm are combined to enhance the training accuracy, stability and speed. Based on the measured electromagnetic characteristics of a 3-phase 12/8-pole SRM, the nonlinear simulation model is built by hybrid trained WNN in Matlab. The phase current and mechanical characteristics from simulation under different working conditions meet well with those from experiments, which indicates the accuracy of the model for dynamic and static performance evaluation of SRM and verifies the effectiveness of the proposed modeling method.

  19. A hamster model for Marburg virus infection accurately recapitulates Marburg hemorrhagic fever

    PubMed Central

    Marzi, Andrea; Banadyga, Logan; Haddock, Elaine; Thomas, Tina; Shen, Kui; Horne, Eva J.; Scott, Dana P.; Feldmann, Heinz; Ebihara, Hideki

    2016-01-01

    Marburg virus (MARV), a close relative of Ebola virus, is the causative agent of a severe human disease known as Marburg hemorrhagic fever (MHF). No licensed vaccine or therapeutic exists to treat MHF, and MARV is therefore classified as a Tier 1 select agent and a category A bioterrorism agent. In order to develop countermeasures against this severe disease, animal models that accurately recapitulate human disease are required. Here we describe the development of a novel, uniformly lethal Syrian golden hamster model of MHF using a hamster-adapted MARV variant Angola. Remarkably, this model displayed almost all of the clinical features of MHF seen in humans and non-human primates, including coagulation abnormalities, hemorrhagic manifestations, petechial rash, and a severely dysregulated immune response. This MHF hamster model represents a powerful tool for further dissecting MARV pathogenesis and accelerating the development of effective medical countermeasures against human MHF. PMID:27976688

  20. A hamster model for Marburg virus infection accurately recapitulates Marburg hemorrhagic fever.

    PubMed

    Marzi, Andrea; Banadyga, Logan; Haddock, Elaine; Thomas, Tina; Shen, Kui; Horne, Eva J; Scott, Dana P; Feldmann, Heinz; Ebihara, Hideki

    2016-12-15

    Marburg virus (MARV), a close relative of Ebola virus, is the causative agent of a severe human disease known as Marburg hemorrhagic fever (MHF). No licensed vaccine or therapeutic exists to treat MHF, and MARV is therefore classified as a Tier 1 select agent and a category A bioterrorism agent. In order to develop countermeasures against this severe disease, animal models that accurately recapitulate human disease are required. Here we describe the development of a novel, uniformly lethal Syrian golden hamster model of MHF using a hamster-adapted MARV variant Angola. Remarkably, this model displayed almost all of the clinical features of MHF seen in humans and non-human primates, including coagulation abnormalities, hemorrhagic manifestations, petechial rash, and a severely dysregulated immune response. This MHF hamster model represents a powerful tool for further dissecting MARV pathogenesis and accelerating the development of effective medical countermeasures against human MHF.

  1. Accurate modeling of switched reluctance machine based on hybrid trained WNN

    SciTech Connect

    Song, Shoujun Ge, Lefei; Ma, Shaojie; Zhang, Man

    2014-04-15

    According to the strong nonlinear electromagnetic characteristics of switched reluctance machine (SRM), a novel accurate modeling method is proposed based on hybrid trained wavelet neural network (WNN) which combines improved genetic algorithm (GA) with gradient descent (GD) method to train the network. In the novel method, WNN is trained by GD method based on the initial weights obtained per improved GA optimization, and the global parallel searching capability of stochastic algorithm and local convergence speed of deterministic algorithm are combined to enhance the training accuracy, stability and speed. Based on the measured electromagnetic characteristics of a 3-phase 12/8-pole SRM, the nonlinear simulation model is built by hybrid trained WNN in Matlab. The phase current and mechanical characteristics from simulation under different working conditions meet well with those from experiments, which indicates the accuracy of the model for dynamic and static performance evaluation of SRM and verifies the effectiveness of the proposed modeling method.

  2. Adaptive Mesh Refinement in Reactive Transport Modeling of Subsurface Environments

    NASA Astrophysics Data System (ADS)

    Molins, S.; Day, M.; Trebotich, D.; Graves, D. T.

    2015-12-01

    Adaptive mesh refinement (AMR) is a numerical technique for locally adjusting the resolution of computational grids. AMR makes it possible to superimpose levels of finer grids on the global computational grid in an adaptive manner allowing for more accurate calculations locally. AMR codes rely on the fundamental concept that the solution can be computed in different regions of the domain with different spatial resolutions. AMR codes have been applied to a wide range of problem including (but not limited to): fully compressible hydrodynamics, astrophysical flows, cosmological applications, combustion, blood flow, heat transfer in nuclear reactors, and land ice and atmospheric models for climate. In subsurface applications, in particular, reactive transport modeling, AMR may be particularly useful in accurately capturing concentration gradients (hence, reaction rates) that develop in localized areas of the simulation domain. Accurate evaluation of reaction rates is critical in many subsurface applications. In this contribution, we will discuss recent applications that bring to bear AMR capabilities on reactive transport problems from the pore scale to the flood plain scale.

  3. Beyond Ellipse(s): Accurately Modelling the Isophotal Structure of Galaxies with ISOFIT and CMODEL

    NASA Astrophysics Data System (ADS)

    Ciambur, B. C.

    2015-09-01

    This work introduces a new fitting formalism for isophotes that enables more accurate modeling of galaxies with non-elliptical shapes, such as disk galaxies viewed edge-on or galaxies with X-shaped/peanut bulges. Within this scheme, the angular parameter that defines quasi-elliptical isophotes is transformed from the commonly used, but inappropriate, polar coordinate to the “eccentric anomaly.” This provides a superior description of deviations from ellipticity, better capturing the true isophotal shape. Furthermore, this makes it possible to accurately recover both the surface brightness profile, using the correct azimuthally averaged isophote, and the two-dimensional model of any galaxy: the hitherto ubiquitous, but artificial, cross-like features in residual images are completely removed. The formalism has been implemented into the Image Reduction and Analysis Facility tasks Ellipse and Bmodel to create the new tasks “Isofit,” and “Cmodel.” The new tools are demonstrated here with application to five galaxies, chosen to be representative case-studies for several areas where this technique makes it possible to gain new scientific insight. Specifically: properly quantifying boxy/disky isophotes via the fourth harmonic order in edge-on galaxies, quantifying X-shaped/peanut bulges, higher-order Fourier moments for modeling bars in disks, and complex isophote shapes. Higher order (n > 4) harmonics now become meaningful and may correlate with structural properties, as boxyness/diskyness is known to do. This work also illustrates how the accurate construction, and subtraction, of a model from a galaxy image facilitates the identification and recovery of over-lapping sources such as globular clusters and the optical counterparts of X-ray sources.

  4. BEYOND ELLIPSE(S): ACCURATELY MODELING THE ISOPHOTAL STRUCTURE OF GALAXIES WITH ISOFIT AND CMODEL

    SciTech Connect

    Ciambur, B. C.

    2015-09-10

    This work introduces a new fitting formalism for isophotes that enables more accurate modeling of galaxies with non-elliptical shapes, such as disk galaxies viewed edge-on or galaxies with X-shaped/peanut bulges. Within this scheme, the angular parameter that defines quasi-elliptical isophotes is transformed from the commonly used, but inappropriate, polar coordinate to the “eccentric anomaly.” This provides a superior description of deviations from ellipticity, better capturing the true isophotal shape. Furthermore, this makes it possible to accurately recover both the surface brightness profile, using the correct azimuthally averaged isophote, and the two-dimensional model of any galaxy: the hitherto ubiquitous, but artificial, cross-like features in residual images are completely removed. The formalism has been implemented into the Image Reduction and Analysis Facility tasks Ellipse and Bmodel to create the new tasks “Isofit,” and “Cmodel.” The new tools are demonstrated here with application to five galaxies, chosen to be representative case-studies for several areas where this technique makes it possible to gain new scientific insight. Specifically: properly quantifying boxy/disky isophotes via the fourth harmonic order in edge-on galaxies, quantifying X-shaped/peanut bulges, higher-order Fourier moments for modeling bars in disks, and complex isophote shapes. Higher order (n > 4) harmonics now become meaningful and may correlate with structural properties, as boxyness/diskyness is known to do. This work also illustrates how the accurate construction, and subtraction, of a model from a galaxy image facilitates the identification and recovery of over-lapping sources such as globular clusters and the optical counterparts of X-ray sources.

  5. A multiscale red blood cell model with accurate mechanics, rheology, and dynamics.

    PubMed

    Fedosov, Dmitry A; Caswell, Bruce; Karniadakis, George Em

    2010-05-19

    Red blood cells (RBCs) have highly deformable viscoelastic membranes exhibiting complex rheological response and rich hydrodynamic behavior governed by special elastic and bending properties and by the external/internal fluid and membrane viscosities. We present a multiscale RBC model that is able to predict RBC mechanics, rheology, and dynamics in agreement with experiments. Based on an analytic theory, the modeled membrane properties can be uniquely related to the experimentally established RBC macroscopic properties without any adjustment of parameters. The RBC linear and nonlinear elastic deformations match those obtained in optical-tweezers experiments. The rheological properties of the membrane are compared with those obtained in optical magnetic twisting cytometry, membrane thermal fluctuations, and creep followed by cell recovery. The dynamics of RBCs in shear and Poiseuille flows is tested against experiments and theoretical predictions, and the applicability of the latter is discussed. Our findings clearly indicate that a purely elastic model for the membrane cannot accurately represent the RBC's rheological properties and its dynamics, and therefore accurate modeling of a viscoelastic membrane is necessary.

  6. Computational modeling of ion transport through nanopores.

    PubMed

    Modi, Niraj; Winterhalter, Mathias; Kleinekathöfer, Ulrich

    2012-10-21

    Nanoscale pores are ubiquitous in biological systems while artificial nanopores are being fabricated for an increasing number of applications. Biological pores are responsible for the transport of various ions and substrates between the different compartments of biological systems separated by membranes while artificial pores are aimed at emulating such transport properties. As an experimental method, electrophysiology has proven to be an important nano-analytical tool for the study of substrate transport through nanopores utilizing ion current measurements as a probe for the detection. Independent of the pore type, i.e., biological or synthetic, and objective of the study, i.e., to model cellular processes of ion transport or electrophysiological experiments, it has become increasingly important to understand the dynamics of ions in nanoscale confinements. To this end, numerical simulations have established themselves as an indispensable tool to decipher ion transport processes through biological as well as artificial nanopores. This article provides an overview of different theoretical and computational methods to study ion transport in general and to calculate ion conductance in particular. Potential new improvements in the existing methods and their applications are highlighted wherever applicable. Moreover, representative examples are given describing the ion transport through biological and synthetic nanopores as well as the high selectivity of ion channels. Special emphasis is placed on the usage of molecular dynamics simulations which already have demonstrated their potential to unravel ion transport properties at an atomic level.

  7. Modeling gas transport in the Martian subsurface

    NASA Astrophysics Data System (ADS)

    Gloesener, Elodie; Karatekin, Özgür; Dehant, Véronique

    2015-04-01

    Modeling gas transport through Martian subsurface and outgassing processes is essential in the study of atmospheric evolution of Mars. We present an overview of gas transport in Martian soil focusing on water vapor and methane diffusion to explain the recent observations of methane in Martian atmosphere with a diffusive transport model. The range of parameters that have the largest effect on transport in Martian conditions is investigated. Among the possible sources of methane, clathrate hydrates destabilization is one potential mechanism. Hydrate stability zone in subsurface is also investigated. In 2016, ExoMars Trace Gas Orbiter (TGO) will have the capabilities to detect and characterize trace gases in Martian atmosphere and will bring additional information to validate the different possible outgassing scenarios.

  8. What input data are needed to accurately model electromagnetic fields from mobile phone base stations?

    PubMed

    Beekhuizen, Johan; Kromhout, Hans; Bürgi, Alfred; Huss, Anke; Vermeulen, Roel

    2015-01-01

    The increase in mobile communication technology has led to concern about potential health effects of radio frequency electromagnetic fields (RF-EMFs) from mobile phone base stations. Different RF-EMF prediction models have been applied to assess population exposure to RF-EMF. Our study examines what input data are needed to accurately model RF-EMF, as detailed data are not always available for epidemiological studies. We used NISMap, a 3D radio wave propagation model, to test models with various levels of detail in building and antenna input data. The model outcomes were compared with outdoor measurements taken in Amsterdam, the Netherlands. Results showed good agreement between modelled and measured RF-EMF when 3D building data and basic antenna information (location, height, frequency and direction) were used: Spearman correlations were >0.6. Model performance was not sensitive to changes in building damping parameters. Antenna-specific information about down-tilt, type and output power did not significantly improve model performance compared with using average down-tilt and power values, or assuming one standard antenna type. We conclude that 3D radio wave propagation modelling is a feasible approach to predict outdoor RF-EMF levels for ranking exposure levels in epidemiological studies, when 3D building data and information on the antenna height, frequency, location and direction are available.

  9. The Community Sediment Transport Modeling System

    DTIC Science & Technology

    2008-01-01

    addition to wave processes, the model includes the influence of flocculation, hindered settling, rheology, and turbulence -suppression by stratification...The extensive upwelling event occurred in March 2002 is better reproduced with evident appearance of submesoscale spiral eddies all over the inner...THE COMMUNITY SEDIMENT TRANSPORT MODELING SYSTEM W. Rockwell Geyer Woods Hole Oceanographic Institution MS 11, Woods Hole, MA 02543 phone

  10. Clinton River Sediment Transport Modeling Study

    EPA Pesticide Factsheets

    The U.S. ACE develops sediment transport models for tributaries to the Great Lakes that discharge to AOCs. The models developed help State and local agencies to evaluate better ways for soil conservation and non-point source pollution prevention.

  11. Accurate verification of the conserved-vector-current and standard-model predictions

    SciTech Connect

    Sirlin, A.; Zucchini, R.

    1986-10-20

    An approximate analytic calculation of O(Z..cap alpha../sup 2/) corrections to Fermi decays is presented. When the analysis of Koslowsky et al. is modified to take into account the new results, it is found that each of the eight accurately studied scrFt values differs from the average by approx. <1sigma, thus significantly improving the comparison of experiments with conserved-vector-current predictions. The new scrFt values are lower than before, which also brings experiments into very good agreement with the three-generation standard model, at the level of its quantum corrections.

  12. The effects of video modeling with voiceover instruction on accurate implementation of discrete-trial instruction.

    PubMed

    Vladescu, Jason C; Carroll, Regina; Paden, Amber; Kodak, Tiffany M

    2012-01-01

    The present study replicates and extends previous research on the use of video modeling (VM) with voiceover instruction to train staff to implement discrete-trial instruction (DTI). After staff trainees reached the mastery criterion when teaching an adult confederate with VM, they taught a child with a developmental disability using DTI. The results showed that the staff trainees' accurate implementation of DTI remained high, and both child participants acquired new skills. These findings provide additional support that VM may be an effective method to train staff members to conduct DTI.

  13. Double Cluster Heads Model for Secure and Accurate Data Fusion in Wireless Sensor Networks

    PubMed Central

    Fu, Jun-Song; Liu, Yun

    2015-01-01

    Secure and accurate data fusion is an important issue in wireless sensor networks (WSNs) and has been extensively researched in the literature. In this paper, by combining clustering techniques, reputation and trust systems, and data fusion algorithms, we propose a novel cluster-based data fusion model called Double Cluster Heads Model (DCHM) for secure and accurate data fusion in WSNs. Different from traditional clustering models in WSNs, two cluster heads are selected after clustering for each cluster based on the reputation and trust system and they perform data fusion independently of each other. Then, the results are sent to the base station where the dissimilarity coefficient is computed. If the dissimilarity coefficient of the two data fusion results exceeds the threshold preset by the users, the cluster heads will be added to blacklist, and the cluster heads must be reelected by the sensor nodes in a cluster. Meanwhile, feedback is sent from the base station to the reputation and trust system, which can help us to identify and delete the compromised sensor nodes in time. Through a series of extensive simulations, we found that the DCHM performed very well in data fusion security and accuracy. PMID:25608211

  14. Fast and accurate computation of system matrix for area integral model-based algebraic reconstruction technique

    NASA Astrophysics Data System (ADS)

    Zhang, Shunli; Zhang, Dinghua; Gong, Hao; Ghasemalizadeh, Omid; Wang, Ge; Cao, Guohua

    2014-11-01

    Iterative algorithms, such as the algebraic reconstruction technique (ART), are popular for image reconstruction. For iterative reconstruction, the area integral model (AIM) is more accurate for better reconstruction quality than the line integral model (LIM). However, the computation of the system matrix for AIM is more complex and time-consuming than that for LIM. Here, we propose a fast and accurate method to compute the system matrix for AIM. First, we calculate the intersection of each boundary line of a narrow fan-beam with pixels in a recursive and efficient manner. Then, by grouping the beam-pixel intersection area into six types according to the slopes of the two boundary lines, we analytically compute the intersection area of the narrow fan-beam with the pixels in a simple algebraic fashion. Overall, experimental results show that our method is about three times faster than the Siddon algorithm and about two times faster than the distance-driven model (DDM) in computation of the system matrix. The reconstruction speed of our AIM-based ART is also faster than the LIM-based ART that uses the Siddon algorithm and DDM-based ART, for one iteration. The fast reconstruction speed of our method was accomplished without compromising the image quality.

  15. Accurate simulation of transient landscape evolution by eliminating numerical diffusion: the TTLEM 1.0 model

    NASA Astrophysics Data System (ADS)

    Campforts, Benjamin; Schwanghart, Wolfgang; Govers, Gerard

    2017-01-01

    Landscape evolution models (LEMs) allow the study of earth surface responses to changing climatic and tectonic forcings. While much effort has been devoted to the development of LEMs that simulate a wide range of processes, the numerical accuracy of these models has received less attention. Most LEMs use first-order accurate numerical methods that suffer from substantial numerical diffusion. Numerical diffusion particularly affects the solution of the advection equation and thus the simulation of retreating landforms such as cliffs and river knickpoints. This has potential consequences for the integrated response of the simulated landscape. Here we test a higher-order flux-limiting finite volume method that is total variation diminishing (TVD-FVM) to solve the partial differential equations of river incision and tectonic displacement. We show that using the TVD-FVM to simulate river incision significantly influences the evolution of simulated landscapes and the spatial and temporal variability of catchment-wide erosion rates. Furthermore, a two-dimensional TVD-FVM accurately simulates the evolution of landscapes affected by lateral tectonic displacement, a process whose simulation was hitherto largely limited to LEMs with flexible spatial discretization. We implement the scheme in TTLEM (TopoToolbox Landscape Evolution Model), a spatially explicit, raster-based LEM for the study of fluvially eroding landscapes in TopoToolbox 2.

  16. Radionuclide Transport Models Under Ambient Conditions

    SciTech Connect

    G. Moridis; Q. Hu

    2000-03-12

    The purpose of this Analysis/Model Report (AMR) is to evaluate (by means of 2-D semianalytical and 3-D numerical models) the transport of radioactive solutes and colloids in the unsaturated zone (UZ) under ambient conditions from the potential repository horizon to the water table at Yucca Mountain (YM), Nevada. This is in accordance with the ''AMR Development Plan U0060, Radionuclide Transport Models Under Ambient Conditions'' (CRWMS M and O 1999a). This AMR supports the UZ Flow and Transport Process Model Report (PMR). This AMR documents the UZ Radionuclide Transport Model (RTM). This model considers: the transport of radionuclides through fractured tuffs; the effects of changes in the intensity and configuration of fracturing from hydrogeologic unit to unit; colloid transport; physical and retardation processes and the effects of perched water. In this AMR they document the capabilities of the UZ RTM, which can describe flow (saturated and/or unsaturated) and transport, and accounts for (a) advection, (b) molecular diffusion, (c) hydrodynamic dispersion (with full 3-D tensorial representation), (d) kinetic or equilibrium physical and/or chemical sorption (linear, Langmuir, Freundlich or combined), (e) first-order linear chemical reaction, (f) radioactive decay and tracking of daughters, (g) colloid filtration (equilibrium, kinetic or combined), and (h) colloid-assisted solute transport. Simulations of transport of radioactive solutes and colloids (incorporating the processes described above) from the repository horizon to the water table are performed to support model development and support studies for Performance Assessment (PA). The input files for these simulations include transport parameters obtained from other AMRs (i.e., CRWMS M and O 1999d, e, f, g, h; 2000a, b, c, d). When not available, the parameter values used are obtained from the literature. The results of the simulations are used to evaluate the transport of radioactive solutes and colloids, and

  17. Accurate method for including solid-fluid boundary interactions in mesoscopic model fluids

    SciTech Connect

    Berkenbos, A. Lowe, C.P.

    2008-04-20

    Particle models are attractive methods for simulating the dynamics of complex mesoscopic fluids. Many practical applications of this methodology involve flow through a solid geometry. As the system is modeled using particles whose positions move continuously in space, one might expect that implementing the correct stick boundary condition exactly at the solid-fluid interface is straightforward. After all, unlike discrete methods there is no mapping onto a grid to contend with. In this article we describe a method that, for axisymmetric flows, imposes both the no-slip condition and continuity of stress at the interface. We show that the new method then accurately reproduces correct hydrodynamic behavior right up to the location of the interface. As such, computed flow profiles are correct even using a relatively small number of particles to model the fluid.

  18. A stochastic model of kinetochore-microtubule attachment accurately describes fission yeast chromosome segregation.

    PubMed

    Gay, Guillaume; Courtheoux, Thibault; Reyes, Céline; Tournier, Sylvie; Gachet, Yannick

    2012-03-19

    In fission yeast, erroneous attachments of spindle microtubules to kinetochores are frequent in early mitosis. Most are corrected before anaphase onset by a mechanism involving the protein kinase Aurora B, which destabilizes kinetochore microtubules (ktMTs) in the absence of tension between sister chromatids. In this paper, we describe a minimal mathematical model of fission yeast chromosome segregation based on the stochastic attachment and detachment of ktMTs. The model accurately reproduces the timing of correct chromosome biorientation and segregation seen in fission yeast. Prevention of attachment defects requires both appropriate kinetochore orientation and an Aurora B-like activity. The model also reproduces abnormal chromosome segregation behavior (caused by, for example, inhibition of Aurora B). It predicts that, in metaphase, merotelic attachment is prevented by a kinetochore orientation effect and corrected by an Aurora B-like activity, whereas in anaphase, it is corrected through unbalanced forces applied to the kinetochore. These unbalanced forces are sufficient to prevent aneuploidy.

  19. Cumulative atomic multipole moments complement any atomic charge model to obtain more accurate electrostatic properties

    NASA Technical Reports Server (NTRS)

    Sokalski, W. A.; Shibata, M.; Ornstein, R. L.; Rein, R.

    1992-01-01

    The quality of several atomic charge models based on different definitions has been analyzed using cumulative atomic multipole moments (CAMM). This formalism can generate higher atomic moments starting from any atomic charges, while preserving the corresponding molecular moments. The atomic charge contribution to the higher molecular moments, as well as to the electrostatic potentials, has been examined for CO and HCN molecules at several different levels of theory. The results clearly show that the electrostatic potential obtained from CAMM expansion is convergent up to R-5 term for all atomic charge models used. This illustrates that higher atomic moments can be used to supplement any atomic charge model to obtain more accurate description of electrostatic properties.

  20. Models for Turbulent Transport Processes.

    ERIC Educational Resources Information Center

    Hill, James C.

    1979-01-01

    Since the statistical theories of turbulence that have developed over the last twenty or thirty years are too abstract and unreliable to be of much use to chemical engineers, this paper introduces the techniques of single point models and suggests some areas of needed research. (BB)

  1. The importance of accurate muscle modelling for biomechanical analyses: a case study with a lizard skull

    PubMed Central

    Gröning, Flora; Jones, Marc E. H.; Curtis, Neil; Herrel, Anthony; O'Higgins, Paul; Evans, Susan E.; Fagan, Michael J.

    2013-01-01

    Computer-based simulation techniques such as multi-body dynamics analysis are becoming increasingly popular in the field of skull mechanics. Multi-body models can be used for studying the relationships between skull architecture, muscle morphology and feeding performance. However, to be confident in the modelling results, models need to be validated against experimental data, and the effects of uncertainties or inaccuracies in the chosen model attributes need to be assessed with sensitivity analyses. Here, we compare the bite forces predicted by a multi-body model of a lizard (Tupinambis merianae) with in vivo measurements, using anatomical data collected from the same specimen. This subject-specific model predicts bite forces that are very close to the in vivo measurements and also shows a consistent increase in bite force as the bite position is moved posteriorly on the jaw. However, the model is very sensitive to changes in muscle attributes such as fibre length, intrinsic muscle strength and force orientation, with bite force predictions varying considerably when these three variables are altered. We conclude that accurate muscle measurements are crucial to building realistic multi-body models and that subject-specific data should be used whenever possible. PMID:23614944

  2. Modeling Vapor and Heat Transport on Io

    NASA Astrophysics Data System (ADS)

    Allen, D. R.; Howell, R. R.

    2012-12-01

    Loki patera, a large, active volcanic depression on Jupiter's innermost Galilean moon Io, shows evidence of sulfur transport and exhibits temperatures that are consistently lower than many other volcanoes on Io. Galileo images of Loki reveal red sulfur deposits exterior to the patera that extend approximately 40 km from the patera's edge. Voyager images show light deposits, colloquially known as sulfur bergs, scattered across the patera floor that range from 3.5 km to 5 km in diameter. In addition, temperature profiles running north to south across the patera vary by only a few degrees and are difficult to explain with current thermal models, which don't include the role of volatiles such as sulfur. We are investigating the role sulfur plays in producing the features seen in images of Loki and in modifying the temperatures at Loki. We used the atmospheric models of Ingersoll (1989) and Moreno et al. (1991) for SO2 transport on Io as a starting point for our own sulfur transport models. We also compared the length scales of deposition predicted by our models and Moreno's models to the morphology and features seen in Galileo and Voyager images. In one case, Ingersoll modeled the sublimation of SO2 from a hot, higher pressure side which moves in one dimension and is deposited on a cold, lower pressure side. Using this case as a starting point, we adapted it for temperatures and pressures appropriate for S8 transport. We also converted his equations to consider the radial expansion of S8 from a point source, which we compared to the models of Moreno et al. (1991). We solved the hot side-cold side Ingersoll adapted model both analytically and numerically and obtained horizontal length scales of sulfur deposition consistent with the red deposits. We scaled the horizontal lengths of SO2 deposition predicted by Moreno's numerical models for S8 and obtained sulfur deposition lengths consistent with the light deposits. In contrast, our radial expansion model gave horizontal

  3. World Energy Projection System Plus Model Documentation: Transportation Model

    EIA Publications

    2011-01-01

    This report documents the objectives, analytical approach and development of the World Energy Projection System Plus (WEPS ) International Transportation model. It also catalogues and describes critical assumptions, computational methodology, parameter estimation techniques, and model source code.

  4. Molybdate transport in a chemically complex aquifer: Field measurements compared with solute-transport model predictions

    USGS Publications Warehouse

    Stollenwerk, K.G.

    1998-01-01

    A natural-gradient tracer test was conducted in an unconfined sand and gravel aquifer on Cape Cod, Massachusetts. Molybdate was included in the injectate to study the effects of variable groundwater chemistry on its aqueous distribution and to evaluate the reliability of laboratory experiments for identifying and quantifying reactions that control the transport of reactive solutes in groundwater. Transport of molybdate in this aquifer was controlled by adsorption. The amount adsorbed varied with aqueous chemistry that changed with depth as freshwater recharge mixed with a plume of sewage-contaminated groundwater. Molybdate adsorption was strongest near the water table where pH (5.7) and the concentration of the competing solutes phosphate (2.3 micromolar) and sulfate (86 micromolar) were low. Adsorption of molybdate decreased with depth as pH increased to 6.5, phosphate increased to 40 micromolar, and sulfate increased to 340 micromolar. A one-site diffuse-layer surface-complexation model and a two-site diffuse-layer surface-complexation model were used to simulate adsorption. Reactions and equilibrium constants for both models were determined in laboratory experiments and used in the reactive-transport model PHAST to simulate the two-dimensional transport of molybdate during the tracer test. No geochemical parameters were adjusted in the simulation to improve the fit between model and field data. Both models simulated the travel distance of the molybdate cloud to within 10% during the 2-year tracer test; however, the two-site diffuse-layer model more accurately simulated the molybdate concentration distribution within the cloud.

  5. Digitalized accurate modeling of SPCB with multi-spiral surface based on CPC algorithm

    NASA Astrophysics Data System (ADS)

    Huang, Yanhua; Gu, Lizhi

    2015-09-01

    The main methods of the existing multi-spiral surface geometry modeling include spatial analytic geometry algorithms, graphical method, interpolation and approximation algorithms. However, there are some shortcomings in these modeling methods, such as large amount of calculation, complex process, visible errors, and so on. The above methods have, to some extent, restricted the design and manufacture of the premium and high-precision products with spiral surface considerably. This paper introduces the concepts of the spatially parallel coupling with multi-spiral surface and spatially parallel coupling body. The typical geometry and topological features of each spiral surface forming the multi-spiral surface body are determined, by using the extraction principle of datum point cluster, the algorithm of coupling point cluster by removing singular point, and the "spatially parallel coupling" principle based on the non-uniform B-spline for each spiral surface. The orientation and quantitative relationships of datum point cluster and coupling point cluster in Euclidean space are determined accurately and in digital description and expression, coupling coalescence of the surfaces with multi-coupling point clusters under the Pro/E environment. The digitally accurate modeling of spatially parallel coupling body with multi-spiral surface is realized. The smooth and fairing processing is done to the three-blade end-milling cutter's end section area by applying the principle of spatially parallel coupling with multi-spiral surface, and the alternative entity model is processed in the four axis machining center after the end mill is disposed. And the algorithm is verified and then applied effectively to the transition area among the multi-spiral surface. The proposed model and algorithms may be used in design and manufacture of the multi-spiral surface body products, as well as in solving essentially the problems of considerable modeling errors in computer graphics and

  6. Can a Global Model Accurately Simulate Land-Atmosphere Interactions under Climate Change Conditions?

    NASA Astrophysics Data System (ADS)

    Zhou, C., VI; Wang, K.

    2015-12-01

    Surface air temperature (Ta) is largely determined by surface net radiation (Rn) and its partitioning into latent (LE) and sensible heat fluxes (H). Existing model evaluations of the absolute values of these fluxes are less helpful because the evaluation results are a blending of inconsistent spatial scales, inaccurate model forcing data and inaccurate parameterizations. This study further evaluates the relationship of LE and H with Rn and environmental parameters, including Ta, relative humidity (RH) and wind speed (WS), using ERA-interim reanalysis data at a grid of 0.125°×0.125° with measurements at AmeriFlux sites from 1998 to 2012. The results demonstrate that ERA-Interim can reproduce the absolute values of environmental parameters, radiation and turbulent fluxes rather accurately. The model performs well in simulating the correlation of LE and H to Rn, except for the notable correlation overestimation of H against Rn over high-density vegetation (e.g., deciduous broadleaf forest (DBF), grassland (GRA) and cropland (CRO)). The sensitivity of LE to Rn in the model is similar to the observations, but that of H to Rn is overestimated by 24.2%. In regions with high-density vegetation, the correlation coefficient between H and Ta is overestimated by more than 0.2, whereas that between H and WS is underestimated by more than 0.43. The sensitivity of H to Ta is overestimated by 0.72 Wm-2 °C-1, whereas that of H to WS in the model is underestimated by 16.15 Wm-2/(ms-1) over all of the sites. Considering both LE and H, the model cannot accurately capture the response of the evaporative fraction (EF=LE/(LE+H)) to Rn and the environmental parameters.

  7. Towards an accurate understanding of UHMWPE visco-dynamic behaviour for numerical modelling of implants.

    PubMed

    Quinci, Federico; Dressler, Matthew; Strickland, Anthony M; Limbert, Georges

    2014-04-01

    Considerable progress has been made in understanding implant wear and developing numerical models to predict wear for new orthopaedic devices. However any model of wear could be improved through a more accurate representation of the biomaterial mechanics, including time-varying dynamic and inelastic behaviour such as viscosity and plastic deformation. In particular, most computational models of wear of UHMWPE implement a time-invariant version of Archard's law that links the volume of worn material to the contact pressure between the metal implant and the polymeric tibial insert. During in-vivo conditions, however, the contact area is a time-varying quantity and is therefore dependent upon the dynamic deformation response of the material. From this observation one can conclude that creep deformations of UHMWPE may be very important to consider when conducting computational wear analyses, in stark contrast to what can be found in the literature. In this study, different numerical modelling techniques are compared with experimental creep testing on a unicondylar knee replacement system in a physiologically representative context. Linear elastic, plastic and time-varying visco-dynamic models are benchmarked using literature data to predict contact deformations, pressures and areas. The aim of this study is to elucidate the contributions of viscoelastic and plastic effects on these surface quantities. It is concluded that creep deformations have a significant effect on the contact pressure measured (experiment) and calculated (computational models) at the surface of the UHMWPE unicondylar insert. The use of a purely elastoplastic constitutive model for UHMWPE lead to compressive deformations of the insert which are much smaller than those predicted by a creep-capturing viscoelastic model (and those measured experimentally). This shows again the importance of including creep behaviour into a constitutive model in order to predict the right level of surface deformation

  8. Modeling Transport of Viruses in Fractured Rock

    NASA Astrophysics Data System (ADS)

    Sleep, B. E.; Mondal, P. K.

    2011-12-01

    Fractured rock aquifers are frequently used for water supply for human consumption. In many instances the fractured rock aquifers are vulnerable to contamination by pathogens, including viruses, due to co-location of on-site septic systems, wastewater discharges, biosolids and agricultural activities. Approximately half of the illnesses associated with groundwater consumption in the Unites States have been attributed to viral contamination. A number of these cases have been related to transport of viruses from septic systems to drinking water wells. Despite the potential for rapid transport of viruses through rock fractures to drinking water wells, the understanding of virus transport in fractured rock is limited. In particular, the impacts of virus size, fracture aperture variability and roughness, matrix porosity, groundwater velocity, and geochemical conditions have not been well studied. In this study, a multidimensional model for virus transport in variable aperture fractures is presented. The model is applied to laboratory experiments on transport of virus-sized latex microspheres (0.02 and 0.2 microns) and bacteriophages (MS2 and PR772) in artificially fractured dolomite rocks. In these experiments significant impacts of particle size, fracture characteristics, groundwater velocity, and geochemistry were observed. Given the variability in aperture distribution and associated spatial variation in groundwater flow field, one-dimensional models were not suitable for a comprehensive evaluation of the mechanisms governing the microsphere and bacteriophage transport. Various relationships for virus retention (attachment and detachment) are evaluated to provide insight into the governing processes in virus transport in fractured rock. In addition, the role of virus size, fracture aperture variability, fracture roughness, fracture surface charge, matrix porosity, groundwater velocity, and ionic strength in virus transport are evaluated. Scale-up to the field is

  9. Validation of an Accurate Three-Dimensional Helical Slow-Wave Circuit Model

    NASA Technical Reports Server (NTRS)

    Kory, Carol L.

    1997-01-01

    The helical slow-wave circuit embodies a helical coil of rectangular tape supported in a metal barrel by dielectric support rods. Although the helix slow-wave circuit remains the mainstay of the traveling-wave tube (TWT) industry because of its exceptionally wide bandwidth, a full helical circuit, without significant dimensional approximations, has not been successfully modeled until now. Numerous attempts have been made to analyze the helical slow-wave circuit so that the performance could be accurately predicted without actually building it, but because of its complex geometry, many geometrical approximations became necessary rendering the previous models inaccurate. In the course of this research it has been demonstrated that using the simulation code, MAFIA, the helical structure can be modeled with actual tape width and thickness, dielectric support rod geometry and materials. To demonstrate the accuracy of the MAFIA model, the cold-test parameters including dispersion, on-axis interaction impedance and attenuation have been calculated for several helical TWT slow-wave circuits with a variety of support rod geometries including rectangular and T-shaped rods, as well as various support rod materials including isotropic, anisotropic and partially metal coated dielectrics. Compared with experimentally measured results, the agreement is excellent. With the accuracy of the MAFIA helical model validated, the code was used to investigate several conventional geometric approximations in an attempt to obtain the most computationally efficient model. Several simplifications were made to a standard model including replacing the helical tape with filaments, and replacing rectangular support rods with shapes conforming to the cylindrical coordinate system with effective permittivity. The approximate models are compared with the standard model in terms of cold-test characteristics and computational time. The model was also used to determine the sensitivity of various

  10. Algal productivity modeling: a step toward accurate assessments of full-scale algal cultivation.

    PubMed

    Béchet, Quentin; Chambonnière, Paul; Shilton, Andy; Guizard, Guillaume; Guieysse, Benoit

    2015-05-01

    A new biomass productivity model was parameterized for Chlorella vulgaris using short-term (<30 min) oxygen productivities from algal microcosms exposed to 6 light intensities (20-420 W/m(2)) and 6 temperatures (5-42 °C). The model was then validated against experimental biomass productivities recorded in bench-scale photobioreactors operated under 4 light intensities (30.6-74.3 W/m(2)) and 4 temperatures (10-30 °C), yielding an accuracy of ± 15% over 163 days of cultivation. This modeling approach addresses major challenges associated with the accurate prediction of algal productivity at full-scale. Firstly, while most prior modeling approaches have only considered the impact of light intensity on algal productivity, the model herein validated also accounts for the critical impact of temperature. Secondly, this study validates a theoretical approach to convert short-term oxygen productivities into long-term biomass productivities. Thirdly, the experimental methodology used has the practical advantage of only requiring one day of experimental work for complete model parameterization. The validation of this new modeling approach is therefore an important step for refining feasibility assessments of algae biotechnologies.

  11. DAC 22 High Speed Civil Transport Model

    NASA Technical Reports Server (NTRS)

    1992-01-01

    Between tests, NASA research engineer Dave Hahne inspects a tenth-scale model of a supersonic transport model in the 30- by 60-Foot Tunnel at NASA Langley Research Center, Hampton, Virginia. The model is being used in support of NASA's High-Speed Research (HSR) program. Langley researchers are applying advance aerodynamic design methods to develop a wing leading-edge flap system which significantly improves low-speed fuel efficiency and reduces noise generated during takeoff operation. Langley is NASA's lead center for the agency's HSR program, aimed at developing technology to help U.S. industry compete in the rapidly expanding trans-oceanic transport market. A U.S. high-speed civil transport is expected to fly in about the year 2010. As envisioned, it would fly 300 passengers across the Pacific in about four hours at Mach 2.4 (approximately 1,600 mph/1950 kph) for a modest increase over business class fares.

  12. Band transport model for discotic liquid crystals

    NASA Astrophysics Data System (ADS)

    Lever, L. J.; Kelsall, R. W.; Bushby, R. J.

    2005-07-01

    A theoretical model is presented for charge transport in discotic liquid crystals in which a charge is delocalized over more than one lattice site. As such, charge transport is via a banded conduction process in a narrow bandwidth system and takes place over coherent lengths of a few molecules. The coherent lengths are disrupted by the geometrical disorder of the system and are treated as being terminated by quantum tunnel barriers. The transmission probabilities at these barriers have been calculated as a function of the charge carrier energy. Phononic interactions are also considered and the charge carrier scattering rates are calculated for intermolecular and intramolecular vibrations. The results of the calculations have been used to develop a Monte Carlo simulation of the charge transport model. Simulated data are presented and used to discuss the nature of the tunnel barriers required to reproduce experimental data. We find that the model successfully reproduces experimental time of flight data including temperature dependence.

  13. Stratospheric Transport Times From Observations and Models

    NASA Astrophysics Data System (ADS)

    Hoor, P. M.; Lelieveld, J.; Boenisch, H.; Joeckel, P.; Steil, B.; Bruehl, C.; Strahan, S.

    2007-12-01

    Transport time scales in the stratosphere are crucial to understand and calculate the effects of chemical active species on stratospheric chemistry. In general CO2 or SF6 have been used to calculate mean ages of air in the stratosphere, whereas shorter lived trace gases like CO are used to investigate cross tropopause transport and mixing on short time-scales close to the tropopause. Besides mean ages and their assocated mean trace gas mixing ratios at a given point in the atmosphere other quantities of the trace gas distributions can be used to constrain stratospheric transport times, such as variability and slope. In particular the younger part of the age spectrum needs to be constrained since it determines the extent to which shorter lived compounds can be transported into the stratosphere. We investigate transport times in the stratosphere based on observations of CO, N2O and CO2 and test a new approach to deduce transport times. For that purpose we compare observations from the ER-2 and other platforms. The approach is applied to global models (ECHAM5/MESSy, Combo GMI) to identify barriers as well as regions of rapid mixing and transport.

  14. GEOS-5 Chemistry Transport Model User's Guide

    NASA Technical Reports Server (NTRS)

    Kouatchou, J.; Molod, A.; Nielsen, J. E.; Auer, B.; Putman, W.; Clune, T.

    2015-01-01

    The Goddard Earth Observing System version 5 (GEOS-5) General Circulation Model (GCM) makes use of the Earth System Modeling Framework (ESMF) to enable model configurations with many functions. One of the options of the GEOS-5 GCM is the GEOS-5 Chemistry Transport Model (GEOS-5 CTM), which is an offline simulation of chemistry and constituent transport driven by a specified meteorology and other model output fields. This document describes the basic components of the GEOS-5 CTM, and is a user's guide on to how to obtain and run simulations on the NCCS Discover platform. In addition, we provide information on how to change the model configuration input files to meet users' needs.

  15. Accurately modeling Gaussian beam propagation in the context of Monte Carlo techniques

    NASA Astrophysics Data System (ADS)

    Hokr, Brett H.; Winblad, Aidan; Bixler, Joel N.; Elpers, Gabriel; Zollars, Byron; Scully, Marlan O.; Yakovlev, Vladislav V.; Thomas, Robert J.

    2016-03-01

    Monte Carlo simulations are widely considered to be the gold standard for studying the propagation of light in turbid media. However, traditional Monte Carlo methods fail to account for diffraction because they treat light as a particle. This results in converging beams focusing to a point instead of a diffraction limited spot, greatly effecting the accuracy of Monte Carlo simulations near the focal plane. Here, we present a technique capable of simulating a focusing beam in accordance to the rules of Gaussian optics, resulting in a diffraction limited focal spot. This technique can be easily implemented into any traditional Monte Carlo simulation allowing existing models to be converted to include accurate focusing geometries with minimal effort. We will present results for a focusing beam in a layered tissue model, demonstrating that for different scenarios the region of highest intensity, thus the greatest heating, can change from the surface to the focus. The ability to simulate accurate focusing geometries will greatly enhance the usefulness of Monte Carlo for countless applications, including studying laser tissue interactions in medical applications and light propagation through turbid media.

  16. Accurate model of electron beam profiles with emittance effects for pierce guns

    NASA Astrophysics Data System (ADS)

    Zeng, Peng; Wang, Guangqiang; Wang, Jianguo; Wang, Dongyang; Li, Shuang

    2016-09-01

    Accurate prediction of electron beam profile is one of the key objectives of electron optics, and the basis for design of the practical electron gun. In this paper, an improved model describing electron beam in Pierce gun with both space charge effects and emittance effects is proposed. The theory developed by Cutler and Hines is still applied for the accelerating region of the Pierce gun, while the motion equations of the electron beams in the anode aperture and drift tunnel are improved by modifying electron optics theory with emittance. As a result, a more universal and accurate formula of the focal length of the lens for the electron beam with both effects is derived for the anode aperture with finite dimension, and a modified universal spread curve considering beam emittance is introduced in drift tunnel region. Based on these improved motion equations of the electron beam, beam profiles with space charge effects and emittance effects can be theoretically predicted, which are subsequently approved to agree well with the experimentally measured ones. The developed model here is helpful to design more applicable Pierce guns at high frequencies.

  17. Accurate and scalable social recommendation using mixed-membership stochastic block models

    PubMed Central

    Godoy-Lorite, Antonia; Moore, Cristopher

    2016-01-01

    With increasing amounts of information available, modeling and predicting user preferences—for books or articles, for example—are becoming more important. We present a collaborative filtering model, with an associated scalable algorithm, that makes accurate predictions of users’ ratings. Like previous approaches, we assume that there are groups of users and of items and that the rating a user gives an item is determined by their respective group memberships. However, we allow each user and each item to belong simultaneously to mixtures of different groups and, unlike many popular approaches such as matrix factorization, we do not assume that users in each group prefer a single group of items. In particular, we do not assume that ratings depend linearly on a measure of similarity, but allow probability distributions of ratings to depend freely on the user’s and item’s groups. The resulting overlapping groups and predicted ratings can be inferred with an expectation-maximization algorithm whose running time scales linearly with the number of observed ratings. Our approach enables us to predict user preferences in large datasets and is considerably more accurate than the current algorithms for such large datasets. PMID:27911773

  18. Past, present and prospect of an Artificial Intelligence (AI) based model for sediment transport prediction

    NASA Astrophysics Data System (ADS)

    Afan, Haitham Abdulmohsin; El-shafie, Ahmed; Mohtar, Wan Hanna Melini Wan; Yaseen, Zaher Mundher

    2016-10-01

    An accurate model for sediment prediction is a priority for all hydrological researchers. Many conventional methods have shown an inability to achieve an accurate prediction of suspended sediment. These methods are unable to understand the behaviour of sediment transport in rivers due to the complexity, noise, non-stationarity, and dynamism of the sediment pattern. In the past two decades, Artificial Intelligence (AI) and computational approaches have become a remarkable tool for developing an accurate model. These approaches are considered a powerful tool for solving any non-linear model, as they can deal easily with a large number of data and sophisticated models. This paper is a review of all AI approaches that have been applied in sediment modelling. The current research focuses on the development of AI application in sediment transport. In addition, the review identifies major challenges and opportunities for prospective research. Throughout the literature, complementary models superior to classical modelling.

  19. A Biomechanical Model of the Scapulothoracic Joint to Accurately Capture Scapular Kinematics during Shoulder Movements

    PubMed Central

    Seth, Ajay; Matias, Ricardo; Veloso, António P.; Delp, Scott L.

    2016-01-01

    The complexity of shoulder mechanics combined with the movement of skin relative to the scapula makes it difficult to measure shoulder kinematics with sufficient accuracy to distinguish between symptomatic and asymptomatic individuals. Multibody skeletal models can improve motion capture accuracy by reducing the space of possible joint movements, and models are used widely to improve measurement of lower limb kinematics. In this study, we developed a rigid-body model of a scapulothoracic joint to describe the kinematics of the scapula relative to the thorax. This model describes scapular kinematics with four degrees of freedom: 1) elevation and 2) abduction of the scapula on an ellipsoidal thoracic surface, 3) upward rotation of the scapula normal to the thoracic surface, and 4) internal rotation of the scapula to lift the medial border of the scapula off the surface of the thorax. The surface dimensions and joint axes can be customized to match an individual’s anthropometry. We compared the model to “gold standard” bone-pin kinematics collected during three shoulder tasks and found modeled scapular kinematics to be accurate to within 2mm root-mean-squared error for individual bone-pin markers across all markers and movement tasks. As an additional test, we added random and systematic noise to the bone-pin marker data and found that the model reduced kinematic variability due to noise by 65% compared to Euler angles computed without the model. Our scapulothoracic joint model can be used for inverse and forward dynamics analyses and to compute joint reaction loads. The computational performance of the scapulothoracic joint model is well suited for real-time applications; it is freely available for use with OpenSim 3.2, and is customizable and usable with other OpenSim models. PMID:26734761

  20. Fractional Order Modeling of Atmospheric Turbulence - A More Accurate Modeling Methodology for Aero Vehicles

    NASA Technical Reports Server (NTRS)

    Kopasakis, George

    2014-01-01

    The presentation covers a recently developed methodology to model atmospheric turbulence as disturbances for aero vehicle gust loads and for controls development like flutter and inlet shock position. The approach models atmospheric turbulence in their natural fractional order form, which provides for more accuracy compared to traditional methods like the Dryden model, especially for high speed vehicle. The presentation provides a historical background on atmospheric turbulence modeling and the approaches utilized for air vehicles. This is followed by the motivation and the methodology utilized to develop the atmospheric turbulence fractional order modeling approach. Some examples covering the application of this method are also provided, followed by concluding remarks.

  1. [Model of active peristaltic transport in biosystems].

    PubMed

    Klochkov, B N; Romanov, A S

    2013-01-01

    A nonlinear distributed mathematical model of soft vessel with the nonmonotonous static characteristic is proposed and considered. The model describes space-time dynamics of vessel clearance change. Wave phenomena in vessels of different nature and the possibility of peristaltic fluid pumping are discussed and analyzed. The model is rather common in character and represents a description of the whole class of transport phenomena. Lymphatic vessels are particularly considered.

  2. Accurate Cold-Test Model of Helical TWT Slow-Wave Circuits

    NASA Technical Reports Server (NTRS)

    Kory, Carol L.; Dayton, James A., Jr.

    1997-01-01

    Recently, a method has been established to accurately calculate cold-test data for helical slow-wave structures using the three-dimensional electromagnetic computer code, MAFIA. Cold-test parameters have been calculated for several helical traveling-wave tube (TWT) slow-wave circuits possessing various support rod configurations, and results are presented here showing excellent agreement with experiment. The helical models include tape thickness, dielectric support shapes and material properties consistent with the actual circuits. The cold-test data from this helical model can be used as input into large-signal helical TWT interaction codes making it possible, for the first time, to design a complete TWT via computer simulation.

  3. Fast and Accurate Prediction of Numerical Relativity Waveforms from Binary Black Hole Coalescences Using Surrogate Models.

    PubMed

    Blackman, Jonathan; Field, Scott E; Galley, Chad R; Szilágyi, Béla; Scheel, Mark A; Tiglio, Manuel; Hemberger, Daniel A

    2015-09-18

    Simulating a binary black hole coalescence by solving Einstein's equations is computationally expensive, requiring days to months of supercomputing time. Using reduced order modeling techniques, we construct an accurate surrogate model, which is evaluated in a millisecond to a second, for numerical relativity (NR) waveforms from nonspinning binary black hole coalescences with mass ratios in [1, 10] and durations corresponding to about 15 orbits before merger. We assess the model's uncertainty and show that our modeling strategy predicts NR waveforms not used for the surrogate's training with errors nearly as small as the numerical error of the NR code. Our model includes all spherical-harmonic _{-2}Y_{ℓm} waveform modes resolved by the NR code up to ℓ=8. We compare our surrogate model to effective one body waveforms from 50M_{⊙} to 300M_{⊙} for advanced LIGO detectors and find that the surrogate is always more faithful (by at least an order of magnitude in most cases).

  4. Construction of feasible and accurate kinetic models of metabolism: A Bayesian approach

    PubMed Central

    Saa, Pedro A.; Nielsen, Lars K.

    2016-01-01

    Kinetic models are essential to quantitatively understand and predict the behaviour of metabolic networks. Detailed and thermodynamically feasible kinetic models of metabolism are inherently difficult to formulate and fit. They have a large number of heterogeneous parameters, are non-linear and have complex interactions. Many powerful fitting strategies are ruled out by the intractability of the likelihood function. Here, we have developed a computational framework capable of fitting feasible and accurate kinetic models using Approximate Bayesian Computation. This framework readily supports advanced modelling features such as model selection and model-based experimental design. We illustrate this approach on the tightly-regulated mammalian methionine cycle. Sampling from the posterior distribution, the proposed framework generated thermodynamically feasible parameter samples that converged on the true values, and displayed remarkable prediction accuracy in several validation tests. Furthermore, a posteriori analysis of the parameter distributions enabled appraisal of the systems properties of the network (e.g., control structure) and key metabolic regulations. Finally, the framework was used to predict missing allosteric interactions. PMID:27417285

  5. Fitmunk: improving protein structures by accurate, automatic modeling of side-chain conformations.

    PubMed

    Porebski, Przemyslaw Jerzy; Cymborowski, Marcin; Pasenkiewicz-Gierula, Marta; Minor, Wladek

    2016-02-01

    Improvements in crystallographic hardware and software have allowed automated structure-solution pipelines to approach a near-`one-click' experience for the initial determination of macromolecular structures. However, in many cases the resulting initial model requires a laborious, iterative process of refinement and validation. A new method has been developed for the automatic modeling of side-chain conformations that takes advantage of rotamer-prediction methods in a crystallographic context. The algorithm, which is based on deterministic dead-end elimination (DEE) theory, uses new dense conformer libraries and a hybrid energy function derived from experimental data and prior information about rotamer frequencies to find the optimal conformation of each side chain. In contrast to existing methods, which incorporate the electron-density term into protein-modeling frameworks, the proposed algorithm is designed to take advantage of the highly discriminatory nature of electron-density maps. This method has been implemented in the program Fitmunk, which uses extensive conformational sampling. This improves the accuracy of the modeling and makes it a versatile tool for crystallographic model building, refinement and validation. Fitmunk was extensively tested on over 115 new structures, as well as a subset of 1100 structures from the PDB. It is demonstrated that the ability of Fitmunk to model more than 95% of side chains accurately is beneficial for improving the quality of crystallographic protein models, especially at medium and low resolutions. Fitmunk can be used for model validation of existing structures and as a tool to assess whether side chains are modeled optimally or could be better fitted into electron density. Fitmunk is available as a web service at http://kniahini.med.virginia.edu/fitmunk/server/ or at http://fitmunk.bitbucket.org/.

  6. Fitmunk: improving protein structures by accurate, automatic modeling of side-chain conformations

    PubMed Central

    Porebski, Przemyslaw Jerzy; Cymborowski, Marcin; Pasenkiewicz-Gierula, Marta; Minor, Wladek

    2016-01-01

    Improvements in crystallographic hardware and software have allowed automated structure-solution pipelines to approach a near-‘one-click’ experience for the initial determination of macromolecular structures. However, in many cases the resulting initial model requires a laborious, iterative process of refinement and validation. A new method has been developed for the automatic modeling of side-chain conformations that takes advantage of rotamer-prediction methods in a crystallographic context. The algorithm, which is based on deterministic dead-end elimination (DEE) theory, uses new dense conformer libraries and a hybrid energy function derived from experimental data and prior information about rotamer frequencies to find the optimal conformation of each side chain. In contrast to existing methods, which incorporate the electron-density term into protein-modeling frameworks, the proposed algorithm is designed to take advantage of the highly discriminatory nature of electron-density maps. This method has been implemented in the program Fitmunk, which uses extensive conformational sampling. This improves the accuracy of the modeling and makes it a versatile tool for crystallographic model building, refinement and validation. Fitmunk was extensively tested on over 115 new structures, as well as a subset of 1100 structures from the PDB. It is demonstrated that the ability of Fitmunk to model more than 95% of side chains accurately is beneficial for improving the quality of crystallographic protein models, especially at medium and low resolutions. Fitmunk can be used for model validation of existing structures and as a tool to assess whether side chains are modeled optimally or could be better fitted into electron density. Fitmunk is available as a web service at http://kniahini.med.virginia.edu/fitmunk/server/ or at http://fitmunk.bitbucket.org/. PMID:26894674

  7. Climate Impact of Transportation A Model Comparison

    SciTech Connect

    Girod, Bastien; Van Vuuren, Detlef; Grahn, Maria; Kitous, Alban; Kim, Son H.; Kyle, G. Page

    2013-06-01

    Transportation contributes to a significant and rising share of global energy use and GHG emissions. Therefore modeling future travel demand, its fuel use, and resulting CO2 emission is highly relevant for climate change mitigation. In this study we compare the baseline projections for global service demand (passenger-kilometers, ton-kilometers), fuel use, and CO2 emissions of five different global transport models using harmonized input assumptions on income and population. For four models we also evaluate the impact of a carbon tax. All models project a steep increase in service demand over the century. Technology is important for limiting energy consumption and CO2 emissions, but quite radical changes in the technology mix are required to stabilize or reverse the trend. While all models project liquid fossil fuels dominating up to 2050, they differ regarding the use of alternative fuels (natural gas, hydrogen, biofuels, and electricity), because of different fuel price projections. The carbon tax of US$200/tCO2 in 2050 stabilizes or reverses global emission growth in all models. Besides common findings many differences in the model assumptions and projections indicate room for improvement in modeling and empirical description of the transport system.

  8. Accurate ab initio tight-binding Hamiltonians: Effective tools for electronic transport and optical spectroscopy from first principles

    NASA Astrophysics Data System (ADS)

    D'Amico, Pino; Agapito, Luis; Catellani, Alessandra; Ruini, Alice; Curtarolo, Stefano; Fornari, Marco; Nardelli, Marco Buongiorno; Calzolari, Arrigo

    2016-10-01

    The calculations of electronic transport coefficients and optical properties require a very dense interpolation of the electronic band structure in reciprocal space that is computationally expensive and may have issues with band crossing and degeneracies. Capitalizing on a recently developed pseudoatomic orbital projection technique, we exploit the exact tight-binding representation of the first-principles electronic structure for the purposes of (i) providing an efficient strategy to explore the full band structure En(k ) , (ii) computing the momentum operator differentiating directly the Hamiltonian, and (iii) calculating the imaginary part of the dielectric function. This enables us to determine the Boltzmann transport coefficients and the optical properties within the independent particle approximation. In addition, the local nature of the tight-binding representation facilitates the calculation of the ballistic transport within the Landauer theory for systems with hundreds of atoms. In order to validate our approach we study the multivalley band structure of CoSb3 and a large core-shell nanowire using the ACBN0 functional. In CoSb3 we point the many band minima contributing to the electronic transport that enhance the thermoelectric properties; for the core-shell nanowire we identify possible mechanisms for photo-current generation and justify the presence of protected transport channels in the wire.

  9. Lattice Boltzmann modeling of phonon transport

    NASA Astrophysics Data System (ADS)

    Guo, Yangyu; Wang, Moran

    2016-06-01

    A novel lattice Boltzmann scheme is proposed for phonon transport based on the phonon Boltzmann equation. Through the Chapman-Enskog expansion, the phonon lattice Boltzmann equation under the gray relaxation time approximation recovers the classical Fourier's law in the diffusive limit. The numerical parameters in the lattice Boltzmann model are therefore rigorously correlated to the bulk material properties. The new scheme does not only eliminate the fictitious phonon speed in the diagonal direction of a square lattice system in the previous lattice Boltzmann models, but also displays very robust performances in predicting both temperature and heat flux distributions consistent with analytical solutions for diverse numerical cases, including steady-state and transient, macroscale and microscale, one-dimensional and multi-dimensional phonon heat transport. This method may provide a powerful numerical tool for deep studies of nonlinear and nonlocal heat transports in nanosystems.

  10. Contamination transport modeling with CTSP (Conference Presentation)

    NASA Astrophysics Data System (ADS)

    Brieda, Lubos

    2016-09-01

    CTSP (Contamination Transport Simulation Program) is a simulation program for performing detailed molecular and particulate contaminant transport analyses using complex, CAD-generated geometries. CTSP concurrently traces many simulation macroparticles, allowing it to compute contaminant partial pressures. The code uses a detailed surface model that supports multiple trapped gases and a multi-component surface layer. The molecular residence time is computed by considering surface temperature and activation energies. This paper describes the implemented algorithms and demonstrates the code with several test cases. These include outgassing in a vacuum chamber, spacecraft venting, particulate transport in an air flow, and redistribution of paint flakes on an orbiting satellite. The paper is concluded by summarizing the on-going effort to parallelize the code and utilize GPUs, and to add support for electrostatic return modeling by computing space potential using Green's functions.

  11. A Simple and Accurate Model to Predict Responses to Multi-electrode Stimulation in the Retina.

    PubMed

    Maturana, Matias I; Apollo, Nicholas V; Hadjinicolaou, Alex E; Garrett, David J; Cloherty, Shaun L; Kameneva, Tatiana; Grayden, David B; Ibbotson, Michael R; Meffin, Hamish

    2016-04-01

    Implantable electrode arrays are widely used in therapeutic stimulation of the nervous system (e.g. cochlear, retinal, and cortical implants). Currently, most neural prostheses use serial stimulation (i.e. one electrode at a time) despite this severely limiting the repertoire of stimuli that can be applied. Methods to reliably predict the outcome of multi-electrode stimulation have not been available. Here, we demonstrate that a linear-nonlinear model accurately predicts neural responses to arbitrary patterns of stimulation using in vitro recordings from single retinal ganglion cells (RGCs) stimulated with a subretinal multi-electrode array. In the model, the stimulus is projected onto a low-dimensional subspace and then undergoes a nonlinear transformation to produce an estimate of spiking probability. The low-dimensional subspace is estimated using principal components analysis, which gives the neuron's electrical receptive field (ERF), i.e. the electrodes to which the neuron is most sensitive. Our model suggests that stimulation proportional to the ERF yields a higher efficacy given a fixed amount of power when compared to equal amplitude stimulation on up to three electrodes. We find that the model captures the responses of all the cells recorded in the study, suggesting that it will generalize to most cell types in the retina. The model is computationally efficient to evaluate and, therefore, appropriate for future real-time applications including stimulation strategies that make use of recorded neural activity to improve the stimulation strategy.

  12. A Simple and Accurate Model to Predict Responses to Multi-electrode Stimulation in the Retina

    PubMed Central

    Maturana, Matias I.; Apollo, Nicholas V.; Hadjinicolaou, Alex E.; Garrett, David J.; Cloherty, Shaun L.; Kameneva, Tatiana; Grayden, David B.; Ibbotson, Michael R.; Meffin, Hamish

    2016-01-01

    Implantable electrode arrays are widely used in therapeutic stimulation of the nervous system (e.g. cochlear, retinal, and cortical implants). Currently, most neural prostheses use serial stimulation (i.e. one electrode at a time) despite this severely limiting the repertoire of stimuli that can be applied. Methods to reliably predict the outcome of multi-electrode stimulation have not been available. Here, we demonstrate that a linear-nonlinear model accurately predicts neural responses to arbitrary patterns of stimulation using in vitro recordings from single retinal ganglion cells (RGCs) stimulated with a subretinal multi-electrode array. In the model, the stimulus is projected onto a low-dimensional subspace and then undergoes a nonlinear transformation to produce an estimate of spiking probability. The low-dimensional subspace is estimated using principal components analysis, which gives the neuron’s electrical receptive field (ERF), i.e. the electrodes to which the neuron is most sensitive. Our model suggests that stimulation proportional to the ERF yields a higher efficacy given a fixed amount of power when compared to equal amplitude stimulation on up to three electrodes. We find that the model captures the responses of all the cells recorded in the study, suggesting that it will generalize to most cell types in the retina. The model is computationally efficient to evaluate and, therefore, appropriate for future real-time applications including stimulation strategies that make use of recorded neural activity to improve the stimulation strategy. PMID:27035143

  13. Optimal Cluster Mill Pass Scheduling With an Accurate and Rapid New Strip Crown Model

    NASA Astrophysics Data System (ADS)

    Malik, Arif S.; Grandhi, Ramana V.; Zipf, Mark E.

    2007-05-01

    Besides the requirement to roll coiled sheet at high levels of productivity, the optimal pass scheduling of cluster-type reversing cold mills presents the added challenge of assigning mill parameters that facilitate the best possible strip flatness. The pressures of intense global competition, and the requirements for increasingly thinner, higher quality specialty sheet products that are more difficult to roll, continue to force metal producers to commission innovative flatness-control technologies. This means that during the on-line computerized set-up of rolling mills, the mathematical model should not only determine the minimum total number of passes and maximum rolling speed, it should simultaneously optimize the pass-schedule so that desired flatness is assured, either by manual or automated means. In many cases today, however, on-line prediction of strip crown and corresponding flatness for the complex cluster-type rolling mills is typically addressed either by trial and error, by approximate deflection models for equivalent vertical roll-stacks, or by non-physical pattern recognition style models. The abundance of the aforementioned methods is largely due to the complexity of cluster-type mill configurations and the lack of deflection models with sufficient accuracy and speed for on-line use. Without adequate assignment of the pass-schedule set-up parameters, it may be difficult or impossible to achieve the required strip flatness. In this paper, we demonstrate optimization of cluster mill pass-schedules using a new accurate and rapid strip crown model. This pass-schedule optimization includes computations of the predicted strip thickness profile to validate mathematical constraints. In contrast to many of the existing methods for on-line prediction of strip crown and flatness on cluster mills, the demonstrated method requires minimal prior tuning and no extensive training with collected mill data. To rapidly and accurately solve the multi-contact problem

  14. Development and application of accurate analytical models for single active electron potentials

    NASA Astrophysics Data System (ADS)

    Miller, Michelle; Jaron-Becker, Agnieszka; Becker, Andreas

    2015-05-01

    The single active electron (SAE) approximation is a theoretical model frequently employed to study scenarios in which inner-shell electrons may productively be treated as frozen spectators to a physical process of interest, and accurate analytical approximations for these potentials are sought as a useful simulation tool. Density function theory is often used to construct a SAE potential, requiring that a further approximation for the exchange correlation functional be enacted. In this study, we employ the Krieger, Li, and Iafrate (KLI) modification to the optimized-effective-potential (OEP) method to reduce the complexity of the problem to the straightforward solution of a system of linear equations through simple arguments regarding the behavior of the exchange-correlation potential in regions where a single orbital dominates. We employ this method for the solution of atomic and molecular potentials, and use the resultant curve to devise a systematic construction for highly accurate and useful analytical approximations for several systems. Supported by the U.S. Department of Energy (Grant No. DE-FG02-09ER16103), and the U.S. National Science Foundation (Graduate Research Fellowship, Grants No. PHY-1125844 and No. PHY-1068706).

  15. Exchange-Hole Dipole Dispersion Model for Accurate Energy Ranking in Molecular Crystal Structure Prediction.

    PubMed

    Whittleton, Sarah R; Otero-de-la-Roza, A; Johnson, Erin R

    2017-02-14

    Accurate energy ranking is a key facet to the problem of first-principles crystal-structure prediction (CSP) of molecular crystals. This work presents a systematic assessment of B86bPBE-XDM, a semilocal density functional combined with the exchange-hole dipole moment (XDM) dispersion model, for energy ranking using 14 compounds from the first five CSP blind tests. Specifically, the set of crystals studied comprises 11 rigid, planar compounds and 3 co-crystals. The experimental structure was correctly identified as the lowest in lattice energy for 12 of the 14 total crystals. One of the exceptions is 4-hydroxythiophene-2-carbonitrile, for which the experimental structure was correctly identified once a quasi-harmonic estimate of the vibrational free-energy contribution was included, evidencing the occasional importance of thermal corrections for accurate energy ranking. The other exception is an organic salt, where charge-transfer error (also called delocalization error) is expected to cause the base density functional to be unreliable. Provided the choice of base density functional is appropriate and an estimate of temperature effects is used, XDM-corrected density-functional theory is highly reliable for the energetic ranking of competing crystal structures.

  16. Fast and accurate analytical model to solve inverse problem in SHM using Lamb wave propagation

    NASA Astrophysics Data System (ADS)

    Poddar, Banibrata; Giurgiutiu, Victor

    2016-04-01

    Lamb wave propagation is at the center of attention of researchers for structural health monitoring of thin walled structures. This is due to the fact that Lamb wave modes are natural modes of wave propagation in these structures with long travel distances and without much attenuation. This brings the prospect of monitoring large structure with few sensors/actuators. However the problem of damage detection and identification is an "inverse problem" where we do not have the luxury to know the exact mathematical model of the system. On top of that the problem is more challenging due to the confounding factors of statistical variation of the material and geometric properties. Typically this problem may also be ill posed. Due to all these complexities the direct solution of the problem of damage detection and identification in SHM is impossible. Therefore an indirect method using the solution of the "forward problem" is popular for solving the "inverse problem". This requires a fast forward problem solver. Due to the complexities involved with the forward problem of scattering of Lamb waves from damages researchers rely primarily on numerical techniques such as FEM, BEM, etc. But these methods are slow and practically impossible to be used in structural health monitoring. We have developed a fast and accurate analytical forward problem solver for this purpose. This solver, CMEP (complex modes expansion and vector projection), can simulate scattering of Lamb waves from all types of damages in thin walled structures fast and accurately to assist the inverse problem solver.

  17. Ab initio calculations to support accurate modelling of the rovibronic spectroscopy calculations of vanadium monoxide (VO)

    NASA Astrophysics Data System (ADS)

    McKemmish, Laura K.; Yurchenko, Sergei N.; Tennyson, Jonathan

    2016-11-01

    Accurate knowledge of the rovibronic near-infrared and visible spectra of vanadium monoxide (VO) is very important for studies of cool stellar and hot planetary atmospheres. Here, the required ab initio dipole moment and spin-orbit coupling curves for VO are produced. This data forms the basis of a new VO line list considering 13 different electronic states and containing over 277 million transitions. Open shell transition, metal diatomics are challenging species to model through ab initio quantum mechanics due to the large number of low-lying electronic states, significant spin-orbit coupling and strong static and dynamic electron correlation. Multi-reference configuration interaction methodologies using orbitals from a complete active space self-consistent-field (CASSCF) calculation are the standard technique for these systems. We use different state-specific or minimal-state CASSCF orbitals for each electronic state to maximise the calculation accuracy. The off-diagonal dipole moment controls the intensity of electronic transitions. We test finite-field off-diagonal dipole moments, but found that (1) the accuracy of the excitation energies were not sufficient to allow accurate dipole moments to be evaluated and (2) computer time requirements for perpendicular transitions were prohibitive. The best off-diagonal dipole moments are calculated using wavefunctions with different CASSCF orbitals.

  18. Magnetic gaps in organic tri-radicals: From a simple model to accurate estimates

    NASA Astrophysics Data System (ADS)

    Barone, Vincenzo; Cacelli, Ivo; Ferretti, Alessandro; Prampolini, Giacomo

    2017-03-01

    The calculation of the energy gap between the magnetic states of organic poly-radicals still represents a challenging playground for quantum chemistry, and high-level techniques are required to obtain accurate estimates. On these grounds, the aim of the present study is twofold. From the one side, it shows that, thanks to recent algorithmic and technical improvements, we are able to compute reliable quantum mechanical results for the systems of current fundamental and technological interest. From the other side, proper parameterization of a simple Hubbard Hamiltonian allows for a sound rationalization of magnetic gaps in terms of basic physical effects, unraveling the role played by electron delocalization, Coulomb repulsion, and effective exchange in tuning the magnetic character of the ground state. As case studies, we have chosen three prototypical organic tri-radicals, namely, 1,3,5-trimethylenebenzene, 1,3,5-tridehydrobenzene, and 1,2,3-tridehydrobenzene, which differ either for geometric or electronic structure. After discussing the differences among the three species and their consequences on the magnetic properties in terms of the simple model mentioned above, accurate and reliable values for the energy gap between the lowest quartet and doublet states are computed by means of the so-called difference dedicated configuration interaction (DDCI) technique, and the final results are discussed and compared to both available experimental and computational estimates.

  19. Modeling effects of multinode wells on solute transport

    USGS Publications Warehouse

    Konikow, L.F.; Hornberger, G.Z.

    2006-01-01

    Long-screen wells or long open boreholes with intraborehole flow potentially provide pathways for contaminants to move from one location to another in a ground water flow system. Such wells also can perturb a flow field so that the well will not provide water samples that are representative of ground water quality a short distance away from the well. A methodology is presented to accurately and efficiently simulate solute transport in ground water systems that include wells longer than the grid spacing used in a simulation model of the system and hence are connected to multiple nodes of the grid. The methods are implemented in a MODFLOW-compatible solute-transport model and use MODFLOW's Multi-Node Well Package but are generic and can be readily implemented in other solute-transport models. For nonpumping multinode wells (used to simulate open boreholes or observation wells, for example) and for low-rate pumping wells (in which the flow between the well and the ground water system is not unidirectional), a simple routing and local mixing model was developed to calculate nodal concentrations within the borehole. For high-rate pumping multinode wells (either withdrawal or injection, in which flow between the well and the ground water system is in the same direction at all well nodes), complete and instantaneous mixing in the wellbore of all inflows is assumed.

  20. Modeling Facilitated Contaminant Transport by Mobile Bacteria

    NASA Astrophysics Data System (ADS)

    Corapcioglu, M. Yavuz; Kim, Seunghyun

    1995-01-01

    Introduction of exogenous biocolloids such as genetically engineered bacteria in a bioremediation operation can enhance the transport of contaminants in groundwater by reducing the retardation effects. Because of their colloidal size and favorable surface conditions, bacteria are efficient contaminant carriers. In cases where contaminants have a low mobility in porous media because of their high partition with solid matrix, facilitated contaminant transport by mobile bacteria can create high contaminant fluxes. When metabolically active mobile bacteria are present in a subsurface environment, the system can be treated as consisting of three phases: water phase, bacterial phase, and stationary solid matrix phase. In this work a mathematical model based on mass balance equations is developed to describe the facilitated transport and fate of a contaminant and bacteria in a porous medium. Bacterial partition between the bulk solution and the stationary solid matrix and contaminant partition among three phases are represented by expressions in terms of measurable quantities. Solutions were obtained to provide estimates of contaminant and bacterial concentrations. A dimensional analysis of the transport model was utilized to estimate model parameters from the experimental data and to assess the effect of several parameters on model behavior. The model results matched favorably with experimental data of Jenkins and Lion (1993). The presence of mobile bacteria enhances the contaminant transport. However, bacterial consumption of the contaminant, which serves as a bacterial nutrient, can attenuate the contaminant mobility. The work presented in this paper is the first three-phase model to include the effects of substrate metabolism on the fate of groundwater contaminants.

  1. Glucose Transport Machinery Reconstituted in Cell Models

    PubMed Central

    Hansen, Jesper S.; Elbing, Karin; Thompson, James R.; Malmstadt, Noah

    2015-01-01

    Here we demonstrate the production of a functioning cell model by formation of giant vesicles reconstituted with the GLUT1 glucose transporter and a glucose oxidase and hydrogen peroxidase linked fluorescent reporter internally. Hence, a simplified artificial cell is formed that is able to take up glucose and process it. PMID:25562394

  2. Glucose transport machinery reconstituted in cell models.

    PubMed

    Hansen, Jesper S; Elbing, Karin; Thompson, James R; Malmstadt, Noah; Lindkvist-Petersson, Karin

    2015-02-11

    Here we demonstrate the production of a functioning cell model by formation of giant vesicles reconstituted with the GLUT1 glucose transporter and a glucose oxidase and hydrogen peroxidase linked fluorescent reporter internally. Hence, a simplified artificial cell is formed that is able to take up glucose and process it.

  3. MHD Modeling of the Transition Region Using Realistic Transport Coefficients

    NASA Astrophysics Data System (ADS)

    Goodman, Michael L.

    1997-05-01

    Most of the transition region (TR) consists of a collision dominated plasma. The dissipation and transport of energy in such a plasma is accurately described by the well known classical transport coefficients which include the electrical and thermal conductivity, viscosity, and thermo- electric tensors. These tensors are anisotropic and are functions of local values of temperature, density, and magnetic field. They may be used in an MHD model to obtain a self consistent, physically realistic description of the TR. The physics of kinetic processes is included in the MHD model through the transport coefficients. As a first step in studying heating and cooling processes in the TR in a realistic, quantitative manner, a 1.5 dimensional, steady state MHD model with a specified temperature profile is considered. The momentum equation includes the inertial, pressure gradient, Lorentz, and gravitational forces. The Ohm's law includes the exact expressions for the electrical conductivity and thermo- electric tensors. The electrical conductivity relates the generalized electric field to the conduction current density while the thermo-electric tensor relates the temperature gradient to the thermo-electric current density. The total current density is the sum of the two. It is found that the thermo-electric current density can be as large as the conduction current density, indicating that thermo-electric effects are probably important in modeling the dynamics of energy dissipation, such as wave dissipation, in the TR. Although the temperature gradient is in the vertical direction, the thermo-electric current density is in the horizontal direction, indicating the importance of the effects of anisotropic transport. The transport coefficients are valid for all magnetic field strengths, and so may be used to study the physics of weakly as well as strongly magnetized regions of the TR. Numerical examples are presented.

  4. Modeling methodology for the accurate and prompt prediction of symptomatic events in chronic diseases.

    PubMed

    Pagán, Josué; Risco-Martín, José L; Moya, José M; Ayala, José L

    2016-08-01

    Prediction of symptomatic crises in chronic diseases allows to take decisions before the symptoms occur, such as the intake of drugs to avoid the symptoms or the activation of medical alarms. The prediction horizon is in this case an important parameter in order to fulfill the pharmacokinetics of medications, or the time response of medical services. This paper presents a study about the prediction limits of a chronic disease with symptomatic crises: the migraine. For that purpose, this work develops a methodology to build predictive migraine models and to improve these predictions beyond the limits of the initial models. The maximum prediction horizon is analyzed, and its dependency on the selected features is studied. A strategy for model selection is proposed to tackle the trade off between conservative but robust predictive models, with respect to less accurate predictions with higher horizons. The obtained results show a prediction horizon close to 40min, which is in the time range of the drug pharmacokinetics. Experiments have been performed in a realistic scenario where input data have been acquired in an ambulatory clinical study by the deployment of a non-intrusive Wireless Body Sensor Network. Our results provide an effective methodology for the selection of the future horizon in the development of prediction algorithms for diseases experiencing symptomatic crises.

  5. Efficient and Accurate Explicit Integration Algorithms with Application to Viscoplastic Models

    NASA Technical Reports Server (NTRS)

    Arya, Vinod K.

    1994-01-01

    Several explicit integration algorithms with self-adative time integration strategies are developed and investigated for efficiency and accuracy. These algorithms involve the Runge-Kutta second order, the lower Runge-Kutta method of orders one and two, and the exponential integration method. The algorithms are applied to viscoplastic models put forth by Freed and Verrilli and Bodner and Partom for thermal/mechanical loadings (including tensile, relaxation, and cyclic loadings). The large amount of computations performed showed that, for comparable accuracy, the efficiency of an integration algorithm depends significantly on the type of application (loading). However, in general, for the aforementioned loadings and viscoplastic models, the exponential integration algorithm with the proposed self-adaptive time integration strategy worked more (or comparably) efficiently and accurately than the other integration algorithms. Using this strategy for integrating viscoplastic models may lead to considerable savings in computer time (better efficiency) without adversely affecting the accuracy of the results. This conclusion should encourage the utilization of viscoplastic models in the stress analysis and design of structural components.

  6. Accurate integral equation theory for the central force model of liquid water and ionic solutions

    NASA Astrophysics Data System (ADS)

    Ichiye, Toshiko; Haymet, A. D. J.

    1988-10-01

    The atom-atom pair correlation functions and thermodynamics of the central force model of water, introduced by Lemberg, Stillinger, and Rahman, have been calculated accurately by an integral equation method which incorporates two new developments. First, a rapid new scheme has been used to solve the Ornstein-Zernike equation. This scheme combines the renormalization methods of Allnatt, and Rossky and Friedman with an extension of the trigonometric basis-set solution of Labik and co-workers. Second, by adding approximate ``bridge'' functions to the hypernetted-chain (HNC) integral equation, we have obtained predictions for liquid water in which the hydrogen bond length and number are in good agreement with ``exact'' computer simulations of the same model force laws. In addition, for dilute ionic solutions, the ion-oxygen and ion-hydrogen coordination numbers display both the physically correct stoichiometry and good agreement with earlier simulations. These results represent a measurable improvement over both a previous HNC solution of the central force model and the ex-RISM integral equation solutions for the TIPS and other rigid molecule models of water.

  7. Accurate and fast simulation of channel noise in conductance-based model neurons by diffusion approximation.

    PubMed

    Linaro, Daniele; Storace, Marco; Giugliano, Michele

    2011-03-01

    Stochastic channel gating is the major source of intrinsic neuronal noise whose functional consequences at the microcircuit- and network-levels have been only partly explored. A systematic study of this channel noise in large ensembles of biophysically detailed model neurons calls for the availability of fast numerical methods. In fact, exact techniques employ the microscopic simulation of the random opening and closing of individual ion channels, usually based on Markov models, whose computational loads are prohibitive for next generation massive computer models of the brain. In this work, we operatively define a procedure for translating any Markov model describing voltage- or ligand-gated membrane ion-conductances into an effective stochastic version, whose computer simulation is efficient, without compromising accuracy. Our approximation is based on an improved Langevin-like approach, which employs stochastic differential equations and no Montecarlo methods. As opposed to an earlier proposal recently debated in the literature, our approximation reproduces accurately the statistical properties of the exact microscopic simulations, under a variety of conditions, from spontaneous to evoked response features. In addition, our method is not restricted to the Hodgkin-Huxley sodium and potassium currents and is general for a variety of voltage- and ligand-gated ion currents. As a by-product, the analysis of the properties emerging in exact Markov schemes by standard probability calculus enables us for the first time to analytically identify the sources of inaccuracy of the previous proposal, while providing solid ground for its modification and improvement we present here.

  8. Evaluation of a quantitative phosphorus transport model for potential improvement of southern phosphorus indices

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Due to a shortage of available phosphorus (P) loss data sets, simulated data from a quantitative P transport model could be used to evaluate a P-index. However, the model would need to accurately predict the P loss data sets that are available. The objective of this study was to compare predictions ...

  9. Sediment and radionuclide transport in rivers: radionuclide transport modeling for Cattaraugus and Buttermilk Creeks, New York

    SciTech Connect

    Onishi, Y.; Yabusaki, S.B.; Kincaid, C.T.; Skaggs, R.L.; Walters, W.H.

    1982-12-01

    SERATRA, a transient, two-dimensional (laterally-averaged) computer model of sediment-contaminant transport in rivers, satisfactorily resolved the distribution of sediment and radionuclide concentrations in the Cattaraugus Creek stream system in New York. By modeling the physical processes of advection, diffusion, erosion, deposition, and bed armoring, SERATRA routed three sediment size fractions, including cohesive soils, to simulate three dynamic flow events. In conjunction with the sediment transport, SERATRA computed radionuclide levels in dissolved, suspended sediment, and bed sediment forms for four radionuclides (/sup 137/Cs, /sup 90/Sr, /sup 239/ /sup 240/Pu, and /sup 3/H). By accounting for time-dependent sediment-radionuclide interaction in the water column and bed, SERATA is a physically explicit model of radionuclide fate and migration. Sediment and radionuclide concentrations calculated by SERATA in the Cattaraugus Creek stream system are in reasonable agreement with measured values. SERATRA is in the field performance phase of an extensive testing program designed to establish the utility of the model as a site assessment tool. The model handles not only radionuclides but other contaminants such as pesticides, heavy metals and other toxic chemicals. Now that the model has been applied to four field sites, including the latest study of the Cattaraugus Creek stream system, it is recommended that a final model be validated through comparison of predicted results with field data from a carefully controlled tracer test at a field site. It is also recommended that a detailed laboratory flume be tested to study cohesive sediment transport, deposition, and erosion characteristics. The lack of current understanding of these characteristics is one of the weakest areas hindering the accurate assessment of the migration of radionuclides sorbed by fine sediments of silt and clay.

  10. Nearshore Tsunami Inundation Model Validation: Toward Sediment Transport Applications

    USGS Publications Warehouse

    Apotsos, Alex; Buckley, Mark; Gelfenbaum, Guy; Jaffe, Bruce; Vatvani, Deepak

    2011-01-01

    Model predictions from a numerical model, Delft3D, based on the nonlinear shallow water equations are compared with analytical results and laboratory observations from seven tsunami-like benchmark experiments, and with field observations from the 26 December 2004 Indian Ocean tsunami. The model accurately predicts the magnitude and timing of the measured water levels and flow velocities, as well as the magnitude of the maximum inundation distance and run-up, for both breaking and non-breaking waves. The shock-capturing numerical scheme employed describes well the total decrease in wave height due to breaking, but does not reproduce the observed shoaling near the break point. The maximum water levels observed onshore near Kuala Meurisi, Sumatra, following the 26 December 2004 tsunami are well predicted given the uncertainty in the model setup. The good agreement between the model predictions and the analytical results and observations demonstrates that the numerical solution and wetting and drying methods employed are appropriate for modeling tsunami inundation for breaking and non-breaking long waves. Extension of the model to include sediment transport may be appropriate for long, non-breaking tsunami waves. Using available sediment transport formulations, the sediment deposit thickness at Kuala Meurisi is predicted generally within a factor of 2.

  11. A General Pairwise Interaction Model Provides an Accurate Description of In Vivo Transcription Factor Binding Sites

    PubMed Central

    Santolini, Marc; Mora, Thierry; Hakim, Vincent

    2014-01-01

    The identification of transcription factor binding sites (TFBSs) on genomic DNA is of crucial importance for understanding and predicting regulatory elements in gene networks. TFBS motifs are commonly described by Position Weight Matrices (PWMs), in which each DNA base pair contributes independently to the transcription factor (TF) binding. However, this description ignores correlations between nucleotides at different positions, and is generally inaccurate: analysing fly and mouse in vivo ChIPseq data, we show that in most cases the PWM model fails to reproduce the observed statistics of TFBSs. To overcome this issue, we introduce the pairwise interaction model (PIM), a generalization of the PWM model. The model is based on the principle of maximum entropy and explicitly describes pairwise correlations between nucleotides at different positions, while being otherwise as unconstrained as possible. It is mathematically equivalent to considering a TF-DNA binding energy that depends additively on each nucleotide identity at all positions in the TFBS, like the PWM model, but also additively on pairs of nucleotides. We find that the PIM significantly improves over the PWM model, and even provides an optimal description of TFBS statistics within statistical noise. The PIM generalizes previous approaches to interdependent positions: it accounts for co-variation of two or more base pairs, and predicts secondary motifs, while outperforming multiple-motif models consisting of mixtures of PWMs. We analyse the structure of pairwise interactions between nucleotides, and find that they are sparse and dominantly located between consecutive base pairs in the flanking region of TFBS. Nonetheless, interactions between pairs of non-consecutive nucleotides are found to play a significant role in the obtained accurate description of TFBS statistics. The PIM is computationally tractable, and provides a general framework that should be useful for describing and predicting TFBSs beyond

  12. Application of thin plate splines for accurate regional ionosphere modeling with multi-GNSS data

    NASA Astrophysics Data System (ADS)

    Krypiak-Gregorczyk, Anna; Wielgosz, Pawel; Borkowski, Andrzej

    2016-04-01

    GNSS-derived regional ionosphere models are widely used in both precise positioning, ionosphere and space weather studies. However, their accuracy is often not sufficient to support precise positioning, RTK in particular. In this paper, we presented new approach that uses solely carrier phase multi-GNSS observables and thin plate splines (TPS) for accurate ionospheric TEC modeling. TPS is a closed solution of a variational problem minimizing both the sum of squared second derivatives of a smoothing function and the deviation between data points and this function. This approach is used in UWM-rt1 regional ionosphere model developed at UWM in Olsztyn. The model allows for providing ionospheric TEC maps with high spatial and temporal resolutions - 0.2x0.2 degrees and 2.5 minutes, respectively. For TEC estimation, EPN and EUPOS reference station data is used. The maps are available with delay of 15-60 minutes. In this paper we compare the performance of UWM-rt1 model with IGS global and CODE regional ionosphere maps during ionospheric storm that took place on March 17th, 2015. During this storm, the TEC level over Europe doubled comparing to earlier quiet days. The performance of the UWM-rt1 model was validated by (a) comparison to reference double-differenced ionospheric corrections over selected baselines, and (b) analysis of post-fit residuals to calibrated carrier phase geometry-free observational arcs at selected test stations. The results show a very good performance of UWM-rt1 model. The obtained post-fit residuals in case of UWM maps are lower by one order of magnitude comparing to IGS maps. The accuracy of UWM-rt1 -derived TEC maps is estimated at 0.5 TECU. This may be directly translated to the user positioning domain.

  13. Accurate force fields and methods for modelling organic molecular crystals at finite temperatures.

    PubMed

    Nyman, Jonas; Pundyke, Orla Sheehan; Day, Graeme M

    2016-06-21

    We present an assessment of the performance of several force fields for modelling intermolecular interactions in organic molecular crystals using the X23 benchmark set. The performance of the force fields is compared to several popular dispersion corrected density functional methods. In addition, we present our implementation of lattice vibrational free energy calculations in the quasi-harmonic approximation, using several methods to account for phonon dispersion. This allows us to also benchmark the force fields' reproduction of finite temperature crystal structures. The results demonstrate that anisotropic atom-atom multipole-based force fields can be as accurate as several popular DFT-D methods, but have errors 2-3 times larger than the current best DFT-D methods. The largest error in the examined force fields is a systematic underestimation of the (absolute) lattice energy.

  14. Accurate Modeling of Organic Molecular Crystals by Dispersion-Corrected Density Functional Tight Binding (DFTB).

    PubMed

    Brandenburg, Jan Gerit; Grimme, Stefan

    2014-06-05

    The ambitious goal of organic crystal structure prediction challenges theoretical methods regarding their accuracy and efficiency. Dispersion-corrected density functional theory (DFT-D) in principle is applicable, but the computational demands, for example, to compute a huge number of polymorphs, are too high. Here, we demonstrate that this task can be carried out by a dispersion-corrected density functional tight binding (DFTB) method. The semiempirical Hamiltonian with the D3 correction can accurately and efficiently model both solid- and gas-phase inter- and intramolecular interactions at a speed up of 2 orders of magnitude compared to DFT-D. The mean absolute deviations for interaction (lattice) energies for various databases are typically 2-3 kcal/mol (10-20%), that is, only about two times larger than those for DFT-D. For zero-point phonon energies, small deviations of <0.5 kcal/mol compared to DFT-D are obtained.

  15. SMARTIES: Spheroids Modelled Accurately with a Robust T-matrix Implementation for Electromagnetic Scattering

    NASA Astrophysics Data System (ADS)

    Somerville, W. R. C.; Auguié, B.; Le Ru, E. C.

    2016-03-01

    SMARTIES calculates the optical properties of oblate and prolate spheroidal particles, with comparable capabilities and ease-of-use as Mie theory for spheres. This suite of MATLAB codes provides a fully documented implementation of an improved T-matrix algorithm for the theoretical modelling of electromagnetic scattering by particles of spheroidal shape. Included are scripts that cover a range of scattering problems relevant to nanophotonics and plasmonics, including calculation of far-field scattering and absorption cross-sections for fixed incidence orientation, orientation-averaged cross-sections and scattering matrix, surface-field calculations as well as near-fields, wavelength-dependent near-field and far-field properties, and access to lower-level functions implementing the T-matrix calculations, including the T-matrix elements which may be calculated more accurately than with competing codes.

  16. Development of Accurate Chemical Equilibrium Models for the Hanford Waste Tanks: New Thermodynamic Measurements and Model Applications

    SciTech Connect

    Felmy, Andrew R.; Mason, Marvin; Qafoku, Odeta; Xia, Yuanxian; Wang, Zheming; MacLean, Graham

    2003-03-27

    Developing accurate thermodynamic models for predicting the chemistry of the high-level waste tanks at Hanford is an extremely daunting challenge in electrolyte and radionuclide chemistry. These challenges stem from the extremely high ionic strength of the tank waste supernatants, presence of chelating agents in selected tanks, wide temperature range in processing conditions and the presence of important actinide species in multiple oxidation states. This presentation summarizes progress made to date in developing accurate models for these tank waste solutions, how these data are being used at Hanford and the important challenges that remain. New thermodynamic measurements on Sr and actinide complexation with specific chelating agents (EDTA, HEDTA and gluconate) will also be presented.

  17. Stochastic models for convective momentum transport.

    PubMed

    Majda, Andrew J; Stechmann, Samuel N

    2008-11-18

    The improved parameterization of unresolved features of tropical convection is a central challenge in current computer models for long-range ensemble forecasting of weather and short-term climate change. Observations, theory, and detailed smaller-scale numerical simulations suggest that convective momentum transport (CMT) from the unresolved scales to the resolved scales is one of the major deficiencies in contemporary computer models. Here, a combination of mathematical and physical reasoning is utilized to build simple stochastic models that capture the significant intermittent upscale transports of CMT on the large scales due to organized unresolved convection from squall lines. Properties of the stochastic model for CMT are developed below in a test column model environment for the large-scale variables. The effects of CMT from the stochastic model on a large-scale convectively coupled wave in an idealized setting are presented below as a nontrivial test problem. Here, the upscale transports from stochastic effects are significant and even generate a large-scale mean flow which can interact with the convectively coupled wave.

  18. Oxygen-enhanced MRI accurately identifies, quantifies, and maps tumor hypoxia in preclinical cancer models

    PubMed Central

    O’Connor, James PB; Boult, Jessica KR; Jamin, Yann; Babur, Muhammad; Finegan, Katherine G; Williams, Kaye J; Little, Ross A; Jackson, Alan; Parker, Geoff JM; Reynolds, Andrew R; Waterton, John C; Robinson, Simon P

    2015-01-01

    There is a clinical need for non-invasive biomarkers of tumor hypoxia for prognostic and predictive studies, radiotherapy planning and therapy monitoring. Oxygen enhanced MRI (OE-MRI) is an emerging imaging technique for quantifying the spatial distribution and extent of tumor oxygen delivery in vivo. In OE-MRI, the longitudinal relaxation rate of protons (ΔR1) changes in proportion to the concentration of molecular oxygen dissolved in plasma or interstitial tissue fluid. Therefore, well-oxygenated tissues show positive ΔR1. We hypothesized that the fraction of tumor tissue refractory to oxygen challenge (lack of positive ΔR1, termed “Oxy-R fraction”) would be a robust biomarker of hypoxia in models with varying vascular and hypoxic features. Here we demonstrate that OE-MRI signals are accurate, precise and sensitive to changes in tumor pO2 in highly vascular 786-0 renal cancer xenografts. Furthermore, we show that Oxy-R fraction can quantify the hypoxic fraction in multiple models with differing hypoxic and vascular phenotypes, when used in combination with measurements of tumor perfusion. Finally, Oxy-R fraction can detect dynamic changes in hypoxia induced by the vasomodulator agent hydralazine. In contrast, more conventional biomarkers of hypoxia (derived from blood oxygenation-level dependent MRI and dynamic contrast-enhanced MRI) did not relate to tumor hypoxia consistently. Our results show that the Oxy-R fraction accurately quantifies tumor hypoxia non-invasively and is immediately translatable to the clinic. PMID:26659574

  19. ACE-Asia Chemical Transport Modeling Overview

    NASA Astrophysics Data System (ADS)

    UNO, I.; Chin, M.; Collins, W.; Ginoux, P.; Rasch, P.; Carmichael, G. R.; Yienger, J. J.

    2001-12-01

    ACE-Asia (Asia Pacific Regional Aerosol Characterization Experiment) was designed to increase our understanding of how atmospheric aerosol particles affect the Earth?s climate system. The intensive observation period was carried out during March to May, 2001, and more than 100 researchers from several countries (United States, Japan, Korea, China, and many other Asian countries) participated using aircraft, a research vessel, surface stations and numerical models. Aerosol transport forecast activities played an important role during the ACE-Asia intensive observation period. Three independent modeling groups operated chemical transport models in forecast mode and participated in flight planning activities at the operations center. These models were: MATCH (Model of Atmospheric Transport and Chemistry; Rasch and Collins); GOCART (Georgia Tech/Goddard Global Ozone Chemistry Aerosol Radiation and Transport model; Chin and Ginour) and CFORS (Research Institute for Applied Mechanics, Kyushu University + University of Iowa - Chemical weather FORecast System; Uno, Carmichael and Yienger). The MATCH model used in ACE-Asia was a transport model applied for the Asia region, driven by NCEP forecast meteorology. A unique feature of this model was that it assimilated satellite derived optical depths into its forecast algorithm. The GOCART model provided global aerosol forecast using forecast meteorological fields provided by the Goddard Earth Observing System Data Assimilation System (GEOS DAS). The CFORS model provided regional forecasts using a limited area transport model coupled with Regional Meteorological Modeling System (RAMS), initialized by NCEP and JMA forecasts. All models produced 3-d aerosol forecast products consisting of aerosol mass distributions and optical depths for sulfate, black carbon, organic carbon, sea salt, and dust. In the field these model products were made available to all participating scientists via the Web, and were also presented during the

  20. A model of axonal transport drug delivery

    NASA Astrophysics Data System (ADS)

    Kuznetsov, Andrey V.

    2012-04-01

    In this paper a model of targeted drug delivery by means of active (motor-driven) axonal transport is developed. The model is motivated by recent experimental research by Filler et al. (A.G. Filler, G.T. Whiteside, M. Bacon, M. Frederickson, F.A. Howe, M.D. Rabinowitz, A.J. Sokoloff, T.W. Deacon, C. Abell, R. Munglani, J.R. Griffiths, B.A. Bell, A.M.L. Lever, Tri-partite complex for axonal transport drug delivery achieves pharmacological effect, Bmc Neuroscience 11 (2010) 8) that reported synthesis and pharmacological efficiency tests of a tri-partite complex designed for axonal transport drug delivery. The developed model accounts for two populations of pharmaceutical agent complexes (PACs): PACs that are transported retrogradely by dynein motors and PACs that are accumulated in the axon at the Nodes of Ranvier. The transitions between these two populations of PACs are described by first-order reactions. An analytical solution of the coupled system of transient equations describing conservations of these two populations of PACs is obtained by using Laplace transform. Numerical results for various combinations of parameter values are presented and their physical significance is discussed.

  1. Discrete state model and accurate estimation of loop entropy of RNA secondary structures.

    PubMed

    Zhang, Jian; Lin, Ming; Chen, Rong; Wang, Wei; Liang, Jie

    2008-03-28

    Conformational entropy makes important contribution to the stability and folding of RNA molecule, but it is challenging to either measure or compute conformational entropy associated with long loops. We develop optimized discrete k-state models of RNA backbone based on known RNA structures for computing entropy of loops, which are modeled as self-avoiding walks. To estimate entropy of hairpin, bulge, internal loop, and multibranch loop of long length (up to 50), we develop an efficient sampling method based on the sequential Monte Carlo principle. Our method considers excluded volume effect. It is general and can be applied to calculating entropy of loops with longer length and arbitrary complexity. For loops of short length, our results are in good agreement with a recent theoretical model and experimental measurement. For long loops, our estimated entropy of hairpin loops is in excellent agreement with the Jacobson-Stockmayer extrapolation model. However, for bulge loops and more complex secondary structures such as internal and multibranch loops, we find that the Jacobson-Stockmayer extrapolation model has large errors. Based on estimated entropy, we have developed empirical formulae for accurate calculation of entropy of long loops in different secondary structures. Our study on the effect of asymmetric size of loops suggest that loop entropy of internal loops is largely determined by the total loop length, and is only marginally affected by the asymmetric size of the two loops. Our finding suggests that the significant asymmetric effects of loop length in internal loops measured by experiments are likely to be partially enthalpic. Our method can be applied to develop improved energy parameters important for studying RNA stability and folding, and for predicting RNA secondary and tertiary structures. The discrete model and the program used to calculate loop entropy can be downloaded at http://gila.bioengr.uic.edu/resources/RNA.html.

  2. Random generalized linear model: a highly accurate and interpretable ensemble predictor

    PubMed Central

    2013-01-01

    Background Ensemble predictors such as the random forest are known to have superior accuracy but their black-box predictions are difficult to interpret. In contrast, a generalized linear model (GLM) is very interpretable especially when forward feature selection is used to construct the model. However, forward feature selection tends to overfit the data and leads to low predictive accuracy. Therefore, it remains an important research goal to combine the advantages of ensemble predictors (high accuracy) with the advantages of forward regression modeling (interpretability). To address this goal several articles have explored GLM based ensemble predictors. Since limited evaluations suggested that these ensemble predictors were less accurate than alternative predictors, they have found little attention in the literature. Results Comprehensive evaluations involving hundreds of genomic data sets, the UCI machine learning benchmark data, and simulations are used to give GLM based ensemble predictors a new and careful look. A novel bootstrap aggregated (bagged) GLM predictor that incorporates several elements of randomness and instability (random subspace method, optional interaction terms, forward variable selection) often outperforms a host of alternative prediction methods including random forests and penalized regression models (ridge regression, elastic net, lasso). This random generalized linear model (RGLM) predictor provides variable importance measures that can be used to define a “thinned” ensemble predictor (involving few features) that retains excellent predictive accuracy. Conclusion RGLM is a state of the art predictor that shares the advantages of a random forest (excellent predictive accuracy, feature importance measures, out-of-bag estimates of accuracy) with those of a forward selected generalized linear model (interpretability). These methods are implemented in the freely available R software package randomGLM. PMID:23323760

  3. Modeling of transport phenomena in tokamak plasmas with neural networks

    NASA Astrophysics Data System (ADS)

    Meneghini, O.; Luna, C. J.; Smith, S. P.; Lao, L. L.

    2014-06-01

    A new transport model that uses neural networks (NNs) to yield electron and ion heat flux profiles has been developed. Given a set of local dimensionless plasma parameters similar to the ones that the highest fidelity models use, the NN model is able to efficiently and accurately predict the ion and electron heat transport profiles. As a benchmark, a NN was built, trained, and tested on data from the 2012 and 2013 DIII-D experimental campaigns. It is found that NN can capture the experimental behavior over the majority of the plasma radius and across a broad range of plasma regimes. Although each radial location is calculated independently from the others, the heat flux profiles are smooth, suggesting that the solution found by the NN is a smooth function of the local input parameters. This result supports the evidence of a well-defined, non-stochastic relationship between the input parameters and the experimentally measured transport fluxes. The numerical efficiency of this method, requiring only a few CPU-μs per data point, makes it ideal for scenario development simulations and real-time plasma control.

  4. Modeling of transport phenomena in tokamak plasmas with neural networks

    SciTech Connect

    Meneghini, O.; Luna, C. J.; Smith, S. P.; Lao, L. L.

    2014-06-15

    A new transport model that uses neural networks (NNs) to yield electron and ion heat flux profiles has been developed. Given a set of local dimensionless plasma parameters similar to the ones that the highest fidelity models use, the NN model is able to efficiently and accurately predict the ion and electron heat transport profiles. As a benchmark, a NN was built, trained, and tested on data from the 2012 and 2013 DIII-D experimental campaigns. It is found that NN can capture the experimental behavior over the majority of the plasma radius and across a broad range of plasma regimes. Although each radial location is calculated independently from the others, the heat flux profiles are smooth, suggesting that the solution found by the NN is a smooth function of the local input parameters. This result supports the evidence of a well-defined, non-stochastic relationship between the input parameters and the experimentally measured transport fluxes. The numerical efficiency of this method, requiring only a few CPU-μs per data point, makes it ideal for scenario development simulations and real-time plasma control.

  5. Development of a Fast and Accurate PCRTM Radiative Transfer Model in the Solar Spectral Region

    NASA Technical Reports Server (NTRS)

    Liu, Xu; Yang, Qiguang; Li, Hui; Jin, Zhonghai; Wu, Wan; Kizer, Susan; Zhou, Daniel K.; Yang, Ping

    2016-01-01

    A fast and accurate principal component-based radiative transfer model in the solar spectral region (PCRTMSOLAR) has been developed. The algorithm is capable of simulating reflected solar spectra in both clear sky and cloudy atmospheric conditions. Multiple scattering of the solar beam by the multilayer clouds and aerosols are calculated using a discrete ordinate radiative transfer scheme. The PCRTM-SOLAR model can be trained to simulate top-of-atmosphere radiance or reflectance spectra with spectral resolution ranging from 1 cm(exp -1) resolution to a few nanometers. Broadband radiances or reflectance can also be calculated if desired. The current version of the PCRTM-SOLAR covers a spectral range from 300 to 2500 nm. The model is valid for solar zenith angles ranging from 0 to 80 deg, the instrument view zenith angles ranging from 0 to 70 deg, and the relative azimuthal angles ranging from 0 to 360 deg. Depending on the number of spectral channels, the speed of the current version of PCRTM-SOLAR is a few hundred to over one thousand times faster than the medium speed correlated-k option MODTRAN5. The absolute RMS error in channel radiance is smaller than 10(exp -3) mW/cm)exp 2)/sr/cm(exp -1) and the relative error is typically less than 0.2%.

  6. Development of a fast and accurate PCRTM radiative transfer model in the solar spectral region.

    PubMed

    Liu, Xu; Yang, Qiguang; Li, Hui; Jin, Zhonghai; Wu, Wan; Kizer, Susan; Zhou, Daniel K; Yang, Ping

    2016-10-10

    A fast and accurate principal component-based radiative transfer model in the solar spectral region (PCRTM-SOLAR) has been developed. The algorithm is capable of simulating reflected solar spectra in both clear sky and cloudy atmospheric conditions. Multiple scattering of the solar beam by the multilayer clouds and aerosols are calculated using a discrete ordinate radiative transfer scheme. The PCRTM-SOLAR model can be trained to simulate top-of-atmosphere radiance or reflectance spectra with spectral resolution ranging from 1  cm-1 resolution to a few nanometers. Broadband radiances or reflectance can also be calculated if desired. The current version of the PCRTM-SOLAR covers a spectral range from 300 to 2500 nm. The model is valid for solar zenith angles ranging from 0 to 80 deg, the instrument view zenith angles ranging from 0 to 70 deg, and the relative azimuthal angles ranging from 0 to 360 deg. Depending on the number of spectral channels, the speed of the current version of PCRTM-SOLAR is a few hundred to over one thousand times faster than the medium speed correlated-k option MODTRAN5. The absolute RMS error in channel radiance is smaller than 10-3  mW/cm2/sr/cm-1 and the relative error is typically less than 0.2%.

  7. Accurate Models of Formation Enthalpy Created using Machine Learning and Voronoi Tessellations

    NASA Astrophysics Data System (ADS)

    Ward, Logan; Liu, Rosanne; Krishna, Amar; Hegde, Vinay; Agrawal, Ankit; Choudhary, Alok; Wolverton, Chris

    Several groups in the past decade have used high-throughput Density Functional Theory to predict the properties of hundreds of thousands of compounds. These databases provide the unique capability of being able to quickly query the properties of many compounds. Here, we explore how these datasets can also be used to create models that can predict the properties of compounds at rates several orders of magnitude faster than DFT. Our method relies on using Voronoi tessellations to derive attributes that quantitatively characterize the local environment around each atom, which then are used as input to a machine learning model. In this presentation, we will discuss the application of this technique to predicting the formation enthalpy of compounds using data from the Open Quantum Materials Database (OQMD). To date, we have found that this technique can be used to create models that are about twice as accurate as those created using the Coulomb Matrix and Partial Radial Distribution approaches and are equally as fast to evaluate.

  8. A murine model of neurofibromatosis type 2 that accurately phenocopies human schwannoma formation

    PubMed Central

    Gehlhausen, Jeffrey R.; Park, Su-Jung; Hickox, Ann E.; Shew, Matthew; Staser, Karl; Rhodes, Steven D.; Menon, Keshav; Lajiness, Jacquelyn D.; Mwanthi, Muithi; Yang, Xianlin; Yuan, Jin; Territo, Paul; Hutchins, Gary; Nalepa, Grzegorz; Yang, Feng-Chun; Conway, Simon J.; Heinz, Michael G.; Stemmer-Rachamimov, Anat; Yates, Charles W.; Wade Clapp, D.

    2015-01-01

    Neurofibromatosis type 2 (NF2) is an autosomal dominant genetic disorder resulting from germline mutations in the NF2 gene. Bilateral vestibular schwannomas, tumors on cranial nerve VIII, are pathognomonic for NF2 disease. Furthermore, schwannomas also commonly develop in other cranial nerves, dorsal root ganglia and peripheral nerves. These tumors are a major cause of morbidity and mortality, and medical therapies to treat them are limited. Animal models that accurately recapitulate the full anatomical spectrum of human NF2-related schwannomas, including the characteristic functional deficits in hearing and balance associated with cranial nerve VIII tumors, would allow systematic evaluation of experimental therapeutics prior to clinical use. Here, we present a genetically engineered NF2 mouse model generated through excision of the Nf2 gene driven by Cre expression under control of a tissue-restricted 3.9kbPeriostin promoter element. By 10 months of age, 100% of Postn-Cre; Nf2flox/flox mice develop spinal, peripheral and cranial nerve tumors histologically identical to human schwannomas. In addition, the development of cranial nerve VIII tumors correlates with functional impairments in hearing and balance, as measured by auditory brainstem response and vestibular testing. Overall, the Postn-Cre; Nf2flox/flox tumor model provides a novel tool for future mechanistic and therapeutic studies of NF2-associated schwannomas. PMID:25113746

  9. Symposium on unsaturated flow and transport modeling

    SciTech Connect

    Arnold, E.M.; Gee, G.W.; Nelson, R.W.

    1982-09-01

    This document records the proceedings of a symposium on flow and transport processes in partially saturated groundwater systems, conducted at the Battelle Seattle Research Center on March 22-24, 1982. The symposium was sponsored by the US Nuclear Regulatory Commission for the purpose of assessing the state-of-the-art of flow and transport modeling for use in licensing low-level nuclear waste repositories in partially saturated zones. The first day of the symposium centered around research in flow through partially saturated systems. Papers were presented with the opportunity for questions following each presentation. In addition, after all the talks, a formal panel discussion was held during which written questions were addressed to the panel of the days speakers. The second day of the Symposium was devoted to solute and contaminant transport in partially saturated media in an identical format. Individual papers are abstracted.

  10. Molecular modeling of auxin transport inhibitors

    SciTech Connect

    Gardner, G.; Black-Schaefer, C.; Bures, M.G. )

    1990-05-01

    Molecular modeling techniques have been used to study the chemical and steric properties of auxin transport inhibitors. These bind to a specific site on the plant plasma membrane characterized by its affinity for N-1-naphthylphthalamic acid (NPA). A three-dimensional model was derived from critical features of ligands for the NPA receptor, and a suggested binding conformation is proposed. This model, along with three-dimensional structural searching techniques, was then used to search the Abbott corporate database of chemical structures. Of the 467 compounds that satisfied the search criteria, 77 representative molecules were evaluated for their ability to compete for ({sup 3}H)NPA binding to corn microsomal membranes. Nineteen showed activity that ranged from 16 to 85% of the maximum NPA binding. Four of the most active of these, from chemical classes not included in the original compound set, also inhibited polar auxin transport through corn coleoptile sections.

  11. Modeling radium and radon transport through soil and vegetation

    USGS Publications Warehouse

    Kozak, J.A.; Reeves, H.W.; Lewis, B.A.

    2003-01-01

    A one-dimensional flow and transport model was developed to describe the movement of two fluid phases, gas and water, within a porous medium and the transport of 226Ra and 222Rn within and between these two phases. Included in this model is the vegetative uptake of water and aqueous 226Ra and 222Rn that can be extracted from the soil via the transpiration stream. The mathematical model is formulated through a set of phase balance equations and a set of species balance equations. Mass exchange, sink terms and the dependence of physical properties upon phase composition couple the two sets of equations. Numerical solution of each set, with iteration between the sets, is carried out leading to a set-iterative compositional model. The Petrov-Galerkin finite element approach is used to allow for upstream weighting if required for a given simulation. Mass lumping improves solution convergence and stability behavior. The resulting numerical model was applied to four problems and was found to produce accurate, mass conservative solutions when compared to published experimental and numerical results and theoretical column experiments. Preliminary results suggest that the model can be used as an investigative tool to determine the feasibility of phytoremediating radium and radon-contaminated soil. ?? 2003 Elsevier Science B.V. All rights reserved.

  12. A Radiative Transport Model for Blazars

    NASA Astrophysics Data System (ADS)

    Lewis, Tiffany; Justin, Finke; Becker, Peter A.

    2017-01-01

    Blazars are observed across the electromagnetic spectrum, often with strong variability throughout. The underlying electron distribution associated with the observed emission is typically not computed from first principles. We start from first-principles to build up a transport model, whose solution is the electron distribution, rather than assuming a convenient functional form. Our analytical transport model considers shock acceleration, adiabatic expansion, stochastic acceleration, Bohm diffusion, and synchrotron radiation. We use this solution to generate predictions for the X-ray spectrum and time lags, and compare the results with data products from BeppoSAX observations of X-ray flares from Mrk 421. This new self-consistent model provides an unprecedented view into the jet physics at play in this source, especially the strength of the shock and stochastic acceleration components and the size of the acceleration region.More recently, we augmented the transport model to incorporate Compton scattering, including Klein-Nishina effects. In this case, an analytical solution cannot be derived, and therefore we obtain the steady-state electron distribution computationally. We compare the resulting radiation spectrum with multi-wavelength data for 3C 279. We show that our new Compton + synchrotron blazar model is the first to successfully fit the FermiLAT gamma-ray data for this source based on a first-principles physical calculation.

  13. A Radiative Transport Model for Blazars

    NASA Astrophysics Data System (ADS)

    Lewis, Tiffany; Finke, Justin; Becker, Peter

    2017-01-01

    Blazars are observed across the electromagnetic spectrum, often with strong variability throughout. We start from first-principles to build up a transport model, whose solution is the electron distribution, rather than assuming a convenient functional form. Our analytical transport model considers shock acceleration, adiabatic expansion, stochastic acceleration, Bohm diffusion, and synchrotron radiation. We use this solution to give predictions for the X-ray spectrum and time lags, comparing the results with BeppoSAX observations of X-ray flares from Mrk 421. This new self-consistent model provides an unprecedented view into the jet physics at play in this source, especially the strength of the shock and stochastic acceleration components and the size of the acceleration region. More recently, we augmented the transport model to incorporate Compton scattering, including Klein-Nishina effects. Here, an analytical solution cannot be derived. Therefore we obtain the steady-state electron distribution computationally. We compare the resulting radiation spectrum with multi-wavelength data for 3C 279. We show that our new Compton + synchrotron blazar model is the first to successfully fit the FermiLAT gamma-ray data for this source based on a first-principles physical calculation.

  14. Accurate state estimation from uncertain data and models: an application of data assimilation to mathematical models of human brain tumors

    PubMed Central

    2011-01-01

    Background Data assimilation refers to methods for updating the state vector (initial condition) of a complex spatiotemporal model (such as a numerical weather model) by combining new observations with one or more prior forecasts. We consider the potential feasibility of this approach for making short-term (60-day) forecasts of the growth and spread of a malignant brain cancer (glioblastoma multiforme) in individual patient cases, where the observations are synthetic magnetic resonance images of a hypothetical tumor. Results We apply a modern state estimation algorithm (the Local Ensemble Transform Kalman Filter), previously developed for numerical weather prediction, to two different mathematical models of glioblastoma, taking into account likely errors in model parameters and measurement uncertainties in magnetic resonance imaging. The filter can accurately shadow the growth of a representative synthetic tumor for 360 days (six 60-day forecast/update cycles) in the presence of a moderate degree of systematic model error and measurement noise. Conclusions The mathematical methodology described here may prove useful for other modeling efforts in biology and oncology. An accurate forecast system for glioblastoma may prove useful in clinical settings for treatment planning and patient counseling. Reviewers This article was reviewed by Anthony Almudevar, Tomas Radivoyevitch, and Kristin Swanson (nominated by Georg Luebeck). PMID:22185645

  15. Numerical modelling of ion transport in flames

    NASA Astrophysics Data System (ADS)

    Han, Jie; Belhi, Memdouh; Bisetti, Fabrizio; Mani Sarathy, S.

    2015-11-01

    This paper presents a modelling framework to compute the diffusivity and mobility of ions in flames. The (n, 6, 4) interaction potential is adopted to model collisions between neutral and charged species. All required parameters in the potential are related to the polarizability of the species pair via semi-empirical formulas, which are derived using the most recently published data or best estimates. The resulting framework permits computation of the transport coefficients of any ion found in a hydrocarbon flame. The accuracy of the proposed method is evaluated by comparing its predictions with experimental data on the mobility of selected ions in single-component neutral gases. Based on this analysis, the value of a model constant available in the literature is modified in order to improve the model's predictions. The newly determined ion transport coefficients are used as part of a previously developed numerical approach to compute the distribution of charged species in a freely propagating premixed lean CH4/O2 flame. Since a significant scatter of polarizability data exists in the literature, the effects of changes in polarizability on ion transport properties and the spatial distribution of ions in flames are explored. Our analysis shows that changes in polarizability propagate with decreasing effect from binary transport coefficients to species number densities. We conclude that the chosen polarizability value has a limited effect on the ion distribution in freely propagating flames. We expect that the modelling framework proposed here will benefit future efforts in modelling the effect of external voltages on flames. Supplemental data for this article can be accessed at http://dx.doi.org/10.1080/13647830.2015.1090018.

  16. Mesoscopic Modeling of Reactive Transport Processes

    NASA Astrophysics Data System (ADS)

    Kang, Q.; Chen, L.; Deng, H.

    2012-12-01

    Reactive transport processes involving precipitation and/or dissolution are pervasive in geochemical, biological and engineered systems. Typical examples include self-assembled patterns such as Liesegang rings or bands, cones of stalactites in limestones caves, biofilm growth in aqueous environment, formation of mineral deposits in boilers and heat exchangers, uptake of toxic metal ions from polluted water by calcium carbonate, and mineral trapping of CO2. Compared to experimental studies, a numerical approach enables a systematic study of the reaction kinetics, mass transport, and mechanisms of nucleation and crystal growth, and hence provides a detailed description of reactive transport processes. In this study, we enhance a previously developed lattice Boltzmann pore-scale model by taking into account the nucleation process, and develop a mesoscopic approach to simulate reactive transport processes involving precipitation and/or dissolution of solid phases. The model is then used to simulate the formation of Liesegang precipitation patterns and investigate the effects of gel on the morphology of the precipitates. It is shown that this model can capture the porous structures of the precipitates and can account for the effects of the gel concentration and material. A wide range of precipitation patterns is predicted under different gel concentrations, including regular bands, treelike patterns, and for the first time with numerical models, transition patterns from regular bands to treelike patterns. The model is also applied to study the effect of secondary precipitate on the dissolution of primary mineral. Several types of dissolution and precipitation processes are identified based on the morphology and structures of the precipitates and on the extent to which the precipitates affect the dissolution of the primary mineral. Finally the model is applied to study the formation of pseudomorph. It is demonstrated for the first time by numerical simulation that a

  17. Fast and Accurate Radiative Transfer Calculations Using Principal Component Analysis for (Exo-)Planetary Retrieval Models

    NASA Astrophysics Data System (ADS)

    Kopparla, P.; Natraj, V.; Shia, R. L.; Spurr, R. J. D.; Crisp, D.; Yung, Y. L.

    2015-12-01

    Radiative transfer (RT) computations form the engine of atmospheric retrieval codes. However, full treatment of RT processes is computationally expensive, prompting usage of two-stream approximations in current exoplanetary atmospheric retrieval codes [Line et al., 2013]. Natraj et al. [2005, 2010] and Spurr and Natraj [2013] demonstrated the ability of a technique using principal component analysis (PCA) to speed up RT computations. In the PCA method for RT performance enhancement, empirical orthogonal functions are developed for binned sets of inherent optical properties that possess some redundancy; costly multiple-scattering RT calculations are only done for those few optical states corresponding to the most important principal components, and correction factors are applied to approximate radiation fields. Kopparla et al. [2015, in preparation] extended the PCA method to a broadband spectral region from the ultraviolet to the shortwave infrared (0.3-3 micron), accounting for major gas absorptions in this region. Here, we apply the PCA method to a some typical (exo-)planetary retrieval problems. Comparisons between the new model, called Universal Principal Component Analysis Radiative Transfer (UPCART) model, two-stream models and line-by-line RT models are performed, for spectral radiances, spectral fluxes and broadband fluxes. Each of these are calculated at the top of the atmosphere for several scenarios with varying aerosol types, extinction and scattering optical depth profiles, and stellar and viewing geometries. We demonstrate that very accurate radiance and flux estimates can be obtained, with better than 1% accuracy in all spectral regions and better than 0.1% in most cases, as compared to a numerically exact line-by-line RT model. The accuracy is enhanced when the results are convolved to typical instrument resolutions. The operational speed and accuracy of UPCART can be further improved by optimizing binning schemes and parallelizing the codes, work

  18. 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.

  19. Modeling multispecies reactive transport in ground water

    SciTech Connect

    Clement, T.P.; Sun, Y.; Hooker, B.S.; Petersen, J.N.

    1998-12-31

    In this paper, the details of RT3D, a general purpose, multispecies, reactive transport code, are presented. The code uses MODFLOW to simulate flow and several MT3D sub-programs to simulate advection and dispersion. A set of reaction modules were developed and incorporated into RT3D to simulate various types of multispecies reactive transport. This new computer model can be used for analyzing different types of subsurface contaminant reactions, microbial metabolisms, and microbial transport kinetics. Details of the model and numerical solution procedure are presented. The numerical formulation of the code is general enough to allow description of any type of reaction with any number of mobile/immobile species. Several example problems are presented to test the performance of the code, and to illustrate its features. The presented numerical model is shown to be a useful tool for analyzing different types of subsurface bioremediation systems. Prediction based on this model can be used for screening remediation alternatives including natural attenuation and/or for forecasting contaminant exposure levels and environmental risks at sensitive, downgradient receptors.

  20. Physical and Numerical Model Studies of Cross-flow Turbines Towards Accurate Parameterization in Array Simulations

    NASA Astrophysics Data System (ADS)

    Wosnik, M.; Bachant, P.

    2014-12-01

    Cross-flow turbines, often referred to as vertical-axis turbines, show potential for success in marine hydrokinetic (MHK) and wind energy applications, ranging from small- to utility-scale installations in tidal/ocean currents and offshore wind. As turbine designs mature, the research focus is shifting from individual devices to the optimization of turbine arrays. It would be expensive and time-consuming to conduct physical model studies of large arrays at large model scales (to achieve sufficiently high Reynolds numbers), and hence numerical techniques are generally better suited to explore the array design parameter space. However, since the computing power available today is not sufficient to conduct simulations of the flow in and around large arrays of turbines with fully resolved turbine geometries (e.g., grid resolution into the viscous sublayer on turbine blades), the turbines' interaction with the energy resource (water current or wind) needs to be parameterized, or modeled. Models used today--a common model is the actuator disk concept--are not able to predict the unique wake structure generated by cross-flow turbines. This wake structure has been shown to create "constructive" interference in some cases, improving turbine performance in array configurations, in contrast with axial-flow, or horizontal axis devices. Towards a more accurate parameterization of cross-flow turbines, an extensive experimental study was carried out using a high-resolution turbine test bed with wake measurement capability in a large cross-section tow tank. The experimental results were then "interpolated" using high-fidelity Navier--Stokes simulations, to gain insight into the turbine's near-wake. The study was designed to achieve sufficiently high Reynolds numbers for the results to be Reynolds number independent with respect to turbine performance and wake statistics, such that they can be reliably extrapolated to full scale and used for model validation. The end product of

  1. Structure-based constitutive model can accurately predict planar biaxial properties of aortic wall tissue.

    PubMed

    Polzer, S; Gasser, T C; Novak, K; Man, V; Tichy, M; Skacel, P; Bursa, J

    2015-03-01

    Structure-based constitutive models might help in exploring mechanisms by which arterial wall histology is linked to wall mechanics. This study aims to validate a recently proposed structure-based constitutive model. Specifically, the model's ability to predict mechanical biaxial response of porcine aortic tissue with predefined collagen structure was tested. Histological slices from porcine thoracic aorta wall (n=9) were automatically processed to quantify the collagen fiber organization, and mechanical testing identified the non-linear properties of the wall samples (n=18) over a wide range of biaxial stretches. Histological and mechanical experimental data were used to identify the model parameters of a recently proposed multi-scale constitutive description for arterial layers. The model predictive capability was tested with respect to interpolation and extrapolation. Collagen in the media was predominantly aligned in circumferential direction (planar von Mises distribution with concentration parameter bM=1.03 ± 0.23), and its coherence decreased gradually from the luminal to the abluminal tissue layers (inner media, b=1.54 ± 0.40; outer media, b=0.72 ± 0.20). In contrast, the collagen in the adventitia was aligned almost isotropically (bA=0.27 ± 0.11), and no features, such as families of coherent fibers, were identified. The applied constitutive model captured the aorta biaxial properties accurately (coefficient of determination R(2)=0.95 ± 0.03) over the entire range of biaxial deformations and with physically meaningful model parameters. Good predictive properties, well outside the parameter identification space, were observed (R(2)=0.92 ± 0.04). Multi-scale constitutive models equipped with realistic micro-histological data can predict macroscopic non-linear aorta wall properties. Collagen largely defines already low strain properties of media, which explains the origin of wall anisotropy seen at this strain level. The structure and mechanical

  2. New possibilities of accurate particle characterisation by applying direct boundary models to analytical centrifugation.

    PubMed

    Walter, Johannes; Thajudeen, Thaseem; Süss, Sebastian; Segets, Doris; Peukert, Wolfgang

    2015-04-21

    Analytical centrifugation (AC) is a powerful technique for the characterisation of nanoparticles in colloidal systems. As a direct and absolute technique it requires no calibration or measurements of standards. Moreover, it offers simple experimental design and handling, high sample throughput as well as moderate investment costs. However, the full potential of AC for nanoparticle size analysis requires the development of powerful data analysis techniques. In this study we show how the application of direct boundary models to AC data opens up new possibilities in particle characterisation. An accurate analysis method, successfully applied to sedimentation data obtained by analytical ultracentrifugation (AUC) in the past, was used for the first time in analysing AC data. Unlike traditional data evaluation routines for AC using a designated number of radial positions or scans, direct boundary models consider the complete sedimentation boundary, which results in significantly better statistics. We demonstrate that meniscus fitting, as well as the correction of radius and time invariant noise significantly improves the signal-to-noise ratio and prevents the occurrence of false positives due to optical artefacts. Moreover, hydrodynamic non-ideality can be assessed by the residuals obtained from the analysis. The sedimentation coefficient distributions obtained by AC are in excellent agreement with the results from AUC. Brownian dynamics simulations were used to generate numerical sedimentation data to study the influence of diffusion on the obtained distributions. Our approach is further validated using polystyrene and silica nanoparticles. In particular, we demonstrate the strength of AC for analysing multimodal distributions by means of gold nanoparticles.

  3. Accurate modeling of cache replacement policies in a Data-Grid.

    SciTech Connect

    Otoo, Ekow J.; Shoshani, Arie

    2003-01-23

    Caching techniques have been used to improve the performance gap of storage hierarchies in computing systems. In data intensive applications that access large data files over wide area network environment, such as a data grid,caching mechanism can significantly improve the data access performance under appropriate workloads. In a data grid, it is envisioned that local disk storage resources retain or cache the data files being used by local application. Under a workload of shared access and high locality of reference, the performance of the caching techniques depends heavily on the replacement policies being used. A replacement policy effectively determines which set of objects must be evicted when space is needed. Unlike cache replacement policies in virtual memory paging or database buffering, developing an optimal replacement policy for data grids is complicated by the fact that the file objects being cached have varying sizes and varying transfer and processing costs that vary with time. We present an accurate model for evaluating various replacement policies and propose a new replacement algorithm referred to as ''Least Cost Beneficial based on K backward references (LCB-K).'' Using this modeling technique, we compare LCB-K with various replacement policies such as Least Frequently Used (LFU), Least Recently Used (LRU), Greedy DualSize (GDS), etc., using synthetic and actual workload of accesses to and from tertiary storage systems. The results obtained show that (LCB-K) and (GDS) are the most cost effective cache replacement policies for storage resource management in data grids.

  4. GIS-Based Population Model Applied to Nevada Transportation Routes

    SciTech Connect

    Mills, G.S.; Neuhauser, K.S.

    1999-03-04

    Recently, a model based on geographic information system (GIS) processing of US Census Block data has made high-resolution population analysis for transportation risk analysis technically and economically feasible. Population density bordering each kilometer of a route may be tabulated with specific route sections falling into each of three categories (Rural, Suburban or Urban) identified for separate risk analysis. In addition to the improvement in resolution of Urban areas along a route, the model provides a statistically-based correction to population densities in Rural and Suburban areas where Census Block dimensions may greatly exceed the 800-meter scale of interest. A semi-automated application of the GIS model to a subset of routes in Nevada (related to the Yucca Mountain project) are presented, and the results compared to previous models including a model based on published Census and other data. These comparisons demonstrate that meaningful improvement in accuracy and specificity of transportation risk analyses is dependent on correspondingly accurate and geographically-specific population density data.

  5. Turbulent transport models for scramjet flowfields

    NASA Technical Reports Server (NTRS)

    Sindir, M. M.; Harsha, P. T.

    1984-01-01

    Turbulence modeling approaches were examined from the standpoint of their capability to predict the complex flowfield features observed in scramjet combustions. Thus, for example, the accuracy of each turbulence model, with respect to the prediction of recirculating flows, was examined. It was observed that for large diameter ratio axisymmetric sudden expansion flows, a choice of turbulence model was not critical because of the domination of their flowfields by pressure forces. For low diameter ratio axisymmetric sudden expansions and planar backward-facing steps flows, where turbulent shear stresses are of greater significance, the algebraic Reynolds stress approach, modified to increase its sensitivity to streamline curvature, was found to provide the best results. Results of the study also showed that strongly swirling flows provide a stringent test of turbulence model assumptions. Thus, although flows with very high swirl are not of great practical interest, they are useful for turbulence model development. Finally, it was also noted that numerical flowfields solution techniques have a strong interrelation with turbulence models, particularly with the turbulent transport models which involve source-dominated transport equations.

  6. Variational multiscale models for charge transport

    PubMed Central

    Wei, Guo-Wei; Zheng, Qiong; Chen, Zhan; Xia, Kelin

    2012-01-01

    This work presents a few variational multiscale models for charge transport in complex physical, chemical and biological systems and engineering devices, such as fuel cells, solar cells, battery cells, nanofluidics, transistors and ion channels. An essential ingredient of the present models, introduced in an earlier paper (Bulletin of Mathematical Biology, 72, 1562-1622, 2010), is the use of differential geometry theory of surfaces as a natural means to geometrically separate the macroscopic domain from the microscopic domain, meanwhile, dynamically couple discrete and continuum descriptions. Our main strategy is to construct the total energy functional of a charge transport system to encompass the polar and nonpolar free energies of solvation, and chemical potential related energy. By using the Euler-Lagrange variation, coupled Laplace-Beltrami and Poisson-Nernst-Planck (LB-PNP) equations are derived. The solution of the LB-PNP equations leads to the minimization of the total free energy, and explicit profiles of electrostatic potential and densities of charge species. To further reduce the computational complexity, the Boltzmann distribution obtained from the Poisson-Boltzmann (PB) equation is utilized to represent the densities of certain charge species so as to avoid the computationally expensive solution of some Nernst-Planck (NP) equations. Consequently, the coupled Laplace-Beltrami and Poisson-Boltzmann-Nernst-Planck (LB-PBNP) equations are proposed for charge transport in heterogeneous systems. A major emphasis of the present formulation is the consistency between equilibrium LB-PB theory and non-equilibrium LB-PNP theory at equilibrium. Another major emphasis is the capability of the reduced LB-PBNP model to fully recover the prediction of the LB-PNP model at non-equilibrium settings. To account for the fluid impact on the charge transport, we derive coupled Laplace-Beltrami, Poisson-Nernst-Planck and Navier-Stokes equations from the variational principle

  7. Modelling sediment clasts transport during landscape evolution

    NASA Astrophysics Data System (ADS)

    Carretier, Sébastien; Martinod, Pierre; Reich, Martin; Godderis, Yves

    2016-03-01

    Over thousands to millions of years, the landscape evolution is predicted by models based on fluxes of eroded, transported and deposited material. The laws describing these fluxes, corresponding to averages over many years, are difficult to prove with the available data. On the other hand, sediment dynamics are often tackled by studying the distribution of certain grain properties in the field (e.g. heavy metals, detrital zircons, 10Be in gravel, magnetic tracers). There is a gap between landscape evolution models based on fluxes and these field data on individual clasts, which prevent the latter from being used to calibrate the former. Here we propose an algorithm coupling the landscape evolution with mobile clasts. Our landscape evolution model predicts local erosion, deposition and transfer fluxes resulting from hillslope and river processes. Clasts of any size are initially spread in the basement and are detached, moved and deposited according to probabilities using these fluxes. Several river and hillslope laws are studied. Although the resulting mean transport rate of the clasts does not depend on the time step or the model cell size, our approach is limited by the fact that their scattering rate is cell-size-dependent. Nevertheless, both their mean transport rate and the shape of the scattering-time curves fit the predictions. Different erosion-transport laws generate different clast movements. These differences show that studying the tracers in the field may provide a way to establish these laws on the hillslopes and in the rivers. Possible applications include the interpretation of cosmogenic nuclides in individual gravel deposits, provenance analyses, placers, sediment coarsening or fining, the relationship between magnetic tracers in rivers and the river planform, and the tracing of weathered sediment.

  8. Accurate numerical forward model for optimal retracking of SIRAL2 SAR echoes over open ocean

    NASA Astrophysics Data System (ADS)

    Phalippou, L.; Demeestere, F.

    2011-12-01

    The SAR mode of SIRAL-2 on board Cryosat-2 has been designed to measure primarily sea-ice and continental ice (Wingham et al. 2005). In 2005, K. Raney (KR, 2005) pointed out the improvements brought by SAR altimeter for open ocean. KR results were mostly based on 'rule of thumb' considerations on speckle noise reduction due to the higher PRF and to speckle decorrelation after SAR processing. In 2007, Phalippou and Enjolras (PE,2007) provided the theoretical background for optimal retracking of SAR echoes over ocean with a focus on the forward modelling of the power-waveforms. The accuracies of geophysical parameters (range, significant wave heights, and backscattering coefficient) retrieved from SAR altimeter data were derived accounting for SAR echo shape and speckle noise accurate modelling. The step forward to optimal retracking using numerical forward model (NFM) was also pointed out. NFM of the power waveform avoids analytical approximation, a warranty to minimise the geophysical dependent biases in the retrieval. NFM have been used for many years, in operational meteorology in particular, for retrieving temperature and humidity profiles from IR and microwave radiometers as the radiative transfer function is complex (Eyre, 1989). So far this technique was not used in the field of ocean conventional altimetry as analytical models (e.g. Brown's model for instance) were found to give sufficient accuracy. However, although NFM seems desirable even for conventional nadir altimetry, it becomes inevitable if one wish to process SAR altimeter data as the transfer function is too complex to be approximated by a simple analytical function. This was clearly demonstrated in PE 2007. The paper describes the background to SAR data retracking over open ocean. Since PE 2007 improvements have been brought to the forward model and it is shown that the altimeter on-ground and in flight characterisation (e.g antenna pattern range impulse response, azimuth impulse response

  9. Accurate De Novo Prediction of Protein Contact Map by Ultra-Deep Learning Model

    PubMed Central

    Li, Zhen; Zhang, Renyu

    2017-01-01

    Motivation Protein contacts contain key information for the understanding of protein structure and function and thus, contact prediction from sequence is an important problem. Recently exciting progress has been made on this problem, but the predicted contacts for proteins without many sequence homologs is still of low quality and not very useful for de novo structure prediction. Method This paper presents a new deep learning method that predicts contacts by integrating both evolutionary coupling (EC) and sequence conservation information through an ultra-deep neural network formed by two deep residual neural networks. The first residual network conducts a series of 1-dimensional convolutional transformation of sequential features; the second residual network conducts a series of 2-dimensional convolutional transformation of pairwise information including output of the first residual network, EC information and pairwise potential. By using very deep residual networks, we can accurately model contact occurrence patterns and complex sequence-structure relationship and thus, obtain higher-quality contact prediction regardless of how many sequence homologs are available for proteins in question. Results Our method greatly outperforms existing methods and leads to much more accurate contact-assisted folding. Tested on 105 CASP11 targets, 76 past CAMEO hard targets, and 398 membrane proteins, the average top L long-range prediction accuracy obtained by our method, one representative EC method CCMpred and the CASP11 winner MetaPSICOV is 0.47, 0.21 and 0.30, respectively; the average top L/10 long-range accuracy of our method, CCMpred and MetaPSICOV is 0.77, 0.47 and 0.59, respectively. Ab initio folding using our predicted contacts as restraints but without any force fields can yield correct folds (i.e., TMscore>0.6) for 203 of the 579 test proteins, while that using MetaPSICOV- and CCMpred-predicted contacts can do so for only 79 and 62 of them, respectively. Our contact

  10. Upscaling Reactive Transport in Porous Media: Laboratory Visualizations and Stochastic Models

    NASA Astrophysics Data System (ADS)

    Oates, P.; Harvey, C. F.

    2007-12-01

    We present a field-scale model of reactive transport that describes the segregation and mixing of reactants at the small-scale by their joint distribution, thereby avoiding the nearly impossible task of explicitly resolving centimeter- scale patterns of reactant concentrations in field-scale models. We tested this model by collecting detailed quantitative images of colorimetric reactions during transport through translucent porous media. These novel experimental results reveal that: (1) The distributions of local solute concentrations are accurately parameterized by beta distributions; (2) The evolution of these distributions is predicted by coupling transport equations for the variance and covariance of local reactant concentrations with conventional transport and chemical reaction equations; and (3) The rate of concentration variance destruction, that drives chemical reaction, quickly equilibrates with the rate of variance production. We demonstrate this reactive-transport model for both our experimental results and through numerical simulation of double-Monod kinetic oxidation of hydrocarbons subject to linear adsorption.

  11. Updated Delft Mass Transport model DMT-2: computation and validation

    NASA Astrophysics Data System (ADS)

    Hashemi Farahani, Hassan; Ditmar, Pavel; Inacio, Pedro; Klees, Roland; Guo, Jing; Guo, Xiang; Liu, Xianglin; Zhao, Qile; Didova, Olga; Ran, Jiangjun; Sun, Yu; Tangdamrongsub, Natthachet; Gunter, Brian; Riva, Ricardo; Steele-Dunne, Susan

    2014-05-01

    A number of research centers compute models of mass transport in the Earth's system using primarily K-Band Ranging (KBR) data from the Gravity Recovery And Climate Experiment (GRACE) satellite mission. These models typically consist of a time series of monthly solutions, each of which is defined in terms of a set of spherical harmonic coefficients up to degree 60-120. One of such models, the Delft Mass Transport, release 2 (DMT-2), is computed at the Delft University of Technology (The Netherlands) in collaboration with Wuhan University. An updated variant of this model has been produced recently. A unique feature of the computational scheme designed to compute DMT-2 is the preparation of an accurate stochastic description of data noise in the frequency domain using an Auto-Regressive Moving-Average (ARMA) model, which is derived for each particular month. The benefits of such an approach are a proper frequency-dependent data weighting in the data inversion and an accurate variance-covariance matrix of noise in the estimated spherical harmonic coefficients. Furthermore, the data prior to the inversion are subject to an advanced high-pass filtering, which makes use of a spatially-dependent weighting scheme, so that noise is primarily estimated on the basis of data collected over areas with minor mass transport signals (e.g., oceans). On the one hand, this procedure efficiently suppresses noise, which are caused by inaccuracies in satellite orbits and, on the other hand, preserves mass transport signals in the data. Finally, the unconstrained monthly solutions are filtered using a Wiener filter, which is based on estimates of the signal and noise variance-covariance matrices. In combination with a proper data weighting, this noticeably improves the spatial resolution of the monthly gravity models and the associated mass transport models.. For instance, the computed solutions allow long-term negative trends to be clearly seen in sufficiently small regions notorious

  12. SPARC: Mass Models for 175 Disk Galaxies with Spitzer Photometry and Accurate Rotation Curves

    NASA Astrophysics Data System (ADS)

    Lelli, Federico; McGaugh, Stacy S.; Schombert, James M.

    2016-12-01

    We introduce SPARC (Spitzer Photometry and Accurate Rotation Curves): a sample of 175 nearby galaxies with new surface photometry at 3.6 μm and high-quality rotation curves from previous H i/Hα studies. SPARC spans a broad range of morphologies (S0 to Irr), luminosities (∼5 dex), and surface brightnesses (∼4 dex). We derive [3.6] surface photometry and study structural relations of stellar and gas disks. We find that both the stellar mass–H i mass relation and the stellar radius–H i radius relation have significant intrinsic scatter, while the H i mass–radius relation is extremely tight. We build detailed mass models and quantify the ratio of baryonic to observed velocity (V bar/V obs) for different characteristic radii and values of the stellar mass-to-light ratio (ϒ⋆) at [3.6]. Assuming ϒ⋆ ≃ 0.5 M ⊙/L ⊙ (as suggested by stellar population models), we find that (i) the gas fraction linearly correlates with total luminosity (ii) the transition from star-dominated to gas-dominated galaxies roughly corresponds to the transition from spiral galaxies to dwarf irregulars, in line with density wave theory; and (iii) V bar/V obs varies with luminosity and surface brightness: high-mass, high-surface-brightness galaxies are nearly maximal, while low-mass, low-surface-brightness galaxies are submaximal. These basic properties are lost for low values of ϒ⋆ ≃ 0.2 M ⊙/L ⊙ as suggested by the DiskMass survey. The mean maximum-disk limit in bright galaxies is ϒ⋆ ≃ 0.7 M ⊙/L ⊙ at [3.6]. The SPARC data are publicly available and represent an ideal test bed for models of galaxy formation.

  13. Modeling of Non-Gravitational Forces for Precise and Accurate Orbit Determination

    NASA Astrophysics Data System (ADS)

    Hackel, Stefan; Gisinger, Christoph; Steigenberger, Peter; Balss, Ulrich; Montenbruck, Oliver; Eineder, Michael

    2014-05-01

    Remote sensing satellites support a broad range of scientific and commercial applications. The two radar imaging satellites TerraSAR-X and TanDEM-X provide spaceborne Synthetic Aperture Radar (SAR) and interferometric SAR data with a very high accuracy. The precise reconstruction of the satellite's trajectory is based on the Global Positioning System (GPS) measurements from a geodetic-grade dual-frequency Integrated Geodetic and Occultation Receiver (IGOR) onboard the spacecraft. The increasing demand for precise radar products relies on validation methods, which require precise and accurate orbit products. An analysis of the orbit quality by means of internal and external validation methods on long and short timescales shows systematics, which reflect deficits in the employed force models. Following the proper analysis of this deficits, possible solution strategies are highlighted in the presentation. The employed Reduced Dynamic Orbit Determination (RDOD) approach utilizes models for gravitational and non-gravitational forces. A detailed satellite macro model is introduced to describe the geometry and the optical surface properties of the satellite. Two major non-gravitational forces are the direct and the indirect Solar Radiation Pressure (SRP). The satellite TerraSAR-X flies on a dusk-dawn orbit with an altitude of approximately 510 km above ground. Due to this constellation, the Sun almost constantly illuminates the satellite, which causes strong across-track accelerations on the plane rectangular to the solar rays. The indirect effect of the solar radiation is called Earth Radiation Pressure (ERP). This force depends on the sunlight, which is reflected by the illuminated Earth surface (visible spectra) and the emission of the Earth body in the infrared spectra. Both components of ERP require Earth models to describe the optical properties of the Earth surface. Therefore, the influence of different Earth models on the orbit quality is assessed. The scope of

  14. Azimuthal anisotropies as stringent test for nuclear transport models

    NASA Astrophysics Data System (ADS)

    Crochet, P.; Rami, F.; Donà, R.; Coffin, J. P.; Fintz, P.; Guillaume, G.; Jundt, F.; Kuhn, C.; Roy, C.; de Schauenburg, B.; Tizniti, L.; Wagner, P.; Alard, J. P.; Andronic, A.; Basrak, Z.; Bastid, N.; Belyaev, I.; Bendarag, A.; Berek, G.; Best, D.; Biegansky, J.; Buta, A.; Čaplar, R.; Cindro, N.; Dupieux, P.; Dželalija, M.; Fan, Z. G.; Fodor, Z.; Fraysse, L.; Freifelder, R. P.; Gobbi, A.; Herrmann, N.; Hildenbrand, K. D.; Hong, B.; Jeong, S. C.; Kecskemeti, J.; Kirejczyk, M.; Koncz, P.; Korolija, M.; Kotte, R.; Lebedev, A.; Leifels, Y.; Manko, V.; Moisa, D.; Mösner, J.; Neubert, W.; Pelte, D.; Petrovici, M.; Pinkenburg, C.; Reisdorf, W.; Ritman, J. L.; Sadchikov, A. G.; Schüll, D.; Seres, Z.; Sikora, B.; Simion, V.; Siwek-Wilczyńska, K.; Sodan, U.; Teh, K. M.; Trzaska, M.; Wang, G. S.; Wessels, J. P.; Wienold, T.; Wisniewski, K.; Wohlfarth, D.; Zhilin, A.; Hartnack, C.; FOPI Collaboration

    1997-02-01

    Azimuthal distributions of charged particles and intermediate mass fragments emitted in Au+Au collisions at 600 A MeV have been measured using the FOPI facility at GSI-Darmstadt. Data show a strong increase of the in-plane azimuthal anisotropy ratio with the charge of the detected fragment. Intermediate mass fragments are found to exhibit a strong momentum-space alignment with respect of the reaction plane. The experimental results are presented as a function of the polar centre-of-mass angle and over a broad range of impact parameters. They are compared to the predictions of the Isospin Quantum Molecular Dynamics model using three different parametrisations of the equation of state. We show that such highly accurate data provide stringent test for microscopic transport models and can potentially constrain separately the stiffness of the nuclear equation of state and the momentum dependence of the nuclear interaction.

  15. Representations of transport, convection, and the hydrologic cycle in chemical transport models: Implications for the modeling of short-lived and soluble species

    NASA Astrophysics Data System (ADS)

    Rasch, P. J.; Mahowald, N. M.; Eaton, B. E.

    1997-12-01

    We compare chemical transport simulations performed in a model using archived meteorological data (an off-line transport model) to those performed in a model in which the meteorological data are predicted every time step (an on-line model). We identify the errors associated with using data sampled at timescales much longer than those operating in the atmosphere or in the on-line model, and strategies for ameleorating those errors. The evaluation is performed in the context of a global off-line chemical transport model called the Model of Atmospheric Transport and Chemistry (MATCH) for three test problems: (1) the passive advection of blobs initially concentrated in the lower and upper troposphere; (2) the surface emission of radon and its decay to lead; and (3) the removal of lead from the atmosphere by wet and dry deposition processes. These problems exercise the important processes of transport by resolved scale winds, rapid transport by smaller scale convection processes, and wet removal (which depends on the representation of the hydrologic cycle). We show that the errors in off-line model simulations (compared to the on-line simulations) can be made small when the sampling interval is order 6 hours or less. We also show that one can accurately reproduce the subgrid-scale processes within the off-line model, rather than needing to archive the results of those processes as input to the off-line model. This suggests that for the spatial and temporal scales treated in global models it is possible to treat many problems nearly as accurately in an off-line mode as one can with an on-line treatment.

  16. Do modelled or satellite-based estimates of surface solar irradiance accurately describe its temporal variability?

    NASA Astrophysics Data System (ADS)

    Bengulescu, Marc; Blanc, Philippe; Boilley, Alexandre; Wald, Lucien

    2017-02-01

    This study investigates the characteristic time-scales of variability found in long-term time-series of daily means of estimates of surface solar irradiance (SSI). The study is performed at various levels to better understand the causes of variability in the SSI. First, the variability of the solar irradiance at the top of the atmosphere is scrutinized. Then, estimates of the SSI in cloud-free conditions as provided by the McClear model are dealt with, in order to reveal the influence of the clear atmosphere (aerosols, water vapour, etc.). Lastly, the role of clouds on variability is inferred by the analysis of in-situ measurements. A description of how the atmosphere affects SSI variability is thus obtained on a time-scale basis. The analysis is also performed with estimates of the SSI provided by the satellite-derived HelioClim-3 database and by two numerical weather re-analyses: ERA-Interim and MERRA2. It is found that HelioClim-3 estimates render an accurate picture of the variability found in ground measurements, not only globally, but also with respect to individual characteristic time-scales. On the contrary, the variability found in re-analyses correlates poorly with all scales of ground measurements variability.

  17. Accurate two-dimensional model of an arrayed-waveguide grating demultiplexer and optimal design based on the reciprocity theory.

    PubMed

    Dai, Daoxin; He, Sailing

    2004-12-01

    An accurate two-dimensional (2D) model is introduced for the simulation of an arrayed-waveguide grating (AWG) demultiplexer by integrating the field distribution along the vertical direction. The equivalent 2D model has almost the same accuracy as the original three-dimensional model and is more accurate for the AWG considered here than the conventional 2D model based on the effective-index method. To further improve the computational efficiency, the reciprocity theory is applied to the optimal design of a flat-top AWG demultiplexer with a special input structure.

  18. Optimal Filtering in Mass Transport Modeling From Satellite Gravimetry Data

    NASA Astrophysics Data System (ADS)

    Ditmar, P.; Hashemi Farahani, H.; Klees, R.

    2011-12-01

    investigation. For instance, processes of hydrological origin occur at short time scales, so that the input time series is typically short (1 month or less), which implies a relatively strong noise in the derived model. On the contrary, study of a long-term ice mass depletion requires a long time series of satellite data, which leads to a reduction of noise in the mass transport model. Of course, the spatial pattern (and therefore, the signal covariance matrices) of various mass transport processes are also very different. In the presented study, we compare various strategies to build the signal and noise covariance matrices in the context of mass transport modeling. In this way, we demonstrate the benefits of an accurate construction of an optimal filter as outlined above, compared to simplified strategies. Furthermore, we consider both models based on GRACE data alone and combined GRACE/GOCE models. In this way, we shed more light on a potential synergy of the GRACE and GOCE satellite mission. This is important nor only for the best possible mass transport modeling on the basis of all available data, but also for the optimal planning of future satellite gravity missions.

  19. Meeting in Turkey: WASP Transport Modeling and WASP Ecological Modeling

    EPA Science Inventory

    A combination of lectures, demonstrations, and hands-on excercises will be used to introduce pollutant transport modeling with the U.S. EPA's general water quality model, WASP (Water Quality Analysis Simulation Program). WASP features include a user-friendly Windows-based interfa...

  20. Meeting in Korea: WASP Transport Modeling and WASP Ecological Modeling

    EPA Science Inventory

    A combination of lectures, demonstrations, and hands-on excercises will be used to introduce pollutant transport modeling with the U.S. EPA's general water quality model, WASP (Water Quality Analysis Simulation Program). WASP features include a user-friendly Windows-based interfa...

  1. Thermal Transport Model for Heat Sink Design

    NASA Technical Reports Server (NTRS)

    Chervenak, James A.; Kelley, Richard L.; Brown, Ari D.; Smith, Stephen J.; Kilbourne, Caroline a.

    2009-01-01

    A document discusses the development of a finite element model for describing thermal transport through microcalorimeter arrays in order to assist in heat-sinking design. A fabricated multi-absorber transition edge sensor (PoST) was designed in order to reduce device wiring density by a factor of four. The finite element model consists of breaking the microcalorimeter array into separate elements, including the transition edge sensor (TES) and the silicon substrate on which the sensor is deposited. Each element is then broken up into subelements, whose surface area subtends 10 10 microns. The heat capacity per unit temperature, thermal conductance, and thermal diffusivity of each subelement are the model inputs, as are the temperatures of each subelement. Numerical integration using the Finite in Time Centered in Space algorithm of the thermal diffusion equation is then performed in order to obtain a temporal evolution of the subelement temperature. Thermal transport across interfaces is modeled using a thermal boundary resistance obtained using the acoustic mismatch model. The document concludes with a discussion of the PoST fabrication. PoSTs are novel because they enable incident x-ray position sensitivity with good energy resolution and low wiring density.

  2. Understanding transport in model water desalination membranes

    NASA Astrophysics Data System (ADS)

    Chan, Edwin

    Polyamide based thin film composites represent the the state-of-the-art nanofiltration and reverse osmosis membranes used in water desalination. The performance of these membranes is enabled by the ultrathin (~100 nm) crosslinked polyamide film in facilitating the selective transport of water over salt ions. While these materials have been refined over the last several decades, understanding the relationships between polyamide structure and membrane performance remains a challenge because of the complex and heterogeneous nature of the polyamide film. In this contribution, we present our approach to addressing this challenge by studying the transport properties of model polyamide membranes synthesized via molecular layer-by-layer (mLbL) assembly. First, we demonstrate that mLbL can successfully construct polyamide membranes with well-defined nanoscale thickness and roughness using a variety of monomer formulations. Next, we present measurement tools for characterizing the network structure and transport of these model polyamide membranes. Specifically, we used X-ray and neutron scattering techniques to characterize their structure as well as a recently-developed indentation based poromechanics approach to extrapolate their water diffusion coefficient. Finally, we illustrate how these measurements can provide insight into the original problem by linking the key polyamide network properties, i.e. water-polyamide interaction parameter and characteristic network mesh size, to the membrane performance.

  3. Transports and budgets of volume, heat, and salt from a global eddy-resolving ocean model

    SciTech Connect

    McCann, M.P.; Semtner, A.J. Jr.; Chervin, R.M.

    1994-07-01

    The results from an integration of a global ocean circulation model have been condensed into an analysis of the volume, heat, and salt transports among the major ocean basins. Transports are also broken down between the model`s Ekman, thermocline, and deep layers. Overall, the model does well. Horizontal exchanges of mass, heat, and salt between ocean basins have reasonable values: and the volume of North Atlantic Deep Water (NADW) transport is in general agreement with what limited observations exist. On a global basis the zonally integrated meridional heat transport is poleward at all latitudes except for the latitude band 30{degrees}S to 45{degrees}S. This anomalous transport is most likely a signature of the model`s inability to form Antarctic Intermediate (AAIW) and Antarctic bottom water (AABW) properly. Eddy heat transport is strong at the equator where its convergence heats the equatorial Pacific about twice as much as it heats the equatorial Atlantic. The greater heating in the Pacific suggests that mesoscale eddies may be a vital mechanism for warming and maintaining an upwelling portion of the global conveyor-belt circulation. The model`s fresh water transport compares well with observations. However, in the Atlantic there is an excessive southward transport of fresh water due to the absence of the Mediterranean outflow and weak northward flow of AAIW. Perhaps the model`s greatest weakness is the lack of strong AAIW and AABW circulation cells. Accurate thermohaline forcing in the North Atlantic (based on numerous hydrographic observations) helps the model adequately produce NADW. In contrast, the southern ocean is an area of sparse observation. Better thermohaline observations in this area may be needed if models such as this are to produce the deep convection that will achieve more accurate simulations of the global 3-dimensional circulation. 41 refs., 18 figs., 1 tab.

  4. Transport Model of Underground Sediment in Soils

    PubMed Central

    Guangqian, Wang

    2013-01-01

    Studies about sediment erosion were mainly concentrated on the river channel sediment, the terrestrial sediment, and the underground sediment. The transport process of underground sediment is studied in the paper. The concept of the flush potential sediment is founded. The transport equation with stable saturated seepage is set up, and the relations between the flush potential sediment and water sediment are discussed. Flushing of underground sediment begins with small particles, and large particles will be taken away later. The pore ratio of the soil increases gradually. The flow ultimately becomes direct water seepage, and the sediment concentration at the same position in the water decreases over time. The concentration of maximal flushing potential sediment decreases along the path. The underground sediment flushing model reflects the flushing mechanism of underground sediment. PMID:24288479

  5. Toward accurate tooth segmentation from computed tomography images using a hybrid level set model

    SciTech Connect

    Gan, Yangzhou; Zhao, Qunfei; Xia, Zeyang E-mail: jing.xiong@siat.ac.cn; Hu, Ying; Xiong, Jing E-mail: jing.xiong@siat.ac.cn; Zhang, Jianwei

    2015-01-15

    Purpose: A three-dimensional (3D) model of the teeth provides important information for orthodontic diagnosis and treatment planning. Tooth segmentation is an essential step in generating the 3D digital model from computed tomography (CT) images. The aim of this study is to develop an accurate and efficient tooth segmentation method from CT images. Methods: The 3D dental CT volumetric images are segmented slice by slice in a two-dimensional (2D) transverse plane. The 2D segmentation is composed of a manual initialization step and an automatic slice by slice segmentation step. In the manual initialization step, the user manually picks a starting slice and selects a seed point for each tooth in this slice. In the automatic slice segmentation step, a developed hybrid level set model is applied to segment tooth contours from each slice. Tooth contour propagation strategy is employed to initialize the level set function automatically. Cone beam CT (CBCT) images of two subjects were used to tune the parameters. Images of 16 additional subjects were used to validate the performance of the method. Volume overlap metrics and surface distance metrics were adopted to assess the segmentation accuracy quantitatively. The volume overlap metrics were volume difference (VD, mm{sup 3}) and Dice similarity coefficient (DSC, %). The surface distance metrics were average symmetric surface distance (ASSD, mm), RMS (root mean square) symmetric surface distance (RMSSSD, mm), and maximum symmetric surface distance (MSSD, mm). Computation time was recorded to assess the efficiency. The performance of the proposed method has been compared with two state-of-the-art methods. Results: For the tested CBCT images, the VD, DSC, ASSD, RMSSSD, and MSSD for the incisor were 38.16 ± 12.94 mm{sup 3}, 88.82 ± 2.14%, 0.29 ± 0.03 mm, 0.32 ± 0.08 mm, and 1.25 ± 0.58 mm, respectively; the VD, DSC, ASSD, RMSSSD, and MSSD for the canine were 49.12 ± 9.33 mm{sup 3}, 91.57 ± 0.82%, 0.27 ± 0.02 mm, 0

  6. Three dimensional printing as an effective method of producing anatomically accurate models for studies in thermal ecology.

    PubMed

    Watson, Charles M; Francis, Gamal R

    2015-07-01

    Hollow copper models painted to match the reflectance of the animal subject are standard in thermal ecology research. While the copper electroplating process results in accurate models, it is relatively time consuming, uses caustic chemicals, and the models are often anatomically imprecise. Although the decreasing cost of 3D printing can potentially allow the reproduction of highly accurate models, the thermal performance of 3D printed models has not been evaluated. We compared the cost, accuracy, and performance of both copper and 3D printed lizard models and found that the performance of the models were statistically identical in both open and closed habitats. We also find that 3D models are more standard, lighter, durable, and inexpensive, than the copper electroformed models.

  7. Modeling Electrical Transport through Nucleic Acids

    NASA Astrophysics Data System (ADS)

    Qi, Jianqing

    Nucleic acids play a vital role in many biological systems and activities. In recent years, engineers and scientists have been interested in studying their electrical properties. The motivation for these studies stems from the following facts: (1) the bases, which form the building blocks of nucleic acids, have unique ionization potentials. Further, nucleic acids are one of the few nanomaterials that can be reproducibly manufactured with a high degree of accuracy (though admittedly their placement at desired locations remains a challenge). As a result, designed strands with specific sequences may offer unique device properties; (2) electrical methods offer potential for sequencing nucleic acids based on a single molecule; (3) electrical methods for disease detection based on the current flowing through nucleic acids are beginning to be demonstrated. While experiments in the above mentioned areas is promising, a deeper understanding of the electrical current flow through the nucleic acids needs to be developed. The modeling of current flowing in these molecules is complex because: (1) they are based on atomic scale contacts between nucleic acids and metal, which cannot be reproducibly built; (2) the conductivity of nucleic acids is easily influenced by the environment, which is constantly changing; and (3) the nucleic acids by themselves are floppy. This thesis focuses on the modeling of electrical transport through nucleic acids that are connected to two metal electrodes at nanoscale. We first develop a decoherent transport model for the double-stranded helix based on the Landauer-Buttiker framework. This model is rationalized by comparison with an experiment that measured the conductance of four different DNA strands. The developed model is then used to study the: (1) potential to make barriers and wells for quantum transport using specifically engineered sequences; (2) change in the electrical properties of a specific DNA strand with and without methylation; (3

  8. Io Volcanism: Modeling Vapor And Heat Transport

    NASA Astrophysics Data System (ADS)

    Allen, Daniel R.; Howell, R. R.

    2010-10-01

    Loki is a large, active volcanic source on Jupiter's moon, Io, whose overall temperatures are well explained by current cooling models, but there are unexplainable subtleties. Using the SO2 atmospheric models of Ingersoll (1989) as a starting point, we are investigating how volatiles, specifically sulfur, are transported on the surface and how they modify the temperatures at Loki and other volcanoes. Voyager images reveal light colored deposits, colloquially called "sulfur bergs,” on Loki's dark patera floor that may be sulfur fumaroles. Galileo images show the presence of red short-chain sulfur deposits around the patera. We are investigating the mechanisms that lead to these features. The light deposits are a few kilometers across. Calculations of the mean free paths for day time conditions on Io indicate lengths on the order of 0.1 km while poorly constrained night time conditions indicate mean free paths about 100 times greater, on the order of what is needed to produce the deposits under ballistic conditions. Preliminary calculations reveal horizontal transport length scales for diffuse transport in a collisional atmosphere of approximately 30 km for sublimating S8 sulfur at 300 K. These length scales would be sufficient to move the sulfur from the warm patera floor to the locations of the red sulfur deposits. At a typical Loki temperature of 300 K, the sublimation/evaporation rate of S8 is a few tens of microns/day. It then requires just a few days to deposit an optically thick 100 µm layer of material. Preliminary length scales and sublimation rates are thus of sufficient scale to produce the deposits. Investigations into the sulfur transport and its effect on temperature are ongoing.

  9. Accurate Monte Carlo modeling of cyclotrons for optimization of shielding and activation calculations in the biomedical field

    NASA Astrophysics Data System (ADS)

    Infantino, Angelo; Marengo, Mario; Baschetti, Serafina; Cicoria, Gianfranco; Longo Vaschetto, Vittorio; Lucconi, Giulia; Massucci, Piera; Vichi, Sara; Zagni, Federico; Mostacci, Domiziano

    2015-11-01

    Biomedical cyclotrons for production of Positron Emission Tomography (PET) radionuclides and radiotherapy with hadrons or ions are widely diffused and established in hospitals as well as in industrial facilities and research sites. Guidelines for site planning and installation, as well as for radiation protection assessment, are given in a number of international documents; however, these well-established guides typically offer analytic methods of calculation of both shielding and materials activation, in approximate or idealized geometry set up. The availability of Monte Carlo codes with accurate and up-to-date libraries for transport and interactions of neutrons and charged particles at energies below 250 MeV, together with the continuously increasing power of nowadays computers, makes systematic use of simulations with realistic geometries possible, yielding equipment and site specific evaluation of the source terms, shielding requirements and all quantities relevant to radiation protection. In this work, the well-known Monte Carlo code FLUKA was used to simulate two representative models of cyclotron for PET radionuclides production, including their targetry; and one type of proton therapy cyclotron including the energy selection system. Simulations yield estimates of various quantities of radiological interest, including the effective dose distribution around the equipment, the effective number of neutron produced per incident proton and the activation of target materials, the structure of the cyclotron, the energy degrader, the vault walls and the soil. The model was validated against experimental measurements and comparison with well-established reference data. Neutron ambient dose equivalent H*(10) was measured around a GE PETtrace cyclotron: an average ratio between experimental measurement and simulations of 0.99±0.07 was found. Saturation yield of 18F, produced by the well-known 18O(p,n)18F reaction, was calculated and compared with the IAEA recommended

  10. Quantifying Fluxes of Chemical and Biological Species in Great Lakes Watersheds: A Reactive Transport Modeling Framework

    NASA Astrophysics Data System (ADS)

    Niu, J.; Phanikumar, M. S.

    2012-12-01

    Understanding and quantifying the interactions between hydro-climatic processes and the fate and transport of aquatic pollutants and the resultant threats to human and ecosystem health is a high priority research area in many parts of the world. In the Great Lakes region, harmful algal blooms, increased beach closures due to microbiological pollution and drinking water related issues continue to be causes for concern in recent years highlighting the need for accurate transport models. In this presentation we describe the development of a watershed-scale multi-component reactive transport modeling framework to describe fluxes of nutrients and bacteria exported to the Great Lakes. We describe an operator-splitting strategy combined with a particle transport modeling approach with reactions to describe transport in different hydrologic units with interactions between domains. The algorithms are tested using analytical solutions (where available), data from plot-scale experiments and monitoring data from watersheds in the Great Lakes region.

  11. 3 Lectures: "Lagrangian Models", "Numerical Transport Schemes", and "Chemical and Transport Models"

    NASA Technical Reports Server (NTRS)

    Douglass, A.

    2005-01-01

    The topics for the three lectures for the Canadian Summer School are Lagrangian Models, numerical transport schemes, and chemical and transport models. In the first lecture I will explain the basic components of the Lagrangian model (a trajectory code and a photochemical code), the difficulties in using such a model (initialization) and show some applications in interpretation of aircraft and satellite data. If time permits I will show some results concerning inverse modeling which is being used to evaluate sources of tropospheric pollutants. In the second lecture I will discuss one of the core components of any grid point model, the numerical transport scheme. I will explain the basics of shock capturing schemes, and performance criteria. I will include an example of the importance of horizontal resolution to polar processes. We have learned from NASA's global modeling initiative that horizontal resolution matters for predictions of the future evolution of the ozone hole. The numerical scheme will be evaluated using performance metrics based on satellite observations of long-lived tracers. The final lecture will discuss the evolution of chemical transport models over the last decade. Some of the problems with assimilated winds will be demonstrated, using satellite data to evaluate the simulations.

  12. Generation of Accurate Lateral Boundary Conditions for a Surface-Water Groundwater Interaction Model

    NASA Astrophysics Data System (ADS)

    Khambhammettu, P.; Tsou, M.; Panday, S. M.; Kool, J.; Wei, X.

    2010-12-01

    The 106 mile long Peace River in Florida flows south from Lakeland to Charlotte Harbor and has a drainage basin of approximately 2,350 square miles. A long-term decline in stream flows and groundwater potentiometric levels has been observed in the region. Long-term trends in rainfall, along with effects of land use changes on runoff, surface-water storage, recharge and evapotranspiration patterns, and increased groundwater and surface-water withdrawals have contributed to this decline. The South West Florida Water Management District (SWFWMD) has funded the development of the Peace River Integrated Model (PRIM) to assess the effects of land use, water use, and climatic changes on stream flows and to evaluate the effectiveness of various management alternatives for restoring stream flows. The PRIM was developed using MODHMS, a fully integrated surface-water groundwater flow and transport simulator developed by HydroGeoLogic, Inc. The development of the lateral boundary conditions (groundwater inflow and outflow) for the PRIM in both historical and predictive contexts is discussed in this presentation. Monthly-varying specified heads were used to define the lateral boundary conditions for the PRIM. These head values were derived from the coarser Southern District Groundwater Model (SDM). However, there were discrepancies between the simulated SDM heads and measured heads: the likely causes being spatial (use of a coarser grid) and temporal (monthly average pumping rates and recharge rates) approximations in the regional SDM. Finer re-calibration of the SDM was not feasible, therefore, an innovative approach was adopted to remove the discrepancies. In this approach, point discrepancies/residuals between the observed and simulated heads were kriged with an appropriate variogram to generate a residual surface. This surface was then added to the simulated head surface of the SDM to generate a corrected head surface. This approach preserves the trends associated with

  13. Transport Studies and Modeling in PEM Fuel Cells

    SciTech Connect

    Mittelsteadt, Cortney K.; Xu, Hui; Brawn, Shelly

    2014-07-30

    This project’s aim was to develop fuel cell components (i.e. membranes, gas-diffusion media (GDM), bipolar plates and flow fields) that possess specific properties (i.e. water transport and conductivity). A computational fluid dynamics model was developed to elucidate the effect of certain parameters on these specific properties. Ultimately, the model will be used to determine sensitivity of fuel cell performance to component properties to determine limiting components and to guide research. We have successfully reached our objectives and achieved most of the milestones of this project. We have designed and synthesized a variety of hydrocarbon block polymer membranes with lower equivalent weight, structure, chemistry, phase separation and process conditions. These membranes provide a broad selection with optimized water transport properties. We have also designed and constructed a variety of devices that are capable of accurately measuring the water transport properties (water uptake, water diffusivity and electro-osmatic drag) of these membranes. These transport properties are correlated to the membranes’ structures derived from X-ray and microscopy techniques to determine the structure-property relationship. We successfully integrated hydrocarbon membrane MEAs with a current distribution board (CBD) to study the impact of hydrocarbon membrane on water transport in fuel cells. We have designed and fabricated various GDM with varying substrate, diffusivity and micro-porous layers (MPL) and characterized their pore structure, tortuosity and hydrophobicity. We have derived a universal chart (MacMullin number as function of wet proofing and porosity) that can be used to characterize various GDM. The abovementioned GDMs have been evaluated in operating fuel cells; their performance is correlated to various pore structure, tortuosity and hydrophobicity of the GDM. Unfortunately, determining a universal relationship between the MacMullin number and these properties

  14. Full-waveform modeling of Zero-Offset Electromagnetic Induction for Accurate Characterization of Subsurface Electrical Properties

    NASA Astrophysics Data System (ADS)

    Moghadas, D.; André, F.; Vereecken, H.; Lambot, S.

    2009-04-01

    Water is a vital resource for human needs, agriculture, sanitation and industrial supply. The knowledge of soil water dynamics and solute transport is essential in agricultural and environmental engineering as it controls plant growth, hydrological processes, and the contamination of surface and subsurface water. Increased irrigation efficiency has also an important role for water conservation, reducing drainage and mitigating some of the water pollution and soil salinity. Geophysical methods are effective techniques for monitoring the vadose zone. In particular, electromagnetic induction (EMI) can provide in a non-invasive way important information about the soil electrical properties at the field scale, which are mainly correlated to important variables such as soil water content, salinity, and texture. EMI is based on the radiation of a VLF EM wave into the soil. Depending on its electrical conductivity, Foucault currents are generated and produce a secondary EM field which is then recorded by the EMI system. Advanced techniques for EMI data interpretation resort to inverse modeling. Yet, a major gap in current knowledge is the limited accuracy of the forward model used for describing the EMI-subsurface system, usually relying on strongly simplifying assumptions. We present a new low frequency EMI method based on Vector Network Analyzer (VNA) technology and advanced forward modeling using a linear system of complex transfer functions for describing the EMI loop antenna and a three-dimensional solution of Maxwell's equations for wave propagation in multilayered media. VNA permits simple, international standard calibration of the EMI system. We derived a Green's function for the zero-offset, off-ground horizontal loop antenna and also proposed an optimal integration path for faster evaluation of the spatial-domain Green's function from its spectral counterpart. This new integration path shows fewer oscillations compared with the real path and permits to avoid the

  15. A space transportation system operations model

    NASA Technical Reports Server (NTRS)

    Morris, W. Douglas; White, Nancy H.

    1987-01-01

    Presented is a description of a computer program which permits assessment of the operational support requirements of space transportation systems functioning in both a ground- and space-based environment. The scenario depicted provides for the delivery of payloads from Earth to a space station and beyond using upper stages based at the station. Model results are scenario dependent and rely on the input definitions of delivery requirements, task times, and available resources. Output is in terms of flight rate capabilities, resource requirements, and facility utilization. A general program description, program listing, input requirements, and sample output are included.

  16. Conceptual and Numerical Models for UZ Flow and Transport

    SciTech Connect

    H. Liu

    2000-03-03

    The purpose of this Analysis/Model Report (AMR) is to document the conceptual and numerical models used for modeling of unsaturated zone (UZ) fluid (water and air) flow and solute transport processes. This is in accordance with ''AMR Development Plan for U0030 Conceptual and Numerical Models for Unsaturated Zone (UZ) Flow and Transport Processes, Rev 00''. The conceptual and numerical modeling approaches described in this AMR are used for models of UZ flow and transport in fractured, unsaturated rock under ambient and thermal conditions, which are documented in separate AMRs. This AMR supports the UZ Flow and Transport Process Model Report (PMR), the Near Field Environment PMR, and the following models: Calibrated Properties Model; UZ Flow Models and Submodels; Mountain-Scale Coupled Processes Model; Thermal-Hydrologic-Chemical (THC) Seepage Model; Drift Scale Test (DST) THC Model; Seepage Model for Performance Assessment (PA); and UZ Radionuclide Transport Models.

  17. Model of reversible vesicular transport with exclusion

    NASA Astrophysics Data System (ADS)

    Bressloff, Paul C.; Karamched, Bhargav R.

    2016-08-01

    A major question in neurobiology concerns the mechanics behind the motor-driven transport and delivery of vesicles to synaptic targets along the axon of a neuron. Experimental evidence suggests that the distribution of vesicles along the axon is relatively uniform and that vesicular delivery to synapses is reversible. A recent modeling study has made explicit the crucial role that reversibility in vesicular delivery to synapses plays in achieving uniformity in vesicle distribution, so called synaptic democracy (Bressloff et al 2015 Phys. Rev. Lett. 114 168101). In this paper we generalize the previous model by accounting for exclusion effects (hard-core repulsion) that may occur between molecular motor-cargo complexes (particles) moving along the same microtubule track. The resulting model takes the form of an exclusion process with four internal states, which distinguish between motile and stationary particles, and whether or not a particle is carrying vesicles. By applying a mean field approximation and an adiabatic approximation we reduce the system of ODEs describing the evolution of occupation numbers of the sites on a 1D lattice to a system of hydrodynamic equations in the continuum limit. We find that reversibility in vesicular delivery allows for synaptic democracy even in the presence of exclusion effects, although exclusion does exacerbate nonuniform distributions of vesicles in an axon when compared with a model without exclusion. We also uncover the relationship between our model and other models of exclusion processes with internal states.

  18. A COMSOL-GEMS interface for modeling coupled reactive-transport geochemical processes

    NASA Astrophysics Data System (ADS)

    Azad, Vahid Jafari; Li, Chang; Verba, Circe; Ideker, Jason H.; Isgor, O. Burkan

    2016-07-01

    An interface was developed between COMSOL MultiphysicsTM finite element analysis software and (geo)chemical modeling platform, GEMS, for the reactive-transport modeling of (geo)chemical processes in variably saturated porous media. The two standalone software packages are managed from the interface that uses a non-iterative operator splitting technique to couple the transport (COMSOL) and reaction (GEMS) processes. The interface allows modeling media with complex chemistry (e.g. cement) using GEMS thermodynamic database formats. Benchmark comparisons show that the developed interface can be used to predict a variety of reactive-transport processes accurately. The full functionality of the interface was demonstrated to model transport processes, governed by extended Nernst-Plank equation, in Class H Portland cement samples in high pressure and temperature autoclaves simulating systems that are used to store captured carbon dioxide (CO2) in geological reservoirs.

  19. Modeling transport in polymer-electrolyte fuel cells.

    PubMed

    Weber, Adam Z; Newman, John

    2004-10-01

    membrane transport modes, nonisothermal effects, especially in the directions perpendicular to the sandwich, and multidimensional effects such as changing gas composition along the channel, among others. For any model, a balance must be struck between the complexity required to describe the physical reality and the additional costs of such complexity. In other words, while more complex models more accurately describe the physics of the transport processes, they are more computationally costly and may have so many unknown parameters that their results are not as meaningful. Hopefully, this review has shown and broken down for the reader the vast complexities of transport within polymer-electrolyte fuel cells and the various ways they have been and can be modeled.

  20. Experimental & Numerical Modeling of Non-combusting Model Firebrands' Transport

    NASA Astrophysics Data System (ADS)

    Tohidi, Ali; Kaye, Nigel

    2016-11-01

    Fire spotting is one of the major mechanisms of wildfire spread. Three phases of this phenomenon are firebrand formation and break-off from burning vegetation, lofting and downwind transport of firebrands through the velocity field of the wildfire, and spot fire ignition upon landing. The lofting and downwind transport phase is modeled by conducting large-scale wind tunnel experiments. Non-combusting rod-like model firebrands with different aspect ratios are released within the velocity field of a jet in a boundary layer cross-flow that approximates the wildfire velocity field. Characteristics of the firebrand dispersion are quantified by capturing the full trajectory of the model firebrands using the developed image processing algorithm. The results show that the lofting height has a direct impact on the maximum travel distance of the model firebrands. Also, the experimental results are utilized for validation of a highly scalable coupled stochastic & parametric firebrand flight model that, couples the LES-resolved velocity field of a jet-in-nonuniform-cross-flow (JINCF) with a 3D fully deterministic 6-degrees-of-freedom debris transport model. The validation results show that the developed numerical model is capable of estimating average statistics of the firebrands' flight. Authors would like to thank support of the National Science Foundation under Grant No. 1200560. Also, the presenter (Ali Tohid) would like to thank Dr. Michael Gollner from the University of Maryland College Park for the conference participation support.

  1. Modeling photon transport in transabdominal fetal oximetry

    NASA Astrophysics Data System (ADS)

    Jacques, Steven L.; Ramanujam, Nirmala; Vishnoi, Gargi; Choe, Regine; Chance, Britton

    2000-07-01

    The possibility of optical oximetry of the blood in the fetal brain measured across the maternal abdomen just prior to birth is under investigated. Such measurements could detect fetal distress prior to birth and aid in the clinical decision regarding Cesarean section. This paper uses a perturbation method to model photon transport through a 8- cm-diam fetal brain located at a constant 2.5 cm below a curved maternal abdominal surface with an air/tissue boundary. In the simulation, a near-infrared light source delivers light to the abdomen and a detector is positioned up to 10 cm from the source along the arc of the abdominal surface. The light transport [W/cm2 fluence rate per W incident power] collected at the 10 cm position is Tm equals 2.2 X 10-6 cm-2 if the fetal brain has the same optical properties as the mother and Tf equals 1.0 X 10MIN6 cm-2 for an optically perturbing fetal brain with typical brain optical properties. The perturbation P equals (Tf - Tm)/Tm is -53% due to the fetal brain. The model illustrates the challenge and feasibility of transabdominal oximetry of the fetal brain.

  2. Modeling the quasistatic energy transport between nanoparticles

    NASA Astrophysics Data System (ADS)

    Panasyuk, George Y.; Yerkes, Kirk L.

    2015-12-01

    We consider phononic energy transport between nanoparticles mediated by a quantum particle. The nanoparticles are considered as thermal reservoirs described by ensembles of finite numbers of harmonic oscillators within the Drude-Ullersma model having, in general, unequal mode spacings Δ1 and Δ2, which amount to different numbers of atoms in the nanoparticles. The quasistatic energy transport between the nanoparticles on the time scale t ˜1 /Δ1 ,2 is investigated using the generalized quantum Langevin equation. We find that double degeneracy of system's eigenfrequencies, which occurs in the case of identical nanoparticles, is removed when the mode spacings become unequal. The equations describing the dynamics of the averaged eigenmode energies are derived and solved, and the resulting expression for the energy current between the nanoparticles is obtained and explored. Unlike the case when the thermodynamic limit is assumed resulting in time-independent energy current, finite-size effects result in temporal behavior of the energy current that evinces reversibility features combined with decay and possesses peculiarities at time moments t =2 π n /Δ1+2 π m /Δ2 for non-negative integers n and m . When Δ1 ,2→0 , an expression for the heat current obtained previously under assumption of the thermodynamic limit is reproduced. The energy current between two platinum nanoparticles mediated by a carbon oxide molecule is considered as an application of the developed model.

  3. Modeling the quasistatic energy transport between nanoparticles.

    PubMed

    Panasyuk, George Y; Yerkes, Kirk L

    2015-12-01

    We consider phononic energy transport between nanoparticles mediated by a quantum particle. The nanoparticles are considered as thermal reservoirs described by ensembles of finite numbers of harmonic oscillators within the Drude-Ullersma model having, in general, unequal mode spacings Δ(1) and Δ(2), which amount to different numbers of atoms in the nanoparticles. The quasistatic energy transport between the nanoparticles on the time scale t∼1/Δ(1,2) is investigated using the generalized quantum Langevin equation. We find that double degeneracy of system's eigenfrequencies, which occurs in the case of identical nanoparticles, is removed when the mode spacings become unequal. The equations describing the dynamics of the averaged eigenmode energies are derived and solved, and the resulting expression for the energy current between the nanoparticles is obtained and explored. Unlike the case when the thermodynamic limit is assumed resulting in time-independent energy current, finite-size effects result in temporal behavior of the energy current that evinces reversibility features combined with decay and possesses peculiarities at time moments t=2πn/Δ(1)+2πm/Δ(2) for non-negative integers n and m. When Δ(1,2)→0, an expression for the heat current obtained previously under assumption of the thermodynamic limit is reproduced. The energy current between two platinum nanoparticles mediated by a carbon oxide molecule is considered as an application of the developed model.

  4. Documentation of TRU biological transport model (BIOTRAN)

    SciTech Connect

    Gallegos, A.F.; Garcia, B.J.; Sutton, C.M.

    1980-01-01

    Inclusive of Appendices, this document describes the purpose, rationale, construction, and operation of a biological transport model (BIOTRAN). This model is used to predict the flow of transuranic elements (TRU) through specified plant and animal environments using biomass as a vector. The appendices are: (A) Flows of moisture, biomass, and TRU; (B) Intermediate variables affecting flows; (C) Mnemonic equivalents (code) for variables; (D) Variable library (code); (E) BIOTRAN code (Fortran); (F) Plants simulated; (G) BIOTRAN code documentation; (H) Operating instructions for BIOTRAN code. The main text is presented with a specific format which uses a minimum of space, yet is adequate for tracking most relationships from their first appearance to their formulation in the code. Because relationships are treated individually in this manner, and rely heavily on Appendix material for understanding, it is advised that the reader familiarize himself with these materials before proceeding with the main text.

  5. Is scintillometer measurement accurate enough for evaluating remote sensing based energy balance ET models?

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The three evapotranspiration (ET) measurement/retrieval techniques used in this study, lysimeter, scintillometer and remote sensing vary in their level of complexity, accuracy, resolution and applicability. The lysimeter with its point measurement is the most accurate and direct method to measure ET...

  6. Accurate Modeling of Stability and Control Properties for Fighter Aircraft from CFD

    DTIC Science & Technology

    2012-03-01

    accurately placed and calibrated , etc. The results of the wind tunnel test must then be properly filtered and scaled to the proper size while taking...1 1.2 Background . . . . . . . . . . . . . . . . . . . . . . . . . 2 1.2.1 Wind Tunnel . . . . . . . . . . . . . . . . . . . 2...analysis, wind tunnel testing, flight testing, and Com- putational Fluid Dynamics (CFD). Analytical analysis includes linear aerodynamic techniques

  7. Modeling transport phenomena and uncertainty quantification in solidification processes

    NASA Astrophysics Data System (ADS)

    Fezi, Kyle S.

    Direct chill (DC) casting is the primary processing route for wrought aluminum alloys. This semicontinuous process consists of primary cooling as the metal is pulled through a water cooled mold followed by secondary cooling with a water jet spray and free falling water. To gain insight into this complex solidification process, a fully transient model of DC casting was developed to predict the transport phenomena of aluminum alloys for various conditions. This model is capable of solving mixture mass, momentum, energy, and species conservation equations during multicomponent solidification. Various DC casting process parameters were examined for their effect on transport phenomena predictions in an alloy of commercial interest (aluminum alloy 7050). The practice of placing a wiper to divert cooling water from the ingot surface was studied and the results showed that placement closer to the mold causes remelting at the surface and increases susceptibility to bleed outs. Numerical models of metal alloy solidification, like the one previously mentioned, are used to gain insight into physical phenomena that cannot be observed experimentally. However, uncertainty in model inputs cause uncertainty in results and those insights. The analysis of model assumptions and probable input variability on the level of uncertainty in model predictions has not been calculated in solidification modeling as yet. As a step towards understanding the effect of uncertain inputs on solidification modeling, uncertainty quantification (UQ) and sensitivity analysis were first performed on a transient solidification model of a simple binary alloy (Al-4.5wt.%Cu) in a rectangular cavity with both columnar and equiaxed solid growth models. This analysis was followed by quantifying the uncertainty in predictions from the recently developed transient DC casting model. The PRISM Uncertainty Quantification (PUQ) framework quantified the uncertainty and sensitivity in macrosegregation, solidification

  8. Modeling transport in transient ground-water flow: An unacknowledged approximation

    USGS Publications Warehouse

    Goode, Daniel J.

    1992-01-01

    During unsteady or transient ground-water flow, the fluid mass per unit volume of aquifer changes as the potentiometric head changes, and solute transport is affected by this change in fluid storage. Three widely applied numerical models of two-dimensional transport partially account for the effects of transient flow by removing terms corresponding to the fluid continuity equation from the transport equation, resulting in a simpler governing equation. However, fluid-storage terms remaining in the transport equation that change during transient flow are, in certain cases, held constant in time in these models. For the case of increasing heads, this approximation, which is unacknowledged in these models' documentation, leads to transport velocities that are too high, and increased concentration at fluid and solute sources. If heads are dropping in time, computed transport velocities are too low. Using parameters that somewhat exaggerate the effects of this approximation, an example numerical simulation indicates solute travel time error of about 14 percent but only minor errors due to incorrect dilution volume. For horizontal flow and transport models that assume fluid density is constant, the product of porosity and aquifer thickness changes in time: initial porosity times initial thickness plus the change in head times the storage coefficient. This formula reduces to the saturated thickness in unconfined aquifers if porosity is assumed to be constant and equal to specific yield. The computational cost of this more accurate representation is insignificant and is easily incorporated in numerical models of solute transport.

  9. ANALYZING NUMERICAL ERRORS IN DOMAIN HEAT TRANSPORT MODELS USING THE CVBEM.

    USGS Publications Warehouse

    Hromadka, T.V.; ,

    1985-01-01

    Besides providing an exact solution for steady-state heat conduction processes (Laplace Poisson equations), the CVBEM (complex variable boundary element method) can be used for the numerical error analysis of domain model solutions. For problems where soil water phase change latent heat effects dominate the thermal regime, heat transport can be approximately modeled as a time-stepped steady-state condition in the thawed and frozen regions, respectively. The CVBEM provides an exact solution of the two-dimensional steady-state heat transport problem, and also provides the error in matching the prescribed boundary conditions by the development of a modeling error distribution or an approximative boundary generation. This error evaluation can be used to develop highly accurate CVBEM models of the heat transport process, and the resulting model can be used as a test case for evaluating the precision of domain models based on finite elements or finite differences.

  10. Measurement and modeling of oil slick transport

    NASA Astrophysics Data System (ADS)

    Jones, Cathleen E.; Dagestad, Knut-Frode; Breivik, Åyvind; Holt, Benjamin; Röhrs, Johannes; Christensen, Kai Hâkon; Espeseth, Martine; Brekke, Camilla; Skrunes, Stine

    2016-10-01

    Transport characteristics of oil slicks are reported from a controlled release experiment conducted in the North Sea in June 2015, during which mineral oil emulsions of different volumetric oil fractions and a look-alike biogenic oil were released and allowed to develop naturally. The experiment used the Uninhabited Aerial Vehicle Synthetic Aperture Radar (UAVSAR) to track slick location, size, and shape for ˜8 h following release. Wind conditions during the exercise were at the high end of the range considered suitable for radar-based slick detection, but the slicks were easily detectable in all images acquired by the low noise, L-band imaging radar. The measurements are used to constrain the entrainment length and representative droplet radii for oil elements in simulations generated using the OpenOil advanced oil drift model. Simultaneously released drifters provide near-surface current estimates for the single biogenic release and one emulsion release, and are used to test model sensitivity to upper ocean currents and mixing. Results of the modeling reveal a distinct difference between the transport of the biogenic oil and the mineral oil emulsion, in particular in the vertical direction, with faster and deeper entrainment of significantly smaller droplets of the biogenic oil. The difference in depth profiles for the two types of oils is substantial, with most of the biogenic oil residing below depths of 10 m, compared to the majority of the emulsion remaining above 10 m depth. This difference was key to fitting the observed evolution of the two different types of slicks.

  11. RAETRAD MODEL OF RADON GAS GENERATION, TRANSPORT, AND INDOOR ENTRY

    EPA Science Inventory

    The report describes the theoretical basis, implementation, and validation of the Radon Emanation and Transport into Dwellings (RAETRAD) model, a conceptual and mathematical approach for simulating radon (222Rn) gas generation and transport from soils and building foundations to ...

  12. Accurate ampacity determination: Temperature-Sag Model for operational real time ratings

    SciTech Connect

    Seppa, T.O.

    1995-07-01

    This report presents a method for determining transmission line ratings based on the relationship between the conductor`s temperature and its sag. The method is based on the Ruling Span principle and the use of transmission line tension monitoring systems. The report also presents a method of accurately calibrating the final sag of the conductor and determining the actual Ruling Span length of the line sections between deadend structures. Main error sources for two other real time methods are also examined.

  13. Advanced propulsion for LEO-Moon transport. 3: Transportation model. M.S. Thesis - California Univ.

    NASA Technical Reports Server (NTRS)

    Henley, Mark W.

    1992-01-01

    A simplified computational model of low Earth orbit-Moon transportation system has been developed to provide insight into the benefits of new transportation technologies. A reference transportation infrastructure, based upon near-term technology developments, is used as a departure point for assessing other, more advanced alternatives. Comparison of the benefits of technology application, measured in terms of a mass payback ratio, suggests that several of the advanced technology alternatives could substantially improve the efficiency of low Earth orbit-Moon transportation.

  14. Numerical modeling of colloid facilitated virus transport in porus media

    NASA Astrophysics Data System (ADS)

    Katzourakis, Vasileios E.; Chrysikopoulos, Constantinos V.

    2013-04-01

    A conceptual mathematical model was developed to describethe simultaneous transport (cotransport) of viruses and colloids in three-dimensional, water saturated, homogeneous porous media with uniform flow. The model accounts for the migration of individual virus and colloid particles as well as viruses attached onto colloids. Viruses can be suspended in the aqueous phase, attached onto suspended colloids and the solid matrix, and attached onto colloids previously attached on the solid matrix. Colloids can be suspended in the aqueous phase or attached on the solid matrix. Viruses in all four phases (suspended in the aqueous phase, attached onto suspended colloid particles, attached onto the solid matrix, and attached onto colloids previously attached on the solid matrix) may undergo inactivation with different inactivation coefficients. The governing coupled partial differential equations were solved numerically by employing finite difference methods, which were implemented explicitly or implicitly so that both stability and accuracy factors were satisfied. Furthermore, available experimental data were used to test the newly developed cotransport model. The model was shown to simulate quite accurately the available experimental data.

  15. A Systems Approach to Scalable Transportation Network Modeling

    SciTech Connect

    Perumalla, Kalyan S

    2006-01-01

    Emerging needs in transportation network modeling and simulation are raising new challenges with respect to scal-ability of network size and vehicular traffic intensity, speed of simulation for simulation-based optimization, and fidel-ity of vehicular behavior for accurate capture of event phe-nomena. Parallel execution is warranted to sustain the re-quired detail, size and speed. However, few parallel simulators exist for such applications, partly due to the challenges underlying their development. Moreover, many simulators are based on time-stepped models, which can be computationally inefficient for the purposes of modeling evacuation traffic. Here an approach is presented to de-signing a simulator with memory and speed efficiency as the goals from the outset, and, specifically, scalability via parallel execution. The design makes use of discrete event modeling techniques as well as parallel simulation meth-ods. Our simulator, called SCATTER, is being developed, incorporating such design considerations. Preliminary per-formance results are presented on benchmark road net-works, showing scalability to one million vehicles simu-lated on one processor.

  16. A multimedia fate and chemical transport modeling system for pesticides: II. Model evaluation

    NASA Astrophysics Data System (ADS)

    Li, Rong; Scholtz, M. Trevor; Yang, Fuquan; Sloan, James J.

    2011-07-01

    Pesticides have adverse health effects and can be transported over long distances to contaminate sensitive ecosystems. To address problems caused by environmental pesticides we developed a multimedia multi-pollutant modeling system, and here we present an evaluation of the model by comparing modeled results against measurements. The modeled toxaphene air concentrations for two sites, in Louisiana (LA) and Michigan (MI), are in good agreement with measurements (average concentrations agree to within a factor of 2). Because the residue inventory showed no soil residues at these two sites, resulting in no emissions, the concentrations must be caused by transport; the good agreement between the modeled and measured concentrations suggests that the model simulates atmospheric transport accurately. Compared to the LA and MI sites, the measured air concentrations at two other sites having toxaphene soil residues leading to emissions, in Indiana and Arkansas, showed more pronounced seasonal variability (higher in warmer months); this pattern was also captured by the model. The model-predicted toxaphene concentration fraction on particles (0.5-5%) agrees well with measurement-based estimates (3% or 6%). There is also good agreement between modeled and measured dry (1:1) and wet (within a factor of less than 2) depositions in Lake Ontario. Additionally this study identified erroneous soil residue data around a site in Texas in a published US toxaphene residue inventory, which led to very low modeled air concentrations at this site. Except for the erroneous soil residue data around this site, the good agreement between the modeled and observed results implies that both the US and Mexican toxaphene soil residue inventories are reasonably good. This agreement also suggests that the modeling system is capable of simulating the important physical and chemical processes in the multimedia compartments.

  17. A Critical Review for Developing Accurate and Dynamic Predictive Models Using Machine Learning Methods in Medicine and Health Care.

    PubMed

    Alanazi, Hamdan O; Abdullah, Abdul Hanan; Qureshi, Kashif Naseer

    2017-04-01

    Recently, Artificial Intelligence (AI) has been used widely in medicine and health care sector. In machine learning, the classification or prediction is a major field of AI. Today, the study of existing predictive models based on machine learning methods is extremely active. Doctors need accurate predictions for the outcomes of their patients' diseases. In addition, for accurate predictions, timing is another significant factor that influences treatment decisions. In this paper, existing predictive models in medicine and health care have critically reviewed. Furthermore, the most famous machine learning methods have explained, and the confusion between a statistical approach and machine learning has clarified. A review of related literature reveals that the predictions of existing predictive models differ even when the same dataset is used. Therefore, existing predictive models are essential, and current methods must be improved.

  18. Edge and coupled core/edge transport modeling in tokamak

    SciTech Connect

    Pearlstein, L D; Casper, T A; Cohen, R H; LoDestro, L L; Mattor, N; Porter, G D; Rensink, M E; Rognlien, T D; Ryutov, D D; Scott, H A; Wan, A

    1998-10-14

    Recent advances in the theory and modelling of tokamak edge, scrape-off-layer and divertor plasmas are described. The effects of the poloidal ExB drift on inner/outer divertor-plate asymmetries within a 1D analysis are shown to be in good agreement with experimental observations; above a critical v ExB, the model predicts transitions to supersonic SOL flow at the inboard midplane. Two-dimensional simulations show the importance of ExB flow in the private-flux region and B-drift effects. A theory of rough plasma-facing surfaces is given, and interesting effects, some traveling back up the magnetic field-lines to the SOL plasma, are predicted. The parametric dependence of detached-plasma states in slab geometry has been explored; with sufficient pumping, the location of the ionization front can be controlled; otherwise only fronts at the plate or the X-point are stable. Studies with a more accurate Monte-Carlo neutrals model and a detailed non-LTE radiation-transport code indicate various effects are important for quantitative rnodelling. Long-lived oscillatory UEDGE solutions in both ITER and DIII-D are reported. Detailed simulations of the DIII-D core and edge are presented; impurity and plasma flow are shown to be well modelled with UEDGE, and the roles of impurity and neutral transport in the edge and SOL are discussed.

  19. Simplified risk score models accurately predict the risk of major in-hospital complications following percutaneous coronary intervention.

    PubMed

    Resnic, F S; Ohno-Machado, L; Selwyn, A; Simon, D I; Popma, J J

    2001-07-01

    The objectives of this analysis were to develop and validate simplified risk score models for predicting the risk of major in-hospital complications after percutaneous coronary intervention (PCI) in the era of widespread stenting and use of glycoprotein IIb/IIIa antagonists. We then sought to compare the performance of these simplified models with those of full logistic regression and neural network models. From January 1, 1997 to December 31, 1999, data were collected on 4,264 consecutive interventional procedures at a single center. Risk score models were derived from multiple logistic regression models using the first 2,804 cases and then validated on the final 1,460 cases. The area under the receiver operating characteristic (ROC) curve for the risk score model that predicted death was 0.86 compared with 0.85 for the multiple logistic model and 0.83 for the neural network model (validation set). For the combined end points of death, myocardial infarction, or bypass surgery, the corresponding areas under the ROC curves were 0.74, 0.78, and 0.81, respectively. Previously identified risk factors were confirmed in this analysis. The use of stents was associated with a decreased risk of in-hospital complications. Thus, risk score models can accurately predict the risk of major in-hospital complications after PCI. Their discriminatory power is comparable to those of logistic models and neural network models. Accurate bedside risk stratification may be achieved with these simple models.

  20. Modeling Oxygen Transport in the Human Placenta

    NASA Astrophysics Data System (ADS)

    Serov, Alexander; Filoche, Marcel; Salafia, Carolyn; Grebenkov, Denis

    Efficient functioning of the human placenta is crucial for the favorable pregnancy outcome. We construct a 3D model of oxygen transport in the placenta based on its histological cross-sections. The model accounts for both diffusion and convention of oxygen in the intervillous space and allows one to estimate oxygen uptake of a placentone. We demonstrate the existence of an optimal villi density maximizing the uptake and explain it as a trade-off between the incoming oxygen flow and the absorbing villous surface. Calculations performed for arbitrary shapes of fetal villi show that only two geometrical characteristics - villi density and the effective villi radius - are required to predict fetal oxygen uptake. Two combinations of physiological parameters that determine oxygen uptake are also identified: maximal oxygen inflow of a placentone and the Damköhler number. An automatic image analysis method is developed and applied to 22 healthy placental cross-sections demonstrating that villi density of a healthy human placenta lies within 10% of the optimal value, while overall geometry efficiency is rather low (around 30-40%). In a perspective, the model can constitute the base of a reliable tool of post partum oxygen exchange efficiency assessment in the human placenta. Also affiliated with Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA 90095, USA.

  1. Bottom-up coarse-grained models that accurately describe the structure, pressure, and compressibility of molecular liquids

    SciTech Connect

    Dunn, Nicholas J. H.; Noid, W. G.

    2015-12-28

    The present work investigates the capability of bottom-up coarse-graining (CG) methods for accurately modeling both structural and thermodynamic properties of all-atom (AA) models for molecular liquids. In particular, we consider 1, 2, and 3-site CG models for heptane, as well as 1 and 3-site CG models for toluene. For each model, we employ the multiscale coarse-graining method to determine interaction potentials that optimally approximate the configuration dependence of the many-body potential of mean force (PMF). We employ a previously developed “pressure-matching” variational principle to determine a volume-dependent contribution to the potential, U{sub V}(V), that approximates the volume-dependence of the PMF. We demonstrate that the resulting CG models describe AA density fluctuations with qualitative, but not quantitative, accuracy. Accordingly, we develop a self-consistent approach for further optimizing U{sub V}, such that the CG models accurately reproduce the equilibrium density, compressibility, and average pressure of the AA models, although the CG models still significantly underestimate the atomic pressure fluctuations. Additionally, by comparing this array of models that accurately describe the structure and thermodynamic pressure of heptane and toluene at a range of different resolutions, we investigate the impact of bottom-up coarse-graining upon thermodynamic properties. In particular, we demonstrate that U{sub V} accounts for the reduced cohesion in the CG models. Finally, we observe that bottom-up coarse-graining introduces subtle correlations between the resolution, the cohesive energy density, and the “simplicity” of the model.

  2. Improved model for mercury emission, transport and deposition

    NASA Astrophysics Data System (ADS)

    Gbor, Philip K.; Wen, Deyong; Meng, Fan; Yang, Fuquan; Zhang, Baoning; Sloan, James J.

    Most regional models that have been developed to study the behaviour of mercury (Hg) in the environment do not include detailed treatment of natural (i.e. non-anthropogenic) Hg emissions. We have developed a Hg emission model including natural sources; incorporated it into the CMAQ-Hg model (US EPA) and used it to study the behaviour of Hg in the atmosphere. Our natural Hg emission model uses an algorithm based on meteorology to calculate the emission from vegetation, soil and water using Hg concentrations in soil and water. Using our new model, we carried out simulations for the months of May to September 2000 inclusive on a domain covering eastern North America containing 75 by 70 grid cells at a resolution of 36 km. The simulated daily average natural Hg emission flux varied between 1.8 and 3.7 ng m -2 h -1, with the maximum occurring in July. The simulation found that the total natural emission averaged across the domain is about twice the anthropogenic emission. Hg concentration in the air and wet deposition amounts were higher in the eastern part of the domain than in the western part and reflected both local sources and transport. We report for the first time comparisons of hourly and daily Hg concentrations measured by CAMNet monitoring stations with model simulations done at the same timescales. The correlation coefficients ( R) between modelled daily average total gaseous Hg concentrations and measurements for Point Petre, Egbert and Burnt Island are between 0.74 and 0.82. Neglecting natural emissions led to poorer correlations (between 0.22 and 0.51), indicating the importance of including an accurate and detailed treatment of natural Hg emissions in atmospheric Hg models.

  3. Effective and accurate approach for modeling of commensurate–incommensurate transition in krypton monolayer on graphite

    SciTech Connect

    Ustinov, E. A.

    2014-10-07

    Commensurate–incommensurate (C-IC) transition of krypton molecular layer on graphite received much attention in recent decades in theoretical and experimental researches. However, there still exists a possibility of generalization of the phenomenon from thermodynamic viewpoint on the basis of accurate molecular simulation. Recently, a new technique was developed for analysis of two-dimensional (2D) phase transitions in systems involving a crystalline phase, which is based on accounting for the effect of temperature and the chemical potential on the lattice constant of the 2D layer using the Gibbs–Duhem equation [E. A. Ustinov, J. Chem. Phys. 140, 074706 (2014)]. The technique has allowed for determination of phase diagrams of 2D argon layers on the uniform surface and in slit pores. This paper extends the developed methodology on systems accounting for the periodic modulation of the substrate potential. The main advantage of the developed approach is that it provides highly accurate evaluation of the chemical potential of crystalline layers, which allows reliable determination of temperature and other parameters of various 2D phase transitions. Applicability of the methodology is demonstrated on the krypton–graphite system. Analysis of phase diagram of the krypton molecular layer, thermodynamic functions of coexisting phases, and a method of prediction of adsorption isotherms is considered accounting for a compression of the graphite due to the krypton–carbon interaction. The temperature and heat of C-IC transition has been reliably determined for the gas–solid and solid–solid system.

  4. Effective and accurate approach for modeling of commensurate-incommensurate transition in krypton monolayer on graphite.

    PubMed

    Ustinov, E A

    2014-10-07

    Commensurate-incommensurate (C-IC) transition of krypton molecular layer on graphite received much attention in recent decades in theoretical and experimental researches. However, there still exists a possibility of generalization of the phenomenon from thermodynamic viewpoint on the basis of accurate molecular simulation. Recently, a new technique was developed for analysis of two-dimensional (2D) phase transitions in systems involving a crystalline phase, which is based on accounting for the effect of temperature and the chemical potential on the lattice constant of the 2D layer using the Gibbs-Duhem equation [E. A. Ustinov, J. Chem. Phys. 140, 074706 (2014)]. The technique has allowed for determination of phase diagrams of 2D argon layers on the uniform surface and in slit pores. This paper extends the developed methodology on systems accounting for the periodic modulation of the substrate potential. The main advantage of the developed approach is that it provides highly accurate evaluation of the chemical potential of crystalline layers, which allows reliable determination of temperature and other parameters of various 2D phase transitions. Applicability of the methodology is demonstrated on the krypton-graphite system. Analysis of phase diagram of the krypton molecular layer, thermodynamic functions of coexisting phases, and a method of prediction of adsorption isotherms is considered accounting for a compression of the graphite due to the krypton-carbon interaction. The temperature and heat of C-IC transition has been reliably determined for the gas-solid and solid-solid system.

  5. Testing a method-of-characteristics model of three-dimensional solute transport in ground water

    USGS Publications Warehouse

    Goode, Daniel J.; Konikow, Leonard F.; ,

    1991-01-01

    A new three-dimensional model of solute transport in groundwater that is based on a widely used two-dimensional method of characteristics model and is coupled to a modular finite-difference flow model is under development. The model's accuracy for ideal aquifers having homogeneous properties, uniform boundary conditions, and steady flow along a grid direction is demonstrated by comparison with conventional analytical solutions. The effect of spatially and temporally variable flow velocities is investigated by comparison with special analytical solutions. To test the performance of the model for typical hydrogeologic conditions, we compare results with those from other models as well as with results from the same model using smaller grid spacings and time steps. This model generally provides accurate results for realistic simulations, and is particularly efficient for advection-dominated transport.

  6. An accurate elasto-plastic frictional tangential force displacement model for granular-flow simulations: Displacement-driven formulation

    NASA Astrophysics Data System (ADS)

    Zhang, Xiang; Vu-Quoc, Loc

    2007-07-01

    We present in this paper the displacement-driven version of a tangential force-displacement (TFD) model that accounts for both elastic and plastic deformations together with interfacial friction occurring in collisions of spherical particles. This elasto-plastic frictional TFD model, with its force-driven version presented in [L. Vu-Quoc, L. Lesburg, X. Zhang. An accurate tangential force-displacement model for granular-flow simulations: contacting spheres with plastic deformation, force-driven formulation, Journal of Computational Physics 196(1) (2004) 298-326], is consistent with the elasto-plastic frictional normal force-displacement (NFD) model presented in [L. Vu-Quoc, X. Zhang. An elasto-plastic contact force-displacement model in the normal direction: displacement-driven version, Proceedings of the Royal Society of London, Series A 455 (1991) 4013-4044]. Both the NFD model and the present TFD model are based on the concept of additive decomposition of the radius of contact area into an elastic part and a plastic part. The effect of permanent indentation after impact is represented by a correction to the radius of curvature. The effect of material softening due to plastic flow is represented by a correction to the elastic moduli. The proposed TFD model is accurate, and is validated against nonlinear finite element analyses involving plastic flows in both the loading and unloading conditions. The proposed consistent displacement-driven, elasto-plastic NFD and TFD models are designed for implementation in computer codes using the discrete-element method (DEM) for granular-flow simulations. The model is shown to be accurate and is validated against nonlinear elasto-plastic finite-element analysis.

  7. Accurate, precise, and efficient theoretical methods to calculate anion-π interaction energies in model structures.

    PubMed

    Mezei, Pál D; Csonka, Gábor I; Ruzsinszky, Adrienn; Sun, Jianwei

    2015-01-13

    A correct description of the anion-π interaction is essential for the design of selective anion receptors and channels and important for advances in the field of supramolecular chemistry. However, it is challenging to do accurate, precise, and efficient calculations of this interaction, which are lacking in the literature. In this article, by testing sets of 20 binary anion-π complexes of fluoride, chloride, bromide, nitrate, or carbonate ions with hexafluorobenzene, 1,3,5-trifluorobenzene, 2,4,6-trifluoro-1,3,5-triazine, or 1,3,5-triazine and 30 ternary π-anion-π' sandwich complexes composed from the same monomers, we suggest domain-based local-pair natural orbital coupled cluster energies extrapolated to the complete basis-set limit as reference values. We give a detailed explanation of the origin of anion-π interactions, using the permanent quadrupole moments, static dipole polarizabilities, and electrostatic potential maps. We use symmetry-adapted perturbation theory (SAPT) to calculate the components of the anion-π interaction energies. We examine the performance of the direct random phase approximation (dRPA), the second-order screened exchange (SOSEX), local-pair natural-orbital (LPNO) coupled electron pair approximation (CEPA), and several dispersion-corrected density functionals (including generalized gradient approximation (GGA), meta-GGA, and double hybrid density functional). The LPNO-CEPA/1 results show the best agreement with the reference results. The dRPA method is only slightly less accurate and precise than the LPNO-CEPA/1, but it is considerably more efficient (6-17 times faster) for the binary complexes studied in this paper. For 30 ternary π-anion-π' sandwich complexes, we give dRPA interaction energies as reference values. The double hybrid functionals are much more efficient but less accurate and precise than dRPA. The dispersion-corrected double hybrid PWPB95-D3(BJ) and B2PLYP-D3(BJ) functionals perform better than the GGA and meta

  8. Modeling flow and solute transport in irrigation furrows

    Technology Transfer Automated Retrieval System (TEKTRAN)

    This paper presents an internally coupled flow and solute transport model for free-draining irrigation furrows. Furrow hydraulics is simulated with a numerical zero-inertia model and solute transport is computed with a model based on a numerical solution of the cross-section averaged advection-dispe...

  9. 2016 KIVA-hpFE Development: A Robust and Accurate Engine Modeling Software

    SciTech Connect

    Carrington, David Bradley; Waters, Jiajia

    2016-10-25

    Los Alamos National Laboratory and its collaborators are facilitating engine modeling by improving accuracy and robustness of the modeling, and improving the robustness of software. We also continue to improve the physical modeling methods. We are developing and implementing new mathematical algorithms, those that represent the physics within an engine. We provide software that others may use directly or that they may alter with various models e.g., sophisticated chemical kinetics, different turbulent closure methods or other fuel injection and spray systems.

  10. Preliminary characterization of materials for a reactive transport model validation experiment

    SciTech Connect

    Siegel, M.D.; Ward, D.B.; Cheng, W.C.; Bryant, C.; Chocas, C.S.; Reynolds, C.G.

    1993-03-01

    The geochemical properties of a porous sand and several tracers (Ni, Br, and Li) have been characterized for use in a caisson experiment designed to validate sorption models used in models of inactive transport. The surfaces of the sand grains have been examined by a combination of techniques including potentiometric titration, acid leaching, optical microscopy, and scanning electron microscopy with energy-dispersive spectroscopy. The surface studies indicate the presence of small amounts of carbonate, kaolinite and iron-oxyhydroxides. Adsorption of nickel, lithium and bromide by the sand was measured using batch techniques. Bromide was not sorbed by the sand. A linear (K{sub d}) or an isotherm sorption model may adequately describe transport of Li; however, a model describing the changes of pH and the concentrations of other solution species as a function of time and position within the caisson and the concomitant effects on Ni sorption may be required for accurate predictions of nickel transport.

  11. Parameters estimation for reactive transport: A way to test the validity of a reactive model

    NASA Astrophysics Data System (ADS)

    Aggarwal, Mohit; Cheikh Anta Ndiaye, Mame; Carrayrou, Jérôme

    The chemical parameters used in reactive transport models are not known accurately due to the complexity and the heterogeneous conditions of a real domain. We will present an efficient algorithm in order to estimate the chemical parameters using Monte-Carlo method. Monte-Carlo methods are very robust for the optimisation of the highly non-linear mathematical model describing reactive transport. Reactive transport of tributyltin (TBT) through natural quartz sand at seven different pHs is taken as the test case. Our algorithm will be used to estimate the chemical parameters of the sorption of TBT onto the natural quartz sand. By testing and comparing three models of surface complexation, we show that the proposed adsorption model cannot explain the experimental data.

  12. How to Construct More Accurate Student Models: Comparing and Optimizing Knowledge Tracing and Performance Factor Analysis

    ERIC Educational Resources Information Center

    Gong, Yue; Beck, Joseph E.; Heffernan, Neil T.

    2011-01-01

    Student modeling is a fundamental concept applicable to a variety of intelligent tutoring systems (ITS). However, there is not a lot of practical guidance on how to construct and train such models. This paper compares two approaches for student modeling, Knowledge Tracing (KT) and Performance Factors Analysis (PFA), by evaluating their predictive…

  13. Models in biology: ‘accurate descriptions of our pathetic thinking’

    PubMed Central

    2014-01-01

    In this essay I will sketch some ideas for how to think about models in biology. I will begin by trying to dispel the myth that quantitative modeling is somehow foreign to biology. I will then point out the distinction between forward and reverse modeling and focus thereafter on the former. Instead of going into mathematical technicalities about different varieties of models, I will focus on their logical structure, in terms of assumptions and conclusions. A model is a logical machine for deducing the latter from the former. If the model is correct, then, if you believe its assumptions, you must, as a matter of logic, also believe its conclusions. This leads to consideration of the assumptions underlying models. If these are based on fundamental physical laws, then it may be reasonable to treat the model as ‘predictive’, in the sense that it is not subject to falsification and we can rely on its conclusions. However, at the molecular level, models are more often derived from phenomenology and guesswork. In this case, the model is a test of its assumptions and must be falsifiable. I will discuss three models from this perspective, each of which yields biological insights, and this will lead to some guidelines for prospective model builders. PMID:24886484

  14. Modeling and analysis of transport in the mammary glands

    NASA Astrophysics Data System (ADS)

    Quezada, Ana; Vafai, Kambiz

    2014-08-01

    The transport of three toxins moving from the blood stream into the ducts of the mammary glands is analyzed in this work. The model predictions are compared with experimental data from the literature. The utility of the model lies in its potential to improve our understanding of toxin transport as a pre-disposing factor to breast cancer. This work is based on a multi-layer transport model to analyze the toxins present in the breast milk. The breast milk in comparison with other sampling strategies allows us to understand the mass transport of toxins once inside the bloodstream of breastfeeding women. The multi-layer model presented describes the transport of caffeine, DDT and cimetidine. The analysis performed takes into account the unique transport mechanisms for each of the toxins. Our model predicts the movement of toxins and/or drugs within the mammary glands as well as their bioaccumulation in the tissues.

  15. Towards more accurate isoscapes encouraging results from wine, water and marijuana data/model and model/model comparisons.

    NASA Astrophysics Data System (ADS)

    West, J. B.; Ehleringer, J. R.; Cerling, T.

    2006-12-01

    Understanding how the biosphere responds to change it at the heart of biogeochemistry, ecology, and other Earth sciences. The dramatic increase in human population and technological capacity over the past 200 years or so has resulted in numerous, simultaneous changes to biosphere structure and function. This, then, has lead to increased urgency in the scientific community to try to understand how systems have already responded to these changes, and how they might do so in the future. Since all biospheric processes exhibit some patchiness or patterns over space, as well as time, we believe that understanding the dynamic interactions between natural systems and human technological manipulations can be improved if these systems are studied in an explicitly spatial context. We present here results of some of our efforts to model the spatial variation in the stable isotope ratios (δ2H and δ18O) of plants over large spatial extents, and how these spatial model predictions compare to spatially explicit data. Stable isotopes trace and record ecological processes and as such, if modeled correctly over Earth's surface allow us insights into changes in biosphere states and processes across spatial scales. The data-model comparisons show good agreement, in spite of the remaining uncertainties (e.g., plant source water isotopic composition). For example, inter-annual changes in climate are recorded in wine stable isotope ratios. Also, a much simpler model of leaf water enrichment driven with spatially continuous global rasters of precipitation and climate normals largely agrees with complex GCM modeling that includes leaf water δ18O. Our results suggest that modeling plant stable isotope ratios across large spatial extents may be done with reasonable accuracy, including over time. These spatial maps, or isoscapes, can now be utilized to help understand spatially distributed data, as well as to help guide future studies designed to understand ecological change across

  16. Accurate and efficient modeling of global seismic wave propagation for an attenuative Earth model including the center

    NASA Astrophysics Data System (ADS)

    Toyokuni, Genti; Takenaka, Hiroshi

    2012-06-01

    We propose a method for modeling global seismic wave propagation through an attenuative Earth model including the center. This method enables accurate and efficient computations since it is based on the 2.5-D approach, which solves wave equations only on a 2-D cross section of the whole Earth and can correctly model 3-D geometrical spreading. We extend a numerical scheme for the elastic waves in spherical coordinates using the finite-difference method (FDM), to solve the viscoelastodynamic equation. For computation of realistic seismic wave propagation, incorporation of anelastic attenuation is crucial. Since the nature of Earth material is both elastic solid and viscous fluid, we should solve stress-strain relations of viscoelastic material, including attenuative structures. These relations represent the stress as a convolution integral in time, which has had difficulty treating viscoelasticity in time-domain computation such as the FDM. However, we now have a method using so-called memory variables, invented in the 1980s, followed by improvements in Cartesian coordinates. Arbitrary values of the quality factor (Q) can be incorporated into the wave equation via an array of Zener bodies. We also introduce the multi-domain, an FD grid of several layers with different grid spacings, into our FDM scheme. This allows wider lateral grid spacings with depth, so as not to perturb the FD stability criterion around the Earth center. In addition, we propose a technique to avoid the singularity problem of the wave equation in spherical coordinates at the Earth center. We develop a scheme to calculate wavefield variables on this point, based on linear interpolation for the velocity-stress, staggered-grid FDM. This scheme is validated through a comparison of synthetic seismograms with those obtained by the Direct Solution Method for a spherically symmetric Earth model, showing excellent accuracy for our FDM scheme. As a numerical example, we apply the method to simulate seismic

  17. Status of the solar and infrared radiation submodels in the LLNL 1-D and 2-D chemical-transport models

    SciTech Connect

    Grant, K.E.; Taylor, K.E.; Ellis, J.S.; Wuebbles, D.J.

    1987-07-01

    The authors have implemented a series of state of the art radiation transport submodels in previously developed one dimensional and two dimensional chemical transport models of the troposphere and stratosphere. These submodels provide the capability of calculating accurate solar and infrared heating rates. They are a firm basis for further radiation submodel development as well as for studying interactions between radiation and model dynamics under varying conditions of clear sky, clouds, and aerosols. 37 refs., 3 figs.

  18. Guidelines for effective radiation transport for cable SGEMP modeling

    SciTech Connect

    Drumm, Clifton Russell; Fan, Wesley C.; Turner, C. David

    2014-07-01

    This report describes experiences gained in performing radiation transport computations with the SCEPTRE radiation transport code for System Generated ElectroMagnetic Pulse (SGEMP) applications. SCEPTRE is a complex code requiring a fairly sophisticated user to run the code effectively, so this report provides guidance for analysts interested in performing these types of calculations. One challenge in modeling coupled photon/electron transport for SGEMP is to provide a spatial mesh that is sufficiently resolved to accurately model surface charge emission and charge deposition near material interfaces. The method that has been most commonly used to date to compute cable SGEMP typically requires a sub-micron mesh size near material interfaces, which may be difficult for meshing software to provide for complex geometries. We present here an alternative method for computing cable SGEMP that appears to substantially relax this requirement. The report also investigates the effect of refining the energy mesh and increasing the order of the angular approximation to provide some guidance on determining reasonable parameters for the energy/angular approximation needed for x-ray environments. Conclusions for γ-ray environments may be quite different and will be treated in a subsequent report. In the course of the energy-mesh refinement studies, a bug in the cross-section generation software was discovered that may cause underprediction of the result by as much as an order of magnitude for the test problem studied here, when the electron energy group widths are much smaller than those for the photons. Results will be presented and compared using cross sections generated before and after the fix. We also describe adjoint modeling, which provides sensitivity of the total charge drive to the source energy and angle of incidence, which is quite useful for comparing the effect of changing the source environment and for determining most stressing angle of incidence and source

  19. Accurate and self-consistent procedure for determining pH in seawater desalination brines and its manifestation in reverse osmosis modeling.

    PubMed

    Nir, Oded; Marvin, Esra; Lahav, Ori

    2014-11-01

    Measuring and modeling pH in concentrated aqueous solutions in an accurate and consistent manner is of paramount importance to many R&D and industrial applications, including RO desalination. Nevertheless, unified definitions and standard procedures have yet to be developed for solutions with ionic strength higher than ∼0.7 M, while implementation of conventional pH determination approaches may lead to significant errors. In this work a systematic yet simple methodology for measuring pH in concentrated solutions (dominated by Na(+)/Cl(-)) was developed and evaluated, with the aim of achieving consistency with the Pitzer ion-interaction approach. Results indicate that the addition of 0.75 M of NaCl to NIST buffers, followed by assigning a new standard pH (calculated based on the Pitzer approach), enabled reducing measured errors to below 0.03 pH units in seawater RO brines (ionic strength up to 2 M). To facilitate its use, the method was developed to be both conceptually and practically analogous to the conventional pH measurement procedure. The method was used to measure the pH of seawater RO retentates obtained at varying recovery ratios. The results matched better the pH values predicted by an accurate RO transport model. Calibrating the model by the measured pH values enabled better boron transport prediction. A Donnan-induced phenomenon, affecting pH in both retentate and permeate streams, was identified and quantified.

  20. THE IMPACT OF ACCURATE EXTINCTION MEASUREMENTS FOR X-RAY SPECTRAL MODELS

    SciTech Connect

    Smith, Randall K.; Valencic, Lynne A.; Corrales, Lia

    2016-02-20

    Interstellar extinction includes both absorption and scattering of photons from interstellar gas and dust grains, and it has the effect of altering a source's spectrum and its total observed intensity. However, while multiple absorption models exist, there are no useful scattering models in standard X-ray spectrum fitting tools, such as XSPEC. Nonetheless, X-ray halos, created by scattering from dust grains, are detected around even moderately absorbed sources, and the impact on an observed source spectrum can be significant, if modest, compared to direct absorption. By convolving the scattering cross section with dust models, we have created a spectral model as a function of energy, type of dust, and extraction region that can be used with models of direct absorption. This will ensure that the extinction model is consistent and enable direct connections to be made between a source's X-ray spectral fits and its UV/optical extinction.

  1. Development of accurate waveform models for eccentric compact binaries with numerical relativity simulations

    NASA Astrophysics Data System (ADS)

    Huerta, Eliu; Agarwal, Bhanu; Chua, Alvin; George, Daniel; Haas, Roland; Hinder, Ian; Kumar, Prayush; Moore, Christopher; Pfeiffer, Harald

    2017-01-01

    We recently constructed an inspiral-merger-ringdown (IMR) waveform model to describe the dynamical evolution of compact binaries on eccentric orbits, and used this model to constrain the eccentricity with which the gravitational wave transients currently detected by LIGO could be effectively recovered with banks of quasi-circular templates. We now present the second generation of this model, which is calibrated using a large catalog of eccentric numerical relativity simulations. We discuss the new features of this model, and show that its enhance accuracy makes it a powerful tool to detect eccentric signals with LIGO.

  2. An Efficient and Accurate Quantum Lattice-Gas Model for the Many-Body Schroedinger Wave Equation

    DTIC Science & Technology

    2002-01-01

    CONTRACT NUMBER AN EFFICIENT AND ACCURATE QUANTUM LATTICE-GAS MODEL FOR THE MANY-BODY SCHROEDINGER WAVE EQUATION 5b. GRANT NUMBER SC. PROGRAM ELEMENT...for simulating the time-dependent evolution of a many-body jiiantum mechanical system of particles governed by the non-relativistic Schroedinger " wave...the numerical dispersion of the simulated wave packets is compared with the analytical solutions. 15. SUBJECT TERM: Schroedinger wave equation

  3. Offline tracer transport modeling with global WRF model data

    NASA Astrophysics Data System (ADS)

    Belikov, Dmitry; Maksytov, Shamil; Zaripov, Radomir; Bart, Andrey; Starchenko, Alexander

    2013-04-01

    This work describes the one-way coupling between a global configuration of the Weather Research and Forecasting (WRF) weather prediction model (http://wrf-model.org/) and the National Institute for Environmental Studies (NIES) three-dimensional offline chemical transport model (version NIES-08.1i). The primary motivation for developing this coupled model has been to reduce transport errors in global-scale simulation of greenhouse gases through a more detailed description of the meteorological conditions. We have implemented a global configuration of WRF model (version 3.4.1, ARW core) with 2.5 degree horizontal resolution and 32 vertical levels. The WRF model was driving with NCEP Final Analysis (FNL) reanalysis using combined techniques: FDDA + Cyclic Incremental Correction (like in intermittent data assimilation). Time-averaged mass-coupled horizontal velocities on sigma levels with approach supposed by Nehrkorn et al. (2010) are calculated to drive NIES TM. The NIES TM is designed to simulate natural and anthropogenic synoptic-scale variations in atmospheric constituents at diurnal, seasonal and interannual timescales. The model uses a mass-conservative flux-form formulation that consists of a third-order van Leer advection scheme and a horizontal dry-air mass flux correction. The horizontal latitude-longitude grid is a reduced rectangular grid (i.e., the grid size is doubled several times approaching the poles), with an initial spatial resolution of 2.5 deg x 2.5 deg and 32 vertical levels from the surface up to the level of 3 hPa. A simulations of the atmospheric tracer are used to evaluate the performance of the coupled WRF-NIES model. Simulated distributions are validated against in situ observations and compared with output from "standard" version of NIES TM driven by the Japanese 25-year Reanalysis/the Japan Meteorological Agency Climate Data Assimilation System (JRA-25/JCDAS) dataset. Fields calculated by WRF and used to drive NIES TM were also evaluated

  4. Aerosols and clouds in chemical transport models and climate models.

    SciTech Connect

    Lohmann,U.; Schwartz, S. E.

    2008-03-02

    Clouds exert major influences on both shortwave and longwave radiation as well as on the hydrological cycle. Accurate representation of clouds in climate models is a major unsolved problem because of high sensitivity of radiation and hydrology to cloud properties and processes, incomplete understanding of these processes, and the wide range of length scales over which these processes occur. Small changes in the amount, altitude, physical thickness, and/or microphysical properties of clouds due to human influences can exert changes in Earth's radiation budget that are comparable to the radiative forcing by anthropogenic greenhouse gases, thus either partly offsetting or enhancing the warming due to these gases. Because clouds form on aerosol particles, changes in the amount and/or composition of aerosols affect clouds in a variety of ways. The forcing of the radiation balance due to aerosol-cloud interactions (indirect aerosol effect) has large uncertainties because a variety of important processes are not well understood precluding their accurate representation in models.

  5. Application of pesticide transport model for simulating diazinon runoff in California’s central valley

    NASA Astrophysics Data System (ADS)

    Joyce, Brian A.; Wallender, Wesley W.; Mailapalli, Damodhara R.

    2010-12-01

    Dormant spray application of pesticides to almond and other stone fruit orchards is the main source of diazinon during the winter in California's central valley. Understanding the pesticide transport and the tradeoffs associated with the various management practices is greatly facilitated by the use of physically-based contaminant transport models. In this study, performance of Joyce's et al. (2008) pesticide transport model was evaluated using experimental data collected from two ground treatments such as resident vegetation and bare soil. The model simulation results obtained in calibration and validation process were analyzed for pesticide concentration and total load. The pesticide transport model accurately predicted the pesticide concentrations and total load in the runoff from bare field and was capable of simulating chemical responses to rainfall-runoff events. In case of resident vegetation, the model results exhibited a larger range of variation than was observed in the bare soil simulations due to increased model parameterization with the addition of foliage and thatch compartments. Furthermore, the model was applied to study the effect of runoff lag time, extent of crop cover, organic content of soil and post-application irrigation on the pesticide peak concentration and total load. Based on the model results, recommendations were suggested to growers prior to implementing certain management decisions to mitigate diazinon transport in the orchard's spray runoff.

  6. Investigating long-range transport of pollution to the Arctic troposphere using aircraft observations and a global chemical transport model

    NASA Astrophysics Data System (ADS)

    Monks, S.; Arnold, S.; Chipperfield, M.; Turquety, S.; Ancellet, G.; Law, K.; Schlager, H.

    2009-04-01

    Surface temperatures in the Arctic have increased more than in any other region over the past few decades. A better understanding of the processes governing this warming, including the role of short-lived greenhouse gases, is therefore urgently required. During summer 2008, the POLARCAT campaign aimed to collect an extensive gas-phase and aerosol dataset within the Arctic troposphere, which will aid the evaluation of our understanding of oxidant photochemistry and aerosol processing in the region. Previous comparisons of global chemical transport models have shown that they exhibit large variability in their Arctic chemical budgets, indicating that the processes controlling Arctic tropospheric composition are not well understood or represented within models. Here, we will use new trace-gas observations from the French ATR and German DLR Falcon aircraft during the POLARCAT experiment to evaluate the ability of a global chemical transport model (TOMCAT) to simulate the summertime transport of pollutants to the Arctic, and their impact on oxidant budgets. In particular, we aim to quantify the impact of anthropogenic and biomass burning sources on the Arctic tropospheric ozone budget. Initial results show that the model underestimates observed concentrations of CO which has led to a re-evaluation of the different sources of CO to the region. Model performance in the Arctic is highly sensitive to the treatment of boreal biomass burning emissions. Boreal biomass burning plumes were sampled frequently over the course of the campaign therefore accurate representation of emission injection heights and fire locations is essential. Model CO is improved with real-time satellite derived daily biomass burning emissions, however large uncertainties in these emissions result in large variability in the Arctic CO budget. We will also present results on the ability of the model to capture pollution transport pathways to the Arctic and contributions to the oxidant and NOy budgets

  7. Modeling transportation of efavirenz: inference on possibility of mixed modes of transportation and kinetic solubility.

    PubMed

    Nemaura, Tafireyi

    2015-01-01

    Understanding drug transportation mechanisms in the human body is of paramount importance in modeling Pharmacokinetic-Pharmacodynamic relationships. This work gives a novel general model of efavirenz transportation projections based on concentrations simulated from patients on a dose of 600 mg. The work puts forward a proposition that transportation can wholly be modeled by concentration and time in a uniform volumetric space. Furthermore, movement entities are used to inform the state of "kinetic solubility" of a solution. There is use of Ricker's model, and forms of the Hill's equation in modeling transportation. Characterization on the movement rates of solution particle are suggested in relation to advection rate of solution particle. At turning points on the transportation rate of solution particle vs. concentration curve, a suggestion of possibly change of dominance in the mode of transportation and saturation is made. There are four movement rates postulated at primary micro-level transportation, that are attributed to convection, diffusion [passive transportation (EI )] and energy dependent system transportation (ED ) in relation to advection. Furthermore, a new parameter is introduced which is defined as an advection rate constant of solution particle. It is postulated to be dependent on two rate constants of solution particle, that is a convection rate constant of solution particle and a saturable transportation rate constant of solution particle. At secondary micro-level transportation, the results show convection as sum of advection and saturable transportation. The kinetics of dissolution of efavirenz in the solution space is postulated. Relatively, a good level of kinetics of dissolution is projected in the concentration region 0 - 32.82 μg/ml.

  8. Efficient and accurate local model for colorimetric characterization of liquid-crystal displays.

    PubMed

    Zou, Wenhai; Xu, Haisong; Gong, Rui

    2012-01-01

    Taking the chromaticity inconstancy of LCDs and the inverse efficiency into account, a novel local colorimetric characterization model was developed in this Letter. Rather than dividing the device color space into many subspaces to refine the chromaticity description as existent local models, the proposed model tailored the transformation relationship uniquely for each characterized color with look-up tables and a local chromaticity matrix. Based on this model, the characterization task could be efficiently accomplished within a few steps for either the forward or the inverse transformation. Test experiments on several commercial LCDs indicated that the average color difference between the estimated and measured tristimulus values could be achieved in a low level of about 0.4 CIEDE2000 units, effectively demonstrating the proposed model.

  9. Active appearance model and deep learning for more accurate prostate segmentation on MRI

    NASA Astrophysics Data System (ADS)

    Cheng, Ruida; Roth, Holger R.; Lu, Le; Wang, Shijun; Turkbey, Baris; Gandler, William; McCreedy, Evan S.; Agarwal, Harsh K.; Choyke, Peter; Summers, Ronald M.; McAuliffe, Matthew J.

    2016-03-01

    Prostate segmentation on 3D MR images is a challenging task due to image artifacts, large inter-patient prostate shape and texture variability, and lack of a clear prostate boundary specifically at apex and base levels. We propose a supervised machine learning model that combines atlas based Active Appearance Model (AAM) with a Deep Learning model to segment the prostate on MR images. The performance of the segmentation method is evaluated on 20 unseen MR image datasets. The proposed method combining AAM and Deep Learning achieves a mean Dice Similarity Coefficient (DSC) of 0.925 for whole 3D MR images of the prostate using axial cross-sections. The proposed model utilizes the adaptive atlas-based AAM model and Deep Learning to achieve significant segmentation accuracy.

  10. Accurate coarse-grained models for mixtures of colloids and linear polymers under good-solvent conditions

    SciTech Connect

    D’Adamo, Giuseppe; Pelissetto, Andrea; Pierleoni, Carlo

    2014-12-28

    A coarse-graining strategy, previously developed for polymer solutions, is extended here to mixtures of linear polymers and hard-sphere colloids. In this approach, groups of monomers are mapped onto a single pseudoatom (a blob) and the effective blob-blob interactions are obtained by requiring the model to reproduce some large-scale structural properties in the zero-density limit. We show that an accurate parametrization of the polymer-colloid interactions is obtained by simply introducing pair potentials between blobs and colloids. For the coarse-grained (CG) model in which polymers are modelled as four-blob chains (tetramers), the pair potentials are determined by means of the iterative Boltzmann inversion scheme, taking full-monomer (FM) pair correlation functions at zero-density as targets. For a larger number n of blobs, pair potentials are determined by using a simple transferability assumption based on the polymer self-similarity. We validate the model by comparing its predictions with full-monomer results for the interfacial properties of polymer solutions in the presence of a single colloid and for thermodynamic and structural properties in the homogeneous phase at finite polymer and colloid density. The tetramer model is quite accurate for q ≲ 1 (q=R{sup ^}{sub g}/R{sub c}, where R{sup ^}{sub g} is the zero-density polymer radius of gyration and R{sub c} is the colloid radius) and reasonably good also for q = 2. For q = 2, an accurate coarse-grained description is obtained by using the n = 10 blob model. We also compare our results with those obtained by using single-blob models with state-dependent potentials.

  11. Evaluation of Tropical Transport in a Global Chemistry and Transport Model

    NASA Technical Reports Server (NTRS)

    Douglass, Anne R.; DaSilva, A. M.; Lin, S.-J.; Pawson, S.; Rood, R. B.; Bhartia, P. K. (Technical Monitor)

    2001-01-01

    Observations of constituents from satellite, aircraft and sondes can be utilized to develop diagnostics of various aspects of tropical transport. These include tropical mid-latitude isolation, the seasonal transport from the upper tropical troposphere to the mid-latitude lowermost stratosphere, the seasonal cycle of the tropical total ozone and its variability. These diagnostics will be applied to constituent fields from an off-line chemistry and transport model (CTM) driven by winds from two sources. These are the Finite Volume Community Climate Model (FV-CCM), a general circulation model that uses the NCAR CCM physics and the Lin and Rood dynamical core, and an assimilation system developed by the Data Assimilation Office at the Goddard Space Flight Center that uses the FV-CCM at its core. Signatures of the quasi-biennial oscillation present in the observations will be emphasized to understand differences between the two model transports and the transport inferred from the observations.

  12. Revisiting low-fidelity two-fluid models for gas–solids transport

    SciTech Connect

    Adeleke, Najeem Adewumi, Michael Ityokumbul, Thaddeus

    2016-08-15

    Two-phase gas–solids transport models are widely utilized for process design and automation in a broad range of industrial applications. Some of these applications include proppant transport in gaseous fracking fluids, air/gas drilling hydraulics, coal-gasification reactors and food processing units. Systems automation and real time process optimization stand to benefit a great deal from availability of efficient and accurate theoretical models for operations data processing. However, modeling two-phase pneumatic transport systems accurately requires a comprehensive understanding of gas–solids flow behavior. In this study we discuss the prevailing flow conditions and present a low-fidelity two-fluid model equation for particulate transport. The model equations are formulated in a manner that ensures the physical flux term remains conservative despite the inclusion of solids normal stress through the empirical formula for modulus of elasticity. A new set of Roe–Pike averages are presented for the resulting strictly hyperbolic flux term in the system of equations, which was used to develop a Roe-type approximate Riemann solver. The resulting scheme is stable regardless of the choice of flux-limiter. The model is evaluated by the prediction of experimental results from both pneumatic riser and air-drilling hydraulics systems. We demonstrate the effect and impact of numerical formulation and choice of numerical scheme on model predictions. We illustrate the capability of a low-fidelity one-dimensional two-fluid model in predicting relevant flow parameters in two-phase particulate systems accurately even under flow regimes involving counter-current flow.

  13. Revisiting low-fidelity two-fluid models for gas-solids transport

    NASA Astrophysics Data System (ADS)

    Adeleke, Najeem; Adewumi, Michael; Ityokumbul, Thaddeus

    2016-08-01

    Two-phase gas-solids transport models are widely utilized for process design and automation in a broad range of industrial applications. Some of these applications include proppant transport in gaseous fracking fluids, air/gas drilling hydraulics, coal-gasification reactors and food processing units. Systems automation and real time process optimization stand to benefit a great deal from availability of efficient and accurate theoretical models for operations data processing. However, modeling two-phase pneumatic transport systems accurately requires a comprehensive understanding of gas-solids flow behavior. In this study we discuss the prevailing flow conditions and present a low-fidelity two-fluid model equation for particulate transport. The model equations are formulated in a manner that ensures the physical flux term remains conservative despite the inclusion of solids normal stress through the empirical formula for modulus of elasticity. A new set of Roe-Pike averages are presented for the resulting strictly hyperbolic flux term in the system of equations, which was used to develop a Roe-type approximate Riemann solver. The resulting scheme is stable regardless of the choice of flux-limiter. The model is evaluated by the prediction of experimental results from both pneumatic riser and air-drilling hydraulics systems. We demonstrate the effect and impact of numerical formulation and choice of numerical scheme on model predictions. We illustrate the capability of a low-fidelity one-dimensional two-fluid model in predicting relevant flow parameters in two-phase particulate systems accurately even under flow regimes involving counter-current flow.

  14. Simplified versus geometrically accurate models of forefoot anatomy to predict plantar pressures: A finite element study.

    PubMed

    Telfer, Scott; Erdemir, Ahmet; Woodburn, James; Cavanagh, Peter R

    2016-01-25

    Integration of patient-specific biomechanical measurements into the design of therapeutic footwear has been shown to improve clinical outcomes in patients with diabetic foot disease. The addition of numerical simulations intended to optimise intervention design may help to build on these advances, however at present the time and labour required to generate and run personalised models of foot anatomy restrict their routine clinical utility. In this study we developed second-generation personalised simple finite element (FE) models of the forefoot with varying geometric fidelities. Plantar pressure predictions from barefoot, shod, and shod with insole simulations using simplified models were compared to those obtained from CT-based FE models incorporating more detailed representations of bone and tissue geometry. A simplified model including representations of metatarsals based on simple geometric shapes, embedded within a contoured soft tissue block with outer geometry acquired from a 3D surface scan was found to provide pressure predictions closest to the more complex model, with mean differences of 13.3kPa (SD 13.4), 12.52kPa (SD 11.9) and 9.6kPa (SD 9.3) for barefoot, shod, and insole conditions respectively. The simplified model design could be produced in <1h compared to >3h in the case of the more detailed model, and solved on average 24% faster. FE models of the forefoot based on simplified geometric representations of the metatarsal bones and soft tissue surface geometry from 3D surface scans may potentially provide a simulation approach with improved clinical utility, however further validity testing around a range of therapeutic footwear types is required.

  15. Modeling and laboratory investigations of microbial transport phenomena in porous media

    SciTech Connect

    Chang, Ming-Ming; Bryant, R.S.; Chung, Ting-Horng; Gao, H.W.

    1991-11-01

    Simulation and experimental results on the transport of microbes and nutrients in one-dimensional cores are presented, and the development of a three-dimensional, three-phase, multiple-component numerical model to describe the microbial transport phenomena in porous media is described. The governing equations in the mathematical model include net flux of microbes by convection and dispersion, decay and growth rates of microbes, chemotaxis and nutrient consumption, and deposition of microbes on rock grain surfaces. Porosity and permeability reductions due to cell clogging have been considered, and the production of gas by microbial metabolism has been incorporated. Governing equations for microbial and nutrient transport are coupled with continuity and flow equations under conditions appropriate for a black oil reservoir. The computer simulator has been used to determine the effects of various transport parameters on microbial transport phenomena. The model can accurately describe the observed transport of microbes, nutrients, and metabolites in coreflooding experiments. Input parameters are determined by matching laboratory experimental results. The model can be used to predict the propagation of microbes and nutrients in a model reservoir and to optimize injection strategies. Optimization of injection strategy results in increased oil recovery due to improvements in sweep efficiency. 16 refs., 9 figs., 5 tabs.

  16. Accurate Sloshing Modes Modeling: A New Analytical Solution and its Consequences on Control

    NASA Astrophysics Data System (ADS)

    Gonidou, Luc-Olivier; Desmariaux, Jean

    2014-06-01

    This study addresses the issue of sloshing modes modeling for GNC analyses purposes. On European launchers, equivalent mechanical systems are commonly used for modeling sloshing effects on launcher dynamics. The representativeness of such a methodology is discussed here. First an exact analytical formulation of the launcher dynamics fitted with sloshing modes is proposed and discrepancies with equivalent mechanical system approach are emphasized. Then preliminary comparative GNC analyses are performed using the different models of dynamics in order to evaluate the impact of the aforementioned discrepancies from GNC standpoint. Special attention is paid to system stability.

  17. Generalized Stoner-Wohlfarth model accurately describing the switching processes in pseudo-single ferromagnetic particles

    SciTech Connect

    Cimpoesu, Dorin Stoleriu, Laurentiu; Stancu, Alexandru

    2013-12-14

    We propose a generalized Stoner-Wohlfarth (SW) type model to describe various experimentally observed angular dependencies of the switching field in non-single-domain magnetic particles. Because the nonuniform magnetic states are generally characterized by complicated spin configurations with no simple analytical description, we maintain the macrospin hypothesis and we phenomenologically include the effects of nonuniformities only in the anisotropy energy, preserving as much as possible the elegance of SW model, the concept of critical curve and its geometric interpretation. We compare the results obtained with our model with full micromagnetic simulations in order to evaluate the performance and limits of our approach.

  18. Empirical approaches to more accurately predict benthic-pelagic coupling in biogeochemical ocean models

    NASA Astrophysics Data System (ADS)

    Dale, Andy; Stolpovsky, Konstantin; Wallmann, Klaus

    2016-04-01

    The recycling and burial of biogenic material in the sea floor plays a key role in the regulation of ocean chemistry. Proper consideration of these processes in ocean biogeochemical models is becoming increasingly recognized as an important step in model validation and prediction. However, the rate of organic matter remineralization in sediments and the benthic flux of redox-sensitive elements are difficult to predict a priori. In this communication, examples of empirical benthic flux models that can be coupled to earth system models to predict sediment-water exchange in the open ocean are presented. Large uncertainties hindering further progress in this field include knowledge of the reactivity of organic carbon reaching the sediment, the importance of episodic variability in bottom water chemistry and particle rain rates (for both the deep-sea and margins) and the role of benthic fauna. How do we meet the challenge?

  19. Accurate modeling of F-region electron densities. Annual progress report, 1993-1994

    SciTech Connect

    Not Available

    1994-01-01

    In the past year, the authors have made considerable progress in a number of areas including algorithm development, completion of two major case studies, and the development of a new EUV flux model. As a result, there has been a major improvement in the ability to model global emissions in support of NASA's imaging plans. Activity highlights include the following: developed a new algorithm to allow physical models to reproduce observed NmF2; investigated the relationship between NmF2 and F10.7 at Millstone Hill during 1990; developed a new solar EUV flux model; statistical survey of anomalously high nighttime electron T(sub e) at Millstone Hill; conducted a case study of the March 1990 magnetic storm; and conducted a comparison between theory and data of magnetically quiet behavior of the winter ionosphere at Millstone Hill.

  20. A Two-Phase Space Resection Model for Accurate Topographic Reconstruction from Lunar Imagery with PushbroomScanners

    PubMed Central

    Xu, Xuemiao; Zhang, Huaidong; Han, Guoqiang; Kwan, Kin Chung; Pang, Wai-Man; Fang, Jiaming; Zhao, Gansen

    2016-01-01

    Exterior orientation parameters’ (EOP) estimation using space resection plays an important role in topographic reconstruction for push broom scanners. However, existing models of space resection are highly sensitive to errors in data. Unfortunately, for lunar imagery, the altitude data at the ground control points (GCPs) for space resection are error-prone. Thus, existing models fail to produce reliable EOPs. Motivated by a finding that for push broom scanners, angular rotations of EOPs can be estimated independent of the altitude data and only involving the geographic data at the GCPs, which are already provided, hence, we divide the modeling of space resection into two phases. Firstly, we estimate the angular rotations based on the reliable geographic data using our proposed mathematical model. Then, with the accurate angular rotations, the collinear equations for space resection are simplified into a linear problem, and the global optimal solution for the spatial position of EOPs can always be achieved. Moreover, a certainty term is integrated to penalize the unreliable altitude data for increasing the error tolerance. Experimental results evidence that our model can obtain more accurate EOPs and topographic maps not only for the simulated data, but also for the real data from Chang’E-1, compared to the existing space resection model. PMID:27077855

  1. A Weibull statistics-based lignocellulose saccharification model and a built-in parameter accurately predict lignocellulose hydrolysis performance.

    PubMed

    Wang, Mingyu; Han, Lijuan; Liu, Shasha; Zhao, Xuebing; Yang, Jinghua; Loh, Soh Kheang; Sun, Xiaomin; Zhang, Chenxi; Fang, Xu

    2015-09-01

    Renewable energy from lignocellulosic biomass has been deemed an alternative to depleting fossil fuels. In order to improve this technology, we aim to develop robust mathematical models for the enzymatic lignocellulose degradation process. By analyzing 96 groups of previously published and newly obtained lignocellulose saccharification results and fitting them to Weibull distribution, we discovered Weibull statistics can accurately predict lignocellulose saccharification data, regardless of the type of substrates, enzymes and saccharification conditions. A mathematical model for enzymatic lignocellulose degradation was subsequently constructed based on Weibull statistics. Further analysis of the mathematical structure of the model and experimental saccharification data showed the significance of the two parameters in this model. In particular, the λ value, defined the characteristic time, represents the overall performance of the saccharification system. This suggestion was further supported by statistical analysis of experimental saccharification data and analysis of the glucose production levels when λ and n values change. In conclusion, the constructed Weibull statistics-based model can accurately predict lignocellulose hydrolysis behavior and we can use the λ parameter to assess the overall performance of enzymatic lignocellulose degradation. Advantages and potential applications of the model and the λ value in saccharification performance assessment were discussed.

  2. A Two-Phase Space Resection Model for Accurate Topographic Reconstruction from Lunar Imagery with PushbroomScanners.

    PubMed

    Xu, Xuemiao; Zhang, Huaidong; Han, Guoqiang; Kwan, Kin Chung; Pang, Wai-Man; Fang, Jiaming; Zhao, Gansen

    2016-04-11

    Exterior orientation parameters' (EOP) estimation using space resection plays an important role in topographic reconstruction for push broom scanners. However, existing models of space resection are highly sensitive to errors in data. Unfortunately, for lunar imagery, the altitude data at the ground control points (GCPs) for space resection are error-prone. Thus, existing models fail to produce reliable EOPs. Motivated by a finding that for push broom scanners, angular rotations of EOPs can be estimated independent of the altitude data and only involving the geographic data at the GCPs, which are already provided, hence, we divide the modeling of space resection into two phases. Firstly, we estimate the angular rotations based on the reliable geographic data using our proposed mathematical model. Then, with the accurate angular rotations, the collinear equations for space resection are simplified into a linear problem, and the global optimal solution for the spatial position of EOPs can always be achieved. Moreover, a certainty term is integrated to penalize the unreliable altitude data for increasing the error tolerance. Experimental results evidence that our model can obtain more accurate EOPs and topographic maps not only for the simulated data, but also for the real data from Chang'E-1, compared to the existing space resection model.

  3. Dynamic saturation in Semiconductor Optical Amplifiers: accurate model, role of carrier density, and slow light.

    PubMed

    Berger, Perrine; Alouini, Mehdi; Bourderionnet, Jérôme; Bretenaker, Fabien; Dolfi, Daniel

    2010-01-18

    We developed an improved model in order to predict the RF behavior and the slow light properties of the SOA valid for any experimental conditions. It takes into account the dynamic saturation of the SOA, which can be fully characterized by a simple measurement, and only relies on material fitting parameters, independent of the optical intensity and the injected current. The present model is validated by showing a good agreement with experiments for small and large modulation indices.

  4. Accurate 3D Modeling of Breast Deformation for Temporal Mammogram Registration

    DTIC Science & Technology

    2008-09-01

    SUPPLEMENTARY NOTES 14. ABSTRACT In this research project, we have developed mathematical model of breast deformation to simulate breast compression during...proposed to simulate and analyze breast deformation that can significantly improve the accuracy of matching in temporal mammograms and thus, the...performance of diagnosis and treatment. In this research project, we have developed a mathematical model of breast deformation to simulate breast

  5. Accurate model annotation of a near-atomic resolution cryo-EM map

    PubMed Central

    Hryc, Corey F.; Chen, Dong-Hua; Afonine, Pavel V.; Jakana, Joanita; Wang, Zhao; Haase-Pettingell, Cameron; Jiang, Wen; Adams, Paul D.; King, Jonathan A.; Schmid, Michael F.; Chiu, Wah

    2017-01-01

    Electron cryomicroscopy (cryo-EM) has been used to determine the atomic coordinates (models) from density maps of biological assemblies. These models can be assessed by their overall fit to the experimental data and stereochemical information. However, these models do not annotate the actual density values of the atoms nor their positional uncertainty. Here, we introduce a computational procedure to derive an atomic model from a cryo-EM map with annotated metadata. The accuracy of such a model is validated by a faithful replication of the experimental cryo-EM map computed using the coordinates and associated metadata. The functional interpretation of any structural features in the model and its utilization for future studies can be made in the context of its measure of uncertainty. We applied this protocol to the 3.3-Å map of the mature P22 bacteriophage capsid, a large and complex macromolecular assembly. With this protocol, we identify and annotate previously undescribed molecular interactions between capsid subunits that are crucial to maintain stability in the absence of cementing proteins or cross-linking, as occur in other bacteriophages. PMID:28270620

  6. Making it Easy to Construct Accurate Hydrological Models that Exploit High Performance Computers (Invited)

    NASA Astrophysics Data System (ADS)

    Kees, C. E.; Farthing, M. W.; Terrel, A.; Certik, O.; Seljebotn, D.

    2013-12-01

    This presentation will focus on two barriers to progress in the hydrological modeling community, and research and development conducted to lessen or eliminate them. The first is a barrier to sharing hydrological models among specialized scientists that is caused by intertwining the implementation of numerical methods with the implementation of abstract numerical modeling information. In the Proteus toolkit for computational methods and simulation, we have decoupled these two important parts of computational model through separate "physics" and "numerics" interfaces. More recently we have begun developing the Strong Form Language for easy and direct representation of the mathematical model formulation in a domain specific language embedded in Python. The second major barrier is sharing ANY scientific software tools that have complex library or module dependencies, as most parallel, multi-physics hydrological models must have. In this setting, users and developer are dependent on an entire distribution, possibly depending on multiple compilers and special instructions depending on the environment of the target machine. To solve these problem we have developed, hashdist, a stateless package management tool and a resulting portable, open source scientific software distribution.

  7. Statistical tests with accurate size and power for balanced linear mixed models.

    PubMed

    Muller, Keith E; Edwards, Lloyd J; Simpson, Sean L; Taylor, Douglas J

    2007-08-30

    The convenience of linear mixed models for Gaussian data has led to their widespread use. Unfortunately, standard mixed model tests often have greatly inflated test size in small samples. Many applications with correlated outcomes in medical imaging and other fields have simple properties which do not require the generality of a mixed model. Alternately, stating the special cases as a general linear multivariate model allows analysing them with either the univariate or multivariate approach to repeated measures (UNIREP, MULTIREP). Even in small samples, an appropriate UNIREP or MULTIREP test always controls test size and has a good power approximation, in sharp contrast to mixed model tests. Hence, mixed model tests should never be used when one of the UNIREP tests (uncorrected, Huynh-Feldt, Geisser-Greenhouse, Box conservative) or MULTIREP tests (Wilks, Hotelling-Lawley, Roy's, Pillai-Bartlett) apply. Convenient methods give exact power for the uncorrected and Box conservative tests. Simulations demonstrate that new power approximations for all four UNIREP tests eliminate most inaccuracy in existing methods. In turn, free software implements the approximations to give a better choice of sample size. Two repeated measures power analyses illustrate the methods. The examples highlight the advantages of examining the entire response surface of power as a function of sample size, mean differences, and variability.

  8. Single Neuron Optimization as a Basis for Accurate Biophysical Modeling: The Case of Cerebellar Granule Cells.

    PubMed

    Masoli, Stefano; Rizza, Martina F; Sgritta, Martina; Van Geit, Werner; Schürmann, Felix; D'Angelo, Egidio

    2017-01-01

    In realistic neuronal modeling, once the ionic channel complement has been defined, the maximum ionic conductance (Gi-max) values need to be tuned in order to match the firing pattern revealed by electrophysiological recordings. Recently, selection/mutation genetic algorithms have been proposed to efficiently and automatically tune these parameters. Nonetheless, since similar firing patterns can be achieved through different combinations of Gi-max values, it is not clear how well these algorithms approximate the corresponding properties of real cells. Here we have evaluated the issue by exploiting a unique opportunity offered by the cerebellar granule cell (GrC), which is electrotonically compact and has therefore allowed the direct experimental measurement of ionic currents. Previous models were constructed using empirical tuning of Gi-max values to match the original data set. Here, by using repetitive discharge patterns as a template, the optimization procedure yielded models that closely approximated the experimental Gi-max values. These models, in addition to repetitive firing, captured additional features, including inward rectification, near-threshold oscillations, and resonance, which were not used as features. Thus, parameter optimization using genetic algorithms provided an efficient modeling strategy for reconstructing the biophysical properties of neurons and for the subsequent reconstruction of large-scale neuronal network models.

  9. Accurate model annotation of a near-atomic resolution cryo-EM map.

    PubMed

    Hryc, Corey F; Chen, Dong-Hua; Afonine, Pavel V; Jakana, Joanita; Wang, Zhao; Haase-Pettingell, Cameron; Jiang, Wen; Adams, Paul D; King, Jonathan A; Schmid, Michael F; Chiu, Wah

    2017-03-21

    Electron cryomicroscopy (cryo-EM) has been used to determine the atomic coordinates (models) from density maps of biological assemblies. These models can be assessed by their overall fit to the experimental data and stereochemical information. However, these models do not annotate the actual density values of the atoms nor their positional uncertainty. Here, we introduce a computational procedure to derive an atomic model from a cryo-EM map with annotated metadata. The accuracy of such a model is validated by a faithful replication of the experimental cryo-EM map computed using the coordinates and associated metadata. The functional interpretation of any structural features in the model and its utilization for future studies can be made in the context of its measure of uncertainty. We applied this protocol to the 3.3-Å map of the mature P22 bacteriophage capsid, a large and complex macromolecular assembly. With this protocol, we identify and annotate previously undescribed molecular interactions between capsid subunits that are crucial to maintain stability in the absence of cementing proteins or cross-linking, as occur in other bacteriophages.

  10. Single Neuron Optimization as a Basis for Accurate Biophysical Modeling: The Case of Cerebellar Granule Cells

    PubMed Central

    Masoli, Stefano; Rizza, Martina F.; Sgritta, Martina; Van Geit, Werner; Schürmann, Felix; D'Angelo, Egidio

    2017-01-01

    In realistic neuronal modeling, once the ionic channel complement has been defined, the maximum ionic conductance (Gi-max) values need to be tuned in order to match the firing pattern revealed by electrophysiological recordings. Recently, selection/mutation genetic algorithms have been proposed to efficiently and automatically tune these parameters. Nonetheless, since similar firing patterns can be achieved through different combinations of Gi-max values, it is not clear how well these algorithms approximate the corresponding properties of real cells. Here we have evaluated the issue by exploiting a unique opportunity offered by the cerebellar granule cell (GrC), which is electrotonically compact and has therefore allowed the direct experimental measurement of ionic currents. Previous models were constructed using empirical tuning of Gi-max values to match the original data set. Here, by using repetitive discharge patterns as a template, the optimization procedure yielded models that closely approximated the experimental Gi-max values. These models, in addition to repetitive firing, captured additional features, including inward rectification, near-threshold oscillations, and resonance, which were not used as features. Thus, parameter optimization using genetic algorithms provided an efficient modeling strategy for reconstructing the biophysical properties of neurons and for the subsequent reconstruction of large-scale neuronal network models. PMID:28360841

  11. Estimation and upscaling of dual-permeability model parameters for the transport of E.coli D21g in soils with preferential flow

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Dual-permeability models are increasingly used to quantify the transport of solutes and microorganisms in soils with preferential flow. An ability to accurately determine the model parameters and their variation with preferential pathway characteristics is crucial for predicting the transport of mi...

  12. A Fibre-Reinforced Poroviscoelastic Model Accurately Describes the Biomechanical Behaviour of the Rat Achilles Tendon

    PubMed Central

    Heuijerjans, Ashley; Matikainen, Marko K.; Julkunen, Petro; Eliasson, Pernilla; Aspenberg, Per; Isaksson, Hanna

    2015-01-01

    Background Computational models of Achilles tendons can help understanding how healthy tendons are affected by repetitive loading and how the different tissue constituents contribute to the tendon’s biomechanical response. However, available models of Achilles tendon are limited in their description of the hierarchical multi-structural composition of the tissue. This study hypothesised that a poroviscoelastic fibre-reinforced model, previously successful in capturing cartilage biomechanical behaviour, can depict the biomechanical behaviour of the rat Achilles tendon found experimentally. Materials and Methods We developed a new material model of the Achilles tendon, which considers the tendon’s main constituents namely: water, proteoglycan matrix and collagen fibres. A hyperelastic formulation of the proteoglycan matrix enabled computations of large deformations of the tendon, and collagen fibres were modelled as viscoelastic. Specimen-specific finite element models were created of 9 rat Achilles tendons from an animal experiment and simulations were carried out following a repetitive tensile loading protocol. The material model parameters were calibrated against data from the rats by minimising the root mean squared error (RMS) between experimental force data and model output. Results and Conclusions All specimen models were successfully fitted to experimental data with high accuracy (RMS 0.42-1.02). Additional simulations predicted more compliant and soft tendon behaviour at reduced strain-rates compared to higher strain-rates that produce a stiff and brittle tendon response. Stress-relaxation simulations exhibited strain-dependent stress-relaxation behaviour where larger strains produced slower relaxation rates compared to smaller strain levels. Our simulations showed that the collagen fibres in the Achilles tendon are the main load-bearing component during tensile loading, where the orientation of the collagen fibres plays an important role for the tendon

  13. Enhancing the Fever Workup Utilizing a Multi-Technique Modeling Approach to Diagnose Infections More Accurately

    PubMed Central

    Fadlalla, Adam M.A.; Golob, Joseph F.

    2012-01-01

    Abstract Background Differentiation between infectious and non-infectious etiologies of the systemic inflammatory response syndrome (SIRS) in trauma patients remains elusive. We hypothesized that mathematical modeling in combination with computerized clinical decision support would assist with this differentiation. The purpose of this study was to determine the capability of various mathematical modeling techniques to predict infectious complications in critically ill trauma patients and compare the performance of these models with a standard fever workup practice (identifying infections on the basis of fever or leukocytosis). Methods An 18-mo retrospective database was created using information collected daily from critically ill trauma patients admitted to an academic surgical and trauma intensive care unit. Two hundred forty-three non-infected patient-days were chosen randomly to combine with the 243 infected-days, which created a modeling sample of 486 patient-days. Utilizing ten variables known to be associated with infectious complications, decision trees, neural networks, and logistic regression analysis models were created to predict the presence of urinary tract infections (UTIs), bacteremia, and respiratory tract infections (RTIs). The data sample was split into a 70% training set and a 30% testing set. Models were compared by calculating sensitivity, specificity, positive predictive value, negative predictive value, overall accuracy, and discrimination. Results Decision trees had the best modeling performance, with a sensitivity of 83%, an accuracy of 82%, and a discrimination of 0.91 for identifying infections. Both neural networks and decision trees outperformed logistic regression analysis. A second analysis was performed utilizing the same 243 infected days and only those non-infected patient-days associated with negative microbiologic cultures (n = 236). Decision trees again had the best modeling performance for infection identification, with a

  14. Computational methods toward accurate RNA structure prediction using coarse-grained and all-atom models.

    PubMed

    Krokhotin, Andrey; Dokholyan, Nikolay V

    2015-01-01

    Computational methods can provide significant insights into RNA structure and dynamics, bridging the gap in our understanding of the relationship between structure and biological function. Simulations enrich and enhance our understanding of data derived on the bench, as well as provide feasible alternatives to costly or technically challenging experiments. Coarse-grained computational models of RNA are especially important in this regard, as they allow analysis of events occurring in timescales relevant to RNA biological function, which are inaccessible through experimental methods alone. We have developed a three-bead coarse-grained model of RNA for discrete molecular dynamics simulations. This model is efficient in de novo prediction of short RNA tertiary structure, starting from RNA primary sequences of less than 50 nucleotides. To complement this model, we have incorporated additional base-pairing constraints and have developed a bias potential reliant on data obtained from hydroxyl probing experiments that guide RNA folding to its correct state. By introducing experimentally derived constraints to our computer simulations, we are able to make reliable predictions of RNA tertiary structures up to a few hundred nucleotides. Our refined model exemplifies a valuable benefit achieved through integration of computation and experimental methods.

  15. A cortico-subcortical model for generation of spatially accurate sequential saccades.

    PubMed

    Dominey, P F; Arbib, M A

    1992-01-01

    This article provides a systems framework for the analysis of cortical and subcortical interactions in the control of saccadic eye movements, A major thesis of this model is that a topography of saccade direction and amplitude is preserved through multiple projections between brain regions until they are finally transformed into a temporal pattern of activity that drives the eyes to the target. The control of voluntary saccades to visual and remembered targets is modeled in terms of interactions between posterior parietal cortex, frontal eye fields, the basal ganglia (caudate and substantia nigra), superior colliculus, mediodorsal thalamus, and the saccade generator of the brainstem. Interactions include the modulation of eye movement motor error maps by topographic inhibitory projections, dynamic remapping of spatial target representations in saccade motor error maps, and sustained neural activity that embodies spatial memory. Models of these mechanisms implemented in our Neural Simulation Language simulate behavior and neural activity described in the literature, and suggest new experiments.

  16. An accurate, fast and stable material model for shape memory alloys

    NASA Astrophysics Data System (ADS)

    Junker, Philipp

    2014-10-01

    Shape memory alloys possess several features that make them interesting for industrial applications. However, due to their complex and thermo-mechanically coupled behavior, direct use of shape memory alloys in engineering construction is problematic. There is thus a demand for tools to achieve realistic, predictive simulations that are numerically robust when computing complex, coupled load states, are fast enough to calculate geometries of industrial interest, and yield realistic and reliable results without the use of fitting curves. In this paper a new and numerically fast material model for shape memory alloys is presented. It is based solely on energetic quantities, which thus creates a quite universal approach. In the beginning, a short derivation is given before it is demonstrated how this model can be easily calibrated by means of tension tests. Then, several examples of engineering applications under mechanical and thermal loads are presented to demonstrate the numerical stability and high computation speed of the model.

  17. Making Transporter Models for Drug-Drug Interaction Prediction Mobile.

    PubMed

    Ekins, Sean; Clark, Alex M; Wright, Stephen H

    2015-10-01

    The past decade has seen increased numbers of studies publishing ligand-based computational models for drug transporters. Although they generally use small experimental data sets, these models can provide insights into structure-activity relationships for the transporter. In addition, such models have helped to identify new compounds as substrates or inhibitors of transporters of interest. We recently proposed that many transporters are promiscuous and may require profiling of new chemical entities against multiple substrates for a specific transporter. Furthermore, it should be noted that virtually all of the published ligand-based transporter models are only accessible to those involved in creating them and, consequently, are rarely shared effectively. One way to surmount this is to make models shareable or more accessible. The development of mobile apps that can access such models is highlighted here. These apps can be used to predict ligand interactions with transporters using Bayesian algorithms. We used recently published transporter data sets (MATE1, MATE2K, OCT2, OCTN2, ASBT, and NTCP) to build preliminary models in a commercial tool and in open software that can deliver the model in a mobile app. In addition, several transporter data sets extracted from the ChEMBL database were used to illustrate how such public data and models can be shared. Predicting drug-drug interactions for various transporters using computational models is potentially within reach of anyone with an iPhone or iPad. Such tools could help prioritize which substrates should be used for in vivo drug-drug interaction testing and enable open sharing of models.

  18. One-Dimensional Transport with Equilibrium Chemistry (OTEQ) - A Reactive Transport Model for Streams and Rivers

    USGS Publications Warehouse

    Runkel, Robert L.

    2010-01-01

    OTEQ is a mathematical simulation model used to characterize the fate and transport of waterborne solutes in streams and rivers. The model is formed by coupling a solute transport model with a chemical equilibrium submodel. The solute transport model is based on OTIS, a model that considers the physical processes of advection, dispersion, lateral inflow, and transient storage. The equilibrium submodel is based on MINTEQ, a model that considers the speciation and complexation of aqueous species, acid-base reactions, precipitation/dissolution, and sorption. Within OTEQ, reactions in the water column may result in the formation of solid phases (precipitates and sorbed species) that are subject to downstream transport and settling processes. Solid phases on the streambed may also interact with the water column through dissolution and sorption/desorption reactions. Consideration of both mobile (waterborne) and immobile (streambed) solid phases requires a unique set of governing differential equations and solution techniques that are developed herein. The partial differential equations describing physical transport and the algebraic equations describing chemical equilibria are coupled using the sequential iteration approach. The model's ability to simulate pH, precipitation/dissolution, and pH-dependent sorption provides a means of evaluating the complex interactions between instream chemistry and hydrologic transport at the field scale. This report details the development and application of OTEQ. Sections of the report describe model theory, input/output specifications, model applications, and installation instructions. OTEQ may be obtained over the Internet at http://water.usgs.gov/software/OTEQ.

  19. Improved image quality in pinhole SPECT by accurate modeling of the point spread function in low magnification systems

    SciTech Connect

    Pino, Francisco; Roé, Nuria; Aguiar, Pablo; Falcon, Carles; Ros, Domènec; Pavía, Javier

    2015-02-15

    Purpose: Single photon emission computed tomography (SPECT) has become an important noninvasive imaging technique in small-animal research. Due to the high resolution required in small-animal SPECT systems, the spatially variant system response needs to be included in the reconstruction algorithm. Accurate modeling of the system response should result in a major improvement in the quality of reconstructed images. The aim of this study was to quantitatively assess the impact that an accurate modeling of spatially variant collimator/detector response has on image-quality parameters, using a low magnification SPECT system equipped with a pinhole collimator and a small gamma camera. Methods: Three methods were used to model the point spread function (PSF). For the first, only the geometrical pinhole aperture was included in the PSF. For the second, the septal penetration through the pinhole collimator was added. In the third method, the measured intrinsic detector response was incorporated. Tomographic spatial resolution was evaluated and contrast, recovery coefficients, contrast-to-noise ratio, and noise were quantified using a custom-built NEMA NU 4–2008 image-quality phantom. Results: A high correlation was found between the experimental data corresponding to intrinsic detector response and the fitted values obtained by means of an asymmetric Gaussian distribution. For all PSF models, resolution improved as the distance from the point source to the center of the field of view increased and when the acquisition radius diminished. An improvement of resolution was observed after a minimum of five iterations when the PSF modeling included more corrections. Contrast, recovery coefficients, and contrast-to-noise ratio were better for the same level of noise in the image when more accurate models were included. Ring-type artifacts were observed when the number of iterations exceeded 12. Conclusions: Accurate modeling of the PSF improves resolution, contrast, and recovery

  20. Numerical Computation of a Continuous-thrust State Transition Matrix Incorporating Accurate Hardware and Ephemeris Models

    NASA Technical Reports Server (NTRS)

    Ellison, Donald; Conway, Bruce; Englander, Jacob

    2015-01-01

    A significant body of work exists showing that providing a nonlinear programming (NLP) solver with expressions for the problem constraint gradient substantially increases the speed of program execution and can also improve the robustness of convergence, especially for local optimizers. Calculation of these derivatives is often accomplished through the computation of spacecraft's state transition matrix (STM). If the two-body gravitational model is employed as is often done in the context of preliminary design, closed form expressions for these derivatives may be provided. If a high fidelity dynamics model, that might include perturbing forces such as the gravitational effect from multiple third bodies and solar radiation pressure is used then these STM's must be computed numerically. We present a method for the power hardward model and a full ephemeris model. An adaptive-step embedded eight order Dormand-Prince numerical integrator is discussed and a method for the computation of the time of flight derivatives in this framework is presented. The use of these numerically calculated derivatieves offer a substantial improvement over finite differencing in the context of a global optimizer. Specifically the inclusion of these STM's into the low thrust missiondesign tool chain in use at NASA Goddard Spaceflight Center allows for an increased preliminary mission design cadence.

  1. Advancements and challenges in generating accurate animal models of gestational diabetes mellitus.

    PubMed

    Pasek, Raymond C; Gannon, Maureen

    2013-12-01

    The maintenance of glucose homeostasis during pregnancy is critical to the health and well-being of both the mother and the developing fetus. Strikingly, approximately 7% of human pregnancies are characterized by insufficient insulin production or signaling, resulting in gestational diabetes mellitus (GDM). In addition to the acute health concerns of hyperglycemia, women diagnosed with GDM during pregnancy have an increased incidence of complications during pregnancy as well as an increased risk of developing type 2 diabetes (T2D) later in life. Furthermore, children born to mothers diagnosed with GDM have increased incidence of perinatal complications, including hypoglycemia, respiratory distress syndrome, and macrosomia, as well as an increased risk of being obese or developing T2D as adults. No single environmental or genetic factor is solely responsible for the disease; instead, a variety of risk factors, including weight, ethnicity, genetics, and family history, contribute to the likelihood of developing GDM, making the generation of animal models that fully recapitulate the disease difficult. Here, we discuss and critique the various animal models that have been generated to better understand the etiology of diabetes during pregnancy and its physiological impacts on both the mother and the fetus. Strategies utilized are diverse in nature and include the use of surgical manipulation, pharmacological treatment, nutritional manipulation, and genetic approaches in a variety of animal models. Continued development of animal models of GDM is essential for understanding the consequences of this disease as well as providing insights into potential treatments and preventative measures.

  2. Accurate prediction of the refractive index of polymers using first principles and data modeling

    NASA Astrophysics Data System (ADS)

    Afzal, Mohammad Atif Faiz; Cheng, Chong; Hachmann, Johannes

    Organic polymers with a high refractive index (RI) have recently attracted considerable interest due to their potential application in optical and optoelectronic devices. The ability to tailor the molecular structure of polymers is the key to increasing the accessible RI values. Our work concerns the creation of predictive in silico models for the optical properties of organic polymers, the screening of large-scale candidate libraries, and the mining of the resulting data to extract the underlying design principles that govern their performance. This work was set up to guide our experimentalist partners and allow them to target the most promising candidates. Our model is based on the Lorentz-Lorenz equation and thus includes the polarizability and number density values for each candidate. For the former, we performed a detailed benchmark study of different density functionals, basis sets, and the extrapolation scheme towards the polymer limit. For the number density we devised an exceedingly efficient machine learning approach to correlate the polymer structure and the packing fraction in the bulk material. We validated the proposed RI model against the experimentally known RI values of 112 polymers. We could show that the proposed combination of physical and data modeling is both successful and highly economical to characterize a wide range of organic polymers, which is a prerequisite for virtual high-throughput screening.

  3. Towards Relaxing the Spherical Solar Radiation Pressure Model for Accurate Orbit Predictions

    NASA Astrophysics Data System (ADS)

    Lachut, M.; Bennett, J.

    2016-09-01

    The well-known cannonball model has been used ubiquitously to capture the effects of atmospheric drag and solar radiation pressure on satellites and/or space debris for decades. While it lends itself naturally to spherical objects, its validity in the case of non-spherical objects has been debated heavily for years throughout the space situational awareness community. One of the leading motivations to improve orbit predictions by relaxing the spherical assumption, is the ongoing demand for more robust and reliable conjunction assessments. In this study, we explore the orbit propagation of a flat plate in a near-GEO orbit under the influence of solar radiation pressure, using a Lambertian BRDF model. Consequently, this approach will account for the spin rate and orientation of the object, which is typically determined in practice using a light curve analysis. Here, simulations will be performed which systematically reduces the spin rate to demonstrate the point at which the spherical model no longer describes the orbital elements of the spinning plate. Further understanding of this threshold would provide insight into when a higher fidelity model should be used, thus resulting in improved orbit propagations. Therefore, the work presented here is of particular interest to organizations and researchers that maintain their own catalog, and/or perform conjunction analyses.

  4. The Effects of Video Modeling with Voiceover Instruction on Accurate Implementation of Discrete-Trial Instruction

    ERIC Educational Resources Information Center

    Vladescu, Jason C.; Carroll, Regina; Paden, Amber; Kodak, Tiffany M.

    2012-01-01

    The present study replicates and extends previous research on the use of video modeling (VM) with voiceover instruction to train staff to implement discrete-trial instruction (DTI). After staff trainees reached the mastery criterion when teaching an adult confederate with VM, they taught a child with a developmental disability using DTI. The…

  5. A Cartesian quasi-classical model to nonequilibrium quantum transport: the Anderson impurity model.

    PubMed

    Li, Bin; Levy, Tal J; Swenson, David W H; Rabani, Eran; Miller, William H

    2013-03-14

    We apply the recently proposed quasi-classical approach for a second quantized many-electron Hamiltonian in Cartesian coordinates [B. Li and W. H. Miller, J. Chem. Phys. 137, 154107 (2012)] to correlated nonequilibrium quantum transport. The approach provides accurate results for the resonant level model for a wide range of temperatures, bias, and gate voltages, correcting the flaws of our recently proposed mapping using action-angle variables. When electron-electron interactions are included, a Gaussian function scheme is required to map the two-electron integrals, leading to quantitative results for the Anderson impurity model. In particular, we show that the current mapping is capable of capturing quantitatively the Coulomb blockade effect and the temperature dependence of the current below and above the blockade.

  6. Accurate 2D/3D electromagnetic modeling for time-domain airborne EM systems

    NASA Astrophysics Data System (ADS)

    Yin, C.; Hodges, G.

    2012-12-01

    The existing industry software cannot deliver correct results for 3D time-domain airborne EM responses. In this paper, starting from the Fourier transform and convolution, we compare the stability of different modeling techniques and analyze the reason for instable calculations of the time-domain airborne EM responses. We find that the singularity of the impulse responses of EM systems at very early time that are used in the convolution is responsible for the instability of the modeling (Fig.1). Based on this finding, we put forward an algorithm that uses step response rather than impulse response of the airborne EM system for the convolution and create a stable algorithm that delivers precise results and maintains well the integral/derivative relationship between the magnetic field B and the magnetic induction dB/dt. A three-step transformation procedure for the modeling is proposed: 1) output the frequency-domain EM response data from the existing software; 2) transform into step-response by digital Fourier/Hankel transform; 3) convolve the step response with the transmitting current or its derivatives. The method has proved to be working very well (Fig. 2). The algorithm can be extended to the modeling of other time-domain ground and airborne EM system responses.Fig. 1: Comparison of impulse and step responses for an airborne EM system Fig. 2: Bz and dBz/dt calculated from step (middle panel) and impulse responses (lower panel) for the same 3D model as in Fig.1.

  7. Statistically accurate low-order models for uncertainty quantification in turbulent dynamical systems.

    PubMed

    Sapsis, Themistoklis P; Majda, Andrew J

    2013-08-20

    A framework for low-order predictive statistical modeling and uncertainty quantification in turbulent dynamical systems is developed here. These reduced-order, modified quasilinear Gaussian (ROMQG) algorithms apply to turbulent dynamical systems in which there is significant linear instability or linear nonnormal dynamics in the unperturbed system and energy-conserving nonlinear interactions that transfer energy from the unstable modes to the stable modes where dissipation occurs, resulting in a statistical steady state; such turbulent dynamical systems are ubiquitous in geophysical and engineering turbulence. The ROMQG method involves constructing a low-order, nonlinear, dynamical system for the mean and covariance statistics in the reduced subspace that has the unperturbed statistics as a stable fixed point and optimally incorporates the indirect effect of non-Gaussian third-order statistics for the unperturbed system in a systematic calibration stage. This calibration procedure is achieved through information involving only the mean and covariance statistics for the unperturbed equilibrium. The performance of the ROMQG algorithm is assessed on two stringent test cases: the 40-mode Lorenz 96 model mimicking midlatitude atmospheric turbulence and two-layer baroclinic models for high-latitude ocean turbulence with over 125,000 degrees of freedom. In the Lorenz 96 model, the ROMQG algorithm with just a single mode captures the transient response to random or deterministic forcing. For the baroclinic ocean turbulence models, the inexpensive ROMQG algorithm with 252 modes, less than 0.2% of the total, captures the nonlinear response of the energy, the heat flux, and even the one-dimensional energy and heat flux spectra.

  8. The development and verification of a highly accurate collision prediction model for automated noncoplanar plan delivery

    SciTech Connect

    Yu, Victoria Y.; Tran, Angelia; Nguyen, Dan; Cao, Minsong; Ruan, Dan; Low, Daniel A.; Sheng, Ke

    2015-11-15

    Purpose: Significant dosimetric benefits had been previously demonstrated in highly noncoplanar treatment plans. In this study, the authors developed and verified an individualized collision model for the purpose of delivering highly noncoplanar radiotherapy and tested the feasibility of total delivery automation with Varian TrueBeam developer mode. Methods: A hand-held 3D scanner was used to capture the surfaces of an anthropomorphic phantom and a human subject, which were positioned with a computer-aided design model of a TrueBeam machine to create a detailed virtual geometrical collision model. The collision model included gantry, collimator, and couch motion degrees of freedom. The accuracy of the 3D scanner was validated by scanning a rigid cubical phantom with known dimensions. The collision model was then validated by generating 300 linear accelerator orientations corresponding to 300 gantry-to-couch and gantry-to-phantom distances, and comparing the corresponding distance measurements to their corresponding models. The linear accelerator orientations reflected uniformly sampled noncoplanar beam angles to the head, lung, and prostate. The distance discrepancies between measurements on the physical and virtual systems were used to estimate treatment-site-specific safety buffer distances with 0.1%, 0.01%, and 0.001% probability of collision between the gantry and couch or phantom. Plans containing 20 noncoplanar beams to the brain, lung, and prostate optimized via an in-house noncoplanar radiotherapy platform were converted into XML script for automated delivery and the entire delivery was recorded and timed to demonstrate the feasibility of automated delivery. Results: The 3D scanner measured the dimension of the 14 cm cubic phantom within 0.5 mm. The maximal absolute discrepancy between machine and model measurements for gantry-to-couch and gantry-to-phantom was 0.95 and 2.97 cm, respectively. The reduced accuracy of gantry-to-phantom measurements was

  9. The development and verification of a highly accurate collision prediction model for automated noncoplanar plan delivery

    PubMed Central

    Yu, Victoria Y.; Tran, Angelia; Nguyen, Dan; Cao, Minsong; Ruan, Dan; Low, Daniel A.; Sheng, Ke

    2015-01-01

    Purpose: Significant dosimetric benefits had been previously demonstrated in highly noncoplanar treatment plans. In this study, the authors developed and verified an individualized collision model for the purpose of delivering highly noncoplanar radiotherapy and tested the feasibility of total delivery automation with Varian TrueBeam developer mode. Methods: A hand-held 3D scanner was used to capture the surfaces of an anthropomorphic phantom and a human subject, which were positioned with a computer-aided design model of a TrueBeam machine to create a detailed virtual geometrical collision model. The collision model included gantry, collimator, and couch motion degrees of freedom. The accuracy of the 3D scanner was validated by scanning a rigid cubical phantom with known dimensions. The collision model was then validated by generating 300 linear accelerator orientations corresponding to 300 gantry-to-couch and gantry-to-phantom distances, and comparing the corresponding distance measurements to their corresponding models. The linear accelerator orientations reflected uniformly sampled noncoplanar beam angles to the head, lung, and prostate. The distance discrepancies between measurements on the physical and virtual systems were used to estimate treatment-site-specific safety buffer distances with 0.1%, 0.01%, and 0.001% probability of collision between the gantry and couch or phantom. Plans containing 20 noncoplanar beams to the brain, lung, and prostate optimized via an in-house noncoplanar radiotherapy platform were converted into XML script for automated delivery and the entire delivery was recorded and timed to demonstrate the feasibility of automated delivery. Results: The 3D scanner measured the dimension of the 14 cm cubic phantom within 0.5 mm. The maximal absolute discrepancy between machine and model measurements for gantry-to-couch and gantry-to-phantom was 0.95 and 2.97 cm, respectively. The reduced accuracy of gantry-to-phantom measurements was

  10. Membrane transport of several ions during peritoneal dialysis: mathematical modeling.

    PubMed

    Galach, Magda; Waniewski, Jacek

    2012-09-01

    Peritoneal dialysis utilizes a complex mass exchange device created by natural permselective membranes of the visceral and abdominal muscle tissues. In mathematical modeling of solute transport during peritoneal dialysis, each solute is typically considered as a neutral, independent particle. However, such mathematical models cannot predict transport parameters for small ions. Therefore, the impact of the electrostatic interactions between ions on the estimated transport parameters needs to be investigated. In this study, transport of sodium, chloride, and a third ion through a permselective membrane with characteristics of the peritoneal transport barrier was described using two models: a model with the Nernst-Planck (NP) equations for a set of interacting ions and a model with combined diffusive and convective transport of each ion separately (DC). Transport parameters for the NP model were calculated using the pore theory, while the parameters for the DC model were estimated by fitting the model to the predictions from the NP model. Solute concentration profiles in the membrane obtained by computer simulations based on these two models were similar, whereas the transport parameters (diffusive mass transport parameters and sieving coefficients) were generally different. The presence of the third ion could substantially modify the values of diffusive mass parameter for sodium and chloride ions estimated using the DC model compared with those predicted by NP. The extent of this modification depended on the molecular mass and concentration of the third ion, and the rate of volumetric flow. Closed formulas for the transport parameters of the DC model in terms of the NP model parameters, ion concentration profiles in the membrane, and volumetric flow across the membrane were derived. Their reliable approximations, which include only boundary ion concentrations instead of spatial intramembrane concentration profiles, were formulated. The precision of this approximation

  11. A parallel high-order accurate finite element nonlinear Stokes ice sheet model and benchmark experiments: A PARALLEL FEM STOKES ICE SHEET MODEL

    SciTech Connect

    Leng, Wei; Ju, Lili; Gunzburger, Max; Price, Stephen; Ringler, Todd

    2012-01-04

    The numerical modeling of glacier and ice sheet evolution is a subject of growing interest, in part because of the potential for models to inform estimates of global sea level change. This paper focuses on the development of a numerical model that determines the velocity and pressure fields within an ice sheet. Our numerical model features a high-fidelity mathematical model involving the nonlinear Stokes system and combinations of no-sliding and sliding basal boundary conditions, high-order accurate finite element discretizations based on variable resolution grids, and highly scalable parallel solution strategies, all of which contribute to a numerical model that can achieve accurate velocity and pressure approximations in a highly efficient manner. We demonstrate the accuracy and efficiency of our model by analytical solution tests, established ice sheet benchmark experiments, and comparisons with other well-established ice sheet models.

  12. Accurate dynamic power estimation for CMOS combinational logic circuits with real gate delay model.

    PubMed

    Fadl, Omnia S; Abu-Elyazeed, Mohamed F; Abdelhalim, Mohamed B; Amer, Hassanein H; Madian, Ahmed H

    2016-01-01

    Dynamic power estimation is essential in designing VLSI circuits where many parameters are involved but the only circuit parameter that is related to the circuit operation is the nodes' toggle rate. This paper discusses a deterministic and fast method to estimate the dynamic power consumption for CMOS combinational logic circuits using gate-level descriptions based on the Logic Pictures concept to obtain the circuit nodes' toggle rate. The delay model for the logic gates is the real-delay model. To validate the results, the method is applied to several circuits and compared against exhaustive, as well as Monte Carlo, simulations. The proposed technique was shown to save up to 96% processing time compared to exhaustive simulation.

  13. An accurate two-phase approximate solution to the acute viral infection model

    SciTech Connect

    Perelson, Alan S

    2009-01-01

    During an acute viral infection, virus levels rise, reach a peak and then decline. Data and numerical solutions suggest the growth and decay phases are linear on a log scale. While viral dynamic models are typically nonlinear with analytical solutions difficult to obtain, the exponential nature of the solutions suggests approximations can be found. We derive a two-phase approximate solution to the target cell limited influenza model and illustrate the accuracy using data and previously established parameter values of six patients infected with influenza A. For one patient, the subsequent fall in virus concentration was not consistent with our predictions during the decay phase and an alternate approximation is derived. We find expressions for the rate and length of initial viral growth in terms of the parameters, the extent each parameter is involved in viral peaks, and the single parameter responsible for virus decay. We discuss applications of this analysis in antiviral treatments and investigating host and virus heterogeneities.

  14. Modeling of Weakly Collisional Parallel Electron Transport for Edge Plasma Simulations

    NASA Astrophysics Data System (ADS)

    Umansky, M. V.; Dimits, A. M.; Joseph, I.; Omotani, J. T.; Rognlien, T. D.

    2014-10-01

    The parallel electron heat transport in a weakly collisional regime can be represented in the framework of the Landau-fluid (LF) model. Practical implementation of LF-based transport models has become possible due to the recent invention of an efficient non- spectral method for the non-local closure operators. Here the implementation of a LF based model for the parallel plasma transport is described, and the model is tested for different collisionality regimes against a Fokker-Plank code. The new method appears to represent weakly collisional parallel electron transport more accurately than the conventional flux-limiter based models; on the other hand it is computationally efficient enough to be used in tokamak edge plasma simulations. Implementation of an LF-based model for the parallel plasma transport in the UEDGE code is described, and applications to realistic divertor simulations are discussed. Work performed for U.S. DoE by LLNL under Contract DE-AC52-07NA27344.

  15. Robust and Accurate Modeling Approaches for Migraine Per-Patient Prediction from Ambulatory Data.

    PubMed

    Pagán, Josué; De Orbe, M Irene; Gago, Ana; Sobrado, Mónica; Risco-Martín, José L; Mora, J Vivancos; Moya, José M; Ayala, José L

    2015-06-30

    Migraine is one of the most wide-spread neurological disorders, and its medical treatment represents a high percentage of the costs of health systems. In some patients, characteristic symptoms that precede the headache appear. However, they are nonspecific, and their prediction horizon is unknown and pretty variable; hence, these symptoms are almost useless for prediction, and they are not useful to advance the intake of drugs to be effective and neutralize the pain. To solve this problem, this paper sets up a realistic monitoring scenario where hemodynamic variables from real patients are monitored in ambulatory conditions with a wireless body sensor network (WBSN). The acquired data are used to evaluate the predictive capabilities and robustness against noise and failures in sensors of several modeling approaches. The obtained results encourage the development of per-patient models based on state-space models (N4SID) that are capable of providing average forecast windows of 47 min and a low rate of false positives.

  16. Towards a More Accurate Solar Power Forecast By Improving NWP Model Physics

    NASA Astrophysics Data System (ADS)

    Köhler, C.; Lee, D.; Steiner, A.; Ritter, B.

    2014-12-01

    The growing importance and successive expansion of renewable energies raise new challenges for decision makers, transmission system operators, scientists and many more. In this interdisciplinary field, the role of Numerical Weather Prediction (NWP) is to reduce the uncertainties associated with the large share of weather-dependent power sources. Precise power forecast, well-timed energy trading on the stock market, and electrical grid stability can be maintained. The research project EWeLiNE is a collaboration of the German Weather Service (DWD), the Fraunhofer Institute (IWES) and three German transmission system operators (TSOs). Together, wind and photovoltaic (PV) power forecasts shall be improved by combining optimized NWP and enhanced power forecast models. The conducted work focuses on the identification of critical weather situations and the associated errors in the German regional NWP model COSMO-DE. Not only the representation of the model cloud characteristics, but also special events like Sahara dust over Germany and the solar eclipse in 2015 are treated and their effect on solar power accounted for. An overview of the EWeLiNE project and results of the ongoing research will be presented.

  17. Robust and Accurate Modeling Approaches for Migraine Per-Patient Prediction from Ambulatory Data

    PubMed Central

    Pagán, Josué; Irene De Orbe, M.; Gago, Ana; Sobrado, Mónica; Risco-Martín, José L.; Vivancos Mora, J.; Moya, José M.; Ayala, José L.

    2015-01-01

    Migraine is one of the most wide-spread neurological disorders, and its medical treatment represents a high percentage of the costs of health systems. In some patients, characteristic symptoms that precede the headache appear. However, they are nonspecific, and their prediction horizon is unknown and pretty variable; hence, these symptoms are almost useless for prediction, and they are not useful to advance the intake of drugs to be effective and neutralize the pain. To solve this problem, this paper sets up a realistic monitoring scenario where hemodynamic variables from real patients are monitored in ambulatory conditions with a wireless body sensor network (WBSN). The acquired data are used to evaluate the predictive capabilities and robustness against noise and failures in sensors of several modeling approaches. The obtained results encourage the development of per-patient models based on state-space models (N4SID) that are capable of providing average forecast windows of 47 min and a low rate of false positives. PMID:26134103

  18. Morphometric analysis of Russian Plain's small lakes on the base of accurate digital bathymetric models

    NASA Astrophysics Data System (ADS)

    Naumenko, Mikhail; Guzivaty, Vadim; Sapelko, Tatiana

    2016-04-01

    Lake morphometry refers to physical factors (shape, size, structure, etc) that determine the lake depression. Morphology has a great influence on lake ecological characteristics especially on water thermal conditions and mixing depth. Depth analyses, including sediment measurement at various depths, volumes of strata and shoreline characteristics are often critical to the investigation of biological, chemical and physical properties of fresh waters as well as theoretical retention time. Management techniques such as loading capacity for effluents and selective removal of undesirable components of the biota are also dependent on detailed knowledge of the morphometry and flow characteristics. During the recent years a lake bathymetric surveys were carried out by using echo sounder with a high bottom depth resolution and GPS coordinate determination. Few digital bathymetric models have been created with 10*10 m spatial grid for some small lakes of Russian Plain which the areas not exceed 1-2 sq. km. The statistical characteristics of the depth and slopes distribution of these lakes calculated on an equidistant grid. It will provide the level-surface-volume variations of small lakes and reservoirs, calculated through combination of various satellite images. We discuss the methodological aspects of creating of morphometric models of depths and slopes of small lakes as well as the advantages of digital models over traditional methods.

  19. Review of petroleum transport network models and their applicability to a national refinery model

    SciTech Connect

    Hooker, J. N.

    1982-04-01

    This report examines four petroleum transport network models to determine whether parts of them can be incorporated into the transportation component of a national refinery model. Two questions in particular are addressed. (a) How do the models under examination represent the oil transport network, estimate link capacities, and calculate transport costs. (b) Are any of these network representations, capacity estimates, or cost functions suitable for inclusion in a linear programming model of oil refinery and primary distribution in the US. Only pipeline and waterway transport is discussed. The models examined are the Department of Energy's OILNET model, the Department of Transportation's Freight Energy Model, the Federal Energy Administration Petroleum Transportation Network Model, and an Oak Ridge National Laboratory oil pipeline energy model. Link capacity and cost functions are recommended for each transport mode. The coefficients of the recommended pipeline cost functions remain to be estimated.

  20. Using OTIS to model solute transport in streams and rivers

    USGS Publications Warehouse

    Runkel, Robert L.

    2000-01-01

    Solute transport in streams and rivers is governed by a suite of hydrologic and geochemical processes. Knowledge of these processes is needed when assessing the fate of contaminants that are released into surface waters. The study of solute fate and transport often is aided by solute transport models that mathematically describe the underlying processes. This fact sheet describes a model that considers One-Dimensional Transport with Inflow and Storage (OTIS). As shown by several example applications, OTIS may be used in conjunction with field-scale data to quantify hydrologic processes (advection, dispersion, and transient storage) and certain chemical reactions (sorption and first-order decay).

  1. Accurate 3d Textured Models of Vessels for the Improvement of the Educational Tools of a Museum

    NASA Astrophysics Data System (ADS)

    Soile, S.; Adam, K.; Ioannidis, C.; Georgopoulos, A.

    2013-02-01

    Besides the demonstration of the findings, modern museums organize educational programs which aim to experience and knowledge sharing combined with entertainment rather than to pure learning. Toward that effort, 2D and 3D digital representations are gradually replacing the traditional recording of the findings through photos or drawings. The present paper refers to a project that aims to create 3D textured models of two lekythoi that are exhibited in the National Archaeological Museum of Athens in Greece; on the surfaces of these lekythoi scenes of the adventures of Odysseus are depicted. The project is expected to support the production of an educational movie and some other relevant interactive educational programs for the museum. The creation of accurate developments of the paintings and of accurate 3D models is the basis for the visualization of the adventures of the mythical hero. The data collection was made by using a structured light scanner consisting of two machine vision cameras that are used for the determination of geometry of the object, a high resolution camera for the recording of the texture, and a DLP projector. The creation of the final accurate 3D textured model is a complicated and tiring procedure which includes the collection of geometric data, the creation of the surface, the noise filtering, the merging of individual surfaces, the creation of a c-mesh, the creation of the UV map, the provision of the texture and, finally, the general processing of the 3D textured object. For a better result a combination of commercial and in-house software made for the automation of various steps of the procedure was used. The results derived from the above procedure were especially satisfactory in terms of accuracy and quality of the model. However, the procedure was proved to be time consuming while the use of various software packages presumes the services of a specialist.

  2. Accurate, full chip 3D electromagnetic field model for non-Manhattan mask corners

    NASA Astrophysics Data System (ADS)

    Lam, Michael; Clifford, Chris; Oliver, Michael; Fryer, David; Tejnil, Edita; Adam, Kostas

    2015-03-01

    The physical process of mask manufacturing produces absorber geometry with significantly less than 90 degree fidelity at corners. The non-Manhattan mask geometry is an essential contributor to the aerial image and resulting patterning performance through focus. Current state of the art models for corner rounding employ "chopping" a 90 degree mask corner, replacing the corner with a small 45 degree edge. In this paper, a methodology is presented to approximate the impact of 3D EMF effects introduced by corners with rounded edges. The approach is integrated into a full chip 3D mask simulation methodology based on the Domain Decomposition Method (DDM) with edge to edge crosstalk correction.

  3. Can an Atmospherically Forced Ocean Model Accurately Simulate Sea Surface Temperature During ENSO Events?

    DTIC Science & Technology

    2010-01-01

    Mateger, Herley E. Hurlburt, Alan J. Walloraft H a inleficed to offer this paper to the (Nanm of Confe ounce) (Dafe. P/ace and Classification of...temperature during ENSO events? By A. BIROL KARA.HARLEY E. HURLBURT*. CHARLIE N. BARRON. ALAN J. WALLCRAFT andE. JOSEPH METZGER, Naval Research...Quantifying SST errors from an OGCM in relation to atmospheric forcing variables. Ocean Modell. 29, 43-57. Urge. W. G., McWilliams , J. C. and Doney. S. C

  4. Modeling atmospheric deposition using a stochastic transport model

    SciTech Connect

    Buckley, R.L.

    1999-12-17

    An advanced stochastic transport model has been modified to include the removal mechanisms of dry and wet deposition. Time-dependent wind and turbulence fields are generated with a prognostic mesoscale numerical model and are used to advect and disperse individually released particles that are each assigned a mass. These particles are subjected to mass reduction in two ways depending on their physical location. Particles near the surface experience a decrease in mass using the concept of a dry deposition velocity, while the mass of particles located within areas of precipitation are depleted using a scavenging coefficient. Two levels of complexity are incorporated into the particle model. The simple case assumes constant values of dry deposition velocity and scavenging coefficient, while the more complex case varies the values according to meteorology, surface conditions, release material, and precipitation intensity. Instantaneous and cumulative dry and wet deposition are determined from the mass loss due to these physical mechanisms. A useful means of validating the model results is with data available from a recent accidental release of Cesium-137 from a steel-processing furnace in Algeciras, Spain in May, 1998. This paper describes the deposition modeling technique, as well as a comparison of simulated concentration and deposition with measurements taken for the Algeciras release.

  5. Considering mask pellicle effect for more accurate OPC model at 45nm technology node

    NASA Astrophysics Data System (ADS)

    Wang, Ching-Heng; Liu, Qingwei; Zhang, Liguo

    2008-11-01

    Now it comes to the 45nm technology node, which should be the first generation of the immersion micro-lithography. And the brand-new lithography tool makes many optical effects, which can be ignored at 90nm and 65nm nodes, now have significant impact on the pattern transmission process from design to silicon. Among all the effects, one that needs to be pay attention to is the mask pellicle effect's impact on the critical dimension variation. With the implement of hyper-NA lithography tools, light transmits the mask pellicle vertically is not a good approximation now, and the image blurring induced by the mask pellicle should be taken into account in the computational microlithography. In this works, we investigate how the mask pellicle impacts the accuracy of the OPC model. And we will show that considering the extremely tight critical dimension control spec for 45nm generation node, to take the mask pellicle effect into the OPC model now becomes necessary.

  6. Accurate early-time and late-time modeling of countercurrent spontaneous imbibition

    NASA Astrophysics Data System (ADS)

    March, Rafael; Doster, Florian; Geiger, Sebastian

    2016-08-01

    Spontaneous countercurrent imbibition into a finite porous medium is an important physical mechanism for many applications, included but not limited to irrigation, CO2 storage, and oil recovery. Symmetry considerations that are often valid in fractured porous media allow us to study the process in a one-dimensional domain. In 1-D, for incompressible fluids and homogeneous rocks, the onset of imbibition can be captured by self-similar solutions and the imbibed volume scales with √t. At later times, the imbibition rate decreases and the finite size of the medium has to be taken into account. This requires numerical solutions. Here we present a new approach to approximate the whole imbibition process semianalytically. The onset is captured by a semianalytical solution. We also provide an a priori estimate of the time until which the imbibed volume scales with √t. This time is significantly longer than the time it takes until the imbibition front reaches the model boundary. The remainder of the imbibition process is obtained from a self-similarity solution. We test our approach against numerical solutions that employ parametrizations relevant for oil recovery and CO2 sequestration. We show that this concept improves common first-order approaches that heavily underestimate early-time behavior and note that it can be readily included into dual-porosity models.

  7. Accurate modeling of SiPM detectors coupled to FE electronics for timing performance analysis

    NASA Astrophysics Data System (ADS)

    Ciciriello, F.; Corsi, F.; Licciulli, F.; Marzocca, C.; Matarrese, G.; Del Guerra, A.; Bisogni, M. G.

    2013-08-01

    It has already been shown how the shape of the current pulse produced by a SiPM in response to an incident photon is sensibly affected by the characteristics of the front-end electronics (FEE) used to read out the detector. When the application requires to approach the best theoretical time performance of the detection system, the influence of all the parasitics associated to the coupling SiPM-FEE can play a relevant role and must be adequately modeled. In particular, it has been reported that the shape of the current pulse is affected by the parasitic inductance of the wiring connection between SiPM and FEE. In this contribution, we extend the validity of a previously presented SiPM model to account for the wiring inductance. Various combinations of the main performance parameters of the FEE (input resistance and bandwidth) have been simulated in order to evaluate their influence on the time accuracy of the detection system, when the time pick-off of each single event is extracted by means of a leading edge discriminator (LED) technique.

  8. A new modelling concept for aeolian sediment transport on beaches

    NASA Astrophysics Data System (ADS)

    de Vries, S.; Arens, S. M.; Stive, M. J. F.; Ranasinghe, R.

    2012-04-01

    This paper presents a new modelling concept for aeolian transport on beaches. Many research is invested in describing aeolian sediment transport for desert situations. Some of the principles of aeolian sediment transport in deserts are valid for application at the coastal zone but, where in deserts abundant sand is available for transport, in coastal situations sediment availability is limited. Sediment availability (or supply) is limited due to supply limiting factors such as moisture content of the bed, fetch effects and armouring of the surface. We propose a new sediment transport concept where we quantify aeolian sediment transport while quantifying the sediment availability rather than the more conventional (Bagnold, 1954) wind driven transport capacity. The concept is illustrated using field data. The field data is collected during a measurement campaign which has been designed to measure aeolian transport with special focus on sediment availability. Wind and sediment transport rates are measured on a beach for a period of 1 week. During this week onshore wind occurred allowing the analysis of aeolian transport across the beach towards the dunes. A total of 5 sediment transport gauges are dynamically placed over the cross section of the beach from locations in the intertidal zone (at low tide) until the dunefoot. The observations show that the amount of aeolian transport is very much dependent on the tidal phase. Low tides correspond to large aeolian transport and high tides to significantly lower aeolian transport across the beach. Wind conditions during the experiment were relatively constant implying that the specific variability in time of the measured aeolian transport is caused by variability with respect to the source rather than variability in wind conditions. Additional to this specific case, existing data of similar experiments (Arens, 1996) are analysed. Re-analysing this data, from experiments covering larger timespans, more evidence is found for

  9. Reduced Fast Ion Transport Model For The Tokamak Transport Code TRANSP

    SciTech Connect

    Podesta,, Mario; Gorelenkova, Marina; White, Roscoe

    2014-02-28

    Fast ion transport models presently implemented in the tokamak transport code TRANSP [R. J. Hawryluk, in Physics of Plasmas Close to Thermonuclear Conditions, CEC Brussels, 1 , 19 (1980)] are not capturing important aspects of the physics associated with resonant transport caused by instabilities such as Toroidal Alfv en Eigenmodes (TAEs). This work describes the implementation of a fast ion transport model consistent with the basic mechanisms of resonant mode-particle interaction. The model is formulated in terms of a probability distribution function for the particle's steps in phase space, which is consistent with the MonteCarlo approach used in TRANSP. The proposed model is based on the analysis of fast ion response to TAE modes through the ORBIT code [R. B. White et al., Phys. Fluids 27 , 2455 (1984)], but it can be generalized to higher frequency modes (e.g. Compressional and Global Alfv en Eigenmodes) and to other numerical codes or theories.

  10. Modeling oil weathering and transport in sea ice.

    PubMed

    Afenyo, Mawuli; Khan, Faisal; Veitch, Brian; Yang, Ming

    2016-06-15

    This paper presents a model of oil weathering and transport in sea ice. It contains a model formulation and scenario simulation to test the proposed model. The model formulation is based on state-of-the-art models for individual weathering and transport processes. The approach incorporates the dependency of weathering and transport processes on each other, as well as their simultaneous occurrence after an oil spill in sea ice. The model is calibrated with available experimental data. The experimental data and model prediction show close agreement. A sensitivity analysis is conducted to determine the most sensitive parameters in the model. The model is useful for contingency planning of a potential oil spill in sea ice. It is suitable for coupling with a level IV fugacity model, to estimate the concentration and persistence of hydrocarbons in air, ice, water and sediments for risk assessment purposes.

  11. Combined Modeling of Acceleration, Transport, and Hydrodynamic Response in Solar Flares. 1; The Numerical Model

    NASA Technical Reports Server (NTRS)

    Liu, Wei; Petrosian, Vahe; Mariska, John T.

    2009-01-01

    Acceleration and transport of high-energy particles and fluid dynamics of atmospheric plasma are interrelated aspects of solar flares, but for convenience and simplicity they were artificially separated in the past. We present here self consistently combined Fokker-Planck modeling of particles and hydrodynamic simulation of flare plasma. Energetic electrons are modeled with the Stanford unified code of acceleration, transport, and radiation, while plasma is modeled with the Naval Research Laboratory flux tube code. We calculated the collisional heating rate directly from the particle transport code, which is more accurate than those in previous studies based on approximate analytical solutions. We repeated the simulation of Mariska et al. with an injection of power law, downward-beamed electrons using the new heating rate. For this case, a -10% difference was found from their old result. We also used a more realistic spectrum of injected electrons provided by the stochastic acceleration model, which has a smooth transition from a quasi-thermal background at low energies to a non thermal tail at high energies. The inclusion of low-energy electrons results in relatively more heating in the corona (versus chromosphere) and thus a larger downward heat conduction flux. The interplay of electron heating, conduction, and radiative loss leads to stronger chromospheric evaporation than obtained in previous studies, which had a deficit in low-energy electrons due to an arbitrarily assumed low-energy cutoff. The energy and spatial distributions of energetic electrons and bremsstrahlung photons bear signatures of the changing density distribution caused by chromospheric evaporation. In particular, the density jump at the evaporation front gives rise to enhanced emission, which, in principle, can be imaged by X-ray telescopes. This model can be applied to investigate a variety of high-energy processes in solar, space, and astrophysical plasmas.

  12. Coarse-graining intermittent intracellular transport: Two- and three-dimensional models

    NASA Astrophysics Data System (ADS)

    Lawley, Sean D.; Tuft, Marie; Brooks, Heather A.

    2015-10-01

    Viruses and other cellular cargo that lack locomotion must rely on diffusion and cellular transport systems to navigate through a biological cell. Indeed, advances in single particle tracking have revealed that viral motion alternates between (a) diffusion in the cytoplasm and (b) active transport along microtubules. This intermittency makes quantitative analysis of trajectories difficult. Therefore, the purpose of this paper is to construct mathematical methods to approximate intermittent dynamics by effective stochastic differential equations. The coarse-graining method that we develop is more accurate than existing techniques and applicable to a wide range of intermittent transport models. In particular, we apply our method to two- and three-dimensional cell geometries (disk, sphere, and cylinder) and demonstrate its accuracy. In addition to these specific applications, we also explain our method in full generality for use on future intermittent models.

  13. TRIM—3D: a three-dimensional model for accurate simulation of shallow water flow

    USGS Publications Warehouse

    Casulli, Vincenzo; Bertolazzi, Enrico; Cheng, Ralph T.

    1993-01-01

    A semi-implicit finite difference formulation for the numerical solution of three-dimensional tidal circulation is discussed. The governing equations are the three-dimensional Reynolds equations in which the pressure is assumed to be hydrostatic. A minimal degree of implicitness has been introduced in the finite difference formula so that the resulting algorithm permits the use of large time steps at a minimal computational cost. This formulation includes the simulation of flooding and drying of tidal flats, and is fully vectorizable for an efficient implementation on modern vector computers. The high computational efficiency of this method has made it possible to provide the fine details of circulation structure in complex regions that previous studies were unable to obtain. For proper interpretation of the model results suitable interactive graphics is also an essential tool.

  14. Accurate, full-chip, three-dimensional electromagnetic field model for non-Manhattan mask corners

    NASA Astrophysics Data System (ADS)

    Lam, Michael C.; Clifford, Chris; Oliver, Mike; Fryer, David; Tejnil, Edita; Adam, Kostas

    2016-04-01

    The physical process of mask manufacturing produces absorber geometry with significant deviations from the 90-deg corners, which are typically assumed in the mask design. The non-Manhattan mask geometry is an essential contributor to the aerial image and resulting patterning performance through focus. Current state-of-the-art models for corner rounding employ "chopping" a 90-deg mask corner, replacing the corner with a small 45-deg edge. A methodology is presented to approximate the impact of three-dimensional (3-D) EMF effects introduced by corners with rounded edges. The approach is integrated into a full-chip 3-D mask simulation methodology based on the domain decomposition method with edge to edge crosstalk correction.

  15. Secular Orbit Evolution in Systems with a Strong External Perturber - A Simple and Accurate Model

    NASA Astrophysics Data System (ADS)

    Andrade-Ines, Eduardo; Eggl, Siegfried

    2017-04-01

    We present a semi-analytical correction to the seminal solution for the secular motion of a planet’s orbit under gravitational influence of an external perturber derived by Heppenheimer. A comparison between analytical predictions and numerical simulations allows us to determine corrective factors for the secular frequency and forced eccentricity in the coplanar restricted three-body problem. The correction is given in the form of a polynomial function of the system’s parameters that can be applied to first-order forced eccentricity and secular frequency estimates. The resulting secular equations are simple, straight forward to use, and improve the fidelity of Heppenheimers solution well beyond higher-order models. The quality and convergence of the corrected secular equations are tested for a wide range of parameters and limits of its applicability are given.

  16. A microbial clock provides an accurate estimate of the postmortem interval in a mouse model system

    PubMed Central

    Metcalf, Jessica L; Wegener Parfrey, Laura; Gonzalez, Antonio; Lauber, Christian L; Knights, Dan; Ackermann, Gail; Humphrey, Gregory C; Gebert, Matthew J; Van Treuren, Will; Berg-Lyons, Donna; Keepers, Kyle; Guo, Yan; Bullard, James; Fierer, Noah; Carter, David O; Knight, Rob

    2013-01-01

    Establishing the time since death is critical in every death investigation, yet existing techniques are susceptible to a range of errors and biases. For example, forensic entomology is widely used to assess the postmortem interval (PMI), but errors can range from days to months. Microbes may provide a novel method for estimating PMI that avoids many of these limitations. Here we show that postmortem microbial community changes are dramatic, measurable, and repeatable in a mouse model system, allowing PMI to be estimated within approximately 3 days over 48 days. Our results provide a detailed understanding of bacterial and microbial eukaryotic ecology within a decomposing corpse system and suggest that microbial community data can be developed into a forensic tool for estimating PMI. DOI: http://dx.doi.org/10.7554/eLife.01104.001 PMID:24137541

  17. Biomechanical modeling provides more accurate data for neuronavigation than rigid registration

    PubMed Central

    Garlapati, Revanth Reddy; Roy, Aditi; Joldes, Grand Roman; Wittek, Adam; Mostayed, Ahmed; Doyle, Barry; Warfield, Simon Keith; Kikinis, Ron; Knuckey, Neville; Bunt, Stuart; Miller, Karol

    2015-01-01

    It is possible to improve neuronavigation during image-guided surgery by warping the high-quality preoperative brain images so that they correspond with the current intraoperative configuration of the brain. In this work, the accuracy of registration results obtained using comprehensive biomechanical models is compared to the accuracy of rigid registration, the technology currently available to patients. This comparison allows us to investigate whether biomechanical modeling provides good quality image data for neuronavigation for a larger proportion of patients than rigid registration. Preoperative images for 33 cases of neurosurgery were warped onto their respective intraoperative configurations using both biomechanics-based method and rigid registration. We used a Hausdorff distance-based evaluation process that measures the difference between images to quantify the performance of both methods of registration. A statistical test for difference in proportions was conducted to evaluate the null hypothesis that the proportion of patients for whom improved neuronavigation can be achieved, is the same for rigid and biomechanics-based registration. The null hypothesis was confidently rejected (p-value<10−4). Even the modified hypothesis that less than 25% of patients would benefit from the use of biomechanics-based registration was rejected at a significance level of 5% (p-value = 0.02). The biomechanics-based method proved particularly effective for cases experiencing large craniotomy-induced brain deformations. The outcome of this analysis suggests that our nonlinear biomechanics-based methods are beneficial to a large proportion of patients and can be considered for use in the operating theatre as one possible method of improving neuronavigation and surgical outcomes. PMID:24460486

  18. A new method based on the subpixel Gaussian model for accurate estimation of asteroid coordinates

    NASA Astrophysics Data System (ADS)

    Savanevych, V. E.; Briukhovetskyi, O. B.; Sokovikova, N. S.; Bezkrovny, M. M.; Vavilova, I. B.; Ivashchenko, Yu. M.; Elenin, L. V.; Khlamov, S. V.; Movsesian, Ia. S.; Dashkova, A. M.; Pogorelov, A. V.

    2015-08-01

    We describe a new iteration method to estimate asteroid coordinates, based on a subpixel Gaussian model of the discrete object image. The method operates by continuous parameters (asteroid coordinates) in a discrete observational space (the set of pixel potentials) of the CCD frame. In this model, the kind of coordinate distribution of the photons hitting a pixel of the CCD frame is known a priori, while the associated parameters are determined from a real digital object image. The method that is developed, which is flexible in adapting to any form of object image, has a high measurement accuracy along with a low calculating complexity, due to the maximum-likelihood procedure that is implemented to obtain the best fit instead of a least-squares method and Levenberg-Marquardt algorithm for minimization of the quadratic form. Since 2010, the method has been tested as the basis of our Collection Light Technology (COLITEC) software, which has been installed at several observatories across the world with the aim of the automatic discovery of asteroids and comets in sets of CCD frames. As a result, four comets (C/2010 X1 (Elenin), P/2011 NO1(Elenin), C/2012 S1 (ISON) and P/2013 V3 (Nevski)) as well as more than 1500 small Solar system bodies (including five near-Earth objects (NEOs), 21 Trojan asteroids of Jupiter and one Centaur object) have been discovered. We discuss these results, which allowed us to compare the accuracy parameters of the new method and confirm its efficiency. In 2014, the COLITEC software was recommended to all members of the Gaia-FUN-SSO network for analysing observations as a tool to detect faint moving objects in frames.

  19. Comparative study of chemo-electro-mechanical transport models for an electrically stimulated hydrogel

    NASA Astrophysics Data System (ADS)

    Elshaer, S. E.; Moussa, W. A.

    2014-07-01

    The main objective of this work is to introduce a new expression for the hydrogel’s hydration for use within the Poisson Nernst-Planck chemo electro mechanical (PNP CEM) transport models. This new contribution to the models support large deformation by considering the higher order terms in the Green-Lagrangian strain tensor. A detailed discussion of the CEM transport models using Poisson Nernst-Planck (PNP) and Poisson logarithmic Nernst-Planck (PLNP) equations for chemically and electrically stimulated hydrogels will be presented. The assumptions made to simplify both CEM transport models for electric field application in the order of 0.833 kV m-1 and a highly diluted electrolyte solution (97% is water) will be explained. This PNP CEM model has been verified accurately against experimental and numerical results. In addition, different definitions for normalizing the parameters are used to derive the dimensionless forms of both the PNP and PLNP CEM. Four models, PNP CEM, PLNP CEM, dimensionless PNP CEM and dimensionless PNLP CEM transport models were employed on an axially symmetric cylindrical hydrogel problem with an aspect ratio (diameter to thickness) of 175:3. The displacement and osmotic pressure obtained for the four models are compared against the variation of the number of elements for finite element analysis, simulation duration and solution rate when using the direct numerical solver.

  20. Particle Tracking Model and Abstraction of Transport Processes

    SciTech Connect

    B. Robinson

    2004-10-21

    The purpose of this report is to document the abstraction model being used in total system performance assessment (TSPA) model calculations for radionuclide transport in the unsaturated zone (UZ). The UZ transport abstraction model uses the particle-tracking method that is incorporated into the finite element heat and mass model (FEHM) computer code (Zyvoloski et al. 1997 [DIRS 100615]) to simulate radionuclide transport in the UZ. This report outlines the assumptions, design, and testing of a model for calculating radionuclide transport in the UZ at Yucca Mountain. In addition, methods for determining and inputting transport parameters are outlined for use in the TSPA for license application (LA) analyses. Process-level transport model calculations are documented in another report for the UZ (BSC 2004 [DIRS 164500]). Three-dimensional, dual-permeability flow fields generated to characterize UZ flow (documented by BSC 2004 [DIRS 169861]; DTN: LB03023DSSCP9I.001 [DIRS 163044]) are converted to make them compatible with the FEHM code for use in this abstraction model. This report establishes the numerical method and demonstrates the use of the model that is intended to represent UZ transport in the TSPA-LA. Capability of the UZ barrier for retarding the transport is demonstrated in this report, and by the underlying process model (BSC 2004 [DIRS 164500]). The technical scope, content, and management of this report are described in the planning document ''Technical Work Plan for: Unsaturated Zone Transport Model Report Integration'' (BSC 2004 [DIRS 171282]). Deviations from the technical work plan (TWP) are noted within the text of this report, as appropriate. The latest version of this document is being prepared principally to correct parameter values found to be in error due to transcription errors, changes in source data that were not captured in the report, calculation errors, and errors in interpretation of source data.

  1. Nearshore Berm Sediment Transport & Migration: Measurements & Modeling

    DTIC Science & Technology

    2013-02-13

    of nourishment • How much is it accreting by? • Shoreline change or profile volume • What is the long-term fate of the material? Coarser...18% +9% Volume Change o Accurate means of determining sand volume within and adjacent to the nourished area o Quantitative method to describe...parameters and coastal engineering design practices o Automated wave parameter extraction; user-defined beach profile; draft depth and

  2. Communication: Accurate higher-order van der Waals coefficients between molecules from a model dynamic multipole polarizability

    SciTech Connect

    Tao, Jianmin; Rappe, Andrew M.

    2016-01-21

    Due to the absence of the long-range van der Waals (vdW) interaction, conventional density functional theory (DFT) often fails in the description of molecular complexes and solids. In recent years, considerable progress has been made in the development of the vdW correction. However, the vdW correction based on the leading-order coefficient C{sub 6} alone can only achieve limited accuracy, while accurate modeling of higher-order coefficients remains a formidable task, due to the strong non-additivity effect. Here, we apply a model dynamic multipole polarizability within a modified single-frequency approximation to calculate C{sub 8} and C{sub 10} between small molecules. We find that the higher-order vdW coefficients from this model can achieve remarkable accuracy, with mean absolute relative deviations of 5% for C{sub 8} and 7% for C{sub 10}. Inclusion of accurate higher-order contributions in the vdW correction will effectively enhance the predictive power of DFT in condensed matter physics and quantum chemistry.

  3. The human skin/chick chorioallantoic membrane model accurately predicts the potency of cosmetic allergens.

    PubMed

    Slodownik, Dan; Grinberg, Igor; Spira, Ram M; Skornik, Yehuda; Goldstein, Ronald S

    2009-04-01

    The current standard method for predicting contact allergenicity is the murine local lymph node assay (LLNA). Public objection to the use of animals in testing of cosmetics makes the development of a system that does not use sentient animals highly desirable. The chorioallantoic membrane (CAM) of the chick egg has been extensively used for the growth of normal and transformed mammalian tissues. The CAM is not innervated, and embryos are sacrificed before the development of pain perception. The aim of this study was to determine whether the sensitization phase of contact dermatitis to known cosmetic allergens can be quantified using CAM-engrafted human skin and how these results compare with published EC3 data obtained with the LLNA. We studied six common molecules used in allergen testing and quantified migration of epidermal Langerhans cells (LC) as a measure of their allergic potency. All agents with known allergic potential induced statistically significant migration of LC. The data obtained correlated well with published data for these allergens generated using the LLNA test. The human-skin CAM model therefore has great potential as an inexpensive, non-radioactive, in vivo alternative to the LLNA, which does not require the use of sentient animals. In addition, this system has the advantage of testing the allergic response of human, rather than animal skin.

  4. Structural Design of Oligopeptides for Intestinal Transport Model.

    PubMed

    Hong, Seong-Min; Tanaka, Mitsuru; Koyanagi, Riho; Shen, Weilin; Matsui, Toshiro

    2016-03-16

    Glycyl-sarcosine (Gly-Sar) is a well-known model substrate for the intestinal uptake of dipeptides through peptide transporter 1 (PepT1). However, there are no other model peptides larger than tripeptides to evaluate their intestinal transport ability. In this study, we designed new oligopeptides based on the Gly-Sar structure in terms of protease resistance. Gly-Sar-Sar was found to be an appropriate transport model for tripeptides because it does not degrade during the transport across the rat intestinal membrane, while Gly-Gly-Sar was degraded to Gly-Sar during the 60 min transport. Caco-2 cell transport experiments revealed that the designed oligopeptides based on Gly-Sar-Sar showed a significantly (p < 0.05) lower transport ability by factors of 1/10-, 1/25-, and 1/40-fold for Gly-Sar-Sar, Gly-Sar-Sar-Sar, and Gly-Sar-Sar-Sar-Sar, respectively, compared to Gly-Sar (apparent permeability coefficient: 38.6 ± 11.4 cm/s). Cell experiments also showed that the designed tripeptide and Gly-Sar were transported across Caco-2 cell via PepT1, whereas the tetra- and pentapeptides were transported through the paracellular tight-junction pathway.

  5. Molecular modeling and ligand docking for Solute Carrier (SLC) transporters

    PubMed Central

    Schlessinger, Avner; Khuri, Natalia; Giacomini, Kathleen M.; Sali, Andrej

    2014-01-01

    Solute Carrier (SLC) transporters are membrane proteins that transport solutes, such as ions, metabolites, peptides, and drugs, across biological membranes, using diverse energy coupling mechanisms. In human, there are 386 SLC transporters, many of which contribute to the absorption, distribution, metabolism, and excretion of drugs and/or can be targeted directly by therapeutics. Recent atomic structures of SLC transporters determined by X-ray crystallography and NMR spectroscopy have significantly expanded the applicability of structure-based prediction of SLC transporter ligands, by enabling both comparative modeling of additional SLC transporters and virtual screening of small molecules libraries against experimental structures as well as comparative models. In this review, we begin by describing computational tools, including sequence analysis, comparative modeling, and virtual screening, that are used to predict the structures and functions of membrane proteins such as SLC transporters. We then illustrate the applications of these tools to predicting ligand specificities of select SLC transporters, followed by experimental validation using uptake kinetic measurements and other assays. We conclude by discussing future directions in the discovery of the SLC transporter ligands. PMID:23578028

  6. Model Validation of an RSRM Transporter Through Full-scale Operational and Modal Testing

    NASA Technical Reports Server (NTRS)

    Brillhart, Ralph; Davis, Joshua; Allred, Bradley

    2009-01-01

    The Reusable Solid Rocket Motor (RSRM) segments, which are part of the current Space Shuttle system and will provide the first stage of the Ares launch vehicle, must be transported from their manufacturing facility in Promontory, Utah, to a railhead in Corinne, Utah. This approximately 25-mile trip on secondary paved roads is accomplished using a special transporter system which lifts and conveys each individual segment. ATK Launch Systems (ATK) has recently obtained a new set of these transporters from Scheuerle, a company in Germany. The transporter is a 96-wheel, dual tractor vehicle that supports the payload via a hydraulic suspension. Since this system is a different design than was previously used, computer modeling with validation via test is required to ensure that the environment to which the segment is exposed is not too severe for this space-critical hardware. Accurate prediction of the loads imparted to the rocket motor is essential in order to prevent damage to the segment. To develop and validate a finite element model capable of such accurate predictions, ATA Engineering, Inc., teamed with ATK to perform a modal survey of the transport system, including a forward RSRM segment. A set of electrodynamic shakers was placed around the transporter at locations capable of exciting the transporter vehicle dynamics. Forces from the shakers with varying phase combinations were applied using sinusoidal sweep excitation. The relative phase of the shaker forcing functions was adjusted to match the shape characteristics of each of several target modes, thereby customizing each sweep run for exciting a particular mode. The resulting frequency response functions (FRF) from this series of sine sweeps allowed identification of all target modes and other higher-order modes, allowing good comparison to the finite element model. Furthermore, the survey-derived modal frequencies were correlated with peak frequencies observed during road-going operating tests. This

  7. Synchronizing production and air transportation scheduling using mathematical programming models

    NASA Astrophysics Data System (ADS)

    Zandieh, M.; Molla-Alizadeh-Zavardehi, S.

    2009-08-01

    Traditional scheduling problems assume that there are always infinitely many resources for delivering finished jobs to their destinations, and no time is needed for their transportation, so that finished products can be transported to customers without delay. So, for coordination of these two different activities in the implementation of a supply chain solution, we studied the problem of synchronizing production and air transportation scheduling using mathematical programming models. The overall problem is decomposed into two sub-problems, which consists of air transportation allocation problem and a single machine scheduling problem which they are considered together. We have taken into consideration different constraints and assumptions in our modeling such as special flights, delivery tardiness and no delivery tardiness. For these purposes, a variety of models have been proposed to minimize supply chain total cost which encompass transportation, makespan, delivery earliness tardiness and departure time earliness tardiness costs.

  8. Comparison of transport properties models for numerical simulations of Mars entry vehicles

    NASA Astrophysics Data System (ADS)

    Hao, Jiaao; Wang, Jingying; Gao, Zhenxun; Jiang, Chongwen; Lee, Chunhian

    2017-01-01

    Effects of two different models for transport properties, including the approximate model and the collision integral model, on hypersonic flow simulations of Mars entry vehicles are numerically investigated. A least square fitting is firstly performed using the best-available data of collision integrals for Martian atmosphere species within the temperature range of 300-20,000 K. Then, the performance of these two transport properties models are compared for an equilibrium Martian atmosphere gas mixture at 10 kPa and temperatures ranging from 1000 to 10,000 K. Finally, four flight conditions chosen from the trajectory of the Mars Pathfinder entry vehicle are numerically simulated. It is indicated that the approximate model is capable of accurately providing the distributions of species mass fractions and temperatures in the flowfield. Both models give similar translational-rotational and vibrational heat fluxes. However, the chemical diffusion heat fluxes predicted by the approximate model are significantly larger than the results computed by the collision integral model, particularly in the vicinity of the forebody stagnation point, whose maximum relative error of 15% for the super-catalytic case. The diffusion model employed in the approximate model is responsible to the discrepancy. In addition, the wake structure is largely unaffected by the transport properties models.

  9. Evaluation of Transport in the Lower Tropical Stratosphere in a Global Chemistry and Transport Model

    NASA Technical Reports Server (NTRS)

    Douglass, Anne R.; Schoeberl, Mark R.; Rood, Richard B.; Pawson, Steven

    2002-01-01

    A general circulation model (GCM) relies on various physical parameterizations and provides a solution to the atmospheric equations of motion. A data assimilation system (DAS) combines information from observations with a GCM forecast and produces analyzed meteorological fields that represent the observed atmospheric state. An off-line chemistry and transport model (CTM) can use winds and temperatures from a either a GCM or a DAS. The latter application is in common usage for interpretation of observations from various platforms under the assumption that the DAS transport represents the actual atmospheric transport. Here we compare the transport produced by a DAS with that produced by the particular GCM that is combined with observations to produce the analyzed fields. We focus on transport in the tropics and middle latitudes by comparing the age-of-air inferred from observations of SF6 and CO2 with the age-of-air calculated using GCM fields and DAS fields. We also compare observations of ozone, total reactive nitrogen, and methane with results from the two simulations. These comparisons show that DAS fields produce rapid upward tropical transport and excessive mixing between the tropics and middle latitudes. The unrealistic transport produced by the DAS fields may be due to implicit forcing that is required by the assimilation process when there is bias between the GCM forecast and observations that are combined to produce the analyzed fields. For example, the GCM does not produce a quasi-biennial oscillation (QBO). The QBO is present in the analyzed fields because it is present in the observations, and systematic implicit forcing is required by the DAS. Any systematic bias between observations and the GCM forecast used to produce the DAS analysis is likely to corrupt the transport produced by the analyzed fields. Evaluation of transport in the lower tropical stratosphere in a global chemistry and transport model.

  10. Transmission line model for strained quantum well lasers including carrier transport and carrier heating effects.

    PubMed

    Xia, Mingjun; Ghafouri-Shiraz, H

    2016-03-01

    This paper reports a new model for strained quantum well lasers, which are based on the quantum well transmission line modeling method where effects of both carrier transport and carrier heating have been included. We have applied this new model and studied the effect of carrier transport on the output waveform of a strained quantum well laser both in time and frequency domains. It has been found that the carrier transport increases the turn-on, turn-off delay times and damping of the quantum well laser transient response. Also, analysis in the frequency domain indicates that the carrier transport causes the output spectrum of the quantum well laser in steady state to exhibit a redshift which has a narrower bandwidth and lower magnitude. The simulation results of turning-on transients obtained by the proposed model are compared with those obtained by the rate equation laser model. The new model has also been used to study the effects of pump current spikes on the laser output waveforms properties, and it was found that the presence of current spikes causes (i) wavelength blueshift, (ii) larger bandwidth, and (iii) reduces the magnitude and decreases the side-lobe suppression ratio of the laser output spectrum. Analysis in both frequency and time domains confirms that the new proposed model can accurately predict the temporal and spectral behaviors of strained quantum well lasers.

  11. Keratin Dynamics: Modeling the Interplay between Turnover and Transport

    PubMed Central

    Portet, Stéphanie; Madzvamuse, Anotida; Chung, Andy; Leube, Rudolf E.; Windoffer, Reinhard

    2015-01-01

    Keratin are among the most abundant proteins in epithelial cells. Functions of the keratin network in cells are shaped by their dynamical organization. Using a collection of experimentally-driven mathematical models, different hypotheses for the turnover and transport of the keratin material in epithelial cells are tested. The interplay between turnover and transport and their effects on the keratin organization in cells are hence investigated by combining mathematical modeling and experimental data. Amongst the collection of mathematical models considered, a best model strongly supported by experimental data is identified. Fundamental to this approach is the fact that optimal parameter values associated with the best fit for each model are established. The best candidate among the best fits is characterized by the disassembly of the assembled keratin material in the perinuclear region and an active transport of the assembled keratin. Our study shows that an active transport of the assembled keratin is required to explain the experimentally observed keratin organization. PMID:25822661

  12. Antenna modeling considerations for accurate SAR calculations in human phantoms in close proximity to GSM cellular base station antennas.

    PubMed

    van Wyk, Marnus J; Bingle, Marianne; Meyer, Frans J C

    2005-09-01

    International bodies such as International Commission on Non-Ionizing Radiation Protection (ICNIRP) and the Institute for Electrical and Electronic Engineering (IEEE) make provision for human exposure assessment based on SAR calculations (or measurements) and basic restrictions. In the case of base station exposure this is mostly applicable to occupational exposure scenarios in the very near field of these antennas where the conservative reference level criteria could be unnecessarily restrictive. This study presents a variety of critical aspects that need to be considered when calculating SAR in a human body close to a mobile phone base station antenna. A hybrid FEM/MoM technique is proposed as a suitable numerical method to obtain accurate results. The verification of the FEM/MoM implementation has been presented in a previous publication; the focus of this study is an investigation into the detail that must be included in a numerical model of the antenna, to accurately represent the real-world scenario. This is accomplished by comparing numerical results to measurements for a generic GSM base station antenna and appropriate, representative canonical and human phantoms. The results show that it is critical to take the disturbance effect of the human phantom (a large conductive body) on the base station antenna into account when the antenna-phantom spacing is less than 300 mm. For these small spacings, the antenna structure must be modeled in detail. The conclusion is that it is feasible to calculate, using the proposed techniques and methodology, accurate occupational compliance zones around base station antennas based on a SAR profile and basic restriction guidelines.

  13. Modeling pollutant transport in the atmosphere boundary layer

    SciTech Connect

    O`Steen, B.L.

    1990-12-31

    The two basic methods for modeling the atmospheric transport of pollutants (diagnostic and prognostic) are examined along with the current models utilized at SRS for emergency response (WINDS). The ability of a limited-area (mesoscale) model, nested within a synoptic scale model, to represent a wide range of flow behavior, makes it the method of choice for predicting pollutant transport. Such a mesoscale model can provide an invaluable research tool and, with a periodic processing strategy for wind field calculation and/or sufficient computer capability, can be utilized in an emergency response capacity. Various models are compared.

  14. Modeling pollutant transport in the atmosphere boundary layer

    SciTech Connect

    O'Steen, B.L.

    1990-01-01

    The two basic methods for modeling the atmospheric transport of pollutants (diagnostic and prognostic) are examined along with the current models utilized at SRS for emergency response (WINDS). The ability of a limited-area (mesoscale) model, nested within a synoptic scale model, to represent a wide range of flow behavior, makes it the method of choice for predicting pollutant transport. Such a mesoscale model can provide an invaluable research tool and, with a periodic processing strategy for wind field calculation and/or sufficient computer capability, can be utilized in an emergency response capacity. Various models are compared.

  15. Rolling mill optimization using an accurate and rapid new model for mill deflection and strip thickness profile

    NASA Astrophysics Data System (ADS)

    Malik, Arif Sultan

    This work presents improved technology for attaining high-quality rolled metal strip. The new technology is based on an innovative method to model both the static and dynamic characteristics of rolling mill deflection, and it applies equally to both cluster-type and non cluster-type rolling mill configurations. By effectively combining numerical Finite Element Analysis (FEA) with analytical solid mechanics, the devised approach delivers a rapid, accurate, flexible, high-fidelity model useful for optimizing many important rolling parameters. The associated static deflection model enables computation of the thickness profile and corresponding flatness of the rolled strip. Accurate methods of predicting the strip thickness profile and strip flatness are important in rolling mill design, rolling schedule set-up, control of mill flatness actuators, and optimization of ground roll profiles. The corresponding dynamic deflection model enables solution of the standard eigenvalue problem to determine natural frequencies and modes of vibration. The presented method for solving the roll-stack deflection problem offers several important advantages over traditional methods. In particular, it includes continuity of elastic foundations, non-iterative solution when using pre-determined elastic foundation moduli, continuous third-order displacement fields, simple stress-field determination, the ability to calculate dynamic characteristics, and a comparatively faster solution time. Consistent with the most advanced existing methods, the presented method accommodates loading conditions that represent roll crowning, roll bending, roll shifting, and roll crossing mechanisms. Validation of the static model is provided by comparing results and solution time with large-scale, commercial finite element simulations. In addition to examples with the common 4-high vertical stand rolling mill, application of the presented method to the most complex of rolling mill configurations is demonstrated

  16. Using Transport Diagnostics to Understand Chemistry Climate Model Ozone Simulations

    NASA Technical Reports Server (NTRS)

    Strahan, S. E.; Douglass, A. R.; Stolarski, R. S.; Akiyoshi, H.; Bekki, S.; Braesicke, P.; Butchart, N.; Chipperfield, M. P.; Cugnet, D.; Dhomse, S.; Frith, S. M.; Gettleman, A.; Hardiman, S. C.; Kinnison, D. E.; Lamarque, J.-F.; Mancini, E.; Marchand, M.; Michou, M.; Morgenstern, O.; Nakamura, T.; Olivie, D.; Pawson, S.; Pitari, G.; Plummer, D. A.; Pyle, J. A.

    2010-01-01

    We demonstrate how observations of N2O and mean age in the tropical and midlatitude lower stratosphere (LS) can be used to identify realistic transport in models. The results are applied to 15 Chemistry Climate Models (CCMs) participating in the 2010 WMO assessment. Comparison of the observed and simulated N2O/mean age relationship identifies models with fast or slow circulations and reveals details of model ascent and tropical isolation. The use of this process-oriented N2O/mean age diagnostic identifies models with compensating transport deficiencies that produce fortuitous agreement with mean age. We compare the diagnosed model transport behavior with a model's ability to produce realistic LS O3 profiles in the tropics and midlatitudes. Models with the greatest tropical transport problems show the poorest agreement with observations. Models with the most realistic LS transport agree more closely with LS observations and each other. We incorporate the results of the chemistry evaluations in the SPARC CCMVal Report (2010) to explain the range of CCM predictions for the return-to-1980 dates for global (60 S-60 N) and Antarctic column ozone. Later (earlier) Antarctic return dates are generally correlated to higher (lower) vortex Cl(sub y) levels in the LS, and vortex Cl(sub y) is generally correlated with the model's circulation although model Cl(sub y) chemistry or Cl(sub y) conservation can have a significant effect. In both regions, models that have good LS transport produce a smaller range of predictions for the return-to-1980 ozone values. This study suggests that the current range of predicted return dates is unnecessarily large due to identifiable model transport deficiencies.

  17. Fast and Accurate Hybrid Stream PCRTMSOLAR Radiative Transfer Model for Reflected Solar Spectrum Simulation in the Cloudy Atmosphere

    NASA Technical Reports Server (NTRS)

    Yang, Qiguang; Liu, Xu; Wu, Wan; Kizer, Susan; Baize, Rosemary R.

    2016-01-01

    A hybrid stream PCRTM-SOLAR model has been proposed for fast and accurate radiative transfer simulation. It calculates the reflected solar (RS) radiances with a fast coarse way and then, with the help of a pre-saved matrix, transforms the results to obtain the desired high accurate RS spectrum. The methodology has been demonstrated with the hybrid stream discrete ordinate (HSDO) radiative transfer (RT) model. The HSDO method calculates the monochromatic radiances using a 4-stream discrete ordinate method, where only a small number of monochromatic radiances are simulated with both 4-stream and a larger N-stream (N = 16) discrete ordinate RT algorithm. The accuracy of the obtained channel radiance is comparable to the result from N-stream moderate resolution atmospheric transmission version 5 (MODTRAN5). The root-mean-square errors are usually less than 5x10(exp -4) mW/sq cm/sr/cm. The computational speed is three to four-orders of magnitude faster than the medium speed correlated-k option MODTRAN5. This method is very efficient to simulate thousands of RS spectra under multi-layer clouds/aerosols and solar radiation conditions for climate change study and numerical weather prediction applications.

  18. Combining Structural Modeling with Ensemble Machine Learning to Accurately Predict Protein Fold Stability and Binding Affinity Effects upon Mutation

    PubMed Central

    Garcia Lopez, Sebastian; Kim, Philip M.

    2014-01-01

    Advances in sequencing have led to a rapid accumulation of mutations, some of which are associated with diseases. However, to draw mechanistic conclusions, a biochemical understanding of these mutations is necessary. For coding mutations, accurate prediction of significant changes in either the stability of proteins or their affinity to their binding partners is required. Traditional methods have used semi-empirical force fields, while newer methods employ machine learning of sequence and structural features. Here, we show how combining both of these approaches leads to a marked boost in accuracy. We introduce ELASPIC, a novel ensemble machine learning approach that is able to predict stability effects upon mutation in both, domain cores and domain-domain interfaces. We combine semi-empirical energy terms, sequence conservation, and a wide variety of molecular details with a Stochastic Gradient Boosting of Decision Trees (SGB-DT) algorithm. The accuracy of our predictions surpasses existing methods by a considerable margin, achieving correlation coefficients of 0.77 for stability, and 0.75 for affinity predictions. Notably, we integrated homology modeling to enable proteome-wide prediction and show that accurate prediction on modeled structures is possible. Lastly, ELASPIC showed significant differences between various types of disease-associated mutations, as well as between disease and common neutral mutations. Unlike pure sequence-based prediction methods that try to predict phenotypic effects of mutations, our predictions unravel the molecular details governing the protein instability, and help us better understand the molecular causes of diseases. PMID:25243403

  19. MO-A-BRD-10: A Fast and Accurate GPU-Based Proton Transport Monte Carlo Simulation for Validating Proton Therapy Treatment Plans

    SciTech Connect

    Wan Chan Tseung, H; Ma, J; Beltran, C

    2014-06-15

    Purpose: To build a GPU-based Monte Carlo (MC) simulation of proton transport with detailed modeling of elastic and non-elastic (NE) protonnucleus interactions, for use in a very fast and cost-effective proton therapy treatment plan verification system. Methods: Using the CUDA framework, we implemented kernels for the following tasks: (1) Simulation of beam spots from our possible scanning nozzle configurations, (2) Proton propagation through CT geometry, taking into account nuclear elastic and multiple scattering, as well as energy straggling, (3) Bertini-style modeling of the intranuclear cascade stage of NE interactions, and (4) Simulation of nuclear evaporation. To validate our MC, we performed: (1) Secondary particle yield calculations in NE collisions with therapeutically-relevant nuclei, (2) Pencil-beam dose calculations in homogeneous phantoms, (3) A large number of treatment plan dose recalculations, and compared with Geant4.9.6p2/TOPAS. A workflow was devised for calculating plans from a commercially available treatment planning system, with scripts for reading DICOM files and generating inputs for our MC. Results: Yields, energy and angular distributions of secondaries from NE collisions on various nuclei are in good agreement with the Geant4.9.6p2 Bertini and Binary cascade models. The 3D-gamma pass rate at 2%–2mm for 70–230 MeV pencil-beam dose distributions in water, soft tissue, bone and Ti phantoms is 100%. The pass rate at 2%–2mm for treatment plan calculations is typically above 98%. The net computational time on a NVIDIA GTX680 card, including all CPU-GPU data transfers, is around 20s for 1×10{sup 7} proton histories. Conclusion: Our GPU-based proton transport MC is the first of its kind to include a detailed nuclear model to handle NE interactions on any nucleus. Dosimetric calculations demonstrate very good agreement with Geant4.9.6p2/TOPAS. Our MC is being integrated into a framework to perform fast routine clinical QA of pencil

  20. Boltzmann Transport in Hybrid PIC HET Modeling

    DTIC Science & Technology

    2015-07-01

    the device. Experimental measurements and computational simulations have consistently indicated that the electron transport perpendicular to the...plasma conditions experienced in HPHall. 1. Electron mobility in HET simulation The most widely used computational simulations of HETs, including HPHall...Figure 1: Cartoon schematic of anomalous electron trans- port regions in typical HET II. Computational setup As the stalwart HET simulation code in the EP

  1. Modeling atmospheric transport to the Marshall Islands

    NASA Astrophysics Data System (ADS)

    Merrill, John T.; Bleck, Rainer; Avila, Lixion

    1985-12-01

    Isentropic trajectory analyses are presented which support the hypothesis that atmospheric continental material found at Enewetak Atoll (11.3°N, 162.3°E) during the Sea-Air Exchange (SEAREX) experiments in 1979 had its origin primarily in Asia in the springtime (dry season experiment) and in North and Central America in the summer (wet season experiment). Fields of wind, Montgomery potential, and pressure on isentropic surfaces are obtained from global isobaric analyses by vertical interpolation. Trajectories backward in time from the area at and upwind of the experiment site were calculated using these fields. In April and May 1979 the atmospheric chemistry at Enewetak was influenced strongly by long-range transport from Asia; this transport was primarily in the potential temperature range 305-315 K with travel times of 8-13 days. Westerly winds over Asia at 350-600 mbar carry continental materials over the ocean, and as the air moves southward, subsidence occurs until the air is entrained in the trade wind flow. During July and August 1979 the transport paths were from open ocean areas and from near North and Central America at 305-310 K with travel times of 17-21 days. The trajectories remained at low levels within the boundary layer during this period. Also discussed is a meteorological analysis of dust storms in China, which shows that a mechanism exists for lifting eolian material to the upper troposphere. There is substantial uncertainty in the individual trajectories, and the factors limiting their accuracy are discussed. Given the consistency of the trajectory analyses with the chemical results, we now have a coherent picture of some of the processes responsible for long-range transport to the subtropical open ocean.

  2. Feedback network models for quantum transport

    NASA Astrophysics Data System (ADS)

    Gough, John

    2014-12-01

    Quantum feedback networks have been introduced in quantum optics as a framework for constructing arbitrary networks of quantum mechanical systems connected by unidirectional quantum optical fields, and has allowed for a system theoretic approach to open quantum optics systems. Our aim here is to establish a network theory for quantum transport systems where typically the mediating fields between systems are bidirectional. Mathematically, this leads us to study quantum feedback networks where fields arrive at ports in input-output pairs, making it a special case of the unidirectional theory where inputs and outputs are paired. However, it is conceptually important to develop this theory in the context of quantum transport theory—the resulting theory extends traditional approaches which tend to view the components in quantum transport as scatterers for the various fields, in the process allowing us to consider emission and absorption of field quanta by these components. The quantum feedback network theory is applicable to both Bose and Fermi fields, moreover, it applies to nonlinear dynamics for the component systems. We advance the general theory, but study the case of linear passive quantum components in some detail.

  3. Feedback network models for quantum transport.

    PubMed

    Gough, John

    2014-12-01

    Quantum feedback networks have been introduced in quantum optics as a framework for constructing arbitrary networks of quantum mechanical systems connected by unidirectional quantum optical fields, and has allowed for a system theoretic approach to open quantum optics systems. Our aim here is to establish a network theory for quantum transport systems where typically the mediating fields between systems are bidirectional. Mathematically, this leads us to study quantum feedback networks where fields arrive at ports in input-output pairs, making it a special case of the unidirectional theory where inputs and outputs are paired. However, it is conceptually important to develop this theory in the context of quantum transport theory-the resulting theory extends traditional approaches which tend to view the components in quantum transport as scatterers for the various fields, in the process allowing us to consider emission and absorption of field quanta by these components. The quantum feedback network theory is applicable to both Bose and Fermi fields, moreover, it applies to nonlinear dynamics for the component systems. We advance the general theory, but study the case of linear passive quantum components in some detail.

  4. Metal transport across biomembranes: emerging models for a distinct chemistry.

    PubMed

    Argüello, José M; Raimunda, Daniel; González-Guerrero, Manuel

    2012-04-20

    Transition metals are essential components of important biomolecules, and their homeostasis is central to many life processes. Transmembrane transporters are key elements controlling the distribution of metals in various compartments. However, due to their chemical properties, transition elements require transporters with different structural-functional characteristics from those of alkali and alkali earth ions. Emerging structural information and functional studies have revealed distinctive features of metal transport. Among these are the relevance of multifaceted events involving metal transfer among participating proteins, the importance of coordination geometry at transmembrane transport sites, and the presence of the largely irreversible steps associated with vectorial transport. Here, we discuss how these characteristics shape novel transition metal ion transport models.

  5. A deterministic computational model for the two dimensional electron and photon transport

    NASA Astrophysics Data System (ADS)

    Badavi, Francis F.; Nealy, John E.

    2014-12-01

    A deterministic (non-statistical) two dimensional (2D) computational model describing the transport of electron and photon typical of space radiation environment in various shield media is described. The 2D formalism is casted into a code which is an extension of a previously developed one dimensional (1D) deterministic electron and photon transport code. The goal of both 1D and 2D codes is to satisfy engineering design applications (i.e. rapid analysis) while maintaining an accurate physics based representation of electron and photon transport in space environment. Both 1D and 2D transport codes have utilized established theoretical representations to describe the relevant collisional and radiative interactions and transport processes. In the 2D version, the shield material specifications are made more general as having the pertinent cross sections. In the 2D model, the specification of the computational field is in terms of a distance of traverse z along an axial direction as well as a variable distribution of deflection (i.e. polar) angles θ where -π/2<θ<π/2, and corresponding symmetry is assumed for the range of azimuth angles (0<φ<2π). In the transport formalism, a combined mean-free-path and average trajectory approach is used. For candidate shielding materials, using the trapped electron radiation environments at low Earth orbit (LEO), geosynchronous orbit (GEO) and Jupiter moon Europa, verification of the 2D formalism vs. 1D and an existing Monte Carlo code are presented.

  6. Skin mechanics measured in vivo using torsion: a new and accurate model more sensitive to age, sex and moisturizing treatment.

    PubMed

    Salter, D C; McArthur, H C; Crosse, J E; Dickens, A D

    1993-10-01

    Summary Measurements of skin mechanics are required to understand better cracking and flaking of the epidermis and loss of 'elasticity'with age in the dermis. Improvements in torsional testing are described here. The resulting data was fitted to algebraic models, the parameters of which can serve both as a concise description of the responses and as a means of relating them to skin structure and physiology. This investigation looks into the suitability of seven such algebraic models. Five of the models examined here appear to be new. Using the commercially available Dia-Stron DTM Torque Meter with our own software, model parameters were studied as indicators of the effects of age and sex in 41 people, and of skin moisturizing treatments in a further 10 people. The two models in the literature were both found to be substantially less accurate and sensitive representations of experimental data than one of the new models proposed here based on the Weibull distribution. This 'WB model'was consistently the one best able to distinguish differences and detect changes which were statistically significant. The WB model appears to be the most powerful and efficient available. Use of this model makes it possible to demonstrate in vivo a statistically significant mechanical difference between male and pre-menopausal female skin using only one parameter (p= 0.0163, with 18 males and 19 females) and to demonstrate a statistically significant mechanical difference between successive decades of age in female skin using only one parameter (p= 0.0124, n= 24). The two parameters of the model most sensitive to skin structure, function and treatment have been combined to form the axes of a 'Skin condition chart'. Any person can be located on this chart at a point indicating their overall skin condition in mechanical terms and any changes in that condition can be clearly demonstrated by movement across the plot.

  7. Electronic transport in VO{sub 2}—Experimentally calibrated Boltzmann transport modeling

    SciTech Connect

    Kinaci, Alper; Rosenmann, Daniel; Chan, Maria K. Y. E-mail: mchan@anl.gov; Kado, Motohisa; Ling, Chen; Zhu, Gaohua; Banerjee, Debasish E-mail: mchan@anl.gov

    2015-12-28

    Materials that undergo metal-insulator transitions (MITs) are under intense study, because the transition is scientifically fascinating and technologically promising for various applications. Among these materials, VO{sub 2} has served as a prototype due to its favorable transition temperature. While the physical underpinnings of the transition have been heavily investigated experimentally and computationally, quantitative modeling of electronic transport in the two phases has yet to be undertaken. In this work, we establish a density-functional-theory (DFT)-based approach with Hubbard U correction (DFT + U) to model electronic transport properties in VO{sub 2} in the semiconducting and metallic regimes, focusing on band transport using the Boltzmann transport equations. We synthesized high quality VO{sub 2} films and measured the transport quantities across the transition, in order to calibrate the free parameters in the model. We find that the experimental calibration of the Hubbard correction term can efficiently and adequately model the metallic and semiconducting phases, allowing for further computational design of MIT materials for desirable transport properties.

  8. Accurate and efficient prediction of fine-resolution hydrologic and carbon dynamic simulations from coarse-resolution models

    NASA Astrophysics Data System (ADS)

    Pau, George Shu Heng; Shen, Chaopeng; Riley, William J.; Liu, Yaning

    2016-02-01

    The topography, and the biotic and abiotic parameters are typically upscaled to make watershed-scale hydrologic-biogeochemical models computationally tractable. However, upscaling procedure can produce biases when nonlinear interactions between different processes are not fully captured at coarse resolutions. Here we applied the Proper Orthogonal Decomposition Mapping Method (PODMM) to downscale the field solutions from a coarse (7 km) resolution grid to a fine (220 m) resolution grid. PODMM trains a reduced-order model (ROM) with coarse-resolution and fine-resolution solutions, here obtained using PAWS+CLM, a quasi-3-D watershed processes model that has been validated for many temperate watersheds. Subsequent fine-resolution solutions were approximated based only on coarse-resolution solutions and the ROM. The approximation errors were efficiently quantified using an error estimator. By jointly estimating correlated variables and temporally varying the ROM parameters, we further reduced the approximation errors by up to 20%. We also improved the method's robustness by constructing multiple ROMs using different set of variables, and selecting the best approximation based on the error estimator. The ROMs produced accurate downscaling of soil moisture, latent heat flux, and net primary production with O(1000) reduction in computational cost. The subgrid distributions were also nearly indistinguishable from the ones obtained using the fine-resolution model. Compared to coarse-resolution solutions, biases in upscaled ROM solutions were reduced by up to 80%. This method has the potential to help address the long-standing spatial scaling problem in hydrology and enable long-time integration, parameter estimation, and stochastic uncertainty analysis while accurately representing the heterogeneities.

  9. A Lagrangian stochastic model for aerial spray transport above an oak forest

    USGS Publications Warehouse

    Wang, Yansen; Miller, David R.; Anderson, Dean E.; McManus, Michael L.

    1995-01-01

    An aerial spray droplets' transport model has been developed by applying recent advances in Lagrangian stochastic simulation of heavy particles. A two-dimensional Lagrangian stochastic model was adopted to simulate the spray droplet dispersion in atmospheric turbulence by adjusting the Lagrangian integral time scale along the drop trajectory. The other major physical processes affecting the transport of spray droplets above a forest canopy, the aircraft wingtip vortices and the droplet evaporation, were also included in each time step of the droplets' transport.The model was evaluated using data from an aerial spray field experiment. In generally neutral stability conditions, the accuracy of the model predictions varied from run-to-run as expected. The average root-mean-square error was 24.61 IU cm−2, and the average relative error was 15%. The model prediction was adequate in two-dimensional steady wind conditions, but was less accurate in variable wind condition. The results indicated that the model can simulate successfully the ensemble; average transport of aerial spray droplets under neutral, steady atmospheric wind conditions.

  10. Modeling of active transmembrane transport in a mixture theory framework.

    PubMed

    Ateshian, Gerard A; Morrison, Barclay; Hung, Clark T

    2010-05-01

    This study formulates governing equations for active transport across semi-permeable membranes within the framework of the theory of mixtures. In mixture theory, which models the interactions of any number of fluid and solid constituents, a supply term appears in the conservation of linear momentum to describe momentum exchanges among the constituents. In past applications, this momentum supply was used to model frictional interactions only, thereby describing passive transport processes. In this study, it is shown that active transport processes, which impart momentum to solutes or solvent, may also be incorporated in this term. By projecting the equation of conservation of linear momentum along the normal to the membrane, a jump condition is formulated for the mechano-electrochemical potential of fluid constituents which is generally applicable to nonequilibrium processes involving active transport. The resulting relations are simple and easy to use, and address an important need in the membrane transport literature.

  11. Application of a data assimilation method via an ensemble Kalman filter to reactive urea hydrolysis transport modeling

    SciTech Connect

    Juxiu Tong; Bill X. Hu; Hai Huang; Luanjin Guo; Jinzhong Yang

    2014-03-01

    With growing importance of water resources in the world, remediations of anthropogenic contaminations due to reactive solute transport become even more important. A good understanding of reactive rate parameters such as kinetic parameters is the key to accurately predicting reactive solute transport processes and designing corresponding remediation schemes. For modeling reactive solute transport, it is very difficult to estimate chemical reaction rate parameters due to complex processes of chemical reactions and limited available data. To find a method to get the reactive rate parameters for the reactive urea hydrolysis transport modeling and obtain more accurate prediction for the chemical concentrations, we developed a data assimilation method based on an ensemble Kalman filter (EnKF) method to calibrate reactive rate parameters for modeling urea hydrolysis transport in a synthetic one-dimensional column at laboratory scale and to update modeling prediction. We applied a constrained EnKF method to pose constraints to the updated reactive rate parameters and the predicted solute concentrations based on their physical meanings after the data assimilation calibration. From the study results we concluded that we could efficiently improve the chemical reactive rate parameters with the data assimilation method via the EnKF, and at the same time we could improve solute concentration prediction. The more data we assimilated, the more accurate the reactive rate parameters and concentration prediction. The filter divergence problem was also solved in this study.

  12. Lagrangian Transport in a coupled Chemistry Climate Model

    NASA Astrophysics Data System (ADS)

    Hoppe, C.; Müller, R.; Günther, G.; Hoffmann, L.

    2012-04-01

    We describe the implementation of a Lagrangian transport core in a chemistry climate model (CCM). This is motivated by the problem that in many cases trace gas distributions in the stratosphere can not be represented properly in a classical Eulerian framework with a fixed model grid, especially in regions where strong trace gas gradients occur. Here, we focus on stratospheric water vapor, which is an important driver of surface climate change on decadal scales. In this case, the transport representation is particularly important in the tropical tropopause layer (TTL), where tropospheric air enters into the stratosphere, i.e. , where the entry level of stratospheric water vapor is determined. For this purpose, the Chemical Lagrangian Model of the Stratosphere (CLaMS) is coupled with the ECHAM/MESSy Atmospheric Chemistry Model (EMAC). The latter includes the ECHAM5 climate model, and a coupling interface, which allows for flexible coupling and switching between different submodels. The chemistry transport model CLaMS provides a full Lagrangian transport representation to calculate constituent transport on a set of air parcels that move along trajectories. In the Lagrangian frame of reference, different vertical velocity representations can be used to drive the trajectories: - kinematic transport in isobaric coordinates with omega as vertical velocity, - diabatic transport in isentropic coordinates, where thetadot calculated from diabatic heatingrates is used as vertical velocity. Since vertical winds in the statosphere derived with the kinematic method from the continuity equation often suffer from excessive numerical noise and errors, we expect that constituent transport using the diabatic method will improve the simulations of stratospheric water vapor. We will present preliminary results illustrating how the different transport representations influence simulated tracer distributions.

  13. Accurate Time-Dependent Traveling-Wave Tube Model Developed for Computational Bit-Error-Rate Testing

    NASA Technical Reports Server (NTRS)

    Kory, Carol L.

    2001-01-01

    The phenomenal growth of the satellite communications industry has created a large demand for traveling-wave tubes (TWT's) operating with unprecedented specifications requiring the design and production of many novel devices in record time. To achieve this, the TWT industry heavily relies on computational modeling. However, the TWT industry's computational modeling capabilities need to be improved because there are often discrepancies between measured TWT data and that predicted by conventional two-dimensional helical TWT interaction codes. This limits the analysis and design of novel devices or TWT's with parameters differing from what is conventionally manufactured. In addition, the inaccuracy of current computational tools limits achievable TWT performance because optimized designs require highly accurate models. To address these concerns, a fully three-dimensional, time-dependent, helical TWT interaction model was developed using the electromagnetic particle-in-cell code MAFIA (Solution of MAxwell's equations by the Finite-Integration-Algorithm). The model includes a short section of helical slow-wave circuit with excitation fed by radiofrequency input/output couplers, and an electron beam contained by periodic permanent magnet focusing. A cutaway view of several turns of the three-dimensional helical slow-wave circuit with input/output couplers is shown. This has been shown to be more accurate than conventionally used two-dimensional models. The growth of the communications industry has also imposed a demand for increased data rates for the transmission of large volumes of data. To achieve increased data rates, complex modulation and multiple access techniques are employed requiring minimum distortion of the signal as it is passed through the TWT. Thus, intersymbol interference (ISI) becomes a major consideration, as well as suspected causes such as reflections within the TWT. To experimentally investigate effects of the physical TWT on ISI would be

  14. Models of motor-assisted transport of intracellular particles.

    PubMed Central

    Smith, D A; Simmons, R M

    2001-01-01

    One-dimensional models are presented for the macroscopic intracellular transport of vesicles and organelles by molecular motors on a network of aligned intracellular filaments. A motor-coated vesicle or organelle is described as a diffusing particle binding intermittently to filaments, when it is transported at the motor velocity. Two models are treated in detail: 1) a unidirectional model, where only one kind of motor is operative and all filaments have the same polarity; and 2) a bidirectional model, in which filaments of both polarities exist (for example, a randomly polarized actin network for myosin motors) and/or particles have plus-end and minus-end motors operating on unipolar filaments (kinesin and dynein on microtubules). The unidirectional model provides net particle transport in the absence of a concentration gradient. A symmetric bidirectional model, with equal mixtures of filament polarities or plus-end and minus-end motors of the same characteristics, provides rapid transport down a concentration gradient and enhanced dispersion of particles from a point source by motor-assisted diffusion. Both models are studied in detail as a function of the diffusion constant and motor velocity of bound particles, and their rates of binding to and detachment from filaments. These models can form the basis of more realistic models for particle transport in axons, melanophores, and the dendritic arms of melanocytes, in which networks of actin filaments and microtubules coexist and motors for both types of filament are implicated. PMID:11159382

  15. Transported PDF Modeling of Nonpremixed Turbulent CO/H-2/N-2 Jet Flames

    SciTech Connect

    Zhao, xinyu; Haworth, D. C.; Huckaby, E. David

    2012-01-01

    Turbulent CO/H{sub 2}/N{sub 2} (“syngas”) flames are simulated using a transported composition probability density function (PDF) method. A consistent hybrid Lagrangian particle/Eulerian mesh algorithm is used to solve the modeled PDF transport equation. The model includes standard k–ϵ turbulence, gradient transport for scalars, and Euclidean minimum spanning tree (EMST) mixing. Sensitivities of model results to variations in the turbulence model, the treatment of radiation heat transfer, the choice of chemical mechanism, and the PDF mixing model are explored. A baseline model reproduces the measured mean and rms temperature, major species, and minor species profiles reasonably well, and captures the scaling that is observed in the experiments. Both our results and the literature suggest that further improvements can be realized with adjustments in the turbulence model, the radiation heat transfer model, and the chemical mechanism. Although radiation effects are relatively small in these flames, consideration of radiation is important for accurate NO prediction. Chemical mechanisms that have been developed specifically for fuels with high concentrations of CO and H{sub 2} perform better than a methane mechanism that was not designed for this purpose. It is important to account explicitly for turbulence–chemistry interactions, although the details of the mixing model do not make a large difference in the results, within reasonable limits.

  16. Improving representation of convective transport for scale-aware parameterization: 2. Analysis of cloud-resolving model simulations

    NASA Astrophysics Data System (ADS)

    Liu, Yi-Chin; Fan, Jiwen; Zhang, Guang J.; Xu, Kuan-Man; Ghan, Steven J.

    2015-04-01

    Following Part I, in which 3-D cloud-resolving model (CRM) simulations of a squall line and mesoscale convective complex in the midlatitude continental and the tropical regions are conducted and evaluated, we examine the scale dependence of eddy transport of water vapor, evaluate different eddy transport formulations, and improve the representation of convective transport across all scales by proposing a new formulation that more accurately represents the CRM-calculated eddy flux. CRM results show that there are strong grid-spacing dependencies of updraft and downdraft fractions regardless of altitudes, cloud life stage, and geographical location. As for the eddy transport of water vapor, updraft eddy flux is a major contributor to total eddy flux in the lower and middle troposphere. However, downdraft eddy transport can be as large as updraft eddy transport in the lower atmosphere especially at the mature stage of midlatitude continental convection. We show that the single-updraft approach significantly underestimates updraft eddy transport of water vapor because it fails to account for the large internal variability of updrafts, while a single downdraft represents the downdraft eddy transport of water vapor well. We find that using as few as three updrafts can account for the internal variability of updrafts well. Based on the evaluation with the CRM simulated data, we recommend a simplified eddy transport formulation that considers three updrafts and one downdraft. Such formulation is similar to the conventional one but much more accurately represents CRM-simulated eddy flux across all grid scales.

  17. Object-oriented data model of the municipal transportation

    NASA Astrophysics Data System (ADS)

    Pan, Yuqing; Sheng, Yehua; Zhang, Guiying

    2008-10-01

    The transportation problem is always one of main questions each big city all over the world faces. Managing the municipal transportation using GIS is becoming the important trend. And the data model is the transportation information system foundation. The organization and storage of the data must consider well in the system design. The data model not only needs to meet the demand that the transportation navigates, but also needs to achieve the good visual effects, also can carry on the management and the maintenance to the traffic information. According to the object-oriented theory and the method, the road is divided into segment, intersection. This paper analyzed the driveway, marking, sign and other transportation facilities and the relationship with the segment, intersection and constructed the municipal transportation data model which is adequate to the demand of vehicles navigation, visual and management. The paper also schemes the the all kinds of transportation data. The practice proves that this data model can satisfy the application demands of traffic management system.

  18. Parameter Set Uniqueness and Confidence Limits in Model Identification of Insulin Transport Models for Simulation Data Diabetic Patient Models

    PubMed Central

    Farmer, Terry G.; Edgar, Thomas F.; Peppas, Nicholas A.

    2011-01-01

    Background The use of patient models describing the dynamics of glucose, insulin, and possibly other metabolic species associated with glucose regulation allows diabetes researchers to gain insights regarding novel therapies via simulation. However, such models are only useful when model parameters are effectively estimated with patient data. Methods The use of least squares to effectively estimate model parameters from simulation data was investigated by observing factors that influence the accuracy of estimates for the model parameters from a data set generated using a model with known parameters. An intravenous insulin pharmacokinetic model was used to generate the insulin response of a patient with type 1 diabetes mellitus to a series of step changes in the insulin infusion rate from an external insulin pump. The effects of using user-defined gradient and Hessian calculations on both parameter estimations and the 95% confidence limits of the estimated parameter sets were investigated. Results Estimations performed by either solver without user-supplied quantities were highly dependent on the initial guess of the parameter set, with relative confidence limits greater than ±100%. The use of user-defined quantities allowed the one-compartment model parameters to be effectively estimated. While the two-compartment model parameter estimation still depended on the initial parameter set specification, confidence limits were decreased, and all fits to simulation data were very good. Conclusions The use of user-defined gradients and Hessian matrices results in more accurate parameter estimations for insulin transport models. Improved estimation could result in more accurate simulations for use in glucose control system design. PMID:18260776

  19. Uranium transport in a crushed granodiorite: Experiments and reactive transport modeling

    DOE PAGES

    Dittrich, T. M.; Reimus, P. W.

    2015-02-12

    The primary objective of this study was to develop and demonstrate an experimental method to refine and better parameterize process models for reactive contaminant transport in aqueous subsurface environments and to reduce conservatism in such models without attempting to fully describe the geochemical system.

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

    NASA Astrophysics Data System (ADS)

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

    2014-05-01

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

  1. Fokker-Planck/Transport model for neutral beam driven tokamaks

    SciTech Connect

    Killeen, J.; Mirin, A.A.; McCoy, M.G.

    1980-01-01

    The application of nonlinear Fokker-Planck models to the study of beam-driven plasmas is briefly reviewed. This evolution of models has led to a Fokker-Planck/Transport (FPT) model for neutral-beam-driven Tokamaks, which is described in detail. The FPT code has been applied to the PLT, PDX, and TFTR Tokamaks, and some representative results are presented.

  2. Insights on the role of accurate state estimation in coupled model parameter estimation by a conceptual climate model study

    NASA Astrophysics Data System (ADS)

    Yu, Xiaolin; Zhang, Shaoqing; Lin, Xiaopei; Li, Mingkui

    2017-03-01

    The uncertainties in values of coupled model parameters are an important source of model bias that causes model climate drift. The values can be calibrated by a parameter estimation procedure that projects observational information onto model parameters. The signal-to-noise ratio of error covariance between the model state and the parameter being estimated directly determines whether the parameter estimation succeeds or not. With a conceptual climate model that couples the stochastic atmosphere and slow-varying ocean, this study examines the sensitivity of state-parameter covariance on the accuracy of estimated model states in different model components of a coupled system. Due to the interaction of multiple timescales, the fast-varying atmosphere with a chaotic nature is the major source of the inaccuracy of estimated state-parameter covariance. Thus, enhancing the estimation accuracy of atmospheric states is very important for the success of coupled model parameter estimation, especially for the parameters in the air-sea interaction processes. The impact of chaotic-to-periodic ratio in state variability on parameter estimation is also discussed. This simple model study provides a guideline when real observations are used to optimize model parameters in a coupled general circulation model for improving climate analysis and predictions.

  3. Transport lattice models of heat transport in skin with spatially heterogeneous, temperature-dependent perfusion

    PubMed Central

    Gowrishankar, TR; Stewart, Donald A; Martin, Gregory T; Weaver, James C

    2004-01-01

    Background Investigation of bioheat transfer problems requires the evaluation of temporal and spatial distributions of temperature. This class of problems has been traditionally addressed using the Pennes bioheat equation. Transport of heat by conduction, and by temperature-dependent, spatially heterogeneous blood perfusion is modeled here using a transport lattice approach. Methods We represent heat transport processes by using a lattice that represents the Pennes bioheat equation in perfused tissues, and diffusion in nonperfused regions. The three layer skin model has a nonperfused viable epidermis, and deeper regions of dermis and subcutaneous tissue with perfusion that is constant or temperature-dependent. Two cases are considered: (1) surface contact heating and (2) spatially distributed heating. The model is relevant to the prediction of the transient and steady state temperature rise for different methods of power deposition within the skin. Accumulated thermal damage is estimated by using an Arrhenius type rate equation at locations where viable tissue temperature exceeds 42°C. Prediction of spatial temperature distributions is also illustrated with a two-dimensional model of skin created from a histological image. Results The transport lattice approach was validated by comparison with an analytical solution for a slab with homogeneous thermal properties and spatially distributed uniform sink held at constant temperatures at the ends. For typical transcutaneous blood gas sensing conditions the estimated damage is small, even with prolonged skin contact to a 45°C surface. Spatial heterogeneity in skin thermal properties leads to a non-uniform temperature distribution during a 10 GHz electromagnetic field exposure. A realistic two-dimensional model of the skin shows that tissue heterogeneity does not lead to a significant local temperature increase when heated by a hot wire tip. Conclusions The heat transport system model of the skin was solved by

  4. Sand transport on Mars: Preliminary results from models

    NASA Technical Reports Server (NTRS)

    Greeley, R.; Anderson, F. S.; Blumberg, D.; Lo, E.; Xu, P.; Pollack, J.

    1993-01-01

    Most studies of active aeolian processes on Mars have focused on dust, i.e., particles approximately 1 micron in diameter that are transported in suspension by wind. The presence of sand dunes on Mars indicates that larger grains (approximately greater than 60 microns, transported primarily in saltation) are also present. Although indirect evidence suggests that some dunes may be active, definitive evidence is lacking. Nonetheless, numerous studies demonstrate that sand is substantially easier to transport by wind than dust, and it is reasonable to infer that sand transportation in saltation occurs under present Martian conditions. In order to assess potential source regions, transportation pathways, and sites of deposition for sand on Mars, an iterative sand transport algorithm was developed that is based on the Mars General Circulation Model of Pollack et al. The results of the dust transport model are then compared with observed surface features, such as dune field locations observed on images, and surficial deposits as inferred from Viking IRTM observations. Preliminary results suggest that the north polar dune fields in the vicinity of 270 degrees W, 70 degrees N originated from weathered polar layered plains centered at 280 degrees W, 85 degrees N, and that Thaumasia Fossae, southern Hellas Planitia, and the area west of Hellespontus Montes are sand depositional sites. Examples of transportation 'corridors' include a westward pathway in the latitudinal band 35 degrees N to 45 degrees N, and a pathway southward from Solis Planum to Thaumasia Fossae, among others.

  5. Lab-on-a-brane: A novel physiologically relevant planar arterial model to study transendothelial transport

    NASA Astrophysics Data System (ADS)

    Budhwani, Karim Ismail

    The tremendous quality of life impact notwithstanding, cardiovascular diseases and Cancer add up to over US$ 700bn each year in financial costs alone. Aging and population growth are expected to further expand the problem space while drug research and development remain expensive. However, preclinical costs can be substantially mitigated by substituting animal models with in vitro devices that accurately model human cardiovascular transport. Here we present a novel physiologically relevant lab-on-a-brane that simulates in vivo pressure, flow, strain, and shear waveforms associated with normal and pathological conditions in large and small blood vessels for studying molecular transport across the endothelial monolayer. The device builds upon previously demonstrated integrated microfluidic loop design by: (a) introducing nanoscale pores in the substrate membrane to enable transmembrane molecular transport, (b) transforming the substrate membrane into a nanofibrous matrix for 3D smooth muscle cell (SMC) tissue culture, (c) integrating electrospinning fabrication methods, (d) engineering an invertible sandwich cell culture device architecture, and (e) devising a healthy co-culture mechanism for human arterial endothelial cell (HAEC) monolayer and multiple layers of human smooth muscle cells (HSMC) to accurately mimic arterial anatomy. Structural and mechanical characterization was conducted using confocal microscopy, SEM, stress/strain analysis, and infrared spectroscopy. Transport was characterized using FITC-Dextran hydraulic permeability protocol. Structure and transport characterization successfully demonstrate device viability as a physiologically relevant arterial mimic for testing transendothelial transport. Thus, our lab-on-a-brane provides a highly effective and efficient, yet considerably inexpensive, physiologically relevant alternative for pharmacokinetic evaluation; possibly reducing animals used in pre-clinical testing, clinical trials cost from false

  6. Mineralogical compositions of aquifer matrix as necessary initial conditions in reactive contaminant transport models

    NASA Astrophysics Data System (ADS)

    Zhu, Chen; Burden, David S.

    2001-10-01

    Mineralogical compositions and their spatial distributions are important initial conditions for reactive transport modeling. However, popular Kd-based "reactive" transport models only require contaminant concentrations in the pore fluids as initial conditions, and minerals implicitly represent infinite sources and sinks in these models. That situation results in a general neglect of mineralogical characterization in site investigations. This study uses a coupled multi-component reactive mass transport model to predict the natural attenuation of a ground water plume at a uranium mill tailings site in western USA. Numerous ground water geochemistry data are available at this site, but mineralogical data are sketchy. Even given the well-defined pore fluid chemistry, variations of secondary mineral species and mineral abundances in the aquifer resulted in significantly different modeling outcomes. Results show that the amount of calcite in the aquifer determines the distances of plume migration. The possible presence of jurbanite, an aluminum sulfate phase, can store acidity temporarily but cause more severe contamination on a later date. The surfaces of iron oxyhydroxides can store significant amounts of sulfate and protons and serve as a second source for prolonged contamination. These simulations under field conditions illustrate that mineralogical compositions are an essential requirement for accurate prediction of contaminant fate and transport.

  7. Mineralogical compositions of aquifer matrix as necessary initial conditions in reactive contaminant transport models.

    PubMed

    Zhu, C; Burden, D S

    2001-10-01

    Mineralogical compositions and their spatial distributions are important initial conditions for reactive transport modeling. However, popular Kd-based "reactive" transport models only require contaminant concentrations in the pore fluids as initial conditions, and minerals implicitly represent infinite sources and sinks in these models. That situation results in a general neglect of mineralogical characterization in site investigations. This study uses a coupled multi-component reactive mass transport model to predict the natural attenuation of a ground water plume at a uranium mill tailings site in western USA. Numerous ground water geochemistry data are available at this site, but mineralogical data are sketchy. Even given the well-defined pore fluid chemistry, variations of secondary mineral species and mineral abundances in the aquifer resulted in significantly different modeling outcomes. Results show that the amount of calcite in the aquifer determines the distances of plume migration. The possible presence of jurbanite, an aluminum sulfate phase, can store acidity temporarily but cause more severe contamination on a later date. The surfaces of iron oxyhydroxides can store significant amounts of sulfate and protons and serve as a second source for prolonged contamination. These simulations under field conditions illustrate that mineralogical compositions are an essential requirement for accurate prediction of contaminant fate and transport.

  8. Numerical study on pollutant transport in Dalian bay based on hydrodynamic model

    NASA Astrophysics Data System (ADS)

    Qiao, Huiting; Li, Jin; Zhang, Hongxing; Zhao, Kaibin; Zhang, Mingliang

    2017-01-01

    Based on the depth-averaged two-dimensional shallow water and pollutant transport equation, the coupling model of water flow and water quality with explicit scheme is developed in this study. The unstructured triangular grid is adopted to locally refine the mesh around sewage outlet or in high-gradient regions of terrain change for the coupling model. The finite volume method is applied to ensure the conservation of mass for each element. This hydrodynamic model applies the Roe solver approximate Riemann solution with second-order accuracy to compute the water momentum flux on the grid interface. Taking Dalian Bay as the research object, the numerical model established is used to simulate the hydrodynamic characteristics and pollutant transport process. The computed results of the tide level, flow current and flow direction agree well with the measured data in Dalian Bay. The spatial and temporal distribution of pollutant in water are analyzed and discussed in this study. Simulated results show that the two-dimensional hydrodynamic and pollutant transport model can accurately simulate the mass transport in coastal waters, and it can provide a scientific basis on coastal water environment protection for the research water.

  9. Kinase-kernel models: accurate in silico screening of 4 million compounds across the entire human kinome.

    PubMed

    Martin, Eric; Mukherjee, Prasenjit

    2012-01-23

    Reliable in silico prediction methods promise many advantages over experimental high-throughput screening (HTS): vastly lower time and cost, affinity magnitude estimates, no requirement for a physical sample, and a knowledge-driven exploration of chemical space. For the specific case of kinases, given several hundred experimental IC(50) training measurements, the empirically parametrized profile-quantitative structure-activity relationship (profile-QSAR) and surrogate AutoShim methods developed at Novartis can predict IC(50) with a reliability approaching experimental HTS. However, in the absence of training data, prediction is much harder. The most common a priori prediction method is docking, which suffers from many limitations: It requires a protein structure, is slow, and cannot predict affinity. (1) Highly accurate profile-QSAR (2) models have now been built for roughly 100 kinases covering most of the kinome. Analyzing correlations among neighboring kinases shows that near neighbors share a high degree of SAR similarity. The novel chemogenomic kinase-kernel method reported here predicts activity for new kinases as a weighted average of predicted activities from profile-QSAR models for nearby neighbor kinases. Three different factors for weighting the neighbors were evaluated: binding site sequence identity to the kinase neighbors, similarity of the training set for each neighbor model to the compound being predicted, and accuracy of each neighbor model. Binding site sequence identity was by far most important, followed by chemical similarity. Model quality had almost no relevance. The median R(2) = 0.55 for kinase-kernel interpolations on 25% of the data of each set held out from method optimization for 51 kinase assays, approached the accuracy of median R(2) = 0.61 for the trained profile-QSAR predictions on the same held out 25% data of each set, far faster and far more accurate than docking. Validation on the full data sets from 18 additional kinase assays

  10. A method for simple and accurate estimation of fog deposition in a mountain forest using a meteorological model

    NASA Astrophysics Data System (ADS)

    Katata, Genki; Kajino, Mizuo; Hiraki, Takatoshi; Aikawa, Masahide; Kobayashi, Tomiki; Nagai, Haruyasu

    2011-10-01

    To apply a meteorological model to investigate fog occurrence, acidification and deposition in mountain forests, the meteorological model WRF was modified to calculate fog deposition accurately by the simple linear function of fog deposition onto vegetation derived from numerical experiments using the detailed multilayer atmosphere-vegetation-soil model (SOLVEG). The modified version of WRF that includes fog deposition (fog-WRF) was tested in a mountain forest on Mt. Rokko in Japan. fog-WRF provided a distinctly better prediction of liquid water content of fog (LWC) than the original version of WRF. It also successfully simulated throughfall observations due to fog deposition inside the forest during the summer season that excluded the effect of forest edges. Using the linear relationship between fog deposition and altitude given by the fog-WRF calculations and the data from throughfall observations at a given altitude, the vertical distribution of fog deposition can be roughly estimated in mountain forests. A meteorological model that includes fog deposition will be useful in mapping fog deposition in mountain cloud forests.

  11. Towards an accurate model of redshift-space distortions: a bivariate Gaussian description for the galaxy pairwise velocity distributions

    NASA Astrophysics Data System (ADS)

    Bianchi, Davide; Chiesa, Matteo; Guzzo, Luigi

    2016-10-01

    As a step towards a more accurate modelling of redshift-space distortions (RSD) in galaxy surveys, we develop a general description of the probability distribution function of galaxy pairwise velocities within the framework of the so-called streaming model. For a given galaxy separation , such function can be described as a superposition of virtually infinite local distributions. We characterize these in terms of their moments and then consider the specific case in which they are Gaussian functions, each with its own mean μ and variance σ2. Based on physical considerations, we make the further crucial assumption that these two parameters are in turn distributed according to a bivariate Gaussian, with its own mean and covariance matrix. Tests using numerical simulations explicitly show that with this compact description one can correctly model redshift-space distorsions on all scales, fully capturing the overall linear and nonlinear dynamics of the galaxy flow at different separations. In particular, we naturally obtain Gaussian/exponential, skewed/unskewed distribution functions, depending on separation as observed in simulations and data. Also, the recently proposed single-Gaussian description of redshift-space distortions is included in this model as a limiting case, when the bivariate Gaussian is collapsed to a two-dimensional Dirac delta function. More work is needed, but these results indicate a very promising path to make definitive progress in our program to improve RSD estimators.

  12. Use of transport models for wildfire behavior simulations

    SciTech Connect

    Linn, R.R.; Harlow, F.H.

    1998-01-01

    Investigators have attempted to describe the behavior of wildfires for over fifty years. Current models for numerical description are mainly algebraic and based on statistical or empirical ideas. The authors have developed a transport model called FIRETEC. The use of transport formulations connects the propagation rates to the full conservation equations for energy, momentum, species concentrations, mass, and turbulence. In this paper, highlights of the model formulation and results are described. The goal of the FIRETEC model is to describe most probable average behavior of wildfires in a wide variety of conditions. FIRETEC represents the essence of the combination of many small-scale processes without resolving each process in complete detail.

  13. Biogeochemical Transport and Reaction Model (BeTR) v1

    SciTech Connect

    TANG, JINYUN

    2016-04-18

    The Biogeochemical Transport and Reaction Model (BeTR) is a F90 code that enables reactive transport modeling in land modules of earth system models (e.g. CESM, ACME). The code adopts the Objective-Oriented-Design, and allows users to plug in their own biogeochemical (BGC) formulations/codes, and compare them to other existing BGC codes in those ESMs. The code takes information of soil physics variables, such as variables, such as temperature, moisture, soil density profile; water flow, etc., from a land model to track the movement of different chemicals in presence of biogeochemical reactions.

  14. Aquifer Heterogeneity and Solute-Transport Modeling in the Floridan Aquifer System

    NASA Astrophysics Data System (ADS)

    Guo, W.; Maliva, R. G.; Missimer, T. M.

    2008-05-01

    The Floridan Aquifer System (FAS) is one of the most prolific aquifers in the world and is widely used for public and irrigation water supply. The FAS is also increasingly being used as a storage zone for aquifer storage and recovery (ASR) systems, including a 333-well system that is planned as part of the Comprehensive Everglades Restoration Plan (CERP). The FAS is highly heterogeneous with respect to hydraulic conductivity, with meter- scale inter-bed variation exceeding seven orders of magnitude in some cases, even in South Florida where mega-karst is not well developed. Aquifer heterogeneity can have a major impact on ASR system performance because of its affects on the movement and mixing of stored water. Aquifer heterogeneity poses challenges for accurate modeling of the FAS, including solute transport modeling of ASR systems and variable density flow modeling of the freshwater/saltwater interface along coastal areas. Dispersivity is an important parameter in solute transport modeling, which is associated with aquifer heterogeneity. Commonly the values of dispersivity used in solute-transport modeling are derived from literature review and adjusted during model calibration process. Artificially large dispersivity values are often used in solute-transport models of ASR systems as a "fudge factor" to simulate the apparent greater mixing caused by inter-bed heterogeneity. This approach is problematic because the use of artificial hydraulic parameters for calibration opens the results of predictive simulations to question. The use of large dispersivity values to simulate aquifer heterogeneity also does not incorporate other impacts of aquifer heterogeneity, such as differential flow rates and migration distances between beds. The technical challenge is to incorporate aquifer heterogeneity into groundwater models at a scale that is sufficient to adequately simulate its effect on ASR system performance and coastal groundwater flow, while maintaining acceptable

  15. Chemical Kinetic Modeling of Advanced Transportation Fuels

    SciTech Connect

    PItz, W J; Westbrook, C K; Herbinet, O

    2009-01-20

    Development of detailed chemical kinetic models for advanced petroleum-based and nonpetroleum based fuels is a difficult challenge because of the hundreds to thousands of different components in these fuels and because some of these fuels contain components that have not been considered in the past. It is important to develop detailed chemical kinetic models for these fuels since the models can be put into engine simulation codes used for optimizing engine design for maximum efficiency and minimal pollutant emissions. For example, these chemistry-enabled engine codes can be used to optimize combustion chamber shape and fuel injection timing. They also allow insight into how the composition of advanced petroleum-based and non-petroleum based fuels affect engine performance characteristics. Additionally, chemical kinetic models can be used separately to interpret important in-cylinder experimental data and gain insight into advanced engine combustion processes such as HCCI and lean burn engines. The objectives are: (1) Develop detailed chemical kinetic reaction models for components of advanced petroleum-based and non-petroleum based fuels. These fuels models include components from vegetable-oil-derived biodiesel, oil-sand derived fuel, alcohol fuels and other advanced bio-based and alternative fuels. (2) Develop detailed chemical kinetic reaction models for mixtures of non-petroleum and petroleum-based components to represent real fuels and lead to efficient reduced combustion models needed for engine modeling codes. (3) Characterize the role of fuel composition on efficiency and pollutant emissions from practical automotive engines.

  16. Turbulent Transport In Global Models of Magnetized Accretion Disks

    NASA Astrophysics Data System (ADS)

    Sorathia, Kareem

    of local models is predicated on the assumption that these models accurately capture the dynamics of a small patch of a global astrophysical disk. This assumption is tested in detail through the study of local regions of global simulations. To reach resolutions comparable to those used in local simulations an orbital advection algorithm, a semi-Lagrangian reformulation of the fluid equations, is used which allows an order of magnitude increase in computational efficiency. It is found that the turbulence in global simulations agrees at intermediate- and small-scales with local models and that the presence of magnetic flux stimulates angular momentum transport in global simulations in a similar manner to that observed for local ones. However, the importance of this flux-stress connection is shown to cast doubt on the validity of local models due to their inability to accurately capture the temporal evolution of the magnetic flux seen in global simulations. The use of orbital advection allows the ability to probe previously-inaccessible resolutions in global simulations and is the basis for a rigorous resolution study presented here. Included are the results of a study utilizing a series of global simulations of varying resolutions and initial magnetic field topologies where a collection of proposed metrics of numerical convergence are explored. The resolution constraints necessary to establish numerical convergence of astrophysically-important measurements are presented along with evidence suggesting that the use of proper azimuthal resolution, while computationally-demanding, is vital to achieving convergence. The majority of the proposed metrics are found to be useful diagnostics of MRI-driven turbulence, however they suffer as metrics of convergence due to their dependence on the initial magnetic field topology. In contrast to this, the magnetic tilt angle, a measure of the planar anisotropy of the magnetic field, is found to be a powerful tool for diagnosing

  17. Modelling hillslope evolution: linear and nonlinear transport relations

    NASA Astrophysics Data System (ADS)

    Martin, Yvonne

    2000-08-01

    Many recent models of landscape evolution have used a diffusion relation to simulate hillslope transport. In this study, a linear diffusion equation for slow, quasi-continuous mass movement (e.g., creep), which is based on a large data compilation, is adopted in the hillslope model. Transport relations for rapid, episodic mass movements are based on an extensive data set covering a 40-yr period from the Queen Charlotte Islands, British Columbia. A hyperbolic tangent relation, in which transport increases nonlinearly with gradient above some threshold gradient, provided the best fit to the data. Model runs were undertaken for typical hillslope profiles found in small drainage basins in the Queen Charlotte Islands. Results, based on linear diffusivity values defined in the present study, are compared to results based on diffusivities used in earlier studies. Linear diffusivities, adopted in several earlier studies, generally did not provide adequate approximations of hillslope evolution. The nonlinear transport relation was tested and found to provide acceptable simulations of hillslope evolution. Weathering is introduced into the final set of model runs. The incorporation of weathering into the model decreases the rate of hillslope change when theoretical rates of sediment transport exceed sediment supply. The incorporation of weathering into the model is essential to ensuring that transport rates at high gradients obtained in the model reasonably replicate conditions observed in real landscapes. An outline of landscape progression is proposed based on model results. Hillslope change initially occurs at a rapid rate following events that result in oversteepened gradients (e.g., tectonic forcing, glaciation, fluvial undercutting). Steep gradients are eventually eliminated and hillslope transport is reduced significantly.

  18. Modeling variably saturated subsurface solute transport with MODFLOW-UZF and MT3DMS

    USGS Publications Warehouse

    Morway, Eric D.; Niswonger, Richard G.; Langevin, Christian D.; Bailey, Ryan T.; Healy, Richard W.

    2013-01-01

    The MT3DMS groundwater solute transport model was modified to simulate solute transport in the unsaturated zone by incorporating the unsaturated-zone flow (UZF1) package developed for MODFLOW. The modified MT3DMS code uses a volume-averaged approach in which Lagrangian-based UZF1 fluid fluxes and storage changes are mapped onto a fixed grid. Referred to as UZF-MT3DMS, the linked model was tested against published benchmarks solved analytically as well as against other published codes, most frequently the U.S. Geological Survey's Variably-Saturated Two-Dimensional Flow and Transport Model. Results from a suite of test cases demonstrate that the modified code accurately simulates solute advection, dispersion, and reaction in the unsaturated zone. Two- and three-dimensional simulations also were investigated to ensure unsaturated-saturated zone interaction was simulated correctly. Because the UZF1 solution is analytical, large-scale flow and transport investigations can be performed free from the computational and data burdens required by numerical solutions to Richards' equation. Results demonstrate that significant simulation runtime savings can be achieved with UZF-MT3DMS, an important development when hundreds or thousands of model runs are required during parameter estimation and uncertainty analysis. Three-dimensional variably saturated flow and transport simulations revealed UZF-MT3DMS to have runtimes that are less than one tenth of the time required by models that rely on Richards' equation. Given its accuracy and efficiency, and the wide-spread use of both MODFLOW and MT3DMS, the added capability of unsaturated-zone transport in this familiar modeling framework stands to benefit a broad user-ship.

  19. Modeling variably saturated subsurface solute transport with MODFLOW-UZF and MT3DMS.

    PubMed

    Morway, Eric D; Niswonger, Richard G; Langevin, Christian D; Bailey, Ryan T; Healy, Richard W

    2013-03-01

    The MT3DMS groundwater solute transport model was modified to simulate solute transport in the unsaturated zone by incorporating the unsaturated-zone flow (UZF1) package developed for MODFLOW. The modified MT3DMS code uses a volume-averaged approach in which Lagrangian-based UZF1 fluid fluxes and storage changes are mapped onto a fixed grid. Referred to as UZF-MT3DMS, the linked model was tested against published benchmarks solved analytically as well as against other published codes, most frequently the U.S. Geological Survey's Variably-Saturated Two-Dimensional Flow and Transport Model. Results from a suite of test cases demonstrate that the modified code accurately simulates solute advection, dispersion, and reaction in the unsaturated zone. Two- and three-dimensional simulations also were investigated to ensure unsaturated-saturated zone interaction was simulated correctly. Because the UZF1 solution is analytical, large-scale flow and transport investigations can be performed free from the computational and data burdens required by numerical solutions to Richards' equation. Results demonstrate that significant simulation runtime savings can be achieved with UZF-MT3DMS, an important development when hundreds or thousands of model runs are required during parameter estimation and uncertainty analysis. Three-dimensional variably saturated flow and transport simulations revealed UZF-MT3DMS to have runtimes that are less than one tenth of the time required by models that rely on Richards' equation. Given its accuracy and efficiency, and the wide-spread use of both MODFLOW and MT3DMS, the added capability of unsaturated-zone transport in this familiar modeling framework stands to benefit a broad user-ship.

  20. Mathematical Model of Estuarial Sediment Transport.

    DTIC Science & Technology

    1977-10-01

    NUMBERS» Contract No. ^Ar DACW39-75-C-0080 ^^ 9. PERFORMING ORGANIZATION NAME AND ADDRESS Department of Civil Engineering...The original model, SEDIMENT I, was verified by comparison with measurements in a recirculating flume. The modified model, SEDIMENT II, developed for... organic matter from contiguous drainage areas, and waste materials. Clay minerals are hydrated aluminum silicates in a layer lattice crystal

  1. Transportation Sector Model of the National Energy Modeling System. Volume 2 -- Appendices: Part 1

    SciTech Connect

    1998-01-01

    This volume contains input data and parameters used in the model of the transportation sector of the National Energy Modeling System. The list of Transportation Sector Model variables includes parameters for the following: Light duty vehicle modules (fuel economy, regional sales, alternative fuel vehicles); Light duty vehicle stock modules; Light duty vehicle fleet module; Air travel module (demand model and fleet efficiency model); Freight transport module; Miscellaneous energy demand module; and Transportation emissions module. Also included in these appendices are: Light duty vehicle market classes; Maximum light duty vehicle market penetration parameters; Aircraft fleet efficiency model adjustment factors; and List of expected aircraft technology improvements.

  2. Cosmic-Ray Transport in Heliospheric Magnetic Structures. II. Modeling Particle Transport through Corotating Interaction Regions

    NASA Astrophysics Data System (ADS)

    Kopp, Andreas; Wiengarten, Tobias; Fichtner, Horst; Effenberger, Frederic; Kühl, Patrick; Heber, Bernd; Raath, Jan-Louis; Potgieter, Marius S.

    2017-03-01

    The transport of cosmic rays (CRs) in the heliosphere is determined by the properties of the solar wind plasma. The heliospheric plasma environment has been probed by spacecraft for decades and provides a unique opportunity for testing transport theories. Of particular interest for the three-dimensional (3D) heliospheric CR transport are structures such as corotating interaction regions (CIRs), which, due to the enhancement of the magnetic field strength and magnetic fluctuations within and due to the associated shocks as well as stream interfaces, do influence the CR diffusion and drift. In a three-fold series of papers, we investigate these effects by modeling inner-heliospheric solar wind conditions with the numerical magnetohydrodynamic (MHD) framework Cronos (Wiengarten et al., referred as Paper I), and the results serve as input to a transport code employing a stochastic differential equation approach (this paper). While, in Paper I, we presented results from 3D simulations with Cronos, the MHD output is now taken as an input to the CR transport modeling. We discuss the diffusion and drift behavior of Galactic cosmic rays using the example of different theories, and study the effects of CIRs on these transport processes. In particular, we point out the wide range of possible particle fluxes at a given point in space resulting from these different theories. The restriction of this variety by fitting the numerical results to spacecraft data will be the subject of the third paper of this series.

  3. Computer modeling of electron and proton transport in chloroplasts.

    PubMed

    Tikhonov, Alexander N; Vershubskii, Alexey V

    2014-07-01

    Photosynthesis is one of the most important biological processes in biosphere, which provides production of organic substances from atmospheric CO2 and water at expense of solar energy. In this review, we contemplate computer models of oxygenic photosynthesis in the context of feedback regulation of photosynthetic electron transport in chloroplasts, the energy-transducing organelles of the plant cell. We start with a brief overview of electron and proton transport processes in chloroplasts coupled to ATP synthesis and consider basic regulatory mechanisms of oxygenic photosynthesis. General approaches to computer simulation of photosynthetic processes are considered, including the random walk models of plastoquinone diffusion in thylakoid membranes and deterministic approach to modeling electron transport in chloroplasts based on the mass action law. Then we focus on a kinetic model of oxygenic photosynthesis that includes key stages of the linear electron transport, alternative pathways of electron transfer around photosystem I (PSI), transmembrane proton transport and ATP synthesis in chloroplasts. This model includes different regulatory processes: pH-dependent control of the intersystem electron transport, down-regulation of photosystem II (PSII) activity (non-photochemical quenching), the light-induced activation of the Bassham-Benson-Calvin (BBC) cycle. The model correctly describes pH-dependent feedback control of electron transport in chloroplasts and adequately reproduces a variety of experimental data on induction events observed under different experimental conditions in intact chloroplasts (variations of CO2 and O2 concentrations in atmosphere), including a complex kinetics of P700 (primary electron donor in PSI) photooxidation, CO2 consumption in the BBC cycle, and photorespiration. Finally, we describe diffusion-controlled photosynthetic processes in chloroplasts within the framework of the model that takes into account complex architecture of

  4. A finite-volume ELLAM for three-dimensional solute-transport modeling

    USGS Publications Warehouse

    Russell, T.F.; Heberton, C.I.; Konikow, L.F.; Hornberger, G.Z.

    2003-01-01

    A three-dimensional finite-volume ELLAM method has been developed, tested, and successfully implemented as part of the U.S. Geological Survey (USGS) MODFLOW-2000 ground water modeling package. It is included as a solver option for the Ground Water Transport process. The FVELLAM uses space-time finite volumes oriented along the streamlines of the flow field to solve an integral form of the solute-transport equation, thus combining local and global mass conservation with the advantages of Eulerian-Lagrangian characteristic methods. The USGS FVELLAM code simulates solute transport in flowing ground water for a single dissolved solute constituent and represents the processes of advective transport, hydrodynamic dispersion, mixing from fluid sources, retardation, and decay. Implicit time discretization of the dispersive and source/sink terms is combined with a Lagrangian treatment of advection, in which forward tracking moves mass to the new time level, distributing mass among destination cells using approximate indicator functions. This allows the use of large transport time increments (large Courant numbers) with accurate results, even for advection-dominated systems (large Peclet numbers). Four test cases, including comparisons with analytical solutions and benchmarking against other numerical codes, are presented that indicate that the FVELLAM can usually yield excellent results, even if relatively few transport time steps are used, although the quality of the results is problem-dependent.

  5. High Fidelity Non-Gravitational Force Models for Precise and Accurate Orbit Determination of TerraSAR-X

    NASA Astrophysics Data System (ADS)

    Hackel, Stefan; Montenbruck, Oliver; Steigenberger, -Peter; Eineder, Michael; Gisinger, Christoph

    Remote sensing satellites support a broad range of scientific and commercial applications. The two radar imaging satellites TerraSAR-X and TanDEM-X provide spaceborne Synthetic Aperture Radar (SAR) and interferometric SAR data with a very high accuracy. The increasing demand for precise radar products relies on sophisticated validation methods, which require precise and accurate orbit products. Basically, the precise reconstruction of the satellite’s trajectory is based on the Global Positioning System (GPS) measurements from a geodetic-grade dual-frequency receiver onboard the spacecraft. The Reduced Dynamic Orbit Determination (RDOD) approach utilizes models for the gravitational and non-gravitational forces. Following a proper analysis of the orbit quality, systematics in the orbit products have been identified, which reflect deficits in the non-gravitational force models. A detailed satellite macro model is introduced to describe the geometry and the optical surface properties of the satellite. Two major non-gravitational forces are the direct and the indirect Solar Radiation Pressure (SRP). Due to the dusk-dawn orbit configuration of TerraSAR-X, the satellite is almost constantly illuminated by the Sun. Therefore, the direct SRP has an effect on the lateral stability of the determined orbit. The indirect effect of the solar radiation principally contributes to the Earth Radiation Pressure (ERP). The resulting force depends on the sunlight, which is reflected by the illuminated Earth surface in the visible, and the emission of the Earth body in the infrared spectra. Both components of ERP require Earth models to describe the optical properties of the Earth surface. Therefore, the influence of different Earth models on the orbit quality is assessed within the presentation. The presentation highlights the influence of non-gravitational force and satellite macro models on the orbit quality of TerraSAR-X.

  6. Modelling of human transplacental transport as performed in Copenhagen, Denmark.

    PubMed

    Mathiesen, Line; Mørck, Thit Aarøe; Zuri, Giuseppina; Andersen, Maria Helena; Pehrson, Caroline; Frederiksen, Marie; Mose, Tina;