Active and passive transport of cargo in a corrugated channel: A lattice model study

NASA Astrophysics Data System (ADS)

Dey, Supravat; Ching, Kevin; Das, Moumita

2018-04-01

Inside cells, cargos such as vesicles and organelles are transported by molecular motors to their correct locations via active motion on cytoskeletal tracks and passive, Brownian diffusion. During the transportation of cargos, motor-cargo complexes (MCCs) navigate the confining and crowded environment of the cytoskeletal network and other macromolecules. Motivated by this, we study a minimal two-state model of motor-driven cargo transport in confinement and predict transport properties that can be tested in experiments. We assume that the motion of the MCC is directly affected by the entropic barrier due to confinement if it is in the passive, unbound state but not in the active, bound state where it moves with a constant bound velocity. We construct a lattice model based on a Fokker Planck description of the two-state system, study it using a kinetic Monte Carlo method and compare our numerical results with analytical expressions for a mean field limit. We find that the effect of confinement strongly depends on the bound velocity and the binding kinetics of the MCC. Confinement effectively reduces the effective diffusivity and average velocity, except when it results in an enhanced average binding rate and thereby leads to a larger average velocity than when unconfined.

Network aggregation in transportation planning models

DOT National Transportation Integrated Search

1979-06-01

This report contains six papers addressed at mathematical and computation aspects of an extraction aggregation model often employed in transportation planning studies. This model concerns the optimal flowing of an extracted subnetwork of a given netw...

Iontophoretic transport of oligonucleotides across human epidermal membrane: a study of the Nernst-Planck model.

PubMed

Li, S K; Ghanem, A H; Teng, C L; Hardee, G E; Higuchi, W I

2001-07-01

The objective of this study was to investigate the transport behavior of a series of oligonucleotides with human epidermal membrane (HEM) and to examine the applicability of the modified NERNST-PLANCK model to transdermal iontophoresis of these macromolecules. Iontophoretic transport experiments were first carried out in a synthetic model membrane system (Nuclepore membranes) with a four-electrode potentiostat to examine the baseline modified NERNST-PLANCK model. The modified NERNST-PLANCK model derived from the Einstein relation and the Stokes-Einstein equation taken from previous work did not hold for the oligonucleotides. Results obtained in the Nuclepore studies were, however, consistent with predictions of the modified NERNST-PLANCK model using the experimentally determined electromobilities and diffusion coefficients. The electromobilities of the oligonucleotides (determined by capillary electrophoresis) were found to be more than a factor of two smaller than expected from the Einstein relation between electromobilities and diffusion coefficients (the latter determined in diffusion cell experiments). A correlation between these electromobilities and the theoretical electromobilities estimated by considering the effects of counterion binding and the effects of mobility reduction according to colloid theory was also observed. These results suggest that the modified NERNST-PLANCK model predictions are satisfactory only when the electromobilities and the effective molecular size of the oligonucleotides are known and are used directly to predict the iontophoretically enhanced transport. Results with the HEM experiments generally agreed with model predictions based on the experimental electromobilities. The oligonucleotide HEM flux data also suggest the existence of pores with effective pore radii greater than the effective radii estimated in previous studies with small molecular weight model permeants.

Oxygen Transport: A Simple Model for Study and Examination.

ERIC Educational Resources Information Center

Gaar, Kermit A., Jr.

1985-01-01

Describes an oxygen transport model computer program (written in Applesoft BASIC) which uses such variables as amount of time lapse from beginning of the simulation, arterial blood oxygen concentration, alveolar oxygen pressure, and venous blood oxygen concentration and pressure. Includes information on obtaining the program and its documentation.…

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. Copyright © 2015 by The American Society for Pharmacology and Experimental Therapeutics.

Uranium transport in a crushed granodiorite: Experiments and reactive transport modeling

DOE PAGES

Dittrich, T. M.; Reimus, P. W.

2015-02-12

The primary objective of this study was to develop and demonstrate an experimental method to refine and better parameterize process models for reactive contaminant transport in aqueous subsurface environments and to reduce conservatism in such models without attempting to fully describe the geochemical system.

Impact of Transport Zone Number in Simulation Models on Cost-Benefit Analysis Results in Transport Investments

NASA Astrophysics Data System (ADS)

Chmielewski, Jacek

2017-10-01

Nowadays, feasibility studies need to be prepared for all planned transport investments, mainly those co-financed with UE grants. One of the fundamental aspect of feasibility study is the economic justification of an investment, evaluated in an area of so called cost-benefit analysis (CBA). The main goal of CBA calculation is to prove that a transport investment is really important for the society and should be implemented as economically efficient one. It can be said that the number of hours (PH - passengers hours) in trips and travelled kilometres (PK - passengers kilometres) are the most important for CBA results. The differences between PH and PK calculated for particular investment scenarios are the base for benefits calculation. Typically, transport simulation models are the best source for such data. Transport simulation models are one of the most powerful tools for transport network planning. They make it possible to evaluate forecast traffic volume and passenger flows in a public transport system for defined scenarios of transport and area development. There are many different transport models. Their construction is often similar, and they mainly differ in the level of their accuracy. Even models for the same area may differ in this matter. Typically, such differences come from the accuracy of supply side representation: road and public transport network representation. In many cases only main roads and a public transport network are represented, while local and service roads are eliminated as a way of reality simplification. This also enables a faster and more effective calculation process. On the other hand, the description of demand part of these models based on transport zones is often stable. Difficulties with data collection, mainly data on land use, resulted in the lack of changes in the analysed land division into so called transport zones. In this paper the author presents an influence of land division on the results of traffic analyses, and hence

Maximum likelihood Bayesian model averaging and its predictive analysis for groundwater reactive transport models

USGS Publications Warehouse

Curtis, Gary P.; Lu, Dan; Ye, Ming

2015-01-01

While Bayesian model averaging (BMA) has been widely used in groundwater modeling, it is infrequently applied to groundwater reactive transport modeling because of multiple sources of uncertainty in the coupled hydrogeochemical processes and because of the long execution time of each model run. To resolve these problems, this study analyzed different levels of uncertainty in a hierarchical way, and used the maximum likelihood version of BMA, i.e., MLBMA, to improve the computational efficiency. This study demonstrates the applicability of MLBMA to groundwater reactive transport modeling in a synthetic case in which twenty-seven reactive transport models were designed to predict the reactive transport of hexavalent uranium (U(VI)) based on observations at a former uranium mill site near Naturita, CO. These reactive transport models contain three uncertain model components, i.e., parameterization of hydraulic conductivity, configuration of model boundary, and surface complexation reactions that simulate U(VI) adsorption. These uncertain model components were aggregated into the alternative models by integrating a hierarchical structure into MLBMA. The modeling results of the individual models and MLBMA were analyzed to investigate their predictive performance. The predictive logscore results show that MLBMA generally outperforms the best model, suggesting that using MLBMA is a sound strategy to achieve more robust model predictions relative to a single model. MLBMA works best when the alternative models are structurally distinct and have diverse model predictions. When correlation in model structure exists, two strategies were used to improve predictive performance by retaining structurally distinct models or assigning smaller prior model probabilities to correlated models. Since the synthetic models were designed using data from the Naturita site, the results of this study are expected to provide guidance for real-world modeling. Limitations of applying MLBMA to the

Maximum likelihood Bayesian model averaging and its predictive analysis for groundwater reactive transport models

DOE PAGES

Lu, Dan; Ye, Ming; Curtis, Gary P.

2015-08-01

While Bayesian model averaging (BMA) has been widely used in groundwater modeling, it is infrequently applied to groundwater reactive transport modeling because of multiple sources of uncertainty in the coupled hydrogeochemical processes and because of the long execution time of each model run. To resolve these problems, this study analyzed different levels of uncertainty in a hierarchical way, and used the maximum likelihood version of BMA, i.e., MLBMA, to improve the computational efficiency. Our study demonstrates the applicability of MLBMA to groundwater reactive transport modeling in a synthetic case in which twenty-seven reactive transport models were designed to predict themore » reactive transport of hexavalent uranium (U(VI)) based on observations at a former uranium mill site near Naturita, CO. Moreover, these reactive transport models contain three uncertain model components, i.e., parameterization of hydraulic conductivity, configuration of model boundary, and surface complexation reactions that simulate U(VI) adsorption. These uncertain model components were aggregated into the alternative models by integrating a hierarchical structure into MLBMA. The modeling results of the individual models and MLBMA were analyzed to investigate their predictive performance. The predictive logscore results show that MLBMA generally outperforms the best model, suggesting that using MLBMA is a sound strategy to achieve more robust model predictions relative to a single model. MLBMA works best when the alternative models are structurally distinct and have diverse model predictions. When correlation in model structure exists, two strategies were used to improve predictive performance by retaining structurally distinct models or assigning smaller prior model probabilities to correlated models. Since the synthetic models were designed using data from the Naturita site, the results of this study are expected to provide guidance for real-world modeling. Finally

Groundwater flow and transport modeling

USGS Publications Warehouse

Konikow, Leonard 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.

ADVANCED CUTTINGS TRANSPORT STUDY

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

Stefan Miska; Troy Reed; Ergun Kuru

2004-09-30

The Advanced Cuttings Transport Study (ACTS) was a 5-year JIP project undertaken at the University of Tulsa (TU). The project was sponsored by the U.S. Department of Energy (DOE) and JIP member companies. The objectives of the project were: (1) to develop and construct a new research facility that would allow three-phase (gas, liquid and cuttings) flow experiments under ambient and EPET (elevated pressure and temperature) conditions, and at different angle of inclinations and drill pipe rotation speeds; (2) to conduct experiments and develop a data base for the industry and academia; and (3) to develop mechanistic models for optimizationmore » of drilling hydraulics and cuttings transport. This project consisted of research studies, flow loop construction and instrumentation development. Following a one-year period for basic flow loop construction, a proposal was submitted by TU to the DOE for a five-year project that was organized in such a manner as to provide a logical progression of research experiments as well as additions to the basic flow loop. The flow loop additions and improvements included: (1) elevated temperature capability; (2) two-phase (gas and liquid, foam etc.) capability; (3) cuttings injection and removal system; (4) drill pipe rotation system; and (5) drilling section elevation system. In parallel with the flow loop construction, hydraulics and cuttings transport studies were preformed using drilling foams and aerated muds. In addition, hydraulics and rheology of synthetic drilling fluids were investigated. The studies were performed under ambient and EPET conditions. The effects of temperature and pressure on the hydraulics and cuttings transport were investigated. Mechanistic models were developed to predict frictional pressure loss and cuttings transport in horizontal and near-horizontal configurations. Model predictions were compared with the measured data. Predominantly, model predictions show satisfactory agreements with the measured

A new turbulence-based model for sand transport

NASA Astrophysics Data System (ADS)

Mayaud, Jerome; Wiggs, Giles; Bailey, Richard

2016-04-01

Knowledge of the changing rate of sediment flux in space and time is essential for quantifying surface erosion and deposition in desert landscapes. While many aeolian studies have relied on time-averaged parameters such as wind velocity (U) and wind shear velocity (u*) to determine sediment flux, there is increasing evidence that high-frequency turbulence is an important driving force behind the entrainment and transport of sand. However, turbulence has yet to be incorporated into a functional sand transport model that can be used for predictive purposes. In this study we present a new transport model (the 'turbulence model') that accounts for high-frequency variations in the horizontal (u) and vertical (w) components of wind flow. The turbulence model is fitted to wind velocity and sediment transport data from a field experiment undertaken in Namibia's Skeleton Coast National Park, and its performance at three temporal resolutions (10 Hz, 1 Hz, 1 min) is compared to two existing models that rely on time-averaged wind velocity data (Radok, 1977; Dong et al., 2003). The validity of the three models is analysed under a variety of saltation conditions, using a 2-hour (1 Hz measurement resolution) dataset from the Skeleton Coast and a 5-hour (1 min measurement resolution) dataset from the southwestern Kalahari Desert. The turbulence model is shown to outperform the Radok and Dong models when predicting total saltation count over the three experimental periods. For all temporal resolutions presented in this study (10 Hz-10 min), the turbulence model predicted total saltation count to within at least 0.34%, whereas the Radok and Dong models over- or underestimated total count by up to 5.50% and 20.53% respectively. The strong performance of the turbulence model can be attributed to a lag in mass flux response built into its formulation, which can be adapted depending on the temporal resolution of investigation. This accounts for the inherent lag within the physical

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.

Modelling of human transplacental transport as performed in Copenhagen, Denmark.

PubMed

Mathiesen, Line; Mørck, Thit Aarøe; Zuri, Giuseppina; Andersen, Maria Helena; Pehrson, Caroline; Frederiksen, Marie; Mose, Tina; Rytting, Erik; Poulsen, Marie S; Nielsen, Jeanette K S; Knudsen, Lisbeth E

2014-07-01

Placenta perfusion models are very effective when studying the placental mechanisms in order to extrapolate to real-life situations. The models are most often used to investigate the transport of substances between mother and foetus, including the potential metabolism of these. We have studied the relationships between maternal and foetal exposures to various compounds including pollutants such as polychlorinated biphenyls, polybrominated flame retardants, nanoparticles as well as recombinant human antibodies. The compounds have been studied in the human placenta perfusion model and to some extent in vitro with an established human monolayer trophoblast cell culture model. Results from our studies distinguish placental transport of substances by physicochemical properties, adsorption to placental tissue, binding to transport and receptor proteins and metabolism. We have collected data from different classes of chemicals and nanoparticles for comparisons across chemical structures as well as different test systems. Our test systems are based on human material to bypass the extrapolation from animal data. By combining data from our two test systems, we are able to rank and compare the transport of different classes of substances according to their transport ability. Ultimately, human data including measurements in cord blood contribute to the study of placental transport. © 2014 Nordic Association for the Publication of BCPT (former Nordic Pharmacological Society).

A Transportation Modeling Primer

DOT National Transportation Integrated Search

2006-06-01

This primer is intended to explain the urban transportation modeling process works, the assumptions made and the steps used to forecast travel demand for urban transportation planning. This is done in order to help to understand the process and its i...

HYDRODYNAMIC AND TRANSPORT MODELING STUDY IN A HIGHLY STRATIFIED ESTUARY

EPA Science Inventory

This paper presents the preliminary results of hydrodynamic and salinity predictions and the implications to an ongoing contaminated sediment transport and fate modeling effort in the Lower Duwamish Waterway (LDW), Seattle, Washington. The LDW is highly strati-fied when freshwate...

Analytical mesoscale modeling of aeolian sand transport

NASA Astrophysics Data System (ADS)

Lämmel, Marc; Kroy, Klaus

2017-11-01

The mesoscale structure of aeolian sand transport determines a variety of natural phenomena studied in planetary and Earth science. We analyze it theoretically beyond the mean-field level, based on the grain-scale transport kinetics and splash statistics. A coarse-grained analytical model is proposed and verified by numerical simulations resolving individual grain trajectories. The predicted height-resolved sand flux and other important characteristics of the aeolian transport layer agree remarkably well with a comprehensive compilation of field and wind-tunnel data, suggesting that the model robustly captures the essential mesoscale physics. By comparing the predicted saturation length with field data for the minimum sand-dune size, we elucidate the importance of intermittent turbulent wind fluctuations for field measurements and reconcile conflicting previous models for this most enigmatic emergent aeolian scale.

Composite Transport Model and Water and Solute Transport across Plant Roots: An Update.

PubMed

Kim, Yangmin X; Ranathunge, Kosala; Lee, Seulbi; Lee, Yejin; Lee, Deogbae; Sung, Jwakyung

2018-01-01

The present review examines recent experimental findings in root transport phenomena in terms of the composite transport model (CTM). It has been a well-accepted conceptual model to explain the complex water and solute flows across the root that has been related to the composite anatomical structure. There are three parallel pathways involved in the transport of water and solutes in roots - apoplast, symplast, and transcellular paths. The role of aquaporins (AQPs), which facilitate water flows through the transcellular path, and root apoplast is examined in terms of the CTM. The contribution of the plasma membrane bound AQPs for the overall water transport in the whole plant level was varying depending on the plant species, age of roots with varying developmental stages of apoplastic barriers, and driving forces (hydrostatic vs. osmotic). Many studies have demonstrated that the apoplastic barriers, such as Casparian bands in the primary anticlinal walls and suberin lamellae in the secondary cell walls, in the endo- and exodermis are not perfect barriers and unable to completely block the transport of water and some solute transport into the stele. Recent research on water and solute transport of roots with and without exodermis triggered the importance of the extension of conventional CTM adding resistances that arrange in series (epidermis, exodermis, mid-cortex, endodermis, and pericycle). The extension of the model may answer current questions about the applicability of CTM for composite water and solute transport of roots that contain complex anatomical structures with heterogeneous cell layers.

On modeling heterogeneous coastal sediment transport - A numerical study using multiphase Eulerian and Euler-Lagrangian approaches

NASA Astrophysics Data System (ADS)

Cheng, Z.; Yu, X.; Hsu, T. J.; Calantoni, J.; Chauchat, J.

2016-02-01

Regional scale coastal evolution models do not explicitly resolve wave-driven sediment transport and must rely on bedload/suspended modules that utilize empirical assumptions. Under extreme wave events or in regions of high sediment heterogeneity, these empirical bedload/suspended load modules may need to be reevaluated with detailed observation and more sophisticated small-scale models. In the past decade, significant research efforts have been devoted to modeling sediment transport using multiphase Eulerian or Euler-Lagrangian approaches. Recently, an open-source multi-dimensional Reynolds-averaged two-phase sediment transport model, SedFOAM is developed by the authors and it has been adopted by many researchers to study momentary bed failure, granular rheology in sheet flow and scour around structures. In this abstract, we further report our recent progress made in extending the model with 3D turbulence-resolving capability and to model the sediment phase with the Discrete Element method (DEM). Adopting the large-eddy simulation methodology, we validate the 3D model with measured fine sediment transport is oscillatory sheet flow and demonstrate that the model is able to resolve sediment burst events during flow reversals. To better resolve the intergranular interactions and to model heterogeneous properties of sediment (e.g., mixed grain sizes and grain shape), we use an Euler-Lagrangian solver called CFDEM, which couples OpenFOAM for the fluid phase and LIGGGHTS for the particle phase. We improve the model by better enforcing conservation of mass in the pressure solver. The modified CFDEM solver is validated with measured oscillatory sheet flow data for coarse sand and we demonstrated that the model can reproduce the well-known armoring effects. We show that under Stokes second-order wave forcing, the armoring effect is more significant during the energetic positive peak, and hence the net onshore transport is reduced. Preliminary results modeling the shape

A model study of sediment transport across the shelf break

NASA Astrophysics Data System (ADS)

Marchal, Olivier

2017-04-01

A variety of dynamical processes can contribute to the transport of material (e.g., particulate matter) across the shelf break - the region separating the continental shelf from the continental slope. Among these processes are (i) the reflection of internal waves on the outer shelf and upper slope, and (ii) the instability of hydrographic fronts, roughly aligned with isobaths, that are often present at the shelf break. On the one hand, internal waves reflecting on a sloping boundary can produce bottom shear stresses that are large enough to resuspend non-cohesive sediments into the water column. On the other hand, eddies shed from unstable shelf break fronts can incorporate into their core particle-rich waters from the outer shelf and upper slope, and transport these waters offshore. Here we present numerical experiments with a three-dimensional numerical model of ocean circulation and sediment transport, which illustrate the joint effect of internal waves and eddies on sediment transport across the shelf break. The model is based on the primitive equations and terrain-following coordinates. The model domain is square and idealized, comprising a flat continental shelf, a constant continental slope, and a flat abyssal basin. The model grid has O(1 km) horizontal resolution, so that (sub)mesoscale eddies observed in the vicinity of shelf breaks, such as south of New England, can be represented in detail. Internal waves are excited through the specification of a periodic variation in the across-slope component of velocity at the offshore boundary of the domain, and eddies are generated from the baroclinic instability of a shelf break jet that is initially in strict thermal wind balance. Numerical experiments are conducted that are characterized by (i) different slopes of internal wave characteristics relative to the continental slope, representing sub-critical, critical, and super-critical regimes, and (ii) different values for the dimensionless ratios that emerge

Computational models for predicting interactions with membrane transporters.

PubMed

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

2013-01-01

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

Sealed reticulocyte ghosts. An experimental model for the study of Fe2+ transport.

PubMed

Núñez, M T; Escobar, A; Ahumada, A; Gonzalez-Sepulveda, M

1992-06-05

Sealed right-side-out reticulocyte ghosts transported and accumulated iron offered as 59Fe(2+)-ascorbate (Km = 1.1 microM). The uptake of iron by ghosts presented the characteristics of a transporter-mediated process: it responded to osmotic challenge, the rate of transport increased when iron was present in the opposing side, and the transport rate showed the temperature dependence typical of membrane-mediated processes. The transport of iron was dependent on an associated influx of Cl- in order to keep electroneutrality. Other transition metals, such as Cu2+, Zn2+, and Co2+, inhibited the transport of Fe2+. The overall characteristics of the system make reticulocyte sealed ghosts a very useful model in determining the basic mechanisms of membrane iron transport.

NMR studies of cation transport across membranes

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

Shochet, N.R.

1985-01-01

/sup 23/Na NMR Studies of cation transport across membranes were conducted both on model and biological membranes. Two ionophores, the carrier monensin and the channel-former gramicidin, were chosen to induce cation transport in large unilamellar phosphatidylcholine vesicles. The distinction between the NMR signals arising from the two sides of the membrane was achieved by the addition of an anionic paramagnetic shift reagent to the outer solution. The kinetics of the cation transport across the membrane was observed simultaneously monitoring the changes in the /sup 23/Na NMR signals of both compartments. Two mathematical models were developed for the estimation of themore » transport parameters of the monensin- and gramicidin-induced cation transport. The models were able to fit the experimental data very well. A new method for the estimation of the volume trapped inside the vesicles was developed. The method uses the relative areas of the intra- and extravesicular NMR signals arising from a suspension of vesicles bathed in the same medium they contain, as a measure for the relative volumes of these compartments. Sodium transport across biological membranes was studied by /sup 23/ NMR, using suspensions of cultured nerve cells. The sodium influx through voltage-gated channels was studied using the channel modifier batrachotoxin in combination with scorpion toxin.« less

A three-dimensional transport model for the middle atmosphere

NASA Technical Reports Server (NTRS)

Rasch, Philip J.; Tie, Xuexi; Boville, Byron A.; Williamson, David L.

1994-01-01

In this paper we describe fundamental properties of an 'off-line' three-dimensional transport model, that is, a model which uses prescribed rather than predicted winds. The model is currently used primarily for studying problems of the middle atmosphere because we have not (yet) incorporated a formulation for the convective transport of trace species, a prerequisite for many tropospheric problems. The off-line model is simpler and less expensive than a model which predicts the wind and mass evolution (an 'on-line' model), but it is more complex than the two-dimensional (2-D) zonally averaged transport models often used in the study of chemistry and transport in the middle atmosphere. It thus serves as a model of intermediate complexity and can fill a useful niche for the study of transport and chemistry. We compare simulations of four tracers, released in the lower stratosphere, in both the on- and off-line models to document the difference resulting from differences in modeling the same problem with this intermediate model. These differences identify the price to be paid in going to a cheaper and simpler calculation. The off-line model transports a tracer in three dimensions. For this reason, it requires fewer approximations than 2-D transport model, which must parameterize the effects of mixing by transient and zonally asymmetric wind features. We compare simulations of the off-line model with simulations of a 2-D model for two problems. First, we compare 2-D and three-dimensional (3-D) models by simulating the emission of an NO(x)-like tracer by a fleet of high-speed aircraft. The off-line model is then used to simulate the transport of C-14 and to contrast its simulation properties to that of the host of 2-D models which participated in an identical simulation in a recent NASA model intercomparison. The off-line model is shown to be somewhat sensitive to the sampling strategy for off-line winds. Simulations with daily averaged winds are in very good qualitative

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.

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.

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).

The effect on Arctic climate of atmospheric meridional energy-transport changes studied based on the CESM climate model

NASA Astrophysics Data System (ADS)

Grand Graversen, Rune

2017-04-01

The Arctic amplification of global warming, and the pronounced Arctic sea-ice retreat constitute some of the most alarming signs of global climate change. These Arctic changes are likely a consequence of a combination of several processes, for instance enhanced uptake of solar radiation in the Arctic due to a decrease of sea ice (the ice-albedo feedback), and increase in the local Arctic greenhouse effect due to enhanced moister flux from lower latitudes. Many of the proposed processes appear to be dependent on each other, for instance an increase in water-vapour advection to the Arctic enhances the greenhouse effect in the Arctic and the longwave radiation to the surface, leading to sea-ice melt and enhancement of the ice-albedo feedback. The effects of albedo changes and other radiative feedbacks have been investigated in earlier studies based on model experiments designed to examine these effects specifically. Here we instead focus on the effects of meridional transport changes into the Arctic, both of moister and dry-static energy. Hence we here present results of model experiments with the CESM climate model designed specifically to extract the effects of the changes of the two transport components. In the CESM model the moister transport to the Arctic increases, whereas the dry-static transport decreases in response to a doubling of CO2. This is in agreement with other model results. The model is now forced with these transport changes of water-vapour and dry-static energy associated with a CO2 doubling. The results show that changes of the water-vapour transport lead to Arctic warming. This is partly a consequence of the ice-albedo feedback due to sea-ice melt caused by the change of the water-vapour advection. The changes of the dry-static transport lead to Arctic cooling, which however is smaller than the warming induced by the water-vapour component. Hence this study support the hypothesis that changes in the atmospheric circulation contribute to the

Bottom currents and sediment transport in Long Island Sound: A modeling study

USGS Publications Warehouse

Signell, R.P.; List, J.H.; Farris, A.S.

2000-01-01

A high resolution (300-400 m grid spacing), process oriented modeling study was undertaken to elucidate the physical processes affecting the characteristics and distribution of sea-floor sedimentary environments in Long Island Sound. Simulations using idealized forcing and high-resolution bathymetry were performed using a three-dimensional circulation model ECOM (Blumberg and Mellor, 1987) and a stationary shallow water wave model HISWA (Holthuijsen et al., 1989). The relative contributions of tide-, density-, wind- and wave-driven bottom currents are assessed and related to observed characteristics of the sea-floor environments, and simple bedload sediment transport simulations are performed. The fine grid spacing allows features with scales of several kilometers to be resolved. The simulations clearly show physical processes that affect the observed sea-floor characteristics at both regional and local scales. Simulations of near-bottom tidal currents reveal a strong gradient in the funnel-shaped eastern part of the Sound, which parallels an observed gradient in sedimentary environments from erosion or nondeposition, through bedload transport and sediment sorting, to fine-grained deposition. A simulation of estuarine flow driven by the along-axis gradient in salinity shows generally westward bottom currents of 2-4 cm/s that are locally enhanced to 6-8 cm/s along the axial depression of the Sound. Bottom wind-driven currents flow downwind along the shallow margins of the basin, but flow against the wind in the deeper regions. These bottom flows (in opposition to the wind) are strongest in the axial depression and add to the estuarine flow when winds are from the west. The combination of enhanced bottom currents due to both estuarine circulation and the prevailing westerly winds provide an explanation for the relatively coarse sediments found along parts of the axial depression. Climatological simulations of wave-driven bottom currents show that frequent high

A Lagrangian mixing frequency model for transported PDF modeling

NASA Astrophysics Data System (ADS)

Turkeri, Hasret; Zhao, Xinyu

2017-11-01

In this study, a Lagrangian mixing frequency model is proposed for molecular mixing models within the framework of transported probability density function (PDF) methods. The model is based on the dissipations of mixture fraction and progress variables obtained from Lagrangian particles in PDF methods. The new model is proposed as a remedy to the difficulty in choosing the optimal model constant parameters when using conventional mixing frequency models. The model is implemented in combination with the Interaction by exchange with the mean (IEM) mixing model. The performance of the new model is examined by performing simulations of Sandia Flame D and the turbulent premixed flame from the Cambridge stratified flame series. The simulations are performed using the pdfFOAM solver which is a LES/PDF solver developed entirely in OpenFOAM. A 16-species reduced mechanism is used to represent methane/air combustion, and in situ adaptive tabulation is employed to accelerate the finite-rate chemistry calculations. The results are compared with experimental measurements as well as with the results obtained using conventional mixing frequency models. Dynamic mixing frequencies are predicted using the new model without solving additional transport equations, and good agreement with experimental data is observed.

Modeling Fate and Transport of Rotavirus in Surface Flow by Integrating WEPP and a Pathogen Transport Model

NASA Astrophysics Data System (ADS)

Bhattarai, R.; Kalita, P. K.; Davidson, P. C.; Kuhlenschmidt, M. S.

2012-12-01

More than 3.5 million people die each year from a water related diseases in this world. Every 20 seconds, a child dies from a water-related illness. Even in a developed country like the United States, there have been at least 1870 outbreaks associated with drinking water during the period of 1920 to 2002, causing 883,806 illnesses. Most of these outbreaks are resulted due to the presence of microbial pathogens in drinking water. Rotavirus infection has been recognized as the most common cause of diarrhea in young children throughout the world. Laboratory experiments conducted at the University of Illinois have demonstrated that recovery of rotavirus has been significantly affected by climatic and soil-surface conditions like slope, soil types, and ground cover. The objective of this study is to simulate the fate and transport of Rotavirus in overland and near-surface flow using a process-based model. In order to capture the dynamics of sediment-bound pathogens, the Water Erosion Prediction Project (WEPP) is coupled with the pathogen transport model. Transport of pathogens in overland flow can be simulated mathematically by including terms for the concentration of the pathogens in the liquid phase (in suspension or free-floating) and the solid phase (adsorbed to the fine solid particles like clay and silt). Advection, adsorption, and decay processes are considered. The mass balance equations are solved using numerical technique to predict spatial and temporal changes in pathogen concentrations in two phases. Outputs from WEPP simulations (flow velocity, depth, saturated conductivity and the soil particle fraction exiting in flow) are transferred as input for the pathogen transport model. Three soil types and three different surface cover conditions have been used in the experimental investigations. Results from these conditions have been used in calibrating and validating the simulation results. Bare surface conditions have produced very good agreement between

Influence of Transport on Two-Dimensional Model Simulation. Tracer Sensitivity to 2-D Model Transport. 1; Long Lived Tracers

NASA Technical Reports Server (NTRS)

Fleming, Eric L.; Jackman, Charles H.; Considine, David B.; Stolarski, Richard S.

1999-01-01

In this study, we examine the sensitivity of long lived tracers to changes in the base transport components in our 2-D model. Changes to the strength of the residual circulation in the upper troposphere and stratosphere and changes to the lower stratospheric K(sub zz) had similar effects in that increasing the transport rates decreased the overall stratospheric mean age, and increased the rate of removal of material from the stratosphere. Increasing the stratospheric K(sub yy) increased the mean age due to the greater recycling of air parcels through the middle atmosphere, via the residual circulation, before returning to the troposphere. However, increasing K(sub yy) along with self-consistent increases in the corresponding planetary wave drive, which leads to a stronger residual circulation, more than compensates for the K(sub yy)-effect, and produces significantly younger ages throughout the stratosphere. Simulations with very small tropical stratospheric K(sub yy) decreased the globally averaged age of air by as much as 25% in the middle and upper stratosphere, and resulted in substantially weaker vertical age gradients above 20 km in the extratropics. We found only very small stratospheric tracer sensitivity to the magnitude of the horizontal mixing across the tropopause, and to the strength of the mesospheric gravity wave drag and diffusion used in the model. We also investigated the transport influence on chemically active tracers and found a strong age-tracer correlation, both in concentration and calculated lifetimes. The base model transport gives the most favorable overall comparison with a variety of inert tracer observations, and provides a significant improvement over our previous 1995 model transport. Moderate changes to the base transport were found to provide modest agreement with some of the measurements. Transport scenarios with residence times ranging from moderately shorter to slightly longer relative to the base case simulated N2O lifetimes

Vadose Zone Transport Field Study: Summary Report

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

Ward, Andy L.; Conrad, Mark E.; Daily, William D.

2006-07-31

From FY 2000 through FY 2003, a series of vadose zone transport field experiments were conducted as part of the U.S. Department of Energy’s Groundwater/Vadose Zone Integration Project Science and Technology Project, now known as the Remediation and Closure Science Project, and managed by the Pacific Northwest National Laboratory (PNNL). The series of experiments included two major field campaigns, one at a 299-E24-11 injection test site near PUREX and a second at a clastic dike site off Army Loop Road. The goals of these experiments were to improve our understanding of vadose zone transport processes; to develop data sets tomore » validate and calibrate vadose zone flow and transport models; and to identify advanced monitoring techniques useful for evaluating flow-and-transport mechanisms and delineating contaminant plumes in the vadose zone at the Hanford Site. This report summarizes the key findings from the field studies and demonstrates how data collected from these studies are being used to improve conceptual models and develop numerical models of flow and transport in Hanford’s vadose zone. Results of these tests have led to a better understanding of the vadose zone. Fine-scale geologic heterogeneities, including grain fabric and lamination, were observed to have a strong effect on the large-scale behavior of contaminant plumes, primarily through increased lateral spreading resulting from anisotropy. Conceptual models have been updated to include lateral spreading and numerical models of unsaturated flow and transport have revised accordingly. A new robust model based on the concept of a connectivity tensor was developed to describe saturation-dependent anisotropy in strongly heterogeneous soils and has been incorporated into PNNL’s Subsurface Transport Over Multiple Phases (STOMP) simulator. Application to field-scale transport problems have led to a better understanding plume behavior at a number of sites where lateral spreading may have dominated

Polycyclic aromatic hydrocarbons - fate and long-range atmospheric transport studied using a global model, EMAC-SVOC

NASA Astrophysics Data System (ADS)

Octaviani, Mega; Tost, Holger; Lammel, Gerhard

2017-04-01

Polycyclic aromatic hydrocarbons (PAHs) are emitted by incomplete combustion from fossil fuel, vehicles, and biomass burning. They may persist in environmental compartments, pose a health hazard and may bio accumulate along food chains. The ECHAM/MESSy Atmospheric Chemistry (EMAC) model had been used to simulate global tropospheric, stratospheric chemistry and climate. In this study, we improve the model to include simulations of the transport and fate of semi-volatile organic compounds (SVOC). The EMAC-SVOC model takes into account essential environmental processes including gas-particle partitioning, dry and wet deposition, chemical and bio-degradation, and volatilization from sea surface, soils, vegetation, and snow. The model was evaluated against observational data in the Arctic, mid-latitudes, and tropics, and further applied to study total environmental lifetime and long-range transport potential (LRTP) of PAHs. We selected four compounds for study, spanning a wide range of volatility, i.e., phenanthrene, fluoranthene, pyrene, and benzo[a]pyrene. Several LRTP indicators were investigated, including the Arctic contamination potential, meridional spreading, and zonal and meridional fluxes to remote regions.

Hybrid transport and diffusion modeling using electron thermal transport Monte Carlo SNB in DRACO

NASA Astrophysics Data System (ADS)

Chenhall, Jeffrey; Moses, Gregory

2017-10-01

The iSNB (implicit Schurtz Nicolai Busquet) multigroup diffusion electron thermal transport method is adapted into an Electron Thermal Transport Monte Carlo (ETTMC) transport method to better model angular and long mean free path non-local effects. Previously, the ETTMC model had been implemented in the 2D DRACO multiphysics code and found to produce consistent results with the iSNB method. Current work is focused on a hybridization of the computationally slower but higher fidelity ETTMC transport method with the computationally faster iSNB diffusion method in order to maximize computational efficiency. Furthermore, effects on the energy distribution of the heat flux divergence are studied. Work to date on the hybrid method will be presented. This work was supported by Sandia National Laboratories and the Univ. of Rochester Laboratory for Laser Energetics.

Understanding Transportation Systems : An Integrated Approach to Modeling Complex Transportation Systems

DOT National Transportation Integrated Search

2013-01-01

The ability to model and understand the complex dynamics of intelligent agents as they interact within a transportation system could lead to revolutionary advances in transportation engineering and intermodal surface transportation in the United Stat...

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

NASA Astrophysics Data System (ADS)

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

2005-12-01

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

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.

[Study on transport mechanism of baicalin in Scutellariae radix extracts and effect of Angelica dahurica extracts on transport of baicalin by Caco-2 cell monolayer model].

PubMed

Liang, Xin-Li; Zhu, Meng-Liang; Zhao, Li-Jun; Zhao, Guo-Wei; Liao, Zheng-Gen; Cao, Yun-Chao; Yang, Ming

2013-07-01

To study the transport mechanism of baicalin of Scutellariae Radix extracts and the effect of Angelica dahurica extracts on the intestinal absorption of baicalin by using Caco-2 cell monolayer model, in order to analyze the effect mechanism of Angelica dahurica extracts on the intestinal absorption of baicalin. The Caco-2 cell monolayer model was established with human colonic adenocarcinoma cells, and used to study the effect of pH, time, drug concentration and temperature on the transport of baicalin in Scutellariae Radix extracts, the effect of P-gp and MRP protein-dedicated inhibitors on the bidirectional transport of baicalin in Caco-2 cell model, and the effect of angelica root extracts on baicalin absorption and transport. Baicalin was absorbed well at 37 degrees C and under pH 7.4 condition and concentration dependent. Its proteins became inactive at 4 degrees C, with a low transport. The bi-drectional transfer PDR was 0. 54. After P-gp inhibitor verapamil and MRP inhibitor probenecid were added, the value of PappBL-AP of baicalin decreased, but without any difference in PDR. The transport of baicalin was improved by 2.34, 3.31 and 3.13 times, after A. dahurica extract coumarin, volatile oil, and mixture of coumarin and volatile oil. The transport mechanism of baicalin is mainly passive transfer and supplemented with efflux proteins involved. A. dahurica extracts can enhance the absorption of baicalin, which may be related to the passive transfer merchanism of baicalin. A. dahurica extracts' effect in opening the close junction among cells may be related to its expression or function in inhibiting efflux proteins.

Evaluation of unsaturated-zone solute-transport models for studies of agricultural chemicals

USGS Publications Warehouse

Nolan, Bernard T.; Bayless, E. Randall; Green, Christopher T.; Garg, Sheena; Voss, Frank D.; Lampe, David C.; Barbash, Jack E.; Capel, Paul D.; Bekins, Barbara A.

2005-01-01

Of the models tested, RZWQM, HYDRUS2D, VS2DT, GLEAMS and PRZM had graphical user interfaces. Extensive documentation was available for RZWQM, HYDRUS2D, and VS2DT. RZWQM can explicitly simulate water and solute flux in macropores, and both HYDRUS2D and VS2DT can simulate water and solute flux in two dimensions. The version of RZWQM tested had a maximum simulation depth of 3 meters. The complex models simulate the formation, transport, and fate of degradates of up to three to five compounds including the parent, with the exception of VS2DT, which simulates the transport and fate of a single compound.

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.

Glucose Transport into Everted Sacks of Intestine of Mice: A Model for the Study of Active Transport.

ERIC Educational Resources Information Center

Deyrup-Olsen, Ingrith; Linder, Alison R.

1979-01-01

Described is a laboratory procedure which uses the small intestines of mice as models for the transport of glucose and other solutes. Demonstrations are suitable for either introductory or advanced physiology courses. (RE)

Application of rrm as behavior mode choice on modelling transportation

NASA Astrophysics Data System (ADS)

Surbakti, M. S.; Sadullah, A. F.

2018-03-01

Transportation mode selection, the first step in transportation planning process, is probably one of the most important planning elements. The development of models that can explain the preference of passengers regarding their chosen mode of public transport option will contribute to the improvement and development of existing public transport. Logit models have been widely used to determine the mode choice models in which the alternative are different transport modes. Random Regret Minimization (RRM) theory is a theory developed from the behavior to choose (choice behavior) in a state of uncertainty. During its development, the theory was used in various disciplines, such as marketing, micro economy, psychology, management, and transportation. This article aims to show the use of RRM in various modes of selection, from the results of various studies that have been conducted both in north sumatera and western Java.

A bilayer model for bedload sediment transport as generalization of Exner models

NASA Astrophysics Data System (ADS)

Escalante, Cipriano; Fernandez-Nieto, Enrique; Morales de Luna, Tomas; Narbona Reina, Gladys

2017-04-01

Sediment can be transported in several ways by the action of a river. During low transport stages, particles move by sliding and rolling over the surface of the bed. This type of transport is usually called bedload transport. The usual approach to model these phenomena is to use the Saint-Venant-Exner model (SVE) which consists in a shallow water model coupled with a morphodynamical component for the bedload transport. The bedload transport depends on an empirical flux. Nevertheless, this approach presents some drawbacks, for instance, gravitational effects for bedload transport is neglected and the momentum equation for the sediment is missing. In this work we present a two-layer shallow water type model in order to better describe bedload transport. We consider an upper layer consisting in clear water and a lower layer which accounts for the sediment material. This allows to better describe the phenomena. The key point is the definition of the friction laws between the two layers. The model is a generalization of classic models as it allows to recover SVE system when the ratio between the hydrodynamic and morphodynamic time scales is small, as commonly done to derive SVE models.

Functional Characterization Of Peptide Transporters In MDCKII -MDR1 Cell line As A Model For Oral Absorption Studies

PubMed Central

Agarwal, Sheetal; Jain, Ritesh; Pal, Dhananjay; K.Mitra, Ashim

2007-01-01

MDCKII-MDR1 cell line has been extensively selected as a model to study P-gp-mediated drug efflux. Recently, investigators have employed this cell line for studying influx of peptide prodrug derivatives of parent compounds which are P-gp substrates. Therefore, the objective of this study is to functionally characterize the peptide mediated uptake and transport of [3H] Glycylsarcosine ([3H] Gly-Sar), a model peptide substrate across MDCKII-MDR1 cells. [3H] Gly-Sar uptake from apical (AP) and basolateral (BL) membranes was found to be time dependent and saturable. Michaelis-Menten (Km) constants of [3H] Gly-Sar uptake across the AP and BL directions in MDCKII-MDR1 cell line were found to be 457 ± 37 μM and 464 ± 85 μM respectively. Vmax values in AP and BL directions for the peptide transporters in MDCKII-MDR1 cell line were calculated to be 0.035 ± 0.001 and 0.35 ± 0.034 pmol/min/mg protein respectively. Uptake of [3H] Gly-Sar was significantly inhibited in the presence of aminocephalosporins and ACE-Inhibitors, known substrates for peptide transporters in both the AP and BL directions. Permeability of [3H] Gly-Sar in the BL direction was maximal at pH 4 as compared to pH 5, 6 and 7.4 whereas such permeability in the AP direction was optimal at pH 7.4. Transepithelial transport of [3H] Gly-Sar in the AP-BL direction was significantly lower than from BL-AP direction at all observed pHs. No statistical difference was observed in the transepithelial permeability of [3H] Gly-Sar across both AP and BL directions over 4–10 days of growth period. The present study indicates that peptide transporters are effectively involved in the bidirectional transport of Gly-Sar across MDCKII-MDR1 cell line; the BL peptide transporter can transport Gly-Sar at a greater rate as compared to the AP peptide transporter. Results from these studies suggest the application of MDCKII-MDR1 cell line as a rapid effective tool to study peptide mediated influx of compounds that may be

Assessment of parametric uncertainty for groundwater reactive transport modeling,

USGS Publications Warehouse

Shi, Xiaoqing; Ye, Ming; Curtis, Gary P.; Miller, Geoffery L.; Meyer, Philip D.; Kohler, Matthias; Yabusaki, Steve; Wu, Jichun

2014-01-01

The validity of using Gaussian assumptions for model residuals in uncertainty quantification of a groundwater reactive transport model was evaluated in this study. Least squares regression methods explicitly assume Gaussian residuals, and the assumption leads to Gaussian likelihood functions, model parameters, and model predictions. While the Bayesian methods do not explicitly require the Gaussian assumption, Gaussian residuals are widely used. This paper shows that the residuals of the reactive transport model are non-Gaussian, heteroscedastic, and correlated in time; characterizing them requires using a generalized likelihood function such as the formal generalized likelihood function developed by Schoups and Vrugt (2010). For the surface complexation model considered in this study for simulating uranium reactive transport in groundwater, parametric uncertainty is quantified using the least squares regression methods and Bayesian methods with both Gaussian and formal generalized likelihood functions. While the least squares methods and Bayesian methods with Gaussian likelihood function produce similar Gaussian parameter distributions, the parameter distributions of Bayesian uncertainty quantification using the formal generalized likelihood function are non-Gaussian. In addition, predictive performance of formal generalized likelihood function is superior to that of least squares regression and Bayesian methods with Gaussian likelihood function. The Bayesian uncertainty quantification is conducted using the differential evolution adaptive metropolis (DREAM(zs)) algorithm; as a Markov chain Monte Carlo (MCMC) method, it is a robust tool for quantifying uncertainty in groundwater reactive transport models. For the surface complexation model, the regression-based local sensitivity analysis and Morris- and DREAM(ZS)-based global sensitivity analysis yield almost identical ranking of parameter importance. The uncertainty analysis may help select appropriate likelihood

Modelling the optical properties of aerosols in a chemical transport model

NASA Astrophysics Data System (ADS)

Andersson, E.; Kahnert, M.

2015-12-01

According to the IPCC fifth assessment report (2013), clouds and aerosols still contribute to the largest uncertainty when estimating and interpreting changes to the Earth's energy budget. Therefore, understanding the interaction between radiation and aerosols is both crucial for remote sensing observations and modelling the climate forcing arising from aerosols. Carbon particles are the largest contributor to the aerosol absorption of solar radiation, thereby enhancing the warming of the planet. Modelling the radiative properties of carbon particles is a hard task and involves many uncertainties arising from the difficulties of accounting for the morphologies and heterogeneous chemical composition of the particles. This study aims to compare two ways of modelling the optical properties of aerosols simulated by a chemical transport model. The first method models particle optical properties as homogeneous spheres and are externally mixed. This is a simple model that is particularly easy to use in data assimilation methods, since the optics model is linear. The second method involves a core-shell internal mixture of soot, where sulphate, nitrate, ammonia, organic carbon, sea salt, and water are contained in the shell. However, by contrast to previously used core-shell models, only part of the carbon is concentrated in the core, while the remaining part is homogeneously mixed with the shell. The chemical transport model (CTM) simulations are done regionally over Europe with the Multiple-scale Atmospheric Transport and CHemistry (MATCH) model, developed by the Swedish Meteorological and Hydrological Institute (SMHI). The MATCH model was run with both an aerosol dynamics module, called SALSA, and with a regular "bulk" approach, i.e., a mass transport model without aerosol dynamics. Two events from 2007 are used in the analysis, one with high (22/12-2007) and one with low (22/6-2007) levels of elemental carbon (EC) over Europe. The results of the study help to assess the

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...

Collisional transport across the magnetic field in drift-fluid models

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

Madsen, J., E-mail: jmad@fysik.dtu.dk; Naulin, V.; Nielsen, A. H.

2016-03-15

Drift ordered fluid models are widely applied in studies of low-frequency turbulence in the edge and scrape-off layer regions of magnetically confined plasmas. Here, we show how collisional transport across the magnetic field is self-consistently incorporated into drift-fluid models without altering the drift-fluid energy integral. We demonstrate that the inclusion of collisional transport in drift-fluid models gives rise to diffusion of particle density, momentum, and pressures in drift-fluid turbulence models and, thereby, obviates the customary use of artificial diffusion in turbulence simulations. We further derive a computationally efficient, two-dimensional model, which can be time integrated for several turbulence de-correlation timesmore » using only limited computational resources. The model describes interchange turbulence in a two-dimensional plane perpendicular to the magnetic field located at the outboard midplane of a tokamak. The model domain has two regions modeling open and closed field lines. The model employs a computational expedient model for collisional transport. Numerical simulations show good agreement between the full and the simplified model for collisional transport.« less

Macroscopic Modeling of In Vivo Drug Transport in Electroporated Tissue.

PubMed

Boyd, Bradley; Becker, Sid

2016-03-01

This study develops a macroscopic model of mass transport in electroporated biological tissue in order to predict the cellular drug uptake. The change in the macroscopic mass transport coefficient is related to the increase in electrical conductivity resulting from the applied electric field. Additionally, the model considers the influences of both irreversible electroporation (IRE) and the transient resealing of the cell membrane associated with reversible electroporation. Two case studies are conducted to illustrate the applicability of this model by comparing transport associated with two electrode arrangements: side-by-side arrangement and the clamp arrangement. The results show increased drug transmission to viable cells is possible using the clamp arrangement due to the more uniform electric field.

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.;

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.

Coupling between geochemical reactions and multicomponent gas and solute transport in unsaturated media: A reactive transport modeling study

USGS Publications Warehouse

Molins, S.; Mayer, K.U.

2007-01-01

The two‐way coupling that exists between biogeochemical reactions and vadose zone transport processes, in particular gas phase transport, determines the composition of soil gas. To explore these feedback processes quantitatively, multicomponent gas diffusion and advection are implemented into an existing reactive transport model that includes a full suite of geochemical reactions. Multicomponent gas diffusion is described on the basis of the dusty gas model, which accounts for all relevant gas diffusion mechanisms. The simulation of gas attenuation in partially saturated landfill soil covers, methane production, and oxidation in aquifers contaminated by organic compounds (e.g., an oil spill site) and pyrite oxidation in mine tailings demonstrate that both diffusive and advective gas transport can be affected by geochemical reactions. Methane oxidation in landfill covers reduces the existing upward pressure gradient, thereby decreasing the contribution of advective methane emissions to the atmosphere and enhancing the net flux of atmospheric oxygen into the soil column. At an oil spill site, methane oxidation causes a reversal in the direction of gas advection, which results in advective transport toward the zone of oxidation both from the ground surface and the deeper zone of methane production. Both diffusion and advection contribute to supply atmospheric oxygen into the subsurface, and methane emissions to the atmosphere are averted. During pyrite oxidation in mine tailings, pressure reduction in the reaction zone drives advective gas flow into the sediment column, enhancing the oxidation process. In carbonate‐rich mine tailings, calcite dissolution releases carbon dioxide, which partly offsets the pressure reduction caused by O2 consumption.

Computational modeling of ion transport through nanopores.

PubMed

Modi, Niraj; Winterhalter, Mathias; Kleinekathöfer, Ulrich

2012-10-21

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

Sensitivity of chemical transport model simulations to the duration of chemical and transport operators: a case study with GEOS-Chem v10-01

NASA Astrophysics Data System (ADS)

Philip, S.; Martin, R. V.; Keller, C. A.

2015-11-01

Chemical transport models involve considerable computational expense. Fine temporal resolution offers accuracy at the expense of computation time. Assessment is needed of the sensitivity of simulation accuracy to the duration of chemical and transport operators. We conduct a series of simulations with the GEOS-Chem chemical transport model at different temporal and spatial resolutions to examine the sensitivity of simulated atmospheric composition to temporal resolution. Subsequently, we compare the tracers simulated with operator durations from 10 to 60 min as typically used by global chemical transport models, and identify the timesteps that optimize both computational expense and simulation accuracy. We found that longer transport timesteps increase concentrations of emitted species such as nitrogen oxides and carbon monoxide since a more homogeneous distribution reduces loss through chemical reactions and dry deposition. The increased concentrations of ozone precursors increase ozone production at longer transport timesteps. Longer chemical timesteps decrease sulfate and ammonium but increase nitrate due to feedbacks with in-cloud sulfur dioxide oxidation and aerosol thermodynamics. The simulation duration decreases by an order of magnitude from fine (5 min) to coarse (60 min) temporal resolution. We assess the change in simulation accuracy with resolution by comparing the root mean square difference in ground-level concentrations of nitrogen oxides, ozone, carbon monoxide and secondary inorganic aerosols with a finer temporal or spatial resolution taken as truth. Simulation error for these species increases by more than a factor of 5 from the shortest (5 min) to longest (60 min) temporal resolution. Chemical timesteps twice that of the transport timestep offer more simulation accuracy per unit computation. However, simulation error from coarser spatial resolution generally exceeds that from longer timesteps; e.g. degrading from 2° × 2.5° to 4° × 5�

A Mercury Model of Atmospheric Transport

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

Christensen, Alex B.; Chodash, Perry A.; Procassini, R. J.

Using the particle transport code Mercury, accurate models were built of the two sources used in Operation BREN, a series of radiation experiments performed by the United States during the 1960s. In the future, these models will be used to validate Mercury’s ability to simulate atmospheric transport.

A batch adsorption study on bentonite clay Pertinence to transport modeling?

NASA Astrophysics Data System (ADS)

BOURG, I.; BOURG, A. C.; SPOSITO, G.

2001-12-01

Bentonite clay is often used as a component of engineered barriers for the isolation of high-level toxic wastes. This swelling clay is used for its physical (impermeability, self-healing) but also for its chemical properties, mostly a high cation exchange capacity (CEC). The adsorbed cations being temporarily immobilized, this should slow down the release of cations from the waste to the surrounding environment. In order to assess the performance of the engineered barrier, the partitioning of solutes between the liquid and solid phases needs to be quantified for use in transport models. The usual method for characterizing the adsorption is through batch adsorption experiments on dispersed suspensions of the solid, yielding an adsorption isotherm (adsorbed concentration vs. dissolved concentration). This isotherm however should be a function of various environmental variables (e.g., pH, ionic strength, concentrations of various ligands and competing adsorbents), so that extrapolation of lab data to performance assessment in the field is problematic. We present results from a study of the adsorption of cesium, strontium, cadmium and lead on dispersed suspensions of the standard BX-80 bentonite. Through a wide range of experimental parameters (pH, ionic strength, reaction time, reactor open or closed to the atmosphere, study of a range of cations of differing properties), we seek a mechanistic interpretation of the results instead of an empirical determination of adsorption parameters. Depending on the mechanisms that control the adsorption in different experimental ranges, we discuss the degree to which the partitioning coefficient (Kd) obtained in the lab can be extrapolated to a transport model through compacted bentonite in a natural environment.

Erosion and Sediment Transport Modelling in Shallow Waters: A Review on Approaches, Models and Applications.

PubMed

Hajigholizadeh, Mohammad; Melesse, Assefa M; Fuentes, Hector R

2018-03-14

The erosion and sediment transport processes in shallow waters, which are discussed in this paper, begin when water droplets hit the soil surface. The transport mechanism caused by the consequent rainfall-runoff process determines the amount of generated sediment that can be transferred downslope. Many significant studies and models are performed to investigate these processes, which differ in terms of their effecting factors, approaches, inputs and outputs, model structure and the manner that these processes represent. This paper attempts to review the related literature concerning sediment transport modelling in shallow waters. A classification based on the representational processes of the soil erosion and sediment transport models (empirical, conceptual, physical and hybrid) is adopted, and the commonly-used models and their characteristics are listed. This review is expected to be of interest to researchers and soil and water conservation managers who are working on erosion and sediment transport phenomena in shallow waters. The paper format should be helpful for practitioners to identify and generally characterize the types of available models, their strengths and their basic scope of applicability.

Erosion and Sediment Transport Modelling in Shallow Waters: A Review on Approaches, Models and Applications

PubMed Central

Fuentes, Hector R.

2018-01-01

The erosion and sediment transport processes in shallow waters, which are discussed in this paper, begin when water droplets hit the soil surface. The transport mechanism caused by the consequent rainfall-runoff process determines the amount of generated sediment that can be transferred downslope. Many significant studies and models are performed to investigate these processes, which differ in terms of their effecting factors, approaches, inputs and outputs, model structure and the manner that these processes represent. This paper attempts to review the related literature concerning sediment transport modelling in shallow waters. A classification based on the representational processes of the soil erosion and sediment transport models (empirical, conceptual, physical and hybrid) is adopted, and the commonly-used models and their characteristics are listed. This review is expected to be of interest to researchers and soil and water conservation managers who are working on erosion and sediment transport phenomena in shallow waters. The paper format should be helpful for practitioners to identify and generally characterize the types of available models, their strengths and their basic scope of applicability. PMID:29538335

Sediment transport and deposition on a river-dominated tidal flat: An idealized model study

USGS Publications Warehouse

Sherwood, Christopher R.; Chen, Shih-Nan; Geyer, W. Rockwell; Ralston, David K.

2010-01-01

A 3-D hydrodynamic model is used to investigate how different size classes of river-derived sediment are transported, exported and trapped on an idealized, river-dominated tidal flat. The model is composed of a river channel flanked by sloping tidal flats, a configuration motivated by the intertidal region of the Skagit River mouth in Washington State, United States. It is forced by mixed tides and a pulse of freshwater and sediment with various settling velocities. In this system, the river not only influences stratification but also contributes a significant cross-shore transport. As a result, the bottom stress is strongly ebb-dominated in the channel because of the seaward advance of strong river flow as the tidal flats drain during ebbs. Sediment deposition patterns and mass budgets are sensitive to settling velocity. The lateral sediment spreading scales with an advective distance (settling time multiplied by lateral flow speed), thereby confining the fast settling sediment classes in the channel. Residual sediment transport is landward on the flats, because of settling lag, but is strongly seaward in the channel. The seaward transport mainly occurs during big ebbs and is controlled by a length scale ratio Ld/XWL, where Ld is a cross-shore advective distance (settling time multiplied by river outlet velocity), and XWL is the immersed cross-shore length of the intertidal zone. Sediment trapping requires Ld/XWL < 1, leading to more trapping for the faster settling classes. Sensitivity studies show that including stratification and reducing tidal range both favor sediment trapping, whereas varying channel geometries and asymmetry of tides has relatively small impacts. Implications of the modeling results on the south Skagit intertidal region are discussed.

Colloid transport in model fracture filling materials

NASA Astrophysics Data System (ADS)

Wold, S.; Garcia-Garcia, S.; Jonsson, M.

2010-12-01

Colloid transport in model fracture filling materials Susanna Wold*, Sandra García-García and Mats Jonsson KTH Chemical Science and Engineering Royal Institute of Technology, SE-100 44 Stockholm, Sweden *Corresponding author: E-mail: wold@kth.se Phone: +46 8 790 6295 In colloid transport in water-bearing fractures, the retardation depends on interactions with the fracture surface by sorption or filtration. These mechanisms are difficult to separate. A rougher surface will give a larger area available for sorption, and also when a particle is physically hindered, it approaches the surface and enables further sorption. Sorption can be explained by electrostatics were the strongest sorption on minerals always is observed at pH below pHpzc (Filby et al., 2008). The adhesion of colloids to mineral surfaces is related to the surface roughness according to a recent study (Darbha et al., 2010). There is a large variation in the characteristics of water-bearing fractures in bedrock in terms of aperture distribution, flow velocity, surface roughness, mineral distributions, presence of fracture filling material, and biological and organic material, which is hard to implement in modeling. The aim of this work was to study the transport of negatively charged colloids in model fracture filling material in relation to flow, porosity, mineral type, colloid size, and surface charge distribution. In addition, the impact on transport of colloids of mixing model fracture filling materials with different retention and immobilization capacities, determined by batch sorption experiments, was investigated. The transport of Na-montmorillonite colloids and well-defined negatively charged latex microspheres of 50, 100, and 200 nm diameter were studied in either columns containing quartz or quartz mixed with biotite. The ionic strength in the solution was exclusively 0.001 and pH 6 or 8.5. The flow rates used were 0.002, 0.03, and 0.6 mL min-1. Sorption of the colloids on the model fracture

A comprehensive one-dimensional numerical model for solute transport in rivers

NASA Astrophysics Data System (ADS)

Barati Moghaddam, Maryam; Mazaheri, Mehdi; MohammadVali Samani, Jamal

2017-01-01

One of the mechanisms that greatly affect the pollutant transport in rivers, especially in mountain streams, is the effect of transient storage zones. The main effect of these zones is to retain pollutants temporarily and then release them gradually. Transient storage zones indirectly influence all phenomena related to mass transport in rivers. This paper presents the TOASTS (third-order accuracy simulation of transient storage) model to simulate 1-D pollutant transport in rivers with irregular cross-sections under unsteady flow and transient storage zones. The proposed model was verified versus some analytical solutions and a 2-D hydrodynamic model. In addition, in order to demonstrate the model applicability, two hypothetical examples were designed and four sets of well-established frequently cited tracer study data were used. These cases cover different processes governing transport, cross-section types and flow regimes. The results of the TOASTS model, in comparison with two common contaminant transport models, shows better accuracy and numerical stability.

Community Sediment Transport Model

DTIC Science & Technology

2007-01-01

Woods Hole, MA 02543-1598 Phone: (508) 457-2269 Fax: (508) 457-2310 email: csherwood@usgs.gov Timothy Keen Naval Research Laboratory, Code...intended to be used as both a research tool and for practical applications. An accurate and useful model will require coupling sediment-transport with...and time steps range from seconds to minutes. We include higher-resolution sediment- transport calculation modules for research problems but, for

Development of the Transport Class Model (TCM) Aircraft Simulation From a Sub-Scale Generic Transport Model (GTM) Simulation

NASA Technical Reports Server (NTRS)

Hueschen, Richard M.

2011-01-01

A six degree-of-freedom, flat-earth dynamics, non-linear, and non-proprietary aircraft simulation was developed that is representative of a generic mid-sized twin-jet transport aircraft. The simulation was developed from a non-proprietary, publicly available, subscale twin-jet transport aircraft simulation using scaling relationships and a modified aerodynamic database. The simulation has an extended aerodynamics database with aero data outside the normal transport-operating envelope (large angle-of-attack and sideslip values). The simulation has representative transport aircraft surface actuator models with variable rate-limits and generally fixed position limits. The simulation contains a generic 40,000 lb sea level thrust engine model. The engine model is a first order dynamic model with a variable time constant that changes according to simulation conditions. The simulation provides a means for interfacing a flight control system to use the simulation sensor variables and to command the surface actuators and throttle position of the engine model.

Equilibrium, kinetic, and reactive transport models for plutonium

NASA Astrophysics Data System (ADS)

Schwantes, Jon Michael

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

Experimental study of UTM-LST generic half model transport aircraft

NASA Astrophysics Data System (ADS)

Ujang, M. I.; Mat, S.; Perumal, K.; Mohd. Nasir, M. N.

2016-10-01

This paper presents the experimental results from the investigation carried out at the UTM Low Speed wind tunnel facility (UTM-LST) on a half model generic transport aircraft at several configurations of primary control surfaces (flap, aileron and elevator). The objective is to measure the aerodynamic forces and moments due to the configuration changes. The study is carried out at two different speeds of 26.1 m/s and 43.1 m/s at corresponding Reynolds number of 1 × 106 and 2 × 106, respectively. Angle of attack of the model is varied between -2o to 20o. For the flaps, the deflection applied is 0o, 5o and 10o. Meanwhile, for aileron and elevator, the deflection applied is between -10o and 10o. The results show the differences in aerodynamic characteristics of the aircraft at different control surfaces configurations. The results obtained indicate that a laminar separation bubble developed on the surface of the wing at lower angles of attack and show that the separation process is delayed when the Reynolds number is increased.

Animal models for studying transport across the blood-brain barrier.

PubMed

Bonate, P L

1995-01-01

There are many reasons for wishing to determine the rate of uptake of a drug from blood into brain parenchyma. However, when faced with doing so for the first time, choosing a method can be a formidable task. There are at least 7 methods from which to choose: indicator dilution, brain uptake index, microdialysis, external registration, PET scanning, in situ perfusion, and compartmental modeling. Each method has advantages and disadvantages. Some methods require very little equipment while others require equipment that can cost millions of dollars. Some methods require very little technical experience whereas others require complex surgical manipulation. The mathematics alone for the various methods range from simple algebra to complex integral calculus and differential equations. Like most things in science, as the complexity of the technique increases, so does the quantity of information it provides. This review is meant to serve as a starting point for the researcher who wishes to study transport and uptake across the blood-brain barrier in animal models. An overview of the mathematical theory, as well as an introduction to the techniques, is presented.

Freight Transportation Energy Use : Appendix. Transportation Network Model Output.

DOT National Transportation Integrated Search

1978-07-01

The overall design of the TSC Freight Energy Model is presented. A hierarchical modeling strategy is used, in which detailed modal simulators estimate the performance characteristics of transportation network elements, and the estimates are input to ...

Applying Simulation and Logistics Modeling to Transportation Issues

DOT National Transportation Integrated Search

1995-08-15

This paper describes an application where transportation logistics and simulation tools are integrated to create a modeling environment for transportation planning. The Transportation Planning Model (TPM) is a tool developed for the Department of Ene...

Modeling of active transmembrane transport in a mixture theory framework.

PubMed

Ateshian, Gerard A; Morrison, Barclay; Hung, Clark T

2010-05-01

This study formulates governing equations for active transport across semi-permeable membranes within the framework of the theory of mixtures. In mixture theory, which models the interactions of any number of fluid and solid constituents, a supply term appears in the conservation of linear momentum to describe momentum exchanges among the constituents. In past applications, this momentum supply was used to model frictional interactions only, thereby describing passive transport processes. In this study, it is shown that active transport processes, which impart momentum to solutes or solvent, may also be incorporated in this term. By projecting the equation of conservation of linear momentum along the normal to the membrane, a jump condition is formulated for the mechano-electrochemical potential of fluid constituents which is generally applicable to nonequilibrium processes involving active transport. The resulting relations are simple and easy to use, and address an important need in the membrane transport literature.

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...

Modeling firebrand transport in wildfires using HIGRAD/FIRETEC

Treesearch

Eunmo Koo; Rodman R. Linn; Patrick J. Pagni; Carleton B. Edminster

2012-01-01

Firebrand transport is studied for disc and cylindrical firebrands by modelling their trajectories with a coupled-physics fire model, HIGRAD/FIRETEC. Through HIGRAD/FIRETEC simulations, the size of possible firebrands and travelled distances are analysed to assess spot ignition hazard. Trajectories modelled with and without the assumption that the firebrands'...

Integrating wildfire plume rises within atmospheric transport models

NASA Astrophysics Data System (ADS)

Mallia, D. V.; Kochanski, A.; Wu, D.; Urbanski, S. P.; Krueger, S. K.; Lin, J. C.

2016-12-01

Wildfires can generate significant pyro-convection that is responsible for releasing pollutants, greenhouse gases, and trace species into the free troposphere, which are then transported a significant distance downwind from the fire. Oftentimes, atmospheric transport and chemistry models have a difficult time resolving the transport of smoke from these wildfires, primarily due to deficiencies in estimating the plume injection height, which has been highlighted in previous work as the most important aspect of simulating wildfire plume transport. As a result of the uncertainties associated with modeled wildfire plume rise, researchers face difficulties modeling the impacts of wildfire smoke on air quality and constraining fire emissions using inverse modeling techniques. Currently, several plume rise parameterizations exist that are able to determine the injection height of fire emissions; however, the success of these parameterizations has been mixed. With the advent of WRF-SFIRE, the wildfire plume rise and injection height can now be explicitly calculated using a fire spread model (SFIRE) that is dynamically linked with the atmosphere simulated by WRF. However, this model has only been tested on a limited basis due to computational costs. Here, we will test the performance of WRF-SFIRE in addition to several commonly adopted plume parameterizations (Freitas, Sofiev, and Briggs) for the 2013 Patch Springs (Utah) and 2012 Baker Canyon (Washington) fires, for both of which observations of plume rise heights are available. These plume rise techniques will then be incorporated within a Lagrangian atmospheric transport model (STILT) in order to simulate CO and CO2 concentrations during NASA's CARVE Earth Science Airborne Program over Alaska during the summer of 2012. Initial model results showed that STILT model simulations were unable to reproduce enhanced CO concentrations produced by Alaskan fires observed during 2012. Near-surface concentrations were drastically

Lab-on-a-brane: A novel physiologically relevant planar arterial model to study transendothelial transport

NASA Astrophysics Data System (ADS)

Budhwani, Karim Ismail

The tremendous quality of life impact notwithstanding, cardiovascular diseases and Cancer add up to over US$ 700bn each year in financial costs alone. Aging and population growth are expected to further expand the problem space while drug research and development remain expensive. However, preclinical costs can be substantially mitigated by substituting animal models with in vitro devices that accurately model human cardiovascular transport. Here we present a novel physiologically relevant lab-on-a-brane that simulates in vivo pressure, flow, strain, and shear waveforms associated with normal and pathological conditions in large and small blood vessels for studying molecular transport across the endothelial monolayer. The device builds upon previously demonstrated integrated microfluidic loop design by: (a) introducing nanoscale pores in the substrate membrane to enable transmembrane molecular transport, (b) transforming the substrate membrane into a nanofibrous matrix for 3D smooth muscle cell (SMC) tissue culture, (c) integrating electrospinning fabrication methods, (d) engineering an invertible sandwich cell culture device architecture, and (e) devising a healthy co-culture mechanism for human arterial endothelial cell (HAEC) monolayer and multiple layers of human smooth muscle cells (HSMC) to accurately mimic arterial anatomy. Structural and mechanical characterization was conducted using confocal microscopy, SEM, stress/strain analysis, and infrared spectroscopy. Transport was characterized using FITC-Dextran hydraulic permeability protocol. Structure and transport characterization successfully demonstrate device viability as a physiologically relevant arterial mimic for testing transendothelial transport. Thus, our lab-on-a-brane provides a highly effective and efficient, yet considerably inexpensive, physiologically relevant alternative for pharmacokinetic evaluation; possibly reducing animals used in pre-clinical testing, clinical trials cost from false

A Comparative Study of Spectral Auroral Intensity Predictions From Multiple Electron Transport Models

NASA Astrophysics Data System (ADS)

Grubbs, Guy; Michell, Robert; Samara, Marilia; Hampton, Donald; Hecht, James; Solomon, Stanley; Jahn, Jorg-Micha

2018-01-01

It is important to routinely examine and update models used to predict auroral emissions resulting from precipitating electrons in Earth's magnetotail. These models are commonly used to invert spectral auroral ground-based images to infer characteristics about incident electron populations when in situ measurements are unavailable. In this work, we examine and compare auroral emission intensities predicted by three commonly used electron transport models using varying electron population characteristics. We then compare model predictions to same-volume in situ electron measurements and ground-based imaging to qualitatively examine modeling prediction error. Initial comparisons showed differences in predictions by the GLobal airglOW (GLOW) model and the other transport models examined. Chemical reaction rates and radiative rates in GLOW were updated using recent publications, and predictions showed better agreement with the other models and the same-volume data, stressing that these rates are important to consider when modeling auroral processes. Predictions by each model exhibit similar behavior for varying atmospheric constants, energies, and energy fluxes. Same-volume electron data and images are highly correlated with predictions by each model, showing that these models can be used to accurately derive electron characteristics and ionospheric parameters based solely on multispectral optical imaging data.

Transportation Sector Model of the National Energy Modeling System. Volume 1

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

NONE

1998-01-01

This report documents the objectives, analytical approach and development of the National Energy Modeling System (NEMS) Transportation Model (TRAN). The report catalogues and describes the model assumptions, computational methodology, parameter estimation techniques, model source code, and forecast results generated by the model. The NEMS Transportation Model comprises a series of semi-independent models which address different aspects of the transportation sector. The primary purpose of this model is to provide mid-term forecasts of transportation energy demand by fuel type including, but not limited to, motor gasoline, distillate, jet fuel, and alternative fuels (such as CNG) not commonly associated with transportation. Themore » current NEMS forecast horizon extends to the year 2010 and uses 1990 as the base year. Forecasts are generated through the separate consideration of energy consumption within the various modes of transport, including: private and fleet light-duty vehicles; aircraft; marine, rail, and truck freight; and various modes with minor overall impacts, such as mass transit and recreational boating. This approach is useful in assessing the impacts of policy initiatives, legislative mandates which affect individual modes of travel, and technological developments. The model also provides forecasts of selected intermediate values which are generated in order to determine energy consumption. These elements include estimates of passenger travel demand by automobile, air, or mass transit; estimates of the efficiency with which that demand is met; projections of vehicle stocks and the penetration of new technologies; and estimates of the demand for freight transport which are linked to forecasts of industrial output. Following the estimation of energy demand, TRAN produces forecasts of vehicular emissions of the following pollutants by source: oxides of sulfur, oxides of nitrogen, total carbon, carbon dioxide, carbon monoxide, and volatile organic

Sensitivity of chemistry-transport model simulations to the duration of chemical and transport operators: a case study with GEOS-Chem v10-01

NASA Astrophysics Data System (ADS)

Philip, Sajeev; Martin, Randall V.; Keller, Christoph A.

2016-05-01

Chemistry-transport models involve considerable computational expense. Fine temporal resolution offers accuracy at the expense of computation time. Assessment is needed of the sensitivity of simulation accuracy to the duration of chemical and transport operators. We conduct a series of simulations with the GEOS-Chem chemistry-transport model at different temporal and spatial resolutions to examine the sensitivity of simulated atmospheric composition to operator duration. Subsequently, we compare the species simulated with operator durations from 10 to 60 min as typically used by global chemistry-transport models, and identify the operator durations that optimize both computational expense and simulation accuracy. We find that longer continuous transport operator duration increases concentrations of emitted species such as nitrogen oxides and carbon monoxide since a more homogeneous distribution reduces loss through chemical reactions and dry deposition. The increased concentrations of ozone precursors increase ozone production with longer transport operator duration. Longer chemical operator duration decreases sulfate and ammonium but increases nitrate due to feedbacks with in-cloud sulfur dioxide oxidation and aerosol thermodynamics. The simulation duration decreases by up to a factor of 5 from fine (5 min) to coarse (60 min) operator duration. We assess the change in simulation accuracy with resolution by comparing the root mean square difference in ground-level concentrations of nitrogen oxides, secondary inorganic aerosols, ozone and carbon monoxide with a finer temporal or spatial resolution taken as "truth". Relative simulation error for these species increases by more than a factor of 5 from the shortest (5 min) to longest (60 min) operator duration. Chemical operator duration twice that of the transport operator duration offers more simulation accuracy per unit computation. However, the relative simulation error from coarser spatial resolution generally

Chemical element transport in stellar evolution models

PubMed Central

Cassisi, Santi

2017-01-01

Stellar evolution computations provide the foundation of several methods applied to study the evolutionary properties of stars and stellar populations, both Galactic and extragalactic. The accuracy of the results obtained with these techniques is linked to the accuracy of the stellar models, and in this context the correct treatment of the transport of chemical elements is crucial. Unfortunately, in many respects calculations of the evolution of the chemical abundance profiles in stars are still affected by sometimes sizable uncertainties. Here, we review the various mechanisms of element transport included in the current generation of stellar evolution calculations, how they are implemented, the free parameters and uncertainties involved, the impact on the models and the observational constraints. PMID:28878972

Chemical element transport in stellar evolution models.

PubMed

Salaris, Maurizio; Cassisi, Santi

2017-08-01

Stellar evolution computations provide the foundation of several methods applied to study the evolutionary properties of stars and stellar populations, both Galactic and extragalactic. The accuracy of the results obtained with these techniques is linked to the accuracy of the stellar models, and in this context the correct treatment of the transport of chemical elements is crucial. Unfortunately, in many respects calculations of the evolution of the chemical abundance profiles in stars are still affected by sometimes sizable uncertainties. Here, we review the various mechanisms of element transport included in the current generation of stellar evolution calculations, how they are implemented, the free parameters and uncertainties involved, the impact on the models and the observational constraints.

Reactive transport modeling

USDA-ARS?s Scientific Manuscript database

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

Multiscale modelling of dual-porosity porous media; a computational pore-scale study for flow and solute transport

NASA Astrophysics Data System (ADS)

de Vries, Enno T.; Raoof, Amir; van Genuchten, Martinus Th.

2017-07-01

Many environmental and agricultural applications involve the transport of water and dissolved constituents through aggregated soil profiles, or porous media that are structured, fractured or macroporous in other ways. During the past several decades, various process-based macroscopic models have been used to simulate contaminant transport in such media. Many of these models consider advective-dispersive transport through relatively large inter-aggregate pore domains, while exchange with the smaller intra-aggregate pores is assumed to be controlled by diffusion. Exchange of solute between the two domains is often represented using a first-order mass transfer coefficient, which is commonly obtained by fitting to observed data. This study aims to understand and quantify the solute exchange term by applying a dual-porosity pore-scale network model to relatively large domains, and analysing the pore-scale results in terms of the classical dual-porosity (mobile-immobile) transport formulation. We examined the effects of key parameters (notably aggregate porosity and aggregate permeability) on the main dual-porosity model parameters, i.e., the mobile water fraction (ϕm) and the mass transfer coefficient (α). Results were obtained for a wide range of aggregate porosities (between 0.082 and 0.700). The effect of aggregate permeability was explored by varying pore throat sizes within the aggregates. Solute breakthrough curves (BTCs) obtained with the pore-scale network model at several locations along the domain were analysed using analytical solutions of the dual-porosity model to obtain estimates of ϕm and α. An increase in aggregate porosity was found to decrease ϕm and increase α, leading to considerable tailing in the BTCs. Changes in the aggregate pore throat size affected the relative flow velocity between the intra- and inter-aggregate domains. Higher flow velocities within the aggregates caused a change in the transport regime from diffusion dominated to more

Object-oriented data model of the municipal transportation

NASA Astrophysics Data System (ADS)

Pan, Yuqing; Sheng, Yehua; Zhang, Guiying

2008-10-01

The transportation problem is always one of main questions each big city all over the world faces. Managing the municipal transportation using GIS is becoming the important trend. And the data model is the transportation information system foundation. The organization and storage of the data must consider well in the system design. The data model not only needs to meet the demand that the transportation navigates, but also needs to achieve the good visual effects, also can carry on the management and the maintenance to the traffic information. According to the object-oriented theory and the method, the road is divided into segment, intersection. This paper analyzed the driveway, marking, sign and other transportation facilities and the relationship with the segment, intersection and constructed the municipal transportation data model which is adequate to the demand of vehicles navigation, visual and management. The paper also schemes the the all kinds of transportation data. The practice proves that this data model can satisfy the application demands of traffic management system.

Role of sediment transport model to improve the tsunami numerical simulation

NASA Astrophysics Data System (ADS)

Sugawara, D.; Yamashita, K.; Takahashi, T.; Imamura, F.

2015-12-01

Are we overlooking an important factor for improved numerical prediction of tsunamis in shallow sea to onshore? In this presentation, several case studies on numerical modeling of tsunami-induced sediment transport are reviewed, and the role of sediment transport models for tsunami inundation simulation is discussed. Large-scale sediment transport and resulting geomorphological change occurred in the coastal areas of Tohoku, Japan, due to the 2011 Tohoku Earthquake Tsunami. Datasets obtained after the tsunami, including geomorphological and sedimentological data as well as hydrodynamic records, allows us to validate the numerical model in detail. The numerical modeling of the sediment transport by the 2011 tsunami depicted the severest erosion of sandy beach, as well as characteristic spatial patterns of erosion and deposition on the seafloor, which have taken place in Hirota Bay, Sanriku Coast. Quantitative comparisons of observation and simulation of the geomorphological changes in Sanriku Coast and Sendai Bay showed that the numerical model can predict the volumes of erosion and deposition with a right order. In addition, comparison of the simulation with aerial video footages demonstrated the numerical model is capable of tracking the overall processes of tsunami sediment transport. Although tsunami-induced sediment erosion and deposition sometimes cause significant geomorphological change, and may enhance tsunami hydrodynamic impact to the coastal zones, most tsunami simulations do not include sediment transport modeling. A coupled modeling of tsunami hydrodynamics and sediment transport draws a different picture of tsunami hazard, comparing with simple hydrodynamic modeling of tsunami inundation. Since tsunami-induced erosion, deposition and geomorphological change sometimes extend more than several kilometers across the coastline, two-dimensional horizontal model are typically used for the computation of tsunami hydrodynamics and sediment transport

Wave-induced bedload transport - a study of the southern Baltic coastal zone

NASA Astrophysics Data System (ADS)

Dudkowska, Aleksandra; Gic-Grusza, Gabriela

2017-03-01

The wave-induced bedload transport and spatial distribution of its magnitude in the southern Baltic coastal zone of Poland are estimated. The vicinity of Lubiatowo was selected as a representative part of the Polish coast. It was assumed that transport is a function of shear stress; alternative approaches, based on force balances and discharge relationships, were not considered in the present study. Four models were studied and compared over a wide range of bottom shear stress and wind-wave conditions. The set of models comprises classic theories that assume a simplified influence of turbulence on sediment transport (e.g., advocated by authors such as Du Boys, Meyer-Peter and Müller, Ribberink, Engelund and Hansen). It is shown that these models allow to estimate transport comparable to measured values under similar environmental conditions. A united general model for bedload transport is proposed, and a set of maps of wave bedload transport for various wind conditions in the study area is presented.

Module-oriented modeling of reactive transport with HYTEC

NASA Astrophysics Data System (ADS)

van der Lee, Jan; De Windt, Laurent; Lagneau, Vincent; Goblet, Patrick

2003-04-01

The paper introduces HYTEC, a coupled reactive transport code currently used for groundwater pollution studies, safety assessment of nuclear waste disposals, geochemical studies and interpretation of laboratory column experiments. Based on a known permeability field, HYTEC evaluates the groundwater flow paths, and simulates the migration of mobile matter (ions, organics, colloids) subject to geochemical reactions. The code forms part of a module-oriented structure which facilitates maintenance and improves coding flexibility. In particular, using the geochemical module CHESS as a common denominator for several reactive transport models significantly facilitates the development of new geochemical features which become automatically available to all models. A first example shows how the model can be used to assess migration of uranium from a sub-surface source under the effect of an oxidation front. The model also accounts for alteration of hydrodynamic parameters (local porosity, permeability) due to precipitation and dissolution of mineral phases, which potentially modifies the migration properties in general. The second example illustrates this feature.

Crystal Growth of ZnSe by Physical Vapor Transport: A Modeling Study

NASA Technical Reports Server (NTRS)

Ramachandran, Narayanan; Su, Ching-Hua

1998-01-01

Crystal growth from the vapor phase has various advantages over melt growth. The main advantage is from a lower processing temperature which makes the process more amenable in instances where the melting temperature of the crystal is high. Other benefits stem from the inherent purification mechanism in the process due to differences in the vapor pressures of the native elements and impurities, and the enhanced interfacial morphological stability during the growth process. Further, the implementation of Physical Vapor Transport (PVT) growth in closed ampoules affords experimental simplicity with minimal needs for complex process control which makes it an ideal candidate for space investigations in systems where gravity tends to have undesirable effects on the growth process. Bulk growth of wide band gap II-VI semiconductors by physical vapor transport has been developed and refined over the past several years at NASA MSFC. Results from a modeling study of PVT crystal growth of ZnSe arc reported in this paper. The PVI process is numerically investigated using both two-dimensional and fully three-dimensional formulation of the governing equations and associated boundary conditions. Both the incompressible Boussinesq approximation and the compressible model are tested to determine the influence of gravity on the process and to discern the differences between the two approaches. The influence of a residual gas is included in the models. The preliminary results show that both the incompressible and compressible approximations provide comparable results and the presence of a residual gas tends to measurably reduce the mass flux in the system. Detailed flow, thermal and concentration profiles will be provided in the final manuscript along with computed heat and mass transfer rates. Comparisons with the 1-D model will also be provided.

A model of ion transport processes along and across the neuronal membrane.

PubMed

Xiang, Z X; Liu, G Z; Tang, C X; Yan, L X

2017-01-01

In this study, we provide a foundational model of ion transport processes in the intracellular and extracellular compartments of neurons at the nanoscale. There are two different kinds of ionic transport processes: (i) ionic transport across the neuronal membrane (trans-membrane), and (ii) ionic transport along both the intracellular and extracellular surfaces of the membrane. Brownian dynamics simulations are used to give a description of ionic trans-membrane transport. Electro-diffusion is used to model ion transport along the membrane surface, and the two transport processes can be linked analytically. In our model, we found that the interactions between ions and ion channels result in high-frequency ionic oscillations during trans-membrane transport. In ion transport along the membrane, high-frequency ionic oscillations may be evoked on both the intracellular and extracellular surfaces of the plasma membrane. The electric field caused by Coulomb interactions between the ions is found to be the most likely origin of those ionic oscillations.

Design, Modeling and Simulations in the RACE Project: Preliminary study for the development of a transport line

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

Maidana, C. O.; Hunt, A. W.; Idaho State University, Department of Physics, PO Box 8106, Pocatello, ID 83209

2007-02-12

As part of the Reactor Accelerator Coupling Experiment (RACE) a set of preliminary studies were conducted to design a transport beam line that could bring a 25 MeV electron beam from a Linear Accelerator to a neutron-producing target inside a subcritical system. Because of the relatively low energy beam, the beam size and a relatively long beam line (implicating a possible divergence problem) different parameters and models were studied before a final design could be submitted for assembly. This report shows the first results obtained from different simulations of the transport line optics and dynamics.

Effects of varying the step particle distribution on a probabilistic transport model

NASA Astrophysics Data System (ADS)

Bouzat, S.; Farengo, R.

2005-12-01

The consequences of varying the step particle distribution on a probabilistic transport model, which captures the basic features of transport in plasmas and was recently introduced in Ref. 1 [B. Ph. van Milligen et al., Phys. Plasmas 11, 2272 (2004)], are studied. Different superdiffusive transport mechanisms generated by a family of distributions with algebraic decays (Tsallis distributions) are considered. It is observed that the possibility of changing the superdiffusive transport mechanism improves the flexibility of the model for describing different situations. The use of the model to describe the low (L) and high (H) confinement modes is also analyzed.

Transport properties of puerarin and effect of Radix Angelicae Dahuricae extract on the transport of puerarin in Caco-2 cell model.

PubMed

Liang, Xin-Li; Zhao, Li-Jun; Liao, Zheng-Gen; Zhao, Guo-Wei; Zhang, Jing; Chao, Yun-Chao; Yang, Ming; Yin, Rong-Li

2012-12-18

Angelicae Dahurica (Hoffm.)Benth.& Hook.f.ex Franch.&Sav combined with Pueraria labota (Willd.)Ohwi has been widely used as herb-pairs in traditional Chinese medicine (TCM) for utilization of antipyretic analgesic and anti-inflammatory drugs, and modern pharmacological studies have shown that application compatibility of the two drugs has the effects of cardiovascular disease treatment. The previous study has proved that Radix Angelicae Dahuricae extract could enhance the intestinal absorption of puerarin in Pueraria. But the underlying compatibility mechanism of the two herbs remains unknown. In this study we tried to further evaluate the improvement of Radix Angelicae Dahuricae extract on the puerarin using the Caco-2 cell model and explore the transport properties of puerarin through the above research to discuss the possible effect mechanism of Radix Angelicae Dahuricae extract on the transport of puerarin and the underlying compatibility mechanism of the two herbs. The aim of this work was to study the transport properties of puerarin in Radix Pueraria across Caco-2 cell membrane and to explore how the Radix Angelicae Dahuricae extract affected the transport of puerarin using the well-characterized, human-based intestinal Caco-2 cell model as a platform. The bidirectional transport, and the effects of time, drug concentration, pH, P-gp inhibitors (Verapamil, Cyclosporin A), MRP inhibitor (MK-571) and EDTA-Na(2) (tight junction modulator) on the absorption of puerarin were observed. Then the influence of extract of Radix Angelicae Dahuricae on the transport of puerarin was studied. Drug concentration was measured by HPLC and the apparent permeability coefficients (Papp) and apparent permeability ratio (PDR) were calculated. The results showed that the transport (Papp) of puerarin in Caco-2 cell monolayer model had time and concentration dependence, and the transport showed saturation characteristics with the time and concentration of puerarin to a certain

Transport lattice models of heat transport in skin with spatially heterogeneous, temperature-dependent perfusion

PubMed Central

Gowrishankar, TR; Stewart, Donald A; Martin, Gregory T; Weaver, James C

2004-01-01

Background Investigation of bioheat transfer problems requires the evaluation of temporal and spatial distributions of temperature. This class of problems has been traditionally addressed using the Pennes bioheat equation. Transport of heat by conduction, and by temperature-dependent, spatially heterogeneous blood perfusion is modeled here using a transport lattice approach. Methods We represent heat transport processes by using a lattice that represents the Pennes bioheat equation in perfused tissues, and diffusion in nonperfused regions. The three layer skin model has a nonperfused viable epidermis, and deeper regions of dermis and subcutaneous tissue with perfusion that is constant or temperature-dependent. Two cases are considered: (1) surface contact heating and (2) spatially distributed heating. The model is relevant to the prediction of the transient and steady state temperature rise for different methods of power deposition within the skin. Accumulated thermal damage is estimated by using an Arrhenius type rate equation at locations where viable tissue temperature exceeds 42°C. Prediction of spatial temperature distributions is also illustrated with a two-dimensional model of skin created from a histological image. Results The transport lattice approach was validated by comparison with an analytical solution for a slab with homogeneous thermal properties and spatially distributed uniform sink held at constant temperatures at the ends. For typical transcutaneous blood gas sensing conditions the estimated damage is small, even with prolonged skin contact to a 45°C surface. Spatial heterogeneity in skin thermal properties leads to a non-uniform temperature distribution during a 10 GHz electromagnetic field exposure. A realistic two-dimensional model of the skin shows that tissue heterogeneity does not lead to a significant local temperature increase when heated by a hot wire tip. Conclusions The heat transport system model of the skin was solved by

Transport lattice models of heat transport in skin with spatially heterogeneous, temperature-dependent perfusion.

PubMed

Gowrishankar, T R; Stewart, Donald A; Martin, Gregory T; Weaver, James C

2004-11-17

Investigation of bioheat transfer problems requires the evaluation of temporal and spatial distributions of temperature. This class of problems has been traditionally addressed using the Pennes bioheat equation. Transport of heat by conduction, and by temperature-dependent, spatially heterogeneous blood perfusion is modeled here using a transport lattice approach. We represent heat transport processes by using a lattice that represents the Pennes bioheat equation in perfused tissues, and diffusion in nonperfused regions. The three layer skin model has a nonperfused viable epidermis, and deeper regions of dermis and subcutaneous tissue with perfusion that is constant or temperature-dependent. Two cases are considered: (1) surface contact heating and (2) spatially distributed heating. The model is relevant to the prediction of the transient and steady state temperature rise for different methods of power deposition within the skin. Accumulated thermal damage is estimated by using an Arrhenius type rate equation at locations where viable tissue temperature exceeds 42 degrees C. Prediction of spatial temperature distributions is also illustrated with a two-dimensional model of skin created from a histological image. The transport lattice approach was validated by comparison with an analytical solution for a slab with homogeneous thermal properties and spatially distributed uniform sink held at constant temperatures at the ends. For typical transcutaneous blood gas sensing conditions the estimated damage is small, even with prolonged skin contact to a 45 degrees C surface. Spatial heterogeneity in skin thermal properties leads to a non-uniform temperature distribution during a 10 GHz electromagnetic field exposure. A realistic two-dimensional model of the skin shows that tissue heterogeneity does not lead to a significant local temperature increase when heated by a hot wire tip. The heat transport system model of the skin was solved by exploiting the mathematical

Workshop discusses community models for coastal sediment transport

NASA Astrophysics Data System (ADS)

Sherwood, Christopher R.; Signell, Richard P.; Harris, Courtney K.; Butman, Bradford

Numerical models of coastal sediment transport are increasingly used to address problems ranging from remediation of contaminated sediments, to siting of sewage outfalls and disposal sites, to evaluating impacts of coastal development. They are also used as a test bed for sediment-transport algorithms, to provide realistic settings for biological and geochemical models, and for a variety of other research, both fundamental and applied. However, there are few full-featured, publicly available coastal sediment-transport models, and fewer still that are well tested and have been widely applied.This was the motivation for a workshop in Woods Hole, Massachusetts, on June 22-23, 2000, that explored the establishment of community models for coastal sediment-transport processes.

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

USGS Publications Warehouse

Stollenwerk, Kenneth G.

1998-01-01

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

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

Scattering and transport statistics at the metal-insulator transition: A numerical study of the power-law banded random-matrix model

NASA Astrophysics Data System (ADS)

Méndez-Bermúdez, J. A.; Gopar, Victor A.; Varga, Imre

2010-09-01

We study numerically scattering and transport statistical properties of the one-dimensional Anderson model at the metal-insulator transition described by the power-law banded random matrix (PBRM) model at criticality. Within a scattering approach to electronic transport, we concentrate on the case of a small number of single-channel attached leads. We observe a smooth crossover from localized to delocalized behavior in the average-scattering matrix elements, the conductance probability distribution, the variance of the conductance, and the shot noise power by varying b (the effective bandwidth of the PBRM model) from small (b≪1) to large (b>1) values. We contrast our results with analytic random matrix theory predictions which are expected to be recovered in the limit b→∞ . We also compare our results for the PBRM model with those for the three-dimensional (3D) Anderson model at criticality, finding that the PBRM model with bɛ[0.2,0.4] reproduces well the scattering and transport properties of the 3D Anderson model.

How Sensitive Are Transdermal Transport Predictions by Microscopic Stratum Corneum Models to Geometric and Transport Parameter Input?

PubMed

Wen, Jessica; Koo, Soh Myoung; Lape, Nancy

2018-02-01

While predictive models of transdermal transport have the potential to reduce human and animal testing, microscopic stratum corneum (SC) model output is highly dependent on idealized SC geometry, transport pathway (transcellular vs. intercellular), and penetrant transport parameters (e.g., compound diffusivity in lipids). Most microscopic models are limited to a simple rectangular brick-and-mortar SC geometry and do not account for variability across delivery sites, hydration levels, and populations. In addition, these models rely on transport parameters obtained from pure theory, parameter fitting to match in vivo experiments, and time-intensive diffusion experiments for each compound. In this work, we develop a microscopic finite element model that allows us to probe model sensitivity to variations in geometry, transport pathway, and hydration level. Given the dearth of experimentally-validated transport data and the wide range in theoretically-predicted transport parameters, we examine the model's response to a variety of transport parameters reported in the literature. Results show that model predictions are strongly dependent on all aforementioned variations, resulting in order-of-magnitude differences in lag times and permeabilities for distinct structure, hydration, and parameter combinations. This work demonstrates that universally predictive models cannot fully succeed without employing experimentally verified transport parameters and individualized SC structures. Copyright © 2018 American Pharmacists Association®. Published by Elsevier Inc. All rights reserved.

A mobile-mobile transport model for simulating reactive transport in connected heterogeneous fields

NASA Astrophysics Data System (ADS)

Lu, Chunhui; Wang, Zhiyuan; Zhao, Yue; Rathore, Saubhagya Singh; Huo, Jinge; Tang, Yuening; Liu, Ming; Gong, Rulan; Cirpka, Olaf A.; Luo, Jian

2018-05-01

Mobile-immobile transport models can be effective in reproducing heavily tailed breakthrough curves of concentration. However, such models may not adequately describe transport along multiple flow paths with intermediate velocity contrasts in connected fields. We propose using the mobile-mobile model for simulating subsurface flow and associated mixing-controlled reactive transport in connected fields. This model includes two local concentrations, one in the fast- and the other in the slow-flow domain, which predict both the concentration mean and variance. The normalized total concentration variance within the flux is found to be a non-monotonic function of the discharge ratio with a maximum concentration variance at intermediate values of the discharge ratio. We test the mobile-mobile model for mixing-controlled reactive transport with an instantaneous, irreversible bimolecular reaction in structured and connected random heterogeneous domains, and compare the performance of the mobile-mobile to the mobile-immobile model. The results indicate that the mobile-mobile model generally predicts the concentration breakthrough curves (BTCs) of the reactive compound better. Particularly, for cases of an elliptical inclusion with intermediate hydraulic-conductivity contrasts, where the travel-time distribution shows bimodal behavior, the prediction of both the BTCs and maximum product concentration is significantly improved. Our results exemplify that the conceptual model of two mobile domains with diffusive mass transfer in between is in general good for predicting mixing-controlled reactive transport, and particularly so in cases where the transfer in the low-conductivity zones is by slow advection rather than diffusion.

Transport and Chemical Production of Ozone in the East Asian Pacific Rim Region: -Modeling Study Based on Observation-

NASA Astrophysics Data System (ADS)

Akimoto, H.; Li, J.; Wang, Z.; Yamaji, K.; Pochanart, P.; Ohara, T.; Uno, I.; Gao, C.; Wang, X.; Tanimoto, H.; Kurokawa, J.

2007-12-01

Form satellite observational data, east-central China covering the North China Plain (NCP) and Yanzi Delta (YZD) has been identified as the most widely spread source area of air pollutants in the East Asian Pacific region. In order to quantify transport and chemical production of ozone in this region, both of observational and modeling studies in both of source and outflow region are necessary. In the present study, we investigated the budgets of ozone over East Asia by using regional chemical transport models (NAQPMS and CMAQ) based on observations at newly founded three mountain sites (Mt. Tai, Hua and Huang) in east-central China, and several sites from EANET and regional WMO/GAW. The observations show that a striking pattern of two sharp high ozone peaks in May-June and September-October at the three mountain sites. The budget analysis by the model confirms that maximum of net photochemical ozone production reaches 31.8, 15.1 and 11.4 ppb/day at Mt. Tai, Hua and Huang, respectively. The net chemical production dominates the formation of ozone maximum at Mt. Tai and Hua in June, and the importing transport also plays a comparable importance at Mt. Huang. In the outflow region at Oki, Japan, transport of ozone produced by East Asian emissions accounts up to 21 ppb in summer but less than 3 ppb in winter agreeing with the model analysis. The contribution of ozone due to East Asian emission is the largest (53.6%) in July-August, and somewhat smaller in May-June (34.0%) and September-October (30.7%) on the transect between Japan and the Asian continent.

Galactic Cosmic-ray Transport in the Global Heliosphere: A Four-Dimensional Stochastic Model

NASA Astrophysics Data System (ADS)

Florinski, V.

2009-04-01

We study galactic cosmic-ray transport in the outer heliosphere and heliosheath using a newly developed transport model based on stochastic integration of the phase-space trajectories of Parker's equation. The model employs backward integration of the diffusion-convection transport equation using Ito calculus and is four-dimensional in space+momentum. We apply the model to the problem of galactic proton transport in the heliosphere during a negative solar minimum. Model results are compared with the Voyager measurements of galactic proton radial gradients and spectra in the heliosheath. We show that the heliosheath is not as efficient in diverting cosmic rays during solar minima as predicted by earlier two-dimensional models.

Characterization of Transport Errors in Chemical Forecasts from a Global Tropospheric Chemical Transport Model

NASA Technical Reports Server (NTRS)

Bey, I.; Jacob, D. J.; Liu, H.; Yantosca, R. M.; Sachse, G. W.

2004-01-01

We propose a new methodology to characterize errors in the representation of transport processes in chemical transport models. We constrain the evaluation of a global three-dimensional chemical transport model (GEOS-CHEM) with an extended dataset of carbon monoxide (CO) concentrations obtained during the Transport and Chemical Evolution over the Pacific (TRACE-P) aircraft campaign. The TRACEP mission took place over the western Pacific, a region frequently impacted by continental outflow associated with different synoptic-scale weather systems (such as cold fronts) and deep convection, and thus provides a valuable dataset. for our analysis. Model simulations using both forecast and assimilated meteorology are examined. Background CO concentrations are computed as a function of latitude and altitude and subsequently subtracted from both the observed and the model datasets to focus on the ability of the model to simulate variability on a synoptic scale. Different sampling strategies (i.e., spatial displacement and smoothing) are applied along the flight tracks to search for systematic model biases. Statistical quantities such as correlation coefficient and centered root-mean-square difference are computed between the simulated and the observed fields and are further inter-compared using Taylor diagrams. We find no systematic bias in the model for the TRACE-P region when we consider the entire dataset (i.e., from the surface to 12 km ). This result indicates that the transport error in our model is globally unbiased, which has important implications for using the model to conduct inverse modeling studies. Using the First-Look assimilated meteorology only provides little improvement of the correlation, in comparison with the forecast meteorology. These general statements can be refined when the entire dataset is divided into different vertical domains, i.e., the lower troposphere (less than 2 km), the middle troposphere (2-6 km), and the upper troposphere (greater than

Data-based mathematical modeling of vectorial transport across double-transfected polarized cells.

PubMed

Bartholomé, Kilian; Rius, Maria; Letschert, Katrin; Keller, Daniela; Timmer, Jens; Keppler, Dietrich

2007-09-01

Vectorial transport of endogenous small molecules, toxins, and drugs across polarized epithelial cells contributes to their half-life in the organism and to detoxification. To study vectorial transport in a quantitative manner, an in vitro model was used that includes polarized MDCKII cells stably expressing the recombinant human uptake transporter OATP1B3 in their basolateral membrane and the recombinant ATP-driven efflux pump ABCC2 in their apical membrane. These double-transfected cells enabled mathematical modeling of the vectorial transport of the anionic prototype substance bromosulfophthalein (BSP) that has frequently been used to examine hepatobiliary transport. Time-dependent analyses of (3)H-labeled BSP in the basolateral, intracellular, and apical compartments of cells cultured on filter membranes and efflux experiments in cells preloaded with BSP were performed. A mathematical model was fitted to the experimental data. Data-based modeling was optimized by including endogenous transport processes in addition to the recombinant transport proteins. The predominant contributions to the overall vectorial transport of BSP were mediated by OATP1B3 (44%) and ABCC2 (28%). Model comparison predicted a previously unrecognized endogenous basolateral efflux process as a negative contribution to total vectorial transport, amounting to 19%, which is in line with the detection of the basolateral efflux pump Abcc4 in MDCKII cells. Rate-determining steps in the vectorial transport were identified by calculating control coefficients. Data-based mathematical modeling of vectorial transport of BSP as a model substance resulted in a quantitative description of this process and its components. The same systems biology approach may be applied to other cellular systems and to different substances.

Transport of Asian Aerosols and Trace Gases to North America During the INTEX-B Field Campaign: A Regional Chemical Transport Model Analysis.

NASA Astrophysics Data System (ADS)

Adhikary, B.; Kulkarni, S.; Carmichael, G. R.; Tang, Y.; Dallura, A.; Mena, M.; Streets, D.; Zhang, Q.

2007-12-01

The Intercontinental Chemical Transport Experiment-Phase B (INTEX-B) was conducted over the Pacific Ocean during the 2006 North American spring season. One of the scientific objectives of the INTEX-B field campaign was to quantify the transport and chemical evolution/aging of Asian air pollution into North America. The field campaign deployed multiple experimental platforms such as satellites, aircrafts and surface measurements stations to study the pollution outflow to North America. Three dimensional chemical transport models were used to provide chemical weather forecasts and assist in flight planning during the mission. The Sulfur Transport and dEposition Model (STEM) is a regional chemical transport model developed at the University of Iowa. The STEM model was involved in providing chemical weather forecasts and assist in flight planning during the INTEX-B intensive field campaign. In this study we will report the STEM model performance of aerosols and trace gases in its ability to capture the pollutant plume with experimental observations obtained from the field campaign. The study will then relate the emissions of trace gases and aerosols to atmospheric composition, sources and sinks using the newly developed emissions inventory for the INTEX-B field campaign.

Quantifying errors in trace species transport modeling.

PubMed

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

2008-12-16

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

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.

Experimental and AI-based numerical modeling of contaminant transport in porous media

NASA Astrophysics Data System (ADS)

Nourani, Vahid; Mousavi, Shahram; Sadikoglu, Fahreddin; Singh, Vijay P.

2017-10-01

This study developed a new hybrid artificial intelligence (AI)-meshless approach for modeling contaminant transport in porous media. The key innovation of the proposed approach is that both black box and physically-based models are combined for modeling contaminant transport. The effectiveness of the approach was evaluated using experimental and real world data. Artificial neural network (ANN) and adaptive neuro-fuzzy inference system (ANFIS) were calibrated to predict temporal contaminant concentrations (CCs), and the effect of noisy and de-noised data on the model performance was evaluated. Then, considering the predicted CCs at test points (TPs, in experimental study) and piezometers (in Myandoab plain) as interior conditions, the multiquadric radial basis function (MQ-RBF), as a meshless approach which solves partial differential equation (PDE) of contaminant transport in porous media, was employed to estimate the CC values at any point within the study area where there was no TP or piezometer. Optimal values of the dispersion coefficient in the advection-dispersion PDE and shape coefficient of MQ-RBF were determined using the imperialist competitive algorithm. In temporal contaminant transport modeling, de-noised data enhanced the performance of ANN and ANFIS methods in terms of the determination coefficient, up to 6 and 5%, respectively, in the experimental study and up to 39 and 18%, respectively, in the field study. Results showed that the efficiency of ANFIS-meshless model was more than ANN-meshless model up to 2 and 13% in the experimental and field studies, respectively.

Modeling sediment transport with an integrated view of the biofilm effects

NASA Astrophysics Data System (ADS)

Fang, H. W.; Lai, H. J.; Cheng, W.; Huang, L.; He, G. J.

2017-09-01

Most natural sediment is invariably covered by biofilms in reservoirs and lakes, which have significant influence on bed form dynamics and sediment transport, and also play a crucial role in natural river evolution, pollutant transport, and habitat changes. However, most models for sediment transport are based on experiments using clean sediments without biological materials. In this study, a three-dimensional mathematical model of hydrodynamics and sediment transport is presented with a comprehensive consideration of the biofilm effects. The changes of the bed resistance mainly due to the different bed form dynamics of the biofilm-coated sediment (biosediment), which affect the hydrodynamic characteristics, are considered. Moreover, the variations of parameters related to sediment transport after the biofilm growth are integrated, including the significant changes of the incipient velocity, settling velocity, reference concentration, and equilibrium bed load transport rate. The proposed model is applied to evaluate the effects of biofilms on the hydrodynamic characteristics and sediment transport in laboratory experiments. Results indicate that the mean velocity increases after the biofilm growth, and the turbulence intensity near the river bed decreases under the same flow condition. Meanwhile, biofilm inhibits sediment from moving independently. Thus, the moderate erosion is observed for biosediment resulting in smaller suspended sediment concentrations. The proposed model can reasonably reflect these sediment transport characteristics with biofilms, and the approach to integration of the biological impact could also be used in other modeling of sediment transport, which can be further applied to provide references for the integrated management of natural aqueous systems.

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.

Numerical modelling of bedload sediment transport

NASA Astrophysics Data System (ADS)

Langlois, Vincent J.

2010-05-01

We present a numerical study of sediment transport in the bedload regime. Classical bedload transport laws only describe the variation of the vertically integrated flux of grains as a function of the Shields number. However, these relations are only valid if the moving layer of the bed is at equilibrium with the external flow. Besides, they do not contain enough information for many geomorphological applications. For instance, understanding inertial effects in the moving bed requires models that are able to account for the variability of hydrodynamical conditions, and the discrete nature of the sediment material. We developped a numerical modelling of the behaviour of a three-dimensional bed of grains sheared by a unidirectional fluid flow. These simulations are based on a combination of discrete and continuum approaches: sediment particles are modelled by hard spheres interacting through simple contact forces, whereas the fluid flow is described by a 'mean field' model. Both the drag exerted on grains by the fluid and the retroactive effect of the presence of grains on the flow are accounted for, allowing the system to converge to its equilibrium state (no assumption is made on the fluid velocity profile inside the layer of moving grains). Above the motion threshold, the variation of the flux of grains in the steady state is found to vary like the cube of the Shields number (as predicted by Bagnold). Besides, our simulations allow us to obtain new insights into the detailed mechanisms of bedload transport, by giving access to non-integral quantities, such as the trajectories of each individual grains, the detailed velocity and packing fraction profiles inside the granular bed, etc. It is therefore possible to investigate some effects that are not accounted for in usual continuum models, such as the polydispersity of grains, the ageing of the bed, the response to a variation of the flowrate, etc.

Evaluate transport processes in MERRA driven chemical transport models using updated 222Rn emission inventories and global observations

NASA Astrophysics Data System (ADS)

Zhang, B.; Liu, H.; Crawford, J. H.; Fairlie, T. D.; Chen, G.; Chambers, S. D.; Kang, C. H.; Williams, A. G.; Zhang, K.; Considine, D. B.; Payer Sulprizio, M.; Yantosca, R.

2015-12-01

Convective and synoptic processes play a major role in determining the transport and distribution of trace gases and aerosols in the troposphere. The representation of these processes in global models (at ~100-1000 km horizontal resolution) is challenging, because convection is a sub-grid process and needs to be parameterized, while synoptic processes are close to the grid scale. Depending on the parameterization schemes used in climate models, the role of convection in transporting trace gases and aerosols may vary from model to model. 222Rn is a chemically inert and radioactive gas constantly emitted from soil and has a half-life (3.8 days) comparable to synoptic timescale, which makes it an effective tracer for convective and synoptic transport. In this study, we evaluate the convective and synoptic transport in two chemical transport models (GMI and GEOS-Chem), both driven by the NASA's MERRA reanalysis. Considering the uncertainties in 222Rn emissions, we incorporate two more recent scenarios with regionally varying 222Rn emissions into GEOS-Chem/MERRA and compare the simulation results with those using the relatively uniform 222Rn emissions in the standard model. We evaluate the global distribution and seasonality of 222Rn concentrations simulated by the two models against an extended collection of 222Rn observations from 1970s to 2010s. The intercomparison will improve our understanding of the spatial variability in global 222Rn emissions, including the suspected excessive 222Rn emissions in East Asia, and provide useful feedbacks on 222Rn emission models. We will assess 222Rn vertical distributions at different latitudes in the models using observations at surface sites and in the upper troposphere and lower stratosphere. Results will be compared with previous models driven by other meteorological fields (e.g., fvGCM and GEOS4). Since the decay of 222Rn is the source of 210Pb, a useful radionuclide tracer attached to submicron aerosols, improved

Transportation and socioeconomic impacts of bypasses on communities : an integrated synthesis of panel data, multilevel, and spatial econometric models with case studies.

DOT National Transportation Integrated Search

2011-09-21

Title: Transportation and Socioeconomic Impacts of Bypasses on Communities: An Integrated Synthesis of Panel Data, Multilevel, and Spatial Econometric Models with Case Studies. The title used at the start of this project was Transportation and Soc...

Modeling preferential water flow and solute transport in unsaturated soil using the active region model

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

Sheng, F.; Wang, K.; Zhang, R.

2009-03-15

Preferential flow and solute transport are common processes in the unsaturated soil, in which distributions of soil water content and solute concentrations are often characterized as fractal patterns. An active region model (ARM) was recently proposed to describe the preferential flow and transport patterns. In this study, ARM governing equations were derived to model the preferential soil water flow and solute transport processes. To evaluate the ARM equations, dye infiltration experiments were conducted, in which distributions of soil water content and Cl{sup -} concentration were measured. Predicted results using the ARM and the mobile-immobile region model (MIM) were compared withmore » the measured distributions of soil water content and Cl{sup -} concentration. Although both the ARM and the MIM are two-region models, they are fundamental different in terms of treatments of the flow region. The models were evaluated based on the modeling efficiency (ME). The MIM provided relatively poor prediction results of the preferential flow and transport with negative ME values or positive ME values less than 0.4. On the contrary, predicted distributions of soil water content and Cl- concentration using the ARM agreed reasonably well with the experimental data with ME values higher than 0.8. The results indicated that the ARM successfully captured the macroscopic behavior of preferential flow and solute transport in the unsaturated soil.« less

Modeling flow and solute transport in irrigation furrows

USDA-ARS?s Scientific Manuscript database

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...

Mathematical modeling of kidney transport.

PubMed

Layton, Anita T

2013-01-01

In addition to metabolic waste and toxin excretion, the kidney also plays an indispensable role in regulating the balance of water, electrolytes, nitrogen, and acid-base. In this review, we describe representative mathematical models that have been developed to better understand kidney physiology and pathophysiology, including the regulation of glomerular filtration, the regulation of renal blood flow by means of the tubuloglomerular feedback mechanisms and of the myogenic mechanism, the urine concentrating mechanism, epithelial transport, and regulation of renal oxygen transport. We discuss the extent to which these modeling efforts have expanded our understanding of renal function in both health and disease. Copyright © 2013 Wiley Periodicals, Inc.

Modeling neuropeptide transport in various types of nerve terminals containing en passant boutons.

PubMed

Kuznetsov, I A; Kuznetsov, A V

2015-03-01

We developed a mathematical model for simulating neuropeptide transport inside dense core vesicles (DCVs) in axon terminals containing en passant boutons. The motivation for this research is a recent experimental study by Levitan and colleagues (Bulgari et al., 2014) which described DCV transport in nerve terminals of type Ib and type III as well as in nerve terminals of type Ib with the transcription factor DIMM. The goal of our modeling is validating the proposition put forward by Levitan and colleagues that the dramatic difference in DCV number in type Ib and type III terminals can be explained by the difference in DCV capture in type Ib and type III boutons rather than by differences in DCV anterograde transport and half-life of resident DCVs. The developed model provides a tool for studying the dynamics of DCV transport in various types of nerve terminals. The model is also an important step in gaining a better mechanistic understanding of transport processes in axons and identifying directions for the development of new models in this area. Copyright © 2014 Elsevier Inc. All rights reserved.

The absorption and transport of magnolol in Caco-2 cell model.

PubMed

Wu, An-Guo; Zeng, Bao; Huang, Meng-Qiu; Li, Sheng-Mei; Chen, Jian-Nan; Lai, Xiao-Ping

2013-03-01

To investigate the absorption and transport mechanism of magnolol in Caco-2 cell model. A human intestinal epithelial cell model Caco-2 cell in vitro cultured was applied to study the absorption and transport of magnolol, the effects of time, donor concentration, P-gp inhibitor verapamil, pH and temperature on the absorption and transport of magnolol were investigated. The determination of magnolol was performed by high performance liquid chromatography, then the values of apparent permeability coefficient (P app ) and P ratio Basolateral-to-Apical (BL-to-AP)/Apical-to-Basolateral (AP-to-BL) were calculated. In Caco-2 cell model, comparing the amounts of transport of AP-to-BL and BL-to-AP, the latter was larger. At the same donor concentration, either the amounts of transport of AP-to-BL or BL-to-AP increased with increase in donor concentration and incubation time. Verapamil could significantly improve the amounts of transport of AP-to-BL. The transport of AP-to-BL and BL-to-AP depended on temperature, and there was no significant effect of pH on the transport of AP-to-BL. Magnolol could be transported through the intestinal mucosa via a passive diffusion mechanism primarily, coexisting with a carrier-mediated transport, at the same time, the efflux mechanism could be involved.

Modeling sediment transport after ditch network maintenance of a forested peatland

NASA Astrophysics Data System (ADS)

Haahti, K.; Marttila, H.; Warsta, L.; Kokkonen, T.; Finér, L.; Koivusalo, H.

2016-11-01

Elevated suspended sediment (SS) loads released from peatlands after drainage operations and the resulting negative effect on the ecological status of the receiving water bodies have been widely recognized. Understanding the processes controlling erosion and sediment transport within the ditch network forms a prerequisite for adequate sediment control. While numerous experimental studies have been reported in this field, model based assessments are rare. This study presents a modeling approach to investigate sediment transport in a peatland ditch network. The transport model describes bed erosion, rain-induced bank erosion, floc deposition, and consolidation of the bed. Coupled to a distributed hydrological model, sediment transport was simulated in a 5.2 ha forestry-drained peatland catchment for 2 years after ditch cleaning. Comparing simulation results to measured SS concentrations suggested that the loose peat material, produced during excavation, contributed markedly to elevated SS concentrations immediately after ditch cleaning. Both snowmelt and summer rainstorms contributed critically to annual loads. Springtime peat erosion during snowmelt was driven by ditch flow whereas during summer rainfalls, bank erosion by raindrop impact was identified as an important process. Relating modeling results to observed spatial topographic changes in the ditch network was challenging and the results were difficult to verify. Nevertheless, the model has potential to identify risk areas for erosion. The results demonstrate that modeling is effective in separating the importance of different processes and complements pure experimental approaches. Modeling results can aid planning and designing efficient sediment control measures and guide the focus of experimental studies.

The Importance of Protons in Reactive Transport Modeling

NASA Astrophysics Data System (ADS)

McNeece, C. J.; Hesse, M. A.

2014-12-01

The importance of pH in aqueous chemistry is evident; yet, its role in reactive transport is complex. Consider a column flow experiment through silica glass beads. Take the column to be saturated and flowing with solution of a distinct pH. An instantaneous change in the influent solution pH can yield a breakthrough curve with both a rarefaction and shock component (composite wave). This behavior is unique among aqueous ions in transport and is more complex than intuition would tell. Analysis of the hyperbolic limit of this physical system can explain these first order transport phenomenon. This analysis shows that transport behavior is heavily dependent on the shape of the adsorption isotherm. Hence it is clear that accurate surface chemistry models are important in reactive transport. The proton adsorption isotherm has nonconstant concavity due to the proton's ability to partition into hydroxide. An eigenvalue analysis shows that an inflection point in the adsorption isotherm allows the development of composite waves. We use electrostatic surface complexation models to calculate realistic proton adsorption isotherms. Surface characteristics such as specific surface area, and surface site density were determined experimentally. We validate the model by comparison against silica glass bead flow through experiments. When coupled to surface complexation models, the transport equation captures the timing and behavior of breakthrough curves markedly better than with commonly used Langmuir assumptions. Furthermore, we use the adsorption isotherm to predict, a priori, the transport behavior of protons across pH composition space. Expansion of the model to multicomponent systems shows that proton adsorption can force composite waves to develop in the breakthrough curves of ions that would not otherwise exhibit such behavior. Given the abundance of reactive surfaces in nature and the nonlinearity of chemical systems, we conclude that building a greater understanding of

Experimental Study and Reactive Transport Modeling of Boric Acid Leaching of Concrete

NASA Astrophysics Data System (ADS)

Pabalan, R. T.; Chiang, K.-T. K.

2013-07-01

Borated water leakage through spent fuel pools (SFPs) at pressurized water reactors is a concern because it could cause corrosion of reinforcement steel in the concrete structure, compromise the integrity of the structure, or cause unmonitored releases of contaminated water to the environment. Experimental data indicate that pH is a critical parameter that determines the corrosion susceptibility of rebar in borated water and the degree of concrete degradation by boric acid leaching. In this study, reactive transport modeling of concrete leaching by borated water was performed to provide information on the solution pH in the concrete crack or matrix and the degree of concrete degradation at different locations of an SFP concrete structure exposed to borated water. Simulations up to 100 years were performed using different boric acid concentrations, crack apertures, and solution flow rates. Concrete cylinders were immersed in boric acid solutions for several months and the mineralogical changes and boric acid penetration in the concrete cylinder were evaluated as a function of time. The depths of concrete leaching by boric acid solution derived from the reactive transport simulations were compared with the measured boric acid penetration depth.

Transportation network policy modeling for congestion and pollution control: A variational inequality approach

NASA Astrophysics Data System (ADS)

Ramanujam, Padma

1999-08-01

Public concern over the state of the environment has grown over the past decade. All indications are that this concern will continue to influence policy making into the foreseeable future. Road transport is seen as the major contributor to environmental degradation. Transportation planners around the world face the question: cleaner air and/or faster commutes? While individual vehicles can be made more environmentally friendly, the sheer scale of growth in world-wide vehicle numbers is projected to cause significant environmental degradation in the longer run, and in the absence of newer and stricter polices. It is a challenge for governments to find policies that ensure congestion-free metropolitan areas while guaranteeing both critical environmental quality levels and a sufficient infrastructure access to all groups involved. The objective of the dissertation is to provide a mathematical framework to study transportation policy models for the purpose of controlling congestion and pollution. Towards this objective. a series of transportation policy models are developed to study travel behavior and to quantity the reductions in congestion and automobile emissions. The dissertation begins with a brief historical overview of some of the pioneering works in urban transportation economics and later presents the theoretical foundation for the transportation policy models developed. The dissertation introduces single modal and multimodal transportation network policy models that accomplish road pricing with the imposition of goal targets on link loads. as well as, integrated traffic equilibrium models with marketable mobile emission permits. Furthermore, equilibrium conditions are derived for each model, and both qualitative analysis and computational procedures are studied. Finally, the dissertation concludes with a comparative study of the relationship between regulatory pricing models and marketable emission permit transportation models and a discussion on key factors

Reactive transport modeling in fractured rock: A state-of-the-science review

NASA Astrophysics Data System (ADS)

MacQuarrie, Kerry T. B.; Mayer, K. Ulrich

2005-10-01

The field of reactive transport modeling has expanded significantly in the past two decades and has assisted in resolving many issues in Earth Sciences. Numerical models allow for detailed examination of coupled transport and reactions, or more general investigation of controlling processes over geologic time scales. Reactive transport models serve to provide guidance in field data collection and, in particular, enable researchers to link modeling and hydrogeochemical studies. In this state-of-science review, the key objectives were to examine the applicability of reactive transport codes for exploring issues of redox stability to depths of several hundreds of meters in sparsely fractured crystalline rock, with a focus on the Canadian Shield setting. A conceptual model of oxygen ingress and redox buffering, within a Shield environment at time and space scales relevant to nuclear waste repository performance, is developed through a review of previous research. This conceptual model describes geochemical and biological processes and mechanisms materially important to understanding redox buffering capacity and radionuclide mobility in the far-field. Consistent with this model, reactive transport codes should ideally be capable of simulating the effects of changing recharge water compositions as a result of long-term climate change, and fracture-matrix interactions that may govern water-rock interaction. Other aspects influencing the suitability of reactive transport codes include the treatment of various reaction and transport time scales, the ability to apply equilibrium or kinetic formulations simultaneously, the need to capture feedback between water-rock interactions and porosity-permeability changes, and the representation of fractured crystalline rock environments as discrete fracture or dual continuum media. A review of modern multicomponent reactive transport codes indicates a relatively high-level of maturity. Within the Yucca Mountain nuclear waste disposal

Using Multiscale Modeling to Study Coupled Flow, Transport, Reaction and Biofilm Growth Processes in Porous Media

NASA Astrophysics Data System (ADS)

Valocchi, A. J.; Laleian, A.; Werth, C. J.

2017-12-01

Perturbation of natural subsurface systems by fluid inputs may induce geochemical or microbiological reactions that change porosity and permeability, leading to complex coupled feedbacks between reaction and transport processes. Some examples are precipitation/dissolution processes associated with carbon capture and storage and biofilm growth associated with contaminant transport and remediation. We study biofilm growth due to mixing controlled reaction of multiple substrates. As biofilms grow, pore clogging occurs which alters pore-scale flow paths thus changing the mixing and reaction. These interactions are challenging to quantify using conventional continuum-scale porosity-permeability relations. Pore-scale models can accurately resolve coupled reaction, biofilm growth and transport processes, but modeling at this scale is not feasible for practical applications. There are two approaches to address this challenge. Results from pore-scale models in generic pore structures can be used to develop empirical relations between porosity and continuum-scale parameters, such as permeability and dispersion coefficients. The other approach is to develop a multiscale model of biofilm growth in which non-overlapping regions at pore and continuum spatial scales are coupled by a suitable method that ensures continuity of flux across the interface. Thus, regions of high reactivity where flow alteration occurs are resolved at the pore scale for accuracy while regions of low reactivity are resolved at the continuum scale for efficiency. This approach thus avoids the need for empirical upscaling relations in regions with strong feedbacks between reaction and porosity change. We explore and compare these approaches for several two-dimensional cases.

Experimental and AI-based numerical modeling of contaminant transport in porous media.

PubMed

Nourani, Vahid; Mousavi, Shahram; Sadikoglu, Fahreddin; Singh, Vijay P

2017-10-01

This study developed a new hybrid artificial intelligence (AI)-meshless approach for modeling contaminant transport in porous media. The key innovation of the proposed approach is that both black box and physically-based models are combined for modeling contaminant transport. The effectiveness of the approach was evaluated using experimental and real world data. Artificial neural network (ANN) and adaptive neuro-fuzzy inference system (ANFIS) were calibrated to predict temporal contaminant concentrations (CCs), and the effect of noisy and de-noised data on the model performance was evaluated. Then, considering the predicted CCs at test points (TPs, in experimental study) and piezometers (in Myandoab plain) as interior conditions, the multiquadric radial basis function (MQ-RBF), as a meshless approach which solves partial differential equation (PDE) of contaminant transport in porous media, was employed to estimate the CC values at any point within the study area where there was no TP or piezometer. Optimal values of the dispersion coefficient in the advection-dispersion PDE and shape coefficient of MQ-RBF were determined using the imperialist competitive algorithm. In temporal contaminant transport modeling, de-noised data enhanced the performance of ANN and ANFIS methods in terms of the determination coefficient, up to 6 and 5%, respectively, in the experimental study and up to 39 and 18%, respectively, in the field study. Results showed that the efficiency of ANFIS-meshless model was more than ANN-meshless model up to 2 and 13% in the experimental and field studies, respectively. Copyright © 2017. Published by Elsevier B.V.

Unsteady Aerodynamic Modeling in Roll for the NASA Generic Transport Model

NASA Technical Reports Server (NTRS)

Murphy, Patrick C.; Klein, Vladislav; Frink, Neal T.

2012-01-01

Reducing the impact of loss-of-control conditions on commercial transport aircraft is a primary goal of the NASA Aviation Safety Program. One aspect in developing the supporting technologies is to improve the aerodynamic models that represent these adverse conditions. Aerodynamic models appropriate for loss of control conditions require a more general mathematical representation to predict nonlinear unsteady behaviors. In this paper, a more general mathematical model is proposed for the subscale NASA Generic Transport Model (GTM) that covers both low and high angles of attack. Particular attention is devoted to the stall region where full-scale transports have demonstrated a tendency for roll instability. The complete aerodynamic model was estimated from dynamic wind-tunnel data. Advanced computational methods are used to improve understanding and visualize the flow physics within the region where roll instability is a factor.

Metal Transport across Biomembranes: Emerging Models for a Distinct Chemistry*

PubMed Central

Argüello, José M.; Raimunda, Daniel; González-Guerrero, Manuel

2012-01-01

Transition metals are essential components of important biomolecules, and their homeostasis is central to many life processes. Transmembrane transporters are key elements controlling the distribution of metals in various compartments. However, due to their chemical properties, transition elements require transporters with different structural-functional characteristics from those of alkali and alkali earth ions. Emerging structural information and functional studies have revealed distinctive features of metal transport. Among these are the relevance of multifaceted events involving metal transfer among participating proteins, the importance of coordination geometry at transmembrane transport sites, and the presence of the largely irreversible steps associated with vectorial transport. Here, we discuss how these characteristics shape novel transition metal ion transport models. PMID:22389499

Metal transport across biomembranes: emerging models for a distinct chemistry.

PubMed

Argüello, José M; Raimunda, Daniel; González-Guerrero, Manuel

2012-04-20

Transition metals are essential components of important biomolecules, and their homeostasis is central to many life processes. Transmembrane transporters are key elements controlling the distribution of metals in various compartments. However, due to their chemical properties, transition elements require transporters with different structural-functional characteristics from those of alkali and alkali earth ions. Emerging structural information and functional studies have revealed distinctive features of metal transport. Among these are the relevance of multifaceted events involving metal transfer among participating proteins, the importance of coordination geometry at transmembrane transport sites, and the presence of the largely irreversible steps associated with vectorial transport. Here, we discuss how these characteristics shape novel transition metal ion transport models.

Application of model abstraction techniques to simulate transport in soils

USDA-ARS?s Scientific Manuscript database

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...

Modelling atmospheric transport of α-hexachlorocyclohexane in the Northern Hemispherewith a 3-D dynamical model: DEHM-POP

NASA Astrophysics Data System (ADS)

Hansen, K. M.; Christensen, J. H.; Brandt, J.; Frohn, L. M.; Geels, C.

2004-07-01

The Danish Eulerian Hemispheric Model (DEHM) is a 3-D dynamical atmospheric transport model originally developed to describe the atmospheric transport of sulphur into the Arctic. A new version of the model, DEHM-POP, developed to study the atmospheric transport and environmental fate of persistent organic pollutants (POPs) is presented. During environmental cycling, POPs can be deposited and re-emitted several times before reaching a final destination. A description of the exchange processes between the land/ocean surfaces and the atmosphere is included in the model to account for this multi-hop transport. The α-isomer of the pesticide hexachlorocyclohexane (α-HCH) is used as tracer in the model development. The structure of the model and processes included are described in detail. The results from a model simulation showing the atmospheric transport for the years 1991 to 1998 are presented and evaluated against measurements. The annual averaged atmospheric concentration of α-HCH for the 1990s is well described by the model; however, the shorter-term average concentration for most of the stations is not well captured. This indicates that the present simple surface description needs to be refined to get a better description of the air-surface exchange processes of POPs.

Lagrangian transport model forecasts and a transport climatology for the Intercontinental Transport and Chemical Transformation 2002 (ITCT 2K2) measurement campaign

NASA Astrophysics Data System (ADS)

Forster, Caroline; Cooper, Owen; Stohl, Andreas; Eckhardt, Sabine; James, Paul; Dunlea, Edward; Nicks, Dennis K.; Holloway, John S.; Hübler, Gerd; Parrish, David D.; Ryerson, Tom B.; Trainer, Michael

2004-04-01

On the basis of Lagrangian tracer transport simulations this study presents an intercontinental transport climatology and tracer forecasts for the Intercontinental Transport and Chemical Transformation 2002 (ITCT 2K2) aircraft measurement campaign, which took place at Monterey, California, in April-May 2002 to measure Asian pollution arriving at the North American West Coast. For the climatology the average transport of an Asian CO tracer was calculated over a time period of 15 years using the particle dispersion model FLEXPART. To determine by how much the transport from Asia to North America during ITCT 2K2 deviated from the climatological mean, the 15-year average for April and May was compared with the average for April and May 2002 and that for the ITCT 2K2 period. It was found that 8% less Asian CO tracer arrived at the North American West Coast during the ITCT 2K2 period compared to the climatological mean. Below 8-km altitude, the maximum altitude of the research aircraft, 13% less arrived. Nevertheless, pronounced layers of Asian pollution were measured during 3 of the 13 ITCT 2K2 flights. FLEXPART was also successfully used as a forecasting tool for the flight planning during ITCT 2K2. It provided 3-day forecasts for three different anthropogenic CO tracers originating from Asia, North America, and Europe. In two case studies the forecast abilities of FLEXPART are analyzed and discussed by comparing the forecasts with measurement data and infrared satellite images. The model forecasts underestimated the measured CO enhancements by about a factor of 4, mainly because of an underestimation of the Asian emissions in the emission inventory and because of biomass-burning influence that was not modeled. Nevertheless, the intercontinental transport and dispersion of pollution plumes were qualitatively well predicted, and on the basis of the model results the aircraft could successfully be guided into the polluted air masses.

A Mechanistic Pharmacokinetic Model for Liver Transporter Substrates Under Liver Cirrhosis Conditions

PubMed Central

Li, R; Barton, HA; Maurer, TS

2015-01-01

Liver cirrhosis is a disease characterized by the loss of functional liver mass. Physiologically based pharmacokinetic (PBPK) modeling was applied to interpret and predict how the interplay among physiological changes in cirrhosis affects pharmacokinetics. However, previous PBPK models under cirrhotic conditions were developed for permeable cytochrome P450 substrates and do not directly apply to substrates of liver transporters. This study characterizes a PBPK model for liver transporter substrates in relation to the severity of liver cirrhosis. A published PBPK model structure for liver transporter substrates under healthy conditions and the physiological changes for cirrhosis are combined to simulate pharmacokinetics of liver transporter substrates in patients with mild and moderate cirrhosis. The simulated pharmacokinetics under liver cirrhosis reasonably approximate observations. This analysis includes meta-analysis to obtain system-dependent parameters in cirrhosis patients and a top-down approach to improve understanding of the effect of cirrhosis on transporter-mediated drug disposition under cirrhotic conditions. PMID:26225262

A conceptual network model of the air transportation system. the basic level 1 model.

DOT National Transportation Integrated Search

1971-04-01

A basic conceptual model of the entire Air Transportation System is being developed to serve as an analytical tool for studying the interactions among the system elements. The model is being designed to function in an interactive computer graphics en...

Component Design Report: International Transportation Energy Demand Determinants Model

EIA Publications

2017-01-01

This Component Design Report discusses working design elements for a new model to replace the International Transportation Model (ITran) in the World Energy Projection System Plus (WEPS ) that is maintained by the U.S. Energy Information Administration. The key objective of the new International Transportation Energy Demand Determinants (ITEDD) model is to enable more rigorous, quantitative research related to energy consumption in the international transportation sectors.

Interactive 4D Visualization of Sediment Transport Models

NASA Astrophysics Data System (ADS)

Butkiewicz, T.; Englert, C. M.

2013-12-01

Coastal sediment transport models simulate the effects that waves, currents, and tides have on near-shore bathymetry and features such as beaches and barrier islands. Understanding these dynamic processes is integral to the study of coastline stability, beach erosion, and environmental contamination. Furthermore, analyzing the results of these simulations is a critical task in the design, placement, and engineering of coastal structures such as seawalls, jetties, support pilings for wind turbines, etc. Despite the importance of these models, there is a lack of available visualization software that allows users to explore and perform analysis on these datasets in an intuitive and effective manner. Existing visualization interfaces for these datasets often present only one variable at a time, using two dimensional plan or cross-sectional views. These visual restrictions limit the ability to observe the contents in the proper overall context, both in spatial and multi-dimensional terms. To improve upon these limitations, we use 3D rendering and particle system based illustration techniques to show water column/flow data across all depths simultaneously. We can also encode multiple variables across different perceptual channels (color, texture, motion, etc.) to enrich surfaces with multi-dimensional information. Interactive tools are provided, which can be used to explore the dataset and find regions-of-interest for further investigation. Our visualization package provides an intuitive 4D (3D, time-varying) visualization of sediment transport model output. In addition, we are also integrating real world observations with the simulated data to support analysis of the impact from major sediment transport events. In particular, we have been focusing on the effects of Superstorm Sandy on the Redbird Artificial Reef Site, offshore of Delaware Bay. Based on our pre- and post-storm high-resolution sonar surveys, there has significant scour and bedform migration around the

Numerical Modeling Studies of Wake Vortex Transport and Evolution Within the Planetary Boundary Layer

NASA Technical Reports Server (NTRS)

Lin, Yuh-Lang; Arya, S. Pal; Kaplan, Michael L.; Shen, Shaohua

1998-01-01

In support of the wake vortex effect of the Terminal Area Productivity program, we have put forward four tasks to be accomplished in our proposal. The first task is validation of two-dimensional wake vortex-turbulence interaction. The second task is investigation of three-dimensional interaction between wake vortices and atmospheric boundary layer (ABL) turbulence. The third task is ABL studies. The, fourth task is addition of a Klemp-Durran condition at the top boundary for TASS model. The accomplishment of these tasks will increase our understanding of the dynamics of wake vortex and improve forecasting systems responsible for air safety and efficiency. The first two tasks include following three parts: (a) Determine significant length scale for vortex decay and transport, especially the length scales associated with the onset of Crow instability (Crow, 1970); (b) Study the effects of atmospheric turbulence on the decay of the wake vortices; and (c) Determine the relationships between decay rate, transport properties and atmospheric parameters based on large eddy simulation (LES) results and the observational data. These parameters may include turbulence kinetic energy, dissipation rate, wind shear and atmospheric stratification. The ABL studies cover LES modeling of turbulence structure within planetary boundary layer under transition and stable stratification conditions. Evidences have shown that the turbulence in the stable boundary layer can be highly intermittent and the length scales of eddies are very small compared to those in convective case. We proposed to develop a nesting grid mesh scheme and a modified Klemp-Durran conditions (Klemp and Wilhelmson, 1978) at the top boundary for TASS model to simulate planetary boundary layer under stable stratification conditions. During the past year, our group has made great efforts to carry out the above mentioned four tasks simultaneously. The work accomplished in the last year will be described in the next

A Combined Observational and Modeling Approach to Study Modern Dust Transport from the Patagonia Desert to East Antarctica

NASA Technical Reports Server (NTRS)

Gasso, S.; Stein, A.; Marino, F.; Castellano, E.; Udisti, R.; Ceratto, J.

2010-01-01

The understanding of present atmospheric transport processes from Southern Hemisphere (SH) landmasses to Antarctica can improve the interpretation of stratigraphic data in Antarctic ice cores. In addition, long range transport can deliver key nutrients normally not available to marine ecosystems in the Southern Ocean and may trigger or enhance primary productivity. However, there is a dearth of observational based studies of dust transport in the SH. This work aims to improve current understanding of dust transport in the SH by showing a characterization of two dust events originating in the Patagonia desert (south end of South America). The approach is based on a combined and complementary use of satellite retrievals (detectors MISR, MODIS, GLAS ,POLDER, OMI,), transport model simulation (HYSPLIT) and surface observations near the sources and aerosol measurements in Antarctica (Neumayer and Concordia sites). Satellite imagery and visibility observations confirm dust emission in a stretch of dry lakes along the coast of the Tierra del Fuego (TdF) island (approx.54deg S) and from the shores of the Colihue Huapi lake in Central Patagonia (approx.46deg S) in February 2005. Model simulations initialized by these observations reproduce the timing of an observed increase in dust concentration at the Concordia Station and some of the observed increases in atmospheric aerosol absorption (here used as a dust proxy) in the Neumayer station. The TdF sources were the largest contributors of dust at both sites. The transit times from TdF to the Neumayer and Concordia sites are 6-7 and 9-10 days respectively. Lidar observations and model outputs coincide in placing most of the dust cloud in the boundary layer and suggest significant de- position over the ocean immediately downwind. Boundary layer dust was detected as far as 1800 km from the source and approx.800 km north of the South Georgia Island over the central sub-Antarctic Atlantic Ocean. Although the analysis suggests the

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

NASA Astrophysics Data System (ADS)

Tohidi, Ali; Kaye, Nigel

2016-11-01

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

A continuum mechanics-based musculo-mechanical model for esophageal transport

NASA Astrophysics Data System (ADS)

Kou, Wenjun; Griffith, Boyce E.; Pandolfino, John E.; Kahrilas, Peter J.; Patankar, Neelesh A.

2017-11-01

In this work, we extend our previous esophageal transport model using an immersed boundary (IB) method with discrete fiber-based structural model, to one using a continuum mechanics-based model that is approximated based on finite elements (IB-FE). To deal with the leakage of flow when the Lagrangian mesh becomes coarser than the fluid mesh, we employ adaptive interaction quadrature points to deal with Lagrangian-Eulerian interaction equations based on a previous work (Griffith and Luo [1]). In particular, we introduce a new anisotropic adaptive interaction quadrature rule. The new rule permits us to vary the interaction quadrature points not only at each time-step and element but also at different orientations per element. This helps to avoid the leakage issue without sacrificing the computational efficiency and accuracy in dealing with the interaction equations. For the material model, we extend our previous fiber-based model to a continuum-based model. We present formulations for general fiber-reinforced material models in the IB-FE framework. The new material model can handle non-linear elasticity and fiber-matrix interactions, and thus permits us to consider more realistic material behavior of biological tissues. To validate our method, we first study a case in which a three-dimensional short tube is dilated. Results on the pressure-displacement relationship and the stress distribution matches very well with those obtained from the implicit FE method. We remark that in our IB-FE case, the three-dimensional tube undergoes a very large deformation and the Lagrangian mesh-size becomes about 6 times of Eulerian mesh-size in the circumferential orientation. To validate the performance of the method in handling fiber-matrix material models, we perform a second study on dilating a long fiber-reinforced tube. Errors are small when we compare numerical solutions with analytical solutions. The technique is then applied to the problem of esophageal transport. We use two

Predicting the use of public transportation: a case study from Putrajaya, Malaysia.

PubMed

Borhan, Muhamad Nazri; Syamsunur, Deprizon; Akhir, Norliza Mohd; Yazid, Muhamad Razuhanafi Mat; Ismail, Amiruddin; Rahmat, Riza Atiq

2014-01-01

Putrajaya is a new federal administrative capital of Malaysia which has been set to achieve a 70% share of all travels by public transport in the city area. However, the current modal split between the public transport and private transport is 15:85. In order to understand travelers' willingness to use the public transport, a conceptual model has been developed to determine the factors that affect them to use the public transport instead of travelling in their own cars. Various variables such as service quality, environmental impact, attitude, and behavior intention were analyzed and tested using structural equation model (SEM). Results indicate that the service quality and attitude are found to have positive effects on the behavioral intention of taking the public transport. Other than this, this study also shows that the service quality and environmental impact have some positive influences on the attitude to using the public transport. However, environmental impact has no significant, positive, and direct effect on behavioral intention. The results of this study demonstrate that the model that was developed is useful in predicting the public transport and it could provide a more complete understanding of behavioral intention towards public transport use.

Safety improvements through Intelligent Transport Systems: a South African case study based on microscopic simulation modelling.

PubMed

Vanderschuren, Marianne

2008-03-01

Intelligent Transport Systems (ITS) can facilitate the delivery of a wide range of policy objectives. There are six main objectives/benefits identified in the international literature: Safety (reduction of (potential) crashes), mobility (reduction of delays and travel times), efficiency (optimise the use of existing infrastructure), productivity (cost saving), energy/environment and customer satisfaction [Mitretek Systems, 2001. Intelligent Transport System Benefits: 2001 update, Under Contract to the Federal Highway Administration, US Department of Transportation, Washington, DC, US]. In the South African context, there is an interest for measures that can reduce (potential) crashes. In South Africa the number of year on year traffic related fatalities is still increasing. In 2005 the number of fatalities was 15393 (from 14135 in 2004) while the estimated costs for the same period increased from R8.89-billion to R9.99-billion [RTMC, 2007. Interim Road Traffic and Fatal Crash Report 2006, Road Traffic Management Corporation, Pretoria, SA]. Given the extent of the road safety problem and the potential benefits of ITS, the need for further research is apparent. A study with regards to the potential of different types of models (macroscopic, mesoscopic and miscroscopic simulation models) led to the use of Paramics. Two corridors and three types of ITS measures were investigated and safety benefits were estimated.

Modeling axisymmetric flow and transport

USGS Publications Warehouse

Langevin, C.D.

2008-01-01

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

Transport of carboxymethyl cellulose stabilized nanoscale zerovalent iron in porous media, an experimental and modeling study

NASA Astrophysics Data System (ADS)

Sleep, Brent; Mondal, Pulin; Furbacher, Paul; Cui, Ziteng; Krol, Magdalena

2015-04-01

Nano-scale zero valent iron (nZVI) is capable of reacting with a wide variety of groundwater contaminants. Therefore, during the last decade nZVI has received significant attention for application in subsurface remediation, particularly for sites contaminated with chlorinated compounds and heavy metals. However, due to agglomeration of the nZVI, delivery into the contaminated subsurface zones is challenging. Polymer stabilization of nZVI can enhance the mobility of the iron particles in the subsurface. In this study, a set of laboratory-scale transport experiments and numerical simulations were performed to evaluate carboxymethyl cellulose (CMC) polymer stabilized nZVI transport in porous media. Experiments were conducted in a two-dimensional water-saturated lab-scale glass-walled sandbox, uniformly packed with silica sand, to identify the effects of water specific discharge and CMC concentration on nZVI transport. Experiments were also performed using Lissamine Green B (LGB) dye as a non-reactive tracer to characterize the sand media. The CMC stabilized nZVI was synthesized freshly at a concentration of 1000 mg/L before each transport experiment. The synthesized CMC-nZVI mixture was characterized using transmission electron microscopy, dynamic light scattering, and UV-visual spectrophotometry. The movement of the LGB dye and nZVI in the sandbox during the experiments was monitored using time-lapsed images captured using a light source and a dark box. The transport of LGB, CMC, and CMC-nZVI was evaluated through analysis of the breakthrough curves at the outlet and the retained nZVI in the sandbox. The LGB, CMC, and nZVI transport was also modeled using a multiphase flow and transport model considering LGB and CMC as solutes, and nZVI as a colloid. Analysis of the breakthrough data showed that the mass recovery of LGB and CMC was greater than 95 % indicating conservative transport in silica sand. However, the mean residence time of CMC was significantly higher than

Source tagging modeling study of heavy haze episodes under complex regional transport processes over Wuhan megacity, Central China.

PubMed

Lu, Miaomiao; Tang, Xiao; Wang, Zifa; Gbaguidi, Alex; Liang, Shengwen; Hu, Ke; Wu, Lin; Wu, Huangjian; Huang, Zhen; Shen, Longjiao

2017-12-01

Wuhan as a megacity of Central China was suffering from severe particulate matter pollution according to previous observation studies, however, the mechanism behind the pollution formation especially the impact of regional chemical transport is still unclear. This study, carried out on the Nested Air Quality Prediction Modeling System (NAQPMS) coupled with an on-line source-tagging module, explores different roles regional transport had in two strong haze episodes over Wuhan in October 2014 and quantitatively assesses the contributions from local and regional sources to PM 2.5 concentration. Validation of predictions based on observations shows modeling system good skills in reproducing key meteorological and chemical features. The first short-time haze episode occurred on 12 October under strong northerly winds, with a hourly PM 2.5 peak of 180 μg m -3 , and was found to be caused primarily by the long-range transport from the northern regions, which contributed 60.6% of the episode's PM 2.5 concentration (versus a total of 32.7% from sources in and near Wuhan). The second episode lasted from the 15-20 October under stable regional large-scale synoptic conditions and weak winds, and had an hourly PM 2.5 peak of 231.0 μg m -3 . In this episode, both the long-distance transport from far regions and short-range transport from the Wuhan-cluster were the primary causes of the haze episode and account for 24.8% and 29.2% of the PM 2.5 concentration respectively. Therefore, regional transport acts as a crucial driver of haze pollution over Wuhan through not only long-range transfer of pollutants, but also short-range aerosol movement under specific meteorological conditions. The present findings highlight the important role of regional transport in urban haze formation and indicate that the joint control of multi city-clusters are needed to reduce the particulate pollution level in Wuhan. Copyright © 2017 Elsevier Ltd. All rights reserved.

Modelling the transport of optical photons in scintillation detectors for diagnostic and radiotherapy imaging

NASA Astrophysics Data System (ADS)

Roncali, Emilie; Mosleh-Shirazi, Mohammad Amin; Badano, Aldo

2017-10-01

Computational modelling of radiation transport can enhance the understanding of the relative importance of individual processes involved in imaging systems. Modelling is a powerful tool for improving detector designs in ways that are impractical or impossible to achieve through experimental measurements. Modelling of light transport in scintillation detectors used in radiology and radiotherapy imaging that rely on the detection of visible light plays an increasingly important role in detector design. Historically, researchers have invested heavily in modelling the transport of ionizing radiation while light transport is often ignored or coarsely modelled. Due to the complexity of existing light transport simulation tools and the breadth of custom codes developed by users, light transport studies are seldom fully exploited and have not reached their full potential. This topical review aims at providing an overview of the methods employed in freely available and other described optical Monte Carlo packages and analytical models and discussing their respective advantages and limitations. In particular, applications of optical transport modelling in nuclear medicine, diagnostic and radiotherapy imaging are described. A discussion on the evolution of these modelling tools into future developments and applications is presented. The authors declare equal leadership and contribution regarding this review.

Studies of potential intelligent transportation systems benefits using traffic simulation modeling

DOT National Transportation Integrated Search

1996-06-01

This report documents five studies performed by Mitretek Systems, Inc. to analyze potential : benefits of Intelligent Transportation Systems (ITS) deployment, in support of the ITS : Architecture Development Program. The studies explore the operation...

Use of Models in Urban Transportation Planning

DOT National Transportation Integrated Search

1973-04-01

The report describes the most commonly used models in urban transportation planning. A background on urban transportation planning is given including changes in planning objectives and the effects of Federal legislation. General concepts and problems...

Investigating the role of transportation models in epidemiologic studies of traffic related air pollution and health effects.

PubMed

Shekarrizfard, Maryam; Valois, Marie-France; Goldberg, Mark S; Crouse, Dan; Ross, Nancy; Parent, Marie-Elise; Yasmin, Shamsunnahar; Hatzopoulou, Marianne

2015-07-01

In two earlier case-control studies conducted in Montreal, nitrogen dioxide (NO2), a marker for traffic-related air pollution was found to be associated with the incidence of postmenopausal breast cancer and prostate cancer. These studies relied on a land use regression model (LUR) for NO2 that is commonly used in epidemiologic studies for deriving estimates of traffic-related air pollution. Here, we investigate the use of a transportation model developed during the summer season to generate a measure of traffic emissions as an alternative to the LUR model. Our traffic model provides estimates of emissions of nitrogen oxides (NOx) at the level of individual roads, as does the LUR model. Our main objective was to compare the distribution of the spatial estimates of NOx computed from our transportation model to the distribution obtained from the LUR model. A secondary objective was to compare estimates of risk using these two exposure estimates. We observed that the correlation (spearman) between our two measures of exposure (NO2 and NOx) ranged from less than 0.3 to more than 0.9 across Montreal neighborhoods. The most important factor affecting the "agreement" between the two measures in a specific area was found to be the length of roads. Areas affected by a high level of traffic-related air pollution had a far better agreement between the two exposure measures. A comparison of odds ratios (ORs) obtained from NO2 and NOx used in two case-control studies of breast and prostate cancer, showed that the differences between the ORs associated with NO2 exposure vs NOx exposure differed by 5.2-8.8%. Copyright © 2015 Elsevier Inc. All rights reserved.

Two dimensional model study of atmospheric transport using carbon-14 and strontium-90 as inert tracers

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

Kinnison, D.E.; Wuebbles, D.J.; Johnston, H.S.

1992-02-01

This study tests the transport processes in the LLNL two-dimensional chemical-radiative-transport model using recently reanalyzed carbon-14 and strontium-90 data. These radioactive tracers were produced bythe atmospheric nuclear bomb tests of 1952--58 and 1961--62, and they were measured at a few latitudes up to 35 kilometers over the period 1955--1970. Selected horizontal and vertical eddy diffusion coefficients were varied in the model to test their sensitivity to short and long term transpose of carbon-14. A sharp transition of K[sub zz] and K[sub yy] through the tropopause, as opposed to a slow transition between the same limiting values, shows a distinct improvementmore » in the calculated carbon-14 distributions, a distinct improvement in the calculated seasonal and latitudinal distribution of ozone columns (relative to TOMS observations), and a very large difference in the calculated ozone reduction by a possible fleet of High Speed Civil Transports. Calculated northern hemisphere carbon-14 is more sensitive to variation of K[sub yy] than are global ozone columns. Strontium-90 was used to test the LLNL tropopause height at four different latitudes. Starting with the 1960 background distribution of carbon-14, we calculate the input of carbon-14 as the sum of each nuclear test of the 1961--62 series, using two bomb-cloud rise models. With the Seitz bomb-rise formulation in the LLNL model, we find good agreement between calculated and observedcarbon-14 (with noticeable exceptions at the north polar tropopause and the short-term mid-latitude mid-stratosphere) between 1963 and 1970.« less

Two dimensional model study of atmospheric transport using carbon-14 and strontium-90 as inert tracers

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

Kinnison, D.E.; Wuebbles, D.J.; Johnston, H.S.

1992-02-01

This study tests the transport processes in the LLNL two-dimensional chemical-radiative-transport model using recently reanalyzed carbon-14 and strontium-90 data. These radioactive tracers were produced bythe atmospheric nuclear bomb tests of 1952--58 and 1961--62, and they were measured at a few latitudes up to 35 kilometers over the period 1955--1970. Selected horizontal and vertical eddy diffusion coefficients were varied in the model to test their sensitivity to short and long term transpose of carbon-14. A sharp transition of K{sub zz} and K{sub yy} through the tropopause, as opposed to a slow transition between the same limiting values, shows a distinct improvementmore » in the calculated carbon-14 distributions, a distinct improvement in the calculated seasonal and latitudinal distribution of ozone columns (relative to TOMS observations), and a very large difference in the calculated ozone reduction by a possible fleet of High Speed Civil Transports. Calculated northern hemisphere carbon-14 is more sensitive to variation of K{sub yy} than are global ozone columns. Strontium-90 was used to test the LLNL tropopause height at four different latitudes. Starting with the 1960 background distribution of carbon-14, we calculate the input of carbon-14 as the sum of each nuclear test of the 1961--62 series, using two bomb-cloud rise models. With the Seitz bomb-rise formulation in the LLNL model, we find good agreement between calculated and observedcarbon-14 (with noticeable exceptions at the north polar tropopause and the short-term mid-latitude mid-stratosphere) between 1963 and 1970.« less

Cosmic-Ray Transport in Heliospheric Magnetic Structures. II. Modeling Particle Transport through Corotating Interaction Regions

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

Kopp, Andreas; Wiengarten, Tobias; Fichtner, Horst

The transport of cosmic rays (CRs) in the heliosphere is determined by the properties of the solar wind plasma. The heliospheric plasma environment has been probed by spacecraft for decades and provides a unique opportunity for testing transport theories. Of particular interest for the three-dimensional (3D) heliospheric CR transport are structures such as corotating interaction regions (CIRs), which, due to the enhancement of the magnetic field strength and magnetic fluctuations within and due to the associated shocks as well as stream interfaces, do influence the CR diffusion and drift. In a three-fold series of papers, we investigate these effects bymore » modeling inner-heliospheric solar wind conditions with the numerical magnetohydrodynamic (MHD) framework Cronos (Wiengarten et al., referred as Paper I), and the results serve as input to a transport code employing a stochastic differential equation approach (this paper). While, in Paper I, we presented results from 3D simulations with Cronos, the MHD output is now taken as an input to the CR transport modeling. We discuss the diffusion and drift behavior of Galactic cosmic rays using the example of different theories, and study the effects of CIRs on these transport processes. In particular, we point out the wide range of possible particle fluxes at a given point in space resulting from these different theories. The restriction of this variety by fitting the numerical results to spacecraft data will be the subject of the third paper of this series.« less

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.

A review of model applications for structured soils: b) Pesticide transport.

PubMed

Köhne, John Maximilian; Köhne, Sigrid; Simůnek, Jirka

2009-02-16

The past decade has seen considerable progress in the development of models simulating pesticide transport in structured soils subject to preferential flow (PF). Most PF pesticide transport models are based on the two-region concept and usually assume one (vertical) dimensional flow and transport. Stochastic parameter sets are sometimes used to account for the effects of spatial variability at the field scale. In the past decade, PF pesticide models were also coupled with Geographical Information Systems (GIS) and groundwater flow models for application at the catchment and larger regional scales. A review of PF pesticide model applications reveals that the principal difficulty of their application is still the appropriate parameterization of PF and pesticide processes. Experimental solution strategies involve improving measurement techniques and experimental designs. Model strategies aim at enhancing process descriptions, studying parameter sensitivity, uncertainty, inverse parameter identification, model calibration, and effects of spatial variability, as well as generating model emulators and databases. Model comparison studies demonstrated that, after calibration, PF pesticide models clearly outperform chromatographic models for structured soils. Considering nonlinear and kinetic sorption reactions further enhanced the pesticide transport description. However, inverse techniques combined with typically available experimental data are often limited in their ability to simultaneously identify parameters for describing PF, sorption, degradation and other processes. On the other hand, the predictive capacity of uncalibrated PF pesticide models currently allows at best an approximate (order-of-magnitude) estimation of concentrations. Moreover, models should target the entire soil-plant-atmosphere system, including often neglected above-ground processes such as pesticide volatilization, interception, sorption to plant residues, root uptake, and losses by runoff. The

A multi-ion generalized transport model of the polar wind

NASA Technical Reports Server (NTRS)

Demars, H. G.; Schunk, R. W.

1994-01-01

The higher-order generalizations of the equations of standard hydrodynamics, known collectively as generalized transport theories, have been used since the early 1980s to describe the terrestrial polar wind. Inherent in the structure of generalized transport theories is the ability to describe not only interparticle collisions but also certain non-Maxwellian processes, such as heat flow and viscous stress, that are characteristic of any plasma flow that is not collision dominated. Because the polar wind exhibits a transition from collision-dominated to collisionless flow, generalized transport theories possess advantages for polar wind modeling not shared by either collision-dominated models (such as standard hydrodynamics) or collisionless models (such as those based on solving the collisionless Boltzmann equation). In general, previous polar wind models have used generalized transport equations to describe electrons and only one species of ion (H(+)). If other ion species were included in the models at all, it was in a simplified or semiempirical manner. The model described in this paper is the first polar wind model that uses a generalized transport theory (bi-Maxwellian-based 16-moment theory) to describe all of the species, both major and minor, in the polar wind plasma. In the model, electrons and three ion species (H(+), He(+), O(+)) are assumed to be major and several ion species are assumed to be minor (NO(+), Fe(+), O(++)). For all species, a complete 16-moment transport formulation is used, so that profiles of density, drift velocity, parallel and perpendicular temperatures, and the field-aligned parallel and perpendicular energy flows are obtained. In the results presented here, emphasis is placed on describing those constituents of the polar wind that have received little attention in past studies. In particular, characteristic solutions are presented for supersonic H(+) outflow and for both supersonic and subsonic outflows of the major ion He

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.

Forest Canopy Processes in a Regional Chemical Transport Model

NASA Astrophysics Data System (ADS)

Makar, Paul; Staebler, Ralf; Akingunola, Ayodeji; Zhang, Junhua; McLinden, Chris; Kharol, Shailesh; Moran, Michael; Robichaud, Alain; Zhang, Leiming; Stroud, Craig; Pabla, Balbir; Cheung, Philip

2016-04-01

Forest canopies have typically been absent or highly parameterized in regional chemical transport models. Some forest-related processes are often considered - for example, biogenic emissions from the forests are included as a flux lower boundary condition on vertical diffusion, as is deposition to vegetation. However, real forest canopies comprise a much more complicated set of processes, at scales below the "transport model-resolved scale" of vertical levels usually employed in regional transport models. Advective and diffusive transport within the forest canopy typically scale with the height of the canopy, and the former process tends to dominate over the latter. Emissions of biogenic hydrocarbons arise from the foliage, which may be located tens of metres above the surface, while emissions of biogenic nitric oxide from decaying plant matter are located at the surface - in contrast to the surface flux boundary condition usually employed in chemical transport models. Deposition, similarly, is usually parameterized as a flux boundary condition, but may be differentiated between fluxes to vegetation and fluxes to the surface when the canopy scale is considered. The chemical environment also changes within forest canopies: shading, temperature, and relativity humidity changes with height within the canopy may influence chemical reaction rates. These processes have been observed in a host of measurement studies, and have been simulated using site-specific one-dimensional forest canopy models. Their influence on regional scale chemistry has been unknown, until now. In this work, we describe the results of the first attempt to include complex canopy processes within a regional chemical transport model (GEM-MACH). The original model core was subdivided into "canopy" and "non-canopy" subdomains. In the former, three additional near-surface layers based on spatially and seasonally varying satellite-derived canopy height and leaf area index were added to the original model

Mathematical interpretation of Brownian motor model: Limit cycles and directed transport phenomena

NASA Astrophysics Data System (ADS)

Yang, Jianqiang; Ma, Hong; Zhong, Suchuang

2018-03-01

In this article, we first suggest that the attractor of Brownian motor model is one of the reasons for the directed transport phenomenon of Brownian particle. We take the classical Smoluchowski-Feynman (SF) ratchet model as an example to investigate the relationship between limit cycles and directed transport phenomenon of the Brownian particle. We study the existence and variation rule of limit cycles of SF ratchet model at changing parameters through mathematical methods. The influences of these parameters on the directed transport phenomenon of a Brownian particle are then analyzed through numerical simulations. Reasonable mathematical explanations for the directed transport phenomenon of Brownian particle in SF ratchet model are also formulated on the basis of the existence and variation rule of the limit cycles and numerical simulations. These mathematical explanations provide a theoretical basis for applying these theories in physics, biology, chemistry, and engineering.

Diffusion Dominant Solute Transport Modelling in Fractured Media Under Deep Geological Environment - 12211

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

Kwong, S.; Jivkov, A.P.

2012-07-01

Deep geologic disposal of high activity and long-lived radioactive waste is gaining increasing support in many countries, where suitable low permeability geological formation in combination with engineered barriers are used to provide long term waste contaminant and minimise the impacts to the environment and risk to the biosphere. This modelling study examines the solute transport in fractured media under low flow velocities that are relevant to a deep geological environment. In particular, reactive solute transport through fractured media is studied using a 2-D model, that considers advection and diffusion, to explore the coupled effects of kinetic and equilibrium chemical processes.more » The effects of water velocity in the fracture, matrix porosity and diffusion on solute transport are investigated and discussed. Some illustrative modelled results are presented to demonstrate the use of the model to examine the effects of media degradation on solute transport, under the influences of hydrogeological (diffusion dominant) and microbially mediated chemical processes. The challenges facing the prediction of long term degradation such as cracks evolution, interaction and coalescence are highlighted. The potential of a novel microstructure informed modelling approach to account for these effects is discussed, particularly with respect to investigating multiple phenomena impact on material performance. The GRM code is used to examine the effects of media degradation for a geological waste disposal package, under the combined hydrogeological (diffusion dominant) and chemical effects in low groundwater flow conditions that are typical of deep geological disposal systems. An illustrative reactive transport modelling application demonstrates the use of the code to examine the interplay of kinetic controlled biogeochemical reactive processes with advective and diffusive transport, under the influence of media degradation. The initial model results are encouraging which

Expression analysis of MDR1, BCRP and MRP3 transporter proteins in different in vitro and ex vivo cornea models for drug absorption studies.

PubMed

Verstraelen, Jessica; Reichl, Stephan

2013-01-30

Ocular drug absorption studies are required for the development of new drugs or drug delivery systems for eye treatment. Such preclinical investigations on transcorneal drug absorption are performed ex vivo with the excised corneas of experimental animals or in vitro using corneal cell culture models. The data currently available on the expression of ABC transporter proteins in corneal tissue is limited or contradictory. This study describes, for the first time, the comparison of the expression of ABC transporters, in particular, MDR1, BCRP and MRP3, between human cornea cell culture models and the most commonly used ex vivo models, namely, rabbit and porcine corneas, conducted in the same laboratory. The expression levels and functionality were determined by means of PCR, western blot, immunohistochemistry and bidirectional permeation studies using specific substrates and inhibitors. The results clearly indicate species-dependent expression of the studied efflux transporters. In the rabbit cornea, the expression and activity of MDR1 transporter was confirmed, whereas human cell culture models and porcine corneas did not show MDR1 expression. However, human cornea models possessed MRP3 and BCRP expression, whereas no functional expression was found in rabbit and porcine corneas. Therefore, the translation of transcorneal permeation data from animal experiments to humans should be performed with caution. Copyright © 2012 Elsevier B.V. All rights reserved.

Predicting the Use of Public Transportation: A Case Study from Putrajaya, Malaysia

PubMed Central

Borhan, Muhamad Nazri; Mohd Akhir, Norliza; Mat Yazid, Muhamad Razuhanafi; Ismail, Amiruddin; Rahmat, Riza Atiq

2014-01-01

Putrajaya is a new federal administrative capital of Malaysia which has been set to achieve a 70% share of all travels by public transport in the city area. However, the current modal split between the public transport and private transport is 15 : 85. In order to understand travelers' willingness to use the public transport, a conceptual model has been developed to determine the factors that affect them to use the public transport instead of travelling in their own cars. Various variables such as service quality, environmental impact, attitude, and behavior intention were analyzed and tested using structural equation model (SEM). Results indicate that the service quality and attitude are found to have positive effects on the behavioral intention of taking the public transport. Other than this, this study also shows that the service quality and environmental impact have some positive influences on the attitude to using the public transport. However, environmental impact has no significant, positive, and direct effect on behavioral intention. The results of this study demonstrate that the model that was developed is useful in predicting the public transport and it could provide a more complete understanding of behavioral intention towards public transport use. PMID:25110744

Integrated urban systems model with multiple transportation supply agents.

DOT National Transportation Integrated Search

2012-10-01

This project demonstrates the feasibility of developing quantitative models that can forecast future networks under : current and alternative transportation planning processes. The current transportation planning process is modeled : based on empiric...

Variational multiscale models for charge transport.

PubMed

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

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

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.

Preliminary Evaluation of the DUSTRAN Modeling Suite for Modeling Atmospheric Chloride Transport

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

Jensen, Philip; Tran, Tracy; Fritz, Bradley

2016-05-03

This study investigates the potential of DUSTRAN, a dust dispersion modeling system developed by Pacific Northwest National Laboratory, to model the transport of sea salt aerosols (SSA). Results from DUSTRAN simulations run with historical meteorological data were compared against privately-measured chloride data at the near coastal Maine Yankee Nuclear Power Plant (NPP) and the Environmental Protection Agency-measured CASTNET data from Acadia National Park (NP). The comparisons have provided both encouragement as to the practical value of DUSTRAN’s CALPUFF model and suggestions for further software development opportunities. All modeled concentrations were within one order of magnitude of those measured and amore » few test cases showed excellent agreement between modeled and measured concentrations. However, there is a lack of consistency in discrepancy which may be due to inaccurate extrapolation of meteorological data, underlying model physics, and the source term. Future research will refine the software to better capture physical phenomena. Overall, results indicate that with parameter refinement, DUSTRAN has the potential to simulate atmospheric chloride transport from known sources to inland sites for the purpose of determining the corrosion susceptibility of various structures, systems, and components at the site.« less

Generalized heat-transport equations: parabolic and hyperbolic models

NASA Astrophysics Data System (ADS)

Rogolino, Patrizia; Kovács, Robert; Ván, Peter; Cimmelli, Vito Antonio

2018-03-01

We derive two different generalized heat-transport equations: the most general one, of the first order in time and second order in space, encompasses some well-known heat equations and describes the hyperbolic regime in the absence of nonlocal effects. Another, less general, of the second order in time and fourth order in space, is able to describe hyperbolic heat conduction also in the presence of nonlocal effects. We investigate the thermodynamic compatibility of both models by applying some generalizations of the classical Liu and Coleman-Noll procedures. In both cases, constitutive equations for the entropy and for the entropy flux are obtained. For the second model, we consider a heat-transport equation which includes nonlocal terms and study the resulting set of balance laws, proving that the corresponding thermal perturbations propagate with finite speed.

Atmospheric transport of persistent organic pollutants - development of a 3-d dynamical transport model covering the northern hemisphere

NASA Astrophysics Data System (ADS)

Hansen, K. M.; Christensen, J. H.; Geels, C.; Frohn, L. M.; Brandt, J.

2003-04-01

The Danish Eulerian Hemispheric Model (DEHM) is a 3-D dynamical atmospheric transport model originally developed to describe the atmospheric transport of sulphur, lead, and mercury to the Arctic. The model has been validated carefully for these compounds. A new version of DEHM is currently being developed to describe the atmospheric transport of persistent organic pollutants (POPs) which are toxic, lipophilic and bio-accumulating compounds showing great persistence in the environment. The model has a horizontal resolution of 150 km x 150 km and 18 vertical layers, and it is driven by meteorological data from the numerical weather prediction model MM5V2. During environmental cycling POPs can be deposited and re-emitted several times before reaching a final destination. A description of the exchange processes between the land/ocean surfaces and the atmosphere is included in the model to account for this multi-hop transport. The present model version describes the atmospheric transport of the pesticide alpha-hexachlorocyclohexane (alpha-HCH). Other POPs may be included when proper data on emissions and physical-chemical parameters becomes available. The model-processes and the first model results are presented. The atmospheric transport of alpha-HCH for the 1990s is well described by the model.

Modeling tracer transport in randomly heterogeneous porous media by nonlocal moment equations: Anomalous transport

NASA Astrophysics Data System (ADS)

Morales-Casique, E.; Lezama-Campos, J. L.; Guadagnini, A.; Neuman, S. P.

2013-05-01

Modeling tracer transport in geologic porous media suffers from the corrupt characterization of the spatial distribution of hydrogeologic properties of the system and the incomplete knowledge of processes governing transport at multiple scales. Representations of transport dynamics based on a Fickian model of the kind considered in the advection-dispersion equation (ADE) fail to capture (a) the temporal variation associated with the rate of spreading of a tracer, and (b) the distribution of early and late arrival times which are often observed in field and/or laboratory scenarios and are considered as the signature of anomalous transport. Elsewhere we have presented exact stochastic moment equations to model tracer transport in randomly heterogeneous aquifers. We have also developed a closure scheme which enables one to provide numerical solutions of such moment equations at different orders of approximations. The resulting (ensemble) average and variance of concentration fields were found to display a good agreement against Monte Carlo - based simulation results for mildly heterogeneous (or well-conditioned strongly heterogeneous) media. Here we explore the ability of the moment equations approach to describe the distribution of early arrival times and late time tailing effects which can be observed in Monte-Carlo based breakthrough curves (BTCs) of the (ensemble) mean concentration. We show that BTCs of mean resident concentration calculated at a fixed space location through higher-order approximations of moment equations display long tailing features of the kind which is typically associated with anomalous transport behavior and are not represented by an ADE model with constant dispersive parameter, such as the zero-order approximation.

Process based modeling of total longshore sediment transport

USGS Publications Warehouse

Haas, K.A.; Hanes, D.M.

2004-01-01

Waves, currents, and longshore sand transport are calculated locally as a function of position in the nearshore region using process based numerical models. The resultant longshore sand transport is then integrated across the nearshore to provide predictions of the total longshore transport of sand due to waves and longshore currents. Model results are in close agreement with the I1-P1 correlation described by Komar and Inman (1970) and the CERC (1984) formula. Model results also indicate that the proportionality constant in the I1-P1 formula depends weakly upon the sediment size, the shape of the beach profile, and the particular local sediment flux formula that is employed. Model results indicate that the various effects and influences of sediment size tend to cancel out, resulting in little overall dependence on sediment size.

Modeling transport kinetics in clinoptilolite-phosphate rock systems

NASA Technical Reports Server (NTRS)

Allen, E. R.; Ming, D. W.; Hossner, L. R.; Henninger, D. L.

1995-01-01

Nutrient release in clinoptilolite-phosphate rock (Cp-PR) systems occurs through dissolution and cation-exchange reactions. Investigating the kinetics of these reactions expands our understanding of nutrient release processes. Research was conducted to model transport kinetics of nutrient release in Cp-PR systems. The objectives were to identify empirical models that best describe NH4, K, and P release and define diffusion-controlling processes. Materials included a Texas clinoptilolite (Cp) and North Carolina phosphate rock (PR). A continuous-flow thin-disk technique was used. Models evaluated included zero order, first order, second order, parabolic diffusion, simplified Elovich, Elovich, and power function. The power-function, Elovich, and parabolic-diffusion models adequately described NH4, K, and P release. The power-function model was preferred because of its simplicity. Models indicated nutrient release was diffusion controlled. Primary transport processes controlling nutrient release for the time span observed were probably the result of a combination of several interacting transport mechanisms.

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

NASA Astrophysics Data System (ADS)

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

2014-05-01

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

A model of axonal transport drug delivery

NASA Astrophysics Data System (ADS)

Kuznetsov, Andrey V.

2012-04-01

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

A kinetic Monte Carlo approach to study fluid transport in pore networks

NASA Astrophysics Data System (ADS)

Apostolopoulou, M.; Day, R.; Hull, R.; Stamatakis, M.; Striolo, A.

2017-10-01

The mechanism of fluid migration in porous networks continues to attract great interest. Darcy's law (phenomenological continuum theory), which is often used to describe macroscopically fluid flow through a porous material, is thought to fail in nano-channels. Transport through heterogeneous and anisotropic systems, characterized by a broad distribution of pores, occurs via a contribution of different transport mechanisms, all of which need to be accounted for. The situation is likely more complicated when immiscible fluid mixtures are present. To generalize the study of fluid transport through a porous network, we developed a stochastic kinetic Monte Carlo (KMC) model. In our lattice model, the pore network is represented as a set of connected finite volumes (voxels), and transport is simulated as a random walk of molecules, which "hop" from voxel to voxel. We simulated fluid transport along an effectively 1D pore and we compared the results to those expected by solving analytically the diffusion equation. The KMC model was then implemented to quantify the transport of methane through hydrated micropores, in which case atomistic molecular dynamic simulation results were reproduced. The model was then used to study flow through pore networks, where it was able to quantify the effect of the pore length and the effect of the network's connectivity. The results are consistent with experiments but also provide additional physical insights. Extension of the model will be useful to better understand fluid transport in shale rocks.

A case study on the influences of long-range transport to Taiwan`s acid deposition using Taiwan air quality model

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

Ken-Hui Chang; Fu-Tien Jeng

1996-12-31

The long-range and transboundary transport of precursors of add deposition in East Asia became important due to the industrial development around this area. We started to develop Taiwan Air Quality Model (TAQM) system since 1992, which is based on regional Acid Deposition Model (RADM) system. A typical episode in Mei-Yu season has been selected to study. A case considering all emissions within simulated domain has been run as a reference case, and another perturbed case, not including Taiwan`s emission, has been also run for analyzing quantitatively the influence of long-range transport to Taiwan`s wet deposition during the episode are 31%more » and 24% for total sulfur compounds and total nitrogen compounds respectively; but for dry deposition, only 6% is contributed by long range transport for sulfur compounds and 29% for total nitrogen compounds. Therefore, the percentages of total acid deposition contributed by long-range transport are 27% and 25% for total sulfur compounds and total nitrogen compounds, respectively.« less

Modeling coupled nanoparticle aggregation and transport in porous media: A Lagrangian approach

NASA Astrophysics Data System (ADS)

Taghavy, Amir; Pennell, Kurt D.; Abriola, Linda M.

2015-01-01

Changes in nanoparticle size and shape due to particle-particle interactions (i.e., aggregation or agglomeration) may significantly alter particle mobility and retention in porous media. To date, however, few modeling studies have considered the coupling of transport and particle aggregation processes. The majority of particle transport models employ an Eulerian modeling framework and are, consequently, limited in the types of collisions and aggregate sizes that can be considered. In this work, a more general Lagrangian modeling framework is developed and implemented to explore coupled nanoparticle aggregation and transport processes. The model was verified through comparison of model simulations to published results of an experimental and Eulerian modeling study (Raychoudhury et al., 2012) of carboxymethyl cellulose (CMC)-modified nano-sized zero-valent iron particle (nZVI) transport and retention in water-saturated sand columns. A model sensitivity analysis reveals the influence of influent particle concentration (ca. 70 to 700 mg/L), primary particle size (10-100 nm) and pore water velocity (ca. 1-6 m/day) on particle-particle, and, consequently, particle-collector interactions. Model simulations demonstrate that, when environmental conditions promote particle-particle interactions, neglecting aggregation effects can lead to under- or over-estimation of nanoparticle mobility. Results also suggest that the extent to which higher order particle-particle collisions influence aggregation kinetics will increase with the fraction of primary particles. This work demonstrates the potential importance of time-dependent aggregation processes on nanoparticle mobility and provides a numerical model capable of capturing/describing these interactions in water-saturated porous media.

Modeling coupled nanoparticle aggregation and transport in porous media: a Lagrangian approach.

PubMed

Taghavy, Amir; Pennell, Kurt D; Abriola, Linda M

2015-01-01

Changes in nanoparticle size and shape due to particle-particle interactions (i.e., aggregation or agglomeration) may significantly alter particle mobility and retention in porous media. To date, however, few modeling studies have considered the coupling of transport and particle aggregation processes. The majority of particle transport models employ an Eulerian modeling framework and are, consequently, limited in the types of collisions and aggregate sizes that can be considered. In this work, a more general Lagrangian modeling framework is developed and implemented to explore coupled nanoparticle aggregation and transport processes. The model was verified through comparison of model simulations to published results of an experimental and Eulerian modeling study (Raychoudhury et al., 2012) of carboxymethyl cellulose (CMC)-modified nano-sized zero-valent iron particle (nZVI) transport and retention in water-saturated sand columns. A model sensitivity analysis reveals the influence of influent particle concentration (ca. 70 to 700 mg/L), primary particle size (10-100 nm) and pore water velocity (ca. 1-6 m/day) on particle-particle, and, consequently, particle-collector interactions. Model simulations demonstrate that, when environmental conditions promote particle-particle interactions, neglecting aggregation effects can lead to under- or over-estimation of nanoparticle mobility. Results also suggest that the extent to which higher order particle-particle collisions influence aggregation kinetics will increase with the fraction of primary particles. This work demonstrates the potential importance of time-dependent aggregation processes on nanoparticle mobility and provides a numerical model capable of capturing/describing these interactions in water-saturated porous media. Copyright © 2014 Elsevier B.V. All rights reserved.

Bioinformatics for transporter pharmacogenomics and systems biology: data integration and modeling with UML.

PubMed

Yan, Qing

2010-01-01

Bioinformatics is the rational study at an abstract level that can influence the way we understand biomedical facts and the way we apply the biomedical knowledge. Bioinformatics is facing challenges in helping with finding the relationships between genetic structures and functions, analyzing genotype-phenotype associations, and understanding gene-environment interactions at the systems level. One of the most important issues in bioinformatics is data integration. The data integration methods introduced here can be used to organize and integrate both public and in-house data. With the volume of data and the high complexity, computational decision support is essential for integrative transporter studies in pharmacogenomics, nutrigenomics, epigenetics, and systems biology. For the development of such a decision support system, object-oriented (OO) models can be constructed using the Unified Modeling Language (UML). A methodology is developed to build biomedical models at different system levels and construct corresponding UML diagrams, including use case diagrams, class diagrams, and sequence diagrams. By OO modeling using UML, the problems of transporter pharmacogenomics and systems biology can be approached from different angles with a more complete view, which may greatly enhance the efforts in effective drug discovery and development. Bioinformatics resources of membrane transporters and general bioinformatics databases and tools that are frequently used in transporter studies are also collected here. An informatics decision support system based on the models presented here is available at http://www.pharmtao.com/transporter . The methodology developed here can also be used for other biomedical fields.

Self-Consistent Chaotic Transport in a High-Dimensional Mean-Field Hamiltonian Map Model

DOE PAGES

Martínez-del-Río, D.; del-Castillo-Negrete, D.; Olvera, A.; ...

2015-10-30

We studied the self-consistent chaotic transport in a Hamiltonian mean-field model. This model provides a simplified description of transport in marginally stable systems including vorticity mixing in strong shear flows and electron dynamics in plasmas. Self-consistency is incorporated through a mean-field that couples all the degrees-of-freedom. The model is formulated as a large set of N coupled standard-like area-preserving twist maps in which the amplitude and phase of the perturbation, rather than being constant like in the standard map, are dynamical variables. Of particular interest is the study of the impact of periodic orbits on the chaotic transport and coherentmore » structures. Furthermore, numerical simulations show that self-consistency leads to the formation of a coherent macro-particle trapped around the elliptic fixed point of the system that appears together with an asymptotic periodic behavior of the mean field. To model this asymptotic state, we introduced a non-autonomous map that allows a detailed study of the onset of global transport. A turnstile-type transport mechanism that allows transport across instantaneous KAM invariant circles in non-autonomous systems is discussed. As a first step to understand transport, we study a special type of orbits referred to as sequential periodic orbits. Using symmetry properties we show that, through replication, high-dimensional sequential periodic orbits can be generated starting from low-dimensional periodic orbits. We show that sequential periodic orbits in the self-consistent map can be continued from trivial (uncoupled) periodic orbits of standard-like maps using numerical and asymptotic methods. Normal forms are used to describe these orbits and to find the values of the map parameters that guarantee their existence. Numerical simulations are used to verify the prediction from the asymptotic methods.« less

Self-Consistent Chaotic Transport in a High-Dimensional Mean-Field Hamiltonian Map Model

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

Martínez-del-Río, D.; del-Castillo-Negrete, D.; Olvera, A.

We studied the self-consistent chaotic transport in a Hamiltonian mean-field model. This model provides a simplified description of transport in marginally stable systems including vorticity mixing in strong shear flows and electron dynamics in plasmas. Self-consistency is incorporated through a mean-field that couples all the degrees-of-freedom. The model is formulated as a large set of N coupled standard-like area-preserving twist maps in which the amplitude and phase of the perturbation, rather than being constant like in the standard map, are dynamical variables. Of particular interest is the study of the impact of periodic orbits on the chaotic transport and coherentmore » structures. Furthermore, numerical simulations show that self-consistency leads to the formation of a coherent macro-particle trapped around the elliptic fixed point of the system that appears together with an asymptotic periodic behavior of the mean field. To model this asymptotic state, we introduced a non-autonomous map that allows a detailed study of the onset of global transport. A turnstile-type transport mechanism that allows transport across instantaneous KAM invariant circles in non-autonomous systems is discussed. As a first step to understand transport, we study a special type of orbits referred to as sequential periodic orbits. Using symmetry properties we show that, through replication, high-dimensional sequential periodic orbits can be generated starting from low-dimensional periodic orbits. We show that sequential periodic orbits in the self-consistent map can be continued from trivial (uncoupled) periodic orbits of standard-like maps using numerical and asymptotic methods. Normal forms are used to describe these orbits and to find the values of the map parameters that guarantee their existence. Numerical simulations are used to verify the prediction from the asymptotic methods.« less

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

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

Adeleke, Najeem, E-mail: najm@psu.edu; Adewumi, Michael, E-mail: m2a@psu.edu; Ityokumbul, Thaddeus

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 modelmore » 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.« less

Aircraft wake vortex transport model

DOT National Transportation Integrated Search

1974-03-31

A wake vortex transport model has been developed which includes the effects of wind and wind : shear, buoyancy, mutual and self-induction, ground plane interaction, viscous decay, finite core : and Crow instability effects. Photographic and ground-wi...

Computer modeling of electron and proton transport in chloroplasts.

PubMed

Tikhonov, Alexander N; Vershubskii, Alexey V

2014-07-01

Photosynthesis is one of the most important biological processes in biosphere, which provides production of organic substances from atmospheric CO2 and water at expense of solar energy. In this review, we contemplate computer models of oxygenic photosynthesis in the context of feedback regulation of photosynthetic electron transport in chloroplasts, the energy-transducing organelles of the plant cell. We start with a brief overview of electron and proton transport processes in chloroplasts coupled to ATP synthesis and consider basic regulatory mechanisms of oxygenic photosynthesis. General approaches to computer simulation of photosynthetic processes are considered, including the random walk models of plastoquinone diffusion in thylakoid membranes and deterministic approach to modeling electron transport in chloroplasts based on the mass action law. Then we focus on a kinetic model of oxygenic photosynthesis that includes key stages of the linear electron transport, alternative pathways of electron transfer around photosystem I (PSI), transmembrane proton transport and ATP synthesis in chloroplasts. This model includes different regulatory processes: pH-dependent control of the intersystem electron transport, down-regulation of photosystem II (PSII) activity (non-photochemical quenching), the light-induced activation of the Bassham-Benson-Calvin (BBC) cycle. The model correctly describes pH-dependent feedback control of electron transport in chloroplasts and adequately reproduces a variety of experimental data on induction events observed under different experimental conditions in intact chloroplasts (variations of CO2 and O2 concentrations in atmosphere), including a complex kinetics of P700 (primary electron donor in PSI) photooxidation, CO2 consumption in the BBC cycle, and photorespiration. Finally, we describe diffusion-controlled photosynthetic processes in chloroplasts within the framework of the model that takes into account complex architecture of

Mathematical modeling of urea transport in the kidney.

PubMed

Layton, Anita T

2014-01-01

Mathematical modeling techniques have been useful in providing insights into biological systems, including the kidney. This article considers some of the mathematical models that concern urea transport in the kidney. Modeling simulations have been conducted to investigate, in the context of urea cycling and urine concentration, the effects of hypothetical active urea secretion into pars recta. Simulation results suggest that active urea secretion induces a "urea-selective" improvement in urine concentrating ability. Mathematical models have also been built to study the implications of the highly structured organization of tubules and vessels in the renal medulla on urea sequestration and cycling. The goal of this article is to show how physiological problems can be formulated and studied mathematically, and how such models may provide insights into renal functions.

Comparison of mechanistic transport cycle models of ABC exporters.

PubMed

Szöllősi, Dániel; Rose-Sperling, Dania; Hellmich, Ute A; Stockner, Thomas

2018-04-01

ABC (ATP binding cassette) transporters, ubiquitous in all kingdoms of life, carry out essential substrate transport reactions across cell membranes. Their transmembrane domains bind and translocate substrates and are connected to a pair of nucleotide binding domains, which bind and hydrolyze ATP to energize import or export of substrates. Over four decades of investigations into ABC transporters have revealed numerous details from atomic-level structural insights to their functional and physiological roles. Despite all these advances, a comprehensive understanding of the mechanistic principles of ABC transporter function remains elusive. The human multidrug resistance transporter ABCB1, also referred to as P-glycoprotein (P-gp), is one of the most intensively studied ABC exporters. Using ABCB1 as the reference point, we aim to compare the dominating mechanistic models of substrate transport and ATP hydrolysis for ABC exporters and to highlight the experimental and computational evidence in their support. In particular, we point out in silico studies that enhance and complement available biochemical data. "This article is part of a Special Issue entitled: Beyond the Structure-Function Horizon of Membrane Proteins edited by Ute Hellmich, Rupak Doshi and Benjamin McIlwain." Copyright © 2017 The Authors. Published by Elsevier B.V. All rights reserved.

Modeling Biodegradation and Reactive Transport: Analytical and Numerical Models

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

Sun, Y; Glascoe, L

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 requirementsmore » 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.« less

Modelling Suspended Sediment Transport in Monsoon Season: A Case Study of Pahang River Estuary, Pahang, Malaysia

NASA Astrophysics Data System (ADS)

Zakariya, Razak; Ahmad, Zuhairi; Saad, Shahbudin; Yaakop, Rosnan

2013-04-01

Sediment transport based on 2-dimensional real time model was applied to Pahang River estuary, Pahang, Malaysia and has been evaluated and verified with time series of tidal elevation, flow and suspended sediment load. Period of modelling was during highest high tide and lowest low tide in Northeast Monsoon (NE) which happened in December 2010 and Southwest Monsoon (SW) in July 2011. Simulated model outputs has been verify using Pearson's coefficient and has showed high accuracy. The validated model was used to simulate hydrodynamic and sediment transport of extreme conditions during both monsoon seasons. Based on field measurement and model simulation, tidal elevation and flow velocity, freshwater discharge of Pahang River were found to be higher during NE Monsoon. Based on the fluxes, the estuary also showed 'ebb-dominant' characteristic during highest high tide and lowest low tide in NE monsoon and normal ebbing-flooding characteristics during SW monsoon. In the Pahang River estuary, inflow and outflow patterns were perpendicular to the open boundary with circular flow formed at the shallow area in the middle of estuary during both monsoons. Referring to sea water intrusion from the river mouth, both seasons show penetration of more than 9 km (upstream input boundary) during higher high water tide. During higher lower water tide, the water intrusion stated varies which 5.6km during NE monsoon and 7.8km during SW monsoon. Regarding to the times lap during high tide, the sea water takes 2.8 hours to reach 9km upstream during NE monsoon compared to 1.9 hour during SW monsoon. The averages of suspended sediment concentration and suspended sediment load were higher during Northeast monsoon which increased the sedimentation potentials.Total of suspended sediment load discharged to the South China Sea yearly from Pahang River is approximately 96727.5 tonnes/day or 3.33 tonnes/km2/day which 442.6 tonnes/day during Northeast Monsoon and 25.3 tonnes/day during Southwest

Studies of HZE particle interactions and transport for space radiation protection purposes

NASA Technical Reports Server (NTRS)

Townsend, Lawrence W.; Wilson, John W.; Schimmerling, Walter; Wong, Mervyn

1987-01-01

The main emphasis is on developing general methods for accurately predicting high-energy heavy ion (HZE) particle interactions and transport for use by researchers in mission planning studies, in evaluating astronaut self-shielding factors, and in spacecraft shield design and optimization studies. The two research tasks are: (1) to develop computationally fast and accurate solutions to the Boltzmann (transport) equation; and (2) to develop accurate HZE interaction models, from fundamental physical considerations, for use as inputs into these transport codes. Accurate solutions to the HZE transport problem have been formulated through a combination of analytical and numerical techniques. In addition, theoretical models for the input interaction parameters are under development: stopping powers, nuclear absorption cross sections, and fragmentation parameters.

Tritium environmental transport studies at TFTR

NASA Astrophysics Data System (ADS)

Ritter, P. D.; Dolan, T. J.; Longhurst, G. R.

1993-06-01

Environmental tritium concentrations will be measured near the Tokamak Fusion Test Reactor (TFTR) to help validate dynamic models of tritium transport in the environment. For model validation the database must contain sequential measurements of tritium concentrations in key environmental compartments. Since complete containment of tritium is an operational goal, the supplementary monitoring program should be able to glean useful data from an unscheduled acute release. Portable air samplers will be used to take samples automatically every 4 hours for a week after an acute release, thus obtaining the time resolution needed for code validation. Samples of soil, vegetation, and foodstuffs will be gathered daily at the same locations as the active air monitors. The database may help validate the plant/soil/air part of tritium transport models and enhance environmental tritium transport understanding for the International Thermonuclear Experimental Reactor (ITER).

A sigma-coordinate primitive equation model for studying the circulation in the South Atlantic Part II: Meridional transports and seasonal variability

NASA Astrophysics Data System (ADS)

Marchesiello, P.; Barnier, B.; de Miranda, A. P.

1998-04-01

The mean and seasonal variability of the circulation and meridional heat transport in the South Atlantic are investigated using a set of numerical experiments. The primitive equation model uses a topography-following (sigma) coordinate. The model domain is limited to the South Atlantic basin. Artificial boundaries at Drake Passage, between Brazil and Angola, and between South Africa and Antarctica are treated as open boundaries. Finally, recent and self-consistent estimates of seasonal fluxes are used to define a model-dependent atmospheric forcing. Quasi-diagnostic simulations forced by constant climatological winds are first conducted to determine the sensitivity of model solutions to bottom topography smoothing, and to diagnose meridional fluxes from a mass field that is relaxed to the annual climatology of Levitus (1982). Model results show good agreement with known climatological circulation features in this basin, especially in the Confluence Region, where coarse resolution models usually give smooth structures. Sensitivity studies show that the more detailed features of the circulation are influenced by the model bathymetry. The model simulates a meridional circulation whose upper branch (the return flow that balances the southward flow of North Atlantic Deep Water) is composed of Intermediate (IW) and Thermocline (TW) Waters. The transport of IW is found to be predominant, and the value of meridional heat transport consequently falls within the low estimates. We notice that the meridional heat balance is sensitive to the position of the Confluence. When this region occurs too far south, the amount of IW contributing to the return flow of the overturning cell is reduced. Prognostic simulations forced by seasonal winds and heat fluxes are studied to quantify the impact of wind forcing on the circulation in the South Atlantic. Particular attention is focused on meridional transports at 30°S. Analysis of the mean annual circulation confirms that the upper

Significance of flow clustering and sequencing on sediment transport: 1D sediment transport modelling

NASA Astrophysics Data System (ADS)

Hassan, Kazi; Allen, Deonie; Haynes, Heather

2016-04-01

This paper considers 1D hydraulic model data on the effect of high flow clusters and sequencing on sediment transport. Using observed flow gauge data from the River Caldew, England, a novel stochastic modelling approach was developed in order to create alternative 50 year flow sequences. Whilst the observed probability density of gauge data was preserved in all sequences, the order in which those flows occurred was varied using the output from a Hidden Markov Model (HMM) with generalised Pareto distribution (GP). In total, one hundred 50 year synthetic flow series were generated and used as the inflow boundary conditions for individual flow series model runs using the 1D sediment transport model HEC-RAS. The model routed graded sediment through the case study river reach to define the long-term morphological changes. Comparison of individual simulations provided a detailed understanding of the sensitivity of channel capacity to flow sequence. Specifically, each 50 year synthetic flow sequence was analysed using a 3-month, 6-month or 12-month rolling window approach and classified for clusters in peak discharge. As a cluster is described as a temporal grouping of flow events above a specified threshold, the threshold condition used herein is considered as a morphologically active channel forming discharge event. Thus, clusters were identified for peak discharges in excess of 10%, 20%, 50%, 100% and 150% of the 1 year Return Period (RP) event. The window of above-peak flows also required cluster definition and was tested for timeframes 1, 2, 10 and 30 days. Subsequently, clusters could be described in terms of the number of events, maximum peak flow discharge, cumulative flow discharge and skewness (i.e. a description of the flow sequence). The model output for each cluster was analysed for the cumulative flow volume and cumulative sediment transport (mass). This was then compared to the total sediment transport of a single flow event of equivalent flow volume

Mechanistic Study of Human Glucose Transport Mediated by GLUT1.

PubMed

Fu, Xuegang; Zhang, Gang; Liu, Ran; Wei, Jing; Zhang-Negrerie, Daisy; Jian, Xiaodong; Gao, Qingzhi

2016-03-28

The glucose transporter 1 (GLUT1) belongs to the major facilitator superfamily (MFS) and is responsible for the constant uptake of glucose. However, the molecular mechanism of sugar transport remains obscure. In this study, homology modeling and molecular dynamics (MD) simulations in lipid bilayers were performed to investigate the combination of the alternate and multisite transport mechanism of glucose with GLUT1 in atomic detail. To explore the substrate recognition mechanism, the outward-open state human GLUT1 homology model was generated based on the template of xylose transporter XylE (PDB ID: 4GBZ), which shares up to 29% sequence identity and 49% similarity with GLUT1. Through the MD simulation study of glucose across lipid bilayer with both the outward-open GLUT1 and the GLUT1 inward-open crystal structure, we investigated six different conformational states and identified four key binding sites in both exofacial and endofacial loops that are essential for glucose recognition and transport. The study further revealed that four flexible gates consisting of W65/Y292/Y293-M420/TM10b-W388 might play important roles in the transport cycle. The study showed that some side chains close to the central ligand binding site underwent larger position changes. These conformational interchanges formed gated networks within an S-shaped central channel that permitted staged ligand diffusion across the transporter. This study provides new inroads for the understanding of GLUT1 ligand recognition paradigm and configurational features which are important for molecular, structural, and physiological research of the MFS members, especially for GLUT1-targeted drug design and discovery.

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.

Analysis of Intelligent Transportation Systems Using Model-Driven Simulations.

PubMed

Fernández-Isabel, Alberto; Fuentes-Fernández, Rubén

2015-06-15

Intelligent Transportation Systems (ITSs) integrate information, sensor, control, and communication technologies to provide transport related services. Their users range from everyday commuters to policy makers and urban planners. Given the complexity of these systems and their environment, their study in real settings is frequently unfeasible. Simulations help to address this problem, but present their own issues: there can be unintended mistakes in the transition from models to code; their platforms frequently bias modeling; and it is difficult to compare works that use different models and tools. In order to overcome these problems, this paper proposes a framework for a model-driven development of these simulations. It is based on a specific modeling language that supports the integrated specification of the multiple facets of an ITS: people, their vehicles, and the external environment; and a network of sensors and actuators conveniently arranged and distributed that operates over them. The framework works with a model editor to generate specifications compliant with that language, and a code generator to produce code from them using platform specifications. There are also guidelines to help researchers in the application of this infrastructure. A case study on advanced management of traffic lights with cameras illustrates its use.

Analysis of Intelligent Transportation Systems Using Model-Driven Simulations

PubMed Central

Fernández-Isabel, Alberto; Fuentes-Fernández, Rubén

2015-01-01

Intelligent Transportation Systems (ITSs) integrate information, sensor, control, and communication technologies to provide transport related services. Their users range from everyday commuters to policy makers and urban planners. Given the complexity of these systems and their environment, their study in real settings is frequently unfeasible. Simulations help to address this problem, but present their own issues: there can be unintended mistakes in the transition from models to code; their platforms frequently bias modeling; and it is difficult to compare works that use different models and tools. In order to overcome these problems, this paper proposes a framework for a model-driven development of these simulations. It is based on a specific modeling language that supports the integrated specification of the multiple facets of an ITS: people, their vehicles, and the external environment; and a network of sensors and actuators conveniently arranged and distributed that operates over them. The framework works with a model editor to generate specifications compliant with that language, and a code generator to produce code from them using platform specifications. There are also guidelines to help researchers in the application of this infrastructure. A case study on advanced management of traffic lights with cameras illustrates its use. PMID:26083232

Modeling Transportation Systems : an Overview

DOT National Transportation Integrated Search

1971-06-01

The purpose of this report is to outline the role of systems analysis and mathematical modeling in the planning of transportation systems. The planning process is divided into three sectors (demand, supply, and policy) reflecting the demand for trans...

Modeling of gravitational separation using the NIES global atmospheric tracer transport model

NASA Astrophysics Data System (ADS)

Belikov, D.; Ishidoya, S.; Sugawara, S.; Maksyutov, S. S.; Hasebe, F.

2017-12-01

The existence of gravitational separation (separation of atmospheric molecules depending on their molar masses) in the stratosphere was confirmed both experimentally from high-precision measurements of the isotopic ratios of N2, O2, Ar (Ishidoya et al., ACP, 2008), and theoretically by numerical simulations using the 2-dimensional model of the middle atmosphere (SOCRATES) (Ishidoya et al., ACP, 2013). It was also shown, that the gravitational separation, as well as their relationship with age of air, is usable as a new indicator of long-term changes in the Brewer-Dobson Circulation (BDC).For more detailed examination of the relationship between gravitational separation and the stratospheric circulation, we used the NIES (National Institute for Environmental Studies) three-dimensional global atmospheric tracer transport model with molecular diffusivity parameterization. The NIES transport model uses a flexible hybrid sigma-isentropic vertical coordinate, in which a vertical transport in the stratosphere was controlled by the heating rate from reanalysis. The simulated gravitational separation and age of air are validated through comparison with observations carried out using a balloon-borne cryogenic air sampler over Kiruna (68°N, 21°E), Sweden, Sanriku (39°N, 142°E) and Taiki (43°N, 143°E), Japan, Syowa Station (69°S, 39°E), Antarctica for 1995-2010.Our further study is an analysis of gravitational separation in respect of the major stratospheric processes including variabilities/changes in association with quasi-biennial oscillation, Asian summer monsoon, Sudden Stratospheric Warming events, acceleration of the BDC due to global warming.

Modelling atmospheric transport of persistent organic pollutants in the Northern Hemisphere with a 3-D dynamical model: DEHM-POP

NASA Astrophysics Data System (ADS)

Hansen, K. M.; Christensen, J. H.; Brandt, J.; Frohn, L. M.; Geels, C.

2004-03-01

The Danish Eulerian Hemispheric Model (DEHM) is a 3-D dynamical atmospheric transport model originally developed to describe the atmospheric transport of sulphur into the Arctic. A new version of the model, DEHM-POP, developed to study the atmospheric transport and environmental fate of persistent organic pollutants (POPs) is presented. During environmental cycling, POPs can be deposited and re-emitted several times before reaching a final destination. A description of the exchange processes between the land/ocean surfaces and the atmosphere is included in the model to account for this multi-hop transport. The α-isomer of the pesticide hexachlorocyclohexane (α-HCH) is used as tracer in the model development. The structure of the model and processes included are described in detail. The results from a model simulation showing the atmospheric transport for the years 1991 to 1998 are presented and evaluated against measurements. The annual averaged atmospheric concentration of α-HCH for the 1990s is well described by the model; however, the shorter-term average concentration for most of the stations is not well captured. This indicates that the present simple surface description needs to be refined to get a better description of the air-surface exchange proceses of POPs.

Visualization and modeling of smoke transport over landscape scales

Treesearch

Glenn P. Forney; William Mell

2007-01-01

Computational tools have been developed at the National Institute of Standards and Technology (NIST) for modeling fire spread and smoke transport. These tools have been adapted to address fire scenarios that occur in the wildland urban interface (WUI) over kilometer-scale distances. These models include the smoke plume transport model ALOFT (A Large Open Fire plume...

Stated choice for transportation demand management models : using a disaggregate truth set to study predictive validity

DOT National Transportation Integrated Search

1997-01-01

Discrete choice models have expanded the ability of transportation planners to forecast future trends. Where new services or policies are proposed, the stated-choice approach can provide an objective basis for forecasts. Stated-choice models are subj...

Mathematical Modeling and Experimental Validation of Nanoemulsion-Based Drug Transport across Cellular Barriers.

PubMed

Kadakia, Ekta; Shah, Lipa; Amiji, Mansoor M

2017-07-01

Nanoemulsions have shown potential in delivering drug across epithelial and endothelial cell barriers, which express efflux transporters. However, their transport mechanisms are not entirely understood. Our goal was to investigate the cellular permeability of nanoemulsion-encapsulated drugs and apply mathematical modeling to elucidate transport mechanisms and sensitive nanoemulsion attributes. Transport studies were performed in Caco-2 cells, using fish oil nanoemulsions and a model substrate, rhodamine-123. Permeability data was modeled using a semi-mechanistic approach, capturing the following cellular processes: endocytotic uptake of the nanoemulsion, release of rhodamine-123 from the nanoemulsion, efflux and passive permeability of rhodamine-123 in aqueous solution. Nanoemulsions not only improved the permeability of rhodamine-123, but were also less sensitive to efflux transporters. The model captured bidirectional permeability results and identified sensitive processes, such as the release of the nanoemulsion-encapsulated drug and cellular uptake of the nanoemulsion. Mathematical description of cellular processes, improved our understanding of transport mechanisms, such as nanoemulsions don't inhibit efflux to improve drug permeability. Instead, their endocytotic uptake, results in higher intracellular drug concentrations, thereby increasing the concentration gradient and transcellular permeability across biological barriers. Modeling results indicated optimizing nanoemulsion attributes like the droplet size and intracellular drug release rate, may further improve drug permeability.

Vadose Zone Transport Field Study: Status Report

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

Gee, Glendon W.; Ward, Anderson L.

2001-11-30

Studies were initiated at the Hanford Site to evaluate the process controlling the transport of fluids in the vadose zone and to develop a reliable database upon which vadose-zone transport models can be calibrated. These models are needed to evaluate contaminant migration through the vadose zone to underlying groundwaters at Hanford. A study site that had previously been extensively characterized using geophysical monitoring techniques was selected in the 200 E Area. Techniques used previously included neutron probe for water content, spectral gamma logging for radionuclide tracers, and gamma scattering for wet bulk density. Building on the characterization efforts of themore » past 20 years, the site was instrumented to facilitate the comparison of nine vadose-zone characterization methods: advanced tensiometers, neutron probe, electrical resistance tomography (ERT), high-resolution resistivity (HRR), electromagnetic induction imaging (EMI), cross-borehole radar (XBR), and cross-borehole seismic (XBS). Soil coring was used to obtain soil samples for analyzing ionic and isotopic tracers.« less

Evaluation of Transport in the Lower Tropical Stratosphere in a Global Chemistry and Transport Model

NASA Technical Reports Server (NTRS)

Douglass, Anne R.; Schoeberl, Mark R.; Rood, Richard B.; Pawson, Steven

2002-01-01

A general circulation model (GCM) relies on various physical parameterizations and provides a solution to the atmospheric equations of motion. A data assimilation system (DAS) combines information from observations with a GCM forecast and produces analyzed meteorological fields that represent the observed atmospheric state. An off-line chemistry and transport model (CTM) can use winds and temperatures from a either a GCM or a DAS. The latter application is in common usage for interpretation of observations from various platforms under the assumption that the DAS transport represents the actual atmospheric transport. Here we compare the transport produced by a DAS with that produced by the particular GCM that is combined with observations to produce the analyzed fields. We focus on transport in the tropics and middle latitudes by comparing the age-of-air inferred from observations of SF6 and CO2 with the age-of-air calculated using GCM fields and DAS fields. We also compare observations of ozone, total reactive nitrogen, and methane with results from the two simulations. These comparisons show that DAS fields produce rapid upward tropical transport and excessive mixing between the tropics and middle latitudes. The unrealistic transport produced by the DAS fields may be due to implicit forcing that is required by the assimilation process when there is bias between the GCM forecast and observations that are combined to produce the analyzed fields. For example, the GCM does not produce a quasi-biennial oscillation (QBO). The QBO is present in the analyzed fields because it is present in the observations, and systematic implicit forcing is required by the DAS. Any systematic bias between observations and the GCM forecast used to produce the DAS analysis is likely to corrupt the transport produced by the analyzed fields. Evaluation of transport in the lower tropical stratosphere in a global chemistry and transport model.

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.

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...

Modeling of patient's blood pressure variation during ambulance transportation

NASA Astrophysics Data System (ADS)

Sakatani, Kenji; Ono, Takahiko; Kobayasi, Yasuhide; Hikita, Shinichi; Saito, Mitsuyuki

2007-12-01

In an emergency transportation by ambulance, a patient is transported in a supine position. In this position, a patient's blood pressure (BP) variation depending on an inertial force which occurs when an ambulance accelerates or decelerates. This BP variation causes a critical damage for a patent with brain disorder. In order to keep a patient stable during transportation, it is required to maintain small BP variation. To analyze the BP variation during transportation, a model of the BP variation has so far been made. But, it can estimate the BP variation only in braking. The purpose of this paper is to make a dynamical model of the BP variation which can simulate it in both braking and accelerating. First, to obtain the data to construct the model, we used a tilting bed to measure a head-to-foot acceleration and BP of fingertip. Based on this data, we build a mathematical model whose input is the head-to-foot acceleration and output is the Mean BP variation. It is a switched model which switches two models depending on the jerk. We add baroreceptor reflex to the model as a offset value.

A nonequilibrium model for reactive contaminant transport through fractured porous media: Model development and semianalytical solution

NASA Astrophysics Data System (ADS)

Joshi, Nitin; Ojha, C. S. P.; Sharma, P. K.

2012-10-01

In this study a conceptual model that accounts for the effects of nonequilibrium contaminant transport in a fractured porous media is developed. Present model accounts for both physical and sorption nonequilibrium. Analytical solution was developed using the Laplace transform technique, which was then numerically inverted to obtain solute concentration in the fracture matrix system. The semianalytical solution developed here can incorporate both semi-infinite and finite fracture matrix extent. In addition, the model can account for flexible boundary conditions and nonzero initial condition in the fracture matrix system. The present semianalytical solution was validated against the existing analytical solutions for the fracture matrix system. In order to differentiate between various sorption/transport mechanism different cases of sorption and mass transfer were analyzed by comparing the breakthrough curves and temporal moments. It was found that significant differences in the signature of sorption and mass transfer exists. Applicability of the developed model was evaluated by simulating the published experimental data of Calcium and Strontium transport in a single fracture. The present model simulated the experimental data reasonably well in comparison to the model based on equilibrium sorption assumption in fracture matrix system, and multi rate mass transfer model.

Health Impact Modelling of Active Travel Visions for England and Wales Using an Integrated Transport and Health Impact Modelling Tool (ITHIM)

PubMed Central

Woodcock, James; Givoni, Moshe; Morgan, Andrei Scott

2013-01-01

Background Achieving health benefits while reducing greenhouse gas emissions from transport offers a potential policy win-win; the magnitude of potential benefits, however, is likely to vary. This study uses an Integrated Transport and Health Impact Modelling tool (ITHIM) to evaluate the health and environmental impacts of high walking and cycling transport scenarios for English and Welsh urban areas outside London. Methods Three scenarios with increased walking and cycling and lower car use were generated based upon the Visions 2030 Walking and Cycling project. Changes to carbon dioxide emissions were estimated by environmental modelling. Health impact assessment modelling was used to estimate changes in Disability Adjusted Life Years (DALYs) resulting from changes in exposure to air pollution, road traffic injury risk, and physical activity. We compare the findings of the model with results generated using the World Health Organization's Health Economic Assessment of Transport (HEAT) tools. Results This study found considerable reductions in disease burden under all three scenarios, with the largest health benefits attributed to reductions in ischemic heart disease. The pathways that produced the largest benefits were, in order, physical activity, road traffic injuries, and air pollution. The choice of dose response relationship for physical activity had a large impact on the size of the benefits. Modelling the impact on all-cause mortality rather than through individual diseases suggested larger benefits. Using the best available evidence we found fewer road traffic injuries for all scenarios compared with baseline but alternative assumptions suggested potential increases. Conclusions Methods to estimate the health impacts from transport related physical activity and injury risk are in their infancy; this study has demonstrated an integration of transport and health impact modelling approaches. The findings add to the case for a move from car transport to

Health impact modelling of active travel visions for England and Wales using an Integrated Transport and Health Impact Modelling Tool (ITHIM).

PubMed

Woodcock, James; Givoni, Moshe; Morgan, Andrei Scott

2013-01-01

Achieving health benefits while reducing greenhouse gas emissions from transport offers a potential policy win-win; the magnitude of potential benefits, however, is likely to vary. This study uses an Integrated Transport and Health Impact Modelling tool (ITHIM) to evaluate the health and environmental impacts of high walking and cycling transport scenarios for English and Welsh urban areas outside London. Three scenarios with increased walking and cycling and lower car use were generated based upon the Visions 2030 Walking and Cycling project. Changes to carbon dioxide emissions were estimated by environmental modelling. Health impact assessment modelling was used to estimate changes in Disability Adjusted Life Years (DALYs) resulting from changes in exposure to air pollution, road traffic injury risk, and physical activity. We compare the findings of the model with results generated using the World Health Organization's Health Economic Assessment of Transport (HEAT) tools. This study found considerable reductions in disease burden under all three scenarios, with the largest health benefits attributed to reductions in ischemic heart disease. The pathways that produced the largest benefits were, in order, physical activity, road traffic injuries, and air pollution. The choice of dose response relationship for physical activity had a large impact on the size of the benefits. Modelling the impact on all-cause mortality rather than through individual diseases suggested larger benefits. Using the best available evidence we found fewer road traffic injuries for all scenarios compared with baseline but alternative assumptions suggested potential increases. Methods to estimate the health impacts from transport related physical activity and injury risk are in their infancy; this study has demonstrated an integration of transport and health impact modelling approaches. The findings add to the case for a move from car transport to walking and cycling, and have implications

Effects of engine emissions from high-speed civil transport aircraft: A two-dimensional modeling study, part 2

NASA Technical Reports Server (NTRS)

Ko, Malcolm K. W.; Weisenstein, Debra K.; Sze, Nein Dak; Shia, Run-Lie; Rodriguez, Jose M.; Heisey, Curtis

1991-01-01

The AER two-dimensional chemistry-transport model is used to study the effect of supersonic and subsonic aircraft operation in the 2010 atmosphere on stratospheric ozone (O3). The results show that: (1) the calculated O3 response is smaller in the 2010 atmosphere compared to previous calculations performed in the 1980 atmosphere; (2) with the emissions provided, the calculated decrease in O3 column is less than 1 percent; and (3) the effect of model grid resolution on O3 response is small provided that the physics is not modified.

Routing and Scheduling Optimization Model of Sea Transportation

NASA Astrophysics Data System (ADS)

barus, Mika debora br; asyrafy, Habib; nababan, Esther; mawengkang, Herman

2018-01-01

This paper examines the routing and scheduling optimization model of sea transportation. One of the issues discussed is about the transportation of ships carrying crude oil (tankers) which is distributed to many islands. The consideration is the cost of transportation which consists of travel costs and the cost of layover at the port. Crude oil to be distributed consists of several types. This paper develops routing and scheduling model taking into consideration some objective functions and constraints. The formulation of the mathematical model analyzed is to minimize costs based on the total distance visited by the tanker and minimize the cost of the ports. In order for the model of the problem to be more realistic and the cost calculated to be more appropriate then added a parameter that states the multiplier factor of cost increases as the charge of crude oil is filled.

On the modelling of scalar and mass transport in combustor flows

NASA Technical Reports Server (NTRS)

Nikjooy, M.; So, R. M. C.

1989-01-01

Results are presented of a numerical study of swirling and nonswirling combustor flows with and without density variations. Constant-density arguments are used to justify closure assumptions invoked for the transport equations for turbulent momentum and scalar fluxes, which are written in terms of density-weighted variables. Comparisons are carried out with measurements obtained from three different axisymmetric model combustor experiments covering recirculating flow, swirling flow, and variable-density swirling flow inside the model combustors. Results show that the Reynolds stress/flux models do a credible job of predicting constant-density swirling and nonswirling combustor flows with passive scalar transport. However, their improvements over algebraic stress/flux models are marginal. The extension of the constant-density models to variable-density flow calculations shows that the models are equally valid for such flows.

Evaluation of Stratospheric Transport in New 3D Models Using the Global Modeling Initiative Grading Criteria

NASA Technical Reports Server (NTRS)

Strahan, Susan E.; Douglass, Anne R.; Einaudi, Franco (Technical Monitor)

2001-01-01

The Global Modeling Initiative (GMI) Team developed objective criteria for model evaluation in order to identify the best representation of the stratosphere. This work created a method to quantitatively and objectively discriminate between different models. In the original GMI study, 3 different meteorological data sets were used to run an offline chemistry and transport model (CTM). Observationally-based grading criteria were derived and applied to these simulations and various aspects of stratospheric transport were evaluated; grades were assigned. Here we report on the application of the GMI evaluation criteria to CTM simulations integrated with a new assimilated wind data set and a new general circulation model (GCM) wind data set. The Finite Volume Community Climate Model (FV-CCM) is a new GCM developed at Goddard which uses the NCAR CCM physics and the Lin and Rood advection scheme. The FV-Data Assimilation System (FV-DAS) is a new data assimilation system which uses the FV-CCM as its core model. One year CTM simulations of 2.5 degrees longitude by 2 degrees latitude resolution were run for each wind data set. We present the evaluation of temperature and annual transport cycles in the lower and middle stratosphere in the two new CTM simulations. We include an evaluation of high latitude transport which was not part of the original GMI criteria. Grades for the new simulations will be compared with those assigned during the original GMT evaluations and areas of improvement will be identified.

Developing of Watershed Radionuclide Transport Model DHSVM-R as Modification and Extension of Distributed Hydrological and Sediment Dynamics Model DHSVM

NASA Astrophysics Data System (ADS)

Zheleznyak, M.; Kivva, S.; Onda, Y.; Nanba, K.; Wakiyama, Y.; Konoplev, A.

2015-12-01

The reliable modeling tools for prediction wash - off radionuclides from watersheds are needed as for assessment the consequences of accidental and industrial releases of radionuclides, as for soil erosion studies using the radioactive tracers. The distributed model of radionuclide transport through watershed in exchangeable and nonexchangeable forms in solute and with sediments was developed and validated for small Chernobyl watersheds in 90th within EU SPARTACUS project (van der Perk et al., 1996). New tendency is coupling of radionuclide transport models and the widely validated hydrological distributed models. To develop radionuclide transport model DHSVM-R the open source Distributed Hydrology Soil Vegetation Model -DHSVM http://www.hydro.washington.edu/Lettenmaier/Models/DHSVM was modified and extended. The main changes provided in the hydrological and sediment transport modules of DHSVM are as follows: Morel-Seytoux infiltration model is added; four-directions schematization for the model's cells flows (D4) is replaced by D8 approach; the finite-difference schemes for solution of kinematic wave equations for overland water flow, stream net flow, and sediment transport are replaced by new computationally efficient scheme. New radionuclide transport module, coupled with hydrological and sediment transport modules, continues SPARTACUS's approach, - it describes radionuclide wash-off from watershed and transport via stream network in soluble phase and on suspended sediments. The hydrological module of DHSVM-R was calibrated and validated for the watersheds of Ukrainian Carpathian mountains and for the subwatersheds of Niida river flowing 137Cs in solute and with suspended sediments to Pacific Ocean at 30 km north of the Fukushima Daiichi NPP. The modules of radionuclide and sediment transport were calibrated and validated versus experimental data for USLE experimental plots in Fukushima Prefecture and versus monitoring data collected in Niida watershed. The role

A non-Linear transport model for determining shale rock characteristics

NASA Astrophysics Data System (ADS)

Ali, Iftikhar; Malik, Nadeem

2016-04-01

); doi: 10.1063/1.2721253 [3] Ali, I. "A numerical study of shale gas flow in tight porous media through non-linear transport model", PhD Dissertation, King Fahd University of Petroleum and Minerals. Submitted (2016). [4]. Civan, F., Rai, C.S., Sondergeld, C.H.: Shale-gas permeability and diffusivity inferred by improved formulation of relevant retention and transport mechanisms. Transport in Porous Media, 86(3), 925-944 (2011). Acknowledgement: The authors would like to acknowledge the support provided by King Abdulaziz City for Science and Technology (KACST) through the Science Technology Unit at King Fahd University of Petroleum and Minerals (KFUPM) for funding this work through project No. 14-OIL280-04.

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)

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...

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...

Some Sensitivity Studies of Chemical Transport Simulated in Models of the Soil-Plant-Litter System

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

Begovich, C.L.

2002-10-28

Fifteen parameters in a set of five coupled models describing carbon, water, and chemical dynamics in the soil-plant-litter system were varied in a sensitivity analysis of model response. Results are presented for chemical distribution in the components of soil, plants, and litter along with selected responses of biomass, internal chemical transport (xylem and phloem pathways), and chemical uptake. Response and sensitivity coefficients are presented for up to 102 model outputs in an appendix. Two soil properties (chemical distribution coefficient and chemical solubility) and three plant properties (leaf chemical permeability, cuticle thickness, and root chemical conductivity) had the greatest influence onmore » chemical transport in the soil-plant-litter system under the conditions examined. Pollutant gas uptake (SO{sub 2}) increased with change in plant properties that increased plant growth. Heavy metal dynamics in litter responded to plant properties (phloem resistance, respiration characteristics) which induced changes in the chemical cycling to the litter system. Some of the SO{sub 2} and heavy metal responses were not expected but became apparent through the modeling analysis.« less

Digital-transport model study of Diisopropylmethylphosphonate (DIMP) ground-water contamination at the Rocky Mountain Arsenal, Colorado

USGS Publications Warehouse

Warner, James W.

1979-01-01

Diisopropylmethylphosphonate (DIMP) is an organic compound produced as a by-product of the manufacture and detoxification of GB nerve gas. Ground-water contamination by DIMP from the disposal of wastes into unlined surface ponds at the Rocky Mountain Arsenal occurred from 1952 to 1956. A digital-transport model was used to determine the effects on ground-water movement and on DIMP concentrations in the ground water of a bentonite barrier in the aquifer near the northern boundary of the arsenal. The transport model is based on an iterative-alternating-direction-implicit mathematical solution of the ground-water-flow equation coupled with a method-of-characteristics solution of the solute-transport equation. The model assumes conservative (nonreactive) transient transport of DIMP and steady-state ground-water flow. In the model simulations, a bentonite barrier was assumed that was impermeable and penetrated the entire saturated thickness of the aquifer. Ground water intercepted by the barrier was assumed to be pumped by wells located south (upgradient) of the barrier, to be treated to remove DIMP, and to be recharged by pits or wells to the aquifer north (downgradient) of the barrier. The amount of DIMP transported across the northern boundary of the arsenal was substantially reduced by a ground-water-barrier system of this type. For a 1,500-foot-long bentonite barrier located along the northern boundary of the arsenal near D Street, about 50 percent of the DIMP that would otherwise cross the boundary would be intercepted by the barrier. This barrier configuration and location were proposed by the U.S. Army. Of the ground water with DIMP concentrations greater than 500 micrograms per liter, the safe DIMP-concentration level determined by the U.S. Army, about 72 percent would be intercepted by the barrier system. The amount of DIMP underflow intercepted may be increased to 65 percent by doubling the pumpage, or to 73 percent by doubling the length of the barrier

Users manual for a one-dimensional Lagrangian transport model

USGS Publications Warehouse

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

1986-01-01

A Users Manual for the Lagrangian Transport Model (LTM) is presented. The LTM uses Lagrangian calculations that are based on a reference frame moving with the river flow. The Lagrangian reference frame eliminates the need to numerically solve the convective term of the convection-diffusion equation and provides significant numerical advantages over the more commonly used Eulerian reference frame. When properly applied, the LTM can simulate riverine transport and decay processes within the accuracy required by most water quality studies. The LTM is applicable to steady or unsteady one-dimensional unidirectional flows in fixed channels with tributary and lateral inflows. Application of the LTM is relatively simple and optional capabilities improve the model 's convenience. Appendices give file formats and three example LTM applications that include the incorporation of the QUAL II water quality model 's reaction kinetics into the LTM. (Author 's abstract)

Modeling of natural organic matter transport processes in groundwater.

PubMed Central

Yeh, T C; Mas-Pla, J; McCarthy, J F; Williams, T M

1995-01-01

A forced-gradient tracer test was conducted at the Georgetown site to study the transport of natural organic matter (NOM) in groundwater. In particular, the goal of this experiment was to investigate the interactions between NOM and the aquifer matrix. A detailed three-dimensional characterization of the hydrologic conductivity heterogeneity of the site was obtained using slug tests. The transport of a conservative tracer (chloride) was successfully reproduced using these conductivity data. Despite the good simulation of the flow field, NOM breakthrough curves could not be reproduced using a two-site sorption model with spatially constant parameters. Preliminary results suggest that different mechanisms for the adsorption/desorption processes, as well as their spatial variability, may significantly affect the transport and fate of NOM. PMID:7621798

Worldwide transportation/energy demand, 1975-2000. Revised Variflex model projections

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

Ayres, R.U.; Ayres, L.W.

1980-03-01

The salient features of the transportation-energy relationships that characterize the world of 1975 are reviewed, and worldwide (34 countries) long-range transportation demand by mode to the year 2000 is reviewed. A worldwide model is used to estimate future energy demand for transportation. Projections made by the forecasting model indicate that in the year 2000, every region will be more dependent on petroleum for the transportation sector than it was in 1975. This report is intended to highlight certain trends and to suggest areas for further investigation. Forecast methodology and model output are described in detail in the appendices. The reportmore » is one of a series addressing transportation energy consumption; it supplants and replaces an earlier version published in October 1978 (ORNL/Sub-78/13536/1).« less

A Lagrangian Transport Eulerian Reaction Spatial (LATERS) Markov Model for Prediction of Effective Bimolecular Reactive Transport

NASA Astrophysics Data System (ADS)

Sund, Nicole; Porta, Giovanni; Bolster, Diogo; Parashar, Rishi

2017-11-01

Prediction of effective transport for mixing-driven reactive systems at larger scales, requires accurate representation of mixing at small scales, which poses a significant upscaling challenge. Depending on the problem at hand, there can be benefits to using a Lagrangian framework, while in others an Eulerian might have advantages. Here we propose and test a novel hybrid model which attempts to leverage benefits of each. Specifically, our framework provides a Lagrangian closure required for a volume-averaging procedure of the advection diffusion reaction equation. This hybrid model is a LAgrangian Transport Eulerian Reaction Spatial Markov model (LATERS Markov model), which extends previous implementations of the Lagrangian Spatial Markov model and maps concentrations to an Eulerian grid to quantify closure terms required to calculate the volume-averaged reaction terms. The advantage of this approach is that the Spatial Markov model is known to provide accurate predictions of transport, particularly at preasymptotic early times, when assumptions required by traditional volume-averaging closures are least likely to hold; likewise, the Eulerian reaction method is efficient, because it does not require calculation of distances between particles. This manuscript introduces the LATERS Markov model and demonstrates by example its ability to accurately predict bimolecular reactive transport in a simple benchmark 2-D porous medium.

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.

Catalog of selected heavy duty transport energy management models

NASA Technical Reports Server (NTRS)

Colello, R. G.; Boghani, A. B.; Gardella, N. C.; Gott, P. G.; Lee, W. D.; Pollak, E. C.; Teagan, W. P.; Thomas, R. G.; Snyder, C. M.; Wilson, R. P., Jr.

1983-01-01

A catalog of energy management models for heavy duty transport systems powered by diesel engines is presented. The catalog results from a literature survey, supplemented by telephone interviews and mailed questionnaires to discover the major computer models currently used in the transportation industry in the following categories: heavy duty transport systems, which consist of highway (vehicle simulation), marine (ship simulation), rail (locomotive simulation), and pipeline (pumping station simulation); and heavy duty diesel engines, which involve models that match the intake/exhaust system to the engine, fuel efficiency, emissions, combustion chamber shape, fuel injection system, heat transfer, intake/exhaust system, operating performance, and waste heat utilization devices, i.e., turbocharger, bottoming cycle.

Effects of engine emissions from high-speed civil transport aircraft: A two-dimensional modeling study, part 1

NASA Technical Reports Server (NTRS)

Ko, Malcolm K. W.; Weisenstein, Debra K.; Sze, Nein Dak; Rodriguez, Jose M.; Heisey, Curtis

1991-01-01

The AER two-dimensional chemistry-transport model is used to study the effect on stratospheric ozone (O3) from operations of supersonic and subsonic aircraft. The study is based on six emission scenarios provided to AER. The study showed that: (1) the O3 response is dominated by the portion of the emitted nitrogen compounds that is entrained in the stratosphere; (2) the entrainment is a sensitive function of the altitude at which the material is injected; (3) the O3 removal efficiency of the emitted material depends on the concentrations of trace gases in the background atmosphere; and (4) evaluation of the impact of fleet operations in the future atmosphere must take into account the expected changes in trace gas concentrations from other activities. Areas for model improvements in future studies are also discussed.

A statistical study of gyro-averaging effects in a reduced model of drift-wave transport

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

Fonseca, Julio; Del-Castillo-Negrete, Diego B.; Sokolov, Igor M.

2016-08-25

Here, a statistical study of finite Larmor radius (FLR) effects on transport driven by electrostatic driftwaves is presented. The study is based on a reduced discrete Hamiltonian dynamical system known as the gyro-averaged standard map (GSM). In this system, FLR effects are incorporated through the gyro-averaging of a simplified weak-turbulence model of electrostatic fluctuations. Formally, the GSM is a modified version of the standard map in which the perturbation amplitude, K 0, becomes K 0J 0(more » $$\\hat{p}$$), where J 0 is the zeroth-order Bessel function and $$\\hat{p}$$ s the Larmor radius. Assuming a Maxwellian probability density function (pdf) for $$\\hat{p}$$ , we compute analytically and numerically the pdf and the cumulative distribution function of the effective drift-wave perturba- tion amplitude K 0J 0($$\\hat{p}$$). Using these results, we compute the probability of loss of confinement (i.e., global chaos), P c provides an upper bound for the escape rate, and that P t rovides a good estimate of the particle trapping rate. Lastly. the analytical results are compared with direct numerical Monte-Carlo simulations of particle transport.« less

A consistent transported PDF model for treating differential molecular diffusion

NASA Astrophysics Data System (ADS)

Wang, Haifeng; Zhang, Pei

2016-11-01

Differential molecular diffusion is a fundamentally significant phenomenon in all multi-component turbulent reacting or non-reacting flows caused by the different rates of molecular diffusion of energy and species concentrations. In the transported probability density function (PDF) method, the differential molecular diffusion can be treated by using a mean drift model developed by McDermott and Pope. This model correctly accounts for the differential molecular diffusion in the scalar mean transport and yields a correct DNS limit of the scalar variance production. The model, however, misses the molecular diffusion term in the scalar variance transport equation, which yields an inconsistent prediction of the scalar variance in the transported PDF method. In this work, a new model is introduced to remedy this problem that can yield a consistent scalar variance prediction. The model formulation along with its numerical implementation is discussed, and the model validation is conducted in a turbulent mixing layer problem.

Bacteria transport simulation using apex model in the toenepi watershed, New Zealand

USDA-ARS?s Scientific Manuscript database

The Agricultural Policy/Environmental eXtender (APEX) model is a distributed, continuous, daily-timestep small watershed-scale hydrologic and water quality model. In this study, the newly developed fecal-derived bacteria fate and transport subroutine was applied and validated using APEX model. The ...

Electron Temperature Fluctuation Measurements and Transport Model Validation at Alcator C-Mod

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

White, Anne

The tokamak is a type of toroidal device used to confine a fusion plasma using large magnetic fields. Tokamaks and stellarators the leading devices for confining plasmas for fusion, and the capability to predict performance in these magnetically confined plasmas is essential for developing a sustainable fusion energy source. The magnetic configuration of tokamaks and stellarators does not exist in Nature, yet, the fundamental processes governing transport in fusion plasmas are universal – turbulence and instabilities, driven by inhomogeneity and asymmetry in the plasma, conspire to transport heat and particles across magnetic field lines and can play critical roles inmore » impurity confinement and generation of intrinsic rotation. Turbulence exists in all plasmas, and in neutral fluids as well. The study of turbulence is essential to developing a fundamental understanding of the nature of the fourth state of matter, plasmas. Experimental studies of turbulence in tokamaks date back to early scattering observations from the late 1970s. Since that time, great advances in turbulence diagnostics have been made, all of which have significantly enhanced our knowledge and understanding of turbulence in tokamaks. Through comparisons with advanced gyrokinetic theory and turbulent-transport models a great deal of evidence exists to implicate turbulent-driven transport as an important mechanism determining transport in all channels: heat, particle and momentum However, prediction and control of turbulent-driven transport remains elusive. Key to development of predictive transport models for magnetically confined fusion plasmas is validation of the nonlinear gyrokinetic transport model, which describes transport due to turbulence. Validation of gyrokinetic codes must include detailed and quantitative comparisons with measured turbulence characteristics, in addition to comparisons with inferred transport levels and equilibrium profiles. For this reason, advanced plasma

Erosion, Transportation, and Deposition on Outer Solar System Satellites: Landform Evolution Modeling Studies

NASA Technical Reports Server (NTRS)

Moore, Jeffrey Morgan; Howard, Alan D.; Schenk, Paul M.

2013-01-01

Mass movement and landform degradation reduces topographic relief by moving surface materials to a lower gravitational potential. In addition to the obvious role of gravity, abrasive mechanical erosion plays a role, often in combination with the lowering of cohesion, which allows disaggregation of the relief-forming material. The identification of specific landform types associated with mass movement and landform degradation provides information about local sediment particle size and abundance and transportation processes. Generally, mass movements can be classified in terms of the particle sizes of the transported material and the speed the material moved during transport. Most degradation on outer planet satellites appears consistent with sliding or slumping, impact erosion, and regolith evolution. Some satellites, such as Callisto and perhaps Hyperion and Iapetus, have an appearance that implies that some additional process is at work, most likely sublimation-driven landform modification and mass wasting. A variant on this process is thermally driven frost segregation as seen on all three icy Galilean satellites and perhaps elsewhere. Titan is unique among outer planet satellites in that Aeolian and fluvial processes also operate to erode, transport, and deposit material. We will evaluate the sequence and extent of various landform-modifying erosional and volatile redistribution processes that have shaped these icy satellites using a 3-D model that simulates the following surface and subsurface processes: 1) sublimation and re-condensation of volatiles; 2) development of refractory lag deposits; 3) disaggregation and downward sloughing of surficial material; 4) radiative heating/cooling of the surface (including reflection, emission, and shadowing by other surface elements); 5) thermal diffusion; and 6) vapor diffusion. The model will provide explicit simulations of landform development and thusly predicts the topographic and volatile evolution of the surface

Enhancements to the Branched Lagrangian Transport Modeling System

USGS Publications Warehouse

Jobson, Harvey E.

1997-01-01

The Branched Lagrangian Transport Model (BLTM) has received wide use within the U.S. Geological Survey over the past 10 years. This report documents the enhancements and modifications that have been made to this modeling system since it was first introduced. The programs in the modeling system are arranged into five levels?programs to generate time-series of meteorological data (EQULTMP, SOLAR), programs to process time-series data (INTRP, MRG), programs to build input files for transport model (BBLTM, BQUAL2E), the model with defined reaction kinetics (BLTM, QUAL2E), and post processor plotting programs (CTPLT, CXPLT). An example application is presented to illustrate how the modeling system can be used to simulate 10 water-quality constituents in the Chattahoochee River below Atlanta, Georgia.

An implicit dispersive transport algorithm for the US Geological Survey MOC3D solute-transport model

USGS Publications Warehouse

Kipp, K.L.; Konikow, Leonard F.; Hornberger, G.Z.

1998-01-01

This report documents an extension to the U.S. Geological Survey MOC3D transport model that incorporates an implicit-in-time difference approximation for the dispersive transport equation, including source/sink terms. The original MOC3D transport model (Version 1) uses the method of characteristics to solve the transport equation on the basis of the velocity field. The original MOC3D solution algorithm incorporates particle tracking to represent advective processes and an explicit finite-difference formulation to calculate dispersive fluxes. The new implicit procedure eliminates several stability criteria required for the previous explicit formulation. This allows much larger transport time increments to be used in dispersion-dominated problems. The decoupling of advective and dispersive transport in MOC3D, however, is unchanged. With the implicit extension, the MOC3D model is upgraded to Version 2. A description of the numerical method of the implicit dispersion calculation, the data-input requirements and output options, and the results of simulator testing and evaluation are presented. Version 2 of MOC3D was evaluated for the same set of problems used for verification of Version 1. These test results indicate that the implicit calculation of Version 2 matches the accuracy of Version 1, yet is more efficient than the explicit calculation for transport problems that are characterized by a grid Peclet number less than about 1.0.

ITC Recommendations for Transporter Kinetic Parameter Estimation and Translational Modeling of Transport-Mediated PK and DDIs in Humans

PubMed Central

Zamek-Gliszczynski, MJ; Lee, CA; Poirier, A; Bentz, J; Chu, X; Ellens, H; Ishikawa, T; Jamei, M; Kalvass, JC; Nagar, S; Pang, KS; Korzekwa, K; Swaan, PW; Taub, ME; Zhao, P; Galetin, A

2013-01-01

This white paper provides a critical analysis of methods for estimating transporter kinetics and recommendations on proper parameter calculation in various experimental systems. Rational interpretation of transporter-knockout animal findings and application of static and dynamic physiologically based modeling approaches for prediction of human transporter-mediated pharmacokinetics and drug–drug interactions (DDIs) are presented. The objective is to provide appropriate guidance for the use of in vitro, in vivo, and modeling tools in translational transporter science. PMID:23588311

Pharmacokinetic interplay of phase II metabolism and transport: a theoretical study.

PubMed

Wu, Baojian

2012-01-01

Understanding of the interdependence of cytochrome P450 enzymes and P-glycoprotein in disposition of drugs (also termed "transport-metabolism interplay") has been significantly advanced in recent years. However, whether such "interplay" exists between phase II metabolic enzymes and efflux transporters remains largely unknown. The objective of this article is to explore the role of efflux transporters (acting on the phase II metabolites) in disposition of the parent drug in Caco-2 cells, liver, and intestine via simulations utilizing a catenary model (for Caco-2 system) and physiologically based pharmacokinetic (PBPK) models (for the liver and intestine). In all three models, "transport-metabolism interplay" (i.e., inhibition of metabolite efflux decreases the metabolism) can be observed only when futile recycling (or deconjugation) occurred. Futile recycling appeared to bridge the two processes (i.e., metabolite formation and excretion) and enable the interplay thereof. Without futile recycling, metabolite formation was independent on its downstream process excretion, thus impact of metabolite excretion on its formation was impossible. Moreover, in liver PBPK model with futile recycling, impact of biliary metabolite excretion on the exposure of parent drug [(systemic (reservoir) area under the concentration-time curve (AUC(R1))] was limited; a complete inhibition of efflux resulted in AUC(R1) increases of less than 1-fold only. In intestine PBPK model with futile recycling, even though a complete inhibition of efflux could result in large elevations (e.g., 3.5-6.0-fold) in AUC(R1), an incomplete inhibition of efflux (e.g., with a residual activity of ≥ 20% metabolic clearance) saw negligible increases (<0.9-fold) in AUC(R1). In conclusion, this study presented mechanistic observations of pharmacokinetic interplay between phase II enzymes and efflux transporters. Those studying such "interplay" are encouraged to adequately consider potential consequences of

A Comparison of Geographic Information Systems, Complex Networks, and Other Models for Analyzing Transportation Network Topologies

NASA Technical Reports Server (NTRS)

Alexandrov, Natalia (Technical Monitor); Kuby, Michael; Tierney, Sean; Roberts, Tyler; Upchurch, Christopher

2005-01-01

This report reviews six classes of models that are used for studying transportation network topologies. The report is motivated by two main questions. First, what can the "new science" of complex networks (scale-free, small-world networks) contribute to our understanding of transport network structure, compared to more traditional methods? Second, how can geographic information systems (GIS) contribute to studying transport networks? The report defines terms that can be used to classify different kinds of models by their function, composition, mechanism, spatial and temporal dimensions, certainty, linearity, and resolution. Six broad classes of models for analyzing transport network topologies are then explored: GIS; static graph theory; complex networks; mathematical programming; simulation; and agent-based modeling. Each class of models is defined and classified according to the attributes introduced earlier. The paper identifies some typical types of research questions about network structure that have been addressed by each class of model in the literature.

Entity-Centric Abstraction and Modeling Framework for Transportation Architectures

NASA Technical Reports Server (NTRS)

Lewe, Jung-Ho; DeLaurentis, Daniel A.; Mavris, Dimitri N.; Schrage, Daniel P.

2007-01-01

A comprehensive framework for representing transpportation architectures is presented. After discussing a series of preceding perspectives and formulations, the intellectual underpinning of the novel framework using an entity-centric abstraction of transportation is described. The entities include endogenous and exogenous factors and functional expressions are offered that relate these and their evolution. The end result is a Transportation Architecture Field which permits analysis of future concepts under the holistic perspective. A simulation model which stems from the framework is presented and exercised producing results which quantify improvements in air transportation due to advanced aircraft technologies. Finally, a modeling hypothesis and its accompanying criteria are proposed to test further use of the framework for evaluating new transportation solutions.

Computational modeling of transport and electrochemical reactions in proton-exchange membrane fuel cells

NASA Astrophysics Data System (ADS)

Um, Sukkee

A comprehensive, multi-physics computational fuel cell dynamics (CFCD) model integrating electrochemical kinetics, charge transport, mass transport (particularly water transport), and flow dynamics is developed in this thesis. The numerical model is validated against published experimental data and utilized to generate results that reveal the internal operation of a PEM fuel cell. A number of model applications are demonstrated in the present work. First, the CFCD model is applied to explore hydrogen dilution effects in the anode feed. Detailed two-dimensional electrochemical and flow/transport simulations are provided to examine substantial anode concentration polarization due to hydrogen depletion at the reaction sites. A transient simulation of the cell current response to a step change in cell voltage is also attempted to elucidate characteristics of the dynamic response of a fuel cell for the first time. After the two-dimensional computational study, the CFCD model is applied to illustrate three-dimensional interactions between mass transfer and electrochemical kinetics. Emphasis is placed on obtaining a fundamental understanding of fully three-dimensional flow in the air cathode with interdigitated flowfield design and how it impacts the transport and electrochemical reaction processes. The innovative design concept for enhanced oxygen transport to, and effective water removal from the cathode, is explored numerically. Next, an analytical study of water transport is performed to investigate various water transport regimes of practical interest. The axial locations characteristic of anode water loss and cathode flooding are predicted theoretically and compared with numerical results. A continuous stirred fuel cell reactor (CSFCR) model is also proposed for the limiting situation where the anode and cathode sides reach equilibrium in water concentration with a thin ionomer membrane in between. In addition to the analytical solutions, a detailed water transport

Bacteria transport simulation using APEX model in the Toenepi watershed, New Zealand

USDA-ARS?s Scientific Manuscript database

The Agricultural Policy/Environmental eXtender (APEX) model is a distributed, continuous, daily-time step small watershed-scale hydrologic and water quality model. In this study, the newly developed fecal-derived bacteria fate and transport subroutine was applied and evalated using APEX model. The e...

Web-based reactive transport modeling using PFLOTRAN

NASA Astrophysics Data System (ADS)

Zhou, H.; Karra, S.; Lichtner, P. C.; Versteeg, R.; Zhang, Y.

2017-12-01

Actionable understanding of system behavior in the subsurface is required for a wide spectrum of societal and engineering needs by both commercial firms and government entities and academia. These needs include, for example, water resource management, precision agriculture, contaminant remediation, unconventional energy production, CO2 sequestration monitoring, and climate studies. Such understanding requires the ability to numerically model various coupled processes that occur across different temporal and spatial scales as well as multiple physical domains (reservoirs - overburden, surface-subsurface, groundwater-surface water, saturated-unsaturated zone). Currently, this ability is typically met through an in-house approach where computational resources, model expertise, and data for model parameterization are brought together to meet modeling needs. However, such an approach has multiple drawbacks which limit the application of high-end reactive transport codes such as the Department of Energy funded[?] PFLOTRAN code. In addition, while many end users have a need for the capabilities provided by high-end reactive transport codes, they do not have the expertise - nor the time required to obtain the expertise - to effectively use these codes. We have developed and are actively enhancing a cloud-based software platform through which diverse users are able to easily configure, execute, visualize, share, and interpret PFLOTRAN models. This platform consists of a web application and available on-demand HPC computational infrastructure. The web application consists of (1) a browser-based graphical user interface which allows users to configure models and visualize results interactively, and (2) a central server with back-end relational databases which hold configuration, data, modeling results, and Python scripts for model configuration, and (3) a HPC environment for on-demand model execution. We will discuss lessons learned in the development of this platform, the

Tracer transport in soils and shallow groundwater: model abstraction with modern tools

USDA-ARS?s Scientific Manuscript database

Vadose zone controls contaminant transport from the surface to groundwater, and modeling transport in vadose zone has become a burgeoning field. Exceedingly complex models of subsurface contaminant transport are often inefficient. Model abstraction is the methodology for reducing the complexity of a...

A case study of pollutants transported from HPCL (vishakhapatnam) accidental fire through synergy of flexpart model and ground-based instruments

NASA Astrophysics Data System (ADS)

Wankhede, Tushar

Tushar Wankhede*, Harish Gadhavi, Amit K. Pandit National Atmospheric Research Laboratory (NARL), Gadanki-517112, Chittoor, A.P. *tushar1771@gmail.com, Mobile: +91-8297152481 A fire at Hindustan Petroleum Corporation Limited (HPCL) in Vishakhapatnam (17.70 ˚N, 83.24˚E) resulted from a gas leak in the salt water cooling tower system. This led to the release of various pollutants like hydrocarbons, black carbon, carbon mono-oxide and carbon dioxide etc(other gases) in just 44 min of fire in system a very huge amount of particles were emitted. The transport of these pollutants has been studied through FLEXPART which is a Lagrangian particle dispersion model having wide range of applications in atmospheric transport modeling. FLEXPART simulation of this accidental fire shows the direction and sensitivity of dispersed pollutants from its source. It was observed that the pollutants reached Gadanki, a rural site located at 13.45 ˚N, 79.18 ˚E in Southern-India. The concentration of pollutant obtained from FLEXPART output we are comparing with ground based instruments data collected at the observation site (Indian Climate Observatory Network-ICON, NARL Gadanki). This case-study provides significant information about the life-time of dispersed pollutants and their long-range transport pattern under the influence of small weather variability en-route from source to receptor. The detailed work of FLEXPART for the Long range transport of the particles will be presented later on in conference.

Statewide Transportation Needs & Funding Study

DOT National Transportation Integrated Search

1995-05-01

The State Transportation Policy Initiative (STPI)is multi-phase study to examine : current transportation planning, growth management, and transportation funding : practices in Florida and to develop recommendations that can be the basis of : future ...

A transport model for computer simulation of wildfires

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

Linn, R.

1997-12-31

Realistic self-determining simulation of wildfires is a difficult task because of a large variety of important length scales (including scales on the size of twigs or grass and the size of large trees), imperfect data, complex fluid mechanics and heat transfer, and very complicated chemical reactions. The author uses a transport approach to produce a model that exhibits a self-determining propagation rate. The transport approach allows him to represent a large number of environments such as those with nonhomogeneous vegetation and terrain. He accounts for the microscopic details of a fire with macroscopic resolution by dividing quantities into mean andmore » fluctuating parts similar to what is done in traditional turbulence modeling. These divided quantities include fuel, wind, gas concentrations, and temperature. Reaction rates are limited by the mixing process and not the chemical kinetics. The author has developed a model that includes the transport of multiple gas species, such as oxygen and volatile hydrocarbons, and tracks the depletion of various fuels and other stationary solids and liquids. From this model he develops a simplified local burning model with which he performs a number of simulations that demonstrate that he is able to capture the important physics with the transport approach. With this simplified model he is able to pick up the essence of wildfire propagation, including such features as acceleration when transitioning to upsloping terrain, deceleration of fire fronts when they reach downslopes, and crowning in the presence of high winds.« less

Modeling spin magnetization transport in a spatially varying magnetic field

NASA Astrophysics Data System (ADS)

Picone, Rico A. R.; Garbini, Joseph L.; Sidles, John A.

2015-01-01

We present a framework for modeling the transport of any number of globally conserved quantities in any spatial configuration and apply it to obtain a model of magnetization transport for spin-systems that is valid in new regimes (including high-polarization). The framework allows an entropy function to define a model that explicitly respects the laws of thermodynamics. Three facets of the model are explored. First, it is expressed as nonlinear partial differential equations that are valid for the new regime of high dipole-energy and polarization. Second, the nonlinear model is explored in the limit of low dipole-energy (semi-linear), from which is derived a physical parameter characterizing separative magnetization transport (SMT). It is shown that the necessary and sufficient condition for SMT to occur is that the parameter is spatially inhomogeneous. Third, the high spin-temperature (linear) limit is shown to be equivalent to the model of nuclear spin transport of Genack and Redfield (1975) [1]. Differences among the three forms of the model are illustrated by numerical solution with parameters corresponding to a magnetic resonance force microscopy (MRFM) experiment (Degen et al., 2009 [2]; Kuehn et al., 2008 [3]; Sidles et al., 2003 [4]; Dougherty et al., 2000 [5]). A family of analytic, steady-state solutions to the nonlinear equation is derived and shown to be the spin-temperature analog of the Langevin paramagnetic equation and Curie's law. Finally, we analyze the separative quality of magnetization transport, and a steady-state solution for the magnetization is shown to be compatible with Fenske's separative mass transport equation (Fenske, 1932 [6]).

Implementation of Gravity Model to Estimation of Transportation Market Shares

NASA Astrophysics Data System (ADS)

Krata, Przemysław

2010-03-01

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

Tropospheric transport differences between models using the same large-scale meteorological fields

NASA Astrophysics Data System (ADS)

Orbe, Clara; Waugh, Darryn W.; Yang, Huang; Lamarque, Jean-Francois; Tilmes, Simone; Kinnison, Douglas E.

2017-01-01

The transport of chemicals is a major uncertainty in the modeling of tropospheric composition. A common approach is to transport gases using the winds from meteorological analyses, either using them directly in a chemical transport model or by constraining the flow in a general circulation model. Here we compare the transport of idealized tracers in several different models that use the same meteorological fields taken from Modern-Era Retrospective analysis for Research and Applications (MERRA). We show that, even though the models use the same meteorological fields, there are substantial differences in their global-scale tropospheric transport related to large differences in parameterized convection between the simulations. Furthermore, we find that the transport differences between simulations constrained with the same-large scale flow are larger than differences between free-running simulations, which have differing large-scale flow but much more similar convective mass fluxes. Our results indicate that more attention needs to be paid to convective parameterizations in order to understand large-scale tropospheric transport in models, particularly in simulations constrained with analyzed winds.

Impact of intercontinental pollution transport on North American ozone air pollution: an HTAP phase 2 multi-model study

NASA Astrophysics Data System (ADS)

Huang, Min; Carmichael, Gregory R.; Pierce, R. Bradley; Jo, Duseong S.; Park, Rokjin J.; Flemming, Johannes; Emmons, Louisa K.; Bowman, Kevin W.; Henze, Daven K.; Davila, Yanko; Sudo, Kengo; Eiof Jonson, Jan; Tronstad Lund, Marianne; Janssens-Maenhout, Greet; Dentener, Frank J.; Keating, Terry J.; Oetjen, Hilke; Payne, Vivienne H.

2017-05-01

The recent update on the US National Ambient Air Quality Standards (NAAQS) of the ground-level ozone (O3) can benefit from a better understanding of its source contributions in different US regions during recent years. In the Hemispheric Transport of Air Pollution experiment phase 1 (HTAP1), various global models were used to determine the O3 source-receptor (SR) relationships among three continents in the Northern Hemisphere in 2001. In support of the HTAP phase 2 (HTAP2) experiment that studies more recent years and involves higher-resolution global models and regional models' participation, we conduct a number of regional-scale Sulfur Transport and dEposition Model (STEM) air quality base and sensitivity simulations over North America during May-June 2010. STEM's top and lateral chemical boundary conditions were downscaled from three global chemical transport models' (i.e., GEOS-Chem, RAQMS, and ECMWF C-IFS) base and sensitivity simulations in which the East Asian (EAS) anthropogenic emissions were reduced by 20 %. The mean differences between STEM surface O3 sensitivities to the emission changes and its corresponding boundary condition model's are smaller than those among its boundary condition models, in terms of the regional/period-mean (< 10 %) and the spatial distributions. An additional STEM simulation was performed in which the boundary conditions were downscaled from a RAQMS (Realtime Air Quality Modeling System) simulation without EAS anthropogenic emissions. The scalability of O3 sensitivities to the size of the emission perturbation is spatially varying, and the full (i.e., based on a 100 % emission reduction) source contribution obtained from linearly scaling the North American mean O3 sensitivities to a 20 % reduction in the EAS anthropogenic emissions may be underestimated by at least 10 %. The three boundary condition models' mean O3 sensitivities to the 20 % EAS emission perturbations are ˜ 8 % (May-June 2010)/˜ 11 % (2010 annual) lower than

Impact of intercontinental pollution transport on North American ozone air pollution: an HTAP phase 2 multi-model study.

PubMed

Huang, Min; Carmichael, Gregory R; Pierce, R Bradley; Jo, Duseong S; Park, Rokjin J; Flemming, Johannes; Emmons, Louisa K; Bowman, Kevin W; Henze, Daven K; Davila, Yanko; Sudo, Kengo; Jonson, Jan Eiof; Lund, Marianne Tronstad; Janssens-Maenhout, Greet; Dentener, Frank J; Keating, Terry J; Oetjen, Hilke; Payne, Vivienne H

2017-05-08

The recent update on the US National Ambient Air Quality Standards (NAAQS) of the ground-level ozone (O 3 / can benefit from a better understanding of its source contributions in different US regions during recent years. In the Hemispheric Transport of Air Pollution experiment phase 1 (HTAP1), various global models were used to determine the O 3 source-receptor (SR) relationships among three continents in the Northern Hemisphere in 2001. In support of the HTAP phase 2 (HTAP2) experiment that studies more recent years and involves higher-resolution global models and regional models' participation, we conduct a number of regional-scale Sulfur Transport and dEposition Model (STEM) air quality base and sensitivity simulations over North America during May-June 2010. STEM's top and lateral chemical boundary conditions were downscaled from three global chemical transport models' (i.e., GEOS-Chem, RAQMS, and ECMWF C-IFS) base and sensitivity simulations in which the East Asian (EAS) anthropogenic emissions were reduced by 20 %. The mean differences between STEM surface O 3 sensitivities to the emission changes and its corresponding boundary condition model's are smaller than those among its boundary condition models, in terms of the regional/period-mean (<10 %) and the spatial distributions. An additional STEM simulation was performed in which the boundary conditions were downscaled from a RAQMS (Realtime Air Quality Modeling System) simulation without EAS anthropogenic emissions. The scalability of O 3 sensitivities to the size of the emission perturbation is spatially varying, and the full (i.e., based on a 100% emission reduction) source contribution obtained from linearly scaling the North American mean O 3 sensitivities to a 20% reduction in the EAS anthropogenic emissions may be underestimated by at least 10 %. The three boundary condition models' mean O 3 sensitivities to the 20% EAS emission perturbations are ~8% (May-June 2010)/~11% (2010 annual) lower than those

Implementation of an anomalous radial transport model for continuum kinetic edge codes

NASA Astrophysics Data System (ADS)

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

2007-11-01

Radial plasma transport in magnetic fusion devices is often dominated by plasma turbulence compared to neoclassical collisional transport. Continuum kinetic edge codes [such as the (2d,2v) transport version of TEMPEST and also EGK] compute the collisional transport directly, but there is a need to model the anomalous transport from turbulence for long-time transport simulations. Such a model is presented and results are shown for its implementation in the TEMPEST gyrokinetic edge code. The model includes velocity-dependent convection and diffusion coefficients expressed as a Hermite polynominals in velocity. The specification of the Hermite coefficients can be set, e.g., by specifying the ratio of particle and energy transport as in fluid transport codes. The anomalous transport terms preserve the property of no particle flux into unphysical regions of velocity space. TEMPEST simulations are presented showing the separate control of particle and energy anomalous transport, and comparisons are made with neoclassical transport also included.

Image-based modeling of flow and reactive transport in porous media

NASA Astrophysics Data System (ADS)

Qin, Chao-Zhong; Hoang, Tuong; Verhoosel, Clemens V.; Harald van Brummelen, E.; Wijshoff, Herman M. A.

2017-04-01

Due to the availability of powerful computational resources and high-resolution acquisition of material structures, image-based modeling has become an important tool in studying pore-scale flow and transport processes in porous media [Scheibe et al., 2015]. It is also playing an important role in the upscaling study for developing macroscale porous media models. Usually, the pore structure of a porous medium is directly discretized by the voxels obtained from visualization techniques (e.g. micro CT scanning), which can avoid the complex generation of computational mesh. However, this discretization may considerably overestimate the interfacial areas between solid walls and pore spaces. As a result, it could impact the numerical predictions of reactive transport and immiscible two-phase flow. In this work, two types of image-based models are used to study single-phase flow and reactive transport in a porous medium of sintered glass beads. One model is from a well-established voxel-based simulation tool. The other is based on the mixed isogeometric finite cell method [Hoang et al., 2016], which has been implemented in the open source Nutils (http://www.nutils.org). The finite cell method can be used in combination with isogeometric analysis to enable the higher-order discretization of problems on complex volumetric domains. A particularly interesting application of this immersed simulation technique is image-based analysis, where the geometry is smoothly approximated by segmentation of a B-spline level set approximation of scan data [Verhoosel et al., 2015]. Through a number of case studies by the two models, we will show the advantages and disadvantages of each model in modeling single-phase flow and reactive transport in porous media. Particularly, we will highlight the importance of preserving high-resolution interfaces between solid walls and pore spaces in image-based modeling of porous media. References Hoang, T., C. V. Verhoosel, F. Auricchio, E. H. van

A residence-time-based transport approach for the groundwater pathway in performance assessment models

NASA Astrophysics Data System (ADS)

Robinson, Bruce A.; Chu, Shaoping

2013-03-01

This paper presents the theoretical development and numerical implementation of a new modeling approach for representing the groundwater pathway in risk assessment or performance assessment model of a contaminant transport system. The model developed in the present study, called the Residence Time Distribution (RTD) Mixing Model (RTDMM), allows for an arbitrary distribution of fluid travel times to be represented, to capture the effects on the breakthrough curve of flow processes such as channelized flow and fast pathways and complex three-dimensional dispersion. Mathematical methods for constructing the model for a given RTD are derived directly from the theory of residence time distributions in flowing systems. A simple mixing model is presented, along with the basic equations required to enable an arbitrary RTD to be reproduced using the model. The practical advantages of the RTDMM include easy incorporation into a multi-realization probabilistic simulation; computational burden no more onerous than a one-dimensional model with the same number of grid cells; and straightforward implementation into available flow and transport modeling codes, enabling one to then utilize advanced transport features of that code. For example, in this study we incorporated diffusion into the stagnant fluid in the rock matrix away from the flowing fractures, using a generalized dual porosity model formulation. A suite of example calculations presented herein showed the utility of the RTDMM for the case of a radioactive decay chain, dual porosity transport and sorption.

Generalized free-space diffuse photon transport model based on the influence analysis of a camera lens diaphragm.

PubMed

Chen, Xueli; Gao, Xinbo; Qu, Xiaochao; Chen, Duofang; Ma, Xiaopeng; Liang, Jimin; Tian, Jie

2010-10-10

The camera lens diaphragm is an important component in a noncontact optical imaging system and has a crucial influence on the images registered on the CCD camera. However, this influence has not been taken into account in the existing free-space photon transport models. To model the photon transport process more accurately, a generalized free-space photon transport model is proposed. It combines Lambertian source theory with analysis of the influence of the camera lens diaphragm to simulate photon transport process in free space. In addition, the radiance theorem is also adopted to establish the energy relationship between the virtual detector and the CCD camera. The accuracy and feasibility of the proposed model is validated with a Monte-Carlo-based free-space photon transport model and physical phantom experiment. A comparison study with our previous hybrid radiosity-radiance theorem based model demonstrates the improvement performance and potential of the proposed model for simulating photon transport process in free space.

Sorafenib metabolism, transport, and enterohepatic recycling: physiologically based modeling and simulation in mice.

PubMed

Edginton, Andrea N; Zimmerman, Eric I; Vasilyeva, Aksana; Baker, Sharyn D; Panetta, John C

2016-05-01

This study used uncertainty and sensitivity analysis to evaluate a physiologically based pharmacokinetic (PBPK) model of the complex mechanisms of sorafenib and its two main metabolites, sorafenib glucuronide and sorafenib N-oxide in mice. A PBPK model for sorafenib and its two main metabolites was developed to explain disposition in mice. It included relevant influx (Oatp) and efflux (Abcc2 and Abcc3) transporters, hepatic metabolic enzymes (CYP3A4 and UGT1A9), and intestinal β-glucuronidase. Parameterization of drug-specific processes was based on in vitro, ex vivo, and in silico data along with plasma and liver pharmacokinetic data from single and multiple transporter knockout mice. Uncertainty analysis demonstrated that the model structure and parameter values could explain the observed variability in the pharmacokinetic data. Global sensitivity analysis demonstrated the global effects of metabolizing enzymes on sorafenib and metabolite disposition and the local effects of transporters on their respective substrate exposures. In addition, through hypothesis testing, the model supported that the influx transporter Oatp is a weak substrate for sorafenib and a strong substrate for sorafenib glucuronide and that the efflux transporter Abcc2 is not the only transporter affected in the Abcc2 knockout mouse. Translation of the mouse model to humans for the purpose of explaining exceptionally high human pharmacokinetic variability and its relationship with exposure-dependent dose-limiting toxicities will require delineation of the importance of these processes on disposition.

Modeling of Dense Water Production and Salt Transport from Alaskan Coastal Polynyas

NASA Technical Reports Server (NTRS)

Signorini, Sergio R.; Cavalieri, Donald J.

2000-01-01

The main significance of this paper is that a realistic, three-dimensional, high-resolution primitive equation model has been developed to study the effects of dense water formation in Arctic coastal polynyas. The model includes realistic ambient stratification, realistic bottom topography, and is forced by time-variant surface heat flux, surface salt flux, and time-dependent coastal flow. The salt and heat fluxes, and the surface ice drift, are derived from satellite observations (SSM/I and NSCAT sensors). The model is used to study the stratification, salt transport, and circulation in the vicinity of Barrow Canyon during the 1996/97 winter season. The coastal flow (Alaska coastal current), which is an extension of the Bering Sea throughflow, is formulated in the model using the wind-transport regression. The results show that for the 1996/97 winter the northeastward coastal current exports 13% to 26% of the salt produced by coastal polynyas upstream of Barrow Canyon in 20 to 30 days. The salt export occurs more rapidly during less persistent polynyas. The inclusion of ice-water stress in the model makes the coastal current slightly weaker and much wider due to the combined effects of surface drag and offshore Ekman transport.

Use of transport models for wildfire behavior simulations

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

Linn, R.R.; Harlow, F.H.

1998-01-01

Investigators have attempted to describe the behavior of wildfires for over fifty years. Current models for numerical description are mainly algebraic and based on statistical or empirical ideas. The authors have developed a transport model called FIRETEC. The use of transport formulations connects the propagation rates to the full conservation equations for energy, momentum, species concentrations, mass, and turbulence. In this paper, highlights of the model formulation and results are described. The goal of the FIRETEC model is to describe most probable average behavior of wildfires in a wide variety of conditions. FIRETEC represents the essence of the combination ofmore » many small-scale processes without resolving each process in complete detail.« less

A musculo-mechanical model of esophageal transport based on an immersed boundary-finite element approach

NASA Astrophysics Data System (ADS)

Kou, Wenjun; Griffith, Boyce E.; Pandolfino, John E.; Kahrilas, Peter J.; Patankar, Neelesh A.

2015-11-01

This work extends a fiber-based immersed boundary (IB) model of esophageal transport by incorporating a continuum model of the deformable esophageal wall. The continuum-based esophagus model adopts finite element approach that is capable of describing more complex and realistic material properties and geometries. The leakage from mismatch between Lagrangian and Eulerian meshes resulting from large deformations of the esophageal wall is avoided by careful choice of interaction points. The esophagus model, which is described as a multi-layered, fiber-reinforced nonlinear elastic material, is coupled to bolus and muscle-activation models using the IB approach to form the esophageal transport model. Cases of esophageal transport with different esophagus models are studied. Results on the transport characteristics, including pressure field and esophageal wall kinematics and stress, are analyzed and compared. Support from NIH grant R01 DK56033 and R01 DK079902 is gratefully acknowledged. BEG is supported by NSF award ACI 1460334.

Investigation of the potential for long-range transport of mercury to the Everglades using the organic chemistry integrated dispersion (ORCHID) model

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

Burns, D.S.; Kienzle, M.A.; Ferris, D.C.

1996-12-31

The objective of this study is to identify potential long-range sources of mercury within the southeast region of the United States. Preliminary results of a climatological study using the Short-range Layered Atmospheric Model (SLAM) transport model from a select source in the southeast U.S. are presented. The potential for long-range transport from Oak Ridge, Tennessee to Florida is discussed. The transport and transformation of mercury during periods of favorable transport to south Florida is modeled using the Organic Chemistry Integrated Dispersion (ORCHID) model, which contains the transport model used in the climatology study. SLAM/ORCHID results indicate the potential for mercurymore » reaching southeast Florida from the source and the atmospheric oxidation of mercury during transport.« less

A Stochastic Multi-Media Model of Microbial Transport in Watersheds

NASA Astrophysics Data System (ADS)

Yeghiazarian, L.; Safwat, A.; Whiteaker, T.; Teklitz, A.; Nietch, C.; Maidment, D. R.; Best, E. P.

2012-12-01

Fecal contamination is the leading cause of surface-water impairment in the US, and fecal pathogens are capable of triggering massive outbreaks of gastrointestinal disease. The difficulty in prediction of water contamination has its roots in the stochastic variability of fecal pathogens in the environment, and in the complexity of microbial dynamics and interactions on the soil surface and in water. To address these challenges, we have developed a stochastic model whereby the transport of microorganisms in watersheds is considered in two broad categories: microorganisms that are attached to mineral or organic substrates in suspended sediment; and unattached microorganisms suspended in overland flow. The interactions of microorganisms with soil particles on the soil surface and in the overland flow lead to transitions of microorganisms between solid and aqueous media. The strength of attachment of microorganisms to soil particles is determined by the chemical characteristics of soils which are highly correlated with the particle size. The particle size class distribution in the suspended sediment is predicted by the Water Erosion Prediction Project (WEPP). The model is integrated with ArcGIS, resulting in a general transport-modeling framework applicable to a variety of biological and chemical surface water contaminants. Simulations are carried out for a case study of contaminant transport in the East Fork Little Miami River Watershed in Ohio. Model results include the spatial probability distribution of microbes in the watershed and can be used for assessment of (1) mechanisms dominating microbial transport, and (2) time and location of highest likelihood of microbial occurrence, thus yielding information on best water sampling strategies.

Investigation of energy transport in DIII-D high- β P EAST-demonstration discharges with the TGLF turbulent and NEO neoclassical transport models [Investigation of energy transport in DIII-D high- β P EAST-demonstration discharges with turbulent and neoclassical transport models

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

Pan, Chengkang; Staebler, Gary M.; Lao, Lang L.

Here, energy transport analyses of DIII-D high-β P EAST-demonstration discharges have been performed using the TGYRO transport package with TGLF turbulent and NEO neoclassical transport models under the OMFIT integrated modeling framework. Ion energy transport is shown to be dominated by neoclassical transport and ion temperature profiles predicted by TGYRO agree closely with the experimental measured profiles for these high-β P discharges. Ion energy transport is largely insensitive to reductions in the E × B flow shear stabilization. The Shafranov shift is shown to play a role in the suppression of the ion turbulent energy transport below the neoclassical level.more » Electron turbulent energy transport is under-predicted by TGLF and a significant shortfall in the electron energy transport over the whole core plasma is found with TGLF predictions for these high-β P discharges. TGYRO can successfully predict the experimental ion and electron temperature profiles by artificially increasing the saturated turbulence level for ETG driven modes used in TGLF.« less

Investigation of energy transport in DIII-D high- β P EAST-demonstration discharges with the TGLF turbulent and NEO neoclassical transport models [Investigation of energy transport in DIII-D high- β P EAST-demonstration discharges with turbulent and neoclassical transport models

DOE PAGES

Pan, Chengkang; Staebler, Gary M.; Lao, Lang L.; ...

2017-01-11

Here, energy transport analyses of DIII-D high-β P EAST-demonstration discharges have been performed using the TGYRO transport package with TGLF turbulent and NEO neoclassical transport models under the OMFIT integrated modeling framework. Ion energy transport is shown to be dominated by neoclassical transport and ion temperature profiles predicted by TGYRO agree closely with the experimental measured profiles for these high-β P discharges. Ion energy transport is largely insensitive to reductions in the E × B flow shear stabilization. The Shafranov shift is shown to play a role in the suppression of the ion turbulent energy transport below the neoclassical level.more » Electron turbulent energy transport is under-predicted by TGLF and a significant shortfall in the electron energy transport over the whole core plasma is found with TGLF predictions for these high-β P discharges. TGYRO can successfully predict the experimental ion and electron temperature profiles by artificially increasing the saturated turbulence level for ETG driven modes used in TGLF.« less

The cell line NCl-H441 is a useful in vitro model for transport studies of human distal lung epithelial barrier.

PubMed

Salomon, Johanna J; Muchitsch, Viktoria E; Gausterer, Julia C; Schwagerus, Elena; Huwer, Hanno; Daum, Nicole; Lehr, Claus-Michael; Ehrhardt, Carsten

2014-03-03

The lack of a well characterized, continuously growing in vitro model of human distal lung epithelial phenotype constitutes a serious limitation in the area of inhalation biopharmaceutics, particularly in the context of transepithelial transport studies. Here, we investigated if a human lung adenocarcinoma cell line, NCl-H441, has potential to serve as an in vitro model of human distal lung epithelium. The development of barrier properties was studied by immunocytochemistry (ICC) against the junction proteins zonula occludens protein 1 (ZO-1) and E-cadherin and measurement of transepithelial electrical resistance (TEER). Moreover, transport studies with the paracellular marker compounds fluorescein sodium and fluorescein isothiocyanate (FITC)-labeled dextrans of molecular weights ranging from 4 to 70 kDa were carried out. The expression of P-glycoprotein (P-gp; ABCB1) and organic cation transporters (OCT/Ns; SLC22A1-A5) was investigated by ICC and immunoblot. P-gp function was assessed by monolayer release and bidirectional transport studies using rhodamine 123 (Rh123) and the inhibitors verapamil and LY335979. Uptake of 4-(4-(dimethylamino)styryl)-N-methylpyridinium iodide (ASP(+)) was measured, in order to assess organic cation transporter function in vitro. Furthermore, the inhibitory potential of several organic cations on ASP(+) uptake was studied. NCl-H441 cells, when grown under liquid-covered conditions, formed confluent, electrically tight monolayers with peak TEER values of approximately 1000 Ω·cm(2), after 8-12 days in culture. These monolayers were able to differentiate paracellularly transported substrates according to their molecular weight. Presence of P-gp, OCT1, OCT2, OCT3, OCTN1, and OCTN2 was confirmed by Western blot and ICC and was similar to data from freshly isolated human alveolar epithelial cells in primary culture. Rh123 release from NCI-H441 monolayers was time-dependent and showed low, albeit significant attenuation by both inhibitors

Electron Transport Modeling of Molecular Nanoscale Bridges Used in Energy Conversion Schemes

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

Dunietz, Barry D

2016-08-09

The goal of the research program is to reliably describe electron transport and transfer processes at the molecular level. Such insight is essential for improving molecular applications of solar and thermal energy conversion. We develop electronic structure models to study (1) photoinduced electron transfer and transport processes in organic semiconducting materials, and (2) charge and heat transport through molecular bridges. We seek fundamental understanding of key processes, which lead to design new experiments and ultimately to achieve systems with improved properties.

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

DOE PAGES

Locatelli, R.; Bousquet, P.; Chevallier, F.; ...

2013-10-08

A modelling experiment has been conceived to assess the impact of transport model errors on methane emissions estimated in an atmospheric inversion system. Synthetic methane observations, obtained from 10 different model outputs from the international TransCom-CH4 model inter-comparison exercise, are combined with a prior scenario of methane emissions and sinks, and integrated into the three-component PYVAR-LMDZ-SACS (PYthon VARiational-Laboratoire de Météorologie Dynamique model with Zooming capability-Simplified Atmospheric Chemistry System) inversion system to produce 10 different methane emission estimates at the global scale for the year 2005. The same methane sinks, emissions and initial conditions have been applied to produce the 10more » synthetic observation datasets. The same inversion set-up (statistical errors, prior emissions, inverse procedure) is then applied to derive flux estimates by inverse modelling. Consequently, only differences in the modelling of atmospheric transport may cause differences in the estimated fluxes. Here in our framework, we show that transport model errors lead to a discrepancy of 27 Tg yr -1 at the global scale, representing 5% of total methane emissions. At continental and annual scales, transport model errors are proportionally larger than at the global scale, with errors ranging from 36 Tg yr -1 in North America to 7 Tg yr -1 in Boreal Eurasia (from 23 to 48%, respectively). At the model grid-scale, the spread of inverse estimates can reach 150% of the prior flux. Therefore, transport model errors contribute significantly to overall uncertainties in emission estimates by inverse modelling, especially when small spatial scales are examined. Sensitivity tests have been carried out to estimate the impact of the measurement network and the advantage of higher horizontal resolution in transport models. The large differences found between methane flux estimates inferred in these different configurations highly question the

Electrical and Thermal Transport Property Studies of High-Temperature Thermoelectric Materials.

DTIC Science & Technology

1985-06-01

THERMAL TRANSPORT PROPERTY STUDIES OF HIGH-TEMPERATURE THERMOELECTRIC MATERIALS: INTERIM TECHNICAL REPORT FOR THE PERIOD MAY 15, 1984 TO MAY 15, 1985 J. L...transport property data base has been expanded oy continued measurements in several systems under study, and a theoretical model for thermoelectric ...6.0 REFERENCES . . . . . . . . . . . . 6.1 APPENDIX A - THERMOELECTRIC PROPERTY DATA . . . . . . . A. I 1l FIGURES 3.1 Dimensionless Figure of Merit

Intercomparison of Multiscale Modeling Approaches in Simulating Subsurface Flow and Transport

NASA Astrophysics Data System (ADS)

Yang, X.; Mehmani, Y.; Barajas-Solano, D. A.; Song, H. S.; Balhoff, M.; Tartakovsky, A. M.; Scheibe, T. D.

2016-12-01

Hybrid multiscale simulations that couple models across scales are critical to advance predictions of the larger system behavior using understanding of fundamental processes. In the current study, three hybrid multiscale methods are intercompared: multiscale loose-coupling method, multiscale finite volume (MsFV) method and multiscale mortar method. The loose-coupling method enables a parallel workflow structure based on the Swift scripting environment that manages the complex process of executing coupled micro- and macro-scale models without being intrusive to the at-scale simulators. The MsFV method applies microscale and macroscale models over overlapping subdomains of the modeling domain and enforces continuity of concentration and transport fluxes between models via restriction and prolongation operators. The mortar method is a non-overlapping domain decomposition approach capable of coupling all permutations of pore- and continuum-scale models with each other. In doing so, Lagrange multipliers are used at interfaces shared between the subdomains so as to establish continuity of species/fluid mass flux. Subdomain computations can be performed either concurrently or non-concurrently depending on the algorithm used. All the above methods have been proven to be accurate and efficient in studying flow and transport in porous media. However, there has not been any field-scale applications and benchmarking among various hybrid multiscale approaches. To address this challenge, we apply all three hybrid multiscale methods to simulate water flow and transport in a conceptualized 2D modeling domain of the hyporheic zone, where strong interactions between groundwater and surface water exist across multiple scales. In all three multiscale methods, fine-scale simulations are applied to a thin layer of riverbed alluvial sediments while the macroscopic simulations are used for the larger subsurface aquifer domain. Different numerical coupling methods are then applied between

ATLAS - A new Lagrangian transport and mixing model with detailed stratospheric chemistry

NASA Astrophysics Data System (ADS)

Wohltmann, I.; Rex, M.; Lehmann, R.

2009-04-01

We present a new global Chemical Transport Model (CTM) with full stratospheric chemistry and Lagrangian transport and mixing called ATLAS. Lagrangian models have some crucial advantages over Eulerian grid-box based models, like no numerical diffusion, no limitation of the time step of the model by the CFL criterion, conservation of mixing ratios by design and easy parallelization of code. The transport module is based on a trajectory code developed at the Alfred Wegener Institute. The horizontal and vertical resolution, the vertical coordinate system (pressure, potential temperature, hybrid coordinate) and the time step of the model are flexible, so that the model can be used both for process studies and long-time runs over several decades. Mixing of the Lagrangian air parcels is parameterized based on the local shear and strain of the flow with a method similar to that used in the CLaMS model, but with some modifications like a triangulation that introduces no vertical layers. The stratospheric chemistry module was developed at the Institute and includes 49 species and 170 reactions and a detailed treatment of heterogenous chemistry on polar stratospheric clouds. We present an overview over the model architecture, the transport and mixing concept and some validation results. Comparison of model results with tracer data from flights of the ER2 aircraft in the stratospheric polar vortex in 1999/2000 which are able to resolve fine tracer filaments show that excellent agreement with observed tracer structures can be achieved with a suitable mixing parameterization.

Time-dependent Perpendicular Transport of Energetic Particles for Different Turbulence Configurations and Parallel Transport Models

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

Lasuik, J.; Shalchi, A., E-mail: andreasm4@yahoo.com

Recently, a new theory for the transport of energetic particles across a mean magnetic field was presented. Compared to other nonlinear theories the new approach has the advantage that it provides a full time-dependent description of the transport. Furthermore, a diffusion approximation is no longer part of that theory. The purpose of this paper is to combine this new approach with a time-dependent model for parallel transport and different turbulence configurations in order to explore the parameter regimes for which we get ballistic transport, compound subdiffusion, and normal Markovian diffusion.

A three-dimensional cohesive sediment transport model with data assimilation: Model development, sensitivity analysis and parameter estimation

NASA Astrophysics Data System (ADS)

Wang, Daosheng; Cao, Anzhou; Zhang, Jicai; Fan, Daidu; Liu, Yongzhi; Zhang, Yue

2018-06-01

Based on the theory of inverse problems, a three-dimensional sigma-coordinate cohesive sediment transport model with the adjoint data assimilation is developed. In this model, the physical processes of cohesive sediment transport, including deposition, erosion and advection-diffusion, are parameterized by corresponding model parameters. These parameters are usually poorly known and have traditionally been assigned empirically. By assimilating observations into the model, the model parameters can be estimated using the adjoint method; meanwhile, the data misfit between model results and observations can be decreased. The model developed in this work contains numerous parameters; therefore, it is necessary to investigate the parameter sensitivity of the model, which is assessed by calculating a relative sensitivity function and the gradient of the cost function with respect to each parameter. The results of parameter sensitivity analysis indicate that the model is sensitive to the initial conditions, inflow open boundary conditions, suspended sediment settling velocity and resuspension rate, while the model is insensitive to horizontal and vertical diffusivity coefficients. A detailed explanation of the pattern of sensitivity analysis is also given. In ideal twin experiments, constant parameters are estimated by assimilating 'pseudo' observations. The results show that the sensitive parameters are estimated more easily than the insensitive parameters. The conclusions of this work can provide guidance for the practical applications of this model to simulate sediment transport in the study area.

Can the three pore model correctly describe peritoneal transport of protein?

PubMed

Waniewski, Jacek; Poleszczuk, Jan; Antosiewicz, Stefan; Baczynński, Daniel; Gałach, Magda; Pietribiasi, Mauro; Wanńkowicz, Zofia

2014-01-01

The three pore model (3PM) includes large pores for the description of protein leak to the peritoneal cavity during peritoneal dialysis. However, the reliability of this description has been not fully tested against clinical data yet. Peritoneal transport parameters were estimated using 3PM, extended 3p model (with estimation of fraction of large pores, ext3PM), ext3PM with modified size of pores and proteins (mext3PM), and simplified two pore (2PM, small and ultrasmall pores) models for 32 patients on peritoneal dialysis investigated using the sequential peritoneal equilibration test (consecutive peritoneal equilibration test [PET]: glucose 2.27%, 4 h, and miniPET: glucose 3.86%, 1 h). Urea, creatinine, glucose, sodium, phosphate, albumin, and IgM concentrations were measured in dialysis fluid and plasma. Ext3PM and mext3PM, with large pore fraction of about 0.14, provided a good description of fluid and small solute kinetics, but their predictions for albumin transport were less accurate. Two pore model precisely described the data on fluid and small solute transport. The 3p models could not describe the diffusive-convective transport of albumin as precisely as the transport of fluid, small solutes, and IgM. The 2p model (not applicable for proteins) was an efficient tool for modeling fluid and small solute transport.

Space evolution model and empirical analysis of an urban public transport network

NASA Astrophysics Data System (ADS)

Sui, Yi; Shao, Feng-jing; Sun, Ren-cheng; Li, Shu-jing

2012-07-01

This study explores the space evolution of an urban public transport network, using empirical evidence and a simulation model validated on that data. Public transport patterns primarily depend on traffic spatial-distribution, demands of passengers and expected utility of investors. Evolution is an iterative process of satisfying the needs of passengers and investors based on a given traffic spatial-distribution. The temporal change of urban public transport network is evaluated both using topological measures and spatial ones. The simulation model is validated using empirical data from nine big cities in China. Statistical analyses on topological and spatial attributes suggest that an evolution network with traffic demands characterized by power-law numerical values which distribute in a mode of concentric circles tallies well with these nine cities.

A time fractional convection-diffusion equation to model gas transport through heterogeneous soil and gas reservoirs

NASA Astrophysics Data System (ADS)

Chang, Ailian; Sun, HongGuang; Zheng, Chunmiao; Lu, Bingqing; Lu, Chengpeng; Ma, Rui; Zhang, Yong

2018-07-01

Fractional-derivative models have been developed recently to interpret various hydrologic dynamics, such as dissolved contaminant transport in groundwater. However, they have not been applied to quantify other fluid dynamics, such as gas transport through complex geological media. This study reviewed previous gas transport experiments conducted in laboratory columns and real-world oil-gas reservoirs and found that gas dynamics exhibit typical sub-diffusive behavior characterized by heavy late-time tailing in the gas breakthrough curves (BTCs), which cannot be effectively captured by classical transport models. Numerical tests and field applications of the time fractional convection-diffusion equation (fCDE) have shown that the fCDE model can capture the observed gas BTCs including their apparent positive skewness. Sensitivity analysis further revealed that the three parameters used in the fCDE model, including the time index, the convection velocity, and the diffusion coefficient, play different roles in interpreting the delayed gas transport dynamics. In addition, the model comparison and analysis showed that the time fCDE model is efficient in application. Therefore, the time fractional-derivative models can be conveniently extended to quantify gas transport through natural geological media such as complex oil-gas reservoirs.

Modeling the transport of nitrogen in an NPP-2006 reactor circuit

NASA Astrophysics Data System (ADS)

Stepanov, O. E.; Galkin, I. Yu.; Sledkov, R. M.; Melekh, S. S.; Strebnev, N. A.

2016-07-01

Efficient radiation protection of the public and personnel requires detecting an accident-initiating event quickly. Specifically, if a heat-exchange tube in a steam generator is ruptured, the 16N radioactive nitrogen isotope, which contributes to a sharp increase in the steam activity before the turbine, may serve as the signaling component. This isotope is produced in the core coolant and is transported along the circulation circuit. The aim of the present study was to model the transport of 16N in the primary and the secondary circuits of a VVER-1000 reactor facility (RF) under nominal operation conditions. KORSAR/GP and RELAP5/Mod.3.2 codes were used to perform the calculations. Computational models incorporating the major components of the primary and the secondary circuits of an NPP-2006 RF were constructed. These computational models were subjected to cross-verification, and the calculation results were compared to the experimental data on the distribution of the void fraction over the steam generator height. The models were proven to be valid. It was found that the time of nitrogen transport from the core to the heat-exchange tube leak was no longer than 1 s under RF operation at a power level of 100% N nom with all primary circuit pumps activated. The time of nitrogen transport from the leak to the γ-radiation detection unit under the same operating conditions was no longer than 9 s, and the nitrogen concentration in steam was no less than 1.4% (by mass) of its concentration at the reactor outlet. These values were obtained using conservative approaches to estimating the leak flow and the transport time, but the radioactive decay of nitrogen was not taken into account. Further research concerned with the calculation of thermohydraulic processes should be focused on modeling the transport of nitrogen under RF operation with some primary circuit pumps deactivated.

A dual-porosity model for simulating solute transport in oil shale

USGS Publications Warehouse

Glover, K.C.

1987-01-01

A model is described for simulating three-dimensional groundwater flow and solute transport in oil shale and associated geohydrologic units. The model treats oil shale as a dual-porosity medium by simulating flow and transport within fractures using the finite-element method. Diffusion of solute between fractures and the essentially static water of the shale matrix is simulated by including an analytical solution that acts as a source-sink term to the differential equation of solute transport. While knowledge of fracture orientation and spacing is needed to effectively use the model, it is not necessary to map the locations of individual fractures. The computer program listed in the report incorporates many of the features of previous dual-porosity models while retaining a practical approach to solving field problems. As a result the theory of solute transport is not extended in any appreciable way. The emphasis is on bringing together various aspects of solute transport theory in a manner that is particularly suited to the unusual groundwater flow and solute transport characteristics of oil shale systems. (Author 's abstract)

Numerical Modeling of Transport of Biomass Burning Emissions on South America

NASA Technical Reports Server (NTRS)

RibeirodeFreitas, Saulo

2001-01-01

Our research efforts have addressed theoretical and numerical modeling of sources emissions and transport processes of trace gases and aerosols emitted by biomass burning on the central of Brazil and Amazon basin. For this effort we coupled all Eulerian transport model with the mesoscale atmospheric model RAMS (Regional Atmospheric Modeling System).

Fuzzy multi-objective chance-constrained programming model for hazardous materials transportation

NASA Astrophysics Data System (ADS)

Du, Jiaoman; Yu, Lean; Li, Xiang

2016-04-01

Hazardous materials transportation is an important and hot issue of public safety. Based on the shortest path model, this paper presents a fuzzy multi-objective programming model that minimizes the transportation risk to life, travel time and fuel consumption. First, we present the risk model, travel time model and fuel consumption model. Furthermore, we formulate a chance-constrained programming model within the framework of credibility theory, in which the lengths of arcs in the transportation network are assumed to be fuzzy variables. A hybrid intelligent algorithm integrating fuzzy simulation and genetic algorithm is designed for finding a satisfactory solution. Finally, some numerical examples are given to demonstrate the efficiency of the proposed model and algorithm.

Validation of the Activities of Community Transportation model for individuals with cognitive impairments.

PubMed

Sohlberg, McKay Moore; Fickas, Stephen; Lemoncello, Rik; Hung, Pei-Fang

2009-01-01

To develop a theoretical, functional model of community navigation for individuals with cognitive impairments: the Activities of Community Transportation (ACTs). Iterative design using qualitative methods (i.e. document review, focus groups and observations). Four agencies providing travel training to adults with cognitive impairments in the USA participated in the validation study. A thorough document review and series of focus groups led to the development of a comprehensive model (ACTs Wheels) delineating the requisite steps and skills for community navigation. The model was validated and updated based on observations of 395 actual trips by travellers with navigational challenges from the four participating agencies. Results revealed that the 'ACTs Wheel' models were complete and comprehensive. The 'ACTs Wheels' represent a comprehensive model of the steps needed to navigate to destinations using paratransit and fixed-route public transportation systems for travellers with cognitive impairments. Suggestions are made for future investigations of community transportation for this population.

Reactive solute transport in streams: 1. Development of an equilibrium- based model

USGS Publications Warehouse

Runkel, Robert L.; Bencala, Kenneth E.; Broshears, Robert E.; Chapra, Steven C.

1996-01-01

An equilibrium-based solute transport model is developed for the simulation of trace metal fate and transport in streams. The model is formed by coupling a solute transport model with a chemical equilibrium submodel based on MINTEQ. The solute transport model considers the physical processes of advection, dispersion, lateral inflow, and transient storage, while the equilibrium submodel considers the speciation and complexation of aqueous species, precipitation/dissolution and sorption. Within the model, 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 (water-borne) 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.

Modelling inflation in transportation, comunication and financial services using B-Spline time series model

NASA Astrophysics Data System (ADS)

Suparti; Prahutama, Alan; Santoso, Rukun

2018-05-01

Inflation is an increase in the price of goods and services in general where the goods and services are the basic needs of society or the decline of the selling power of a country’s currency. Significant inflationary increases occurred in 2013. This increase was contributed by a significant increase in some inflation sectors / groups i.e transportation, communication and financial services; the foodstuff sector, and the housing, water, electricity, gas and fuel sectors. However, significant contributions occurred in the transportation, communications and financial services sectors. In the model of IFIs in the transportation, communication and financial services sector use the B-Spline time series approach, where the predictor variable is Yt, whereas the predictor is a significant lag (in this case Yt-1). In modeling B-spline time series determined the order and the optimum knot point. Optimum knot determination using Generalized Cross Validation (GCV). In inflation modeling for transportation sector, communication and financial services obtained model of B-spline order 2 with 2 points knots produce MAPE less than 50%.

Unified computational model of transport in metal-insulating oxide-metal systems

NASA Astrophysics Data System (ADS)

Tierney, B. D.; Hjalmarson, H. P.; Jacobs-Gedrim, R. B.; Agarwal, Sapan; James, C. D.; Marinella, M. J.

2018-04-01

A unified physics-based model of electron transport in metal-insulator-metal (MIM) systems is presented. In this model, transport through metal-oxide interfaces occurs by electron tunneling between the metal electrodes and oxide defect states. Transport in the oxide bulk is dominated by hopping, modeled as a series of tunneling events that alter the electron occupancy of defect states. Electron transport in the oxide conduction band is treated by the drift-diffusion formalism and defect chemistry reactions link all the various transport mechanisms. It is shown that the current-limiting effect of the interface band offsets is a function of the defect vacancy concentration. These results provide insight into the underlying physical mechanisms of leakage currents in oxide-based capacitors and steady-state electron transport in resistive random access memory (ReRAM) MIM devices. Finally, an explanation of ReRAM bipolar switching behavior based on these results is proposed.

Surrogate model approach for improving the performance of reactive transport simulations

NASA Astrophysics Data System (ADS)

Jatnieks, Janis; De Lucia, Marco; Sips, Mike; Dransch, Doris

2016-04-01

Reactive transport models can serve a large number of important geoscientific applications involving underground resources in industry and scientific research. It is common for simulation of reactive transport to consist of at least two coupled simulation models. First is a hydrodynamics simulator that is responsible for simulating the flow of groundwaters and transport of solutes. Hydrodynamics simulators are well established technology and can be very efficient. When hydrodynamics simulations are performed without coupled geochemistry, their spatial geometries can span millions of elements even when running on desktop workstations. Second is a geochemical simulation model that is coupled to the hydrodynamics simulator. Geochemical simulation models are much more computationally costly. This is a problem that makes reactive transport simulations spanning millions of spatial elements very difficult to achieve. To address this problem we propose to replace the coupled geochemical simulation model with a surrogate model. A surrogate is a statistical model created to include only the necessary subset of simulator complexity for a particular scenario. To demonstrate the viability of such an approach we tested it on a popular reactive transport benchmark problem that involves 1D Calcite transport. This is a published benchmark problem (Kolditz, 2012) for simulation models and for this reason we use it to test the surrogate model approach. To do this we tried a number of statistical models available through the caret and DiceEval packages for R, to be used as surrogate models. These were trained on randomly sampled subset of the input-output data from the geochemical simulation model used in the original reactive transport simulation. For validation we use the surrogate model to predict the simulator output using the part of sampled input data that was not used for training the statistical model. For this scenario we find that the multivariate adaptive regression splines

Comparing Lagrangian and Eulerian models for CO2 transport - a step towards Bayesian inverse modeling using WRF/STILT-VPRM

NASA Astrophysics Data System (ADS)

Pillai, D.; Gerbig, C.; Kretschmer, R.; Beck, V.; Karstens, U.; Neininger, B.; Heimann, M.

2012-01-01

We present simulations of atmospheric CO2 concentrations provided by two modeling systems, run at high spatial resolution: the Eulerian-based Weather Research Forecasting (WRF) model and the Lagrangian-based Stochastic Time-Inverted Lagrangian Transport (STILT) model, both of which are coupled to a diagnostic biospheric model, the Vegetation Photosynthesis and Respiration Model (VPRM). The consistency of the simulations is assessed with special attention paid to the details of horizontal as well as vertical transport and mixing of CO2 concentrations in the atmosphere. The dependence of model mismatch (Eulerian vs. Lagrangian) on models' spatial resolution is further investigated. A case study using airborne measurements during which both models showed large deviations from each other is analyzed in detail as an extreme case. Using aircraft observations and pulse release simulations, we identified differences in the representation of details in the interaction between turbulent mixing and advection through wind shear as the main cause of discrepancies between WRF and STILT transport at a spatial resolution such as 2 and 6 km. Based on observations and inter-model comparisons of atmospheric CO2 concentrations, we show that a refinement of the parameterization of turbulent velocity variance and Lagrangian time-scale in STILT is needed to achieve a better match between the Eulerian and the Lagrangian transport at such a high spatial resolution (e.g. 2 and 6 km). Nevertheless, the inter-model differences in simulated CO2 time series for a tall tower observatory at Ochsenkopf in Germany are about a factor of two smaller than the model-data mismatch and about a factor of three smaller than the mismatch between the current global model simulations and the data. Thus suggests that it is reasonable to use STILT as an adjoint model of WRF atmospheric transport.

Consistency between 2D-3D Sediment Transport models

NASA Astrophysics Data System (ADS)

Villaret, Catherine; Jodeau, Magali

2017-04-01

Sediment transport models have been developed and applied by the engineering community to estimate transport rates and morphodynamic bed evolutions in river flows, coastal and estuarine conditions. Environmental modelling systems like the open-source Telemac modelling system include a hierarchy of models from 1D (Mascaret), 2D (Telemac-2D/Sisyphe) and 3D (Telemac-3D/Sedi-3D) and include a wide range of processes to represent sediment flow interactions under more and more complex situations (cohesive, non-cohesive and mixed sediment). Despite some tremendous progresses in the numerical techniques and computing resources, the quality/accuracy of model results mainly depend on the numerous choices and skills of the modeler. In complex situations involving stratification effects, complex geometry, recirculating flows… 2D model assumptions are no longer valid. A full 3D turbulent flow model is then required in order to capture the vertical mixing processes and to represent accurately the coupled flow/sediment distribution. However a number of theoretical and numerical difficulties arise when dealing with sediment transport modelling in 3D which will be high-lighted : (1) Dependency of model results to the vertical grid refinement and choice of boundary conditions and numerical scheme (2) The choice of turbulence model determines also the sediment vertical distribution which is governed by a balance between the downward settling term and upward turbulent diffusion. (3) The use of different numerical schemes for both hydrodynamics (mean and turbulent flow) and sediment transport modelling can lead to some inconsistency including a mismatch in the definition of numerical cells and definition of boundary conditions. We discuss here those present issues and present some detailed comparison between 2D and 3D simulations on a set of validation test cases which are available in the Telemac 7.2 release using both cohesive and non-cohesive sediments.

Transition From Ideal To Viscous Mach Cones In A Partonic Transport Model

NASA Astrophysics Data System (ADS)

Bouras, I.; El, A.; Fochler, O.; Niemi, H.; Xu, Z.; Greiner, C.

2013-09-01

Using a partonic transport model we investigate the evolution of conical structures in ultrarelativistic matter. Using two different source terms and varying the transport properties of the matter we study the formation of Mach Cones. Furthermore, in an additional study we extract the two-particle correlations from the numerical calculations and compare them to an analytical approximation. The influence of the viscosity to the shape of Mach Cones and the corresponding two-particle correlations is studied by adjusting the cross section of the medium.

Bubble-facilitated VOC transport: Laboratory experiments and numerical modelling

NASA Astrophysics Data System (ADS)

Mumford, K. G.; Soucy, N. C.

2017-12-01

Most conceptual and numerical models of vapor intrusion assume that the transport of volatile organic compounds (VOCs) from the source to near the building foundation is a diffusion-limited processes. However, the transport of VOCs by mobilized gas bubbles through the saturated zone could lead to increased rates of transport and advection through the unsaturated zone, thereby increasing mass flux and risks associated with vapor intrusion. This mobilized gas could be biogenic (methanogenic) but could also result from the partitioning of VOC to trapped atmospheric gases in light non-aqueous phase liquid (LNAPL) smear zones. The potential for bubble-facilitated VOC transport to increase mass flux was investigated in a series of 1D and 2D laboratory experiments. Pentane source zones were emplaced in sand using sequential drainage and imbibition steps to mimic a water table fluctuation and trap air alongside LNAPL residual. This source was placed below an uncontaminated, water saturated sand (occlusion zone) and a gravel-sized (glass beads) unsaturated zone. Water was pumped laterally through the source zone and occlusion zone to deliver the dissolved gases (air) that are required for the expansion of trapped gas bubbles. Images from 2D flow cell experiments were used to demonstrate fluid rearrangement in the source zone and gas expansion to the occlusion zone, and 1D column experiments were used to measure gas-phase pentane mass flux. This flux was found to be 1-2 orders of magnitude greater than that measured in diffusion-dominated control columns, and showed intermittent behavior consistent with bubble transport by repeated expansion, mobilization, coalescence and trapping. Numerical simulation results under a variety of conditions using an approach that couples macroscopic invasion percolation with mass transfer (MIP-MT) between the aqueous and gas phases will also be presented. The results of this study demonstrate the potential for bubble-facilitated transport to

MODELING FINE SEDIMENT TRANSPORT IN ESTUARIES

EPA Science Inventory

A sediment transport model (SEDIMENT IIIA) was developed to assist in predicting the fate of chemical pollutants sorbed to cohesive sediments in rivers and estuaries. Laboratory experiments were conducted to upgrade an existing two-dimensional, depth-averaged, finite element, coh...

Modeling emissions for three-dimensional atmospheric chemistry transport models.

PubMed

Matthias, Volker; Arndt, Jan A; Aulinger, Armin; Bieser, Johannes; Denier Van Der Gon, Hugo; Kranenburg, Richard; Kuenen, Jeroen; Neumann, Daniel; Pouliot, George; Quante, Markus

2018-01-24

Poor air quality is still a threat for human health in many parts of the world. In order to assess measures for emission reductions and improved air quality, three-dimensional atmospheric chemistry transport modeling systems are used in numerous research institutions and public authorities. These models need accurate emission data in appropriate spatial and temporal resolution as input. This paper reviews the most widely used emission inventories on global and regional scale and looks into the methods used to make the inventory data model ready. Shortcomings of using standard temporal profiles for each emission sector are discussed and new methods to improve the spatio-temporal distribution of the emissions are presented. These methods are often neither top-down nor bottom-up approaches but can be seen as hybrid methods that use detailed information about the emission process to derive spatially varying temporal emission profiles. These profiles are subsequently used to distribute bulk emissions like national totals on appropriate grids. The wide area of natural emissions is also summarized and the calculation methods are described. Almost all types of natural emissions depend on meteorological information, which is why they are highly variable in time and space and frequently calculated within the chemistry transport models themselves. The paper closes with an outlook for new ways to improve model ready emission data, for example by using external databases about road traffic flow or satellite data to determine actual land use or leaf area. In a world where emission patterns change rapidly, it seems appropriate to use new types of statistical and observational data to create detailed emission data sets and keep emission inventories up-to-date. Emission data is probably the most important input for chemistry transport model (CTM) systems. It needs to be provided in high temporal and spatial resolution and on a grid that is in agreement with the CTM grid. Simple

Revisiting Temporal Markov Chains for Continuum modeling of Transport in Porous Media

NASA Astrophysics Data System (ADS)

Delgoshaie, A. H.; Jenny, P.; Tchelepi, H.

2017-12-01

The transport of fluids in porous media is dominated by flow­-field heterogeneity resulting from the underlying permeability field. Due to the high uncertainty in the permeability field, many realizations of the reference geological model are used to describe the statistics of the transport phenomena in a Monte Carlo (MC) framework. There has been strong interest in working with stochastic formulations of the transport that are different from the standard MC approach. Several stochastic models based on a velocity process for tracer particle trajectories have been proposed. Previous studies have shown that for high variances of the log-conductivity, the stochastic models need to account for correlations between consecutive velocity transitions to predict dispersion accurately. The correlated velocity models proposed in the literature can be divided into two general classes of temporal and spatial Markov models. Temporal Markov models have been applied successfully to tracer transport in both the longitudinal and transverse directions. These temporal models are Stochastic Differential Equations (SDEs) with very specific drift and diffusion terms tailored for a specific permeability correlation structure. The drift and diffusion functions devised for a certain setup would not necessarily be suitable for a different scenario, (e.g., a different permeability correlation structure). The spatial Markov models are simple discrete Markov chains that do not require case specific assumptions. However, transverse spreading of contaminant plumes has not been successfully modeled with the available correlated spatial models. Here, we propose a temporal discrete Markov chain to model both the longitudinal and transverse dispersion in a two-dimensional domain. We demonstrate that these temporal Markov models are valid for different correlation structures without modification. Similar to the temporal SDEs, the proposed model respects the limited asymptotic transverse spreading of

Anomalous solute transport in saturated porous media: Relating transport model parameters to electrical and nuclear magnetic resonance properties

USGS Publications Warehouse

Swanson, Ryan D; Binley, Andrew; Keating, Kristina; France, Samantha; Osterman, Gordon; Day-Lewis, Frederick D.; Singha, Kamini

2015-01-01

The advection-dispersion equation (ADE) fails to describe commonly observed non-Fickian solute transport in saturated porous media, necessitating the use of other models such as the dual-domain mass-transfer (DDMT) model. DDMT model parameters are commonly calibrated via curve fitting, providing little insight into the relation between effective parameters and physical properties of the medium. There is a clear need for material characterization techniques that can provide insight into the geometry and connectedness of pore spaces related to transport model parameters. Here, we consider proton nuclear magnetic resonance (NMR), direct-current (DC) resistivity, and complex conductivity (CC) measurements for this purpose, and assess these methods using glass beads as a control and two different samples of the zeolite clinoptilolite, a material that demonstrates non-Fickian transport due to intragranular porosity. We estimate DDMT parameters via calibration of a transport model to column-scale solute tracer tests, and compare NMR, DC resistivity, CC results, which reveal that grain size alone does not control transport properties and measured geophysical parameters; rather, volume and arrangement of the pore space play important roles. NMR cannot provide estimates of more-mobile and less-mobile pore volumes in the absence of tracer tests because these estimates depend critically on the selection of a material-dependent and flow-dependent cutoff time. Increased electrical connectedness from DC resistivity measurements are associated with greater mobile pore space determined from transport model calibration. CC was hypothesized to be related to length scales of mass transfer, but the CC response is unrelated to DDMT.

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

PubMed

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

2011-03-25

The activity of microorganisms often plays an important role in dynamic natural attenuation or engineered bioremediation of subsurface contaminants, such as chlorinated solvents, metals, and radionuclides. To evaluate and/or design bioremediated systems, quantitative reactive transport models are needed. State-of-the-art reactive transport models often ignore the microbial effects or simulate the microbial effects with static growth yield and constant reaction rate parameters over simulated conditions, while in reality microorganisms can dynamically modify their functionality (such as utilization of alternative respiratory pathways) in response to spatial and temporal variations in environmental conditions. Constraint-based genome-scale microbial in silico models, using genomic data and multiple-pathway reaction networks, have been shown to be able to simulate transient metabolism of some well studied microorganisms and identify growth rate, substrate uptake rates, and byproduct rates under different growth conditions. These rates can be identified and used to replace specific microbially-mediated reaction rates in a reactive transport model using local geochemical conditions as constraints. We previously demonstrated the potential utility of integrating a constraint-based microbial metabolism model with a reactive transport simulator as applied to bioremediation of uranium in groundwater. However, that work relied on an indirect coupling approach that was effective for initial demonstration but may not be extensible to more complex problems that are of significant interest (e.g., communities of microbial species and multiple constraining variables). Here, we extend that work by presenting and demonstrating a method of directly integrating a reactive transport model (FORTRAN code) with constraint-based in silico models solved with IBM ILOG CPLEX linear optimizer base system (C library). The models were integrated with BABEL, a language interoperability tool. The

Lagrangian Transport Model Forecasts as Useful Support of the Flight Planning During the Intercontinental Transport and Chemical Transformation 2002 (ITCT 2k2) Measurement Campaign

NASA Astrophysics Data System (ADS)

Forster, C.; Cooper, O.; Stohl, A.; Eckhardt, S.; James, P.; Dunlea, E.; Nicks, D. K.; Holloway, J. S.; Hübler, G.; Parrish, D. D.; Ryerson, T. B.; Trainer, M.

2002-12-01

In this study, the Lagrangian tracer transport model FLEXPART is shown to be a useful forecasting tool for the flight planning during the ITCT 2k2 (Intercontinental Transport and Chemical Transformation 2002) aircraft measurement campaign. The advantages of this model are that it requires only a short computation time, has a finer spatial resolution and does not suffer numerical diffusion compared to chemistry transport models (CTMs). It is a compromise between simple trajectory calculations and complex CTMs that makes best use of available computer hardware. During the campaign FLEXPART provided three-day forecasts for four different anthropogenic CO tracers: Asian, North American, Japanese, and European. The forecasts were based on data from the Aviation model (AVN) of the National Center for Environmental Prediction (NCEP) and relied on the EDGAR emission inventory for the base year 1990. In two case studies, the forecast abilities of FLEXPART are analysed and discussed by comparing the forecasts with measurement data, results from the post analysis modelling, infrared satellite images, and backward trajectories calculated with two different Lagrangian trajectory models. It is shown that intercontinental transport and dispersion of pollution plumes were qualitatively well predicted, and the aircraft could successfully be directed into the polluted air masses.

Effect of different transport observations on inverse modeling results: case study of a long-term groundwater tracer test monitored at high resolution

NASA Astrophysics Data System (ADS)

Rasa, Ehsan; Foglia, Laura; Mackay, Douglas M.; Scow, Kate M.

2013-11-01

Conservative tracer experiments can provide information useful for characterizing various subsurface transport properties. This study examines the effectiveness of three different types of transport observations for sensitivity analysis and parameter estimation of a three-dimensional site-specific groundwater flow and transport model: conservative tracer breakthrough curves (BTCs), first temporal moments of BTCs ( m 1), and tracer cumulative mass discharge ( M d) through control planes combined with hydraulic head observations ( h). High-resolution data obtained from a 410-day controlled field experiment at Vandenberg Air Force Base, California (USA), have been used. In this experiment, bromide was injected to create two adjacent plumes monitored at six different transects (perpendicular to groundwater flow) with a total of 162 monitoring wells. A total of 133 different observations of transient hydraulic head, 1,158 of BTC concentration, 23 of first moment, and 36 of mass discharge were used for sensitivity analysis and parameter estimation of nine flow and transport parameters. The importance of each group of transport observations in estimating these parameters was evaluated using sensitivity analysis, and five out of nine parameters were calibrated against these data. Results showed the advantages of using temporal moment of conservative tracer BTCs and mass discharge as observations for inverse modeling.

Modelling of Sediment Transport of the Mehadica River, Caras Severin County, Romania

NASA Astrophysics Data System (ADS)

Grozav, Adia; Beilicci, Robert; Beilicci, Erika

2017-10-01

Study case is situated in Caras-Severin County. Every sediment transport model application is different both in terms of time and space scale, study objectives, required accuracy, allocated resources, background of the study team etc. For sediment transport modelling, it is necessary to know the characteristics of the sediment in the river bed. Therefore, it is recommended to collect a number of bed sediment grap samples. These samples should be analysing in terms of grain size distribution. To solve theoretical problems of movement of water in the river Mehadica, it requires modelling of water flow in this case. Numerical modelling was performed using the program MIKE11. MIKE 11 is a user-friendly, fully dynamic, one-dimensional modelling tool for the detailed analysis, design, management and operation of both simple and complex river and channel systems. With its exceptional flexibility, speed and user friendly environment, MIKE 11 provides a complete and effective design environment for engineering, water resources, water quality management and planning applications. The Hydrodynamic (HD) module is the nucleus of the MIKE 11 modelling system and forms the basis for most modules including Flood Forecasting, Advection- Dispersion, Water Quality and Non-cohesive sediment transport modules. The MIKE 11 HD module solves the vertically integrated equations for the conservation of mass and momentum, i.e. the Saint-Venant equations. The input data are: area plan with location of cross sections; cross sections topographical data and roughness of river bed; flood discharge hydrograph. Advanced computational modules are included for description of flow over hydraulic structures, including possibilities to describe structure operation.

Placental sulphate transport: a review of functional and molecular studies.

PubMed

Shennan, D B

2012-08-01

Sulphate is required by the feto-placental unit for a number of important conjugation and biosynthetic pathways. Functional studies performed several decades ago established that sulphate transport in human placental microvillus and basal membrane vesicles was mainly via a DIDS-sensitive anion-exchange mechanism. In contrast, no evidence was found for Na⁺-dependent transport. Studies performed using isolated human placental tissue confirmed anion-exchange as the main mechanism. More recently, molecular studies have established the presence of anion-exchange proteins which could play a role in transplacental sulphate movement. However, the presence of transcripts for NaS2 has been reported and has prompted the suggestion that Na⁺-sulphate cotransport may play an important role in maternal-fetal sulphate transport. This article reviews our present knowledge of placental sulphate transport, both functional and molecular, and attempts to form a model based on the available evidence. Copyright © 2012 Elsevier Ltd. All rights reserved.

Applying Input-Output Model to Estimate Broader Economic Impact of Transportation Infrastructure Investment

NASA Astrophysics Data System (ADS)

Anas, Ridwan; Tamin, Ofyar; Wibowo, Sony S.

2016-09-01

The purpose of this study is to identify the relationships between infrastructure improvement and economic growth in the surrounding region. Traditionally, microeconomic and macroeconomic analyses are the mostly used tools for analyzing the linkage between transportation sectors and economic growth but offer little clues to the mechanisms linking transport improvements and the broader economy impacts. This study will estimate the broader economic benefits of the new transportation infrastructure investment, Cipularangtollway in West Java province, Indonesia, to the region connected (Bandung district) using Input-Output model. The result show the decrease of freight transportation costs by at 17 % and the increase of 1.2 % of Bandung District's GDP after the operation of Cipularangtollway.

Study on multimodal transport route under low carbon background

NASA Astrophysics Data System (ADS)

Liu, Lele; Liu, Jie

2018-06-01

Low-carbon environmental protection is the focus of attention around the world, scientists are constantly researching on production of carbon emissions and living carbon emissions. However, there is little literature about multimodal transportation based on carbon emission at home and abroad. Firstly, this paper introduces the theory of multimodal transportation, the multimodal transport models that didn't consider carbon emissions and consider carbon emissions are analyzed. On this basis, a multi-objective programming 0-1 programming model with minimum total transportation cost and minimum total carbon emission is proposed. The idea of weight is applied to Ideal point method for solving problem, multi-objective programming is transformed into a single objective function. The optimal solution of carbon emission to transportation cost under different weights is determined by a single objective function with variable weights. Based on the model and algorithm, an example is given and the results are analyzed.

Parameterization and Modeling of Coupled Heat and Mass Transport in the Vadose Zone

NASA Astrophysics Data System (ADS)

Mohanty, B.; Yang, Z.

2016-12-01

The coupled heat and mass transport in the vadose zone is essentially a multiphysics issue. Addressing this issue appropriately has remarkable impacts on soil physical, chemical and biological processes. To data, most coupled heat and water transport modeling has focused on the interactions between liquid water, water vapor and heat transport in homogeneous and layered soils. Comparatively little work has been done on structured soils where preferential infiltration and evaporation flow occurs. Moreover, the traditional coupled heat and water model usually neglects the nonwetting phase air flow, which was found to be significant in the state-of-the-art modeling framework for coupled heat and water transport investigation. However, the parameterizations for the nonwetting phase air permeability largely remain elusive so far. In order to address the above mentioned limitations, this study aims to develop and validate a predictive multiphysics modeling framework for coupled soil heat and water transport in the heterogeneous shallow subsurface. To this end, the following research work is specifically conducted: (a) propose an improved parameterization to better predict the nonwetting phase relative permeability; (b) determine the dynamics, characteristics and processes of simultaneous soil moisture and heat movement in homogeneous and layered soils; and (c) develop a nonisothermal dual permeability model for heterogeneous structured soils. The results of our studies showed that: (a) the proposed modified nonwetting phase relative permeability models are much more accurate, which can be adopted for better parameterization in the subsequent nonisothermal two phase flow models; (b) the isothermal liquid film flow, nonwetting phase gas flow and liquid-vapor phase change non-equilibrium effects are significant in the arid and semiarid environments (Riverside, California and Audubon, Arizona); and (c) the developed nonisothermal dual permeability model is capable of

Model simulation and experiments of flow and mass transport through a nano-material gas filter

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

Yang, Xiaofan; Zheng, Zhongquan C.; Winecki, Slawomir

2013-11-01

A computational model for evaluating the performance of nano-material packed-bed filters was developed. The porous effects of the momentum and mass transport within the filter bed were simulated. For the momentum transport, an extended Ergun-type model was employed and the energy loss (pressure drop) along the packed-bed was simulated and compared with measurement. For the mass transport, a bulk dsorption model was developed to study the adsorption process (breakthrough behavior). Various types of porous materials and gas flows were tested in the filter system where the mathematical models used in the porous substrate were implemented and validated by comparing withmore » experimental data and analytical solutions under similar conditions. Good agreements were obtained between experiments and model predictions.« less

Flow and transport model of the Savannah River Site Old Burial Grounds using Data Fusion modeling (DFM)

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

NONE

1995-11-01

The Data Fusion Modeling (DFM) approach has been used to develop a groundwater flow and transport model of the Old Burial Grounds (OBG) at the US Department of Energy`s Savannah River Site (SRS). The resulting DFM model was compared to an existing model that was calibrated via the typical trial-and-error method. The OBG was chosen because a substantial amount of hydrogeologic information is available, a FACT (derivative of VAM3DCG) flow and transport model of the site exists, and the calibration and numerics were challenging with standard approaches. The DFM flow model developed here is similar to the flow model bymore » Flach et al. This allows comparison of the two flow models and validates the utility of DFM. The contaminant of interest for this study is tritium, because it is a geochemically conservative tracer that has been monitored along the seepline near the F-Area effluent and Fourmile Branch for several years.« less

Multi-process herbicide transport in structured soil columns: Experiments and model analysis

NASA Astrophysics Data System (ADS)

Köhne, J. Maximilian; Köhne, Sigrid; Šimůnek, Jirka

2006-05-01

Model predictions of pesticide transport in structured soils are complicated by multiple processes acting concurrently. In this study, the hydraulic, physical, and chemical nonequilibrium (HNE, PNE, and CNE, respectively) processes governing herbicide transport under variably saturated flow conditions were studied. Bromide (Br -), isoproturon (IPU, 3-(4-isoprpylphenyl)-1,1-dimethylurea) and terbuthylazine (TER, N2-tert-butyl-6-chloro- N4-ethyl-1,3,5-triazine-2,4-diamine) were applied to two soil columns. An aggregated Ap soil column and a macroporous, aggregated Ah soil column were irrigated at a rate of 1 cm h - 1 for 3 h. Two more irrigations at the same rate and duration followed in weekly intervals. Nonlinear (Freundlich) equilibrium and two-site kinetic sorption parameters were determined for IPU and TER using batch experiments. The observed water flow and Br - transport were inversely simulated using mobile-immobile (MIM), dual-permeability (DPM), and combined triple-porosity (DP-MIM) numerical models implemented in HYDRUS-1D, with improving correspondence between empirical data and model results. Using the estimated HNE and PNE parameters together with batch-test derived equilibrium sorption parameters, the preferential breakthrough of the weakly adsorbed IPU in the Ah soil could be reasonably well predicted with the DPM approach, whereas leaching of the strongly adsorbed TER was predicted less well. The transport of IPU and TER through the aggregated Ap soil could be described consistently only when HNE, PNE, and CNE were simultaneously accounted for using the DPM. Inverse parameter estimation suggested that two-site kinetic sorption in inter-aggregate flow paths was reduced as compared to within aggregates, and that large values for the first-order degradation rate were an artifact caused by irreversible sorption. Overall, our results should be helpful to enhance the understanding and modeling of multi-process pesticide transport through structured soils

Modeling charge transport in organic photovoltaic materials.

PubMed

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

2009-11-17

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

Anomalous diffusion for bed load transport with a physically-based model

NASA Astrophysics Data System (ADS)

Fan, N.; Singh, A.; Foufoula-Georgiou, E.; Wu, B.

2013-12-01

Diffusion of bed load particles shows both normal and anomalous behavior for different spatial-temporal scales. Understanding and quantifying these different types of diffusion is important not only for the development of theoretical models of particle transport but also for practical purposes, e.g., river management. Here we extend a recently proposed physically-based model of particle transport by Fan et al. [2013] to further develop an Episodic Langevin equation (ELE) for individual particle motion which reproduces the episodic movement (start and stop) of sediment particles. Using the proposed ELE we simulate particle movements for a large number of uniform size particles, incorporating different probability distribution functions (PDFs) of particle waiting time. For exponential PDFs of waiting times, particles reveal ballistic motion in short time scales and turn to normal diffusion at long time scales. The PDF of simulated particle travel distances also shows a change in its shape from exponential to Gamma to Gaussian with a change in timescale implying different diffusion scaling regimes. For power-law PDF (with power - μ) of waiting times, the asymptotic behavior of particles at long time scales reveals both super-diffusion and sub-diffusion, however, only very heavy tailed waiting times (i.e. 1.0 < μ < 1.5) could result in sub-diffusion. We suggest that the contrast between our results and previous studies (for e.g., studies based on fractional advection-diffusion models of thin/heavy tailed particle hops and waiting times) results could be due the assumption in those studies that the hops are achieved instantaneously, but in reality, particles achieve their hops within finite times (as we simulate here) instead of instantaneously, even if the hop times are much shorter than waiting times. In summary, this study stresses on the need to rethink the alternative models to the previous models, such as, fractional advection-diffusion equations, for studying

Genetic linkage study of bipolar disorder and the serotonin transporter

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

Kelsoe, J.R.; Morison, M.; Mroczkowski-Parker, Z.

1996-04-09

The serotonin transporter (HTT) is an important candidate gene for the genetic transmission of bipolar disorder. It is the site of action of many antidepressants, and plays a key role in the regulation of serotonin neurotransmission. Many studies of affectively ill patients have found abnormalities in serotonin metabolism, and dysregulation of the transporter itself. The human serotonin transporter has been recently cloned and mapped to chromosome 17. We have identified a PstI RFLP at the HTT locus, and here report our examination of this polymorphism for possible linkage to bipolar disorder. Eighteen families were examined from three populations: the Oldmore » Order Amish, Iceland, and the general North American population. In addition to HTT, three other microsatellite markers were examined, which span an interval known to contain HTT. Linkage analyses were conducted under both dominant and recessive models, as well as both narrow (bipolar only) and broad (bipolar + recurrent unipolar) diagnostic models. Linkage could be excluded to HTT under all models examined. Linkage to the interval spanned by the microsatellites was similarly excluded under the dominant models. In two individual families, maximum lod scores of 1.02 and 0.84 were obtained at D17S798 and HTT, respectively. However, these data overall do not support the presence of a susceptibility locus for bipolar disorder near the serotonin transporter. 20 refs., 2 tabs.« less

Steepest entropy ascent quantum thermodynamic model of electron and phonon transport

NASA Astrophysics Data System (ADS)

Li, Guanchen; von Spakovsky, Michael R.; Hin, Celine

2018-01-01

An advanced nonequilibrium thermodynamic model for electron and phonon transport is formulated based on the steepest-entropy-ascent quantum thermodynamics framework. This framework, based on the principle of steepest entropy ascent (or the equivalent maximum entropy production principle), inherently satisfies the laws of thermodynamics and mechanics and is applicable at all temporal and spatial scales even in the far-from-equilibrium realm. Specifically, the model is proven to recover the Boltzmann transport equations in the near-equilibrium limit and the two-temperature model of electron-phonon coupling when no dispersion is assumed. The heat and mass transport at a temperature discontinuity across a homogeneous interface where the dispersion and coupling of electron and phonon transport are both considered are then modeled. Local nonequilibrium system evolution and nonquasiequilibrium interactions are predicted and the results discussed.

Intermittency inhibited by transport: An exactly solvable model

NASA Astrophysics Data System (ADS)

Zanette, Damián H.

1994-04-01

Transport is incorporated in a discrete-time stochastic model of a system undergoing autocatalytic reactions of the type A-->2A and A-->0, whose population field is known to exhibit spatiotemporal intermittency. The temporal evolution is exactly solved, and it is shown that if the transport process is strong enough, intermittency is inhibited. This inhibition is nonuniform, in the sense that, as transport is strengthened, low-order population moments are affected before the high-order ones. Numerical simulations are presented to support the analytical results.

Colloid Transport in Saturated Porous Media: Elimination of Attachment Efficiency in a New Colloid Transport Model

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

Landkamer, Lee L.; Harvey, Ronald W.; Scheibe, Timothy D.

A new colloid transport model is introduced that is conceptually simple but captures the essential features of complicated attachment and detachment behavior of colloids when conditions of secondary minimum attachment exist. This model eliminates the empirical concept of collision efficiency; the attachment rate is computed directly from colloid filtration theory. Also, a new paradigm for colloid detachment based on colloid population heterogeneity is introduced. Assuming the dispersion coefficient can be estimated from tracer behavior, this model has only two fitting parameters: (1) the fraction of colloids that attach irreversibly and (2) the rate at which reversibly attached colloids leave themore » surface. These two parameters were correlated to physical parameters that control colloid transport such as the depth of the secondary minimum and pore water velocity. Given this correlation, the model serves as a heuristic tool for exploring the influence of physical parameters such as surface potential and fluid velocity on colloid transport. This model can be extended to heterogeneous systems characterized by both primary and secondary minimum deposition by simply increasing the fraction of colloids that attach irreversibly.« less

Inter-machine validation study of neoclassical transport modelling in medium- to high-density stellarator-heliotron plasmas

NASA Astrophysics Data System (ADS)

Dinklage, A.; Yokoyama, M.; Tanaka, K.; Velasco, J. L.; López-Bruna, D.; Beidler, C. D.; Satake, S.; Ascasíbar, E.; Arévalo, J.; Baldzuhn, J.; Feng, Y.; Gates, D.; Geiger, J.; Ida, K.; Isaev, M.; Jakubowski, M.; López-Fraguas, A.; Maaßberg, H.; Miyazawa, J.; Morisaki, T.; Murakami, S.; Pablant, N.; Kobayashi, S.; Seki, R.; Suzuki, C.; Suzuki, Y.; Turkin, Yu.; Wakasa, A.; Wolf, R.; Yamada, H.; Yoshinuma, M.; LHD Exp. Group; TJ-II Team; W7-AS Team

2013-06-01

A comparative study of energy transport for medium- to high-density discharges in the stellarator-heliotrons TJ-II, W7-AS and LHD is carried out. The specific discharge parameters are chosen to apply a recently concluded benchmarking study of neoclassical (NC) transport coefficients (Beidler et al 2011 Nucl. Fusion 51 076001) to perform this validation study. In contrast to previous experiments at low densities for which electron transport was predominant (Yokoyama et al 2007 Nucl. Fusion 47 1213), the current discharges also exhibit significant ion energy transport. As it affects the energy transport in 3D devices, the ambipolar radial electric field is addressed as well. For the discharges described, ion-root conditions, i.e. a small negative radial electric field were found. The energy transport in the peripheral region cannot be explained by NC theory. Within a ‘core region’(r/a < 1/2 ˜ 2/3), the predicted NC energy fluxes comply with experimental findings for W7-AS. For TJ-II, compliance in the core region is found for the particle transport and the electron energy transport. For the specific LHD discharges, the core energy transport complied with NC theory except for the electron energy transport in the inward-shifted magnetic configuration. The NC radial electric field tends to agree with experimental results for all devices but is measured to be more negative in the core of both LHD and TJ-II. As a general observation, the energy confinement time approaches the gyro-Bohm-type confinement scaling ISS04 (Yamada et al 2005 Nucl. Fusion 45 1684). This work is carried out within the International Stellarator-Heliotron Profile Database (www.ipp.mpg.de/ISS and http://ishpdb.nifs.ac.jp/index.html).

Modeling of turbulent transport as a volume process

NASA Technical Reports Server (NTRS)

Jennings, Mark J.; Morel, Thomas

1987-01-01

An alternative type of modeling was proposed for the turbulent transport terms in Reynolds-averaged equations. One particular implementation of the model was considered, based on the two-point velocity correlations. The model was found to reproduce the trends but not the magnitude of the nonisotropic behavior of the turbulent transport. Some interesting insights were developed concerning the shape of the contracted two-point correlation volume. This volume is strongly deformed by mean shear from the spherical shape found in unstrained flows. Of particular interest is the finding that the shape is sharply waisted, indicating preferential lines of communication, which should have a direct effect on turbulent transfer and on other processes.

GIS Modelling of Radionuclide Transport from the Semipalatinsk Test Site

NASA Astrophysics Data System (ADS)

Balakay, L.; Zakarin, E.; Mahura, A.; Baklanov, A.; Sorensen, J. H.

2009-04-01

In this study, the software complex GIS-project MigRad (Migration of Radionuclide) was developed, tested and applied for the territory of the Semipalatinsk test site/ polygon (Republic of Kazakhstan), where since 1961, in total 348 underground nuclear explosions were conducted. The MigRad is oriented on integration of large volumes of different information (mapping, ground-based, and satellite-based survey): and also includes modeling on its base local redistribution of radionuclides by precipitation and surface waters and by long-range transport of radioactive aerosols. The existing thermal anomaly on territory of the polygon was investigated in details, and the object-oriented analysis was applied for the studied area. Employing the RUNOFF model, the simulation of radionuclides migration with surface waters was performed. Employing the DERMA model, the simulation of long-term atmospheric transport, dispersion and deposition patterns for cesium was conducted from 3 selected locations (Balapan, Delegen, and Experimental Field). Employing geoinformation technology, the mapping of the of the high temperature zones and epicenters of radioactive aerosols transport for the territory of the test site was carried out with post-processing and integration of modelling results into GIS environment. Contamination levels of pollution due to former nuclear explosions for population and environment of the surrounding polygon territories of Kazakhstan as well as adjacent countries were analyzed and evaluated. The MigRad was designed as instrument for comprehensive analysis of complex territorial processes influenced by former nuclear explosions on the territory of Semipalatinsk test site. It provides possibilities in detailed analyses for (i) extensive cartographic material, remote sensing, and field measurements data collected in different level databases; (ii) radionuclide migration with flows using accumulation and redistribution of soil particles; (iii) thermal anomalies

GNAQPMS-Hg v1.0, a global nested atmospheric mercury transport model: model description, evaluation and application to trans-boundary transport of Chinese anthropogenic emissions

NASA Astrophysics Data System (ADS)

Chen, H. S.; Wang, Z. F.; Li, J.; Tang, X.; Ge, B. Z.; Wu, X. L.; Wild, O.; Carmichael, G. R.

2014-10-01

Atmospheric mercury (Hg) is a toxic pollutant and can be transported over the whole globe due to its long lifetime in the atmosphere. For the purpose of assessing Hg hemispheric transport and better characterizing regional Hg pollution, a global nested atmospheric Hg transport model (GNAQPMS-Hg) has been developed. In GNAQPMS-Hg, the gas and aqueous phase Hg chemistry representing the transformation among three forms of Hg: elemental mercury (Hg(0)), divalent mercury (Hg(II)), and primary particulate mercury (Hg(P)) are calculated. A detailed description of the model, including mercury emissions, gas and aqueous phase chemistry, and dry and wet deposition is given in this study. Worldwide observations including extensive data in China have been collected for model evaluation. Comparison results show that the model reasonably simulates the global mercury budget and the spatial-temporal variation of surface mercury concentrations and deposition. Overall, model predictions of annual total gaseous mercury (TGM) and wet deposition agree with observations within a factor of two, and within a factor of five for oxidized mercury and dry deposition. The model performs significantly better in North America and Europe than in East Asia. This can probably be attributed to the large uncertainties in emission inventories, coarse model resolution and to the inconsistency between the simulation and observation periods in East Asia. Compared to the global simulation, the nested simulation shows improved skill at capturing the high spatial variability of Hg concentrations and deposition over East Asia. In particular, the root mean square error (RMSE) of simulated Hg wet deposition over East Asia is reduced by 24% in the nested simulation. Model sensitivity studies indicate that Chinese primary anthropogenic emissions account for 30 and 62% of surface mercury concentrations and deposition over China, respectively. Along the rim of the western Pacific, the contributions from Chinese

Human intestinal transporter database: QSAR modeling and virtual profiling of drug uptake, efflux and interactions.

PubMed

Sedykh, Alexander; Fourches, Denis; Duan, Jianmin; Hucke, Oliver; Garneau, Michel; Zhu, Hao; Bonneau, Pierre; Tropsha, Alexander

2013-04-01

Membrane transporters mediate many biological effects of chemicals and play a major role in pharmacokinetics and drug resistance. The selection of viable drug candidates among biologically active compounds requires the assessment of their transporter interaction profiles. Using public sources, we have assembled and curated the largest, to our knowledge, human intestinal transporter database (>5,000 interaction entries for >3,700 molecules). This data was used to develop thoroughly validated classification Quantitative Structure-Activity Relationship (QSAR) models of transport and/or inhibition of several major transporters including MDR1, BCRP, MRP1-4, PEPT1, ASBT, OATP2B1, OCT1, and MCT1. QSAR models have been developed with advanced machine learning techniques such as Support Vector Machines, Random Forest, and k Nearest Neighbors using Dragon and MOE chemical descriptors. These models afforded high external prediction accuracies of 71-100% estimated by 5-fold external validation, and showed hit retrieval rates with up to 20-fold enrichment in the virtual screening of DrugBank compounds. The compendium of predictive QSAR models developed in this study can be used for virtual profiling of drug candidates and/or environmental agents with the optimal transporter profiles.

Impact of intercontinental pollution transport on North American ozone air pollution: an HTAP phase 2 multi-model study

PubMed Central

Huang, Min; Carmichael, Gregory R.; Pierce, R. Bradley; Jo, Duseong S.; Park, Rokjin J.; Flemming, Johannes; Emmons, Louisa K.; Bowman, Kevin W.; Henze, Daven K.; Davila, Yanko; Sudo, Kengo; Jonson, Jan Eiof; Lund, Marianne Tronstad; Janssens-Maenhout, Greet; Dentener, Frank J.; Keating, Terry J.; Oetjen, Hilke; Payne, Vivienne H.

2018-01-01

The recent update on the US National Ambient Air Quality Standards (NAAQS) of the ground-level ozone (O3/ can benefit from a better understanding of its source contributions in different US regions during recent years. In the Hemispheric Transport of Air Pollution experiment phase 1 (HTAP1), various global models were used to determine the O3 source–receptor (SR) relationships among three continents in the Northern Hemisphere in 2001. In support of the HTAP phase 2 (HTAP2) experiment that studies more recent years and involves higher-resolution global models and regional models’ participation, we conduct a number of regional-scale Sulfur Transport and dEposition Model (STEM) air quality base and sensitivity simulations over North America during May–June 2010. STEM’s top and lateral chemical boundary conditions were downscaled from three global chemical transport models’ (i.e., GEOS-Chem, RAQMS, and ECMWF C-IFS) base and sensitivity simulations in which the East Asian (EAS) anthropogenic emissions were reduced by 20 %. The mean differences between STEM surface O3 sensitivities to the emission changes and its corresponding boundary condition model’s are smaller than those among its boundary condition models, in terms of the regional/period-mean (<10 %) and the spatial distributions. An additional STEM simulation was performed in which the boundary conditions were downscaled from a RAQMS (Realtime Air Quality Modeling System) simulation without EAS anthropogenic emissions. The scalability of O3 sensitivities to the size of the emission perturbation is spatially varying, and the full (i.e., based on a 100% emission reduction) source contribution obtained from linearly scaling the North American mean O3 sensitivities to a 20% reduction in the EAS anthropogenic emissions may be underestimated by at least 10 %. The three boundary condition models’ mean O3 sensitivities to the 20% EAS emission perturbations are ~8% (May–June 2010)/~11% (2010 annual) lower

Nucleotide-induced conformational dynamics in ABC transporters from structure-based coarse grained modelling.

NASA Astrophysics Data System (ADS)

Flechsig, Holger

2016-02-01

ATP-binding cassette (ABC) transporters are integral membrane proteins which mediate the exchange of diverse substrates across membranes powered by ATP molecules. Our understanding of their activity is still hampered since the conformational dynamics underlying the operation of such proteins cannot yet be resolved in detailed molecular dynamics studies. Here a coarse grained model which allows to mimic binding of nucleotides and follow subsequent conformational motions of full-length transporter structures in computer simulations is proposed and implemented. To justify its explanatory quality, the model is first applied to the maltose transporter system for which multiple conformations are known and we find that the model predictions agree remarkably well with the experimental data. For the MalK subunit the switching from open to the closed dimer configuration upon ATP binding is reproduced and, moreover, for the full-length maltose transporter, progression from inward-facing to the outward-facing state is correctly obtained. For the heme transporter HmuUV, for which only the free structure could yet be determined, the model was then applied to predict nucleotide-induced conformational motions. Upon binding of ATP-mimicking ligands the structure changed from a conformation in which the nucleotide-binding domains formed an open shape, to a conformation in which they were found in tight contact, while, at the same time, a pronounced rotation of the transmembrane domains was observed. This finding is supported by normal mode analysis, and, comparison with structural data of the homologous vitamin B12 transporter BtuCD suggests that the observed rotation mechanism may contribute a common functional aspect for this class of ABC transporters. Although in HmuuV noticeable rearrangement of essential transmembrane helices was detected, there are no indications from our simulations that ATP binding alone may facilitate propagation of substrate molecules in this transporter

Recommended direct simulation Monte Carlo collision model parameters for modeling ionized air transport processes

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

Swaminathan-Gopalan, Krishnan; Stephani, Kelly A., E-mail: ksteph@illinois.edu

2016-02-15

A systematic approach for calibrating the direct simulation Monte Carlo (DSMC) collision model parameters to achieve consistency in the transport processes is presented. The DSMC collision cross section model parameters are calibrated for high temperature atmospheric conditions by matching the collision integrals from DSMC against ab initio based collision integrals that are currently employed in the Langley Aerothermodynamic Upwind Relaxation Algorithm (LAURA) and Data Parallel Line Relaxation (DPLR) high temperature computational fluid dynamics solvers. The DSMC parameter values are computed for the widely used Variable Hard Sphere (VHS) and the Variable Soft Sphere (VSS) models using the collision-specific pairing approach.more » The recommended best-fit VHS/VSS parameter values are provided over a temperature range of 1000-20 000 K for a thirteen-species ionized air mixture. Use of the VSS model is necessary to achieve consistency in transport processes of ionized gases. The agreement of the VSS model transport properties with the transport properties as determined by the ab initio collision integral fits was found to be within 6% in the entire temperature range, regardless of the composition of the mixture. The recommended model parameter values can be readily applied to any gas mixture involving binary collisional interactions between the chemical species presented for the specified temperature range.« less

Model study of atmospheric transport using carbon 14 and strontium 90 as inert tracers

NASA Technical Reports Server (NTRS)

Kinnison, D. E.; Johnston, H. S.; Wuebbles, D. J.

1994-01-01

The observed excess carbon 14 in the atmosphere from 1963 to 1970 provides unique, but limited, data up to an altitude of about 35 km for testing the air motions calculated by 11 multidimensional atmospheric models. Strontium 90 measurements in the atmosphere from 1964 to mid-1967 provide data that have more latitude coverage than those of carbon 14 and are useful for testing combined models of air motions and aerosol settling. Model calculations for carbon 14 begin at October 1963, 9 months after the conclusion of the nuclear bomb tests; the initial conditions for the calculations are derived by three methods, each of which agrees fairly well with measured carbon 14 in October 1963 and each of which has widely different values in regions of the stratosphere where there were no carbon 14 measurements. The model results are compared to the stratospheric measurements, not as if the observed data were absolute standards, but in an effort to obtain new insight about the models and about the atmosphere. The measured carbon 14 vertical profiles at 31 deg N are qualitatively different from all of the models; the measured vertical profiles show a maximum mixing ratio in the altitude range of 20 to 25 km from October 1963 through July 1966, but all modeled profiles show mixing ratio maxima that increase in altitude from 20 km in October 1963 to greater than 40 km by April 1966. Both carbon 14 and strontium 90 data indicate that the models differ substantially among themselves with respect to stratosphere-troposphere exchange rate, but the modeled carbon 14 stratospheric residence times indicate that differences among the models are small with respect to transport rate between the middle stratosphere and the lower stratosphere. Strontium 90 data indicate that aerosol settling is important up to at least 35 km altitude. Relative to the measurements, about three quarters of the models transport carbon 14 from the lower stratosphere to the troposphere too rapidly, and all