Distributed modeling of diffusive solute transport in peritoneal dialysis.

PubMed

Waniewski, Jacek

2002-01-01

The diffusive transport between blood and an ex-tissue medium (dialysis fluid) is evaluated using a mathematical model that takes into account the (quasicontinuous) distribution of capillaries within the tissue at various distances from the tissue surface, and includes diffusive-convective transport through the capillary wall and lymphatic absorption from the tissue. General formulas for solute penetration depth, lambda, and for the diffusive mass transport coefficient for the transport between blood and dialysis fluid, K(BD), are provided in terms of local transport coefficients for capillary wall, tissue, and lymphatic absorption. For pure diffusive transport between blood and dialysis fluid and thick tissue layers (i.e., if the solute penetration depth is much lower than the tissue thickness) these formulas yield previously known expressions. It is shown that apparent tissue layers, with widths lambdaTBL and lambdaT, respectively, may be defined according to the values of local transport parameters in such a way that K(BD) is equal to the solute clearance K(TBL) from the tissue by blood and lymph for a layer with width lambdaTBL or to the solute clearance K(T) from blood to dialysate by diffusion through the tissue layer with width lambdaT. For tissue layers with width much higher than the penetration depth: lambdaT approximately = lambdaTBL approximately = lambda. These characteristic width lengths depend on the transport parameters (and thus on the size) of solutes. Effective blood flow, which may be related to the exchange of the solute between blood and dialysate, is defined using an analogy to the extraction/absorption coefficients for blood-tissue exchange. Various approximations for the distributed model formula for diffusive mass transport coefficient (K(BD)) are possible. The appropriate range for their application is obtained from the general formula.

Peclet number as affected by molecular diffusion controls transient anomalous transport in alluvial aquifer-aquitard complexes

USGS Publications Warehouse

Zhang, Yong; Green, Christopher T.; Tick, Geoffrey R.

2015-01-01

This study evaluates the role of the Peclet number as affected by molecular diffusion in transient anomalous transport, which is one of the major knowledge gaps in anomalous transport, by combining Monte Carlo simulations and stochastic model analysis. Two alluvial settings containing either short- or long-connected hydrofacies are generated and used as media for flow and transport modeling. Numerical experiments show that 1) the Peclet number affects both the duration of the power-law segment of tracer breakthrough curves (BTCs) and the transition rate from anomalous to Fickian transport by determining the solute residence time for a given low-permeability layer, 2) mechanical dispersion has a limited contribution to the anomalous characteristics of late-time transport as compared to molecular diffusion due to an almost negligible velocity in floodplain deposits, and 3) the initial source dimensions only enhance the power-law tail of the BTCs at short travel distances. A tempered stable stochastic (TSS) model is then applied to analyze the modeled transport. Applications show that the time-nonlocal parameters in the TSS model relate to the Peclet number, Pe. In particular, the truncation parameter in the TSS model increases nonlinearly with a decrease in Pe due to the decrease of the mean residence time, and the capacity coefficient increases with an increase in molecular diffusion which is probably due to the increase in the number of immobile particles. The above numerical experiments and stochastic analysis therefore reveal that the Peclet number as affected by molecular diffusion controls transient anomalous transport in alluvial aquifer–aquitard complexes.

Mathematical modelling of the Phloem: the importance of diffusion on sugar transport at osmotic equilibrium.

PubMed

Payvandi, S; Daly, K R; Zygalakis, K C; Roose, T

2014-11-01

Plants rely on the conducting vessels of the phloem to transport the products of photosynthesis from the leaves to the roots, or to any other organs, for growth, metabolism, and storage. Transport within the phloem is due to an osmotically-generated pressure gradient and is hence inherently nonlinear. Since convection dominates over diffusion in the main bulk flow, the effects of diffusive transport have generally been neglected by previous authors. However, diffusion is important due to boundary layers that form at the ends of the phloem, and at the leaf-stem and stem-root boundaries. We present a mathematical model of transport which includes the effects of diffusion. We solve the system analytically in the limit of high Münch number which corresponds to osmotic equilibrium and numerically for all parameter values. We find that the bulk solution is dependent on the diffusion-dominated boundary layers. Hence, even for large Péclet number, it is not always correct to neglect diffusion. We consider the cases of passive and active sugar loading and unloading. We show that for active unloading, the solutions diverge with increasing Péclet. For passive unloading, the convergence of the solutions is dependent on the magnitude of loading. Diffusion also permits the modelling of an axial efflux of sugar in the root zone which may be important for the growing root tip and for promoting symbiotic biological interactions in the soil. Therefore, diffusion is an essential mechanism for transport in the phloem and must be included to accurately predict flow.

Transport of polar and non-polar volatile compounds in polystyrene foam and oriented strand board

NASA Astrophysics Data System (ADS)

Yuan, Huali; Little, John C.; Hodgson, Alfred T.

Transport of hexanal and styrene in polystyrene foam (PSF) and oriented strand board (OSB) was characterized. A microbalance was used to measure sorption/desorption kinetics and equilibrium data. While styrene transport in PSF can be described by Fickian diffusion with a symmetrical and reversible sorption/desorption process, hexanal transport in both PSF and OSB exhibited significant hysteresis, with desorption being much slower than sorption. A porous media diffusion model that assumes instantaneous local equilibrium governed by a nonlinear Freundlich isotherm was found to explain the hysteresis in hexanal transport. A new nonlinear sorption and porous diffusion emissions model was, therefore, developed and partially validated using independent chamber data. The results were also compared to the more conventional linear Fickian-diffusion emissions model. While the linear emissions model predicts styrene emissions from PSF with reasonable accuracy, it substantially underestimates the rate of hexanal emissions from OSB. Although further research and more rigorous validation is needed, the new nonlinear emissions model holds promise for predicting emissions of polar VOCs such as hexanal from porous building materials.

Cross-stream diffusion under pressure-driven flow in microchannels with arbitrary aspect ratios: a phase diagram study using a three-dimensional analytical model

PubMed Central

Song, Hongjun; Wang, Yi; Pant, Kapil

2011-01-01

This article presents a three-dimensional analytical model to investigate cross-stream diffusion transport in rectangular microchannels with arbitrary aspect ratios under pressure-driven flow. The Fourier series solution to the three-dimensional convection–diffusion equation is obtained using a double integral transformation method and associated eigensystem calculation. A phase diagram derived from the dimensional analysis is presented to thoroughly interrogate the characteristics in various transport regimes and examine the validity of the model. The analytical model is verified against both experimental and numerical models in terms of the concentration profile, diffusion scaling law, and mixing efficiency with excellent agreement (with <0.5% relative error). Quantitative comparison against other prior analytical models in extensive parameter space is also performed, which demonstrates that the present model accommodates much broader transport regimes with significantly enhanced applicability. PMID:22247719

Cross-stream diffusion under pressure-driven flow in microchannels with arbitrary aspect ratios: a phase diagram study using a three-dimensional analytical model.

PubMed

Song, Hongjun; Wang, Yi; Pant, Kapil

2012-01-01

This article presents a three-dimensional analytical model to investigate cross-stream diffusion transport in rectangular microchannels with arbitrary aspect ratios under pressure-driven flow. The Fourier series solution to the three-dimensional convection-diffusion equation is obtained using a double integral transformation method and associated eigensystem calculation. A phase diagram derived from the dimensional analysis is presented to thoroughly interrogate the characteristics in various transport regimes and examine the validity of the model. The analytical model is verified against both experimental and numerical models in terms of the concentration profile, diffusion scaling law, and mixing efficiency with excellent agreement (with <0.5% relative error). Quantitative comparison against other prior analytical models in extensive parameter space is also performed, which demonstrates that the present model accommodates much broader transport regimes with significantly enhanced applicability.

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 show the disposal system to evolve in a physically realistic manner. In the example presented the reactive-transport coupling develops chemically reducing zones, which limit the transport of uranium. This illustrates the potential significance of media degradation and chemical effect on the transport of radionuclides which would need to be taken into account when examining the long-term behaviour and containment properties of the geological disposal system. Microstructure-informed modelling and its potential linkage with continuum flow modelling is a subject of ongoing studies. The approach of microstructure-informed modelling is discussed to provide insight and a mechanistic understanding of macroscopic parameters and their evolution. The proposed theoretical and methodological basis for microstructure-informed modelling of porous quasi-brittle media has the potential to develop into an explanatory and predictive tool for deriving mechanism-based, as opposed to phenomenological, evolution laws for macroscopic properties. These concepts in micro-scale modelling are likely to be applicable to the diffusion process, in addition to advective transport illustrated here for porous media. (authors)« less

Anisotropic mesoscale eddy transport in ocean general circulation models

NASA Astrophysics Data System (ADS)

Reckinger, Scott; Fox-Kemper, Baylor; Bachman, Scott; Bryan, Frank; Dennis, John; Danabasoglu, Gokhan

2014-11-01

In modern climate models, the effects of oceanic mesoscale eddies are introduced by relating subgrid eddy fluxes to the resolved gradients of buoyancy or other tracers, where the proportionality is, in general, governed by an eddy transport tensor. The symmetric part of the tensor, which represents the diffusive effects of mesoscale eddies, is universally treated isotropically. However, the diffusive processes that the parameterization approximates, such as shear dispersion and potential vorticity barriers, typically have strongly anisotropic characteristics. Generalizing the eddy diffusivity tensor for anisotropy extends the number of parameters from one to three: major diffusivity, minor diffusivity, and alignment. The Community Earth System Model (CESM) with the anisotropic eddy parameterization is used to test various choices for the parameters, which are motivated by observations and the eddy transport tensor diagnosed from high resolution simulations. Simply setting the ratio of major to minor diffusivities to a value of five globally, while aligning the major axis along the flow direction, improves biogeochemical tracer ventilation and reduces temperature and salinity biases. These effects can be improved by parameterizing the oceanic anisotropic transport mechanisms.

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.

Transport properties of interacting magnetic islands in tokamak plasmas

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

Gianakon, T.A.; Callen, J.D.; Hegna, C.C.

1993-10-01

This paper explores the equilibrium and transient transport properties of a mixed magnetic topology model for tokamak equilibria. The magnetic topology is composed of a discrete set of mostly non-overlapping magnetic islands centered on the low-order rational surfaces. Transport across the island regions is fast due to parallel transport along the stochastic magnetic field lines about the separatrix of each island. Transport between island regions is assumed to be slow due to a low residual cross-field transport. In equilibrium, such a model leads to: a nonlinear dependence of the heat flux on the pressure gradient; a power balance diffusion coefficientmore » which increases from core to edge; and profile resiliency. Transiently, such a model also exhibits a heat pulse diffusion coefficient larger than the power balance diffusion coefficient.« less

A fully coupled 3D transport model in SPH for multi-species reaction-diffusion systems

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

Adami, Stefan; Hu, X. Y.; Adams, N. A.

2011-08-23

Abstract—In this paper we present a fully generalized transport model for multiple species in complex two and threedimensional geometries. Based on previous work [1] we have extended our interfacial reaction-diffusion model to handle arbitrary numbers of species allowing for coupled reaction models. Each species is tracked independently and we consider different physics of a species with respect to the bulk phases in contact. We use our SPH model to simulate the reaction-diffusion problem on a pore-scale level of a solid oxide fuel cell (SOFC) with special emphasize on the effect of surface diffusion.

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 the anomalous diffusion of bed load particles. The implications of these results for modeling sediment transport are discussed.

Peclet number as affected by molecular diffusion controls transient anomalous transport in alluvial aquifer-aquitard complexes.

PubMed

Zhang, Yong; Green, Christopher T; Tick, Geoffrey R

2015-01-01

This study evaluates the role of the Peclet number as affected by molecular diffusion in transient anomalous transport, which is one of the major knowledge gaps in anomalous transport, by combining Monte Carlo simulations and stochastic model analysis. Two alluvial settings containing either short- or long-connected hydrofacies are generated and used as media for flow and transport modeling. Numerical experiments show that 1) the Peclet number affects both the duration of the power-law segment of tracer breakthrough curves (BTCs) and the transition rate from anomalous to Fickian transport by determining the solute residence time for a given low-permeability layer, 2) mechanical dispersion has a limited contribution to the anomalous characteristics of late-time transport as compared to molecular diffusion due to an almost negligible velocity in floodplain deposits, and 3) the initial source dimensions only enhance the power-law tail of the BTCs at short travel distances. A tempered stable stochastic (TSS) model is then applied to analyze the modeled transport. Applications show that the time-nonlocal parameters in the TSS model relate to the Peclet number, Pe. In particular, the truncation parameter in the TSS model increases nonlinearly with a decrease in Pe due to the decrease of the mean residence time, and the capacity coefficient increases with an increase in molecular diffusion which is probably due to the increase in the number of immobile particles. The above numerical experiments and stochastic analysis therefore reveal that the Peclet number as affected by molecular diffusion controls transient anomalous transport in alluvial aquifer-aquitard complexes. Copyright © 2015 Elsevier B.V. All rights reserved.

DEVELOPMENT OF SPLIT-OPERATOR, PETROV-GALERKIN METHODS TO SIMULATE TRANSPORT AND DIFFUSION PROBLEMS

EPA Science Inventory

The rate at which contaminants in groundwater undergo sorption and desorption is routinely described using diffusion models. Such approaches, when incorporated into transport models, lead to large systems of coupled equations, often nonlinear. This has restricted applications of ...

GALACTIC WINDS DRIVEN BY ISOTROPIC AND ANISOTROPIC COSMIC-RAY DIFFUSION IN DISK GALAXIES

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

Pakmor, R.; Pfrommer, C.; Simpson, C. M.

2016-06-20

The physics of cosmic rays (CRs) is a promising candidate for explaining the driving of galactic winds and outflows. Recent galaxy formation simulations have demonstrated the need for active CR transport either in the form of diffusion or streaming to successfully launch winds in galaxies. However, due to computational limitations, most previous simulations have modeled CR transport isotropically. Here, we discuss high-resolution simulations of isolated disk galaxies in a 10{sup 11} M {sub ⊙} halo with the moving-mesh code Arepo that include injection of CRs from supernovae, advective transport, CR cooling, and CR transport through isotropic or anisotropic diffusion. Wemore » show that either mode of diffusion leads to the formation of strong bipolar outflows. However, they develop significantly later in the simulation with anisotropic diffusion compared to the simulation with isotropic diffusion. Moreover, we find that isotropic diffusion allows most of the CRs to quickly diffuse out of the disk, while in the simulation with anisotropic diffusion, most CRs remain in the disk once the magnetic field becomes dominated by its azimuthal component, which occurs after ∼300 Myr. This has important consequences for the gas dynamics in the disk. In particular, we show that isotropic diffusion strongly suppresses the amplification of the magnetic field in the disk compared to anisotropic or no diffusion models. We therefore conclude that reliable simulations which include CR transport inevitably need to account for anisotropic diffusion.« less

Density-driven transport of gas phase chemicals in unsaturated soils

NASA Astrophysics Data System (ADS)

Fen, Chiu-Shia; Sun, Yong-tai; Cheng, Yuen; Chen, Yuanchin; Yang, Whaiwan; Pan, Changtai

2018-01-01

Variations of gas phase density are responsible for advective and diffusive transports of organic vapors in unsaturated soils. Laboratory experiments were conducted to explore dense gas transport (sulfur hexafluoride, SF6) from different source densities through a nitrogen gas-dry soil column. Gas pressures and SF6 densities at transient state were measured along the soil column for three transport configurations (horizontal, vertically upward and vertically downward transport). These measurements and others reported in the literature were compared with simulation results obtained from two models based on different diffusion approaches: the dusty gas model (DGM) equations and a Fickian-type molar fraction-based diffusion expression. The results show that the DGM and Fickian-based models predicted similar dense gas density profiles which matched the measured data well for horizontal transport of dense gas at low to high source densities, despite the pressure variations predicted in the soil column were opposite to the measurements. The pressure evolutions predicted by both models were in trend similar to the measured ones for vertical transport of dense gas. However, differences between the dense gas densities predicted by the DGM and Fickian-based models were discernible for vertically upward transport of dense gas even at low source densities, as the DGM-based predictions matched the measured data better than the Fickian results did. For vertically downward transport, the dense gas densities predicted by both models were not greatly different from our experimental measurements, but substantially greater than the observations obtained from the literature, especially at high source densities. Further research will be necessary for exploring factors affecting downward transport of dense gas in soil columns. Use of the measured data to compute flux components of SF6 showed that the magnitudes of diffusive flux component based on the Fickian-type diffusion expressions in terms of molar concentration, molar fraction and mass density fraction gradient were almost the same. However, they were greater than the result computed with the mass fraction gradient for > 24% and the DGM-based result for more than one time. As a consequence, the DGM-based total flux of SF6 was in magnitude greatly less than the Fickian result not only for horizontal transport (diffusion-dominating) but also for vertical transport (advection and diffusion) of dense gas. Particularly, the Fickian-based total flux was more than two times in magnitude as much as the DGM result for vertically upward transport of dense gas.

A model of oscillatory transport in granular soils, with application to barometric pumping and earth tides.

PubMed

Neeper, D A

2001-04-01

A simple algebraic model is proposed to estimate the transport of a volatile or soluble chemical caused by oscillatory flow of fluid in a porous medium. The model is applied to the barometric pumping of vapors in the vadose zone, and to the transport of dissolved species by earth tides in an aquifer. In the model, the fluid moves sinusoidally with time in the porosity of the soil. The chemical concentration in the mobile fluid is considered to equilibrate with the concentration in the surrounding matrix according to a characteristic time governed by diffusion, sorption, or other rate processes. The model provides a closed form solution, to which barometric pressure data are applied in an example of pore gas motion in the vadose zone. The model predicts that the additional diffusivity due barometric pumping in an unfractured vadose zone would be comparable to the diffusivity in stagnant pore gas if the equilibration time is 1 day or longer. Water motion due to the M2 lunar tide is examined as an example of oscillatory transport in an aquifer. It is shown that the tidal motion of the water in an aquifer might significantly increase the vertical diffusivity of dissolved species when compared to diffusion in an absolutely stagnant aquifer, but the hydrodynamic dispersivity due to tidal motion or gravitational flow would probably exceed the diffusivity due to oscillatory advection.

Quantum Transmission Conditions for Diffusive Transport in Graphene with Steep Potentials

NASA Astrophysics Data System (ADS)

Barletti, Luigi; Negulescu, Claudia

2018-05-01

We present a formal derivation of a drift-diffusion model for stationary electron transport in graphene, in presence of sharp potential profiles, such as barriers and steps. Assuming the electric potential to have steep variations within a strip of vanishing width on a macroscopic scale, such strip is viewed as a quantum interface that couples the classical regions at its left and right sides. In the two classical regions, where the potential is assumed to be smooth, electron and hole transport is described in terms of semiclassical kinetic equations. The diffusive limit of the kinetic model is derived by means of a Hilbert expansion and a boundary layer analysis, and consists of drift-diffusion equations in the classical regions, coupled by quantum diffusive transmission conditions through the interface. The boundary layer analysis leads to the discussion of a four-fold Milne (half-space, half-range) transport problem.

Pore and Continuum Scale Study of the Effect of Subgrid Transport Heterogeneity on Redox Reaction Rates

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

Liu, Yuanyuan; Liu, Chongxuan; Zhang, Changyong

2015-08-01

A micromodel system with a pore structure for heterogeneous flow and transport was used to investigate the effect of subgrid transport heterogeneity on redox reaction rates. Hematite reductive dissolution by injecting a reduced form of flavin mononucleotide (FMNH2) at variable flow rates was used as an example to probe the variations of redox reaction rates in different subgrid transport domains. Experiments, pore-scale simulations, and macroscopic modeling were performed to measure and simulate in-situ hematite reduction and to evaluate the scaling behavior of the redox reaction rates from the pore to macroscopic scales. The results indicated that the measured pore-scale ratesmore » of hematite reduction were consistent with the predictions from a pore scale reactive transport model. A general trend is that hematite reduction followed reductant transport pathways, starting from the advection-dominated pores toward the interior of diffusion-dominated domains. Two types of diffusion domains were considered in the micromodel: a micropore diffusion domain, which locates inside solid grains or aggregates where reactant transport is limited by diffusion; and a macropore diffusion domain, which locates at wedged, dead-end pore spaces created by the grain-grain contacts. The rate of hematite reduction in the advection-dominated domain was faster than those in the diffusion-controlled domains, and the rate in the macropore diffusion domain was faster than that in the micropore domain. The reduction rates in the advection and macropore diffusion domains increased with increasing flow rate, but were affected by different mechanisms. The rate increase in the advection domain was controlled by the mass action effect as a faster flow supplied more reactants, and the rate increase in the macropore domain was more affected by the rate of mass exchange with the advection domain, which increased with increasing flow rate. The hematite reduction rate in the micropore domain was, however, not affected by the flow rate because molecular diffusion limits reductant supply to the micropore domain interior. Domain-based macroscopic models were evaluated to scale redox reaction rates from the pore to macroscopic scales. A single domain model, which ignores subgrid transport heterogeneity deviated significantly from the pore-scale results. Further analysis revealed that the rate expression for hematite reduction was not scalable from the pore to porous media using the single domain model. A three-domain model, which effectively considers subgrid reactive diffusion in the micropore and macropore domains, significantly improved model description. Overall this study revealed the importance of subgrid transport heterogeneity in the manifestation of redox reaction rates in porous media and in scaling reactions from the pore to porous media. The research also supported that the domain-based scaling approach can be used to directly scale redox reactions in porous media with subgrid transport heterogeneity.« less

WE-AB-204-07: Spatiotemporal Distribution of the FDG PET Tracer in Solid Tumors: Contributions of Diffusion and Convection Mechanisms

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

Soltani, M; Sefidgar, M; Bazmara, H

2015-06-15

Purpose: In this study, a mathematical model is utilized to simulate FDG distribution in tumor tissue. In contrast to conventional compartmental modeling, tracer distributions across space and time are directly linked together (i.e. moving beyond ordinary differential equations (ODEs) to utilizing partial differential equations (PDEs) coupling space and time). The diffusion and convection transport mechanisms are both incorporated to model tracer distribution. We aimed to investigate the contributions of these two mechanisms on FDG distribution for various tumor geometries obtained from PET/CT images. Methods: FDG transport was simulated via a spatiotemporal distribution model (SDM). The model is based on amore » 5K compartmental model. We model the fact that tracer concentration in the second compartment (extracellular space) is modulated via convection and diffusion. Data from n=45 patients with pancreatic tumors as imaged using clinical FDG PET/CT imaging were analyzed, and geometrical information from the tumors including size, shape, and aspect ratios were classified. Tumors with varying shapes and sizes were assessed in order to investigate the effects of convection and diffusion mechanisms on FDG transport. Numerical methods simulating interstitial flow and solute transport in tissue were utilized. Results: We have shown the convection mechanism to depend on the shape and size of tumors whereas diffusion mechanism is seen to exhibit low dependency on shape and size. Results show that concentration distribution of FDG is relatively similar for the considered tumors; and that the diffusion mechanism of FDG transport significantly dominates the convection mechanism. The Peclet number which shows the ratio of convection to diffusion rates was shown to be of the order of 10−{sup 3} for all considered tumors. Conclusion: We have demonstrated that even though convection leads to varying tracer distribution profiles depending on tumor shape and size, the domination of the diffusion phenomenon prevents these factors from modulating FDG distribution.« less

Spatial model of convective solute transport in brain extracellular space does not support a “glymphatic” mechanism

PubMed Central

Jin, Byung-Ju; Smith, Alex J.

2016-01-01

A “glymphatic system,” which involves convective fluid transport from para-arterial to paravenous cerebrospinal fluid through brain extracellular space (ECS), has been proposed to account for solute clearance in brain, and aquaporin-4 water channels in astrocyte endfeet may have a role in this process. Here, we investigate the major predictions of the glymphatic mechanism by modeling diffusive and convective transport in brain ECS and by solving the Navier–Stokes and convection–diffusion equations, using realistic ECS geometry for short-range transport between para-arterial and paravenous spaces. Major model parameters include para-arterial and paravenous pressures, ECS volume fraction, solute diffusion coefficient, and astrocyte foot-process water permeability. The model predicts solute accumulation and clearance from the ECS after a step change in solute concentration in para-arterial fluid. The principal and robust conclusions of the model are as follows: (a) significant convective transport requires a sustained pressure difference of several mmHg between the para-arterial and paravenous fluid and is not affected by pulsatile pressure fluctuations; (b) astrocyte endfoot water permeability does not substantially alter the rate of convective transport in ECS as the resistance to flow across endfeet is far greater than in the gaps surrounding them; and (c) diffusion (without convection) in the ECS is adequate to account for experimental transport studies in brain parenchyma. Therefore, our modeling results do not support a physiologically important role for local parenchymal convective flow in solute transport through brain ECS. PMID:27836940

Spatial model of convective solute transport in brain extracellular space does not support a "glymphatic" mechanism.

PubMed

Jin, Byung-Ju; Smith, Alex J; Verkman, Alan S

2016-12-01

A "glymphatic system," which involves convective fluid transport from para-arterial to paravenous cerebrospinal fluid through brain extracellular space (ECS), has been proposed to account for solute clearance in brain, and aquaporin-4 water channels in astrocyte endfeet may have a role in this process. Here, we investigate the major predictions of the glymphatic mechanism by modeling diffusive and convective transport in brain ECS and by solving the Navier-Stokes and convection-diffusion equations, using realistic ECS geometry for short-range transport between para-arterial and paravenous spaces. Major model parameters include para-arterial and paravenous pressures, ECS volume fraction, solute diffusion coefficient, and astrocyte foot-process water permeability. The model predicts solute accumulation and clearance from the ECS after a step change in solute concentration in para-arterial fluid. The principal and robust conclusions of the model are as follows: (a) significant convective transport requires a sustained pressure difference of several mmHg between the para-arterial and paravenous fluid and is not affected by pulsatile pressure fluctuations; (b) astrocyte endfoot water permeability does not substantially alter the rate of convective transport in ECS as the resistance to flow across endfeet is far greater than in the gaps surrounding them; and (c) diffusion (without convection) in the ECS is adequate to account for experimental transport studies in brain parenchyma. Therefore, our modeling results do not support a physiologically important role for local parenchymal convective flow in solute transport through brain ECS. © 2016 Jin et al.

Modeling Particle Acceleration and Transport at a 2-D CME-Driven Shock

NASA Astrophysics Data System (ADS)

Hu, Junxiang; Li, Gang; Ao, Xianzhi; Zank, Gary P.; Verkhoglyadova, Olga

2017-11-01

We extend our earlier Particle Acceleration and Transport in the Heliosphere (PATH) model to study particle acceleration and transport at a coronal mass ejection (CME)-driven shock. We model the propagation of a CME-driven shock in the ecliptic plane using the ZEUS-3D code from 20 solar radii to 2 AU. As in the previous PATH model, the initiation of the CME-driven shock is simplified and modeled as a disturbance at the inner boundary. Different from the earlier PATH model, the disturbance is now longitudinally dependent. Particles are accelerated at the 2-D shock via the diffusive shock acceleration mechanism. The acceleration depends on both the parallel and perpendicular diffusion coefficients κ|| and κ⊥ and is therefore shock-obliquity dependent. Following the procedure used in Li, Shalchi, et al. (k href="#jgra53857-bib-0045"/>), we obtain the particle injection energy, the maximum energy, and the accelerated particle spectra at the shock front. Once accelerated, particles diffuse and convect in the shock complex. The diffusion and convection of these particles are treated using a refined 2-D shell model in an approach similar to Zank et al. (k href="#jgra53857-bib-0089"/>). When particles escape from the shock, they propagate along and across the interplanetary magnetic field. The propagation is modeled using a focused transport equation with the addition of perpendicular diffusion. We solve the transport equation using a backward stochastic differential equation method where adiabatic cooling, focusing, pitch angle scattering, and cross-field diffusion effects are all included. Time intensity profiles and instantaneous particle spectra as well as particle pitch angle distributions are shown for two example CME shocks.

Conceptual model for transport processes in the Culebra Dolomite Member, Rustler Formation

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

Holt, R.M.

1997-08-01

The Culebra Dolomite Member of the Rustler Formation represents a possible pathway for contaminants from the Waste Isolation Pilot Plant underground repository to the accessible environment. The geologic character of the Culebra is consistent with a double-porosity, multiple-rate model for transport in which the medium is conceptualized as consisting of advective porosity, where solutes are carried by the groundwater flow, and fracture-bounded zones of diffusive porosity, where solutes move through slow advection or diffusion. As the advective travel length or travel time increases, the nature of transport within a double-porosity medium changes. This behavior is important for chemical sorption, becausemore » the specific surface area per unit mass of the diffusive porosity is much greater than in the advective porosity. Culebra transport experiments conducted at two different length scales show behavior consistent with a multiple-rate, double-porosity conceptual model for Culebra transport. Tracer tests conducted on intact core samples from the Culebra show no evidence of significant diffusion, suggesting that at the core scale the Culebra can be modeled as a single-porosity medium where only the advective porosity participates in transport. Field tracer tests conducted in the Culebra show strong double-porosity behavior that is best explained using a multiple-rate model.« less

Interplay between inhibited transport and reaction in nanoporous materials

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

Ackerman, David Michael

2013-01-01

This work presents a detailed formulation of reaction and diffusion dynamics of molecules in confined pores such as mesoporous silica and zeolites. A general reaction-diffusion model and discrete Monte Carlo simulations are presented. Both transient and steady state behavior is covered. Failure of previous mean-field models for these systems is explained and discussed. A coarse-grained, generalized hydrodynamic model is developed that accurately captures the interplay between reaction and restricted transport in these systems. This method incorporates the non-uniform chemical diffusion behavior present in finite pores with multi-component diffusion. Two methods of calculating these diffusion values are developed: a random walkmore » based approach and a driven diffusion model based on an extension of Fick's law. The effects of reaction, diffusion, pore length, and catalytic site distribution are investigated. In addition to strictly single file motion, quasi-single file diffusion is incorporated into the model to match a range of experimental systems. The connection between these experimental systems and model parameters is made through Langevin dynamics modeling of particles in confined pores.« less

A compartment model of alveolar-capillary oxygen diffusion with ventilation-perfusion gradient and dynamics of air transport through the respiratory tract.

PubMed

Jaworski, Jacek; Redlarski, Grzegorz

2014-08-01

This paper presents a model of alveolar-capillary oxygen diffusion with dynamics of air transport through the respiratory tract. For this purpose electrical model representing the respiratory tract mechanics and differential equations representing oxygen membrane diffusion are combined. Relevant thermodynamic relations describing the mass of oxygen transported into the human body are proposed as the connection between these models, as well as the influence of ventilation-perfusion mismatch on the oxygen diffusion. The model is verified based on simulation results of varying exercise intensities and statistical calculations of the results obtained during various clinical trials. The benefit of the approach proposed is its application in simulation-based research aimed to generate quantitative data of normal and pathological conditions. Based on the model presented, taking into account many essential physiological processes and air transport dynamics, comprehensive and combined studies of the respiratory efficiency can be performed. The impact of physical exercise, precise changes in respiratory tract mechanics and alterations in breathing pattern can be analyzed together with the impact of various changes in alveolar-capillary oxygen diffusion. This may be useful in simulation of effects of many severe medical conditions and increased activity level. Copyright © 2014 Elsevier Ltd. All rights reserved.

Numerical simulation of double‐diffusive finger convection

USGS Publications Warehouse

Hughes, Joseph D.; Sanford, Ward E.; Vacher, H. Leonard

2005-01-01

A hybrid finite element, integrated finite difference numerical model is developed for the simulation of double‐diffusive and multicomponent flow in two and three dimensions. The model is based on a multidimensional, density‐dependent, saturated‐unsaturated transport model (SUTRA), which uses one governing equation for fluid flow and another for solute transport. The solute‐transport equation is applied sequentially to each simulated species. Density coupling of the flow and solute‐transport equations is accounted for and handled using a sequential implicit Picard iterative scheme. High‐resolution data from a double‐diffusive Hele‐Shaw experiment, initially in a density‐stable configuration, is used to verify the numerical model. The temporal and spatial evolution of simulated double‐diffusive convection is in good agreement with experimental results. Numerical results are very sensitive to discretization and correspond closest to experimental results when element sizes adequately define the spatial resolution of observed fingering. Numerical results also indicate that differences in the molecular diffusivity of sodium chloride and the dye used to visualize experimental sodium chloride concentrations are significant and cause inaccurate mapping of sodium chloride concentrations by the dye, especially at late times. As a result of reduced diffusion, simulated dye fingers are better defined than simulated sodium chloride fingers and exhibit more vertical mass transfer.

Methane Hydrate Formation in Thick Sand Reservoirs: Long-range Gas Transport or Short-range Methane Diffusion?

NASA Astrophysics Data System (ADS)

You, K.; Flemings, P. B.

2016-12-01

We developed two 2-D numerical models to simulate hydrate formation by long range methane gas transport and short-range methane diffusion. We interpret that methane hydrates in thick sands are most likely formed by long range gas transport where methane gas is transported upward into the hydrate stability zone (HSZ) under buoyancy and locally forms hydrate to its stability limit. In short-range methane diffusion, methane is generated locally by biodegradation of organic matter in mud and diffused into bounding sands where it forms hydrate. We could not simulate enough methane transport by diffusion to account for its observed concentration in thick sands. In our models, we include the capillary effect on dissolved methane solubility and on the hydrate phase boundary, sedimentation and different compaction in sand and mud, fracture generation as well as the fully coupled multiphase flow and multicomponent transport. We apply our models to a 12 meter-thick hydrate-bearing sand layer at Walker Ridge 313, Northern Gulf of Mexico. With the long-range gas transport, hydrate saturation is greater than 90% and salinity is increased from seawater to about 8 wt.% through the entire sand. With short-range diffusion, hydrate saturation is more than 90% at the sand base and is less than 10% in the overlying section; salinity is close to seawater when sand is deposited to 800 meter below seafloor by short-range methane diffusion. With short-range diffusion, the amount of hydrate formed is much less than that interpreted from the well log data. Two transient gas layers separated by a hydrate layer are formed from short-range diffusion caused by capillary effect. This could be interpreted as a double bottom simulating reflector. This study provides further insights into different hydrate formation mechanisms, and could serve as a base to confirm the hydrate formation mechanism in fields.

Transport of neutral solute across articular cartilage: the role of zonal diffusivities.

PubMed

Arbabi, V; Pouran, B; Weinans, H; Zadpoor, A A

2015-07-01

Transport of solutes through diffusion is an important metabolic mechanism for the avascular cartilage tissue. Three types of interconnected physical phenomena, namely mechanical, electrical, and chemical, are all involved in the physics of transport in cartilage. In this study, we use a carefully designed experimental-computational setup to separate the effects of mechanical and chemical factors from those of electrical charges. Axial diffusion of a neutral solute Iodixanol into cartilage was monitored using calibrated microcomputed tomography micro-CT images for up to 48 hr. A biphasic-solute computational model was fitted to the experimental data to determine the diffusion coefficients of cartilage. Cartilage was modeled either using one single diffusion coefficient (single-zone model) or using three diffusion coefficients corresponding to superficial, middle, and deep cartilage zones (multizone model). It was observed that the single-zone model cannot capture the entire concentration-time curve and under-predicts the near-equilibrium concentration values, whereas the multizone model could very well match the experimental data. The diffusion coefficient of the superficial zone was found to be at least one order of magnitude larger than that of the middle zone. Since neutral solutes were used, glycosaminoglycan (GAG) content cannot be the primary reason behind such large differences between the diffusion coefficients of the different cartilage zones. It is therefore concluded that other features of the different cartilage zones such as water content and the organization (orientation) of collagen fibers may be enough to cause large differences in diffusion coefficients through the cartilage thickness.

Modeling anomalous radial transport in kinetic transport codes

NASA Astrophysics Data System (ADS)

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

2009-11-01

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

Position-Dependent Diffusion Tensors in Anisotropic Media from Simulation: Oxygen Transport in and through Membranes.

PubMed

Ghysels, An; Venable, Richard M; Pastor, Richard W; Hummer, Gerhard

2017-06-13

A Bayesian-based methodology is developed to estimate diffusion tensors from molecular dynamics simulations of permeants in anisotropic media, and is applied to oxygen in lipid bilayers. By a separation of variables in the Smoluchowski diffusion equation, the multidimensional diffusion is reduced to coupled one-dimensional diffusion problems that are treated by discretization. The resulting diffusivity profiles characterize the membrane transport dynamics as a function of the position across the membrane, discriminating between diffusion normal and parallel to the membrane. The methodology is first validated with neat water, neat hexadecane, and a hexadecane slab surrounded by water, the latter being a simple model for a lipid membrane. Next, a bilayer consisting of pure 1-palmitoyl 2-oleoylphosphatidylcholine (POPC), and a bilayer mimicking the lipid composition of the inner mitochondrial membrane, including cardiolipin, are investigated. We analyze the detailed time evolution of oxygen molecules, in terms of both normal diffusion through and radial diffusion inside the membrane. Diffusion is fast in the more loosely packed interleaflet region, and anisotropic, with oxygen spreading more rapidly in the membrane plane than normal to it. Visualization of the propagator shows that oxygen enters the membrane rapidly, reaching its thermodynamically favored center in about 1 ns, despite the free energy barrier at the headgroup region. Oxygen transport is quantified by computing the oxygen permeability of the membranes and the average radial diffusivity, which confirm the anisotropy of the diffusion. The position-dependent diffusion constants and free energies are used to construct compartmental models and test assumptions used in estimating permeability, including Overton's rule. In particular, a hexadecane slab surrounded by water is found to be a poor model of oxygen transport in membranes because the relevant energy barriers differ substantially.

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.

ICF target 2D modeling using Monte Carlo SNB electron thermal transport in DRACO

NASA Astrophysics Data System (ADS)

Chenhall, Jeffrey; Cao, Duc; Moses, Gregory

2016-10-01

The iSNB (implicit Schurtz Nicolai Busquet multigroup diffusion electron thermal transport method is adapted into a Monte Carlo (MC) transport method to better model angular and long mean free path non-local effects. The MC model was first implemented in the 1D LILAC code to verify consistency with the iSNB model. Implementation of the MC SNB model in the 2D DRACO code enables higher fidelity non-local thermal transport modeling in 2D implosions such as polar drive experiments on NIF. The final step is to optimize the MC model by hybridizing it with a MC version of the iSNB diffusion method. The hybrid method will combine the efficiency of a diffusion method in intermediate mean free path regions with the accuracy of a transport method in long mean free path regions allowing for improved computational efficiency while maintaining accuracy. Work to date on the method will be presented. This work was supported by Sandia National Laboratories and the Univ. of Rochester Laboratory for Laser Energetics.

Modeling of tritium transport in a fusion reactor pin-type solid breeder blanket using the diffuse code

NASA Astrophysics Data System (ADS)

Martin, Rodger; Ghoniem, Nasr M.

1986-11-01

A pin-type fusion reactor blanket is designed using γ-LiAlO 2 solid tritium breeder. Tritium transport and diffusive inventory are modeled using the DIFFUSE code. Two approaches are used to obtain characteristic LiAlO 2 grain temperatures. DIFFUSE provides intragranular diffusive inventories which scale up to blanket size. These results compare well with a numerical analysis, giving a steady-state blanket tritium inventory of 13 g. Start-up transient inventories are modeled using DIFFUSE for both full and restricted coolant flow. Full flow gives rapid inventory buildup while restricted flow prevents this buildup. Inventories after shutdown are modeled: reduced cooling is found to have little effect on removing tritium, but preheating rapidly purges inventory. DIFFUSE provides parametric modeling of solid breeder density, radiation, and surface effects. 100% dense pins are found to give massive inventory and marginal tritium release. Only large trapping energies and concentrations significantly increase inventory. Diatomic surface recombination is only significant at high temperatures.

Relative contributions of active mediated transport and passive diffusion of fluoroquinolones with various lipophilicities in a Calu-3 lung epithelial cell model.

PubMed

Brillault, Julien; De Castro, Whocely Victor; Couet, William

2010-01-01

The transport characteristics of six fluoroquinolones (FQs) with various lipophilicities were compared in a Calu-3 cell model. For each FQ, an active polarized transport was observed in the direction of the apical side. However, the apparent permeability of FQs resulted from active transport and passive diffusion that were highly variable between compounds and mainly governed by lipophilicity. Therefore, active transport was predominant for compounds with relatively low lipophilicity but minor for FQs with higher lipophilicity.

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.

Diffusion Dominant Solute Transport Modelling In Deep Repository Under The Effect of Emplacement Media Degradation - 13285

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

Kwong, S.; Jivkov, A.P.

2013-07-01

Deep geologic disposal of high activity and long-lived radioactive waste is being actively considered and pursued in many countries, where low permeability geological formations are used to provide long term waste contaminant with minimum impact to the environment and risk to the biosphere. A multi-barrier approach that makes use of both engineered and natural barriers (i.e. geological formations) is often used to further enhance the containment performance of the repository. As the deep repository system subjects to a variety of thermo-hydro-chemo-mechanical (THCM) effects over its long 'operational' lifespan (e.g. 0.1 to 1.0 million years, the integrity of the barrier systemmore » will decrease over time (e.g. fracturing in rock or clay)). This is broadly referred as media degradation in the present study. This modelling study examines the effects of media degradation on diffusion dominant solute transport in fractured media that are typical of 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, while the effects of degradation is studied using a pore network model that considers the media diffusivity and network changes. Model results are presented to demonstrate the use of a 3D pore-network model, using a novel architecture, to calculate macroscopic properties of the medium such as diffusivity, subject to pore space changes as the media degrade. Results from a reactive transport model of a representative geological waste disposal package are also presented to demonstrate the effect of media property change on the solute migration behaviour, illustrating the complex interplay between kinetic biogeochemical processes and diffusion dominant transport. The initial modelling results demonstrate the feasibility of a coupled modelling approach (using pore-network model and reactive transport model) to examine the long term behaviour of deep geological repositories with media property change under complex geochemical conditions. (authors)« less

Time-dependent transport of energetic particles in magnetic turbulence: computer simulations versus analytical theory

NASA Astrophysics Data System (ADS)

Arendt, V.; Shalchi, A.

2018-06-01

We explore numerically the transport of energetic particles in a turbulent magnetic field configuration. A test-particle code is employed to compute running diffusion coefficients as well as particle distribution functions in the different directions of space. Our numerical findings are compared with models commonly used in diffusion theory such as Gaussian distribution functions and solutions of the cosmic ray Fokker-Planck equation. Furthermore, we compare the running diffusion coefficients across the mean magnetic field with solutions obtained from the time-dependent version of the unified non-linear transport theory. In most cases we find that particle distribution functions are indeed of Gaussian form as long as a two-component turbulence model is employed. For turbulence setups with reduced dimensionality, however, the Gaussian distribution can no longer be obtained. It is also shown that the unified non-linear transport theory agrees with simulated perpendicular diffusion coefficients as long as the pure two-dimensional model is excluded.

A radially resolved kinetic model for nonlocal electron ripple diffusion losses in tokamaks

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

Robertson, Scott

A relatively simple radially resolved kinetic model is applied to the ripple diffusion problem for electrons in tokamaks. The distribution function f(r,v) is defined on a two-dimensional grid, where r is the radial coordinate and v is the velocity coordinate. Particle transport in the radial direction is from ripple and banana diffusion and transport in the velocity direction is described by the Fokker-Planck equation. Particles and energy are replaced by source functions that are adjusted to maintain a constant central density and temperature. The relaxed profiles of f(r,v) show that the electron distribution function at the wall contains suprathermal electronsmore » that have diffused from the interior that enhance ripple transport. The transport at the periphery is therefore nonlocal. The energy replacement times from the computational model are near to the experimental replacement times for tokamak discharges in the compilation by Pfeiffer and Waltz [Nucl. Fusion 19, 51 (1979)].« less

Model unification and scale-adaptivity in the Eddy-Diffusivity Mass-Flux (EDMF) approach

NASA Astrophysics Data System (ADS)

Neggers, R.; Siebesma, P.

2011-12-01

It has long been understood that the turbulent-convective transport of heat, moisture and momentum plays an important role in the dynamics and climate of the earth's atmosphere. Accordingly, the representation of these processes in General Circulation Models (GCMs) has always been an active research field. Turbulence and convection act on temporal and spatial scales that are unresolved by most present-day GCMs, and have to be represented through parametric relations. Over the years a variety of schemes has been successfully developed. Although differing widely in their details, only two basic transport models stand at the basis of most of these schemes. The first is the diffusive transport model, which can only act down-gradient. An example is the turbulent mixing at small scales. The second is the advective transport model, which can act both down-gradient and counter-gradient. A good example is the transport of heat and moisture by convective updrafts that overshoot into stable layers of air. In practice, diffusive models often make use of a K-profile method or a prognostic TKE budget, while advective models make use of a rising (and entraining) plume budget. While most transport schemes classicaly apply either the diffusive model or advective model, the relatively recently introduced Eddy-Diffusivity Mass-Flux (EDMF) approach aims to combine both techniques. By applying advection and diffusion simultaneously, one can make use of the benefits of both approaches. Since its emergence about a decade ago, the EDMF approach has been successfully applied in both research and operational circulation models. This presentation is dedicated to the EDMF framework. Apart from a short introduction to the EDMF concept and a short overview of its current implementations, our main goal is to elaborate on the opportunities EDMF brings in addressing some long-standing problems in the parameterization of turbulent-convective transport. The first problem is the need for a unified approach in the parameterization of distinct transport regimes. The main objections to a separate representation of regimes are i) artificially discrete regime-transitions, and ii) superfluous and intransparent coding. For a unified approach we need to establish what complexity is sufficient to achieve general applicability. We argue that adding only little complexity already enables the standard EDMF framework to represent multiple boundary-layer transport regimes and smooth transitions between those. The second long-standing problem is that the ever increasing computational capacity and speed has lead to increasingly fine discretizations in GCMs, which requires scale-adaptivity in a sub-grid transport model. It is argued that a flexible partitioning between advection and diffusion within EDMF, as well as the potential to introduce stochastic elements in the advective part of EDMF, creates opportunities to introduce such adaptivity. In the final part of the presentation we will attempt to give an overview of currently ongoing developments of the EDMF framework, both concerning model formulation as well as evaluation efforts of key assumptions against observational datasets and large-eddy simulation results.

Transport Corrections in Nodal Diffusion Codes for HTR Modeling

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

Abderrafi M. Ougouag; Frederick N. Gleicher

2010-08-01

The cores and reflectors of High Temperature Reactors (HTRs) of the Next Generation Nuclear Plant (NGNP) type are dominantly diffusive media from the point of view of behavior of the neutrons and their migration between the various structures of the reactor. This means that neutron diffusion theory is sufficient for modeling most features of such reactors and transport theory may not be needed for most applications. Of course, the above statement assumes the availability of homogenized diffusion theory data. The statement is true for most situations but not all. Two features of NGNP-type HTRs require that the diffusion theory-based solutionmore » be corrected for local transport effects. These two cases are the treatment of burnable poisons (BP) in the case of the prismatic block reactors and, for both pebble bed reactor (PBR) and prismatic block reactor (PMR) designs, that of control rods (CR) embedded in non-multiplying regions near the interface between fueled zones and said non-multiplying zones. The need for transport correction arises because diffusion theory-based solutions appear not to provide sufficient fidelity in these situations.« less

Development of Tokamak Transport Solvers for Stiff Confinement Systems

NASA Astrophysics Data System (ADS)

St. John, H. E.; Lao, L. L.; Murakami, M.; Park, J. M.

2006-10-01

Leading transport models such as GLF23 [1] and MM95 [2] describe turbulent plasma energy, momentum and particle flows. In order to accommodate existing transport codes and associated solution methods effective diffusivities have to be derived from these turbulent flow models. This can cause significant problems in predicting unique solutions. We have developed a parallel transport code solver, GCNMP, that can accommodate both flow based and diffusivity based confinement models by solving the discretized nonlinear equations using modern Newton, trust region, steepest descent and homotopy methods. We present our latest development efforts, including multiple dynamic grids, application of two-level parallel schemes, and operator splitting techniques that allow us to combine flow based and diffusivity based models in tokamk simulations. 6pt [1] R.E. Waltz, et al., Phys. Plasmas 4, 7 (1997). [2] G. Bateman, et al., Phys. Plasmas 5, 1793 (1998).

Tomographic imaging of non-local media based on space-fractional diffusion models

NASA Astrophysics Data System (ADS)

Buonocore, Salvatore; Semperlotti, Fabio

2018-06-01

We investigate a generalized tomographic imaging framework applicable to a class of inhomogeneous media characterized by non-local diffusive energy transport. Under these conditions, the transport mechanism is well described by fractional-order continuum models capable of capturing anomalous diffusion that would otherwise remain undetected when using traditional integer-order models. Although the underlying idea of the proposed framework is applicable to any transport mechanism, the case of fractional heat conduction is presented as a specific example to illustrate the methodology. By using numerical simulations, we show how complex inhomogeneous media involving non-local transport can be successfully imaged if fractional order models are used. In particular, results will show that by properly recognizing and accounting for the fractional character of the host medium not only allows achieving increased resolution but, in case of strong and spatially distributed non-locality, it represents the only viable approach to achieve a successful reconstruction.

Transport through a network of capillaries from ultrametric diffusion equation with quadratic nonlinearity

NASA Astrophysics Data System (ADS)

Oleschko, K.; Khrennikov, A.

2017-10-01

This paper is about a novel mathematical framework to model transport (of, e.g., fluid or gas) through networks of capillaries. This framework takes into account the tree structure of the networks of capillaries. (Roughly speaking, we use the tree-like system of coordinates.) As is well known, tree-geometry can be topologically described as the geometry of an ultrametric space, i.e., a metric space in which the metric satisfies the strong triangle inequality: in each triangle, the third side is less than or equal to the maximum of two other sides. Thus transport (e.g., of oil or emulsion of oil and water in porous media, or blood and air in biological organisms) through networks of capillaries can be mathematically modelled as ultrametric diffusion. Such modelling was performed in a series of recently published papers of the authors. However, the process of transport through capillaries can be only approximately described by the linear diffusion, because the concentration of, e.g., oil droplets, in a capillary can essentially modify the dynamics. Therefore nonlinear dynamical equations provide a more adequate model of transport in a network of capillaries. We consider a nonlinear ultrametric diffusion equation with quadratic nonlinearity - to model transport in such a network. Here, as in the linear case, we apply the theory of ultrametric wavelets. The paper also contains a simple introduction to theory of ultrametric spaces and analysis on them.

Anisotropic Mesoscale Eddy Transport in Ocean General Circulation Models

NASA Astrophysics Data System (ADS)

Reckinger, S. J.; Fox-Kemper, B.; Bachman, S.; Bryan, F.; Dennis, J.; Danabasoglu, G.

2014-12-01

Modern climate models are limited to coarse-resolution representations of large-scale ocean circulation that rely on parameterizations for mesoscale eddies. The effects of eddies are typically introduced by relating subgrid eddy fluxes to the resolved gradients of buoyancy or other tracers, where the proportionality is, in general, governed by an eddy transport tensor. The symmetric part of the tensor, which represents the diffusive effects of mesoscale eddies, is universally treated isotropically in general circulation models. Thus, only a single parameter, namely the eddy diffusivity, is used at each spatial and temporal location to impart the influence of mesoscale eddies on the resolved flow. However, the diffusive processes that the parameterization approximates, such as shear dispersion, potential vorticity barriers, oceanic turbulence, and instabilities, typically have strongly anisotropic characteristics. Generalizing the eddy diffusivity tensor for anisotropy extends the number of parameters to three: a major diffusivity, a minor diffusivity, and the principal axis of alignment. The Community Earth System Model (CESM) with the anisotropic eddy parameterization is used to test various choices for the newly introduced parameters, which are motivated by observations and the eddy transport tensor diagnosed from high resolution simulations. Simply setting the ratio of major to minor diffusivities to a value of five globally, while aligning the major axis along the flow direction, improves biogeochemical tracer ventilation and reduces global temperature and salinity biases. These effects can be improved even further by parameterizing the anisotropic transport mechanisms in the ocean.

Computing eddy-driven effective diffusivity using Lagrangian particles

DOE PAGES

Wolfram, Phillip J.; Ringler, Todd D.

2017-08-14

A novel method to derive effective diffusivity from Lagrangian particle trajectory data sets is developed and then analyzed relative to particle-derived meridional diffusivity for eddy-driven mixing in an idealized circumpolar current. Quantitative standard dispersion- and transport-based mixing diagnostics are defined, compared and contrasted to motivate the computation and use of effective diffusivity derived from Lagrangian particles. We compute the effective diffusivity by first performing scalar transport on Lagrangian control areas using stored trajectories computed from online Lagrangian In-situ Global High-performance particle Tracking (LIGHT) using the Model for Prediction Across Scales Ocean (MPAS-O). Furthermore, the Lagrangian scalar transport scheme is comparedmore » against an Eulerian scalar transport scheme. Spatially-variable effective diffusivities are computed from resulting time-varying cumulative concentrations that vary as a function of cumulative area. The transport-based Eulerian and Lagrangian effective diffusivity diagnostics are found to be qualitatively consistent with the dispersion-based diffusivity. All diffusivity estimates show a region of increased subsurface diffusivity within the core of an idealized circumpolar current and results are within a factor of two of each other. The Eulerian and Lagrangian effective diffusivities are most similar; smaller and more spatially diffused values are obtained with the dispersion-based diffusivity computed with particle clusters.« less

Computing eddy-driven effective diffusivity using Lagrangian particles

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

Wolfram, Phillip J.; Ringler, Todd D.

A novel method to derive effective diffusivity from Lagrangian particle trajectory data sets is developed and then analyzed relative to particle-derived meridional diffusivity for eddy-driven mixing in an idealized circumpolar current. Quantitative standard dispersion- and transport-based mixing diagnostics are defined, compared and contrasted to motivate the computation and use of effective diffusivity derived from Lagrangian particles. We compute the effective diffusivity by first performing scalar transport on Lagrangian control areas using stored trajectories computed from online Lagrangian In-situ Global High-performance particle Tracking (LIGHT) using the Model for Prediction Across Scales Ocean (MPAS-O). Furthermore, the Lagrangian scalar transport scheme is comparedmore » against an Eulerian scalar transport scheme. Spatially-variable effective diffusivities are computed from resulting time-varying cumulative concentrations that vary as a function of cumulative area. The transport-based Eulerian and Lagrangian effective diffusivity diagnostics are found to be qualitatively consistent with the dispersion-based diffusivity. All diffusivity estimates show a region of increased subsurface diffusivity within the core of an idealized circumpolar current and results are within a factor of two of each other. The Eulerian and Lagrangian effective diffusivities are most similar; smaller and more spatially diffused values are obtained with the dispersion-based diffusivity computed with particle clusters.« less

Recycling of Kinesin-1 Motors by Diffusion after Transport

PubMed Central

Blasius, T. Lynne; Reed, Nathan; Slepchenko, Boris M.; Verhey, Kristen J.

2013-01-01

Kinesin motors drive the long-distance anterograde transport of cellular components along microtubule tracks. Kinesin-dependent transport plays a critical role in neurogenesis and neuronal function due to the large distance separating the soma and nerve terminal. The fate of kinesin motors after delivery of their cargoes is unknown but has been postulated to involve degradation at the nerve terminal, recycling via retrograde motors, and/or recycling via diffusion. We set out to test these models concerning the fate of kinesin-1 motors after completion of transport in neuronal cells. We find that kinesin-1 motors are neither degraded nor returned by retrograde motors. By combining mathematical modeling and experimental analysis, we propose a model in which the distribution and recycling of kinesin-1 motors fits a “loose bucket brigade” where individual motors alter between periods of active transport and free diffusion within neuronal processes. These results suggest that individual kinesin-1 motors are utilized for multiple rounds of transport. PMID:24098765

Mathematical modeling of molecular diffusion through mucus

PubMed Central

Cu, Yen; Saltzman, W. Mark

2008-01-01

The rate of molecular transport through the mucus gel can be an important determinant of efficacy for therapeutic agents delivered by oral, intranasal, intravaginal/rectal, and intraocular routes. Transport through mucus can be described by mathematical models based on principles of physical chemistry and known characteristics of the mucus gel, its constituents, and of the drug itself. In this paper, we review mathematical models of molecular diffusion in mucus, as well as the techniques commonly used to measure diffusion of solutes in the mucus gel, mucus gel mimics, and mucosal epithelia. PMID:19135488

Background Error Correlation Modeling with Diffusion Operators

DTIC Science & Technology

2013-01-01

RESPONSIBLE PERSON 19b. TELEPHONE NUMBER (Include area code) 07-10-2013 Book Chapter Background Error Correlation Modeling with Diffusion Operators...normalization Unclassified Unclassified Unclassified UU 27 Max Yaremchuk (228) 688-5259 Reset Chapter 8 Background error correlation modeling with diffusion ...field, then a structure like this simulates enhanced diffusive transport of model errors in the regions of strong cur- rents on the background of

Anomalous Diffusion of Single Particles in Cytoplasm

PubMed Central

Regner, Benjamin M.; Vučinić, Dejan; Domnisoru, Cristina; Bartol, Thomas M.; Hetzer, Martin W.; Tartakovsky, Daniel M.; Sejnowski, Terrence J.

2013-01-01

The crowded intracellular environment poses a formidable challenge to experimental and theoretical analyses of intracellular transport mechanisms. Our measurements of single-particle trajectories in cytoplasm and their random-walk interpretations elucidate two of these mechanisms: molecular diffusion in crowded environments and cytoskeletal transport along microtubules. We employed acousto-optic deflector microscopy to map out the three-dimensional trajectories of microspheres migrating in the cytosolic fraction of a cellular extract. Classical Brownian motion (BM), continuous time random walk, and fractional BM were alternatively used to represent these trajectories. The comparison of the experimental and numerical data demonstrates that cytoskeletal transport along microtubules and diffusion in the cytosolic fraction exhibit anomalous (nonFickian) behavior and posses statistically distinct signatures. Among the three random-walk models used, continuous time random walk provides the best representation of diffusion, whereas microtubular transport is accurately modeled with fractional BM. PMID:23601312

Modelling uncertainties in the diffusion-advection equation for radon transport in soil using interval arithmetic.

PubMed

Chakraverty, S; Sahoo, B K; Rao, T D; Karunakar, P; Sapra, B K

2018-02-01

Modelling radon transport in the earth crust is a useful tool to investigate the changes in the geo-physical processes prior to earthquake event. Radon transport is modeled generally through the deterministic advection-diffusion equation. However, in order to determine the magnitudes of parameters governing these processes from experimental measurements, it is necessary to investigate the role of uncertainties in these parameters. Present paper investigates this aspect by combining the concept of interval uncertainties in transport parameters such as soil diffusivity, advection velocity etc, occurring in the radon transport equation as applied to soil matrix. The predictions made with interval arithmetic have been compared and discussed with the results of classical deterministic model. The practical applicability of the model is demonstrated through a case study involving radon flux measurements at the soil surface with an accumulator deployed in steady-state mode. It is possible to detect the presence of very low levels of advection processes by applying uncertainty bounds on the variations in the observed concentration data in the accumulator. The results are further discussed. Copyright © 2017 Elsevier Ltd. All rights reserved.

The structure of the solution obtained with Reynolds-stress-transport models at the free-stream edges of turbulent flows

NASA Astrophysics Data System (ADS)

Cazalbou, J.-B.; Chassaing, P.

2002-02-01

The behavior of Reynolds-stress-transport models at the free-stream edges of turbulent flows is investigated. Current turbulent-diffusion models are found to produce propagative (possibly weak) solutions of the same type as those reported earlier by Cazalbou, Spalart, and Bradshaw [Phys. Fluids 6, 1797 (1994)] for two-equation models. As in the latter study, an analysis is presented that provides qualitative information on the flow structure predicted near the edge if a condition on the values of the diffusion constants is satisfied. In this case, the solution appears to be fairly insensitive to the residual free-stream turbulence levels needed with conventional numerical methods. The main specific result is that, depending on the diffusion model, the propagative solution can force turbulence toward definite and rather extreme anisotropy states at the edge (one- or two-component limit). This is not the case with the model of Daly and Harlow [Phys. Fluids 13, 2634 (1970)]; it may be one of the reasons why this "old" scheme is still the most widely used, even in recent Reynolds-stress-transport models. In addition, the analysis helps us to interpret some difficulties encountered in computing even very simple flows with Lumley's pressure-diffusion model [Adv. Appl. Mech. 18, 123 (1978)]. A new realizability condition, according to which the diffusion model should not globally become "anti-diffusive," is introduced, and a recalibration of Lumley's model satisfying this condition is performed using information drawn from the analysis.

The nature and role of advection in advection-diffusion equations used for modelling bed load transport

NASA Astrophysics Data System (ADS)

Ancey, Christophe; Bohorquez, Patricio; Heyman, Joris

2016-04-01

The advection-diffusion equation arises quite often in the context of sediment transport, e.g., for describing time and space variations in the particle activity (the solid volume of particles in motion per unit streambed area). Stochastic models can also be used to derive this equation, with the significant advantage that they provide information on the statistical properties of particle activity. Stochastic models are quite useful when sediment transport exhibits large fluctuations (typically at low transport rates), making the measurement of mean values difficult. We develop an approach based on birth-death Markov processes, which involves monitoring the evolution of the number of particles moving within an array of cells of finite length. While the topic has been explored in detail for diffusion-reaction systems, the treatment of advection has received little attention. We show that particle advection produces nonlocal effects, which are more or less significant depending on the cell size and particle velocity. Albeit nonlocal, these effects look like (local) diffusion and add to the intrinsic particle diffusion (dispersal due to velocity fluctuations), with the important consequence that local measurements depend on both the intrinsic properties of particle displacement and the dimensions of the measurement system.

Dual control of flow field heterogeneity and immobile porosity on non-Fickian transport in Berea sandstone

NASA Astrophysics Data System (ADS)

Gjetvaj, Filip; Russian, Anna; Gouze, Philippe; Dentz, Marco

2015-10-01

Both flow field heterogeneity and mass transfer between mobile and immobile domains have been studied separately for explaining observed anomalous transport. Here we investigate non-Fickian transport using high-resolution 3-D X-ray microtomographic images of Berea sandstone containing microporous cement with pore size below the setup resolution. Transport is computed for a set of representative elementary volumes and results from advection and diffusion in the resolved macroporosity (mobile domain) and diffusion in the microporous phase (immobile domain) where the effective diffusion coefficient is calculated from the measured local porosity using a phenomenological model that includes a porosity threshold (ϕθ) below which diffusion is null and the exponent n that characterizes tortuosity-porosity power-law relationship. We show that both flow field heterogeneity and microporosity trigger anomalous transport. Breakthrough curve (BTC) tailing is positively correlated to microporosity volume and mobile-immobile interface area. The sensitivity analysis showed that the BTC tailing increases with the value of ϕθ, due to the increase of the diffusion path tortuosity until the volume of the microporosity becomes negligible. Furthermore, increasing the value of n leads to an increase in the standard deviation of the distribution of effective diffusion coefficients, which in turn results in an increase of the BTC tailing. Finally, we propose a continuous time random walk upscaled model where the transition time is the sum of independently distributed random variables characterized by specific distributions. It allows modeling a 1-D equivalent macroscopic transport honoring both the control of the flow field heterogeneity and the multirate mass transfer between mobile and immobile domains.

Mathematical Model for the Mineralization of Bone

NASA Technical Reports Server (NTRS)

Martin, Bruce

1994-01-01

A mathematical model is presented for the transport and precipitation of mineral in refilling osteons. One goal of this model was to explain calcification 'halos,' in which the bone near the haversian canal is more highly mineralized than the more peripheral lamellae, which have been mineralizing longer. It was assumed that the precipitation rate of mineral is proportional to the difference between the local concentration of calcium ions and an equilibrium concentration and that the transport of ions is by either diffusion or some other concentration gradient-dependent process. Transport of ions was assumed to be slowed by the accumulation of mineral in the matrix along the transport path. ne model also mimics bone apposition, slowing of apposition during refilling, and mineralization lag time. It was found that simple diffusion cannot account for the transport of calcium ions into mineralizing bone, because the diffusion coefficient is two orders of magnitude too low. If a more rapid concentration gradient-driven means of transport exists, the model demonstrates that osteonal geometry and variable rate of refilling work together to produce calcification halos, as well as the primary and secondary calcification effect reported in the literature.

Diffusive mass transport in agglomerated glassy fallout from a near-surface nuclear test

NASA Astrophysics Data System (ADS)

Weisz, David G.; Jacobsen, Benjamin; Marks, Naomi E.; Knight, Kim B.; Isselhardt, Brett H.; Matzel, Jennifer E.

2018-02-01

Aerodynamically-shaped glassy fallout is formed when vapor phase constituents from the nuclear device are incorporated into molten carriers (i.e. fallout precursor materials derived from soil or other near-field environmental debris). The effects of speciation and diffusive transport of condensing constituents are not well defined in models of fallout formation. Previously we reported observations of diffuse micrometer scale layers enriched in Na, Fe, Ca, and 235U, and depleted in Al and Ti, at the interfaces of agglomerated fallout objects. Here, we derive the timescales of uranium mass transport in such fallout as it cools from 2500 K to 1500 K by applying a 1-dimensional planar diffusion model to the observed 235U/30Si variation at the interfaces. By modeling the thermal transport between the fireball and the carrier materials, the time of mass transport is calculated to be <0.6 s, <1 s, <2 s, and <3.5 s for fireball yields of 0.1 kt, 1 kt, 10 kt, and 100 kt respectively. Based on the calculated times of mass transport, a maximum temperature of deposition of uranium onto the carrier material of ∼2200 K is inferred (1σ uncertainty of ∼200 K). We also determine that the occurrence of micrometer scale layers of material enriched in relatively volatile Na-species as well as more refractory Ca-species provides evidence for an oxygen-rich fireball based on the vapor pressure of the two species under oxidizing conditions. These results represent the first application of diffusion-based modeling to derive material transport, thermal environments, and oxidation-speciation in near-surface nuclear detonation environments.

Diffusive mass transport in agglomerated glassy fallout from a near-surface nuclear test

DOE PAGES

Weisz, David G.; Jacobsen, Benjamin; Marks, Naomi E.; ...

2017-12-15

Aerodynamically-shaped glassy fallout is formed when vapor phase constituents from the nuclear device are incorporated into molten carriers (i.e. fallout precursor materials derived from soil or other near-field environmental debris). The effects of speciation and diffusive transport of condensing constituents are not well defined in models of fallout formation. Previously we reported observations of diffuse micrometer scale layers enriched in Na, Fe, Ca, and 235U, and depleted in Al and Ti, at the interfaces of agglomerated fallout objects. Here in this paper, we derive the timescales of uranium mass transport in such fallout as it cools from 2500 K tomore » 1500 K by applying a 1-dimensional planar diffusion model to the observed 235U/ 30Si variation at the interfaces. By modeling the thermal transport between the fireball and the carrier materials, the time of mass transport is calculated to be <0.6 s, <1 s, <2 s, and <3.5 s for fireball yields of 0.1 kt, 1 kt, 10 kt, and 100 kt respectively. Based on the calculated times of mass transport, a maximum temperature of deposition of uranium onto the carrier material of ~2200 K is inferred (1σ uncertainty of ~200 K). We also determine that the occurrence of micrometer scale layers of material enriched in relatively volatile Na-species as well as more refractory Ca-species provides evidence for an oxygen-rich fireball based on the vapor pressure of the two species under oxidizing conditions. These results represent the first application of diffusion-based modeling to derive material transport, thermal environments, and oxidation-speciation in near-surface nuclear detonation environments.« less

Diffusive mass transport in agglomerated glassy fallout from a near-surface nuclear test

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

Weisz, David G.; Jacobsen, Benjamin; Marks, Naomi E.

Aerodynamically-shaped glassy fallout is formed when vapor phase constituents from the nuclear device are incorporated into molten carriers (i.e. fallout precursor materials derived from soil or other near-field environmental debris). The effects of speciation and diffusive transport of condensing constituents are not well defined in models of fallout formation. Previously we reported observations of diffuse micrometer scale layers enriched in Na, Fe, Ca, and 235U, and depleted in Al and Ti, at the interfaces of agglomerated fallout objects. Here in this paper, we derive the timescales of uranium mass transport in such fallout as it cools from 2500 K tomore » 1500 K by applying a 1-dimensional planar diffusion model to the observed 235U/ 30Si variation at the interfaces. By modeling the thermal transport between the fireball and the carrier materials, the time of mass transport is calculated to be <0.6 s, <1 s, <2 s, and <3.5 s for fireball yields of 0.1 kt, 1 kt, 10 kt, and 100 kt respectively. Based on the calculated times of mass transport, a maximum temperature of deposition of uranium onto the carrier material of ~2200 K is inferred (1σ uncertainty of ~200 K). We also determine that the occurrence of micrometer scale layers of material enriched in relatively volatile Na-species as well as more refractory Ca-species provides evidence for an oxygen-rich fireball based on the vapor pressure of the two species under oxidizing conditions. These results represent the first application of diffusion-based modeling to derive material transport, thermal environments, and oxidation-speciation in near-surface nuclear detonation environments.« less

Diffusive smoothing of surfzone bathymetry by gravity-driven sediment transport

NASA Astrophysics Data System (ADS)

Moulton, M. R.; Elgar, S.; Raubenheimer, B.

2012-12-01

Gravity-driven sediment transport often is assumed to have a small effect on the evolution of nearshore morphology. Here, it is shown that down-slope gravity-driven sediment transport is an important process acting to smooth steep bathymetric features in the surfzone. Gravity-driven transport can be modeled as a diffusive term in the sediment continuity equation governing temporal (t) changes in bed level (h): ∂h/∂t ≈ κ ▽2h, where κ is a sediment diffusion coefficient that is a function of the bed shear stress (τb) and sediment properties, such as the grain size and the angle of repose. Field observations of waves, currents, and the evolution of large excavated holes (initially 10-m wide and 2-m deep, with sides as steep as 35°) in an energetic surfzone are consistent with diffusive smoothing by gravity. Specifically, comparisons of κ estimated from the measured bed evolution with those estimated with numerical model results for several transport theories suggest that gravity-driven sediment transport dominates the bed evolution, with κ proportional to a power of τb. The models are initiated with observed bathymetry and forced with observed waves and currents. The diffusion coefficients from the measurements and from the model simulations were on average of order 10-5 m2/s, implying evolution time scales of days for features with length scales of 10 m. The dependence of κ on τb varies for different transport theories and for high and low shear stress regimes. The US Army Corps of Engineers Field Research Facility, Duck, NC provided excellent logistical support. Funded by a National Security Science and Engineering Faculty Fellowship, a National Defense Science and Engineering Graduate Fellowship, and the Office of Naval Research.

A multiscale MD-FE model of diffusion in composite media with internal surface interaction based on numerical homogenization procedure.

PubMed

Kojic, M; Milosevic, M; Kojic, N; Kim, K; Ferrari, M; Ziemys, A

2014-02-01

Mass transport by diffusion within composite materials may depend not only on internal microstructural geometry, but also on the chemical interactions between the transported substance and the material of the microstructure. Retrospectively, there is a gap in methods and theory to connect material microstructure properties with macroscale continuum diffusion characteristics. Here we present a new hierarchical multiscale model for diffusion within composite materials that couples material microstructural geometry and interactions between diffusing particles and the material matrix. This model, which bridges molecular dynamics (MD) and the finite element (FE) method, is employed to construct a continuum diffusion model based on a novel numerical homogenization procedure. The procedure is general and robust for evaluating constitutive material parameters of the continuum model. These parameters include the traditional bulk diffusion coefficients and, additionally, the distances from the solid surface accounting for surface interaction effects. We implemented our models to glucose diffusion through the following two geometrical/material configurations: tightly packed silica nanospheres, and a complex fibrous structure surrounding nanospheres. Then, rhodamine 6G diffusion analysis through an aga-rose gel network was performed, followed by a model validation using our experimental results. The microstructural model, numerical homogenization and continuum model offer a new platform for modeling and predicting mass diffusion through complex biological environment and within composite materials that are used in a wide range of applications, like drug delivery and nanoporous catalysts.

A multiscale MD–FE model of diffusion in composite media with internal surface interaction based on numerical homogenization procedure

PubMed Central

Kojic, M.; Milosevic, M.; Kojic, N.; Kim, K.; Ferrari, M.; Ziemys, A.

2014-01-01

Mass transport by diffusion within composite materials may depend not only on internal microstructural geometry, but also on the chemical interactions between the transported substance and the material of the microstructure. Retrospectively, there is a gap in methods and theory to connect material microstructure properties with macroscale continuum diffusion characteristics. Here we present a new hierarchical multiscale model for diffusion within composite materials that couples material microstructural geometry and interactions between diffusing particles and the material matrix. This model, which bridges molecular dynamics (MD) and the finite element (FE) method, is employed to construct a continuum diffusion model based on a novel numerical homogenization procedure. The procedure is general and robust for evaluating constitutive material parameters of the continuum model. These parameters include the traditional bulk diffusion coefficients and, additionally, the distances from the solid surface accounting for surface interaction effects. We implemented our models to glucose diffusion through the following two geometrical/material configurations: tightly packed silica nanospheres, and a complex fibrous structure surrounding nanospheres. Then, rhodamine 6G diffusion analysis through an aga-rose gel network was performed, followed by a model validation using our experimental results. The microstructural model, numerical homogenization and continuum model offer a new platform for modeling and predicting mass diffusion through complex biological environment and within composite materials that are used in a wide range of applications, like drug delivery and nanoporous catalysts. PMID:24578582

Diffusive flux in a model of stochastically gated oxygen transport in insect respiration

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

Berezhkovskii, Alexander M.; Shvartsman, Stanislav Y.

Oxygen delivery to insect tissues is controlled by transport through a branched tubular network that is connected to the atmosphere by valve-like gates, known as spiracles. In certain physiological regimes, the spiracles appear to be randomly switching between open and closed states. Quantitative analysis of this regime leads a reaction-diffusion problem with stochastically switching boundary condition. We derive an expression for the diffusive flux at long times in this problem. Our approach starts with the derivation of the passage probability for a single particle that diffuses between a stochastically gated boundary, which models the opening and closing spiracle, and themore » perfectly absorbing boundary, which models oxygen absorption by the tissue. This passage probability is then used to derive an expression giving the diffusive flux as a function of the geometric parameters of the tube and characteristic time scales of diffusion and gate dynamics.« less

Diffusive flux in a model of stochastically gated oxygen transport in insect respiration.

PubMed

Berezhkovskii, Alexander M; Shvartsman, Stanislav Y

2016-05-28

Oxygen delivery to insect tissues is controlled by transport through a branched tubular network that is connected to the atmosphere by valve-like gates, known as spiracles. In certain physiological regimes, the spiracles appear to be randomly switching between open and closed states. Quantitative analysis of this regime leads a reaction-diffusion problem with stochastically switching boundary condition. We derive an expression for the diffusive flux at long times in this problem. Our approach starts with the derivation of the passage probability for a single particle that diffuses between a stochastically gated boundary, which models the opening and closing spiracle, and the perfectly absorbing boundary, which models oxygen absorption by the tissue. This passage probability is then used to derive an expression giving the diffusive flux as a function of the geometric parameters of the tube and characteristic time scales of diffusion and gate dynamics.

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

Perriot, Romain; Uberuaga, Blas P.; Zamora, Richard J.

Diffusion in complex oxides is critical to ionic transport, radiation damage evolution, sintering, and aging. In complex oxides such as pyrochlores, anionic diffusion is dramatically affected by cation disorder. However, little is known about how disorder influences cation transport. Here, we report results from classical and accelerated molecular dynamics simulations of vacancy-mediated cation diffusion in Gd 2Ti 2O 7 pyrochlore, on the microsecond timescale. We find that diffusion is slow at low levels of disorder, while higher disorder allows for fast diffusion, which is then accompanied by antisite annihilation and reordering, and thus a slowing of cation transport. Cation diffusivitymore » is therefore not constant, but decreases as the material reorders. We also show that fast cation diffusion is triggered by the formation of a percolation network of antisites. This is in contrast with observations from other complex oxides and disordered media models, suggesting a fundamentally different relation between disorder and mass transport.« less

Ionic-Electronic Ambipolar Transport in Metal Halide Perovskites: Can Electronic Conductivity Limit Ionic Diffusion?

PubMed

Kerner, Ross A; Rand, Barry P

2018-01-04

Ambipolar transport describes the nonequilibrium, coupled motion of positively and negatively charged particles to ensure that internal electric fields remain small. It is commonly invoked in the semiconductor community where the motion of excess electrons and holes drift and diffuse together. However, the concept of ambipolar transport is not limited to semiconductor physics. Materials scientists working on ion conducting ceramics understand ambipolar transport dictates the coupled diffusion of ions and the rate is limited by the ion with the lowest diffusion coefficient. In this Perspective, we review a third application of ambipolar transport relevant to mixed ionic-electronic conducting materials for which the motion of ions is expected to be coupled to electronic carriers. In this unique situation, the ambipolar diffusion model has been successful at explaining the photoenhanced diffusion of metal ions in chalcogenide glasses and other properties of materials. Recent examples of photoenhanced phenomena in metal halide perovskites are discussed and indicate that mixed ionic-electronic ambipolar transport is similarly important for a deep understanding of these emerging materials.

The role of intraluminal thrombus on oxygen transport in abdominal aortic aneurysms

NASA Astrophysics Data System (ADS)

Madhavan, Sudharsan; Cherry Kemmerling, Erica

2017-11-01

Abdominal aortic aneurysm is ranked as the 13th leading cause of death in the United States. The presence of intraluminal thrombus is thought to cause hypoxia in the vessel wall eventually aggravating the condition. Our work investigates oxygen transport and consumption in a patient-specific model of an abdominal aortic aneurysm. The model includes intraluminal thrombus and consists of the abdominal aorta, renal arteries, and iliac arteries. Oxygen transport to and within the aortic wall layer was modeled, accounting for oxygen consumption and diffusion. Flow and transport in the lumen layer were modeled using coupled Navier-Stokes and scalar transport equations. The thrombus layer was assumed to be biomechanically inactive but permeable to oxygen transport in accordance with previously-measured diffusion coefficients. Plots of oxygen concentration through the layers illustrating reduced oxygen supply to the vessel walls in parts of the model that include thrombus will be presented.

An improved model of fission gas atom transport in irradiated uranium dioxide

NASA Astrophysics Data System (ADS)

Shea, J. H.

2018-04-01

The hitherto standard approach to predicting fission gas release has been a pure diffusion gas atom transport model based upon Fick's law. An additional mechanism has subsequently been identified from experimental data at high burnup and has been summarised in an empirical model that is considered to embody a so-called fuel matrix 'saturation' phenomenon whereby the fuel matrix has become saturated with fission gas so that the continued addition of extra fission gas atoms results in their expulsion from the fuel matrix into the fuel rod plenum. The present paper proposes a different approach by constructing an enhanced fission gas transport law consisting of two components: 1) Fick's law and 2) a so-called drift term. The new transport law can be shown to be effectively identical in its predictions to the 'saturation' approach and is more readily physically justifiable. The method introduces a generalisation of the standard diffusion equation which is dubbed the Drift Diffusion Equation. According to the magnitude of a dimensionless Péclet number, P, the new equation can vary from pure diffusion to pure drift, which latter represents a collective motion of the fission gas atoms through the fuel matrix at a translational velocity. Comparison is made between the saturation and enhanced transport approaches. Because of its dependence on P, the Drift Diffusion Equation is shown to be more effective at managing the transition from one type of limiting transport phenomenon to the other. Thus it can adapt appropriately according to the reactor operation.

Transport Imaging of Spatial Distribution of Mobility-Lifetime (Micro Tau) Product in Bulk Semiconductors for Nuclear Radiation Detection

DTIC Science & Technology

2012-06-01

the diffusion length L and the mobility-lifetime product  from the luminescence distribution using the 2D model for transport imaging in bulk...C. Scandrett, and N. M. Haegel, “Three-dimensional transport imaging for the spatially resolved determination of carrier diffusion length in bulk...that allows measurements of the diffusion length and extraction of the  product in luminescent materials without the need for device processing

Measurement and modelling of reactive transport in geological barriers for nuclear waste containment

DOE PAGES

Xiong, Qingrong; Joseph, Claudia; Schmeide, Katja; ...

2015-10-26

Compacted clays are considered as excellent candidates for barriers to radionuclide transport in future repositories for nuclear waste due to their very low hydraulic permeability. Diffusion is the dominant transport mechanism, controlled by a nano-scale pore system. Assessment of the clays' long-term containment function requires adequate modelling of such pore systems and their evolution. Existing characterisation techniques do not provide complete pore space information for effective modelling, such as pore and throat size distributions and connectivity. Special network models for reactive transport are proposed here using the complimentary character of the pore space and the solid phase. Here, this balancesmore » the insufficient characterisation information and provides the means for future mechanical–physical–chemical coupling. The anisotropy and heterogeneity of clays is represented using different length parameters and percentage of pores in different directions. Resulting networks are described as mathematical graphs with efficient discrete calculus formulation of transport. Opalinus Clay (OPA) is chosen as an example. Experimental data for the tritiated water (HTO) and U(VI) diffusion through OPA are presented. Calculated diffusion coefficients of HTO and uranium species are within the ranges of the experimentally determined data in different clay directions. This verifies the proposed pore network model and validates that uranium complexes are diffusing as neutral species in OPA. In the case of U(VI) diffusion the method is extended to account for sorption and convection. Finally, rather than changing pore radii by coarse grained mathematical formula, physical sorption is simulated in each pore, which is more accurate and realistic.« less

Measurement and modelling of reactive transport in geological barriers for nuclear waste containment.

PubMed

Xiong, Qingrong; Joseph, Claudia; Schmeide, Katja; Jivkov, Andrey P

2015-11-11

Compacted clays are considered as excellent candidates for barriers to radionuclide transport in future repositories for nuclear waste due to their very low hydraulic permeability. Diffusion is the dominant transport mechanism, controlled by a nano-scale pore system. Assessment of the clays' long-term containment function requires adequate modelling of such pore systems and their evolution. Existing characterisation techniques do not provide complete pore space information for effective modelling, such as pore and throat size distributions and connectivity. Special network models for reactive transport are proposed here using the complimentary character of the pore space and the solid phase. This balances the insufficient characterisation information and provides the means for future mechanical-physical-chemical coupling. The anisotropy and heterogeneity of clays is represented using different length parameters and percentage of pores in different directions. Resulting networks are described as mathematical graphs with efficient discrete calculus formulation of transport. Opalinus Clay (OPA) is chosen as an example. Experimental data for the tritiated water (HTO) and U(vi) diffusion through OPA are presented. Calculated diffusion coefficients of HTO and uranium species are within the ranges of the experimentally determined data in different clay directions. This verifies the proposed pore network model and validates that uranium complexes are diffusing as neutral species in OPA. In the case of U(vi) diffusion the method is extended to account for sorption and convection. Rather than changing pore radii by coarse grained mathematical formula, physical sorption is simulated in each pore, which is more accurate and realistic.

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.

From conservative to reactive transport under diffusion-controlled conditions

NASA Astrophysics Data System (ADS)

Babey, Tristan; de Dreuzy, Jean-Raynald; Ginn, Timothy R.

2016-05-01

We assess the possibility to use conservative transport information, such as that contained in transit time distributions, breakthrough curves and tracer tests, to predict nonlinear fluid-rock interactions in fracture/matrix or mobile/immobile conditions. Reference simulated data are given by conservative and reactive transport simulations in several diffusive porosity structures differing by their topological organization. Reactions includes nonlinear kinetically controlled dissolution and desorption. Effective Multi-Rate Mass Transfer models (MRMT) are calibrated solely on conservative transport information without pore topology information and provide concentration distributions on which effective reaction rates are estimated. Reference simulated reaction rates and effective reaction rates evaluated by MRMT are compared, as well as characteristic desorption and dissolution times. Although not exactly equal, these indicators remain very close whatever the porous structure, differing at most by 0.6% and 10% for desorption and dissolution. At early times, this close agreement arises from the fine characterization of the diffusive porosity close to the mobile zone that controls fast mobile-diffusive exchanges. At intermediate to late times, concentration gradients are strongly reduced by diffusion, and reactivity can be captured by a very limited number of rates. We conclude that effective models calibrated solely on conservative transport information like MRMT can accurately estimate monocomponent kinetically controlled nonlinear fluid-rock interactions. Their relevance might extend to more advanced biogeochemical reactions because of the good characterization of conservative concentration distributions, even by parsimonious models (e.g., MRMT with 3-5 rates). We propose a methodology to estimate reactive transport from conservative transport in mobile-immobile conditions.

Monte Carlo Transport for Electron Thermal Transport

NASA Astrophysics Data System (ADS)

Chenhall, Jeffrey; Cao, Duc; Moses, Gregory

2015-11-01

The iSNB (implicit Schurtz Nicolai Busquet multigroup electron thermal transport method of Cao et al. is adapted into a Monte Carlo transport method in order to better model the effects of non-local behavior. The end goal is a hybrid transport-diffusion method that combines Monte Carlo Transport with a discrete diffusion Monte Carlo (DDMC). The hybrid method will combine the efficiency of a diffusion method in short mean free path regions with the accuracy of a transport method in long mean free path regions. The Monte Carlo nature of the approach allows the algorithm to be massively parallelized. Work to date on the method will be presented. This work was supported by Sandia National Laboratory - Albuquerque and the University of Rochester Laboratory for Laser Energetics.

Calculation of effective transport properties of partially saturated gas diffusion layers

NASA Astrophysics Data System (ADS)

Bednarek, Tomasz; Tsotridis, Georgios

2017-02-01

A large number of currently available Computational Fluid Dynamics numerical models of Polymer Electrolyte Membrane Fuel Cells (PEMFC) are based on the assumption that porous structures are mainly considered as thin and homogenous layers, hence the mass transport equations in structures such as Gas Diffusion Layers (GDL) are usually modelled according to the Darcy assumptions. Application of homogenous models implies that the effects of porous structures are taken into consideration via the effective transport properties of porosity, tortuosity, permeability (or flow resistance), diffusivity, electric and thermal conductivity. Therefore, reliable values of those effective properties of GDL play a significant role for PEMFC modelling when employing Computational Fluid Dynamics, since these parameters are required as input values for performing the numerical calculations. The objective of the current study is to calculate the effective transport properties of GDL, namely gas permeability, diffusivity and thermal conductivity, as a function of liquid water saturation by using the Lattice-Boltzmann approach. The study proposes a method of uniform water impregnation of the GDL based on the "Fine-Mist" assumption by taking into account the surface tension of water droplets and the actual shape of GDL pores.

Finite Difference Formulation for Prediction of Water Pollution

NASA Astrophysics Data System (ADS)

Johari, Hanani; Rusli, Nursalasawati; Yahya, Zainab

2018-03-01

Water is an important component of the earth. Human being and living organisms are demand for the quality of water. Human activity is one of the causes of the water pollution. The pollution happened give bad effect to the physical and characteristic of water contents. It is not practical to monitor all aspects of water flow and transport distribution. So, in order to help people to access to the polluted area, a prediction of water pollution concentration must be modelled. This study proposed a one-dimensional advection diffusion equation for predicting the water pollution concentration transport. The numerical modelling will be produced in order to predict the transportation of water pollution concentration. In order to approximate the advection diffusion equation, the implicit Crank Nicolson is used. For the purpose of the simulation, the boundary condition and initial condition, the spatial steps and time steps as well as the approximations of the advection diffusion equation have been encoded. The results of one dimensional advection diffusion equation have successfully been used to predict the transportation of water pollution concentration by manipulating the velocity and diffusion parameters.

Direct monitoring of wind-induced pressure-pumping on gas transport in soil

NASA Astrophysics Data System (ADS)

Laemmel, Thomas; Mohr, Manuel; Schindler, Dirk; Schack-Kirchner, Helmer; Maier, Martin

2017-04-01

Gas exchange between soil and atmosphere is important for the biogeochemistry of soils and is commonly assumed to be governed by molecular diffusion. Yet a few previous field studies identified other gas transport processes such as wind-induced pressure-pumping to enhance soil-atmosphere fluxes significantly. However, since these wind-induced non-diffusive gas transport processes in soil often occur intermittently, the quantification of their contribution to soil gas emissions is challenging. To quantify the effects of wind-induced pressure-pumping on soil gas transport, we developed a method for in situ monitoring of soil gas transport. The method includes the use of Helium (He) as a tracer gas which was continuously injected into the soil. The resulting He steady-state concentration profile was monitored. Gas transport parameters of the soil were inversely modelled. We used our method during a field campaign in a well-aerated forest soil over three months. During periods of low wind speed, soil gas transport was modelled assuming diffusion as transport process. During periods of high wind speed, the previously steady diffusive He concentration profile showed temporary concentration decreases in the topsoil, indicating an increase of the effective gas transport rate in the topsoil up to 30%. The enhancement of effective topsoil soil gas diffusivity resulted from wind-induced air pressure fluctuations which are referred to as pressure-pumping. These air pressure fluctuations had frequencies between 0.1 and 0.01 Hz and amplitudes up to 10 Pa and occurred at above-canopy wind speeds greater than 5 m s-1. We could show the importance of the enhancement of the gas transport rate in relation with the wind intensity and corresponding air pressure fluctuations characteristics. We directly detected and quantified the pressure-pumping effect on gas transport in soil in a field study for the first time, and could thus validate and underpin the importance of this non-diffusive gas transport process. Our method can also be used to study other non-diffusive gas transport processes occurring in soil and snow, and their possible feedbacks or interactions with biogeochemical processes.

Anomalous transport in the crowded world of biological cells

NASA Astrophysics Data System (ADS)

Höfling, Felix; Franosch, Thomas

2013-04-01

A ubiquitous observation in cell biology is that the diffusive motion of macromolecules and organelles is anomalous, and a description simply based on the conventional diffusion equation with diffusion constants measured in dilute solution fails. This is commonly attributed to macromolecular crowding in the interior of cells and in cellular membranes, summarizing their densely packed and heterogeneous structures. The most familiar phenomenon is a sublinear, power-law increase of the mean-square displacement (MSD) as a function of the lag time, but there are other manifestations like strongly reduced and time-dependent diffusion coefficients, persistent correlations in time, non-Gaussian distributions of spatial displacements, heterogeneous diffusion and a fraction of immobile particles. After a general introduction to the statistical description of slow, anomalous transport, we summarize some widely used theoretical models: Gaussian models like fractional Brownian motion and Langevin equations for visco-elastic media, the continuous-time random walk model, and the Lorentz model describing obstructed transport in a heterogeneous environment. Particular emphasis is put on the spatio-temporal properties of the transport in terms of two-point correlation functions, dynamic scaling behaviour, and how the models are distinguished by their propagators even if the MSDs are identical. Then, we review the theory underlying commonly applied experimental techniques in the presence of anomalous transport like single-particle tracking, fluorescence correlation spectroscopy (FCS) and fluorescence recovery after photobleaching (FRAP). We report on the large body of recent experimental evidence for anomalous transport in crowded biological media: in cyto- and nucleoplasm as well as in cellular membranes, complemented by in vitro experiments where a variety of model systems mimic physiological crowding conditions. Finally, computer simulations are discussed which play an important role in testing the theoretical models and corroborating the experimental findings. The review is completed by a synthesis of the theoretical and experimental progress identifying open questions for future investigation.

Mathematical modelling of the uptake and transport of salt in plant roots.

PubMed

Foster, Kylie J; Miklavcic, Stanley J

2013-11-07

In this paper, we present and discuss a mathematical model of ion uptake and transport in roots of plants. The underlying physical model of transport is based on the mechanisms of forced diffusion and convection. The model can take account of local variations in effective ion and water permeabilities across the major tissue regions of plant roots, represented through a discretized coupled system of governing equations including mass balance, forced diffusion, convection and electric potential. We present simulation results of an exploration of the consequent enormous parameter space. Among our findings we identify the electric potential as a major factor affecting ion transport across, and accumulation in, root tissues. We also find that under conditions of a constant but realistic level of bulk soil salt concentration and plant-soil hydraulic pressure, diffusion plays a significant role even when convection by the water transpiration stream is operating. Crown Copyright © 2013 Published by Elsevier Ltd. All rights reserved.

Three mechanisms model of shale gas in real state transport through a single nanopore

NASA Astrophysics Data System (ADS)

Li, Dongdong; Zhang, Yanyu; Sun, Xiaofei; Li, Peng; Zhao, Fengkai

2018-02-01

At present, the apparent permeability models of shale gas consider only the viscous flow and Knudsen diffusion of free gas, but do not take into account the influence of surface diffusion. Moreover, it is assumed that shale gas is in ideal state. In this paper, shale gas is assumed in real state, a new apparent permeability model for shale gas transport through a single nanopore is developed that captures many important migration mechanisms, such as viscous flow and Knudsen diffusion of free gas, surface diffusion of adsorbed gas. According to experimental data, the accuracy of apparent permeability model was verified. What’s more, the effects of pressure and pore radius on apparent permeability, and the effects on the permeability fraction of viscous flow, Knudsen diffusion and surface diffusion were analysed, separately. Finally, the results indicate that the error of the developed model in this paper was 3.02%, which is less than the existing models. Pressure and pore radius seriously affect the apparent permeability of shale gas. When the pore radius is small or pressure is low, the surface diffusion cannot be ignored. When the pressure and the pore radius is big, the viscous flow occupies the main position.

Evidence for percolation diffusion of cations and reordering in disordered pyrochlore from accelerated molecular dynamics

DOE PAGES

Perriot, Romain; Uberuaga, Blas P.; Zamora, Richard J.; ...

2017-09-20

Diffusion in complex oxides is critical to ionic transport, radiation damage evolution, sintering, and aging. In complex oxides such as pyrochlores, anionic diffusion is dramatically affected by cation disorder. However, little is known about how disorder influences cation transport. Here, we report results from classical and accelerated molecular dynamics simulations of vacancy-mediated cation diffusion in Gd 2Ti 2O 7 pyrochlore, on the microsecond timescale. We find that diffusion is slow at low levels of disorder, while higher disorder allows for fast diffusion, which is then accompanied by antisite annihilation and reordering, and thus a slowing of cation transport. Cation diffusivitymore » is therefore not constant, but decreases as the material reorders. We also show that fast cation diffusion is triggered by the formation of a percolation network of antisites. This is in contrast with observations from other complex oxides and disordered media models, suggesting a fundamentally different relation between disorder and mass transport.« less

A diffusive ink transport model for lipid dip-pen nanolithography.

PubMed

Urtizberea, A; Hirtz, M

2015-10-14

Despite diverse applications, phospholipid membrane stacks generated by dip-pen nanolithography (DPN) still lack a thorough and systematic characterization that elucidates the whole ink transport process from writing to surface spreading, with the aim of better controlling the resulting feature size and resolution. We report a quantitative analysis and modeling of the dependence of lipid DPN features (area, height and volume) on dwell time and relative humidity. The ink flow rate increases with humidity in agreement with meniscus size growth, determining the overall feature size. The observed time dependence indicates the existence of a balance between surface spreading and the ink flow rate that promotes differences in concentration at the meniscus/substrate interface. Feature shape is controlled by the substrate surface energy. The results are analyzed within a modified model for the ink transport of diffusive inks. At any humidity the dependence of the area spread on the dwell time shows two diffusion regimes: at short dwell times growth is controlled by meniscus diffusion while at long dwell times surface diffusion governs the process. The critical point for the switch of regime depends on the humidity.

The improvement of the method of equivalent cross section in HTR

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

Guo, J.; Li, F.

The Method of Equivalence Cross-Sections (MECS) is a combined transport-diffusion method. By appropriately adjusting the diffusion coefficient of homogenized absorber region, the diffusion theory could yield satisfactory results for the full core model with strong neutron absorber material, for example the control rod in High temperature gas cooled reactor (HTR). Original implementation of MECS based on 1-D cell transport model has some limitation on accuracy and applicability, a new implementation of MECS based on 2-D transport model are proposed and tested in this paper. This improvement can extend the MECS to the calculation of twin small absorber ball system whichmore » have a non-circular boring in graphite reflector and different radial position. A least-square algorithm for the calculation of equivalent diffusion coefficient is adopted, and special treatment for diffusion coefficient for higher energy group is proposed in the case that absorber is absent. Numerical results to adopt MECS into control rod calculation in HTR are encouraging. However, there are some problems left. (authors)« less

Random walk, diffusion and mixing in simulations of scalar transport in fluid flows

NASA Astrophysics Data System (ADS)

Klimenko, A. Y.

2008-12-01

Physical similarity and mathematical equivalence of continuous diffusion and particle random walk form one of the cornerstones of modern physics and the theory of stochastic processes. In many applied models used in simulation of turbulent transport and turbulent combustion, mixing between particles is used to reflect the influence of the continuous diffusion terms in the transport equations. We show that the continuous scalar transport and diffusion can be accurately specified by means of mixing between randomly walking Lagrangian particles with scalar properties and assess errors associated with this scheme. This gives an alternative formulation for the stochastic process which is selected to represent the continuous diffusion. This paper focuses on statistical errors and deals with relatively simple cases, where one-particle distributions are sufficient for a complete description of the problem.

DESCRIPTION OF ATMOSPHERIC TRANSPORT PROCESSES IN EULERIAN AIR QUALITY MODELS

EPA Science Inventory

Key differences among many types of air quality models are the way atmospheric advection and turbulent diffusion processes are treated. Gaussian models use analytical solutions of the advection-diffusion equations. Lagrangian models use a hypothetical air parcel concept effecti...

Role of Electrostatic Interactions on the Transport of Druglike Molecules in Hydrogel-Based Articular Cartilage Mimics: Implications for Drug Delivery.

PubMed

Ye, Fengbin; Baldursdottir, Stefania; Hvidt, Søren; Jensen, Henrik; Larsen, Susan W; Yaghmur, Anan; Larsen, Claus; Østergaard, Jesper

2016-03-07

In the field of drug delivery to the articular cartilage, it is advantageous to apply artificial tissue models as surrogates of cartilage for investigating drug transport and release properties. In this study, artificial cartilage models consisting of 0.5% (w/v) agarose gel containing 0.5% (w/v) chondroitin sulfate or 0.5% (w/v) hyaluronic acid were developed, and their rheological and morphological properties were characterized. UV imaging was utilized to quantify the transport properties of the following four model compounds in the agarose gel and in the developed artificial cartilage models: H-Ala-β-naphthylamide, H-Lys-Lys-β-naphthylamide, lysozyme, and α-lactalbumin. The obtained results showed that the incorporation of the polyelectrolytes chondroitin sulfate or hyaluronic acid into agarose gel induced a significant reduction in the apparent diffusivities of the cationic model compounds as compared to the pure agarose gel. The decrease in apparent diffusivity of the cationic compounds was not caused by a change in the gel structure since a similar reduction in apparent diffusivity was not observed for the net negatively charged protein α-lactalbumin. The apparent diffusivity of the cationic compounds in the negatively charged hydrogels was highly dependent on the ionic strength, pointing out the importance of electrostatic interactions between the diffusant and the polyelectrolytes. Solution based affinity studies between the model compounds and the two investigated polyelectrolytes further confirmed the electrostatic nature of their interactions. The results obtained from the UV imaging diffusion studies are important for understanding the effect of drug physicochemical properties on the transport in articular cartilage. The extracted information may be useful in the development of hydrogels for in vitro release testing having features resembling the articular cartilage.

Phonon cross-plane transport and thermal boundary resistance: effect of heat source size and thermal boundary resistance on phonon characteristics

NASA Astrophysics Data System (ADS)

Ali, H.; Yilbas, B. S.

2016-09-01

Phonon cross-plane transport across silicon and diamond thin films pair is considered, and thermal boundary resistance across the films pair interface is examined incorporating the cut-off mismatch and diffusive mismatch models. In the cut-off mismatch model, phonon frequency mismatch for each acoustic branch is incorporated across the interface of the silicon and diamond films pair in line with the dispersion relations of both films. The frequency-dependent and transient solution of the Boltzmann transport equation is presented, and the equilibrium phonon intensity ratios at the silicon and diamond film edges are predicted across the interface for each phonon acoustic branch. Temperature disturbance across the edges of the films pair is incorporated to assess the phonon transport characteristics due to cut-off and diffusive mismatch models across the interface. The effect of heat source size, which is allocated at high-temperature (301 K) edge of the silicon film, on the phonon transport characteristics at the films pair interface is also investigated. It is found that cut-off mismatch model predicts higher values of the thermal boundary resistance across the films pair interface as compared to that of the diffusive mismatch model. The ratio of equilibrium phonon intensity due to the cut-off mismatch over the diffusive mismatch models remains >1 at the silicon edge, while it becomes <1 at the diamond edge for all acoustic branches.

Diffusive-convective physical vapor transport of PbTe from a Te-rich solid source

NASA Technical Reports Server (NTRS)

Zoutendyk, J.; Akutagawa, W.

1982-01-01

Crystal growth of PbTe by physical vapor transport (sublimation) in a closed ampoule is governed by the vapor species in thermal equilibrium with the solid compound. Deviations from stoichiometry in the source material cause diffusion limitation of the transport rate, which can be modified by natural (gravity-driven) convection. Mass-transport experiments have been performed using Te-rich material wherein sublimation rates have been measured in order to study the effects of natural convection in diffusion-limited vapor transport. Linear velocities for both crystal growth and evaporation (back sublimation) have been measured for transport in the direction of gravity, horizontally, and opposite to gravity. The experimental results are discussed in terms of both the one-dimensional diffusive-advective model and current, more sophisticated theory which includes natural convection. There is some evidence that convection effects from radial temperature gradients and solutal density gradients have been observed.

Application of Paramagnetically Tagged Molecules for Magnetic Resonance Imaging of Biofilm Mass Transport Processes▿

PubMed Central

Ramanan, B.; Holmes, W. M.; Sloan, W. T.; Phoenix, V. R.

2010-01-01

Molecules become readily visible by magnetic resonance imaging (MRI) when labeled with a paramagnetic tag. Consequently, MRI can be used to image their transport through porous media. In this study, we demonstrated that this method could be applied to image mass transport processes in biofilms. The transport of a complex of gadolinium and diethylenetriamine pentaacetic acid (Gd-DTPA), a commercially available paramagnetic molecule, was imaged both in agar (as a homogeneous test system) and in a phototrophic biofilm. The images collected were T1 weighted, where T1 is an MRI property of the biofilm and is dependent on Gd-DTPA concentration. A calibration protocol was applied to convert T1 parameter maps into concentration maps, thus revealing the spatially resolved concentrations of this tracer at different time intervals. Comparing the data obtained from the agar experiment with data from a one-dimensional diffusion model revealed that transport of Gd-DTPA in agar was purely via diffusion, with a diffusion coefficient of 7.2 × 10−10 m2 s−1. In contrast, comparison of data from the phototrophic biofilm experiment with data from a two-dimensional diffusion model revealed that transport of Gd-DTPA inside the biofilm was by both diffusion and advection, equivalent to a diffusion coefficient of 1.04 × 10−9 m2 s−1. This technology can be used to further explore mass transport processes in biofilms, either by using the wide range of commercially available paramagnetically tagged molecules and nanoparticles or by using bespoke tagged molecules. PMID:20435773

Modeling Nitrogen Fate and Transport at the Sediment-Water Interface

EPA Science Inventory

Diffusive mass transfer at media interfaces exerts control on the fate and transport of pollutants originating from agricultural and urban landscapes and affects the con-ditions of water bodies. Diffusion is essentially a physical process affecting the distribution and fate of va...

Diffuse Optics for Tissue Monitoring and Tomography

PubMed Central

Durduran, T; Choe, R; Baker, W B; Yodh, A G

2015-01-01

This review describes the diffusion model for light transport in tissues and the medical applications of diffuse light. Diffuse optics is particularly useful for measurement of tissue hemodynamics, wherein quantitative assessment of oxy- and deoxy-hemoglobin concentrations and blood flow are desired. The theoretical basis for near-infrared or diffuse optical spectroscopy (NIRS or DOS, respectively) is developed, and the basic elements of diffuse optical tomography (DOT) are outlined. We also discuss diffuse correlation spectroscopy (DCS), a technique whereby temporal correlation functions of diffusing light are transported through tissue and are used to measure blood flow. Essential instrumentation is described, and representative brain and breast functional imaging and monitoring results illustrate the workings of these new tissue diagnostics. PMID:26120204

Mathematical modeling of liquid/liquid hollow fiber membrane contactor accounting for interfacial transport phenomena: Extraction of lanthanides as a surrogate for actinides

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

Rogers, J.D.

1994-08-04

This report is divided into two parts. The second part is divided into the following sections: experimental protocol; modeling the hollow fiber extractor using film theory; Graetz model of the hollow fiber membrane process; fundamental diffusive-kinetic model; and diffusive liquid membrane device-a rigorous model. The first part is divided into: membrane and membrane process-a concept; metal extraction; kinetics of metal extraction; modeling the membrane contactor; and interfacial phenomenon-boundary conditions-applied to membrane transport.

Diffusion of a particle in the spatially correlated exponential random energy landscape: Transition from normal to anomalous diffusion.

PubMed

Novikov, S V

2018-01-14

Diffusive transport of a particle in a spatially correlated random energy landscape having exponential density of states has been considered. We exactly calculate the diffusivity in the nondispersive quasi-equilibrium transport regime for the 1D transport model and found that for slow decaying correlation functions the diffusivity becomes singular at some particular temperature higher than the temperature of the transition to the true non-equilibrium dispersive transport regime. It means that the diffusion becomes anomalous and does not follow the usual ∝ t 1/2 law. In such situation, the fully developed non-equilibrium regime emerges in two stages: first, at some temperature there is the transition from the normal to anomalous diffusion, and then at lower temperature the average velocity for the infinite medium goes to zero, thus indicating the development of the true dispersive regime. Validity of the Einstein relation is discussed for the situation where the diffusivity does exist. We provide also some arguments in favor of conservation of the major features of the new transition scenario in higher dimensions.

Mathematical model of water transport in Bacon and alkaline matrix-type hydrogen-oxygen fuel cells

NASA Technical Reports Server (NTRS)

Prokopius, P. R.; Easter, R. W.

1972-01-01

Based on general mass continuity and diffusive transport equations, a mathematical model was developed that simulates the transport of water in Bacon and alkaline-matrix fuel cells. The derived model was validated by using it to analytically reproduce various Bacon and matrix-cell experimental water transport transients.

Verification of Modelica-Based Models with Analytical Solutions for Tritium Diffusion

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

Rader, Jordan D.; Greenwood, Michael Scott; Humrickhouse, Paul W.

Here, tritium transport in metal and molten salt fluids combined with diffusion through high-temperature structural materials is an important phenomenon in both magnetic confinement fusion (MCF) and molten salt reactor (MSR) applications. For MCF, tritium is desirable to capture for fusion fuel. For MSRs, uncaptured tritium potentially can be released to the environment. In either application, quantifying the time- and space-dependent tritium concentration in the working fluid(s) and structural components is necessary.Whereas capability exists specifically for calculating tritium transport in such systems (e.g., using TMAP for fusion reactors), it is desirable to unify the calculation of tritium transport with othermore » system variables such as dynamic fluid and structure temperature combined with control systems such as those that might be found in a system code. Some capability for radioactive trace substance transport exists in thermal-hydraulic systems codes (e.g., RELAP5-3D); however, this capability is not coupled to species diffusion through solids. Combined calculations of tritium transport and thermal-hydraulic solution have been demonstrated with TRIDENT but only for a specific type of MSR.Researchers at Oak Ridge National Laboratory have developed a set of Modelica-based dynamic system modeling tools called TRANsient Simulation Framework Of Reconfigurable Models (TRANSFORM) that were used previously to model advanced fission reactors and associated systems. In this system, the augmented TRANSFORM library includes dynamically coupled fluid and solid trace substance transport and diffusion. Results from simulations are compared against analytical solutions for verification.« less

Verification of Modelica-Based Models with Analytical Solutions for Tritium Diffusion

DOE PAGES

Rader, Jordan D.; Greenwood, Michael Scott; Humrickhouse, Paul W.

2018-03-20

Here, tritium transport in metal and molten salt fluids combined with diffusion through high-temperature structural materials is an important phenomenon in both magnetic confinement fusion (MCF) and molten salt reactor (MSR) applications. For MCF, tritium is desirable to capture for fusion fuel. For MSRs, uncaptured tritium potentially can be released to the environment. In either application, quantifying the time- and space-dependent tritium concentration in the working fluid(s) and structural components is necessary.Whereas capability exists specifically for calculating tritium transport in such systems (e.g., using TMAP for fusion reactors), it is desirable to unify the calculation of tritium transport with othermore » system variables such as dynamic fluid and structure temperature combined with control systems such as those that might be found in a system code. Some capability for radioactive trace substance transport exists in thermal-hydraulic systems codes (e.g., RELAP5-3D); however, this capability is not coupled to species diffusion through solids. Combined calculations of tritium transport and thermal-hydraulic solution have been demonstrated with TRIDENT but only for a specific type of MSR.Researchers at Oak Ridge National Laboratory have developed a set of Modelica-based dynamic system modeling tools called TRANsient Simulation Framework Of Reconfigurable Models (TRANSFORM) that were used previously to model advanced fission reactors and associated systems. In this system, the augmented TRANSFORM library includes dynamically coupled fluid and solid trace substance transport and diffusion. Results from simulations are compared against analytical solutions for verification.« less

The influence of vertical sorbed phase transport on the fate of organic chemicals in surface soils.

PubMed

McLachlan, Michael S; Czub, Gertje; Wania, Frank

2002-11-15

Gaseous exchange between surface soil and the atmosphere is an important process in the environmental fate of many chemicals. It was hypothesized that this process is influenced by vertical transport of chemicals sorbed to soil particles. Vertical sorbed phase transport in surface soils occurs by many processes such as bioturbation, cryoturbation, and erosion into cracks formed by soil drying. The solution of the advection/diffusion equation proposed by Jury et al. to describe organic chemical fate in a uniformly contaminated surface soil was modified to include vertical sorbed phase transport This process was modeled using a sorbed phase diffusion coefficient, the value of which was derived from soil carbon mass balances in the literature. The effective diffusivity of the chemical in a typical soil was greater in the modified model than in the model without sorbed phase transport for compounds with log K(OW) > 2 and log K(OA) > 6. Within this chemical partitioning space, the rate of volatilization from the surface soil was larger in the modified model than in the original model by up to a factor of 65. The volatilization rate was insensitive to the value of the sorbed phase diffusion coefficient throughout much of this chemical partitioning space, indicating that the surface soil layer was essentially well-mixed and that the mass transfer coefficient was determined by diffusion through the atmospheric boundary layer only. When this process was included in a non-steady-state regional multimedia chemical fate model running with a generic emissions scenario to air, the predicted soil concentrations increased by upto a factor of 25,whilethe air concentrations decreased by as much as a factor of approximately 3. Vertical sorbed phase transport in the soil thus has a major impact on predicted air and soil concentrations, the state of equilibrium, and the direction and magnitude of the chemical flux between air and soil. It is a key process influencing the environmental fate of persistent organic pollutants (POPs).

Diffusion impact on atmospheric moisture transport

NASA Astrophysics Data System (ADS)

Moseley, C.; Haerter, J.; Göttel, H.; Hagemann, S.; Jacob, D.

2009-04-01

To ensure numerical stability, many global and regional climate models employ numerical diffusion to dampen short wavelength modes. Terrain following sigma diffusion is known to cause unphysical effects near the surface in orographically structured regions. They can be reduced by applying z-diffusion on geopotential height levels. We investigate the effect of the diffusion scheme on atmospheric moisture transport and precipitation formation at different resolutions in the European region. With respect to a better understanding of diffusion in current and future grid-space global models, current day regional models may serve as the appropriate tool for studies of the impact of diffusion schemes: Results can easily be constrained to a small test region and checked against reliable observations, which often are unavailable on a global scale. Special attention is drawn to the Alps - a region of strong topographic gradients and good observational coverage. Our study is further motivated by the appearance of the "summer drying problem" in South Eastern Europe. This too warm and too dry simulation of climate is common to many regional climate models and also to some global climate models, and remains a permanent unsolved problem in the community. We perform a systematic comparison of the two diffusion-schemes with respect to the hydrological cycle. In particular, we investigate how local meteorological quantities - such as the atmospheric moisture in the region east of the Alps - depend on the spatial model resolution. Higher model resolution would lead to a more accurate representation of the topography and entail larger gradients in the Alps. This could lead to consecutively stronger transport of moisture along the slopes in the case of sigma-diffusion with subsequent orographic precipitation, whereas the effect could be qualitatively different in the case of z-diffusion. For our study, we analyse a sequence of simulations of the regional climate model REMO employing the different diffusion methods over Europe. For these simulations, REMO was forced at the lateral boundaries with ERA40 reanalysis data for a five year period. For our higher resolution simulations we employ the double nesting technique.

Modelling effects of tree population dynamics, tree throw and pit-mound formation/diffusion on microtopography over time in different forest settings

NASA Astrophysics Data System (ADS)

Martin, Y. E.; Johnson, E. A.; Gallaway, J.; Chaikina, O.

2011-12-01

Herein we conduct a followup investigation to an earlier research project in which we developed a numerical model of tree population dynamics, tree throw, and sediment transport associated with the formation of pit-mound features for Hawk Creek watershed, Canadian Rockies (Gallaway et al., 2009). We extend this earlier work by exploring the most appropriate transport relations to simulate the diffusion over time of newly-formed pit-pound features due to tree throw. We combine our earlier model with a landscape development model that can incorporate these diffusive transport relations. Using these combined models, changes in hillslope microtopography over time associated with the formation of pit-mound features and their decay will be investigated. The following ideas have motivated this particular study: (i) Rates of pit-mound degradation remain a source of almost complete speculation, as there is almost no long-term information on process rates. Therefore, we will attempt to tackle the issue of pit-mound degradation in a methodical way that can guide future field studies; (ii) The degree of visible pit-mound topography at any point in time on the landscape is a joint function of the rate of formation of new pit-mound features due to tree death/topple and their magnitude vs. the rate of decay of pit-mound features. An example of one interesting observation that arises is the following: it appears that pit-mound topography is often more pronounced in some eastern North American forests vs. field sites along the eastern slopes of the Canadian Rockies. Why is this the case? Our investigation begins by considering whether pit-mound decay might occur by linear or nonlinear diffusion. What differences might arise depending on which diffusive approach is adopted? What is the magnitude of transport rates associated with these possible forms of transport relations? We explore linear and nonlinear diffusion at varying rates and for different sizes of pit-mound pairs using a numerical modelling approach. Model results suggest that longevity of pit-mound features is dependent on: (i) magnitude/dimensions of initial pit-mound features for forests in different regions; (ii) defining appropriate pit-mound diffusion rates for these different forests (unfortunately, almost no appropriate field observations exist for calibration of these transport relations). In the next stage of this research, we will combine our earlier model of forest disturbance/tree population dynamics, tree throw and pit-mound formation with the numerical model LandMod (Martin, 1998, 2000, 2007); the latter will be used to simulate pit-mound diffusion over time. In this way, we can observe changes in hillslope microtopographic signatures over time that are found in different forest settings.

Gas diffusivity and permeability through the firn column at Summit, Greenland: measurements and comparison to microstructural properties

NASA Astrophysics Data System (ADS)

Adolph, A. C.; Albert, M. R.

2014-02-01

The physical structure of polar firn plays a key role in the mechanisms by which glaciers and ice sheets preserve a natural archive of past atmospheric composition. This study presents the first measurements of gas diffusivity and permeability along with microstructural information measured from the near-surface firn through the firn column to pore close-off. Both fine- and coarse-grained firn from Summit, Greenland are included in this study to investigate the variability in firn caused by seasonal and storm-event layering. Our measurements reveal that the porosity of firn (derived from density) is insufficient to describe the full profiles of diffusivity and permeability, particularly at porosity values above 0.5. Thus, even a model that could perfectly predict the density profile would be insufficient for application to issues involving gas transport. The measured diffusivity profile presented here is compared to two diffusivity profiles modeled from firn air measurements from Summit. Because of differences in scale and in firn processes between the true field situation, firn modeling, and laboratory measurements, the results follow a similar overall pattern but do not align; our results constitute a lower bound on diffusive transport. In comparing our measurements of both diffusivity and permeability to previous parameterizations from numerical 3-D lattice-Boltzmann modeling, it is evident that the previous relationships to porosity are likely site-specific. We present parameterizations relating diffusivity and permeability to porosity as a possible tool, though use of direct measurements would be far more accurate when feasible. The relationships between gas transport properties and microstructural properties are characterized and compared to existing relationships for general porous media, specifically the Katz-Thompson (KT), Kozeny-Carman (KC), and Archie's law approximations. While those approximations can capture the general trend of gas transport relationships, they result in high errors for individual samples and fail to fully describe firn variability, particularly the differences between coarse- and fine-grained firn. We present a direct power law relationship between permeability and gas diffusivity based on our co-located measurements; further research will indicate if this type of relationship is site-specific. This set of measurements and relationships contributes a unique starting point for future investigations in developing more physically based models of firn gas transport.

A diffusive ink transport model for lipid dip-pen nanolithography

NASA Astrophysics Data System (ADS)

Urtizberea, A.; Hirtz, M.

2015-09-01

Despite diverse applications, phospholipid membrane stacks generated by dip-pen nanolithography (DPN) still lack a thorough and systematic characterization that elucidates the whole ink transport process from writing to surface spreading, with the aim of better controlling the resulting feature size and resolution. We report a quantitative analysis and modeling of the dependence of lipid DPN features (area, height and volume) on dwell time and relative humidity. The ink flow rate increases with humidity in agreement with meniscus size growth, determining the overall feature size. The observed time dependence indicates the existence of a balance between surface spreading and the ink flow rate that promotes differences in concentration at the meniscus/substrate interface. Feature shape is controlled by the substrate surface energy. The results are analyzed within a modified model for the ink transport of diffusive inks. At any humidity the dependence of the area spread on the dwell time shows two diffusion regimes: at short dwell times growth is controlled by meniscus diffusion while at long dwell times surface diffusion governs the process. The critical point for the switch of regime depends on the humidity.Despite diverse applications, phospholipid membrane stacks generated by dip-pen nanolithography (DPN) still lack a thorough and systematic characterization that elucidates the whole ink transport process from writing to surface spreading, with the aim of better controlling the resulting feature size and resolution. We report a quantitative analysis and modeling of the dependence of lipid DPN features (area, height and volume) on dwell time and relative humidity. The ink flow rate increases with humidity in agreement with meniscus size growth, determining the overall feature size. The observed time dependence indicates the existence of a balance between surface spreading and the ink flow rate that promotes differences in concentration at the meniscus/substrate interface. Feature shape is controlled by the substrate surface energy. The results are analyzed within a modified model for the ink transport of diffusive inks. At any humidity the dependence of the area spread on the dwell time shows two diffusion regimes: at short dwell times growth is controlled by meniscus diffusion while at long dwell times surface diffusion governs the process. The critical point for the switch of regime depends on the humidity. Electronic supplementary information (ESI) available. See DOI: 10.1039/c5nr04352b

Multidrug efflux transporter activity in sea urchin embryos:Does localization provide a diffusive advantage?

NASA Astrophysics Data System (ADS)

Song, Xianfeng; Setayeshgar, Sima; Cole, Bryan; Hamdoun, Amro; Epel, David

2008-03-01

Experiments have shown upregulation of multidrug efflux transporter activity approximately 30 min after fertilization in the sea urchin embryo [1]. These ATP-hydrolyzing transporter proteins pump moderately hydrophobic molecules out of the cell and represent the cell's first line of defense againstexogenous toxins. It has also been shown that transporters are moved in vesicles along microfilaments and localized to tips of microvilli prior to activation. We have constructed a geometrically realistic model of the embryo, including microvilli, to explore the functional role of this localization in the efficient elimination of toxins from the standpoint of diffusion. We compute diffusion of toxins in extracellular, membrane and intracellular spaces coupled with transporter activity, using experimentally derived values for physical parameters. For transporters uniformly distributed along microvilli and tip-localized transporters we compare regions in parameter space where each distribution provides diffusive advantage, and comment on the physically expected conditions. [1] A. M. Hamdoun, G. N. Cherr, T. A. Roepke and D. Epel, Developmental Biology 276 452 (2004).

Predicting the weathering of fuel and oil spills: A diffusion-limited evaporation model.

PubMed

Kotzakoulakis, Konstantinos; George, Simon C

2018-01-01

The majority of the evaporation models currently available in the literature for the prediction of oil spill weathering do not take into account diffusion-limited mass transport and the formation of a concentration gradient in the oil phase. The altered surface concentration of the spill caused by diffusion-limited transport leads to a slower evaporation rate compared to the predictions of diffusion-agnostic evaporation models. The model presented in this study incorporates a diffusive layer in the oil phase and predicts the diffusion-limited evaporation rate. The information required is the composition of the fluid from gas chromatography or alternatively the distillation data. If the density or a single viscosity measurement is available the accuracy of the predictions is higher. Environmental conditions such as water temperature, air pressure and wind velocity are taken into account. The model was tested with synthetic mixtures, petroleum fuels and crude oils with initial viscosities ranging from 2 to 13,000 cSt. The tested temperatures varied from 0 °C to 23.4 °C and wind velocities from 0.3 to 3.8 m/s. The average absolute deviation (AAD) of the diffusion-limited model ranged between 1.62% and 24.87%. In comparison, the AAD of a diffusion-agnostic model ranged between 2.34% and 136.62% against the same tested fluids. Copyright © 2017 Elsevier Ltd. All rights reserved.

Experimental validation of convection-diffusion discretisation scheme employed for computational modelling of biological mass transport

PubMed Central

2010-01-01

Background The finite volume solver Fluent (Lebanon, NH, USA) is a computational fluid dynamics software employed to analyse biological mass-transport in the vasculature. A principal consideration for computational modelling of blood-side mass-transport is convection-diffusion discretisation scheme selection. Due to numerous discretisation schemes available when developing a mass-transport numerical model, the results obtained should either be validated against benchmark theoretical solutions or experimentally obtained results. Methods An idealised aneurysm model was selected for the experimental and computational mass-transport analysis of species concentration due to its well-defined recirculation region within the aneurysmal sac, allowing species concentration to vary slowly with time. The experimental results were obtained from fluid samples extracted from a glass aneurysm model, using the direct spectrophometric concentration measurement technique. The computational analysis was conducted using the four convection-diffusion discretisation schemes available to the Fluent user, including the First-Order Upwind, the Power Law, the Second-Order Upwind and the Quadratic Upstream Interpolation for Convective Kinetics (QUICK) schemes. The fluid has a diffusivity of 3.125 × 10-10 m2/s in water, resulting in a Peclet number of 2,560,000, indicating strongly convection-dominated flow. Results The discretisation scheme applied to the solution of the convection-diffusion equation, for blood-side mass-transport within the vasculature, has a significant influence on the resultant species concentration field. The First-Order Upwind and the Power Law schemes produce similar results. The Second-Order Upwind and QUICK schemes also correlate well but differ considerably from the concentration contour plots of the First-Order Upwind and Power Law schemes. The computational results were then compared to the experimental findings. An average error of 140% and 116% was demonstrated between the experimental results and those obtained from the First-Order Upwind and Power Law schemes, respectively. However, both the Second-Order upwind and QUICK schemes accurately predict species concentration under high Peclet number, convection-dominated flow conditions. Conclusion Convection-diffusion discretisation scheme selection has a strong influence on resultant species concentration fields, as determined by CFD. Furthermore, either the Second-Order or QUICK discretisation schemes should be implemented when numerically modelling convection-dominated mass-transport conditions. Finally, care should be taken not to utilize computationally inexpensive discretisation schemes at the cost of accuracy in resultant species concentration. PMID:20642816

Atomistic models of Cu diffusion in CuInSe2 under variations in composition

NASA Astrophysics Data System (ADS)

Sommer, David E.; Dunham, Scott T.

2018-03-01

We construct an analytic model for the composition dependence of the vacancy-mediated Cu diffusion coefficient in undoped CuInSe2 using parameters from density functional theory. The applicability of this model is supported numerically with kinetic lattice Monte Carlo and Onsager transport tensors. We discuss how this model relates to experimental measurements of Cu diffusion, arguing that our results can account for significant contributions to the bulk diffusion of Cu tracers in non-stoichiometric CuInSe2.

A novel in-situ method for real-time monitoring of gas transport in soil

NASA Astrophysics Data System (ADS)

Laemmel, Thomas; Maier, Martin; Schack-Kirchner, Helmer; Lang, Friederike

2017-04-01

Gas exchange between soil and atmosphere is important for the biogeochemistry of soils. Gas transport in soil is commonly assumed to be governed by molecular diffusion and is usually described by the soil gas diffusion coefficient DS characterizing the ability of the soil to "transport passively" gas through the soil. One way to determine DS is sampling soil cores in the field and measuring DS in the lab. Unfortunately this method is destructive and laborious. Moreover, a few previous field studies identified other gas transport processes in soil to significantly enhance the diffusive gas transport. However, until now, no method is available to measure gas transport in situ in the soil. We developed a novel method to monitor gas transport in soil in situ. The method includes a custom made gas sampling device, the continuous injection of an inert tracer gas and inverse gas transport modelling in the soil. The gas sampling device has several sampling depths and can be easily installed into a vertical hole drilled by an auger, which allows for fast installation of the system. Helium (He) as inert tracer gas was injected continuously at the lower end of the device. The resulting steady state distribution of He was used to deduce the depth profile of DS. Gas transport in the soil surrounding the gas-sampling-device/soil system was modeled using the Finite Element Modeling program COMSOL . We tested our new method both in the lab and during two short field studies and compared the results with a reference method using soil cores. DS profiles obtained by our in-situ method were consistent with DS profiles determined based on soil core analyses. During a longer monitoring field campaign, typical soil-moisture effects upon gas diffusivity such as an increase during a drying period or a decrease after rain could be observed consistently. Under windy conditions we additionally measured for the first time the direct enhancement of gas transport in soil due to wind-induced pressure-pumping which could increase the effective DS up to 30% in the topsoil. Our novel monitoring method can be quickly and easily installed and allows for monitoring continuously soil gas transport over a long time. It allows monitoring physical modifications of soil gas diffusivity due to rain events or evaporation but it also allows studying non-diffusive gas transport processes in the soil.

Permeability and diffusion in vitreous humor: implications for drug delivery.

PubMed

Xu, J; Heys, J J; Barocas, V H; Randolph, T W

2000-06-01

Previous experimental work suggests that convection may be important in determining the biodistribution of drugs implanted or injected in the vitreous humor. To develop accurate biodistribution models, the relative importance of diffusion and convection in intravitreal transport must be assessed. This requires knowledge of both the diffusivity of candidate drugs and the hydraulic conductivity of the vitreous humor. Hydraulic conductivity of cadaveric bovine vitreous humor was measured by confined compression tests at constant loads of 0.15 and 0.2 N and analyzed numerically using a two-phase model. Diffusion coefficient of acid orange 8, a model compound, in the same medium was measured in a custom-built diffusion cell. Acid orange 8 diffusivity within vitreous humor is about half that in free solution. When viscous effects are properly accounted for, the hydraulic conductivity of bovine vitreous humor is 8.4+/-4.5 x 10(-7) cm2/Pa x s. We predict that convection does not contribute significantly to transport in the mouse eye, particularly for low-molecular-weight compounds. For delivery to larger animals, such as humans we conclude that convection accounts for roughly 30% of the total intravitreal drug transport. This effect should be magnified for higher-molecular-weight compounds, which diffuse more slowly, and in glaucoma, which involves higher intraocular pressure and thus potentially faster convective flow. Thus, caution should be exercised in the extrapolation of small-animal-model biodistribution data to human scale.

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.

Implementation of a diffusion convection surface evolution model in WallDYN

NASA Astrophysics Data System (ADS)

Schmid, K.

2013-07-01

In thermonuclear fusion experiments with multiple plasma facing materials the formation of mixed materials is inevitable. The formation of these mixed material layers is a dynamic process driven the tight interaction between transport in the plasma scrape off layer and erosion/(re-) deposition at the surface. To track this global material erosion/deposition balance and the resulting formation of mixed material layers the WallDYN code has been developed which couples surface processes and plasma transport. The current surface model in WallDYN cannot fully handle the growth of layers nor does it include diffusion. However at elevated temperatures diffusion is a key process in the formation of mixed materials. To remedy this shortcoming a new surface model has been developed which, for the first time, describes both layer growth/recession and diffusion in a single continuous diffusion/convection equation. The paper will detail the derivation of the new surface model and compare it to TRIDYN calculations.

Numerical study of influence of molecular diffusion in the Mild combustion regime

NASA Astrophysics Data System (ADS)

Mardani, Amir; Tabejamaat, Sadegh; Ghamari, Mohsen

2010-09-01

In this paper, the importance of molecular diffusion versus turbulent transport in the moderate or intense low-oxygen dilution (Mild) combustion mode has been numerically studied. The experimental conditions of Dally et al. [Proc. Combust. Inst. 29 (2002) 1147-1154] were used for modelling. The EDC model was used to describe the turbulence-chemistry interaction. The DRM-22 reduced mechanism and the GRI 2.11 full mechanism were used to represent the chemical reactions of an H2/methane jet flame. The importance of molecular diffusion for various O2 levels, jet Reynolds numbers and H2 fuel contents was investigated. Results show that the molecular diffusion in Mild combustion cannot be ignored in comparison with the turbulent transport. Also, the method of inclusion of molecular diffusion in combustion modelling has a considerable effect on the accuracy of numerical modelling of Mild combustion. By decreasing the jet Reynolds number, decreasing the oxygen concentration in the airflow or increasing H2 in the fuel mixture, the influence of molecular diffusion on Mild combustion increases.

The Influence of Turbulent Coherent Structure on Suspended Sediment Transport

NASA Astrophysics Data System (ADS)

Huang, S. H.; Tsai, C.

2017-12-01

The anomalous diffusion of turbulent sedimentation has received more and more attention in recent years. With the advent of new instruments and technologies, researchers have found that sediment behavior may deviate from Fickian assumptions when particles are heavier. In particle-laden flow, bursting phenomena affects instantaneous local concentrations, and seems to carry suspended particles for a longer distance. Instead of the pure diffusion process in an analogy to Brownian motion, Levy flight which allows particles to move in response to bursting phenomena is suspected to be more suitable for describing particle movement in turbulence. And the fractional differential equation is a potential candidate to improve the concentration profile. However, stochastic modeling (the Differential Chapmen-Kolmogorov Equation) also provides an alternative mathematical framework to describe system transits between different states through diffusion/the jump processes. Within this framework, the stochastic particle tracking model linked with advection diffusion equation is a powerful tool to simulate particle locations in the flow field. By including the jump process to this model, a more comprehensive description for suspended sediment transport can be provided with a better physical insight. This study also shows the adaptability and expandability of the stochastic particle tracking model for suspended sediment transport modeling.

Equivalence of two approaches for modeling ion permeation through a transmembrane channel with an internal binding site

NASA Astrophysics Data System (ADS)

Zhou, Huan-Xiang

2011-04-01

Ion permeation through transmembrane channels has traditionally been modeled using two different approaches. In one approach, the translocation of the permeant ion through the channel pore is modeled as continuous diffusion and the rate of ion transport is obtained from solving the steady-state diffusion equation. In the other approach, the translocation of the permeant ion through the pore is modeled as hopping along a discrete set of internal binding sites and the rate of ion transport is obtained from solving a set of steady-state rate equations. In a recent work [Zhou, J. Phys. Chem. Lett. 1, 1973 (2010)], the rate constants for binding to an internal site were further calculated by modeling binding as diffusion-influenced reactions. That work provided the foundation for bridging the two approaches. Here we show that, by representing a binding site as an energy well, the two approaches indeed give the same result for the rate of ion transport.

Scale-Dependent Fracture-Matrix Interactions And Their Impact on Radionuclide Transport - Final Report

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

Detwiler, Russell

Matrix diffusion and adsorption within a rock matrix are widely regarded as important mechanisms for retarding the transport of radionuclides and other solutes in fractured rock (e.g., Neretnieks, 1980; Tang et al., 1981; Maloszewski and Zuber, 1985; Novakowski and Lapcevic, 1994; Jardine et al., 1999; Zhou and Xie, 2003; Reimus et al., 2003a,b). When remediation options are being evaluated for old sources of contamination, where a large fraction of contaminants reside within the rock matrix, slow diffusion out of the matrix greatly increases the difficulty and timeframe of remediation. Estimating the rates of solute exchange between fractures and the adjacentmore » rock matrix is a critical factor in quantifying immobilization and/or remobilization of DOE-relevant contaminants within the subsurface. In principle, the most rigorous approach to modeling solute transport with fracture-matrix interaction would be based on local-scale coupled advection-diffusion/dispersion equations for the rock matrix and in discrete fractures that comprise the fracture network (Discrete Fracture Network and Matrix approach, hereinafter referred to as DFNM approach), fully resolving aperture variability in fractures and matrix property heterogeneity. However, such approaches are computationally demanding, and thus, many predictive models rely upon simplified models. These models typically idealize fracture rock masses as a single fracture or system of parallel fractures interacting with slabs of porous matrix or as a mobile-immobile or multi-rate mass transfer system. These idealizations provide tractable approaches for interpreting tracer tests and predicting contaminant mobility, but rely upon a fitted effective matrix diffusivity or mass-transfer coefficients. However, because these fitted parameters are based upon simplified conceptual models, their effectiveness at predicting long-term transport processes remains uncertain. Evidence of scale dependence of effective matrix diffusion coefficients obtained from tracer tests highlights this point and suggests that the underlying mechanisms and relationship between rock and fracture properties are not fully understood in large complex fracture networks. In this project, we developed a high-resolution DFN model of solute transport in fracture networks to explore and quantify the mechanisms that control transport in complex fracture networks and how these may give rise to observed scale-dependent matrix diffusion coefficients. Results demonstrate that small scale heterogeneity in the flow field caused by local aperture variability within individual fractures can lead to long-tailed breakthrough curves indicative of matrix diffusion, even in the absence of interactions with the fracture matrix. Furthermore, the temporal and spatial scale dependence of these processes highlights the inability of short-term tracer tests to estimate transport parameters that will control long-term fate and transport of contaminants in fractured aquifers.« less

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

Control of reaction-diffusion equations on time-evolving manifolds.

PubMed

Rossi, Francesco; Duteil, Nastassia Pouradier; Yakoby, Nir; Piccoli, Benedetto

2016-12-01

Among the main actors of organism development there are morphogens, which are signaling molecules diffusing in the developing organism and acting on cells to produce local responses. Growth is thus determined by the distribution of such signal. Meanwhile, the diffusion of the signal is itself affected by the changes in shape and size of the organism. In other words, there is a complete coupling between the diffusion of the signal and the change of the shapes. In this paper, we introduce a mathematical model to investigate such coupling. The shape is given by a manifold, that varies in time as the result of a deformation given by a transport equation. The signal is represented by a density, diffusing on the manifold via a diffusion equation. We show the non-commutativity of the transport and diffusion evolution by introducing a new concept of Lie bracket between the diffusion and the transport operator. We also provide numerical simulations showing this phenomenon.

Stochastic interpretation of the advection-diffusion equation and its relevance to bed load transport

NASA Astrophysics Data System (ADS)

Ancey, C.; Bohorquez, P.; Heyman, J.

2015-12-01

The advection-diffusion equation is one of the most widespread equations in physics. It arises quite often in the context of sediment transport, e.g., for describing time and space variations in the particle activity (the solid volume of particles in motion per unit streambed area). Phenomenological laws are usually sufficient to derive this equation and interpret its terms. Stochastic models can also be used to derive it, with the significant advantage that they provide information on the statistical properties of particle activity. These models are quite useful when sediment transport exhibits large fluctuations (typically at low transport rates), making the measurement of mean values difficult. Among these stochastic models, the most common approach consists of random walk models. For instance, they have been used to model the random displacement of tracers in rivers. Here we explore an alternative approach, which involves monitoring the evolution of the number of particles moving within an array of cells of finite length. Birth-death Markov processes are well suited to this objective. While the topic has been explored in detail for diffusion-reaction systems, the treatment of advection has received no attention. We therefore look into the possibility of deriving the advection-diffusion equation (with a source term) within the framework of birth-death Markov processes. We show that in the continuum limit (when the cell size becomes vanishingly small), we can derive an advection-diffusion equation for particle activity. Yet while this derivation is formally valid in the continuum limit, it runs into difficulty in practical applications involving cells or meshes of finite length. Indeed, within our stochastic framework, particle advection produces nonlocal effects, which are more or less significant depending on the cell size and particle velocity. Albeit nonlocal, these effects look like (local) diffusion and add to the intrinsic particle diffusion (dispersal due to velocity fluctuations), with the important consequence that local measurements depend on both the intrinsic properties of particle displacement and the dimensions of the measurement system.

Modeling boundary measurements of scattered light using the corrected diffusion approximation

PubMed Central

Lehtikangas, Ossi; Tarvainen, Tanja; Kim, Arnold D.

2012-01-01

We study the modeling and simulation of steady-state measurements of light scattered by a turbid medium taken at the boundary. In particular, we implement the recently introduced corrected diffusion approximation in two spatial dimensions to model these boundary measurements. This implementation uses expansions in plane wave solutions to compute boundary conditions and the additive boundary layer correction, and a finite element method to solve the diffusion equation. We show that this corrected diffusion approximation models boundary measurements substantially better than the standard diffusion approximation in comparison to numerical solutions of the radiative transport equation. PMID:22435102

Cosmic-ray propagation with DRAGON2: I. numerical solver and astrophysical ingredients

NASA Astrophysics Data System (ADS)

Evoli, Carmelo; Gaggero, Daniele; Vittino, Andrea; Di Bernardo, Giuseppe; Di Mauro, Mattia; Ligorini, Arianna; Ullio, Piero; Grasso, Dario

2017-02-01

We present version 2 of the DRAGON code designed for computing realistic predictions of the CR densities in the Galaxy. The code numerically solves the interstellar CR transport equation (including inhomogeneous and anisotropic diffusion, either in space and momentum, advective transport and energy losses), under realistic conditions. The new version includes an updated numerical solver and several models for the astrophysical ingredients involved in the transport equation. Improvements in the accuracy of the numerical solution are proved against analytical solutions and in reference diffusion scenarios. The novel features implemented in the code allow to simulate the diverse scenarios proposed to reproduce the most recent measurements of local and diffuse CR fluxes, going beyond the limitations of the homogeneous galactic transport paradigm. To this end, several applications using DRAGON2 are presented as well. This new version facilitates the users to include their own physical models by means of a modular C++ structure.

Modeling Bimolecular Reactive Transport With Mixing-Limitation: Theory and Application to Column Experiments

NASA Astrophysics Data System (ADS)

Ginn, T. R.

2018-01-01

The challenge of determining mixing extent of solutions undergoing advective-dispersive-diffusive transport is well known. In particular, reaction extent between displacing and displaced solutes depends on mixing at the pore scale, that is, generally smaller than continuum scale quantification that relies on dispersive fluxes. Here a novel mobile-mobile mass transfer approach is developed to distinguish diffusive mixing from dispersive spreading in one-dimensional transport involving small-scale velocity variations with some correlation, such as occurs in hydrodynamic dispersion, in which short-range ballistic transports give rise to dispersed but not mixed segregation zones, termed here ballisticules. When considering transport of a single solution, this approach distinguishes self-diffusive mixing from spreading, and in the case of displacement of one solution by another, each containing a participant reactant of an irreversible bimolecular reaction, this results in time-delayed diffusive mixing of reactants. The approach generates models for both kinetically controlled and equilibrium irreversible reaction cases, while honoring independently measured reaction rates and dispersivities. The mathematical solution for the equilibrium case is a simple analytical expression. The approach is applied to published experimental data on bimolecular reactions for homogeneous porous media under postasymptotic dispersive conditions with good results.

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

Stagg, Alan K; Yoon, Su-Jong

This report describes the Consortium for Advanced Simulation of Light Water Reactors (CASL) work conducted for completion of the Thermal Hydraulics Methods (THM) Level 3 Milestone THM.CFD.P11.02: Hydra-TH Extensions for Multispecies and Thermosolutal Convection. A critical requirement for modeling reactor thermal hydraulics is to account for species transport within the fluid. In particular, this capability is needed for modeling transport and diffusion of boric acid within water for emergency, reactivity-control scenarios. To support this need, a species transport capability has been implemented in Hydra-TH for binary systems (for example, solute within a solvent). A species transport equation is solved formore » the species (solute) mass fraction, and both thermal and solutal buoyancy effects are handled with specification of a Boussinesq body force. Species boundary conditions can be specified with a Dirichlet condition on mass fraction or a Neumann condition on diffusion flux. To enable enhanced species/fluid mixing in turbulent flow, the molecular diffusivity for the binary system is augmented with a turbulent diffusivity in the species transport calculation. The new capabilities are demonstrated by comparison of Hydra-TH calculations to the analytic solution for a thermosolutal convection problem, and excellent agreement is obtained.« less

A non-Linear transport model for determining shale rock characteristics

NASA Astrophysics Data System (ADS)

Ali, Iftikhar; Malik, Nadeem

2016-04-01

Unconventional hydrocarbon reservoirs consist of tight porous rocks which are characterised by nano-scale size porous networks with ultra-low permeability [1,2]. Transport of gas through them is not well understood at the present time, and realistic transport models are needed in order to determine rock properties and for estimating future gas pressure distribution in the reservoirs. Here, we consider a recently developed non-linear gas transport equation [3], ∂p-+ U ∂p- = D ∂2p-, t > 0, (1) ∂t ∂x ∂x2 complimented with suitable initial and boundary conditions, in order to determine shale rock properties such as the permeability K, the porosity φ and the tortuosity, τ. In our new model, the apparent convection velocity, U = U(p,px), and the apparent diffusivity D = D(p), are both highly non-linear functions of the pressure. The model incorporate various flow regimes (slip, surface diffusion, transition, continuum) based upon the Knudsen number Kn, and also includes Forchchiemers turbulence correction terms. In application, the model parameters and associated compressibility factors are fully pressure dependent, giving the model more realism than previous models. See [4]. Rock properties are determined by solving an inverse problem, with model parameters adjustment to minimise the error between the model simulation and available data. It is has been found that the proposed model performs better than previous models. Results and details of the model will be presented at the conference. Corresponding author: namalik@kfupm.edu.sa and nadeem_malik@cantab.net References [1] Cui, X., Bustin, A.M. and Bustin, R., "Measurements of gas permeability and diffusivity of tight reservoir rocks: different approaches and their applications", Geofluids 9, 208-223 (2009). [2] Chiba R., Fomin S., Chugunov V., Niibori Y. and Hashida T., "Numerical Simulation of Non Fickian Diffusion and Advection in a Fractured Porous Aquifer", AIP Conference Proceedings 898, 75 (2007); 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.

Bulk Growth of Wide Band Gap II-VI Compound Semiconductors by Physical Vapor Transport

NASA Technical Reports Server (NTRS)

Su, Ching-Hua

1997-01-01

The mechanism of physical vapor transport of II-VI semiconducting compounds was studied both theoretically, using a one-dimensional diffusion model, as well as experimentally. It was found that the vapor phase stoichiometry is critical in determining the vapor transport rate. The experimental heat treatment methods to control the vapor composition over the starting materials were investigated and the effectiveness of the heat treatments was confirmed by partial pressure measurements using an optical absorption technique. The effect of residual (foreign) gas on the transport rate was also studies theoretically by the diffusion model and confirmed experimentally by the measurements of total pressure and compositions of the residual gas. An in-situ dynamic technique for the transport rate measurements and a further extension of the technique that simultaneously measured the partial pressures and transport rates were performed and, for the first time, the experimentally determined mass fluxes were compared with those calculated, without any adjustable parameters, from the diffusion model. Using the information obtained from the experimental transport rate measurements as guideline high quality bulk crystal of wide band gap II-VI semiconductor were grown from the source materials which undergone the same heat treatment methods. The grown crystals were then extensively characterized with emphasis on the analysis of the crystalline structural defects.

Insight into the grain boundary effect on the ionic transport of yttria-stabilized zirconia at elevated temperatures from a molecular modeling perspective

NASA Astrophysics Data System (ADS)

Chang, Kai-Shiun; Lin, Yi-Feng; Tung, Kuo-Lun

A molecular dynamics (MD) simulation is used to reveal the grain boundary effect on the ionic transport of yttria-stabilized zirconia (YSZ). The oxygen ion displacements and diffusivities of the ideal and grain boundary-inserted YSZ models are analyzed at elevated temperatures. An optimized Y 2O 3 concentration within YSZ for the best ionic conductivity is achieved by balancing the trade-off between the increased vacancies and the decreased accessible free space. The mass transfer resistance of the grain boundary in YSZ can be more easily found at higher temperatures by observing the oxygen ion diffusivities or traveling trajectories. At lower temperatures, the grain interior and the grain boundary control the ionic transport. In contrast, the grain boundary effect on the diffusion barrier is gradually eliminated at elevated temperatures. The modeled results in this work agree well with previous experimental data.

14 CFR Appendix I to Part 417 - Methodologies for Toxic Release Hazard Analysis and Operational Procedures

Code of Federal Regulations, 2014 CFR

2014-01-01

... physics on the transport and diffusion of each toxicant. (5) Meteorological conditions at the time of..., or for use in any real-time physics models used to ensure compliance with the toxic flight commit... atmospheric physics on the transport and diffusion of toxic propellants released; (5) Meteorological...

14 CFR Appendix I to Part 417 - Methodologies for Toxic Release Hazard Analysis and Operational Procedures

Code of Federal Regulations, 2012 CFR

2012-01-01

... physics on the transport and diffusion of each toxicant. (5) Meteorological conditions at the time of..., or for use in any real-time physics models used to ensure compliance with the toxic flight commit... atmospheric physics on the transport and diffusion of toxic propellants released; (5) Meteorological...

14 CFR Appendix I to Part 417 - Methodologies for Toxic Release Hazard Analysis and Operational Procedures

Code of Federal Regulations, 2011 CFR

2011-01-01

... physics on the transport and diffusion of each toxicant. (5) Meteorological conditions at the time of..., or for use in any real-time physics models used to ensure compliance with the toxic flight commit... atmospheric physics on the transport and diffusion of toxic propellants released; (5) Meteorological...

14 CFR Appendix I to Part 417 - Methodologies for Toxic Release Hazard Analysis and Operational Procedures

Code of Federal Regulations, 2013 CFR

2013-01-01

... physics on the transport and diffusion of each toxicant. (5) Meteorological conditions at the time of..., or for use in any real-time physics models used to ensure compliance with the toxic flight commit... atmospheric physics on the transport and diffusion of toxic propellants released; (5) Meteorological...

Room-Temperature Micron-Scale Exciton Migration in a Stabilized Emissive Molecular Aggregate.

PubMed

Caram, Justin R; Doria, Sandra; Eisele, Dörthe M; Freyria, Francesca S; Sinclair, Timothy S; Rebentrost, Patrick; Lloyd, Seth; Bawendi, Moungi G

2016-11-09

We report 1.6 ± 1 μm exciton transport in self-assembled supramolecular light-harvesting nanotubes (LHNs) assembled from amphiphillic cyanine dyes. We stabilize LHNs in a sucrose glass matrix, greatly reducing light and oxidative damage and allowing the observation of exciton-exciton annihilation signatures under weak excitation flux. Fitting to a one-dimensional diffusion model, we find an average exciton diffusion constant of 55 ± 20 cm 2 /s, among the highest measured for an organic system. We develop a simple model that uses cryogenic measurements of static and dynamic energetic disorder to estimate a diffusion constant of 32 cm 2 /s, in agreement with experiment. We ascribe large exciton diffusion lengths to low static and dynamic energetic disorder in LHNs. We argue that matrix-stabilized LHNS represent an excellent model system to study coherent excitonic transport.

Perfluoroalkyl phosphonic and phosphinic acids as proton conductors for anhydrous proton-exchange membranes.

PubMed

Herath, Mahesha B; Creager, Stephen E; Kitaygorodskiy, Alex; DesMarteau, Darryl D

2010-09-10

A study of proton-transport rates and mechanisms under anhydrous conditions using a series of acid model compounds, analogous to comb-branch perfluorinated ionomers functionalized with phosphonic, phosphinic, sulfonic, and carboxylic acid protogenic groups, is reported. Model compounds are characterized with respect to proton conductivity, viscosity, proton, and anion (conjugate base) self-diffusion coefficients, and Hammett acidity. The highest conductivities, and also the highest viscosities, are observed for the phosphonic and phosphinic acid model compounds. Arrhenius analysis of conductivity and viscosity for these two acids reveals much lower activation energies for ion transport than for viscous flow. Additionally, the proton self-diffusion coefficients are much higher than the conjugate-base self-diffusion coefficients for these two acids. Taken together, these data suggest that anhydrous proton transport in the phosphonic and phosphinic acid model compounds occurs primarily by a structure-diffusion, hopping-based mechanism rather than a vehicle mechanism. Further analysis of ionic conductivity and ion self-diffusion rates by using the Nernst-Einstein equation reveals that the phosphonic and phosphinic acid model compounds are relatively highly dissociated even under anhydrous conditions. In contrast, sulfonic and carboxylic acid-based systems exhibit relatively low degrees of dissociation under anhydrous conditions. These findings suggest that fluoroalkyl phosphonic and phosphinic acids are good candidates for further development as anhydrous, high-temperature proton conductors.

Modeling bioluminescent photon transport in tissue based on Radiosity-diffusion model

NASA Astrophysics Data System (ADS)

Sun, Li; Wang, Pu; Tian, Jie; Zhang, Bo; Han, Dong; Yang, Xin

2010-03-01

Bioluminescence tomography (BLT) is one of the most important non-invasive optical molecular imaging modalities. The model for the bioluminescent photon propagation plays a significant role in the bioluminescence tomography study. Due to the high computational efficiency, diffusion approximation (DA) is generally applied in the bioluminescence tomography. But the diffusion equation is valid only in highly scattering and weakly absorbing regions and fails in non-scattering or low-scattering tissues, such as a cyst in the breast, the cerebrospinal fluid (CSF) layer of the brain and synovial fluid layer in the joints. A hybrid Radiosity-diffusion model is proposed for dealing with the non-scattering regions within diffusing domains in this paper. This hybrid method incorporates a priori information of the geometry of non-scattering regions, which can be acquired by magnetic resonance imaging (MRI) or x-ray computed tomography (CT). Then the model is implemented using a finite element method (FEM) to ensure the high computational efficiency. Finally, we demonstrate that the method is comparable with Mont Carlo (MC) method which is regarded as a 'gold standard' for photon transportation simulation.

Arctic sea-ice diffusion from observed and simulated Lagrangian trajectories

NASA Astrophysics Data System (ADS)

Rampal, Pierre; Bouillon, Sylvain; Bergh, Jon; Ólason, Einar

2016-07-01

We characterize sea-ice drift by applying a Lagrangian diffusion analysis to buoy trajectories from the International Arctic Buoy Programme (IABP) dataset and from two different models: the standalone Lagrangian sea-ice model neXtSIM and the Eulerian coupled ice-ocean model used for the TOPAZ reanalysis. By applying the diffusion analysis to the IABP buoy trajectories over the period 1979-2011, we confirm that sea-ice diffusion follows two distinct regimes (ballistic and Brownian) and we provide accurate values for the diffusivity and integral timescale that could be used in Eulerian or Lagrangian passive tracers models to simulate the transport and diffusion of particles moving with the ice. We discuss how these values are linked to the evolution of the fluctuating displacements variance and how this information could be used to define the size of the search area around the position predicted by the mean drift. By comparing observed and simulated sea-ice trajectories for three consecutive winter seasons (2007-2011), we show how the characteristics of the simulated motion may differ from or agree well with observations. This comparison illustrates the usefulness of first applying a diffusion analysis to evaluate the output of modeling systems that include a sea-ice model before using these in, e.g., oil spill trajectory models or, more generally, to simulate the transport of passive tracers in sea ice.

Diffusive transport of energetic electrons in the solar corona: X-ray and radio diagnostics

NASA Astrophysics Data System (ADS)

Musset, S.; Kontar, E. P.; Vilmer, N.

2018-02-01

Context. Imaging spectroscopy in X-rays with RHESSI provides the possibility to investigate the spatial evolution of X-ray emitting electron distribution and therefore, to study transport effects on energetic electrons during solar flares. Aims: We study the energy dependence of the scattering mean free path of energetic electrons in the solar corona. Methods: We used imaging spectroscopy with RHESSI to study the evolution of energetic electrons distribution in various parts of the magnetic loop during the 2004 May 21 flare. We compared these observations with the radio observations of the gyrosynchrotron radiation of the same flare and with the predictions of a diffusive transport model. Results: X-ray analysis shows a trapping of energetic electrons in the corona and a spectral hardening of the energetic electron distribution between the top of the loop and the footpoints. Coronal trapping of electrons is stronger for radio-emitting electrons than for X-ray-emitting electrons. These observations can be explained by a diffusive transport model. Conclusions: We show that the combination of X-ray and radio diagnostics is a powerful tool to study electron transport in the solar corona in different energy domains. We show that the diffusive transport model can explain our observations, and in the range 25-500 keV, the scattering mean free path of electrons decreases with electron energy. We can estimate for the first time the scattering mean free path dependence on energy in the corona.

Analytical solutions for a soil vapor extraction model that incorporates gas phase dispersion and molecular diffusion

NASA Astrophysics Data System (ADS)

Huang, Junqi; Goltz, Mark N.

2017-06-01

To greatly simplify their solution, the equations describing radial advective/dispersive transport to an extraction well in a porous medium typically neglect molecular diffusion. While this simplification is appropriate to simulate transport in the saturated zone, it can result in significant errors when modeling gas phase transport in the vadose zone, as might be applied when simulating a soil vapor extraction (SVE) system to remediate vadose zone contamination. A new analytical solution for the equations describing radial gas phase transport of a sorbing contaminant to an extraction well is presented. The equations model advection, dispersion (including both mechanical dispersion and molecular diffusion), and rate-limited mass transfer of dissolved, separate phase, and sorbed contaminants into the gas phase. The model equations are analytically solved by using the Laplace transform with respect to time. The solutions are represented by confluent hypergeometric functions in the Laplace domain. The Laplace domain solutions are then evaluated using a numerical Laplace inversion algorithm. The solutions can be used to simulate the spatial distribution and the temporal evolution of contaminant concentrations during operation of a soil vapor extraction well. Results of model simulations show that the effect of gas phase molecular diffusion upon concentrations at the extraction well is relatively small, although the effect upon the distribution of concentrations in space is significant. This study provides a tool that can be useful in designing SVE remediation strategies, as well as verifying numerical models used to simulate SVE system performance.

Multiple-tracer tests for contaminant transport process identification in saturated municipal solid waste

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

Woodman, N.D., E-mail: n.d.woodman@soton.ac.uk; Rees-White, T.C.; Stringfellow, A.M.

2015-04-15

Highlights: • Multiple tracers were applied to saturated MSW to test dual-porosity properties. • Lithium demonstrated to be non-conservative as a tracer. • 260 mm diameter column too small to test transport properties of MSW. • The classical advection-dispersion mode was rejected due to high dispersivity. • Characteristic diffusion times did not vary with the tracer. - Abstract: Two column tests were performed in conditions emulating vertical flow beneath the leachate table in a biologically active landfill to determine dominant transport mechanisms occurring in landfills. An improved understanding of contaminant transport process in wastes is required for developing better predictionsmore » about potential length of the long term aftercare of landfills, currently measured in timescales of centuries. Three tracers (lithium, bromide and deuterium) were used. Lithium did not behave conservatively. Given that lithium has been used extensively for tracing in landfill wastes, the tracer itself and the findings of previous tests which assume that it has behaved conservatively may need revisiting. The smaller column test could not be fitted with continuum models, probably because the volume of waste was below a representative elemental volume. Modelling compared advection-dispersion (AD), dual porosity (DP) and hybrid AD–DP models. Of these models, the DP model was found to be the most suitable. Although there is good evidence to suggest that diffusion is an important transport mechanism, the breakthrough curves of the different tracers did not differ from each other as would be predicted based on the free-water diffusion coefficients. This suggested that solute diffusion in wastes requires further study.« less

Using spatially detailed water-quality data and solute-transport modeling to improve support total maximum daily load development

USGS Publications Warehouse

Walton-Day, Katherine; Runkel, Robert L.; Kimball, Briant A.

2012-01-01

Spatially detailed mass-loading studies and solute-transport modeling using OTIS (One-dimensional Transport with Inflow and Storage) demonstrate how natural attenuation and loading from distinct and diffuse sources control stream water quality and affect load reductions predicted in total maximum daily loads (TMDLs). Mass-loading data collected during low-flow from Cement Creek (a low-pH, metal-rich stream because of natural and mining sources, and subject to TMDL requirements) were used to calibrate OTIS and showed spatially variable effects of natural attenuation (instream reactions) and loading from diffuse (groundwater) and distinct sources. OTIS simulations of the possible effects of TMDL-recommended remediation of mine sites showed less improvement to dissolved zinc load and concentration (14% decrease) than did the TMDL (53-63% decrease). The TMDL (1) assumed conservative transport, (2) accounted for loads removed by remediation by subtracting them from total load at the stream mouth, and (3) did not include diffuse-source loads. In OTIS, loads were reduced near their source; the resulting concentration was decreased by natural attenuation and increased by diffuse-source loads during downstream transport. Thus, by not including natural attenuation and loading from diffuse sources, the TMDL overestimated remediation effects at low flow. Use of the techniques presented herein could improve TMDLs by incorporating these processes during TMDL development.

IMPORTANCE OF MERIDIONAL CIRCULATION IN FLUX TRANSPORT DYNAMO: THE POSSIBILITY OF A MAUNDER-LIKE GRAND MINIMUM

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

Karak, Bidya Binay, E-mail: bidya_karak@physics.iisc.ernet.i

2010-12-01

Meridional circulation is an important ingredient in flux transport dynamo models. We have studied its importance on the period, the amplitude of the solar cycle, and also in producing Maunder-like grand minima in these models. First, we model the periods of the last 23 sunspot cycles by varying the meridional circulation speed. If the dynamo is in a diffusion-dominated regime, then we find that most of the cycle amplitudes also get modeled up to some extent when we model the periods. Next, we propose that at the beginning of the Maunder minimum the amplitude of meridional circulation dropped to amore » low value and then after a few years it increased again. Several independent studies also favor this assumption. With this assumption, a diffusion-dominated dynamo is able to reproduce many important features of the Maunder minimum remarkably well. If the dynamo is in a diffusion-dominated regime, then a slower meridional circulation means that the poloidal field gets more time to diffuse during its transport through the convection zone, making the dynamo weaker. This consequence helps to model both the cycle amplitudes and the Maunder-like minima. We, however, fail to reproduce these results if the dynamo is in an advection-dominated regime.« less

Diapycnal Transport and Pattern Formation in Double-Diffusive Convection

DTIC Science & Technology

2015-12-01

of knowledge. The effects of turbulent-dominated and purely double-diffusive regimes are compared to dual turbulent/double-diffusive systems and...is presented to remedy this dearth of knowledge. The effects of turbulent-dominated and purely double-diffusive regimes are compared to dual...8 2. Double-Diffusion: The Constant Flux Ratio Model ..........................9 3. The Combined Effects of

Modeling diffusion and reaction in soils: 9. The Buckingham-Burdine-Campbell equation for gas diffusivity in undisturbed soil

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

Moldrup, P.; Olesen, T.; Yamaguchi, T.

1999-08-01

Accurate description of gas diffusivity (ratio of gas diffusion coefficients in soil and free air, D{sub s}/D{sub 0}) in undisturbed soils is a prerequisite for predicting in situ transport and fate of volatile organic chemicals and greenhouse gases. Reference point gas diffusivities (R{sub p}) in completely dry soil were estimated for 20 undisturbed soils by assuming a power function relation between gas diffusivity and air-filled porosity ({epsilon}). Among the classical gas diffusivity models, the Buckingham (1904) expression, equal to the soil total porosity squared, best described R{sub p}. Inasmuch, as their previous works implied a soil-type dependency of D{sub s}/D{submore » 0}({epsilon}) in undisturbed soils, the Buckingham R{sub p} expression was inserted in two soil-type-dependent D{sub s}/D{sub 0}({epsilon}) models. One D{sub s}/D{sub 0}({epsilon}) model is a function of pore-size distribution (the Campbell water retention parameter used in a modified Burdine capillary tube model), and the other is a calibrated, empirical function of soil texture (silt + sand fraction). Both the Buckingham-Burdine-Campbell (BBC) and the Buckingham/soil texture-based D{sub s}/D{sub 0}({epsilon}) models described well the observed soil type effects on gas diffusivity and gave improved predictions compared with soil type independent models when tested against an independent data set for six undisturbed surface soils. This study emphasizes that simple but soil-type-dependent power function D{sub s}/D{sub 0}({epsilon}) models can adequately describe and predict gas diffusivity in undisturbed soil. The authors recommend the new BBC model as basis for modeling gas transport and reactions in undisturbed soil systems.« less

Modelling of processes occurring in deep geological repository - Development of new modules in the GoldSim environment

NASA Astrophysics Data System (ADS)

Vopálka, D.; Lukin, D.; Vokál, A.

2006-01-01

Three new modules modelling the processes that occur in a deep geological repository have been prepared in the GoldSim computer code environment (using its Transport Module). These modules help to understand the role of selected parameters in the near-field region of the final repository and to prepare an own complex model of the repository behaviour. The source term module includes radioactive decay and ingrowth in the canister, first order degradation of fuel matrix, solubility limitation of the concentration of the studied nuclides, and diffusive migration through the surrounding bentonite layer controlled by the output boundary condition formulated with respect to the rate of water flow in the rock. The corrosion module describes corrosion of canisters made of carbon steel and transport of corrosion products in the near-field region. This module computes balance equations between dissolving species and species transported by diffusion and/or advection from the surface of a solid material. The diffusion module that includes also non-linear form of the interaction isotherm can be used for an evaluation of small-scale diffusion experiments.

Evolution of porosity and diffusivity associated with chemical weathering of a basalt clast

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

Navarre-Sitchler, A.; Steefel, C.I.; Yang, L.

Weathering of rocks as a result of exposure to water and the atmosphere can cause significant changes in their chemistry and porosity. In low-porosity rocks, such as basalts, changes in porosity, resulting from chemical weathering, are likely to modify the rock's effective diffusivity and permeability, affecting the rate of solute transport and thus potentially the rate of overall weathering to the extent that transport is the rate limiting step. Changes in total porosity as a result of mineral dissolution and precipitation have typically been used to calculate effective diffusion coefficients through Archie's law for reactive transport simulations of chemical weathering,more » but this approach fails to account for unconnected porosity that does not contribute to transport. In this study, we combine synchrotron X-ray microcomputed tomography ({mu}CT) and laboratory and numerical diffusion experiments to examine changes in both total and effective porosity and effective diffusion coefficients across a weathering interface in a weathered basalt clast from Costa Rica. The {mu}CT data indicate that below a critical value of {approx}9%, the porosity is largely unconnected in the basalt clast. The {mu}CT data were further used to construct a numerical pore network model to determine upscaled, effective diffusivities as a function of total porosity (ranging from 3 to 30%) for comparison with diffusivities determined in laboratory tracer experiments. By using effective porosity as the scaling parameter and accounting for critical porosity, a model is developed that accurately predicts continuum-scale effective diffusivities across the weathering interface of the basalt clast.« less

Transport of Internetwork Magnetic Flux Elements in the Solar Photosphere

NASA Astrophysics Data System (ADS)

Agrawal, Piyush; Rast, Mark P.; Gošić, Milan; Bellot Rubio, Luis R.; Rempel, Matthias

2018-02-01

The motions of small-scale magnetic flux elements in the solar photosphere can provide some measure of the Lagrangian properties of the convective flow. Measurements of these motions have been critical in estimating the turbulent diffusion coefficient in flux-transport dynamo models and in determining the Alfvén wave excitation spectrum for coronal heating models. We examine the motions of internetwork flux elements in Hinode/Narrowband Filter Imager magnetograms and study the scaling of their mean squared displacement and the shape of their displacement probability distribution as a function of time. We find that the mean squared displacement scales super-diffusively with a slope of about 1.48. Super-diffusive scaling has been observed in other studies for temporal increments as small as 5 s, increments over which ballistic scaling would be expected. Using high-cadence MURaM simulations, we show that the observed super-diffusive scaling at short increments is a consequence of random changes in barycenter positions due to flux evolution. We also find that for long temporal increments, beyond granular lifetimes, the observed displacement distribution deviates from that expected for a diffusive process, evolving from Rayleigh to Gaussian. This change in distribution can be modeled analytically by accounting for supergranular advection along with granular motions. These results complicate the interpretation of magnetic element motions as strictly advective or diffusive on short and long timescales and suggest that measurements of magnetic element motions must be used with caution in turbulent diffusion or wave excitation models. We propose that passive tracer motions in measured photospheric flows may yield more robust transport statistics.

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.

Application of multiphysics models to efficient design of experiments of solute transport across articular cartilage.

PubMed

Pouran, Behdad; Arbabi, Vahid; Weinans, Harrie; Zadpoor, Amir A

2016-11-01

Transport of solutes helps to regulate normal physiology and proper function of cartilage in diarthrodial joints. Multiple studies have shown the effects of characteristic parameters such as concentration of proteoglycans and collagens and the orientation of collagen fibrils on the diffusion process. However, not much quantitative information and accurate models are available to help understand how the characteristics of the fluid surrounding articular cartilage influence the diffusion process. In this study, we used a combination of micro-computed tomography experiments and biphasic-solute finite element models to study the effects of three parameters of the overlying bath on the diffusion of neutral solutes across cartilage zones. Those parameters include bath size, degree of stirring of the bath, and the size and concentration of the stagnant layer that forms at the interface of cartilage and bath. Parametric studies determined the minimum of the finite bath size for which the diffusion behavior reduces to that of an infinite bath. Stirring of the bath proved to remarkably influence neutral solute transport across cartilage zones. The well-stirred condition was achieved only when the ratio of the diffusivity of bath to that of cartilage was greater than ≈1000. While the thickness of the stagnant layer at the cartilage-bath interface did not significantly influence the diffusion behavior, increase in its concentration substantially elevated solute concentration in cartilage. Sufficient stirring attenuated the effects of the stagnant layer. Our findings could be used for efficient design of experimental protocols aimed at understanding the transport of molecules across articular cartilage. Copyright © 2016 Elsevier Ltd. All rights reserved.

Extravascular transport of drugs in tumor tissue: effect of lipophilicity on diffusion of tirapazamine analogues in multicellular layer cultures.

PubMed

Pruijn, Frederik B; Sturman, Joanna R; Liyanage, H D Sarath; Hicks, Kevin O; Hay, Michael P; Wilson, William R

2005-02-24

The extravascular diffusion of antitumor agents is a key determinant of their therapeutic activity, but the relationships between physicochemical properties of drugs and their extravascular transport are poorly understood. It is well-known that drug lipophilicity plays an important role in transport across biological membranes, but the net effect of lipophilicity on transport through multiple layers of tumor cells is less clear. This study examines the influence of lipophilicity (measured as the octanol-water partition coefficient P) on the extravascular transport properties of the hypoxic cytotoxin tirapazamine (TPZ, 1) and a series of 13 neutral analogues, using multicellular layers (MCLs) of HT29 human colon carcinoma cells as an in vitro model for the extravascular compartment of tumors. Flux of drugs across MCLs was determined using diffusion chambers, with the concentration-time profile on both sides of the MCL measured by HPLC. Diffusion coefficients in the MCLs (D(MCL)) were inversely proportional to M(r)(0.5) (M(r), relative molecular weight), although this was a minor contributor to differences between compounds over the narrow M(r) range investigated. Differences in lipophilicity had a larger effect, with a sigmoidal dependence of D(MCL) on log P. Correcting for M(r) differences, lipophilic compounds (log P > 1.5) had ca. 15-fold higher D(MCL) than hydrophilic compounds (log P < -1). Using a pharmacokinetic/pharmacodynamic (PK/PD) model in which diffusion in the extravascular compartment of tumors is considered explicitly, we demonstrated that hypoxic cell kill is very sensitive to changes in extravascular diffusion coefficient of TPZ analogues within this range. This study shows that simple monosubstitution of TPZ can alter log P enough to markedly improve extravascular transport and activity against target cells, especially if rates of metabolic activation are also optimized.

Diffusional Transport of Organic Solutes in Subsurface Clay Lenses and Layers

NASA Astrophysics Data System (ADS)

Demond, A. H.; Ayral, D.; Goltz, M. N.

2009-12-01

The storage of organic solvents in clay lenses and layers in the subsurface creates long-term contaminant sources. Because of the low hydraulic conductivities of clay, it is thought that organic movement into clay lenses occurs through the process of diffusion. The ratio of the effective diffusion coefficient in the porous medium and the diffusion coefficient in bulk water is usually given by the tortuosity factor which accounts for the reduced area and the increased path length in the porous medium. However, there is field evidence which suggests that the concentrations in these lenses exceed that which can be accounted for by simple diffusion. There are reports, for example, of tortuosity factors greater than 1.0, which theoretically is not possible. Clays such as montmorillonite or bentonite shrink and swell depending on water content, and similar behavior can occur in the presence of organic solvents. In fact, research has shown that the basal spacing of bentonite can decrease by 50% when permeated with heptane. Such contraction of the clay structure can lead to the formation of cracks and macropores, with a concomitant alteration of the diffusional pathways that solutes follow. Models formulated for diffusional transport in soil are available to calculate the tortuosity factor as a function of water content. In addition, models are available to simulate phenomena in which the diffusion coefficient is concentration dependent. However, calculations of diffusional transport using such models show that they may not adequately reflect the impact of the alteration of the clay structure. However, modeling the transport of organic solutes in clay as a dual-domain system with some minimal advective transport in macropores can yield tortuosity factors greater than 1.0. Thus, it appears the cracking of clay in contact with organic solvents and a resultant advective component to transport of the solute may be an explanation of field observations.

A computational kinetic model of diffusion for molecular systems.

PubMed

Teo, Ivan; Schulten, Klaus

2013-09-28

Regulation of biomolecular transport in cells involves intra-protein steps like gating and passage through channels, but these steps are preceded by extra-protein steps, namely, diffusive approach and admittance of solutes. The extra-protein steps develop over a 10-100 nm length scale typically in a highly particular environment, characterized through the protein's geometry, surrounding electrostatic field, and location. In order to account for solute energetics and mobility of solutes in this environment at a relevant resolution, we propose a particle-based kinetic model of diffusion based on a Markov State Model framework. Prerequisite input data consist of diffusion coefficient and potential of mean force maps generated from extensive molecular dynamics simulations of proteins and their environment that sample multi-nanosecond durations. The suggested diffusion model can describe transport processes beyond microsecond duration, relevant for biological function and beyond the realm of molecular dynamics simulation. For this purpose the systems are represented by a discrete set of states specified by the positions, volumes, and surface elements of Voronoi grid cells distributed according to a density function resolving the often intricate relevant diffusion space. Validation tests carried out for generic diffusion spaces show that the model and the associated Brownian motion algorithm are viable over a large range of parameter values such as time step, diffusion coefficient, and grid density. A concrete application of the method is demonstrated for ion diffusion around and through the Eschericia coli mechanosensitive channel of small conductance ecMscS.

Properties of interfaces and transport across them.

PubMed

Cabezas, H

2000-01-01

Much of the biological activity in cell cytoplasm occurs in compartments some of which may be formed, as suggested in this book, by phase separation, and many of the functions of such compartments depend on the transport or exchange of molecules across interfaces. Thus a fundamentally based discussion of the properties of phases, interfaces, and diffusive transport across interfaces has been given to further elucidate these phenomena. An operational criterion for the width of interfaces is given in terms of molecular and physical arguments, and the properties of molecules inside phases and interfaces are discussed in terms of molecular arguments. In general, the properties of the interface become important when the molecules diffusing across are smaller than the width of the interface. Equilibrium partitioning, Donnan phenomena, and electrochemical potentials at interfaces are also discussed in detail. The mathematical expressions for modeling transport across interfaces are discussed in detail. These describe a practical and detailed model for transport across interfaces. For molecules smaller than the width of the interface, this includes a detailed model for diffusion inside the interface. Last, the question of the time scale for phase formation and equilibration in biological systems is discussed.

Room-temperature ballistic energy transport in molecules with repeating units

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

Rubtsova, Natalia I.; Nyby, Clara M.; Zhang, Hong

2015-06-07

In materials, energy can propagate by means of two limiting regimes: diffusive and ballistic. Ballistic energy transport can be fast and efficient and often occurs with a constant speed. Using two-dimensional infrared spectroscopy methods, we discovered ballistic energy transport via individual polyethylene chains with a remarkably high speed of 1440 m/s and the mean free path length of 14.6 Å in solution at room temperature. Whereas the transport via the chains occurs ballistically, the mechanism switches to diffusive with the effective transport speed of 130 m/s at the end-groups attached to the chains. A unifying model of the transport inmore » molecules is presented with clear time separation and additivity among the transport along oligomeric fragments, which occurs ballistically, and the transport within the disordered fragments, occurring diffusively. The results open new avenues for making novel elements for molecular electronics, including ultrafast energy transporters, controlled chemical reactors, and sub-wavelength quantum nanoseparators.« less

Diffusive vs. impulsive energetic electron transport during radiation belt storms

NASA Astrophysics Data System (ADS)

Vassiliadis, D.; Koepke, M.; Tornquist, M.

2008-12-01

Earth's electron radiation belts are continually replenished by inward particle transport (as well as other, local acceleration processes) taking place during radiation belt storms. For some storms the radial transport is primarily diffusive while for others it is impulsive, or characterized by injections. To distinguish between these types of inward transport, we first use a dynamic model of the phase-space density as measured by POLAR/HIST and expressed in terms of adiabatic invariants [Green and Kivelson, 2004]. In a review of storms from 1997 to 2004 the coefficients of the model are peaked at characteristic temporal and phase- space (mu, k, L*) scales during specific storms. The transport is quantified in terms of those invariants which are violated and identified with peaks of the electron distribution in invariant space. Second, we run guiding- center simulations in wave fields fitted to in situ measurements complemented at low and high L by ground ULF pulsations. The modes of response identified in earlier studies from SAMPEX and POLAR electron flux measurements are now associated with primarily diffusive transport in the central range of the outer belt, L=4-8, and primarily impulsive transport near the plasmapause boundary, L=3-4.

On modeling pressure diffusion in non-homogeneous shear flows

NASA Technical Reports Server (NTRS)

Demuren, A. O.; Rogers, M. M.; Durbin, P.; Lele, S. K.

1996-01-01

New models are proposed for the 'slow and 'rapid' parts of the pressure diffusive transport based on the examination of DNS databases for plane mixing layers and wakes. The model for the 'slow' part is non-local, but requires the distribution of the triple-velocity correlation as a local source. The latter can be computed accurately for the normal component from standard gradient diffusion models, but such models are inadequate for the cross component. More work is required to remedy this situation.

Practical and adequate approach to modeling light propagation in an adult head with low-scattering regions by use of diffusion theory.

PubMed

Koyama, Tatsuya; Iwasaki, Atsushi; Ogoshi, Yosuke; Okada, Eiji

2005-04-10

A practical and adequate approach to modeling light propagation in an adult head with a low-scattering cerebrospinal fluid (CSF) region by use of diffusion theory was investigated. The diffusion approximation does not hold in a nonscattering or low-scattering regions. The hybrid radiosity-diffusion method was adopted to model the light propagation in the head with a nonscattering region. In the hybrid method the geometry of the nonscattering region is acquired as a priori information. In reality, low-level scattering occurs in the CSF region and may reduce the error caused by the diffusion approximation. The partial optical path length and the spatial sensitivity profile calculated by the finite-element method agree well with those calculated by the Monte Carlo method in the case in which the transport scattering coefficient of the CSF layer is greater than 0.3 mm(-1). Because it is feasible to assume that the transport scattering coefficient of a CSF layer is 0.3 mm(-1), it is practical to adopt diffusion theory to the modeling of light propagation in an adult head as an alternative to the hybrid method.

Practical and adequate approach to modeling light propagation in an adult head with low-scattering regions by use of diffusion theory

NASA Astrophysics Data System (ADS)

Koyama, Tatsuya; Iwasaki, Atsushi; Ogoshi, Yosuke; Okada, Eiji

2005-04-01

A practical and adequate approach to modeling light propagation in an adult head with a low-scattering cerebrospinal fluid (CSF) region by use of diffusion theory was investigated. The diffusion approximation does not hold in a nonscattering or low-scattering regions. The hybrid radiosity-diffusion method was adopted to model the light propagation in the head with a nonscattering region. In the hybrid method the geometry of the nonscattering region is acquired as a priori information. In reality, low-level scattering occurs in the CSF region and may reduce the error caused by the diffusion approximation. The partial optical path length and the spatial sensitivity profile calculated by the finite-element method agree well with those calculated by the Monte Carlo method in the case in which the transport scattering coefficient of the CSF layer is greater than 0.3 mm^-1. Because it is feasible to assume that the transport scattering coefficient of a CSF layer is 0.3 mm^-1, it is practical to adopt diffusion theory to the modeling of light propagation in an adult head as an alternative to the hybrid method.

Simulating Bioremediation of Chloroethenes in a Fractured Rock Aquifer.

NASA Astrophysics Data System (ADS)

Curtis, G. P.

2016-12-01

Reactive transport simulations are being conducted to synthesize the results of a field experiment on the enhanced bioremediation of chloroethenes in a heterogeneous fractured-rock aquifer near West Trenton, NJ. The aquifer consists of a sequence of dipping mudstone beds, with water-conducting bedding-plane fractures separated by low-permeability rock where transport is diffusion-limited. The enhanced bioremediation experiment was conducted by injecting emulsified vegetable oil as an electron donor (EOS™) and a microbial consortium (KB1™) that contained dehalococcoides ethenogenes into a fracture zone that had maximum trichloroethene (TCE) concentrations of 84µM. TCE was significantly biodegraded to dichloroethene, chloroethene and ethene or CO2 at the injection well and at a downgradient well. The results also show the concomitant reduction of Fe(III) and S(6) and the production of methane . The results were used to calibrate transport models for quantifying the dominant mass-removal mechanisms. A nonreactive transport model was developed to simulate advection, dispersion and matrix diffusion of bromide and deuterium tracers present in the injection solution. This calibrated model matched tracer concentrations at the injection well and a downgradient observation well and demonstrated that matrix diffusion was a dominant control on tracer transport. A reactive transport model was developed to extend the nonreactive transport model to simulate the microbially mediated sequential dechlorination reactions, reduction of Fe(III) and S(6), and methanogenesis. The reactive transport model was calibrated to concentrations of chloride, chloroethenes, pH, alkalinity, redox-sensitive species and major ions, to estimate key biogeochemical kinetic parameters. The simulation results generally match the diverse set of observations at the injection and observation wells throughout the three year experiment. In addition, the observations and model simulations indicate that a significant pool of TCE that was initially sorbed to either the fracture surfaces or in the matrix was degraded during the field experiment. The calibrated reactive transport model will be used to quantify the extent of chloroethene mass removal from a range of hypothetical aquifers.

Characterizing acid diffusion lengths in chemically amplified resists from measurements of deprotection kinetics

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

Patil, Abhijit A.; Pandey, Yogendra Narayan; Doxastakis, Manolis

2014-10-01

The acid-catalyzed deprotection of glassy poly(4-hydroxystyrene-co-tertbutyl acrylate) films was studied with infrared absorbance spectroscopy and stochastic simulations. Experimental data were interpreted with a simple description of subdiffusive acid transport coupled to second-order acid loss. This model predicts key attributes of observed deprotection rates, such as fast reaction at short times, slow reaction at long times, and a nonlinear dependence on acid loading. Fickian diffusion is approached by increasing the post-exposure bake temperature or adding plasticizing agents to the polymer resin. These findings demonstrate that acid mobility and overall deprotection kinetics are coupled to glassy matrix dynamics. To complement the analysismore » of bulk kinetics, acid diffusion lengths were calculated from the anomalous transport model and compared with nanopattern line widths. The consistent scaling between experiments and simulations suggests that the anomalous diffusion model could be further developed into a predictive lithography tool.« less

Using MLT Composition Observations to Evaluate Transport in a Comprehensive High Top Model

NASA Astrophysics Data System (ADS)

Smith, A. K.

2016-12-01

Gravity waves play an outsized role in the MLT: driving the mean meridional circulation, exerting a large degree of control over the mean winds and seasonal variations in temperature, and leading to diffusive vertical transport of heat and trace species. These waves are represented using a parameterization in the NCAR Whole Atmosphere Community Climate Model (WACCM), as in many other GCMs. To evaluate their impact, we need to consider not just the mean temperature and wind but the distributions of trace species that are affected by advection due to resolved winds and waves and diffusion associated with gravity wave dissipation. The responses of chemical species to changes in the gravity wave forcing are complex and sometimes unexpected. Transport and diffusion simultaneously affect all species and the heat and momentum budgets; subsequent interactions, and the strong dependence of reaction rates on temperature, affect the net impact of transport on the composition. In evaluating the model, we evaluate the simulations using a range of available observations of composition, including O, O3, CO, CO2, NO, NO2, OH, and H2O.

Hydroxide Solvation and Transport in Anion Exchange Membranes

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

Chen, Chen; Tse, Ying-Lung Steve; Lindberg, Gerrick E.

Understanding hydroxide solvation and transport in anion exchange membranes (AEMs) can provide important insight into the design principles of these new membranes. To accurately model hydroxide solvation and transport, we developed a new multiscale reactive molecular dynamics model for hydroxide in aqueous solution, which was then subsequently modified for an AEM material. With this model, we investigated the hydroxide solvation structure and transport mechanism in the membrane. We found that a relatively even separation of the rigid side chains produces a continuous overlapping region for hydroxide transport that is made up of the first hydration shell of the tethered cationicmore » groups. Our results show that hydroxide has a significant preference for this overlapping region, transporting through it and between the AEM side chains with substantial contributions from both vehicular (standard diffusion) and Grotthuss (proton hopping) mechanisms. Comparison of the AEM with common proton exchange membranes (PEMs) showed that the excess charge is less delocalized in the AEM than the PEMs, which is correlated with a higher free energy barrier for proton transfer reactions. The vehicular mechanism also contributes considerably more than the Grotthuss mechanism for hydroxide transport in the AEM, while our previous studies of PEM systems showed a larger contribution from the Grotthuss mechanism than the vehicular mechanism for proton transport. The activation energy barrier for hydroxide diffusion in the AEM is greater than that for proton diffusion in PEMs, implying a more significant enhancement of ion transport in the AEM at elevated temperatures.« less

Hydroxide Solvation and Transport in Anion Exchange Membranes.

PubMed

Chen, Chen; Tse, Ying-Lung Steve; Lindberg, Gerrick E; Knight, Chris; Voth, Gregory A

2016-01-27

Understanding hydroxide solvation and transport in anion exchange membranes (AEMs) can provide important insight into the design principles of these new membranes. To accurately model hydroxide solvation and transport, we developed a new multiscale reactive molecular dynamics model for hydroxide in aqueous solution, which was then subsequently modified for an AEM material. With this model, we investigated the hydroxide solvation structure and transport mechanism in the membrane. We found that a relatively even separation of the rigid side chains produces a continuous overlapping region for hydroxide transport that is made up of the first hydration shell of the tethered cationic groups. Our results show that hydroxide has a significant preference for this overlapping region, transporting through it and between the AEM side chains with substantial contributions from both vehicular (standard diffusion) and Grotthuss (proton hopping) mechanisms. Comparison of the AEM with common proton exchange membranes (PEMs) showed that the excess charge is less delocalized in the AEM than the PEMs, which is correlated with a higher free energy barrier for proton transfer reactions. The vehicular mechanism also contributes considerably more than the Grotthuss mechanism for hydroxide transport in the AEM, while our previous studies of PEM systems showed a larger contribution from the Grotthuss mechanism than the vehicular mechanism for proton transport. The activation energy barrier for hydroxide diffusion in the AEM is greater than that for proton diffusion in PEMs, implying a more significant enhancement of ion transport in the AEM at elevated temperatures.

Relationship between the anomalous diffusion and the fractal dimension of the environment

NASA Astrophysics Data System (ADS)

Zhokh, Alexey; Trypolskyi, Andrey; Strizhak, Peter

2018-03-01

In this letter, we provide an experimental study highlighting a relation between the anomalous diffusion and the fractal dimension of the environment using the methanol anomalous transport through the porous solid pellets with various pores geometries and different chemical compositions. The anomalous diffusion exponent was derived from the non-integer order of the time-fractional diffusion equation that describes the methanol anomalous transport through the solid media. The surface fractal dimension was estimated from the nitrogen adsorption isotherms using the Frenkel-Halsey-Hill method. Our study shows that decreasing the fractal dimension leads to increasing the anomalous diffusion exponent, whereas the anomalous diffusion constant is independent on the fractal dimension. We show that the obtained results are in a good agreement with the anomalous diffusion model on a fractal mesh.

USER'S MANUAL FOR THE INSTREAM SEDIMENT-CONTAMINANT TRANSPORT MODEL SERATRA

EPA Science Inventory

This manual guides the user in applying the sediment-contaminant transport model SERATRA. SERATRA is an unsteady, two-dimensional code that uses the finite element computation method with the Galerkin weighted residual technique. The model has general convection-diffusion equatio...

On the statistical and transport properties of a non-dissipative Fermi-Ulam model

NASA Astrophysics Data System (ADS)

Livorati, André L. P.; Dettmann, Carl P.; Caldas, Iberê L.; Leonel, Edson D.

2015-10-01

The transport and diffusion properties for the velocity of a Fermi-Ulam model were characterized using the decay rate of the survival probability. The system consists of an ensemble of non-interacting particles confined to move along and experience elastic collisions with two infinitely heavy walls. One is fixed, working as a returning mechanism of the colliding particles, while the other one moves periodically in time. The diffusion equation is solved, and the diffusion coefficient is numerically estimated by means of the averaged square velocity. Our results show remarkably good agreement of the theory and simulation for the chaotic sea below the first elliptic island in the phase space. From the decay rates of the survival probability, we obtained transport properties that can be extended to other nonlinear mappings, as well to billiard problems.

Role of Passive Diffusion, Transporters, and Membrane Trafficking-Mediated Processes in Cellular Drug Transport.

PubMed

Cocucci, E; Kim, J Y; Bai, Y; Pabla, N

2017-01-01

Intracellular drug accumulation is thought to be dictated by two major processes, passive diffusion through the lipid membrane or membrane transporters. The relative role played by these distinct processes remains actively debated. Moreover, the role of membrane-trafficking in drug transport remains underappreciated and unexplored. Here we discuss the distinct processes involved in cellular drug distribution and propose that better experimental models are required to elucidate the differential contributions of various processes in intracellular drug accumulation. © 2016 American Society for Clinical Pharmacology and Therapeutics.

Transport Studies and Modeling in PEM Fuel Cells

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

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

2014-07-30

This project’s aim was to develop fuel cell components (i.e. membranes, gas-diffusion media (GDM), bipolar plates and flow fields) that possess specific properties (i.e. water transport and conductivity). A computational fluid dynamics model was developed to elucidate the effect of certain parameters on these specific properties. Ultimately, the model will be used to determine sensitivity of fuel cell performance to component properties to determine limiting components and to guide research. We have successfully reached our objectives and achieved most of the milestones of this project. We have designed and synthesized a variety of hydrocarbon block polymer membranes with lower equivalentmore » weight, structure, chemistry, phase separation and process conditions. These membranes provide a broad selection with optimized water transport properties. We have also designed and constructed a variety of devices that are capable of accurately measuring the water transport properties (water uptake, water diffusivity and electro-osmatic drag) of these membranes. These transport properties are correlated to the membranes’ structures derived from X-ray and microscopy techniques to determine the structure-property relationship. We successfully integrated hydrocarbon membrane MEAs with a current distribution board (CBD) to study the impact of hydrocarbon membrane on water transport in fuel cells. We have designed and fabricated various GDM with varying substrate, diffusivity and micro-porous layers (MPL) and characterized their pore structure, tortuosity and hydrophobicity. We have derived a universal chart (MacMullin number as function of wet proofing and porosity) that can be used to characterize various GDM. The abovementioned GDMs have been evaluated in operating fuel cells; their performance is correlated to various pore structure, tortuosity and hydrophobicity of the GDM. Unfortunately, determining a universal relationship between the MacMullin number and these properties was not achieved. We have simulated fuel cell performance, current distribution and water distribution at various values of the water uptake, membrane diffusivity, and electro-osmotic drag coefficient (EODC) and compared modeling results with segmented-cell data for both serpentine and parallel flow-fields. We have developed iterations of fuel cell flow fields to achieve specific water transport and thermal management targets. This work demonstrated the importance of membrane diffusivity on fuel cell performance, the necessity of a high membrane diffusion coefficient, and the desirability of a low EODC at low levels of relative humidity.« less

Two-time quantum transport and quantum diffusion.

PubMed

Kleinert, P

2009-05-01

Based on the nonequilibrium Green's function technique, a unified theory is developed that covers quantum transport and quantum diffusion in bulk semiconductors on the same footing. This approach, which is applicable to transport via extended and localized states, extends previous semiphenomenological studies and puts them on a firm microscopic basis. The approach is sufficiently general and applies not only to well-studied quantum-transport problems, but also to models, in which the Hamiltonian does not commute with the dipole operator. It is shown that even for the unified treatment of quantum transport and quantum diffusion in homogeneous systems, all quasimomenta of the carrier distribution function are present and fulfill their specific function. Particular emphasis is put on the double-time nature of quantum kinetics. To demonstrate the existence of robust macroscopic transport effects that have a true double-time character, a phononless steady-state current is identified that appears only beyond the generalized Kadanoff-Baym ansatz.

Anomalous Transport of High Energy Cosmic Rays in Galactic Superbubbles

NASA Technical Reports Server (NTRS)

Barghouty, Nasser F.

2014-01-01

High-energy cosmic rays may exhibit anomalous transport as they traverse and are accelerated by a collection of supernovae explosions in a galactic superbubble. Signatures of this anomalous transport can show up in the particles' evolution and their spectra. In a continuous-time-random- walk (CTRW) model assuming standard diffusive shock acceleration theory (DSA) for each shock encounter, and where the superbubble (an OB stars association) is idealized as a heterogeneous region of particle sources and sinks, acceleration and transport in the superbubble can be shown to be sub-diffusive. While the sub-diffusive transport can be attributed to the stochastic nature of the acceleration time according to DSA theory, the spectral break appears to be an artifact of transport in a finite medium. These CTRW simulations point to a new and intriguing phenomenon associated with the statistical nature of collective acceleration of high energy cosmic rays in galactic superbubbles.

Simulating Donnan equilibria based on the Nernst-Planck equation

NASA Astrophysics Data System (ADS)

Gimmi, Thomas; Alt-Epping, Peter

2018-07-01

Understanding ion transport through clays and clay membranes is important for many geochemical and environmental applications. Ion transport is affected by electrostatic forces exerted by charged clay surfaces. Anions are partly excluded from pore water near these surfaces, whereas cations are enriched. Such effects can be modeled by the Donnan approach. Here we introduce a new, comparatively simple way to represent Donnan equilibria in transport simulations. We include charged surfaces as immobile ions in the balance equation and calculate coupled transport of all components, including the immobile charges, with the Nernst-Planck equation. This results in an additional diffusion potential that influences ion transport, leading to Donnan ion distributions while maintaining local charge balance. The validity of our new approach was demonstrated by comparing Nernst-Planck simulations using the reactive transport code Flotran with analytical solutions available for simple Donnan systems. Attention has to be paid to the numerical evaluation of the electrochemical migration term in the Nernst-Planck equation to obtain correct results for asymmetric electrolytes. Sensitivity simulations demonstrate the influence of various Donnan model parameters on simulated anion accessible porosities. It is furthermore shown that the salt diffusion coefficient in a Donnan pore depends on local concentrations, in contrast to the aqueous salt diffusion coefficient. Our approach can be easily implemented into other transport codes. It is versatile and facilitates, for instance, assessing the implications of different activity models for the Donnan porosity.

Comparative study of expression and activity of glucose transporters between stem cell-derived brain microvascular endothelial cells and hCMEC/D3 cells.

PubMed

Al-Ahmad, Abraham J

2017-10-01

Glucose constitutes a major source of energy of mammalian brains. Glucose uptake at the blood-brain barrier (BBB) occurs through a facilitated glucose transport, through glucose transporter 1 (GLUT1), although other isoforms have been described at the BBB. Mutations in GLUT1 are associated with the GLUT1 deficiency syndrome, yet none of the current in vitro models of the human BBB maybe suited for modeling such a disorder. In this study, we investigated the expression of glucose transporters and glucose diffusion across brain microvascular endothelial cells (BMECs) derived from healthy patient-derived induced pluripotent stem cells (iPSCs). We investigated the expression of different glucose transporters at the BBB using immunocytochemistry and flow cytometry and measured glucose uptake and diffusion across BMEC monolayers obtained from two iPSC lines and from hCMEC/D3 cells. BMEC monolayers showed expression of several glucose transporters, in particular GLUT1, GLUT3, and GLUT4. Diffusion of glucose across the monolayers was mediated via a saturable transcellular mechanism and partially inhibited by pharmacological inhibitors. Taken together, our study suggests the presence of several glucose transporters isoforms at the human BBB and demonstrates the feasibility of modeling glucose across the BBB using patient-derived stem cells. Copyright © 2017 the American Physiological Society.

Calculation of Transport Coefficients in Dense Plasma Mixtures

NASA Astrophysics Data System (ADS)

Haxhimali, T.; Cabot, W. H.; Caspersen, K. J.; Greenough, J.; Miller, P. L.; Rudd, R. E.; Schwegler, E. R.

2011-10-01

We use classical molecular dynamics (MD) to estimate species diffusivity and viscosity in mixed dense plasmas. The Yukawa potential is used to describe the screened Coulomb interaction between the ions. This potential has been used widely, providing the basis for models of dense stellar materials, inertial confined plasmas, and colloidal particles in electrolytes. We calculate transport coefficients in equilibrium simulations using the Green- Kubo relation over a range of thermodynamic conditions including the viscosity and the self - diffusivity for each component of the mixture. The interdiffusivity (or mutual diffusivity) can then be related to the self-diffusivities by using a generalization of the Darken equation. We have also employed non-equilibrium MD to estimate interdiffusivity during the broadening of the interface between two regions each with a high concentration of either species. Here we present results for an asymmetric mixture between Ar and H. These can easily be extended to other plasma mixtures. A main motivation for this study is to develop accurate transport models that can be incorporated into the hydrodynamic codes to study hydrodynamic instabilities. We use classical molecular dynamics (MD) to estimate species diffusivity and viscosity in mixed dense plasmas. The Yukawa potential is used to describe the screened Coulomb interaction between the ions. This potential has been used widely, providing the basis for models of dense stellar materials, inertial confined plasmas, and colloidal particles in electrolytes. We calculate transport coefficients in equilibrium simulations using the Green- Kubo relation over a range of thermodynamic conditions including the viscosity and the self - diffusivity for each component of the mixture. The interdiffusivity (or mutual diffusivity) can then be related to the self-diffusivities by using a generalization of the Darken equation. We have also employed non-equilibrium MD to estimate interdiffusivity during the broadening of the interface between two regions each with a high concentration of either species. Here we present results for an asymmetric mixture between Ar and H. These can easily be extended to other plasma mixtures. A main motivation for this study is to develop accurate transport models that can be incorporated into the hydrodynamic codes to study hydrodynamic instabilities. This work was performed under the auspices of the US Dept. of Energy by Lawrence Livermore National Security, LLC under Contract DE-AC52-07NA27344.

Computation of the unsteady facilitated transport of oxygen in hemoglobin

NASA Technical Reports Server (NTRS)

Davis, Sanford

1990-01-01

The transport of a reacting permeant diffusing through a thin membrane is extended to more realistic dissociation models. A new nonlinear analysis of the reaction-diffusion equations, using implicit finite-difference methods and direct block solvers, is used to study the limits of linearized and equilibrium theories. Computed curves of molecular oxygen permeating through hemoglobin solution are used to illustrate higher-order reaction models, the effect of concentration boundary layers at the membrane interfaces, and the transient buildup of oxygen flux.

Effects of sorption competition on caesium diffusion through compacted argillaceous rock

NASA Astrophysics Data System (ADS)

Jakob, Andreas; Pfingsten, Wilfried; Van Loon, Luc

2009-05-01

We carried out a small-scale laboratory diffusion experiment on a disk-like sample of Opalinus clay from the Mont Terri underground laboratory (Switzerland) using 134Cs as tracer. A through-diffusion phase was followed by an out-diffusion phase where the tracer taken up by the sample was released again. Since the tracer concentration at both boundaries was monitored, careful mass-balance considerations were feasible. A first analysis of the experimental data was done in the frame of a single-species model accounting only for transport and non-linear sorption of caesium. The model could match the data of the through-diffusion phase, however only, when strongly reducing the sorption data based on batch sorption experiments. Yet, such a procedure was in strong contradiction with sorption measurements performed on dispersed and compacted systems. In addition, predictions concerning tracer out-diffusion and mass-balance considerations clearly revealed the shortcomings of this type of model. In a second attempt we applied a multi-species transport model where now the whole water chemistry and a sorption model for caesium were considered. First, the value for the diffusion coefficient was fixed to the best-fit value of the single-species model. But again, the sorption site densities had to be reduced strongly albeit the reduction factor was smaller. Only when fixing the sorption site densities to those values of the sorption model and letting the effective diffusion coefficient D e free for the adjustment, could through-diffusion data be reasonably well fitted and out-diffusion as well as mass-balances be predicted in a satisfying manner. The main results are: (1) The best-fit could be achieved with a value for D e of 1.8 × 10 -10 m 2 s -1 which is rather high but corroborated by results of a molecular modelling study. (2) If caesium arrives in the Opalinus clay sample potassium and sodium (calcium etc.) ions are released and caesium ions are sorbed. The released cations diffuse to lower concentration regions according to their individual concentration gradients. Since locally the cation concentration for potassium, (sodium and calcium) is increased, sorption of these cations is also locally enhanced, affecting in return the sorption behaviour of migrating caesium. Consequently, the sorption process of caesium in such diffusion experiments cannot be addressed by a non-linear isotherm formalism any longer. (3) A reasonable analysis of such single tracer diffusion experiments therefore requires the combined description of transport (diffusion) and sorption of many cations and the whole complex water chemistry of the system. Thus, single-species models can only be applied with care in the considered concentration ranges.

The relative importance of decomposition and transport mechanisms in accounting for soil organic carbon profiles

NASA Astrophysics Data System (ADS)

Guenet, B.; Eglin, T.; Vasilyeva, N.; Peylin, P.; Ciais, P.; Chenu, C.

2013-04-01

Soil is the major terrestrial reservoir of carbon and a substantial part of this carbon is stored in deep layers, typically deeper than 50 cm below the surface. Several studies underlined the quantitative importance of this deep soil organic carbon (SOC) pool and models are needed to better understand this stock and its evolution under climate and land-uses changes. In this study, we tested and compared three simple theoretical models of vertical transport for SOC against SOC profiles measurements from a long-term bare fallow experiment carried out by the Central-Chernozem State Natural Biosphere Reserve in the Kursk Region of Russia. The transport schemes tested are diffusion, advection and both diffusion and advection. They are coupled to three different formulations of soil carbon decomposition kinetics. The first formulation is a first order kinetics widely used in global SOC decomposition models; the second one, so-called "priming" model, links SOC decomposition rate to the amount of fresh organic matter, representing the substrate interactions. The last one is also a first order kinetics, but SOC is split into two pools. Field data are from a set of three bare fallow plots where soil received no input during the past 20, 26 and 58 yr, respectively. Parameters of the models were optimised using a Bayesian method. The best results are obtained when SOC decomposition is assumed to be controlled by fresh organic matter (i.e., the priming model). In comparison to the first-order kinetic model, the priming model reduces the overestimation in the deep layers. We also observed that the transport scheme that improved the fit with the data depended on the soil carbon mineralisation formulation chosen. When soil carbon decomposition was modelled to depend on the fresh organic matter amount, the transport mechanism which improved best the fit to the SOC profile data was the model representing both advection and diffusion. Interestingly, the older the bare fallow is, the lesser the need for diffusion is, suggesting that stabilised carbon may not be transported within the profile by the same mechanisms than more labile carbon.

Numerical modeling of coupled variably saturated fluid flow and reactive transport with fast and slow chemical reactions

NASA Astrophysics Data System (ADS)

Yeh, Gour-Tsyh (George); Siegel, Malcolm D.; Li, Ming-Hsu

2001-02-01

The couplings among chemical reaction rates, advective and diffusive transport in fractured media or soils, and changes in hydraulic properties due to precipitation and dissolution within fractures and in rock matrix are important for both nuclear waste disposal and remediation of contaminated sites. This paper describes the development and application of LEHGC2.0, a mechanistically based numerical model for simulation of coupled fluid flow and reactive chemical transport, including both fast and slow reactions in variably saturated media. Theoretical bases and numerical implementations are summarized, and two example problems are demonstrated. The first example deals with the effect of precipitation/dissolution on fluid flow and matrix diffusion in a two-dimensional fractured media. Because of the precipitation and decreased diffusion of solute from the fracture into the matrix, retardation in the fractured medium is not as large as the case wherein interactions between chemical reactions and transport are not considered. The second example focuses on a complicated but realistic advective-dispersive-reactive transport problem. This example exemplifies the need for innovative numerical algorithms to solve problems involving stiff geochemical reactions.

Cosmic-ray propagation with DRAGON2: I. numerical solver and astrophysical ingredients

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

Evoli, Carmelo; Gaggero, Daniele; Vittino, Andrea

2017-02-01

We present version 2 of the DRAGON code designed for computing realistic predictions of the CR densities in the Galaxy. The code numerically solves the interstellar CR transport equation (including inhomogeneous and anisotropic diffusion, either in space and momentum, advective transport and energy losses), under realistic conditions. The new version includes an updated numerical solver and several models for the astrophysical ingredients involved in the transport equation. Improvements in the accuracy of the numerical solution are proved against analytical solutions and in reference diffusion scenarios. The novel features implemented in the code allow to simulate the diverse scenarios proposed tomore » reproduce the most recent measurements of local and diffuse CR fluxes, going beyond the limitations of the homogeneous galactic transport paradigm. To this end, several applications using DRAGON2 are presented as well. This new version facilitates the users to include their own physical models by means of a modular C++ structure.« less

MODELING AND ANALYSIS OF FISSION PRODUCT TRANSPORT IN THE AGR-3/4 EXPERIMENT

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

Humrickhouse, Paul W.; Collin, Blaise P.; Hawkes, Grant L.

In this work we describe the ongoing modeling and analysis efforts in support of the AGR-3/4 experiment. AGR-3/4 is intended to provide data to assess fission product retention and transport (e.g., diffusion coefficients) in fuel matrix and graphite materials. We describe a set of pre-test predictions that incorporate the results of detailed thermal and fission product release models into a coupled 1D radial diffusion model of the experiment, using diffusion coefficients reported in the literature for Ag, Cs, and Sr. We make some comparisons of the predicted Cs profiles to preliminary measured data for Cs and find these to bemore » reasonable, in most cases within an order of magnitude. Our ultimate objective is to refine the diffusion coefficients using AGR-3/4 data, so we identify an analytical method for doing so and demonstrate its efficacy via a series of numerical experiments using the model predictions. Finally, we discuss development of a post-irradiation examination plan informed by the modeling effort and simulate some of the heating tests that are tentatively planned.« less

Transport and concentration controls for chloride, strontium, potassium and lead in Uvas Creek, a small cobble-bed stream in Santa Clara County, California, U.S.A. 2. Mathematical modeling

USGS Publications Warehouse

Jackman, A.P.; Walters, R.A.; Kennedy, V.C.

1984-01-01

Three models describing solute transport of conservative ion species and another describing transport of species which adsorb linearly and reversibly on bed sediments are developed and tested. The conservative models are based on three different conceptual models of the transient storage of solute in the bed. One model assumes the bed to be a well-mixed zone with flux of solute into the bed proportional to the difference between stream concentration and bed concentration. The second model assumes solute in the bed is transported by a vertical diffusion process described by Fick's law. The third model assumes that convection occurs in a selected portion of the bed while the mechanism of the first model functions everywhere. The model for adsorbing species assumes that the bed consists of particles of uniform size with the rate of uptake controlled by an intraparticle diffusion process. All models are tested using data collected before, during and after a 24-hr. pulse injection of chloride, strontium, potassium and lead ions into Uvas Creek near Morgan Hill, California, U.S.A. All three conservative models accurately predict chloride ion concentrations in the stream. The model employing the diffusion mechanism for bed transport predicts better than the others. The adsorption model predicts both strontium and potassium ion concentrations well during the injection of the pulse but somewhat overestimates the observed concentrations after the injection ceases. The overestimation may be due to the convection of solute deep into the bed where it is retained longer than the 3-week post-injection observation period. The model, when calibrated for strontium, predicts potassium equally well when the adsorption equilibrium constant for strontium is replaced by that for potassium. ?? 1984.

Enhanced drug transport through alginate biofilms using magnetic nanoparticles

NASA Astrophysics Data System (ADS)

McGill, Shayna L.; Cuylear, Carla; Adolphi, Natalie L.; Osinski, Marek; Smyth, Hugh

2009-02-01

The development of microbiological biofilms greatly reduces the efficacy of antibiotic therapies and is a serious problem in chronic infection and for implantable medical devices. We investigated the potential of superparamagnetic nanoparticles to increase transport through in vitro models of alginate biofilms. An in vitro alginate biofilm model was developed to mimic the composition of in vivo samples of P. aeruginosa infections. Transport through this model biofilm was performed using both bulk diffusion methods and single particle tracking techniques in the presence and absence of an external magnetic field. Bulk diffusion of nanoparticles through the biofilm was significantly enhanced in the presence of a magnetic field, both visually and quantitatively. Nanoparticle trajectories also showed transport increases were significantly higher when magnetic fields were applied. We also showed that surface chemistry (cationic, anioni, or neutral) of the nanoparticles significantly influenced transport rates. Finally, nanoparticle size also influenced the transport rates and variability of transport rates through the biofilm. In these first studies using magnetic nanoparticles in bacterial biofilms, we demonstrate that transport enhancement can be achieved and further studies are warranted.

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

NASA Astrophysics Data System (ADS)

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

2005-05-01

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

Third-moment closure of turbulence for predictions of separating and reattaching shear flows: A study of Reynolds-stress closure model

NASA Technical Reports Server (NTRS)

Amano, R. S.; Goel, P.

1986-01-01

A numerical study of computations in backward-facing steps with flow separation and reattachment, using the Reynolds stress closure is presented. The highlight of this study is the improvement of the Reynold-stress model (RSM) by modifying the diffusive transport of the Reynolds stresses through the formulation, solution and subsequent incorporation of the transport equations of the third moments, bar-u(i)u(j)u(k), into the turbulence model. The diffusive transport of the Reynolds stresses, represented by the gradients of the third moments, attains greater significance in recirculating flows. The third moments evaluated by the development and solution of the complete transport equations are superior to those obtained by existing algebraic correlations. A low-Reynolds number model for the transport equations of the third moments is developed and considerable improvement in the near-wall profiles of the third moments is observed. The values of the empirical constants utilized in the development of the model are recommended. The Reynolds-stress closure is consolidated by incorporating the equations of k and e, containing the modified diffusion coefficients, and the transport equations of the third moments into the Reynolds stress equations. Computational results obtained by the original k-e model, the original RSM and the consolidated and modified RSM are compared with experimental data. Overall improvement in the predictions is seen by consolidation of the RMS and a marked improvement in the profiles of bar-u(i)u(j)u(k) is obtained around the reattachment region.

Morphogen transport

PubMed Central

Müller, Patrick; Rogers, Katherine W.; Yu, Shuizi R.; Brand, Michael; Schier, Alexander F.

2013-01-01

The graded distribution of morphogens underlies many of the tissue patterns that form during development. How morphogens disperse from a localized source and how gradients in the target tissue form has been under debate for decades. Recent imaging studies and biophysical measurements have provided evidence for various morphogen transport models ranging from passive mechanisms, such as free or hindered extracellular diffusion, to cell-based dispersal by transcytosis or cytonemes. Here, we analyze these transport models using the morphogens Nodal, fibroblast growth factor and Decapentaplegic as case studies. We propose that most of the available data support the idea that morphogen gradients form by diffusion that is hindered by tortuosity and binding to extracellular molecules. PMID:23533171

Quantifying the transport properties of lipid mesophases by theoretical modelling of diffusion experiments

NASA Astrophysics Data System (ADS)

Antognini, Luca M.; Assenza, Salvatore; Speziale, Chiara; Mezzenga, Raffaele

2016-08-01

Lyotropic Liquid Crystals (LLCs) are a class of lipid-based membranes with a strong potential for drug-delivery employment. The characterization and control of their transport properties is a central issue in this regard, and has recently prompted a notable volume of research on the topic. A promising experimental approach is provided by the so-called diffusion setup, where the drug molecules diffuse from a feeding chamber filled with water to a receiving one passing through a LLC. In the present work we provide a theoretical framework for the proper description of this setup, and validate it by means of targeted experiments. Due to the inhomogeneity of the system, a rich palette of different diffusion dynamics emerges from the interplay of the different time- and lengthscales thereby present. Our work paves the way to the employment of diffusion experiments to quantitatively characterize the transport properties of LLCs, and provides the basic tools for device diffusion setups with controlled kinetic properties.

Transport dissipative particle dynamics model for mesoscopic advection- diffusion-reaction problems

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

Zhen, Li; Yazdani, Alireza; Tartakovsky, Alexandre M.

2015-07-07

We present a transport dissipative particle dynamics (tDPD) model for simulating mesoscopic problems involving advection-diffusion-reaction (ADR) processes, along with a methodology for implementation of the correct Dirichlet and Neumann boundary conditions in tDPD simulations. tDPD is an extension of the classic DPD framework with extra variables for describing the evolution of concentration fields. The transport of concentration is modeled by a Fickian flux and a random flux between particles, and an analytical formula is proposed to relate the mesoscopic concentration friction to the effective diffusion coefficient. To validate the present tDPD model and the boundary conditions, we perform three tDPDmore » simulations of one-dimensional diffusion with different boundary conditions, and the results show excellent agreement with the theoretical solutions. We also performed two-dimensional simulations of ADR systems and the tDPD simulations agree well with the results obtained by the spectral element method. Finally, we present an application of the tDPD model to the dynamic process of blood coagulation involving 25 reacting species in order to demonstrate the potential of tDPD in simulating biological dynamics at the mesoscale. We find that the tDPD solution of this comprehensive 25-species coagulation model is only twice as computationally expensive as the DPD simulation of the hydrodynamics only, which is a significant advantage over available continuum solvers.« less

Transport of Solar Energetic Particles across the Parker field direction due to field line meandering

NASA Astrophysics Data System (ADS)

Laitinen, T. L.; Kopp, A.; Effenberger, F.; Dalla, S.; Marsh, M. S.

2014-12-01

Multi-spacecraft observations of Solar Energetic Particles (SEPs) show that the SEPs can spread large distances across the mean Parker spiral field. The SEPs accelerated during a solar eruption can be observed 360° around the Sun, and the dependence of SEP peak intensity on heliographic longitude at 1 AU has been fitted with Gaussian profiles with σ=30-50° for several events (e.g., Dresing et al 2014; Richardson et al 2014). SEP anisotropy measurements suggest that interplanetary transport is an important factor to the SEP cross-field extent (Dresing et al 2014). However, the currently used diffusive Fokker Planck (FP) description of SEP transport, with realistic diffusion coefficients, has been found insufficient to explain the SEP event cross-field extents. Recently Laitinen et al (2013) emphasised the importance of particle propagation along meandering field lines, which cannot be described as diffusion. They showed that early in an event field line meandering dominates particle cross-field transport and produces events wider than the FP description. They also introduced a new FP model that incorporates both field line meandering and SEP cross-field diffusion using stochastic differential equations and a constant background magnetic field. In this work, we implement the new FP model into Parker field geometry, to study the evolution of an SEP event in the interplanetary space. We compare the new model to the traditional FP approach by using particle and field line diffusion coefficients that are calculated consistently for both models using an assumed radial and spectral description of the turbulence evolution. We find that while the traditional SEP propagation modelling gives typically longitudinal extent with σ=10-20°, the new model results in values σ=30-50°, which is consistent with SEP observations. We conclude that field line meandering must be taken into account when modelling SEP propagation in the interplanetary space.

Modeling cytoskeletal traffic: an interplay between passive diffusion and active transport.

PubMed

Neri, Izaak; Kern, Norbert; Parmeggiani, Andrea

2013-03-01

We introduce the totally asymmetric simple exclusion process with Langmuir kinetics on a network as a microscopic model for active motor protein transport on the cytoskeleton, immersed in the diffusive cytoplasm. We discuss how the interplay between active transport along a network and infinite diffusion in a bulk reservoir leads to a heterogeneous matter distribution on various scales: we find three regimes for steady state transport, corresponding to the scale of the network, of individual segments, or local to sites. At low exchange rates strong density heterogeneities develop between different segments in the network. In this regime one has to consider the topological complexity of the whole network to describe transport. In contrast, at moderate exchange rates the transport through the network decouples, and the physics is determined by single segments and the local topology. At last, for very high exchange rates the homogeneous Langmuir process dominates the stationary state. We introduce effective rate diagrams for the network to identify these different regimes. Based on this method we develop an intuitive but generic picture of how the stationary state of excluded volume processes on complex networks can be understood in terms of the single-segment phase diagram.

Multiphasic modeling of charged solute transport across articular cartilage: Application of multi-zone finite-bath model.

PubMed

Arbabi, Vahid; Pouran, Behdad; Weinans, Harrie; Zadpoor, Amir A

2016-06-14

Charged and uncharged solutes penetrate through cartilage to maintain the metabolic function of chondrocytes and to possibly restore or further breakdown the cartilage tissue in different stages of osteoarthritis. In this study the transport of charged solutes across the various zones of cartilage was quantified, taken into account the physicochemical interactions between the solute and the cartilage constituents. A multiphasic finite-bath finite element (FE) model was developed to simulate equine cartilage diffusion experiments that used a negatively charged contrast agent (ioxaglate) in combination with serial micro-computed tomography (micro-CT) to measure the diffusion. By comparing the FE model with the experimental data both the diffusion coefficient of ioxaglate and the fixed charge density (FCD) were obtained. In the multiphasic model, cartilage was divided into multiple (three) zones to help understand how diffusion coefficient and FCD vary across cartilage thickness. The direct effects of charged solute-FCD interaction on diffusion were investigated by comparing the diffusion coefficients derived from the multiphasic and biphasic-solute models. We found a relationship between the FCD obtained by the multiphasic model and ioxaglate partitioning obtained from micro-CT experiments. Using our multi-zone multiphasic model, diffusion coefficient of the superficial zone was up to ten-fold higher than that of the middle zone, while the FCD of the middle zone was up to almost two-fold higher than that of the superficial zone. In conclusion, the developed finite-bath multiphasic model provides us with a non-destructive method by which we could obtain both diffusion coefficient and FCD of different cartilage zones. The outcomes of the current work will also help understand how charge of the bath affects the diffusion of a charged molecule and also predict the diffusion behavior of a charged solute across articular cartilage. Copyright © 2016 Elsevier Ltd. All rights reserved.

Proton transport by phosphate diffusion--a mechanism of facilitated CO2 transfer

PubMed Central

1976-01-01

We have measured CO2 fluxes across phosphate solutions at different carbonic anhydrase concentrations, bicarbonate concentration gradients, phosphate concentrations, and mobilities. Temperature was 22-25 degrees C, the pH of the phosphate solutions was 7.0-7.3. We found that under physiological conditions of pH and pCO2 a facilitated diffusion of CO2 occurs in addition to free diffusion when (a) sufficient carbonic anhydrase is present, and (b) a concentration gradient of HCO3- is established along with a pCO2 gradient, and (c) the phosphate buffer has a mobility comparable to that of bicarbonate. When the phosphate was immobilized by attaching 0.25-mm-long cellulose particles, no facilitation of CO2 diffusion was detectable. A mechanism of facilitated CO2 diffusion in phosphate solutions analogous to that in albumin solutions was proposed on the basis of these findings: bicarbonate diffusion together with a facilitated proton transport by phosphate diffusion. A mathematical model of this mechanism was formulated. The CO2 fluxed predicted by the model agree quantitatively with the experimentally determined fluxes. It is concluded that a highly effective proton transport mechanism acts in solutions of mobile phosphate buffers. By this mechanism; CO2 transfer may be increased up to fivefold and proton transfer may be increased to 10,000-fold. PMID:6619

A Reactive-Transport Model Describing Methanogen Growth and Methane Production in Diffuse Flow Vents at Axial Seamount

NASA Astrophysics Data System (ADS)

Algar, C. K.

2015-12-01

Hydrogenotrophic methanogenesis is an important mode of metabolism in deep-sea hydrothermal vents. Diffuse vent fluids often show a depletion in hydrogen with a corresponding increase in methane relative to pure-mixing of end member fluid and seawater, and genomic surveys show an enrichment in genetic sequences associated with known methanogens. However, because we cannot directly sample the subseafloor habitat where these organisms are living, constraining the size and activity of these populations remains a challenge and limits our ability to quantify the role they play in vent biogeochemistry. Reactive-transport modeling may provide a useful tool for approaching this problem. Here we present a reactive-transport model describing methane production along the flow-path of hydrothermal fluid from its high temperature end-member to diffuse venting at the seafloor. The model is set up to reflect conditions at several diffuse vents in the Axial Seamount. The model describes the growth of the two dominant thermophilic methanogens, Methanothermococcus and Methanocaldococcus, observed at Axial seamount. Monod and Arrhenius constants for Methanothermococcus thermolithotrophicus and Methanocaldococcus jannaschii were obtained for the model using chemostat and bottle experiments at varying temperatures. The model is used to investigate the influence of different mixing regimes on the subseafloor populations of these methanogens. By varying the model flow path length and subseafloor cell concentrations, and fitting to observed hydrogen and methane concentrations in the venting fluid, the subseafloor biomass, fluid residence time, and methane production rate can be constrained.

Introduction of Shear-Based Transport Mechanisms in Radial-Axial Hybrid Hall Thruster Simulations

NASA Astrophysics Data System (ADS)

Scharfe, Michelle; Gascon, Nicolas; Scharfe, David; Cappelli, Mark; Fernandez, Eduardo

2007-11-01

Electron diffusion across magnetic field lines in Hall effect thrusters is experimentally observed to be higher than predicted by classical diffusion theory. Motivated by theoretical work for fusion applications and experimental measurements of Hall thrusters, numerical models for the electron transport are implemented in radial-axial hybrid simulations in order to compute the electron mobility using simulated plasma properties and fitting parameters. These models relate the cross-field transport to the imposed magnetic field distribution through shear suppression of turbulence-enhanced transport. While azimuthal waves likely enhance cross field mobility, axial shear in the electron fluid may reduce transport due to a reduction in turbulence amplitudes and modification of phase shifts between fluctuating properties. The sensitivity of the simulation results to the fitting parameters is evaluated and an examination is made of the transportability of these parameters to several Hall thruster devices.

Modeling Transport of Cesium in Grimsel Granodiorite With Micrometer Scale Heterogeneities and Dynamic Update of Kd

NASA Astrophysics Data System (ADS)

Voutilainen, Mikko; Kekäläinen, Pekka; Siitari-Kauppi, Marja; Sardini, Paul; Muuri, Eveliina; Timonen, Jussi; Martin, Andrew

2017-11-01

Transport and retardation of cesium in Grimsel granodiorite taking into account heterogeneity of mineral and pore structure was studied using rock samples overcored from an in situ diffusion test at the Grimsel Test Site. The field test was part of the Long-Term Diffusion (LTD) project designed to characterize retardation properties (diffusion and distribution coefficients) under in situ conditions. Results of the LTD experiment for cesium showed that in-diffusion profiles and spatial concentration distributions were strongly influenced by the heterogeneous pore structure and mineral distribution. In order to study the effect of heterogeneity on the in-diffusion profile and spatial concentration distribution, a Time Domain Random Walk (TDRW) method was applied along with a feature for modeling chemical sorption in geological materials. A heterogeneous mineral structure of Grimsel granodiorite was constructed using X-ray microcomputed tomography (X-μCT) and the map was linked to previous results for mineral specific porosities and distribution coefficients (Kd) that were determined using C-14-PMMA autoradiography and batch sorption experiments, respectively. After this the heterogeneous structure contains information on local porosity and Kd in 3-D. It was found that the heterogeneity of the mineral structure on the micrometer scale affects significantly the diffusion and sorption of cesium in Grimsel granodiorite at the centimeter scale. Furthermore, the modeled in-diffusion profiles and spatial concentration distributions show similar shape and pattern to those from the LTD experiment. It was concluded that the use of detailed structure characterization and quantitative data on heterogeneity can significantly improve the interpretation and evaluation of transport experiments.

Experimental tests of truncated diffusion in fault damage zones

NASA Astrophysics Data System (ADS)

Suzuki, Anna; Hashida, Toshiyuki; Li, Kewen; Horne, Roland N.

2016-11-01

Fault zones affect the flow paths of fluids in groundwater aquifers and geological reservoirs. Fault-related fracture damage decreases to background levels with increasing distance from the fault core according to a power law. This study investigated mass transport in such a fault-related structure using nonlocal models. A column flow experiment is conducted to create a permeability distribution that varies with distance from a main conduit. The experimental tracer response curve is preasymptotic and implies subdiffusive transport, which is slower than the normal Fickian diffusion. If the surrounding area is a finite domain, an upper truncated behavior in tracer response (i.e., exponential decline at late times) is observed. The tempered anomalous diffusion (TAD) model captures the transition from subdiffusive to Fickian transport, which is characterized by a smooth transition from power-law to an exponential decline in the late-time breakthrough curves.

Ratchet effect for nanoparticle transport in hair follicles.

PubMed

Radtke, Matthias; Patzelt, Alexa; Knorr, Fanny; Lademann, Jürgen; Netz, Roland R

2017-07-01

The motion of a single rigid nanoparticle inside a hair follicle is investigated by means of Brownian dynamics simulations. The cuticular hair structure is modeled as a periodic asymmetric ratchet-shaped surface. Induced by oscillating radial hair motion we find directed nanoparticle transport into the hair follicle with maximal velocity at a specific optimal frequency and an optimal particle size. We observe flow reversal when switching from radial to axial oscillatory hair motion. We also study the diffusion behavior and find strongly enhanced diffusion for axial motion with a diffusivity significantly larger than for free diffusion. Copyright © 2016 Elsevier B.V. All rights reserved.

The relative importance of decomposition and transport mechanisms in accounting for C profiles

NASA Astrophysics Data System (ADS)

Guenet, B.; Eglin, T.; Vasilyeva, N.; Peylin, P.; Ciais, P.; Chenu, C.

2012-10-01

Soil is the major terrestrial reservoirs of carbon, and a substantial part of this carbon is stored in deep layers, typically deeper than 50 cm below the surface. Several studies underlined the quantitative importance of this deep Soil Organic Carbon (SOC) pool and models are needed to better understand this stock and its evolution under climate and land-uses changes. In this study, we test and compare 3 simple theoretical models of vertical transport for SOC against SOC profiles measurements from a long-term bare fallow experiment carried out by the Central-Chernozem State Natural Biosphere Reserve named after V.V. Alekhin, in the Kursk Region of Russia. The transport schemes tested are diffusion, advection or both diffusion and advection. They are coupled to two different formulations of soil carbon decomposition kinetics. The first formulation is a first order kinetics widely used in global SOC decomposition models; the second one links SOC decomposition rate to the amount of fresh organic matter, representing a "priming effect". Field data are from a set of three bare fallow plots where soil received no input during the past 20, 26 and 58 yr respectively. Parameters of the models were optimized using a Bayesian method. The best results are obtained when SOC decomposition is assumed to be controlled by fresh organic matter. In comparison to the first-order kinetic model, the "priming" model reduces the underestimation of SOC decomposition in the top layers and the over estimation in the deep layers. We also observe that the transport scheme that improved the fit with the data depends on the soil carbon mineralization formulation chosen. When soil carbon decomposition is modelled to depend on the fresh organic matter amount, the transport mechanisms which improves best the fit to the SOC profile data is the model representing both advection and diffusion. Interestingly, the older the bare fallow is, the lesser the need for diffusion is. This suggests that stabilized carbon may not be transported within the profile by the same mechanisms than more labile carbon.

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

Morales, George J.; Maggs, James E.

The project expanded and developed mathematical descriptions, and corresponding numerical modeling, of non-diffusive transport to incorporate new perspectives derived from basic transport experiments performed in the LAPD device at UCLA, and at fusion devices throughout the world. By non-diffusive it is meant that the transport of fundamental macroscopic parameters of a system, such as temperature and density, does not follow the standard diffusive behavior predicted by a classical Fokker-Planck equation. The appearance of non-diffusive behavior is often related to underlying microscopic processes that cause the value of a system parameter, at one spatial position, to be linked to distant events,more » i.e., non-locality. In the LAPD experiments the underlying process was traced to large amplitude, coherent drift-waves that give rise to chaotic trajectories. Significant advances were made in this project. The results have lead to a new perspective about the fundamentals of edge transport in magnetically confined plasmas; the insight has important consequences for worldwide studies in fusion devices. Progress was also made in advancing the mathematical techniques used to describe fractional diffusion.« less

Prediction of oxygen distribution in aortic valve leaflet considering diffusion and convection.

PubMed

Wang, Ling; Korossis, Sotirios; Fisher, John; Ingham, Eileen; Jin, Zhongmin

2011-07-01

Oxygen supply and transport is an important consideration in the development of tissue engineered constructs. Previous studies from our group have focused on the effect of tissue thickness on the oxygen diffusion within a three-dimensional aortic valve leaflet model, and highlighted the necessity for additional transport mechanisms such as oxygen convection. The aims of this study were to investigate the effect of interstitial fluid flow within the aortic valve leaflet, induced by the cyclic loading of the leaflet, on oxygen transport. Indentation testing and finite element modelings were employed to derive the biphasic properties of the leaflet tissue. The biphasic properties were subsequently used in the computational modeling of oxygen convection in the leaflet, which was based on the effective interstitial fluid velocity and the tissue deformation. Subsequently, the oxygen profile was predicted within the valve leaflet model by solving the diffusion and convection equation simultaneously utilizing the finite difference method. The compression modulus (E) and hydraulic permeability were determined by adapting a finite element model to the experimental indentation test on valvular tissue, E = 0.05MPa, and k =2.0 mm4/Ns. Finite element model of oxygen convection in valvular tissue incorporating the predicted biphasic properties was developed and the interstitial fluid flow rate was calculated falling in range of 0.025-0.25 mm/s depending on the tissue depth. Oxygen distribution within valvular tissue was predicted using one-dimensional oxygen diffusion model taking into consider the interstitial fluid effect. It was found that convection did enhance the oxygen transport in valvular tissue by up to 68% increase in the minimum oxygen tension within the tissue, depending on the strain level of the tissue as reaction of the magnitude and frequencies of the cardiac loading. The effective interstitial fluid velocity was found to play an important role in enhancing the oxygen transport within the valve leaflet. Such an understanding is important in the development of valvular tissue engineered constructs.

Simulation of Ultra-Small MOSFETs Using a 2-D Quantum-Corrected Drift-Diffusion Model

NASA Technical Reports Server (NTRS)

Biegel, Bryan A.; Rafferty, Conor S.; Yu, Zhiping; Dutton, Robert W.; Ancona, Mario G.; Saini, Subhash (Technical Monitor)

1998-01-01

We describe an electronic transport model and an implementation approach that respond to the challenges of device modeling for gigascale integration. We use the density-gradient (DG) transport model, which adds tunneling and quantum smoothing of carrier density profiles to the drift-diffusion model. We present the current implementation of the DG model in PROPHET, a partial differential equation solver developed by Lucent Technologies. This implementation approach permits rapid development and enhancement of models, as well as run-time modifications and model switching. We show that even in typical bulk transport devices such as P-N diodes and BJTs, DG quantum effects can significantly modify the I-V characteristics. Quantum effects are shown to be even more significant in small, surface transport devices, such as sub-0.1 micron MOSFETs. In thin-oxide MOS capacitors, we find that quantum effects may reduce gate capacitance by 25% or more. The inclusion of quantum effects in simulations dramatically improves the match between C-V simulations and measurements. Significant quantum corrections also occur in the I-V characteristics of short-channel MOSFETs due to the gate capacitance correction.

The effect of solution nonideality on modeling transmembrane water transport and diffusion-limited intracellular ice formation during cryopreservation

NASA Astrophysics Data System (ADS)

Zhao, Gang; Takamatsu, Hiroshi; He, Xiaoming

2014-04-01

A new model was developed to predict transmembrane water transport and diffusion-limited ice formation in cells during freezing without the ideal-solution assumption that has been used in previous models. The model was applied to predict cell dehydration and intracellular ice formation (IIF) during cryopreservation of mouse oocytes and bovine carotid artery endothelial cells in aqueous sodium chloride (NaCl) solution with glycerol as the cryoprotectant or cryoprotective agent. A comparison of the predictions between the present model and the previously reported models indicated that the ideal-solution assumption results in under-prediction of the amount of intracellular ice at slow cooling rates (<50 K/min). In addition, the lower critical cooling rates for IIF that is lethal to cells predicted by the present model were much lower than those estimated with the ideal-solution assumption. This study represents the first investigation on how accounting for solution nonideality in modeling water transport across the cell membrane could affect the prediction of diffusion-limited ice formation in biological cells during freezing. Future studies are warranted to look at other assumptions alongside nonideality to further develop the model as a useful tool for optimizing the protocol of cell cryopreservation for practical applications.

The effect of solution nonideality on modeling transmembrane water transport and diffusion-limited intracellular ice formation during cryopreservation.

PubMed

Zhao, Gang; Takamatsu, Hiroshi; He, Xiaoming

2014-04-14

A new model was developed to predict transmembrane water transport and diffusion-limited ice formation in cells during freezing without the ideal-solution assumption that has been used in previous models. The model was applied to predict cell dehydration and intracellular ice formation (IIF) during cryopreservation of mouse oocytes and bovine carotid artery endothelial cells in aqueous sodium chloride (NaCl) solution with glycerol as the cryoprotectant or cryoprotective agent. A comparison of the predictions between the present model and the previously reported models indicated that the ideal-solution assumption results in under-prediction of the amount of intracellular ice at slow cooling rates (<50 K/min). In addition, the lower critical cooling rates for IIF that is lethal to cells predicted by the present model were much lower than those estimated with the ideal-solution assumption. This study represents the first investigation on how accounting for solution nonideality in modeling water transport across the cell membrane could affect the prediction of diffusion-limited ice formation in biological cells during freezing. Future studies are warranted to look at other assumptions alongside nonideality to further develop the model as a useful tool for optimizing the protocol of cell cryopreservation for practical applications.

Conformable derivative approach to anomalous diffusion

NASA Astrophysics Data System (ADS)

Zhou, H. W.; Yang, S.; Zhang, S. Q.

2018-02-01

By using a new derivative with fractional order, referred to conformable derivative, an alternative representation of the diffusion equation is proposed to improve the modeling of anomalous diffusion. The analytical solutions of the conformable derivative model in terms of Gauss kernel and Error function are presented. The power law of the mean square displacement for the conformable diffusion model is studied invoking the time-dependent Gauss kernel. The parameters related to the conformable derivative model are determined by Levenberg-Marquardt method on the basis of the experimental data of chloride ions transportation in reinforced concrete. The data fitting results showed that the conformable derivative model agrees better with the experimental data than the normal diffusion equation. Furthermore, the potential application of the proposed conformable derivative model of water flow in low-permeability media is discussed.

Revisiting point FRAP to quantitatively characterize anomalous diffusion in live cells.

PubMed

Daddysman, Matthew K; Fecko, Christopher J

2013-02-07

Fluorescence recovery after photobleaching (FRAP) is widely used to interrogate diffusion and binding of proteins in live cells. Herein, we apply two-photon excited FRAP with a diffraction limited bleaching and observation volume to study anomalous diffusion of unconjugated green fluorescence protein (GFP) in vitro and in cells. Experiments performed on dilute solutions of GFP reveal that reversible fluorophore bleaching can be mistakenly interpreted as anomalous diffusion. We derive a reaction-diffusion FRAP model that includes reversible photobleaching, and demonstrate that it properly accounts for these photophysics. We then apply this model to investigate the diffusion of GFP in HeLa cells and polytene cells of Drosophila larval salivary glands. GFP exhibits anomalous diffusion in the cytoplasm of both cell types and in HeLa nuclei. Polytene nuclei contain optically resolvable chromosomes, permitting FRAP experiments that focus separately on chromosomal or interchrosomal regions. We find that GFP exhibits anomalous diffusion in chromosomal regions but diffuses normally in regions devoid of chromatin. This observation indicates that obstructed transport through chromatin and not crowding by macromolecules is a source of anomalous diffusion in polytene nuclei. This behavior is likely true in other cells, so it will be important to account for this type of transport physics and for reversible photobleaching to properly interpret future FRAP experiments on DNA-binding proteins.

Effective matrix diffusion in kilometer‐scale transport in fractured crystalline rock

USGS Publications Warehouse

Shapiro, Allen M.

2001-01-01

Concentrations of tritium (3H) and dichlorodifluoromethane (CFC‐12) in water samples taken from glacial drift and fractured crystalline rock over 4 km2 in central New Hampshire are interpreted to identify a conceptual model of matrix diffusion and the magnitude of the diffusion coefficient. Dispersion and mass transfer to and from fractures has affected the 3H concentration to the extent that the peak 3H concentration of the 1960s is no longer distinguishable. Because of heterogeneity in the bedrock the sparsely distributed chemical data do not warrant a three‐dimensional transport model. Instead, a one‐dimensional model of CFC‐12 and 3H migration along flow lines in the glacial drift and bedrock is used to place bounds on the processes affecting kilometer‐scale transport, arid model parameters are varied to reproduce the measured relation between 3H and CFC‐12, rather than their spatial distributions. A model of mass exchange to and from fractures that is dependent on the time‐varying concentration gradient at fracture surfaces qualitatively reproduces the measured relation between 3H and CFC‐12 with an upper bound for the fracture dispersivity approximately equal to 250 m and a lower bound for the effective matrix diffusion coefficient equal to 1 m2 yr−1. The diffusion coefficient at the kilometer scale is at least 3 orders of magnitude greater than laboratory estimates of diffusion in crystalline rock. The large diffusion coefficient indicates that diffusion into an immobile fluid phase (rock matrix) is masked at the kilometer scale by advective mass exchange between fractures with large contrasts in trarismissivity. The measured transmissivity of fractures in the study area varies over more than 6 orders of magnitude. Advective mass exchange from high‐permeability fractures to low‐permeability fractures results in short migration distances of a chemical constituent in low‐permeability fractures over an extended period of time before reentering high‐permeability fractures; viewed at the kilometer scale, this process is analogous to the chemical constituent diffusing into and out of an immobile fluid phase.

Modeling gas displacement kinetics in coal with Maxwell-Stefan diffusion theory

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

Wei, X.R.; Wang, G.X.; Massarotto, P.

2007-12-15

The kinetics of binary gas counter-diffusion and Darcy flow in a large coal sample were modeled, and the results compared with data from experimental laboratory investigations. The study aimed for a better understanding of the CO{sub 2}-sequestration enhanced coalbed methane (ECBM) recovery process. The transport model used was based on the bidisperse diffusion mechanism and Maxwell-Stefan (MS) diffusion theory. This provides an alternative approach to simulate multicomponent gas diffusion and flow in bulk coals. A series of high-stress core flush tests were performed on a large coal sample sourced from a Bowen Basin coal mine in Queensland, Australia to investigatemore » the kinetics of one gas displacing another. These experimental results were used to derive gas diffusivities, and to examine the predictive capability of the diffusion model. The simulations show good agreements with the displacement experiments revealing that MS diffusion theory is superior for describing diffusion of mixed gases in coals compared with the constant Fick diffusivity model. The optimized effective micropore and macropore diffusivities are comparable with experimental measurements achieved by other researchers.« less

Principles for the dynamic maintenance of cortical polarity

PubMed Central

Marco, Eugenio; Wedlich-Soldner, Roland; Li, Rong; Altschuler, Steven J.; Wu, Lani F.

2007-01-01

Summary Diverse cell types require the ability to dynamically maintain polarized membrane protein distributions through balancing transport and diffusion. However, design principles underlying dynamically maintained cortical polarity are not well understood. Here we constructed a mathematical model for characterizing the morphology of dynamically polarized protein distributions. We developed analytical approaches for measuring all model parameters from single-cell experiments. We applied our methods to a well-characterized system for studying polarized membrane proteins: budding yeast cells expressing activated Cdc42. We found that balanced diffusion and colocalized transport to and from the plasma membrane were sufficient for accurately describing polarization morphologies. Surprisingly, the model predicts that polarized regions are defined with a precision that is nearly optimal for measured transport rates, and that polarity can be dynamically stabilized through positive feedback with directed transport. Our approach provides a step towards understanding how biological systems shape spatially precise, unambiguous cortical polarity domains using dynamic processes. PMID:17448998

AN OPTIMAL ADAPTIVE LOCAL GRID REFINEMENT APPROACH TO MODELING CONTAMINANT TRANSPORT

EPA Science Inventory

A Lagrangian-Eulerian method with an optimal adaptive local grid refinement is used to model contaminant transport equations. pplication of this approach to two bench-mark problems indicates that it completely resolves difficulties of peak clipping, numerical diffusion, and spuri...

Two-photon time-lapse microscopy of BODIPY-cholesterol reveals anomalous sterol diffusion in chinese hamster ovary cells

PubMed Central

2012-01-01

Background Cholesterol is an important membrane component, but our knowledge about its transport in cells is sparse. Previous imaging studies using dehydroergosterol (DHE), an intrinsically fluorescent sterol from yeast, have established that vesicular and non-vesicular transport modes contribute to sterol trafficking from the plasma membrane. Significant photobleaching, however, limits the possibilities for in-depth analysis of sterol dynamics using DHE. Co-trafficking studies with DHE and the recently introduced fluorescent cholesterol analog BODIPY-cholesterol (BChol) suggested that the latter probe has utility for prolonged live-cell imaging of sterol transport. Results We found that BChol is very photostable under two-photon (2P)-excitation allowing the acquisition of several hundred frames without significant photobleaching. Therefore, long-term tracking and diffusion measurements are possible. Two-photon temporal image correlation spectroscopy (2P-TICS) provided evidence for spatially heterogeneous diffusion constants of BChol varying over two orders of magnitude from the cell interior towards the plasma membrane, where D ~ 1.3 μm2/s. Number and brightness (N&B) analysis together with stochastic simulations suggest that transient partitioning of BChol into convoluted membranes slows local sterol diffusion. We observed sterol endocytosis as well as fusion and fission of sterol-containing endocytic vesicles. The mobility of endocytic vesicles, as studied by particle tracking, is well described by a model for anomalous subdiffusion on short time scales with an anomalous exponent α ~ 0.63 and an anomalous diffusion constant of Dα = 1.95 x 10-3 μm2/sα. On a longer time scale (t > ~5 s), a transition to superdiffusion consistent with slow directed transport with an average velocity of v ~ 6 x 10-3 μm/s was observed. We present an analytical model that bridges the two regimes and fit this model to vesicle trajectories from control cells and cells with disrupted microtubule or actin filaments. Both treatments reduced the anomalous diffusion constant and the velocity by ~40-50%. Conclusions The mobility of sterol-containing vesicles on the short time scale could reflect dynamic rearrangements of the cytoskeleton, while directed transport of sterol vesicles occurs likely along both, microtubules and actin filaments. Spatially varying anomalous diffusion could contribute to fine-tuning and local regulation of intracellular sterol transport. PMID:23078907

Volume Diffusion Growth Kinetics and Step Geometry in Crystal Growth

NASA Technical Reports Server (NTRS)

Mazuruk, Konstantin; Ramachandran, Narayanan

1998-01-01

The role of step geometry in two-dimensional stationary volume diff4sion process used in crystal growth kinetics models is investigated. Three different interface shapes: a) a planar interface, b) an equidistant hemispherical bumps train tAx interface, and c) a train of right angled steps, are used in this comparative study. The ratio of the super-saturation to the diffusive flux at the step position is used as a control parameter. The value of this parameter can vary as much as 50% for different geometries. An approximate analytical formula is derived for the right angled steps geometry. In addition to the kinetic models, this formula can be utilized in macrostep growth models. Finally, numerical modeling of the diffusive and convective transport for equidistant steps is conducted. In particular, the role of fluid flow resulting from the advancement of steps and its contribution to the transport of species to the steps is investigated.

Modeling Nitrogen Fate and Transport at the Sediment-Water ...

EPA Pesticide Factsheets

Diffusive mass transfer at media interfaces exerts control on the fate and transport of pollutants originating from agricultural and urban landscapes and affects the con-ditions of water bodies. Diffusion is essentially a physical process affecting the distribution and fate of various environmental pollutants such as nutrients, pesticides, metals, PCBs, PAHs, etc. Environmental problems caused by excessive use of agricultural chemicals (e.g., pesticides and fertilizers) and improper discharge of industrial waste and fuel leaks are all influenced by the diffusive nature of pollutants in the environment. Eutrophication is one such environmental problem where the sediment-water interface exerts a significant physical and geochemical control on the eutrophic condition of the stressed water body. Exposure of streams and lakes to contaminated sediment is another common environmental problem whereby transport of the contaminant (PCBs, PAHs, and other organic contaminants) across the sediment water can increase the risk for exposure to the chemicals and pose a significant health hazard to aquatic life and human beings. This chapter presents analytical and numerical models describing fate and transport phenomena at the sediment-water interface in freshwater ecosystems, with the primary focus on nitrogen cycling and the applicability of the models to real-world environmental problems and challenges faced in their applications. The first model deals with nitrogen cycling

Modeling diffuse phosphorus emissions to assist in best management practice designing

NASA Astrophysics Data System (ADS)

Kovacs, Adam; Zessner, Matthias; Honti, Mark; Clement, Adrienne

2010-05-01

A diffuse emission modeling tool has been developed, which is appropriate to support decision-making in watershed management. The PhosFate (Phosphorus Fate) tool allows planning best management practices (BMPs) in catchments and simulating their possible impacts on the phosphorus (P) loads. PhosFate is a simple fate model to calculate diffuse P emissions and their transport within a catchment. The model is a semi-empirical, catchment scale, distributed parameter and long-term (annual) average model. It has two main parts: (a) the emission and (b) the transport model. The main input data of the model are digital maps (elevation, soil types and landuse categories), statistical data (crop yields, animal numbers, fertilizer amounts and precipitation distribution) and point information (precipitation, meteorology, soil humus content, point source emissions and reservoir data). The emission model calculates the diffuse P emissions at their source. It computes the basic elements of the hydrology as well as the soil loss. The model determines the accumulated P surplus of the topsoil and distinguishes the dissolved and the particulate P forms. Emissions are calculated according to the different pathways (surface runoff, erosion and leaching). The main outputs are the spatial distribution (cell values) of the runoff components, the soil loss and the P emissions within the catchment. The transport model joins the independent cells based on the flow tree and it follows the further fate of emitted P from each cell to the catchment outlets. Surface runoff and P fluxes are accumulated along the tree and the field and in-stream retention of the particulate forms are computed. In case of base flow and subsurface P loads only the channel transport is taken into account due to the less known hydrogeological conditions. During the channel transport, point sources and reservoirs are also considered. Main results of the transport algorithm are the discharge, dissolved and sediment-bounded P load values at any arbitrary point within the catchment. Finally, a simple design procedure has been built up to plan BMPs in the catchments and simulate their possible impacts on diffuse P fluxes as well as calculate their approximately costs. Both source and transport controlling measures have been involved into the planning procedure. The model also allows examining the impacts of alterations of fertilizer application, point source emissions as well as the climate change on the river loads. Besides this, a simple optimization algorithm has been developed to select the most effective source areas (real hot spots), which should be targeted by the interventions. The fate model performed well in Hungarian pilot catchments. Using the calibrated and validated model, different management scenarios were worked out and their effects and costs evaluated and compared to each other. The results show that the approach is suitable to effectively design BMP measures at local scale. Combinative application of the source and transport controlling BMPs can result in high P reduction efficiency. Optimization of the interventions can remarkably reduce the area demand of the necessary BMPs, consequently the establishment costs can be decreased. The model can be coupled with a larger scale catchment model to form a "screening and planning" modeling system.

Pore network modeling to explore the effects of compression on multiphase transport in polymer electrolyte membrane fuel cell gas diffusion layers

NASA Astrophysics Data System (ADS)

Fazeli, Mohammadreza; Hinebaugh, James; Fishman, Zachary; Tötzke, Christian; Lehnert, Werner; Manke, Ingo; Bazylak, Aimy

2016-12-01

Understanding how compression affects the distribution of liquid water and gaseous oxygen in the polymer electrolyte membrane fuel cell gas diffusion layer (GDL) is vital for informing the design of improved porous materials for effective water management strategies. Pore networks extracted from synchrotron-based micro-computed tomography images of compressed GDLs were employed to simulate liquid water transport in GDL materials over a range of compression pressures. The oxygen transport resistance was predicted for each sample under dry and partially saturated conditions. A favorable GDL compression value for a preferred liquid water distribution and oxygen diffusion was found for Toray TGP-H-090 (10%), yet an optimum compression value was not recognized for SGL Sigracet 25BC. SGL Sigracet 25BC exhibited lower transport resistance values compared to Toray TGP-H-090, and this is attributed to the additional diffusion pathways provided by the microporous layer (MPL), an effect that is particularly significant under partially saturated conditions.

A unified multicomponent stress-diffusion model of drug release from non-biodegradable polymeric matrix tablets.

PubMed

Salehi, Ali; Zhao, Jin; Cabelka, Tim D; Larson, Ronald G

2016-02-28

We propose a new transport model of drug release from hydrophilic polymeric matrices, based on Stefan-Maxwell flux laws for multicomponent transport. Polymer stress is incorporated in the total mixing free energy, which contributes directly to the diffusion driving force while leading to time-dependent boundary conditions at the tablet interface. Given that hydrated matrix tablets are dense multicomponent systems, extended Stefan-Maxwell (ESM) flux laws are adopted to ensure consistency with the Onsager reciprocity principle and the Gibbs-Duhem thermodynamic constraint. The ESM flux law for any given component takes into account the friction exerted by all other species and is invariant with respect to reference velocity, thus satisfying Galilean translational invariance. Our model demonstrates that penetrant-induced plasticization of polymer chains partially or even entirely offsets the steady decline of chemical potential gradients at the tablet-medium interface that drive drug release. Utilizing a Flory-Huggins thermodynamic model, a modified form of the upper convected Maxwell constitutive equation for polymer stress and a Fujita-type dependence of mutual diffusivities on composition, depending on parameters, Fickian, anomalous or case II drug transport arises naturally from the model, which are characterized by quasi-power-law release profiles with exponents ranging from 0.5 to 1, respectively. A necessary requirement for non-Fickian release in our model is that the matrix stress relaxation time is comparable to the time scale for water diffusion. Mutual diffusivities and their composition dependence are the most decisive factors in controlling drug release characteristics in our model. Regression of the experimental polymer dissolution and drug release profiles in a system of Theophylline/cellulose (K15M) demonstrate that API-water mutual diffusivity in the presence of excipient cannot generally be taken as a constant. Copyright © 2016 Elsevier B.V. All rights reserved.

Controlling reactivity of nanoporous catalyst materials by tuning reaction product-pore interior interactions: Statistical mechanical modeling

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

Wang, Jing; Ackerman, David M.; Lin, Victor S.-Y.

2013-04-02

Statistical mechanical modeling is performed of a catalytic conversion reaction within a functionalized nanoporous material to assess the effect of varying the reaction product-pore interior interaction from attractive to repulsive. A strong enhancement in reactivity is observed not just due to the shift in reaction equilibrium towards completion but also due to enhanced transport within the pore resulting from reduced loading. The latter effect is strongest for highly restricted transport (single-file diffusion), and applies even for irreversible reactions. The analysis is performed utilizing a generalized hydrodynamic formulation of the reaction-diffusion equations which can reliably capture the complex interplay between reactionmore » and restricted transport.« less

Fractional derivatives in the transport of drugs across biological materials and human skin

NASA Astrophysics Data System (ADS)

Caputo, Michele; Cametti, Cesare

2016-11-01

The diffusion of drugs across a composite structure such as a biological membrane is a rather complex phenomenon, because of its inhomogeneous nature, yielding a diffusion rate and a drug solubility strongly dependent on the local position across the membrane itself. These problems are particularly strengthened in composite structures of a considerable thickness like, for example, the human skin, where the high heterogeneity provokes the transport through different simultaneous pathways. In this note, we propose a generalization of the diffusion model based on Fick's 2nd equation by substituting a diffusion constant by means of the memory formalism approach (diffusion with memory). In particular, we employ two different definitions of the fractional derivative, i.e., the usual Caputo fractional derivative and a new definition recently proposed by Caputo and Fabrizio. The model predictions have been compared to experimental results concerning the permeation of two different compounds through human skin in vivo, such as piroxicam, an anti-inflammatory drug, and 4-cyanophenol, a test chemical model compound. Moreover, we have also considered water penetration across human stratum corneum and the diffusion of an antiviral agent employed as model drugs across the skin of male hairless rats. In all cases, a satisfactory good agreement based on the diffusion with memory has been found. However, the model based on the new definition of fractional derivative gives a better description of the experimental data, on the basis of the residuals analysis. The use of the new definition widens the applicability of the fractional derivative to diffusion processes in highly heterogeneous systems.

Advanced Atmospheric Modeling for Emergency Response.

NASA Astrophysics Data System (ADS)

Fast, Jerome D.; O'Steen, B. Lance; Addis, Robert P.

1995-03-01

Atmospheric transport and diffusion models are an important part of emergency response systems for industrial facilities that have the potential to release significant quantities of toxic or radioactive material into the atmosphere. An advanced atmospheric transport and diffusion modeling system for emergency response and environmental applications, based upon a three-dimensional mesoscale model, has been developed for the U.S. Department of Energy's Savannah River Site so that complex, time-dependent flow fields not explicitly measured can be routinely simulated. To overcome some of the current computational demands of mesoscale models, two operational procedures for the advanced atmospheric transport and diffusion modeling system are described including 1) a semiprognostic calculation to produce high-resolution wind fields for local pollutant transport in the vicinity of the Savannah River Site and 2) a fully prognostic calculation to produce a regional wind field encompassing the southeastern United States for larger-scale pollutant problems. Local and regional observations and large-scale model output are used by the mesoscale model for the initial conditions, lateral boundary conditions, and four-dimensional data assimilation procedure. This paper describes the current status of the modeling system and presents two case studies demonstrating the capabilities of both modes of operation. While the results from the case studies shown in this paper are preliminary and certainly not definitive, they do suggest that the mesoscale model has the potential for improving the prognostic capabilities of atmospheric modeling for emergency response at the Savannah River Site. Long-term model evaluation will be required to determine under what conditions significant forecast errors exist.

Transscleral diffusion of ethacrynic acid and sodium fluorescein

PubMed Central

Lin, Cheng-Wen; Wang, Yong; Challa, Pratap; Epstein, David L.

2007-01-01

Purpose One of the current limitations in developing novel glaucoma drugs that target the trabecular meshwork (TM) is the induced corneal toxicity from eyedrop formulations. To avoid the corneal toxicity, an alternative approach would be to deliver TM drugs through the sclera. To this end, we quantified ex vivo diffusion coefficient of a potential TM drug, ethacrynic acid (ECA), and investigated mechanisms of ECA transport in the sclera. Methods An Ussing-type diffusion apparatus was built to measure the apparent diffusion coefficient of ECA in fresh porcine sclera at 4 °C. To understand mechanisms of ECA transport, we quantified the transscleral transport of a fluorescent tracer, sodium fluorescein (NaF), that has a similar molecular weight but is more hydrophilic compared to ECA. Furthermore, we developed a mathematical model to simulate the transport processes and used it to analyze the experimental data. The model was also used to investigate the dependence of diffusion coefficients on volume fraction of viable cells and the binding of NaF and ECA to scleral tissues. Results The diffusion coefficients of ECA and NaF in the sclera were 48.5±15.1x10-7 cm2/s (n=9) and 5.23±1.93x10-7 cm2/s (n=8), respectively. Both diffusion coefficients were insensitive to cell shrinkage caused by ECA during the diffusion experiments and cell damage caused by the storage of tissues ex vivo before the experiments. Binding of ECA to scleral tissues could not be detected. The apparent maximum binding capacity and the apparent equilibrium dissociation constant for NaF were 80±5 mM and 2.5±0.5 mM (n=3), respectively. Conclusions These data demonstrated that ECA diffusion was minimally hindered by structures in the sclera, presumably due to the lack of cells and binding sites for ECA in the sclera. PMID:17356511

Anomalous Extracellular Diffusion in Rat Cerebellum

PubMed Central

Xiao, Fanrong; Hrabe, Jan; Hrabetova, Sabina

2015-01-01

Extracellular space (ECS) is a major channel transporting biologically active molecules and drugs in the brain. Diffusion-mediated transport of these substances is hindered by the ECS structure but the microscopic basis of this hindrance is not fully understood. One hypothesis proposes that the hindrance originates in large part from the presence of dead-space (DS) microdomains that can transiently retain diffusing molecules. Because previous theoretical and modeling work reported an initial period of anomalous diffusion in similar environments, we expected that brain regions densely populated by DS microdomains would exhibit anomalous extracellular diffusion. Specifically, we targeted granular layers (GL) of rat and turtle cerebella that are populated with large and geometrically complex glomeruli. The integrative optical imaging (IOI) method was employed to evaluate diffusion of fluorophore-labeled dextran (MW 3000) in GL, and the IOI data analysis was adapted to quantify the anomalous diffusion exponent dw from the IOI records. Diffusion was significantly anomalous in rat GL, where dw reached 4.8. In the geometrically simpler turtle GL, dw was elevated but not robustly anomalous (dw = 2.6). The experimental work was complemented by numerical Monte Carlo simulations of anomalous ECS diffusion in several three-dimensional tissue models containing glomeruli-like structures. It demonstrated that both the duration of transiently anomalous diffusion and the anomalous exponent depend on the size of model glomeruli and the degree of their wrapping. In conclusion, we have found anomalous extracellular diffusion in the GL of rat cerebellum. This finding lends support to the DS microdomain hypothesis. Transiently anomalous diffusion also has a profound effect on the spatiotemporal distribution of molecules released into the ECS, especially at diffusion distances on the order of a few cell diameters, speeding up short-range diffusion-mediated signals in less permeable structures. PMID:25954895

Numerical Test of the Additivity Principle in Anomalous Transport

NASA Astrophysics Data System (ADS)

Tamaki, Shuji

2017-10-01

The additivity principle (AP) is one of the remarkable predictions that systematically generates all information on current fluctuations once the value of average current in the linear response regime is input. However, conditions to justify the AP are still ambiguous. We hence consider three tractable models, and discuss possible conditions. The models include the harmonic chain (HC), momentum exchange (ME) model, and momentum flip (MF) model, which respectively show ballistic, anomalous, and diffusive transport. We compare the heat current cumulants predicted by the AP with exact numerical data obtained for these models. The HC does not show the AP, whereas the MF model satisfies it, as expected, since the AP was originally proposed for diffusive systems. Surprisingly, the ME model also shows the AP. The ME model is known to show the anomalous transport similar to that shown in nonlinear systems such as the Fermi-Pasta-Ulam model. Our finding indicates that general nonlinear systems may satisfy the AP. Possible conditions for satisfying the AP are discussed.

Wavy membranes and the growth rate of a planar chemical garden: Enhanced diffusion and bioenergetics.

PubMed

Ding, Yang; Batista, Bruno; Steinbock, Oliver; Cartwright, Julyan H E; Cardoso, Silvana S S

2016-08-16

To model ion transport across protocell membranes in Hadean hydrothermal vents, we consider both theoretically and experimentally the planar growth of a precipitate membrane formed at the interface between two parallel fluid streams in a 2D microfluidic reactor. The growth rate of the precipitate is found to be proportional to the square root of time, which is characteristic of diffusive transport. However, the dependence of the growth rate on the concentrations of hydroxide and metal ions is approximately linear and quadratic, respectively. We show that such a difference in ionic transport dynamics arises from the enhanced transport of metal ions across a thin gel layer present at the surface of the precipitate. The fluctuations in transverse velocity in this wavy porous gel layer allow an enhanced transport of the cation, so that the effective diffusivity is about one order of magnitude higher than that expected from molecular diffusion alone. Our theoretical predictions are in excellent agreement with our laboratory measurements of the growth of a manganese hydroxide membrane in a microfluidic channel, and this enhanced transport is thought to have been needed to account for the bioenergetics of the first single-celled organisms.

Diffusion in random networks

DOE PAGES

Zhang, Duan Z.; Padrino, Juan C.

2017-06-01

The ensemble averaging technique is applied to model mass transport by diffusion in random networks. The system consists of an ensemble of random networks, where each network is made of pockets connected by tortuous channels. Inside a channel, fluid transport is assumed to be governed by the one-dimensional diffusion equation. Mass balance leads to an integro-differential equation for the pocket mass density. The so-called dual-porosity model is found to be equivalent to the leading order approximation of the integration kernel when the diffusion time scale inside the channels is small compared to the macroscopic time scale. As a test problem,more » we consider the one-dimensional mass diffusion in a semi-infinite domain. Because of the required time to establish the linear concentration profile inside a channel, for early times the similarity variable is xt $-$1/4 rather than xt $-$1/2 as in the traditional theory. We found this early time similarity can be explained by random walk theory through the network.« less

Convective diffusion of nanoparticles from the epithelial barrier toward regional lymph nodes.

PubMed

Dukhin, Stanislav S; Labib, Mohamed E

2013-11-01

Drug delivery using nanoparticles as drug carriers has recently attracted the attention of many investigators. Targeted delivery of nanoparticles to the lymph nodes is especially important to prevent cancer metastasis or infection, and to diagnose disease stage. However, systemic injection of nanoparticles often results in organ toxicity because they reach and accumulate in all the lymph nodes in the body. An attractive strategy would be to deliver the drug-loaded nanoparticles to a subset of draining lymph nodes corresponding to a specific site or organ to minimize systemic toxicity. In this respect, mucosal delivery of nanoparticles to regional draining lymph nodes of a selected site creates a new opportunity to accomplish this task with minimal toxicity. One example is the delivery of nanoparticles from the vaginal lumen to draining lymph nodes to prevent the transmission of HIV in women. Other known examples include mucosal delivery of vaccines to induce immunity. In all cases, molecular and particle transport by means of diffusion and convective diffusion play a major role. The corresponding transport processes have common inherent regularities and are addressed in this review. Here we use nanoparticle delivery from the vaginal lumen to the lymph nodes as an example to address the many aspects of associated transport processes. In this case, nanoparticles penetrate the epithelial barrier and move through the interstitium (tissue) to the initial lymphatics until they finally reach the lymph nodes. Since the movement of interstitial liquid near the epithelial barrier is retarded, nanoparticle transport was found to take place through special foci present in the epithelium. Immediately after nanoparticles emerge from the foci, they move through the interstitium due to diffusion affected by convection (convective diffusion). Specifically, the convective transport of nanoparticles occurs due to their convection together with interstitial fluid through the interstitium toward the initial lymph capillaries. Afterwards, nanoparticles move together with the lymph flow along the initial lymph capillaries and then enter the afferent lymphatics and ultimately reach the lymph node. As the liquid moves through the interstitium toward the initial lymph capillaries due to the axial movement of lymph along the lymphatics, the theory for coupling between lymph flow and concomitant flow through the interstitium is developed to describe this general case. The developed theory is applied to interpret the large uptake of Qdots by lymph nodes during inflammation, which is induced by pre-treating mouse vagina with the surfactant Nonoxynol-9 prior to instilling the Qdots. Inflammation is viewed here to cause broadening of the pores within the interstitium with the concomitant formation of transport channels which function as conduits to transport the nanoparticles to the initial lymph capillaries. We introduced the term "effective channels" to denote those channels which interconnect with foci present in the epithelial barrier and which function to transport nanoparticles to initial lymph capillaries. The time of transport toward the lymph node, predicated by the theory, increases rapidly with increasing the distance y0 between the epithelial barrier and the initial lymph capillaries. Transport time is only a few hours, when y0 is small, about some R (where R is the initial lymph capillary radius), due to the predomination of a rather rapid convection in this case. This transport time to the lymph nodes may be tens of hours (or longer) when y0 is essentially larger and the slow diffusion controls the transport rate in a zone not far from the epithelial barrier, where convection is weak at large y0. Accounting for transport by diffusion only, which is mainly considered in many relevant publications, is not sufficient to explain our nanoparticle uptake kinetics because the possibility of fast transport due to convection is overlooked. Our systematic investigations have revealed that the information about the main transport conditions, namely, y0 and the pore broadening up to the dimension of the interstitial transport channels, is necessary to create the quantitative model of enhanced transport during inflammation with the use of the proposed model as a prerequisite. The modeling for convective diffusion of nanoparticles from the epithelial barrier to the lymph node has been mainly accomplished here, while the diffusion only scenario is accounted for in other studies. This first modeling is a semi-quantitative one. A more rigorous mathematical approach is almost impossible at this stage because the transport properties of the model are introduced here for the first time. These properties include: discovery of foci in the epithelium, formation of transport channels, definition of channels interconnecting with foci (effective foci and channels), generation of flow in the interstitium toward the initial lymph capillaries due to axial flow within afferent lymphatics, deformation of this flow due to hydrodynamic impermeability of the squamous layer with the formation of the hydrodynamic stagnation zone near the epithelial barrier, predomination of slow diffusion transport within the above zone, and predomination of fast convection of nanoparticles near the initial lymph capillaries. Copyright © 2013 Elsevier B.V. All rights reserved.

Convective diffusion of nanoparticles from the epithelial barrier towards regional lymph nodes

PubMed Central

Dukhin, Stanislav S; Labib, Mohamed E.

2013-01-01

Drug delivery using nanoparticles as drug carriers has recently attracted the attention of many investigators. Targeted delivery of nanoparticles to lymph nodes is especially important to prevent cancer metastasis or infection, and to diagnose disease stage. However, systemic injection of nanoparticles often results in organ toxicity because they reach and accumulate in all the lymph nodes in the body. An attractive strategy would be to deliver the drug-loaded nanoparticles to a subset of draining lymph nodes corresponding to a specific site or organ to minimize systemic toxicity. In this respect, mucosal delivery of nanoparticles to regional draining lymph nodes of a selected site creates a new opportunity to accomplish this task with minimal toxicity. One example is the delivery of nanoparticles from the vaginal lumen to draining lymph nodes to prevent the transmission of HIV in women. Other known examples include mucosal delivery of vaccines to induce immunity. In all cases, molecular and particle transport by means of diffusion and convective diffusion play a major role. The corresponding transport processes have common inherent regularities and are addressed in this review. Here we use nanoparticles delivery from the vaginal lumen to lymph nodes as an example to address the many aspects of associated transport processes. In this case, nanoparticles penetrate the epithelial barrier and move through the interstitium (tissue) to the initial lymphatics until they finally reach the lymph nodes. Since the movement of interstitial liquid near the epithelial barrier is retarded, nanoparticles transport was found to take place through special foci present in the epithelium. Immediately after nanoparticles emerge from the foci, they move through the interstitium due to diffusion affected by convection (convective diffusion). Specifically, the convective transport of nanoparticles occurs due to their convection together with interstitial fluid through the interstitium towards the initial lymph capillaries. Afterwards, nanoparticles move together with the lymph flow along the initial lymph capillaries and then enter the afferent lymphatics and ultimately reach the lymph node. As the liquid moves through the interstitium towards the initial lymph capillaries due to the axial movement of lymph along the lymphatics, the theory for coupling between lymph flow and concomitant flow through the interstitium is developed to describe this general case. The developed theory is applied to interpret the large uptake of Qdots by lymph nodes during inflammation, which is induced by pre-treating mouse vagina with the surfactant Nonoxynol-9 prior to instilling the Qdots. Inflammation is viewed here to cause broadening of the pores within the interstitium with the concomitant formation of transport channels which function as conduits to transport the nanoparticles to the initial lymph capillaries. We introduced the term “effective channels” to denote those channels which interconnect with foci present in the epithelial barrier and which function to transport nanoparticles to initial lymph capillaries. The time of transport towards the lymph node, predicated by the theory, increases rapidly with increasing the distance y0 between the epithelial barrier and the initial lymph capillaries. Transport time is only a few hours, when y0 is small, about some R (where R is the initial lymph capillary radius), due to the predomination of a rather rapid convection in this case. This transport time to lymph nodes may be tens of hours (or longer) when y0 is essentially larger and the slow diffusion controls the transport rate in a zone not far from the epithelial barrier, where convection is weak at large y0. Accounting for transport by diffusion only, which is mainly considered in many relevant publications, is not sufficient to explain our nanoparticles uptake kinetics because the possibility of fast transport due to convection is overlooked. Our systematic investigations have revealed that the information about the main transport conditions, namely, y0 and the pore broadening up to the dimension of the interstitial transport channels, is necessary to create the quantitative model of enhanced transport during inflammation with the use of the proposed model as a prerequisite. The modeling for convective diffusion of nanoparticles from the epithelial barrier to the lymph node has been mainly accomplished here, while the diffusion only scenario is accounted for in other studies. This first modeling is a semi-quantitative one. A more rigorous mathematical approach is almost impossible at this stage because the transport properties of the model are introduced here for the first time. These properties include: discovery of foci in the epithelium, formation of transport channels, definition of channels interconnecting with foci (effective foci and channels), generation of flow in the interstitium towards the initial lymph capillaries due to axial flow within afferent lymphatics, deformation of this flow due to hydrodynamic impermeability of the squamous layer with the formation of the hydrodynamic stagnation zone near the epithelial barrier, predomination of slow diffusion transport within the above zone, and predomination of fast convection of nanoparticles near the initial lymph capillaries. PMID:23859221

Transport dissipative particle dynamics model for mesoscopic advection-diffusion-reaction problems

PubMed Central

Yazdani, Alireza; Tartakovsky, Alexandre; Karniadakis, George Em

2015-01-01

We present a transport dissipative particle dynamics (tDPD) model for simulating mesoscopic problems involving advection-diffusion-reaction (ADR) processes, along with a methodology for implementation of the correct Dirichlet and Neumann boundary conditions in tDPD simulations. tDPD is an extension of the classic dissipative particle dynamics (DPD) framework with extra variables for describing the evolution of concentration fields. The transport of concentration is modeled by a Fickian flux and a random flux between tDPD particles, and the advection is implicitly considered by the movements of these Lagrangian particles. An analytical formula is proposed to relate the tDPD parameters to the effective diffusion coefficient. To validate the present tDPD model and the boundary conditions, we perform three tDPD simulations of one-dimensional diffusion with different boundary conditions, and the results show excellent agreement with the theoretical solutions. We also performed two-dimensional simulations of ADR systems and the tDPD simulations agree well with the results obtained by the spectral element method. Finally, we present an application of the tDPD model to the dynamic process of blood coagulation involving 25 reacting species in order to demonstrate the potential of tDPD in simulating biological dynamics at the mesoscale. We find that the tDPD solution of this comprehensive 25-species coagulation model is only twice as computationally expensive as the conventional DPD simulation of the hydrodynamics only, which is a significant advantage over available continuum solvers. PMID:26156459

A deterministic Lagrangian particle separation-based method for advective-diffusion problems

NASA Astrophysics Data System (ADS)

Wong, Ken T. M.; Lee, Joseph H. W.; Choi, K. W.

2008-12-01

A simple and robust Lagrangian particle scheme is proposed to solve the advective-diffusion transport problem. The scheme is based on relative diffusion concepts and simulates diffusion by regulating particle separation. This new approach generates a deterministic result and requires far less number of particles than the random walk method. For the advection process, particles are simply moved according to their velocity. The general scheme is mass conservative and is free from numerical diffusion. It can be applied to a wide variety of advective-diffusion problems, but is particularly suited for ecological and water quality modelling when definition of particle attributes (e.g., cell status for modelling algal blooms or red tides) is a necessity. The basic derivation, numerical stability and practical implementation of the NEighborhood Separation Technique (NEST) are presented. The accuracy of the method is demonstrated through a series of test cases which embrace realistic features of coastal environmental transport problems. Two field application examples on the tidal flushing of a fish farm and the dynamics of vertically migrating marine algae are also presented.

Influence of surface wettability on transport mechanisms governing water droplet evaporation.

PubMed

Pan, Zhenhai; Weibel, Justin A; Garimella, Suresh V

2014-08-19

Prediction and manipulation of the evaporation of small droplets is a fundamental problem with importance in a variety of microfluidic, microfabrication, and biomedical applications. A vapor-diffusion-based model has been widely employed to predict the interfacial evaporation rate; however, its scope of applicability is limited due to incorporation of a number of simplifying assumptions of the physical behavior. Two key transport mechanisms besides vapor diffusion-evaporative cooling and natural convection in the surrounding gas-are investigated here as a function of the substrate wettability using an augmented droplet evaporation model. Three regimes are distinguished by the instantaneous contact angle (CA). In Regime I (CA ≲ 60°), the flat droplet shape results in a small thermal resistance between the liquid-vapor interface and substrate, which mitigates the effect of evaporative cooling; upward gas-phase natural convection enhances evaporation. In Regime II (60 ≲ CA ≲ 90°), evaporative cooling at the interface suppresses evaporation with increasing contact angle and counterbalances the gas-phase convection enhancement. Because effects of the evaporative cooling and gas-phase convection mechanisms largely neutralize each other, the vapor-diffusion-based model can predict the overall evaporation rates in this regime. In Regime III (CA ≳ 90°), evaporative cooling suppresses the evaporation rate significantly and reverses entirely the direction of natural convection induced by vapor concentration gradients in the gas phase. Delineation of these counteracting mechanisms reconciles previous debate (founded on single-surface experiments or models that consider only a subset of the governing transport mechanisms) regarding the applicability of the classic vapor-diffusion model. The vapor diffusion-based model cannot predict the local evaporation flux along the interface for high contact angle (CA ≥ 90°) when evaporative cooling is strong and the temperature gradient along the interface determines the peak local evaporation flux.

Spatial Variation in Mobility-Lifetime Product in Bulk TlBr and CZT

NASA Astrophysics Data System (ADS)

Phillips, David; Haegel, Nancy; Blaine, Kevin; Kim, Hadong; Ciampi, Guido; Cirignano, Len

2012-02-01

The energy resolution of a semiconductor radiation detector depends on the charge transport properties of the semiconductor, and the mobility-lifetime (μτ) product is a key figure of merit for charge transport. In this work, we investigate the effects of two impurities, Na and Cu, on the μτ product in bulk thallium bromide (TlBr) using cathodoluminescence (CL) and transport imaging. Transport imaging uses a scanning electron microscope to generate a line of charge carriers on the surface of a bulk sample, and the intensity and spatial distribution of the recombination luminescence are recorded. A Green's function approach is used to model the generation, diffusion, and recombination of charge carriers under steady-state conditions. The luminescence distribution is fit to the model to extract the ambipolar diffusion length and the μτ product, providing a high-resolution correlation between the luminescence variations due to dopants/defects and the quantitative transport behavior. The μτ product has been mapped across a 40 μm segment of TlBr at a resolution of 2 μm. Additionally, this approach has been used to locally map variations in ambipolar diffusion length and μτ product due to extended defects in cadmium zinc telluride (CZT).

Liquid Water Saturation and Oxygen Transport Resistance in Polymer Electrolyte Membrane Fuel Cell Gas Diffusion Layers

NASA Astrophysics Data System (ADS)

Muirhead, Daniel

In this thesis, the relative humidity (RH) of the cathode reactant gas was investigated as a factor which influences gas diffusion layer (GDL) liquid water accumulation and mass transport-related efficiency losses over a range of operating current densities in a polymer electrolyte membrane (PEM) fuel cell. Limiting current measurements were used to characterize fuel cell oxygen transport resistance while simultaneous measurements of liquid water accumulation were conducted using synchrotron X-ray radiography. GDL porosity distributions were characterized with micro-computed tomography (microCT). The work presented here can be used by researchers to develop improved numerical models to predict GDL liquid water accumulation and to inform the design of next-generation GDL materials to mitigate mass transport-related efficiency losses. This work also contributes an extensive set of concurrent performance and liquid water visualization data to the PEM fuel cell field that can be used for validating multiphase transport models.

Carrier mobility in organic field-effect transistors

NASA Astrophysics Data System (ADS)

Xu, Yong; Benwadih, Mohamed; Gwoziecki, Romain; Coppard, Romain; Minari, Takeo; Liu, Chuan; Tsukagoshi, Kazuhito; Chroboczek, Jan; Balestra, Francis; Ghibaudo, Gerard

2011-11-01

A study of carrier transport in top-gate and bottom-contact TIPS-pentacene organic field-effect transistors (OFETs) based on mobility is presented. Among three mobilities extracted by different methods, the low-field mobility obtained by the Y function exhibits the best reliability and ease for use, whereas the widely applied field-effect mobility is not reliable, particularly in short-channel transistors and at low temperatures. A detailed study of contact transport reveals its strong impact on short-channel transistors, suggesting that a more intrinsic transport analysis is better implemented in relatively longer-channel devices. The observed temperature dependences of mobility are well explained by a transport model with Gaussian-like diffusivity band tails, different from diffusion in localized states band tails. This model explicitly interprets the non-zero constant mobility at low temperatures and clearly demonstrates the effects of disorder and hopping transport on temperature and carrier density dependences of mobility in organic transistors.

INFLUENCES OF DIFFUSION AND ADVECTIVE FLOW ON THE DISTRIBUTION OF RADON ACTIVITY WITHIN U.S. EPA'S SOIL CHAMBER

EPA Science Inventory

The paper presents an analysis of steady-state diffusion in the soil for two different conditions of moisture. The model accounts for multiphase emanation and transport. When the position dependence of the moisture profile is taken into account, the model and measurements agree w...

Active diffusion and microtubule-based transport oppose myosin forces to position organelles in cells

PubMed Central

Lin, Congping; Schuster, Martin; Guimaraes, Sofia Cunha; Ashwin, Peter; Schrader, Michael; Metz, Jeremy; Hacker, Christian; Gurr, Sarah Jane; Steinberg, Gero

2016-01-01

Even distribution of peroxisomes (POs) and lipid droplets (LDs) is critical to their role in lipid and reactive oxygen species homeostasis. How even distribution is achieved remains elusive, but diffusive motion and directed motility may play a role. Here we show that in the fungus Ustilago maydis ∼95% of POs and LDs undergo diffusive motions. These movements require ATP and involve bidirectional early endosome motility, indicating that microtubule-associated membrane trafficking enhances diffusion of organelles. When early endosome transport is abolished, POs and LDs drift slowly towards the growing cell end. This pole-ward drift is facilitated by anterograde delivery of secretory cargo to the cell tip by myosin-5. Modelling reveals that microtubule-based directed transport and active diffusion support distribution, mobility and mixing of POs. In mammalian COS-7 cells, microtubules and F-actin also counteract each other to distribute POs. This highlights the importance of opposing cytoskeletal forces in organelle positioning in eukaryotes. PMID:27251117

Water Transport in the Micro Porous Layer and Gas Diffusion Layer of a Polymer Electrolyte Fuel Cell

NASA Astrophysics Data System (ADS)

Qin, C.; Hassanizadeh, S. M.

2015-12-01

In this work, a recently developed dynamic pore-network model is presented [1]. The model explicitly solves for both water pressure and capillary pressure. A semi-implicit scheme is used in updating water saturation in each pore body, which considerably increases the numerical stability at low capillary number values. Furthermore, a multiple-time-step algorithm is introduced to reduce the computational effort. A number of case studies of water transport in the micro porous layer (MPL) and gas diffusion layer (GDL) are conducted. We illustrate the role of MPL in reducing water flooding in the GDL. Also, the dynamic water transport through the MPL-GDL interface is explored in detail. This information is essential to the reduced continua model (RCM), which was developed for multiphase flow through thin porous layers [2, 3]. C.Z. Qin, Water transport in the gas diffusion layer of a polymer electrolyte fuel cell: dynamic pore-network modeling, J Electrochimical. Soci., 162, F1036-F1046, 2015. C.Z. Qin and S.M. Hassanizadeh, Multiphase flow through multilayers of thin porous media: general balance equations and constitutive relationships for a solid-gas-liquid three-phase system, Int. J. Heat Mass Transfer, 70, 693-708, 2014. C.Z. Qin and S.M. Hassanizadeh, A new approach to modeling water flooding in a polymer electrolyte fuel cell, Int. J. Hydrogen Energy, 40, 3348-3358, 2015.

Modeling Biogeochemical Cycling of Heavy Metals in Lake Coeur d'Alene Sediments

NASA Astrophysics Data System (ADS)

Sengor, S. S.; Spycher, N.; Belding, E.; Curthoys, K.; Ginn, T. R.

2005-12-01

Mining of precious metals since the late 1800's have left Lake Coeur d'Alene (LCdA) sediments heavily enriched with toxic metals, including Cd, Cu, Pb, and Zn. Indigenous microbes however are capable of catalyzing reactions that detoxify the benthic and aqueous lake environments, and thus constitute an important driving component in the biogeochemical cycles of these metals. Here we report on the development of a quantitative model of transport, fate, exposure and effects of toxic compounds on benthic microbial communities at LCdA. First, chemical data from the LCdA area have been compiled from multiple sources to investigate trends in chemical occurrence, as well as to define model boundary conditions. The model is structured as 1-D diffusive reactive transport model to simulate spatial and temporal distribution of metals through the benthic sediments. Inorganic reaction processes included in the model are aqueous speciation, surface complexation, mineral precipitation/dissolution and abiotic redox reactions. Simulations with and without surface complexation are carried out to evaluate the effect of sorption and the conservative behaviour of metals within the benthic sediments under abiotic and purely diffusive transport. The 1-D inorganic diffusive transport model is then coupled to a biotic reaction network including consortium biodegradation kinetics with multiple electron acceptors, product toxicity, and energy partitioning. Multiyear simulations are performed, with water column chemistry established as a boundary condition from extant data, to explore the role of biogeochemical dynamics on benthic fluxes of metals in the long term.

Characterization of Magma-Driven Hydrothermal Systems at Oceanic Spreading Centers

NASA Astrophysics Data System (ADS)

Farough, A.; Lowell, R. P.; Corrigan, R.

2012-12-01

Fluid circulation in high-temperature hydrothermal systems involves complex water-rock chemical reactions and phase separation. Numerical modeling of reactive transport in multi-component, multiphase systems is required to obtain a full understanding of the characteristics and evolution of hydrothermal vent systems. We use a single-pass parameterized model of high-temperature hydrothermal circulation at oceanic spreading centers constrained by observational parameters such as vent temperature, heat output, and vent field area, together with surface area and depth of the sub-axial magma chamber, to deduce fundamental hydrothermal parameters such as mass flow rate, bulk permeability, conductive boundary layer thickness at the base of the system, magma replenishment rate, and residence time in the discharge zone. All of these key subsurface characteristics are known for fewer than 10 sites out of 300 known hydrothermal systems. The principal limitations of this approach stem from the uncertainty in heat output and vent field area. For systems where data are available on partitioning of heat and chemical output between focused and diffuse flow, we determined the fraction of high-temperature vent fluid incorporated into diffuse flow using a two-limb single pass model. For EPR 9°50` N and ASHES, the diffuse flow temperatures calculated assuming conservative mixing are nearly equal to the observed temperatures indicating that approximately 80%-90% of the hydrothermal heat output occurs as high-temperature flow derived from magmatic heat even though most of the heat output appears as low-temperature diffuse discharge. For the Main Endeavour Field and Lucky Strike, diffuse flow fluids show significant conductive cooling and heating respectively. Finally, we calculate the transport of various geochemical constituents in focused and diffuse flow at the vent field scale and compare the results with estimates of geochemical transports from the Rainbow hydrothermal field where diffuse flow is absent.

Application of Local Discretization Methods in the NASA Finite-Volume General Circulation Model

NASA Technical Reports Server (NTRS)

Yeh, Kao-San; Lin, Shian-Jiann; Rood, Richard B.

2002-01-01

We present the basic ideas of the dynamics system of the finite-volume General Circulation Model developed at NASA Goddard Space Flight Center for climate simulations and other applications in meteorology. The dynamics of this model is designed with emphases on conservative and monotonic transport, where the property of Lagrangian conservation is used to maintain the physical consistency of the computational fluid for long-term simulations. As the model benefits from the noise-free solutions of monotonic finite-volume transport schemes, the property of Lagrangian conservation also partly compensates the accuracy of transport for the diffusion effects due to the treatment of monotonicity. By faithfully maintaining the fundamental laws of physics during the computation, this model is able to achieve sufficient accuracy for the global consistency of climate processes. Because the computing algorithms are based on local memory, this model has the advantage of efficiency in parallel computation with distributed memory. Further research is yet desirable to reduce the diffusion effects of monotonic transport for better accuracy, and to mitigate the limitation due to fast-moving gravity waves for better efficiency.

Multimodal transport and dispersion of organelles in narrow tubular cells

NASA Astrophysics Data System (ADS)

Mogre, Saurabh S.; Koslover, Elena F.

2018-04-01

Intracellular components explore the cytoplasm via active motor-driven transport in conjunction with passive diffusion. We model the motion of organelles in narrow tubular cells using analytical techniques and numerical simulations to study the efficiency of different transport modes in achieving various cellular objectives. Our model describes length and time scales over which each transport mode dominates organelle motion, along with various metrics to quantify exploration of intracellular space. For organelles that search for a specific target, we obtain the average capture time for given transport parameters and show that diffusion and active motion contribute to target capture in the biologically relevant regime. Because many organelles have been found to tether to microtubules when not engaged in active motion, we study the interplay between immobilization due to tethering and increased probability of active transport. We derive parameter-dependent conditions under which tethering enhances long-range transport and improves the target capture time. These results shed light on the optimization of intracellular transport machinery and provide experimentally testable predictions for the effects of transport regulation mechanisms such as tethering.

Modeling the Impact of Heterogeneous Spatial Distribution of Soil Microbes on Pesticide Biodegradation at the Centimeter Scale

NASA Astrophysics Data System (ADS)

Babey, T.; De Dreuzy, J. R.; Pinheiro, M.; Garnier, P.; Vieublé-Gonod, L.; Rapaport, A.

2015-12-01

Micro-organisms and substrates may be heterogeneously distributed in soils. This repartition as well as transport mechanisms bringing them into contact are expected to impact the biodegradation rates. Pinheiro et al [2015] have measured in cm-large reconstructed soil cores the fate of an injection of 2,4-D pesticide for different injection conditions and initial distributions of soil pesticide degraders. Through the calibration of a reactive transport model of these experiments, we show that: i) biodegradation of diffusion-controlled pesticide fluxes is favored by a high Damköhler number (high reaction rate compared to flux rate); ii) abiotic sorption processes are negligible and do not interact strongly with biodegradation; iii) biodegradation is primarily governed by the initial repartition of pesticide and degraders for diffusion-controlled transport, as diffusion greatly limits the flux of pesticide reaching the microbial hotspot due to dilution. These results suggest that for biodegradation to be substantial, a spatial heterogeneity in the repartition of microbes and substrate has to be associated with intermittent and fast transport processes to mix them.

Update on Advection-Diffusion Purge Flow Model

NASA Technical Reports Server (NTRS)

Brieda, Lubos

2015-01-01

Gaseous purge is commonly used in sensitive spacecraft optical or electronic instruments to prevent infiltration of contaminants and/or water vapor. Typically, purge is sized using simplistic zero-dimensional models that do not take into account instrument geometry, surface effects, and the dependence of diffusive flux on the concentration gradient. For this reason, an axisymmetric computational fluid dynamics (CFD) simulation was recently developed to model contaminant infiltration and removal by purge. The solver uses a combined Navier-Stokes and Advection-Diffusion approach. In this talk, we report on updates in the model, namely inclusion of a particulate transport model.

Optical measurement of transverse molecular diffusion in a microchannel.

PubMed Central

Kamholz, A E; Schilling, E A; Yager, P

2001-01-01

Quantitative analysis of molecular diffusion is a necessity for the efficient design of most microfluidic devices as well as an important biophysical method in its own right. This study demonstrates the rapid measurement of diffusion coefficients of large and small molecules in a microfluidic device, the T-sensor, by means of conventional epifluorescence microscopy. Data were collected by monitoring the transverse flux of analyte from a sample stream into a second stream flowing alongside it. As indicated by the low Reynolds numbers of the system (< 1), flow is laminar, and molecular transport between streams occurs only by diffusion. Quantitative determinations were made by fitting data with predictions of a one-dimensional model. Analysis was made of the flow development and its effect on the distribution of diffusing analyte using a three-dimensional modeling software package. Diffusion coefficients were measured for four fluorescently labeled molecules: fluorescein-biotin, insulin, ovalbumin, and streptavidin. The resulting values differed from accepted results by an average of 2.4%. Microfluidic system parameters can be selected to achieve accurate diffusion coefficient measurements and to optimize other microfluidic devices that rely on precise transverse transport of molecules. PMID:11259309

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.

Evaluation of multidimensional transport through a field-scale compacted soil liner

USGS Publications Warehouse

Willingham, T.W.; Werth, C.J.; Valocchi, A.J.; Krapac, I.G.; Toupiol, C.; Stark, T.D.; Daniel, D.E.

2004-01-01

A field-scale compacted soil liner was constructed at the University of Illinois at Urbana-Champaign by the U.S. Environmental Protection Agency (USEPA) and Illinois State Geological Survey in 1988 to investigate chemical transport rates through low permeability compacted clay liners (CCLs). Four tracers (bromide and three benzoic acid tracers) were each added to one of four large ring infiltrometers (LRIs) while tritium was added to the pond water (excluding the infiltrometers). Results from the long-term transport of Br- from the localized source zone of LRI are presented in this paper. Core samples were taken radially outward from the center of the Br- LRI and concentration depth profiles were obtained. Transport properties were evaluated using an axially symmetric transport model. Results indicate that (1) transport was diffusion controlled; (2) transport due to advection was negligible and well within the regulatory limits of ksat???1 ?? 10-7 cm/s; (3) diffusion rates in the horizontal and vertical directions were the same; and (4) small positioning errors due to compression during soil sampling did not affect the best fit advection and diffusion values. The best-fit diffusion coefficient for bromide was equal to the molecular diffusion coefficient multiplied by a tortuosity factor of 0.27, which is within 8% of the tortuosity factor (0.25) found in a related study where tritium transport through the same liner was evaluated. This suggests that the governing mechanisms for the transport of tritium and bromide through the CCL were similar. These results are significant because they address transport through a composite liner from a localized source zone which occurs when defects or punctures in the geomembrane of a composite system are present. ?? ASCE.

Howard Brenner's Legacy for Biological Transport Processes

NASA Astrophysics Data System (ADS)

Nitsche, Johannes

2014-11-01

This talk discusses the manner in which Howard Brenner's theoretical contributions have had, and long will have, strong and direct impact on the understanding of transport processes occurring in biological systems. His early work on low Reynolds number resistance/mobility coefficients of arbitrarily shaped particles, and particles near walls and in pores, is an essential component of models of hindered diffusion through many types of membranes and tissues, and convective transport in microfluidic diagnostic systems. His seminal contributions to macrotransport (coarse-graining, homogenization) theory presaged the growing discipline of multiscale modeling. For biological systems they represent the key to infusing diffusion models of a wide variety of tissues with a sound basis in their microscopic structure and properties, often over a hierarchy of scales. Both scientific currents are illustrated within the concrete context of diffusion models of drug/chemical diffusion through the skin. This area of theory, which is key to transdermal drug development and risk assessment of chemical exposure, has benefitted very directly from Brenner's contributions. In this as in other areas, Brenner's physicochemical insight, mathematical virtuosity, drive for fully justified analysis free of ad hoc assumptions, quest for generality, and impeccable exposition, have consistently elevated the level of theoretical understanding and presentation. We close with anecdotes showing how his personal qualities and warmth helped to impart high standards of rigor to generations of grateful research students. Authors are Johannes M. Nitsche, Ludwig C. Nitsche and Gerald B. Kasting.

Effective scattering coefficient of the cerebral spinal fluid in adult head models for diffuse optical imaging

NASA Astrophysics Data System (ADS)

Custo, Anna; Wells, William M., III; Barnett, Alex H.; Hillman, Elizabeth M. C.; Boas, David A.

2006-07-01

An efficient computation of the time-dependent forward solution for photon transport in a head model is a key capability for performing accurate inversion for functional diffuse optical imaging of the brain. The diffusion approximation to photon transport is much faster to simulate than the physically correct radiative transport equation (RTE); however, it is commonly assumed that scattering lengths must be much smaller than all system dimensions and all absorption lengths for the approximation to be accurate. Neither of these conditions is satisfied in the cerebrospinal fluid (CSF). Since line-of-sight distances in the CSF are small, of the order of a few millimeters, we explore the idea that the CSF scattering coefficient may be modeled by any value from zero up to the order of the typical inverse line-of-sight distance, or approximately 0.3 mm-1, without significantly altering the calculated detector signals or the partial path lengths relevant for functional measurements. We demonstrate this in detail by using a Monte Carlo simulation of the RTE in a three-dimensional head model based on clinical magnetic resonance imaging data, with realistic optode geometries. Our findings lead us to expect that the diffusion approximation will be valid even in the presence of the CSF, with consequences for faster solution of the inverse problem.

Particle transport through hydrogels is charge asymmetric.

PubMed

Zhang, Xiaolu; Hansing, Johann; Netz, Roland R; DeRouchey, Jason E

2015-02-03

Transport processes within biological polymer networks, including mucus and the extracellular matrix, play an important role in the human body, where they serve as a filter for the exchange of molecules and nanoparticles. Such polymer networks are complex and heterogeneous hydrogel environments that regulate diffusive processes through finely tuned particle-network interactions. In this work, we present experimental and theoretical studies to examine the role of electrostatics on the basic mechanisms governing the diffusion of charged probe molecules inside model polymer networks. Translational diffusion coefficients are determined by fluorescence correlation spectroscopy measurements for probe molecules in uncharged as well as cationic and anionic polymer solutions. We show that particle transport in the charged hydrogels is highly asymmetric, with diffusion slowed down much more by electrostatic attraction than by repulsion, and that the filtering capability of the gel is sensitive to the solution ionic strength. Brownian dynamics simulations of a simple model are used to examine key parameters, including interaction strength and interaction range within the model networks. Simulations, which are in quantitative agreement with our experiments, reveal the charge asymmetry to be due to the sticking of particles at the vertices of the oppositely charged polymer networks. Copyright © 2015 Biophysical Society. Published by Elsevier Inc. All rights reserved.

The effect of turbulence strength on meandering field lines and Solar Energetic Particle event extents

NASA Astrophysics Data System (ADS)

Laitinen, Timo; Effenberger, Frederic; Kopp, Andreas; Dalla, Silvia

2018-02-01

Insights into the processes of Solar Energetic Particle (SEP) propagation are essential for understanding how solar eruptions affect the radiation environment of near-Earth space. SEP propagation is influenced by turbulent magnetic fields in the solar wind, resulting in stochastic transport of the particles from their acceleration site to Earth. While the conventional approach for SEP modelling focuses mainly on the transport of particles along the mean Parker spiral magnetic field, multi-spacecraft observations suggest that the cross-field propagation shapes the SEP fluxes at Earth strongly. However, adding cross-field transport of SEPs as spatial diffusion has been shown to be insufficient in modelling the SEP events without use of unrealistically large cross-field diffusion coefficients. Recently, Laitinen et al. [ApJL 773 (2013b); A&A 591 (2016)] demonstrated that the early-time propagation of energetic particles across the mean field direction in turbulent fields is not diffusive, with the particles propagating along meandering field lines. This early-time transport mode results in fast access of the particles across the mean field direction, in agreement with the SEP observations. In this work, we study the propagation of SEPs within the new transport paradigm, and demonstrate the significance of turbulence strength on the evolution of the SEP radiation environment near Earth. We calculate the transport parameters consistently using a turbulence transport model, parametrised by the SEP parallel scattering mean free path at 1 AU, λ∥*, and show that the parallel and cross-field transport are connected, with conditions resulting in slow parallel transport corresponding to wider events. We find a scaling σφ,max∝(1/λ∥*)1/4 for the Gaussian fitting of the longitudinal distribution of maximum intensities. The longitudes with highest intensities are shifted towards the west for strong scattering conditions. Our results emphasise the importance of understanding both the SEP transport and the interplanetary turbulence conditions for modelling and predicting the SEP radiation environment at Earth.

A Rayleighian approach for modeling kinetics of ionic transport in polymeric media

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

Kumar, Rajeev

2017-02-14

Here, we report a theoretical approach for analyzing impedance of ionic liquids (ILs) and charged polymers such as polymerized ionic liquids (PolyILs) within linear response. The approach is based on the Rayleigh dissipation function formalism, which provides a computational framework for a systematic study of various factors, including polymer dynamics, in affecting the impedance. We present an analytical expression for the impedance within linear response by constructing a one-dimensional model for ionic transport in ILs/PolyILs. This expression is used to extract mutual diffusion constants, the length scale of mutual diffusion, and thicknesses of a low-dielectric layer on the electrodes frommore » the broadband dielectric spectroscopy (BDS) measurements done for an IL and three PolyILs. Also, static dielectric permittivities of the IL and the PolyILs are determined. The extracted mutual diffusion constants are compared with the self diffusion constants of ions measured using pulse field gradient (PFG) fluorine nuclear magnetic resonance (NMR). For the first time, excellent agreements between the diffusivities extracted from the Electrode Polarization spectra (EPS) of IL/PolyILs and those measured using the PFG-NMR are found, which allows the use of the EPS and the PFG-NMR techniques in a complimentary manner for a general understanding of the ionic transport.« less

Modeling and simulation of Cu diffusion and drift in porous CMOS backend dielectrics

NASA Astrophysics Data System (ADS)

Ali, R.; Fan, Y.; King, S.; Orlowski, M.

2018-06-01

With the advent of porous dielectrics, Cu drift-diffusion reliability issues in CMOS backend have only been exacerbated. In this regard, a modeling and simulation study of Cu atom/ion drift-diffusion in porous dielectrics is presented to assess the backend reliability and to explore conditions for a reliable Resistive Random Access Memory (RRAM) operation. The numerical computation, using elementary jump frequencies for a random walk in 2D and 3D, is based on an extended adjacency tensor concept. It is shown that Cu diffusion and drift transport are affected as much by the level of porosity as by the pore morphology. Allowance is made for different rates of Cu dissolution into the dielectric and for Cu absorption and transport at and on the inner walls of the pores. Most of the complex phenomena of the drift-diffusion transport in porous media can be understood in terms of local lateral and vertical gradients and the degree of their perturbation caused by the presence of pores in the transport domain. The impact of pore morphology, related to the concept of tortuosity, is discussed in terms of "channeling" and "trapping" effects. The simulations are calibrated to experimental results of porous SiCOH layers of 25 nm thickness, sandwiched between Cu and Pt(W) electrodes with experimental porosity levels of 0%, 8%, 12%, and 25%. We find that porous SICOH is more immune to Cu+ drift at 300 K than non-porous SICOH.

Uncertainty Quantification For Physical and Numerical Diffusion Models In Inertial Confinement Fusion Simulations

NASA Astrophysics Data System (ADS)

Rana, Verinder S.

This thesis concerns simulations of Inertial Confinement Fusion. Inertial confinement is carried out in a large scale facility at National Ignition Facility. The experiments have failed to reproduce design calculations, and so uncertainty quantification of calculations is an important asset. Uncertainties can be classified as aleatoric or epistemic. This thesis is concerned with aleatoric uncertainty quantification. Among the many uncertain aspects that affect the simulations, we have narrowed our study of possible uncertainties. The first source of uncertainty we present is the amount of pre-heating of the fuel done by hot electrons. The second source of uncertainty we consider is the effect of the algorithmic and physical transport diffusion and their effect on the hot spot thermodynamics. Physical transport mechanisms play an important role for the entire duration of the ICF capsule, so modeling them correctly becomes extremely vital. In addition, codes that simulate material mixing introduce numerical (algorithmically) generated transport across the material interfaces. This adds another layer of uncertainty in the solution through the artificially added diffusion. The third source of uncertainty we consider is physical model uncertainty. The fourth source of uncertainty we focus on a single localized surface perturbation (a divot) which creates a perturbation to the solution that can potentially enter the hot spot to diminish the thermonuclear environment. Jets of ablator material are hypothesized to enter the hot spot and cool the core, contributing to the observed lower reactions than predicted levels. A plasma transport package, Transport for Inertial Confinement Fusion (TICF) has been implemented into the Radiation Hydrodynamics code FLASH, from the University of Chicago. TICF has thermal, viscous and mass diffusion models that span the entire ICF implosion regime. We introduced a Quantum Molecular Dynamics calibrated thermal conduction model due to Hu for thermal transport. The numerical approximation uncertainties are introduced by the choice of a hydrodynamic solver for a particular flow. Solvers tend to be diffusive at material interfaces and the Front Tracking (FT) algorithm, which is an already available software code in the form of an API, helps to ameliorate such effects. The FT algorithm has also been implemented in FLASH and we use this to study the effect that divots can have on the hot spot properties.

Unsteady Crystal Growth Due to Step-Bunch Cascading

NASA Technical Reports Server (NTRS)

Vekilov, Peter G.; Lin, Hong; Rosenberger, Franz

1997-01-01

Based on our experimental findings of growth rate fluctuations during the crystallization of the protein lysozym, we have developed a numerical model that combines diffusion in the bulk of a solution with diffusive transport to microscopic growth steps that propagate on a finite crystal facet. Nonlinearities in layer growth kinetics arising from step interaction by bulk and surface diffusion, and from step generation by surface nucleation, are taken into account. On evaluation of the model with properties characteristic for the solute transport, and the generation and propagation of steps in the lysozyme system, growth rate fluctuations of the same magnitude and characteristic time, as in the experiments, are obtained. The fluctuation time scale is large compared to that of step generation. Variations of the governing parameters of the model reveal that both the nonlinearity in step kinetics and mixed transport-kinetics control of the crystallization process are necessary conditions for the fluctuations. On a microscopic scale, the fluctuations are associated with a morphological instability of the vicinal face, in which a step bunch triggers a cascade of new step bunches through the microscopic interfacial supersaturation distribution.

Effect of Gravity Level on the Particle Shape and Size During Zeolite Crystal Growth

NASA Technical Reports Server (NTRS)

Song, Hong-Wei; Ilebusi, Olusegun J.; Sacco, Albert, Jr.

2003-01-01

A microscopic diffusion model is developed to represent solute transport in the boundary layer of a growing zeolite crystal. This model is used to describe the effect of gravity on particle shape and solute distribution. Particle dynamics and crystal growth kinetics serve as the boundary conditions of flow and convection-diffusion equations. A statistical rate theory is used to obtain the rate of solute transport across the growing interface, which is expressed in terms of concentration and velocity of solute species. Microgravity can significantly decrease the solute velocity across the growing interface compared to its earth-based counterpart. The extent of this reduction highly depends on solute diffusion constant in solution. Under gravity, the flow towards the crystal enhances solute transport rate across the growing interface while the flow away from crystals reduces this rate, suggesting a non-uniform growth rate and thus an elliptic final shape. However, microgravity can significantly reduce the influence of flow and obtain a final product with perfect spherical shape. The model predictions compare favorably with the data of space experiment of zeolites grown in space.

Spin-scattering rates in metallic thin films measured by ferromagnetic resonance damping enhanced by spin-pumping

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

Boone, C. T.; Shaw, J. M.; Nembach, H. T.

2015-06-14

We determined the spin-transport properties of Pd and Pt thin films by measuring the increase in ferromagnetic resonance damping due to spin-pumping in ferromagnetic (FM)-nonferromagnetic metal (NM) multilayers with varying NM thicknesses. The increase in damping with NM thickness depends strongly on both the spin- and charge-transport properties of the NM, as modeled by diffusion equations that include both momentum- and spin-scattering parameters. We use the analytical solution to the spin-diffusion equations to obtain spin-diffusion lengths for Pt and Pd. By measuring the dependence of conductivity on NM thickness, we correlate the charge- and spin-transport parameters, and validate the applicabilitymore » of various models for momentum-scattering and spin-scattering rates in these systems: constant, inverse-proportional (Dyakanov-Perel), and linear-proportional (Elliot-Yafet). We confirm previous reports that the spin-scattering time appears to be shorter than the momentum scattering time in Pt, and the Dyakanov-Perel-like model is the best fit to the data.« less

Transport of volatile organic compounds across the capillary fringe

USGS Publications Warehouse

McCarthy, Kathleen A.; Johnson, Richard L.

1993-01-01

Physical experiments were conducted to investigate the transport of a dissolved volatile organic compound (trichloroethylene, TCE) from shallow groundwater to the unsaturated zone under a variety of conditions including changes in the soil moisture profile and water table position. Experimental data indicated that at moderate groundwater velocities (0.1 m/d), vertical mechanical dispersion was negligible and molecular diffusion was the dominant vertical transport mechanism. Under these conditions, TCE concentrations decreased nearly 3 orders of magnitude across the capillary fringe and soil gas concentrations remained low relative to those of underlying groundwater. Data collected during a water table drop showed a short-term increase in concentrations throughout most of the unsaturated zone, but these concentrations quickly declined and approached initial values after the water table was returned to its original level. In the deep part of the unsaturated zone, the water table drop resulted in a long-term decrease in concentrations, illustrating the effects of hysteresis in the soil moisture profile. A two-dimensional random walk advection-diffusion model was developed to simulate the experimental conditions, and numerical simulations agreed well with experimental data. A simpler, one-dimensional finite-difference diffusion-dispersion model was also developed. One-dimensional simulations based on molecular diffusion also agreed well with experimental data. Simulations which incorporated mechanical dispersion tended to overestimate flux across the capillary fringe. Good agreement between the one- and two-dimensional models suggested that a simple, one-dimensional approximation of vertical transport across the capillary fringe can be useful when conditions are appropriate.

Modeling a Single SEP Event from Multiple Vantage Points Using the iPATH Model

NASA Astrophysics Data System (ADS)

Hu, Junxiang; Li, Gang; Fu, Shuai; Zank, Gary; Ao, Xianzhi

2018-02-01

Using the recently extended 2D improved Particle Acceleration and Transport in the Heliosphere (iPATH) model, we model an example gradual solar energetic particle event as observed at multiple locations. Protons and ions that are energized via the diffusive shock acceleration mechanism are followed at a 2D coronal mass ejection-driven shock where the shock geometry varies across the shock front. The subsequent transport of energetic particles, including cross-field diffusion, is modeled by a Monte Carlo code that is based on a stochastic differential equation method. Time intensity profiles and particle spectra at multiple locations and different radial distances, separated in longitudes, are presented. The results shown here are relevant to the upcoming Parker Solar Probe mission.

Thermal conductivity of III-V semiconductor superlattices

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

Mei, S., E-mail: song.mei@wisc.edu; Knezevic, I., E-mail: irena.knezevic@wisc.edu

2015-11-07

This paper presents a semiclassical model for the anisotropic thermal transport in III-V semiconductor superlattices (SLs). An effective interface rms roughness is the only adjustable parameter. Thermal transport inside a layer is described by the Boltzmann transport equation in the relaxation time approximation and is affected by the relevant scattering mechanisms (three-phonon, mass-difference, and dopant and electron scattering of phonons), as well as by diffuse scattering from the interfaces captured via an effective interface scattering rate. The in-plane thermal conductivity is obtained from the layer conductivities connected in parallel. The cross-plane thermal conductivity is calculated from the layer thermal conductivitiesmore » in series with one another and with thermal boundary resistances (TBRs) associated with each interface; the TBRs dominate cross-plane transport. The TBR of each interface is calculated from the transmission coefficient obtained by interpolating between the acoustic mismatch model (AMM) and the diffuse mismatch model (DMM), where the weight of the AMM transmission coefficient is the same wavelength-dependent specularity parameter related to the effective interface rms roughness that is commonly used to describe diffuse interface scattering. The model is applied to multiple III-arsenide superlattices, and the results are in very good agreement with experimental findings. The method is both simple and accurate, easy to implement, and applicable to complicated SL systems, such as the active regions of quantum cascade lasers. It is also valid for other SL material systems with high-quality interfaces and predominantly incoherent phonon transport.« less

Oxygen self-diffusion mechanisms in monoclinic Zr O2 revealed and quantified by density functional theory, random walk analysis, and kinetic Monte Carlo calculations

NASA Astrophysics Data System (ADS)

Yang, Jing; Youssef, Mostafa; Yildiz, Bilge

2018-01-01

In this work, we quantify oxygen self-diffusion in monoclinic-phase zirconium oxide as a function of temperature and oxygen partial pressure. A migration barrier of each type of oxygen defect was obtained by first-principles calculations. Random walk theory was used to quantify the diffusivities of oxygen interstitials by using the calculated migration barriers. Kinetic Monte Carlo simulations were used to calculate diffusivities of oxygen vacancies by distinguishing the threefold- and fourfold-coordinated lattice oxygen. By combining the equilibrium defect concentrations obtained in our previous work together with the herein calculated diffusivity of each defect species, we present the resulting oxygen self-diffusion coefficients and the corresponding atomistically resolved transport mechanisms. The predicted effective migration barriers and diffusion prefactors are in reasonable agreement with the experimentally reported values. This work provides insights into oxygen diffusion engineering in Zr O2 -related devices and parametrization for continuum transport modeling.

The Role of Subsurface Properties on Transport of Water and Trace Gases: 1D Simulations at Selected Mars Landing Sites.

NASA Astrophysics Data System (ADS)

Karatekin, O.; Gloesener, E.; Dehant, V. M. A.

2017-12-01

In this work, water ice stability and water vapour transport through porous martian subsurface are studied using a 1D diffusive model. The role of adsorption on water transfer in martian conditions is investigated as well as the range of parameters that have the largest effect on gas transport. In addition, adsorption kinetics is considered to examine its influence on the water vapor exchange between the subsurface and the atmosphere. As methane has been detected in the martian atmosphere, the subsurface model is then used to study methane diffusion in the CH4/CO2/H2O system from variable depths under the surface. The results of subsurface gas transport at selected locations/landing sites are shown and implications for present/future observations are discussed.

A mathematical model of water and nutrient transport in xylem vessels of a wheat plant.

PubMed

Payvandi, S; Daly, K R; Jones, D L; Talboys, P; Zygalakis, K C; Roose, T

2014-03-01

At a time of increasing global demand for food, dwindling land and resources, and escalating pressures from climate change, the farming industry is undergoing financial strain, with a need to improve efficiency and crop yields. In order to improve efficiencies in farming, and in fertiliser usage in particular, understanding must be gained of the fertiliser-to-crop-yield pathway. We model one aspect of this pathway; the transport of nutrients within the vascular tissues of a crop plant from roots to leaves. We present a mathematical model of the transport of nutrients within the xylem vessels in response to the evapotranspiration of water. We determine seven different classes of flow, including positive unidirectional flow, which is optimal for nutrient transport from the roots to the leaves; and root multidirectional flow, which is similar to the hydraulic lift process observed in plants. We also investigate the effect of diffusion on nutrient transport and find that diffusion can be significant at the vessel termini especially if there is an axial efflux of nutrient, and at night when transpiration is minimal. Models such as these can then be coupled to whole-plant models to be used for optimisation of nutrient delivery scenarios.

Modelling of soot formation in laminar diffusion flames using a comprehensive CFD-PBE model with detailed gas-phase chemistry

NASA Astrophysics Data System (ADS)

Akridis, Petros; Rigopoulos, Stelios

2017-01-01

A discretised population balance equation (PBE) is coupled with an in-house computational fluid dynamics (CFD) code in order to model soot formation in laminar diffusion flames. The unsteady Navier-Stokes, species and enthalpy transport equations and the spatially-distributed discretised PBE for the soot particles are solved in a coupled manner, together with comprehensive gas-phase chemistry and an optically thin radiation model, thus yielding the complete particle size distribution of the soot particles. Nucleation, surface growth and oxidation are incorporated into the PBE using an acetylene-based soot model. The potential of the proposed methodology is investigated by comparing with experimental results from the Santoro jet burner [Santoro, Semerjian and Dobbins, Soot particle measurements in diffusion flames, Combustion and Flame, Vol. 51 (1983), pp. 203-218; Santoro, Yeh, Horvath and Semerjian, The transport and growth of soot particles in laminar diffusion flames, Combustion Science and Technology, Vol. 53 (1987), pp. 89-115] for three laminar axisymmetric non-premixed ethylene flames: a non-smoking, an incipient smoking and a smoking flame. Overall, good agreement is observed between the numerical and the experimental results.

Effects of Anomalous Cosmic Rays on the Structure of the Outer Heliosphere

NASA Astrophysics Data System (ADS)

Guo, Xiaocheng; Florinski, Vladimir; Wang, Chi

2018-06-01

Based on Voyager 1 observations, some anomalous cosmic rays (ACRs) may have crossed the heliopause and escaped into the interstellar medium, providing a mechanism of energy transfer between the inner and outer heliosheaths that is not included in conventional magnetohydrodynamics (MHD) models. In this paper, we study the effect of energetic particles’ escape through the heliopause on the size and shape of the heliosphere using a simple model that includes diffusive transport of cosmic rays. We show that the presence of ACRs significantly changes the heliosphere structure, including the location of the heliopause and termination shock. It was found that the heliopause would contract for certain values of the ACR diffusion coefficients when the diffusive particles’ pressure is comparable to the pressure of the plasma background. The difference in Voyager 1 and 2 observations of energetic particles during their respective termination shock crossings is interpreted here as due to the differences in diffusion environments during the different phases of the solar cycle. The shorter period of enhanced ACR intensities upstream of the shock measured by Voyager 2 may have been caused by weaker radial diffusive transport compared with the time of Voyager 1 crossing. We conclude that ACR diffusive effects could be prominent and should be included in MHD models of the heliosphere.

Multiparameter Analysis of Gas Transport Phenomena in Shale Gas Reservoirs: Apparent Permeability Characterization.

PubMed

Shen, Yinghao; Pang, Yu; Shen, Ziqi; Tian, Yuanyuan; Ge, Hongkui

2018-02-08

The large amount of nanoscale pores in shale results in the inability to apply Darcy's law. Moreover, the gas adsorption of shale increases the complexity of pore size characterization and thus decreases the accuracy of flow regime estimation. In this study, an apparent permeability model, which describes the adsorptive gas flow behavior in shale by considering the effects of gas adsorption, stress dependence, and non-Darcy flow, is proposed. The pore size distribution, methane adsorption capacity, pore compressibility, and matrix permeability of the Barnett and Eagle Ford shales are measured in the laboratory to determine the critical parameters of gas transport phenomena. The slip coefficients, tortuosity, and surface diffusivity are predicted via the regression analysis of the permeability data. The results indicate that the apparent permeability model, which considers second-order gas slippage, Knudsen diffusion, and surface diffusion, could describe the gas flow behavior in the transition flow regime for nanoporous shale. Second-order gas slippage and surface diffusion play key roles in the gas flow in nanopores for Knudsen numbers ranging from 0.18 to 0.5. Therefore, the gas adsorption and non-Darcy flow effects, which involve gas slippage, Knudsen diffusion, and surface diffusion, are indispensable parameters of the permeability model for shale.

Comparison of Experimental Methods for Estimating Matrix Diffusion Coefficients for Contaminant Transport Modeling

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

Telfeyan, Katherine Christina; Ware, Stuart Douglas; Reimus, Paul William

Diffusion cell and diffusion wafer experiments were conducted to compare methods for estimating matrix diffusion coefficients in rock core samples from Pahute Mesa at the Nevada Nuclear Security Site (NNSS). A diffusion wafer method, in which a solute diffuses out of a rock matrix that is pre-saturated with water containing the solute, is presented as a simpler alternative to the traditional through-diffusion (diffusion cell) method. Both methods yielded estimates of matrix diffusion coefficients that were within the range of values previously reported for NNSS volcanic rocks. The difference between the estimates of the two methods ranged from 14 to 30%,more » and there was no systematic high or low bias of one method relative to the other. From a transport modeling perspective, these differences are relatively minor when one considers that other variables (e.g., fracture apertures, fracture spacings) influence matrix diffusion to a greater degree and tend to have greater uncertainty than diffusion coefficients. For the same relative random errors in concentration measurements, the diffusion cell method yields diffusion coefficient estimates that have less uncertainty than the wafer method. However, the wafer method is easier and less costly to implement and yields estimates more quickly, thus allowing a greater number of samples to be analyzed for the same cost and time. Given the relatively good agreement between the methods, and the lack of any apparent bias between the methods, the diffusion wafer method appears to offer advantages over the diffusion cell method if better statistical representation of a given set of rock samples is desired.« less

Comparison of experimental methods for estimating matrix diffusion coefficients for contaminant transport modeling

NASA Astrophysics Data System (ADS)

Telfeyan, Katherine; Ware, S. Doug; Reimus, Paul W.; Birdsell, Kay H.

2018-02-01

Diffusion cell and diffusion wafer experiments were conducted to compare methods for estimating effective matrix diffusion coefficients in rock core samples from Pahute Mesa at the Nevada Nuclear Security Site (NNSS). A diffusion wafer method, in which a solute diffuses out of a rock matrix that is pre-saturated with water containing the solute, is presented as a simpler alternative to the traditional through-diffusion (diffusion cell) method. Both methods yielded estimates of effective matrix diffusion coefficients that were within the range of values previously reported for NNSS volcanic rocks. The difference between the estimates of the two methods ranged from 14 to 30%, and there was no systematic high or low bias of one method relative to the other. From a transport modeling perspective, these differences are relatively minor when one considers that other variables (e.g., fracture apertures, fracture spacings) influence matrix diffusion to a greater degree and tend to have greater uncertainty than effective matrix diffusion coefficients. For the same relative random errors in concentration measurements, the diffusion cell method yields effective matrix diffusion coefficient estimates that have less uncertainty than the wafer method. However, the wafer method is easier and less costly to implement and yields estimates more quickly, thus allowing a greater number of samples to be analyzed for the same cost and time. Given the relatively good agreement between the methods, and the lack of any apparent bias between the methods, the diffusion wafer method appears to offer advantages over the diffusion cell method if better statistical representation of a given set of rock samples is desired.

Origin of halides (Cl- and Br-) and of their stable isotopes (d37Cl and d81Br) at the Tournemire URL (France) - Experimental and numerical approach

NASA Astrophysics Data System (ADS)

Bachir-Bey, Nassim; Matray, Jean-Michel

2014-05-01

This work is part of research conducted by the Institute of Radiological and Nuclear Safety (IRSN) on the geological disposal of High-Level and Intermediate-Level Long-Lived (HL-ILLL) radioactive waste in deep clayrocks. In France, the choice of the potential host rock for the geological storage is focused on the Callovian-Oxfordian (COx) of Meuse/Haute-Marne from its low permeability, capacity for self- sealing, high sorption and ability to radionuclide (RN) transport by diffusion. IRSN, which plays an expert role for ASN has its own underground research laboratory in a clayrock which has strong analogies to the COx. This is the Toarcian/Domerian clayrock located at Tournemire in southern Aveyron in France. The purpose of this study was to assess the transfer of RN in the Tournemire clayrock through the study of halides contents and of their stable isotopes (Cl-, Br-, Cl-/Br-, d37Cl, d81Br). The approach used was multiple and consisted for halides to: 1) Assess their stock in different fractions of the rock by applying several techniques including i) alkaline fusion for their total stock, ii) leaching to access their stock in porewater and to mineral phases sensitive to dissolution iii) cubic diffusion for their stock in porewater, 2) Get their diffusive transport parameters of a selection of samples from the upper Toarcian by cubic diffusion experiments modelled using the Hytec transport code developed by Mines ParisTech and 3) Model their transport after palaeohydrogeological known changes of the Tournemire massif. The experimental approach, conducted at the LAME lab, did not lead to an operational protocol for the alkaline fusion due to an incomplete rock dissolution. Leaching was used to characterize the concentrations of halides in the fractions of pore water and of minerals sensitive to dissolution. The results show levels of halides much higher than those of pore water with very low Cl/Br ratios likely resulting from the dissolution of mineral species. The cubic diffusion produced the pore diffusion coefficients for Cl and Br as well as their concentration in the porewater. Cubic diffusion also allowed to estimate a Cl to Br pore diffusion coefficient ratio, necessary to calculate the profiles of Cl/Br. These estimates have required the use of the transport code Hytec i) for dimensioning and implementing the experiment in a time frame compatible with the work period, ii) for analysing the sensitiveness of the model to the accessible porosity and to the diffusion coefficient which act respectively to the steady phase and transient phase of the experiments, and finally, iii ) for adjusting the pore diffusion coefficients of Cl and Br to an accessible porosity of 3-4%. The Hytec code was then used to check the consistency of the current profiles of chlorides, bromides, 35Cl , 37Cl , d37Cl, Cl/Br in 1D, a fake drilling assumed crossing the entire clayrock. The assumption is that halides have undergone a diffusive transport between seawater trapped during sedimentation and meteoric waters infiltrated at different times to domain boundaries. Four scenarios were tested according to the paleohydrogeological history of the massif. All tracers and scenarios are consistent with a unique marine source of halides more or less diluted by meteoric waters. The duration of the diffusive exchange initially suggested 85 ± 10 Ma (Bensenouci, 2010) is never contradicted despite uncertainties related to changes in boundary conditions. This body of evidence would suggest that molecular diffusion is the transport process which has affected and still affect the Tournemire clayrock, outside fault zones. The d37Cl results expected on the surrounding carbonated aquifers, leachates and fracture waters (including d81Br values) should help to refine the models and the results.

A model of recovering the parameters of fast nonlocal heat transport in magnetic fusion plasmas

NASA Astrophysics Data System (ADS)

Kukushkin, A. B.; Kulichenko, A. A.; Sdvizhenskii, P. A.; Sokolov, A. V.; Voloshinov, V. V.

2017-12-01

A model is elaborated for interpreting the initial stage of the fast nonlocal transport events, which exhibit immediate response, in the diffusion time scale, of the spatial profile of electron temperature to its local perturbation, while the net heat flux is directed opposite to ordinary diffusion (i.e. along the temperature gradient). We solve the inverse problem of recovering the kernel of the integral equation, which describes nonlocal (superdiffusive) transport of energy due to emission and absorption of electromagnetic (EM) waves with long free path and strong reflection from the vacuum vessel’s wall. To allow for the errors of experimental data, we use the method based on the regularized (in the framework of an ill-posed problem, using the parametric models) approximation of available experimental data. The model is applied to interpreting the data from stellarator LHD and tokamak TFTR. The EM wave transport is considered here in the single-group approximation, however the limitations of the physics model enable us to identify the spectral range of the EM waves which might be responsible for the observed phenomenon.

Anomalous diffusion of brain metabolites evidenced by diffusion-weighted magnetic resonance spectroscopy in vivo

PubMed Central

Marchadour, Charlotte; Brouillet, Emmanuel; Hantraye, Philippe; Lebon, Vincent; Valette, Julien

2012-01-01

Translational displacement of molecules within cells is a key process in cellular biology. Molecular motion potentially depends on many factors, including active transport, cytosol viscosity and molecular crowding, tortuosity resulting from cytoskeleton and organelles, and restriction barriers. However, the relative contribution of these factors to molecular motion in the cytoplasm remains poorly understood. In this work, we designed an original diffusion-weighted magnetic resonance spectroscopy strategy to probe molecular motion at subcellular scales in vivo. This led to the first observation of anomalous diffusion, that is, dependence of the apparent diffusion coefficient (ADC) on the diffusion time, for endogenous intracellular metabolites in the brain. The observed increase of the ADC at short diffusion time yields evidence that metabolite motion is characteristic of hindered random diffusion rather than active transport, for time scales up to the dozen milliseconds. Armed with this knowledge, data modeling based on geometrically constrained diffusion was performed. Results suggest that metabolite diffusion occurs in a low-viscosity cytosol hindered by ∼2-μm structures, which is consistent with known intracellular organization. PMID:22929443

Analytical transport network theory to guide the design of 3-D microstructural networks in energy materials: Part 1. Flow without reactions

NASA Astrophysics Data System (ADS)

Cocco, Alex P.; Nakajo, Arata; Chiu, Wilson K. S.

2017-12-01

We present a fully analytical, heuristic model - the "Analytical Transport Network Model" - for steady-state, diffusive, potential flow through a 3-D network. Employing a combination of graph theory, linear algebra, and geometry, the model explicitly relates a microstructural network's topology and the morphology of its channels to an effective material transport coefficient (a general term meant to encompass, e.g., conductivity or diffusion coefficient). The model's transport coefficient predictions agree well with those from electrochemical fin (ECF) theory and finite element analysis (FEA), but are computed 0.5-1.5 and 5-6 orders of magnitude faster, respectively. In addition, the theory explicitly relates a number of morphological and topological parameters directly to the transport coefficient, whereby the distributions that characterize the structure are readily available for further analysis. Furthermore, ATN's explicit development provides insight into the nature of the tortuosity factor and offers the potential to apply theory from network science and to consider the optimization of a network's effective resistance in a mathematically rigorous manner. The ATN model's speed and relative ease-of-use offer the potential to aid in accelerating the design (with respect to transport), and thus reducing the cost, of energy materials.

A HIGHWAY MODEL FOR THE ADVECTION, DIFFUSION AND CHEMICAL REACTION OF POLLUTANTS RELEASED BY AUTOMOBILES: PART I. ADVECTION AND DIFFUSION OF SF6 TRACER GAS

EPA Science Inventory

A two-dimensional, finite-difference model simulating a highway has been developed which is able to handle linear and nonlinear chemical reactions. Transport of the pollutants is accomplished by use of an upstream-flux-corrected algorithm developed at the Naval Research Laborator...

Scaling Law for Cross-stream Diffusion in Microchannels under Combined Electroosmotic and Pressure Driven Flow.

PubMed

Song, Hongjun; Wang, Yi; Pant, Kapil

2013-01-01

This paper presents an analytical study of the cross-stream diffusion of an analyte in a rectangular microchannel under combined electroosmotic flow (EOF) and pressure driven flow to investigate the heterogeneous transport behavior and spatially-dependent diffusion scaling law. An analytical model capable of accurately describing 3D steady-state convection-diffusion in microchannels with arbitrary aspect ratios is developed based on the assumption of the thin Electric Double Layer (EDL). The model is verified against high-fidelity numerical simulation in terms of flow velocity and analyte concentration profiles with excellent agreement (<0.5% relative error). An extensive parametric analysis is then undertaken to interrogate the effect of the combined flow velocity field on the transport behavior in both the positive pressure gradient (PPG) and negative pressure gradient (NPG) cases. For the first time, the evolution from the spindle-shaped concentration profile in the PPG case, via the stripe-shaped profile (pure EOF), and finally to the butterfly-shaped profile in the PPG case is obtained using the analytical model along with a quantitative depiction of the spatially-dependent diffusion layer thickness and scaling law across a wide range of the parameter space.

Scaling Law for Cross-stream Diffusion in Microchannels under Combined Electroosmotic and Pressure Driven Flow

PubMed Central

Song, Hongjun; Wang, Yi; Pant, Kapil

2012-01-01

This paper presents an analytical study of the cross-stream diffusion of an analyte in a rectangular microchannel under combined electroosmotic flow (EOF) and pressure driven flow to investigate the heterogeneous transport behavior and spatially-dependent diffusion scaling law. An analytical model capable of accurately describing 3D steady-state convection-diffusion in microchannels with arbitrary aspect ratios is developed based on the assumption of the thin Electric Double Layer (EDL). The model is verified against high-fidelity numerical simulation in terms of flow velocity and analyte concentration profiles with excellent agreement (<0.5% relative error). An extensive parametric analysis is then undertaken to interrogate the effect of the combined flow velocity field on the transport behavior in both the positive pressure gradient (PPG) and negative pressure gradient (NPG) cases. For the first time, the evolution from the spindle-shaped concentration profile in the PPG case, via the stripe-shaped profile (pure EOF), and finally to the butterfly-shaped profile in the PPG case is obtained using the analytical model along with a quantitative depiction of the spatially-dependent diffusion layer thickness and scaling law across a wide range of the parameter space. PMID:23554584

Diffusion of a Concentrated Lattice Gas in a Regular Comb Structure

NASA Astrophysics Data System (ADS)

Garcia, Paul; Wentworth, Christopher

2008-10-01

Understanding diffusion in constrained geometries is of interest in a variety of contexts as varied as mass transport in disordered solids, such as a percolation cluster, or intercellular transport of water molecules in biological tissue. In this investigation we explore diffusion in a very simple constrained geometry: a comb-like structure involving a one-dimensional backbone of lattice sites with regularly spaced teeth of fixed length. The model considered assumes a fixed concentration of diffusing particles can hop to nearest-neighbor sites only, and they do not interact with each other except that double occupancy is not allowed. The system is simulated using a Monte Carlo simulation procedure. The mean-square displacement of a tagged particle is calculated from the simulation as a function of time. The simulation shows normal diffusive behavior after a period of anomalous diffusion that increases as the tooth size increases.

Effects of energy-related activities on the Atlantic Continental Shelf

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

Manowitz, B

1975-01-01

Sixteen papers were presented and are announced separately. Coastal waters, continental shelf geology and aquatic ecosystems are studied for modelling basic data for assessment of possible environmental impacts from offshore energy development. Sediment transport and wave phenomena are modelled for understanding water pollution transport and diffusion. (PCS)

Phospholipid Diffusion Coefficients of Cushioned Model Membranes determined via Z-Scan Fluorescence Correlation Spectroscopy

PubMed Central

Sterling, Sarah M.; Allgeyer, Edward S.; Fick, Jörg; Prudovsky, Igor; Mason, Michael D.; Neivandt, David J.

2013-01-01

Model cellular membranes enable the study of biological processes in a controlled environment and reduce the traditional challenges associated with live or fixed cell studies. However, model membrane systems based on the air/water or oil/solution interface do not allow for incorporation of transmembrane proteins, or for the study of protein transport mechanisms. Conversely, a phospholipid bilayer deposited via the Langmuir-Blodgett/Langmuir Schaefer method on a hydrogel layer is potentially an effective mimic of the cross-section of a biological membrane, and facilitates both protein incorporation and transport studies. Prior to application, however, such membranes must be fully characterized, particularly with respect to the phospholipid bilayer phase transition temperature. Here we present a detailed characterization of the phase transition temperature of the inner and outer leaflets of a chitosan supported model membrane system. Specifically, the lateral diffusion coefficient of each individual leaflet has been determined as a function of temperature. Measurements were performed utilizing z-scan fluorescence correlation spectroscopy (FCS), a technique that yields calibration-free diffusion information. Analysis via the method of Wawrezinieck and coworkers, revealed that phospholipid diffusion changes from raft-like to free diffusion as the temperature is increased; an insight into the dynamic behavior of hydrogel supported membranes not previously reported. PMID:23705855

Stormtime ring current and radiation belt ion transport: Simulations and interpretations

NASA Technical Reports Server (NTRS)

Lyons, Larry R.; Gorney, David J.; Chen, Margaret W.; Schulz, Michael

1995-01-01

We use a dynamical guiding-center model to investigate the stormtime transport of ring current and radiation-belt ions. We trace the motion of representative ions' guiding centers in response to model substorm-associated impulses in the convection electric field for a range of ion energies. Our simple magnetospheric model allows us to compare our numerical results quantitatively with analytical descriptions of particle transport, (e.g., with the quasilinear theory of radial diffusion). We find that 10-145-keV ions gain access to L approximately 3, where they can form the stormtime ring current, mainly from outside the (trapping) region in which particles execute closed drift paths. Conversely, the transport of higher-energy ions (approximately greater than 145 keV at L approximately 3) turns out to resemble radial diffusion. The quasilinear diffusion coefficient calculated for our model storm does not vary smoothly with particle energy, since our impulses occur at specific (although randomly determined) times. Despite the spectral irregularity, quasilinear theory provides a surprisingly accurate description of the transport process for approximately greater than 145-keV ions, even for the case of an individual storm. For 4 different realizations of our model storm, the geometric mean discrepancies between diffusion coefficients D(sup sim, sub LL) obtained from the simulations and the quasilinear diffusion coefficient D(sup ql, sub LL) amount to factors of 2.3, 2.3, 1.5, and 3.0, respectively. We have found that these discrepancies between D(sup sim, sub LL) and D(sup ql, sub LL) can be reduced slightly by invoking drift-resonance broadening to smooth out the sharp minima and maxima in D(sup ql, sub LL). The mean of the remaining discrepancies between D(sup sim, sub LL) and D(sup ql, sub LL) for the 4 different storms then amount to factors of 1.9, 2.1, 1.5, and 2.7, respectively. We find even better agreement when we reduce the impulse amplitudes systematically in a given model storm (e.g., reduction of all the impulse amplitudes by half reduces the discrepancy factor by at least its square root) and also when we average our results over an ensemble of 20 model storms (agreement is within a factor of 1.2 without impulse-amplitude reduction). We use our simulation results also to map phase-space densities f in accordance with Liouville's theorem. We find that the stormtime transport of approximately greater than 145-keV ions produces little change in f-bar the drift-averaged phase-space density on any drift shell of interest. However, the stormtime transport produces a major enhancement from the pre-storm phase-space density at energies approximately 30-145 keV, which are representative of the stormtime ring current.

Fluid flow and convective transport of solutes within the intervertebral disc.

PubMed

Ferguson, Stephen J; Ito, Keita; Nolte, Lutz P

2004-02-01

Previous experimental and analytical studies of solute transport in the intervertebral disc have demonstrated that for small molecules diffusive transport alone fulfils the nutritional needs of disc cells. It has been often suggested that fluid flow into and within the disc may enhance the transport of larger molecules. The goal of the study was to predict the influence of load-induced interstitial fluid flow on mass transport in the intervertebral disc. An iterative procedure was used to predict the convective transport of physiologically relevant molecules within the disc. An axisymmetric, poroelastic finite-element structural model of the disc was developed. The diurnal loading was divided into discrete time steps. At each time step, the fluid flow within the disc due to compression or swelling was calculated. A sequentially coupled diffusion/convection model was then employed to calculate solute transport, with a constant concentration of solute being provided at the vascularised endplates and outer annulus. Loading was simulated for a complete diurnal cycle, and the relative convective and diffusive transport was compared for solutes with molecular weights ranging from 400 Da to 40 kDa. Consistent with previous studies, fluid flow did not enhance the transport of low-weight solutes. During swelling, interstitial fluid flow increased the unidirectional penetration of large solutes by approximately 100%. Due to the bi-directional temporal nature of disc loading, however, the net effect of convective transport over a full diurnal cycle was more limited (30% increase). Further study is required to determine the significance of large solutes and the timing of their delivery for disc physiology.

Cytoskeletal Network Morphology Regulates Intracellular Transport Dynamics

PubMed Central

Ando, David; Korabel, Nickolay; Huang, Kerwyn Casey; Gopinathan, Ajay

2015-01-01

Intracellular transport is essential for maintaining proper cellular function in most eukaryotic cells, with perturbations in active transport resulting in several types of disease. Efficient delivery of critical cargos to specific locations is accomplished through a combination of passive diffusion and active transport by molecular motors that ballistically move along a network of cytoskeletal filaments. Although motor-based transport is known to be necessary to overcome cytoplasmic crowding and the limited range of diffusion within reasonable timescales, the topological features of the cytoskeletal network that regulate transport efficiency and robustness have not been established. Using a continuum diffusion model, we observed that the time required for cellular transport was minimized when the network was localized near the nucleus. In simulations that explicitly incorporated network spatial architectures, total filament mass was the primary driver of network transit times. However, filament traps that redirect cargo back to the nucleus caused large variations in network transport. Filament polarity was more important than filament orientation in reducing average transit times, and transport properties were optimized in networks with intermediate motor on and off rates. Our results provide important insights into the functional constraints on intracellular transport under which cells have evolved cytoskeletal structures, and have potential applications for enhancing reactions in biomimetic systems through rational transport network design. PMID:26488648

A novel (ex situ) method to quantify oxygen diffusion coefficient of polymer fuel cells backing and catalyst layers

NASA Astrophysics Data System (ADS)

Baricci, Andrea; Casalegno, Andrea

2016-09-01

Limiting current density of oxygen reduction reaction in polymer electrolyte fuel cells is determined by several mass transport resistances that lower the concentration of oxygen on the catalyst active site. Among them, diffusion across porous media plays a significant role. Despite the extensive experimental activity documented in PEMFC literature, only few efforts have been dedicated to the measurement of the effective transport properties in porous layers. In the present work, a methodology for ex situ measurement of the effective diffusion coefficient and Knudsen radius of porous layers for polymer electrolyte fuel cells (gas diffusion layer, micro porous layer and catalyst layer) is described and applied to high temperature polymer fuel cells State of Art materials. Regression of the measured quantities by means of a quasi 2D physical model is performed to quantify the Knudsen effect, which is reported to account, respectively, for 30% and 50% of the mass transport resistance in micro porous layer and catalyst layer. On the other side, the model reveals that pressure gradient consequent to permeation in porous layers of high temperature polymer fuel cells has a negligible effect on oxygen concentration in relevant operating conditions.

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.

Modeling packed bed sorbent systems with the Pore Surface Diffusion Model: Evidence of facilitated surface diffusion of arsenate in nano-metal (hydr)oxide hybrid ion exchange media.

PubMed

Dale, Sachie; Markovski, Jasmina; Hristovski, Kiril D

2016-09-01

This study explores the possibility of employing the Pore Surface Diffusion Model (PSDM) to predict the arsenic breakthrough curve of a packed bed system operated under continuous flow conditions with realistic groundwater, and consequently minimize the need to conduct pilot scale tests. To provide the nano-metal (hydr)oxide hybrid ion exchange media's performance in realistic water matrices without engaging in taxing pilot scale testing, the multi-point equilibrium batch sorption tests under pseudo-equilibrium conditions were performed; arsenate breakthrough curve of short bed column (SBC) was predicted by the PSDM in the continuous flow experiments; SBC tests were conducted under the same conditions to validate the model. The overlapping Freundlich isotherms suggested that the water matrix and competing ions did not have any denoting effect on sorption capacity of the media when the matrix was changed from arsenic-only model water to real groundwater. As expected, the PSDM provided a relatively good prediction of the breakthrough profile for arsenic-only model water limited by intraparticle mass transports. In contrast, the groundwater breakthrough curve demonstrated significantly faster intraparticle mass transport suggesting to a surface diffusion process, which occurs in parallel to the pore diffusion. A simple selection of DS=1/2 DP appears to be sufficient when describing the facilitated surface diffusion of arsenate inside metal (hydr)oxide nano-enabled hybrid ion-exchange media in presence of sulfate, however, quantification of the factors determining the surface diffusion coefficient's magnitude under different treatment scenarios remained unexplored. Copyright © 2015 Elsevier B.V. All rights reserved.

Influence of wind-induced air pressure fluctuations on topsoil gas concentrations within a Scots pine forest

NASA Astrophysics Data System (ADS)

Mohr, Manuel; Laemmel, Thomas; Maier, Martin; Schindler, Dirk

2017-04-01

Commonly it is assumed that soil gas transport is dominated by molecular diffusion. Few recent studies indicate that the atmosphere above the soil triggers non-diffusive gas transport processes in the soil, which can enhance soil gas transport and therefore soil gas efflux significantly. During high wind speed conditions, the so called pressure pumping effect has been observed: the enhancement of soil gas transport through dynamic changes in the air pressure field above the soil. However, the amplitudes and frequencies of the air pressure fluctuations responsible for pressure pumping are still uncertain. Moreover, an in situ observation of the pressure pumping effect is still missing. To investigate the pressure pumping effect, airflow measurements above and below the canopy of a Scots pine forest and high-precision relative air pressure measurements were conducted in the below-canopy space and in the soil over a measurement period of 16 weeks. To monitor the soil gas transport, a newly developed gas measurement system was used. The gas measurement system continuously injects helium as a tracer gas into the soil until a diffusive steady state is reached. With the steady state concentration profile of the tracer gas, it is possible to inversely model the gas diffusion coefficient profile of the soil. If the gas diffusion coefficient profile differed from steady state, we deduced that the soil gas transport is not only diffusive, but also influenced by non-diffusive processes. Results show that the occurrence of small air pressure fluctuations is strongly dependent on the mean above-canopy wind speed. The wind-induced air pressure fluctuations have mean amplitudes up to 10 Pa and lie in the frequency range 0.01-0.1 Hz. To describe the pumping motion of the air pressure field, the pressure pumping coefficient (PPC) was defined as the mean change in pressure per second. The PPC shows a clear quadratic dependence on mean above-canopy wind speed. Empirical modelling of the measured topsoil helium concentration demonstrated that the PPC is the most important predictor for changes in the topsoil helium concentration. Comparison of time periods with high PPC and periods of low PPC showed that the soil gas diffusion coefficient in depths between 5-10 cm increased up to 30% during periods of high PPC compared to steady state. Thus, the air pressure fluctuations observed in the atmosphere and described by the PPC penetrate into the soil and influence the topsoil gas transport.

Coarse-grained model of nanoscale segregation, water diffusion, and proton transport in Nafion membranes

NASA Astrophysics Data System (ADS)

Vishnyakov, Aleksey; Mao, Runfang; Lee, Ming-Tsung; Neimark, Alexander V.

2018-01-01

We present a coarse-grained model of the acid form of Nafion membrane that explicitly includes proton transport. This model is based on a soft-core bead representation of the polymer implemented into the dissipative particle dynamics (DPD) simulation framework. The proton is introduced as a separate charged bead that forms dissociable Morse bonds with water beads. Morse bond formation and breakup artificially mimics the Grotthuss hopping mechanism of proton transport. The proposed DPD model is parameterized to account for the specifics of the conformations and flexibility of the Nafion backbone and sidechains; it treats electrostatic interactions in the smeared charge approximation. The simulation results qualitatively, and in many respects quantitatively, predict the specifics of nanoscale segregation in the hydrated Nafion membrane into hydrophobic and hydrophilic subphases, water diffusion, and proton mobility. As the hydration level increases, the hydrophilic subphase exhibits a percolation transition from a collection of isolated water clusters to a 3D network of pores filled with water embedded in the hydrophobic matrix. The segregated morphology is characterized in terms of the pore size distribution with the average size growing with hydration from ˜1 to ˜4 nm. Comparison of the predicted water diffusivity with the experimental data taken from different sources shows good agreement at high and moderate hydration and substantial deviation at low hydration, around and below the percolation threshold. This discrepancy is attributed to the dynamic percolation effects of formation and rupture of merging bridges between the water clusters, which become progressively important at low hydration, when the coarse-grained model is unable to mimic the fine structure of water network that includes singe molecule bridges. Selected simulations of water diffusion are performed for the alkali metal substituted membrane which demonstrate the effects of the counter-ions on membrane self-assembly and transport. The hydration dependence of the proton diffusivity reproduces semi-qualitatively the trend of the diverse experimental data, showing a sharp decrease around the percolation threshold. Overall, the proposed model opens up an opportunity to study self-assembly and water and proton transport in polyelectrolytes using computationally efficient DPD simulations, and, with further refinement, it may become a practical tool for theory informed design and optimization of perm-selective and ion-conducting membranes with improved properties.

Comparisons of anomalous and collisional radial transport with a continuum kinetic edge code

NASA Astrophysics Data System (ADS)

Bodi, K.; Krasheninnikov, S.; Cohen, R.; Rognlien, T.

2009-05-01

Modeling of anomalous (turbulence-driven) radial transport in controlled-fusion plasmas is necessary for long-time transport simulations. Here the focus is 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, but the model also has wider application. Our previously developed anomalous diagonal transport matrix model with velocity-dependent convection and diffusion coefficients allows contact with typical fluid transport models (e.g., UEDGE). Results are presented that combine the anomalous transport model and collisional transport owing to ion drift orbits utilizing a Krook collision operator that conserves density and energy. Comparison is made of the relative magnitudes and possible synergistic effects of the two processes for typical tokamak device parameters.

Modeling of FMISO [F18] nanoparticle PET tracer in normal-cancerous tissue based on real clinical image.

PubMed

Asgari, Hanie; Soltani, M; Sefidgar, Mostafa

2018-07-01

Hypoxia as one of the principal properties of tumor cells is a reaction to the deprivation of oxygen. The location of tumor cells could be identified by assessment of oxygen and nutrient level in human body. Positron emission tomography (PET) is a well-known non-invasive method that is able to measure hypoxia based on the FMISO (Fluoromisonidazole) tracer dynamic. This paper aims to study the PET tracer concentration through convection-diffusion-reaction equations in a real human capillary-like network. A non-uniform oxygen pressure along the capillary path and convection mechanism for FMISO transport are taken into account to accurately model the characteristics of the tracer. To this end, a multi-scale model consists of laminar blood flow through the capillary network, interstitial pressure, oxygen pressure, FMISO diffusion and FMISO convection transport in the extravascular region is developed. The present model considers both normal and tumor tissue regions in computational domain. The accuracy of numerical model is verified with the experimental results available in the literature. The convection and diffusion types of transport mechanism are employed in order to calculate the concentration of FMISO in the normal and tumor sub-domain. The influences of intravascular oxygen pressure, FMISO transport mechanisms, capillary density and different types of tissue on the FMISO concentration have been investigated. According to result (Table 4) the convection mechanism of FMISO molecules transportation is negligible, but it causes more accuracy of the proposed model. The approach of present study can be employed in order to investigate the effects of various parameters, such as tumor shape, on the dynamic behavior of different PET tracers, such as FDG, can be extended to different case study problems, such as drug delivery. Copyright © 2018 Elsevier Inc. All rights reserved.

Comparison of transport properties models for numerical simulations of Mars entry vehicles

NASA Astrophysics Data System (ADS)

Hao, Jiaao; Wang, Jingying; Gao, Zhenxun; Jiang, Chongwen; Lee, Chunhian

2017-01-01

Effects of two different models for transport properties, including the approximate model and the collision integral model, on hypersonic flow simulations of Mars entry vehicles are numerically investigated. A least square fitting is firstly performed using the best-available data of collision integrals for Martian atmosphere species within the temperature range of 300-20,000 K. Then, the performance of these two transport properties models are compared for an equilibrium Martian atmosphere gas mixture at 10 kPa and temperatures ranging from 1000 to 10,000 K. Finally, four flight conditions chosen from the trajectory of the Mars Pathfinder entry vehicle are numerically simulated. It is indicated that the approximate model is capable of accurately providing the distributions of species mass fractions and temperatures in the flowfield. Both models give similar translational-rotational and vibrational heat fluxes. However, the chemical diffusion heat fluxes predicted by the approximate model are significantly larger than the results computed by the collision integral model, particularly in the vicinity of the forebody stagnation point, whose maximum relative error of 15% for the super-catalytic case. The diffusion model employed in the approximate model is responsible to the discrepancy. In addition, the wake structure is largely unaffected by the transport properties models.

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 chloroplasts and lateral heterogeneity of lamellar system of thylakoids. The lateral profiles of pH in the thylakoid lumen and in the narrow gap between grana thylakoids have been calculated under different metabolic conditions. Analyzing topological aspects of diffusion-controlled stages of electron and proton transport in chloroplasts, we conclude that along with the NPQ mechanism of attenuation of PSII activity and deceleration of PQH2 oxidation by the cytochrome b6f complex caused by the lumen acidification, the intersystem electron transport may be down-regulated due to the light-induced alkalization of the narrow partition between adjacent thylakoids of grana. The computer models of electron and proton transport described in this article may be integrated as appropriate modules into a comprehensive model of oxygenic photosynthesis. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

High-energy phosphate transfer in human muscle: diffusion of phosphocreatine.

PubMed

Gabr, Refaat E; El-Sharkawy, Abdel-Monem M; Schär, Michael; Weiss, Robert G; Bottomley, Paul A

2011-07-01

The creatine kinase (CK) reaction is central to muscle energetics, buffering ATP levels during periods of intense activity via consumption of phosphocreatine (PCr). PCr is believed to serve as a spatial shuttle of high-energy phosphate between sites of energy production in the mitochondria and sites of energy utilization in the myofibrils via diffusion. Knowledge of the diffusion coefficient of PCr (D(PCr)) is thus critical for modeling and understanding energy transport in the myocyte, but D(PCr) has not been measured in humans. Using localized phosphorus magnetic resonance spectroscopy, we measured D(PCr) in the calf muscle of 11 adults as a function of direction and diffusion time. The results show that the diffusion of PCr is anisotropic, with significantly higher diffusion along the muscle fibers, and that the diffusion of PCr is restricted to a ∼28-μm pathlength assuming a cylindrical model, with an unbounded diffusion coefficient of ∼0.69 × 10(-3) mm(2)/s. This distance is comparable in size to the myofiber radius. On the basis of prior measures of CK reaction kinetics in human muscle, the expected diffusion distance of PCr during its half-life in the CK reaction is ∼66 μm. This distance is much greater than the average distances between mitochondria and myofibrils. Thus these first measurements of PCr diffusion in human muscle in vivo support the view that PCr diffusion is not a factor limiting high-energy phosphate transport between the mitochondria and the myofibrils in healthy resting myocytes.

High-energy phosphate transfer in human muscle: diffusion of phosphocreatine

PubMed Central

Gabr, Refaat E.; El-Sharkawy, AbdEl-Monem M.; Schär, Michael; Weiss, Robert G.

2011-01-01

The creatine kinase (CK) reaction is central to muscle energetics, buffering ATP levels during periods of intense activity via consumption of phosphocreatine (PCr). PCr is believed to serve as a spatial shuttle of high-energy phosphate between sites of energy production in the mitochondria and sites of energy utilization in the myofibrils via diffusion. Knowledge of the diffusion coefficient of PCr (DPCr) is thus critical for modeling and understanding energy transport in the myocyte, but DPCr has not been measured in humans. Using localized phosphorus magnetic resonance spectroscopy, we measured DPCr in the calf muscle of 11 adults as a function of direction and diffusion time. The results show that the diffusion of PCr is anisotropic, with significantly higher diffusion along the muscle fibers, and that the diffusion of PCr is restricted to a ∼28-μm pathlength assuming a cylindrical model, with an unbounded diffusion coefficient of ∼0.69 × 10−3 mm2/s. This distance is comparable in size to the myofiber radius. On the basis of prior measures of CK reaction kinetics in human muscle, the expected diffusion distance of PCr during its half-life in the CK reaction is ∼66 μm. This distance is much greater than the average distances between mitochondria and myofibrils. Thus these first measurements of PCr diffusion in human muscle in vivo support the view that PCr diffusion is not a factor limiting high-energy phosphate transport between the mitochondria and the myofibrils in healthy resting myocytes. PMID:21368292

Strain-based diffusion solver for realistic representation of diffusion front in physical reactions

PubMed Central

2017-01-01

When simulating fluids, such as water or fire, interacting with solids, it is a challenging problem to represent details of diffusion front in physical reaction. Previous approaches commonly use isotropic or anisotropic diffusion to model the transport of a quantity through a medium or long interface. We have identified unrealistic monotonous patterns with previous approaches and therefore, propose to extend these approaches by integrating the deformation of the material with the diffusion process. Specifically, stretching deformation represented by strain is incorporated in a divergence-constrained diffusion model. A novel diffusion model is introduced to increase the global rate at which the solid acquires relevant quantities, such as heat or saturation. This ensures that the equations describing fluid flow are linked to the change of solid geometry, and also satisfy the divergence-free condition. Experiments show that our method produces convincing results. PMID:28448591

Hopping Conduction and Bacteria: Transport Properties of Disordered Reaction-Diffusion Systems

NASA Astrophysics Data System (ADS)

Missel, Andrew; Dahmen, Karin

2008-03-01

Reaction-diffusion (RD) systems are used to model everything from the formation of animal coat patterns to the spread of genes in a population to the seasonal variation of plankton density in the ocean. In all of these problems, disorder plays a large role, but determining its effects on transport properties in RD systems has been a challenge. We present here both analytical and numerical studies of a particular disordered RD system consisting of particles which are allowed to diffuse and compete for resources (2A->A) with spatially homogeneous rates, reproduce (A->2A) in certain areas (``oases''), and die (A->0) everywhere else (the ``desert''). In the low oasis density regime, transport is mediated through rare ``hopping events'' in which a small number of particles diffuse through the desert from one oasis to another; the situation is mathematically analogous to hopping conduction in doped semiconductors, and this analogy, along with some ideas from first passage percolation theory, allows us to make some quantitative predictions about the transport properties of the system on a large scale.

Decay of the zincate concentration gradient at an alkaline zinc cathode after charging

NASA Technical Reports Server (NTRS)

Kautz, H. E.; May, C. E.

1979-01-01

The study was carried out by observing the decay of the zincate concentration gradient at a horizontal zinc cathode after charging. This decay was found to approximate first order kinetics as expected from a proposed boundary layer model. The decay half life was shown to be a linear function of the thickness of porous zinc deposit on the cathode indicating a very rapid transport of zincate through porous zinc metal. The rapid transport is attributed to an electrochemical mechanism. The data also indicated a relatively sharp transition between the diffusion and convection transport regions. The diffusion of zincate ion through asbestos submerged in alkaline electrolyte was shown to be comparable with that predicted from the bulk diffusion coefficient of the zincate ion in alkali.

Numerical analysis of the diffusive mass transport in brain tissues with applications to optical sensors

NASA Astrophysics Data System (ADS)

Neculae, Adrian P.; Otte, Andreas; Curticapean, Dan

2013-03-01

In the brain-cell microenvironment, diffusion plays an important role: apart from delivering glucose and oxygen from the vascular system to brain cells, it also moves informational substances between cells. The brain is an extremely complex structure of interwoven, intercommunicating cells, but recent theoretical and experimental works showed that the classical laws of diffusion, cast in the framework of porous media theory, can deliver an accurate quantitative description of the way molecules are transported through this tissue. The mathematical modeling and the numerical simulations are successfully applied in the investigation of diffusion processes in tissues, replacing the costly laboratory investigations. Nevertheless, modeling must rely on highly accurate information regarding the main parameters (tortuosity, volume fraction) which characterize the tissue, obtained by structural and functional imaging. The usual techniques to measure the diffusion mechanism in brain tissue are the radiotracer method, the real time iontophoretic method and integrative optical imaging using fluorescence microscopy. A promising technique for obtaining the values for characteristic parameters of the transport equation is the direct optical investigation using optical fibers. The analysis of these parameters also reveals how the local geometry of the brain changes with time or under pathological conditions. This paper presents a set of computations concerning the mass transport inside the brain tissue, for different types of cells. By measuring the time evolution of the concentration profile of an injected substance and using suitable fitting procedures, the main parameters characterizing the tissue can be determined. This type of analysis could be an important tool in understanding the functional mechanisms of effective drug delivery in complex structures such as the brain tissue. It also offers possibilities to realize optical imaging methods for in vitro and in vivo measurements using optical fibers. The model also may help in radiotracer biomarker models for the understanding of the mechanism of action of new chemical entities.

Modeling the Impact of Cracking in Low Permeability Layers in a Groundwater Contamination Source Zone on Dissolved Contaminant Fate and Transport

NASA Astrophysics Data System (ADS)

Sievers, K. W.; Goltz, M. N.; Huang, J.; Demond, A. H.

2011-12-01

Dense Non-Aqueous Phase Liquids (DNAPLs), which are chemicals and chemical mixtures that are heavier than and only slightly soluble in water, are a significant source of groundwater contamination. Even with the removal or destruction of most DNAPL mass, small amounts of remaining DNAPL can dissolve into flowing groundwater and continue as a contamination source for decades. One category of DNAPLs is the chlorinated aliphatic hydrocarbons (CAHs). CAHs, such as trichloroethylene and carbon tetrachloride, are found to contaminate groundwater at numerous DoD and industrial sites. DNAPLs move through soils and groundwater leaving behind residual separate phase contamination as well as pools sitting atop low permeability layers. Recently developed models are based on the assumption that dissolved CAHs diffuse slowly from pooled DNAPL into the low permeability layers. Subsequently, when the DNAPL pools and residual DNAPL are depleted, perhaps as a result of a remediation effort, the dissolved CAHs in these low permeability layers still remain to serve as long-term sources of contamination, due to so-called "back diffusion." These recently developed models assume that transport in the low permeability zones is strictly diffusive; however field observations suggest that more DNAPL and/or dissolved CAH is stored in the low permeability zones than can be explained on the basis of diffusion alone. One explanation for these field observations is that there is enhanced transport of dissolved CAHs and/or DNAPL into the low permeability layers due to cracking. Cracks may allow for advective flow of water contaminated with dissolved CAHs into the layer as well as possible movement of pure phase DNAPL into the layer. In this study, a multiphase numerical flow and transport model is employed in a dual domain (high and low permeability layers) to investigate the impact of cracking on DNAPL and CAH movement. Using literature values, the crack geometry and spacing was varied to model and compare four scenarios: (1) CAH diffusion only into cracks, (2) CAH advection-dispersion into cracks, (3) separate phase DNAPL movement into the cracks, and (4) CAH diffusion into an uncracked low permeability clay layer. For each scenario, model simulations are used to show the evolution and persistence of groundwater contamination downgradient of the DNAPL source.

A multi-scale Lattice Boltzmann model for simulating solute transport in 3D X-ray micro-tomography images of aggregated porous materials

NASA Astrophysics Data System (ADS)

Zhang, Xiaoxian; Crawford, John W.; Flavel, Richard J.; Young, Iain M.

2016-10-01

The Lattice Boltzmann (LB) model and X-ray computed tomography (CT) have been increasingly used in combination over the past decade to simulate water flow and chemical transport at pore scale in porous materials. Because of its limitation in resolution and the hierarchical structure of most natural soils, the X-ray CT tomography can only identify pores that are greater than its resolution and treats other pores as solid. As a result, the so-called solid phase in X-ray images may in reality be a grey phase, containing substantial connected pores capable of conducing fluids and solute. Although modified LB models have been developed to simulate fluid flow in such media, models for solute transport are relatively limited. In this paper, we propose a LB model for simulating solute transport in binary soil images containing permeable solid phase. The model is based on the single-relaxation time approach and uses a modified partial bounce-back method to describe the resistance caused by the permeable solid phase to chemical transport. We derive the relationship between the diffusion coefficient and the parameter introduced in the partial bounce-back method, and test the model against analytical solution for movement of a pulse of tracer. We also validate it against classical finite volume method for solute diffusion in a simple 2D image, and then apply the model to a soil image acquired using X-ray tomography at resolution of 30 μm in attempts to analyse how the ability of the solid phase to diffuse solute at micron-scale affects the behaviour of the solute at macro-scale after a volumetric average. Based on the simulated results, we discuss briefly the danger in interpreting experimental results using the continuum model without fully understanding the pore-scale processes, as well as the potential of using pore-scale modelling and tomography to help improve the continuum models.

Mathematical modeling of synthesis gas fueled electrochemistry and transport including H2/CO co-oxidation and surface diffusion in solid oxide fuel cell

NASA Astrophysics Data System (ADS)

Bao, Cheng; Jiang, Zeyi; Zhang, Xinxin

2015-10-01

Fuel flexibility is a significant advantage of solid oxide fuel cell (SOFC). A comprehensive macroscopic framework is proposed for synthesis gas (syngas) fueled electrochemistry and transport in SOFC anode with two main novelties, i.e. analytical H2/CO electrochemical co-oxidation, and correction of gas species concentration at triple phase boundary considering competitive absorption and surface diffusion. Staring from analytical approximation of the decoupled charge and mass transfer, we present analytical solutions of two defined variables, i.e. hydrogen current fraction and enhancement factor. Giving explicit answer (rather than case-by-case numerical calculation) on how many percent of the current output contributed by H2 or CO and on how great the water gas shift reaction plays role on, this approach establishes at the first time an adaptive superposition mechanism of H2-fuel and CO-fuel electrochemistry for syngas fuel. Based on the diffusion equivalent circuit model, assuming series-connected resistances of surface diffusion and bulk diffusion, the model predicts well at high fuel utilization by keeping fixed porosity/tortuosity ratio. The model has been validated by experimental polarization behaviors in a wide range of operation on a button cell for H2-H2O-CO-CO2-N2 fuel systems. The framework could be helpful to narrow the gap between macro-scale and meso-scale SOFC modeling.

Experimental determination of barium isotope fractionation during diffusion and adsorption processes at low temperatures

NASA Astrophysics Data System (ADS)

van Zuilen, Kirsten; Müller, Thomas; Nägler, Thomas F.; Dietzel, Martin; Küsters, Tim

2016-08-01

Variations in barium (Ba) stable isotope abundances measured in low and high temperature environments have recently received increasing attention. The actual processes controlling Ba isotope fractionation, however, remain mostly elusive. In this study, we present the first experimental approach to quantify the contribution of diffusion and adsorption on mass-dependent Ba isotope fractionation during transport of aqueous Ba2+ ions through a porous medium. Experiments have been carried out in which a BaCl2 solution of known isotopic composition diffused through u-shaped glass tubes filled with silica hydrogel at 10 °C and 25 °C for up to 201 days. The diffused Ba was highly fractionated by up to -2.15‰ in δ137/134Ba, despite the low relative difference in atomic mass. The time-dependent isotope fractionation can be successfully reproduced by a diffusive transport model accounting for mass-dependent differences in the effective diffusivities of the Ba isotope species (D137Ba /D134Ba =(m134 /m137) β). Values of β extracted from the transport model were in the range of 0.010-0.011. Independently conducted batch experiments revealed that adsorption of Ba onto the surface of silica hydrogel favoured the heavier Ba isotopes (α = 1.00015 ± 0.00008). The contribution of adsorption on the overall isotope fractionation in the diffusion experiments, however, was found to be small. Our results contribute to the understanding of Ba isotope fractionation processes, which is crucial for interpreting natural isotope variations and the assessment of Ba isotope ratios as geochemical proxies.

Measurements of True Leak Rates of MEMS Packages

PubMed Central

Han, Bongtae

2012-01-01

Gas transport mechanisms that characterize the hermetic behavior of MEMS packages are fundamentally different depending upon which sealing materials are used in the packages. In metallic seals, gas transport occurs through a few nanoscale leak channels (gas conduction) that are produced randomly during the solder reflow process, while gas transport in polymeric seals occurs through the bulk material (gas diffusion). In this review article, the techniques to measure true leak rates of MEMS packages with the two sealing materials are described and discussed: a Helium mass spectrometer based technique for metallic sealing and a gas diffusion based model for polymeric sealing. PMID:22736994

Impact of multi-component diffusion in turbulent combustion using direct numerical simulations

DOE PAGES

Bruno, Claudio; Sankaran, Vaidyanathan; Kolla, Hemanth; ...

2015-08-28

This study presents the results of DNS of a partially premixed turbulent syngas/air flame at atmospheric pressure. The objective was to assess the importance and possible effects of molecular transport on flame behavior and structure. To this purpose DNS were performed at with two proprietary DNS codes and with three different molecular diffusion transport models: fully multi-component, mixture averaged, and imposing the Lewis number of all species to be unity.

Aquaporins and membrane diffusion of CO2 in living organisms.

PubMed

Kaldenhoff, Ralf; Kai, Lei; Uehlein, Norbert

2014-05-01

Determination of CO2 diffusion rates in living cells revealed inconsistencies with existing models about the mechanisms of membrane gas transport. Mainly, these discrepancies exist in the determined CO2 diffusion rates of bio-membranes, which were orders of magnitudes below those for pure lipid bilayers or theoretical considerations as well as in the observation that membrane insertion of specific aquaporins was rescuing high CO2 transport rates. This effect was confirmed by functional aquaporin protein analysis in heterologous expression systems as well as in bacteria, plants and partly in mammals. This review summarizes the arguments in favor of and against aquaporin facilitated membrane diffusion of CO2 and reports about its importance for the physiology of living organisms. Most likely, the aquaporin tetramer forming an additional fifth pore is required for CO2 diffusion facilitation. Aquaporin tetramer formation, membrane integration and disintegration could provide a mechanism for regulation of cellular CO2 exchange. The physiological importance of aquaporin mediated CO2 membrane diffusion could be shown for plants and cyanobacteria and partly for mammals. Taking the mentioned results into account, consequences for our current picture of cell membrane transport emerge. It appears that in some or many instances, membranes might not be as permeable as it was suggested by current bio-membrane models, opening an additional way of controlling the cellular influx or efflux of volatile substances like CO2. This article is part of a Special Issue entitled Aquaporins. © 2013.

Efficient micromagnetic modelling of spin-transfer torque and spin-orbit torque

NASA Astrophysics Data System (ADS)

Abert, Claas; Bruckner, Florian; Vogler, Christoph; Suess, Dieter

2018-05-01

While the spin-diffusion model is considered one of the most complete and accurate tools for the description of spin transport and spin torque, its solution in the context of dynamical micromagnetic simulations is numerically expensive. We propose a procedure to retrieve the free parameters of a simple macro-spin like spin-torque model through the spin-diffusion model. In case of spin-transfer torque the simplified model complies with the model of Slonczewski. A similar model can be established for the description of spin-orbit torque. In both cases the spin-diffusion model enables the retrieval of free model parameters from the geometry and the material parameters of the system. Since these parameters usually have to be determined phenomenologically through experiments, the proposed method combines the strength of the diffusion model to resolve material parameters and geometry with the high performance of simple torque models.

Energy Models for One-Carrier Transport in Semiconductor Devices

NASA Technical Reports Server (NTRS)

Jerome, Joseph W.; Shu, Chi-Wang

1991-01-01

Moment models of carrier transport, derived from the Boltzmann equation, made possible the simulation of certain key effects through such realistic assumptions as energy dependent mobility functions. This type of global dependence permits the observation of velocity overshoot in the vicinity of device junctions, not discerned via classical drift-diffusion models, which are primarily local in nature. It was found that a critical role is played in the hydrodynamic model by the heat conduction term. When ignored, the overshoot is inappropriately damped. When the standard choice of the Wiedemann-Franz law is made for the conductivity, spurious overshoot is observed. Agreement with Monte-Carlo simulation in this regime required empirical modification of this law, or nonstandard choices. Simulations of the hydrodynamic model in one and two dimensions, as well as simulations of a newly developed energy model, the RT model, are presented. The RT model, intermediate between the hydrodynamic and drift-diffusion model, was developed to eliminate the parabolic energy band and Maxwellian distribution assumptions, and to reduce the spurious overshoot with physically consistent assumptions. The algorithms employed for both models are the essentially non-oscillatory shock capturing algorithms. Some mathematical results are presented and contrasted with the highly developed state of the drift-diffusion model.

Penetration of Cosmic Rays into Dense Molecular Clouds: Role of Diffuse Envelopes

NASA Astrophysics Data System (ADS)

Ivlev, A. V.; Dogiel, V. A.; Chernyshov, D. O.; Caselli, P.; Ko, C.-M.; Cheng, K. S.

2018-03-01

A flux of cosmic rays (CRs) propagating through a diffuse ionized gas can excite MHD waves, thus generating magnetic disturbances. We propose a generic model of CR penetration into molecular clouds through their diffuse envelopes, and identify the leading physical processes controlling their transport on the way from a highly ionized interstellar medium to the dense interior of the cloud. The model allows us to describe a transition between a free streaming of CRs and their diffusive propagation, determined by the scattering on the self-generated disturbances. A self-consistent set of equations, governing the diffusive transport regime in an envelope and the MHD turbulence generated by the modulated CR flux, is characterized by two dimensionless numbers. We demonstrate a remarkable mutual complementarity of different mechanisms leading to the onset of the diffusive regime, which results in a universal energy spectrum of the modulated CRs. In conclusion, we briefly discuss implications of our results for several fundamental astrophysical problems, such as the spatial distribution of CRs in the Galaxy as well as the ionization, heating, and chemistry in dense molecular clouds. This paper is dedicated to the memory of Prof. Vadim Tsytovich.

Computational Study of Poloidal Angular Momentum Transport in DIII-D

NASA Astrophysics Data System (ADS)

Pankin, Alexei; Kruger, Scott; Kritz, Arnold; Rafiq, Tariq; Weiland, Jan

2013-10-01

The new Multi-Mode Model, MMM8.1, includes the capability to predict the anomalous poloidal momentum diffusivity [T. Rafiq et al., Phys. Plasmas 20, 032506 (2013)]. It is important to consider the effect of this diffusivity on the poloidal rotation of tokamak plasmas since some experimental observations suggest that neoclassical effects are not always sufficient to explain the observed poloidal rotation [B.A. Grierson et al., Phys. Plasmas 19, 056107 (2012)]. One of the objectives of this research is to determine if the anomalous contribution to the poloidal rotation can be significant in the regions of internal transport barriers (ITBs). In this study, the MMM8.1 model is used to compute the poloidal momentum diffusivity for a range of plasma parameters that correspond to the parameters that occur in DIII-D discharges. The parameters that are considered include the temperature and density gradients, and magnetic shear. The role of anomalous poloidal transport in the possible poloidal spin up in the ITB regions is discussed. Progress in the implementation of poloidal transport equations in the ASTRA transport code is reported and initial predictive simulation results for the poloidal rotation profiles are presented. This research is partially support by the DOE Grants DE-SC0006629 and DE-FG02-92ER54141.

Influence of Structural Heterogeneity on Diffusion of CH4 and CO2 in Silicon Carbide-Derived Nanoporous Carbon

PubMed Central

2015-01-01

We investigate the influence of structural heterogeneity on the transport properties of simple gases in a Hybrid Reverse Monte Carlo (HRMC) constructed model of silicon carbide-derived carbon (SiC-DC). The energy landscape of the system is determined based on free energy analysis of the atomistic model. The overall energy barriers of the system for different gases are computed along with important properties, such as Henry constant and differential enthalpy of adsorption at infinite dilution, and indicate hydrophobicity of the SiC-DC structure and its affinity for CO2 and CH4 adsorption. We also study the effect of molecular geometry, pore structure and energy heterogeneity considering different hopping scenarios for diffusion of CO2 and CH4 through ultramicropores using the Nudged Elastic Band (NEB) method. It is shown that the energy barrier of a hopping molecule is very sensitive to the shape of the pore entry. We provide evidence for the influence of structural heterogeneity on self-diffusivity of methane and carbon dioxide using molecular dynamics simulation, based on a maximum in the variation of self-diffusivity with loading. A comparison of the MD simulation results with self-diffusivities from quasi-elastic neutron scattering (QENS) measurements and, with macroscopic uptake-based low-density transport coefficients, reveals the existence of internal barriers not captured in MD simulation and QENS experiments. Nevertheless, the simulation and macroscopic uptake-based diffusion coefficients agree within a factor of 2–3, indicating that our HRMC model structure captures most of the important energy barriers affecting the transport of CH4 in the nanostructure of SiC-DC. PMID:24932319

Influence of Structural Heterogeneity on Diffusion of CH4 and CO2 in Silicon Carbide-Derived Nanoporous Carbon.

PubMed

Farmahini, Amir H; Shahtalebi, Ali; Jobic, Hervé; Bhatia, Suresh K

2014-06-05

We investigate the influence of structural heterogeneity on the transport properties of simple gases in a Hybrid Reverse Monte Carlo (HRMC) constructed model of silicon carbide-derived carbon (SiC-DC). The energy landscape of the system is determined based on free energy analysis of the atomistic model. The overall energy barriers of the system for different gases are computed along with important properties, such as Henry constant and differential enthalpy of adsorption at infinite dilution, and indicate hydrophobicity of the SiC-DC structure and its affinity for CO 2 and CH 4 adsorption. We also study the effect of molecular geometry, pore structure and energy heterogeneity considering different hopping scenarios for diffusion of CO 2 and CH 4 through ultramicropores using the Nudged Elastic Band (NEB) method. It is shown that the energy barrier of a hopping molecule is very sensitive to the shape of the pore entry. We provide evidence for the influence of structural heterogeneity on self-diffusivity of methane and carbon dioxide using molecular dynamics simulation, based on a maximum in the variation of self-diffusivity with loading. A comparison of the MD simulation results with self-diffusivities from quasi-elastic neutron scattering (QENS) measurements and, with macroscopic uptake-based low-density transport coefficients, reveals the existence of internal barriers not captured in MD simulation and QENS experiments. Nevertheless, the simulation and macroscopic uptake-based diffusion coefficients agree within a factor of 2-3, indicating that our HRMC model structure captures most of the important energy barriers affecting the transport of CH 4 in the nanostructure of SiC-DC.

Predicting the influence of long-range molecular interactions on macroscopic-scale diffusion by homogenization of the Smoluchowski equation

NASA Astrophysics Data System (ADS)

Kekenes-Huskey, P. M.; Gillette, A. K.; McCammon, J. A.

2014-05-01

The macroscopic diffusion constant for a charged diffuser is in part dependent on (1) the volume excluded by solute "obstacles" and (2) long-range interactions between those obstacles and the diffuser. Increasing excluded volume reduces transport of the diffuser, while long-range interactions can either increase or decrease diffusivity, depending on the nature of the potential. We previously demonstrated [P. M. Kekenes-Huskey et al., Biophys. J. 105, 2130 (2013)] using homogenization theory that the configuration of molecular-scale obstacles can both hinder diffusion and induce diffusional anisotropy for small ions. As the density of molecular obstacles increases, van der Waals (vdW) and electrostatic interactions between obstacle and a diffuser become significant and can strongly influence the latter's diffusivity, which was neglected in our original model. Here, we extend this methodology to include a fixed (time-independent) potential of mean force, through homogenization of the Smoluchowski equation. We consider the diffusion of ions in crowded, hydrophilic environments at physiological ionic strengths and find that electrostatic and vdW interactions can enhance or depress effective diffusion rates for attractive or repulsive forces, respectively. Additionally, we show that the observed diffusion rate may be reduced independent of non-specific electrostatic and vdW interactions by treating obstacles that exhibit specific binding interactions as "buffers" that absorb free diffusers. Finally, we demonstrate that effective diffusion rates are sensitive to distribution of surface charge on a globular protein, Troponin C, suggesting that the use of molecular structures with atomistic-scale resolution can account for electrostatic influences on substrate transport. This approach offers new insight into the influence of molecular-scale, long-range interactions on transport of charged species, particularly for diffusion-influenced signaling events occurring in crowded cellular environments.

Impact of charge transport on current–voltage characteristics and power-conversion efficiency of organic solar cells

PubMed Central

Würfel, Uli; Neher, Dieter; Spies, Annika; Albrecht, Steve

2015-01-01

This work elucidates the impact of charge transport on the photovoltaic properties of organic solar cells. Here we show that the analysis of current–voltage curves of organic solar cells under illumination with the Shockley equation results in values for ideality factor, photocurrent and parallel resistance, which lack physical meaning. Drift-diffusion simulations for a wide range of charge-carrier mobilities and illumination intensities reveal significant carrier accumulation caused by poor transport properties, which is not included in the Shockley equation. As a consequence, the separation of the quasi Fermi levels in the organic photoactive layer (internal voltage) differs substantially from the external voltage for almost all conditions. We present a new analytical model, which considers carrier transport explicitly. The model shows excellent agreement with full drift-diffusion simulations over a wide range of mobilities and illumination intensities, making it suitable for realistic efficiency predictions for organic solar cells. PMID:25907581

Pore-scale lattice Boltzmann simulation of micro-gaseous flow considering surface diffusion effect

DOE PAGES

Wang, Junjian; Kang, Qinjun; Chen, Li; ...

2016-11-21

Some recent studies have shown that adsorbed gas and its surface diffusion have profound influence on micro-gaseous flow through organic pores in shale gas reservoirs. Here, a multiple-relaxation-time (MRT) LB model is adopted to estimate the apparent permeability of organic shale and a new boundary condition, which combines Langmuir adsorption theory with Maxwellian diffusive reflection boundary condition, is proposed to capture gas slip and surface diffusion of adsorbed gas. The simulation results match well with previous studies carried out using Molecular Dynamics (MD) and show that Maxwell slip boundary condition fails to characterize gas transport in the near wall regionmore » under the influence of the adsorbed gas. The total molar flux can be either enhanced or reduced depending on variations in adsorbed gas coverage and surface diffusion velocity. The effects of pore width, pressure as well as Langmuir properties on apparent permeability of methane transport in organic pores are further studied. It is found that the surface transport plays a significant role in determining the apparent permeability, and the variation of apparent permeability with pore size and pressure is affected by the adsorption and surface diffusion.« less

Spatio-temporal Model of Xenobiotic Distribution and Metabolism in an in Silico Mouse Liver Lobule

NASA Astrophysics Data System (ADS)

Fu, Xiao; Sluka, James; Clendenon, Sherry; Glazier, James; Ryan, Jennifer; Dunn, Kenneth; Wang, Zemin; Klaunig, James

Our study aims to construct a structurally plausible in silico model of a mouse liver lobule to simulate the transport of xenobiotics and the production of their metabolites. We use a physiologically-based model to calculate blood-flow rates in a network of mouse liver sinusoids and simulate transport, uptake and biotransformation of xenobiotics within the in silico lobule. Using our base model, we then explore the effects of variations of compound-specific (diffusion, transport and metabolism) and compound-independent (temporal alteration of blood flow pattern) parameters, and examine their influence on the distribution of xenobiotics and metabolites. Our simulations show that the transport mechanism (diffusive and transporter-mediated) of xenobiotics and blood flow both impact the regional distribution of xenobiotics in a mouse hepatic lobule. Furthermore, differential expression of metabolic enzymes along each sinusoid's portal to central axis, together with differential cellular availability of xenobiotics, induce non-uniform production of metabolites. Thus, the heterogeneity of the biochemical and biophysical properties of xenobiotics, along with the complexity of blood flow, result in different exposures to xenobiotics for hepatocytes at different lobular locations. We acknowledge support from National Institute of Health GM 077138 and GM 111243.

Finite Larmor radius effects on weak turbulence transport

NASA Astrophysics Data System (ADS)

Kryukov, N.; Martinell, J. J.

2018-06-01

Transport of test particles in two-dimensional weak turbulence with waves propagating along the poloidal direction is studied using a reduced model. Finite Larmor radius (FLR) effects are included by gyroaveraging over one particle orbit. For low wave amplitudes the motion is mostly regular with particles trapped in the potential wells. As the amplitude increases the trajectories become chaotic and the Larmor radius modifies the orbits. For a thermal distribution of Finite Larmor radii the particle distribution function (PDF) is Gaussian for small th$ (thermal gyroradius) but becomes non-Gaussian for large th$ . However, the time scaling of transport is diffusive, as characterized by a linear dependence of the variance of the PDF with time. An explanation for this behaviour is presented that provides an expression for an effective diffusion coefficient and reproduces the numerical results for large wave amplitudes which implies generalized chaos. When a shear flow is added in the direction of wave propagation, a modified model is obtained that produces free-streaming particle trajectories in addition to trapped ones; these contribute to ballistic transport for low wave amplitude but produce super-ballistic transport in the chaotic regime. As in the previous case, the PDF is Gaussian for low th$ becoming non-Gaussian as it increases. The perpendicular transport presents the same behaviour as in the case with no flow but the diffusion is faster in the presence of the flow.

A Fractional PDE Approach to Turbulent Mixing; Part II: Numerical Simulation

NASA Astrophysics Data System (ADS)

Samiee, Mehdi; Zayernouri, Mohsen

2016-11-01

We propose a generalizing fractional order transport model of advection-diffusion kind with fractional time- and space-derivatives, governing the evolution of passive scalar turbulence. This approach allows one to incorporate the nonlocal and memory effects in the underlying anomalous diffusion i.e., sub-to-standard diffusion to model the trapping of particles inside the eddied, and super-diffusion associated with the sudden jumps of particles from one coherent region to another. For this nonlocal model, we develop a high order numerical (spectral) method in addition to a fast solver, examined in the context of some canonical problems. PhD student, Department of Mechanical Engineering, & Department Computational Mathematics, Science, and Engineering.

Cosmic Ray Propagation through the Magnetic Fields of the Galaxy with Extended Halo

NASA Technical Reports Server (NTRS)

Zhang, Ming

2005-01-01

In this project we perform theoretical studies of 3-dimensional cosmic ray propagation in magnetic field configurations of the Galaxy with an extended halo. We employ our newly developed Markov stochastic process methods to solve the diffusive cosmic ray transport equation. We seek to understand observations of cosmic ray spectra, composition under the constraints of the observations of diffuse gamma ray and radio emission from the Galaxy. The model parameters are directly are related to properties of our Galaxy, such as the size of the Galactic halo, particle transport in Galactic magnetic fields, distribution of interstellar gas, primary cosmic ray source distribution and their confinement in the Galaxy. The core of this investigation is the development of software for cosmic ray propagation models with the Markov stochastic process approach. Values of important model parameters for the halo diffusion model are examined in comparison with observations of cosmic ray spectra, composition and the diffuse gamma-ray background. This report summarizes our achievement in the grant period at the Florida Institute of Technology. Work at the co-investigator's institution, the University of New Hampshire, under a companion grant, will be covered in detail by a separate report.

Physics-based agent to simulant correlations for vapor phase mass transport.

PubMed

Willis, Matthew P; Varady, Mark J; Pearl, Thomas P; Fouse, Janet C; Riley, Patrick C; Mantooth, Brent A; Lalain, Teri A

2013-12-15

Chemical warfare agent simulants are often used as an agent surrogate to perform environmental testing, mitigating exposure hazards. This work specifically addresses the assessment of downwind agent vapor concentration resulting from an evaporating simulant droplet. A previously developed methodology was used to estimate the mass diffusivities of the chemical warfare agent simulants methyl salicylate, 2-chloroethyl ethyl sulfide, di-ethyl malonate, and chloroethyl phenyl sulfide. Along with the diffusivity of the chemical warfare agent bis(2-chloroethyl) sulfide, the simulant diffusivities were used in an advection-diffusion model to predict the vapor concentrations downwind from an evaporating droplet of each chemical at various wind velocities and temperatures. The results demonstrate that the simulant-to-agent concentration ratio and the corresponding vapor pressure ratio are equivalent under certain conditions. Specifically, the relationship is valid within ranges of measurement locations relative to the evaporating droplet and observation times. The valid ranges depend on the relative transport properties of the agent and simulant, and whether vapor transport is diffusion or advection dominant. Published by Elsevier B.V.

Finite Element Analysis Modeling of Chemical Vapor Deposition of Silicon Carbide

DTIC Science & Technology

2014-06-19

thesis primarily focuses on mass transport by gas -phase flow and diffusion , chemical reaction in gas phase and on solid surfaces, and thin film...chemical vapor deposition (CVD). This thesis primarily focuses on mass transport by gas -phase flow and diffusion , chemical reaction in gas phase and...9 Fluid Flow…………………………………………..…………………..…………….9 Thermodynamics………………………………………..………………….….…….11 Chemical Reaction and Diffusion

Including carrier-mediated transport in oral uptake prediction of nutrients and pharmaceuticals in humans.

PubMed

O'Connor, Isabel A; Veltman, Karin; Huijbregts, Mark A J; Ragas, Ad M J; Russel, Frans G M; Hendriks, A Jan

2014-11-01

Most toxicokinetic models consider passive diffusion as the only mechanism when modeling the oral uptake of chemicals. However, the overall uptake of nutrients and xenobiotics, such as pharmaceuticals and environmental pollutants, can be increased by influx transport proteins. We incorporated carrier-mediated transport into a one-compartment toxicokinetic model originally developed for passive diffusion only. The predictions were compared with measured oral uptake efficiencies of nutrients and pharmaceuticals, i.e. the fraction of the chemical reaching systemic circulation. Including carrier-mediated uptake improved model predictions for hydrophilic nutrients (RMSE=10% vs. 56%, Coefficient of Efficiency CoE=0.5 vs. -9.6) and for pharmaceuticals (RMSE=21% vs. 28% and CoE=-0.4 vs. -1.1). However, the negative CoE for pharmaceuticals indicates that further improvements are needed. Most important in this respect is a more accurate estimation of vMAX and KM as well as the determination of the amount of expressed and functional transport proteins both in vivo and in vitro. Copyright © 2014 Elsevier B.V. All rights reserved.

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.

Anomalous extracellular diffusion in rat cerebellum.

PubMed

Xiao, Fanrong; Hrabe, Jan; Hrabetova, Sabina

2015-05-05

Extracellular space (ECS) is a major channel transporting biologically active molecules and drugs in the brain. Diffusion-mediated transport of these substances is hindered by the ECS structure but the microscopic basis of this hindrance is not fully understood. One hypothesis proposes that the hindrance originates in large part from the presence of dead-space (DS) microdomains that can transiently retain diffusing molecules. Because previous theoretical and modeling work reported an initial period of anomalous diffusion in similar environments, we expected that brain regions densely populated by DS microdomains would exhibit anomalous extracellular diffusion. Specifically, we targeted granular layers (GL) of rat and turtle cerebella that are populated with large and geometrically complex glomeruli. The integrative optical imaging (IOI) method was employed to evaluate diffusion of fluorophore-labeled dextran (MW 3000) in GL, and the IOI data analysis was adapted to quantify the anomalous diffusion exponent dw from the IOI records. Diffusion was significantly anomalous in rat GL, where dw reached 4.8. In the geometrically simpler turtle GL, dw was elevated but not robustly anomalous (dw = 2.6). The experimental work was complemented by numerical Monte Carlo simulations of anomalous ECS diffusion in several three-dimensional tissue models containing glomeruli-like structures. It demonstrated that both the duration of transiently anomalous diffusion and the anomalous exponent depend on the size of model glomeruli and the degree of their wrapping. In conclusion, we have found anomalous extracellular diffusion in the GL of rat cerebellum. This finding lends support to the DS microdomain hypothesis. Transiently anomalous diffusion also has a profound effect on the spatiotemporal distribution of molecules released into the ECS, especially at diffusion distances on the order of a few cell diameters, speeding up short-range diffusion-mediated signals in less permeable structures. Copyright © 2015 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Comparison of experimental methods for estimating matrix diffusion coefficients for contaminant transport modeling

DOE PAGES

Telfeyan, Katherine Christina; Ware, Stuart Doug; Reimus, Paul William; ...

2018-01-31

Here, diffusion cell and diffusion wafer experiments were conducted to compare methods for estimating effective matrix diffusion coefficients in rock core samples from Pahute Mesa at the Nevada Nuclear Security Site (NNSS). A diffusion wafer method, in which a solute diffuses out of a rock matrix that is pre-saturated with water containing the solute, is presented as a simpler alternative to the traditional through-diffusion (diffusion cell) method. Both methods yielded estimates of effective matrix diffusion coefficients that were within the range of values previously reported for NNSS volcanic rocks. The difference between the estimates of the two methods ranged frommore » 14 to 30%, and there was no systematic high or low bias of one method relative to the other. From a transport modeling perspective, these differences are relatively minor when one considers that other variables (e.g., fracture apertures, fracture spacings) influence matrix diffusion to a greater degree and tend to have greater uncertainty than effective matrix diffusion coefficients. For the same relative random errors in concentration measurements, the diffusion cell method yields effective matrix diffusion coefficient estimates that have less uncertainty than the wafer method. However, the wafer method is easier and less costly to implement and yields estimates more quickly, thus allowing a greater number of samples to be analyzed for the same cost and time. Given the relatively good agreement between the methods, and the lack of any apparent bias between the methods, the diffusion wafer method appears to offer advantages over the diffusion cell method if better statistical representation of a given set of rock samples is desired.« less

Comparison of experimental methods for estimating matrix diffusion coefficients for contaminant transport modeling

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

Telfeyan, Katherine Christina; Ware, Stuart Doug; Reimus, Paul William

Here, diffusion cell and diffusion wafer experiments were conducted to compare methods for estimating effective matrix diffusion coefficients in rock core samples from Pahute Mesa at the Nevada Nuclear Security Site (NNSS). A diffusion wafer method, in which a solute diffuses out of a rock matrix that is pre-saturated with water containing the solute, is presented as a simpler alternative to the traditional through-diffusion (diffusion cell) method. Both methods yielded estimates of effective matrix diffusion coefficients that were within the range of values previously reported for NNSS volcanic rocks. The difference between the estimates of the two methods ranged frommore » 14 to 30%, and there was no systematic high or low bias of one method relative to the other. From a transport modeling perspective, these differences are relatively minor when one considers that other variables (e.g., fracture apertures, fracture spacings) influence matrix diffusion to a greater degree and tend to have greater uncertainty than effective matrix diffusion coefficients. For the same relative random errors in concentration measurements, the diffusion cell method yields effective matrix diffusion coefficient estimates that have less uncertainty than the wafer method. However, the wafer method is easier and less costly to implement and yields estimates more quickly, thus allowing a greater number of samples to be analyzed for the same cost and time. Given the relatively good agreement between the methods, and the lack of any apparent bias between the methods, the diffusion wafer method appears to offer advantages over the diffusion cell method if better statistical representation of a given set of rock samples is desired.« less

Transport equations in an enzymatic glucose fuel cell

NASA Astrophysics Data System (ADS)

Jariwala, Soham; Krishnamurthy, Balaji

2018-01-01

A mathematical model is developed to study the effects of convective flux and operating temperature on the performance of an enzymatic glucose fuel cell with a membrane. The model assumes isothermal operating conditions and constant feed rate of glucose. The glucose fuel cell domain is divided into five sections, with governing equations describing transport characteristics in each region, namely - anode diffusion layer, anode catalyst layer (enzyme layer), membrane, cathode catalyst layer and cathode diffusion layer. The mass transport is assumed to be one-dimensional and the governing equations are solved numerically. The effects flow rate of glucose feed on the performance of the fuel cell are studied as it contributes significantly to the convective flux. The effects of operating temperature on the performance of a glucose fuel cell are also modeled. The cell performances are compared using cell polarization curves, which were found compliant with experimental observations.

NOR-USA Scientific Traverse of East Antarctica: Science and Logistics on a Three-Month Expedition Across Antarctica's Farthest Frontier

NASA Technical Reports Server (NTRS)

Albert, Mary R.

2012-01-01

Dr. Albert's current research is centered on transfer processes in porous media, including air-snow exchange in the Polar Regions and in soils in temperate areas. Her research includes field measurements, laboratory experiments, and theoretical modeling. Mary conducts field and laboratory measurements of the physical properties of natural terrain surfaces, including permeability, microstructure, and thermal conductivity. Mary uses the measurements to examine the processes of diffusion and advection of heat, mass, and chemical transport through snow and other porous media. She has developed numerical models for investigation of a variety of problems, from interstitial transport to freezing of flowing liquids. These models include a two-dimensional finite element code for air flow with heat, water vapor, and chemical transport in porous media, several multidimensional codes for diffusive transfer, as well as a computational fluid dynamics code for analysis of turbulent water flow in moving-boundary phase change problems.

Gyrokinetic modelling of the quasilinear particle flux for plasmas with neutral-beam fuelling

NASA Astrophysics Data System (ADS)

Narita, E.; Honda, M.; Nakata, M.; Yoshida, M.; Takenaga, H.; Hayashi, N.

2018-02-01

A quasilinear particle flux is modelled based on gyrokinetic calculations. The particle flux is estimated by determining factors, namely, coefficients of off-diagonal terms and a particle diffusivity. In this paper, the methodology to estimate the factors is presented using a subset of JT-60U plasmas. First, the coefficients of off-diagonal terms are estimated by linear gyrokinetic calculations. Next, to obtain the particle diffusivity, a semi-empirical approach is taken. Most experimental analyses for particle transport have assumed that turbulent particle fluxes are zero in the core region. On the other hand, even in the stationary state, the plasmas in question have a finite turbulent particle flux due to neutral-beam fuelling. By combining estimates of the experimental turbulent particle flux and the coefficients of off-diagonal terms calculated earlier, the particle diffusivity is obtained. The particle diffusivity should reflect a saturation amplitude of instabilities. The particle diffusivity is investigated in terms of the effects of the linear instability and linear zonal flow response, and it is found that a formula including these effects roughly reproduces the particle diffusivity. The developed framework for prediction of the particle flux is flexible to add terms neglected in the current model. The methodology to estimate the quasilinear particle flux requires so low computational cost that a database consisting of the resultant coefficients of off-diagonal terms and particle diffusivity can be constructed to train a neural network. The development of the methodology is the first step towards a neural-network-based particle transport model for fast prediction of the particle flux.

Including scattering within the room acoustics diffusion model: An analytical approach.

PubMed

Foy, Cédric; Picaut, Judicaël; Valeau, Vincent

2016-10-01

Over the last 20 years, a statistical acoustic model has been developed to predict the reverberant sound field in buildings. This model is based on the assumption that the propagation of the reverberant sound field follows a transport process and, as an approximation, a diffusion process that can be easily solved numerically. This model, initially designed and validated for rooms with purely diffuse reflections, is extended in the present study to mixed reflections, with a proportion of specular and diffuse reflections defined by a scattering coefficient. The proposed mathematical developments lead to an analytical expression of the diffusion constant that is a function of the scattering coefficient, but also on the absorption coefficient of the walls. The results obtained with this extended diffusion model are then compared with the classical diffusion model, as well as with a sound particles tracing approach considering mixed wall reflections. The comparison shows a good agreement for long rooms with uniform low absorption (α = 0.01) and uniform scattering. For a larger absorption (α = 0.1), the agreement is moderate, due to the fact that the proposed expression of the diffusion coefficient does not vary spatially. In addition, the proposed model is for now limited to uniform diffusion and should be extended in the future to more general cases.

Influence of tissue metabolism and capillary oxygen supply on arteriolar oxygen transport: a computational model.

PubMed

Moschandreou, T E; Ellis, C G; Goldman, D

2011-07-01

We present a theoretical model for steady-state radial and longitudinal oxygen transport in arterioles containing flowing blood (plasma and red blood cells) and surrounded by living tissue. This model combines a detailed description of convective and diffusive oxygen transport inside the arteriole with a novel boundary condition at the arteriolar lumen surface, and the results provide new mass transfer coefficients for computing arteriolar O(2) losses based on far-field tissue O(2) tension and in the presence of spatially distributed capillaries. A numerical procedure is introduced for calculating O(2) diffusion from an arteriole to a continuous capillary-tissue matrix immediately adjacent to the arteriole. The tissue O(2) consumption rate is assumed to be constant and capillaries act as either O(2) sources or sinks depending on the local O(2) environment. Using the model, O(2) saturation (SO(2)) and tension (PO(2)) are determined for the intraluminal region of the arteriole, as well as for the extraluminal region in the neighbouring tissue. Our model gives results that are consistent with available experimental data and previous intraluminal transport models, including appreciable radial decreases in intraluminal PO(2) for all vessel diameters considered (12-100 μm) and slower longitudinal decreases in PO(2) for larger vessels than for smaller ones, and predicts substantially less diffusion of O(2) from arteriolar blood than do models with PO(2) specified at the edge of the lumen. The dependence of the new mass transfer coefficients on vessel diameter, SO(2) and far-field PO(2) is calculated allowing their application to a wide range of physiological situations. This novel arteriolar O(2) transport model will be a vital component of future integrated models of microvascular regulation of O(2) supply to capillary beds and the tissue regions they support. Copyright © 2011 Elsevier Inc. All rights reserved.

Plasma transport in an Eulerian AMR code

DOE PAGES

Vold, E. L.; Rauenzahn, R. M.; Aldrich, C. H.; ...

2017-04-04

A plasma transport model has been implemented in an Eulerian AMR radiation-hydrodynamics code, xRage, which includes plasma viscosity in the momentum tensor, viscous dissipation in the energy equations, and binary species mixing with consistent species mass and energy fluxes driven by concentration gradients, ion and electron baro-diffusion terms and temperature gradient forces. The physics basis, computational issues, numeric options, and results from several test problems are discussed. The transport coefficients are found to be relatively insensitive to the kinetic correction factors when the concentrations are expressed with the molar fractions and the ion mass differences are large. The contributions tomore » flow dynamics from plasma viscosity and mass diffusion were found to increase significantly as scale lengths decrease in an inertial confinement fusion relevant Kelvin-Helmholtz instability mix layer. The mixing scale lengths in the test case are on the order of 100 μm and smaller for viscous effects to appear and 10 μm or less for significant ion species diffusion, evident over durations on the order of nanoseconds. The temperature gradient driven mass flux is seen to deplete a high Z tracer ion at the ion shock front. The plasma transport model provides the generation of the atomic mix per unit of interfacial area between two species with no free parameters. The evolution of the total atomic mix then depends also on an accurate resolution or estimate of the interfacial area between the species mixing by plasma transport. High resolution simulations or a more Lagrangian-like treatment of species interfaces may be required to distinguish plasma transport and numerical diffusion in an Eulerian computation of complex and dynamically evolving mix regions.« less

Plasma transport in an Eulerian AMR code

NASA Astrophysics Data System (ADS)

Vold, E. L.; Rauenzahn, R. M.; Aldrich, C. H.; Molvig, K.; Simakov, A. N.; Haines, B. M.

2017-04-01

A plasma transport model has been implemented in an Eulerian AMR radiation-hydrodynamics code, xRage, which includes plasma viscosity in the momentum tensor, viscous dissipation in the energy equations, and binary species mixing with consistent species mass and energy fluxes driven by concentration gradients, ion and electron baro-diffusion terms and temperature gradient forces. The physics basis, computational issues, numeric options, and results from several test problems are discussed. The transport coefficients are found to be relatively insensitive to the kinetic correction factors when the concentrations are expressed with the molar fractions and the ion mass differences are large. The contributions to flow dynamics from plasma viscosity and mass diffusion were found to increase significantly as scale lengths decrease in an inertial confinement fusion relevant Kelvin-Helmholtz instability mix layer. The mixing scale lengths in the test case are on the order of 100 μm and smaller for viscous effects to appear and 10 μm or less for significant ion species diffusion, evident over durations on the order of nanoseconds. The temperature gradient driven mass flux is seen to deplete a high Z tracer ion at the ion shock front. The plasma transport model provides the generation of the atomic mix per unit of interfacial area between two species with no free parameters. The evolution of the total atomic mix then depends also on an accurate resolution or estimate of the interfacial area between the species mixing by plasma transport. High resolution simulations or a more Lagrangian-like treatment of species interfaces may be required to distinguish plasma transport and numerical diffusion in an Eulerian computation of complex and dynamically evolving mix regions.

Transport mechanisms through PE-CVD coatings: influence of temperature, coating properties and defects on permeation of water vapour

NASA Astrophysics Data System (ADS)

Kirchheim, Dennis; Jaritz, Montgomery; Mitschker, Felix; Gebhard, Maximilian; Brochhagen, Markus; Hopmann, Christian; Böke, Marc; Devi, Anjana; Awakowicz, Peter; Dahlmann, Rainer

2017-03-01

Gas transport mechanisms through plastics are usually described by the temperature-dependent Arrhenius-model and compositions of several plastic layers are represented by the CLT. When it comes to thin films such as plasma-enhanced chemical vapour deposition (PE-CVD) or plasma-enhanced atomic layer deposition (PE-ALD) coatings on substrates of polymeric material, a universal model is lacking. While existing models describe diffusion through defects, these models presume that permeation does not occur by other means of transport mechanisms. This paper correlates the existing transport models with data from water vapour transmission experiments.

Ion transport and loss in the Earth's quiet ring current. 2: Diffusion and magnetosphere-ionosphere coupling

NASA Technical Reports Server (NTRS)

Sheldon, R. B.

1994-01-01

We have studied the transport and loss of H(+), He(+), and He(++) ions in the Earth's quiet time ring current (1 to 300 keV/e, 3 to 7 R(sub E), Kp less than 2+, absolute value of Dst less than 11, 70 to 110 degs pitchangles, all LT) comparing the standard radial diffusion model developed for the higher-energy radiation belt particles with measurements of the lower energy ring current ions in a previous paper. Large deviations of that model, which fit only 50% of the data to within a factor of 10, suggested that another transport mechanism is operating in the ring current. Here we derive a modified diffusion coefficient corrected for electric field effects on ring current energy ions that fit nearly 80% of the data to within a factor of 2. Thus we infer that electric field fluctuations from the low-latitude to midlatitude ionosphere (ionospheric dynamo) dominated the ring current transport, rather than high-latitude or solar wind fluctuations. Much of the remaining deviation may arise from convective electric field transport of the E less than 30 keV particles. Since convection effects cannot be correctly treated with this azimuthally symmetric model, we defer treatment of the lowest-energy ions to a another paper. We give chi(exp 2) contours for the best fit, showing the dependence of the fit upon the internal/external spectral power of the predicted electric and magnetic field fluctuations.

An efficient transport solver for tokamak plasmas

DOE PAGES

Park, Jin Myung; Murakami, Masanori; St. John, H. E.; ...

2017-01-03

A simple approach to efficiently solve a coupled set of 1-D diffusion-type transport equations with a stiff transport model for tokamak plasmas is presented based on the 4th order accurate Interpolated Differential Operator scheme along with a nonlinear iteration method derived from a root-finding algorithm. Here, numerical tests using the Trapped Gyro-Landau-Fluid model show that the presented high order method provides an accurate transport solution using a small number of grid points with robust nonlinear convergence.

Upper Bound on Diffusivity

NASA Astrophysics Data System (ADS)

Hartman, Thomas; Hartnoll, Sean A.; Mahajan, Raghu

2017-10-01

The linear growth of operators in local quantum systems leads to an effective light cone even if the system is nonrelativistic. We show that the consistency of diffusive transport with this light cone places an upper bound on the diffusivity: D ≲v2τeq. The operator growth velocity v defines the light cone, and τeq is the local equilibration time scale, beyond which the dynamics of conserved densities is diffusive. We verify that the bound is obeyed in various weakly and strongly interacting theories. In holographic models, this bound establishes a relation between the hydrodynamic and leading nonhydrodynamic quasinormal modes of planar black holes. Our bound relates transport data—including the electrical resistivity and the shear viscosity—to the local equilibration time, even in the absence of a quasiparticle description. In this way, the bound sheds light on the observed T -linear resistivity of many unconventional metals, the shear viscosity of the quark-gluon plasma, and the spin transport of unitary fermions.

An in vitro assay for entry into cilia reveals unique properties of the soluble diffusion barrier

PubMed Central

Breslow, David K.; Koslover, Elena F.; Seydel, Federica; Spakowitz, Andrew J.

2013-01-01

Specific proteins are concentrated within primary cilia, whereas others remain excluded. To understand the mechanistic basis of entry into cilia, we developed an in vitro assay using cells in which the plasma membrane was permeabilized, but the ciliary membrane was left intact. Using a diffusion-to-capture system and quantitative analysis, we find that proteins >9 nm in diameter (∼100 kD) are restricted from entering cilia, and we confirm these findings in vivo. Interference with the nuclear pore complex (NPC) or the actin cytoskeleton in permeabilized cells demonstrated that the ciliary diffusion barrier is mechanistically distinct from those of the NPC or the axon initial segment. Moreover, applying a mass transport model to this system revealed diffusion coefficients for soluble and membrane proteins within cilia that are compatible with rapid exploration of the ciliary space in the absence of active transport. Our results indicate that large proteins require active transport for entry into cilia but not necessarily for movement inside cilia. PMID:24100294

Transport properties in dilute UN (X ) solid solutions (X =Xe ,Kr )

NASA Astrophysics Data System (ADS)

Claisse, Antoine; Schuler, Thomas; Lopes, Denise Adorno; Olsson, Pär

2016-11-01

Uranium nitride (UN) is a candidate fuel for current GEN III fission reactors, for which it is investigated as an accident-tolerant fuel, as well as for future GEN IV reactors. In this study, we investigate the kinetic properties of gas fission products (Xe and Kr) in UN. Binding and migration energies are obtained using density functional theory, with an added Hubbard correlation to model f electrons, and the occupation matrix control scheme to avoid metastable states. These energies are then used as input for the self-consistent mean field method which enables to determine transport coefficients for vacancy-mediated diffusion of Xe and Kr on the U sublattice. The magnetic ordering of the UN structure is explicitly taken into account, for both energetic and transport properties. Solute diffusivities are compared with experimental measurements and the effect of various parameters on the theoretical model is carefully investigated. We find that kinetic correlations are very strong in this system, and that despite atomic migration anisotropy, macroscopic solute diffusivities show limited anisotropy. Our model indicates that the discrepancy between experimental measurements probably results from different irradiation conditions, and hence different defect concentrations.

Modeling the transport of chemical warfare agents and simulants in polymeric substrates for reactive decontamination

NASA Astrophysics Data System (ADS)

Pearl, Thomas; Mantooth, Brent; Varady, Mark; Willis, Matthew

2014-03-01

Chemical warfare agent simulants are often used for environmental testing in place of highly toxic agents. This work sets the foundation for modeling decontamination of absorbing polymeric materials with the focus on determining relationships between agents and simulants. The correlations of agents to simulants must consider the three way interactions in the chemical-material-decontaminant system where transport and reaction occur in polymer materials. To this end, diffusion modeling of the subsurface transport of simulants and live chemical warfare agents was conducted for various polymer systems (e.g., paint coatings) with and without reaction pathways with applied decontamination. The models utilized 1D and 2D finite difference diffusion and reaction models to simulate absorption and reaction in the polymers, and subsequent flux of the chemicals out of the polymers. Experimental data including vapor flux measurements and dynamic contact angle measurements were used to determine model input parameters. Through modeling, an understanding of the relationship of simulant to live chemical warfare agent was established, focusing on vapor emission of agents and simulants from materials.

Preliminary study: Moisture-polymer interaction. Stuby objectives

NASA Technical Reports Server (NTRS)

Wen, L. C.

1985-01-01

The problems associated with mathematically modeling water-module interaction phenomena, including sorption and desorption, diffusion, and permeation are discussed. With reliable analytical models, an extensive materials data base, and solar radiation surface meteorological observations (SOLMET) weather data, predicting module lifetimes in realistic environments can become a practical reality. The status of the present techniques of simulating the various transport mechanisms was reported. The Dent model (a modified Brunauer-Emmet-Teller) approach represented polyvinyl butyral (PVB) sorption data. A 100-layer material model and Fick's diffusion model gave diffusivity values exhibiting adequate agreement with those measured for PVB. Diffusivity of PVB is concentration dependent, decreasing as the water content in PVB increases. The temperature dependence of diffusion in PVB is well modeled by the Arrhenius rate equation. Equilibrium conductivity and leakage current data are well represented by Hearle's model for bulk ionic conductivity. A nodal network analysis using the Systems Improved Numerical Differencing Analyzer (SINDA) Thermal Analyzer gave reasonable correlation with measurable data. It is concluded that realistic lifetime predictions seem to be feasible.

Proton transfer and the diffusion of H+ and OH- ions along water wires.

PubMed

Lee, Song Hi; Rasaiah, Jayendran C

2013-09-28

Hydrogen and hydroxide ion transport in narrow carbon nanotubes (CNTs) of diameter 8.1 Å and lengths up to 582 Å are investigated by molecular dynamics simulations using a dissociating water model. The diffusion coefficients of the free ions in an open chain are significantly larger than in periodically replicated wires that necessarily contain D or L end defects, and both are higher than they are in bulk water. The free hydroxide ion diffuses faster than the free hydronium ion in short CNTs, unlike diffusion in liquid water, and both coefficients increase and converge to nearly the same value with increasing tube length. The diffusion coefficients of the two ions increase further when the tubes are immersed in a water reservoir and they move easily out of the tube, suggesting an additional pathway for proton transport via OH(-) ions in biological channels.

Generic Transport Mechanisms for Molecular Traffic in Cellular Protrusions

NASA Astrophysics Data System (ADS)

Graf, Isabella R.; Frey, Erwin

2017-03-01

Transport of molecular motors along protein filaments in a half-closed geometry is a common feature of biologically relevant processes in cellular protrusions. Using a lattice-gas model we study how the interplay between active and diffusive transport and mass conservation leads to localized domain walls and tip localization of the motors. We identify a mechanism for task sharing between the active motors (maintaining a gradient) and the diffusive motion (transport to the tip), which ensures that energy consumption is low and motor exchange mostly happens at the tip. These features are attributed to strong nearest-neighbor correlations that lead to a strong reduction of active currents, which we calculate analytically using an exact moment identity, and might prove useful for the understanding of correlations and active transport also in more elaborate systems.

An interdisciplinary computational/experimental approach to evaluate drug-loaded gold nanoparticle tumor cytotoxicity

PubMed Central

Curtis, Louis T; England, Christopher G; Wu, Min; Lowengrub, John; Frieboes, Hermann B

2016-01-01

Aim: Clinical translation of cancer nanotherapy has largely failed due to the infeasibility of optimizing the complex interaction of nano/drug/tumor/patient parameters. We develop an interdisciplinary approach modeling diffusive transport of drug-loaded gold nanoparticles in heterogeneously-vascularized tumors. Materials & methods: Evaluated lung cancer cytotoxicity to paclitaxel/cisplatin using novel two-layer (hexadecanethiol/phosphatidylcholine) and three-layer (with high-density-lipoprotein) nanoparticles. Computer simulations calibrated to in-vitro data simulated nanotherapy of heterogeneously-vascularized tumors. Results: Evaluation of free-drug cytotoxicity between monolayer/spheroid cultures demonstrates a substantial differential, with increased resistance conferred by diffusive transport. Nanoparticles had significantly higher efficacy than free-drug. Simulations of nanotherapy demonstrate 9.5% (cisplatin) and 41.3% (paclitaxel) tumor radius decrease. Conclusion: Interdisciplinary approach evaluating gold nanoparticle cytotoxicity and diffusive transport may provide insight into cancer nanotherapy. PMID:26829163

Plasma transport in the Io torus - The importance of microscopic diffusion

NASA Technical Reports Server (NTRS)

Mei, YI; Thorne, Richard M.

1991-01-01

This paper considers the question of whether the distribution of mass in the Io plasma torus is consistent with the concept of interchange eddy transport. Specifically, the flux tube content exhibits a gradual decrease with increasing radial distance from the source near Io without any evidence for substantial density irregularity associated with the plasma source or loss. Using a simple one-dimensional numerical model to simulate macroscopic interchange eddy transport, it is demonstrated that this smooth equilibrium distribution of mass can occur but only with the inclusion of a minimal level of small scale microscopic mixing at a rate approaching Bohm diffusion. Otherwise, the system exhibits a chaotic appearance which never approaches an equilibrium distribution. Various physical mechanisms for the microscopic diffusion process which is required to provide a sufficiently rapid mixing of material between the macroscopic eddies are discussed.

Ion radial diffusion in an electrostatic impulse model for stormtime ring current formation

NASA Technical Reports Server (NTRS)

Chen, Margaret W.; Schulz, Michael; Lyons, Larry R.; Gorney, David J.

1992-01-01

Two refinements to the quasi-linear theory of ion radial diffusion are proposed and examined analytically with simulations of particle trajectories. The resonance-broadening correction by Dungey (1965) is applied to the quasi-linear diffusion theory by Faelthammar (1965) for an individual model storm. Quasi-linear theory is then applied to the mean diffusion coefficients resulting from simulations of particle trajectories in 20 model storms. The correction for drift-resonance broadening results in quasi-linear diffusion coefficients with discrepancies from the corresponding simulated values that are reduced by a factor of about 3. Further reductions in the discrepancies are noted following the averaging of the quasi-linear diffusion coefficients, the simulated coefficients, and the resonance-broadened coefficients for the 20 storms. Quasi-linear theory provides good descriptions of particle transport for a single storm but performs even better in conjunction with the present ensemble-averaging.

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

Wong, May Wai San; Ovchinnikov, Mikhail; Wang, Minghuai

Potential ways of parameterizing vertical turbulent fluxes of hydrometeors are examined using a high-resolution cloud-resolving model. The cloud-resolving model uses the Morrison microphysics scheme, which contains prognostic variables for rain, graupel, ice, and snow. A benchmark simulation with a horizontal grid spacing of 250 m of a deep convection case carried out to evaluate three different ways of parameterizing the turbulent vertical fluxes of hydrometeors: an eddy-diffusion approximation, a quadrant-based decomposition, and a scaling method that accounts for within-quadrant (subplume) correlations. Results show that the down-gradient nature of the eddy-diffusion approximation tends to transport mass away from concentrated regions, whereasmore » the benchmark simulation indicates that the vertical transport tends to transport mass from below the level of maximum to aloft. Unlike the eddy-diffusion approach, the quadri-modal decomposition is able to capture the signs of the flux gradient but underestimates the magnitudes. The scaling approach is shown to perform the best by accounting for within-quadrant correlations, and improves the results for all hydrometeors except for snow. A sensitivity study is performed to examine how vertical transport may affect the microphysics of the hydrometeors. The vertical transport of each hydrometeor type is artificially suppressed in each test. Results from the sensitivity tests show that cloud-droplet-related processes are most sensitive to suppressed rain or graupel transport. In particular, suppressing rain or graupel transport has a strong impact on the production of snow and ice aloft. Lastly, a viable subgrid-scale hydrometeor transport scheme in an assumed probability density function parameterization is discussed.« less

Cytoskeletal Network Morphology Regulates Intracellular Transport Dynamics.

PubMed

Ando, David; Korabel, Nickolay; Huang, Kerwyn Casey; Gopinathan, Ajay

2015-10-20

Intracellular transport is essential for maintaining proper cellular function in most eukaryotic cells, with perturbations in active transport resulting in several types of disease. Efficient delivery of critical cargos to specific locations is accomplished through a combination of passive diffusion and active transport by molecular motors that ballistically move along a network of cytoskeletal filaments. Although motor-based transport is known to be necessary to overcome cytoplasmic crowding and the limited range of diffusion within reasonable timescales, the topological features of the cytoskeletal network that regulate transport efficiency and robustness have not been established. Using a continuum diffusion model, we observed that the time required for cellular transport was minimized when the network was localized near the nucleus. In simulations that explicitly incorporated network spatial architectures, total filament mass was the primary driver of network transit times. However, filament traps that redirect cargo back to the nucleus caused large variations in network transport. Filament polarity was more important than filament orientation in reducing average transit times, and transport properties were optimized in networks with intermediate motor on and off rates. Our results provide important insights into the functional constraints on intracellular transport under which cells have evolved cytoskeletal structures, and have potential applications for enhancing reactions in biomimetic systems through rational transport network design. Copyright © 2015 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Simulations of reactive transport and precipitation with smoothed particle hydrodynamics

NASA Astrophysics Data System (ADS)

Tartakovsky, Alexandre M.; Meakin, Paul; Scheibe, Timothy D.; Eichler West, Rogene M.

2007-03-01

A numerical model based on smoothed particle hydrodynamics (SPH) was developed for reactive transport and mineral precipitation in fractured and porous materials. Because of its Lagrangian particle nature, SPH has several advantages for modeling Navier-Stokes flow and reactive transport including: (1) in a Lagrangian framework there is no non-linear term in the momentum conservation equation, so that accurate solutions can be obtained for momentum dominated flows and; (2) complicated physical and chemical processes such as surface growth due to precipitation/dissolution and chemical reactions are easy to implement. In addition, SPH simulations explicitly conserve mass and linear momentum. The SPH solution of the diffusion equation with fixed and moving reactive solid-fluid boundaries was compared with analytical solutions, Lattice Boltzmann [Q. Kang, D. Zhang, P. Lichtner, I. Tsimpanogiannis, Lattice Boltzmann model for crystal growth from supersaturated solution, Geophysical Research Letters, 31 (2004) L21604] simulations and diffusion limited aggregation (DLA) [P. Meakin, Fractals, scaling and far from equilibrium. Cambridge University Press, Cambridge, UK, 1998] model simulations. To illustrate the capabilities of the model, coupled three-dimensional flow, reactive transport and precipitation in a fracture aperture with a complex geometry were simulated.

A simulation of water pollution model parameter estimation

NASA Technical Reports Server (NTRS)

Kibler, J. F.

1976-01-01

A parameter estimation procedure for a water pollution transport model is elaborated. A two-dimensional instantaneous-release shear-diffusion model serves as representative of a simple transport process. Pollution concentration levels are arrived at via modeling of a remote-sensing system. The remote-sensed data are simulated by adding Gaussian noise to the concentration level values generated via the transport model. Model parameters are estimated from the simulated data using a least-squares batch processor. Resolution, sensor array size, and number and location of sensor readings can be found from the accuracies of the parameter estimates.

Simultaneous Modeling of Gradual SEP Events at the Earth and the Mars

NASA Astrophysics Data System (ADS)

Hu, J.; Li, G.

2017-12-01

Solar Energetic Particles (SEP) event is the number one space hazard for spacecraft instruments and astronauts' safety. Recent studies have shown that both longitudinal and radial extent of SEP events can be very significant. In this work, we use the improved Particle Acceleration and Transport in the Heliosphere (iPATH) model to simulate gradual SEP events that have impacts upon both the Earth and the Mars. We follow the propagation of a 2D CME-driven shock. Particles are accelerated at the shock via the diffusive shock acceleration (DSA) mechanism. Transport of the escaped particles to the Earth and the Mars is then followed using a backward stochastic differential equation method. Perpendicular diffusion is considered in both the DSA and the transport process. Model results such as time intensity profile and energetic particle spectrum at the two locations are compared to understand the spatial extent of an SEP event. Observational data at the Earth and the Mars are also studied to validate the model.

Galerkin methods for Boltzmann-Poisson transport with reflection conditions on rough boundaries

NASA Astrophysics Data System (ADS)

Morales Escalante, José A.; Gamba, Irene M.

2018-06-01

We consider in this paper the mathematical and numerical modeling of reflective boundary conditions (BC) associated to Boltzmann-Poisson systems, including diffusive reflection in addition to specularity, in the context of electron transport in semiconductor device modeling at nano scales, and their implementation in Discontinuous Galerkin (DG) schemes. We study these BC on the physical boundaries of the device and develop a numerical approximation to model an insulating boundary condition, or equivalently, a pointwise zero flux mathematical condition for the electron transport equation. Such condition balances the incident and reflective momentum flux at the microscopic level, pointwise at the boundary, in the case of a more general mixed reflection with momentum dependant specularity probability p (k →). We compare the computational prediction of physical observables given by the numerical implementation of these different reflection conditions in our DG scheme for BP models, and observe that the diffusive condition influences the kinetic moments over the whole domain in position space.

Numerical Modeling of High-Temperature Corrosion Processes

NASA Technical Reports Server (NTRS)

Nesbitt, James A.

1995-01-01

Numerical modeling of the diffusional transport associated with high-temperature corrosion processes is reviewed. These corrosion processes include external scale formation and internal subscale formation during oxidation, coating degradation by oxidation and substrate interdiffusion, carburization, sulfidation and nitridation. The studies that are reviewed cover such complexities as concentration-dependent diffusivities, cross-term effects in ternary alloys, and internal precipitation where several compounds of the same element form (e.g., carbides of Cr) or several compounds exist simultaneously (e.g., carbides containing varying amounts of Ni, Cr, Fe or Mo). In addition, the studies involve a variety of boundary conditions that vary with time and temperature. Finite-difference (F-D) techniques have been applied almost exclusively to model either the solute or corrodant transport in each of these studies. Hence, the paper first reviews the use of F-D techniques to develop solutions to the diffusion equations with various boundary conditions appropriate to high-temperature corrosion processes. The bulk of the paper then reviews various F-D modeling studies of diffusional transport associated with high-temperature corrosion.

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.

Effects of spin transition on diffusion of Fe2+ in ferropericlase in Earth's lower mantle

NASA Astrophysics Data System (ADS)

Saha, Saumitra; Bengtson, Amelia; Crispin, Katherine L.; van Orman, James A.; Morgan, Dane

2011-11-01

Knowledge of Fe composition in lower-mantle minerals (primarily perovskite and ferropericlase) is essential to a complete understanding of the Earth's interior. Fe cation diffusion potentially controls many aspects of the distribution of Fe in the Earth's lower mantle, including mixing of chemical heterogeneities, element partitioning, and the extent of core-mantle communications. Fe in ferropericlase has been shown to undergo a spin transition starting at about 40 GPa and exists in a mixture of high-spin and low-spin states over a wide range of pressures. Present experimental data on Fe transport in ferropericlase is limited to pressures below 35 GPa and provides little information on the pressure dependence of the activation volume and none on the impact of the spin transition on diffusion. Therefore, known experimental data on Fe diffusion cannot be reliably extrapolated to predict diffusion throughout the lower mantle. Here, first-principles and statistical modeling are combined to predict diffusion of Fe in ferropericlase over the entire lower mantle, including the effects of the Fe spin transition. A thorough statistical thermodynamic treatment is given to fully incorporate the coexistence of high- and low-spin Fe in the model of overall Fe diffusion in the lower mantle. Pure low-spin Fe diffuses approximately 104 times slower than high-spin Fe in ferropericlase but Fe diffusion of the mixed-spin state is only about 10 times slower than that of high-spin Fe. The predicted Fe diffusivities demonstrate that ferropericlase is unlikely to be rate limiting in transporting Fe in deep earth since much slower Fe diffusion in perovskite is predicted.

Determination of Diffusion Coefficients in Cement-Based Materials: An Inverse Problem for the Nernst-Planck and Poisson Models

NASA Astrophysics Data System (ADS)

Szyszkiewicz-Warzecha, Krzysztof; Jasielec, Jerzy J.; Fausek, Janusz; Filipek, Robert

2016-08-01

Transport properties of ions have significant impact on the possibility of rebars corrosion thus the knowledge of a diffusion coefficient is important for reinforced concrete durability. Numerous tests for the determination of diffusion coefficients have been proposed but analysis of some of these tests show that they are too simplistic or even not valid. Hence, more rigorous models to calculate the coefficients should be employed. Here we propose the Nernst-Planck and Poisson equations, which take into account the concentration and electric potential field. Based on this model a special inverse method is presented for determination of a chloride diffusion coefficient. It requires the measurement of concentration profiles or flux on the boundary and solution of the NPP model to define the goal function. Finding the global minimum is equivalent to the determination of diffusion coefficients. Typical examples of the application of the presented method are given.

Spatially Different Tissue-Scale Diffusivity Shapes ANGUSTIFOLIA3 Gradient in Growing Leaves.

PubMed

Kawade, Kensuke; Tanimoto, Hirokazu; Horiguchi, Gorou; Tsukaya, Hirokazu

2017-09-05

The spatial gradient of signaling molecules is pivotal for establishing developmental patterns of multicellular organisms. It has long been proposed that these gradients could arise from the pure diffusion process of signaling molecules between cells, but whether this simplest mechanism establishes the formation of the tissue-scale gradient remains unclear. Plasmodesmata are unique channel structures in plants that connect neighboring cells for molecular transport. In this study, we measured cellular- and tissue-scale kinetics of molecular transport through plasmodesmata in Arabidopsis thaliana developing leaf primordia by fluorescence recovery assays. These trans-scale measurements revealed biophysical properties of diffusive molecular transport through plasmodesmata and revealed that the tissue-scale diffusivity, but not the cellular-scale diffusivity, is spatially different along the leaf proximal-to-distal axis. We found that the gradient in cell size along the developmental axis underlies this spatially different tissue-scale diffusivity. We then asked how this diffusion-based framework functions in establishing a signaling gradient of endogenous molecules. ANGUSTIFOLIA3 (AN3) is a transcriptional co-activator, and as we have shown here, it forms a long-range signaling gradient along the leaf proximal-to-distal axis to determine a cell-proliferation domain. By genetically engineering AN3 mobility, we assessed each contribution of cell-to-cell movement and tissue growth to the distribution of the AN3 gradient. We constructed a diffusion-based theoretical model using these quantitative data to analyze the AN3 gradient formation and demonstrated that it could be achieved solely by the diffusive molecular transport in a growing tissue. Our results indicate that the spatially different tissue-scale diffusivity is a core mechanism for AN3 gradient formation. This provides evidence that the pure diffusion process establishes the formation of the long-range signaling gradient in leaf development. Copyright © 2017 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Modeling growth kinetics of thin films made by atomic layer deposition in lateral high-aspect-ratio structures

NASA Astrophysics Data System (ADS)

Ylilammi, Markku; Ylivaara, Oili M. E.; Puurunen, Riikka L.

2018-05-01

The conformality of thin films grown by atomic layer deposition (ALD) is studied using all-silicon test structures with long narrow lateral channels. A diffusion model, developed in this work, is used for studying the propagation of ALD growth in narrow channels. The diffusion model takes into account the gas transportation at low pressures, the dynamic Langmuir adsorption model for the film growth and the effect of channel narrowing due to film growth. The film growth is calculated by solving the diffusion equation with surface reactions. An efficient analytic approximate solution of the diffusion equation is developed for fitting the model to the measured thickness profile. The fitting gives the equilibrium constant of adsorption and the sticking coefficient. This model and Gordon's plug flow model are compared. The simulations predict the experimental measurement results quite well for Al2O3 and TiO2 ALD processes.

Computational modeling of diffusion in the cerebellum.

PubMed

Marinov, Toma M; Santamaria, Fidel

2014-01-01

Diffusion is a major transport mechanism in living organisms. In the cerebellum, diffusion is responsible for the propagation of molecular signaling involved in synaptic plasticity and metabolism, both intracellularly and extracellularly. In this chapter, we present an overview of the cerebellar structure and function. We then discuss the types of diffusion processes present in the cerebellum and their biological importance. We particularly emphasize the differences between extracellular and intracellular diffusion and the presence of tortuosity and anomalous diffusion in different parts of the cerebellar cortex. We provide a mathematical introduction to diffusion and a conceptual overview of various computational modeling techniques. We discuss their scope and their limit of application. Although our focus is the cerebellum, we have aimed at presenting the biological and mathematical foundations as general as possible to be applicable to any other area in biology in which diffusion is of importance. © 2014 Elsevier Inc. All rights reserved.

In Vivo Evaluation of White Matter Integrity and Anterograde Transport in Visual System After Excitotoxic Retinal Injury With Multimodal MRI and OCT

PubMed Central

Ho, Leon C.; Wang, Bo; Conner, Ian P.; van der Merwe, Yolandi; Bilonick, Richard A.; Kim, Seong-Gi; Wu, Ed X.; Sigal, Ian A.; Wollstein, Gadi; Schuman, Joel S.; Chan, Kevin C.

2015-01-01

Purpose. Excitotoxicity has been linked to the pathogenesis of ocular diseases and injuries and may involve early degeneration of both anterior and posterior visual pathways. However, their spatiotemporal relationships remain unclear. We hypothesized that the effects of excitotoxic retinal injury (ERI) on the visual system can be revealed in vivo by diffusion tensor magnetic resonance imagining (DTI), manganese-enhanced magnetic resonance imagining (MRI), and optical coherence tomography (OCT). Methods. Diffusion tensor MRI was performed at 9.4 Tesla to monitor white matter integrity changes after unilateral N-methyl-D-aspartate (NMDA)-induced ERI in six Sprague-Dawley rats and six C57BL/6J mice. Additionally, four rats and four mice were intravitreally injected with saline to compare with NMDA-injected animals. Optical coherence tomography of the retina and manganese-enhanced MRI of anterograde transport were evaluated and correlated with DTI parameters. Results. In the rat optic nerve, the largest axial diffusivity decrease and radial diffusivity increase occurred within the first 3 and 7 days post ERI, respectively, suggestive of early axonal degeneration and delayed demyelination. The optic tract showed smaller directional diffusivity changes and weaker DTI correlations with retinal thickness compared with optic nerve, indicative of anterograde degeneration. The splenium of corpus callosum was also reorganized at 4 weeks post ERI. The DTI profiles appeared comparable between rat and mouse models. Furthermore, the NMDA-injured visual pathway showed reduced anterograde manganese transport, which correlated with diffusivity changes along but not perpendicular to optic nerve. Conclusions. Diffusion tensor MRI, manganese-enhanced MRI, and OCT provided an in vivo model system for characterizing the spatiotemporal changes in white matter integrity, the eye–brain relationships and structural–physiological relationships in the visual system after ERI. PMID:26066747

RANS modeling of scalar dispersion from localized sources within a simplified urban-area model

NASA Astrophysics Data System (ADS)

Rossi, Riccardo; Capra, Stefano; Iaccarino, Gianluca

2011-11-01

The dispersion of a passive scalar downstream a localized source within a simplified urban-like geometry is examined by means of RANS scalar flux models. The computations are conducted under conditions of neutral stability and for three different incoming wind directions (0°, 45°, 90°) at a roughness Reynolds number of Ret = 391. A Reynolds stress transport model is used to close the flow governing equations whereas both the standard eddy-diffusivity closure and algebraic flux models are employed to close the transport equation for the passive scalar. The comparison with a DNS database shows improved reliability from algebraic scalar flux models towards predicting both the mean concentration and the plume structure. Since algebraic flux models do not increase substantially the computational effort, the results indicate that the use of tensorial-diffusivity can be promising tool for dispersion simulations for the urban environment.

Summer Work Experience: Determining Methane Combustion Mechanisms and Sub-Scale Diffuser Properties for Space Transporation System Engine Testing

NASA Technical Reports Server (NTRS)

Williams, Powtawche N.

1998-01-01

To assess engine performance during the testing of Space Shuttle Main Engines (SSMEs), the design of an optimal altitude diffuser is studied for future Space Transportation Systems (STS). For other Space Transportation Systems, rocket propellant using kerosene is also studied. Methane and dodecane have similar reaction schemes as kerosene, and are used to simulate kerosene combustion processes at various temperatures. The equations for the methane combustion mechanism at high temperature are given, and engine combustion is simulated on the General Aerodynamic Simulation Program (GASP). The successful design of an altitude diffuser depends on the study of a sub-scaled diffuser model tested through two-dimensional (2-D) flow-techniques. Subroutines given calculate the static temperature and pressure at each Mach number within the diffuser flow. Implementing these subroutines into program code for the properties of 2-D compressible fluid flow determines all fluid characteristics, and will be used in the development of an optimal diffuser design.

The Role of Diffusivity Quenching in Flux-transport Dynamo Models

NASA Astrophysics Data System (ADS)

Guerrero, Gustavo; Dikpati, Mausumi; de Gouveia Dal Pino, Elisabete M.

2009-08-01

In the nonlinear phase of a dynamo process, the back-reaction of the magnetic field upon the turbulent motion results in a decrease of the turbulence level and therefore in a suppression of both the magnetic field amplification (the α-quenching effect) and the turbulent magnetic diffusivity (the η-quenching effect). While the former has been widely explored, the effects of η-quenching in the magnetic field evolution have rarely been considered. In this work, we investigate the role of the suppression of diffusivity in a flux-transport solar dynamo model that also includes a nonlinear α-quenching term. Our results indicate that, although for α-quenching the dependence of the magnetic field amplification with the quenching factor is nearly linear, the magnetic field response to η-quenching is nonlinear and spatially nonuniform. We have found that the magnetic field can be locally amplified in this case, forming long-lived structures whose maximum amplitude can be up to ~2.5 times larger at the tachocline and up to ~2 times larger at the center of the convection zone than in models without quenching. However, this amplification leads to unobservable effects and to a worse distribution of the magnetic field in the butterfly diagram. Since the dynamo cycle period increases when the efficiency of the quenching increases, we have also explored whether the η-quenching can cause a diffusion-dominated model to drift into an advection-dominated regime. We have found that models undergoing a large suppression in η produce a strong segregation of magnetic fields that may lead to unsteady dynamo-oscillations. On the other hand, an initially diffusion-dominated model undergoing a small suppression in η remains in the diffusion-dominated regime.

Surface transport processes in charged porous media

DOE PAGES

Gabitto, Jorge; Tsouris, Costas

2017-03-03

Surface transport processes are important in chemistry, colloidal sciences, engineering, biology, and geophysics. Natural or externally produced charges on surfaces create electrical double layers (EDLs) at the solid-liquid interface. The existence of the EDLs produces several complex processes including bulk and surface transport of ions. In this work, a model is presented to simulate bulk and transport processes in homogeneous porous media comprising big pores. It is based on a theory for capacitive charging by ideally polarizable porous electrodes without Faradaic reactions or specific adsorption of ions. A volume averaging technique is used to derive the averaged transport equations inmore » the limit of thin electrical double layers. Description of the EDL between the electrolyte solution and the charged wall is accomplished using the Gouy-Chapman-Stern (GCS) model. The surface transport terms enter into the average equations due to the use of boundary conditions for diffuse interfaces. Two extra surface transports terms appear in the closed average equations. One is a surface diffusion term equivalent to the transport process in non-charged porous media. The second surface transport term is a migration term unique to charged porous media. The effective bulk and transport parameters for isotropic porous media are calculated solving the corresponding closure problems.« less

Surface transport processes in charged porous media

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

Gabitto, Jorge; Tsouris, Costas

Surface transport processes are important in chemistry, colloidal sciences, engineering, biology, and geophysics. Natural or externally produced charges on surfaces create electrical double layers (EDLs) at the solid-liquid interface. The existence of the EDLs produces several complex processes including bulk and surface transport of ions. In this work, a model is presented to simulate bulk and transport processes in homogeneous porous media comprising big pores. It is based on a theory for capacitive charging by ideally polarizable porous electrodes without Faradaic reactions or specific adsorption of ions. A volume averaging technique is used to derive the averaged transport equations inmore » the limit of thin electrical double layers. Description of the EDL between the electrolyte solution and the charged wall is accomplished using the Gouy-Chapman-Stern (GCS) model. The surface transport terms enter into the average equations due to the use of boundary conditions for diffuse interfaces. Two extra surface transports terms appear in the closed average equations. One is a surface diffusion term equivalent to the transport process in non-charged porous media. The second surface transport term is a migration term unique to charged porous media. The effective bulk and transport parameters for isotropic porous media are calculated solving the corresponding closure problems.« less

Understanding of flux-limited behaviors of heat transport in nonlinear regime

NASA Astrophysics Data System (ADS)

Guo, Yangyu; Jou, David; Wang, Moran

2016-01-01

The classical Fourier's law of heat transport breaks down in highly nonequilibrium situations as in nanoscale heat transport, where nonlinear effects become important. The present work is aimed at exploring the flux-limited behaviors based on a categorization of existing nonlinear heat transport models in terms of their theoretical foundations. Different saturation heat fluxes are obtained, whereas the same qualitative variation trend of heat flux versus exerted temperature gradient is got in diverse nonlinear models. The phonon hydrodynamic model is proposed to act as a standard to evaluate other heat flux limiters because of its more rigorous physical foundation. A deeper knowledge is thus achieved about the phenomenological generalized heat transport models. The present work provides deeper understanding and accurate modeling of nonlocal and nonlinear heat transport beyond the diffusive limit.

Continuous-time random-walk model for anomalous diffusion in expanding media

NASA Astrophysics Data System (ADS)

Le Vot, F.; Abad, E.; Yuste, S. B.

2017-09-01

Expanding media are typical in many different fields, e.g., in biology and cosmology. In general, a medium expansion (contraction) brings about dramatic changes in the behavior of diffusive transport properties such as the set of positional moments and the Green's function. Here, we focus on the characterization of such effects when the diffusion process is described by the continuous-time random-walk (CTRW) model. As is well known, when the medium is static this model yields anomalous diffusion for a proper choice of the probability density function (pdf) for the jump length and the waiting time, but the behavior may change drastically if a medium expansion is superimposed on the intrinsic random motion of the diffusing particle. For the case where the jump length and the waiting time pdfs are long-tailed, we derive a general bifractional diffusion equation which reduces to a normal diffusion equation in the appropriate limit. We then study some particular cases of interest, including Lévy flights and subdiffusive CTRWs. In the former case, we find an analytical exact solution for the Green's function (propagator). When the expansion is sufficiently fast, the contribution of the diffusive transport becomes irrelevant at long times and the propagator tends to a stationary profile in the comoving reference frame. In contrast, for a contracting medium a competition between the spreading effect of diffusion and the concentrating effect of contraction arises. In the specific case of a subdiffusive CTRW in an exponentially contracting medium, the latter effect prevails for sufficiently long times, and all the particles are eventually localized at a single point in physical space. This "big crunch" effect, totally absent in the case of normal diffusion, stems from inefficient particle spreading due to subdiffusion. We also derive a hierarchy of differential equations for the moments of the transport process described by the subdiffusive CTRW model in an expanding medium. From this hierarchy, the full time evolution of the second-order moment is obtained for some specific types of expansion. In the case of an exponential expansion, exact recurrence relations for the Laplace-transformed moments are obtained, whence the long-time behavior of moments of arbitrary order is subsequently inferred. Our analytical and numerical results for both Lévy flights and subdiffusive CTRWs confirm the intuitive expectation that the medium expansion hinders the mixing of diffusive particles occupying separate regions. In the case of Lévy flights, we quantify this effect by means of the so-called "Lévy horizon."

Continuous-time random-walk model for anomalous diffusion in expanding media.

PubMed

Le Vot, F; Abad, E; Yuste, S B

2017-09-01

Expanding media are typical in many different fields, e.g., in biology and cosmology. In general, a medium expansion (contraction) brings about dramatic changes in the behavior of diffusive transport properties such as the set of positional moments and the Green's function. Here, we focus on the characterization of such effects when the diffusion process is described by the continuous-time random-walk (CTRW) model. As is well known, when the medium is static this model yields anomalous diffusion for a proper choice of the probability density function (pdf) for the jump length and the waiting time, but the behavior may change drastically if a medium expansion is superimposed on the intrinsic random motion of the diffusing particle. For the case where the jump length and the waiting time pdfs are long-tailed, we derive a general bifractional diffusion equation which reduces to a normal diffusion equation in the appropriate limit. We then study some particular cases of interest, including Lévy flights and subdiffusive CTRWs. In the former case, we find an analytical exact solution for the Green's function (propagator). When the expansion is sufficiently fast, the contribution of the diffusive transport becomes irrelevant at long times and the propagator tends to a stationary profile in the comoving reference frame. In contrast, for a contracting medium a competition between the spreading effect of diffusion and the concentrating effect of contraction arises. In the specific case of a subdiffusive CTRW in an exponentially contracting medium, the latter effect prevails for sufficiently long times, and all the particles are eventually localized at a single point in physical space. This "big crunch" effect, totally absent in the case of normal diffusion, stems from inefficient particle spreading due to subdiffusion. We also derive a hierarchy of differential equations for the moments of the transport process described by the subdiffusive CTRW model in an expanding medium. From this hierarchy, the full time evolution of the second-order moment is obtained for some specific types of expansion. In the case of an exponential expansion, exact recurrence relations for the Laplace-transformed moments are obtained, whence the long-time behavior of moments of arbitrary order is subsequently inferred. Our analytical and numerical results for both Lévy flights and subdiffusive CTRWs confirm the intuitive expectation that the medium expansion hinders the mixing of diffusive particles occupying separate regions. In the case of Lévy flights, we quantify this effect by means of the so-called "Lévy horizon."

Unsteady Oxygen Transfer in Space-Filling Models of the Pulmonary Acinus

NASA Astrophysics Data System (ADS)

Hofemeier, Philipp; Shachar-Berman, Lihi; Filoche, Marcel; Sznitman, Josue

2014-11-01

Diffusional screening in the pulmonary acinus is a well-known physical phenomenon that results from the depletion of fresh oxygen in proximal acinar generations diffusing through the alveolar wall membranes and effectively creating a gradient in the oxygen partial pressure along the acinar airways. Until present, most studies have focused on steady-state oxygen diffusion in generic sub-acinar structures and discarded convective oxygen transport due to low Peclet numbers in this region. Such studies, however, fall typically short in capturing the complex morphology of acinar airways as well as the oscillatory nature of convecive acinar breathing. Here, we revisit this problem and solve the convective-diffusive transport equations in breathing 3D acinar structures, underlining the significance of convective flows in proximal acinar generations as well as recirculating alveolar flow patterns. In particular, to assess diffusional screening, we monitor time-dependent efficiencies of the acinus under cyclic breathing motion. Our study emphasizes the necessity of capturing both a dynamically breathing and anatomically-realistic model of the sub-acinus to characterize unsteady oxygen transport across the acinar walls.

Diffusive, supersonic x-ray transport in radiatively heated foam cylinders

NASA Astrophysics Data System (ADS)

Back, C. A.; Bauer, J. D.; Hammer, J. H.; Lasinski, B. F.; Turner, R. E.; Rambo, P. W.; Landen, O. L.; Suter, L. J.; Rosen, M. D.; Hsing, W. W.

2000-05-01

Diffusive supersonic radiation transport, where the ratio of the diffusive radiation front velocity to the material sound speed >2 has been studied in experiments on low density (40 mg/cc to 50 mg/cc) foams. Laser-heated Au hohlraums provided a radiation drive that heated SiO2 and Ta2O5 aerogel foams of varying lengths. Face-on emission measurements at 550 eV provided clean signatures of the radiation breakout. The high quality data provides new detailed information on the importance of both the fill and wall material opacities and heat capacities in determining the radiation front speed and curvature. The Marshak radiation wave transport is studied in a geometry that allows direct comparisons with analytic models and two-dimensional code simulations. Experiments show important effects that will affect even nondiffusive and transonic radiation transport experiments studied by others in the field. This work is of basic science interest with applications to inertial confinement fusion and astrophysics.

Characterization of transport phenomena in porous transport layers using X-ray microtomography

NASA Astrophysics Data System (ADS)

Hasanpour, S.; Hoorfar, M.; Phillion, A. B.

2017-06-01

Among different methods available for estimating the transport properties of porous transport layers (PTLs) of polymer electrolyte membrane fuel cells, X-ray micro computed tomography (X-μCT) imaging in combination with image-based numerical simulation has been recognized as a viable tool. In this study, four commercially-available single-layer and dual-layer PTLs are analyzed using this method in order to compare and contrast transport properties between different PTLs, as well as the variability within a single sheet. Complete transport property datasets are created for each PTL. The simulation predictions indicate that PTLs with high porosity show considerable variability in permeability and effective diffusivity, while PTLs with low porosity do not. Furthermore, it is seen that the Tomadakis-Sotirchos (TS) analytical expressions for porous media match the image-based simulations when porosity is relatively low but predict higher permeability and effective diffusivity for porosity values greater than 80%. Finally, the simulations show that cracks within MPL of dual-layer PTLs have a significant effect on the overall permeability and effective diffusivity of the PTLs. This must be considered when estimating the transport properties of dual-layer PTLs. These findings can be used to improve macro-scale models of product and reactant transport within fuel cells, and ultimately, fuel cell efficiency.

Photon migration in non-scattering tissue and the effects on image reconstruction

NASA Astrophysics Data System (ADS)

Dehghani, H.; Delpy, D. T.; Arridge, S. R.

1999-12-01

Photon propagation in tissue can be calculated using the relationship described by the transport equation. For scattering tissue this relationship is often simplified and expressed in terms of the diffusion approximation. This approximation, however, is not valid for non-scattering regions, for example cerebrospinal fluid (CSF) below the skull. This study looks at the effects of a thin clear layer in a simple model representing the head and examines its effect on image reconstruction. Specifically, boundary photon intensities (total number of photons exiting at a point on the boundary due to a source input at another point on the boundary) are calculated using the transport equation and compared with data calculated using the diffusion approximation for both non-scattering and scattering regions. The effect of non-scattering regions on the calculated boundary photon intensities is presented together with the advantages and restrictions of the transport code used. Reconstructed images are then presented where the forward problem is solved using the transport equation for a simple two-dimensional system containing a non-scattering ring and the inverse problem is solved using the diffusion approximation to the transport equation.

Evolution and Transport of Water in the Upper Regolith of Mars

NASA Technical Reports Server (NTRS)

Hudson, T. L.; Aharonson, O.; Schorghofer, N.; Hecht, M. H.; Bridges, N. T.; Green, J. R.

2003-01-01

Long standing theoretical predictions [1-3], as well as recent spacecraft observations [4] indicate that large quantities of ice is present in the high latitudes upper decimeters to meters of the Martian regolith. At shallower depths and warmer locations small amounts of H2O, either adsorbed or free, may be present transiently. An understanding of the evolution of water based on theoretical and experimental considerations of the processes operating at the Martian environment is required. In particular, the porosity, diffusivity, and permeability of soils and their effect on water vapor transport under Mars-like conditions have been estimated, but experimental validation of such models is lacking. Goal: Three related mechanisms may affect water transport in the upper Martian regolith. 1) diffusion along a concentration gradient under isobaric conditions, 2) diffusion along a thermal gradient, which may give rise to a concentration gradient as ice sublimes or molecules desorb from the regolith, and 3) hydraulic flow, or mass motion in response to a pressure gradient. Our combined theoretical and experimental investigation seeks to disentangle these mechanisms and determine which process(es) are dominant in the upper regolith over various timescales. A detailed one-dimensional model of the upper regolith is being created which incorporates water adsorption/ desorption, condensation, porosity, diffusivity, and permeability effects. Certain factors such as diffusivity are difficult to determine theoretically due to the wide range of intrinsic grain properties such as particle sizes, shapes, packing densities, and emergent properties such as tortuosity. An experiment is being designed which will allow us to more accurately determine diffusivity, permeability, and water desorption isotherms for regolith simulants.

Information loss and reconstruction in diffuse fluorescence tomography

PubMed Central

Bonfert-Taylor, Petra; Leblond, Frederic; Holt, Robert W.; Tichauer, Kenneth; Pogue, Brian W.; Taylor, Edward C.

2012-01-01

This paper is a theoretical exploration of spatial resolution in diffuse fluorescence tomography. It is demonstrated that, given a fixed imaging geometry, one cannot—relative to standard techniques such as Tikhonov regularization and truncated singular value decomposition—improve the spatial resolution of the optical reconstructions via increasing the node density of the mesh considered for modeling light transport. Using techniques from linear algebra, it is shown that, as one increases the number of nodes beyond the number of measurements, information is lost by the forward model. It is demonstrated that this information cannot be recovered using various common reconstruction techniques. Evidence is provided showing that this phenomenon is related to the smoothing properties of the elliptic forward model that is used in the diffusion approximation to light transport in tissue. This argues for reconstruction techniques that are sensitive to boundaries, such as L1-reconstruction and the use of priors, as well as the natural approach of building a measurement geometry that reflects the desired image resolution. PMID:22472763

Quasi-two-layer morphodynamic model for bedload-dominated problems: bed slope-induced morphological diffusion

NASA Astrophysics Data System (ADS)

Maldonado, Sergio; Borthwick, Alistair G. L.

2018-02-01

We derive a two-layer depth-averaged model of sediment transport and morphological evolution for application to bedload-dominated problems. The near-bed transport region is represented by the lower (bedload) layer which has an arbitrarily constant, vanishing thickness (of approx. 10 times the sediment particle diameter), and whose average sediment concentration is free to vary. Sediment is allowed to enter the upper layer, and hence the total load may also be simulated, provided that concentrations of suspended sediment remain low. The model conforms with established theories of bedload, and is validated satisfactorily against empirical expressions for sediment transport rates and the morphodynamic experiment of a migrating mining pit by Lee et al. (1993 J. Hydraul. Eng. 119, 64-80 (doi:10.1061/(ASCE)0733-9429(1993)119:1(64))). Investigation into the effect of a local bed gradient on bedload leads to derivation of an analytical, physically meaningful expression for morphological diffusion induced by a non-zero local bed slope. Incorporation of the proposed morphological diffusion into a conventional morphodynamic model (defined as a coupling between the shallow water equations, Exner equation and an empirical formula for bedload) improves model predictions when applied to the evolution of a mining pit, without the need either to resort to special numerical treatment of the equations or to use additional tuning parameters.

Modeling of the anode of a liquid-feed DMFC: Inhomogeneous compression effects and two-phase transport phenomena

NASA Astrophysics Data System (ADS)

García-Salaberri, Pablo A.; Vera, Marcos; Iglesias, Immaculada

2014-01-01

An isothermal two-phase 2D/1D across-the-channel model for the anode of a liquid-feed Direct Methanol Fuel Cell (DMFC) is presented. The model takes into account the effects of the inhomogeneous assembly compression of the Gas Diffusion Layer (GDL), including the spatial variations of porosity, diffusivity, permeability, capillary pressure, and electrical conductivity. The effective anisotropic properties of the GDL are evaluated from empirical data reported in the literature corresponding to Toray carbon paper TGP-H series. Multiphase transport is modeled according to the classical theory of porous media (two-fluid model), considering the effect of non-equilibrium evaporation and condensation of methanol and water. The numerical results evidence that the hydrophobic Leverett J-function approach is physically inconsistent to describe capillary transport in the anode of a DMFC when assembly compression effects are considered. In contrast, more realistic results are obtained when GDL-specific capillary pressure curves reflecting the mixed-wettability characteristics of GDLs are taken into account. The gas coverage factor at the GDL/channel interface also exhibits a strong influence on the gas-void fraction distribution in the GDL, which in turn depends on the relative importance between the capillary resistance induced by the inhomogeneous compression, Rc(∝ ∂pc / ∂ ε) , and the capillary diffusivity, Dbarc(∝ ∂pc / ∂ s) .

Quasi-two-layer morphodynamic model for bedload-dominated problems: bed slope-induced morphological diffusion.

PubMed

Maldonado, Sergio; Borthwick, Alistair G L

2018-02-01

We derive a two-layer depth-averaged model of sediment transport and morphological evolution for application to bedload-dominated problems. The near-bed transport region is represented by the lower (bedload) layer which has an arbitrarily constant, vanishing thickness (of approx. 10 times the sediment particle diameter), and whose average sediment concentration is free to vary. Sediment is allowed to enter the upper layer, and hence the total load may also be simulated, provided that concentrations of suspended sediment remain low. The model conforms with established theories of bedload, and is validated satisfactorily against empirical expressions for sediment transport rates and the morphodynamic experiment of a migrating mining pit by Lee et al. (1993 J. Hydraul. Eng. 119 , 64-80 (doi:10.1061/(ASCE)0733-9429(1993)119:1(64))). Investigation into the effect of a local bed gradient on bedload leads to derivation of an analytical, physically meaningful expression for morphological diffusion induced by a non-zero local bed slope. Incorporation of the proposed morphological diffusion into a conventional morphodynamic model (defined as a coupling between the shallow water equations, Exner equation and an empirical formula for bedload) improves model predictions when applied to the evolution of a mining pit, without the need either to resort to special numerical treatment of the equations or to use additional tuning parameters.

Regression-based model of skin diffuse reflectance for skin color analysis

NASA Astrophysics Data System (ADS)

Tsumura, Norimichi; Kawazoe, Daisuke; Nakaguchi, Toshiya; Ojima, Nobutoshi; Miyake, Yoichi

2008-11-01

A simple regression-based model of skin diffuse reflectance is developed based on reflectance samples calculated by Monte Carlo simulation of light transport in a two-layered skin model. This reflectance model includes the values of spectral reflectance in the visible spectra for Japanese women. The modified Lambert Beer law holds in the proposed model with a modified mean free path length in non-linear density space. The averaged RMS and maximum errors of the proposed model were 1.1 and 3.1%, respectively, in the above range.

Systematic derivation of reaction-diffusion equations with distributed delays and relations to fractional reaction-diffusion equations and hyperbolic transport equations: application to the theory of Neolithic transition.

PubMed

Vlad, Marcel Ovidiu; Ross, John

2002-12-01

We introduce a general method for the systematic derivation of nonlinear reaction-diffusion equations with distributed delays. We study the interactions among different types of moving individuals (atoms, molecules, quasiparticles, biological organisms, etc). The motion of each species is described by the continuous time random walk theory, analyzed in the literature for transport problems, whereas the interactions among the species are described by a set of transformation rates, which are nonlinear functions of the local concentrations of the different types of individuals. We use the time interval between two jumps (the transition time) as an additional state variable and obtain a set of evolution equations, which are local in time. In order to make a connection with the transport models used in the literature, we make transformations which eliminate the transition time and derive a set of nonlocal equations which are nonlinear generalizations of the so-called generalized master equations. The method leads under different specified conditions to various types of nonlocal transport equations including a nonlinear generalization of fractional diffusion equations, hyperbolic reaction-diffusion equations, and delay-differential reaction-diffusion equations. Thus in the analysis of a given problem we can fit to the data the type of reaction-diffusion equation and the corresponding physical and kinetic parameters. The method is illustrated, as a test case, by the study of the neolithic transition. We introduce a set of assumptions which makes it possible to describe the transition from hunting and gathering to agriculture economics by a differential delay reaction-diffusion equation for the population density. We derive a delay evolution equation for the rate of advance of agriculture, which illustrates an application of our analysis.

Effect of particle- and specimen-level transport on product state in compacted-powder combustion synthesis and thermal debinding of polymers from molded powders

NASA Astrophysics Data System (ADS)

Oliveira, Amir Antonio Martins

The existence of large gradients within particles and fast temporal variations in the temperature and species concentration prevents the use of asymptotic approximations for the closure of the volume-averaged, specimen-level formulations. In this case a solution of the particle-level transport problem is needed to complement the specimen-level volume-averaged equations. Here, the use of combined specimen-level and particle-level models for transport in reactive porous media is demonstrated with two examples. For the gasless compacted-powder combustion synthesis, a three-scale model is developed. The specimen-level model is based on the volume-averaged equations for species and temperature. Local thermal equilibrium is assumed and the macroscopic mass diffusion and convection fluxes are neglected. The particle-level model accounts for the interparticle diffusion (i.e., the liquid migration from liquid-rich to liquid-lean regions) and the intraparticle diffusion (i.e., the species mass diffusion within the product layer formed at the surface of the high melting temperature component). It is found that the interparticle diffusion controls the extent of conversion to the final product, the maximum temperature, and to a smaller degree the propagation velocity. The intraparticle diffusion controls the propagation velocity and to a smaller degree the maximum temperature. The initial stages of thermal degradation of EVA from molded specimens is modeled using volume-averaged equations for the species and empirical models for the kinetics of the thermal degradation, the vapor-liquid equilibrium, and the diffusion coefficient of acetic acid in the molten polymer. It is assumed that a bubble forms when the partial pressure of acetic acid exceeds the external ambient pressure. It is found that the removal of acetic acid is characterized by two regimes, a pre-charge dominated regime and a generation dominated regime. For the development of an optimum debinding schedule, the heating rate is modulated to avoid bubbling, while the concentration and temperature follow the bubble-point line for the mixture. The results show a strong dependence on the presence of a pre-charge. It is shown that isolation of the pre-charge effect by using temporary lower heating rates results in an optimum schedule for which the process time is reduced by over 70% when compared to a constant heating rate schedule.

Active Brownian motion in a narrow channel

NASA Astrophysics Data System (ADS)

Ao, X.; Ghosh, P. K.; Li, Y.; Schmid, G.; Hänggi, P.; Marchesoni, F.

2014-12-01

We review recent advances in rectification control of artificial microswimmers, also known as Janus particles, diffusing along narrow, periodically corrugated channels. The swimmer self-propulsion mechanism is modeled so as to incorporate a nonzero torque (propulsion chirality). We first summarize the effects of chirality on the autonomous current of microswimmers freely diffusing in channels of different geometries. In particular, left-right and upside-down asymmetric channels are shown to exhibit different transport properties. We then report new results on the dependence of the diffusivity of chiral microswimmers on the channel geometry and their own self-propulsion mechanism. The self-propulsion torque turns out to play a key role as a transport control parameter.

The influence of mass transfer on solute transport in column experiments with an aggregated soil

NASA Astrophysics Data System (ADS)

Roberts, Paul V.; Goltz, Mark N.; Summers, R. Scott; Crittenden, John C.; Nkedi-Kizza, Peter

1987-06-01

The spreading of concentration fronts in dynamic column experiments conducted with a porous, aggregated soil is analyzed by means of a previously documented transport model (DFPSDM) that accounts for longitudinal dispersion, external mass transfer in the boundary layer surrounding the aggregate particles, and diffusion in the intra-aggregate pores. The data are drawn from a previous report on the transport of tritiated water, chloride, and calcium ion in a column filled with Ione soil having an average aggregate particle diameter of 0.34 cm, at pore water velocities from 3 to 143 cm/h. The parameters for dispersion, external mass transfer, and internal diffusion were predicted for the experimental conditions by means of generalized correlations, independent of the column data. The predicted degree of solute front-spreading agreed well with the experimental observations. Consistent with the aggregate porosity of 45%, the tortuosity factor for internal pore diffusion was approximately equal to 2. Quantitative criteria for the spreading influence of the three mechanisms are evaluated with respect to the column data. Hydrodynamic dispersion is thought to have governed the front shape in the experiments at low velocity, and internal pore diffusion is believed to have dominated at high velocity; the external mass transfer resistance played a minor role under all conditions. A transport model such as DFPSDM is useful for interpreting column data with regard to the mechanisms controlling concentration front dynamics, but care must be exercised to avoid confounding the effects of the relevant processes.

The role of boundary variability in polycrystalline grain-boundary diffusion

NASA Astrophysics Data System (ADS)

Moghadam, M. M.; Rickman, J. M.; Harmer, M. P.; Chan, H. M.

2015-01-01

We investigate the impact of grain-boundary variability on mass transport in a polycrystal. More specifically, we perform both numerical and analytical studies of steady-state diffusion in prototypical microstructures in which there is either a discrete spectrum of grain-boundary activation energies or else a complex distribution of grain-boundary character, and hence a continuous spectrum of boundary activation energies. An effective diffusivity is calculated for these structures using simplified multi-state models and, for the case of a continuous spectrum, employing experimentally obtained grain-boundary energy data. We identify different diffusive regimes for these cases and quantify deviations from Arrhenius behavior using effective medium theory. Finally, we examine the diffusion kinetics of a simplified model of an interfacial layering (i.e., complexion) transition.

Hemoglobin diffusion and the dynamics of oxygen capture by red blood cells.

PubMed

Longeville, Stéphane; Stingaciu, Laura-Roxana

2017-09-05

Translational diffusion of macromolecules in cell is generally assumed to be anomalous due high macromolecular crowding of the milieu. Red blood cells are a special case of cells filled quasi exclusively (95% of the dry weight of the cell) with an almost spherical protein: hemoglobin. Hemoglobin diffusion has since a long time been recognized as facilitating the rate of oxygen diffusion through a solution. We address in this paper the question on how hemoglobin diffusion in the red blood cells can help the oxygen capture at the cell level and hence to improve oxygen transport. We report a measurement by neutron spin echo spectroscopy of the diffusion of hemoglobin in solutions with increasing protein concentration. We show that hemoglobin diffusion in solution can be described as Brownian motion up to physiological concentration and that hemoglobin diffusion in the red blood cells and in solutions at similar concentration are the same. Finally, using a simple model and the concentration dependence of the diffusion of the protein reported here, we show that hemoglobin concentration observed in human red blood cells ([Formula: see text]330 g.L -1 ) corresponds to an optimum for oxygen transport for individuals under strong activity.

Hemoglobin diffusion and the dynamics of oxygen capture by red blood cells

DOE PAGES

Longeville, Stéphane; Stingaciu, Laura-Roxana

2017-09-05

Translational diffusion of macromolecules in cell is generally assumed to be anomalous due high macromolecular crowding of the milieu. Red blood cells are a special case of cells filled quasi exclusively (95% of the dry weight of the cell) with an almost spherical protein: hemoglobin. Hemoglobin diffusion has since a long time been recognized as facilitating the rate of oxygen diffusion through a solution. We address in this paper the question on how hemoglobin diffusion in the red blood cells can help the oxygen capture at the cell level and hence to improve oxygen transport. We report a measurement bymore » neutron spin echo spectroscopy of the diffusion of hemoglobin in solutions with increasing protein concentration. We show that hemoglobin diffusion in solution can be described as Brownian motion up to physiological concentration and that hemoglobin diffusion in the red blood cells and in solutions at similar concentration are the same. Finally, using a simple model and the concentration dependence of the diffusion of the protein reported here, we show that hemoglobin concentration observed in human red blood cells (≃330 g.L -1) corresponds to an optimum for oxygen transport for individuals under strong activity.« less

Hemoglobin diffusion and the dynamics of oxygen capture by red blood cells

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

Longeville, Stéphane; Stingaciu, Laura-Roxana

Translational diffusion of macromolecules in cell is generally assumed to be anomalous due high macromolecular crowding of the milieu. Red blood cells are a special case of cells filled quasi exclusively (95% of the dry weight of the cell) with an almost spherical protein: hemoglobin. Hemoglobin diffusion has since a long time been recognized as facilitating the rate of oxygen diffusion through a solution. We address in this paper the question on how hemoglobin diffusion in the red blood cells can help the oxygen capture at the cell level and hence to improve oxygen transport. We report a measurement bymore » neutron spin echo spectroscopy of the diffusion of hemoglobin in solutions with increasing protein concentration. We show that hemoglobin diffusion in solution can be described as Brownian motion up to physiological concentration and that hemoglobin diffusion in the red blood cells and in solutions at similar concentration are the same. Finally, using a simple model and the concentration dependence of the diffusion of the protein reported here, we show that hemoglobin concentration observed in human red blood cells (≃330 g.L -1) corresponds to an optimum for oxygen transport for individuals under strong activity.« less

Mesophyll conductance and reaction-diffusion models for CO2 transport in C3 leaves; needs, opportunities and challenges.

PubMed

Berghuijs, Herman N C; Yin, Xinyou; Ho, Q Tri; Driever, Steven M; Retta, Moges A; Nicolaï, Bart M; Struik, Paul C

2016-11-01

One way to increase potential crop yield could be increasing mesophyll conductance g m . This variable determines the difference between the CO 2 partial pressure in the intercellular air spaces (C i ) and that near Rubisco (C c ). Various methods can determine g m from gas exchange measurements, often combined with measurements of chlorophyll fluorescence or carbon isotope discrimination. g m lumps all biochemical and physical factors that cause the difference between C c and C i . g m appears to vary with C i . This variability indicates that g m does not satisfy the physical definition of a conductance according to Fick's first law and is thus an apparent parameter. Uncertainty about the mechanisms that determine g m can be limited to some extent by using analytical models that partition g m into separate conductances. Such models are still only capable of describing the CO 2 diffusion pathway to a limited extent, as they make implicit assumptions about the position of mitochondria in the cells, which affect the re-assimilation of (photo)respired CO 2 . Alternatively, reaction-diffusion models may be used. Rather than quantifying g m , these models explicitly account for factors that affect the efficiency of CO 2 transport in the mesophyll. These models provide a better mechanistic description of the CO 2 diffusion pathways than mesophyll conductance models. Therefore, we argue that reaction-diffusion models should be used as an alternative to mesophyll conductance models, in case the aim of such a study is to identify traits that can be improved to increase g m . Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Atomistic simulations of carbon diffusion and segregation in liquid silicon

NASA Astrophysics Data System (ADS)

Luo, Jinping; Alateeqi, Abdullah; Liu, Lijun; Sinno, Talid

2017-12-01

The diffusivity of carbon atoms in liquid silicon and their equilibrium distribution between the silicon melt and crystal phases are key, but unfortunately not precisely known parameters for the global models of silicon solidification processes. In this study, we apply a suite of molecular simulation tools, driven by multiple empirical potential models, to compute diffusion and segregation coefficients of carbon at the silicon melting temperature. We generally find good consistency across the potential model predictions, although some exceptions are identified and discussed. We also find good agreement with the range of available experimental measurements of segregation coefficients. However, the carbon diffusion coefficients we compute are significantly lower than the values typically assumed in continuum models of impurity distribution. Overall, we show that currently available empirical potential models may be useful, at least semi-quantitatively, for studying carbon (and possibly other impurity) transport in silicon solidification, especially if a multi-model approach is taken.

Fast Ion and Thermal Plasma Transport in Turbulent Waves in the Large Plasma Device (LAPD)

NASA Astrophysics Data System (ADS)

Zhou, Shu

2011-10-01

The transport of fast ions and thermal plasmas in electrostatic microturbulence is studied. Strong density and potential fluctuations (δn / n ~ δϕ / kTe ~ 0 . 5 , f ~5-50 kHz) are observed in the LAPD in density gradient regions produced by obstacles with slab or cylindrical geometry. Wave characteristics and the associated plasma transport are modified by driving sheared E ×B drift through biasing the obstacle, and by modification of the axial magnetic fields (Bz) and the plasma species. Cross-field plasma transport is suppressed with small bias and large Bz, and is enhanced with large bias and small Bz. Suppressed cross-field thermal transport coincides with a 180° phase shift between the density and potential fluctuations in the radial direction, while the enhanced thermal transport is associated with modes having low mode number (m = 1) and long radial correlation length. Large gyroradius lithium ions (ρfast /ρs ~ 10) orbit through the turbulent region. Scans with a collimated analyzer and with Langmuir probes give detailed profiles of the fast ion spatial-temporal distribution and of the fluctuating fields. Fast-ion transport decreases rapidly with increasing fast-ion gyroradius. Background waves with different scale lengths also alter the fast ion transport: Beam diffusion is smaller in waves with smaller structures (higher mode number); also, coherent waves with long correlation length cause less beam diffusion than turbulent waves. Experimental results agree well with gyro-averaging theory. When the fast ion interacts with the wave for most of a wave period, a transition from super-diffusive to sub-diffusive transport is observed, as predicted by diffusion theory. A Monte Carlo trajectory-following code simulates the interaction of the fast ions with the measured turbulent fields. Good agreement between observation and modeling is observed. Work funded by DOE and NSF and performed at the Basic Plasma Science Facility.

A priori analysis of differential diffusion for model development for scale-resolving simulations

NASA Astrophysics Data System (ADS)

Hunger, Franziska; Dietzsch, Felix; Gauding, Michael; Hasse, Christian

2018-01-01

The present study analyzes differential diffusion and the mechanisms responsible for it with regard to the turbulent/nonturbulent interface (TNTI) with special focus on model development for scale-resolving simulations. In order to analyze differences between resolved and subfilter phenomena, direct numerical simulation (DNS) data are compared with explicitly filtered data. The DNS database stems from a temporally evolving turbulent plane jet transporting two passive scalars with Schmidt numbers of unity and 0.25 presented by Hunger et al. [F. Hunger et al., J. Fluid Mech. 802, R5 (2016), 10.1017/jfm.2016.471]. The objective of this research is twofold: (i) to compare the position of the turbulent-nonturbulent interface between the original DNS data and the filtered data and (ii) to analyze differential diffusion and the impact of the TNTI with regard to scale resolution in the filtered DNS data. For the latter, differential diffusion quantities are studied, clearly showing the decrease of differential diffusion at the resolved scales with increasing filter width. A transport equation for the scalar differences is evaluated. Finally, the existence of large scalar gradients, gradient alignment, and the diffusive fluxes being the physical mechanisms responsible for the separation of the two scalars are compared between the resolved and subfilter scales.

Application of quasi-steady state methods to molecular motor transport on microtubules in fungal hyphae.

PubMed

Dauvergne, Duncan; Edelstein-Keshet, Leah

2015-08-21

We consider bidirectional transport of cargo by molecular motors dynein and kinesin that walk along microtubules, and/or diffuse in the cell. The motors compete to transport cargo in opposite directions with respect to microtubule polarity (towards the plus or minus end of the microtubule). In recent work, Gou et al. (2014) used a hierarchical set of models, each consisting of continuum transport equations to track the evolution of motors and their cargo (early endosomes) in the specific case of the fungus Ustilago maydis. We complement their work using a framework of quasi-steady state analysis developed by Newby and Bressloff (2010) and Bressloff and Newby (2013) to reduce the models to an approximating steady state Fokker-Plank equation. This analysis allows us to find analytic approximations to the steady state solutions in many cases where the full models are not easily solved. Consequently, we can make predictions about parameter dependence of the resulting spatial distributions. We also characterize the overall rates of bulk transport and diffusion, and how these are related to state transition parameters, motor speeds, microtubule polarity distribution, and specific assumptions made. Copyright © 2015 Elsevier Ltd. All rights reserved.

Monte Carlo simulation based on dynamic disorder model in organic semiconductors: From coherent to incoherent transport

NASA Astrophysics Data System (ADS)

Yao, Yao; Si, Wei; Hou, Xiaoyuan; Wu, Chang-Qin

2012-06-01

The dynamic disorder model for charge carrier transport in organic semiconductors has been extensively studied in recent years. Although it is successful on determining the value of bandlike mobility in the organic crystalline materials, the incoherent hopping, the typical transport characteristic in amorphous molecular semiconductors, cannot be described. In this work, the decoherence process is taken into account via a phenomenological parameter, say, decoherence time, and the projective and Monte Carlo method are applied for this model to determine the waiting time and thus the diffusion coefficient. It is obtained that the type of transport is changed from coherent to incoherent with a sufficiently short decoherence time, which indicates the essential role of decoherence time in determining the type of transport in organics. We have also discussed the spatial extent of carriers for different decoherence time, and the transition from delocalization (carrier resides in about 10 molecules) to localization is observed. Based on the experimental results of spatial extent, we estimate that the decoherence time in pentacene has the order of 1 ps. Furthermore, the dependence of diffusion coefficient on decoherence time is also investigated, and corresponding experiments are discussed.

Monte Carlo simulation based on dynamic disorder model in organic semiconductors: from coherent to incoherent transport.

PubMed

Yao, Yao; Si, Wei; Hou, Xiaoyuan; Wu, Chang-Qin

2012-06-21

The dynamic disorder model for charge carrier transport in organic semiconductors has been extensively studied in recent years. Although it is successful on determining the value of bandlike mobility in the organic crystalline materials, the incoherent hopping, the typical transport characteristic in amorphous molecular semiconductors, cannot be described. In this work, the decoherence process is taken into account via a phenomenological parameter, say, decoherence time, and the projective and Monte Carlo method are applied for this model to determine the waiting time and thus the diffusion coefficient. It is obtained that the type of transport is changed from coherent to incoherent with a sufficiently short decoherence time, which indicates the essential role of decoherence time in determining the type of transport in organics. We have also discussed the spatial extent of carriers for different decoherence time, and the transition from delocalization (carrier resides in about 10 molecules) to localization is observed. Based on the experimental results of spatial extent, we estimate that the decoherence time in pentacene has the order of 1 ps. Furthermore, the dependence of diffusion coefficient on decoherence time is also investigated, and corresponding experiments are discussed.

Dynamical patterns and regime shifts in the nonlinear model of soil microorganisms growth

NASA Astrophysics Data System (ADS)

Zaitseva, Maria; Vladimirov, Artem; Winter, Anna-Marie; Vasilyeva, Nadezda

2017-04-01

Dynamical model of soil microorganisms growth and turnover is formulated as a system of nonlinear partial differential equations of reaction-diffusion type. We consider spatial distributions of concentrations of several substrates and microorganisms. Biochemical reactions are modelled by chemical kinetic equations. Transport is modelled by simple linear diffusion for all chemical substances, while for microorganisms we use different transport functions, e.g. some of them can actively move along gradient of substrate concentration, while others cannot move. We solve our model in two dimensions, starting from uniform state with small initial perturbations for various parameters and find parameter range, where small initial perturbations grow and evolve. We search for bifurcation points and critical regime shifts in our model and analyze time-space profile and phase portraits of these solutions approaching critical regime shifts in the system, exploring possibility to detect such shifts in advance. This work is supported by NordForsk, project #81513.

A new solar cycle model including meridional circulation

NASA Technical Reports Server (NTRS)

Wang, Y.-M.; Sheeley, N. R., Jr.; Nash, A. G.

1991-01-01

A kinematic model is presented for the solar cycle which includes not only the transport of magnetic flux by supergranular diffusion and a poleward bulk flow at the sun's surface, but also the effects of turbulent diffusion and an equatorward 'return flow' beneath the surface. As in the earlier models of Babcock and Leighton, the rotational shearing of a subsurface poloidal field generates toroidal flux that erupts at the surface in the form of bipolar magnetic regions. However, such eruptions do not result in any net loss of toroidal flux from the sun (as assumed by Babcock and Leighton); instead, the large-scale toroidal field is destroyed both by 'unwinding' as the local poloidal field reverses its polarity, and by diffusion as the toroidal flux is transported equatorward by the subsurface flow and merged with its opposite hemisphere counterpart. The inclusion of meridional circulation allows stable oscillations of the magnetic field, accompanied by the equatorward progression of flux eruptions, to be achieved even in the absence of a radial gradient in the angular velocity. An illustrative case in which a subsurface flow speed of order 1 m/s and subsurface diffusion rate of order 10 sq km/s yield 22-yr oscillations in qualitative agreement with observations.

Coarsening of physics for biogeochemical model in NEMO

NASA Astrophysics Data System (ADS)

Bricaud, Clement; Le Sommer, Julien; Madec, Gurvan; Deshayes, Julie; Chanut, Jerome; Perruche, Coralie

2017-04-01

Ocean mesoscale and submesoscale turbulence contribute to ocean tracer transport and to shaping ocean biogeochemical tracers distribution. Representing adequately tracer transport in ocean models therefore requires to increase model resolution so that the impact of ocean turbulence is adequately accounted for. But due to supercomputers power and storage limitations, global biogeochemical models are not yet run routinely at eddying resolution. Still, because the "effective resolution" of eddying ocean models is much coarser than the physical model grid resolution, tracer transport can be reconstructed to a large extent by computing tracer transport and diffusion with a model grid resolution close to the effective resolution of the physical model. This observation has motivated the implementation of a new capability in NEMO ocean model (http://www.nemo-ocean.eu/) that allows to run the physical model and the tracer transport model at different grid resolutions. In a first time, we present results obtained with this new capability applied to a synthetic age tracer in a global eddying model configuration. In this model configuration, ocean dynamic is computed at ¼° resolution but tracer transport is computed at 3/4° resolution. The solution obtained is compared to 2 reference setup ,one at ¼° resolution for both physics and passive tracer models and one at 3/4° resolution for both physics and passive tracer model. We discuss possible options for defining the vertical diffusivity coefficient for the tracer transport model based on information from the high resolution grid. We describe the impact of this choice on the distribution and one the penetration of the age tracer. In a second time we present results obtained by coupling the physics with the biogeochemical model PISCES. We look at the impact of this methodology on some tracers distribution and dynamic. The method described here can found applications in ocean forecasting, such as the Copernicus Marine service operated by Mercator-Ocean, and in Earth System Models for climate applications.

Anomalous transport in turbulent plasmas and continuous time random walks

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

Balescu, R.

1995-05-01

The possibility of a model of anomalous transport problems in a turbulent plasma by a purely stochastic process is investigated. The theory of continuous time random walks (CTRW`s) is briefly reviewed. It is shown that a particular class, called the standard long tail CTRW`s is of special interest for the description of subdiffusive transport. Its evolution is described by a non-Markovian diffusion equation that is constructed in such a way as to yield exact values for all the moments of the density profile. The concept of a CTRW model is compared to an exact solution of a simple test problem:more » transport of charged particles in a fluctuating magnetic field in the limit of infinite perpendicular correlation length. Although the well-known behavior of the mean square displacement proportional to {ital t}{sup 1/2} is easily recovered, the exact density profile cannot be modeled by a CTRW. However, the quasilinear approximation of the kinetic equation has the form of a non-Markovian diffusion equation and can thus be generated by a CTRW.« less

Fokker-Planck diffusive law: its interpretation in the context of plasma transport modeling

NASA Astrophysics Data System (ADS)

Sanchez, Raul; Carreras, Ben A.; van Milligen, Boudewijn Ph.

2006-10-01

It was recently proposed that, when building phenomenological transport models for particle transport in tokamaks, use of the Fokker-Planck diffusive law might be preferable to Fick's law to express particle fluxes [1]. In particular, it might offer a possible explanation for the excessive pinch velocites observed in some experimental situations with respect to the values expected from the forces and asymmetries existent in the system. In spite of the fact that Fokker-Planck's law was first proposed many years ago, it produces a series of counterintuitive results that at first sight seem in contradiction with the second law of thermodynamics. In this contribution we will review the basic concepts behind its formulation and show that, through the use of simple examples relevant to plasma physics, the second law of thermodynamics is not violated in any manner if properly used. The benefits of its use within the modelling of transport in tokamaks will also be clarified.REFERENCES: [1] R. Sanchez et al, Phys. Plasmas 12, 056105 (2005); B.Ph. van Milligen et al, Plasma Phys.Contr.Fusion 47, B743 (2005)

Electron temperature critical gradient and transport stiffness in DIII-D

DOE PAGES

Smith, Sterling P.; Petty, Clinton C.; White, Anne E.; ...

2015-07-06

The electron energy flux has been probed as a function of electron temperature gradient on the DIII-D tokamak, in a continuing effort to validate turbulent transport models. In the scan of gradient, a critical electron temperature gradient has been found in the electron heat fluxes and stiffness at various radii in L-mode plasmas. The TGLF reduced turbulent transport model [G.M. Staebler et al, Phys. Plasmas 14, 055909 (2007)] and full gyrokinetic GYRO model [J. Candy and R.E. Waltz, J. Comput. Phys. 186, 545 (2003)] recover the general trend of increasing electron energy flux with increasing electron temperature gradient scale length,more » but they do not predict the absolute level of transport at all radii and gradients. Comparing the experimental observations of incremental (heat pulse) diffusivity and stiffness to the models’ reveals that TGLF reproduces the trends in increasing diffusivity and stiffness with increasing electron temperature gradient scale length with a critical gradient behavior. Furthermore, the critical gradient of TGLF is found to have a dependence on q 95, contrary to the independence of the experimental critical gradient from q 95.« less

Hydrodynamics of steady state phloem transport with radial leakage of solute

PubMed Central

Cabrita, Paulo; Thorpe, Michael; Huber, Gregor

2013-01-01

Long-distance phloem transport occurs under a pressure gradient generated by the osmotic exchange of water associated with solute exchange in source and sink regions. But these exchanges also occur along the pathway, and yet their physiological role has almost been ignored in mathematical models of phloem transport. Here we present a steady state model for transport phloem which allows solute leakage, based on the Navier-Stokes and convection-diffusion equations which describe fluid motion rigorously. Sieve tube membrane permeability Ps for passive solute exchange (and correspondingly, membrane reflection coefficient) influenced model results strongly, and had to lie in the bottom range of the values reported for plant cells for the results to be realistic. This smaller permeability reflects the efficient specialization of sieve tube elements, minimizing any diffusive solute loss favored by the large concentration difference across the sieve tube membrane. We also found there can be a specific reflection coefficient for which pressure profiles and sap velocities can both be similar to those predicted by the Hagen-Poiseuille equation for a completely impermeable tube. PMID:24409189

Modeling of sediment transport in a saltwater lake with supplemental sandy freshwater.

PubMed

Liang, Li; Deng, Yun; Li, Ran; Li, Jia

2018-06-22

Considering the highly complex flow structure of saltwater lakes during freshwater supplementation, a three-dimensional numerical model was developed to simulate suspended sediment transport in saltwater lakes. The model was validated using measurements of the salinity and sediment concentration during a pumping test at Yamdrok Lake. The simulation results were in quantitative agreement with the measured data. The observed and simulated results also indicated that the wind stress and vertical salinity gradient have a significant influence on salinity and sediment transport in a saltwater lake. The validated model was then used to predict and analyze the contributions of wind, the supplement flow rate and salinity stratification to the sediment transport process in Yamdrok Lake during continuous river water supplementation. The simulation results showed that after the sandy river water was continuously discharged into the saltwater lake, the lateral diffusion trends of the sediment exhibited three stages: linear growth in the inflow direction, logarithmic growth in the wind direction, and stabilization. Furthermore, wind was the dominant factor in driving the lake flow pattern and sediment transport. Specifically, wind can effectively reduce the area of the sediment diffusion zone by increasing the lateral sediment carrying and dilution capacities. The effect of inflow on the lake current is negligible, but the extent of the sediment turbidity zone mainly depends on the inflow. Reducing the inflow discharge can decrease the area of the sediment turbidity zone to proportions that far exceed the proportions of inflow discharge reductions. In addition, the high-salinity lake water can support the supplemented freshwater via buoyancy forces, which weaken vertical mixing and sediment settlement and increase lake currents and sediment diffusion near the surface.

Magnon spin transport driven by the magnon chemical potential in a magnetic insulator

NASA Astrophysics Data System (ADS)

Cornelissen, L. J.; Peters, K. J. H.; Bauer, G. E. W.; Duine, R. A.; van Wees, B. J.

2016-07-01

We develop a linear-response transport theory of diffusive spin and heat transport by magnons in magnetic insulators with metallic contacts. The magnons are described by a position-dependent temperature and chemical potential that are governed by diffusion equations with characteristic relaxation lengths. Proceeding from a linearized Boltzmann equation, we derive expressions for length scales and transport coefficients. For yttrium iron garnet (YIG) at room temperature we find that long-range transport is dominated by the magnon chemical potential. We compare the model's results with recent experiments on YIG with Pt contacts [L. J. Cornelissen et al., Nat. Phys. 11, 1022 (2015), 10.1038/nphys3465] and extract a magnon spin conductivity of σm=5 ×105 S/m. Our results for the spin Seebeck coefficient in YIG agree with published experiments. We conclude that the magnon chemical potential is an essential ingredient for energy and spin transport in magnetic insulators.

Diffusive Silicon Nanopore Membranes for Hemodialysis Applications

PubMed Central

Kim, Steven; Feinberg, Benjamin; Kant, Rishi; Chui, Benjamin; Goldman, Ken; Park, Jaehyun; Moses, Willieford; Blaha, Charles; Iqbal, Zohora; Chow, Clarence; Wright, Nathan; Fissell, William H.; Zydney, Andrew; Roy, Shuvo

2016-01-01

Hemodialysis using hollow-fiber membranes provides life-sustaining treatment for nearly 2 million patients worldwide with end stage renal disease (ESRD). However, patients on hemodialysis have worse long-term outcomes compared to kidney transplant or other chronic illnesses. Additionally, the underlying membrane technology of polymer hollow-fiber membranes has not fundamentally changed in over four decades. Therefore, we have proposed a fundamentally different approach using microelectromechanical systems (MEMS) fabrication techniques to create thin-flat sheets of silicon-based membranes for implantable or portable hemodialysis applications. The silicon nanopore membranes (SNM) have biomimetic slit-pore geometry and uniform pores size distribution that allow for exceptional permeability and selectivity. A quantitative diffusion model identified structural limits to diffusive solute transport and motivated a new microfabrication technique to create SNM with enhanced diffusive transport. We performed in vitro testing and extracorporeal testing in pigs on prototype membranes with an effective surface area of 2.52 cm2 and 2.02 cm2, respectively. The diffusive clearance was a two-fold improvement in with the new microfabrication technique and was consistent with our mathematical model. These results establish the feasibility of using SNM for hemodialysis applications with additional scale-up. PMID:27438878

Exact Solutions of Linear Reaction-Diffusion Processes on a Uniformly Growing Domain: Criteria for Successful Colonization

PubMed Central

Simpson, Matthew J

2015-01-01

Many processes during embryonic development involve transport and reaction of molecules, or transport and proliferation of cells, within growing tissues. Mathematical models of such processes usually take the form of a reaction-diffusion partial differential equation (PDE) on a growing domain. Previous analyses of such models have mainly involved solving the PDEs numerically. Here, we present a framework for calculating the exact solution of a linear reaction-diffusion PDE on a growing domain. We derive an exact solution for a general class of one-dimensional linear reaction—diffusion process on 0

Exact solutions of linear reaction-diffusion processes on a uniformly growing domain: criteria for successful colonization.

PubMed

Simpson, Matthew J

2015-01-01

Many processes during embryonic development involve transport and reaction of molecules, or transport and proliferation of cells, within growing tissues. Mathematical models of such processes usually take the form of a reaction-diffusion partial differential equation (PDE) on a growing domain. Previous analyses of such models have mainly involved solving the PDEs numerically. Here, we present a framework for calculating the exact solution of a linear reaction-diffusion PDE on a growing domain. We derive an exact solution for a general class of one-dimensional linear reaction-diffusion process on 0

Diffusion of residual monomer in polymer resins.

PubMed Central

Piver, W T

1976-01-01

A simplified mathematical model which made use of Fick's laws of diffusion written in spherical coordinates was developed to describe the rate of diffusion of residual monomers from polymer resins. The properties of the monomer-polymer system which influenced the amount of monomer remaining in the polymer as a function of time were the diffusivity and solubility of the monomer in the polymer, and the particle size of the polymer resin. This model was used to analyze literature data on the diffusion of residual vinyl chloride monomer in polyvinyl chloride resins made by the suspension process. It was concluded that particle size of the resin was a significant parameter which should be taken advantage of in process equipment designed to remove residual monomer from PVC resins. The diffusivity of the monomer in the polymer was a function of the solubility of the monomer in the polymer. Monomer solubility can be determined from Henry's law. It was suggested that this model could be adapted to describe diffusion of monomers from any monomer-polymer system, and would be a useful approach to modeling the transport of nonreactive chemical additives from plastics. PMID:1026410

Diffusion in random networks: Asymptotic properties, and numerical and engineering approximations

NASA Astrophysics Data System (ADS)

Padrino, Juan C.; Zhang, Duan Z.

2016-11-01

The ensemble phase averaging technique is applied to model mass transport by diffusion in random networks. The system consists of an ensemble of random networks, where each network is made of a set of pockets connected by tortuous channels. Inside a channel, we assume that fluid transport is governed by the one-dimensional diffusion equation. Mass balance leads to an integro-differential equation for the pores mass density. The so-called dual porosity model is found to be equivalent to the leading order approximation of the integration kernel when the diffusion time scale inside the channels is small compared to the macroscopic time scale. As a test problem, we consider the one-dimensional mass diffusion in a semi-infinite domain, whose solution is sought numerically. Because of the required time to establish the linear concentration profile inside a channel, for early times the similarity variable is xt- 1 / 4 rather than xt- 1 / 2 as in the traditional theory. This early time sub-diffusive similarity can be explained by random walk theory through the network. In addition, by applying concepts of fractional calculus, we show that, for small time, the governing equation reduces to a fractional diffusion equation with known solution. We recast this solution in terms of special functions easier to compute. Comparison of the numerical and exact solutions shows excellent agreement.

Understanding Diffusion in Hierarchical Zeolites with House-of-Cards Nanosheets.

PubMed

Bai, Peng; Haldoupis, Emmanuel; Dauenhauer, Paul J; Tsapatsis, Michael; Siepmann, J Ilja

2016-08-23

Introducing mesoporosity to conventional microporous sorbents or catalysts is often proposed as a solution to enhance their mass transport rates. Here, we show that diffusion in these hierarchical materials is more complex and exhibits non-monotonic dependence on sorbate loading. Our atomistic simulations of n-hexane in a model system containing microporous nanosheets and mesopore channels indicate that diffusivity can be smaller than in a conventional zeolite with the same micropore structure, and this observation holds true even if we confine the analysis to molecules completely inside the microporous nanosheets. Only at high sorbate loadings or elevated temperatures, when the mesopores begin to be sufficiently populated, does the overall diffusion in the hierarchical material exceed that in conventional microporous zeolites. Our model system is free of structural defects, such as pore blocking or surface disorder, that are typically invoked to explain slower-than-expected diffusion phenomena in experimental measurements. Examination of free energy profiles and visualization of molecular diffusion pathways demonstrates that the large free energy cost (mostly enthalpic in origin) for escaping from the microporous region into the mesopores leads to more tortuous diffusion paths and causes this unusual transport behavior in hierarchical nanoporous materials. This knowledge allows us to re-examine zero-length-column chromatography data and show that these experimental measurements are consistent with the simulation data when the crystallite size instead of the nanosheet thickness is used for the nominal diffusional length.

Self-diffusion of electrolyte species in model battery electrodes using Magic Angle Spinning and Pulsed Field Gradient Nuclear Magnetic Resonance

NASA Astrophysics Data System (ADS)

Tambio, Sacris Jeru; Deschamps, Michaël; Sarou-Kanian, Vincent; Etiemble, Aurélien; Douillard, Thierry; Maire, Eric; Lestriez, Bernard

2017-09-01

Lithium-ion batteries are electrochemical storage devices using the electrochemical activity of the lithium ion in relation to intercalation compounds owing to mass transport phenomena through diffusion. Diffusion of the lithium ion in the electrode pores has been poorly understood due to the lack of experimental techniques for measuring its self-diffusion coefficient in porous media. Magic-Angle Spinning, Pulsed Field Gradient, Stimulated-Echo Nuclear Magnetic Resonance (MAS-PFG-STE NMR) was used here for the first time to measure the self-diffusion coefficients of the electrolyte species in the LP30 battery electrolyte (i.e. a 1 M solution of LiPF6 dissolved in 1:1 Ethylene Carbonate - Dimethyl Carbonate) in model composites. These composite electrodes were made of alumina, carbon black and PVdF-HFP. Alumina's magnetic susceptibility is close to the measured magnetic susceptibility of the LP30 electrolyte thereby limiting undesirable internal field gradients. Interestingly, the self-diffusion coefficient of lithium ions decreases with increasing carbon content. FIB-SEM was used to describe the 3D geometry of the samples. The comparison between the reduction of self-diffusion coefficients as measured by PFG-NMR and as geometrically derived from FIB/SEM tortuosity values highlights the contribution of specific interactions at the material/electrolyte interface on the lithium transport properties.

Numerical modeling of physical vapor transport under microgravity conditions: Effect of thermal creep and stress

NASA Technical Reports Server (NTRS)

Mackowski, Daniel W.; Knight, Roy W.

1993-01-01

One of the most promising applications of microgravity (micro-g) environments is the manufacture of exotic and high-quality crystals in closed cylindrical ampoules using physical vapor transport (PVT) processes. The quality enhancements are believed to be due to the absence of buoyant convection in the weightless environment - resulting in diffusion-limited transport of the vapor. In a typical experiment, solid-phase sample material is initially contained at one end of the ampoule. The sample is made to sublime into the vapor phase and deposit onto the opposite end by maintaining the source at an elevated temperature with respect to the deposit. Identification of the physical factors governing both the rates and uniformity of crystal growth, and the optimization of the micro-g technology, will require an accurate modeling of the vapor transport within the ampoule. Previous micro-g modeling efforts have approached the problem from a 'classical' convective/diffusion formulation, in which convection is driven by the action of buoyancy on thermal and solutal density differences. The general conclusion of these works have been that in low gravity environments the effect of buoyancy on vapor transport is negligible, and vapor transport occurs in a diffusion-limited mode. However, it has been recently recognized than in the non-isothermal (and often low total pressure) conditions encountered in ampoules, the commonly-assumed no-slip boundary condition to the differential equations governing fluid motion can be grossly unrepresentative of the actual situation. Specifically, the temperature gradients can give rise to thermal creep flows at the ampoule side walls. In addition, temperature gradients in the vapor itself can, through the action of thermal stress, lead to bulk fluid convection.

Non-Linear Dynamics and Emergence in Laboratory Fusion Plasmas

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

Hnat, B.

2011-09-22

Turbulent behaviour of laboratory fusion plasma system is modelled using extended Hasegawa-Wakatani equations. The model is solved numerically using finite difference techniques. We discuss non-linear effects in such a system in the presence of the micro-instabilities, specifically a drift wave instability. We explore particle dynamics in different range of parameters and show that the transport changes from diffusive to non-diffusive when large directional flows are developed.

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

Guo, X.; Florinski, V.

We present a new model that couples galactic cosmic-ray (GCR) propagation with magnetic turbulence transport and the MHD background evolution in the heliosphere. The model is applied to the problem of the formation of corotating interaction regions (CIRs) during the last solar minimum from the period between 2007 and 2009. The numerical model simultaneously calculates the large-scale supersonic solar wind properties and its small-scale turbulent content from 0.3 au to the termination shock. Cosmic rays are then transported through the background, and thus computed, with diffusion coefficients derived from the solar wind turbulent properties, using a stochastic Parker approach. Ourmore » results demonstrate that GCR variations depend on the ratio of diffusion coefficients in the fast and slow solar winds. Stream interfaces inside the CIRs always lead to depressions of the GCR intensity. On the other hand, heliospheric current sheet (HCS) crossings do not appreciably affect GCR intensities in the model, which is consistent with the two observations under quiet solar wind conditions. Therefore, variations in diffusion coefficients associated with CIR stream interfaces are more important for GCR propagation than the drift effects of the HCS during a negative solar minimum.« less

Transverse thermal conductivity of porous materials made from aligned nano- and microcylindrical pores

NASA Astrophysics Data System (ADS)

Prasher, Ravi

2006-09-01

Nanoporous and microporous materials made from aligned cylindrical pores play important roles in present technologies and will play even bigger roles in future technologies. The insight into the phonon thermal conductivity of these materials is important and relevant in many technologies and applications. Since the mean free path of phonons can be comparable to the pore size and interpore distance, diffusion-approximation based effective medium models cannot be used to predict the thermal conductivity of these materials. Strictly speaking, the Boltzmann transport equation (BTE) must be solved to capture the ballistic nature of thermal transport; however, solving BTE in such a complex network of pores is impractical. As an alternative, we propose an approximate ballistic-diffusive microscopic effective medium model for predicting the thermal conductivity of phonons in two-dimensional nanoporous and microporous materials made from aligned cylindrical pores. The model captures the size effects due to the pore diameter and the interpore distance and reduces to diffusion-approximation based models for macroporous materials. The results are in good agreement with experimental data.

Coherent pulses in the diffusive transport of charged particles`

NASA Technical Reports Server (NTRS)

Kota, J.

1994-01-01

We present exact solutions to the diffusive transport of charged particles following impulsive injection for a simple model of scattering. A modified, two-parameter relaxation-time model is considered that simulates the low rate of scattering through perpendicular pitch-angle. Scattering is taken to be isotropic within each of the foward- and backward-pointing hemispheres, respectively, but, at the same time, a reduced rate of sccattering is assumed from one hemisphere to the other one. By applying a technique of Fourier- and Laplace-transform, the inverse transformation can be performed and exact solutions can be reached. By contrast with the first, and so far only exact solutions of Federov and Shakov, this wider class of solutions gives rise to coherent pulses to appear. The present work addresses omnidirectional densities for isotropic injection from an instantaneous and localized source. The dispersion relations are briefly discussed. We find, for this particular model, two diffusive models to exist up to a certain limiting wavenumber. The corresponding eigenvalues are real at the lowest wavenumbers. Complex eigenvalues, which are responsible for coherent pulses, appear at higher wavenumbers.

Applicability of a diffusion model to lateral transport in the terrestrial and lunar exospheres.

NASA Technical Reports Server (NTRS)

Hodges, R. R., Jr.

1972-01-01

Kinetic theory is used to determine a series expansion of the vertical flux of particles in an exosphere in terms of time and space derivatives of particle concentration, exobase velocity, and temperature. For sufficiently large scale variations of these parameters in time and space, the series can be truncated to a form that is similar to a diffusion equation. Owing to this analogy, it is possible to unite the mathematical description of molecular diffusion, which governs thermospheric flow, and the corresponding exospheric equation by using effective transport coefficients which change smoothly with altitude through the transition from thermosphere to exosphere. A new definition of the exobase for lateral flow emerges from the analogy of exospheric and thermospheric diffusion, as the altitude where the horizontal mean free path length equals the mean horizontal extent of ballistic trajectories of the transported gas, as opposed to the scale height of the dominant gas which determines the exobase for escape. It is shown that the approximation of exospheric lateral flow as a diffusion process is applicable to global scale problems concerning terrestrial helium and heavier gases, and lunar gases heavier than helium.

Light source distribution and scattering phase function influence light transport in diffuse multi-layered media

NASA Astrophysics Data System (ADS)

Vaudelle, Fabrice; L'Huillier, Jean-Pierre; Askoura, Mohamed Lamine

2017-06-01

Red and near-Infrared light is often used as a useful diagnostic and imaging probe for highly scattering media such as biological tissues, fruits and vegetables. Part of diffusively reflected light gives interesting information related to the tissue subsurface, whereas light recorded at further distances may probe deeper into the interrogated turbid tissues. However, modelling diffusive events occurring at short source-detector distances requires to consider both the distribution of the light sources and the scattering phase functions. In this report, a modified Monte Carlo model is used to compute light transport in curved and multi-layered tissue samples which are covered with a thin and highly diffusing tissue layer. Different light source distributions (ballistic, diffuse or Lambertian) are tested with specific scattering phase functions (modified or not modified Henyey-Greenstein, Gegenbauer and Mie) to compute the amount of backscattered and transmitted light in apple and human skin structures. Comparisons between simulation results and experiments carried out with a multispectral imaging setup confirm the soundness of the theoretical strategy and may explain the role of the skin on light transport in whole and half-cut apples. Other computational results show that a Lambertian source distribution combined with a Henyey-Greenstein phase function provides a higher photon density in the stratum corneum than in the upper dermis layer. Furthermore, it is also shown that the scattering phase function may affect the shape and the magnitude of the Bidirectional Reflectance Distribution (BRDF) exhibited at the skin surface.

k-space image correlation to probe the intracellular dynamics of gold nanoparticles

NASA Astrophysics Data System (ADS)

Bouzin, M.; Sironi, L.; Chirico, G.; D'Alfonso, L.; Inverso, D.; Pallavicini, P.; Collini, M.

2016-04-01

The collective action of dynein, kinesin and myosin molecular motors is responsible for the intracellular active transport of cargoes, vesicles and organelles along the semi-flexible oriented filaments of the cytoskeleton. The overall mobility of the cargoes upon binding and unbinding to motor proteins can be modeled as an intermittency between Brownian diffusion in the cell cytoplasm and active ballistic excursions along actin filaments or microtubules. Such an intermittent intracellular active transport, exhibited by star-shaped gold nanoparticles (GNSs, Gold Nanostars) upon internalization in HeLa cancer cells, is investigated here by combining live-cell time-lapse confocal reflectance microscopy and the spatio-temporal correlation, in the reciprocal Fourier space, of the acquired image sequences. At first, the analytical theoretical framework for the investigation of a two-state intermittent dynamics is presented for Fourier-space Image Correlation Spectroscopy (kICS). Then simulated kICS correlation functions are employed to evaluate the influence of, and sensitivity to, all the kinetic and dynamic parameters the model involves (the transition rates between the diffusive and the active transport states, the diffusion coefficient and drift velocity of the imaged particles). The optimal procedure for the analysis of the experimental data is outlined and finally exploited to derive whole-cell maps for the parameters underlying the GNSs super-diffusive dynamics. Applied here to the GNSs subcellular trafficking, the proposed kICS analysis can be adopted for the characterization of the intracellular (super-) diffusive dynamics of any fluorescent or scattering biological macromolecule.

Transport properties of active Brownian particles in a modified energy-depot model driven by correlated noises

NASA Astrophysics Data System (ADS)

Guan, Lin; Fang, Yuwen; Li, Kongzhai; Zeng, Chunhua; Yang, Fengzao

2018-09-01

In this paper, we investigate the role of correlated multiplicative (κ1) and additive (κ2) noises in a modified energy conversion depot model, at which it is added a linear term in the conversion of internal energy of active Brownian particles (ABPs). The linear term (a1 ≠ 0 . 0) in energy conversion model breaks the symmetry of the potential to generate motion of the ABPs with a net transport velocity. Adopt a nonlinear Langevin approach, the transport properties of the ABPs have been discussed, and our results show that: (i) the transport velocity <υ1 > of the ABPs are always positive whether the correlation intensity λ = 0 . 0 or not; (ii) for a small value of the multiplicative noise intensity κ1, the variation of <υ1 > with λ shows a minimum, there exists an optimal value of the correlation intensity λ at which the <υ1 > of the ABPs is minimized. But for a large value of κ1, the <υ1 > monotonically decreases; (iii) the transport velocity <υ1 > increases with the increase of the κ1 or κ2, i.e., the multiplicative or additive noise can facilitate the transport of the ABPs; and (iv) the effective diffusion increases with the increase of a1, namely, the linear term in modified energy conversion model of the ABPs can enhance the diffusion of the ABPs.

Pharmacokinetic Model of the Transport of Fast-Acting Insulin From the Subcutaneous and Intradermal Spaces to Blood.

PubMed

Lv, Dayu; Kulkarni, Sandip D; Chan, Alice; Keith, Stephen; Pettis, Ron; Kovatchev, Boris P; Farhi, Leon S; Breton, Marc D

2015-07-01

Pharmacokinetic (PK) models describing the transport of insulin from the injection site to blood assist clinical decision making and are part of in silico platforms for developing and testing of insulin delivery strategies for treatment of patients with diabetes. The ability of these models to accurately describe all facets of the in vivo insulin transport is therefore critical for their application. Here, we propose a new model of fast-acting insulin analogs transport from the subcutaneous and intradermal spaces to blood that can accommodate clinically observed biphasic appearance and delayed clearance of injected insulin, 2 phenomena that are not captured by existing PK models. To develop the model we compare 9 insulin transport PK models which describe hypothetical insulin delivery pathways potentially capable of approximating biphasic appearance of exogenous insulin. The models are tested with respect to their ability to describe clinical data from 10 healthy volunteers which received 1 subcutaneous and 2 intradermal insulin injections on 3 different occasions. The optimal model, selected based on information and posterior identifiability criteria, assumes that insulin is delivered at the administrative site and is then transported to the bloodstream via 2 independent routes (1) diffusion-like process to the blood and (2) combination of diffusion-like processes followed by an additional compartment before entering the blood. This optimal model accounts for biphasic appearance and delayed clearance of exogenous insulin. It agrees better with the clinical data as compared to commonly used models and is expected to improve the in silico development and testing of insulin treatment strategies, including artificial pancreas systems. © 2015 Diabetes Technology Society.

Ebullition, Plant-Mediated Transport, and Subsurface Horizontal Water Flow Dominate Methane Transport in an Arctic Sphagnum Bog

NASA Astrophysics Data System (ADS)

Wehr, R. A.; McCalley, C. K.; Logan, T. A.; Chanton, J.; Crill, P. M.; Rich, V. I.; Saleska, S. R.

2017-12-01

Emission of the greenhouse gas methane from wetlands is of prime concern in the prediction of climate change - especially emission associated with thawing permafrost, which may drive a positive feedback loop of emission and warming. In addition to the biochemistry of methane production and consumption, wetland methane emission depends critically on the transport mechanisms by which methane moves through and out of the ecosystem. We therefore developed a model of methane biochemistry and transport for a sphagnum bog representing an intermediate permafrost thaw stage in Stordalen Mire, Sweden. In order to simultaneously reproduce measured profiles of both the concentrations and isotopic compositions of both methane and carbon dioxide in the peat pore water (Fig. 1) - as well as the surface methane emission - it was necessary for the model to include ebullition, plant-mediated transport via aerenchyma, and subsurface horizontal water flow. Diffusion of gas through the pore water was relatively unimportant. As a result, 90% of the produced methane escaped the wetland rather than being consumed by methanotrophic organisms in the near-surface pore water. Our model provides a comprehensive picture of methane emission from this bog site by quantifying the vertical profiles of: acetoclastic methanogenesis, hydrogenotrophic methanogenesis, methane oxidation, aerobic respiration, ebullition, plant-mediated transport, subsurface horizontal water flow, and diffusion.

A one-dimensional heat-transport model for conduit flow in karst aquifers

USGS Publications Warehouse

Long, Andrew J.; Gilcrease, P.C.

2009-01-01

A one-dimensional heat-transport model for conduit flow in karst aquifers is presented as an alternative to two or three-dimensional distributed-parameter models, which are data intensive and require knowledge of conduit locations. This model can be applied for cases where water temperature in a well or spring receives all or part of its water from a phreatic conduit. Heat transport in the conduit is simulated by using a physically-based heat-transport equation that accounts for inflow of diffuse flow from smaller openings and fissures in the surrounding aquifer during periods of low recharge. Additional diffuse flow that is within the zone of influence of the well or spring but has not interacted with the conduit is accounted for with a binary mixing equation to proportion these different water sources. The estimation of this proportion through inverse modeling is useful for the assessment of contaminant vulnerability and well-head or spring protection. The model was applied to 7 months of continuous temperature data for a sinking stream that recharges a conduit and a pumped well open to the Madison aquifer in western South Dakota. The simulated conduit-flow fraction to the well ranged from 2% to 31% of total flow, and simulated conduit velocity ranged from 44 to 353 m/d.

Lévy walks

NASA Astrophysics Data System (ADS)

Zaburdaev, V.; Denisov, S.; Klafter, J.

2015-04-01

Random walk is a fundamental concept with applications ranging from quantum physics to econometrics. Remarkably, one specific model of random walks appears to be ubiquitous across many fields as a tool to analyze transport phenomena in which the dispersal process is faster than dictated by Brownian diffusion. The Lévy-walk model combines two key features, the ability to generate anomalously fast diffusion and a finite velocity of a random walker. Recent results in optics, Hamiltonian chaos, cold atom dynamics, biophysics, and behavioral science demonstrate that this particular type of random walk provides significant insight into complex transport phenomena. This review gives a self-consistent introduction to Lévy walks, surveys their existing applications, including latest advances, and outlines further perspectives.

Micro-porous layer stochastic reconstruction and transport parameter determination

NASA Astrophysics Data System (ADS)

El Hannach, Mohamed; Singh, Randhir; Djilali, Ned; Kjeang, Erik

2015-05-01

The Micro-Porous Layer (MPL) is a porous, thin layer commonly used in fuel cells at the interfaces between the catalyst layers and gas diffusion media. It is generally made from spherical carbon nanoparticles and PTFE acting as hydrophobic agent. The scale and brittle nature of the MPL structure makes it challenging to study experimentally. In the present work, a 3D stochastic model is developed to virtually reconstruct the MPL structure. The carbon nanoparticle and PTFE phases are fully distinguished by the algorithm. The model is shown to capture the actual structural morphology of the MPL and is validated by comparing the results to available experimental data. The model shows a good capability in generating a realistic MPL successfully using a set of parameters introduced to capture specific morphological features of the MPL. A numerical model that resolves diffusive transport at the pore scale is used to compute the effective transport properties of the reconstructed MPLs. A parametric study is conducted to illustrate the capability of the model as an MPL design tool that can be used to guide and optimize the functionality of the material.

Protein diffusiophoresis and salt osmotic diffusion in aqueous solutions.

PubMed

Annunziata, Onofrio; Buzatu, Daniela; Albright, John G

2012-10-25

Diffusion of a solute can be induced by the concentration gradient of another solute in solution. This transport mechanism is known as cross-diffusion. We have investigated cross-diffusion in a ternary protein-salt-water system. Specifically, we measured the two cross-diffusion coefficients for the lysozyme-NaCl-water system at 25 °C and pH 4.5 as a function of protein and salt concentrations by Rayleigh interferometry. One cross-diffusion coefficient characterizes salt osmotic diffusion induced by a protein concentration gradient, and is related to protein-salt thermodynamic interactions as described by the theories of Donnan membrane equilibrium and protein preferential hydration. The other cross-diffusion coefficient characterizes protein diffusiophoresis induced by a salt concentration gradient, and is described as the difference between a preferential-interaction coefficient and a transport parameter. We first relate our experimental results to the protein net charge and the thermodynamic excess of water near the protein surface. We then extract the Stefan-Maxwell diffusion coefficient describing protein-salt interactions in water. We find that the value of this coefficient is negative, contrary to the friction interpretation of Stefan-Maxwell equations. This result is explained by considering protein hydration. Finally, protein diffusiophoresis is quantitatively examined by considering electrophoretic and hydration effects on protein migration and utilized to accurately estimate lysozyme electrophoretic mobility. To our knowledge, this is the first time that protein diffusiophoresis has been experimentally characterized and a protein-salt Stefan-Maxwell diffusion coefficient reported. This work represents a significant contribution for understanding and modeling the effect of concentration gradients in protein-salt aqueous systems relevant to diffusion-based mass-transfer technologies and transport in living systems.

Suspended sediment diffusion mechanisms in the Yangtze Estuary influenced by wind fields

NASA Astrophysics Data System (ADS)

Wang, Lihua; Zhou, Yunxuan; Shen, Fang

2018-01-01

The complexity of suspended sediment concentration (SSC) distribution and diffusion has been widely recognized because it is influenced by sediment supply and various hydrodynamic forcing conditions that vary over space and over time. Sediment suspended by waves and transported by currents are the dominant sediment transport mechanisms in estuarine and coastal areas. However, it is unclear to what extent the SSC distribution is impacted by each hydrodynamic factor. Research on the quantitative influence of wind fields on the SSC diffusion range will contribute to a better understanding of the characteristics of sediment transport change and sedimentary geomorphic evolution. This study determined SSC from three Envisat Medium-Resolution Imaging Spectrometer acquisitions, covering the Yangtze Estuary and adjacent water area under the same season and tidal conditions but with varying wind conditions. SSC was examined based on the Semi-Empirical Radiative Transfer model, which has been well validated with the observation data. Integrating the corresponding wind field information from European Centre for Medium-Range Weather Forecasts further facilitated the discussion of wind fields affecting SSC, and in turn the influence of water and suspended sediment transportation and diffusion in the Yangtze estuarine and coastal area. The results demonstrated that the SSC present much more distinctive fluvial features in the inner estuary and wind fields are one of the major factors controlling the range of turbid water diffusion.

A class of exact solutions for biomacromolecule diffusion-reaction in live cells.

PubMed

Sadegh Zadeh, Kouroush; Montas, Hubert J

2010-06-07

A class of novel explicit analytic solutions for a system of n+1 coupled partial differential equations governing biomolecular mass transfer and reaction in living organisms are proposed, evaluated, and analyzed. The solution process uses Laplace and Hankel transforms and results in a recursive convolution of an exponentially scaled Gaussian with modified Bessel functions. The solution is developed for wide range of biomolecular binding kinetics from pure diffusion to multiple binding reactions. The proposed approach provides solutions for both Dirac and Gaussian laser beam (or fluorescence-labeled biomacromolecule) profiles during the course of a Fluorescence Recovery After Photobleaching (FRAP) experiment. We demonstrate that previous models are simplified forms of our theory for special cases. Model analysis indicates that at the early stages of the transport process, biomolecular dynamics is governed by pure diffusion. At large times, the dominant mass transfer process is effective diffusion. Analysis of the sensitivity equations, derived analytically and verified by finite difference differentiation, indicates that experimental biologists should use full space-time profile (instead of the averaged time series) obtained at the early stages of the fluorescence microscopy experiments to extract meaningful physiological information from the protocol. Such a small time frame requires improved bioinstrumentation relative to that in use today. Our mathematical analysis highlights several limitations of the FRAP protocol and provides strategies to improve it. The proposed model can be used to study biomolecular dynamics in molecular biology, targeted drug delivery in normal and cancerous tissues, motor-driven axonal transport in normal and abnormal nervous systems, kinetics of diffusion-controlled reactions between enzyme and substrate, and to validate numerical simulators of biological mass transport processes in vivo. Copyright (c) 2010 Elsevier Ltd. All rights reserved.

Modelling of the mercury loss in fluorescent lamps under the influence of metal oxide coatings

NASA Astrophysics Data System (ADS)

Santos Abreu, A.; Mayer, J.; Lenk, D.; Horn, S.; Konrad, A.; Tidecks, R.

2016-11-01

The mercury transport and loss mechanisms in the metal oxide coatings of mercury low pressure discharge fluorescent lamps have been investigated. An existing model based on a ballistic process is discussed in the context of experimental mercury loss data. Two different approaches to the modeling of the mercury loss have been developed. The first one is based on mercury transition rates between the plasma, the coating, and the glass without specifying the underlying physical processes. The second one is based on a transport process driven by diffusion and a binding process of mercury reacting to mercury oxide inside the layers. Moreover, we extended the diffusion based model to handle multi-component coatings. All approaches are applied to describe mercury loss experiments under the influence of an Al 2 O 3 coating.

Transport processes in partially saturate concrete: Testing and liquid properties

NASA Astrophysics Data System (ADS)

Villani, Chiara

The measurement of transport properties of concrete is considered by many to have the potential to serve as a performance criterion that can be related to concrete durability. However, the sensitivity of transport tests to several parameters combined with the low permeability of concrete complicates the testing. Gas permeability and diffusivity test methods are attractive due to the ease of testing, their non-destructive nature and their potential to correlate to in-field carbonation of reinforced concrete structures. This work was aimed at investigating the potential of existing gas transport tests as a way to reliably quantify transport properties in concrete. In this study gas permeability and diffusivity test methods were analyzed comparing their performance in terms of repeatability and variability. The influence of several parameters was investigated such as moisture content, mixture proportions and gas flow. A closer look to the influence of pressure revealed an anomalous trend of permeability with respect to pressure. An alternative calculation is proposed in an effort to move towards the determination of intrinsic material properties that can serve as an input for service life prediction models. The impact of deicing salts exposure was also analyzed with respect to their alteration of the degree of saturation as this may affect gas transport in cementitious materials. Limited information were previously available on liquid properties over a wide range of concentrations. To overcome this limitation, this study quantified surface tension, viscosity in presence of deicing salts in a broad concentration range and at different temperatures. Existing models were applied to predict the change of fluid properties during drying. Vapor desorption isotherms were obtained to investigate the influence of deicing salts presence on the non-linear moisture diffusion coefficient. Semi-empirical models were used to quantify the initiation and the rate of drying using liquid properties and pore structure information as inputs. Concrete exposed to deicing salts resulted to have a reduced gas transport due to the higher degree of saturation (DOS). The higher DOS is believed to contribute to the premature deterioration observed in concrete pavements exposed to deicing salts. Moisture diffusion and moisture profiles in concrete are known to directly relate with the stresses generated during shrinkage and creep mechanisms. The alteration due to the presence of shrinkage reducing admixtures on drying was also investigated in this work. Liquid properties were used to predict the diffusion coefficient in presence of SRA. Moisture profiles obtained using Fick's second law for diffusion were compared to relative humidity profiles measured on concrete slabs. Results confirm that a qualitative prediction of drying in concrete elements is realistic when using this type of approach.

Space shuttle exhaust plumes in the lower thermosphere: Advective transport and diffusive spreading

NASA Astrophysics Data System (ADS)

Stevens, Michael H.; Lossow, Stefan; Siskind, David E.; Meier, R. R.; Randall, Cora E.; Russell, James M.; Urban, Jo; Murtagh, Donal

2014-02-01

The space shuttle main engine plume deposited between 100 and 115 km altitude is a valuable tracer for global-scale dynamical processes. Several studies have shown that this plume can reach the Arctic or Antarctic to form bursts of polar mesospheric clouds (PMCs) within a few days. The rapid transport of the shuttle plume is currently not reproduced by general circulation models and is not well understood. To help delineate the issues, we present the complete satellite datasets of shuttle plume observations by the Sounding of the Atmosphere using Broadband Emission Radiometry instrument and the Sub-Millimeter Radiometer instrument. From 2002 to 2011 these two instruments observed 27 shuttle plumes in over 600 limb scans of water vapor emission, from which we derive both advective meridional transport and diffusive spreading. Each plume is deposited at virtually the same place off the United States east coast so our results are relevant to northern mid-latitudes. We find that the advective transport for the first 6-18 h following deposition depends on the local time (LT) of launch: shuttle plumes deposited later in the day (~13-22 LT) typically move south whereas they otherwise typically move north. For these younger plumes rapid transport is most favorable for launches at 6 and 18 LT, when the displacement is 10° in latitude corresponding to an average wind speed of 30 m/s. For plumes between 18 and 30 h old some show average sustained meridional speeds of 30 m/s. For plumes between 30 and 54 h old the observations suggest a seasonal dependence to the meridional transport, peaking near the beginning of year at 24 m/s. The diffusive spreading of the plume superimposed on the transport is on average 23 m/s in 24 h. The plume observations show large variations in both meridional transport and diffusive spreading so that accurate modeling requires knowledge of the winds specific to each case. The combination of transport and spreading from the STS-118 plume in August 2007 formed bright PMCs between 75 and 85°N a day after launch. These are the highest latitude Arctic PMCs formed by shuttle exhaust reported to date.

Neutral solute transport across osteochondral interface: A finite element approach.

PubMed

Arbabi, Vahid; Pouran, Behdad; Weinans, Harrie; Zadpoor, Amir A

2016-12-08

Investigation of the solute transfer across articular cartilage and subchondral bone plate could nurture the understanding of the mechanisms of osteoarthritis (OA) progression. In the current study, we approached the transport of neutral solutes in human (slight OA) and equine (healthy) samples using both computed tomography and biphasic-solute finite element modeling. We developed a multi-zone biphasic-solute finite element model (FEM) accounting for the inhomogeneity of articular cartilage (superficial, middle and deep zones) and subchondral bone plate. Fitting the FEM model to the concentration-time curves of the cartilage and the equilibrium concentration of the subchondral plate/calcified cartilage enabled determination of the diffusion coefficients in the superficial, middle and deep zones of cartilage and subchondral plate. We found slightly higher diffusion coefficients for all zones in the human samples as compared to the equine samples. Generally the diffusion coefficient in the superficial zone of human samples was about 3-fold higher than the middle zone, the diffusion coefficient of the middle zone was 1.5-fold higher than that of the deep zone, and the diffusion coefficient of the deep zone was 1.5-fold higher than that of the subchondral plate/calcified cartilage. Those ratios for equine samples were 9, 2 and 1.5, respectively. Regardless of the species considered, there is a gradual decrease of the diffusion coefficient as one approaches the subchondral plate, whereas the rate of decrease is dependent on the type of species. Copyright © 2016 Elsevier Ltd. All rights reserved.

Semianalytical Solutions for Transport in Aquifer and Fractured Clay Matrix System

EPA Science Inventory

A three-dimensional mathematical model that describes transport of contaminant in a horizontal aquifer with simultaneous diffusion into a fractured clay formation is proposed. A group of analytical solutions is derived based on specific initial and boundary conditions as well as ...

Diffusion-advection within dynamic biological gaps driven by structural motion

NASA Astrophysics Data System (ADS)

Asaro, Robert J.; Zhu, Qiang; Lin, Kuanpo

2018-04-01

To study the significance of advection in the transport of solutes, or particles, within thin biological gaps (channels), we examine theoretically the process driven by stochastic fluid flow caused by random thermal structural motion, and we compare it with transport via diffusion. The model geometry chosen resembles the synaptic cleft; this choice is motivated by the cleft's readily modeled structure, which allows for well-defined mechanical and physical features that control the advection process. Our analysis defines a Péclet-like number, AD, that quantifies the ratio of time scales of advection versus diffusion. Another parameter, AM, is also defined by the analysis that quantifies the full potential extent of advection in the absence of diffusion. These parameters provide a clear and compact description of the interplay among the well-defined structural, geometric, and physical properties vis-a ̀-vis the advection versus diffusion process. For example, it is found that AD˜1 /R2 , where R is the cleft diameter and hence diffusion distance. This curious, and perhaps unexpected, result follows from the dependence of structural motion that drives fluid flow on R . AM, on the other hand, is directly related (essentially proportional to) the energetic input into structural motion, and thereby to fluid flow, as well as to the mechanical stiffness of the cleftlike structure. Our model analysis thus provides unambiguous insight into the prospect of competition of advection versus diffusion within biological gaplike structures. The importance of the random, versus a regular, nature of structural motion and of the resulting transient nature of advection under random motion is made clear in our analysis. Further, by quantifying the effects of geometric and physical properties on the competition between advection and diffusion, our results clearly demonstrate the important role that metabolic energy (ATP) plays in this competitive process.

Transport of solar electrons in the turbulent interplanetary magnetic field

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

Ablaßmayer, J.; Tautz, R. C., E-mail: robert.c.tautz@gmail.com; Dresing, N., E-mail: dresing@physik.uni-kiel.de

2016-01-15

The turbulent transport of solar energetic electrons in the interplanetary magnetic field is investigated by means of a test-particle Monte-Carlo simulation. The magnetic fields are modeled as a combination of the Parker field and a turbulent component. In combination with the direct calculation of diffusion coefficients via the mean-square displacements, this approach allows one to analyze the effect of the initial ballistic transport phase. In that sense, the model complements the main other approach in which a transport equation is solved. The major advancement is that, by recording the flux of particles arriving at virtual detectors, intensity and anisotropy-time profilesmore » can be obtained. Observational indications for a longitudinal asymmetry can thus be explained by tracing the diffusive spread of the particle distribution. The approach may be of future help for the systematic interpretation of observations for instance by the solar terrestrial relations observatory (STEREO) and advanced composition explorer (ACE) spacecrafts.« less

The vacuole system is a significant intracellular pathway for longitudinal solute transport in basidiomycete fungi.

PubMed

Darrah, P R; Tlalka, M; Ashford, A; Watkinson, S C; Fricker, M D

2006-07-01

Mycelial fungi have a growth form which is unique among multicellular organisms. The data presented here suggest that they have developed a unique solution to internal solute translocation involving a complex, extended vacuole. In all filamentous fungi examined, this extended vacuole forms an interconnected network, dynamically linked by tubules, which has been hypothesized to act as an internal distribution system. We have tested this hypothesis directly by quantifying solute movement within the organelle by photobleaching a fluorescent vacuolar marker. Predictive simulation models were then used to determine the transport characteristics over extended length scales. This modeling showed that the vacuolar organelle forms a functionally important, bidirectional diffusive transport pathway over distances of millimeters to centimeters. Flux through the pathway is regulated by the dynamic tubular connections involving homotypic fusion and fission. There is also a strongly predicted interaction among vacuolar organization, predicted diffusion transport distances, and the architecture of the branching colony margin.

The Steady-State Transport of Oxygen through Hemoglobin Solutions

PubMed Central

Keller, K. H.; Friedlander, S. K.

1966-01-01

The steady-state transport of oxygen through hemoglobin solutions was studied to identify the mechanism of the diffusion augmentation observed at low oxygen tensions. A novel technique employing a platinum-silver oxygen electrode was developed to measure the effective diffusion coefficient of oxygen in steady-state transport. The measurements were made over a wider range of hemoglobin and oxygen concentrations than previously reported. Values of the Brownian motion diffusion coefficient of oxygen in hemoglobin solution were obtained as well as measurements of facilitated transport at low oxygen tensions. Transport rates up to ten times greater than ordinary diffusion rates were found. Predictions of oxygen flux were made assuming that the oxyhemoglobin transport coefficient was equal to the Brownian motion diffusivity which was measured in a separate set of experiments. The close correlation between prediction and experiment indicates that the diffusion of oxyhemoglobin is the mechanism by which steady-state oxygen transport is facilitated. PMID:5943608

pH Dependent but not P-gp Dependent Bidirectional Transport Study of S-propranolol: The Importance of Passive Diffusion.

PubMed

Zheng, Yi; Benet, Leslie Z; Okochi, Hideaki; Chen, Xijing

2015-08-01

Recent controversial publications, citing studies purporting to show that P-gp mediates the transport of propranolol, proposed that passive biological membrane transport is negligible. Based on the BDDCS, the extensively metabolized-highly permeable-highly soluble BDDCS class 1 drug, propranolol, shows a high passive permeability at concentrations unrestricted by solubility that can overwhelm any potential transporter effects. Here we reinvestigate the effects of passive diffusion and carrier-mediated transport on S-propranolol. Bidirectional permeability and inhibition of efflux transport studies were carried out in MDCK, MDCK-MDR1 and Caco-2 cell lines at different concentrations. Transcellular permeability studies were conducted at different apical pHs in the rat jejunum Ussing chamber model and PAMPA system. S-propranolol exhibited efflux ratios lower than 1 in MDCK, MDCK-MDR1 and Caco-2 cells. No significant differences of Papp, B->A in the presence and absence of the efflux inhibitor GG918 were observed. However, an efflux ratio of 3.63 was found at apical pH 6.5 with significant decrease in Papp, A->B and increase in Papp, B->A compared to apical pH 7.4 in Caco-2 cell lines. The pH dependent permeability was confirmed in the Ussing chamber model. S-propranolol flux was unchanged during inhibition by verapamil and rifampin. Furthermore, pH dependent permeability was also observed in the PAMPA system. S-propranolol does not exhibit active transport as proposed previously. The "false" positive efflux ratio can be explained by the pH partition theory. As expected, passive diffusion, but not active transport, plays the primary role in the permeability of the BDDCS class 1 drug propranolol.

pH dependent but not P-gp dependent bidirectional transport study of S-propranolol: the importance of passive diffusion

PubMed Central

Zheng, Yi; Benet, Leslie Z.; Okochi, Hideaki; Chen, Xijing

2016-01-01

Purpose Recent controversial publications, citing studies purporting to show that P-gp mediates the transport of propranolol, proposed that passive biological membrane transport is negligible. Based on the BDDCS, the extensively metabolized-highly permeable-highly soluble BDDCS class 1 drug, propranolol, shows a high passive permeability at concentrations unrestricted by solubility that can overwhelm any potential transporter effects. Here we reinvestigate the effects of passive diffusion and carrier-mediated transport on S-propranolol. Methods Bidirectional permeability and inhibition of efflux transport studies were carried out in MDCK, MDCK-MDR1 and Caco-2 cell lines at different concentrations. Transcellular permeability studies were conducted at different apical pHs in the rat jejunum Ussing chamber model and PAMPA system. Results S-propranolol exhibited efflux ratios lower than 1 in MDCK, MDCK-MDR1 and Caco-2 cells. No significant differences of Papp, B->A in the presence and absence of the efflux inhibitor GG918 were observed. However, an efflux ratio of 3.63 was found at apical pH 6.5 with significant decrease in Papp, A->B and increase in Papp, B->A compared to apical pH 7.4 in Caco-2 cell lines. The pH dependent permeability was confirmed in the Ussing chamber model. S-propranolol flux was unchanged during inhibition by verapamil and rifampin. Furthermore, pH dependent permeability was also observed in the PAMPA system. Conclusions S-propranolol does not exhibit active transport as proposed previously. The "false" positive efflux ratio can be explained by the pH partition theory. As expected, passive diffusion, but not active transport, plays the primary role in the permeability of the BDDCS class 1 drug propranolol. PMID:25690341

Transport of Carbon Tetrachloride in a Fractured Vadose Zone due to Atmospheric Pressure Fluctuations, Diffusion, and Vapor Density

NASA Astrophysics Data System (ADS)

McCray, J. E.; Downs, W.; Falta, R. W.; Housley, T.

2005-12-01

DNAPL sources of carbon tetrachloride (CT) vapors are of interest at the Radioactive Waste Management Complex (RWMC) at the Idaho National Engineering and Environmental Laboratory (INEEL). The site is underlain by thick fractured basalt that includes sedimentary interbeds, each are a few meters thick. Daily atmospheric pressure fluctuations serve as driving forces for CT vapor transport in the subsurface. Other important transport processes for vapor movement include gas-phase diffusion and density-driven transport. The objective of this research is to investigate the influence and relative importance of these processes on gaseous transport of CT. Gas pressure and vapor concentration measurements were conducted at various depths in two wells. A numerical multiphase flow model (TOUGH2), calibrated to field pressure data, is used to conduct sensitivity analyses to elucidate the importance of the different transport mechanisms. Results show that the basalt is highly permeable to vertical air flow. The pressure dampening occurs mainly in the sedimentary interbeds. Model-calibrated permeability values for the interbeds are similar to those obtained in a study by the U.S. Geological Survey for shallow sediments, and an order of magnitude higher than column-scale values obtained by previous studies conducted by INEEL scientists. The transport simulations indicate that considering the effect of barometric pressure changes is critical to simulating transport of pollutants in the vadose zone above the DNAPL source. Predicted concentrations can be orders of magnitude smaller than actual concentrations if the effect is not considered. Below the DNAPL vapor source, accounting for density and diffusion alone would yield acceptable results provided that a 20% error in concentrations are acceptable, and that simulating concentrations trends (and not actual concentrations) is the primary goal.

Charge effects on the hindered transport of macromolecules across the endothelial surface glycocalyx layer.

PubMed

Sugihara-Seki, Masako; Akinaga, Takeshi; O-Tani, Hideyuki

2012-01-01

A fluid mechanical and electrostatic model for the transport of solute molecules across the vascular endothelial surface glycocalyx layer (EGL) was developed to study the charge effect on the diffusive and convective transport of the solutes. The solute was assumed to be a spherical particle with a constant surface charge density, and the EGL was represented as an array of periodically arranged circular cylinders of like charge, with a constant surface charge density. By combining the fluid mechanical analyses for the flow around a solute suspended in an electrolyte solution and the electrostatic analyses for the free energy of the interaction between the solute and cylinders based on a mean field theory, we estimated the transport coefficients of the solute across the EGL. Both of diffusive and convective transports are reduced compared to those for an uncharged system, due to the stronger exclusion of the solute that results from the repulsive electrostatic interaction. The model prediction for the reflection coefficient for serum albumin agreed well with experimental observations if the charge density in the EGL is ranged from approximately -10 to -30 mEq/l.

Geomorphic control of radionuclide diffusion in desert soils

USGS Publications Warehouse

Pelletier, J.D.; Harrington, C.D.; Whitney, J.W.; Cline, M.; DeLong, S.B.; Keating, G.; Ebert, T.K.

2005-01-01

Diffusion is a standard model for the vertical migration of radionuclides in soil profiles. Here we show that diffusivity values inferred from fallout 137CS profiles in soils on the Fortymile Wash alluvial fan, Nye County, Nevada, have a strong inverse correlation with the age of the geomorphic surface. This result suggests that radionuclide-bound particles are predominantly transported by infiltration rather than by bulk-mixing processes such as wetting/ drying, freeze/thaw, and bioturbation. Our results provide a preliminary basis for using soil-geomorphic mapping, point-based calibration data, and the diffusion model to predict radionuclide trans desert soils within a pedotransfer-function approach. Copyright 2005 by the American Geophysical Union.

Kinetic multi-layer model of aerosol surface and bulk chemistry (KM-SUB): the influence of interfacial transport and bulk diffusion on the oxidation of oleic acid by ozone

NASA Astrophysics Data System (ADS)

Shiraiwa, Manabu; Pfrang, Christian; Pöschl, Ulrich

2010-05-01

Aerosols are ubiquitous in the atmosphere and have strong effects on climate and public health. Gas-particle interactions can significantly change the physical and chemical properties of aerosols such as toxicity, reactivity, hygroscopicity and radiative properties. Chemical reactions and mass transport lead to continuous transformation and changes in the composition of atmospheric aerosols ("chemical aging"). Resistor model formulations are widely used to describe and investigate heterogeneous reactions and multiphase processes in laboratory, field and model studies of atmospheric chemistry. The traditional resistor models, however, are usually based on simplifying assumptions such as steady state conditions, homogeneous mixing, and limited numbers of non-interacting species and processes. In order to overcome these limitations, Pöschl, Rudich and Ammann have developed a kinetic model framework (PRA framework) with a double-layer surface concept and universally applicable rate equations and parameters for mass transport and chemical reactions at the gas-particle interface of aerosols and clouds [1]. Based on the PRA framework, we present a novel kinetic multi-layer model that explicitly resolves mass transport and chemical reaction at the surface and in the bulk of aerosol particles (KM-SUB) [2]. The model includes reversible adsorption, surface reactions and surface-bulk exchange as well as bulk diffusion and reaction. Unlike earlier models, KM-SUB does not require simplifying assumptions about steady-state conditions and radial mixing. The temporal evolution and concentration profiles of volatile and non-volatile species at the gas-particle interface and in the particle bulk can be modeled along with surface concentrations and gas uptake coefficients. In this study we explore and exemplify the effects of bulk diffusion on the rate of reactive gas uptake for a simple reference system, the ozonolysis of oleic acid particles, in comparison to experimental data and earlier model studies. We demonstrate how KM-SUB can be used to interpret and analyze experimental data from laboratory studies, and how the results can be extrapolated to atmospheric conditions. In particular, we show how interfacial transport and bulk transport, i.e., surface accommodation, bulk accommodation and bulk diffusion, influence the kinetics of the chemical reaction. Sensitivity studies suggest that in fine air particulate matter oleic acid and compounds with similar reactivity against ozone (C=C double bonds) can reach chemical life-times of multiple hours only if they are embedded in a (semi-)solid matrix with very low diffusion coefficients (~10-10 cm2 s-1). Depending on the complexity of the investigated system, unlimited numbers of volatile and non-volatile species and chemical reactions can be flexibly added and treated with KM-SUB. We propose and intend to pursue the application of KM-SUB as a basis for the development of a detailed master mechanism of aerosol chemistry as well as for the derivation of simplified but realistic parameterizations for large-scale atmospheric and climate models. References [1] Pöschl et al., Atmos. Chem. and Phys., 7, 5989-6023 (2007). [2] Shiraiwa et al., Atmos. Chem. Phys. Discuss., 10, 281-326 (2010).

Finite element modelling of creep cavity filling by solute diffusion

NASA Astrophysics Data System (ADS)

Versteylen, C. D.; Szymański, N. K.; Sluiter, M. H. F.; van Dijk, N. H.

2018-04-01

In recently discovered self healing creep steels, open-volume creep cavities are filled by the precipitation of supersaturated solute. These creep cavities form on the grain boundaries oriented perpendicular to the applied stress. The presence of a free surface triggers a flux of solute from the matrix, over the grain boundaries towards the creep cavities. We studied the creep cavity filling by finite element modelling and found that the filling time critically depends on (i) the ratio of diffusivities in the grain boundary and the bulk, and (ii) on the ratio of the intercavity distance and the cavity size. For a relatively large intercavity spacing 3D transport is observed when the grain boundary and volume diffusivities are of a similar order of magnitude, while a 2D behaviour is observed when the grain boundary diffusivity is dominant. Instead when the intercavity distance is small, the transport behaviour tends to a 1D behaviour in all cases, as the amount of solute available in the grain boundary is insufficient. A phase diagram with the transition lines is constructed.

Fractional derivatives in the diffusion process in heterogeneous systems: The case of transdermal patches.

PubMed

Caputo, Michele; Cametti, Cesare

2017-09-01

In this note, we present a simple mathematical model of drug delivery through transdermal patches by introducing a memory formalism in the classical Fick diffusion equation based on the fractional derivative. This approach is developed in the case of a medicated adhesive patch placed on the skin to deliver a time released dose of medication through the skin towards the bloodstream.The main resistance to drug transport across the skin resides in the diffusion through its outermost layer (the stratum corneum). Due to the complicated architecture of this region, a model based on a constant diffusivity in a steady-state condition results in too simplistic assumptions and more refined models are required.The introduction of a memory formalism in the diffusion process, where diffusion parameters depend at a certain time or position on what happens at preceeding times, meets this requirement and allows a significantly better description of the experimental results.The present model may be useful not only for analyzing the rate of skin permeation but also for predicting the drug concentration after transdermal drug delivery depending on the diffusion characteristics of the patch (its thickness and pseudo-diffusion coefficient). Copyright © 2017 Elsevier Inc. All rights reserved.

Continuous versus discontinuous albedo representations in a simple diffusive climate model

NASA Astrophysics Data System (ADS)

Simmons, P. A.; Griffel, D. H.

1988-07-01

A one-dimensional annually and zonally averaged energy-balance model, with diffusive meridional heat transport and including icealbedo feedback, is considered. This type of model is found to be very sensitive to the form of albedo used. The solutions for a discontinuous step-function albedo are compared to those for a more realistic smoothly varying albedo. The smooth albedo gives a closer fit to present conditions, but the discontinuous form gives a better representation of climates in earlier epochs.

Towards nonaxisymmetry; initial results using the Flux Coordinate Independent method in BOUT++

NASA Astrophysics Data System (ADS)

Shanahan, B. W.; Hill, P.; Dudson, B. D.

2016-11-01

Fluid simulation of stellarator edge transport is difficult due to the complexities of mesh generation; the stochastic edge and strong nonaxisymmetry inhibit the use of field aligned coordinate systems. The recent implementation of the Flux Coordinate Independent method for calculating parallel derivatives in BOUT++ has allowed for more complex geometries. Here we present initial results of nonaxisymmetric diffusion modelling as a step towards stellarator turbulence modelling. We then present initial (non-turbulent) transport modelling using the FCI method and compare the results with analytical calculations. The prospects for future stellarator transport and turbulence modelling are discussed.

Radionuclide transport behavior in a generic geological radioactive waste repository.

PubMed

Bianchi, Marco; Liu, Hui-Hai; Birkholzer, Jens T

2015-01-01

We performed numerical simulations of groundwater flow and radionuclide transport to study the influence of several factors, including the ambient hydraulic gradient, groundwater pressure anomalies, and the properties of the excavation damaged zone (EDZ), on the prevailing transport mechanism (i.e., advection or molecular diffusion) in a generic nuclear waste repository within a clay-rich geological formation. By comparing simulation results, we show that the EDZ plays a major role as a preferential flowpath for radionuclide transport. When the EDZ is not taken into account, transport is dominated by molecular diffusion in almost the totality of the simulated domain, and transport velocity is about 40% slower. Modeling results also show that a reduction in hydraulic gradient leads to a greater predominance of diffusive transport, slowing down radionuclide transport by about 30% with respect to a scenario assuming a unit gradient. In addition, inward flow caused by negative pressure anomalies in the clay-rich formation further reduces transport velocity, enhancing the ability of the geological barrier to contain the radioactive waste. On the other hand, local high gradients associated with positive pressure anomalies can speed up radionuclide transport with respect to steady-state flow systems having the same regional hydraulic gradients. Transport behavior was also found to be sensitive to both geometrical and hydrogeological parameters of the EDZ. Results from this work can provide useful knowledge toward correctly assessing the post-closure safety of a geological disposal system. © 2014, National Ground Water Association.

A preliminary compressible second-order closure model for high speed flows

NASA Technical Reports Server (NTRS)

Speziale, Charles G.; Sarkar, Sutanu

1989-01-01

A preliminary version of a compressible second-order closure model that was developed in connection with the National Aero-Space Plane Project is presented. The model requires the solution of transport equations for the Favre-averaged Reynolds stress tensor and dissipation rate. Gradient transport hypotheses are used for the Reynolds heat flux, mass flux, and turbulent diffusion terms. Some brief remarks are made about the direction of future research to generalize the model.

Continuum mesoscopic framework for multiple interacting species and processes on multiple site types and/or crystallographic planes.

PubMed

Chatterjee, Abhijit; Vlachos, Dionisios G

2007-07-21

While recently derived continuum mesoscopic equations successfully bridge the gap between microscopic and macroscopic physics, so far they have been derived only for simple lattice models. In this paper, general deterministic continuum mesoscopic equations are derived rigorously via nonequilibrium statistical mechanics to account for multiple interacting surface species and multiple processes on multiple site types and/or different crystallographic planes. Adsorption, desorption, reaction, and surface diffusion are modeled. It is demonstrated that contrary to conventional phenomenological continuum models, microscopic physics, such as the interaction potential, determines the final form of the mesoscopic equation. Models of single component diffusion and binary diffusion of interacting particles on single-type site lattice and of single component diffusion on complex microporous materials' lattices consisting of two types of sites are derived, as illustrations of the mesoscopic framework. Simplification of the diffusion mesoscopic model illustrates the relation to phenomenological models, such as the Fickian and Maxwell-Stefan transport models. It is demonstrated that the mesoscopic equations are in good agreement with lattice kinetic Monte Carlo simulations for several prototype examples studied.

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 structure. Process methodology for deposition, biogenic emissions, shading, vertical diffusion, advection, chemical reactive environment and particle microphysics were modified to account for expected conditions within the forest canopy and the additional layers. The revised and original models were compared for a 10km resolution domain covering North America, for a one-month duration simulation. The canopy processes were found to have a very significant impact on model results. We will present a comparison to network observations which suggests that forest canopy processes may account for previously unexplained local and regional biases in model ozone predictions noted in GEM-MACH and other models. The impact of the canopy processes on NO2, PM2.5, and SO2 performance will also be presented and discussed.

Diffusive transport and reaction in clay rocks: A storage (nuclear waste, CO2, H2), energy (shale gas) and water quality issue

NASA Astrophysics Data System (ADS)

Charlet, Laurent; Alt-Epping, Peter; Wersin, Paul; Gilbert, Benjamin

2017-08-01

Clay rocks are low permeability sedimentary formations that provide records of Earth history, influence the quality of water resources, and that are increasingly used for the extraction or storage of energy resources and the sequestration of waste materials. Informed use of clay rock formations to achieve low-carbon or carbon-free energy goals requires the ability to predict the rates of diffusive transport processes for chemically diverse dissolved and gaseous species over periods up to thousands of years. We survey the composition, properties and uses of clay rock and summarize fundamental science challenges in developing confident conceptual and quantitative gas and solute transport models.

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.

Tailorable Exciton Transport in Doped Peptide–Amphiphile Assemblies

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

Solomon, Lee A.; Sykes, Matthew E.; Wu, Yimin A.

Light-harvesting biomaterials are an attractive target in photovoltaics, photocatalysis, and artificial photosynthesis. Through peptide self-assembly, complex nanostructures can be engineered to study the role of chromophore organization during light absorption and energy transport. To this end, we demonstrate the one-dimensional transport of excitons along naturally occurring, light-harvesting, Zn-protoporphyrin IX chromophores within self-assembled peptide-amphiphile nanofibers. The internal structure of the nanofibers induces packing of the porphyrins into linear chains. We find that this peptide assembly can enable long-range exciton diffusion, yet it also induces the formation of excimers between adjacent molecules, which serve as exciton traps. Electronic coupling between neighboring porphyrinmore » molecules is confirmed by various spectroscopic methods. The exciton diffusion process is then probed through transient photoluminescence and absorption measurements and fit to a model for one-dimensional hopping. Because excimer formation impedes exciton hopping, increasing the interchromophore spacing allows for improved diffusivity, which we control through porphyrin doping levels. We show that diffusion lengths of over 60 nm are possible at low porphyrin doping, representing an order of magnitude improvement over the highest doping fractions.« less

Grain Boundaries Act as Solid Walls for Charge Carrier Diffusion in Large Crystal MAPI Thin Films.

PubMed

Ciesielski, Richard; Schäfer, Frank; Hartmann, Nicolai F; Giesbrecht, Nadja; Bein, Thomas; Docampo, Pablo; Hartschuh, Achim

2018-03-07

Micro- and nanocrystalline methylammonium lead iodide (MAPI)-based thin-film solar cells today reach power conversion efficiencies of over 20%. We investigate the impact of grain boundaries on charge carrier transport in large crystal MAPI thin films using time-resolved photoluminescence (PL) microscopy and numerical model calculations. Crystal sizes in the range of several tens of micrometers allow for the spatially and time resolved study of boundary effects. Whereas long-ranged diffusive charge carrier transport is observed within single crystals, no detectable diffusive transport occurs across grain boundaries. The observed PL transients are found to crucially depend on the microscopic geometry of the crystal and the point of observation. In particular, spatially restricted diffusion of charge carriers leads to slower PL decay near crystal edges as compared to the crystal center. In contrast to many reports in the literature, our experimental results show no quenching or additional loss channels due to grain boundaries for the studied material, which thus do not negatively affect the performance of the derived thin-film devices.

Tailorable Exciton Transport in Doped Peptide-Amphiphile Assemblies.

PubMed

Solomon, Lee A; Sykes, Matthew E; Wu, Yimin A; Schaller, Richard D; Wiederrecht, Gary P; Fry, H Christopher

2017-09-26

Light-harvesting biomaterials are an attractive target in photovoltaics, photocatalysis, and artificial photosynthesis. Through peptide self-assembly, complex nanostructures can be engineered to study the role of chromophore organization during light absorption and energy transport. To this end, we demonstrate the one-dimensional transport of excitons along naturally occurring, light-harvesting, Zn-protoporphyrin IX chromophores within self-assembled peptide-amphiphile nanofibers. The internal structure of the nanofibers induces packing of the porphyrins into linear chains. We find that this peptide assembly can enable long-range exciton diffusion, yet it also induces the formation of excimers between adjacent molecules, which serve as exciton traps. Electronic coupling between neighboring porphyrin molecules is confirmed by various spectroscopic methods. The exciton diffusion process is then probed through transient photoluminescence and absorption measurements and fit to a model for one-dimensional hopping. Because excimer formation impedes exciton hopping, increasing the interchromophore spacing allows for improved diffusivity, which we control through porphyrin doping levels. We show that diffusion lengths of over 60 nm are possible at low porphyrin doping, representing an order of magnitude improvement over the highest doping fractions.

Need-based activation of ammonium uptake in Escherichia coli

PubMed Central

Kim, Minsu; Zhang, Zhongge; Okano, Hiroyuki; Yan, Dalai; Groisman, Alexander; Hwa, Terence

2012-01-01

The efficient sequestration of nutrients is vital for the growth and survival of microorganisms. Some nutrients, such as CO2 and NH3, are readily diffusible across the cell membrane. The large membrane permeability of these nutrients obviates the need of transporters when the ambient level is high. When the ambient level is low, however, maintaining a high intracellular nutrient level against passive back diffusion is both challenging and costly. Here, we study the delicate management of ammonium (NH4+/NH3) sequestration by E. coli cells using microfluidic chemostats. We find that as the ambient ammonium concentration is reduced, E. coli cells first maximize their ability to assimilate the gaseous NH3 diffusing into the cytoplasm and then abruptly activate ammonium transport. The onset of transport varies under different growth conditions, but always occurring just as needed to maintain growth. Quantitative modeling of known interactions reveals an integral feedback mechanism by which this need-based uptake strategy is implemented. This novel strategy ensures that the expensive cost of upholding the internal ammonium concentration against back diffusion is kept at a minimum. PMID:23010999

Simulating contaminant attenuation, double-porosity exchange, and water age in aquifers using MOC3D

USGS Publications Warehouse

Goode, Daniel J.

1999-01-01

MOC3D is a general-purpose computer model developed by the U.S. Geological Survey (USGS) for simulation of three-dimensional solute transport in ground water (Konikow and others, 1996). The model is an update to the widely used USGS two-dimensional solute-transport model (MOC) and is implemented as an optional “package” for the ground-water flow model MODFLOW (Harbaugh and McDonald, 1996). Directly coupling the time-tested MOC transport algorithms with the widely used MODFLOW program makes MOC3D a powerful tool for simulation of solute transport in ground water in many hydrogeologic settings. The model simulates transport processes that include:Advection - Transport of dissolved solutes at the same rate as the average ground-water flow velocity.Diffusion - Spreading of solute from areas of high concentration to areas of low concentration, caused by “random” molecular motionDispersion - Diffusion-like spreading of solute that is caused primarily by spatial variability in aquifer properties, which results in spatial variability in transport velocity.Retardation - Reduction in the apparent solute velocity, compared to the ground-water velocity, caused by linear equilibrium sorption on aquifer materials.Decay - Disappearance of solute caused by reactions such as radioactive decay or biodegradation that are proportional to concentration.Growth - Creation (or disappearance) of solute mass caused by reactions that proceed independent of the solute concentration, such as some cases of biodegradationDouble-porosity exchange - rate-limited exchange of solute mass between mobile and immobile zones; for example, between fractures and the rock matrix.

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.

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

Barbante, Paolo; Frezzotti, Aldo; Gibelli, Livio

The unsteady evaporation of a thin planar liquid film is studied by molecular dynamics simulations of Lennard-Jones fluid. The obtained results are compared with the predictions of a diffuse interface model in which capillary Korteweg contributions are added to hydrodynamic equations, in order to obtain a unified description of the liquid bulk, liquid-vapor interface and vapor region. Particular care has been taken in constructing a diffuse interface model matching the thermodynamic and transport properties of the Lennard-Jones fluid. The comparison of diffuse interface model and molecular dynamics results shows that, although good agreement is obtained in equilibrium conditions, remarkable deviationsmore » of diffuse interface model predictions from the reference molecular dynamics results are observed in the simulation of liquid film evaporation. It is also observed that molecular dynamics results are in good agreement with preliminary results obtained from a composite model which describes the liquid film by a standard hydrodynamic model and the vapor by the Boltzmann equation. The two mathematical model models are connected by kinetic boundary conditions assuming unit evaporation coefficient.« less

Diffusion related isotopic fractionation effects with one-dimensional advective-dispersive transport.

PubMed

Xu, Bruce S; Lollar, Barbara Sherwood; Passeport, Elodie; Sleep, Brent E

2016-04-15

Aqueous phase diffusion-related isotope fractionation (DRIF) for carbon isotopes was investigated for common groundwater contaminants in systems in which transport could be considered to be one-dimensional. This paper focuses not only on theoretically observable DRIF effects in these systems but introduces the important concept of constraining "observable" DRIF based on constraints imposed by the scale of measurements in the field, and on standard limits of detection and analytical uncertainty. Specifically, constraints for the detection of DRIF were determined in terms of the diffusive fractionation factor, the initial concentration of contaminants (C0), the method detection limit (MDL) for isotopic analysis, the transport time, and the ratio of the longitudinal mechanical dispersion coefficient to effective molecular diffusion coefficient (Dmech/Deff). The results allow a determination of field conditions under which DRIF may be an important factor in the use of stable carbon isotope measurements for evaluation of contaminant transport and transformation for one-dimensional advective-dispersive transport. This study demonstrates that for diffusion-dominated transport of BTEX, MTBE, and chlorinated ethenes, DRIF effects are only detectable for the smaller molar mass compounds such as vinyl chloride for C0/MDL ratios of 50 or higher. Much larger C0/MDL ratios, corresponding to higher source concentrations or lower detection limits, are necessary for DRIF to be detectable for the higher molar mass compounds. The distance over which DRIF is observable for VC is small (less than 1m) for a relatively young diffusive plume (<100years), and DRIF will not easily be detected by using the conventional sampling approach with "typical" well spacing (at least several meters). With contaminant transport by advection, mechanical dispersion, and molecular diffusion this study suggests that in field sites where Dmech/Deff is larger than 10, DRIF effects will likely not be observable for common groundwater contaminants. Importantly, under most field conditions, Dmech/Deff≥10 is usually satisfied in the longitudinal direction, suggesting that DRIF is not likely to be observable in most groundwater systems in which contaminant transport is predominantly one-dimensional. Given the importance in the MDL it is recommended that MDL should always be explicitly reported in both modeling and field studies. Copyright © 2016. Published by Elsevier B.V.

The influence of vibrational state-resolved transport coefficients on the wave propagation in diatomic gases

NASA Astrophysics Data System (ADS)

Kremer, Gilberto M.; Kunova, Olga V.; Kustova, Elena V.; Oblapenko, George P.

2018-01-01

A detailed kinetic-theory model for the vibrationally state-resolved transport coefficients is developed taking into account the dependence of the collision cross section on the size of vibrationally excited molecule. Algorithms for the calculation of shear and bulk viscosity, thermal conductivity, thermal diffusion and diffusion coefficients for vibrational states are proposed. The transport coefficients are evaluated for single-component diatomic gases N2, O2, NO, H2, Cl2 in the wide range of temperature, and the effects of molecular diameters and the number of accounted states are discussed. The developed model is applied to study wave propagation in diatomic gases. For the case of initial Boltzmann distribution, the influence of vibrational excitation on the phase velocity and attenuation coefficient is found to be weak. We expect more significant effect in the case of initial thermal non-equilibrium, for instance in gases with optically pumped selected vibrational states.

Modeling methanol transfer in the mesoporous catalyst for the methanol-to-olefins reaction by the time-fractional diffusion equation

NASA Astrophysics Data System (ADS)

Zhokh, Alexey A.; Strizhak, Peter E.

2018-04-01

The solutions of the time-fractional diffusion equation for the short and long times are obtained via an application of the asymptotic Green's functions. The derived solutions are applied to analysis of the methanol mass transfer through H-ZSM-5/alumina catalyst grain. It is demonstrated that the methanol transport in the catalysts pores may be described by the obtained solutions in a fairly good manner. The measured fractional exponent is equal to 1.20 ± 0.02 and reveals the super-diffusive regime of the methanol mass transfer. The presence of the anomalous transport may be caused by geometrical restrictions and the adsorption process on the internal surface of the catalyst grain's pores.

Lagrangian particles with mixing. I. Simulating scalar transport

NASA Astrophysics Data System (ADS)

Klimenko, A. Y.

2009-06-01

The physical similarity and mathematical equivalence of continuous diffusion and particle random walk forms one of the cornerstones of modern physics and the theory of stochastic processes. The randomly walking particles do not need to posses any properties other than location in physical space. However, particles used in many models dealing with simulating turbulent transport and turbulent combustion do posses a set of scalar properties and mixing between particle properties is performed to reflect the dissipative nature of the diffusion processes. We show that the continuous scalar transport and diffusion can be accurately specified by means of localized mixing between randomly walking Lagrangian particles with scalar properties and assess errors associated with this scheme. Particles with scalar properties and localized mixing represent an alternative formulation for the process, which is selected to represent the continuous diffusion. Simulating diffusion by Lagrangian particles with mixing involves three main competing requirements: minimizing stochastic uncertainty, minimizing bias introduced by numerical diffusion, and preserving independence of particles. These requirements are analyzed for two limited cases of mixing between two particles and mixing between a large number of particles. The problem of possible dependences between particles is most complicated. This problem is analyzed using a coupled chain of equations that has similarities with Bogolubov-Born-Green-Kirkwood-Yvon chain in statistical physics. Dependences between particles can be significant in close proximity of the particles resulting in a reduced rate of mixing. This work develops further ideas introduced in the previously published letter [Phys. Fluids 19, 031702 (2007)]. Paper I of this work is followed by Paper II [Phys. Fluids 19, 065102 (2009)] where modeling of turbulent reacting flows by Lagrangian particles with localized mixing is specifically considered.

Control of the photosynthetic electron transport by PQ diffusion microdomains in thylakoids of higher plants.

PubMed

Kirchhoff, H; Horstmann, S; Weis, E

2000-07-20

We investigate the role of plastoquinone (PQ) diffusion in the control of the photosynthetic electron transport. A control analysis reveals an unexpected flux control of the whole chain electron transport by photosystem (PS) II. The contribution of PSII to the flux control of whole chain electron transport was high in stacked thylakoids (control coefficient, CJ(PSII) =0.85), but decreased after destacking (CJ(PSII)=0.25). From an 'electron storage' experiment, we conclude that in stacked thylakoids only about 50 to 60% of photoreducable PQ is involved in the light-saturated linear electron transport. No redox equilibration throughout the membrane between fixed redox groups at PSII and cytochrome (cyt) bf complexes, and the diffusable carrier PQ is achieved. The data support the PQ diffusion microdomain concept by Lavergne et al. [J. Lavergne, J.-P. Bouchaud, P. Joliot, Biochim. Biophys. Acta 1101 (1992) 13-22], but we come to different conclusions about size, structure and size distribution of domains. From an analysis of cyt b6 reduction, as a function of PSII inhibition, we conclude that in stacked thylakoids about 70% of PSII is located in small domains, where only 1 to 2 PSII share a local pool of a few PQ molecules. Thirty percent of PSII is located in larger domains. No small domains were found in destacked thylakoids. We present a structural model assuming a hierarchy of specific, strong and weak interactions between PSII core, light harvesting complexes (LHC) II and cyt bf. Peripheral LHCII's may serve to connect PSII-LHCII supercomplexes to a flexible protein network, by which small closed lipid diffusion compartments are formed. Within each domain, PQ moves rapidly and shuttles electrons between PSII and cyt bf complexes in the close vicinity. At the same time, long range diffusion is slow. We conclude, that in high light, cyt bfcomplexes located in distant stromal lamellae (20 to 30%) are not involved in the linear electron transport.

Diffusive deposition of aerosols in Phebus containment during FPT-2 test

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

Kontautas, A.; Urbonavicius, E.

2012-07-01

At present the lumped-parameter codes is the main tool to investigate the complex response of the containment of Nuclear Power Plant in case of an accident. Continuous development and validation of the codes is required to perform realistic investigation of the processes that determine the possible source term of radioactive products to the environment. Validation of the codes is based on the comparison of the calculated results with the measurements performed in experimental facilities. The most extensive experimental program to investigate fission product release from the molten fuel, transport through the cooling circuit and deposition in the containment is performedmore » in PHEBUS test facility. Test FPT-2 performed in this facility is considered for analysis of processes taking place in containment. Earlier performed investigations using COCOSYS code showed that the code could be successfully used for analysis of thermal-hydraulic processes and deposition of aerosols, but there was also noticed that diffusive deposition on the vertical walls does not fit well with the measured results. In the CPA module of ASTEC code there is implemented different model for diffusive deposition, therefore the PHEBUS containment model was transferred from COCOSYS code to ASTEC-CPA to investigate the influence of the diffusive deposition modelling. Analysis was performed using PHEBUS containment model of 16 nodes. The calculated thermal-hydraulic parameters are in good agreement with measured results, which gives basis for realistic simulation of aerosol transport and deposition processes. Performed investigations showed that diffusive deposition model has influence on the aerosol deposition distribution on different surfaces in the test facility. (authors)« less

Modeling hexavalent chromium reduction in groundwater in field-scale transport and laboratory batch experiments

USGS Publications Warehouse

Friedly, J.C.; Davis, J.A.; Kent, D.B.

1995-01-01

A plausible and consistent model is developed to obtain a quantitative description of the gradual disappearance of hexavalent chromium (Cr(VI)) from groundwater in a small-scale field tracer test and in batch kinetic experiments using aquifer sediments under similar chemical conditions. The data exhibit three distinct timescales. Fast reduction occurs in well-stirred batch reactors in times much less than 1 hour and is followed by slow reduction over a timescale of the order of 2 days. In the field, reduction occurs on a timescale of the order of 8 days. The model is based on the following hypotheses. The chemical reduction reaction occurs very fast, and the longer timescales are caused by diffusion resistance. Diffusion into the secondary porosity of grains causes the apparent slow reduction rate in batch experiments. In the model of the field experiments, the reducing agent, heavy Fe(II)-bearing minerals, is heterogeneously distributed in thin strata located between larger nonreducing sand lenses that comprise the bulk of the aquifer solids. It is found that reducing strata of the order of centimeters thick are sufficient to contribute enough diffusion resistance to cause the observed longest timescale in the field. A one-dimensional advection/dispersion model is formulated that describes the major experimental trends. Diffusion rates are estimated in terms of an elementary physical picture of flow through a stratified medium containing identically sized spherical grains. Both reduction and sorption reactions are included. Batch simulation results are sensitive to the fraction of reductant located at or near the surface of grains, which controls the amount of rapid reduction, and the secondary porosity, which controls the rate of slow reduction observed in batch experiments. Results of Cr(VI) transport simulations are sensitive to the thickness and relative size of the reducing stratum. Transport simulation results suggest that nearly all of the reductant must be located in the reducing stratum. Within this context and as long as there is adequate reductive capacity present, the transport simulation results are insensitive to the parameters important for the batch simulations. The results illustrate how a combination of field measurements and batch laboratory studies can be used to improve predictive modeling of contaminant transport.

Isotope effect of mercury diffusion in air

PubMed Central

Koster van Groos, Paul G.; Esser, Bradley K.; Williams, Ross W.; Hunt, James R.

2014-01-01

Identifying and reducing impacts from mercury sources in the environment remains a considerable challenge and requires process based models to quantify mercury stocks and flows. The stable isotope composition of mercury in environmental samples can help address this challenge by serving as a tracer of specific sources and processes. Mercury isotope variations are small and result only from isotope fractionation during transport, equilibrium, and transformation processes. Because these processes occur in both industrial and environmental settings, knowledge of their associated isotope effects is required to interpret mercury isotope data. To improve the mechanistic modeling of mercury isotope effects during gas phase diffusion, an experimental program tested the applicability of kinetic gas theory. Gas-phase elemental mercury diffusion through small bore needles from finite sources demonstrated mass dependent diffusivities leading to isotope fractionation described by a Rayleigh distillation model. The measured relative atomic diffusivities among mercury isotopes in air are large and in agreement with kinetic gas theory. Mercury diffusion in air offers a reasonable explanation of recent field results reported in the literature. PMID:24364380

Isotope effect of mercury diffusion in air.

PubMed

Koster van Groos, Paul G; Esser, Bradley K; Williams, Ross W; Hunt, James R

2014-01-01

Identifying and reducing impacts from mercury sources in the environment remains a considerable challenge and requires process based models to quantify mercury stocks and flows. The stable isotope composition of mercury in environmental samples can help address this challenge by serving as a tracer of specific sources and processes. Mercury isotope variations are small and result only from isotope fractionation during transport, equilibrium, and transformation processes. Because these processes occur in both industrial and environmental settings, knowledge of their associated isotope effects is required to interpret mercury isotope data. To improve the mechanistic modeling of mercury isotope effects during gas phase diffusion, an experimental program tested the applicability of kinetic gas theory. Gas-phase elemental mercury diffusion through small bore needles from finite sources demonstrated mass dependent diffusivities leading to isotope fractionation described by a Rayleigh distillation model. The measured relative atomic diffusivities among mercury isotopes in air are large and in agreement with kinetic gas theory. Mercury diffusion in air offers a reasonable explanation of recent field results reported in the literature.

Simple Analytical Forms of the Perpendicular Diffusion Coefficient for Two-component Turbulence. III. Damping Model of Dynamical Turbulence

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

Gammon, M.; Shalchi, A., E-mail: andreasm4@yahoo.com

2017-10-01

In several astrophysical applications one needs analytical forms of cosmic-ray diffusion parameters. Some examples are studies of diffusive shock acceleration and solar modulation. In the current article we explore perpendicular diffusion based on the unified nonlinear transport theory. While we focused on magnetostatic turbulence in Paper I, we included the effect of dynamical turbulence in Paper II of the series. In the latter paper we assumed that the temporal correlation time does not depend on the wavenumber. More realistic models have been proposed in the past, such as the so-called damping model of dynamical turbulence. In the present paper wemore » derive analytical forms for the perpendicular diffusion coefficient of energetic particles in two-component turbulence for this type of time-dependent turbulence. We present new formulas for the perpendicular diffusion coefficient and we derive a condition for which the magnetostatic result is recovered.« less

Heavy metal transport in large river systems: heavy metal emissions and loads in the Rhine and Elbe river basins

NASA Astrophysics Data System (ADS)

Vink, Rona; Behrendt, Horst

2002-11-01

Pollutant transport and management in the Rhine and Elbe basins is still of international concern, since certain target levels set by the international committees for protection of both rivers have not been reached. The analysis of the chain of emissions of point and diffuse sources to river loads will provide policy makers with a tool for effective management of river basins. The analysis of large river basins such as the Elbe and Rhine requires information on the spatial and temporal characteristics of both emissions and physical information of the entire river basin. In this paper, an analysis has been made of heavy metal emissions from various point and diffuse sources in the Rhine and Elbe drainage areas. Different point and diffuse pathways are considered in the model, such as inputs from industry, wastewater treatment plants, urban areas, erosion, groundwater, atmospheric deposition, tile drainage, and runoff. In most cases the measured heavy metal loads at monitoring stations are lower than the sum of the heavy metal emissions. This behaviour in large river systems can largely be explained by retention processes (e.g. sedimentation) and is dependent on the specific runoff of a catchment. Independent of the method used to estimate emissions, the source apportionment analysis of observed loads was used to determine the share of point and diffuse sources in the heavy metal load at a monitoring station by establishing a discharge dependency. The results from both the emission analysis and the source apportionment analysis of observed loads were compared and gave similar results. Between 51% (for Hg) and 74% (for Pb) of the total transport in the Elbe basin is supplied by inputs from diffuse sources. In the Rhine basin diffuse source inputs dominate the total transport and deliver more than 70% of the total transport. The diffuse hydrological pathways with the highest share are erosion and urban areas.

Physiologically based pharmacokinetic modeling of deltamethrin: Development of a rat and human diffusion-limited model

EPA Science Inventory

Mirfazaelian et al. (2006) developed a physiologically based pharmacokinetic (PBPK) model for the pyrethroid pesticide deltamethrin in the rat. This model describes gastrointestinal tract absorption as a saturable process mediated by phase III efflux transporters which pump delta...

The influence of layering and barometric pumping on firn air transport in a 2-D model

NASA Astrophysics Data System (ADS)

Birner, Benjamin; Buizert, Christo; Wagner, Till J. W.; Severinghaus, Jeffrey P.

2018-06-01

Ancient air trapped in ice core bubbles has been paramount to developing our understanding of past climate and atmospheric composition. Before air bubbles become isolated in ice, the atmospheric signal is altered in the firn column by transport processes such as advection and diffusion. However, the influence of low-permeability layers and barometric pumping (driven by surface pressure variability) on firn air transport is not well understood and is not readily captured in conventional one-dimensional (1-D) firn air models. Here we present a two-dimensional (2-D) trace gas advection-diffusion-dispersion model that accounts for discontinuous horizontal layers of reduced permeability. We find that layering or barometric pumping individually yields too small a reduction in gravitational settling to match observations. In contrast, when both effects are active, the model's gravitational fractionation is suppressed as observed. Layering focuses airflows in certain regions in the 2-D model, which acts to amplify the dispersive mixing resulting from barometric pumping. Hence, the representation of both factors is needed to obtain a realistic emergence of the lock-in zone. In contrast to expectations, we find that the addition of barometric pumping in the layered 2-D model does not substantially change the differential kinetic fractionation of fast- and slow-diffusing trace gases. Like 1-D models, the 2-D model substantially underestimates the amount of differential kinetic fractionation seen in actual observations, suggesting that further subgrid-scale processes may be missing in the current generation of firn air transport models. However, we find robust scaling relationships between kinetic isotope fractionation of different noble gas isotope and elemental ratios. These relationships may be used to correct for kinetic fractionation in future high-precision ice core studies and can amount to a bias of up to 0.45 °C in noble-gas-based mean ocean temperature reconstructions at WAIS Divide, Antarctica.

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 the plume in two-dimensional problems.

Effects of Spatial N nutrient mobility relevant to plants, soils and microtopograhy on plant growth and soil organic matter accumulation by using coupled CLM-PFLOTRAN biogeochemical model in an Area in NGEE-Arctic Intensive Study Sites, Barrow, AK.

NASA Astrophysics Data System (ADS)

Yuan, F.; Thornton, P. E.; Tang, G.; Xu, X.; Kumar, J.; Iversen, C. M.; Bisht, G.; Hammond, G. E.; Mills, R. T.; Wullschleger, S. D.

2015-12-01

At fine-scale spatially-explicit reactive-transport (RT) and hydrological coupled modeling for likely soil nutrient N transport mechanisms driven by gradients, soil properties and micro-topography is critical to spatial distribution of plants and thus soil organic matter stocks accumulation or changes. In this study we successfully carried out a fully coupled fine-scale CLM-PFLOTRAN soil biogeochemical (BGC) RT model simulation on Titan at 2.5mx2.5m resolution for the Area C of 100mx100m in the NGEE-Arctic Intensive Study Sites, Barrow, AK. The Area spatially varies in terms of plant function types (PFT) and soil thermal-hydraulic properties associated with locally polygonal landscape features. The spatially explicit CLM-PFLOTRAN coupled RT model allows soil N nutrient mobility driven either by diffusion or by advection or both. The modeling experiments are conducted with three soil nutrient N (NH4+ and NO3-) mobility mechanisms within the CLM-PFLOTAN: no transport, diffusion only, and diffusion and advection in 3-D soils. It shows that CLM-PFLOTRAN model simulated higher SOM C density in both lower troughs and neighbored areas when transport mechanism allowed, compared to no-transport, although with similar ranges (about 0.1~20 kgC m-3). It also simulates slightly higher LAI (0.16~0.84 vs. 0.11~0.85) in growing season, especially in lower troughs and neighbored regions. It's likely because CLM-PFLOTRAN can explicitly simulate transport of nutrients and others both vertically and laterally. So it can more mechanically mimic plant root N extract caused relatively low concentration in root zone and thus allow transport from surrounding high N concentration regions. The lateral mobility also implies that N nutrient can transport from initially high-production columns to the neighbored low-production area where then production could be improved. The results suggest that taking account of locally mobility of soil N nutrients may be critical to plant growth and thus long-term soil organic carbon stocks in this polygonal coastal tundra ecosystem at fine scale. It also implies that regional or global scale modelings should consider vertical transport (2D) due to shallow soil root zones, for which a feature in CLM-PFLOTRAN is available as well.

Numerical Modeling of the Vertical Heat Transport Through the Diffusive Layer of the Arctic Ocean

DTIC Science & Technology

2013-03-01

vertical heat transport through Arctic thermohaline staircases over time . Re-engaging in the inverse modeling technique that was started by Chaplin ...reporting burden for this collection of information is estimated to average 1 hour per response, including the time for reviewing instruction, searching...function. ........................................42 Figure 23. Temperature—Salinity plots for ITPs 1-6 (After Chaplin 2009

Glucose diffusion in pancreatic islets of Langerhans.

PubMed Central

Bertram, R; Pernarowski, M

1998-01-01

We investigate the time required for glucose to diffuse through an isolated pancreatic islet of Langerhans and reach an equilibrium. This question is relevant in the context of in vitro electrophysiological studies of the response of an islet to step changes in the bath glucose concentration. Islet cells are electrically coupled by gap junctions, so nonuniformities in islet glucose concentration may be reflected in the activity of cells on the islet periphery, where electrical recordings are made. Using a mathematical model of hindered glucose diffusion, we investigate the effects of the islet porosity and the permeability of a surrounding layer of acinar cells. A major factor in the determination of the equilibrium time is the transport of glucose into islet beta-cells, which removes glucose from the interstitial spaces where diffusion occurs. This transport is incorporated by using a model of the GLUT-2 glucose transporter. We find that several minutes are required for the islet to equilibrate to a 10 mM change in bath glucose, a typical protocol in islet experiments. It is therefore likely that in electrophysiological islet experiments the glucose distribution is nonuniform for several minutes after a step change in bath glucose. The delay in glucose penetration to the inner portions of the islet may be a major contributing factor to the 1-2-min delay in islet electrical activity typically observed after bath application of a stimulatory concentration of glucose. PMID:9545035

Surface conservation laws at microscopically diffuse interfaces.

PubMed

Chu, Kevin T; Bazant, Martin Z

2007-11-01

In studies of interfaces with dynamic chemical composition, bulk and interfacial quantities are often coupled via surface conservation laws of excess surface quantities. While this approach is easily justified for microscopically sharp interfaces, its applicability in the context of microscopically diffuse interfaces is less theoretically well-established. Furthermore, surface conservation laws (and interfacial models in general) are often derived phenomenologically rather than systematically. In this article, we first provide a mathematically rigorous justification for surface conservation laws at diffuse interfaces based on an asymptotic analysis of transport processes in the boundary layer and derive general formulae for the surface and normal fluxes that appear in surface conservation laws. Next, we use nonequilibrium thermodynamics to formulate surface conservation laws in terms of chemical potentials and provide a method for systematically deriving the structure of the interfacial layer. Finally, we derive surface conservation laws for a few examples from diffusive and electrochemical transport.

Optimized Diffusion of Run-and-Tumble Particles in Crowded Environments

NASA Astrophysics Data System (ADS)

Bertrand, Thibault; Zhao, Yongfeng; Bénichou, Olivier; Tailleur, Julien; Voituriez, Raphaël

2018-05-01

We study the transport of self-propelled particles in dynamic complex environments. To obtain exact results, we introduce a model of run-and-tumble particles (RTPs) moving in discrete time on a d -dimensional cubic lattice in the presence of diffusing hard-core obstacles. We derive an explicit expression for the diffusivity of the RTP, which is exact in the limit of low density of fixed obstacles. To do so, we introduce a generalization of Kac's theorem on the mean return times of Markov processes, which we expect to be relevant for a large class of lattice gas problems. Our results show the diffusivity of RTPs to be nonmonotonic in the tumbling probability for low enough obstacle mobility. These results prove the potential for the optimization of the transport of RTPs in crowded and disordered environments with applications to motile artificial and biological systems.

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

18,000 displacement vectors and 44 positions surveys of RFID tracers show a normal diffusion of the bedload in a proglacial stream (Bossons glacier, France)

NASA Astrophysics Data System (ADS)

Guillon, Hervé; Mugnier, Jean-Louis; Buoncristiani, Jean-François

2016-04-01

Bedload transport is a stochastic process during which each particle hops for a random length then rests for a random duration. In recent years, this probabilistic approach was investigated by theoretical models, numerical simulations and laboratory experiments. These experiments are generally carried out on short time scales with sand, but underline the diffusive behaviour of the bedload. Conversely, marked pebbles in natural streams have mainly be used to infer about transport processes and transport time of the bedload. In this study, the stochastic characteristics of bedload transport are inferred from the radio-frequency identification (RFID) of pebbles. In particular, we provide insights for answering the following question : is the bedload transport sub-diffusive, normally diffusive or super-diffusive at the long time scale (i.e. global range)? Experiments designed to investigate the phenomenology of bedload transport have been carried out in the proglacial area of Bossons glacier. This 350 m long alluvial plain exhibits daily flood from the glacial system and is still redistributing material from catastrophic events pre-dating our investigations. From 2011 to 2014, the position of the ˜ 1000 RFID tracers have been measured by a mobile antenna and a differential GPS during 44 surveys providing ˜ 2500 tracer positions. Additionnaly, in 2014, 650 new tracers were seeded upstream from a static RFID antenna located at the outlet of the study area. For the 1 to 32 cm fraction surveyed, both mobile and static antenna results show no evidence for a significant export outside of the surveyed zone. Initial data have been maximized by using each possible campaign pairs leading to ˜700 campaign pairs and more than 18,000 displacement vectors. To our knowledge, this is one of the most extensive dataset of tracers positions measured in a natural stream using the RFID methodology. Using 152 campaigns pairs with at least 20 retrieved tracers,r standard probability distributions were tested against the observed travel distances. Regardless of the time scale, heavy- and light-tailed distributions provide a convincing statistical description of measured data. No single distribution is significantly better than the others. Conversely, the distribution of tracers positions in the system and its time evolution is best described by the normal distribution. Its standard deviation scales with time as σ ∝ t0.45±0.12 which suggests a nearly normal diffusive behaviour. The measured virtual velocities and a simple probabilistic model using the time evolution of the mean (i.e. drift) and standard deviation (i.e diffusion) show that the mean bedload transfer time is greater than 5 years. RFID tracers appear as a promising tool to investigate stochastic characteristics of bedload transport.

Filling high aspect ratio trenches by superconformal chemical vapor deposition: Predictive modeling and experiment

NASA Astrophysics Data System (ADS)

Wang, Wenjiao B.; Abelson, John R.

2014-11-01

Complete filling of a deep recessed structure with a second material is a challenge in many areas of nanotechnology fabrication. A newly discovered superconformal coating method, applicable in chemical vapor deposition systems that utilize a precursor in combination with a co-reactant, can solve this problem. However, filling is a dynamic process in which the trench progressively narrows and the aspect ratio (AR) increases. This reduces species diffusion within the trench and may drive the component partial pressures out of the regime for superconformal coating. We therefore derive two theoretical models that can predict the possibility for filling. First, we recast the diffusion-reaction equation for the case of a sidewall with variable taper angle. This affords a definition of effective AR, which is larger than the nominal AR due to the reduced species transport. We then derive the coating profile, both for superconformal and for conformal coating. The critical (most difficult) step in the filling process occurs when the sidewalls merge at the bottom of the trench to form the V shape. Experimentally, for the Mg(DMADB)2/H2O system and a starting AR = 9, this model predicts that complete filling will not be possible, whereas experimentally we do obtain complete filling. We then hypothesize that glancing-angle, long-range transport of species may be responsible for the better than predicted filling. To account for the variable range of species transport, we construct a ballistic transport model. This incorporates the incident flux from outside the structure, cosine law re-emission from surfaces, and line-of-sight transport between internal surfaces. We cast the transport probability between all positions within the trench into a matrix that represents the redistribution of flux after one cycle of collisions. Matrix manipulation then affords a computationally efficient means to determine the steady-state flux distribution and growth rate for a given taper angle. The ballistic transport model predicts a deeper position for the peak of the super-conformal growth rate than the diffusion-reaction model, and successfully explains the observation of complete filling. These models can be used to predict the behavior of any system given a small set of kinetic coefficients to describe the growth rate.

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

Luo, Qingtao; Li, Liyu; Nie, Zimin

We will show a new method to differentiate the vanadium transport from concentration gradient and that from electric field. Flow batteries with vanadium and iron redox couples as the electro-active species were employed to investigate the transport behavior of vanadium ions in the presence of electric field. It was shown that electric field accelerated the positive-to-negative and reduced the negative-to-positive vanadium ions transport in charge process and affected the vanadium ions transport in an opposite way in discharge process. In addition, a method was designed to differentiate the concentration gradient-driven vanadium ions diffusion and electric field-driven vanadium ions migration. Simplifiedmore » mathematical model was established to simulate the vanadium ions transport in real charge-discharge operation of flow battery. The concentration gradient diffusion coefficients and electric-migration coefficients of V2+, V3+, VO2+, and VO2+ across Nafion membrane were obtained by fitting the experimental data.« less

Spatially inhomogeneous acceleration of electrons in solar flares

NASA Astrophysics Data System (ADS)

Stackhouse, Duncan J.; Kontar, Eduard P.

2018-04-01

The imaging spectroscopy capabilities of the Reuven Ramaty high energy solar spectroscopic imager (RHESSI) enable the examination of the accelerated electron distribution throughout a solar flare region. In particular, it has been revealed that the energisation of these particles takes place over a region of finite size, sometimes resolved by RHESSI observations. In this paper, we present, for the first time, a spatially distributed acceleration model and investigate the role of inhomogeneous acceleration on the observed X-ray emission properties. We have modelled transport explicitly examining scatter-free and diffusive transport within the acceleration region and compare with the analytic leaky-box solution. The results show the importance of including this spatial variation when modelling electron acceleration in solar flares. The presence of an inhomogeneous, extended acceleration region produces a spectral index that is, in most cases, different from the simple leaky-box prediction. In particular, it results in a generally softer spectral index than predicted by the leaky-box solution, for both scatter-free and diffusive transport, and thus should be taken into account when modelling stochastic acceleration in solar flares.

Semianalytical solutions for transport in aquifer and fractured clay matrix system

NASA Astrophysics Data System (ADS)

Huang, Junqi; Goltz, Mark N.

2015-09-01

A three-dimensional mathematical model that describes transport of contaminant in a horizontal aquifer with simultaneous diffusion into a fractured clay formation is proposed. A group of semianalytical solutions is derived based on specific initial and boundary conditions as well as various source functions. The analytical model solutions are evaluated by numerical Laplace inverse transformation and analytical Fourier inverse transformation. The model solutions can be used to study the fate and transport in a three-dimensional spatial domain in which a nonaqueous phase liquid exists as a pool atop a fractured low-permeability clay layer. The nonaqueous phase liquid gradually dissolves into the groundwater flowing past the pool, while simultaneously diffusing into the fractured clay formation below the aquifer. Mass transfer of the contaminant into the clay formation is demonstrated to be significantly enhanced by the existence of the fractures, even though the volume of fractures is relatively small compared to the volume of the clay matrix. The model solution is a useful tool in assessing contaminant attenuation processes in a confined aquifer underlain by a fractured clay formation.

Explaining CO2 fluctuations observed in snowpacks

NASA Astrophysics Data System (ADS)

Graham, Laura; Risk, David

2018-02-01

Winter soil carbon dioxide (CO2) respiration is a significant and understudied component of the global carbon (C) cycle. Winter soil CO2 fluxes can be surprisingly variable, owing to physical factors such as snowpack properties and wind. This study aimed to quantify the effects of advective transport of CO2 in soil-snow systems on the subdiurnal to diurnal (hours to days) timescale, use an enhanced diffusion model to replicate the effects of CO2 concentration depletions from persistent winds, and use a model-measure pairing to effectively explore what is happening in the field. We took continuous measurements of CO2 concentration gradients and meteorological data at a site in the Cape Breton Highlands of Nova Scotia, Canada, to determine the relationship between wind speeds and CO2 levels in snowpacks. We adapted a soil CO2 diffusion model for the soil-snow system and simulated stepwise changes in transport rate over a broad range of plausible synthetic cases. The goal was to mimic the changes we observed in CO2 snowpack concentration to help elucidate the mechanisms (diffusion, advection) responsible for observed variations. On subdiurnal to diurnal timescales with varying winds and constant snow levels, a strong negative relationship between wind speed and CO2 concentration within the snowpack was often identified. Modelling clearly demonstrated that diffusion alone was unable to replicate the high-frequency CO2 fluctuations, but simulations using above-atmospheric snowpack diffusivities (simulating advective transport within the snowpack) reproduced snow CO2 changes of the observed magnitude and speed. This confirmed that wind-induced ventilation contributed to episodic pulsed emissions from the snow surface and to suppressed snowpack concentrations. This study improves our understanding of winter CO2 dynamics to aid in continued quantification of the annual global C cycle and demonstrates a preference for continuous wintertime CO2 flux measurement systems.

Adapting HYDRUS-1D to Simulate Overland Flow and Reactive Transport During Sheet Flow Deviations

NASA Astrophysics Data System (ADS)

Liang, J.; Bradford, S. A.; Simunek, J.; Hartmann, A.

2017-12-01

The HYDRUS-1D code is a popular numerical model for solving the Richards equation for variably-saturated water flow and solute transport in porous media. This code was adapted to solve rather than the Richards equation for subsurface flow the diffusion wave equation for overland flow at the soil surface. The numerical results obtained by the new model produced an excellent agreement with the analytical solution of the kinematic wave equation. Model tests demonstrated its applicability to simulate the transport and fate of many different solutes, such as non-adsorbing tracers, nutrients, pesticides, and microbes. However, the diffusion wave or kinematic wave equations describe surface runoff as sheet flow with a uniform depth and velocity across the slope. In reality, overland water flow and transport processes are rarely uniform. Local soil topography, vegetation, and spatial soil heterogeneity control directions and magnitudes of water fluxes, and strongly influence runoff characteristics. There is increasing evidence that variations in soil surface characteristics influence the distribution of overland flow and transport of pollutants. These spatially varying surface characteristics are likely to generate non-equilibrium flow and transport processes. HYDRUS-1D includes a hierarchical series of models of increasing complexity to account for both physical equilibrium and non-equilibrium, e.g., dual-porosity and dual-permeability models, up to a dual-permeability model with immobile water. The same conceptualization as used for the subsurface was implemented to simulate non-equilibrium overland flow and transport at the soil surface. The developed model improves our ability to describe non-equilibrium overland flow and transport processes and to improves our understanding of factors that cause this behavior. The HYDRUS-1D overland flow and transport model was additionally also extended to simulate soil erosion. The HYDRUS-1D Soil Erosion Model has been verified by comparing with other soil erosion models. The model performed well when the average soil particle size is relatively large. The performance of the soil erosion model has been further validated by comparing with selected experimental datasets from the literature.

Transport properties of carbon dioxide and methane from molecular dynamics simulations.

PubMed

Aimoli, C G; Maginn, E J; Abreu, C R A

2014-10-07

Transport properties of carbon dioxide and methane are predicted for temperatures between (273.15 and 573.15) K and pressures up to 800 MPa by molecular dynamics simulations. Viscosities and thermal conductivities were obtained through the Green-Kubo formalism, whereas the Einstein relation was used to provide self-diffusion coefficient estimates. The differences in property predictions due to the force field nature and parametrization were investigated by the comparison of seven different CO2 models (two single-site models, three rigid three-site models, and two fully flexible three-site models) and three different CH4 models (two single-site models and one fully flexible five-site model). The simulation results show good agreement with experimental data, except for thermal conductivities at low densities. The molecular structure and force field parameters play an important role in the accuracy of the simulations, which is within the experimental deviations reported for viscosities and self-diffusion coefficients considering the most accurate CO2 and CH4 models studied. On the other hand, the molecular flexibility does not seem to improve accuracy, since the explicit account of vibrational and bending degrees of freedom in the CO2 flexible models leads to slightly less accurate results. Nonetheless, the use of a correctional term to account for vibrational modes in rigid models generally improves estimations of thermal conductivity values. At extreme densities, the caging effect observed with single-site representations of the molecules restrains mobility and leads to an unphysical overestimation of viscosities and, conversely, to the underestimation of self-diffusion coefficients. This result may help to better understand the limits of applicability of such force fields concerning structural and transport properties of dense systems.

Catalytic conversion in nanoporous materials: Concentration oscillations and spatial correlations due to inhibited transport and intermolecular interactions

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

Garcia, Andres; Evans, James W.

2016-11-03

We show that steady-state catalytic conversion in nanoporous materials can occur in a quasi-counter-diffusion mode with the reactant (product) concentration strongly decaying (growing) into the pore, but also with oscillations in the total concentration. These oscillations reflect the response of the fluid to the transition from an extended to a confined environment near the pore opening. We focus on the regime of strongly inhibited transport in narrow pores corresponding to single-file diffusion. Here, limited penetration of the reactant into the pores and the associated low reaction yield is impacted by strong spatial correlations induced by both reaction (non-equilibrium correlations) andmore » also by intermolecular interactions (thermodynamic correlations). We develop a generalized hydrodynamic formulation to effectively describe inhibited transport accounting for the effect of these correlations, and incorporate this description of transport into appropriate reaction-diffusion equations. These equations accurately describe both shorter-range concentration oscillations near the pore opening and the longer-range mesoscale variation of concentration profiles in the pore (and thus also describe reaction yield). Success of the analytic theory is validated by comparison with a precise kinetic Monte Carlo simulation of an appropriate molecular-level stochastic reaction-diffusion model. As a result, this work elucidates unconventional chemical kinetics in interacting confined systems.« less

Thermal Transport Model for Heat Sink Design

NASA Technical Reports Server (NTRS)

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

2009-01-01

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

Stormtime transport of ring current and radiation belt ions

NASA Technical Reports Server (NTRS)

Chen, Margaret W.; Schulz, Michael; Lyons, L. R.; Gorney, David J.

1993-01-01

This is an investigation of stormtime particle transport that leads to formation of the ring current. Our method is to trace the guiding-center motion of representative ions (having selected first adiabatic invariants mu) in response to model substorm-associated impulses in the convection electric field. We compare our simulation results qualitatively with existing analytically tractable idealizations of particle transport (direct convective access and radial diffusion) in order to assess the limits of validity of these approximations. For mu approximately less than 10 MeV/G (E approximately less than 10 keV at L equivalent to 3) the ion drift period on the final (ring-current) drift shell of interest (L equivalent to 3) exceeds the duration of the main phase of our model storm, and we find that the transport of ions to this drift shell is appropriately idealized as direct convective access, typically from open drift paths. Ion transport to a final closed drift path from an open (plasma-sheet) drift trajectory is possible for those portions of that drift path that lie outside the mean stormtime separatrix between closed and open drift trajectories, For mu approximately 10-25 MeV/G (110 keV approximately less than E approximately less than 280 keV at L equivalent to 3) the drift period at L equivalent to 3 is comparable to the postulated 3-hr duration of the storm, and the mode of transport is transitional between direct convective access and transport that resembles radial diffusion. (This particle population is transitional between the ring current and radiation belt). For mu approximately greater than 25 MeV/G (radiation-belt ions having E approximately greater than 280 keV at L equivalent to 3) the ion drift period is considerably shorter than the main phase of a typical storm, and ions gain access to the ring-current region essentially via radial diffusion. By computing the mean and mean-square cumulative changes in 1/L among (in this case) 12 representative ions equally spaced in drift time around the steady-state drift shell of interest (L equivalent to 3), we have estimated (from both our forward and our time-reversed simulations) the time-integrated radial-diffusion coefficients D(sup sim)(sub LL) for particles having selected values of mu approximately greater than 15 MeV/G. The results agree surprisingly well with the predictions (D(sup ql)(sub LL)) of quasilinear radial diffusion theory, despite the rather brief duration (approximately 3 hrs) of our model storm and despite the extreme variability (with frequency) of the spectral-density function that characterizes the applied electric field during our model storm. As expected, the values of D(sup sim)(sub LL) deduced (respectively) from our forward and time-reversed simulations agree even better with each other and with D(sup sim)(sub LL) when the impulse amplitudes which characterize the individual substorms of our model storm are systematically reduced.

Transport and Deposition of Nanoparticles in the Pore Network of a Reservoir Rock: Effects of Pore Surface Heterogeneity and Radial Diffusion

NASA Astrophysics Data System (ADS)

Pham, Ngoc; Papavassiliou, Dimitrios

2014-03-01

In this study, transport behavior of nanoparticles under different pore surface conditions of consolidated Berea sandstone is numerically investigated. Micro-CT scanning technique is applied to obtain 3D grayscale images of the rock sample geometry. Quantitative characterization, which is based on image analysis is done to obtain physical properties of the pore network, such as the pore size distribution and the type of each pore (dead-end, isolated, and fully connected pore). Transport of water through the rock is simulated by employing a 3D lattice Boltzmann method. The trajectories of nanopaticles moving under convection in the simulated flow field and due to molecular diffusion are monitored in the Lagrangian framework. It is assumed in the model that the particle adsorption on the pore surface, which is modeled as a pseudo-first order adsorption, is the only factor hindering particle propagation. The effect of pore surface heterogeneity to the particle breakthrough is considered, and the role of particle radial diffusion is also addressed in details. The financial support of the Advanced Energy Consortium (AEC BEG08-022) and the computational support of XSEDE (CTS090017) are acknowledged.

Finite element analysis of ion transport in solid state nuclear waste form materials

NASA Astrophysics Data System (ADS)

Rabbi, F.; Brinkman, K.; Amoroso, J.; Reifsnider, K.

2017-09-01

Release of nuclear species from spent fuel ceramic waste form storage depends on the individual constituent properties as well as their internal morphology, heterogeneity and boundary conditions. Predicting the release rate is essential for designing a ceramic waste form, which is capable of effectively storing the spent fuel without contaminating the surrounding environment for a longer period of time. To predict the release rate, in the present work a conformal finite element model is developed based on the Nernst Planck Equation. The equation describes charged species transport through different media by convection, diffusion, or migration. And the transport can be driven by chemical/electrical potentials or velocity fields. The model calculates species flux in the waste form with different diffusion coefficient for each species in each constituent phase. In the work reported, a 2D approach is taken to investigate the contributions of different basic parameters in a waste form design, i.e., volume fraction, phase dispersion, phase surface area variation, phase diffusion co-efficient, boundary concentration etc. The analytical approach with preliminary results is discussed. The method is postulated to be a foundation for conformal analysis based design of heterogeneous waste form materials.

Forward Osmosis Membranes under Null-Pressure Condition: Do Hydraulic and Osmotic Pressures Have Identical Nature?

PubMed

Kook, Seungho; Swetha, Chivukula D; Lee, Jangho; Lee, Chulmin; Fane, Tony; Kim, In S

2018-03-20

Forward osmosis (FO) membranes fall into the category of nonporous membranes, based on the assumption that water and solute transport occur solely based on diffusion. The solution-diffusion (S-D) model has been widely used in predicting their performances in the coexistence of hydraulic and osmotic driving forces, a model that postulates the hydraulic and osmotic driving forces have identical nature. It was suggested, however, such membranes may have pores and mass transport could occur both by convection (i.e., volumetric flow) as well as by diffusion assuming that the dense active layer of the membranes is composed of a nonporous structure with defects which induce volumetric flow through the membranes. In addition, the positron annihilation technique has revealed that the active layers can involve relatively uniform porous structures. As such, the assumption of a nonporous active layer in association with hydraulic pressure is questionable. To validate this assumption, we have tested FO membranes under the conditions where hydraulic and osmotic pressures are equivalent yet in opposite directions for water transport, namely the null-pressure condition. We have also established a practically valid characterization method which quantifies the vulnerability of the FO membranes to hydraulic pressure.

Cell-free study of F plasmid partition provides evidence for cargo transport by a diffusion-ratchet mechanism

PubMed Central

Vecchiarelli, Anthony G.; Hwang, Ling Chin; Mizuuchi, Kiyoshi

2013-01-01

Increasingly diverse types of cargo are being found to be segregated and positioned by ParA-type ATPases. Several minimalistic systems described in bacteria are self-organizing and are known to affect the transport of plasmids, protein machineries, and chromosomal loci. One well-studied model is the F plasmid partition system, SopABC. In vivo, SopA ATPase forms dynamic patterns on the nucleoid in the presence of the ATPase stimulator, SopB, which binds to the sopC site on the plasmid, demarcating it as the cargo. To understand the relationship between nucleoid patterning and plasmid transport, we established a cell-free system to study plasmid partition reactions in a DNA-carpeted flowcell. We observed depletion zones of the partition ATPase on the DNA carpet surrounding partition complexes. The findings favor a diffusion-ratchet model for plasmid motion whereby partition complexes create an ATPase concentration gradient and then climb up this gradient toward higher concentrations of the ATPase. Here, we report on the dynamic properties of the Sop system on a DNA-carpet substrate, which further support the proposed diffusion-ratchet mechanism. PMID:23479605

Modeling Issues and Results for Hydrogen Isotopes in NIF Materials

NASA Astrophysics Data System (ADS)

Grossman, Arthur A.; Doerner, R. P.; Luckhardt, S. C.; Seraydarian, R.; Sze, D.; Burnham, A.

1998-11-01

The TMAP4 (G. Longhurst, et al. INEL 1992) model of hydrogen isotope transport in solid materials includes a particle diffusion calculation with Fick's Law modified for Soret Effect (Thermal Diffusion or Thermomigration), coupled to heat transport calculations which are needed because of the strong temperature dependence of diffusivity. These TMAP4 calculations applied to NIF show that high temperatures approaching the melting point and strong thermal gradients of 10^6 K/cm are reached in the first micron of wall material during the SXR pulse. These strong thermal gradients can drive hydrogen isotope migration up or down the thermal gradient depending on the sign of the heat of transport (Soret coefficient) which depends on whether the material dissolves hydrogen endothermically or exothermically. Two candidates for NIF wall material-boron carbide and stainless steel are compared. Boron carbide dissolves hydrogen exothermically so it may drive Soret migration down the thermal gradient deeper into the material, although the thermal gradient is not as large and hydrogen is not as mobile as in stainless steel. Stainless steel dissolves hydrogen endothermically, with a negative Soret coefficient which can drive hydrogen up the thermal gradient and out of the wall.

Optimal-mass-transfer-based estimation of glymphatic transport in living brain

NASA Astrophysics Data System (ADS)

Ratner, Vadim; Zhu, Liangjia; Kolesov, Ivan; Nedergaard, Maiken; Benveniste, Helene; Tannenbaum, Allen

2015-03-01

It was recently shown that the brain-wide cerebrospinal fluid (CSF) and interstitial fluid exchange system designated the `glymphatic pathway' plays a key role in removing waste products from the brain, similarly to the lymphatic system in other body organs . It is therefore important to study the flow patterns of glymphatic transport through the live brain in order to better understand its functionality in normal and pathological states. Unlike blood, the CSF does not flow rapidly through a network of dedicated vessels, but rather through para-vascular channels and brain parenchyma in a slower time-domain, and thus conventional fMRI or other blood-flow sensitive MRI sequences do not provide much useful information about the desired flow patterns. We have accordingly analyzed a series of MRI images, taken at different times, of the brain of a live rat, which was injected with a paramagnetic tracer into the CSF via the lumbar intrathecal space of the spine. Our goal is twofold: (a) find glymphatic (tracer) flow directions in the live rodent brain; and (b) provide a model of a (healthy) brain that will allow the prediction of tracer concentrations given initial conditions. We model the liquid flow through the brain by the diffusion equation. We then use the Optimal Mass Transfer (OMT) approach to derive the glymphatic flow vector field, and estimate the diffusion tensors by analyzing the (changes in the) flow. Simulations show that the resulting model successfully reproduces the dominant features of the experimental data. Keywords: inverse problem, optimal mass transport, diffusion equation, cerebrospinal fluid flow in brain, optical flow, liquid flow modeling, Monge Kantorovich problem, diffusion tensor estimation