Biomolecular interactions modulate macromolecular structure and dynamics in atomistic model of a bacterial cytoplasm

PubMed Central

Yu, Isseki; Mori, Takaharu; Ando, Tadashi; Harada, Ryuhei; Jung, Jaewoon; Sugita, Yuji; Feig, Michael

2016-01-01

Biological macromolecules function in highly crowded cellular environments. The structure and dynamics of proteins and nucleic acids are well characterized in vitro, but in vivo crowding effects remain unclear. Using molecular dynamics simulations of a comprehensive atomistic model cytoplasm we found that protein-protein interactions may destabilize native protein structures, whereas metabolite interactions may induce more compact states due to electrostatic screening. Protein-protein interactions also resulted in significant variations in reduced macromolecular diffusion under crowded conditions, while metabolites exhibited significant two-dimensional surface diffusion and altered protein-ligand binding that may reduce the effective concentration of metabolites and ligands in vivo. Metabolic enzymes showed weak non-specific association in cellular environments attributed to solvation and entropic effects. These effects are expected to have broad implications for the in vivo functioning of biomolecules. This work is a first step towards physically realistic in silico whole-cell models that connect molecular with cellular biology. DOI: http://dx.doi.org/10.7554/eLife.19274.001 PMID:27801646

Anisotropic Mesoscale Eddy Transport in Ocean General Circulation Models

NASA Astrophysics Data System (ADS)

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

2014-12-01

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

Diffusion impact on atmospheric moisture transport

NASA Astrophysics Data System (ADS)

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

2009-04-01

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

Parametric studies with an atmospheric diffusion model that assesses toxic fuel hazards due to the ground clouds generated by rocket launches

NASA Technical Reports Server (NTRS)

Stewart, R. B.; Grose, W. L.

1975-01-01

Parametric studies were made with a multilayer atmospheric diffusion model to place quantitative limits on the uncertainty of predicting ground-level toxic rocket-fuel concentrations. Exhaust distributions in the ground cloud, cloud stabilized geometry, atmospheric coefficients, the effects of exhaust plume afterburning of carbon monoxide CO, assumed surface mixing-layer division in the model, and model sensitivity to different meteorological regimes were studied. Large-scale differences in ground-level predictions are quantitatively described. Cloud alongwind growth for several meteorological conditions is shown to be in error because of incorrect application of previous diffusion theory. In addition, rocket-plume calculations indicate that almost all of the rocket-motor carbon monoxide is afterburned to carbon dioxide CO2, thus reducing toxic hazards due to CO. The afterburning is also shown to have a significant effect on cloud stabilization height and on ground-level concentrations of exhaust products.

Lateral carrier diffusion and current gain in terahertz InGaAs/InP double-heterojunction bipolar transistors

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

Chiang, Han-Wei; Rode, Johann C.; Choudhary, Prateek

2014-01-21

The DC current gain in In{sub 0.53}Ga{sub 0.47}As/InP double-heterojunction bipolar transistors is computed based on a drift-diffusion model, and is compared with experimental data. Even in the absence of other scaling effects, lateral diffusion of electrons to the base Ohmic contacts causes a rapid reduction in DC current gain as the emitter junction width and emitter-base contact spacing are reduced. The simulation and experimental data are compared in order to examine the effect of carrier lateral diffusion on current gain. The impact on current gain due to device scaling and approaches to increase current gain are discussed.

Convective drying of osmo-dehydrated apple slices: kinetics and spatial behavior of effective mass diffusivity and moisture content

NASA Astrophysics Data System (ADS)

de Farias Aires, Juarez Everton; da Silva, Wilton Pereira; de Almeida Farias Aires, Kalina Lígia Cavalcante; da Silva Júnior, Aluízio Freire; da Silva e Silva, Cleide Maria Diniz Pereira

2018-04-01

The main objective of this study is the presentation of a numerical model of liquid diffusion for the description of the convective drying of apple slices submitted to pretreatment of osmotic dehydration able of predicting the spatial distribution of effective mass diffusivity values in apple slabs. Two models that use numerical solutions of the two-dimensional diffusion equation in Cartesian coordinates with the boundary condition of third kind were proposed to describe drying. The first one does not consider the shrinkage of the product and assumes that the process parameters remain constant along the convective drying. The second one considers the shrinkage of the product and assumes that the effective mass diffusivity of water varies according to the local value of the water content in the apple samples. Process parameters were estimated from experimental data through an optimizer coupled to the numerical solutions. The osmotic pretreatment did not reduce the drying time in relation to the fresh fruits when the drying temperature was equal to 40 °C. The use of the temperature of 60 °C led to a reduction in the drying time. The model that considers the variations in the dimensions of the product and the variation in the effective mass diffusivity proved to be more adequate to describe the process.

Urban stormwater inundation simulation based on SWMM and diffusive overland-flow model.

PubMed

Chen, Wenjie; Huang, Guoru; Zhang, Han

2017-12-01

With rapid urbanization, inundation-induced property losses have become more and more severe. Urban inundation modeling is an effective way to reduce these losses. This paper introduces a simplified urban stormwater inundation simulation model based on the United States Environmental Protection Agency Storm Water Management Model (SWMM) and a geographic information system (GIS)-based diffusive overland-flow model. SWMM is applied for computation of flows in storm sewer systems and flooding flows at junctions, while the GIS-based diffusive overland-flow model simulates surface runoff and inundation. One observed rainfall scenario on Haidian Island, Hainan Province, China was chosen to calibrate the model and the other two were used for validation. Comparisons of the model results with field-surveyed data and InfoWorks ICM (Integrated Catchment Modeling) modeled results indicated the inundation model in this paper can provide inundation extents and reasonable inundation depths even in a large study area.

Dissipation of ionospheric irregularities by wave-particle and collisional interactions

NASA Technical Reports Server (NTRS)

Bernhardt, P. A.; Pongratz, M. B.; Gray, S. P.; Thomsen, M. F.

1982-01-01

The nonlinear dissipation of plasma irregularities aligned parallel to an ambient magnetic field is studied numerically using a model which employs both wave-particle and collisional diffusion. A wave-particle diffusion coefficient derived from a local theory of the universal drift instability is used. This coefficient is effective in regions of nonzero plasma gradients and produces triangular-shaped irregularities with spectra which vary as f to the -4th, where f is the spatial frequency. Collisional diffusion acts rapidly on the vertices of the irregularities to reduce their amplitude. The simultaneous action of the two dissipative processes is more efficient than collisions acting alone. In this model, wave-particle diffusion mimics the forward cascade process of wave-wave coupling.

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

NASA Astrophysics Data System (ADS)

Mardani, Amir; Tabejamaat, Sadegh; Ghamari, Mohsen

2010-09-01

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

A battery model that enables consideration of realistic anisotropic environment surrounding an active material particle and its application

NASA Astrophysics Data System (ADS)

Lin, Xianke; Lu, Wei

2017-07-01

This paper proposes a model that enables consideration of the realistic anisotropic environment surrounding an active material particle by incorporating both diffusion and migration of lithium ions and electrons in the particle. This model makes it possible to quantitatively evaluate effects such as fracture on capacity degradation. In contrast, the conventional model assumes isotropic environment and only considers diffusion in the active particle, which cannot capture the effect of fracture since it would predict results contradictory to experimental observations. With the developed model we have investigated the effects of active material electronic conductivity, particle size, and State of Charge (SOC) swing window when fracture exists. The study shows that the low electronic conductivity of active material has a significant impact on the lithium ion pattern. Fracture increases the resistance for electron transport and therefore reduces lithium intercalation/deintercalation. Particle size plays an important role in lithium ion transport. Smaller particle size is preferable for mitigating capacity loss when fracture happens. The study also shows that operating at high SOC reduces the impact of fracture.

Relevance of anisotropy and spatial variability of gas diffusivity for soil-gas transport

NASA Astrophysics Data System (ADS)

Schack-Kirchner, Helmer; Kühne, Anke; Lang, Friederike

2017-04-01

Models of soil gas transport generally do not consider neither direction dependence of gas diffusivity, nor its small-scale variability. However, in a recent study, we could provide evidence for anisotropy favouring vertical gas diffusion in natural soils. We hypothesize that gas transport models based on gas diffusion data measured with soil rings are strongly influenced by both, anisotropy and spatial variability and the use of averaged diffusivities could be misleading. To test this we used a 2-dimensional model of soil gas transport to under compacted wheel tracks to model the soil-air oxygen distribution in the soil. The model was parametrized with data obtained from soil-ring measurements with its central tendency and variability. The model includes vertical parameter variability as well as variation perpendicular to the elongated wheel track. Different parametrization types have been tested: [i)]Averaged values for wheel track and undisturbed. em [ii)]Random distribution of soil cells with normally distributed variability within the strata. em [iii)]Random distributed soil cells with uniformly distributed variability within the strata. All three types of small-scale variability has been tested for [j)] isotropic gas diffusivity and em [jj)]reduced horizontal gas diffusivity (constant factor), yielding in total six models. As expected the different parametrizations had an important influence to the aeration state under wheel tracks with the strongest oxygen depletion in case of uniformly distributed variability and anisotropy towards higher vertical diffusivity. The simple simulation approach clearly showed the relevance of anisotropy and spatial variability in case of identical central tendency measures of gas diffusivity. However, until now it did not consider spatial dependency of variability, that could even aggravate effects. To consider anisotropy and spatial variability in gas transport models we recommend a) to measure soil-gas transport parameters spatially explicit including different directions and b) to use random-field stochastic models to assess the possible effects for gas-exchange models.

Effect of diffusive and nondiffusive surfaces combinations on sound diffusion

NASA Astrophysics Data System (ADS)

Shafieian, Masoume; Kashani, Farokh Hodjat

2010-05-01

One of room acoustic goals, especially in small to medium rooms, is sound diffusion in low frequencies, which have been the subject of lots of researches. Sound diffusion is a very important consideration in acoustics because it minimizes the coherent reflections that cause problems. It also tends to make an enclosed space sound larger than it is. Diffusion is an excellent alternative or complement to sound absorption in acoustic treatment because it doesn’t really remove much energy, which means it can be used to effectively reduce reflections while still leaving an ambient or live sounding space. Distribution of diffusive and nondiffusive surfaces on room walls affect sound diffusion in room, but the amount, combination, and location of these surfaces are still the matter of question. This paper investigates effects of these issues on room acoustic frequency response in different parts of the room with different source-receiver locations. Room acoustic model based on wave method is used (implemented) which is very accurate and convenient for low frequencies in such rooms. Different distributions of acoustic surfaces on room walls have been introduced to the model and room frequency response results are calculated. For the purpose of comparison, some measurements results are presented. Finally for more smooth frequency response in small and medium rooms, some suggestions are made.

Effect of porous structure of catalyst layer on effective oxygen diffusion coefficient in polymer electrolyte fuel cell

NASA Astrophysics Data System (ADS)

Inoue, Gen; Kawase, Motoaki

2016-09-01

It is important to reduce the oxygen diffusion resistance through PEFC porous electrode, because it is the key to reduce the PEFC cost. However, the gas diffusion coefficient of CL is lower than MPL in spite of framework consisted of same carbon blacks. In this study, in order to understand the reasons of the lower gas diffusion performance of CL, the relationship between a carbon black agglomerate structure and ionomer adhesion condition is evaluated by a numerical analysis with an actual reconstructed structure and a simulated structure. As a result, the gas diffusion property of CL strongly depends on the ionomer adhesion shape. In the case of adhesion shape with the same curvature of ionomer interface, each pore can not be connected enough. So the pore tortuosity increases. Moreover, in the case of existence of inefficient large pores formed by carbon black agglomerate and ununiformly coated ionomer, the gas diffusion performance decrease rapidly. As the measurement values in actual CL are almost equal to that with model structure with inefficient large pores. These characteristics can be confirmed by actual cross-section image obtained by FIB-SEM.

Gas depletion through single gas bubble diffusive growth and its effect on subsequent bubbles

NASA Astrophysics Data System (ADS)

Moreno Soto, Alvaro; Prosperetti, Andrea; Lohse, Detlef; van der Meer, Devaraj; Physics of Fluid Group Collaboration; MCEC Netherlands CenterMultiscale Catalytic Energy Conversion Collaboration

2016-11-01

In weakly supersaturated mixtures, bubbles are known to grow quasi-statically as diffusion-driven mass transfer governs the process. In the final stage of the evolution, before detachment, there is an enhancement of mass transfer, which changes from diffusion to natural convection. Once the bubble detaches, it leaves behind a gas-depleted area. The diffusive mass transfer towards that region cannot compensate for the amount of gas which is taken away by the bubble. Consequently, the consecutive bubble will grow in an environment which contains less gas than for the previous one. This reduces the local supersaturation of the mixture around the nucleation site, leading to a reduced bubble growth rate. We present quantitative experimental data on this effect and the theoretical model for depletion during the bubble growth rate. This work was supported by the Netherlands Center for Multiscale Catalytic Energy Conversion (MCEC), an NWO Gravitation programme funded by the Ministry of Education, Culture and Science of the government of the Netherlands.

An analytical model for contaminant transport in landfill composite liners considering coupled effect of consolidation, diffusion, and degradation.

PubMed

Xie, Haijian; Yan, Huaxiang; Feng, Shijin; Wang, Qiao; Chen, Peixiong

2016-10-01

One-dimensional mathematical model is developed to investigate the behavior of contaminant transport in landfill composite liner system considering coupled effect of consolidation, diffusion, and degradation. The first- and second-type bottom boundary conditions are used to derive the steady-state and quasi-steady-state analytical solutions. The concentration profiles obtained by the proposed analytical solution are in good agreement with those obtained by the laboratory tests. The bottom concentration and flux of the soil liners can be greatly reduced when the degradation effect and porosity changing are considered. For the case under steady-state, the bottom flux and concentration for the case with t 1/2 =10 years can be 2.8 and 5.5 times lower than those of the case with t 1/2 =100 years, respectively. The bottom concentration and flux of the soil liners can be greatly reduced when the coefficient of volume compressibility decreases. For quasi-steady-state and with t 1/2 = 10 years, the bottom flux and concentration for the case with m v  = 0.02/MPa can be 17.4 and 21 times lower than the case with m v  = 0.5/MPa. This may be due to the fact that the true fluid velocity induced by consolidation is greater for the case with high coefficient of volume compressibility. The bottom flux for the case with single compacted clay liner (CCL) can be 1.5 times larger than that for the case with GMB/CCL considering diffusion and consolidation for DCM. The proposed analytical model can be used for verification of more complicated numerical models and assessment of the coupled effect of diffusion, consolidation, and degradation on contaminant transport in landfill liner systems.

Understanding the anisotropic strain effects on lithium diffusion in graphite anodes: A first-principles study

NASA Astrophysics Data System (ADS)

Ji, Xiang; Wang, Yang; Zhang, Junqian

2018-06-01

The lithium diffusion in graphite anode, which is the most widely used commercial electrode material today, affects the charge/discharge performance of lithium-ion batteries. In this study, the anisotropic strain effects on lithium diffusion in graphite anodes are systematically investigated using first-principles calculations based on density functional theory (DFT) with van der Waals corrections. It is found that the effects of external applied strains along various directions of LixC6 (i.e., perpendicular or parallel to the basal planes of the graphite host) on lithium diffusivity are different. Along the direction perpendicular to the graphite planes, the tensile strain facilitates in-plane Li diffusion by reducing the energy barrier, and the compressive strain hinders in-plane Li diffusion by raising the energy barrier. In contrast, the in-plane biaxial tensile strain (parallel to the graphite planes) hinders in-plane Li diffusion, and the in-plane biaxial compressive strain facilitates in-plane Li diffusion. Furthermore, both in-plane and transverse shear strains slightly influence Li diffusion in graphite anodes. A discussion is presented to explain the anisotropic strain dependence of lithium diffusion. This research provides data for the continuum modelling of the electrodes in the lithium-ion batteries.

Development of high-efficiency solar cells on silicon web

NASA Technical Reports Server (NTRS)

Meier, D. L.; Greggi, J.; Rai-Choudhury, P.

1986-01-01

Work is reported aimed at identifying and reducing sources of carrier recombination both in the starting web silicon material and in the processed cells. Cross-sectional transmission electron microscopy measurements of several web cells were made and analyzed. The effect of the heavily twinned region on cell efficiency was modeled, and the modeling results compared to measured values for processed cells. The effects of low energy, high dose hydrogen ion implantation on cell efficiency and diffusion length were examined. Cells were fabricated from web silicon known to have a high diffusion length, with a new double layer antireflection coating being applied to these cells. A new contact system, to be used with oxide passivated cells and which greatly reduces the area of contact between metal and silicon, was designed. The application of DLTS measurements to beveled samples was further investigated.

Modeling the effect of glutamate diffusion and uptake on NMDA and non-NMDA receptor saturation.

PubMed Central

Holmes, W R

1995-01-01

One- and two-dimensional models of glutamate diffusion, uptake, and binding in the synaptic cleft were developed to determine if the release of single vesicles of glutamate would saturate NMDA and non-NMDA receptors. Ranges of parameter values were used in the simulations to determine the conditions when saturation could occur. Single vesicles of glutamate did not saturate NMDA receptors unless diffusion was very slow and the number of glutamate molecules in a vesicle was large. However, the release of eight vesicles at 400 Hz caused NMDA receptor saturation for all parameter values tested. Glutamate uptake was found to reduce NMDA receptor saturation, but the effect was smaller than that of changes in the diffusion coefficient or in the number of glutamate molecules in a vesicle. Non-NMDA receptors were not saturated unless diffusion was very slow and the number of glutamate molecules in a vesicle was large. The release of eight vesicles at 400 Hz caused significant non-NMDA receptor desensitization. The results suggest that NMDA and non-NMDA receptors are not saturated by single vesicles of glutamate under usual conditions, and that tetanic input, of the type typically used to induce long-term potentiation, will increase calcium influx by increasing receptor binding as well as by reducing voltage-dependent block of NMDA receptors. Images FIGURE 1 PMID:8580317

Downstream boundary effects on the frequency of self-excited oscillations in transonic diffuser flows

NASA Astrophysics Data System (ADS)

Hsieh, T.

1986-10-01

Investigation of downstream boundary effects on the frequency of self-excited oscillations in two-dimensional, separated transonic diffuser flows were conducted numerically by solving the compressible, Reynolds-averaged, thin-layer Navier-Stokes equation with two equation turbulence models. It was found that the flow fields are very sensitive to the location of the downstream boundary. Extension of the diffuser downstream boundary significantly reduces the frequency and amplitude of oscillations for pressure, velocity, and shock. The existence of a suction slot in the experimental setpup obscures the physical downstream boundary and therefore presents a difficulty for quantitative comparisons between computation and experiment.

The coupled effects of chemistry and diffusion on the stratospheric ozone reduction

NASA Technical Reports Server (NTRS)

Gupta, R. N.; Grose, W. L.

1980-01-01

The effect of diffusive-mixing on O3-depletion is estimated using the five-step chemistry model. The coupled treatment uses an equilibrium turbulence field and retains the key features of the kinetics while keeping the chemistry simple. Results indicate that those calculations of Hilst and Donaldson (1973) employing the conservation of NO2/NO will yield erroneous results, and it is found that any significant level of turbulence will reduce the severity of the NOx catalytic cycle for O3 destruction.

Effects of Drift-Shell Splitting by Chorus Waves on Radiation Belt Electrons

NASA Astrophysics Data System (ADS)

Chan, A. A.; Zheng, L.; O'Brien, T. P., III; Tu, W.; Cunningham, G.; Elkington, S. R.; Albert, J.

2015-12-01

Drift shell splitting in the radiation belts breaks all three adiabatic invariants of charged particle motion via pitch angle scattering, and produces new diffusion terms that fully populate the diffusion tensor in the Fokker-Planck equation. Based on the stochastic differential equation method, the Radbelt Electron Model (REM) simulation code allows us to solve such a fully three-dimensional Fokker-Planck equation, and to elucidate the sources and transport mechanisms behind the phase space density variations. REM has been used to perform simulations with an empirical initial phase space density followed by a seed electron injection, with a Tsyganenko 1989 magnetic field model, and with chorus wave and ULF wave diffusion models. Our simulation results show that adding drift shell splitting changes the phase space location of the source to smaller L shells, which typically reduces local electron energization (compared to neglecting drift-shell splitting effects). Simulation results with and without drift-shell splitting effects are compared with Van Allen Probe measurements.

Numerical Modelling of the Sound Fields in Urban Streets with Diffusely Reflecting Boundaries

NASA Astrophysics Data System (ADS)

KANG, J.

2002-12-01

A radiosity-based theoretical/computer model has been developed to study the fundamental characteristics of the sound fields in urban streets resulting from diffusely reflecting boundaries, and to investigate the effectiveness of architectural changes and urban design options on noise reduction. Comparison between the theoretical prediction and the measurement in a scale model of an urban street shows very good agreement. Computations using the model in hypothetical rectangular streets demonstrate that though the boundaries are diffusely reflective, the sound attenuation along the length is significant, typically at 20-30 dB/100 m. The sound distribution in a cross-section is generally even unless the cross-section is very close to the source. In terms of the effectiveness of architectural changes and urban design options, it has been shown that over 2-4 dB extra attenuation can be obtained either by increasing boundary absorption evenly or by adding absorbent patches on the façades or the ground. Reducing building height has a similar effect. A gap between buildings can provide about 2-3 dB extra sound attenuation, especially in the vicinity of the gap. The effectiveness of air absorption on increasing sound attenuation along the length could be 3-9 dB at high frequencies. If a treatment is effective with a single source, it is also effective with multiple sources. In addition, it has been demonstrated that if the façades in a street are diffusely reflective, the sound field of the street does not change significantly whether the ground is diffusely or geometrically reflective.

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

NASA Astrophysics Data System (ADS)

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

2014-05-01

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

Seasonal Variability in Global Eddy Diffusion and the Effect on Thermospheric Neutral Density

NASA Astrophysics Data System (ADS)

Pilinski, M.; Crowley, G.

2014-12-01

We describe a method for making single-satellite estimates of the seasonal variability in global-average eddy diffusion coefficients. Eddy diffusion values as a function of time between January 2004 and January 2008 were estimated from residuals of neutral density measurements made by the CHallenging Minisatellite Payload (CHAMP) and simulations made using the Thermosphere Ionosphere Mesosphere Electrodynamics - Global Circulation Model (TIME-GCM). The eddy diffusion coefficient results are quantitatively consistent with previous estimates based on satellite drag observations and are qualitatively consistent with other measurement methods such as sodium lidar observations and eddy-diffusivity models. The eddy diffusion coefficient values estimated between January 2004 and January 2008 were then used to generate new TIME-GCM results. Based on these results, the RMS difference between the TIME-GCM model and density data from a variety of satellites is reduced by an average of 5%. This result, indicates that global thermospheric density modeling can be improved by using data from a single satellite like CHAMP. This approach also demonstrates how eddy diffusion could be estimated in near real-time from satellite observations and used to drive a global circulation model like TIME-GCM. Although the use of global values improves modeled neutral densities, there are some limitations of this method, which are discussed, including that the latitude-dependence of the seasonal neutral-density signal is not completely captured by a global variation of eddy diffusion coefficients. This demonstrates the need for a latitude-dependent specification of eddy diffusion consistent with diffusion observations made by other techniques.

Seasonal variability in global eddy diffusion and the effect on neutral density

NASA Astrophysics Data System (ADS)

Pilinski, M. D.; Crowley, G.

2015-04-01

We describe a method for making single-satellite estimates of the seasonal variability in global-average eddy diffusion coefficients. Eddy diffusion values as a function of time were estimated from residuals of neutral density measurements made by the Challenging Minisatellite Payload (CHAMP) and simulations made using the thermosphere-ionosphere-mesosphere electrodynamics global circulation model (TIME-GCM). The eddy diffusion coefficient results are quantitatively consistent with previous estimates based on satellite drag observations and are qualitatively consistent with other measurement methods such as sodium lidar observations and eddy diffusivity models. Eddy diffusion coefficient values estimated between January 2004 and January 2008 were then used to generate new TIME-GCM results. Based on these results, the root-mean-square sum for the TIME-GCM model is reduced by an average of 5% when compared to density data from a variety of satellites, indicating that the fidelity of global density modeling can be improved by using data from a single satellite like CHAMP. This approach also demonstrates that eddy diffusion could be estimated in near real-time from satellite observations and used to drive a global circulation model like TIME-GCM. Although the use of global values improves modeled neutral densities, there are limitations to this method, which are discussed, including that the latitude dependence of the seasonal neutral-density signal is not completely captured by a global variation of eddy diffusion coefficients. This demonstrates the need for a latitude-dependent specification of eddy diffusion which is also consistent with diffusion observations made by other techniques.

Analysis of Molecular Movement Reveals Latticelike Obstructions to Diffusion in Heart Muscle Cells

PubMed Central

Illaste, Ardo; Laasmaa, Martin; Peterson, Pearu; Vendelin, Marko

2012-01-01

Intracellular diffusion in muscle cells is known to be restricted. Although characteristics and localization of these restrictions is yet to be elucidated, it has been established that ischemia-reperfusion injury reduces the overall diffusion restriction. Here we apply an extended version of raster image correlation spectroscopy to determine directional anisotropy and coefficients of diffusion in rat cardiomyocytes. Our experimental results indicate that diffusion of a smaller molecule (1127 MW fluorescently labeled ATTO633-ATP) is restricted more than that of a larger one (10,000 MW Alexa647-dextran), when comparing diffusion in cardiomyocytes to that in solution. We attempt to provide a resolution to this counterintuitive result by applying a quantitative stochastic model of diffusion. Modeling results suggest the presence of periodic intracellular barriers situated ∼1 μm apart having very low permeabilities and a small effect of molecular crowding in volumes between the barriers. Such intracellular structuring could restrict diffusion of molecules of energy metabolism, reactive oxygen species, and apoptotic signals, enacting a significant role in normally functioning cardiomyocytes as well as in pathological conditions of the heart. PMID:22385844

Experimental study of the possibility of reducing the resistance and unevenness of output field of velocities in flat diffuser channels with large opening angles

NASA Astrophysics Data System (ADS)

Dmitriev, S. S.; Vasil'ev, K. E.; Mokhamed, S. M. S. O.; Gusev, A. A.; Barbashin, A. V.

2017-11-01

In modern combined cycle gas turbines (CCGT), when designing the reducers from the output diffuser of a gas turbine to a boiler-utilizer, wide-angle diffusers are used, in which practically from the input a flow separation and transition to jet stream regime occurs. In such channels, the energy loss in the field of velocities sharply rise and the field of velocities in the output from them is characterized by considerable unevenness that worsens the heat transfer process in the first by motion tube bundles of the boiler-utilizer. The results of experimental research of the method for reducing the energy loss and alignment of the field of velocities at the output from a flat asymmetrical diffuser channel with one deflecting wall with the opening angle of 40° by means of placing inside the channel the flat plate parallel to the deflecting wall are presented in the paper. It is revealed that, at this placement of the plate in the channel, it has a chance to reduce the energy loss by 20%, considerably align the output field of velocities, and decrease the dynamic loads on the walls in the output cross-section. The studied method of resistance reduction and alignment of the fields of velocities in the flat diffuser channels was used for optimization of the reducer from the output diffuser of the gas turbine to the boiler-utilizer of CCGT of PGU-450T type of Kaliningrad Thermal Power Plant-2. The obtained results are evidence that the configuration of the reducer installed in the PGU-450T of Kaliningrad Thermal Power Plant-2 is not optimal. It follows also from the obtained data that working-off the reducer should be necessarily conducted by the test results of the channel consisting of the model of reducer with the model of boiler-utilizer installed behind it. Application of the method of alignment of output field of velocities and reducing the resistance in the wide-angle diffusers investigated in the work made it possible—when using the known model of diffusion reducer for PGU-450T, which is bad from the standpoint of aerodynamics— to reduce the value of the coefficient of the total loss by almost 20% as compared with the model of real reducer of PGU-450T.

Transverse thermal conductivity of porous materials made from aligned nano- and microcylindrical pores

NASA Astrophysics Data System (ADS)

Prasher, Ravi

2006-09-01

Nanoporous and microporous materials made from aligned cylindrical pores play important roles in present technologies and will play even bigger roles in future technologies. The insight into the phonon thermal conductivity of these materials is important and relevant in many technologies and applications. Since the mean free path of phonons can be comparable to the pore size and interpore distance, diffusion-approximation based effective medium models cannot be used to predict the thermal conductivity of these materials. Strictly speaking, the Boltzmann transport equation (BTE) must be solved to capture the ballistic nature of thermal transport; however, solving BTE in such a complex network of pores is impractical. As an alternative, we propose an approximate ballistic-diffusive microscopic effective medium model for predicting the thermal conductivity of phonons in two-dimensional nanoporous and microporous materials made from aligned cylindrical pores. The model captures the size effects due to the pore diameter and the interpore distance and reduces to diffusion-approximation based models for macroporous materials. The results are in good agreement with experimental data.

Why do proton conducting polybenzimidazole phosphoric acid membranes perform well in high-temperature PEM fuel cells?

PubMed

Melchior, Jan-Patrick; Majer, Günter; Kreuer, Klaus-Dieter

2016-12-21

Transport properties and hydration behavior of phosphoric acid/(benz)imidazole mixtures are investigated by diverse NMR techniques, thermogravimetric analysis (TGA) and conductivity measurements. The monomeric systems can serve as models for phosphoric acid/poly-benzimidazole membranes which are known for their exceptional performance in high temperature PEM fuel cells. 1 H- and 31 P-NMR data show benzimidazole acting as a strong Brønsted base with respect to neat phosphoric acid. Since benzimidazole's nitrogens are fully protonated with a low rate for proton exchange with phosphate species, proton diffusion and conduction processes must take place within the hydrogen bond network of phosphoric acid only. The proton exchange dynamics between phosphate and benzimidazole species pass through the intermediate exchange regime (with respect to NMR line separations) with exchange times being close to typical diffusion times chosen in PFG-NMR diffusion measurements (ms regime). The resulting effects, as described by the Kärger equation, are included into the evaluation of PFG-NMR data for obtaining precise proton diffusion coefficients. The highly reduced proton diffusion coefficient within the phosphoric acid part of the model systems compared to neat phosphoric acid is suggested to be the immediate consequence of proton subtraction from phosphoric acid. This reduces hydrogen bond network frustration (imbalance of the number of proton donors and acceptors) and therefore also the rate of structural proton diffusion, phosphoric acid's acidity and hygroscopicity. Reduced water uptake, shown by TGA, goes along with reduced electroosmotic water drag which is suggested to be the reason for PBI-phosphoric acid membranes performing better in fuel cells than other phosphoric-acid-containing electrolytes with higher protonic conductivity.

Diffusion of biostimulators into plant tissues

NASA Astrophysics Data System (ADS)

Kolomazník, Karel; Pecha, Jiří; Friebrová, Veronika; Janáčová, Dagmar; Vašek, Vladimír

2012-09-01

Biostimulators are substances able to enhance the immune system of cultivated crops and support plant metabolism. Their utilization helps to reduce the amount of chemicals used in agriculture. To perform the desired effect, a biostimulator must be able to penetrate into the plant tissue. The time of penetration however, is limited, since the biostimulator must remain in a liquid state. This is of great importance—especially in field conditions, where the treated plants are exposed to different weather condition and other extrinsic factors. A mathematical model based on diffusion mechanisms has been elaborated to describe the biostimulator transport process from penetration of the leaves into the plant's inner tissues. By means of the effective diffusion coefficient of the prepared specific protein hydrolyzate, this model can be used to estimate the time necessary for the uptake of the minimal active amount of the biostimulator.

Poisson-Nernst-Planck Equations for Simulating Biomolecular Diffusion-Reaction Processes II: Size Effects on Ionic Distributions and Diffusion-Reaction Rates

PubMed Central

Lu, Benzhuo; Zhou, Y.C.

2011-01-01

The effects of finite particle size on electrostatics, density profiles, and diffusion have been a long existing topic in the study of ionic solution. The previous size-modified Poisson-Boltzmann and Poisson-Nernst-Planck models are revisited in this article. In contrast to many previous works that can only treat particle species with a single uniform size or two sizes, we generalize the Borukhov model to obtain a size-modified Poisson-Nernst-Planck (SMPNP) model that is able to treat nonuniform particle sizes. The numerical tractability of the model is demonstrated as well. The main contributions of this study are as follows. 1), We show that an (arbitrarily) size-modified PB model is indeed implied by the SMPNP equations under certain boundary/interface conditions, and can be reproduced through numerical solutions of the SMPNP. 2), The size effects in the SMPNP effectively reduce the densities of highly concentrated counterions around the biomolecule. 3), The SMPNP is applied to the diffusion-reaction process for the first time, to our knowledge. In the case of low substrate density near the enzyme reactive site, it is observed that the rate coefficients predicted by SMPNP model are considerably larger than those by the PNP model, suggesting both ions and substrates are subject to finite size effects. 4), An accurate finite element method and a convergent Gummel iteration are developed for the numerical solution of the completely coupled nonlinear system of SMPNP equations. PMID:21575582

Effect of Drag Reducing Polymer and Suspended Solid on the Rate of Diffusion Controlled Corrosion in 90° Copper Elbow

NASA Astrophysics Data System (ADS)

Fouad, Mohamed Ahmed; Zewail, Taghreed Mohamed; Amine, Nieven Kamal Abbes

2017-06-01

Rate of diffusion controlled corrosion in 90° Copper Elbow acidified dichromate has been investigated in relation to the following parameters: effect of solution velocity in the absence and presence of drag- reducing polymer on the rate of diffusion controlled corrosion, and effect of the presence of suspended solids on the rate of diffusion controlled corrosion. It was found that the presence of drag reducing polymer inhibited the rate of mass transfer, while the presence of suspended solid increased significantly the rate of mass transfer.

Can Disorder Enhance Incoherent Exciton Diffusion?

PubMed

Lee, Elizabeth M Y; Tisdale, William A; Willard, Adam P

2015-07-30

Recent experiments aimed at probing the dynamics of excitons have revealed that semiconducting films composed of disordered molecular subunits, unlike expectations for their perfectly ordered counterparts, can exhibit a time-dependent diffusivity in which the effective early time diffusion constant is larger than that of the steady state. This observation has led to speculation about what role, if any, microscopic disorder may play in enhancing exciton transport properties. In this article, we present the results of a model study aimed at addressing this point. Specifically, we introduce a general model, based upon Förster theory, for incoherent exciton diffusion in a material composed of independent molecular subunits with static energetic disorder. Energetic disorder leads to heterogeneity in molecule-to-molecule transition rates, which we demonstrate has two important consequences related to exciton transport. First, the distribution of local site-specific hopping rates is broadened in a manner that results in a decrease in average exciton diffusivity relative to that in a perfectly ordered film. Second, since excitons prefer to make transitions that are downhill in energy, the steady state distribution of exciton energies is biased toward low-energy molecular subunits, those that exhibit reduced diffusivity relative to a perfectly ordered film. These effects combine to reduce the net diffusivity in a manner that is time dependent and grows more pronounced as disorder is increased. Notably, however, we demonstrate that the presence of energetic disorder can give rise to a population of molecular subunits with exciton transfer rates exceeding those of subunits in an energetically uniform material. Such enhancements may play an important role in processes that are sensitive to molecular-scale fluctuations in exciton density field.

Computationally effective solution of the inverse problem in time-of-flight spectroscopy.

PubMed

Kamran, Faisal; Abildgaard, Otto H A; Subash, Arman A; Andersen, Peter E; Andersson-Engels, Stefan; Khoptyar, Dmitry

2015-03-09

Photon time-of-flight (PTOF) spectroscopy enables the estimation of absorption and reduced scattering coefficients of turbid media by measuring the propagation time of short light pulses through turbid medium. The present investigation provides a comparison of the assessed absorption and reduced scattering coefficients from PTOF measurements of intralipid 20% and India ink-based optical phantoms covering a wide range of optical properties relevant for biological tissues and dairy products. Three different models are used to obtain the optical properties by fitting to measured temporal profiles: the Liemert-Kienle model (LKM), the diffusion model (DM) and a white Monte-Carlo (WMC) simulation-based algorithm. For the infinite space geometry, a very good agreement is found between the LKM and WMC, while the results obtained by the DM differ, indicating that the LKM can provide accurate estimation of the optical parameters beyond the limits of the diffusion approximation in a computational effective and accurate manner. This result increases the potential range of applications for PTOF spectroscopy within industrial and biomedical applications.

Generalized two-temperature model for coupled phonon-magnon diffusion.

PubMed

Liao, Bolin; Zhou, Jiawei; Chen, Gang

2014-07-11

We generalize the two-temperature model [Sanders and Walton, Phys. Rev. B 15, 1489 (1977)] for coupled phonon-magnon diffusion to include the effect of the concurrent magnetization flow, with a particular emphasis on the thermal consequence of the magnon flow driven by a nonuniform magnetic field. Working within the framework of the Boltzmann transport equation, we derive the constitutive equations for coupled phonon-magnon transport driven by gradients of both temperature and external magnetic fields, and the corresponding conservation laws. Our equations reduce to the original Sanders-Walton two-temperature model under a uniform external field, but predict a new magnon cooling effect driven by a nonuniform magnetic field in a homogeneous single-domain ferromagnet. We estimate the magnitude of the cooling effect in an yttrium iron garnet, and show it is within current experimental reach. With properly optimized materials, the predicted cooling effect can potentially supplement the conventional magnetocaloric effect in cryogenic applications in the future.

Modeling the reversible, diffusive sink effect in response to transient contaminant sources.

PubMed

Zhao, D; Little, J C; Hodgson, A T

2002-09-01

A physically based diffusion model is used to evaluate the sink effect of diffusion-controlled indoor materials and to predict the transient contaminant concentration in indoor air in response to several time-varying contaminant sources. For simplicity, it is assumed the predominant indoor material is a homogeneous slab, initially free of contaminant, and the air within the room is well mixed. The model enables transient volatile organic compound (VOC) concentrations to be predicted based on the material/air partition coefficient (K) and the material-phase diffusion coefficient (D) of the sink. Model predictions are made for three scenarios, each mimicking a realistic situation in a building. Styrene, phenol, and naphthalene are used as representative VOCs. A styrene butadiene rubber (SBR) backed carpet, vinyl flooring (VF), and a polyurethane foam (PUF) carpet cushion are considered as typical indoor sinks. In scenarios involving a sinusoidal VOC input and a double exponential decaying input, the model predicts the sink has a modest impact for SBR/styrene, but the effect increases for VF/phenol and PUF/naphthalene. In contrast, for an episodic chemical spill, SBR is predicted to reduce the peak styrene concentration considerably. A parametric study reveals for systems involving a large equilibrium constant (K), the kinetic constant (D) will govern the shape of the resulting gasphase concentration profile. On the other hand, for systems with a relaxed mass transfer resistance, K will dominate the profile.

Effects of anisotropies in turbulent magnetic diffusion in mean-field solar dynamo models

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

Pipin, V. V.; Kosovichev, A. G.

2014-04-10

We study how anisotropies of turbulent diffusion affect the evolution of large-scale magnetic fields and the dynamo process on the Sun. The effect of anisotropy is calculated in a mean-field magnetohydrodynamics framework assuming that triple correlations provide relaxation to the turbulent electromotive force (so-called the 'minimal τ-approximation'). We examine two types of mean-field dynamo models: the well-known benchmark flux-transport model and a distributed-dynamo model with a subsurface rotational shear layer. For both models, we investigate effects of the double- and triple-cell meridional circulation, recently suggested by helioseismology and numerical simulations. To characterize the anisotropy effects, we introduce a parameter ofmore » anisotropy as a ratio of the radial and horizontal intensities of turbulent mixing. It is found that the anisotropy affects the distribution of magnetic fields inside the convection zone. The concentration of the magnetic flux near the bottom and top boundaries of the convection zone is greater when the anisotropy is stronger. It is shown that the critical dynamo number and the dynamo period approach to constant values for large values of the anisotropy parameter. The anisotropy reduces the overlap of toroidal magnetic fields generated in subsequent dynamo cycles, in the time-latitude 'butterfly' diagram. If we assume that sunspots are formed in the vicinity of the subsurface shear layer, then the distributed dynamo model with the anisotropic diffusivity satisfies the observational constraints from helioseismology and is consistent with the value of effective turbulent diffusion estimated from the dynamics of surface magnetic fields.« less

The effect of solute concentration on hindered gradient diffusion in polymeric gels

NASA Astrophysics Data System (ADS)

Buck, Kristan K. S.; Dungan, Stephanie R.; Phillips, Ronald J.

1999-10-01

The effect of solute concentration on hindered diffusion of sphere-like colloidal solutes in stiff polymer hydrogels is examined theoretically and experimentally. In the theoretical development, it is shown that the presence of the gel fibres enhances the effect of concentration on the thermodynamic driving force for gradient diffusion, while simultaneously reducing the effect of concentration on the hydrodynamic drag. The result is that gradient diffusion depends more strongly on solute concentration in gels than it does in pure solution, by an amount that depends on the partition coefficient and hydraulic permeability of the gel solute system. Quantitative calculations are made to determine the concentration-dependent diffusivity correct to first order in solute concentration. In order to compare the theoretical predictions with experimental data, rates of diffusion have been measured for nonionic micelles and globular proteins in solution and agarose hydrogels at two gel concentrations. The measurements were performed by using holographic interferometry, through which one monitors changes in refractive index as gradient diffusion takes place within a transparent gel. If the solutes are modelled as spheres with short-range repulsive interactions, then the experimentally measured concentration dependence of the diffusivities of both the protein and micelles is in good agreement with the theoretical predictions.

Effects of Wind and Freshwater on the Atlantic Meridional Overturning Circulation: Role of Sea Ice and Vertical Diffusion

NASA Astrophysics Data System (ADS)

Wang, Kun; Yang, Haijun; Dai, Haijin; Wang, Yuxing; Li, Qing

2015-04-01

Effects of wind and fresh water on the Atlantic meridional overturning circulation (AMOC) are investigated in a fully coupled climate model (CESM1.0). The AMOC can change significantly when perturbing either the wind stress or fresh water flux in the northern North Atlantic. This work pays special attention on the wind stress effect. Our model results show that the wind forcing is a crucial element in maintaining the AMOC. When the wind-stress is reduced, the vertical convection and diffusion are weakened immediately, triggering a salt deficit in the northern North Atlantic that prevents the deep water formation there. The salinity advection from the south, however, plays a contrary role to salt the upper ocean. As the AMOC weakens, the sea ice expends southward and melts, freshening the upper ocean that weakens the AMOC further. There is a positive feedback between the sea ice melting and AMOC strength, which eventually determines the AMOC strength in the reduced wind world.

The EZ diffusion model provides a powerful test of simple empirical effects.

PubMed

van Ravenzwaaij, Don; Donkin, Chris; Vandekerckhove, Joachim

2017-04-01

Over the last four decades, sequential accumulation models for choice response times have spread through cognitive psychology like wildfire. The most popular style of accumulator model is the diffusion model (Ratcliff Psychological Review, 85, 59-108, 1978), which has been shown to account for data from a wide range of paradigms, including perceptual discrimination, letter identification, lexical decision, recognition memory, and signal detection. Since its original inception, the model has become increasingly complex in order to account for subtle, but reliable, data patterns. The additional complexity of the diffusion model renders it a tool that is only for experts. In response, Wagenmakers et al. (Psychonomic Bulletin & Review, 14, 3-22, 2007) proposed that researchers could use a more basic version of the diffusion model, the EZ diffusion. Here, we simulate experimental effects on data generated from the full diffusion model and compare the power of the full diffusion model and EZ diffusion to detect those effects. We show that the EZ diffusion model, by virtue of its relative simplicity, will be sometimes better able to detect experimental effects than the data-generating full diffusion model.

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

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

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

2013-04-02

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

Theoretical examination of effective oxygen diffusion coefficient and electrical conductivity of polymer electrolyte fuel cell porous components

NASA Astrophysics Data System (ADS)

Inoue, Gen; Yokoyama, Kouji; Ooyama, Junpei; Terao, Takeshi; Tokunaga, Tomomi; Kubo, Norio; Kawase, Motoaki

2016-09-01

The reduction of oxygen transfer resistance through porous components consisting of a gas diffusion layer (GDL), microporous layer (MPL), and catalyst layer (CL) is very important to reduce the cost and improve the performance of a PEFC system. This study involves a systematic examination of the relationship between the oxygen transfer resistance of the actual porous components and their three-dimensional structure by direct measurement with FIB-SEM and X-ray CT. Numerical simulations were carried out to model the properties of oxygen transport. Moreover, based on the model structure and theoretical equations, an approach to the design of new structures is proposed. In the case of the GDL, the binder was found to obstruct gas diffusion with a negative effect on performance. The relative diffusion coefficient of the MPL is almost equal to that of the model structure of particle packing. However, that of CL is an order of magnitude less than those of the other two components. Furthermore, an equation expressing the relative diffusion coefficient of each component can be obtained with the function of porosity. The electrical conductivity of MPL, which is lower than that of the carbon black packing, is considered to depend on the contact resistance.

Bidirectional reflectance distribution function effects in ladar-based reflection tomography.

PubMed

Jin, Xuemin; Levine, Robert Y

2009-07-20

Light reflection from a surface is described by the bidirectional reflectance distribution function (BRDF). In this paper, BRDF effects in reflection tomography are studied using modeled range-resolved reflection from well-characterized geometrical surfaces. It is demonstrated that BRDF effects can cause a darkening at the interior boundary of the reconstructed surface analogous to the well-known beam hardening artifact in x-ray transmission computed tomography (CT). This artifact arises from reduced reflection at glancing incidence angles to the surface. It is shown that a purely Lambertian surface without shadowed components is perfectly reconstructed from range-resolved measurements. This result is relevant to newly fabricated carbon nanotube materials. Shadowing is shown to cause crossed streak artifacts similar to limited-angle effects in CT reconstruction. In tomographic reconstruction, these effects can overwhelm highly diffuse components in proximity to specularly reflecting elements. Diffuse components can be recovered by specialized processing, such as reducing glints via thresholded measurements.

Diffusion maps, clustering and fuzzy Markov modeling in peptide folding transitions

NASA Astrophysics Data System (ADS)

Nedialkova, Lilia V.; Amat, Miguel A.; Kevrekidis, Ioannis G.; Hummer, Gerhard

2014-09-01

Using the helix-coil transitions of alanine pentapeptide as an illustrative example, we demonstrate the use of diffusion maps in the analysis of molecular dynamics simulation trajectories. Diffusion maps and other nonlinear data-mining techniques provide powerful tools to visualize the distribution of structures in conformation space. The resulting low-dimensional representations help in partitioning conformation space, and in constructing Markov state models that capture the conformational dynamics. In an initial step, we use diffusion maps to reduce the dimensionality of the conformational dynamics of Ala5. The resulting pretreated data are then used in a clustering step. The identified clusters show excellent overlap with clusters obtained previously by using the backbone dihedral angles as input, with small—but nontrivial—differences reflecting torsional degrees of freedom ignored in the earlier approach. We then construct a Markov state model describing the conformational dynamics in terms of a discrete-time random walk between the clusters. We show that by combining fuzzy C-means clustering with a transition-based assignment of states, we can construct robust Markov state models. This state-assignment procedure suppresses short-time memory effects that result from the non-Markovianity of the dynamics projected onto the space of clusters. In a comparison with previous work, we demonstrate how manifold learning techniques may complement and enhance informed intuition commonly used to construct reduced descriptions of the dynamics in molecular conformation space.

Diffusion maps, clustering and fuzzy Markov modeling in peptide folding transitions

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

Nedialkova, Lilia V.; Amat, Miguel A.; Kevrekidis, Ioannis G., E-mail: yannis@princeton.edu, E-mail: gerhard.hummer@biophys.mpg.de

Using the helix-coil transitions of alanine pentapeptide as an illustrative example, we demonstrate the use of diffusion maps in the analysis of molecular dynamics simulation trajectories. Diffusion maps and other nonlinear data-mining techniques provide powerful tools to visualize the distribution of structures in conformation space. The resulting low-dimensional representations help in partitioning conformation space, and in constructing Markov state models that capture the conformational dynamics. In an initial step, we use diffusion maps to reduce the dimensionality of the conformational dynamics of Ala5. The resulting pretreated data are then used in a clustering step. The identified clusters show excellent overlapmore » with clusters obtained previously by using the backbone dihedral angles as input, with small—but nontrivial—differences reflecting torsional degrees of freedom ignored in the earlier approach. We then construct a Markov state model describing the conformational dynamics in terms of a discrete-time random walk between the clusters. We show that by combining fuzzy C-means clustering with a transition-based assignment of states, we can construct robust Markov state models. This state-assignment procedure suppresses short-time memory effects that result from the non-Markovianity of the dynamics projected onto the space of clusters. In a comparison with previous work, we demonstrate how manifold learning techniques may complement and enhance informed intuition commonly used to construct reduced descriptions of the dynamics in molecular conformation space.« less

Diffusion maps, clustering and fuzzy Markov modeling in peptide folding transitions

PubMed Central

Nedialkova, Lilia V.; Amat, Miguel A.; Kevrekidis, Ioannis G.; Hummer, Gerhard

2014-01-01

Using the helix-coil transitions of alanine pentapeptide as an illustrative example, we demonstrate the use of diffusion maps in the analysis of molecular dynamics simulation trajectories. Diffusion maps and other nonlinear data-mining techniques provide powerful tools to visualize the distribution of structures in conformation space. The resulting low-dimensional representations help in partitioning conformation space, and in constructing Markov state models that capture the conformational dynamics. In an initial step, we use diffusion maps to reduce the dimensionality of the conformational dynamics of Ala5. The resulting pretreated data are then used in a clustering step. The identified clusters show excellent overlap with clusters obtained previously by using the backbone dihedral angles as input, with small—but nontrivial—differences reflecting torsional degrees of freedom ignored in the earlier approach. We then construct a Markov state model describing the conformational dynamics in terms of a discrete-time random walk between the clusters. We show that by combining fuzzy C-means clustering with a transition-based assignment of states, we can construct robust Markov state models. This state-assignment procedure suppresses short-time memory effects that result from the non-Markovianity of the dynamics projected onto the space of clusters. In a comparison with previous work, we demonstrate how manifold learning techniques may complement and enhance informed intuition commonly used to construct reduced descriptions of the dynamics in molecular conformation space. PMID:25240340

Analysis of molecular movement reveals latticelike obstructions to diffusion in heart muscle cells.

PubMed

Illaste, Ardo; Laasmaa, Martin; Peterson, Pearu; Vendelin, Marko

2012-02-22

Intracellular diffusion in muscle cells is known to be restricted. Although characteristics and localization of these restrictions is yet to be elucidated, it has been established that ischemia-reperfusion injury reduces the overall diffusion restriction. Here we apply an extended version of raster image correlation spectroscopy to determine directional anisotropy and coefficients of diffusion in rat cardiomyocytes. Our experimental results indicate that diffusion of a smaller molecule (1127 MW fluorescently labeled ATTO633-ATP) is restricted more than that of a larger one (10,000 MW Alexa647-dextran), when comparing diffusion in cardiomyocytes to that in solution. We attempt to provide a resolution to this counterintuitive result by applying a quantitative stochastic model of diffusion. Modeling results suggest the presence of periodic intracellular barriers situated ∼1 μm apart having very low permeabilities and a small effect of molecular crowding in volumes between the barriers. Such intracellular structuring could restrict diffusion of molecules of energy metabolism, reactive oxygen species, and apoptotic signals, enacting a significant role in normally functioning cardiomyocytes as well as in pathological conditions of the heart. Copyright © 2012 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Restricted diffusion in a model acinar labyrinth by NMR: Theoretical and numerical results

NASA Astrophysics Data System (ADS)

Grebenkov, D. S.; Guillot, G.; Sapoval, B.

2007-01-01

A branched geometrical structure of the mammal lungs is known to be crucial for rapid access of oxygen to blood. But an important pulmonary disease like emphysema results in partial destruction of the alveolar tissue and enlargement of the distal airspaces, which may reduce the total oxygen transfer. This effect has been intensively studied during the last decade by MRI of hyperpolarized gases like helium-3. The relation between geometry and signal attenuation remained obscure due to a lack of realistic geometrical model of the acinar morphology. In this paper, we use Monte Carlo simulations of restricted diffusion in a realistic model acinus to compute the signal attenuation in a diffusion-weighted NMR experiment. We demonstrate that this technique should be sensitive to destruction of the branched structure: partial removal of the interalveolar tissue creates loops in the tree-like acinar architecture that enhance diffusive motion and the consequent signal attenuation. The role of the local geometry and related practical applications are discussed.

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

NASA Technical Reports Server (NTRS)

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

1998-01-01

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

On Diffusive Climatological Models.

NASA Astrophysics Data System (ADS)

Griffel, D. H.; Drazin, P. G.

1981-11-01

A simple, zonally and annually averaged, energy-balance climatological model with diffusive heat transport and nonlinear albedo feedback is solved numerically. Some parameters of the model are varied, one by one, to find the resultant effects on the steady solution representing the climate. In particular, the outward radiation flux, the insulation distribution and the albedo parameterization are varied. We have found an accurate yet simple analytic expression for the mean annual insolation as a function of latitude and the obliquity of the Earth's rotation axis; this has enabled us to consider the effects of the oscillation of the obliquity. We have used a continuous albedo function which fits the observed values; it considerably reduces the sensitivity of the model. Climatic cycles, calculated by solving the time-dependent equation when parameters change slowly and periodically, are compared qualitatively with paleoclimatic records.

The effect of humic acids on biodegradation of polycyclic aromatic hydrocarbons depends on the exposure regime.

PubMed

Tejeda-Agredano, Maria-Carmen; Mayer, Philipp; Ortega-Calvo, Jose-Julio

2014-01-01

Binding of polycyclic aromatic hydrocarbons (PAHs) to dissolved organic matter (DOM) can reduce the freely dissolved concentration, increase apparent solubility or enhance diffusive mass transfer. To study the effects of DOM on biodegradation, we used phenanthrene and pyrene as model PAHs, soil humic acids as model DOM and a soil Mycobacterium strain as a representative degrader organism. Humic acids enhanced the biodegradation of pyrene when present as solid crystals but not when initially dissolved or provided by partitioning from a polymer. Synchronous fluorescence spectrophotometry, scintillation counting and a microscale diffusion technique were applied in order to determine the kinetics of dissolution and diffusive mass transfer of pyrene. We suggest that humic acids can enhance or inhibit biodegradation as a result of the balance of two opposite effects, namely, solubilization of the chemicals on the one hand and inhibition of cell adhesion to the pollutant source on the other. Copyright © 2013 Elsevier Ltd. All rights reserved.

Diffusion of macromolecules in self-assembled cellulose/hemicellulose hydrogels.

PubMed

Lopez-Sanchez, Patricia; Schuster, Erich; Wang, Dongjie; Gidley, Michael J; Strom, Anna

2015-05-28

Cellulose hydrogels are extensively applied in many biotechnological fields and are also used as models for plant cell walls. We synthesised model cellulosic hydrogels containing hemicelluloses, as a biomimetic of plant cell walls, in order to study the role of hemicelluloses on their mass transport properties. Microbial cellulose is able to self-assemble into composites when hemicelluloses, such as xyloglucan and arabinoxylan, are present in the incubation media, leading to hydrogels with different nano and microstructures. We investigated the diffusivities of a series of fluorescently labelled dextrans, of different molecular weight, and proteins, including a plant pectin methyl esterase (PME), using fluorescence recovery after photobleaching (FRAP). The presence of xyloglucan, known to be able to crosslink cellulose fibres, confirmed by scanning electron microscopy (SEM) and (13)C NMR, reduced mobility of macromolecules of molecular weight higher than 10 kDa, reflected in lower diffusion coefficients. Furthermore PME diffusion was reduced in composites containing xyloglucan, despite the lack of a particular binding motif in PME for this polysaccharide, suggesting possible non-specific interactions between PME and this hemicellulose. In contrast, hydrogels containing arabinoxylan coating cellulose fibres showed enhanced diffusivity of the molecules studied. The different diffusivities were related to the architectural features found in the composites as a function of polysaccharide composition. Our results show the effect of model hemicelluloses in the mass transport properties of cellulose networks in highly hydrated environments relevant to understanding the role of hemicelluloses in the permeability of plant cell walls and aiding design of plant based materials with tailored properties.

Vortex Generators in a Streamline-Traced, External-Compression Supersonic Inlet

NASA Technical Reports Server (NTRS)

Baydar, Ezgihan; Lu, Frank K.; Slater, John W.; Trefny, Charles J.

2017-01-01

Vortex generators within a streamline-traced, external-compression supersonic inlet for Mach 1.66 were investigated to determine their ability to increase total pressure recovery and reduce total pressure distortion. The vortex generators studied were rectangular vanes arranged in counter-rotating and co-rotating arrays. The vane geometric factors of interest included height, length, spacing, angle-of-incidence, and positions upstream and downstream of the inlet terminal shock. The flow through the inlet was simulated numerically through the solution of the steady-state, Reynolds-averaged Navier-Stokes equations on multi-block, structured grids using the Wind-US flow solver. The vanes were simulated using a vortex generator model. The inlet performance was characterized by the inlet total pressure recovery and the radial and circumferential total pressure distortion indices at the engine face. Design of experiments and statistical analysis methods were applied to quantify the effect of the geometric factors of the vanes and search for optimal vane arrays. Co-rotating vane arrays with negative angles-of-incidence positioned on the supersonic diffuser were effective in sweeping low-momentum flow from the top toward the sides of the subsonic diffuser. This distributed the low-momentum flow more evenly about the circumference of the subsonic diffuser and reduced distortion. Co-rotating vane arrays with negative angles-of-incidence or counter-rotating vane arrays positioned downstream of the terminal shock were effective in mixing higher-momentum flow with lower-momentum flow to increase recovery and decrease distortion. A strategy of combining a co-rotating vane array on the supersonic diffuser with a counter-rotating vane array on the subsonic diffuser was effective in increasing recovery and reducing distortion.

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

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

Kwong, S.; Jivkov, A.P.

2012-07-01

Deep geologic disposal of high activity and long-lived radioactive waste is gaining increasing support in many countries, where suitable low permeability geological formation in combination with engineered barriers are used to provide long term waste contaminant and minimise the impacts to the environment and risk to the biosphere. This modelling study examines the solute transport in fractured media under low flow velocities that are relevant to a deep geological environment. In particular, reactive solute transport through fractured media is studied using a 2-D model, that considers advection and diffusion, to explore the coupled effects of kinetic and equilibrium chemical processes.more » The effects of water velocity in the fracture, matrix porosity and diffusion on solute transport are investigated and discussed. Some illustrative modelled results are presented to demonstrate the use of the model to examine the effects of media degradation on solute transport, under the influences of hydrogeological (diffusion dominant) and microbially mediated chemical processes. The challenges facing the prediction of long term degradation such as cracks evolution, interaction and coalescence are highlighted. The potential of a novel microstructure informed modelling approach to account for these effects is discussed, particularly with respect to investigating multiple phenomena impact on material performance. The GRM code is used to examine the effects of media degradation for a geological waste disposal package, under the combined hydrogeological (diffusion dominant) and chemical effects in low groundwater flow conditions that are typical of deep geological disposal systems. An illustrative reactive transport modelling application demonstrates the use of the code to examine the interplay of kinetic controlled biogeochemical reactive processes with advective and diffusive transport, under the influence of media degradation. The initial model results are encouraging which show the disposal system to evolve in a physically realistic manner. In the example presented the reactive-transport coupling develops chemically reducing zones, which limit the transport of uranium. This illustrates the potential significance of media degradation and chemical effect on the transport of radionuclides which would need to be taken into account when examining the long-term behaviour and containment properties of the geological disposal system. Microstructure-informed modelling and its potential linkage with continuum flow modelling is a subject of ongoing studies. The approach of microstructure-informed modelling is discussed to provide insight and a mechanistic understanding of macroscopic parameters and their evolution. The proposed theoretical and methodological basis for microstructure-informed modelling of porous quasi-brittle media has the potential to develop into an explanatory and predictive tool for deriving mechanism-based, as opposed to phenomenological, evolution laws for macroscopic properties. These concepts in micro-scale modelling are likely to be applicable to the diffusion process, in addition to advective transport illustrated here for porous media. (authors)« less

Continuous-time random-walk model for anomalous diffusion in expanding media

NASA Astrophysics Data System (ADS)

Le Vot, F.; Abad, E.; Yuste, S. B.

2017-09-01

Expanding media are typical in many different fields, e.g., in biology and cosmology. In general, a medium expansion (contraction) brings about dramatic changes in the behavior of diffusive transport properties such as the set of positional moments and the Green's function. Here, we focus on the characterization of such effects when the diffusion process is described by the continuous-time random-walk (CTRW) model. As is well known, when the medium is static this model yields anomalous diffusion for a proper choice of the probability density function (pdf) for the jump length and the waiting time, but the behavior may change drastically if a medium expansion is superimposed on the intrinsic random motion of the diffusing particle. For the case where the jump length and the waiting time pdfs are long-tailed, we derive a general bifractional diffusion equation which reduces to a normal diffusion equation in the appropriate limit. We then study some particular cases of interest, including Lévy flights and subdiffusive CTRWs. In the former case, we find an analytical exact solution for the Green's function (propagator). When the expansion is sufficiently fast, the contribution of the diffusive transport becomes irrelevant at long times and the propagator tends to a stationary profile in the comoving reference frame. In contrast, for a contracting medium a competition between the spreading effect of diffusion and the concentrating effect of contraction arises. In the specific case of a subdiffusive CTRW in an exponentially contracting medium, the latter effect prevails for sufficiently long times, and all the particles are eventually localized at a single point in physical space. This "big crunch" effect, totally absent in the case of normal diffusion, stems from inefficient particle spreading due to subdiffusion. We also derive a hierarchy of differential equations for the moments of the transport process described by the subdiffusive CTRW model in an expanding medium. From this hierarchy, the full time evolution of the second-order moment is obtained for some specific types of expansion. In the case of an exponential expansion, exact recurrence relations for the Laplace-transformed moments are obtained, whence the long-time behavior of moments of arbitrary order is subsequently inferred. Our analytical and numerical results for both Lévy flights and subdiffusive CTRWs confirm the intuitive expectation that the medium expansion hinders the mixing of diffusive particles occupying separate regions. In the case of Lévy flights, we quantify this effect by means of the so-called "Lévy horizon."

Continuous-time random-walk model for anomalous diffusion in expanding media.

PubMed

Le Vot, F; Abad, E; Yuste, S B

2017-09-01

Expanding media are typical in many different fields, e.g., in biology and cosmology. In general, a medium expansion (contraction) brings about dramatic changes in the behavior of diffusive transport properties such as the set of positional moments and the Green's function. Here, we focus on the characterization of such effects when the diffusion process is described by the continuous-time random-walk (CTRW) model. As is well known, when the medium is static this model yields anomalous diffusion for a proper choice of the probability density function (pdf) for the jump length and the waiting time, but the behavior may change drastically if a medium expansion is superimposed on the intrinsic random motion of the diffusing particle. For the case where the jump length and the waiting time pdfs are long-tailed, we derive a general bifractional diffusion equation which reduces to a normal diffusion equation in the appropriate limit. We then study some particular cases of interest, including Lévy flights and subdiffusive CTRWs. In the former case, we find an analytical exact solution for the Green's function (propagator). When the expansion is sufficiently fast, the contribution of the diffusive transport becomes irrelevant at long times and the propagator tends to a stationary profile in the comoving reference frame. In contrast, for a contracting medium a competition between the spreading effect of diffusion and the concentrating effect of contraction arises. In the specific case of a subdiffusive CTRW in an exponentially contracting medium, the latter effect prevails for sufficiently long times, and all the particles are eventually localized at a single point in physical space. This "big crunch" effect, totally absent in the case of normal diffusion, stems from inefficient particle spreading due to subdiffusion. We also derive a hierarchy of differential equations for the moments of the transport process described by the subdiffusive CTRW model in an expanding medium. From this hierarchy, the full time evolution of the second-order moment is obtained for some specific types of expansion. In the case of an exponential expansion, exact recurrence relations for the Laplace-transformed moments are obtained, whence the long-time behavior of moments of arbitrary order is subsequently inferred. Our analytical and numerical results for both Lévy flights and subdiffusive CTRWs confirm the intuitive expectation that the medium expansion hinders the mixing of diffusive particles occupying separate regions. In the case of Lévy flights, we quantify this effect by means of the so-called "Lévy horizon."

Modelling Detailed-Chemistry Effects on Turbulent Diffusion Flames using a Parallel Solution-Adaptive Scheme

NASA Astrophysics Data System (ADS)

Jha, Pradeep Kumar

Capturing the effects of detailed-chemistry on turbulent combustion processes is a central challenge faced by the numerical combustion community. However, the inherent complexity and non-linear nature of both turbulence and chemistry require that combustion models rely heavily on engineering approximations to remain computationally tractable. This thesis proposes a computationally efficient algorithm for modelling detailed-chemistry effects in turbulent diffusion flames and numerically predicting the associated flame properties. The cornerstone of this combustion modelling tool is the use of parallel Adaptive Mesh Refinement (AMR) scheme with the recently proposed Flame Prolongation of Intrinsic low-dimensional manifold (FPI) tabulated-chemistry approach for modelling complex chemistry. The effect of turbulence on the mean chemistry is incorporated using a Presumed Conditional Moment (PCM) approach based on a beta-probability density function (PDF). The two-equation k-w turbulence model is used for modelling the effects of the unresolved turbulence on the mean flow field. The finite-rate of methane-air combustion is represented here by using the GRI-Mech 3.0 scheme. This detailed mechanism is used to build the FPI tables. A state of the art numerical scheme based on a parallel block-based solution-adaptive algorithm has been developed to solve the Favre-averaged Navier-Stokes (FANS) and other governing partial-differential equations using a second-order accurate, fully-coupled finite-volume formulation on body-fitted, multi-block, quadrilateral/hexahedral mesh for two-dimensional and three-dimensional flow geometries, respectively. A standard fourth-order Runge-Kutta time-marching scheme is used for time-accurate temporal discretizations. Numerical predictions of three different diffusion flames configurations are considered in the present work: a laminar counter-flow flame; a laminar co-flow diffusion flame; and a Sydney bluff-body turbulent reacting flow. Comparisons are made between the predicted results of the present FPI scheme and Steady Laminar Flamelet Model (SLFM) approach for diffusion flames. The effects of grid resolution on the predicted overall flame solutions are also assessed. Other non-reacting flows have also been considered to further validate other aspects of the numerical scheme. The present schemes predict results which are in good agreement with published experimental results and reduces the computational cost involved in modelling turbulent diffusion flames significantly, both in terms of storage and processing time.

Drying kinetics of apricot halves in a microwave-hot air hybrid oven

NASA Astrophysics Data System (ADS)

Horuz, Erhan; Bozkurt, Hüseyin; Karataş, Haluk; Maskan, Medeni

2017-06-01

Drying behavior and kinetics of apricot halves were investigated in a microwave-hot air domestic hybrid oven at 120, 150 and 180 W microwave power and 50, 60 and 70 °C air temperature. Drying operation was finished when the moisture content reached to 25% (wet basis) from 77% (w.b). Increase in microwave power and air temperature increased drying rates and reduced drying time. Only falling rate period was observed in drying of apricot halves in hybrid oven. Eleven mathematical models were used for describing the drying kinetics of apricots. Modified logistic model gave the best fitting to the experimental data. The model has never been used to explain drying behavior of any kind of food materials up to now. Fick's second law was used for determination of both effective moisture diffusivity and thermal diffusivity values. Activation energy values of dried apricots were calculated from Arrhenius equation. Those that obtained from effective moisture diffusivity, thermal diffusivity and drying rate constant values ranged from 31.10 to 39.4 kJ/mol, 29.56 to 35.19 kJ/mol, and 26.02 to 32.36 kJ/mol, respectively.

Analysis of the moisture diffusion transfer through fibrous porous membrane used for waterproof breathable fabrics

NASA Astrophysics Data System (ADS)

Zhu, Fanglong; Zhou, Yu; Liu, Suyan

2013-10-01

In this paper, we propose a new fractal model to determine the moisture effective diffusivity of porous membrane such as expanded polytetrafluorethylene membrane, by taking account of both parallel and perpendicular channels to diffusion flow direction. With the consideration of both the Knudsen and bulk diffusion effect, a relationship between micro-structural parameters and effective moisture diffusivity is deduced. The effective moisture diffusivities predicted by the present fractal model are compared with moisture diffusion experiment data and calculated values obtained from other theoretical models.

Effects of stomata clustering on leaf gas exchange.

PubMed

Lehmann, Peter; Or, Dani

2015-09-01

A general theoretical framework for quantifying the stomatal clustering effects on leaf gaseous diffusive conductance was developed and tested. The theory accounts for stomatal spacing and interactions among 'gaseous concentration shells'. The theory was tested using the unique measurements of Dow et al. (2014) that have shown lower leaf diffusive conductance for a genotype of Arabidopsis thaliana with clustered stomata relative to uniformly distributed stomata of similar size and density. The model accounts for gaseous diffusion: through stomatal pores; via concentration shells forming at pore apertures that vary with stomata spacing and are thus altered by clustering; and across the adjacent air boundary layer. Analytical approximations were derived and validated using a numerical model for 3D diffusion equation. Stomata clustering increases the interactions among concentration shells resulting in larger diffusive resistance that may reduce fluxes by 5-15%. A similar reduction in conductance was found for clusters formed by networks of veins. The study resolves ambiguities found in the literature concerning stomata end-corrections and stomatal shape, and provides a new stomata density threshold for diffusive interactions of overlapping vapor shells. The predicted reduction in gaseous exchange due to clustering, suggests that guard cell function is impaired, limiting stomatal aperture opening. © 2015 The Authors. New Phytologist © 2015 New Phytologist Trust.

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

PubMed

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

2016-11-01

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

q-Space Deep Learning: Twelve-Fold Shorter and Model-Free Diffusion MRI Scans.

PubMed

Golkov, Vladimir; Dosovitskiy, Alexey; Sperl, Jonathan I; Menzel, Marion I; Czisch, Michael; Samann, Philipp; Brox, Thomas; Cremers, Daniel

2016-05-01

Numerous scientific fields rely on elaborate but partly suboptimal data processing pipelines. An example is diffusion magnetic resonance imaging (diffusion MRI), a non-invasive microstructure assessment method with a prominent application in neuroimaging. Advanced diffusion models providing accurate microstructural characterization so far have required long acquisition times and thus have been inapplicable for children and adults who are uncooperative, uncomfortable, or unwell. We show that the long scan time requirements are mainly due to disadvantages of classical data processing. We demonstrate how deep learning, a group of algorithms based on recent advances in the field of artificial neural networks, can be applied to reduce diffusion MRI data processing to a single optimized step. This modification allows obtaining scalar measures from advanced models at twelve-fold reduced scan time and detecting abnormalities without using diffusion models. We set a new state of the art by estimating diffusion kurtosis measures from only 12 data points and neurite orientation dispersion and density measures from only 8 data points. This allows unprecedentedly fast and robust protocols facilitating clinical routine and demonstrates how classical data processing can be streamlined by means of deep learning.

Water diffusion-exchange effect on the paramagnetic relaxation enhancement in off-resonance rotating frame

NASA Astrophysics Data System (ADS)

Zhang, Huiming; Xie, Yang; Ji, Tongyu

2007-06-01

The off-resonance rotating frame technique based on the spin relaxation properties of off-resonance T1 ρ can significantly increase the sensitivity of detecting paramagnetic labeling at high magnetic fields by MRI. However, the in vivo detectable dimension for labeled cell clusters/tissues in T1 ρ-weighted images is limited by the water diffusion-exchange between mesoscopic scale compartments. An experimental investigation of the effect of water diffusion-exchange between compartments on the paramagnetic relaxation enhancement of paramagnetic agent compartment is presented for in vitro/ in vivo models. In these models, the size of paramagnetic agent compartment is comparable to the mean diffusion displacement of water molecules during the long RF pulses that are used to generate the off-resonance rotating frame. The three main objectives of this study were: (1) to qualitatively correlate the effect of water diffusion-exchange with the RF parameters of the long pulse and the rates of water diffusion, (2) to explore the effect of water diffusion-exchange on the paramagnetic relaxation enhancement in vitro, and (3) to demonstrate the paramagnetic relaxation enhancement in vivo. The in vitro models include the water permeable dialysis tubes or water permeable hollow fibers embedded in cross-linked proteins gels. The MWCO of the dialysis tubes was chosen from 0.1 to 15 kDa to control the water diffusion rate. Thin hollow fibers were chosen to provide sub-millimeter scale compartments for the paramagnetic agents. The in vivo model utilized the rat cerebral vasculatures as a paramagnetic agent compartment, and intravascular agents (Gd-DTPA) 30-BSA were administrated into the compartment via bolus injections. Both in vitro and in vivo results demonstrate that the paramagnetic relaxation enhancement is predominant in the T1 ρ-weighted image in the presence of water diffusion-exchange. The T1 ρ contrast has substantially higher sensitivity than the conventional T1 contrast in detecting paramagnetic agents, especially at low paramagnetic agent volumetric fractions, low paramagnetic agent concentrations, and low RF amplitudes. Short pulse duration, short pulse recycle delay and efficient paramagnetic relaxation can reduce the influence of water diffusion-exchange on the paramagnetic enhancement. This study paves the way for the design of off-resonance rotating experiments to detect labeled cell clusters/tissue compartments in vivo at a sub-millimeter scale.

Extracting surface diffusion coefficients from batch adsorption measurement data: application of the classic Langmuir kinetics model.

PubMed

Chu, Khim Hoong

2017-11-09

Surface diffusion coefficients may be estimated by fitting solutions of a diffusion model to batch kinetic data. For non-linear systems, a numerical solution of the diffusion model's governing equations is generally required. We report here the application of the classic Langmuir kinetics model to extract surface diffusion coefficients from batch kinetic data. The use of the Langmuir kinetics model in lieu of the conventional surface diffusion model allows derivation of an analytical expression. The parameter estimation procedure requires determining the Langmuir rate coefficient from which the pertinent surface diffusion coefficient is calculated. Surface diffusion coefficients within the 10 -9 to 10 -6  cm 2 /s range obtained by fitting the Langmuir kinetics model to experimental kinetic data taken from the literature are found to be consistent with the corresponding values obtained from the traditional surface diffusion model. The virtue of this simplified parameter estimation method is that it reduces the computational complexity as the analytical expression involves only an algebraic equation in closed form which is easily evaluated by spreadsheet computation.

Effect of EMIC Wave Normal Angle Distribution on Relativistic Electron Scattering in Outer RB

NASA Technical Reports Server (NTRS)

Khazanov, G. V.; Gamayunov, K. V.

2007-01-01

We present the equatorial and bounce average pitch angle diffusion coefficients for scattering of relativistic electrons by the H+ mode of EMIC waves. Both the model (prescribed) and self consistent distributions over the wave normal angle are considered. The main results of our calculation can be summarized as follows: First, in comparison with field aligned waves, the intermediate and highly oblique waves reduce the pitch angle range subject to diffusion, and strongly suppress the scattering rate for low energy electrons (E less than 2 MeV). Second, for electron energies greater than 5 MeV, the |n| = 1 resonances operate only in a narrow region at large pitch-angles, and despite their greatest contribution in case of field aligned waves, cannot cause electron diffusion into the loss cone. For those energies, oblique waves at |n| greater than 1 resonances are more effective, extending the range of pitch angle diffusion down to the loss cone boundary, and increasing diffusion at small pitch angles by orders of magnitude.

From conservative to reactive transport under diffusion-controlled conditions

NASA Astrophysics Data System (ADS)

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

2016-05-01

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

Approximate series solution of multi-dimensional, time fractional-order (heat-like) diffusion equations using FRDTM.

PubMed

Singh, Brajesh K; Srivastava, Vineet K

2015-04-01

The main goal of this paper is to present a new approximate series solution of the multi-dimensional (heat-like) diffusion equation with time-fractional derivative in Caputo form using a semi-analytical approach: fractional-order reduced differential transform method (FRDTM). The efficiency of FRDTM is confirmed by considering four test problems of the multi-dimensional time fractional-order diffusion equation. FRDTM is a very efficient, effective and powerful mathematical tool which provides exact or very close approximate solutions for a wide range of real-world problems arising in engineering and natural sciences, modelled in terms of differential equations.

Approximate series solution of multi-dimensional, time fractional-order (heat-like) diffusion equations using FRDTM

PubMed Central

Singh, Brajesh K.; Srivastava, Vineet K.

2015-01-01

The main goal of this paper is to present a new approximate series solution of the multi-dimensional (heat-like) diffusion equation with time-fractional derivative in Caputo form using a semi-analytical approach: fractional-order reduced differential transform method (FRDTM). The efficiency of FRDTM is confirmed by considering four test problems of the multi-dimensional time fractional-order diffusion equation. FRDTM is a very efficient, effective and powerful mathematical tool which provides exact or very close approximate solutions for a wide range of real-world problems arising in engineering and natural sciences, modelled in terms of differential equations. PMID:26064639

Nonlinear Porous Diffusion Modeling of Hydrophilic Ionic Agrochemicals in Astomatous Plant Cuticle Aqueous Pores: A Mechanistic Approach.

PubMed

Tredenick, Eloise C; Farrell, Troy W; Forster, W Alison; Psaltis, Steven T P

2017-01-01

The agricultural industry requires improved efficacy of sprays being applied to crops and weeds in order to reduce their environmental impact and deliver improved financial returns. Enhanced foliar uptake is one means of improving efficacy. The plant leaf cuticle is known to be the main barrier to diffusion of agrochemicals within the leaf. The usefulness of a mathematical model to simulate uptake of agrochemicals in plant cuticles has been noted previously in the literature, as the results of each uptake experiment are specific to each formulation of active ingredient, plant species and environmental conditions. In this work we develop a mathematical model and numerical simulation for the uptake of hydrophilic ionic agrochemicals through aqueous pores in plant cuticles. We propose a novel, nonlinear, porous diffusion model for ionic agrochemicals in isolated cuticles, which extends simple diffusion through the incorporation of parameters capable of simulating: plant species variations, evaporation of surface droplet solutions, ion binding effects on the cuticle surface and swelling of the aqueous pores with water. We validate our theoretical results against appropriate experimental data, discuss the key sensitivities in the model and relate theoretical predictions to appropriate physical mechanisms. Major influencing factors have been found to be cuticle structure, including tortuosity and density of the aqueous pores, and to a lesser extent humidity and cuticle surface ion binding effects.

Nonlinear Porous Diffusion Modeling of Hydrophilic Ionic Agrochemicals in Astomatous Plant Cuticle Aqueous Pores: A Mechanistic Approach

PubMed Central

Tredenick, Eloise C.; Farrell, Troy W.; Forster, W. Alison; Psaltis, Steven T. P.

2017-01-01

The agricultural industry requires improved efficacy of sprays being applied to crops and weeds in order to reduce their environmental impact and deliver improved financial returns. Enhanced foliar uptake is one means of improving efficacy. The plant leaf cuticle is known to be the main barrier to diffusion of agrochemicals within the leaf. The usefulness of a mathematical model to simulate uptake of agrochemicals in plant cuticles has been noted previously in the literature, as the results of each uptake experiment are specific to each formulation of active ingredient, plant species and environmental conditions. In this work we develop a mathematical model and numerical simulation for the uptake of hydrophilic ionic agrochemicals through aqueous pores in plant cuticles. We propose a novel, nonlinear, porous diffusion model for ionic agrochemicals in isolated cuticles, which extends simple diffusion through the incorporation of parameters capable of simulating: plant species variations, evaporation of surface droplet solutions, ion binding effects on the cuticle surface and swelling of the aqueous pores with water. We validate our theoretical results against appropriate experimental data, discuss the key sensitivities in the model and relate theoretical predictions to appropriate physical mechanisms. Major influencing factors have been found to be cuticle structure, including tortuosity and density of the aqueous pores, and to a lesser extent humidity and cuticle surface ion binding effects. PMID:28539930

Modeling and experiments for the time-dependent diffusion coefficient during methane desorption from coal

NASA Astrophysics Data System (ADS)

Cheng-Wu, Li; Hong-Lai, Xue; Cheng, Guan; Wen-biao, Liu

2018-04-01

Statistical analysis shows that in the coal matrix, the diffusion coefficient for methane is time-varying, and its integral satisfies the formula μt κ /(1 + β κ ). Therefore, a so-called dynamic diffusion coefficient model (DDC model) is developed. To verify the suitability and accuracy of the DDC model, a series of gas diffusion experiments were conducted using coal particles of different sizes. The results show that the experimental data can be accurately described by the DDC and bidisperse models, but the fit to the DDC model is slightly better. For all coal samples, as time increases, the effective diffusion coefficient first shows a sudden drop, followed by a gradual decrease before stabilizing at longer times. The effective diffusion coefficient has a negative relationship with the size of the coal particle. Finally, the relationship between the constants of the DDC model and the effective diffusion coefficient is discussed. The constant α (μ/R 2 ) denotes the effective coefficient at the initial time, and the constants κ and β control the attenuation characteristic of the effective diffusion coefficient.

Effective Stochastic Model for Reactive Transport

NASA Astrophysics Data System (ADS)

Tartakovsky, A. M.; Zheng, B.; Barajas-Solano, D. A.

2017-12-01

We propose an effective stochastic advection-diffusion-reaction (SADR) model. Unlike traditional advection-dispersion-reaction models, the SADR model describes mechanical and diffusive mixing as two separate processes. In the SADR model, the mechanical mixing is driven by random advective velocity with the variance given by the coefficient of mechanical dispersion. The diffusive mixing is modeled as a fickian diffusion with the effective diffusion coefficient. Both coefficients are given in terms of Peclet number (Pe) and the coefficient of molecular diffusion. We use the experimental results of to demonstrate that for transport and bimolecular reactions in porous media the SADR model is significantly more accurate than the traditional dispersion model, which overestimates the mass of the reaction product by as much as 25%.

Magnetic field line random walk in models and simulations of reduced magnetohydrodynamic turbulence

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

Snodin, A. P.; Ruffolo, D.; Oughton, S.

2013-12-10

The random walk of magnetic field lines is examined numerically and analytically in the context of reduced magnetohydrodynamic (RMHD) turbulence, which provides a useful description of plasmas dominated by a strong mean field, such as in the solar corona. A recently developed non-perturbative theory of magnetic field line diffusion is compared with the diffusion coefficients obtained by accurate numerical tracing of magnetic field lines for both synthetic models and direct numerical simulations of RMHD. Statistical analysis of an ensemble of trajectories confirms the applicability of the theory, which very closely matches the numerical field line diffusion coefficient as a functionmore » of distance z along the mean magnetic field for a wide range of the Kubo number R. This theory employs Corrsin's independence hypothesis, sometimes thought to be valid only at low R. However, the results demonstrate that it works well up to R = 10, both for a synthetic RMHD model and an RMHD simulation. The numerical results from the RMHD simulation are compared with and without phase randomization, demonstrating a clear effect of coherent structures on the field line random walk for a very low Kubo number.« less

Efficient Multi-Dimensional Simulation of Quantum Confinement Effects in Advanced MOS Devices

NASA Technical Reports Server (NTRS)

Biegel, Bryan A.; Ancona, Mario G.; Rafferty, Conor S.; Yu, Zhiping

2000-01-01

We investigate the density-gradient (DG) transport model for efficient multi-dimensional simulation of quantum confinement effects in advanced MOS devices. The formulation of the DG model is described as a quantum correction ot the classical drift-diffusion model. Quantum confinement effects are shown to be significant in sub-100nm MOSFETs. In thin-oxide MOS capacitors, quantum effects may reduce gate capacitance by 25% or more. As a result, the inclusion of quantum effects may reduce gate capacitance by 25% or more. As a result, the inclusion of quantum effects in simulations dramatically improves the match between C-V simulations and measurements for oxide thickness down to 2 nm. Significant quantum corrections also occur in the I-V characteristics of short-channel (30 to 100 nm) n-MOSFETs, with current drive reduced by up to 70%. This effect is shown to result from reduced inversion charge due to quantum confinement of electrons in the channel. Also, subthreshold slope is degraded by 15 to 20 mV/decade with the inclusion of quantum effects via the density-gradient model, and short channel effects (in particular, drain-induced barrier lowering) are noticeably increased.

New approach to effective diffusion coefficient evaluation in the nanostructured two-phase media

NASA Astrophysics Data System (ADS)

Lyashenko, Yu. O.; Liashenko, O. Y.; Morozovich, V. V.

2018-03-01

Most widely used basic and combined models for evaluation of the effective diffusion parameters of inhomogeneous two-phase zone are reviewed. A new combined model of effective medium is analyzed for the description of diffusion processes in the two-phase zones. In this model the effective diffusivity depends on the growth kinetic coefficients of each phase, the volume fractions of phases and on the additional parameter that generally characterizes the structure type of the two-phase zone. Our combined model describes two-phase zone evolution in the binary systems based on consideration of the diffusion fluxes through both phases. The Lattice Monte Carlo method was used to test the validity of different phenomenological models for evaluation of the effective diffusivity in nanostructured two-phase zones with different structural morphology.

Modeling the radiative effects of biomass burning aerosols on carbon fluxes in the Amazon region

NASA Astrophysics Data System (ADS)

Moreira, Demerval S.; Longo, Karla M.; Freitas, Saulo R.; Yamasoe, Marcia A.; Mercado, Lina M.; Rosário, Nilton E.; Gloor, Emauel; Viana, Rosane S. M.; Miller, John B.; Gatti, Luciana V.; Wiedemann, Kenia T.; Domingues, Lucas K. G.; Correia, Caio C. S.

2017-12-01

Every year, a dense smoke haze covers a large portion of South America originating from fires in the Amazon Basin and central parts of Brazil during the dry biomass burning season between August and October. Over a large portion of South America, the average aerosol optical depth at 550 nm exceeds 1.0 during the fire season, while the background value during the rainy season is below 0.2. Biomass burning aerosol particles increase scattering and absorption of the incident solar radiation. The regional-scale aerosol layer reduces the amount of solar energy reaching the surface, cools the near-surface air, and increases the diffuse radiation fraction over a large disturbed area of the Amazon rainforest. These factors affect the energy and CO2 fluxes at the surface. In this work, we applied a fully integrated atmospheric model to assess the impact of biomass burning aerosols in CO2 fluxes in the Amazon region during 2010. We address the effects of the attenuation of global solar radiation and the enhancement of the diffuse solar radiation flux inside the vegetation canopy. Our results indicate that biomass burning aerosols led to increases of about 27 % in the gross primary productivity of Amazonia and 10 % in plant respiration as well as a decline in soil respiration of 3 %. Consequently, in our model Amazonia became a net carbon sink; net ecosystem exchange during September 2010 dropped from +101 to -104 TgC when the aerosol effects are considered, mainly due to the aerosol diffuse radiation effect. For the forest biome, our results point to a dominance of the diffuse radiation effect on CO2 fluxes, reaching a balance of 50-50 % between the diffuse and direct aerosol effects for high aerosol loads. For C3 grasses and savanna (cerrado), as expected, the contribution of the diffuse radiation effect is much lower, tending to zero with the increase in aerosol load. Taking all biomes together, our model shows the Amazon during the dry season, in the presence of high biomass burning aerosol loads, changing from being a source to being a sink of CO2 to the atmosphere.

Sb lattice diffusion in Si1-xGex/Si(001) heterostructures: Chemical and stress effects

NASA Astrophysics Data System (ADS)

Portavoce, A.; Gas, P.; Berbezier, I.; Ronda, A.; Christensen, J. S.; Kuznetsov, A. Yu.; Svensson, B. G.

2004-04-01

The Sb diffusion coefficient in Si1-xGex/Si1-yGey(001) heterostructures grown by molecular beam epitaxy (MBE) was measured for temperatures ranging from 700 to 850 °C, Ge composition from 0 to 20 % and biaxial pressure from -0.8 (tension) to 1.4 GPa (compression). A quantitative separation of composition and biaxial stress effects is made. We show that the Sb lattice diffusion coefficient: (i) increases with Ge concentration in relaxed layers or at constant biaxial pressure and (ii) increases with compressive biaxial stress and decreases with tensile biaxial stress at constant Ge composition. The enhancement of Sb lattice diffusion in Si1-xGex layers in epitaxy on Si(001) is thus due to the cooperative effect of Ge composition and induced compressive biaxial stress. However, the first effect (composition) is predominant. The activation volume of Sb diffusion in Si1-xGex layers is deduced from the variation of the Sb diffusion coefficients with biaxial pressure. This volume is negative. The sign of the activation volume, its absolute value and its variation with temperature confirm the prediction of the thermodynamic model proposed by Aziz, namely, that under a biaxial stress the activation volume is reduced to the relaxation volume.

Model-based analysis of multi-shell diffusion MR data for tractography: How to get over fitting problems

PubMed Central

Jbabdi, Saad; Sotiropoulos, Stamatios N; Savio, Alexander M; Graña, Manuel; Behrens, Timothy EJ

2012-01-01

In this article, we highlight an issue that arises when using multiple b-values in a model-based analysis of diffusion MR data for tractography. The non-mono-exponential decay, commonly observed in experimental data, is shown to induce over-fitting in the distribution of fibre orientations when not considered in the model. Extra fibre orientations perpendicular to the main orientation arise to compensate for the slower apparent signal decay at higher b-values. We propose a simple extension to the ball and stick model based on a continuous Gamma distribution of diffusivities, which significantly improves the fitting and reduces the over-fitting. Using in-vivo experimental data, we show that this model outperforms a simpler, noise floor model, especially at the interfaces between brain tissues, suggesting that partial volume effects are a major cause of the observed non-mono-exponential decay. This model may be helpful for future data acquisition strategies that may attempt to combine multiple shells to improve estimates of fibre orientations in white matter and near the cortex. PMID:22334356

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

PubMed Central

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

2013-01-01

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

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

USGS Publications Warehouse

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

2012-01-01

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

Validation of a numerical method for interface-resolving simulation of multicomponent gas-liquid mass transfer and evaluation of multicomponent diffusion models

NASA Astrophysics Data System (ADS)

Woo, Mino; Wörner, Martin; Tischer, Steffen; Deutschmann, Olaf

2018-03-01

The multicomponent model and the effective diffusivity model are well established diffusion models for numerical simulation of single-phase flows consisting of several components but are seldom used for two-phase flows so far. In this paper, a specific numerical model for interfacial mass transfer by means of a continuous single-field concentration formulation is combined with the multicomponent model and effective diffusivity model and is validated for multicomponent mass transfer. For this purpose, several test cases for one-dimensional physical or reactive mass transfer of ternary mixtures are considered. The numerical results are compared with analytical or numerical solutions of the Maxell-Stefan equations and/or experimental data. The composition-dependent elements of the diffusivity matrix of the multicomponent and effective diffusivity model are found to substantially differ for non-dilute conditions. The species mole fraction or concentration profiles computed with both diffusion models are, however, for all test cases very similar and in good agreement with the analytical/numerical solutions or measurements. For practical computations, the effective diffusivity model is recommended due to its simplicity and lower computational costs.

Efficient Multi-Dimensional Simulation of Quantum Confinement Effects in Advanced MOS Devices

NASA Technical Reports Server (NTRS)

Biegel, Bryan A.; Rafferty, Conor S.; Ancona, Mario G.; Yu, Zhi-Ping

2000-01-01

We investigate the density-gradient (DG) transport model for efficient multi-dimensional simulation of quantum confinement effects in advanced MOS devices. The formulation of the DG model is described as a quantum correction to the classical drift-diffusion model. Quantum confinement effects are shown to be significant in sub-100nm MOSFETs. In thin-oxide MOS capacitors, quantum effects may reduce gate capacitance by 25% or more. As a result, the inclusion or quantum effects in simulations dramatically improves the match between C-V simulations and measurements for oxide thickness down to 2 nm. Significant quantum corrections also occur in the I-V characteristics of short-channel (30 to 100 nm) n-MOSFETs, with current drive reduced by up to 70%. This effect is shown to result from reduced inversion charge due to quantum confinement of electrons in the channel. Also, subthreshold slope is degraded by 15 to 20 mV/decade with the inclusion of quantum effects via the density-gradient model, and short channel effects (in particular, drain-induced barrier lowering) are noticeably increased.

Hybrid MD-Nernst Planck Model of Alpha-hemolysin Conductance Properties

NASA Technical Reports Server (NTRS)

Cozmuta, Ioana; O'Keefer, James T.; Bose, Deepak; Stolc, Viktor

2006-01-01

Motivated by experiments in which an applied electric field translocates polynucleotides through an alpha-hemolysin protein channel causing ionic current transient blockade, a hybrid simulation model is proposed to predict the conductance properties of the open channel. Time scales corresponding to ion permeation processes are reached using the Poisson-Nemst-Planck (PNP) electro-diffusion model in which both solvent and local ion concentrations are represented as a continuum. The diffusion coefficients of the ions (K(+) and Cl(-)) input in the PNP model are, however, calculated from all-atom molecular dynamics (MD). In the MD simulations, a reduced representation of the channel is used. The channel is solvated in a 1 M KCI solution, and an external electric field is applied. The pore specific diffusion coefficients for both ionic species are reduced 5-7 times in comparison to bulk values. Significant statistical variations (17-45%) of the pore-ions diffusivities are observed. Within the statistics, the ionic diffusivities remain invariable for a range of external applied voltages between 30 and 240mV. In the 2D-PNP calculations, the pore stem is approximated by a smooth cylinder of radius approx. 9A with two constriction blocks where the radius is reduced to approx. 6A. The electrostatic potential includes the contribution from the atomistic charges. The MD-PNP model shows that the atomic charges are responsible for the rectifying behaviour and for the slight anion selectivity of the a-hemolysin pore. Independent of the hierarchy between the anion and cation diffusivities, the anionic contribution to the total ionic current will dominate. The predictions of the MD-PNP model are in good agreement with experimental data and give confidence in the present approach of bridging time scales by combining a microscopic and macroscopic model.

Effect of Temperature and Sheet Temper on Isothermal Solidification Kinetics in Clad Aluminum Brazing Sheet

NASA Astrophysics Data System (ADS)

Benoit, Michael J.; Whitney, Mark A.; Wells, Mary A.; Winkler, Sooky

2016-09-01

Isothermal solidification (IS) is a phenomenon observed in clad aluminum brazing sheets, wherein the amount of liquid clad metal is reduced by penetration of the liquid clad into the core. The objective of the current investigation is to quantify the rate of IS through the use of a previously derived parameter, the Interface Rate Constant (IRC). The effect of peak temperature and initial sheet temper on IS kinetics were investigated. The results demonstrated that IS is due to the diffusion of silicon (Si) from the liquid clad layer into the solid core. Reduced amounts of liquid clad at long liquid duration times, a roughened sheet surface, and differences in resolidified clad layer morphology between sheet tempers were observed. Increased IS kinetics were predicted at higher temperatures by an IRC model as well as by experimentally determined IRC values; however, the magnitudes of these values are not in good agreement due to deficiencies in the model when applied to alloys. IS kinetics were found to be higher for sheets in the fully annealed condition when compared with work-hardened sheets, due to the influence of core grain boundaries providing high diffusivity pathways for Si diffusion, resulting in more rapid liquid clad penetration.

Effects of lateral diffusion on morphology and dynamics of a microscopic lattice-gas model of pulsed electrodeposition.

PubMed

Frank, Stefan; Roberts, Daniel E; Rikvold, Per Arne

2005-02-08

The influence of nearest-neighbor diffusion on the decay of a metastable low-coverage phase (monolayer adsorption) in a square lattice-gas model of electrochemical metal deposition is investigated by kinetic Monte Carlo simulations. The phase-transformation dynamics are compared to the well-established Kolmogorov-Johnson-Mehl-Avrami theory. The phase transformation is accelerated by diffusion, but remains in accord with the theory for continuous nucleation up to moderate diffusion rates. At very high diffusion rates the phase-transformation kinetic shows a crossover to instantaneous nucleation. Then, the probability of medium-sized clusters is reduced in favor of large clusters. Upon reversal of the supersaturation, the adsorbate desorbs, but large clusters still tend to grow during the initial stages of desorption. Calculation of the free energy of subcritical clusters by enumeration of lattice animals yields a quasiequilibrium distribution which is in reasonable agreement with the simulation results. This is an improvement relative to classical droplet theory, which fails to describe the distributions, since the macroscopic surface tension is a bad approximation for small clusters.

Self-crowding of AMPA receptors in the excitatory postsynaptic density can effectuate anomalous receptor sub-diffusion.

PubMed

Gupta, Rahul

2018-02-01

AMPA receptors (AMPARs) and their associations with auxiliary transmembrane proteins are bulky structures with large steric-exclusion volumes. Hence, self-crowding of AMPARs, depending on the local density, may affect their lateral diffusion in the postsynaptic membrane as well as in the highly crowded postsynaptic density (PSD) at excitatory synapses. Earlier theoretical studies considered only the roles of transmembrane obstacles and the AMPAR-binding submembranous scaffold proteins in shaping receptor diffusion within PSD. Using lattice model of diffusion, the present study investigates the additional impacts of self-crowding on the anomalousity and effective diffusion coefficient (Deff) of AMPAR diffusion. A recursive algorithm for avoiding false self-blocking during diffusion simulation is also proposed. The findings suggest that high density of AMPARs in the obstacle-free membrane itself engenders strongly anomalous diffusion and severe decline in Deff. Adding transmembrane obstacles to the membrane accentuates the anomalousity arising from self-crowding due to the reduced free diffusion space. Contrarily, enhanced AMPAR-scaffold binding, either through increase in binding strength or scaffold density or both, ameliorates the anomalousity resulting from self-crowding. However, binding has differential impacts on Deff depending on the receptor density. Increase in binding causes consistent decrease in Deff for low and moderate receptor density. For high density, binding increases Deff as long as it reduces anomalousity associated with intense self-crowding. Given a sufficiently strong binding condition when diffusion acquires normal behavior, further increase in binding causes decrease in Deff. Supporting earlier experimental observations are mentioned and implications of present findings to the experimental observations on AMPAR diffusion are also drawn.

Energy Models for One-Carrier Transport in Semiconductor Devices

NASA Technical Reports Server (NTRS)

Jerome, Joseph W.; Shu, Chi-Wang

1991-01-01

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

A simple model for closure temperature of a trace element in cooling bi-mineralic systems

NASA Astrophysics Data System (ADS)

Liang, Yan

2015-09-01

Closure temperature is defined as the lower temperature limit at which the element of interest effectively ceases diffusive exchange with its surrounding medium during cooling. Here we generalize the classic equation of Dodson (1973) for cooling mono-mineralic systems to cooling bi-mineralic aggregates by considering diffusive exchange of a trace element between the two minerals in a closed system. We present a simple analytical model that includes key parameters affecting the closure temperature of a trace element in cooling bi-mineralic systems: cooling rate, temperature-dependent diffusion coefficients for the trace element in the two minerals, temperature-dependent partition coefficient of the trace element between the two minerals, effective grain sizes of the two minerals, and volume proportions of the minerals in the system. We show that closure temperatures of a trace element in cooling bi-mineralic systems are bounded by the closure temperatures of the trace element in the two mono-mineralic systems and that our generalized model reduces to Dodson's equation when one of the mineral serves as "an effective infinite" reservoir to the other mineral. Application to closure temperatures of REE in orthopyroxene and clinopyroxene bi-mineralic systems highlights the importance of REE diffusion and partitioning in the pyroxenes as well as clinopyroxene modal abundance and grain size in the systems. Closure temperatures for REE in two-pyroxene bearing equigranular rocks are controlled primarily by diffusion in orthopyroxene unless the modal abundance of clinopyroxene is very small. This has important bearings on the interpretation of temperatures derived from the REE-in-two-pyroxene thermometer.

Stability of wave processes in a rotating electrically conducting fluid

NASA Astrophysics Data System (ADS)

Peregudin, S. I.; Peregudina, E. S.; Kholodova, S. E.

2018-05-01

The paper puts forward a mathematical model of dynamics of spatial large-scale motions in a rotating layer of electrically conducting incompressible perfect fluid of variable depth with due account of dissipative effects. The resulting boundary-value problem is reduced to a vector system of partial differential equations for any values of the Reynolds number. Theoretical analysis of the so-obtained analytical solution reveals the effect of the magnetic field diffusion on the stability of the wave mode — namely, with the removed external magnetic field, the diffusion of the magnetic field promotes its damping. Besides, a criterion of stability of a wave mode is obtained.

Enriched Brain Omega-3 Polyunsaturated Fatty Acids Confer Neuroprotection against Microinfarction.

PubMed

Luo, Chuanming; Ren, Huixia; Yao, Xiaoli; Shi, Zhe; Liang, Fengyin; Kang, Jing X; Wan, Jian-Bo; Pei, Zhong; Su, Kuan-Pin; Su, Huanxing

2018-06-01

Cerebral microinfarcts have significant effects on the development of geriatric neurological disorders, including vascular dementia and Alzheimer's disease. However, little is known about the pathophysiological mechanisms involved in the evolution of microinfarcts and potential treatment and prevention against these microvascular ischemic lesions. In the present study, the "single cortical microinfarct model" generated via occluding a penetrating arteriole by femtosecond laser ablation and the "multiple diffuse microinfarcts model" induced by unilateral injection of cholesterol crystals through the internal carotid artery were established to investigate the pathophysiological mechanisms underlying the evolution of microinfarcts and the effects of omega-3 polyunsaturated fatty acids (ω-3 PUFAs) on alleviating microinfarct burdens and functional deficits. The occlusion of a single penetrating arteriole led to a distinct cortical microinfarct, which manifested as neuronal loss and occupation of activated glial cells in the ischemic core. Using Fat-1 transgenic mice and fish oil supplements, we demonstrated that both endogenously-generated and exogenously-delivered ω-3 PUFAs significantly inhibited the activation of receptor-interacting serine/threonine protein kinases 1 (RIPK1) and its downstream apoptosis-associated proteins, mitigated cell apoptosis, and anatomically reduced the microinfarct size. The protective effects of ω-3 PUFAs against microinfarcts were further verified in a multiple diffuse microinfarcts model, where ω-3 PUFAs significantly attenuated cell apoptosis as revealed by TUNEL staining, alleviated the diffuse microinfarct burdens and remarkably improved the functional deficits as evidenced by reduced spontaneous anxiety, increased preference for the novel object, and improved hippocampal-based learning and short-term memory. Together, these findings demonstrate that enriched brain ω-3 PUFAs are effective for reducing microinfarct burdens and improving the function deficits, which support the clinical research and application of ω-3 PUFAs in the treatment or prophylaxis in vascular dementia. Copyright © 2018 The Authors. Published by Elsevier B.V. All rights reserved.

Extinguishment of a Diffusion Flame Over a PMMA Cylinder by Depressurization in Reduced-Gravity

NASA Technical Reports Server (NTRS)

Goldmeer, Jeffrey Scott

1996-01-01

Extinction of a diffusion flame burning over horizontal PMMA (Polymethyl methacrylate) cylinders in low-gravity was examined experimentally and via numerical simulations. Low-gravity conditions were obtained using the NASA Lewis Research Center's reduced-gravity aircraft. The effects of velocity and pressure on the visible flame were examined. The flammability of the burning solid was examined as a function of pressure and the solid-phase centerline temperature. As the solid temperature increased, the extinction pressure decreased, and with a centerline temperature of 525 K, the flame was sustained to 0.1 atmospheres before extinguishing. The numerical simulation iteratively coupled a two-dimensional quasi-steady, gas-phase model with a transient solid-phase model which included conductive heat transfer and surface regression. This model employed an energy balance at the gas/solid interface that included the energy conducted by the gas-phase to the gas/solid interface, Arrhenius pyrolysis kinetics, surface radiation, and the energy conducted into the solid. The ratio of the solid and gas-phase conductive fluxes Phi was a boundary condition for the gas-phase model at the solid-surface. Initial simulations modeled conditions similar to the low-gravity experiments and predicted low-pressure extinction limits consistent with the experimental limits. Other simulations examined the effects of velocity, depressurization rate and Phi on extinction.

Effect of electron Monte Carlo collisions on a hybrid simulation of a low-pressure capacitively coupled plasma

NASA Astrophysics Data System (ADS)

Hwang, Seok Won; Lee, Ho-Jun; Lee, Hae June

2014-12-01

Fluid models have been widely used and conducted successfully in high pressure plasma simulations where the drift-diffusion and the local-field approximation are valid. However, fluid models are not able to demonstrate non-local effects related to large electron energy relaxation mean free path in low pressure plasmas. To overcome this weakness, a hybrid model coupling electron Monte Carlo collision (EMCC) method with the fluid model is introduced to obtain precise electron energy distribution functions using pseudo-particles. Steady state simulation results by a one-dimensional hybrid model which includes EMCC method for the collisional reactions but uses drift-diffusion approximation for electron transport in a fluid model are compared with those of a conventional particle-in-cell (PIC) and a fluid model for low pressure capacitively coupled plasmas. At a wide range of pressure, the hybrid model agrees well with the PIC simulation with a reduced calculation time while the fluid model shows discrepancy in the results of the plasma density and the electron temperature.

Differential effects of black currant anthocyanins on diffuser- or negative lens-induced ocular elongation in chicks.

PubMed

Iida, Hiroyuki; Nakamura, Yuko; Matsumoto, Hitoshi; Kawahata, Keiko; Koga, Jinichiro; Katsumi, Osamu

2013-01-01

To compare the inhibitory effects of 4 different types of black currant anthocyanins (BCAs) on ocular elongation in 2 different chick myopia models. In the first model, diffusers were used to induce form vision deprivation. In the second model, negative (-8D) spherical lenses were used to create a defocused retinal image. Either the diffusers or the -8D lenses were placed on the right eyes of 8-day-old chicks for 4 days. Ocular biometric components were measured using an A-scan ultrasound instrument on the third day after application of either the diffusers or -8D lenses. Interocular differences (globe component dimensions of the right diffuser or eyes covered with -8D lenses minus those of the open left eyes) were considered to evaluate the effect of BCAs. The BCAs used were cyanidin-3-glucoside (C3G), cyanidin-3-rutinoside (C3R), delphinidin-3-rutinoside (D3R), and delphinidin-3-glucoside (D3G). Each anthocyanin was administered intravenously at a dose of 0.027 μmol/kg once a day for 3 days. Compared to the vehicle treatment, C3G and C3R treatments significantly reduced both differential increases (positive values of interocular differences) of the ocular axial length induced by diffusers or -8D lenses (diffusers; C3G, C3R, and control: 0.32±0.051 mm, P<0.05; 0.25±0.034 mm, P<0.01; and 0.52±0.047 mm, -8D lenses; C3G, C3R, and control: 0.25±0.049 mm, P<0.01; 0.17±0.049 mm, P<0.001; and 0.50±0.056 mm). In contrast, compared to vehicle treatment, D3R treatment significantly decreased the differential increases in the ocular axial length only in chicks with myopia induced by -8D lenses (D3R and control: 0.17±0.049 mm and 0.50±0.056 mm, P<0.001). D3G did not inhibit the differential increase in the ocular axial length induced by either diffusers or -8D lenses. This study showed that the 4 tested BCAs had different effects on the 2 different experimental models of myopia.

Pattern formation in diffusive excitable systems under magnetic flow effects

NASA Astrophysics Data System (ADS)

Mvogo, Alain; Takembo, Clovis N.; Ekobena Fouda, H. P.; Kofané, Timoléon C.

2017-07-01

We study the spatiotemporal formation of patterns in a diffusive FitzHugh-Nagumo network where the effect of electromagnetic induction has been introduced in the standard mathematical model by using magnetic flux, and the modulation of magnetic flux on membrane potential is realized by using memristor coupling. We use the multi-scale expansion to show that the system equations can be reduced to a single differential-difference nonlinear equation. The linear stability analysis is performed and discussed with emphasis on the impact of magnetic flux. It is observed that the effect of memristor coupling importantly modifies the features of modulational instability. Our analytical results are supported by the numerical experiments, which reveal that the improved model can lead to nonlinear quasi-periodic spatiotemporal patterns with some features of synchronization. It is observed also the generation of pulses and rhythmics behaviors like breathing or swimming which are important in brain researches.

Enzyme localization, crowding, and buffers collectively modulate diffusion-influenced signal transduction: Insights from continuum diffusion modeling

PubMed Central

Kekenes-Huskey, Peter M.; Eun, Changsun; McCammon, J. A.

2015-01-01

Biochemical reaction networks consisting of coupled enzymes connect substrate signaling events with biological function. Substrates involved in these reactions can be strongly influenced by diffusion “barriers” arising from impenetrable cellular structures and macromolecules, as well as interactions with biomolecules, especially within crowded environments. For diffusion-influenced reactions, the spatial organization of diffusion barriers arising from intracellular structures, non-specific crowders, and specific-binders (buffers) strongly controls the temporal and spatial reaction kinetics. In this study, we use two prototypical biochemical reactions, a Goodwin oscillator, and a reaction with a periodic source/sink term to examine how a diffusion barrier that partitions substrates controls reaction behavior. Namely, we examine how conditions representative of a densely packed cytosol, including reduced accessible volume fraction, non-specific interactions, and buffers, impede diffusion over nanometer length-scales. We find that diffusion barriers can modulate the frequencies and amplitudes of coupled diffusion-influenced reaction networks, as well as give rise to “compartments” of decoupled reactant populations. These effects appear to be intensified in the presence of buffers localized to the diffusion barrier. These findings have strong implications for the role of the cellular environment in tuning the dynamics of signaling pathways. PMID:26342355

Combined fetal inflammation and postnatal hypoxia causes myelin deficits and autism-like behavior in a rat model of diffuse white matter injury.

PubMed

van Tilborg, Erik; Achterberg, E J Marijke; van Kammen, Caren M; van der Toorn, Annette; Groenendaal, Floris; Dijkhuizen, Rick M; Heijnen, Cobi J; Vanderschuren, Louk J M J; Benders, Manon N J L; Nijboer, Cora H A

2018-01-01

Diffuse white matter injury (WMI) is a serious problem in extremely preterm infants, and is associated with adverse neurodevelopmental outcome, including cognitive impairments and an increased risk of autism-spectrum disorders. Important risk factors include fetal or perinatal inflammatory insults and fluctuating cerebral oxygenation. However, the exact mechanisms underlying diffuse WMI are not fully understood and no treatment options are currently available. The use of clinically relevant animal models is crucial to advance knowledge on the pathophysiology of diffuse WMI, allowing the definition of novel therapeutic targets. In the present study, we developed a multiple-hit animal model of diffuse WMI by combining fetal inflammation and postnatal hypoxia in rats. We characterized the effects on white matter development and functional outcome by immunohistochemistry, MRI and behavioral paradigms. Combined fetal inflammation and postnatal hypoxia resulted in delayed cortical myelination, microglia activation and astrogliosis at P18, together with long-term changes in oligodendrocyte maturation as observed in 10 week old animals. Furthermore, rats with WMI showed impaired motor performance, increased anxiety and signs of autism-like behavior, i.e. reduced social play behavior and increased repetitive grooming. In conclusion, the combination of fetal inflammation and postnatal hypoxia in rats induces a pattern of brain injury and functional impairments that closely resembles the clinical situation of diffuse WMI. This animal model provides the opportunity to elucidate pathophysiological mechanisms underlying WMI, and can be used to develop novel treatment options for diffuse WMI in preterm infants. © 2017 The Authors GLIA Published by Wiley Periodicals, Inc.

Combined fetal inflammation and postnatal hypoxia causes myelin deficits and autism‐like behavior in a rat model of diffuse white matter injury

PubMed Central

van Tilborg, Erik; Achterberg, E. J. Marijke; van Kammen, Caren M.; van der Toorn, Annette; Groenendaal, Floris; Dijkhuizen, Rick M.; Heijnen, Cobi J.; Vanderschuren, Louk J. M. J.; Benders, Manon N. J. L.

2017-01-01

Abstract Diffuse white matter injury (WMI) is a serious problem in extremely preterm infants, and is associated with adverse neurodevelopmental outcome, including cognitive impairments and an increased risk of autism‐spectrum disorders. Important risk factors include fetal or perinatal inflammatory insults and fluctuating cerebral oxygenation. However, the exact mechanisms underlying diffuse WMI are not fully understood and no treatment options are currently available. The use of clinically relevant animal models is crucial to advance knowledge on the pathophysiology of diffuse WMI, allowing the definition of novel therapeutic targets. In the present study, we developed a multiple‐hit animal model of diffuse WMI by combining fetal inflammation and postnatal hypoxia in rats. We characterized the effects on white matter development and functional outcome by immunohistochemistry, MRI and behavioral paradigms. Combined fetal inflammation and postnatal hypoxia resulted in delayed cortical myelination, microglia activation and astrogliosis at P18, together with long‐term changes in oligodendrocyte maturation as observed in 10 week old animals. Furthermore, rats with WMI showed impaired motor performance, increased anxiety and signs of autism‐like behavior, i.e. reduced social play behavior and increased repetitive grooming. In conclusion, the combination of fetal inflammation and postnatal hypoxia in rats induces a pattern of brain injury and functional impairments that closely resembles the clinical situation of diffuse WMI. This animal model provides the opportunity to elucidate pathophysiological mechanisms underlying WMI, and can be used to develop novel treatment options for diffuse WMI in preterm infants. PMID:28925578

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, where intragranular 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 had been previously described using a semiempirical, multirate model. Compared with the multirate model, the diffusion models have the advantage to provide spatiotemporal speciation evolution within the diffusion domains.

Modelling of agricultural diffuse pollution and mitigation measures effectiveness in Wallonia (Belgium)

NASA Astrophysics Data System (ADS)

Sohier, C.; Deraedt, D.; Degré, A.

2012-04-01

Implementation of European directives in the environmental field and, specially, in the water management field, generates a request from policy-makers for news tools able to evaluate impact of management measures aiming at reducing pressures on ecosystems. In Wallonia (Southern Region of Belgium), the Nitrate Directive (EEC/676/91) was transposed into the "Walloon action plan for nitrogen sustainable management in agriculture" (PGDA1) in 2002. In 2007, a second plan was launched to reinforce some topics (PGDA2). Furthermore, the goal of "good quality" of surface waters and groundwater imposed by the Water Framework Directive poses new challenges in water management. In this context, a "soil and vadose" hydrological model is used in order to evaluate diffuse pollutions and efficiency of mitigation measures. This model, called EPICgrid, has been developed at catchment scale with an original modular concept on the basis of the field scale "water-soil-plant" EPIC model (Williams J.R., Jones C.A., Dyke P.T. (1984). A modelling approach to determining the relationship between erosion and soil productivity. Transactions of the ASAE. 27, 129-144). The model estimates, for each HRU identified into a 1km2 grid, water and nutrients flows into the plant-soil-vadose zone system (Sohier C., Degré A., Dautrebande S. (2009). From root zone modelling to regional forecasting of nitrate concentration in recharge flows - The case of the Walloon Region (Belgium). Journal of Hydrology, Volume 369, Issues 3-4, 15 May 2009, Pages 350-359). The model is used to make prospective simulations in order to evaluate the impact of measures currently performed to reduce the effect of diffuse pollution on water surface quality and groundwater quality, at regional scale. Response of the soil-vadose zone to agricultural practices modification is analyzed for the deadlines of the Water Framework Directive: 2015, 2021 and 2027, taking into account two climatic scenarios. Simulations results showed that actual measures are not sufficient in some areas and that new actions are necessary. The EPICgrid model was also used to evaluate effectiveness of further measures that could be implemented in order to reduce agricultural diffuse pollution. The increasing of catch crops in vulnerable zones has shown a limited impact in the Walloon context. The modifications of agricultural practices such as crop rotations or mineral fertilizing amounts have shown a more significant impact on water quality. Furthermore, the farmers' practices are evaluated each year by a measuring campaign of the soil nitrogen residue after harvest. These data allow us to improve the representativeness of the EPICgrid model in areas in which agricultural practices largely differs from regional statistics.

Diffusional dynamics of an active rhodamine-labeled 1,4-dihydropyridine in sarcolemmal lipid multibilayers.

PubMed Central

Mason, R P; Chester, D W

1989-01-01

A "membrane bilayer pathway" model, involving ligand partition into the bilayer, lateral diffusion, and receptor binding has been invoked to describe the 1,4-dihydropyridine (DHP) calcium channel antagonist receptor binding mechanism. In an earlier study (Chester et al. 1987. Biophys. J. 52:1021-1030), the diffusional component of this model was examined using an active fluorescence labeled DHP calcium channel antagonist, nisoldipine-lissamine rhodamine B (Ns-R), in purified cardiac sarcolemmal (CSL) lipid multibilayers. Diffusion coefficient measurements on membrane-bound drug and phospholipid at maximum bilayer hydration yielded similar values (3.8 x 10(-8) cm2/s). However, decreases in bilayer hydration resulted in dramatically reduced diffusion coefficient values for both probes with substantially greater impact on Ns-R diffusion. These data suggested that hydration dependent diffusional differences could be a function of relative probe location along the bilayer normal. In this communication, we have addressed the relative effect of the rhodamine substituent on Ns-R diffusion complex by examining the diffusional dynamics of free rhodamine B under the same conditions used to evaluate Ns-R complex and phospholipid diffusion. X-ray diffraction studies were performed to determine the Ns-R location in the membrane and model the CSL lipid bilayer profile structure to give a rationale for the differences in probe diffusional dynamics as a function of interbilayer water space. PMID:2611332

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

DOE PAGES

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

2016-11-21

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

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

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

Liu, Yuanyuan; Liu, Chongxuan; Zhang, Changyong

2015-08-01

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

Interdiffusion, Intrinsic Diffusion, Atomic Mobility, and Vacancy Wind Effect in γ(bcc) Uranium-Molybdenum Alloy

NASA Astrophysics Data System (ADS)

Huang, Ke; Keiser, Dennis D.; Sohn, Yongho

2013-02-01

U-Mo alloys are being developed as low enrichment uranium fuels under the Reduced Enrichment for Research and Test Reactor (RERTR) Program. In order to understand the fundamental diffusion behavior of this system, solid-to-solid pure U vs Mo diffusion couples were assembled and annealed at 923 K, 973 K, 1073 K, 1173 K, and 1273 K (650 °C, 700 °C, 800 °C, 900 °C, and 1000 °C) for various times. The interdiffusion microstructures and concentration profiles were examined via scanning electron microscopy and electron probe microanalysis, respectively. As the Mo concentration increased from 2 to 26 at. pct, the interdiffusion coefficient decreased, while the activation energy increased. A Kirkendall marker plane was clearly identified in each diffusion couple and utilized to determine intrinsic diffusion coefficients. Uranium intrinsically diffused 5-10 times faster than Mo. Molar excess Gibbs free energy of U-Mo alloy was applied to calculate the thermodynamic factor using ideal, regular, and subregular solution models. Based on the intrinsic diffusion coefficients and thermodynamic factors, Manning's formalism was used to calculate the tracer diffusion coefficients, atomic mobilities, and vacancy wind parameters of U and Mo at the marker composition. The tracer diffusion coefficients and atomic mobilities of U were about five times larger than those of Mo, and the vacancy wind effect increased the intrinsic flux of U by approximately 30 pct.

An adaptive tau-leaping method for stochastic simulations of reaction-diffusion systems

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

Padgett, Jill M. A.; Ilie, Silvana, E-mail: silvana@ryerson.ca

2016-03-15

Stochastic modelling is critical for studying many biochemical processes in a cell, in particular when some reacting species have low population numbers. For many such cellular processes the spatial distribution of the molecular species plays a key role. The evolution of spatially heterogeneous biochemical systems with some species in low amounts is accurately described by the mesoscopic model of the Reaction-Diffusion Master Equation. The Inhomogeneous Stochastic Simulation Algorithm provides an exact strategy to numerically solve this model, but it is computationally very expensive on realistic applications. We propose a novel adaptive time-stepping scheme for the tau-leaping method for approximating themore » solution of the Reaction-Diffusion Master Equation. This technique combines effective strategies for variable time-stepping with path preservation to reduce the computational cost, while maintaining the desired accuracy. The numerical tests on various examples arising in applications show the improved efficiency achieved by the new adaptive method.« less

The narrow pulse approximation and long length scale determination in xenon gas diffusion NMR studies of model porous media

NASA Technical Reports Server (NTRS)

Mair, R. W.; Sen, P. N.; Hurlimann, M. D.; Patz, S.; Cory, D. G.; Walsworth, R. L.

2002-01-01

We report a systematic study of xenon gas diffusion NMR in simple model porous media, random packs of mono-sized glass beads, and focus on three specific areas peculiar to gas-phase diffusion. These topics are: (i) diffusion of spins on the order of the pore dimensions during the application of the diffusion encoding gradient pulses in a PGSE experiment (breakdown of the narrow pulse approximation and imperfect background gradient cancellation), (ii) the ability to derive long length scale structural information, and (iii) effects of finite sample size. We find that the time-dependent diffusion coefficient, D(t), of the imbibed xenon gas at short diffusion times in small beads is significantly affected by the gas pressure. In particular, as expected, we find smaller deviations between measured D(t) and theoretical predictions as the gas pressure is increased, resulting from reduced diffusion during the application of the gradient pulse. The deviations are then completely removed when water D(t) is observed in the same samples. The use of gas also allows us to probe D(t) over a wide range of length scales and observe the long time asymptotic limit which is proportional to the inverse tortuosity of the sample, as well as the diffusion distance where this limit takes effect (approximately 1-1.5 bead diameters). The Pade approximation can be used as a reference for expected xenon D(t) data between the short and the long time limits, allowing us to explore deviations from the expected behavior at intermediate times as a result of finite sample size effects. Finally, the application of the Pade interpolation between the long and the short time asymptotic limits yields a fitted length scale (the Pade length), which is found to be approximately 0.13b for all bead packs, where b is the bead diameter. c. 2002 Elsevier Sciences (USA).

The narrow pulse approximation and long length scale determination in xenon gas diffusion NMR studies of model porous media.

PubMed

Mair, R W; Sen, P N; Hürlimann, M D; Patz, S; Cory, D G; Walsworth, R L

2002-06-01

We report a systematic study of xenon gas diffusion NMR in simple model porous media, random packs of mono-sized glass beads, and focus on three specific areas peculiar to gas-phase diffusion. These topics are: (i) diffusion of spins on the order of the pore dimensions during the application of the diffusion encoding gradient pulses in a PGSE experiment (breakdown of the narrow pulse approximation and imperfect background gradient cancellation), (ii) the ability to derive long length scale structural information, and (iii) effects of finite sample size. We find that the time-dependent diffusion coefficient, D(t), of the imbibed xenon gas at short diffusion times in small beads is significantly affected by the gas pressure. In particular, as expected, we find smaller deviations between measured D(t) and theoretical predictions as the gas pressure is increased, resulting from reduced diffusion during the application of the gradient pulse. The deviations are then completely removed when water D(t) is observed in the same samples. The use of gas also allows us to probe D(t) over a wide range of length scales and observe the long time asymptotic limit which is proportional to the inverse tortuosity of the sample, as well as the diffusion distance where this limit takes effect (approximately 1-1.5 bead diameters). The Padé approximation can be used as a reference for expected xenon D(t) data between the short and the long time limits, allowing us to explore deviations from the expected behavior at intermediate times as a result of finite sample size effects. Finally, the application of the Padé interpolation between the long and the short time asymptotic limits yields a fitted length scale (the Padé length), which is found to be approximately 0.13b for all bead packs, where b is the bead diameter. c. 2002 Elsevier Sciences (USA).

Random diffusion and leverage effect in financial markets.

PubMed

Perelló, Josep; Masoliver, Jaume

2003-03-01

We prove that Brownian market models with random diffusion coefficients provide an exact measure of the leverage effect [J-P. Bouchaud et al., Phys. Rev. Lett. 87, 228701 (2001)]. This empirical fact asserts that past returns are anticorrelated with future diffusion coefficient. Several models with random diffusion have been suggested but without a quantitative study of the leverage effect. Our analysis lets us to fully estimate all parameters involved and allows a deeper study of correlated random diffusion models that may have practical implications for many aspects of financial markets.

The diffusivity and solubility of deuterium in a high chromium martensitic steel

NASA Astrophysics Data System (ADS)

Forcey, K. S.; Iordanova, I.; Yaneva, M.

1997-01-01

The permeability, diffusivity and solubility of deuterium in the martensitic stainless steel MANET II have been studied in the temperature range 194-465°C by applying a time dependent gas-phase permeation technique. It was found that the temperature dependence of diffusivity and solubility could not be described by a simple Arrhenius expression over the entire temperature range investigated. At lower temperatures (below about 330°C) the diffusivity was found to be greatly reduced by the effects of trapping. Oriani's model has been applied to obtain the trapping energy and number density of the traps as well as the relative amounts of deuterium dissolved at lattice and trap sites. It is suggested that the most likely sites for trapping are at interfaces between the martensitic laths and between second phase particles and the surrounding metal matrix.

Brownian ratchets: How stronger thermal noise can reduce diffusion

NASA Astrophysics Data System (ADS)

Spiechowicz, Jakub; Kostur, Marcin; Łuczka, Jerzy

2017-02-01

We study diffusion properties of an inertial Brownian motor moving on a ratchet substrate, i.e., a periodic structure with broken reflection symmetry. The motor is driven by an unbiased time-periodic symmetric force that takes the system out of thermal equilibrium. For selected parameter sets, the system is in a non-chaotic regime in which we can identify a non-monotonic dependence of the diffusion coefficient on temperature: for low temperature, it initially increases as the temperature grows, passes through its local maximum, next starts to diminish reaching its local minimum, and finally it monotonically increases in accordance with the Einstein linear relation. Particularly interesting is the temperature interval in which diffusion is suppressed by the thermal noise, and we explain this effect in terms of transition rates of a three-state stochastic model.

Brownian ratchets: How stronger thermal noise can reduce diffusion.

PubMed

Spiechowicz, Jakub; Kostur, Marcin; Łuczka, Jerzy

2017-02-01

We study diffusion properties of an inertial Brownian motor moving on a ratchet substrate, i.e., a periodic structure with broken reflection symmetry. The motor is driven by an unbiased time-periodic symmetric force that takes the system out of thermal equilibrium. For selected parameter sets, the system is in a non-chaotic regime in which we can identify a non-monotonic dependence of the diffusion coefficient on temperature: for low temperature, it initially increases as the temperature grows, passes through its local maximum, next starts to diminish reaching its local minimum, and finally it monotonically increases in accordance with the Einstein linear relation. Particularly interesting is the temperature interval in which diffusion is suppressed by the thermal noise, and we explain this effect in terms of transition rates of a three-state stochastic model.

Impact of nitrogen reduction measures on the nitrogen loads of the river Ems and Rhine (Germany)

NASA Astrophysics Data System (ADS)

Wendland, F.; Bogena, H.; Goemann, H.; Hake, J. F.; Kreins, P.; Kunkel, R.

The REGFLUD-project, commissioned by Germany’s Federal Research Ministry (BMBF), addresses the problem of reducing diffuse pollution from agricultural production. The objective of the project is the development and application of multi-criteria scientific methods, which are able to predict diffuse pollution in river basins subject to economic feasibility and social acceptability. The selected river basins (the entire Ems basin and sub-catchments of the Rhine) cover a variety of landscape units with different hydrological, hydrogeological and socio-economic characteristics. This paper focuses on the analysis of the effects of certain policy measures to reduce diffuse pollution by nitrogen. For this purpose, a model system consisting of an agricultural sector model, a water balance model and a residence time/denitrification model was combined and applied. First results indicate a wide range of annual nitrogen surpluses for the rural areas between less than 10 N ha -1 a -1 up 200 kg N ha -1 a -1, or more depending on the type and intensity of farming. Compared to the level of nitrogen surpluses the level of nitrogen inputs into the surface waters is relatively moderate because of degradation processes during transport in soil and groundwater. Policy impact analyses for a nitrogen tax and a limitation of the livestock density stress the importance of regionally adjusted measures.

Self-crowding of AMPA receptors in the excitatory postsynaptic density can effectuate anomalous receptor sub-diffusion

PubMed Central

Gupta, Rahul

2018-01-01

AMPA receptors (AMPARs) and their associations with auxiliary transmembrane proteins are bulky structures with large steric-exclusion volumes. Hence, self-crowding of AMPARs, depending on the local density, may affect their lateral diffusion in the postsynaptic membrane as well as in the highly crowded postsynaptic density (PSD) at excitatory synapses. Earlier theoretical studies considered only the roles of transmembrane obstacles and the AMPAR-binding submembranous scaffold proteins in shaping receptor diffusion within PSD. Using lattice model of diffusion, the present study investigates the additional impacts of self-crowding on the anomalousity and effective diffusion coefficient (Deff) of AMPAR diffusion. A recursive algorithm for avoiding false self-blocking during diffusion simulation is also proposed. The findings suggest that high density of AMPARs in the obstacle-free membrane itself engenders strongly anomalous diffusion and severe decline in Deff. Adding transmembrane obstacles to the membrane accentuates the anomalousity arising from self-crowding due to the reduced free diffusion space. Contrarily, enhanced AMPAR-scaffold binding, either through increase in binding strength or scaffold density or both, ameliorates the anomalousity resulting from self-crowding. However, binding has differential impacts on Deff depending on the receptor density. Increase in binding causes consistent decrease in Deff for low and moderate receptor density. For high density, binding increases Deff as long as it reduces anomalousity associated with intense self-crowding. Given a sufficiently strong binding condition when diffusion acquires normal behavior, further increase in binding causes decrease in Deff. Supporting earlier experimental observations are mentioned and implications of present findings to the experimental observations on AMPAR diffusion are also drawn. PMID:29444074

Effects of Lewis Number on Temperatures of Spherical Diffusion Flames

NASA Technical Reports Server (NTRS)

Santa, K. J.; Sun, Z.; Chao, B. H.; Sunderland, P. B.; Axelbaum, R. I.; Urban, D. L.; Stocker, D. P.

2007-01-01

Spherical diffusion flames supported on a porous sphere were studied numerically and experimentally. Experiments were performed in 2.2 s and 5.2 s microgravity facilities. Numerical results were obtained from a Chemkin-based program. The program simulates flow from a porous sphere into a quiescent environment, yields both steady-state and transient results, and accounts for optically thick gas-phase radiation. The low flow velocities and long residence times in these diffusion flames lead to enhanced radiative and diffusive effects. Despite similar adiabatic flame temperatures, the measured and predicted temperatures varied by as much as 700 K. The temperature reduction correlates with flame size but characteristic flow times and, importantly, Lewis number also influence temperature. The numerical results show that the ambient gas Lewis number would have a strong effect on flame temperature if the flames were steady and nonradiating. For example, a 10% decrease in Lewis number would increase the steady-state flame temperature by 200 K. However, for these transient, radiating flames the effect of Lewis number is small. Transient predictions of flame sizes are larger than those observed in microgravity experiments. Close agreement could not be obtained without either increasing the model s thermal and mass diffusion properties by 30% or reducing mass flow rate by 25%.

Radiative transfer model of snow for bare ice regions

NASA Astrophysics Data System (ADS)

Tanikawa, T.; Aoki, T.; Niwano, M.; Hosaka, M.; Shimada, R.; Hori, M.; Yamaguchi, S.

2016-12-01

Modeling a radiative transfer (RT) for coupled atmosphere-snow-bare ice systems is of fundamental importance for remote sensing applications to monitor snow and bare ice regions in the Greenland ice sheet and for accurate climate change predictions by regional and global climate models. Recently, the RT model for atmosphere-snow system was implemented for our regional and global climate models. However, the bare ice region where recently it has been expanded on the Greenland ice sheet due to the global warming, has not been implemented for these models, implying that this region leads miscalculations in these climate models. Thus, the RT model of snow for bare ice regions is needed for accurate climate change predictions. We developed the RT model for coupled atmosphere-snow-bare ice systems, and conducted a sensitivity analysis of the RT model to know the effect of snow, bare ice and geometry parameters on the spectral radiant quantities. The RT model considers snow and bare-ice inherent optical properties (IOPs), including snow grain size, air bubble size and its concentration and bare ice thickness. The conventional light scattering theory, Mie theory, was used for IOP calculations. Monte Carlo method was used for the multiple scattering. The sensitivity analyses showed that spectral albedo for the bare ice increased with increasing the concentration of the air bubble in the bare ice for visible wavelengths because the air bubble is scatterer with no absorption. For near infrared wavelengths, spectral albedo has no dependence on the air bubble due to the strong light absorption by ice. When increasing solar zenith angle, the spectral albedo were increased for all wavelengths. This is the similar trend with spectral snow albedo. Cloud cover influenced the bare ice spectral albedo by covering direct radiation into diffuse radiation. The purely diffuse radiation has an effective solar zenith angle near 50°. Converting direct into diffuse radiation reduces the effective solar zenith angle, resulting in reducing the spectral albedo. This is also the similar trend with spectral snow albedo. Further work should focus on the validation of the RT model using in situ measurement data through field and laboratory experiments.

Simulations on the Influence of Myelin Water in Diffusion-Weighted Imaging

PubMed Central

Harkins, Kevin D.; Does, Mark D.

2016-01-01

While myelinated axons present an important barrier to water diffusion, many models used to interpret DWI signal neglect other potential influences of myelin. In this work, Monte Carlo simulations were used to test the sensitivity of DWI results to the diffusive properties of water within myelin. Within these simulations, the apparent diffusion coefficient (Dapp) varied slowly over several orders of magnitude of the coefficient of myelin water diffusion (Dm), but exhibited important differences compared to Dapp values simulated that neglect Dm (=0). Compared to Dapp, the apparent diffusion kurtosis (Kapp) was generally more sensitive to Dm. Simulations also tested the sensitivity of Dapp and Kapp to the amount of myelin present. Unique variations in Dapp and Kapp caused by differences in the myelin volume fraction were diminished when myelin water diffusion was included. Also, expected trends in Dapp and Kapp with experimental echo time were reduced or inverted when accounting for myelin water diffusion, and these reduced/inverted trends were seen experimentally in ex vivo rat brain DWI experiments. In general, myelin water has the potential to subtly influence DWI results and bias models of DWI that neglect these components of white matter. PMID:27271991

The Focusing of Light Scattered from Diffuse Reflectors Using Phase Modulation

DTIC Science & Technology

2012-03-22

was recently demonstrated for imaging otherwise hidden scene information through the collection and radiometric modeling of light reflecting off of...effectively reducing the radiometric model to that of the previously demonstrated dual photography, and leading to much-simplified results. This...angle. The fundamental geometric descriptor of reflectance is given by the bidirectional reflectance distribution function ( BRDF ) fr (θi, φi; θs, φs

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

Liang, Linyun; Mei, Zhi-Gang; Yacout, Abdellatif M.

We have developed a mesoscale phase-field model for studying the effect of recrystallization on the gas-bubble-driven swelling in irradiated U-Mo alloy fuel. The model can simulate the microstructural evolution of the intergranular gas bubbles on the grain boundaries as well as the recrystallization process. Our simulation results show that the intergranular gas-bubble-induced fuel swelling exhibits two stages: slow swelling kinetics before recrystallization and rapid swelling kinetics with recrystallization. We observe that the recrystallization can significantly expedite the formation and growth of gas bubbles at high fission densities. The reason is that the recrystallization process increases the nucleation probability of gasmore » bubbles and reduces the diffusion time of fission gases from grain interior to grain boundaries by increasing the grain boundary area and decreasing the diffusion distance. The simulated gas bubble shape, size distribution, and density on the grain boundaries are consistent with experimental measurements. We investigate the effect of the recrystallization on the gas-bubble-driven fuel swelling in UMo through varying the initial grain size and grain aspect ratio. We conclude that the initial microstructure of fuel, such as grain size and grain aspect ratio, can be used to effectively control the recrystallization and therefore reduce the swelling in U-Mo fuel.« less

Electrostatic coupling between DNA and its counterions modulates the observed translational diffusion coefficients.

PubMed

Stellwagen, Earle; Stellwagen, Nancy C

2015-09-01

Free solution capillary electrophoresis (CE) is a useful technique for measuring the translational diffusion coefficients of charged analytes. The measurements are relatively fast if the polarity of the electric field is reversed to drive the analyte back and forth past the detection window during each run. We have tested the validity of the resulting diffusion coefficients using double-stranded DNA molecules ranging in size from 20 to 960 base pairs as the model system. The diffusion coefficients of small DNAs are equal to values in the literature measured by other techniques. However, the diffusion coefficients of DNA molecules larger than ∼30 base pairs are anomalously high and deviate increasingly from the literature values with increasing DNA molar mass. The anomalously high diffusion coefficients are due to electrostatic coupling between the DNA and its counterions. As a result, the measured diffusion coefficients vary with the diffusion coefficient of the counterion, as well as with cation concentration and electric field strength. These effects can be reduced or eliminated by measuring apparent diffusion coefficients of the DNA at several different electric field strengths and extrapolating the results to zero electric field.

Symmetrical and overloaded effect of diffusion in information filtering

NASA Astrophysics Data System (ADS)

Zhu, Xuzhen; Tian, Hui; Chen, Guilin; Cai, Shimin

2017-10-01

In physical dynamics, mass diffusion theory has been applied to design effective information filtering models on bipartite network. In previous works, researchers unilaterally believe objects' similarities are determined by single directional mass diffusion from the collected object to the uncollected, meanwhile, inadvertently ignore adverse influence of diffusion overload. It in some extent veils the essence of diffusion in physical dynamics and hurts the recommendation accuracy and diversity. After delicate investigation, we argue that symmetrical diffusion effectively discloses essence of mass diffusion, and high diffusion overload should be published. Accordingly, in this paper, we propose an symmetrical and overload penalized diffusion based model (SOPD), which shows excellent performances in extensive experiments on benchmark datasets Movielens and Netflix.

Simulation analysis of the effect of initial delay on flight delay diffusion

NASA Astrophysics Data System (ADS)

Que, Zufu; Yao, Hongguang; Yue, Wei

2018-01-01

The initial delay of the flight is an important factor affecting the spread of flight delays, so clarifying their relationship conduces to control flight delays in the aeronautical network. Through establishing a model of the chain aviation network and making simulation analysis of the effects of initial delay on the delay longitudinal diffusion, it’s found that the number of delayed airports in the air network, the total delay time and the average delay time of the delayed airport are generally positively correlated with the initial delay. This indicates that the occurrence of the initial delay should be avoided or reduced as much as possible to improve the punctuality of the flight.

Modification method to reduce the impact of blood vessel on noncontact discrimination of human blood based on ;M+N; theory

NASA Astrophysics Data System (ADS)

Zhang, Linna; Ding, Hongyan; Lin, Ling; Wang, Yimin; Guo, Xin

2018-01-01

Noncontact discriminating human blood is significantly crucial for import-export ports and inspection and quarantine departments. We had already demonstrated that visible diffuse reflectance spectroscopy combining PLS-DA method can successfully realize noncontact human blood discrimination. However, the circulated blood vessels may be produced with different materials. The use of various kinds of blood tubes may have a negative effect on the discrimination, based on ;M+N; theory (Li et al., 2016). In this research, we explored the impact of different material of blood vessels, such as glass tube and plastic tube, on the prediction ability of the discrimination model. Furthermore, we searched for the modification method to reduce the influence from the blood tubes. Our work indicated that generalized diffuse reflectance method can greatly improve the discrimination accuracy. This research can greatly facilitate the application of noncontact discrimination method based on visible and near-infrared diffuse reflectance spectroscopy.

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

NASA Technical Reports Server (NTRS)

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

2002-01-01

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

Self diffusion of alkaline-Earth in Ca-Mg-aluminosilicate melts: Experimental improvements on the determination of the self-diffusion coefficients

NASA Technical Reports Server (NTRS)

Paillat, O.; Wasserburg, G. J.

1993-01-01

Experimental studies of self-diffusion isotopes in silicate melts often have quite large uncertainties when comparing one study to another. We designed an experiment in order to improve the precision of the results by simultaneously studying several elements (Mg, Ca, Sr, Ba) during the same experiment thereby greatly reducing the relative experimental uncertainties. Results show that the uncertainties on the diffusion coefficients can be reduced to 10 percent, allowing a more reliable comparison of differences of self-diffusion coefficients of the elements. This type of experiment permits us to study precisely and simultaneously several elements with no restriction on any element. We also designed an experiment to investigate the possible effects of multicomponent diffusion during Mg self-diffusion experiments by comparing cases where the concentrations of the elements and the isotopic compositions are different. The results suggest that there are differences between the effective means of transport. This approach should allow us to investigate the importance of multicomponent diffusion in silicate melts.

A Simplified Ab Initio Cosmic-ray Modulation Model with Simulated Time Dependence and Predictive Capability

NASA Astrophysics Data System (ADS)

Moloto, K. D.; Engelbrecht, N. E.; Burger, R. A.

2018-06-01

A simplified ab initio approach is followed to model cosmic-ray proton modulation, using a steady-state three-dimensional stochastic solver of the Parker transport equation that simulates some effects of time dependence. Standard diffusion coefficients based on Quasilinear Theory and Nonlinear Guiding Center Theory are employed. The spatial and temporal dependences of the various turbulence quantities required as inputs for the diffusion, as well as the turbulence-reduced drift coefficients, follow from parametric fits to results from a turbulence transport model as well as from spacecraft observations of these turbulence quantities. Effective values are used for the solar wind speed, magnetic field magnitude, and tilt angle in the modulation model to simulate temporal effects due to changes in the large-scale heliospheric plasma. The unusually high cosmic-ray intensities observed during the 2009 solar minimum follow naturally from the current model for most of the energies considered. This demonstrates that changes in turbulence contribute significantly to the high intensities during that solar minimum. We also discuss and illustrate how this model can be used to predict future cosmic-ray intensities, and comment on the reliability of such predictions.

Multiscale Modeling of Diffusion in a Crowded Environment.

PubMed

Meinecke, Lina

2017-11-01

We present a multiscale approach to model diffusion in a crowded environment and its effect on the reaction rates. Diffusion in biological systems is often modeled by a discrete space jump process in order to capture the inherent noise of biological systems, which becomes important in the low copy number regime. To model diffusion in the crowded cell environment efficiently, we compute the jump rates in this mesoscopic model from local first exit times, which account for the microscopic positions of the crowding molecules, while the diffusing molecules jump on a coarser Cartesian grid. We then extract a macroscopic description from the resulting jump rates, where the excluded volume effect is modeled by a diffusion equation with space-dependent diffusion coefficient. The crowding molecules can be of arbitrary shape and size, and numerical experiments demonstrate that those factors together with the size of the diffusing molecule play a crucial role on the magnitude of the decrease in diffusive motion. When correcting the reaction rates for the altered diffusion we can show that molecular crowding either enhances or inhibits chemical reactions depending on local fluctuations of the obstacle density.

Sorption and modeling of mass transfer of toxic chemical vapors in activated-carbon fiber-cloth adsorbers

USGS Publications Warehouse

Lordgooei, M.; Sagen, J.; Rood, M.J.; Rostam-Abadi, M.

1998-01-01

A new activated-carbon fiber-cloth (ACFC) adsorber coupled with an electrothermal regenerator and a cryogenic condenser was designed and developed to efficiently capture and recover toxic chemical vapors (TCVs) from simulated industrial gas streams. The system was characterized for adsorption by ACFC, electrothermal desorption, and cryogenic condensation to separate acetone and methyl ethyl ketone from gas streams. Adsorption dynamics are numerically modeled to predict system characteristics during scale-up and optimization of the process in the future. The model requires diffusivities of TCVs into an activated-carbon fiber (ACF) as an input. Effective diffusivities of TCVs into ACFs were modeled as a function of temperature, concentration, and pore size distribution. Effective diffusivities for acetone at 65 ??C and 30-60 ppmv were measured using a chromatography method. The energy factor for surface diffusion was determined from comparison between the experimental and modeled effective diffusivities. The modeled effective diffusivities were used in a dispersive computational model to predict mass transfer zones of TCVs in fixed beds of ACFC under realistic conditions for industrial applications.

On the Effects of Pickup Ion-driven Waves on the Diffusion Tensor of Low-energy Electrons in the Heliosphere

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

Engelbrecht, N. Eugene, E-mail: n.eugene.engelbrecht@gmail.com

The effects of Alfvén cyclotron waves generated due to the formation in the outer heliosphere of pickup ions on the transport coefficients of low-energy electrons is investigated here. To this end, parallel mean free path (MFP) expressions are derived from quasilinear theory, employing the damping model of dynamical turbulence. These are then used as inputs for existing expressions for the perpendicular MFP and turbulence-reduced drift coefficient. Using outputs generated by a two-component turbulence transport model, the resulting diffusion coefficients are compared with those derived using a more typically assumed turbulence spectral form, which neglects the effects of pickup ion-generated waves.more » It is found that the inclusion of pickup ion effects greatly leads to considerable reductions in the parallel and perpendicular MFPs of 1–10 MeV electrons beyond ∼10 au, which are argued to have significant consequences for studies of the transport of these particles.« less

Utilizing Diffusion Theory to predict carbon dioxide concentration in an indoor environment

NASA Astrophysics Data System (ADS)

Kramer, Andrew R.

This research details a new method of relating sources of carbon dioxide to carbon dioxide concentration in a room operating in a reduced ventilation mode by utilizing Diffusion Theory. The theoretical basis of this research involved solving Fick's Second Law of Diffusion in spherical coordinates for a source of carbon dioxide flowing at a constant rate and located in the center of an impermeable spherical boundary. The solution was developed using a Laplace Transformation. A spherical diffusion test chamber was constructed and used to validate and benchmark the developed theory. The method was benchmarked by using Dispersion Coefficients for large carbon dioxide flow rates due to diffusion induced convection. The theoretical model was adapted to model a room operating with restricted ventilation in the presence of a known, constant source of carbon dioxide. The room was modeled as a sphere of volume equal to the room and utilized a Dispersion Coefficient that is consistent with published values. The developed Diffusion Model successfully predicted the spatial concentration of carbon dioxide in a room operating in a reduced ventilation mode in the presence of a source of carbon dioxide. The flow rates of carbon dioxide that were used in the room are comparable to the average flow rate of carbon dioxide from a person during quiet breathing, also known as the Tidal Breathing. This indicates the Diffusion Model developed from this research has the potential to correlate carbon dioxide concentration with static occupancy levels which can lead to energy savings through a reduction in air exchange rates when low occupancy is detected.

Relationships between self-diffusivity, packing fraction, and excess entropy in simple bulk and confined fluids.

PubMed

Mittal, Jeetain; Errington, Jeffrey R; Truskett, Thomas M

2007-08-30

Static measures such as density and entropy, which are intimately connected to structure, have featured prominently in modern thinking about the dynamics of the liquid state. Here, we explore the connections between self-diffusivity, density, and excess entropy for two of the most widely used model "simple" liquids, the equilibrium Lennard-Jones and square-well fluids, in both bulk and confined environments. We find that the self-diffusivity data of the Lennard-Jones fluid can be approximately collapsed onto a single curve (i) versus effective packing fraction and (ii) in appropriately reduced form versus excess entropy, as suggested by two well-known scaling laws. Similar data collapse does not occur for the square-well fluid, a fact that can be understood on the basis of the nontrivial effects that temperature has on its static structure. Nonetheless, we show that the implications of confinement for the self-diffusivity of both of these model fluids, over a broad range of equilibrium conditions, can be predicted on the basis of knowledge of the bulk fluid behavior and either the effective packing fraction or the excess entropy of the confined fluid. Excess entropy is perhaps the most preferable route due to its superior predictive ability and because it is a standard, unambiguous thermodynamic quantity that can be readily predicted via classical density functional theories of inhomogeneous fluids.

ANALYTIC FORMS OF THE PERPENDICULAR DIFFUSION COEFFICIENT IN NRMHD TURBULENCE

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

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

2015-02-01

In the past different analytic limits for the perpendicular diffusion coefficient of energetic particles interacting with magnetic turbulence were discussed. These different limits or cases correspond to different transport modes describing how the particles are diffusing across the large-scale magnetic field. In the current paper we describe a new transport regime by considering the model of noisy reduced magnetohydrodynamic turbulence. We derive different analytic forms of the perpendicular diffusion coefficient, and while we do this, we focus on the aforementioned new transport mode. We show that for this turbulence model a small perpendicular diffusion coefficient can be obtained so thatmore » the latter diffusion coefficient is more than hundred times smaller than the parallel diffusion coefficient. This result is relevant to explain observations in the solar system where such small perpendicular diffusion coefficients have been reported.« less

Effects of H{sub 2} and H preferential diffusion and unity Lewis number on superadiabatic flame temperatures in rich premixed methane flames

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

Liu, Fengshan; Guelder, OEmer L.

2005-11-01

The structures of freely propagating rich CH{sub 4}/air and CH{sub 4}/O{sub 2} flames were studied numerically using a relatively detailed reaction mechanism. Species diffusion was modeled using five different methods/assumptions to investigate the effects of species diffusion, in particular H{sub 2} and H, on superadiabatic flame temperature. With the preferential diffusion of H{sub 2} and H accounted for, significant amount of H{sub 2} and H produced in the flame front diffuse from the reaction zone to the preheat zone. The preferential diffusion of H{sub 2} from the reaction zone to the preheat zone has negligible effects on the phenomenon ofmore » superadiabatic flame temperature in both CH{sub 4}/air and CH{sub 4}/O{sub 2} flames. It is therefore demonstrated that the superadiabatic flame temperature phenomenon in rich hydrocarbon flames is not due to the preferential diffusion of H{sub 2} from the reaction zone to the preheat zone as recently suggested by Zamashchikov et al. [V.V. Zamashchikov, I.G. Namyatov, V.A. Bunev, V.S. Babkin, Combust. Explosion Shock Waves 40 (2004) 32]. The suppression of the preferential diffusion of H radicals from the reaction zone to the preheat zone drastically reduces the degree of superadiabaticity in rich CH{sub 4}/O{sub 2} flames. The preferential diffusion of H radicals plays an important role in the occurrence of superadiabatic flame temperature. The assumption of unity Lewis number for all species leads to the suppression of H radical diffusion from the reaction zone to the preheat zone and significant diffusion of CO{sub 2} from the postflame zone to the reaction zone. Consequently, the degree of superadiabaticity of flame temperature is also significantly reduced. Through reaction flux analyses and numerical experiments, the chemical nature of the superadiabatic flame temperature phenomenon in rich CH{sub 4}/air and CH{sub 4}/O{sub 2} flames was identified to be the relative scarcity of H radical, which leads to overshoot of H{sub 2}O and CH{sub 2}CO in CH{sub 4}/air flames and overshoot of H{sub 2}O in CH{sub 4}/O{sub 2} flames.« less

Solvent and solute ingress into hydrogels resolved by a combination of imaging techniques

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

Wagner, D.; Burbach, J.; Egelhaaf, S. U.

2016-05-28

Using simultaneous neutron, fluorescence, and optical brightfield transmission imaging, the diffusion of solvent, fluorescent dyes, and macromolecules into a crosslinked polyacrylamide hydrogel was investigated. This novel combination of different imaging techniques enables us to distinguish the movements of the solvent and fluorescent molecules. Additionally, the swelling or deswelling of the hydrogels can be monitored. From the sequence of images, dye and solvent concentrations were extracted spatially and temporally resolved. Diffusion equations and different boundary conditions, represented by different models, were used to quantitatively analyze the temporal evolution of these concentration profiles and to determine the diffusion coefficients of solvent andmore » solutes. Solute size and network properties were varied and their effect was investigated. Increasing the crosslinking ratio or partially drying the hydrogel was found to hinder solute diffusion due to the reduced pore size. By contrast, solvent diffusion seemed to be slightly faster if the hydrogel was only partially swollen and hence solvent uptake enhanced.« less

Ammonia Diffusion through Nalophan Double Bags: Effect of Concentration Gradient Reduction

PubMed Central

Capelli, Laura; Boiardi, Emanuela; Del Rosso, Renato

2014-01-01

The ammonia loss through Nalophan bags has been studied. The losses observed for storage conditions and times as allowed by the reference standard for dynamic olfactometry (EN 13725:2003) indicate that odour concentration values due to the presence of small molecules may be significantly underestimated if samples are not analysed immediately after sampling. A diffusion model was used in order to study diffusion through the bag. The study discusses the effect of concentration gradient (ΔC) across the polymeric membrane of the analyte. The ΔC was controlled by using a setup bag called “double bags.” Experimental data show a reduction of ammonia percentage losses due to the effect of the external multibarrier. The expedient of the double bag loaded with the same gas mixture allows a reduced diffusion of ammonia into the inner bag. Comparing the inner bag losses with those of the single bag stored in the same conditions (T, P, u) and with equal geometrical characteristics (S/V, z), it was observed that the inner bag of the double bag displays a 16% loss while the single bag displays a 37% loss. Acting on the ΔC it is possible to achieve a gross reduction of 57% in the ammonia leakage due to diffusion. PMID:25506608

Modified chloride diffusion model for concrete under the coupling effect of mechanical load and chloride salt environment

NASA Astrophysics Data System (ADS)

Lei, Mingfeng; Lin, Dayong; Liu, Jianwen; Shi, Chenghua; Ma, Jianjun; Yang, Weichao; Yu, Xiaoniu

2018-03-01

For the purpose of investigating lining concrete durability, this study derives a modified chloride diffusion model for concrete based on the odd continuation of boundary conditions and Fourier transform. In order to achieve this, the linear stress distribution on a sectional structure is considered, detailed procedures and methods are presented for model verification and parametric analysis. Simulation results show that the chloride diffusion model can reflect the effects of linear stress distribution of the sectional structure on the chloride diffusivity with reliable accuracy. Along with the natural environmental characteristics of practical engineering structures, reference value ranges of model parameters are provided. Furthermore, a chloride diffusion model is extended for the consideration of multi-factor coupling of linear stress distribution, chloride concentration and diffusion time. Comparison between model simulation and typical current research results shows that the presented model can produce better considerations with a greater universality.

Reaction-diffusion basis of retroviral infectivity

NASA Astrophysics Data System (ADS)

Sadiq, S. Kashif

2016-11-01

Retrovirus particle (virion) infectivity requires diffusion and clustering of multiple transmembrane envelope proteins (Env3) on the virion exterior, yet is triggered by protease-dependent degradation of a partially occluding, membrane-bound Gag polyprotein lattice on the virion interior. The physical mechanism underlying such coupling is unclear and only indirectly accessible via experiment. Modelling stands to provide insight but the required spatio-temporal range far exceeds current accessibility by all-atom or even coarse-grained molecular dynamics simulations. Nor do such approaches account for chemical reactions, while conversely, reaction kinetics approaches handle neither diffusion nor clustering. Here, a recently developed multiscale approach is considered that applies an ultra-coarse-graining scheme to treat entire proteins at near-single particle resolution, but which also couples chemical reactions with diffusion and interactions. A model is developed of Env3 molecules embedded in a truncated Gag lattice composed of membrane-bound matrix proteins linked to capsid subunits, with freely diffusing protease molecules. Simulations suggest that in the presence of Gag but in the absence of lateral lattice-forming interactions, Env3 diffuses comparably to Gag-absent Env3. Initial immobility of Env3 is conferred through lateral caging by matrix trimers vertically coupled to the underlying hexameric capsid layer. Gag cleavage by protease vertically decouples the matrix and capsid layers, induces both matrix and Env3 diffusion, and permits Env3 clustering. Spreading across the entire membrane surface reduces crowding, in turn, enhancing the effect and promoting infectivity. This article is part of the themed issue 'Multiscale modelling at the physics-chemistry-biology interface'.

Modeling of sediment transport in a saltwater lake with supplemental sandy freshwater.

PubMed

Liang, Li; Deng, Yun; Li, Ran; Li, Jia

2018-06-22

Considering the highly complex flow structure of saltwater lakes during freshwater supplementation, a three-dimensional numerical model was developed to simulate suspended sediment transport in saltwater lakes. The model was validated using measurements of the salinity and sediment concentration during a pumping test at Yamdrok Lake. The simulation results were in quantitative agreement with the measured data. The observed and simulated results also indicated that the wind stress and vertical salinity gradient have a significant influence on salinity and sediment transport in a saltwater lake. The validated model was then used to predict and analyze the contributions of wind, the supplement flow rate and salinity stratification to the sediment transport process in Yamdrok Lake during continuous river water supplementation. The simulation results showed that after the sandy river water was continuously discharged into the saltwater lake, the lateral diffusion trends of the sediment exhibited three stages: linear growth in the inflow direction, logarithmic growth in the wind direction, and stabilization. Furthermore, wind was the dominant factor in driving the lake flow pattern and sediment transport. Specifically, wind can effectively reduce the area of the sediment diffusion zone by increasing the lateral sediment carrying and dilution capacities. The effect of inflow on the lake current is negligible, but the extent of the sediment turbidity zone mainly depends on the inflow. Reducing the inflow discharge can decrease the area of the sediment turbidity zone to proportions that far exceed the proportions of inflow discharge reductions. In addition, the high-salinity lake water can support the supplemented freshwater via buoyancy forces, which weaken vertical mixing and sediment settlement and increase lake currents and sediment diffusion near the surface.

Effects of curved midline and varying width on the description of the effective diffusivity of Brownian particles

NASA Astrophysics Data System (ADS)

Chávez, Yoshua; Chacón-Acosta, Guillermo; Dagdug, Leonardo

2018-05-01

Axial diffusion in channels and tubes of smoothly-varying geometry can be approximately described as one-dimensional diffusion in the entropy potential with a position-dependent effective diffusion coefficient, by means of the modified Fick–Jacobs equation. In this work, we derive analytical expressions for the position-dependent effective diffusivity for two-dimensional asymmetric varying-width channels, and for three-dimensional curved midline tubes, formed by straight walls. To this end, we use a recently developed theoretical framework using the Frenet–Serret moving frame as the coordinate system (2016 J. Chem. Phys. 145 074105). For narrow tubes and channels, an effective one-dimensional description reducing the diffusion equation to a Fick–Jacobs-like equation in general coordinates is used. From this last equation, one can calculate the effective diffusion coefficient applying Neumann boundary conditions.

Numerical investigation of biogas diffusion flames characteristics under several operation conditions in counter-flow configuration with an emphasis on thermal and chemical effects of CO2 in the fuel mixture

NASA Astrophysics Data System (ADS)

Mameri, A.; Tabet, F.; Hadef, A.

2017-08-01

This study addresses the influence of several operating conditions (composition and ambient pressure) on biogas diffusion flame structure and NO emissions with particular attention on thermal and chemical effect of CO2. The biogas flame is modeled by a counter flow diffusion flame and analyzed in mixture fraction space using flamelet approach. The GRI Mech-3.0 mechanism that involves 53 species and 325 reactions is adopted for the oxidation chemistry. It has been observed that flame properties are very sensitive to biogas composition and pressure. CO2 addition decreases flame temperature by both thermal and chemical effects. Added CO2 may participate in chemical reaction due to thermal dissociation (chemical effect). Excessively supplied CO2 plays the role of pure diluent (thermal effect). The ambient pressure rise increases temperature and reduces flame thickness, radiation losses and dissociation amount. At high pressure, recombination reactions coupled with chain carrier radicals reduction, diminishes NO mass fraction.

Temperature Variations in Lubricating Films Induced by Viscous Dissipation

NASA Astrophysics Data System (ADS)

Mozaffari, Farshad; Metcalfe, Ralph

2015-11-01

We have studied temperature distributions of lubricating films. The study has applications in tribology where temperature-reduced viscosity decreases load carrying capacity of bearings, or degrades elastomeric seals. The viscosity- temperature dependency is modeled according to ASTM D341-09. We have modeled the film temperature distribution by our finite element program. The program is made up of three modules: the first one solves the general form of Reynolds equation for the film pressure and velocity gradients. The other two solve the energy equation for the film and its solid boundary temperature distributions. The modules are numerically coupled and iteratively converged to the solutions. We have shown that the temperature distribution in the film is strongly coupled with the thermal response at the boundary. In addition, only thermal diffusion across film thickness is dominant. Moreover, thermal diffusion in the lateral directions, as well as all the convection terms, are negligible. The approximation reduces the energy equation to an ordinary differential equation, which significantly simplifies the modeling of temperature -viscosity effects in thin films. Supported by Kalsi Engineering, Inc.

Simulations on the influence of myelin water in diffusion-weighted imaging

NASA Astrophysics Data System (ADS)

Harkins, K. D.; Does, M. D.

2016-07-01

While myelinated axons present an important barrier to water diffusion, many models used to interpret DWI signal neglect other potential influences of myelin. In this work, Monte Carlo simulations were used to test the sensitivity of DWI results to the diffusive properties of water within myelin. Within these simulations, the apparent diffusion coefficient (D app) varied slowly over several orders of magnitude of the coefficient of myelin water diffusion (D m), but exhibited important differences compared to D app values simulated that neglect D m (=0). Compared to D app, the apparent diffusion kurtosis (K app) was generally more sensitive to D m. Simulations also tested the sensitivity of D app and K app to the amount of myelin present. Unique variations in D app and K app caused by differences in the myelin volume fraction were diminished when myelin water diffusion was included. Also, expected trends in D app and K app with experimental echo time were reduced or inverted when accounting for myelin water diffusion, and these reduced/inverted trends were seen experimentally in ex vivo rat brain DWI experiments. In general, myelin water has the potential to subtly influence DWI results and bias models of DWI that neglect these components of white matter.

Simulations on the influence of myelin water in diffusion-weighted imaging.

PubMed

Harkins, K D; Does, M D

2016-07-07

While myelinated axons present an important barrier to water diffusion, many models used to interpret DWI signal neglect other potential influences of myelin. In this work, Monte Carlo simulations were used to test the sensitivity of DWI results to the diffusive properties of water within myelin. Within these simulations, the apparent diffusion coefficient (D app) varied slowly over several orders of magnitude of the coefficient of myelin water diffusion (D m), but exhibited important differences compared to D app values simulated that neglect D m (=0). Compared to D app, the apparent diffusion kurtosis (K app) was generally more sensitive to D m. Simulations also tested the sensitivity of D app and K app to the amount of myelin present. Unique variations in D app and K app caused by differences in the myelin volume fraction were diminished when myelin water diffusion was included. Also, expected trends in D app and K app with experimental echo time were reduced or inverted when accounting for myelin water diffusion, and these reduced/inverted trends were seen experimentally in ex vivo rat brain DWI experiments. In general, myelin water has the potential to subtly influence DWI results and bias models of DWI that neglect these components of white matter.

A counterflow diffusion flame study of branched octane isomers

DOE PAGES

Sarathy, S. Mani; Niemann, Ulrich; Yeung, Coleman; ...

2012-09-25

Conventional petroleum, Fischer–Tropsch (FT), and other alternative hydrocarbon fuels typically contain a high concentration of lightly methylated iso-alkanes. However, until recently little work has been done on this important class of hydrocarbon components. In order to better understand the combustion characteristics of real fuels, this study presents new experimental data for 3-methylheptane and 2,5-dimethylhexane in counterflow diffusion flames. This new dataset includes flame ignition, extinction, and speciation profiles. The high temperature oxidation of these fuels has been modeled using an extended transport database and a high temperature skeletal chemical kinetic model. The skeletal model is generated from a detailed modelmore » reduced using the directed relation graph with expert knowledge (DRG-X) methodology. The proposed skeletal model contains sufficient chemical fidelity to accurately predict the experimental speciation data in flames. The predictions are compared to elucidate the effects of number and location of the methyl substitutions. The location is found to have little effect on ignition and extinction in these counterflow diffusion flames. However, increasing the number of methyl substitutions was found to inhibit ignition and promote extinction. Chemical kinetic modelling simulations were used to correlate a fuel’s extinction propensity with its ability to populate the H radical concentration. In conclusion, species composition measurements indicate that the location and number of methyl substitutions was found to particularly affect the amount and type of alkenes observed.« less

Fokker-Planck analysis of transverse collective instabilities in electron storage rings

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

Lindberg, Ryan R.

We analyze single bunch transverse instabilities due to wakefields using a Fokker-Planck model. We first expand on the work of T. Suzuki, Part. Accel. 12, 237 (1982) to derive the theoretical model including chromaticity, both dipolar and quadrupolar transverse wakefields, and the effects of damping and diffusion due to the synchrotron radiation. We reduce the problem to a linear matrix equation, whose eigenvalues and eigenvectors determine the collective stability of the beam. We then show that various predictions of the theory agree quite well with results from particle tracking simulations, including the threshold current for transverse instability and the profilemore » of the unstable mode. In particular, we find that predicting collective stability for high energy electron beams at moderate to large values of chromaticity requires the full Fokker-Planck analysis to properly account for the effects of damping and diffusion due to synchrotron radiation.« less

Mathematical modeling of vesicle drug delivery systems 2: targeted vesicle interactions with cells, tumors, and the body.

PubMed

Ying, Chong T; Wang, Juntian; Lamm, Robert J; Kamei, Daniel T

2013-02-01

Vesicles have been studied for several years in their ability to deliver drugs. Mathematical models have much potential in reducing time and resources required to engineer optimal vesicles, and this review article summarizes these models that aid in understanding the ability of targeted vesicles to bind and internalize into cancer cells, diffuse into tumors, and distribute in the body. With regard to binding and internalization, radiolabeling and surface plasmon resonance experiments can be performed to determine optimal vesicle size and the number and type of ligands conjugated. Binding and internalization properties are also inputs into a mathematical model of vesicle diffusion into tumor spheroids, which highlights the importance of the vesicle diffusion coefficient and the binding affinity of the targeting ligand. Biodistribution of vesicles in the body, along with their half-life, can be predicted with compartmental models for pharmacokinetics that include the effect of targeting ligands, and these predictions can be used in conjunction with in vivo models to aid in the design of drug carriers. Mathematical models can prove to be very useful in drug carrier design, and our hope is that this review will encourage more investigators to combine modeling with quantitative experimentation in the field of vesicle-based drug delivery.

A Theory for Stability and Buzz Pulsation Amplitude in Ram Jets and an Experimental Investigation Including Scale Effects

NASA Technical Reports Server (NTRS)

Trimpi, Robert L

1956-01-01

From a theory developed on a quasi-one-dimensional-flow basis, it is found that the stability of the ram jet is dependent upon the instantaneous values of mass flow and total pressure recovery of the supersonic diffuser and immediate neighboring subsonic diffuser. Conditions for stable and unstable flow are presented. The theory developed in the report is in agreement with the experimental data of NACA-TN-3506 and NACA-RM-L50K30. A simple theory for predicting the approximate amplitude of small pressure pulsation in terms of mass-flow decrement from minimum-stable mass flow is developed and found to agree with experiments. Cold-flow tests at a Mach number of 1.94 of ram-jet models having scale factors of 3.15:1 and Reynolds number ratios of 4.75:1 with several supersonic diffuser configurations showed only small variations in performance between geometrically similar models. The predominant variation in steady-flow performance resulted from the larger boundary layer in the combustion chamber of the low Reynolds number models. The conditions at which buzz originated were nearly the same for the same supersonic diffuser (cowling-position angle) configurations in both large and small diameter models. There was no appreciable variation in stability limits of any of the models when the combustion-chamber length was increased by a factor of three. The unsteady-flow performance and wave patterns were also similar when considered on a reduced-frequency basis determined from the relative lengths of the model. The negligible effect of Reynolds number on stability of the off-design configurations was not anticipated in view of the importance of boundary layer to stability, and this result should not be construed to be generally applicable. (author)

Zero-gravity aerosol behavior

NASA Technical Reports Server (NTRS)

Edwards, H. W.

1981-01-01

The feasibility and scientific benefits of a zero gravity aerosol study in an orbiting laboratory were examined. A macroscopic model was devised to deal with the simultaneous effects of diffusion and coagulation of particles in the confined aerosol. An analytical solution was found by treating the particle coagulation and diffusion constants as ensemble parameters and employing a transformation of variables. The solution was used to carry out simulated zero gravity aerosol decay experiments in a compact cylindrical chamber. The results demonstrate that the limitations of physical space and time imposed by the orbital situation are not prohibitive in terms of observing the history of an aerosol confined under zero gravity conditions. While the absence of convective effects would be a definite benefit for the experiment, the mathematical complexity of the problem is not greatly reduced when the gravitational term drops out of the equation. Since the model does not deal directly with the evolution of the particle size distribution, it may be desirable to develop more detailed models before undertaking an orbital experiment.

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

NASA Technical Reports Server (NTRS)

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

1992-01-01

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

Beyond self-serving bias: diffusion of responsibility reduces sense of agency and outcome monitoring

PubMed Central

Sidarus, Nura; Bonicalzi, Sofia; Haggard, Patrick

2017-01-01

Abstract Diffusion of responsibility across agents has been proposed to underlie decreased helping and increased aggression in group behaviour. However, few studies have directly investigated effects of the presence of other people on how we experience the consequences of our actions. This EEG study investigated whether diffusion of responsibility simply reflects a post-hoc self-serving bias, or rather has direct effects on how we process the outcomes of our actions, and our experience of agency over them. Participants made voluntary actions whose outcomes were more or less negative. Presence of another potential agent reduced participants’ sense of agency over those outcomes, even though it was always obvious who caused each outcome. Further, presence of another agent reduced the amplitude of feedback-related negativity evoked by outcome stimuli, suggesting reduced outcome monitoring. The presence of other agents may lead to diffusion of responsibility by weakening the neural linkage between one’s actions and their outcomes. PMID:27803288

Beyond self-serving bias: diffusion of responsibility reduces sense of agency and outcome monitoring.

PubMed

Beyer, Frederike; Sidarus, Nura; Bonicalzi, Sofia; Haggard, Patrick

2017-01-01

Diffusion of responsibility across agents has been proposed to underlie decreased helping and increased aggression in group behaviour. However, few studies have directly investigated effects of the presence of other people on how we experience the consequences of our actions. This EEG study investigated whether diffusion of responsibility simply reflects a post-hoc self-serving bias, or rather has direct effects on how we process the outcomes of our actions, and our experience of agency over them. Participants made voluntary actions whose outcomes were more or less negative. Presence of another potential agent reduced participants' sense of agency over those outcomes, even though it was always obvious who caused each outcome. Further, presence of another agent reduced the amplitude of feedback-related negativity evoked by outcome stimuli, suggesting reduced outcome monitoring. The presence of other agents may lead to diffusion of responsibility by weakening the neural linkage between one's actions and their outcomes. © The Author (2016). Published by Oxford University Press.

FADTTS: functional analysis of diffusion tensor tract statistics.

PubMed

Zhu, Hongtu; Kong, Linglong; Li, Runze; Styner, Martin; Gerig, Guido; Lin, Weili; Gilmore, John H

2011-06-01

The aim of this paper is to present a functional analysis of a diffusion tensor tract statistics (FADTTS) pipeline for delineating the association between multiple diffusion properties along major white matter fiber bundles with a set of covariates of interest, such as age, diagnostic status and gender, and the structure of the variability of these white matter tract properties in various diffusion tensor imaging studies. The FADTTS integrates five statistical tools: (i) a multivariate varying coefficient model for allowing the varying coefficient functions in terms of arc length to characterize the varying associations between fiber bundle diffusion properties and a set of covariates, (ii) a weighted least squares estimation of the varying coefficient functions, (iii) a functional principal component analysis to delineate the structure of the variability in fiber bundle diffusion properties, (iv) a global test statistic to test hypotheses of interest, and (v) a simultaneous confidence band to quantify the uncertainty in the estimated coefficient functions. Simulated data are used to evaluate the finite sample performance of FADTTS. We apply FADTTS to investigate the development of white matter diffusivities along the splenium of the corpus callosum tract and the right internal capsule tract in a clinical study of neurodevelopment. FADTTS can be used to facilitate the understanding of normal brain development, the neural bases of neuropsychiatric disorders, and the joint effects of environmental and genetic factors on white matter fiber bundles. The advantages of FADTTS compared with the other existing approaches are that they are capable of modeling the structured inter-subject variability, testing the joint effects, and constructing their simultaneous confidence bands. However, FADTTS is not crucial for estimation and reduces to the functional analysis method for the single measure. Copyright © 2011 Elsevier Inc. All rights reserved.

Characterization, scaling, and partial representation of diffuse and discrete input junctions to CA3 hippocampus.

PubMed

Ascarrunz, F G; Kisley, M A; Flach, K A; Hamilton, R W; MacGregor, R J

1995-07-01

This paper applies a general mathematical system for characterizing and scaling functional connectivity and information flow across the diffuse (EC) and discrete (DG) input junctions to the CA3 hippocampus. Both gross connectivity and coordinated multiunit informational firing patterns are quantitatively characterized in terms of 32 defining parameters interrelated by 17 equations, and then scaled down according to rules for uniformly proportional scaling and for partial representation. The diffuse EC-CA3 junction is shown to be uniformly scalable with realistic representation of both essential spatiotemporal cooperativity and coordinated firing patterns down to populations of a few hundred neurons. Scaling of the discrete DG-CA3 junction can be effected with a two-step process, which necessarily deviates from uniform proportionality but nonetheless produces a valuable and readily interpretable reduced model, also utilizing a few hundred neurons in the receiving population. Partial representation produces a reduced model of only a portion of the full network where each model neuron corresponds directly to a biological neuron. The mathematical analysis illustrated here shows that although omissions and distortions are inescapable in such an application, satisfactorily complete and accurate models the size of pattern modules are possible. Finally, the mathematical characterization of these junctions generates a theory which sees the DG as a definer of the fine structure of embedded traces in the hippocampus and entire coordinated patterns of sequences of 14-cell links in CA3 as triggered by the firing of sequences of individual neurons in DG.

Effects of Buoyancy on Laminar, Transitional, and Turbulent Gas Jet Diffusion Flames

NASA Technical Reports Server (NTRS)

Bahadori, M. Yousef; Stocker, Dennis P.; Vaughan, David F.; Zhou, Liming; Edelman, Raymond B.

1993-01-01

Gas jet diffusion flames have been a subject of research for many years. However, a better understanding of the physical and chemical phenomena occurring in these flames is still needed, and, while the effects of gravity on the burning process have been observed, the basic mechanisms responsible for these changes have yet to be determined. The fundamental mechanisms that control the combustion process are in general coupled and quite complicated. These include mixing, radiation, kinetics, soot formation and disposition, inertia, diffusion, and viscous effects. In order to understand the mechanisms controlling a fire, laboratory-scale laminar and turbulent gas-jet diffusion flames have been extensively studied, which have provided important information in relation to the physico-chemical processes occurring in flames. However, turbulent flames are not fully understood and their understanding requires more fundamental studies of laminar diffusion flames in which the interplay of transport phenomena and chemical kinetics is more tractable. But even this basic, relatively simple flame is not completely characterized in relation to soot formation, radiation, diffusion, and kinetics. Therefore, gaining an understanding of laminar flames is essential to the understanding of turbulent flames, and particularly fires, in which the same basic phenomena occur. In order to improve and verify the theoretical models essential to the interpretation of data, the complexity and degree of coupling of the controlling mechanisms must be reduced. If gravity is isolated, the complication of buoyancy-induced convection would be removed from the problem. In addition, buoyant convection in normal gravity masks the effects of other controlling parameters on the flame. Therefore, the combination of normal-gravity and microgravity data would provide the information, both theoretical and experimental, to improve our understanding of diffusion flames in general, and the effects of gravity on the burning process in particular.

Diffusing diffusivity: Rotational diffusion in two and three dimensions

NASA Astrophysics Data System (ADS)

Jain, Rohit; Sebastian, K. L.

2017-06-01

We consider the problem of calculating the probability distribution function (pdf) of angular displacement for rotational diffusion in a crowded, rearranging medium. We use the diffusing diffusivity model and following our previous work on translational diffusion [R. Jain and K. L. Sebastian, J. Phys. Chem. B 120, 3988 (2016)], we show that the problem can be reduced to that of calculating the survival probability of a particle undergoing Brownian motion, in the presence of a sink. We use the approach to calculate the pdf for the rotational motion in two and three dimensions. We also propose new dimensionless, time dependent parameters, αr o t ,2 D and αr o t ,3 D, which can be used to analyze the experimental/simulation data to find the extent of deviation from the normal behavior, i.e., constant diffusivity, and obtain explicit analytical expressions for them, within our model.

Inhomogeneous Oxygen Vacancy Distribution in Semiconductor Gas Sensors: Formation, Migration and Determination on Gas Sensing Characteristics

PubMed Central

Liu, Jianqiao; Gao, Yinglin; Wu, Xu; Jin, Guohua; Zhai, Zhaoxia; Liu, Huan

2017-01-01

The density of oxygen vacancies in semiconductor gas sensors was often assumed to be identical throughout the grain in the numerical discussion of the gas-sensing mechanism of the devices. In contrast, the actual devices had grains with inhomogeneous distribution of oxygen vacancy under non-ideal conditions. This conflict between reality and discussion drove us to study the formation and migration of the oxygen defects in semiconductor grains. A model of the gradient-distributed oxygen vacancy was proposed based on the effects of cooling rate and re-annealing on semiconductive thin films. The model established the diffusion equations of oxygen vacancy according to the defect kinetics of diffusion and exclusion. We described that the steady-state and transient-state oxygen vacancy distributions, which were used to calculate the gas-sensing characteristics of the sensor resistance and response to reducing gases under two different conditions. The gradient-distributed oxygen vacancy model had the applications in simulating the sensor performances, such as the power law, the grain size effect and the effect of depletion layer width. PMID:28796167

Inhomogeneous Oxygen Vacancy Distribution in Semiconductor Gas Sensors: Formation, Migration and Determination on Gas Sensing Characteristics.

PubMed

Liu, Jianqiao; Gao, Yinglin; Wu, Xu; Jin, Guohua; Zhai, Zhaoxia; Liu, Huan

2017-08-10

The density of oxygen vacancies in semiconductor gas sensors was often assumed to be identical throughout the grain in the numerical discussion of the gas-sensing mechanism of the devices. In contrast, the actual devices had grains with inhomogeneous distribution of oxygen vacancy under non-ideal conditions. This conflict between reality and discussion drove us to study the formation and migration of the oxygen defects in semiconductor grains. A model of the gradient-distributed oxygen vacancy was proposed based on the effects of cooling rate and re-annealing on semiconductive thin films. The model established the diffusion equations of oxygen vacancy according to the defect kinetics of diffusion and exclusion. We described that the steady-state and transient-state oxygen vacancy distributions, which were used to calculate the gas-sensing characteristics of the sensor resistance and response to reducing gases under two different conditions. The gradient-distributed oxygen vacancy model had the applications in simulating the sensor performances, such as the power law, the grain size effect and the effect of depletion layer width.

Role of insulin receptor and insulin signaling on αPS2CβPS integrins' lateral diffusion.

PubMed

Mainali, Dipak; Syed, Aleem; Arora, Neha; Smith, Emily A

2014-12-01

Integrins are ubiquitous transmembrane receptors with adhesion and signaling properties. The influence of insulin receptor and insulin signaling on αPS2CβPS integrins' lateral diffusion was studied using single particle tracking in S2 cells before and after reducing the insulin receptor expression or insulin stimulation. Insulin signaling was monitored by Western blotting for phospho-Akt expression. The expression of the insulin receptor was reduced using RNA interference (RNAi). After insulin receptor RNAi, four significant changes were measured in integrin diffusion properties: (1) there was a 24% increase in the mobile integrin population, (2) 14% of the increase was represented by integrins with Brownian diffusion, (3) for integrins that reside in confined zones of diffusion, there was a 45% increase in the diameter of the confined zone, and (4) there was a 29% increase in the duration integrins spend in confined zones of diffusion. In contrast to reduced expression of the insulin receptor, which alters integrin diffusion properties, insulin stimulation alone or insulin stimulation under conditions of reduced insulin receptor expression have minimal effects on altering the measured integrin diffusion properties. The differences in integrin diffusion measured after insulin receptor RNAi in the presence or absence of insulin stimulation may be the result of other insulin signaling pathways that are activated at reduced insulin receptor conditions. No change in the average integrin diffusion coefficient was measured for any conditions included in this study.

Light-Cone and Diffusive Propagation of Correlations in a Many-Body Dissipative System.

PubMed

Bernier, Jean-Sébastien; Tan, Ryan; Bonnes, Lars; Guo, Chu; Poletti, Dario; Kollath, Corinna

2018-01-12

We analyze the propagation of correlations after a sudden interaction change in a strongly interacting quantum system in contact with an environment. In particular, we consider an interaction quench in the Bose-Hubbard model, deep within the Mott-insulating phase, under the effect of dephasing. We observe that dissipation effectively speeds up the propagation of single-particle correlations while reducing their coherence. In contrast, for two-point density correlations, the initial ballistic propagation regime gives way to diffusion at intermediate times. Numerical simulations, based on a time-dependent matrix product state algorithm, are supplemented by a quantitatively accurate fermionic quasiparticle approach providing an intuitive description of the initial dynamics in terms of holon and doublon excitations.

A non-linear dimension reduction methodology for generating data-driven stochastic input models

NASA Astrophysics Data System (ADS)

Ganapathysubramanian, Baskar; Zabaras, Nicholas

2008-06-01

Stochastic analysis of random heterogeneous media (polycrystalline materials, porous media, functionally graded materials) provides information of significance only if realistic input models of the topology and property variations are used. This paper proposes a framework to construct such input stochastic models for the topology and thermal diffusivity variations in heterogeneous media using a data-driven strategy. Given a set of microstructure realizations (input samples) generated from given statistical information about the medium topology, the framework constructs a reduced-order stochastic representation of the thermal diffusivity. This problem of constructing a low-dimensional stochastic representation of property variations is analogous to the problem of manifold learning and parametric fitting of hyper-surfaces encountered in image processing and psychology. Denote by M the set of microstructures that satisfy the given experimental statistics. A non-linear dimension reduction strategy is utilized to map M to a low-dimensional region, A. We first show that M is a compact manifold embedded in a high-dimensional input space Rn. An isometric mapping F from M to a low-dimensional, compact, connected set A⊂Rd(d≪n) is constructed. Given only a finite set of samples of the data, the methodology uses arguments from graph theory and differential geometry to construct the isometric transformation F:M→A. Asymptotic convergence of the representation of M by A is shown. This mapping F serves as an accurate, low-dimensional, data-driven representation of the property variations. The reduced-order model of the material topology and thermal diffusivity variations is subsequently used as an input in the solution of stochastic partial differential equations that describe the evolution of dependant variables. A sparse grid collocation strategy (Smolyak algorithm) is utilized to solve these stochastic equations efficiently. We showcase the methodology by constructing low-dimensional input stochastic models to represent thermal diffusivity in two-phase microstructures. This model is used in analyzing the effect of topological variations of two-phase microstructures on the evolution of temperature in heat conduction processes.

Diffusion of multiple species with excluded-volume effects.

PubMed

Bruna, Maria; Chapman, S Jonathan

2012-11-28

Stochastic models of diffusion with excluded-volume effects are used to model many biological and physical systems at a discrete level. The average properties of the population may be described by a continuum model based on partial differential equations. In this paper we consider multiple interacting subpopulations/species and study how the inter-species competition emerges at the population level. Each individual is described as a finite-size hard core interacting particle undergoing brownian motion. The link between the discrete stochastic equations of motion and the continuum model is considered systematically using the method of matched asymptotic expansions. The system for two species leads to a nonlinear cross-diffusion system for each subpopulation, which captures the enhancement of the effective diffusion rate due to excluded-volume interactions between particles of the same species, and the diminishment due to particles of the other species. This model can explain two alternative notions of the diffusion coefficient that are often confounded, namely collective diffusion and self-diffusion. Simulations of the discrete system show good agreement with the analytic results.

Testing stellar evolution models with detached eclipsing binaries

NASA Astrophysics Data System (ADS)

Higl, J.; Weiss, A.

2017-12-01

Stellar evolution codes, as all other numerical tools, need to be verified. One of the standard stellar objects that allow stringent tests of stellar evolution theory and models, are detached eclipsing binaries. We have used 19 such objects to test our stellar evolution code, in order to see whether standard methods and assumptions suffice to reproduce the observed global properties. In this paper we concentrate on three effects that contain a specific uncertainty: atomic diffusion as used for standard solar model calculations, overshooting from convective regions, and a simple model for the effect of stellar spots on stellar radius, which is one of the possible solutions for the radius problem of M dwarfs. We find that in general old systems need diffusion to allow for, or at least improve, an acceptable fit, and that systems with convective cores indeed need overshooting. Only one system (AI Phe) requires the absence of it for a successful fit. To match stellar radii for very low-mass stars, the spot model proved to be an effective approach, but depending on model details, requires a high percentage of the surface being covered by spots. We briefly discuss improvements needed to further reduce the freedom in modelling and to allow an even more restrictive test by using these objects.

One-dimensional energetic particle quasilinear diffusion for realistic TAE instabilities

NASA Astrophysics Data System (ADS)

Duarte, Vinicius; Ghantous, Katy; Berk, Herbert; Gorelenkov, Nikolai

2014-10-01

Owing to the proximity of the characteristic phase (Alfvén) velocity and typical energetic particle (EP) superthermal velocities, toroidicity-induced Alfvén eigenmodes (TAEs) can be resonantly destabilized endangering the plasma performance. Thus, it is of ultimate importance to understand the deleterious effects on the confinement resulting from fast ion driven instabilities expected in fusion-grade plasmas. We propose to study the interaction of EPs and TAEs using a line broadened quasilinear model, which captures the interaction in both regimes of isolated and overlapping modes. The resonance particles diffuse in the phase space where the problem essentially reduces to one dimension with constant kinetic energy and the diffusion mainly along the canonical toroidal angular momentum. Mode structure and wave particle resonances are computed by the NOVA code and are used in a quasilinear diffusion code that is being written to study the evolution of the distribution function, under the assumption that they can be considered virtually unalterable during the diffusion. A new scheme for the resonant particle diffusion is being proposed that builds on the 1-D nature of the diffusion from a single mode, which leads to a momentum conserving difference scheme even when there is mode overlap.

Modeling Thermal Pressurization Around Shallow Dikes Using Temperature-Dependent Hydraulic Properties: Implications for Deformation Around Intrusions

NASA Astrophysics Data System (ADS)

Townsend, Meredith R.

2018-01-01

Pressurization and flow of groundwater around igneous intrusions depend in part on the hydraulic diffusivity of the host rocks and processes that enhance diffusivity, such as fracturing, or decrease diffusivity, such as mineral precipitation during chemical alteration. Characterizing and quantifying the coupled effects of alteration, pore pressurization, and deformation have significant implications for deformation around intrusions, geothermal energy, contact metamorphism, and heat transfer at mid-ocean ridges. Fractures around dikes at Ship Rock, New Mexico, indicate that pore pressures in the host rocks exceeded hydrostatic conditions by at least 15 MPa following dike emplacement. Hydraulic measurements and petrographic analysis indicate that mineral precipitation clogged the pores of the host rock, reducing porosity from 0.25 to <0.10 and reducing permeability by 5 orders of magnitude. Field data from Ship Rock are used to motivate and constrain numerical models for thermal pore fluid pressurization adjacent to a meter-scale dike, using temperature-dependent hydraulic properties in the host rock as a proxy for porosity loss by mineral precipitation during chemical alteration. Reduction in permeability by chemical alteration has a negligible effect on pressurization. However, reduction in porosity by mineral precipitation increases fluid pressure by constricting pore volume and is identified as a potentially significant source of pressure. A scaling relationship is derived to determine when porosity loss becomes important; if permeability is low enough, pressurization by porosity loss outweighs pressurization by thermal expansion of fluids.

Atomistic Simulation of High-Density Uranium Fuels

DOE PAGES

Garcés, Jorge Eduardo; Bozzolo, Guillermo

2011-01-01

We apply an atomistic modeling approach to deal with interfacial phenomena in high-density uranium fuels. The effects of Si, as additive to Al or as U-Mo-particles coating, on the behavior of the Al/U-Mo interface is modeled by using the Bozzolo-Ferrante-Smith (BFS) method for alloys. The basic experimental features characterizing the real system are identified, via simulations and atom-by-atom analysis. These include (1) the trend indicating formation of interfacial compounds, (2) much reduced diffusion of Al into U-Mo solid solution due to the high Si concentration, (3) Si depletion in the Al matrix, (4) an unexpected interaction between Mo and Simore » which inhibits Si diffusion to deeper layers in the U-Mo solid solution, and (5) the minimum amount of Si needed to perform as an effective diffusion barrier. Simulation results related to alternatives to Si dispersed in the Al matrix, such as the use of C coating of U-Mo particles or Zr instead of the Al matrix, are also shown. Recent experimental results confirmed early theoretical proposals, along the lines of the results reported in this work, showing that atomistic computational modeling could become a valuable tool to aid the experimental work in the development of nuclear fuels.« less

Transient in-plane thermal transport in nanofilms with internal heating

PubMed Central

Cao, Bing-Yang

2016-01-01

Wide applications of nanofilms in electronics necessitate an in-depth understanding of nanoscale thermal transport, which significantly deviates from Fourier's law. Great efforts have focused on the effective thermal conductivity under temperature difference, while it is still ambiguous whether the diffusion equation with an effective thermal conductivity can accurately characterize the nanoscale thermal transport with internal heating. In this work, transient in-plane thermal transport in nanofilms with internal heating is studied via Monte Carlo (MC) simulations in comparison to the heat diffusion model and mechanism analyses using Fourier transform. Phonon-boundary scattering leads to larger temperature rise and slower thermal response rate when compared with the heat diffusion model based on Fourier's law. The MC simulations are also compared with the diffusion model with effective thermal conductivity. In the first case of continuous internal heating, the diffusion model with effective thermal conductivity under-predicts the temperature rise by the MC simulations at the initial heating stage, while the deviation between them gradually decreases and vanishes with time. By contrast, for the one-pulse internal heating case, the diffusion model with effective thermal conductivity under-predicts both the peak temperature rise and the cooling rate, so the deviation can always exist. PMID:27118903

Transient in-plane thermal transport in nanofilms with internal heating.

PubMed

Hua, Yu-Chao; Cao, Bing-Yang

2016-02-01

Wide applications of nanofilms in electronics necessitate an in-depth understanding of nanoscale thermal transport, which significantly deviates from Fourier's law. Great efforts have focused on the effective thermal conductivity under temperature difference, while it is still ambiguous whether the diffusion equation with an effective thermal conductivity can accurately characterize the nanoscale thermal transport with internal heating. In this work, transient in-plane thermal transport in nanofilms with internal heating is studied via Monte Carlo (MC) simulations in comparison to the heat diffusion model and mechanism analyses using Fourier transform. Phonon-boundary scattering leads to larger temperature rise and slower thermal response rate when compared with the heat diffusion model based on Fourier's law. The MC simulations are also compared with the diffusion model with effective thermal conductivity. In the first case of continuous internal heating, the diffusion model with effective thermal conductivity under-predicts the temperature rise by the MC simulations at the initial heating stage, while the deviation between them gradually decreases and vanishes with time. By contrast, for the one-pulse internal heating case, the diffusion model with effective thermal conductivity under-predicts both the peak temperature rise and the cooling rate, so the deviation can always exist.

Feature Modeling of HfO2 Atomic Layer Deposition Using HfCl4/H2O

NASA Astrophysics Data System (ADS)

Stout, Phillip J.; Adams, Vance; Ventzek, Peter L. G.

2003-03-01

A Monte Carlo based feature scale model (Papaya) has been applied to atomic layer deposition (ALD) of HfO2 using HfCl_4/H_20. The model includes physical effects of transport to surface, specular and diffusive reflection within feature, adsorption, surface diffusion, deposition and etching. Discussed will be the 3D feature modeling of HfO2 deposition in assorted features (vias and trenches). The effect of feature aspect ratios, pulse times, cycle number, and temperature on film thickness, feature coverage, and film Cl fraction (surface/bulk) will be discussed. Differences between HfO2 ALD on blanket wafers and in features will be highlighted. For instance, the minimum pulse times sufficient for surface reaction saturation on blanket wafers needs to be increased when depositing on features. Also, HCl products created during the HfCl4 and H_20 pulses are more likely to react within a feature than at the field, reducing OH coverage within the feature (vs blanket wafer) thus limiting the maximum coverage attainable for a pulse over a feature.

Effect of particle- and specimen-level transport on product state in compacted-powder combustion synthesis and thermal debinding of polymers from molded powders

NASA Astrophysics Data System (ADS)

Oliveira, Amir Antonio Martins

The existence of large gradients within particles and fast temporal variations in the temperature and species concentration prevents the use of asymptotic approximations for the closure of the volume-averaged, specimen-level formulations. In this case a solution of the particle-level transport problem is needed to complement the specimen-level volume-averaged equations. Here, the use of combined specimen-level and particle-level models for transport in reactive porous media is demonstrated with two examples. For the gasless compacted-powder combustion synthesis, a three-scale model is developed. The specimen-level model is based on the volume-averaged equations for species and temperature. Local thermal equilibrium is assumed and the macroscopic mass diffusion and convection fluxes are neglected. The particle-level model accounts for the interparticle diffusion (i.e., the liquid migration from liquid-rich to liquid-lean regions) and the intraparticle diffusion (i.e., the species mass diffusion within the product layer formed at the surface of the high melting temperature component). It is found that the interparticle diffusion controls the extent of conversion to the final product, the maximum temperature, and to a smaller degree the propagation velocity. The intraparticle diffusion controls the propagation velocity and to a smaller degree the maximum temperature. The initial stages of thermal degradation of EVA from molded specimens is modeled using volume-averaged equations for the species and empirical models for the kinetics of the thermal degradation, the vapor-liquid equilibrium, and the diffusion coefficient of acetic acid in the molten polymer. It is assumed that a bubble forms when the partial pressure of acetic acid exceeds the external ambient pressure. It is found that the removal of acetic acid is characterized by two regimes, a pre-charge dominated regime and a generation dominated regime. For the development of an optimum debinding schedule, the heating rate is modulated to avoid bubbling, while the concentration and temperature follow the bubble-point line for the mixture. The results show a strong dependence on the presence of a pre-charge. It is shown that isolation of the pre-charge effect by using temporary lower heating rates results in an optimum schedule for which the process time is reduced by over 70% when compared to a constant heating rate schedule.

Modeling of Diffuse-Diffuse Photon Coupling via a Nonscattering Region: a Comparative Study

NASA Astrophysics Data System (ADS)

Lee, Jae Hoon; Kim, Seunghwan; Kim, Youn Tae

2004-06-01

It is well established that diffusion approximation is valid for light propagation in highly scattering media, but it breaks down in nonscattering regions. The previous methods that manipulate nonscattering regions are essentially boundary-to-boundary coupling (BBC) methods through a nonscattering void region based on the radiosity theory. We present a boundary-to-interior coupling (BIC) method. BIC is based on the fact that the collimated pencil beam incident on the medium can be replaced by an isotropic point source positioned at one reduced scattering length inside the medium from an illuminated point. A similar replacement is possible for the nondiffuse lights that enter the diffuse medium through the void, and it is formulated as the BIC method. We implemented both coupling methods using the finite element method (FEM) and tested for the circle with a void gap and for a four-layer adult head model. For mean time of flight, the BIC shows better agreement with Monte Carlo (MC) simulation results than BBC. For intensity, BIC shows a comparable match with MC data compared with that of BBC. The effect of absorption of the clear layer in the adult head model was investigated. Both mean time and intensity decrease as absorption of the clear layer increases.

Modeling of diffuse-diffuse photon coupling via a nonscattering region: a comparative study.

PubMed

Lee, Jae Hoon; Kim, Seunghwan; Kim, Youn Tae

2004-06-20

It is well established that diffusion approximation is valid for light propagation in highly scattering media, but it breaks down in nonscattering regions. The previous methods that manipulate nonscattering regions are essentially boundary-to-boundary coupling (BBC) methods through a nonscattering void region based on the radiosity theory. We present a boundary-to-interior coupling (BIC) method. BIC is based on the fact that the collimated pencil beam incident on the medium can be replaced by an isotropic point source positioned at one reduced scattering length inside the medium from an illuminated point. A similar replacement is possible for the nondiffuse lights that enter the diffuse medium through the void, and it is formulated as the BIC method. We implemented both coupling methods using the finite element method (FEM) and tested for the circle with a void gap and for a four-layer adult head model. For mean time of flight, the BIC shows better agreement with Monte Carlo (MC) simulation results than BBC. For intensity, BIC shows a comparable match with MC data compared with that of BBC. The effect of absorption of the clear layer in the adult head model was investigated. Both mean time and intensity decrease as absorption of the clear layer increases.

Diapycnal Transport and Pattern Formation in Double-Diffusive Convection

DTIC Science & Technology

2015-12-01

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

General Model of Hindered Diffusion.

PubMed

Eloul, Shaltiel; Compton, Richard G

2016-11-03

The diffusion of a particle from bulk solution is slowed as it moves close to an adsorbing surface. A general model is reported that is easily applied by theoreticians and experimentalists. Specifically, it is shown here that in general and regardless of the space size, the magnitude of the effect of hindered diffusion on the flux is a property of the diffusion layer thickness. We explain and approximate the effect. Predictions of concentration profiles show that a "hindered diffusion layer" is formed near the adsorbing surface within the diffusion layer, observed even when the particle radius is just a 0.1% of the diffusion layer thickness. In particular, we focus on modern electrochemistry processes involving with impact of particles with either ultrasmall electrodes or particles in convective systems. The concept of the "hindered diffusion layer" is generally important for example in recent biophysical models of particles diffusion to small targets.

Increased Accuracy of Ligand Sensing by Receptor Internalization and Lateral Receptor Diffusion

NASA Astrophysics Data System (ADS)

Aquino, Gerardo; Endres, Robert

2010-03-01

Many types of cells can sense external ligand concentrations with cell-surface receptors at extremely high accuracy. Interestingly, ligand-bound receptors are often internalized, a process also known as receptor-mediated endocytosis. While internalization is involved in a vast number of important functions for the life of a cell, it was recently also suggested to increase the accuracy of sensing ligand as overcounting of the same ligand molecules is reduced. A similar role may be played by receptor diffusion om the cell membrane. Fast, lateral receptor diffusion is known to be relevant in neurotransmission initiated by release of neurotransmitter glutamate in the synaptic cleft between neurons. By binding ligand and removal by diffusion from the region of release of the neurotransmitter, diffusing receptors can be reasonably expected to reduce the local overcounting of the same ligand molecules in the region of signaling. By extending simple ligand-receptor models to out-of-equilibrium thermodynamics, we show that both receptor internalization and lateral diffusion increase the accuracy with which cells can measure ligand concentrations in the external environment. We confirm this with our model and give quantitative predictions for experimental parameters values. We give quantitative predictions, which compare favorably to experimental data of real receptors.

Neuronal calcium wave propagation varies with changes in endoplasmic reticulum parameters: a computer model

PubMed Central

Neymotin, Samuel A.; McDougal, Robert A.; Sherif, Mohamed A.; Fall, Christopher P.; Hines, Michael L.; Lytton, William W.

2015-01-01

Calcium (Ca2+) waves provide a complement to neuronal electrical signaling, forming a key part of a neuron’s second messenger system. We developed a reaction-diffusion model of an apical dendrite with diffusible inositol triphosphate (IP3), diffusible Ca2+, IP3 receptors (IP3Rs), endoplasmic reticulum (ER) Ca2+ leak, and ER pump (SERCA) on ER. Ca2+ is released from ER stores via IP3Rs upon binding of IP3 and Ca2+. This results in Ca2+-induced-Ca2+-release (CICR) and increases Ca2+ spread. At least two modes of Ca2+ wave spread have been suggested: a continuous mode based on presumed relative homogeneity of ER within the cell; and a pseudo-saltatory model where Ca2+ regeneration occurs at discrete points with diffusion between them. We compared the effects of three patterns of hypothesized IP3R distribution: 1. continuous homogeneous ER, 2. hotspots with increased IP3R density (IP3R hotspots), 3. areas of increased ER density (ER stacks). All three modes produced Ca2+ waves with velocities similar to those measured in vitro (~50–90µm /sec). Continuous ER showed high sensitivity to IP3R density increases, with time to onset reduced and speed increased. Increases in SERCA density resulted in opposite effects. The measures were sensitive to changes in density and spacing of IP3R hotspots and stacks. Increasing the apparent diffusion coefficient of Ca2+ substantially increased wave speed. An extended electrochemical model, including voltage gated calcium channels and AMPA synapses, demonstrated that membrane priming via AMPA stimulation enhances subsequent Ca2+ wave amplitude and duration. Our modeling suggests that pharmacological targeting of IP3Rs and SERCA could allow modulation of Ca2+ wave propagation in diseases where Ca2+ dysregulation has been implicated. PMID:25734493

Retrospective Correction of Physiological Noise in DTI Using an Extended Tensor Model and Peripheral Measurements

PubMed Central

Mohammadi, Siawoosh; Hutton, Chloe; Nagy, Zoltan; Josephs, Oliver; Weiskopf, Nikolaus

2013-01-01

Diffusion tensor imaging is widely used in research and clinical applications, but this modality is highly sensitive to artefacts. We developed an easy-to-implement extension of the original diffusion tensor model to account for physiological noise in diffusion tensor imaging using measures of peripheral physiology (pulse and respiration), the so-called extended tensor model. Within the framework of the extended tensor model two types of regressors, which respectively modeled small (linear) and strong (nonlinear) variations in the diffusion signal, were derived from peripheral measures. We tested the performance of four extended tensor models with different physiological noise regressors on nongated and gated diffusion tensor imaging data, and compared it to an established data-driven robust fitting method. In the brainstem and cerebellum the extended tensor models reduced the noise in the tensor-fit by up to 23% in accordance with previous studies on physiological noise. The extended tensor model addresses both large-amplitude outliers and small-amplitude signal-changes. The framework of the extended tensor model also facilitates further investigation into physiological noise in diffusion tensor imaging. The proposed extended tensor model can be readily combined with other artefact correction methods such as robust fitting and eddy current correction. PMID:22936599

Electrochemical Ionization and Analyte Charging in the Array of Micromachined UltraSonic Electrospray (AMUSE) Ion Source

PubMed Central

Forbes, Thomas P.; Degertekin, F. Levent; Fedorov, Andrei G.

2010-01-01

Electrochemistry and ion transport in a planar array of mechanically-driven, droplet-based ion sources are investigated using an approximate time scale analysis and in-depth computational simulations. The ion source is modeled as a controlled-current electrolytic cell, in which the piezoelectric transducer electrode, which mechanically drives the charged droplet generation using ultrasonic atomization, also acts as the oxidizing/corroding anode (positive mode). The interplay between advective and diffusive ion transport of electrochemically generated ions is analyzed as a function of the transducer duty cycle and electrode location. A time scale analysis of the relative importance of advective vs. diffusive ion transport provides valuable insight into optimality, from the ionization prospective, of alternative design and operation modes of the ion source operation. A computational model based on the solution of time-averaged, quasi-steady advection-diffusion equations for electroactive species transport is used to substantiate the conclusions of the time scale analysis. The results show that electrochemical ion generation at the piezoelectric transducer electrodes located at the back-side of the ion source reservoir results in poor ionization efficiency due to insufficient time for the charged analyte to diffuse away from the electrode surface to the ejection location, especially at near 100% duty cycle operation. Reducing the duty cycle of droplet/analyte ejection increases the analyte residence time and, in turn, improves ionization efficiency, but at an expense of the reduced device throughput. For applications where this is undesirable, i.e., multiplexed and disposable device configurations, an alternative electrode location is incorporated. By moving the charging electrode to the nozzle surface, the diffusion length scale is greatly reduced, drastically improving ionization efficiency. The ionization efficiency of all operating conditions considered is expressed as a function of the dimensionless Peclet number, which defines the relative effect of advection as compared to diffusion. This analysis is general enough to elucidate an important role of electrochemistry in ionization efficiency of any arrayed ion sources, be they mechanically-driven or electrosprays, and is vital for determining optimal design and operation conditions. PMID:20607111

Apparent Anomalous Diffusion in the Cytoplasm of Human Cells: The Effect of Probes' Polydispersity.

PubMed

Kalwarczyk, Tomasz; Kwapiszewska, Karina; Szczepanski, Krzysztof; Sozanski, Krzysztof; Szymanski, Jedrzej; Michalska, Bernadeta; Patalas-Krawczyk, Paulina; Duszynski, Jerzy; Holyst, Robert

2017-10-26

This work, based on in vivo and in vitro measurements, as well as in silico simulations, provides a consistent analysis of diffusion of polydisperse nanoparticles in the cytoplasm of living cells. Using the example of fluorescence correlation spectroscopy (FCS), we show the effect of polydispersity of probes on the experimental results. Although individual probes undergo normal diffusion, in the ensemble of probes, an effective broadening of the distribution of diffusion times occurs-similar to anomalous diffusion. We introduced fluorescently labeled dextrans into the cytoplasm of HeLa cells and found that cytoplasmic hydrodynamic drag, exponentially dependent on probe size, extraordinarily broadens the distribution of diffusion times across the focal volume. As a result, the in vivo FCS data were effectively fitted with the anomalous subdiffusion model while for a monodisperse probe the normal diffusion model was most suitable. Diffusion time obtained from the anomalous diffusion model corresponds to a probe whose size is determined by the weight-average molecular weight of the polymer. The apparent anomaly exponent decreases with increasing polydispersity of the probes. Our results and methodology can be applied in intracellular studies of the mobility of nanoparticles, polymers, or oligomerizing proteins.

Does the diffusion dark matter-dark energy interaction model solve cosmological puzzles?

NASA Astrophysics Data System (ADS)

Szydłowski, Marek; Stachowski, Aleksander

2016-08-01

We study dynamics of cosmological models with diffusion effects modeling dark matter and dark energy interactions. We show the simple model with diffusion between the cosmological constant sector and dark matter, where the canonical scaling law of dark matter (ρd m ,0a-3(t )) is modified by an additive ɛ (t )=γ t a-3(t ) to the form ρd m=ρd m ,0a-3(t )+ɛ (t ). We reduced this model to the autonomous dynamical system and investigate it using dynamical system methods. This system possesses a two-dimensional invariant submanifold on which the dark matter-dark energy (DM-DE) interaction can be analyzed on the phase plane. The state variables are density parameter for matter (dark and visible) and parameter δ characterizing the rate of growth of energy transfer between the dark sectors. A corresponding dynamical system belongs to a general class of jungle type of cosmologies represented by coupled cosmological models in a Lotka-Volterra framework. We demonstrate that the de Sitter solution is a global attractor for all trajectories in the phase space and there are two repellers: the Einstein-de Sitter universe and the de Sitter universe state dominating by the diffusion effects. We distinguish in the phase space trajectories, which become in good agreement with the data. They should intersect a rectangle with sides of Ωm ,0∈[0.2724 ,0.3624 ] , δ ∈[0.0000 ,0.0364 ] at the 95% CL. Our model could solve some of the puzzles of the Λ CDM model, such as the coincidence and fine-tuning problems. In the context of the coincidence problem, our model can explain the present ratio of ρm to ρd e, which is equal 0.457 6-0.0831+0.1109 at a 2 σ confidence level.

Problems in Catalytic Oxidation of Hydrocarbons and Detailed Simulation of Combustion Processes

NASA Astrophysics Data System (ADS)

Xin, Yuxuan

This dissertation research consists of two parts, with Part I on the kinetics of catalytic oxidation of hydrocarbons and Part II on aspects on the detailed simulation of combustion processes. In Part I, the catalytic oxidation of C1--C3 hydrocarbons, namely methane, ethane, propane and ethylene, was investigated for lean hydrocarbon-air mixtures over an unsupported Pd-based catalyst, from 600 to 800 K and under atmospheric pressure. In Chapter 2, the experimental facility of wire microcalorimetry and simulation configuration were described in details. In Chapter 3 and 4, the oxidation rate of C1--C 3 hydrocarbons is demonstrated to be determined by the dissociative adsorption of hydrocarbons. A detailed surface kinetics model is proposed with deriving the rate coefficient of hydrocarbon dissociative adsorption from the wire microcalorimetry data. In Part II, four fundamental studies were conducted through detailed combustion simulations. In Chapter 5, self-accelerating hydrogen-air flames are studied via two-dimensional detailed numerical simulation (DNS). The increase in the global flame velocity is shown to be caused by the increase of flame surface area, and the fractal structure of the flame front is demonstrated by the box-counting method. In Chapter 6, skeletal reaction models for butane combustion are derived by using directed relation graph (DRG) and DRG-aided sensitivity analysis (DRGASA), and uncertainty minimization by polynomial chaos expansion (MUM-PCE) mothodes. The dependence of model uncertainty is subjected to the completeness of the model. In Chapter 7, a systematic strategy is proposed to reduce the cost of the multicomponent diffusion model by accurately accounting for the species whose diffusivity is important to the global responses of the combustion systems, and approximating those of less importance by the mixture-averaged model. The reduced model is validated in an n-heptane mechanism with 88 species. In Chapter 8, the influence of Soret diffusion on the n-heptane/air flames is investigated numerically. In the unstretched flames, Soret diffusion primarily affects the chemical kinetics embedded in the flame structure and the net effect is small; while in the stretched flames, its impact is mainly through those of n-heptane and the secondary fuel, H2, in modifying the flame temperature, with substantial effects.

Impact of aerosols on solar energy production - Scenarios from the Sahel Zone

NASA Astrophysics Data System (ADS)

Neher, Ina; Meilinger, Stefanie; Crewell, Susanne

2017-04-01

Solar energy is one option to serve the rising global energy demand with low environmental impact. Building an energy system with a considerable share of solar power requires long-term investment and a careful investigation of potential sites. Therefore, understanding the impacts from varying regionally and locally determined meteorological conditions on solar energy production will influence energy yield projections. Aerosols reduce global solar radiation due to absorption and scattering and therewith solar energy yields. Depending on aerosol size distribution they reduce the direct component of the solar radiation and modify the direction of the diffuse component compared to standard atmospheric conditions without aerosols. The aerosol size distribution and composition in the atmosphere is highly variable due to meteorological and land surface conditions. A quantitative assessment of aerosol effects on solar power yields and its relation to land use change is of particular interest for developing countries countries when analyzing the potential of local power production. This study aims to identify the effect of atmospheric aerosols in three different land use regimes, namely desert, urban/polluted and maritime on the tilted plane of photovoltaic energy modules. Here we focus on the Sahel zone, i.e. Niamey, Niger (13.5 N;2.1 E), located at the edge of the Sahara where also detailed measurements of the atmospheric state are available over the year 2006. Guided by observations a model chain is used to determine power yields. The atmospheric aerosol composition will be defined by using the Optical Properties of Aerosols and Clouds (OPAC) library. Direct and diffuse radiation (up- and downward component) are then calculated by the radiative transfer model libRadtran which allows to calculate the diffuse component of the radiance from different azimuth and zenith angles. Then the diffuse radiance will be analytically transformed to an east, south and west facing module with different tilting angles (between 0° and 45°) from each direction and compared to the tilted diffuse radiation derived by the Perez-model (Loutzenhiser et al. 2007) which is widely used in the photovoltaic community. This will allow an assessment how well standard approaches work in tropical region under various aerosol conditions including strong dust outbreaks from the Sahara. This presentation will introduce the modeling chain to assess solar power yields for different photovoltaic modules in the Sahel zone and address their relative dependence on aerosol conditions.

Computational investigation of longitudinal diffusion, eddy dispersion, and trans-particle mass transfer in bulk, random packings of core-shell particles with varied shell thickness and shell diffusion coefficient.

PubMed

Daneyko, Anton; Hlushkou, Dzmitry; Baranau, Vasili; Khirevich, Siarhei; Seidel-Morgenstern, Andreas; Tallarek, Ulrich

2015-08-14

In recent years, chromatographic columns packed with core-shell particles have been widely used for efficient and fast separations at comparatively low operating pressure. However, the influence of the porous shell properties on the mass transfer kinetics in core-shell packings is still not fully understood. We report on results obtained with a modeling approach to simulate three-dimensional advective-diffusive transport in bulk random packings of monosized core-shell particles, covering a range of reduced mobile phase flow velocities from 0.5 up to 1000. The impact of the effective diffusivity of analyte molecules in the porous shell and the shell thickness on the resulting plate height was investigated. An extension of Giddings' theory of coupled eddy dispersion to account for retention of analyte molecules due to stagnant regions in porous shells with zero mobile phase flow velocity is presented. The plate height equation involving a modified eddy dispersion term excellently describes simulated data obtained for particle-packings with varied shell thickness and shell diffusion coefficient. It is confirmed that the model of trans-particle mass transfer resistance of core-shell particles by Kaczmarski and Guiochon [42] is applicable up to a constant factor. We analyze individual contributions to the plate height from different mass transfer mechanisms in dependence of the shell parameters. The simulations demonstrate that a reduction of plate height in packings of core-shell relative to fully porous particles arises mainly due to reduced trans-particle mass transfer resistance and transchannel eddy dispersion. Copyright © 2015 Elsevier B.V. All rights reserved.

Modelling mitigation options to reduce diffuse nitrogen water pollution from agriculture.

PubMed

Bouraoui, Fayçal; Grizzetti, Bruna

2014-01-15

Agriculture is responsible for large scale water quality degradation and is estimated to contribute around 55% of the nitrogen entering the European Seas. The key policy instrument for protecting inland, transitional and coastal water resources is the Water Framework Directive (WFD). Reducing nutrient losses from agriculture is crucial to the successful implementation of the WFD. There are several mitigation measures that can be implemented to reduce nitrogen losses from agricultural areas to surface and ground waters. For the selection of appropriate measures, models are useful for quantifying the expected impacts and the associated costs. In this article we review some of the models used in Europe to assess the effectiveness of nitrogen mitigation measures, ranging from fertilizer management to the construction of riparian areas and wetlands. We highlight how the complexity of models is correlated with the type of scenarios that can be tested, with conceptual models mostly used to evaluate the impact of reduced fertilizer application, and the physically-based models used to evaluate the timing and location of mitigation options and the response times. We underline the importance of considering the lag time between the implementation of measures and effects on water quality. Models can be effective tools for targeting mitigation measures (identifying critical areas and timing), for evaluating their cost effectiveness, for taking into consideration pollution swapping and considering potential trade-offs in contrasting environmental objectives. Models are also useful for involving stakeholders during the development of catchments mitigation plans, increasing their acceptability. © 2013.

Adsorption-Coupled Diffusion of Gold Nanoclusters within a Large-Pore Protein Crystal Scaffold.

PubMed

Hartje, Luke F; Munsky, Brian; Ni, Thomas W; Ackerson, Christopher J; Snow, Christopher D

2017-08-17

Large-pore protein crystals (LPCs) are ordered biologically derived nanoporous materials exhibiting pore diameters greater than 8 nm. These substantial pores distinguish LPCs from typical nanoporous scaffolds, enabling engineered LPC materials to readily uptake, immobilize, and release macromolecular guests. In this study, macromolecular transport within an LPC environment was experimentally and computationally investigated by studying adsorption-coupled diffusion of Au 25 (glutathione) 18 nanoclusters within a cross-linked LPC scaffold via time-lapse confocal microscopy, bulk equilibrium adsorption, and hindered diffusion simulation. Equilibrium adsorption data is congruent with a Langmuir adsorption model, exhibiting strong binding behavior between nanoclusters and the scaffold. The standard Gibbs free energy of binding is equivalent to -37.2 kJ/mol, and the maximum binding capacity of 1.25 × 10 3 mg/g corresponds to approximately 29 nanoclusters per LPC unit cell. The hindered diffusion model showed good agreement with experimental data, revealing a pore diffusion coefficient of 3.7 × 10 -7 cm 2 /s under low nanocluster concentration. Furthermore, the model was sufficient to determine adsorption and desorption kinetic values for k a and k d equal to 13 cm 3 /mol·s and 1.7 × 10 -7 s -1 , respectively. At higher nanocluster concentrations, the simulated pore diffusion coefficient could be reduced by 3 orders of magnitude to 3.4 × 10 -10 cm 2 /s due to the effects of pore occlusion. This study demonstrates a strategy to analyze adsorption-coupled diffusion data to better understand complex transport of fluorescent macromolecules into LPCs. This approach fits the observable fluorescence data to the key molecular details and will benefit downstream efforts to engineer LPC-based nanoporous materials.

Microscopic Interpretation and Generalization of the Bloch-Torrey Equation for Diffusion Magnetic Resonance

PubMed Central

Seroussi, Inbar; Grebenkov, Denis S.; Pasternak, Ofer; Sochen, Nir

2017-01-01

In order to bridge microscopic molecular motion with macroscopic diffusion MR signal in complex structures, we propose a general stochastic model for molecular motion in a magnetic field. The Fokker-Planck equation of this model governs the probability density function describing the diffusion-magnetization propagator. From the propagator we derive a generalized version of the Bloch-Torrey equation and the relation to the random phase approach. This derivation does not require assumptions such as a spatially constant diffusion coefficient, or ad-hoc selection of a propagator. In particular, the boundary conditions that implicitly incorporate the microstructure into the diffusion MR signal can now be included explicitly through a spatially varying diffusion coefficient. While our generalization is reduced to the conventional Bloch-Torrey equation for piecewise constant diffusion coefficients, it also predicts scenarios in which an additional term to the equation is required to fully describe the MR signal. PMID:28242566

Spatiotemporal Patterns in a Predator-Prey Model with Cross-Diffusion Effect

NASA Astrophysics Data System (ADS)

Sambath, M.; Balachandran, K.; Guin, L. N.

The present research deals with the emergence of spatiotemporal patterns of a two-dimensional (2D) continuous predator-prey system with cross-diffusion effect. First, we work out the critical lines of Hopf and Turing bifurcations of the current model system in a 2D spatial domain by means of bifurcation theory. More specifically, the exact Turing region is specified in a two-parameter space. In effect, by choosing the cross-diffusion coefficient as one of the momentous parameter, we demonstrate that the model system undergoes a sequence of spatiotemporal patterns in a homogeneous environment through diffusion-driven instability. Our results via numerical simulation authenticate that cross-diffusion be able to create stationary patterns which enrich the findings of pattern formation in an ecosystem.

Lattice Boltzmann scheme for mixture modeling: analysis of the continuum diffusion regimes recovering Maxwell-Stefan model and incompressible Navier-Stokes equations.

PubMed

Asinari, Pietro

2009-11-01

A finite difference lattice Boltzmann scheme for homogeneous mixture modeling, which recovers Maxwell-Stefan diffusion model in the continuum limit, without the restriction of the mixture-averaged diffusion approximation, was recently proposed [P. Asinari, Phys. Rev. E 77, 056706 (2008)]. The theoretical basis is the Bhatnagar-Gross-Krook-type kinetic model for gas mixtures [P. Andries, K. Aoki, and B. Perthame, J. Stat. Phys. 106, 993 (2002)]. In the present paper, the recovered macroscopic equations in the continuum limit are systematically investigated by varying the ratio between the characteristic diffusion speed and the characteristic barycentric speed. It comes out that the diffusion speed must be at least one order of magnitude (in terms of Knudsen number) smaller than the barycentric speed, in order to recover the Navier-Stokes equations for mixtures in the incompressible limit. Some further numerical tests are also reported. In particular, (1) the solvent and dilute test cases are considered, because they are limiting cases in which the Maxwell-Stefan model reduces automatically to Fickian cases. Moreover, (2) some tests based on the Stefan diffusion tube are reported for proving the complete capabilities of the proposed scheme in solving Maxwell-Stefan diffusion problems. The proposed scheme agrees well with the expected theoretical results.

Diffusion of environmentally-friendly energy technologies: buy versus lease differences in residential PV markets

NASA Astrophysics Data System (ADS)

Rai, Varun; Sigrin, Benjamin

2013-03-01

Diffusion of microgeneration technologies, particularly rooftop photovoltaic (PV), represents a key option in reducing emissions in the residential sector. We use a uniquely rich dataset from the burgeoning residential PV market in Texas to study the nature of the consumer’s decision-making process in the adoption of these technologies. In particular, focusing on the financial metrics and the information decision-makers use to base their decisions upon, we study how the leasing and buying models affect individual choices and, thereby, the adoption of capital-intensive energy technologies. Overall, our findings suggest that the leasing model more effectively addresses consumers’ informational requirements and that, contrary to some other studies, buyers and lessees of PV do not necessarily differ significantly along socio-demographic variables. Instead, we find that the leasing model has opened up the residential PV market to a new, and potentially very large, consumer segment—those with a tight cash-flow situation.

Oblique incidence reflectometry: optical models and measurements using a side-viewing gradient index lens-based endoscopic imaging system

NASA Astrophysics Data System (ADS)

Wall, R. Andrew; Barton, Jennifer K.

2014-06-01

A side-viewing, 2.3-mm diameter oblique incidence reflectometry endoscope has been designed to obtain optical property measurements of turbid samples. Light from a single-mode fiber is relayed obliquely onto the tissue with a gradient index lens-based distal optics assembly and the resulting diffuse reflectance profile is imaged and collected with a 30,000 element, 0.72 mm clear aperture fiber bundle. Sampling the diffuse reflectance in two-dimensions allows for fitting of the reflected intensity profile to a well-known theoretical model, permitting the extraction of both absorption and reduced scattering coefficients of the tissue sample. Models and measurements of the endoscopic imaging system are presented in tissue phantoms and in vivo mouse colon, verifying the endoscope's capabilities to accurately measure effective attenuation coefficient and differentiate diseased from normal colon.

Model of bidirectional reflectance distribution function for metallic materials

NASA Astrophysics Data System (ADS)

Wang, Kai; Zhu, Jing-Ping; Liu, Hong; Hou, Xun

2016-09-01

Based on the three-component assumption that the reflection is divided into specular reflection, directional diffuse reflection, and ideal diffuse reflection, a bidirectional reflectance distribution function (BRDF) model of metallic materials is presented. Compared with the two-component assumption that the reflection is composed of specular reflection and diffuse reflection, the three-component assumption divides the diffuse reflection into directional diffuse and ideal diffuse reflection. This model effectively resolves the problem that constant diffuse reflection leads to considerable error for metallic materials. Simulation and measurement results validate that this three-component BRDF model can improve the modeling accuracy significantly and describe the reflection properties in the hemisphere space precisely for the metallic materials.

Local Antibiotic Delivery by a Bioabsorbable Gel Is Superior to PMMA Bead Depot in Reducing Infection in an Open Fracture Model

DTIC Science & Technology

2014-06-01

be achieved in the wound while avoiding the side effects and cost of systemic administration. Beads molded from polymethylmethacrylate cement are... polymethylmethacrylate antibiotic beads is less effective because this method has to rely on diffusion of the antibiotic from the high concentration close...antibiotics in clinical use is polymethylmethacrylate (PMMA) blended with antibiotics and molded into beads.6–8 There are, however, disadvantages

Effect of drying conditions on drying kinetics and quality of aromatic Pandanus amaryllifolius leaves.

PubMed

Rayaguru, Kalpana; Routray, Winny

2010-12-01

Pandanus amaryllifolius is a plant with aromatic leaves, which impart the characteristic flavour of aromatic rice. The quality of aromatic Pandanus leaves dried at low temperature (35 °C) and low RH (27%) in a heat pump dryer was evaluated and compared with those obtained from hot air drying at 45 °C. Thin-layer drying kinetics has been studied for both the conditions. To determine the kinetic parameters, the drying data were fitted to various semi-theoretical models. The goodness of fit was determined using the coefficient of determination, reduced chi square, and root mean square error. Aroma, colour, and overall acceptability determination of fresh and dried leaves were made using sensory evaluation. Drying of leaves took place mainly under the falling-rate period. The Page equation was found to be best among the proposed models to describe the thin-layer drying of Pandanus leaves with higher coefficient of determination. The effective moisture diffusivity values were also determined. The effect of low RH was prominent during the initial drying when the product was moist. The effect of temperature was prominent in the later part of drying, which acted as a driving force for moisture diffusion and hence the total drying time was reduced. Retention of aromatic compound 2-acetyl-1-pyrroline content was more in low temperature dried samples with higher sensory scores.

Physical Processes at Turnoff

NASA Astrophysics Data System (ADS)

Michaud, Georges

Stellar evolution models taking into account atomic diffusion including radiative accelerations of 28 species have been calculated for Pop II stars of 0.5 to 1.2 solar mass with [Fe/H] from -4.31 to -0.71. Overabundances are expected in some turnoff stars with effective temperatures larger than 5900 K. They depend strongly on the metallicity of the cluster. At the metallicity of M92 they reach a factor of 10 for many species at 12 Gyr but a factor of at most 2 at 13.5 Gyr. Series of models were also calculated with turbulence to determine to what extent turbulence reduces predicted abundance anomalies. The level of abundance anomalies observed in turnoff stars may then determine a level of turbulence. Even in the presence of turbulence however allowance for diffusive processes leads to a 10%-12% reduction in age at a given turnoff luminosity. For M 92 an age of 13.5 Gyr is determined which is about 1.5 Gyr younger than obtained in the absence of diffusion. In clusters atomic diffusion is now known to play a role in white dwarfs HB stars for age determination and for abundance anomalies in some turnoff stars.

Physical Processes at Turnoff

NASA Astrophysics Data System (ADS)

Michaud, Georges

Stellar evolution models taking into account atomic diffusion including radiative accelerations of 28 species have been calculated for Pop II stars of 0.5 to 1.2 solar mass with [Fe/H] from -4.31 to -0.71. Overabundances are expected in some turnoff stars with effective temperatures larger than 5900 K. They depend strongly on the metallicity of the cluster. At the metallicity of M92 they reach a factor of 10 for many species at 12 Gyr but a factor of at most 2 at 13.5 Gyr. Series of models were also calculated with turbulence to determine to what extent turbulence reduces predicted abundance anomalies. The level of abundance anomalies observed in turnoff stars may then determine a level of turbulence. Even in the presence of turbulence however allowance for diffusive processes leads to a 10%-12% reduction in age at a given turnoff luminosity. For M 92 an age of 13.5 Gyr is determined which is about 1.5 Gyr younger than obtained in the absence of diffusion. In clusters atomic diffusion is now known to play a role in white dwarfs HB stars for age determination and for abundance anomalies in some turnoff stars

Processes at the turnoff

NASA Astrophysics Data System (ADS)

Michaud, Georges; Richard, Olivier; Richer, Jacques

2005-01-01

Stellar evolution models taking into account atomic diffusion including radiative accelerations of 28 species have been calculated for Pop II stars of 0.5 to 1.2 solar mass with [Fe/H] from -4.31 to -0.71. Overabundances are expected in some turnoff stars with effective temperatures larger than 5900 K. They depend strongly on the metallicity of the cluster. At the metallicity of M92 they reach a factor of 10 for many species at 12 Gyr but a factor of at most 2 at 13.5 Gyr. Series of models were also calculated with turbulence to determine to what extent turbulence reduces predicted abundance anomalies. The level of abundance anomalies observed in turnoff stars may then determine a level of turbulence. Even in the presence of turbulence however allowance for diffusive processes leads to a 10%-12% reduction in age at a given turnoff luminosity. For M 92 an age of 13.5 Gyr is determined which is about 1.5 Gyr younger than obtained in the absence of diffusion. In clusters atomic diffusion is now known to play a role in white dwarfs HB stars for age determination and for abundance anomalies in some turnoff stars.

Influence of Diffuse Radiation and Its Timescale Effects on Gross Primary Productivity in a Mid-subtropical Planted Coniferous Forest Ecosystem.

NASA Astrophysics Data System (ADS)

Han, J.; Zhang, L.; Li, S.

2017-12-01

The mid-subtropical forests in East Asia monsoon zone act as an important carbon sink. Planted coniferous forests are important vegetation types in this area. However, we lack an in-depth understanding of both controlling mechanisms of environmental and biotic factors in gross primary productivity (GPP) and their timescale effects. Based on eddy covariance carbon flux data and micro-meteorological data (2003-2015) observed at a mid-subtropical planted coniferous forest in Qianyanzhou, along with leaf area index derived from MODIS products, we used the path analysis mothed to quantify standardized total effects (STE) of environmental factors on GPP and their variabilities at different timescales. We found that GPP was mainly affected by photosynthetically active radiation (PAR) at half-hour scale. Furthermore, GPP under cloudy weather conditions was greater than under sunny weather conditions across seasons. From daily to yearly scales, PAR had the positive STE with GPP, but such STE was gradually reduced toward yearly scale; diffuse radiation or air temperature had the positive STE with GPP at daily and monthly scales, while negative STE occurred at seasonal and yearly scales. Vapor pressure deficit exhibited the negative STE with GPP at all timescales, and such STE increased gradually toward the yearly scale. Therefore, on one hand, GPP was controlled by light conditions, but on the other hand, high air temperature in summer and water availability had a significant restraining effect over GPP, and such effect increased with the timescales from day to year. Based on the simulation results by the light use efficiency (LUE) model, it indicated that modelled GPP agreed well with the measurements when the influence of the seasonal variations of LUE and diffuse radiation were incorporated into the model, especially at the yearly scale. This further indicated that diffuse radiation, together with changes in air temperature and water supply, had a significant effect on the variations of yearly GPP.

Effect of stress on the diffusion kinetics of methane during gas desorption in coal matrix under different equilibrium pressures

NASA Astrophysics Data System (ADS)

Li, Chengwu; Xue, Honglai; Hu, Po; Guan, Cheng; Liu, Wenbiao

2018-06-01

Stress has a significant influence on gas diffusion, which is a key factor for methane recovery in coal mines. In this study, a series of experiments were performed to investigate effect of stress on the gas diffusivity during desorption in tectonic coal. Additionally, the desorbed data were modeled using the unipore and bidisperse models. The results show that the bidisperse model better describes the diffusion kinetics than the unipore model in this study. Additionally, the modeling results using the bidisperse approach suggest that the stress impact on the macropore diffusivity is greater than the stress on the micropore diffusivity. Under the same equilibrium pressure, the diffusivity varies with stress according to a four-stage function, which shows an ‘M-shape’. As the equilibrium gas pressure increased from 0.6 to 1.7 MPa, the critical point between stage 2 and stage 3 and between stage 3 and stage 4 transferred to a low stress. This difference is attributed to the gas pressure effects on the physical and mechanical properties of coal. These observations indicate that both the stress and gas pressure can significantly impact gas diffusion and may have significant implications on methane recovery in coal mines.

Modelling the impacts of agricultural management practices on river water quality in Eastern England.

PubMed

Taylor, Sam D; He, Yi; Hiscock, Kevin M

2016-09-15

Agricultural diffuse water pollution remains a notable global pressure on water quality, posing risks to aquatic ecosystems, human health and water resources and as a result legislation has been introduced in many parts of the world to protect water bodies. Due to their efficiency and cost-effectiveness, water quality models have been increasingly applied to catchments as Decision Support Tools (DSTs) to identify mitigation options that can be introduced to reduce agricultural diffuse water pollution and improve water quality. In this study, the Soil and Water Assessment Tool (SWAT) was applied to the River Wensum catchment in eastern England with the aim of quantifying the long-term impacts of potential changes to agricultural management practices on river water quality. Calibration and validation were successfully performed at a daily time-step against observations of discharge, nitrate and total phosphorus obtained from high-frequency water quality monitoring within the Blackwater sub-catchment, covering an area of 19.6 km(2). A variety of mitigation options were identified and modelled, both singly and in combination, and their long-term effects on nitrate and total phosphorus losses were quantified together with the 95% uncertainty range of model predictions. Results showed that introducing a red clover cover crop to the crop rotation scheme applied within the catchment reduced nitrate losses by 19.6%. Buffer strips of 2 m and 6 m width represented the most effective options to reduce total phosphorus losses, achieving reductions of 12.2% and 16.9%, respectively. This is one of the first studies to quantify the impacts of agricultural mitigation options on long-term water quality for nitrate and total phosphorus at a daily resolution, in addition to providing an estimate of the uncertainties of those impacts. The results highlighted the need to consider multiple pollutants, the degree of uncertainty associated with model predictions and the risk of unintended pollutant impacts when evaluating the effectiveness of mitigation options, and showed that high-frequency water quality datasets can be applied to robustly calibrate water quality models, creating DSTs that are more effective and reliable. Copyright © 2016 The Authors. Published by Elsevier Ltd.. All rights reserved.

A localized Richardson-Lucy algorithm for fiber orientation estimation in high angular resolution diffusion imaging.

PubMed

Liu, Xiaozheng; Yuan, Zhenming; Guo, Zhongwei; Xu, Dongrong

2015-05-01

Diffusion tensor imaging is widely used for studying neural fiber trajectories in white matter and for quantifying changes in tissue using diffusion properties at each voxel in the brain. To better model the nature of crossing fibers within complex architectures, rather than using a simplified tensor model that assumes only a single fiber direction at each image voxel, a model mixing multiple diffusion tensors is used to profile diffusion signals from high angular resolution diffusion imaging (HARDI) data. Based on the HARDI signal and a multiple tensors model, spherical deconvolution methods have been developed to overcome the limitations of the diffusion tensor model when resolving crossing fibers. The Richardson-Lucy algorithm is a popular spherical deconvolution method used in previous work. However, it is based on a Gaussian distribution, while HARDI data are always very noisy, and the distribution of HARDI data follows a Rician distribution. This current work aims to present a novel solution to address these issues. By simultaneously considering both the Rician bias and neighbor correlation in HARDI data, the authors propose a localized Richardson-Lucy (LRL) algorithm to estimate fiber orientations for HARDI data. The proposed method can simultaneously reduce noise and correct the Rician bias. Mean angular error (MAE) between the estimated Fiber orientation distribution (FOD) field and the reference FOD field was computed to examine whether the proposed LRL algorithm offered any advantage over the conventional RL algorithm at various levels of noise. Normalized mean squared error (NMSE) was also computed to measure the similarity between the true FOD field and the estimated FOD filed. For MAE comparisons, the proposed LRL approach obtained the best results in most of the cases at different levels of SNR and b-values. For NMSE comparisons, the proposed LRL approach obtained the best results in most of the cases at b-value = 3000 s/mm(2), which is the recommended schema for HARDI data acquisition. In addition, the FOD fields estimated by the proposed LRL approach in regions of fiber crossing regions using real data sets also showed similar fiber structures which agreed with common acknowledge in these regions. The novel spherical deconvolution method for improved accuracy in investigating crossing fibers can simultaneously reduce noise and correct Rician bias. With the noise smoothed and bias corrected, this algorithm is especially suitable for estimation of fiber orientations in HARDI data. Experimental results using both synthetic and real imaging data demonstrated the success and effectiveness of the proposed LRL algorithm.

Probe diffusion of labeled polymers inside polyacrylic acid solutions: A polyelectrolyte effect

NASA Astrophysics Data System (ADS)

Mishra, Banani; Mithra, K.; Khandai, Santripti; Jena, Sidhartha S.

2018-05-01

Probe diffusion of fluorescently labeled Dextran 40 inside polyelectrolyte solution of polyacrylic acid (PAA) was investigated using Fluorescence Recovery After Photobleaching technique. The crowding and interaction effects on probe diffusion were controlled by tuning background polymer and added external electrolyte concentration. For all the salt concentration, an overall decrease in diffusion coefficient is observed with rise in polymer concentration. The diffusion coefficient decreases with decrease in salt concentration whereas the solution viscosity increases, indicating a competition between viscous drag and electrostatic interaction. A large positive deviation from the ideal Stokes-Einstein relation is observed for high polymer and low salt concentration, which reduces markedly with addition of salt confirming polyelectrolyte effects, plays a major role in deciding the probe diffusion.

Suppression of Soot Formation and Shapes of Laminar Jet Diffusion Flames

NASA Technical Reports Server (NTRS)

Xu, F.; Dai, Z.; Faeth, G. M.

2001-01-01

Laminar nonpremixed (diffusion) flames are of interest because they provide model flame systems that are far more tractable for analysis and experiments than practical turbulent flames. In addition, many properties of laminar diffusion flames are directly relevant to turbulent diffusion flames using laminar flamelet concepts. Finally, laminar diffusion flame shapes have been of interest since the classical study of Burke and Schumann because they involve a simple nonintrusive measurement that is convenient for evaluating flame shape predictions. Motivated by these observations, the shapes of round hydrocarbon-fueled laminar jet diffusion flames were considered, emphasizing conditions where effects of buoyancy are small because most practical flames are not buoyant. Earlier studies of shapes of hydrocarbon-fueled nonbuoyant laminar jet diffusion flames considered combustion in still air and have shown that flames at the laminar smoke point are roughly twice as long as corresponding soot-free (blue) flames and have developed simple ways to estimate their shapes. Corresponding studies of hydrocarbon-fueled weakly-buoyant laminar jet diffusion flames in coflowing air have also been reported. These studies were limited to soot-containing flames at laminar smoke point conditions and also developed simple ways to estimate their shapes but the behavior of corresponding soot-free flames has not been addressed. This is unfortunate because ways of selecting flame flow properties to reduce soot concentrations are of great interest; in addition, soot-free flames are fundamentally important because they are much more computationally tractable than corresponding soot-containing flames. Thus, the objectives of the present investigation were to observe the shapes of weakly-buoyant laminar jet diffusion flames at both soot-free and smoke point conditions and to use the results to evaluate simplified flame shape models. The present discussion is brief.

Final Report: The Influence of Novel Behavioral Strategies in Promoting the Diffusion of Solar Energy

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

Gillingham, Kenneth; Bollinger, Bryan

This is the final report for a systematic, evidence-based project using an unprecedented series of large-scale field experiments to examine the effectiveness and cost-effectiveness of novel approaches to reduce the soft costs of solar residential photovoltaics. The approaches were based around grassroots marketing campaigns called ‘Solarize’ campaigns, that were designed to lower costs and increase adoption of solar technology. This study quantified the effectiveness and cost-effectiveness of the Solarize programs and tested new approaches to further improve the model.

An analytical and experimental evaluation of shadow shields and their support members

NASA Technical Reports Server (NTRS)

Stochl, R. J.; Boyle, R. J.

1972-01-01

Experimental tests were performed on a model shadow shield thermal protection system to examine the effect of certain configuration variables. The experimental results were used to verify the ability of an analytical program to predict the shadow shield performance including the shield-support interaction. In general, the analysis (assuming diffuse surfaces) agreed well with the experimental support temperature profiles. The agreement for the shield profiles was not as good. The results demonstrated: (1) shadow shields can be effective in reducing the heat transfer into cryogenic propellant tanks, and (2) the conductive heat transfer through supports can be reduced by selective surface coatings.

Derivation of effective fission gas diffusivities in UO2 from lower length scale simulations and implementation of fission gas diffusion models in BISON

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

Andersson, Anders David Ragnar; Pastore, Giovanni; Liu, Xiang-Yang

2014-11-07

This report summarizes the development of new fission gas diffusion models from lower length scale simulations and assessment of these models in terms of annealing experiments and fission gas release simulations using the BISON fuel performance code. Based on the mechanisms established from density functional theory (DFT) and empirical potential calculations, continuum models for diffusion of xenon (Xe) in UO 2 were derived for both intrinsic conditions and under irradiation. The importance of the large X eU3O cluster (a Xe atom in a uranium + oxygen vacancy trap site with two bound uranium vacancies) is emphasized, which is a consequencemore » of its high mobility and stability. These models were implemented in the MARMOT phase field code, which is used to calculate effective Xe diffusivities for various irradiation conditions. The effective diffusivities were used in BISON to calculate fission gas release for a number of test cases. The results are assessed against experimental data and future directions for research are outlined based on the conclusions.« less

Study of Water Absorption in Raffia vinifera Fibres from Bandjoun, Cameroon

PubMed Central

Sikame Tagne, N. R.; Njeugna, E.; Fogue, M.; Drean, J.-Y.; Nzeukou, A.; Fokwa, D.

2014-01-01

The study is focused on the water diffusion phenomenon through the Raffia vinifera fibre from the stem. The knowledge on the behavior of those fibres in presence of liquid during the realization of biocomposite, is necessary. The parameters like percentage of water gain at the point of saturation, modelling of the kinetic of water absorption, and the effective diffusion coefficient were the main objectives. Along a stem of raffia, twelve zones of sampling were defined. From Fick's 2nd law of diffusion, a new model was proposed and evaluated compared to four other models at a constant temperature of 23°C. From the proposed model, the effective diffusion coefficient was deduced. The percentage of water gain was in the range of 303–662%. The proposed model fitted better to the experimental data. The estimated diffusion coefficient was evaluated during the initial phase and at the final phase. In any cross section located along the stem of Raffia vinifera, it was found that the effective diffusion coefficient increases from the periphery to the centre during the initial and final phases. PMID:24592199

Evaluation of the mass transfer process on thin layer drying of papaya seeds from the perspective of diffusive models

NASA Astrophysics Data System (ADS)

Dotto, Guilherme Luiz; Meili, Lucas; Tanabe, Eduardo Hiromitsu; Chielle, Daniel Padoin; Moreira, Marcos Flávio Pinto

2018-02-01

The mass transfer process that occurs in the thin layer drying of papaya seeds was studied under different conditions. The external mass transfer resistance and the dependence of effective diffusivity ( D EFF ) in relation to the moisture ratio ( \\overline{MR} ) and temperature ( T) were investigated from the perspective of diffusive models. It was verified that the effective diffusivity was affected by the moisture content and temperature. A new correlation was proposed for drying of papaya seeds in order to describe these influences. Regarding the use of diffusive models, the results showed that, at conditions of low drying rates ( T ≤ 70 °C), the external mass transfer resistance, as well as the dependence of the effective diffusivity with respect to the temperature and moisture content should be considered. At high drying rates ( T > 90 °C), the dependence of the effective diffusivity with respect to the temperature and moisture content can be neglected, but the external mass transfer resistance was still considerable in the range of air velocities used in this work.

Eddy current compensated double diffusion encoded (DDE) MRI.

PubMed

Mueller, Lars; Wetscherek, Andreas; Kuder, Tristan Anselm; Laun, Frederik Bernd

2017-01-01

Eddy currents might lead to image distortions in diffusion-weighted echo planar imaging. A method is proposed to reduce their effects on double diffusion encoding (DDE) MRI experiments and the thereby derived microscopic fractional anisotropy (μFA). The twice-refocused spin echo scheme was adapted for DDE measurements. To assess the effect of individual diffusion encodings on the image distortions, measurements of a grid of plastic rods in water were performed. The effect of eddy current compensation on μFA measurements was evaluated in the brains of six healthy volunteers. The use of an eddy current compensation reduced the signal variation. As expected, the distortions caused by the second encoding were larger than those of the first encoding, entailing a stronger need to compensate for them. For an optimal result, however, both encodings had to be compensated. The artifact reduction strongly improved the measurement of the μFA in ventricles and gray matter by reducing the overestimation. An effect of the compensation on absolute μFA values in white matter was not observed. It is advisable to compensate both encodings in DDE measurements for eddy currents. Magn Reson Med 77:328-335, 2017. © 2015 Wiley Periodicals, Inc. © 2015 Wiley Periodicals, Inc.

The Influence of Acute Hyperglycemia in an Animal Model of Lacunar Stroke That Is Induced by Artificial Particle Embolization

PubMed Central

Tsai, Ming-Jun; Lin, Ming-Wei; Huang, Yaw-Bin; Kuo, Yu-Min; Tsai, Yi-Hung

2016-01-01

Animal and clinical studies have revealed that hyperglycemia during ischemic stroke increases the stroke's severity and the infarct size in clinical and animal studies. However, no conclusive evidence demonstrates that acute hyperglycemia worsens post-stroke outcomes and increases infarct size in lacunar stroke. In this study, we developed a rat model of lacunar stroke that was induced via the injection of artificial embolic particles during full consciousness. We then used this model to compare the acute influence of hyperglycemia in lacunar stroke and diffuse infarction, by evaluating neurologic behavior and the rate, size, and location of the infarction. The time course of the neurologic deficits was clearly recorded from immediately after induction to 24 h post-stroke in both types of stroke. We found that acute hyperglycemia aggravated the neurologic deficit in diffuse infarction at 24 h after stroke, and also aggravated the cerebral infarct. Furthermore, the infarct volumes of the basal ganglion, thalamus, hippocampus, and cerebellum but not the cortex were positively correlated with serum glucose levels. In contrast, acute hyperglycemia reduced the infarct volume and neurologic symptoms in lacunar stroke within 4 min after stroke induction, and this effect persisted for up to 24 h post-stroke. In conclusion, acute hyperglycemia aggravated the neurologic outcomes in diffuse infarction, although it significantly reduced the size of the cerebral infarct and improved the neurologic deficits in lacunar stroke. PMID:27226775

Phase-Field Simulation of Concentration and Temperature Distribution During Dendritic Growth in a Forced Liquid Metal Flow

NASA Astrophysics Data System (ADS)

Du, Lifei; Zhang, Rong

2014-12-01

A phase-field model with convection is employed to investigate the effect of liquid flow on the dendritic structure formation of a Ni-Cu alloy during rapid solidification. Temperature and solute diffusion are significantly changed with induced liquid metal flow, and distribution changes of concentration and temperature are also analyzed and discussed. The solute segregation is affected due to the concentration diffusion layer thickness change caused by the liquid flow. The flow reduces the solute segregation in the upstream and leads to a fast dendrite growing, while solidifying in the downstream gets constrained with the large solute diffusion layer. Increasing flow velocity increases the asymmetry of dendrite morphology with much more suppressed growth in the downstream. The temperature distribution is also asymmetrical due to the non-uniform latent heat released during solidification coupling with heat diffusion changed by the liquid flow. Therefore, the forced liquid flow significantly affects the dendrite morphology, concentration, and temperature distributions in the solidifying microstructure.

Predicting X-ray diffuse scattering from translation–libration–screw structural ensembles

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

Van Benschoten, Andrew H.; Afonine, Pavel V.; Terwilliger, Thomas C.

2015-07-28

A method of simulating X-ray diffuse scattering from multi-model PDB files is presented. Despite similar agreement with Bragg data, different translation–libration–screw refinement strategies produce unique diffuse intensity patterns. Identifying the intramolecular motions of proteins and nucleic acids is a major challenge in macromolecular X-ray crystallography. Because Bragg diffraction describes the average positional distribution of crystalline atoms with imperfect precision, the resulting electron density can be compatible with multiple models of motion. Diffuse X-ray scattering can reduce this degeneracy by reporting on correlated atomic displacements. Although recent technological advances are increasing the potential to accurately measure diffuse scattering, computational modeling andmore » validation tools are still needed to quantify the agreement between experimental data and different parameterizations of crystalline disorder. A new tool, phenix.diffuse, addresses this need by employing Guinier’s equation to calculate diffuse scattering from Protein Data Bank (PDB)-formatted structural ensembles. As an example case, phenix.diffuse is applied to translation–libration–screw (TLS) refinement, which models rigid-body displacement for segments of the macromolecule. To enable the calculation of diffuse scattering from TLS-refined structures, phenix.tls-as-xyz builds multi-model PDB files that sample the underlying T, L and S tensors. In the glycerophosphodiesterase GpdQ, alternative TLS-group partitioning and different motional correlations between groups yield markedly dissimilar diffuse scattering maps with distinct implications for molecular mechanism and allostery. These methods demonstrate how, in principle, X-ray diffuse scattering could extend macromolecular structural refinement, validation and analysis.« less

Analysis and correction of gradient nonlinearity bias in apparent diffusion coefficient measurements.

PubMed

Malyarenko, Dariya I; Ross, Brian D; Chenevert, Thomas L

2014-03-01

Gradient nonlinearity of MRI systems leads to spatially dependent b-values and consequently high non-uniformity errors (10-20%) in apparent diffusion coefficient (ADC) measurements over clinically relevant field-of-views. This work seeks practical correction procedure that effectively reduces observed ADC bias for media of arbitrary anisotropy in the fewest measurements. All-inclusive bias analysis considers spatial and time-domain cross-terms for diffusion and imaging gradients. The proposed correction is based on rotation of the gradient nonlinearity tensor into the diffusion gradient frame where spatial bias of b-matrix can be approximated by its Euclidean norm. Correction efficiency of the proposed procedure is numerically evaluated for a range of model diffusion tensor anisotropies and orientations. Spatial dependence of nonlinearity correction terms accounts for the bulk (75-95%) of ADC bias for FA = 0.3-0.9. Residual ADC non-uniformity errors are amplified for anisotropic diffusion. This approximation obviates need for full diffusion tensor measurement and diagonalization to derive a corrected ADC. Practical scenarios are outlined for implementation of the correction on clinical MRI systems. The proposed simplified correction algorithm appears sufficient to control ADC non-uniformity errors in clinical studies using three orthogonal diffusion measurements. The most efficient reduction of ADC bias for anisotropic medium is achieved with non-lab-based diffusion gradients. Copyright © 2013 Wiley Periodicals, Inc.

ADC Quantification of the Vertebral Bone Marrow Water Component: Removing the Confounding Effect of Residual Fat.

PubMed

Dieckmeyer, Michael; Ruschke, Stefan; Eggers, Holger; Kooijman, Hendrik; Rummeny, Ernst J; Kirschke, Jan S; Baum, Thomas; Karampinos, Dimitrios C

2017-10-01

To remove the confounding effect of unsuppressed fat on the imaging-based apparent diffusion coefficient (ADC) of the vertebral bone marrow water component when using spectrally selective fat suppression and to compare and validate the proposed quantification strategy against diffusion-weighted magnetic resonance spectroscopy (DW-MRS). Twelve subjects underwent diffusion-weighted imaging (DWI) and DW-MRS of the vertebral bone marrow. A theoretical model was developed to take into account and correct the effects of residual fat on ADC, incorporating additional measurements for proton density fat fraction (PDFF) and water T 2 (T 2w ). Uncorrected and corrected DWI-based ADC was compared with DW-MRS-based ADC using the Bland-Altman method. There was a systematic bias equal to 0.118 ± 0.116 × 10 -3 mm 2 /s between DWI and DW-MRS when no correction was performed. Taking into account measured PDFF and constant T 2w reduced the bias to 0.006 ± 0.128 × 10 -3 mm 2 /s. Using the proposed approach with both individually measured PDFF and T 2w reduced both the bias and the limits of agreement between DWI and DW-MRS (0.018 ± 0.065 × 10 -3 mm 2 /s). By taking into account the presence of residual fat in a modified signal model that incorporates additional individual measurements of PDFF and T 2w , good agreement of imaging-based ADC with MRS-based ADC can be achieved in vertebral bone marrow. Magn Reson Med 78:1432-1441, 2017. © 2016 International Society for Magnetic Resonance in Medicine. © 2016 International Society for Magnetic Resonance in Medicine.

Collective dissolution of microbubbles

NASA Astrophysics Data System (ADS)

Michelin, Sébastien; Guérin, Etienne; Lauga, Eric

2018-04-01

A microscopic bubble of soluble gas always dissolves in finite time in an undersaturated fluid. This diffusive process is driven by the difference between the gas concentration near the bubble, whose value is governed by the internal pressure through Henry's law, and the concentration in the far field. The presence of neighboring bubbles can significantly slow down this process by increasing the effective background concentration and reducing the diffusing flux of dissolved gas experienced by each bubble. We develop theoretical modeling of such diffusive shielding process in the case of small microbubbles whose internal pressure is dominated by Laplace pressure. We first use an exact semianalytical solution to capture the case of two bubbles and analyze in detail the shielding effect as a function of the distance between the bubbles and their size ratio. While we also solve exactly for the Stokes flow around the bubble, we show that hydrodynamic effects are mostly negligible except in the case of almost-touching bubbles. In order to tackle the case of multiple bubbles, we then derive and validate two analytical approximate yet generic frameworks, first using the method of reflections and then by proposing a self-consistent continuum description. Using both modeling frameworks, we examine the dissolution of regular one-, two-, and three-dimensional bubble lattices. Bubbles located at the edge of the lattices dissolve first, while innermost bubbles benefit from the diffusive shielding effect, leading to the inward propagation of a dissolution front within the lattice. We show that diffusive shielding leads to severalfold increases in the dissolution time, which grows logarithmically with the number of bubbles in one-dimensional lattices and algebraically in two and three dimensions, scaling respectively as its square root and 2 /3 power. We further illustrate the sensitivity of the dissolution patterns to initial fluctuations in bubble size or arrangement in the case of large and dense lattices, as well as nonintuitive oscillatory effects.

Permeability-diffusivity modeling vs. fractional anisotropy on white matter integrity assessment and application in schizophrenia.

PubMed

Kochunov, P; Chiappelli, J; Hong, L E

2013-01-01

Diffusion tensor imaging (DTI) assumes a single pool of anisotropically diffusing water to calculate fractional anisotropy (FA) and is commonly used to ascertain white matter (WM) deficits in schizophrenia. At higher b-values, diffusion-signal decay becomes bi-exponential, suggesting the presence of two, unrestricted and restricted, water pools. Theoretical work suggests that semi-permeable cellular membrane rather than the presence of two physical compartments is the cause. The permeability-diffusivity (PD) parameters measured from bi-exponential modeling may offer advantages, over traditional DTI-FA, in identifying WM deficits in schizophrenia. Imaging was performed in N = 26/26 patients/controls (age = 20-61 years, average age = 40.5 ± 12.6). Imaging consisted of fifteen b-shells: b = 250-3800 s/mm(2) with 30 directions/shell, covering seven slices of mid-sagittal corpus callosum (CC) at 1.7 × 1.7 × 4.6 mm. 64-direction DTI was also collected. Permeability-diffusivity-index (PDI), the ratio of restricted to unrestricted apparent diffusion coefficients, and the fraction of unrestricted compartment (Mu) were calculated for CC and cingulate gray matter (GM). FA values for CC were calculated using tract-based-spatial-statistics. Patients had significantly reduced PDI in CC (p ≅ 10(- 4)) and cingulate GM (p = 0.002), while differences in CC FA were modest (p ≅ .03). There was no group-related difference in Mu. Additional theoretical-modeling analysis suggested that reduced PDI in patients may be caused by reduced cross-membrane water molecule exchanges. PDI measurements for cerebral WM and GM yielded more robust patient-control differences than DTI-FA. Theoretical work offers an explanation that patient-control PDI differences should implicate abnormal active membrane permeability. This would implicate abnormal activities in ion-channels that use water as substrate for ion exchange, in cerebral tissues of schizophrenia patients.

Diffusion tensor imaging reveals adolescent binge ethanol-induced brain structural integrity alterations in adult rats that correlate with behavioral dysfunction.

PubMed

Vetreno, Ryan P; Yaxley, Richard; Paniagua, Beatriz; Crews, Fulton T

2016-07-01

Adolescence is characterized by considerable brain maturation that coincides with the development of adult behavior. Binge drinking is common during adolescence and can have deleterious effects on brain maturation because of the heightened neuroplasticity of the adolescent brain. Using an animal model of adolescent intermittent ethanol [AIE; 5.0 g/kg, intragastric, 20 percent EtOH w/v; 2 days on/2 days off from postnatal day (P)25 to P55], we assessed the adult brain structural volumes and integrity on P80 and P220 using diffusion tensor imaging (DTI). While we did not observe a long-term effect of AIE on structural volumes, AIE did reduce axial diffusivity (AD) in the cerebellum, hippocampus and neocortex. Radial diffusivity (RD) was reduced in the hippocampus and neocortex of AIE-treated animals. Prior AIE treatment did not affect fractional anisotropy (FA), but did lead to long-term reductions of mean diffusivity (MD) in both the cerebellum and corpus callosum. AIE resulted in increased anxiety-like behavior and diminished object recognition memory, the latter of which was positively correlated with DTI measures. Across aging, whole brain volumes increased, as did volumes of the corpus callosum and neocortex. This was accompanied by age-associated AD reductions in the cerebellum and neocortex as well as RD and MD reductions in the cerebellum. Further, we found that FA increased in both the cerebellum and corpus callosum as rats aged from P80 to P220. Thus, both age and AIE treatment caused long-term changes to brain structural integrity that could contribute to cognitive dysfunction. © 2015 Society for the Study of Addiction.

Optimizing Filter-Probe Diffusion Weighting in the Rat Spinal Cord for Human Translation

PubMed Central

Budde, Matthew D.; Skinner, Nathan P.; Muftuler, L. Tugan; Schmit, Brian D.; Kurpad, Shekar N.

2017-01-01

Diffusion tensor imaging (DTI) is a promising biomarker of spinal cord injury (SCI). In the acute aftermath, DTI in SCI animal models consistently demonstrates high sensitivity and prognostic performance, yet translation of DTI to acute human SCI has been limited. In addition to technical challenges, interpretation of the resulting metrics is ambiguous, with contributions in the acute setting from both axonal injury and edema. Novel diffusion MRI acquisition strategies such as double diffusion encoding (DDE) have recently enabled detection of features not available with DTI or similar methods. In this work, we perform a systematic optimization of DDE using simulations and an in vivo rat model of SCI and subsequently implement the protocol to the healthy human spinal cord. First, two complementary DDE approaches were evaluated using an orientationally invariant or a filter-probe diffusion encoding approach. While the two methods were similar in their ability to detect acute SCI, the filter-probe DDE approach had greater predictive power for functional outcomes. Next, the filter-probe DDE was compared to an analogous single diffusion encoding (SDE) approach, with the results indicating that in the spinal cord, SDE provides similar contrast with improved signal to noise. In the SCI rat model, the filter-probe SDE scheme was coupled with a reduced field of view (rFOV) excitation, and the results demonstrate high quality maps of the spinal cord without contamination from edema and cerebrospinal fluid, thereby providing high sensitivity to injury severity. The optimized protocol was demonstrated in the healthy human spinal cord using the commercially-available diffusion MRI sequence with modifications only to the diffusion encoding directions. Maps of axial diffusivity devoid of CSF partial volume effects were obtained in a clinically feasible imaging time with a straightforward analysis and variability comparable to axial diffusivity derived from DTI. Overall, the results and optimizations describe a protocol that mitigates several difficulties with DTI of the spinal cord. Detection of acute axonal damage in the injured or diseased spinal cord will benefit the optimized filter-probe diffusion MRI protocol outlined here. PMID:29311786

Atomisti modeling of the microstructure and transport properties of lead-free solder alloys

NASA Astrophysics Data System (ADS)

Sellers, Michael S.

Damage mechanics models of lead-free solder joints in nanoelectronics continue to improve, and in doing so begin to utilize quantitative values describing processes at the atomic level, governing phenomena like electromigration and thermomigration. In particular, knowledge of the transport properties of specific microstructures helps continuum level models fully describe these larger-scale damage phenomena via multi-scale analysis. For example, diffusivities for different types of grain boundaries (fast diffusion paths for solvent and solute atoms, and vacancies), and a description of the boundary structure as a function of temperature, are critical in modeling solder microstructure evolution and, consequently, joint behavior under extreme temperature and electric current. Moreover, for damage that develops at larger length scales, surface energies and diffusivities play important roles in characterizing void stability and morphology. Unfortunately, experiments that investigate these kind of damage phenomena in the atomistic realm are often inconsistent or unable to directly quantify important parameters. One case is the particular transport and structural properties of grain boundaries in Sn (the main component in lead-free solder alloys) and their behavior in the presence of Ag and Cu impurities. This information is crucial in determining accurate diffusivity values for the common SnAgCu (SAC) type solder. Although an average grain boundary diffusivity has been reported for polycrystalline Sn in several works, the value for grain boundary width is estimated and specific diffusivities for boundaries known to occur in Sn have not been reported, to say nothing of solute effects on Sn diffusivity and grain boundary structure. Similarly, transport properties of Sn surfaces remain relatively uninvestigated as well. These gaps and inconsistencies in atomistic data must be remedied for micro- and macro-scale modeling to improve. As a complement to experimental work and possessing the ability to fill in the gaps, molecular simulation serves to reinforce experimental predictions and provide insight into the atomistic processes that govern studied phenomena. In the present body of work, we employ molecular statics and dynamics simulations in the characterization and computation of betaSn surface energies and surface diffusivities, the determination of diffusivities and structural properties of specific betaSn grain boundaries, and the investigation of Cu and Ag solute effects on betaSn grain boundaries. In our study of betaSn surfaces, energies for low number Miller index surfaces are computed and the (100) plane is found to have the lowest un-relaxed energy. We then find that two simple hopping mechanisms dominate adatom diffusion transitions on this surface. For each, we determine hopping rates of the adatom and compute its tracer diffusivity. Our work on grain boundaries investigates the self-diffusion properties and structure of several betaSn symmetric tilt grain boundaries using molecular dynamics simulations. We find that larger diffusive widths are exhibited by higher excess potential energy grain boundaries. Diffusivities in the directions parallel to the interface plane are also computed and activation energies are found with the Arrhenius relation. These are shown to agree well with experimental data. Finally, we examine the effect that solute atoms of Ag and Cu have on the microstructure of betaSn. Excess energies of the (101) symmetric tilt betaSn grain boundary are computed as a function of solute concentration at the interface, and we show that Ag lowers the energy at a greater rate than Cu. We also quantify segregation enthalpies and critical solute concentrations (where the excess energy of the boundary is reduced to zero). The effect of solute type on shear stress is also examined, and we show that solute has a strong effect on the stabilization of higher energy grain boundaries under shear stress. We then look at the self-diffusivity of Sn in the (101) symmetric tilt betaSn grain boundary and show that adding both Ag or Cu decrease the grain boundary self-diffusivity of Sn as solute amount in the interface increases. Effects of larger concentrations of Cu in particular are also investigated.

Effect of screens in wide-angle diffusers

NASA Technical Reports Server (NTRS)

Schubauer, G B; Spangenberg, W G

1949-01-01

An experimental investigation at low airspeeds was made of the filling effect observed when a screen or similar resistance is placed across a diffuser. The filling effect is found to be real in that screens can prevent separation or restore separated flow in diffusers even of extreme divergence and to depend principally on screen location and pressure-drop coefficient of the screen. Results are given for three different diffusers of circular cross section with a variety of screen arrangements. Effects of single screens and multiple screens are shown. The mechanics of the filling effect is explained, and possible efficiencies are discussed. Results of arrangements of multiple screens in wide-angle diffusers are given to show a possible application to damping screens as used in wind tunnels to reduce turbulence. (author)

A Systematic Procedure to Describe Shale Gas Permeability Evolution during the Production Process

NASA Astrophysics Data System (ADS)

Jia, B.; Tsau, J. S.; Barati, R.

2017-12-01

Gas flow behavior in shales is complex due to the multi-physics nature of the process. Pore size reduces as the in-situ stress increases during the production process, which will reduce intrinsic permeability of the porous media. Slip flow/pore diffusion enhances gas apparent permeability, especially under low reservoir pressures. Adsorption not only increases original gas in place but also influences gas flow behavior because of the adsorption layer. Surface diffusion between free gas and adsorption phase enhances gas permeability. Pore size reduction and the adsorption layer both have complex impacts on gas apparent permeability and non-Darcy flow might be a major component in nanopores. Previously published literature is generally incomplete in terms of coupling of all these four physics with fluid flow during gas production. This work proposes a methodology to simultaneously take them into account to describe a permeability evolution process. Our results show that to fully describe shale gas permeability evolution during gas production, three sets of experimental data are needed initially: 1) intrinsic permeability under different in-situ stress, 2) adsorption isotherm under reservoir conditions and 3) surface diffusivity measurement by the pulse-decay method. Geomechanical effects, slip flow/pore diffusion, adsorption layer and surface diffusion all play roles affecting gas permeability. Neglecting any of them might lead to misleading results. The increasing in-situ stress during shale gas production is unfavorable to shale gas flow process. Slip flow/pore diffusion is important for gas permeability under low pressures in the tight porous media. They might overwhelm the geomechanical effect and enhance gas permeability at low pressures. Adsorption layer reduces the gas permeability by reducing the effective pore size, but the effect is limited. Surface diffusion increases gas permeability more under lower pressures. The total gas apparent permeability might keep increasing during the gas production process when the surface diffusivity is larger than a critical value. We believe that our workflow proposed in this study will help describe shale gas permeability evolution considering all the underlying physics altogether.

What Can the Diffusion Model Tell Us About Prospective Memory?

PubMed Central

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

2011-01-01

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 analyze 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 tradeoffs. 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 (Smith, 2003) was analyzed 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 RT. PMID:21443332

Effect of users' opinion evolution on information diffusion in online social networks

NASA Astrophysics Data System (ADS)

Zhu, Hengmin; Kong, Yuehan; Wei, Jing; Ma, Jing

2018-02-01

The process of topic propagation always interweaves information diffusion and opinion evolution, but most previous works studied the models of information diffusion and opinion evolution separately, and seldom focused on their interaction of each other. To shed light on the effect of users' opinion evolution on information diffusion in online social networks, we proposed a model which incorporates opinion evolution into the process of topic propagation. Several real topics propagating on Sina Microblog were collected to analyze individuals' propagation intentions, and different propagation intentions were considered in the model. The topic propagation was simulated to explore the impact of different opinion distributions and intervention with opposite opinion on information diffusion. Results show that the topic with one-sided opinions can spread faster and more widely, and intervention with opposite opinion is an effective measure to guide the topic propagation. The earlier to intervene, the more effectively the topic propagation would be guided.

Modeling of photon migration in the human lung using a finite volume solver

NASA Astrophysics Data System (ADS)

Sikorski, Zbigniew; Furmanczyk, Michal; Przekwas, Andrzej J.

2006-02-01

The application of the frequency domain and steady-state diffusive optical spectroscopy (DOS) and steady-state near infrared spectroscopy (NIRS) to diagnosis of the human lung injury challenges many elements of these techniques. These include the DOS/NIRS instrument performance and accurate models of light transport in heterogeneous thorax tissue. The thorax tissue not only consists of different media (e.g. chest wall with ribs, lungs) but its optical properties also vary with time due to respiration and changes in thorax geometry with contusion (e.g. pneumothorax or hemothorax). This paper presents a finite volume solver developed to model photon migration in the diffusion approximation in heterogeneous complex 3D tissues. The code applies boundary conditions that account for Fresnel reflections. We propose an effective diffusion coefficient for the void volumes (pneumothorax) based on the assumption of the Lambertian diffusion of photons entering the pleural cavity and accounting for the local pleural cavity thickness. The code has been validated using the MCML Monte Carlo code as a benchmark. The code environment enables a semi-automatic preparation of 3D computational geometry from medical images and its rapid automatic meshing. We present the application of the code to analysis/optimization of the hybrid DOS/NIRS/ultrasound technique in which ultrasound provides data on the localization of thorax tissue boundaries. The code effectiveness (3D complex case computation takes 1 second) enables its use to quantitatively relate detected light signal to absorption and reduced scattering coefficients that are indicators of the pulmonary physiologic state (hemoglobin concentration and oxygenation).

Fem Simulation of Triple Diffusive Natural Convection Along Inclined Plate in Porous Medium: Prescribed Surface Heat, Solute and Nanoparticles Flux

NASA Astrophysics Data System (ADS)

Goyal, M.; Goyal, R.; Bhargava, R.

2017-12-01

In this paper, triple diffusive natural convection under Darcy flow over an inclined plate embedded in a porous medium saturated with a binary base fluid containing nanoparticles and two salts is studied. The model used for the nanofluid is the one which incorporates the effects of Brownian motion and thermophoresis. In addition, the thermal energy equations include regular diffusion and cross-diffusion terms. The vertical surface has the heat, mass and nanoparticle fluxes each prescribed as a power law function of the distance along the wall. The boundary layer equations are transformed into a set of ordinary differential equations with the help of group theory transformations. A wide range of parameter values are chosen to bring out the effect of buoyancy ratio, regular Lewis number and modified Dufour parameters of both salts and nanofluid parameters with varying angle of inclinations. The effects of parameters on the velocity, temperature, solutal and nanoparticles volume fraction profiles, as well as on the important parameters of heat and mass transfer, i.e., the reduced Nusselt, regular and nanofluid Sherwood numbers, are discussed. Such problems find application in extrusion of metals, polymers and ceramics, production of plastic films, insulation of wires and liquid packaging.

Ultrasound speckle reduction based on fractional order differentiation.

PubMed

Shao, Dangguo; Zhou, Ting; Liu, Fan; Yi, Sanli; Xiang, Yan; Ma, Lei; Xiong, Xin; He, Jianfeng

2017-07-01

Ultrasound images show a granular pattern of noise known as speckle that diminishes their quality and results in difficulties in diagnosis. To preserve edges and features, this paper proposes a fractional differentiation-based image operator to reduce speckle in ultrasound. An image de-noising model based on fractional partial differential equations with balance relation between k (gradient modulus threshold that controls the conduction) and v (the order of fractional differentiation) was constructed by the effective combination of fractional calculus theory and a partial differential equation, and the numerical algorithm of it was achieved using a fractional differential mask operator. The proposed algorithm has better speckle reduction and structure preservation than the three existing methods [P-M model, the speckle reducing anisotropic diffusion (SRAD) technique, and the detail preserving anisotropic diffusion (DPAD) technique]. And it is significantly faster than bilateral filtering (BF) in producing virtually the same experimental results. Ultrasound phantom testing and in vivo imaging show that the proposed method can improve the quality of an ultrasound image in terms of tissue SNR, CNR, and FOM values.

Cellular automata approach for the dynamics of HIV infection under antiretroviral therapies: The role of the virus diffusion

NASA Astrophysics Data System (ADS)

González, Ramón E. R.; de Figueirêdo, Pedro Hugo; Coutinho, Sérgio

2013-10-01

We study a cellular automata model to test the timing of antiretroviral therapy strategies for the dynamics of infection with human immunodeficiency virus (HIV). We focus on the role of virus diffusion when its population is included in previous cellular automata model that describes the dynamics of the lymphocytes cells population during infection. This inclusion allows us to consider the spread of infection by the virus-cell interaction, beyond that which occurs by cell-cell contagion. The results show an acceleration of the infectious process in the absence of treatment, but show better efficiency in reducing the risk of the onset of AIDS when combined antiretroviral therapies are used even with drugs of low effectiveness. Comparison of results with clinical data supports the conclusions of this study.

Modelling of nectarine drying under near infrared - Vacuum conditions.

PubMed

Alaei, Behnam; Chayjan, Reza Amiri

2015-01-01

Drying of nectarine slices was performed to determine the thermal and physical properties in order to reduce product deterioration due to chemical reactions, facilitate storage and lower transportation costs. Because nectarine slices are sensitive to heat with long drying period, the selection of a suitable drying approach is a challenging task. Infrared-vacuum drying can be used as an appropriate method for susceptible materials with high moisture content such as nectarine slices. Modelling of nectarine slices drying was carried out in a thin layer near infraredvacuum conditions. Drying of the samples was implemented at the absolute pressures of 20, 40 and 60 kPa and drying temperatures of 50, 60 and 70°C. Drying behaviour of nectarine slices, as well as the effect of drying conditions on moisture loss trend, drying rate, effective diffusion coefficient, activation energy, shrinkage, colour and energy consumption of nectarine slices, dried in near infrared-vacuum dryer are discussed in this study. Six mathematical models were used to predict the moisture ratio of the samples in thin layer drying. The Midilli model had supremacy in prediction of nectarine slices drying behaviour. The maximum drying rates of the samples were between 0.014-0.047 gwater/gdry material·min. Effective moisture diffusivity of the samples was estimated in the ranges of 2.46·10-10 to 6.48·10-10 m2/s. Activation energy were computed between 31.28 and 35.23 kJ/mol. Minimum shrinkage (48.4%) and total colour difference (15.1) were achieved at temperature of 50°C and absolute pressure of 20 kPa. Energy consumption of the tests was estimated in the ranges of 0.129 to 0.247 kWh. Effective moisture diffusivity was increased with decrease of vacuum pressure and increase of drying temperature but effect of drying temperature on effective moisture diffusivity of nectarine slices was more than vacuum pressure. Activation energy was decreased with decrease in absolute pressure. Total colour difference and shrinkage of nectarine slices on near infrared-vacuum drying was decreased with decrease of vacuum pressure and decrease of drying temperature.

Reduction of molecular gas diffusion through gaskets in leaf gas exchange cuvettes by leaf-mediated pores.

PubMed

Boesgaard, Kristine S; Mikkelsen, Teis N; Ro-Poulsen, Helge; Ibrom, Andreas

2013-07-01

There is an ongoing debate on how to correct leaf gas exchange measurements for the unavoidable diffusion leakage that occurs when measurements are done in non-ambient CO2 concentrations. In this study, we present a theory on how the CO2 diffusion gradient over the gasket is affected by leaf-mediated pores (LMP) and how LMP reduce diffusive exchange across the gaskets. Recent discussions have so far neglected the processes in the quasi-laminar boundary layer around the gasket. Counter intuitively, LMP reduce the leakage through gaskets, which can be explained by assuming that the boundary layer at the exterior of the cuvette is enriched with air from the inside of the cuvette. The effect can thus be reduced by reducing the boundary layer thickness. The theory clarifies conflicting results from earlier studies. We developed leaf adaptor frames that eliminate LMP during measurements on delicate plant material such as grass leaves with circular cross section, and the effectiveness is shown with respiration measurements on a harp of Deschampsia flexuosa leaves. We conclude that the best solution for measurements with portable photosynthesis systems is to avoid LMP rather than trying to correct for the effects. © 2013 John Wiley & Sons Ltd.

Predicting X-ray diffuse scattering from translation–libration–screw structural ensembles

PubMed Central

Van Benschoten, Andrew H.; Afonine, Pavel V.; Terwilliger, Thomas C.; Wall, Michael E.; Jackson, Colin J.; Sauter, Nicholas K.; Adams, Paul D.; Urzhumtsev, Alexandre; Fraser, James S.

2015-01-01

Identifying the intramolecular motions of proteins and nucleic acids is a major challenge in macromolecular X-ray crystallography. Because Bragg diffraction describes the average positional distribution of crystalline atoms with imperfect precision, the resulting electron density can be compatible with multiple models of motion. Diffuse X-ray scattering can reduce this degeneracy by reporting on correlated atomic displacements. Although recent technological advances are increasing the potential to accurately measure diffuse scattering, computational modeling and validation tools are still needed to quantify the agreement between experimental data and different parameterizations of crystalline disorder. A new tool, phenix.diffuse, addresses this need by employing Guinier’s equation to calculate diffuse scattering from Protein Data Bank (PDB)-formatted structural ensembles. As an example case, phenix.diffuse is applied to translation–libration–screw (TLS) refinement, which models rigid-body displacement for segments of the macromolecule. To enable the calculation of diffuse scattering from TLS-refined structures, phenix.tls_as_xyz builds multi-model PDB files that sample the underlying T, L and S tensors. In the glycerophos­phodiesterase GpdQ, alternative TLS-group partitioning and different motional correlations between groups yield markedly dissimilar diffuse scattering maps with distinct implications for molecular mechanism and allostery. These methods demonstrate how, in principle, X-ray diffuse scattering could extend macromolecular structural refinement, validation and analysis. PMID:26249347

Predicting X-ray diffuse scattering from translation–libration–screw structural ensembles

DOE PAGES

Van Benschoten, Andrew H.; Afonine, Pavel V.; Terwilliger, Thomas C.; ...

2015-07-28

Identifying the intramolecular motions of proteins and nucleic acids is a major challenge in macromolecular X-ray crystallography. Because Bragg diffraction describes the average positional distribution of crystalline atoms with imperfect precision, the resulting electron density can be compatible with multiple models of motion. Diffuse X-ray scattering can reduce this degeneracy by reporting on correlated atomic displacements. Although recent technological advances are increasing the potential to accurately measure diffuse scattering, computational modeling and validation tools are still needed to quantify the agreement between experimental data and different parameterizations of crystalline disorder. A new tool, phenix.diffuse, addresses this need by employing Guinier'smore » equation to calculate diffuse scattering from Protein Data Bank (PDB)-formatted structural ensembles. As an example case, phenix.diffuse is applied to translation–libration–screw (TLS) refinement, which models rigid-body displacement for segments of the macromolecule. To enable the calculation of diffuse scattering from TLS-refined structures, phenix.tls_as_xyz builds multi-model PDB files that sample the underlying T, L and S tensors. In the glycerophosphodiesterase GpdQ, alternative TLS-group partitioning and different motional correlations between groups yield markedly dissimilar diffuse scattering maps with distinct implications for molecular mechanism and allostery. In addition, these methods demonstrate how, in principle, X-ray diffuse scattering could extend macromolecular structural refinement, validation and analysis.« less

Repeatability of the efficiency of columns packed with sub-3μm core-shell particles: Part III. 2.7μm Poroshell 120 EC-C18 particles in 4.6mm and 2.1mm × 100mm column formats.

PubMed

Gritti, Fabrice; Guiochon, Georges

2012-08-24

As part of an investigation of the column-to-column repeatability of the efficiency of columns packed with sub-3μm shell particles, the parameters of the mass transfer kinetics of twelve columns packed with the same batch of 2.7μm Poroshell 120 EC-C(18) particles (Agilent Technologies, Little Fall, DE, USA) were sequentially measured, using columns provided by the manufacturers that were representative of the efficiency distribution given by the quality test control. The reduced longitudinal diffusion term (B) was measured using the peak parking (PP) method; the reduced solid-liquid mass transfer resistance term (C) was given by a combination of the PP results and the most accurate model of effective diffusion in ternary composite materials. The overall eddy diffusion term (A) was obtained by subtraction of these two HETP terms from the overall reduced HETP derived from the peak moments measured by numerical integration of the entire peak profiles. The results demonstrate that the dispersion of the column efficiencies is a result of the random nature of the packing process and the eddy diffusion term resulting from the lack of homogeneity of the column bed. At the highest reduced velocity achieved for small analytes, the relative standard deviations (RSD) of the eddy diffusion term for the 2.1mm I.D. columns were ca. 3 and 11% (with average values h(eddy)= 2.5 and 13.5) for naphthalene (k=3) and uracil (k=0), respectively. For the 4.6mm I.D. columns, these RSDs were 5 and 13%, respectively, with average values h(eddy)= 1.4 and 2.9. For insulin at reduced velocities as high as 160, the RSDs of the total reduced plate heights were 3 and 8% for the 2.1 and 4.6mm I.D. columns, respectively. Copyright © 2012 Elsevier B.V. All rights reserved.

Diffusion in Brain Extracellular Space

PubMed Central

Syková, Eva; Nicholson, Charles

2009-01-01

Diffusion in the extracellular space (ECS) of the brain is constrained by the volume fraction and the tortuosity and a modified diffusion equation represents the transport behavior of many molecules in the brain. Deviations from the equation reveal loss of molecules across the blood-brain barrier, through cellular uptake, binding or other mechanisms. Early diffusion measurements used radiolabeled sucrose and other tracers. Presently, the real-time iontophoresis (RTI) method is employed for small ions and the integrative optical imaging (IOI) method for fluorescent macromolecules, including dextrans or proteins. Theoretical models and simulations of the ECS have explored the influence of ECS geometry, effects of dead-space microdomains, extracellular matrix and interaction of macromolecules with ECS channels. Extensive experimental studies with the RTI method employing the cation tetramethylammonium (TMA) in normal brain tissue show that the volume fraction of the ECS typically is about 20% and the tortuosity about 1.6 (i.e. free diffusion coefficient of TMA is reduced by 2.6), although there are regional variations. These parameters change during development and aging. Diffusion properties have been characterized in several interventions, including brain stimulation, osmotic challenge and knockout of extracellular matrix components. Measurements have also been made during ischemia, in models of Alzheimer's and Parkinson's diseases and in human gliomas. Overall, these studies improve our conception of ECS structure and the roles of glia and extracellular matrix in modulating the ECS microenvironment. Knowledge of ECS diffusion properties are valuable in contexts ranging from understanding extrasynaptic volume transmission to the development of paradigms for drug delivery to the brain. PMID:18923183

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

Lienhard, D. M.; Huisman, A. J.; Krieger, U. K.

New measurements of water diffusion in secondary organic aerosol (SOA) material produced by oxidation of α-pinene and in a number of organic/inorganic model mixtures (3-methylbutane-1,2,3-tricarboxylic acid (3-MBTCA), levoglucosan, levoglucosan/NH 4HSO 4, raffinose) are presented. These indicate that water diffusion coefficients are determined by several properties of the aerosol substance and cannot be inferred from the glass transition temperature or bouncing properties. Our results suggest that water diffusion in SOA particles is faster than often assumed and imposes no significant kinetic limitation on water uptake and release at temperatures above 220 K. The fast diffusion of water suggests that heterogeneous icemore » nucleation on a glassy core is very unlikely in these systems. At temperatures below 220 K, model simulations of SOA particles suggest that heterogeneous ice nucleation may occur in the immersion mode on glassy cores which remain embedded in a liquid shell when experiencing fast updraft velocities. The particles absorb significant quantities of water during these updrafts which plasticize their outer layers such that these layers equilibrate readily with the gas phase humidity before the homogeneous ice nucleation threshold is reached. Glass formation is thus unlikely to restrict homogeneous ice nucleation. Only under most extreme conditions near the very high tropical tropopause may the homogeneous ice nucleation rate coefficient be reduced as a consequence of slow condensed-phase water diffusion. Since the differences between the behavior limited or non limited by diffusion are small even at the very high tropical tropopause, condensed-phase water diffusivity is unlikely to have significant consequences on the direct climatic effects of SOA particles under tropospheric conditions.« less

Reactive diffusion in the presence of a diffusion barrier: Experiment and model

NASA Astrophysics Data System (ADS)

Mangelinck, D.; Luo, T.; Girardeaux, C.

2018-05-01

Reactions in thin films and diffusion barriers are important for applications such as protective coatings, electrical contact, and interconnections. In this work, the effect of a barrier on the kinetics of the formation for a single phase by reactive diffusion is investigated from both experimental and modeling point of views. Two types of diffusion barriers are studied: (i) a thin layer of W deposited between a Ni film and Si substrate and (ii) Ni alloy films, Ni(1%W) and Ni(5%Pt), that form a diffusion barrier during the reaction with the Si substrate. The effect of the barriers on the kinetics of δ-Ni2Si formation is determined by in situ X ray diffraction and compared to models that explain the kinetic slowdown induced by both types of barrier. A linear parabolic growth is found for the deposited barrier with an increasing linear contribution for increasing barrier thickness. On the contrary, the growth is mainly parabolic for the barrier formed by the reaction between an alloy film and the substrate. The permeability of the two types of barrier is determined and discussed. The developed models fit well with the dedicated model experiments, leading to a better understanding of the barrier effect on the reactive diffusion and allowing us to predict the barrier behaviour in various applications.

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

NASA Technical Reports Server (NTRS)

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

1992-01-01

Guiding-center simulations of stormtime transport of ring-current and radiation-belt ions having first adiabatic invariants mu is approximately greater than 15 MeV/G (E is approximately greater than 165 keV at L is approximately 3) are surprisingly well described (typically within a factor of approximately less than 4) by the quasilinear theory of radial diffusion. This holds even for the case of an individual model storm characterized by substorm-associated impulses in the convection electric field, provided that the actual spectrum of the electric field is incorporated in the quasilinear theory. Correction of the quasilinear diffusion coefficient D(sub LL)(sup ql) for drift-resonance broadening (so as to define D(sub LL)(sup ql)) reduced the typical discrepancy with the diffusion coefficients D(sub LL)(sup sim) deduced from guiding-center simulations of representative-particle trajectories to a factor of approximately 3. The typical discrepancy was reduced to a factor of approximately 1.4 by averaging D(sub LL)(sup sim), D(sub LL)(sup ql), and D(sub LL)(sup rb) over an ensemble of model storms characterized by different (but statistically equivalent) sets of substorm-onset times.

Viscous organic aerosol particles in the upper troposphere: diffusivity-controlled water uptake and ice nucleation?

DOE PAGES

Lienhard, D. M.; Huisman, A. J.; Krieger, U. K.; ...

2015-01-01

New measurements of water diffusion in secondary organic aerosol (SOA) material produced by oxidation of α-pinene and in a number of organic/inorganic model mixtures (3-methylbutane-1,2,3-tricarboxylic acid (3-MBTCA), levoglucosan, levoglucosan/NH 4HSO 4, raffinose) are presented. These indicate that water diffusion coefficients are determined by several properties of the aerosol substance and cannot be inferred from the glass transition temperature or bouncing properties. Our results suggest that water diffusion in SOA particles is faster than often assumed and imposes no significant kinetic limitation on water uptake and release at temperatures above 220 K. The fast diffusion of water suggests that heterogeneous icemore » nucleation on a glassy core is very unlikely in these systems. At temperatures below 220 K, model simulations of SOA particles suggest that heterogeneous ice nucleation may occur in the immersion mode on glassy cores which remain embedded in a liquid shell when experiencing fast updraft velocities. The particles absorb significant quantities of water during these updrafts which plasticize their outer layers such that these layers equilibrate readily with the gas phase humidity before the homogeneous ice nucleation threshold is reached. Glass formation is thus unlikely to restrict homogeneous ice nucleation. Only under most extreme conditions near the very high tropical tropopause may the homogeneous ice nucleation rate coefficient be reduced as a consequence of slow condensed-phase water diffusion. Since the differences between the behavior limited or non limited by diffusion are small even at the very high tropical tropopause, condensed-phase water diffusivity is unlikely to have significant consequences on the direct climatic effects of SOA particles under tropospheric conditions.« less

Evaluation of diffusion models in breast cancer.

PubMed

Panek, Rafal; Borri, Marco; Orton, Matthew; O'Flynn, Elizabeth; Morgan, Veronica; Giles, Sharon L; deSouza, Nandita; Leach, Martin O; Schmidt, Maria A

2015-08-01

The purpose of this study is to investigate whether the microvascular pseudodiffusion effects resulting with non-monoexponential behavior are present in breast cancer, taking into account tumor spatial heterogeneity. Additionally, methodological factors affecting the signal in low and high diffusion-sensitizing gradient ranges were explored in phantom studies. The effect of eddy currents and accuracy of b-value determination using a multiple b-value diffusion-weighted MR imaging sequence were investigated in test objects. Diffusion model selection and noise were then investigated in volunteers (n = 5) and breast tumor patients (n = 21) using the Bayesian information criterion. 54.3% of lesion voxels were best fitted by a monoexponential, 26.2% by a stretched-exponential, and 19.5% by a biexponential intravoxel incoherent motion (IVIM) model. High correlation (0.92) was observed between diffusion coefficients calculated using mono- and stretched-exponential models and moderate (0.59) between monoexponential and IVIM (medians: 0.96/0.84/0.72 × 10(-3) mm(2)/s, respectively). Distortion due to eddy currents depended on the direction of the diffusion gradient and displacement varied between 1 and 6 mm for high b-value images. Shift in the apparent diffusion coefficient due to intrinsic field gradients was compensated for by averaging diffusion data obtained from opposite directions. Pseudodiffusion and intravoxel heterogeneity effects were not observed in approximately half of breast cancer and normal tissue voxels. This result indicates that stretched and IVIM models should be utilized in regional analysis rather than global tumor assessment. Cross terms between diffusion-sensitization gradients and other imaging or susceptibility-related gradients are relevant in clinical protocols, supporting the use of geometric averaging of diffusion-weighted images acquired with diffusion-sensitization gradients in opposite directions.

Temperature effects on multiphase reactions of organic molecular markers: A modeling study

NASA Astrophysics Data System (ADS)

Pratap, Vikram; Chen, Ying; Yao, Guangming; Nakao, Shunsuke

2018-04-01

Various molecular markers are used in source apportionment studies. In early studies, molecular markers were assumed to be inert. However, recent studies suggest that molecular markers can decay rapidly through multiphase reactions, which makes interpretation of marker measurements challenging. This study presents a simplified model to account for the effects of temperature and relative humidity on the lifetime of molecular markers through a shift in gas-particle partitioning as well as a change in viscosity of the condensed phase. As a model case, this study examines the stability of levoglucosan, a key marker species of biomass burning, over a wide temperature range relevant to summertime and wintertime. Despite the importance of wood combustion for space heating in winter, the lifetime of levoglucosan in wintertime is not well understood. The model predicts that in low-temperature conditions, levoglucosan predominantly remains in the particle phase, and therefore its loss due to gas-phase oxidation reactions is significantly reduced. Furthermore, the movement of the levoglucosan from the bulk of the particle to the particle surface is reduced due to low diffusivity in the semi-solid state. The simplified model developed in this study reasonably reproduces upper and lower bounds of the lifetime of levoglucosan investigated in previous studies. The model results show that the levoglucosan depletion after seven days reduces significantly from ∼98% at 25 °C to <1% at 0 °C under dry conditions. The depletion of levoglucosan increases at higher relative humidities. However, at temperatures below 0 °C, levoglucosan appears to be a useful marker (lifetime > 1 week) even at 60% relative humidity irrespective of the assumed fragility parameter D that controls estimated diffusivity. The model shows that lifetime of an organic molecular marker strongly depends on assumed D especially when a semi-volatile marker is in semi-solid organic aerosol.

In Situ Effective Diffusion Coefficient Profiles in Live Biofilms Using Pulsed-Field Gradient Nuclear Magnetic Resonance

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

Renslow, Ryan S.; Majors, Paul D.; McLean, Jeffrey S.

2010-08-15

Diffusive mass transfer in biofilms is characterized by the effective diffusion coefficient. It is well-documented that the effective diffusion coefficient can vary by location in a biofilm. The current literature is dominated by effective diffusion coefficient measurements for distinct cell clusters and stratified biofilms showing this spatial variation. Regardless of whether distinct cell clusters or surface-averaging methods are used, position-dependent measurements of the effective diffusion coefficient are currently: 1) invasive to the biofilm, 2) performed under unnatural conditions, 3) lethal to cells, and/or 4) spatially restricted to only certain regions of the biofilm. Invasive measurements can lead to inaccurate resultsmore » and prohibit further (time dependent) measurements which are important for the mathematical modeling of biofilms. In this study our goals were to: 1) measure the effective diffusion coefficient for water in live biofilms, 2) monitor how the effective diffusion coefficient changes over time under growth conditions, and 3) correlate the effective diffusion coefficient with depth in the biofilm. We measured in situ two-dimensional effective diffusion coefficient maps within Shewanella oneidensis MR-1biofilms using pulsed-field gradient nuclear magnetic resonance methods, and used them to calculate surface-averaged relative effective diffusion coefficient (Drs) profiles. We found that 1) Drs decreased from the top of the biofilm to the bottom, 2) Drs profiles differed for biofilms of different ages, 3) Drs profiles changed over time and generally decreased with time, 4) all the biofilms showed very similar Drs profiles near the top of the biofilm, and 5) the Drs profile near the bottom of the biofilm was different for each biofilm. Practically, our results demonstrate that advanced biofilm models should use a variable effective diffusivity which changes with time and location in the biofilm.« less

The effect of metal (hydr)oxide nano-enabling on intraparticle mass transport of organic contaminants in hybrid granular activated carbon.

PubMed

Garcia, Jose; Markovski, Jasmina; McKay Gifford, J; Apul, Onur; Hristovski, Kiril D

2017-05-15

The overarching goal of this study was to ascertain the changes in intraparticle mass transport rates for organic contaminants resulting from nano-enabled hybridization of commercially available granular activated carbon (GAC). Three different nano-enabled hybrid media were fabricated by in-situ synthesizing titanium dioxide nanoparticles inside the pores of GAC sorbent, characterized, and evaluated for removal of two model organic contaminants under realistic conditions to obtain the intraparticle mass transport (pore and surface diffusion) coefficients. The results validated the two hypotheses that: (H1) the pore diffusion rates of organic contaminants linearly decrease with decrease in cumulative pore volume caused by increase in metal (hydr)oxide nanoparticle content inside the pores of the hybrid GAC sorbent; and (H2) introduction of metal (hydr)oxide nanoparticles initially increases surface diffusivity, but additional loading causes its decrease as the increase in metal (hydr)oxide nanoparticles content continues to reduce the porosity of the GAC sorbent. Nano-enabled hybridization of commercially available GAC with metal (hydr)oxides has the potential to significantly increase the intraparticle mass transport limitations for organic contaminants. Introduction of metal (hydr)oxide nanoparticles inside the pores of a pristine sorbent causes the pore diffusion rates of organic contaminants to decrease as the cumulative pore volume is reduced. In contrast, the introduction of limited amounts of metal (hydr)oxide nanoparticles appears to facilitate the surface diffusion rates of these contaminants. Copyright © 2017 Elsevier B.V. All rights reserved.

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.

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

NASA Astrophysics Data System (ADS)

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

2018-02-01

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

Major diffusion leaks of clamp-on leaf cuvettes still unaccounted: how erroneous are the estimates of Farquhar et al. model parameters?

PubMed

Rodeghiero, Mirco; Niinemets, Ulo; Cescatti, Alessandro

2007-08-01

Estimates of leaf gas-exchange characteristics using standard clamp-on leaf chambers are prone to errors because of diffusion leaks. While some consideration has been given to CO(2) diffusion leaks, potential water vapour diffusion leaks through chamber gaskets have been neglected. We estimated diffusion leaks of two clamp-on Li-Cor LI-6400 (Li-Cor, Inc., Lincoln, NE, USA) leaf chambers with polymer foam gaskets and enclosing either 2 or 6 cm(2) leaf area, and conducted a sensitivity analysis of the diffusion leak effects on Farquhar et al. photosynthesis model parameters - the maximum carboxylase activity of ribulose 1 x 5-bisphosphate carboxylase/oxygenase (Rubisco) (V(cmax)), capacity for photosynthetic electron transport (J(max)) and non-photorespiratory respiration rate in light (R(d)). In addition, net assimilation rate (A(n)) versus intercellular CO(2) (C(i)) responses were measured in leaves of Mediterranean evergreen species Quercus ilex L. enclosing the whole leaf chamber in a polyvinyl fluoride bag flushed with the exhaust air of leaf chamber, thereby effectively reducing the CO(2) and water vapour gradients between ambient air and leaf chamber. For the empty chambers, average diffusion leak for CO(2), K(CO2), (molar flow rate corresponding to unit CO(2) mole fraction difference) was ca. 0.40 micromol s(-1). K(CO2) increased ca. 50% if a dead leaf was clamped between the leaf chamber. Average diffusion leak for H(2)O was ca. 5- to 10-fold larger than the diffusion leak for CO(2). Sensitivity analyses demonstrated that the consequence of a CO(2) diffusion leak was apparent enhancement of A(n) at high CO(2) mole fraction and reduction at lower CO(2) mole fraction, and overall compression of C(i) range. As the result of these modifications, Farquhar et al. model parameters were overestimated. The degree of overestimation increased in the order of V(cmax) < J(max) < R(d), and was larger for smaller chambers and for leaves with lower photosynthetic capacity, leading to overestimation of all three parameters by 70-290% for 2 cm(2), and by 10-60% for 6 cm(2) chamber. Significant diffusion corrections (5-36%) were even required for leaves with high photosynthetic capacity measured in largest chamber. Water vapour diffusion leaks further enhanced the overestimation of model parameters. For small chambers and low photosynthetic capacities, apparent C(i) was simulated to decrease with increasing A(n) because of simultaneous CO(2) and H(2)O diffusion leaks. Measurements in low photosynthetic capacity Quercus ilex leaves enclosed in 2 cm(2) leaf chamber exhibited negative apparent C(i) values at highest A(n). For the same leaves measured with the entire leaf chamber enclosed in the polyvinyl fluoride bag, C(i) and A(n) increased monotonically. While the measurements without the bag could be corrected for diffusion leaks, the required correction in A(n) and transpiration rates was 100-500%, and there was large uncertainty in Farquhar et al. model parameters derived from 'corrected'A(n)/C(i) response curves because of uncertainties in true diffusion leaks. These data demonstrate that both CO(2) and water vapour diffusion leaks need consideration in measurements with clamp-on leaf cuvettes. As plants in natural environments are often characterized by low photosynthetic capacities, cuvette designs need to be improved for reliable measurements in such species.

Wind effect on the Atlantic meridional overturning circulation via sea ice and vertical diffusion

NASA Astrophysics Data System (ADS)

Yang, Haijun; Wang, Kun; Dai, Haijin; Wang, Yuxing; Li, Qing

2016-06-01

Effects of wind and fresh water on the Atlantic meridional overturning circulation (AMOC) are investigated using a fully coupled climate model. The AMOC can change significantly when perturbed by either wind stress or freshwater flux in the North Atlantic. This study focuses on wind stress effect. Our model results show that the wind forcing is crucial in maintaining the AMOC. Reducing wind forcing over the ocean can cause immediately weakening of the vertical salinity diffusion and convection in the mid-high latitudes Atlantic, resulting in an enhancement of vertical salinity stratification that restrains the deep water formation there, triggering a slowdown of the thermohaline circulation. As the thermohaline circulation weakens, the sea ice expands southward and melts, providing the upper ocean with fresh water that weakens the thermohaline circulation further. The wind perturbation experiments suggest a positive feedback between sea-ice and thermohaline circulation strength, which can eventually result in a complete shutdown of the AMOC. This study also suggests that sea-ice variability may be also important to the natural AMOC variability on decadal and longer timescales.

Working memory load and the retro-cue effect: A diffusion model account.

PubMed

Shepherdson, Peter; Oberauer, Klaus; Souza, Alessandra S

2018-02-01

Retro-cues (i.e., cues presented between the offset of a memory array and the onset of a probe) have consistently been found to enhance performance in working memory tasks, sometimes ameliorating the deleterious effects of increased memory load. However, the mechanism by which retro-cues exert their influence remains a matter of debate. To inform this debate, we applied a hierarchical diffusion model to data from 4 change detection experiments using single item, location-specific probes (i.e., a local recognition task) with either visual or verbal memory stimuli. Results showed that retro-cues enhanced the quality of information entering the decision process-especially for visual stimuli-and decreased the time spent on nondecisional processes. Further, cues interacted with memory load primarily on nondecision time, decreasing or abolishing load effects. To explain these findings, we propose an account whereby retro-cues act primarily to reduce the time taken to access the relevant representation in memory upon probe presentation, and in addition protect cued representations from visual interference. (PsycINFO Database Record (c) 2018 APA, all rights reserved).

Effects of Transition-Metal Mixing on Na Ordering and Kinetics in Layered P 2 Oxides

NASA Astrophysics Data System (ADS)

Zheng, Chen; Radhakrishnan, Balachandran; Chu, Iek-Heng; Wang, Zhenbin; Ong, Shyue Ping

2017-06-01

Layered P 2 oxides are promising cathode materials for rechargeable sodium-ion batteries. In this work, we systematically investigate the effects of transition-metal (TM) mixing on Na ordering and kinetics in the NaxCo1 -yMnyO2 model system using density-functional-theory (DFT) calculations. The DFT-predicted 0-K stability diagrams indicate that Co-Mn mixing reduces the energetic differences between Na orderings, which may account for the reduction of the number of phase transformations observed during the cycling of mixed-TM P 2 layered oxides compared to a single TM. Using ab initio molecular-dynamics simulations and nudged elastic-band calculations, we show that the TM composition at the Na(1) (face-sharing) site has a strong influence on the Na site energies, which in turn impacts the kinetics of Na diffusion towards the end of the charge. By employing a site-percolation model, we establish theoretical upper and lower bounds for TM concentrations based on their effect on Na(1) site energies, providing a framework to rationally tune mixed-TM compositions for optimal Na diffusion.

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

PubMed

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

2016-11-09

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

Repeatability of the efficiency of columns packed with sub-3μm core-shell particles: Part II. 2.7 μm Halo-ES-Peptide-C18 particles in 4.6mm and 2.1mm×100mm column formats.

PubMed

Gritti, Fabrice; Guiochon, Georges

2012-08-24

The column-to-column repeatability of the mass transfer kinetics in columns packed with sub-3μm shell particles was investigated. The parameters of this kinetics were measured for twelve columns (six 2.1mm×100mm and six 4.6mm×100mm) packed with the same batch of 2.7μm Halo-ES-Peptide-C(18) particles (Advanced Material Technologies, Wilmington, DE, USA). For both series, the manufacturer provided columns at different positions in the efficiency distribution given by the quality test control. Three compounds were used, uracil, naphthalene and insulin. The reduced longitudinal diffusion term was measured with the peak parking (PP) method; the reduced solid-liquid mass transfer resistance term was given by a combination of the PP results and the most accurate model of effective diffusion in ternary composite materials (non-porous cores, concentric porous shell, and eluent matrix), validated previously. The overall eddy diffusion term was obtained by subtraction of these two HETP terms from the overall reduced HETP measured by numerical integration of the entire peak profiles. The results demonstrate that the dispersion of the column efficiencies is mostly due to the random nature of the packing process and the associated eddy diffusion term. At the highest reduced velocity achieved, the relative standard deviations (RSDs) of the eddy diffusion term for the 2.1mm I.D. columns were ca. 5 and 10% (with average values A(ν)=2.3 and 8.5) for naphthalene and uracil, respectively. For the 4.6mm I.D. columns, these RSDs were 3 and 5%, respectively, with average values A(ν)=1.5 and 2.7. Copyright © 2012 Elsevier B.V. All rights reserved.

Repeatability of the efficiency of columns packed with sub-3μm core-shell particles: Part I. 2.6μm Kinetex-C(18) particles in 4.6mm and 2.1mm×100mm column formats.

PubMed

Gritti, Fabrice; Guiochon, Georges

2012-08-24

The column-to-column repeatability of the mass transfer mechanism in columns packed with sub-3μm shell particles was investigated. The parameters of this mechanism were measured for twelve columns (six 2.1mm×100mm and six 4.6mm×100mm) packed with the same batch of 2.6μm Kinetex-C(18) particles (Phenomenex, CA, USA). For both series, the manufacturer provided columns at different positions in the efficiency distribution given by the quality test control. Three compounds were used, uracil, naphthalene and insulin. The reduced longitudinal diffusion term was measured with the peak parking (PP) method, the reduced solid-liquid mass transfer resistance term was given by a combination of the PP results and a model of effective diffusion in ternary composite materials (non-porous cores, concentric porous shell, and eluent matrix), validated previously. The overall eddy diffusion term was obtained by subtraction of these two HETP terms from the overall reduced HETP measured by numerical integration of the entire peak profiles. The results demonstrate that the dispersion of the column efficiencies is only due to the random nature of the packing process. At the highest reduced velocity achieved, the relative standard deviations (RSDs) of the eddy diffusion term for the 2.1mm I.D. columns were ca. 7% and 3% for the low molecular weight compounds and for insulin, respectively. For the 4.6mm I.D. columns, these RSDs were 15% and 5%, respectively. The larger RSDs for the 4.6mm I.D. columns is explained by the exceptionally low value of the eddy diffusion term. Copyright © 2012 Elsevier B.V. All rights reserved.

Sedimentation dynamics and diffusion of suspensions of swimming E. coli

NASA Astrophysics Data System (ADS)

Arratia, Paulo; Patteson, Alison; Singh, Jaspreet; Purohit, Prashant

2017-11-01

Sedimentation in active fluids has come into focus due to the ubiquity of swimming micro-organisms in natural and man-made environments. Here, we experimentally investigate sedimentation of passive particles in water containing various concentrations of the bacterium E. coli. Results show that the presence of live bacteria reduces the velocity of the sedimentation front even in the dilute regime, where constant sedimentation velocity is expected to be independent of particle concentration. The presence of live bacteria increases the effective diffusion coefficient, which determines the width of the sedimentation front. For higher bacteria concentration, we find the development of two sedimentation fronts due to bacterial death. A model in which the advection-diffusion equation describing the settling of particles under gravity is coupled to the population dynamics of the bacteria captures the experimental trends relatively well. This work is supported by NSF-CBET-1437482.

The effect of atmospheric sulfate reductions on diffuse radiation and photosynthesis in the eastern United States

NASA Astrophysics Data System (ADS)

Keppel-Aleks, G.; Washenfelder, R. A.

2016-12-01

Aerosol optical depth (AOD) has been shown to influence ecosystem carbon uptake by increasing the fraction of diffuse light, which increases photosynthesis over a greater fraction of the vegetated canopy. Several modeling studies have hypothesized that this effect may be a significant driver of the historical terrestrial carbon sink, and may therefore be an important climate feedback associated with changing air quality. In this study, we quantify the impact of anthropogenic aerosols on gross primary production (GPP) in the eastern United States. We focus on the eastern U.S. because 1) rapid decreases in SO2 emissions over the past two decades create an opportunity to examine the effects of reduced SO4 mass and aerosol optical depth; 2) SO2 emissions in the United States have been well quantified; 3) carbon fluxes within temperate ecosystems in the eastern United States have been well observed. We use accurate SO2 emission data for 1995-2013 in the Community Earth System Model (CESM) to determine trends in AOD, surface radiation, and photosynthesis. Between 1995 and 2013, U.S. SO2 emissions declined by over 70%, coinciding with observed AOD reductions of 3.0 ± 0.6% y-1 over the eastern U.S. In the Community Earth System Model (CESM), these trends cause diffuse light to decrease regionally by almost 0.6% y-1, leading to declines GPP of 0.07% y-1. Integrated over the analysis period and domain, this represents 0.5 PgC of omitted GPP. A separate upscaling calculation that used published relationships between GPP and diffuse light agreed with the CESM model results within 20%. The agreement between simulated and data-constrained upscaling results strongly suggests that anthropogenic sulfate trends have a small impact on carbon uptake in temperate forests due to scattered light.

Active compound diffusivity of particle size reduced S. aromaticum and C. cassia fused starch edible films and the shelf life of mutton (Capra aegagrus hircus) meat.

PubMed

Chandra Mohan, C; Radha Krishnan, K; Babuskin, S; Sudharsan, K; Aafrin, Vajiha; Lalitha Priya, U; Mariyajenita, P; Harini, K; Madhushalini, D; Sukumar, M

2017-06-01

In the present study, mathematical models were used to examine the effect of active compound diffusion from edible film (supplemented with S. aromaticum and C. cassia) on the microbial, physical and chemical quality of mutton stored at 4 and 10°C. Cinnamaldehyde and eugenol release from edible film into liquid was found to be 80% and 75% of the equilibrium concentration. Active compound release into meat was 42-51% for cinnamaldehyde and 38-48% for eugenol, in storage temperatures of 4-15°C. Developed mathematical models showed the diffusivity of cinnamaldehyde (0.45×10 -15 ±0.04×10 -15 ) and eugenol (0.63×10 -10 ±0.01×10 -10 ) into meat, which was about 40% of that in liquid medium. On comparing physical, chemical and microbial results, shelf life of mutton meat was found to be increased by 1week at storage temperature of 10°C and 3weeks at storage temperature of 4°C. Copyright © 2017 Elsevier Ltd. All rights reserved.

Study of sorption-retarded U(VI) diffusion in Hanford silt/clay material.

PubMed

Bai, Jing; Liu, Chongxuan; Ball, William P

2009-10-15

A diffusion cell method was applied to measure the effective pore diffusion coefficient (Dp) for U(VI) under strictly controlled chemical conditions in a silt/clay sediment from the U.S. Department of Energy Hanford site, WA. "Inward-flux" diffusion studies were conducted in which [U(VI)] in both aqueous and solid phases was measured as a function of distance in the diffusion cell under conditions of constant concentration at the cell boundaries. A sequential extraction method was developed to measure sorbed contaminant U(VI) in the solid phase containing extractable background U(VI). The effect of sorption kinetics on U(VI) interparticle diffusion was evaluated by comparing sorption-retarded diffusion models with sorption described either as equilibrium or intraparticle diffusion-limited processes. Both experimental and modeling results indicated that (1) a single pore diffusion coefficient can simulate the diffusion of total aqueous U(VI), and (2) the local equilibrium assumption (LEA) is appropriate for modeling sorption-retarded diffusion under the given experimental conditions. Dp of 1.6-1.7 x 10(-6) cm2/s was estimated in aqueous solution at pH 8.0 and saturated with respect to calcite, as relevant to some subsurface regions of the Hanford site.

Interfacial strain effects on lithium diffusion pathways in the spinel solid electrolyte Li-doped MgAl2O4

NASA Astrophysics Data System (ADS)

O'Rourke, Conn; Morgan, Benjamin J.

2018-04-01

The (Li,Al)-codoped magnesium spinel (LixMg1 -2 xAl2 +xO4 ) is a solid lithium-ion electrolyte with potential use in all-solid-state lithium-ion batteries. The spinel structure means that interfaces with spinel electrodes, such as LiyMn2O4 and Li4 +3 zTi5O12 , may be lattice matched, with potentially low interfacial resistances. Small lattice parameter differences across a lattice-matched interface are unavoidable, causing residual epitaxial strain. This strain potentially modifies lithium diffusion near the electrolyte-electrode interface, contributing to interfacial resistance. Here, we report a density functional theory study of strain effects on lithium diffusion pathways for (Li,Al)-codoped magnesium spinel, for xLi=0.25 and xLi=0.5 . We have calculated diffusion profiles for the unstrained materials, and for isotropic and biaxial tensile strains of up to 6 % , corresponding to {100 } epitaxial interfaces with LiyMn2O4 and Li4 +3 zTi5O12 . We find that isotropic tensile strain reduces lithium diffusion barriers by as much as 0.32 eV , with typical barriers reduced by ˜0.1 eV. This effect is associated with increased volumes of transitional octahedral sites, and broadly follows qualitative changes in local electrostatic potentials. For biaxial (epitaxial) strain, which more closely approximates strain at a lattice-matched electrolyte-electrode interface, changes in octahedral site volumes and in lithium diffusion barriers are much smaller than under isotropic strain. Typical barriers are reduced by only ˜0.05 eV. Individual effects, however, depend on the pathway considered and the relative strain orientation. These results predict that isotropic strain strongly affects ionic conductivities in (Li,Al)-codoped magnesium spinel electrolytes, and that tensile strain is a potential route to enhanced lithium transport. For a lattice-matched interface with candidate spinel-structured electrodes, however, epitaxial strain has a small, but complex, effect on lithium diffusion barriers.

Molecular dynamics simulation of real-fluid mutual diffusion coefficients with the Lennard-Jones potential model

NASA Astrophysics Data System (ADS)

Stoker, J. M.; Rowley, R. L.

1989-09-01

Mutual diffusion coefficients for selected alkanes in carbon tetrachloride were calculated using molecular dynamics and Lennard-Jones (LJ) potentials. Use of effective spherical LJ parameters is desirable when possible for two reasons: (i) computer time is saved due to the simplicity of the model and (ii) the number of parameters in the model is kept to a minimum. Results of this study indicate that mutual diffusivity is particularly sensitive to the molecular size cross parameter, σ12, and that the commonly used Lorentz-Berthelot rules are inadequate for mixtures in which the component structures differ significantly. Good agreement between simulated and experimental mutual diffusivities is obtained with a combining rule for σ12 which better represents these asymmetric mixtures using pure component LJ parameters obtained from self-diffusion coefficient data. The effect of alkane chain length on the mutual diffusion coefficient is correctly predicted. While the effects of alkane branching upon the diffusion coefficient are comparable in size to the uncertainty of these calculations, the qualitative trend due to branching is also correctly predicted by the MD results.

Diffusion on social networks: Survey data from rural villages in central China.

PubMed

Xiong, Hang; Wang, Puqing; Zhu, Yueji

2016-06-01

Empirical studies on social diffusions are often restricted by the access to data of diffusion and social relations on the same objects. We present a set of first-hand data that we collected in ten rural villages in central China through household surveys. The dataset contains detailed and comprehensive data of the diffusion of an innovation, the major social relationships and the household level demographic characteristics in these villages. The data have been used to study peer effects in social diffusion using simulation models, "Peer Effects and Social Network: The Case of Rural Diffusion in Central China" [1]. They can also be used to estimate spatial econometric models. Data are supplied with this article.

Mathematical analysis of a sharp-diffuse interfaces model for seawater intrusion

NASA Astrophysics Data System (ADS)

Choquet, C.; Diédhiou, M. M.; Rosier, C.

2015-10-01

We consider a new model mixing sharp and diffuse interface approaches for seawater intrusion phenomena in free aquifers. More precisely, a phase field model is introduced in the boundary conditions on the virtual sharp interfaces. We thus include in the model the existence of diffuse transition zones but we preserve the simplified structure allowing front tracking. The three-dimensional problem then reduces to a two-dimensional model involving a strongly coupled system of partial differential equations of parabolic type describing the evolution of the depths of the two free surfaces, that is the interface between salt- and freshwater and the water table. We prove the existence of a weak solution for the model completed with initial and boundary conditions. We also prove that the depths of the two interfaces satisfy a coupled maximum principle.

Exits in order: How crowding affects particle lifetimes

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

Penington, Catherine J.; Simpson, Matthew J.; Baker, Ruth E.

2016-06-28

Diffusive processes are often represented using stochastic random walk frameworks. The amount of time taken for an individual in a random walk to intersect with an absorbing boundary is a fundamental property that is often referred to as the particle lifetime, or the first passage time. The mean lifetime of particles in a random walk model of diffusion is related to the amount of time required for the diffusive process to reach a steady state. Mathematical analysis describing the mean lifetime of particles in a standard model of diffusion without crowding is well known. However, the lifetime of agents inmore » a random walk with crowding has received much less attention. Since many applications of diffusion in biology and biophysics include crowding effects, here we study a discrete model of diffusion that incorporates crowding. Using simulations, we show that crowding has a dramatic effect on agent lifetimes, and we derive an approximate expression for the mean agent lifetime that includes crowding effects. Our expression matches simulation results very well, and highlights the importance of crowding effects that are sometimes overlooked.« less

Scaling-law equilibria for calcium in canopy-type models of the solar chromosphere

NASA Technical Reports Server (NTRS)

Jones, H. P.

1982-01-01

Scaling laws for resonance line formation are used to obtain approximate excitation and ionization equilibria for a three-level model of singly ionized calcium. The method has been developed for and is applied to the study of magnetograph response in the 8542 A infrared triplet line to magnetostatic canopies which schematically model diffuse, nearly horizontal fields in the low solar chromosphere. For this application, the method is shown to be efficient and semi-quantitative, and the results indicate the type and range of effects on calcium-line radiation which result from reduced gas pressure inside the magnetic regions.

A non-linear dimension reduction methodology for generating data-driven stochastic input models

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

Ganapathysubramanian, Baskar; Zabaras, Nicholas

Stochastic analysis of random heterogeneous media (polycrystalline materials, porous media, functionally graded materials) provides information of significance only if realistic input models of the topology and property variations are used. This paper proposes a framework to construct such input stochastic models for the topology and thermal diffusivity variations in heterogeneous media using a data-driven strategy. Given a set of microstructure realizations (input samples) generated from given statistical information about the medium topology, the framework constructs a reduced-order stochastic representation of the thermal diffusivity. This problem of constructing a low-dimensional stochastic representation of property variations is analogous to the problem ofmore » manifold learning and parametric fitting of hyper-surfaces encountered in image processing and psychology. Denote by M the set of microstructures that satisfy the given experimental statistics. A non-linear dimension reduction strategy is utilized to map M to a low-dimensional region, A. We first show that M is a compact manifold embedded in a high-dimensional input space R{sup n}. An isometric mapping F from M to a low-dimensional, compact, connected set A is contained in R{sup d}(d<

Fractional Diffusion Equations and Anomalous Diffusion

NASA Astrophysics Data System (ADS)

Evangelista, Luiz Roberto; Kaminski Lenzi, Ervin

2018-01-01

Preface; 1. Mathematical preliminaries; 2. A survey of the fractional calculus; 3. From normal to anomalous diffusion; 4. Fractional diffusion equations: elementary applications; 5. Fractional diffusion equations: surface effects; 6. Fractional nonlinear diffusion equation; 7. Anomalous diffusion: anisotropic case; 8. Fractional Schrödinger equations; 9. Anomalous diffusion and impedance spectroscopy; 10. The Poisson–Nernst–Planck anomalous (PNPA) models; References; Index.

Finite Larmor radius effects on weak turbulence transport

NASA Astrophysics Data System (ADS)

Kryukov, N.; Martinell, J. J.

2018-06-01

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

Effects of intravenous dimethyl sulfoxide on ischemia evolution in a rat permanent occlusion model

PubMed Central

Bardutzky, Juergen; Meng, Xianjun; Bouley, James; Duong, Timothy Q; Ratan, Rajiv; Fisher, Marc

2010-01-01

Dimethyl sulfoxide (DMSO) has a variety of biological actions that suggest efficacy as a neuroprotectant. We (1) tested the neuroprotective potential of DMSO at different time windows on infarct size using 2,3,5-triphenyltetrazolium staining and (2) investigated the effects of DMSO on ischemia evolution using quantitative diffusion and perfusion imaging in a permanent middle cerebral artery occlusion (MCAO) model in rats. In experiment 1, DMSO treatment (1.5 g/kg intravenously over 3 h) reduced infarct volume 24 h after MCAO by 65% (P<0.00001) when initiated 20 h before MCAO, by 44% (P=0.0006) when initiated 1 h after MCAO, and by 17% (P=0.11) when started 2 h after MCAO. Significant infarct reduction was also observed after a 3-day survival in animals treated 1 h after MCAO (P=0.005). In experiment 2, treatment was initiated 1 h after MCAO and maps for cerebral blood flow (CBF) and apparent diffusion coefficient (ADC) were acquired before treatment and then every 30 mins up to 4 h. Cerebral blood flow characteristics and CBF-derived lesion volumes did not differ between treated and untreated animals, whereas the ADC-derived lesion volume essentially stopped progressing during DMSO treatment, resulting in a persistent diffusion/perfusion mismatch. This effect was mainly observed in the cortex. Our data suggest that DMSO represents an interesting candidate for acute stroke treatment. PMID:15744247

Determination of drying kinetics and convective heat transfer coefficients of ginger slices

NASA Astrophysics Data System (ADS)

Akpinar, Ebru Kavak; Toraman, Seda

2016-10-01

In the present work, the effects of some parametric values on convective heat transfer coefficients and the thin layer drying process of ginger slices were investigated. Drying was done in the laboratory by using cyclone type convective dryer. The drying air temperature was varied as 40, 50, 60 and 70 °C and the air velocity is 0.8, 1.5 and 3 m/s. All drying experiments had only falling rate period. The drying data were fitted to the twelve mathematical models and performance of these models was investigated by comparing the determination of coefficient ( R 2), reduced Chi-square ( χ 2) and root mean square error between the observed and predicted moisture ratios. The effective moisture diffusivity and activation energy were calculated using an infinite series solution of Fick's diffusion equation. The average effective moisture diffusivity values and activation energy values varied from 2.807 × 10-10 to 6.977 × 10-10 m2/s and 19.313-22.722 kJ/mol over the drying air temperature and velocity range, respectively. Experimental data was used to evaluate the values of constants in Nusselt number expression by using linear regression analysis and consequently, convective heat transfer coefficients were determined in forced convection mode. Convective heat transfer coefficient of ginger slices showed changes in ranges 0.33-2.11 W/m2 °C.

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

PubMed

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

2005-04-10

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

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

NASA Astrophysics Data System (ADS)

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

2005-04-01

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

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

NASA Astrophysics Data System (ADS)

Qin, C.; Hassanizadeh, S. M.

2015-12-01

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

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

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

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

2007-12-15

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

Reduced order modeling of mechanical degradation induced performance decay in lithium-ion battery porous electrodes

DOE PAGES

Barai, Pallab; Smith, Kandler; Chen, Chien -Fan; ...

2015-06-17

In this paper, a one-dimensional computational framework is developed that can solve for the evolution of voltage and current in a lithium-ion battery electrode under different operating conditions. A reduced order model is specifically constructed to predict the growth of mechanical degradation within the active particles of the carbon anode as a function of particle size and C-rate. Using an effective diffusivity relation, the impact of microcracks on the diffusivity of the active particles has been captured. Reduction in capacity due to formation of microcracks within the negative electrode under different operating conditions (constant current discharge and constant current constantmore » voltage charge) has been investigated. At the beginning of constant current discharge, mechanical damage to electrode particles predominantly occurs near the separator. As the reaction front shifts, mechanical damage spreads across the thickness of the negative electrode and becomes relatively uniform under multiple discharge/charge cycles. Mechanical degradation under different drive cycle conditions has been explored. It is observed that electrodes with larger particle sizes are prone to capacity fade due to microcrack formation. Finally, under drive cycle conditions, small particles close to the separator and large particles close to the current collector can help in reducing the capacity fade due to mechanical degradation.« less

Static and Dynamic Effects of Lateral Carrier Diffusion in Semiconductor Lasers

NASA Technical Reports Server (NTRS)

Li, Jian-Zhong; Cheung, Samson H.; Ning, C. Z.; Biegel, Bryan A. (Technical Monitor)

2002-01-01

Electron and hole diffusions in the plane of semiconductor quantum wells play an important part in the static and dynamic operations of semiconductor lasers. It is well known that the value of diffusion coefficients affects the threshold pumping current of a semiconductor laser. At the same time, the strength of carrier diffusion process is expected to affect the modulation bandwidth of an AC-modulated laser. It is important not only to investigate the combined DC and AC effects due to carrier diffusion, but also to separate the AC effects from that of the combined effects in order to provide design insights for high speed modulation. In this presentation, we apply a hydrodynamic model developed by the present authors recently from the semiconductor Bloch equations. The model allows microscopic calculation of the lateral carrier diffusion coefficient, which is a nonlinear function of the carrier density and plasma temperature. We first studied combined AC and DC effects of lateral carrier diffusion by studying the bandwidth dependence on diffusion coefficient at a given DC current under small signal modulation. The results show an increase of modulation bandwidth with decrease in the diffusion coefficient. We simultaneously studied the effects of nonlinearity in the diffusion coefficient. To clearly identify how much of the bandwidth increase is a result of decrease in the threshold pumping current for smaller diffusion coefficient, thus an effective increase of DC pumping, we study the bandwidth dependence on diffusion coefficient at a given relative pumping. A detailed comparison of the two cases will be presented.

Effects of Channel Modification on Detection and Dating of Fault Scarps

NASA Astrophysics Data System (ADS)

Sare, R.; Hilley, G. E.

2016-12-01

Template matching of scarp-like features could potentially generate morphologic age estimates for individual scarps over entire regions, but data noise and scarp modification limits detection of fault scarps by this method. Template functions based on diffusion in the cross-scarp direction may fail to accurately date scarps near channel boundaries. Where channels reduce scarp amplitudes, or where cross-scarp noise is significant, signal-to-noise ratios decrease and the scarp may be poorly resolved. In this contribution, we explore the bias in morphologic age of a complex scarp produced by systematic changes in fault scarp curvature. For example, fault scarps may be modified by encroaching channel banks and mass failure, lateral diffusion of material into a channel, or undercutting parallel to the base of a scarp. We quantify such biases on morphologic age estimates using a block offset model subject to two-dimensional linear diffusion. We carry out a synthetic study of the effects of two-dimensional transport on morphologic age calculated using a profile model, and compare these results to a well- studied and constrained site along the San Andreas Fault at Wallace Creek, CA. This study serves as a first step towards defining regions of high confidence in template matching results based on scarp length, channel geometry, and near-scarp topography.

Real Diffusion-Weighted MRI Enabling True Signal Averaging and Increased Diffusion Contrast

PubMed Central

Eichner, Cornelius; Cauley, Stephen F; Cohen-Adad, Julien; Möller, Harald E; Turner, Robert; Setsompop, Kawin; Wald, Lawrence L

2015-01-01

This project aims to characterize the impact of underlying noise distributions on diffusion-weighted imaging. The noise floor is a well-known problem for traditional magnitude-based diffusion-weighted MRI (dMRI) data, leading to biased diffusion model fits and inaccurate signal averaging. Here, we introduce a total-variation-based algorithm to eliminate shot-to-shot phase variations of complex-valued diffusion data with the intention to extract real-valued dMRI datasets. The obtained real-valued diffusion data are no longer superimposed by a noise floor but instead by a zero-mean Gaussian noise distribution, yielding dMRI data without signal bias. We acquired high-resolution dMRI data with strong diffusion weighting and, thus, low signal-to-noise ratio. Both the extracted real-valued and traditional magnitude data were compared regarding signal averaging, diffusion model fitting and accuracy in resolving crossing fibers. Our results clearly indicate that real-valued diffusion data enables idealized conditions for signal averaging. Furthermore, the proposed method enables unbiased use of widely employed linear least squares estimators for model fitting and demonstrates an increased sensitivity to detect secondary fiber directions with reduced angular error. The use of phase-corrected, real-valued data for dMRI will therefore help to clear the way for more detailed and accurate studies of white matter microstructure and structural connectivity on a fine scale. PMID:26241680

Load Diffusion in Composite and Smart Structures

NASA Technical Reports Server (NTRS)

Horgan, Cornelius O.; Ambur, D. (Technical Monitor); Nemeth, M. P. (Technical Monitor)

2003-01-01

The research carried out here builds on our previous NASA supported research on the general topic of edge effects and load diffusion in composite structures. Further fundamental solid mechanics studies were carried out to provide a basis for assessing the complicated modeling necessary for the multi-functional large scale structures used by NASA. An understanding of the fundamental mechanisms of load diffusion in composite subcomponents is essential in developing primary composite structures. Some specific problems recently considered were those of end effects in smart materials and structures, study of the stress response of pressurized linear piezoelectric cylinders for both static and steady rotating configurations, an analysis of the effect of pre-stressing and pre-polarization on the decay of end effects in piezoelectric solids and investigation of constitutive models for hardening rubber-like materials. Our goal in the study of load diffusion is the development of readily applicable results for the decay lengths in terms of non-dimensional material and geometric parameters. Analytical models of load diffusion behavior are extremely valuable in building an intuitive base for developing refined modeling strategies and assessing results from finite element analyses.

Mitigating effects of captopril and losartan on lung histopathology in a rat model of fat embolism.

PubMed

McIff, Terence E; Poisner, Alan M; Herndon, Betty; Lankachandra, Kamani; Molteni, Agostino; Adler, Federico

2011-05-01

Fat embolization (FE) is an often overlooked and poorly understood complication of skeletal trauma and some orthopedic procedures. Fat embolism can lead to major pulmonary damage associated with fat embolism syndrome (FES). A model of FE in unanesthetized rats, using intravenous injection of the neutral fat triolein, was used to study the potential therapeutic effect on lung histopathology of altering the production of, or response to, endogenous angiotensin (Ang) II. Either captopril, an Ang I converting enzyme inhibitor, or losartan, an Ang II type 1 receptor blocker, was injected 1 hour after FE by triolein injection. After euthanasia at 48 hours, histopathologic evaluation was used to compare the drug-treated animals with control animals that received only triolein. Histology of the lungs of rats treated only with triolein revealed severe, diffuse pathology. Alveolar septa showed severe, diffuse inflammation. Bronchial lumina showed severe mucosal epithelial loss. The media of the pulmonary small arteries and arterioles was thicker, and the lumen patency was reduced 60% to 70%. Trichrome staining confirmed the abundant presence of collagen in the media and adventitia, as well as collagen infiltrating the bronchial musculature. Both captopril and losartan treatments reduced the inflammatory, vasoconstrictor, and profibrotic effects present at 48 hours (p<0.001). With treatment, the vascular lumen remained patent, and the fat droplets were reduced in size and number. There was a reduction in the number of infiltrating leukocytes, macrophages, myofibroblasts, and eosinophils, along with a significant decrease in hemorrhage and collagen deposition (p<0.001). Pathologic changes in bronchial epithelium were also diminished. The results suggest that the use of drugs that act on the renin-Ang system might provide an effective and targeted therapy for fat embolism syndrome.

A Numerical Study of Forbush Decreases with a 3D Cosmic-Ray Modulation Model Based on an SDE Approach

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

Luo, Xi; Feng, Xueshang; Potgieter, Marius S.

Based on the reduced diffusion mechanism for producing Forbush decreases (Fds) in the heliosphere, we constructed a three-dimensional (3D) diffusion barrier, and by incorporating it into a stochastic differential equation (SDE) based time-dependent, cosmic-ray transport model, a 3D numerical model for simulating Fds is built and applied to a period of relatively quiet solar activity. This SDE model generally corroborates previous Fd simulations concerning the effects of the solar magnetic polarity, the tilt angle of the heliospheric current sheet (HCS), and cosmic-ray particle energy. Because the modulation processes in this 3D model are multi-directional, the barrier’s geometrical features affect themore » intensity profiles of Fds differently. We find that both the latitudinal and longitudinal extent of the barrier have relatively fewer effects on these profiles than its radial extent and the level of decreased diffusion inside the disturbance. We find, with the 3D approach, that the HCS rotational motion causes the relative location from the observation point to the HCS to vary, so that a periodic pattern appears in the cosmic-ray intensity at the observing location. Correspondingly, the magnitude and recovery time of an Fd change, and the recovering intensity profile contains oscillation as well. Investigating the Fd magnitude variation with heliocentric radial distance, we find that the magnitude decreases overall and, additionally, that the Fd magnitude exhibits an oscillating pattern as the radial distance increases, which coincides well with the wavy profile of the HCS under quiet solar modulation conditions.« less

Molecular dynamics simulation of solute diffusion in Lennard-Jones fluids

NASA Astrophysics Data System (ADS)

Yamaguchi, T.; Kimura, Y.; Hirota, N.

We performed a molecular dynamics (MD) simulation for a system of 5 solute molecules in 495 solvent molecules interacting through the Lennard-Jones (LJ) 12-6 potential, in order to study solvent density effects on the diffusion coefficients in supercritical fluids. The effects of the size of the solute and the strength of the solute-solvent attractive interaction on the diffusion coefficient of the solute were examined. The diffusion coefficients of the solute molecules were calculated at T = 1.5 (in the LJ reduced unit), slightly above the critical temperature, from rho = 0.1 to rho = 0.95, where rho is the number density in the LJ reduced unit. The memory function in the generalized Langevin equation was calculated, in order to know the molecular origin of the friction on a solute. The memory function is separated into fast and slow components. The former arises from the solute-solvent repulsive interaction, and is interpreted as collisional Enskog-like friction. The interaction strength dependence of the collisional friction is larger in the low- and medium-density regions, which is consistent with the 'clustering' picture, i.e., the local density enhancement due to the solute-solvent attractive interaction. However, the slow component of the memory function suppresses the effect of the local density on the diffusion coefficients, and as a result the effect of the attractive interaction is smaller on the diffusion coefficients than on the local density. Nonetheless, the solvent density dependence of the effect of the attraction on the diffusion coefficient varies with the local density, and it is concluded that the local density is the principal factor that determines the interaction strength dependence of the diffusion coefficient in the low- and medium-density regions (p < 0.6).

A helium-based model for the effects of radiation damage annealing on helium diffusion kinetics in apatite

NASA Astrophysics Data System (ADS)

Willett, Chelsea D.; Fox, Matthew; Shuster, David L.

2017-11-01

Widely used to study surface processes and the development of topography through geologic time, (U-Th)/He thermochronometry in apatite depends on a quantitative description of the kinetics of 4He diffusion across a range of temperatures, timescales, and geologic scenarios. Empirical observations demonstrate that He diffusivity in apatite is not solely a function of temperature, but also depends on damage to the crystal structure from radioactive decay processes. Commonly-used models accounting for the influence of thermal annealing of radiation damage on He diffusivity assume the net effects evolve in proportion to the rate of fission track annealing, although the majority of radiation damage results from α-recoil. While existing models adequately quantify the net effects of damage annealing in many geologic scenarios, experimental work suggests different annealing rates for the two damage types. Here, we introduce an alpha-damage annealing model (ADAM) that is independent of fission track annealing kinetics, and directly quantifies the influence of thermal annealing on He diffusivity in apatite. We present an empirical fit to diffusion kinetics data and incorporate this fit into a model that tracks the competing effects of radiation damage accumulation and annealing on He diffusivity in apatite through geologic time. Using time-temperature paths to illustrate differences between models, we highlight the influence of damage annealing on data interpretation. In certain, but not all, geologic scenarios, the interpretation of low-temperature thermochronometric data can be strongly influenced by which model of radiation damage annealing is assumed. In particular, geologic scenarios involving 1-2 km of sedimentary burial are especially sensitive to the assumed rate of annealing and its influence on He diffusivity. In cases such as basement rocks in Grand Canyon and the Canadian Shield, (U-Th)/He ages predicted from the ADAM can differ by hundreds of Ma from those predicted by other models for a given thermal path involving extended residence between ∼40-80 °C.

The Analytical Limits of Modeling Short Diffusion Timescales

NASA Astrophysics Data System (ADS)

Bradshaw, R. W.; Kent, A. J.

2016-12-01

Chemical and isotopic zoning in minerals is widely used to constrain the timescales of magmatic processes such as magma mixing and crystal residence, etc. via diffusion modeling. Forward modeling of diffusion relies on fitting diffusion profiles to measured compositional gradients. However, an individual measurement is essentially an average composition for a segment of the gradient defined by the spatial resolution of the analysis. Thus there is the potential for the analytical spatial resolution to limit the timescales that can be determined for an element of given diffusivity, particularly where the scale of the gradient approaches that of the measurement. Here we use a probabilistic modeling approach to investigate the effect of analytical spatial resolution on estimated timescales from diffusion modeling. Our method investigates how accurately the age of a synthetic diffusion profile can be obtained by modeling an "unknown" profile derived from discrete sampling of the synthetic compositional gradient at a given spatial resolution. We also include the effects of analytical uncertainty and the position of measurements relative to the diffusion gradient. We apply this method to the spatial resolutions of common microanalytical techniques (LA-ICP-MS, SIMS, EMP, NanoSIMS). Our results confirm that for a given diffusivity, higher spatial resolution gives access to shorter timescales, and that each analytical spacing has a minimum timescale, below which it overestimates the timescale. For example, for Ba diffusion in plagioclase at 750 °C timescales are accurate (within 20%) above 10, 100, 2,600, and 71,000 years at 0.3, 1, 5, and 25 mm spatial resolution, respectively. For Sr diffusion in plagioclase at 750 °C, timescales are accurate above 0.02, 0.2, 4, and 120 years at the same spatial resolutions. Our results highlight the importance of selecting appropriate analytical techniques to estimate accurate diffusion-based timescales.

On The Molecular Mechanism Of Positive Novolac Resists

NASA Astrophysics Data System (ADS)

Huang, Jian-Ping; Kwei, T. K.; Reiser, Arnost

1989-08-01

A molecular mechanism for the dissolution of novolac is proposed, based on the idea of a critical degree of deprotonation as being the condition for the transfer of polymer into solution. The rate at which the critical deprotonation condition is achieved is controlled by the supply of developer into a thin penetration zone, and depends in particular on the rate of diffusion of the base cations which are the developer component with the lowest mobility. The penetration zone contains phenolate ions and ion-bound water, but it retains the structure of a rigid polymer membrane, as evidenced by the diffusion coefficient of cations in the pene;tration zone which is several orders of magnitude slower than in an open gel of the same material. When the critical degree of deprotonation is reached, the membrane structure unravels and all subsequent events, chain rearrangement and transfer into solution, occur rapidly. The supralinear dependence of dissolution rate on base concentration and the effect of the size of the base cation are plausibly interpreted by the model. The diffusion of developer components is assumed to occur preferentially via hydrophilic sites in the polymer matrix. These sites define a diffusion path which acts like a hydrophilic diffusion channel. Suitably designed hydrophobic molecules can block some of the channels and in this way alter the dissolution rate. They reduce in effect the diffusion crossect ion of the material. Hydrophilic additives, on the other hand, introduce additional channels into the system and promote dissolution. The concept of diffusion channels appears to provide a unified interpretation for a number of common observations.

Role Diffusion and Role Reversal: Structural Variations in Divorced Families and Children's Functioning.

ERIC Educational Resources Information Center

Johnston, Janet R.

1990-01-01

Tested model of family structure and process using 133 children where both divorced parents remained in children's lives about 3 years after separation. Found role diffusion, lack of coparental alliance, parental boundary problems, parent-child rejection associated with reduced social competence and behavioral difficulties (especially in boys and…

Simulation of Deep Convective Clouds with the Dynamic Reconstruction Turbulence Closure

NASA Astrophysics Data System (ADS)

Shi, X.; Chow, F. K.; Street, R. L.; Bryan, G. H.

2017-12-01

The terra incognita (TI), or gray zone, in simulations is a range of grid spacing comparable to the most energetic eddy diameter. Spacing in mesoscale and simulations is much larger than the eddies, and turbulence is parameterized with one-dimensional vertical-mixing. Large eddy simulations (LES) have grid spacing much smaller than the energetic eddies, and use three-dimensional models of turbulence. Studies of convective weather use convection-permitting resolutions, which are in the TI. Neither mesoscale-turbulence nor LES models are designed for the TI, so TI turbulence parameterization needs to be discussed. Here, the effects of sub-filter scale (SFS) closure schemes on the simulation of deep tropical convection are evaluated by comparing three closures, i.e. Smagorinsky model, Deardorff-type TKE model and the dynamic reconstruction model (DRM), which partitions SFS turbulence into resolvable sub-filter scales (RSFS) and unresolved sub-grid scales (SGS). The RSFS are reconstructed, and the SGS are modeled with a dynamic eddy viscosity/diffusivity model. The RSFS stresses/fluxes allow backscatter of energy/variance via counter-gradient stresses/fluxes. In high-resolution (100m) simulations of tropical convection use of these turbulence models did not lead to significant differences in cloud water/ice distribution, precipitation flux, or vertical fluxes of momentum and heat. When model resolutions are coarsened, the Smagorinsky and TKE models overestimate cloud ice and produces large-amplitude downward heat flux in the middle troposphere (not found in the high-resolution simulations). This error is a result of unrealistically large eddy diffusivities, i.e., the eddy diffusivity of the DRM is on the order of 1 for the coarse resolution simulations, the eddy diffusivity of the Smagorinsky and TKE model is on the order of 100. Splitting the eddy viscosity/diffusivity scalars into vertical and horizontal components by using different length scales and strain rate components helps to reduce the errors, but does not completely remedy the problem. In contrast, the coarse resolution simulations using the DRM produce results that are more consistent with the high-resolution results, suggesting that the DRM is a more appropriate turbulence model for simulating convection in the TI.

Response of an eddy-permitting ocean model to the assimilation of sparse in situ data

NASA Astrophysics Data System (ADS)

Li, Jian-Guo; Killworth, Peter D.; Smeed, David A.

2003-04-01

The response of an eddy-permitting ocean model to changes introduced by data assimilation is studied when the available in situ data are sparse in both space and time (typical for the majority of the ocean). Temperature and salinity (T&S) profiles from the WOCE upper ocean thermal data set were assimilated into a primitive equation ocean model over the North Atlantic, using a simple nudging scheme with a time window of about 2 days and a horizontal spatial radius of about 1°. When data are sparse the model returns to its unassimilated behavior, locally "forgetting" or rejecting the assimilation, on timescales determined by the local advection and diffusion. Increasing the spatial weighting radius effectively reduces both processes and hence lengthens the model restoring time (and with it, the impact of assimilation). Increasing the nudging factor enhances the assimilation effect but has little effect on the model restoring time.

Contribution of cardiac-induced brain pulsation to the noise of the diffusion tensor in Turboprop diffusion tensor imaging (DTI).

PubMed

Gui, Minzhi; Tamhane, Ashish A; Arfanakis, Konstantinos

2008-05-01

To assess the effects of cardiac-induced brain pulsation on the noise of the diffusion tensor in Turboprop (a form of periodically rotated overlapping parallel lines with enhanced reconstruction [PROPELLER] imaging) diffusion tensor imaging (DTI). A total of six healthy human subjects were imaged with cardiac-gated as well as nongated Turboprop DTI. Gated and nongated Turboprop DTI datasets were also simulated using actual data acquired exclusively during the diastolic or systolic period of the cardiac cycle. The total variance of the diffusion tensor (TVDT) was measured and compared between acquisitions. The TVDT near the ventricles was significantly reduced in cardiac-gated compared to nongated Turboprop DTI acquisitions. Furthermore, the effects of brain pulsation were reduced, but not eliminated, when increasing the amount of data collected. Finally, data corrupted by cardiac-induced pulsation were not consistently detected by the step of the conventional Turboprop reconstruction algorithm that evaluates the quality of data in different blades. Thus, the inherent quality weighting of the conventional Turboprop reconstruction algorithm was unable to compensate for the increased noise in the diffusion tensor due to brain pulsation. Cardiac-induced brain pulsation increases the TVDT in Turboprop DTI. Use of cardiac gating to limit data acquisition to the diastolic period of the cardiac cycle reduces the TVDT at the expense of imaging time. (c) 2008 Wiley-Liss, Inc.

Gallium diffusion in zinc oxide via the paired dopant-vacancy mechanism

NASA Astrophysics Data System (ADS)

Sky, T. N.; Johansen, K. M.; Riise, H. N.; Svensson, B. G.; Vines, L.

2018-02-01

Isochronal and isothermal diffusion experiments of gallium (Ga) in zinc oxide (ZnO) have been performed in the temperature range of 900-1050 °C. The samples used consisted of a sputter-deposited and highly Ga-doped ZnO film at the surface of a single-crystal bulk material. We use a novel reaction diffusion (RD) approach to demonstrate that the diffusion behavior of Ga in ZnO is consistent with zinc vacancy (VZn) mediation via the formation and dissociation of GaZnVZn complexes. In the RD modeling, experimental diffusion data are fitted utilizing recent density-functional-theory estimates of the VZn formation energy and the binding energy of GaZnVZn. From the RD modeling, a migration energy of 2.3 eV is deduced for GaZnVZn, and a total/effective activation energy of 3.0 eV is obtained for the Ga diffusion. Furthermore, and for comparison, employing the so-called Fair model, a total/effective activation energy of 2.7 eV is obtained for the Ga diffusion, reasonably close to the total value extracted from the RD-modeling.

Radiative effects of biomass burning aerosols and cloudiness on seasonal carbon cycle in the Amazon region

NASA Astrophysics Data System (ADS)

Moreira, D. S.; Longo, K.; Freitas, S.; Mercado, L. M.; Miller, J. B.; Rosario, N. M. E. D.; Gatti, L.; Yamasoe, M. A.

2017-12-01

The Amazon region is characterized by high cloudiness, mainly due to convective clouds during most of the year due to the high humidity, and heat availability. However, during the Austral winter, the northward movement of the inter-tropical convergence zone (ITCZ) from its climatological position, significantly reducing cloudiness and precipitation, facilitating vegetation fires. Consequently, during these dry months, biomass burning aerosols contribute to relatively high values of aerosol optical depth (AOD) in Amazonia, typically exceeding 1.0 in the 550 nm wavelength. Both clouds and aerosols scatter solar radiation, reducing the direct irradiance and increasing the diffuse fraction that reaches the surface, decreasing near surface temperature and increasing photosynthetically active radiation (PAR) availability. This, in turn, affects energy and CO2 fluxes within the vegetation canopy. We applied an atmospheric model fully coupled to terrestrial carbon cycle model to assess the relative impact of biomass burning aerosols and clouds on CO2 fluxes in the Amazon region. Our results indicate that during most of the year, gross primary productivity (GPP) is high mainly due to high soil moisture and high values of the diffuse fraction of solar irradiation due to cloudiness. Therefore, heterotrophic and autotrophic respiration are both high, increasing the NEE values (i.e. reducing the net land sink). On the other hand, during the dry season, with a significant reduction of cloudiness, the biomass burning aerosol is mainly responsible for the increase in the diffuse fraction of solar irradiation and the GPP of the forest. However, the low soil moisture during the dry season, especially in the eastern Amazon, reduces heterotrophic and autotrophic respiration and thus compensates for reduced GPP compared to the wet season. Different reasons, an anthropogenic one (human induced fires during the dry season) and a natural one (cloudiness), lead to a somewhat stable value of NEE all year long in Amazonia.

Motion immune diffusion imaging using augmented MUSE (AMUSE) for high-resolution multi-shot EPI

PubMed Central

Guhaniyogi, Shayan; Chu, Mei-Lan; Chang, Hing-Chiu; Song, Allen W.; Chen, Nan-kuei

2015-01-01

Purpose To develop new techniques for reducing the effects of microscopic and macroscopic patient motion in diffusion imaging acquired with high-resolution multi-shot EPI. Theory The previously reported Multiplexed Sensitivity Encoding (MUSE) algorithm is extended to account for macroscopic pixel misregistrations as well as motion-induced phase errors in a technique called Augmented MUSE (AMUSE). Furthermore, to obtain more accurate quantitative DTI measures in the presence of subject motion, we also account for the altered diffusion encoding among shots arising from macroscopic motion. Methods MUSE and AMUSE were evaluated on simulated and in vivo motion-corrupted multi-shot diffusion data. Evaluations were made both on the resulting imaging quality and estimated diffusion tensor metrics. Results AMUSE was found to reduce image blurring resulting from macroscopic subject motion compared to MUSE, but yielded inaccurate tensor estimations when neglecting the altered diffusion encoding. Including the altered diffusion encoding in AMUSE produced better estimations of diffusion tensors. Conclusion The use of AMUSE allows for improved image quality and diffusion tensor accuracy in the presence of macroscopic subject motion during multi-shot diffusion imaging. These techniques should facilitate future high-resolution diffusion imaging. PMID:25762216

A critical examination of the validity of simplified models for radiant heat transfer analysis.

NASA Technical Reports Server (NTRS)

Toor, J. S.; Viskanta, R.

1972-01-01

Examination of the directional effects of the simplified models by comparing the experimental data with the predictions based on simple and more detailed models for the radiation characteristics of surfaces. Analytical results indicate that the constant property diffuse and specular models do not yield the upper and lower bounds on local radiant heat flux. In general, the constant property specular analysis yields higher values of irradiation than the constant property diffuse analysis. A diffuse surface in the enclosure appears to destroy the effect of specularity of the other surfaces. Semigray and gray analyses predict the irradiation reasonably well provided that the directional properties and the specularity of the surfaces are taken into account. The uniform and nonuniform radiosity diffuse models are in satisfactory agreement with each other.

Simulations of eddy kinetic energy transport in barotropic turbulence

NASA Astrophysics Data System (ADS)

Grooms, Ian

2017-11-01

Eddy energy transport in rotating two-dimensional turbulence is investigated using numerical simulation. Stochastic forcing is used to generate an inhomogeneous field of turbulence and the time-mean energy profile is diagnosed. An advective-diffusive model for the transport is fit to the simulation data by requiring the model to accurately predict the observed time-mean energy distribution. Isotropic harmonic diffusion of energy is found to be an accurate model in the case of uniform, solid-body background rotation (the f plane), with a diffusivity that scales reasonably well with a mixing-length law κ ∝V ℓ , where V and ℓ are characteristic eddy velocity and length scales. Passive tracer dynamics are added and it is found that the energy diffusivity is 75 % of the tracer diffusivity. The addition of a differential background rotation with constant vorticity gradient β leads to significant changes to the energy transport. The eddies generate and interact with a mean flow that advects the eddy energy. Mean advection plus anisotropic diffusion (with reduced diffusivity in the direction of the background vorticity gradient) is moderately accurate for flows with scale separation between the eddies and mean flow, but anisotropic diffusion becomes a much less accurate model of the transport when scale separation breaks down. Finally, it is observed that the time-mean eddy energy does not look like the actual eddy energy distribution at any instant of time. In the future, stochastic models of the eddy energy transport may prove more useful than models of the mean transport for predicting realistic eddy energy distributions.

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

NASA Astrophysics Data System (ADS)

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

2007-11-01

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

Evaluation of Land Use, Land Management and Soil Conservation Strategies to Reduce Non-Point Source Pollution Loads in the Three Gorges Region, China

NASA Astrophysics Data System (ADS)

Strehmel, Alexander; Schmalz, Britta; Fohrer, Nicola

2016-11-01

The construction of the Three Gorges Dam in China and the subsequent impoundment of the Yangtze River have induced a major land use change in the Three Gorges Reservoir Region, which fosters increased inputs of sediment and nutrients from diffuse sources into the water bodies. Several government programs have been implemented to mitigate high sediment and nutrient loads to the reservoir. However, institutional weaknesses and a focus on economic development have so far widely counteracted the effectiveness of these programs. In this study, the eco-hydrological model soil and water assessment tool is used to assess the effects of changes in fertilizer amounts and the conditions of bench terraces in the Xiangxi catchment in the Three Gorges Reservoir Region on diffuse matter releases. With this, the study aims at identifying efficient management measures, which should have priority. The results show that a reduction of fertilizer amounts cannot reduce phosphorus loads considerably without inhibiting crop productivity. The condition of terraces in the catchment has a strong impact on soil erosion and phosphorus releases from agricultural areas. Hence, if economically feasible, programmes focusing on the construction and maintenance of terraces in the region should be implemented. Additionally, intercropping on corn fields as well as more efficient fertilization schemes for agricultural land were identified as potential instruments to reduce diffuse matter loads further. While the study was carried out in the Three Gorges Region, its findings may also beneficial for the reduction of water pollution in other mountainous areas with strong agricultural use.

Evaluation of Land Use, Land Management and Soil Conservation Strategies to Reduce Non-Point Source Pollution Loads in the Three Gorges Region, China.

PubMed

Strehmel, Alexander; Schmalz, Britta; Fohrer, Nicola

2016-11-01

The construction of the Three Gorges Dam in China and the subsequent impoundment of the Yangtze River have induced a major land use change in the Three Gorges Reservoir Region, which fosters increased inputs of sediment and nutrients from diffuse sources into the water bodies. Several government programs have been implemented to mitigate high sediment and nutrient loads to the reservoir. However, institutional weaknesses and a focus on economic development have so far widely counteracted the effectiveness of these programs. In this study, the eco-hydrological model soil and water assessment tool is used to assess the effects of changes in fertilizer amounts and the conditions of bench terraces in the Xiangxi catchment in the Three Gorges Reservoir Region on diffuse matter releases. With this, the study aims at identifying efficient management measures, which should have priority. The results show that a reduction of fertilizer amounts cannot reduce phosphorus loads considerably without inhibiting crop productivity. The condition of terraces in the catchment has a strong impact on soil erosion and phosphorus releases from agricultural areas. Hence, if economically feasible, programmes focusing on the construction and maintenance of terraces in the region should be implemented. Additionally, intercropping on corn fields as well as more efficient fertilization schemes for agricultural land were identified as potential instruments to reduce diffuse matter loads further. While the study was carried out in the Three Gorges Region, its findings may also beneficial for the reduction of water pollution in other mountainous areas with strong agricultural use.

Hydroxylamine diffusion can enhance N₂O emissions in nitrifying biofilms: a modeling study.

PubMed

Sabba, Fabrizio; Picioreanu, Cristian; Pérez, Julio; Nerenberg, Robert

2015-02-03

Wastewater treatment plants can be significant sources of nitrous oxide (N2O), a potent greenhouse gas. However, little is known about N2O emissions from biofilm processes. We adapted an existing suspended-growth mathematical model to explore N2O emissions from nitrifying biofilms. The model included N2O formation by ammonia-oxidizing bacteria (AOB) via the hydroxylamine and the nitrifier denitrification pathways. Our model suggested that N2O emissions from nitrifying biofilms could be significantly greater than from suspended growth systems under similar conditions. The main cause was the formation and diffusion of hydroxylamine, an AOB nitrification intermediate, from the aerobic to the anoxic regions of the biofilm. In the anoxic regions, hydroxylamine oxidation by AOB provided reducing equivalents used solely for nitrite reduction to N2O, since there was no competition with oxygen. For a continuous system, very high and very low dissolved oxygen (DO) concentrations resulted in lower emissions, while intermediate values led to higher emissions. Higher bulk ammonia concentrations and greater biofilm thicknesses increased emissions. The model effectively predicted N2O emissions from an actual pilot-scale granular sludge reactor for sidestream nitritation, but significantly underestimated the emissions when the NH2OH diffusion coefficient was assumed to be minimal. This numerical study suggests an unexpected and important role of hydroxylamine in N2O emission in biofilms.

The influence of polarizability and charge transfer on specific ion effects in the dynamics of aqueous salt solutions

NASA Astrophysics Data System (ADS)

Nguyen, Mary; Rick, Steven W.

2018-06-01

The diffusion rates for water molecules in salt solutions depend on the identity of the ions, as well as their concentration. Among the alkali metal ions, cesium and potassium increase and sodium strongly decreases the diffusion constant of water. The origin of the difference can be understood by examining the simulation results using different potential models. In this work, aqueous solutions of salts are simulated with a variety of models. Commonly used non-polarizable models, which otherwise reproduce many experimental properties, do not capture the trend in the diffusion constant, while models which include polarization and/or charge transfer interactions do. For the non-polarizable models, the diffusion constant decreases too strongly with salt concentration. The changes in the water diffusion constant with increasing salt concentration match the diffusion constant of the ion. The ion diffusion constant is dependent on the residence time for water in the ion solvation shell. The non-polarizable models over-estimate the residence time, relative to the translational diffusion constant and so tend to under-estimate the ion and water diffusion constants.

Reconciling transport models across scales: The role of volume exclusion

NASA Astrophysics Data System (ADS)

Taylor, P. R.; Yates, C. A.; Simpson, M. J.; Baker, R. E.

2015-10-01

Diffusive transport is a universal phenomenon, throughout both biological and physical sciences, and models of diffusion are routinely used to interrogate diffusion-driven processes. However, most models neglect to take into account the role of volume exclusion, which can significantly alter diffusive transport, particularly within biological systems where the diffusing particles might occupy a significant fraction of the available space. In this work we use a random walk approach to provide a means to reconcile models that incorporate crowding effects on different spatial scales. Our work demonstrates that coarse-grained models incorporating simplified descriptions of excluded volume can be used in many circumstances, but that care must be taken in pushing the coarse-graining process too far.

Jump rates for surface diffusion of large molecules from first principles

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

Shea, Patrick, E-mail: patrick.shea@dal.ca; Kreuzer, Hans Jürgen

2015-04-21

We apply a recently developed stochastic model for the surface diffusion of large molecules to calculate jump rates for 9,10-dithioanthracene on a Cu(111) surface. The necessary input parameters for the stochastic model are calculated from first principles using density functional theory (DFT). We find that the inclusion of van der Waals corrections to the DFT energies is critical to obtain good agreement with experimental results for the adsorption geometry and energy barrier for diffusion. The predictions for jump rates in our model are in excellent agreement with measured values and show a marked improvement over transition state theory (TST). Wemore » find that the jump rate prefactor is reduced by an order of magnitude from the TST estimate due to frictional damping resulting from energy exchange with surface phonons, as well as a rotational mode of the diffusing molecule.« less

Modeling of hydrogen-air diffusion flame

NASA Technical Reports Server (NTRS)

Isaac, Kakkattukuzhy

1988-01-01

The present research objective is to determine the effects of contaminants on extinction limits of simple, well defined, counterflow Hydrogen 2-air diffusion flames, with combustion at 1 atmosphere. Results of extinction studies and other flame characterizations, with appropriate mechanistic modeling (presently underway), will be used to rationalize the observed effects of contamination over a reasonably wide range of diffusion flame conditions. The knowledge gained should help efforts to anticipate the effects of contaminants on combustion processes in Hydrogen 2-fueled scramjets.

Methane oxidation and formation of EPS in compost: effect of oxygen concentration.

PubMed

Wilshusen, J H; Hettiaratchi, J P A; De Visscher, A; Saint-Fort, R

2004-05-01

Oxygen concentration plays an important role in the regulation of methane oxidation and the microbial ecology of methanotrophs. However, this effect is still poorly quantified in soil and compost ecosystems. The effect of oxygen on the formation of exopolymeric substances (EPS) is as yet unknown. We studied the effect of oxygen on the evolution of methanotrophic activity. At both high and low oxygen concentrations, peak activity was observed twice within a period of 6 months. Phospholipid fatty acid analysis showed that there was a shift from type I to type II methanotrophs during this period. At high oxygen concentration, EPS production was about 250% of the amount at low oxygen concentration. It is hypothesized that EPS serves as a carbon cycling mechanism for type I methanotrophs when inorganic nitrogen is limiting. Simultaneously, EPS stimulates nitrogenase activity in type II methanotrophs by creating oxygen-depleted zones. The kinetic results were incorporated in a simulation model for gas transport and methane oxidation in a passively aerated biofilter. Comparison between the model and experimental data showed that, besides acting as a micro-scale diffusion barrier, EPS can act as a barrier to macro-scale diffusion, reducing the performance of such biofilters.

Peltier-based cloud chamber

NASA Astrophysics Data System (ADS)

Nar, Sevda Yeliz; Cakir, Altan

2018-02-01

Particles produced by nuclear decay, cosmic radiation and reactions can be identified through various methods. One of these methods that has been effective in the last century is the cloud chamber. The chamber makes visible cosmic particles that we are exposed to radiation per second. Diffusion cloud chamber is a kind of cloud chamber that is cooled by dry ice. This traditional model has some application difficulties. In this work, Peltier-based cloud chamber cooled by thermoelectric modules is studied. The new model provided uniformly cooled base of the chamber, moreover, it has longer lifetime than the traditional chamber in terms of observation time. This gain has reduced the costs which spent each time for cosmic particle observation. The chamber is an easy-to-use system according to traditional diffusion cloud chamber. The new model is portable, easier to make, and can be used in the nuclear physics experiments. In addition, it would be very useful to observe Muons which are the direct evidence for Lorentz contraction and time expansion predicted by Einsteins special relativity principle.

Structure and Dynamics of Solvent Landscapes in Charge-Transfer Reactions

NASA Astrophysics Data System (ADS)

Leite, Vitor B. Pereira

The dynamics of solvent polarization plays a major role in the control of charge transfer reactions. The success of Marcus theory describing the solvent influence via a single collective quadratic polarization coordinate has been remarkable. Onuchic and Wolynes have recently proposed (J. Chem Phys 98 (3) 2218, 1993) a simple model demonstrating how a many-dimensional-complex model composed by several dipole moments (representing solvent molecules or polar groups in proteins) can be reduced under the appropriate limits into the Marcus Model. This work presents a dynamical study of the same model, which is characterized by two parameters, an average dipole-dipole interaction as a term associated with the potential energy landscape roughness. It is shown why the effective potential, obtained using a thermodynamic approach, is appropriate for the dynamics of the system. At high temperatures, the system exhibits effective diffusive one-dimensional dynamics, where the Born-Marcus limit is recovered. At low temperatures, a glassy phase appears with a slow non-self-averaging dynamics. At intermediate temperatures, the concept of equivalent diffusion paths and polarization dependence effects are discussed. This approach is extended to treat more realistic solvent models. Real solvents are discussed in terms of simple parameters described above, and an analysis of how different regimes affect the rate of charge transfer is presented. Finally, these ideas are correlated to analogous problems in other areas.

Numerical simulations of short-mixing-time double-wave-vector diffusion-weighting experiments with multiple concatenations on whole-body MR systems

NASA Astrophysics Data System (ADS)

Finsterbusch, Jürgen

2010-12-01

Double- or two-wave-vector diffusion-weighting experiments with short mixing times in which two diffusion-weighting periods are applied in direct succession, are a promising tool to estimate cell sizes in the living tissue. However, the underlying effect, a signal difference between parallel and antiparallel wave vector orientations, is considerably reduced for the long gradient pulses required on whole-body MR systems. Recently, it has been shown that multiple concatenations of the two wave vectors in a single acquisition can double the modulation amplitude if short gradient pulses are used. In this study, numerical simulations of such experiments were performed with parameters achievable with whole-body MR systems. It is shown that the theoretical model yields a good approximation of the signal behavior if an additional term describing free diffusion is included. More importantly, it is demonstrated that the shorter gradient pulses sufficient to achieve the desired diffusion weighting for multiple concatenations, increase the signal modulation considerably, e.g. by a factor of about five for five concatenations. Even at identical echo times, achieved by a shortened diffusion time, a moderate number of concatenations significantly improves the signal modulation. Thus, experiments on whole-body MR systems may benefit from multiple concatenations.

Double-spin-echo diffusion weighting with a modified eddy current adjustment.

PubMed

Finsterbusch, Jürgen

2010-04-01

Magnetic field inhomogeneities like eddy current-related gradient fields cause geometric distortions in echo-planar imaging (EPI). This in particular affects diffusion-weighted imaging where these distortions vary with the direction of the diffusion weighting and hamper the accurate determination of diffusion parameters. The double-spin-echo preparation often used aims to reduce the cumulative eddy current effect by adjusting the diffusion-weighting gradient pulse durations to the time constant of the dominant eddy current contribution. However, eddy currents with a variety of time constants may be present and cause residual distortions. Here, a modification is proposed where the two bipolar gradient pairs of the preparation are adjusted independently to different time constants. At the expense of a slightly prolonged echo time, residual geometric distortions and correspondingly increased values of the diffusion anisotropy can be reduced as is demonstrated in phantoms and the human brain. Thus, it may help to improve the reliability of diffusion-weighted EPI. Copyright 2010 Elsevier Inc. All rights reserved.

Identification and location tasks rely on different mental processes: a diffusion model account of validity effects in spatial cueing paradigms with emotional stimuli.

PubMed

Imhoff, Roland; Lange, Jens; Germar, Markus

2018-02-22

Spatial cueing paradigms are popular tools to assess human attention to emotional stimuli, but different variants of these paradigms differ in what participants' primary task is. In one variant, participants indicate the location of the target (location task), whereas in the other they indicate the shape of the target (identification task). In the present paper we test the idea that although these two variants produce seemingly comparable cue validity effects on response times, they rest on different underlying processes. Across four studies (total N = 397; two in the supplement) using both variants and manipulating the motivational relevance of cue content, diffusion model analyses revealed that cue validity effects in location tasks are primarily driven by response biases, whereas the same effect rests on delay due to attention to the cue in identification tasks. Based on this, we predict and empirically support that a symmetrical distribution of valid and invalid cues would reduce cue validity effects in location tasks to a greater extent than in identification tasks. Across all variants of the task, we fail to replicate the effect of greater cue validity effects for arousing (vs. neutral) stimuli. We discuss the implications of these findings for best practice in spatial cueing research.

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

PubMed Central

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

2015-01-01

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

Diffusion and sorption of organic micropollutants in biofilms with varying thicknesses.

PubMed

Torresi, Elena; Polesel, Fabio; Bester, Kai; Christensson, Magnus; Smets, Barth F; Trapp, Stefan; Andersen, Henrik R; Plósz, Benedek Gy

2017-10-15

Solid-liquid partitioning is one of the main fate processes determining the removal of micropollutants in wastewater. Little is known on the sorption of micropollutants in biofilms, where molecular diffusion may significantly influence partitioning kinetics. In this study, the diffusion and the sorption of 23 micropollutants were investigated in novel moving bed biofilm reactor (MBBR) carriers with controlled biofilm thickness (50, 200 and 500 μm) using targeted batch experiments (initial concentration = 1 μg L -1 , for X-ray contrast media 15 μg L -1 ) and mathematical modelling. We assessed the influence of biofilm thickness and density on the dimensionless effective diffusivity coefficient f (equal to the biofilm-to-aqueous diffusivity ratio) and the distribution coefficient K d,eq (L g -1 ). Sorption was significant only for eight positively charged micropollutants (atenolol, metoprolol, propranolol, citalopram, venlafaxine, erythromycin, clarithromycin and roxithromycin), revealing the importance of electrostatic interactions with solids. Sorption equilibria were likely not reached within the duration of batch experiments (4 h), particularly for the thickest biofilm, requiring the calculation of the distribution coefficient K d,eq based on the approximation of the asymptotic equilibrium concentration (t > 4 h). K d,eq values increased with increasing biofilm thickness for all sorptive micropollutants (except atenolol), possibly due to higher porosity and accessible surface area in the thickest biofilm. Positive correlations between K d,eq and micropollutant properties (polarity and molecular size descriptors) were identified but not for all biofilm thicknesses, thus confirming the challenge of improving predictive sorption models for positively charged compounds. A diffusion-sorption model was developed and calibrated against experimental data, and estimated f values also increased with increasing biofilm thickness. This indicates that diffusion in thin biofilms may be strongly limited (f ≪ 0.1) by the high biomass density (reduced porosity). Copyright © 2017 Elsevier Ltd. All rights reserved.

Reducing uncertainty in Climate Response Time Scale by Bayesian Analysis of the 8.2 ka event

NASA Astrophysics Data System (ADS)

Lorenz, A.; Held, H.; Bauer, E.; Schneider von Deimling, T.

2009-04-01

We analyze the possibility of uncertainty reduction in Climate Response Time Scale by utilizing Greenland ice-core data that contain the 8.2 ka event within a Bayesian model-data intercomparison with the Earth system model of intermediate complexity, CLIMBER-2.3. Within a stochastic version of the model it has been possible to mimic the 8.2 ka event within a plausible experimental setting and with relatively good accuracy considering the timing of the event in comparison to other modeling exercises [1]. The simulation of the centennial cold event is effectively determined by the oceanic cooling rate which depends largely on the ocean diffusivity described by diffusion coefficients of relatively wide uncertainty ranges. The idea now is to discriminate between the different values of diffusivities according to their likelihood to rightly represent the duration of the 8.2 ka event and thus to exploit the paleo data to constrain uncertainty in model parameters in analogue to [2]. Implementing this inverse Bayesian Analysis with this model the technical difficulty arises to establish the related likelihood numerically in addition to the uncertain model parameters: While mainstream uncertainty analyses can assume a quasi-Gaussian shape of likelihood, with weather fluctuating around a long term mean, the 8.2 ka event as a highly nonlinear effect precludes such an a priori assumption. As a result of this study [3] the Bayesian Analysis showed a reduction of uncertainty in vertical ocean diffusivity parameters of factor 2 compared to prior knowledge. This learning effect on the model parameters is propagated to other model outputs of interest; e.g. the inverse ocean heat capacity, which is important for the dominant time scale of climate response to anthropogenic forcing which, in combination with climate sensitivity, strongly influences the climate systems reaction for the near- and medium-term future. 1 References [1] E. Bauer, A. Ganopolski, M. Montoya: Simulation of the cold climate event 8200 years ago by meltwater outburst from lake Agassiz. Paleoceanography 19:PA3014, (2004) [2] T. Schneider von Deimling, H. Held, A. Ganopolski, S. Rahmstorf, Climate sensitivity estimated from ensemble simulations of glacial climates, Climate Dynamics 27, 149-163, DOI 10.1007/s00382-006-0126-8 (2006). [3] A. Lorenz, Diploma Thesis, U Potsdam (2007).

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

NASA Astrophysics Data System (ADS)

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

2017-12-01

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

Interplay between inhibited transport and reaction in nanoporous materials

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

Ackerman, David Michael

2013-01-01

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

The influence of clouds and diffuse radiation on ecosystem-atmosphere CO2 and CO18O exhanges

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

Still, C.J.; Riley, W.J.; Biraud, S.C.

2009-05-01

This study evaluates the potential impact of clouds on ecosystem CO{sub 2} and CO{sub 2} isotope fluxes ('isofluxes') in two contrasting ecosystems (a broadleaf deciduous forest and a C{sub 4} grassland), in a region for which cloud cover, meteorological, and isotope data are available for driving the isotope-enabled land surface model, ISOLSM. Our model results indicate a large impact of clouds on ecosystem CO{sub 2} fluxes and isofluxes. Despite lower irradiance on partly cloudy and cloudy days, predicted forest canopy photosynthesis was substantially higher than on clear, sunny days, and the highest carbon uptake was achieved on the cloudiest day.more » This effect was driven by a large increase in light-limited shade leaf photosynthesis following an increase in the diffuse fraction of irradiance. Photosynthetic isofluxes, by contrast, were largest on partly cloudy days, as leaf water isotopic composition was only slightly depleted and photosynthesis was enhanced, as compared to adjacent clear sky days. On the cloudiest day, the forest exhibited intermediate isofluxes: although photosynthesis was highest on this day, leaf-to-atmosphere isofluxes were reduced from a feedback of transpiration on canopy relative humidity and leaf water. Photosynthesis and isofluxes were both reduced in the C{sub 4} grass canopy with increasing cloud cover and diffuse fraction as a result of near-constant light limitation of photosynthesis. These results suggest that some of the unexplained variation in global mean {delta}{sup 18}O of CO{sub 2} may be driven by large-scale changes in clouds and aerosols and their impacts on diffuse radiation, photosynthesis, and relative humidity.« less

[Study on the characteristics of radiance calibration using nonuniformity extended source].

PubMed

Wang, Jian-Wei; Huang, Min; Xiangli, Bin; Tu, Xiao-Long

2013-07-01

Integrating sphere and diffuser are always used as extended source, and they have different effects on radiance calibration of imaging spectrometer with parameter difference. In the present paper, a mathematical model based on the theory of radiative transfer and calibration principle is founded to calculate the irradiance and calibration coefficients on CCD, taking relatively poor uniformity lights-board calibration system for example. The effects of the nonuniformity on the calibration was analyzed, which makes up the correlation of calibration coefficient matrix under ideal and unideal situation. The results show that the nonuniformity makes the viewing angle and the position of the point of intersection of the optical axis and the diffuse reflection plate have relatively large effects on calibration, while the observing distance's effect is small; under different viewing angles, a deviation value can be found that makes the calibration results closest to the desired results. So, the calibration error can be reduced by choosing appropriate deviation value.

Wavenumber distribution in Hopf-wave instability: the reversible Selkov model of glycolytic oscillation.

PubMed

Dutt, Arun K

2005-09-22

We have investigated the short-wave instability due to Hopf bifurcation in a reaction-diffusion model of glycolytic oscillations. Very low values of the ratio d of the diffusion coefficient of the inhibitor (ATP) and that of the activator (ADP) do help to create short waves, whereas high values of the ratio d and the complexing reaction of the activator ADP reduces drastically the wave-instability domain, generating much longer wavelengths.

Kinetic modeling of ultrasound-assisted extraction of phenolic compounds from grape marc: influence of acoustic energy density and temperature.

PubMed

Tao, Yang; Zhang, Zhihang; Sun, Da-Wen

2014-07-01

The effects of acoustic energy density (6.8-47.4 W/L) and temperature (20-50 °C) on the extraction yields of total phenolics and tartaric esters during ultrasound-assisted extraction from grape marc were investigated in this study. The ultrasound treatment was performed in a 25-kHz ultrasound bath system and the 50% aqueous ethanol was used as the solvent. The initial extraction rate and final extraction yield increased with the increase of acoustic energy density and temperature. The two site kinetic model was used to simulate the kinetics of extraction process and the diffusion model based on the Fick's second law was employed to determine the effective diffusion coefficient of phenolics in grape marc. Both models gave satisfactory quality of data fit. The diffusion process was divided into one fast stage and one slow stage and the diffusion coefficients in both stages were calculated. Within the current experimental range, the diffusion coefficients of total phenolics and tartaric esters for both diffusion stages increased with acoustic energy density. Meanwhile, the rise of temperature also resulted in the increase of diffusion coefficients of phenolics except the diffusion coefficient of total phenolics in the fast stage, the value of which being the highest at 40 °C. Moreover, an empirical equation was suggested to correlate the effective diffusion coefficient of phenolics in grape marc with acoustic energy density and temperature. In addition, the performance comparison of ultrasound-assisted extraction and convention methods demonstrates that ultrasound is an effective and promising technology to extract bioactive substances from grape marc. Copyright © 2014 Elsevier B.V. All rights reserved.

Study on low intensity aeration oxygenation model and optimization for shallow water

NASA Astrophysics Data System (ADS)

Chen, Xiao; Ding, Zhibin; Ding, Jian; Wang, Yi

2018-02-01

Aeration/oxygenation is an effective measure to improve self-purification capacity in shallow water treatment while high energy consumption, high noise and expensive management refrain the development and the application of this process. Based on two-film theory, the theoretical model of the three-dimensional partial differential equation of aeration in shallow water is established. In order to simplify the equation, the basic assumptions of gas-liquid mass transfer in vertical direction and concentration diffusion in horizontal direction are proposed based on engineering practice and are tested by the simulation results of gas holdup which are obtained by simulating the gas-liquid two-phase flow in aeration tank under low-intensity condition. Based on the basic assumptions and the theory of shallow permeability, the model of three-dimensional partial differential equations is simplified and the calculation model of low-intensity aeration oxygenation is obtained. The model is verified through comparing the aeration experiment. Conclusions as follows: (1)The calculation model of gas-liquid mass transfer in vertical direction and concentration diffusion in horizontal direction can reflect the process of aeration well; (2) Under low-intensity conditions, the long-term aeration and oxygenation is theoretically feasible to enhance the self-purification capacity of water bodies; (3) In the case of the same total aeration intensity, the effect of multipoint distributed aeration on the diffusion of oxygen concentration in the horizontal direction is obvious; (4) In the shallow water treatment, reducing the volume of aeration equipment with the methods of miniaturization, array, low-intensity, mobilization to overcome the high energy consumption, large size, noise and other problems can provide a good reference.

Water diffusion in silicate glasses: the effect of glass structure

NASA Astrophysics Data System (ADS)

Kuroda, M.; Tachibana, S.

2016-12-01

Water diffusion in silicate melts (glasses) is one of the main controlling factors of magmatism in a volcanic system. Water diffusivity in silicate glasses depends on its own concentration. However, the mechanism causing those dependences has not been fully understood yet. In order to construct a general model for water diffusion in various silicate glasses, we performed water diffusion experiments in silica glass and proposed a new water diffusion model [Kuroda et al., 2015]. In the model, water diffusivity is controlled by the concentration of both main diffusion species (i.e. molecular water) and diffusion pathways, which are determined by the concentrations of hydroxyl groups and network modifier cations. The model well explains the water diffusivity in various silicate glasses from silica glass to basalt glass. However, pre-exponential factors of water diffusivity in various glasses show five orders of magnitude variations although the pre-exponential factor should ideally represent the jump frequency and the jump distance of molecular water and show a much smaller variation. Here, we attribute the large variation of pre-exponential factors to a glass structure dependence of activation energy for molecular water diffusion. It has been known that the activation energy depends on the water concentration [Nowak and Behrens, 1997]. The concentration of hydroxyls, which cut Si-O-Si network in the glass structure, increases with water concentration, resulting in lowering the activation energy for water diffusion probably due to more fragmented structure. Network modifier cations are likely to play the same role as water. With taking the effect of glass structure into account, we found that the variation of pre-exponential factors of water diffusivity in silicate glasses can be much smaller than the five orders of magnitude, implying that the diffusion of molecular water in silicate glasses is controlled by the same atomic process.

Using Perturbation Theory to Reduce Noise in Diffusion Tensor Fields

PubMed Central

Bansal, Ravi; Staib, Lawrence H.; Xu, Dongrong; Laine, Andrew F.; Liu, Jun; Peterson, Bradley S.

2009-01-01

We propose the use of Perturbation theory to reduce noise in Diffusion Tensor (DT) fields. Diffusion Tensor Imaging (DTI) encodes the diffusion of water molecules along different spatial directions in a positive-definite, 3 × 3 symmetric tensor. Eigenvectors and eigenvalues of DTs allow the in vivo visualization and quantitative analysis of white matter fiber bundles across the brain. The validity and reliability of these analyses are limited, however, by the low spatial resolution and low Signal-to-Noise Ratio (SNR) in DTI datasets. Our procedures can be applied to improve the validity and reliability of these quantitative analyses by reducing noise in the tensor fields. We model a tensor field as a three-dimensional Markov Random Field and then compute the likelihood and the prior terms of this model using Perturbation theory. The prior term constrains the tensor field to be smooth, whereas the likelihood term constrains the smoothed tensor field to be similar to the original field. Thus, the proposed method generates a smoothed field that is close in structure to the original tensor field. We evaluate the performance of our method both visually and quantitatively using synthetic and real-world datasets. We quantitatively assess the performance of our method by computing the SNR for eigenvalues and the coherence measures for eigenvectors of DTs across tensor fields. In addition, we quantitatively compare the performance of our procedures with the performance of one method that uses a Riemannian distance to compute the similarity between two tensors, and with another method that reduces noise in tensor fields by anisotropically filtering the diffusion weighted images that are used to estimate diffusion tensors. These experiments demonstrate that our method significantly increases the coherence of the eigenvectors and the SNR of the eigenvalues, while simultaneously preserving the fine structure and boundaries between homogeneous regions, in the smoothed tensor field. PMID:19540791

Chemical ageing and transformation of diffusivity in semi-solid multi-component organic aerosol particles

NASA Astrophysics Data System (ADS)

Pfrang, C.; Shiraiwa, M.; Pöschl, U.

2011-04-01

Recent experimental evidence underlines the importance of reduced diffusivity in amorphous semi-solid or glassy atmospheric aerosols. This paper investigates the impact of diffusivity on the ageing of multi-component reactive organic particles representative of atmospheric cooking aerosols. We apply and extend the recently developed KM-SUB model in a study of a 12-component mixture containing oleic and palmitoleic acids. We demonstrate that changes in the diffusivity may explain the evolution of chemical loss rates in ageing semi-solid particles, and we resolve surface and bulk processes under transient reaction conditions considering diffusivities altered by oligomerisation. This new model treatment allows prediction of the ageing of mixed organic multi-component aerosols over atmospherically relevant time scales and conditions. We illustrate the impact of changing diffusivity on the chemical half-life of reactive components in semi-solid particles, and we demonstrate how solidification and crust formation at the particle surface can affect the chemical transformation of organic aerosols.

Chemical ageing and transformation of diffusivity in semi-solid multi-component organic aerosol particles

NASA Astrophysics Data System (ADS)

Pfrang, C.; Shiraiwa, M.; Pöschl, U.

2011-07-01

Recent experimental evidence underlines the importance of reduced diffusivity in amorphous semi-solid or glassy atmospheric aerosols. This paper investigates the impact of diffusivity on the ageing of multi-component reactive organic particles approximating atmospheric cooking aerosols. We apply and extend the recently developed KM-SUB model in a study of a 12-component mixture containing oleic and palmitoleic acids. We demonstrate that changes in the diffusivity may explain the evolution of chemical loss rates in ageing semi-solid particles, and we resolve surface and bulk processes under transient reaction conditions considering diffusivities altered by oligomerisation. This new model treatment allows prediction of the ageing of mixed organic multi-component aerosols over atmospherically relevant timescales and conditions. We illustrate the impact of changing diffusivity on the chemical half-life of reactive components in semi-solid particles, and we demonstrate how solidification and crust formation at the particle surface can affect the chemical transformation of organic aerosols.

Analysis and correction of gradient nonlinearity bias in ADC measurements

PubMed Central

Malyarenko, Dariya I.; Ross, Brian D.; Chenevert, Thomas L.

2013-01-01

Purpose Gradient nonlinearity of MRI systems leads to spatially-dependent b-values and consequently high non-uniformity errors (10–20%) in ADC measurements over clinically relevant field-of-views. This work seeks practical correction procedure that effectively reduces observed ADC bias for media of arbitrary anisotropy in the fewest measurements. Methods All-inclusive bias analysis considers spatial and time-domain cross-terms for diffusion and imaging gradients. The proposed correction is based on rotation of the gradient nonlinearity tensor into the diffusion gradient frame where spatial bias of b-matrix can be approximated by its Euclidean norm. Correction efficiency of the proposed procedure is numerically evaluated for a range of model diffusion tensor anisotropies and orientations. Results Spatial dependence of nonlinearity correction terms accounts for the bulk (75–95%) of ADC bias for FA = 0.3–0.9. Residual ADC non-uniformity errors are amplified for anisotropic diffusion. This approximation obviates need for full diffusion tensor measurement and diagonalization to derive a corrected ADC. Practical scenarios are outlined for implementation of the correction on clinical MRI systems. Conclusions The proposed simplified correction algorithm appears sufficient to control ADC non-uniformity errors in clinical studies using three orthogonal diffusion measurements. The most efficient reduction of ADC bias for anisotropic medium is achieved with non-lab-based diffusion gradients. PMID:23794533

Effect of Ionic Diffusion on Extracellular Potentials in Neural Tissue

PubMed Central

Halnes, Geir; Mäki-Marttunen, Tuomo; Keller, Daniel; Pettersen, Klas H.; Andreassen, Ole A.

2016-01-01

Recorded potentials in the extracellular space (ECS) of the brain is a standard measure of population activity in neural tissue. Computational models that simulate the relationship between the ECS potential and its underlying neurophysiological processes are commonly used in the interpretation of such measurements. Standard methods, such as volume-conductor theory and current-source density theory, assume that diffusion has a negligible effect on the ECS potential, at least in the range of frequencies picked up by most recording systems. This assumption remains to be verified. We here present a hybrid simulation framework that accounts for diffusive effects on the ECS potential. The framework uses (1) the NEURON simulator to compute the activity and ionic output currents from multicompartmental neuron models, and (2) the electrodiffusive Kirchhoff-Nernst-Planck framework to simulate the resulting dynamics of the potential and ion concentrations in the ECS, accounting for the effect of electrical migration as well as diffusion. Using this framework, we explore the effect that ECS diffusion has on the electrical potential surrounding a small population of 10 pyramidal neurons. The neural model was tuned so that simulations over ∼100 seconds of biological time led to shifts in ECS concentrations by a few millimolars, similar to what has been seen in experiments. By comparing simulations where ECS diffusion was absent with simulations where ECS diffusion was included, we made the following key findings: (i) ECS diffusion shifted the local potential by up to ∼0.2 mV. (ii) The power spectral density (PSD) of the diffusion-evoked potential shifts followed a 1/f2 power law. (iii) Diffusion effects dominated the PSD of the ECS potential for frequencies up to several hertz. In scenarios with large, but physiologically realistic ECS concentration gradients, diffusion was thus found to affect the ECS potential well within the frequency range picked up in experimental recordings. PMID:27820827

Effect of Ionic Diffusion on Extracellular Potentials in Neural Tissue.

PubMed

Halnes, Geir; Mäki-Marttunen, Tuomo; Keller, Daniel; Pettersen, Klas H; Andreassen, Ole A; Einevoll, Gaute T

2016-11-01

Recorded potentials in the extracellular space (ECS) of the brain is a standard measure of population activity in neural tissue. Computational models that simulate the relationship between the ECS potential and its underlying neurophysiological processes are commonly used in the interpretation of such measurements. Standard methods, such as volume-conductor theory and current-source density theory, assume that diffusion has a negligible effect on the ECS potential, at least in the range of frequencies picked up by most recording systems. This assumption remains to be verified. We here present a hybrid simulation framework that accounts for diffusive effects on the ECS potential. The framework uses (1) the NEURON simulator to compute the activity and ionic output currents from multicompartmental neuron models, and (2) the electrodiffusive Kirchhoff-Nernst-Planck framework to simulate the resulting dynamics of the potential and ion concentrations in the ECS, accounting for the effect of electrical migration as well as diffusion. Using this framework, we explore the effect that ECS diffusion has on the electrical potential surrounding a small population of 10 pyramidal neurons. The neural model was tuned so that simulations over ∼100 seconds of biological time led to shifts in ECS concentrations by a few millimolars, similar to what has been seen in experiments. By comparing simulations where ECS diffusion was absent with simulations where ECS diffusion was included, we made the following key findings: (i) ECS diffusion shifted the local potential by up to ∼0.2 mV. (ii) The power spectral density (PSD) of the diffusion-evoked potential shifts followed a 1/f2 power law. (iii) Diffusion effects dominated the PSD of the ECS potential for frequencies up to several hertz. In scenarios with large, but physiologically realistic ECS concentration gradients, diffusion was thus found to affect the ECS potential well within the frequency range picked up in experimental recordings.

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

NASA Astrophysics Data System (ADS)

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

2018-02-01

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

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.

Direct determination of minority carrier diffusion lengths at axial GaAs nanowire p-n junctions.

PubMed

Gutsche, Christoph; Niepelt, Raphael; Gnauck, Martin; Lysov, Andrey; Prost, Werner; Ronning, Carsten; Tegude, Franz-Josef

2012-03-14

Axial GaAs nanowire p-n diodes, possibly one of the core elements of future nanowire solar cells and light emitters, were grown via the Au-assisted vapor-liquid-solid mode, contacted by electron beam lithography, and investigated using electron beam induced current measurements. The minority carrier diffusion lengths and dynamics of both, electrons and holes, were determined directly at the vicinity of the p-n junction. The generated photocurrent shows an exponential decay on both sides of the junction and the extracted diffusion lengths are about 1 order of magnitude lower compared to bulk material due to surface recombination. Moreover, the observed strong diameter-dependence is well in line with the surface-to-volume ratio of semiconductor nanowires. Estimating the surface recombination velocities clearly indicates a nonabrupt p-n junction, which is in essential agreement with the model of delayed dopant incorporation in the Au-assisted vapor-liquid-solid mechanism. Surface passivation using ammonium sulfide effectively reduces the surface recombination and thus leads to higher minority carrier diffusion lengths. © 2012 American Chemical Society

Hydrodynamic and Thermal Slip Effect on Double-Diffusive Free Convective Boundary Layer Flow of a Nanofluid Past a Flat Vertical Plate in the Moving Free Stream

PubMed Central

Khan, Waqar A.; Uddin, Md Jashim; Ismail, A. I. Md.

2013-01-01

The effects of hydrodynamic and thermal slip boundary conditions on the double-diffusive free convective flow of a nanofluid along a semi-infinite flat solid vertical plate are investigated numerically. It is assumed that free stream is moving. The governing boundary layer equations are non-dimensionalized and transformed into a system of nonlinear, coupled similarity equations. The effects of the controlling parameters on the dimensionless velocity, temperature, solute and nanofluid concentration as well as on the reduced Nusselt number, reduced Sherwood number and the reduced nanoparticle Sherwood number are investigated and presented graphically. To the best of our knowledge, the effects of hydrodynamic and thermal slip boundary conditions have not been investigated yet. It is found that the reduced local Nusselt, local solute and the local nanofluid Sherwood numbers increase with hydrodynamic slip and decrease with thermal slip parameters. PMID:23533566

Studies on Molecular and Ion Transport in Silicalite Membranes and Applications as Ion Separator for Redox Flow Battery

NASA Astrophysics Data System (ADS)

Yang, Ruidong

Microporous zeolite membranes have been widely studied for molecular separations based on size exclusion or preferential adsorption-diffusion mechanisms. The MFI-type zeolite membranes were also demonstrated for brine water desalination by molecular sieving effect. In this research, the pure silica MFI-type zeolite (i.e. silicalite) membrane has been for the first time demonstrated for selective permeation of hydrated proton (i.e. H3O+) in acidic electrolyte solutions. The silicalite membrane allows for permeation of H 3O+ ions, but is inaccessible to the large hydrated multivalent vanadium ions due to steric effect. The silicalite membrane has been further demonstrated as an effective ion separator in the all-vanadium redox flow battery (RFB).The silicalite is nonionic and its proton conductivity relies on the electric field-driven H3O+ transport through the sub nanometer-sized pores under the RFB operation conditions. The silicalite membrane displayed a significantly reduced self-discharge rate because of its high proton-to-vanadium ion transport selectivity. However, the nonionic nature of the silicalite membrane and very small diffusion channel size render low proton conductivity and is therefore inefficient as ion exchange membranes (IEMs) for practical applications. The proton transport efficiency may be improved by reducing the membrane thickness. However, the zeolite thin films are extremely fragile and must be supported on mechanically strong and rigid porous substrates. In this work, silicalite-Nafion composite membranes were synthesized to achieve a colloidal silicalite skin on the Nafion thin film base. The "colloidal zeolite-ionic polymer" layered composite membrane combines the advantages of high proton-selectivity of the zeolite layer and the mechanical flexibility and low proton transport resistance of the ionic polymer membrane. The composite membrane exhibited higher proton/vanadium ion separation selectivity and lower electrical resistance than the commercial Nafion 117 membrane. The high proton transport selectivity is a result of the molecular sieving effect between the H3O+ and multivalent vanadium ions by the zeolitic pores; thus the zeolite particles significantly reduced the effective membrane surface area for vanadium ion permeation. The low resistance of the composite membrane can be attributed to the reduced thickness of the Nafion base film and the thinness of the colloidal silicalite top layer. The composite membrane outperformed the Nafion 117 membrane in the vanadium RFB operation in terms of the overall charge-discharge energy efficiency. Efforts have been made in further investigation of ion and molecular transport diffusivity in the polycrystalline silicalite film using zeolite-coated optical fiber interferometers. A physical model has been established for analyzing the molecular diffusivity in the zeolite layer based on the temporal responses of the optical interferometric signals during the transient process of molecular sorption. Experiments were first carried out to study the diffusivity of isobutane to evaluate the effectiveness of the proposed optical method. The isobutane diffusivities in silicalite measured by this method were in good agreement with the values reported in literature. The zeolite coated fiber optic interferometer was however ineffective in monitoring ion sorption or ion exchange in the silicalite films. It is suggested that more sensitive fiber optic devices are needed for studying the ion diffusion.

Multiscale diffusion in the mitotic Drosophila melanogaster syncytial blastoderm

PubMed Central

Daniels, Brian R.; Rikhy, Richa; Renz, Malte; Dobrowsky, Terrence M.; Lippincott-Schwartz, Jennifer

2012-01-01

Despite the fundamental importance of diffusion for embryonic morphogen gradient formation in the early Drosophila melanogaster embryo, there remains controversy regarding both the extent and the rate of diffusion of well-characterized morphogens. Furthermore, the recent observation of diffusional “compartmentalization” has suggested that diffusion may in fact be nonideal and mediated by an as-yet-unidentified mechanism. Here, we characterize the effects of the geometry of the early syncytial Drosophila embryo on the effective diffusivity of cytoplasmic proteins. Our results demonstrate that the presence of transient mitotic membrane furrows results in a multiscale diffusion effect that has a significant impact on effective diffusion rates across the embryo. Using a combination of live-cell experiments and computational modeling, we characterize these effects and relate effective bulk diffusion rates to instantaneous diffusion coefficients throughout the syncytial blastoderm nuclear cycle phase of the early embryo. This multiscale effect may be related to the effect of interphase nuclei on effective diffusion, and thus we propose that an as-yet-unidentified role of syncytial membrane furrows is to temporally regulate bulk embryonic diffusion rates to balance the multiscale effect of interphase nuclei, which ultimately stabilizes the shapes of various morphogen gradients. PMID:22592793

An axisymmetric non-hydrostatic model for double-diffusive water systems

NASA Astrophysics Data System (ADS)

Hilgersom, Koen; Zijlema, Marcel; van de Giesen, Nick

2018-02-01

The three-dimensional (3-D) modelling of water systems involving double-diffusive processes is challenging due to the large computation times required to solve the flow and transport of constituents. In 3-D systems that approach axisymmetry around a central location, computation times can be reduced by applying a 2-D axisymmetric model set-up. This article applies the Reynolds-averaged Navier-Stokes equations described in cylindrical coordinates and integrates them to guarantee mass and momentum conservation. The discretized equations are presented in a way that a Cartesian finite-volume model can be easily extended to the developed framework, which is demonstrated by the implementation into a non-hydrostatic free-surface flow model. This model employs temperature- and salinity-dependent densities, molecular diffusivities, and kinematic viscosity. One quantitative case study, based on an analytical solution derived for the radial expansion of a dense water layer, and two qualitative case studies demonstrate a good behaviour of the model for seepage inflows with contrasting salinities and temperatures. Four case studies with respect to double-diffusive processes in a stratified water body demonstrate that turbulent flows are not yet correctly modelled near the interfaces and that an advanced turbulence model is required.

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.

Mapping the parameter space of a T2-dependent model of water diffusion MR in brain tissue.

PubMed

Hansen, Brian; Vestergaard-Poulsen, Peter

2006-10-01

We present a new model for describing the diffusion-weighted (DW) proton nuclear magnetic resonance signal obtained from normal grey matter. Our model is analytical and, in some respects, is an extension of earlier model schemes. We model tissue as composed of three separate compartments with individual properties of diffusion and transverse relaxation. Our study assumes slow exchange between compartments. We attempt to take cell morphology into account, along with its effect on water diffusion in tissues. Using this model, we simulate diffusion-sensitive MR signals and compare model output to experimental data from human grey matter. In doing this comparison, we perform a global search for good fits in the parameter space of the model. The characteristic nonmonoexponential behavior of the signal as a function of experimental b value is reproduced quite well, along with established values for tissue-specific parameters such as volume fraction, tortuosity and apparent diffusion coefficient. We believe that the presented approach to modeling diffusion in grey matter adds new aspects to the treatment of a longstanding problem.

Vertical distribution and composition of phytoplankton under the influence of an upper mixed layer.

PubMed

Ryabov, Alexei B; Rudolf, Lars; Blasius, Bernd

2010-03-07

The vertical distribution of phytoplankton is of fundamental importance for the dynamics and structure of aquatic communities. Here, using an advection-reaction-diffusion model, we investigate the distribution and competition of phytoplankton species in a water column, in which inverse resource gradients of light and a nutrient can limit growth of the biomass. This problem poses a challenge for ecologists, as the location of a production layer is not fixed, but rather depends on many internal parameters and environmental factors. In particular, we study the influence of an upper mixed layer (UML) in this system and show that it leads to a variety of dynamic effects: (i) Our model predicts alternative density profiles with a maximum of biomass either within or below the UML, thereby the system may be bistable or the relaxation from an unstable state may require a long-lasting transition. (ii) Reduced mixing in the deep layer can induce oscillations of the biomass; we show that a UML can sustain these oscillations even if the diffusivity is less than the critical mixing for a sinking phytoplankton population. (iii) A UML can strongly modify the outcome of competition between different phytoplankton species, yielding bistability both in the spatial distribution and in the species composition. (iv) A light limited species can obtain a competitive advantage if the diffusivity in the deep layers is reduced below a critical value. This yields a subtle competitive exclusion effect, where the oscillatory states in the deep layers are displaced by steady solutions in the UML. Finally, we present a novel graphical approach for deducing the competition outcome and for the analysis of the role of a UML in aquatic systems. 2009 Elsevier Ltd. All rights reserved.

Multi-mode Li diffusion in natural zircons: Evidence for diffusion in the presence of step-function concentration boundaries

NASA Astrophysics Data System (ADS)

Tang, Ming; Rudnick, Roberta L.; McDonough, William F.; Bose, Maitrayee; Goreva, Yulia

2017-09-01

Micron- to submicron-scale observations of Li distribution and Li isotope composition profiles can be used to infer the mechanisms of Li diffusion in natural zircon. Extreme fractionation (20-30‰) within each single crystal studied here confirms that Li diffusion commonly occurs in zircon. Sharp Li concentration gradients frequently seen in zircons suggest that the effective diffusivity of Li is significantly slower than experimentally determined (Cherniak and Watson, 2010; Trail et al., 2016), otherwise the crystallization/metamorphic heating of these zircons would have to be unrealistically fast (years to tens of years). Charge coupling with REE and Y has been suggested as a mechanism that may considerably reduce Li diffusivity in zircon (Ushikubo et al., 2008; Bouvier et al., 2012). We show that Li diffused in the direction of decreasing Li/Y ratio and increasing Li concentration (uphill diffusion) in one of the zircons, demonstrating charge coupling with REE and Y. Quantitative modeling reveals that Li may diffuse in at least two modes in natural zircons: one being slow and possibly coupled with REE+Y, and the other one being fast and not coupled with REE+Y. The partitioning of Li between these two modes during its diffusion may depend on the pre-diffusion substitution mechanism of REE and Y in the zircon lattice. Based on our results, sharp Li concentration gradients are not indicative of limited diffusion, and can be preserved at temperatures >700 °C on geologic timescales. Finally, large δ7 Li variations observed in the Hadean Jack Hills zircons may record kinetic fractionation, rather than a record of ancient intense weathering in the granite source materials.

On the role of adhesion in single-file dynamics

NASA Astrophysics Data System (ADS)

Fouad, Ahmed M.; Noel, John A.

2017-08-01

For a one-dimensional interacting system of Brownian particles with hard-core interactions (a single-file model), we study the effect of adhesion on both the collective diffusion (diffusion of the entire system with respect to its center of mass) and the tracer diffusion (diffusion of the individual tagged particles). For the case with no adhesion, all properties of these particle systems that are independent of particle labeling (symmetric in all particle coordinates and velocities) are identical to those of non-interacting particles (Lebowitz and Percus, 1967). We clarify this last fact twice. First, we derive our analytical predictions that show that the probability-density functions of single-file (ρsf) and ordinary (ρord) diffusion are identical, ρsf =ρord, predicting a nonanomalous (ordinary) behavior for the collective single-file diffusion, where the average second moment with respect to the center of mass, < x(t) 2 > , is calculated from ρ for both diffusion processes. Second, for single-file diffusion, we show, both analytically and through large-scale simulations, that < x(t) 2 > grows linearly with time, confirming the nonanomalous behavior. This nonanomalous collective behavior comes in contrast to the well-known anomalous sub-diffusion behavior of the individual tagged particles (Harris, 1965). We introduce adhesion to single-file dynamics as a second inter-particle interaction rule and, interestingly, we show that adding adhesion does reduce the magnitudes of both < x(t) 2 > and the mean square displacement per particle Δx2; but the diffusion behavior remains intact independent of adhesion in both cases. Moreover, we study the dependence of both the collective diffusion constant D and the tracer diffusion constant DT on the adhesion coefficient α.

A sun-crown-sensor model and adapted C-correction logic for topographic correction of high resolution forest imagery

NASA Astrophysics Data System (ADS)

Fan, Yuanchao; Koukal, Tatjana; Weisberg, Peter J.

2014-10-01

Canopy shadowing mediated by topography is an important source of radiometric distortion on remote sensing images of rugged terrain. Topographic correction based on the sun-canopy-sensor (SCS) model significantly improved over those based on the sun-terrain-sensor (STS) model for surfaces with high forest canopy cover, because the SCS model considers and preserves the geotropic nature of trees. The SCS model accounts for sub-pixel canopy shadowing effects and normalizes the sunlit canopy area within a pixel. However, it does not account for mutual shadowing between neighboring pixels. Pixel-to-pixel shadowing is especially apparent for fine resolution satellite images in which individual tree crowns are resolved. This paper proposes a new topographic correction model: the sun-crown-sensor (SCnS) model based on high-resolution satellite imagery (IKONOS) and high-precision LiDAR digital elevation model. An improvement on the C-correction logic with a radiance partitioning method to address the effects of diffuse irradiance is also introduced (SCnS + C). In addition, we incorporate a weighting variable, based on pixel shadow fraction, on the direct and diffuse radiance portions to enhance the retrieval of at-sensor radiance and reflectance of highly shadowed tree pixels and form another variety of SCnS model (SCnS + W). Model evaluation with IKONOS test data showed that the new SCnS model outperformed the STS and SCS models in quantifying the correlation between terrain-regulated illumination factor and at-sensor radiance. Our adapted C-correction logic based on the sun-crown-sensor geometry and radiance partitioning better represented the general additive effects of diffuse radiation than C parameters derived from the STS or SCS models. The weighting factor Wt also significantly enhanced correction results by reducing within-class standard deviation and balancing the mean pixel radiance between sunlit and shaded slopes. We analyzed these improvements with model comparison on the red and near infrared bands. The advantages of SCnS + C and SCnS + W on both bands are expected to facilitate forest classification and change detection applications.

Effect of Oblique Electromagnetic Ion Cyclotron Waves on Relativistic Electron Scattering: CRRES Based Calculation

NASA Technical Reports Server (NTRS)

Gamayunov, K. V.; Khazanov, G. V.

2007-01-01

We consider the effect of oblique EMIC waves on relativistic electron scattering in the outer radiation belt using simultaneous observations of plasma and wave parameters from CRRES. The main findings can be s ummarized as follows: 1. In 1comparison with field-aligned waves, int ermediate and highly oblique distributions decrease the range of pitc h-angles subject to diffusion, and reduce the local scattering rate b y an order of magnitude at pitch-angles where the principle absolute value of n = 1 resonances operate. Oblique waves allow the absolute va lue of n > 1 resonances to operate, extending the range of local pitc h-angle diffusion down to the loss cone, and increasing the diffusion at lower pitch angles by orders of magnitude; 2. The local diffusion coefficients derived from CRRES data are qualitatively similar to the local results obtained for prescribed plasma/wave parameters. Conseq uently, it is likely that the bounce-averaged diffusion coefficients, if estimated from concurrent data, will exhibit the dependencies similar to those we found for model calculations; 3. In comparison with f ield-aligned waves, intermediate and highly oblique waves decrease th e bounce-averaged scattering rate near the edge of the equatorial lo ss cone by orders of magnitude if the electron energy does not excee d a threshold (approximately equal to 2 - 5 MeV) depending on specified plasma and/or wave parameters; 4. For greater electron energies_ ob lique waves operating the absolute value of n > 1 resonances are more effective and provide the same bounce_averaged diffusion rate near the loss cone as fiel_aligned waves do.

Report on simulation of fission gas and fission product diffusion in UO 2

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

Andersson, Anders David; Perriot, Romain Thibault; Pastore, Giovanni

2016-07-22

In UO 2 nuclear fuel, the retention and release of fission gas atoms such as xenon (Xe) are important for nuclear fuel performance by, for example, reducing the fuel thermal conductivity, causing fuel swelling that leads to mechanical interaction with the clad, increasing the plenum pressure and reducing the fuel–clad gap thermal conductivity. We use multi-­scale simulations to determine fission gas diffusion mechanisms as well as the corresponding rates in UO 2 under both intrinsic and irradiation conditions. In addition to Xe and Kr, the fission products Zr, Ru, Ce, Y, La, Sr and Ba have been investigated. Density functionalmore » theory (DFT) calculations are used to study formation, binding and migration energies of small clusters of Xe atoms and vacancies. Empirical potential calculations enable us to determine the corresponding entropies and attempt frequencies for migration as well as investigate the properties of large clusters or small fission gas bubbles. A continuum reaction-­diffusion model is developed for Xe and point defects based on the mechanisms and rates obtained from atomistic simulations. Effective fission gas diffusivities are then obtained by solving this set of equations for different chemical and irradiation conditions using the MARMOT phase field code. The predictions are compared to available experimental data. The importance of the large Xe U3O cluster (a Xe atom in a uranium + oxygen vacancy trap site with two bound uranium vacancies) is emphasized, which is a consequence of its high mobility and high binding energy. We find that the Xe U3O cluster gives Xe diffusion coefficients that are higher for intrinsic conditions than under irradiation over a wide range of temperatures. Under irradiation the fast-­moving Xe U3O cluster recombines quickly with irradiation-induced interstitial U ions, while this mechanism is less important for intrinsic conditions. The net result is higher concentration of the Xe U3O cluster for intrinsic conditions than under irradiation. We speculate that differences in the irradiation conditions and their impact on the Xe U3O cluster can explain the wide range of diffusivities reported in experimental studies. However, all vacancy-­mediated mechanisms underestimate the Xe diffusivity compared to the empirical radiation-­enhanced rate used in most fission gas release models. We investigate the possibility that diffusion of small fission gas bubbles or extended Xe-­vacancy clusters may give rise to the observed radiation-­enhanced diffusion coefficient. These studies highlight the importance of U divacancies and an octahedron coordination of uranium vacancies encompassing a Xe fission gas atom. The latter cluster can migrate via a multistep mechanism with a rather low effective barrier, which together with irradiation-induced clusters of uranium vacancies, gives rise to the irradiation-enhanced diffusion coefficient observed in experiments.« less

Application of screened Coulomb potential in fitting DBV star PG 0112+104

NASA Astrophysics Data System (ADS)

Chen, Y. H.

2018-03-01

With 78.7 d of observations for PG 0112+104, a pulsating DB star, from Campaign 8 of Kepler 2 mission, Hermes et al. made a detailed mode identification. A reliable mode identification, with 5 l = 1 modes, 3 l = 2 modes, and 3 l = 1 or 2 modes, was identified. Grids of DBV star models are evolved by WDEC with element diffusion effect of pure Coulomb potential and screened Coulomb potential. Fitting the identified modes of PG 0112+104 by the calculated ones, we studied the difference of element diffusion effect between adopting pure Coulomb potential and screened Coulomb potential. Our aim is to reduce the fitting error by studying new input physics. The starting models including their chemical composition profile are from white dwarf models evolved by MESA. They were calculated following the stellar evolution from the main sequence to the start of the white dwarf cooling sequences. The optimal parameters are basically consistent with that of previous spectroscopic and asteroseismological studies. The pure and screened Coulomb potential lead to different composition profiles of the C/O-He interface area. High k modes are very sensitive to the area. However, most of the observed modes for PG 0112+104 are low k modes. The σRMS taking the screened Coulomb potential is reduced by 4 per cent compared with taking the pure Coulomb potential when fitting the identified low k modes of PG 0112+104. Fitting the Kepler 2 data with our models improved the σRMS of the fit by 27 per cent.

Molecular Dynamics Simulations of Grain Boundary and Bulk Diffusion in Metals.

NASA Astrophysics Data System (ADS)

Plimpton, Steven James

Diffusion is a microscopic mass transport mechanism that underlies many important macroscopic phenomena affecting the structural, electrical, and mechanical properties of metals. This thesis presents results from atomistic simulation studies of diffusion both in bulk and in the fast diffusion paths known as grain boundaries. Using the principles of molecular dynamics single boundaries are studied and their structure and dynamic properties characterized. In particular, tilt boundary bicrystal and bulk models of fcc Al and bcc alpha-Fe are simulated. Diffusion coefficients and activation energies for atomic motion are calculated for both models and compared to experimental data. The influence of the interatomic pair potential on the diffusion is studied in detail. A universal relation between the melting temperature that a pair potential induces in a simulated bulk model and the potential energy barrier height for atomic hopping is derived and used to correlate results for a wide variety of pair potentials. Using these techniques grain boundary and bulk diffusion coefficients for any fcc material can be estimated from simple static calculations without the need to perform more time-consuming dynamic simulations. The influences of two other factors on grain boundary diffusion are also studied because of the interest of the microelectronics industry in the diffusion related reliability problem known as electromigration. The first factor, known to affect the self diffusion rate of Al, is the presence of Cu impurity atoms in Al tilt boundaries. The bicrystal model for Al is seeded randomly with Cu atoms and a simple hybrid Morse potential used to model the Al-Cu interaction. While some effect due to the Cu is noted, it is concluded that pair potentials are likely an inadequate approximation for the alloy system. The second factor studied is the effect of the boundary orientation angle on the diffusion rate. Symmetric bcc Fe boundaries are relaxed to find optimal structures and their diffusion coefficients calculated. Good agreement is found with the dislocation pipe model for tilt boundary diffusion.

Strain effect on the adsorption, diffusion, and molecular dissociation of hydrogen on Mg (0001) surface

NASA Astrophysics Data System (ADS)

Lei, Huaping; Wang, Caizhuang; Yao, Yongxin; Wang, Yangang; Hupalo, Myron; McDougall, Dan; Tringides, Michael; Ho, Kaiming

2013-12-01

The adsorption, diffusion, and molecular dissociation of hydrogen on the biaxially strained Mg (0001) surface have been systematically investigated by the first principle calculations based on density functional theory. When the strain changes from the compressive to tensile state, the adsorption energy of H atom linearly increases while its diffusion barrier linearly decreases oppositely. The dissociation barrier of H2 molecule linearly reduces in the tensile strain region. Through the chemical bonding analysis including the charge density difference, the projected density of states and the Mulliken population, the mechanism of the strain effect on the adsorption of H atom and the dissociation of H2 molecule has been elucidated by an s-p charge transfer model. With the reduction of the orbital overlap between the surface Mg atoms upon the lattice expansion, the charge transfers from p to s states of Mg atoms, which enhances the hybridization of H s and Mg s orbitals. Therefore, the bonding interaction of H with Mg surface is strengthened and then the atomic diffusion and molecular dissociation barriers of hydrogen decrease accordingly. Our works will be helpful to understand and to estimate the influence of the lattice deformation on the performance of Mg-containing hydrogen storage materials.

Thin Layer Drying Kinetics of By-Products from Olive Oil Processing

PubMed Central

Montero, Irene; Miranda, Teresa; Arranz, Jose Ignacio; Rojas, Carmen Victoria

2011-01-01

The thin-layer behavior of by-products from olive oil production was determined in a solar dryer in passive and active operation modes for a temperature range of 20–50 °C. The increase in the air temperature reduced the drying time of olive pomace, sludge and olive mill wastewater. Moisture ratio was analyzed to obtain effective diffusivity values, varying in the oil mill by-products from 9.136 × 10−11 to 1.406 × 10−9 m2/s in forced convection (ma = 0.22 kg/s), and from 9.296 × 10−11 to 6.277 × 10−10 m2/s in natural convection (ma = 0.042 kg/s). Diffusivity values at each temperature were obtained using the Fick’s diffusion model and, regardless of the convection, they increased with the air temperature. The temperature dependence on the effective diffusivity was determined by an Arrhenius type relationship. The activation energies were found to be 38.64 kJ/mol, 30.44 kJ/mol and 47.64 kJ/mol for the olive pomace, the sludge and the olive mill wastewater in active mode, respectively, and 91.35 kJ/mol, 14.04 kJ/mol and 77.15 kJ/mol in natural mode, in that order. PMID:22174639

Modelling of point and diffuse pollution: application of the Moneris model in the Ipojuca river basin, Pernambuco State, Brazil.

PubMed

de Lima Barros, Alessandra Maciel; do Carmo Sobral, Maria; Gunkel, Günter

2013-01-01

Emissions of pollutants and nutrients are causing several problems in aquatic ecosystems, and in general an excess of nutrients, specifically nitrogen and phosphorus, is responsible for the eutrophication process in water bodies. In most developed countries, more attention is given to diffuse pollution because problems with point pollution have already been solved. In many non-developed countries basic data for point and diffuse pollution are not available. The focus of the presented studies is to quantify nutrient emissions from point and diffuse sources in the Ipojuca river basin, Pernambuco State, Brazil, using the Moneris model (Modelling Nutrient Emissions in River Systems). This model has been developed in Germany and has already been implemented in more than 600 river basins. The model is mainly based on river flow, water quality and geographical information system data. According to the Moneris model results, untreated domestic sewage is the major source of nutrients in the Ipojuca river basin. The Moneris model has shown itself to be a useful tool that allows the identification and quantification of point and diffuse nutrient sources, thus enabling the adoption of measures to reduce them. The Moneris model, conducted for the first time in a tropical river basin with intermittent flow, can be used as a reference for implementation in other watersheds.

Polymer/riblet combination for hydrodynamic skin friction reduction

NASA Technical Reports Server (NTRS)

Reed, Jason C. (Inventor); Bushnell, Dennis M. (Inventor)

1995-01-01

A process is disclosed for reducing skin friction and inhibiting the effects of liquid turbulence in a system involving the flow of a liquid along the surface of a body, e.g. a marine vehicle. This process includes injecting a drag reducing polymer into the valleys of adjacent, evenly spaced, longitudinal grooves extending along the length of the surface of the body, so that the rate of diffusion of the polymer from individual grooves into the liquid flow is predictably controlled by the groove dimensions. When the polymer has diffused over the tips of the grooves into the near wall region of the boundary layer, the polymer effectively reduces the turbulent skin friction. A substantial drag reducing effect is achieved with less polymer than must be used to lower skin friction when the surface of the body is smooth.

Polymer/riblet combination for hydrodynamic skin friction reduction

NASA Technical Reports Server (NTRS)

Bushnell, Dennis M. (Inventor); Reed, Jason C. (Inventor)

1990-01-01

A process is disclosed for reducing skin friction and inhibiting the effects of liquid turbulence in a system involving the flow of a liquid along the surface of a body, e.g., a marine vehicle. This process includes injecting a drag reducing polymer into the valleys of adjacent, evenly spaced, longitudinal grooves extending along the length of the surface of the body, so that the rate of diffusion of the polymer from individual grooves into the liquid flow is predictably controlled by the groove dimensions. When the polymer has diffused over the tips of the grooves into the near wall region of the boundary layer, the polymer effectively reduces the turbulent skin friction. A substantial drag reducing effect is achieved with less polymer than must be used to lower skin friction when the surface of the body is smooth.

Characteristics of Perforated Diffusers at Free-stream Mach Number 1.90

NASA Technical Reports Server (NTRS)

Hunczak, Henry R; Kremzier, Emil J

1950-01-01

An investigation was conducted at Mach number 1.90 to determine pressure recovery and mass-flow characteristics of series of perforated convergent-divergent supersonic diffusers. Pressure recoveries as high as 96 percent were obtained, but at reduced mass flows through the diffuser. Theoretical considerations of effect of perforation distribution on shock stability in converging section of diffuser are presented and correlated with experimental data. A method of estimating relative importance of pressure recovery and mass flow on internal thrust coefficient basis is given and a comparison of various diffusers investigated is made.

Quantitative diffusion MRI using reduced field-of-view and multi-shot acquisition techniques: Validation in phantoms and prostate imaging.

PubMed

Zhang, Yuxin; Holmes, James; Rabanillo, Iñaki; Guidon, Arnaud; Wells, Shane; Hernando, Diego

2018-09-01

To evaluate the reproducibility of quantitative diffusion measurements obtained with reduced Field of View (rFOV) and Multi-shot EPI (msEPI) acquisitions, using single-shot EPI (ssEPI) as a reference. Diffusion phantom experiments, and prostate diffusion-weighted imaging in healthy volunteers and patients with known or suspected prostate cancer were performed across the three different sequences. Quantitative diffusion measurements of apparent diffusion coefficient, and diffusion kurtosis parameters (healthy volunteers), were obtained and compared across diffusion sequences (rFOV, msEPI, and ssEPI). Other possible confounding factors like b-value combinations and acquisition parameters were also investigated. Both msEPI and rFOV have shown reproducible quantitative diffusion measurements relative to ssEPI; no significant difference in ADC was observed across pulse sequences in the standard diffusion phantom (p = 0.156), healthy volunteers (p ≥ 0.12) or patients (p ≥ 0.26). The ADC values within the non-cancerous central gland and peripheral zone of patients were 1.29 ± 0.17 × 10 -3  mm 2 /s and 1.74 ± 0.23 × 10 -3  mm 2 /s respectively. However, differences in quantitative diffusion parameters were observed across different number of averages for rFOV, and across b-value groups and diffusion models for all the three sequences. Both rFOV and msEPI have the potential to provide high image quality with reproducible quantitative diffusion measurements in prostate diffusion MRI. Copyright © 2018 Elsevier Inc. All rights reserved.

Detailed numerical investigation of the Bohm limit in cosmic ray diffusion theory

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

Hussein, M.; Shalchi, A., E-mail: m_hussein@physics.umanitoba.ca, E-mail: andreasm4@yahoo.com

2014-04-10

A standard model in cosmic ray diffusion theory is the so-called Bohm limit in which the particle mean free path is assumed to be equal to the Larmor radius. This type of diffusion is often employed to model the propagation and acceleration of energetic particles. However, recent analytical and numerical work has shown that standard Bohm diffusion is not realistic. In the present paper, we perform test-particle simulations to explore particle diffusion in the strong turbulence limit in which the wave field is much stronger than the mean magnetic field. We show that there is indeed a lower limit ofmore » the particle mean free path along the mean field. In this limit, the mean free path is directly proportional to the unperturbed Larmor radius like in the traditional Bohm limit, but it is reduced by the factor δB/B {sub 0} where B {sub 0} is the mean field and δB the turbulent field. Although we focus on parallel diffusion, we also explore diffusion across the mean field in the strong turbulence limit.« less

Reduction of numerical diffusion in three-dimensional vortical flows using a coupled Eulerian/Lagrangian solution procedure

NASA Technical Reports Server (NTRS)

Felici, Helene M.; Drela, Mark

1993-01-01

A new approach based on the coupling of an Eulerian and a Lagrangian solver, aimed at reducing the numerical diffusion errors of standard Eulerian time-marching finite-volume solvers, is presented. The approach is applied to the computation of the secondary flow in two bent pipes and the flow around a 3D wing. Using convective point markers the Lagrangian approach provides a correction of the basic Eulerian solution. The Eulerian flow in turn integrates in time the Lagrangian state-vector. A comparison of coarse and fine grid Eulerian solutions makes it possible to identify numerical diffusion. It is shown that the Eulerian/Lagrangian approach is an effective method for reducing numerical diffusion errors.

Diffusion of subsidized ACTs in accredited drug shops in Tanzania: determinants of stocking and characteristics of early and late adopters

PubMed Central

2013-01-01

Background Many households in sub-Saharan Africa utilize the private sector as a primary source of treatment for malaria episodes. Expanding access to effective treatment in private drug shops may help reduce incidence of severe disease and mortality. This research leveraged a longitudinal survey of stocking of subsidized artemisinin combination therapies (ACTs), an effective anti-malarial, in Accredited Drug Dispensing Outlets (ADDOs) in two regions of Tanzania. This provided a unique opportunity to explore shop and market level determinants of product diffusion in a developing country retail market. Methods 356 ADDOs in the Rukwa and Mtwara regions of Tanzania were surveyed at seven points between Feb 2011 and May 2012. Shop level audits were used to measure the availability of subsidized ACTs at each shop. Data on market and shop level factors were collected during the survey and also extracted from GIS layers. Regression and network based methodologies were used. Shops classified as early and late adopters, following Rogers’ model of product diffusion, were compared. The Bass model of product diffusion was applied to determine whether shops stocked ACTs out of a need to imitate market competitors or a desire to satisfy customer needs. Results Following the introduction of a subsidy for ACTs, stocking increased from 12% to nearly 80% over the seven survey rounds. Stocking was influenced by higher numbers of proximal shops and clinics, larger customer traffic and the presence of a licensed pharmacist. Early adopters were characterized by a larger percentage of customers seeking care for malaria, a larger catchment and sourcing from specific wholesalers/suppliers. The Bass model of product diffusion indicated that shops were adopting products in response to competitor behavior, rather than customer demand. Conclusions Decisions to stock new pharmaceutical products in Tanzanian ADDOs are influenced by a combination of factors related to both market competition and customer demand, but are particularly influenced by the behavior of competing shops. Efforts to expand access to new pharmaceutical products in developing country markets could benefit from initial targeting of high profile shops in competitive markets and wholesale suppliers to encourage faster product diffusion across all drug retailers. PMID:24350611

Diffusion of subsidized ACTs in accredited drug shops in Tanzania: determinants of stocking and characteristics of early and late adopters.

PubMed

Larson, Peter S; Yadav, Prashant; Alphs, Sarah; Arkedis, Jean; Massaga, Julius; Sabot, Oliver; Cohen, Jessica L

2013-12-18

Many households in sub-Saharan Africa utilize the private sector as a primary source of treatment for malaria episodes. Expanding access to effective treatment in private drug shops may help reduce incidence of severe disease and mortality. This research leveraged a longitudinal survey of stocking of subsidized artemisinin combination therapies (ACTs), an effective anti-malarial, in Accredited Drug Dispensing Outlets (ADDOs) in two regions of Tanzania. This provided a unique opportunity to explore shop and market level determinants of product diffusion in a developing country retail market. 356 ADDOs in the Rukwa and Mtwara regions of Tanzania were surveyed at seven points between Feb 2011 and May 2012. Shop level audits were used to measure the availability of subsidized ACTs at each shop. Data on market and shop level factors were collected during the survey and also extracted from GIS layers. Regression and network based methodologies were used. Shops classified as early and late adopters, following Rogers' model of product diffusion, were compared. The Bass model of product diffusion was applied to determine whether shops stocked ACTs out of a need to imitate market competitors or a desire to satisfy customer needs. Following the introduction of a subsidy for ACTs, stocking increased from 12% to nearly 80% over the seven survey rounds. Stocking was influenced by higher numbers of proximal shops and clinics, larger customer traffic and the presence of a licensed pharmacist. Early adopters were characterized by a larger percentage of customers seeking care for malaria, a larger catchment and sourcing from specific wholesalers/suppliers. The Bass model of product diffusion indicated that shops were adopting products in response to competitor behavior, rather than customer demand. Decisions to stock new pharmaceutical products in Tanzanian ADDOs are influenced by a combination of factors related to both market competition and customer demand, but are particularly influenced by the behavior of competing shops. Efforts to expand access to new pharmaceutical products in developing country markets could benefit from initial targeting of high profile shops in competitive markets and wholesale suppliers to encourage faster product diffusion across all drug retailers.

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

The contribution of the diffuse light component to the topographic effect on remotely sensed data

NASA Technical Reports Server (NTRS)

Justice, C.; Holben, B.

1980-01-01

The topographic effect is measured by the difference between the global radiance from inclined surfaces as a function of their orientation relative to the sensor position and light source. The short wave radiant energy incident on a surface is composed of direct sunlight, scattered skylight, and light reflected from surrounding terrain. The latter two components are commonly known as the diffuse component. The contribution of the diffuse light component to the topographic effect was examined and the significance of this diffuse component with respect to two direct radiance models was assessed. Diffuse and global spectral radiances were measured for a series of slopes and aspects of a uniform and surface in the red and photographic infrared parts of the spectrum, using a nadir pointing two channel handheld radiometer. The diffuse light was found to produce a topographic effect which varied from the topographic effect for direct light. The topographic effect caused by diffuse light was found to increase slightly with solar elevation and wavelength for the channels examined. The correlations between data derived from two simple direct radiance simulation models and the field data were not significantly affected when the diffuse component was removed from the radiances. Radiances from a 60 percent reflective surface, assuming no atmospheric path radiance, the diffuse light topographic effect contributed a maximum range of 3 pixel values in simulated LANDSAT data from all aspects with slopes up to 30 degrees.

A Novel Diffuse Fraction-Based Two-Leaf Light Use Efficiency Model: An Application Quantifying Photosynthetic Seasonality across 20 AmeriFlux Flux Tower Sites

NASA Astrophysics Data System (ADS)

Yan, Hao; Wang, Shao-Qiang; Yu, Kai-Liang; Wang, Bin; Yu, Qin; Bohrer, Gil; Billesbach, Dave; Bracho, Rosvel; Rahman, Faiz; Shugart, Herman H.

2017-10-01

Diffuse radiation can increase canopy light use efficiency (LUE). This creates the need to differentiate the effects of direct and diffuse radiation when simulating terrestrial gross primary production (GPP). Here, we present a novel GPP model, the diffuse-fraction-based two-leaf model (DTEC), which includes the leaf response to direct and diffuse radiation, and treats maximum LUE for shaded leaves (ɛmsh defined as a power function of the diffuse fraction (Df)) and sunlit leaves (ɛmsu defined as a constant) separately. An Amazonian rainforest site (KM67) was used to calibrate the model by simulating the linear relationship between monthly canopy LUE and Df. This showed a positive response of forest GPP to atmospheric diffuse radiation, and suggested that diffuse radiation was more limiting than global radiation and water availability for Amazon rainforest GPP on a monthly scale. Further evaluation at 20 independent AmeriFlux sites showed that the DTEC model, when driven by monthly meteorological data and MODIS leaf area index (LAI) products, explained 70% of the variability observed in monthly flux tower GPP. This exceeded the 51% accounted for by the MODIS 17A2 big-leaf GPP product. The DTEC model's explicit accounting for the impacts of diffuse radiation and soil water stress along with its parameterization for C4 and C3 plants was responsible for this difference. The evaluation of DTEC at Amazon rainforest sites demonstrated its potential to capture the unique seasonality of higher GPP during the diffuse radiation-dominated wet season. Our results highlight the importance of diffuse radiation in seasonal GPP simulation.