Science.gov

Sample records for accurate transport models

  1. Accurate mask model for advanced nodes

    NASA Astrophysics Data System (ADS)

    Zine El Abidine, Nacer; Sundermann, Frank; Yesilada, Emek; Ndiaye, El Hadji Omar; Mishra, Kushlendra; Paninjath, Sankaranarayanan; Bork, Ingo; Buck, Peter; Toublan, Olivier; Schanen, Isabelle

    2014-07-01

    Standard OPC models consist of a physical optical model and an empirical resist model. The resist model compensates the optical model imprecision on top of modeling resist development. The optical model imprecision may result from mask topography effects and real mask information including mask ebeam writing and mask process contributions. For advanced technology nodes, significant progress has been made to model mask topography to improve optical model accuracy. However, mask information is difficult to decorrelate from standard OPC model. Our goal is to establish an accurate mask model through a dedicated calibration exercise. In this paper, we present a flow to calibrate an accurate mask enabling its implementation. The study covers the different effects that should be embedded in the mask model as well as the experiment required to model them.

  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. Accurate modeling of parallel scientific computations

    NASA Technical Reports Server (NTRS)

    Nicol, David M.; Townsend, James C.

    1988-01-01

    Scientific codes are usually parallelized by partitioning a grid among processors. To achieve top performance it is necessary to partition the grid so as to balance workload and minimize communication/synchronization costs. This problem is particularly acute when the grid is irregular, changes over the course of the computation, and is not known until load time. Critical mapping and remapping decisions rest on the ability to accurately predict performance, given a description of a grid and its partition. This paper discusses one approach to this problem, and illustrates its use on a one-dimensional fluids code. The models constructed are shown to be accurate, and are used to find optimal remapping schedules.

  4. 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

  5. Accurate measurement of liquid transport through nanoscale conduits

    NASA Astrophysics Data System (ADS)

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

    2016-04-01

    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.

  6. Accurate measurement of liquid transport through nanoscale conduits.

    PubMed

    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. Universality: Accurate Checks in Dyson's Hierarchical Model

    NASA Astrophysics Data System (ADS)

    Godina, J. J.; Meurice, Y.; Oktay, M. B.

    2003-06-01

    In this talk we present high-accuracy calculations of the susceptibility near βc for Dyson's hierarchical model in D = 3. Using linear fitting, we estimate the leading (γ) and subleading (Δ) exponents. Independent estimates are obtained by calculating the first two eigenvalues of the linearized renormalization group transformation. We found γ = 1.29914073 ± 10 -8 and, Δ = 0.4259469 ± 10-7 independently of the choice of local integration measure (Ising or Landau-Ginzburg). After a suitable rescaling, the approximate fixed points for a large class of local measure coincide accurately with a fixed point constructed by Koch and Wittwer.

  8. The importance of accurate atmospheric modeling

    NASA Astrophysics Data System (ADS)

    Payne, Dylan; Schroeder, John; Liang, Pang

    2014-11-01

    This paper will focus on the effect of atmospheric conditions on EO sensor performance using computer models. We have shown the importance of accurately modeling atmospheric effects for predicting the performance of an EO sensor. A simple example will demonstrated how real conditions for several sites in China will significantly impact on image correction, hyperspectral imaging, and remote sensing. The current state-of-the-art model for computing atmospheric transmission and radiance is, MODTRAN® 5, developed by the US Air Force Research Laboratory and Spectral Science, Inc. Research by the US Air Force, Navy and Army resulted in the public release of LOWTRAN 2 in the early 1970's. Subsequent releases of LOWTRAN and MODTRAN® have continued until the present. Please verify that (1) all pages are present, (2) all figures are correct, (3) all fonts and special characters are correct, and (4) all text and figures fit within the red margin lines shown on this review document. Complete formatting information is available at http://SPIE.org/manuscripts Return to the Manage Active Submissions page at http://spie.org/submissions/tasks.aspx and approve or disapprove this submission. Your manuscript will not be published without this approval. Please contact author_help@spie.org with any questions or concerns. The paper will demonstrate the importance of using validated models and local measured meteorological, atmospheric and aerosol conditions to accurately simulate the atmospheric transmission and radiance. Frequently default conditions are used which can produce errors of as much as 75% in these values. This can have significant impact on remote sensing applications.

  9. SPECTROPOLARIMETRICALLY ACCURATE MAGNETOHYDROSTATIC SUNSPOT MODEL FOR FORWARD MODELING IN HELIOSEISMOLOGY

    SciTech Connect

    Przybylski, D.; Shelyag, S.; Cally, P. S.

    2015-07-01

    We present a technique to construct a spectropolarimetrically accurate magnetohydrostatic model of a large-scale solar magnetic field concentration, mimicking a sunspot. Using the constructed model we perform a simulation of acoustic wave propagation, conversion, and absorption in the solar interior and photosphere with the sunspot embedded into it. With the 6173 Å magnetically sensitive photospheric absorption line of neutral iron, we calculate observable quantities such as continuum intensities, Doppler velocities, as well as the full Stokes vector for the simulation at various positions at the solar disk, and analyze the influence of non-locality of radiative transport in the solar photosphere on helioseismic measurements. Bisector shapes were used to perform multi-height observations. The differences in acoustic power at different heights within the line formation region at different positions at the solar disk were simulated and characterized. An increase in acoustic power in the simulated observations of the sunspot umbra away from the solar disk center was confirmed as the slow magnetoacoustic wave.

  10. 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.

  11. 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

  12. Faster and more accurate transport procedures for HZETRN

    NASA Astrophysics Data System (ADS)

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

    2010-12-01

    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 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 2 of aluminum, polyethylene, and water. The new algorithms are found to be almost 100 times faster for solar particle event simulations and almost 10

  13. 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.

  14. 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.

  15. Accurate Drawbead Modeling in Stamping Simulations

    NASA Astrophysics Data System (ADS)

    Sester, M.; Burchitz, I.; Saenz de Argandona, E.; Estalayo, F.; Carleer, B.

    2016-08-01

    An adaptive line bead model that continually updates according to the changing conditions during the forming process has been developed. In these calculations, the adaptive line bead's geometry is treated as a 3D object where relevant phenomena like hardening curve, yield surface, through thickness stress effects and contact description are incorporated. The effectiveness of the adaptive drawbead model will be illustrated by an industrial example.

  16. 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.

  17. Accurate theoretical chemistry with coupled pair models.

    PubMed

    Neese, Frank; Hansen, Andreas; Wennmohs, Frank; Grimme, Stefan

    2009-05-19

    Quantum chemistry has found its way into the everyday work of many experimental chemists. Calculations can predict the outcome of chemical reactions, afford insight into reaction mechanisms, and be used to interpret structure and bonding in molecules. Thus, contemporary theory offers tremendous opportunities in experimental chemical research. However, even with present-day computers and algorithms, we cannot solve the many particle Schrodinger equation exactly; inevitably some error is introduced in approximating the solutions of this equation. Thus, the accuracy of quantum chemical calculations is of critical importance. The affordable accuracy depends on molecular size and particularly on the total number of atoms: for orientation, ethanol has 9 atoms, aspirin 21 atoms, morphine 40 atoms, sildenafil 63 atoms, paclitaxel 113 atoms, insulin nearly 800 atoms, and quaternary hemoglobin almost 12,000 atoms. Currently, molecules with up to approximately 10 atoms can be very accurately studied by coupled cluster (CC) theory, approximately 100 atoms with second-order Møller-Plesset perturbation theory (MP2), approximately 1000 atoms with density functional theory (DFT), and beyond that number with semiempirical quantum chemistry and force-field methods. The overwhelming majority of present-day calculations in the 100-atom range use DFT. Although these methods have been very successful in quantum chemistry, they do not offer a well-defined hierarchy of calculations that allows one to systematically converge to the correct answer. Recently a number of rather spectacular failures of DFT methods have been found-even for seemingly simple systems such as hydrocarbons, fueling renewed interest in wave function-based methods that incorporate the relevant physics of electron correlation in a more systematic way. Thus, it would be highly desirable to fill the gap between 10 and 100 atoms with highly correlated ab initio methods. We have found that one of the earliest (and now

  18. 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.

  19. In-band asymmetry compensation for accurate time/phase transport over optical transport network.

    PubMed

    Siu, Sammy; Tseng, Wen-Hung; 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.

  20. An articulated statistical shape model for accurate hip joint segmentation.

    PubMed

    Kainmueller, Dagmar; Lamecker, Hans; Zachow, Stefan; Hege, Hans-Christian

    2009-01-01

    In this paper we propose a framework for fully automatic, robust and accurate segmentation of the human pelvis and proximal femur in CT data. We propose a composite statistical shape model of femur and pelvis with a flexible hip joint, for which we extend the common definition of statistical shape models as well as the common strategy for their adaptation. We do not analyze the joint flexibility statistically, but model it explicitly by rotational parameters describing the bent in a ball-and-socket joint. A leave-one-out evaluation on 50 CT volumes shows that image driven adaptation of our composite shape model robustly produces accurate segmentations of both proximal femur and pelvis. As a second contribution, we evaluate a fine grain multi-object segmentation method based on graph optimization. It relies on accurate initializations of femur and pelvis, which our composite shape model can generate. Simultaneous optimization of both femur and pelvis yields more accurate results than separate optimizations of each structure. Shape model adaptation and graph based optimization are embedded in a fully automatic framework. PMID:19964159

  1. Methods for accurate homology modeling by global optimization.

    PubMed

    Joo, Keehyoung; Lee, Jinwoo; Lee, Jooyoung

    2012-01-01

    High accuracy protein modeling from its sequence information is an important step toward revealing the sequence-structure-function relationship of proteins and nowadays it becomes increasingly more useful for practical purposes such as in drug discovery and in protein design. We have developed a protocol for protein structure prediction that can generate highly accurate protein models in terms of backbone structure, side-chain orientation, hydrogen bonding, and binding sites of ligands. To obtain accurate protein models, we have combined a powerful global optimization method with traditional homology modeling procedures such as multiple sequence alignment, chain building, and side-chain remodeling. We have built a series of specific score functions for these steps, and optimized them by utilizing conformational space annealing, which is one of the most successful combinatorial optimization algorithms currently available.

  2. 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.

  3. 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. PMID:18384599

  4. 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.

  5. 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.

  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. 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. PMID:16662241

  9. Accurate transport properties for H-CO and H-CO2

    NASA Astrophysics Data System (ADS)

    Dagdigian, Paul J.

    2015-08-01

    Transport properties for collisions of hydrogen atoms with CO and CO2 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-CO2 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.

  10. 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.

  11. On the importance of having accurate data for astrophysical modelling

    NASA Astrophysics Data System (ADS)

    Lique, Francois

    2016-06-01

    The Herschel telescope and the ALMA and NOEMA interferometers have opened new windows of observation for wavelengths ranging from far infrared to sub-millimeter with spatial and spectral resolutions previously unmatched. To make the most of these observations, an accurate knowledge of the physical and chemical processes occurring in the interstellar and circumstellar media is essential.In this presentation, I will discuss what are the current needs of astrophysics in terms of molecular data and I will show that accurate molecular data are crucial for the proper determination of the physical conditions in molecular clouds.First, I will focus on collisional excitation studies that are needed for molecular lines modelling beyond the Local Thermodynamic Equilibrium (LTE) approach. In particular, I will show how new collisional data for the HCN and HNC isomers, two tracers of star forming conditions, have allowed solving the problem of their respective abundance in cold molecular clouds. I will also present the last collisional data that have been computed in order to analyse new highly resolved observations provided by the ALMA interferometer.Then, I will present the calculation of accurate rate constants for the F+H2 → HF+H and Cl+H2 ↔ HCl+H reactions, which have allowed a more accurate determination of the physical conditions in diffuse molecular clouds. I will also present the recent work on the ortho-para-H2 conversion due to hydrogen exchange that allow more accurate determination of the ortho-to-para-H2 ratio in the universe and that imply a significant revision of the cooling mechanism in astrophysical media.

  12. Accurate method of modeling cluster scaling relations in modified gravity

    NASA Astrophysics Data System (ADS)

    He, Jian-hua; Li, Baojiu

    2016-06-01

    We propose a new method to model cluster scaling relations in modified gravity. Using a suite of nonradiative hydrodynamical simulations, we show that the scaling relations of accumulated gas quantities, such as the Sunyaev-Zel'dovich effect (Compton-y parameter) and the x-ray Compton-y parameter, can be accurately predicted using the known results in the Λ CDM model with a precision of ˜3 % . This method provides a reliable way to analyze the gas physics in modified gravity using the less demanding and much more efficient pure cold dark matter simulations. Our results therefore have important theoretical and practical implications in constraining gravity using cluster surveys.

  13. 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.

  14. Optimal monotonization of a high-order accurate bicompact scheme for the nonstationary multidimensional transport equation

    NASA Astrophysics Data System (ADS)

    Aristova, E. N.; Rogov, B. V.; Chikitkin, A. V.

    2016-06-01

    A hybrid scheme is proposed for solving the nonstationary inhomogeneous transport equation. The hybridization procedure is based on two baseline schemes: (1) a bicompact one that is fourth-order accurate in all space variables and third-order accurate in time and (2) a monotone first-order accurate scheme from the family of short characteristic methods with interpolation over illuminated faces. It is shown that the first-order accurate scheme has minimal dissipation, so it is called optimal. The solution of the hybrid scheme depends locally on the solutions of the baseline schemes at each node of the space-time grid. A monotonization procedure is constructed continuously and uniformly in all mesh cells so as to keep fourth-order accuracy in space and third-order accuracy in time in domains where the solution is smooth, while maintaining a high level of accuracy in domains of discontinuous solution. Due to its logical simplicity and uniformity, the algorithm is well suited for supercomputer simulation.

  15. 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.

  16. 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

  17. 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

  18. 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.

  19. Robust and accurate transient light transport decomposition via convolutional sparse coding.

    PubMed

    Hu, Xuemei; Deng, Yue; Lin, Xing; Suo, Jinli; Dai, Qionghai; Barsi, Christopher; Raskar, Ramesh

    2014-06-01

    Ultrafast sources and detectors have been used to record the time-resolved scattering of light propagating through macroscopic scenes. In the context of computational imaging, decomposition of this transient light transport (TLT) is useful for applications, such as characterizing materials, imaging through diffuser layers, and relighting scenes dynamically. Here, we demonstrate a method of convolutional sparse coding to decompose TLT into direct reflections, inter-reflections, and subsurface scattering. The method relies on the sparsity composition of the time-resolved kernel. We show that it is robust and accurate to noise during the acquisition process.

  20. 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

  1. An accurate, efficient algorithm for calculation of quantum transport in extended structures

    SciTech Connect

    Godin, T.J.; Haydock, R.

    1994-05-01

    In device structures with dimensions comparable to carrier inelastic scattering lengths, the quantum nature of carriers will cause interference effects that cannot be modeled by conventional techniques. The basic equations that govern these ``quantum`` circuit elements present significant numerical challenges. The authors describe the block recursion method, an accurate, efficient method for solving the quantum circuit problem. They demonstrate this method by modeling dirty inversion layers.

  2. 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.

  3. Chewing simulation with a physically accurate deformable model.

    PubMed

    Pascale, Andra Maria; Ruge, Sebastian; Hauth, Steffen; Kordaß, Bernd; Linsen, Lars

    2015-01-01

    Nowadays, CAD/CAM software is being used to compute the optimal shape and position of a new tooth model meant for a patient. With this possible future application in mind, we present in this article an independent and stand-alone interactive application that simulates the human chewing process and the deformation it produces in the food substrate. Chewing motion sensors are used to produce an accurate representation of the jaw movement. The substrate is represented by a deformable elastic model based on the finite linear elements method, which preserves physical accuracy. Collision detection based on spatial partitioning is used to calculate the forces that are acting on the deformable model. Based on the calculated information, geometry elements are added to the scene to enhance the information available for the user. The goal of the simulation is to present a complete scene to the dentist, highlighting the points where the teeth came into contact with the substrate and giving information about how much force acted at these points, which therefore makes it possible to indicate whether the tooth is being used incorrectly in the mastication process. Real-time interactivity is desired and achieved within limits, depending on the complexity of the employed geometric models. The presented simulation is a first step towards the overall project goal of interactively optimizing tooth position and shape under the investigation of a virtual chewing process using real patient data (Fig 1). PMID:26389135

  4. Particle Image Velocimetry Measurements in an Anatomically-Accurate Scaled Model of the Mammalian Nasal Cavity

    NASA Astrophysics Data System (ADS)

    Rumple, Christopher; Krane, Michael; Richter, Joseph; Craven, Brent

    2013-11-01

    The mammalian nose is a multi-purpose organ that houses a convoluted airway labyrinth responsible for respiratory air conditioning, filtering of environmental contaminants, and chemical sensing. 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 respiratory airflow and olfactory transport phenomena in anatomically-accurate reconstructions of the nasal cavity. Here, we focus on efforts to manufacture an anatomically-accurate transparent model for stereoscopic particle image velocimetry (SPIV) measurements. Challenges in the design and manufacture of an index-matched anatomical model are addressed. PIV measurements are presented, which are used to validate concurrent computational fluid dynamics (CFD) simulations of mammalian nasal airflow. Supported by the National Science Foundation.

  5. Accurate, low-cost 3D-models of gullies

    NASA Astrophysics Data System (ADS)

    Onnen, Nils; Gronz, Oliver; Ries, Johannes B.; Brings, Christine

    2015-04-01

    Soil erosion is a widespread problem in arid and semi-arid areas. The most severe form is the gully erosion. They often cut into agricultural farmland and can make a certain area completely unproductive. To understand the development and processes inside and around gullies, we calculated detailed 3D-models of gullies in the Souss Valley in South Morocco. Near Taroudant, we had four study areas with five gullies different in size, volume and activity. By using a Canon HF G30 Camcorder, we made varying series of Full HD videos with 25fps. Afterwards, we used the method Structure from Motion (SfM) to create the models. To generate accurate models maintaining feasible runtimes, it is necessary to select around 1500-1700 images from the video, while the overlap of neighboring images should be at least 80%. In addition, it is very important to avoid selecting photos that are blurry or out of focus. Nearby pixels of a blurry image tend to have similar color values. That is why we used a MATLAB script to compare the derivatives of the images. The higher the sum of the derivative, the sharper an image of similar objects. MATLAB subdivides the video into image intervals. From each interval, the image with the highest sum is selected. E.g.: 20min. video at 25fps equals 30.000 single images. The program now inspects the first 20 images, saves the sharpest and moves on to the next 20 images etc. Using this algorithm, we selected 1500 images for our modeling. With VisualSFM, we calculated features and the matches between all images and produced a point cloud. Then, MeshLab has been used to build a surface out of it using the Poisson surface reconstruction approach. Afterwards we are able to calculate the size and the volume of the gullies. It is also possible to determine soil erosion rates, if we compare the data with old recordings. The final step would be the combination of the terrestrial data with the data from our aerial photography. So far, the method works well and we

  6. 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.

  7. Towards accurate observation and modelling of Antarctic glacial isostatic adjustment

    NASA Astrophysics Data System (ADS)

    King, M.

    2012-04-01

    The response of the solid Earth to glacial mass changes, known as glacial isostatic adjustment (GIA), has received renewed attention in the recent decade thanks to the Gravity Recovery and Climate Experiment (GRACE) satellite mission. GRACE measures Earth's gravity field every 30 days, but cannot partition surface mass changes, such as present-day cryospheric or hydrological change, from changes within the solid Earth, notably due to GIA. If GIA cannot be accurately modelled in a particular region the accuracy of GRACE estimates of ice mass balance for that region is compromised. This lecture will focus on Antarctica, where models of GIA are hugely uncertain due to weak constraints on ice loading history and Earth structure. Over the last years, however, there has been a step-change in our ability to measure GIA uplift with the Global Positioning System (GPS), including widespread deployments of permanent GPS receivers as part of the International Polar Year (IPY) POLENET project. I will particularly focus on the Antarctic GPS velocity field and the confounding effect of elastic rebound due to present-day ice mass changes, and then describe the construction and calibration of a new Antarctic GIA model for application to GRACE data, as well as highlighting areas where further critical developments are required.

  8. An accurate and simple quantum model for liquid water.

    PubMed

    Paesani, Francesco; Zhang, Wei; Case, David A; Cheatham, Thomas E; Voth, Gregory A

    2006-11-14

    The path-integral molecular dynamics and centroid molecular dynamics methods have been applied to investigate the behavior of liquid water at ambient conditions starting from a recently developed simple point charge/flexible (SPC/Fw) model. Several quantum structural, thermodynamic, and dynamical properties have been computed and compared to the corresponding classical values, as well as to the available experimental data. The path-integral molecular dynamics simulations show that the inclusion of quantum effects results in a less structured liquid with a reduced amount of hydrogen bonding in comparison to its classical analog. The nuclear quantization also leads to a smaller dielectric constant and a larger diffusion coefficient relative to the corresponding classical values. Collective and single molecule time correlation functions show a faster decay than their classical counterparts. Good agreement with the experimental measurements in the low-frequency region is obtained for the quantum infrared spectrum, which also shows a higher intensity and a redshift relative to its classical analog. A modification of the original parametrization of the SPC/Fw model is suggested and tested in order to construct an accurate quantum model, called q-SPC/Fw, for liquid water. The quantum results for several thermodynamic and dynamical properties computed with the new model are shown to be in a significantly better agreement with the experimental data. Finally, a force-matching approach was applied to the q-SPC/Fw model to derive an effective quantum force field for liquid water in which the effects due to the nuclear quantization are explicitly distinguished from those due to the underlying molecular interactions. Thermodynamic and dynamical properties computed using standard classical simulations with this effective quantum potential are found in excellent agreement with those obtained from significantly more computationally demanding full centroid molecular dynamics

  9. 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.

  10. 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

  11. A new algorithm for generating highly accurate benchmark solutions to transport test problems

    SciTech Connect

    Azmy, Y.Y.

    1997-06-01

    We present a new algorithm for solving the neutron transport equation in its discrete-variable form. The new algorithm is based on computing the full matrix relating the scalar flux spatial moments in all cells to the fixed neutron source spatial moments, foregoing the need to compute the angular flux spatial moments, and thereby eliminating the need for sweeping the spatial mesh in each discrete-angular direction. The matrix equation is solved exactly in test cases, producing a solution vector that is free from iteration convergence error, and subject only to truncation and roundoff errors. Our algorithm is designed to provide method developers with a quick and simple solution scheme to test their new methods on difficult test problems without the need to develop sophisticated solution techniques, e.g. acceleration, before establishing the worthiness of their innovation. We demonstrate the utility of the new algorithm by applying it to the Arbitrarily High Order Transport Nodal (AHOT-N) method, and using it to solve two of Burre`s Suite of Test Problems (BSTP). Our results provide highly accurate benchmark solutions, that can be distributed electronically and used to verify the pointwise accuracy of other solution methods and algorithms.

  12. 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.

  13. 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.

  14. 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

  15. 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

  16. 3ARM: A Fast, Accurate Radiative Transfer Model for Use in Climate Models

    NASA Technical Reports Server (NTRS)

    Bergstrom, R. W.; Kinne, S.; Sokolik, I. N.; Toon, O. B.; Mlawer, E. J.; Clough, S. A.; Ackerman, T. P.; Mather, J.

    1996-01-01

    A new radiative transfer model combining the efforts of three groups of researchers is discussed. The model accurately computes radiative transfer in a inhomogeneous absorbing, scattering and emitting atmospheres. As an illustration of the model, results are shown for the effects of dust on the thermal radiation.

  17. 3ARM: A Fast, Accurate Radiative Transfer Model for use in Climate Models

    NASA Technical Reports Server (NTRS)

    Bergstrom, R. W.; Kinne, S.; Sokolik, I. N.; Toon, O. B.; Mlawer, E. J.; Clough, S. A.; Ackerman, T. P.; Mather, J.

    1996-01-01

    A new radiative transfer model combining the efforts of three groups of researchers is discussed. The model accurately computes radiative transfer in a inhomogeneous absorbing, scattering and emitting atmospheres. As an illustration of the model, results are shown for the effects of dust on the thermal radiation.

  18. 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.

  19. Models in biology: 'accurate descriptions of our pathetic thinking'.

    PubMed

    Gunawardena, Jeremy

    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

  20. 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.

  1. 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.

  2. Accurate Model Selection of Relaxed Molecular Clocks in Bayesian Phylogenetics

    PubMed Central

    Baele, Guy; Li, Wai Lok Sibon; Drummond, Alexei J.; Suchard, Marc A.; Lemey, Philippe

    2013-01-01

    Recent implementations of path sampling (PS) and stepping-stone sampling (SS) have been shown to outperform the harmonic mean estimator (HME) and a posterior simulation-based analog of Akaike’s information criterion through Markov chain Monte Carlo (AICM), in Bayesian model selection of demographic and molecular clock models. Almost simultaneously, a Bayesian model averaging approach was developed that avoids conditioning on a single model but averages over a set of relaxed clock models. This approach returns estimates of the posterior probability of each clock model through which one can estimate the Bayes factor in favor of the maximum a posteriori (MAP) clock model; however, this Bayes factor estimate may suffer when the posterior probability of the MAP model approaches 1. Here, we compare these two recent developments with the HME, stabilized/smoothed HME (sHME), and AICM, using both synthetic and empirical data. Our comparison shows reassuringly that MAP identification and its Bayes factor provide similar performance to PS and SS and that these approaches considerably outperform HME, sHME, and AICM in selecting the correct underlying clock model. We also illustrate the importance of using proper priors on a large set of empirical data sets. PMID:23090976

  3. 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.

  4. Accurate and computationally efficient mixing models for the simulation of turbulent mixing with PDF methods

    NASA Astrophysics Data System (ADS)

    Meyer, Daniel W.; Jenny, Patrick

    2013-08-01

    Different simulation methods are applicable to study turbulent mixing. When applying probability density function (PDF) methods, turbulent transport, and chemical reactions appear in closed form, which is not the case in second moment closure methods (RANS). Moreover, PDF methods provide the entire joint velocity-scalar PDF instead of a limited set of moments. In PDF methods, however, a mixing model is required to account for molecular diffusion. In joint velocity-scalar PDF methods, mixing models should also account for the joint velocity-scalar statistics, which is often under appreciated in applications. The interaction by exchange with the conditional mean (IECM) model accounts for these joint statistics, but requires velocity-conditional scalar means that are expensive to compute in spatially three dimensional settings. In this work, two alternative mixing models are presented that provide more accurate PDF predictions at reduced computational cost compared to the IECM model, since no conditional moments have to be computed. All models are tested for different mixing benchmark cases and their computational efficiencies are inspected thoroughly. The benchmark cases involve statistically homogeneous and inhomogeneous settings dealing with three streams that are characterized by two passive scalars. The inhomogeneous case clearly illustrates the importance of accounting for joint velocity-scalar statistics in the mixing model. Failure to do so leads to significant errors in the resulting scalar means, variances and other statistics.

  5. 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.

  6. Methods for testing transport models

    SciTech Connect

    Singer, C.; Cox, D.

    1991-11-14

    Substantial progress has been made over the past year on six aspects of the work supported by this grant. As a result, we have in hand for the first time a fairly complete set of transport models and improved statistical methods for testing them against large databases. We also have initial results of such tests. These results indicate that careful application of presently available transport theories can reasonably well produce a remarkably wide variety of tokamak data.

  7. Accurate Low-mass Stellar Models of KOI-126

    NASA Astrophysics Data System (ADS)

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

    2011-10-01

    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.

  8. Inflation model building with an accurate measure of e -folding

    NASA Astrophysics Data System (ADS)

    Chongchitnan, Sirichai

    2016-08-01

    It has become standard practice to take the logarithmic growth of the scale factor as a measure of the amount of inflation, despite the well-known fact that this is only an approximation for the true amount of inflation required to solve the horizon and flatness problems. The aim of this work is to show how this approximation can be completely avoided using an alternative framework for inflation model building. We show that using the inverse Hubble radius, H =a H , as the key dynamical parameter, the correct number of e -folding arises naturally as a measure of inflation. As an application, we present an interesting model in which the entire inflationary dynamics can be solved analytically and exactly, and, in special cases, reduces to the familiar class of power-law models.

  9. 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.

  10. 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.

  11. Simulation model accurately estimates total dietary iodine intake.

    PubMed

    Verkaik-Kloosterman, Janneke; van 't Veer, Pieter; Ocké, Marga C

    2009-07-01

    One problem with estimating iodine intake is the lack of detailed data about the discretionary use of iodized kitchen salt and iodization of industrially processed foods. To be able to take into account these uncertainties in estimating iodine intake, a simulation model combining deterministic and probabilistic techniques was developed. Data from the Dutch National Food Consumption Survey (1997-1998) and an update of the Food Composition database were used to simulate 3 different scenarios: Dutch iodine legislation until July 2008, Dutch iodine legislation after July 2008, and a potential future situation. Results from studies measuring iodine excretion during the former legislation are comparable with the iodine intakes estimated with our model. For both former and current legislation, iodine intake was adequate for a large part of the Dutch population, but some young children (<5%) were at risk of intakes that were too low. In the scenario of a potential future situation using lower salt iodine levels, the percentage of the Dutch population with intakes that were too low increased (almost 10% of young children). To keep iodine intakes adequate, salt iodine levels should not be decreased, unless many more foods will contain iodized salt. Our model should be useful in predicting the effects of food reformulation or fortification on habitual nutrient intakes.

  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. Mathematical modeling of kidney transport.

    PubMed

    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.

  14. 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

  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. 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...

  17. A practical Lagrangian transport model

    USGS Publications Warehouse

    Jobson, Harvey E.

    1980-01-01

    An unconditionally stable and practical transport model for use in upland streams and rivers has been developed and verified. Basing the model on the Lagrangian, rather than the Eulerian, reference frame greatly reduces the numerical problems associated with solving the advective terms of the convective-diffusion equation. The model contains almost no numerical dispersion, is conceptually simple, and is relatively easy to code. Model results closely simulated dye concentrations measured in the Chattahoochee River near Atlanta, Ga. under highly unsteady flow conditions. (USGS)

  18. 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.

  19. 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

  20. An Accurately Stable Thermo-Hydro-Mechanical Model for Geo-Environmental Simulations

    NASA Astrophysics Data System (ADS)

    Gambolati, G.; Castelletto, N.; Ferronato, M.

    2011-12-01

    In real-world applications involving complex 3D heterogeneous domains the use of advanced numerical algorithms is of paramount importance to stabily, accurately and efficiently solve the coupled system of partial differential equations governing the mass and the energy balance in deformable porous media. The present communication discusses a novel coupled 3-D numerical model based on a suitable combination of Finite Elements (FEs), Mixed FEs (MFEs), and Finite Volumes (FVs) developed with the aim at stabilizing the numerical solution. Elemental pressures and temperatures, nodal displacements and face normal Darcy and Fourier fluxes are the selected primary variables. Such an approach provides an element-wise conservative velocity field, with both pore pressure and stress having the same order of approximation, and allows for the accurate prediction of sharp temperature convective fronts. In particular, the flow-deformation problem is addressed jointly by FEs and MFEs and is coupled to the heat transfer equation using an ad hoc time splitting technique that separates the time temperature evolution into two partial differential equations, accounting for the convective and the diffusive contribution, respectively. The convective part is addressed by a FV scheme which proves effective in treating sharp convective fronts, while the diffusive part is solved by a MFE formulation. A staggered technique is then implemented for the global solution of the coupled thermo-hydro-mechanical problem, solving iteratively the flow-deformation and the heat transport at each time step. Finally, the model is successfully experimented with in realistic applications dealing with geothermal energy extraction and injection.

  1. Modeling anomalous radial transport in kinetic transport codes

    NASA Astrophysics Data System (ADS)

    Bodi, K.; Krasheninnikov, S. I.; Cohen, R. H.; Rognlien, T. D.

    2009-11-01

    Anomalous transport is typically the dominant component of the radial transport in magnetically confined plasmas, where the physical origin of this transport is believed to be plasma turbulence. A model is presented for anomalous transport that can be used in continuum kinetic edge codes like TEMPEST, NEO and the next-generation code being developed by the Edge Simulation Laboratory. The model can also be adapted to particle-based codes. It is demonstrated that the model with a velocity-dependent diffusion and convection terms can match a diagonal gradient-driven transport matrix as found in contemporary fluid codes, but can also include off-diagonal effects. The anomalous transport model is also combined with particle drifts and a particle/energy-conserving Krook collision operator to study possible synergistic effects with neoclassical transport. For the latter study, a velocity-independent anomalous diffusion coefficient is used to mimic the effect of long-wavelength ExB turbulence.

  2. Modeling of radon transport in unsaturated soil

    SciTech Connect

    Chen, C.; Thomas, D.M.; Green, R.

    1995-08-10

    This study applies a recently developed model, LEACHV, to simulate transport of radon through unsaturated soil and compares calculated soil radon activities against field-measured values. For volatile and gas phase transport, LEACHV is modified from LEACHP, a pesticide version of LEACHM, as well-documented one-dimensional model for water and chemical movement through unsaturated soil. LEACHV adds consideration of air temperature changes and air flow driven by barometric pressure change to the other soil variables currently used in LEACHP. It applies diurnal barometric pressure and air temperature changes to reflect more accurately the typical field conditions, Sensitivity analysis and simulated results have clearly demonstrated the relative importance of barometric pressure change, rainfall events, changes in water content, gas advection, and radon source term in radon transport process. Comparisons among simulated results illustrated that the importance of barometric pressure change and its pumping phenomenon produces both fluctuation in soil gas radon activities and an elevation of the long-term average radon activity in shallow soils of an equal magnitude to the disturbed source parameter. Comparisons between measured and simulated soil radon activities showed that LEACHV can provide realistic estimates of radon activity concentration in the soil profile. 41 refs., 10 figs., 2 tabs.

  3. Modeling hydrogen transport by dislocations

    NASA Astrophysics Data System (ADS)

    Dadfarnia, Mohsen; Martin, May L.; Nagao, Akihide; Sofronis, Petros; Robertson, Ian M.

    2015-05-01

    Recent experimental studies of the microstructure beneath fracture surfaces of specimens fractured in the presence of high concentrations of hydrogen suggest that the dislocation structure and hydrogen transported by mobile dislocations play important roles in establishing the local conditions that promote failure. The experiments demonstrate that hydrogen is responsible for the copious plasticity in large volumes of material before the onset of fracture and further afield from a crack tip. A revised model for hydrogen transport that accounts for hydrogen carried by dislocations along with stress driven diffusion and trapping at other microstructural defects is proposed. With the use of this new model, numerical simulation results for transient hydrogen profiles in the neighborhood of a crack tip are presented. Based on hydrogen-enhanced dislocation mobility and density, the results indicate that dislocation transport can contribute to the elevation of the local hydrogen concentrations ahead of the crack to levels above those predicted by the classical diffusion model and to distributions that extend farther afield.

  4. 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.

  5. 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. PMID:26026447

  6. Modeling VOC transport in simulated waste drums

    SciTech Connect

    Liekhus, K.J.; Gresham, G.L.; Peterson, E.S.; Rae, C.; Hotz, N.J.; Connolly, M.J.

    1993-06-01

    A volatile organic compound (VOC) transport model has been developed to describe unsteady-state VOC permeation and diffusion within a waste drum. Model equations account for three primary mechanisms for VOC transport from a void volume within the drum. These mechanisms are VOC permeation across a polymer boundary, VOC diffusion across an opening in a volume boundary, and VOC solubilization in a polymer boundary. A series of lab-scale experiments was performed in which the VOC concentration was measured in simulated waste drums under different conditions. A lab-scale simulated waste drum consisted of a sized-down 55-gal metal drum containing a modified rigid polyethylene drum liner. Four polyethylene bags were sealed inside a large polyethylene bag, supported by a wire cage, and placed inside the drum liner. The small bags were filled with VOC-air gas mixture and the VOC concentration was measured throughout the drum over a period of time. Test variables included the type of VOC-air gas mixtures introduced into the small bags, the small bag closure type, and the presence or absence of a variable external heat source. Model results were calculated for those trials where the VOC permeability had been measured. Permeabilities for five VOCs [methylene chloride, 1,1,2-trichloro-1,2,2-trifluoroethane (Freon-113), 1,1,1-trichloroethane, carbon tetrachloride, and trichloroethylene] were measured across a polyethylene bag. Comparison of model and experimental results of VOC concentration as a function of time indicate that model accurately accounts for significant VOC transport mechanisms in a lab-scale waste drum.

  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. Accurate mask model implementation in optical proximity correction model for 14-nm nodes and beyond

    NASA Astrophysics Data System (ADS)

    Zine El Abidine, Nacer; Sundermann, Frank; Yesilada, Emek; Farys, Vincent; Huguennet, Frederic; Armeanu, Ana-Maria; Bork, Ingo; Chomat, Michael; Buck, Peter; Schanen, Isabelle

    2016-04-01

    In a previous work, we demonstrated that the current optical proximity correction model assuming the mask pattern to be analogous to the designed data is no longer valid. An extreme case of line-end shortening shows a gap up to 10 nm difference (at mask level). For that reason, an accurate mask model has been calibrated for a 14-nm logic gate level. A model with a total RMS of 1.38 nm at mask level was obtained. Two-dimensional structures, such as line-end shortening and corner rounding, were well predicted using scanning electron microscopy pictures overlaid with simulated contours. The first part of this paper is dedicated to the implementation of our improved model in current flow. The improved model consists of a mask model capturing mask process and writing effects, and a standard optical and resist model addressing the litho exposure and development effects at wafer level. The second part will focus on results from the comparison of the two models, the new and the regular.

  9. Accurate mask model implementation in OPC model for 14nm nodes and beyond

    NASA Astrophysics Data System (ADS)

    Zine El Abidine, Nacer; Sundermann, Frank; Yesilada, Emek; Farys, Vincent; Huguennet, Frederic; Armeanu, Ana-Maria; Bork, Ingo; Chomat, Michael; Buck, Peter; Schanen, Isabelle

    2015-10-01

    In a previous work [1] we demonstrated that current OPC model assuming the mask pattern to be analogous to the designed data is no longer valid. Indeed as depicted in figure 1, an extreme case of line-end shortening shows a gap up to 10 nm difference (at mask level). For that reason an accurate mask model, for a 14nm logic gate level has been calibrated. A model with a total RMS of 1.38nm at mask level was obtained. 2D structures such as line-end shortening and corner rounding were well predicted using SEM pictures overlaid with simulated contours. The first part of this paper is dedicated to the implementation of our improved model in current flow. The improved model consists of a mask model capturing mask process and writing effects and a standard optical and resist model addressing the litho exposure and development effects at wafer level. The second part will focus on results from the comparison of the two models, the new and the regular, as depicted in figure 2.

  10. 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.

  11. 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.

  12. MONA: An accurate two-phase well flow model based on phase slippage

    SciTech Connect

    Asheim, H.

    1984-10-01

    In two phase flow, holdup and pressure loss are related to interfacial slippage. A model based on the slippage concept has been developed and tested using production well data from Forties, the Ekofisk area, and flowline data from Prudhoe Bay. The model developed turned out considerably more accurate than the standard models used for comparison.

  13. Accurate Modeling of the Terrestrial Gamma-Ray Background for Homeland Security Applications

    SciTech Connect

    Sandness, Gerald A.; Schweppe, John E.; Hensley, Walter K.; Borgardt, James D.; Mitchell, Allison L.

    2009-10-24

    Abstract–The Pacific Northwest National Laboratory has developed computer models to simulate the use of radiation portal monitors to screen vehicles and cargo for the presence of illicit radioactive material. The gamma radiation emitted by the vehicles or cargo containers must often be measured in the presence of a relatively large gamma-ray background mainly due to the presence of potassium, uranium, and thorium (and progeny isotopes) in the soil and surrounding building materials. This large background is often a significant limit to the detection sensitivity for items of interest and must be modeled accurately for analyzing homeland security situations. Calculations of the expected gamma-ray emission from a disk of soil and asphalt were made using the Monte Carlo transport code MCNP and were compared to measurements made at a seaport with a high-purity germanium detector. Analysis revealed that the energy spectrum of the measured background could not be reproduced unless the model included gamma rays coming from the ground out to distances of at least 300 m. The contribution from beyond about 50 m was primarily due to gamma rays that scattered in the air before entering the detectors rather than passing directly from the ground to the detectors. These skyshine gamma rays contribute tens of percent to the total gamma-ray spectrum, primarily at energies below a few hundred keV. The techniques that were developed to efficiently calculate the contributions from a large soil disk and a large air volume in a Monte Carlo simulation are described and the implications of skyshine in portal monitoring applications are discussed.

  14. 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.

  15. 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.

  16. An adaptive atmospheric transport model for the Nevada Test Site

    SciTech Connect

    Pepper, D.W.; Randerson, D.

    1998-12-31

    The need to accurately calculate the transport of hazardous material is paramount to environmental safety and health activities, as well as to establish a sound emergency response capability, in the western United States and at the Nevada Test Site (NTS). Current efforts are under way at the University of Nevada, Las Vegas (UNLV) and the NOAA Air Resources Laboratory in Las Vegas to develop a state-of-the-art atmospheric flow and species transport model that will accurately calculate wind fields and atmospheric particulate transport over complex terrain. In addition, research efforts are needed to improve predictive capabilities for catastrophic events, e.g., volcanic eruptions, thunderstorms, heavy rains and floods, and dust storms. The model has a wide range of environmental, safety, and health applications as required by the US Department of Energy for NTS programs, including those activities associated with emergency response, the Hazard Material Spill Center, and site restoration and remediation.

  17. A parallel high-order accurate finite element nonlinear Stokes ice sheet model and benchmark experiments

    SciTech Connect

    Leng, Wei; Ju, Lili; Gunzburger, Max; Price, Stephen; Ringler, Todd

    2012-01-01

    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.

  18. Getting a Picture that Is Both Accurate and Stable: Situation Models and Epistemic Validation

    ERIC Educational Resources Information Center

    Schroeder, Sascha; Richter, Tobias; Hoever, Inga

    2008-01-01

    Text comprehension entails the construction of a situation model that prepares individuals for situated action. In order to meet this function, situation model representations are required to be both accurate and stable. We propose a framework according to which comprehenders rely on epistemic validation to prevent inaccurate information from…

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

    DOE PAGES

    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.

  20. MODELING CONTAMINANT TRANSPORT THROUGH SUBSURFACE SYSTEMS

    EPA Science Inventory

    Modeling of contaminant transport through soil to groundwater to a receptor requires that consideration be given to the many processes which control the transport and fate of chemical constituents in the subsurface environment. These processes include volatilization, degradation,...

  1. Cholesterol transport in model membranes

    NASA Astrophysics Data System (ADS)

    Garg, Sumit; Porcar, Lionel; Butler, Paul; Perez-Salas, Ursula

    2010-03-01

    Physiological processes distribute cholesterol unevenly within the cell. The levels of cholesterol are maintained by intracellular transport and a disruption in the cell's ability to keep these normal levels will lead to disease. Exchange rates of cholesterol are generally studied in model systems using labeled lipid vesicles. Initially donor vesicles have all the cholesterol and acceptor vesicles are devoid of it. They are mixed and after some time the vesicles are separated and cholesterol is traced in each vesicle. The studies performed up to date have significant scatter indicating that the methodologies are not consistent. The present work shows in-situ Time-Resolved SANS studies of cholesterol exchange rates in unsaturated PC lipid vesicles. Molecular dynamics simulations were done to investigate the energetic and kinetic behavior of cholesterol in this system. This synergistic approach will provide insight into our efforts to understand cholesterol traffic.

  2. 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.

  3. Accurate FDTD modelling for dispersive media using rational function and particle swarm optimisation

    NASA Astrophysics Data System (ADS)

    Chung, Haejun; Ha, Sang-Gyu; Choi, Jaehoon; Jung, Kyung-Young

    2015-07-01

    This article presents an accurate finite-difference time domain (FDTD) dispersive modelling suitable for complex dispersive media. A quadratic complex rational function (QCRF) is used to characterise their dispersive relations. To obtain accurate coefficients of QCRF, in this work, we use an analytical approach and a particle swarm optimisation (PSO) simultaneously. In specific, an analytical approach is used to obtain the QCRF matrix-solving equation and PSO is applied to adjust a weighting function of this equation. Numerical examples are used to illustrate the validity of the proposed FDTD dispersion model.

  4. Studies of Trace Gas Chemical Cycles Using Observations, Inverse Methods and Global Chemical Transport Models

    NASA Technical Reports Server (NTRS)

    Prinn, Ronald G.

    2001-01-01

    For interpreting observational data, and in particular for use in inverse methods, accurate and realistic chemical transport models are essential. Toward this end we have, in recent years, helped develop and utilize a number of three-dimensional models including the Model for Atmospheric Transport and Chemistry (MATCH).

  5. Continuous Modeling of Calcium Transport Through Biological Membranes

    NASA Astrophysics Data System (ADS)

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

    2016-06-01

    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).

  6. 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).

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

    NASA Astrophysics Data System (ADS)

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

    2016-10-01

    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.

  8. 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

  9. SATURATED ZONE FLOW AND TRANSPORT MODEL ABSTRACTION

    SciTech Connect

    B.W. ARNOLD

    2004-10-27

    The purpose of the saturated zone (SZ) flow and transport model abstraction task is to provide radionuclide-transport simulation results for use in the total system performance assessment (TSPA) for license application (LA) calculations. This task includes assessment of uncertainty in parameters that pertain to both groundwater flow and radionuclide transport in the models used for this purpose. This model report documents the following: (1) The SZ transport abstraction model, which consists of a set of radionuclide breakthrough curves at the accessible environment for use in the TSPA-LA simulations of radionuclide releases into the biosphere. These radionuclide breakthrough curves contain information on radionuclide-transport times through the SZ. (2) The SZ one-dimensional (I-D) transport model, which is incorporated in the TSPA-LA model to simulate the transport, decay, and ingrowth of radionuclide decay chains in the SZ. (3) The analysis of uncertainty in groundwater-flow and radionuclide-transport input parameters for the SZ transport abstraction model and the SZ 1-D transport model. (4) The analysis of the background concentration of alpha-emitting species in the groundwater of the SZ.

  10. 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

  11. 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.

  12. Built-in templates speed up process for making accurate models

    NASA Technical Reports Server (NTRS)

    1964-01-01

    From accurate scale drawings of a model, photographic negatives of the cross sections are printed on thin sheets of aluminum. These cross-section images are cut out and mounted, and mahogany blocks placed between them. The wood can be worked down using the aluminum as a built-in template.

  13. 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 ...

  14. 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.

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

    PubMed

    Elbasiouny, Sherif M

    2014-12-01

    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.

  16. A model for fast axonal transport.

    PubMed

    Blum, J J; Reed, M C

    1985-01-01

    A model for fast axonal transport is developed in which the essential features are that organelles may interact with mechanochemical cross-bridges that in turn interact with microtubules, forming an organelle-engine-microtubule complex which is transported along the microtubules. Computer analysis of the equations derived to describe such a system show that most of the experimental observations on fast axonal transport can be simulated by the model, indicating that the model is useful for the interpretation and design of experiments aimed at clarifying the mechanism of fast axonal transport. PMID:2416456

  17. Fast, Accurate RF Propagation Modeling and Simulation Tool for Highly Cluttered Environments

    SciTech Connect

    Kuruganti, Phani Teja

    2007-01-01

    As network centric warfare and distributed operations paradigms unfold, there is a need for robust, fast wireless network deployment tools. These tools must take into consideration the terrain of the operating theater, and facilitate specific modeling of end to end network performance based on accurate RF propagation predictions. It is well known that empirical models can not provide accurate, site specific predictions of radio channel behavior. In this paper an event-driven wave propagation simulation is proposed as a computationally efficient technique for predicting critical propagation characteristics of RF signals in cluttered environments. Convincing validation and simulator performance studies confirm the suitability of this method for indoor and urban area RF channel modeling. By integrating our RF propagation prediction tool, RCSIM, with popular packetlevel network simulators, we are able to construct an end to end network analysis tool for wireless networks operated in built-up urban areas.

  18. Accurate identification of waveform of evoked potentials by component decomposition using discrete cosine transform modeling.

    PubMed

    Bai, O; Nakamura, M; Kanda, M; Nagamine, T; Shibasaki, H

    2001-11-01

    This study introduces a method for accurate identification of the waveform of the evoked potentials by decomposing the component responses. The decomposition was achieved by zero-pole modeling of the evoked potentials in the discrete cosine transform (DCT) domain. It was found that the DCT coefficients of a component response in the evoked potentials could be modeled sufficiently by a second order transfer function in the DCT domain. The decomposition of the component responses was approached by using partial expansion of the estimated model for the evoked potentials, and the effectiveness of the decomposition method was evaluated both qualitatively and quantitatively. Because of the overlap of the different component responses, the proposed method enables an accurate identification of the evoked potentials, which is useful for clinical and neurophysiological investigations.

  19. 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. PMID:19229307

  20. 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

  1. 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.

  2. 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.

  3. 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.

  4. Accurate and interpretable nanoSAR models from genetic programming-based decision tree construction approaches.

    PubMed

    Oksel, Ceyda; Winkler, David A; Ma, Cai Y; Wilkins, Terry; Wang, Xue Z

    2016-09-01

    The number of engineered nanomaterials (ENMs) being exploited commercially is growing rapidly, due to the novel properties they exhibit. Clearly, it is important to understand and minimize any risks to health or the environment posed by the presence of ENMs. Data-driven models that decode the relationships between the biological activities of ENMs and their physicochemical characteristics provide an attractive means of maximizing the value of scarce and expensive experimental data. Although such structure-activity relationship (SAR) methods have become very useful tools for modelling nanotoxicity endpoints (nanoSAR), they have limited robustness and predictivity and, most importantly, interpretation of the models they generate is often very difficult. New computational modelling tools or new ways of using existing tools are required to model the relatively sparse and sometimes lower quality data on the biological effects of ENMs. The most commonly used SAR modelling methods work best with large datasets, are not particularly good at feature selection, can be relatively opaque to interpretation, and may not account for nonlinearity in the structure-property relationships. To overcome these limitations, we describe the application of a novel algorithm, a genetic programming-based decision tree construction tool (GPTree) to nanoSAR modelling. We demonstrate the use of GPTree in the construction of accurate and interpretable nanoSAR models by applying it to four diverse literature datasets. We describe the algorithm and compare model results across the four studies. We show that GPTree generates models with accuracies equivalent to or superior to those of prior modelling studies on the same datasets. GPTree is a robust, automatic method for generation of accurate nanoSAR models with important advantages that it works with small datasets, automatically selects descriptors, and provides significantly improved interpretability of models.

  5. 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.

  6. 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.

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

    PubMed Central

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

    2015-01-01

    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. PMID:26510769

  8. Modeling pollutant transport using a meshless-lagrangian particle model

    SciTech Connect

    Carrington, D. B.; Pepper, D. W.

    2002-01-01

    A combined meshless-Lagrangian particle transport model is used to predict pollutant transport over irregular terrain. The numerical model for initializing the velocity field is based on a meshless approach utilizing multiquadrics established by Kansa. The Lagrangian particle transport technique uses a random walk procedure to depict the advection and dispersion of pollutants over any type of surface, including street and city canyons

  9. 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.

  10. Can phenological models predict tree phenology accurately in the future? The unrevealed hurdle of endodormancy break.

    PubMed

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

    2016-10-01

    The onset of the growing season of trees has been earlier by 2.3 days per decade during the last 40 years in temperate Europe because of global warming. 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 endodormancy, and, on the other hand, higher temperatures are necessary to promote bud cell growth afterward. Different process-based models have been developed in the last decades to predict the date of budbreak of woody species. They predict that global warming should delay or compromise endodormancy break at the species equatorward range limits leading to a delay or even impossibility to flower or set new leaves. These models are classically parameterized with flowering or budbreak dates only, with no information on the endodormancy break date because this information is very scarce. Here, we evaluated the efficiency of a set of phenological models to accurately predict the endodormancy break dates of three fruit trees. Our results show that models calibrated solely with budbreak dates usually do not accurately predict the endodormancy break date. Providing endodormancy break date for the model parameterization results in much more accurate prediction of this latter, with, however, a higher error than that on budbreak dates. Most importantly, we show that models not calibrated with endodormancy break dates can generate large discrepancies in forecasted budbreak dates when using climate scenarios as compared to models calibrated with endodormancy break dates. This discrepancy increases with mean annual temperature and is therefore the strongest after 2050 in the southernmost regions. Our results claim for the urgent need of massive measurements of endodormancy break dates in forest and fruit trees to yield more robust projections of phenological changes in a near future. PMID:27272707

  11. 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.

  12. Can phenological models predict tree phenology accurately in the future? The unrevealed hurdle of endodormancy break.

    PubMed

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

    2016-10-01

    The onset of the growing season of trees has been earlier by 2.3 days per decade during the last 40 years in temperate Europe because of global warming. 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 endodormancy, and, on the other hand, higher temperatures are necessary to promote bud cell growth afterward. Different process-based models have been developed in the last decades to predict the date of budbreak of woody species. They predict that global warming should delay or compromise endodormancy break at the species equatorward range limits leading to a delay or even impossibility to flower or set new leaves. These models are classically parameterized with flowering or budbreak dates only, with no information on the endodormancy break date because this information is very scarce. Here, we evaluated the efficiency of a set of phenological models to accurately predict the endodormancy break dates of three fruit trees. Our results show that models calibrated solely with budbreak dates usually do not accurately predict the endodormancy break date. Providing endodormancy break date for the model parameterization results in much more accurate prediction of this latter, with, however, a higher error than that on budbreak dates. Most importantly, we show that models not calibrated with endodormancy break dates can generate large discrepancies in forecasted budbreak dates when using climate scenarios as compared to models calibrated with endodormancy break dates. This discrepancy increases with mean annual temperature and is therefore the strongest after 2050 in the southernmost regions. Our results claim for the urgent need of massive measurements of endodormancy break dates in forest and fruit trees to yield more robust projections of phenological changes in a near future.

  13. 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.

  14. Method for modeling radiative transport in luminescent particulate media.

    PubMed

    Hughes, Michael D; Borca-Tasciuc, Diana-Andra; Kaminski, Deborah A

    2016-04-20

    Modeling radiative transport in luminescent particulate media is important to a variety of applications, from biomedical imaging to solar power harvesting. When absorption and scattering from individual particles must be considered, the description of radiative transport is not straightforward. For large particles and interparticle spacing, geometrical optics can be employed. However, this approach requires accurate knowledge of several particle properties, such as index of refraction and absorption coefficient, along with particle geometry and positioning. Because the determination of these variables is often nontrivial, we developed an approach for modeling radiative transport in such media, which combines two simple experiments with Monte Carlo simulations to determine the particle extinction coefficient (Γ) and the probability of absorption of light by a particle (PA). The method is validated on samples consisting of luminescent phosphor powder dispersed in a silicone matrix. PMID:27140095

  15. 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

  16. Accurate Analytic Results for the Steady State Distribution of the Eigen Model

    NASA Astrophysics Data System (ADS)

    Huang, Guan-Rong; Saakian, David B.; Hu, Chin-Kun

    2016-04-01

    Eigen model of molecular evolution is popular in studying complex biological and biomedical systems. Using the Hamilton-Jacobi equation method, we have calculated analytic equations for the steady state distribution of the Eigen model with a relative accuracy of O(1/N), where N is the length of genome. Our results can be applied for the case of small genome length N, as well as the cases where the direct numerics can not give accurate result, e.g., the tail of distribution.

  17. 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.

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

    PubMed

    Yates, M V; Ouyang, Y

    1992-05-01

    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.

  19. 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.

  20. An accurate simulation model for single-photon avalanche diodes including important statistical effects

    NASA Astrophysics Data System (ADS)

    Qiuyang, He; Yue, Xu; Feifei, Zhao

    2013-10-01

    An accurate and complete circuit simulation model for single-photon avalanche diodes (SPADs) is presented. The derived model is not only able to simulate the static DC and dynamic AC behaviors of an SPAD operating in Geiger-mode, but also can emulate the second breakdown and the forward bias behaviors. In particular, it considers important statistical effects, such as dark-counting and after-pulsing phenomena. The developed model is implemented using the Verilog-A description language and can be directly performed in commercial simulators such as Cadence Spectre. The Spectre simulation results give a very good agreement with the experimental results reported in the open literature. This model shows a high simulation accuracy and very fast simulation rate.

  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. 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.

  3. An Accurate and Computationally Efficient Model for Membrane-Type Circular-Symmetric Micro-Hotplates

    PubMed Central

    Khan, Usman; Falconi, Christian

    2014-01-01

    Ideally, the design of high-performance micro-hotplates would require a large number of simulations because of the existence of many important design parameters as well as the possibly crucial effects of both spread and drift. However, the computational cost of FEM simulations, which are the only available tool for accurately predicting the temperature in micro-hotplates, is very high. As a result, micro-hotplate designers generally have no effective simulation-tools for the optimization. In order to circumvent these issues, here, we propose a model for practical circular-symmetric micro-hot-plates which takes advantage of modified Bessel functions, computationally efficient matrix-approach for considering the relevant boundary conditions, Taylor linearization for modeling the Joule heating and radiation losses, and external-region-segmentation strategy in order to accurately take into account radiation losses in the entire micro-hotplate. The proposed model is almost as accurate as FEM simulations and two to three orders of magnitude more computationally efficient (e.g., 45 s versus more than 8 h). The residual errors, which are mainly associated to the undesired heating in the electrical contacts, are small (e.g., few degrees Celsius for an 800 °C operating temperature) and, for important analyses, almost constant. Therefore, we also introduce a computationally-easy single-FEM-compensation strategy in order to reduce the residual errors to about 1 °C. As illustrative examples of the power of our approach, we report the systematic investigation of a spread in the membrane thermal conductivity and of combined variations of both ambient and bulk temperatures. Our model enables a much faster characterization of micro-hotplates and, thus, a much more effective optimization prior to fabrication. PMID:24763214

  4. 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.

  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. A Multiscale Red Blood Cell Model with Accurate Mechanics, Rheology, and Dynamics

    PubMed Central

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

    2010-01-01

    Abstract 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. PMID:20483330

  7. Towards more accurate numerical modeling of impedance based high frequency harmonic vibration

    NASA Astrophysics Data System (ADS)

    Lim, Yee Yan; Kiong Soh, Chee

    2014-03-01

    The application of smart materials in various fields of engineering has recently become increasingly popular. For instance, the high frequency based electromechanical impedance (EMI) technique employing smart piezoelectric materials is found to be versatile in structural health monitoring (SHM). Thus far, considerable efforts have been made to study and improve the technique. Various theoretical models of the EMI technique have been proposed in an attempt to better understand its behavior. So far, the three-dimensional (3D) coupled field finite element (FE) model has proved to be the most accurate. However, large discrepancies between the results of the FE model and experimental tests, especially in terms of the slope and magnitude of the admittance signatures, continue to exist and are yet to be resolved. This paper presents a series of parametric studies using the 3D coupled field finite element method (FEM) on all properties of materials involved in the lead zirconate titanate (PZT) structure interaction of the EMI technique, to investigate their effect on the admittance signatures acquired. FE model updating is then performed by adjusting the parameters to match the experimental results. One of the main reasons for the lower accuracy, especially in terms of magnitude and slope, of previous FE models is the difficulty in determining the damping related coefficients and the stiffness of the bonding layer. In this study, using the hysteretic damping model in place of Rayleigh damping, which is used by most researchers in this field, and updated bonding stiffness, an improved and more accurate FE model is achieved. The results of this paper are expected to be useful for future study of the subject area in terms of research and application, such as modeling, design and optimization.

  8. 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.

  9. Vertical transport and sources in flux models

    SciTech Connect

    Canavan, G.H.

    1997-01-01

    Vertical transport in flux models in examined and shown to reproduce expected limits for densities and fluxes. Disparities with catalog distributions are derived and inverted to find the sources required to rectify them.

  10. 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.

  11. 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. PMID:24472756

  12. Mathematical modeling plasma transport in tokamaks

    SciTech Connect

    Quiang, Ji

    1995-12-31

    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 10{sup 20}/m{sup 3} 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%.

  13. Accurate description of aqueous carbonate ions: an effective polarization model verified by neutron scattering.

    PubMed

    Mason, Philip E; Wernersson, Erik; Jungwirth, Pavel

    2012-07-19

    The carbonate ion plays a central role in the biochemical formation of the shells of aquatic life, which is an important path for carbon dioxide sequestration. Given the vital role of carbonate in this and other contexts, it is imperative to develop accurate models for such a high charge density ion. As a divalent ion, carbonate has a strong polarizing effect on surrounding water molecules. This raises the question whether it is possible to describe accurately such systems without including polarization. It has recently been suggested the lack of electronic polarization in nonpolarizable water models can be effectively compensated by introducing an electronic dielectric continuum, which is with respect to the forces between atoms equivalent to rescaling the ionic charges. Given how widely nonpolarizable models are used to model electrolyte solutions, establishing the experimental validity of this suggestion is imperative. Here, we examine a stringent test for such models: a comparison of the difference of the neutron scattering structure factors of K2CO3 vs KNO3 solutions and that predicted by molecular dynamics simulations for various models of the same systems. We compare standard nonpolarizable simulations in SPC/E water to analogous simulations with effective ion charges, as well as simulations in explicitly polarizable POL3 water (which, however, has only about half the experimental polarizability). It is found that the simulation with rescaled charges is in a very good agreement with the experimental data, which is significantly better than for the nonpolarizable simulation and even better than for the explicitly polarizable POL3 model.

  14. 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.

  15. Double cluster heads model for secure and accurate data fusion in wireless sensor networks.

    PubMed

    Fu, Jun-Song; Liu, Yun

    2015-01-19

    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.

  16. 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.

  17. Applying an accurate spherical model to gamma-ray burst afterglow observations

    NASA Astrophysics Data System (ADS)

    Leventis, K.; van der Horst, A. J.; van Eerten, H. J.; Wijers, R. A. M. J.

    2013-05-01

    We present results of model fits to afterglow data sets of GRB 970508, GRB 980703 and GRB 070125, characterized by long and broad-band coverage. The model assumes synchrotron radiation (including self-absorption) from a spherical adiabatic blast wave and consists of analytic flux prescriptions based on numerical results. For the first time it combines the accuracy of hydrodynamic simulations through different stages of the outflow dynamics with the flexibility of simple heuristic formulas. The prescriptions are especially geared towards accurate description of the dynamical transition of the outflow from relativistic to Newtonian velocities in an arbitrary power-law density environment. We show that the spherical model can accurately describe the data only in the case of GRB 970508, for which we find a circumburst medium density n ∝ r-2. We investigate in detail the implied spectra and physical parameters of that burst. For the microphysics we show evidence for equipartition between the fraction of energy density carried by relativistic electrons and magnetic field. We also find that for the blast wave to be adiabatic, the fraction of electrons accelerated at the shock has to be smaller than 1. We present best-fitting parameters for the afterglows of all three bursts, including uncertainties in the parameters of GRB 970508, and compare the inferred values to those obtained by different authors.

  18. 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.

  19. 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

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

    PubMed

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

    2013-07-01

    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

  1. Multidimensional modeling of pyrolysis gas transport inside orthotropic charring ablators

    NASA Astrophysics Data System (ADS)

    Weng, Haoyue

    During hypersonic atmospheric entry, spacecraft are exposed to enormous aerodynamic heat. To prevent the payload from overheating, charring ablative materials are favored to be applied as the heat shield at the exposing surface of the vehicle. Accurate modeling not only prevents mission failures, but also helps reduce cost. Existing models were mostly limited to one-dimensional and discrepancies were shown against measured experiments and flight-data. To help improve the models and analyze the charring ablation problems, a multidimensional material response module is developed, based on a finite volume method framework. The developed computer program is verified through a series of test-cases, and through code-to-code comparisons with a validated code. Several novel models are proposed, including a three-dimensional pyrolysis gas transport model and an orthotropic material model. The effects of these models are numerically studied and demonstrated to be significant.

  2. 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

  3. 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

  4. 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

  5. Sediment Transport and Water Quality Model of Cedar Lake, Indiana

    NASA Astrophysics Data System (ADS)

    James, S. C.; Jones, C. A.; Roberts, J. D.; Ahlmann, M.; Bucaro, D. A.

    2006-12-01

    The EPA-supported Environmental Fluid Dynamics Code, EFDC, is used to model hydrodynamics, sediment transport, and water quality in coastal regions, estuaries, rivers, and lakes. However, the empirical formulations used for sediment transport are not always adequate to accurately characterize cohesive sediment erosion and transport. New sediment transport subroutines have been incorporated into EFDC and the new model is called SNL-EFDC. The updated model provides an improved, coupled hydrodynamics, sediment transport, and water quality framework. The newly incorporated sediment transport subroutines facilitate direct use of measured erosion rate data from the Sediment Erosion with Depth Flume (SEDflume). Erosion rates are included as functions of both depth within the sediment bed and applied shear stresses. This bypasses problems associated with empirical erosion formulations often based on disaggregated particle size. Restoration alternatives are under consideration for Cedar Lake in Indiana and SNL-EFDC models its hydrodynamics, sediment transport, and water quality. The water quality model as implemented on Cedar Lake tracks algae, oxygen, temperature, carbon, phosphorous, and nitrogen kinetics, as well as, sediment bed diagenesis. Environmental conditions, wind, temperature, rainfall, and sunlight, were based on data collected in 2005. Tributary loading was modeled using L-THIA and provided influxes of water, nutrients (phosphorous, nitrogen, etc.), and sediments. The calibrated model was used to simulate a nine month period from March to November 2005. Results suggest that the model simulates sediments transport and associated water quality correctly. The calibrated model is being used to evaluate several restoration measures throughout the lake and watershed and their effect on water quality. Because Cedar Lake is a nitrogen limited lake, changes in the level of eutrophication from each measure are being tracked by calculating the Carlson trophic state index

  6. Transportation energy: data, forecasting, policy, and models

    SciTech Connect

    Morris, M.; Talvitie, A.; Hartgen, D.T.; Erlbaum, N.S.; Lee, M.E.H.

    1980-01-01

    The 16 papers in this report deal with the following areas: assessment of energy and petroleum consumption of different transportation modes in the Buffalo area; long-range forecasts of transportation energy consumption in New York state; use of disaggregate data to evaluate gasoline conservation policies: smaller cars and carpooling; how much fuel does vanpooling really save; evaluating the costs and benefits of plans to reduce gasoline queues; queuing and search delays due to gasoline station closings: simple equilibrium framework; demand for travel and the gasoline crisis; simple analytical model for understanding gasoline station lines; review of analytical models of gasoline demand during an energy emergency; direct energy accounts for urban transportation planning; transportation energy effects on urban growth: results of simulations; effect of urban development patterns on transportation energy use; travel demand and estimation of energy consumption by a constrained model; assessment of the Wharton EFA automobile demand model; forecasting equilibrium motor vehicle holdings by means of disaggregate models; and transportation system management actions - a study of the energy costs.

  7. Charge transport model to predict intrinsic reliability for dielectric materials

    SciTech Connect

    Ogden, Sean P.; Borja, Juan; Plawsky, Joel L. Gill, William N.; Lu, T.-M.; Yeap, Kong Boon

    2015-09-28

    Several lifetime models, mostly empirical in nature, are used to predict reliability for low-k dielectrics used in integrated circuits. There is a dispute over which model provides the most accurate prediction for device lifetime at operating conditions. As a result, there is a need to transition from the use of these largely empirical models to one built entirely on theory. Therefore, a charge transport model was developed to predict the device lifetime of low-k interconnect systems. The model is based on electron transport and donor-type defect formation. Breakdown occurs when a critical defect concentration accumulates, resulting in electron tunneling and the emptying of positively charged traps. The enhanced local electric field lowers the barrier for electron injection into the dielectric, causing a positive feedforward failure. The charge transport model is able to replicate experimental I-V and I-t curves, capturing the current decay at early stress times and the rapid current increase at failure. The model is based on field-driven and current-driven failure mechanisms and uses a minimal number of parameters. All the parameters have some theoretical basis or have been measured experimentally and are not directly used to fit the slope of the time-to-failure versus applied field curve. Despite this simplicity, the model is able to accurately predict device lifetime for three different sources of experimental data. The simulation's predictions at low fields and very long lifetimes show that the use of a single empirical model can lead to inaccuracies in device reliability.

  8. Charge transport model to predict intrinsic reliability for dielectric materials

    NASA Astrophysics Data System (ADS)

    Ogden, Sean P.; Borja, Juan; Plawsky, Joel L.; Lu, T.-M.; Yeap, Kong Boon; Gill, William N.

    2015-09-01

    Several lifetime models, mostly empirical in nature, are used to predict reliability for low-k dielectrics used in integrated circuits. There is a dispute over which model provides the most accurate prediction for device lifetime at operating conditions. As a result, there is a need to transition from the use of these largely empirical models to one built entirely on theory. Therefore, a charge transport model was developed to predict the device lifetime of low-k interconnect systems. The model is based on electron transport and donor-type defect formation. Breakdown occurs when a critical defect concentration accumulates, resulting in electron tunneling and the emptying of positively charged traps. The enhanced local electric field lowers the barrier for electron injection into the dielectric, causing a positive feedforward failure. The charge transport model is able to replicate experimental I-V and I-t curves, capturing the current decay at early stress times and the rapid current increase at failure. The model is based on field-driven and current-driven failure mechanisms and uses a minimal number of parameters. All the parameters have some theoretical basis or have been measured experimentally and are not directly used to fit the slope of the time-to-failure versus applied field curve. Despite this simplicity, the model is able to accurately predict device lifetime for three different sources of experimental data. The simulation's predictions at low fields and very long lifetimes show that the use of a single empirical model can lead to inaccuracies in device reliability.

  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. 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. PMID:25502920

  12. Simple and accurate modelling of the gravitational potential produced by thick and thin exponential discs

    NASA Astrophysics Data System (ADS)

    Smith, R.; Flynn, C.; Candlish, G. N.; Fellhauer, M.; Gibson, B. K.

    2015-04-01

    We present accurate models of the gravitational potential produced by a radially exponential disc mass distribution. The models are produced by combining three separate Miyamoto-Nagai discs. Such models have been used previously to model the disc of the Milky Way, but here we extend this framework to allow its application to discs of any mass, scalelength, and a wide range of thickness from infinitely thin to near spherical (ellipticities from 0 to 0.9). The models have the advantage of simplicity of implementation, and we expect faster run speeds over a double exponential disc treatment. The potentials are fully analytical, and differentiable at all points. The mass distribution of our models deviates from the radial mass distribution of a pure exponential disc by <0.4 per cent out to 4 disc scalelengths, and <1.9 per cent out to 10 disc scalelengths. We tabulate fitting parameters which facilitate construction of exponential discs for any scalelength, and a wide range of disc thickness (a user-friendly, web-based interface is also available). Our recipe is well suited for numerical modelling of the tidal effects of a giant disc galaxy on star clusters or dwarf galaxies. We consider three worked examples; the Milky Way thin and thick disc, and a discy dwarf galaxy.

  13. 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.

  14. 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.

  15. Oxygen-Enhanced MRI Accurately Identifies, Quantifies, and Maps Tumor Hypoxia in Preclinical Cancer Models.

    PubMed

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

    2016-02-15

    There is a clinical need for noninvasive 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 noninvasively and is immediately translatable to the clinic.

  16. An accurate parameterization of the infrared radiative properties of cirrus clouds for climate models

    SciTech Connect

    Fu, Q.; Sun, W.B.; Yang, P.

    1998-09-01

    An accurate parameterization is presented for the infrared radiative properties of cirrus clouds. For the single-scattering calculations, a composite scheme is developed for randomly oriented hexagonal ice crystals by comparing results from Mie theory, anomalous diffraction theory (ADT), the geometric optics method (GOM), and the finite-difference time domain technique. This scheme employs a linear combination of single-scattering properties from the Mie theory, ADT, and GOM, which is accurate for a wide range of size parameters. Following the approach of Q. Fu, the extinction coefficient, absorption coefficient, and asymmetry factor are parameterized as functions of the cloud ice water content and generalized effective size (D{sub ge}). The present parameterization of the single-scattering properties of cirrus clouds is validated by examining the bulk radiative properties for a wide range of atmospheric conditions. Compared with reference results, the typical relative error in emissivity due to the parameterization is {approximately}2.2%. The accuracy of this parameterization guarantees its reliability in applications to climate models. The present parameterization complements the scheme for the solar radiative properties of cirrus clouds developed by Q. Fu for use in numerical models.

  17. A Flexible Fringe Projection Vision System with Extended Mathematical Model for Accurate Three-Dimensional Measurement

    PubMed Central

    Xiao, Suzhi; Tao, Wei; Zhao, Hui

    2016-01-01

    In order to acquire an accurate three-dimensional (3D) measurement, the traditional fringe projection technique applies complex and laborious procedures to compensate for the errors that exist in the vision system. However, the error sources in the vision system are very complex, such as lens distortion, lens defocus, and fringe pattern nonsinusoidality. Some errors cannot even be explained or rendered with clear expressions and are difficult to compensate directly as a result. In this paper, an approach is proposed that avoids the complex and laborious compensation procedure for error sources but still promises accurate 3D measurement. It is realized by the mathematical model extension technique. The parameters of the extended mathematical model for the ’phase to 3D coordinates transformation’ are derived using the least-squares parameter estimation algorithm. In addition, a phase-coding method based on a frequency analysis is proposed for the absolute phase map retrieval to spatially isolated objects. The results demonstrate the validity and the accuracy of the proposed flexible fringe projection vision system on spatially continuous and discontinuous objects for 3D measurement. PMID:27136553

  18. 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.

  19. An Accurate Parameterization of the Infrared Radiative Properties of Cirrus Clouds for Climate Models.

    NASA Astrophysics Data System (ADS)

    Fu, Qiang; Yang, Ping; Sun, W. B.

    1998-09-01

    An accurate parameterization is presented for the infrared radiative properties of cirrus clouds. For the single-scattering calculations, a composite scheme is developed for randomly oriented hexagonal ice crystals by comparing results from Mie theory, anomalous diffraction theory (ADT), the geometric optics method (GOM), and the finite-difference time domain technique. This scheme employs a linear combination of single-scattering properties from the Mie theory, ADT, and GOM, which is accurate for a wide range of size parameters. Following the approach of Q. Fu, the extinction coefficient, absorption coefficient, and asymmetry factor are parameterized as functions of the cloud ice water content and generalized effective size (Dge). The present parameterization of the single-scattering properties of cirrus clouds is validated by examining the bulk radiative properties for a wide range of atmospheric conditions. Compared with reference results, the typical relative error in emissivity due to the parameterization is 2.2%. The accuracy of this parameterization guarantees its reliability in applications to climate models. The present parameterization complements the scheme for the solar radiative properties of cirrus clouds developed by Q. Fu for use in numerical models.

  20. A Flexible Fringe Projection Vision System with Extended Mathematical Model for Accurate Three-Dimensional Measurement.

    PubMed

    Xiao, Suzhi; Tao, Wei; Zhao, Hui

    2016-01-01

    In order to acquire an accurate three-dimensional (3D) measurement, the traditional fringe projection technique applies complex and laborious procedures to compensate for the errors that exist in the vision system. However, the error sources in the vision system are very complex, such as lens distortion, lens defocus, and fringe pattern nonsinusoidality. Some errors cannot even be explained or rendered with clear expressions and are difficult to compensate directly as a result. In this paper, an approach is proposed that avoids the complex and laborious compensation procedure for error sources but still promises accurate 3D measurement. It is realized by the mathematical model extension technique. The parameters of the extended mathematical model for the 'phase to 3D coordinates transformation' are derived using the least-squares parameter estimation algorithm. In addition, a phase-coding method based on a frequency analysis is proposed for the absolute phase map retrieval to spatially isolated objects. The results demonstrate the validity and the accuracy of the proposed flexible fringe projection vision system on spatially continuous and discontinuous objects for 3D measurement. PMID:27136553

  1. 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.

  2. 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

  3. 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.

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

    NASA Technical Reports Server (NTRS)

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

    1998-01-01

    Recently, a method has been established to accurately calculate cold-test data for helical slow-wave structures using the three-dimensional (3-D) 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.

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

    NASA Technical Reports Server (NTRS)

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

    1998-01-01

    Recently, a method has been established to accurately calculate cold-test data for helical slow-wave structures using the three-dimensional (3-D) electromagnetic computer code, MAxwell's equations by the Finite Integration Algorithm (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 complete TWT via computer simulation.

  6. Allowable forward model misspecification for accurate basis decomposition in a silicon detector based spectral CT.

    PubMed

    Bornefalk, Hans; Persson, Mats; Danielsson, Mats

    2015-03-01

    Material basis decomposition in the sinogram domain requires accurate knowledge of the forward model in spectral computed tomography (CT). Misspecifications over a certain limit will result in biased estimates and make quantum limited (where statistical noise dominates) quantitative CT difficult. We present a method whereby users can determine the degree of allowed misspecification error in a spectral CT forward model and still have quantification errors that are limited by the inherent statistical uncertainty. For a particular silicon detector based spectral CT system, we conclude that threshold determination is the most critical factor and that the bin edges need to be known to within 0.15 keV in order to be able to perform quantum limited material basis decomposition. The method as such is general to all multibin systems.

  7. 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).

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

    PubMed

    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

  9. 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). PMID:26430979

  10. 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

  11. Are Quasi-Steady-State Approximated Models Suitable for Quantifying Intrinsic Noise Accurately?

    PubMed Central

    Sengupta, Dola; Kar, Sandip

    2015-01-01

    Large gene regulatory networks (GRN) are often modeled with quasi-steady-state approximation (QSSA) to reduce the huge computational time required for intrinsic noise quantification using Gillespie stochastic simulation algorithm (SSA). However, the question still remains whether the stochastic QSSA model measures the intrinsic noise as accurately as the SSA performed for a detailed mechanistic model or not? To address this issue, we have constructed mechanistic and QSSA models for few frequently observed GRNs exhibiting switching behavior and performed stochastic simulations with them. Our results strongly suggest that the performance of a stochastic QSSA model in comparison to SSA performed for a mechanistic model critically relies on the absolute values of the mRNA and protein half-lives involved in the corresponding GRN. The extent of accuracy level achieved by the stochastic QSSA model calculations will depend on the level of bursting frequency generated due to the absolute value of the half-life of either mRNA or protein or for both the species. For the GRNs considered, the stochastic QSSA quantifies the intrinsic noise at the protein level with greater accuracy and for larger combinations of half-life values of mRNA and protein, whereas in case of mRNA the satisfactory accuracy level can only be reached for limited combinations of absolute values of half-lives. Further, we have clearly demonstrated that the abundance levels of mRNA and protein hardly matter for such comparison between QSSA and mechanistic models. Based on our findings, we conclude that QSSA model can be a good choice for evaluating intrinsic noise for other GRNs as well, provided we make a rational choice based on experimental half-life values available in literature. PMID:26327626

  12. 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/.

  13. 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

  14. 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/. PMID:26894674

  15. 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. PMID:27035143

  16. 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

  17. Radionuclide Transport Models Under Ambient Conditions

    SciTech Connect

    G. Moridis; Q. Hu

    2001-12-20

    The purpose of Revision 00 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.

  18. 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.

  19. Advective transport in heterogeneous aquifers: Are proxy models predictive?

    NASA Astrophysics Data System (ADS)

    Fiori, A.; Zarlenga, A.; Gotovac, H.; Jankovic, I.; Volpi, E.; Cvetkovic, V.; Dagan, G.

    2015-12-01

    We examine the prediction capability of two approximate models (Multi-Rate Mass Transfer (MRMT) and Continuous Time Random Walk (CTRW)) of non-Fickian transport, by comparison with accurate 2-D and 3-D numerical simulations. Both nonlocal in time approaches circumvent the need to solve the flow and transport equations by using proxy models to advection, providing the breakthrough curves (BTC) at control planes at any x, depending on a vector of five unknown parameters. Although underlain by different mechanisms, the two models have an identical structure in the Laplace Transform domain and have the Markovian property of independent transitions. We show that also the numerical BTCs enjoy the Markovian property. Following the procedure recommended in the literature, along a practitioner perspective, we first calibrate the parameters values by a best fit with the numerical BTC at a control plane at x1, close to the injection plane, and subsequently use it for prediction at further control planes for a few values of σY2≤8. Due to a similar structure and Markovian property, the two methods perform equally well in matching the numerical BTC. The identified parameters are generally not unique, making their identification somewhat arbitrary. The inverse Gaussian model and the recently developed Multi-Indicator Model (MIM), which does not require any fitting as it relates the BTC to the permeability structure, are also discussed. The application of the proxy models for prediction requires carrying out transport field tests of large plumes for a long duration.

  20. 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

  1. 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

  2. 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).

  3. 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.

  4. Development of a New Model for Accurate Prediction of Cloud Water Deposition on Vegetation

    NASA Astrophysics Data System (ADS)

    Katata, G.; Nagai, H.; Wrzesinsky, T.; Klemm, O.; Eugster, W.; Burkard, R.

    2006-12-01

    Scarcity of water resources in arid and semi-arid areas is of great concern in the light of population growth and food shortages. Several experiments focusing on cloud (fog) water deposition on the land surface suggest that cloud water plays an important role in water resource in such regions. A one-dimensional vegetation model including the process of cloud water deposition on vegetation has been developed to better predict cloud water deposition on the vegetation. New schemes to calculate capture efficiency of leaf, cloud droplet size distribution, and gravitational flux of cloud water were incorporated in the model. Model calculations were compared with the data acquired at the Norway spruce forest at the Waldstein site, Germany. High performance of the model was confirmed by comparisons of calculated net radiation, sensible and latent heat, and cloud water fluxes over the forest with measurements. The present model provided a better prediction of measured turbulent and gravitational fluxes of cloud water over the canopy than the Lovett model, which is a commonly used cloud water deposition model. Detailed calculations of evapotranspiration and of turbulent exchange of heat and water vapor within the canopy and the modifications are necessary for accurate prediction of cloud water deposition. Numerical experiments to examine the dependence of cloud water deposition on the vegetation species (coniferous and broad-leaved trees, flat and cylindrical grasses) and structures (Leaf Area Index (LAI) and canopy height) are performed using the presented model. The results indicate that the differences of leaf shape and size have a large impact on cloud water deposition. Cloud water deposition also varies with the growth of vegetation and seasonal change of LAI. We found that the coniferous trees whose height and LAI are 24 m and 2.0 m2m-2, respectively, produce the largest amount of cloud water deposition in all combinations of vegetation species and structures in the

  5. 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.

  6. 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

  7. 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. PMID:27260782

  8. Do Ecological Niche Models Accurately Identify Climatic Determinants of Species Ranges?

    PubMed

    Searcy, Christopher A; Shaffer, H Bradley

    2016-04-01

    Defining species' niches is central to understanding their distributions and is thus fundamental to basic ecology and climate change projections. Ecological niche models (ENMs) are a key component of making accurate projections and include descriptions of the niche in terms of both response curves and rankings of variable importance. In this study, we evaluate Maxent's ranking of environmental variables based on their importance in delimiting species' range boundaries by asking whether these same variables also govern annual recruitment based on long-term demographic studies. We found that Maxent-based assessments of variable importance in setting range boundaries in the California tiger salamander (Ambystoma californiense; CTS) correlate very well with how important those variables are in governing ongoing recruitment of CTS at the population level. This strong correlation suggests that Maxent's ranking of variable importance captures biologically realistic assessments of factors governing population persistence. However, this result holds only when Maxent models are built using best-practice procedures and variables are ranked based on permutation importance. Our study highlights the need for building high-quality niche models and provides encouraging evidence that when such models are built, they can reflect important aspects of a species' ecology. PMID:27028071

  9. Universal model for accurate calculation of tracer diffusion coefficients in gas, liquid and supercritical systems.

    PubMed

    Lito, Patrícia F; Magalhães, Ana L; Gomes, José R B; Silva, Carlos M

    2013-05-17

    In this work it is presented a new model for accurate calculation of binary diffusivities (D12) of solutes infinitely diluted in gas, liquid and supercritical solvents. It is based on a Lennard-Jones (LJ) model, and contains two parameters: the molecular diameter of the solvent and a diffusion activation energy. The model is universal since it is applicable to polar, weakly polar, and non-polar solutes and/or solvents, over wide ranges of temperature and density. Its validation was accomplished with the largest database ever compiled, namely 487 systems with 8293 points totally, covering polar (180 systems/2335 points) and non-polar or weakly polar (307 systems/5958 points) mixtures, for which the average errors were 2.65% and 2.97%, respectively. With regard to the physical states of the systems, the average deviations achieved were 1.56% for gaseous (73 systems/1036 points), 2.90% for supercritical (173 systems/4398 points), and 2.92% for liquid (241 systems/2859 points). Furthermore, the model exhibited excellent prediction ability. Ten expressions from the literature were adopted for comparison, but provided worse results or were not applicable to polar systems. A spreadsheet for D12 calculation is provided online for users in Supplementary Data.

  10. An accurate and efficient Lagrangian sub-grid model for multi-particle dispersion

    NASA Astrophysics Data System (ADS)

    Toschi, Federico; Mazzitelli, Irene; Lanotte, Alessandra S.

    2014-11-01

    Many natural and industrial processes involve the dispersion of particle in turbulent flows. Despite recent theoretical progresses in the understanding of particle dynamics in simple turbulent flows, complex geometries often call for numerical approaches based on eulerian Large Eddy Simulation (LES). One important issue related to the Lagrangian integration of tracers in under-resolved velocity fields is connected to the lack of spatial correlations at unresolved scales. Here we propose a computationally efficient Lagrangian model for the sub-grid velocity of tracers dispersed in statistically homogeneous and isotropic turbulent flows. The model incorporates the multi-scale nature of turbulent temporal and spatial correlations that are essential to correctly reproduce the dynamics of multi-particle dispersion. The new model is able to describe the Lagrangian temporal and spatial correlations in clouds of particles. In particular we show that pairs and tetrads dispersion compare well with results from Direct Numerical Simulations of statistically isotropic and homogeneous 3d turbulence. This model may offer an accurate and efficient way to describe multi-particle dispersion in under resolved turbulent velocity fields such as the one employed in eulerian LES. This work is part of the research programmes FP112 of the Foundation for Fundamental Research on Matter (FOM), which is part of the Netherlands Organisation for Scientific Research (NWO). We acknowledge support from the EU COST Action MP0806.

  11. 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.

  12. 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.

  13. Accurate calculation of conductive conductances in complex geometries for spacecrafts thermal models

    NASA Astrophysics Data System (ADS)

    Garmendia, Iñaki; Anglada, Eva; Vallejo, Haritz; Seco, Miguel

    2016-02-01

    The thermal subsystem of spacecrafts and payloads is always designed with the help of Thermal Mathematical Models. In the case of the Thermal Lumped Parameter (TLP) method, the non-linear system of equations that is created is solved to calculate the temperature distribution and the heat power that goes between nodes. The accuracy of the results depends largely on the appropriate calculation of the conductive and radiative conductances. Several established methods for the determination of conductive conductances exist but they present some limitations for complex geometries. Two new methods are proposed in this paper to calculate accurately these conductive conductances: The Extended Far Field method and the Mid-Section method. Both are based on a finite element calculation but while the Extended Far Field method uses the calculation of node mean temperatures, the Mid-Section method is based on assuming specific temperature values. They are compared with traditionally used methods showing the advantages of these two new methods.

  14. 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.

  15. A fast and accurate PCA based radiative transfer model: Extension to the broadband shortwave region

    NASA Astrophysics Data System (ADS)

    Kopparla, Pushkar; Natraj, Vijay; Spurr, Robert; Shia, Run-Lie; Crisp, David; Yung, Yuk L.

    2016-04-01

    Accurate radiative transfer (RT) calculations are necessary for many earth-atmosphere applications, from remote sensing retrieval to climate modeling. A Principal Component Analysis (PCA)-based spectral binning method has been shown to provide an order of magnitude increase in computational speed while maintaining an overall accuracy of 0.01% (compared to line-by-line calculations) over narrow spectral bands. In this paper, we have extended the PCA method for RT calculations over the entire shortwave region of the spectrum from 0.3 to 3 microns. The region is divided into 33 spectral fields covering all major gas absorption regimes. We find that the RT performance runtimes are shorter by factors between 10 and 100, while root mean square errors are of order 0.01%.

  16. Accurate calculation of control-augmented structural eigenvalue sensitivities using reduced-order models

    NASA Technical Reports Server (NTRS)

    Livne, Eli

    1989-01-01

    A method is presented for generating mode shapes for model order reduction in a way that leads to accurate calculation of eigenvalue derivatives and eigenvalues for a class of control augmented structures. The method is based on treating degrees of freedom where control forces act or masses are changed in a manner analogous to that used for boundary degrees of freedom in component mode synthesis. It is especially suited for structures controlled by a small number of actuators and/or tuned by a small number of concentrated masses whose positions are predetermined. A control augmented multispan beam with closely spaced natural frequencies is used for numerical experimentation. A comparison with reduced-order eigenvalue sensitivity calculations based on the normal modes of the structure shows that the method presented produces significant improvements in accuracy.

  17. 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.

  18. Parallel kinetic Monte Carlo simulation framework incorporating accurate models of adsorbate lateral interactions

    NASA Astrophysics Data System (ADS)

    Nielsen, Jens; d'Avezac, Mayeul; Hetherington, James; Stamatakis, Michail

    2013-12-01

    Ab initio kinetic Monte Carlo (KMC) simulations have been successfully applied for over two decades to elucidate the underlying physico-chemical phenomena on the surfaces of heterogeneous catalysts. These simulations necessitate detailed knowledge of the kinetics of elementary reactions constituting the reaction mechanism, and the energetics of the species participating in the chemistry. The information about the energetics is encoded in the formation energies of gas and surface-bound species, and the lateral interactions between adsorbates on the catalytic surface, which can be modeled at different levels of detail. The majority of previous works accounted for only pairwise-additive first nearest-neighbor interactions. More recently, cluster-expansion Hamiltonians incorporating long-range interactions and many-body terms have been used for detailed estimations of catalytic rate [C. Wu, D. J. Schmidt, C. Wolverton, and W. F. Schneider, J. Catal. 286, 88 (2012)]. In view of the increasing interest in accurate predictions of catalytic performance, there is a need for general-purpose KMC approaches incorporating detailed cluster expansion models for the adlayer energetics. We have addressed this need by building on the previously introduced graph-theoretical KMC framework, and we have developed Zacros, a FORTRAN2003 KMC package for simulating catalytic chemistries. To tackle the high computational cost in the presence of long-range interactions we introduce parallelization with OpenMP. We further benchmark our framework by simulating a KMC analogue of the NO oxidation system established by Schneider and co-workers [J. Catal. 286, 88 (2012)]. We show that taking into account only first nearest-neighbor interactions may lead to large errors in the prediction of the catalytic rate, whereas for accurate estimates thereof, one needs to include long-range terms in the cluster expansion.

  19. The S-model: A highly accurate MOST model for CAD

    NASA Astrophysics Data System (ADS)

    Satter, J. H.

    1986-09-01

    A new MOST model which combines simplicity and a logical structure with a high accuracy of only 0.5-4.5% is presented. The model is suited for enhancement and depletion devices with either large or small dimensions. It includes the effects of scattering and carrier-velocity saturation as well as the influence of the intrinsic source and drain series resistance. The decrease of the drain current due to substrate bias is incorporated too. The model is in the first place intended for digital purposes. All necessary quantities are calculated in a straightforward manner without iteration. An almost entirely new way of determining the parameters is described and a new cluster parameter is introduced, which is responsible for the high accuracy of the model. The total number of parameters is 7. A still simpler β expression is derived, which is suitable for only one value of the substrate bias and contains only three parameters, while maintaining the accuracy. The way in which the parameters are determined is readily suited for automatic measurement. A simple linear regression procedure programmed in the computer, which controls the measurements, produces the parameter values.

  20. 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

  1. Accurate characterization of delay discounting: a multiple model approach using approximate Bayesian model selection and a unified discounting measure.

    PubMed

    Franck, Christopher T; Koffarnus, Mikhail N; House, Leanna L; Bickel, Warren K

    2015-01-01

    The study of delay discounting, or valuation of future rewards as a function of delay, has contributed to understanding the behavioral economics of addiction. Accurate characterization of discounting can be furthered by statistical model selection given that many functions have been proposed to measure future valuation of rewards. The present study provides a convenient Bayesian model selection algorithm that selects the most probable discounting model among a set of candidate models chosen by the researcher. The approach assigns the most probable model for each individual subject. Importantly, effective delay 50 (ED50) functions as a suitable unifying measure that is computable for and comparable between a number of popular functions, including both one- and two-parameter models. The combined model selection/ED50 approach is illustrated using empirical discounting data collected from a sample of 111 undergraduate students with models proposed by Laibson (1997); Mazur (1987); Myerson & Green (1995); Rachlin (2006); and Samuelson (1937). Computer simulation suggests that the proposed Bayesian model selection approach outperforms the single model approach when data truly arise from multiple models. When a single model underlies all participant data, the simulation suggests that the proposed approach fares no worse than the single model approach.

  2. 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.

  3. 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

  4. Kinetic Relaxation Models for Energy Transport

    NASA Astrophysics Data System (ADS)

    Aoki, Kazuo; Markowich, Peter; Takata, Shigeru

    2007-04-01

    Kinetic equations with relaxation collision kernels are considered under the basic assumption of two collision invariants, namely mass and energy. The collision kernels are of BGK-type with a general local Gibbs state, which may be quite different from the Gaussian. By the use of the diffusive length/time scales, energy transport systems consisting of two parabolic equations with the position density and the energy density as unknowns are derived on a formal level. The H theorem for the kinetic model is presented, and the entropy for the energy transport systems, which is inherited from the kinetic model, is derived. The energy transport systems for specific examples of the global Gibbs state, such as a power law with negative exponent, a cut-off power law with positive exponent, the Maxwellian, Bose-Einstein, and Fermi-Dirac distributions, arepresented.

  5. 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.

  6. Linear transport models for adsorbing solutes

    NASA Astrophysics Data System (ADS)

    Roth, K.; Jury, W. A.

    1993-04-01

    A unified linear theory for the transport of adsorbing solutes through soils is presented and applied to analyze movement of napropamide through undisturbed soil columns. The transport characteristics of the soil are expressed in terms of the travel time distribution of the mobile phase which is then used to incorporate local interaction processes. This approach permits the analysis of all linear transport processes, not only the small subset for which a differential description is known. From a practical point of view, it allows the direct use of measured concentrations or fluxes of conservative solutes to characterize the mobile phase without first subjecting them to any model. For complicated flow regimes, this may vastly improve the identification of models and estimation of their parameters for the local adsorption processes.

  7. 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.

  8. Global climate modeling of Saturn's atmosphere: fast and accurate radiative transfer and exploration of seasonal variability

    NASA Astrophysics Data System (ADS)

    Guerlet, Sandrine; Spiga, A.; Sylvestre, M.; Fouchet, T.; Millour, E.; Wordsworth, R.; Leconte, J.; Forget, F.

    2013-10-01

    Recent observations of Saturn’s stratospheric thermal structure and composition revealed new phenomena: an equatorial oscillation in temperature, reminiscent of the Earth's Quasi-Biennal Oscillation ; strong meridional contrasts of hydrocarbons ; a warm “beacon” associated with the powerful 2010 storm. Those signatures cannot be reproduced by 1D photochemical and radiative models and suggest that atmospheric dynamics plays a key role. This motivated us to develop a complete 3D General Circulation Model (GCM) for Saturn, based on the LMDz hydrodynamical core, to explore the circulation, seasonal variability, and wave activity in Saturn's atmosphere. In order to closely reproduce Saturn's radiative forcing, a particular emphasis was put in obtaining fast and accurate radiative transfer calculations. Our radiative model uses correlated-k distributions and spectral discretization tailored for Saturn's atmosphere. We include internal heat flux, ring shadowing and aerosols. We will report on the sensitivity of the model to spectral discretization, spectroscopic databases, and aerosol scenarios (varying particle sizes, opacities and vertical structures). We will also discuss the radiative effect of the ring shadowing on Saturn's atmosphere. We will present a comparison of temperature fields obtained with this new radiative equilibrium model to that inferred from Cassini/CIRS observations. In the troposphere, our model reproduces the observed temperature knee caused by heating at the top of the tropospheric aerosol layer. In the lower stratosphere (20mbar modeled temperature is 5-10K too low compared to measurements. This suggests that processes other than radiative heating/cooling by trace

  9. 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

  10. An Approach to More Accurate Model Systems for Purple Acid Phosphatases (PAPs).

    PubMed

    Bernhardt, Paul V; Bosch, Simone; Comba, Peter; Gahan, Lawrence R; Hanson, Graeme R; Mereacre, Valeriu; Noble, Christopher J; Powell, Annie K; Schenk, Gerhard; Wadepohl, Hubert

    2015-08-01

    The active site of mammalian purple acid phosphatases (PAPs) have a dinuclear iron site in two accessible oxidation states (Fe(III)2 and Fe(III)Fe(II)), and the heterovalent is the active form, involved in the regulation of phosphate and phosphorylated metabolite levels in a wide range of organisms. Therefore, two sites with different coordination geometries to stabilize the heterovalent active form and, in addition, with hydrogen bond donors to enable the fixation of the substrate and release of the product, are believed to be required for catalytically competent model systems. Two ligands and their dinuclear iron complexes have been studied in detail. The solid-state structures and properties, studied by X-ray crystallography, magnetism, and Mössbauer spectroscopy, and the solution structural and electronic properties, investigated by mass spectrometry, electronic, nuclear magnetic resonance (NMR), electron paramagnetic resonance (EPR), and Mössbauer spectroscopies and electrochemistry, are discussed in detail in order to understand the structures and relative stabilities in solution. In particular, with one of the ligands, a heterovalent Fe(III)Fe(II) species has been produced by chemical oxidation of the Fe(II)2 precursor. The phosphatase reactivities of the complexes, in particular, also of the heterovalent complex, are reported. These studies include pH-dependent as well as substrate concentration dependent studies, leading to pH profiles, catalytic efficiencies and turnover numbers, and indicate that the heterovalent diiron complex discussed here is an accurate PAP model system. PMID:26196255

  11. Accurate assessment of mass, models and resolution by small-angle scattering

    PubMed Central

    Rambo, Robert P.; Tainer, John A.

    2013-01-01

    Modern small angle scattering (SAS) experiments with X-rays or neutrons provide a comprehensive, resolution-limited observation of the thermodynamic state. However, methods for evaluating mass and validating SAS based models and resolution have been inadequate. Here, we define the volume-of-correlation, Vc: a SAS invariant derived from the scattered intensities that is specific to the structural state of the particle, yet independent of concentration and the requirements of a compact, folded particle. We show Vc defines a ratio, Qr, that determines the molecular mass of proteins or RNA ranging from 10 to 1,000 kDa. Furthermore, we propose a statistically robust method for assessing model-data agreements (X2free) akin to cross-validation. Our approach prevents over-fitting of the SAS data and can be used with a newly defined metric, Rsas, for quantitative evaluation of resolution. Together, these metrics (Vc, Qr, X2free, and Rsas) provide analytical tools for unbiased and accurate macromolecular structural characterizations in solution. PMID:23619693

  12. 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. PMID:25562394

  13. 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

  14. Accurate Universal Models for the Mass Accretion Histories and Concentrations of Dark Matter Halos

    NASA Astrophysics Data System (ADS)

    Zhao, D. H.; Jing, Y. P.; Mo, H. J.; Börner, G.

    2009-12-01

    A large amount of observations have constrained cosmological parameters and the initial density fluctuation spectrum to a very high accuracy. However, cosmological parameters change with time and the power index of the power spectrum dramatically varies with mass scale in the so-called concordance ΛCDM cosmology. Thus, any successful model for its structural evolution should work well simultaneously for various cosmological models and different power spectra. We use a large set of high-resolution N-body simulations of a variety of structure formation models (scale-free, standard CDM, open CDM, and ΛCDM) to study the mass accretion histories, the mass and redshift dependence of concentrations, and the concentration evolution histories of dark matter halos. We find that there is significant disagreement between the much-used empirical models in the literature and our simulations. Based on our simulation results, we find that the mass accretion rate of a halo is tightly correlated with a simple function of its mass, the redshift, parameters of the cosmology, and of the initial density fluctuation spectrum, which correctly disentangles the effects of all these factors and halo environments. We also find that the concentration of a halo is strongly correlated with the universe age when its progenitor on the mass accretion history first reaches 4% of its current mass. According to these correlations, we develop new empirical models for both the mass accretion histories and the concentration evolution histories of dark matter halos, and the latter can also be used to predict the mass and redshift dependence of halo concentrations. These models are accurate and universal: the same set of model parameters works well for different cosmological models and for halos of different masses at different redshifts, and in the ΛCDM case the model predictions match the simulation results very well even though halo mass is traced to about 0.0005 times the final mass, when

  15. ACCURATE UNIVERSAL MODELS FOR THE MASS ACCRETION HISTORIES AND CONCENTRATIONS OF DARK MATTER HALOS

    SciTech Connect

    Zhao, D. H.; Jing, Y. P.; Mo, H. J.; Boerner, G.

    2009-12-10

    A large amount of observations have constrained cosmological parameters and the initial density fluctuation spectrum to a very high accuracy. However, cosmological parameters change with time and the power index of the power spectrum dramatically varies with mass scale in the so-called concordance LAMBDACDM cosmology. Thus, any successful model for its structural evolution should work well simultaneously for various cosmological models and different power spectra. We use a large set of high-resolution N-body simulations of a variety of structure formation models (scale-free, standard CDM, open CDM, and LAMBDACDM) to study the mass accretion histories, the mass and redshift dependence of concentrations, and the concentration evolution histories of dark matter halos. We find that there is significant disagreement between the much-used empirical models in the literature and our simulations. Based on our simulation results, we find that the mass accretion rate of a halo is tightly correlated with a simple function of its mass, the redshift, parameters of the cosmology, and of the initial density fluctuation spectrum, which correctly disentangles the effects of all these factors and halo environments. We also find that the concentration of a halo is strongly correlated with the universe age when its progenitor on the mass accretion history first reaches 4% of its current mass. According to these correlations, we develop new empirical models for both the mass accretion histories and the concentration evolution histories of dark matter halos, and the latter can also be used to predict the mass and redshift dependence of halo concentrations. These models are accurate and universal: the same set of model parameters works well for different cosmological models and for halos of different masses at different redshifts, and in the LAMBDACDM case the model predictions match the simulation results very well even though halo mass is traced to about 0.0005 times the final mass

  16. Cumulus parameterizations in chemical transport models

    NASA Astrophysics Data System (ADS)

    Mahowald, Natalie M.; Rasch, Philip J.; Prinn, Ronald G.

    1995-12-01

    Global three-dimensional chemical transport models (CTMs) are valuable tools for studying processes controlling the distribution of trace constituents in the atmosphere. A major uncertainty in these models is the subgrid-scale parametrization of transport by cumulus convection. This study seeks to define the range of behavior of moist convective schemes and point toward more reliable formulations for inclusion in chemical transport models. The emphasis is on deriving convective transport from meteorological data sets (such as those from the forecast centers) which do not routinely include convective mass fluxes. Seven moist convective parameterizations are compared in a column model to examine the sensitivity of the vertical profile of trace gases to the parameterization used in a global chemical transport model. The moist convective schemes examined are the Emanuel scheme [Emanuel, 1991], the Feichter-Crutzen scheme [Feichter and Crutzen, 1990], the inverse thermodynamic scheme (described in this paper), two versions of a scheme suggested by Hack [Hack, 1994], and two versions of a scheme suggested by Tiedtke (one following the formulation used in the ECMWF (European Centre for Medium-Range Weather Forecasting) and ECHAM3 (European Centre and Hamburg Max-Planck-Institut) models [Tiedtke, 1989], and one formulated as in the TM2 (Transport Model-2) model (M. Heimann, personal communication, 1992). These convective schemes vary in the closure used to derive the mass fluxes, as well as the cloud model formulation, giving a broad range of results. In addition, two boundary layer schemes are compared: a state-of-the-art nonlocal boundary layer scheme [Holtslag and Boville, 1993] and a simple adiabatic mixing scheme described in this paper. Three tests are used to compare the moist convective schemes against observations. Although the tests conducted here cannot conclusively show that one parameterization is better than the others, the tests are a good measure of the

  17. 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.

  18. 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.

  19. 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

  20. 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

  1. 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.

  2. 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.

  3. 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.

  4. Application of automatic differentiation to groundwater transport models

    SciTech Connect

    Bischof, C.H.; Ross, A.A.; Whiffen, G.J.; Shoemaker, C.A.; Carle, A.

    1994-06-01

    Automatic differentiation (AD) is a technique for generating efficient and reliable derivative codes from computer programs with a minimum of human effort. Derivatives of model output with respect to input are obtained exactly. No intrinsic limits to program length or complexity exist for this procedure. Calculation of derivatives of complex numerical models is required in systems optimization, parameter identification, and systems identification. We report on our experiences with the ADIFOR (Automatic Differentiation of Fortran) tool on a two-dimensional groundwater flow and contaminant transport finite-element model, ISOQUAD, and a three-dimensional contaminant transport finite-element model, TLS3D. Derivative values and computational times for the automatic differentiation procedure axe compared with values obtained from the divided differences and handwritten analytic approaches. We found that the derivative codes generated by ADIFOR provided accurate derivatives and ran significantly faster than divided-differences approximations, typically in a tenth of the CPU time required for the imprecise divided-differences method for both codes. We also comment on the impact of automatic differentiation technology with respect to accelerating the transfer of general techniques developed for using water resource computer models, such as optimal design, sensitivity analysis, and inverse modeling problems to field problems.

  5. 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.

  6. Public transport networks: empirical analysis and modeling

    NASA Astrophysics Data System (ADS)

    von Ferber, C.; Holovatch, T.; Holovatch, Yu.; Palchykov, V.

    2009-03-01

    Public transport networks of fourteen cities of so far unexplored network size are analyzed in standardized graph representations: the simple graph of the network map, the bipartite graph of routes and stations, and both one mode projections of the latter. Special attention is paid to the inter-relations and spatial embedding of transport routes. This systematic approach reveals rich behavior beyond that of the ubiquitous scale-free complex network. We find strong evidence for structures in PTNs that are counter-intuitive and need to be explained, among these a pronounced diversity in the expression of typical network characteristics within the present sample of cities, a surprising geometrical behavior with respect to the two-dimensional geographical embedding and an unexpected attraction between transport routes. A simple model based on these observations reproduces many of the identified PTN properties by growing networks of attractive self-avoiding walks.

  7. Fire and materials modeling for transportation systems

    SciTech Connect

    Skocypec, R.D.; Gritzo, L.A.; Moya, J.L.; Nicolette, V.F.; Tieszen, S.R.; Thomas, R.

    1994-10-01

    Fire is an important threat to the safety of transportation systems. Therefore, understanding the effects of fire (and its interaction with materials) on transportation systems is crucial to quantifying and mitigating the impact of fire on the safety of those systems. Research and development directed toward improving the fire safety of transportation systems must address a broad range of phenomena and technologies, including: crash dynamics, fuel dispersion, fire environment characterization, material characterization, and system/cargo thermal response modeling. In addition, if the goal of the work is an assessment and/or reduction of risk due to fires, probabilistic risk assessment technology is also required. The research currently underway at Sandia National Laboratories in each of these areas is summarized in this paper.

  8. 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.

  9. Modeling human nonalcoholic steatohepatitis-associated changes in drug transporter expression using experimental rodent models.

    PubMed

    Canet, Mark J; Hardwick, Rhiannon N; Lake, April D; Dzierlenga, Anika L; Clarke, John D; Cherrington, Nathan J

    2014-04-01

    Nonalcoholic fatty liver disease is a prevalent form of chronic liver disease that can progress to the more advanced stage of nonalcoholic steatohepatitis (NASH). NASH has been shown to alter drug transporter regulation and may have implications in the development of adverse drug reactions. Several experimental rodent models have been proposed for the study of NASH, but no single model fully recapitulates all aspects of the human disease. The purpose of the current study was to determine which experimental NASH model best reflects the known alterations in human drug transporter expression to enable more accurate drug disposition predictions in NASH. Both rat and mouse NASH models were used in this investigation and include the methionine and choline deficient (MCD) diet model, atherogenic diet model, ob/ob and db/db mice, and fa/fa rats. Pathologic scoring evaluations demonstrated that MCD and atherogenic rats, as well as ob/ob and db/db mice, developed NASH. Liver mRNA and protein expression analyses of drug transporters showed that in general, efflux transporters were induced and uptake transporters were repressed in the rat MCD and the mouse ob/ob and db/db models. Lastly, concordance analyses suggest that both the mouse and rat MCD models as well as mouse ob/ob and db/db NASH models show the most similarity to human transporter mRNA and protein expression. These results suggest that the MCD rat and mouse model, as well as the ob/ob and db/db mouse models, may be useful for predicting altered disposition of drugs with similar kinetics across humans and rodents.

  10. 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.

  11. 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

  12. 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.

  13. Stable, accurate and efficient computation of normal modes for horizontal stratified models

    NASA Astrophysics Data System (ADS)

    Wu, Bo; Chen, Xiaofei

    2016-06-01

    We propose an adaptive root-determining strategy that is very useful when dealing with trapped modes or Stoneley modes whose energies become very insignificant on the free surface in the presence of low-velocity layers or fluid layers in the model. Loss of modes in these cases or inaccuracy in the calculation of these modes may then be easily avoided. Built upon the generalized reflection/transmission coefficients, the concept of "family of secular functions" that we herein call "adaptive mode observers", is thus naturally introduced to implement this strategy, the underlying idea of which has been distinctly noted for the first time and may be generalized to other applications such as free oscillations or applied to other methods in use when these cases are encountered. Additionally, we have made further improvements upon the generalized reflection/transmission coefficient method; mode observers associated with only the free surface and low-velocity layers (and the fluid/solid interface if the model contains fluid layers) are adequate to guarantee no loss and high precision at the same time of any physically existent modes without excessive calculations. Finally, the conventional definition of the fundamental mode is reconsidered, which is entailed in the cases under study. Some computational aspects are remarked on. With the additional help afforded by our superior root-searching scheme and the possibility of speeding calculation using a less number of layers aided by the concept of "turning point", our algorithm is remarkably efficient as well as stable and accurate and can be used as a powerful tool for widely related applications.

  14. Stable, accurate and efficient computation of normal modes for horizontal stratified models

    NASA Astrophysics Data System (ADS)

    Wu, Bo; Chen, Xiaofei

    2016-08-01

    We propose an adaptive root-determining strategy that is very useful when dealing with trapped modes or Stoneley modes whose energies become very insignificant on the free surface in the presence of low-velocity layers or fluid layers in the model. Loss of modes in these cases or inaccuracy in the calculation of these modes may then be easily avoided. Built upon the generalized reflection/transmission coefficients, the concept of `family of secular functions' that we herein call `adaptive mode observers' is thus naturally introduced to implement this strategy, the underlying idea of which has been distinctly noted for the first time and may be generalized to other applications such as free oscillations or applied to other methods in use when these cases are encountered. Additionally, we have made further improvements upon the generalized reflection/transmission coefficient method; mode observers associated with only the free surface and low-velocity layers (and the fluid/solid interface if the model contains fluid layers) are adequate to guarantee no loss and high precision at the same time of any physically existent modes without excessive calculations. Finally, the conventional definition of the fundamental mode is reconsidered, which is entailed in the cases under study. Some computational aspects are remarked on. With the additional help afforded by our superior root-searching scheme and the possibility of speeding calculation using a less number of layers aided by the concept of `turning point', our algorithm is remarkably efficient as well as stable and accurate and can be used as a powerful tool for widely related applications.

  15. Precise and accurate assessment of uncertainties in model parameters from stellar interferometry. Application to stellar diameters

    NASA Astrophysics Data System (ADS)

    Lachaume, Regis; Rabus, Markus; Jordan, Andres

    2015-08-01

    In stellar interferometry, the assumption that the observables can be seen as Gaussian, independent variables is the norm. In particular, neither the optical interferometry FITS (OIFITS) format nor the most popular fitting software in the field, LITpro, offer means to specify a covariance matrix or non-Gaussian uncertainties. Interferometric observables are correlated by construct, though. Also, the calibration by an instrumental transfer function ensures that the resulting observables are not Gaussian, even if uncalibrated ones happened to be so.While analytic frameworks have been published in the past, they are cumbersome and there is no generic implementation available. We propose here a relatively simple way of dealing with correlated errors without the need to extend the OIFITS specification or making some Gaussian assumptions. By repeatedly picking at random which interferograms, which calibrator stars, and which are the errors on their diameters, and performing the data processing on the bootstrapped data, we derive a sampling of p(O), the multivariate probability density function (PDF) of the observables O. The results can be stored in a normal OIFITS file. Then, given a model m with parameters P predicting observables O = m(P), we can estimate the PDF of the model parameters f(P) = p(m(P)) by using a density estimation of the observables' PDF p.With observations repeated over different baselines, on nights several days apart, and with a significant set of calibrators systematic errors are de facto taken into account. We apply the technique to a precise and accurate assessment of stellar diameters obtained at the Very Large Telescope Interferometer with PIONIER.

  16. 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.

  17. 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

  18. Using transportation demand models to assess regional noise exposure

    NASA Astrophysics Data System (ADS)

    Kaliski, Kenneth

    2005-09-01

    In the United States, most metropolitan areas run some type of transportation demand model to estimate regional travel patterns, and, to some extent, air pollution. The more advanced of these models accurately represent the geographic contours of the roadways (in contrast to the older straight-line node and link models). This allows an almost seamless integration of these new transportation demand models into noise prediction models. Combined with the locations of individual homes from a separate E911 database, we can readily make estimates of the noise exposure of populations over large areas. In this paper, the regional traffic noise exposure of residences of Chittenden County, VT is estimated and mapped. It was found that 30% of the residences are exposed to noise levels exceeding the WHO sleep disturbance level of 45 dB LAeq(8) and 20% of residences are exposed to levels exceeding the WHO ``serious annoyance'' level of 55 dB LAeq(16). Maps show noise contours as well as individual homes color coded based on relative day and night noise exposure levels. Measured sound level data are given for particular locations to validate the predictions.

  19. 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. PMID:25965016

  20. 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.

  1. Towards accurate kinetic modeling of prompt NO formation in hydrocarbon flames via the NCN pathway

    SciTech Connect

    Sutton, Jeffrey A.; Fleming, James W.

    2008-08-15

    A basic kinetic mechanism that can predict the appropriate prompt-NO precursor NCN, as shown by experiment, with relative accuracy while still producing postflame NO results that can be calculated as accurately as or more accurately than through the former HCN pathway is presented for the first time. The basic NCN submechanism should be a starting point for future NCN kinetic and prompt NO formation refinement.

  2. 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

  3. Resistive Plate Chambers: electron transport and modeling

    NASA Astrophysics Data System (ADS)

    Bošnjaković, D.; Petrović, Z. Lj; Dujko, S.

    2014-12-01

    We study the electron transport in gas mixtures used by Resistive Plate Chambers (RPCs) in high energy physics experiments at CERN. Calculations are performed using a multi term theory for solving the Boltzmann equation. We identify the effects induced by non-conservative nature of electron attachment, including attachment heating of electrons and negative differential conductivity (NDC). NDC was observed only in the bulk component of drift velocity. Using our Monte Carlo technique, we calculate the spatially resolved transport properties in order to investigate the origin of these effects. We also present our microscopic approach to modeling of RPCs which is based on Monte Carlo method. Calculated results for a timing RPC show good agreement with an analytical model and experimental data. Different cross section sets for electron scattering in C2H2F4 are used for comparison and analysis.

  4. 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

  5. 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.

  6. 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

  7. Abstracts of the symposium on unsaturated flow and transport modeling

    SciTech Connect

    Not Available

    1982-03-01

    Abstract titles are: Recent developments in modeling variably saturated flow and transport; Unsaturated flow modeling as applied to field problems; Coupled heat and moisture transport in unsaturated soils; Influence of climatic parameters on movement of radionuclides in a multilayered saturated-unsaturated media; Modeling water and solute transport in soil containing roots; Simulation of consolidation in partially saturated soil materials; modeling of water and solute transport in unsaturated heterogeneous fields; Fluid dynamics and mass transfer in variably-saturated porous media; Solute transport through soils; One-dimensional analytical transport modeling; Convective transport of ideal tracers in unsaturated soils; Chemical transport in macropore-mesopore media under partially saturated conditions; Influence of the tension-saturated zone on contaminant migration in shallow water regimes; Influence of the spatial distribution of velocities in porous media on the form of solute transport; Stochastic vs deterministic models for solute movement in the field; and Stochastic analysis of flow and solute transport. (DMC)

  8. A velocity-dependent anomalous radial transport model for (2-D, 2-V) kinetic transport codes

    NASA Astrophysics Data System (ADS)

    Bodi, Kowsik; Krasheninnikov, Sergei; Cohen, Ron; Rognlien, Tom

    2008-11-01

    Plasma turbulence constitutes a significant part of radial plasma transport in magnetically confined plasmas. This turbulent transport is modeled in the form of anomalous convection and diffusion coefficients in fluid transport codes. There is a need to model the same in continuum kinetic edge codes [such as the (2-D, 2-V) transport version of TEMPEST, NEO, and the code being developed by the Edge Simulation Laboratory] with non-Maxwellian distributions. We present an anomalous transport model with velocity-dependent convection and diffusion coefficients leading to a diagonal transport matrix similar to that used in contemporary fluid transport models (e.g., UEDGE). Also presented are results of simulations corresponding to radial transport due to long-wavelength ExB turbulence using a velocity-independent diffusion coefficient. A BGK collision model is used to enable comparison with fluid transport codes.

  9. Discrete element modelling of bedload transport

    NASA Astrophysics Data System (ADS)

    Loyer, A.; Frey, P.

    2011-12-01

    Discrete element modelling (DEM) has been widely used in solid mechanics and in granular physics. In this type of modelling, each individual particle is taken into account and intergranular interactions are modelled with simple laws (e.g. Coulomb friction). Gravity and contact forces permit to solve the dynamical behaviour of the system. DEM is interesting to model configurations and access to parameters not directly available in laboratory experimentation, hence the term "numerical experimentations" sometimes used to describe DEM. DEM was used to model bedload transport experiments performed at the particle scale with spherical glass beads in a steep and narrow flume. Bedload is the larger material that is transported on the bed on stream channels. It has a great geomorphic impact. Physical processes ruling bedload transport and more generally coarse-particle/fluid systems are poorly known, arguably because granular interactions have been somewhat neglected. An existing DEM code (PFC3D) already computing granular interactions was used. We implemented basic hydrodynamic forces to model the fluid interactions (buoyancy, drag, lift). The idea was to use the minimum number of ingredients to match the experimental results. Experiments were performed with one-size and two-size mixtures of coarse spherical glass beads entrained by a shallow turbulent and supercritical water flow down a steep channel with a mobile bed. The particle diameters were 4 and 6mm, the channel width 6.5mm (about the same width as the coarser particles) and the channel inclination was typically 10%. The water flow rate and the particle rate were kept constant at the upstream entrance and adjusted to obtain bedload transport equilibrium. Flows were filmed from the side by a high-speed camera. Using image processing algorithms made it possible to determine the position, velocity and trajectory of both smaller and coarser particles. Modelled and experimental particle velocity and concentration depth

  10. 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...

  11. 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...

  12. 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.

  13. 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.

  14. 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.

  15. 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

  16. 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.

  17. 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.

  18. Modeling charge transport in organic photovoltaic materials.

    PubMed

    Nelson, Jenny; Kwiatkowski, Joe J; Kirkpatrick, James; Frost, Jarvist M

    2009-11-17

    The performance of an organic photovoltaic cell depends critically on the mobility of charge carriers within the constituent molecular semiconductor materials. However, a complex combination of phenomena that span a range of length and time scales control charge transport in disordered organic semiconductors. As a result, it is difficult to rationalize charge transport properties in terms of material parameters. Until now, efforts to improve charge mobilities in molecular semiconductors have proceeded largely by trial and error rather than through systematic design. However, recent developments have enabled the first predictive simulation studies of charge transport in disordered organic semiconductors. This Account describes a set of computational methods, specifically molecular modeling methods, to simulate molecular packing, quantum chemical calculations of charge transfer rates, and Monte Carlo simulations of charge transport. Using case studies, we show how this combination of methods can reproduce experimental mobilities with few or no fitting parameters. Although currently applied to material systems of high symmetry or well-defined structure, further developments of this approach could address more complex systems such anisotropic or multicomponent solids and conjugated polymers. Even with an approximate treatment of packing disorder, these computational methods simulate experimental mobilities within an order of magnitude at high electric fields. We can both reproduce the relative values of electron and hole mobility in a conjugated small molecule and rationalize those values based on the symmetry of frontier orbitals. Using fully atomistic molecular dynamics simulations of molecular packing, we can quantitatively replicate vertical charge transport along stacks of discotic liquid crystals which vary only in the structure of their side chains. We can reproduce the trends in mobility with molecular weight for self-organizing polymers using a cheap, coarse

  19. 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

  20. 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.

  1. 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.

  2. 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.

  3. 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.

  4. Reactive transport modeling of Li isotope fractionation

    NASA Astrophysics Data System (ADS)

    Wanner, C.; Sonnenthal, E. L.

    2013-12-01

    The fractionation of Li isotopes has been used as a proxy for interaction processes between silicate rocks and any kind of fluids. In particular, Li isotope measurements are powerful because Li is almost exclusively found in silicate minerals. Moreover, the two stable Li isotopes, 6Li and 7Li, differ by 17% in mass introducing a large mass dependent isotope fractionation even at high temperature. Typical applications include Li isotope measurements along soil profiles and of river waters to track silicate weathering patterns and Li isotope measurements of geothermal wells and springs to assess water-rock interaction processes in geothermal systems. For this contribution we present a novel reactive transport modeling approach for the simulation of Li isotope fractionation using the code TOUGHREACT [1]. It is based on a 6Li-7Li solid solution approach similar to the one recently described for simulating Cr isotope fractionation [2]. Model applications include the simulation of granite weathering along a 1D flow path as well as the simulation of a column experiment related to an enhanced geothermal system. Results show that measured δ7Li values are mainly controlled by (i) the degree of interaction between Li bearing primary silicate mineral phases (e.g., micas, feldspars) and the corresponding fluid, (ii) the Li isotope fractionation factor during precipitation of secondary mineral phases (e.g., clays), (iii) the Li concentration in primary and secondary Li bearing mineral phases and (iv) the proportion of dissolved Li that adsorbs to negatively charged surfaces (e.g., clays, Fe/Al-hydroxides). To date, most of these parameters are not very well constrained. Reactive transport modeling thus currently has to rely on many assumptions. Nevertheless, such models are powerful because they are the only viable option if individual contributions of all potential processes on the resulting (i.e., measured) Li isotopic ratio have to be quantitatively assessed. Accordingly, we

  5. Flow characteristics in a crowded transport model

    NASA Astrophysics Data System (ADS)

    Burger, Martin; Pietschmann, Jan-Frederik

    2016-11-01

    The aim of this paper is to discuss the appropriate modelling of in- and outflow boundary conditions for nonlinear drift-diffusion models for the transport of particles including size exclusion and their effect on the behaviour of solutions. We use a derivation from a microscopic asymmetric exclusion process and its extension to particles entering or leaving on the boundaries. This leads to specific Robin-type boundary conditions for inflow and outflow, respectively. For the stationary equation we prove the existence of solutions in a suitable set-up. Moreover, we investigate the flow characteristics for a small diffusion parameter \\varepsilon , which yields the occurrence of a maximal current phase in addition to well-known one-sided boundary layer effects for linear drift-diffusion problems. In a 1D set-up we provide rigorous estimates in terms of ε, which confirm three different phases. Finally, we derive a numerical approach to solve the problem also in multiple dimensions.

  6. 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.

  7. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2015-12-01

    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, UV(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 UV, 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 UV 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.

  9. Fast algorithms for transport models. Final report

    SciTech Connect

    Manteuffel, T.A.

    1994-10-01

    This project has developed a multigrid in space algorithm for the solution of the S{sub N} equations with isotropic scattering in slab geometry. The algorithm was developed for the Modified Linear Discontinuous (MLD) discretization in space which is accurate in the thick diffusion limit. It uses a red/black two-cell {mu}-line relaxation. This relaxation solves for all angles on two adjacent spatial cells simultaneously. It takes advantage of the rank-one property of the coupling between angles and can perform this inversion in O(N) operations. A version of the multigrid in space algorithm was programmed on the Thinking Machines Inc. CM-200 located at LANL. It was discovered that on the CM-200 a block Jacobi type iteration was more efficient than the block red/black iteration. Given sufficient processors all two-cell block inversions can be carried out simultaneously with a small number of parallel steps. The bottleneck is the need for sums of N values, where N is the number of discrete angles, each from a different processor. These are carried out by machine intrinsic functions and are well optimized. The overall algorithm has computational complexity O(log(M)), where M is the number of spatial cells. The algorithm is very efficient and represents the state-of-the-art for isotropic problems in slab geometry. For anisotropic scattering in slab geometry, a multilevel in angle algorithm was developed. A parallel version of the multilevel in angle algorithm has also been developed. Upon first glance, the shifted transport sweep has limited parallelism. Once the right-hand-side has been computed, the sweep is completely parallel in angle, becoming N uncoupled initial value ODE`s. The author has developed a cyclic reduction algorithm that renders it parallel with complexity O(log(M)). The multilevel in angle algorithm visits log(N) levels, where shifted transport sweeps are performed. The overall complexity is O(log(N)log(M)).

  10. Modeling birch pollen emission and transport with the chemistry-transport model CHIMERE

    NASA Astrophysics Data System (ADS)

    Potier, Aurelie; Khvorostyanov, Dmitry; Menut, Laurent; Sofiev, Mikhail; Viovy, Nicolas; Vautard, Robert; Thibaudon, Michel; Tao, Phikune

    2013-04-01

    Among pollen species, birch pollen is recognized to have one of the highest allergenic effects. Its emission as well as its transport with air masses depend on several meteorological parameters. If the conditions are favourable (typically sunny and windy days), the pollen can travel at distances of hundred kilometers in only one day. For analysis and source-oriented forecast, the chemistry-transport models are promising tools to simulate emissions and concentrations over large domains such as Europe. In addition to pollution gaseous and particulate species, the birch pollen related processes were recently added in the chemistry-transport model CHIMERE. This first includes an emission module based on a double-threshold temperature sum concept which describes the onset of the flowering season as well as its propagation using a birch pollen source emission. The parameterization is defined following Sofiev et al. (2012). Second, the processes such as transport, turbulent vertical mixing, dry deposition, wash out and resuspension were updated in CHIMERE to account for the specificities of the pollen grains. In this study, we present a simulation of pollen emissions and transport over Europe with an horizontal resolution of 15km. The CHIMERE model is driven by the WRF meteorological fields and the simulation covers the complete spring of 2008. The modeled pollen concentrations are compared to the R.N.S.A. french national aerobiological survey network measurements. The strength and weaknesses of the modeled results are discussed in terms of emissions data available, meteorology and all specific processes added in the model.

  11. 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.

  12. Modeling solute/contaminant transport in heterogeneous aquifers.

    PubMed

    Kocabas, Ibrahim; Bulbul, Mahmut

    2015-03-01

    A fissured aquifer may be considered as a dense network of fissures separated by low permeability matrix blocks. A conceptual modeling of such a system consists of an infinite number of parallel fractures separated by constant width matrix slabs. While the fissures are assumed to be main flow conduits, the fluid in the porous matrix blocks are considered to be virtually immobile. The mathematical model of the transport of a solute and/or contaminant which assumes a purely convective flow in fissures and diffusion into the matrix blocks consists of two coupled differential equations. An analytical solution of this model for the case of solute entering into the system at a constant concentration has been presented by Skopp and Warrick in Soil Sci Soc Am Proc 38:545-550, 1974. Note however, Skopp and Warrick (Soil Sci Soc Am Proc 38:545-550, 1974) have not considered the additional processes of adsorption and radioactive decay. Unfortunately, their solution had computational limitations as it involved numerical integration of a quite complex expression. Therefore, one had to turn to employing numerical Laplace transform inverters to compute the solutions. This work presents simple real space analytical solutions for the contaminant transport model described above including the adsorption and radioactive decay. The real space solutions have been developed using the method of double Laplace transform and binomial series approximation. An accurate approximate solution has also been presented which converges to the exact solution only after computing three terms in the series full solution. The developed model has been used for 1) assessment of the efficiency of numerical Laplace transform algorithms and 2) investigation of the degree and scale of contamination, and 3) designing remediation schemes for the already contaminated aquifers.

  13. Surface electron density models for accurate ab initio molecular dynamics with electronic friction

    NASA Astrophysics Data System (ADS)

    Novko, D.; Blanco-Rey, M.; Alducin, M.; Juaristi, J. I.

    2016-06-01

    Ab initio molecular dynamics with electronic friction (AIMDEF) is a valuable methodology to study the interaction of atomic particles with metal surfaces. This method, in which the effect of low-energy electron-hole (e-h) pair excitations is treated within the local density friction approximation (LDFA) [Juaristi et al., Phys. Rev. Lett. 100, 116102 (2008), 10.1103/PhysRevLett.100.116102], can provide an accurate description of both e-h pair and phonon excitations. In practice, its applicability becomes a complicated task in those situations of substantial surface atoms displacements because the LDFA requires the knowledge at each integration step of the bare surface electron density. In this work, we propose three different methods of calculating on-the-fly the electron density of the distorted surface and we discuss their suitability under typical surface distortions. The investigated methods are used in AIMDEF simulations for three illustrative adsorption cases, namely, dissociated H2 on Pd(100), N on Ag(111), and N2 on Fe(110). Our AIMDEF calculations performed with the three approaches highlight the importance of going beyond the frozen surface density to accurately describe the energy released into e-h pair excitations in case of large surface atom displacements.

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

    PubMed

    Ustinov, E A

    2014-10-01

    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.

  15. Accurate cortical tissue classification on MRI by modeling cortical folding patterns.

    PubMed

    Kim, Hosung; Caldairou, Benoit; Hwang, Ji-Wook; Mansi, Tommaso; Hong, Seok-Jun; Bernasconi, Neda; Bernasconi, Andrea

    2015-09-01

    Accurate tissue classification is a crucial prerequisite to MRI morphometry. Automated methods based on intensity histograms constructed from the entire volume are challenged by regional intensity variations due to local radiofrequency artifacts as well as disparities in tissue composition, laminar architecture and folding patterns. Current work proposes a novel anatomy-driven method in which parcels conforming cortical folding were regionally extracted from the brain. Each parcel is subsequently classified using nonparametric mean shift clustering. Evaluation was carried out on manually labeled images from two datasets acquired at 3.0 Tesla (n = 15) and 1.5 Tesla (n = 20). In both datasets, we observed high tissue classification accuracy of the proposed method (Dice index >97.6% at 3.0 Tesla, and >89.2% at 1.5 Tesla). Moreover, our method consistently outperformed state-of-the-art classification routines available in SPM8 and FSL-FAST, as well as a recently proposed local classifier that partitions the brain into cubes. Contour-based analyses localized more accurate white matter-gray matter (GM) interface classification of the proposed framework compared to the other algorithms, particularly in central and occipital cortices that generally display bright GM due to their highly degree of myelination. Excellent accuracy was maintained, even in the absence of correction for intensity inhomogeneity. The presented anatomy-driven local classification algorithm may significantly improve cortical boundary definition, with possible benefits for morphometric inference and biomarker discovery.

  16. 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.

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

    PubMed

    Ustinov, E A

    2014-10-01

    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. PMID:25296827

  18. Accurate cortical tissue classification on MRI by modeling cortical folding patterns.

    PubMed

    Kim, Hosung; Caldairou, Benoit; Hwang, Ji-Wook; Mansi, Tommaso; Hong, Seok-Jun; Bernasconi, Neda; Bernasconi, Andrea

    2015-09-01

    Accurate tissue classification is a crucial prerequisite to MRI morphometry. Automated methods based on intensity histograms constructed from the entire volume are challenged by regional intensity variations due to local radiofrequency artifacts as well as disparities in tissue composition, laminar architecture and folding patterns. Current work proposes a novel anatomy-driven method in which parcels conforming cortical folding were regionally extracted from the brain. Each parcel is subsequently classified using nonparametric mean shift clustering. Evaluation was carried out on manually labeled images from two datasets acquired at 3.0 Tesla (n = 15) and 1.5 Tesla (n = 20). In both datasets, we observed high tissue classification accuracy of the proposed method (Dice index >97.6% at 3.0 Tesla, and >89.2% at 1.5 Tesla). Moreover, our method consistently outperformed state-of-the-art classification routines available in SPM8 and FSL-FAST, as well as a recently proposed local classifier that partitions the brain into cubes. Contour-based analyses localized more accurate white matter-gray matter (GM) interface classification of the proposed framework compared to the other algorithms, particularly in central and occipital cortices that generally display bright GM due to their highly degree of myelination. Excellent accuracy was maintained, even in the absence of correction for intensity inhomogeneity. The presented anatomy-driven local classification algorithm may significantly improve cortical boundary definition, with possible benefits for morphometric inference and biomarker discovery. PMID:26037453

  19. 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.

  20. Transport characteristics of a finite-difference dynamics model combined with a spectral transport model of the middle atmosphere

    NASA Technical Reports Server (NTRS)

    Duncan, T.; Fairlie, A.; Turner, Richard E.; Siskind, David E.

    1994-01-01

    A three-dimensional off-line spectral transport model has been combined with a global, mechanistic, finite-difference dynamics model of the middle atmosphere in order to study transport and photochemistry in the middle atmosphere for specific, observed episodes. In this paper, the basic transport characteristics of the combined models are examined, first using steady, idealized flow fields and second using time-dependent flow fields closely related to observed atmospheric behavior. Transport conducted with the combined models is found to compare favorably with transport conducted on-line in the dynamics model, given appropriate time averaging of the flow fields and suitable choice of artificial diffusion.

  1. Modeling Transport of Flushed Reservoir Sediment

    NASA Astrophysics Data System (ADS)

    Dubinski, I. M.

    2014-12-01

    Drawdown flushing of a reservoir is often part of a reservoir sediment management program. Flushing can deliver higher than normal sediment loads to the river channel located downstream of a reservoir. The flushed sediment may contain a higher proportion of finer sediment than what was delivered to a channel prior to the presence of the reservoir. The extent of long-term impacts caused by the flushed sediment on the channel morphology and habitat will in part depend on the residence time of the sediment within the channel. In this study we used MIKE 21C to model the fate of flushed sediment through a river channel where the bed material consists of an armoring layer of gravels overlying finer sediment. MIKE 21C is a two-dimensional curvilinear morphological model for rivers developed by DHI. Curvilinear means that the model grid may curve to better follow the channel and flow direction, for example in a meandering channel. Multiple bed material layers are included in the model to represent the armoring and underlying layers existing in the bed separately from the overlying flushed sediment. These layers may also mix. The nature of the interactions between these two layers helps regulate transport and deposition of the flushed sediment, thus are critical to assessing the fate of the flushed sediment and associated potential impacts.

  2. Signal Processing Model for Radiation Transport

    SciTech Connect

    Chambers, D H

    2008-07-28

    This note describes the design of a simplified gamma ray transport model for use in designing a sequential Bayesian signal processor for low-count detection and classification. It uses a simple one-dimensional geometry to describe the emitting source, shield effects, and detector (see Fig. 1). At present, only Compton scattering and photoelectric absorption are implemented for the shield and the detector. Other effects may be incorporated in the future by revising the expressions for the probabilities of escape and absorption. Pair production would require a redesign of the simulator to incorporate photon correlation effects. The initial design incorporates the physical effects that were present in the previous event mode sequence simulator created by Alan Meyer. The main difference is that this simulator transports the rate distributions instead of single photons. Event mode sequences and other time-dependent photon flux sequences are assumed to be marked Poisson processes that are entirely described by their rate distributions. Individual realizations can be constructed from the rate distribution using a random Poisson point sequence generator.

  3. 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 ...

  4. 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.

  5. Multi Sensor Data Integration for AN Accurate 3d Model Generation

    NASA Astrophysics Data System (ADS)

    Chhatkuli, S.; Satoh, T.; Tachibana, K.

    2015-05-01

    The aim of this paper is to introduce a novel technique of data integration between two different data sets, i.e. laser scanned RGB point cloud and oblique imageries derived 3D model, to create a 3D model with more details and better accuracy. In general, aerial imageries are used to create a 3D city model. Aerial imageries produce an overall decent 3D city models and generally suit to generate 3D model of building roof and some non-complex terrain. However, the automatically generated 3D model, from aerial imageries, generally suffers from the lack of accuracy in deriving the 3D model of road under the bridges, details under tree canopy, isolated trees, etc. Moreover, the automatically generated 3D model from aerial imageries also suffers from undulated road surfaces, non-conforming building shapes, loss of minute details like street furniture, etc. in many cases. On the other hand, laser scanned data and images taken from mobile vehicle platform can produce more detailed 3D road model, street furniture model, 3D model of details under bridge, etc. However, laser scanned data and images from mobile vehicle are not suitable to acquire detailed 3D model of tall buildings, roof tops, and so forth. Our proposed approach to integrate multi sensor data compensated each other's weakness and helped to create a very detailed 3D model with better accuracy. Moreover, the additional details like isolated trees, street furniture, etc. which were missing in the original 3D model derived from aerial imageries could also be integrated in the final model automatically. During the process, the noise in the laser scanned data for example people, vehicles etc. on the road were also automatically removed. Hence, even though the two dataset were acquired in different time period the integrated data set or the final 3D model was generally noise free and without unnecessary details.

  6. A Hybrid Micro-Scale Model for Transport in Connected Macro-Pores in Porous Media

    SciTech Connect

    Ryan, Emily M.; Tartakovsky, Alexandre M.

    2011-07-13

    This paper presents a multi-scale approach for modeling the transport of species in fractured porous media. The multi-scale approach consists of a hybrid model and a pore-scale model that is used to parameterize the hybrid model. The hybrid model explicitly models the advection and diffusion of species in the fracture and treats the porous matrix as a continuum with effective transport properties. The pore-scale model is used to calculate the effective transport properties of the hybrid model. This approach negates the need to calibrate the hybrid model against experimental data, which is common for continuum-scale models of porous media, and allows an arbitrary microstructure to be considered. The paper presents the multi-scale modeling approach along with the details of the hybrid and pore-scale models. Validation of the model is also presented along with several case studies investigating the applicability of the multi-scale modeling approach to different geometries and transport conditions. The case studies show that the multi-scale modeling approach is accurate for various fracture geometries given that the matrix porosity is sufficiently small. The accuracy of the hybrid model decreases with increasing porosity of the matrix.

  7. 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

  8. 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…

  9. 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.

  10. 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

  11. Accurate modeling and inversion of electrical resistivity data in the presence of metallic infrastructure with known location and dimension

    SciTech Connect

    Johnson, Timothy C.; Wellman, Dawn M.

    2015-06-26

    Electrical resistivity tomography (ERT) has been widely used in environmental applications to study processes associated with subsurface contaminants and contaminant remediation. Anthropogenic alterations in subsurface electrical conductivity associated with contamination often originate from highly industrialized areas with significant amounts of buried metallic infrastructure. The deleterious influence of such infrastructure on imaging results generally limits the utility of ERT where it might otherwise prove useful for subsurface investigation and monitoring. In this manuscript we present a method of accurately modeling the effects of buried conductive infrastructure within the forward modeling algorithm, thereby removing them from the inversion results. The method is implemented in parallel using immersed interface boundary conditions, whereby the global solution is reconstructed from a series of well-conditioned partial solutions. Forward modeling accuracy is demonstrated by comparison with analytic solutions. Synthetic imaging examples are used to investigate imaging capabilities within a subsurface containing electrically conductive buried tanks, transfer piping, and well casing, using both well casings and vertical electrode arrays as current sources and potential measurement electrodes. Results show that, although accurate infrastructure modeling removes the dominating influence of buried metallic features, the presence of metallic infrastructure degrades imaging resolution compared to standard ERT imaging. However, accurate imaging results may be obtained if electrodes are appropriately located.

  12. 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

  13. Modelling total solar irradiance using a flux transport model

    NASA Astrophysics Data System (ADS)

    Dasi Espuig, Maria; Jiang, Jie; Krivova, Natalie; Solanki, Sami

    2014-05-01

    Reconstructions of solar irradiance into the past are of considerable interest for studies of solar influence on climate. Models based on the assumption that irradiance changes are caused by the evolution of the photospheric magnetic field have been the most successful in reproducing the measured irradiance variations. Our SATIRE-S model is one of these. It uses solar full-disc magnetograms as an input, and these are available for less than four decades. Thus, to reconstruct the irradiance back to times when no observed magnetograms are available, we combine the SATIRE-S model with synthetic magnetograms, produced using a surface flux transport model. The model is fed with daily, observed or modelled statistically, records of sunspot positions, areas, and tilt angles. To describe the secular change in the irradiance, we used the concept of overlapping ephemeral region cycles. With this technique TSI can be reconstructed back to 1700.

  14. 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.

  15. Genome-Scale Metabolic Model for the Green Alga Chlorella vulgaris UTEX 395 Accurately Predicts Phenotypes under Autotrophic, Heterotrophic, and Mixotrophic Growth Conditions.

    PubMed

    Zuñiga, Cristal; Li, Chien-Ting; Huelsman, Tyler; Levering, Jennifer; Zielinski, Daniel C; McConnell, Brian O; Long, Christopher P; Knoshaug, Eric P; Guarnieri, Michael T; Antoniewicz, Maciek R; Betenbaugh, Michael J; Zengler, Karsten

    2016-09-01

    The green microalga Chlorella vulgaris has been widely recognized as a promising candidate for biofuel production due to its ability to store high lipid content and its natural metabolic versatility. Compartmentalized genome-scale metabolic models constructed from genome sequences enable quantitative insight into the transport and metabolism of compounds within a target organism. These metabolic models have long been utilized to generate optimized design strategies for an improved production process. Here, we describe the reconstruction, validation, and application of a genome-scale metabolic model for C. vulgaris UTEX 395, iCZ843. The reconstruction represents the most comprehensive model for any eukaryotic photosynthetic organism to date, based on the genome size and number of genes in the reconstruction. The highly curated model accurately predicts phenotypes under photoautotrophic, heterotrophic, and mixotrophic conditions. The model was validated against experimental data and lays the foundation for model-driven strain design and medium alteration to improve yield. Calculated flux distributions under different trophic conditions show that a number of key pathways are affected by nitrogen starvation conditions, including central carbon metabolism and amino acid, nucleotide, and pigment biosynthetic pathways. Furthermore, model prediction of growth rates under various medium compositions and subsequent experimental validation showed an increased growth rate with the addition of tryptophan and methionine. PMID:27372244

  16. Ut-Minimos a Hierarchical Transport Model Based Simulator for Deep Submicron Silicon Devices

    NASA Astrophysics Data System (ADS)

    Yeap, Choh-Fei

    1995-01-01

    The challenge of Ultra Large Scale Integration (ULSI) of integrated circuits reinforces the need for accurate and efficient simulations to speed development and reduce cost. The predictive power of conventional simulation based on the drift-diffusion (DD) model has diminished to a critically low level. An improved transport model must now replace, what has been the foundation of semiconductor device simulation, the DD model. The hydrodynamic (HD) transport model, that addresses non-local effects such as velocity overshoot and carrier heating, is an attractive candidate. The true viability of the HD models in replacing the DD model rests on their availability in well-accepted device simulators, physical accuracy and ease of solution. This work is an attempt to hasten and facilitate this replacement. The focus of this dissertation is an effort towards implementing a hierarchy of promising HD transport model candidates in an established and well-accepted device simulator using robust and efficient discretization and solution methods. Thus, UT-MiniMOS 3.0, a 2-D two -carrier integrated simulator for deep submicron silicon devices, has been developed to include a hierarchy of transport models and to construct a programming environment for easy implementation and maintenance of the physical models and numerical techniques. The hierarchy of transport models includes the DD model, post-processing current contour HD model, parabolic HD model, Stratton's energy balance model, Chen's energy transport model, Lee's HD model, Stettler's HD model, Bordelon's non-parabolic HD (NPHD) model, lattice temperature model, and Monte Carlo (MC) model. Each of these HD models is cast into a generalized HD formulation with four controlling parameters. This generalized HD formulation allows a unified discretization for all HD models. The NPHD model has been shown to provide the best overall agreement to MC energy, velocity and concentration. HD simulation in UT-MiniMOS for a bias point

  17. 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.

  18. Efficient and accurate approach to modeling the microstructure and defect properties of LaCoO3

    NASA Astrophysics Data System (ADS)

    Buckeridge, J.; Taylor, F. H.; Catlow, C. R. A.

    2016-04-01

    Complex perovskite oxides are promising materials for cathode layers in solid oxide fuel cells. Such materials have intricate electronic, magnetic, and crystalline structures that prove challenging to model accurately. We analyze a wide range of standard density functional theory approaches to modeling a highly promising system, the perovskite LaCoO3, focusing on optimizing the Hubbard U parameter to treat the self-interaction of the B-site cation's d states, in order to determine the most appropriate method to study defect formation and the effect of spin on local structure. By calculating structural and electronic properties for different magnetic states we determine that U =4 eV for Co in LaCoO3 agrees best with available experiments. We demonstrate that the generalized gradient approximation (PBEsol +U ) is most appropriate for studying structure versus spin state, while the local density approximation (LDA +U ) is most appropriate for determining accurate energetics for defect properties.

  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. 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.

  1. Accurate calculation of binding energies for molecular clusters - Assessment of different models

    NASA Astrophysics Data System (ADS)

    Friedrich, Joachim; Fiedler, Benjamin

    2016-06-01

    In this work we test different strategies to compute high-level benchmark energies for medium-sized molecular clusters. We use the incremental scheme to obtain CCSD(T)/CBS energies for our test set and carefully validate the accuracy for binding energies by statistical measures. The local errors of the incremental scheme are <1 kJ/mol. Since they are smaller than the basis set errors, we obtain higher total accuracy due to the applicability of larger basis sets. The final CCSD(T)/CBS benchmark values are ΔE = - 278.01 kJ/mol for (H2O)10, ΔE = - 221.64 kJ/mol for (HF)10, ΔE = - 45.63 kJ/mol for (CH4)10, ΔE = - 19.52 kJ/mol for (H2)20 and ΔE = - 7.38 kJ/mol for (H2)10 . Furthermore we test state-of-the-art wave-function-based and DFT methods. Our benchmark data will be very useful for critical validations of new methods. We find focal-point-methods for estimating CCSD(T)/CBS energies to be highly accurate and efficient. For foQ-i3CCSD(T)-MP2/TZ we get a mean error of 0.34 kJ/mol and a standard deviation of 0.39 kJ/mol.

  2. Accurate characterization and modeling of transmission lines for GaAs MMIC's

    NASA Astrophysics Data System (ADS)

    Finlay, Hugh J.; Jansen, Rolf H.; Jenkins, John A.; Eddison, Ian G.

    1988-06-01

    The authors discuss computer-aided design (CAD) tools together with high-accuracy microwave measurements to realize improved design data for GaAs monolithic microwave integrated circuits (MMICs). In particular, a combined theoretical and experimental approach to the generation of an accurate design database for transmission lines on GaAs MMICs is presented. The theoretical approach is based on an improved transmission-line theory which is part of the spectral-domain hybrid-mode computer program MCLINE. The benefit of this approach in the design of multidielectric-media transmission lines is described. The program was designed to include loss mechanisms in all dielectric layers and to include conductor and surface roughness loss contributions. As an example, using GaAs ring resonator techniques covering 2 to 24 GHz, accuracies in effective dielectric constant and loss of 1 percent and 15 percent respectively, are presented. By combining theoretical and experimental techniques, a generalized MMIC microstrip design database is outlined.

  3. Modelling of minority-carrier transport in heavily doped silicon emitters

    NASA Astrophysics Data System (ADS)

    del Alamo, Jesús A.; Swanson, Richard M.

    1987-11-01

    The transport and recombination of minority carriers in heavily doped emitters plays a crucial role in the performance of silicon bipolar transistors and solar cells. In the past, only order-of-magnitude prediction of the value of the current injected into a heavily doped emitter was possible. The limitations to a more accurate modelling stemmed from: (1) the incomplete understanding of the physics of minority carriers in heavily doped semiconductors; (2) the lack of precise measurements of the relevant material parameters; (3) the difficulties encountered with the modelling of transport and recombination in non-homogeneously doped regions, and (4) problems with the characterization of "real" emitters of bipolar devices. This paper reviews recent experimental and theoretical efforts that addressed some of these issues, with the goal of being able to achieve accurate modelling of the current injected into an arbitrary heavily doped region in a silicon device.

  4. A nonlinear model for the layer between plates in acoustic noncontact transportation

    NASA Astrophysics Data System (ADS)

    Li, Jin; Cao, Wenwu; Zhang, Wenjun

    2014-12-01

    To more accurately describe the noncontact transport behavior of traveling acoustic waves, a nonlinear model is presented in this paper for the squeeze gas film with consideration of gas inertia in the case of a large amplitude motion and low viscosity of the gas. A closed form solution is derived for the vertical and horizontal forces of the film from this model. Our results have shown that the gas inertia has a significant influence on the pressure distribution in the squeeze film, and the inertial force is higher than the viscous force. The predicted levitation and horizontal driving forces are found to be in good agreement with our experimental measurements. Our inertia model provides a powerful tool for the force estimation and its potential benefits could be far reaching. The accurate prediction of these forces is useful to design the system for levitating and transporting planar objects, such as MEMS devices, glass substrates, and IC chips

  5. 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.

  6. Development of versatile molecular transport model for modeling spacecraft contamination

    NASA Astrophysics Data System (ADS)

    Chang, Chien W.; Kannenberg, Keith; Chidester, Michael H.

    2010-08-01

    This paper describes a MATLAB-based molecular transport model developed for modeling contamination of spacecraft and optical instruments in space. The model adopts the Gebhart inverse-matrix theory for thermal radiation to analyze mass (molecular) transfer due to direct and reflected flux processes by balancing the mass fluxes instead of heat fluxes among surfaces with prescribed boundary conditions (contamination sticking fractions). The model can easily input view factor results from current thermal tools as well as measured outgassing data from ASTM E 1559 tests or vacuum bake-outs of flight components. Application examples of a geosynchronous satellite and an optical telescope are given to demonstrate versatile applications of the developed model.

  7. Modeling Phosphorous and Sediment Transport in the Cayuga Lake Watershed

    NASA Astrophysics Data System (ADS)

    Menzies, E.; Walter, M. T.

    2014-12-01

    Excess sediment and nutrient loading to surface waters, especially nitrogen and phosphorus, is a common and significant problem throughout the United States. While pollution remediation efforts are continuously improving, the most effective treatment remains to limit the source. The southern end of Cayuga Lake, near Ithaca, NY, is listed by the New York State Department of Environmental Conservation (NYS DEC) as an impaired water body for both sediment and nutrient pollution. In an effort to determine appropriate remediation measures and as little is currently known about the pollutants cycling through the lake, the NYS DEC is conducting a large scale investigation to fully understand how Cayuga Lake is impacted by sediment and nutrient pollution. This study, as part of the greater effort, explores the contribution of phosphorous and sediment from the surrounding tributaries of Cayuga Lake. The evaluation will include an analysis of the sources and transport pathways of these pollutants in the Cayuga Lake watershed using ArcSWAT. Preliminary execution of the model was carried out on two large watersheds thought to be major contributors of phosphorous to the lake. Data from a number of sources are being used to ensure that model outputs provide an accurate understanding of the watersheds. The calibrated model, combined with information from other sources, will help the NYS DEC determine if a Total Maximum Daily Load (TMDL) is an appropriate remediation tool for the south end of Cayuga Lake.

  8. 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.

  9. A Simple, Accurate Model for Alkyl Adsorption on Late Transition Metals

    SciTech Connect

    Montemore, Matthew M.; Medlin, James W.

    2013-01-18

    A simple model that predicts the adsorption energy of an arbitrary alkyl in the high-symmetry sites of late transition metal fcc(111) and related surfaces is presented. The model makes predictions based on a few simple attributes of the adsorbate and surface, including the d-shell filling and the matrix coupling element, as well as the adsorption energy of methyl in the top sites. We use the model to screen surfaces for alkyl chain-growth properties and to explain trends in alkyl adsorption strength, site preference, and vibrational softening.

  10. Accurate Fabrication of Hydroxyapatite Bone Models with Porous Scaffold Structures by Using Stereolithography

    NASA Astrophysics Data System (ADS)

    Maeda, Chiaki; Tasaki, Satoko; Kirihara, Soshu

    2011-05-01

    Computer graphic models of bioscaffolds with four-coordinate lattice structures of solid rods in artificial bones were designed by using a computer aided design. The scaffold models composed of acryl resin with hydroxyapatite particles at 45vol. % were fabricated by using stereolithography of a computer aided manufacturing. After dewaxing and sintering heat treatment processes, the ceramics scaffold models with four-coordinate lattices and fine hydroxyapatite microstructures were obtained successfully. By using a computer aided analysis, it was found that bio-fluids could flow extensively inside the sintered scaffolds. This result shows that the lattice structures will realize appropriate bio-fluid circulations and promote regenerations of new bones.

  11. 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.

  12. Better Understanding Transport Related Differences Between CCMs and Trace Gas Measurements With an Idealized Stratospheric Model

    NASA Astrophysics Data System (ADS)

    Ray, E. A.; Moore, F. L.; Rosenlof, K. H.; Plummer, D. A.; Kolonjari, F.; Walker, K. A.

    2015-12-01

    We use a modified version of the tropical leaky pipe (TLP) model of the stratosphere to explore how well an idealized model can (1) reproduce global chemistry-climate model (CCM) output and (2) constrain transport characteristics necessary to replicate measurements of long-lived trace gases. The version of the TLP model we use includes the simulation of long-lived trace gases, such as SF6 and CO2, as well as photochemically active trace gases such as CFC-11, CFC-12 and N2O. The TLP model was found to accurately replicate trace gas output from the Canadian Middle Atmosphere Model (CMAM) for time-averaged profiles in the tropics and each extratropical region. With confidence that the TLP model could represent the basic transport features in CMAM we then used the TLP model to interpret differences between ACE satellite and balloon measurements and CMAM output. The TLP model is shown to uniquely determine mean circulation and recirculation (mixing between the extratropics and tropics) changes necessary for CMAM to more accurately simulate the measurements. This guidance on transport changes is novel, and cannot readily be obtained from direct comparison of CCM output with measurements. The TLP model can thus be used as a bridge between measurements and CCMs to allow more targeted modification of the CCMs than would otherwise be possible.

  13. 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?

  14. A model for the accurate computation of the lateral scattering of protons in water.

    PubMed

    Bellinzona, E V; Ciocca, M; Embriaco, A; Ferrari, A; Fontana, A; Mairani, A; Parodi, K; Rotondi, A; Sala, P; Tessonnier, T

    2016-02-21

    A pencil beam model for the calculation of the lateral scattering in water of protons for any therapeutic energy and depth is presented. It is based on the full Molière theory, taking into account the energy loss and the effects of mixtures and compounds. Concerning the electromagnetic part, the model has no free parameters and is in very good agreement with the FLUKA Monte Carlo (MC) code. The effects of the nuclear interactions are parametrized with a two-parameter tail function, adjusted on MC data calculated with FLUKA. The model, after the convolution with the beam and the detector response, is in agreement with recent proton data in water from HIT. The model gives results with the same accuracy of the MC codes based on Molière theory, with a much shorter computing time.

  15. Accurate calculations of the hydration free energies of druglike molecules using the reference interaction site model.

    PubMed

    Palmer, David S; Sergiievskyi, Volodymyr P; Jensen, Frank; Fedorov, Maxim V

    2010-07-28

    We report on the results of testing the reference interaction site model (RISM) for the estimation of the hydration free energy of druglike molecules. The optimum model was selected after testing of different RISM free energy expressions combined with different quantum mechanics and empirical force-field methods of structure optimization and atomic partial charge calculation. The final model gave a systematic error with a standard deviation of 2.6 kcal/mol for a test set of 31 molecules selected from the SAMPL1 blind challenge set [J. P. Guthrie, J. Phys. Chem. B 113, 4501 (2009)]. After parametrization of this model to include terms for the excluded volume and the number of atoms of different types in the molecule, the root mean squared error for a test set of 19 molecules was less than 1.2 kcal/mol.

  16. A model for the accurate computation of the lateral scattering of protons in water

    NASA Astrophysics Data System (ADS)

    Bellinzona, E. V.; Ciocca, M.; Embriaco, A.; Ferrari, A.; Fontana, A.; Mairani, A.; Parodi, K.; Rotondi, A.; Sala, P.; Tessonnier, T.

    2016-02-01

    A pencil beam model for the calculation of the lateral scattering in water of protons for any therapeutic energy and depth is presented. It is based on the full Molière theory, taking into account the energy loss and the effects of mixtures and compounds. Concerning the electromagnetic part, the model has no free parameters and is in very good agreement with the FLUKA Monte Carlo (MC) code. The effects of the nuclear interactions are parametrized with a two-parameter tail function, adjusted on MC data calculated with FLUKA. The model, after the convolution with the beam and the detector response, is in agreement with recent proton data in water from HIT. The model gives results with the same accuracy of the MC codes based on Molière theory, with a much shorter computing time.

  17. 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.

  18. 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.

  19. 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.

  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 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.

  2. 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. PMID:26121186

  3. 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

  4. Physical resist models and their calibration: their readiness for accurate EUV lithography simulation

    NASA Astrophysics Data System (ADS)

    Klostermann, U. K.; Mülders, T.; Schmöller, T.; Lorusso, G. F.; Hendrickx, E.

    2010-04-01

    In this paper, we discuss the performance of EUV resist models in terms of predictive accuracy, and we assess the readiness of the corresponding model calibration methodology. The study is done on an extensive OPC data set collected at IMEC for the ShinEtsu resist SEVR-59 on the ASML EUV Alpha Demo Tool (ADT), with the data set including more than thousand CD values. We address practical aspects such as the speed of calibration and selection of calibration patterns. The model is calibrated on 12 process window data series varying in pattern width (32, 36, 40 nm), orientation (H, V) and pitch (dense, isolated). The minimum measured feature size at nominal process condition is a 32 nm CD at a dense pitch of 64 nm. Mask metrology is applied to verify and eventually correct nominal width of the drawn CD. Cross-sectional SEM information is included in the calibration to tune the simulated resist loss and sidewall angle. The achieved calibration RMS is ~ 1.0 nm. We show what elements are important to obtain a well calibrated model. We discuss the impact of 3D mask effects on the Bossung tilt. We demonstrate that a correct representation of the flare level during the calibration is important to achieve a high predictability at various flare conditions. Although the model calibration is performed on a limited subset of the measurement data (one dimensional structures only), its accuracy is validated based on a large number of OPC patterns (at nominal dose and focus conditions) not included in the calibration; validation RMS results as small as 1 nm can be reached. Furthermore, we study the model's extendibility to two-dimensional end of line (EOL) structures. Finally, we correlate the experimentally observed fingerprint of the CD uniformity to a model, where EUV tool specific signatures are taken into account.

  5. Use of human in vitro skin models for accurate and ethical risk assessment: metabolic considerations.

    PubMed

    Hewitt, Nicola J; Edwards, Robert J; Fritsche, Ellen; Goebel, Carsten; Aeby, Pierre; Scheel, Julia; Reisinger, Kerstin; Ouédraogo, Gladys; Duche, Daniel; Eilstein, Joan; Latil, Alain; Kenny, Julia; Moore, Claire; Kuehnl, Jochen; Barroso, Joao; Fautz, Rolf; Pfuhler, Stefan

    2013-06-01

    Several human skin models employing primary cells and immortalized cell lines used as monocultures or combined to produce reconstituted 3D skin constructs have been developed. Furthermore, these models have been included in European genotoxicity and sensitization/irritation assay validation projects. In order to help interpret data, Cosmetics Europe (formerly COLIPA) facilitated research projects that measured a variety of defined phase I and II enzyme activities and created a complete proteomic profile of xenobiotic metabolizing enzymes (XMEs) in native human skin and compared them with data obtained from a number of in vitro models of human skin. Here, we have summarized our findings on the current knowledge of the metabolic capacity of native human skin and in vitro models and made an overall assessment of the metabolic capacity from gene expression, proteomic expression, and substrate metabolism data. The known low expression and function of phase I enzymes in native whole skin were reflected in the in vitro models. Some XMEs in whole skin were not detected in in vitro models and vice versa, and some major hepatic XMEs such as cytochrome P450-monooxygenases were absent or measured only at very low levels in the skin. Conversely, despite varying mRNA and protein levels of phase II enzymes, functional activity of glutathione S-transferases, N-acetyltransferase 1, and UDP-glucuronosyltransferases were all readily measurable in whole skin and in vitro skin models at activity levels similar to those measured in the liver. These projects have enabled a better understanding of the contribution of XMEs to toxicity endpoints. PMID:23539547

  6. 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.

  7. 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...

  8. Toward Accurate Modeling of the Effect of Ion-Pair Formation on Solute Redox Potential.

    PubMed

    Qu, Xiaohui; Persson, Kristin A

    2016-09-13

    A scheme to model the dependence of a solute redox potential on the supporting electrolyte is proposed, and the results are compared to experimental observations and other reported theoretical models. An improved agreement with experiment is exhibited if the effect of the supporting electrolyte on the redox potential is modeled through a concentration change induced via ion pair formation with the salt, rather than by only considering the direct impact on the redox potential of the solute itself. To exemplify the approach, the scheme is applied to the concentration-dependent redox potential of select molecules proposed for nonaqueous flow batteries. However, the methodology is general and enables rational computational electrolyte design through tuning of the operating window of electrochemical systems by shifting the redox potential of its solutes; including potentially both salts as well as redox active molecules. PMID:27500744

  9. Geo-accurate model extraction from three-dimensional image-derived point clouds

    NASA Astrophysics Data System (ADS)

    Nilosek, David; Sun, Shaohui; Salvaggio, Carl

    2012-06-01

    A methodology is proposed for automatically extracting primitive models of buildings in a scene from a three-dimensional point cloud derived from multi-view depth extraction techniques. By exploring the information provided by the two-dimensional images and the three-dimensional point cloud and the relationship between the two, automated methods for extraction are presented. Using the inertial measurement unit (IMU) and global positioning system (GPS) data that accompanies the aerial imagery, the geometry is derived in a world-coordinate system so the model can be used with GIS software. This work uses imagery collected by the Rochester Institute of Technology's Digital Imaging and Remote Sensing Laboratory's WASP sensor platform. The data used was collected over downtown Rochester, New York. Multiple target buildings have their primitive three-dimensional model geometry extracted using modern point-cloud processing techniques.

  10. Lateral impact validation of a geometrically accurate full body finite element model for blunt injury prediction.

    PubMed

    Vavalle, Nicholas A; Moreno, Daniel P; Rhyne, Ashley C; Stitzel, Joel D; Gayzik, F Scott

    2013-03-01

    This study presents four validation cases of a mid-sized male (M50) full human body finite element model-two lateral sled tests at 6.7 m/s, one sled test at 8.9 m/s, and a lateral drop test. Model results were compared to transient force curves, peak force, chest compression, and number of fractures from the studies. For one of the 6.7 m/s impacts (flat wall impact), the peak thoracic, abdominal and pelvic loads were 8.7, 3.1 and 14.9 kN for the model and 5.2 ± 1.1 kN, 3.1 ± 1.1 kN, and 6.3 ± 2.3 kN for the tests. For the same test setup in the 8.9 m/s case, they were 12.6, 6, and 21.9 kN for the model and 9.1 ± 1.5 kN, 4.9 ± 1.1 kN, and 17.4 ± 6.8 kN for the experiments. The combined torso load and the pelvis load simulated in a second rigid wall impact at 6.7 m/s were 11.4 and 15.6 kN, respectively, compared to 8.5 ± 0.2 kN and 8.3 ± 1.8 kN experimentally. The peak thorax load in the drop test was 6.7 kN for the model, within the range in the cadavers, 5.8-7.4 kN. When analyzing rib fractures, the model predicted Abbreviated Injury Scale scores within the reported range in three of four cases. Objective comparison methods were used to quantitatively compare the model results to the literature studies. The results show a good match in the thorax and abdomen regions while the pelvis results over predicted the reaction loads from the literature studies. These results are an important milestone in the development and validation of this globally developed average male FEA model in lateral impact.

  11. 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.

  12. 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.

  13. 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.

  14. 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.

  15. 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…

  16. Compact and accurate linear and nonlinear autoregressive moving average model parameter estimation using laguerre functions.

    PubMed

    Chon, K H; Cohen, R J; Holstein-Rathlou, N H

    1997-01-01

    A linear and nonlinear autoregressive moving average (ARMA) identification algorithm is developed for modeling time series data. The algorithm uses Laguerre expansion of kernals (LEK) to estimate Volterra-Wiener kernals. However, instead of estimating linear and nonlinear system dynamics via moving average models, as is the case for the Volterra-Wiener analysis, we propose an ARMA model-based approach. The proposed algorithm is essentially the same as LEK, but this algorithm is extended to include past values of the output as well. Thus, all of the advantages associated with using the Laguerre function remain with our algorithm; but, by extending the algorithm to the linear and nonlinear ARMA model, a significant reduction in the number of Laguerre functions can be made, compared with the Volterra-Wiener approach. This translates into a more compact system representation and makes the physiological interpretation of higher order kernels easier. Furthermore, simulation results show better performance of the proposed approach in estimating the system dynamics than LEK in certain cases, and it remains effective in the presence of significant additive measurement noise. PMID:9236985

  17. 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

  18. 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.

  19. Statistically accurate low-order models for uncertainty quantification in turbulent dynamical systems

    PubMed Central

    Sapsis, Themistoklis P.; Majda, Andrew J.

    2013-01-01

    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. PMID:23918398

  20. 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 -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 under prediction 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

  1. 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

  2. Are satellite based rainfall estimates accurate enough for crop modelling under Sahelian climate?

    NASA Astrophysics Data System (ADS)

    Ramarohetra, J.; Sultan, B.

    2012-04-01

    Agriculture is considered as the most climate dependant human activity. In West Africa and especially in the sudano-sahelian zone, rain-fed agriculture - that represents 93% of cultivated areas and is the means of support of 70% of the active population - is highly vulnerable to precipitation variability. To better understand and anticipate climate impacts on agriculture, crop models - that estimate crop yield from climate information (e.g rainfall, temperature, insolation, humidity) - have been developed. These crop models are useful (i) in ex ante analysis to quantify the impact of different strategies implementation - crop management (e.g. choice of varieties, sowing date), crop insurance or medium-range weather forecast - on yields, (ii) for early warning systems and to (iii) assess future food security. Yet, the successful application of these models depends on the accuracy of their climatic drivers. In the sudano-sahelian zone , the quality of precipitation estimations is then a key factor to understand and anticipate climate impacts on agriculture via crop modelling and yield estimations. Different kinds of precipitation estimations can be used. Ground measurements have long-time series but an insufficient network density, a large proportion of missing values, delay in reporting time, and they have limited availability. An answer to these shortcomings may lie in the field of remote sensing that provides satellite-based precipitation estimations. However, satellite-based rainfall estimates (SRFE) are not a direct measurement but rather an estimation of precipitation. Used as an input for crop models, it determines the performance of the simulated yield, hence SRFE require validation. The SARRAH crop model is used to model three different varieties of pearl millet (HKP, MTDO, Souna3) in a square degree centred on 13.5°N and 2.5°E, in Niger. Eight satellite-based rainfall daily products (PERSIANN, CMORPH, TRMM 3b42-RT, GSMAP MKV+, GPCP, TRMM 3b42v6, RFEv2 and

  3. 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

  4. Fast and accurate low-dimensional reduction of biophysically detailed neuron models.

    PubMed

    Marasco, Addolorata; Limongiello, Alessandro; Migliore, Michele

    2012-01-01

    Realistic modeling of neurons are quite successful in complementing traditional experimental techniques. However, their networks require a computational power beyond the capabilities of current supercomputers, and the methods used so far to reduce their complexity do not take into account the key features of the cells nor critical physiological properties. Here we introduce a new, automatic and fast method to map realistic neurons into equivalent reduced models running up to > 40 times faster while maintaining a very high accuracy of the membrane potential dynamics during synaptic inputs, and a direct link with experimental observables. The mapping of arbitrary sets of synaptic inputs, without additional fine tuning, would also allow the convenient and efficient implementation of a new generation of large-scale simulations of brain regions reproducing the biological variability observed in real neurons, with unprecedented advances to understand higher brain functions. PMID:23226594

  5. An accurate in vitro model of the E. coli envelope.

    PubMed

    Clifton, Luke A; Holt, Stephen A; Hughes, Arwel V; Daulton, Emma L; Arunmanee, Wanatchaporn; Heinrich, Frank; Khalid, Syma; Jefferies, Damien; Charlton, Timothy R; Webster, John R P; Kinane, Christian J; Lakey, Jeremy H

    2015-10-01

    Gram-negative bacteria are an increasingly serious source of antibiotic-resistant infections, partly owing to their characteristic protective envelope. This complex, 20 nm thick barrier includes a highly impermeable, asymmetric bilayer outer membrane (OM), which plays a pivotal role in resisting antibacterial chemotherapy. Nevertheless, the OM molecular structure and its dynamics are poorly understood because the structure is difficult to recreate or study in vitro. The successful formation and characterization of a fully asymmetric model envelope using Langmuir-Blodgett and Langmuir-Schaefer methods is now reported. Neutron reflectivity and isotopic labeling confirmed the expected structure and asymmetry and showed that experiments with antibacterial proteins reproduced published in vivo behavior. By closely recreating natural OM behavior, this model provides a much needed robust system for antibiotic development. PMID:26331292

  6. Fast and accurate low-dimensional reduction of biophysically detailed neuron models.

    PubMed

    Marasco, Addolorata; Limongiello, Alessandro; Migliore, Michele

    2012-01-01

    Realistic modeling of neurons are quite successful in complementing traditional experimental techniques. However, their networks require a computational power beyond the capabilities of current supercomputers, and the methods used so far to reduce their complexity do not take into account the key features of the cells nor critical physiological properties. Here we introduce a new, automatic and fast method to map realistic neurons into equivalent reduced models running up to > 40 times faster while maintaining a very high accuracy of the membrane potential dynamics during synaptic inputs, and a direct link with experimental observables. The mapping of arbitrary sets of synaptic inputs, without additional fine tuning, would also allow the convenient and efficient implementation of a new generation of large-scale simulations of brain regions reproducing the biological variability observed in real neurons, with unprecedented advances to understand higher brain functions.

  7. 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.

  8. 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

  9. Simulating Dissolution of Intravitreal Triamcinolone Acetonide Suspensions in an Anatomically Accurate Rabbit Eye Model

    PubMed Central

    Horner, Marc; Muralikrishnan, R.

    2010-01-01

    ABSTRACT Purpose A computational fluid dynamics (CFD) study examined the impact of particle size on dissolution rate and residence of intravitreal suspension depots of Triamcinolone Acetonide (TAC). Methods A model for the rabbit eye was constructed using insights from high-resolution NMR imaging studies (Sawada 2002). The current model was compared to other published simulations in its ability to predict clearance of various intravitreally injected materials. Suspension depots were constructed explicitly rendering individual particles in various configurations: 4 or 16 mg drug confined to a 100 μL spherical depot, or 4 mg exploded to fill the entire vitreous. Particle size was reduced systematically in each configuration. The convective diffusion/dissolution process was simulated using a multiphase model. Results Release rate became independent of particle diameter below a certain value. The size-independent limits occurred for particle diameters ranging from 77 to 428 μM depending upon the depot configuration. Residence time predicted for the spherical depots in the size-independent limit was comparable to that observed in vivo. Conclusions Since the size-independent limit was several-fold greater than the particle size of commercially available pharmaceutical TAC suspensions, differences in particle size amongst such products are predicted to be immaterial to their duration or performance. PMID:20467888

  10. Mathematical model accurately predicts protein release from an affinity-based delivery system.

    PubMed

    Vulic, Katarina; Pakulska, Malgosia M; Sonthalia, Rohit; Ramachandran, Arun; Shoichet, Molly S

    2015-01-10

    Affinity-based controlled release modulates the delivery of protein or small molecule therapeutics through transient dissociation/association. To understand which parameters can be used to tune release, we used a mathematical model based on simple binding kinetics. A comprehensive asymptotic analysis revealed three characteristic regimes for therapeutic release from affinity-based systems. These regimes can be controlled by diffusion or unbinding kinetics, and can exhibit release over either a single stage or two stages. This analysis fundamentally changes the way we think of controlling release from affinity-based systems and thereby explains some of the discrepancies in the literature on which parameters influence affinity-based release. The rate of protein release from affinity-based systems is determined by the balance of diffusion of the therapeutic agent through the hydrogel and the dissociation kinetics of the affinity pair. Equations for tuning protein release rate by altering the strength (KD) of the affinity interaction, the concentration of binding ligand in the system, the rate of dissociation (koff) of the complex, and the hydrogel size and geometry, are provided. We validated our model by collapsing the model simulations and the experimental data from a recently described affinity release system, to a single master curve. Importantly, this mathematical analysis can be applied to any single species affinity-based system to determine the parameters required for a desired release profile. PMID:25449806

  11. 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.

  12. 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.

  13. Anisotropic distributions in a multiphase transport model

    NASA Astrophysics Data System (ADS)

    Zhou, You; Xiao, Kai; Feng, Zhao; Liu, Feng; Snellings, Raimond

    2016-03-01

    With a multiphase transport (AMPT) model we investigate the relation between the magnitude, fluctuations, and correlations of the initial state spatial anisotropy ɛn and the final state anisotropic flow coefficients vn in Au+Au collisions at √{s NN}=200 GeV. It is found that the relative eccentricity fluctuations in AMPT account for the observed elliptic flow fluctuations, both are in agreement with the elliptic flow fluctuation measurements from the STAR collaboration. In addition, the studies based on two- and multiparticle correlations and event-by-event distributions of the anisotropies suggest that the elliptic-power function is a promising candidate of the underlying probability density function of the event-by-event distributions of ɛn as well as vn. Furthermore, the correlations between different order symmetry planes and harmonics in the initial coordinate space and final state momentum space are presented. Nonzero values of these correlations have been observed. The comparison between our calculations and data will, in the future, shed new insight into the nature of the fluctuations of the quark-gluon plasma produced in heavy ion collisions.

  14. Effects of the inlet conditions and blood models on accurate prediction of hemodynamics in the stented coronary arteries

    NASA Astrophysics Data System (ADS)

    Jiang, Yongfei; Zhang, Jun; Zhao, Wanhua

    2015-05-01

    Hemodynamics altered by stent implantation is well-known to be closely related to in-stent restenosis. Computational fluid dynamics (CFD) method has been used to investigate the hemodynamics in stented arteries in detail and help to analyze the performances of stents. In this study, blood models with Newtonian or non-Newtonian properties were numerically investigated for the hemodynamics at steady or pulsatile inlet conditions respectively employing CFD based on the finite volume method. The results showed that the blood model with non-Newtonian property decreased the area of low wall shear stress (WSS) compared with the blood model with Newtonian property and the magnitude of WSS varied with the magnitude and waveform of the inlet velocity. The study indicates that the inlet conditions and blood models are all important for accurately predicting the hemodynamics. This will be beneficial to estimate the performances of stents and also help clinicians to select the proper stents for the patients.

  15. 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.

  16. 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.

  17. Application of divided convective-dispersive transport model to simulate conservative transport processes in planted horizontal sub-surface flow constructed wetlands.

    PubMed

    Dittrich, Ernő; Klincsik, Mihály

    2015-11-01

    We have created a divided convective-dispersive transport (D-CDT) model that can be used to provide an accurate simulation of conservative transport processes in planted horizontal sub-surface flow constructed wetlands filled with coarse gravel (HSFCW-C). This model makes a fitted response curve from the sum of two independent CDT curves, which show the contributions of the main and side streams. The analytical solutions of both CDT curves are inverse Gaussian distribution functions. We used Fréchet distribution to provide a fast optimization mathematical procedure. As a result of our detailed analysis, we concluded that the most important role in the fast upward part of the tracer response curve is played by the main stream, with high porous velocity and dispersion. This gives the first inverse Gaussian distribution function. The side stream shows slower transport processes in the micro-porous system, and this shows the impact of back-mixing and dead zones, too. The significance of this new model is that it can simulate transport processes in this kind of systems more accurately than the conventionally used convective-dispersive transport (CDT) model. The calculated velocity and dispersion coefficients with the D-CDT model gave differences of 24-54% (of velocity) and 22-308% (of dispersion coeff.) from the conventional CDT model, and were closer to actual hydraulic behaviour.

  18. A Simple Iterative Model Accurately Captures Complex Trapline Formation by Bumblebees Across Spatial Scales and Flower Arrangements

    PubMed Central

    Reynolds, Andrew M.; Lihoreau, Mathieu; Chittka, Lars

    2013-01-01

    Pollinating bees develop foraging circuits (traplines) to visit multiple flowers in a manner that minimizes overall travel distance, a task analogous to the travelling salesman problem. We report on an in-depth exploration of an iterative improvement heuristic model of bumblebee traplining previously found to accurately replicate the establishment of stable routes by bees between flowers distributed over several hectares. The critical test for a model is its predictive power for empirical data for which the model has not been specifically developed, and here the model is shown to be consistent with observations from different research groups made at several spatial scales and using multiple configurations of flowers. We refine the model to account for the spatial search strategy of bees exploring their environment, and test several previously unexplored predictions. We find that the model predicts accurately 1) the increasing propensity of bees to optimize their foraging routes with increasing spatial scale; 2) that bees cannot establish stable optimal traplines for all spatial configurations of rewarding flowers; 3) the observed trade-off between travel distance and prioritization of high-reward sites (with a slight modification of the model); 4) the temporal pattern with which bees acquire approximate solutions to travelling salesman-like problems over several dozen foraging bouts; 5) the instability of visitation schedules in some spatial configurations of flowers; 6) the observation that in some flower arrays, bees' visitation schedules are highly individually different; 7) the searching behaviour that leads to efficient location of flowers and routes between them. Our model constitutes a robust theoretical platform to generate novel hypotheses and refine our understanding about how small-brained insects develop a representation of space and use it to navigate in complex and dynamic environments. PMID:23505353

  19. A simple iterative model accurately captures complex trapline formation by bumblebees across spatial scales and flower arrangements.

    PubMed

    Reynolds, Andrew M; Lihoreau, Mathieu; Chittka, Lars

    2013-01-01

    Pollinating bees develop foraging circuits (traplines) to visit multiple flowers in a manner that minimizes overall travel distance, a task analogous to the travelling salesman problem. We report on an in-depth exploration of an iterative improvement heuristic model of bumblebee traplining previously found to accurately replicate the establishment of stable routes by bees between flowers distributed over several hectares. The critical test for a model is its predictive power for empirical data for which the model has not been specifically developed, and here the model is shown to be consistent with observations from different research groups made at several spatial scales and using multiple configurations of flowers. We refine the model to account for the spatial search strategy of bees exploring their environment, and test several previously unexplored predictions. We find that the model predicts accurately 1) the increasing propensity of bees to optimize their foraging routes with increasing spatial scale; 2) that bees cannot establish stable optimal traplines for all spatial configurations of rewarding flowers; 3) the observed trade-off between travel distance and prioritization of high-reward sites (with a slight modification of the model); 4) the temporal pattern with which bees acquire approximate solutions to travelling salesman-like problems over several dozen foraging bouts; 5) the instability of visitation schedules in some spatial configurations of flowers; 6) the observation that in some flower arrays, bees' visitation schedules are highly individually different; 7) the searching behaviour that leads to efficient location of flowers and routes between them. Our model constitutes a robust theoretical platform to generate novel hypotheses and refine our understanding about how small-brained insects develop a representation of space and use it to navigate in complex and dynamic environments.

  20. Development of a Godunov-type model for the accurate simulation of dispersion dominated waves

    NASA Astrophysics Data System (ADS)

    Bradford, Scott F.

    2016-10-01

    A new numerical model based on the Navier-Stokes equations is presented for the simulation of dispersion dominated waves. The equations are solved by splitting the pressure into hydrostatic and non-hydrostatic components. The Godunov approach is utilized to solve the hydrostatic flow equations and the resulting velocity field is then corrected to be divergence free. Alternative techniques for the time integration of the non-hydrostatic pressure gradients are presented and investigated in order to improve the accuracy of dispersion dominated wave simulations. Numerical predictions are compared with analytical solutions and experimental data for test cases involving standing, shoaling, refracting, and breaking waves.

  1. 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.

  2. 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.

  3. Affine-response model of molecular solvation of ions: Accurate predictions of asymmetric charging free energies

    PubMed Central

    Bardhan, Jaydeep P.; Jungwirth, Pavel; Makowski, Lee

    2012-01-01

    Two mechanisms have been proposed to drive asymmetric solvent response to a solute charge: a static potential contribution similar to the liquid-vapor potential, and a steric contribution associated with a water molecule's structure and charge distribution. In this work, we use free-energy perturbation molecular-dynamics calculations in explicit water to show that these mechanisms act in complementary regimes; the large static potential (∼44 kJ/mol/e) dominates asymmetric response for deeply buried charges, and the steric contribution dominates for charges near the solute-solvent interface. Therefore, both mechanisms must be included in order to fully account for asymmetric solvation in general. Our calculations suggest that the steric contribution leads to a remarkable deviation from the popular “linear response” model in which the reaction potential changes linearly as a function of charge. In fact, the potential varies in a piecewise-linear fashion, i.e., with different proportionality constants depending on the sign of the charge. This discrepancy is significant even when the charge is completely buried, and holds for solutes larger than single atoms. Together, these mechanisms suggest that implicit-solvent models can be improved using a combination of affine response (an offset due to the static potential) and piecewise-linear response (due to the steric contribution). PMID:23020318

  4. Modeling of Anomalous Transport in Tokamaks with FACETS code

    NASA Astrophysics Data System (ADS)

    Pankin, A. Y.; Batemann, G.; Kritz, A.; Rafiq, T.; Vadlamani, S.; Hakim, A.; Kruger, S.; Miah, M.; Rognlien, T.

    2009-05-01

    The FACETS code, a whole-device integrated modeling code that self-consistently computes plasma profiles for the plasma core and edge in tokamaks, has been recently developed as a part of the SciDAC project for core-edge simulations. A choice of transport models is available in FACETS through the FMCFM interface [1]. Transport models included in FMCFM have specific ranges of applicability, which can limit their use to parts of the plasma. In particular, the GLF23 transport model does not include the resistive ballooning effects that can be important in the tokamak pedestal region and GLF23 typically under-predicts the anomalous fluxes near the magnetic axis [2]. The TGLF and GYRO transport models have similar limitations [3]. A combination of transport models that covers the entire discharge domain is studied using FACETS in a realistic tokamak geometry. Effective diffusivities computed with the FMCFM transport models are extended to the region near the separatrix to be used in the UEDGE code within FACETS. 1. S. Vadlamani et al. (2009) %First time-dependent transport simulations using GYRO and NCLASS within FACETS (this meeting).2. T. Rafiq et al. (2009) %Simulation of electron thermal transport in H-mode discharges Submitted to Phys. Plasmas.3. C. Holland et al. (2008) %Validation of gyrokinetic transport simulations using %DIII-D core turbulence measurements Proc. of IAEA FEC (Switzerland, 2008)

  5. 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.

  6. Trapped gyro-Landau-fluid transport modeling of DIII-D hybrid discharges

    SciTech Connect

    Kinsey, J. E.; Staebler, G. M.; Petty, C. C.

    2010-12-15

    Previous work has summarized the physics and first results of benchmarking the trapped gyro-Landau-fluid (TGLF) model for turbulent transport driven by trapped ion and electron modes, ion and electron temperature gradient (ETG) modes, and electromagnetic kinetic ballooning modes including the effects of shaped geometry. Recently, an improved collision model was implemented which provides a more accurate fit to a transport database of nonlinear collisional GYRO[J. Candy and R. E. Waltz, J. Comput. Phys. 186, 545 (2003)] simulations of long wavelength driftwave turbulence. The impact of the new collision model on TGLF modeling results was unknown. Using the improved TGLF model we obtain excellent agreement with the ion and electron temperature profiles from 30 DIII-D [A. Mahdavi and J. L. Luxon, Fusion Sci. Technol. 48, 2 (2005)] hybrid discharges. The transport results show that the electron energy transport tends to be dominated by short wavelength ETG modes in cases where the ion energy transport approaches neoclassical levels. The hybrid regime has significant energy confinement improvement from ExB velocity shear which is well predicted by TGLF. Weak magnetic shear and low safety factor are also shown to enhance the hybrid regime energy confinement. In high normalized {beta} hybrids, we find that finite {beta} effects noticably reduce the predicted electron energy transport and improve agreement with the measured electron temperature profiles.

  7. Trapped gyro-Landau-fluid transport modeling of DIII-D hybrid discharges

    NASA Astrophysics Data System (ADS)

    Kinsey, J. E.; Staebler, G. M.; Petty, C. C.

    2010-12-01

    Previous work has summarized the physics and first results of benchmarking the trapped gyro-Landau-fluid (TGLF) model for turbulent transport driven by trapped ion and electron modes, ion and electron temperature gradient (ETG) modes, and electromagnetic kinetic ballooning modes including the effects of shaped geometry. Recently, an improved collision model was implemented which provides a more accurate fit to a transport database of nonlinear collisional GYRO [J. Candy and R. E. Waltz, J. Comput. Phys. 186, 545 (2003)] simulations of long wavelength driftwave turbulence. The impact of the new collision model on TGLF modeling results was unknown. Using the improved TGLF model we obtain excellent agreement with the ion and electron temperature profiles from 30 DIII-D [A. Mahdavi and J. L. Luxon, Fusion Sci. Technol. 48, 2 (2005)] hybrid discharges. The transport results show that the electron energy transport tends to be dominated by short wavelength ETG modes in cases where the ion energy transport approaches neoclassical levels. The hybrid regime has significant energy confinement improvement from E ×B velocity shear which is well predicted by TGLF. Weak magnetic shear and low safety factor are also shown to enhance the hybrid regime energy confinement. In high normalized β hybrids, we find that finite β effects noticably reduce the predicted electron energy transport and improve agreement with the measured electron temperature profiles.

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

    PubMed Central

    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. PMID:26106329

  9. 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.

  10. 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.

  11. 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

  12. Accurate programmable electrocardiogram generator using a dynamical model implemented on a microcontroller

    NASA Astrophysics Data System (ADS)

    Chien Chang, Jia-Ren; Tai, Cheng-Chi

    2006-07-01

    This article reports on the design and development of a complete, programmable electrocardiogram (ECG) generator, which can be used for the testing, calibration and maintenance of electrocardiograph equipment. A modified mathematical model, developed from the three coupled ordinary differential equations of McSharry et al. [IEEE Trans. Biomed. Eng. 50, 289, (2003)], was used to locate precisely the positions of the onset, termination, angle, and duration of individual components in an ECG. Generator facilities are provided so the user can adjust the signal amplitude, heart rate, QRS-complex slopes, and P- and T-wave settings. The heart rate can be adjusted in increments of 1BPM (beats per minute), from 20to176BPM, while the amplitude of the ECG signal can be set from 0.1to400mV with a 0.1mV resolution. Experimental results show that the proposed concept and the resulting system are feasible.

  13. Communication: Accurate higher-order van der Waals coefficients between molecules from a model dynamic multipole polarizability

    NASA Astrophysics Data System (ADS)

    Tao, Jianmin; Rappe, Andrew M.

    2016-01-01

    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 C6 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 C8 and C10 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 C8 and 7% for C10. 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.

  14. Accurate analytical modelling of cosmic ray induced failure rates of power semiconductor devices

    NASA Astrophysics Data System (ADS)

    Bauer, Friedhelm D.

    2009-06-01

    A new, simple and efficient approach is presented to conduct estimations of the cosmic ray induced failure rate for high voltage silicon power devices early in the design phase. This allows combining common design issues such as device losses and safe operating area with the constraints imposed by the reliability to result in a better and overall more efficient design methodology. Starting from an experimental and theoretical background brought forth a few yeas ago [Kabza H et al. Cosmic radiation as a cause for power device failure and possible countermeasures. In: Proceedings of the sixth international symposium on power semiconductor devices and IC's, Davos, Switzerland; 1994. p. 9-12, Zeller HR. Cosmic ray induced breakdown in high voltage semiconductor devices, microscopic model and possible countermeasures. In: Proceedings of the sixth international symposium on power semiconductor devices and IC's, Davos, Switzerland; 1994. p. 339-40, and Matsuda H et al. Analysis of GTO failure mode during d.c. blocking. In: Proceedings of the sixth international symposium on power semiconductor devices and IC's, Davos, Switzerland; 1994. p. 221-5], an exact solution of the failure rate integral is derived and presented in a form which lends itself to be combined with the results available from commercial semiconductor simulation tools. Hence, failure rate integrals can be obtained with relative ease for realistic two- and even three-dimensional semiconductor geometries. Two case studies relating to IGBT cell design and planar junction termination layout demonstrate the purpose of the method.

  15. Accurate Estimation of Protein Folding and Unfolding Times: Beyond Markov State Models.

    PubMed

    Suárez, Ernesto; Adelman, Joshua L; Zuckerman, Daniel M

    2016-08-01

    Because standard molecular dynamics (MD) simulations are unable to access time scales of interest in complex biomolecular systems, it is common to "stitch together" information from multiple shorter trajectories using approximate Markov state model (MSM) analysis. However, MSMs may require significant tuning and can yield biased results. Here, by analyzing some of the longest protein MD data sets available (>100 μs per protein), we show that estimators constructed based on exact non-Markovian (NM) principles can yield significantly improved mean first-passage times (MFPTs) for protein folding and unfolding. In some cases, MSM bias of more than an order of magnitude can be corrected when identical trajectory data are reanalyzed by non-Markovian approaches. The NM analysis includes "history" information, higher order time correlations compared to MSMs, that is available in every MD trajectory. The NM strategy is insensitive to fine details of the states used and works well when a fine time-discretization (i.e., small "lag time") is used. PMID:27340835

  16. A quantum energy transport model for semiconductor device simulation

    SciTech Connect

    Sho, Shohiro; Odanaka, Shinji

    2013-02-15

    This paper describes numerical methods for a quantum energy transport (QET) model in semiconductors, which is derived by using a diffusion scaling in the quantum hydrodynamic (QHD) model. We newly drive a four-moments QET model similar with a classical ET model. Space discretization is performed by a new set of unknown variables. Numerical stability and convergence are obtained by developing numerical schemes and an iterative solution method with a relaxation method. Numerical simulations of electron transport in a scaled MOSFET device are discussed. The QET model allows simulations of quantum confinement transport, and nonlocal and hot-carrier effects in scaled MOSFETs.

  17. Small pores in soils: Is the physico-chemical environment accurately reflected in biogeochemical models ?

    NASA Astrophysics Data System (ADS)

    Weber, Tobias K. D.; Riedel, Thomas

    2015-04-01

    Free water is a prerequesite to chemical reactions and biological activity in earth's upper crust essential to life. The void volume between the solid compounds provides space for water, air, and organisms that thrive on the consumption of minerals and organic matter thereby regulating soil carbon turnover. However, not all water in the pore space in soils and sediments is in its liquid state. This is a result of the adhesive forces which reduce the water activity in small pores and charged mineral surfaces. This water has a lower tendency to react chemically in solution as this additional binding energy lowers its activity. In this work, we estimated the amount of soil pore water that is thermodynamically different from a simple aqueous solution. The quantity of soil pore water with properties different to liquid water was found to systematically increase with increasing clay content. The significance of this is that the grain size and surface area apparently affects the thermodynamic state of water. This implies that current methods to determine the amount of water content, traditionally determined from bulk density or gravimetric water content after drying at 105°C overestimates the amount of free water in a soil especially at higher clay content. Our findings have consequences for biogeochemical processes in soils, e.g. nutrients may be contained in water which is not free which could enhance preservation. From water activity measurements on a set of various soils with 0 to 100 wt-% clay, we can show that 5 to 130 mg H2O per g of soil can generally be considered as unsuitable for microbial respiration. These results may therefore provide a unifying explanation for the grain size dependency of organic matter preservation in sedimentary environments and call for a revised view on the biogeochemical environment in soils and sediments. This could allow a different type of process oriented modelling.

  18. 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. PMID:26199424

  19. 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.

  20. Comparison of model results transporting the odd nitrogen family with results transporting separate odd nitrogen species

    NASA Technical Reports Server (NTRS)

    Douglass, Anne R.; Jackman, Charles H.; Stolarski, Richard S.

    1989-01-01

    A fast two-dimensional residual circulation stratospheric family transport model, designed to minimize computer requirements, is developed. The model was used to calculate the ambient and perturbed atmospheres in which odd nitrogen species are transported as a family, and the results were compared with calculations in which HNO3, N2O5, ClONO2, and HO2NO2 are transported separately. It was found that ozone distributions computed by the two models for a present-day atmosphere are nearly identical. Good agreement was also found between calculated species concentrations and the ozone response, indicating the general applicability of the odd-nitrogen family approximations.

  1. 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

  2. Prognostic models and risk scores: can we accurately predict postoperative nausea and vomiting in children after craniotomy?

    PubMed

    Neufeld, Susan M; Newburn-Cook, Christine V; Drummond, Jane E

    2008-10-01

    Postoperative nausea and vomiting (PONV) is a problem for many children after craniotomy. Prognostic models and risk scores help identify who is at risk for an adverse event such as PONV to help guide clinical care. The purpose of this article is to assess whether an existing prognostic model or risk score can predict PONV in children after craniotomy. The concepts of transportability, calibration, and discrimination are presented to identify what is required to have a valid tool for clinical use. Although previous work may inform clinical practice and guide future research, existing prognostic models and risk scores do not appear to be options for predicting PONV in children undergoing craniotomy. However, until risk factors are further delineated, followed by the development and validation of prognostic models and risk scores that include children after craniotomy, clinical judgment in the context of current research may serve as a guide for clinical care in this population. PMID:18939320

  3. 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.

  4. 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

  5. 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.

  6. Mathematical Modelling of Cation Transport and Regulation in Yeast.

    PubMed

    Kahm, Matthiasé; Kschischo, Maik

    2016-01-01

    Mathematical modelling of ion transport is a strategy to understand the complex interplay between various ionic species and their transporters. Such models should provide new insights and suggest new interesting experiments. Two essential variables in models for ion transport and control are the membrane potential and the intracellular pH, which generates an additional layer of complexity absent from many other models of biochemical reaction pathways. The aim of this text is to introduce the reader to the basic principles and assumptions of modelling in this field. A simplified model of potassium transport will be used as an example and will be derived in a step by step manner. This forms the basis for understanding the advantages and limitations of more complex models. These are briefly reviewed at the end of this chapter.

  7. Implementation of Gravity Model to Estimation of Transportation Market Shares

    NASA Astrophysics Data System (ADS)

    Krata, Przemysław

    2010-03-01

    The theoretical consideration presented in the paper is inspired by market gravity models, as an interesting attitude towards operations research on a market. The transportation market issues are emphasized. The mathematical model of relations, taking place between transportation companies and their customers on the market, which is applied in the course of the research is based on continuous functions characteristics. This attitude enables the use of the field theory notions. The resultant vector-type utility function facilitates obtaining of competitive advantage areas for all transportation companies located on the considered transportation market.

  8. 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.

  9. Modeling of cellular arginine uptake by more than one transporter.

    PubMed

    Nel, Marietha J; Woodiwiss, Angela J; Candy, Geoffrey P

    2012-01-01

    Determining the kinetic constants of arginine uptake by endothelial cells mediated by more than one transporter from linearization of data as Eadie-Hofstee plots or modeling which does not include the concentration of trace radiolabeled amino acid used to measure uptake may not be correct. The initial rate of uptake of trace [³H]L-arginine by HUVECs and ECV₃₀₄ cells in the presence of a range of unlabeled arginine and modifiers was used in nonlinear models to calculate the constants of arginine uptake using GraphPad Prism. Theoretical plots of uptake derived from constants determined from Eadie-Hofstee graphs overestimated uptake, whereas those from the nonlinear modeling approach agreed with experimental data. The contribution of uptake by individual transporters could be modeled and showed that leucine inhibited the individual transporters differently and not necessarily competitively. N-Ethylmaleimide inhibited only y⁺ transport, and BCH may be a selective inhibitor of y⁺L transport. The absence of sodium reduced arginine uptake by y⁺L transport and reduced the K(m)', whereas reducing sodium decreased arginine uptake by y⁺ transport without affecting the K (m)'. The nonlinear modeling approach using raw data avoided the errors inherent in methods deriving constants from the linearization of the uptake processes following Michaelian kinetics. This study provides explanations for discrepancies in the literature and suggests that a nonlinear modeling approach better characterizes the kinetics of amino acid uptake into cells by more than one transporter.

  10. Accurate prediction model of bead geometry in crimping butt of the laser brazing using generalized regression neural network

    NASA Astrophysics Data System (ADS)

    Rong, Y. M.; Chang, Y.; Huang, Y.; Zhang, G. J.; Shao, X. Y.

    2015-12-01

    There are few researches that concentrate on the prediction of the bead geometry for laser brazing with crimping butt. This paper addressed the accurate prediction of the bead profile by developing a generalized regression neural network (GRNN) algorithm. Firstly GRNN model was developed and trained to decrease the prediction error that may be influenced by the sample size. Then the prediction accuracy was demonstrated by comparing with other articles and back propagation artificial neural network (BPNN) algorithm. Eventually the reliability and stability of GRNN model were discussed from the points of average relative error (ARE), mean square error (MSE) and root mean square error (RMSE), while the maximum ARE and MSE were 6.94% and 0.0303 that were clearly less than those (14.28% and 0.0832) predicted by BPNN. Obviously, it was proved that the prediction accuracy was improved at least 2 times, and the stability was also increased much more.

  11. In pursuit of an accurate spatial and temporal model of biomolecules at the atomistic level: a perspective on computer simulation

    PubMed Central

    Gray, Alan; Harlen, Oliver G.; Harris, Sarah A.; Khalid, Syma; Leung, Yuk Ming; Lonsdale, Richard; Mulholland, Adrian J.; Pearson, Arwen R.; Read, Daniel J.; Richardson, Robin A.

    2015-01-01

    Despite huge advances in the computational techniques available for simulating biomolecules at the quantum-mechanical, atomistic and coarse-grained levels, there is still a widespread perception amongst the experimental community that these calculations are highly specialist and are not generally applicable by researchers outside the theoretical community. In this article, the successes and limitations of biomolecular simulation and the further developments that are likely in the near future are discussed. A brief overview is also provided of the experimental biophysical methods that are commonly used to probe biomolecular structure and dynamics, and the accuracy of the information that can be obtained from each is compared with that from modelling. It is concluded that progress towards an accurate spatial and temporal model of biomacromolecules requires a combination of all of these biophysical techniques, both experimental and computational. PMID:25615870

  12. A coupling model of the radiative transport equation for calculating photon migration in biological tissue

    NASA Astrophysics Data System (ADS)

    Fujii, Hiroyuki; Okawa, Shinpei; Yamada, Yukio; Hoshi, Yoko; Watanabe, Masao

    2015-12-01

    Development of a physically accurate and computationally efficient photon migration model for turbid media is crucial for optical computed tomography such as diffuse optical tomography. For the development, this paper constructs a space-time coupling model of the radiative transport equation with the photon diffusion equation. In the coupling model, a space-time regime of the photon migration is divided into the ballistic and diffusive regimes with the interaction between the both regimes to improve the accuracy of the results and the efficiency of computation. The coupling model provides an accurate description of the photon migration in various turbid media in a wide range of the optical properties, and reduces computational loads when compared with those of full calculation of the RTE.

  13. 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.

  14. 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. PMID:27130467

  15. 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.

  16. Coarse-graining intermittent intracellular transport: Two- and three-dimensional models.

    PubMed

    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.

  17. 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.

  18. A comparison of total reaction cross section models used in particle and heavy ion transport codes

    NASA Astrophysics Data System (ADS)

    Sihver, Lembit; Lantz, M.; Takechi, M.; Kohama, A.; Ferrari, A.; Cerutti, F.; Sato, T.

    To be able to calculate the nucleon-nucleus and nucleus-nucleus total reaction cross sections with precision is very important for studies of basic nuclear properties, e.g. nuclear structure. This is also of importance for particle and heavy ion transport calculations because, in all particle and heavy ion transport codes, the probability function that a projectile particle will collide within a certain distance x in the matter depends on the total reaction cross sections. Furthermore, the total reaction cross sections will also scale the calculated partial fragmentation cross sections. It is therefore crucial that accurate total reaction cross section models are used in the transport calculations. In this paper, different models for calculating nucleon-nucleus and nucleus-nucleus total reaction cross sections are compared and discussed.

  19. 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.

  20. Predictive modelling and simulations of internal transport barriers in tokamaks

    NASA Astrophysics Data System (ADS)

    Zhu, Ping

    2001-09-01

    An Internal Transport Barrier (ITB) is a localized region inside a (tokamak) plasma where a steep temperature and/or density gradient forms due to much lower thermal and/or particle transport than in the surrounding regions. Internal transport barriers have now been observed in all large tokamaks after they were first discovered in the Japan Atomic Energy Research Institute Tokamak-60 Upgrade (JT-60U) in 1993. While suggesting a promising practical approach to the realization of fusion ignition conditions, this high performance regime poses a great challenge to our understanding of tokamak anomalous transport physics. In this work, the formation and evolution of internal transport barriers in tokamaks are studied through predictive transport modelling and simulations. Neoclassical and anomalous transport of particles, energy, and toroidal momentum are systematically formulated from the ensemble-averaged gyrokinetic equation, for a tokamak plasma with large toroidal flow on the order of the ion thermal speed. This formulation is then used to construct an updated Multi-Mode model (MMM) based on (1)the Weiland fluid model for the drift wave transport, (2)the Scott-Bateman model for drift-Alfvèn mode at the tokamak edge, and (3)poloidal and toroidal momentum transport models by Zhu, Horton and Sugama. The formation of internal transport barriers observed in two optimized shear discharges in the Joint European Torus (JET) and two negative central shear discharges in the Doublet III-D Tokamak (DIII-D) are reproduced in predictive transport simulations that use the updated MultiMode model embedded in the time-dependent one/one and half dimensional transport code BALDUR. The Weiland model for drift modes in the MultiMode model is implemented in combination with either the Hahm-Burrell or the Hamaguchi-Horton flow shear stabilization mechanisms, where the radial electric field is inferred from both the measured toroidal velocity profile and the poloidal velocity profile

  1. An evolutionary model-based algorithm for accurate phylogenetic breakpoint mapping and subtype prediction in HIV-1.

    PubMed

    Kosakovsky Pond, Sergei L; Posada, David; Stawiski, Eric; Chappey, Colombe; Poon, Art F Y; Hughes, Gareth; Fearnhill, Esther; Gravenor, Mike B; Leigh Brown, Andrew J; Frost, Simon D W

    2009-11-01

    Genetically diverse pathogens (such as Human Immunodeficiency virus type 1, HIV-1) are frequently stratified into phylogenetically or immunologically defined subtypes for classification purposes. Computational identification of such subtypes is helpful in surveillance, epidemiological analysis and detection of novel variants, e.g., circulating recombinant forms in HIV-1. A number of conceptually and technically different techniques have been proposed for determining the subtype of a query sequence, but there is not a universally optimal approach. We present a model-based phylogenetic method for automatically subtyping an HIV-1 (or other viral or bacterial) sequence, mapping the location of breakpoints and assigning parental sequences in recombinant strains as well as computing confidence levels for the inferred quantities. Our Subtype Classification Using Evolutionary ALgorithms (SCUEAL) procedure is shown to perform very well in a variety of simulation scenarios, runs in parallel when multiple sequences are being screened, and matches or exceeds the performance of existing approaches on typical empirical cases. We applied SCUEAL to all available polymerase (pol) sequences from two large databases, the Stanford Drug Resistance database and the UK HIV Drug Resistance Database. Comparing with subtypes which had previously been assigned revealed that a minor but substantial (approximately 5%) fraction of pure subtype sequences may in fact be within- or inter-subtype recombinants. A free implementation of SCUEAL is provided as a module for the HyPhy package and the Datamonkey web server. Our method is especially useful when an accurate automatic classification of an unknown strain is desired, and is positioned to complement and extend faster but less accurate methods. Given the increasingly frequent use of HIV subtype information in studies focusing on the effect of subtype on treatment, clinical outcome, pathogenicity and vaccine design, the importance of accurate

  2. 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

  3. 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

  4. SU-E-T-475: An Accurate Linear Model of Tomotherapy MLC-Detector System for Patient Specific Delivery QA

    SciTech Connect

    Chen, Y; Mo, X; Chen, M; Olivera, G; Parnell, D; Key, S; Lu, W; Reeher, M; Galmarini, D

    2014-06-01

    Purpose: An accurate leaf fluence model can be used in applications such as patient specific delivery QA and in-vivo dosimetry for TomoTherapy systems. It is known that the total fluence is not a linear combination of individual leaf fluence due to leakage-transmission, tongue-and-groove, and source occlusion effect. Here we propose a method to model the nonlinear effects as linear terms thus making the MLC-detector system a linear system. Methods: A leaf pattern basis (LPB) consisting of no-leaf-open, single-leaf-open, double-leaf-open and triple-leaf-open patterns are chosen to represent linear and major nonlinear effects of leaf fluence as a linear system. An arbitrary leaf pattern can be expressed as (or decomposed to) a linear combination of the LPB either pulse by pulse or weighted by dwelling time. The exit detector responses to the LPB are obtained by processing returned detector signals resulting from the predefined leaf patterns for each jaw setting. Through forward transformation, detector signal can be predicted given a delivery plan. An equivalent leaf open time (LOT) sinogram containing output variation information can also be inversely calculated from the measured detector signals. Twelve patient plans were delivered in air. The equivalent LOT sinograms were compared with their planned sinograms. Results: The whole calibration process was done in 20 minutes. For two randomly generated leaf patterns, 98.5% of the active channels showed differences within 0.5% of the local maximum between the predicted and measured signals. Averaged over the twelve plans, 90% of LOT errors were within +/−10 ms. The LOT systematic error increases and shows an oscillating pattern when LOT is shorter than 50 ms. Conclusion: The LPB method models the MLC-detector response accurately, which improves patient specific delivery QA and in-vivo dosimetry for TomoTherapy systems. It is sensitive enough to detect systematic LOT errors as small as 10 ms.

  5. Toward accurate modelling of the non-linear matter bispectrum: standard perturbation theory and transients from initial conditions

    NASA Astrophysics Data System (ADS)

    McCullagh, Nuala; Jeong, Donghui; Szalay, Alexander S.

    2016-01-01

    Accurate modelling of non-linearities in the galaxy bispectrum, the Fourier transform of the galaxy three-point correlation function, is essential to fully exploit it as a cosmological probe. In this paper, we present numerical and theoretical challenges in modelling the non-linear bispectrum. First, we test the robustness of the matter bispectrum measured from N-body simulations using different initial conditions generators. We run a suite of N-body simulations using the Zel'dovich approximation and second-order Lagrangian perturbation theory (2LPT) at different starting redshifts, and find that transients from initial decaying modes systematically reduce the non-linearities in the matter bispectrum. To achieve 1 per cent accuracy in the matter bispectrum at z ≤ 3 on scales k < 1 h Mpc-1, 2LPT initial conditions generator with initial redshift z ≳ 100 is required. We then compare various analytical formulas and empirical fitting functions for modelling the non-linear matter bispectrum, and discuss the regimes for which each is valid. We find that the next-to-leading order (one-loop) correction from standard perturbation theory matches with N-body results on quasi-linear scales for z ≥ 1. We find that the fitting formula in Gil-Marín et al. accurately predicts the matter bispectrum for z ≤ 1 on a wide range of scales, but at higher redshifts, the fitting formula given in Scoccimarro & Couchman gives the best agreement with measurements from N-body simulations.

  6. Molecular modeling and ligand docking for solute carrier (SLC) transporters.

    PubMed

    Schlessinger, Avner; Khuri, Natalia; Giacomini, Kathleen M; Sali, Andrej

    2013-01-01

    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.

  7. Accurate prediction of interfacial residues in two-domain proteins using evolutionary information: implications for three-dimensional modeling.

    PubMed

    Bhaskara, Ramachandra M; Padhi, Amrita; Srinivasan, Narayanaswamy

    2014-07-01

    With the preponderance of multidomain proteins in eukaryotic genomes, it is essential to recognize the constituent domains and their functions. Often function involves communications across the domain interfaces, and the knowledge of the interacting sites is essential to our understanding of the structure-function relationship. Using evolutionary information extracted from homologous domains in at least two diverse domain architectures (single and multidomain), we predict the interface residues corresponding to domains from the two-domain proteins. We also use information from the three-dimensional structures of individual domains of two-domain proteins to train naïve Bayes classifier model to predict the interfacial residues. Our predictions are highly accurate (∼85%) and specific (∼95%) to the domain-domain interfaces. This method is specific to multidomain proteins which contain domains in at least more than one protein architectural context. Using predicted residues to constrain domain-domain interaction, rigid-body docking was able to provide us with accurate full-length protein structures with correct orientation of domains. We believe that these results can be of considerable interest toward rational protein and interaction design, apart from providing us with valuable information on the nature of interactions.

  8. 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

  9. A homotopy-based sparse representation for fast and accurate shape prior modeling in liver surgical planning.

    PubMed

    Wang, Guotai; Zhang, Shaoting; Xie, Hongzhi; Metaxas, Dimitris N; Gu, Lixu

    2015-01-01

    Shape prior plays an important role in accurate and robust liver segmentation. However, liver shapes have complex variations and accurate modeling of liver shapes is challenging. Using large-scale training data can improve the accuracy but it limits the computational efficiency. In order to obtain accurate liver shape priors without sacrificing the efficiency when dealing with large-scale training data, we investigate effective and scalable shape prior modeling method that is more applicable in clinical liver surgical planning system. We employed the Sparse Shape Composition (SSC) to represent liver shapes by an optimized sparse combination of shapes in the repository, without any assumptions on parametric distributions of liver shapes. To leverage large-scale training data and improve the computational efficiency of SSC, we also introduced a homotopy-based method to quickly solve the L1-norm optimization problem in SSC. This method takes advantage of the sparsity of shape modeling, and solves the original optimization problem in SSC by continuously transforming it into a series of simplified problems whose solution is fast to compute. When new training shapes arrive gradually, the homotopy strategy updates the optimal solution on the fly and avoids re-computing it from scratch. Experiments showed that SSC had a high accuracy and efficiency in dealing with complex liver shape variations, excluding gross errors and preserving local details on the input liver shape. The homotopy-based SSC had a high computational efficiency, and its runtime increased very slowly when repository's capacity and vertex number rose to a large degree. When repository's capacity was 10,000, with 2000 vertices on each shape, homotopy method cost merely about 11.29 s to solve the optimization problem in SSC, nearly 2000 times faster than interior point method. The dice similarity coefficient (DSC), average symmetric surface distance (ASD), and maximum symmetric surface distance measurement

  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. PMID:26974607

  11. Programmers manual for a one-dimensional Lagrangian transport model

    USGS Publications Warehouse

    Schoellhamer, D.H.; Jobson, H.E.

    1986-01-01

    A one-dimensional Lagrangian transport model for simulating water-quality constituents such as temperature, dissolved oxygen , and suspended sediment in rivers is presented in this Programmers Manual. Lagrangian transport modeling techniques, the model 's subroutines, and the user-written decay-coefficient subroutine are discussed in detail. Appendices list the program codes. The Programmers Manual is intended for the model user who needs to modify code either to adapt the model to a particular need or to use reaction kinetics not provided with the model. (Author 's abstract)

  12. Keratin dynamics: modeling the interplay between turnover and transport.

    PubMed

    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.

  13. Improvement of sediment transport models using the shallow water framework

    NASA Astrophysics Data System (ADS)

    Morales de Luna, Tomás; Castro Diaz, Manuel J.; Fernandez Nieto, Enrique D.; Narbona Reina, Gladys

    2016-04-01

    Sediment can be transported in several ways by the action of a river. During low transport stages, particles move by sliding and rolling over the surface of the bed. This type of transport is usually called bedload transport. With the increase of the velocity, the sediment is entrained into suspension and travels significant distances before being deposed again. One can observe a continuous exchange between sediment at the riverbed and sediment in suspension. One possible approach to model these phenomena is to use a shallow water model coupled with transport equations for sediment in suspension and a morphodynamical component for the bedload transport, which depends on an empirical flux. Nevertheless, this approach presents some drawbacks, for instance, the vertical distribution of the sediment in suspension is lost, gravitational effects for bedload transport is neglected and the models are usually too simplified for practical situations. We present here some recent advances in sediment transport modeling that aim to overcome the difficulties present in classic models. In particular, for suspended transport, a multilayer approach results as a promising tool. This allows to keep track of the vertical distribution of sediment and the computational cost is less expensive than a fully 3D approach. In what concerns bedload transport, a new general formulation will be introduced that recovers classic formulae as a particular case, but incorporates more information on the physics of the problem. This makes the model more suitable for practical applications. ACKNOWLEDGMENTS This research has been partially supported by the Junta de Andalucía research project TESELA (P11-RNM7069) and by the Spanish Government and FEDER through the research project DAIFLUID (MTM2012-38383-C02-01 and MTM2012-38383-C02-02)

  14. Reactive Transport Modeling of the Yucca Mountain Site, Nevada

    SciTech Connect

    G. Bodvarsson

    2004-04-20

    The Yucca Mountain site has a dry climate and deep water table, with the repository located in the middle of an unsaturated zone approximately 600 m thick. Radionuclide transport processes from the repository to the water table are sensitive to the unsaturated zone flow field, as well as to sorption, matrix diffusion, radioactive decay, and colloid transport mechanisms. The unsaturated zone flow and transport models are calibrated against both physical and chemical data, including pneumatic pressure, liquid saturation, water potential, temperature, chloride, and calcite. The transport model predictions are further compared with testing specific to unsaturated zone transport: at Alcove 1 in the Exploratory Studies Facility (ESF), at Alcove 8 and Niche 3 of the ESF, and at the Busted Butte site. The models are applied to predict the breakthroughs at the water table for nonsorbing and sorbing radionuclides, with faults shown as the important paths for radionuclide transport. Daughter products of some important radionuclides, such as {sup 239}Pu and {sup 241}Am, have faster transport than the parents and must be considered in the unsaturated zone transport model. Colloid transport is significantly affected by colloid size, but only negligibly affected by lunetic declogging (reverse filtering) mechanisms. Unsaturated zone model uncertainties are discussed, including the sensitivity of breakthrough to the active fracture model parameter, as an example of uncertainties related to detailed flow characteristics and fracture-matrix interaction. It is expected that additional benefits from the unsaturated zone barrier for transport can be achieved by full implementation of the shadow zone concept immediately below the radionuclide release points in the waste emplacement drifts.

  15. The SLC6 transporters: perspectives on structure, functions, regulation, and models for transporter dysfunction

    PubMed Central

    Rudnick, Gary; Krämer, Reinhard; Blakely, Randy D.; Murphy, Dennis L.

    2014-01-01

    The human SLC6 family is composed of approximately 20 structurally related symporters (co-transporters) that use the transmembrane electrochemical gradient to actively import their substrates into cells. Approximately half of the substrates of these transporters are amino acids, with others transporting biogenic amines and/or closely related compounds, such as nutrients and compatible osmolytes. In this short review, five leaders in the field discuss a number of currently important research themes that involve SLC6 transporters, highlighting the integrative role they play across a wide spectrum of different functions. The first essay, by Gary Rudnick, describes the molecular mechanism of their coupled transport which is being progressively better understood based on new crystal structures, functional studies, and modeling. Next, the question of multiple levels of transporter regulation is discussed by Reinhard Krämer, in the context of osmoregulation and stress response by the related bacterial betaine transporter BetP. The role of selected members of the human SLC6 family that function as nutrient amino acid transporters is then reviewed by François Verrey. He discusses how some of these transporters mediate the active uptake of (essential) amino acids into epithelial cells of the gut and the kidney tubule to support systemic amino acid requirements, whereas others are expressed in specific cells to support their specialized metabolism and/or growth. The most extensively studied members of the human SLC6 family are neurotransmitter reuptake transporters, many of which are important drug targets for the treatment of neuropsychiatric disorders. Randy Blakely discusses the role of posttranscriptional modifications of these proteins in regulating transporter subcellular localization and activity state. Finally, Dennis Murphy reviews how natural gene variants and mouse genetic models display consistent behavioral alterations that relate to altered extracellular

  16. A Coupled Model of Multiphase Flow, Reactive Biogeochemical Transport, Thermal Transport and Geo-Mechanics.

    NASA Astrophysics Data System (ADS)

    Tsai, C. H.; Yeh, G. T.

    2015-12-01

    In this investigation, a coupled model of multiphase flow, reactive biogeochemical transport, thermal transport and geo-mechanics in subsurface media is presented. It iteratively solves the mass conservation equation for fluid flow, thermal transport equation for temperature, reactive biogeochemical transport equations for concentration distributions, and solid momentum equation for displacement with successive linearization algorithm. With species-based equations of state, density of a phase in the system is obtained by summing up concentrations of all species. This circumvents the problem of having to use empirical functions. Moreover, reaction rates of all species are incorporated in mass conservation equation for fluid flow. Formation enthalpy of all species is included in the law of energy conservation as a source-sink term. Finite element methods are used to discretize the governing equations. Numerical experiments are presented to examine the accuracy and robustness of the proposed model. The results demonstrate the feasibility and capability of present model in subsurface media.

  17. 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.

  18. Accurate coronary modeling procedure using 2D calibrated projections based on 2D centerline points on a single projection

    NASA Astrophysics Data System (ADS)

    Movassaghi, Babak; Rasche, Volker; Viergever, Max A.; Niessen, Wiro J.

    2004-05-01

    For the diagnosis of ischemic heart disease, accurate quantitative analysis of the coronary arteries is important. In coronary angiography, a number of projections is acquired from which 3D models of the coronaries can be reconstructed. A signifcant limitation of the current 3D modeling procedures is the required user interaction for defining the centerlines of the vessel structures in the 2D projections. Currently, the 3D centerlines of the coronary tree structure are calculated based on the interactively determined centerlines in two projections. For every interactively selected centerline point in a first projection the corresponding point in a second projection has to be determined interactively by the user. The correspondence is obtained based on the epipolar-geometry. In this paper a method is proposed to retrieve all the information required for the modeling procedure, by the interactive determination of the 2D centerline-points in only one projection. For every determined 2D centerline-point the corresponding 3D centerline-point is calculated by the analysis of the 1D gray value functions of the corresponding epipolarlines in space for all available 2D projections. This information is then used to build a 3D representation of the coronary arteries using coronary modeling techniques. The approach is illustrated on the analysis of calibrated phantom and calibrated coronary projection data.

  19. 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.

  20. 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.

  1. Modelling transport of decay chains by particle displacement along random trajectories

    NASA Astrophysics Data System (ADS)

    Cvetkovic, V.; Painter, S.; Frampton, A.

    2005-12-01

    The streamtube/trajectory approach to modelling solute transport in the subsurface is widely used in applications, from numerical simulations (method of characteristics) to analytical models (Dagan). The trajectory approach has a solid foundation in chemical engineering and hydrodynamics. However, its main limitation is that the (semi)analytical solutions for incorporating retention processes, as proposed by Dagan and Cvetkovic among others, are applicable only to a single species partitioned into mobile and immobile phases. We propose a new methodology for simulating transport of multiple species (exemplified by decay chains) subject to random advection and retention in heterogeneous porous media. The method is based on displacing dynamically inert particles along random trajectories. We first demonstrate the accuracy of the method for a two-component chain with linear equilibrium sorption and hydrodynamic transport governed by the advection-dispersion equation, where an analytical solution is available. We then test the applicability of the method by considering a three- component decay chain in a two-dimensional fractured porous medium, where highly non-Gaussian advective transport has been simulated using a discrete fracture network model, and the retention processes are controlled by Fickian diffusion into the rock matrix. These tests in combination demonstrate that the proposed methodology is efficient and accurate, thus opening possibilities for studying transport of interacting species subject to more complex chemical reactions, where random advection and retention (Gaussian or non-Gaussian) can be fully incorporated into the modelling.

  2. Computational models for predicting interactions with membrane transporters.

    PubMed

    Xu, Y; Shen, Q; Liu, X; Lu, J; Li, S; Luo, C; Gong, L; Luo, X; Zheng, M; Jiang, H

    2013-01-01

    Membrane transporters, including two members: ATP-binding cassette (ABC) transporters and solute carrier (SLC) transporters are proteins that play important roles to facilitate molecules into and out of cells. Consequently, these transporters can be major determinants of the therapeutic efficacy, toxicity and pharmacokinetics of a variety of drugs. Considering the time and expense of bio-experiments taking, research should be driven by evaluation of efficacy and safety. Computational methods arise to be a complementary choice. In this article, we provide an overview of the contribution that computational methods made in transporters field in the past decades. At the beginning, we present a brief introduction about the structure and function of major members of two families in transporters. In the second part, we focus on widely used computational methods in different aspects of transporters research. In the absence of a high-resolution structure of most of transporters, homology modeling is a useful tool to interpret experimental data and potentially guide experimental studies. We summarize reported homology modeling in this review. Researches in computational methods cover major members of transporters and a variety of topics including the classification of substrates and/or inhibitors, prediction of protein-ligand interactions, constitution of binding pocket, phenotype of non-synonymous single-nucleotide polymorphisms, and the conformation analysis that try to explain the mechanism of action. As an example, one of the most important transporters P-gp is elaborated to explain the differences and advantages of various computational models. In the third part, the challenges of developing computational methods to get reliable prediction, as well as the potential future directions in transporter related modeling are discussed.

  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. Towards an accurate model of the redshift-space clustering of haloes in the quasi-linear regime

    NASA Astrophysics Data System (ADS)

    Reid, Beth A.; White, Martin

    2011-11-01

    Observations of redshift-space distortions in spectroscopic galaxy surveys offer an attractive method for measuring the build-up of cosmological structure, which depends both on the expansion rate of the Universe and on our theory of gravity. The statistical precision with which redshift-space distortions can now be measured demands better control of our theoretical systematic errors. While many recent studies focus on understanding dark matter clustering in redshift space, galaxies occupy special places in the universe: dark matter haloes. In our detailed study of halo clustering and velocity statistics in 67.5 h-3 Gpc3 of N-body simulations, we uncover a complex dependence of redshift-space clustering on halo bias. We identify two distinct corrections which affect the halo redshift-space correlation function on quasi-linear scales (˜30-80 h-1 Mpc): the non-linear mapping between real-space and redshift-space positions, and the non-linear suppression of power in the velocity divergence field. We model the first non-perturbatively using the scale-dependent Gaussian streaming model, which we show is accurate at the <0.5 (2) per cent level in transforming real-space clustering and velocity statistics into redshift space on scales s > 10 (s > 25) h-1 Mpc for the monopole (quadrupole) halo correlation functions. The dominant correction to the Kaiser limit in this model scales like b3. We use standard perturbation theory to predict the real-space pairwise halo velocity statistics. Our fully analytic model is accurate at the 2 per cent level only on scales s > 40 h-1 Mpc for the range of halo masses we studied (with b= 1.4-2.8). We find that recent models of halo redshift-space clustering that neglect the corrections from the bispectrum and higher order terms from the non-linear real-space to redshift-space mapping will not have the accuracy required for current and future observational analyses. Finally, we note that our simulation results confirm the essential but non

  5. Modeling Reactive Transport in Coupled Groundwater-Conduit Systems

    NASA Astrophysics Data System (ADS)

    Spiessl, S. M.; Sauter, M.; Zheng, C.; Viswanathan, H. S.

    2002-05-01

    Modeling reactive transport in coupled groundwater-conduit systems requires consideration of two transport time scales in the flow and transport models. Consider for example a subsurface mine consisting of a network of highly conductive shafts, drifts or ventilation raises (i.e., conduits) within the considerably less permeable ore material (i.e., matrix). In the conduits, potential contaminants can travel much more rapidly than in the background aquifer (matrix). Since conduits cannot necessarily be regarded as a continuum, double continuum models are only of limited use for simulation of contaminant transport in such coupled groundwater-conduit systems. This study utilizes a "hybrid" flow and transport model in which contaminants can in essence be transported at a slower time scale in the matrix and at a faster time scale in the conduits. The hybrid flow model uses an approach developed by Clemens et al. (1996), which is based on the modelling of flow in a discrete pipe network, coupled to a continuum representing the low-permeability inter-conduit matrix blocks. Laminar or turbulent flow can be simulated in the different pipes depending on the flow conditions in the model domain. The three-dimensional finite-difference groundwater flow model MODFLOW (Harbaugh and McDonald, 1996) is used to simulate flow in the continuum. Contaminant transport within the matrix is simulated with a continuum approach using the three-dimensional multi-species solute transport model MT3DMS (Zheng and Wang, 1999), while that in the conduit system is simulated with a one-dimensional advective transport model. As a first step for reactive transport modeling in such systems, only equilibrium reactions among multiple species are considered by coupling the hybrid transport model to a geochemical speciation package. An idealized mine network developed by Viswanathan and Sauter (2001) is used as a test problem in this study. The numerical experiment is based on reference date collected from

  6. 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.

  7. 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.

  8. 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.

  9. Virtus, a model of virus transport in unsaturated soils

    SciTech Connect

    Yates, M.V.; Ouyang, Y.

    1993-01-01

    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. The purpose of the 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 laws 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 percent confidence limits of the measured concentrations.

  10. Kinetic modelling of coupled transport across biological membranes.

    PubMed

    Korla, Kalyani; Mitra, Chanchal K

    2014-04-01

    In this report, we have modelled a secondary active co-transporter (symport and antiport), based on the classical kinetics model. Michaelis-Menten model of enzyme kinetics for a single substrate, single intermediate enzyme catalyzed reaction was proposed more than a hundred years ago. However, no single model for the kinetics of co-transport of molecules across a membrane is available in the literature We have made several simplifying assumptions and have followed the basic Michaelis-Menten approach. The results have been simulated using GNU Octave. The results will be useful in general kinetic simulations and modelling.

  11. Fast and accurate global multiphase arrival tracking: the irregular shortest-path method in a 3-D spherical earth model

    NASA Astrophysics Data System (ADS)

    Huang, Guo-Jiao; Bai, Chao-Ying; Greenhalgh, Stewart

    2013-09-01

    The traditional grid/cell-based wavefront expansion algorithms, such as the shortest path algorithm, can only find the first arrivals or multiply reflected (or mode converted) waves transmitted from subsurface interfaces, but cannot calculate the other later reflections/conversions having a minimax time path. In order to overcome the above limitations, we introduce the concept of a stationary minimax time path of Fermat's Principle into the multistage irregular shortest path method. Here we extend it from Cartesian coordinates for a flat earth model to global ray tracing of multiple phases in a 3-D complex spherical earth model. The ray tracing results for 49 different kinds of crustal, mantle and core phases show that the maximum absolute traveltime error is less than 0.12 s and the average absolute traveltime error is within 0.09 s when compared with the AK135 theoretical traveltime tables for a 1-D reference model. Numerical tests in terms of computational accuracy and CPU time consumption indicate that the new scheme is an accurate, efficient and a practical way to perform 3-D multiphase arrival tracking in regional or global traveltime tomography.

  12. Numerical simulation of pharyngeal airflow applied to obstructive sleep apnea: effect of the nasal cavity in anatomically accurate airway models.

    PubMed

    Cisonni, Julien; Lucey, Anthony D; King, Andrew J C; Islam, Syed Mohammed Shamsul; Lewis, Richard; Goonewardene, Mithran S

    2015-11-01

    Repetitive brief episodes of soft-tissue collapse within the upper airway during sleep characterize obstructive sleep apnea (OSA), an extremely common and disabling disorder. Failure to maintain the patency of the upper airway is caused by the combination of sleep-related loss of compensatory dilator muscle activity and aerodynamic forces promoting closure. The prediction of soft-tissue movement in patient-specific airway 3D mechanical models is emerging as a useful contribution to clinical understanding and decision making. Such modeling requires reliable estimations of the pharyngeal wall pressure forces. While nasal obstruction has been recognized as a risk factor for OSA, the need to include the nasal cavity in upper-airway models for OSA studies requires consideration, as it is most often omitted because of its complex shape. A quantitative analysis of the flow conditions generated by the nasal cavity and the sinuses during inspiration upstream of the pharynx is presented. Results show that adequate velocity boundary conditions and simple artificial extensions of the flow domain can reproduce the essential effects of the nasal cavity on the pharyngeal flow field. Therefore, the overall complexity and computational cost of accurate flow predictions can be reduced.

  13. 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.

  14. 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.

  15. The use of sparse CT datasets for auto-generating accurate FE models of the femur and pelvis.

    PubMed

    Shim, Vickie B; Pitto, Rocco P; Streicher, Robert M; Hunter, Peter J; Anderson, Iain A

    2007-01-01

    The finite element (FE) method when coupled with computed tomography (CT) is a powerful tool in orthopaedic biomechanics. However, substantial data is required for patient-specific modelling. Here we present a new method for generating a FE model with a minimum amount of patient data. Our method uses high order cubic Hermite basis functions for mesh generation and least-square fits the mesh to the dataset. We have tested our method on seven patient data sets obtained from CT assisted osteodensitometry of the proximal femur. Using only 12 CT slices we generated smooth and accurate meshes of the proximal femur with a geometric root mean square (RMS) error of less than 1 mm and peak errors less than 8 mm. To model the complex geometry of the pelvis we developed a hybrid method which supplements sparse patient data with data from the visible human data set. We tested this method on three patient data sets, generating FE meshes of the pelvis using only 10 CT slices with an overall RMS error less than 3 mm. Although we have peak errors about 12 mm in these meshes, they occur relatively far from the region of interest (the acetabulum) and will have minimal effects on the performance of the model. Considering that linear meshes usually require about 70-100 pelvic CT slices (in axial mode) to generate FE models, our method has brought a significant data reduction to the automatic mesh generation step. The method, that is fully automated except for a semi-automatic bone/tissue boundary extraction part, will bring the benefits of FE methods to the clinical environment with much reduced radiation risks and data requirement.

  16. Do inverse ecosystem models accurately reconstruct plankton trophic flows? Comparing two solution methods using field data from the California Current

    NASA Astrophysics Data System (ADS)

    Stukel, Michael R.; Landry, Michael R.; Ohman, Mark D.; Goericke, Ralf; Samo, Ty; Benitez-Nelson, Claudia R.

    2012-03-01

    Despite the increasing use of linear inverse modeling techniques to elucidate fluxes in undersampled marine ecosystems, the accuracy with which they estimate food web flows has not been resolved. New Markov Chain Monte Carlo (MCMC) solution methods have also called into question the biases of the commonly used L2 minimum norm (L 2MN) solution technique. Here, we test the abilities of MCMC and L 2MN methods to recover field-measured ecosystem rates that are sequentially excluded from the model input. For data, we use experimental measurements from process cruises of the California Current Ecosystem (CCE-LTER) Program that include rate estimates of phytoplankton and bacterial production, micro- and mesozooplankton grazing, and carbon export from eight study sites varying from rich coastal upwelling to offshore oligotrophic conditions. Both the MCMC and L 2MN methods predicted well-constrained rates of protozoan and mesozooplankton grazing with reasonable accuracy, but the MCMC method overestimated primary production. The MCMC method more accurately predicted the poorly constrained rate of vertical carbon export than the L 2MN method, which consistently overestimated export. Results involving DOC and bacterial production were equivocal. Overall, when primary production is provided as model input, the MCMC method gives a robust depiction of ecosystem processes. Uncertainty in inverse ecosystem models is large and arises primarily from solution under-determinacy. We thus suggest that experimental programs focusing on food web fluxes expand the range of experimental measurements to include the nature and fate of detrital pools, which play large roles in the model.

  17. Probabilistic transport models for plasma transport in the presence of critical thresholds: Beyond the diffusive paradigma)

    NASA Astrophysics Data System (ADS)

    Sánchez, R.; van Milligen, B. Ph.; Carreras, B. A.

    2005-05-01

    It is argued that the modeling of plasma transport in tokamaks may benefit greatly from extending the usual local paradigm to accommodate scale-free transport mechanisms. This can be done by combining Lévy distributions and a nonlinear threshold condition within the continuous time random walk concept. The advantages of this nonlocal, nonlinear extension are illustrated by constructing a simple particle density transport model that, as a result of these ideas, spontaneously exhibits much of nondiffusive phenomenology routinely observed in tokamaks. The fluid limit of the system shows that the kind of equations that are appropriate to capture these dynamics are based on fractional differential operators. In them, effective diffusivities and pinch velocities are found that are dynamically set by the system in response to the specific characteristics of the fueling source and external perturbations. This fact suggests some dramatic consequences for the extrapolation of these transport properties to larger size systems.

  18. 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.

  19. Prognostic breast cancer signature identified from 3D culture model accurately predicts clinical outcome across independent datasets

    SciTech Connect

    Martin, Katherine J.; Patrick, Denis R.; Bissell, Mina J.; Fournier, Marcia V.

    2008-10-20

    One of the major tenets in breast cancer research is that early detection is vital for patient survival by increasing treatment options. To that end, we have previously used a novel unsupervised approach to identify a set of genes whose expression predicts prognosis of breast cancer patients. The predictive genes were selected in a well-defined three dimensional (3D) cell culture model of non-malignant human mammary epithelial cell morphogenesis as down-regulated during breast epithelial cell acinar formation and cell cycle arrest. Here we examine the ability of this gene signature (3D-signature) to predict prognosis in three independent breast cancer microarray datasets having 295, 286, and 118 samples, respectively. Our results show that the 3D-signature accurately predicts prognosis in three unrelated patient datasets. At 10 years, the probability of positive outcome was 52, 51, and 47 percent in the group with a poor-prognosis signature and 91, 75, and 71 percent in the group with a good-prognosis signature for the three datasets, respectively (Kaplan-Meier survival analysis, p<0.05). Hazard ratios for poor outcome were 5.5 (95% CI 3.0 to 12.2, p<0.0001), 2.4 (95% CI 1.6 to 3.6, p<0.0001) and 1.9 (95% CI 1.1 to 3.2, p = 0.016) and remained significant for the two larger datasets when corrected for estrogen receptor (ER) status. Hence the 3D-signature accurately predicts breast cancer outcome in both ER-positive and ER-negative tumors, though individual genes differed in their prognostic ability in the two subtypes. Genes that were prognostic in ER+ patients are AURKA, CEP55, RRM2, EPHA2, FGFBP1, and VRK1, while genes prognostic in ER patients include ACTB, FOXM1 and SERPINE2 (Kaplan-Meier p<0.05). Multivariable Cox regression analysis in the largest dataset showed that the 3D-signature was a strong independent factor in predicting breast cancer outcome. The 3D-signature accurately predicts breast cancer outcome across multiple datasets and holds prognostic

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

    NASA Astrophysics Data System (ADS)

    Yogurtcu, Osman N.; Johnson, Margaret E.

    2015-08-01

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

  3. Simulating the Cranfield geological carbon sequestration project with high-resolution static models and an accurate equation of state

    DOE PAGES

    Soltanian, Mohamad Reza; Amooie, Mohammad Amin; Cole, David R.; Graham, David E.; Hosseini, Seyyed Abolfazl; Hovorka, Susan; Pfiffner, Susan M.; Phelps, Tommy Joe; Moortgat, Joachim

    2016-10-11

    In this study, a field-scale carbon dioxide (CO2) injection pilot project was conducted as part of the Southeast Regional Sequestration Partnership (SECARB) at Cranfield, Mississippi. We present higher-order finite element simulations of the compositional two-phase CO2-brine flow and transport during the experiment. High- resolution static models of the formation geology in the Detailed Area Study (DAS) located below the oil- water contact (brine saturated) are used to capture the impact of connected flow paths on breakthrough times in two observation wells. Phase behavior is described by the cubic-plus-association (CPA) equation of state, which takes into account the polar nature ofmore » water molecules. Parameter studies are performed to investigate the importance of Fickian diffusion, permeability heterogeneity, relative permeabilities, and capillarity. Simulation results for the pressure response in the injection well and the CO2 breakthrough times at the observation wells show good agreement with the field data. For the high injection rates and short duration of the experiment, diffusion is relatively unimportant (high P clet numbers), while relative permeabilities have a profound impact on the pressure response. High-permeability pathways, created by fluvial deposits, strongly affect the CO2 transport and highlight the importance of properly characterizing the formation heterogeneity in future carbon sequestration projects.« less

  4. 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.

  5. 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. PMID:11588823

  6. Modeling hydrology, metribuzin degradation and metribuzin transport in macroporous tilled and no-till silt loam soil using RZWQM.

    PubMed

    Malone, Robert W; Ma, Liwang; Wauchope, R Don; Ahuja, Lajpat R; Rojas, Kenneth W; Ma, Qingli; Warner, Richard; Byers, Matt

    2004-03-01

    Due to the complex nature of pesticide transport, process-based models can be difficult to use. For example, pesticide transport can be effected by macropore flow, and can be further complicated by sorption, desorption and degradation occurring at different rates in different soil compartments. We have used the Root Zone Water Quality Model (RZWQM) to investigate these phenomena with field data that included two management conditions (till and no-till) and metribuzin concentrations in percolate, runoff and soil. Metribuzin degradation and transport were simulated using three pesticide sorption models available in RZWQM: (a) instantaneous equilibrium-only (EO); (b) equilibrium-kinetic (EK, includes sites with slow desorption and no degradation); (c) equilibrium-bound (EB, includes irreversibly bound sites with relatively slow degradation). Site-specific RZWQM input included water retention curves from four soil depths, saturated hydraulic conductivity from four soil depths and the metribuzin partition coefficient. The calibrated parameters were macropore radius, surface crust saturated hydraulic conductivity, kinetic parameters, irreversible binding parameters and metribuzin half-life. The results indicate that (1) simulated metribuzin persistence was more accurate using the EK (root mean square error, RMSE = 0.03 kg ha(-1)) and EB (RMSE = 0.03 kg ha(-1)) sorption models compared to the EO (RMSE = 0.08 kg ha(-1)) model because of slowing metribuzin degradation rate with time and (2) simulating macropore flow resulted in prediction of metribuzin transport in percolate over the simulation period within a factor of two of that observed using all three pesticide sorption models. Moreover, little difference in simulated daily transport was observed between the three pesticide sorption models, except that the EB model substantially under-predicted metribuzin transport in runoff and percolate >30 days after application when transported concentrations were relatively low

  7. Modeling hydrology, metribuzin degradation and metribuzin transport in macroporous tilled and no-till silt loam soil using RZWQM.

    PubMed

    Malone, Robert W; Ma, Liwang; Wauchope, R Don; Ahuja, Lajpat R; Rojas, Kenneth W; Ma, Qingli; Warner, Richard; Byers, Matt

    2004-03-01

    Due to the complex nature of pesticide transport, process-based models can be difficult to use. For example, pesticide transport can be effected by macropore flow, and can be further complicated by sorption, desorption and degradation occurring at different rates in different soil compartments. We have used the Root Zone Water Quality Model (RZWQM) to investigate these phenomena with field data that included two management conditions (till and no-till) and metribuzin concentrations in percolate, runoff and soil. Metribuzin degradation and transport were simulated using three pesticide sorption models available in RZWQM: (a) instantaneous equilibrium-only (EO); (b) equilibrium-kinetic (EK, includes sites with slow desorption and no degradation); (c) equilibrium-bound (EB, includes irreversibly bound sites with relatively slow degradation). Site-specific RZWQM input included water retention curves from four soil depths, saturated hydraulic conductivity from four soil depths and the metribuzin partition coefficient. The calibrated parameters were macropore radius, surface crust saturated hydraulic conductivity, kinetic parameters, irreversible binding parameters and metribuzin half-life. The results indicate that (1) simulated metribuzin persistence was more accurate using the EK (root mean square error, RMSE = 0.03 kg ha(-1)) and EB (RMSE = 0.03 kg ha(-1)) sorption models compared to the EO (RMSE = 0.08 kg ha(-1)) model because of slowing metribuzin degradation rate with time and (2) simulating macropore flow resulted in prediction of metribuzin transport in percolate over the simulation period within a factor of two of that observed using all three pesticide sorption models. Moreover, little difference in simulated daily transport was observed between the three pesticide sorption models, except that the EB model substantially under-predicted metribuzin transport in runoff and percolate >30 days after application when transported concentrations were relatively low

  8. 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

  9. Predictive transport simulations of internal transport barriers using the Multi-Mode model

    NASA Astrophysics Data System (ADS)

    Zhu, P.; Bateman, G.; Kritz, A. H.; Horton, W.

    2000-07-01

    The formation of internal transport barriers observed in both Joint European Torus (JET) [P. H. Rebut, R. J. Bickerton, and B. E. Keen, Nucl. Fusion 25, 1011 (1985)] and Doublet III-D Tokamak (DIII-D) [J. L. Luxon and L. G. Davis, Fusion Technol. 8, 441 (1985)] are reproduced in predictive transport simulations. These simulations are carried out for two JET-optimized shear discharges and two DIII-D negative central shear discharges using the Multi-Mode model in the time-dependent 1-1/2-D BALDUR transport code [C. E. Singer et al., Comput. Phys. Commun. 49, 275 (1988)]. The Weiland model is used for drift modes in the Multi-Mode model in combination with either Hahm-Burrell or Hamaguchi-Horton flow shear stabilization mechanisms, where the radial electric field is inferred from the measured toroidal velocity profile and the poloidal velocity profile computed using neoclassical theory. The transport barriers are apparent in both the ion temperature and thermal diffusivity profiles of the simulations. The timing and location of the internal transport barriers in the simulations and experimental data for the DIII-D cases are in good agreement, though some differences remain for the JET discharges. The formations of internal transport barriers are interpreted as resulting from a combination of E×B flow shear and weak magnetic shear mechanisms.

  10. ELIST 8.0 Transportation Model

    SciTech Connect

    Braun, M. B.; Van Groningen, C. N.

    2002-03-06

    The Enhanced Logistics Intratheater Support Tool (ELIST) Version 8 is a software tool designed to allow military analysts to model the deployment of cargo and personnel into theaters of operation from ports of debarkation through staging areas and theater-staging bases to in-theater destinations, usually tactical assembly areas. This document defines the parameters and heuristics to be modeled. All design and implementation decisions are derived from this document. Validation and verification of the model are based on this document.

  11. 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.

  12. An accurate numerical solution to the Saint-Venant-Hirano model for mixed-sediment morphodynamics in rivers

    NASA Astrophysics Data System (ADS)

    Stecca, Guglielmo; Siviglia, Annunziato; Blom, Astrid

    2016-07-01

    We present an accurate numerical approximation to the Saint-Venant-Hirano model for mixed-sediment morphodynamics in one space dimension. Our solution procedure originates from the fully-unsteady matrix-vector formulation developed in [54]. The principal part of the problem is solved by an explicit Finite Volume upwind method of the path-conservative type, by which all the variables are updated simultaneously in a coupled fashion. The solution to the principal part is embedded into a splitting procedure for the treatment of frictional source terms. The numerical scheme is extended to second-order accuracy and includes a bookkeeping procedure for handling the evolution of size stratification in the substrate. We develop a concept of balancedness for the vertical mass flux between the substrate and active layer under bed degradation, which prevents the occurrence of non-physical oscillations in the grainsize distribution of the substrate. We suitably modify the numerical scheme to respect this principle. We finally verify the accuracy in our solution to the equations, and its ability to reproduce one-dimensional morphodynamics due to streamwise and vertical sorting, using three test cases. In detail, (i) we empirically assess the balancedness of vertical mass fluxes under degradation; (ii) we study the convergence to the analytical linearised solution for the propagation of infinitesimal-amplitude waves [54], which is here employed for the first time to assess a mixed-sediment model; (iii) we reproduce Ribberink's E8-E9 flume experiment [46].

  13. In pursuit of an accurate spatial and temporal model of biomolecules at the atomistic level: a perspective on computer simulation

    SciTech Connect

    Gray, Alan; Harlen, Oliver G.; Harris, Sarah A.; Khalid, Syma; Leung, Yuk Ming; Lonsdale, Richard; Mulholland, Adrian J.; Pearson, Arwen R.; Read, Daniel J.; Richardson, Robin A.

    2015-01-01

    The current computational techniques available for biomolecular simulation are described, and the successes and limitations of each with reference to the experimental biophysical methods that they complement are presented. Despite huge advances in the computational techniques available for simulating biomolecules at the quantum-mechanical, atomistic and coarse-grained levels, there is still a widespread perception amongst the experimental community that these calculations are highly specialist and are not generally applicable by researchers outside the theoretical community. In this article, the successes and limitations of biomolecular simulation and the further developments that are likely in the near future are discussed. A brief overview is also provided of the experimental biophysical methods that are commonly used to probe biomolecular structure and dynamics, and the accuracy of the information that can be obtained from each is compared with that from modelling. It is concluded that progress towards an accurate spatial and temporal model of biomacromolecules requires a combination of all of these biophysical techniques, both experimental and computational.

  14. A fast and accurate implementation of tunable algorithms used for generation of fractal-like aggregate models

    NASA Astrophysics Data System (ADS)

    Skorupski, Krzysztof; Mroczka, Janusz; Wriedt, Thomas; Riefler, Norbert

    2014-06-01

    In many branches of science experiments are expensive, require specialist equipment or are very time consuming. Studying the light scattering phenomenon by fractal aggregates can serve as an example. Light scattering simulations can overcome these problems and provide us with theoretical, additional data which complete our study. For this reason a fractal-like aggregate model as well as fast aggregation codes are needed. Until now various computer models, that try to mimic the physics behind this phenomenon, have been developed. However, their implementations are mostly based on a trial-and-error procedure. Such approach is very time consuming and the morphological parameters of resulting aggregates are not exact because the postconditions (e.g. the position error) cannot be very strict. In this paper we present a very fast and accurate implementation of a tunable aggregation algorithm based on the work of Filippov et al. (2000). Randomization is reduced to its necessary minimum (our technique can be more than 1000 times faster than standard algorithms) and the position of a new particle, or a cluster, is calculated with algebraic methods. Therefore, the postconditions can be extremely strict and the resulting errors negligible (e.g. the position error can be recognized as non-existent). In our paper two different methods, which are based on the particle-cluster (PC) and the cluster-cluster (CC) aggregation processes, are presented.

  15. X-ray and microwave emissions from the July 19, 2012 solar flare: Highly accurate observations and kinetic models

    NASA Astrophysics Data System (ADS)

    Gritsyk, P. A.; Somov, B. V.

    2016-08-01

    The M7.7 solar flare of July 19, 2012, at 05:58 UT was observed with high spatial, temporal, and spectral resolutions in the hard X-ray and optical ranges. The flare occurred at the solar limb, which allowed us to see the relative positions of the coronal and chromospheric X-ray sources and to determine their spectra. To explain the observations of the coronal source and the chromospheric one unocculted by the solar limb, we apply an accurate analytical model for the kinetic behavior of accelerated electrons in a flare. We interpret the chromospheric hard X-ray source in the thick-target approximation with a reverse current and the coronal one in the thin-target approximation. Our estimates of the slopes of the hard X-ray spectra for both sources are consistent with the observations. However, the calculated intensity of the coronal source is lower than the observed one by several times. Allowance for the acceleration of fast electrons in a collapsing magnetic trap has enabled us to remove this contradiction. As a result of our modeling, we have estimated the flux density of the energy transferred by electrons with energies above 15 keV to be ˜5 × 1010 erg cm-2 s-1, which exceeds the values typical of the thick-target model without a reverse current by a factor of ˜5. To independently test the model, we have calculated the microwave spectrum in the range 1-50 GHz that corresponds to the available radio observations.

  16. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2016-02-01

    We present a numerical method for multiphase chemical equilibrium calculations based on a Gibbs energy minimization approach. The method can accurately and efficiently determine the stable phase assemblage at equilibrium independently of the type of phases and species that constitute the chemical system. We have successfully applied our chemical equilibrium algorithm in reactive transport simulations to demonstrate its effective