Science.gov

Sample records for accurate transport models

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

    PubMed

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

    2015-09-17

    We used NMR imaging (MRI) combined with data analysis based on inverse modeling of the mass transport problem to determine ionic diffusion coefficients and transference numbers in electrolyte solutions of interest for Li-ion batteries. Sensitivity analyses have shown that accurate estimates of these parameters (as a function of concentration) are critical to the reliability of the predictions provided by models of porous electrodes. The inverse modeling (IM) solution was generated with an extension of the Planck-Nernst model for the transport of ionic species in electrolyte solutions. Concentration-dependent diffusion coefficients and transference numbers were derived using concentration profiles obtained from in situ (19)F MRI measurements. Material properties were reconstructed under minimal assumptions using methods of variational optimization to minimize the least-squares deviation between experimental and simulated concentration values with uncertainty of the reconstructions quantified using a Monte Carlo analysis. The diffusion coefficients obtained by pulsed field gradient NMR (PFG-NMR) fall within the 95% confidence bounds for the diffusion coefficient values obtained by the MRI+IM method. The MRI+IM method also yields the concentration dependence of the Li(+) transference number in agreement with trends obtained by electrochemical methods for similar systems and with predictions of theoretical models for concentrated electrolyte solutions, in marked contrast to the salt concentration dependence of transport numbers determined from PFG-NMR data. PMID:26247105

  2. METEOROLOGICAL AND TRANSPORT MODELING

    EPA Science Inventory

    Advanced air quality simulation models, such as CMAQ, as well as other transport and dispersion models, require accurate and detailed meteorology fields. These meteorology fields include primary 3-dimensional dynamical and thermodynamical variables (e.g., winds, temperature, mo...

  3. Anatomically accurate individual face modeling.

    PubMed

    Zhang, Yu; Prakash, Edmond C; Sung, Eric

    2003-01-01

    This paper presents a new 3D face model of a specific person constructed from the anatomical perspective. By exploiting the laser range data, a 3D facial mesh precisely representing the skin geometry is reconstructed. Based on the geometric facial mesh, we develop a deformable multi-layer skin model. It takes into account the nonlinear stress-strain relationship and dynamically simulates the non-homogenous behavior of the real skin. The face model also incorporates a set of anatomically-motivated facial muscle actuators and underlying skull structure. Lagrangian mechanics governs the facial motion dynamics, dictating the dynamic deformation of facial skin in response to the muscle contraction. PMID:15455936

  4. 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.

  5. 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…

  6. New model accurately predicts reformate composition

    SciTech Connect

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

    1994-01-31

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

  7. 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.

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

    PubMed

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

    2016-02-18

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

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

    PubMed Central

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

    2016-01-01

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

  10. 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.

  11. 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

  12. 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

  13. 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.

  14. 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.

  15. Anisotropic Turbulence Modeling for Accurate Rod Bundle Simulations

    SciTech Connect

    Baglietto, Emilio

    2006-07-01

    An improved anisotropic eddy viscosity model has been developed for accurate predictions of the thermal hydraulic performances of nuclear reactor fuel assemblies. The proposed model adopts a non-linear formulation of the stress-strain relationship in order to include the reproduction of the anisotropic phenomena, and in combination with an optimized low-Reynolds-number formulation based on Direct Numerical Simulation (DNS) to produce correct damping of the turbulent viscosity in the near wall region. This work underlines the importance of accurate anisotropic modeling to faithfully reproduce the scale of the turbulence driven secondary flows inside the bundle subchannels, by comparison with various isothermal and heated experimental cases. The very low scale secondary motion is responsible for the increased turbulence transport which produces a noticeable homogenization of the velocity distribution and consequently of the circumferential cladding temperature distribution, which is of main interest in bundle design. Various fully developed bare bundles test cases are shown for different geometrical and flow conditions, where the proposed model shows clearly improved predictions, in close agreement with experimental findings, for regular as well as distorted geometries. Finally the applicability of the model for practical bundle calculations is evaluated through its application in the high-Reynolds form on coarse grids, with excellent results. (author)

  16. Accurate astronomical atmospheric dispersion models in ZEMAX

    NASA Astrophysics Data System (ADS)

    Spanò, P.

    2014-07-01

    ZEMAX provides a standard built-in atmospheric model to simulate atmospheric refraction and dispersion. This model has been compared with other ones to assess its intrinsic accuracy, critical for very demanding application like ADCs for AO-assisted extremely large telescopes. A revised simple model, based on updated published data of the air refractivity, is proposed by using the "Gradient 5" surface of Zemax. At large zenith angles (65 deg), discrepancies up to 100 mas in the differential refraction are expected near the UV atmospheric transmission cutoff. When high-accuracy modeling is required, the latter model should be preferred.

  17. Turbulence Models for Accurate Aerothermal Prediction in Hypersonic Flows

    NASA Astrophysics Data System (ADS)

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

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

  18. 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

  19. 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.

  20. 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.

  1. 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

  2. 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.

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

    PubMed Central

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

    2014-01-01

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

  4. Model Comparison for Electron Thermal Transport

    NASA Astrophysics Data System (ADS)

    Moses, Gregory; Chenhall, Jeffrey; Cao, Duc; Delettrez, Jacques

    2015-11-01

    Four electron thermal transport models are compared for their ability to accurately and efficiently model non-local behavior in ICF simulations. Goncharov's transport model has accurately predicted shock timing in implosion simulations but is computationally slow and limited to 1D. The iSNB (implicit Schurtz Nicolai Busquet electron thermal transport method of Cao et al. uses multigroup diffusion to speed up the calculation. Chenhall has expanded upon the iSNB diffusion model to a higher order simplified P3 approximation and a Monte Carlo transport model, to bridge the gap between the iSNB and Goncharov models while maintaining computational efficiency. Comparisons of the above models for several test problems will be presented. This work was supported by Sandia National Laboratory - Albuquerque and the University of Rochester Laboratory for Laser Energetics.

  5. Water wave model with accurate dispersion and vertical vorticity

    NASA Astrophysics Data System (ADS)

    Bokhove, Onno

    2010-05-01

    Cotter and Bokhove (Journal of Engineering Mathematics 2010) derived a variational water wave model with accurate dispersion and vertical vorticity. In one limit, it leads to Luke's variational principle for potential flow water waves. In the another limit it leads to the depth-averaged shallow water equations including vertical vorticity. Presently, focus will be put on the Hamiltonian formulation of the variational model and its boundary conditions.

  6. 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.

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

    NASA Technical Reports Server (NTRS)

    Bednarcyk, Brett A.; Arnold, Steven M.

    2001-01-01

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

  8. 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

  9. 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

  10. 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.

  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. 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.

  14. 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.

  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. Mouse models of human AML accurately predict chemotherapy response.

    PubMed

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

    2009-04-01

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

  18. An accurate model potential for alkali neon systems.

    PubMed

    Zanuttini, D; Jacquet, E; Giglio, E; Douady, J; Gervais, B

    2009-12-01

    We present a detailed investigation of the ground and lowest excited states of M-Ne dimers, for M=Li, Na, and K. We show that the potential energy curves of these Van der Waals dimers can be obtained accurately by considering the alkali neon systems as one-electron systems. Following previous authors, the model describes the evolution of the alkali valence electron in the combined potentials of the alkali and neon cores by means of core polarization pseudopotentials. The key parameter for an accurate model is the M(+)-Ne potential energy curve, which was obtained by means of ab initio CCSD(T) calculation using a large basis set. For each MNe dimer, a systematic comparison with ab initio computation of the potential energy curve for the X, A, and B states shows the remarkable accuracy of the model. The vibrational analysis and the comparison with existing experimental data strengthens this conclusion and allows for a precise assignment of the vibrational levels. PMID:19968334

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

    NASA Astrophysics Data System (ADS)

    Mehmani, Yashar; Oostrom, Mart; Balhoff, Matthew T.

    2014-03-01

    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 validated against micromodel experiments; excellent matches were obtained 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 3-D disordered granular media.

  20. 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.

  1. 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. PMID:26355331

  2. 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

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

    NASA Astrophysics Data System (ADS)

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

    2010-10-01

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

  4. 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

  5. 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.

  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. 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

  8. 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

  9. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2015-12-01

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

  11. Modeling Nonequilibrium Flow and Transport Processes Using HYDRUS

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Accurate process-based modeling of nonequilibrium water flow and solute transport remains a major challenge in vadose zone hydrology. The objective of this paper is to describe a wide range of nonequilibrium flow and transport modeling approaches available within the latest version of the HYDRUS-1D ...

  12. Minority Transportation Expenditure Allocation Model

    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. New process model proves accurate in tests on catalytic reformer

    SciTech Connect

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

    1994-07-25

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

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

    NASA Astrophysics Data System (ADS)

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

    2012-11-01

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

  16. Coupling Efforts to the Accurate and Efficient Tsunami Modelling System

    NASA Astrophysics Data System (ADS)

    Son, S.

    2015-12-01

    In the present study, we couple two different types of tsunami models, i.e., nondispersive shallow water model of characteristic form(MOST ver.4) and dispersive Boussinesq model of non-characteristic form(Son et al. (2011)) in an attempt to improve modelling accuracy and efficiency. Since each model deals with different type of primary variables, additional care on matching boundary condition is required. Using an absorbing-generating boundary condition developed by Van Dongeren and Svendsen(1997), model coupling and integration is achieved. Characteristic variables(i.e., Riemann invariants) in MOST are converted to non-characteristic variables for Boussinesq solver without any loss of physical consistency. Established modelling system has been validated through typical test problems to realistic tsunami events. Simulated results reveal good performance of developed modelling system. Since coupled modelling system provides advantageous flexibility feature during implementation, great efficiencies and accuracies are expected to be gained through spot-focusing application of Boussinesq model inside the entire domain of tsunami propagation.

  17. 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.

  18. Accurate modelling of flow induced stresses in rigid colloidal aggregates

    NASA Astrophysics Data System (ADS)

    Vanni, Marco

    2015-07-01

    A method has been developed to estimate the motion and the internal stresses induced by a fluid flow on a rigid aggregate. The approach couples Stokesian dynamics and structural mechanics in order to take into account accurately the effect of the complex geometry of the aggregates on hydrodynamic forces and the internal redistribution of stresses. The intrinsic error of the method, due to the low-order truncation of the multipole expansion of the Stokes solution, has been assessed by comparison with the analytical solution for the case of a doublet in a shear flow. In addition, it has been shown that the error becomes smaller as the number of primary particles in the aggregate increases and hence it is expected to be negligible for realistic reproductions of large aggregates. The evaluation of internal forces is performed by an adaptation of the matrix methods of structural mechanics to the geometric features of the aggregates and to the particular stress-strain relationship that occurs at intermonomer contacts. A preliminary investigation on the stress distribution in rigid aggregates and their mode of breakup has been performed by studying the response to an elongational flow of both realistic reproductions of colloidal aggregates (made of several hundreds monomers) and highly simplified structures. A very different behaviour has been evidenced between low-density aggregates with isostatic or weakly hyperstatic structures and compact aggregates with highly hyperstatic configuration. In low-density clusters breakup is caused directly by the failure of the most stressed intermonomer contact, which is typically located in the inner region of the aggregate and hence originates the birth of fragments of similar size. On the contrary, breakup of compact and highly cross-linked clusters is seldom caused by the failure of a single bond. When this happens, it proceeds through the removal of a tiny fragment from the external part of the structure. More commonly, however

  19. 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.

  20. Modeling colloid transport for performance assessment.

    PubMed

    Contardi, J S; Turner, D R; Ahn, T M

    2001-02-01

    The natural system is expected to contribute to isolation at the proposed high-level nuclear waste (HLW) geologic repository at Yucca Mountain, NV (YM). In developing performance assessment (PA) computer models to simulate long-term behavior at YM, colloidal transport of radionuclides has been proposed as a critical factor because of the possible reduced interaction with the geologic media. Site-specific information on the chemistry and natural colloid concentration of saturated zone groundwaters in the vicinity of YM is combined with a surface complexation sorption model to evaluate the impact of natural colloids on calculated retardation factors (RF) for several radioelements of concern in PA. Inclusion of colloids into the conceptual model can reduce the calculated effective retardation significantly. Strongly sorbed radionuclides such as americium and thorium are most affected by pseudocolloid formation and transport, with a potential reduction in RF of several orders of magnitude. Radioelements that are less strongly sorbed under YM conditions, such as uranium and neptunium, are not affected significantly by colloid transport, and transport of plutonium in the valence state is only moderately enhanced. Model results showed no increase in the peak mean annual total effective dose equivalent (TEDE) within a compliance period of 10,000 years, although this is strongly dependent on container life in the base case scenario. At longer times, simulated container failures increase and the TEDE from the colloidal models increased by a factor of 60 from the base case. By using mechanistic models and sensitivity analyses to determine what parameters and transport processes affect the TEDE, colloidal transport in future versions of the TPA code can be represented more accurately. PMID:11288586

  1. An Accurate In Vitro Model of the E. coli Envelope

    PubMed Central

    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

    2015-01-01

    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

  2. Leidenfrost effect: accurate drop shape modeling and new scaling laws

    NASA Astrophysics Data System (ADS)

    Sobac, Benjamin; Rednikov, Alexey; Dorbolo, Stéphane; Colinet, Pierre

    2014-11-01

    In this study, we theoretically investigate the shape of a drop in a Leidenfrost state, focusing on the geometry of the vapor layer. The drop geometry is modeled by numerically matching the solution of the hydrostatic shape of a superhydrophobic drop (for the upper part) with the solution of the lubrication equation of the vapor flow underlying the drop (for the bottom part). The results highlight that the vapor layer, fed by evaporation, forms a concave depression in the drop interface that becomes increasingly marked with the drop size. The vapor layer then consists of a gas pocket in the center and a thin annular neck surrounding it. The film thickness increases with the size of the drop, and the thickness at the neck appears to be of the order of 10--100 μm in the case of water. The model is compared to recent experimental results [Burton et al., Phys. Rev. Lett., 074301 (2012)] and shows an excellent agreement, without any fitting parameter. New scaling laws also emerge from this model. The geometry of the vapor pocket is only weakly dependent on the superheat (and thus on the evaporation rate), this weak dependence being more pronounced in the neck region. In turn, the vapor layer characteristics strongly depend on the drop size.

  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. 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.

  5. Next Generation Transport Phenomenology Model

    NASA Technical Reports Server (NTRS)

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

    2004-01-01

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

  6. 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

  7. 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...

  8. 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.

  9. 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)

  10. 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

  11. 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.

  12. Modeling Tokamak Transport with Neural-Network Based Models

    NASA Astrophysics Data System (ADS)

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

    2014-10-01

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

  13. 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.

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

    PubMed

    Takahashi, F; Shigemori, Y; Seki, A

    2009-01-01

    A system has been developed to assess radiation dose distribution inside the body of exposed persons in a radiological accident by utilising radiation transport calculation codes-MCNP and MCNPX. The system consists mainly of two parts, pre-processor and post-processor of the radiation transport calculation. Programs for the pre-processor are used to set up a 'problem-dependent' input file, which defines the accident condition and dosimetric quantities to be estimated. The program developed for the post-processor part can effectively indicate dose information based upon the output file of the code. All of the programs in the dosimetry system can be executed with a generally used personal computer and accurately give the dose profile to an exposed person in a radiological accident without complicated procedures. An experiment using a physical phantom was carried out to verify the availability of the dosimetry system with the developed programs in a gamma ray irradiation field. PMID:19181661

  15. 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

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

    NASA Astrophysics Data System (ADS)

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

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

  17. 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.

  18. Ab initio electronic transport model with explicit solution to the linearized Boltzmann transport equation

    NASA Astrophysics Data System (ADS)

    Faghaninia, Alireza; Ager, Joel W.; Lo, Cynthia S.

    2015-06-01

    Accurate models of carrier transport are essential for describing the electronic properties of semiconductor materials. To the best of our knowledge, the current models following the framework of the Boltzmann transport equation (BTE) either rely heavily on experimental data (i.e., semiempirical), or utilize simplifying assumptions, such as the constant relaxation time approximation (BTE-cRTA). While these models offer valuable physical insights and accurate calculations of transport properties in some cases, they often lack sufficient accuracy—particularly in capturing the correct trends with temperature and carrier concentration. We present here a transport model for calculating low-field electrical drift mobility and Seebeck coefficient of n -type semiconductors, by explicitly considering relevant physical phenomena (i.e., elastic and inelastic scattering mechanisms). We first rewrite expressions for the rates of elastic scattering mechanisms, in terms of ab initio properties, such as the band structure, density of states, and polar optical phonon frequency. We then solve the linear BTE to obtain the perturbation to the electron distribution—resulting from the dominant scattering mechanisms—and use this to calculate the overall mobility and Seebeck coefficient. Therefore, we have developed an ab initio model for calculating mobility and Seebeck coefficient using the Boltzmann transport (aMoBT) equation. Using aMoBT, we accurately calculate electrical transport properties of the compound n -type semiconductors, GaAs and InN, over various ranges of temperature and carrier concentration. aMoBT is fully predictive and provides high accuracy when compared to experimental measurements on both GaAs and InN, and vastly outperforms both semiempirical models and the BTE-cRTA. Therefore, we assert that this approach represents a first step towards a fully ab initio carrier transport model that is valid in all compound semiconductors.

  19. 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.

  20. 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.

  1. 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.

  2. The general AMBER force field (GAFF) can accurately predict thermodynamic and transport properties of many ionic liquids.

    PubMed

    Sprenger, K G; Jaeger, Vance W; Pfaendtner, Jim

    2015-05-01

    We have applied molecular dynamics to calculate thermodynamic and transport properties of a set of 19 room-temperature ionic liquids. Since accurately simulating the thermophysical properties of solvents strongly depends upon the force field of choice, we tested the accuracy of the general AMBER force field, without refinement, for the case of ionic liquids. Electrostatic point charges were developed using ab initio calculations and a charge scaling factor of 0.8 to more accurately predict dynamic properties. The density, heat capacity, molar enthalpy of vaporization, self-diffusivity, and shear viscosity of the ionic liquids were computed and compared to experimentally available data, and good agreement across a wide range of cation and anion types was observed. Results show that, for a wide range of ionic liquids, the general AMBER force field, with no tuning of parameters, can reproduce a variety of thermodynamic and transport properties with similar accuracy to that of other published, often IL-specific, force fields. PMID:25853313

  3. An accurate modeling, simulation, and analysis tool for predicting and estimating Raman LIDAR system performance

    NASA Astrophysics Data System (ADS)

    Grasso, Robert J.; Russo, Leonard P.; Barrett, John L.; Odhner, Jefferson E.; Egbert, Paul I.

    2007-09-01

    BAE Systems presents the results of a program to model the performance of Raman LIDAR systems for the remote detection of atmospheric gases, air polluting hydrocarbons, chemical and biological weapons, and other molecular species of interest. Our model, which integrates remote Raman spectroscopy, 2D and 3D LADAR, and USAF atmospheric propagation codes permits accurate determination of the performance of a Raman LIDAR system. The very high predictive performance accuracy of our model is due to the very accurate calculation of the differential scattering cross section for the specie of interest at user selected wavelengths. We show excellent correlation of our calculated cross section data, used in our model, with experimental data obtained from both laboratory measurements and the published literature. In addition, the use of standard USAF atmospheric models provides very accurate determination of the atmospheric extinction at both the excitation and Raman shifted wavelengths.

  4. How accurately does the public perceive differences in transport risks? An exploratory analysis of scales representing perceived risk.

    PubMed

    Elvik, Rune; Bjørnskau, Torkel

    2005-11-01

    This paper probes the extent to which the public accurately perceives differences in transport risks. The paper is based on a survey of a random sample of the Norwegian population, conducted in September 2003. In the survey, respondents were asked: "How safe do you think it is to travel by means of (bus, train, etc.)?" Answers were given as: very safe, safe, a little unsafe, and very unsafe. A cursory examination of the answers suggested that the Norwegian public was quite well informed about differences in the risk of accident between different modes of transport, as well as between groups formed according to age and gender for each mode of transport. This paper probes the relationship between statistical estimates of risk and summary representations of perceived risk more systematically. It is found that the differences in fatality rate between different modes of transport are quite well perceived by the Norwegian public, irrespective of the way in which perceived risk is represented numerically. The relationship between statistical estimates of risk and numerical representations of perceived risk for each mode of transport is more sensitive to the choice of a numerical representation of perceived risk. A scale in which the answer "very safe" is assigned the value of 0.01 and the answer "very unsafe" is assigned the value of 10 is found to perform quite well. When the perception of risk is represented numerically according to this scale, a positive correlation between statistically estimated risk and perceived risk is found in seven of the eight comparisons that were made to determine how well variation in accident rates according to age and gender for car occupants, car drivers, cyclists and pedestrians are perceived. PMID:16054102

  5. 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.

  6. Coupled transport in rotor models

    NASA Astrophysics Data System (ADS)

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

    2016-08-01

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

  7. Fast algorithms for transport models

    SciTech Connect

    Manteuffel, T.A.

    1992-12-01

    The objective of this project is the development of numerical solution techniques for deterministic models of the transport of neutral and charged particles and the demonstration of their effectiveness in both a production environment and on advanced architecture computers. The primary focus is on various versions of the linear Boltzman equation. These equations are fundamental in many important applications. This project is an attempt to integrate the development of numerical algorithms with the process of developing production software. A major thrust of this reject will be the implementation of these algorithms on advanced architecture machines that reside at the Advanced Computing Laboratory (ACL) at Los Alamos National Laboratories (LANL).

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

    SciTech Connect

    Sun, Y; Glascoe, L

    2005-06-09

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

  9. 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.

  10. 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.

  11. 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.

  12. 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).

  13. 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

  14. Improved inline model for nonlocal electron transport in HYDRA

    NASA Astrophysics Data System (ADS)

    Marinak, M. M.; Kerbel, G. D.; Patel, M. V.; Robey, H.; Ridgers, C. P.; Kingham, R. J.

    2014-10-01

    The nonlocal electron transport model in HYDRA has been improved in several respects. The original multigroup model has been extended to include the cascade in energy as particles slow down, yielding a more accurate range. The model was also extended to account for contributions to the energy loss rate due to bound electrons. These are among the important modifications that have enabled the package to simulate classes of suprathermal electrons. We show recent calculations using the model that suggest superthermal electrons could be having a significant effect on performance of cryogenic capsule implosions on the National Ignition Facility. We evaluate the nonlocal transport model's accuracy by comparison with an electron VFP code. Comparisons assess the accuracy of the calculated thermal transport for plasmas relevant to NIF experiments. This work was performed under the auspices of the Lawrence Livermore National Security, LLC, (LLNS) under Contract No. DE-AC52-07NA27344.

  15. 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).

  16. Identification of accurate nonlinear rainfall-runoff models with unique parameters

    NASA Astrophysics Data System (ADS)

    Schoups, G.; Vrugt, J. A.; Fenicia, F.; van de Giesen, N.

    2009-04-01

    We propose a strategy to identify models with unique parameters that yield accurate streamflow predictions, given a time-series of rainfall inputs. The procedure consists of five general steps. First, an a priori range of model structures is specified based on prior general and site-specific hydrologic knowledge. To this end, we rely on a flexible model code that allows a specification of a wide range of model structures, from simple to complex. Second, using global optimization each model structure is calibrated to a record of rainfall-runoff data, yielding optimal parameter values for each model structure. Third, accuracy of each model structure is determined by estimating model prediction errors using independent validation and statistical theory. Fourth, parameter identifiability of each calibrated model structure is estimated by means of Monte Carlo Markov Chain simulation. Finally, an assessment is made about each model structure in terms of its accuracy of mimicking rainfall-runoff processes (step 3), and the uniqueness of its parameters (step 4). The procedure results in the identification of the most complex and accurate model supported by the data, without causing parameter equifinality. As such, it provides insight into the information content of the data for identifying nonlinear rainfall-runoff models. We illustrate the method using rainfall-runoff data records from several MOPEX basins in the US.

  17. Benchmarking of a Markov multizone model of contaminant transport.

    PubMed

    Jones, Rachael M; Nicas, Mark

    2014-10-01

    A Markov chain model previously applied to the simulation of advection and diffusion process of gaseous contaminants is extended to three-dimensional transport of particulates in indoor environments. The model framework and assumptions are described. The performance of the Markov model is benchmarked against simple conventional models of contaminant transport. The Markov model is able to replicate elutriation predictions of particle deposition with distance from a point source, and the stirred settling of respirable particles. Comparisons with turbulent eddy diffusion models indicate that the Markov model exhibits numerical diffusion in the first seconds after release, but over time accurately predicts mean lateral dispersion. The Markov model exhibits some instability with grid length aspect when turbulence is incorporated by way of the turbulent diffusion coefficient, and advection is present. However, the magnitude of prediction error may be tolerable for some applications and can be avoided by incorporating turbulence by way of fluctuating velocity (e.g. turbulence intensity). PMID:25143517

  18. Material Models for Accurate Simulation of Sheet Metal Forming and Springback

    NASA Astrophysics Data System (ADS)

    Yoshida, Fusahito

    2010-06-01

    For anisotropic sheet metals, modeling of anisotropy and the Bauschinger effect is discussed in the framework of Yoshida-Uemori kinematic hardening model incorporating with anisotropic yield functions. The performances of the models in predicting yield loci, cyclic stress-strain responses on several types of steel and aluminum sheets are demonstrated by comparing the numerical simulation results with the corresponding experimental observations. From some examples of FE simulation of sheet metal forming and springback, it is concluded that modeling of both the anisotropy and the Bauschinger effect is essential for the accurate numerical simulation.

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

    PubMed Central

    2014-01-01

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

  20. 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.

  1. 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 ...

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

    NASA Astrophysics Data System (ADS)

    Wang, Qian; Li, Bincheng

    2015-12-01

    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.

  3. 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.

  4. 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.

  5. One-dimensional transport equation models for sound energy propagation in long spaces: simulations and experiments.

    PubMed

    Jing, Yun; Xiang, Ning

    2010-04-01

    In this paper, the accuracy and efficiency of the previously discussed one-dimensional transport equation models [Y. Jing et al., J. Acoust. Soc. Am. 127, 2312-2322 (2010)] are examined both numerically and experimentally. The finite element method is employed to solve the equations. Artificial diffusion is applied in the numerical implementation to suppress oscillations of the solution. The transport equation models are then compared with the ray-tracing based method for different scenarios. In general, they are in good agreement, and the transport equation models are substantially less time consuming. In addition, the two-group model is found to yield more accurate results than the one-group model for the tested cases. Lastly, acoustic experimental results obtained from a 1:10 long room scale-model are used to verify the transport equation models. The results suggest that the transport equation models are able to accurately model the sound field in a long space. PMID:20370014

  6. Methodology to set up accurate OPC model using optical CD metrology and atomic force microscopy

    NASA Astrophysics Data System (ADS)

    Shim, Yeon-Ah; Kang, Jaehyun; Lee, Sang-Uk; Kim, Jeahee; Kim, Keeho

    2007-03-01

    For the 90nm node and beyond, smaller Critical Dimension(CD) control budget is required and the ways to control good CD uniformity are needed. Moreover Optical Proximity Correction(OPC) for the sub-90nm node demands more accurate wafer CD data in order to improve accuracy of OPC model. Scanning Electron Microscope (SEM) is the typical method for measuring CD until ArF process. However SEM can give serious attack such as shrinkage of Photo Resist(PR) by burning of weak chemical structure of ArF PR due to high energy electron beam. In fact about 5nm CD narrowing occur when we measure CD by using CD-SEM in ArF photo process. Optical CD Metrology(OCD) and Atomic Force Microscopy(AFM) has been considered to the method for measuring CD without attack of organic materials. Also the OCD and AFM measurement system have the merits of speed, easiness and accurate data. For model-based OPC, the model is generated using CD data of test patterns transferred onto the wafer. In this study we discuss to generate accurate OPC model using OCD and AFM measurement system.

  7. 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

  8. Building an accurate 3D model of a circular feature for robot vision

    NASA Astrophysics Data System (ADS)

    Li, L.

    2012-06-01

    In this paper, an accurate 3D model analysis of a circular feature is built with error compensation for robot vision. We propose an efficient method of fitting ellipses to data points by minimizing the algebraic distance subject to the constraint that a conic should be an ellipse and solving the ellipse parameters through a direct ellipse fitting method by analysing the 3D geometrical representation in a perspective projection scheme, the 3D position of a circular feature with known radius can be obtained. A set of identical circles, machined on a calibration board whose centres were known, was calibrated with a camera and did the model analysis that our method developed. Experimental results show that our method is more accurate than other methods.

  9. 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.

  10. 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. PMID:26956430

  11. 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

  12. 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

    2015-01-01

    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

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

    NASA Astrophysics Data System (ADS)

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

    2015-10-01

    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.

  14. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2015-09-01

    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 -2Yℓm waveform modes resolved by the NR code up to ℓ=8 . We compare our surrogate model to effective one body waveforms from 50 M⊙ to 300 M⊙ for advanced LIGO detectors and find that the surrogate is always more faithful (by at least an order of magnitude in most cases).

  16. 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

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

    PubMed Central

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

    2012-01-01

    While information from homologous structures plays a central role in X-ray structure determination by molecular replacement, such information is rarely used in NMR structure determination because it can be incorrect, both locally and globally, when evolutionary relationships are inferred incorrectly or there has been considerable evolutionary structural divergence. Here we describe a method that allows robust modeling of protein structures of up to 225 residues by combining , 13C, and 15N backbone and 13Cβ chemical shift data, distance restraints derived from homologous structures, and a physically realistic all-atom energy function. Accurate models are distinguished from inaccurate models generated using incorrect sequence alignments by requiring that (i) the all-atom energies of models generated using the restraints are lower than models generated in unrestrained calculations and (ii) the low-energy structures converge to within 2.0 Å backbone rmsd over 75% of the protein. Benchmark calculations on known structures and blind targets show that the method can accurately model protein structures, even with very remote homology information, to a backbone rmsd of 1.2–1.9 Å relative to the conventional determined NMR ensembles and of 0.9–1.6 Å relative to X-ray structures for well-defined regions of the protein structures. This approach facilitates the accurate modeling of protein structures using backbone chemical shift data without need for side-chain resonance assignments and extensive analysis of NOESY cross-peak assignments. PMID:22665781

  18. 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. PMID:25195174

  19. 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

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

    PubMed

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

    2009-01-01

    We present a coarse-grained red blood cell (RBC) model with accurate and realistic mechanical properties, rheology and dynamics. The modeled membrane is represented by a triangular mesh which incorporates shear inplane energy, bending energy, and area and volume conservation constraints. The macroscopic membrane elastic properties are imposed through semi-analytic theory, and are matched with those obtained in optical tweezers stretching experiments. Rheological measurements characterized by time-dependent complex modulus are extracted from the membrane thermal fluctuations, and compared with those obtained from the optical magnetic twisting cytometry results. The results allow us to define a meaningful characteristic time of the membrane. The dynamics of RBCs observed in shear flow suggests that a purely elastic model for the RBC membrane is not appropriate, and therefore a viscoelastic model is required. The set of proposed analyses and numerical tests can be used as a complete model testbed in order to calibrate the modeled viscoelastic membranes to accurately represent RBCs in health and disease. PMID:19965026

  1. 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.

  2. 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.

  3. 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.

  4. 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

  5. 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

  6. 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.

  7. 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.

  8. Accurate, efficient, and (iso)geometrically flexible collocation methods for phase-field models

    NASA Astrophysics Data System (ADS)

    Gomez, Hector; Reali, Alessandro; Sangalli, Giancarlo

    2014-04-01

    We propose new collocation methods for phase-field models. Our algorithms are based on isogeometric analysis, a new technology that makes use of functions from computational geometry, such as, for example, Non-Uniform Rational B-Splines (NURBS). NURBS exhibit excellent approximability and controllable global smoothness, and can represent exactly most geometries encapsulated in Computer Aided Design (CAD) models. These attributes permitted us to derive accurate, efficient, and geometrically flexible collocation methods for phase-field models. The performance of our method is demonstrated by several numerical examples of phase separation modeled by the Cahn-Hilliard equation. We feel that our method successfully combines the geometrical flexibility of finite elements with the accuracy and simplicity of pseudo-spectral collocation methods, and is a viable alternative to classical collocation methods.

  9. 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.

  10. An accurate and computationally efficient model for membrane-type circular-symmetric micro-hotplates.

    PubMed

    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

  11. 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

  12. A Method for Accurate in silico modeling of Ultrasound Transducer Arrays

    PubMed Central

    Guenther, Drake A.; Walker, William F.

    2009-01-01

    This paper presents a new approach to improve the in silico modeling of ultrasound transducer arrays. While current simulation tools accurately predict the theoretical element spatio-temporal pressure response, transducers do not always behave as theorized. In practice, using the probe's physical dimensions and published specifications in silico, often results in unsatisfactory agreement between simulation and experiment. We describe a general optimization procedure used to maximize the correlation between the observed and simulated spatio-temporal response of a pulsed single element in a commercial ultrasound probe. A linear systems approach is employed to model element angular sensitivity, lens effects, and diffraction phenomena. A numerical deconvolution method is described to characterize the intrinsic electro-mechanical impulse response of the element. Once the response of the element and optimal element characteristics are known, prediction of the pressure response for arbitrary apertures and excitation signals is performed through direct convolution using available tools. We achieve a correlation of 0.846 between the experimental emitted waveform and simulated waveform when using the probe's physical specifications in silico. A far superior correlation of 0.988 is achieved when using the optimized in silico model. Electronic noise appears to be the main effect preventing the realization of higher correlation coefficients. More accurate in silico modeling will improve the evaluation and design of ultrasound transducers as well as aid in the development of sophisticated beamforming strategies. PMID:19041997

  13. 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.

  14. 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

  15. Multiple mode model of tokamak transport

    SciTech Connect

    Singer, C.E.; Ghanem, E.S.; Bateman, G.; Stotler, D.P.

    1989-07-01

    Theoretical models for radical transport of energy and particles in tokamaks due to drift waves, rippling modes, and resistive ballooning modes have been combined in a predictive transport code. The resulting unified model has been used to simulate low confinement mode (L-mode) energy confinement scalings. Dependence of global energy confinement on electron density for the resulting model is also described. 26 refs., 1 fig., 2 tabs.

  16. 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.

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

    PubMed Central

    Fu, Jun-Song; Liu, Yun

    2015-01-01

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

  18. 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.

  19. Fully Automated Generation of Accurate Digital Surface Models with Sub-Meter Resolution from Satellite Imagery

    NASA Astrophysics Data System (ADS)

    Wohlfeil, J.; Hirschmüller, H.; Piltz, B.; Börner, A.; Suppa, M.

    2012-07-01

    Modern pixel-wise image matching algorithms like Semi-Global Matching (SGM) are able to compute high resolution digital surface models from airborne and spaceborne stereo imagery. Although image matching itself can be performed automatically, there are prerequisites, like high geometric accuracy, which are essential for ensuring the high quality of resulting surface models. Especially for line cameras, these prerequisites currently require laborious manual interaction using standard tools, which is a growing problem due to continually increasing demand for such surface models. The tedious work includes partly or fully manual selection of tie- and/or ground control points for ensuring the required accuracy of the relative orientation of images for stereo matching. It also includes masking of large water areas that seriously reduce the quality of the results. Furthermore, a good estimate of the depth range is required, since accurate estimates can seriously reduce the processing time for stereo matching. In this paper an approach is presented that allows performing all these steps fully automated. It includes very robust and precise tie point selection, enabling the accurate calculation of the images' relative orientation via bundle adjustment. It is also shown how water masking and elevation range estimation can be performed automatically on the base of freely available SRTM data. Extensive tests with a large number of different satellite images from QuickBird and WorldView are presented as proof of the robustness and reliability of the proposed method.

  20. 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.

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

    PubMed Central

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

    2013-01-01

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

  2. 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

  3. An accurate and comprehensive model of thin fluid flows with inertia on curved substrates

    NASA Astrophysics Data System (ADS)

    Roberts, A. J.; Li, Zhenquan

    2006-04-01

    Consider the three-dimensional flow of a viscous Newtonian fluid upon a curved two-dimensional substrate when the fluid film is thin, as occurs in many draining, coating and biological flows. We derive a comprehensive model of the dynamics of the film, the model being expressed in terms of the film thickness eta and the average lateral velocity bar{bm u}. Centre manifold theory assures us that the model accurately and systematically includes the effects of the curvature of substrate, gravitational body force, fluid inertia and dissipation. The model resolves wavelike phenomena in the dynamics of viscous fluid flows over arbitrarily curved substrates such as cylinders, tubes and spheres. We briefly illustrate its use in simulating drop formation on cylindrical fibres, wave transitions, three-dimensional instabilities, Faraday waves, viscous hydraulic jumps, flow vortices in a compound channel and flow down and up a step. These models are the most complete models for thin-film flow of a Newtonian fluid; many other thin-film models can be obtained by different restrictions and truncations of the model derived here.

  4. Anomalous transport modelling of tokamak plasmas

    SciTech Connect

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

    1992-12-31

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

  5. Anomalous transport modelling of tokamak plasmas

    SciTech Connect

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

    1992-01-01

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

  6. 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

  7. Transport model of nucleon-nucleus reaction

    NASA Technical Reports Server (NTRS)

    Wilson, J. W.; Townsend, L. W.; Cucinotta, F. A.

    1986-01-01

    A simplified model of nucleon-nucleus reaction is developed and some of its properties are examined. Comparisons with proton production measured for targets of Al-27, Ni-58, Zr-90, and Bi-209 show some hope for developing an accurate model for these complex reactions. It is suggested that binding effects are the next step required for further development.

  8. 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

  9. 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.

  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. PMID:25502920

  11. Turtle utricle dynamic behavior using a combined anatomically accurate model and experimentally measured hair bundle stiffness

    PubMed Central

    Davis, J.L.; Grant, J.W.

    2014-01-01

    Anatomically correct turtle utricle geometry was incorporated into two finite element models. The geometrically accurate model included appropriately shaped macular surface and otoconial layer, compact gel and column filament (or shear) layer thicknesses and thickness distributions. The first model included a shear layer where the effects of hair bundle stiffness was included as part of the shear layer modulus. This solid model’s undamped natural frequency was matched to an experimentally measured value. This frequency match established a realistic value of the effective shear layer Young’s modulus of 16 Pascals. We feel this is the most accurate prediction of this shear layer modulus and fits with other estimates (Kondrachuk, 2001b). The second model incorporated only beam elements in the shear layer to represent hair cell bundle stiffness. The beam element stiffness’s were further distributed to represent their location on the neuroepithelial surface. Experimentally measured striola hair cell bundles mean stiffness values were used in the striolar region and the mean extrastriola hair cell bundles stiffness values were used in this region. The results from this second model indicated that hair cell bundle stiffness contributes approximately 40% to the overall stiffness of the shear layer– hair cell bundle complex. This analysis shows that high mass saccules, in general, achieve high gain at the sacrifice of frequency bandwidth. We propose the mechanism by which this can be achieved is through increase the otoconial layer mass. The theoretical difference in gain (deflection per acceleration) is shown for saccules with large otoconial layer mass relative to saccules and utricles with small otoconial layer mass. Also discussed is the necessity of these high mass saccules to increase their overall system shear layer stiffness. Undamped natural frequencies and mode shapes for these sensors are shown. PMID:25445820

  12. 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

  13. 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.

  14. 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.

  15. 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

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

    PubMed

    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 2 mm 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

  17. 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.

  18. 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.

  19. Achieving accurate nuetron-multiplicity analysis of metals and oxides with weighted point model equations.

    SciTech Connect

    Burward-Hoy, J. M.; Geist, W. H.; Krick, M. S.; Mayo, D. R.

    2004-01-01

    Neutron multiplicity counting is a technique for the rapid, nondestructive measurement of plutonium mass in pure and impure materials. This technique is very powerful because it uses the measured coincidence count rates to determine the sample mass without requiring a set of representative standards for calibration. Interpreting measured singles, doubles, and triples count rates using the three-parameter standard point model accurately determines plutonium mass, neutron multiplication, and the ratio of ({alpha},n) to spontaneous-fission neutrons (alpha) for oxides of moderate mass. However, underlying standard point model assumptions - including constant neutron energy and constant multiplication throughout the sample - cause significant biases for the mass, multiplication, and alpha in measurements of metal and large, dense oxides.

  20. 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.

  1. 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.

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

    NASA Technical Reports Server (NTRS)

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

    1997-01-01

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

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

    PubMed

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

    2015-09-18

    Simulating a binary black hole coalescence by solving Einstein's equations is computationally expensive, requiring days to months of supercomputing time. Using reduced order modeling techniques, we construct an accurate surrogate model, which is evaluated in a millisecond to a second, for numerical relativity (NR) waveforms from nonspinning binary black hole coalescences with mass ratios in [1, 10] and durations corresponding to about 15 orbits before merger. We assess the model's uncertainty and show that our modeling strategy predicts NR waveforms not used for the surrogate's training with errors nearly as small as the numerical error of the NR code. Our model includes all spherical-harmonic _{-2}Y_{ℓm} waveform modes resolved by the NR code up to ℓ=8. We compare our surrogate model to effective one body waveforms from 50M_{⊙} to 300M_{⊙} for advanced LIGO detectors and find that the surrogate is always more faithful (by at least an order of magnitude in most cases). PMID:26430979

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

    PubMed Central

    Saa, Pedro A.; Nielsen, Lars K.

    2016-01-01

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

  5. An Accurate Model for Biomolecular Helices and Its Application to Helix Visualization

    PubMed Central

    Wang, Lincong; Qiao, Hui; Cao, Chen; Xu, Shutan; Zou, Shuxue

    2015-01-01

    Helices are the most abundant secondary structural elements in proteins and the structural forms assumed by double stranded DNAs (dsDNA). Though the mathematical expression for a helical curve is simple, none of the previous models for the biomolecular helices in either proteins or DNAs use a genuine helical curve, likely because of the complexity of fitting backbone atoms to helical curves. In this paper we model a helix as a series of different but all bona fide helical curves; each one best fits the coordinates of four consecutive backbone Cα atoms for a protein or P atoms for a DNA molecule. An implementation of the model demonstrates that it is more accurate than the previous ones for the description of the deviation of a helix from a standard helical curve. Furthermore, the accuracy of the model makes it possible to correlate deviations with structural and functional significance. When applied to helix visualization, the ribbon diagrams generated by the model are less choppy or have smaller side chain detachment than those by the previous visualization programs that typically model a helix as a series of low-degree splines. PMID:26126117

  6. Fast and Accurate Radiative Transfer Calculations Using Principal Component Analysis for Climate Modeling

    NASA Astrophysics Data System (ADS)

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

    2014-12-01

    Radiative transfer (RT) computations are an essential component of energy budget calculations in climate models. However, full treatment of RT processes is computationally expensive, prompting usage of 2-stream approximations in operational climate models. This simplification introduces errors of the order of 10% in the top of the atmosphere (TOA) fluxes [Randles 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 simulations. 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. Here, we extend 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. Comparisons between the new model, called Universal Principal Component Analysis model for Radiative Transfer (UPCART), 2-stream models (such as those used in climate applications) and line-by-line RT models are performed, in order for spectral radiances, spectral fluxes and broadband fluxes. Each of these are calculated at the TOA for several scenarios with varying aerosol types, extinction and scattering optical depth profiles, and solar and viewing geometries. We demonstrate that very accurate radiative forcing estimates can be obtained, with better than 1% accuracy in all spectral regions and better than 0.1% in most cases as compared to an exact line-by-line RT model. The model is comparable in speeds to 2-stream models, potentially rendering UPCART useful for operational General Circulation Models (GCMs). The operational speed and accuracy of UPCART can be further

  7. 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%.

  8. A community firn densification and gas transport model

    NASA Astrophysics Data System (ADS)

    Stevens, C.; Lundin, J.; Harris, P.; Leahy, W.; Waddington, E. D.

    2012-12-01

    Gas bubbles trapped in ice preserve a record of Earth's climate history. Interpretation of ice-core records is complicated by the difference in age (called delta age) between the gas trapped in bubbles and the ice enclosing the gas. Determining delta age requires understanding both densification of polar firn and gas transport through the firn. Independent models of firn densification and firn gas transport have been developed in the past by individual research groups. We are developing a web-based model of firn densification and gas transport that combines the best features of those models and is freely accessible to research teams. Users input site-specific data, and the model provides depth-density-age and delta-age results. In addition to the web-based model, state-of-the-art transient firn-densification and gas-transport models are in development. These models allow physical properties to evolve, which results in more accurate delta-age approximations at times of rapid climate change in the past. These community models will be downloadable as open-source code. They will provide a baseline to make intercomparisons between datasets or other models. The models are modular, allowing users to choose preferred physical models and physical processes to include, based on available pre-coded options. Alternatively, users can adapt the code to include new or different physics. Here, we present results from the web-based model and early stages of the transient models and compare with known firn-density and gas-concentration profiles.

  9. 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

  10. 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

  11. 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

  12. Continuum descriptions of membranes and their interaction with proteins: Towards chemically accurate models.

    PubMed

    Argudo, David; Bethel, Neville P; Marcoline, Frank V; Grabe, Michael

    2016-07-01

    Biological membranes deform in response to resident proteins leading to a coupling between membrane shape and protein localization. Additionally, the membrane influences the function of membrane proteins. Here we review contributions to this field from continuum elastic membrane models focusing on the class of models that couple the protein to the membrane. While it has been argued that continuum models cannot reproduce the distortions observed in fully-atomistic molecular dynamics simulations, we suggest that this failure can be overcome by using chemically accurate representations of the protein. We outline our recent advances along these lines with our hybrid continuum-atomistic model, and we show the model is in excellent agreement with fully-atomistic simulations of the nhTMEM16 lipid scramblase. We believe that the speed and accuracy of continuum-atomistic methodologies will make it possible to simulate large scale, slow biological processes, such as membrane morphological changes, that are currently beyond the scope of other computational approaches. This article is part of a Special Issue entitled: Membrane Proteins edited by J.C. Gumbart and Sergei Noskov. PMID:26853937

  13. 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

  14. Hybridization modeling of oligonucleotide SNP arrays for accurate DNA copy number estimation

    PubMed Central

    Wan, Lin; Sun, Kelian; Ding, Qi; Cui, Yuehua; Li, Ming; Wen, Yalu; Elston, Robert C.; Qian, Minping; Fu, Wenjiang J

    2009-01-01

    Affymetrix SNP arrays have been widely used for single-nucleotide polymorphism (SNP) genotype calling and DNA copy number variation inference. Although numerous methods have achieved high accuracy in these fields, most studies have paid little attention to the modeling of hybridization of probes to off-target allele sequences, which can affect the accuracy greatly. In this study, we address this issue and demonstrate that hybridization with mismatch nucleotides (HWMMN) occurs in all SNP probe-sets and has a critical effect on the estimation of allelic concentrations (ACs). We study sequence binding through binding free energy and then binding affinity, and develop a probe intensity composite representation (PICR) model. The PICR model allows the estimation of ACs at a given SNP through statistical regression. Furthermore, we demonstrate with cell-line data of known true copy numbers that the PICR model can achieve reasonable accuracy in copy number estimation at a single SNP locus, by using the ratio of the estimated AC of each sample to that of the reference sample, and can reveal subtle genotype structure of SNPs at abnormal loci. We also demonstrate with HapMap data that the PICR model yields accurate SNP genotype calls consistently across samples, laboratories and even across array platforms. PMID:19586935

  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. 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.

  17. 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.

  18. 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

  19. 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.

  20. 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).

  1. Application of model abstraction techniques to simulate transport in soils

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Successful understanding and modeling of contaminant transport in soils is the precondition of risk-informed predictions of the subsurface contaminant transport. Exceedingly complex models of subsurface contaminant transport are often inefficient. Model abstraction is the methodology for reducing th...

  2. 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.

  3. 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

  4. Accurate and Fast Simulation of Channel Noise in Conductance-Based Model Neurons by Diffusion Approximation

    PubMed Central

    Linaro, Daniele; Storace, Marco; Giugliano, Michele

    2011-01-01

    Stochastic channel gating is the major source of intrinsic neuronal noise whose functional consequences at the microcircuit- and network-levels have been only partly explored. A systematic study of this channel noise in large ensembles of biophysically detailed model neurons calls for the availability of fast numerical methods. In fact, exact techniques employ the microscopic simulation of the random opening and closing of individual ion channels, usually based on Markov models, whose computational loads are prohibitive for next generation massive computer models of the brain. In this work, we operatively define a procedure for translating any Markov model describing voltage- or ligand-gated membrane ion-conductances into an effective stochastic version, whose computer simulation is efficient, without compromising accuracy. Our approximation is based on an improved Langevin-like approach, which employs stochastic differential equations and no Montecarlo methods. As opposed to an earlier proposal recently debated in the literature, our approximation reproduces accurately the statistical properties of the exact microscopic simulations, under a variety of conditions, from spontaneous to evoked response features. In addition, our method is not restricted to the Hodgkin-Huxley sodium and potassium currents and is general for a variety of voltage- and ligand-gated ion currents. As a by-product, the analysis of the properties emerging in exact Markov schemes by standard probability calculus enables us for the first time to analytically identify the sources of inaccuracy of the previous proposal, while providing solid ground for its modification and improvement we present here. PMID:21423712

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

    NASA Astrophysics Data System (ADS)

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

    1988-10-01

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

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

    NASA Technical Reports Server (NTRS)

    Arya, Vinod K.

    1994-01-01

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

  7. 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.

  8. 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

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

    PubMed Central

    Santolini, Marc; Mora, Thierry; Hakim, Vincent

    2014-01-01

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

  10. 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.

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

    SciTech Connect

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

    2003-03-27

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

  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. 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%.

  15. 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. PMID:27230942

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

    PubMed Central

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

    2015-01-01

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

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

    SciTech Connect

    Nielsen, Jens; D’Avezac, Mayeul; Hetherington, James; Stamatakis, Michail

    2013-12-14

    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.

  18. 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.

  19. 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

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

    PubMed

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

    2008-03-28

    Conformational entropy makes important contribution to the stability and folding of RNA molecule, but it is challenging to either measure or compute conformational entropy associated with long loops. We develop optimized discrete k-state models of RNA backbone based on known RNA structures for computing entropy of loops, which are modeled as self-avoiding walks. To estimate entropy of hairpin, bulge, internal loop, and multibranch loop of long length (up to 50), we develop an efficient sampling method based on the sequential Monte Carlo principle. Our method considers excluded volume effect. It is general and can be applied to calculating entropy of loops with longer length and arbitrary complexity. For loops of short length, our results are in good agreement with a recent theoretical model and experimental measurement. For long loops, our estimated entropy of hairpin loops is in excellent agreement with the Jacobson-Stockmayer extrapolation model. However, for bulge loops and more complex secondary structures such as internal and multibranch loops, we find that the Jacobson-Stockmayer extrapolation model has large errors. Based on estimated entropy, we have developed empirical formulae for accurate calculation of entropy of long loops in different secondary structures. Our study on the effect of asymmetric size of loops suggest that loop entropy of internal loops is largely determined by the total loop length, and is only marginally affected by the asymmetric size of the two loops. Our finding suggests that the significant asymmetric effects of loop length in internal loops measured by experiments are likely to be partially enthalpic. Our method can be applied to develop improved energy parameters important for studying RNA stability and folding, and for predicting RNA secondary and tertiary structures. The discrete model and the program used to calculate loop entropy can be downloaded at http://gila.bioengr.uic.edu/resources/RNA.html. PMID:18376982

  1. Efficient yet accurate solution of the linear transport equation in the presence of internal sources - The exponential-linear-in-depth approximation

    NASA Technical Reports Server (NTRS)

    Kylling, Arve; Stamnes, Knut

    1992-01-01

    The present solutions to the linear transport equation pertain to monoenergetic particles' interaction with a multiple scattering/absorbing layered medium with a general anisotropic internal source term. Attention is given to a novel exponential-linear approximation to the internal source, as a function of scattering depth, which furnishes an at-once efficient and accurate solution to the linear transport equation through its reduction of the spatial mesh size. The great superiority of the proposed method is demonstrated by the numerical results obtained in the illustrative cases of (1) an embedded thermal source and (2) a rapidly varying beam pseudosource.

  2. 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.

  3. A stochastic model of kinetochore–microtubule attachment accurately describes fission yeast chromosome segregation

    PubMed Central

    Gay, Guillaume; Courtheoux, Thibault; Reyes, Céline

    2012-01-01

    In fission yeast, erroneous attachments of spindle microtubules to kinetochores are frequent in early mitosis. Most are corrected before anaphase onset by a mechanism involving the protein kinase Aurora B, which destabilizes kinetochore microtubules (ktMTs) in the absence of tension between sister chromatids. In this paper, we describe a minimal mathematical model of fission yeast chromosome segregation based on the stochastic attachment and detachment of ktMTs. The model accurately reproduces the timing of correct chromosome biorientation and segregation seen in fission yeast. Prevention of attachment defects requires both appropriate kinetochore orientation and an Aurora B–like activity. The model also reproduces abnormal chromosome segregation behavior (caused by, for example, inhibition of Aurora B). It predicts that, in metaphase, merotelic attachment is prevented by a kinetochore orientation effect and corrected by an Aurora B–like activity, whereas in anaphase, it is corrected through unbalanced forces applied to the kinetochore. These unbalanced forces are sufficient to prevent aneuploidy. PMID:22412019

  4. Computationally efficient and accurate enantioselectivity modeling by clusters of molecular dynamics simulations.

    PubMed

    Wijma, Hein J; Marrink, Siewert J; Janssen, Dick B

    2014-07-28

    Computational approaches could decrease the need for the laborious high-throughput experimental screening that is often required to improve enzymes by mutagenesis. Here, we report that using multiple short molecular dynamics (MD) simulations makes it possible to accurately model enantioselectivity for large numbers of enzyme-substrate combinations at low computational costs. We chose four different haloalkane dehalogenases as model systems because of the availability of a large set of experimental data on the enantioselective conversion of 45 different substrates. To model the enantioselectivity, we quantified the frequency of occurrence of catalytically productive conformations (near attack conformations) for pairs of enantiomers during MD simulations. We found that the angle of nucleophilic attack that leads to carbon-halogen bond cleavage was a critical variable that limited the occurrence of productive conformations; enantiomers for which this angle reached values close to 180° were preferentially converted. A cluster of 20-40 very short (10 ps) MD simulations allowed adequate conformational sampling and resulted in much better agreement to experimental enantioselectivities than single long MD simulations (22 ns), while the computational costs were 50-100 fold lower. With single long MD simulations, the dynamics of enzyme-substrate complexes remained confined to a conformational subspace that rarely changed significantly, whereas with multiple short MD simulations a larger diversity of conformations of enzyme-substrate complexes was observed. PMID:24916632

  5. Accurate models for P-gp drug recognition induced from a cancer cell line cytotoxicity screen.

    PubMed

    Levatić, Jurica; Ćurak, Jasna; Kralj, Marijeta; Šmuc, Tomislav; Osmak, Maja; Supek, Fran

    2013-07-25

    P-glycoprotein (P-gp, MDR1) is a promiscuous drug efflux pump of substantial pharmacological importance. Taking advantage of large-scale cytotoxicity screening data involving 60 cancer cell lines, we correlated the differential biological activities of ∼13,000 compounds against cellular P-gp levels. We created a large set of 934 high-confidence P-gp substrates or nonsubstrates by enforcing agreement with an orthogonal criterion involving P-gp overexpressing ADR-RES cells. A support vector machine (SVM) was 86.7% accurate in discriminating P-gp substrates on independent test data, exceeding previous models. Two molecular features had an overarching influence: nearly all P-gp substrates were large (>35 atoms including H) and dense (specific volume of <7.3 Å(3)/atom) molecules. Seven other descriptors and 24 molecular fragments ("effluxophores") were found enriched in the (non)substrates and incorporated into interpretable rule-based models. Biological experiments on an independent P-gp overexpressing cell line, the vincristine-resistant VK2, allowed us to reclassify six compounds previously annotated as substrates, validating our method's predictive ability. Models are freely available at http://pgp.biozyne.com . PMID:23772653

  6. 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.

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

    PubMed Central

    2011-01-01

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

  8. Models for Turbulent Transport Processes.

    ERIC Educational Resources Information Center

    Hill, James C.

    1979-01-01

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

  9. Accurate mathematical models to describe the lactation curve of Lacaune dairy sheep under intensive management.

    PubMed

    Elvira, L; Hernandez, F; Cuesta, P; Cano, S; Gonzalez-Martin, J-V; Astiz, S

    2013-06-01

    Although the intensive production system of Lacaune dairy sheep is the only profitable method for producers outside of the French Roquefort area, little is known about this type of systems. This study evaluated yield records of 3677 Lacaune sheep under intensive management between 2005 and 2010 in order to describe the lactation curve of this breed and to investigate the suitability of different mathematical functions for modeling this curve. A total of 7873 complete lactations during a 40-week lactation period corresponding to 201 281 pieces of weekly yield data were used. First, five mathematical functions were evaluated on the basis of the residual mean square, determination coefficient, Durbin Watson and Runs Test values. The two better models were found to be Pollott Additive and fractional polynomial (FP). In the second part of the study, the milk yield, peak of milk yield, day of peak and persistency of the lactations were calculated with Pollot Additive and FP models and compared with the real data. The results indicate that both models gave an extremely accurate fit to Lacaune lactation curves in order to predict milk yields (P = 0.871), with the FP model being the best choice to provide a good fit to an extensive amount of real data and applicable on farm without specific statistical software. On the other hand, the interpretation of the parameters of the Pollott Additive function helps to understand the biology of the udder of the Lacaune sheep. The characteristics of the Lacaune lactation curve and milk yield are affected by lactation number and length. The lactation curves obtained in the present study allow the early identification of ewes with low milk yield potential, which will help to optimize farm profitability. PMID:23257242

  10. 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

  11. 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

  12. Mapping of photon distribution and imaging of MR-derived anatomically accurate optical models of the female breast

    NASA Astrophysics Data System (ADS)

    Barbour, San-Lian S.; Barbour, Randall L.; Koo, Ping C.; Graber, Harry L.; Chang, Jenghwa

    1995-05-01

    We have computed optical images of the female breast based on analysis of tomographic data obtained from simulated time-independent optical measurements of anatomically accurate maps derived from segmented 3D magnetic resonance (MR) images. Images were segmented according to the measured MR contrast levels for fat and parenchymal tissue from T1 weighted acquisitions. Computed images were obtained from analysis of solutions to the forward problem for breasts containing 'added pathologies', representing tumors, to breasts lacking these inclusions. Both breast size and its optical properties have been examined in tissue. In each case, two small simulated tumors were 'added' to the background issue. Values of absorption and scattering coefficients of the tumors have been examined that are both greater and less than the surrounding tissue. Detector responses and the required imaging operators were computed by numerically solving the diffusion equation for inhomogeneous media. Detectors were distributed uniformly, in a circular fashion, around the breast in a plane positioned parallel and half-way between the chest wall and the nipple. A total of 20 sources were used, and for each 20 detectors. Reconstructed images were obtained by solving a linear perturbation equation derived from transport theory. Three algorithms were tested to solve the perturbation equation and include, the methods of conjugate gradient decent (CGD), projection onto convex sets (POCS), and simultaneous algebraic reconstruction technique (SART). Results obtained showed that in each case, high quality reconstructions were obtained. The computed images correctly resolved and identified the spatial position of the two tumors. Additional studies showed that computed images were stable to large systematic errors in the imaging operators and to added noise. Further, examination of the computed detector readings indicate that images of tissue up to approximately 10 cm in thickness should be possible. The

  13. 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.

  14. The secret to successful solute-transport modeling.

    PubMed

    Konikow, Leonard F

    2011-01-01

    Modeling subsurface solute transport is difficult-more so than modeling heads and flows. The classical governing equation does not always adequately represent what we see at the field scale. In such cases, commonly used numerical models are solving the wrong equation. Also, the transport equation is hyperbolic where advection is dominant, and parabolic where hydrodynamic dispersion is dominant. No single numerical method works well for all conditions, and for any given complex field problem, where seepage velocity is highly variable, no one method will be optimal everywhere. Although we normally expect a numerically accurate solution to the governing groundwater-flow equation, errors in concentrations from numerical dispersion and/or oscillations may be large in some cases. The accuracy and efficiency of the numerical solution to the solute-transport equation are more sensitive to the numerical method chosen than for typical groundwater-flow problems. However, numerical errors can be kept within acceptable limits if sufficient computational effort is expended. But impractically long simulation times may promote a tendency to ignore or accept numerical errors. One approach to effective solute-transport modeling is to keep the model relatively simple and use it to test and improve conceptual understanding of the system and the problem at hand. It should not be expected that all concentrations observed in the field can be reproduced. Given a knowledgeable analyst, a reasonable description of a hydrogeologic framework, and the availability of solute-concentration data, the secret to successful solute-transport modeling may simply be to lower expectations. PMID:21039449

  15. 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

  16. 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

  17. 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

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

    SciTech Connect

    Otoo, Ekow J.; Shoshani, Arie

    2003-01-23

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

  19. 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

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

    NASA Astrophysics Data System (ADS)

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

    2015-04-01

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

  1. DAC 22 High Speed Civil Transport Model

    NASA Technical Reports Server (NTRS)

    1992-01-01

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

  2. 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.

  3. 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

  4. Chemistry and transport in a multi-dimensional model

    NASA Technical Reports Server (NTRS)

    Yung, Yuk L.

    1993-01-01

    The focus of our research program is the achievement of a quantitative understanding of the spatial distribution and temporal variation of chemical species in the terrestrial middle atmosphere, with emphasis on ozone. Although not directed at assessments of anthropogenic impacts, our activities contribute to a refinement of model descriptions of chemical and dynamical processes that are needed for assessment tasks. A unique feature of our research effort is a close interaction with the chemical kinetics group at JPL and the field measurement groups at JPL. The principal tools used in our investigations are l-D and 2-D photochemical models. The advective component of the meridional transport in these models is approximated by the diabatic circulation, which is derived diagnostically from the net radiative heating rates. We are developing accurate radiative transfer algorithms to find the net heating rates and the diabatic circulation for use in the 2-D model.

  5. An accurate parameterization of the radiative properties of water clouds suitable for use in climate models

    SciTech Connect

    Hu, Y.X.; Stamnes, K. )

    1993-04-01

    A new parameterization of the radiative Properties of water clouds is presented. Cloud optical properties for valent radius throughout the solar and both solar and terrestrial spectra and for cloud equivalent radii in the range 2.5-60 [mu]m are calculated from Mie theory. It is found that cloud optical properties depend mainly on equivalent radius throughout the solar and terrestrial spectrum and are insensitive to the details of the droplet size distribution, such as shape, skewness, width, and modality (single or bimodal). This suggests that in cloud models, aimed at predicting the evolution of cloud microphysics with climate change, it is sufficient to determine the third and the second moments of the size distribution (the ratio of which determines the equivalent radius). It also implies that measurements of the cloud liquid water content and the extinction coefficient are sufficient to determine cloud optical properties experimentally (i.e., measuring the complete droplet size distribution is not required). Based on the detailed calculations, the optical properties are parameterized as a function of cloud liquid water path and equivalent cloud droplet radius by using a nonlinear least-square fitting. The parameterization is performed separately for the range of radii 2.5-12 [mu]m, 12-30,[mu]m, and 30-60 [mu]m. Cloud heating and cooling rates are computed from this parameterization by using a comprehensive radiation model. Comparison with similar results obtained from exact Mie scattering calculations shows that this parameterization yields very accurate results and that it is several thousand times faster. This parameterization separates the dependence of cloud optical properties on droplet size and liquid water content, and is suitable for inclusion into climate models. 22 refs., 7 figs., 6 tabs.

  6. 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

  7. Climate Impact of Transportation A Model Comparison

    SciTech Connect

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

    2013-06-01

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

  8. Multidrug resistance ABC transporter structure predictions by homology modeling approaches.

    PubMed

    Honorat, Mylène; Falson, Pierre; Terreux, Raphael; Di Pietro, Attilio; Dumontet, Charles; Payen, Léa

    2011-03-01

    Human multidrug resistance ABC transporters are ubiquitous membrane proteins responsible for the efflux of multiple, endogenous or exogenous, compounds out of the cells, and therefore they are involved in multi-drug resistance phenotype (MDR). They thus deeply impact the pharmacokinetic parameters and toxicity properties of drugs. A great pressure to develop inhibitors of these pumps is carried out, by either ligand-based drug design or (more ideally) structure-based drug design. In that goal, many biochemical studies have been carried out to characterize their transport functions, and many efforts have been spent to get high-resolution structures. Currently, beside the 3D-structures of bacterial ABC transporters Sav1866 and MsbA, only the mouse ABCB1 complete structure has been published at high-resolution, illustrating the tremendous difficulty in getting such information, taking into account that the human genome accounts for 48 ABC transporters encoding genes. Homology modeling is consequently a reasonable approach to overcome this obstacle. The present review describes, in the first part, the different approaches which have been published to set up human ABC pump 3D-homology models allowing the localization of binding sites for drug candidates, and the identification of critical residues therein. In a second part, the review proposes a more accurate strategy and practical keys to use such biological tools for initiating structure-based drug design. PMID:21470105

  9. Model for assessing bronchial mucus transport

    SciTech Connect

    Agnew, J.E.; Bateman, J.R.M.; Pavia, D.; Clarke, S.W.

    1984-02-01

    The authors propose a scheme for the assessment of regional mucus transport using inhaled Tc-99m aerosol particles and quantitative analysis of serial gamma-camera images. The model treats input to inner and intermediate lung regions as the total of initial deposition there plus subsequent transport into these regions from more peripheral airways. It allows for interregional differences in the proportion of particles deposited on the mucus-bearing conducting airways, and does not require a gamma image 24 hr after particle inhalation. Instead, distribution of particles reaching the respiratory bronchioles or alveoli is determined from a Kr-81m ventilation image, while the total amount of such deposition is obtained from 24-hr Tc-99m retention measured with a sensitive counter system. The model is applicable to transport by mucociliary action or by cough, and has been tested in ten normal and ten asthmatic subjects.

  10. 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.

  11. 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.

  12. 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.

  13. Modeling Facilitated Contaminant Transport by Mobile Bacteria

    NASA Astrophysics Data System (ADS)

    Corapcioglu, M. Yavuz; Kim, Seunghyun

    1995-01-01

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

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

    PubMed

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

    2015-04-21

    Analytical centrifugation (AC) is a powerful technique for the characterisation of nanoparticles in colloidal systems. As a direct and absolute technique it requires no calibration or measurements of standards. Moreover, it offers simple experimental design and handling, high sample throughput as well as moderate investment costs. However, the full potential of AC for nanoparticle size analysis requires the development of powerful data analysis techniques. In this study we show how the application of direct boundary models to AC data opens up new possibilities in particle characterisation. An accurate analysis method, successfully applied to sedimentation data obtained by analytical ultracentrifugation (AUC) in the past, was used for the first time in analysing AC data. Unlike traditional data evaluation routines for AC using a designated number of radial positions or scans, direct boundary models consider the complete sedimentation boundary, which results in significantly better statistics. We demonstrate that meniscus fitting, as well as the correction of radius and time invariant noise significantly improves the signal-to-noise ratio and prevents the occurrence of false positives due to optical artefacts. Moreover, hydrodynamic non-ideality can be assessed by the residuals obtained from the analysis. The sedimentation coefficient distributions obtained by AC are in excellent agreement with the results from AUC. Brownian dynamics simulations were used to generate numerical sedimentation data to study the influence of diffusion on the obtained distributions. Our approach is further validated using polystyrene and silica nanoparticles. In particular, we demonstrate the strength of AC for analysing multimodal distributions by means of gold nanoparticles. PMID:25789666

  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. 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.

  17. 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.

  18. 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

  19. MODEL OF VIRUS TRANSPORT IN UNSATURATED SOIL

    EPA Science Inventory

    As a result of the recently-proposed mandatory ground-water disinfection requirements to inactivate viruses in potable water supplies, there has been increasing interest in virus fate and transport in the subsurface. everal models have been developed to predict the fate of viruse...

  20. 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

  1. SEWAGE SLUDGE PATHOGEN TRANSPORT MODEL PROJECT

    EPA Science Inventory

    The sewage sludge pathogen transport model predicts the number of Salmonella, Ascaris, and polioviruses which might be expected to occur at various points in the environment along 13 defined pathways. These pathways describe the use of dried or liquid, raw or anaerobically digest...

  2. Accurate calculation and modeling of the adiabatic connection in density functional theory

    NASA Astrophysics Data System (ADS)

    Teale, A. M.; Coriani, S.; Helgaker, T.

    2010-04-01

    AC. When parametrized in terms of the same input data, the AC-CI model offers improved performance over the corresponding AC-D model, which is shown to be the lowest-order contribution to the AC-CI model. The utility of the accurately calculated AC curves for the analysis of standard density functionals is demonstrated for the BLYP exchange-correlation functional and the interaction-strength-interpolation (ISI) model AC integrand. From the results of this analysis, we investigate the performance of our proposed two-parameter AC-D and AC-CI models when a simple density functional for the AC at infinite interaction strength is employed in place of information at the fully interacting point. The resulting two-parameter correlation functionals offer a qualitatively correct behavior of the AC integrand with much improved accuracy over previous attempts. The AC integrands in the present work are recommended as a basis for further work, generating functionals that avoid spurious error cancellations between exchange and correlation energies and give good accuracy for the range of densities and types of correlation contained in the systems studied here.

  3. 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

  4. Modeling Unsaturated Flow and Transport using Zones: Aliasing Errors

    NASA Astrophysics Data System (ADS)

    Schafer, A. L.; Holt, R. M.

    2001-12-01

    It is difficult and costly to accurately determine the spatial statistics of unsaturated hydraulic properties, whereas it is often easier to define hydraulic property zones. When heterogeneous hydraulic property fields are subdivided into zones, however, flow and transport predictions show aliasing errors that alter predicted concentrations and breakthrough curves. The amount of error varies with the number of zones, the character of the heterogeneity, and boundary and initial conditions. The objective of this work is to determine the number of zones required to preserve critical transport behavior during numerical simulation of flow and transport. For this exercise, we consider unsaturated flow and non-reactive transport only. We assume that Richard?s Equation is valid and that the Gardner-Russo parametric model exactly describes unsaturated constitutive relationships. Correlated random parameter fields are generated and unsaturated flow and transport through these fields is simulated. The fields are then zoned using quantiles (0.25, 0.1, 0.05, and 0.025), appropriate zonal averages are determined, and flow and transport is simulated through the zoned fields. Aliasing errors are assessed by comparing the first, second and third moments of concentration for the full and zoned fields. The number of zones is varied to elucidate the character of aliasing error. The style of heterogeneity is varied to reflect geologically relevant end members (statistically isotropic vs. perfectly layered fields). Simulations are repeated under unit gradient conditions at mean tensions of 10, 100, and 1000 cm. Aliasing errors will tend to be smallest in layered systems with flow perpendicular to layering, because zonal averaging does not obscure fast paths. In statistically isotropic systems, fast paths are reduced as the coarseness of the zones increases. At higher tensions, finer zones are required to preserve transport behavior.

  5. 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.

  6. 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

  7. 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.

  8. 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.

  9. 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.

  10. 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.

  11. A model of axonal transport drug delivery

    NASA Astrophysics Data System (ADS)

    Kuznetsov, Andrey

    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.

  12. Mathematical models for accurate prediction of atmospheric visibility with particular reference to the seasonal and environmental patterns in Hong Kong.

    PubMed

    Mui, K W; Wong, L T; Chung, L Y

    2009-11-01

    Atmospheric visibility impairment has gained increasing concern as it is associated with the existence of a number of aerosols as well as common air pollutants and produces unfavorable conditions for observation, dispersion, and transportation. This study analyzed the atmospheric visibility data measured in urban and suburban Hong Kong (two selected stations) with respect to time-matched mass concentrations of common air pollutants including nitrogen dioxide (NO(2)), nitrogen monoxide (NO), respirable suspended particulates (PM(10)), sulfur dioxide (SO(2)), carbon monoxide (CO), and meteorological parameters including air temperature, relative humidity, and wind speed. No significant difference in atmospheric visibility was reported between the two measurement locations (p > or = 0.6, t test); and good atmospheric visibility was observed more frequently in summer and autumn than in winter and spring (p < 0.01, t test). It was also found that atmospheric visibility increased with temperature but decreased with the concentrations of SO(2), CO, PM(10), NO, and NO(2). The results showed that atmospheric visibility was season dependent and would have significant correlations with temperature, the mass concentrations of PM(10) and NO(2), and the air pollution index API (correlation coefficients mid R: R mid R: > or = 0.7, p < or = 0.0001, t test). Mathematical expressions catering to the seasonal variations of atmospheric visibility were thus proposed. By comparison, the proposed visibility prediction models were more accurate than some existing regional models. In addition to improving visibility prediction accuracy, this study would be useful for understanding the context of low atmospheric visibility, exploring possible remedial measures, and evaluating the impact of air pollution and atmospheric visibility impairment in this region. PMID:18951139

  13. 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

  14. 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.

  15. DIVIMP Modeling of Impurity Transport in EAST

    NASA Astrophysics Data System (ADS)

    Wang, Fuqiong; Chen, Yiping; Hu, Liqun

    2014-07-01

    Simulations of carbon impurity transport in SOL/divertor plasmas with Ohmic heating on EAST tokamak were performed using the two-dimensional (2D) Monte Carlo impurity transport code DIVIMP. The background plasmas for DIVIMP simulations were externally taken from B2.5/Eirene calculation. Besides the basic output of DIVIMP, the 2D density distributions of the carbon impurity with different ionization states and neutral carbon atoms were obtained, the 2D distributions of CII and CIII emissivities from C+1 and C+2 radiation respectively were also calculated. Comparison between the measured and calculated CIII emissivities showed favorable agreement, indicating that the impurity physics transport models, as implemented in the DIVIMP code, are suitable for the EAST tokamak plasma condition.

  16. 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.

  17. 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.

  18. 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.

  19. 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.

  20. Numerical modeling of transport barrier formation

    SciTech Connect

    Tokar, Mikhail Z.

    2010-04-01

    In diverse media the characteristics of mass and heat transfer may undergo spontaneous and abrupt changes in time and space. This can lead to the formation of regions with strongly reduced transport, so called transport barriers (TB). The presence of interfaces between regions with qualitatively and quantitatively different transport characteristics impose severe requirements to methods and numerical schemes used by solving of transport equations. In particular the assumptions made in standard methods about the solution behavior by representing its derivatives fail in points where the transport changes abruptly. The situation is complicated further by the fact that neither the formation time nor the positions of interfaces are known a priori. A numerical approach, operating reliably under such conditions, is proposed. It is based on the introduction of a new dependent variable related to the variation after one time step of the original one integrated over the volume. In the vicinity of any grid knot the resulting differential equation is approximated by a second order ordinary differential equation with constant coefficients. Exact analytical solutions of these equations are conjugated between knots by demanding the continuity of the total solution and its first derivative. As an example the heat transfer in media with heat conductivity decreasing abruptly when the temperature e-folding length exceeds a critical value is considered. The formation of TB both at a heating power above the critical level and caused with radiation energy losses non-linearly dependent on the temperature is modeled.

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

    SciTech Connect

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

    1999-03-04

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

  2. 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.

  3. 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.

  4. Reactive Transport Modeling Approach and its Initial Saltcake Dilution Chemical Modeling

    SciTech Connect

    Onishi, Yasuo

    2002-11-29

    During waste retrieval, chemical reactions, waste property changes, and waste movements/mixing interact. Thus,to be accurate, a waste process assessment methodology must account for these physical and chemical waste characteristics and mechanisms. This study provides suggestions for column tests and simulation modeling efforts to investigate saltwell pumping of Hanford Tank S-112. In addition, GMIN chemical modeling was initiated for S-112 saltcake dilution with 50% and 100% water as the first step of evaluating the feasibility of the reactive transport code ARIEL as a waste retrieval assessment methodology. The chemical modeling predicted the S-112 saltcake chemistry reasonably well. Although it is too early to conclude the usefulness of this reactive transport modeling approach, it is worth further evaluating its applicability to the waste retrieval process.

  5. Modeling sediment transport as a spatio-temporal Markov process.

    NASA Astrophysics Data System (ADS)

    Heyman, Joris; Ancey, Christophe

    2014-05-01

    Despite a century of research about sediment transport by bedload occuring in rivers, its constitutive laws remain largely unknown. The proof being that our ability to predict mid-to-long term transported volumes within reasonable confidence interval is almost null. The intrinsic fluctuating nature of bedload transport may be one of the most important reasons why classical approaches fail. Microscopic probabilistic framework has the advantage of taking into account these fluctuations at the particle scale, to understand their effect on the macroscopic variables such as sediment flux. In this framework, bedload transport is seen as the random motion of particles (sand, gravel, pebbles...) over a two-dimensional surface (the river bed). The number of particles in motion, as well as their velocities, are random variables. In this talk, we show how a simple birth-death Markov model governing particle motion on a regular lattice accurately reproduces the spatio-temporal correlations observed at the macroscopic level. Entrainment, deposition and transport of particles by the turbulent fluid (air or water) are supposed to be independent and memoryless processes that modify the number of particles in motion. By means of the Poisson representation, we obtained a Fokker-Planck equation that is exactly equivalent to the master equation and thus valid for all cell sizes. The analysis shows that the number of moving particles evolves locally far from thermodynamic equilibrium. Several analytical results are presented and compared to experimental data. The index of dispersion (or variance over mean ratio) is proved to grow from unity at small scales to larger values at larger scales confirming the non Poisonnian behavior of bedload transport. Also, we study the one and two dimensional K-function, which gives the average number of moving particles located in a ball centered at a particle centroid function of the ball's radius.

  6. 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.

  7. Evaluating Conceptual Site Models with Multicomponent Reactive Transport Modeling

    NASA Astrophysics Data System (ADS)

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

    2005-05-01

    Modeling ground-water flow and multicomponent reactive chemical transport is a useful approach for testing conceptual site models and assessing the design of monitoring networks. A graded approach with three conceptual site models is presented here with a field case of tetrachloroethene (PCE) transport and biodegradation near Charleston, SC. The first model assumed a one-layer homogeneous aquifer structure with semi-infinite boundary conditions, in which an analytical solution of the reactive solute transport can be obtained with BIOCHLOR (Aziz et al., 1999). Due to the over-simplification of the aquifer structure, this simulation cannot reproduce the monitoring data. In the second approach we used GMS to develop the conceptual site model, a layer-cake multi-aquifer system, and applied a numerical module (MODFLOW and RT3D within GMS) to solve the flow and reactive transport problem. The results were better than the first approach but still did not fit the plume well because the geological structures were still inadequately defined. In the third approach we developed a complex conceptual site model by interpreting log and seismic survey data with Petra and PetraSeis. We detected a major channel and a younger channel, through the PCE source area. These channels control the local ground-water flow direction and provide a preferential chemical transport pathway. Results using the third conceptual site model agree well with the monitoring concentration data. This study confirms that the bias and uncertainty from inadequate conceptual models are much larger than those introduced from an inadequate choice of model parameter values (Neuman and Wierenga, 2003; Meyer et al., 2004). Numerical modeling in this case provides key insight into the hydrogeology and geochemistry of the field site for predicting contaminant transport in the future. Finally, critical monitoring points and performance indicator parameters are selected for future monitoring to confirm system

  8. 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

  9. 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

  10. 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.

  11. Modelling sediment clasts transport during landscape evolution

    NASA Astrophysics Data System (ADS)

    Carretier, S.; Martinod, P.; Reich, M.; Godderis, Y.

    2015-10-01

    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, detrial zircons, 10Be in gravel, magnetic tracers, etc.). 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.

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

  13. Impact of transport model errors on the global and regional methane emissions estimated by inverse modelling

    NASA Astrophysics Data System (ADS)

    Locatelli, R.; Bousquet, P.; Chevallier, F.; Fortems-Cheney, A.; Szopa, S.; Saunois, M.; Agusti-Panareda, A.; Bergmann, D.; Bian, H.; Cameron-Smith, P.; Chipperfield, M. P.; Gloor, E.; Houweling, S.; Kawa, S. R.; Krol, M.; Patra, P. K.; Prinn, R. G.; Rigby, M.; Saito, R.; Wilson, C.

    2013-10-01

    transport model errors in current inverse systems. Future inversions should include more accurately prescribed observation covariances matrices in order to limit the impact of transport model errors on estimated methane fluxes.

  14. Aeolian sand transport: a wind tunnel model

    NASA Astrophysics Data System (ADS)

    Dong, Zhibao; Liu, Xiaoping; Wang, Hongtao; Wang, Xunming

    2003-09-01

    Wind sand transport is an important geological process on earth and some other planets. Formulating the wind sand transport model has been of continuing significance. Majority of the existing models relate sand transport rate to the wind shear velocity based on dynamic analysis. However, the wind shear velocity readapted to blown sand is difficult to determine from the measured wind profiles when sand movement occurs, especially at high wind velocity. Moreover, the effect of grain size on sand transport is open to argument. Detailed wind tunnel tests were carried out with respect to the threshold velocity, threshold shear velocity, and transport rate of differently sized, loose dry sand at different wind velocities to reformulate the transport model. The results suggest that the relationship between threshold shear velocity and grain size basically follow the Bagnold-type equation for the grain size d>0.1 mm. However, the threshold coefficient A in the equation is not constant as suggested by Bagnold, but decreases with the particle Reynolds number. The threshold velocity at the centerline height of the wind tunnel proved to be directly proportional to the square root of grain diameter. Attempts have been made to relate sand transport rate to both the wind velocity and shear velocity readapted to the blown sand movement. The reformulated transport model for loose dry sand follows the modified O'Brien-Rindlaub-type equation: Q= f1( d)(1- Ru) 2( ρ/ g) V3, or the modified Bagnold-type equation: Q= f2( d)(1- Rt) 0.25( ρ/ g) U*3. Where Q is the sand transport rate, the sand flux per unit time and per unit width, in kg m -1 s -1; ρ is the air density, 1.25 kg m -3; g is the acceleration due to gravity, 9.81 m s -2; Ru= Vt/ V; Rt= U*t/ U*; V is the wind velocity at the centerline of the wind tunnel, in m s -1; Vt is the threshold velocity measured at the same height as V, in m s -1; U* is the shear velocity with saltating flux, in m s -1; U*t is threshold shear

  15. Making the most of your prognostic factors: presenting a more accurate survival model for breast cancer patients.

    PubMed

    Knorr, K L; Hilsenbeck, S G; Wenger, C R; Pounds, G; Oldaker, T; Vendely, P; Pandian, M R; Harrington, D; Clark, G M

    1992-01-01

    Determining an appropriate level of adjuvant therapy is one of the most difficult facets of treating breast cancer patients. Although the myriad of prognostic factors aid in this decision, often they give conflicting reports of a patient's prognosis. What we need is a survival model which can properly utilize the information contained in these factors and give an accurate, reliable account of the patient's probability of recurrence. We also need a method of evaluating these models' predictive ability instead of simply measuring goodness-of-fit, as is currently done. Often, prognostic factors are broken into two categories such as positive or negative. But this dichotomization may hide valuable prognostic information. We investigated whether continuous representations of factors, including standard transformations--logarithmic, square root, categorical, and smoothers--might more accurately estimate the underlying relationship between each factor and survival. We chose the logistic regression model, a special case of the commonly used Cox model, to test our hypothesis. The model containing continuous transformed factors fit the data more closely than the model containing the traditional dichotomized factors. In order to appropriately evaluate these models, we introduce three predictive validity statistics--the Calibration score, the Overall Calibration score, and the Brier score--designed to assess the model's accuracy and reliability. These standardized scores showed the transformed factors predicted three year survival accurately and reliably. The scores can also be used to assess models or compare across studies. PMID:1391991

  16. 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...

  17. 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...

  18. MODELING TRANSPORT BY CONVECTIVE CLOUDS FOR REGIONAL AIR POLLUTION MODELS

    EPA Science Inventory

    A model is developed to account for regional scale vertical transport of pollutants from the mixed layer to the overlying free troposphere by an ensemble of non-precipitating cumulus convective clouds. The model determines acceptable cloud classes for given atmospheric state repr...

  19. 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

  20. 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.

  1. Thermal Transport Model for Heat Sink Design

    NASA Technical Reports Server (NTRS)

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

    2009-01-01

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

  2. 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.

  3. Modeling transport phenomena in porous media

    SciTech Connect

    Bear, J.

    1996-12-31

    The paper reviews the continuum approach to modelling the transport of mass, momentum and energy, of phases and of their components in a porous medium domain. The review begins with the definition of a porous medium, making use of the concept of a Representative Elementary Volume (REV) as a tool for overcoming the effect of the microscopic heterogeneity resulting from the presence of a solid matrix and a void space. The microscopic and macroscopic levels of description are defined. By averaging the description of a transport phenomenon at the microscopic level over an REV, using certain {open_quote}averaging rules{close_quote}, the macroscopic or continuum description of the same phenomenon is obtained. This methodology is first introduced in general terms for any extensive quantity, and then demonstrated for the transport of mass, momentum and energy. In the process of deriving the macroscopic models, expressions are presented also for the advective, dispersive and diffusive fluxes of extensive quantities that appear in them, in terms of averaged, measurable values of state variables.

  4. 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.

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

    NASA Astrophysics Data System (ADS)

    Niu, J.; Phanikumar, M. S.

    2012-12-01

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

  6. 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

  7. GUIDELINES FOR FIELD TESTING AQUATIC FATE AND TRANSPORT MODELS

    EPA Science Inventory

    This guidance has been developed for those attempting to field validate aquatic fate and transport models. Included are discussions of the major steps in validating models and sections on the individual fate and transport processes: biodegradation, oxidation, hydrolysis, photolys...

  8. MULTIMEDIA CONTAMINANT FATE, TRANSPORT, AND EXPOSURE MODEL (MMSOILS)

    EPA Science Inventory

    The Multimedia Contaminant Fate, Transport, and Exposure Model (MMSOILS) estimates the human exposure and health risk associated with releases of contamination from hazardous waste sites. The methodology consists of a multimedia model that addresses the transport of a chemical in...

  9. 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.

  10. Discrete element modelling of bed load transport

    NASA Astrophysics Data System (ADS)

    Maurin, Raphael; Chareyre, Bruno; Chauchat, Julien; Frey, Philippe

    2013-04-01

    Discrete element method (DEM) is a numerical method to simulate an assembly of particles, which has been widely used in mechanics (soil, rock) and granular physics. DEM consists in considering undeformable particles and modelling the intergranular interactions with simple laws (e.g. linear elastic and Coulomb friction law). The expression of the equation of motion on each particle considering the nearest neighbor interactions allows then to solve the dynamical behavior of the system explicitely. Since its introduction more than thirty years ago, this type of model has proven its ability to well describe the behavior of granular media in several different situations, from quasi-static system to flow of granular media. Bedload transport in streams is characterized by particle transport restricted to the interface between fluid flow and immerged granular media, where particles are rolling, sliding or in saltation over the bed. This situation corresponds to the larger particles transported on the bed in stream channels and has a great influence on geomorphology. Physical mechanisms and processes ruling bedload transport and more generally coarse-particle/fluid systems are poorly known. This is partly due to the small attention given to the role of granular interactions. Starting from these considerations, we used DEM to reproduce experiments carried out with spherical glass beads in an experimental steep and narrow flume. This was done in order to focus on granular interactions and to have access to parameters not available in the experiment. DEM open-source code Yade was coupled with a simplified fluid model, taking into account the different hydrodynamical interactions (buoyancy, drag, lift...) experienced by the particles. Numerical results obtained from the simulation are compared with an experimental data set established previously at the laboratory. It consists in monodisperse and bidisperse mixtures of coarse spherical glass beads entrained by a shallow

  11. 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.

  12. 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

  13. 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.

  14. 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

  15. 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

  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. 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.

  18. 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.

  19. Modeling of tokamak divertor plasma for weakly collisional parallel electron transport

    NASA Astrophysics Data System (ADS)

    Umansky, M. V.; Dimits, A. M.; Joseph, I.; Omotani, J. T.; Rognlien, T. D.

    2015-08-01

    The parallel electron heat transport in a weakly collisional regime can be represented in the framework of the Landau-fluid model (Hammett et al., 1990). Practical implementation of Landau-fluid transport has become possible due to the recent invention of an efficient non-spectral method for the non-local closure operators (Dimits et al., 2014). Here the implementation of a Landau-fluid based model for the parallel plasma transport is described, and the model is tested for different collisionality regimes against Fokker-Planck simulations. The new method appears to represent the weakly collisional electron transport more accurately than the conventional flux-limiter based models, on the other hand it is computationally efficient enough to be incorporated in comprehensive edge plasma simulations.

  20. 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.

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

    NASA Astrophysics Data System (ADS)

    Zhang, Xiang; Vu-Quoc, Loc

    2007-07-01

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

  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. 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.

  4. 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…

  5. 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

  6. 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

  7. Modeling the quasistatic energy transport between nanoparticles.

    PubMed

    Panasyuk, George Y; Yerkes, Kirk L

    2015-12-01

    We consider phononic energy transport between nanoparticles mediated by a quantum particle. The nanoparticles are considered as thermal reservoirs described by ensembles of finite numbers of harmonic oscillators within the Drude-Ullersma model having, in general, unequal mode spacings Δ(1) and Δ(2), which amount to different numbers of atoms in the nanoparticles. The quasistatic energy transport between the nanoparticles on the time scale t∼1/Δ(1,2) is investigated using the generalized quantum Langevin equation. We find that double degeneracy of system's eigenfrequencies, which occurs in the case of identical nanoparticles, is removed when the mode spacings become unequal. The equations describing the dynamics of the averaged eigenmode energies are derived and solved, and the resulting expression for the energy current between the nanoparticles is obtained and explored. Unlike the case when the thermodynamic limit is assumed resulting in time-independent energy current, finite-size effects result in temporal behavior of the energy current that evinces reversibility features combined with decay and possesses peculiarities at time moments t=2πn/Δ(1)+2πm/Δ(2) for non-negative integers n and m. When Δ(1,2)→0, an expression for the heat current obtained previously under assumption of the thermodynamic limit is reproduced. The energy current between two platinum nanoparticles mediated by a carbon oxide molecule is considered as an application of the developed model. PMID:26764663

  8. Modeling photon transport in transabdominal fetal oximetry

    NASA Astrophysics Data System (ADS)

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

    2000-07-01

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

  9. Modeling of Carbon Impurity Anomalous Transport

    NASA Astrophysics Data System (ADS)

    Stamm, Roland; Voitsekhovitch, Irina; Benkadda, Sadri; Beyer, Peter; Koubiti, Mohamed; Marandet, Yannick; Godbert-Mouret, Laurence; Bateman, Glenn; Kritz, Arnold; Pankin, Andre

    2001-10-01

    An improvement of plasma confinement by impurity seeding has been observed on different Tokamak. The understanding of the physics of the impurity transport is an important step towards the control of the plasma confinement in such regimes. Different physical mechanisms of the anomalous transport of carbon impurity and their impact on the evolution of the scenario of a tokamak discharge are analyzed in this work. This is done by using a self-consistent modeling of thermal electron and ion energy, and main ion and carbon impurity content with the multi-mode model taking into account the contributions from different types of plasma instabilities [1]. This study has been performed for the medium size tokamak with a central heating of the electron and ion species, and with both central (NBI) and wall particle source. The L-mode scenario and the scenario with an improved particle and energy confinement due to the reversed q-profile has been analyzed and the influence of the carbon impurity on the plasma evolution has been investigated by varying the starting time and the magnitude of the carbon influx. The effect of the main ion dilution on the growth rate as well as the effect of radiative cooling at the plasma edge on the power balance are analyzed under different conditions. 1. Bateman G., et al., Phys. Plasmas, 5 (1998) 1793

  10. More accurate predictions with transonic Navier-Stokes methods through improved turbulence modeling

    NASA Technical Reports Server (NTRS)

    Johnson, Dennis A.

    1989-01-01

    Significant improvements in predictive accuracies for off-design conditions are achievable through better turbulence modeling; and, without necessarily adding any significant complication to the numerics. One well established fact about turbulence is it is slow to respond to changes in the mean strain field. With the 'equilibrium' algebraic turbulence models no attempt is made to model this characteristic and as a consequence these turbulence models exaggerate the turbulent boundary layer's ability to produce turbulent Reynolds shear stresses in regions of adverse pressure gradient. As a consequence, too little momentum loss within the boundary layer is predicted in the region of the shock wave and along the aft part of the airfoil where the surface pressure undergoes further increases. Recently, a 'nonequilibrium' algebraic turbulence model was formulated which attempts to capture this important characteristic of turbulence. This 'nonequilibrium' algebraic model employs an ordinary differential equation to model the slow response of the turbulence to changes in local flow conditions. In its original form, there was some question as to whether this 'nonequilibrium' model performed as well as the 'equilibrium' models for weak interaction cases. However, this turbulence model has since been further improved wherein it now appears that this turbulence model performs at least as well as the 'equilibrium' models for weak interaction cases and for strong interaction cases represents a very significant improvement. The performance of this turbulence model relative to popular 'equilibrium' models is illustrated for three airfoil test cases of the 1987 AIAA Viscous Transonic Airfoil Workshop, Reno, Nevada. A form of this 'nonequilibrium' turbulence model is currently being applied to wing flows for which similar improvements in predictive accuracy are being realized.

  11. 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.

  12. A framework for modeling rail transport vulnerability

    SciTech Connect

    Peterson, Steven K; Church, Richard L.

    2008-01-01

    Railroads represent one of the most efficient methods of long-haul transport for bulk commodities, from coal to agricultural products. Over the past fifty years, the rail network has contracted while tonnage has increased. Service, geographically, has been abandoned along short haul routes and increased along major long haul routes, resulting in a network that is more streamlined. The current rail network may be very vulnerable to disruptions, like the failure of a trestle. This paper proposes a framework to model rail network vulnerability and gives an application of this modeling framework in analyzing rail network vulnerability for the State of Washington. It concludes with a number of policy related issues that need to be addressed in order to identify, plan, and mitigate the risks associated with the sudden loss of a bridge or trestle.

  13. 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.

  14. 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

  15. 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

  16. A Viscoelastic Constitutive Model Can Accurately Represent Entire Creep Indentation Tests of Human Patella Cartilage

    PubMed Central

    Pal, Saikat; Lindsey, Derek P.; Besier, Thor F.; Beaupre, Gary S.

    2013-01-01

    Cartilage material properties provide important insights into joint health, and cartilage material models are used in whole-joint finite element models. Although the biphasic model representing experimental creep indentation tests is commonly used to characterize cartilage, cartilage short-term response to loading is generally not characterized using the biphasic model. The purpose of this study was to determine the short-term and equilibrium material properties of human patella cartilage using a viscoelastic model representation of creep indentation tests. We performed 24 experimental creep indentation tests from 14 human patellar specimens ranging in age from 20 to 90 years (median age 61 years). We used a finite element model to reproduce the experimental tests and determined cartilage material properties from viscoelastic and biphasic representations of cartilage. The viscoelastic model consistently provided excellent representation of the short-term and equilibrium creep displacements. We determined initial elastic modulus, equilibrium elastic modulus, and equilibrium Poisson’s ratio using the viscoelastic model. The viscoelastic model can represent the short-term and equilibrium response of cartilage and may easily be implemented in whole-joint finite element models. PMID:23027200

  17. 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)).

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

    USGS Publications Warehouse

    Hromadka, T.V., II

    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.

  19. 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

  20. 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.

  1. Accurate determination of the superfluid-insulator transition in the one-dimensional Bose-Hubbard model

    NASA Astrophysics Data System (ADS)

    Zakrzewski, Jakub; Delande, Dominique

    2008-11-01

    The quantum phase transition point between the insulator and the superfluid phase at unit filling factor of the infinite one-dimensional Bose-Hubbard model is numerically computed with a high accuracy. The method uses the infinite system version of the time evolving block decimation algorithm, here tested in a challenging case. We provide also the accurate estimate of the phase transition point at double occupancy.

  2. Accurate analytical method for the extraction of solar cell model parameters

    NASA Astrophysics Data System (ADS)

    Phang, J. C. H.; Chan, D. S. H.; Phillips, J. R.

    1984-05-01

    Single diode solar cell model parameters are rapidly extracted from experimental data by means of the presently derived analytical expressions. The parameter values obtained have a less than 5 percent error for most solar cells, in light of the extraction of model parameters for two cells of differing quality which were compared with parameters extracted by means of the iterative method.

  3. Development and Implementation of a Bayesian Model for Sediment Transport in Fluvial Systems

    NASA Astrophysics Data System (ADS)

    Schmelter, M. L.; Hooten, M.

    2010-12-01

    Recent studies in the field of sediment transport in fluvial systems underscore the difficulty in reliably estimating transport model parameters, collecting accurate observations, and making predictions due to measurement error and uncertainty in conceptual models. While much of the initial research in sediment transport recognized the process as being inherently statistical, developing a sediment transport model in a statistical framework that can manage and account for measurement error, process uncertainty, and provide credible intervals of parameter estimates and transport predictions still presents many opportunities for discovery. In this research, we propose a uni-size bedload sediment transport model in which inference on the critical Shields Number and measurement error along with credible intervals of transport prediction are sought. This model is realized through the application of a Bayesian framework in which posterior distributions of model parameters are evaluated given both simulated data and uni-size sediment transport observations pulled from the literature. Our model provides a sediment rating curve that is delineated in terms of credible intervals for prediction. Credible ranges of the critical Shields Number and process/measurement uncertainty are inferred from simulated and observed data as well. While the application of these methods are currently being tested using simulated and laboratory flume data, the proposed framework can be applied to fluvial systems of arbitrary size. Additionally, our model presents opportunities to evaluate the suitability of different transport relations. The initial findings of applying a sediment transport relation in a Bayesian framework show great promise for managing uncertainty and variability in associated process models and measurements.

  4. 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.

  5. Fast and accurate Monte Carlo sampling of first-passage times from Wiener diffusion models

    PubMed Central

    Drugowitsch, Jan

    2016-01-01

    We present a new, fast approach for drawing boundary crossing samples from Wiener diffusion models. Diffusion models are widely applied to model choices and reaction times in two-choice decisions. Samples from these models can be used to simulate the choices and reaction times they predict. These samples, in turn, can be utilized to adjust the models’ parameters to match observed behavior from humans and other animals. Usually, such samples are drawn by simulating a stochastic differential equation in discrete time steps, which is slow and leads to biases in the reaction time estimates. Our method, instead, facilitates known expressions for first-passage time densities, which results in unbiased, exact samples and a hundred to thousand-fold speed increase in typical situations. In its most basic form it is restricted to diffusion models with symmetric boundaries and non-leaky accumulation, but our approach can be extended to also handle asymmetric boundaries or to approximate leaky accumulation. PMID:26864391

  6. 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.

  7. 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.

  8. 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. PMID:25058737

  9. 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.

  10. 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.

  11. conSSert: Consensus SVM Model for Accurate Prediction of Ordered Secondary Structure.

    PubMed

    Kieslich, Chris A; Smadbeck, James; Khoury, George A; Floudas, Christodoulos A

    2016-03-28

    Accurate prediction of protein secondary structure remains a crucial step in most approaches to the protein-folding problem, yet the prediction of ordered secondary structure, specifically beta-strands, remains a challenge. We developed a consensus secondary structure prediction method, conSSert, which is based on support vector machines (SVM) and provides exceptional accuracy for the prediction of beta-strands with QE accuracy of over 0.82 and a Q2-EH of 0.86. conSSert uses as input probabilities for the three types of secondary structure (helix, strand, and coil) that are predicted by four top performing methods: PSSpred, PSIPRED, SPINE-X, and RAPTOR. conSSert was trained/tested using 4261 protein chains from PDBSelect25, and 8632 chains from PISCES. Further validation was performed using targets from CASP9, CASP10, and CASP11. Our data suggest that poor performance in strand prediction is likely a result of training bias and not solely due to the nonlocal nature of beta-sheet contacts. conSSert is freely available for noncommercial use as a webservice: http://ares.tamu.edu/conSSert/ . PMID:26928531

  12. 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.

  13. 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. PMID:26708965

  14. A new geometric-based model to accurately estimate arm and leg inertial estimates.

    PubMed

    Wicke, Jason; Dumas, Geneviève A

    2014-06-01

    Segment estimates of mass, center of mass and moment of inertia are required input parameters to analyze the forces and moments acting across the joints. The objectives of this study were to propose a new geometric model for limb segments, to evaluate it against criterion values obtained from DXA, and to compare its performance to five other popular models. Twenty five female and 24 male college students participated in the study. For the criterion measures, the participants underwent a whole body DXA scan, and estimates for segment mass, center of mass location, and moment of inertia (frontal plane) were directly computed from the DXA mass units. For the new model, the volume was determined from two standing frontal and sagittal photographs. Each segment was modeled as a stack of slices, the sections of which were ellipses if they are not adjoining another segment and sectioned ellipses if they were adjoining another segment (e.g. upper arm and trunk). Length of axes of the ellipses was obtained from the photographs. In addition, a sex-specific, non-uniform density function was developed for each segment. A series of anthropometric measurements were also taken by directly following the definitions provided of the different body segment models tested, and the same parameters determined for each model. Comparison of models showed that estimates from the new model were consistently closer to the DXA criterion than those from the other models, with an error of less than 5% for mass and moment of inertia and less than about 6% for center of mass location. PMID:24735506

  15. A Systems Approach to Scalable Transportation Network Modeling

    SciTech Connect

    Perumalla, Kalyan S

    2006-01-01

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

  16. 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.

  17. 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.

  18. 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 ...

  19. IDENTIFICATION AND EVALUATION OF FUNDAMENTAL TRANSPORT AND TRANSFORMATION PROCESS MODELS

    EPA Science Inventory

    Chemical fate models require explicit algorithms for computing the effects of transformation and transport processes on the spatial and temporal distribution of chemical concentrations. Transport processes in aquatic systems are driven by physical characteristics on the system an...

  20. 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?

  1. 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. PMID:26808380

  2. 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.

  3. 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

  4. 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

  5. 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

    2016-01-01

    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

  6. 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. PMID:20173888

  7. 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.

  8. Heterogeneous Chemistry in Global Chemistry Transport Models

    NASA Astrophysics Data System (ADS)

    Stadtler, Scarlet; Simpson, David; Schultz, Martin; Bott, Andreas

    2016-04-01

    The impact of six tropospheric heterogeneous reactions on ozone and nitrogen species was studied using two chemical transport models EMEP MSC-W and ECHAM6-HAMMOZ. Since heterogeneous reactions depend on reactant concentrations (in this study these are N_2O_5, NO_3, NO_2, O_3, HNO_3, HO_2) and aerosol surface area S_a, the modeled surface area of both models was compared to a satellite product retrieving the surface area. This comparison shows a good agreement in global pattern and especially the capability of both models to capture the extreme aerosol loadings in East Asia. Further, the impact of the heterogeneous reactions was evaluated by the simulation of a reference run containing all heterogeneous reactions and several sensitivity runs. One reaction was turned off in each sensitivity run to compare it with the reference run. As previously shown, the analysis of the sensitivity runs shows that the globally most important heterogeneous reaction is the one of N_2O_5. Nevertheless, NO_2, NO_3, HNO3 and HO2 heterogeneous reactions gain relevance particular in East China due to presence of high NOx concentrations and high Sa in the same region. The heterogeneous reaction of O3 itself on dust is compared to the other heterogeneous reactions of minor relevance. Evaluation of the models with northern hemispheric ozone surface observations yields a better agreement of the models with observations when the heterogeneous reactions are incorporated. Impacts of emission changes on the importance of the heterogeneous chemistry will be discussed.

  9. 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.

  10. 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

  11. The transport exponent in percolation models with additional loops

    NASA Astrophysics Data System (ADS)

    Babalievski, F.

    1994-10-01

    Several percolation models with additional loops were studied. The transport exponents for these models were estimated numerically by means of a transfer-matrix approach. It was found that the transport exponent has a drastically changed value for some of the models. This result supports some previous numerical studies on the vibrational properties of similar models (with additional loops).

  12. MODELLING SEDIMENT TRANSPORT FOR THE LAKE MICHIGAN MASS BALANCE PROJECT

    EPA Science Inventory

    A sediment transport model is one component of the overall ensemble of models being developed for the Lake Michigan Mass Balance. The SEDZL model is being applied to simulate the fine-grained sediment transport in Lake Michigan for the 1982-1983 and 1994-1995 periods. Model perf...

  13. How accurate are polymer models in the analysis of Förster resonance energy transfer experiments on proteins?

    NASA Astrophysics Data System (ADS)

    O'Brien, Edward P.; Morrison, Greg; Brooks, Bernard R.; Thirumalai, D.

    2009-03-01

    Single molecule Förster resonance energy transfer (FRET) experiments are used to infer the properties of the denatured state ensemble (DSE) of proteins. From the measured average FRET efficiency, ⟨E⟩, the distance distribution P(R ) is inferred by assuming that the DSE can be described as a polymer. The single parameter in the appropriate polymer model (Gaussian chain, wormlike chain, or self-avoiding walk) for P(R ) is determined by equating the calculated and measured ⟨E⟩. In order to assess the accuracy of this "standard procedure," we consider the generalized Rouse model (GRM), whose properties [⟨E⟩ and P(R )] can be analytically computed, and the Molecular Transfer Model for protein L for which accurate simulations can be carried out as a function of guanadinium hydrochloride (GdmCl) concentration. Using the precisely computed ⟨E⟩ for the GRM and protein L, we infer P(R ) using the standard procedure. We find that the mean end-to-end distance can be accurately inferred (less than 10% relative error) using ⟨E⟩ and polymer models for P(R ). However, the value extracted for the radius of gyration (Rg) and the persistence length (lp) are less accurate. For protein L, the errors in the inferred properties increase as the GdmCl concentration increases for all polymer models. The relative error in the inferred Rg and lp, with respect to the exact values, can be as large as 25% at the highest GdmCl concentration. We propose a self-consistency test, requiring measurements of ⟨E⟩ by attaching dyes to different residues in the protein, to assess the validity of describing DSE using the Gaussian model. Application of the self-consistency test to the GRM shows that even for this simple model, which exhibits an order→disorder transition, the Gaussian P(R ) is inadequate. Analysis of experimental data of FRET efficiencies with dyes at several locations for the cold shock protein, and simulations results for protein L, for which accurate FRET

  14. 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.

  15. 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

  16. 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.

  17. 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

  18. Network diffusion accurately models the relationship between structural and functional brain connectivity networks

    PubMed Central

    Abdelnour, Farras; Voss, Henning U.; Raj, Ashish

    2014-01-01

    The relationship between anatomic connectivity of large-scale brain networks and their functional connectivity is of immense importance and an area of active research. Previous attempts have required complex simulations which model the dynamics of each cortical region, and explore the coupling between regions as derived by anatomic connections. While much insight is gained from these non-linear simulations, they can be computationally taxing tools for predicting functional from anatomic connectivities. Little attention has been paid to linear models. Here we show that a properly designed linear model appears to be superior to previous non-linear approaches in capturing the brain’s long-range second order correlation structure that governs the relationship between anatomic and functional connectivities. We derive a linear network of brain dynamics based on graph diffusion, whereby the diffusing quantity undergoes a random walk on a graph. We test our model using subjects who underwent diffusion MRI and resting state fMRI. The network diffusion model applied to the structural networks largely predicts the correlation structures derived from their fMRI data, to a greater extent than other approaches. The utility of the proposed approach is that it can routinely be used to infer functional correlation from anatomic connectivity. And since it is linear, anatomic connectivity can also be inferred from functional data. The success of our model confirms the linearity of ensemble average signals in the brain, and implies that their long-range correlation structure may percolate within the brain via purely mechanistic processes enacted on its structural connectivity pathways. PMID:24384152

  19. Fast and accurate modeling of molecular atomization energies with machine learning.

    PubMed

    Rupp, Matthias; Tkatchenko, Alexandre; Müller, Klaus-Robert; von Lilienfeld, O Anatole

    2012-02-01

    We introduce a machine learning model to predict atomization energies of a diverse set of organic molecules, based on nuclear charges and atomic positions only. The problem of solving the molecular Schrödinger equation is mapped onto a nonlinear statistical regression problem of reduced complexity. Regression models are trained on and compared to atomization energies computed with hybrid density-functional theory. Cross validation over more than seven thousand organic molecules yields a mean absolute error of ∼10  kcal/mol. Applicability is demonstrated for the prediction of molecular atomization potential energy curves. PMID:22400967

  20. 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

  1. 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

  2. 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…

  3. 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.

  4. 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.

  5. 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

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

    PubMed

    Sapsis, Themistoklis P; Majda, Andrew J

    2013-08-20

    A framework for low-order predictive statistical modeling and uncertainty quantification in turbulent dynamical systems is developed here. These reduced-order, modified quasilinear Gaussian (ROMQG) algorithms apply to turbulent dynamical systems in which there is significant linear instability or linear nonnormal dynamics in the unperturbed system and energy-conserving nonlinear interactions that transfer energy from the unstable modes to the stable modes where dissipation occurs, resulting in a statistical steady state; such turbulent dynamical systems are ubiquitous in geophysical and engineering turbulence. The ROMQG method involves constructing a low-order, nonlinear, dynamical system for the mean and covariance statistics in the reduced subspace that has the unperturbed statistics as a stable fixed point and optimally incorporates the indirect effect of non-Gaussian third-order statistics for the unperturbed system in a systematic calibration stage. This calibration procedure is achieved through information involving only the mean and covariance statistics for the unperturbed equilibrium. The performance of the ROMQG algorithm is assessed on two stringent test cases: the 40-mode Lorenz 96 model mimicking midlatitude atmospheric turbulence and two-layer baroclinic models for high-latitude ocean turbulence with over 125,000 degrees of freedom. In the Lorenz 96 model, the ROMQG algorithm with just a single mode captures the transient response to random or deterministic forcing. For the baroclinic ocean turbulence models, the inexpensive ROMQG algorithm with 252 modes, less than 0.2% of the total, captures the nonlinear response of the energy, the heat flux, and even the one-dimensional energy and heat flux spectra. PMID:23918398

  7. 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.

  8. The development and verification of a highly accurate collision prediction model for automated noncoplanar plan delivery

    SciTech Connect

    Yu, Victoria Y.; Tran, Angelia; Nguyen, Dan; Cao, Minsong; Ruan, Dan; Low, Daniel A.; Sheng, Ke

    2015-11-15

    Purpose: Significant dosimetric benefits had been previously demonstrated in highly noncoplanar treatment plans. In this study, the authors developed and verified an individualized collision model for the purpose of delivering highly noncoplanar radiotherapy and tested the feasibility of total delivery automation with Varian TrueBeam developer mode. Methods: A hand-held 3D scanner was used to capture the surfaces of an anthropomorphic phantom and a human subject, which were positioned with a computer-aided design model of a TrueBeam machine to create a detailed virtual geometrical collision model. The collision model included gantry, collimator, and couch motion degrees of freedom. The accuracy of the 3D scanner was validated by scanning a rigid cubical phantom with known dimensions. The collision model was then validated by generating 300 linear accelerator orientations corresponding to 300 gantry-to-couch and gantry-to-phantom distances, and comparing the corresponding distance measurements to their corresponding models. The linear accelerator orientations reflected uniformly sampled noncoplanar beam angles to the head, lung, and prostate. The distance discrepancies between measurements on the physical and virtual systems were used to estimate treatment-site-specific safety buffer distances with 0.1%, 0.01%, and 0.001% probability of collision between the gantry and couch or phantom. Plans containing 20 noncoplanar beams to the brain, lung, and prostate optimized via an in-house noncoplanar radiotherapy platform were converted into XML script for automated delivery and the entire delivery was recorded and timed to demonstrate the feasibility of automated delivery. Results: The 3D scanner measured the dimension of the 14 cm cubic phantom within 0.5 mm. The maximal absolute discrepancy between machine and model measurements for gantry-to-couch and gantry-to-phantom was 0.95 and 2.97 cm, respectively. The reduced accuracy of gantry-to-phantom measurements was

  9. 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

  10. A Framework for Accurate Geospatial Modeling of Recharge and Discharge Maps using Image Ranking and Machine Learning

    NASA Astrophysics Data System (ADS)

    Yahja, A.; Kim, C.; Lin, Y.; Bajcsy, P.

    2008-12-01

    This paper addresses the problem of accurate estimation of geospatial models from a set of groundwater recharge & discharge (R&D) maps and from auxiliary remote sensing and terrestrial raster measurements. The motivation for our work is driven by the cost of field measurements, and by the limitations of currently available physics-based modeling techniques that do not include all relevant variables and allow accurate predictions only at coarse spatial scales. The goal is to improve our understanding of the underlying physical phenomena and increase the accuracy of geospatial models--with a combination of remote sensing, field measurements and physics-based modeling. Our approach is to process a set of R&D maps generated from interpolated sparse field measurements using existing physics-based models, and identify the R&D map that would be the most suitable for extracting a set of rules between the auxiliary variables of interest and the R&D map labels. We implemented this approach by ranking R&D maps using information entropy and mutual information criteria, and then by deriving a set of rules using a machine learning technique, such as the decision tree method. The novelty of our work is in developing a general framework for building geospatial models with the ultimate goal of minimizing cost and maximizing model accuracy. The framework is demonstrated for groundwater R&D rate models but could be applied to other similar studies, for instance, to understanding hypoxia based on physics-based models and remotely sensed variables. Furthermore, our key contribution is in designing a ranking method for R&D maps that allows us to analyze multiple plausible R&D maps with a different number of zones which was not possible in our earlier prototype of the framework called Spatial Pattern to Learn. We will present experimental results using examples R&D and other maps from an area in Wisconsin.

  11. Time-dependent recycling modeling with edge plasma transport codes

    NASA Astrophysics Data System (ADS)

    Pigarov, A.; Krasheninnikov, S.; Rognlien, T.; Taverniers, S.; Hollmann, E.

    2013-10-01

    First,we discuss extensions to Macroblob approach which allow to simulate more accurately dynamics of ELMs, pedestal and edge transport with UEDGE code. Second,we present UEDGE modeling results for H mode discharge with infrequent ELMs and large pedestal losses on DIII-D. In modeled sequence of ELMs this discharge attains a dynamic equilibrium. Temporal evolution of pedestal plasma profiles, spectral line emission, and surface temperature matching experimental data over ELM cycle is discussed. Analysis of dynamic gas balance highlights important role of material surfaces. We quantified the wall outgassing between ELMs as 3X the NBI fueling and the recycling coefficient as 0.8 for wall pumping via macroblob-wall interactions. Third,we also present results from multiphysics version of UEDGE with built-in, reduced, 1-D wall models and analyze the role of various PMI processes. Progress in framework-coupled UEDGE/WALLPSI code is discussed. Finally, implicit coupling schemes are important feature of multiphysics codes and we report on the results of parametric analysis of convergence and performance for Picard and Newton iterations in a system of coupled deterministic-stochastic ODE and proposed modifications enhancing convergence.

  12. An Accurate In Vitro Model of the E. coli Envelope

    PubMed Central

    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.

    2015-01-01

    Abstract 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:27346898

  13. 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

  14. 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.

  15. Features of creation of highly accurate models of triumphal pylons for archaeological reconstruction

    NASA Astrophysics Data System (ADS)

    Grishkanich, A. S.; Sidorov, I. S.; Redka, D. N.

    2015-12-01

    Cited a measuring operation for determining the geometric characteristics of objects in space and geodetic survey objects on the ground. In the course of the work, data were obtained on a relative positioning of the pylons in space. There are deviations from verticality. In comparison with traditional surveying this testing method is preferable because it allows you to get in semi-automated mode, the CAD model of the object is high for subsequent analysis that is more economical-ly advantageous.

  16. 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.

  17. 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

  18. Robust and Accurate Modeling Approaches for Migraine Per-Patient Prediction from Ambulatory Data.

    PubMed

    Pagán, Josué; De Orbe, M Irene; Gago, Ana; Sobrado, Mónica; Risco-Martín, José L; Mora, J Vivancos; Moya, José M; Ayala, José L

    2015-01-01

    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

  19. 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.

  20. 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

  1. 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.

  2. 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.

  3. 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

  4. Key Issues for an Accurate Modelling of GaSb TPV Converters

    NASA Astrophysics Data System (ADS)

    Martín, Diego; Algora, Carlos

    2003-01-01

    GaSb TPV devices are commonly manufactured by Zn diffusion from the vapour phase on a n-type substrate, leading to very high doping concentrations in a narrow emitter. This fact emphasizes the need of a careful modelling that must include high doping effects to simulate the optoelectronic behaviour of devices. In this work the key parameters that have strong influence on the performance of GaSb TPV devices are underlined, more reliable values are suggested and our first results on the study of the absorption coefficient dependence with p-type high doping concentration are presented.

  5. PLUME FORMATION, TRANSPORT AND MODELING, PRESENTED IN RENO, NEVADA

    EPA Science Inventory

    This presentation presents information on plume formation, transport and modeling. The outline for the presentation is: conceptualization of hydrocarbon releases; factors affecting plume length and concentration; modeling considerations; and uncertainty in model calculations.

  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. Multiconjugate adaptive optics applied to an anatomically accurate human eye model.

    PubMed

    Bedggood, P A; Ashman, R; Smith, G; Metha, A B

    2006-09-01

    Aberrations of both astronomical telescopes and the human eye can be successfully corrected with conventional adaptive optics. This produces diffraction-limited imagery over a limited field of view called the isoplanatic patch. A new technique, known as multiconjugate adaptive optics, has been developed recently in astronomy to increase the size of this patch. The key is to model atmospheric turbulence as several flat, discrete layers. A human eye, however, has several curved, aspheric surfaces and a gradient index lens, complicating the task of correcting aberrations over a wide field of view. Here we utilize a computer model to determine the degree to which this technology may be applied to generate high resolution, wide-field retinal images, and discuss the considerations necessary for optimal use with the eye. The Liou and Brennan schematic eye simulates the aspheric surfaces and gradient index lens of real human eyes. We show that the size of the isoplanatic patch of the human eye is significantly increased through multiconjugate adaptive optics. PMID:19529172

  8. Accurate modeling of SiPM detectors coupled to FE electronics for timing performance analysis

    NASA Astrophysics Data System (ADS)

    Ciciriello, F.; Corsi, F.; Licciulli, F.; Marzocca, C.; Matarrese, G.; Del Guerra, A.; Bisogni, M. G.

    2013-08-01

    It has already been shown how the shape of the current pulse produced by a SiPM in response to an incident photon is sensibly affected by the characteristics of the front-end electronics (FEE) used to read out the detector. When the application requires to approach the best theoretical time performance of the detection system, the influence of all the parasitics associated to the coupling SiPM-FEE can play a relevant role and must be adequately modeled. In particular, it has been reported that the shape of the current pulse is affected by the parasitic inductance of the wiring connection between SiPM and FEE. In this contribution, we extend the validity of a previously presented SiPM model to account for the wiring inductance. Various combinations of the main performance parameters of the FEE (input resistance and bandwidth) have been simulated in order to evaluate their influence on the time accuracy of the detection system, when the time pick-off of each single event is extracted by means of a leading edge discriminator (LED) technique.

  9. 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.

  10. Coupled reactive mass transport and fluid flow: Issues in model verification

    SciTech Connect

    Freedman, Vicky L.; Ibaraki, Motomu

    2003-01-03

    Model verification and validation are both important steps in the development of reactive transport models. In this paper, a distinction is made between verification and validation, and the focus is on codifying the issues of verification for a numerical, reactive transport flow model. First, the conceptual basis of model verification is reviewed, which shows that verification should be understood as a first step in model development, and be followed by a protocol that assures that the model accurately represents system behavior. Second, commonly used procedures and methods of model verification are presented. In the third part of this paper, an intercomparison of models is used to demonstrate that model verification can be performed despite differences in hydrogeochemical transport code formulations. Results of an example simulation of transport are presented in which the numerical model is tested against other hydrogeochemical codes. Different kinetic formulations between solid and aqueous phases used among numerical models complicates model verification. This test problem involves uranium transport under conditions of varying pH and oxidation potential, with reversible precipitation of calcium uranate and coffinite. Results between the different hydrogeochemical transport codes show differences in oxidation potentials, but similarities in mineral assemblages and aqueous transport patterns. Because model verification can be further complicated by differences in the approach for solving redox problems, a comparison of a fugacity approach to both the external approach (based on hypothetical electron activity) and effective internal approach (based on conservation of electrons) is performed. The comparison demonstrates that the oxygen fugacity approach produces different redox potentials and mineral assemblages than both the effective internal and external approaches.

  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. Reactive transport in porous media: pore-network model approach compared to pore-scale model.

    PubMed

    Varloteaux, Clément; Vu, Minh Tan; Békri, Samir; Adler, Pierre M

    2013-02-01

    Accurate determination of three macroscopic parameters governing reactive transport in porous media, namely, the apparent solute velocity, the dispersion, and the apparent reaction rate, is of key importance for predicting solute migration through reservoir aquifers. Two methods are proposed to calculate these parameters as functions of the Péclet and the Péclet-Dahmköhler numbers. In the first method called the pore-scale model (PSM), the porous medium is discretized by the level set method; the Stokes and convection-diffusion equations with reaction at the wall are solved by a finite-difference scheme. In the second method, called the pore-network model (PNM), the void space of the porous medium is represented by an idealized geometry of pore bodies joined by pore throats; the flow field is computed by solving Kirchhoff's laws and transport calculations are performed in the asymptotic regime where the solute concentration undergoes an exponential evolution with time. Two synthetic geometries of porous media are addressed by using both numerical codes. The first geometry is constructed in order to validate the hypotheses implemented in PNM. PSM is also used for a better understanding of the various reaction patterns observed in the asymptotic regime. Despite the PNM approximations, a very good agreement between the models is obtained, which shows that PNM is an accurate description of reactive transport. PNM, which can address much larger pore volumes than PSM, is used to evaluate the influence of the concentration distribution on macroscopic properties of a large irregular network reconstructed from microtomography images. The role of the dimensionless numbers and of the location and size of the largest pore bodies is highlighted. PMID:23496613

  14. 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...

  15. Accurate modeling of light trapping in thin film silicon solar cells

    SciTech Connect

    Abouelsaood, A.A.; Ghannam, M.Y.; Poortmans, J.; Mertens, R.P.

    1997-12-31

    An attempt is made to assess the accuracy of the simplifying assumption of total retransmission of light inside the escape or loss cone which is made in many models of optical confinement in thin-film silicon solar cells. A closed form expression is derived for the absorption enhancement factor as a function of the refractive index in the low-absorption limit for a thin-film cell with a flat front surface and a lambertian back reflector. Numerical calculations are carried out to investigate similar systems with antireflection coatings, and the investigation of cells with a textured front surface is achieved using a modified version of the existing ray-tracing computer simulation program TEXTURE.

  16. 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.

  17. 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.

  18. 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

  19. Biomechanical modeling provides more accurate data for neuronavigation than rigid registration

    PubMed Central

    Garlapati, Revanth Reddy; Roy, Aditi; Joldes, Grand Roman; Wittek, Adam; Mostayed, Ahmed; Doyle, Barry; Warfield, Simon Keith; Kikinis, Ron; Knuckey, Neville; Bunt, Stuart; Miller, Karol

    2015-01-01

    It is possible to improve neuronavigation during image-guided surgery by warping the high-quality preoperative brain images so that they correspond with the current intraoperative configuration of the brain. In this work, the accuracy of registration results obtained using comprehensive biomechanical models is compared to the accuracy of rigid registration, the technology currently available to patients. This comparison allows us to investigate whether biomechanical modeling provides good quality image data for neuronavigation for a larger proportion of patients than rigid registration. Preoperative images for 33 cases of neurosurgery were warped onto their respective intraoperative configurations using both biomechanics-based method and rigid registration. We used a Hausdorff distance-based evaluation process that measures the difference between images to quantify the performance of both methods of registration. A statistical test for difference in proportions was conducted to evaluate the null hypothesis that the proportion of patients for whom improved neuronavigation can be achieved, is the same for rigid and biomechanics-based registration. The null hypothesis was confidently rejected (p-value<10−4). Even the modified hypothesis that less than 25% of patients would benefit from the use of biomechanics-based registration was rejected at a significance level of 5% (p-value = 0.02). The biomechanics-based method proved particularly effective for cases experiencing large craniotomy-induced brain deformations. The outcome of this analysis suggests that our nonlinear biomechanics-based methods are beneficial to a large proportion of patients and can be considered for use in the operating theatre as one possible method of improving neuronavigation and surgical outcomes. PMID:24460486

  20. A new method based on the subpixel Gaussian model for accurate estimation of asteroid coordinates

    NASA Astrophysics Data System (ADS)

    Savanevych, V. E.; Briukhovetskyi, O. B.; Sokovikova, N. S.; Bezkrovny, M. M.; Vavilova, I. B.; Ivashchenko, Yu. M.; Elenin, L. V.; Khlamov, S. V.; Movsesian, Ia. S.; Dashkova, A. M.; Pogorelov, A. V.

    2015-08-01

    We describe a new iteration method to estimate asteroid coordinates, based on a subpixel Gaussian model of the discrete object image. The method operates by continuous parameters (asteroid coordinates) in a discrete observational space (the set of pixel potentials) of the CCD frame. In this model, the kind of coordinate distribution of the photons hitting a pixel of the CCD frame is known a priori, while the associated parameters are determined from a real digital object image. The method that is developed, which is flexible in adapting to any form of object image, has a high measurement accuracy along with a low calculating complexity, due to the maximum-likelihood procedure that is implemented to obtain the best fit instead of a least-squares method and Levenberg-Marquardt algorithm for minimization of the quadratic form. Since 2010, the method has been tested as the basis of our Collection Light Technology (COLITEC) software, which has been installed at several observatories across the world with the aim of the automatic discovery of asteroids and comets in sets of CCD frames. As a result, four comets (C/2010 X1 (Elenin), P/2011 NO1(Elenin), C/2012 S1 (ISON) and P/2013 V3 (Nevski)) as well as more than 1500 small Solar system bodies (including five near-Earth objects (NEOs), 21 Trojan asteroids of Jupiter and one Centaur object) have been discovered. We discuss these results, which allowed us to compare the accuracy parameters of the new method and confirm its efficiency. In 2014, the COLITEC software was recommended to all members of the Gaia-FUN-SSO network for analysing observations as a tool to detect faint moving objects in frames.

  1. Uncertainties of modelling emissions from road transport

    NASA Astrophysics Data System (ADS)

    Kühlwein, J.; Friedrich, R.

    To determine emission data from road transport, complex methods and models are applied. Emission data are characterized by a huge variety of source types as well as a high resolution of the spatial allocation and temporal variation. So far, the uncertainties of such calculated emission data have been largely unknown. As emission data is used to aid policy decisions, the accuracy of the data should be known. So, in the following, the determination of uncertainties of emission data is described. Using the IER emission model for generating regional or national emission data, the uncertainties of model input data and the total errors on different aggregation levels are exemplarily investigated for the pollutants NO x and NMHC in 1994 for the area of West Germany. The results of statistical error analysis carried out for annual emissions on road sections show variation coefficients (68.3% confidence interval) of 15-25%. In addition, systematic errors of common input data sets have been identified especially affecting emissions on motorway sections. The statistical errors of urban emissions with warm engine on town level amount to 35%. Therefore they are considerably higher than the errors outside towns. Error ranges of additional cold start emissions determined so far have been found in the same order. Additional uncertainties of temporally highly resolved (hourly) emission data depend strongly on the daytime, the weekday and the road category. Variation coefficients have been determined in the range between 10 and 70% for light-duty vehicles and between 15 and 100% for heavy-duty vehicles. All total errors determined here have to be regarded as lower limits of the real total errors.

  2. 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

  3. 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.

  4. Accurate estimation of retinal vessel width using bagged decision trees and an extended multiresolution Hermite model.

    PubMed

    Lupaşcu, Carmen Alina; Tegolo, Domenico; Trucco, Emanuele

    2013-12-01

    We present an algorithm estimating the width of retinal vessels in fundus camera images. The algorithm uses a novel parametric surface model of the cross-sectional intensities of vessels, and ensembles of bagged decision trees to estimate the local width from the parameters of the best-fit surface. We report comparative tests with REVIEW, currently the public database of reference for retinal width estimation, containing 16 images with 193 annotated vessel segments and 5066 profile points annotated manually by three independent experts. Comparative tests are reported also with our own set of 378 vessel widths selected sparsely in 38 images from the Tayside Scotland diabetic retinopathy screening programme and annotated manually by two clinicians. We obtain considerably better accuracies compared to leading methods in REVIEW tests and in Tayside tests. An important advantage of our method is its stability (success rate, i.e., meaningful measurement returned, of 100% on all REVIEW data sets and on the Tayside data set) compared to a variety of methods from the literature. We also find that results depend crucially on testing data and conditions, and discuss criteria for selecting a training set yielding optimal accuracy. PMID:24001930

  5. 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.

  6. The human skin/chick chorioallantoic membrane model accurately predicts the potency of cosmetic allergens.

    PubMed

    Slodownik, Dan; Grinberg, Igor; Spira, Ram M; Skornik, Yehuda; Goldstein, Ronald S

    2009-04-01

    The current standard method for predicting contact allergenicity is the murine local lymph node assay (LLNA). Public objection to the use of animals in testing of cosmetics makes the development of a system that does not use sentient animals highly desirable. The chorioallantoic membrane (CAM) of the chick egg has been extensively used for the growth of normal and transformed mammalian tissues. The CAM is not innervated, and embryos are sacrificed before the development of pain perception. The aim of this study was to determine whether the sensitization phase of contact dermatitis to known cosmetic allergens can be quantified using CAM-engrafted human skin and how these results compare with published EC3 data obtained with the LLNA. We studied six common molecules used in allergen testing and quantified migration of epidermal Langerhans cells (LC) as a measure of their allergic potency. All agents with known allergic potential induced statistically significant migration of LC. The data obtained correlated well with published data for these allergens generated using the LLNA test. The human-skin CAM model therefore has great potential as an inexpensive, non-radioactive, in vivo alternative to the LLNA, which does not require the use of sentient animals. In addition, this system has the advantage of testing the allergic response of human, rather than animal skin. PMID:19054059

  7. 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

  8. Offline tracer transport modeling with global WRF model data

    NASA Astrophysics Data System (ADS)

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

    2013-04-01

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

  9. Simulation models for conservative and nonconservative solute transport in streams

    USGS Publications Warehouse

    Runkel, R.L.

    1995-01-01

    Solute transport in streams is governed by a suite of hydrologic and chemical processes. Interactions between hydrologic processes and chemical reactions may be quantified through a combination of field-scale experimentation and simulation modeling. Two mathematical models that simulate conservative and nonconservative solute transport in streams are presented. A model for conservative solutes that considers One Dimensional Transport with Inflow and Storage (OTIS) may be used in conjunction with tracer-dilution methods to quantify hydrologic transport processes (advection, dispersion, lateral inflow and transient storage). For nonconservative solutes, a model known as OTEQ may be used to quantify chemical processes within the context of hydrologic transport. OTEQ combines the transport mechanisms in OTIS with a chemical equilibrium sub-model that considers complexation, precipitation/dissolution and sorption. OTEQ has been used to quantify processes affecting trace metals in two streams in the Rocky Mountains of Colorado, USA.

  10. 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.

  11. 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.

  12. 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.

  13. 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. PMID:26178828

  14. 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.

  15. 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.

  16. Antenna modeling considerations for accurate SAR calculations in human phantoms in close proximity to GSM cellular base station antennas.

    PubMed

    van Wyk, Marnus J; Bingle, Marianne; Meyer, Frans J C

    2005-09-01

    International bodies such as International Commission on Non-Ionizing Radiation Protection (ICNIRP) and the Institute for Electrical and Electronic Engineering (IEEE) make provision for human exposure assessment based on SAR calculations (or measurements) and basic restrictions. In the case of base station exposure this is mostly applicable to occupational exposure scenarios in the very near field of these antennas where the conservative reference level criteria could be unnecessarily restrictive. This study presents a variety of critical aspects that need to be considered when calculating SAR in a human body close to a mobile phone base station antenna. A hybrid FEM/MoM technique is proposed as a suitable numerical method to obtain accurate results. The verification of the FEM/MoM implementation has been presented in a previous publication; the focus of this study is an investigation into the detail that must be included in a numerical model of the antenna, to accurately represent the real-world scenario. This is accomplished by comparing numerical results to measurements for a generic GSM base station antenna and appropriate, representative canonical and human phantoms. The results show that it is critical to take the disturbance effect of the human phantom (a large conductive body) on the base station antenna into account when the antenna-phantom spacing is less than 300 mm. For these small spacings, the antenna structure must be modeled in detail. The conclusion is that it is feasible to calculate, using the proposed techniques and methodology, accurate occupational compliance zones around base station antennas based on a SAR profile and basic restriction guidelines. PMID:15931680

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

    NASA Astrophysics Data System (ADS)

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

    2009-04-01

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

  18. What makes an accurate and reliable subject-specific finite element model? A case study of an elephant femur.

    PubMed

    Panagiotopoulou, O; Wilshin, S D; Rayfield, E J; Shefelbine, S J; Hutchinson, J R

    2012-02-01

    Finite element modelling is well entrenched in comparative vertebrate biomechanics as a tool to assess the mechanical design of skeletal structures and to better comprehend the complex interaction of their form-function relationships. But what makes a reliable subject-specific finite element model? To approach this question, we here present a set of convergence and sensitivity analyses and a validation study as an example, for finite element analysis (FEA) in general, of ways to ensure a reliable model. We detail how choices of element size, type and material properties in FEA influence the results of simulations. We also present an empirical model for estimating heterogeneous material properties throughout an elephant femur (but of broad applicability to FEA). We then use an ex vivo experimental validation test of a cadaveric femur to check our FEA results and find that the heterogeneous model matches the experimental results extremely well, and far better than the homogeneous model. We emphasize how considering heterogeneous material properties in FEA may be critical, so this should become standard practice in comparative FEA studies along with convergence analyses, consideration of element size, type and experimental validation. These steps may be required to obtain accurate models and derive reliable conclusions from them. PMID:21752810

  19. 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.

  20. 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.

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

  2. 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)

  3. Accurate prediction of interference minima in linear molecular harmonic spectra by a modified two-center model

    NASA Astrophysics Data System (ADS)

    Xin, Cui; Di-Yu, Zhang; Gao, Chen; Ji-Gen, Chen; Si-Liang, Zeng; Fu-Ming, Guo; Yu-Jun, Yang

    2016-03-01

    We demonstrate that the interference minima in the linear molecular harmonic spectra can be accurately predicted by a modified two-center model. Based on systematically investigating the interference minima in the linear molecular harmonic spectra by the strong-field approximation (SFA), it is found that the locations of the harmonic minima are related not only to the nuclear distance between the two main atoms contributing to the harmonic generation, but also to the symmetry of the molecular orbital. Therefore, we modify the initial phase difference between the double wave sources in the two-center model, and predict the harmonic minimum positions consistent with those simulated by SFA. Project supported by the National Basic Research Program of China (Grant No. 2013CB922200) and the National Natural Science Foundation of China (Grant Nos. 11274001, 11274141, 11304116, 11247024, and 11034003), and the Jilin Provincial Research Foundation for Basic Research, China (Grant Nos. 20130101012JC and 20140101168JC).

  4. 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.

  5. 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

  6. 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.

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

    PubMed

    Nemaura, Tafireyi

    2015-01-01

    Understanding drug transportation mechanisms in the human body is of paramount importance in modeling Pharmacokinetic-Pharmacodynamic relationships. This work gives a novel general model of efavirenz transportation projections based on concentrations simulated from patients on a dose of 600 mg. The work puts forward a proposition that transportation can wholly be modeled by concentration and time in a uniform volumetric space. Furthermore, movement entities are used to inform the state of "kinetic solubility" of a solution. There is use of Ricker's model, and forms of the Hill's equation in modeling transportation. Characterization on the movement rates of solution particle are suggested in relation to advection rate of solution particle. At turning points on the transportation rate of solution particle vs. concentration curve, a suggestion of possibly change of dominance in the mode of transportation and saturation is made. There are four movement rates postulated at primary micro-level transportation, that are attributed to convection, diffusion [passive transportation (EI )] and energy dependent system transportation (ED ) in relation to advection. Furthermore, a new parameter is introduced which is defined as an advection rate constant of solution particle. It is postulated to be dependent on two rate constants of solution particle, that is a convection rate constant of solution particle and a saturable transportation rate constant of solution particle. At secondary micro-level transportation, the results show convection as sum of advection and saturable transportation. The kinetics of dissolution of efavirenz in the solution space is postulated. Relatively, a good level of kinetics of dissolution is projected in the concentration region 0 - 32.82 μg/ml. PMID:26106329

  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. Heat transport model within the hyporheic zone

    NASA Astrophysics Data System (ADS)

    Marzadri, Alessandra; Tonina, Daniele; Bellin, Alberto

    2010-05-01

    Temperature is a key quantity in controlling water quality, aquatic habitats and the distribution of aquatic invertebrates within the hyporheic zone. Despite its importance in all processes (e.g., biogeochemical reactions and organism metabolism, growth, movement and migration) occurring within the streambed sediment, only few experimental and numerical works analyzed temperature distribution within the hyporheic zone, while little is known on the control that river morphology exerts on temperature dynamics. In the present work, we analyze the effects of river morphology on the thermal regime of the hyporheic zone from a modelling perspective. Our goal is to identify the dominant processes that affect the hyporheic thermal regime and gradients, which influence the rates of microbial and biogeochemical processes. With this objective in mind, we developed a simplified process-based model, which predicts the temperature pattern within the streambed sediment taking into account the external forcing due to the daily temperature variations of the in-stream water and the hyporheic exchange due to streambed morphology. To simplify the analysis the hydraulic conductivity of the streambed sediment is assumed homogeneous and isotropic, and the hyporheic velocity field is obtained analytically by solving the flow equation with the near-bed piezometric head of the stream flow as the linkage between surface and subsurface flows. Furthermore, we solved the heat transport equation with a Lagrangian approach and by neglecting transverse dispersivity. Our model results show a complex near-bed hyporheic temperature distributions, which vary temporally and are strongly related to the in-stream water residence time into the hyporheic zone and consequently to the bed morphology and flow discharge. We compared the temperature dynamics within the hyporheic zone of both large low-gradient and small steep streams to investigate the effect of stream morphology. Results show that the

  10. 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.

  11. Contaminant Transport in the Unsaturated Zone Theory and Modeling

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Mathematical models are increasingly used to better understand and quantify site-specific subsurface water flow and solute transport processes. This chapter reviews mathematical models for solute transport in predominantly variably-saturated media. After a brief description of the physics and mathe...

  12. 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

  13. 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

  14. Development of a variational flux inversion system (INVICAT v1.0) using the TOMCAT chemical transport model

    NASA Astrophysics Data System (ADS)

    Wilson, C.; Chipperfield, M. P.; Gloor, M.; Chevallier, F.

    2014-10-01

    We present a new variational inverse transport model, named INVICAT (v1.0), which is based on the global chemical transport model TOMCAT, and a new corresponding adjoint transport model, ATOMCAT. The adjoint model is constructed through manually derived discrete adjoint algorithms, and includes subroutines governing advection, convection and boundary layer mixing, all of which are linear in the TOMCAT model. We present extensive testing of the adjoint and inverse models, and also thoroughly assess the accuracy of the TOMCAT forward model's representation of atmospheric transport through comparison with observations of the atmospheric trace gas SF6. The forward model is shown to perform well in comparison with these observations, capturing the latitudinal gradient and seasonal cycle of SF6 to within acceptable tolerances. The adjoint model is shown, through numerical identity tests and novel transport reciprocity tests, to be extremely accurate in comparison with the forward model, with no error shown at the level of accuracy possible with our machines. The potential for the variational system as a tool for inverse modelling is investigated through an idealised test using simulated observations, and the system demonstrates an ability to retrieve known fluxes from a perturbed state accurately. Using basic off-line chemistry schemes, the inverse model is ready and available to perform inversions of trace gases with relatively simple chemical interactions, including CH4, CO2 and CO.

  15. Accurate Segmentation of CT Male Pelvic Organs via Regression-Based Deformable Models and Multi-Task Random Forests.

    PubMed

    Gao, Yaozong; Shao, Yeqin; Lian, Jun; Wang, Andrew Z; Chen, Ronald C; Shen, Dinggang

    2016-06-01

    Segmenting male pelvic organs from CT images is a prerequisite for prostate cancer radiotherapy. The efficacy of radiation treatment highly depends on segmentation accuracy. However, accurate segmentation of male pelvic organs is challenging due to low tissue contrast of CT images, as well as large variations of shape and appearance of the pelvic organs. Among existing segmentation methods, deformable models are the most popular, as shape prior can be easily incorporated to regularize the segmentation. Nonetheless, the sensitivity to initialization often limits their performance, especially for segmenting organs with large shape variations. In this paper, we propose a novel approach to guide deformable models, thus making them robust against arbitrary initializations. Specifically, we learn a displacement regressor, which predicts 3D displacement from any image voxel to the target organ boundary based on the local patch appearance. This regressor provides a non-local external force for each vertex of deformable model, thus overcoming the initialization problem suffered by the traditional deformable models. To learn a reliable displacement regressor, two strategies are particularly proposed. 1) A multi-task random forest is proposed to learn the displacement regressor jointly with the organ classifier; 2) an auto-context model is used to iteratively enforce structural information during voxel-wise prediction. Extensive experiments on 313 planning CT scans of 313 patients show that our method achieves better results than alternative classification or regression based methods, and also several other existing methods in CT pelvic organ segmentation. PMID:26800531

  16. Efficiency of a statistical transport model for turbulent particle dispersion

    NASA Astrophysics Data System (ADS)

    Litchford, Ron J.; Jeng, San-Mou

    1992-05-01

    In developing its theory for turbulent dispersion transport, the Litchford and Jeng (1991) statistical transport model for turbulent particle dispersion took a generalized approach in which the perturbing influence of each turbulent eddy on consequent interactions was transported through all subsequent eddies. Nevertheless, examinations of this transport relation shows it to be able to decay rapidly: this implies that additional computational efficiency may be obtained via truncation of unneccessary transport terms. Attention is here given to the criterion for truncation, as well as to expected efficiency gains.

  17. Efficiency of a statistical transport model for turbulent particle dispersion

    SciTech Connect

    Litchford, R.J.; Jeng, San-Mou )

    1992-05-01

    In developing its theory for turbulent dispersion transport, the Litchford and Jeng (1991) statistical transport model for turbulent particle dispersion took a generalized approach in which the perturbing influence of each turbulent eddy on consequent interactions was transported through all subsequent eddies. Nevertheless, examinations of this transport relation shows it to be able to decay rapidly: this implies that additional computational efficiency may be obtained via truncation of unneccessary transport terms. Attention is here given to the criterion for truncation, as well as to expected efficiency gains. 2 refs.

  18. Efficiency of a statistical transport model for turbulent particle dispersion

    NASA Technical Reports Server (NTRS)

    Litchford, Ron J.; Jeng, San-Mou

    1992-01-01

    In developing its theory for turbulent dispersion transport, the Litchford and Jeng (1991) statistical transport model for turbulent particle dispersion took a generalized approach in which the perturbing influence of each turbulent eddy on consequent interactions was transported through all subsequent eddies. Nevertheless, examinations of this transport relation shows it to be able to decay rapidly: this implies that additional computational efficiency may be obtained via truncation of unneccessary transport terms. Attention is here given to the criterion for truncation, as well as to expected efficiency gains.

  19. 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.

  20. 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.

  1. 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.

  2. 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.

  3. 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.

  4. 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. PMID:24375512

  5. 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.

  6. 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

  7. 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.

  8. 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.

  9. Development and testing of conceptual models describing plutonium subsurface transport (Invited)

    NASA Astrophysics Data System (ADS)

    Powell, B. A.

    2009-12-01

    , a conceptual model describing the effects of plutonium redox cycling on subsurface transport was developed. This model accurately described downward movement of plutonium in a series of field lysimeters. Research related to these lysimeters has continued using a combination of long-term field observations, laboratory measurements, and computer modeling which have provided a unique and detailed conceptual and quantitative model describing plutonium subsurface transport. Field and laboratory experiments indicate that biogeochemical processes such as ligand complexation and redox cycling profoundly influence plutonium subsurface transport. This presentation will focus on laboratory efforts to develop these conceptual models and provide a quantitative framework for reactive transport modeling efforts.

  10. Development of a variational flux inversion system (INVICAT v1.0) within the TOMCAT chemical transport model

    NASA Astrophysics Data System (ADS)

    Wilson, C.; Chipperfield, M. P.; Gloor, M.; Chevallier, F.

    2013-12-01

    We present a new variational inverse transport model, named INVICAT (v1.0), which is based upon the global chemical transport model TOMCAT, and a new corresponding adjoint transport model, ATOMCAT. The adjoint model is constructed through manually derived discrete adjoint algorithms, and includes subroutines governing advection, convection and boundary layer mixing. We present extensive testing of the adjoint and inverse models, and also thoroughly assess the accuracy of the TOMCAT forward model's representation of atmospheric transport through comparison with observations of the atmospheric trace gas SF6. The forward model is shown to perform well in comparison with these observations, capturing the latitudinal gradient and seasonal cycle of SF6 to within acceptable tolerances. The adjoint model is shown, through numerical identity tests and novel transport reciprocity tests, to be extremely accurate in comparison with the forward model, with no error shown at the level of accuracy possible with our machines. The potential for the variational system as a tool for inverse modelling is investigated through an idealised test using simulated observations, and the system demonstrates an ability to retrieve known fluxes from a perturbed state accurately. Using basic off-line chemistry schemes, the inverse model is ready and available to perform inversions of trace gases with relatively simple chemical interactions, including CH4, CO2 and CO.

  11. A reduced-dimensional model for near-wall transport in cardiovascular flows.

    PubMed

    Hansen, Kirk B; Shadden, Shawn C

    2016-06-01

    Near-wall mass transport plays an important role in many cardiovascular processes, including the initiation of atherosclerosis, endothelial cell vasoregulation, and thrombogenesis. These problems are characterized by large Péclet and Schmidt numbers as well as a wide range of spatial and temporal scales, all of which impose computational difficulties. In this work, we develop an analytical relationship between the flow field and near-wall mass transport for high-Schmidt-number flows. This allows for the development of a wall-shear-stress-driven transport equation that lies on a codimension-one vessel-wall surface, significantly reducing computational cost in solving the transport problem. Separate versions of this equation are developed for the reaction-rate-limited and transport-limited cases, and numerical results in an idealized abdominal aortic aneurysm are compared to those obtained by solving the full transport equations over the entire domain. The reaction-rate-limited model matches the expected results well. The transport-limited model is accurate in the developed flow regions, but overpredicts wall flux at entry regions and reattachment points in the flow. PMID:26298313

  12. The DOE National Transportation Program Cost-Estimating Model

    SciTech Connect

    Rawl, R.R.

    2001-09-25

    The United States Department of Energy (DOE) carries out a significant amount of transportation each year, including waste remediation activities at the sites for which it is responsible. In future years, the amount of material transported is expected to increase, and the costs of this transportation are expected to be large. To support the assessment of such costs, a cost-estimating model was developed in 1996, peer-reviewed against other available packaging and transportation cost data, and used to calculate the costs for a significant number of shipping campaigns of radioactive waste. This cost-estimating model, known as the Ten-year Plan Transportation Model (TEPTRAM), served as the cost-estimating model for radioactive material shipments in developing the DOE Office of Environmental Management's Ten Year Plan. The TEPTRAM model considered costs for recovery and processing of the wastes, packaging of the wastes for transport, carriage of the waste and a rough estimate of labor cost s associated with preparing and undertaking the shipments. At the user's direction, the model could also include the cost for DOE's interaction with its external stakeholders (e.g., state and local governments and tribal entities) and the cost associated with tracking and communication (e.g., use of the DOE TRANSCOM system). By considering all of these sources of costs, it provided a mechanism for assessing and comparing the costs of various waste processing and shipping campaign alternatives to help guide decision-making. Recognizing that a more user-friendly version of a cost-estimating model would be more useful to the DOE packaging and transportation community, the National Transportation Program sponsored an update of the TEPTRAM model. The new Transportation Cost Estimating Model (TRANSCOST) was developed to fulfill this need. TRANSCOST utilizes a series of input and output screens to facilitate information flow, and a number of new features were added on the basis of features

  13. 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.

  14. Relevance of deterministic structures for modeling of transport: the Lauswiesen case study.

    PubMed

    Händel, Falk; Dietrich, Peter

    2012-01-01

    Knowledge of site-specific contaminant transport processes is an essential requirement for performing various tasks concerning the protection and management of groundwater resources. However, prediction of their behavior is often difficult, especially in heterogeneous aquifers because of the lack of information about flow- and transport-governing subsurface structures and parameters. Hence, stochastic approaches have been developed and frequently used. However, extensive modeling studies on sedimentary structures have shown that consideration of hydrogeological subunits and their distribution can be essential for transport modeling. A case study from the intensely investigated Lauswiesen site is used to demonstrate that more accurate predictions are possible with improved knowledge of deterministic structures. Results of this case study using direct-push injection logging (DPIL) provide a more reliable characterization of hydraulic conductivity than sieve and flow meter data. PMID:22582812

  15. Particle Tracking Model and Abstraction of Transport Processes

    SciTech Connect

    B. Robinson

    2000-04-07

    The purpose of the transport methodology and component analysis is to provide the numerical methods for simulating radionuclide transport and model setup for transport in the unsaturated zone (UZ) site-scale model. The particle-tracking method of simulating radionuclide transport is incorporated into the FEHM computer code and the resulting changes in the FEHM code are to be submitted to the software configuration management system. This Analysis and Model Report (AMR) outlines the assumptions, design, and testing of a model for calculating radionuclide transport in the unsaturated zone at Yucca Mountain. In addition, methods for determining colloid-facilitated transport parameters are outlined for use in the Total System Performance Assessment (TSPA) analyses. Concurrently, process-level flow model calculations are being carrier out in a PMR for the unsaturated zone. The computer code TOUGH2 is being used to generate three-dimensional, dual-permeability flow fields, that are supplied to the Performance Assessment group for subsequent transport simulations. These flow fields are converted to input files compatible with the FEHM code, which for this application simulates radionuclide transport using the particle-tracking algorithm outlined in this AMR. Therefore, this AMR establishes the numerical method and demonstrates the use of the model, but the specific breakthrough curves presented do not necessarily represent the behavior of the Yucca Mountain unsaturated zone.

  16. Comparative study of chemo-electro-mechanical transport models for an electrically stimulated hydrogel

    NASA Astrophysics Data System (ADS)

    Elshaer, S. E.; Moussa, W. A.

    2014-07-01

    The main objective of this work is to introduce a new expression for the hydrogel’s hydration for use within the Poisson Nernst-Planck chemo electro mechanical (PNP CEM) transport models. This new contribution to the models support large deformation by considering the higher order terms in the Green-Lagrangian strain tensor. A detailed discussion of the CEM transport models using Poisson Nernst-Planck (PNP) and Poisson logarithmic Nernst-Planck (PLNP) equations for chemically and electrically stimulated hydrogels will be presented. The assumptions made to simplify both CEM transport models for electric field application in the order of 0.833 kV m-1 and a highly diluted electrolyte solution (97% is water) will be explained. This PNP CEM model has been verified accurately against experimental and numerical results. In addition, different definitions for normalizing the parameters are used to derive the dimensionless forms of both the PNP and PLNP CEM. Four models, PNP CEM, PLNP CEM, dimensionless PNP CEM and dimensionless PNLP CEM transport models were employed on an axially symmetric cylindrical hydrogel problem with an aspect ratio (diameter to thickness) of 175:3. The displacement and osmotic pressure obtained for the four models are compared against the variation of the number of elements for finite element analysis, simulation duration and solution rate when using the direct numerical solver.

  17. 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

  18. 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

  19. Particle Tracking Model and Abstraction of Transport Processes

    SciTech Connect

    B. Robinson

    2004-10-21

    The purpose of this report is to document the abstraction model being used in total system performance assessment (TSPA) model calculations for radionuclide transport in the unsaturated zone (UZ). The UZ transport abstraction model uses the particle-tracking method that is incorporated into the finite element heat and mass model (FEHM) computer code (Zyvoloski et al. 1997 [DIRS 100615]) to simulate radionuclide transport in the UZ. This report outlines the assumptions, design, and testing of a model for calculating radionuclide transport in the UZ at Yucca Mountain. In addition, methods for determining and inputting transport parameters are outlined for use in the TSPA for license application (LA) analyses. Process-level transport model calculations are documented in another report for the UZ (BSC 2004 [DIRS 164500]). Three-dimensional, dual-permeability flow fields generated to characterize UZ flow (documented by BSC 2004 [DIRS 169861]; DTN: LB03023DSSCP9I.001 [DIRS 163044]) are converted to make them compatible with the FEHM code for use in this abstraction model. This report establishes the numerical method and demonstrates the use of the model that is intended to represent UZ transport in the TSPA-LA. Capability of the UZ barrier for retarding the transport is demonstrated in this report, and by the underlying process model (BSC 2004 [DIRS 164500]). The technical scope, content, and management of this report are described in the planning document ''Technical Work Plan for: Unsaturated Zone Transport Model Report Integration'' (BSC 2004 [DIRS 171282]). Deviations from the technical work plan (TWP) are noted within the text of this report, as appropriate. The latest version of this document is being prepared principally to correct parameter values found to be in error due to transcription errors, changes in source data that were not captured in the report, calculation errors, and errors in interpretation of source data.

  20. 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.

  1. 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.

  2. 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

  3. A robust and accurate approach to computing compressible multiphase flow: Stratified flow model and AUSM{sup +}-up scheme

    SciTech Connect

    Chang, Chih-Hao . E-mail: chchang@engineering.ucsb.edu; Liou, Meng-Sing . E-mail: meng-sing.liou@grc.nasa.gov

    2007-07-01

    In this paper, we propose a new approach to compute compressible multifluid equations. Firstly, a single-pressure compressible multifluid model based on the stratified flow model is proposed. The stratified flow model, which defines different fluids in separated regions, is shown to be amenable to the finite volume method. We can apply the conservation law to each subregion and obtain a set of balance equations. Secondly, the AUSM{sup +} scheme, which is originally designed for the compressible gas flow, is extended to solve compressible liquid flows. By introducing additional dissipation terms into the numerical flux, the new scheme, called AUSM{sup +}-up, can be applied to both liquid and gas flows. Thirdly, the contribution to the numerical flux due to interactions between different phases is taken into account and solved by the exact Riemann solver. We will show that the proposed approach yields an accurate and robust method for computing compressible multiphase flows involving discontinuities, such as shock waves and fluid interfaces. Several one-dimensional test problems are used to demonstrate the capability of our method, including the Ransom's water faucet problem and the air-water shock tube problem. Finally, several two dimensional problems will show the capability to capture enormous details and complicated wave patterns in flows having large disparities in the fluid density and velocities, such as interactions between water shock wave and air bubble, between air shock wave and water column(s), and underwater explosion.

  4. 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.

  5. COMBINED SEWER OVERFLOW SEDIMENT TRANSPORT MODEL: DOCUMENTATION AND EVALUATION

    EPA Science Inventory

    A modeling package for studying the movement and fate of combined sewer overflow (CSO) sediment in receiving waters is described. The package contains a linear, implicit, finite-difference flow model and an explicit, finite-difference sediment transport model. The sediment model ...

  6. 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.

  7. Computational Modeling of Transport Limitations in Li-Air Batteries

    SciTech Connect

    Ryan, Emily M.; Ferris, Kim F.; Tartakovsky, Alexandre M.; Khaleel, Mohammad A.

    2013-02-22

    In this paper we investigate transport limitations in the electrodes of lithium-air batteries through computational modeling. We use meso-scale models to consider the effects of dendrites on the current and potential at the anode surface, and to investigate the effects of reaction and transport parameters on the formation of precipitates in the cathode. The formation of dendrites on the anode surface during cycling reduces the transport of ions and can lead to short circuits in the cell. Growth of precipitates in the cathode reduces the specific capacity of the cell due to surface passivation and pore clogging. Both of these degradation mechanisms depend on meso-scale phenomena, such as the pore-scale reactive transport in the cathode. To understand the effects of the meso-scale transport and precipitation on the performance and lifetime of Li-air batteries, meso-scale modeling is needed that is able to resolve the electrodes and their microstructures.

  8. 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

  9. 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)

  10. 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

  11. GROUNDWATER MASS TRANSPORT AND EQUILIBRIUM CHEMISTRY MODEL FOR MULTICOMPONENT SYSTEMS

    EPA Science Inventory

    A mass transport model, TRANQL, for a multicomponent solution system has been developed. The equilibrium interaction chemistry is posed independently of the mass transport equations which leads to a set of algebraic equations for the chemistry coupled to a set of differential equ...

  12. 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.

  13. 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.

  14. Monte Carlo impurity transport modeling in the DIII-D transport

    SciTech Connect

    Evans, T.E.; Finkenthal, D.F.

    1998-04-01

    A description of the carbon transport and sputtering physics contained in the Monte Carlo Impurity (MCI) transport code is given. Examples of statistically significant carbon transport pathways are examined using MCI`s unique tracking visualizer and a mechanism for enhanced carbon accumulation on the high field side of the divertor chamber is discussed. Comparisons between carbon emissions calculated with MCI and those measured in the DIII-D tokamak are described. Good qualitative agreement is found between 2D carbon emission patterns calculated with MCI and experimentally measured carbon patterns. While uncertainties in the sputtering physics, atomic data, and transport models have made quantitative comparisons with experiments more difficult, recent results using a physics based model for physical and chemical sputtering has yielded simulations with about 50% of the total carbon radiation measured in the divertor. These results and plans for future improvement in the physics models and atomic data are discussed.

  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. 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.

  17. 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].

  18. An accurate locally active memristor model for S-type negative differential resistance in NbOx

    NASA Astrophysics Data System (ADS)

    Gibson, Gary A.; Musunuru, Srinitya; Zhang, Jiaming; Vandenberghe, Ken; Lee, James; Hsieh, Cheng-Chih; Jackson, Warren; Jeon, Yoocharn; Henze, Dick; Li, Zhiyong; Stanley Williams, R.

    2016-01-01

    A number of important commercial applications would benefit from the introduction of easily manufactured devices that exhibit current-controlled, or "S-type," negative differential resistance (NDR). A leading example is emerging non-volatile memory based on crossbar array architectures. Due to the inherently linear current vs. voltage characteristics of candidate non-volatile memristor memory elements, individual memory cells in these crossbar arrays can be addressed only if a highly non-linear circuit element, termed a "selector," is incorporated in the cell. Selectors based on a layer of niobium oxide sandwiched between two electrodes have been investigated by a number of groups because the NDR they exhibit provides a promisingly large non-linearity. We have developed a highly accurate compact dynamical model for their electrical conduction that shows that the NDR in these devices results from a thermal feedback mechanism. A series of electrothermal measurements and numerical simulations corroborate this model. These results reveal that the leakage currents can be minimized by thermally isolating the selector or by incorporating materials with larger activation energies for electron motion.

  19. Accurate modeling of fluorescence line narrowing difference spectra: Direct measurement of the single-site fluorescence spectrum

    NASA Astrophysics Data System (ADS)

    Reppert, Mike; Naibo, Virginia; Jankowiak, Ryszard

    2010-07-01

    Accurate lineshape functions for modeling fluorescence line narrowing (FLN) difference spectra (ΔFLN spectra) in the low-fluence limit are derived and examined in terms of the physical interpretation of various contributions, including photoproduct absorption and emission. While in agreement with the earlier results of Jaaniso [Proc. Est. Acad. Sci., Phys., Math. 34, 277 (1985)] and Fünfschilling et al. [J. Lumin. 36, 85 (1986)], the derived formulas differ substantially from functions used recently [e.g., M. Rätsep et al., Chem. Phys. Lett. 479, 140 (2009)] to model ΔFLN spectra. In contrast to traditional FLN spectra, it is demonstrated that for most physically reasonable parameters, the ΔFLN spectrum reduces simply to the single-site fluorescence lineshape function. These results imply that direct measurement of a bulk-averaged single-site fluorescence lineshape function can be accomplished with no complicated extraction process or knowledge of any additional parameters such as site distribution function shape and width. We argue that previous analysis of ΔFLN spectra obtained for many photosynthetic complexes led to strong artificial lowering of apparent electron-phonon coupling strength, especially on the high-energy side of the pigment site distribution function.

  20. Increasingly accurate dynamic molecular models of G-protein coupled receptor oligomers: Panacea or Pandora's box for novel drug discovery?

    PubMed Central

    Filizola, Marta

    2009-01-01

    For years conventional drug design at G-protein coupled receptors (GPCRs) has mainly focused on the inhibition of a single receptor at a usually well-defined ligand-binding site. The recent discovery of more and more physiologically relevant GPCR dimers/oligomers suggests that selectively targeting these complexes or designing small molecules that inhibit receptor-receptor interactions might provide new opportunities for novel drug discovery. To uncover the fundamental mechanisms and dynamics governing GPCR dimerization/oligomerization, it is crucial to understand the dynamic process of receptor-receptor association, and to identify regions that are suitable for selective drug binding. This minireview highlights current progress in the development of increasingly accurate dynamic molecular models of GPCR oligomers based on structural, biochemical, and biophysical information that has recently appeared in the literature. In view of this new information, there has never been a more exciting time for computational research into GPCRs than at present. Information-driven modern molecular models of GPCR complexes are expected to efficiently guide the rational design of GPCR oligomer-specific drugs, possibly allowing researchers to reach for the high-hanging fruits in GPCR drug discovery, i.e. more potent and selective drugs for efficient therapeutic interventions. PMID:19465029