Science.gov

Sample records for diffusion models part

  1. Repulsive interactions induced by specific adsorption: Anomalous step diffusivity and inadequacy of nearest-neighbor Ising model. (part I experimental)

    NASA Astrophysics Data System (ADS)

    Al-Shakran, Mohammad; Kibler, Ludwig A.; Jacob, Timo; Ibach, Harald; Beltramo, Guillermo L.; Giesen, Margret

    2016-09-01

    This is Part I of two closely related papers, where we show that the specific adsorption of anions leads to a failure of the nearest-neighbor Ising model to describe island perimeter curvatures on Au(100) electrodes in dilute KBr, HCl and H2SO4 electrolytes and the therewith derived step diffusivity vs. step orientation. This result has major consequences for theoretical studies aiming at the understanding of growth, diffusion and degradation phenomena. Part I focuses on the experimental data. As shown theoretically in detail in Part II (doi:10.1016/j.susc.2016.03.022), a set of nearest-neighbor and next-nearest-neighbor interaction energies (ɛNN, ɛNNN) can uniquely be derived from the diffusivity of steps along <100> and <110>. We find strong repulsive next-nearest neighbor (NNN) interaction in KBr and HCl, whereas NNN interaction is negligibly for H2SO4. The NNN repulsive interaction energy ɛNNN therefore correlates positively with the Gibbs adsorption energy of the anions. We find furthermore that ɛNNN increases with increasing Br- and Cl- coverage. The results for ɛNN and ɛNNN are quantitatively consistent with the coverage dependence of the step line tension. We thereby establish a sound experimental base for theoretical studies on the energetics of steps in the presence of specific adsorption.

  2. Updating applied diffusion models

    SciTech Connect

    Weil, J.C.

    1985-11-01

    Most diffusion models currently used in air quality applications are substantially out of date with understanding of turbulence and diffusion in the planetary boundary layer. Under a Cooperative Agreement with the Environmental Protection Agency, the American Meteorological Society organized a workshop to help improve the basis of such models, their physics and hopefuly their performance. Reviews and recommendations were made on models in three areas: diffusion in the convective boundary layer (CBL), diffusion in the stabe boundary layer (SBL), and model uncertainty.

  3. Updating applied diffusion models

    SciTech Connect

    Weil, J.C.

    1985-01-01

    Most diffusion models currently used in air-quality applications are substantially out of date with understanding of turbulence and diffusion in the planetary boundary layer. Under a Cooperative Agreement with the Environmental Protection Agency, the American Meteorological Society organized a workshop to help improve the basis of such models, their physics and hopefully their performance. Reviews and recommendations were made on models in three areas: diffusion in the convective boundary layer (CBL), diffusion in the stable boundary layer (SBL), and model uncertainty. Progress has been made in all areas, but it is most significant and ready for application to practical models in the case of the CBL. This has resulted from a clear understanding of the vertical structure and diffusion in the CBL, as demonstrated by laboratory experiments, numerical simulations, and field observations. Understanding of turbulence structure and diffusion in the SBL is less complete and not yet ready for general use in applications.

  4. Diffusing Diffusivity: A Model for Anomalous, yet Brownian, Diffusion

    NASA Astrophysics Data System (ADS)

    Chubynsky, Mykyta V.; Slater, Gary W.

    2014-08-01

    Wang et al. [Proc. Natl. Acad. Sci. U.S.A. 106, 15160 (2009)] have found that in several systems the linear time dependence of the mean-square displacement (MSD) of diffusing colloidal particles, typical of normal diffusion, is accompanied by a non-Gaussian displacement distribution G(x ,t), with roughly exponential tails at short times, a situation they termed "anomalous yet Brownian" diffusion. The diversity of systems in which this is observed calls for a generic model. We present such a model where there is diffusivity memory but no direction memory in the particle trajectory, and we show that it leads to both a linear MSD and a non-Gaussian G(x ,t) at short times. In our model, the diffusivity is undergoing a (perhaps biased) random walk, hence the expression "diffusing diffusivity". G(x ,t) is predicted to be exactly exponential at short times if the distribution of diffusivities is itself exponential, but an exponential remains a good fit for a variety of diffusivity distributions. Moreover, our generic model can be modified to produce subdiffusion.

  5. Random diffusion model.

    PubMed

    Mazenko, Gene F

    2008-09-01

    We study the random diffusion model. This is a continuum model for a conserved scalar density field varphi driven by diffusive dynamics. The interesting feature of the dynamics is that the bare diffusion coefficient D is density dependent. In the simplest case, D=D[over ]+D_{1}deltavarphi , where D[over ] is the constant average diffusion constant. In the case where the driving effective Hamiltonian is quadratic, the model can be treated using perturbation theory in terms of the single nonlinear coupling D1 . We develop perturbation theory to fourth order in D1 . The are two ways of analyzing this perturbation theory. In one approach, developed by Kawasaki, at one-loop order one finds mode-coupling theory with an ergodic-nonergodic transition. An alternative more direct interpretation at one-loop order leads to a slowing down as the nonlinear coupling increases. Eventually one hits a critical coupling where the time decay becomes algebraic. Near this critical coupling a weak peak develops at a wave number well above the peak at q=0 associated with the conservation law. The width of this peak in Fourier space decreases with time and can be identified with a characteristic kinetic length which grows with a power law in time. For stronger coupling the system becomes metastable and then unstable. At two-loop order it is shown that the ergodic-nonergodic transition is not supported. It is demonstrated that the critical properties of the direct approach survive, going to higher order in perturbation theory.

  6. Diffuse Cystic Lung Disease. Part II.

    PubMed

    Gupta, Nishant; Vassallo, Robert; Wikenheiser-Brokamp, Kathryn A; McCormack, Francis X

    2015-07-01

    The diffuse cystic lung diseases have a broad differential diagnosis. A wide variety of pathophysiological processes spanning the spectrum from airway obstruction to lung remodeling can lead to multifocal cyst development in the lung. Although lymphangioleiomyomatosis and pulmonary Langerhans cell histiocytosis are perhaps more frequently seen in the clinic, disorders such as Birt-Hogg-Dubé syndrome, lymphocytic interstitial pneumonia, follicular bronchiolitis, and light-chain deposition disease are increasingly being recognized. Obtaining an accurate diagnosis can be challenging, and management approaches are highly disease dependent. Unique imaging features, genetic tests, serum studies, and clinical features provide invaluable clues that help clinicians distinguish among the various etiologies, but biopsy is often required for definitive diagnosis. In part II of this review, we present an overview of the diffuse cystic lung diseases caused by lymphoproliferative disorders, genetic mutations, or aberrant lung development and provide an approach to aid in their diagnosis and management.

  7. 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.

  8. Simplification of physics-based electrochemical model for lithium ion battery on electric vehicle. Part I: Diffusion simplification and single particle model

    NASA Astrophysics Data System (ADS)

    Han, Xuebing; Ouyang, Minggao; Lu, Languang; Li, Jianqiu

    2015-03-01

    Now the lithium ion batteries are widely used in electrical vehicles (EV). The battery modeling and state estimation is of great significance. The rigorous physic based electrochemical model is too complicated for on-line simulation in vehicle. In this work, the simplification of physics-based model lithium ion battery for application in battery management system (BMS) on real electrical vehicle is proposed. Approximate method for solving the solid phase diffusion and electrolyte concentration distribution problems is introduced. The approximate result is very close to the rigorous model but fewer computations are needed. An extended single particle model is founded based on these approximated results and the on-line state of charge (SOC) estimation algorithm using the extended Kalman filter with this single particle model is discussed. This SOC estimation algorithm could be used in the BMS in real vehicle.

  9. Fractal model of anomalous diffusion.

    PubMed

    Gmachowski, Lech

    2015-12-01

    An equation of motion is derived from fractal analysis of the Brownian particle trajectory in which the asymptotic fractal dimension of the trajectory has a required value. The formula makes it possible to calculate the time dependence of the mean square displacement for both short and long periods when the molecule diffuses anomalously. The anomalous diffusion which occurs after long periods is characterized by two variables, the transport coefficient and the anomalous diffusion exponent. An explicit formula is derived for the transport coefficient, which is related to the diffusion constant, as dependent on the Brownian step time, and the anomalous diffusion exponent. The model makes it possible to deduce anomalous diffusion properties from experimental data obtained even for short time periods and to estimate the transport coefficient in systems for which the diffusion behavior has been investigated. The results were confirmed for both sub and super-diffusion.

  10. Diffusion in silicate melts: III. Empirical models for multicomponent diffusion

    NASA Astrophysics Data System (ADS)

    Yan, Liang; Richter, Frank M.; Chamberlin, Laurinda

    1997-12-01

    Empirical models for multicomponent diffusion in an isotropic fluid were derived by splitting the component's dispersion velocity into two parts: (a) an intrinsic velocity which is proportional to each component's electrochemical potential gradient and independent of reference frame and (b) a net interaction velocity which is both model and reference frame dependent. Simple molecules (e.g., M pO q) were chosen as endmember components. The interaction velocity is assumed to be either the same for each component (leading to a common relaxation velocity U) or proportional to a common interaction force ( F). U or F is constrained by requiring no local buildup in either volume or charge. The most general form of the model-derived diffusion matrix [ D] can be written as a product of a model-dependent kinetic matrix [ L] and a model independent thermodynamic matrix [ G], [ D] = [ L] · [ G]. The elements of [ G] are functions of derivatives of chemical potential with respect to concentration. The elements of [ L] are functions of concentration and partial molar volume of the endmember components, Cio and Vio, and self diffusivity Di, and charge number zi of individual diffusing species. When component n is taken as the dependent variable they can be written in a common form L ij = D jδ ij + C io[V noD n - V joD j)A i + (p nz nD n - p jz jD j)B i] where the functional forms of the scaling factors Ai and Bi depend on the model considered. The off-diagonal element Lij ( i ≠ j) is directly proportional to the concentration of component i, and thus negligible when i is a dilute component. The salient feature of kinetic interaction or relaxation is to slow down larger (volume or charge) and faster diffusing components and to speed up smaller (volume or charge) and slower moving species, in order to prevent local volume or charge buildup. Empirical models for multicomponent diffusion were tested in the ternary system CaOAl 2O 3SiO 2 at 1500°C and 1 GPa over a large

  11. Multispecies diffusion models: A study of uranyl species diffusion

    SciTech Connect

    Liu, Chongxuan; Shang, Jianying; Zachara, John M.

    2011-12-14

    Rigorous numerical description of multi-species diffusion requires coupling of species, charge, and aqueous and surface complexation reactions that collectively affect diffusive fluxes. The applicability of a fully coupled diffusion model is, however, often constrained by the availability of species self-diffusion coefficients, as well as by computational complication for imposing charge conservation. In this study, several diffusion models with variable complexity in charge and species coupling were formulated and compared to describe reactive multi-species diffusion in groundwater. Diffusion of uranyl [U(VI)] species was used as an example in demonstrating the effectiveness of the models in describing multi-species diffusion. Numerical simulations found that a diffusion model with a single, common diffusion coefficient for all species was sufficient to describe multi-species U(VI) diffusion under steady-state condition of major chemical composition, but not under transient chemical conditions. Simulations revealed that a fully coupled diffusion model can be well approximated by a component-based diffusion model, which considers difference in diffusion coefficients between chemical components, but not between the species within each chemical component. This treatment significantly enhanced computational efficiency at the expense of minor charge conservation. The charge balance in the component-based diffusion model can be rigorously enforced, if necessary, by adding an artificial kinetic reaction term induced by the charge separation. The diffusion models were applied to describe U(VI) diffusive mass transfer in intragranular domains in two sediments collected from US Department of Energy's Hanford 300A where intragrain diffusion is a rate-limiting process controlling U(VI) adsorption and desorption. The grain-scale reactive diffusion model was able to describe U(VI) adsorption/desorption kinetics that has been described using a semi-empirical, multi-rate model

  12. Multispecies diffusion models: A study of uranyl species diffusion

    NASA Astrophysics Data System (ADS)

    Liu, Chongxuan; Shang, Jianying; Zachara, John M.

    2011-12-01

    Rigorous numerical description of multispecies diffusion requires coupling of species, charge, and aqueous and surface complexation reactions that collectively affect diffusive fluxes. The applicability of a fully coupled diffusion model is, however, often constrained by the availability of species self-diffusion coefficients, as well as by computational complication in imposing charge conservation. In this study, several diffusion models with variable complexity in charge and species coupling were formulated and compared to describe reactive multispecies diffusion in groundwater. Diffusion of uranyl [U(VI)] species was used as an example in demonstrating the effectiveness of the models in describing multispecies diffusion. Numerical simulations found that a diffusion model with a single, common diffusion coefficient for all species was sufficient to describe multispecies U(VI) diffusion under a steady state condition of major chemical composition, but not under transient chemical conditions. Simulations revealed that for multispecies U(VI) diffusion under transient chemical conditions, a fully coupled diffusion model could be well approximated by a component-based diffusion model when the diffusion coefficient for each chemical component was properly selected. The component-based diffusion model considers the difference in diffusion coefficients between chemical components, but not between the species within each chemical component. This treatment significantly enhanced computational efficiency at the expense of minor charge conservation. The charge balance in the component-based diffusion model can be enforced, if necessary, by adding a secondary migration term resulting from model simplification. The effect of ion activity coefficient gradients on multispecies diffusion is also discussed. The diffusion models were applied to describe U(VI) diffusive mass transfer in intragranular domains in two sediments collected from U.S. Department of Energy's Hanford 300A

  13. In-silico model of skin penetration based on experimentally determined input parameters. Part I: experimental determination of partition and diffusion coefficients.

    PubMed

    Hansen, Steffi; Henning, Andreas; Naegel, Arne; Heisig, Michael; Wittum, Gabriel; Neumann, Dirk; Kostka, Karl-Heinz; Zbytovska, Jarmila; Lehr, Claus-Michael; Schaefer, Ulrich F

    2008-02-01

    Mathematical modeling of skin transport is considered a valuable alternative of in-vitro and in-vivo investigations especially considering ethical and economical questions. Mechanistic diffusion models describe skin transport by solving Fick's 2nd law of diffusion in time and space; however models relying entirely on a consistent experimental data set are missing. For a two-dimensional model membrane consisting of a biphasic stratum corneum (SC) and a homogeneous epidermal/dermal compartment (DSL) methods are presented to determine all relevant input parameters. The data were generated for flufenamic acid (M(W) 281.24g/mol; logK(Oct/H2O) 4.8; pK(a) 3.9) and caffeine (M(W) 194.2g/mol; logK(Oct/H2O) -0.083; pK(a) 1.39) using female abdominal skin. K(lip/don) (lipid-donor partition coefficient) was determined in equilibration experiments with human SC lipids. K(cor/lip) (corneocyte-lipid) and K(DSL/lip) (DSL-lipid) were derived from easily available experimental data, i.e. K(SC/don) (SC-donor), K(lip/don) and K(SC/DSL) (SC-DSL) considering realistic volume fractions of the lipid and corneocyte phases. Lipid and DSL diffusion coefficients D(lip) and D(DSL) were calculated based on steady state flux. The corneocyte diffusion coefficient D(cor) is not accessible experimentally and needs to be estimated by simulation. Based on these results time-dependent stratum corneum concentration-depth profiles were simulated and compared to experimental profiles in an accompanying study.

  14. Numerical study on convection diffusion for gasification agent in underground coal gasification. Part I: establishment of mathematical models and solving method

    SciTech Connect

    Yang, L.H.; Ding, Y.M.

    2009-07-01

    The aim of this article is to discuss the distribution law of the gasification agent concentration in a deep-going way during underground coal gasification and the new method of solving the problem for the convection diffusion of the gas. In this paper, the basic features of convection diffusion for the gas produced in underground coal gasification are studied. On the basis of the model experiment, through the analysis of the distribution and patterns of variation for the fluid concentration field in the process of the combustion and gasification of the coal seams within the gasifier, the 3-D non-linear unstable mathematical models on the convection diffusion for oxygen are established. In order to curb such pseudo-physical effects as numerical oscillation and surfeit which frequently occurred in the solution of the complex mathematical models, the novel finite unit algorithm, the upstream weighted multi-cell balance method is advanced in this article, and its main derivation process is introduced.

  15. Lithium isotope fractionation by diffusion in minerals. Part 1: Pyroxenes

    NASA Astrophysics Data System (ADS)

    Richter, Frank; Watson, Bruce; Chaussidon, Marc; Mendybaev, Ruslan; Ruscitto, Dan

    2014-02-01

    Several recent studies found large lithium isotopic fractionations correlated with concentration gradients in pyroxene minerals from lava flows and mantle nodules that were interpreted as indicating diffusion of lithium into the grains. Motivated by these findings experiments were undertaken in which powdered spodumene (LiAlSi2O6) or Li2SiO3 was used to diffuse lithium into Templeton augite or Dekalb diopside grains at 900 °C and oxygen fugacity ranging from log fO2 = -17 to log fO2 = -12. The purpose of these experiments was to determine the diffusion coefficient of lithium in pyroxene minerals and to measure the isotopic fractionation of lithium in the diffusion boundary layer due to the relative mobility of 6Li compared to 7Li. The diffusion profiles of lithium that had not yet reached the center of Templeton augite grains were in most cases sharp steps propagating in from each boundary. In one case a more usual profile with smoothly decreasing lithium concentration with distance from the grain boundary was found. A model in which lithium occupies two different sites - one being fast diffusing interstitial lithium, the other much less mobile lithium in a metal site, reproduced both types of profiles. The step-like profiles arise in the model when interstitial lithium diffusing into the grain is strongly partitioned into abundant metal sites and thus does not penetrate further into the grain until all the metal sites at a given distance become filled. While the rate of propagation of the concentration step can be used to calculate an effective diffusivity for the penetration of lithium into the augite grains, the multiple speciation of lithium precludes making a separate precise determination of the diffusion coefficient of the interstitial lithium. Isotopic fractionations of 7Li/6Li of about 30‰ were found in the step-like diffusion boundary layers, which translate into a ratio of the isotope diffusion coefficients D/D=0.9592 (i.e., (6/7)β with β = 0

  16. Effects of inlet flow field conditions on the performance of centrifugal compressor diffusers: Part 2 -- Straight-channel diffuser

    SciTech Connect

    Deniz, S.; Greitzer, E.M.; Cumpsty, N.A.

    2000-01-01

    This is Part 2 of an examination of the influence of inlet flow conditions on the performance and operating range of centrifugal compressor vaned diffusers. The paper describes tests of a straight-channel type diffuser, sometimes called a wedge-vane diffuser, and compares the results with those from the discrete-passage diffusers described in Part 1. Effects of diffuser inlet Mach number, flow angle, blockage, and axial flow nonuniformity on diffuser pressure recovery and operating range are addressed. The straight-channel diffuser investigated has 30 vanes and was designed for the same aerodynamic duty as the discrete-passage diffuser described in Part 1. The ranges of the overall pressure recovery coefficients were 0.50--0.78 for the straight-channel diffuser and 0.50--0.70 for the discrete-passage diffuser, except when the diffuser was choked. In other words, the maximum pressure recovery of the straight-channel diffuser was found to be roughly 10% higher than that of the discrete-passage diffuser investigated. The two types of diffuser showed similar behavior regarding the dependence of pressure recovery on diffuser inlet flow angle and the insensitivity of the performance to inlet flow field axial distortion and Mach number. The operating range of the straight-channel diffuser, as for the discrete-passage diffusers, was limited by the onset of rotating stall at a fixed momentum-averaged flow angle into the diffuser, which was for the straight-channel diffuser, {alpha}{sub crit} = 70 {+-} 0.5 deg. The background, nomenclature, and description of the facility and method are all given in Part 1.

  17. Random diffusion model with structure corrections

    NASA Astrophysics Data System (ADS)

    McCowan, David D.; Mazenko, Gene F.

    2010-05-01

    The random diffusion model is a continuum model for a conserved scalar density field ϕ driven by diffusive dynamics where the bare diffusion coefficient is density dependent. We generalize the model from one with a sharp wave-number cutoff to one with a more natural large wave-number cutoff. We investigate whether the features seen previously—namely, a slowing down of the system and the development of a prepeak in the dynamic structure factor at a wave number below the first structure peak—survive in this model. A method for extracting information about a hidden prepeak in experimental data is presented.

  18. Connectionist and diffusion models of reaction time.

    PubMed

    Ratcliff, R; Van Zandt, T; McKoon, G

    1999-04-01

    Two connectionist frameworks, GRAIN (J. L. McClelland, 1993) and brain-state-in-a-box (J. A. Anderson, 1991), and R. Ratcliff's (1978) diffusion model were evaluated using data from a signal detection task. Dependent variables included response probabilities, reaction times for correct and error responses, and shapes of reaction-time distributions. The diffusion model accounted for all aspects of the data, including error reaction times that had previously been a problem for all response-time models. The connectionist models accounted for many aspects of the data adequately, but each failed to a greater or lesser degree in important ways except for one model that was similar to the diffusion model. The findings advance the development of the diffusion model and show that the long tradition of reaction-time research and theory is a fertile domain for development and testing of connectionist assumptions about how decisions are generated over time.

  19. Effects of inlet flow field conditions on the performance of centrifugal compressor diffusers: Part 1 -- Discrete-passage diffuser

    SciTech Connect

    Filipenco, V.G.; Deniz, S.; Johnston, J.M.; Greitzer, E.M.; Cumpsty, N.A.

    2000-01-01

    This is Part 1 of a two-part paper considering the performance of radial diffusers for use in a high-performance centrifugal compressor. Part 1 reports on discrete-passage diffusers, while Part 2 describes a test of a straight-channel diffuser designed for equivalent duty. Two builds of discrete-passage diffuser were tested, with 30 and 38 separate passages. Both the 30 and 38 passage diffusers investigated showed comparable range of unstalled operation and similar level of overall diffuser pressure recovery. The paper concentrates on the influence of inlet flow conditions on the pressure recovery and operating range of radial diffusers for centrifugal compressor stages. The flow conditions examined include diffuser inlet Mach number, flow angle, blockage, and axial flow nonuniformity. The investigation was carried out in a specially built test facility, designed to provide a controlled inlet flow field to the test diffusers. The facility can provide a wide range of diffuser inlet velocity profile distortion and skew with Mach numbers up to unity and flow angles of 63 to 75 deg from the radical direction. The consequences of different averaging methods for the inlet total pressure distributions, which are needed in the definition of diffuser pressure recovery coefficient for nonuniform diffuser inlet conditions, were also assessed. The overall diffuser pressure recovery coefficient, based on suitably averaged inlet total pressure, was found to correlate well with the momentum-averaged flow angle into the diffuser. It is shown that the generally accepted sensitivity of diffuser pressure recovery performance to inlet flow distortion and boundary layer blockage can be largely attributed to inappropriate quantification of the average dynamic pressure at diffuser inlet. Use of an inlet dynamic pressure based on availability or mass-averaging in combination with definition of inlet flow angle based on mass average of the radial and tangential velocity at diffuser inlet

  20. Patch-based anisotropic diffusion scheme for fluorescence diffuse optical tomography—part 1: technical principles

    NASA Astrophysics Data System (ADS)

    Correia, Teresa; Arridge, Simon

    2016-02-01

    Fluorescence diffuse optical tomography (fDOT) provides 3D images of fluorescence distributions in biological tissue, which represent molecular and cellular processes. The image reconstruction problem is highly ill-posed and requires regularisation techniques to stabilise and find meaningful solutions. Quadratic regularisation tends to either oversmooth or generate very noisy reconstructions, depending on the regularisation strength. Edge preserving methods, such as anisotropic diffusion regularisation (AD), can preserve important features in the fluorescence image and smooth out noise. However, AD has limited ability to distinguish an edge from noise. In this two-part paper, we propose a patch-based anisotropic diffusion regularisation (PAD), where regularisation strength is determined by a weighted average according to the similarity between patches around voxels within a search window, instead of a simple local neighbourhood strategy. However, this method has higher computational complexity and, hence, we wavelet compress the patches (PAD-WT) to speed it up, while simultaneously taking advantage of the denoising properties of wavelet thresholding. The proposed method combines the nonlocal means (NLM), AD and wavelet shrinkage methods, which are image processing methods. Therefore, in this first paper, we used a denoising test problem to analyse the performance of the new method. Our results show that the proposed PAD-WT method provides better results than the AD or NLM methods alone. The efficacy of the method for fDOT image reconstruction problem is evaluated in part 2.

  1. Patch-based anisotropic diffusion scheme for fluorescence diffuse optical tomography--part 1: technical principles.

    PubMed

    Correia, Teresa; Arridge, Simon

    2016-02-21

    Fluorescence diffuse optical tomography (fDOT) provides 3D images of fluorescence distributions in biological tissue, which represent molecular and cellular processes. The image reconstruction problem is highly ill-posed and requires regularisation techniques to stabilise and find meaningful solutions. Quadratic regularisation tends to either oversmooth or generate very noisy reconstructions, depending on the regularisation strength. Edge preserving methods, such as anisotropic diffusion regularisation (AD), can preserve important features in the fluorescence image and smooth out noise. However, AD has limited ability to distinguish an edge from noise. In this two-part paper, we propose a patch-based anisotropic diffusion regularisation (PAD), where regularisation strength is determined by a weighted average according to the similarity between patches around voxels within a search window, instead of a simple local neighbourhood strategy. However, this method has higher computational complexity and, hence, we wavelet compress the patches (PAD-WT) to speed it up, while simultaneously taking advantage of the denoising properties of wavelet thresholding. The proposed method combines the nonlocal means (NLM), AD and wavelet shrinkage methods, which are image processing methods. Therefore, in this first paper, we used a denoising test problem to analyse the performance of the new method. Our results show that the proposed PAD-WT method provides better results than the AD or NLM methods alone. The efficacy of the method for fDOT image reconstruction problem is evaluated in part 2.

  2. Modeling diffusion in foamed polymer nanocomposites.

    PubMed

    Ippalapalli, Sandeep; Ranaprathapan, A Dileep; Singh, Sachchida N; Harikrishnan, G

    2013-04-15

    Two-way multicomponent diffusion processes in polymeric nanocomposite foams, where the condensed phase is nanoscopically reinforced with impermeable fillers, are investigated. The diffusion process involves simultaneous outward permeation of the components of the dispersed gas phase and inward diffusion of atmospheric air. The transient variation in thermal conductivity of foam is used as the macroscopic property to track the compositional variations of the dispersed gases due to the diffusion process. In the continuum approach adopted, the unsteady-state diffusion process is combined with tortuosity theory. The simulations conducted at ambient temperature reveal distinct regimes of diffusion processes in the nanocomposite foams owing to the reduction in the gas-transport rate induced by nanofillers. Simulations at a higher temperature are also conducted and the predictions are compared with experimentally determined thermal conductivities under accelerated diffusion conditions for polyurethane foams reinforced with clay nanoplatelets of varying individual lamellar dimensions. Intermittent measurements of foam thermal conductivity are performed while the accelerated diffusion proceeded. The predictions under accelerated diffusion conditions show good agreement with experimentally measured thermal conductivities for nanocomposite foams reinforced with low and medium aspect-ratios fillers. The model shows higher deviations for foams with fillers that have a high aspect ratio.

  3. Circumnutation modeled by reaction-diffusion equations

    SciTech Connect

    Lubkin, S.R.

    1992-01-01

    In studies of biological oscillators, plants are only rarely examined. The authors study a common sub-diurnal oscillation of plants, called circumnutation. Based on experimental evidence that the oscillations consist of a turgor wave traveling around a growing plant part, circumnutation is modeled by a nonlinear reaction-diffusion system with cylindrical geometry. Because of its simplicity, and because biological oscillations are so common, an oscillatory [lambda]-[omega] reaction-diffusion system is chosen for the model. The authors study behavior of traveling waves in [lambda]-[omega] systems. The authors show the existence of Hopf bifurcations and the stability of the limit cycles born at the Hopf bifurcation for some parameter values. Using a Lindstedt-type perturbation scheme, the authors construct periodic solutions of the [lambda]-[omega] system near a Hopf bifurcation and show that the periodic solutions superimposed on the original traveling wave have the effect of altering its overall frequency and amplitude. Circumnutating plants generally display a strong directional preference to their oscillations, which is species-dependent. Circumnutation is modeled by a [lambda]-[omega] system on an annulus of variable width, which does not possess reflection symmetry about any axis. The annulus represents a region of high potassium concentration in the cross-section of the stem. The asymmetry of the annulus represents the anatomical asymmetry of the plant. Traveling waves are constructed on this variable-width annulus by a perturbation scheme, and perturbing the width of the annulus alters the amplitude and frequency of traveling waves on the domain by a small (order [epsilon][sup 2]) amount. The speed, frequency, and stability are unaffected by the direction of travel of the wave on the annulus. This indicates that the [lambda]-[omega] system on a variable-width domain cannot account for directional preferences of traveling waves in biological systems.

  4. SiC Recession Due to SiO2 Scale Volatility Under Combustion Conditions. Part 2; Thermodynamics and Gaseous Diffusion Model

    NASA Technical Reports Server (NTRS)

    Opila, Elizabeth J.; Smialek, James L.; Robinson, Raymond C.; Fox, Dennis S.; Jacobson, Nathan S.

    1998-01-01

    In combustion environments, volatilization of SiO2 to Si-O-H(g) species is a critical issue. Available thermochemical data for Si-O-H(g) species were used to calculate boundary layer controlled fluxes from SiO2. Calculated fluxes were compared to volatilization rates Of SiO2 scales grown on SiC which were measured in Part 1 of this paper. Calculated volatilization rates were also compared to those measured in synthetic combustion gas furnace tests. Probable vapor species were identified in both fuel-lean and fuel-rich combustion environments based on the observed pressure, temperature and velocity dependencies as well as the magnitude of the volatility rate. Water vapor is responsible for the degradation of SiO2 in the fuel-lean environment. Silica volatility in fuel-lean combustion environments is attributed primarily to the formation of Si(OH)4(g) with a small contribution of SiO(OH)2(g).

  5. Models (Part 1).

    ERIC Educational Resources Information Center

    Callison, Daniel

    2002-01-01

    Defines models and describes information search models that can be helpful to instructional media specialists in meeting users' abilities and information needs. Explains pathfinders and Kuhlthau's information search process, including the pre-writing information search process. (LRW)

  6. Stochastic models for surface diffusion of molecules

    SciTech Connect

    Shea, Patrick Kreuzer, Hans Jürgen

    2014-07-28

    We derive a stochastic model for the surface diffusion of molecules, starting from the classical equations of motion for an N-atom molecule on a surface. The equation of motion becomes a generalized Langevin equation for the center of mass of the molecule, with a non-Markovian friction kernel. In the Markov approximation, a standard Langevin equation is recovered, and the effect of the molecular vibrations on the diffusion is seen to lead to an increase in the friction for center of mass motion. This effective friction has a simple form that depends on the curvature of the lowest energy diffusion path in the 3N-dimensional coordinate space. We also find that so long as the intramolecular forces are sufficiently strong, memory effects are usually not significant and the Markov approximation can be employed, resulting in a simple one-dimensional model that can account for the effect of the dynamics of the molecular vibrations on the diffusive motion.

  7. Models, Part IV: Inquiry Models.

    ERIC Educational Resources Information Center

    Callison, Daniel

    2002-01-01

    Discusses models for information skills that include inquiry-oriented activities. Highlights include WebQuest, which uses Internet resources supplemented with videoconferencing; Minnesota's Inquiry Process based on the Big Six model for information problem-solving; Indiana's Student Inquiry Model; constructivist learning models for inquiry; and…

  8. Patch-based anisotropic diffusion scheme for fluorescence diffuse optical tomography—part 2: image reconstruction

    NASA Astrophysics Data System (ADS)

    Correia, Teresa; Koch, Maximilian; Ale, Angelique; Ntziachristos, Vasilis; Arridge, Simon

    2016-02-01

    Fluorescence diffuse optical tomography (fDOT) provides 3D images of fluorescence distributions in biological tissue, which represent molecular and cellular processes. The image reconstruction problem is highly ill-posed and requires regularisation techniques to stabilise and find meaningful solutions. Quadratic regularisation tends to either oversmooth or generate very noisy reconstructions, depending on the regularisation strength. Edge preserving methods, such as anisotropic diffusion regularisation (AD), can preserve important features in the fluorescence image and smooth out noise. However, AD has limited ability to distinguish an edge from noise. We propose a patch-based anisotropic diffusion regularisation (PAD), where regularisation strength is determined by a weighted average according to the similarity between patches around voxels within a search window, instead of a simple local neighbourhood strategy. However, this method has higher computational complexity and, hence, we wavelet compress the patches (PAD-WT) to speed it up, while simultaneously taking advantage of the denoising properties of wavelet thresholding. Furthermore, structural information can be incorporated into the image reconstruction with PAD-WT to improve image quality and resolution. In this case, the weights used to average voxels in the image are calculated using the structural image, instead of the fluorescence image. The regularisation strength depends on both structural and fluorescence images, which guarantees that the method can preserve fluorescence information even when it is not structurally visible in the anatomical images. In part 1, we tested the method using a denoising problem. Here, we use simulated and in vivo mouse fDOT data to assess the algorithm performance. Our results show that the proposed PAD-WT method provides high quality and noise free images, superior to those obtained using AD.

  9. Flux-mediated diffuse mismatch model

    NASA Astrophysics Data System (ADS)

    Loh, G. C.; Tay, B. K.; Teo, E. H. T.

    2010-09-01

    The diffuse mismatch model (DMM) is modified to account for the effect of thermal flux on phonon transmission at interfaces. This new model, the flux-mediated diffuse mismatch model (FMDMM) takes a slightly different approach in its formulation, and does not employ the principle of detailed balance. Two competing processes—an increase in the flux coefficient, and a decrease in the rest of the transmission term, may result in either a rise or fall in thermal boundary resistance when thermal flux is increased. This might partially explain the large disparities between experimental, theoretical, and simulated results of thermal boundary resistance.

  10. 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

  11. Configurational diffusion of asphaltenes in fresh and aged catalysts extrudates. [Mathematical configurational diffusion model

    SciTech Connect

    Guin, J.A.; Tarrer, A.R.

    1992-01-01

    The objective of this research is to determine the relationship between the size and shape of coal and petroleum macromolecules and their diffusion rates i.e., effective diffusivities, in catalyst pore structures. That is, how do the effective intrapore diffusivities depend on molecule configuration and pore geometry. This quarter we made a more comprehensive literature survey concerning configurational diffusion in porous catalysts or catalyst supports. A detailed literature review is reported. Also, a mathematical configurational diffusion model was developed. By using this model, the effective diffusivity for model compounds diffusing in porous media and a linear adsorption constant can be determined by fitting experimental data.

  12. MODIS Solar Diffuser: Modelled and Actual Performance

    NASA Technical Reports Server (NTRS)

    Waluschka, Eugene; Xiong, Xiao-Xiong; Esposito, Joe; Wang, Xin-Dong; Krebs, Carolyn (Technical Monitor)

    2001-01-01

    The Moderate Resolution Imaging Spectroradiometer (MODIS) instrument's solar diffuser is used in its radiometric calibration for the reflective solar bands (VIS, NTR, and SWIR) ranging from 0.41 to 2.1 micron. The sun illuminates the solar diffuser either directly or through a attenuation screen. The attenuation screen consists of a regular array of pin holes. The attenuated illumination pattern on the solar diffuser is not uniform, but consists of a multitude of pin-hole images of the sun. This non-uniform illumination produces small, but noticeable radiometric effects. A description of the computer model used to simulate the effects of the attenuation screen is given and the predictions of the model are compared with actual, on-orbit, calibration measurements.

  13. Models, Part V: Composition Models.

    ERIC Educational Resources Information Center

    Callison, Daniel

    2003-01-01

    Describes four models: The Authoring Cycle, a whole language approach that reflects the inquiry process; I-Search, an approach to research that uses the power of student interests; Cultural Celebration, using local heritage topics; and Science Lab Report, for the composition of a lab report. (LRW)

  14. Modelling Diffusion of a Personalized Learning Framework

    ERIC Educational Resources Information Center

    Karmeshu; Raman, Raghu; Nedungadi, Prema

    2012-01-01

    A new modelling approach for diffusion of personalized learning as an educational process innovation in social group comprising adopter-teachers is proposed. An empirical analysis regarding the perception of 261 adopter-teachers from 18 schools in India about a particular personalized learning framework has been made. Based on this analysis,…

  15. Generalized Drift-Diffusion Model In Semiconductors

    SciTech Connect

    Mesbah, S.; Bendib-Kalache, K.; Bendib, A.

    2008-09-23

    A new drift-diffusion model is proposed based on the computation of the stationary nonlocal current density. The semi classical Boltzmann equation is solved keeping all the anisotropies of the distribution function with the use of the continued fractions. The conductivity is calculated in the linear approximation and for arbitrary collision frequency with respect to Kv{sub t} where K{sup -1} is the characteristic length scale of the system and V{sub t} is the thermal velocity. The nonlocal conductivity can be used to close the generalized drift-diffusion equations valid for arbitrary collisionality.

  16. Coupled chemical and diffusion model for compacted bentonite

    SciTech Connect

    Olin, M.; Lehikoinen, J.; Muurinen, A.

    1995-12-31

    A chemical equilibrium model has been developed for ion-exchange and to a limited extent for other reactions, such as precipitation or dissolution of calcite or gypsum, in compacted bentonite water systems. The model was successfully applied to some bentonite experiments, especially as far as monovalent ions were concerned. The fitted log-binding constants for the exchange of sodium for potassium, magnesium, and calcium were 0.27, 1.50, and 2.10, respectively. In addition, a coupled chemical and diffusion model has been developed to take account of diffusion in pore water, surface diffusion and ion-exchange.d the model was applied to the same experiments as the chemical equilibrium model, and its validation was found partly successful. The above values for binding constants were used also in the coupled model. The apparent (both for anions and cations) and surface diffusion (only for cations) constants yielding the best agreement between calculated and experimental data were 3.0 {times} 10{sup {minus}11} m{sup 2}/s and 6.0 {times} 10{sup {minus}12} m{sup 2}/s, respectively. These values are questionable, however, as experimental results good enough for fitting are currently not available.

  17. Modeling Demic and Cultural Diffusion: An Introduction.

    PubMed

    Fort, Joaquim; Crema, Enrico R; Madella, Marco

    2015-07-01

    Identifying the processes by which human cultures spread across different populations is one of the most topical objectives shared among different fields of study. Seminal works have analyzed a variety of data and attempted to determine whether empirically observed patterns are the result of demic and/or cultural diffusion. This special issue collects articles exploring several themes (from modes of cultural transmission to drivers of dispersal mechanisms) and contexts (from the Neolithic in Europe to the spread of computer programming languages), which offer new insights that will augment the theoretical and empirical basis for the study of demic and cultural diffusion. In this introduction we outline the state of art in the modeling of these processes, briefly discuss the pros and cons of two of the most commonly used frameworks (equation-based models and agent-based models), and summarize the significance of each article in this special issue.

  18. Modeling Demic and Cultural Diffusion: An Introduction.

    PubMed

    Fort, Joaquim; Crema, Enrico R; Madella, Marco

    2015-07-01

    Identifying the processes by which human cultures spread across different populations is one of the most topical objectives shared among different fields of study. Seminal works have analyzed a variety of data and attempted to determine whether empirically observed patterns are the result of demic and/or cultural diffusion. This special issue collects articles exploring several themes (from modes of cultural transmission to drivers of dispersal mechanisms) and contexts (from the Neolithic in Europe to the spread of computer programming languages), which offer new insights that will augment the theoretical and empirical basis for the study of demic and cultural diffusion. In this introduction we outline the state of art in the modeling of these processes, briefly discuss the pros and cons of two of the most commonly used frameworks (equation-based models and agent-based models), and summarize the significance of each article in this special issue. PMID:26932566

  19. Relativistic diffusion processes and random walk models

    SciTech Connect

    Dunkel, Joern; Talkner, Peter; Haenggi, Peter

    2007-02-15

    The nonrelativistic standard model for a continuous, one-parameter diffusion process in position space is the Wiener process. As is well known, the Gaussian transition probability density function (PDF) of this process is in conflict with special relativity, as it permits particles to propagate faster than the speed of light. A frequently considered alternative is provided by the telegraph equation, whose solutions avoid superluminal propagation speeds but suffer from singular (noncontinuous) diffusion fronts on the light cone, which are unlikely to exist for massive particles. It is therefore advisable to explore other alternatives as well. In this paper, a generalized Wiener process is proposed that is continuous, avoids superluminal propagation, and reduces to the standard Wiener process in the nonrelativistic limit. The corresponding relativistic diffusion propagator is obtained directly from the nonrelativistic Wiener propagator, by rewriting the latter in terms of an integral over actions. The resulting relativistic process is non-Markovian, in accordance with the known fact that nontrivial continuous, relativistic Markov processes in position space cannot exist. Hence, the proposed process defines a consistent relativistic diffusion model for massive particles and provides a viable alternative to the solutions of the telegraph equation.

  20. Analytic modeling of a spray diffusion flame

    NASA Technical Reports Server (NTRS)

    Harsha, P. T.; Edelman, R. B.

    1984-01-01

    A detailed model for a spray diffusion flame is described. The model is based on the boundary layer form of the equations of motion, with droplet transport accounted for using a discretized droplet size distribution function. Interphase transport of mass and energy are accounted for, with a flame-sheet model used to describe the combustion process on a droplet scale. Near dynamic equilibrium is assumed for the description of droplet transport; droplets can diffuse relative to the gas phase. Gas-phase mixing is accounted for using a two-equation turbulence model; buoyancy effects are included, with a temperature fluctuation equation used to account for buoyancy effects on turbulence structure. Thermal radiation from gas-phase CO2 and H2O is included. Gas-phase chemical kinetics are modeled using a 20-reaction, 10-species version of the advanced quasi-global chemical kinetics formulation. Results are compared with data for a vaporizing Freon spray and a pentane spray flame. It is shown that the computational approach provides a reasonably valid picture of the overall development of a spray diffusion flame, and, furthermore, provides a useful tool for the parametric examination of the spray combustion process.

  1. Modeling diffuse pollution with a distributed approach.

    PubMed

    León, L F; Soulis, E D; Kouwen, N; Farquhar, G J

    2002-01-01

    The transferability of parameters for non-point source pollution models to other watersheds, especially those in remote areas without enough data for calibration, is a major problem in diffuse pollution modeling. A water quality component was developed for WATFLOOD (a flood forecast hydrological model) to deal with sediment and nutrient transport. The model uses a distributed group response unit approach for water quantity and quality modeling. Runoff, sediment yield and soluble nutrient concentrations are calculated separately for each land cover class, weighted by area and then routed downstream. The distributed approach for the water quality model for diffuse pollution in agricultural watersheds is described in this paper. Integrating the model with data extracted using GIS technology (Geographical Information Systems) for a local watershed, the model is calibrated for the hydrologic response and validated for the water quality component. With the connection to GIS and the group response unit approach used in this paper, model portability increases substantially, which will improve non-point source modeling at the watershed scale level.

  2. [Radiation diagnosis of diffuse lung diseases: Part I].

    PubMed

    Stashuk, G A; Dubrova, S E

    2005-01-01

    Based on the data on 150 patients with diffuse lung diseases, the authors present the X-ray and computed topographic semiotics of changes in lung tissue in a number of diseases from this group. The differential diagnosis of diffuse lung diseases has certain difficulties whose solution is association with the application of complex radiation studies (digital fluorography, classical X-ray study, X-ray computed tomography, and magnetic resonance imaging). These techniques not only assess the status of the parenchyma of the lung and the extent of a process, but also permit a follow-up monitoring and evaluation of the efficiency of the therapy performed.

  3. A Diffuse Interface Model with Immiscibility Preservation

    PubMed Central

    Tiwari, Arpit; Freund, Jonathan B.; Pantano, Carlos

    2013-01-01

    A new, simple, and computationally efficient interface capturing scheme based on a diffuse interface approach is presented for simulation of compressible multiphase flows. Multi-fluid interfaces are represented using field variables (interface functions) with associated transport equations that are augmented, with respect to an established formulation, to enforce a selected interface thickness. The resulting interface region can be set just thick enough to be resolved by the underlying mesh and numerical method, yet thin enough to provide an efficient model for dynamics of well-resolved scales. A key advance in the present method is that the interface regularization is asymptotically compatible with the thermodynamic mixture laws of the mixture model upon which it is constructed. It incorporates first-order pressure and velocity non-equilibrium effects while preserving interface conditions for equilibrium flows, even within the thin diffused mixture region. We first quantify the improved convergence of this formulation in some widely used one-dimensional configurations, then show that it enables fundamentally better simulations of bubble dynamics. Demonstrations include both a spherical bubble collapse, which is shown to maintain excellent symmetry despite the Cartesian mesh, and a jetting bubble collapse adjacent a wall. Comparisons show that without the new formulation the jet is suppressed by numerical diffusion leading to qualitatively incorrect results. PMID:24058207

  4. Anomalous diffusion in generalized Dykhne model

    SciTech Connect

    Dvoretskaya, O. A.; Kondratenko, P. S. Matveev, L. V.

    2010-01-15

    Contaminant transport is investigated in the generalized Dykhne model differing from the original Dykhne model by the presence of advection in the high-permeability medium. An analysis is presented of transport regimes and concentration tail behavior in the high-permeability medium. It is found that the transport regimes include anomalous ones: subdiffusion and quasi-diffusion. A difference is revealed between longitudinal and transverse transport. Regime change over time leads to multiple-regime long-distance asymptotic behavior of concentration distributions. An analogy is drawn between the problems examined here and transport through comb structures.

  5. Distributed Energy Resources Market Diffusion Model

    SciTech Connect

    Maribu, Karl Magnus; Firestone, Ryan; Marnay, Chris; Siddiqui,Afzal S.

    2006-06-16

    Distributed generation (DG) technologies, such as gas-fired reciprocating engines and microturbines, have been found to be economically beneficial in meeting commercial-sector electrical, heating, and cooling loads. Even though the electric-only efficiency of DG is lower than that offered by traditional central stations, combined heat and power (CHP) applications using recovered heat can make the overall system energy efficiency of distributed energy resources (DER) greater. From a policy perspective, however, it would be useful to have good estimates of penetration rates of DER under various economic and regulatory scenarios. In order to examine the extent to which DER systems may be adopted at a national level, we model the diffusion of DER in the US commercial building sector under different technical research and technology outreach scenarios. In this context, technology market diffusion is assumed to depend on the system's economic attractiveness and the developer's knowledge about the technology. The latter can be spread both by word-of-mouth and by public outreach programs. To account for regional differences in energy markets and climates, as well as the economic potential for different building types, optimal DER systems are found for several building types and regions. Technology diffusion is then predicted via two scenarios: a baseline scenario and a program scenario, in which more research improves DER performance and stronger technology outreach programs increase DER knowledge. The results depict a large and diverse market where both optimal installed capacity and profitability vary significantly across regions and building types. According to the technology diffusion model, the West region will take the lead in DER installations mainly due to high electricity prices, followed by a later adoption in the Northeast and Midwest regions. Since the DER market is in an early stage, both technology research and outreach programs have the potential to increase

  6. Diffusion through thin membranes: Modeling across scales

    NASA Astrophysics Data System (ADS)

    Aho, Vesa; Mattila, Keijo; Kühn, Thomas; Kekäläinen, Pekka; Pulkkinen, Otto; Minussi, Roberta Brondani; Vihinen-Ranta, Maija; Timonen, Jussi

    2016-04-01

    From macroscopic to microscopic scales it is demonstrated that diffusion through membranes can be modeled using specific boundary conditions across them. The membranes are here considered thin in comparison to the overall size of the system. In a macroscopic scale the membrane is introduced as a transmission boundary condition, which enables an effective modeling of systems that involve multiple scales. In a mesoscopic scale, a numerical lattice-Boltzmann scheme with a partial-bounceback condition at the membrane is proposed and analyzed. It is shown that this mesoscopic approach provides a consistent approximation of the transmission boundary condition. Furthermore, analysis of the mesoscopic scheme gives rise to an expression for the permeability of a thin membrane as a function of a mesoscopic transmission parameter. In a microscopic model, the mean waiting time for a passage of a particle through the membrane is in accordance with this permeability. Numerical results computed with the mesoscopic scheme are then compared successfully with analytical solutions derived in a macroscopic scale, and the membrane model introduced here is used to simulate diffusive transport between the cell nucleus and cytoplasm through the nuclear envelope in a realistic cell model based on fluorescence microscopy data. By comparing the simulated fluorophore transport to the experimental one, we determine the permeability of the nuclear envelope of HeLa cells to enhanced yellow fluorescent protein.

  7. Distributed Wind Diffusion Model Overview (Presentation)

    SciTech Connect

    Preus, R.; Drury, E.; Sigrin, B.; Gleason, M.

    2014-07-01

    Distributed wind market demand is driven by current and future wind price and performance, along with several non-price market factors like financing terms, retail electricity rates and rate structures, future wind incentives, and others. We developed a new distributed wind technology diffusion model for the contiguous United States that combines hourly wind speed data at 200m resolution with high resolution electricity load data for various consumer segments (e.g., residential, commercial, industrial), electricity rates and rate structures for utility service territories, incentive data, and high resolution tree cover. The model first calculates the economics of distributed wind at high spatial resolution for each market segment, and then uses a Bass diffusion framework to estimate the evolution of market demand over time. The model provides a fundamental new tool for characterizing how distributed wind market potential could be impacted by a range of future conditions, such as electricity price escalations, improvements in wind generator performance and installed cost, and new financing structures. This paper describes model methodology and presents sample results for distributed wind market potential in the contiguous U.S. through 2050.

  8. Diffuse Interface Model for Microstructure Evolution

    NASA Astrophysics Data System (ADS)

    Nestler, Britta

    A phase-field model for a general class of multi-phase metallic alloys is proposed which describes both, multi-phase solidification phenomena as well as polycrystalline grain structures. The model serves as a computational method to simulate the motion and kinetics of multiple phase boundaries and enables the visualization of the diffusion processes and of the phase transitions in multi-phase systems. Numerical simulations are presented which illustrate the capability of the phase-field model to recover a variety of complex experimental growth structures. In particular, the phase-field model can be used to simulate microstructure evolutions in eutectic, peritectic and monotectic alloys. In addition, polycrystalline grain structures with effects such as wetting, grain growth, symmetry properties of adjacent triple junctions in thin film samples and stability criteria at multiple junctions are described by phase-field simulations.

  9. Extended source model for diffusive coupling.

    PubMed

    González-Ochoa, Héctor O; Flores-Moreno, Roberto; Reyes, Luz M; Femat, Ricardo

    2016-01-01

    Motivated by the prevailing approach to diffusion coupling phenomena which considers point-like diffusing sources, we derived an analogous expression for the concentration rate of change of diffusively coupled extended containers. The proposed equation, together with expressions based on solutions to the diffusion equation, is intended to be applied to the numerical solution of systems exclusively composed of ordinary differential equations, however is able to account for effects due the finite size of the coupled sources.

  10. Extended source model for diffusive coupling.

    PubMed

    González-Ochoa, Héctor O; Flores-Moreno, Roberto; Reyes, Luz M; Femat, Ricardo

    2016-01-01

    Motivated by the prevailing approach to diffusion coupling phenomena which considers point-like diffusing sources, we derived an analogous expression for the concentration rate of change of diffusively coupled extended containers. The proposed equation, together with expressions based on solutions to the diffusion equation, is intended to be applied to the numerical solution of systems exclusively composed of ordinary differential equations, however is able to account for effects due the finite size of the coupled sources. PMID:26802012

  11. Recommendation Based on Trust Diffusion Model

    PubMed Central

    Li, Li

    2014-01-01

    Recommender system is emerging as a powerful and popular tool for online information relevant to a given user. The traditional recommendation system suffers from the cold start problem and the data sparsity problem. Many methods have been proposed to solve these problems, but few can achieve satisfactory efficiency. In this paper, we present a method which combines the trust diffusion (DiffTrust) algorithm and the probabilistic matrix factorization (PMF). DiffTrust is first used to study the possible diffusions of trust between various users. It is able to make use of the implicit relationship of the trust network, thus alleviating the data sparsity problem. The probabilistic matrix factorization (PMF) is then employed to combine the users' tastes with their trusted friends' interests. We evaluate the algorithm on Flixster, Moviedata, and Epinions datasets, respectively. The experimental results show that the recommendation based on our proposed DiffTrust + PMF model achieves high performance in terms of the root mean square error (RMSE), Recall, and F Measure. PMID:25009827

  12. A Void Diffusion Model of Granular Flow

    NASA Astrophysics Data System (ADS)

    Rudra, Jayanta; Vieth, Paul

    2009-03-01

    In an earlier paper^1 we derived a nonlinear diffusion equation to describe the dynamics in granular flow based on a Diffusion Void Model (DVM). The equation was successfully used to describe the flow of a homogeneous granular material through the hole of a container under gravity. It also properly described similar flow in the presence of a flat horizontal barrier placed above the hole. Recently, however, we have found out that the above nonlinear equation does not lead to correct static equilibrium. For example, the stability of the free surface of a granular aggregate cannot be described by the equation. The equation also fails to describe, say, how an unstable vertical column of a granular material will change to a stable λ-shaped pile at the angle of repose. In this paper work we derive an equation using an appropriate current density of voids that can explain all the observed dynamical characteristics of a simple granular state. ^1Jayanta K. Rudra and D. C. Hong, Phys. Rev. E47, R1459(1993).

  13. Recommendation based on trust diffusion model.

    PubMed

    Yuan, Jinfeng; Li, Li

    2014-01-01

    Recommender system is emerging as a powerful and popular tool for online information relevant to a given user. The traditional recommendation system suffers from the cold start problem and the data sparsity problem. Many methods have been proposed to solve these problems, but few can achieve satisfactory efficiency. In this paper, we present a method which combines the trust diffusion (DiffTrust) algorithm and the probabilistic matrix factorization (PMF). DiffTrust is first used to study the possible diffusions of trust between various users. It is able to make use of the implicit relationship of the trust network, thus alleviating the data sparsity problem. The probabilistic matrix factorization (PMF) is then employed to combine the users' tastes with their trusted friends' interests. We evaluate the algorithm on Flixster, Moviedata, and Epinions datasets, respectively. The experimental results show that the recommendation based on our proposed DiffTrust + PMF model achieves high performance in terms of the root mean square error (RMSE), Recall, and F Measure.

  14. a Diffusivity Model for Gas Diffusion in Dry Porous Media Composed of Converging-Diverging Capillaries

    NASA Astrophysics Data System (ADS)

    Wang, Shifang; Wu, Tao; Deng, Yongju; Zheng, Qiusha; Zheng, Qian

    2016-08-01

    Gas diffusion in dry porous media has been a hot topic in several areas of technology for many years. In this paper, a diffusivity model for gas diffusion in dry porous media is developed based on fractal theory and Fick’s law, which incorporates the effects of converging-diverging pores and tortuous characteristics of capillaries as well as Knudsen diffusion. The effective gas diffusivity model is expressed as a function of the fluctuation amplitude of the capillary cross-section size variations, the porosity, the pore area fractal dimension and the tortuosity fractal dimension. The results show that the relative diffusivity decreases with the increase of the fluctuation amplitude and increases with the increase of pore area fractal dimension. To verify the validity of the present model, the relative diffusivity from the proposed fractal model is compared with the existing experimental data as well as two available models of Bruggeman and Shou. Our proposed diffusivity model with pore converging-diverging effect included is in good agreement with reported experimental data.

  15. a Diffusivity Model for Gas Diffusion in Dry Porous Media Composed of Converging-Diverging Capillaries

    NASA Astrophysics Data System (ADS)

    Wang, Shifang; Wu, Tao; Deng, Yongju; Zheng, Qiusha; Zheng, Qian

    2016-08-01

    Gas diffusion in dry porous media has been a hot topic in several areas of technology for many years. In this paper, a diffusivity model for gas diffusion in dry porous media is developed based on fractal theory and Fick’s law, which incorporates the effects of converging-diverging pores and tortuous characteristics of capillaries as well as Knudsen diffusion. The effective gas diffusivity model is expressed as a function of the fluctuation amplitude of the capillary cross-section size variations, the porosity, the pore area fractal dimension and the tortuosity fractal dimension. The results show that the relative diffusivity decreases with the increase of the fluctuation amplitude and increases with the increase of pore area fractal dimension. To verify the validity of the present model, the relative diffusivity from the proposed fractal model is compared with the existing experimental data as well as two available models of Bruggeman and Shou. Our proposed diffusivity model with pore converging-diverging effect included is in good agreement with reported experimental data.

  16. Modeling of hydrogen-air diffusion flame

    NASA Technical Reports Server (NTRS)

    Isaac, K. M.

    1988-01-01

    Work performed during the first six months of the project duration for NASA Grant (NAG-1-861) is reported. An analytical and computational study of opposed jet diffusion flame for the purpose of understanding the effects of contaminants in the reactants and thermal diffusion of light species on extinction and reignition of diffusion flames is in progress. The methodologies attempted so far are described.

  17. Modeling of hydrogen-air diffusion flame

    NASA Technical Reports Server (NTRS)

    Isaac, K. M.

    1989-01-01

    An analytical and computational study of opposed jet diffusion flame for the purpose of understanding the effects of contaminants in the reactants and thermal diffusion of light species on extinction and reignition of diffusion flames is in progress. The methodologies that have been attempted so far are described. Results using a simple, one-step reaction for the hydrogen-air counterflow diffusion flame are presented. These results show the correct trends in the profiles of chemical species and temperature. The extinction limit can be clearly seen in the plot of temperature vs. Damkohler number.

  18. A diffusion model of a neuron and neural nets.

    PubMed

    Dabrowski, L

    1993-01-01

    In the paper a diffusion model of a neuron is treated. A new, less restrictive than usually, condition of applicability of a diffusion model is presented. As a result the point-process-to-point-process model of a neuron is obtained, which produces an output signal of the same kind as the accepted input signals.

  19. Some Problems in Using Diffusion Models for New Products

    ERIC Educational Resources Information Center

    Bernhardt, Irwin; Mackenzie, Kenneth D.

    1972-01-01

    Analyzes some of the problems involved in using diffusion models to formulate marketing strategies for introducing new products. Six models, which remove some of the theoretical and methodological restrictions inherent in current models of the adoption and diffusion process, are presented. (Author/JH)

  20. Sedimentary radioactive tracers and diffusive models.

    PubMed

    Carroll, J; Lerche, I

    2010-08-01

    This paper examines the underlying assumptions and consequences of applying a steady-state equation to sediment profiles of radioactive tracers in order to deconvolute sedimentation from bioturbation processes modelled as a diffusive type process. Several factors follow immediately from this investigation: (i) if the observed radioactive concentration increases with depth over any finite depth range then the proposed steady-state, constant flux equation is not applicable. Any increase in radioactive concentration with depth implies a negative mixing coefficient which is a physical impossibility; (ii) when the radioactive concentration systematically decreases with increasing sedimentary depth then solutions to the steady-state conservation equation exist only when either the constant solid state flux to the sediment surface is small enough so that a positive mixing coefficient results or when the mixing coefficient is small enough so that a positive flux results. If the radioactive concentration, porosity and/or density of the solid phase are such that the proposed equation is inappropriate (because no physically acceptable solution exists) then one must abandon the proposed steady-state equation. Further: if the flux of solid sediment to the sediment surface varies with time then, of course, a steady-state conservation equation is also inappropriate. Simple examples illustrate that the assumption of steady-state restricts the applicability of this modelling approach to a relatively small sub-set of expected situations in the real world.

  1. Models to assess perfume diffusion from skin.

    PubMed

    Schwarzenbach, R; Bertschi, L

    2001-04-01

    Temperature, fragrance concentration on the skin and power of ventilation have been determined as crucial parameters in fragrance diffusion from skin. A tool has been developed to simulate perfume diffusion from skin over time, allowing headspace analysis and fragrance profile assessments in a highly reproducible way.

  2. An Ion Diffusion Model in Semi-Permeable Clay Materials

    SciTech Connect

    Liu, Chongxuan

    2007-08-01

    Ion diffusion in semi-impermeable clay materials dynamically interacts with electrostatic fields (or diffuse double layers) associated with clay particles. Current theory of ion transport in porous media containing fixed charges on solid materials, however, cannot explicitly account for the dynamic interactions. Here we proposed a model by coupling electrodynamics and nonequilibrium thermodynamics to describe ion diffusion in the clay materials. The developed model was validated by comparing the calculated and measured apparent ion diffusion coefficients in clay materials as a function of ionic strength, which affects the overlap extent of the electrostatic double layers associated with adjacent clay particles. The model shows that ion diffusion in clay materials is a complex function of factors including surface charge density, tortuosity, porosity, chemico-osmotic coefficient, and ion self-diffusivity. At transitional states, ion diffusive fluxes are dynamically related to the electrostatic fields, which shrink or expand as ion diffusion. At steady states, the electrostatic fields are time-invariant and ion diffusive fluxes conform to flux and concentration gradient relationships; and apparent diffusivity can be expressed by the ion diffusivity in bulk electrolytes corrected by a tortuosity factor and concentration gradient variations at the interfaces between clay materials and bulk solutions.

  3. Diffusion model of the non-stoichiometric uranium dioxide

    SciTech Connect

    Moore, Emily; Guéneau, Christine; Crocombette, Jean-Paul

    2013-07-15

    Uranium dioxide (UO{sub 2}), which is used in light water reactors, exhibits a large range of non-stoichiometry over a wide temperature scale up to 2000 K. Understanding diffusion behavior of uranium oxides under such conditions is essential to ensure safe reactor operation. The current understanding of diffusion properties is largely limited by the stoichiometric deviations inherent to the fuel. The present DICTRA-based model considers diffusion across non-stoichiometric ranges described by experimentally available data. A vacancy and interstitial model of diffusion is applied to the U–O system as a function of its defect structure derived from CALPHAD-type thermodynamic descriptions. Oxygen and uranium self and tracer diffusion coefficients are assessed for the construction of a mobility database. Chemical diffusion coefficients of oxygen are derived with respect to the Darken relation and migration energies of defects are evaluated as a function of stoichiometric deviation. - Graphical abstract: Complete description of Oxygen–Uranium diffusion as a function of composition at various temperatures according to the developed Dictra model. - Highlights: • Assessment of a uranium–oxygen diffusion model with Dictra. • Complete description of U–O diffusion over wide temperature and composition range. • Oxygen model includes terms for interstitial and vacancy migration. • Interaction terms between defects help describe non-stoichiometric domain of UO{sub 2±x}. • Uranium model is separated into mobility terms for the cationic species.

  4. Modeling diffusion in miscible polymer blend films.

    PubMed

    Indrakanti, Ananth; Ramesh, Narayan; Duda, J Larry; Kumar, Sanat K

    2004-07-01

    Recent experiments designed to probe polymer transport in the bulk and in the vicinity of surfaces have examined the interdiffusion of multilayer sandwiches of isotopically labeled polymers. The measured time dependent concentration profiles normal to the surface are typically fit to Fick's law, with a single fitting parameter, the mutual binary diffusion coefficient (MBDC). The resulting MBDCs are found to vary over a broad range of film thicknesses and time, with the time dependence being viewed as a unique signature of the reptation mechanism of long chain motion, and the thickness dependence being attributed to the slowing down of chain dynamics near surfaces. Since the experiments are conducted at finite concentration, the MBDC, which is a product of the bare mobility and the concentration derivative of the chemical potential, could be dominated by the time and thickness dependence of this second term (which is ignored in Fick's law). To quantify this conjecture we consider the more rigorous Cahn formulation of the diffusion problem in terms of chemical potential gradients. We use square gradient theory to evaluate chemical potentials, and fit the resulting time dependent concentration profiles to the analytical solution of Fick's law. By thus mimicking the experimental analysis we find that the apparent MBDCs vary with time as t(-1/2) at short times, in good agreement with existing experiments. We show that this time dependence reflects the system's desire to minimize concentration gradients, a fact ignored in Fick's law. Since these arguments make no reference to the mechanism of chain motion, we argue that the time dependence of MBDC derived from interdiffusion experiments does not provide unequivocal support for the reptation mechanism of long chain transport. The MBDC values, which also vary with the degree of confinement, are predicted to increase with decreasing thickness for model parameters corresponding to experimental systems. In contrast, since the

  5. Radon diffusion through multilayer earthen covers: models and simulations

    SciTech Connect

    Mayer, D.W.; Oster, C.A.; Nelson, R.W.; Gee, G.W.

    1981-09-01

    A capability to model and analyze the fundamental interactions that influence the diffusion of radon gas through uranium mill tailings and cover systems has been investigated. The purpose of this study is to develop the theoretical basis for modeling radon diffusion and to develop an understanding of the fundamental interactions that influence radon diffusion. This study develops the theoretical basis for modeling radon diffusion in one, two and three dimensions. The theory has been incorporated into three computer models that are used to analyze several tailings and cover configurations. This report contains a discussion of the theoretical basis for modeling radon diffusion, a discussion of the computer models used to analyze uranium mill tailings and multilayered cover systems, and presents the results that have been obtained.

  6. A social diffusion model with an application on election simulation.

    PubMed

    Lou, Jing-Kai; Wang, Fu-Min; Tsai, Chin-Hua; Hung, San-Chuan; Kung, Perng-Hwa; Lin, Shou-De; Chen, Kuan-Ta; Lei, Chin-Laung

    2014-01-01

    Issues about opinion diffusion have been studied for decades. It has so far no empirical approach to model the interflow and formation of crowd's opinion in elections due to two reasons. First, unlike the spread of information or flu, individuals have their intrinsic attitudes to election candidates in advance. Second, opinions are generally simply assumed as single values in most diffusion models. However, in this case, an opinion should represent preference toward multiple candidates. Previously done models thus may not intuitively interpret such scenario. This work is to design a diffusion model which is capable of managing the aforementioned scenario. To demonstrate the usefulness of our model, we simulate the diffusion on the network built based on a publicly available bibliography dataset. We compare the proposed model with other well-known models such as independent cascade. It turns out that our model consistently outperforms other models. We additionally investigate electoral issues with our model simulator.

  7. A Social Diffusion Model with an Application on Election Simulation

    PubMed Central

    Wang, Fu-Min; Hung, San-Chuan; Kung, Perng-Hwa; Lin, Shou-De

    2014-01-01

    Issues about opinion diffusion have been studied for decades. It has so far no empirical approach to model the interflow and formation of crowd's opinion in elections due to two reasons. First, unlike the spread of information or flu, individuals have their intrinsic attitudes to election candidates in advance. Second, opinions are generally simply assumed as single values in most diffusion models. However, in this case, an opinion should represent preference toward multiple candidates. Previously done models thus may not intuitively interpret such scenario. This work is to design a diffusion model which is capable of managing the aforementioned scenario. To demonstrate the usefulness of our model, we simulate the diffusion on the network built based on a publicly available bibliography dataset. We compare the proposed model with other well-known models such as independent cascade. It turns out that our model consistently outperforms other models. We additionally investigate electoral issues with our model simulator. PMID:24995351

  8. Some Problems in Using Diffusion Models for New Products.

    ERIC Educational Resources Information Center

    Bernhardt, Irwin; Mackenzie, Kenneth D.

    This paper analyzes some of the problems of using diffusion models to formulate marketing strategies for new products. Though future work in this area appears justified, many unresolved problems limit its application. There is no theory for adoption and diffusion processes; such a theory is outlined in this paper. The present models are too…

  9. Parameter Variability and Distributional Assumptions in the Diffusion Model

    ERIC Educational Resources Information Center

    Ratcliff, Roger

    2013-01-01

    If the diffusion model (Ratcliff & McKoon, 2008) is to account for the relative speeds of correct responses and errors, it is necessary that the components of processing identified by the model vary across the trials of a task. In standard applications, the rate at which information is accumulated by the diffusion process is assumed to be normally…

  10. A Comparison of Competing Models of the News Diffusion Process.

    ERIC Educational Resources Information Center

    Mayer, Michael E.; And Others

    1990-01-01

    Investigates the diffusion of information about the space shuttle Challenger explosion by comparing loglinear models of the diffusion process. Finds that the most parsimonious model with adequate goodness of fit was a linear one in which a person's location affected how the information was heard, which in turn affected when the information was…

  11. Modeling realistic breast lesions using diffusion limited aggregation

    NASA Astrophysics Data System (ADS)

    Rashidnasab, Alaleh; Elangovan, Premkumar; Dance, David R.; Young, Kenneth C.; Diaz, Oliver; Wells, Kevin

    2012-03-01

    Synthesizing the appearance of malignant masses and inserting these into digital mammograms can be used as part of a wider framework for investigating the radiological detection task in X-ray mammography. However, the randomness associated with cell division within cancerous masses and the associated complex morphology challenges the realism of the modeling process. In this paper, Diffusion Limited Aggregation (DLA), a type of fractal growth process is proposed and utilized for modeling breast lesions. Masses of different sizes, shapes and densities were grown by controlling DLA growth parameters either prior to growth, or dynamically updating these during growth. A validation study was conducted by presenting 30 real and 30 simulated masses in a random order to a team of radiologists. The results from the validation study suggest that the observers found it difficult to differentiate between the real and simulated lesions.

  12. Asmparts: assembly of biological model parts.

    PubMed

    Rodrigo, Guillermo; Carrera, Javier; Jaramillo, Alfonso

    2007-12-01

    We propose a new computational tool to produce models of biological systems by assembling models from biological parts. Our software not only takes advantage of modularity, but it also enforces standardisation in part characterisation by considering a model of each part. We have used model parts in SBML to design transcriptional networks. Our software is open source, it works in linux and windows platforms, and it could be used to automatically produce models in a server. Our tool not only facilitates model design, but it will also help to promote the establishment of a registry of model parts.

  13. Asmparts: assembly of biological model parts

    PubMed Central

    Rodrigo, Guillermo; Carrera, Javier

    2008-01-01

    We propose a new computational tool to produce models of biological systems by assembling models from biological parts. Our software not only takes advantage of modularity, but it also enforces standardisation in part characterisation by considering a model of each part. We have used model parts in SBML to design transcriptional networks. Our software is open source, it works in linux and windows platforms, and it could be used to automatically produce models in a server. Our tool not only facilitates model design, but it will also help to promote the establishment of a registry of model parts. PMID:19003441

  14. A memory diffusion model for molecular anisotropic diffusion in siliceous β-zeolite.

    PubMed

    Ji, Xiangfei; An, Zhuanzhuan; Yang, Xiaofeng

    2016-01-01

    A memory diffusion model of molecules on β-zeolite is proposed. In the model, molecular diffusion in β-zeolites is treated as jumping from one adsorption site to its neighbors and the jumping probability is a compound probability which includes that provided by the transitional state theory as well as that derived from the information about which direction the target molecule comes from. The proposed approach reveals that the diffusivities along two crystal axes on β-zeolite are correlated. The model is tested by molecular dynamics simulations on diffusion of benzene and other simple molecules in β-zeolites. The results show that the molecules with larger diameters fit the prediction much better and that the "memory effects" are important in all cases.

  15. Dynamic hysteresis modeling including skin effect using diffusion equation model

    NASA Astrophysics Data System (ADS)

    Hamada, Souad; Louai, Fatima Zohra; Nait-Said, Nasreddine; Benabou, Abdelkader

    2016-07-01

    An improved dynamic hysteresis model is proposed for the prediction of hysteresis loop of electrical steel up to mean frequencies, taking into account the skin effect. In previous works, the analytical solution of the diffusion equation for low frequency (DELF) was coupled with the inverse static Jiles-Atherton (JA) model in order to represent the hysteresis behavior for a lamination. In the present paper, this approach is improved to ensure the reproducibility of measured hysteresis loops at mean frequency. The results of simulation are compared with the experimental ones. The selected results for frequencies 50 Hz, 100 Hz, 200 Hz and 400 Hz are presented and discussed.

  16. Modeling Diffusion Induced Stresses for Lithium-Ion Battery Materials

    NASA Astrophysics Data System (ADS)

    Chiu Huang, Cheng-Kai

    rate (C-rate) during charging/discharging affects diffusion induced stresses inside electrode materials. For the experimental part we first conduct charging/discharging under different C-rates to observe the voltage responses for commercial LiFePO4 batteries. Then Time-of-Flight Secondary Ion Mass Spectrometry technique is applied to measure the lithium ion intensities in different C-rate charged/discharged samples. These experimental results could be used to support that a more significant voltage fluctuation under high C-rates is due to different lithium insertion mechanisms, rather than the amount of lithium ions intercalated into electrode materials. Thus the investigation of C-rate-dependent stress evolution is required for the development of a more durable lithium ion battery. In this dissertation, we extend the single particle finite element model to investigate the C-rate-dependent diffusion induced stresses in a multi-particle system. Concentration dependent anisotropic material properties, C-rate-dependent volume misfits and concentration dependent Li-ion diffusivity are incorporated in the model. The concentration gradients, diffusion induced stresses, and strain energies under different C-rates are discussed in this study. Particle fractures have been observed in many experimental results, in this study we further discuss the effect of the crack surface orientation on the lithium concentration profile and stress level in cathode materials. The results of this dissertation provide a better understanding of diffusion induced stresses in electrode materials and contribute to our fundamental knowledge of interplay between lithium intercalations, stress evolutions, particle fractures and the capacity fade in lithium-ion batteries.

  17. A diffusivity model for predicting VOC diffusion in porous building materials based on fractal theory.

    PubMed

    Liu, Yanfeng; Zhou, Xiaojun; Wang, Dengjia; Song, Cong; Liu, Jiaping

    2015-12-15

    Most building materials are porous media, and the internal diffusion coefficients of such materials have an important influences on the emission characteristics of volatile organic compounds (VOCs). The pore structure of porous building materials has a significant impact on the diffusion coefficient. However, the complex structural characteristics bring great difficulties to the model development. The existing prediction models of the diffusion coefficient are flawed and need to be improved. Using scanning electron microscope (SEM) observations and mercury intrusion porosimetry (MIP) tests of typical porous building materials, this study developed a new diffusivity model: the multistage series-connection fractal capillary-bundle (MSFC) model. The model considers the variable-diameter capillaries formed by macropores connected in series as the main mass transfer paths, and the diameter distribution of the capillary bundles obeys a fractal power law in the cross section. In addition, the tortuosity of the macrocapillary segments with different diameters is obtained by the fractal theory. Mesopores serve as the connections between the macrocapillary segments rather than as the main mass transfer paths. The theoretical results obtained using the MSFC model yielded a highly accurate prediction of the diffusion coefficients and were in a good agreement with the VOC concentration measurements in the environmental test chamber. PMID:26291782

  18. 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.

  19. Anisotropy-resolving models for predicting separation in 3--D asymmetric diffusers

    NASA Astrophysics Data System (ADS)

    Jeyapaul, Elbert; Durbin, Paul

    2011-11-01

    All linear eddy-viscosity models are qualitatively incorrect in predicting separation in 3-D asymmetric diffusers. The failure to predict normal stress and shear stress anisotropy at high production-dissipation ratios is the cause. The Explicit algebraic Reynolds stress model (Wallin and Johansson, 2000) predicts the mean flow field in the diffuser accurately, but not the wall pressure and Reynolds stresses. Recalibrating the coefficients of the rapid part of pressure-strain model improves the wall pressure prediction. Including the convective, diffusive, streamline curvature effects on anisotropy has not been beneficial. The model has been tested using a family of diffusers having the same nominal streamwise pressure gradient, LES data is used as a reference. Professor

  20. Comparison of Turbulent Thermal Diffusivity and Scalar Variance Models

    NASA Technical Reports Server (NTRS)

    Yoder, Dennis A.

    2016-01-01

    This paper will include a detailed comparison of heat transfer models that rely upon the thermal diffusivity. The goals are to inform users of the development history of the various models and the resulting differences in model formulations, as well as to evaluate the models on a variety of validation cases so that users might better understand which models are more broadly applicable.

  1. Model calculations for diffuse molecular clouds. [interstellar hydrogen cloud model

    NASA Technical Reports Server (NTRS)

    Glassgold, A. E.; Langer, W. D.

    1974-01-01

    A steady state isobaric cloud model is developed. The pressure, thermal, electrical, and chemical balance equations are solved simultaneously with a simple one dimensional approximation to the equation of radiative transfer appropriate to diffuse clouds. Cooling is mainly by CII fine structure transitions, and a variety of heating mechanisms are considered. Particular attention is given to the abundance variation of H2. Inhomogeneous density distributions are obtained because of the attenuation of the interstellar UV field and the conversion from atomic to molecular hyrodgen. The effects of changing the model parameters are described and the applicability of the model to OAO-3 observations is discussed. Good qualitative agreement with the fractional H2 abundance determinations has been obtained. The observed kinetic temperatures near 80 K can also be achieved by grain photoelectron heating. The problem of the electron density is solved taking special account of the various hydrogen ions as well as heavier ones.

  2. Nonequilibrium drift-diffusion model for organic semiconductor devices

    NASA Astrophysics Data System (ADS)

    Felekidis, Nikolaos; Melianas, Armantas; Kemerink, Martijn

    2016-07-01

    Two prevailing formalisms are currently used to model charge transport in organic semiconductor devices. Drift-diffusion calculations, on the one hand, are time effective but assume local thermodynamic equilibrium, which is not always realistic. Kinetic Monte Carlo models, on the other hand, do not require this assumption but are computationally expensive. Here, we present a nonequilibrium drift-diffusion model that bridges this gap by fusing the established multiple trap and release formalism with the drift-diffusion transport equation. For a prototypical photovoltaic system the model is shown to quantitatively describe, with a single set of parameters, experiments probing (1) temperature-dependent steady-state charge transport—space-charge limited currents, and (2) time-resolved charge transport and relaxation of nonequilibrated photocreated charges. Moreover, the outputs of the developed kinetic drift-diffusion model are an order of magnitude, or more, faster to compute and in good agreement with kinetic Monte Carlo calculations.

  3. What can the diffusion model tell us about prospective memory?

    PubMed

    Horn, Sebastian S; Bayen, Ute J; Smith, Rebekah E

    2011-03-01

    Cognitive process models, such as Ratcliff's (1978) diffusion model, are useful tools for examining cost or interference effects in event-based prospective memory (PM). The diffusion model includes several parameters that provide insight into how and why ongoing-task performance may be affected by a PM task and is ideally suited to analyse performance because both reaction time and accuracy are taken into account. Separate analyses of these measures can easily yield misleading interpretations in cases of speed-accuracy trade-offs. The diffusion model allows us to measure possible criterion shifts and is thus an important methodological improvement over standard analyses. Performance in an ongoing lexical-decision task was analysed with the diffusion model. The results suggest that criterion shifts play an important role when a PM task is added, but do not fully explain the cost effect on reaction time. PMID:21443332

  4. Modeling Intragranular Diffusion in Low-Connectivity Granular Media

    SciTech Connect

    Ewing, Robert G.; Liu, Chongxuan; Hu, Qinhong

    2012-03-20

    Diffusive exchange of solutes between bulk water in an aquifer and water in the intragranular pores of the solid phase remains confusing after decades of study. In a previous paper, we reviewed some of the explanations, and suggested that the disparities between observation and theory were largely due to low connectivity of the intragranular pores. Low connectivity indicates that a useful conceptual framework is percolation theory, which guided our analysis. The present study was initiated to improve the finite difference (FD) model presented in the previous paper, and to test that new model rigorously against new random walk (RW) simulations of diffusion in low-connectivity porous spheres starting from non-equilibrium. The new FD model calculates diffusion separately in the infinite cluster and the finite clusters, and closely matches the new, more complex RW results. The percolation-theory based description of the new model is fairly simple, and can readily be incorporated into existing FD models. The simulations showed that the combination of low intragranular pore connectivity, and out-diffusion initiated at diffusive non-equilibrium, can produce diffusive behavior that appears as if the solute had undergone slow sorption, even in the absence of any sorption process. This mechanism may help explain some hitherto confusing aspects of intragranular diffusion.

  5. Diffusion models for Jupiter's radiation belt

    NASA Technical Reports Server (NTRS)

    Jacques, S. A.; Davis, L., Jr.

    1972-01-01

    Solutions are given for the diffusion of trapped particles in a planetary magnetic field in which the first and second adiabatic invariants are preserved but the third is not, using as boundary conditions a fixed density at the outer boundary (the magnetopause) and a zero density at an inner boundary (the planetary surface). Losses to an orbiting natural satellite are included and an approximate evaluation is made of the effects of the synchrotron radiation on the energy of relativistic electrons. Choosing parameters appropriate to Jupiter, the electrons required to produce the observed synchrotron radiation are explained. If a speculative mechanism in which the diffusion is driven by ionospheric wind is the true explanation of the electrons producing the synchrotron emission it can be concluded that Jupiter's inner magnetosphere is occupied by an energetic proton flux that would be a serious hazard to spacecraft.

  6. Addition of Diffusion Model to MELCOR and Comparison with Data

    SciTech Connect

    Brad Merrill; Richard Moore; Chang Oh

    2004-06-01

    A chemical diffusion model was incorporated into the thermal-hydraulics package of the MELCOR Severe Accident code (Reference 1) for analyzing air ingress events for a very high temperature gas-cooled reactor.

  7. Modelling oxygen self-diffusion in UO2 under pressure

    DOE PAGESBeta

    Cooper, Michael William D.; Grimes, R. W.; Fitzpatrick, M. E.; Chroneos, A.

    2015-10-22

    Access to values for oxygen self-diffusion over a range of temperatures and pressures in UO2 is important to nuclear fuel applications. Here, elastic and expansivity data are used in the framework of a thermodynamic model, the cBΩ model, to derive the oxygen self-diffusion coefficient in UO2 over a range of pressures (0–10 GPa) and temperatures (300–1900 K). Furthermore, the significant reduction in oxygen self-diffusion as a function of increasing hydrostatic pressure, and the associated increase in activation energy, is identified.

  8. A model for diffusive systems: Beyond the Arrhenius mechanism

    NASA Astrophysics Data System (ADS)

    Rosa, A. C. P.; Vaveliuk, Pablo; Mundim, Kleber C.; Moret, M. A.

    2016-05-01

    Diffusivity in supercooled liquids was observed to exhibit a non-Arrhenius behavior near the glass-transition temperature. This process, which occurs where the activation energy depends on the temperature, suggests the possibility of a metastable equilibrium. This peculiar phenomenon cannot be explained using the usual Markovian stochastic models. Based on a non-linear Fokker-Planck equation, we propose a diffusion coefficient that is proportional to the supercooled-liquid concentration. The proposed model allows us to explain the anomalous behavior of the diffusivity robustly. We demonstrate that this new approach is consistent with experimental patterns. Besides, it could be applied to non-Arrhenius chemical kinetics.

  9. A 1D coupled Schroedinger drift-diffusion model including collisions

    SciTech Connect

    Baro, M. . E-mail: baro@wias-berlin.de; Abdallah, N. Ben . E-mail: naoufel@mip.ups-tlse.fr; Degond, P. . E-mail: degond@mip.ups-tlse.fr; El Ayyadi, A. . E-mail: elayyadi@mathematik.uni-mainz.de

    2005-02-10

    We consider a one-dimensional coupled stationary Schroedinger drift-diffusion model for quantum semiconductor device simulations. The device domain is decomposed into a part with large quantum effects (quantum zone) and a part where quantum effects are negligible (classical zone). We give boundary conditions at the classic-quantum interface which are current preserving. Collisions within the quantum zone are introduced via a Pauli master equation. To illustrate the validity we apply the model to three resonant tunneling diodes.

  10. Postural control model interpretation of stabilogram diffusion analysis

    NASA Technical Reports Server (NTRS)

    Peterka, R. J.

    2000-01-01

    Collins and De Luca [Collins JJ. De Luca CJ (1993) Exp Brain Res 95: 308-318] introduced a new method known as stabilogram diffusion analysis that provides a quantitative statistical measure of the apparently random variations of center-of-pressure (COP) trajectories recorded during quiet upright stance in humans. This analysis generates a stabilogram diffusion function (SDF) that summarizes the mean square COP displacement as a function of the time interval between COP comparisons. SDFs have a characteristic two-part form that suggests the presence of two different control regimes: a short-term open-loop control behavior and a longer-term closed-loop behavior. This paper demonstrates that a very simple closed-loop control model of upright stance can generate realistic SDFs. The model consists of an inverted pendulum body with torque applied at the ankle joint. This torque includes a random disturbance torque and a control torque. The control torque is a function of the deviation (error signal) between the desired upright body position and the actual body position, and is generated in proportion to the error signal, the derivative of the error signal, and the integral of the error signal [i.e. a proportional, integral and derivative (PID) neural controller]. The control torque is applied with a time delay representing conduction, processing, and muscle activation delays. Variations in the PID parameters and the time delay generate variations in SDFs that mimic real experimental SDFs. This model analysis allows one to interpret experimentally observed changes in SDFs in terms of variations in neural controller and time delay parameters rather than in terms of open-loop versus closed-loop behavior.

  11. BF{sub 3} PIII modeling: Implantation, amorphisation and diffusion

    SciTech Connect

    Essa, Z.; Cristiano, F.; Spiegel, Y.; Boulenc, P.; Qiu, Y.; Quillec, M.; Taleb, N.; Burenkov, A.; Hackenberg, M.; Bedel-Pereira, E.; Mortet, V.; Torregrosa, Frank; Tavernier, C.

    2012-11-06

    In the race for highly doped ultra-shallow junctions (USJs) in complementary metal oxide semi-conductor (CMOS) technologies, plasma immersion ion implantation (PIII) is a promising alternative to traditional beamline implantation. Currently, no commercial technology computer aided design (TCAD) process simulator allows modeling the complete USJ fabrication process by PIII, including as-implanted dopant profiles, damage formation, dopant diffusion and activation. In this work, a full simulation of a p-type BF{sub 3} PIII USJ has been carried out. In order to investigate the various physical phenomena mentioned above, process conditions included a high energy/high dose case (10 kV, 5 Multiplication-Sign 10{sup 15} cm{sup -2}), specifically designed to increase damage formation, as well as more technology relevant implant conditions (0.5 kV) for comparison. All implanted samples were annealed at different temperatures and times. As implanted profiles for both boron and fluorine in BF{sub 3} implants were modeled and compared to Secondary Ion Mass Spectrometry (SIMS) measurements. Amorphous/crystalline (a/c) interface depths were measured by transmission electron microscopy (TEM) and successfully simulated. Diffused profiles simulations agreed with SIMS data at low thermal budgets. A boron peak behind the a/c interface was observed in all annealed SIMS profiles for the 10 kV case, indicating boron trapping from EOR defects in this region even after high thermal budgets. TEM measurements on the annealed samples showed an end of range (EOR) defects survival behind the a/c interface, including large dislocation loops (DLs) lying on (001) plane parallel to the surface. In the last part of this work, activation simulations were compared to Hall measurements and confirmed the need to develop a (001) large BICs model.

  12. A reaction-diffusion model of human brain development.

    PubMed

    Lefèvre, Julien; Mangin, Jean-François

    2010-04-01

    Cortical folding exhibits both reproducibility and variability in the geometry and topology of its patterns. These two properties are obviously the result of the brain development that goes through local cellular and molecular interactions which have important consequences on the global shape of the cortex. Hypotheses to explain the convoluted aspect of the brain are still intensively debated and do not focus necessarily on the variability of folds. Here we propose a phenomenological model based on reaction-diffusion mechanisms involving Turing morphogens that are responsible for the differential growth of two types of areas, sulci (bottom of folds) and gyri (top of folds). We use a finite element approach of our model that is able to compute the evolution of morphogens on any kind of surface and to deform it through an iterative process. Our model mimics the progressive folding of the cortical surface along foetal development. Moreover it reveals patterns of reproducibility when we look at several realizations of the model from a noisy initial condition. However this reproducibility must be tempered by the fact that a same fold engendered by the model can have different topological properties, in one or several parts. These two results on the reproducibility and variability of the model echo the sulcal roots theory that postulates the existence of anatomical entities around which the folding organizes itself. These sulcal roots would correspond to initial conditions in our model. Last but not least, the parameters of our model are able to produce different kinds of patterns that can be linked to developmental pathologies such as polymicrogyria and lissencephaly. The main significance of our model is that it proposes a first approach to the issue of reproducibility and variability of the cortical folding. PMID:20421989

  13. The Defect Diffusion Model of Glass-Forming Liquids

    NASA Astrophysics Data System (ADS)

    Fontanella, John; Bendler, John; Wintersgill, Mary; Shlesinger, Michael

    2013-03-01

    The defect diffusion model (DDM) provides an explanation of many properties of glass-forming liquids. For example, it has been used to interpret dielectric relaxation (alpha and beta relaxations and the boson peak), viscosity, ionic conductivity, (including the effects of temperature and pressure) positron annihilation lifetime spectroscopy data, the physical basis of fragility, scaling, the ratio of the apparent isochoric activation energy to the isobaric activation enthalpy and its relationship to monomer volume, and correlation lengths. In the model, the glass transition, Tg, occurs because of rigidity percolation. In addition the transition at TB (or TLL) is associated with mobility percolation. In the simplest form of the DDM, a supercooled liquid contains mobile single defects (MSDs) and immobile, clustered single defects (ICSDs). Consequently, dynamic heterogeneity is a natural feature of the model. If the glass transition did not intervene, all MSDs would disappear at a critical temperature Tc. In the present talk, the model will be used to comment on the change of heat capacity, thermal expansion coefficient and compressibility at Tg. Work supported in part by the Office of Naval Research

  14. Whole Cell Model of Actin Diffusion and Reaction based on Single Molecule Speckle Microscopy Measurements

    NASA Astrophysics Data System (ADS)

    McMillen, Laura; Vavylonis, Dimitrios; Vavylonis Group Team

    It is debated whether transport of actin across the cell by diffusion alone is sufficiently fast to account for the rapid reorganization of actin filaments at the leading edge of motile cells. In order to investigate this question, we created a 3D model of the whole cell that includes reaction and diffusion of actin using a particle Monte Carlo method. For the lamellipodium of the simulated cell we use the model by Smith et al. Biophys. J 104:247 (2013), which includes two diffuse pools of actin, one which is slowly diffusing and the other which diffuses more quickly, as well as a pool of filamentous actin undergoing retrograde flow towards the cell center. We adjusted this model to fit a circular geometry around the whole cell. We also consider actin in the cell center which is either diffusing or in stationary filamentous form, representing cortical actin or actin in stress fibers. The local rates of polymerization and the lifetime distributions of polymerized actin were estimated from single molecule speckle microscopy experiments by the group of N. Watanabe. With this model we are able to simulate prior experiments that monitored the redistribution of actin after photoactivation or fluorescence recovery after photobleaching in various parts of the cell. We find that transport by diffusion is sufficient to fit these data, without the need for an active transport mechanism, however significant concentration gradients may develop at steady state.

  15. The diffusion and telegraph equations in diagenetic modeling

    SciTech Connect

    Boudreau, B.P. )

    1989-08-01

    This paper considers the practical aspects of differentiating between the solutions of the Diffusion and Telegraph Equations when they are used to model molecular diffusion in sediment pore waters and the diffusive bioturbation of solids. If molecular diffusion is the only transport mechanism in pore water, then the results from a simple random-walk model coupled to the hydrodynamic or kinetic theories of diffusion indicate that the solute profiles predicted by these two equations differ measurably only for periods up to 10{sup {minus}10} s after the introduction of a transient and for spatial scales less than 10{sup {minus}6} cm. In addition, the distinct propagating front predicted by the Telegraph Equation moves so fast and is so attenuated as to be unmeasurable. In this situation, the Telegraph Equation offers no practical advantage over the Diffusion Equation for the description of diagenetic pore water profiles. These findings also hold when advection due to burial and chemical reaction are included in the model. The time scales associated with bioturbation of solids are sufficiently long compared to normal sampling times that the profiles of some transients, both in deep-sea and near-shore sediments, should exhibit behavior characteristic of the Telegraph Equation if mixing is diffusive (local).

  16. Scaling in the Diffusion Limited Aggregation Model

    NASA Astrophysics Data System (ADS)

    Menshutin, Anton

    2012-01-01

    We present a self-consistent picture of diffusion limited aggregation (DLA) growth based on the assumption that the probability density P(r,N) for the next particle to be attached within the distance r to the center of the cluster is expressible in the scale-invariant form P[r/Rdep(N)]. It follows from this assumption that there is no multiscaling issue in DLA and there is only a single fractal dimension D for all length scales. We check our assumption self-consistently by calculating the particle-density distribution with a measured P(r/Rdep) function on an ensemble with 1000 clusters of 5×107 particles each. We also show that a nontrivial multiscaling function D(x) can be obtained only when small clusters (N<10000) are used to calculate D(x). Hence, multiscaling is a finite-size effect and is not intrinsic to DLA.

  17. Diffusive feed of reactants and Hopf bifurcations in an oscillatory reaction-diffusion model

    NASA Astrophysics Data System (ADS)

    von Haeften, B.; Izús, G. G.

    1999-01-01

    We study an oscillatory chemical model (the "Brusselator") with the aim of analyzing the effect of a controlled diffusive feed of reactants in the appearance of chemical oscillations. The reflectivities of the boundary, which adjust the external fluxes, act as control parameters capable to alter the attractive basin of the thermodynamic branch, leading to oscillatory behavior.

  18. Innovation Diffusion Model in Higher Education: Case Study of E-Learning Diffusion

    ERIC Educational Resources Information Center

    Buc, Sanjana; Divjak, Blaženka

    2015-01-01

    The diffusion of innovation (DOI) is critical for any organization and especially nowadays for higher education institutions (HEIs) in the light of vast pressure of emerging educational technologies as well as of the demand of economy and society. DOI takes into account the initial and the implementation phase. The conceptual model of DOI in…

  19. SOLVING THE TWO-DIMENSIONAL DIFFUSION FLOW MODEL.

    USGS Publications Warehouse

    Hromadka, T.V.; Lai, Chintu

    1985-01-01

    A simplification of the two-dimensional (2-D) continuity and momentum equations is the diffusion equation. To investigate its capability, the numerical model using the diffusion approach is applied to a hypothetical failure problem of a regional water reservoir. The model is based on an explicit, integrated finite-difference scheme, and the floodplain is simulated by a popular home computer which supports 64K FORTRAN. Though simple, the 2-D model can simulate some interesting flooding effects that a 1-D full dynamic model cannot.

  20. 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.

  1. Modeling cation diffusion in compacted water-saturatedNa-bentonite at low ionic strength

    SciTech Connect

    Bourg, Ian C.; Sposito, Garrison; Bourg, Alain C.M.

    2007-08-28

    Sodium bentonites are used as barrier materials for the isolation of landfills and are under consideration for a similar use in the subsurface storage of high-level radioactive waste. The performance of these barriers is determined in large part by molecular diffusion in the bentonite pore space. We tested two current models of cation diffusion in bentonite against experimental data on the relative apparent diffusion coefficients of two representative cations, sodium and strontium. On the 'macropore/nanopore' model, solute molecules are divided into two categories, with unequal pore-scale diffusion coefficients, based on location: in macropores or in interlayer nanopores. On the 'surface diffusion' model, solute molecules are divided into categories based on chemical speciation: dissolved or adsorbed. The macropore/nanopore model agrees with all experimental data at partial montmorillonite dry densities ranging from 0.2 (a dilute bentonite gel) to 1.7 kg dm{sup -3} (a highly compacted bentonite with most of its pore space located in interlayer nanopores), whereas the surface diffusion model fails at partial montmorillonite dry densities greater than about 1.2 kg dm{sup -3}.

  2. Modeling cation diffusion in compacted water-saturated sodium bentonite at low ionic strength.

    PubMed

    Bourg, Ian C; Sposito, Garrison; Bourg, Alain C M

    2007-12-01

    Sodium bentonites are used as barrier materials for the isolation of landfills and are under consideration for a similar use in the subsurface storage of high-level radioactive waste. The performance of these barriers is determined in large part by molecular diffusion in the bentonite pore space. We tested two current models of cation diffusion in bentonite against experimental data on the relative apparent diffusion coefficients of two representative cations, sodium and strontium. On the "macropore/nanopore" model, solute molecules are divided into two categories, with unequal pore-scale diffusion coefficients, based on location: in macropores or in interlayer nanopores. On the "surface diffusion" model, solute molecules are divided into categories based on chemical speciation: dissolved or adsorbed. The macropore/nanopore model agrees with all experimental data at partial montmorillonite dry densities ranging from 0.2 (a dilute bentonite gel) to 1.7 kg dm(-3) (a highly compacted bentonite with most of its pore space located in interlayer nanopores), whereas the surface diffusion model fails at partial montmorillonite dry densities greater than about 1.3 kg dm(-3). PMID:18186346

  3. Characterizing time dependent anomalous diffusion process: A survey on fractional derivative and nonlinear models

    NASA Astrophysics Data System (ADS)

    Wei, Song; Chen, Wen; Hon, Y. C.

    2016-11-01

    This paper investigates the temporal effects in the modeling of flows through porous media and particles transport. Studies will be made among the time fractional diffusion model and two classical nonlinear diffusion models. The effects of the parameters upon the mentioned models have been studied. By simulating the sub-diffusion processes and comparing the numerical results of these models under different boundary conditions, we can conclude that the time fractional diffusion model is more suitable for simulating the sub-diffusion with steady diffusion rate; whereas the nonlinear models are more appropriate for depicting the sub-diffusion under changing diffusion rate.

  4. Diffusion tensor imaging of diffuse axonal injury in a rat brain trauma model.

    PubMed

    van de Looij, Yohan; Mauconduit, Franck; Beaumont, Marine; Valable, Samuel; Farion, Régine; Francony, Gilles; Payen, Jean-François; Lahrech, Hana

    2012-01-01

    Diffusion tensor imaging (DTI) was used to study traumatic brain injury. The impact-acceleration trauma model was used in rats. Here, in addition to diffusivities (mean, axial and radial), fractional anisotropy (FA) was used, in particular, as a parameter to characterize the cerebral tissue early after trauma. DTI was implemented at 7 T using fast spiral k-space sampling and the twice-refocused spin echo radiofrequency sequence for eddy current minimization. The method was carefully validated on different phantom measurements. DTI of a trauma group (n = 5), as well as a sham group (n = 5), was performed at different time points during 6 h following traumatic brain injury. Two cerebral regions, the cortex and corpus callosum, were analyzed carefully. A significant decrease in diffusivity in the trauma group versus the sham group was observed, suggesting the predominance of cellular edema in both cerebral regions. No significant FA change was detected in the cortex. In the corpus callosum of the trauma group, the FA indices were significantly lower. A net discontinuity in fiber reconstructions in the corpus callosum was observed by fiber tracking using DTI. Histological analysis using Hoechst, myelin basic protein and Bielschowsky staining showed fiber disorganization in the corpus callosum in the brains of the trauma group. On the basis of our histology results and the characteristics of the impact-acceleration model responsible for the presence of diffuse axonal injury, the detection of low FA caused by a drastic reduction in axial diffusivity and the presence of fiber disconnections of the DTI track in the corpus callosum were considered to be related to the presence of diffuse axonal injury. PMID:21618304

  5. Scaling in the diffusion limited aggregation model.

    PubMed

    Menshutin, Anton

    2012-01-01

    We present a self-consistent picture of diffusion limited aggregation (DLA) growth based on the assumption that the probability density P(r,N) for the next particle to be attached within the distance r to the center of the cluster is expressible in the scale-invariant form P[r/R{dep}(N)]. It follows from this assumption that there is no multiscaling issue in DLA and there is only a single fractal dimension D for all length scales. We check our assumption self-consistently by calculating the particle-density distribution with a measured P(r/R{dep}) function on an ensemble with 1000 clusters of 5×10{7} particles each. We also show that a nontrivial multiscaling function D(x) can be obtained only when small clusters (N<10 000) are used to calculate D(x). Hence, multiscaling is a finite-size effect and is not intrinsic to DLA. PMID:22304265

  6. A model for restricted diffusion in complex fluids

    NASA Astrophysics Data System (ADS)

    de Bruyn, John; Wylie, Jonathan

    2014-03-01

    We use a model originally due to Tanner to study the diffusion of tracer particles in complex fluids both analytically and through Monte-Carlo simulations. The model consists of regions through which the particles diffuse freely, separated by membranes with a specified low permeability. The mean squared displacement of the particles calculated from the model agrees well with experimental data on the diffusion of particles in a concentrated colloidal suspension when the membrane permeability is used as an adjustable parameter. Data on a micro-phase-separated polymer system can be well modeled by considering two populations of particles constrained by membranes with different permeabilites. Supported by the Hong Kong Research Grants Council and the Natural Sciences and Engineering Research Council of Canada.

  7. A Novel Restricted Diffusion Model of Evoked Dopamine

    PubMed Central

    2015-01-01

    In vivo fast-scan cyclic voltammetry provides high-fidelity recordings of electrically evoked dopamine release in the rat striatum. The evoked responses are suitable targets for numerical modeling because the frequency and duration of the stimulus are exactly known. Responses recorded in the dorsal and ventral striatum of the rat do not bear out the predictions of a numerical model that assumes the presence of a diffusion gap interposed between the recording electrode and nearby dopamine terminals. Recent findings, however, suggest that dopamine may be subject to restricted diffusion processes in brain extracellular space. A numerical model cast to account for restricted diffusion produces excellent agreement between simulated and observed responses recorded under a broad range of anatomical, stimulus, and pharmacological conditions. The numerical model requires four, and in some cases only three, adjustable parameters and produces meaningful kinetic parameter values. PMID:24983330

  8. Cohabitation reaction-diffusion model for virus focal infections

    NASA Astrophysics Data System (ADS)

    Amor, Daniel R.; Fort, Joaquim

    2014-12-01

    The propagation of virus infection fronts has been typically modeled using a set of classical (noncohabitation) reaction-diffusion equations for interacting species. However, for some single-species systems it has been recently shown that noncohabitation reaction-diffusion equations may lead to unrealistic descriptions. We argue that previous virus infection models also have this limitation, because they assume that a virion can simultaneously reproduce inside a cell and diffuse away from it. For this reason, we build a several-species cohabitation model that does not have this limitation. Furthermore, we perform a sensitivity analysis for the most relevant parameters of the model, and we compare the predicted infection speed with observed data for two different strains of the T7 virus.

  9. Langevin equation with fluctuating diffusivity: A two-state model.

    PubMed

    Miyaguchi, Tomoshige; Akimoto, Takuma; Yamamoto, Eiji

    2016-07-01

    Recently, anomalous subdiffusion, aging, and scatter of the diffusion coefficient have been reported in many single-particle-tracking experiments, though the origins of these behaviors are still elusive. Here, as a model to describe such phenomena, we investigate a Langevin equation with diffusivity fluctuating between a fast and a slow state. Namely, the diffusivity follows a dichotomous stochastic process. We assume that the sojourn time distributions of these two states are given by power laws. It is shown that, for a nonequilibrium ensemble, the ensemble-averaged mean-square displacement (MSD) shows transient subdiffusion. In contrast, the time-averaged MSD shows normal diffusion, but an effective diffusion coefficient transiently shows aging behavior. The propagator is non-Gaussian for short time and converges to a Gaussian distribution in a long-time limit; this convergence to Gaussian is extremely slow for some parameter values. For equilibrium ensembles, both ensemble-averaged and time-averaged MSDs show only normal diffusion and thus we cannot detect any traces of the fluctuating diffusivity with these MSDs. Therefore, as an alternative approach to characterizing the fluctuating diffusivity, the relative standard deviation (RSD) of the time-averaged MSD is utilized and it is shown that the RSD exhibits slow relaxation as a signature of the long-time correlation in the fluctuating diffusivity. Furthermore, it is shown that the RSD is related to a non-Gaussian parameter of the propagator. To obtain these theoretical results, we develop a two-state renewal theory as an analytical tool. PMID:27575079

  10. Langevin equation with fluctuating diffusivity: A two-state model

    NASA Astrophysics Data System (ADS)

    Miyaguchi, Tomoshige; Akimoto, Takuma; Yamamoto, Eiji

    2016-07-01

    Recently, anomalous subdiffusion, aging, and scatter of the diffusion coefficient have been reported in many single-particle-tracking experiments, though the origins of these behaviors are still elusive. Here, as a model to describe such phenomena, we investigate a Langevin equation with diffusivity fluctuating between a fast and a slow state. Namely, the diffusivity follows a dichotomous stochastic process. We assume that the sojourn time distributions of these two states are given by power laws. It is shown that, for a nonequilibrium ensemble, the ensemble-averaged mean-square displacement (MSD) shows transient subdiffusion. In contrast, the time-averaged MSD shows normal diffusion, but an effective diffusion coefficient transiently shows aging behavior. The propagator is non-Gaussian for short time and converges to a Gaussian distribution in a long-time limit; this convergence to Gaussian is extremely slow for some parameter values. For equilibrium ensembles, both ensemble-averaged and time-averaged MSDs show only normal diffusion and thus we cannot detect any traces of the fluctuating diffusivity with these MSDs. Therefore, as an alternative approach to characterizing the fluctuating diffusivity, the relative standard deviation (RSD) of the time-averaged MSD is utilized and it is shown that the RSD exhibits slow relaxation as a signature of the long-time correlation in the fluctuating diffusivity. Furthermore, it is shown that the RSD is related to a non-Gaussian parameter of the propagator. To obtain these theoretical results, we develop a two-state renewal theory as an analytical tool.

  11. A combinatorial model of malware diffusion via bluetooth connections.

    PubMed

    Merler, Stefano; Jurman, Giuseppe

    2013-01-01

    We outline here the mathematical expression of a diffusion model for cellphones malware transmitted through Bluetooth channels. In particular, we provide the deterministic formula underlying the proposed infection model, in its equivalent recursive (simple but computationally heavy) and closed form (more complex but efficiently computable) expression. PMID:23555677

  12. An Urban Diffusion Simulation Model for Carbon Monoxide

    ERIC Educational Resources Information Center

    Johnson, W. B.; And Others

    1973-01-01

    A relatively simple Gaussian-type diffusion simulation model for calculating urban carbon (CO) concentrations as a function of local meteorology and the distribution of traffic is described. The model can be used in two ways: in the synoptic mode and in the climatological mode. (Author/BL)

  13. A combinatorial model of malware diffusion via bluetooth connections.

    PubMed

    Merler, Stefano; Jurman, Giuseppe

    2013-01-01

    We outline here the mathematical expression of a diffusion model for cellphones malware transmitted through Bluetooth channels. In particular, we provide the deterministic formula underlying the proposed infection model, in its equivalent recursive (simple but computationally heavy) and closed form (more complex but efficiently computable) expression.

  14. A Diffusion Model Account of the Lexical Decision Task

    ERIC Educational Resources Information Center

    Ratcliff, Roger; Gomez, Pablo; McKoon, Gail

    2004-01-01

    The diffusion model for 2-choice decisions (R. Ratcliff, 1978) was applied to data from lexical decision experiments in which word frequency, proportion of high- versus low-frequency words, and type of nonword were manipulated. The model gave a good account of all of the dependent variables--accuracy, correct and error response times, and their…

  15. Modeling Copper Diffusion in Polycrystalline CdTe Solar Cells

    SciTech Connect

    Akis, Richard; Brinkman, Daniel; Sankin, Igor; Fang, Tian; Guo, Da; Vasileska, Dragica; Ringhofer, Christain

    2014-06-06

    It is well known that Cu plays an important role in CdTe solar cell performance as a dopant. In this work, a finite-difference method is developed and used to simulate Cu diffusion in CdTe solar cells. In the simulations, which are done on a two-dimensional (2D) domain, the CdTe is assumed to be polycrystalline, with the individual grains separated by grain boundaries. When used to fit experimental Cu concentration data, bulk and grain boundary diffusion coefficients and activation energies for CdTe can be extracted. In the past, diffusion coefficients have been typically obtained by fitting data to simple functional forms of limited validity. By doing full simulations, the simplifying assumptions used in those analytical models are avoided and diffusion parameters can thus be determined more accurately

  16. Modelling of monovacancy diffusion in W over wide temperature range

    SciTech Connect

    Bukonte, L. Ahlgren, T.; Heinola, K.

    2014-03-28

    The diffusion of monovacancies in tungsten is studied computationally over a wide temperature range from 1300 K until the melting point of the material. Our modelling is based on Molecular Dynamics technique and Density Functional Theory. The monovacancy migration barriers are calculated using nudged elastic band method for nearest and next-nearest neighbour monovacancy jumps. The diffusion pre-exponential factor for monovacancy diffusion is found to be two to three orders of magnitude higher than commonly used in computational studies, resulting in attempt frequency of the order 10{sup 15} Hz. Multiple nearest neighbour jumps of monovacancy are found to play an important role in the contribution to the total diffusion coefficient, especially at temperatures above 2/3 of T{sub m}, resulting in an upward curvature of the Arrhenius diagram. The probabilities for different nearest neighbour jumps for monovacancy in W are calculated at different temperatures.

  17. A three-dimensional spin-diffusion model for micromagnetics

    NASA Astrophysics Data System (ADS)

    Abert, Claas; Ruggeri, Michele; Bruckner, Florian; Vogler, Christoph; Hrkac, Gino; Praetorius, Dirk; Suess, Dieter

    2015-10-01

    We solve a time-dependent three-dimensional spin-diffusion model coupled to the Landau-Lifshitz-Gilbert equation numerically. The presented model is validated by comparison to two established spin-torque models: The model of Slonzewski that describes spin-torque in multi-layer structures in the presence of a fixed layer and the model of Zhang and Li that describes current driven domain-wall motion. It is shown that both models are incorporated by the spin-diffusion description, i.e., the nonlocal effects of the Slonzewski model are captured as well as the spin-accumulation due to magnetization gradients as described by the model of Zhang and Li. Moreover, the presented method is able to resolve the time dependency of the spin-accumulation.

  18. A three-dimensional spin-diffusion model for micromagnetics

    PubMed Central

    Abert, Claas; Ruggeri, Michele; Bruckner, Florian; Vogler, Christoph; Hrkac, Gino; Praetorius, Dirk; Suess, Dieter

    2015-01-01

    We solve a time-dependent three-dimensional spin-diffusion model coupled to the Landau-Lifshitz-Gilbert equation numerically. The presented model is validated by comparison to two established spin-torque models: The model of Slonzewski that describes spin-torque in multi-layer structures in the presence of a fixed layer and the model of Zhang and Li that describes current driven domain-wall motion. It is shown that both models are incorporated by the spin-diffusion description, i.e., the nonlocal effects of the Slonzewski model are captured as well as the spin-accumulation due to magnetization gradients as described by the model of Zhang and Li. Moreover, the presented method is able to resolve the time dependency of the spin-accumulation. PMID:26442796

  19. Numerical modelling of swirling diffusive flames

    NASA Astrophysics Data System (ADS)

    Parra-Santos, Teresa; Perez, Ruben; Szasz, Robert Z.; Gutkowski, Artur N.; Castro, Francisco

    2016-03-01

    Computational Fluid Dynamics has been used to study the mixing and combustion of two confined jets whose setup and operating conditions are those of the benchmark of Roback and Johnson. Numerical model solves 3D transient Navier Stokes for turbulent and reactive flows. Averaged velocity profiles using RNG swirl dominated k-epsilon model have been validated with experimental measurements from other sources for the non reactive case. The combustion model is Probability Density Function. Bearing in mind the annular jet has swirl number over 0.5, a vortex breakdown appears in the axis of the burner. Besides, the sudden expansion with a ratio of 2 in diameter between nozzle exits and the test chamber produces the boundary layer separation with the corresponding torus shape recirculation. Contrasting the mixing and combustion models, the last one produces the reduction of the vortex breakdown.

  20. Modelling on cavitation in a diffuser with vortex generator

    NASA Astrophysics Data System (ADS)

    Jablonská, J.

    2013-04-01

    Based on cavitation modelling in Laval nozzle results and experience, problem with the diffuser with vortex generator was defined. The problem describes unsteady multiphase flow of water. Different cavitation models were used when modelling in Fluent, flow condition is inlet and pressure condition is outlet. Boundary conditions were specified by Energy Institute, Victor Kaplan's Department of Fluid Engineering, Faculty of Mechanical Engineering, Brno University of Technology. Numerical modelling is compared with experiment.

  1. A diffuse interface Lox/hydrogen transcritical flame model

    NASA Astrophysics Data System (ADS)

    Gaillard, Pierre; Giovangigli, Vincent; Matuszewski, Lionel

    2016-05-01

    We present a diffuse-interface all-pressure flame model that transitions smoothly between subcritical and supercritical conditions. The model involves a non-equilibrium liquid/gas diffuse interface of van der Waals/Korteweg type embedded into a non-ideal multicomponent reactive fluid. The multicomponent transport fluxes are evaluated in their thermodynamic form in order to avoid singularities at thermodynamic mechanical stability limits. The model also takes into account condensing liquid water in order to avoid thermodynamic chemical instabilities. The resulting equations are used to investigate the interface between cold dense and hot light oxygen as well as the structure of diffusion flames between cold dense oxygen and gaseous-like hydrogen at all pressures, either subcritical or supercritical.

  2. Diffusion Models for the Doping of Semiconductor Crystals.

    NASA Astrophysics Data System (ADS)

    Hearne, M. T.

    Available from UMI in association with The British Library. Requires signed TDF. Discrete models, based on the physics of diffusion at the atomic level, are presented in the form of difference equations, thus providing explicit numerical techniques for evaluating concentration profiles. Models are developed for three diffusion mechanisms. All three of the models are used to study diffusion of dopant in semiconductor crystals during growth by the Czochralski technique. This study is motivated by previously published experimental data which showed dopant concentration profiles for grown gallium arsenide crystals. For these results the distribution of dopant, in this case chromium, was found to deviate significantly from the concentration profile which would be expected if no diffusion of dopant is assumed to take place. Four problems are modelled in one dimension. The first model to be developed is equivalent to Fick's first law of diffusion (the standard diffusion equation). Computed results are obtained for a given set of values of parameters, and the sensitivity of the model to variation of a number of these parameters is investigated. A more sophisticated model is then developed for which the dopant is assumed to diffuse substitutionally. The effect of the vacancy concentration is considered in a more rigorous manner than for the preceding model, and self-diffusion is taken into account. The corresponding partial differential equations are derived, although these are highly non-linear, and cannot be solved for the Czochralski growth problem. Results are again presented demonstrating the effect of varying certain parameters. For the third model, dopant is assumed to diffuse interstitially with effectively infinite diffusivity. Most of the dopant is, however, assumed to exist in the form of substitutionals which are "created" by interstitials occupying lattices. This model is applied, in one dimension, to two problems. The first application is not to Czochralski

  3. Hierarchical set of models to estimate soil thermal diffusivity

    NASA Astrophysics Data System (ADS)

    Arkhangelskaya, Tatiana; Lukyashchenko, Ksenia

    2016-04-01

    Soil thermal properties significantly affect the land-atmosphere heat exchange rates. Intra-soil heat fluxes depend both on temperature gradients and soil thermal conductivity. Soil temperature changes due to energy fluxes are determined by soil specific heat. Thermal diffusivity is equal to thermal conductivity divided by volumetric specific heat and reflects both the soil ability to transfer heat and its ability to change temperature when heat is supplied or withdrawn. The higher soil thermal diffusivity is, the thicker is the soil/ground layer in which diurnal and seasonal temperature fluctuations are registered and the smaller are the temperature fluctuations at the soil surface. Thermal diffusivity vs. moisture dependencies for loams, sands and clays of the East European Plain were obtained using the unsteady-state method. Thermal diffusivity of different soils differed greatly, and for a given soil it could vary by 2, 3 or even 5 times depending on soil moisture. The shapes of thermal diffusivity vs. moisture dependencies were different: peak curves were typical for sandy soils and sigmoid curves were typical for loamy and especially for compacted soils. The lowest thermal diffusivities and the smallest range of their variability with soil moisture were obtained for clays with high humus content. Hierarchical set of models will be presented, allowing an estimate of soil thermal diffusivity from available data on soil texture, moisture, bulk density and organic carbon. When developing these models the first step was to parameterize the experimental thermal diffusivity vs. moisture dependencies with a 4-parameter function; the next step was to obtain regression formulas to estimate the function parameters from available data on basic soil properties; the last step was to evaluate the accuracy of suggested models using independent data on soil thermal diffusivity. The simplest models were based on soil bulk density and organic carbon data and provided different

  4. Notes on the Langevin model for turbulent diffusion of ``marked`` particles

    SciTech Connect

    Rodean, H.C.

    1994-01-26

    Three models for scalar diffusion in turbulent flow (eddy diffusivity, random displacement, and on the Langevin equation) are briefly described. These models random velocity increment based Fokker-Planck equation is introduced as are then examined in more detail in the reverse order. The Fokker-Planck equation is the Eulerian equivalent of the Lagrangian Langevin equation, and the derivation of e outlined. The procedure for obtaining the deterministic and stochastic components of the Langevin equation from Kolmogorov`s 1941 inertial range theory and the Fokker-Planck equation is described. it is noted that a unique form of the Langevin equation can be determined for diffusion in one dimension but not in two or three. The Langevin equation for vertical diffusion in the non-Gaussian convective boundary layer is presented and successively simplified for Gaussian inhomogeneous turbulence and Gaussian homogeneous turbulence in turn. The Langevin equation for Gaussian inhomogeneous turbulence is mathematically transformed into the random displacement model. It is shown how the Fokker-Planck equation for the random displacement model is identical in form to the partial differential equation for the eddy diffusivity model. It is noted that the Langevin model is applicable in two cases in which the other two are not valid: (1) very close in time and distance to the point of scalar release and (2) the non-Gaussian convective boundary layer. The two- and three-dimensional cases are considered in Part III.

  5. Groundwater transport modeling with nonlinear sorption and intraparticle diffusion

    NASA Astrophysics Data System (ADS)

    Singh, Anshuman; Allen-King, Richelle M.; Rabideau, Alan J.

    2014-08-01

    Despite recent advances in the mechanistic understanding of sorption in groundwater systems, most contaminant transport models provide limited support for nonideal sorption processes such as nonlinear isotherms and/or diffusion-limited sorption. However, recent developments in the conceptualization of "dual mode" sorption for hydrophobic organic contaminants have provided more realistic and mechanistically sound alternatives to the commonly used Langmuir and Freundlich models. To support the inclusion of both nonlinear and diffusion-limited sorption processes in groundwater transport models, this paper presents two numerical algorithms based on the split operator approach. For the nonlinear equilibrium scenario, the commonly used two-step split operator algorithm has been modified to provide a more robust treatment of complex multi-parameter isotherms such as the Polanyi-partitioning model. For diffusion-limited sorption, a flexible three step split-operator procedure is presented to simulate intraparticle diffusion in multiple spherical particles with different sizes and nonlinear isotherms. Numerical experiments confirmed the accuracy of both algorithms for several candidate isotherms. However, the primary advantages of the algorithms are: (1) flexibility to accommodate any isotherm equation including "dual mode" and similar expressions, and (2) ease of adapting existing grid-based transport models of any dimensionality to include nonlinear sorption and/or intraparticle diffusion. Comparisons are developed for one-dimensional transport scenarios with different isotherms and particle configurations. Illustrative results highlight (1) the potential influence of isotherm model selection on solute transport predictions, and (2) the combined effects of intraparticle diffusion and nonlinear sorption on the plume transport and flushing for both single-particle and multi-particle scenarios.

  6. Lattice Boltzmann model for nonlinear convection-diffusion equations.

    PubMed

    Shi, Baochang; Guo, Zhaoli

    2009-01-01

    A lattice Boltzmann model for convection-diffusion equation with nonlinear convection and isotropic-diffusion terms is proposed through selecting equilibrium distribution function properly. The model can be applied to the common real and complex-valued nonlinear evolutionary equations, such as the nonlinear Schrödinger equation, complex Ginzburg-Landau equation, Burgers-Fisher equation, nonlinear heat conduction equation, and sine-Gordon equation, by using a real and complex-valued distribution function and relaxation time. Detailed simulations of these equations are performed, and it is found that the numerical results agree well with the analytical solutions and the numerical solutions reported in previous studies.

  7. A multiple mapping conditioning model for differential diffusion

    NASA Astrophysics Data System (ADS)

    Dialameh, L.; Cleary, M. J.; Klimenko, A. Y.

    2014-02-01

    This work introduces modeling of differential diffusion within the multiple mapping conditioning (MMC) turbulent mixing and combustion framework. The effect of differential diffusion on scalar variance decay is analyzed and, following a number of publications, is found to scale as Re-1/2. The ability to model the differential decay rates is the most important aim of practical differential diffusion models, and here this is achieved in MMC by introducing what is called the side-stepping method. The approach is practical and, as it does not involve an increase in the number of MMC reference variables, economical. In addition we also investigate the modeling of a more refined and difficult to reproduce differential diffusion effect - the loss of correlation between the different scalars. For this we develop an alternative MMC model with two reference variables but which also makes use of the side-stepping method. The new models are successfully validated against DNS results available in literature for homogenous, isotropic two scalar mixing.

  8. Models of geochemical systems from mixture theory: diffusion

    SciTech Connect

    Kirwan, A.D. Jr; Kump, L.R.

    1987-05-01

    The problem of diffusion of a geochemical component in a natural environment is investigated from the standpoint of mixture theory. The approach here differs from previous diffusion studies in that both the conservation of mass and momentum for the component is considered. This approach avoids parameterizing the diffusive flux in the mass equation by Fick's law. It is shown that when the momentum equation is included with the mass equation, the linear approximation for the space-time distribution of a solute in a binary system is the telegraph equation, well known from electrodynamics. This contrasts with the diffusion equation, which relies on introducing the Fick's law assumption into the conservation of mass equation for the solute. Solutions for both the diffusion and telegraph equation models are obtained and compared for the case of migration of a minor component into the sea bed when the sediment-water interface concentration is a prescribed function of time. Although the stationary, steady state solutions of the telegraph and diffusion equations are identical, the former has a transient solution in which fluctuations propagate at finite speed. The Fickian assumption, in contrast, requires an infinite speed of propagation.

  9. A Mathematical Model of Diffusion-Limited Gas Bubble Dynamics in Tissue with Varying Diffusion Region Thickness

    NASA Technical Reports Server (NTRS)

    Srinivasan, R. Srini; Gerth, Wayne A.; Powell, Michael R.; Paloski, William H. (Technical Monitor)

    2000-01-01

    A three-region mathematical model of gas bubble dynamics has been shown suitable for describing diffusion-limited dynamics of more than one bubble in a given volume of extravascular tissue. The model is based on the dynamics of gas exchange between a bubble and a well-stirred tissue region through an intervening unperfused diffusion region previously assumed to have constant thickness and uniform gas diffusivity. As a result, the gas content of the diffusion region remains constant as the volume of the region increases with bubble growth, causing dissolved gas in the region to violate Henry's law. Earlier work also neglected the relationship between the varying diffusion region volume and the fixed total tissue volume, because only cases in which the diffusion region volume is a small fraction of the overall tissue volume were considered. We herein extend the three-region model to correct these theoretical inconsistencies by allowing both the thickness and gas content of the diffusion region to vary during bubble evolution. A postulated difference in gas diffusivity between an infinitesimally thin layer at the bubble surface and the remainder of the diffusion region leads to variation in diffusion region gas content and thickness during bubble growth and resolution. This variable thickness, differential diffusivity (VTDD) model can yield bubble lifetimes considerably longer than those yielded by earlier three-region models for given model and decompression parameters, and meets a need for theoretically consistent but relatively simple bubble dynamics models for use in studies of decompression sickness (DCS) in human subjects, Keywords: decompression sickness, gas diffusion in tissue, diffusivity

  10. MESOI: an interactive Lagrangian trajectory puff diffusion model

    SciTech Connect

    Ramsdell, J.V.; Athey, G.F.

    1981-12-01

    MESOI is an interactive Lagrangian trajectory puff diffusion model based on an earlier model by Start and Wendell at the Air Resources Laboratory Field Office at Idaho Falls, Idaho. Puff trajectories are determined using spatially and temporally varying wind fields. Diffusion in the puffs is computed as a function of distance traveled and atmospheric stability. Exposures are computed at nodes of a 31 by 31 grid. There is also provision for interpolation of short term exposures at off-grid locations. This report discusses: the theoretical bases of the model, the numerical approach used in the model, and the sensitivity and accuracy of the model. It contains a description of the computer program and a listing of the code. MESOI is written in FORTRAN. A companion report (Athey, Allwine and Ramsdell, 1981) contains a user's guide to MESOI and documents utility programs that maintain the data files needed by the model.

  11. Toxicological Models Part B: Environmental Models

    NASA Astrophysics Data System (ADS)

    Garric, Jeanne; Thybaud, Eric

    Assessment of ecotoxicological risks due to chemical substances is based in part on establishing concentration-response relationships for different organisms, including plants, invertebrates, and vertebrates living on land, fresh water, or sea water. European regulations for assessing the risks due to chemical products thus recommend the measurement of toxic effects on at least three taxons (algae, crustacea, fish) [1]. The assessment becomes more relevant when based upon a variety of different organisms, with a range of different biological and ecological features (autotrophic or heterotrophic, benthic or pelagic habitat, and different modes of reproduction, growth, respiration, or feeding, etc.), but also when it describes the effects of contaminants on sensitive physiological functions such as growth and reproduction, which determine the balance of populations of terrestrial and aquatic species in their environment.

  12. Nonlinear diffusion model for Rayleigh-Taylor mixing.

    PubMed

    Boffetta, G; De Lillo, F; Musacchio, S

    2010-01-22

    The complex evolution of turbulent mixing in Rayleigh-Taylor convection is studied in terms of eddy diffusivity models for the mean temperature profile. It is found that a nonlinear model, derived within the general framework of Prandtl mixing theory, reproduces accurately the evolution of turbulent profiles obtained from numerical simulations. Our model allows us to give very precise predictions for the turbulent heat flux and for the Nusselt number in the ultimate state regime of thermal convection.

  13. Computer modelling of nanoscale diffusion phenomena at epitaxial interfaces

    NASA Astrophysics Data System (ADS)

    Michailov, M.; Ranguelov, B.

    2014-05-01

    The present study outlines an important area in the application of computer modelling to interface phenomena. Being relevant to the fundamental physical problem of competing atomic interactions in systems with reduced dimensionality, these phenomena attract special academic attention. On the other hand, from a technological point of view, detailed knowledge of the fine atomic structure of surfaces and interfaces correlates with a large number of practical problems in materials science. Typical examples are formation of nanoscale surface patterns, two-dimensional superlattices, atomic intermixing at an epitaxial interface, atomic transport phenomena, structure and stability of quantum wires on surfaces. We discuss here a variety of diffusion mechanisms that control surface-confined atomic exchange, formation of alloyed atomic stripes and islands, relaxation of pure and alloyed atomic terraces, diffusion of clusters and their stability in an external field. The computational model refines important details of diffusion of adatoms and clusters accounting for the energy barriers at specific atomic sites: smooth domains, terraces, steps and kinks. The diffusion kinetics, integrity and decomposition of atomic islands in an external field are considered in detail and assigned to specific energy regions depending on the cluster stability in mass transport processes. The presented ensemble of diffusion scenarios opens a way for nanoscale surface design towards regular atomic interface patterns with exotic physical features.

  14. Some Approaches to Modeling Diffuse Flow at Mid-Ocean Ridges

    NASA Astrophysics Data System (ADS)

    Farough, A.; Lowell, R. P.; Craft, K.; Germanovich, L. N.

    2011-12-01

    To obtain a sound understanding of subsurface temperatures and the extent of the subsurface biosphere in young oceanic crust, one must understand the mechanisms of diffuse flow at oceanic spreading centers. Mathematical modeling of diffuse flow at oceanic spreading centers has received relatively little attention compared to high-temperature black smoker discharge, in part because the temperature and fluid flow data required to constrain the models are scarce. We review a number of different approaches to modelling diffuse flow: (1) The simplest method considers 1-D steady-state uniform upflow from below subject to a heat transfer boundary condition at the surface, which represents the effects of mixing of hydrothermal fluid with seawater. These models, in which the heat transfer coefficient and the velocity of the ascending fluid are constrained by observed diffuse flow vent temperature and heat flux, typically result in a steep temperature gradient near the seafloor and subsurface biological activity may be limited to the upper few cm of the crust. (2) A related method uses data on the partitioning of heat flux between focused and diffuse flow and chemical data from the focused and diffuse flow components in a two-limb single pass modeling approach to determine the fraction of high-temperature fluid that is incorporated in the diffuse flow. Using data available from EPR 950', the Main Endeavour Field, and ASHES vent field at Axial Volcano on the Juan de Fuca Ridge in conjunction with Mg as a passive tracer, we find that the mixing ratio of high temperature in diffuse flow is <10%. The high-temperature contribution to the diffuse heat flux remains large, however, and high-temperature vent fluid ultimately contributes ~ 90% of the total heat output from the vent field. In these models mixing between high-temperature fluid and seawater may occur over a considerable depth, and the subsurface biosphere may be ~ 100 m deep beneath diffuse flow sites. (3) Finally, in

  15. GIS-BASED 1-D DIFFUSIVE WAVE OVERLAND FLOW MODEL

    SciTech Connect

    KALYANAPU, ALFRED; MCPHERSON, TIMOTHY N.; BURIAN, STEVEN J.

    2007-01-17

    This paper presents a GIS-based 1-d distributed overland flow model and summarizes an application to simulate a flood event. The model estimates infiltration using the Green-Ampt approach and routes excess rainfall using the 1-d diffusive wave approximation. The model was designed to use readily available topographic, soils, and land use/land cover data and rainfall predictions from a meteorological model. An assessment of model performance was performed for a small catchment and a large watershed, both in urban environments. Simulated runoff hydrographs were compared to observations for a selected set of validation events. Results confirmed the model provides reasonable predictions in a short period of time.

  16. Impacts of regional mixing on the temperature structure of the equatorial Pacific Ocean. Part 1: Vertically uniform vertical diffusion

    NASA Astrophysics Data System (ADS)

    Furue, Ryo; Jia, Yanli; McCreary, Julian P.; Schneider, Niklas; Richards, Kelvin J.; Müller, Peter; Cornuelle, Bruce D.; Avellaneda, Nidia Martínez; Stammer, Detlef; Liu, Chuanyu; Köhl, Armin

    2015-07-01

    We investigate the sensitivity of numerical-model solutions to regional changes in vertical diffusion. Specifically, we vary the background diffusion coefficient, κb, within spatially distinct subregions of the tropical Pacific, assess the impacts of those changes, and diagnose the processes that account for them. Solutions respond to a diffusion anomaly, δκb, in three ways. Initially, there is a fast response (several months), due to the interaction of rapidly-propagating, barotropic and gravity waves with eddies and other mesoscale features. It is followed by a local response (roughly one year), the initial growth and spatial pattern of which can be explained by one-dimensional (vertical) diffusion. At this stage, temperature and salinity anomalies are generated that are either associated with a change in density ("dynamical" anomalies) or without one ("spiciness" anomalies). In a final adjustment stage, the dynamical and spiciness anomalies spread to remote regions by radiation of Rossby and Kelvin waves and by advection, respectively. In near-equilibrium solutions, dynamical anomalies are generally much larger in the latitude band of the forcing, but the impact of off-equatorial forcing by δκb on the equatorial temperature structure is still significant. Spiciness anomalies spread equatorward within the pycnocline, where they are carried to the equator as part of the subsurface branch of the Pacific Subtropical Cells, and spiciness also extends to the equator via western-boundary currents. Forcing near and at the equator generates strong dynamical anomalies, and sometimes additional spiciness anomalies, at pycnocline depths. The total response of the equatorial temperature structure to δκb in various regions depends on the strength and spatial pattern of the generation of each signal within the forcing region as well as on the processes of its spreading to the equator.

  17. Lattice Boltzmann Modeling of Gaseous Diffusion in Unsaturated Porous Media under Variable Gravity Conditions

    NASA Astrophysics Data System (ADS)

    Chau, J. F.; Or, D.; Jones, S.; Sukop, M.

    2004-05-01

    Liquid distribution in unsaturated porous media under different gravitational forces and resulting gaseous diffusion coefficients were investigated to enhance understanding of plant growth conditions in microgravity. Different fluid behavior in plant growth media under microgravity conditions as compared to earth presents a challenge to plant growth in long duration space exploration missions. Our primary objective was to provide qualitative description and quantitative measures of the role of reduced gravity on hydraulic and gaseous transport properties in simulated porous media. We implemented a multi-phase lattice Boltzmann code for equilibrium distribution of liquid in an idealized two-dimensional porous medium under microgravity and "normal" gravity conditions. The information was then used to provide boundary conditions for simulation of gaseous diffusion through the equilibrium domains (considering diffusion through liquid phase negligibly small). The models were tested by comparison with several analytical solutions to the diffusion equation, with excellent results. The relative diffusion coefficient for both series of simulations (with and without gravity) as functions of air-filled porosity was in good agreement with established models of Millington-Quirk. Liquid distribution under earth's gravity featured increased water content at the lower part of the medium relative to the distribution in reduced gravity, which resulted in decreased gas diffusion through a vertically oriented column of a porous medium. Simulation results for larger domains under various orientations will be presented.

  18. Turing instability in reaction-diffusion models on complex networks

    NASA Astrophysics Data System (ADS)

    Ide, Yusuke; Izuhara, Hirofumi; Machida, Takuya

    2016-09-01

    In this paper, the Turing instability in reaction-diffusion models defined on complex networks is studied. Here, we focus on three types of models which generate complex networks, i.e. the Erdős-Rényi, the Watts-Strogatz, and the threshold network models. From analysis of the Laplacian matrices of graphs generated by these models, we numerically reveal that stable and unstable regions of a homogeneous steady state on the parameter space of two diffusion coefficients completely differ, depending on the network architecture. In addition, we theoretically discuss the stable and unstable regions in the cases of regular enhanced ring lattices which include regular circles, and networks generated by the threshold network model when the number of vertices is large enough.

  19. Cosmic ray anisotropy in fractional differential models of anomalous diffusion

    SciTech Connect

    Uchaikin, V. V.

    2013-06-15

    The problem of galactic cosmic ray anisotropy is considered in two versions of the fractional differential model for anomalous diffusion. The simplest problem of cosmic ray propagation from a point instantaneous source in an unbounded medium is used as an example to show that the transition from the standard diffusion model to the Lagutin-Uchaikin fractional differential model (with characteristic exponent {alpha} = 3/5 and a finite velocity of free particle motion), which gives rise to a knee in the energy spectrum at 10{sup 6} GeV, increases the anisotropy coefficient only by 20%, while the anisotropy coefficient in the Lagutin-Tyumentsev model (with exponents {alpha} = 0.3 and {beta} = 0.8, a long stay of particles in traps, and an infinite velocity of their jumps) is close to one. This is because the parameters of the Lagutin-Tyumentsev model have been chosen improperly.

  20. Mathematical modeling of clearing liquid drop diffusion after intradermal injection

    NASA Astrophysics Data System (ADS)

    Stolnitz, Mikhail M.; Bashkatov, Alexey N.; Genina, Elina A.; Tuchin, Valery V.

    2007-05-01

    The mathematical model of clearing agent diffusion after intradermal injection has been developed. Skin was presented as multilayer medium, but one layer with proper boundary conditions is considered. Analytical solution of the boundary problem for small and large time intervals is obtained.

  1. Modeling development of inhibition zones in an agar diffusion bioassay

    PubMed Central

    Chandrasekar, Vaishnavi; Knabel, Stephen J; Anantheswaran, Ramaswamy C

    2015-01-01

    A two-temperature agar diffusion bioassay is commonly used to quantify the concentration of nisin using Micrococcus luteus as the indicator microorganism. A finite element computational model based on Fick's second law of diffusion was used to predict the radius of the inhibition zone in this diffusion bioassay. The model developed was used to calculate nisin concentration profiles as a function of time and position within the agar. The minimum inhibitory concentration (MIC) of nisin against M. luteus was determined experimentally. The critical time (Tc) for growth of M. luteus within the agar diffusion bioassay was experimentally determined using incubation studies with nisin. The radius of the inhibition zone was predicted from the computational model as the location where the predicted nisin concentration at Tc was equal to MIC. The MIC was experimentally determined to be 0.156 μg mL−1, and Tc was determined to be 7 h. Good agreement (R2 = 0.984) was obtained between model-predicted and experimentally determined inhibition zone radii. PMID:26405525

  2. Decomposing Task-Switching Costs with the Diffusion Model

    ERIC Educational Resources Information Center

    Schmitz, Florian; Voss, Andreas

    2012-01-01

    In four experiments, task-switching processes were investigated with variants of the alternating runs paradigm and the explicit cueing paradigm. The classical diffusion model for binary decisions (Ratcliff, 1978) was used to dissociate different components of task-switching costs. Findings can be reconciled with the view that task-switching…

  3. A simple reaction-rate model for turbulent diffusion flames

    NASA Technical Reports Server (NTRS)

    Bangert, L. H.

    1975-01-01

    A simple reaction rate model is proposed for turbulent diffusion flames in which the reaction rate is proportional to the turbulence mixing rate. The reaction rate is also dependent on the mean mass fraction and the mean square fluctuation of mass fraction of each reactant. Calculations are compared with experimental data and are generally successful in predicting the measured quantities.

  4. Reaction Diffusion Modeling of Calcium Dynamics with Realistic ER Geometry

    PubMed Central

    Means, Shawn; Smith, Alexander J.; Shepherd, Jason; Shadid, John; Fowler, John; Wojcikiewicz, Richard J. H.; Mazel, Tomas; Smith, Gregory D.; Wilson, Bridget S.

    2006-01-01

    We describe a finite-element model of mast cell calcium dynamics that incorporates the endoplasmic reticulum's complex geometry. The model is built upon a three-dimensional reconstruction of the endoplasmic reticulum (ER) from an electron tomographic tilt series. Tetrahedral meshes provide volumetric representations of the ER lumen, ER membrane, cytoplasm, and plasma membrane. The reaction-diffusion model simultaneously tracks changes in cytoplasmic and ER intraluminal calcium concentrations and includes luminal and cytoplasmic protein buffers. Transport fluxes via PMCA, SERCA, ER leakage, and Type II IP3 receptors are also represented. Unique features of the model include stochastic behavior of IP3 receptor calcium channels and comparisons of channel open times when diffusely distributed or aggregated in clusters on the ER surface. Simulations show that IP3R channels in close proximity modulate activity of their neighbors through local Ca2+ feedback effects. Cytoplasmic calcium levels rise higher, and ER luminal calcium concentrations drop lower, after IP3-mediated release from receptors in the diffuse configuration. Simulation results also suggest that the buffering capacity of the ER, and not restricted diffusion, is the predominant factor influencing average luminal calcium concentrations. PMID:16617072

  5. Modeling development of inhibition zones in an agar diffusion bioassay.

    PubMed

    Chandrasekar, Vaishnavi; Knabel, Stephen J; Anantheswaran, Ramaswamy C

    2015-09-01

    A two-temperature agar diffusion bioassay is commonly used to quantify the concentration of nisin using Micrococcus luteus as the indicator microorganism. A finite element computational model based on Fick's second law of diffusion was used to predict the radius of the inhibition zone in this diffusion bioassay. The model developed was used to calculate nisin concentration profiles as a function of time and position within the agar. The minimum inhibitory concentration (MIC) of nisin against M. luteus was determined experimentally. The critical time (T c) for growth of M. luteus within the agar diffusion bioassay was experimentally determined using incubation studies with nisin. The radius of the inhibition zone was predicted from the computational model as the location where the predicted nisin concentration at T c was equal to MIC. The MIC was experimentally determined to be 0.156 μg mL(-1), and T c was determined to be 7 h. Good agreement (R (2) = 0.984) was obtained between model-predicted and experimentally determined inhibition zone radii.

  6. A Mixed-Culture Biofilm Model with Cross-Diffusion.

    PubMed

    Rahman, Kazi A; Sudarsan, Rangarajan; Eberl, Hermann J

    2015-11-01

    We propose a deterministic continuum model for mixed-culture biofilms. A crucial aspect is that movement of one species is affected by the presence of the other. This leads to a degenerate cross-diffusion system that generalizes an earlier single-species biofilm model. Two derivations of this new model are given. One, like cellular automata biofilm models, starts from a discrete in space lattice differential equation where the spatial interaction is described by microscopic rules. The other one starts from the same continuous mass balances that are the basis of other deterministic biofilm models, but it gives up a simplifying assumption of these models that has recently been criticized as being too restrictive in terms of ecological structure. We show that both model derivations lead to the same PDE model, if corresponding closure assumptions are introduced. To investigate the role of cross-diffusion, we conduct numerical simulations of three biofilm systems: competition, allelopathy and a mixed system formed by an aerobic and an anaerobic species. In all cases, we find that accounting for cross-diffusion affects local distribution of biomass, but it does not affect overall lumped quantities such as the total amount of biomass in the system. PMID:26582360

  7. A Mixed-Culture Biofilm Model with Cross-Diffusion.

    PubMed

    Rahman, Kazi A; Sudarsan, Rangarajan; Eberl, Hermann J

    2015-11-01

    We propose a deterministic continuum model for mixed-culture biofilms. A crucial aspect is that movement of one species is affected by the presence of the other. This leads to a degenerate cross-diffusion system that generalizes an earlier single-species biofilm model. Two derivations of this new model are given. One, like cellular automata biofilm models, starts from a discrete in space lattice differential equation where the spatial interaction is described by microscopic rules. The other one starts from the same continuous mass balances that are the basis of other deterministic biofilm models, but it gives up a simplifying assumption of these models that has recently been criticized as being too restrictive in terms of ecological structure. We show that both model derivations lead to the same PDE model, if corresponding closure assumptions are introduced. To investigate the role of cross-diffusion, we conduct numerical simulations of three biofilm systems: competition, allelopathy and a mixed system formed by an aerobic and an anaerobic species. In all cases, we find that accounting for cross-diffusion affects local distribution of biomass, but it does not affect overall lumped quantities such as the total amount of biomass in the system.

  8. User's Manual for the APRAC-1A Urban Diffusion Model Computer Program.

    ERIC Educational Resources Information Center

    Mancuso, R. L.; And Others

    The APRAC-1A diffusion model was developed as a versatile and practical model for computing the concentrations of pollutants at any point within a city. The model calculates pollutant contributions from diffusion on various scales, including: extra-urban diffusion, mainly from sources in upwind cities; intra-urban diffusion from freeway, arterial,…

  9. Modeling the diffusion of phosphorus in silicon in 3-D

    SciTech Connect

    Baker, K.R.

    1994-12-31

    The use of matrix preconditioning in semiconductor process simulation is examined. The simplified nonlinear single-species model for the diffusion of phosphorus into silicon is considered. The experimental three-dimensional simulator, PEPPER3, which uses finite differences and the numerical method of lines to implement the reaction-diffusion equation is modified to allow NSPCG to be called to solve the linear system in the inner Newton loop. Use of NSPCG allowed various accelerators such as Generalized Minimal Residual (GMRES) and Conjugate Gradient (CG) to be used in conjunction with preconditioners such as Richardson, Jacobi, and Incomplete Cholesky.

  10. Reaction-diffusion modelling of bacterial colony patterns

    NASA Astrophysics Data System (ADS)

    Mimura, Masayasu; Sakaguchi, Hideo; Matsushita, Mitsugu

    2000-07-01

    It is well known from experiments that bacterial species Bacillus subtilis exhibit various colony patterns. These are essentially classified into five types in the morphological diagram, depending on the substrate softness and nutrient concentration. (A) diffusion-limited aggregation-like; (B) Eden-like; (C) concentric ring-like; (D) disk-like; and (E) dense branching morphology-like. There arises the naive question of whether the diversity of colony patterns observed in experiments is caused by different effects or governed by the same underlying principles. Our research has led us to propose reaction-diffusion models to describe the morphological diversity of colony patterns except for Eden-like ones.

  11. A Diffusion Model Account of the Lexical Decision Task

    PubMed Central

    Ratcliff, Roger; Gomez, Pablo; McKoon, Gail

    2005-01-01

    The diffusion model for 2-choice decisions (R. Ratcliff, 1978) was applied to data from lexical decision experiments in which word frequency, proportion of high- versus low-frequency words, and type of nonword were manipulated. The model gave a good account of all of the dependent variables—accuracy, correct and error response times, and their distributions—and provided a description of how the component processes involved in the lexical decision task were affected by experimental variables. All of the variables investigated affected the rate at which information was accumulated from the stimuli—called drift rate in the model. The different drift rates observed for the various classes of stimuli can all be explained by a 2-dimensional signal-detection representation of stimulus information. The authors discuss how this representation and the diffusion model’s decision process might be integrated with current models of lexical access. PMID:14756592

  12. Continuum modeling of diffusion and dispersion in dense granular flows

    NASA Astrophysics Data System (ADS)

    Christov, Ivan C.; Stone, Howard A.

    2014-03-01

    Continuum modeling of granular flows remains a challenge of modern statistical physics. Granular materials do not perform Brownian motion, yet diffusion and shear dispersion can be observed in such systems when agitation causes inelastic collisions between particles. In a number of canonical flow regimes (e.g., in a rotating container or down an incline), granular materials can behave like fluids. We formulate and solve the granular counterparts to two basic fluid mechanics problems: diffusion of a pulse and shear dispersion of a pulse for dense granular materials in rapid flow. We provide a theory to account for the concentration-dependent diffusivity of bidisperse granular mixtures, and we give an asymptotic argument for the self-similar behavior of such a diffusion process for which an exact self-similar analytical solution does not exist. For shear dispersion, we show that the effective dispersivity of the depth-averaged concentration of the dispersing powder varies as the Péclet number squared, as in classical Taylor-Aris dispersion of molecular solutes. The calculation is extended to generic shear profiles, showing a significant enhancement for convex profiles due to the shear-rate dependence of the diffusivity of granular materials. ICC was supported by NSF Grant DMS-1104047 and the U.S. DOE through the LANL/LDRD Program; HAS was supported by NSF Grant CBET-1234500.

  13. Continuum modeling of diffusion and dispersion in dense granular flows

    NASA Astrophysics Data System (ADS)

    Christov, Ivan C.; Stone, Howard A.

    2014-11-01

    Continuum modeling of granular flows remains a challenge of modern statistical physics. Granular materials do not perform Brownian motion, yet diffusion and shear dispersion can be observed in such systems when agitation causes inelastic collisions between particles. In a number of canonical flow regimes (e.g., in a rotating container or down an incline), granular materials can behave like fluids. We formulate and solve the granular counterparts to two basic fluid mechanics problems: diffusion of a pulse and shear dispersion of a pulse for dense granular materials in rapid flow. We provide a theory to account for the concentration-dependent diffusivity of bidisperse granular mixtures, and we give an asymptotic argument for the self-similar behavior of such a diffusion process for which an exact self-similar analytical solution does not exist. For shear dispersion, we show that the effective dispersivity of the depth-averaged concentration of the dispersing powder varies as the Péclet number squared, as in classical Taylor-Aris dispersion of molecular solutes. The calculation is extended to generic shear profiles, showing a significant enhancement for convex profiles due to the shear-rate dependence of the diffusivity of granular materials. ICC was supported by NSF Grant DMS-1104047 and the U.S. DOE through the LANL/LDRD Program; HAS was supported by NSF Grant CBET-1234500.

  14. Modeling and quality assessment of halftoning by error diffusion.

    PubMed

    Kite, T D; Evans, B L; Bovik, A C

    2000-01-01

    Digital halftoning quantizes a graylevel image to one bit per pixel. Halftoning by error diffusion reduces local quantization error by filtering the quantization error in a feedback loop. In this paper, we linearize error diffusion algorithms by modeling the quantizer as a linear gain plus additive noise. We confirm the accuracy of the linear model in three independent ways. Using the linear model, we quantify the two primary effects of error diffusion: edge sharpening and noise shaping. For each effect, we develop an objective measure of its impact on the subjective quality of the halftone. Edge sharpening is proportional to the linear gain, and we give a formula to estimate the gain from a given error filter. In quantifying the noise, we modify the input image to compensate for the sharpening distortion and apply a perceptually weighted signal-to-noise ratio to the residual of the halftone and modified input image. We compute the correlation between the residual and the original image to show when the residual can be considered signal independent. We also compute a tonality measure similar to total harmonic distortion. We use the proposed measures for edge sharpening, noise shaping, and tonality to evaluate the quality of error diffusion algorithms. PMID:18255461

  15. Predicting vulnerability to sleep deprivation using diffusion model parameters.

    PubMed

    Patanaik, Amiya; Zagorodnov, Vitali; Kwoh, Chee Keong; Chee, Michael W L

    2014-10-01

    We used diffusion modelling to predict vulnerability to decline in psychomotor vigilance task (PVT) performance following a night of total sleep deprivation (SD). A total of 135 healthy young adults (69 women, age = 21.9 ± 1.7 years) participated in several within-subject cross-over design studies that incorporated the PVT. Participants were classified as vulnerable (lower tertile) or non-vulnerable (upper tertile) according to their change in lapse rate [lapse = reaction time (RT) ≥ 500 ms] between the evening before (ESD) and the morning after SD. RT data were fitted using Ratcliff's diffusion model. Although both groups showed significant change in RT during SD, there was no significant group difference in RT during the ESD session. In contrast, during ESD, the mean diffusion drift of vulnerable subjects was significantly lower than for non-vulnerable subjects. Mean drift and non-decision times were both adversely affected by sleep deprivation. Both mean drift and non-decision time showed significant state × vulnerability interaction. Diffusion modelling appears to have promise in predicting vulnerability to vigilance decline induced by a night of total sleep deprivation.

  16. Fitting degradation of shoreline scarps by a nonlinear diffusion model

    USGS Publications Warehouse

    Andrews, D.J.; Buckna, R.C.

    1987-01-01

    The diffusion model of degradation of topographic features is a promising means by which vertical offsets on Holocene faults might be dated. In order to calibrate the method, we have examined present-day profiles of wave-cut shoreline scarps of late Pleistocene lakes Bonneville and Lahontan. A table is included that allows easy application of the model to scarps with simple initial shape. -from Authors

  17. A Diffusion Model for Two-sided Service Systems

    NASA Astrophysics Data System (ADS)

    Homma, Koichi; Yano, Koujin; Funabashi, Motohisa

    A diffusion model is proposed for two-sided service systems. ‘Two-sided’ refers to the existence of an economic network effect between two different and interrelated groups, e.g., card holders and merchants in an electronic money service. The service benefit for a member of one side depends on the number and quality of the members on the other side. A mathematical model by J. H. Rohlfs explains the network (or bandwagon) effect of communications services. In Rohlfs' model, only the users' group exists and the model is one-sided. This paper extends Rohlfs' model to a two-sided model. We propose, first, a micro model that explains individual behavior in regard to service subscription of both sides and a computational method that drives the proposed model. Second, we develop macro models with two diffusion-rate variables by simplifying the micro model. As a case study, we apply the models to an electronic money service and discuss the simulation results and actual statistics.

  18. Modeling hydrogen diffusion for solar cell passivation and process optimization

    NASA Astrophysics Data System (ADS)

    Zhang, Yi

    A diffusion model for hydrogen (H) in crystalline silicon was established which takes into account the charged state conversion, junction field, mobile traps, and complex formation and dissociation at dopant and trap sites. Carrier exchange among the various charged species is a "fast" process compared to the diffusion process. A numerical method was developed to solve the densities of various charged species from the Poisson's equation that involves shallow-level dopants and one "negative U" impurity, e.g., H. Time domain implicit method was adopted in finite difference scheme to solve the fully coupled equations. Limiting versions of the model were applied to the problems that are of interest to photovoltaics. Simplified trap-limited model was used to describe the low temperature diffusion profiles, assuming process-induced traps, a constant bulk trap level, and trapping/detrapping mechanisms. The results of the simulation agreed with those obtained from experiments. The best fit yielded a low surface free H concentration, Cs, (˜10 14 cm-3) from high temperature extrapolated diffusivity value. In the case of ion beam hydrogenation, mobile traps needed to be considered. PAS analysis showed the existence of vacancy-type defects in implanted Si substrates. Simulation of hydrogen diffusion in p-n junction was first attempted in this work. The order of magnitude of Cs (˜10 14 cm-3) was confirmed. Simulation results showed that the preferred charged state of H is H- (H +) in n- (p-) side of the junction. The accumulation of H- (H+) species on n+ (p+) side of the n+-p (p+-n) junction was observed, which could retard the diffusion in junction. The diffusion of hydrogen through heavily doped region in a junction is trap-limited. Several popular hydrogenation techniques were evaluated by means of modeling and experimental observations. In particular, PECVD followed by RTP hydrogenation was found to be two-step process: PECVD deposition serves as a predeposition step of H

  19. Extended model of the channel diffusivity in the rutile structure

    NASA Astrophysics Data System (ADS)

    Ruebenbauer, K.; Wdowik, U. D.; Kwater, M.; Kowalik, J. T.

    1996-11-01

    A model describing the diffusivity of a highly diluted and randomly distributed substitutional cationic impurity via the open and almost empty <001> channels in the rutile structure has been developed recently. The above model is based upon the assumption that the insignificant fraction of the impurities resides in the channels. An extended model is developed that allows for a significant fraction of the impurities to stay within channels, and it is used to evaluate emission Mössbauer spectra originating from the diffusing impurities embedded in single-crystalline samples. Final results are shown for the 14.4-keV Mössbauer line in 57Co(Fe). It is shown that spectral line positions depend upon the wave-vector transfer to the system, and that the data are sensitive to the fraction of both parent and daughter impurities residing in the channels.

  20. Numerical modelling and image reconstruction in diffuse optical tomography

    PubMed Central

    Dehghani, Hamid; Srinivasan, Subhadra; Pogue, Brian W.; Gibson, Adam

    2009-01-01

    The development of diffuse optical tomography as a functional imaging modality has relied largely on the use of model-based image reconstruction. The recovery of optical parameters from boundary measurements of light propagation within tissue is inherently a difficult one, because the problem is nonlinear, ill-posed and ill-conditioned. Additionally, although the measured near-infrared signals of light transmission through tissue provide high imaging contrast, the reconstructed images suffer from poor spatial resolution due to the diffuse propagation of light in biological tissue. The application of model-based image reconstruction is reviewed in this paper, together with a numerical modelling approach to light propagation in tissue as well as generalized image reconstruction using boundary data. A comprehensive review and details of the basis for using spatial and structural prior information are also discussed, whereby the use of spectral and dual-modality systems can improve contrast and spatial resolution. PMID:19581256

  1. A model of the diffuse galactic gamma ray emission

    NASA Technical Reports Server (NTRS)

    Sreekumar, Parameswaran

    1990-01-01

    The galaxy was observed to be a source of high energy gamma rays as shown by the two successful satellite experiments, SAS-2 and COS-B. It is generally understood that these diffuse gamma rays result from interactions between energetic cosmic rays and interstellar gas. This work makes use of the most recent data on the distribution of atomic and molecular hydrogen in the galaxy along with new estimates of gamma ray production functions to model the diffuse galactic gamma ray emission. The model allows various spatial distributions for cosmic rays in the Galaxy including non-axisymmetric ones. In the light of the expected data from EGRET (Energetic Gamma-Ray Experiment Telescope), an improved model of cosmic ray-matter-gamma ray interaction will provide new insights into the distribution of cosmic rays and the strength of its coupling to matter.

  2. Assessment of a Molecular Diffusion Model in MELCOR

    SciTech Connect

    Chang OH; Richard Moore

    2005-06-01

    The MELCOR (version 1.8.5) [1] computer code with INEEL revisions is being improved for the analysis of very high temperature gas-cooled reactors [2]. Following a loss-of-coolant accident, flow through the reactor vessel may initially stagnate due to a non-uniform concentration of helium and air. However, molecular diffusion will eventually result in a uniform concentration of air and helium. The differences in fluid temperatures within the reactor vessel will then result in the establishment of a natural circulation flow that can supply significant amounts of air to the reactor core. The heat released by the resulting oxidation of graphite in the reactor core has the potential to increase the peak fuel temperature. In order to analyze the effects of oxidation on the response of the reactor during accidents, a molecular diffusion model was added to MELCOR. The model is based on Fick's Second Law for spatially uniform pressure and temperature. This paper describes equimolal counter diffusion experiments in a two bulb diffusion cell and the results of the assessment calculations.

  3. Characterization and modeling of thermal diffusion and aggregation in nanofluids.

    SciTech Connect

    Gharagozloo, Patricia E.; Goodson, Kenneth E.

    2010-05-01

    Fluids with higher thermal conductivities are sought for fluidic cooling systems in applications including microprocessors and high-power lasers. By adding high thermal conductivity nanoscale metal and metal oxide particles to a fluid the thermal conductivity of the fluid is enhanced. While particle aggregates play a central role in recent models for the thermal conductivity of nanofluids, the effect of particle diffusion in a temperature field on the aggregation and transport has yet to be studied in depth. The present work separates the effects of particle aggregation and diffusion using parallel plate experiments, infrared microscopy, light scattering, Monte Carlo simulations, and rate equations for particle and heat transport in a well dispersed nanofluid. Experimental data show non-uniform temporal increases in thermal conductivity above effective medium theory and can be well described through simulation of the combination of particle aggregation and diffusion. The simulation shows large concentration distributions due to thermal diffusion causing variations in aggregation, thermal conductivity and viscosity. Static light scattering shows aggregates form more quickly at higher concentrations and temperatures, which explains the increased enhancement with temperature reported by other research groups. The permanent aggregates in the nanofluid are found to have a fractal dimension of 2.4 and the aggregate formations that grow over time are found to have a fractal dimension of 1.8, which is consistent with diffusion limited aggregation. Calculations show as aggregates grow the viscosity increases at a faster rate than thermal conductivity making the highly aggregated nanofluids unfavorable, especially at the low fractal dimension of 1.8. An optimum nanoparticle diameter for these particular fluid properties is calculated to be 130 nm to optimize the fluid stability by reducing settling, thermal diffusion and aggregation.

  4. Performance of turbulence models for transonic flows in a diffuser

    NASA Astrophysics Data System (ADS)

    Liu, Yangwei; Wu, Jianuo; Lu, Lipeng

    2016-09-01

    Eight turbulence models frequently used in aerodynamics have been employed in the detailed numerical investigations for transonic flows in the Sajben diffuser, to assess the predictive capabilities of the turbulence models for shock wave/turbulent boundary layer interactions (SWTBLI) in internal flows. The eight turbulence models include: the Spalart-Allmaras model, the standard k - 𝜀 model, the RNG k - 𝜀 model, the realizable k - 𝜀 model, the standard k - ω model, the SST k - ω model, the v2¯ - f model and the Reynolds stress model. The performance of the different turbulence models adopted has been systematically assessed by comparing the numerical results with the available experimental data. The comparisons show that the predictive performance becomes worse as the shock wave becomes stronger. The v2¯ - f model and the SST k - ω model perform much better than other models, and the SST k - ω model predicts a little better than the v2¯ - f model for pressure on walls and velocity profile, whereas the v2¯ - f model predicts a little better than the SST k - ω model for separation location, reattachment location and separation length for strong shock case.

  5. Thermomechanics of damageable materials under diffusion: modelling and analysis

    NASA Astrophysics Data System (ADS)

    Roubíček, Tomáš; Tomassetti, Giuseppe

    2015-12-01

    We propose a thermodynamically consistent general-purpose model describing diffusion of a solute or a fluid in a solid undergoing possible phase transformations and damage, beside possible visco-inelastic processes. Also heat generation/consumption/transfer is considered. Damage is modelled as rate-independent. The applications include metal-hydrogen systems with metal/hydride phase transformation, poroelastic rocks, structural and ferro/para-magnetic phase transformation, water and heat transport in concrete, and if diffusion is neglected, plasticity with damage and viscoelasticity, etc. For the ensuing system of partial differential equations and inclusions, we prove existence of solutions by a carefully devised semi-implicit approximation scheme of the fractional-step type.

  6. Chaotic map models of soot fluctuations in turbulent diffusion flames

    SciTech Connect

    Mukerji, S.; McDonough, J.M.; Menguec, M.P.; Manickavasagam, S.; Chung, S.

    1998-10-01

    In this paper, the authors introduce a methodology to characterize time-dependent soot volume fraction fluctuations in turbulent diffusion flames via chaotic maps. The approach is based on the hypothesis that fluctuations of properties in turbulent flames are deterministic in nature, rather than statistical. The objective is to develop models of these fluctuations to be used in comprehensive algorithms to study the nature of turbulent flames and the interaction of turbulence with radiation. To this end the authors measured the time series of soot scattering coefficient in an ethylene diffusion flame from light scattering experiments and fit these data to linear combinations of chaotic maps of the unit interval. Both time series and power spectra can be modeled with reasonable accuracy in this way.

  7. Model-free simulation approach to molecular diffusion tensors.

    PubMed

    Chevrot, Guillaume; Hinsen, Konrad; Kneller, Gerald R

    2013-10-21

    In the present work, we propose a simple model-free approach for the computation of molecular diffusion tensors from molecular dynamics trajectories. The method uses a rigid body trajectory of the molecule under consideration, which is constructed a posteriori by an accumulation of quaternion-based superposition fits of consecutive conformations. From the rigid body trajectory, we compute the translational and angular velocities of the molecule and by integration of the latter also the corresponding angular trajectory. All quantities can be referred to the laboratory frame and a molecule-fixed frame. The 6 × 6 diffusion tensor is computed from the asymptotic slope of the tensorial mean square displacement and, for comparison, also from the Kubo integral of the velocity correlation tensor. The method is illustrated for two simple model systems - a water molecule and a lysozyme molecule in bulk water. We give estimations of the statistical accuracy of the calculations. PMID:24160503

  8. Model-free simulation approach to molecular diffusion tensors

    NASA Astrophysics Data System (ADS)

    Chevrot, Guillaume; Hinsen, Konrad; Kneller, Gerald R.

    2013-10-01

    In the present work, we propose a simple model-free approach for the computation of molecular diffusion tensors from molecular dynamics trajectories. The method uses a rigid body trajectory of the molecule under consideration, which is constructed a posteriori by an accumulation of quaternion-based superposition fits of consecutive conformations. From the rigid body trajectory, we compute the translational and angular velocities of the molecule and by integration of the latter also the corresponding angular trajectory. All quantities can be referred to the laboratory frame and a molecule-fixed frame. The 6 × 6 diffusion tensor is computed from the asymptotic slope of the tensorial mean square displacement and, for comparison, also from the Kubo integral of the velocity correlation tensor. The method is illustrated for two simple model systems - a water molecule and a lysozyme molecule in bulk water. We give estimations of the statistical accuracy of the calculations.

  9. A surface diffusion model for Dip Pen Nanolithography line writing

    NASA Astrophysics Data System (ADS)

    Saha, Sourabh K.; Culpepper, Martin L.

    2010-06-01

    Dip Pen Nanolithography is a direct write process that creates nanoscale dots and lines. Models typically predict dot and line size via assumption of constant ink flow rate from tip to substrate. This is appropriate for dot writing. It is however well-known, though models rarely reflect, that the ink flow rate depends upon writing speed during line writing. Herein, we explain the physical phenomenon that governs line writing and use this to model tip-substrate diffusion in line writing. We accurately predict (i) the increase in flow rate with writing speed and (ii) line width within 12.5%.

  10. Forecasting Diffusion of Technology by using Bass Model

    NASA Astrophysics Data System (ADS)

    Kim, Do-Hoi; Shin, Young-Geun; Park, Sang-Sung; Jang, Dong-Sik

    2009-08-01

    Generally, researching method of technology forecasting has been depended on intuition of expert until now. So there were many defects like consuming much time and money and so on. In this paper, we forecast diffusion of technology by using Bass model that is one of the quantitative analysis methods. We applied this model at technology market. And for input data of experiment, we use patent data that is representing each technology in technology market. We expect this research will be suggest new possibility that patent data can be applied in Bass model.

  11. Consistent flamelet modeling of differential molecular diffusion for turbulent non-premixed flames

    NASA Astrophysics Data System (ADS)

    Wang, Haifeng

    2016-03-01

    Treating differential molecular diffusion correctly and accurately remains as a great challenge to the modeling of turbulent non-premixed combustion. The aim of this paper is to develop consistent modeling strategies for differential molecular diffusion in flamelet models. Two types of differential molecular diffusion models are introduced, linear differential diffusion models and nonlinear differential diffusion models. A multi-component turbulent mixing layer problem is analyzed in detail to gain insights into differential molecular diffusion and its characteristics, particularly the dependence of differential molecular diffusion on the Reynolds number and the Lewis number. These characteristics are then used to validate the differential molecular diffusion models. Finally, the new models are applied to the modeling of a series of laboratory-scale turbulent non-premixed jet flames with different Reynolds number (Sandia Flames B, C, and D) to further assess the models' performance.

  12. Extending the Diffuse Layer Model of Surface Acidity Constant Behavior: IV. Diffuse Layer Charge/Potential Relationships

    EPA Science Inventory

    Most current electrostatic surface complexation models describing ionic binding at the particle/water interface rely on the use of Poisson - Boltzmann (PB) theory for relating diffuse layer charge densities to diffuse layer electrostatic potentials. PB theory is known to contain ...

  13. Molecular Diffusive Motion in a Monolayer of a Model Lubricant

    NASA Astrophysics Data System (ADS)

    Diama, A.; Criswell, L.; Mo, H.; Taub, H.; Herwig, K. W.; Hansen, F. Y.; Volkmann, U. G.; Dimeo, R.; Neumann, D.

    2003-03-01

    Squalane (C_30H_62), a branched alkane of intermediate length consisting of a tetracosane backbone (n-C_24H_50 or C24) and six symmetrically placed methyl sidegroups, is frequently taken as a model lubricant. We have conducted quasielastic neutron scattering (QNS) experiments to investigate the diffusive motion on different time scales in a squalane monolayer adsorbed on the (0001) surfaces of an exfoliated graphite substrate. Unlike tetracosane, high-energy resolution spectra (time scale ˜0.1 - 4 ns) at temperatures of 215 K and 230 K show the energy width of the QNS to have a maximum near Q = 1.2 ÅThis nonmonotonic Q dependence suggests a more complicated diffusive motion than the simple rotation about the long molecular axis believed to occur in a C24 monolayer at this temperature. Lower-energy-resolution spectra (time scale ˜4 - 40 ps) show evidence of two types of diffusive motion whose rates have opposite temperature dependences. The rate of the faster motion decreases as the monolayer is heated, and we speculate that it is due to hindered rotation of the methyl groups. The rate of the slower motion increases with temperature and may involve both uniaxial rotation and translational diffusion. Our experimental results will be compared with molecular dynamics simulations.

  14. Modeling diffusive transport with a fractional derivative without singular kernel

    NASA Astrophysics Data System (ADS)

    Gómez-Aguilar, J. F.; López-López, M. G.; Alvarado-Martínez, V. M.; Reyes-Reyes, J.; Adam-Medina, M.

    2016-04-01

    In this paper we present an alternative representation of the diffusion equation and the diffusion-advection equation using the fractional calculus approach, the spatial-time derivatives are approximated using the fractional definition recently introduced by Caputo and Fabrizio in the range β , γ ∈(0 ; 2 ] for the space and time domain respectively. In this representation two auxiliary parameters σx and σt are introduced, these parameters related to equation results in a fractal space-time geometry provide an entire new family of solutions for the diffusion processes. The numerical results showed different behaviors when compared with classical model solutions. In the range β , γ ∈(0 ; 1) , the concentration exhibits the non-Markovian Lévy flights and the subdiffusion phenomena; when β = γ = 1 the classical case is recovered; when β , γ ∈(1 ; 2 ] the concentration exhibits the Markovian Lévy flights and the superdiffusion phenomena; finally when β = γ = 2 the concentration is anomalous dispersive and we found ballistic diffusion.

  15. Reaction-diffusion processes and metapopulation models on duplex networks

    NASA Astrophysics Data System (ADS)

    Xuan, Qi; Du, Fang; Yu, Li; Chen, Guanrong

    2013-03-01

    Reaction-diffusion processes, used to model various spatially distributed dynamics such as epidemics, have been studied mostly on regular lattices or complex networks with simplex links that are identical and invariant in transferring different kinds of particles. However, in many self-organized systems, different particles may have their own private channels to keep their purities. Such division of links often significantly influences the underlying reaction-diffusion dynamics and thus needs to be carefully investigated. This article studies a special reaction-diffusion process, named susceptible-infected-susceptible (SIS) dynamics, given by the reaction steps β→α and α+β→2β, on duplex networks where links are classified into two groups: α and β links used to transfer α and β particles, which, along with the corresponding nodes, consist of an α subnetwork and a β subnetwork, respectively. It is found that the critical point of particle density to sustain reaction activity is independent of the network topology if there is no correlation between the degree sequences of the two subnetworks, and this critical value is suppressed or extended if the two degree sequences are positively or negatively correlated, respectively. Based on the obtained results, it is predicted that epidemic spreading may be promoted on positive correlated traffic networks but may be suppressed on networks with modules composed of different types of diffusion links.

  16. Diffuse interface modeling of a radial vapor bubble collapse

    NASA Astrophysics Data System (ADS)

    Magaletti, Francesco; Marino, Luca; Massimo Casciola, Carlo

    2015-12-01

    A diffuse interface model is exploited to study in details the dynamics of a cavitation vapor bubble, by including phase change, transition to supercritical conditions, shock wave propagation and thermal conduction. The numerical experiments show that the actual dynamic is a sequence of collapses and rebounds demonstrating the importance of nonequilibrium phase changes. In particular the transition to supercritical conditions avoids the full condensation and leads to shockwave emission after the collapse and to successive bubble rebound.

  17. Modeling of Diffusion in Liquid Ge and Its Alloys

    NASA Technical Reports Server (NTRS)

    Stroud, David G.

    1998-01-01

    This report summarizes progress made on NASA Grant NAG3-1437, Modeling of diffusion in Liquid Ge and Its Alloys, which was in effect from January 15, 1993 through July 10, 1997. It briefly describes the purpose of the grant, and the work accomplished in simulations and other studies of thermophysical properties of liquid semiconductors and related materials. A list of publications completed with the support of the grant is also given.

  18. Pricing turbo warrants under mixed-exponential jump diffusion model

    NASA Astrophysics Data System (ADS)

    Yu, Jianfeng; Xu, Weidong

    2016-06-01

    Turbo warrant is a special type of barrier options in which the rebate is calculated as another exotic option. In this paper, using Laplace transforms we obtain the valuation of turbo warrant under the mixed-exponential jump diffusion model, which is able to approximate any jump size distribution. The numerical Laplace inversion examples verify that the analytical solutions are accurate. The results of simulation confirm the argument that jump risk should not be ignored in the valuation of turbo warrants.

  19. Lattice Boltzmann model for the convection-diffusion equation.

    PubMed

    Chai, Zhenhua; Zhao, T S

    2013-06-01

    We propose a lattice Boltzmann (LB) model for the convection-diffusion equation (CDE) and show that the CDE can be recovered correctly from the model by the Chapman-Enskog analysis. The most striking feature of the present LB model is that it enables the collision process to be implemented locally, making it possible to retain the advantage of the lattice Boltzmann method in the study of the heat and mass transfer in complex geometries. A local scheme for computing the heat and mass fluxes is then proposed to replace conventional nonlocal finite-difference schemes. We further validate the present model and the local scheme for computing the flux against analytical solutions to several classical problems, and we show that both the model for the CDE and the computational scheme for the flux have a second-order convergence rate in space. It is also demonstrated the present model is more accurate than existing LB models for the CDE.

  20. An epidemic model of rumor diffusion in online social networks

    NASA Astrophysics Data System (ADS)

    Cheng, Jun-Jun; Liu, Yun; Shen, Bo; Yuan, Wei-Guo

    2013-01-01

    So far, in some standard rumor spreading models, the transition probability from ignorants to spreaders is always treated as a constant. However, from a practical perspective, the case that individual whether or not be infected by the neighbor spreader greatly depends on the trustiness of ties between them. In order to solve this problem, we introduce a stochastic epidemic model of the rumor diffusion, in which the infectious probability is defined as a function of the strength of ties. Moreover, we investigate numerically the behavior of the model on a real scale-free social site with the exponent γ = 2.2. We verify that the strength of ties plays a critical role in the rumor diffusion process. Specially, selecting weak ties preferentially cannot make rumor spread faster and wider, but the efficiency of diffusion will be greatly affected after removing them. Another significant finding is that the maximum number of spreaders max( S) is very sensitive to the immune probability μ and the decay probability v. We show that a smaller μ or v leads to a larger spreading of the rumor, and their relationships can be described as the function ln(max( S)) = Av + B, in which the intercept B and the slope A can be fitted perfectly as power-law functions of μ. Our findings may offer some useful insights, helping guide the application in practice and reduce the damage brought by the rumor.

  1. Reaction-diffusion processes and metapopulation models in heterogeneous networks

    NASA Astrophysics Data System (ADS)

    Colizza, Vittoria; Pastor-Satorras, Romualdo; Vespignani, Alessandro

    2007-04-01

    Dynamical reaction-diffusion processes and metapopulation models are standard modelling approaches for a wide array of phenomena in which local quantities-such as density, potentials and particles-diffuse and interact according to the physical laws. Here, we study the behaviour of the basic reaction-diffusion process (given by the reaction steps B-->A and B+A-->2B) defined on networks with heterogeneous topology and no limit on the nodes' occupation number. We investigate the effect of network topology on the basic properties of the system's phase diagram and find that the network heterogeneity sustains the reaction activity even in the limit of a vanishing density of particles, eventually suppressing the critical point in density-driven phase transitions, whereas phase transition and critical points independent of the particle density are not altered by topological fluctuations. This work lays out a theoretical and computational microscopic framework for the study of a wide range of realistic metapopulation and agent-based models that include the complex features of real-world networks.

  2. A Model Based on Facilitated Passive Diffusion is Needed to Describe Root Water Entry through Aquaporins.

    PubMed

    Beaudette, Pc; Salon, C; Emery, Rjn

    2007-09-01

    Despite abundant evidence that water transfer from soil to xylem occurs along a pathway regulated by aquaporins (AQPs) water entry is still modeled using principles of ordinary passive diffusion. Problems with this model have been known for some time and include variable intrinsic properties of conductivity Lp, changing reflection coefficients, sigma, and an inability to accurately resolve osmotic differentials between the soil and xylem. Here we propose a model of water entry based on principles of facilitated passive diffusion and following Michaelis-Menten formalism. If one accepts that water entry is controlled, at least in part, by AQPs, then a model of ordinary passive diffusion is precluded, as it does not allow for facilitation kinetics. By contrast, recognition of facilitated water entry through protein channels could explain shortcomings of ordinary passive diffusion, such as diurnal variability in conductivity which we have recently shown is directly correlated to diurnal changes in PsPIP2-1 mRNA levels in Pisum sativum.

  3. Impact Acceleration Model of Diffuse Traumatic Brain Injury.

    PubMed

    Hellewell, Sarah C; Ziebell, Jenna M; Lifshitz, Jonathan; Morganti-Kossmann, M Cristina

    2016-01-01

    The impact acceleration (I/A) model of traumatic brain injury (TBI) was developed to reliably induce diffuse traumatic axonal injury in rats in the absence of skull fractures and parenchymal focal lesions. This model replicates a pathophysiology that is commonly observed in humans with diffuse axonal injury (DAI) caused by acceleration-deceleration forces. Such injuries are typical consequences of motor vehicle accidents and falls, which do not necessarily require a direct impact to the closed skull. There are several desirable characteristics of the I/A model, including the extensive axonal injury produced in the absence of a focal contusion, the suitability for secondary insult modeling, and the adaptability for mild/moderate injury through alteration of height and/or weight. Furthermore, the trauma device is inexpensive and readily manufactured in any laboratory, and the induction of injury is rapid (~45 min per animal from weighing to post-injury recovery) allowing multiple animal experiments per day. In this chapter, we describe in detail the methodology and materials required to produce the rat model of I/A in the laboratory. We also review current adaptations to the model to alter injury severity, discuss frequent complications and technical issues encountered using this model, and provide recommendations to ensure technically sound injury induction. PMID:27604723

  4. THE LOS ALAMOS NATIONAL LABORATORY ATMOSPHERIC TRANSPORT AND DIFFUSION MODELS

    SciTech Connect

    M. WILLIAMS

    1999-08-01

    The LANL atmospheric transport and diffusion models are composed of two state-of-the-art computer codes. The first is an atmospheric wind model called HOThlAC, Higher Order Turbulence Model for Atmospheric circulations. HOTMAC generates wind and turbulence fields by solving a set of atmospheric dynamic equations. The second is an atmospheric diffusion model called RAPTAD, Random Particle Transport And Diffusion. RAPTAD uses the wind and turbulence output from HOTMAC to compute particle trajectories and concentration at any location downwind from a source. Both of these models, originally developed as research codes on supercomputers, have been modified to run on microcomputers. Because the capability of microcomputers is advancing so rapidly, the expectation is that they will eventually become as good as today's supercomputers. Now both models are run on desktop or deskside computers, such as an IBM PC/AT with an Opus Pm 350-32 bit coprocessor board and a SUN workstation. Codes have also been modified so that high level graphics, NCAR Graphics, of the output from both models are displayed on the desktop computer monitors and plotted on a laser printer. Two programs, HOTPLT and RAPLOT, produce wind vector plots of the output from HOTMAC and particle trajectory plots of the output from RAPTAD, respectively. A third CONPLT provides concentration contour plots. Section II describes step-by-step operational procedures, specifically for a SUN-4 desk side computer, on how to run main programs HOTMAC and RAPTAD, and graphics programs to display the results. Governing equations, boundary conditions and initial values of HOTMAC and RAPTAD are discussed in Section III. Finite-difference representations of the governing equations, numerical solution procedures, and a grid system are given in Section IV.

  5. Simultaneous estimation of model parameters and diffuse pollution sources for river water quality modeling.

    PubMed

    Jun, K S; Kang, J W; Lee, K S

    2007-01-01

    Diffuse pollution sources along a stream reach are very difficult to both monitor and estimate. In this paper, a systematic method using an optimal estimation algorithm is presented for simultaneous estimation of diffuse pollution and model parameters in a stream water quality model. It was applied with the QUAL2E model to the South Han River in South Korea for optimal estimation of kinetic constants and diffuse loads along the river. Initial calibration results for kinetic constants selected from a sensitivity analysis reveal that diffuse source inputs for nitrogen and phosphorus are essential to satisfy the system mass balance. Diffuse loads for total nitrogen and total phosphorus were estimated by solving the expanded inverse problem. Comparison of kinetic constants estimated simultaneously with diffuse sources to those estimated without diffuse loads, suggests that diffuse sources must be included in the optimization not only for its own estimation but also for adequate estimation of the model parameters. Application of the optimization method to river water quality modeling is discussed in terms of the sensitivity coefficient matrix structure.

  6. Assessment of diffuse transmission and reflection modes in near-infrared quantification, part 2: DIFFuse reflection information depth.

    PubMed

    Saeed, Muhanned; Probst, Leila; Betz, Gabriele

    2011-03-01

    Near-infrared spectroscopy offers tremendous advantages for pharmaceutical manufacturing as a fast and nondestructive method of quantitative and qualitative analysis. Content uniformity (end-product analytics) and process analytics are two important applications of the method. Diffuse reflection (DR) information depth (vertical sampling span) assessment is of equal importance in content prediction applications and to understand the effect of inhomogeneities in the sample. Three experiments were conducted: (a) 0.5 to 10.0 mm incremental thickness MCC tablets with constant porosity, (b) MCC/phenylbutazone (PBZ) double-layered (DL) tablets (PBZ layer 0%-100% in 0.5 mm steps), and (c) Comparison of placebo and 30% caffeine tablet cores with incremental film coating (film thickness of 0-0.35 mm). Incremental thickness and cluster analysis of DL tablets showed that DR information depth was <0.5 mm, whereas the data fitting from incremental coating showed that signal drop reached 50% at 0.05 to 0.07 mm, depending on the wavenumber and 90% signal drop (10% information content) can be seen between 0.20 and 0.25 mm without extrapolation. These results mean that DR mode for pharmaceutical tablets obtains spectral information from the very surface, and radiation is barely reflected back from beyond thin-film coatings, making it less useful than diffuse transmission mode for core content analysis, especially for thick-coated, multilayer, multicore, or highly inhomogeneous tablets.

  7. Diffusion of an effective tobacco prevention program. Part II: Evaluation of the adoption phase.

    PubMed

    Parcel, G S; O'Hara-Tompkins, N M; Harrist, R B; Basen-Engquist, K M; McCormick, L K; Gottlieb, N H; Eriksen, M P

    1995-09-01

    This paper presents the results of theory-based intervention strategies to increase the adoption of a tobacco prevention program. The adoption intervention followed a series of dissemination intervention strategies targeted at 128 school districts in Texas. Informed by Social Cognitive Theory, the intervention provided opportunities for districts to learn about and model themselves after 'successful' school districts that had adopted the program, and to see the potential for social reinforcement through the knowledge that the program had the potential to have an important influence on students' lives. The proportion of districts in the Intervention condition that adopted the program was significantly greater than in the Comparison condition (P < 0.001). Stepwise logistic regression indicated that the variables most closely related to adoption among intervention districts were teacher attitudes toward the innovation and organizational considerations of administrators. Recommendations for the development of effective strategies for the diffusion of innovations are presented.

  8. Boussinesq modeling of HB06 tracer releases Part 2: Tracer plumes

    NASA Astrophysics Data System (ADS)

    Clark, D. B.; Feddersen, F.; Guza, R. T.

    2010-12-01

    Tracer plumes simulated with a Boussinesq surfzone model (funwaveC) are compared with 5 plumes observed during the HB06 experiment (Huntington Beach, Fall 2006). Surfzone tracer plumes were formed by continuously releasing dye tracer into the wave-driven alongshore current. Bulk cross-shore eddy diffusivities, O(1 m2 s-1), were estimated from the observed plumes and agreed best with a mixing-length scaling based on large 2D eddies [Clark et al., JGR, in press 2010]. The mechanisms for surfzone cross-shore tracer dispersion are not well known, and are explored here with the time-dependent, wave and horizontal eddy resolving, funwaveC model. The funwaveC model is run with observed bathymetry, and initialized in 4m depth with the observed obliquely incident and directionally spread waves. Modeled and observed waves and currents are similar, and discussed in Part 1. Model tracer is dispersed by the surfzone horizontal eddy field, a breaking wave eddy diffusivity, and a small O(0.01 m2 s-1) background diffusivity. Modeled and observed mean plume structures agree, but can be degraded by a mismatch between observed and modeled alongshore currents, especially near the tracer source. Bulk tracer eddy diffusivities agree with HB06 observations, and the long narrow plume assumption (used for diffusion analysis) is discussed with modeled tracer fluxes. The model suggests that cross-shore mixing at time scales of many wave periods is dominated by horizontal eddies, not by the breaking eddy diffusivity.

  9. Reaction-diffusion models of within-feather pigmentation patterning.

    PubMed

    Prum, Richard O; Williamson, Scott

    2002-04-22

    Feathers are complex, branched keratin structures that exhibit a diversity of pigmentation patterns. Feather pigments are transferred into developing feather keratinocytes from pigment cells that migrate into the tubular feather germ from the dermis. Within-feather pigment patterns are determined by differential pigmentation of keratinocytes within independent barb ridges during feather development. Little is known about the molecular mechanisms that determine which keratinocytes receive pigment. We apply reaction-diffusion models to the growth of within-feather pigment patterns based on a realistic model of feather growth. These models accurately simulate the growth of a diversity of the within-feather pigmentation patterns found in real feathers, including a central patch, a 'hollow' central patch, concentric central patches, bars, chevrons, a central circular spot, rows of paired spots, and arrays of offset dots. The models can also simulate the complex transitions between distinct pigmentation patterns among feathers observed in real avian plumages, including transitions from bars to chevrons, bars to paired dots, and bars to arrays of dots. The congruence between the developmental dynamics of the simulated and observed feather patterns indicates that the reaction-diffusion models provide a realistic and accurate description of the determination of pigment pattern within avian feather follicles. The models support the hypothesis that within-feather pigmentation patterning is determined by antagonistic interactions among molecular expression gradients within the tubular follicle and feather germ.

  10. A pore-pressure diffusion model for estimating landslide-inducing rainfall

    USGS Publications Warehouse

    Reid, M.E.

    1994-01-01

    Many types of landslide movement are induced by large rainstorms, and empirical rainfall intensity/duration thresholds for initiating movement have been determined for various parts of the world. In this paper, I present a simple pressure diffusion model that provides a physically based hydrologic link between rainfall intensity/duration at the ground surface and destabilizing pore-water pressures at depth. The model approximates rainfall infiltration as a sinusoidally varying flux over time and uses physical parameters that can be determined independently. Using a comprehensive data set from an intensively monitored landslide, I demonstrate that the model is capable of distinguishing movement-inducing rainstorms. -Author

  11. An anisotropic model of diffuse solar radiation with application to an optimization of compound parabolic collectors

    NASA Astrophysics Data System (ADS)

    Perez, R. R.

    Based on a simple geometrical description of the sky hemisphere and the magnitude of the horizontal diffuse radiation, a model for estimating diffuse radiation impinging on sloping surfaces was developed. Tests against data show that substantial improvement is achieved over the classical isotropic model for any collector slope or orientation. Improvement is found for instantaneous as well as accumulated data. The application of the model to compound parabolic collectors (CPC) accounts partly for the role played by forward scattered radiation in the total energy they receive. An optimization of CPC's geometrical characteristics is performed for photovoltaic generation in the area of Albany, NY. This calculation is used to assess the relative effects of meteorological conditions and economic assumptions or optimum concentration values, and provides the reader with information pertaining to the variation of the cost of electrical energy produced as a function of the cost of silicon solar cells.

  12. A Temporal Model of Technology Diffusion into Small Firms in Wales.

    ERIC Educational Resources Information Center

    Thomas, Brychan; Packham, Gary; Miller, Chris

    2001-01-01

    Discusses technology diffusion through formal and informal networks. Develops a model that includes channels and mechanisms involved in transferring technology into innovative small businesses. The model depicts influences that increase or slow the rate of diffusion. (SK)

  13. Super-resolution image reconstruction using diffuse source models.

    PubMed

    Ellis, Michael A; Viola, Francesco; Walker, William F

    2010-06-01

    Image reconstruction is central to many scientific fields, from medical ultrasound and sonar to computed tomography and computer vision. Although lenses play a critical reconstruction role in these fields, digital sensors enable more sophisticated computational approaches. A variety of computational methods have thus been developed, with the common goal of increasing contrast and resolution to extract the greatest possible information from raw data. This paper describes a new image reconstruction method named the Diffuse Time-domain Optimized Near-field Estimator (dTONE). dTONE represents each hypothetical target in the system model as a diffuse region of targets rather than a single discrete target, which more accurately represents the experimental data that arise from signal sources in continuous space, with no additional computational requirements at the time of image reconstruction. Simulation and experimental ultrasound images of animal tissues show that dTONE achieves image resolution and contrast far superior to those of conventional image reconstruction methods. We also demonstrate the increased robustness of the diffuse target model to major sources of image degradation through the addition of electronic noise, phase aberration and magnitude aberration to ultrasound simulations. Using experimental ultrasound data from a tissue-mimicking phantom containing a 3-mm-diameter anechoic cyst, the conventionally reconstructed image has a cystic contrast of -6.3 dB, whereas the dTONE image has a cystic contrast of -14.4 dB.

  14. Measurements and modeling of explosive vapor diffusion in snow

    NASA Astrophysics Data System (ADS)

    Albert, Mary R.; Cragin, James H.; Leggett, Daniel C.

    2000-08-01

    The detection of buried mines is important to both for humanitarian and military strategic de-mining both at home and abroad, and recent efforts in chemical detection show promise for definitive identification of buried miens. The impact of weather has a large effect on the fate and transport of the explosives vapor that these systems sense. In many areas of military conflict, and at Army military training grounds in cold regions, winter weather affects military operations for many months of the year. In cold regions, the presence of freezing ground or a snow cover may provide increased temporary storage of the explosive, potentially leading to opportunities for more optimal sensing conditions later. This paper discusses the result of a controlled laboratory experiment to investigate explosives diffusion through snow, quantitative microscopy measurements of snow microstructure including specific surface, and verifications of our transport model using this data. In experiments measuring 1,3-DNB, 2,4-DNT and 2,4,6-TNT we determined an effective diffusion coefficient of 1.5 X 10-6 cm2/s from measurements through isothermal sieved snow with equivalent sphere radius of 0.11 mm. Adsorption is a major factor in diffusive transport of these explosives through snow. The data was used to verify our finite element mole of explosives transport. Measurements and model results show close agreement.

  15. Cosmic ray diffusion: Detailed investigation of a recent model

    SciTech Connect

    Lerche, Ian; Tautz, R. C.

    2011-08-15

    A recently proposed model [A. Shalchi, Astrophys. J. 720, L127 (2010)] of perpendicular cosmic ray scattering is investigated in detail, with special emphasis to the relevant diffusion coefficients. Solution of a pair of critical equations, as well as a fundamental integral needed to describe the particle transport, are represented via a mathematically correct expansion procedure, thus modifying the previously available approximations. It is hoped that these significant improvements will aid in allowing a clearer understanding of precisely what the model is capable of evaluating.

  16. Affinity based information diffusion model in social networks

    NASA Astrophysics Data System (ADS)

    Liu, Hongli; Xie, Yun; Hu, Haibo; Chen, Zhigao

    2014-12-01

    There is a widespread intuitive sense that people prefer participating in spreading the information in which they are interested. The affinity of people with information disseminated can affect the information propagation in social networks. In this paper, we propose an information diffusion model incorporating the mechanism of affinity of people with information which considers the fitness of affinity values of people with affinity threshold of the information. We find that the final size of information diffusion is affected by affinity threshold of the information, average degree of the network and the probability of people's losing their interest in the information. We also explore the effects of other factors on information spreading by numerical simulations and find that the probabilities of people's questioning and confirming the information can affect the propagation speed, but not the final scope.

  17. Time Fractional Diffusion Equations and Analytical Solvable Models

    NASA Astrophysics Data System (ADS)

    Bakalis, Evangelos; Zerbetto, Francesco

    2016-08-01

    The anomalous diffusion of a particle that moves in complex environments is analytically studied by means of the time fractional diffusion equation. The influence on the dynamics of a random moving particle caused by a uniform external field is taken into account. We extract analytical solutions in terms either of the Mittag-Leffler functions or of the M- Wright function for the probability distribution, for the velocity autocorrelation function as well as for the mean and the mean square displacement. Discussion of the applicability of the model to real systems is made in order to provide new insight of the medium from the analysis of the motion of a particle embedded in it.

  18. A mathematical model of diffusion-limited gas bubble dynamics in tissue with varying diffusion region thickness.

    PubMed

    Srinivasan, R S; Gerth, W A; Powell, M R

    2000-10-01

    The three-region model of gas bubble dynamics consists of a bubble and a well-stirred tissue region with an intervening unperfused diffusion region previously assumed to have constant thickness and uniform gas diffusivity. As a result, the diffusion region gas content remains unchanged as its volume increases with bubble growth, causing dissolved gas in the region to violate Henry's law. Earlier work also neglected the relationship between the varying diffusion region volume and the fixed total tissue volume. The present work corrects these theoretical inconsistencies by postulating a difference in gas diffusivity between an infinitesimally thin layer at the bubble surface and the remainder of the diffusion region, thus allowing both thickness and gas content of the diffusion region to vary during bubble evolution. The corrected model can yield bubble lifetimes considerably longer than those yielded by earlier three-region models, and meets a need for theoretically consistent but relatively simple bubble dynamics models for use in studies of decompression sickness (DCS) in human subjects.

  19. A Discrete Model to Study Reaction-Diffusion-Mechanics Systems

    PubMed Central

    Weise, Louis D.; Nash, Martyn P.; Panfilov, Alexander V.

    2011-01-01

    This article introduces a discrete reaction-diffusion-mechanics (dRDM) model to study the effects of deformation on reaction-diffusion (RD) processes. The dRDM framework employs a FitzHugh-Nagumo type RD model coupled to a mass-lattice model, that undergoes finite deformations. The dRDM model describes a material whose elastic properties are described by a generalized Hooke's law for finite deformations (Seth material). Numerically, the dRDM approach combines a finite difference approach for the RD equations with a Verlet integration scheme for the equations of the mass-lattice system. Using this framework results were reproduced on self-organized pacemaking activity that have been previously found with a continuous RD mechanics model. Mechanisms that determine the period of pacemakers and its dependency on the medium size are identified. Finally it is shown how the drift direction of pacemakers in RDM systems is related to the spatial distribution of deformation and curvature effects. PMID:21804911

  20. A discrete model to study reaction-diffusion-mechanics systems.

    PubMed

    Weise, Louis D; Nash, Martyn P; Panfilov, Alexander V

    2011-01-01

    This article introduces a discrete reaction-diffusion-mechanics (dRDM) model to study the effects of deformation on reaction-diffusion (RD) processes. The dRDM framework employs a FitzHugh-Nagumo type RD model coupled to a mass-lattice model, that undergoes finite deformations. The dRDM model describes a material whose elastic properties are described by a generalized Hooke's law for finite deformations (Seth material). Numerically, the dRDM approach combines a finite difference approach for the RD equations with a Verlet integration scheme for the equations of the mass-lattice system. Using this framework results were reproduced on self-organized pacemaking activity that have been previously found with a continuous RD mechanics model. Mechanisms that determine the period of pacemakers and its dependency on the medium size are identified. Finally it is shown how the drift direction of pacemakers in RDM systems is related to the spatial distribution of deformation and curvature effects.

  1. Subgrid models for mass and thermal diffusion in turbulent mixing

    NASA Astrophysics Data System (ADS)

    Lim, H.; Yu, Y.; Glimm, J.; Li, X.-L.; Sharp, D. H.

    2010-12-01

    We propose a new method for the large eddy simulation (LES) of turbulent mixing flows. The method yields convergent probability distribution functions (PDFs) for temperature and concentration and a chemical reaction rate when applied to reshocked Richtmyer-Meshkov (RM) unstable flows. Because such a mesh convergence is an unusual and perhaps original capability for LES of RM flows, we review previous validation studies of the principal components of the algorithm. The components are (i) a front tracking code, FronTier, to control numerical mass diffusion and (ii) dynamic subgrid scale (SGS) models to compensate for unresolved scales in the LES. We also review the relevant code comparison studies. We compare our results to a simple model based on 1D diffusion, taking place in the geometry defined statistically by the interface (the 50% isoconcentration surface between the two fluids). Several conclusions important to physics could be drawn from our study. We model chemical reactions with no closure approximations beyond those in the LES of the fluid variables itself, and as with dynamic SGS models, these closures contain no adjustable parameters. The chemical reaction rate is specified by the joint PDF for temperature and concentration. We observe a bimodal distribution for the PDF and we observe significant dependence on fluid transport parameters.

  2. A multiphase solute diffusion model for dendritic alloy solidification

    SciTech Connect

    Wang, C.Y.; Beckermann, C.

    1993-12-01

    A solute diffusion model, aimed at predicting microstructure formation in metal castings, is proposed for dendritic solidification of alloys. The model accounts for the different length scales existing in a dendritic structure. This is accomplished by utilizing a multiphase approach, in which not only the various physical phases but also phases associated with different length scales are considered separately. The macroscopic conservation equations are derived for each phase using the volume averaging technique, with constitutive relations developed for the interfacial transfer terms. It is shown that the multiphase model can rigorously incorporate the growth of dendrite tips and coarsening of dendrite arms. In addition, the distinction of different length scales enables the inclusion of realistic descriptions of the dendrite topology and relations to key metallurgical parameters. Another novel aspect of the model is that a single set of conservation equations for solute diffusion is developed for both equiaxed and columnar dendritic solidification. Finally, illustrative calculations for equiaxed, columnar, and mixed columnar-equiaxed solidification are carried out to provide quantitative comparisons with previous studies, and a variety of fundamental phenomena such as recalescence, dendrite tip undercooling, and columnar-to-equiaxed transition (CET) are predicted.

  3. A Reaction-Diffusion Model of Cholinergic Retinal Waves

    PubMed Central

    Lansdell, Benjamin; Ford, Kevin; Kutz, J. Nathan

    2014-01-01

    Prior to receiving visual stimuli, spontaneous, correlated activity in the retina, called retinal waves, drives activity-dependent developmental programs. Early-stage waves mediated by acetylcholine (ACh) manifest as slow, spreading bursts of action potentials. They are believed to be initiated by the spontaneous firing of Starburst Amacrine Cells (SACs), whose dense, recurrent connectivity then propagates this activity laterally. Their inter-wave interval and shifting wave boundaries are the result of the slow after-hyperpolarization of the SACs creating an evolving mosaic of recruitable and refractory cells, which can and cannot participate in waves, respectively. Recent evidence suggests that cholinergic waves may be modulated by the extracellular concentration of ACh. Here, we construct a simplified, biophysically consistent, reaction-diffusion model of cholinergic retinal waves capable of recapitulating wave dynamics observed in mice retina recordings. The dense, recurrent connectivity of SACs is modeled through local, excitatory coupling occurring via the volume release and diffusion of ACh. In addition to simulation, we are thus able to use non-linear wave theory to connect wave features to underlying physiological parameters, making the model useful in determining appropriate pharmacological manipulations to experimentally produce waves of a prescribed spatiotemporal character. The model is used to determine how ACh mediated connectivity may modulate wave activity, and how parameters such as the spontaneous activation rate and sAHP refractory period contribute to critical wave size variability. PMID:25474327

  4. Dense-gas dispersion advection-diffusion model

    SciTech Connect

    Ermak, D.L.

    1992-07-01

    A dense-gas version of the ADPIC particle-in-cell, advection- diffusion model was developed to simulate the atmospheric dispersion of denser-than-air releases. In developing the model, it was assumed that the dense-gas effects could be described in terms of the vertically-averaged thermodynamic properties and the local height of the cloud. The dense-gas effects were treated as a perturbation to the ambient thermodynamic properties (density and temperature), ground level heat flux, turbulence level (diffusivity), and windfield (gravity flow) within the local region of the dense-gas cloud. These perturbations were calculated from conservation of energy and conservation of momentum principles along with the ideal gas law equation of state for a mixture of gases. ADPIC, which is generally run in conjunction with a mass-conserving wind flow model to provide the advection field, contains all the dense-gas modifications within it. This feature provides the versatility of coupling the new dense-gas ADPIC with alternative wind flow models. The new dense-gas ADPIC has been used to simulate the atmospheric dispersion of ground-level, colder-than-ambient, denser-than-air releases and has compared favorably with the results of field-scale experiments.

  5. Anomalous diffusion in neutral evolution of model proteins

    NASA Astrophysics Data System (ADS)

    Nelson, Erik D.; Grishin, Nick V.

    2015-06-01

    Protein evolution is frequently explored using minimalist polymer models, however, little attention has been given to the problem of structural drift, or diffusion. Here, we study neutral evolution of small protein motifs using an off-lattice heteropolymer model in which individual monomers interact as low-resolution amino acids. In contrast to most earlier models, both the length and folded structure of the polymers are permitted to change. To describe structural change, we compute the mean-square distance (MSD) between monomers in homologous folds separated by n neutral mutations. We find that structural change is episodic, and, averaged over lineages (for example, those extending from a single sequence), exhibits a power-law dependence on n . We show that this exponent depends on the alignment method used, and we analyze the distribution of waiting times between neutral mutations. The latter are more disperse than for models required to maintain a specific fold, but exhibit a similar power-law tail.

  6. Diffusive spatio-temporal noise in a first-passage time model for intracellular calcium release

    NASA Astrophysics Data System (ADS)

    Flegg, Mark B.; Rüdiger, Sten; Erban, Radek

    2013-04-01

    The intracellular release of calcium from the endoplasmic reticulum is controlled by ion channels. The resulting calcium signals exhibit a rich spatio-temporal signature, which originates at least partly from microscopic fluctuations. While stochasticity in the gating transition of ion channels has been incorporated into many models, the distribution of calcium is usually described by deterministic reaction-diffusion equations. Here we test the validity of the latter modeling approach by using two different models to calculate the frequency of localized calcium signals (calcium puffs) from clustered IP3 receptor channels. The complexity of the full calcium system is here limited to the basic opening mechanism of the ion channels and, in the mathematical reduction simplifies to the calculation of a first passage time. Two models are then studied: (i) a hybrid model, where channel gating is treated stochastically, while calcium concentration is deterministic and (ii) a fully stochastic model with noisy channel gating and Brownian calcium ion motion. The second model utilises the recently developed two-regime method [M. B. Flegg, S. J. Chapman, and R. Erban, "The two-regime method for optimizing stochastic reaction-diffusion simulations," J. R. Soc., Interface 9, 859-868 (2012)], 10.1098/rsif.2011.0574 in order to simulate a large domain with precision required only near the Ca2+ absorbing channels. The expected time for a first channel opening that results in a calcium puff event is calculated. It is found that for a large diffusion constant, predictions of the interpuff time are significantly overestimated using the model (i) with a deterministic non-spatial calcium variable. It is thus demonstrated that the presence of diffusive noise in local concentrations of intracellular Ca2+ ions can substantially influence the occurrence of calcium signals. The presented approach and results may also be relevant for other cell-physiological first-passage time problems with

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

    SciTech Connect

    Moldrup, P.; Olesen, T.; Yamaguchi, T.; Schjoenning, P.; Rolston, D.E.

    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{sub 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.

  8. Parametric Pattern Selection in a Reaction-Diffusion Model

    PubMed Central

    Stich, Michael; Ghoshal, Gourab; Pérez-Mercader, Juan

    2013-01-01

    We compare spot patterns generated by Turing mechanisms with those generated by replication cascades, in a model one-dimensional reaction-diffusion system. We determine the stability region of spot solutions in parameter space as a function of a natural control parameter (feed-rate) where degenerate patterns with different numbers of spots coexist for a fixed feed-rate. While it is possible to generate identical patterns via both mechanisms, we show that replication cascades lead to a wider choice of pattern profiles that can be selected through a tuning of the feed-rate, exploiting hysteresis and directionality effects of the different pattern pathways. PMID:24204813

  9. Reading and a diffusion model analysis of reaction time.

    PubMed

    Naples, Adam; Katz, Leonard; Grigorenko, Elena L

    2012-01-01

    Processing speed is associated with reading performance. However, the literature is not clear either on the definition of processing speed or on why and how it contributes to reading performance. In this study we demonstrated that processing speed, as measured by reaction time, is not a unitary construct. Using the diffusion model of two-choice reaction time, we assessed processing speed in a series of same-different reaction time tasks for letter and number strings. We demonstrated that the association between reaction time and reading performance is driven by processing speed for reading-related information, but not motor or sensory encoding speed.

  10. Reading and a Diffusion Model Analysis of Reaction Time

    PubMed Central

    Naples, Adam; Katz, Leonard; Grigorenko, Elena L.

    2012-01-01

    Processing speed is associated with reading performance. However, the literature is not clear either on the definition of processing speed or on why and how it contributes to reading performance. In this study we demonstrated that processing speed, as measured by reaction time, is not a unitary construct. Using the diffusion model of two-choice reaction time, we assessed processing speed in a series of same-different reaction time tasks for letter and number strings. We demonstrated that the association between reaction time and reading performance is driven by processing speed for reading-related information, but not motor or sensory encoding speed. PMID:22612543

  11. A study of hydrogen diffusion flames using PDF turbulence model

    NASA Technical Reports Server (NTRS)

    Hsu, Andrew T.

    1991-01-01

    The application of probability density function (pdf) turbulence models is addressed in this work. For the purpose of accurate prediction of turbulent combustion, an algorithm that combines a conventional CFD flow solver with the Monte Carlo simulation of the pdf evolution equation has been developed. The algorithm has been validated using experimental data for a heated turbulent plane jet. The study of H2-F2 diffusion flames has been carried out using this algorithm. Numerical results compared favorably with experimental data. The computuations show that the flame center shifts as the equivalence ratio changes, and that for the same equivalence ratio, similarity solutions for flames exist.

  12. A study of hydrogen diffusion flames using PDF turbulence model

    NASA Technical Reports Server (NTRS)

    Hsu, Andrew T.

    1991-01-01

    The application of probability density function (pdf) turbulence models is addressed. For the purpose of accurate prediction of turbulent combustion, an algorithm that combines a conventional computational fluid dynamic (CFD) flow solver with the Monte Carlo simulation of the pdf evolution equation was developed. The algorithm was validated using experimental data for a heated turbulent plane jet. The study of H2-F2 diffusion flames was carried out using this algorithm. Numerical results compared favorably with experimental data. The computations show that the flame center shifts as the equivalence ratio changes, and that for the same equivalence ratio, similarity solutions for flames exist.

  13. Hybrid diffusion and two-flux approximation for multilayered tissue light propagation modeling.

    PubMed

    Yudovsky, Dmitry; Durkin, Anthony J

    2011-07-20

    Accurate and rapid estimation of fluence, reflectance, and absorbance in multilayered biological media has been essential in many biophotonics applications that aim to diagnose, cure, or model in vivo tissue. The radiative transfer equation (RTE) rigorously models light transfer in absorbing and scattering media. However, analytical solutions to the RTE are limited even in simple homogeneous or plane media. Monte Carlo simulation has been used extensively to solve the RTE. However, Monte Carlo simulation is computationally intensive and may not be practical for applications that demand real-time results. Instead, the diffusion approximation has been shown to provide accurate estimates of light transport in strongly scattering tissue. The diffusion approximation is a greatly simplified model and produces analytical solutions for the reflectance and absorbance in tissue. However, the diffusion approximation breaks down if tissue is strongly absorbing, which is common in the visible part of the spectrum or in applications that involve darkly pigmented skin and/or high local volumes of blood such as port-wine stain therapy or reconstructive flap monitoring. In these cases, a model of light transfer that can accommodate both strongly and weakly absorbing regimes is required. Here we present a model of light transfer through layered biological media that represents skin with two strongly scattering and one strongly absorbing layer.

  14. Hybrid diffusion and two-flux approximation for multilayered tissue light propagation modeling

    NASA Astrophysics Data System (ADS)

    Yudovsky, Dmitry; Durkin, Anthony J.

    2011-07-01

    Accurate and rapid estimation of fluence, reflectance, and absorbance in multilayered biological media has been essential in many biophotonics applications that aim to diagnose, cure, or model in vivo tissue. The radiative transfer equation (RTE) rigorously models light transfer in absorbing and scattering media. However, analytical solutions to the RTE are limited even in simple homogeneous or plane media. Monte Carlo simulation has been used extensively to solve the RTE. However, Monte Carlo simulation is computationally intensive and may not be practical for applications that demand real-time results. Instead, the diffusion approximation has been shown to provide accurate estimates of light transport in strongly scattering tissue. The diffusion approximation is a greatly simplified model and produces analytical solutions for the reflectance and absorbance in tissue. However, the diffusion approximation breaks down if tissue is strongly absorbing, which is common in the visible part of the spectrum or in applications that involve darkly pigmented skin and/or high local volumes of blood such as port-wine stain therapy or reconstructive flap monitoring. In these cases, a model of light transfer that can accommodate both strongly and weakly absorbing regimes is required. Here we present a model of light transfer through layered biological media that represents skin with two strongly scattering and one strongly absorbing layer.

  15. SHIR competitive information diffusion model for online social media

    NASA Astrophysics Data System (ADS)

    Liu, Yun; Diao, Su-Meng; Zhu, Yi-Xiang; Liu, Qing

    2016-11-01

    In online social media, opinion divergences and differentiations generally exist as a result of individuals' extensive participation and personalization. In this paper, a Susceptible-Hesitated-Infected-Removed (SHIR) model is proposed to study the dynamics of competitive dual information diffusion. The proposed model extends the classical SIR model by adding hesitators as a neutralized state of dual information competition. It is both hesitators and stable spreaders that facilitate information dissemination. Researching on the impacts of diffusion parameters, it is found that the final density of stiflers increases monotonically as infection rate increases and removal rate decreases. And the advantage information with larger stable transition rate takes control of whole influence of dual information. The density of disadvantage information spreaders slightly grows with the increase of its stable transition rate, while whole spreaders of dual information and the relaxation time remain almost unchanged. Moreover, simulations imply that the final result of competition is closely related to the ratio of stable transition rates of dual information. If the stable transition rates of dual information are nearly the same, a slightly reduction of the smaller one brings out a significant disadvantage in its propagation coverage. Additionally, the relationship of the ratio of final stiflers versus the ratio of stable transition rates presents power characteristic.

  16. A chaotic model for advertising diffusion problem with competition

    NASA Astrophysics Data System (ADS)

    Ip, W. H.; Yung, K. L.; Wang, Dingwei

    2012-08-01

    In this article, the author extends Dawid and Feichtinger's chaotic advertising diffusion model into the duopoly case. A computer simulation system is used to test this enhanced model. Based on the analysis of simulation results, it is found that the best advertising strategy in duopoly is to increase the advertising investment to reach the best Win-Win situation where the oscillation of market portion will not occur. In order to effectively arrive at the best situation, we define a synthetic index and two thresholds. An estimation method for the parameters of the index and thresholds is proposed in this research. We can reach the Win-Win situation by simply selecting the control parameters to make the synthetic index close to the threshold of min-oscillation state. The numerical example and computational results indicated that the proposed chaotic model is useful to describe and analyse advertising diffusion process in duopoly, it is an efficient tool for the selection and optimisation of advertising strategy.

  17. The impact of hardpans and cemented layers on oxygen diffusivity in mining waste heaps: diffusion experiments and modelling studies.

    PubMed

    Kohfahl, Claus; Graupner, Torsten; Fetzer, Christian; Holzbecher, Ekkehard; Pekdeger, Asaf

    2011-08-01

    This study reports column tests and modelling results to assess the impact of hardpans and cemented layers on oxygen supply in mine waste sediments. The analysed sediment samples were obtained from a low-sulphide and low-carbonate polymetallic mine waste tailings impoundment located in the Freiberg mining district in Germany. The three samples were characterised by different degrees and types of cementation. After physical and mineralogical properties of the samples had been determined, breakthrough curves of oxygen were measured in column studies at different degrees of water saturation, and the diffusivities were assessed using a numerical modelling approach. Results demonstrate that cemented layers and hardpans in undisturbed sediments associated with fine-grained material operate as preferential pathways for diffusive gas transport during rewetting, leading to higher oxygen diffusivities compared to disturbed sediments. Under air-dry conditions, the disturbed samples show higher diffusivities than the undisturbed sample, indicating clogging of the porosity by precipitation of secondary minerals such as trivalent Fe oxyhydroxides acting as a barrier and thereby decreasing the diffusivity of the undisturbed sample. In contrast to sediments without cementation, diffusion experiments of sediments with cemented layers used in this study yield similar tortuosities in spite of their different grain size distributions, pointing to the important role of these heterogeneities for gas diffusion.

  18. Modeling the Determinants Influencing the Diffusion of Mobile Internet

    NASA Astrophysics Data System (ADS)

    Alwahaishi, Saleh; Snášel, Václav

    2013-04-01

    Understanding individual acceptance and use of Information and Communication Technology (ICT) is one of the most mature streams of information systems research. In Information Technology and Information System research, numerous theories are used to understand users' adoption of new technologies. Various models were developed including the Innovation Diffusion Theory, Theory of Reasoned Action, Theory of Planned Behavior, Technology Acceptance Model, and recently, the Unified Theory of Acceptance and Use of Technology. This research composes a new hybrid theoretical framework to identify the factors affecting the acceptance and use of Mobile Internet -as an ICT application- in a consumer context. The proposed model incorporates eight constructs: Performance Expectancy (PE), Effort Expectancy (EE), Facilitating Conditions (FC), Social Influences (SI), Perceived Value (PV), Perceived Playfulness (PP), Attention Focus (AF), and Behavioral intention (BI). Individual differences-namely, age, gender, education, income, and experience are moderating the effects of these constructs on behavioral intention and technology use.

  19. A polarizable continuum model for molecules at spherical diffuse interfaces

    NASA Astrophysics Data System (ADS)

    Di Remigio, Roberto; Mozgawa, Krzysztof; Cao, Hui; Weijo, Ville; Frediani, Luca

    2016-03-01

    We present an extension of the Polarizable Continuum Model (PCM) to simulate solvent effects at diffuse interfaces with spherical symmetry, such as nanodroplets and micelles. We derive the form of the Green's function for a spatially varying dielectric permittivity with spherical symmetry and exploit the integral equation formalism of the PCM for general dielectric environments to recast the solvation problem into a continuum solvation framework. This allows the investigation of the solvation of ions and molecules in nonuniform dielectric environments, such as liquid droplets, micelles or membranes, while maintaining the computationally appealing characteristics of continuum solvation models. We describe in detail our implementation, both for the calculation of the Green's function and for its subsequent use in the PCM electrostatic problem. The model is then applied on a few test systems, mainly to analyze the effect of interface curvature on solvation energetics.

  20. A polarizable continuum model for molecules at spherical diffuse interfaces.

    PubMed

    Di Remigio, Roberto; Mozgawa, Krzysztof; Cao, Hui; Weijo, Ville; Frediani, Luca

    2016-03-28

    We present an extension of the Polarizable Continuum Model (PCM) to simulate solvent effects at diffuse interfaces with spherical symmetry, such as nanodroplets and micelles. We derive the form of the Green's function for a spatially varying dielectric permittivity with spherical symmetry and exploit the integral equation formalism of the PCM for general dielectric environments to recast the solvation problem into a continuum solvation framework. This allows the investigation of the solvation of ions and molecules in nonuniform dielectric environments, such as liquid droplets, micelles or membranes, while maintaining the computationally appealing characteristics of continuum solvation models. We describe in detail our implementation, both for the calculation of the Green's function and for its subsequent use in the PCM electrostatic problem. The model is then applied on a few test systems, mainly to analyze the effect of interface curvature on solvation energetics. PMID:27036423

  1. Soot oxidation and agglomeration modeling in a microgravity diffusion flame

    SciTech Connect

    Ezekoye, O.A.; Zhang, Z.

    1997-07-01

    The global evolution of a microgravity diffusion flame is detailed. Gas species evolution is computed using a reduced finite rate chemical mechanism. Soot evolution is computed using various combinations of existing soot mechanisms. Radiative transfer is coupled to the soot and gas phase chemistry processes using a P1 spherical harmonics radiation model. The soot agglomeration model was examined to note the dependence of soot growth and oxidation processes on soot surface area predictions. For limiting cases where agglomeration was excluded from the soot evolution model, soot primary particle sizes and number concentrations were calculated, and the number of primary particles per aggregate was inferred. These computations are compared with experimental results for microgravity and nonbuoyant flame conditions.

  2. Modeling diffusion-induced stress in nanowire electrode structures

    NASA Astrophysics Data System (ADS)

    Deshpande, Rutooj; Cheng, Yang-Tse; Verbrugge, Mark W.

    There is an intense, worldwide effort to develop durable lithium ion batteries with high energy and power densities for a wide range of applications, including electric and hybrid electric vehicles. One of the critical challenges in advancing lithium ion battery technologies is fracture and decrepitation of the electrodes as a result of lithium diffusion during charging and discharging operations. When lithium is inserted in either the positive or negative electrode, a large volume change on the order of a few to several hundred percent, can occur. Diffusion-induced stresses (DISs) can therefore cause the nucleation and growth of cracks, leading to mechanical degradation of the active electrode materials. Our work is aimed at developing a mathematical model relating surface energy with diffusion-induced stresses in nanowire electrodes. With decreasing size of the electrode, the ratio of surface area to volume increases. Thus, surface energy and surface stress can play an important role in mitigating DISs in nanostructured electrodes. In this work, we establish relationships between the surface energy, surface stress, and the magnitude of DISs in nanowires. We find that DISs, especially the tensile stresses, can decrease significantly due to the surface effects. Our model also establishes a relationship between stress and the nanowire radius. We show that, with decreasing size, the electrode material will be less prone to mechanical degradation, leading to an increase in the life of lithium ion batteries, provided other phenomena are unaffected by increased surface area (e.g., chemical degradation reactions). Also we show that, in the case of nanostructures, surface strain energy is significant in magnitude comparing with bulk strain energy. A mathematical tool to calculate total strain energy is developed that can be used to compare strain energy with the fracture energy of that material in electrode system.

  3. Innovation Diffusion: A Deterministic Model of Space-Time Integration with Physical Analog

    ERIC Educational Resources Information Center

    Haynes, Kingsley E.; And Others

    1977-01-01

    Extends a fundamental temporal diffusion model to integrate space and time dimensions of innovation diffusion. Compares analogous developments in the physical sciences and argues that the proposed model may help link the concepts of catalysts in physical science diffusion processes to the role of change agents in social science systems. (Author/JG)

  4. Hybrid approaches for multiple-species stochastic reaction–diffusion models

    SciTech Connect

    Spill, Fabian; Guerrero, Pilar; Alarcon, Tomas; Maini, Philip K.; Byrne, Helen

    2015-10-15

    Reaction–diffusion models are used to describe systems in fields as diverse as physics, chemistry, ecology and biology. The fundamental quantities in such models are individual entities such as atoms and molecules, bacteria, cells or animals, which move and/or react in a stochastic manner. If the number of entities is large, accounting for each individual is inefficient, and often partial differential equation (PDE) models are used in which the stochastic behaviour of individuals is replaced by a description of the averaged, or mean behaviour of the system. In some situations the number of individuals is large in certain regions and small in others. In such cases, a stochastic model may be inefficient in one region, and a PDE model inaccurate in another. To overcome this problem, we develop a scheme which couples a stochastic reaction–diffusion system in one part of the domain with its mean field analogue, i.e. a discretised PDE model, in the other part of the domain. The interface in between the two domains occupies exactly one lattice site and is chosen such that the mean field description is still accurate there. In this way errors due to the flux between the domains are small. Our scheme can account for multiple dynamic interfaces separating multiple stochastic and deterministic domains, and the coupling between the domains conserves the total number of particles. The method preserves stochastic features such as extinction not observable in the mean field description, and is significantly faster to simulate on a computer than the pure stochastic model. - Highlights: • A novel hybrid stochastic/deterministic reaction–diffusion simulation method is given. • Can massively speed up stochastic simulations while preserving stochastic effects. • Can handle multiple reacting species. • Can handle moving boundaries.

  5. A Microscopic Multiphase Diffusion Model of Viable Epidermis Permeability

    PubMed Central

    Nitsche, Johannes M.; Kasting, Gerald B.

    2013-01-01

    A microscopic model of passive transverse mass transport of small solutes in the viable epidermal layer of human skin is formulated on the basis of a hexagonal array of cells (i.e., keratinocytes) bounded by 4-nm-thick, anisotropic lipid bilayers and separated by 1-μm layers of extracellular fluid. Gap junctions and tight junctions with adjustable permeabilities are included to modulate the transport of solutes with low membrane permeabilities. Two keratinocyte aspect ratios are considered to represent basal and spinous cells (longer) and granular cells (more flattened). The diffusion problem is solved in a unit cell using a coordinate system conforming to the hexagonal cross section, and an efficient two-dimensional treatment is applied to describe transport in both the cell membranes and intercellular spaces, given their thinness. Results are presented in terms of an effective diffusion coefficient, D¯epi, and partition coefficient, K¯epi/w, for a homogenized representation of the microtransport problem. Representative calculations are carried out for three small solutes—water, L-glucose, and hydrocortisone—covering a wide range of membrane permeability. The effective transport parameters and their microscopic interpretation can be employed within the context of existing three-layer models of skin transport to provide more realistic estimates of the epidermal concentrations of topically applied solutes. PMID:23708370

  6. Diffusion dynamics in the disordered Bose Hubbard model

    NASA Astrophysics Data System (ADS)

    Wadleigh, Laura; Russ, Philip; Demarco, Brian

    2016-05-01

    We explore the dynamics of diffusion for out-of-equilibrium superfluid, Mott insulator, and Bose glass states using an atomic realization of the disordered Bose Hubbard (DBH) model. Dynamics in strongly correlated systems, especially far from equilibrium, are not well understood. The introduction of disorder further complicates these systems. We realize the DBH model--which has been central to our understanding of quantum phase transitions in disordered systems--using ultracold Rubidium-87 atoms trapped in a cubic disordered optical lattice. By tightly focusing a beam into the center of the gas, we create a hole in the atomic density profile. We achieve Mott insulator, superfluid, or Bose glass states by varying the interaction and disorder strength, and measure the time evolution of the density profile after removing the central barrier. This allows us to infer diffusion rates from the velocities at the edge of the hole and to look for signatures of superfluid puddles in the Bose glass state. We acknowledge funding from NSF Grant PHY 15-05468, NSF Grant DGE-1144245, and ARO Grant W911NF-12-1-0462.

  7. The Approximate Number System Acuity Redefined: A Diffusion Model Approach

    PubMed Central

    Park, Joonkoo; Starns, Jeffrey J.

    2015-01-01

    While all humans are capable of non-verbally representing numerical quantity using so-called the approximate number system (ANS), there exist considerable individual differences in its acuity. For example, in a non-symbolic number comparison task, some people find it easy to discriminate brief presentations of 14 dots from 16 dots while others do not. Quantifying individual ANS acuity from such a task has become an essential practice in the field, as individual differences in such a primitive number sense is thought to provide insights into individual differences in learned symbolic math abilities. However, the dominant method of characterizing ANS acuity—computing the Weber fraction (w)—only utilizes the accuracy data while ignoring response times (RT). Here, we offer a novel approach of quantifying ANS acuity by using the diffusion model, which accounts both accuracy and RT distributions. Specifically, the drift rate in the diffusion model, which indexes the quality of the stimulus information, is used to capture the precision of the internal quantity representation. Analysis of behavioral data shows that w is contaminated by speed-accuracy tradeoff, making it problematic as a measure of ANS acuity, while drift rate provides a measure more independent from speed-accuracy criterion settings. Furthermore, drift rate is a better predictor of symbolic math ability than w, suggesting a practical utility of the measure. These findings demonstrate critical limitations of the use of w and suggest clear advantages of using drift rate as a measure of primitive numerical competence. PMID:26733929

  8. A microscopic multiphase diffusion model of viable epidermis permeability.

    PubMed

    Nitsche, Johannes M; Kasting, Gerald B

    2013-05-21

    A microscopic model of passive transverse mass transport of small solutes in the viable epidermal layer of human skin is formulated on the basis of a hexagonal array of cells (i.e., keratinocytes) bounded by 4-nm-thick, anisotropic lipid bilayers and separated by 1-μm layers of extracellular fluid. Gap junctions and tight junctions with adjustable permeabilities are included to modulate the transport of solutes with low membrane permeabilities. Two keratinocyte aspect ratios are considered to represent basal and spinous cells (longer) and granular cells (more flattened). The diffusion problem is solved in a unit cell using a coordinate system conforming to the hexagonal cross section, and an efficient two-dimensional treatment is applied to describe transport in both the cell membranes and intercellular spaces, given their thinness. Results are presented in terms of an effective diffusion coefficient, D¯(epi), and partition coefficient, K¯(epi/w), for a homogenized representation of the microtransport problem. Representative calculations are carried out for three small solutes-water, L-glucose, and hydrocortisone-covering a wide range of membrane permeability. The effective transport parameters and their microscopic interpretation can be employed within the context of existing three-layer models of skin transport to provide more realistic estimates of the epidermal concentrations of topically applied solutes.

  9. Comparison of Turbulent Thermal Diffusivity and Scalar Variance Models

    NASA Technical Reports Server (NTRS)

    Yoder, Dennis A.

    2016-01-01

    In this study, several variable turbulent Prandtl number formulations are examined for boundary layers, pipe flow, and axisymmetric jets. The model formulations include simple algebraic relations between the thermal diffusivity and turbulent viscosity as well as more complex models that solve transport equations for the thermal variance and its dissipation rate. Results are compared with available data for wall heat transfer and profile measurements of mean temperature, the root-mean-square (RMS) fluctuating temperature, turbulent heat flux and turbulent Prandtl number. For wall-bounded problems, the algebraic models are found to best predict the rise in turbulent Prandtl number near the wall as well as the log-layer temperature profile, while the thermal variance models provide a good representation of the RMS temperature fluctuations. In jet flows, the algebraic models provide no benefit over a constant turbulent Prandtl number approach. Application of the thermal variance models finds that some significantly overpredict the temperature variance in the plume and most underpredict the thermal growth rate of the jet. The models yield very similar fluctuating temperature intensities in jets from straight pipes and smooth contraction nozzles, in contrast to data that indicate the latter should have noticeably higher values. For the particular low subsonic heated jet cases examined, changes in the turbulent Prandtl number had no effect on the centerline velocity decay.

  10. Pre-Clinical Models of Diffuse Intrinsic Pontine Glioma

    PubMed Central

    Misuraca, Katherine L.; Cordero, Francisco J.; Becher, Oren J.

    2015-01-01

    Diffuse intrinsic pontine glioma (DIPG) is a rare and incurable brain tumor that arises in the brainstem of children predominantly between the ages of 6 and 8. Its intricate morphology and involvement of normal pons tissue precludes surgical resection, and the standard of care today remains fractionated radiation alone. In the past 30 years, there have been no significant advances made in the treatment of DIPG. This is largely because we lack good models of DIPG and therefore have little biological basis for treatment. In recent years, however, due to increased biopsy and acquisition of autopsy specimens, research is beginning to unravel the genetic and epigenetic drivers of DIPG. Insight gleaned from these studies has led to improvements in approaches to both model these tumors in the lab and to potentially treat them in the clinic. This review will detail the initial strides toward modeling DIPG in animals, which included allograft and xenograft rodent models using non-DIPG glioma cells. Important advances in the field came with the development of in vitro cell and in vivo xenograft models derived directly from autopsy material of DIPG patients or from human embryonic stem cells. Finally, we will summarize the progress made in the development of genetically engineered mouse models of DIPG. Cooperation of studies incorporating all of these modeling systems to both investigate the unique mechanisms of gliomagenesis in the brainstem and to test potential novel therapeutic agents in a preclinical setting will result in improvement in treatments for DIPG patients. PMID:26258075

  11. Molecular Modeling of Diffusion on a Crystalline PETN Surface

    SciTech Connect

    Lin, P; Khare, R; Gee, R H; Weeks, B L

    2007-07-13

    Surface diffusion on a PETN crystal was investigated by treating the surface diffusion as an activated process in the formalism of transition state theory. In particular, surface diffusion on the (110) and (101) facets, as well as diffusion between these facets, were considered. We successfully obtained the potential energy barriers required for PETN surface diffusion. Our results show that the (110) surface is more thermally active than the (101) surface and PETN molecules mainly diffuses from the (110) to (101) facet. These results are in good agreement with experimental observations and previous simulations.

  12. NMR signal for particles diffusing under potentials: From path integrals and numerical methods to a model of diffusion anisotropy

    NASA Astrophysics Data System (ADS)

    Yolcu, Cem; Memiç, Muhammet; Şimşek, Kadir; Westin, Carl-Fredrik; Özarslan, Evren

    2016-05-01

    We study the influence of diffusion on NMR experiments when the molecules undergo random motion under the influence of a force field and place special emphasis on parabolic (Hookean) potentials. To this end, the problem is studied using path integral methods. Explicit relationships are derived for commonly employed gradient waveforms involving pulsed and oscillating gradients. The Bloch-Torrey equation, describing the temporal evolution of magnetization, is modified by incorporating potentials. A general solution to this equation is obtained for the case of parabolic potential by adopting the multiple correlation function (MCF) formalism, which has been used in the past to quantify the effects of restricted diffusion. Both analytical and MCF results were found to be in agreement with random walk simulations. A multidimensional formulation of the problem is introduced that leads to a new characterization of diffusion anisotropy. Unlike the case of traditional methods that employ a diffusion tensor, anisotropy originates from the tensorial force constant, and bulk diffusivity is retained in the formulation. Our findings suggest that some features of the NMR signal that have traditionally been attributed to restricted diffusion are accommodated by the Hookean model. Under certain conditions, the formalism can be envisioned to provide a viable approximation to the mathematically more challenging restricted diffusion problems.

  13. NMR signal for particles diffusing under potentials: From path integrals and numerical methods to a model of diffusion anisotropy.

    PubMed

    Yolcu, Cem; Memiç, Muhammet; Şimşek, Kadir; Westin, Carl-Fredrik; Özarslan, Evren

    2016-05-01

    We study the influence of diffusion on NMR experiments when the molecules undergo random motion under the influence of a force field and place special emphasis on parabolic (Hookean) potentials. To this end, the problem is studied using path integral methods. Explicit relationships are derived for commonly employed gradient waveforms involving pulsed and oscillating gradients. The Bloch-Torrey equation, describing the temporal evolution of magnetization, is modified by incorporating potentials. A general solution to this equation is obtained for the case of parabolic potential by adopting the multiple correlation function (MCF) formalism, which has been used in the past to quantify the effects of restricted diffusion. Both analytical and MCF results were found to be in agreement with random walk simulations. A multidimensional formulation of the problem is introduced that leads to a new characterization of diffusion anisotropy. Unlike the case of traditional methods that employ a diffusion tensor, anisotropy originates from the tensorial force constant, and bulk diffusivity is retained in the formulation. Our findings suggest that some features of the NMR signal that have traditionally been attributed to restricted diffusion are accommodated by the Hookean model. Under certain conditions, the formalism can be envisioned to provide a viable approximation to the mathematically more challenging restricted diffusion problems. PMID:27300946

  14. A Lattice Boltzmann Model for Oscillating Reaction-Diffusion

    NASA Astrophysics Data System (ADS)

    Rodríguez-Romo, Suemi; Ibañez-Orozco, Oscar; Sosa-Herrera, Antonio

    2016-07-01

    A computational algorithm based on the lattice Boltzmann method (LBM) is proposed to model reaction-diffusion systems. In this paper, we focus on how nonlinear chemical oscillators like Belousov-Zhabotinsky (BZ) and the chlorite-iodide-malonic acid (CIMA) reactions can be modeled by LBM and provide with new insight into the nature and applications of oscillating reactions. We use Gaussian pulse initial concentrations of sulfuric acid in different places of a bidimensional reactor and nondiffusive boundary walls. We clearly show how these systems evolve to a chaotic attractor and produce specific pattern images that are portrayed in the reactions trajectory to the corresponding chaotic attractor and can be used in robotic control.

  15. On Modeling Viral Diffusion in Heterogeneous Wireless Networks

    NASA Astrophysics Data System (ADS)

    Nguyen, Hoai-Nam; Shinoda, Yoichi

    Smart phones and computers now are able to co-work in a wireless environment where malware can propagate. Although many investigations have modeled the spread of malware, little has been done to take into account different characteristics of items to see how they affect disease diffusion in an ad hoc network. We have therefore developed a novel framework, consisting of two models, which consider diversity of objects as well as interactions between their different classes. Our framework is able to produce a huge result space thus makes it appropriate to describe many viral proliferating scenarios. Additionally, we have developed a formula to calculate the possible average number of newly infected devices in the considered system. An important contribution of our work is the comprehension of item diversity, which states that a mixture of device types causes a bigger malware spread as the number of device types in the network increases.

  16. INACTIVATION OF CRYPTOSPORIDIUM OOCYSTS IN A PILOT-SCALE OZONE BUBBLE-DIFFUSER CONTACTOR - II: MODEL VALIDATION AND APPLICATION

    EPA Science Inventory

    The ADR model developed in Part I of this study was successfully validated with experimenta data obtained for the inactivation of C. parvum and C. muris oocysts with a pilot-scale ozone-bubble diffuser contactor operated with treated Ohio River water. Kinetic parameters, required...

  17. Effective Diffusion Coefficient and Controlling Process of P Diffusion in Si Based on the Pair Diffusion Models of Vacancy and Interstitial Mechanisms

    NASA Astrophysics Data System (ADS)

    Yoshida, Masayuki; Morooka, Masami; Takahashi, Manabu; Tomokage, Hajime

    2000-05-01

    Based on the pair diffusion models of vacancy and interstitial (V and I) mechanisms, the V and I components of effective P diffusion coefficient, DP^+,Veff and DP^+,Ieff, and the controlling process of P diffusion in Si are obtained. Assuming that the I mechanism is dominant, not only the I- concentration, CI^-, but also its gradient, d CI^-/d λ , is effective on DP^+,Ieff at high CP^+. DP^+,Ieff is large at d CI^-/d λ <0 and small at d CI^-/d λ >0. P+ and I- are generated by the dissociation of P-I pair. When excess I- thus generated is removed, d CI^-/d λ <0 is obtained. d CI^-/d λ <0 is also obtained by the decrease in quasi self-interstitial formation energy. Several diffusion models simulate the P diffusion profile well under an inert atmosphere. Applying the controlling process to them, the reason why they simulate the P profile well is investigated. Because all of them simulate the P profile well, it is difficult to conclude which model is correct. It is suggested that it is possible to conclude which model is correct from the P profile under oxidation at CP^+s >1× 1020 cm-3 (s: surface).

  18. The Diffusion Model Is Not a Deterministic Growth Model: Comment on Jones and Dzhafarov (2014)

    PubMed Central

    Smith, Philip L.; Ratcliff, Roger; McKoon, Gail

    2015-01-01

    Jones and Dzhafarov (2014) claim that several current models of speeded decision making in cognitive tasks, including the diffusion model, can be viewed as special cases of other general models or model classes. The general models can be made to match any set of response time (RT) distribution and accuracy data exactly by a suitable choice of parameters and so are unfalsifiable. The implication of their claim is that models like the diffusion model are empirically testable only by artificially restricting them to exclude unfalsifiable instances of the general model. We show that Jones and Dzhafarov’s argument depends on enlarging the class of “diffusion” models to include models in which there is little or no diffusion. The unfalsifiable models are deterministic or near-deterministic growth models, from which the effects of within-trial variability have been removed or in which they are constrained to be negligible. These models attribute most or all of the variability in RT and accuracy to across-trial variability in the rate of evidence growth, which is permitted to be distributed arbitrarily and to vary freely across experimental conditions. In contrast, in the standard diffusion model, within-trial variability in evidence is the primary determinant of variability in RT. Across-trial variability, which determines the relative speed of correct responses and errors, is theoretically and empirically constrained. Jones and Dzhafarov’s attempt to include the diffusion model in a class of models that also includes deterministic growth models misrepresents and trivializes it and conveys a misleading picture of cognitive decision-making research. PMID:25347314

  19. Modeling Periodic Impulsive Effects on Online TV Series Diffusion

    PubMed Central

    Fang, Qiwen; Wang, Xi

    2016-01-01

    Background Online broadcasting substantially affects the production, distribution, and profit of TV series. In addition, online word-of-mouth significantly affects the diffusion of TV series. Because on-demand streaming rates are the most important factor that influences the earnings of online video suppliers, streaming statistics and forecasting trends are valuable. In this paper, we investigate the effects of periodic impulsive stimulation and pre-launch promotion on on-demand streaming dynamics. We consider imbalanced audience feverish distribution using an impulsive susceptible-infected-removed(SIR)-like model. In addition, we perform a correlation analysis of online buzz volume based on Baidu Index data. Methods We propose a PI-SIR model to evolve audience dynamics and translate them into on-demand streaming fluctuations, which can be observed and comprehended by online video suppliers. Six South Korean TV series datasets are used to test the model. We develop a coarse-to-fine two-step fitting scheme to estimate the model parameters, first by fitting inter-period accumulation and then by fitting inner-period feverish distribution. Results We find that audience members display similar viewing habits. That is, they seek new episodes every update day but fade away. This outcome means that impulsive intensity plays a crucial role in on-demand streaming diffusion. In addition, the initial audience size and online buzz are significant factors. On-demand streaming fluctuation is highly correlated with online buzz fluctuation. Conclusion To stimulate audience attention and interpersonal diffusion, it is worthwhile to invest in promotion near update days. Strong pre-launch promotion is also a good marketing tool to improve overall performance. It is not advisable for online video providers to promote several popular TV series on the same update day. Inter-period accumulation is a feasible forecasting tool to predict the future trend of the on-demand streaming amount

  20. An intravoxel oriented flow model for diffusion-weighted imaging of the kidney.

    PubMed

    Hilbert, Fabian; Bock, Maximilian; Neubauer, Henning; Veldhoen, Simon; Wech, Tobias; Bley, Thorsten Alexander; Köstler, Herbert

    2016-10-01

    By combining intravoxel incoherent motion (IVIM) and diffusion tensor imaging (DTI) we introduce a new diffusion model called intravoxel oriented flow (IVOF) that accounts for anisotropy of diffusion and the flow-related signal. An IVOF model using a simplified apparent flow fraction tensor (IVOFf ) is applied to diffusion-weighted imaging of human kidneys. The kidneys of 13 healthy volunteers were examined on a 3 T scanner. Diffusion-weighted images were acquired with six b values between 0 and 800 s/mm(2) and 30 diffusion directions. Diffusivity and flow fraction were calculated for different diffusion models. The Akaike information criterion was used to compare the model fit of the proposed IVOFf model to IVIM and DTI. In the majority of voxels the proposed IVOFf model with a simplified apparent flow fraction tensor performs better than IVIM and DTI. Mean diffusivity is significantly higher in DTI compared with models that account for the flow-related signal. The fractional anisotropy of diffusion is significantly reduced when flow fraction is considered to be anisotropic. Anisotropy of the apparent flow fraction tensor is significantly higher in the renal medulla than in the cortex region. The IVOFf model describes diffusion-weighted data in the human kidney more accurately than IVIM or DTI. The apparent flow fraction in the kidney proved to be anisotropic. PMID:27488570

  1. Modelling interactions between soil evolution and diffusive surface processes

    NASA Astrophysics Data System (ADS)

    Kirkby, Mike; Johnson, Michelle; Gloor, Emanual

    2014-05-01

    Bioturbation, combined with settlement under gravity, generates profiles of bulk density, porosity and hydraulic conductivity (Ksat). Rates of bioturbation are linked to rates of diffusive downslope sediment transport (creep) and rates can be compared via the increase in OSL ages of soil aggregate grains with depth. Some primary porosity is also produced by weathering of rock to saprolite, often with little reduction in bulk density but some dilation of joints. Downward percolation of rain water near the surface is controlled by the diffusion-induced decrease in porosity and Ksat, driving lateral subsurface flow in the zone of fluctuating water table, and leaving progressively less water for downward percolation. As the depth to the weathering front is varied, progressively less water is therefore available for weathering, producing the observed decrease in weathering rate with increasing soil depth. These processes are modelled by repeatedly applying a stochastic realisation of daily rainfalls for an area until the annual hydrological cycle stabilises, providing the average partition of rainfall into its components of evapotranspiration, lateral flow and downward percolation, with depth in the soil. The average hydrology is then applied to drive evolution of the weathering profile over longer time spans.

  2. Magnetic field diffusion modeling of a small enclosed firing system

    SciTech Connect

    Warne, L.K.; Merewether, K.O.

    1996-01-01

    Intense magnetic fields exist in the immediate vicinity of a lightning strike (and near power lines). Conducting barriers increase the rise time (and thus decrease the rise rate) interior to the barrier, but typically do not prevent penetration of the magnetic field, since the lightning current fall time may be larger than the barrier diffusion time. Thus, substantial energy is present in the interior field, although the degradation of rise rate makes it more difficult to couple into electrical circuits. This report assesses the threat posed by the diffusive magnetic field to interior components and wire loops (where voltages are induced). Analytical and numerical bounding analyses are carried out on a pill box shaped conducting barrier to develop estimates for the worst case magnetic field threats inside the system. Worst case induced voltages and energies are estimated and compared with threshold charge voltages and energies on the output capacitor of the system. Variability of these quantities with respect to design parameters are indicated. The interior magnetic field and induced voltage estimates given in this report can be used as excitations for more detailed interior and component models.

  3. Analytical model of diffuse reflectance spectrum of skin tissue

    SciTech Connect

    Lisenko, S A; Kugeiko, M M; Firago, V A; Sobchuk, A N

    2014-01-31

    We have derived simple analytical expressions that enable highly accurate calculation of diffusely reflected light signals of skin in the spectral range from 450 to 800 nm at a distance from the region of delivery of exciting radiation. The expressions, taking into account the dependence of the detected signals on the refractive index, transport scattering coefficient, absorption coefficient and anisotropy factor of the medium, have been obtained in the approximation of a two-layer medium model (epidermis and dermis) for the same parameters of light scattering but different absorption coefficients of layers. Numerical experiments on the retrieval of the skin biophysical parameters from the diffuse reflectance spectra simulated by the Monte Carlo method show that commercially available fibre-optic spectrophotometers with a fixed distance between the radiation source and detector can reliably determine the concentration of bilirubin, oxy- and deoxyhaemoglobin in the dermis tissues and the tissue structure parameter characterising the size of its effective scatterers. We present the examples of quantitative analysis of the experimental data, confirming the correctness of estimates of biophysical parameters of skin using the obtained analytical expressions. (biophotonics)

  4. Analytical model of diffuse reflectance spectrum of skin tissue

    NASA Astrophysics Data System (ADS)

    Lisenko, S. A.; Kugeiko, M. M.; Firago, V. A.; Sobchuk, A. N.

    2014-01-01

    We have derived simple analytical expressions that enable highly accurate calculation of diffusely reflected light signals of skin in the spectral range from 450 to 800 nm at a distance from the region of delivery of exciting radiation. The expressions, taking into account the dependence of the detected signals on the refractive index, transport scattering coefficient, absorption coefficient and anisotropy factor of the medium, have been obtained in the approximation of a two-layer medium model (epidermis and dermis) for the same parameters of light scattering but different absorption coefficients of layers. Numerical experiments on the retrieval of the skin biophysical parameters from the diffuse reflectance spectra simulated by the Monte Carlo method show that commercially available fibre-optic spectrophotometers with a fixed distance between the radiation source and detector can reliably determine the concentration of bilirubin, oxy- and deoxyhaemoglobin in the dermis tissues and the tissue structure parameter characterising the size of its effective scatterers. We present the examples of quantitative analysis of the experimental data, confirming the correctness of estimates of biophysical parameters of skin using the obtained analytical expressions.

  5. A seed-diffusion model for tropical tree diversity patterns

    NASA Astrophysics Data System (ADS)

    Derzsi, A.; Néda, Z.

    2012-10-01

    Diversity patterns of tree species in a tropical forest community are approached by a simple lattice model and investigated by Monte Carlo simulations using a backtracking method. Our spatially explicit neutral model is based on a simple statistical physics process, namely the diffusion of seeds. The model has three parameters: the speciation rate, the size of the meta-community in which the studied tree-community is embedded, and the average surviving time of the seeds. By extensive computer simulations we aim towards the reproduction of relevant statistical measures derived from the experimental data of the Barro Colorado Island tree census in 1995. The first two parameters of the model are fixed to known values, characteristic of the studied community, thus obtaining a model with only one freely adjustable parameter. As a result of this, the average number of species in the considered territory, the relative species abundance distribution, the species-area relationship and the spatial auto-correlation function of the individuals in abundant species are simultaneously fitted with only one parameter which is the average surviving time of the seeds.

  6. Reactor-Diffusion Models For Cartilage Pattern Formation

    NASA Astrophysics Data System (ADS)

    Glimm, Tilmann; Hentschel, H. G. E.

    2004-03-01

    In the early stages of the development of the embryonic chick limb, the sites of future skeletal elements are marked by a prepattern formed by condensations of precartilage cells. A number of different theories have been proposed as to what mechanism determines the characteristic size, shape and number of these condensations. Nevertheless, there is still little definite knowledge on this question. In this talk, we present a model of the limb based on recent experiments and additional hypotheses. In this model, it is a ``reactor-diffusion'' mechanism which gives rise to precartilage condensation. The model consists of a system of nonlinear partial differential equations which govern the spatiotemporal distribution of various types of mesenchymal cells and relevant biomolecules. These biomolecules include Fibroblast growth factors (FGFs), transforming growth factor-betas (TGF-βs), the extracellular matrix protein Fibronectin, as well as a laterally-acting inhibitor. We present the results of numerical simulations for the system of PDEs. Also addressed are preliminary results on how this PDE model can be tied in with more biologically realistic cellular automata based models.

  7. A kinetic model for molecular diffusion through pores.

    PubMed

    D'Agostino, Tommaso; Salis, Samuele; Ceccarelli, Matteo

    2016-07-01

    The number of pathogens developing multiple drug resistance is ever increasing. The impact on healthcare systems is huge and the need for novel antibiotics as well a new way to develop them is urgent, especially against Gram-negative bacteria. The first defense of these bacteria is the outer membrane, where unspecific protein channels (porins) modulate nutrients passive diffusion. Also polar antibiotics enter through this path and down-regulation and/or mutation of porins are very common in drug resistant strains. Our inability to come up with novel effective antibiotics mostly relies upon the insufficient comprehension of the key molecular features enabling better penetration through porins. Molecular dynamics simulations offer an extraordinary tool in the study of the dynamics of biological systems; however, one of the major drawbacks of this method is that its use is currently restricted to study time scales of the order of microsecond. Enhanced sampling methods like Metadynamics have been recently used to investigate the diffusion of antibiotics through bacterial porins. The main limitation is that dynamical properties cannot be estimated because of the different potential that the systems under study are experiencing. Recently, the scope of Metadynamics has been extended. By applying an a posteriori analysis one can obtain rates of transitions and rate-limiting steps of the process under study, directly comparable with kinetic data extracted from electrophysiology experiments. In this work, we apply this method to the study of the permeability of Escherichia coli's OmpF with respect to Meropenem, finding good agreement with the residence time obtained analyzing experimental current noise. This article is part of a Special Issue entitled: Membrane Proteins edited by J.C. Gumbart and Sergei Noskov.

  8. Assessment of non-Gaussian diffusion with singly and doubly stretched biexponential models of diffusion-weighted MRI (DWI) signal attenuation in prostate tissue.

    PubMed

    Hall, Matt G; Bongers, Andre; Sved, Paul; Watson, Geoffrey; Bourne, Roger M

    2015-04-01

    Non-Gaussian diffusion dynamics was investigated in the two distinct water populations identified by a biexponential model of diffusion in prostate tissue. Diffusion-weighted MRI (DWI) signal attenuation was measured ex vivo in two formalin-fixed prostates at 9.4 T with diffusion times Δ = 10, 20 and 40 ms, and b values in the range 0.017-8.2 ms/µm(2) . A conventional biexponential model was compared with models in which either the lower diffusivity component or both of the components of the biexponential were stretched. Models were compared using Akaike's Information Criterion (AIC) and a leave-one-out (LOO) test of model prediction accuracy. The doubly stretched (SS) model had the highest LOO prediction accuracy and lowest AIC (highest information content) in the majority of voxels at Δ = 10 and 20 ms. The lower diffusivity stretching factor (α2 ) of the SS model was consistently lower (range ~0.3-0.9) than the higher diffusivity stretching factor (α1 , range ~0.7-1.1), indicating a high degree of diffusion heterogeneity in the lower diffusivity environment, and nearly Gaussian diffusion in the higher diffusivity environment. Stretched biexponential models demonstrate that, in prostate tissue, the two distinct water populations identified by the simple biexponential model individually exhibit non-Gaussian diffusion dynamics.

  9. Weak solutions for a non-Newtonian diffuse interface model with different densities

    NASA Astrophysics Data System (ADS)

    Abels, Helmut; Breit, Dominic

    2016-11-01

    We consider weak solutions for a diffuse interface model of two non-Newtonian viscous, incompressible fluids of power-law type in the case of different densities in a bounded, sufficiently smooth domain. This leads to a coupled system of a nonhomogenouos generalized Navier-Stokes system and a Cahn-Hilliard equation. For the Cahn-Hilliard part a smooth free energy density and a constant, positive mobility is assumed. Using the {{L}∞} -truncation method we prove existence of weak solutions for a power-law exponent p>\\frac{2d+2}{d+2} , d  =  2, 3.

  10. The small ice cap instability in diffusive climate models

    NASA Technical Reports Server (NTRS)

    North, G. R.

    1984-01-01

    Simple climate models which invoke diffusive heat transport and ice cap albedo feedback have equilibrium solutions with no stable ice cap smaller than a radius of about 20 deg on a great circle. Attention is presently given to a solution of this phenomenon which is physically appealing. The ice-free solution has a thermal minimum, and if the minimum temperature is just above the critical value for ice formation, then the artificial addition of a patch of ice leads to a widespread depression of the temperature below the critical freezing temperature. A second stable solution will then exist whose spatial extent is determined by the range of the influence function of a point sink of heat, due to the albedo shift in the patch.

  11. Energy efficient engine diffuser/combustor model technology

    NASA Technical Reports Server (NTRS)

    Gardner, W.

    1980-01-01

    A full scale, full annular diffuser/combustor model test rig was tested to investigate how configurational changes affect pressure loss and flow separation characteristics. The rig was characterized by five major modules: inlet; prediffuser; strut; simulated combustor; and full combustor. The prediffuser featured a short, curved wall dump design. Performance goals included: (1) a separation-free prediffuser flow field; (2) total pressure loss limited to 3.0 percent in the prediffuser and shrouds; and (3) an overall section pressure loss of 5.5 percent P sub T3 at the design airflow distribution. The results indicated that the prediffuser configurations operate well within the program goals for pressure loss and demonstrate separation free operation over a wide range of inlet conditions.

  12. JPEG-2000 Part 10 Verification Model

    2003-03-04

    VM10 is a research software implementation of the ISO/IEC JPEG-2000 Still Image Coding standard (ISO international Standard 15444). JPEG-2000 image coding involves subband codiing and compression of digital raster images to facilitate storage and transmission of such imagery. Images are decomposed into space/scale subbands using cascades of two-dimensional (tensor product) discrete wavelet transforms. The wavelet transforms can be either reversible (integer-to-integer) transforms or irreversible (integer-to-float). The subbands in each resolution level are quantized by uniformmore » scalar quantization in the irreversible case. The resulting integer subbands in each resolution level are partitioned into spatially localized code blocks to facilitate localized entropy decoding. Code blocks are encoded and packaged into an embedded bitstream using binary arithmetic bitplane coding (the MQ Coder algorithm applied to hierarchical bitplane coding (the MQ coder algorithm applied to hierachical bitplane context modeling). The resultant compressed bitstream is configured for use with the JPIP interactive client-server protocol (JPEG-2000 part 9). VM10 is written in ANSI C++ using the Biltz++ array class library. To enable development of multidimensional image coding algorithms, VM10 is templated on the dimension of the array containers. It was developed with the GNU g++ compiler on both Linux (Red Hat) and Windows/cygwin platforms, although it should compile and run under other ANSI C++ compilers as well. Software design is highly modular and object-oriented in order to facilitate rapid development and frequent revision and experimentation. No attempt has been made to optimize the run-time performance of the code. The software performs both the encoding and decoding operations involved in JPEG-2000 image coding, as implemented in apps/compress/main.cpp and apps/expand/main.cpp. VM10 implements all of the JPEG-2000 baseline (Part 1, ISO 15444-1) and portions of the

  13. Phantoms for diffuse optical imaging based on totally absorbing objects, part 2: experimental implementation.

    PubMed

    Martelli, Fabrizio; Di Ninni, Paola; Zaccanti, Giovanni; Contini, Davide; Spinelli, Lorenzo; Torricelli, Alessandro; Cubeddu, Rinaldo; Wabnitz, Heidrun; Mazurenka, Mikhail; Macdonald, Rainer; Sassaroli, Angelo; Pifferi, Antonio

    2014-01-01

    We present the experimental implementation and validation of a phantom for diffuse optical imaging based on totally absorbing objects for which, in the previous paper [J. Biomed. Opt.18(6), 066014, (2013)], we have provided the basic theory. Totally absorbing objects have been manufactured as black polyvinyl chloride (PVC) cylinders and the phantom is a water dilution of intralipid-20% as the diffusive medium and India ink as the absorber, filled into a black scattering cell made of PVC. By means of time-domain measurements and of Monte Carlo simulations, we have shown the reliability, the accuracy, and the robustness of such a phantom in mimicking typical absorbing perturbations of diffuse optical imaging. In particular, we show that such a phantom can be used to generate any absorption perturbation by changing the volume and position of the totally absorbing inclusion.

  14. Diffusion bonding and its application to manufacturing. [for joining of metal parts

    NASA Technical Reports Server (NTRS)

    Spurgeon, W. M.

    1972-01-01

    In its simplest form diffusion bonding is accomplished by placing clean metal surfaces together under a sufficient load and heating. The natural interatomic attractive force between atoms transforms the interface into a natural grain boundary. Therefore, in principle, the properties of the bond area are identical to those of the parent metal. Other advantages of diffusion bonding over conventional methods of bonding include freedom from residual stresses, excessive deformation, foreign metals, or changed crystal structures. Stainless steels, nickel-base superalloys, and aluminum alloys have all been successfully joined. Complex hardware, including integrated flueric devices, jet engine servovalves, and porous woven structures have been fabricated. The processing involved is discussed, along with such theoretical considerations as the role of metal surfaces, the formation of metal contact junctions, and the mechanisms of material transport in diffusion bonding.

  15. Stochastic fire-diffuse-fire model with realistic cluster dynamics

    NASA Astrophysics Data System (ADS)

    Calabrese, Ana; Fraiman, Daniel; Zysman, Daniel; Ponce Dawson, Silvina

    2010-09-01

    Living organisms use waves that propagate through excitable media to transport information. Ca2+ waves are a paradigmatic example of this type of processes. A large hierarchy of Ca2+ signals that range from localized release events to global waves has been observed in Xenopus laevis oocytes. In these cells, Ca2+ release occurs trough inositol 1,4,5-trisphosphate receptors (IP3Rs) which are organized in clusters of channels located on the membrane of the endoplasmic reticulum. In this article we construct a stochastic model for a cluster of IP3R ’s that replicates the experimental observations reported in [D. Fraiman , Biophys. J. 90, 3897 (2006)10.1529/biophysj.105.075911]. We then couple this phenomenological cluster model with a reaction-diffusion equation, so as to have a discrete stochastic model for calcium dynamics. The model we propose describes the transition regimes between isolated release and steadily propagating waves as the IP3 concentration is increased.

  16. A reaction-diffusion model of cytosolic hydrogen peroxide.

    PubMed

    Lim, Joseph B; Langford, Troy F; Huang, Beijing K; Deen, William M; Sikes, Hadley D

    2016-01-01

    As a signaling molecule in mammalian cells, hydrogen peroxide (H2O2) determines the thiol/disulfide oxidation state of several key proteins in the cytosol. Localization is a key concept in redox signaling; the concentrations of signaling molecules within the cell are expected to vary in time and in space in manner that is essential for function. However, as a simplification, all theoretical studies of intracellular hydrogen peroxide and many experimental studies to date have treated the cytosol as a well-mixed compartment. In this work, we incorporate our previously reported reduced kinetic model of the network of reactions that metabolize hydrogen peroxide in the cytosol into a model that explicitly treats diffusion along with reaction. We modeled a bolus addition experiment, solved the model analytically, and used the resulting equations to quantify the spatiotemporal variations in intracellular H2O2 that result from this kind of perturbation to the extracellular H2O2 concentration. We predict that micromolar bolus additions of H2O2 to suspensions of HeLa cells (0.8 × 10(9)cells/l) result in increases in the intracellular concentration that are localized near the membrane. These findings challenge the assumption that intracellular concentrations of H2O2 are increased uniformly throughout the cell during bolus addition experiments and provide a theoretical basis for differing phenotypic responses of cells to intracellular versus extracellular perturbations to H2O2 levels.

  17. A diffuse interface model of grain boundary faceting

    NASA Astrophysics Data System (ADS)

    Abdeljawad, F.; Medlin, D. L.; Zimmerman, J. A.; Hattar, K.; Foiles, S. M.

    2016-06-01

    Interfaces, free or internal, greatly influence the physical properties and stability of materials microstructures. Of particular interest are the processes that occur due to anisotropic interfacial properties. In the case of grain boundaries (GBs) in metals, several experimental observations revealed that an initially flat GB may facet into hill-and-valley structures with well defined planes and corners/edges connecting them. Herein, we present a diffuse interface model that is capable of accounting for strongly anisotropic GB properties and capturing the formation of hill-and-valley morphologies. The hallmark of our approach is the ability to independently examine the various factors affecting GB faceting and subsequent facet coarsening. More specifically, our formulation incorporates higher order expansions to account for the excess energy due to facet junctions and their non-local interactions. As a demonstration of the modeling capability, we consider the Σ5 <001 > tilt GB in body-centered-cubic iron, where faceting along the {210} and {310} planes was experimentally observed. Atomistic calculations were utilized to determine the inclination-dependent GB energy, which was then used as an input in our model. Linear stability analysis and simulation results highlight the role of junction energy and associated non-local interactions on the resulting facet length scales. Broadly speaking, our modeling approach provides a general framework to examine the microstructural stability of polycrystalline systems with highly anisotropic GBs.

  18. Anomalous diffusion in neutral evolution of model proteins.

    PubMed

    Nelson, Erik D; Grishin, Nick V

    2015-06-01

    Protein evolution is frequently explored using minimalist polymer models, however, little attention has been given to the problem of structural drift, or diffusion. Here, we study neutral evolution of small protein motifs using an off-lattice heteropolymer model in which individual monomers interact as low-resolution amino acids. In contrast to most earlier models, both the length and folded structure of the polymers are permitted to change. To describe structural change, we compute the mean-square distance (MSD) between monomers in homologous folds separated by n neutral mutations. We find that structural change is episodic, and, averaged over lineages (for example, those extending from a single sequence), exhibits a power-law dependence on n. We show that this exponent depends on the alignment method used, and we analyze the distribution of waiting times between neutral mutations. The latter are more disperse than for models required to maintain a specific fold, but exhibit a similar power-law tail. PMID:26172648

  19. Multiple-to-dominant path collapse of linked-flux model for diffusion-limited nucleation

    NASA Astrophysics Data System (ADS)

    Lau, Y. H.; Wu, D. T.

    2013-01-01

    While capable of estimating diffusion-limited nucleation rates, Kelton's linked-flux model has no simple solution. To increase the model's usability, we simplify the model by retaining only the dominant nucleation path to obtain a series solution. The solution agrees well with the Kelton's model's predictions of the nucleation rate, and thus provides a simple estimate of diffusion-limited nucleation rates.

  20. Modelling thermal radiation in buoyant turbulent diffusion flames

    NASA Astrophysics Data System (ADS)

    Consalvi, J. L.; Demarco, R.; Fuentes, A.

    2012-10-01

    This work focuses on the numerical modelling of radiative heat transfer in laboratory-scale buoyant turbulent diffusion flames. Spectral gas and soot radiation is modelled by using the Full-Spectrum Correlated-k (FSCK) method. Turbulence-Radiation Interactions (TRI) are taken into account by considering the Optically-Thin Fluctuation Approximation (OTFA), the resulting time-averaged Radiative Transfer Equation (RTE) being solved by the Finite Volume Method (FVM). Emission TRIs and the mean absorption coefficient are then closed by using a presumed probability density function (pdf) of the mixture fraction. The mean gas flow field is modelled by the Favre-averaged Navier-Stokes (FANS) equation set closed by a buoyancy-modified k-ɛ model with algebraic stress/flux models (ASM/AFM), the Steady Laminar Flamelet (SLF) model coupled with a presumed pdf approach to account for Turbulence-Chemistry Interactions, and an acetylene-based semi-empirical two-equation soot model. Two sets of experimental pool fire data are used for validation: propane pool fires 0.3 m in diameter with Heat Release Rates (HRR) of 15, 22 and 37 kW and methane pool fires 0.38 m in diameter with HRRs of 34 and 176 kW. Predicted flame structures, radiant fractions, and radiative heat fluxes on surrounding surfaces are found in satisfactory agreement with available experimental data across all the flames. In addition further computations indicate that, for the present flames, the gray approximation can be applied for soot with a minor influence on the results, resulting in a substantial gain in Computer Processing Unit (CPU) time when the FSCK is used to treat gas radiation.

  1. NASA/MSFC multilayer diffusion models and computer programs, version 5

    NASA Technical Reports Server (NTRS)

    Dumbauld, R. K.; Bjorklund, J. R.

    1975-01-01

    The transport and diffusion models and algorithms developed for use by NASA in predicting concentrations and dosages downwind from normal and abnormal launches of rocket vehicles are described along with the associated computer programs for use in performing the calculations. Topics discussed include: the mathematical specifications and procedures used in the Preprocessor Program to calculate rocket exhaust cloud rise, cloud dimensions, and other input parameters to the transport and diffusion models; the revised mathematical specifications for the Multilayer Diffusion Models; users' instructions for implementing the Preprocessor and Multilayer Diffusion Models Programs; and worked example problems illustrating the use of the models and computer programs.

  2. Protein folding dynamics: the diffusion-collision model and experimental data.

    PubMed Central

    Karplus, M.; Weaver, D. L.

    1994-01-01

    The diffusion-collision model of protein folding is assessed. A description is given of the qualitative aspects and quantitative results of the diffusion-collision model and their relation to available experimental data. We consider alternative mechanisms for folding and point out their relationship to the diffusion-collision model. We show that the diffusion-collision model is supported by a growing body of experimental and theoretical evidence, and we outline future directions for developing the model and its applications. PMID:8003983

  3. Dynamics of velocity gradient invariants in turbulence: Restricted Euler and linear diffusion models

    NASA Astrophysics Data System (ADS)

    Martín, Jesús; Dopazo, César; Valiño, Luis

    1998-08-01

    A complete system of dynamical equations for the invariants of the velocity gradient, the strain rate, and the rate-of-rotation tensors is deduced for an incompressible flow. The equations for the velocity gradient invariants R and Q were first deduced by Cantwell [Phys. Fluids A 4, 782 (1992)] in terms of Hij, the tensor containing the anisotropic part of the pressure Hessian and the viscous diffusion term in the velocity gradient equation. These equations are extended here for the strain rate tensor invariants, RS and QS, and for the rate-of-rotation tensor invariant, QW, using HijS and HijW, the symmetric and the skew-symmetric parts of Hij, respectively. In order to obtain a complete system, an equation for the square of the vortex stretching vector, Vi≡Sijωj, is required. The resulting dynamical system of invariants is closed using a simple model for the velocity gradient evolution: an isotropic approximation for the pressure term and a linear model for the viscous diffusion term. The local topology and the resulting statistics implied by this model reproduce a number of trends similar to known results from numerical experiments for the small scales of turbulence.

  4. Photodynamic therapy: computer modeling of diffusion and reaction phenomena

    NASA Astrophysics Data System (ADS)

    Hampton, James A.; Mahama, Patricia A.; Fournier, Ronald L.; Henning, Jeffery P.

    1996-04-01

    We have developed a transient, one-dimensional mathematical model for the reaction and diffusion phenomena that occurs during photodynamic therapy (PDT). This model is referred to as the PDTmodem program. The model is solved by the Crank-Nicholson finite difference technique and can be used to predict the fates of important molecular species within the intercapillary tissue undergoing PDT. The following factors govern molecular oxygen consumption and singlet oxygen generation within a tumor: (1) photosensitizer concentration; (2) fluence rate; and (3) intercapillary spacing. In an effort to maximize direct tumor cell killing, the model allows educated decisions to be made to insure the uniform generation and exposure of singlet oxygen to tumor cells across the intercapillary space. Based on predictions made by the model, we have determined that the singlet oxygen concentration profile within the intercapillary space is controlled by the product of the drug concentration, and light fluence rate. The model predicts that at high levels of this product, within seconds singlet oxygen generation is limited to a small core of cells immediately surrounding the capillary. The remainder of the tumor tissue in the intercapillary space is anoxic and protected from the generation and toxic effects of singlet oxygen. However, at lower values of this product, the PDT-induced anoxic regions are not observed. An important finding is that an optimal value of this product can be defined that maintains the singlet oxygen concentration throughout the intercapillary space at a near constant level. Direct tumor cell killing is therefore postulated to depend on the singlet oxygen exposure, defined as the product of the uniform singlet oxygen concentration and the time of exposure, and not on the total light dose.

  5. Collective Diffusion Model for Ion Conduction through Microscopic Channels

    PubMed Central

    Liu, Yingting; Zhu, Fangqiang

    2013-01-01

    Ion conduction through microscopic channels is of central importance in both biology and nanotechnology. To better understand the current-voltage (I-V) dependence of ion channels, here we describe and prove a collective diffusion model that quantitatively relates the spontaneous ion permeation at equilibrium to the stationary ionic fluxes driven by small voltages. The model makes it possible to determine the channel conductance in the linear I-V range from equilibrium simulations without the application of a voltage. To validate the theory, we perform molecular-dynamics simulations on two channels—a conical-shaped nanopore and the transmembrane pore of an α-hemolysin—under both equilibrium and nonequilibrium conditions. The simulations reveal substantial couplings between the motions of cations and anions, which are effectively captured by the collective coordinate in the model. Although the two channels exhibit very different linear ranges in the I-V curves, in both cases the channel conductance at small voltages is in reasonable agreement with the prediction from the equilibrium simulation. The simulations also suggest that channel charges, rather than geometric asymmetry, play a more prominent role in current rectification. PMID:23442858

  6. Reaction–diffusion model of hair-bundle morphogenesis

    PubMed Central

    Jacobo, Adrian; Hudspeth, A. J.

    2014-01-01

    The hair bundle, an apical specialization of the hair cell composed of several rows of regularly organized stereocilia and a kinocilium, is essential for mechanotransduction in the ear. Its precise organization allows the hair bundle to convert mechanical stimuli to electrical signals; mutations that alter the bundle’s morphology often cause deafness. However, little is known about the proteins involved in the process of morphogenesis and how the structure of the bundle arises through interactions between these molecules. We present a mathematical model based on simple reaction–diffusion mechanisms that can reproduce the shape and organization of the hair bundle. This model suggests that the boundary of the cell and the kinocilium act as signaling centers that establish the bundle’s shape. The interaction of two proteins forms a hexagonal Turing pattern—a periodic modulation of the concentrations of the morphogens, sustained by local activation and long-range inhibition of the reactants—that sets a blueprint for the location of the stereocilia. Finally we use this model to predict how different alterations to the system might impact the shape and organization of the hair bundle. PMID:25313064

  7. A simple differential diffusion model to account for the discrepancy between 223Ra- and 224Ra-based eddy diffusivities

    NASA Astrophysics Data System (ADS)

    Stachelhaus, Scott L.; Moran, S. Bradley

    2012-03-01

    A series of 223Ra (t1/2 = 11.4 d) and 224Ra (t1/2 = 3.66 d) measurements made in the Mid-Atlantic Bight yield eddy diffusivity (K) estimates of 1.2 ± 0.3 × 102 m2 s-1 and 1.4 ± 0.2 × 102 m2 s-1, respectively. These results fall in line with previous studies from multiple locations throughout the ocean, in which 224Ra-based eddy diffusivities invariably exceed those determined using 223Ra. Such a pattern conflicts with the Fickian model for eddy diffusivity, in which K is constant. Moreover, this trend runs counter to the length scale-dependent view of eddy diffusion, which suggests that K values estimated using 223Ra should exceed those of 224Ra, because the length scale of the former is greater than that of the latter. A finite mixing-length model based on the concept of differential diffusion is used to provide an explanation for this discrepancy.

  8. Distributed-order diffusion equations and multifractality: Models and solutions

    NASA Astrophysics Data System (ADS)

    Sandev, Trifce; Chechkin, Aleksei V.; Korabel, Nickolay; Kantz, Holger; Sokolov, Igor M.; Metzler, Ralf

    2015-10-01

    We study distributed-order time fractional diffusion equations characterized by multifractal memory kernels, in contrast to the simple power-law kernel of common time fractional diffusion equations. Based on the physical approach to anomalous diffusion provided by the seminal Scher-Montroll-Weiss continuous time random walk, we analyze both natural and modified-form distributed-order time fractional diffusion equations and compare the two approaches. The mean squared displacement is obtained and its limiting behavior analyzed. We derive the connection between the Wiener process, described by the conventional Langevin equation and the dynamics encoded by the distributed-order time fractional diffusion equation in terms of a generalized subordination of time. A detailed analysis of the multifractal properties of distributed-order diffusion equations is provided.

  9. Distributed-order diffusion equations and multifractality: Models and solutions.

    PubMed

    Sandev, Trifce; Chechkin, Aleksei V; Korabel, Nickolay; Kantz, Holger; Sokolov, Igor M; Metzler, Ralf

    2015-10-01

    We study distributed-order time fractional diffusion equations characterized by multifractal memory kernels, in contrast to the simple power-law kernel of common time fractional diffusion equations. Based on the physical approach to anomalous diffusion provided by the seminal Scher-Montroll-Weiss continuous time random walk, we analyze both natural and modified-form distributed-order time fractional diffusion equations and compare the two approaches. The mean squared displacement is obtained and its limiting behavior analyzed. We derive the connection between the Wiener process, described by the conventional Langevin equation and the dynamics encoded by the distributed-order time fractional diffusion equation in terms of a generalized subordination of time. A detailed analysis of the multifractal properties of distributed-order diffusion equations is provided. PMID:26565178

  10. Diffuse phosphorus models in the United States and europe: their usages, scales, and uncertainties.

    PubMed

    Radcliffe, D E; Freer, Jim; Schoumans, Oscar

    2009-01-01

    Today there are many well-established computer models that are being used at different spatial and temporal scales to describe water, sediment, and P transport from diffuse sources. In this review, we describe how diffuse P models are commonly being used in the United States and Europe, the challenge presented by different temporal and spatial scales, and the uncertainty in model predictions. In the United States, for water bodies that do not meet water quality standards, a total maximum daily load (TMDL) of the pollutant of concern must be set that will restore water quality and a plan implemented to reduce the pollutant load to meet the TMDL. Models are used to estimate the current maximum daily and annual average load, to estimate the contribution from different nonpoint sources, and to develop scenarios for achieving the TMDL target. In Europe, the EC-Water Framework Directive is the driving force to improve water quality and models are playing a similar role to that in the United States, but the models being used are not the same. European models are more likely to take into account leaching of P and the identification of critical source areas. Scaling up to the watershed scale has led to overparameterized models that cannot be used to test hypotheses regarding nonpoint sources of P or transport processes using the monitoring data that is typically available. There is a need for more parsimonious models and monitoring data that takes advantage of the technological improvements that allow nearly continuous sampling for P and sediment. Tools for measuring model uncertainty must become an integral part of models and be readily available for model users.

  11. The importance of being dispersed: A ranking of diffusion MRI models for fibre dispersion using in vivo human brain data.

    PubMed

    Ferizi, Uran; Schneider, Torben; Tariq, Maira; Wheeler-Kingshott, Claudia A M; Zhang, Hui; Alexander, Daniel C

    2013-01-01

    In this work we compare parametric diffusion MRI models which explicitly seek to explain fibre dispersion in nervous tissue. These models aim at providing more specific biomarkers of disease by disentangling these structural contributions to the signal. Some models are drawn from recent work in the field; others have been constructed from combinations of existing compartments that aim to capture both intracellular and extracellular diffusion. To test these models we use a rich dataset acquired in vivo on the corpus callosum of a human brain, and then compare the models via the Bayesian Information Criteria. We test this ranking via bootstrapping on the data sets, and cross-validate across unseen parts of the protocol. We find that models that capture fibre dispersion are preferred. The results show the importance of modelling dispersion, even in apparently coherent fibres.

  12. Performance of a TKE diffusion scheme in ECMWF IFS Single Column Model

    NASA Astrophysics Data System (ADS)

    Svensson, Jacob; Bazile, Eric; Sandu, Irina; Svensson, Gunilla

    2015-04-01

    Numerical Weather Prediction models (NWP) as well as climate models are used for decision making on all levels in society and their performance and accuracy are of great importance for both economical and safety reasons. Today's extensive use of weather apps and websites that directly uses model output even more highlights the importance of realistic output parameters. The turbulent atmospheric boundary layer (ABL) includes many physical processes which occur on a subgrid scale and need to be parameterized. As the absolute major part of the biosphere is located in the ABL, it is of great importance that these subgrid processes are parametrized so that they give realistic values of e.g. temperature and wind on the levels close to the surface. GEWEX (Global Energy and Water Exchange Project) Atmospheric Boundary Layer Study (GABLS), has the overall objective to improve the understanding and the representation of the atmospheric boundary layers in climate models. The study has pointed out that there is a need for a better understanding and representation of stable atmospheric boundary layers (SBL). Therefore four test cases have been designed to highlight the performance of and differences between a number of climate models and NWP:s in SBL. In the experiments, most global NWP and climate models have shown to be too diffusive in stable conditions and thus give too weak temperature gradients, too strong momentum mixing and too weak ageostrophic Ekman flow. The reason for this is that the models need enhanced diffusion to create enough friction for the large scale weather systems, which otherwise would be too fast and too active. In the GABLS test cases, turbulence schemes that use Turbulent Kinetic Energy (TKE) have shown to be more skilful than schemes that only use stability and gradients. TKE as a prognostic variable allows for advection both vertically and horizontally and gives a "memory" from previous time steps. Therefore, e.g. the ECMWF-GABLS workshop in 2011

  13. Development of Spray on Bag for manufacturing of large composites parts: Diffusivity analysis

    NASA Astrophysics Data System (ADS)

    Dempah, Maxime Joseph

    Bagging materials are utilized in many composites manufacturing processes. The selection is mainly driven by cost, temperature requirements, chemical compatibility and tear properties of the bag. The air barrier properties of the bag are assumed to be adequate or in many cases are not considered at all. However, the gas barrier property of a bag is the most critical parameter, as it can negatively affect the quality of the final laminate. The barrier property is a function of the bag material, uniformity, thickness and temperature. Improved barrier properties are needed for large parts, high pressure consolidated components and structures where air stays entrapped on the part surface. The air resistance property of the film is defined as permeability and is investigated in this thesis. A model was developed to evaluate the gas transport through the film and an experimental cell was implemented to characterize various commercial films. Understanding and characterizing the transport phenomena through the film allows optimization of the bagging material for various manufacturing processes. Spray-on-Bag is a scalable alternative bagging method compared to standard films. The approach allows in-situ fabrication of the bag on large and complex geometry structures where optimization of the bag properties can be varied on a local level. An experimental setup was developed and implemented using a six axis robot and an automated spraying system. Experiments were performed on a flat surface and specimens were characterized and compared to conventional films. Air barrier properties were within range of standard film approaches showing the potential to fabricate net shape bagging structures in an automated process.

  14. Animal Models of Ischemic Stroke. Part One: Modeling Risk Factors

    PubMed Central

    Bacigaluppi, Marco; Comi, Giancarlo; Hermann, Dirk M.

    2010-01-01

    Ischemic stroke is one of the leading causes of long-term disability and death in developed and developing countries. As emerging disease, stroke related mortality and morbidity is going to step up in the next decades. This is both due to the poor identification of risk factors and persistence of unhealthy habits, as well as to the aging of the population. To counteract the estimated increase in stroke incidence, it is of primary importance to identify risk factors, study their effects, to promote primary and secondary prevention, and to extend the therapeutic repertoire that is currently limited to the very first hours after stroke. While epidemiologic studies in the human population are essential to identify emerging risk factors, adequate animal models represent a fundamental tool to dissect stroke risk factors to their molecular mechanism and to find efficacious therapeutic strategies for this complex multi- factorial disorder. The present review is organized into two parts: the first part deals with the animal models that have been developed to study stroke and its related risk factors and the second part analyzes the specific stroke models. These models represent an indispensable tool to investigate the mechanisms of cerebral injury and to develop novel therapies. PMID:20802809

  15. Diffusion Models of the Flanker Task: Discrete versus Gradual Attentional Selection

    ERIC Educational Resources Information Center

    White, Corey N.; Ratcliff, Roger; Starns, Jeffrey J.

    2011-01-01

    The present study tested diffusion models of processing in the flanker task, in which participants identify a target that is flanked by items that indicate the same (congruent) or opposite response (incongruent). Single- and dual-process flanker models were implemented in a diffusion-model framework and tested against data from experiments that…

  16. Applicability of an Adoption-Diffusion Model to Resource Conservation: A Supporting View.

    ERIC Educational Resources Information Center

    Nowak, Peter J.

    At issue is the extent to which one can employ an adoption and diffusion of innovations model(s) to explain and predict the use of soil and water conservation practices. Much, however, can be gained from using models in this area. Four dimensions that should be present in any research design if it is to account for adoption and diffusion of…

  17. Hybrid approaches for multiple-species stochastic reaction-diffusion models

    NASA Astrophysics Data System (ADS)

    Spill, Fabian; Guerrero, Pilar; Alarcon, Tomas; Maini, Philip K.; Byrne, Helen

    2015-10-01

    Reaction-diffusion models are used to describe systems in fields as diverse as physics, chemistry, ecology and biology. The fundamental quantities in such models are individual entities such as atoms and molecules, bacteria, cells or animals, which move and/or react in a stochastic manner. If the number of entities is large, accounting for each individual is inefficient, and often partial differential equation (PDE) models are used in which the stochastic behaviour of individuals is replaced by a description of the averaged, or mean behaviour of the system. In some situations the number of individuals is large in certain regions and small in others. In such cases, a stochastic model may be inefficient in one region, and a PDE model inaccurate in another. To overcome this problem, we develop a scheme which couples a stochastic reaction-diffusion system in one part of the domain with its mean field analogue, i.e. a discretised PDE model, in the other part of the domain. The interface in between the two domains occupies exactly one lattice site and is chosen such that the mean field description is still accurate there. In this way errors due to the flux between the domains are small. Our scheme can account for multiple dynamic interfaces separating multiple stochastic and deterministic domains, and the coupling between the domains conserves the total number of particles. The method preserves stochastic features such as extinction not observable in the mean field description, and is significantly faster to simulate on a computer than the pure stochastic model.

  18. Hybrid approaches for multiple-species stochastic reaction–diffusion models

    PubMed Central

    Spill, Fabian; Guerrero, Pilar; Alarcon, Tomas; Maini, Philip K.; Byrne, Helen

    2015-01-01

    Reaction–diffusion models are used to describe systems in fields as diverse as physics, chemistry, ecology and biology. The fundamental quantities in such models are individual entities such as atoms and molecules, bacteria, cells or animals, which move and/or react in a stochastic manner. If the number of entities is large, accounting for each individual is inefficient, and often partial differential equation (PDE) models are used in which the stochastic behaviour of individuals is replaced by a description of the averaged, or mean behaviour of the system. In some situations the number of individuals is large in certain regions and small in others. In such cases, a stochastic model may be inefficient in one region, and a PDE model inaccurate in another. To overcome this problem, we develop a scheme which couples a stochastic reaction–diffusion system in one part of the domain with its mean field analogue, i.e. a discretised PDE model, in the other part of the domain. The interface in between the two domains occupies exactly one lattice site and is chosen such that the mean field description is still accurate there. In this way errors due to the flux between the domains are small. Our scheme can account for multiple dynamic interfaces separating multiple stochastic and deterministic domains, and the coupling between the domains conserves the total number of particles. The method preserves stochastic features such as extinction not observable in the mean field description, and is significantly faster to simulate on a computer than the pure stochastic model. PMID:26478601

  19. A diffuse interface model of grain boundary faceting

    NASA Astrophysics Data System (ADS)

    Abdeljawad, Fadi; Medlin, Douglas; Zimmerman, Jonathan; Hattar, Khalid; Foiles, Stephen

    Incorporating anisotropy into thermodynamic treatments of interfaces dates back to over a century ago. For a given orientation of two abutting grains in a pure metal, depressions in the grain boundary (GB) energy may exist as a function of GB inclination, defined by the plane normal. Therefore, an initially flat GB may facet resulting in a hill-and-valley structure. Herein, we present a diffuse interface model of GB faceting that is capable of capturing anisotropic GB energies and mobilities, and accounting for the excess energy due to facet junctions and their non-local interactions. The hallmark of our approach is the ability to independently examine the role of each of the interface properties on the faceting behavior. As a demonstration, we consider the Σ 5 < 001 > tilt GB in iron, where faceting along the { 310 } and { 210 } planes was experimentally observed. Linear stability analysis and numerical examples highlight the role of junction energy and associated non-local interactions on the resulting facet length scales. On the whole, our modeling approach provides a general framework to examine the spatio-temporal evolution of highly anisotropic GBs in polycrystalline metals. Sandia National Laboratories is a multi-program laboratory managed and operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Corporation, for the U.S. DOE's National Nuclear Security Administration under Contract DE-AC04-94AL85000.

  20. Antideuteron fluxes from dark matter annihilation in diffusion models

    SciTech Connect

    Donato, F.; Fornengo, N.; Maurin, D.

    2008-08-15

    Antideuterons are among the most promising galactic cosmic-ray-related targets for dark matter indirect detection. Currently only upper limits exist on the flux, but the development of new experiments, such as GAPS and AMS-02, provides exciting perspectives for a positive measurement in the near future. In this paper, we present a novel and updated calculation of both the secondary and primary d fluxes. We employ a two-zone diffusion model which successfully reproduces cosmic-ray nuclear data and the observed antiproton flux. We review the nuclear and astrophysical uncertainties and provide an up to date secondary (i.e. background) antideuteron flux. The primary (i.e. signal) contribution is calculated for generic weakly interactive massive particles (WIMPs) annihilating in the galactic halo: we explicitly consider and quantify the various sources of uncertainty in the theoretical evaluations. Propagation uncertainties, as is the case of antiprotons, are sizeable. Nevertheless, antideuterons offer an exciting target for indirect dark matter detection for low and intermediate mass WIMP dark matter. We then show the reaching capabilities of the future experiments for neutralino dark matter in a variety of supersymmetric models.

  1. 12 CFR Appendix A to Part 233 - Model Notice

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... Federal Regulations (12 CFR part 233) and part 132 of title 31 of the U.S. Code of Federal Regulations (31 CFR part 132). ... FUNDING OF UNLAWFUL INTERNET GAMBLING (REGULATION GG) Part 233, App. A Appendix A to Part 233—Model...

  2. 31 CFR Appendix A to Part 132 - Model Notice

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... one another can be found at part 233 of title 12 of the U.S. Code of Federal Regulations (12 CFR part 233) and part 132 of title 31 of the U.S. Code of Federal Regulations (31 CFR part 132). ... INTERNET GAMBLING Pt. 132, App. A Appendix A to Part 132—Model Notice Re: U.S. Unlawful Internet...

  3. 12 CFR Appendix A to Part 233 - Model Notice

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... Federal Regulations (12 CFR part 233) and part 132 of title 31 of the U.S. Code of Federal Regulations (31 CFR part 132). ... FUNDING OF UNLAWFUL INTERNET GAMBLING (REGULATION GG) Part 233, App. A Appendix A to Part 233—Model...

  4. Perceptual decision making: drift-diffusion model is equivalent to a Bayesian model

    PubMed Central

    Bitzer, Sebastian; Park, Hame; Blankenburg, Felix; Kiebel, Stefan J.

    2014-01-01

    Behavioral data obtained with perceptual decision making experiments are typically analyzed with the drift-diffusion model. This parsimonious model accumulates noisy pieces of evidence toward a decision bound to explain the accuracy and reaction times of subjects. Recently, Bayesian models have been proposed to explain how the brain extracts information from noisy input as typically presented in perceptual decision making tasks. It has long been known that the drift-diffusion model is tightly linked with such functional Bayesian models but the precise relationship of the two mechanisms was never made explicit. Using a Bayesian model, we derived the equations which relate parameter values between these models. In practice we show that this equivalence is useful when fitting multi-subject data. We further show that the Bayesian model suggests different decision variables which all predict equal responses and discuss how these may be discriminated based on neural correlates of accumulated evidence. In addition, we discuss extensions to the Bayesian model which would be difficult to derive for the drift-diffusion model. We suggest that these and other extensions may be highly useful for deriving new experiments which test novel hypotheses. PMID:24616689

  5. Subgrid models for mass and thermal diffusion in turbulent mixing

    SciTech Connect

    Sharp, David H; Lim, Hyunkyung; Li, Xiao - Lin; Gilmm, James G

    2008-01-01

    We are concerned with the chaotic flow fields of turbulent mixing. Chaotic flow is found in an extreme form in multiply shocked Richtmyer-Meshkov unstable flows. The goal of a converged simulation for this problem is twofold: to obtain converged solutions for macro solution features, such as the trajectories of the principal shock waves, mixing zone edges, and mean densities and velocities within each phase, and also for such micro solution features as the joint probability distributions of the temperature and species concentration. We introduce parameterized subgrid models of mass and thermal diffusion, to define large eddy simulations (LES) that replicate the micro features observed in the direct numerical simulation (DNS). The Schmidt numbers and Prandtl numbers are chosen to represent typical liquid, gas and plasma parameter values. Our main result is to explore the variation of the Schmidt, Prandtl and Reynolds numbers by three orders of magnitude, and the mesh by a factor of 8 per linear dimension (up to 3200 cells per dimension), to allow exploration of both DNS and LES regimes and verification of the simulations for both macro and micro observables. We find mesh convergence for key properties describing the molecular level of mixing, including chemical reaction rates between the distinct fluid species. We find results nearly independent of Reynolds number for Re 300, 6000, 600K . Methodologically, the results are also new. In common with the shock capturing community, we allow and maintain sharp solution gradients, and we enhance these gradients through use of front tracking. In common with the turbulence modeling community, we include subgrid scale models with no adjustable parameters for LES. To the authors' knowledge, these two methodologies have not been previously combined. In contrast to both of these methodologies, our use of Front Tracking, with DNS or LES resolution of the momentum equation at or near the Kolmogorov scale, but without resolving the

  6. Model Complexity in Diffusion Modeling: Benefits of Making the Model More Parsimonious

    PubMed Central

    Lerche, Veronika; Voss, Andreas

    2016-01-01

    The diffusion model (Ratcliff, 1978) takes into account the reaction time distributions of both correct and erroneous responses from binary decision tasks. This high degree of information usage allows the estimation of different parameters mapping cognitive components such as speed of information accumulation or decision bias. For three of the four main parameters (drift rate, starting point, and non-decision time) trial-to-trial variability is allowed. We investigated the influence of these variability parameters both drawing on simulation studies and on data from an empirical test-retest study using different optimization criteria and different trial numbers. Our results suggest that less complex models (fixing intertrial variabilities of the drift rate and the starting point at zero) can improve the estimation of the psychologically most interesting parameters (drift rate, threshold separation, starting point, and non-decision time). PMID:27679585

  7. Model Complexity in Diffusion Modeling: Benefits of Making the Model More Parsimonious.

    PubMed

    Lerche, Veronika; Voss, Andreas

    2016-01-01

    The diffusion model (Ratcliff, 1978) takes into account the reaction time distributions of both correct and erroneous responses from binary decision tasks. This high degree of information usage allows the estimation of different parameters mapping cognitive components such as speed of information accumulation or decision bias. For three of the four main parameters (drift rate, starting point, and non-decision time) trial-to-trial variability is allowed. We investigated the influence of these variability parameters both drawing on simulation studies and on data from an empirical test-retest study using different optimization criteria and different trial numbers. Our results suggest that less complex models (fixing intertrial variabilities of the drift rate and the starting point at zero) can improve the estimation of the psychologically most interesting parameters (drift rate, threshold separation, starting point, and non-decision time). PMID:27679585

  8. Model Complexity in Diffusion Modeling: Benefits of Making the Model More Parsimonious

    PubMed Central

    Lerche, Veronika; Voss, Andreas

    2016-01-01

    The diffusion model (Ratcliff, 1978) takes into account the reaction time distributions of both correct and erroneous responses from binary decision tasks. This high degree of information usage allows the estimation of different parameters mapping cognitive components such as speed of information accumulation or decision bias. For three of the four main parameters (drift rate, starting point, and non-decision time) trial-to-trial variability is allowed. We investigated the influence of these variability parameters both drawing on simulation studies and on data from an empirical test-retest study using different optimization criteria and different trial numbers. Our results suggest that less complex models (fixing intertrial variabilities of the drift rate and the starting point at zero) can improve the estimation of the psychologically most interesting parameters (drift rate, threshold separation, starting point, and non-decision time).

  9. Multi-solid and multi-fluid diffuse interface model: Applications to dynamic fracture and fragmentation

    SciTech Connect

    Ndanou, S. Favrie, N. Gavrilyuk, S.

    2015-08-15

    We extend the model of diffuse solid–fluid interfaces developed earlier by authors of this paper to the case of arbitrary number of interacting hyperelastic solids. Plastic transformations of solids are taken into account through a Maxwell type model. The specific energy of each solid is given in separable form: it is the sum of a hydrodynamic part of the energy depending only on the density and the entropy, and an elastic part of the energy which is unaffected by the volume change. It allows us to naturally pass to the fluid description in the limit of vanishing shear modulus. In spite of a large number of governing equations, the model has a quite simple mathematical structure: it is a duplication of a single visco-elastic model. The model is well posed both mathematically and thermodynamically: it is hyperbolic and compatible with the second law of thermodynamics. The resulting model can be applied in the situations involving an arbitrary number of fluids and solids. In particular, we show the ability of the model to describe spallation and penetration phenomena occurring during high velocity impacts.

  10. The impact of different vertical diffusion schemes in a three-dimensional oil spill model in the Bohai Sea

    NASA Astrophysics Data System (ADS)

    Li, Yan; Zhu, Jiang; Wang, Hui

    2013-11-01

    Vertical transport is critical to the movement of oil spills in seawater. Breaking waves play an important role by developing a well-defined mixing layer in the upper part of the water column. A three-dimensional (3-D) Lagrangian random walk oil spill model was used here to study the influence of sea surface waves on the vertical turbulence movement of oil particles. Three vertical diffusion schemes were utilized in the model to compare their impact on oil dispersion and transportation. The first scheme calculated the vertical eddy viscosity semi-empirically. In the second scheme, the vertical diffusion coefficient was obtained directly from an Eulerian hydrodynamic model (Princeton Ocean Model, POM2k) while considering wave-caused turbulence. The third scheme was formulated by solving the Langevin equation. The trajectories, percentages of oil particles intruding into water, and the vertical distribution structures of oil particles were analyzed for a series of numerical experiments with different wind magnitudes. The results showed that the different vertical diffusion schemes could generate different horizontal trajectories and spatial distributions of oil spills on the sea surface. The vertical diffusion schemes caused different water-intruding and resurfacing oil particle behaviors, leading to different horizontal transport of oil particles at the surface and subsurface of the ocean. The vertical diffusion schemes were also applied to a realistic oil spill simulation, and these results were compared to satellite observations. All three schemes yielded acceptable results, and those of the third scheme most closely simulated the observed data.

  11. Monte Carlo Modeling of Diffuse Scattering from Single Crystals: The Program ZMC

    SciTech Connect

    Goossens, D.J.; Heerdegen, A.P.; Chan, E.J.; Welberry, T.R.

    2012-04-30

    Diffuse scattering probes the local ordering in a crystal, whereas Bragg peaks are descriptive of the average long-range ordering. The population of local configurations can be explored by modeling the three-dimensional distribution of diffuse scattering. Local configurations are not constrained by the average crystallographic symmetry, so one way of modeling diffuse scattering is by modeling a disordered (short-range-ordered) structure and then calculating its diffuse scattering. The structure must contain enough unit cells to give a statistically valid model of the populations of local configurations, and so requirements for a program to model this ordering are very different from programs that model average crystal structures (used to fit the Bragg diffraction). ZMC is a program that has been developed to model diffuse scattering, particularly from molecular crystals. The strategies used to tackle the problem and the way in which they are implemented will be discussed.

  12. Investigation of the best model to characterize diffuse correlation spectroscopy measurements acquired directly on the brain

    NASA Astrophysics Data System (ADS)

    Verdecchia, K.; Diop, M.; St. Lawrence, K.

    2015-03-01

    Diffuse correlation spectroscopy (DCS) is a non-invasive optical technique capable of monitoring tissue perfusion changes, particularly in the brain. The normalized temporal intensity autocorrelation function generated by DCS is typically characterized by assuming that the movement of erythrocytes can be modeled as a Brownian diffusion-like process instead of the expected random flow model. Carp et al. [Biomedical Optics Express, 2011] proposed a hybrid model, referred to as the hydrodynamic diffusion model, to capture both the random ballistic and diffusive nature of erythrocyte motion. The purpose of this study was to compare how well the Brownian diffusion and the hydrodynamic diffusion models characterized DCS data acquired directly on the brain, avoiding the confounding effects of scalp and skull. Data were acquired from seven pigs during normocapnia (39.9 +/- 0.7 mmHg) and hypocapnia (22.1 +/- 1.6 mmHg) with the DCS fibers placed 7 mm apart, directly on the cerebral cortex. The hydrodynamic diffusion model was found to provide a consistently better fit to the autocorrelation functions compared to the Brownian diffusion model and was less sensitive to the chosen start and end time points used in the fitting. However, the decrease in cerebral blood flow from normocapnia to hypocapnia determined was similar for the two models (-42.6 +/- 8.6 % for the Brownian model and -42.2 +/- 10.2 % for the hydrodynamic model), suggesting that the latter is reasonable for monitoring flow changes.

  13. Developing A Laser Shockwave Model For Characterizing Diffusion Bonded Interfaces

    SciTech Connect

    James A. Smith; Jeffrey M. Lacy; Barry H. Rabin

    2014-07-01

    12. Other advances in QNDE and related topics: Preferred Session Laser-ultrasonics Developing A Laser Shockwave Model For Characterizing Diffusion Bonded Interfaces 41st Annual Review of Progress in Quantitative Nondestructive Evaluation Conference QNDE Conference July 20-25, 2014 Boise Centre 850 West Front Street Boise, Idaho 83702 James A. Smith, Jeffrey M. Lacy, Barry H. Rabin, Idaho National Laboratory, Idaho Falls, ID ABSTRACT: The US National Nuclear Security Agency has a Global Threat Reduction Initiative (GTRI) which is assigned with reducing the worldwide use of high-enriched uranium (HEU). A salient component of that initiative is the conversion of research reactors from HEU to low enriched uranium (LEU) fuels. An innovative fuel is being developed to replace HEU. The new LEU fuel is based on a monolithic fuel made from a U-Mo alloy foil encapsulated in Al-6061 cladding. In order to complete the fuel qualification process, the laser shock technique is being developed to characterize the clad-clad and fuel-clad interface strengths in fresh and irradiated fuel plates. The Laser Shockwave Technique (LST) is being investigated to characterize interface strength in fuel plates. LST is a non-contact method that uses lasers for the generation and detection of large amplitude acoustic waves to characterize interfaces in nuclear fuel plates. However the deposition of laser energy into the containment layer on specimen’s surface is intractably complex. The shock wave energy is inferred from the velocity on the backside and the depth of the impression left on the surface from the high pressure plasma pulse created by the shock laser. To help quantify the stresses and strengths at the interface, a finite element model is being developed and validated by comparing numerical and experimental results for back face velocities and front face depressions with experimental results. This paper will report on initial efforts to develop a finite element model for laser

  14. Reaction time in ankle movements: a diffusion model analysis

    PubMed Central

    Michmizos, Konstantinos P.; Krebs, Hermano Igo

    2015-01-01

    Reaction time (RT) is one of the most commonly used measures of neurological function and dysfunction. Despite the extensive studies on it, no study has ever examined the RT in the ankle. Twenty-two subjects were recruited to perform simple, 2- and 4-choice RT tasks by visually guiding a cursor inside a rectangular target with their ankle. RT did not change with spatial accuracy constraints imposed by different target widths in the direction of the movement. RT increased as a linear function of potential target stimuli, as would be predicted by Hick–Hyman law. Although the slopes of the regressions were similar, the intercept in dorsal–plantar (DP) direction was significantly smaller than the intercept in inversion–eversion (IE) direction. To explain this difference, we used a hierarchical Bayesian estimation of the Ratcliff's (Psychol Rev 85:59, 1978) diffusion model parameters and divided processing time into cognitive components. The model gave a good account of RTs, their distribution and accuracy values, and hence provided a testimony that the non-decision processing time (overlap of posterior distributions between DP and IE < 0.045), the boundary separation (overlap of the posterior distributions < 0.1) and the evidence accumulation rate (overlap of the posterior distributions < 0.01) components of the RT accounted for the intercept difference between DP and IE. The model also proposed that there was no systematic change in non-decision processing time or drift rate when spatial accuracy constraints were altered. The results were in agreement with the memory drum hypothesis and could be further justified neurophysiologically by the larger innervation of the muscles controlling DP movements. This study might contribute to assessing deficits in sensorimotor control of the ankle and enlighten a possible target for correction in the framework of our on-going effort to develop robotic therapeutic interventions to the ankle of children with cerebral palsy

  15. Superdiffusion in a Model for Diffusion in a Molecularly Crowded Environment

    PubMed Central

    Stauffer, Dietrich; Schulze, Christian

    2008-01-01

    We present a model for diffusion in a molecularly crowded environment. The model consists of random barriers in a percolation network. Random walks in the presence of slowly moving barriers show normal diffusion for long times but anomalous diffusion at intermediate times. The effective exponents for square distance vs time usually are below one at these intermediate times, but they can also be larger than one for high barrier concentrations. Thus, we observe sub- and superdiffusion in a crowded environment. PMID:19669520

  16. Optimization of a Free Water Elimination Two-Compartment Model for Diffusion Tensor Imaging

    PubMed Central

    Hoy, Andrew R.; Koay, Cheng Guan; Kecskemeti, Steven R.; Alexander, Andrew L.

    2014-01-01

    Diffusion tensor imaging is used to measure the diffusion of water in tissue. The diffusion properties carry information about the relative organization and structure of the underlying tissue. In the case of a single voxel containing both tissue and a fast diffusing component such as free water, a single diffusion tensor is no longer appropriate. A two-tensor free water elimination model has previously been proposed to correct for the case of volume mixing. Here, this model was implemented in a straightforward but novel manner without the use of spatial constraints. The optimal acquisition parameters were investigated through Monte Carlo simulations and human brain imaging studies. At a signal-to-noise ratio of 40 with 64 diffusion-weighted encoding images, the most accurate estimates of fast diffusion signal were obtained with two diffusion-weighted shells (b-value in s/mm^2 x number of directions) of 500×32 and 1500×32. The potential bias in fractional anisotropy induced by this two-compartment model was more than an order of magnitude less than the error of using the single diffusion tensor model in the presence of partial volume effects with free water. This strategy may be useful for characterizing the diffusion of tissues adjacent to cerebral spinal fluid (CSF), tissues affected by edema, and removing artifacts from blurring and ghosting of the CSF signal. PMID:25271843

  17. A generalized diffusion model for growth of nanoparticles synthesized by colloidal methods.

    PubMed

    Wen, Tianlong; Brush, Lucien N; Krishnan, Kannan M

    2014-04-01

    A nanoparticle growth model is developed to predict and guide the syntheses of monodisperse colloidal nanoparticles in the liquid phase. The model, without any a priori assumptions, is based on the Fick's law of diffusion, conservation of mass and the Gibbs-Thomson equation for crystal growth. In the limiting case, this model reduces to the same expression as the currently accepted model that requires the assumption of a diffusion layer around each nanoparticle. The present growth model bridges the two limiting cases of the previous model i.e. complete diffusion controlled and adsorption controlled growth of nanoparticles. Specifically, the results show that a monodispersion of nanoparticles can be obtained both with fast monomer diffusion and with surface reaction under conditions of small diffusivity to surface reaction constant ratio that results is growth 'focusing'. This comprehensive description of nanoparticle growth provides new insights and establishes the required conditions for fabricating monodisperse nanoparticles critical for a wide range of applications.

  18. Quantifying the effect of tissue deformation on diffusion-weighted MRI: a mathematical model and an efficient simulation framework applied to cardiac diffusion imaging

    NASA Astrophysics Data System (ADS)

    Mekkaoui, Imen; Moulin, Kevin; Croisille, Pierre; Pousin, Jerome; Viallon, Magalie

    2016-08-01

    Cardiac motion presents a major challenge in diffusion weighted MRI, often leading to large signal losses that necessitate repeated measurements. The diffusion process in the myocardium is difficult to investigate because of the unqualified sensitivity of diffusion measurements to cardiac motion. A rigorous mathematical formalism is introduced to quantify the effect of tissue motion in diffusion imaging. The presented mathematical model, based on the Bloch-Torrey equations, takes into account deformations according to the laws of continuum mechanics. Approximating this mathematical model by using finite elements method, numerical simulations can predict the sensitivity of the diffusion signal to cardiac motion. Different diffusion encoding schemes are considered and the diffusion weighted MR signals, computed numerically, are compared to available results in literature. Our numerical model can identify the existence of two time points in the cardiac cycle, at which the diffusion is unaffected by myocardial strain and cardiac motion. Of course, these time points depend on the type of diffusion encoding scheme. Our numerical results also show that the motion sensitivity of the diffusion sequence can be reduced by using either spin echo technique with acceleration motion compensation diffusion gradients or stimulated echo acquisition mode with unipolar and bipolar diffusion gradients.

  19. Quantifying the effect of tissue deformation on diffusion-weighted MRI: a mathematical model and an efficient simulation framework applied to cardiac diffusion imaging

    NASA Astrophysics Data System (ADS)

    Mekkaoui, Imen; Moulin, Kevin; Croisille, Pierre; Pousin, Jerome; Viallon, Magalie

    2016-08-01

    Cardiac motion presents a major challenge in diffusion weighted MRI, often leading to large signal losses that necessitate repeated measurements. The diffusion process in the myocardium is difficult to investigate because of the unqualified sensitivity of diffusion measurements to cardiac motion. A rigorous mathematical formalism is introduced to quantify the effect of tissue motion in diffusion imaging. The presented mathematical model, based on the Bloch–Torrey equations, takes into account deformations according to the laws of continuum mechanics. Approximating this mathematical model by using finite elements method, numerical simulations can predict the sensitivity of the diffusion signal to cardiac motion. Different diffusion encoding schemes are considered and the diffusion weighted MR signals, computed numerically, are compared to available results in literature. Our numerical model can identify the existence of two time points in the cardiac cycle, at which the diffusion is unaffected by myocardial strain and cardiac motion. Of course, these time points depend on the type of diffusion encoding scheme. Our numerical results also show that the motion sensitivity of the diffusion sequence can be reduced by using either spin echo technique with acceleration motion compensation diffusion gradients or stimulated echo acquisition mode with unipolar and bipolar diffusion gradients.

  20. Quantifying the effect of tissue deformation on diffusion-weighted MRI: a mathematical model and an efficient simulation framework applied to cardiac diffusion imaging.

    PubMed

    Mekkaoui, Imen; Moulin, Kevin; Croisille, Pierre; Pousin, Jerome; Viallon, Magalie

    2016-08-01

    Cardiac motion presents a major challenge in diffusion weighted MRI, often leading to large signal losses that necessitate repeated measurements. The diffusion process in the myocardium is difficult to investigate because of the unqualified sensitivity of diffusion measurements to cardiac motion. A rigorous mathematical formalism is introduced to quantify the effect of tissue motion in diffusion imaging. The presented mathematical model, based on the Bloch-Torrey equations, takes into account deformations according to the laws of continuum mechanics. Approximating this mathematical model by using finite elements method, numerical simulations can predict the sensitivity of the diffusion signal to cardiac motion. Different diffusion encoding schemes are considered and the diffusion weighted MR signals, computed numerically, are compared to available results in literature. Our numerical model can identify the existence of two time points in the cardiac cycle, at which the diffusion is unaffected by myocardial strain and cardiac motion. Of course, these time points depend on the type of diffusion encoding scheme. Our numerical results also show that the motion sensitivity of the diffusion sequence can be reduced by using either spin echo technique with acceleration motion compensation diffusion gradients or stimulated echo acquisition mode with unipolar and bipolar diffusion gradients. PMID:27385441

  1. Phantoms for diffuse optical imaging based on totally absorbing objects, part 1: basic concepts

    PubMed Central

    Pifferi, Antonio; Contini, Davide; Spinelli, Lorenzo; Torricelli, Alessandro; Wabnitz, Heidrun; Macdonald, Rainer; Sassaroli, Angelo; Zaccanti, Giovanni

    2013-01-01

    Abstract. The design of inhomogeneous phantoms for diffuse optical imaging purposes using totally absorbing objects embedded in a diffusive medium is proposed and validated. From time-resolved and continuous-wave Monte Carlo simulations, it is shown that a given or desired perturbation strength caused by a realistic absorbing inhomogeneity of a certain absorption and volume can be approximately mimicked by a small totally absorbing object of a so-called equivalent black volume (equivalence relation). This concept can be useful in two ways. First, it can be exploited to design realistic inhomogeneous phantoms with different perturbation strengths simply using a set of black objects with different volumes. Further, it permits one to grade physiological or pathological changes on a reproducible scale of perturbation strengths given as equivalent black volumes, thus facilitating the performance assessment of clinical instruments. A set of plots and interpolating functions to derive the equivalent black volume corresponding to a given absorption change is provided. The application of the equivalent black volume concept for grading different optical perturbations is demonstrated for some examples. PMID:23778947

  2. Modeling Simple Driving Tasks with a One-Boundary Diffusion Model

    PubMed Central

    Ratcliff, Roger; Strayer, David

    2014-01-01

    A one-boundary diffusion model was applied to the data from two experiments in which subjects were performing a simple simulated driving task. In the first experiment, the same subjects were tested on two driving tasks using a PC-based driving simulator and the psychomotor vigilance test (PVT). The diffusion model fit the response time (RT) distributions for each task and individual subject well. Model parameters were found to correlate across tasks which suggests common component processes were being tapped in the three tasks. The model was also fit to a distracted driving experiment of Cooper and Strayer (2008). Results showed that distraction altered performance by affecting the rate of evidence accumulation (drift rate) and/or increasing the boundary settings. This provides an interpretation of cognitive distraction whereby conversing on a cell phone diverts attention from the normal accumulation of information in the driving environment. PMID:24297620

  3. Drift diffusion model of reward and punishment learning in schizophrenia: Modeling and experimental data.

    PubMed

    Moustafa, Ahmed A; Kéri, Szabolcs; Somlai, Zsuzsanna; Balsdon, Tarryn; Frydecka, Dorota; Misiak, Blazej; White, Corey

    2015-09-15

    In this study, we tested reward- and punishment learning performance using a probabilistic classification learning task in patients with schizophrenia (n=37) and healthy controls (n=48). We also fit subjects' data using a Drift Diffusion Model (DDM) of simple decisions to investigate which components of the decision process differ between patients and controls. Modeling results show between-group differences in multiple components of the decision process. Specifically, patients had slower motor/encoding time, higher response caution (favoring accuracy over speed), and a deficit in classification learning for punishment, but not reward, trials. The results suggest that patients with schizophrenia adopt a compensatory strategy of favoring accuracy over speed to improve performance, yet still show signs of a deficit in learning based on negative feedback. Our data highlights the importance of applying fitting models (particularly drift diffusion models) to behavioral data. The implications of these findings are discussed relative to theories of schizophrenia and cognitive processing.

  4. Drift diffusion model of reward and punishment learning in schizophrenia: Modeling and experimental data.

    PubMed

    Moustafa, Ahmed A; Kéri, Szabolcs; Somlai, Zsuzsanna; Balsdon, Tarryn; Frydecka, Dorota; Misiak, Blazej; White, Corey

    2015-09-15

    In this study, we tested reward- and punishment learning performance using a probabilistic classification learning task in patients with schizophrenia (n=37) and healthy controls (n=48). We also fit subjects' data using a Drift Diffusion Model (DDM) of simple decisions to investigate which components of the decision process differ between patients and controls. Modeling results show between-group differences in multiple components of the decision process. Specifically, patients had slower motor/encoding time, higher response caution (favoring accuracy over speed), and a deficit in classification learning for punishment, but not reward, trials. The results suggest that patients with schizophrenia adopt a compensatory strategy of favoring accuracy over speed to improve performance, yet still show signs of a deficit in learning based on negative feedback. Our data highlights the importance of applying fitting models (particularly drift diffusion models) to behavioral data. The implications of these findings are discussed relative to theories of schizophrenia and cognitive processing. PMID:26005124

  5. Boundedness in a chemotaxis-haptotaxis model with nonlinear diffusion

    NASA Astrophysics Data System (ADS)

    Li, Yan; Lankeit, Johannes

    2016-05-01

    This article deals with an initial-boundary value problem for the coupled chemotaxis-haptotaxis system with nonlinear diffusion under homogeneous Neumann boundary conditions in a bounded smooth domain Ω \\subset {{{R}}n} , n  =  2, 3, 4, where χ,ξ and μ are given nonnegative parameters. The diffusivity D(u) is assumed to satisfy D(u)≥slant δ {{u}m-1} for all u  >  0 with some δ >0 . It is proved that for sufficiently regular initial data global bounded solutions exist whenever m>2-\\frac{2}{n} . For the case of non-degenerate diffusion (i.e. D(0)  >  0) the solutions are classical; for the case of possibly degenerate diffusion (D(0)≥slant 0 ), the existence of bounded weak solutions is shown.

  6. 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.

  7. Computational Analyses in Support of Sub-scale Diffuser Testing for the A-3 Facility. Part 1; Steady Predictions

    NASA Technical Reports Server (NTRS)

    Allgood, Daniel C.; Graham, Jason S.; Ahuja, Vineet; Hosangadi, Ashvin

    2010-01-01

    Simulation technology can play an important role in rocket engine test facility design and development by assessing risks, providing analysis of dynamic pressure and thermal loads, identifying failure modes and predicting anomalous behavior of critical systems. Advanced numerical tools assume greater significance in supporting testing and design of high altitude testing facilities and plume induced testing environments of high thrust engines because of the greater inter-dependence and synergy in the functioning of the different sub-systems. This is especially true for facilities such as the proposed A-3 facility at NASA SSC because of a challenging operating envelope linked to variable throttle conditions at relatively low chamber pressures. Facility designs in this case will require a complex network of diffuser ducts, steam ejector trains, fast operating valves, cooling water systems and flow diverters that need to be characterized for steady state performance. In this paper, we will demonstrate with the use of CFD analyses s advanced capability to evaluate supersonic diffuser and steam ejector performance in a sub-scale A-3 facility at NASA Stennis Space Center (SSC) where extensive testing was performed. Furthermore, the focus in this paper relates to modeling of critical sub-systems and components used in facilities such as the A-3 facility. The work here will address deficiencies in empirical models and current CFD analyses that are used for design of supersonic diffusers/turning vanes/ejectors as well as analyses for confined plumes and venting processes. The primary areas that will be addressed are: (1) supersonic diffuser performance including analyses of thermal loads (2) accurate shock capturing in the diffuser duct; (3) effect of turning duct on the performance of the facility (4) prediction of mass flow rates and performance classification for steam ejectors (5) comparisons with test data from sub-scale diffuser testing and assessment of confidence

  8. The development of a through-diffusion model with a parent-daughter decay chain.

    PubMed

    Chen, Chin-Lung; Wang, Tsing-Hai; Lee, Ching-Hor; Teng, Shi-Ping

    2012-09-01

    A valid performance assessment of radioactive waste repositories strongly depends on the reliability of nuclide transport parameters, including distribution and diffusion coefficients. To reduce the waste produced and time spent conducting diffusion experiments, a robust model is required to accurately interpret the experiment results. Therefore, we developed a through-diffusion model with parent-daughter nuclide decay chain. We validated our model through comparisons with the Moridis model (Moridis, 1999) and Bharat model (Bharat et al., 2009), assessing our model and these two models using the distribution of parent nuclide concentrations. This strongly supports the rationality and functionality of extending our proposed model to daughter nuclides. In this study, we derived analytical solutions for the parent nuclides of the through-diffusion experiment using the multicompartment (MC) model. We also propose a simplified formula for estimating the apparent diffusion coefficient of parent nuclides based on the analytical solutions. Through numerical experiments, we verified the feasibility of the formula. Our models are useful for determining the apparent diffusion coefficient of daughter nuclides when conducting through-diffusion experiments with parent-daughter nuclide decay chains. Additionally, the proposed models offer the advantages of saving time and reducing experimental waste.

  9. Diffusion-controlled reactions modeling in Geant4-DNA

    SciTech Connect

    Karamitros, M.; Luan, S.; Bernal, M.A.; Allison, J.; Baldacchino, G.; Davidkova, M.; Francis, Z.; Friedland, W.; Ivantchenko, V.; Ivantchenko, A.; Mantero, A.; Nieminem, P.; Santin, G.; Tran, H.N.; Stepan, V.; Incerti, S.

    2014-10-01

    Context Under irradiation, a biological system undergoes a cascade of chemical reactions that can lead to an alteration of its normal operation. There are different types of radiation and many competing reactions. As a result the kinetics of chemical species is extremely complex. The simulation becomes then a powerful tool which, by describing the basic principles of chemical reactions, can reveal the dynamics of the macroscopic system. To understand the dynamics of biological systems under radiation, since the 80s there have been on-going efforts carried out by several research groups to establish a mechanistic model that consists in describing all the physical, chemical and biological phenomena following the irradiation of single cells. This approach is generally divided into a succession of stages that follow each other in time: (1) the physical stage, where the ionizing particles interact directly with the biological material; (2) the physico-chemical stage, where the targeted molecules release their energy by dissociating, creating new chemical species; (3) the chemical stage, where the new chemical species interact with each other or with the biomolecules; (4) the biological stage, where the repairing mechanisms of the cell come into play. This article focuses on the modeling of the chemical stage. Method This article presents a general method of speeding-up chemical reaction simulations in fluids based on the Smoluchowski equation and Monte-Carlo methods, where all molecules are explicitly simulated and the solvent is treated as a continuum. The model describes diffusion-controlled reactions. This method has been implemented in Geant4-DNA. The keys to the new algorithm include: (1) the combination of a method to compute time steps dynamically with a Brownian bridge process to account for chemical reactions, which avoids costly fixed time step simulations; (2) a k–d tree data structure for quickly locating, for a given molecule, its closest reactants. The

  10. Diffusion-controlled reactions modeling in Geant4-DNA

    NASA Astrophysics Data System (ADS)

    Karamitros, M.; Luan, S.; Bernal, M. A.; Allison, J.; Baldacchino, G.; Davidkova, M.; Francis, Z.; Friedland, W.; Ivantchenko, V.; Ivantchenko, A.; Mantero, A.; Nieminem, P.; Santin, G.; Tran, H. N.; Stepan, V.; Incerti, S.

    2014-10-01

    Context Under irradiation, a biological system undergoes a cascade of chemical reactions that can lead to an alteration of its normal operation. There are different types of radiation and many competing reactions. As a result the kinetics of chemical species is extremely complex. The simulation becomes then a powerful tool which, by describing the basic principles of chemical reactions, can reveal the dynamics of the macroscopic system. To understand the dynamics of biological systems under radiation, since the 80s there have been on-going efforts carried out by several research groups to establish a mechanistic model that consists in describing all the physical, chemical and biological phenomena following the irradiation of single cells. This approach is generally divided into a succession of stages that follow each other in time: (1) the physical stage, where the ionizing particles interact directly with the biological material; (2) the physico-chemical stage, where the targeted molecules release their energy by dissociating, creating new chemical species; (3) the chemical stage, where the new chemical species interact with each other or with the biomolecules; (4) the biological stage, where the repairing mechanisms of the cell come into play. This article focuses on the modeling of the chemical stage. Method This article presents a general method of speeding-up chemical reaction simulations in fluids based on the Smoluchowski equation and Monte-Carlo methods, where all molecules are explicitly simulated and the solvent is treated as a continuum. The model describes diffusion-controlled reactions. This method has been implemented in Geant4-DNA. The keys to the new algorithm include: (1) the combination of a method to compute time steps dynamically with a Brownian bridge process to account for chemical reactions, which avoids costly fixed time step simulations; (2) a k-d tree data structure for quickly locating, for a given molecule, its closest reactants. The

  11. Evaluating a three dimensional model of diffuse photosynthetically active radiation in maize canopies

    NASA Astrophysics Data System (ADS)

    Wang, Xiping; Guo, Yan; Li, Baoguo; Wang, Xiyong; Ma, Yuntao

    2006-07-01

    Diffuse photosynthetically active radiation (DPAR) is important during overcast days and for plant parts shaded from the direct beam radiation. Simulation of DPAR interception by individual plant parts of a canopy, separately from direct beam photosynthetically active radiation (PAR), may give important insights into plant ecology. This paper presents a model to simulate the interception of DPAR in plant canopies. A sub-model of a virtual maize canopy was reconstructed. Plant surfaces were represented as small triangular facets positioned according to three-dimensionally (3D) digitized data collected in the field. Then a second sub-model to simulate the 3D DPAR distribution in the canopy was developed by dividing the sky hemisphere into a grid of fine cells that allowed for the anisotropic distribution of DPAR over the sky hemisphere. This model, DSHP (Dividing Sky Hemisphere with Projecting), simulates which DSH (Divided Sky Hemisphere) cells are directly visible from a facet in the virtual canopy, i.e. not obscured by other facets. The DPAR reaching the center of a facet was calculated by summing the amounts of DPAR present in every DSH cell. The distribution of DPAR in a canopy was obtained from the calculated DPARs intercepted by all facets in the canopy. This DSHP model was validated against DPAR measurements made in an actual maize ( Zea mays L.) canopy over selected days during the early filling stage. The simulated and measured DPAR at different canopy depths showed a good agreement with a R 2 equaling 0.78 ( n=120).

  12. Quantum-corrected drift-diffusion models for transport in semiconductor devices

    SciTech Connect

    De Falco, Carlo; Gatti, Emilio; Lacaita, Andrea L.; Sacco, Riccardo . E-mail: riccardo.sacco@mate.polimi.it

    2005-04-10

    In this paper, we propose a unified framework for Quantum-corrected drift-diffusion (QCDD) models in nanoscale semiconductor device simulation. QCDD models are presented as a suitable generalization of the classical drift-diffusion (DD) system, each particular model being identified by the constitutive relation for the quantum-correction to the electric potential. We examine two special, and relevant, examples of QCDD models; the first one is the modified DD model named Schroedinger-Poisson-drift-diffusion, and the second one is the quantum-drift-diffusion (QDD) model. For the decoupled solution of the two models, we introduce a functional iteration technique that extends the classical Gummel algorithm widely used in the iterative solution of the DD system. We discuss the finite element discretization of the various differential subsystems, with special emphasis on their stability properties, and illustrate the performance of the proposed algorithms and models on the numerical simulation of nanoscale devices in two spatial dimensions.

  13. Model for radon diffusion through the lunar regolith.

    NASA Technical Reports Server (NTRS)

    Friesen, L. J.; Heymann, D.

    1972-01-01

    Description of a model for radon diffusion through the lunar regolith in which the atom migrates by random walk. The regolith is represented by a system of randomly oriented baffles in which the mean distance which the atom travels between two collisions takes on the role of a mean free path. The effective mean time between two collisions depends on two entities: the actual mean time-of-flight and the mean sticking time on grain surfaces for one collision. The latter depends strongly on the temperature and the heat of adsorption of radon on regolith materials. Both the mean free path as well as the heat of adsorption are either poorly known or unknown for the lunar regolith; hence these quantities are treated as free parameters. Because of the greatly different mean lifetimes against radioactive decay of Rn219, Rn220, and Rn222, the regolith acts as a powerful 'filter' for these species. Rn222 escape is significant (32%) even for a mean free path of 1 micron, a heat of adsorption of 7.0 kcal/mole and a regolith depth of 4 m. Calculations of radon escape from a 4 m thick regolith, using mean free paths of 1, 10, and 80 microns and heats of adsorption of 4.0, 5.2, and 7.0 kcal/mole show that the Rn222/Rn220 escape ratio can be as small as 7.7 and as large as, or larger than 47. The small value of 7.7 is of particular interest, because it is nearly equal to the escape ratio inferred by Turkevich et al. (1970) from their Surveyor 5 results.

  14. Climate stability for a Sellers-type model. [atmospheric diffusive energy balance model

    NASA Technical Reports Server (NTRS)

    Ghil, M.

    1976-01-01

    We study a diffusive energy-balance climate model governed by a nonlinear parabolic partial differential equation. Three positive steady-state solutions of this equation are found; they correspond to three possible climates of our planet: an interglacial (nearly identical to the present climate), a glacial, and a completely ice-covered earth. We consider also models similar to the main one studied, and determine the number of their steady states. All the models have albedo continuously varying with latitude and temperature, and entirely diffusive horizontal heat transfer. The diffusion is taken to be nonlinear as well as linear. We investigate the stability under small perturbations of the main model's climates. A stability criterion is derived, and its application shows that the 'present climate' and the 'deep freeze' are stable, whereas the model's glacial is unstable. A variational principle is introduced to confirm the results of this stability analysis. For a sufficient decrease in solar radiation (about 2%) the glacial and interglacial solutions disappear, leaving the ice-covered earth as the only possible climate.

  15. Bass-SIR model for diffusion of new products in social networks

    NASA Astrophysics Data System (ADS)

    Fibich, Gadi

    2016-09-01

    We consider the diffusion of new products in social networks, where consumers who adopt the product can later "recover" and stop influencing others to adopt the product. We show that the diffusion is not described by the susceptible-infected-recovered (SIR) model, but rather by a new model, the Bass-SIR model, which combines the Bass model for diffusion of new products with the SIR model for epidemics. The phase transition of consumers from nonadopters to adopters is described by a nonstandard Kolmogorov-Johnson-Mehl-Avrami model, in which clusters growth is limited by adopters' recovery. Therefore, diffusion in the Bass-SIR model only depends on the local structure of the social network, but not on the average distance between consumers. Consequently, unlike the SIR model, a small-worlds structure has a negligible effect on the diffusion. Moreover, unlike the SIR model, there is no threshold value above which the diffusion will peter out. Surprisingly, diffusion on scale-free networks is nearly identical to that on Cartesian ones.

  16. Amphiphile diffusion in model membrane systems studied by pulsed NMR.

    PubMed

    Lindblom, G; Wennerström, H

    1977-01-01

    The translational diffusion of the amphiphilic molecules in a number of lyotropic liquid crystalline phases has been measured with the pulsed NMR pulsed magnetic field gradient method. The amphiphiles studied were soaps, monoglycerids and lecithins. Measurements were performed both for oriented lamellar and for cubic phases. The order of magnitude of the diffusion coefficients was found to be the same as in neat liquids of analogous compounds. It was also found that the difussion coefficient depend markedly on the amphiphile end group in a way that parallels the area per polar head group as determined in X-ray studies. When corrections for geometrical factors has been made the diffusion rate is approximately equal in cubic and lamellar phases containing the same amphiphile.

  17. The membrane skeleton of erythrocytes: models of its effect on lateral diffusion.

    PubMed

    Saxton, M J

    1990-01-01

    The membrane skeleton, a network of structural proteins attached to the cytoplasmic surface of the plasma membrane, hinders lateral diffusion of integral proteins. 2. In some types of cells, such as epithelial cells and nerve cells, the obstruction of lateral diffusion by the membrane skeleton is one of the mechanisms by which proteins are localized to domains on the cell surface. 3. The effect of the membrane skeleton on lateral diffusion may involve steric hindrance, transient binding or both. Three pictures of the effect are reviewed, the discrete barrier model, the continuous barrier model and the transient binding model. 4. Experiments to distinguish the models are discussed.

  18. Diffuse ultraviolet erythemal irradiance on inclined planes: a comparison of experimental and modeled data.

    PubMed

    Utrillas, María P; Marín, María J; Esteve, Anna R; Estellés, Victor; Tena, Fernando; Cañada, Javier; Martínez-Lozano, José A

    2009-01-01

    Values of measured and modeled diffuse UV erythemal irradiance (UVER) for all sky conditions are compared on planes inclined at 40 degrees and oriented north, south, east and west. The models used for simulating diffuse UVER are of the geometric-type, mainly the Isotropic, Klucher, Hay, Muneer, Reindl and Schauberger models. To analyze the precision of the models, some statistical estimators were used such as root mean square deviation, mean absolute deviation and mean bias deviation. It was seen that all the analyzed models reproduce adequately the diffuse UVER on the south-facing plane, with greater discrepancies for the other inclined planes. When the models are applied to cloud-free conditions, the errors obtained are higher because the anisotropy of the sky dome acquires more importance and the models do not provide the estimation of diffuse UVER accurately. PMID:19496991

  19. Diffuse ultraviolet erythemal irradiance on inclined planes: a comparison of experimental and modeled data.

    PubMed

    Utrillas, María P; Marín, María J; Esteve, Anna R; Estellés, Victor; Tena, Fernando; Cañada, Javier; Martínez-Lozano, José A

    2009-01-01

    Values of measured and modeled diffuse UV erythemal irradiance (UVER) for all sky conditions are compared on planes inclined at 40 degrees and oriented north, south, east and west. The models used for simulating diffuse UVER are of the geometric-type, mainly the Isotropic, Klucher, Hay, Muneer, Reindl and Schauberger models. To analyze the precision of the models, some statistical estimators were used such as root mean square deviation, mean absolute deviation and mean bias deviation. It was seen that all the analyzed models reproduce adequately the diffuse UVER on the south-facing plane, with greater discrepancies for the other inclined planes. When the models are applied to cloud-free conditions, the errors obtained are higher because the anisotropy of the sky dome acquires more importance and the models do not provide the estimation of diffuse UVER accurately.

  20. Asymptotic profiles of steady states for a diffusive SIS epidemic model with mass action infection mechanism

    NASA Astrophysics Data System (ADS)

    Wu, Yixiang; Zou, Xingfu

    2016-10-01

    Mass action and standard incidence are two major infection mechanisms in modelling spread of infectious diseases. Spatial heterogeneity plays an important role in spread of infectious diseases, and hence, motivates and advocates diffusive models for disease dynamics. By analyzing a diffusive SIS model with the standard incidence infection mechanism, some recent works [2,12] have investigated the asymptotical profiles of the endemic steady state for large and small diffusion rates, and the results show that controlling the diffusion rate of the susceptible individuals can help eradicate the infection, while controlling the diffusion rate of the infectious individuals cannot. This paper aims to reveal the difference between the two infection mechanisms in a spatially heterogeneous environment. To this end, we consider a diffusive SIS model of the same structure but with the mass action infection adopted, and explore the asymptotic profiles of the endemic steady state for small and large diffusion rates. It turns out that the new model poses some new challenges due to the nonlocal term in the equilibrium problem and the unboundedness of the nonlinear term. Our results on this new model reveal some fundamental differences between the two transmission mechanisms in such spatial models, which may provide some implications on disease modelling and controls.

  1. A fractional Fokker-Planck model for anomalous diffusion

    SciTech Connect

    Anderson, Johan; Kim, Eun-jin; Moradi, Sara

    2014-12-15

    In this paper, we present a study of anomalous diffusion using a Fokker-Planck description with fractional velocity derivatives. The distribution functions are found using numerical means for varying degree of fractionality of the stable Lévy distribution. The statistical properties of the distribution functions are assessed by a generalized normalized expectation measure and entropy in terms of Tsallis statistical mechanics. We find that the ratio of the generalized entropy and expectation is increasing with decreasing fractionality towards the well known so-called sub-diffusive domain, indicating a self-organising behavior.

  2. Diffusion Dynamics and Creative Destruction in a Simple Classical Model

    PubMed Central

    2015-01-01

    ABSTRACT The article explores the impact of the diffusion of new methods of production on output and employment growth and income distribution within a Classical one‐sector framework. Disequilibrium paths are studied analytically and in terms of simulations. Diffusion by differential growth affects aggregate dynamics through several channels. The analysis reveals the non‐steady nature of economic change and shows that the adaptation pattern depends both on the innovation's factor‐saving bias and on the extent of the bias, which determines the strength of the selection pressure on non‐innovators. The typology of different cases developed shows various aspects of Schumpeter's concept of creative destruction. PMID:27642192

  3. 12 CFR Appendix B to Part 202 - Model Application Forms

    Code of Federal Regulations, 2013 CFR

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    Code of Federal Regulations, 2011 CFR

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    Code of Federal Regulations, 2013 CFR

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    Code of Federal Regulations, 2014 CFR

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  9. 12 CFR Appendix A to Part 213 - Model Forms

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  14. 12 CFR Appendix A to Part 704 - Model Forms

    Code of Federal Regulations, 2011 CFR

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  15. 12 CFR Appendix A to Part 716 - Model Privacy Form

    Code of Federal Regulations, 2013 CFR

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    Code of Federal Regulations, 2014 CFR

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    Code of Federal Regulations, 2013 CFR

    2013-01-01

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    Code of Federal Regulations, 2012 CFR

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  19. 12 CFR Appendix A to Part 573 - Model Privacy Form

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ...) with black or other contrasting ink color. Spot color may be used to achieve visual interest, so long... languages other than English. C. Information Required in the Model Privacy Form The information in the model... the model form under this part, must comply with section 624 of the FCRA and 12 CFR part 571,...

  20. 12 CFR Appendix A to Part 716 - Model Privacy Form

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ...) with black or other contrasting ink color. Spot color may be used to achieve visual interest, so long... languages other than English. C. Information Required in the Model Privacy Form The information in the model... the model form under this part, must comply with section 624 of the FCRA and 12 CFR part 717,...

  1. 12 CFR Appendix A to Part 716 - Model Privacy Form

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ...) with black or other contrasting ink color. Spot color may be used to achieve visual interest, so long... languages other than English. C. Information Required in the Model Privacy Form The information in the model... the model form under this part, must comply with section 624 of the FCRA and 12 CFR part 717,...

  2. 12 CFR Appendix A to Part 573 - Model Privacy Form

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ...) with black or other contrasting ink color. Spot color may be used to achieve visual interest, so long... languages other than English. C. Information Required in the Model Privacy Form The information in the model... the model form under this part, must comply with section 624 of the FCRA and 12 CFR part 571,...

  3. 12 CFR Appendix A to Part 573 - Model Privacy Form

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ...) with black or other contrasting ink color. Spot color may be used to achieve visual interest, so long... languages other than English. C. Information Required in the Model Privacy Form The information in the model... the model form under this part, must comply with section 624 of the FCRA and 12 CFR part 571,...

  4. 12 CFR Appendix B to Part 202 - Model Application Forms

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 12 Banks and Banking 2 2010-01-01 2010-01-01 false Model Application Forms B Appendix B to Part 202 Banks and Banking FEDERAL RESERVE SYSTEM BOARD OF GOVERNORS OF THE FEDERAL RESERVE SYSTEM EQUAL CREDIT OPPORTUNITY ACT (REGULATION B) Pt. 202, App. B Appendix B to Part 202—Model Application Forms 1. This appendix contains five model...

  5. 12 CFR Appendix A to Part 1013 - Model Forms

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... 12 Banks and Banking 8 2014-01-01 2014-01-01 false Model Forms A Appendix A to Part 1013 Banks and... A to Part 1013—Model Forms A-1—Model Open-End or Finance Vehicle Lease Disclosures A-2—Model Closed-End or Net Vehicle Lease Disclosures A-3—Model Furniture Lease Disclosures ER19DE11.010...

  6. 12 CFR Appendix A to Part 1013 - Model Forms

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... 12 Banks and Banking 8 2013-01-01 2013-01-01 false Model Forms A Appendix A to Part 1013 Banks and... A to Part 1013—Model Forms A-1—Model Open-End or Finance Vehicle Lease Disclosures A-2—Model Closed-End or Net Vehicle Lease Disclosures A-3—Model Furniture Lease Disclosures ER19DE11.010...

  7. 12 CFR Appendix A to Part 1013 - Model Forms

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... 12 Banks and Banking 8 2012-01-01 2012-01-01 false Model Forms A Appendix A to Part 1013 Banks and... A to Part 1013—Model Forms A-1—Model Open-End or Finance Vehicle Lease Disclosures A-2—Model Closed-End or Net Vehicle Lease Disclosures A-3—Model Furniture Lease Disclosures ER19DE11.010...

  8. An entropic quantum drift-diffusion model for electron transport in resonant tunneling diodes

    SciTech Connect

    Degond, Pierre; Gallego, Samy . E-mail: gallego@mip.ups-tlse.fr; Mehats, Florian

    2007-01-20

    We present an entropic quantum drift-diffusion model (eQDD) and show how it can be derived on a bounded domain as the diffusive approximation of the Quantum Liouville equation with a quantum BGK operator. Some links between this model and other existing models are exhibited, especially with the density gradient (DG) model and the Schroedinger-Poisson drift-diffusion model (SPDD). Then a finite difference scheme is proposed to discretize the eQDD model coupled to the Poisson equation and we show how this scheme can be slightly modified to discretize the other models. Numerical results show that the properties listed for the eQDD model are checked, as well as the model captures important features concerning the modeling of a resonant tunneling diode. To finish, some comparisons between the models stated above are realized.

  9. Modeling of the magnetic free energy of self-diffusion in bcc Fe

    NASA Astrophysics Data System (ADS)

    Sandberg, N.; Chang, Z.; Messina, L.; Olsson, P.; Korzhavyi, P.

    2015-11-01

    A first-principles based approach to calculating self-diffusion rates in bcc Fe is discussed with particular focus on the magnetic free energy associated with diffusion activation. First, the enthalpies and entropies of vacancy formation and migration in ferromagnetic bcc Fe are calculated from standard density functional theory methods in combination with transition state theory. Next, the shift in diffusion activation energy when going from the ferromagnetic to the paramagnetic state is estimated by averaging over random spin states. Classical and quantum mechanical Monte Carlo simulations within the Heisenberg model are used to study the effect of spin disordering on the vacancy formation and migration free energy. Finally, a quasiempirical model of the magnetic contribution to the diffusion activation free energy is applied in order to connect the current first-principles results to experimental data. The importance of the zero-point magnon energy in modeling of diffusion in bcc Fe is stressed.

  10. Diffusion versus network models as descriptions for the spread of prion diseases in the brain.

    PubMed

    Matthäus, Franziska

    2006-05-01

    In this paper we will discuss different modeling approaches for the spread of prion diseases in the brain. Firstly, we will compare reaction-diffusion models with models of epidemic diseases on networks. The solutions of the resulting reaction-diffusion equations exhibit traveling wave behavior on a one-dimensional domain, and the wave speed can be estimated. The models can be tested for diffusion-driven (Turing) instability, which could present a possible mechanism for the formation of plaques. We also show that the reaction-diffusion systems are capable of reproducing experimental data on prion spread in the mouse visual system. Secondly, we study classical epidemic models on networks, and use these models to study the influence of the network topology on the disease progression. PMID:16219329

  11. Employing a Modified Diffuser Momentum Model to Simulate Ventilation of the Orion CEV

    NASA Technical Reports Server (NTRS)

    Straus, John; Lewis, John F.

    2011-01-01

    The Ansys CFX CFD modeling tool was used to support the design efforts of the ventilation system for the Orion CEV. CFD modeling was used to establish the flow field within the cabin for several supply configurations. A mesh and turbulence model sensitivity study was performed before the design studies. Results were post-processed for comparison with performance requirements. Most configurations employed straight vaned diffusers to direct and throw the flow. To manage the size of the models, the diffuser vanes were not resolved. Instead, a momentum model was employed to account for the effect of the diffusers. The momentum model was tested against a separate, vane-resolved side study. Results are presented for a single diffuser configuration for a low supply flow case.

  12. Information diffusion, Facebook clusters, and the simplicial model of social aggregation: a computational simulation of simplicial diffusers for community health interventions.

    PubMed

    Kee, Kerk F; Sparks, Lisa; Struppa, Daniele C; Mannucci, Mirco A; Damiano, Alberto

    2016-01-01

    By integrating the simplicial model of social aggregation with existing research on opinion leadership and diffusion networks, this article introduces the constructs of simplicial diffusers (mathematically defined as nodes embedded in simplexes; a simplex is a socially bonded cluster) and simplicial diffusing sets (mathematically defined as minimal covers of a simplicial complex; a simplicial complex is a social aggregation in which socially bonded clusters are embedded) to propose a strategic approach for information diffusion of cancer screenings as a health intervention on Facebook for community cancer prevention and control. This approach is novel in its incorporation of interpersonally bonded clusters, culturally distinct subgroups, and different united social entities that coexist within a larger community into a computational simulation to select sets of simplicial diffusers with the highest degree of information diffusion for health intervention dissemination. The unique contributions of the article also include seven propositions and five algorithmic steps for computationally modeling the simplicial model with Facebook data.

  13. A review of porous media enhanced vapor-phase diffusion mechanisms, models, and data: Does enhanced vapor-phase diffusion exist?

    SciTech Connect

    Ho, C.K.; Webb, S.W.

    1996-05-01

    A review of mechanisms, models, and data relevant to the postulated phenomenon of enhanced vapor-phase diffusion in porous media is presented. Information is obtained from literature spanning two different disciplines (soil science and engineering) to gain a diverse perspective on this topic. Findings indicate that while enhanced vapor diffusion tends to correct the discrepancies observed between past theory and experiments, no direct evidence exists to support the postulated processes causing enhanced vapor diffusion. Numerical modeling analyses of experiments representative of the two disciplines are presented in this paper to assess the sensitivity of different systems to enhanced vapor diffusion. Pore-scale modeling is also performed to evaluate the relative significance of enhanced vapor diffusion mechanisms when compared to Fickian diffusion. The results demonstrate the need for additional experiments so that more discerning analyses can be performed.

  14. A fractal derivative model for the characterization of anomalous diffusion in magnetic resonance imaging

    NASA Astrophysics Data System (ADS)

    Liang, Yingjie; Ye, Allen Q.; Chen, Wen; Gatto, Rodolfo G.; Colon-Perez, Luis; Mareci, Thomas H.; Magin, Richard L.

    2016-10-01

    Non-Gaussian (anomalous) diffusion is wide spread in biological tissues where its effects modulate chemical reactions and membrane transport. When viewed using magnetic resonance imaging (MRI), anomalous diffusion is characterized by a persistent or 'long tail' behavior in the decay of the diffusion signal. Recent MRI studies have used the fractional derivative to describe diffusion dynamics in normal and post-mortem tissue by connecting the order of the derivative with changes in tissue composition, structure and complexity. In this study we consider an alternative approach by introducing fractal time and space derivatives into Fick's second law of diffusion. This provides a more natural way to link sub-voxel tissue composition with the observed MRI diffusion signal decay following the application of a diffusion-sensitive pulse sequence. Unlike previous studies using fractional order derivatives, here the fractal derivative order is directly connected to the Hausdorff fractal dimension of the diffusion trajectory. The result is a simpler, computationally faster, and more direct way to incorporate tissue complexity and microstructure into the diffusional dynamics. Furthermore, the results are readily expressed in terms of spectral entropy, which provides a quantitative measure of the overall complexity of the heterogeneous and multi-scale structure of biological tissues. As an example, we apply this new model for the characterization of diffusion in fixed samples of the mouse brain. These results are compared with those obtained using the mono-exponential, the stretched exponential, the fractional derivative, and the diffusion kurtosis models. Overall, we find that the order of the fractal time derivative, the diffusion coefficient, and the spectral entropy are potential biomarkers to differentiate between the microstructure of white and gray matter. In addition, we note that the fractal derivative model has practical advantages over the existing models from the

  15. Hindered diffusion in agarose gels: test of effective medium model.

    PubMed Central

    Johnson, E M; Berk, D A; Jain, R K; Deen, W M

    1996-01-01

    The diffusivities of uncharged macromolecules in gels (D) are typically lower than in free solution (D infinity), because of a combination of hydrodynamic and steric factors. To examine these factors, we measured D and D infinity for dilute solutions of several fluorescein-labeled macromolecules, using an image-based fluorescence recovery after photobleaching technique. Test macromolecules with Stokes-Einstein radii (rs) of 2.1-6.2 nm, including three globular proteins (bovine serum albumin, ovalbumin, lactalbumin) and four narrow fractions of Ficoll, were studied in agarose gels with agarose volume fractions (phi) of 0.038-0.073. The gels were characterized by measuring the hydraulic permeability of supported agarose membranes, allowing calculation of the Darcy permeability (kappa) for each gel sample. It was found that kappa, which is a measure of the intrinsic hydraulic conductance of the gel, decreased by an order of magnitude as phi was increased over the range indicated. The diffusivity ratio D/D infinity, which varied from 0.20 to 0.63, decreased with increases in rs or phi. Thus as expected, diffusional hindrances were the most severe for large macromolecules and/or relatively concentrated gels. According to a recently proposed theory for hindered diffusion through fibrous media, the diffusivity ratio is given by the product of a hydrodynamic factor (F) and a steric factor (S). The functional form is D/D infinity = F(rs/k1/2) S(f), where f = [(rs+rf)/rf]2 phi and rf is the fiber radius. Values of D/D infinity calculated from this effective medium theory, without use of adjustable parameters, were in much better agreement with the measured values than were predictions based on other approaches. The strengths and limitations of the effective medium theory for predicting diffusivities in gels are discussed. PMID:8789119

  16. Diffusion on a hypersphere: application to the Wright-Fisher model

    NASA Astrophysics Data System (ADS)

    Maruyama, Kishiko; Itoh, Yoshiaki

    2016-04-01

    The eigenfunction expansion by Gegenbauer polynomials for the diffusion on a hypersphere is transformed into the diffusion for the Wright-Fisher model with a particular mutation rate. We use the Ito calculus considering stochastic differential equations. The expansion gives a simple interpretation of the Griffiths eigenfunction expansion for the Wright-Fisher model. Our representation is useful to simulate the Wright-Fisher model as well as Brownian motion on a hypersphere.

  17. An efficient wavelet analysis method to film-pore diffusion model arising in mathematical chemistry.

    PubMed

    Hariharan, G

    2014-04-01

    In this paper, we have established an efficient Legendre wavelet based approximation method to solve film-pore diffusion model arising in engineering. Film-pore diffusion model is widely used to determine study the kinetics of adsorption systems. The use of Legendre wavelet based approximation method is found to be accurate, simple, fast, flexible, convenient, and computationally attractive. It is shown that film-pore diffusion model satisfactorily describe kinetics of methylene blue adsorption onto the three low-cost adsorbents, Guava, teak and gulmohar plant leaf powders, used in this study. PMID:24562792

  18. Computational Analyses in Support of Sub-scale Diffuser Testing for the A-3 Facility. Part 1; Steady Predictions

    NASA Technical Reports Server (NTRS)

    Allgood, Daniel C.; Graham, Jason S.; Ahuja, Vineet; Hosangadi, Ashvin

    2008-01-01

    Simulation technology can play an important role in rocket engine test facility design and development by assessing risks, providing analysis of dynamic pressure and thermal loads, identifying failure modes and predicting anomalous behavior of critical systems. Advanced numerical tools assume greater significance in supporting testing and design of high altitude testing facilities and plume induced testing environments of high thrust engines because of the greater inter-dependence and synergy in the functioning of the different sub-systems. This is especially true for facilities such as the proposed A-3 facility at NASA SSC because of a challenging operating envelope linked to variable throttle conditions at relatively low chamber pressures. Facility designs in this case will require a complex network of diffuser ducts, steam ejector trains, fast operating valves, cooling water systems and flow diverters that need to be characterized for steady state performance. In this paper, we will demonstrate with the use of CFD analyses s advanced capability to evaluate supersonic diffuser and steam ejector performance in a sub-scale A-3 facility at NASA Stennis Space Center (SSC) where extensive testing was performed. Furthermore, the focus in this paper relates to modeling of critical sub-systems and components used in facilities such as the A-3 facility. The work here will address deficiencies in empirical models and current CFD analyses that are used for design of supersonic diffusers/turning vanes/ejectors as well as analyses for confined plumes and venting processes. The primary areas that will be addressed are: (1) supersonic diffuser performance including analyses of thermal loads (2) accurate shock capturing in the diffuser duct; (3) effect of turning duct on the performance of the facility (4) prediction of mass flow rates and performance classification for steam ejectors (5) comparisons with test data from sub-scale diffuser testing and assessment of confidence

  19. Hierarchical Bass model: a product diffusion model considering a diversity of sensitivity to fashion

    NASA Astrophysics Data System (ADS)

    Tashiro, Tohru

    2016-11-01

    We propose a new product diffusion model including the number of how many adopters or advertisements a non-adopter met until he/she adopts the product, where (non-)adopters mean people (not) possessing it. By this effect not considered in the Bass model, we can depict a diversity of sensitivity to fashion. As an application, we utilize the model to fit the iPod and the iPhone unit sales data, and so the better agreement is obtained than the Bass model for the iPod data. We also present a new method to estimate the number of advertisements in a society from fitting parameters of the Bass model and this new model.

  20. A Process for Modelling Diffuse Scattering from Disordered Molecular Crystals, Illustrated by Application to Monoclinic 9-Chloro-10-methylanthracene

    DOE PAGESBeta

    Goossens, D. J.

    2015-01-01

    Diffuse scattering from a crystal contains valuable information about the two-body correlations (related to the nanoscale order) in the material. Despite years of development, the detailed analysis of single crystal diffuse scattering (SCDS) has yet to become part of the everyday toolbox of the structural scientist. Recent decades have seen the pair distribution function approach to diffuse scattering (in fact, total scattering) from powders become a relatively routine tool. However, analysing the detailed, complex, and often highly anisotropic three-dimensional distribution of SCDS remains valuable yet rare because there is no routine method for undertaking the analysis. At present, analysis requiresmore » significant investment of time to develop specialist expertise, which means that the analysis of diffuse scattering, which has much to offer, is not incorporated thorough studies of many compounds even though it has the potential to be a very useful adjunct to existing techniques. This article endeavours to outline in some detail how the diffuse scattering from a molecular crystal can be modelled relatively quickly and largely using existing software tools. It is hoped this will provide a template for other studies. To enable this, the entire simulation is included as deposited material.« less

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

    NASA Astrophysics Data System (ADS)

    Berezhkovskii, Alexander M.; Shvartsman, Stanislav Y.

    2016-05-01

    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.

  2. Radiative diffusivity factors in cirrus and stratocumulus clouds: Application to two-stream models

    NASA Technical Reports Server (NTRS)

    Stephens, Graeme L.; Flatau, P. J.; Tsay, S.-C.; Hein, Paul F.

    1990-01-01

    A diffusion-like description of radiative transfer in clouds and the free atmosphere is often used. The two stream model is probably the best known example of such a description. The main idea behind the approach is that only the first few moments of radiance are needed to describe the radiative field correctly. Integration smooths details of the angular distribution of specific intensity and it is assumed that the closure parameters of the theory (diffusivity factors) are only weakly dependent on the distribution. The diffusivity factors are investigated using the results obtained from both Stratocumulus and Cirrus phases of FIRE experiment. A new theoretical framework is described in which two (upwards and downwards) diffusivity factors are used and a detailed multistream model is used to provide further insight about both the diffusivity factors and their dependence on scattering properties of clouds.

  3. Turing pattern dynamics and adaptive discretization for a super-diffusive Lotka-Volterra model.

    PubMed

    Bendahmane, Mostafa; Ruiz-Baier, Ricardo; Tian, Canrong

    2016-05-01

    In this paper we analyze the effects of introducing the fractional-in-space operator into a Lotka-Volterra competitive model describing population super-diffusion. First, we study how cross super-diffusion influences the formation of spatial patterns: a linear stability analysis is carried out, showing that cross super-diffusion triggers Turing instabilities, whereas classical (self) super-diffusion does not. In addition we perform a weakly nonlinear analysis yielding a system of amplitude equations, whose study shows the stability of Turing steady states. A second goal of this contribution is to propose a fully adaptive multiresolution finite volume method that employs shifted Grünwald gradient approximations, and which is tailored for a larger class of systems involving fractional diffusion operators. The scheme is aimed at efficient dynamic mesh adaptation and substantial savings in computational burden. A numerical simulation of the model was performed near the instability boundaries, confirming the behavior predicted by our analysis.

  4. Numerical study of a cylinder model of the diffusion MRI signal for neuronal dendrite trees.

    PubMed

    Van Nguyen, Dang; Grebenkov, Denis; Le Bihan, Denis; Li, Jing-Rebecca

    2015-03-01

    We study numerically how the neuronal dendrite tree structure can affect the diffusion magnetic resonance imaging (dMRI) signal in brain tissue. For a large set of randomly generated dendrite trees, synthetic dMRI signals are computed and fitted to a cylinder model to estimate the effective longitudinal diffusivity D(L) in the direction of neurites. When the dendrite branches are short compared to the diffusion length, D(L) depends significantly on the ratio between the average branch length and the diffusion length. In turn, D(L) has very weak dependence on the distribution of branch lengths and orientations of a dendrite tree, and the number of branches per node. We conclude that the cylinder model which ignores the connectivity of the dendrite tree, can still be adapted to describe the apparent diffusion coefficient in brain tissue. PMID:25681802

  5. 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.

  6. Turing pattern dynamics and adaptive discretization for a super-diffusive Lotka-Volterra model.

    PubMed

    Bendahmane, Mostafa; Ruiz-Baier, Ricardo; Tian, Canrong

    2016-05-01

    In this paper we analyze the effects of introducing the fractional-in-space operator into a Lotka-Volterra competitive model describing population super-diffusion. First, we study how cross super-diffusion influences the formation of spatial patterns: a linear stability analysis is carried out, showing that cross super-diffusion triggers Turing instabilities, whereas classical (self) super-diffusion does not. In addition we perform a weakly nonlinear analysis yielding a system of amplitude equations, whose study shows the stability of Turing steady states. A second goal of this contribution is to propose a fully adaptive multiresolution finite volume method that employs shifted Grünwald gradient approximations, and which is tailored for a larger class of systems involving fractional diffusion operators. The scheme is aimed at efficient dynamic mesh adaptation and substantial savings in computational burden. A numerical simulation of the model was performed near the instability boundaries, confirming the behavior predicted by our analysis. PMID:26219250

  7. 12 CFR Appendix A to Part 213 - Model Forms

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 12 Banks and Banking 2 2010-01-01 2010-01-01 false Model Forms A Appendix A to Part 213 Banks and Banking FEDERAL RESERVE SYSTEM BOARD OF GOVERNORS OF THE FEDERAL RESERVE SYSTEM CONSUMER LEASING (REGULATION M) Pt. 213, App. A Appendix A to Part 213—Model Forms A-1Model Open-End or Finance Vehicle Lease Disclosures A-2Model Closed-End or...

  8. Modeling of TCE diffusion to the atmosphere and distribution in plant stems.

    PubMed

    Ma, Xingmao; Burken, Joel

    2004-09-01

    Fate of chlorinated solvents in phytoremediation has been delineated by many discoveries made in recent years. Plant uptake, metabolism, rhizosphere degradation, accumulation, and volatilization were shown to occur to differing degrees for many organic contaminants including chlorinated solvents. Among these mechanistic findings, recent research confirmed that volatile organic compounds (VOCs) volatilize from stems and that the resulting diffusive flux to the atmosphere is related to exposure concentration and to height up the stem. A comprehensive model was developed based upon all identified fate and transport mechanisms for VOCs, including translocation in the xylem flow and diffusion. The dispersion and diffusion in the radial direction were considered as one process (effective diffusion) as the two could not be investigated individually. The mechanism-based model mathematically indicates an exponential decrease of concentrations with height. While an analytic solution for the comprehensive model was not attained, it can serve as a starting point for other modeling efforts. The comprehensive model was simplified in this work for practical application to experimentally obtained data on trichloroethylene (TCE) fate. Model output correlated well with experimental results, and effective diffusivities for TCE in plant tissues were obtained through the model calibrations. The simplified model approximated TCE concentrations in the transpiration stream as well as TCE volatilization to the atmosphere. Xylem transport, including advection, dispersion, and diffusion through cell walls with subsequent volatilization to the atmosphere, is a major fate for VOCs in phytoremediation. PMID:15461166

  9. Ages estimated from a diffusion equation model for scarp degradation

    USGS Publications Warehouse

    Colman, Steven M.; Watson, K.E.N.

    1983-01-01

    The diffusion equation derived from the continuity equation for hillslopes is applied to scarp erosion in unconsolidated materials. Solutions to this equation allow direct calculation of the product of the rate coefficient and the age of the scarp from measurements of scarp morphology. Where the rate coefficient can be estimated or can be derived from scarps of known age, this method allows direct calculation of unknown ages of scarps.

  10. Integrating O/S models during conceptual design, part 2

    NASA Technical Reports Server (NTRS)

    Ebeling, Charles E.

    1994-01-01

    This report documents the procedures for utilizing and maintaining the Reliability & Maintainability Model (RAM) developed by the University of Dayton for the National Aeronautics and Space Administration (NASA) Langley Research Center (LaRC) under NASA research grant NAG-1-1327. The purpose of the grant is to provide support to NASA in establishing operational and support parameters and costs of proposed space systems. As part of this research objective, the model described here was developed. Additional documentation concerning the development of this model may be found in Part 1 of this report. This is the 2nd part of a 3 part technical report.

  11. Delayed-exponential approximation of a linear homogeneous diffusion model of neuron.

    PubMed

    Pacut, A; Dabrowski, L

    1988-01-01

    The diffusion models of neuronal activity are general yet conceptually simple and flexible enough to be useful in a variety of modeling problems. Unfortunately, even simple diffusion models lead to tedious numerical calculations. Consequently, the existing neural net models use characteristics of a single neuron taken from the "pre-diffusion" era of neural modeling. Simplistic elements of neural nets forbid to incorporate a single learning neuron structure into the net model. The above drawback cannot be overcome without the use of the adequate structure of the single neuron as an element of a net. A linear (not necessarily homogeneous) diffusion model of a single neuron is a good candidate for such a structure, it must, however, be simplified. In the paper the structure of the diffusion model of neuron is discussed and a linear homogeneous model with reflection is analyzed. For this model an approximation is presented, which is based on the approximation of the first passage time distribution of the Ornstein-Uhlenbeck process by the delayed (shifted) exponential distribution. The resulting model has a simple structure and has a prospective application in neural modeling and in analysis of neural nets.

  12. Optimal prediction for moment models: crescendo diffusion and reordered equations

    NASA Astrophysics Data System (ADS)

    Seibold, Benjamin; Frank, Martin

    2009-12-01

    A direct numerical solution of the radiative transfer equation or any kinetic equation is typically expensive, since the radiative intensity depends on time, space and direction. An expansion in the direction variables yields an equivalent system of infinitely many moments. A fundamental problem is how to truncate the system. Various closures have been presented in the literature. We want to generally study the moment closure within the framework of optimal prediction, a strategy to approximate the mean solution of a large system by a smaller system, for radiation moment systems. We apply this strategy to radiative transfer and show that several closures can be re-derived within this framework, such as P N , diffusion, and diffusion correction closures. In addition, the formalism gives rise to new parabolic systems, the reordered P N equations, that are similar to the simplified P N equations. Furthermore, we propose a modification to existing closures. Although simple and with no extra cost, this newly derived crescendo diffusion yields better approximations in numerical tests.

  13. Inhibition drives configural superiority of illusory Gestalt: Combined behavioral and drift-diffusion model evidence.

    PubMed

    Nie, Qi-Yang; Maurer, Mara; Müller, Hermann J; Conci, Markus

    2016-05-01

    Illusory Kanizsa figures demonstrate that a perceptually completed whole is more than the sum of its composite parts. In the current study, we explored part/whole relationships in object completion using the configural superiority effect (CSE) with illusory figures (Pomerantz & Portillo, 2011). In particular, we investigated to which extent the CSE is modulated by closure in target and distractor configurations. Our results demonstrated a typical CSE, with detection of a configural whole being more efficient than the detection of a corresponding part-level target. Moreover, the CSE was more pronounced when grouped objects were presented in distractors rather than in the target. A follow-up experiment systematically manipulated closure in whole target or, respectively, distractor configurations. The results revealed the effect of closure to be again stronger in distractor, rather than in target configurations, suggesting that closure primarily affects the inhibition of distractors, and to a lesser extent the selection of the target. In addition, a drift-diffusion model analysis of our data revealed that efficient distractor inhibition expedites the rate of evidence accumulation, with closure in distractors particularly speeding the drift toward the decision boundary. In sum, our findings demonstrate that the CSE in Kanizsa figures derives primarily from the inhibition of closed distractor objects, rather than being driven by a conspicuous target configuration. Altogether, these results support a fundamental role of inhibition in driving configural superiority effects in visual search.

  14. 12 CFR Appendix A to Part 40 - Model Privacy Form

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    .... The model form must be printed on white or light color paper (such as cream) with black or other... in color. (e) Languages. The model form may be translated into languages other than English. C... under this part, must comply with section 624 of the FCRA and 12 CFR part 41, subpart C, with respect...

  15. 12 CFR Appendix A to Part 40 - Model Privacy Form

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    .... The model form must be printed on white or light color paper (such as cream) with black or other... in color. (e) Languages. The model form may be translated into languages other than English. C... under this part, must comply with section 624 of the FCRA and 12 CFR part 41, subpart C, with respect...

  16. 12 CFR Appendix A to Part 40 - Model Privacy Form

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    .... The model form must be printed on white or light color paper (such as cream) with black or other... in color. (e) Languages. The model form may be translated into languages other than English. C... under this part, must comply with section 624 of the FCRA and 12 CFR part 41, subpart C, with respect...

  17. 12 CFR Appendix A to Part 40 - Model Privacy Form

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    .... The model form must be printed on white or light color paper (such as cream) with black or other... in color. (e) Languages. The model form may be translated into languages other than English. C... under this part, must comply with section 624 of the FCRA and 12 CFR part 41, subpart C, with respect...

  18. 12 CFR Appendix A to Part 40 - Model Privacy Form

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    .... The model form must be printed on white or light color paper (such as cream) with black or other... in color. (e) Languages. The model form may be translated into languages other than English. C... under this part, must comply with section 624 of the FCRA and 12 CFR part 41, subpart C, with respect...

  19. Measuring and modeling diffuse scattering in protein X-ray crystallography

    PubMed Central

    Van Benschoten, Andrew H.; Liu, Lin; Gonzalez, Ana; Brewster, Aaron S.; Sauter, Nicholas K.; Wall, Michael E.

    2016-01-01

    X-ray diffraction has the potential to provide rich information about the structural dynamics of macromolecules. To realize this potential, both Bragg scattering, which is currently used to derive macromolecular structures, and diffuse scattering, which reports on correlations in charge density variations, must be measured. Until now, measurement of diffuse scattering from protein crystals has been scarce because of the extra effort of collecting diffuse data. Here, we present 3D measurements of diffuse intensity collected from crystals of the enzymes cyclophilin A and trypsin. The measurements were obtained from the same X-ray diffraction images as the Bragg data, using best practices for standard data collection. To model the underlying dynamics in a practical way that could be used during structure refinement, we tested translation–libration–screw (TLS), liquid-like motions (LLM), and coarse-grained normal-modes (NM) models of protein motions. The LLM model provides a global picture of motions and was refined against the diffuse data, whereas the TLS and NM models provide more detailed and distinct descriptions of atom displacements, and only used information from the Bragg data. Whereas different TLS groupings yielded similar Bragg intensities, they yielded different diffuse intensities, none of which agreed well with the data. In contrast, both the LLM and NM models agreed substantially with the diffuse data. These results demonstrate a realistic path to increase the number of diffuse datasets available to the wider biosciences community and indicate that dynamics-inspired NM structural models can simultaneously agree with both Bragg and diffuse scattering. PMID:27035972

  20. Measuring and modeling diffuse scattering in protein X-ray crystallography

    DOE PAGESBeta

    Van Benschoten, Andrew H.; Liu, Lin; Gonzalez, Ana; Brewster, Aaron S.; Sauter, Nicholas K.; Fraser, James S.; Wall, Michael E.

    2016-03-28

    X-ray diffraction has the potential to provide rich information about the structural dynamics of macromolecules. To realize this potential, both Bragg scattering, which is currently used to derive macromolecular structures, and diffuse scattering, which reports on correlations in charge density variations, must be measured. Until now, measurement of diffuse scattering from protein crystals has been scarce because of the extra effort of collecting diffuse data. Here, we present 3D measurements of diffuse intensity collected from crystals of the enzymes cyclophilin A and trypsin. The measurements were obtained from the same X-ray diffraction images as the Bragg data, using best practicesmore » for standard data collection. To model the underlying dynamics in a practical way that could be used during structure refinement, we tested translation–libration–screw (TLS), liquid-like motions (LLM), and coarse-grained normal-modes (NM) models of protein motions. The LLM model provides a global picture of motions and was refined against the diffuse data, whereas the TLS and NM models provide more detailed and distinct descriptions of atom displacements, and only used information from the Bragg data. Whereas different TLS groupings yielded similar Bragg intensities, they yielded different diffuse intensities, none of which agreed well with the data. In contrast, both the LLM and NM models agreed substantially with the diffuse data. In conclusion, these results demonstrate a realistic path to increase the number of diffuse datasets available to the wider biosciences community and indicate that dynamics-inspired NM structural models can simultaneously agree with both Bragg and diffuse scattering.« less

  1. Mathematical modeling of hydrolysate diffusion and utilization in cellulolytic biofilms of the extreme thermophile Caldicellulosiruptor obsidiansis

    SciTech Connect

    Wang, Zhiwu; Hamilton-Brehm, Scott; Lochner, Adriane; Elkins, James G; Morrell-Falvey, Jennifer L

    2011-01-01

    Abstract: The morphological and structural properties of microbial biofilms are influenced by internal substrate diffusion and utilization processes. In the case of microbial hydrolysis of plant cell walls, only thin and uniform biofilm structures are typically formed by cellulolytic microorganisms. In this study, we develop a hydrolysate diffusion and utilization model system to examine factors influencing cellulolytic biofilm formation. Model simulations using Caldicellulosiruptor obsidiansis as a representative organism, reveal that the growth of the cellulolytic biofilm is limited by hydrolysate utilization but not diffusion. As a consequence, the cellulolytic biofilm has a uniform growth rate, and there is a hydrolysate surplus that diffuses through the cellulolytic biofilm into the bulk solution where it is consumed by planktonic cells. Predictions based on the model were tested in a cellulose fermentation study and the results are consistent with the model and previously reported experimental data. The factors determining the rate-limiting step of biofilm growth are also analyzed.

  2. A Functional Model for Teaching Osmosis-Diffusion to Biology Students

    ERIC Educational Resources Information Center

    Olsen, Richard W.; Petry, Douglas E.

    1976-01-01

    Described is a maternal-fetal model, operated by the student, to teach osmosis-diffusion to biology students. Included are materials needed, assembly instructions, and student operating procedures. (SL)

  3. Degenerate mobilities in phase field models are insufficient to capture surface diffusion

    NASA Astrophysics Data System (ADS)

    Lee, Alpha A.; Münch, Andreas; Süli, Endre

    2015-08-01

    Phase field models frequently provide insight into phase transitions and are robust numerical tools to solve free boundary problems corresponding to the motion of interfaces. A body of prior literature suggests that interface motion via surface diffusion is the long-time, sharp interface limit of microscopic phase field models such as the Cahn-Hilliard equation with a degenerate mobility function. Contrary to this conventional wisdom, we show that the long-time behaviour of degenerate Cahn-Hilliard equation with a polynomial free energy undergoes coarsening, reflecting the presence of bulk diffusion, rather than pure surface diffusion. This reveals an important limitation of phase field models that are frequently used to model surface diffusion.

  4. Epidemic model for information diffusion in web forums: experiments in marketing exchange and political dialog.

    PubMed

    Woo, Jiyoung; Chen, Hsinchun

    2016-01-01

    As social media has become more prevalent, its influence on business, politics, and society has become significant. Due to easy access and interaction between large numbers of users, information diffuses in an epidemic style on the web. Understanding the mechanisms of information diffusion through these new publication methods is important for political and marketing purposes. Among social media, web forums, where people in online communities disseminate and receive information, provide a good environment for examining information diffusion. In this paper, we model topic diffusion in web forums using the epidemiology model, the susceptible-infected-recovered (SIR) model, frequently used in previous research to analyze both disease outbreaks and knowledge diffusion. The model was evaluated on a large longitudinal dataset from the web forum of a major retail company and from a general political discussion forum. The fitting results showed that the SIR model is a plausible model to describe the diffusion process of a topic. This research shows that epidemic models can expand their application areas to topic discussion on the web, particularly social media such as web forums.

  5. Epidemic model for information diffusion in web forums: experiments in marketing exchange and political dialog.

    PubMed

    Woo, Jiyoung; Chen, Hsinchun

    2016-01-01

    As social media has become more prevalent, its influence on business, politics, and society has become significant. Due to easy access and interaction between large numbers of users, information diffuses in an epidemic style on the web. Understanding the mechanisms of information diffusion through these new publication methods is important for political and marketing purposes. Among social media, web forums, where people in online communities disseminate and receive information, provide a good environment for examining information diffusion. In this paper, we model topic diffusion in web forums using the epidemiology model, the susceptible-infected-recovered (SIR) model, frequently used in previous research to analyze both disease outbreaks and knowledge diffusion. The model was evaluated on a large longitudinal dataset from the web forum of a major retail company and from a general political discussion forum. The fitting results showed that the SIR model is a plausible model to describe the diffusion process of a topic. This research shows that epidemic models can expand their application areas to topic discussion on the web, particularly social media such as web forums. PMID:26839759

  6. Models of diffusion-limited uptake of trace elements in fossils and rates of fossilization

    NASA Astrophysics Data System (ADS)

    Kohn, Matthew J.

    2008-08-01

    Many fossils are assumed to take up trace elements by a process of combined diffusion plus adsorption (DA), yet in principle composition profiles can be explained by several different diffusion-limited processes, including diffusion plus reaction or recrystallization (DR) and double-medium diffusion (DMD). The DA and DMD models are supported by REE and U composition profiles across fossil teeth, measured by laser-ablation ICP-MS, that show error-function - like diffusion profiles into enamel from the dentine-enamel interface and concentrations in the interior of enamel that are at original biogenic levels or higher. Published composition and age profiles in some Pleistocene bones may be better explained by a DR model. All three diffusion models imply linear behavior between age and distance squared, vastly simplifying U-series dating methods for Pleistocene fossils. Modeled uptake rates for fossil teeth yield a strict minimum bound on durations of about one decade to one century. The similarity of diffusion profiles in teeth, irrespective of depositional ages ranging from ˜30 ka to >30 Ma, implies that uptake occurred quickly, with a maximum duration of a few tens of kyr for typical fossil enamel; faster uptake is implied for typical fossil bone and dentine. Disparities in these uptake estimates compared to some archeological bone may reflect sampling and preservation bias for paleontological vs. archeological materials.

  7. Application of a diffusion-desorption rate equation model in astrochemistry.

    PubMed

    He, Jiao; Vidali, Gianfranco

    2014-01-01

    Desorption and diffusion are two of the most important processes on interstellar grain surfaces; knowledge of them is critical for the understanding of chemical reaction networks in the interstellar medium (ISM). However, a lack of information on desorption and diffusion is preventing further progress in astrochemistry. To obtain desorption energy distributions of molecules from the surfaces of ISM-related materials, one usually carries out adsorption-desorption temperature programmed desorption (TPD) experiments, and uses rate equation models to extract desorption energy distributions. However, the often-used rate equation models fail to adequately take into account diffusion processes and thus are only valid in situations where adsorption is strongly localized. As adsorption-desorption experiments show that adsorbate molecules tend to occupy deep adsorption sites before occupying shallow ones, a diffusion process must be involved. Thus, it is necessary to include a diffusion term in the model that takes into account the morphology of the surface as obtained from analyses of TPD experiments. We take the experimental data of CO desorption from the MgO(100) surface and of D2 desorption from amorphous solid water ice as examples to show how a diffusion-desorption rate equation model explains the redistribution of adsorbate molecules among different adsorption sites. We extract distributions of desorption energies and diffusion energy barriers from TPD profiles. These examples are contrasted with a system where adsorption is strongly localized--HD from an amorphous silicate surface. Suggestions for experimental investigations are provided.

  8. Langevin dynamics modeling of the water diffusion tensor in partially aligned collagen networks

    NASA Astrophysics Data System (ADS)

    Powell, Sean K.; Momot, Konstantin I.

    2012-09-01

    In this work, a Langevin dynamics model of the diffusion of water in articular cartilage was developed. Numerical simulations of the translational dynamics of water molecules and their interaction with collagen fibers were used to study the quantitative relationship between the organization of the collagen fiber network and the diffusion tensor of water in model cartilage. Langevin dynamics was used to simulate water diffusion in both ordered and partially disordered cartilage models. In addition, an analytical approach was developed to estimate the diffusion tensor for a network comprising a given distribution of fiber orientations. The key findings are that (1) an approximately linear relationship was observed between collagen volume fraction and the fractional anisotropy of the diffusion tensor in fiber networks of a given degree of alignment, (2) for any given fiber volume fraction, fractional anisotropy follows a fiber alignment dependency similar to the square of the second Legendre polynomial of cos(θ), with the minimum anisotropy occurring at approximately the magic angle (θMA), and (3) a decrease in the principal eigenvalue and an increase in the transverse eigenvalues is observed as the fiber orientation angle θ progresses from 0∘ to 90∘. The corresponding diffusion ellipsoids are prolate for θ<θMA, spherical for θ≈θMA, and oblate for θ>θMA. Expansion of the model to include discrimination between the combined effects of alignment disorder and collagen fiber volume fraction on the diffusion tensor is discussed.

  9. First principles calculations of alloying element diffusion coefficients in Ni using the five-frequency model

    NASA Astrophysics Data System (ADS)

    Wu, Qiong; Li, Shu-Suo; Ma, Yue; Gong, Sheng-Kai

    2012-10-01

    The diffusion coefficients of several alloying elements (Al, Mo, Co, Ta, Ru, W, Cr, Re) in Ni are directly calculated using the five-frequency model and the first principles density functional theory. The correlation factors provided by the five-frequency model are explicitly calculated. The calculated diffusion coefficients show their excellent agreement with the available experimental data. Both the diffusion pre-factor (D0) and the activation energy (Q) of impurity diffusion are obtained. The diffusion coefficients above 700 K are sorted in the following order: DAl > DCr > DCo > DTa > DMo > DRu > DW > DRe. It is found that there is a positive correlation between the atomic radius of the solute and the jump energy of Ni that results in the rotation of the solute-vacancy pair (E1). The value of E2-E1 (E2 is the solute diffusion energy) and the correlation factor each also show a positive correlation. The larger atoms in the same series have lower diffusion activation energies and faster diffusion coefficients.

  10. A model for the compositions of non-stoichiometric intermediate phases formed by diffusion reactions, and its application to Nb3Sn superconductors

    PubMed Central

    Xu, X.; Sumption, M. D.

    2016-01-01

    In this work we explore the compositions of non-stoichiometric intermediate phases formed by diffusion reactions: a mathematical framework is developed and tested against the specific case of Nb3Sn superconductors. In the first part, the governing equations for the bulk diffusion and inter-phase interface reactions during the growth of a compound are derived, numerical solutions to which give both the composition profile and growth rate of the compound layer. The analytic solutions are obtained with certain approximations made. In the second part, we explain an effect that the composition characteristics of compounds can be quite different depending on whether it is the bulk diffusion or grain boundary diffusion that dominates in the compounds, and that “frozen” bulk diffusion leads to unique composition characteristics that the bulk composition of a compound layer remains unchanged after its initial formation instead of varying with the diffusion reaction system; here the model is modified for the case of grain boundary diffusion. Finally, we apply this model to the Nb3Sn superconductors and propose approaches to control their compositions. PMID:26754774

  11. Modelling oxygen self-diffusion in UO2 under pressure

    SciTech Connect

    Cooper, Michael William D.; Grimes, R. W.; Fitzpatrick, M. E.; Chroneos, A.

    2015-10-22

    Access to values for oxygen self-diffusion over a range of temperatures and pressures in UO2 is important to nuclear fuel applications. Here, elastic and expansivity data are used in the framework of a thermodynamic model, the cBΩ model, to derive the oxygen self-diffusion coefficient in UO2 over a range of pressures (0–10 GPa) and temperatures (300–1900 K). Furthermore, the significant reduction in oxygen self-diffusion as a function of increasing hydrostatic pressure, and the associated increase in activation energy, is identified.

  12. Reaction-diffusion processes and epidemic metapopulation models in complex networks

    NASA Astrophysics Data System (ADS)

    Vespignani, A.

    2008-08-01

    The correct description of reaction-diffusion phenomena requires a detailed knowledge of the contact networks defining the interactions between individuals and groups of individuals. For this reason, the study of reaction-diffusion processes has been recently widened with opportune models and methods dealing with the heterogeneity and large scale fluctuations observed in many real world networks. Here we present a brief overview of some recent results on reaction-diffusion processes in complex networks which provide useful insights into the dynamic behavior of epidemic metapopulation models.

  13. A qualitative model for aggregation and diffusion of β-amyloid in Alzheimer's disease.

    PubMed

    Achdou, Yves; Franchi, Bruno; Marcello, Norina; Tesi, Maria Carla

    2013-12-01

    In this paper we present a mathematical model for the aggregation and diffusion of Aβ amyloid in the brain affected by Alzheimer's disease, at the early stage of the disease. The model is based on a classical discrete Smoluchowski aggregation equation modified to take diffusion into account. We also describe a numerical scheme and discuss the results of the simulations in the light of the recent biomedical literature.

  14. Efficient simulation of diffusion-based choice RT models on CPU and GPU.

    PubMed

    Verdonck, Stijn; Meers, Kristof; Tuerlinckx, Francis

    2016-03-01

    In this paper, we present software for the efficient simulation of a broad class of linear and nonlinear diffusion models for choice RT, using either CPU or graphical processing unit (GPU) technology. The software is readily accessible from the popular scripting languages MATLAB and R (both 64-bit). The speed obtained on a single high-end GPU is comparable to that of a small CPU cluster, bringing standard statistical inference of complex diffusion models to the desktop platform.

  15. Diffuse-interface modeling of liquid-vapor coexistence in equilibrium drops using smoothed particle hydrodynamics

    NASA Astrophysics Data System (ADS)

    Sigalotti, Leonardo Di G.; Troconis, Jorge; Sira, Eloy; Peña-Polo, Franklin; Klapp, Jaime

    2014-07-01

    We study numerically liquid-vapor phase separation in two-dimensional, nonisothermal, van der Waals (vdW) liquid drops using the method of smoothed particle hydrodynamics (SPH). In contrast to previous SPH simulations of drop formation, our approach is fully adaptive and follows the diffuse-interface model for a single-component fluid, where a reversible, capillary (Korteweg) force is added to the equations of motion to model the rapid but smooth transition of physical quantities through the interface separating the bulk phases. Surface tension arises naturally from the cohesive part of the vdW equation of state and the capillary forces. The drop models all start from a square-shaped liquid and spinodal decomposition is investigated for a range of initial densities and temperatures. The simulations predict the formation of stable, subcritical liquid drops with a vapor atmosphere, with the densities and temperatures of coexisting liquid and vapor in the vdW phase diagram closely matching the binodal curve. We find that the values of surface tension, as determined from the Young-Laplace equation, are in good agreement with the results of independent numerical simulations and experimental data. The models also predict the increase of the vapor pressure with temperature and the fitting to the numerical data reproduces very well the Clausius-Clapeyron relation, thus allowing for the calculation of the vaporization pressure for this vdW fluid.

  16. Modeling controlled nutrient release from polymer coated fertilizers: diffusion release from single granules.

    PubMed

    Shaviv, Avi; Raban, Smadar; Zaidel, Elina

    2003-05-15

    A comprehensive model describing the complex and "non-Fickian" (mathematically nonlinear) nature of the release from single granules of membrane coated, controlled release fertilizers (CRFs) is proposed consisting of three stages: i. a lag period during which water penetrates the coating of the granule dissolving part of the solid fertilizer in it ii. a period of linear release during which water penetration into and release out occur concomitantly while the total volume of the granules remains practically constant; and iii. a period of "decaying release", starting as the concentration inside the granule starts to decrease. A mathematical model was developed based on vapor and nutrient diffusion equations. The model predicts the release stages in terms of measurable geometrical and chemophysical parameters such as the following: the product of granule radius and coating thickness, water and solute permeability, saturation concentration of the fertilizer, and its density. The model successfully predicts the complex and "sigmoidal" pattern of release that is essential for matching plant temporal demand to ensure high agronomic and environmental effectiveness. It also lends itself to more complex statistical formulations which account for the large variability within large populations of coated CRFs and can serve for further improving CRF production and performance. PMID:12785532

  17. Diffuse-interface modeling of liquid-vapor coexistence in equilibrium drops using smoothed particle hydrodynamics.

    PubMed

    Sigalotti, Leonardo Di G; Troconis, Jorge; Sira, Eloy; Peña-Polo, Franklin; Klapp, Jaime

    2014-07-01

    We study numerically liquid-vapor phase separation in two-dimensional, nonisothermal, van der Waals (vdW) liquid drops using the method of smoothed particle hydrodynamics (SPH). In contrast to previous SPH simulations of drop formation, our approach is fully adaptive and follows the diffuse-interface model for a single-component fluid, where a reversible, capillary (Korteweg) force is added to the equations of motion to model the rapid but smooth transition of physical quantities through the interface separating the bulk phases. Surface tension arises naturally from the cohesive part of the vdW equation of state and the capillary forces. The drop models all start from a square-shaped liquid and spinodal decomposition is investigated for a range of initial densities and temperatures. The simulations predict the formation of stable, subcritical liquid drops with a vapor atmosphere, with the densities and temperatures of coexisting liquid and vapor in the vdW phase diagram closely matching the binodal curve. We find that the values of surface tension, as determined from the Young-Laplace equation, are in good agreement with the results of independent numerical simulations and experimental data. The models also predict the increase of the vapor pressure with temperature and the fitting to the numerical data reproduces very well the Clausius-Clapeyron relation, thus allowing for the calculation of the vaporization pressure for this vdW fluid. PMID:25122383

  18. Diffuse-interface modeling of liquid-vapor coexistence in equilibrium drops using smoothed particle hydrodynamics

    NASA Astrophysics Data System (ADS)

    Klapp, Jaime; di G Sigalotti, Leonardo; Troconis, Jorge; Sira, Eloy; Pena, Franklin; ININ-IVIC Team; Cinvestav-UAM-A Team

    2014-11-01

    We study numerically liquid-vapor phase separation in two-dimensional, nonisothermal, van der Waals (vdW) liquid drops using the method of Smoothed Particle Hydrodynamics (SPH). In contrast to previous SPH simulations of drop formation, our approach is fully adaptive and follows the diffuse interface model for a single-component fluid, where a reversible, capillary (Korteweg) force is added to the equations of motion to model the rapid but smooth transition of physical quantities through the interface separating the bulk phases. Surface tension arises naturally from the cohesive part of the vdW equation of state and the capillary forces. The drop models all start from a square-shaped liquid and spinodal decomposition is investigated for a range of initial densities and temperatures. The simulations predict the formation of stable, subcritical liquid drops with a vapor atmosphere, with the densities and temperatures of coexisting liquid and vapor in the vdW phase diagram closely matching the binodal curve. We find that the values of surface tension, as determined from the Young-Laplace equation, are in good agreement with the results of independent numerical simulations and experimental data. The models also predict the increase of the vapor pressure with temperature and the fitting to the numerical data reproduces very well the Clausius-Clapeyron relation, thus allowing for the calculation of the vaporization pressure for this vdW fluid. Cinvestav-Abacus.

  19. Diffuse-interface modeling of liquid-vapor coexistence in equilibrium drops using smoothed particle hydrodynamics.

    PubMed

    Sigalotti, Leonardo Di G; Troconis, Jorge; Sira, Eloy; Peña-Polo, Franklin; Klapp, Jaime

    2014-07-01

    We study numerically liquid-vapor phase separation in two-dimensional, nonisothermal, van der Waals (vdW) liquid drops using the method of smoothed particle hydrodynamics (SPH). In contrast to previous SPH simulations of drop formation, our approach is fully adaptive and follows the diffuse-interface model for a single-component fluid, where a reversible, capillary (Korteweg) force is added to the equations of motion to model the rapid but smooth transition of physical quantities through the interface separating the bulk phases. Surface tension arises naturally from the cohesive part of the vdW equation of state and the capillary forces. The drop models all start from a square-shaped liquid and spinodal decomposition is investigated for a range of initial densities and temperatures. The simulations predict the formation of stable, subcritical liquid drops with a vapor atmosphere, with the densities and temperatures of coexisting liquid and vapor in the vdW phase diagram closely matching the binodal curve. We find that the values of surface tension, as determined from the Young-Laplace equation, are in good agreement with the results of independent numerical simulations and experimental data. The models also predict the increase of the vapor pressure with temperature and the fitting to the numerical data reproduces very well the Clausius-Clapeyron relation, thus allowing for the calculation of the vaporization pressure for this vdW fluid.

  20. Modeling controlled nutrient release from polymer coated fertilizers: diffusion release from single granules.

    PubMed

    Shaviv, Avi; Raban, Smadar; Zaidel, Elina

    2003-05-15

    A comprehensive model describing the complex and "non-Fickian" (mathematically nonlinear) nature of the release from single granules of membrane coated, controlled release fertilizers (CRFs) is proposed consisting of three stages: i. a lag period during which water penetrates the coating of the granule dissolving part of the solid fertilizer in it ii. a period of linear release during which water penetration into and release out occur concomitantly while the total volume of the granules remains practically constant; and iii. a period of "decaying release", starting as the concentration inside the granule starts to decrease. A mathematical model was developed based on vapor and nutrient diffusion equations. The model predicts the release stages in terms of measurable geometrical and chemophysical parameters such as the following: the product of granule radius and coating thickness, water and solute permeability, saturation concentration of the fertilizer, and its density. The model successfully predicts the complex and "sigmoidal" pattern of release that is essential for matching plant temporal demand to ensure high agronomic and environmental effectiveness. It also lends itself to more complex statistical formulations which account for the large variability within large populations of coated CRFs and can serve for further improving CRF production and performance.

  1. Modeling of diffusion mechanism of conductive channel oxidation in a Pt/NiO/Pt memory switching structure

    NASA Astrophysics Data System (ADS)

    Sysun, V. I.; Bute, I. V.; Boriskov, P. P.

    2016-09-01

    The transition process from the low resistance state into the high resistance state in a Pt/NiO/Pt memory switching structure has been studied by numerical modeling. Detailed analysis shows, that thermally induced diffusion oxidation by nickel vacancies is the key factor for distortion of the channel metallic conductivity. Spatial dynamics of the process of oxidation defines channel narrowing mainly in its central part, and also sets the critical current through the structure sufficient for final rupture of the channel and the transition to high resistance state. The increase in critical current above the limit even by 10% reduces the switching time by an order of magnitude, which is in agreement with experiments. The developed radial diffusion model of conductive channel (or filaments) oxidation may be suitable for the analysis of switching effect a number of other ReRAM oxide structures.

  2. Delay-induced Turing-like waves for one-species reaction-diffusion model on a network

    NASA Astrophysics Data System (ADS)

    Petit, Julien; Carletti, Timoteo; Asllani, Malbor; Fanelli, Duccio

    2015-09-01

    A one-species time-delay reaction-diffusion system defined on a complex network is studied. Traveling waves are predicted to occur following a symmetry-breaking instability of a homogeneous stationary stable solution, subject to an external nonhomogeneous perturbation. These are generalized Turing-like waves that materialize in a single-species populations dynamics model, as the unexpected byproduct of the imposed delay in the diffusion part. Sufficient conditions for the onset of the instability are mathematically provided by performing a linear stability analysis adapted to time-delayed differential equations. The method here developed exploits the properties of the Lambert W-function. The prediction of the theory are confirmed by direct numerical simulation carried out for a modified version of the classical Fisher model, defined on a Watts-Strogatz network and with the inclusion of the delay.

  3. A diffuse plate boundary model for Indian Ocean tectonics

    NASA Technical Reports Server (NTRS)

    Wiens, D. A.; Demets, C.; Gordon, R. G.; Stein, S.; Argus, D.

    1985-01-01

    It is suggested that motion along the virtually aseismic Owen fracture zone is negligible, so that Arabia and India are contained within a single Indo-Arabian plate divided from the Australian plate by a diffuse boundary. The boundary is a zone of concentrated seismicity and deformation commonly characterized as 'intraplate'. The rotation vector of Australia relative to Indo-Arabia is consistent with the seismologically observed 2 cm/yr of left-lateral strike-slip along the Ninetyeast Ridge, north-south compression in the Central Indian Ocean, and the north-south extension near Chagos.

  4. Electrochemical measurement of lateral diffusion coefficients of ubiquinones and plastoquinones of various isoprenoid chain lengths incorporated in model bilayers.

    PubMed Central

    Marchal, D; Boireau, W; Laval, J M; Moiroux, J; Bourdillon, C

    1998-01-01

    The long-range diffusion coefficients of isoprenoid quinones in a model of lipid bilayer were determined by a method avoiding fluorescent probe labeling of the molecules. The quinone electron carriers were incorporated in supported dimyristoylphosphatidylcholine layers at physiological molar fractions (<3 mol%). The elaborate bilayer template contained a built-in gold electrode at which the redox molecules solubilized in the bilayer were reduced or oxidized. The lateral diffusion coefficient of a natural quinone like UQ10 or PQ9 was 2.0 +/- 0.4 x 10(-8) cm2 s(-1) at 30 degrees C, two to three times smaller than the diffusion coefficient of a lipid analog in the same artificial bilayer. The lateral mobilities of the oxidized or reduced forms could be determined separately and were found to be identical in the 4-13 pH range. For a series of isoprenoid quinones, UQ2 or PQ2 to UQ10, the diffusion coefficient exhibited a marked dependence on the length of the isoprenoid chain. The data fit very well the quantitative behavior predicted by a continuum fluid model in which the isoprenoid chains are taken as rigid particles moving in the less viscous part of the bilayer and rubbing against the more viscous layers of lipid heads. The present study supports the concept of a homogeneous pool of quinone located in the less viscous region of the bilayer. PMID:9545054

  5. Advances in modeling sorption and diffusion of moisture in porous reactive materials.

    PubMed

    Harley, Stephen J; Glascoe, Elizabeth A; Lewicki, James P; Maxwell, Robert S

    2014-06-23

    Water-vapor-uptake experiments were performed on a silica-filled poly(dimethylsiloxane) (PDMS) network and modeled by using two different approaches. The data was modeled by using established methods and the model parameters were used to predict moisture uptake in a sample. The predictions are reasonably good, but not outstanding; many of the shortcomings of the modeling are discussed. A high-fidelity modeling approach is derived and used to improve the modeling of moisture uptake and diffusion. Our modeling approach captures the physics and kinetics of diffusion and adsorption/desorption, simultaneously. It predicts uptake better than the established method; more importantly, it is also able to predict outgassing. The material used for these studies is a filled-PDMS network; physical interpretations concerning the sorption and diffusion of moisture in this network are discussed.

  6. The role of tissue microstructure and water exchange in biophysical modelling of diffusion in white matter.

    PubMed

    Nilsson, Markus; van Westen, Danielle; Ståhlberg, Freddy; Sundgren, Pia C; Lätt, Jimmy

    2013-08-01

    Biophysical models that describe the outcome of white matter diffusion MRI experiments have various degrees of complexity. While the simplest models assume equal-sized and parallel axons, more elaborate ones may include distributions of axon diameters and axonal orientation dispersions. These microstructural features can be inferred from diffusion-weighted signal attenuation curves by solving an inverse problem, validated in several Monte Carlo simulation studies. Model development has been paralleled by microscopy studies of the microstructure of excised and fixed nerves, confirming that axon diameter estimates from diffusion measurements agree with those from microscopy. However, results obtained in vivo are less conclusive. For example, the amount of slowly diffusing water is lower than expected, and the diffusion-encoded signal is apparently insensitive to diffusion time variations, contrary to what may be expected. Recent understandings of the resolution limit in diffusion MRI, the rate of water exchange, and the presence of microscopic axonal undulation and axonal orientation dispersions may, however, explain such apparent contradictions. Knowledge of the effects of biophysical mechanisms on water diffusion in tissue can be used to predict the outcome of diffusion tensor imaging (DTI) and of diffusion kurtosis imaging (DKI) studies. Alterations of DTI or DKI parameters found in studies of pathologies such as ischemic stroke can thus be compared with those predicted by modelling. Observations in agreement with the predictions strengthen the credibility of biophysical models; those in disagreement could provide clues of how to improve them. DKI is particularly suited for this purpose; it is performed using higher b-values than DTI, and thus carries more information about the tissue microstructure. The purpose of this review is to provide an update on the current understanding of how various properties of the tissue microstructure and the rate of water exchange

  7. Comparison and analysis of theoretical models for diffusion-controlled dissolution.

    PubMed

    Wang, Yanxing; Abrahamsson, Bertil; Lindfors, Lennart; Brasseur, James G

    2012-05-01

    Dissolution models require, at their core, an accurate diffusion model. The accuracy of the model for diffusion-dominated dissolution is particularly important with the trend toward micro- and nanoscale drug particles. Often such models are based on the concept of a "diffusion layer." Here a framework is developed for diffusion-dominated dissolution models, and we discuss the inadequacy of classical models that are based on an unphysical constant diffusion layer thickness assumption, or do not correctly modify dissolution rate due to "confinement effects": (1) the increase in bulk concentration from confinement of the dissolution process, (2) the modification of the flux model (the Sherwood number) by confinement. We derive the exact mathematical solution for a spherical particle in a confined fluid with impermeable boundaries. Using this solution, we analyze the accuracy of a time-dependent "infinite domain model" (IDM) and "quasi steady-state model" (QSM), both formally derived for infinite domains but which can be applied in approximate fashion to confined dissolution with proper adjustment of a concentration parameter. We show that dissolution rate is sensitive to the degree of confinement or, equivalently, to the total concentration C(tot). The most practical model, the QSM, is shown to be very accurate for most applications and, consequently, can be used with confidence in design-level dissolution models so long as confinement is accurately treated. The QSM predicts the ratio of diffusion layer thickness to particle radius (the Sherwood number) as a constant plus a correction that depends on the degree of confinement. The QSM also predicts that the time required for complete saturation or dissolution in diffusion-controlled dissolution experiments is singular (i.e., infinite) when total concentration equals the solubility. Using the QSM, we show that measured differences in dissolution rate in a diffusion-controlled dissolution experiment are a result of

  8. Measurement and modeling of CO2 diffusion coefficient in Saline Aquifer at reservoir conditions

    NASA Astrophysics Data System (ADS)

    Azin, Reza; Mahmoudy, Mohamad; Raad, Seyed Mostafa Jafari; Osfouri, Shahriar

    2013-12-01

    Storage of CO2 in deep saline aquifers is a promising techniques to mitigate global warming and reduce greenhouse gases (GHG). Correct measurement of diffusivity is essential for predicting rate of transfer and cumulative amount of trapped gas. Little information is available on diffusion of GHG in saline aquifers. In this study, diffusivity of CO2 into a saline aquifer taken from oil field was measured and modeled. Equilibrium concentration of CO2 at gas-liquid interface was determined using Henry's law. Experimental measurements were reported at temperature and pressure ranges of 32-50°C and 5900-6900 kPa, respectively. Results show that diffusivity of CO2 varies between 3.52-5.98×10-9 m2/s for 5900 kPa and 5.33-6.16×10-9 m2/s for 6900 kPa initial pressure. Also, it was found that both pressure and temperature have a positive impact on the measures of diffusion coefficient. Liquid swelling due to gas dissolution and variations in gas compressibility factor as a result of pressure decay was found negligible. Measured diffusivities were used model the physical model and develop concentration profile of dissolved gas in the liquid phase. Results of this study provide unique measures of CO2 diffusion coefficient in saline aquifer at high pressure and temperature conditions, which can be applied in full-field studies of carbon capture and sequestration projects.

  9. The Diffuse Galactic Gamma-Ray Emission Model for GLAST LAT

    SciTech Connect

    Porter, T.A.; Digel, S.W.; Grenier, I.A.; Moskalenko, I.V.; Strong, A.W.; /Garching, Max Planck Inst., MPE

    2007-06-13

    Diffuse emission from the Milky Way dominates the gamma-ray sky. About 80% of the high-energy luminosity of the Milky Way comes from processes in the interstellar medium. The Galactic diffuse emission traces interactions of energetic particles, primarily protons and electrons, with the interstellar gas and radiation field, thus delivering information about cosmic-ray spectra and interstellar mass in distant locations. Additionally, the Galactic diffuse emission is the celestial foreground for the study of gamma-ray point sources and the extragalactic diffuse gamma-ray emission. We will report on the latest developments in the modeling of the Galactic diffuse emission, which will be used for the Gamma Ray Large Area Space Telescope (GLAST) investigations.

  10. Symmetry breaking in a bulk-surface reaction-diffusion model for signalling networks

    NASA Astrophysics Data System (ADS)

    Rätz, Andreas; Röger, Matthias

    2014-08-01

    Signalling molecules play an important role for many cellular functions. We investigate here a general system of two membrane reaction-diffusion equations coupled to a diffusion equation inside the cell by a Robin-type boundary condition and a flux term in the membrane equations. A specific model of this form was recently proposed by the authors for the GTPase cycle in cells. We investigate here a putative role of diffusive instabilities in cell polarization. By a linearized stability analysis, we identify two different mechanisms. The first resembles a classical Turing instability for the membrane subsystem and requires (unrealistically) large differences in the lateral diffusion of activator and substrate. On the other hand, the second possibility is induced by the difference in cytosolic and lateral diffusion and appears much more realistic. We complement our theoretical analysis by numerical simulations that confirm the new stability mechanism and allow us to investigate the evolution beyond the regime where the linearization applies.

  11. [Estimation of the indoor diffusion of asbestos fibers with the diffusion model for the external environment of Pasquill and Gifford].

    PubMed

    Bellassai, Debora; Spinazzola, Antonio; Silvestri, Stefano

    2015-01-01

    In absence of results of environmental monitoring to proceed with the assessment of occupational exposure, it was developed a model that retraces the one of Pasquill and Gifford, currently used for the estimation of concentrations of pollutants at certain distances from the source in outdoor environment. Purpose of the study is the quantitative estimate of the diffusion of airborne asbestos fibers in function of the distance from the source in an factory where railway carriages were produced during the period when asbestos was sprayed as insulator of the body. The treatment was carried out in a large shed without separation from other operations. The application of the model, given the characteristics of the emitting source, has allowed us to estimate the diffusion of particles inside the shed with an expected decrease in concentration inversely proportional to the distance from the source. By appropriate calculations the concentration by weight has been converted into number offibers by volume, the unit of measure currently used for the definition of asbestos pollution. PMID:26193738

  12. Applicable apparent diffusion coefficient of an orthotopic mouse model of gastric cancer by improved clinical MRI diffusion weighted imaging

    PubMed Central

    Sun, Jia; Zhang, Xiao-Peng; Li, Xiao-Ting; Tang, Lei; Cui, Yong; Zhang, Xiao-Yan; Sun, Ying-Shi

    2014-01-01

    In vivo imaging studies in animal models are hindered by variables that contribute to poor image quality and measurement reliability. As such we sought to improve the diffusion coefficient (ADC) of an orthotopic mouse model of gastric cancer in diffusion-weighted images (DWI) using alginate moulding and Ultrasonic coupling medium. BGC-823 human gastric cancer cells were subcutaneously injected into the abdomen of nude mice and 1 mm3 primary tumour was orthotopically transplanted. Alginate and coupling medium were applied to the mice and MRI (T2 and DWI) was performed for 6 weeks. Regions of interest (ROI) were drawn and liver and tumour ADC were evaluated. Using alginate moulding, the mean quality total score of DW imaging was 8.53; however, in control animals this value was 5.20 (p < 0.001). The coefficient of variation of ADC of liver in experimental and control groups were 0.071 and 0.270 (p < 0.001), respectively, suggesting this method may be helpful for DWI studies of important human diseases such as gastric cancer. PMID:25123166

  13. Random variability in mesoscale wind observations and implications for diffusion models

    SciTech Connect

    Hanna, S.R.

    1994-12-31

    The investigation reported in this paper grew out of a preliminary analysis of methods by which regional air quality models such as the Regional Oxidant Model account for horizontal transport and diffusion. It was discovered that there is a variety of often inconsistent methods used to parameterize horizontal diffusion at meso- and regional scales, and the time seemed ripe to review and compare and contrast these schemes. This paper provides a brief overview of the major issues that were uncovered and lists a few specific examples of the technical approaches that are used. Subsequent sections cover the basic physics of horizontal diffusion, the characteristics of observed wind fields, and methods of parameterizing horizontal diffusion in air quality models.

  14. Quasilinear model for energetic particle diffusion in radial and velocity space

    NASA Astrophysics Data System (ADS)

    Waltz, R. E.; Bass, E. M.; Staebler, G. M.

    2013-04-01

    A quasilinear model for passive energetic particle (EP) turbulent diffusion in radial and velocity space is fitted and tested against nonlinear gyrokinetic tokamak simulations with the GYRO code [J. Candy and R. E. Waltz, Phys. Rev. Lett. 91, 045001 (2003)]. Off diagonal elements of a symmetric positive definite 2×2 EP diffusion matrix account for fluxes up radial (energy) gradients driven by energy (radial) gradients of the EP velocity space distribution function. The quasilinear ratio kernel of the model is provided by a simple analytic formula for the EP radial and velocity space EP diffusivity relative to radial thermal ion energy diffusivity at each linear mode of the turbulence driven by the thermal plasma. The TGLF [G. M. Staebler, J. E. Kinsey, and R. E. Waltz, Phys. Plasmas 14, 0055909 (2007); ibid. 15, 0055908 (2008)] tokamak transport model provides the linear mode frequency and growth rates to the kernel as well as the nonlinear spectral weight for each mode.

  15. Quasilinear model for energetic particle diffusion in radial and velocity space

    SciTech Connect

    Waltz, R. E.; Staebler, G. M.; Bass, E. M.

    2013-04-15

    A quasilinear model for passive energetic particle (EP) turbulent diffusion in radial and velocity space is fitted and tested against nonlinear gyrokinetic tokamak simulations with the GYRO code [J. Candy and R. E. Waltz, Phys. Rev. Lett. 91, 045001 (2003)]. Off diagonal elements of a symmetric positive definite 2 Multiplication-Sign 2 EP diffusion matrix account for fluxes up radial (energy) gradients driven by energy (radial) gradients of the EP velocity space distribution function. The quasilinear ratio kernel of the model is provided by a simple analytic formula for the EP radial and velocity space EP diffusivity relative to radial thermal ion energy diffusivity at each linear mode of the turbulence driven by the thermal plasma. The TGLF [G. M. Staebler, J. E. Kinsey, and R. E. Waltz, Phys. Plasmas 14, 0055909 (2007); ibid. 15, 0055908 (2008)] tokamak transport model provides the linear mode frequency and growth rates to the kernel as well as the nonlinear spectral weight for each mode.

  16. Modelling the effect of diffuse light on canopy photosynthesis in controlled environments.

    PubMed

    Cavazzoni, James; Volk, Tyler; Tubiello, Francesco; Monje, Oscar

    2002-01-01

    A layered canopy model was used to analyze the effects of diffuse light on canopy gross photosynthesis in controlled environment plant growth chambers, where, in contrast to the field, highly diffuse light can occur at high irradiance. The model suggests that high diffuse light fractions (approximately 0.7) and irradiance (1400 micromoles m-2 s-1) may enhance crop life-cycle canopy gross photosynthesis for hydroponic wheat by about 20% compared to direct light at the same irradiance. Our simulations suggest that high accuracy is not needed in specifying diffuse light fractions in chambers between approximately 0.7 and 1, because simulated photosynthesis for closed canopies plateau in this range. We also examined the effect of leaf angle distribution on canopy photosynthesis under growth chamber conditions, as these distributions determine canopy extinction coefficients for direct and diffuse light. We show that the spherical leaf angle distribution is not suitable for modeling photosynthesis of planophile canopies (e.g., soybean and peanut) in growth chambers. Also, the absorption of the light reflected from the surface below the canopy should generally be included in model simulations, as the corresponding albedo values in the photosynthetically active range may be quite high in growth chambers (e.g., approximately 0.5). In addition to the modeling implications, our results suggest that diffuse light conditions should be considered when drawing conclusions from experiments in controlled environments.

  17. Modelling the effect of diffuse light on canopy photosynthesis in controlled environments

    NASA Technical Reports Server (NTRS)

    Cavazzoni, James; Volk, Tyler; Tubiello, Francesco; Monje, Oscar; Janes, H. W. (Principal Investigator)

    2002-01-01

    A layered canopy model was used to analyze the effects of diffuse light on canopy gross photosynthesis in controlled environment plant growth chambers, where, in contrast to the field, highly diffuse light can occur at high irradiance. The model suggests that high diffuse light fractions (approximately 0.7) and irradiance (1400 micromoles m-2 s-1) may enhance crop life-cycle canopy gross photosynthesis for hydroponic wheat by about 20% compared to direct light at the same irradiance. Our simulations suggest that high accuracy is not needed in specifying diffuse light fractions in chambers between approximately 0.7 and 1, because simulated photosynthesis for closed canopies plateau in this range. We also examined the effect of leaf angle distribution on canopy photosynthesis under growth chamber conditions, as these distributions determine canopy extinction coefficients for direct and diffuse light. We show that the spherical leaf angle distribution is not suitable for modeling photosynthesis of planophile canopies (e.g., soybean and peanut) in growth chambers. Also, the absorption of the light reflected from the surface below the canopy should generally be included in model simulations, as the corresponding albedo values in the photosynthetically active range may be quite high in growth chambers (e.g., approximately 0.5). In addition to the modeling implications, our results suggest that diffuse light conditions should be considered when drawing conclusions from experiments in controlled environments.

  18. Modelling the effect of diffuse light on canopy photosynthesis in controlled environments.

    PubMed

    Cavazzoni, James; Volk, Tyler; Tubiello, Francesco; Monje, Oscar

    2002-01-01

    A layered canopy model was used to analyze the effects of diffuse light on canopy gross photosynthesis in controlled environment plant growth chambers, where, in contrast to the field, highly diffuse light can occur at high irradiance. The model suggests that high diffuse light fractions (approximately 0.7) and irradiance (1400 micromoles m-2 s-1) may enhance crop life-cycle canopy gross photosynthesis for hydroponic wheat by about 20% compared to direct light at the same irradiance. Our simulations suggest that high accuracy is not needed in specifying diffuse light fractions in chambers between approximately 0.7 and 1, because simulated photosynthesis for closed canopies plateau in this range. We also examined the effect of leaf angle distribution on canopy photosynthesis under growth chamber conditions, as these distributions determine canopy extinction coefficients for direct and diffuse light. We show that the spherical leaf angle distribution is not suitable for modeling photosynthesis of planophile canopies (e.g., soybean and peanut) in growth chambers. Also, the absorption of the light reflected from the surface below the canopy should generally be included in model simulations, as the corresponding albedo values in the photosynthetically active range may be quite high in growth chambers (e.g., approximately 0.5). In addition to the modeling implications, our results suggest that diffuse light conditions should be considered when drawing conclusions from experiments in controlled environments. PMID:12882223

  19. A Bayesian hierarchical diffusion model decomposition of performance in Approach–Avoidance Tasks

    PubMed Central

    Krypotos, Angelos-Miltiadis; Beckers, Tom; Kindt, Merel; Wagenmakers, Eric-Jan

    2015-01-01

    Common methods for analysing response time (RT) tasks, frequently used across different disciplines of psychology, suffer from a number of limitations such as the failure to directly measure the underlying latent processes of interest and the inability to take into account the uncertainty associated with each individual's point estimate of performance. Here, we discuss a Bayesian hierarchical diffusion model and apply it to RT data. This model allows researchers to decompose performance into meaningful psychological processes and to account optimally for individual differences and commonalities, even with relatively sparse data. We highlight the advantages of the Bayesian hierarchical diffusion model decomposition by applying it to performance on Approach–Avoidance Tasks, widely used in the emotion and psychopathology literature. Model fits for two experimental data-sets demonstrate that the model performs well. The Bayesian hierarchical diffusion model overcomes important limitations of current analysis procedures and provides deeper insight in latent psychological processes of interest. PMID:25491372

  20. Diffusive to quasi-ballistic random laser: incoherent and coherent models

    NASA Astrophysics Data System (ADS)

    Guerin, W.; Chong, Y. D.; Baudouin, Q.; Liertzer, M.; Rotter, S.; Kaiser, R.

    2016-09-01

    We study the crossover between the diffusive and quasi-ballistic regimes of random lasers. In particular, we compare incoherent models based on the diffusion equation and the radiative transfer equation (RTE), which neglect all wave effects, with a coherent wave model for the random laser threshold. We show that both the incoherent and the coherent models predict qualitatively similar thresholds, with a smooth transition from a diffuse to a quasi-ballistic regime. The shape of the intensity distribution in the sample as predicted by the RTE model at threshold is also in good agreement with the coherent model. The approximate incoherent models thus provide useful analytical predictions for the threshold of random lasers as well as the shape of the random laser modes at threshold.

  1. Research article: Watershed management councils and scientific models: Using diffusion literature to explain adoption

    USGS Publications Warehouse

    King, M.D.; Burkardt, N.; Clark, B.T.

    2006-01-01

    Recent literature on the diffusion of innovations concentrates either specifically on public adoption of policy, where social or environmental conditions are the dependent variables for adoption, or on private adoption of an innovation, where emphasis is placed on the characteristics of the innovation itself. This article uses both the policy diffusion literature and the diffusion of innovation literature to assess watershed management councils' decisions to adopt, or not adopt, scientific models. Watershed management councils are a relevant case study because they possess both public and private attributes. We report on a survey of councils in the United States that was conducted to determine the criteria used when selecting scientific models for studying watershed conditions. We found that specific variables from each body of literature play a role in explaining the choice to adopt scientific models by these quasi-public organizations. The diffusion of innovation literature contributes to an understanding of how organizations select models by confirming the importance of a model's ability to provide better data. Variables from the policy diffusion literature showed that watershed management councils that employ consultants are more likely to use scientific models. We found a gap between those who create scientific models and those who use these models. We recommend shrinking this gap through more communication between these actors and advancing the need for developers to provide more technical assistance.

  2. Diffusion of a Sustainable Farming Technique in Sri Lanka: An Agent-Based Modeling Approach

    NASA Astrophysics Data System (ADS)

    Jacobi, J. H.; Gilligan, J. M.; Carrico, A. R.; Truelove, H. B.; Hornberger, G.

    2012-12-01

    We live in a changing world - anthropogenic climate change is disrupting historic climate patterns and social structures are shifting as large scale population growth and massive migrations place unprecedented strain on natural and social resources. Agriculture in many countries is affected by these changes in the social and natural environments. In Sri Lanka, rice farmers in the Mahaweli River watershed have seen increases in temperature and decreases in precipitation. In addition, a government led resettlement project has altered the demographics and social practices in villages throughout the watershed. These changes have the potential to impact rice yields in a country where self-sufficiency in rice production is a point of national pride. Studies of the climate can elucidate physical effects on rice production, while research on social behaviors can illuminate the influence of community dynamics on agricultural practices. Only an integrated approach, however, can capture the combined and interactive impacts of these global changes on Sri Lankan agricultural. As part of an interdisciplinary team, we present an agent-based modeling (ABM) approach to studying the effects of physical and social changes on farmers in Sri Lanka. In our research, the diffusion of a sustainable farming technique, the system of rice intensification (SRI), throughout a farming community is modeled to identify factors that either inhibit or promote the spread of a more sustainable approach to rice farming. Inputs into the ABM are both physical and social and include temperature, precipitation, the Palmer Drought Severity Index (PDSI), community trust, and social networks. Outputs from the ABM demonstrate the importance of meteorology and social structure on the diffusion of SRI throughout a farming community.

  3. MO-G-BRF-07: Anomalously Fast Diffusion of Carbon Nanotubes Carriers in 3D Tissue Model

    SciTech Connect

    Wang, Y; Bahng, J; Kotov, N

    2014-06-15

    Purpose: We aim to investigate and understand diffusion process of carbon nanotubes (CNTs) and other nanoscale particles in tissue and organs. Methods: In this research, we utilized a 3D model tissue of hepatocellular carcinoma (HCC)cultured in inverted colloidal crystal (ICC) scaffolds to compare the diffusivity of CNTs with small molecules such as Rhodamine and FITC in vitro, and further investigated the transportation of CNTs with and without targeting ligand, TGFβ1. The real-time permeation profiles of CNTs in HCC tissue model with high temporal and spatial resolution was demonstrated by using standard confocal microscopy. Quantitative analysis of the diffusion process in 3D was carried out using luminescence intensity in a series of Z-stack images obtained for different time points of the diffusion process after initial addition of CNTs or small molecules to the cell culture and the image data was analyzed by software ImageJ and Mathematica. Results: CNTs display diffusion rate in model tissues substantially faster than small molecules of the similar charge such as FITC, and the diffusion rate of CNTs are significantly enhanced with targeting ligand, TGFβ1. Conclusion: In terms of the advantages of in-vitro model, we were able to have access to measuring the rate of CNT penetration at designed conditions with variable parameters. And the findings by using this model, changed our understanding about advantages of CNTs as nanoscale drug carriers and provides design principles for making new drug carriers for both treatment and diagnostics. Additionally the fast diffusion opens the discussion of the best possible drug carriers to reach deep parts of cancerous tissues, which is often a prerequisite for successful cancer treatment. This work was supported by the Center for Photonic and Multiscale Nanomaterials funded by National Science Foundation Materials Research Science and Engineering Center program DMR 1120923. The work was also partially supported by NSF

  4. Modelling of silica diffusion experiments with 32Si in Boom Clay.

    PubMed

    Aertsens, Marc; De Cannière, Pierre; Moors, Hugo

    2003-03-01

    A mathematical model describing the dissolution of nuclear glass directly disposed in clay combines a first-order dissolution rate law with the diffusion of dissolved silica in clay. According to this model, the main parameters describing the long-term dissolution of the glass are etaR, the product of the diffusion accessible porosity eta and the retardation factor R, and the apparent diffusion coefficient D(app) of dissolved silica in clay. For determining the migration parameters needed for long-term predictions, four Through-Diffusion (T-D) experiments and one percolation test have been performed on undisturbed clay cores. In the Through-Diffusion experiments, the concentration decrease after injection of 32Si (radioactive labelled silica) was measured in the inlet compartment. At the end of the T-D experiments, the clay cores were cut in thin slices and the activity of labelled silica in each slice was determined. The measured activity profiles for these four clay cores are well reproducible. Since no labelled silica could be detected in the outlet compartments, the Through-Diffusion experiments are fitted by two In-Diffusion models: one model assuming linear and reversible sorption equilibrium and a second model taking into account sorption kinetics. Although the kinetic model provides better fits, due to the sufficiently long duration of the experiments, both models give approximately similar values for the fit parameters. The single percolation test leads to an apparent diffusion coefficient value about two to three times lower than those of the Through-Diffusion tests. Therefore, dissolved silica appears to be strongly retarded in Boom Clay. A retardation factor R between 100 and 300 was determined. The corresponding in situ distribution coefficient K(d) is in the range 25-75 cm(3) g(-1). The apparent diffusion coefficient of dissolved silica in Boom Clay is estimated between 2 x 10(-13) and 7 x 10(-13) m(2) s(-1). The pore diffusion coefficient is in the

  5. Modeling of the interplay between single-file diffusion and conversion reaction in mesoporous systems

    SciTech Connect

    Wang, Jing

    2013-01-11

    We analyze the spatiotemporal behavior of species concentrations in a diffusion-mediated conversion reaction which occurs at catalytic sites within linear pores of nanometer diameter. A strict single-file (no passing) constraint occurs in the diffusion within such narrow pores. Both transient and steady-state behavior is precisely characterized by kinetic Monte Carlo simulations of a spatially discrete lattice–gas model for this reaction–diffusion process considering various distributions of catalytic sites. Exact hierarchical master equations can also be developed for this model. Their analysis, after application of mean-field type truncation approximations, produces discrete reaction–diffusion type equations (mf-RDE). For slowly varying concentrations, we further develop coarse-grained continuum hydrodynamic reaction–diffusion equations (h-RDE) incorporating a precise treatment of single-file diffusion (SFD) in this multispecies system. Noting the shortcomings of mf-RDE and h-RDE, we then develop a generalized hydrodynamic (GH) formulation of appropriate gh-RDE which incorporates an unconventional description of chemical diffusion in mixed-component quasi-single-file systems based on a refined picture of tracer diffusion for finite-length pores. The gh-RDE elucidate the non-exponential decay of the steady-state reactant concentration into the pore and the non-mean-field scaling of the reactant penetration depth. Then an extended model of a catalytic conversion reaction within a functionalized nanoporous material is developed to assess the effect of varying the reaction product – pore interior interaction from attractive to repulsive. The analysis is performed utilizing the generalized hydrodynamic formulation of the reaction-diffusion equations which can reliably capture the complex interplay between reaction and restricted transport for both irreversible and reversible reactions.

  6. Sensitivity of Urban Airshed Model (UAM-IV) calculated air pollutant concentrations to the vertical diffusion parameterization during convective meteorological situations

    SciTech Connect

    Nowacki, P.; Samson, P.J.; Sillman, S.

    1996-10-01

    It is shown that Urban Airshed Model (UAM-IV) calculated air pollutant concentrations during photochemical smog episodes in Atlanta, Georgia, depend strongly on the numerical parameterization of the daytime vertical diffusivity. Results found suggest that vertical mixing is overestimated by the UAM-IV during unstable daytime conditions, as calculated vertical diffusivity values exceed measured and comparable literature values. Although deviations between measured and UAM-IV calculated air pollutant concentrations may only in part be due the UAM-IV diffusivity parameterization, results indicate the large error potential in vertical diffusivity parameterization. Easily implemented enhancements to UAM-IV algorithms are proposed, thus improving UAM-IV modeling performance during unstable stratification. 38 refs., 14 figs., 1 tab.

  7. Mathematical Modelling in Physics and Engineering--Part 2.

    ERIC Educational Resources Information Center

    Oke, K. H.; Jones, A. L.

    1982-01-01

    Mathematical modelling and an example used with undergraduates were presented in part 1 (v17, n5, p212-18, 1982). A second example, Power from Windmills, is provided which has considerable potential for development both as a model and as a series of modelling experiences of increasing difficulty for students with different backgrounds. (Author/JN)

  8. Modeling diffusion of adsorbed polymer with explicit solvent.

    PubMed

    Desai, Tapan G; Keblinski, Pawel; Kumar, Sanat K; Granick, Steve

    2007-05-25

    Computer simulations of a polymer chain of length N strongly adsorbed at the solid-liquid interface in the presence of explicit solvent are used to delineate the factors affecting the N dependence of the polymer lateral diffusion coefficient, D(||). We find that surface roughness has a large influence, and D(||) scales as D(||) approximately N(-x), with x approximately 3/4 and x approximately 1 for ideal smooth and corrugated surfaces, respectively. The first result is consistent with the hydrodynamics of a "particle" of radius of gyration R(G) approximately N(nu) (nu=0.75) translating parallel to a planar interface, while the second implies that the friction of the adsorbed chains dominates. These results are discussed in the context of recent measurements.

  9. Reconstruction of two constant coefficients in linear anisotropic diffusion model

    NASA Astrophysics Data System (ADS)

    Mola, Gianluca; Okazawa, Noboru; Yokota, Tomomi

    2016-11-01

    Let (H,< \\cdot ,\\cdot > ) be a complex Hilbert space and A:D(A)\\to H and B:D(B)\\to H be nonnegative and selfadjoint operators. We study the inverse problem consisting in the identification of the function u:[0,T]\\to H and two constants α, β \\in {{{R}}}+=(0,∞ ) (diffusion coefficients) that fulfill the initial-value problem u ‧ ( t ) + α Au ( t ) + β Bu ( t ) = 0 , t ∈ ( 0 , T ) , u ( 0 ) = x , and the additional conditions < Au ( T ) , u ( T ) > = φ and < Bu ( T ) , u ( T ) > = ψ . Under suitable assumptions on the operators A and B, and on the data x\\in H and \\varphi ,\\psi \\gt 0, we shall construct a solution and prove its uniqueness and continuous dependence on the data. Applications are considered.

  10. A novel rumor diffusion model considering the effect of truth in online social media

    NASA Astrophysics Data System (ADS)

    Sun, Ling; Liu, Yun; Zeng, Qing-An; Xiong, Fei

    2015-12-01

    In this paper, we propose a model to investigate how truth affects rumor diffusion in online social media. Our model reveals a relation between rumor and truth — namely, when a rumor is diffusing, the truth about the rumor also diffuses with it. Two patterns of the agents used to identify rumor, self-identification and passive learning are taken into account. Combining theoretical proof and simulation analysis, we find that the threshold value of rumor diffusion is negatively correlated to the connectivity between nodes in the network and the probability β of agents knowing truth. Increasing β can reduce the maximum density of the rumor spreaders and slow down the generation speed of new rumor spreaders. On the other hand, we conclude that the best rumor diffusion strategy must balance the probability of forwarding rumor and the probability of agents losing interest in the rumor. High spread rate λ of rumor would lead to a surge in truth dissemination which will greatly limit the diffusion of rumor. Furthermore, in the case of unknown λ, increasing β can effectively reduce the maximum proportion of agents who do not know the truth, but cannot narrow the rumor diffusion range in a certain interval of β.

  11. A method for modeling oxygen diffusion in an agent-based model with application to host-pathogen infection

    SciTech Connect

    Plimpton, Steven J.; Sershen, Cheryl L.; May, Elebeoba E.

    2015-01-01

    This paper describes a method for incorporating a diffusion field modeling oxygen usage and dispersion in a multi-scale model of Mycobacterium tuberculosis (Mtb) infection mediated granuloma formation. We implemented this method over a floating-point field to model oxygen dynamics in host tissue during chronic phase response and Mtb persistence. The method avoids the requirement of satisfying the Courant-Friedrichs-Lewy (CFL) condition, which is necessary in implementing the explicit version of the finite-difference method, but imposes an impractical bound on the time step. Instead, diffusion is modeled by a matrix-based, steady state approximate solution to the diffusion equation. Moreover, presented in figure 1 is the evolution of the diffusion profiles of a containment granuloma over time.

  12. A method for modeling oxygen diffusion in an agent-based model with application to host-pathogen infection

    DOE PAGESBeta

    Plimpton, Steven J.; Sershen, Cheryl L.; May, Elebeoba E.

    2015-01-01

    This paper describes a method for incorporating a diffusion field modeling oxygen usage and dispersion in a multi-scale model of Mycobacterium tuberculosis (Mtb) infection mediated granuloma formation. We implemented this method over a floating-point field to model oxygen dynamics in host tissue during chronic phase response and Mtb persistence. The method avoids the requirement of satisfying the Courant-Friedrichs-Lewy (CFL) condition, which is necessary in implementing the explicit version of the finite-difference method, but imposes an impractical bound on the time step. Instead, diffusion is modeled by a matrix-based, steady state approximate solution to the diffusion equation. Moreover, presented in figuremore » 1 is the evolution of the diffusion profiles of a containment granuloma over time.« less

  13. Comparison and content of the Wright-Fisher model of random genetic drift, the diffusion approximation, and an intermediate model.

    PubMed

    Waxman, D

    2011-01-21

    We investigate the detailed connection between the Wright-Fisher model of random genetic drift and the diffusion approximation, under the assumption that selection and drift are weak and so cause small changes over a single generation. A representation of the mathematics underlying the Wright-Fisher model is introduced which allows the connection to be made with the corresponding mathematics underlying the diffusion approximation. Two 'hybrid' models are also introduced which lie 'between' the Wright-Fisher model and the diffusion approximation. In model 1 the relative allele frequency takes discrete values while time is continuous; in model 2 time is discrete and relative allele frequency is continuous. While both hybrid models appear to have a similar status and the same level of plausibility, the different nature of time and frequency in the two models leads to significant mathematical differences. Model 2 is mathematically inconsistent and has to be ruled out as being meaningful. Model 1 is used to clarify the content of Kimura's solution of the diffusion equation, which is shown to have the natural interpretation as describing only those populations where alleles are segregating. By contrast the Wright-Fisher model and the solution of the diffusion equation of McKane and Waxman cover populations of all categories, namely populations where alleles segregate, are lost, or fix.

  14. Uncertainty quantification in modeling of microfluidic T-sensor based diffusion immunoassay.

    PubMed

    Jha, Aman Kumar; Bahga, Supreet Singh

    2016-01-01

    Comparison of experimental data with modeling predictions is essential for making quantitative measurements of species properties, such as diffusion coefficients and species concentrations using a T-sensor. To make valid comparisons between experimental data and model predictions, it is necessary to account for uncertainty in model predictions due to uncertain values of model parameters. We present an analysis of uncertainty induced in model predictions of a T-sensor based competitive diffusion immunoassay due to uncertainty in diffusion constants, binding reaction rate constants, and inlet flow speed. We use a non-intrusive stochastic uncertainty quantification method employing polynomial chaos expansions to represent the dependence of uncertain species concentrations on the uncertainty in model parameters. Our simulations show that the uncertainties in model parameters lead to significant spatially varying uncertainty in predicted concentration. In particular, the diffusivity of fluorescently labeled probe antigen dominates the overall uncertainty. The predicted uncertainty in fluorescence intensity is minimum near the centerline of T-sensor and relatively high in the regions with gradients in fluorescence intensity. We show that using centerline fluorescence intensity instead of first derivative of fluorescence intensity as the system response for measuring sample antigen concentration in T-sensor based competitive diffusion immunoassay leads to lower uncertainty and higher detection sensitivity. PMID:26858817

  15. Assessing cognitive processes with diffusion model analyses: a tutorial based on fast-dm-30

    PubMed Central

    Voss, Andreas; Voss, Jochen; Lerche, Veronika

    2015-01-01

    Diffusion models can be used to infer cognitive processes involved in fast binary decision tasks. The model assumes that information is accumulated continuously until one of two thresholds is hit. In the analysis, response time distributions from numerous trials of the decision task are used to estimate a set of parameters mapping distinct cognitive processes. In recent years, diffusion model analyses have become more and more popular in different fields of psychology. This increased popularity is based on the recent development of several software solutions for the parameter estimation. Although these programs make the application of the model relatively easy, there is a shortage of knowledge about different steps of a state-of-the-art diffusion model study. In this paper, we give a concise tutorial on diffusion modeling, and we present fast-dm-30, a thoroughly revised and extended version of the fast-dm software (Voss and Voss, 2007) for diffusion model data analysis. The most important improvement of the fast-dm version is the possibility to choose between different optimization criteria (i.e., Maximum Likelihood, Chi-Square, and Kolmogorov-Smirnov), which differ in applicability for different data sets. PMID:25870575

  16. Modelling and simulations of multi-component lipid membranes and open membranes via diffuse interface approaches.

    PubMed

    Wang, Xiaoqiang; Du, Qiang

    2008-03-01

    Diffuse interface (phase field) models are developed for multi-component vesicle membranes with different lipid compositions and membranes with free boundary. These models are used to simulate the deformation of membranes under the elastic bending energy and the line tension energy with prescribed volume and surface area constraints. By comparing our numerical simulations with recent biological experiments, it is demonstrated that the diffuse interface models can effectively capture the rich phenomena associated with the multi-component vesicle transformation and thus offering great functionality in their simulation and modelling.

  17. Using a Quasipotential Transformation for Modeling Diffusion Media inPolymer-Electrolyte Fuel Cells

    SciTech Connect

    Weber, Adam Z.; Newman, John

    2008-08-29

    In this paper, a quasipotential approach along with conformal mapping is used to model the diffusion media of a polymer-electrolyte fuel cell. This method provides a series solution that is grid independent and only requires integration along a single boundary to solve the problem. The approach accounts for nonisothermal phenomena, two-phase flow, correct placement of the electronic potential boundary condition, and multilayer media. The method is applied to a cathode diffusion medium to explore the interplay between water and thermal management and performance, the impact of the rib-to-channel ratio, and the existence of diffusion under the rib and flooding phenomena.

  18. Finite volume element approximation of an inhomogeneous Brusselator model with cross-diffusion

    NASA Astrophysics Data System (ADS)

    Lin, Zhigui; Ruiz-Baier, Ricardo; Tian, Canrong

    2014-01-01

    This paper is concerned with the study of pattern formation for an inhomogeneous Brusselator model with cross-diffusion, modeling an autocatalytic chemical reaction taking place in a three-dimensional domain. For the spatial discretization of the problem we develop a novel finite volume element (FVE) method associated to a piecewise linear finite element approximation of the cross-diffusion system. We study the main properties of the unique equilibrium of the related dynamical system. A rigorous linear stability analysis around the spatially homogeneous steady state is provided and we address in detail the formation of Turing patterns driven by the cross-diffusion effect. In addition we focus on the spatial accuracy of the FVE method, and a series of numerical simulations confirm the expected behavior of the solutions. In particular we show that, depending on the spatial dimension, the magnitude of the cross-diffusion influences the selection of spatial patterns.

  19. 16 CFR Appendix A to Part 313 - Model Privacy Form

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... form must be printed on white or light color paper (such as cream) with black or other contrasting ink... color. (e) Languages. The model form may be translated into languages other than English. C. Information... under this part, must comply with section 624 of the FCRA and 16 CFR parts 680 and 698 with respect...

  20. 16 CFR Appendix A to Part 313 - Model Privacy Form

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... form must be printed on white or light color paper (such as cream) with black or other contrasting ink... color. (e) Languages. The model form may be translated into languages other than English. C. Information... under this part, must comply with section 624 of the FCRA and 16 CFR parts 680 and 698 with respect...

  1. 16 CFR Appendix A to Part 313 - Model Privacy Form

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... form must be printed on white or light color paper (such as cream) with black or other contrasting ink... color. (e) Languages. The model form may be translated into languages other than English. C. Information... under this part, must comply with section 624 of the FCRA and 16 CFR parts 680 and 698 with respect...

  2. 16 CFR Appendix A to Part 313 - Model Privacy Form

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... form must be printed on white or light color paper (such as cream) with black or other contrasting ink... color. (e) Languages. The model form may be translated into languages other than English. C. Information... under this part, must comply with section 624 of the FCRA and 16 CFR parts 680 and 698 with respect...

  3. 16 CFR Appendix A to Part 313 - Model Privacy Form

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... form must be printed on white or light color paper (such as cream) with black or other contrasting ink... color. (e) Languages. The model form may be translated into languages other than English. C. Information... under this part, must comply with section 624 of the FCRA and 16 CFR parts 680 and 698 with respect...

  4. On the application of kinematic models to simulate the diffusive processes of debris flows

    NASA Astrophysics Data System (ADS)

    Arattano, M.; Franzi, L.

    2010-08-01

    Debris flows generally propagate along steep mountain torrents with dynamics primarily governed by gravitational and frictional forces. Thus, debris flows modelling can be successfully performed through the application of kinematic models, which consider only the effects of slope and friction and neglect the remaining terms of the momentum equation. However, the diffusion processes that can be observed in the field, such as the spreading of the debris flow wave as it flows downstream, can not be theoretically predicted by kinematic models, since diffusion is a second-order process neglected in the kinematic approximation. In this paper, this issue is discussed and an application for both a generalized diffusion wave model and a kinematic model is proposed of a debris flow which occurred in an Italian instrumented torrent to identify, in a real case scenario, the effective value of the neglected terms in the kinematic approximation.

  5. Modeling and Uncertainty Quantification of Vapor Sorption and Diffusion in Heterogeneous Polymers

    SciTech Connect

    Sun, Yunwei; Harley, Stephen J.; Glascoe, Elizabeth A.

    2015-08-13

    A high-fidelity model of kinetic and equilibrium sorption and diffusion is developed and exercised. The gas-diffusion model is coupled with a triple-sorption mechanism: Henry’s law absorption, Langmuir adsorption, and pooling or clustering of molecules at higher partial pressures. Sorption experiments are conducted and span a range of relative humidities (0-95 %) and temperatures (30-60 °C). Kinetic and equilibrium sorption properties and effective diffusivity are determined by minimizing the absolute difference between measured and modeled uptakes. Uncertainty quantification and sensitivity analysis methods are described and exercised herein to demonstrate the capability of this modeling approach. Water uptake in silica-filled and unfilled poly(dimethylsiloxane) networks is investigated; however, the model is versatile enough to be used with a wide range of materials and vapors.

  6. Adsorption rate of phenol from aqueous solution onto organobentonite: surface diffusion and kinetic models.

    PubMed

    Ocampo-Perez, Raul; Leyva-Ramos, Roberto; Mendoza-Barron, Jovita; Guerrero-Coronado, Rosa M

    2011-12-01

    The concentration decay curves for the adsorption of phenol on organobentonite were obtained in an agitated tank batch adsorber. The experimental adsorption rate data were interpreted with diffusional models as well as first-order, second-order and Langmuir kinetic models. The surface diffusion model adjusted the data quite well, revealing that the overall rate of adsorption was controlled by surface diffusion. Furthermore, the surface diffusion coefficient increased raising the mass of phenol adsorbed at equilibrium and was independent of the particle diameter in the range 0.042-0.0126 cm. It was demonstrated that the overall rate of adsorption was essentially not affected by the external mass transfer. The second-order and the Langmuir kinetic models fitted the experimental data quite well; however, the kinetic constants of both models varied without any physical meaning while increasing the particle size and the mass of phenol adsorbed at equilibrium.

  7. A joint model for boundaries of multiple anatomical parts

    NASA Astrophysics Data System (ADS)

    Kerr, Grégoire; Kurtek, Sebastian; Srivastava, Anuj

    2011-03-01

    The use of joint shape analysis of multiple anatomical parts is a promising area of research with applications in medical diagnostics, growth evaluations, and disease characterizations. In this paper, we consider several features (shapes, orientations, scales, and locations) associated with anatomical parts and develop probability models that capture interactions between these features and across objects. The shape component is based on elastic shape analysis of continuous boundary curves. The proposed model is a second order model that considers principal coefficients in tangent spaces of joint manifolds as multivariate normal random variables. Additionally, it models interactions across objects using area-interaction processes. Using given observations of four anatomical parts: caudate, hippocampus, putamen and thalamus, on one side of the brain, we first estimate the model parameters and then generate random samples from them using the Metropolis-Hastings algorithm. The plausibility of these random samples validates the proposed models.

  8. Radiation transport phenomena and modeling. Part A: Codes; Part B: Applications with examples

    SciTech Connect

    Lorence, L.J. Jr.; Beutler, D.E.

    1997-09-01

    This report contains the notes from the second session of the 1997 IEEE Nuclear and Space Radiation Effects Conference Short Course on Applying Computer Simulation Tools to Radiation Effects Problems. Part A discusses the physical phenomena modeled in radiation transport codes and various types of algorithmic implementations. Part B gives examples of how these codes can be used to design experiments whose results can be easily analyzed and describes how to calculate quantities of interest for electronic devices.

  9. Modeling the Growth of Hyperthermophiles in Deep-sea Hydrothermal Diffuse Fluids and Sulfide Deposits

    NASA Astrophysics Data System (ADS)

    Ver Eecke, H. C.; Oslowski, D. M.; Butterfield, D. A.; Olson, E. J.; Lilley, M. D.; Holden, J. F.

    2009-12-01

    In 2008 and 2009, 534 hydrothermal fluid samples and 5 actively-venting black smoker chimneys were collected using Alvin for correlative microbiological and chemical analyses as part of the Endeavour Segment and Axial Volcano Geochemistry and Ecology Research (EAGER) program. Hyperthermophilic, autotrophic Fe(III) oxide reducers, methanogens, and sulfur-reducing heterotrophs were enriched for at 85 and 95°C using most-probable-number estimates from 28 diffuse fluid and 8 chimney samples. Heterotrophs were the most abundant of the three groups in both diffuse fluids and black-smoker chimneys. Iron reducers were more abundant than methanogens, and more abundant in sulfide-hosted vents than in basalt-hosted vents. Fluid chemistry suggests that there is net biogenic methanogenesis at the Marker 113/62 diffuse vent at Axial Volcano but nowhere else sampled. The growth of hyperthermophilic methanogens and heterotrophs was modeled in the lab using pure cultures. Methanocaldococcus jannaschii grew at 82°C in a 2-liter reactor with continuous gas flow at H2 concentrations between 20 and 225 µM with a H2 km of 100 µM. Correlating H2 end-member mixing curves from vent fluids and seawater with our laboratory modeling study suggests that H2 concentrations are limiting for Methanocaldococcus growth at most Mothra, Main Field, and High Rise vent sites at Endeavour but sufficient to support growth at some Axial Volcano vents. Therefore, hyperthermophilic methanogens may depend on H2 syntrophy at low H2 sites. Twenty-one pure hyperthermophilic heterotroph strains each grew on α-1,4 and β-1,4 linked sugars and polypeptides with concomitant H2 production. The H2 production rate (cell-1 doubling-1) for Pyrococcus furiosus at 95°C without sulfur was 29 fmol, 36 fmol, and 53 fmol for growth on α-1,4 sugars, β-1,4 sugars, and peptides, respectively. The CH4 production rate for M. jannaschii was 390 fmol cell-1 doubling-1; therefore, we estimate that it would take approximately

  10. Anomalous diffusion and dynamics of fluorescence recovery after photobleaching in the random-comb model.

    PubMed

    Yuste, S B; Abad, E; Baumgaertner, A

    2016-07-01

    We address the problem of diffusion on a comb whose teeth display varying lengths. Specifically, the length ℓ of each tooth is drawn from a probability distribution displaying power law behavior at large ℓ,P(ℓ)∼ℓ^{-(1+α)} (α>0). To start with, we focus on the computation of the anomalous diffusion coefficient for the subdiffusive motion along the backbone. This quantity is subsequently used as an input to compute concentration recovery curves mimicking fluorescence recovery after photobleaching experiments in comblike geometries such as spiny dendrites. Our method is based on the mean-field description provided by the well-tested continuous time random-walk approach for the random-comb model, and the obtained analytical result for the diffusion coefficient is confirmed by numerical simulations of a random walk with finite steps in time and space along the backbone and the teeth. We subsequently incorporate retardation effects arising from binding-unbinding kinetics into our model and obtain a scaling law characterizing the corresponding change in the diffusion coefficient. Finally, we show that recovery curves obtained with the help of the analytical expression for the anomalous diffusion coefficient cannot be fitted perfectly by a model based on scaled Brownian motion, i.e., a standard diffusion equation with a time-dependent diffusion coefficient. However, differences between the exact curves and such fits are small, thereby providing justification for the practical use of models relying on scaled Brownian motion as a fitting procedure for recovery curves arising from particle diffusion in comblike systems.

  11. Anomalous diffusion and dynamics of fluorescence recovery after photobleaching in the random-comb model

    NASA Astrophysics Data System (ADS)

    Yuste, S. B.; Abad, E.; Baumgaertner, A.

    2016-07-01

    We address the problem of diffusion on a comb whose teeth display varying lengths. Specifically, the length ℓ of each tooth is drawn from a probability distribution displaying power law behavior at large ℓ ,P (ℓ ) ˜ℓ-(1 +α ) (α >0 ). To start with, we focus on the computation of the anomalous diffusion coefficient for the subdiffusive motion along the backbone. This quantity is subsequently used as an input to compute concentration recovery curves mimicking fluorescence recovery after photobleaching experiments in comblike geometries such as spiny dendrites. Our method is based on the mean-field description provided by the well-tested continuous time random-walk approach for the random-comb model, and the obtained analytical result for the diffusion coefficient is confirmed by numerical simulations of a random walk with finite steps in time and space along the backbone and the teeth. We subsequently incorporate retardation effects arising from binding-unbinding kinetics into our model and obtain a scaling law characterizing the corresponding change in the diffusion coefficient. Finally, we show that recovery curves obtained with the help of the analytical expression for the anomalous diffusion coefficient cannot be fitted perfectly by a model based on scaled Brownian motion, i.e., a standard diffusion equation with a time-dependent diffusion coefficient. However, differences between the exact curves and such fits are small, thereby providing justification for the practical use of models relying on scaled Brownian motion as a fitting procedure for recovery curves arising from particle diffusion in comblike systems.

  12. Anomalous diffusion and dynamics of fluorescence recovery after photobleaching in the random-comb model.

    PubMed

    Yuste, S B; Abad, E; Baumgaertner, A

    2016-07-01

    We address the problem of diffusion on a comb whose teeth display varying lengths. Specifically, the length ℓ of each tooth is drawn from a probability distribution displaying power law behavior at large ℓ,P(ℓ)∼ℓ^{-(1+α)} (α>0). To start with, we focus on the computation of the anomalous diffusion coefficient for the subdiffusive motion along the backbone. This quantity is subsequently used as an input to compute concentration recovery curves mimicking fluorescence recovery after photobleaching experiments in comblike geometries such as spiny dendrites. Our method is based on the mean-field description provided by the well-tested continuous time random-walk approach for the random-comb model, and the obtained analytical result for the diffusion coefficient is confirmed by numerical simulations of a random walk with finite steps in time and space along the backbone and the teeth. We subsequently incorporate retardation effects arising from binding-unbinding kinetics into our model and obtain a scaling law characterizing the corresponding change in the diffusion coefficient. Finally, we show that recovery curves obtained with the help of the analytical expression for the anomalous diffusion coefficient cannot be fitted perfectly by a model based on scaled Brownian motion, i.e., a standard diffusion equation with a time-dependent diffusion coefficient. However, differences between the exact curves and such fits are small, thereby providing justification for the practical use of models relying on scaled Brownian motion as a fitting procedure for recovery curves arising from particle diffusion in comblike systems. PMID:27575088

  13. Hierarchical Diffusion Models for Two-Choice Response Times

    ERIC Educational Resources Information Center

    Vandekerckhove, Joachim; Tuerlinckx, Francis; Lee, Michael D.

    2011-01-01

    Two-choice response times are a common type of data, and much research has been devoted to the development of process models for such data. However, the practical application of these models is notoriously complicated, and flexible methods are largely nonexistent. We combine a popular model for choice response times--the Wiener diffusion…

  14. Technological Diffusion within Educational Institutions: Applying the Technology Acceptance Model.

    ERIC Educational Resources Information Center

    Wolski, Stacy; Jackson, Sally

    Expectancy models of behavior such as the Theory of Reasoned Action (TRA) and the Technology Acceptance Model (TAM) offer guidelines that aid efforts to facilitate use of new technology. These models remind us that both acceptance of and resistance to technology use are grounded in beliefs and norms regarding the technology. Although TAM is widely…

  15. Diffusion in pulsar wind nebulae: an investigation using magnetohydrodynamic and particle transport models

    NASA Astrophysics Data System (ADS)

    Porth, O.; Vorster, M. J.; Lyutikov, M.; Engelbrecht, N. E.

    2016-08-01

    We study the transport of high-energy particles in pulsar wind nebulae (PWN) using three-dimensional magnetohydrodynamic (MHD) and test-particle simulations, as well as a Fokker-Planck particle transport model. The latter includes radiative and adiabatic losses, diffusion, and advection on the background flow of the simulated MHD nebula. By combining the models, the spatial evolution of flux and photon index of the X-ray synchrotron emission is modelled for the three nebulae G21.5-0.9, the inner regions of Vela, and 3C 58, thereby allowing us to derive governing parameters: the magnetic field strength, average flow velocity, and spatial diffusion coefficient. For comparison, the nebulae are also modelled with the semi-analytic Kennel & Coroniti model but the Porth et al. model generally yields better fits to the observational data. We find that high velocity fluctuations in the turbulent nebula (downstream of the termination shock) give rise to efficient diffusive transport of particles, with average Péclet number close to unity, indicating that both advection and diffusion play an important role in particle transport. We find that the diffusive transport coefficient of the order of ˜ 2 × 1027(Ls/0.42 Ly) cm2 s- 1 (Ls is the size of the termination shock) is independent of energy up to extreme particle Lorentz factors of γp ˜ 1010.

  16. Tone-dependent error diffusion based on an updated blue-noise model

    NASA Astrophysics Data System (ADS)

    Fung, Yik-Hing; Chan, Yuk-Hee

    2016-01-01

    The conventional blue-noise model that specifies the desired noise characteristics of an ideal halftone has been updated recently, and simulation results showed that the updated model can serve as a better guideline for developing halftone algorithms. At the moment, only a feature-preserving multiscale error diffusion-based algorithm was developed based on the updated noise model. As the algorithm does not support real-time applications, a tone-dependent error diffusion (TDED) algorithm is developed based on the updated noise model. To support the proposed TDED algorithm, we optimize a diffusion filter and a quantizer threshold for each possible input gray level based on the updated noise model, such that the algorithm can adapt its diffusion filter and quantizer according to the input intensity value of a pixel to produce a halftone. Simulation results showed that the proposed TDED algorithm can successfully produce halftones bearing the desired noise characteristics as specified by the updated noise model. As a consequence, it provides better performance than conventional error diffusion-based algorithms in terms of various measures including radially averaged power spectrum density and anisotropy. When processing real images, it can eliminate directional artifacts, regular structure patterns, and unintended sharpening effects in its halftoning outputs.

  17. A study of a diffusive model of asset returns and an empirical analysis of financial markets

    NASA Astrophysics Data System (ADS)

    Alejandro Quinones, Angel Luis

    A diffusive model for market dynamics is studied and the predictions of the model are compared to real financial markets. The model has a non-constant diffusion coefficient which depends both on the asset value and the time. A general solution for the distribution of returns is obtained and shown to match the results of computer simulations for two simple cases, piecewise linear and quadratic diffusion. The effects of discreteness in the market dynamics on the model are also studied. For the quadratic diffusion case, a type of phase transition leading to fat tails is observed as the discrete distribution approaches the continuum limit. It is also found that the model captures some of the empirical stylized facts observed in real markets, including fat-tails and scaling behavior in the distribution of returns. An analysis of empirical data for the EUR/USD currency exchange rate and the S&P 500 index is performed. Both markets show time scaling behavior consistent with a value of 1/2 for the Hurst exponent. Finally, the results show that the distribution of returns for the two markets is well fitted by the model, and the corresponding empirical diffusion coefficients are determined.

  18. Ocean Turbulence I: One-Point Closure Model Momentum and Heat Vertical Diffusivities

    NASA Technical Reports Server (NTRS)

    Canuto, V. M.; Howard, A.; Cheng, Y.; Dubovikov, M. S.

    1999-01-01

    Since the early forties, one-point turbulence closure models have been the canonical tools used to describe turbulent flows in many fields. In geophysics, Mellor and Yamada applied such models using the 1980 state-of-the art. Since then, no improvements were introduced to alleviate two major difficulties: 1) closure of the pressure correlations, which affects the correct determination of the critical Richardson number Ri(sub cr) above which turbulent mixing is no longer possible and 2) the need to express the non-local third-order moments (TOM) in terms of lower order moments rather than via the down-gradient approximation as done thus far, since the latter seriously underestimates the TOMs. Since 1) and 2) are still being dealt with adjustable parameters which weaken the credibility of the models, alternative models, not based on turbulence modeling, have been suggested. The aim of this paper is to show that new information, partly derived from the newest 2-point closure model discussed, can be used to solve these shortcomings. The new one-point closure model, which in its simplest form is algebraic and thus simple to implement, is first shown to reproduce a variety of data. Then, it is used in a Ocean-General Circulation Model (O-GCM) where it reproduces well a large variety of ocean data. While phenomenological models are specifically tuned to ocean turbulence, the present model is not. It is first tested against laboratory data on stably stratified flows and then used in an O-GCM. It is more general, more predictive and more resilient, e.g., it can incorporate phenomena like wave-breaking at the surface, salinity diffusivity, non-locality, etc. One important feature that naturally comes out of the new model is that the predicted Richardson critical value Ri(sub cr) is Ri (sub cr approx. = 1) in agreement with both Large Eddy Simulations (LES) and empirical evidence while all previous models predicted Ri (sub cr approx. = 0.2) which led to a considerable

  19. Integrating O/S models during conceptual design, part 1

    NASA Technical Reports Server (NTRS)

    Ebeling, Charles E.

    1994-01-01

    The University of Dayton is pleased to submit this report to the National Aeronautics and Space Administration (NASA), Langley Research Center, which integrates a set of models for determining operational capabilities and support requirements during the conceptual design of proposed space systems. This research provides for the integration of the reliability and maintainability (R&M) model, both new and existing simulation models, and existing operations and support (O&S) costing equations in arriving at a complete analysis methodology. Details concerning the R&M model and the O&S costing model may be found in previous reports accomplished under this grant (NASA Research Grant NAG1-1327). In the process of developing this comprehensive analysis approach, significant enhancements were made to the R&M model, updates to the O&S costing model were accomplished, and a new simulation model developed. This is the 1st part of a 3 part technical report.

  20. Diffusion of Innovation: A Plea for Indigenous Models

    ERIC Educational Resources Information Center

    Rubdy, Rani

    2008-01-01

    Much of curriculum innovation in English language teaching in the context of former colonial countries has been derivative rather than generative, imitative rather than self-initiated or self-regulatory. This trend is in part the result of historical exigencies that made the importation of ELT approaches, methods, and techniques for classroom…

  1. Ocean Turbulence. Paper 3; Two-Point Closure Model Momentum, Heat and Salt Vertical Diffusivities in the Presence of Shear

    NASA Technical Reports Server (NTRS)

    Canuto, V. M.; Dubovikov, M. S.; Howard, A.; Cheng, Y.

    1999-01-01

    In papers 1 and 2 we have presented the results of the most updated 1-point closure model for the turbulent vertical diffusivities of momentum, heat and salt, K(sub m,h,s). In this paper, we derive the analytic expressions for K(sub m,h,s) using a new 2-point closure model that has recently been developed and successfully tested against some approx. 80 turbulence statistics for different flows. The new model has no free parameters. The expressions for K(sub m, h. s) are analytical functions of two stability parameters: the Turner number R(sub rho) (salinity gradient/temperature gradient) and the Richardson number R(sub i) (temperature gradient/shear). The turbulent kinetic energy K and its rate of dissipation may be taken local or non-local (K-epsilon model). Contrary to all previous models that to describe turbulent mixing below the mixed layer (ML) have adopted three adjustable "background diffusivities" for momentum. heat and salt, we propose a model that avoids such adjustable diffusivities. We assume that below the ML, K(sub m,h,s) have the same functional dependence on R(sub i) and R(sub rho) derived from the turbulence model. However, in order to compute R(sub i) below the ML, we use data of vertical shear due to wave-breaking measured by Gargett et al. (1981). The procedure frees the model from adjustable background diffusivities and indeed we use the same model throughout the entire vertical extent of the ocean. Using the new K(sub m,h, s), we run an O-GCM and present a variety of results that we compare with Levitus and the KPP model. Since the traditional 1-point (used in papers 1 and 2) and the new 2-point closure models used here represent different modeling philosophies and procedures, testing them in an O-GCM is indispensable. The basic motivation is to show that the new 2-point closure model gives results that are overall superior to the 1-point closure in spite of the fact that the latter rely on several adjustable parameters while the new 2-point

  2. A comparison between the fission matrix method, the diffusion model and the transport model

    SciTech Connect

    Dehaye, B.; Hugot, F. X.; Diop, C. M.

    2013-07-01

    The fission matrix method may be used to solve the critical eigenvalue problem in a Monte Carlo simulation. This method gives us access to the different eigenvalues and eigenvectors of the transport or fission operator. We propose to compare the results obtained via the fission matrix method with those of the diffusion model, and an approximated transport model. To do so, we choose to analyse the mono-kinetic and continuous energy cases for a Godiva-inspired critical sphere. The first five eigenvalues are computed with TRIPOLI-4{sup R} and compared to the theoretical ones. An extension of the notion of the extrapolation distance is proposed for the modes other than the fundamental one. (authors)

  3. Modeling chemistry in and above snow at Summit, Greenland - Part 1: Model description and results

    NASA Astrophysics Data System (ADS)

    Thomas, J. L.; Stutz, J.; Lefer, B.; Huey, L. G.; Toyota, K.; Dibb, J. E.; von Glasow, R.

    2011-05-01

    Sun-lit snow is increasingly recognized as a chemical reactor that plays an active role in uptake, transformation, and release of atmospheric trace gases. Snow is known to influence boundary layer air on a local scale, and given the large global surface coverage of snow may also be significant on regional and global scales. We present a new detailed one-dimensional snow chemistry module that has been coupled to the 1-D atmospheric boundary layer model MISTRA. The new 1-D snow module, which is dynamically coupled to the overlaying atmospheric model, includes heat transport in the snowpack, molecular diffusion, and wind pumping of gases in the interstitial air. The model includes gas phase chemical reactions both in the interstitial air and the atmosphere. Heterogeneous and multiphase chemistry on atmospheric aerosol is considered explicitly. The chemical interaction of interstitial air with snow grains is simulated assuming chemistry in a liquid-like layer (LLL) on the grain surface. The coupled model, referred to as MISTRA-SNOW, was used to investigate snow as the source of nitrogen oxides (NOx) and gas phase reactive bromine in the atmospheric boundary layer in the remote snow covered Arctic (over the Greenland ice sheet) as well as to investigate the link between halogen cycling and ozone depletion that has been observed in interstitial air. The model is validated using data taken 10 June-13 June, 2008 as part of the Greenland Summit Halogen-HOx experiment (GSHOX). The model predicts that reactions involving bromide and nitrate impurities in the surface snow can sustain atmospheric NO and BrO mixing ratios measured at Summit, Greenland during this period.

  4. Analysis of the absorptive behavior of photopolymer materials. Part I. Theoretical modeling

    NASA Astrophysics Data System (ADS)

    Li, Haoyu; Qi, Yue; Guo, Jinxin; Sheridan, John T.

    2015-01-01

    Photopolymers have received a great deal of attention due to their broad range of applications. The variation of their absorptive behavior during exposure is pivotal to the study of such materials. A model combining the associated electromagnetics and photochemical kinetics is presented to describe these absorptive processes. Such a model is critical in describing both self-modulations during holographic recording and also self-focusing effects. To describe the photophysical and photochemical changes taking place, a modulated equivalent electrical conductivity is introduced. Temporal variations of the concentrations of dye, monomer, and polymer are then predicted using the modified nonlocal photopolymerization driven diffusion model. The numerical convergence of the model is examined. Comparisons between the predictions of the model and experimental results, for both acrylamide/polyvinyl alcohol and Phenanthrenequinone doped poly(methyl methacrylate) photopolymer materials, are presented and analyzed in Part II of this paper.

  5. Modelling and simulating reaction-diffusion systems using coloured Petri nets.

    PubMed

    Liu, Fei; Blätke, Mary-Ann; Heiner, Monika; Yang, Ming

    2014-10-01

    Reaction-diffusion systems often play an important role in systems biology when developmental processes are involved. Traditional methods of modelling and simulating such systems require substantial prior knowledge of mathematics and/or simulation algorithms. Such skills may impose a challenge for biologists, when they are not equally well-trained in mathematics and computer science. Coloured Petri nets as a high-level and graphical language offer an attractive alternative, which is easily approachable. In this paper, we investigate a coloured Petri net framework integrating deterministic, stochastic and hybrid modelling formalisms and corresponding simulation algorithms for the modelling and simulation of reaction-diffusion processes that may be closely coupled with signalling pathways, metabolic reactions and/or gene expression. Such systems often manifest multiscaleness in time, space and/or concentration. We introduce our approach by means of some basic diffusion scenarios, and test it against an established case study, the Brusselator model. PMID:25150626

  6. Chemical kinetic modeling of a methane opposed flow diffusion flame and comparison to experiments

    SciTech Connect

    Marinov, N.M., Pitz, W.J.; Westbrook, C.K.; Vincitore, A.M.; Senka, S.M.; Lutz, A.E.

    1998-01-01

    The chemical structure of an opposed flow, methane diffusion flame is studied using a chemical kinetic model and the results are compared to experimental measurements. The chemical kinetic paths leading to aromatics and polycyclic aromatics hydrocarbons (PAHs) in the diffusion flame are identified. These paths all involve resonantly stabilized radicals which include propargyl, allyl, cyclopentadienyl, and benzyl radicals. The modeling results show reasonable agreement with the experimental measurements for the large hydrocarbon aliphatic compounds, aromatics, and PAHs. the benzene was predicted to be formed primarily by the reaction sequence of Allyl plus Propargyl equals Fulvene plus H plus H followed by fulvene isomerization to benzene. Naphthalene was modeled using the reaction of benzyl with propargyl, while the combination of cyclopentadienyl radicals were shown to be a minor contributor in the diffusion flame. The agreement between the model and experiment for the four-ring PAHs was poor.

  7. Bilayer mass transport model for determining swelling and diffusion in coated, ultrathin membranes.

    PubMed

    Nadermann, Nichole K; Chan, Edwin P; Stafford, Christopher M

    2015-02-18

    Water transport and swelling properties of an ultrathin, selective polyamide layer with a hydrophilic polymer coating, i.e., a polymer bilayer, are studied using quartz crystal microbalance with dissipation (QCM-D). Specifically, QCM-D is used to measure the dynamic and equilibrium change in mass in a series of differential sorption experiments to determine the dependence of the apparent diffusion coefficient and equilibrium swelling of the bilayer as a function of the water vapor activity. To determine transport properties specific to the polyamide layer, sorption kinetics of the bilayer was modeled with a bilayer mass transport model. The swelling and water diffusion coefficients are interpreted according to the Painter-Shenoy polymer network swelling model and the solution-diffusion model, respectively.

  8. A theoretical model of isotopic fractionation by thermal diffusion and its implementation on silicate melts

    NASA Astrophysics Data System (ADS)

    Xuefang, L.; Liu, Y.

    2015-12-01

    Huang et al (2010) found that Fe, Ca and Mg isotope fractionations of high-temperature silicate melts are only associated with the temperature gradients in thermal diffusion processes and are independent of compositions and mean temperatures [1]. Richter et al (2010) doubted that the existing data are sufficient to obtain such conclusion [2]. A few theoretical models have been proposed for explaining isotopic fractionations in these processes under high temperatures [3, 4]. However, molecular-level mechanisms and theoretical treatments of these processes are still under debating. Here we provide a unified theory based on the local thermodynamic equilibrium treatment (LTE) of statistical mechanics for evaluating thermal isotopic fractionations under a wide range of temperatures. Under high temperatures, our theory however can be reasonably approximated to this equation: where A and B are constants which are related to specific isotope systems and chemical compositions of silicate melts. If the thermal gradient is not very large and the mean temperature is high, the second part of the above equation can be safely neglected and obtain an extremely simple equation which is linearly depended on temperatures, agreeing with what Huang et al (2010) concluded. Based on this terse equation, we can not only easily provide isotope fractionation data for almost all kinds of isotope systems, but also can provide the mechanisms of isotope fractionation in thermal diffusion processes. [1] Huang et al (2010) Nature 464, 396-400. [2] Richter et al (2010) Nature 472, E1-E1. [3] Dominguez et al (2011) Nature 473, 70-73.

  9. Measuring and modeling oxygen diffusion in niobium-vanadium and niobium-palladium alloys

    NASA Astrophysics Data System (ADS)

    Hennessey, Theresa P.

    Niobium alloys are under consideration for high-temperature aerospace applications, but they have poor oxidation resistance and need high-temperature coatings for protection in severe environments. Our approach to creating an oxidation-resistant Nb alloy is to identify substitutional solute elements that lower the diffusivity of oxygen in Nb. In theory, this will induce a transition from internal to external oxidation and promote the formation of a desirable, protective oxide scale. The objective of this particular project is to compare the oxygen diffusivity in Nb alloys that contain either trap or repulsive sites. In Nb, oxygen atoms diffuse via an interstitial mechanism, and they can interact with substitutional solute atoms in different ways. The interstitial sites adjacent to a substitutional atom constitute a "zone of influence". If the sites in this zone have a lower energy than the normal sites, they are called "trap" sites. If these sites have a higher energy, they are called "repulsive" sites. Oxygen diffusion is inhibited in both cases: trap sites hold the oxygen and keep it from diffusing further, while repulsive sites block the path of the oxygen. Two new mathematical models for interstitial diffusion in these systems were derived from probability and statistical thermodynamic theory. The models were verified using a new random-walk computer simulation of oxygen diffusion through Nb alloys. These models were also tested experimentally by measuring oxygen diffusivity in Nb-V and Nb-Pd alloys. These results showed that V atoms create trap sites for oxygen atoms, confirming previous work. However, there was not enough data to prove definitively that Pd atoms create repulsive sites, as expected by theory.

  10. 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

  11. Finite linear diffusion model for design of overcharge protection for rechargeable lithium batteries

    NASA Technical Reports Server (NTRS)

    Narayanan, S. R.; Surampudi, S.; Attia, A. I.

    1991-01-01

    The overcharge condition in secondary lithium batteries employing redox additives for overcharge protection has been theoretically analyzed in terms of a finite linear diffusion model. The analysis leads to expressions relating the steady-state overcharge current density and cell voltage to the concentration, diffusion coefficient, standard reduction potential of the redox couple, and interelectrode distance. The model permits the estimation of the maximum permissible overcharge rate for any chosen set of system conditions. The model has been experimentally verified using 1,1-prime-dimethylferrocene as a redox additive. The theoretical results may be exploited in the design and optimization of overcharge protection by the redox additive approach.

  12. A simplified model for thermal-wave cavity self-consistent measurement of thermal diffusivity

    NASA Astrophysics Data System (ADS)

    Shen, Jun; Zhou, Jianqin; Gu, Caikang; Neill, Stuart; Michaelian, Kirk H.; Fairbridge, Craig; Astrath, Nelson G. C.; Baesso, Mauro L.

    2013-12-01

    A simplified theoretical model was developed for the thermal-wave cavity (TWC) technique in this study. This model takes thermal radiation into account and can be employed for absolute measurements of the thermal diffusivity of gas and liquid samples without any knowledge of geometrical and thermal parameters of the components of the TWC. Using this model and cavity-length scans, thermal diffusivities of air and distilled water were accurately and precisely measured as (2.191 ± 0.004) × 10-5 and (1.427 ± 0.009) × 10-7 m2 s-1, respectively, in very good agreement with accepted literature values.

  13. Combustor diffuser interaction program

    NASA Technical Reports Server (NTRS)

    Srinivasan, Ram; Thorp, Daniel

    1986-01-01

    Advances in gas turbine engine performance are achieved by using compressor systems with high stage loading and low part count, which result in high exit Mach numbers. The diffuser and combustor systems in such engines should be optimized to reduce system pressure loss and to maximize the engine thrust-to-weight ratio and minimize length. The state-of-the-art combustor-diffuser systems do not meet these requirements. Detailed understanding of the combustor-diffuser flow field interaction is required for designing advanced gas turbine engines. An experimental study of the combustor-diffuser interaction (CDI) is being conducted to obtain data for the evaluation and improvement of analytical models applicable to a wide variety of diffuser designs. The CDI program consists of four technical phases: Literature Search; Baseline Configuration; Parametric Configurations; and Performance Configurations. Phase 2 of the program is in progress.

  14. Submodels of model of nonlinear diffusion in the inhomogeneous medium involving absorption

    SciTech Connect

    Chirkunov, Yu. A.

    2015-10-15

    We study the five-parameter model, describing the process of nonlinear diffusion in an inhomogeneous medium in the presence of absorption, for which the differential equation of the model admits a continuous Lie group of transformations, acting on the set of its solutions. We found six submodels of the original model of nonlinear diffusion, with different symmetry properties. Of these six submodels, the five submodels with transient absorption, for which the absorption coefficient depends on time according to a power law, represent the greatest interest with a mathematical point of view and with the point of view of physical applications. For each of these nonlinear submodels, we obtained formulas for producing new solutions that contain arbitrary constants, and we found all invariant submodels. All essentially distinct invariant solutions describing these invariant submodels are found in an explicit form or are reduced to finding the solution of nonlinear integral equations. The presence of the arbitrary constants in the integral equations that determine these solutions provide new opportunities for analytical and numerical study of boundary value problems for the received submodels and, thus, for the original model of nonlinear diffusion. For the received invariant submodels, we studied diffusion processes for which at the initial moment of the time at a fixed point is specified as a concentration and its gradient or as a concentration and its velocity. Solving of boundary value problems describing these processes is reduced to the solving of nonlinear integral equations. We established the existence and uniqueness of solutions of these boundary value problems under some additional conditions. The obtained results can be used to study the diffusion of substances, diffusion of conduction electrons and other particles, diffusion of physical fields and propagation of heat in inhomogeneous medium, and also to study a turbulence (Leith model, differential

  15. Forecasting turbulent modes with nonparametric diffusion models: Learning from noisy data

    NASA Astrophysics Data System (ADS)

    Berry, Tyrus; Harlim, John

    2016-04-01

    In this paper, we apply a recently developed nonparametric modeling approach, the "diffusion forecast", to predict the time-evolution of Fourier modes of turbulent dynamical systems. While the diffusion forecasting method assumes the availability of a noise-free training data set observing the full state space of the dynamics, in real applications we often have only partial observations which are corrupted by noise. To alleviate these practical issues, following the theory of embedology, the diffusion model is built using the delay-embedding coordinates of the data. We show that this delay embedding biases the geometry of the data in a way which extracts the most stable component of the dynamics and reduces the influence of independent additive observation noise. The resulting diffusion forecast model approximates the semigroup solutions of the generator of the underlying dynamics in the limit of large data and when the observation noise vanishes. As in any standard forecasting problem, the forecasting skill depends crucially on the accuracy of the initial conditions. We introduce a novel Bayesian method for filtering the discrete-time noisy observations which works with the diffusion forecast to determine the forecast initial densities. Numerically, we compare this nonparametric approach with standard stochastic parametric models on a wide-range of well-studied turbulent modes, including the Lorenz-96 model in weakly chaotic to fully turbulent regimes and the barotropic modes of a quasi-geostrophic model with baroclinic instabilities. We show that when the only available data is the low-dimensional set of noisy modes that are being modeled, the diffusion forecast is indeed competitive to the perfect model.

  16. A refined model of water and CO2 membrane diffusion: Effects and contribution of sterols and proteins

    PubMed Central

    Kai, Lei; Kaldenhoff, Ralf

    2014-01-01

    Black lipid bilayers, a general model system for biomembranes were studied for diffusion rates of small molecules such as water or CO2 using advanced analysis techniques and cell free synthesized proteins. We provide evidence that by simple insertion of proteins or sterols the diffusion rates of water or those of CO2 decrease. Insertion of cell free synthesized water permeable aquaporins restored water diffusion rates as well as insertion of CO2-facilitating aquaporins the CO2 diffusion. Insertion of water or CO2 impermeable proteins decreased the respective diffusion rates. Therefore, for normal high cellular CO2 diffusion rates specific aquaporins are mandatory. PMID:25331164

  17. Matrix Diffusion and Colloid-Facilitated Transport in Fractured Rocks: Model and Parameter Validation

    SciTech Connect

    Zavarin, M

    2002-08-02

    In this report, we review the results of Reimus et al. (2000a; 2000b) regarding matrix diffusion and colloid-facilitated transport in fractured rock and evaluate the implications of these results on modeling fracture flow at the Nevada Test Site (NTS). In particular, we examine these data in the context of the recent Cheshire hydrologic source term (HST) model results (Pawloski et al., 2001). This report is divided into several sections. In the first, we evaluate the effective diffusion coefficient (D{sub e}) data reported in Reimus et al. (2000a) for conservative tracer species ({sup 3}H, {sup 14}C, and {sup 99}Tc) and fit a simple effective diffusion model to these data. In the second, we use the fitted effective diffusion model, in conjunction with a surface complexation model, to simulate plutonium-colloid transport and compare model results to data reported in Reimus et al. (2000b). In the third, we evaluate the implications of these data with regards to radionuclide transport through fractures at the field scale and, in particular, with regards to the Cheshire HST model (Pawloski et al., 2001). Finally, we make recommendations regarding future radionuclide transport modeling efforts at the NTS.

  18. Stability and bifurcation in a reaction-diffusion model with nonlocal delay effect

    NASA Astrophysics Data System (ADS)

    Guo, Shangjiang

    2015-08-01

    In this paper, the existence, stability, and multiplicity of spatially nonhomogeneous steady-state solution and periodic solutions for a reaction-diffusion model with nonlocal delay effect and Dirichlet boundary condition are investigated by using Lyapunov-Schmidt reduction. Moreover, we illustrate our general results by applications to models with a single delay and one-dimensional spatial domain.

  19. Weak localization as a definitive test of diffusive models in the Casimir effect

    NASA Astrophysics Data System (ADS)

    Allocca, Andrew; Wilson, Justin; Galitski, Victor

    2015-03-01

    Results from many measurements of the Casimir effect suggest that the metallic plates in these experiments should be modeled with the plasma model of free electrons as opposed to the naive diffusive Drude model, while other experiments seem to indicate the exact opposite, with results more in line with a diffusive model. We study the Casimir effect at low temperatures between a thick disordered plate and purely two-dimensional disordered system where the Drude conductivity decreases logarithmically at low temperatures due to weak localization. This effect can be tuned with either temperature or applied magnetic field leading to a measurable change in the Casimir force. On the other hand, a ballistic model cannot experience such an effect and is only weakly dependent on temperature and magnetic field. As a result, we propose that an experiment would unambiguously differentiate between diffusive and ballistic models by measuring the effect at low temperatures with an applied magnetic field. Additionally, we calculate the impact that fluctuations in the disorder distribution have on the Casimir effect. Assuming the validity of a diffusive model, we find that the Drude model is a good approximation of a more exact treatment of disorder. This work was supported by the DOE-BES (Grant No. DESC0001911) (A.A. and V.G.), the JQI-PFC (J.W.), and the Simons Foundation.

  20. Proposing an Educational Scaling-and-Diffusion Model for Inquiry-Based Learning Designs

    ERIC Educational Resources Information Center

    Hung, David; Lee, Shu-Shing

    2015-01-01

    Education cannot adopt the linear model of scaling used by the medical sciences. "Gold standards" cannot be replicated without considering process-in-learning, diversity, and student-variedness in classrooms. This article proposes a nuanced model of educational scaling-and-diffusion, describing the scaling (top-down supports) and…

  1. A time-periodic reaction-diffusion epidemic model with infection period

    NASA Astrophysics Data System (ADS)

    Zhang, Liang; Wang, Zhi-Cheng

    2016-10-01

    In this paper, we propose a time-periodic and diffusive SIR epidemic model with constant infection period. By introducing the basic reproduction number R_0 via a next generation operator for this model, we show that the disease goes extinction if R_0 < 1; while the disease is uniformly persistent if R_0 > 1.

  2. A comparison of molecular dynamics and diffuse interface model predictions of Lennard-Jones fluid evaporation

    SciTech Connect

    Barbante, Paolo; Frezzotti, Aldo; Gibelli, Livio

    2014-12-09

    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 deviations 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.

  3. Comparison of neutron diffusion and Monte Carlo models for a fission wave

    SciTech Connect

    Osborne, A. G.; Deinert, M. R.

    2013-07-01

    Many groups have used neutron diffusion simulations to study fission wave phenomena in natural or depleted uranium. However, few studies of fission wave phenomena have been published that use Monte Carlo simulations to confirm the results of diffusion models for this type of system. In the present work we show the results of a criticality and burnup simulation of a traveling wave reactor using MCNPX 2.7.0. The characteristics of the fission wave in this simulation are compared with those from a simple one-dimensional, one-group neutron diffusion model. The diffusion simulations produce a wave speed of 5.9 cm/yr versus 5.3 cm/yr for the Monte Carlo simulations. The axial flux profile in the Monte Carlo simulation is similar in shape to the diffusion results, but with different peak values, and the two profiles have an R2 value of 0.93. The {sup 238}U, {sup 239}Np and {sup 239}Pu burnup profiles from the diffusion simulation show good agreement with the Monte Carlo simulations, R values of 0.98, 0.93 and 0.97 respectively are observed. (authors)

  4. Fractional motion model for characterization of anomalous diffusion from NMR signals.

    PubMed

    Fan, Yang; Gao, Jia-Hong

    2015-07-01

    Measuring molecular diffusion has been used to characterize the properties of living organisms and porous materials. NMR is able to detect the diffusion process in vivo and noninvasively. The fractional motion (FM) model is appropriate to describe anomalous diffusion phenomenon in crowded environments, such as living cells. However, no FM-based NMR theory has yet been established. Here, we present a general formulation of the FM-based NMR signal under the influence of arbitrary magnetic field gradient waveforms. An explicit analytic solution of the stretched exponential decay format for NMR signals with finite-width Stejskal-Tanner bipolar pulse magnetic field gradients is presented. Signals from a numerical simulation matched well with the theoretical prediction. In vivo diffusion-weighted brain images were acquired and analyzed using the proposed theory, and the resulting parametric maps exhibit remarkable contrasts between different brain tissues.

  5. Learning Information Diffusion Model for Extracting Influential Nodes in a Social Network

    NASA Astrophysics Data System (ADS)

    Kimura, Masahiro; Saito, Kazumi; Nakano, Ryohei; Motoda, Hiroshi

    We address the problem of ranking influential nodes in complex social networks by estimating diffusion probabilities from observed information diffusion data using the popular independent cascade (IC) model. For this purpose we formulate the likelihood for information diffusion data which is a set of time sequence data of active nodes and propose an iterative method to search for the probabilities that maximizes this likelihood. We apply this to two real world social networks in the simplest setting where the probability is uniform for all the links, and show that when there is a reasonable amount of information diffusion data, the accuracy of the probability is outstandingly good, and the proposed method can predict the high ranked influential nodes much more accurately than the well studied conventional four heuristic methods.

  6. Fractional motion model for characterization of anomalous diffusion from NMR signals

    NASA Astrophysics Data System (ADS)

    Fan, Yang; Gao, Jia-Hong

    2015-07-01

    Measuring molecular diffusion has been used to characterize the properties of living organisms and porous materials. NMR is able to detect the diffusion process in vivo and noninvasively. The fractional motion (FM) model is appropriate to describe anomalous diffusion phenomenon in crowded environments, such as living cells. However, no FM-based NMR theory has yet been established. Here, we present a general formulation of the FM-based NMR signal under the influence of arbitrary magnetic field gradient waveforms. An explicit analytic solution of the stretched exponential decay format for NMR signals with finite-width Stejskal-Tanner bipolar pulse magnetic field gradients is presented. Signals from a numerical simulation matched well with the theoretical prediction. In vivo diffusion-weighted brain images were acquired and analyzed using the proposed theory, and the resulting parametric maps exhibit remarkable contrasts between different brain tissues.

  7. Mass loading and velocity diffusion models for heavy pickup ions at comet Grigg-Skjellerup

    NASA Technical Reports Server (NTRS)

    Huddleston, D. E.; Coates, A. J.; Johnstone, A. D.; Neubauer, Fritz M.

    1993-01-01

    We compare model predictions of cometary water group ion densities and the solar wind slow down with measurements made by the Giotto Johnstone plasma analyzer implanted ion sensor at the encounter with comet Grigg-Skjellerup (G-S) on July 10, 1992. The observed slope of the ion density profile on approach to the comet is unexpectedly steep. Possible explanations for this are discussed. We present also a preliminary investigation of the quasilinear velocity-space diffusion of the implanted heavy ion population at G-S using a transport equation including souce, convection, adiabatic compression, and velocity diffusion terms. Resulting distributions are anisotropic, in agreement with observations. We consider theoretically the waves that may be generated by the diffusion process for the observed solar wind conditions. At initial ion injections, waves are generated at omega approximately Omega(sub i) the ion gyrofrequency, and lower frequencies are predicted for diffusion toward a bispherical shell.

  8. 12 CFR Appendix to Part 1016 - Model Privacy Form

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ...) with black or other contrasting ink color. Spot color may be used to achieve visual interest, so long... languages other than English. C. Information Required in the Model Privacy Form The information in the model... CFR part 1022, subpart C, with respect to the initial notice and opt-out and any subsequent...

  9. 12 CFR Appendix to Part 1016 - Model Privacy Form

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ...) with black or other contrasting ink color. Spot color may be used to achieve visual interest, so long... languages other than English. C. Information Required in the Model Privacy Form The information in the model... CFR part 1022, subpart C, with respect to the initial notice and opt-out and any subsequent...

  10. 12 CFR Appendix to Part 1016 - Model Privacy Form

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ...) with black or other contrasting ink color. Spot color may be used to achieve visual interest, so long... languages other than English. C. Information Required in the Model Privacy Form The information in the model... CFR part 1022, subpart C, with respect to the initial notice and opt-out and any subsequent...

  11. Identification of boundary conditions as a part of model correction

    NASA Astrophysics Data System (ADS)

    Pabst, U.; Hagedorn, P.

    1995-05-01

    Experience shows that in mathematical models of elastic systems the boundary conditions, bearings and joints are those parts of the system which are generally much less well known than the main components. The influence of these local parts on the system's dynamic behavior is commonly underestimated. Thus, in model correction, they tend to be modelled in an oversimplified way. Taking this fact into account, the present paper gives a system identification approach that is limited (at least in a first step) to the estimation of boundary conditions by using measured modal data.

  12. Variational Implicit Solvation with Solute Molecular Mechanics: From Diffuse-Interface to Sharp-Interface Models

    PubMed Central

    Li, Bo; Zhao, Yanxiang

    2013-01-01

    Central in a variational implicit-solvent description of biomolecular solvation is an effective free-energy functional of the solute atomic positions and the solute-solvent interface (i.e., the dielectric boundary). The free-energy functional couples together the solute molecular mechanical interaction energy, the solute-solvent interfacial energy, the solute-solvent van der Waals interaction energy, and the electrostatic energy. In recent years, the sharp-interface version of the variational implicit-solvent model has been developed and used for numerical computations of molecular solvation. In this work, we propose a diffuse-interface version of the variational implicit-solvent model with solute molecular mechanics. We also analyze both the sharp-interface and diffuse-interface models. We prove the existence of free-energy minimizers and obtain their bounds. We also prove the convergence of the diffuse-interface model to the sharp-interface model in the sense of Γ-convergence. We further discuss properties of sharp-interface free-energy minimizers, the boundary conditions and the coupling of the Poisson–Boltzmann equation in the diffuse-interface model, and the convergence of forces from diffuse-interface to sharp-interface descriptions. Our analysis relies on the previous works on the problem of minimizing surface areas and on our observations on the coupling between solute molecular mechanical interactions with the continuum solvent. Our studies justify rigorously the self consistency of the proposed diffuse-interface variational models of implicit solvation. PMID:24058213

  13. Mathematical model of diffusion-limited evolution of multiple gas bubbles in tissue.

    PubMed

    Srinivasan, R Srini; Gerth, Wayne A; Powell, Michael R

    2003-04-01

    Models of gas bubble dynamics employed in probabilistic analyses of decompression sickness incidence in man must be theoretically consistent and simple, if they are to yield useful results without requiring excessive computations. They are generally formulated in terms of ordinary differential equations that describe diffusion-limited gas exchange between a gas bubble and the extravascular tissue surrounding it. In our previous model (Ann. Biomed. Eng. 30: 232-246, 2002), we showed that with appropriate representation of sink pressures to account for gas loss or gain due to heterogeneous blood perfusion in the unstirred diffusion region around the bubble, diffusion-limited bubble growth in a tissue of finite volume can be simulated without postulating a boundary layer across which gas flux is discontinuous. However, interactions between two or more bubbles caused by competition for available gas cannot be considered in this model, because the diffusion region has a fixed volume with zero gas flux at its outer boundary. The present work extends the previous model to accommodate interactions among multiple bubbles by allowing the diffusion region volume of each bubble to vary during bubble evolution. For given decompression and tissue volume, bubble growth is sustained only if the bubble number density is below a certain maximum.

  14. Mathematical model of diffusion-limited evolution of multiple gas bubbles in tissue

    NASA Technical Reports Server (NTRS)

    Srinivasan, R. Srini; Gerth, Wayne A.; Powell, Michael R.

    2003-01-01

    Models of gas bubble dynamics employed in probabilistic analyses of decompression sickness incidence in man must be theoretically consistent and simple, if they are to yield useful results without requiring excessive computations. They are generally formulated in terms of ordinary differential equations that describe diffusion-limited gas exchange between a gas bubble and the extravascular tissue surrounding it. In our previous model (Ann. Biomed. Eng. 30: 232-246, 2002), we showed that with appropriate representation of sink pressures to account for gas loss or gain due to heterogeneous blood perfusion in the unstirred diffusion region around the bubble, diffusion-limited bubble growth in a tissue of finite volume can be simulated without postulating a boundary layer across which gas flux is discontinuous. However, interactions between two or more bubbles caused by competition for available gas cannot be considered in this model, because the diffusion region has a fixed volume with zero gas flux at its outer boundary. The present work extends the previous model to accommodate interactions among multiple bubbles by allowing the diffusion region volume of each bubble to vary during bubble evolution. For given decompression and tissue volume, bubble growth is sustained only if the bubble number density is below a certain maximum.

  15. 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. PMID:25348061

  16. Stability and Hopf bifurcation for a prey-predator model with prey-stage structure and diffusion.

    PubMed

    Wang, Mingxin

    2008-04-01

    In this paper, we first propose a prey-predator model with prey-stage structure and diffusion. Then we discuss the following three problems: (1) stability of non-negative constant steady states for the reduced ODE system and the corresponding reaction diffusion system with homogeneous Neumann boundary conditions; (2) Hopf bifurcation for the ODE system; (3) Hopf bifurcation created by diffusion.

  17. Multi-view and 3D deformable part models.

    PubMed

    Pepik, Bojan; Stark, Michael; Gehler, Peter; Schiele, Bernt

    2015-11-01

    As objects are inherently 3D, they have been modeled in 3D in the early days of computer vision. Due to the ambiguities arising from mapping 2D features to 3D models, 3D object representations have been neglected and 2D feature-based models are the predominant paradigm in object detection nowadays. While such models have achieved outstanding bounding box detection performance, they come with limited expressiveness, as they are clearly limited in their capability of reasoning about 3D shape or viewpoints. In this work, we bring the worlds of 3D and 2D object representations closer, by building an object detector which leverages the expressive power of 3D object representations while at the same time can be robustly matched to image evidence. To that end, we gradually extend the successful deformable part model [1] to include viewpoint information and part-level 3D geometry information, resulting in several different models with different level of expressiveness. We end up with a 3D object model, consisting of multiple object parts represented in 3D and a continuous appearance model. We experimentally verify that our models, while providing richer object hypotheses than the 2D object models, provide consistently better joint object localization and viewpoint estimation than the state-of-the-art multi-view and 3D object detectors on various benchmarks (KITTI [2] , 3D object classes [3] , Pascal3D+ [4] , Pascal VOC 2007 [5] , EPFL multi-view cars[6] ). PMID:26440264

  18. Dermic diffusion and stratum corneum: a state of the art review of mathematical models.

    PubMed

    Couto, Ana; Fernandes, Rúben; Cordeiro, M Natália S; Reis, Sara S; Ribeiro, Rogério T; Pessoa, Ana M

    2014-03-10

    Transdermal biotechnologies are an ever increasing field of interest, due to the medical and pharmaceutical applications that they underlie. There are several mathematical models at use that permit a more inclusive vision of pure experimental data and even allow practical extrapolation for new dermal diffusion methodologies. However, they grasp a complex variety of theories and assumptions that allocate their use for specific situations. Models based on Fick's First Law found better use in contexts where scaled particle theory Models would be extensive in time-span but the reciprocal is also true, as context of transdermal diffusion of particular active compounds changes. This article reviews extensively the various theoretical methodologies for studying dermic diffusion in the rate limiting dermic barrier, the stratum corneum, and systematizes its characteristics, their proper context of application, advantages and limitations, as well as future perspectives. PMID:24362041

  19. Dermic diffusion and stratum corneum: a state of the art review of mathematical models.

    PubMed

    Couto, Ana; Fernandes, Rúben; Cordeiro, M Natália S; Reis, Sara S; Ribeiro, Rogério T; Pessoa, Ana M

    2014-03-10

    Transdermal biotechnologies are an ever increasing field of interest, due to the medical and pharmaceutical applications that they underlie. There are several mathematical models at use that permit a more inclusive vision of pure experimental data and even allow practical extrapolation for new dermal diffusion methodologies. However, they grasp a complex variety of theories and assumptions that allocate their use for specific situations. Models based on Fick's First Law found better use in contexts where scaled particle theory Models would be extensive in time-span but the reciprocal is also true, as context of transdermal diffusion of particular active compounds changes. This article reviews extensively the various theoretical methodologies for studying dermic diffusion in the rate limiting dermic barrier, the stratum corneum, and systematizes its characteristics, their proper context of application, advantages and limitations, as well as future perspectives.

  20. A bioreaction-diffusion model for growth of marine sponge explants in bioreactors.

    PubMed

    Garcia Camacho, F; Chileh, T; Cerón García, M C; Sánchez Mirón, A; Belarbi, E H; Chisti, Y; Molina Grima, E

    2006-12-01

    Marine sponges are sources of high-value bioactives. Engineering aspects of in vitro culture of sponges from cuttings (explants) are poorly understood. This work develops a diffusion-controlled growth model for sponge explants. The model assumes that the explant growth is controlled by diffusive transport of at least some nutrients from the surrounding medium into the explant that generally has a poorly developed aquiferous system for internal irrigation during early stages of growth. Growth is assumed to obey Monod-type kinetics. The model is shown to satisfactorily explain the measured growth behavior of the marine sponge Crambe crambe in two different growth media. In addition, the model is generally consistent with published data for growth of explants of the sponges Disidea avara and Hemimycale columella. The model predicted that nutrient concentration profiles for nutrients, such as dissolved oxygen within the explant, are consistent with data published by independent researchers. In view of the proposed model's ability to explain available data for growth of several species of sponge explants, diffusive transport does play a controlling role in explant growth at least until a fully developed aquiferous system has become established. According to the model and experimental observations, the instantaneous growth rate depends on the size of the explant and all those factors that influence the diffusion of critical nutrients within the explant. Growth follows a hyperbolic profile that is consistent with the Monod kinetics.