Distributional behavior of diffusion coefficients obtained by single trajectories in annealed transit time model

NASA Astrophysics Data System (ADS)

Akimoto, Takuma; Yamamoto, Eiji

2016-12-01

Local diffusion coefficients in disordered systems such as spin glass systems and living cells are highly heterogeneous and may change over time. Such a time-dependent and spatially heterogeneous environment results in irreproducibility of single-particle-tracking measurements. Irreproducibility of time-averaged observables has been theoretically studied in the context of weak ergodicity breaking in stochastic processes. Here, we provide rigorous descriptions of equilibrium and non-equilibrium diffusion processes for the annealed transit time model, which is a heterogeneous diffusion model in living cells. We give analytical solutions for the mean square displacement (MSD) and the relative standard deviation of the time-averaged MSD for equilibrium and non-equilibrium situations. We find that the time-averaged MSD grows linearly with time and that the time-averaged diffusion coefficients are intrinsically random (irreproducible) even in the long-time measurements in non-equilibrium situations. Furthermore, the distribution of the time-averaged diffusion coefficients converges to a universal distribution in the sense that it does not depend on initial conditions. Our findings pave the way for a theoretical understanding of distributional behavior of the time-averaged diffusion coefficients in disordered systems.

Measurement of shear-induced diffusion of red blood cells using dynamic light scattering-optical coherence tomography

NASA Astrophysics Data System (ADS)

Tang, Jianbo; Erdener, Sefik Evren; Li, Baoqiang; Fu, Buyin; Sakadzic, Sava; Carp, Stefan A.; Lee, Jonghwan; Boas, David A.

2018-02-01

Dynamic Light Scattering-Optical Coherence Tomography (DLS-OCT) takes the advantages of using DLS to measure particle flow and diffusion within an OCT resolution-constrained 3D volume, enabling the simultaneous measurements of absolute RBC velocity and diffusion coefficient with high spatial resolution. In this work, we applied DLS-OCT to measure both RBC velocity and the shear-induced diffusion coefficient within penetrating venules of the somatosensory cortex of anesthetized mice. Blood flow laminar profile measurements indicate a blunted laminar flow profile, and the degree of blunting decreases with increasing vessel diameter. The measured shear-induced diffusion coefficient was proportional to the flow shear rate with a magnitude of 0.1 to 0.5 × 10-6 mm2 . These results provide important experimental support for the recent theoretical explanation for why DCS is dominantly sensitive to RBC diffusive motion.

Exciton diffusion coefficient measurement in ZnO nanowires under electron beam irradiation.

PubMed

Donatini, Fabrice; Pernot, Julien

2018-03-09

In semiconductor nanowires (NWs) the exciton diffusion coefficient can be determined using a scanning electron microscope fitted with a cathodoluminescence system. High spatial and temporal resolution cathodoluminescence experiments are needed to measure independently the exciton diffusion length and lifetime in single NWs. However, both diffusion length and lifetime can be affected by the electron beam bombardment during observation and measurement. Thus, in this work the exciton lifetime in a ZnO NW is measured versus the electron beam dose (EBD) via a time-resolved cathodoluminescence experiment with a temporal resolution of 50 ps. The behavior of the measured exciton lifetime is consistent with our recent work on the EBD dependence of the exciton diffusion length in similar NWs investigated under comparable SEM conditions. Combining the two results, the exciton diffusion coefficient in ZnO is determined at room temperature and is found constant over the full span of EBD.

Quantification of optical absorption coefficient from acoustic spectra in the optical diffusive regime using photoacoustic microscopy

NASA Astrophysics Data System (ADS)

Guo, Zijian; Favazza, Christopher; Wang, Lihong V.

2012-02-01

Photoacoustic (PA) tomography (PAT) can image optical absorption contrast with ultrasonic spatial resolution in the optical diffusive regime. Multi-wavelength PAT can noninvasively monitor hemoglobin oxygen saturation (sO2) with high sensitivity and fine spatial resolution. However, accurate quantification in PAT requires knowledge of the optical fluence distribution, acoustic wave attenuation, and detection system bandwidth. We propose a method to circumvent this requirement using acoustic spectra of PA signals acquired at two optical wavelengths. With the acoustic spectral method, the absorption coefficients of an oxygenated bovine blood phantom at 560 and 575 nm were quantified with errors of ><5%.

Motion of charged particles normal to an irregular magnetic field. [astrophysical plasmas

NASA Technical Reports Server (NTRS)

Jokipii, J. R.

1975-01-01

The motion is analyzed of charged particles in a fluctuating magnetic field which varies only in directions normal to its mean direction, such as that which would be generated by an ensemble of magnetosonic waves propagating normal to an ambient magnetic field. The appropriate generalization of gradient-drift motion is derived in terms of the power spectrum of the magnetic fluctuations, and an effective spatial diffusion coefficient is obtained. Several special cases are considered, including a Gaussian power spectrum, a power-law spectrum with a cutoff, and a general power-law spectrum. A possible magnitude is calculated for the spatial diffusion coefficient of the solar wind.

Microscale diffusion measurements and simulation of a scaffold with a permeable strut.

PubMed

Lee, Seung Youl; Lee, Byung Ryong; Lee, Jongwan; Kim, Seongjun; Kim, Jung Kyung; Jeong, Young Hun; Jin, Songwan

2013-10-10

Electrospun nanofibrous structures provide good performance to scaffolds in tissue engineering. We measured the local diffusion coefficients of 3-kDa FITC-dextran in line patterns of electrospun nanofibrous structures fabricated by the direct-write electrospinning (DWES) technique using the fluorescence recovery after photobleaching (FRAP) method. No significant differences were detected between DWES line patterns fabricated with polymer supplied at flow rates of 0.1 and 0.5 mL/h. The oxygen diffusion coefficients of samples were estimated to be ~92%-94% of the oxygen diffusion coefficient in water based on the measured diffusion coefficient of 3-kDa FITC-dextran. We also simulated cell growth and distribution within spatially patterned scaffolds with struts consisting of either oxygen-permeable or non-permeable material. The permeable strut scaffolds exhibited enhanced cell growth. Saturated depths at which cells could grow to confluence were 15% deeper for the permeable strut scaffolds than for the non-permeable strut scaffold.

Enhanced Scattering of Diffuse Ions on Front of the Earth's Quasi-Parallel Bow Shock: a Case Study

NASA Astrophysics Data System (ADS)

Kis, A.; Matsukiyo, S.; Otsuka, F.; Hada, T.; Lemperger, I.; Dandouras, I. S.; Barta, V.; Facsko, G. I.

2017-12-01

In the analysis we present a case study of three energetic upstream ion events at the Earth's quasi-parallel bow shock based on multi-spacecraft data recorded by Cluster. The CIS-HIA instrument onboard Cluster provides partial energetic ion densities in 4 energy channels between 10 and 32 keV.The difference of the partial ion densities recorded by the individual spacecraft at various distances from the bow shock surface makes possible the determination of the spatial gradient of energetic ions.Using the gradient values we determined the spatial profile of the energetic ion partial densities as a function of distance from the bow shock and we calculated the e-folding distance and the diffusion coefficient for each event and each ion energy range. Results show that in two cases the scattering of diffuse ions takes place in a normal way, as "by the book", and the e-folding distance and diffusion coefficient values are comparable with previous results. On the other hand, in the third case the e-folding distance and the diffusion coefficient values are significantly lower, which suggests that in this case the scattering process -and therefore the diffusive shock acceleration (DSA) mechanism also- is much more efficient. Our analysis provides an explanation for this "enhanced" scattering process recorded in the third case.

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

PubMed

Foy, Cédric; Picaut, Judicaël; Valeau, Vincent

2016-10-01

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

Homogenization of a Directed Dispersal Model for Animal Movement in a Heterogeneous Environment.

PubMed

Yurk, Brian P

2016-10-01

The dispersal patterns of animals moving through heterogeneous environments have important ecological and epidemiological consequences. In this work, we apply the method of homogenization to analyze an advection-diffusion (AD) model of directed movement in a one-dimensional environment in which the scale of the heterogeneity is small relative to the spatial scale of interest. We show that the large (slow) scale behavior is described by a constant-coefficient diffusion equation under certain assumptions about the fast-scale advection velocity, and we determine a formula for the slow-scale diffusion coefficient in terms of the fast-scale parameters. We extend the homogenization result to predict invasion speeds for an advection-diffusion-reaction (ADR) model with directed dispersal. For periodic environments, the homogenization approximation of the solution of the AD model compares favorably with numerical simulations. Invasion speed approximations for the ADR model also compare favorably with numerical simulations when the spatial period is sufficiently small.

Regulation of NF-κB oscillation by spatial parameters in true intracellular space (TiCS)

NASA Astrophysics Data System (ADS)

Ohshima, Daisuke; Sagara, Hiroshi; Ichikawa, Kazuhisa

2013-10-01

Transcription factor NF-κB is activated by cytokine stimulation, viral infection, or hypoxic environment leading to its translocation to the nucleus. The nuclear NF-κB is exported from the nucleus to the cytoplasm again, and by repetitive import and export, NF-κB shows damped oscillation with the period of 1.5-2.0 h. Oscillation pattern of NF-κB is thought to determine the gene expression profile. We published a report on a computational simulation for the oscillation of nuclear NF-κB in a 3D spherical cell, and showed the importance of spatial parameters such as diffusion coefficient and locus of translation for determining the oscillation pattern. Although the value of diffusion coefficient is inherent to protein species, its effective value can be modified by organelle crowding in intracellular space. Here we tested this possibility by computer simulation. The results indicate that the effective value of diffusion coefficient is significantly changed by the organelle crowding, and this alters the oscillation pattern of nuclear NF-κB.

Data-driven analysis for the temperature and momentum dependence of the heavy-quark diffusion coefficient in relativistic heavy-ion collisions

NASA Astrophysics Data System (ADS)

Xu, Yingru; Bernhard, Jonah E.; Bass, Steffen A.; Nahrgang, Marlene; Cao, Shanshan

2018-01-01

By applying a Bayesian model-to-data analysis, we estimate the temperature and momentum dependence of the heavy quark diffusion coefficient in an improved Langevin framework. The posterior range of the diffusion coefficient is obtained by performing a Markov chain Monte Carlo random walk and calibrating on the experimental data of D -meson RAA and v2 in three different collision systems at the Relativistic Heavy-Ion Collidaer (RHIC) and the Large Hadron Collider (LHC): Au-Au collisions at 200 GeV and Pb-Pb collisions at 2.76 and 5.02 TeV. The spatial diffusion coefficient is found to be consistent with lattice QCD calculations and comparable with other models' estimation. We demonstrate the capability of our improved Langevin model to simultaneously describe the RAA and v2 at both RHIC and the LHC energies, as well as the higher order flow coefficient such as D meson v3. We show that by applying a Bayesian analysis, we are able to quantitatively and systematically study the heavy flavor dynamics in heavy-ion collisions.

Understanding the spectral hardenings and radial distribution of Galactic cosmic rays and Fermi diffuse γ rays with spatially-dependent propagation

NASA Astrophysics Data System (ADS)

Guo, Yi-Qing; Yuan, Qiang

2018-03-01

Recent direct measurements of Galactic cosmic ray spectra by balloon/space-borne detectors reveal spectral hardenings of all major nucleus species at rigidities of a few hundred GV. The all-sky diffuse γ -ray emissions measured by the Fermi Large Area Telescope also show spatial variations of the intensities and spectral indices of cosmic rays. These new observations challenge the traditional simple acceleration and/or propagation scenario of Galactic cosmic rays. In this work, we propose a spatially dependent diffusion scenario to explain all these phenomena. The diffusion coefficient is assumed to be anticorrelated with the source distribution, which is a natural expectation from the charged particle transportation in a turbulent magnetic field. The spatially dependent diffusion model also gives a lower level of anisotropies of cosmic rays, which are consistent with observations by underground muons and air shower experiments. The spectral variations of cosmic rays across the Galaxy can be properly reproduced by this model.

LASERS IN MEDICINE: Determination of the optical characteristics of turbid media by the laser optoacoustic method

NASA Astrophysics Data System (ADS)

Karabutov, Aleksander A.; Pelivanov, Ivan M.; Podymova, N. B.; Skipetrov, S. E.

1999-12-01

A method, based on the optoacoustic effect for determination of the spatial distribution of the light intensity in turbid media and of the optical characteristics of such media was proposed (and implemented experimentally). A temporal profile of the pressure of a thermo-optically excited acoustic pulse was found to be governed by the absorption coefficient and by the spatial distribution of the light intensity in the investigated medium. The absorption coefficient and the reduced light-scattering coefficient of model turbid water-like media were measured by the optoacoustic method. The results of a direct determination of the spatial light-intensity distribution agreed with a theoretical calculation made in the diffusion approximation.

A Hydrodynamic Theory for Spatially Inhomogeneous Semiconductor Lasers. 2; Numerical Results

NASA Technical Reports Server (NTRS)

Li, Jianzhong; Ning, C. Z.; Biegel, Bryan A. (Technical Monitor)

2001-01-01

We present numerical results of the diffusion coefficients (DCs) in the coupled diffusion model derived in the preceding paper for a semiconductor quantum well. These include self and mutual DCs in the general two-component case, as well as density- and temperature-related DCs under the single-component approximation. The results are analyzed from the viewpoint of free Fermi gas theory with many-body effects incorporated. We discuss in detail the dependence of these DCs on densities and temperatures in order to identify different roles played by the free carrier contributions including carrier statistics and carrier-LO phonon scattering, and many-body corrections including bandgap renormalization and electron-hole (e-h) scattering. In the general two-component case, it is found that the self- and mutual- diffusion coefficients are determined mainly by the free carrier contributions, but with significant many-body corrections near the critical density. Carrier-LO phonon scattering is dominant at low density, but e-h scattering becomes important in determining their density dependence above the critical electron density. In the single-component case, it is found that many-body effects suppress the density coefficients but enhance the temperature coefficients. The modification is of the order of 10% and reaches a maximum of over 20% for the density coefficients. Overall, temperature elevation enhances the diffusive capability or DCs of carriers linearly, and such an enhancement grows with density. Finally, the complete dataset of various DCs as functions of carrier densities and temperatures provides necessary ingredients for future applications of the model to various spatially inhomogeneous optoelectronic devices.

Banded Structures in Electron Pitch Angle Diffusion Coefficients from Resonant Wave Particle Interactions

NASA Technical Reports Server (NTRS)

Tripathi, A. K.; Singhal, R. P.; Khazanov, G. V.; Avanov, L. A.

2016-01-01

Electron pitch angle (D (alpha)) and momentum (D(pp)) diffusion coefficients have been calculated due to resonant interactions with electrostatic electron cyclotron harmonic (ECH) and whistler mode chorus waves. Calculations have been performed at two spatial locations L = 4.6 and 6.8 for electron energies 10 keV. Landau (n = 0) resonance and cyclotron harmonic resonances n = +/-1, +/-2,...+/-5 have been included in the calculations. It is found that diffusion coefficient versus pitch angle (alpha) profiles show large dips and oscillations or banded structures. The structures are more pronounced for ECH and lower band chorus (LBC) and particularly at location 4.6. Calculations of diffusion coefficients have also been performed for individual resonances. It is noticed that the main contribution of ECH waves in pitch angle diffusion coefficient is due to resonances n = +1 and n = +2. A major contribution to momentum diffusion coefficients appears from n = +2. However, the banded structures in D alpha and Dpp coefficients appear only in the profile of diffusion coefficients for n = +2. The contribution of other resonances to diffusion coefficients is found to be, in general, quite small or even negligible. For LBC and upper band chorus waves, the banded structures appear only in Landau resonance. The Dpp diffusion coefficient for ECH waves is one to two orders smaller than D alpha coefficients. For chorus waves, Dpp coefficients are about an order of magnitude smaller than D alpha coefficients for the case n does not = 0. In case of Landau resonance, the values of Dpp coefficient are generally larger than the values of D alpha coefficients particularly at lower energies. As an aid to the interpretation of results, we have also determined the resonant frequencies. For ECH waves, resonant frequencies have been estimated for wave normal angle 89 deg and harmonic resonances n = +1, +2, and +3, whereas for whistler mode waves, the frequencies have been calculated for angle 10 deg and Landau resonance. Further, in ECH waves, the banded structures appear for electron energies (is) greater than1 keV, and for whistler mode chorus waves, structures appear for energies greater than 2 keV at L = 4.6 and above 200 eV for L = 6.8. The results obtained in the present work will be helpful in the study of diffusion curves and will have important consequences for diffuse aurora and pancake distributions.

Banded Structures in Electron Pitch Angle Diffusion Coefficients from Resonant Wave-Particle Interactions

NASA Technical Reports Server (NTRS)

Tripathi, A. K.; Singhal, R. P.; Khazanov, G. V.; Avanov, L. A.

2016-01-01

Electron pitch angle (D(sub (alpha alpha))) and momentum (D(sub pp)) diffusion coefficients have been calculated due to resonant interactions with electrostatic electron cyclotron harmonic (ECH) and whistler mode chorus waves. Calculations have been performed at two spatial locations L=4.6 and 6.8 for electron energies less than or equal to 10 keV. Landau (n=0) resonance and cyclotron harmonic resonances n= +/- 1, +/-2, ... +/-5 have been included in the calculations. It is found that diffusion coefficient versus pitch angle (alpha) profiles show large dips and oscillations or banded structures. The structures are more pronounced for ECH and lower band chorus (LBC) and particularly at location 4.6. Calculations of diffusion coefficients have also been performed for individual resonances. It is noticed that the main contribution of ECH waves in pitch angle diffusion coefficient is due to resonances n=+1 and n=+2. A major contribution to momentum diffusion coefficients appears from n=+2. However, the banded structures in D(sub alpha alpha) and D(sub pp) coefficients appear only in the profile of diffusion coefficients for n=+2. The contribution of other resonances to diffusion coefficients is found to be, in general, quite small or even negligible. For LBC and upper band chorus waves, the banded structures appear only in Landau resonance. The D(sub pp) diffusion coefficient for ECH waves is one to two orders smaller than D(sub alpha alpha) coefficients. For chorus waves, D(sub pp) coefficients are about an order of magnitude smaller than D(sub alpha alpha) coefficients for the case n does not equal 0. In case of Landau resonance, the values of D(sub pp) coefficient are generally larger than the values of D(sub alpha alpha) coefficients particularly at lower energies. As an aid to the interpretation of results, we have also determined the resonant frequencies. For ECH waves, resonant frequencies have been estimated for wave normal angle 89 deg and harmonic resonances n= +1, +2, and +3, whereas for whistler mode waves, the frequencies have been calculated for angle 10 deg and Landau resonance. Further, in ECH waves, the banded structures appear for electron energies 1 greater than or equal to keV, and for whistler mode chorus waves, structures appear for energies greater than 2 keV at L=4.6 and above 200 eV for L=6.8. The results obtained in the present work will be helpful in the study of diffusion curves and will have important consequences for diffuse aurora and pancake distributions.

Measurement of Rapid Protein Diffusion in the Cytoplasm by Photo-Converted Intensity Profile Expansion.

PubMed

Gura Sadovsky, Rotem; Brielle, Shlomi; Kaganovich, Daniel; England, Jeremy L

2017-03-14

The fluorescence microscopy methods presently used to characterize protein motion in cells infer protein motion from indirect observables, rather than measuring protein motion directly. Operationalizing these methods requires expertise that can constitute a barrier to their broad utilization. Here, we have developed PIPE (photo-converted intensity profile expansion) to directly measure the motion of tagged proteins and quantify it using an effective diffusion coefficient. PIPE works by pulsing photo-convertible fluorescent proteins, generating a peaked fluorescence signal at the pulsed region, and analyzing the spatial expansion of the signal. We demonstrate PIPE's success in measuring accurate diffusion coefficients in silico and in vitro and compare effective diffusion coefficients of native cellular proteins and free fluorophores in vivo. We apply PIPE to measure diffusion anomality in the cell and use it to distinguish free fluorophores from native cellular proteins. PIPE's direct measurement and ease of use make it appealing for cell biologists. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

Stochastic particle acceleration at shocks in the presence of braided magnetic fields.

NASA Astrophysics Data System (ADS)

Kirk, J. G.; Duffy, P.; Gallant, Y. A.

1996-10-01

The theory of diffusive acceleration of energetic particles at shock fronts assumes charged particles undergo spatial diffusion in a uniform magnetic field. If, however, the magnetic field is not uniform, but has a stochastic or braided structure, the transport of charged particles across the average direction of the field is more complicated. Assuming quasi-linear behaviour of the field lines, the particles undergo sub-diffusion on short time scales. We derive the propagator for such motion, which differs from the Gaussian form relevant for diffusion, and apply it to a configuration with a plane shock front whose normal is perpendicular to the average field direction. Expressions are given for the acceleration time as a function of the diffusion coefficient of the wandering magnetic field lines and the spatial diffusion coefficient of the charged particles parallel to the local field. In addition we calculate the spatial dependence of the particle density in both the upstream and downstream plasmas. In contrast to the diffusive case, the density of particles at the shock front is lower than it is far downstream. This is a consequence of the partial trapping of particles by structures in the magnetic field. As a result, the spectrum of accelerated particles is a power-law in momentum which is steeper than in the diffusive case. For a phase-space density f{prop.to}p^-s^, we find s=s_diff_[1+1/(2ρ_c_)], where ρ_c_ is the compression ratio of the shock front and s_diff_ is the standard result of diffusive acceleration: s_diff_=3ρ_c_/(ρ_c_-1). A strong shock in a monatomic ideal gas yields a spectrum of s=4.5. In the case of electrons, this corresponds to a radio synchrotron spectral index of α=0.75.

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.

Nanoscale Spatiotemporal Diffusion Modes Measured by Simultaneous Confocal and Stimulated Emission Depletion Nanoscopy Imaging.

PubMed

Schneider, Falk; Waithe, Dominic; Galiani, Silvia; Bernardino de la Serna, Jorge; Sezgin, Erdinc; Eggeling, Christian

2018-06-19

The diffusion dynamics in the cellular plasma membrane provide crucial insights into molecular interactions, organization, and bioactivity. Beam-scanning fluorescence correlation spectroscopy combined with super-resolution stimulated emission depletion nanoscopy (scanning STED-FCS) measures such dynamics with high spatial and temporal resolution. It reveals nanoscale diffusion characteristics by measuring the molecular diffusion in conventional confocal mode and super-resolved STED mode sequentially for each pixel along the scanned line. However, to directly link the spatial and the temporal information, a method that simultaneously measures the diffusion in confocal and STED modes is needed. Here, to overcome this problem, we establish an advanced STED-FCS measurement method, line interleaved excitation scanning STED-FCS (LIESS-FCS), that discloses the molecular diffusion modes at different spatial positions with a single measurement. It relies on fast beam-scanning along a line with alternating laser illumination that yields, for each pixel, the apparent diffusion coefficients for two different observation spot sizes (conventional confocal and super-resolved STED). We demonstrate the potential of the LIESS-FCS approach with simulations and experiments on lipid diffusion in model and live cell plasma membranes. We also apply LIESS-FCS to investigate the spatiotemporal organization of glycosylphosphatidylinositol-anchored proteins in the plasma membrane of live cells, which, interestingly, show multiple diffusion modes at different spatial positions.

Molecular dynamics simulation of three plastic additives' diffusion in polyethylene terephthalate.

PubMed

Li, Bo; Wang, Zhi-Wei; Lin, Qin-Bao; Hu, Chang-Ying

2017-06-01

Accurate diffusion coefficient data of additives in a polymer are of paramount importance for estimating the migration of the additives over time. This paper shows how this diffusion coefficient can be estimated for three plastic additives [2-(2'-hydroxy-5'-methylphenyl) (UV-P), 2,6-di-tert-butyl-4-methylphenol (BHT) and di-(2-ethylhexyl) phthalate (DEHP)] in polyethylene terephthalate (PET) using the molecular dynamics (MD) simulation method. MD simulations were performed at temperatures of 293-433 K. The diffusion coefficient was calculated through the Einstein relationship connecting the data of mean-square displacement at different times. Comparison of the diffusion coefficients simulated by the MD simulation technique, predicted by the Piringer model and experiments, showed that, except for a few samples, the MD-simulated values were in agreement with the experimental values within one order of magnitude. Furthermore, the diffusion process for additives is discussed in detail, and four factors - the interaction energy between additive molecules and PET, fractional free volume, molecular shape and size, and self-diffusion of the polymer - are proposed to illustrate the microscopic diffusion mechanism. The movement trajectories of additives in PET cell models suggested that the additive molecules oscillate slowly rather than hopping for a long time. Occasionally, when a sufficiently large hole was created adjacently, the molecule could undergo spatial motion by jumping into the free-volume hole and consequently start a continuous oscillation and hop. The results indicate that MD simulation is a useful approach for predicting the microstructure and diffusion coefficient of plastic additives, and help to estimate the migration level of additives from PET packaging.

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

NASA Astrophysics Data System (ADS)

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

2017-11-01

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

Measuring the Local Diffusion Coefficient with H.E.S.S. Observations of Very High-Energy Electrons

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

Hooper, Dan; Linden, Tim

2017-11-20

The HAWC Collaboration has recently reported the detection of bright and spatially extended multi-TeV gamma-ray emission from Geminga, Monogem, and a handful of other nearby, middle-aged pulsars. The angular profile of the emission observed from these pulsars is surprising, in that it implies that cosmic-ray diffusion is significantly inhibited within ~25 pc of these objects, compared to the expectations of standard Galactic diffusion models. This raises the important question of whether the diffusion coefficient in the local interstellar medium is also low, or whether it is instead better fit by the mean Galactic value. Here, we utilize recent observations ofmore » the cosmic-ray electron spectrum (extending up to ~20 TeV) by the H.E.S.S. Collaboration to show that the local diffusion coefficient cannot be as low as it is in the regions surrounding Geminga and Monogem. Instead, we conclude that cosmic rays efficiently diffuse through the bulk of the local interstellar medium. Among other implications, this further supports the conclusion that pulsars significantly contribute to the observed positron excess.« less

Correlation time and diffusion coefficient imaging: application to a granular flow system.

PubMed

Caprihan, A; Seymour, J D

2000-05-01

A parametric method for spatially resolved measurements for velocity autocorrelation functions, R(u)(tau) = , expressed as a sum of exponentials, is presented. The method is applied to a granular flow system of 2-mm oil-filled spheres rotated in a half-filled horizontal cylinder, which is an Ornstein-Uhlenbeck process with velocity autocorrelation function R(u)(tau) = e(- ||tau ||/tau(c)), where tau(c) is the correlation time and D = tau(c) is the diffusion coefficient. The pulsed-field-gradient NMR method consists of applying three different gradient pulse sequences of varying motion sensitivity to distinguish the range of correlation times present for particle motion. Time-dependent apparent diffusion coefficients are measured for these three sequences and tau(c) and D are then calculated from the apparent diffusion coefficient images. For the cylinder rotation rate of 2.3 rad/s, the axial diffusion coefficient at the top center of the free surface was 5.5 x 10(-6) m(2)/s, the correlation time was 3 ms, and the velocity fluctuation or granular temperature was 1.8 x 10(-3) m(2)/s(2). This method is also applicable to study transport in systems involving turbulence and porous media flows. Copyright 2000 Academic Press.

Direct Imaging of Long-Range Exciton Transport in Quantum Dot Superlattices by Ultrafast Microscopy.

PubMed

Yoon, Seog Joon; Guo, Zhi; Dos Santos Claro, Paula C; Shevchenko, Elena V; Huang, Libai

2016-07-26

Long-range charge and exciton transport in quantum dot (QD) solids is a crucial challenge in utilizing QDs for optoelectronic applications. Here, we present a direct visualization of exciton diffusion in highly ordered CdSe QDs superlattices by mapping exciton population using ultrafast transient absorption microscopy. A temporal resolution of ∼200 fs and a spatial precision of ∼50 nm of this technique provide a direct assessment of the upper limit for exciton transport in QD solids. An exciton diffusion length of ∼125 nm has been visualized in the 3 ns experimental time window and an exciton diffusion coefficient of (2.5 ± 0.2) × 10(-2) cm(2) s(-1) has been measured for superlattices constructed from 3.6 nm CdSe QDs with center-to-center distance of 6.7 nm. The measured exciton diffusion constant is in good agreement with Förster resonance energy transfer theory. We have found that exciton diffusion is greatly enhanced in the superlattices over the disordered films with an order of magnitude higher diffusion coefficient, pointing toward the role of disorder in limiting transport. This study provides important understandings on energy transport mechanisms in both the spatial and temporal domains in QD solids.

Accurate determination of the diffusion coefficient of proteins by Fourier analysis with whole column imaging detection.

PubMed

Zarabadi, Atefeh S; Pawliszyn, Janusz

2015-02-17

Analysis in the frequency domain is considered a powerful tool to elicit precise information from spectroscopic signals. In this study, the Fourier transformation technique is employed to determine the diffusion coefficient (D) of a number of proteins in the frequency domain. Analytical approaches are investigated for determination of D from both experimental and data treatment viewpoints. The diffusion process is modeled to calculate diffusion coefficients based on the Fourier transformation solution to Fick's law equation, and its results are compared to time domain results. The simulations characterize optimum spatial and temporal conditions and demonstrate the noise tolerance of the method. The proposed model is validated by its application for the electropherograms from the diffusion path of a set of proteins. Real-time dynamic scanning is conducted to monitor dispersion by employing whole column imaging detection technology in combination with capillary isoelectric focusing (CIEF) and the imaging plug flow (iPF) experiment. These experimental techniques provide different peak shapes, which are utilized to demonstrate the Fourier transformation ability in extracting diffusion coefficients out of irregular shape signals. Experimental results confirmed that the Fourier transformation procedure substantially enhanced the accuracy of the determined values compared to those obtained in the time domain.

Quantitative photoacoustic microscopy of optical absorption coefficients from acoustic spectra in the optical diffusive regime

NASA Astrophysics Data System (ADS)

Guo, Zijian; Favazza, Christopher; Garcia-Uribe, Alejandro; Wang, Lihong V.

2012-06-01

Photoacoustic (PA) microscopy (PAM) can image optical absorption contrast with ultrasonic spatial resolution in the optical diffusive regime. Conventionally, accurate quantification in PAM requires knowledge of the optical fluence attenuation, acoustic pressure attenuation, and detection bandwidth. We circumvent this requirement by quantifying the optical absorption coefficients from the acoustic spectra of PA signals acquired at multiple optical wavelengths. With the acoustic spectral method, the absorption coefficients of an oxygenated bovine blood phantom at 560, 565, 570, and 575 nm were quantified with errors of <3%. We also quantified the total hemoglobin concentration and hemoglobin oxygen saturation in a live mouse. Compared with the conventional amplitude method, the acoustic spectral method provides greater quantification accuracy in the optical diffusive regime. The limitations of the acoustic spectral method was also discussed.

Quantitative photoacoustic microscopy of optical absorption coefficients from acoustic spectra in the optical diffusive regime

PubMed Central

Guo, Zijian; Favazza, Christopher; Garcia-Uribe, Alejandro

2012-01-01

Abstract. Photoacoustic (PA) microscopy (PAM) can image optical absorption contrast with ultrasonic spatial resolution in the optical diffusive regime. Conventionally, accurate quantification in PAM requires knowledge of the optical fluence attenuation, acoustic pressure attenuation, and detection bandwidth. We circumvent this requirement by quantifying the optical absorption coefficients from the acoustic spectra of PA signals acquired at multiple optical wavelengths. With the acoustic spectral method, the absorption coefficients of an oxygenated bovine blood phantom at 560, 565, 570, and 575 nm were quantified with errors of <3%. We also quantified the total hemoglobin concentration and hemoglobin oxygen saturation in a live mouse. Compared with the conventional amplitude method, the acoustic spectral method provides greater quantification accuracy in the optical diffusive regime. The limitations of the acoustic spectral method was also discussed. PMID:22734767

Quantitative photoacoustic microscopy of optical absorption coefficients from acoustic spectra in the optical diffusive regime.

PubMed

Guo, Zijian; Favazza, Christopher; Garcia-Uribe, Alejandro; Wang, Lihong V

2012-06-01

Photoacoustic (PA) microscopy (PAM) can image optical absorption contrast with ultrasonic spatial resolution in the optical diffusive regime. Conventionally, accurate quantification in PAM requires knowledge of the optical fluence attenuation, acoustic pressure attenuation, and detection bandwidth. We circumvent this requirement by quantifying the optical absorption coefficients from the acoustic spectra of PA signals acquired at multiple optical wavelengths. With the acoustic spectral method, the absorption coefficients of an oxygenated bovine blood phantom at 560, 565, 570, and 575 nm were quantified with errors of <3%. We also quantified the total hemoglobin concentration and hemoglobin oxygen saturation in a live mouse. Compared with the conventional amplitude method, the acoustic spectral method provides greater quantification accuracy in the optical diffusive regime. The limitations of the acoustic spectral method was also discussed.

The Spatial Relationship between Apparent Diffusion Coefficient and Standardized Uptake Value of 18F-Fluorodeoxyglucose Has a Crucial Influence on the Numeric Correlation of Both Parameters in PET/MRI of Lung Tumors

PubMed Central

Stieltjes, Bram; Weikert, Thomas; Gatidis, Sergios; Wiese, Mark; Wild, Damian; Lardinois, Didier

2017-01-01

The minimum apparent diffusion coefficient (ADCmin) derived from diffusion-weighted MRI (DW-MRI) and the maximum standardized uptake value (SUVmax) of FDG-PET are markers of aggressiveness in lung cancer. The numeric correlation of the two parameters has been extensively studied, but their spatial interplay is not well understood. After FDG-PET and DW-MRI coregistration, values and location of ADCmin- and SUVmax-voxels were analyzed. The upper limit of the 95% confidence interval for registration accuracy of sequential PET/MRI was 12 mm, and the mean distance (D) between ADCmin- and SUVmax-voxels was 14.0 mm (average of two readers). Spatial mismatch (D > 12 mm) between ADCmin and SUVmax was found in 9/25 patients. A considerable number of mismatch cases (65%) was also seen in a control group that underwent simultaneous PET/MRI. In the entire patient cohort, no statistically significant correlation between SUVmax and ADCmin was seen, while a moderate negative linear relationship (r = −0.5) between SUVmax and ADCmin was observed in tumors with a spatial match (D ≤ 12 mm). In conclusion, spatial mismatch between ADCmin and SUVmax is found in a considerable percentage of patients. The spatial connection of the two parameters SUVmax and ADCmin has a crucial influence on their numeric correlation. PMID:29391862

The Spatial Relationship between Apparent Diffusion Coefficient and Standardized Uptake Value of 18F-Fluorodeoxyglucose Has a Crucial Influence on the Numeric Correlation of Both Parameters in PET/MRI of Lung Tumors.

PubMed

Sauter, Alexander W; Stieltjes, Bram; Weikert, Thomas; Gatidis, Sergios; Wiese, Mark; Klarhöfer, Markus; Wild, Damian; Lardinois, Didier; Bremerich, Jens; Sommer, Gregor

2017-01-01

The minimum apparent diffusion coefficient (ADC min ) derived from diffusion-weighted MRI (DW-MRI) and the maximum standardized uptake value (SUV max ) of FDG-PET are markers of aggressiveness in lung cancer. The numeric correlation of the two parameters has been extensively studied, but their spatial interplay is not well understood. After FDG-PET and DW-MRI coregistration, values and location of ADC min - and SUV max -voxels were analyzed. The upper limit of the 95% confidence interval for registration accuracy of sequential PET/MRI was 12 mm, and the mean distance ( D ) between ADC min - and SUV max -voxels was 14.0 mm (average of two readers). Spatial mismatch ( D > 12 mm) between ADC min and SUV max was found in 9/25 patients. A considerable number of mismatch cases (65%) was also seen in a control group that underwent simultaneous PET/MRI. In the entire patient cohort, no statistically significant correlation between SUV max and ADC min was seen, while a moderate negative linear relationship ( r = -0.5) between SUV max and ADC min was observed in tumors with a spatial match ( D ≤ 12 mm). In conclusion, spatial mismatch between ADC min and SUV max is found in a considerable percentage of patients. The spatial connection of the two parameters SUV max and ADC min has a crucial influence on their numeric correlation.

Time-dependent diffusive acceleration of test particles at shocks

NASA Astrophysics Data System (ADS)

Drury, L. O'C.

1991-07-01

A theoretical description is developed for the acceleration of test particles at a steady plane nonrelativistic shock. The mean and the variance of the acceleration-time distribution are expressed analytically for the condition under which the diffusion coefficient is arbitrarily dependent on position and momentum. The formula for an acceleration rate with arbitrary spatial variation in the diffusion coefficient developed by Drury (1987) is supplemented by a general theory of time dependence. An approximation scheme is developed by means of the analysis which permits the description of the spectral cutoff resulting from the finite shock age. The formulas developed in the analysis are also of interest for analyzing the observations of heliospheric shocks made from spacecraft.

Kubo formulas for dispersion in heterogeneous periodic nonequilibrium systems.

PubMed

Guérin, T; Dean, D S

2015-12-01

We consider the dispersion properties of tracer particles moving in nonequilibrium heterogeneous periodic media. The tracer motion is described by a Fokker-Planck equation with arbitrary spatially periodic (but constant in time) local diffusion tensors and drifts, eventually with the presence of obstacles. We derive a Kubo-like formula for the time-dependent effective diffusion tensor valid in any dimension. From this general formula, we derive expressions for the late time effective diffusion tensor and drift in these systems. In addition, we find an explicit formula for the late finite-time corrections to these transport coefficients. In one dimension, we give a closed analytical formula for the transport coefficients. The formulas derived here are very general and provide a straightforward method to compute the dispersion properties in arbitrary nonequilibrium periodic advection-diffusion systems.

An integrated fiber-optic probe combined with support vector regression for fast estimation of optical properties of turbid media.

PubMed

Zhou, Yang; Fu, Xiaping; Ying, Yibin; Fang, Zhenhuan

2015-06-23

A fiber-optic probe system was developed to estimate the optical properties of turbid media based on spatially resolved diffuse reflectance. Because of the limitations in numerical calculation of radiative transfer equation (RTE), diffusion approximation (DA) and Monte Carlo simulations (MC), support vector regression (SVR) was introduced to model the relationship between diffuse reflectance values and optical properties. The SVR models of four collection fibers were trained by phantoms in calibration set with a wide range of optical properties which represented products of different applications, then the optical properties of phantoms in prediction set were predicted after an optimal searching on SVR models. The results indicated that the SVR model was capable of describing the relationship with little deviation in forward validation. The correlation coefficient (R) of reduced scattering coefficient μ'(s) and absorption coefficient μ(a) in the prediction set were 0.9907 and 0.9980, respectively. The root mean square errors of prediction (RMSEP) of μ'(s) and μ(a) in inverse validation were 0.411 cm(-1) and 0.338 cm(-1), respectively. The results indicated that the integrated fiber-optic probe system combined with SVR model were suitable for fast and accurate estimation of optical properties of turbid media based on spatially resolved diffuse reflectance. Copyright © 2015 Elsevier B.V. All rights reserved.

An analysis of diffuse light attenuation in the northern Gulf of Mexico hypoxic zone using the SeaWiFS satellite data record

EPA Science Inventory

The water column diffuse attenuation coefficient (Kd) of the Louisiana Continental Shelf (LCS) was examined during ten years to characterize the spatial and temporal variations on monthly scales from 1998 to 2007. This region is well-known for summer hypoxia (dissolved oxygen < 2...

Theory and Simulation of Self- and Mutual-Diffusion of Carrier Density and Temperature in Semiconductor Lasers

NASA Technical Reports Server (NTRS)

Li, Jian-Zhong; Cheung, Samson H.; Ning, C. Z.

2001-01-01

Carrier diffusion and thermal conduction play a fundamental role in the operation of high-power, broad-area semiconductor lasers. Restricted geometry, high pumping level and dynamic instability lead to inhomogeneous spatial distribution of plasma density, temperature, as well as light field, due to strong light-matter interaction. Thus, modeling and simulation of such optoelectronic devices rely on detailed descriptions of carrier dynamics and energy transport in the system. A self-consistent description of lasing and heating in large-aperture, inhomogeneous edge- or surface-emitting lasers (VCSELs) require coupled diffusion equations for carrier density and temperature. In this paper, we derive such equations from the Boltzmann transport equation for the carrier distributions. The derived self- and mutual-diffusion coefficients are in general nonlinear functions of carrier density and temperature including many-body interactions. We study the effects of many-body interactions on these coefficients, as well as the nonlinearity of these coefficients for large-area VCSELs. The effects of mutual diffusions on carrier and temperature distributions in gain-guided VCSELs will be also presented.

Equilibrium distribution of heavy quarks in fokker-planck dynamics

PubMed

Walton; Rafelski

2000-01-03

We obtain an explicit generalization, within Fokker-Planck dynamics, of Einstein's relation between drag, diffusion, and the equilibrium distribution for a spatially homogeneous system, considering both the transverse and longitudinal diffusion for dimension n>1. We provide a complete characterization of the equilibrium distribution in terms of the drag and diffusion transport coefficients. We apply this analysis to charm quark dynamics in a thermal quark-gluon plasma for the case of collisional equilibration.

Banded structures in electron pitch angle diffusion coefficients from resonant wave-particle interactions

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

Tripathi, A. K., E-mail: aktrip2001@yahoo.co.in; Singhal, R. P., E-mail: rpsiitbhu@yahoo.com; Khazanov, G. V., E-mail: George.V.Khazanov@nasa.gov

2016-04-15

Electron pitch angle (D{sub αα}) and momentum (D{sub pp}) diffusion coefficients have been calculated due to resonant interactions with electrostatic electron cyclotron harmonic (ECH) and whistler mode chorus waves. Calculations have been performed at two spatial locations L = 4.6 and 6.8 for electron energies ≤10 keV. Landau (n = 0) resonance and cyclotron harmonic resonances n = ±1, ±2, … ±5 have been included in the calculations. It is found that diffusion coefficient versus pitch angle (α) profiles show large dips and oscillations or banded structures. The structures are more pronounced for ECH and lower band chorus (LBC) and particularly at location 4.6. Calculations of diffusionmore » coefficients have also been performed for individual resonances. It is noticed that the main contribution of ECH waves in pitch angle diffusion coefficient is due to resonances n = +1 and n = +2. A major contribution to momentum diffusion coefficients appears from n = +2. However, the banded structures in D{sub αα} and D{sub pp} coefficients appear only in the profile of diffusion coefficients for n = +2. The contribution of other resonances to diffusion coefficients is found to be, in general, quite small or even negligible. For LBC and upper band chorus waves, the banded structures appear only in Landau resonance. The D{sub pp} diffusion coefficient for ECH waves is one to two orders smaller than D{sub αα} coefficients. For chorus waves, D{sub pp} coefficients are about an order of magnitude smaller than D{sub αα} coefficients for the case n ≠ 0. In case of Landau resonance, the values of D{sub pp} coefficient are generally larger than the values of D{sub αα} coefficients particularly at lower energies. As an aid to the interpretation of results, we have also determined the resonant frequencies. For ECH waves, resonant frequencies have been estimated for wave normal angle 89° and harmonic resonances n = +1, +2, and +3, whereas for whistler mode waves, the frequencies have been calculated for angle 10° and Landau resonance. Further, in ECH waves, the banded structures appear for electron energies ≥1 keV, and for whistler mode chorus waves, structures appear for energies >2 keV at L = 4.6 and above 200 eV for L = 6.8. The results obtained in the present work will be helpful in the study of diffusion curves and will have important consequences for diffuse aurora and pancake distributions.« less

A comment on the position dependent diffusion coefficient representation of structural heterogeneity

NASA Astrophysics Data System (ADS)

Wolfson, Molly; Liepold, Christopher; Lin, Binhua; Rice, Stuart A.

2018-05-01

Experimental studies of the variation of the mean square displacement (MSD) of a particle in a confined colloid suspension that exhibits density variations on the scale length of the particle diameter are not in agreement with the prediction that the spatial variation in MSD should mimic the spatial variation in density. The predicted behavior is derived from the expectation that the MSD of a particle depends on the system density and the assumption that the force acting on a particle is a point function of position. The experimental data are obtained from studies of the MSDs of particles in narrow ribbon channels and between narrowly spaced parallel plates and from new data, reported herein, of the radial and azimuthal MSDs of a colloid particle in a dense colloid suspension confined to a small circular cavity. In each of these geometries, a dense colloid suspension exhibits pronounced density oscillations with spacing of a particle diameter. We remove the discrepancy between prediction and experiment using the Fisher-Methfessel interpretation of how local equilibrium in an inhomogeneous system is maintained to argue that the force acting on a particle is delocalized over a volume with radius equal to a particle diameter. Our interpretation has relevance to the relationship between the scale of inhomogeneity and the utility of translation of the particle MSD into a position dependent diffusion coefficient and to the use of a spatially dependent diffusion coefficient to describe mass transport in a heterogeneous system.

Methodology and apparatus for diffuse photon imaging

DOEpatents

Feng, S.C.; Zeng, F.; Zhao, H.L.

1997-12-09

Non-invasive near infrared optical medical imaging devices for both hematoma detection in the brain and early tumor detection in the breast is achieved using image reconstruction which allows a mapping of the position dependent contrast diffusive propagation constants, which are related to the optical absorption coefficient and scattering coefficient in the tissue, at near infrared wavelengths. Spatial resolutions in the range of 5 mm for adult brain sizes and breast sizes can be achieved. The image reconstruction utilizes WKB approximation on most probable diffusion paths which has as lowest order approximation the straight line-of-sight between the plurality of sources and the plurality of detectors. The WKB approximation yields a set of linear equations in which the contrast optical absorption coefficients are the unknowns and for which signals can be generated to produce a pixel map of the contrast optical resolution of the scanned tissue. 58 figs.

Methodology and apparatus for diffuse photon mimaging

DOEpatents

Feng, Shechao C.; Zeng, Fanan; Zhao, Hui-Lin

1997-12-09

Non-invasive near infrared optical medical imaging devices for both hematoma detection in the brain and early tumor detection in the breast is achieved using image reconstruction which allows a mapping of the position dependent contrast diffusive propagation constants, which are related to the optical absorption coefficient and scattering coefficient in the tissue, at near infrared wavelengths. Spatial resolutions in the range of 5 mm for adult brain sizes and breast sizes can be achieved. The image reconstruction utilizes WKB approximation on most probable diffusion paths which has as lowest order approximation the straight line-of-sight between the plurality of sources and the plurality of detectors. The WKB approximation yields a set of linear equations in which the contrast optical absorption coefficients are the unknowns and for which signals can be generated to produce a pixel map of the contrast optical resolution of the scanned tissue.

Hyperspectral diffuse reflectance for determination of the optical properties of milk and fruit and vegetable juices

NASA Astrophysics Data System (ADS)

Qin, Jianwei; Lu, Renfu

2005-11-01

Absorption and reduced scattering coefficients are two fundamental optical properties for turbid biological materials. This paper presents the technique and method of using hyperspectral diffuse reflectance for fast determination of the optical properties of fruit and vegetable juices and milks. A hyperspectral imaging system was used to acquire spatially resolved steady-state diffuse reflectance over the spectral region between 530 and 900 nm from a variety of fruit and vegetable juices (citrus, grapefruit, orange, and vegetable) and milks with different fat levels (full, skim and mixed). The system collected diffuse reflectance in the source-detector separation range from 1.1 to 10.0 mm. The hyperspectral reflectance data were analyzed by using a diffusion theory model for semi-infinite homogeneous media. The absorption and reduced scattering coefficients of the fruit and vegetable juices and milks were extracted by inverse algorithms from the scattering profiles for wavelengths of 530-900 nm. Values of the absorption and reduced scattering coefficient at 650 nm were highly correlated to the fat content of the milk samples with the correlation coefficient of 0.990 and 0.989, respectively. The hyperspectral imaging technique can be extended to the measurement of other liquid and solid foods in which light scattering is dominant.

TEMPORAL AND SPATIAL VARIATION IN SOLAR RADIATION AND PHOTO-ENHANCED TOXICITY RISKS OF SPILLED OIL IN PRINCE WILLIAM SOUND, ALASKA

EPA Science Inventory

Solar irradiance (W/m2) and downwelling diffuse attenuation coefficients (Kd; m-1) were determined in several locations in Prince William Sound, Alaska, USA, between April 2003 and December 2005 to assess temporal and spatial variation in solar radiation and the risks of photoenh...

Single-molecule diffusion and conformational dynamics by spatial integration of temporal fluctuations

PubMed Central

Serag, Maged F.; Abadi, Maram; Habuchi, Satoshi

2014-01-01

Single-molecule localization and tracking has been used to translate spatiotemporal information of individual molecules to map their diffusion behaviours. However, accurate analysis of diffusion behaviours and including other parameters, such as the conformation and size of molecules, remain as limitations to the method. Here, we report a method that addresses the limitations of existing single-molecular localization methods. The method is based on temporal tracking of the cumulative area occupied by molecules. These temporal fluctuations are tied to molecular size, rates of diffusion and conformational changes. By analysing fluorescent nanospheres and double-stranded DNA molecules of different lengths and topological forms, we demonstrate that our cumulative-area method surpasses the conventional single-molecule localization method in terms of the accuracy of determined diffusion coefficients. Furthermore, the cumulative-area method provides conformational relaxation times of structurally flexible chains along with diffusion coefficients, which together are relevant to work in a wide spectrum of scientific fields. PMID:25283876

The hydrogen diffusion in liquid aluminum alloys from ab initio molecular dynamics

NASA Astrophysics Data System (ADS)

Jakse, N.; Pasturel, A.

2014-09-01

We study the hydrogen diffusion in liquid aluminum alloys through extensive ab initio molecular dynamics simulations. At the microscopic scale, we show that the hydrogen motion is characterized by a broad distribution of spatial jumps that does not correspond to a Brownian motion. To determine the self-diffusion coefficient of hydrogen in liquid aluminum alloys, we use a generalized continuous time random walk model recently developed to describe the hydrogen diffusion in pure aluminum. In particular, we show that the model successfully accounts the effects of alloying elements on the hydrogen diffusion in agreement with experimental features.

Spatiotemporal chaos in the dynamics of buoyantly and diffusively unstable chemical fronts

NASA Astrophysics Data System (ADS)

Baroni, M. P. M. A.; Guéron, E.; De Wit, A.

2012-03-01

Nonlinear dynamics resulting from the interplay between diffusive and buoyancy-driven Rayleigh-Taylor (RT) instabilities of autocatalytic traveling fronts are analyzed numerically for various values of the relevant parameters. These are the Rayleigh numbers of the reactant A and autocatalytic product B solutions as well as the ratio D =DB/DA between the diffusion coefficients of the two key chemical species. The interplay between the coarsening dynamics characteristic of the RT instability and the constant short wavelength modulation of the diffusive instability can lead in some regimes to complex dynamics dominated by irregular succession of birth and death of fingers. By using spectral entropy measurements, we characterize the transition between order and spatial disorder in this system. The analysis of the power spectrum and autocorrelation function, moreover, identifies similarities between the various spatial patterns. The contribution of the diffusive instability to the complex dynamics is discussed.

Consequences of using nonlinear particle trajectories to compute spatial diffusion coefficients. [for charged particles in interplanetary space

NASA Technical Reports Server (NTRS)

Goldstein, M. L.

1976-01-01

The propagation of charged particles through interstellar and interplanetary space has often been described as a random process in which the particles are scattered by ambient electromagnetic turbulence. In general, this changes both the magnitude and direction of the particles' momentum. Some situations for which scattering in direction (pitch angle) is of primary interest were studied. A perturbed orbit, resonant scattering theory for pitch-angle diffusion in magnetostatic turbulence was slightly generalized and then utilized to compute the diffusion coefficient for spatial propagation parallel to the mean magnetic field, Kappa. All divergences inherent in the quasilinear formalism when the power spectrum of the fluctuation field falls off as K to the minus Q power (Q less than 2) were removed. Various methods of computing Kappa were compared and limits on the validity of the theory discussed. For Q less than 1 or 2, the various methods give roughly comparable values of Kappa, but use of perturbed orbits systematically results in a somewhat smaller Kappa than can be obtained from quasilinear theory.

A reaction-diffusion malaria model with seasonality and incubation period.

PubMed

Bai, Zhenguo; Peng, Rui; Zhao, Xiao-Qiang

2018-07-01

In this paper, we propose a time-periodic reaction-diffusion model which incorporates seasonality, spatial heterogeneity and the extrinsic incubation period (EIP) of the parasite. The basic reproduction number [Formula: see text] is derived, and it is shown that the disease-free periodic solution is globally attractive if [Formula: see text], while there is an endemic periodic solution and the disease is uniformly persistent if [Formula: see text]. Numerical simulations indicate that prolonging the EIP may be helpful in the disease control, while spatial heterogeneity of the disease transmission coefficient may increase the disease burden.

Crosstalk and transitions between multiple spatial maps in an attractor neural network model of the hippocampus: Collective motion of the activity

NASA Astrophysics Data System (ADS)

Monasson, R.; Rosay, S.

2014-03-01

The dynamics of a neural model for hippocampal place cells storing spatial maps is studied. In the absence of external input, depending on the number of cells and on the values of control parameters (number of environments stored, level of neural noise, average level of activity, connectivity of place cells), a "clump" of spatially localized activity can diffuse or remains pinned due to crosstalk between the environments. In the single-environment case, the macroscopic coefficient of diffusion of the clump and its effective mobility are calculated analytically from first principles and corroborated by numerical simulations. In the multienvironment case the heights and the widths of the pinning barriers are analytically characterized with the replica method; diffusion within one map is then in competition with transitions between different maps. Possible mechanisms enhancing mobility are proposed and tested.

Hydrogen diffusion in liquid aluminum from ab initio molecular dynamics

NASA Astrophysics Data System (ADS)

Jakse, N.; Pasturel, A.

2014-05-01

Ab initio molecular dynamics simulations are used to describe the diffusion of hydrogen in liquid aluminum at different temperatures. Quasi-instantaneous jumps separating periods of localized vibrations around a mean position are found to characterize the hydrogen motion at the microscopic scale. The hydrogen motion is furthermore analyzed using the van Hove function. We highlight a non-Fickian behavior for the hydrogen diffusion due to a large spatial distribution of hydrogen jumps. We show that a generalized continuous time random walk (CTRW) model describes the experimental diffusion coefficients in a satisfactory manner. Finally, the impact of impurities and alloying elements on hydrogen diffusion in aluminum is discussed.

High-throughput mathematical analysis identifies Turing networks for patterning with equally diffusing signals.

PubMed

Marcon, Luciano; Diego, Xavier; Sharpe, James; Müller, Patrick

2016-04-08

The Turing reaction-diffusion model explains how identical cells can self-organize to form spatial patterns. It has been suggested that extracellular signaling molecules with different diffusion coefficients underlie this model, but the contribution of cell-autonomous signaling components is largely unknown. We developed an automated mathematical analysis to derive a catalog of realistic Turing networks. This analysis reveals that in the presence of cell-autonomous factors, networks can form a pattern with equally diffusing signals and even for any combination of diffusion coefficients. We provide a software (available at http://www.RDNets.com) to explore these networks and to constrain topologies with qualitative and quantitative experimental data. We use the software to examine the self-organizing networks that control embryonic axis specification and digit patterning. Finally, we demonstrate how existing synthetic circuits can be extended with additional feedbacks to form Turing reaction-diffusion systems. Our study offers a new theoretical framework to understand multicellular pattern formation and enables the wide-spread use of mathematical biology to engineer synthetic patterning systems.

High-throughput mathematical analysis identifies Turing networks for patterning with equally diffusing signals

PubMed Central

Marcon, Luciano; Diego, Xavier; Sharpe, James; Müller, Patrick

2016-01-01

The Turing reaction-diffusion model explains how identical cells can self-organize to form spatial patterns. It has been suggested that extracellular signaling molecules with different diffusion coefficients underlie this model, but the contribution of cell-autonomous signaling components is largely unknown. We developed an automated mathematical analysis to derive a catalog of realistic Turing networks. This analysis reveals that in the presence of cell-autonomous factors, networks can form a pattern with equally diffusing signals and even for any combination of diffusion coefficients. We provide a software (available at http://www.RDNets.com) to explore these networks and to constrain topologies with qualitative and quantitative experimental data. We use the software to examine the self-organizing networks that control embryonic axis specification and digit patterning. Finally, we demonstrate how existing synthetic circuits can be extended with additional feedbacks to form Turing reaction-diffusion systems. Our study offers a new theoretical framework to understand multicellular pattern formation and enables the wide-spread use of mathematical biology to engineer synthetic patterning systems. DOI: http://dx.doi.org/10.7554/eLife.14022.001 PMID:27058171

Transport and fluctuation-dissipation relations in asymptotic and preasymptotic diffusion across channels with variable section.

PubMed

Forte, Giuseppe; Cecconi, Fabio; Vulpiani, Angelo

2014-12-01

We study the asymptotic and preasymptotic diffusive properties of Brownian particles in channels whose section varies periodically in space. The effective diffusion coefficient D(eff) is numerically determined by the asymptotic behavior of the root mean square displacement in different geometries, considering even cases of steep variations of the channel boundaries. Moreover, we compared the numerical results to the predictions from the various corrections proposed in the literature to the well known Fick-Jacobs approximation. Building an effective one-dimensional equation for the longitudinal diffusion, we obtain an approximation for the effective diffusion coefficient. Such a result goes beyond a perturbation approach, and it is in good agreement with the actual values obtained by the numerical simulations. We discuss also the preasymptotic diffusion which is observed up to a crossover time whose value, in the presence of strong spatial variation of the channel cross section, can be very large. In addition, we show how the Einstein's relation between the mean drift induced by a small external field and the mean square displacement of the unperturbed system is valid in both asymptotic and preasymptotic regimes.

Spatial Mapping of Translational Diffusion Coefficients Using Diffusion Tensor Imaging: A Mathematical Description

PubMed Central

SHETTY, ANIL N.; CHIANG, SHARON; MALETIC-SAVATIC, MIRJANA; KASPRIAN, GREGOR; VANNUCCI, MARINA; LEE, WESLEY

2016-01-01

In this article, we discuss the theoretical background for diffusion weighted imaging and diffusion tensor imaging. Molecular diffusion is a random process involving thermal Brownian motion. In biological tissues, the underlying microstructures restrict the diffusion of water molecules, making diffusion directionally dependent. Water diffusion in tissue is mathematically characterized by the diffusion tensor, the elements of which contain information about the magnitude and direction of diffusion and is a function of the coordinate system. Thus, it is possible to generate contrast in tissue based primarily on diffusion effects. Expressing diffusion in terms of the measured diffusion coefficient (eigenvalue) in any one direction can lead to errors. Nowhere is this more evident than in white matter, due to the preferential orientation of myelin fibers. The directional dependency is removed by diagonalization of the diffusion tensor, which then yields a set of three eigenvalues and eigenvectors, representing the magnitude and direction of the three orthogonal axes of the diffusion ellipsoid, respectively. For example, the eigenvalue corresponding to the eigenvector along the long axis of the fiber corresponds qualitatively to diffusion with least restriction. Determination of the principal values of the diffusion tensor and various anisotropic indices provides structural information. We review the use of diffusion measurements using the modified Stejskal–Tanner diffusion equation. The anisotropy is analyzed by decomposing the diffusion tensor based on symmetrical properties describing the geometry of diffusion tensor. We further describe diffusion tensor properties in visualizing fiber tract organization of the human brain. PMID:27441031

Label-free hyperspectral dark-field microscopy for quantitative scatter imaging

NASA Astrophysics Data System (ADS)

Cheney, Philip; McClatchy, David; Kanick, Stephen; Lemaillet, Paul; Allen, David; Samarov, Daniel; Pogue, Brian; Hwang, Jeeseong

2017-03-01

A hyperspectral dark-field microscope has been developed for imaging spatially distributed diffuse reflectance spectra from light-scattering samples. In this report, quantitative scatter spectroscopy is demonstrated with a uniform scattering phantom, namely a solution of polystyrene microspheres. A Monte Carlo-based inverse model was used to calculate the reduced scattering coefficients of samples of different microsphere concentrations from wavelength-dependent backscattered signal measured by the dark-field microscope. The results are compared to the measurement results from a NIST double-integrating sphere system for validation. Ongoing efforts involve quantitative mapping of scattering and absorption coefficients in samples with spatially heterogeneous optical properties.

Cosmic ray propagation in interplanetary space

NASA Technical Reports Server (NTRS)

Voelk, H. J.

1975-01-01

The validity of the test-particle picture, the approximation of static fields, and the spatial-diffusion approximation are discussed in a general way before specific technical assumptions are introduced. It is argued that the spatial-diffusion equation for the intensity per unit energy has a much wider range of applicability than the kinetic (Fokker-Planck) equation it is derived from. This gives strong weight to the phenomenological propagation theory. The general success (and possible failure at small energies) of the phenomenological theory for the modulation of galactic cosmic rays and solar events is described. Apparent effects such as the 'free boundary' are given disproportionate weight since they establish the connection with the detailed plasma physics of the solar wind. Greatest attention is paid to the pitch-angle diffusion theory. A general theory is presented which removes the well-known secularities of the quasi-linear approximation. The possible breakdown of any pitch-angle diffusion theory at very small energies is perhaps connected with the observed 'turn up' of the spectrum at low energies. A first attempt to derive the spatial dependence of the diffusion coefficient in the solar cavity, using such a divergence free scattering theory, is described and compared with recent observations out to 5 AU.

Effects of whistler mode hiss waves on the radiation belts structure during quiet times

NASA Astrophysics Data System (ADS)

Ripoll, J. F.; Santolik, O.; Reeves, G. D.; Kurth, W. S.; Denton, M.; Loridan, V.; Thaller, S. A.; Cunningham, G.; Kletzing, C.; Turner, D. L.; Henderson, M. G.; Ukhorskiy, S.; Drozdov, A.; Cervantes Villa, J. S.; Shprits, Y.

2017-12-01

We present dynamic Fokker-Planck simulations of the electron radiation belts and slot formation during the quiet days that can follow a storm. Simulations are made for all energies and L-shells between 2 and 6 in the view of recovering the observations of two particular events. Pitch angle diffusion is essential to energy structure of the belts and slot region. Pitch angle diffusion is computed from data-driven spatially and temporally-resolved whistler mode hiss wave and ambient plasma observations from the Van Allen Probes satellites. The simulations are performed either with a 3D formulation that uses pitch angle diffusion coefficients or with a simpler 1D Fokker-Planck equation based on losses computed from a lifetime. Validation is carried out globally against Magnetic Electron and Ion Spectrometer observations of the belts at all energy. Results are complemented with a sensitivity study involving different radial diffusion coefficients, electron lifetimes, and pitch angle diffusion coefficients. We discuss which models allow to recover the observed "S-shaped" energy-dependent inner boundary to the outer zone that results from the competition between diffusive radial transport and losses. Periods when the plasmasphere extends beyond L 5 favor long-lasting hiss losses from the outer belt. Through these simulations, we explain the full structure in energy and L-shell of the belts and the slot formation by hiss scattering during quiet storm recovery.

Local texture descriptors for the assessment of differences in diffusion magnetic resonance imaging of the brain.

PubMed

Thomsen, Felix Sebastian Leo; Delrieux, Claudio Augusto; de Luis-García, Rodrigo

2017-03-01

Descriptors extracted from magnetic resonance imaging (MRI) of the brain can be employed to locate and characterize a wide range of pathologies. Scalar measures are typically derived within a single-voxel unit, but neighborhood-based texture measures can also be applied. In this work, we propose a new set of descriptors to compute local texture characteristics from scalar measures of diffusion tensor imaging (DTI), such as mean and radial diffusivity, and fractional anisotropy. We employ weighted rotational invariant local operators, namely standard deviation, inter-quartile range, coefficient of variation, quartile coefficient of variation and skewness. Sensitivity and specificity of those texture descriptors were analyzed with tract-based spatial statistics of the white matter on a diffusion MRI group study of elderly healthy controls, patients with mild cognitive impairment (MCI), and mild or moderate Alzheimer's disease (AD). In addition, robustness against noise has been assessed with a realistic diffusion-weighted imaging phantom and the contamination of the local neighborhood with gray matter has been measured. The new texture operators showed an increased ability for finding formerly undetected differences between groups compared to conventional DTI methods. In particular, the coefficient of variation, quartile coefficient of variation, standard deviation and inter-quartile range of the mean and radial diffusivity detected significant differences even between previously not significantly discernible groups, such as MCI versus moderate AD and mild versus moderate AD. The analysis provided evidence of low contamination of the local neighborhood with gray matter and high robustness against noise. The local operators applied here enhance the identification and localization of areas of the brain where cognitive impairment takes place and thus indicate them as promising extensions in diffusion MRI group studies.

Multi-Mission Remote Sensing of Suspended Particulate Matter and Diffuse Attenuation Coefficient in the Yangtze Estuarine and Coastal Waters

NASA Astrophysics Data System (ADS)

Yu, X.; Salama, S.; Shen, F.

2016-08-01

During the Dragon-3 project (ID: 10555) period, we developed and improved the atmospheric correction algorithms (AC) and retrieval models of suspended sediment concentration ( ) and diffuse attenuation coefficient ( ) for the Yangtze estuarine and coastal waters. The developed models were validated by measurements with consistently stable and fairly accurate estimations, reproducing reasonable distribution maps of and over the study area. Spatial-temporal variations of were presented and the mechanisms of the sediment transport were discussed. We further examined the compatibility of the developed AC algorithms and retrieval model and the consistency of satellite products for multi-sensor such as MODIS/Terra/Aqua, MERIS/Envisat, MERSI/ FY-3 and GOCI. The inter-comparison of multi- sensor suggested that different satellite products can be combined to increase revisit frequency and complement a temporal gap of time series satellites that may exist between on-orbit and off- orbit, facilitating a better monitor on the spatial- temporal dynamics of .

Application of underdamped Langevin dynamics simulations for the study of diffusion from a drug-eluting stent

NASA Astrophysics Data System (ADS)

Regev, Shaked; Farago, Oded

2018-10-01

We use a one-dimensional two layer model with a semi-permeable membrane to study the diffusion of a therapeutic drug delivered from a drug-eluting stent (DES). The rate of drug transfer from the stent coating to the arterial wall is calculated by using underdamped Langevin dynamics simulations. Our results reveal that the membrane has virtually no delay effect on the rate of delivery from the DES. The work demonstrates the great potential of underdamped Langevin dynamics simulations as an easy to implement, efficient, method for solving complicated diffusion problems in systems with a spatially-dependent diffusion coefficient.

Glycosylases utilize ``stop and go'' motion to locate DNA damage

NASA Astrophysics Data System (ADS)

Nelson, Shane

2015-03-01

Oxidative damage to DNA results in alterations that are mutagenic or even cytotoxic. Base excision repair is a mechanism that functions to identify and correct these lesions, and is present in organisms ranging from bacteria to humans. DNA glycosylases are the first enzymes in this pathway and function to locate and remove oxidatively damaged bases, and do so utilizing only thermal energy. However, the question remains of how these enzymes locate and recognize a damaged base among millions of undamaged bases. Utilizing fluorescence video microscopy with high spatial and temporal resolution, we have observed a number of different fluorescently labeled glycosylases (including bacterial FPG, NEI, and NTH as well as mammalian MutyH and OGG). These enzymes diffuse along DNA tightropes at approximately 0.01 +/- 0.005 μm2/s with binding lifetimes ranging from one second to several minutes. Chemically induced damage to the DNA substrate causes a ~ 50% reduction in diffusion coefficients and a ~ 400% increase in binding lifetimes, while mutation of the key ``wedge residue'' - which has been shown to be responsible for damage detection - results in a 200% increase in the diffusion coefficient. Utilizing a sliding window approach to measure diffusion coefficients within individual trajectories, we observe that distributions of diffusion coefficients are bimodal, consistent with periods of diffusive motion interspersed with immobile periods. Utilizing a unique chemo-mechanical simulation approach, we demonstrate that the motion of these glycosylases can be explained as free diffusion along the helical pitch of the DNA, punctuated with two different types of pauses: 1) rapid, short-lived pauses as the enzyme rapidly probes DNA bases to interrogate for damage and, 2) less frequent, longer lived pauses that reflect the enzyme bound to and catalytically removing a damaged base. These simulations also indicate that the wedge residue is critical for interrogation and recognition of damage, and thus enzymes missing this residue diffuse faster. Similarly, chemically induced damage increases the frequency with which the enzymes encounter damaged bases, resulting in slower diffusion.

Improvement of gray-scale representation of horizontally scanning holographic display using error diffusion.

PubMed

Matsumoto, Yuji; Takaki, Yasuhiro

2014-06-15

Horizontally scanning holography can enlarge both screen size and viewing zone angle. A microelectromechanical-system spatial light modulator, which can generate only binary images, is used to generate hologram patterns. Thus, techniques to improve gray-scale representation in reconstructed images should be developed. In this study, the error diffusion technique was used for the binarization of holograms. When the Floyd-Steinberg error diffusion coefficients were used, gray-scale representation was improved. However, the linearity in the gray-scale representation was not satisfactory. We proposed the use of a correction table and showed that the linearity was greatly improved.

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.

Selection of intracellular calcium patterns in a model with clustered Ca2+ release channels

NASA Astrophysics Data System (ADS)

Shuai, J. W.; Jung, P.

2003-03-01

A two-dimensional model is proposed for intracellular Ca2+ waves, which incorporates both the discrete nature of Ca2+ release sites in the endoplasmic reticulum membrane and the stochastic dynamics of the clustered inositol 1,4,5-triphosphate (IP3) receptors. Depending on the Ca2+ diffusion coefficient and concentration of IP3, various spontaneous Ca2+ patterns, such as calcium puffs, local waves, abortive waves, global oscillation, and tide waves, can be observed. We further investigate the speed of the global waves as a function of the IP3 concentration and the Ca2+ diffusion coefficient and under what conditions the spatially averaged Ca2+ response can be described by a simple set of ordinary differential equations.

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.

Comparison of Spatial Correlation Parameters between Full and Model Scale Launch Vehicles

NASA Technical Reports Server (NTRS)

Kenny, Jeremy; Giacomoni, Clothilde

2016-01-01

The current vibro-acoustic analysis tools require specific spatial correlation parameters as input to define the liftoff acoustic environment experienced by the launch vehicle. Until recently these parameters have not been very well defined. A comprehensive set of spatial correlation data were obtained during a scale model acoustic test conducted in 2014. From these spatial correlation data, several parameters were calculated: the decay coefficient, the diffuse to propagating ratio, and the angle of incidence. Spatial correlation data were also collected on the EFT-1 flight of the Delta IV vehicle which launched on December 5th, 2014. A comparison of the spatial correlation parameters from full scale and model scale data will be presented.

Correction of Gradient Nonlinearity Bias in Quantitative Diffusion Parameters of Renal Tissue with Intra Voxel Incoherent Motion.

PubMed

Malyarenko, Dariya I; Pang, Yuxi; Senegas, Julien; Ivancevic, Marko K; Ross, Brian D; Chenevert, Thomas L

2015-12-01

Spatially non-uniform diffusion weighting bias due to gradient nonlinearity (GNL) causes substantial errors in apparent diffusion coefficient (ADC) maps for anatomical regions imaged distant from magnet isocenter. Our previously-described approach allowed effective removal of spatial ADC bias from three orthogonal DWI measurements for mono-exponential media of arbitrary anisotropy. The present work evaluates correction feasibility and performance for quantitative diffusion parameters of the two-component IVIM model for well-perfused and nearly isotropic renal tissue. Sagittal kidney DWI scans of a volunteer were performed on a clinical 3T MRI scanner near isocenter and offset superiorly. Spatially non-uniform diffusion weighting due to GNL resulted both in shift and broadening of perfusion-suppressed ADC histograms for off-center DWI relative to unbiased measurements close to isocenter. Direction-average DW-bias correctors were computed based on the known gradient design provided by vendor. The computed bias maps were empirically confirmed by coronal DWI measurements for an isotropic gel-flood phantom. Both phantom and renal tissue ADC bias for off-center measurements was effectively removed by applying pre-computed 3D correction maps. Comparable ADC accuracy was achieved for corrections of both b -maps and DWI intensities in presence of IVIM perfusion. No significant bias impact was observed for IVIM perfusion fraction.

Correction of Gradient Nonlinearity Bias in Quantitative Diffusion Parameters of Renal Tissue with Intra Voxel Incoherent Motion

PubMed Central

Malyarenko, Dariya I.; Pang, Yuxi; Senegas, Julien; Ivancevic, Marko K.; Ross, Brian D.; Chenevert, Thomas L.

2015-01-01

Spatially non-uniform diffusion weighting bias due to gradient nonlinearity (GNL) causes substantial errors in apparent diffusion coefficient (ADC) maps for anatomical regions imaged distant from magnet isocenter. Our previously-described approach allowed effective removal of spatial ADC bias from three orthogonal DWI measurements for mono-exponential media of arbitrary anisotropy. The present work evaluates correction feasibility and performance for quantitative diffusion parameters of the two-component IVIM model for well-perfused and nearly isotropic renal tissue. Sagittal kidney DWI scans of a volunteer were performed on a clinical 3T MRI scanner near isocenter and offset superiorly. Spatially non-uniform diffusion weighting due to GNL resulted both in shift and broadening of perfusion-suppressed ADC histograms for off-center DWI relative to unbiased measurements close to isocenter. Direction-average DW-bias correctors were computed based on the known gradient design provided by vendor. The computed bias maps were empirically confirmed by coronal DWI measurements for an isotropic gel-flood phantom. Both phantom and renal tissue ADC bias for off-center measurements was effectively removed by applying pre-computed 3D correction maps. Comparable ADC accuracy was achieved for corrections of both b-maps and DWI intensities in presence of IVIM perfusion. No significant bias impact was observed for IVIM perfusion fraction. PMID:26811845

Spatially resolved, diffuse reflectance imaging for subsurface pattern visualization toward development of a lensless imaging platform: phantom experiments

NASA Astrophysics Data System (ADS)

Schelkanova, Irina; Pandya, Aditya; Saiko, Guennadi; Nacy, Lidia; Babar, Hannan; Shah, Duoaud; Lilge, Lothar; Douplik, Alexandre

2016-01-01

A portable, spatially resolved, diffuse reflectance lensless imaging technique based on the charge-coupled device or complementary metal-oxide semiconductor sensor directly coupled to the fiber optic bundle is proposed for visualization of subsurface structures such as superficial microvasculature in the epithelium. We discuss an experimental method for emulating a lensless imaging setup via raster scanning a single fiber-optic cable over a microfluidic phantom containing periodic hemoglobin absorption contrast. To evaluate the ability of the technique to recover information about the subsurface linear structures, scattering layers formed of the Sylgard® 184 Silicone Elastomer and titanium dioxide were placed atop the microfluidic phantom. Thickness of the layers ranged from 0.2 to 0.7 mm, and the values of the reduced scattering coefficient (μs‧) were between 0.85 and 4.25 mm-1. The results demonstrate that fiber-optic, lensless platform can be used for two-dimensional imaging of absorbing inclusions in diffuse reflectance mode. In these experiments, it was shown that diffuse reflectance imaging can provide sufficient spatial sampling of the phantom for differentiation of 30 μm structural features of the embedded absorbing pattern inside the scattering media.

Dispersion-relation phase spectroscopy of neuron transport

NASA Astrophysics Data System (ADS)

Wang, Ru; Wang, Zhuo; Millet, Larry; Gillette, Martha; Leigh, Joseph Robert; Sobh, Nahil; Levine, Alex; Popescu, Gabreil

2012-02-01

Molecular motors move materials along prescribed biopolymer tracks. This sort of active transport is required to rapidly move products over large distances within the cell, where passive diffusion is too slow. We examine intracellular traffic patterns using a new application of spatial light interference microscopy (SLIM) and measure the dispersion relation, i.e. decay rate vs. spatial mode, associated with mass transport in live cells. This approach applies equally well to both discrete and continuous mass distributions without the need for particle tracking. From the quadratic experimental curve specific to diffusion, we extracted the diffusion coefficient as the only fitting parameter. The linear portion of the dispersion relation reveals the deterministic component of the intracellular transport. Our data show a universal behavior where the intracellular transport is diffusive at small scales and deterministic at large scales. We further applied this method to studying transport in neurons and are able to use SLIM to map the changes in index of refraction across the neuron and its extended processes. We found that in dendrites and axons, the transport is mostly active, i.e., diffusion is subdominant.

Spatial dynamics of a population with stage-dependent diffusion

NASA Astrophysics Data System (ADS)

Azevedo, F.; Coutinho, R. M.; Kraenkel, R. A.

2015-05-01

We explore the spatial dynamics of a population whose individuals go through life stages with very different dispersal capacities. We model it through a system of partial differential equations of the reaction-diffusion kind, with nonlinear diffusion terms that may depend on population density and on the stage. This model includes a few key biological ingredients: growth and saturation, life stage structure, small population effects, and diffusion dependent on the stage. In particular, we consider that adults exhibit two distinct classes: one highly mobile and the other less mobile but with higher fecundity rate, and the development of juveniles into one or the other depends on population density. We parametrize the model with estimated parameters of an insect species, the brown planthopper. We focus on a situation akin to an invasion of the species in a new habitat and find that the front of invasion is led by the most mobile adult class. We also show that the trade-off between dispersal and fecundity leads to invasion speed attaining its maximum at an intermediate value of the diffusion coefficient of the most mobile class.

Multi-spectral imaging of oxygen saturation

NASA Astrophysics Data System (ADS)

Savelieva, Tatiana A.; Stratonnikov, Aleksander A.; Loschenov, Victor B.

2008-06-01

The system of multi-spectral imaging of oxygen saturation is an instrument that can record both spectral and spatial information about a sample. In this project, the spectral imaging technique is used for monitoring of oxygen saturation of hemoglobin in human tissues. This system can be used for monitoring spatial distribution of oxygen saturation in photodynamic therapy, surgery or sports medicine. Diffuse reflectance spectroscopy in the visible range is an effective and extensively used technique for the non-invasive study and characterization of various biological tissues. In this article, a short review of modeling techniques being currently in use for diffuse reflection from semi-infinite turbid media is presented. A simple and practical model for use with a real-time imaging system is proposed. This model is based on linear approximation of the dependence of the diffuse reflectance coefficient on relation between absorbance and reduced scattering coefficient. This dependence was obtained with the Monte Carlo simulation of photon propagation in turbid media. Spectra of the oxygenated and deoxygenated forms of hemoglobin differ mostly in the red area (520 - 600 nm) and have several characteristic points there. Thus four band-pass filters were used for multi-spectral imaging. After having measured the reflectance, the data obtained are used for fitting the concentration of oxygenated and free hemoglobin, and hemoglobin oxygen saturation.

Diffusion in biofilms respiring on electrodes

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

Renslow, Ryan S.; Babauta, Jerome T.; Majors, Paul D.

2012-11-15

The goal of this study was to measure spatially and temporally resolved effective diffusion coefficients (De) in biofilms respiring on electrodes. Two model electrochemically active biofilms, Geobacter sulfurreducens PCA and Shewanella oneidensis MR-1, were investigated. A novel nuclear magnetic resonance microimaging perfusion probe capable of simultaneous electrochemical and pulsed-field gradient nuclear magnetic resonance (PFG-NMR) techniques was used. PFG-NMR allowed for noninvasive, nondestructive, high spatial resolution in situ De measurements in living biofilms respiring on electrodes. The electrodes were polarized so that they would act as the sole terminal electron acceptor for microbial metabolism. We present our results as both two-dimensionalmore » De heat maps and surface-averaged relative effective diffusion coefficient (Drs) depth profiles. We found that (1) Drs decreases with depth in G. sulfurreducens biofilms, following a sigmoid shape; (2) Drs at a given location decreases with G. sulfurreducens biofilm age; (3) average De and Drs profiles in G. sulfurreducens biofilms are lower than those in S. oneidensis biofilms—the G. sulfurreducens biofilms studied here were on average 10 times denser than the S. oneidensis biofilms; and (4) halting the respiration of a G. sulfurreducens biofilm decreases the De values. Density, reflected by De, plays a major role in the extracellular electron transfer strategies of electrochemically active biofilms.« less

Protic ammonium carboxylate ionic liquids: insight into structure, dynamics and thermophysical properties by alkyl group functionalization.

PubMed

Reddy, Th Dhileep N; Mallik, Bhabani S

2017-04-19

This study is aimed at characterising the structure, dynamics and thermophysical properties of five alkylammonium carboxylate ionic liquids (ILs) from classical molecular dynamics simulations. The structural features of these ILs were characterised by calculating the site-site radial distribution functions, g(r), spatial distribution functions and structure factors. The structural properties demonstrate that ILs show greater interaction between cations and anions when alkyl chain length increases on the cation or anion. In all ILs, spatial distribution functions show that the anion is close to the acidic hydrogen atoms of the ammonium cation. We determined the role of alkyl group functionalization of the charged entities, cations and anions, in the dynamical behavior and the transport coefficients of this family of ionic liquids. The dynamics of ILs are described by studying the mean square displacement (MSD) of the centres of mass of the ions, diffusion coefficients, ionic conductivities and hydrogen bonds as well as residence dynamics. The diffusion coefficients and ionic conductivity decrease with an increase in the size of the cation or anion. The effect of alkyl chain length on ionic conductivity calculated in this article is consistent with the findings of other experimental studies. Hydrogen bond lifetimes and residence times along with structure factors were also calculated, and are related to alkyl chain length.

[Examination of upper abdominal region in high spatial resolution diffusion-weighted imaging using 3-Tesla MRI].

PubMed

Terada, Masaki; Matsushita, Hiroki; Oosugi, Masanori; Inoue, Kazuyasu; Yaegashi, Taku; Anma, Takeshi

2009-03-20

The advantage of the higher signal-to-noise ratio (SNR) of 3-Tesla magnetic resonance imaging (3-Tesla) has the possibility of contributing to the improvement of high spatial resolution without causing image deterioration. In this study, we compared SNR and the apparent diffusion coefficient (ADC) value with 3-Tesla as the condition in the diffusion-weighted image (DWI) parameter of the 1.5-Tesla magnetic resonance imaging (1.5-Tesla) and we examined the high spatial resolution images in the imaging method [respiratory-triggering (RT) method and breath free (BF) method] and artifact (motion and zebra) in the upper abdominal region of DWI at 3-Tesla. We have optimized scan parameters based on phantom and in vivo study. As a result, 3-Tesla was able to obtain about 1.5 times SNR in comparison with the 1.5-Tesla, ADC value had few differences. Moreover, the RT method was effective in correcting the influence of respiratory movement in comparison with the BF method, and image improvement by the effective acquisition of SNR and reduction of the artifact were provided. Thus, DWI of upper abdominal region was a useful sequence for the high spatial resolution in 3-Tesla.

Non-Gaussian diffusion in static disordered media

NASA Astrophysics Data System (ADS)

Luo, Liang; Yi, Ming

2018-04-01

Non-Gaussian diffusion is commonly considered as a result of fluctuating diffusivity, which is correlated in time or in space or both. In this work, we investigate the non-Gaussian diffusion in static disordered media via a quenched trap model, where the diffusivity is spatially correlated. Several unique effects due to quenched disorder are reported. We analytically estimate the diffusion coefficient Ddis and its fluctuation over samples of finite size. We show a mechanism of population splitting in the non-Gaussian diffusion. It results in a sharp peak in the distribution of displacement P (x ,t ) around x =0 , that has frequently been observed in experiments. We examine the fidelity of the coarse-grained diffusion map, which is reconstructed from particle trajectories. Finally, we propose a procedure to estimate the correlation length in static disordered environments, where the information stored in the sample-to-sample fluctuation has been utilized.

MR Scanner Systems Should Be Adequately Characterized in Diffusion-MRI of the Breast

PubMed Central

Giannelli, Marco; Sghedoni, Roberto; Iacconi, Chiara; Iori, Mauro; Traino, Antonio Claudio; Guerrisi, Maria; Mascalchi, Mario; Toschi, Nicola; Diciotti, Stefano

2014-01-01

Breast imaging represents a relatively recent and promising field of application of quantitative diffusion-MRI techniques. In view of the importance of guaranteeing and assessing its reliability in clinical as well as research settings, the aim of this study was to specifically characterize how the main MR scanner system-related factors affect quantitative measurements in diffusion-MRI of the breast. In particular, phantom acquisitions were performed on three 1.5 T MR scanner systems by different manufacturers, all equipped with a dedicated multi-channel breast coil as well as acquisition sequences for diffusion-MRI of the breast. We assessed the accuracy, inter-scan and inter-scanner reproducibility of the mean apparent diffusion coefficient measured along the main orthogonal directions () as well as of diffusion-tensor imaging (DTI)-derived mean diffusivity (MD) measurements. Additionally, we estimated spatial non-uniformity of (NU) and MD (NUMD) maps. We showed that the signal-to-noise ratio as well as overall calibration of high strength diffusion gradients system in typical acquisition sequences for diffusion-MRI of the breast varied across MR scanner systems, introducing systematic bias in the measurements of diffusion indices. While and MD values were not appreciably different from each other, they substantially varied across MR scanner systems. The mean of the accuracies of measured and MD was in the range [−2.3%,11.9%], and the mean of the coefficients of variation for and MD measurements across MR scanner systems was 6.8%. The coefficient of variation for repeated measurements of both and MD was < 1%, while NU and NUMD values were <4%. Our results highlight that MR scanner system-related factors can substantially affect quantitative diffusion-MRI of the breast. Therefore, a specific quality control program for assessing and monitoring the performance of MR scanner systems for diffusion-MRI of the breast is highly recommended at every site, especially in multicenter and longitudinal studies. PMID:24489711

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

PubMed

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

2011-07-01

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

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

PubMed Central

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

2011-01-01

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

Effect of concentration dependence of the diffusion coefficient on homogenization kinetics in multiphase binary alloy systems

NASA Technical Reports Server (NTRS)

Tenney, D. R.; Unnam, J.

1978-01-01

Diffusion calculations were performed to establish the conditions under which concentration dependence of the diffusion coefficient was important in single, two, and three phase binary alloy systems. Finite-difference solutions were obtained for each type of system using diffusion coefficient variations typical of those observed in real alloy systems. Solutions were also obtained using average diffusion coefficients determined by taking a logarithmic average of each diffusion coefficient variation considered. The constant diffusion coefficient solutions were used as reference in assessing diffusion coefficient variation effects. Calculations were performed for planar, cylindrical, and spherical geometries in order to compare the effect of diffusion coefficient variations with the effect of interface geometries. In most of the cases considered, the diffusion coefficient of the major-alloy phase was the key parameter that controlled the kinetics of interdiffusion.

Kubo conductivity of a strongly magnetized two-dimensional plasma.

NASA Technical Reports Server (NTRS)

Montgomery, D.; Tappert, F.

1971-01-01

The Kubo formula is used to evaluate the bulk electrical conductivity of a two-dimensional guiding-center plasma in a strong dc magnetic field. The particles interact only electrostatically. An ?anomalous' electrical conductivity is derived for this system, which parallels a recent result of Taylor and McNamara for the coefficient of spatial diffusion.

Role of spatial inhomogenity in GPCR dimerisation predicted by receptor association-diffusion models

NASA Astrophysics Data System (ADS)

Deshpande, Sneha A.; Pawar, Aiswarya B.; Dighe, Anish; Athale, Chaitanya A.; Sengupta, Durba

2017-06-01

G protein-coupled receptor (GPCR) association is an emerging paradigm with far reaching implications in the regulation of signalling pathways and therapeutic interventions. Recent super resolution microscopy studies have revealed that receptor dimer steady state exhibits sub-second dynamics. In particular the GPCRs, muscarinic acetylcholine receptor M1 (M1MR) and formyl peptide receptor (FPR), have been demonstrated to exhibit a fast association/dissociation kinetics, independent of ligand binding. In this work, we have developed a spatial kinetic Monte Carlo model to investigate receptor homo-dimerisation at a single receptor resolution. Experimentally measured association/dissociation kinetic parameters and diffusion coefficients were used as inputs to the model. To test the effect of membrane spatial heterogeneity on the simulated steady state, simulations were compared to experimental statistics of dimerisation. In the simplest case the receptors are assumed to be diffusing in a spatially homogeneous environment, while spatial heterogeneity is modelled to result from crowding, membrane micro-domains and cytoskeletal compartmentalisation or ‘corrals’. We show that a simple association-diffusion model is sufficient to reproduce M1MR association statistics, but fails to reproduce FPR statistics despite comparable kinetic constants. A parameter sensitivity analysis is required to reproduce the association statistics of FPR. The model reveals the complex interplay between cytoskeletal components and their influence on receptor association kinetics within the features of the membrane landscape. These results constitute an important step towards understanding the factors modulating GPCR organisation.

Regression approach to non-invasive determination of bilirubin in neonatal blood

NASA Astrophysics Data System (ADS)

Lysenko, S. A.; Kugeiko, M. M.

2012-07-01

A statistical ensemble of structural and biophysical parameters of neonatal skin was modeled based on experimental data. Diffuse scattering coefficients of the skin in the visible and infrared regions were calculated by applying a Monte-Carlo method to each realization of the ensemble. The potential accuracy of recovering the bilirubin concentration in dermis (which correlates closely with that in blood) was estimated from spatially resolved spectrometric measurements of diffuse scattering. The possibility to determine noninvasively the bilirubin concentration was shown by measurements of diffuse scattering at λ = 460, 500, and 660 nm at three source-detector separations under conditions of total variability of the skin biophysical parameters.

Exciton diffusion in WSe2 monolayers embedded in a van der Waals heterostructure

NASA Astrophysics Data System (ADS)

Cadiz, F.; Robert, C.; Courtade, E.; Manca, M.; Martinelli, L.; Taniguchi, T.; Watanabe, K.; Amand, T.; Rowe, A. C. H.; Paget, D.; Urbaszek, B.; Marie, X.

2018-04-01

We have combined spatially resolved steady-state micro-photoluminescence with time-resolved photoluminescence to investigate the exciton diffusion in a WSe2 monolayer encapsulated with hexagonal boron nitride. At 300 K, we extract an exciton diffusion length of LX = 0.36 ± 0.02 μm and an exciton diffusion coefficient of DX = 14.5 ± 2 cm2/s. This represents a nearly 10-fold increase in the effective mobility of excitons with respect to several previously reported values on nonencapsulated samples. At cryogenic temperatures, the high optical quality of these samples has allowed us to discriminate the diffusion of the different exciton species: bright and dark neutral excitons, as well as charged excitons. The longer lifetime of dark neutral excitons yields a larger diffusion length of LXD=1.5 ±0.02 μ m.

3D radiation belt diffusion model results using new empirical models of whistler chorus and hiss

NASA Astrophysics Data System (ADS)

Cunningham, G.; Chen, Y.; Henderson, M. G.; Reeves, G. D.; Tu, W.

2012-12-01

3D diffusion codes model the energization, radial transport, and pitch angle scattering due to wave-particle interactions. Diffusion codes are powerful but are limited by the lack of knowledge of the spatial & temporal distribution of waves that drive the interactions for a specific event. We present results from the 3D DREAM model using diffusion coefficients driven by new, activity-dependent, statistical models of chorus and hiss waves. Most 3D codes parameterize the diffusion coefficients or wave amplitudes as functions of magnetic activity indices like Kp, AE, or Dst. These functional representations produce the average value of the wave intensities for a given level of magnetic activity; however, the variability of the wave population at a given activity level is lost with such a representation. Our 3D code makes use of the full sample distributions contained in a set of empirical wave databases (one database for each wave type, including plasmaspheric hiss, lower and upper hand chorus) that were recently produced by our team using CRRES and THEMIS observations. The wave databases store the full probability distribution of observed wave intensity binned by AE, MLT, MLAT and L*. In this presentation, we show results that make use of the wave intensity sample probability distributions for lower-band and upper-band chorus by sampling the distributions stochastically during a representative CRRES-era storm. The sampling of the wave intensity probability distributions produces a collection of possible evolutions of the phase space density, which quantifies the uncertainty in the model predictions caused by the uncertainty of the chorus wave amplitudes for a specific event. A significant issue is the determination of an appropriate model for the spatio-temporal correlations of the wave intensities, since the diffusion coefficients are computed as spatio-temporal averages of the waves over MLT, MLAT and L*. The spatiotemporal correlations cannot be inferred from the wave databases. In this study we use a temporal correlation of ~1 hour for the sampled wave intensities that is informed by the observed autocorrelation in the AE index, a spatial correlation length of ~100 km in the two directions perpendicular to the magnetic field, and a spatial correlation length of 5000 km in the direction parallel to the magnetic field, according to the work of Santolik et al (2003), who used multi-spacecraft measurements from Cluster to quantify the correlation length scales for equatorial chorus . We find that, despite the small correlation length scale for chorus, there remains significant variability in the model outcomes driven by variability in the chorus wave intensities.

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

USGS Publications Warehouse

Shapiro, Allen M.

2001-01-01

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

Active motion assisted by correlated stochastic torques.

PubMed

Weber, Christian; Radtke, Paul K; Schimansky-Geier, Lutz; Hänggi, Peter

2011-07-01

The stochastic dynamics of an active particle undergoing a constant speed and additionally driven by an overall fluctuating torque is investigated. The random torque forces are expressed by a stochastic differential equation for the angular dynamics of the particle determining the orientation of motion. In addition to a constant torque, the particle is supplemented by random torques, which are modeled as an Ornstein-Uhlenbeck process with given correlation time τ(c). These nonvanishing correlations cause a persistence of the particles' trajectories and a change of the effective spatial diffusion coefficient. We discuss the mean square displacement as a function of the correlation time and the noise intensity and detect a nonmonotonic dependence of the effective diffusion coefficient with respect to both correlation time and noise strength. A maximal diffusion behavior is obtained if the correlated angular noise straightens the curved trajectories, interrupted by small pirouettes, whereby the correlated noise amplifies a straightening of the curved trajectories caused by the constant torque.

A Hydrodynamic Theory for Spatially Inhomogeneous Semiconductor Lasers: Microscopic Approach

NASA Technical Reports Server (NTRS)

Li, Jianzhong; Ning, C. Z.; Biegel, Bryan A. (Technical Monitor)

2001-01-01

Starting from the microscopic semiconductor Bloch equations (SBEs) including the Boltzmann transport terms in the distribution function equations for electrons and holes, we derived a closed set of diffusion equations for carrier densities and temperatures with self-consistent coupling to Maxwell's equation and to an effective optical polarization equation. The coherent many-body effects are included within the screened Hartree-Fock approximation, while scatterings are treated within the second Born approximation including both the in- and out-scatterings. Microscopic expressions for electron-hole (e-h) and carrier-LO (c-LO) phonon scatterings are directly used to derive the momentum and energy relaxation rates. These rates expressed as functions of temperatures and densities lead to microscopic expressions for self- and mutual-diffusion coefficients in the coupled density-temperature diffusion equations. Approximations for reducing the general two-component description of the electron-hole plasma (EHP) to a single-component one are discussed. In particular, we show that a special single-component reduction is possible when e-h scattering dominates over c-LO phonon scattering. The ambipolar diffusion approximation is also discussed and we show that the ambipolar diffusion coefficients are independent of e-h scattering, even though the diffusion coefficients of individual components depend sensitively on the e-h scattering rates. Our discussions lead to new perspectives into the roles played in the single-component reduction by the electron-hole correlation in momentum space induced by scatterings and the electron-hole correlation in real space via internal static electrical field. Finally, the theory is completed by coupling the diffusion equations to the lattice temperature equation and to the effective optical polarization which in turn couples to the laser field.

Lab and Pore-Scale Study of Low Permeable Soils Diffusional Tortuosity

NASA Astrophysics Data System (ADS)

Lekhov, V.; Pozdniakov, S. P.; Denisova, L.

2016-12-01

Diffusion plays important role in contaminant spreading in low permeable units. The effective diffusion coefficient of saturated porous medium depends on this coefficient in water, porosity and structural parameter of porous space - tortuosity. Theoretical models of relationship between porosity and diffusional tortuosity are usually derived for conceptual granular models of medium filled by solid particles of simple geometry. These models usually do not represent soils with complex microstructure. The empirical models, like as Archie's law, based on the experimental electrical conductivity data are mostly useful for practical applications. Such models contain empirical parameters that should be defined experimentally for given soil type. In this work, we compared tortuosity values obtained in lab-scale diffusional experiments and pore scale diffusion simulation for the studied soil microstructure and exanimated relationship between tortuosity and porosity. Samples for the study were taken from borehole cores of low-permeable silt-clay formation. Using the samples of 50 cm3 we performed lab scale diffusional experiments and estimated the lab-scale tortuosity. Next using these samples we studied the microstructure with X-ray microtomograph. Shooting performed on undisturbed microsamples of size 1,53 mm with a resolution ×300 (10243 vox). After binarization of each obtained 3-D structure, its spatial correlation analysis was performed. This analysis showed that the spatial correlation scale of the indicator variogram is considerably smaller than microsample length. Then there was the numerical simulation of the Laplace equation with binary coefficients for each microsamples. The total number of simulations at the finite-difference grid of 1753 cells was 3500. As a result the effective diffusion coefficient, tortuosity and porosity values were obtained for all studied microsamples. The results were analyzed in the form of graph of tortuosity versus porosity. The 6 experimental tortuosity values well agree with pore-scale simulations falling in the general pattern that shows nonlinear decreasing of tortuosity with decreasing of porosity. Fitting this graph by Archie model we found exponent value in the range between 1,8 and 2,4. This work was supported by RFBR via grant 14-05-00409.

An algorithm for localization of optical disturbances in turbid media using time-resolved diffuse optical tomography

NASA Astrophysics Data System (ADS)

Potlov, A. Yu.; Frolov, S. V.; Proskurin, S. G.

2018-04-01

Optical structure disturbances localization algorithm for time-resolved diffuse optical tomography of biological objects is described. The key features of the presented algorithm are: the initial approximation for the spatial distribution of the optical characteristics based on the Homogeneity Index and the assumption that all the absorbing and scattering inhomogeneities in an investigated object are spherical and have the same absorption and scattering coefficients. The described algorithm can be used in the brain structures diagnosis, in traumatology and optical mammography.

Geometric distortion correction in prostate diffusion-weighted MRI and its effect on quantitative apparent diffusion coefficient analysis.

PubMed

Nketiah, Gabriel; Selnaes, Kirsten M; Sandsmark, Elise; Teruel, Jose R; Krüger-Stokke, Brage; Bertilsson, Helena; Bathen, Tone F; Elschot, Mattijs

2018-05-01

To evaluate the effect of correction for B 0 inhomogeneity-induced geometric distortion in echo-planar diffusion-weighted imaging on quantitative apparent diffusion coefficient (ADC) analysis in multiparametric prostate MRI. Geometric distortion correction was performed in echo-planar diffusion-weighted images (b = 0, 50, 400, 800 s/mm 2 ) of 28 patients, using two b 0 scans with opposing phase-encoding polarities. Histology-matched tumor and healthy tissue volumes of interest delineated on T 2 -weighted images were mapped to the nondistortion-corrected and distortion-corrected data sets by resampling with and without spatial coregistration. The ADC values were calculated on the volume and voxel level. The effect of distortion correction on ADC quantification and tissue classification was evaluated using linear-mixed models and logistic regression, respectively. Without coregistration, the absolute differences in tumor ADC (range: 0.0002-0.189 mm 2 /s×10 -3 (volume level); 0.014-0.493 mm 2 /s×10 -3 (voxel level)) between the nondistortion-corrected and distortion-corrected were significantly associated (P < 0.05) with distortion distance (mean: 1.4 ± 1.3 mm; range: 0.3-5.3 mm). No significant associations were found upon coregistration; however, in patients with high rectal gas residue, distortion correction resulted in improved spatial representation and significantly better classification of healthy versus tumor voxels (P < 0.05). Geometric distortion correction in DWI could improve quantitative ADC analysis in multiparametric prostate MRI. Magn Reson Med 79:2524-2532, 2018. © 2017 International Society for Magnetic Resonance in Medicine. © 2017 International Society for Magnetic Resonance in Medicine.

Measuring and imaging diffusion with multiple scan speed image correlation spectroscopy.

PubMed

Gröner, Nadine; Capoulade, Jérémie; Cremer, Christoph; Wachsmuth, Malte

2010-09-27

The intracellular mobility of biomolecules is determined by transport and diffusion as well as molecular interactions and is crucial for many processes in living cells. Methods of fluorescence microscopy like confocal laser scanning microscopy (CLSM) can be used to characterize the intracellular distribution of fluorescently labeled biomolecules. Fluorescence correlation spectroscopy (FCS) is used to describe diffusion, transport and photo-physical processes quantitatively. As an alternative to FCS, spatially resolved measurements of mobilities can be implemented using a CLSM by utilizing the spatio-temporal information inscribed into the image by the scan process, referred to as raster image correlation spectroscopy (RICS). Here we present and discuss an extended approach, multiple scan speed image correlation spectroscopy (msICS), which benefits from the advantages of RICS, i.e. the use of widely available instrumentation and the extraction of spatially resolved mobility information, without the need of a priori knowledge of diffusion properties. In addition, msICS covers a broad dynamic range, generates correlation data comparable to FCS measurements, and allows to derive two-dimensional maps of diffusion coefficients. We show the applicability of msICS to fluorophores in solution and to free EGFP in living cells.

Relativistic analysis of stochastic kinematics

NASA Astrophysics Data System (ADS)

Giona, Massimiliano

2017-10-01

The relativistic analysis of stochastic kinematics is developed in order to determine the transformation of the effective diffusivity tensor in inertial frames. Poisson-Kac stochastic processes are initially considered. For one-dimensional spatial models, the effective diffusion coefficient measured in a frame Σ moving with velocity w with respect to the rest frame of the stochastic process is inversely proportional to the third power of the Lorentz factor γ (w ) =(1-w2/c2) -1 /2 . Subsequently, higher-dimensional processes are analyzed and it is shown that the diffusivity tensor in a moving frame becomes nonisotropic: The diffusivities parallel and orthogonal to the velocity of the moving frame scale differently with respect to γ (w ) . The analysis of discrete space-time diffusion processes permits one to obtain a general transformation theory of the tensor diffusivity, confirmed by several different simulation experiments. Several implications of the theory are also addressed and discussed.

Remote sensing of the diffuse attenuation coefficient of ocean water. [coastal zone color scanner

NASA Technical Reports Server (NTRS)

Austin, R. W.

1981-01-01

A technique was devised which uses remotely sensed spectral radiances from the sea to assess the optical diffuse attenuation coefficient, K (lambda) of near-surface ocean water. With spectral image data from a sensor such as the coastal zone color scanner (CZCS) carried on NIMBUS-7, it is possible to rapidly compute the K (lambda) fields for large ocean areas and obtain K "images" which show synoptic, spatial distribution of this attenuation coefficient. The technique utilizes a relationship that has been determined between the value of K and the ratio of the upwelling radiances leaving the sea surface at two wavelengths. The relationship was developed to provide an algorithm for inferring K from the radiance images obtained by the CZCS, thus the wavelengths were selected from those used by this sensor, viz., 443, 520, 550 and 670 nm. The majority of the radiance arriving at the spacecraft is the result of scattering in the atmospheric and is unrelated to the radiance signal generated by the water. A necessary step in the processing of the data received by the sensor is, therefore, the effective removal of these atmospheric path radiance signals before the K algorithm is applied. Examples of the efficacy of these removal techniques are given together with examples of the spatial distributions of K in several ocean areas.

Correlation of human papillomavirus status with apparent diffusion coefficient of diffusion-weighted MRI in head and neck squamous cell carcinomas.

PubMed

Driessen, Juliette P; van Bemmel, Alexander J M; van Kempen, Pauline M W; Janssen, Luuk M; Terhaard, Chris H J; Pameijer, Frank A; Willems, Stefan M; Stegeman, Inge; Grolman, Wilko; Philippens, Marielle E P

2016-04-01

Identification of prognostic patient characteristics in head and neck squamous cell carcinoma (HNSCC) is of great importance. Human papillomavirus (HPV)-positive HNSCCs have favorable response to (chemo)radiotherapy. Apparent diffusion coefficient, derived from diffusion-weighted MRI, has also shown to predict treatment response. The purpose of this study was to evaluate the correlation between HPV status and apparent diffusion coefficient. Seventy-three patients with histologically proven HNSCC were retrospectively analyzed. Mean pretreatment apparent diffusion coefficient was calculated by delineation of total tumor volume on diffusion-weighted MRI. HPV status was analyzed and correlated to apparent diffusion coefficient. Six HNSCCs were HPV-positive. HPV-positive HNSCC showed significantly lower apparent diffusion coefficient compared to HPV-negative. This correlation was independent of other patient characteristics. In HNSCC, positive HPV status correlates with low mean apparent diffusion coefficient. The favorable prognostic value of low pretreatment apparent diffusion coefficient might be partially attributed to patients with a positive HPV status. © 2015 Wiley Periodicals, Inc. Head Neck 38: E613-E618, 2016. © 2015 Wiley Periodicals, Inc.

Light distribution modulated diffuse reflectance spectroscopy.

PubMed

Huang, Pin-Yuan; Chien, Chun-Yu; Sheu, Chia-Rong; Chen, Yu-Wen; Tseng, Sheng-Hao

2016-06-01

Typically, a diffuse reflectance spectroscopy (DRS) system employing a continuous wave light source would need to acquire diffuse reflectances measured at multiple source-detector separations for determining the absorption and reduced scattering coefficients of turbid samples. This results in a multi-fiber probe structure and an indefinite probing depth. Here we present a novel DRS method that can utilize a few diffuse reflectances measured at one source-detector separation for recovering the optical properties of samples. The core of innovation is a liquid crystal (LC) cell whose scattering property can be modulated by the bias voltage. By placing the LC cell between the light source and the sample, the spatial distribution of light in the sample can be varied as the scattering property of the LC cell modulated by the bias voltage, and this would induce intensity variation of the collected diffuse reflectance. From a series of Monte Carlo simulations and phantom measurements, we found that this new light distribution modulated DRS (LDM DRS) system was capable of accurately recover the absorption and scattering coefficients of turbid samples and its probing depth only varied by less than 3% over the full bias voltage variation range. Our results suggest that this LDM DRS platform could be developed to various low-cost, efficient, and compact systems for in-vivo superficial tissue investigation.

Light distribution modulated diffuse reflectance spectroscopy

PubMed Central

Huang, Pin-Yuan; Chien, Chun-Yu; Sheu, Chia-Rong; Chen, Yu-Wen; Tseng, Sheng-Hao

2016-01-01

Typically, a diffuse reflectance spectroscopy (DRS) system employing a continuous wave light source would need to acquire diffuse reflectances measured at multiple source-detector separations for determining the absorption and reduced scattering coefficients of turbid samples. This results in a multi-fiber probe structure and an indefinite probing depth. Here we present a novel DRS method that can utilize a few diffuse reflectances measured at one source-detector separation for recovering the optical properties of samples. The core of innovation is a liquid crystal (LC) cell whose scattering property can be modulated by the bias voltage. By placing the LC cell between the light source and the sample, the spatial distribution of light in the sample can be varied as the scattering property of the LC cell modulated by the bias voltage, and this would induce intensity variation of the collected diffuse reflectance. From a series of Monte Carlo simulations and phantom measurements, we found that this new light distribution modulated DRS (LDM DRS) system was capable of accurately recover the absorption and scattering coefficients of turbid samples and its probing depth only varied by less than 3% over the full bias voltage variation range. Our results suggest that this LDM DRS platform could be developed to various low-cost, efficient, and compact systems for in-vivo superficial tissue investigation. PMID:27375931

Practical estimate of gradient nonlinearity for implementation of apparent diffusion coefficient bias correction.

PubMed

Malkyarenko, Dariya I; Chenevert, Thomas L

2014-12-01

To describe an efficient procedure to empirically characterize gradient nonlinearity and correct for the corresponding apparent diffusion coefficient (ADC) bias on a clinical magnetic resonance imaging (MRI) scanner. Spatial nonlinearity scalars for individual gradient coils along superior and right directions were estimated via diffusion measurements of an isotropicic e-water phantom. Digital nonlinearity model from an independent scanner, described in the literature, was rescaled by system-specific scalars to approximate 3D bias correction maps. Correction efficacy was assessed by comparison to unbiased ADC values measured at isocenter. Empirically estimated nonlinearity scalars were confirmed by geometric distortion measurements of a regular grid phantom. The applied nonlinearity correction for arbitrarily oriented diffusion gradients reduced ADC bias from 20% down to 2% at clinically relevant offsets both for isotropic and anisotropic media. Identical performance was achieved using either corrected diffusion-weighted imaging (DWI) intensities or corrected b-values for each direction in brain and ice-water. Direction-average trace image correction was adequate only for isotropic medium. Empiric scalar adjustment of an independent gradient nonlinearity model adequately described DWI bias for a clinical scanner. Observed efficiency of implemented ADC bias correction quantitatively agreed with previous theoretical predictions and numerical simulations. The described procedure provides an independent benchmark for nonlinearity bias correction of clinical MRI scanners.

Demonstration of Nonlinearity Bias in the Measurement of the Apparent Diffusion Coefficient in Multicenter Trials

PubMed Central

Malyarenko, Dariya; Newitt, David; Wilmes, Lisa; Tudorica, Alina; Helmer, Karl G.; Arlinghaus, Lori R.; Jacobs, Michael A.; Jajamovich, Guido; Taouli, Bachir; Yankeelov, Thomas E.; Huang, Wei; Chenevert, Thomas L.

2015-01-01

Purpose Characterize system-specific bias across common magnetic resonance imaging (MRI) platforms for quantitative diffusion measurements in multicenter trials. Methods Diffusion weighted imaging (DWI) was performed on an ice-water phantom along the superior-inferior (SI) and right-left (RL) orientations spanning ±150 mm. The same scanning protocol was implemented on 14 MRI systems at seven imaging centers. The bias was estimated as a deviation of measured from known apparent diffusion coefficient (ADC) along individual DWI directions. The relative contributions of gradient nonlinearity, shim errors, imaging gradients and eddy currents were assessed independently. The observed bias errors were compared to numerical models. Results The measured systematic ADC errors scaled quadratically with offset from isocenter, and ranged between −55% (SI) and 25% (RL). Nonlinearity bias was dependent on system design and diffusion gradient direction. Consistent with numerical models, minor ADC errors (±5%) due to shim, imaging and eddy currents were mitigated by double echo DWI and image co-registration of individual gradient directions. Conclusion The analysis confirms gradient nonlinearity as a major source of spatial DW bias and variability in off-center ADC measurements across MRI platforms, with minor contributions from shim, imaging gradients and eddy currents. The developed protocol enables empiric description of systematic bias in multicenter quantitative DWI studies. PMID:25940607

Demonstration of nonlinearity bias in the measurement of the apparent diffusion coefficient in multicenter trials.

PubMed

Malyarenko, Dariya I; Newitt, David; J Wilmes, Lisa; Tudorica, Alina; Helmer, Karl G; Arlinghaus, Lori R; Jacobs, Michael A; Jajamovich, Guido; Taouli, Bachir; Yankeelov, Thomas E; Huang, Wei; Chenevert, Thomas L

2016-03-01

Characterize system-specific bias across common magnetic resonance imaging (MRI) platforms for quantitative diffusion measurements in multicenter trials. Diffusion weighted imaging (DWI) was performed on an ice-water phantom along the superior-inferior (SI) and right-left (RL) orientations spanning ± 150 mm. The same scanning protocol was implemented on 14 MRI systems at seven imaging centers. The bias was estimated as a deviation of measured from known apparent diffusion coefficient (ADC) along individual DWI directions. The relative contributions of gradient nonlinearity, shim errors, imaging gradients, and eddy currents were assessed independently. The observed bias errors were compared with numerical models. The measured systematic ADC errors scaled quadratically with offset from isocenter, and ranged between -55% (SI) and 25% (RL). Nonlinearity bias was dependent on system design and diffusion gradient direction. Consistent with numerical models, minor ADC errors (± 5%) due to shim, imaging and eddy currents were mitigated by double echo DWI and image coregistration of individual gradient directions. The analysis confirms gradient nonlinearity as a major source of spatial DW bias and variability in off-center ADC measurements across MRI platforms, with minor contributions from shim, imaging gradients and eddy currents. The developed protocol enables empiric description of systematic bias in multicenter quantitative DWI studies. © 2015 Wiley Periodicals, Inc.

Diffusion coefficients in organic-water solutions and comparison with Stokes-Einstein predictions

NASA Astrophysics Data System (ADS)

Evoy, E.; Kamal, S.; Bertram, A. K.

2017-12-01

Diffusion coefficients of organic species in particles containing secondary organic material (SOM) are necessary for predicting the growth and reactivity of these particles in the atmosphere. Previously, the Stokes-Einstein equation combined with viscosity measurements have been used to predict these diffusion coefficients. However, the accuracy of the Stokes-Einstein equation for predicting diffusion coefficients in SOM-water particles has not been quantified. To test the Stokes-Einstein equation, diffusion coefficients of fluorescent organic probe molecules were measured in citric acid-water and sorbitol-water solutions. These solutions were used as proxies for SOM-water particles found in the atmosphere. Measurements were performed as a function of water activity, ranging from 0.26-0.86, and as a function of viscosity ranging from 10-3 to 103 Pa s. Diffusion coefficients were measured using fluorescence recovery after photobleaching. The measured diffusion coefficients were compared with predictions made using the Stokes-Einstein equation combined with literature viscosity data. Within the uncertainties of the measurements, the measured diffusion coefficients agreed with the predicted diffusion coefficients, in all cases.

Monte Carlo simulation based on dynamic disorder model in organic semiconductors: From coherent to incoherent transport

NASA Astrophysics Data System (ADS)

Yao, Yao; Si, Wei; Hou, Xiaoyuan; Wu, Chang-Qin

2012-06-01

The dynamic disorder model for charge carrier transport in organic semiconductors has been extensively studied in recent years. Although it is successful on determining the value of bandlike mobility in the organic crystalline materials, the incoherent hopping, the typical transport characteristic in amorphous molecular semiconductors, cannot be described. In this work, the decoherence process is taken into account via a phenomenological parameter, say, decoherence time, and the projective and Monte Carlo method are applied for this model to determine the waiting time and thus the diffusion coefficient. It is obtained that the type of transport is changed from coherent to incoherent with a sufficiently short decoherence time, which indicates the essential role of decoherence time in determining the type of transport in organics. We have also discussed the spatial extent of carriers for different decoherence time, and the transition from delocalization (carrier resides in about 10 molecules) to localization is observed. Based on the experimental results of spatial extent, we estimate that the decoherence time in pentacene has the order of 1 ps. Furthermore, the dependence of diffusion coefficient on decoherence time is also investigated, and corresponding experiments are discussed.

Monte Carlo simulation based on dynamic disorder model in organic semiconductors: from coherent to incoherent transport.

PubMed

Yao, Yao; Si, Wei; Hou, Xiaoyuan; Wu, Chang-Qin

2012-06-21

The dynamic disorder model for charge carrier transport in organic semiconductors has been extensively studied in recent years. Although it is successful on determining the value of bandlike mobility in the organic crystalline materials, the incoherent hopping, the typical transport characteristic in amorphous molecular semiconductors, cannot be described. In this work, the decoherence process is taken into account via a phenomenological parameter, say, decoherence time, and the projective and Monte Carlo method are applied for this model to determine the waiting time and thus the diffusion coefficient. It is obtained that the type of transport is changed from coherent to incoherent with a sufficiently short decoherence time, which indicates the essential role of decoherence time in determining the type of transport in organics. We have also discussed the spatial extent of carriers for different decoherence time, and the transition from delocalization (carrier resides in about 10 molecules) to localization is observed. Based on the experimental results of spatial extent, we estimate that the decoherence time in pentacene has the order of 1 ps. Furthermore, the dependence of diffusion coefficient on decoherence time is also investigated, and corresponding experiments are discussed.

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

An Exploration into Diffusion Tensor Imaging in the Bovine Ocular Lens

PubMed Central

Vaghefi, Ehsan; Donaldson, Paul J.

2013-01-01

We describe our development of the diffusion tensor imaging modality for the bovine ocular lens. Diffusion gradients were added to a spin-echo pulse sequence and the relevant parameters of the sequence were refined to achieve good diffusion weighting in the lens tissue, which demonstrated heterogeneous regions of diffusive signal attenuation. Decay curves for b-value (loosely summarizes the strength of diffusion weighting) and TE (determines the amount of magnetic resonance imaging-obtained signal) were used to estimate apparent diffusion coefficients (ADC) and T2 in different lens regions. The ADCs varied by over an order of magnitude and revealed diffusive anisotropy in the lens. Up to 30 diffusion gradient directions, and 8 signal acquisition averages, were applied to lenses in culture in order to improve maps of diffusion tensor eigenvalues, equivalent to ADC, across the lens. From these maps, fractional anisotropy maps were calculated and compared to known spatial distributions of anisotropic molecular fluxes in the lens. This comparison suggested new hypotheses and experiments to quantitatively assess models of circulation in the avascular lens. PMID:23459990

COSMIC-RAY PITCH-ANGLE SCATTERING IN IMBALANCED MHD TURBULENCE SIMULATIONS

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

Weidl, Martin S.; Jenko, Frank; Teaca, Bogdan

2015-09-20

Pitch-angle scattering rates for cosmic-ray particles in MHD simulations with imbalanced turbulence are calculated for fully evolving electromagnetic turbulence. We compare with theoretical predictions derived from the quasilinear theory of cosmic-ray diffusion for an idealized slab spectrum and demonstrate how cross helicity affects the shape of the pitch-angle diffusion coefficient. Additional simulations in evolving magnetic fields or static field configurations provide evidence that the scattering anisotropy in imbalanced turbulence is not primarily due to coherence with propagating Alfvén waves, but an effect of the spatial structure of electric fields in cross-helical MHD turbulence.

Sinc-Galerkin estimation of diffusivity in parabolic problems

NASA Technical Reports Server (NTRS)

Smith, Ralph C.; Bowers, Kenneth L.

1991-01-01

A fully Sinc-Galerkin method for the numerical recovery of spatially varying diffusion coefficients in linear partial differential equations is presented. Because the parameter recovery problems are inherently ill-posed, an output error criterion in conjunction with Tikhonov regularization is used to formulate them as infinite-dimensional minimization problems. The forward problems are discretized with a sinc basis in both the spatial and temporal domains thus yielding an approximate solution which displays an exponential convergence rate and is valid on the infinite time interval. The minimization problems are then solved via a quasi-Newton/trust region algorithm. The L-curve technique for determining an approximate value of the regularization parameter is briefly discussed, and numerical examples are given which show the applicability of the method both for problems with noise-free data as well as for those whose data contains white noise.

Compartmentalization of the outer hair cell demonstrated by slow diffusion in the extracisternal space.

PubMed

Gliko, Olga; Saggau, Peter; Brownell, William E

2009-08-19

In the outer hair cell (OHC), the extracisternal space (ECiS) is a conduit and reservoir of the molecular and ionic substrates of the lateral wall, including those necessary for electromotility. To determine the mechanisms through which molecules are transported in the ECiS of the OHC, we selectively imaged the time-dependent spatial distribution of fluorescent molecules in a <100 nm layer near the cell/glass interface of the recording chamber after their photolytic activation in a diffraction-limited volume. The effective diffusion coefficient was calculated using the analytical solution of the diffusion equation. It was found that diffusion in the ECiS is isotropic and not affected by depolarizing the OHC. Compared with free solution, the diffusion of 10 kDa dextran was slowed down in both the ECiS and the axial core by a factor of 4.6 and 1.6, respectively.

Correlated diffusion of colloidal particles near a liquid-liquid interface.

PubMed

Zhang, Wei; Chen, Song; Li, Na; Zhang, Jia Zheng; Chen, Wei

2014-01-01

Optical microscopy and multi-particle tracking are used to investigate the cross-correlated diffusion of quasi two-dimensional colloidal particles near an oil-water interface. The behaviors of the correlated diffusion along longitudinal and transverse direction are asymmetric. It is shown that the characteristic length for longitudinal and transverse correlated diffusion are particle diameter d and the distance z from particle center to the interface, respectively, for large particle separation z. The longitudinal and transverse correlated diffusion coefficient D||(r) and D[perpendicular](r) are independent of the colloidal area fraction n when n < 0.3, which indicates that the hydrodynamic interactions(HIs) among the particles are dominated by HIs through the surrounding fluid for small n. For high area fraction n > 0.4 the power law exponent for the spatial decay of [Formula: see text] begins to decrease, which suggests the HIs are more contributed from the 2D particle monolayer self for large n.

White matter involvement in sporadic Creutzfeldt-Jakob disease

PubMed Central

Mandelli, Maria Luisa; DeArmond, Stephen J.; Hess, Christopher P.; Vitali, Paolo; Papinutto, Nico; Oehler, Abby; Miller, Bruce L.; Lobach, Irina V.; Bastianello, Stefano; Geschwind, Michael D.; Henry, Roland G.

2014-01-01

Sporadic Creutzfeldt-Jakob disease is considered primarily a disease of grey matter, although the extent of white matter involvement has not been well described. We used diffusion tensor imaging to study the white matter in sporadic Creutzfeldt-Jakob disease compared to healthy control subjects and to correlated magnetic resonance imaging findings with histopathology. Twenty-six patients with sporadic Creutzfeldt-Jakob disease and nine age- and gender-matched healthy control subjects underwent volumetric T1-weighted and diffusion tensor imaging. Six patients had post-mortem brain analysis available for assessment of neuropathological findings associated with prion disease. Parcellation of the subcortical white matter was performed on 3D T1-weighted volumes using Freesurfer. Diffusion tensor imaging maps were calculated and transformed to the 3D-T1 space; the average value for each diffusion metric was calculated in the total white matter and in regional volumes of interest. Tract-based spatial statistics analysis was also performed to investigate the deeper white matter tracts. There was a significant reduction of mean (P = 0.002), axial (P = 0.0003) and radial (P = 0.0134) diffusivities in the total white matter in sporadic Creutzfeldt-Jakob disease. Mean diffusivity was significantly lower in most white matter volumes of interest (P < 0.05, corrected for multiple comparisons), with a generally symmetric pattern of involvement in sporadic Creutzfeldt-Jakob disease. Mean diffusivity reduction reflected concomitant decrease of both axial and radial diffusivity, without appreciable changes in white matter anisotropy. Tract-based spatial statistics analysis showed significant reductions of mean diffusivity within the white matter of patients with sporadic Creutzfeldt-Jakob disease, mainly in the left hemisphere, with a strong trend (P = 0.06) towards reduced mean diffusivity in most of the white matter bilaterally. In contrast, by visual assessment there was no white matter abnormality either on T2-weighted or diffusion-weighted images. Widespread reduction in white matter mean diffusivity, however, was apparent visibly on the quantitative attenuation coefficient maps compared to healthy control subjects. Neuropathological analysis showed diffuse astrocytic gliosis and activated microglia in the white matter, rare prion deposition and subtle subcortical microvacuolization, and patchy foci of demyelination with no evident white matter axonal degeneration. Decreased mean diffusivity on attenuation coefficient maps might be associated with astrocytic gliosis. We show for the first time significant global reduced mean diffusivity within the white matter in sporadic Creutzfeldt-Jakob disease, suggesting possible primary involvement of the white matter, rather than changes secondary to neuronal degeneration/loss. PMID:25367029

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.

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.

Application of a planetary wave breaking parameterization to stratospheric circulation statistics

NASA Technical Reports Server (NTRS)

Randel, William J.; Garcia, Rolando R.

1994-01-01

The planetary wave parameterization scheme developed recently by Garcia is applied to statospheric circulation statistics derived from 12 years of National Meteorological Center operational stratospheric analyses. From the data a planetary wave breaking criterion (based on the ratio of the eddy to zonal mean meridional potential vorticity (PV) gradients), a wave damping rate, and a meridional diffusion coefficient are calculated. The equatorward flank of the polar night jet during winter is identified as a wave breaking region from the observed PV gradients; the region moves poleward with season, covering all high latitudes in spring. Derived damping rates maximize in the subtropical upper stratosphere (the 'surf zone'), with damping time scales of 3-4 days. Maximum diffusion coefficients follow the spatial patterns of the wave breaking criterion, with magnitudes comparable to prior published estimates. Overall, the observed results agree well with the parameterized calculations of Garcia.

Multivariate space - time analysis of PRE-STORM precipitation

NASA Technical Reports Server (NTRS)

Polyak, Ilya; North, Gerald R.; Valdes, Juan B.

1994-01-01

This paper presents the methodologies and results of the multivariate modeling and two-dimensional spectral and correlation analysis of PRE-STORM rainfall gauge data. Estimated parameters of the models for the specific spatial averages clearly indicate the eastward and southeastward wave propagation of rainfall fluctuations. A relationship between the coefficients of the diffusion equation and the parameters of the stochastic model of rainfall fluctuations is derived that leads directly to the exclusive use of rainfall data to estimate advection speed (about 12 m/s) as well as other coefficients of the diffusion equation of the corresponding fields. The statistical methodology developed here can be used for confirmation of physical models by comparison of the corresponding second-moment statistics of the observed and simulated data, for generating multiple samples of any size, for solving the inverse problem of the hydrodynamic equations, and for application in some other areas of meteorological and climatological data analysis and modeling.

Characterization of Tissue Structure at Varying Length Scales Using Temporal Diffusion Spectroscopy

PubMed Central

Gore, John C.; Xu, Junzhong; Colvin, Daniel C.; Yankeelov, Thomas E.; Parsons, Edward C.; Does, Mark D.

2011-01-01

The concepts, theoretical behavior and experimental applications of temporal diffusion spectroscopy are reviewed and illustrated. Temporal diffusion spectra are obtained by using oscillating gradient waveforms in diffusion-weighted measurements, and represent the manner in which various spectral components of molecular velocity correlations vary in different geometrical structures that restrict or hinder free movements. Measurements made at different gradient frequencies reveal information on the scale of restrictions or hindrances to free diffusion, and the shape of a spectrum reveals the relative contributions of spatial restrictions at different distance scales. Such spectra differ from other so-called diffusion spectra which depict spatial frequencies and are defined at a fixed diffusion time. Experimentally, oscillating gradients at moderate frequency are more feasible for exploring restrictions at very short distances, which in tissues correspond to structures smaller than cells. We describe the underlying concepts of temporal diffusion spectra and provide analytical expressions for the behavior of the diffusion coefficient as a function of gradient frequency in simple geometries with different dimensions. Diffusion in more complex model media that mimic tissues has been simulated using numerical methods. Experimental measurements of diffusion spectra have been obtained in suspensions of particles and cells, as well as in vivo in intact animals. An observation of particular interest is the increased contrast and heterogeneity observed in tumors using oscillating gradients at moderate frequency compared to conventional pulse gradient methods, and the potential for detecting changes in tumors early in their response to treatment. Computer simulations suggest that diffusion spectral measurements may be sensitive to intracellular structures such as nuclear size, and that changes in tissue diffusion properties may be measured before there are changes in cell density. PMID:20677208

Chemical morphogenesis: recent experimental advances in reaction–diffusion system design and control

PubMed Central

Szalai, István; Cuiñas, Daniel; Takács, Nándor; Horváth, Judit; De Kepper, Patrick

2012-01-01

In his seminal 1952 paper, Alan Turing predicted that diffusion could spontaneously drive an initially uniform solution of reacting chemicals to develop stable spatially periodic concentration patterns. It took nearly 40 years before the first two unquestionable experimental demonstrations of such reaction–diffusion patterns could be made in isothermal single phase reaction systems. The number of these examples stagnated for nearly 20 years. We recently proposed a design method that made their number increase to six in less than 3 years. In this report, we formally justify our original semi-empirical method and support the approach with numerical simulations based on a simple but realistic kinetic model. To retain a number of basic properties of real spatial reactors but keep calculations to a minimal complexity, we introduce a new way to collapse the confined spatial direction of these reactors. Contrary to similar reduced descriptions, we take into account the effect of the geometric size in the confinement direction and the influence of the differences in the diffusion coefficient on exchange rates of species with their feed environment. We experimentally support the method by the observation of stationary patterns in red-ox reactions not based on oxihalogen chemistry. Emphasis is also brought on how one of these new systems can process different initial conditions and memorize them in the form of localized patterns of different geometries. PMID:23919126

Bio-Optical Properties of the Arabian Sea as Determined by In Situ and Sea WiFS Data

NASA Technical Reports Server (NTRS)

Trees, Charles C.

1997-01-01

The overall objective of this work was to characterize optical and fluorescence properties in the euphotic zone during two British Ocean Flux Study (BOFS) Arabian Sea cruises. This was later expanded in 1995 to include three U.S. JGOFS Arabian Sea Cruises. The region was to be divided into one or more "bio-optical provinces," within each of which a single set of regression models was to be developed to relate the vertical distribution of irradiance attenuation and normalized fluorescence (SF and NF) to remote sensing reflectance and diffuse attenuation coefficient. The working hypothesis was that over relatively large spatial and temporal scales, the vertical profiles of bio-optical properties were predictable. The specific technical objectives were: (1) To characterize the vertical distribution of the inherent and apparent optical properties by measuring downwelling and upwelling irradiances, upwelling radiances, scalar irradiance of PAR, and beam transmissions at each station - from these data, spectral diffuse attenuation coefficients, irradiance reflectances, remote sensing reflectances, surface-leaving radiances and beam attenuation coefficients were determined; (2) To characterize the spectral absorption of total particulate, detrital, and dissolved organic material at each station from discrete water samples; (3) To describe the vertical distribution of photoadaptive properties in the water column by measuring profiles of stimulated (SF) and natural (NF) fluorescence and examining relationships between SF and NF as a function of diffuse optical depth, pigment biomass and primary productivity; and (4) To establish locally derived, in-water algorithms relating remote sensing reflectance spectra to diffuse attenuation coefficients, phytoplankton pigment concentrations and primary productivity, through intercomparisons with in situ measurements, for application to SeaWiFS data.

Thermophoresis of a Brownian particle driven by inhomogeneous thermal fluctuation

NASA Astrophysics Data System (ADS)

Tsuji, Tetsuro; Saita, Sho; Kawano, Satoyuki

2018-03-01

Brownian motion of a spherical particle induced by the interaction with surrounding molecules is considered. If the particle is larger than the molecules and the temperature of surrounding media is spatially non-uniform, the interaction between an individual molecule and the particle is also position-dependent. That is, the particle is subject to inhomogeneous thermal fluctuation. In this paper, we investigate the contribution of the inhomogeneous thermal fluctuation to the thermophoresis, i.e., the Soret coefficient or thermal diffusion factor. The problem is simplified by assuming a hard-sphere potential between the particle and the surrounding molecules and is investigated using the kinetic theory, namely, we consider a linear Boltzmann-type equation for the velocity distribution function of the particle. Using the perturbation analysis with respect to the square root of mass ratio between the molecule and the particle, the drift-diffusion equation of the particle is derived. It is found that the Soret coefficient, or thermal diffusion factor, is dependent on the mass ratio and the excluded volume of the particle. In particular, when the ratio of the mass density of the particle to that of the surrounding media decreases, the Soret coefficient also decreases and may take negative value. The present result well describes the mass-dependency of thermal diffusion factor obtained by the molecular dynamics simulation carried out in an existing study and the one in the present study, where soft potentials of Lennard-Jones-type are used instead of hard-sphere potential.

Multiplexed measurement of protein diffusion in Caenorhabditis elegans embryos with SPIM-FCS

NASA Astrophysics Data System (ADS)

Struntz, Philipp; Weiss, Matthias

2016-02-01

Quantifying the diffusion behavior of proteins in different environments, e.g. on cellular membranes, is a key step in uncovering the vital action of protein networks in living organisms. While several established techniques for local diffusion measurements exist, the life sciences are currently in need of a multiplexed, i.e. spatially parallelized, data acquisition that allows for obtaining diffusion maps with high spatiotemporal resolution. Following this demand, the combination of camera-based single-plane illumination microscopy (SPIM) and fluorescence correlation spectroscopy (FCS) has recently emerged as a promising approach. So far, SPIM-FCS has mainly been used to assess the diffusion of soluble particles and proteins in vitro and in culture cells, but due to a particularly low photobleaching and -toxicity the method is also well applicable to developmental organisms. Here, we have probed the performance of SPIM-FCS on an established developmental model organism, the small nematode Caenorhabditis elegans. In particular, we have quantified the diffusion of the peripheral membrane protein PLC1δ 1 in the embryo’s cytoplasm and on the plasma membrane. As a result, we were able to derive diffusion maps of PLC1δ 1 in both compartments in multiple individuals, showing the spatially varying diffusion coefficients across the embryo. Our data also report on the dissociation kinetics of PLC1δ 1 from the plasma membrane, hence underlining that SPIM-FCS can be used to explore key features of peripheral membrane proteins in fragile developmental model organisms.

The role of intra-NAPL diffusion on mass transfer from MGP residuals

NASA Astrophysics Data System (ADS)

Shafieiyoun, Saeid; Thomson, Neil R.

2018-06-01

An experimental and computational study was performed to investigate the role of multi-component intra-NAPL diffusion on NAPL-water mass transfer. Molecular weight and the NAPL component concentrations were determined to be the most important parameters affecting intra-NAPL diffusion coefficients. Four NAPLs with different viscosities but the same quantified mass were simulated. For a spherical NAPL body, a combination of NAPL properties and interphase mass transfer rate can result in internal diffusion limitations. When the main intra-NAPL diffusion coefficients are in the range of self-diffusion coefficients (10-5 to 10-6 cm2/s), dissolution is not limited by internal diffusion except for high mass transfer rate coefficients (>180 cm/day). For a complex and relatively high viscous NAPL (>50 g/(cm s)), smaller intra-NAPL diffusion coefficients (<10-8) are expected and even low mass transfer rate coefficients ( 6 cm/day) can result in diffusion-limited dissolution.

Spatial distribution of protons at high and low altitudes in the radiation belts. Comparison of theory and experiment

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

Panasyuk, M.I.; Reizman, S.Y.; Sosnovets, E.N.

1986-05-01

A comparative analysis of experimental data on the spatial distributions of protons with energies (E) greater than 0.1 MeV at high and low latitudes, which were obtained on the Molniya-1, Kosmos-900, Elektron, and 1964-45A satellites, is carried out. As a result of the comparison of the experimental data relating to the measurements of protons with E - 0.2 MeV with the calculation including radial drift of particles under the action of electric and magnetic field fluctuations, it is shown that radial diffusion with a diffusion coefficient independent of geomagnetic latitude is the primary mechanism shaping the spatial distributions of protonsmore » at geomagnetic latitudes up to ..lambda.. approx. = 40/sup 0/. The results of the experiments and the calculations agree under the assumption of both magnetic and electric diffusion, but the latter case requires the inclusion of the model of a spatially inhomogeneous convection electric field. At ..lambda.. greater than or equal to 50/sup 0/ pitchangle scattering makes the primary contribution to the shaping of the spatial structure of the protons at low altitudes. A value of 2 less than or equal to n less than or equal to 4 is obtained for the exponent of the slope of the radial distribution of cold electrons N /sub e/ (r)..cap alpha.. /sup -n/ at 2 less than or equal to L less than or equal to 4.« less

The development of the rhizosphere: simulation of root exudation for two contrasting exudates: citrate and mucilage

NASA Astrophysics Data System (ADS)

Sheng, Cheng; Bol, Roland; Vetterlein, Doris; Vanderborght, Jan; Schnepf, Andrea

2017-04-01

Different types of root exudates and their effect on soil/rhizosphere properties have received a lot of attention. Since their influence of rhizosphere properties and processes depends on their concentration in the soil, the assessment of the spatial-temporal exudate concentration distribution around roots is of key importance for understanding the functioning of the rhizosphere. Different root systems have different root architectures. Different types of root exudates diffuse in the rhizosphere with different diffusion coefficient. Both of them are responsible for the dynamics of exudate concentration distribution in the rhizosphere. Hence, simulations of root exudation involving four kinds of plant root systems (Vicia faba, Lupinus albus, Triticum aestivum and Zea mays) and two kinds of root exudates (citrate and mucilage) were conducted. We consider a simplified root architecture where each root is represented by a straight line. Assuming that root tips move at a constant velocity and that mucilage transport is linear, concentration distributions can be obtained from a convolution of the analytical solution of the transport equation in a stationary flow field for an instantaneous point source injection with the spatial-temporal distribution of the source strength. By coupling the analytical equation with a root growth model that delivers the spatial-temporal source term, we simulated exudate concentration distributions for citrate and mucilage with MATLAB. From the simulation results, we inferred the following information about the rhizosphere: (a) the dynamics of the root architecture development is the main effect of exudate distribution in the root zone; (b) a steady rhizosphere with constant width is more likely to develop for individual roots when the diffusion coefficient is small. The simulations suggest that rhizosphere development depends in the following way on the root and exudate properties: the dynamics of the root architecture result in various development patterns of the rhizosphere. Meanwhile, Results improve our understanding of the impact of the spatial and temporal heterogeneity of exudate input on rhizosphere development for different root system types and substances. In future work, we will use the simulation tool to infer critical parameters that determine the spatial-temporal extent of the rhizosphere from experimental data.

In Vivo Fluorescence Resonance Energy Transfer Imaging for Targeted Anti-Cancer Drug Delivery Kinetics

NASA Astrophysics Data System (ADS)

Webb, Kevin; Gaind, Vaibhav; Tsai, Hsiaorho; Bentz, Brian; Chelvam, Venkatesh; Low, Philip

2012-02-01

We describe an approach for the evaluation of targeted anti-cancer drug delivery in vivo. The method emulates the drug release and activation process through acceptor release from a targeted donor-acceptor pair that exhibits fluorescence resonance energy transfer (FRET). In this case, folate targeting of the cancer cells is used - 40 % of all human cancers, including ovarian, lung, breast, kidney, brain and colon cancer, over-express folate receptors. We demonstrate the reconstruction of the spatially-dependent FRET parameters in a mouse model and in tissue phantoms. The FRET parameterization is incorporated into a source for a diffusion equation model for photon transport in tissue, in a variant of optical diffusion tomography (ODT) called FRET-ODT. In addition to the spatially-dependent tissue parameters in the diffusion model (absorption and diffusion coefficients), the FRET parameters (donor-acceptor distance and yield) are imaged as a function of position. Modulated light measurements are made with various laser excitation positions and a gated camera. More generally, our method provides a new vehicle for studying disease at the molecular level by imaging FRET parameters in deep tissue, and allows the nanometer FRET ruler to be utilized in deep tissue.

Spatial modeling of cell signaling networks.

PubMed

Cowan, Ann E; Moraru, Ion I; Schaff, James C; Slepchenko, Boris M; Loew, Leslie M

2012-01-01

The shape of a cell, the sizes of subcellular compartments, and the spatial distribution of molecules within the cytoplasm can all control how molecules interact to produce a cellular behavior. This chapter describes how these spatial features can be included in mechanistic mathematical models of cell signaling. The Virtual Cell computational modeling and simulation software is used to illustrate the considerations required to build a spatial model. An explanation of how to appropriately choose between physical formulations that implicitly or explicitly account for cell geometry and between deterministic versus stochastic formulations for molecular dynamics is provided, along with a discussion of their respective strengths and weaknesses. As a first step toward constructing a spatial model, the geometry needs to be specified and associated with the molecules, reactions, and membrane flux processes of the network. Initial conditions, diffusion coefficients, velocities, and boundary conditions complete the specifications required to define the mathematics of the model. The numerical methods used to solve reaction-diffusion problems both deterministically and stochastically are then described and some guidance is provided in how to set up and run simulations. A study of cAMP signaling in neurons ends the chapter, providing an example of the insights that can be gained in interpreting experimental results through the application of spatial modeling. Copyright © 2012 Elsevier Inc. All rights reserved.

Diffusion properties of conventional and calcium-sensitive MRI contrast agents in the rat cerebral cortex.

PubMed

Hagberg, Gisela E; Mamedov, Ilgar; Power, Anthony; Beyerlein, Michael; Merkle, Hellmut; Kiselev, Valerij G; Dhingra, Kirti; Kubìček, Vojtĕch; Angelovski, Goran; Logothetis, Nikos K

2014-01-01

Calcium-sensitive MRI contrast agents can only yield quantitative results if the agent concentration in the tissue is known. The agent concentration could be determined by diffusion modeling, if relevant parameters were available. We have established an MRI-based method capable of determining diffusion properties of conventional and calcium-sensitive agents. Simulations and experiments demonstrate that the method is applicable both for conventional contrast agents with a fixed relaxivity value and for calcium-sensitive contrast agents. The full pharmacokinetic time-course of gadolinium concentration estimates was observed by MRI before, during and after intracerebral administration of the agent, and the effective diffusion coefficient D* was determined by voxel-wise fitting of the solution to the diffusion equation. The method yielded whole brain coverage with a high spatial and temporal sampling. The use of two types of MRI sequences for sampling of the diffusion time courses was investigated: Look-Locker-based quantitative T(1) mapping, and T(1) -weighted MRI. The observation times of the proposed MRI method is long (up to 20 h) and consequently the diffusion distances covered are also long (2-4 mm). Despite this difference, the D* values in vivo were in agreement with previous findings using optical measurement techniques, based on observation times of a few minutes. The effective diffusion coefficient determined for the calcium-sensitive contrast agents may be used to determine local tissue concentrations and to design infusion protocols that maintain the agent concentration at a steady state, thereby enabling quantitative sensing of the local calcium concentration. Copyright © 2014 John Wiley & Sons, Ltd.

Monitoring and Manipulating Motions of Single Molecules/Nanoparticles

NASA Astrophysics Data System (ADS)

Chen, Fang

This dissertation has two main research components: 1. the study of mass transport in confined environments; 2. the effort toward driving a molecular car on a solid surface. Understanding mass transport processes, e.g., diffusion, migration, and adsorption/desorption in confined space is important not only to fundamental sciences but also to advanced applications. So far, they are poorly understood because of technical challenges: insufficient spatial and/or temporal resolutions. In this dissertation, we made efforts toward understanding molecular/particular dynamics in confined space by combining a recently developed super resolution technique, stimulated depletion emission microscopy (STED), with the high temporal resolution technique, fluorescence correlation spectroscopy (FCS). We first explored the feasibility of using conventional FCS to study diffusion in a model confined space: cylindrical pores. Since there is no analytical solution to solve the autocorrelation function (ACF) in confined space, we simulated single particle diffusion in hundred-nanometer pores using Monte Carlo simulation. We found that confined 2D diffusion and unconfined 1D diffusion dynamics are separated in both intensity traces and autocorrelation functions, which gives a new opportunity to extract the axial diffusion coefficient in cylindrical pores. We then experimentally studied 45 nm particles diffusing in 300 nm alumina pores. The acquired axial diffusion coefficient is consistent with the expected value. Conventional confocal FCS is insufficient to resolve lateral diffusion in confined space because of the diffraction limit in spatial resolution. To pave the way of using STED microscopy to study the anisotropic diffusion in confined space, we theoretically investigated STED-FCS in cylindrical pores. It showed that by reducing the spatial resolution from 250 nm to 50 nm in STED microscopy, we would be able to determine both lateral and axial diffusion coefficients in hundred-nanometer pores in theory. We then experimentally studied nanoparticles diffusing on membrane filters containing 200 nm polyethyleneglycol- or C18-modified pores. Using STED microscopy, we resolved for the first time how small particles are retained by the pores. Trapping by the pore entrances rather than adsorption is responsible for the retention. Further studies on C18-modified pores showed consistency in Gibbs free energy about the retention process. In addition, in order to understand how nanoparticles interact with the surface when they are forced to be on, or very close to, the surface, we studied nanosecond rotation dynamics of gold nanorods with one end attached on the surface. We found that the nanorod motion is dominated by van der Waals interaction-induced immobilization rather Brownian rotational diffusion as previously thought. The actual rotation, during which the nanorod transits from one immobilized state to the other, slows down by 50 times. The second part of the research is the collaboration with Tour's group in Rice University. The ultimate goal is to use light to drive a motorized nanocar at ambient conditions. To fulfill this goal, we first studied the moving kinetics of adamantane-wheeled nanocars on hydroxylated and PEG-modified surfaces using single molecule fluorescence microscopy. We found that nanocars' diffusion slows down on solid surface over time, which is possibly caused by the increased hydrophobicity of the substrate surface due to the adsorbates from the air. A sticky-spots model was proposed to explain the observed slowing down. To find out whether a light-activatable motor works when it is incorporated into a nanocar, we carefully designed a series of molecules containing a regular motor, a slow motor, a nonunidirectional motor, and no motor. We found that a fast unidirectional rotating motor enhanced the diffusion of the molecule in solution upon UV-illumination. Detailed analysis suggested that the unimolecular submersible nanomachine (USN) will give 9-nm step upon each motor actuation. This is the first nanomachine that gives mechanical motion at small molecular scale.

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.

Continuous Diffusion Model for Concentration Dependence of Nitroxide EPR Parameters in Normal and Supercooled Water.

PubMed

Merunka, Dalibor; Peric, Miroslav

2017-05-25

Electron paramagnetic resonance (EPR) spectra of radicals in solution depend on their relative motion, which modulates the Heisenberg spin exchange and dipole-dipole interactions between them. To gain information on radical diffusion from EPR spectra demands both reliable spectral fitting to find the concentration coefficients of EPR parameters and valid expressions between the concentration and diffusion coefficients. Here, we measured EPR spectra of the 14 N- and 15 N-labeled perdeuterated TEMPONE radicals in normal and supercooled water at various concentrations. By fitting the EPR spectra to the functions based on the modified Bloch equations, we obtained the concentration coefficients for the spin dephasing, coherence transfer, and hyperfine splitting parameters. Assuming the continuous diffusion model for radical motion, the diffusion coefficients of radicals were calculated from the concentration coefficients using the standard relations and the relations derived from the kinetic equations for the spin evolution of a radical pair. The latter relations give better agreement between the diffusion coefficients calculated from different concentration coefficients. The diffusion coefficients are similar for both radicals, which supports the presented method. They decrease with lowering temperature slower than is predicted by the Stokes-Einstein relation and slower than the rotational diffusion coefficients, which is similar to the diffusion of water molecules in supercooled water.

Anisotropic diffusion of fluorescently labeled ATP in rat cardiomyocytes determined by raster image correlation spectroscopy

PubMed Central

Vendelin, Marko; Birkedal, Rikke

2008-01-01

A series of experimental data points to the existence of profound diffusion restrictions of ADP/ATP in rat cardiomyocytes. This assumption is required to explain the measurements of kinetics of respiration, sarcoplasmic reticulum loading with calcium, and kinetics of ATP-sensitive potassium channels. To be able to analyze and estimate the role of intracellular diffusion restrictions on bioenergetics, the intracellular diffusion coefficients of metabolites have to be determined. The aim of this work was to develop a practical method for determining diffusion coefficients in anisotropic medium and to estimate the overall diffusion coefficients of fluorescently labeled ATP in rat cardiomyocytes. For that, we have extended raster image correlation spectroscopy (RICS) protocols to be able to discriminate the anisotropy in the diffusion coefficient tensor. Using this extended protocol, we estimated diffusion coefficients of ATP labeled with the fluorescent conjugate Alexa Fluor 647 (Alexa-ATP). In the analysis, we assumed that the diffusion tensor can be described by two values: diffusion coefficient along the myofibril and that across it. The average diffusion coefficients found for Alexa-ATP were as follows: 83 ± 14 μm2/s in the longitudinal and 52 ± 16 μm2/s in the transverse directions (n = 8, mean ± SD). Those values are ∼2 (longitudinal) and ∼3.5 (transverse) times smaller than the diffusion coefficient value estimated for the surrounding solution. Such uneven reduction of average diffusion coefficient leads to anisotropic diffusion in rat cardiomyocytes. Although the source for such anisotropy is uncertain, we speculate that it may be induced by the ordered pattern of intracellular structures in rat cardiomyocytes. PMID:18815224

Fluid self-diffusion in Scots pine sapwood tracheid cells.

PubMed

Johannessen, Espen H; Hansen, Eddy W; Rosenholm, Jarl B

2006-02-09

The self-diffusion coefficients of water and toluene in Scots pine sapwood was measured using low field pulsed field gradient nuclear magnetic resonance (PFG-NMR). Wood chips of 8 mm diameter were saturated with the respective liquids, and liquid self-diffusion was then traced in one dimension orthogonal to the tracheid cell walls in the wood's radial direction. The experimental echo attenuation curves were exponential, and characteristic self-diffusion coefficients were produced for diffusion times spanning from very short times to times on the order of magnitude of seconds. Observed self-diffusion coefficients were decaying asymptotically as a function of diffusion time, an effect which was ascribed to the cell walls' restriction on confined liquid diffusion. The observed self-diffusion behavior in Scots pine sapwood was compared to self-diffusion coefficients obtained from simulations of diffusion in a square. Principles of molecular displacements in confined geometries were used for elucidating the wood's cellular structure from the observed diffusion coefficients. The results were compared with a mathematical model for diffusion between parallel planes.

Ultrafast lithium diffusion in bilayer graphene

NASA Astrophysics Data System (ADS)

Kühne, Matthias; Paolucci, Federico; Popovic, Jelena; Ostrovsky, Pavel M.; Maier, Joachim; Smet, Jurgen H.

2017-09-01

Solids that simultaneously conduct electrons and ions are key elements for the mass transfer and storage required in battery electrodes. Single-phase materials with a high electronic and high ionic conductivity at room temperature are hard to come by, and therefore multiphase systems with separate ion and electron channels have been put forward instead. Here we report on bilayer graphene as a single-phase mixed conductor that demonstrates Li diffusion faster than in graphite and even surpassing the diffusion of sodium chloride in liquid water. To measure Li diffusion, we have developed an on-chip electrochemical cell architecture in which the redox reaction that forces Li intercalation is localized only at a protrusion of the device so that the graphene bilayer remains unperturbed from the electrolyte during operation. We performed time-dependent Hall measurements across spatially displaced Hall probes to monitor the in-plane Li diffusion kinetics within the graphene bilayer and measured a diffusion coefficient as high as 7 × 10-5 cm2 s-1.

On time-dependent diffusion coefficients arising from stochastic processes with memory

NASA Astrophysics Data System (ADS)

Carpio-Bernido, M. Victoria; Barredo, Wilson I.; Bernido, Christopher C.

2017-08-01

Time-dependent diffusion coefficients arise from anomalous diffusion encountered in many physical systems such as protein transport in cells. We compare these coefficients with those arising from analysis of stochastic processes with memory that go beyond fractional Brownian motion. Facilitated by the Hida white noise functional integral approach, diffusion propagators or probability density functions (pdf) are obtained and shown to be solutions of modified diffusion equations with time-dependent diffusion coefficients. This should be useful in the study of complex transport processes.

Estimating the Diffusion Coefficients of Sugars Using Diffusion Experiments in Agar-Gel and Computer Simulations.

PubMed

Miyamoto, Shuichi; Atsuyama, Kenji; Ekino, Keisuke; Shin, Takashi

2018-01-01

The isolation of useful microbes is one of the traditional approaches for the lead generation in drug discovery. As an effective technique for microbe isolation, we recently developed a multidimensional diffusion-based gradient culture system of microbes. In order to enhance the utility of the system, it is favorable to have diffusion coefficients of nutrients such as sugars in the culture medium beforehand. We have, therefore, built a simple and convenient experimental system that uses agar-gel to observe diffusion. Next, we performed computer simulations-based on random-walk concepts-of the experimental diffusion system and derived correlation formulas that relate observable diffusion data to diffusion coefficients. Finally, we applied these correlation formulas to our experimentally-determined diffusion data to estimate the diffusion coefficients of sugars. Our values for these coefficients agree reasonably well with values published in the literature. The effectiveness of our simple technique, which has elucidated the diffusion coefficients of some molecules which are rarely reported (e.g., galactose, trehalose, and glycerol) is demonstrated by the strong correspondence between the literature values and those obtained in our experiments.

Single-Molecule and Superresolution Imaging in Live Bacteria Cells

PubMed Central

Biteen, Julie S.; Moerner, W.E.

2010-01-01

Single-molecule imaging enables biophysical measurements devoid of ensemble averaging, gives enhanced spatial resolution beyond the diffraction limit, and permits superresolution reconstructions. Here, single-molecule and superresolution imaging are applied to the study of proteins in live Caulobacter crescentus cells to illustrate the power of these methods in bacterial imaging. Based on these techniques, the diffusion coefficient and dynamics of the histidine protein kinase PleC, the localization behavior of the polar protein PopZ, and the treadmilling behavior and protein superstructure of the structural protein MreB are investigated with sub-40-nm spatial resolution, all in live cells. PMID:20300204

Study of diffusion coefficient of anhydrous trehalose glasses by using PFG-NMR spectroscopy

NASA Astrophysics Data System (ADS)

Kwon, Hyun-Joung; Takekawa, Reiji; Kawamura, Junichi; Tokuyama, Michio

2013-02-01

We investigated the temperature dependent long time self-diffusion coefficient of the anhydrous trehalose supercooled liquids by using pulsed field gradient nuclear magnetic resonance (PFG-NMR) spectroscopy. At the same temperature ranges, the diffusion coefficient convoluted from the α-relaxation time as Einstein-Smoluchowski relaxation, measured by using the dielectric loss spectroscopy are well overlapped with diffusion coefficients within experimental error. The temperature dependent diffusion coefficients obtained from different methods are normalized by fictive temperature and well satisfied the single master curve, proposed by Tokuyama.

Convergence of lateral dynamic measurements in the plasma membrane of live cells from single particle tracking and STED-FCS

NASA Astrophysics Data System (ADS)

Lagerholm, B. Christoffer; Andrade, Débora M.; Clausen, Mathias P.; Eggeling, Christian

2017-02-01

Fluorescence correlation spectroscopy (FCS) in combination with the super-resolution imaging method STED (STED-FCS), and single-particle tracking (SPT) are able to directly probe the lateral dynamics of lipids and proteins in the plasma membrane of live cells at spatial scales much below the diffraction limit of conventional microscopy. However, a major disparity in interpretation of data from SPT and STED-FCS remains, namely the proposed existence of a very fast (unhindered) lateral diffusion coefficient, ⩾5 µm2 s-1, in the plasma membrane of live cells at very short length scales, ≈⩽ 100 nm, and time scales, ≈1-10 ms. This fast diffusion coefficient has been advocated in several high-speed SPT studies, for lipids and membrane proteins alike, but the equivalent has not been detected in STED-FCS measurements. Resolving this ambiguity is important because the assessment of membrane dynamics currently relies heavily on SPT for the determination of heterogeneous diffusion. A possible systematic error in this approach would thus have vast implications in this field. To address this, we have re-visited the analysis procedure for SPT data with an emphasis on the measurement errors and the effect that these errors have on the measurement outputs. We subsequently demonstrate that STED-FCS and SPT data, following careful consideration of the experimental errors of the SPT data, converge to a common interpretation which for the case of a diffusing phospholipid analogue in the plasma membrane of live mouse embryo fibroblasts results in an unhindered, intra-compartment, diffusion coefficient of  ≈0.7-1.0 µm2 s-1, and a compartment size of about 100-150 nm.

Convergence of lateral dynamic measurements in the plasma membrane of live cells from single particle tracking and STED-FCS

PubMed Central

Lagerholm, B Christoffer; Andrade, Débora M; Clausen, Mathias P; Eggeling, Christian

2017-01-01

Abstract Fluorescence correlation spectroscopy (FCS) in combination with the super-resolution imaging method STED (STED-FCS), and single-particle tracking (SPT) are able to directly probe the lateral dynamics of lipids and proteins in the plasma membrane of live cells at spatial scales much below the diffraction limit of conventional microscopy. However, a major disparity in interpretation of data from SPT and STED-FCS remains, namely the proposed existence of a very fast (unhindered) lateral diffusion coefficient, ⩾5 µm2 s−1, in the plasma membrane of live cells at very short length scales, ≈⩽ 100 nm, and time scales, ≈1–10 ms. This fast diffusion coefficient has been advocated in several high-speed SPT studies, for lipids and membrane proteins alike, but the equivalent has not been detected in STED-FCS measurements. Resolving this ambiguity is important because the assessment of membrane dynamics currently relies heavily on SPT for the determination of heterogeneous diffusion. A possible systematic error in this approach would thus have vast implications in this field. To address this, we have re-visited the analysis procedure for SPT data with an emphasis on the measurement errors and the effect that these errors have on the measurement outputs. We subsequently demonstrate that STED-FCS and SPT data, following careful consideration of the experimental errors of the SPT data, converge to a common interpretation which for the case of a diffusing phospholipid analogue in the plasma membrane of live mouse embryo fibroblasts results in an unhindered, intra-compartment, diffusion coefficient of  ≈0.7–1.0 µm2 s−1, and a compartment size of about 100–150 nm. PMID:28458397

Model of turnover kinetics in the lamellipodium: implications of slow- and fast- diffusing capping protein and Arp2/3 complex

NASA Astrophysics Data System (ADS)

McMillen, Laura M.; Vavylonis, Dimitrios

2016-12-01

Cell protrusion through polymerization of actin filaments at the leading edge of motile cells may be influenced by spatial gradients of diffuse actin and regulators. Here we study the distribution of two of the most important regulators, capping protein and Arp2/3 complex, which regulate actin polymerization in the lamellipodium through capping and nucleation of free barbed ends. We modeled their kinetics using data from prior single molecule microscopy experiments on XTC cells. These experiments have provided evidence for a broad distribution of diffusion coefficients of both capping protein and Arp2/3 complex. The slowly diffusing proteins appear as extended ‘clouds’ while proteins bound to the actin filament network appear as speckles that undergo retrograde flow. Speckle appearance and disappearance events correspond to assembly and dissociation from the actin filament network and speckle lifetimes correspond to the dissociation rate. The slowly diffusing capping protein could represent severed capped actin filament fragments or membrane-bound capping protein. Prior evidence suggests that slowly diffusing Apr2/3 complex associates with the membrane. We use the measured rates and estimates of diffusion coefficients of capping protein and Arp2/3 complex in a Monte Carlo simulation that includes particles in association with a filament network and diffuse in the cytoplasm. We consider two separate pools of diffuse proteins, representing fast and slowly diffusing species. We find a steady state with concentration gradients involving a balance of diffusive flow of fast and slow species with retrograde flow. We show that simulations of FRAP are consistent with prior experiments performed on different cell types. We provide estimates for the ratio of bound to diffuse complexes and calculate conditions where Arp2/3 complex recycling by diffusion may become limiting. We discuss the implications of slowly diffusing populations and suggest experiments to distinguish among mechanisms that influence long range transport.

Basis adaptation and domain decomposition for steady partial differential equations with random coefficients

DOE PAGES

Tipireddy, R.; Stinis, P.; Tartakovsky, A. M.

2017-09-04

In this paper, we present a novel approach for solving steady-state stochastic partial differential equations (PDEs) with high-dimensional random parameter space. The proposed approach combines spatial domain decomposition with basis adaptation for each subdomain. The basis adaptation is used to address the curse of dimensionality by constructing an accurate low-dimensional representation of the stochastic PDE solution (probability density function and/or its leading statistical moments) in each subdomain. Restricting the basis adaptation to a specific subdomain affords finding a locally accurate solution. Then, the solutions from all of the subdomains are stitched together to provide a global solution. We support ourmore » construction with numerical experiments for a steady-state diffusion equation with a random spatially dependent coefficient. Lastly, our results show that highly accurate global solutions can be obtained with significantly reduced computational costs.« less

Basis adaptation and domain decomposition for steady-state partial differential equations with random coefficients

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

Tipireddy, R.; Stinis, P.; Tartakovsky, A. M.

We present a novel approach for solving steady-state stochastic partial differential equations (PDEs) with high-dimensional random parameter space. The proposed approach combines spatial domain decomposition with basis adaptation for each subdomain. The basis adaptation is used to address the curse of dimensionality by constructing an accurate low-dimensional representation of the stochastic PDE solution (probability density function and/or its leading statistical moments) in each subdomain. Restricting the basis adaptation to a specific subdomain affords finding a locally accurate solution. Then, the solutions from all of the subdomains are stitched together to provide a global solution. We support our construction with numericalmore » experiments for a steady-state diffusion equation with a random spatially dependent coefficient. Our results show that highly accurate global solutions can be obtained with significantly reduced computational costs.« less

Real-time absorption and scattering characterization of slab-shaped turbid samples obtained by a combination of angular and spatially resolved measurements.

PubMed

Dam, Jan S; Yavari, Nazila; Sørensen, Søren; Andersson-Engels, Stefan

2005-07-10

We present a fast and accurate method for real-time determination of the absorption coefficient, the scattering coefficient, and the anisotropy factor of thin turbid samples by using simple continuous-wave noncoherent light sources. The three optical properties are extracted from recordings of angularly resolved transmittance in addition to spatially resolved diffuse reflectance and transmittance. The applied multivariate calibration and prediction techniques are based on multiple polynomial regression in combination with a Newton--Raphson algorithm. The numerical test results based on Monte Carlo simulations showed mean prediction errors of approximately 0.5% for all three optical properties within ranges typical for biological media. Preliminary experimental results are also presented yielding errors of approximately 5%. Thus the presented methods show a substantial potential for simultaneous absorption and scattering characterization of turbid media.

Development of a semiclassical method to compute mobility and diffusion coefficient of a Brownian particle in a nonequilibrium environment.

PubMed

Shit, Anindita; Ghosh, Pradipta; Chattopadhyay, Sudip; Chaudhuri, Jyotipratim Ray

2011-03-01

We explore the issue of a quantum-noise-induced directed transport of an overdamped Brownian particle that is allowed to move in a spatially periodic potential. The established system-reservoir model has been employed here to study the quantum-noise-induced transport of a Brownian particle in a periodic potential, where the reservoir is being modulated externally by a Gaussian-colored noise. The mobility of the Brownian particle in the linear response regime has been calculated. Then, using Einstein's relation, the analytical expression for the diffusion rate is evaluated for any arbitrary periodic potential for the high-temperature quantum regime.

Analytic expressions for ULF wave radiation belt radial diffusion coefficients

PubMed Central

Ozeke, Louis G; Mann, Ian R; Murphy, Kyle R; Jonathan Rae, I; Milling, David K

2014-01-01

We present analytic expressions for ULF wave-derived radiation belt radial diffusion coefficients, as a function of L and Kp, which can easily be incorporated into global radiation belt transport models. The diffusion coefficients are derived from statistical representations of ULF wave power, electric field power mapped from ground magnetometer data, and compressional magnetic field power from in situ measurements. We show that the overall electric and magnetic diffusion coefficients are to a good approximation both independent of energy. We present example 1-D radial diffusion results from simulations driven by CRRES-observed time-dependent energy spectra at the outer boundary, under the action of radial diffusion driven by the new ULF wave radial diffusion coefficients and with empirical chorus wave loss terms (as a function of energy, Kp and L). There is excellent agreement between the differential flux produced by the 1-D, Kp-driven, radial diffusion model and CRRES observations of differential electron flux at 0.976 MeV—even though the model does not include the effects of local internal acceleration sources. Our results highlight not only the importance of correct specification of radial diffusion coefficients for developing accurate models but also show significant promise for belt specification based on relatively simple models driven by solar wind parameters such as solar wind speed or geomagnetic indices such as Kp. Key Points Analytic expressions for the radial diffusion coefficients are presented The coefficients do not dependent on energy or wave m value The electric field diffusion coefficient dominates over the magnetic PMID:26167440

NMR investigation of gaseous SF6 confinement into EPDM rubber.

PubMed

Neutzler, Sven; Terekhov, Maxim; Hoepfel, Dieter; Oellrich, Lothar Rainer

2005-02-01

The confinement process of gaseous sulphurhexafluoride (SF6) in ethylene-propylene-diene (EPDM) rubber was investigated by spectroscopic and spatially resolved NMR techniques. A strong elongation of T1 relaxation time of SF6 and a decrease of the diffusion coefficient were found. A possible explanation may be the strong restriction of molecular mobility due to interactions between SF6 and active centers of the EPDM.

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.

Extent of BOLD Vascular Dysregulation Is Greater in Diffuse Gliomas without Isocitrate Dehydrogenase 1 R132H Mutation.

PubMed

Englander, Zachary K; Horenstein, Craig I; Bowden, Stephen G; Chow, Daniel S; Otten, Marc L; Lignelli, Angela; Bruce, Jeffrey N; Canoll, Peter; Grinband, Jack

2018-06-01

Purpose To determine the effect that R132H mutation status of diffuse glioma has on extent of vascular dysregulation and extent of residual blood oxygen level-dependent (BOLD) abnormality after surgical resection. Materials and Methods This study was an institutional review board-approved retrospective analysis of an institutional database of patients, and informed consent was waived. From 2010 to 2017, 39 treatment-naïve patients with diffuse glioma underwent preoperative echo-planar imaging and BOLD functional magnetic resonance imaging. BOLD vascular dysregulation maps were made by identifying voxels with time series similar to tumor and dissimilar to healthy brain. The spatial overlap between tumor and vascular dysregulation was characterized by using the Dice coefficient, and areas of BOLD abnormality outside the tumor margins were quantified as BOLD-only fraction (BOF). Linear regression was used to assess effects of R132H status on the Dice coefficient, BOF, and residual BOLD abnormality after surgical resection. Results When compared with R132H wild-type (R132H-) gliomas, R132H-mutated (R132H+) gliomas showed greater spatial overlap between BOLD abnormality and tumor (mean Dice coefficient, 0.659 ± 0.02 [standard error] for R132H+ and 0.327 ± 0.04 for R132H-; P < .001), less BOLD abnormality beyond the tumor margin (mean BOF, 0.255 ± 0.03 for R132H+ and 0.728 ± 0.04 for R132H-; P < .001), and less postoperative BOLD abnormality (residual fraction, 0.046 ± 0.0047 for R132H+ and 0.397 ± 0.045 for R132H-; P < .001). Receiver operating characteristic curve analysis showed high sensitivity and specificity in the discrimination of R132H+ tumors from R132H- tumors with calculation of both Dice coefficient and BOF (area under the receiver operating characteristic curve, 0.967 and 0.977, respectively). Conclusion R132H mutation status is an important variable affecting the extent of tumor-associated vascular dysregulation and the residual vascular dysregulation after surgical resection. © RSNA, 2018 Online supplemental material is available for this article.

A method of online quantitative interpretation of diffuse reflection profiles of biological tissues

NASA Astrophysics Data System (ADS)

Lisenko, S. A.; Kugeiko, M. M.

2013-02-01

We have developed a method of combined interpretation of spectral and spatial characteristics of diffuse reflection of biological tissues, which makes it possible to determine biophysical parameters of the tissue with a high accuracy in real time under conditions of their general variability. Using the Monte Carlo method, we have modeled a statistical ensemble of profiles of diffuse reflection coefficients of skin, which corresponds to a wave variation of its biophysical parameters. On its basis, we have estimated the retrieval accuracy of biophysical parameters using the developed method and investigated the stability of the method to errors of optical measurements. We have showed that it is possible to determine online the concentrations of melanin, hemoglobin, bilirubin, oxygen saturation of blood, and structural parameters of skin from measurements of its diffuse reflection in the spectral range 450-800 nm at three distances between the radiation source and detector.

The time and spatial behavior of solar flare proton anisotropies observed in deep space on Pioneers 10 and 11

NASA Technical Reports Server (NTRS)

Mccarthy, J.; Ogallagher, J. J.

1975-01-01

The anisotropy of solar flare protons from the direction of the 'garden hose' magnetic field line has been analyzed for 24 events observed by the University of Chicago experiment on Pioneers 10 and 11 in 1972 and 1973. The anisotropy versus time profiles during individual events are in general consistent with diffusive propagation, but several cases are observed where the decay is better described by an exponential time decay. The anisotropy amplitude evaluated at the time of maximum intensity for each event shows evidence for a gradual decrease with increasing distance from the sun which is qualitatively consistent with diffusive propagation and suggests that the effective interplanetary diffusion coefficient parallel to the magnetic field increases slowly with heliocentric distance.

Influences of Exciton Diffusion and Exciton-Exciton Annihilation on Photon Emission Statistics of Carbon Nanotubes.

PubMed

Ma, Xuedan; Roslyak, Oleskiy; Duque, Juan G; Pang, Xiaoying; Doorn, Stephen K; Piryatinski, Andrei; Dunlap, David H; Htoon, Han

2015-07-03

Pump-dependent photoluminescence imaging and second-order photon correlation studies have been performed on individual single-walled carbon nanotubes (SWCNTs) at room temperature. These studies enable the extraction of both the exciton diffusion constant and the Auger recombination coefficient. A linear correlation between these parameters is attributed to the effect of environmental disorder in setting the exciton mean free path and capture-limited Auger recombination at this length scale. A suppression of photon antibunching is attributed to the creation of multiple spatially nonoverlapping excitons in SWCNTs, whose diffusion length is shorter than the laser spot size. We conclude that complete antibunching at room temperature requires an enhancement of the exciton-exciton annihilation rate that may become realizable in SWCNTs allowing for strong exciton localization.

Diffusion coefficient of the protein in various crystallization solutions: The key to growing high-quality crystals in space

NASA Astrophysics Data System (ADS)

Tanaka, Hiroaki; Takahashi, Sachiko; Yamanaka, Mari; Yoshizaki, Izumi; Sato, Masaru; Sano, Satoshi; Motohara, Moritoshi; Kobayashi, Tomoyuki; Yoshitomi, Susumu; Tanaka, Tetsuo; Fukuyama, Seijiro

2006-09-01

The diffusion coefficients of lysozyme and alpha-amylase were measured in the various polyethylene glycol (PEG) solutions. Obtained diffusion coefficients were studied with the viscosity coefficient of the solution. It was found that the diffusion process of the protein was suppressed with a factor of vγ, where ν is a relative viscosity coefficient of the PEG solution. The value of γ is -0.64 at PEG1500 for both proteins. The value increased to -0.48 at PEG8000 for lysozyme, while decreased to -0.72 for alpha-amylase. The equation of an approximate diffusion coefficient at certain PEG molecular weight and concentration was roughly obtained.

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.

Temperature effects on diffusion coefficient for 6-gingerol and 6-shogaol in subcritical water extraction

NASA Astrophysics Data System (ADS)

Ilia Anisa, Nor; Azian, Noor; Sharizan, Mohd; Iwai, Yoshio

2014-04-01

6-gingerol and 6-shogaol are the main constituents as anti-inflammatory or bioactive compounds from zingiber officinale Roscoe. These bioactive compounds have been proven for inflammatory disease, antioxidatives and anticancer. The effect of temperature on diffusion coefficient for 6-gingerol and 6-shogaol were studied in subcritical water extraction. The diffusion coefficient was determined by Fick's second law. By neglecting external mass transfer and solid particle in spherical form, a linear portion of Ln (1-(Ct/Co)) versus time was plotted in determining the diffusion coefficient. 6-gingerol obtained the higher yield at 130°C with diffusion coefficient of 8.582x10-11 m2/s whilst for 6-shogaol, the higher yield and diffusion coefficient at 170°C and 19.417 × 10-11 m2/s.

Heat and mass transport during microwave heating of mashed potato in domestic oven--model development, validation, and sensitivity analysis.

PubMed

Chen, Jiajia; Pitchai, Krishnamoorthy; Birla, Sohan; Negahban, Mehrdad; Jones, David; Subbiah, Jeyamkondan

2014-10-01

A 3-dimensional finite-element model coupling electromagnetics and heat and mass transfer was developed to understand the interactions between the microwaves and fresh mashed potato in a 500 mL tray. The model was validated by performing heating of mashed potato from 25 °C on a rotating turntable in a microwave oven, rated at 1200 W, for 3 min. The simulated spatial temperature profiles on the top and bottom layer of the mashed potato showed similar hot and cold spots when compared to the thermal images acquired by an infrared camera. Transient temperature profiles at 6 locations collected by fiber-optic sensors showed good agreement with predicted results, with the root mean square error ranging from 1.6 to 11.7 °C. The predicted total moisture loss matched well with the observed result. Several input parameters, such as the evaporation rate constant, the intrinsic permeability of water and gas, and the diffusion coefficient of water and gas, are not readily available for mashed potato, and they cannot be easily measured experimentally. Reported values for raw potato were used as baseline values. A sensitivity analysis of these input parameters on the temperature profiles and the total moisture loss was evaluated by changing the baseline values to their 10% and 1000%. The sensitivity analysis showed that the gas diffusion coefficient, intrinsic water permeability, and the evaporation rate constant greatly influenced the predicted temperature and total moisture loss, while the intrinsic gas permeability and the water diffusion coefficient had little influence. This model can be used by the food product developers to understand microwave heating of food products spatially and temporally. This tool will allow food product developers to design food package systems that would heat more uniformly in various microwave ovens. The sensitivity analysis of this study will help us determine the most significant parameters that need to be measured accurately for reliable model prediction. © 2014 Institute of Food Technologists®

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

Tracer counterpermeation analysis of diffusivity in finite-length nanopores with and without single-file dynamics

DOE PAGES

Ackerman, David M.; Evans, James W.

2017-01-19

Here, we perform a tracer counterpermeation (TCP) analysis for a stochastic model of diffusive transport through a narrow linear pore where passing of species within the pore is inhibited or even excluded (single-file diffusion). TCP involves differently labeled but otherwise identical particles from two decoupled infinite reservoirs adsorbing into opposite ends of the pore, and desorbing from either end. In addition to transient behavior, we assess steady-state concentration profiles, spatial correlations, particle number fluctuations, and diffusion fluxes through the pore. From the profiles and fluxes, we determine a generalized tracer diffusion coefficient D tr(x), at various positions x within themore » pore. D tr(x) has a plateau value in the pore center scaling inversely with the pore length, but it is enhanced near the pore openings. The latter feature reflects the effect of fluctuations in adsorption and desorption, and it is also associated with a nontrivial scaling of the concentration profiles near the pore openings.« less

Tracer counterpermeation analysis of diffusivity in finite-length nanopores with and without single-file dynamics

NASA Astrophysics Data System (ADS)

Ackerman, David M.; Evans, James W.

2017-01-01

We perform a tracer counterpermeation (TCP) analysis for a stochastic model of diffusive transport through a narrow linear pore where passing of species within the pore is inhibited or even excluded (single-file diffusion). TCP involves differently labeled but otherwise identical particles from two decoupled infinite reservoirs adsorbing into opposite ends of the pore, and desorbing from either end. In addition to transient behavior, we assess steady-state concentration profiles, spatial correlations, particle number fluctuations, and diffusion fluxes through the pore. From the profiles and fluxes, we determine a generalized tracer diffusion coefficient Dtr(x ) , at various positions x within the pore. Dtr(x ) has a plateau value in the pore center scaling inversely with the pore length, but it is enhanced near the pore openings. The latter feature reflects the effect of fluctuations in adsorption and desorption, and it is also associated with a nontrivial scaling of the concentration profiles near the pore openings.

Comments on the Diffusive Behavior of Two Upwind Schemes

NASA Technical Reports Server (NTRS)

Wood, William A.; Kleb, William L.

1998-01-01

The diffusive characteristics of two upwind schemes, multi-dimensional fluctuation splitting and locally one-dimensional finite volume, are compared for scalar advection-diffusion problems. Algorithms for the two schemes are developed for node-based data representation on median-dual meshes associated with unstructured triangulations in two spatial dimensions. Four model equations are considered: linear advection, non-linear advection, diffusion, and advection-diffusion. Modular coding is employed to isolate the effects of the two approaches for upwind flux evaluation, allowing for head-to-head accuracy and efficiency comparisons. Both the stability of compressive limiters and the amount of artificial diffusion generated by the schemes is found to be grid-orientation dependent, with the fluctuation splitting scheme producing less artificial diffusion than the finite volume scheme. Convergence rates are compared for the combined advection-diffusion problem, with a speedup of 2.5 seen for fluctuation splitting versus finite volume when solved on the same mesh. However, accurate solutions to problems with small diffusion coefficients can be achieved on coarser meshes using fluctuation splitting rather than finite volume, so that when comparing convergence rates to reach a given accuracy, fluctuation splitting shows a speedup of 29 over finite volume.

Diffusion Characteristics of Upwind Schemes on Unstructured Triangulations

NASA Technical Reports Server (NTRS)

Wood, William A.; Kleb, William L.

1998-01-01

The diffusive characteristics of two upwind schemes, multi-dimensional fluctuation splitting and dimensionally-split finite volume, are compared for scalar advection-diffusion problems. Algorithms for the two schemes are developed for node-based data representation on median-dual meshes associated with unstructured triangulations in two spatial dimensions. Four model equations are considered: linear advection, non-linear advection, diffusion, and advection-diffusion. Modular coding is employed to isolate the effects of the two approaches for upwind flux evaluation, allowing for head-to-head accuracy and efficiency comparisons. Both the stability of compressive limiters and the amount of artificial diffusion generated by the schemes is found to be grid-orientation dependent, with the fluctuation splitting scheme producing less artificial diffusion than the dimensionally-split finite volume scheme. Convergence rates are compared for the combined advection-diffusion problem, with a speedup of 2-3 seen for fluctuation splitting versus finite volume when solved on the same mesh. However, accurate solutions to problems with small diffusion coefficients can be achieved on coarser meshes using fluctuation splitting rather than finite volume, so that when comparing convergence rates to reach a given accuracy, fluctuation splitting shows a 20-25 speedup over finite volume.

Derivation of diffusion coefficient of a Brownian particle in tilted periodic potential from the coordinate moments

NASA Astrophysics Data System (ADS)

Zhang, Yunxin

2009-07-01

In this research, diffusion of an overdamped Brownian particle in the tilted periodic potential is investigated. Using the one-dimensional hopping model, the formulations of the mean velocity V and effective diffusion coefficient D of the Brownian particle have been obtained [B. Derrida, J. Stat. Phys. 31 (1983) 433]. Based on the relation between the effective diffusion coefficient and the moments of the mean first passage time, the formulation of effective diffusion coefficient D of the Brownian particle also has been obtained [P. Reimann, et al., Phys. Rev. E 65 (2002) 031104]. In this research, we'll give another analytical expression of the effective diffusion coefficient D from the moments of the particle's coordinate.

Diffusion-Weighted PROPELLER MRI for Quantitative Assessment of Liver Tumor Necrotic Fraction and Viable Tumor Volume in VX2 Rabbits

PubMed Central

Deng, Jie; Virmani, Sumeet; Young, Joseph; Harris, Kathleen; Yang, Guang-Yu; Rademaker, Alfred; Woloschak, Gayle; Omary, Reed A.; Larson, Andrew C.

2010-01-01

Purpose To test the hypothesis that diffusion-weighted (DW)-PROPELLER (periodically rotated overlapping parallel lines with enhanced reconstruction) MRI provides more accurate liver tumor necrotic fraction (NF) and viable tumor volume (VTV) measurements than conventional DW-SE-EPI (spin echo echo-planar imaging) methods. Materials and Methods Our institutional Animal Care and Use Committee approved all experiments. In six rabbits implanted with 10 VX2 liver tumors, DW-PROPELLER and DW-SE-EPI scans were performed at contiguous axial slice positions covering each tumor volume. Apparent diffusion coefficient maps of each tumor were used to generate spatially resolved tumor viability maps for NF and VTV measurements. We compared NF, whole tumor volume (WTV), and VTV measurements to corresponding reference standard histological measurements based on correlation and concordance coefficients and the Bland–Altman analysis. Results DW-PROPELLER generally improved image quality with less distortion compared to DW-SE-EPI. DW-PROPELLER NF, WTV, and VTV measurements were strongly correlated and satisfactorily concordant with histological measurements. DW-SE-EPI NF measurements were weakly correlated and poorly concordant with histological measurements. Bland–Altman analysis demonstrated that DWPROPELLER WTV and VTV measurements were less biased from histological measurements than the corresponding DW-SE-EPI measurements. Conclusion DW-PROPELLER MRI can provide spatially resolved liver tumor viability maps for accurate NF and VTV measurements, superior to DW-SE-EPI approaches. DWPROPELLER measurements may serve as a noninvasive surrogate for pathology, offering the potential for more accurate assessments of therapy response than conventional anatomic size measurements. PMID:18407540

Effective gaseous diffusion coefficients of select ultra-fine, super-fine and medium grain nuclear graphite

DOE PAGES

Kane, Joshua J.; Matthews, Austin C.; Orme, Christopher J.; ...

2018-05-05

Understanding “Where?” and “How much?” oxidation has occurred in a nuclear graphite component is critical to predicting any deleterious effects to physical, mechanical, and thermal properties. A key factor in answering these questions is characterizing the effective mass transport rates of gas species in nuclear graphites. Effective gas diffusion coefficients were determined for twenty-six graphite specimens spanning six modern grades of nuclear graphite. A correlation was established for the majority of grades examined allowing a reasonable estimate of the effective diffusion coefficient to be determined purely from an estimate of total porosity. The importance of Knudsen diffusion to the measuredmore » diffusion coefficients is also shown for modern grades. Furthermore, Knudsen diffusion has not historically been considered to contribute to measured diffusion coefficients of nuclear graphite.« less

Effective gaseous diffusion coefficients of select ultra-fine, super-fine and medium grain nuclear graphite

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

Kane, Joshua J.; Matthews, Austin C.; Orme, Christopher J.

Understanding “Where?” and “How much?” oxidation has occurred in a nuclear graphite component is critical to predicting any deleterious effects to physical, mechanical, and thermal properties. A key factor in answering these questions is characterizing the effective mass transport rates of gas species in nuclear graphites. Effective gas diffusion coefficients were determined for twenty-six graphite specimens spanning six modern grades of nuclear graphite. A correlation was established for the majority of grades examined allowing a reasonable estimate of the effective diffusion coefficient to be determined purely from an estimate of total porosity. The importance of Knudsen diffusion to the measuredmore » diffusion coefficients is also shown for modern grades. Furthermore, Knudsen diffusion has not historically been considered to contribute to measured diffusion coefficients of nuclear graphite.« less

Direct measurement of lateral transport in membranes by using time-resolved spatial photometry.

PubMed Central

Kapitza, H G; McGregor, G; Jacobson, K A

1985-01-01

Spatially resolving light detectors allow, with proper calibration, quantitative analysis of the variations in two-dimensional intensity distributions over time. An ultrasensitive microfluorometer was assembled by using as a detector a microchannel plate-intensified video camera. The camera was interfaced with a software-based digital video analysis system to digitize, average, and process images and to directly control the timing of the experiments to minimize exposure of the specimen to light. The detector system has been characterized to allow its use as a photometer. A major application has been to perform fluorescence recovery after photobleaching measurements by using the camera in place of a photomultiplier tube (video-FRAP) with the goal of detecting possible anisotropic diffusion or convective flow. Analysis of the data on macromolecular diffusion in homogenous aqueous glycol solutions yielded diffusion constants in agreement with previous measurements. Results on lipid probe diffusion in dimyristoylphosphatidylcholine multibilayers indicated that at temperatures above the gel-to-liquid crystalline phase transition diffusion is isotropic, and analysis of video-FRAP data yielded diffusion coefficients consistent with those measured previously by using spot photobleaching. However, lipid probes in these multibilayers held just below the main phase transition temperature exhibited markedly anisotropic diffusive fluxes when the bleaching beam was positioned proximate to domain boundaries in the P beta' phase. Lipid probes and lectin receptor complexes diffused isotropically in fibroblast surface membranes with little evidence for diffusion channeled parallel to stress fibers. A second application was to trace the time evolution of cell surface reactions such as patching. The feasibility of following, on the optical scale, the growth of individual receptor clusters induced by the ligand wheat germ agglutinin was demonstrated. PMID:3858869

Direct measurement of lateral transport in membranes by using time-resolved spatial photometry.

PubMed

Kapitza, H G; McGregor, G; Jacobson, K A

1985-06-01

Spatially resolving light detectors allow, with proper calibration, quantitative analysis of the variations in two-dimensional intensity distributions over time. An ultrasensitive microfluorometer was assembled by using as a detector a microchannel plate-intensified video camera. The camera was interfaced with a software-based digital video analysis system to digitize, average, and process images and to directly control the timing of the experiments to minimize exposure of the specimen to light. The detector system has been characterized to allow its use as a photometer. A major application has been to perform fluorescence recovery after photobleaching measurements by using the camera in place of a photomultiplier tube (video-FRAP) with the goal of detecting possible anisotropic diffusion or convective flow. Analysis of the data on macromolecular diffusion in homogenous aqueous glycol solutions yielded diffusion constants in agreement with previous measurements. Results on lipid probe diffusion in dimyristoylphosphatidylcholine multibilayers indicated that at temperatures above the gel-to-liquid crystalline phase transition diffusion is isotropic, and analysis of video-FRAP data yielded diffusion coefficients consistent with those measured previously by using spot photobleaching. However, lipid probes in these multibilayers held just below the main phase transition temperature exhibited markedly anisotropic diffusive fluxes when the bleaching beam was positioned proximate to domain boundaries in the P beta' phase. Lipid probes and lectin receptor complexes diffused isotropically in fibroblast surface membranes with little evidence for diffusion channeled parallel to stress fibers. A second application was to trace the time evolution of cell surface reactions such as patching. The feasibility of following, on the optical scale, the growth of individual receptor clusters induced by the ligand wheat germ agglutinin was demonstrated.

A review of anisotropic conductivity models of brain white matter based on diffusion tensor imaging.

PubMed

Wu, Zhanxiong; Liu, Yang; Hong, Ming; Yu, Xiaohui

2018-06-01

The conductivity of brain tissues is not only essential for electromagnetic source estimation (ESI), but also a key reflector of the brain functional changes. Different from the other brain tissues, the conductivity of whiter matter (WM) is highly anisotropic and a tensor is needed to describe it. The traditional electrical property imaging methods, such as electrical impedance tomography (EIT) and magnetic resonance electrical impedance tomography (MREIT), usually fail to image the anisotropic conductivity tensor of WM with high spatial resolution. The diffusion tensor imaging (DTI) is a newly developed technique that can fulfill this purpose. This paper reviews the existing anisotropic conductivity models of WM based on the DTI and discusses their advantages and disadvantages, as well as identifies opportunities for future research on this subject. It is crucial to obtain the linear conversion coefficient between the eigenvalues of anisotropic conductivity tensor and diffusion tensor, since they share the same eigenvectors. We conclude that the electrochemical model is suitable for ESI analysis because the conversion coefficient can be directly obtained from the concentration of ions in extracellular liquid and that the volume fraction model is appropriate to study the influence of WM structural changes on electrical conductivity. Graphical abstract ᅟ.

Determination of diffusion coefficients of biocides on their passage through organic resin-based renders.

PubMed

Styszko, Katarzyna; Kupiec, Krzysztof

2016-10-01

In this study the diffusion coefficients of isoproturon, diuron and cybutryn in acrylate and silicone resin-based renders were determined. The diffusion coefficients were determined using measuring concentrations of biocides in the liquid phase after being in contact with renders for specific time intervals. The mathematical solution of the transient diffusion equation for an infinite plate contacted on one side with a limited volume of water was used to calculate the diffusion coefficient. The diffusion coefficients through the acrylate render were 8.10·10(-9) m(2) s(-1) for isoproturon, 1.96·10(-9) m(2) s(-1) for diuron and 1.53·10(-9) m(2) s(-1) for cybutryn. The results for the silicone render were lower by one order of magnitude. The compounds with a high diffusion coefficient for one polymer had likewise high values for the other polymer. Copyright © 2016 Elsevier Ltd. All rights reserved.

Simultaneous Rapid Determination of the Solubility and Diffusion Coefficients of a Poorly Water-Soluble Drug Based on a Novel UV Imaging System.

PubMed

Lu, Yan; Li, Mingzhong

2016-01-01

The solubility and diffusion coefficient are two of the most important physicochemical properties of a drug compound. In practice, both have been measured separately, which is time consuming. This work utilizes a novel technique of UV imaging to determine the solubility and diffusion coefficients of poorly water-soluble drugs simultaneously. A 2-step optimal method is proposed to determine the solubility and diffusion coefficients of a poorly water-soluble pharmaceutical substance based on the Fick's second law of diffusion and UV imaging measurements. Experimental results demonstrate that the proposed method can be used to determine the solubility and diffusion coefficients of a drug with reasonable accuracy, indicating that UV imaging may provide a new opportunity to accurately measure the solubility and diffusion coefficients of a poorly water-soluble drug simultaneously and rapidly. Copyright © 2016 American Pharmacists Association®. Published by Elsevier Inc. All rights reserved.

Diffusion coefficients of organic molecules in sucrose-water solutions and comparison with Stokes-Einstein predictions

NASA Astrophysics Data System (ADS)

Chenyakin, Yuri; Ullmann, Dagny A.; Evoy, Erin; Renbaum-Wolff, Lindsay; Kamal, Saeid; Bertram, Allan K.

2017-02-01

The diffusion coefficients of organic species in secondary organic aerosol (SOA) particles are needed to predict the growth and reactivity of these particles in the atmosphere. Previously, viscosity measurements, along with the Stokes-Einstein relation, have been used to estimate the diffusion rates of organics within SOA particles or proxies of SOA particles. To test the Stokes-Einstein relation, we have measured the diffusion coefficients of three fluorescent organic dyes (fluorescein, rhodamine 6G and calcein) within sucrose-water solutions with varying water activity. Sucrose-water solutions were used as a proxy for SOA material found in the atmosphere. Diffusion coefficients were measured using fluorescence recovery after photobleaching. For the three dyes studied, the diffusion coefficients vary by 4-5 orders of magnitude as the water activity varied from 0.38 to 0.80, illustrating the sensitivity of the diffusion coefficients to the water content in the matrix. At the lowest water activity studied (0.38), the average diffusion coefficients were 1.9 × 10-13, 1.5 × 10-14 and 7.7 × 10-14 cm2 s-1 for fluorescein, rhodamine 6G and calcein, respectively. The measured diffusion coefficients were compared with predictions made using literature viscosities and the Stokes-Einstein relation. We found that at water activity ≥ 0.6 (which corresponds to a viscosity of ≤ 360 Pa s and Tg/T ≤ 0.81), predicted diffusion rates agreed with measured diffusion rates within the experimental uncertainty (Tg represents the glass transition temperature and T is the temperature of the measurements). When the water activity was 0.38 (which corresponds to a viscosity of 3.3 × 106 Pa s and a Tg/T of 0.94), the Stokes-Einstein relation underpredicted the diffusion coefficients of fluorescein, rhodamine 6G and calcein by a factor of 118 (minimum of 10 and maximum of 977), a factor of 17 (minimum of 3 and maximum of 104) and a factor of 70 (minimum of 8 and maximum of 494), respectively. This disagreement is significantly smaller than the disagreement observed when comparing measured and predicted diffusion coefficients of water in sucrose-water mixtures.

Improving diffuse optical tomography with structural a priori from fluorescence diffuse optical tomography

NASA Astrophysics Data System (ADS)

Ma, Wenjuan; Gao, Feng; Duan, Linjing; Zhu, Qingzhen; Wang, Xin; Zhang, Wei; Wu, Linhui; Yi, Xi; Zhao, Huijuan

2012-03-01

We obtain absorption and scattering reconstructed images by incorporating a priori information of target location obtained from fluorescence diffuse optical tomography (FDOT) into the diffuse optical tomography (DOT). The main disadvantage of DOT lies in the low spatial resolution resulting from highly scattering nature of tissue in the near-infrared (NIR), but one can use it to monitor hemoglobin concentration and oxygen saturation simultaneously, as well as several other cheomphores such as water, lipids, and cytochrome-c-oxidase. Up to date, extensive effort has been made to integrate DOT with other imaging modalities such as MRI, CT, to obtain accurate optical property maps of the tissue. However, the experimental apparatus is intricate. In this study, DOT image reconstruction algorithm that incorporates a prior structural information provided by FDOT is investigated in an attempt to optimize recovery of a simulated optical property distribution. By use of a specifically designed multi-channel time-correlated single photon counting system, the proposed scheme in a transmission mode is experimentally validated to achieve simultaneous reconstruction of the fluorescent yield, lifetime, absorption and scattering coefficient. The experimental results demonstrate that the quantitative recovery of the tumor optical properties has doubled and the spatial resolution improves as well by applying the new improved method.

Analysis of spatial diffusion of ferric ions in PVA-GTA gel dosimeters through magnetic resonance imaging

NASA Astrophysics Data System (ADS)

Marrale, Maurizio; Collura, Giorgio; Gallo, Salvatore; Nici, Stefania; Tranchina, Luigi; Abbate, Boris Federico; Marineo, Sandra; Caracappa, Santo; d'Errico, Francesco

2017-04-01

This work focused on the analysis of the temporal diffusion of ferric ions through PVA-GTA gel dosimeters. PVA-GTA gel samples, partly exposed with 6 MV X-rays in order to create an initial steep gradient, were mapped using magnetic resonance imaging on a 7T MRI scanner for small animals. Multiple images of the gels were acquired over several hours after irradiation and were analyzed to quantitatively extract the signal profile. The spatial resolution achieved is 200 μm and this makes this technique particularly suitable for the analysis of steep gradients of ferric ion concentration. The results obtained with PVA-GTA gels were compared with those achieved with agarose gels, which is a standard dosimetric gel formulation. The analysis showed that the diffusion process is much slower (more than five times) for PVA-GTA gels than for agarose ones. Furthermore, it is noteworthy that the diffusion coefficient value obtained through MRI analysis is significantly consistent with that obtained in separate study Marini et al. (Submitted for publication) using a totally independent method such as spectrophotometry. This is a valuable result highlighting that the good dosimetric features of this gel matrix not only can be reproduced but also can be measured through independent experimental techniques based on different physical principles.

Mutual influence of molecular diffusion in gas and surface phases

NASA Astrophysics Data System (ADS)

Hori, Takuma; Kamino, Takafumi; Yoshimoto, Yuta; Takagi, Shu; Kinefuchi, Ikuya

2018-01-01

We develop molecular transport simulation methods that simultaneously deal with gas- and surface-phase diffusions to determine the effect of surface diffusion on the overall diffusion coefficients. The phenomenon of surface diffusion is incorporated into the test particle method and the mean square displacement method, which are typically employed only for gas-phase transport. It is found that for a simple cylindrical pore, the diffusion coefficients in the presence of surface diffusion calculated by these two methods show good agreement. We also confirm that both methods reproduce the analytical solution. Then, the diffusion coefficients for ink-bottle-shaped pores are calculated using the developed method. Our results show that surface diffusion assists molecular transport in the gas phase. Moreover, the surface tortuosity factor, which is known to be uniquely determined by physical structure, is influenced by the presence of gas-phase diffusion. This mutual influence of gas-phase diffusion and surface diffusion indicates that their simultaneous calculation is necessary for an accurate evaluation of the diffusion coefficients.

Molecular modeling of diffusion coefficient and ionic conductivity of CO2 in aqueous ionic solutions.

PubMed

Garcia-Ratés, Miquel; de Hemptinne, Jean-Charles; Bonet Avalos, Josep; Nieto-Draghi, Carlos

2012-03-08

Mass diffusion coefficients of CO(2)/brine mixtures under thermodynamic conditions of deep saline aquifers have been investigated by molecular simulation. The objective of this work is to provide estimates of the diffusion coefficient of CO(2) in salty water to compensate the lack of experimental data on this property. We analyzed the influence of temperature, CO(2) concentration,and salinity on the diffusion coefficient, the rotational diffusion, as well as the electrical conductivity. We observe an increase of the mass diffusion coefficient with the temperature, but no clear dependence is identified with the salinity or with the CO(2) mole fraction, if the system is overall dilute. In this case, we notice an important dispersion on the values of the diffusion coefficient which impairs any conclusive statement about the effect of the gas concentration on the mobility of CO(2) molecules. Rotational relaxation times for water and CO(2) increase by decreasing temperature or increasing the salt concentration. We propose a correlation for the self-diffusion coefficient of CO(2) in terms of the rotational relaxation time which can ultimately be used to estimate the mutual diffusion coefficient of CO(2) in brine. The electrical conductivity of the CO(2)-brine mixtures was also calculated under different thermodynamic conditions. Electrical conductivity tends to increase with the temperature and salt concentration. However, we do not observe any influence of this property with the CO(2) concentration at the studied regimes. Our results give a first evaluation of the variation of the CO(2)-brine mass diffusion coefficient, rotational relaxation times, and electrical conductivity under the thermodynamic conditions typically encountered in deep saline aquifers.

Spin Diffusion Coefficient of A1-PHASE of Superfluid 3He at Low Temperatures

NASA Astrophysics Data System (ADS)

Afzali, R.; Pashaee, F.

The spin diffusion coefficient tensor of the A1-phase of superfluid 3He at low temperatures and melting pressure is calculated using the Boltzmann equation approach and Pfitzner procedure. Then considering Bogoliubov-normal interaction, we show that the total spin diffusion is proportional to 1/T2, the spin diffusion coefficient of superfluid component D\\uparrowxzxz is proportional to T-2, and the spin diffusion coefficient of super-fluid component D\\uparrowxxxx (=D\\uarrowxyxy) is independent of temperature. Furthermore, it is seen that superfluid components play an important role in spin diffusion of the A1-phase.

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.

Diffusion and mobility of atomic particles in a liquid

NASA Astrophysics Data System (ADS)

Smirnov, B. M.; Son, E. E.; Tereshonok, D. V.

2017-11-01

The diffusion coefficient of a test atom or molecule in a liquid is determined for the mechanism where the displacement of the test molecule results from the vibrations and motion of liquid molecules surrounding the test molecule and of the test particle itself. This leads to a random change in the coordinate of the test molecule, which eventually results in the diffusion motion of the test particle in space. Two models parameters of interaction of a particle and a liquid are used to find the activation energy of the diffusion process under consideration: the gas-kinetic cross section for scattering of test molecules in the parent gas and the Wigner-Seitz radius for test molecules. In the context of this approach, we have calculated the diffusion coefficient of atoms and molecules in water, where based on experimental data, we have constructed the dependence of the activation energy for the diffusion of test molecules in water on the interaction parameter and the temperature dependence for diffusion coefficient of atoms or molecules in water within the models considered. The statistically averaged difference of the activation energies for the diffusion coefficients of different test molecules in water that we have calculated based on each of the presented models does not exceed 10% of the diffusion coefficient itself. We have considered the diffusion of clusters in water and present the dependence of the diffusion coefficient on the cluster size. The accuracy of the presented formulas for the diffusion coefficient of atomic particles in water is estimated to be 50%.

Unsaturated soil moisture drying and wetting diffusion coefficient measurements in the laboratory.

DOT National Transportation Integrated Search

2009-09-01

ABSTRACTTransient moisture flow in an unsaturated soil in response to suction changes is controlled by the unsaturated moisture diffusion coefficient. The moisture diffusion coefficient can be determined by measuring suction profiles over time. The l...

A novel approach to interpretation of the time-dependent self-diffusion coefficient as a probe of porous media geometry.

PubMed

Loskutov, V V; Sevriugin, V A

2013-05-01

This article presents a new approximation describing fluid diffusion in porous media. Time dependence of the self-diffusion coefficient D(t) in the permeable porous medium is studied based on the assumption that diffusant molecules move randomly. An analytical expression for time dependence of the self-diffusion coefficient was obtained in the following form: D(t)=(D0-D∞)exp(-D0t/λ)+D∞, where D0 is the self-diffusion coefficient of bulk fluid, D∞ is the asymptotic value of the self-diffusion coefficient in the limit of long time values (t→∞), λ is the characteristic parameter of this porous medium with dimensionality of length. Applicability of the solution obtained to the analysis of experimental data is shown. The possibility of passing to short-time and long-time regimes is discussed. Copyright © 2013 Elsevier Inc. All rights reserved.

Single-image diffusion coefficient measurements of proteins in free solution.

PubMed

Zareh, Shannon Kian; DeSantis, Michael C; Kessler, Jonathan M; Li, Je-Luen; Wang, Y M

2012-04-04

Diffusion coefficient measurements are important for many biological and material investigations, such as studies of particle dynamics and kinetics, and size determinations. Among current measurement methods, single particle tracking (SPT) offers the unique ability to simultaneously obtain location and diffusion information about a molecule while using only femtomoles of sample. However, the temporal resolution of SPT is limited to seconds for single-color-labeled samples. By directly imaging three-dimensional diffusing fluorescent proteins and studying the widths of their intensity profiles, we were able to determine the proteins' diffusion coefficients using single protein images of submillisecond exposure times. This simple method improves the temporal resolution of diffusion coefficient measurements to submilliseconds, and can be readily applied to a range of particle sizes in SPT investigations and applications in which diffusion coefficient measurements are needed, such as reaction kinetics and particle size determinations. Copyright © 2012 Biophysical Society. Published by Elsevier Inc. All rights reserved.

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

PubMed Central

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

2010-01-01

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

Diffusion coefficients in systems with inclusion compounds. 1. alpha. -Cyclodextrin-L-phenylalanine-water at 25 degree C

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

Paduano, L.; Sartorio, R.; Vitagliano, V.

Diffusion coefficients in the ternary system {alpha}-cyclodextrin (at one concentration)-L-phenylalanine (at four concentrations)-water have been measured by using the Gouy interferometric technique. The effect of the inclusion equilibrium on the cross-term diffusion coefficients was observed. The measured diffusion coefficients in the ternary systems were used to calculate values of the binding constants. These values are in good agreement with the value obtained from calorimetric studies.

Anomalously Fast Diffusion of Targeted Carbon Nanotubes in Cellular Spheroids.

PubMed

Wang, Yichun; Bahng, Joong Hwan; Che, Quantong; Han, Jishu; Kotov, Nicholas A

2015-08-25

Understanding transport of carbon nanotubes (CNTs) and other nanocarriers within tissues is essential for biomedical imaging and drug delivery using these carriers. Compared to traditional cell cultures in animal studies, three-dimensional tissue replicas approach the complexity of the actual organs and enable high temporal and spatial resolution of the carrier permeation. We investigated diffusional transport of CNTs in highly uniform spheroids of hepatocellular carcinoma and found that apparent diffusion coefficients of CNTs in these tissue replicas are anomalously high and comparable to diffusion rates of similarly charged molecules with molecular weights 10000× lower. Moreover, diffusivity of CNTs in tissues is enhanced after functionalization with transforming growth factor β1. This unexpected trend contradicts predictions of the Stokes-Einstein equation and previously obtained empirical dependences of diffusivity on molecular mass for permeants in gas, liquid, solid or gel. It is attributed to the planar diffusion (gliding) of CNTs along cellular membranes reducing effective dimensionality of diffusional space. These findings indicate that nanotubes and potentially similar nanostructures are capable of fast and deep permeation into the tissue, which is often difficult to realize with anticancer agents.

Modeling the sound transmission between rooms coupled through partition walls by using a diffusion model.

PubMed

Billon, Alexis; Foy, Cédric; Picaut, Judicaël; Valeau, Vincent; Sakout, Anas

2008-06-01

In this paper, a modification of the diffusion model for room acoustics is proposed to account for sound transmission between two rooms, a source room and an adjacent room, which are coupled through a partition wall. A system of two diffusion equations, one for each room, together with a set of two boundary conditions, one for the partition wall and one for the other walls of a room, is obtained and numerically solved. The modified diffusion model is validated by numerical comparisons with the statistical theory for several coupled-room configurations by varying the coupling area surface, the absorption coefficient of each room, and the volume of the adjacent room. An experimental comparison is also carried out for two coupled classrooms. The modified diffusion model results agree very well with both the statistical theory and the experimental data. The diffusion model can then be used as an alternative to the statistical theory, especially when the statistical theory is not applicable, that is, when the reverberant sound field is not diffuse. Moreover, the diffusion model allows the prediction of the spatial distribution of sound energy within each coupled room, while the statistical theory gives only one sound level for each room.

Bulk diffusion in a kinetically constrained lattice gas

NASA Astrophysics Data System (ADS)

Arita, Chikashi; Krapivsky, P. L.; Mallick, Kirone

2018-03-01

In the hydrodynamic regime, the evolution of a stochastic lattice gas with symmetric hopping rules is described by a diffusion equation with density-dependent diffusion coefficient encapsulating all microscopic details of the dynamics. This diffusion coefficient is, in principle, determined by a Green-Kubo formula. In practice, even when the equilibrium properties of a lattice gas are analytically known, the diffusion coefficient cannot be computed except when a lattice gas additionally satisfies the gradient condition. We develop a procedure to systematically obtain analytical approximations for the diffusion coefficient for non-gradient lattice gases with known equilibrium. The method relies on a variational formula found by Varadhan and Spohn which is a version of the Green-Kubo formula particularly suitable for diffusive lattice gases. Restricting the variational formula to finite-dimensional sub-spaces allows one to perform the minimization and gives upper bounds for the diffusion coefficient. We apply this approach to a kinetically constrained non-gradient lattice gas in two dimensions, viz. to the Kob-Andersen model on the square lattice.

Plasma fluctuations as Markovian noise.

PubMed

Li, B; Hazeltine, R D; Gentle, K W

2007-12-01

Noise theory is used to study the correlations of stationary Markovian fluctuations that are homogeneous and isotropic in space. The relaxation of the fluctuations is modeled by the diffusion equation. The spatial correlations of random fluctuations are modeled by the exponential decay. Based on these models, the temporal correlations of random fluctuations, such as the correlation function and the power spectrum, are calculated. We find that the diffusion process can give rise to the decay of the correlation function and a broad frequency spectrum of random fluctuations. We also find that the transport coefficients may be estimated by the correlation length and the correlation time. The theoretical results are compared with the observed plasma density fluctuations from the tokamak and helimak experiments.

Structure-specific magnetic field inhomogeneities and its effect on the correlation time.

PubMed

Ziener, Christian H; Bauer, Wolfgang R; Melkus, Gerd; Weber, Thomas; Herold, Volker; Jakob, Peter M

2006-12-01

We describe the relationship between the correlation time and microscopic spatial inhomogeneities in the static magnetic field. The theory takes into account diffusion of nuclear spins in the inhomogeneous field created by magnetized objects. A simple general expression for the correlation time is obtained. It is shown that the correlation time is dependent on a characteristic length, the diffusion coefficient of surrounding medium, the permeability of the surface and the volume fraction of the magnetized objects. For specific geometries (spheres and cylinders), exact analytical expressions for the correlation time are given. The theory can be applied to contrast agents (magnetically labeled cells), capillary network, BOLD effect and so forth.

Charge and spin diffusion on the metallic side of the metal-insulator transition: A self-consistent approach

NASA Astrophysics Data System (ADS)

Wellens, Thomas; Jalabert, Rodolfo A.

2016-10-01

We develop a self-consistent theory describing the spin and spatial electron diffusion in the impurity band of doped semiconductors under the effect of a weak spin-orbit coupling. The resulting low-temperature spin-relaxation time and diffusion coefficient are calculated within different schemes of the self-consistent framework. The simplest of these schemes qualitatively reproduces previous phenomenological developments, while more elaborate calculations provide corrections that approach the values obtained in numerical simulations. The results are universal for zinc-blende semiconductors with electron conductance in the impurity band, and thus they are able to account for the measured spin-relaxation times of materials with very different physical parameters. From a general point of view, our theory opens a new perspective for describing the hopping dynamics in random quantum networks.

Measurement of effective air diffusion coefficients for trichloroethene in undisturbed soil cores.

PubMed

Bartelt-Hunt, Shannon L; Smith, James A

2002-06-01

In this study, we measure effective diffusion coefficients for trichloroethene in undisturbed soil samples taken from Picatinny Arsenal, New Jersey. The measured effective diffusion coefficients ranged from 0.0053 to 0.0609 cm2/s over a range of air-filled porosity of 0.23-0.49. The experimental data were compared to several previously published relations that predict diffusion coefficients as a function of air-filled porosity and porosity. A multiple linear regression analysis was developed to determine if a modification of the exponents in Millington's [Science 130 (1959) 100] relation would better fit the experimental data. The literature relations appeared to generally underpredict the effective diffusion coefficient for the soil cores studied in this work. Inclusion of a particle-size distribution parameter, d10, did not significantly improve the fit of the linear regression equation. The effective diffusion coefficient and porosity data were used to recalculate estimates of diffusive flux through the subsurface made in a previous study performed at the field site. It was determined that the method of calculation used in the previous study resulted in an underprediction of diffusive flux from the subsurface. We conclude that although Millington's [Science 130 (1959) 100] relation works well to predict effective diffusion coefficients in homogeneous soils with relatively uniform particle-size distributions, it may be inaccurate for many natural soils with heterogeneous structure and/or non-uniform particle-size distributions.

Quantitative metrics for evaluating parallel acquisition techniques in diffusion tensor imaging at 3 Tesla.

PubMed

Ardekani, Siamak; Selva, Luis; Sayre, James; Sinha, Usha

2006-11-01

Single-shot echo-planar based diffusion tensor imaging is prone to geometric and intensity distortions. Parallel imaging is a means of reducing these distortions while preserving spatial resolution. A quantitative comparison at 3 T of parallel imaging for diffusion tensor images (DTI) using k-space (generalized auto-calibrating partially parallel acquisitions; GRAPPA) and image domain (sensitivity encoding; SENSE) reconstructions at different acceleration factors, R, is reported here. Images were evaluated using 8 human subjects with repeated scans for 2 subjects to estimate reproducibility. Mutual information (MI) was used to assess the global changes in geometric distortions. The effects of parallel imaging techniques on random noise and reconstruction artifacts were evaluated by placing 26 regions of interest and computing the standard deviation of apparent diffusion coefficient and fractional anisotropy along with the error of fitting the data to the diffusion model (residual error). The larger positive values in mutual information index with increasing R values confirmed the anticipated decrease in distortions. Further, the MI index of GRAPPA sequences for a given R factor was larger than the corresponding mSENSE images. The residual error was lowest in the images acquired without parallel imaging and among the parallel reconstruction methods, the R = 2 acquisitions had the least error. The standard deviation, accuracy, and reproducibility of the apparent diffusion coefficient and fractional anisotropy in homogenous tissue regions showed that GRAPPA acquired with R = 2 had the least amount of systematic and random noise and of these, significant differences with mSENSE, R = 2 were found only for the fractional anisotropy index. Evaluation of the current implementation of parallel reconstruction algorithms identified GRAPPA acquired with R = 2 as optimal for diffusion tensor imaging.

Turbulent eddy diffusion models in exposure assessment - Determination of the eddy diffusion coefficient.

PubMed

Shao, Yuan; Ramachandran, Sandhya; Arnold, Susan; Ramachandran, Gurumurthy

2017-03-01

The use of the turbulent eddy diffusion model and its variants in exposure assessment is limited due to the lack of knowledge regarding the isotropic eddy diffusion coefficient, D T . But some studies have suggested a possible relationship between D T and the air changes per hour (ACH) through a room. The main goal of this study was to accurately estimate D T for a range of ACH values by minimizing the difference between the concentrations measured and predicted by eddy diffusion model. We constructed an experimental chamber with a spatial concentration gradient away from the contaminant source, and conducted 27 3-hr long experiments using toluene and acetone under different air flow conditions (0.43-2.89 ACHs). An eddy diffusion model accounting for chamber boundary, general ventilation, and advection was developed. A mathematical expression for the slope based on the geometrical parameters of the ventilation system was also derived. There is a strong linear relationship between D T and ACH, providing a surrogate parameter for estimating D T in real-life settings. For the first time, a mathematical expression for the relationship between D T and ACH has been derived that also corrects for non-ideal conditions, and the calculated value of the slope between these two parameters is very close to the experimentally determined value. The values of D T obtained from the experiments are generally consistent with values reported in the literature. They are also independent of averaging time of measurements, allowing for comparison of values obtained from different measurement settings. These findings make the use of turbulent eddy diffusion models for exposure assessment in workplace/indoor environments more practical.

Material appearance acquisition from a single image

NASA Astrophysics Data System (ADS)

Zhang, Xu; Cui, Shulin; Cui, Hanwen; Yang, Lin; Wu, Tao

2017-01-01

The scope of this paper is to present a method of material appearance acquisition(MAA) from a single image. In this paper, material appearance is represented by spatially varying bidirectional reflectance distribution function(SVBRDF). Therefore, MAA can be reduced to the problem of recovery of each pixel's BRDF parameters from an original input image, which include diffuse coefficient, specular coefficient, normal and glossiness based on the Blinn-Phone model. In our method, the workflow of MAA includes five main phases: highlight removal, estimation of intrinsic images, shape from shading(SFS), initialization of glossiness and refining SVBRDF parameters based on IPOPT. The results indicate that the proposed technique can effectively extract the material appearance from a single image.

Determination of the diffusion coefficient of hydrogen ion in hydrogels.

PubMed

Schuszter, Gábor; Gehér-Herczegh, Tünde; Szűcs, Árpád; Tóth, Ágota; Horváth, Dezső

2017-05-17

The role of diffusion in chemical pattern formation has been widely studied due to the great diversity of patterns emerging in reaction-diffusion systems, particularly in H + -autocatalytic reactions where hydrogels are applied to avoid convection. A custom-made conductometric cell is designed to measure the effective diffusion coefficient of a pair of strong electrolytes containing sodium ions or hydrogen ions with a common anion. This together with the individual diffusion coefficient for sodium ions, obtained from PFGSE-NMR spectroscopy, allows the determination of the diffusion coefficient of hydrogen ions in hydrogels. Numerical calculations are also performed to study the behavior of a diffusion-migration model describing ionic diffusion in our system. The method we present for one particular case may be extended for various hydrogels and diffusing ions (such as hydroxide) which are relevant e.g. for the development of pH-regulated self-healing mechanisms and hydrogels used for drug delivery.

Extensive database of liquid phase diffusion coefficients of some frequently used test molecules in reversed-phase liquid chromatography and hydrophilic interaction liquid chromatography.

PubMed

Song, Huiying; Vanderheyden, Yoachim; Adams, Erwin; Desmet, Gert; Cabooter, Deirdre

2016-07-15

Diffusion plays an important role in all aspects of band broadening in chromatography. An accurate knowledge of molecular diffusion coefficients in different mobile phases is therefore crucial in fundamental column performance studies. Correlations available in literature, such as the Wilke-Chang equation, can provide good approximations of molecular diffusion under reversed-phase conditions. However, these correlations have been demonstrated to be less accurate for mobile phases containing a large percentage of acetonitrile, as is the case in hydrophilic interaction liquid chromatography. A database of experimentally measured molecular diffusion coefficients of some 45 polar and apolar compounds that are frequently used as test molecules under hydrophilic interaction liquid chromatography and reversed-phase conditions is therefore presented. Special attention is given to diffusion coefficients of polar compounds obtained in large percentages of acetonitrile (>90%). The effect of the buffer concentration (5-10mM ammonium acetate) on the obtained diffusion coefficients is investigated and is demonstrated to mainly influence the molecular diffusion of charged molecules. Diffusion coefficients are measured using the Taylor-Aris method and hence deduced from the peak broadening of a solute when flowing through a long open tube. The validity of the set-up employed for the measurement of the diffusion coefficients is demonstrated by ruling out the occurrence of longitudinal diffusion, secondary flow interactions and extra-column effects, while it is also shown that radial equilibration in the 15m long capillary is effective. Copyright © 2016 Elsevier B.V. All rights reserved.

Listening to light scattering in turbid media: quantitative optical scattering imaging using photoacoustic measurements with one-wavelength illumination

NASA Astrophysics Data System (ADS)

Yuan, Zhen; Li, Xiaoqi; Xi, Lei

2014-06-01

Biomedical photoacoustic tomography (PAT), as a potential imaging modality, can visualize tissue structure and function with high spatial resolution and excellent optical contrast. It is widely recognized that the ability of quantitatively imaging optical absorption and scattering coefficients from photoacoustic measurements is essential before PAT can become a powerful imaging modality. Existing quantitative PAT (qPAT), while successful, has been focused on recovering absorption coefficient only by assuming scattering coefficient a constant. An effective method for photoacoustically recovering optical scattering coefficient is presently not available. Here we propose and experimentally validate such a method for quantitative scattering coefficient imaging using photoacoustic data from one-wavelength illumination. The reconstruction method developed combines conventional PAT with the photon diffusion equation in a novel way to realize the recovery of scattering coefficient. We demonstrate the method using various objects having scattering contrast only or both absorption and scattering contrasts embedded in turbid media. The listening-to-light-scattering method described will be able to provide high resolution scattering imaging for various biomedical applications ranging from breast to brain imaging.

Method of producing microporous joints in metal bodies

DOEpatents

Danko, Joseph C.

1982-01-01

Tungsten is placed in contact with either molybdenum, tantalum, niobium, vanadium, rhenium, or other metal of atoms having a different diffusion coefficient than tungsten. The metals are heated so that the atoms having the higher diffusion coefficient migrate to the metal having the lower diffusion rate, leaving voids in the higher diffusion coefficient metal. Heating is continued until the voids are interconnected.

First-principles multiple-barrier diffusion theory. The case study of interstitial diffusion in CdTe

DOE PAGES

Yang, Ji -Hui; Park, Ji -Sang; Kang, Joongoo; ...

2015-02-17

The diffusion of particles in solid-state materials generally involves several sequential thermal-activation processes. However, presently, diffusion coefficient theory only deals with a single barrier, i.e., it lacks an accurate description to deal with multiple-barrier diffusion. Here, we develop a general diffusion coefficient theory for multiple-barrier diffusion. Using our diffusion theory and first-principles calculated hopping rates for each barrier, we calculate the diffusion coefficients of Cd, Cu, Te, and Cl interstitials in CdTe for their full multiple-barrier diffusion pathways. As a result, we found that the calculated diffusivity agrees well with the experimental measurement, thus justifying our theory, which is generalmore » for many other systems.« less

Gas-film coefficients for streams

USGS Publications Warehouse

Rathbun, R.E.; Tai, D.Y.

1983-01-01

Equations for predicting the gas-film coefficient for the volatilization of organic solutes from streams are developed. The film coefficient is a function of windspeed and water temperature. The dependence of the coefficient on windspeed is determined from published information on the evaporation of water from a canal. The dependence of the coefficient on temperature is determined from laboratory studies on the evaporation of water. Procedures for adjusting the coefficients for different organic solutes are based on the molecular diffusion coefficient and the molecular weight. The molecular weight procedure is easiest to use because of the availability of molecular weights. However, the theoretical basis of the procedure is questionable. The diffusion coefficient procedure is supported by considerable data. Questions, however, remain regarding the exact dependence of the film coefficint on the diffusion coefficient. It is suggested that the diffusion coefficient procedure with a 0.68-power dependence be used when precise estimate of the gas-film coefficient are needed and that the molecular weight procedure be used when only approximate estimates are needed.

An Ab Initio and Kinetic Monte Carlo Simulation Study of Lithium Ion Diffusion on Graphene

PubMed Central

Zhong, Kehua; Yang, Yanmin; Xu, Guigui; Zhang, Jian-Min; Huang, Zhigao

2017-01-01

The Li+ diffusion coefficients in Li+-adsorbed graphene systems were determined by combining first-principle calculations based on density functional theory with Kinetic Monte Carlo simulations. The calculated results indicate that the interactions between Li ions have a very important influence on lithium diffusion. Based on energy barriers directly obtained from first-principle calculations for single-Li+ and two-Li+ adsorbed systems, a new equation predicting energy barriers with more than two Li ions was deduced. Furthermore, it is found that the temperature dependence of Li+ diffusion coefficients fits well to the Arrhenius equation, rather than meeting the equation from electrochemical impedance spectroscopy applied to estimate experimental diffusion coefficients. Moreover, the calculated results also reveal that Li+ concentration dependence of diffusion coefficients roughly fits to the equation from electrochemical impedance spectroscopy in a low concentration region; however, it seriously deviates from the equation in a high concentration region. So, the equation from electrochemical impedance spectroscopy technique could not be simply used to estimate the Li+ diffusion coefficient for all Li+-adsorbed graphene systems with various Li+ concentrations. Our work suggests that interactions between Li ions, and among Li ion and host atoms will influence the Li+ diffusion, which determines that the Li+ intercalation dependence of Li+ diffusion coefficient should be changed and complex. PMID:28773122

On the Ageing of High Energy Lithium-Ion Batteries—Comprehensive Electrochemical Diffusivity Studies of Harvested Nickel Manganese Cobalt Electrodes

PubMed Central

Jaguemont, Joris; Van Den Bossche, Peter; Omar, Noshin; Van Mierlo, Joeri

2018-01-01

This paper examines the impact of the characterisation technique considered for the determination of the Li+ solid state diffusion coefficient in uncycled as in cycled Nickel Manganese Cobalt oxide (NMC) electrodes. As major characterisation techniques, Cyclic Voltammetry (CV), Galvanostatic Intermittent Titration Technique (GITT) and Electrochemical Impedance Spectroscopy (EIS) were systematically investigated. Li+ diffusion coefficients during the lithiation process of the uncycled and cycled electrodes determined by CV at 3.71 V are shown to be equal to 3.48×10−10 cm2·s−1 and 1.56×10−10 cm2·s−1 , respectively. The dependency of the Li+ diffusion with the lithium content in the electrodes is further studied in this paper with GITT and EIS. Diffusion coefficients calculated by GITT and EIS characterisations are shown to be in the range between 1.76×10−15 cm2·s−1 and 4.06×10−12 cm2·s−1, while demonstrating the same decreasing trend with the lithiation process of the electrodes. For both electrode types, diffusion coefficients calculated by CV show greater values compared to those determined by GITT and EIS. With ageing, CV and EIS techniques lead to diffusion coefficients in the electrodes at 3.71 V that are decreasing, in contrast to GITT for which results indicate increasing diffusion coefficient. After long-term cycling, ratios of the diffusion coefficients determined by GITT compared to CV become more significant with an increase about 1 order of magnitude, while no significant variation is seen between the diffusion coefficients calculated from EIS in comparison to CV. PMID:29360787

On the Ageing of High Energy Lithium-Ion Batteries-Comprehensive Electrochemical Diffusivity Studies of Harvested Nickel Manganese Cobalt Electrodes.

PubMed

Capron, Odile; Gopalakrishnan, Rahul; Jaguemont, Joris; Van Den Bossche, Peter; Omar, Noshin; Van Mierlo, Joeri

2018-01-23

This paper examines the impact of the characterisation technique considered for the determination of the L i + solid state diffusion coefficient in uncycled as in cycled Nickel Manganese Cobalt oxide (NMC) electrodes. As major characterisation techniques, Cyclic Voltammetry (CV), Galvanostatic Intermittent Titration Technique (GITT) and Electrochemical Impedance Spectroscopy (EIS) were systematically investigated. L i + diffusion coefficients during the lithiation process of the uncycled and cycled electrodes determined by CV at 3.71 V are shown to be equal to 3 . 48 × 10 - 10 cm 2 ·s - 1 and 1 . 56 × 10 - 10 cm 2 ·s - 1 , respectively. The dependency of the L i + diffusion with the lithium content in the electrodes is further studied in this paper with GITT and EIS. Diffusion coefficients calculated by GITT and EIS characterisations are shown to be in the range between 1 . 76 × 10 - 15 cm 2 ·s - 1 and 4 . 06 × 10 - 12 cm 2 ·s - 1 , while demonstrating the same decreasing trend with the lithiation process of the electrodes. For both electrode types, diffusion coefficients calculated by CV show greater values compared to those determined by GITT and EIS. With ageing, CV and EIS techniques lead to diffusion coefficients in the electrodes at 3.71 V that are decreasing, in contrast to GITT for which results indicate increasing diffusion coefficient. After long-term cycling, ratios of the diffusion coefficients determined by GITT compared to CV become more significant with an increase about 1 order of magnitude, while no significant variation is seen between the diffusion coefficients calculated from EIS in comparison to CV.

A new ionospheric electron precipitation module coupled with RAM-SCB within the geospace general circulation model

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

Yu, Yiqun; Jordanova, Vania K.; Ridley, Aaron J.

Electron precipitation down to the atmosphere due to wave-particle scattering in the magnetosphere contributes significantly to the auroral ionospheric conductivity. In order to obtain the auroral conductivity in global MHD models that are incapable of capturing kinetic physics in the magnetosphere, MHD parameters are often used to estimate electron precipitation flux for the conductivity calculation. Such an MHD approach, however, lacks self-consistency in representing the magnetosphere-ionosphere coupling processes. In this study we improve the coupling processes in global models with a more physical method. We calculate the physics-based electron precipitation from the ring current and map it to the ionosphericmore » altitude for solving the ionospheric electrodynamics. In particular, we use the BATS-R-US (Block Adaptive Tree Scheme-Roe type-Upstream) MHD model coupled with the kinetic ring current model RAM-SCB (Ring current-Atmosphere interaction Model with Self-Consistent Magnetic field (B)) that solves pitch angle-dependent electron distribution functions, to study the global circulation dynamics during the 25–26 January 2013 storm event. Since the electron precipitation loss is mostly governed by wave-particle resonant scattering in the magnetosphere, we further investigate two loss methods of specifying electron precipitation loss associated with wave-particle interactions: (1) using pitch angle diffusion coefficients D αα(E,α) determined from the quasi-linear theory, with wave spectral and plasma density obtained from statistical observations (named as “diffusion coefficient method”) and (2) using electron lifetimes τ(E) independent on pitch angles inferred from the above diffusion coefficients (named as “lifetime method”). We found that both loss methods demonstrate similar temporal evolution of the trapped ring current electrons, indicating that the impact of using different kinds of loss rates is small on the trapped electron population. Furthermore, for the precipitated electrons, the lifetime method hardly captures any precipitation in the large L shell (i.e., 4 < L < 6.5) region, while the diffusion coefficient method produces much better agreement with NOAA/POES measurements, including the spatial distribution and temporal evolution of electron precipitation in the region from the premidnight through the dawn to the dayside. Further comparisons of the precipitation energy flux to DMSP observations indicates that the new physics-based precipitation approach using diffusion coefficients for the ring current electron loss can explain the diffuse electron precipitation in the dawn sector, such as the enhanced precipitation flux at auroral latitudes and flux drop near the subauroral latitudes, but the traditional MHD approach largely overestimates the precipitation flux at lower latitudes.« less

A new ionospheric electron precipitation module coupled with RAM-SCB within the geospace general circulation model

DOE PAGES

Yu, Yiqun; Jordanova, Vania K.; Ridley, Aaron J.; ...

2016-09-01

Electron precipitation down to the atmosphere due to wave-particle scattering in the magnetosphere contributes significantly to the auroral ionospheric conductivity. In order to obtain the auroral conductivity in global MHD models that are incapable of capturing kinetic physics in the magnetosphere, MHD parameters are often used to estimate electron precipitation flux for the conductivity calculation. Such an MHD approach, however, lacks self-consistency in representing the magnetosphere-ionosphere coupling processes. In this study we improve the coupling processes in global models with a more physical method. We calculate the physics-based electron precipitation from the ring current and map it to the ionosphericmore » altitude for solving the ionospheric electrodynamics. In particular, we use the BATS-R-US (Block Adaptive Tree Scheme-Roe type-Upstream) MHD model coupled with the kinetic ring current model RAM-SCB (Ring current-Atmosphere interaction Model with Self-Consistent Magnetic field (B)) that solves pitch angle-dependent electron distribution functions, to study the global circulation dynamics during the 25–26 January 2013 storm event. Since the electron precipitation loss is mostly governed by wave-particle resonant scattering in the magnetosphere, we further investigate two loss methods of specifying electron precipitation loss associated with wave-particle interactions: (1) using pitch angle diffusion coefficients D αα(E,α) determined from the quasi-linear theory, with wave spectral and plasma density obtained from statistical observations (named as “diffusion coefficient method”) and (2) using electron lifetimes τ(E) independent on pitch angles inferred from the above diffusion coefficients (named as “lifetime method”). We found that both loss methods demonstrate similar temporal evolution of the trapped ring current electrons, indicating that the impact of using different kinds of loss rates is small on the trapped electron population. Furthermore, for the precipitated electrons, the lifetime method hardly captures any precipitation in the large L shell (i.e., 4 < L < 6.5) region, while the diffusion coefficient method produces much better agreement with NOAA/POES measurements, including the spatial distribution and temporal evolution of electron precipitation in the region from the premidnight through the dawn to the dayside. Further comparisons of the precipitation energy flux to DMSP observations indicates that the new physics-based precipitation approach using diffusion coefficients for the ring current electron loss can explain the diffuse electron precipitation in the dawn sector, such as the enhanced precipitation flux at auroral latitudes and flux drop near the subauroral latitudes, but the traditional MHD approach largely overestimates the precipitation flux at lower latitudes.« less

Diffusion and solubility coefficients determined by permeation and immersion experiments for organic solvents in HDPE geomembrane.

PubMed

Chao, Keh-Ping; Wang, Ping; Wang, Ya-Ting

2007-04-02

The chemical resistance of eight organic solvents in high density polyethylene (HDPE) geomembrane has been investigated using the ASTM F739 permeation method and the immersion test at different temperatures. The diffusion of the experimental organic solvents in HDPE geomembrane was non-Fickian kinetic, and the solubility coefficients can be consistent with the solubility parameter theory. The diffusion coefficients and solubility coefficients determined by the ASTM F739 method were significantly correlated to the immersion tests (p<0.001). The steady state permeation rates also showed a good agreement between ASTM F739 and immersion experiments (r(2)=0.973, p<0.001). Using a one-dimensional diffusion equation based on Fick's second law, the diffusion and solubility coefficients obtained by immersion test resulted in over estimates of the ASTM F739 permeation results. The modeling results indicated that the diffusion and solubility coefficients should be obtained using ASTM F739 method which closely simulates the practical application of HDPE as barriers in the field.

Radon diffusion coefficients in 360 waterproof materials of different chemical composition.

PubMed

Jiránek, M; Kotrbatá, M

2011-05-01

This paper summarises the results of radon diffusion coefficient measurements in 360 common waterproof materials available throughout Europe. The materials were grouped into 26 categories according to their chemical composition. It was found that the diffusion coefficients of materials used for protecting houses against radon vary within eight orders from 10(-15) to 10(-8) m(2) s(-1). The lowest values were obtained for bitumen membranes with an Al carrier film and for ethylene vinyl acetate membranes. The highest radon diffusion coefficient values were discovered for sodium bentonite membranes, rubber membranes made of ethylene propylene diene monomer and polymer cement coatings. The radon diffusion coefficients for waterproofings widely used for protecting houses, i.e. flexible polyvinyl chloride, high-, low-density polyethylene, polypropylene and bitumen membranes, vary in the range from 3 × 10(-12) to 3 × 10(-11) m(2) s(-1). Tests were performed which confirmed that the radon diffusion coefficient is also an effective tool for verifying the air-tightness of joints.

Electronic speckle pattern interferometry: a tool for determining diffusion and partition coefficients for proteins in gels.

PubMed

Karlsson, David; Zacchi, Guido; Axelsson, Anders

2002-01-01

The aim of this study was to demonstrate electronic speckle pattern interferometry (ESPI) as a powerful tool in determining diffusion coefficients and partition coefficients for proteins in gels. ESPI employs a CCD camera instead of a holographic plate as in conventional holographic interferometry. This gives the advantage of being able to choose the reference state freely. If a hologram at the reference state is taken and compared to a hologram during the diffusion process, an interferometric picture can be generated that describes the refraction index gradients and thus the concentration gradients in the gel as well as in the liquid. MATLAB is then used to fit Fick's law to the experimental data to obtain the diffusion coefficients in gel and liquid. The partition coefficient is obtained from the same experiment from the flux condition at the interface between gel and liquid. This makes the comparison between the different diffusants more reliable than when the measurements are performed in separate experiments. The diffusion and partitioning coefficients of lysozyme, BSA, and IgG in 4% agarose gel at pH 5.6 and in 0.1 M NaCl have been determined. In the gel the diffusion coefficients were 11.2 +/- 1.6, 4.8 +/- 0.6, and 3.0 +/- 0.3 m(2)/s for lysozyme, BSA, and IgG, respectively. The partition coefficients were determined to be 0.65 +/- 0.04, 0.44 +/- 0.06, and 0.51 +/- 0.04 for lysozyme, BSA, and IgG, respectively. The current study shows that ESPI is easy to use and gives diffusion coefficients and partition coefficients for proteins with sufficient accuracy from the same experiment.

Diffusion of rhodamine B and bovine serum albumin in fibrin gels seeded with primary endothelial cells.

PubMed

Shkilnyy, Andriy; Proulx, Pierre; Sharp, Jamie; Lepage, Martin; Vermette, Patrick

2012-05-01

Scaffolds with adequate mass transport properties are needed in many tissue engineering applications. Fibrin is considered a good biological material to fabricate such scaffolds. However, very little is known about mass transport in fibrin. Therefore, a method based on the analysis of fluorescence intensity for measuring the apparent diffusion coefficient of rhodamine B and fluorescein-labelled bovine serum albumin (FITC-BSA) is described. The experiments are performed in fibrin gels with and without human umbilical vein endothelial cells (HUVEC). The apparent diffusion coefficients of rhodamine B and FITC-BSA in fibrin (fibrinogen concentration of 4 mg/mL) with different cell densities are reported. A LIVE/DEAD(®) assay is performed to confirm the viability of HUVEC seeded at high densities. Diffusion coefficients for rhodamine B remain more or less constant up to 5×10(5) cells/mL and correlate well with literature values measured by other methods in water systems. This indicates that the presence of HUVEC in the fibrin gels (up to 5×10(5) cells/mL) has almost no effect on the diffusion coefficients. Higher cell densities (>5×10(5) cells/mL) result in a decrease of the diffusion coefficients. Diffusion coefficients of rhodamine B and FITC-BSA obtained by this method agree with diffusion coefficients in water predicted by the Stokes-Einstein equation. The experimental design used in this study can be applied to measure diffusion coefficients in different types of gels seeded or not with living cells. Copyright © 2012 Elsevier B.V. All rights reserved.

Spatial frequency domain spectroscopy of two layer media

NASA Astrophysics Data System (ADS)

Yudovsky, Dmitry; Durkin, Anthony J.

2011-10-01

Monitoring of tissue blood volume and oxygen saturation using biomedical optics techniques has the potential to inform the assessment of tissue health, healing, and dysfunction. These quantities are typically estimated from the contribution of oxyhemoglobin and deoxyhemoglobin to the absorption spectrum of the dermis. However, estimation of blood related absorption in superficial tissue such as the skin can be confounded by the strong absorption of melanin in the epidermis. Furthermore, epidermal thickness and pigmentation varies with anatomic location, race, gender, and degree of disease progression. This study describes a technique for decoupling the effect of melanin absorption in the epidermis from blood absorption in the dermis for a large range of skin types and thicknesses. An artificial neural network was used to map input optical properties to spatial frequency domain diffuse reflectance of two layer media. Then, iterative fitting was used to determine the optical properties from simulated spatial frequency domain diffuse reflectance. Additionally, an artificial neural network was trained to directly map spatial frequency domain reflectance to sets of optical properties of a two layer medium, thus bypassing the need for iteration. In both cases, the optical thickness of the epidermis and absorption and reduced scattering coefficients of the dermis were determined independently. The accuracy and efficiency of the iterative fitting approach was compared with the direct neural network inversion.

Photo-induced Mass Transport through Polymer Networks

NASA Astrophysics Data System (ADS)

Meng, Yuan; Anthamatten, Mitchell

2014-03-01

Among adaptable materials, photo-responsive polymers are especially attractive as they allow for spatiotemporal stimuli and response. We have recently developed a macromolecular network capable of photo-induced mass transport of covalently bound species. The system comprises of crosslinked chains that form an elastic network and photosensitive fluorescent arms that become mobile upon irradiation. We form loosely crosslinked polymer networks by Michael-Addition between multifunctional thiols and small molecule containing acrylate end-groups. The arms are connected to the network by allyl sulfide, that undergoes addition-fragmentation chain transfer (AFCT) in the presence of free radicals, releasing diffusible fluorophore. The networks are loaded with photoinitiator to allow for spatial modulation of the AFCT reactions. FRAP experiments within bulk elastomers are conducted to establish correlations between the fluorophore's diffusion coefficient and experimental variables such as network architecture, temperature and UV intensity. Photo-induced mass transport between two contacted films is demonstrated, and release of fluorophore into a solvent is investigated. Spatial and temporal control of mass transport could benefit drug release, printing, and sensing 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

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.

Complementary studies of lipid membrane dynamics using iSCAT and super-resolved fluorescence correlation spectroscopy

NASA Astrophysics Data System (ADS)

Reina, Francesco; Galiani, Silvia; Shrestha, Dilip; Sezgin, Erdinc; de Wit, Gabrielle; Cole, Daniel; Lagerholm, B. Christoffer; Kukura, Philipp; Eggeling, Christian

2018-06-01

Observation techniques with high spatial and temporal resolution, such as single-particle tracking based on interferometric scattering (iSCAT) microscopy, and fluorescence correlation spectroscopy applied on a super-resolution STED microscope (STED-FCS), have revealed new insights of the molecular organization of membranes. While delivering complementary information, there are still distinct differences between these techniques, most prominently the use of fluorescent dye tagged probes for STED-FCS and a need for larger scattering gold nanoparticle tags for iSCAT. In this work, we have used lipid analogues tagged with a hybrid fluorescent tag–gold nanoparticle construct, to directly compare the results from STED-FCS and iSCAT measurements of phospholipid diffusion on a homogeneous supported lipid bilayer (SLB). These comparative measurements showed that while the mode of diffusion remained free, at least at the spatial (>40 nm) and temporal (50  ⩽  t  ⩽  100 ms) scales probed, the diffussion coefficient was reduced by 20- to 60-fold when tagging with 20 and 40 nm large gold particles as compared to when using dye tagged lipid analogues. These FCS measurements of hybrid fluorescent tag–gold nanoparticle labeled lipids also revealed that commercially supplied streptavidin-coated gold nanoparticles contain large quantities of free streptavidin. Finally, the values of apparent diffusion coefficients obtained by STED-FCS and iSCAT differed by a factor of 2–3 across the techniques, while relative differences in mobility between different species of lipid analogues considered were identical in both approaches. In conclusion, our experiments reveal that large and potentially cross-linking scattering tags introduce a significant slow-down in diffusion on SLBs but no additional bias, and our labeling approach creates a new way of exploiting complementary information from STED-FCS and iSCAT measurements.

Perpendicular Diffusion Coefficient of Comic Rays: The Presence of Weak Adiabatic Focusing

NASA Astrophysics Data System (ADS)

Wang, J. F.; Qin, G.; Ma, Q. M.; Song, T.; Yuan, S. B.

2017-08-01

The influence of adiabatic focusing on particle diffusion is an important topic in astrophysics and plasma physics. In the past, several authors have explored the influence of along-field adiabatic focusing on the parallel diffusion of charged energetic particles. In this paper, using the unified nonlinear transport theory developed by Shalchi and the method of He and Schlickeiser, we derive a new nonlinear perpendicular diffusion coefficient for a non-uniform background magnetic field. This formula demonstrates that the particle perpendicular diffusion coefficient is modified by along-field adiabatic focusing. For isotropic pitch-angle scattering and the weak adiabatic focusing limit, the derived perpendicular diffusion coefficient is independent of the sign of adiabatic focusing characteristic length. For the two-component model, we simplify the perpendicular diffusion coefficient up to the second order of the power series of the adiabatic focusing characteristic quantity. We find that the first-order modifying factor is equal to zero and that the sign of the second order is determined by the energy of the particles.

Thermodynamic properties and diffusion of water + methane binary mixtures

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

Shvab, I.; Sadus, Richard J., E-mail: rsadus@swin.edu.au

2014-03-14

Thermodynamic and diffusion properties of water + methane mixtures in a single liquid phase are studied using NVT molecular dynamics. An extensive comparison is reported for the thermal pressure coefficient, compressibilities, expansion coefficients, heat capacities, Joule-Thomson coefficient, zero frequency speed of sound, and diffusion coefficient at methane concentrations up to 15% in the temperature range of 298–650 K. The simulations reveal a complex concentration dependence of the thermodynamic properties of water + methane mixtures. The compressibilities, heat capacities, and diffusion coefficients decrease with increasing methane concentration, whereas values of the thermal expansion coefficients and speed of sound increase. Increasing methanemore » concentration considerably retards the self-diffusion of both water and methane in the mixture. These effects are caused by changes in hydrogen bond network, solvation shell structure, and dynamics of water molecules induced by the solvation of methane at constant volume conditions.« less

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

NASA Astrophysics Data System (ADS)

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

2016-08-01

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

Kinetics of dodecanoic acid adsorption from caustic solution by activated carbon.

PubMed

Pendleton, Phillip; Wu, Sophie Hua

2003-10-15

This study examines the influences of adsorbent porosity and surface chemistry and of carbon dosage on dodecanoic acid adsorption kinetics from aqueous and 2 M NaOH solutions as batch adsorption processes. Both adsorbents are steam-activated carbons prepared from either coconut or coal precursors. Prior to use the adsorbents were washed in deionized water or 2 M NaOH. Mass transfer coefficients and effective overall diffusion coefficients indicate a minor contribution from adsorbent porosity. In contrast, high surface oxygen content impedes transport to and into the adsorbent structure. Carbon dosage shows a proportional increase in transport coefficients with increasing mass; these coefficients are constant when normalized per unit mass. Neither water nor NaOH treatment of the adsorbents has a significant influence on dodecanoic acid adsorption kinetics. Molecular and Knudsen diffusion coefficients are defined to demonstrate that the overall effective diffusion coefficient values and the diffusion process are controlled by surface diffusion.

A feasibility study for measuring stratospheric turbulence using metrac positioning system

NASA Technical Reports Server (NTRS)

Gage, K. S.; Jasperson, W. H.

1975-01-01

The feasibility of obtaining measurements of Lagrangian turbulence at stratospheric altitudes is demonstrated by using the METRAC System to track constant-level balloons. The basis for current estimates of diffusion coefficients are reviewed and it is pointed out that insufficient data is available upon which to base reliable estimates of vertical diffusion coefficients. It is concluded that diffusion coefficients could be directly obtained from Lagrangian turbulence measurements. The METRAC balloon tracking system is shown to possess the necessary precision in order to resolve the response of constant-level balloons to turbulence at stratospheric altitudes. A small sample of data recorded from a tropospheric tetroon flight tracked by the METRAC System is analyzed to obtain estimates of small-scale three-dimensional diffusion coefficients. It is recommended that this technique be employed to establish a climatology of diffusion coefficients and to ascertain the variation of these coefficients with altitude, season, and latitude.

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%.

Predicting Salt Permeability Coefficients in Highly Swollen, Highly Charged Ion Exchange Membranes.

PubMed

Kamcev, Jovan; Paul, Donald R; Manning, Gerald S; Freeman, Benny D

2017-02-01

This study presents a framework for predicting salt permeability coefficients in ion exchange membranes in contact with an aqueous salt solution. The model, based on the solution-diffusion mechanism, was tested using experimental salt permeability data for a series of commercial ion exchange membranes. Equilibrium salt partition coefficients were calculated using a thermodynamic framework (i.e., Donnan theory), incorporating Manning's counterion condensation theory to calculate ion activity coefficients in the membrane phase and the Pitzer model to calculate ion activity coefficients in the solution phase. The model predicted NaCl partition coefficients in a cation exchange membrane and two anion exchange membranes, as well as MgCl 2 partition coefficients in a cation exchange membrane, remarkably well at higher external salt concentrations (>0.1 M) and reasonably well at lower external salt concentrations (<0.1 M) with no adjustable parameters. Membrane ion diffusion coefficients were calculated using a combination of the Mackie and Meares model, which assumes ion diffusion in water-swollen polymers is affected by a tortuosity factor, and a model developed by Manning to account for electrostatic effects. Agreement between experimental and predicted salt diffusion coefficients was good with no adjustable parameters. Calculated salt partition and diffusion coefficients were combined within the framework of the solution-diffusion model to predict salt permeability coefficients. Agreement between model and experimental data was remarkably good. Additionally, a simplified version of the model was used to elucidate connections between membrane structure (e.g., fixed charge group concentration) and salt transport properties.

Protein diffusiophoresis and salt osmotic diffusion in aqueous solutions.

PubMed

Annunziata, Onofrio; Buzatu, Daniela; Albright, John G

2012-10-25

Diffusion of a solute can be induced by the concentration gradient of another solute in solution. This transport mechanism is known as cross-diffusion. We have investigated cross-diffusion in a ternary protein-salt-water system. Specifically, we measured the two cross-diffusion coefficients for the lysozyme-NaCl-water system at 25 °C and pH 4.5 as a function of protein and salt concentrations by Rayleigh interferometry. One cross-diffusion coefficient characterizes salt osmotic diffusion induced by a protein concentration gradient, and is related to protein-salt thermodynamic interactions as described by the theories of Donnan membrane equilibrium and protein preferential hydration. The other cross-diffusion coefficient characterizes protein diffusiophoresis induced by a salt concentration gradient, and is described as the difference between a preferential-interaction coefficient and a transport parameter. We first relate our experimental results to the protein net charge and the thermodynamic excess of water near the protein surface. We then extract the Stefan-Maxwell diffusion coefficient describing protein-salt interactions in water. We find that the value of this coefficient is negative, contrary to the friction interpretation of Stefan-Maxwell equations. This result is explained by considering protein hydration. Finally, protein diffusiophoresis is quantitatively examined by considering electrophoretic and hydration effects on protein migration and utilized to accurately estimate lysozyme electrophoretic mobility. To our knowledge, this is the first time that protein diffusiophoresis has been experimentally characterized and a protein-salt Stefan-Maxwell diffusion coefficient reported. This work represents a significant contribution for understanding and modeling the effect of concentration gradients in protein-salt aqueous systems relevant to diffusion-based mass-transfer technologies and transport in living systems.

Apparent diffusion coefficient evaluation for secondary changes in the cerebellum of rats after middle cerebral artery occlusion

PubMed Central

Yang, Yunjun; Gao, Lingyun; Fu, Jun; Zhang, Jun; Li, Yuxin; Yin, Bo; Chen, Weijian; Geng, Daoying

2013-01-01

Supratentorial cerebral infarction can cause functional inhibition of remote regions such as the cerebellum, which may be relevant to diaschisis. This phenomenon is often analyzed using positron emission tomography and single photon emission CT. However, these methods are expensive and radioactive. Thus, the present study quantified the changes of infarction core and remote regions after unilateral middle cerebral artery occlusion using apparent diffusion coefficient values. Diffusion-weighted imaging showed that the area of infarction core gradually increased to involve the cerebral cortex with increasing infarction time. Diffusion weighted imaging signals were initially increased and then stabilized by 24 hours. With increasing infarction time, the apparent diffusion coefficient value in the infarction core and remote bilateral cerebellum both gradually decreased, and then slightly increased 3–24 hours after infarction. Apparent diffusion coefficient values at remote regions (cerebellum) varied along with the change of supratentorial infarction core, suggesting that the phenomenon of diaschisis existed at the remote regions. Thus, apparent diffusion coefficient values and diffusion weighted imaging can be used to detect early diaschisis. PMID:25206615

A Spatio-Temporal Model of Notch Signalling in the Zebrafish Segmentation Clock: Conditions for Synchronised Oscillatory Dynamics

PubMed Central

Terry, Alan J.; Sturrock, Marc; Dale, J. Kim; Maroto, Miguel; Chaplain, Mark A. J.

2011-01-01

In the vertebrate embryo, tissue blocks called somites are laid down in head-to-tail succession, a process known as somitogenesis. Research into somitogenesis has been both experimental and mathematical. For zebrafish, there is experimental evidence for oscillatory gene expression in cells in the presomitic mesoderm (PSM) as well as evidence that Notch signalling synchronises the oscillations in neighbouring PSM cells. A biological mechanism has previously been proposed to explain these phenomena. Here we have converted this mechanism into a mathematical model of partial differential equations in which the nuclear and cytoplasmic diffusion of protein and mRNA molecules is explictly considered. By performing simulations, we have found ranges of values for the model parameters (such as diffusion and degradation rates) that yield oscillatory dynamics within PSM cells and that enable Notch signalling to synchronise the oscillations in two touching cells. Our model contains a Hill coefficient that measures the co-operativity between two proteins (Her1, Her7) and three genes (her1, her7, deltaC) which they inhibit. This coefficient appears to be bounded below by the requirement for oscillations in individual cells and bounded above by the requirement for synchronisation. Consistent with experimental data and a previous spatially non-explicit mathematical model, we have found that signalling can increase the average level of Her1 protein. Biological pattern formation would be impossible without a certain robustness to variety in cell shape and size; our results possess such robustness. Our spatially-explicit modelling approach, together with new imaging technologies that can measure intracellular protein diffusion rates, is likely to yield significant new insight into somitogenesis and other biological processes. PMID:21386903

A spatio-temporal model of Notch signalling in the zebrafish segmentation clock: conditions for synchronised oscillatory dynamics.

PubMed

Terry, Alan J; Sturrock, Marc; Dale, J Kim; Maroto, Miguel; Chaplain, Mark A J

2011-02-28

In the vertebrate embryo, tissue blocks called somites are laid down in head-to-tail succession, a process known as somitogenesis. Research into somitogenesis has been both experimental and mathematical. For zebrafish, there is experimental evidence for oscillatory gene expression in cells in the presomitic mesoderm (PSM) as well as evidence that Notch signalling synchronises the oscillations in neighbouring PSM cells. A biological mechanism has previously been proposed to explain these phenomena. Here we have converted this mechanism into a mathematical model of partial differential equations in which the nuclear and cytoplasmic diffusion of protein and mRNA molecules is explicitly considered. By performing simulations, we have found ranges of values for the model parameters (such as diffusion and degradation rates) that yield oscillatory dynamics within PSM cells and that enable Notch signalling to synchronise the oscillations in two touching cells. Our model contains a Hill coefficient that measures the co-operativity between two proteins (Her1, Her7) and three genes (her1, her7, deltaC) which they inhibit. This coefficient appears to be bounded below by the requirement for oscillations in individual cells and bounded above by the requirement for synchronisation. Consistent with experimental data and a previous spatially non-explicit mathematical model, we have found that signalling can increase the average level of Her1 protein. Biological pattern formation would be impossible without a certain robustness to variety in cell shape and size; our results possess such robustness. Our spatially-explicit modelling approach, together with new imaging technologies that can measure intracellular protein diffusion rates, is likely to yield significant new insight into somitogenesis and other biological processes.

Diffusion in the system K2O-SrO-SiO2. II - Cation self-diffusion coefficients.

NASA Technical Reports Server (NTRS)

Varshneya, A. K.; Cooper, A. R.

1972-01-01

The self-diffusion coefficients were measured by introducing a slab of glass previously irradiated in a reactor between two slabs of unirradiated glass. By heating the specimens, etching them sequentially and determining the radioactivity, self-diffusion coefficients for K and Sr were measured. It is pointed out that the results obtained in the investigations appear to support the proposal that the network of the base glass predominantly controls the activation energy for the diffusion of ions.

Spatially constrained incoherent motion method improves diffusion-weighted MRI signal decay analysis in the liver and spleen

PubMed Central

Taimouri, Vahid; Afacan, Onur; Perez-Rossello, Jeannette M.; Callahan, Michael J.; Mulkern, Robert V.; Warfield, Simon K.; Freiman, Moti

2015-01-01

Purpose: To evaluate the effect of the spatially constrained incoherent motion (SCIM) method on improving the precision and robustness of fast and slow diffusion parameter estimates from diffusion-weighted MRI in liver and spleen in comparison to the independent voxel-wise intravoxel incoherent motion (IVIM) model. Methods: We collected diffusion-weighted MRI (DW-MRI) data of 29 subjects (5 healthy subjects and 24 patients with Crohn’s disease in the ileum). We evaluated parameters estimates’ robustness against different combinations of b-values (i.e., 4 b-values and 7 b-values) by comparing the variance of the estimates obtained with the SCIM and the independent voxel-wise IVIM model. We also evaluated the improvement in the precision of parameter estimates by comparing the coefficient of variation (CV) of the SCIM parameter estimates to that of the IVIM. Results: The SCIM method was more robust compared to IVIM (up to 70% in liver and spleen) for different combinations of b-values. Also, the CV values of the parameter estimations using the SCIM method were significantly lower compared to repeated acquisition and signal averaging estimated using IVIM, especially for the fast diffusion parameter in liver (CVIV IM = 46.61 ± 11.22, CVSCIM = 16.85 ± 2.160, p < 0.001) and spleen (CVIV IM = 95.15 ± 19.82, CVSCIM = 52.55 ± 1.91, p < 0.001). Conclusions: The SCIM method characterizes fast and slow diffusion more precisely compared to the independent voxel-wise IVIM model fitting in the liver and spleen. PMID:25832079

Limbic and corpus callosum aberrations in adolescents with bipolar disorder: a tract-based spatial statistics analysis.

PubMed

Barnea-Goraly, Naama; Chang, Kiki D; Karchemskiy, Asya; Howe, Meghan E; Reiss, Allan L

2009-08-01

Bipolar disorder (BD) is a common and debilitating condition, often beginning in adolescence. Converging evidence from genetic and neuroimaging studies indicates that white matter abnormalities may be involved in BD. In this study, we investigated white matter structure in adolescents with familial bipolar disorder using diffusion tensor imaging (DTI) and a whole brain analysis. We analyzed DTI images using tract-based spatial statistics (TBSS), a whole-brain voxel-by-voxel analysis, to investigate white matter structure in 21 adolescents with BD, who also were offspring of at least one parent with BD, and 18 age- and IQ-matched control subjects. Fractional anisotropy (FA; a measure of diffusion anisotropy), trace values (average diffusivity), and apparent diffusion coefficient (ADC; a measure of overall diffusivity) were used as variables in this analysis. In a post hoc analysis, we correlated between FA values, behavioral measures, and medication exposure. Adolescents with BD had lower FA values than control subjects in the fornix, the left mid-posterior cingulate gyrus, throughout the corpus callosum, in fibers extending from the fornix to the thalamus, and in parietal and occipital corona radiata bilaterally. There were no significant between-group differences in trace or ADC values and no significant correlation between behavioral measures, medication exposure, and FA values. Significant white matter tract alterations in adolescents with BD were observed in regions involved in emotional, behavioral, and cognitive regulation. These results suggest that alterations in white matter are present early in the course of disease in familial BD.

Electrokinetics of diffuse soft interfaces. 1. Limit of low Donnan potentials.

PubMed

Duval, Jérôme F L; van Leeuwen, Herman P

2004-11-09

The current theoretical approaches to electrokinetics of gels or polyelectrolyte layers are based on the assumption that the position of the very interface between the aqueous medium and the gel phase is well defined. Within this assumption, spatial profiles for the volume fraction of polymer segments (phi), the density of fixed charges in the porous layer (rho fix), and the coefficient modeling the friction to hydrodynamic flow (k) follow a step-function. In reality, the "fuzzy" nature of the charged soft layer is intrinsically incompatible with the concept of a sharp interface and therefore necessarily calls for more detailed spatial representations for phi, rho fix, and k. In this paper, the notion of diffuse interface is introduced. For the sake of illustration, linear spatial distributions for phi and rho fix are considered in the interfacial zone between the bulk of the porous charged layer and the bulk electrolyte solution. The corresponding distribution for k is inferred from the Brinkman equation, which for low phi reduces to Stokes' equation. Linear electrostatics, hydrodynamics, and electroosmosis issues are analytically solved within the context of streaming current and streaming potential of charged surface layers in a thin-layer cell. The hydrodynamic analysis clearly demonstrates the physical incorrectness of the concept of a discrete slip plane for diffuse interfaces. For moderate to low electrolyte concentrations and nanoscale spatial transition of phi from zero (bulk electrolyte) to phi o (bulk gel), the electrokinetic properties of the soft layer as predicted by the theory considerably deviate from those calculated on the basis of the discontinuous approximation by Ohshima.

Photopolymer holographic recording material

NASA Astrophysics Data System (ADS)

Lawrence, J. R.; O'Neill, F. T.; Sheridan, J. T.

Photopolymers are promising materials for use in holography. They have many advantages, such as ease of preparation, and are capable of efficiencies of up to 100%. A disadvantage of these materials is their inability to record high spatial frequency gratings when compared to other materials such as dichromated gelatin and silver halide photographic emulsion. Until recently, the drop off at high spatial frequencies of the material response was not predicted by any of the diffusion based models available. It has recently been proposed that this effect is due to polymer chains growing away from their initiation point and causing a smeared profile to be recorded. This is termed a non-local material response. Simple analytic expressions have been derived using this model and fits to experimental data have allowed values to be estimated for material parameters such as the diffusion coefficient of monomer, the ratio of polymerisation rate to diffusion rate and the distance that the polymer chains spread during holographic recording. The model predicts that the spatial frequency response might be improved by decreasing the mean polymer chain lengths and/or by increasing the mobility of the molecules used in the material. The experimental work carried out to investigate these predictions is reported here. This work involved (a) the changing of the molecular weights of chemical components within the material (dyes and binders) and (b) the addition of a chemical retarder in order to shorten the polymer chains, thereby decreasing the extent of the non-local effect. Although no significant improvement in spatial frequency response was observed the model appears to offer an improved understanding of the operation of the material.

Phase transition of traveling waves in bacterial colony pattern

NASA Astrophysics Data System (ADS)

Wakano, Joe Yuichiro; Komoto, Atsushi; Yamaguchi, Yukio

2004-05-01

Depending on the growth condition, bacterial colonies can exhibit different morphologies. Many previous studies have used reaction diffusion equations to reproduce spatial patterns. They have revealed that nonlinear reaction term can produce diverse patterns as well as nonlinear diffusion coefficient. Typical reaction term consists of nutrient consumption, bacterial reproduction, and sporulation. Among them, the functional form of sporulation rate has not been biologically investigated. Here we report experimentally measured sporulation rate. Then, based on the result, a reaction diffusion model is proposed. One-dimensional simulation showed the existence of traveling wave solution. We study the wave form as a function of the initial nutrient concentration and find two distinct types of solution. Moreover, transition between them is very sharp, which is analogous to phase transition. The velocity of traveling wave also shows sharp transition in nonlinear diffusion model, which is consistent with the previous experimental result. The phenomenon can be explained by separatrix in reaction term dynamics. Results of two-dimensional simulation are also shown and discussed.

Estimation of Knudsen diffusion coefficients from tracer experiments conducted with a binary gas system and a porous medium.

PubMed

Hibi, Yoshihiko; Kashihara, Ayumi

2018-03-01

A previous study has reported that Knudsen diffusion coefficients obtained by tracer experiments conducted with a binary gas system and a porous medium are consistently smaller than those obtained by permeability experiments conducted with a single-gas system and a porous medium. To date, however, that study is the only one in which tracer experiments have been conducted with a binary gas system. Therefore, to confirm this difference in Knudsen diffusion coefficients, we used a method we had developed previously to conduct tracer experiments with a binary carbon dioxide-nitrogen gas system and five porous media with permeability coefficients ranging from 10 -13 to 10 -11  m 2 . The results showed that the Knudsen diffusion coefficient of N 2 (D N2 ) (cm 2 /s) was related to the effective permeability coefficient k e (m 2 ) as D N2  = 7.39 × 10 7 k e 0.767 . Thus, the Knudsen diffusion coefficients of N 2 obtained by our tracer experiments were consistently 1/27 of those obtained by permeability experiments conducted with many porous media and air by other researchers. By using an inversion simulation to fit the advection-diffusion equation to the distribution of concentrations at observation points calculated by mathematically solving the equation, we confirmed that the method used to obtain the Knudsen diffusion coefficient in this study yielded accurate values. Moreover, because the Knudsen diffusion coefficient did not differ when columns with two different lengths, 900 and 1500 mm, were used, this column property did not influence the flow of gas in the column. The equation of the dusty gas model already includes obstruction factors for Knudsen diffusion and molecular diffusion, which relate to medium heterogeneity and tortuosity and depend only on the structure of the porous medium. Furthermore, there is no need to take account of any additional correction factor for molecular diffusion except the obstruction factor because molecular diffusion is only treated in a multicomponent gas system. Thus, molecular diffusion considers only the obstruction factor related to tortuosity. Therefore, we introduced a correction factor for a multicomponent gas system into the DGM equation, multiplying the Knudsen diffusion coefficient, which includes the obstruction factor related to tortuosity, by this correction factor. From the present experimental results, the value of this correction factor was 1/27, and it depended only on the structure of the gas system in the porous medium. Copyright © 2018 Elsevier B.V. All rights reserved.

Estimation of Knudsen diffusion coefficients from tracer experiments conducted with a binary gas system and a porous medium

NASA Astrophysics Data System (ADS)

Hibi, Yoshihiko; Kashihara, Ayumi

2018-03-01

A previous study has reported that Knudsen diffusion coefficients obtained by tracer experiments conducted with a binary gas system and a porous medium are consistently smaller than those obtained by permeability experiments conducted with a single-gas system and a porous medium. To date, however, that study is the only one in which tracer experiments have been conducted with a binary gas system. Therefore, to confirm this difference in Knudsen diffusion coefficients, we used a method we had developed previously to conduct tracer experiments with a binary carbon dioxide-nitrogen gas system and five porous media with permeability coefficients ranging from 10-13 to 10-11 m2. The results showed that the Knudsen diffusion coefficient of N2 (DN2) (cm2/s) was related to the effective permeability coefficient ke (m2) as DN2 = 7.39 × 107ke0.767. Thus, the Knudsen diffusion coefficients of N2 obtained by our tracer experiments were consistently 1/27 of those obtained by permeability experiments conducted with many porous media and air by other researchers. By using an inversion simulation to fit the advection-diffusion equation to the distribution of concentrations at observation points calculated by mathematically solving the equation, we confirmed that the method used to obtain the Knudsen diffusion coefficient in this study yielded accurate values. Moreover, because the Knudsen diffusion coefficient did not differ when columns with two different lengths, 900 and 1500 mm, were used, this column property did not influence the flow of gas in the column. The equation of the dusty gas model already includes obstruction factors for Knudsen diffusion and molecular diffusion, which relate to medium heterogeneity and tortuosity and depend only on the structure of the porous medium. Furthermore, there is no need to take account of any additional correction factor for molecular diffusion except the obstruction factor because molecular diffusion is only treated in a multicomponent gas system. Thus, molecular diffusion considers only the obstruction factor related to tortuosity. Therefore, we introduced a correction factor for a multicomponent gas system into the DGM equation, multiplying the Knudsen diffusion coefficient, which includes the obstruction factor related to tortuosity, by this correction factor. From the present experimental results, the value of this correction factor was 1/27, and it depended only on the structure of the gas system in the porous medium.

Gene interference regulates aquaporin-4 expression in swollen tissue of rats with cerebral ischemic edema: Correlation with variation in apparent diffusion coefficient.

PubMed

Hu, Hui; Lu, Hong; He, Zhanping; Han, Xiangjun; Chen, Jing; Tu, Rong

2012-07-25

To investigate the effects of mRNA interference on aquaporin-4 expression in swollen tissue of rats with ischemic cerebral edema, and diagnose the significance of diffusion-weighted MRI, we injected 5 μL shRNA- aquaporin-4 (control group) or siRNA- aquaporin-4 solution (1:800) (RNA interference group) into the rat right basal ganglia immediately before occlusion of the middle cerebral artery. At 0.25 hours after occlusion of the middle cerebral artery, diffusion-weighted MRI displayed a high signal; within 2 hours, the relative apparent diffusion coefficient decreased markedly, aquaporin-4 expression increased rapidly, and intracellular edema was obviously aggravated; at 4 and 6 hours, the relative apparent diffusion coefficient slowly returned to control levels, aquaporin-4 expression slightly increased, and angioedema was observed. In the RNA interference group, during 0.25-6 hours after injection of siRNA- aquaporin-4 solution, the relative apparent diffusion coefficient slightly fluctuated and aquaporin-4 expression was upregulated; during 0.5-4 hours, the relative apparent diffusion coefficient was significantly higher, while aquaporin-4 expression was significantly lower when compared with the control group, and intracellular edema was markedly reduced; at 0.25 and 6 hours, the relative apparent diffusion coefficient and aquaporin-4 expression were similar when compared with the control group; obvious angioedema remained at 6 hours. Pearson's correlation test results showed that aquaporin-4 expression was negatively correlated with the apparent diffusion coefficient (r = -0.806, P < 0.01). These findings suggest that upregulated aquaporin-4 expression is likely to be the main molecular mechanism of intracellular edema and may be the molecular basis for decreased relative apparent diffusion coefficient. Aquaporin-4 gene interference can effectively inhibit the upregulation of aquaporin-4 expression during the stage of intracellular edema with time-effectiveness. Moreover, diffusion-weighted MRI can accurately detect intracellular edema.

Combined inverse-forward artificial neural networks for fast and accurate estimation of the diffusion coefficients of cartilage based on multi-physics models.

PubMed

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

2016-09-06

Analytical and numerical methods have been used to extract essential engineering parameters such as elastic modulus, Poisson׳s ratio, permeability and diffusion coefficient from experimental data in various types of biological tissues. The major limitation associated with analytical techniques is that they are often only applicable to problems with simplified assumptions. Numerical multi-physics methods, on the other hand, enable minimizing the simplified assumptions but require substantial computational expertise, which is not always available. In this paper, we propose a novel approach that combines inverse and forward artificial neural networks (ANNs) which enables fast and accurate estimation of the diffusion coefficient of cartilage without any need for computational modeling. In this approach, an inverse ANN is trained using our multi-zone biphasic-solute finite-bath computational model of diffusion in cartilage to estimate the diffusion coefficient of the various zones of cartilage given the concentration-time curves. Robust estimation of the diffusion coefficients, however, requires introducing certain levels of stochastic variations during the training process. Determining the required level of stochastic variation is performed by coupling the inverse ANN with a forward ANN that receives the diffusion coefficient as input and returns the concentration-time curve as output. Combined together, forward-inverse ANNs enable computationally inexperienced users to obtain accurate and fast estimation of the diffusion coefficients of cartilage zones. The diffusion coefficients estimated using the proposed approach are compared with those determined using direct scanning of the parameter space as the optimization approach. It has been shown that both approaches yield comparable results. Copyright © 2016 Elsevier Ltd. All rights reserved.

Effect of diffuser vane shape on the performance of a centrifugal compressor stage

NASA Astrophysics Data System (ADS)

Reddy, T. Ch Siva; Ramana Murty, G. V.; Prasad, M. V. S. S. S. M.

2014-04-01

The present paper reports the results of experimental investigations on the effect of diffuser vane shape on the performance of a centrifugal compressor stage. These studies were conducted on the chosen stage having a backward curved impeller of 500 mm tip diameter and 24.5 mm width and its design flow coefficient is ϕd=0.0535. Three different low solidity diffuser vane shapes namely uncambered aerofoil, constant thickness flat plate and circular arc cambered constant thickness plate were chosen as the variants for diffuser vane shape and all the three shapes have the same thickness to chord ratio (t/c=0.1). Flow coefficient, polytropic efficiency, total head coefficient, power coefficient and static pressure recovery coefficient were chosen as the parameters for evaluating the effect of diffuser vane shape on the stage performance. The results show that there is reasonable improvement in stage efficiency and total head coefficient with the use of the chosen diffuser vane shapes as compared to conventional vaneless diffuser. It is also noticed that the aero foil shaped LSD has shown better performance when compared to flat plate and circular arc profiles. The aerofoil vane shape of the diffuser blade is seen to be tolerant over a considerable range of incidence.

Application of the compensated Arrhenius formalism to self-diffusion: implications for ionic conductivity and dielectric relaxation.

PubMed

Petrowsky, Matt; Frech, Roger

2010-07-08

Self-diffusion coefficients are measured from -5 to 80 degrees C in a series of linear alcohols using pulsed field gradient NMR. The temperature dependence of these data is studied using a compensated Arrhenius formalism that assumes an Arrhenius-like expression for the diffusion coefficient; however, this expression includes a dielectric constant dependence in the exponential prefactor. Scaling temperature-dependent diffusion coefficients to isothermal diffusion coefficients so that the exponential prefactors cancel results in calculated energies of activation E(a). The exponential prefactor is determined by dividing the temperature-dependent diffusion coefficients by the Boltzmann term exp(-E(a)/RT). Plotting the prefactors versus the dielectric constant places the data on a single master curve. This procedure is identical to that previously used to study the temperature dependence of ionic conductivities and dielectric relaxation rate constants. The energies of activation determined from self-diffusion coefficients in the series of alcohols are strikingly similar to those calculated for the same series of alcohols from both dielectric relaxation rate constants and ionic conductivities of dilute electrolytes. The experimental results are described in terms of an activated transport mechanism that is mediated by relaxation of the solution molecules. This microscopic picture of transport is postulated to be common to diffusion, dielectric relaxation, and ionic transport.

Calculation method for steady-state pollutant concentration in mixing zones considering variable lateral diffusion coefficient.

PubMed

Wu, Wen; Wu, Zhouhu; Song, Zhiwen

2017-07-01

Prediction of the pollutant mixing zone (PMZ) near the discharge outfall in Huangshaxi shows large error when using the methods based on the constant lateral diffusion assumption. The discrepancy is due to the lack of consideration of the diffusion coefficient variation. The variable lateral diffusion coefficient is proposed to be a function of the longitudinal distance from the outfall. Analytical solution of the two-dimensional advection-diffusion equation of a pollutant is derived and discussed. Formulas to characterize the geometry of the PMZ are derived based on this solution, and a standard curve describing the boundary of the PMZ is obtained by proper choices of the normalization scales. The change of PMZ topology due to the variable diffusion coefficient is then discussed using these formulas. The criterion of assuming the lateral diffusion coefficient to be constant without large error in PMZ geometry is found. It is also demonstrated how to use these analytical formulas in the inverse problems including estimating the lateral diffusion coefficient in rivers by convenient measurements, and determining the maximum allowable discharge load based on the limitations of the geometrical scales of the PMZ. Finally, applications of the obtained formulas to onsite PMZ measurements in Huangshaxi present excellent agreement.

Optical absorption characteristics in the assessment of powder phosphor-based x-ray detectors: from nano- to micro-scale.

PubMed

Liaparinos, P F

2015-11-21

X-ray phosphor-based detectors have enormously improved the quality of medical imaging examinations through the optimization of optical diffusion. In recent years, with the development of science and technology in the field of materials, improved powder phosphors require structural and optical properties that contribute to better optical signal propagation. The purpose of this paper was to provide a quantitative and qualitative understanding of the optical absorption characteristics in the assessment of powder phosphor-based detectors (from nano- scale up to micro-scale). Variations on the optical absorption parameters (i.e. the light extinction coefficient [Formula: see text] and the percentage probability of light absorption p%) were evaluated based on Mie calculations examining a wide range of light wavelengths, particle refractive indices and sizes. To model and assess the effects of the aforementioned parameters on optical diffusion, Monte Carlo simulation techniques were employed considering: (i) phosphors of different layer thickness, 100 μm (thin layer) and 300 μm (thick layer), respectively, (ii) light extinction coefficient values, 1, 3 and 6 μm(-1), and (iii) percentage probability of light absorption p% in the range 10(-4)-10(-2). Results showed that the [Formula: see text] coefficient is high for phosphor grains in the submicron scale and for low light wavelengths. At higher wavelengths (above 650 nm), optical quanta follow approximately similar depths until interaction for grain diameter 500 nm and 1 μm. Regarding the variability of the refractive index, high variations of the [Formula: see text] coefficient occurred above 1.6. Furthermore, results derived from Monte Carlo modeling showed that high spatial resolution phosphors can be accomplished by increasing the [Formula: see text] parameter. More specifically, the FWHM was found to decrease (i.e. higher resolution): (i) 4.8% at 100 μm and (ii) 9.5%, at 300 μm layer thickness. This study attempted to examine the role of the optical absorption parameters on optical diffusion studies. A significant outcome of the present investigation was that the improvement of phosphor spatial resolution without decreasing the light collection efficiency too much can be better achieved by increasing the parameter [Formula: see text] rather than the parameter p%.

Density profiles around A+B→C reaction-diffusion fronts in partially miscible systems: A general classification.

PubMed

Loodts, V; Trevelyan, P M J; Rongy, L; De Wit, A

2016-10-01

Various spatial density profiles can develop in partially miscible stratifications when a phase A dissolves with a finite solubility into a host phase containing a dissolved reactant B. We investigate theoretically the impact of an A+B→C reaction on such density profiles in the host phase and classify them in a parameter space spanned by the ratios of relative contributions to density and diffusion coefficients of the chemical species. While the density profile is either monotonically increasing or decreasing in the nonreactive case, reactions combined with differential diffusivity can create eight different types of density profiles featuring up to two extrema in density, at the reaction front or below it. We use this framework to predict various possible hydrodynamic instability scenarios inducing buoyancy-driven convection around such reaction fronts when they propagate parallel to the gravity field.

Synchronization of hybrid coupled reaction-diffusion neural networks with time delays via generalized intermittent control with spacial sampled-data.

PubMed

Lu, Binglong; Jiang, Haijun; Hu, Cheng; Abdurahman, Abdujelil

2018-05-04

The exponential synchronization of hybrid coupled reaction-diffusion neural networks with time delays is discussed in this article. At first, a generalized intermittent control with spacial sampled-data is introduced, which is intermittent in time and data sampling in space. This type of control strategy not only can unify the traditional periodic intermittent control and the aperiodic case, but also can lower the update rate of the controller in both temporal and spatial domains. Next, based on the designed control protocol and the Lyapunov-Krasovskii functional approach, some novel and readily verified criteria are established to guarantee the exponential synchronization of the considered networks. These criteria depend on the diffusion coefficients, coupled strengths, time delays as well as control parameters. Finally, the effectiveness of the proposed control strategy is shown by a numerical example. Copyright © 2018 Elsevier Ltd. All rights reserved.

Resistivity bound for hydrodynamic bad metals

PubMed Central

Lucas, Andrew; Hartnoll, Sean A.

2017-01-01

We obtain a rigorous upper bound on the resistivity ρ of an electron fluid whose electronic mean free path is short compared with the scale of spatial inhomogeneities. When such a hydrodynamic electron fluid supports a nonthermal diffusion process—such as an imbalance mode between different bands—we show that the resistivity bound becomes ρ≲AΓ. The coefficient A is independent of temperature and inhomogeneity lengthscale, and Γ is a microscopic momentum-preserving scattering rate. In this way, we obtain a unified mechanism—without umklapp—for ρ∼T2 in a Fermi liquid and the crossover to ρ∼T in quantum critical regimes. This behavior is widely observed in transition metal oxides, organic metals, pnictides, and heavy fermion compounds and has presented a long-standing challenge to transport theory. Our hydrodynamic bound allows phonon contributions to diffusion constants, including thermal diffusion, to directly affect the electrical resistivity. PMID:29073054

Developing semi-analytical solution for multiple-zone transient storage model with spatially non-uniform storage

NASA Astrophysics Data System (ADS)

Deng, Baoqing; Si, Yinbing; Wang, Jia

2017-12-01

Transient storages may vary along the stream due to stream hydraulic conditions and the characteristics of storage. Analytical solutions of transient storage models in literature didn't cover the spatially non-uniform storage. A novel integral transform strategy is presented that simultaneously performs integral transforms to the concentrations in the stream and in storage zones by using the single set of eigenfunctions derived from the advection-diffusion equation of the stream. The semi-analytical solution of the multiple-zone transient storage model with the spatially non-uniform storage is obtained by applying the generalized integral transform technique to all partial differential equations in the multiple-zone transient storage model. The derived semi-analytical solution is validated against the field data in literature. Good agreement between the computed data and the field data is obtained. Some illustrative examples are formulated to demonstrate the applications of the present solution. It is shown that solute transport can be greatly affected by the variation of mass exchange coefficient and the ratio of cross-sectional areas. When the ratio of cross-sectional areas is big or the mass exchange coefficient is small, more reaches are recommended to calibrate the parameter.

Towards a more consistent picture of isopycnal mixing in climate models

NASA Astrophysics Data System (ADS)

Gnanadesikan, A.; Pradal, M. A. S.; Koszalka, I.; Abernathey, R. P.

2014-12-01

The stirring of tracers by mesoscale eddies along isopycnal surfaces is often represented in coarse-resolution models by the Redi diffusion parameter ARedi. Theoretical treatments of ARedi often assume it should scale as the eddy energy or the growth rate of mesoscale eddies,. producing a picture where it is high in boundary currents and low )of order a few hundred m2/s) in the gyre interiors. However, observational estimates suggest that ARedi should be very large (of order thousands of m2/s) in the gyre interior. We present results of recent simulations comparing a range of spatially constant values ARedi (with values of 400, 800, 1200 and 2400 m2/s) to a spatially resolved estimate based on altimetry and a zonally averaged version of the same estimate. In general, increasing the ARedi coefficient destratifies and warms the high latitudes. Relative to our control simulation, the spatially dependent coefficient is lower in the Southern Ocean, but high in the North Pacific, and so the temperature changes mirror this. We also examine the response of ocean hypoxia to these changes. In general, the zonally averaged version of the altimetry-based estimate of ARedi does not capture the full 2d representation.

Diffusion in different models of active Brownian motion

NASA Astrophysics Data System (ADS)

Lindner, B.; Nicola, E. M.

2008-04-01

Active Brownian particles (ABP) have served as phenomenological models of self-propelled motion in biology. We study the effective diffusion coefficient of two one-dimensional ABP models (simplified depot model and Rayleigh-Helmholtz model) differing in their nonlinear friction functions. Depending on the choice of the friction function the diffusion coefficient does or does not attain a minimum as a function of noise intensity. We furthermore discuss the case of an additional bias breaking the left-right symmetry of the system. We show that this bias induces a drift and that it generally reduces the diffusion coefficient. For a finite range of values of the bias, both models can exhibit a maximum in the diffusion coefficient vs. noise intensity.

Ionic diffusion and space charge polarization in structural characterization of biological tissues.

PubMed

Jastrzebska, M; Kocot, A

2004-06-01

In this study, a new approach to the analysis of the low-frequency (1-10(7) Hz) dielectric spectra of biological tissue, has been described. The experimental results are interpreted in terms of ionic diffusion and space charge polarization according to Sawada's theory. The new presentation of dielectric spectra, i.e. ([Formula: see text]) [Formula: see text] has been used. This method results in peaks which are narrower and better resolved than both the measured loss peaks and an alternative loss quantity [Formula: see text]. The presented method and Sawada's expression have been applied to the analysis of changes in the spatial molecular structure of a collagen fibril network in pericardium tissue exposed to glutaraldehyde (GA), with respect to the native tissue. The diffusion coefficient of ions was estimated on the basis of a dielectric dispersion measurement for an aqueous NaCl solution with a well-calibrated distance between the electrodes. The fitting procedure of a theoretical function to the experimental data allowed us to determine three diffusive relaxation regions with three structural distance parameters d(s), describing the spatial arrangement of collagen fibrils in pericardium tissue. It has been found that a significant decrease in the structural distance d(s) from 87 nm to 45 nm may correspond to a reduction in the interfibrillar distance within GA cross-linked tissue.

MEASUREMENT OF EFFECTIVE AIR DIFFUSION COEFFICIENTS FOR TRICHLOROETHENE IN UNDISTURBED SOIL CORES. (R826162)

EPA Science Inventory

Abstract

In this study, we measure effective diffusion coefficients for trichloroethene in undisturbed soil samples taken from Picatinny Arsenal, New Jersey. The measured effective diffusion coefficients ranged from 0.0053 to 0.0609 cm²/s over a range of air...

Thermodiffusion, molecular diffusion and Soret coefficient of binary and ternary mixtures of n-hexane, n-dodecane and toluene.

PubMed

Alonso de Mezquia, David; Wang, Zilin; Lapeira, Estela; Klein, Michael; Wiegand, Simone; Mounir Bou-Ali, M

2014-11-01

In this study, the thermodiffusion, molecular diffusion, and Soret coefficients of 12 binary mixtures composed of toluene, n-hexane and n-dodecane in the whole range of concentrations at atmospheric pressure and temperatures of 298.15 K and 308.15 K have been determined. The experimental measurements have been carried out using the Thermogravitational Column, the Sliding Symmetric Tubes and the Thermal Diffusion Forced Rayleigh Scattering techniques. The results obtained using the different techniques show a maximum deviation of 9% for the thermodiffusion coefficient, 8% for the molecular diffusion coefficient and 2% for the Soret coefficient. For the first time we report a decrease of the thermodiffusion coefficient with increasing ratio of the thermal expansion coefficient and viscosity for a binary mixture of an organic ring compound with a short n-alkane. This observation is discussed in terms of interactions between the different components. Additionally, the thermogravitational technique has been used to measure the thermodiffusion coefficients of four ternary mixtures consisting of toluene, n-hexane and n-dodecane at 298.15 K. In order to complete the study, the values obtained for the molecular diffusion coefficient in binary mixtures, and the thermodiffusion coefficient of binary and ternary mixtures have been compared with recently derived correlations.

Confined active Brownian particles: theoretical description of propulsion-induced accumulation

NASA Astrophysics Data System (ADS)

Das, Shibananda; Gompper, Gerhard; Winkler, Roland G.

2018-01-01

The stationary-state distribution function of confined active Brownian particles (ABPs) is analyzed by computer simulations and analytical calculations. We consider a radial harmonic as well as an anharmonic confinement potential. In the simulations, the ABP is propelled with a prescribed velocity along a body-fixed direction, which is changing in a diffusive manner. For the analytical approach, the Cartesian components of the propulsion velocity are assumed to change independently; active Ornstein-Uhlenbeck particle (AOUP). This results in very different velocity distribution functions. The analytical solution of the Fokker-Planck equation for an AOUP in a harmonic potential is presented and a conditional distribution function is provided for the radial particle distribution at a given magnitude of the propulsion velocity. This conditional probability distribution facilitates the description of the coupling of the spatial coordinate and propulsion, which yields activity-induced accumulation of particles. For the anharmonic potential, a probability distribution function is derived within the unified colored noise approximation. The comparison of the simulation results with theoretical predictions yields good agreement for large rotational diffusion coefficients, e.g. due to tumbling, even for large propulsion velocities (Péclet numbers). However, we find significant deviations already for moderate Péclet number, when the rotational diffusion coefficient is on the order of the thermal one.

Mass transport in polyelectrolyte solutions

NASA Astrophysics Data System (ADS)

Schipper, F. J. M.; Leyte, J. C.

1999-02-01

The self-diffusion coefficients of the three components of a salt-free heavy-water solution of polymethacrylic acid, completely neutralized with tetra-methylammonium hydroxide, were measured over a broad concentration range. Three concentration regions were observed for the self-diffusion of both the polyions and the counterions. At polyion concentrations below 0.01 mol monomer kg-1, the dilute concentration regime for the polymer, the polyion self-diffusion coefficient approaches the self-diffusion coefficient of a freely diffusing rod upon dilution. At polyelectrolyte concentrations above 0.1 mol monomer kg-1, the self-diffusion coefficients of the solvent, the counterions and the polymer decreased with concentration, suggesting that this decrease is due to a topological constraint on the motions of the components. In the intermediate-concentration region, the self-diffusion coefficients of the polyions and the counterions are independent of the concentration. The polyion dynamic behaviour is, in the intermediate- and high-concentration regions, reasonably well described by that of a hard sphere, with a radius of 3.7 nm. A correct prediction for the solvent dynamics is given by the obstruction effect of this hard sphere on the solvent. The relative counterion self-diffusion coefficient is predicted almost quantitatively over the entire concentration range with the Poisson-Boltzmann-Smoluchowski model for the spherical cell, provided that the sphere radius and the number of charges are chosen appropriately (approximately the number of charges in a persistence length). Using this model, the dependence of the counterion self-diffusion coefficient on the ionic strength, polyion concentration and counterion radius is calculated quantitatively over a large concentration range.

Influence of diffuse reflectance measurement accuracy on the scattering coefficient in determination of optical properties with integrating sphere optics (a secondary publication).

PubMed

Horibe, Takuro; Ishii, Katsunori; Fukutomi, Daichi; Awazu, Kunio

2015-12-30

An estimation error of the scattering coefficient of hemoglobin in the high absorption wavelength range has been observed in optical property calculations of blood-rich tissues. In this study, the relationship between the accuracy of diffuse reflectance measurement in the integrating sphere and calculated scattering coefficient was evaluated with a system to calculate optical properties combined with an integrating sphere setup and the inverse Monte Carlo simulation. Diffuse reflectance was measured with the integrating sphere using a small incident port diameter and optical properties were calculated. As a result, the estimation error of the scattering coefficient was improved by accurate measurement of diffuse reflectance. In the high absorption wavelength range, the accuracy of diffuse reflectance measurement has an effect on the calculated scattering coefficient.

A Reaction-Diffusion Model of Vector-Borne Disease with Periodic Delays

NASA Astrophysics Data System (ADS)

Wu, Ruiwen; Zhao, Xiao-Qiang

2018-06-01

A vector-borne disease is caused by a range of pathogens and transmitted to hosts through vectors. To investigate the multiple effects of the spatial heterogeneity, the temperature sensitivity of extrinsic incubation period and intrinsic incubation period, and the seasonality on disease transmission, we propose a nonlocal reaction-diffusion model of vector-borne disease with periodic delays. We introduce the basic reproduction number R_0 for this model and then establish a threshold-type result on its global dynamics in terms of R_0 . In the case where all the coefficients are constants, we also prove the global attractivity of the positive constant steady state when R_0>1 . Numerically, we study the malaria transmission in Maputo Province, Mozambique.

Holographic investigation of silver electromigration in nano-sized As2S3 films

NASA Astrophysics Data System (ADS)

Sainov, S.; Todorov, R.; Bodurov, I.; Yovcheva, Temenuzhka

2013-10-01

Holographic gratings with a diffraction efficiency (DE) greater than 8% and a spatial resolution of 2237 mm-1 are recorded in very thin As2S3 films with a thickness of 100 nm. Silver photo-diffusion is observed during the holographic recording process while applying a corona discharge. We use the method of holographic grating relaxation spectroscopy (forced Rayleigh scattering) based on the evanescent waves to determine that the silver diffusion coefficient in the thin As2S3 film is in the range of (0.9-10.3) × 10-13 cm2 s-1 depending on the corona charge polarity. This work is dedicated to the 90th anniversary of the birth of Academician Jordan Malinowski.

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

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

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

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

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

NASA Astrophysics Data System (ADS)

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

2018-02-01

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

The Analytical Solution of the Transient Radial Diffusion Equation with a Nonuniform Loss Term.

NASA Astrophysics Data System (ADS)

Loridan, V.; Ripoll, J. F.; De Vuyst, F.

2017-12-01

Many works have been done during the past 40 years to perform the analytical solution of the radial diffusion equation that models the transport and loss of electrons in the magnetosphere, considering a diffusion coefficient proportional to a power law in shell and a constant loss term. Here, we propose an original analytical method to address this challenge with a nonuniform loss term. The strategy is to match any L-dependent electron losses with a piecewise constant function on M subintervals, i.e., dealing with a constant lifetime on each subinterval. Applying an eigenfunction expansion method, the eigenvalue problem becomes presently a Sturm-Liouville problem with M interfaces. Assuming the continuity of both the distribution function and its first spatial derivatives, we are able to deal with a well-posed problem and to find the full analytical solution. We further show an excellent agreement between both the analytical solutions and the solutions obtained directly from numerical simulations for different loss terms of various shapes and with a diffusion coefficient DLL L6. We also give two expressions for the required number of eigenmodes N to get an accurate snapshot of the analytical solution, highlighting that N is proportional to 1/√t0, where t0 is a time of interest, and that N increases with the diffusion power. Finally, the equilibrium time, defined as the time to nearly reach the steady solution, is estimated by a closed-form expression and discussed. Applications to Earth and also Jupiter and Saturn are discussed.

Determination of pollutant diffusion coefficients in naturally formed biofilms using a single tube extractive membrane bioreactor

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

Zhang, S.F.; Splendiani, A.; Freitas dos Santos, L.M.

A novel technique has been used to determine the effective diffusion coefficients for 1,1,2-trichloroethane (TCE), a nonreacting tracer, in biofilms growing on the external surface of a silicone rubber membrane tube during degradation of 1,2-dichloroethane (DCE) by Xanthobacter autotrophicus GJ10 and monochlorobenzene (MCB) by Pseudomonas JS150. Experiments were carried out in a single tube extractive membrane bioreactor (STEMB), whose configuration makes it possible to measure the transmembrane flux of substrates. A video imaging technique (VIT) was employed for in situ biofilm thickness measurement and recording. Diffusion coefficients of TCE in the biofilms and TCE mass transfer coefficients in the liquidmore » films adjacent to the biofilms were determined simultaneously using a resistances-in-series diffusion model. It was found that the flux and overall mass transfer coefficient of TCE decrease with increasing biofilm thickness, showing the importance of biofilm diffusion on the mass transfer process. Similar fluxes were observed for the nonreacting tracer (TCE) and the reactive substrates (MCB or DCE), suggesting that membrane-attached biofilm systems can be rate controlled primarily by substrate diffusion. The TCE diffusion coefficient in the JS150 biofilm appeared to be dependent on biofilm thickness, decreasing markedly for biofilm thicknesses of >1 mm. The values of the TCE diffusion coefficients in the JS150 biofilms <1-mm thick are approximately twice those in water and fall to around 30% of the water value for biofilms >1-mm thick.« less

k-Space Image Correlation Spectroscopy: A Method for Accurate Transport Measurements Independent of Fluorophore Photophysics

PubMed Central

Kolin, David L.; Ronis, David; Wiseman, Paul W.

2006-01-01

We present the theory and application of reciprocal space image correlation spectroscopy (kICS). This technique measures the number density, diffusion coefficient, and velocity of fluorescently labeled macromolecules in a cell membrane imaged on a confocal, two-photon, or total internal reflection fluorescence microscope. In contrast to r-space correlation techniques, we show kICS can recover accurate dynamics even in the presence of complex fluorophore photobleaching and/or “blinking”. Furthermore, these quantities can be calculated without nonlinear curve fitting, or any knowledge of the beam radius of the exciting laser. The number densities calculated by kICS are less sensitive to spatial inhomogeneity of the fluorophore distribution than densities measured using image correlation spectroscopy. We use simulations as a proof-of-principle to show that number densities and transport coefficients can be extracted using this technique. We present calibration measurements with fluorescent microspheres imaged on a confocal microscope, which recover Stokes-Einstein diffusion coefficients, and flow velocities that agree with single particle tracking measurements. We also show the application of kICS to measurements of the transport dynamics of α5-integrin/enhanced green fluorescent protein constructs in a transfected CHO cell imaged on a total internal reflection fluorescence microscope using charge-coupled device area detection. PMID:16861272

Diffusion and plasticity at high temperature

NASA Astrophysics Data System (ADS)

Philibert, J.

1991-06-01

High temperature plastic deformation requires atomic migration whatever the mechanism of deformation. The constitutive equations contain a diffusion coefficient and the deformation rate follows an Arrhenius law. This paper will only discuss the case of viscous creep in order to elucidate the nature of the diffusion processes and the expression of the diffusion coefficient involved in alloys or compounds. La déformation plastique à haute température met en jeu des migrations atomiques, quel que soit le mécanisme de déformation. Les lois de comportement contiennent donc un coefficient de diffusion et la vitesse de déformation obéit à une loi d'Arrhenius. Dans cet article, qui ne conceme qu'un seul type de déformation, lefluage visqueux, on s'efforce de préciser la nature des processus de diffusion et du coefficient de diffusion mis en jeu dans le cas des alliages et des composés.

Theoretical and Experimental Investigation of the Translational Diffusion of Proteins in the Vicinity of Temperature-Induced Unfolding Transition.

PubMed

Molchanov, Stanislav; Faizullin, Dzhigangir A; Nesmelova, Irina V

2016-10-06

Translational diffusion is the most fundamental form of transport in chemical and biological systems. The diffusion coefficient is highly sensitive to changes in the size of the diffusing species; hence, it provides important information on the variety of macromolecular processes, such as self-assembly or folding-unfolding. Here, we investigate the behavior of the diffusion coefficient of a macromolecule in the vicinity of heat-induced transition from folded to unfolded state. We derive the equation that describes the diffusion coefficient of the macromolecule in the vicinity of the transition and use it to fit the experimental data from pulsed-field-gradient nuclear magnetic resonance (PFG NMR) experiments acquired for two globular proteins, lysozyme and RNase A, undergoing temperature-induced unfolding. A very good qualitative agreement between the theoretically derived diffusion coefficient and experimental data is observed.

Three FORTRAN programs for finite-difference solutions to binary diffusion in one and two phases with composition-and time-dependent diffusion coefficients

USGS Publications Warehouse

Sanford, R.F.

1982-01-01

Geological examples of binary diffusion are numerous. They are potential indicators of the duration and rates of geological processes. Analytical solutions to the diffusion equations generally do not allow for variable diffusion coefficients, changing boundary conditions, and impingement of diffusion fields. The three programs presented here are based on Crank-Nicholson finite-difference approximations, which can take into account these complicating factors. Program 1 describes the diffusion of a component into an initially homogeneous phase that has a constant surface composition. Specifically it is written for Fe-Mg exchange in olivine at oxygen fugacities appropriate for the lunar crust, but other components, phases, or fugacities may be substituted by changing the values of the diffusion coefficient. Program 2 simulates the growth of exsolution lamellae. Program 3 describes the growth of reaction rims. These two programs are written for pseudobinary Ca-(Mg, Fe) exchange in pyroxenes. In all three programs, the diffusion coefficients and boundary conditions can be varied systematically with time. To enable users to employ widely different numerical values for diffusion coefficients and diffusion distance, the grid spacing in the space dimension and the increment by which the grid spacing in the time dimension is increased at each time step are input constants that can be varied each time the programs are run to yield a solution of the desired accuracy. ?? 1982.

Self diffusion of interacting membrane proteins.

PubMed Central

Abney, J R; Scalettar, B A; Owicki, J C

1989-01-01

A two-dimensional version of the generalized Smoluchowski equation is used to analyze the time (or distance) dependent self diffusion of interacting membrane proteins in concentrated membrane systems. This equation provides a well established starting point for descriptions of the diffusion of particles that interact through both direct and hydrodynamic forces; in this initial work only the effects of direct interactions are explicitly considered. Data describing diffusion in the presence of hard-core repulsions, soft repulsions, and soft repulsions with weak attractions are presented. The effect that interactions have on the self-diffusion coefficient of a real protein molecule from mouse liver gap junctions is also calculated. The results indicate that self diffusion is always inhibited by direct interactions; this observation is interpreted in terms of the caging that will exist at finite protein concentration. It is also noted that, over small distance scales, the diffusion coefficient is determined entirely by the very strong Brownian forces; therefore, as a function of displacement the self-diffusion coefficient decays (rapidly) from its value at infinite dilution to its steady-state interaction-averaged value. The steady-state self-diffusion coefficient describes motion over distance scales that range from approximately 10 nm to cellular dimensions and is the quantity measured in fluorescence recovery after photobleaching experiments. The short-ranged behavior of the diffusion coefficient is important on the interparticle-distance scale and may therefore influence the rate at which nearest-neighbor collisional processes take place. The hard-disk theoretical results presented here are in excellent agreement with lattice Monte-Carlo results obtained by other workers. The concentration dependence of experimentally measured diffusion coefficients of antibody-hapten complexes bound to the membrane surface is consistent with that predicted by the theory. The variation in experimental diffusion coefficients of integral membrane proteins is greater than that predicted by the theory, and may also reflect protein-induced perturbations in membrane viscosity. PMID:2720077

Determination of malignancy and characterization of hepatic tumor type with diffusion-weighted magnetic resonance imaging: comparison of apparent diffusion coefficient and intravoxel incoherent motion-derived measurements.

PubMed

Doblas, Sabrina; Wagner, Mathilde; Leitao, Helena S; Daire, Jean-Luc; Sinkus, Ralph; Vilgrain, Valérie; Van Beers, Bernard E

2013-10-01

The objective of this study was to compare the value of the apparent diffusion coefficient (ADC) determined with 3 b values and the intravoxel incoherent motion (IVIM)-derived parameters in the determination of malignancy and characterization of hepatic tumor type. Seventy-six patients with 86 solid hepatic lesions, including 8 hemangiomas, 20 lesions of focal nodular hyperplasia, 9 adenomas, 30 hepatocellular carcinomas, 13 metastases, and 6 cholangiocarcinomas, were assessed in this prospective study. Diffusion-weighted images were acquired with 11 b values to measure the ADCs (with b = 0, 150, and 500 s/mm) and the IVIM-derived parameters, namely, the pure diffusion coefficient and the perfusion-related diffusion fraction and coefficient. The diffusion parameters were compared between benign and malignant tumors and between tumor types, and their diagnostic value in identifying tumor malignancy was assessed. The apparent and pure diffusion coefficients were significantly higher in benign than in malignant tumors (benign: 2.32 [0.87] × 10 mm/s and 1.42 [0.37] × 10 mm/s vs malignant: 1.64 [0.51] × 10 mm/s and 1.14 [0.28] × 10 mm/s, respectively; P < 0.0001 and P = 0.0005), whereas the perfusion-related diffusion parameters did not differ significantly between the 2 groups. The apparent and pure diffusion coefficients provided similar accuracy in assessing tumor malignancy (areas under the receiver operating characteristic curve of 0.770 and 0.723, respectively). In the multigroup analysis, the ADC was found to be significantly higher in hemangiomas than in hepatocellular carcinomas, metastases, and cholangiocarcinomas. In the same manner, it was higher in lesions of focal nodular hyperplasia than in metastases and cholangiocarcinomas. However, the pure diffusion coefficient was significantly higher only in hemangiomas versus hepatocellular and cholangiocellular carcinomas. Compared with the ADC, the diffusion parameters derived from the IVIM model did not improve the determination of malignancy and characterization of hepatic tumor type.

Maxwell-Stefan diffusion coefficient estimation for ternary systems: an ideal ternary alcohol system.

PubMed

Allie-Ebrahim, Tariq; Zhu, Qingyu; Bräuer, Pierre; Moggridge, Geoff D; D'Agostino, Carmine

2017-06-21

The Maxwell-Stefan model is a popular diffusion model originally developed to model diffusion of gases, which can be considered thermodynamically ideal mixtures, although its application has been extended to model diffusion in non-ideal liquid mixtures as well. A drawback of the model is that it requires the Maxwell-Stefan diffusion coefficients, which are not based on measurable quantities but they have to be estimated. As a result, numerous estimation methods, such as the Darken model, have been proposed to estimate these diffusion coefficients. However, the Darken model was derived, and is only well defined, for binary systems. This model has been extended to ternary systems according to two proposed forms, one by R. Krishna and J. M. van Baten, Ind. Eng. Chem. Res., 2005, 44, 6939-6947 and the other by X. Liu, T. J. H. Vlugt and A. Bardow, Ind. Eng. Chem. Res., 2011, 50, 10350-10358. In this paper, the two forms have been analysed against the ideal ternary system of methanol/butan-1-ol/propan-1-ol and using experimental values of self-diffusion coefficients. In particular, using pulsed gradient stimulated echo nuclear magnetic resonance (PGSTE-NMR) we have measured the self-diffusion coefficients in various methanol/butan-1-ol/propan-1-ol mixtures. The experimental values of self-diffusion coefficients were then used as the input data required for the Darken model. The predictions of the two proposed multicomponent forms of this model were then compared to experimental values of mutual diffusion coefficients for the ideal alcohol ternary system. This experimental-based approach showed that the Liu's model gives better predictions compared to that of Krishna and van Baten, although it was only accurate to within 26%. Nonetheless, the multicomponent Darken model in conjunction with self-diffusion measurements from PGSTE-NMR represents an attractive method for a rapid estimation of mutual diffusion in multicomponent systems, especially when compared to exhaustive MD simulations.

Experimental study of mass diffusion coefficients of hydrogen in dimethyl phosphate and n-heptane

NASA Astrophysics Data System (ADS)

Guo, Y.; Zhu, L. K.; Zhang, Y. P.; Liu, J.; Guo, J. S.

2017-11-01

In this study, a laser holographic interferometer experimental system was developed for studying the gas-liquid mass diffusion coefficient. Then the experimental system’s uncertainty was analyzed to be at most ±0.2% therefore, this system was reliable. The mass diffusion coefficient of hydrogen in dimethyl phosphate and n-heptane was measured at atmospheric pressure in the temperature range of 273.15-338.15 K. Then, the experimental data were used to fit the correlations of the mass diffusion coefficient of hydrogen in dimethyl phosphate and n-heptane with temperature.

Chromatographic determination of the diffusion coefficients of light hydrocarbons in polymers

NASA Astrophysics Data System (ADS)

Yakubenko, E. E.; Korolev, A. A.; Chapala, P. P.; Bermeshev, M. V.; Kanat'eva, A. Yu.; Kurganov, A. A.

2017-01-01

Gas-chromatographic determination of the diffusion coefficients that allows for the compressibility of the mobile phase has been suggested. The diffusion coefficients were determined for light hydrocarbons C1-C4 in four polymers with a high free volume, which are candidates for use as gas-separating membranes. The diffusion coefficients calculated from chromatographic data were shown to be one or two orders of magnitude smaller than the values obtained by the membrane method. This may be due to the presence of an additional flow through the membrane caused by the pressure gradient across the membrane in membrane methods.

Multimodal optical setup based on spectrometer and cameras combination for biological tissue characterization with spatially modulated illumination

NASA Astrophysics Data System (ADS)

Baruch, Daniel; Abookasis, David

2017-04-01

The application of optical techniques as tools for biomedical research has generated substantial interest for the ability of such methodologies to simultaneously measure biochemical and morphological parameters of tissue. Ongoing optimization of optical techniques may introduce such tools as alternative or complementary to conventional methodologies. The common approach shared by current optical techniques lies in the independent acquisition of tissue's optical properties (i.e., absorption and reduced scattering coefficients) from reflected or transmitted light. Such optical parameters, in turn, provide detailed information regarding both the concentrations of clinically relevant chromophores and macroscopic structural variations in tissue. We couple a noncontact optical setup with a simple analysis algorithm to obtain absorption and scattering coefficients of biological samples under test. Technically, a portable picoprojector projects serial sinusoidal patterns at low and high spatial frequencies, while a spectrometer and two independent CCD cameras simultaneously acquire the reflected diffuse light through a single spectrometer and two separate CCD cameras having different bandpass filters at nonisosbestic and isosbestic wavelengths in front of each. This configuration fills the gaps in each other's capabilities for acquiring optical properties of tissue at high spectral and spatial resolution. Experiments were performed on both tissue-mimicking phantoms as well as hands of healthy human volunteers to quantify their optical properties as proof of concept for the present technique. In a separate experiment, we derived the optical properties of the hand skin from the measured diffuse reflectance, based on a recently developed camera model. Additionally, oxygen saturation levels of tissue measured by the system were found to agree well with reference values. Taken together, the present results demonstrate the potential of this integrated setup for diagnostic and research applications.

Buoyancy-driven instabilities around miscible A+B→C reaction fronts: a general classification.

PubMed

Trevelyan, P M J; Almarcha, C; De Wit, A

2015-02-01

Upon contact between miscible solutions of reactants A and B along a horizontal interface in the gravity field, various buoyancy-driven instabilities can develop when an A+B→C reaction takes place and the density varies with the concentrations of the various chemicals. To classify the possible convective instability scenarios, we analyze the spatial dependence of the large time asymptotic density profiles as a function of the key parameters of the problem, which are the ratios of diffusion coefficients and of solutal expansion coefficients of species A, B, and C. We find that 62 different density profiles can develop in the reactive problem, whereas only 6 of them can be obtained in the nonreactive one.

Field-scale effective matrix diffusion coefficient for fractured rock: results from literature survey.

PubMed

Zhou, Quanlin; Liu, Hui-Hai; Molz, Fred J; Zhang, Yingqi; Bodvarsson, Gudmundur S

2007-08-15

Matrix diffusion is an important mechanism for solute transport in fractured rock. We recently conducted a literature survey on the effective matrix diffusion coefficient, D(m)(e), a key parameter for describing matrix diffusion processes at the field scale. Forty field tracer tests at 15 fractured geologic sites were surveyed and selected for the study, based on data availability and quality. Field-scale D(m)(e) values were calculated, either directly using data reported in the literature, or by reanalyzing the corresponding field tracer tests. The reanalysis was conducted for the selected tracer tests using analytic or semi-analytic solutions for tracer transport in linear, radial, or interwell flow fields. Surveyed data show that the scale factor of the effective matrix diffusion coefficient (defined as the ratio of D(m)(e) to the lab-scale matrix diffusion coefficient, D(m), of the same tracer) is generally larger than one, indicating that the effective matrix diffusion coefficient in the field is comparatively larger than the matrix diffusion coefficient at the rock-core scale. This larger value can be attributed to the many mass-transfer processes at different scales in naturally heterogeneous, fractured rock systems. Furthermore, we observed a moderate, on average trend toward systematic increase in the scale factor with observation scale. This trend suggests that the effective matrix diffusion coefficient is likely to be statistically scale-dependent. The scale-factor value ranges from 0.5 to 884 for observation scales from 5 to 2000 m. At a given scale, the scale factor varies by two orders of magnitude, reflecting the influence of differing degrees of fractured rock heterogeneity at different geologic sites. In addition, the surveyed data indicate that field-scale longitudinal dispersivity generally increases with observation scale, which is consistent with previous studies. The scale-dependent field-scale matrix diffusion coefficient (and dispersivity) may have significant implications for assessing long-term, large-scale radionuclide and contaminant transport events in fractured rock, both for nuclear waste disposal and contaminant remediation.

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.

Time of Flight Electrochemistry: Diffusion Coefficient Measurements Using Interdigitated Array (IDA) Electrodes

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

Liu, Fei; Kolesov, Grigory; Parkinson, Bruce A.

2014-09-26

A simple and straightforward method for measuring diffusion coefficients using interdigitated array (IDA) electrodes is reported. The method does not require that the exact electrode area be known but depends only the size of the gap between the IDA electrode pairs. Electroactive molecules produced at the generator electrode of the IDA by a voltage step or scan can diffuse to the collector electrode and the time delay before the current for the reverse electrochemical reaction is detected at the collector is used to calculate the diffusion coefficient. The measurement of the diffusion rate of Ru(NH3)6+2 in aqueous solution has beenmore » used as an example measuring diffusion coefficients using this method. Additionally, a digital simulation of the electrochemical response of the IDA electrodes was used to simulate the entire current/voltage/time behavior of the system and verify the experimentally measured diffusion coefficients. This work was supported as part of the Center for Molecular Electrocatalysis, an Energy Frontier Research Center funded by the Department of Energy, Office of Science, Office of Basic Energy Sciences.« less

Serial diffusion-weighted imaging in subacute sclerosing panencephalitis.

PubMed

Kanemura, Hideaki; Aihara, Masao

2008-06-01

Subacute sclerosing panencephalitis may be associated with clinical features of frontal lobe dysfunction. We previously reported that frontal lobe volume falls significantly as clinical stage progresses, using three-dimensional magnetic resonance imaging-based brain volumetry. The hypothesis that frontal volume increases correlate with clinical improvement, however, was not tested in our previous study. Therefore, we reevaluated our patient with subacute sclerosing panencephalitis, to determine whether apparent diffusion coefficient maps can characterize the clinical course of subacute sclerosing panencephalitis. We studied an 8-year-old boy with subacute sclerosing panencephalitis, using serial diffusion-weighted imaging magnetic resonance imaging, and measured the regional apparent diffusion coefficient. The regional apparent diffusion coefficient of the frontal lobe decreased significantly with clinical progression, whereas it increased to within normal range during clinical improvements. The apparent diffusion coefficient of the other regions did not change. These results suggest that the clinical signs of patients with subacute sclerosing panencephalitis are attributable to frontal lobe dysfunction, and that apparent diffusion coefficient measurements may be useful in predicting the clinical course of subacute sclerosing panencephalitis.

Quantitative differentiation of breast lesions at 3T diffusion-weighted imaging (DWI) using the ratio of distributed diffusion coefficient (DDC).

PubMed

Ertas, Gokhan; Onaygil, Can; Akin, Yasin; Kaya, Handan; Aribal, Erkin

2016-12-01

To investigate the accuracy of diffusion coefficients and diffusion coefficient ratios of breast lesions and of glandular breast tissue from mono- and stretched-exponential models for quantitative diagnosis in diffusion-weighted magnetic resonance imaging (MRI). We analyzed pathologically confirmed 170 lesions (85 benign and 85 malignant) imaged using a 3.0T MR scanner. Small regions of interest (ROIs) focusing on the highest signal intensity for lesions and also for glandular tissue of contralateral breast were obtained. Apparent diffusion coefficient (ADC) and distributed diffusion coefficient (DDC) were estimated by performing nonlinear fittings using mono- and stretched-exponential models, respectively. Coefficient ratios were calculated by dividing the lesion coefficient by the glandular tissue coefficient. A stretched exponential model provides significantly better fits then the monoexponential model (P < 0.001): 65% of the better fits for glandular tissue and 71% of the better fits for lesion. High correlation was found in diffusion coefficients (0.99-0.81 and coefficient ratios (0.94) between the models. The highest diagnostic accuracy was found by the DDC ratio (area under the curve [AUC] = 0.93) when compared with lesion DDC, ADC ratio, and lesion ADC (AUC = 0.91, 0.90, 0.90) but with no statistically significant difference (P > 0.05). At optimal thresholds, the DDC ratio achieves 93% sensitivity, 80% specificity, and 87% overall diagnostic accuracy, while ADC ratio leads to 89% sensitivity, 78% specificity, and 83% overall diagnostic accuracy. The stretched exponential model fits better with signal intensity measurements from both lesion and glandular tissue ROIs. Although the DDC ratio estimated by using the model shows a higher diagnostic accuracy than the ADC ratio, lesion DDC, and ADC, it is not statistically significant. J. Magn. Reson. Imaging 2016;44:1633-1641. © 2016 International Society for Magnetic Resonance in Medicine.

Diffusion coefficients of nitric oxide in water: A molecular dynamics study

NASA Astrophysics Data System (ADS)

Pokharel, Sunil; Pantha, Nurapati; Adhikari, N. P.

2016-09-01

Self-diffusion coefficients along with the mutual diffusion coefficients of nitric oxide (NO) and SPC/E water (H2O) as solute and solvent of the mixture, have been studied within the framework of classical molecular dynamics level of calculations using GROMACS package. The radial distribution function (RDF) of the constituent compounds are calculated to study solute-solute, solute-solvent and solvent-solvent molecular interactions as a function of temperature. A dilute solution of five NO molecules (mole fraction 0.018) and 280 H2O molecules (mole fraction 0.982) has been taken as the sample. The self-diffusion coefficient of the solvent is calculated by using mean square displacement (MSD) where as that for solute (NO) is calculated by using MSD and velocity auto-correlation function (VACF). The results are then compared with the available experimental values. The results from the present work for water come in good agreement, very precise at low temperatures, with the experimental values. The diffusion coefficients of NO, on the other hands, agree well with the available theoretical studies, and also with experiment at low temperatures (up to 310 K). The results at the higher temperatures (up to 333 K), however, deviate significantly with the experimental observations. Also, the mutual diffusion coefficients of NO in water have been calculated by using Darken’s relation. The temperature dependence of the calculated diffusion coefficients follow the Arrhenius behavior.

The Gini coefficient: a methodological pilot study to assess fetal brain development employing postmortem diffusion MRI.

PubMed

Viehweger, Adrian; Riffert, Till; Dhital, Bibek; Knösche, Thomas R; Anwander, Alfred; Stepan, Holger; Sorge, Ina; Hirsch, Wolfgang

2014-10-01

Diffusion-weighted imaging (DWI) is important in the assessment of fetal brain development. However, it is clinically challenging and time-consuming to prepare neuromorphological examinations to assess real brain age and to detect abnormalities. To demonstrate that the Gini coefficient can be a simple, intuitive parameter for modelling fetal brain development. Postmortem fetal specimens(n = 28) were evaluated by diffusion-weighted imaging (DWI) on a 3-T MRI scanner using 60 directions, 0.7-mm isotropic voxels and b-values of 0, 150, 1,600 s/mm(2). Constrained spherical deconvolution (CSD) was used as the local diffusion model. Fractional anisotropy (FA), apparent diffusion coefficient (ADC) and complexity (CX) maps were generated. CX was defined as a novel diffusion metric. On the basis of those three parameters, the Gini coefficient was calculated. Study of fetal brain development in postmortem specimens was feasible using DWI. The Gini coefficient could be calculated for the combination of the three diffusion parameters. This multidimensional Gini coefficient correlated well with age (Adjusted R(2) = 0.59) between the ages of 17 and 26 gestational weeks. We propose a new method that uses an economics concept, the Gini coefficient, to describe the whole brain with one simple and intuitive measure, which can be used to assess the brain's developmental state.

Diffusion Properties and 3D Architecture of Human Lower Leg Muscles Assessed with Ultra-High-Field-Strength Diffusion-Tensor MR Imaging and Tractography: Reproducibility and Sensitivity to Sex Difference and Intramuscular Variability.

PubMed

Fouré, Alexandre; Ogier, Augustin C; Le Troter, Arnaud; Vilmen, Christophe; Feiweier, Thorsten; Guye, Maxime; Gondin, Julien; Besson, Pierre; Bendahan, David

2018-05-01

Purpose To demonstrate the reproducibility of the diffusion properties and three-dimensional structural organization measurements of the lower leg muscles by using diffusion-tensor imaging (DTI) assessed with ultra-high-field-strength (7.0-T) magnetic resonance (MR) imaging and tractography of skeletal muscle fibers. On the basis of robust statistical mapping analyses, this study also aimed at determining the sensitivity of the measurements to sex difference and intramuscular variability. Materials and Methods All examinations were performed with ethical review board approval; written informed consent was obtained from all volunteers. Reproducibility of diffusion tensor indexes assessment including eigenvalues, mean diffusivity, and fractional anisotropy (FA) as well as muscle volume and architecture (ie, fiber length and pennation angle) were characterized in lower leg muscles (n = 8). Intramuscular variability and sex differences were characterized in young healthy men and women (n = 10 in each group). Student t test, statistical parametric mapping, correlation coefficients (Spearman rho and Pearson product-moment) and coefficient of variation (CV) were used for statistical data analysis. Results High reproducibility of measurements (mean CV ± standard deviation, 4.6% ± 3.8) was determined in diffusion properties and architectural parameters. Significant sex differences were detected in FA (4.2% in women for the entire lower leg; P = .001) and muscle volume (21.7% in men for the entire lower leg; P = .008), whereas architecture parameters were almost identical across sex. Additional differences were found independently of sex in diffusion properties and architecture along several muscles of the lower leg. Conclusion The high-spatial-resolution DTI assessed with 7.0-T MR imaging allows a reproducible assessment of structural organization of superficial and deep muscles, giving indirect information on muscle function. © RSNA, 2018 Online supplemental material is available for this article.

Using genetic data to estimate diffusion rates in heterogeneous landscapes.

PubMed

Roques, L; Walker, E; Franck, P; Soubeyrand, S; Klein, E K

2016-08-01

Having a precise knowledge of the dispersal ability of a population in a heterogeneous environment is of critical importance in agroecology and conservation biology as it can provide management tools to limit the effects of pests or to increase the survival of endangered species. In this paper, we propose a mechanistic-statistical method to estimate space-dependent diffusion parameters of spatially-explicit models based on stochastic differential equations, using genetic data. Dividing the total population into subpopulations corresponding to different habitat patches with known allele frequencies, the expected proportions of individuals from each subpopulation at each position is computed by solving a system of reaction-diffusion equations. Modelling the capture and genotyping of the individuals with a statistical approach, we derive a numerically tractable formula for the likelihood function associated with the diffusion parameters. In a simulated environment made of three types of regions, each associated with a different diffusion coefficient, we successfully estimate the diffusion parameters with a maximum-likelihood approach. Although higher genetic differentiation among subpopulations leads to more accurate estimations, once a certain level of differentiation has been reached, the finite size of the genotyped population becomes the limiting factor for accurate estimation.

Effective diffusion coefficients of DNAPL waste components in saturated low permeability soil materials

NASA Astrophysics Data System (ADS)

Ayral-Cinar, Derya; Demond, Avery H.

2017-12-01

Diffusion is regarded as the dominant transport mechanism into and out of low permeable subsurface lenses and layers in the subsurface. But, some reports of mass storage in such zones are higher than what might be attributable to diffusion, based on estimated diffusion coefficients. Despite the importance of diffusion to efforts to estimate the quantity of residual contamination in the subsurface, relatively few studies present measured diffusion coefficients of organic solutes in saturated low permeability soils. This study reports the diffusion coefficients of a trichloroethylene (TCE), and an anionic surfactant, Aerosol OT (AOT), in water-saturated silt and a silt-montmorillonite (25:75) mixture, obtained using steady-state experiments. The relative diffusivity ranged from 0.11 to 0.17 for all three compounds for the silt and the silt-clay mixture that was allowed to expand. In the case in which the swelling was constrained, the relative diffusivity was about 0.07. In addition, the relative diffusivity of 13C-labeled TCE through a water saturated silt-clay mixture that had contacted a field dense non-aqueous phase liquid (DNAPL) for 18 months was measured and equaled 0.001. These experimental results were compared with the estimates generated using common correlations, and it was found that, in all cases, the measured diffusion coefficients were significantly lower than the estimated. Thus, the discrepancy between mass accumulations observed in the field and the mass storage that can attributable to diffusion may be greater than previously believed.

The tracer diffusion coefficient of soft nanoparticles in a linear polymer matrix

DOE PAGES

Imel, Adam E.; Rostom, Sahar; Holley, Wade; ...

2017-03-09

The diffusion properties of nanoparticles in polymer nanocomposites are largely unknown and are often difficult to determine experimentally. To address this shortcoming, we have developed a novel method to determine the tracer diffusion coefficient of soft polystyrene nanoparticles in a linear polystyrene matrix. Monitoring the interdiffusion of soft nanoparticles into a linear polystyrene matrix provides the mutual diffusion coefficient of this system, from which the tracer diffusion coefficient of the soft nanoparticle can be determined using the slow mode theory. Utilizing this protocol, the role of nanoparticle molecular weight and rigidity on its tracer diffusion coefficient is provided. These resultsmore » demonstrate that the diffusive behavior of these soft nanoparticles differ from that of star polymers, which is surprising since our recent studies suggest that the nanoparticle interacts with a linear polymer similarly to that of a star polymer. It appears that these deformable nanoparticles mostly closely mimic the diffusive behavior of fractal macromolecular architectures or microgels, where the transport of the nanoparticle relies on the cooperative motion of neighboring linear chains. Finally, the less cross-linked, and thus more deformable, nanoparticles diffuse faster than the more highly crosslinked nanoparticles, presumably because the increased deformability allows the nanoparticle to distort and fit into available space.« less

The Cool Flames Experiment

NASA Technical Reports Server (NTRS)

Pearlman, Howard; Chapek, Richard; Neville, Donna; Sheredy, William; Wu, Ming-Shin; Tornabene, Robert

2001-01-01

A space-based experiment is currently under development to study diffusion-controlled, gas-phase, low temperature oxidation reactions, cool flames and auto-ignition in an unstirred, static reactor. At Earth's gravity (1g), natural convection due to self-heating during the course of slow reaction dominates diffusive transport and produces spatio-temporal variations in the thermal and thus species concentration profiles via the Arrhenius temperature dependence of the reaction rates. Natural convection is important in all terrestrial cool flame and auto-ignition studies, except for select low pressure, highly dilute (small temperature excess) studies in small vessels (i.e., small Rayleigh number). On Earth, natural convection occurs when the Rayleigh number (Ra) exceeds a critical value of approximately 600. Typical values of the Ra, associated with cool flames and auto-ignitions, range from 104-105 (or larger), a regime where both natural convection and conduction heat transport are important. When natural convection occurs, it alters the temperature, hydrodynamic, and species concentration fields, thus generating a multi-dimensional field that is extremely difficult, if not impossible, to be modeled analytically. This point has been emphasized recently by Kagan and co-workers who have shown that explosion limits can shift depending on the characteristic length scale associated with the natural convection. Moreover, natural convection in unstirred reactors is never "sufficiently strong to generate a spatially uniform temperature distribution throughout the reacting gas." Thus, an unstirred, nonisothermal reaction on Earth does not reduce to that generated in a mechanically, well-stirred system. Interestingly, however, thermal ignition theories and thermokinetic models neglect natural convection and assume a heat transfer correlation of the form: q=h(S/V)(T(bar) - Tw) where q is the heat loss per unit volume, h is the heat transfer coefficient, S/V is the surface to volume ratio, and (T(bar) - Tw ) is the spatially averaged temperature excess. This Newtonian form has been validated in spatially-uniform, well-stirred reactors, provided the effective heat transfer coefficient associated with the unsteady process is properly evaluated. Unfortunately, it is not a valid assumption for spatially-nonuniform temperature distributions induced by natural convection in unstirred reactors. "This is why the analysis of such a system is so difficult." Historically, the complexities associated with natural convection were perhaps recognized as early as 1938 when thermal ignition theory was first developed. In the 1955 text "Diffusion and Heat Exchange in Chemical Kinetics", Frank-Kamenetskii recognized that "the purely conductive theory can be applied at sufficiently low pressure and small dimensions of the vessel when the influence of natural convection can be disregarded." This was reiterated by Tyler in 1966 and further emphasized by Barnard and Harwood in 1974. Specifically, they state: "It is generally assumed that heat losses are purely conductive. While this may be valid for certain low pressure slow combustion regimes, it is unlikely to be true for the cool flame and ignition regimes." While this statement is true for terrestrial experiments, the purely conductive heat transport assumption is valid at microgravity (mu-g). Specifically, buoyant complexities are suppressed at mu-g and the reaction-diffusion structure associated with low temperature oxidation reactions, cool flames and auto-ignitions can be studied. Without natural convection, the system is simpler, does not require determination of the effective heat transfer coefficient, and is a testbed for analytic and numerical models that assume pure diffusive transport. In addition, mu-g experiments will provide baseline data that will improve our understanding of the effects of natural convection on Earth.

Investigation of impurity transport using laser blow-off technique in the HL-2A Ohmic and ECRH plasmas

NASA Astrophysics Data System (ADS)

Kai, Zhang; Zheng-Ying, Cui; Ping, Sun; Chun-Feng, Dong; Wei, Deng; Yun-Bo, Dong; Shao-Dong, Song; Min, Jiang; Yong-Gao, Li; Ping, Lu; Qing-Wei, Yang

2016-06-01

Impurity transports in two neighboring discharges with and without electron cyclotron resonance heating (ECRH) are studied in the HL-2A tokamak by laser blow-off (LBO) technique. The progression of aluminium ions as the trace impurity is monitored by soft x-ray (SXR) and bolometer detector arrays with good temporal and spatial resolutions. Obvious difference in the time trace of the signal between the Ohmic and ECRH L-mode discharges is observed. Based on the numerical simulation with one-dimensional (1D) impurity transport code STRAHL, the radial profiles of impurity diffusion coefficient D and convective velocity V are obtained for each shot. The result shows that the diffusion coefficient D significantly increases throughout the plasma minor radius for the ECRH case with respect to the Ohmic case, and that the convection velocity V changes from negative (inward) for the Ohmic case to partially positive (outward) for the ECRH case. The result on HL-2A confirms the pump out effect of ECRH on impurity profile as reported on various other devices.

Modelling of Dictyostelium discoideum movement in a linear gradient of chemoattractant.

PubMed

Eidi, Zahra; Mohammad-Rafiee, Farshid; Khorrami, Mohammad; Gholami, Azam

2017-11-15

Chemotaxis is a ubiquitous biological phenomenon in which cells detect a spatial gradient of chemoattractant, and then move towards the source. Here we present a position-dependent advection-diffusion model that quantitatively describes the statistical features of the chemotactic motion of the social amoeba Dictyostelium discoideum in a linear gradient of cAMP (cyclic adenosine monophosphate). We fit the model to experimental trajectories that are recorded in a microfluidic setup with stationary cAMP gradients and extract the diffusion and drift coefficients in the gradient direction. Our analysis shows that for the majority of gradients, both coefficients decrease over time and become negative as the cells crawl up the gradient. The extracted model parameters also show that besides the expected drift in the direction of the chemoattractant gradient, we observe a nonlinear dependency of the corresponding variance on time, which can be explained by the model. Furthermore, the results of the model show that the non-linear term in the mean squared displacement of the cell trajectories can dominate the linear term on large time scales.

Simultaneous characterization of lateral lipid and prothrombin diffusion coefficients by z-scan fluorescence correlation spectroscopy.

PubMed

Stefl, Martin; Kułakowska, Anna; Hof, Martin

2009-08-05

A new (to our knowledge) robust approach for the determination of lateral diffusion coefficients of weakly bound proteins is applied for the phosphatidylserine specific membrane interaction of bovine prothrombin. It is shown that z-scan fluorescence correlation spectroscopy in combination with pulsed interleaved dual excitation allows simultaneous monitoring of the lateral diffusion of labeled protein and phospholipids. Moreover, from the dependencies of the particle numbers on the axial sample positions at different protein concentrations phosphatidylserine-dependent equilibrium dissociation constants are derived confirming literature values. Increasing the amount of membrane-bound prothrombin retards the lateral protein and lipid diffusion, indicating coupling of both processes. The lateral diffusion coefficients of labeled lipids are considerably larger than the simultaneously determined lateral diffusion coefficients of prothrombin, which contradicts findings reported for the isolated N-terminus of prothrombin.

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

PubMed

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

2015-07-01

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

Unifying diffusion and seepage for nonlinear gas transport in multiscale porous media

NASA Astrophysics Data System (ADS)

Song, Hongqing; Wang, Yuhe; Wang, Jiulong; Li, Zhengyi

2016-09-01

We unify the diffusion and seepage process for nonlinear gas transport in multiscale porous media via a proposed new general transport equation. A coherent theoretical derivation indicates the wall-molecule and molecule-molecule collisions drive the Knudsen and collective diffusive fluxes, and constitute the system pressure across the porous media. A new terminology, nominal diffusion coefficient can summarize Knudsen and collective diffusion coefficients. Physical and numerical experiments show the support of the new formulation and provide approaches to obtain the diffusion coefficient and permeability simultaneously. This work has important implication for natural gas extraction and greenhouse gases sequestration in geological formations.

Numerical study of centrifugal compressor stage vaneless diffusers

NASA Astrophysics Data System (ADS)

Galerkin, Y.; Soldatova, K.; Solovieva, O.

2015-08-01

The authors analyzed CFD calculations of flow in vaneless diffusers with relative width in range from 0.014 to 0.100 at inlet flow angles in range from 100 to 450 with different inlet velocity coefficients, Reynolds numbers and surface roughness. The aim is to simulate calculated performances by simple algebraic equations. The friction coefficient that represents head losses as friction losses is proposed for simulation. The friction coefficient and loss coefficient are directly connected by simple equation. The advantage is that friction coefficient changes comparatively little in range of studied parameters. Simple equations for this coefficient are proposed by the authors. The simulation accuracy is sufficient for practical calculations. To create the complete algebraic model of the vaneless diffuser the authors plan to widen this method of modeling to diffusers with different relative length and for wider range of Reynolds numbers.

Determination of partition and diffusion coefficients of formaldehyde in selected building materials and impact of relative humidity.

PubMed

Xu, Jing; Zhang, Jianshun S; Liu, Xiaoyu; Gao, Zhi

2012-06-01

The partition and effective diffusion coefficients of formaldehyde were measured for three materials (conventional gypsum wallboard, "green" gypsum wallboard, and "green" carpet) under three relative humidity (RH) conditions (20%, 50%, and 70% RH). The "green" materials contained recycled materials and were friendly to environment. A dynamic dual-chamber test method was used. Results showed that a higher relative humidity led to a larger effective diffusion coefficient for two kinds of wallboards and carpet. The carpet was also found to be very permeable resulting in an effective diffusion coefficient at the same order of magnitude with the formaldehyde diffusion coefficient in air. The partition coefficient (K(ma)) of formaldehyde in conventional wallboard was 1.52 times larger at 50% RH than at 20% RH, whereas it decreased slightly from 50% to 70% RH, presumably due to the combined effects of water solubility of formaldehyde and micro-pore blocking by condensed moisture at the high RH level. The partition coefficient of formaldehyde increased slightly with the increase of relative humidity in "green" wallboard and "green" carpet. At the same relative humidity level, the "green" wallboard had larger partition coefficient and effective diffusion coefficient than the conventional wallboard, presumably due to the micro-pore structure differences between the two materials. The data generated could be used to assess the sorption effects of formaldehyde on building materials and to evaluate its impact on the formaldehyde concentration in buildings.

Determination of diffusion coefficients of various livestock antibiotics in water at infinite dilution

NASA Astrophysics Data System (ADS)

Soriano, Allan N.; Adamos, Kristoni G.; Bonifacio, Pauline B.; Adornado, Adonis P.; Bungay, Vergel C.; Vairavan, Rajendaran

2017-11-01

The fate of antibiotics entering the environment raised concerns on the possible effect of antimicrobial resistance bacteria. Prediction of the fate and transport of these particles are needed to be determined, significantly the diffusion coefficient of antibiotic in water at infinite dilution. A systematic determination of diffusion coefficient of antibiotic in water at infinite dilution of five different kinds of livestock antibiotics namely: Amtyl, Ciprotyl, Doxylak Forte, Trisullak, and Vetracin Gold in the 293.15 to 313.15 K temperature range are reported through the use of the method involving the electrolytic conductivity measurements. A continuous stirred tank reactor is utilized to measure the electrolytic conductivities of the considered systems. These conductivities are correlated by using the Nernst-Haskell equation to determine the infinite dilution diffusion coefficient. Determined diffusion coefficients are based on the assumption that in dilute solution, these antibiotics behave as strong electrolyte from which H+ cation dissociate from the antibiotic's anion.

Determination of molecular diffusion coefficient in n-alkane binary mixtures: empirical correlations.

PubMed

De Mezquia, D Alonso; Bou-Ali, M Mounir; Larrañaga, M; Madariaga, J A; Santamaría, C

2012-03-08

In this work we have measured the molecular diffusion coefficient of the n-alkane binary series nC(i)-nC(6), nC(i)-nC(10), and nC(i)-nC(12) at 298 K and 1 atm and a mass fraction of 0.5 by using the so-called sliding symmetric tubes technique. The results show that the diffusion coefficient at this concentration is proportional to the inverse viscosity of the mixture. In addition, we have also measured the diffusion coefficient of the systems nC(12)-nC(6), nC(12)-nC(7), and nC(12)-nC(8) as a function of concentration. From the data obtained, it is shown that the diffusion coefficient of the n-alkane binary mixtures at any concentration can be calculated from the molecular weight of the components and the dynamic viscosity of the corresponding mixture at 50% mass fraction.

Quantitative, depth-resolved determination of particle motion using multi-exposure, spatial frequency domain laser speckle imaging.

PubMed

Rice, Tyler B; Kwan, Elliott; Hayakawa, Carole K; Durkin, Anthony J; Choi, Bernard; Tromberg, Bruce J

2013-01-01

Laser Speckle Imaging (LSI) is a simple, noninvasive technique for rapid imaging of particle motion in scattering media such as biological tissue. LSI is generally used to derive a qualitative index of relative blood flow due to unknown impact from several variables that affect speckle contrast. These variables may include optical absorption and scattering coefficients, multi-layer dynamics including static, non-ergodic regions, and systematic effects such as laser coherence length. In order to account for these effects and move toward quantitative, depth-resolved LSI, we have developed a method that combines Monte Carlo modeling, multi-exposure speckle imaging (MESI), spatial frequency domain imaging (SFDI), and careful instrument calibration. Monte Carlo models were used to generate total and layer-specific fractional momentum transfer distributions. This information was used to predict speckle contrast as a function of exposure time, spatial frequency, layer thickness, and layer dynamics. To verify with experimental data, controlled phantom experiments with characteristic tissue optical properties were performed using a structured light speckle imaging system. Three main geometries were explored: 1) diffusive dynamic layer beneath a static layer, 2) static layer beneath a diffuse dynamic layer, and 3) directed flow (tube) submerged in a dynamic scattering layer. Data fits were performed using the Monte Carlo model, which accurately reconstructed the type of particle flow (diffusive or directed) in each layer, the layer thickness, and absolute flow speeds to within 15% or better.

Super-resolution study of polymer mobility fluctuations near c*.

PubMed

King, John T; Yu, Changqian; Wilson, William L; Granick, Steve

2014-09-23

Nanoscale dynamic heterogeneities in synthetic polymer solutions are detected using super-resolution optical microscopy. To this end, we map concentration fluctuations in polystyrene-toluene solutions with spatial resolution below the diffraction limit, focusing on critical fluctuations near the polymer overlap concentration, c*. Two-photon super-resolution microscopy was adapted to be applicable in an organic solvent, and a home-built STED-FCS system with stimulated emission depletion (STED) was used to perform fluorescence correlation spectroscopy (FCS). The polystyrene serving as the tracer probe (670 kg mol(-1), radius of gyration RG ≈ 35 nm, end-labeled with a bodipy derivative chromophore) was dissolved in toluene at room temperature (good solvent) and mixed with matrix polystyrene (3,840 kg mol(-1), RG ≈ 97 nm, Mw/Mn = 1.04) whose concentration was varied from dilute to more than 10c*. Whereas for dilute solutions the intensity-intensity correlation function follows a single diffusion process, it splits starting at c* to imply an additional relaxation process provided that the experimental focal area does not greatly exceed the polymer blob size. We identify the slower mode as self-diffusion and the increasingly rapid mode as correlated segment fluctuations that reflect the cooperative diffusion coefficient, Dcoop. These real-space measurements find quantitative agreement between correlation lengths inferred from dynamic measurements and those from determining the limit below which diffusion coefficients are independent of spot size. This study is considered to illustrate the potential of importing into polymer science the techniques of super-resolution imaging.

Pitfalls and Limitations of Diffusion-Weighted Magnetic Resonance Imaging in the Diagnosis of Urinary Bladder Cancer

PubMed Central

Lin, Wei-Ching; Chen, Jeon-Hor

2015-01-01

Adequately selecting a therapeutic approach for bladder cancer depends on accurate grading and staging. Substantial inaccuracy of clinical staging with bimanual examination, cystoscopy, and transurethral resection of bladder tumor has facilitated the increasing utility of magnetic resonance imaging to evaluate bladder cancer. Diffusion-weighted imaging (DWI) is a noninvasive functional magnetic resonance imaging technique. The high tissue contrast between cancers and surrounding tissues on DWI is derived from the difference of water molecules motion. DWI is potentially a useful tool for the detection, characterization, and staging of bladder cancers; it can also monitor posttreatment response and provide information on predicting tumor biophysical behaviors. Despite advancements in DWI techniques and the use of quantitative analysis to evaluate the apparent diffusion coefficient values, there are some inherent limitations in DWI interpretation related to relatively poor spatial resolution, lack of cancer specificity, and lack of standardized image acquisition protocols and data analysis procedures that restrict the application of DWI and reproducibility of apparent diffusion coefficient values. In addition, inadequate bladder distension, artifacts, thinness of bladder wall, cancerous mimickers of normal bladder wall and benign lesions, and variations in the manifestation of bladder cancer may interfere with diagnosis and monitoring of treatment. Recognition of these pitfalls and limitations can minimize their impact on image interpretation, and carefully applying the analyzed results and combining with pathologic grading and staging to clinical practice can contribute to the selection of an adequate treatment method to improve patient care. PMID:26055180

Measurement of the ferric diffusion coefficient in agarose and gelatine gels by utilization of the evolution of a radiation induced edge as reflected in relaxation rate images.

PubMed

Pedersen, T V; Olsen, D R; Skretting, A

1997-08-01

A method has been developed to determine the diffusion coefficients of ferric ions in ferrous sulphate doped gels. A radiation induced edge was created in the gel, and two spin-echo sequences were used to acquire a pair of images of the gel at different points of time. For each of these image pairs, a longitudinal relaxation rate image was derived. From profiles through these images, the standard deviations of the Gaussian functions that characterize diffusion were determined. These data provided the basis for the determination of the ferric diffusion coefficients by two different methods. Simulations indicate that the use of single spin-echo images in this procedure may in some cases lead to a significant underestimation of the diffusion coefficient. The technique was applied to different agarose and gelatine gels that were prepared, irradiated and imaged simultaneously. The results indicate that the diffusion coefficient is lower in a gelatine gel than in an agarose gel. Addition of xylenol orange to a gelatine gel lowers the diffusion coefficient from 1.45 to 0.81 mm2 h-1, at the cost of significantly lower Rl sensitivity. The addition of benzoic acid to the latter gel did not increase the Rl sensitivity.

Effects of different cooling treatments on water diffusion, microcirculation, and water content within exercised muscles: evaluation by magnetic resonance T2-weighted and diffusion-weighted imaging.

PubMed

Yanagisawa, Osamu; Takahashi, Hideyuki; Fukubayashi, Toru

2010-09-01

In this study, we determined the effects of different cooling treatments on exercised muscles. Seven adults underwent four post-exercise treatments (20-min ice-bag application, 60-min gel-pack application at 10 degrees C and 17 degrees C, and non-cooling treatment) with at least 1 week between treatments. Magnetic resonance diffusion- and T2-weighted images were obtained to calculate the apparent diffusion coefficients (apparent diffusion coefficient 1, which reflects intramuscular water diffusion and microcirculation, and apparent diffusion coefficient 2, which is approximately equal to the true diffusion coefficient that excludes as much of the effect of intramuscular microcirculation as possible) and the T2 values (intramuscular water content level) of the ankle dorsiflexors, respectively, before and after ankle dorsiflexion exercise and after post-exercise treatment. The T2 values increased significantly after exercise and returned to pre-exercise values after each treatment; no significant differences were observed among the four post-exercise treatments. Both apparent diffusion coefficients also increased significantly after exercise and decreased significantly after the three cooling treatments; no significant difference was detected among the three cooling treatments. Local cooling suppresses both water diffusion and microcirculation within exercised muscles. Moreover, although the treatment time was longer, adequate cooling effects could be achieved using the gel-pack applications at relatively mild cooling temperatures.

CO2 diffusion in champagne wines: a molecular dynamics study.

PubMed

Perret, Alexandre; Bonhommeau, David A; Liger-Belair, Gérard; Cours, Thibaud; Alijah, Alexander

2014-02-20

Although diffusion is considered as the main physical process responsible for the nucleation and growth of carbon dioxide bubbles in sparkling beverages, the role of each type of molecule in the diffusion process remains unclear. In the present study, we have used the TIP5P and SPC/E water models to perform force field molecular dynamics simulations of CO2 molecules in water and in a water/ethanol mixture respecting Champagne wine proportions. CO2 diffusion coefficients were computed by applying the generalized Fick's law for the determination of multicomponent diffusion coefficients, a law that simplifies to the standard Fick's law in the case of champagnes. The CO2 diffusion coefficients obtained in pure water and water/ethanol mixtures composed of TIP5P water molecules were always found to exceed the coefficients obtained in mixtures composed of SPC/E water molecules, a trend that was attributed to a larger propensity of SPC/E water molecules to form hydrogen bonds. Despite the fact that the SPC/E model is more accurate than the TIP5P model to compute water self-diffusion and CO2 diffusion in pure water, the diffusion coefficients of CO2 molecules in the water/ethanol mixture are in much better agreement with the experimental values of 1.4 - 1.5 × 10(-9) m(2)/s obtained for Champagne wines when the TIP5P model is employed. This difference was deemed to rely on the larger propensity of SPC/E water molecules to maintain the hydrogen-bonded network between water molecules and form new hydrogen bonds with ethanol, although statistical issues cannot be completely excluded. The remarkable agreement between the theoretical CO2 diffusion coefficients obtained within the TIP5P water/ethanol mixture and the experimental data specific to Champagne wines makes us infer that the diffusion coefficient in these emblematic hydroalcoholic sparkling beverages is expected to remain roughly constant whathever their proportions in sugars, glycerol, or peptides.

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

DOE PAGES

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

2018-01-31

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

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

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

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

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

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.

Estimation of diffusion coefficients from voltammetric signals by support vector and gaussian process regression

PubMed Central

2014-01-01

Background Support vector regression (SVR) and Gaussian process regression (GPR) were used for the analysis of electroanalytical experimental data to estimate diffusion coefficients. Results For simulated cyclic voltammograms based on the EC, Eqr, and EqrC mechanisms these regression algorithms in combination with nonlinear kernel/covariance functions yielded diffusion coefficients with higher accuracy as compared to the standard approach of calculating diffusion coefficients relying on the Nicholson-Shain equation. The level of accuracy achieved by SVR and GPR is virtually independent of the rate constants governing the respective reaction steps. Further, the reduction of high-dimensional voltammetric signals by manual selection of typical voltammetric peak features decreased the performance of both regression algorithms compared to a reduction by downsampling or principal component analysis. After training on simulated data sets, diffusion coefficients were estimated by the regression algorithms for experimental data comprising voltammetric signals for three organometallic complexes. Conclusions Estimated diffusion coefficients closely matched the values determined by the parameter fitting method, but reduced the required computational time considerably for one of the reaction mechanisms. The automated processing of voltammograms according to the regression algorithms yields better results than the conventional analysis of peak-related data. PMID:24987463

The influence of screening of the polyion electrostatic potential on the counterion dynamics in polyelectrolyte solutions

NASA Astrophysics Data System (ADS)

Schipper, F. J. M.; Hollander, J. G.; Leyte, J. C.

1998-10-01

The self-diffusion coefficient of tetra-methylammonium counterion in solutions of polymethacrylic acid in 0953-8984/10/41/004/img1 has been measured over a broad polyion concentration range at a constant degree of neutralization and at different ratios of added monovalent or bivalent salt to polyions. A maximum counterion self-diffusion coefficient was observed as a function of polyion concentration. The value of the self-diffusion coefficient at the maximum did not depend on the valency of the added salt. The maximum was found at lower polymer concentrations and with a higher value, when the ratio of added salt to polyions was increased, as predicted by the Poisson-Boltzmann-Smoluchowski equation in the cylindrical cell model for polyelectrolytes. At higher polyion concentrations a maximum counterion self-diffusion coefficient against the ratio of added salt and polyions was observed, which has not been reported before. Upon increasing this ratio the electrostatic potential of the polyelectrolyte gets screened, leading to an increase of the counterion self-diffusion coefficient. Concentration effects of the added salt on the other hand ultimately lead to a decrease of the counterion self-diffusion coefficient, which explains the occurrence of a maximum.

Multilevel Preconditioners for Reaction-Diffusion Problems with Discontinuous Coefficients

DOE PAGES

Kolev, Tzanio V.; Xu, Jinchao; Zhu, Yunrong

2015-08-23

In this study, we extend some of the multilevel convergence results obtained by Xu and Zhu, to the case of second order linear reaction-diffusion equations. Specifically, we consider the multilevel preconditioners for solving the linear systems arising from the linear finite element approximation of the problem, where both diffusion and reaction coefficients are piecewise-constant functions. We discuss in detail the influence of both the discontinuous reaction and diffusion coefficients to the performance of the classical BPX and multigrid V-cycle preconditioner.

Note: On the relation between Lifson-Jackson and Derrida formulas for effective diffusion coefficient

NASA Astrophysics Data System (ADS)

Kalnin, Juris R.; Berezhkovskii, Alexander M.

2013-11-01

The Lifson-Jackson formula provides the effective free diffusion coefficient for a particle diffusing in an arbitrary one-dimensional periodic potential. Its counterpart, when the underlying dynamics is described in terms of an unbiased nearest-neighbor Markovian random walk on a one-dimensional periodic lattice is given by the formula obtained by Derrida. It is shown that the latter formula can be considered as a discretized version of the Lifson-Jackson formula with correctly chosen position-dependent diffusion coefficient.

Translational diffusion coefficients of volatile compounds in various aqueous solutions at low and subzero temperatures.

PubMed

Covarrubias-Cervantes, Marco; Champion, Dominique; Debeaufort, Frédéric; Voilley, Andrée

2005-08-24

Translational diffusion coefficients (D(12)) of volatile compounds were measured in model media with the profile concentration method. The influence of sample temperature (from 25 to -10 degrees C) was studied on translational diffusion in sucrose or maltodextrin solutions at various concentrations. Results show that diffusivity of volatile compounds in sucrose solutions is controlled by temperature, molecule size, and the viscosity of the liquid phase as expected with the Stokes-Einstein equation; moreover, physicochemical interactions between volatile compounds and the medium are determinant for diffusion estimation. At negative temperature, the winding path induced by an ice crystal content of >70% lowered volatile compound diffusion. On the contrary, no influence on translational diffusion coefficients was observed for lower ice content.

Experimental Method Development for Estimating Solid-phase Diffusion Coefficients and Material/Air Partition Coefficients of SVOCs

EPA Science Inventory

The solid-phase diffusion coefficient (Dm) and material-air partition coefficient (Kma) are key parameters for characterizing the sources and transport of semivolatile organic compounds (SVOCs) in the indoor environment. In this work, a new experimental method was developed to es...

Study the effects of varying interference upon the optical properties of turbid samples using NIR spatial light modulation

NASA Astrophysics Data System (ADS)

Shaul, Oren; Fanrazi-Kahana, Michal; Meitav, Omri; Pinhasi, Gad A.; Abookasis, David

2018-03-01

Optical properties of biological tissues are valuable diagnostic parameters which can provide necessary information regarding tissue state during disease pathogenesis and therapy. However, different sources of interference, such as temperature changes may modify these properties, introducing confounding factors and artifacts to data, consequently skewing their interpretation and misinforming clinical decision-making. In the current study, we apply spatial light modulation, a type of diffuse reflectance hyperspectral imaging technique, to monitor the variation in optical properties of highly scattering turbid media in the presence varying levels of the following sources of interference: scattering concentration, temperature, and pressure. Spatial near-infrared (NIR) light modulation is a wide-field, non-contact emerging optical imaging platform capable of separating the effects of tissue scattering from those of absorption, thereby accurately estimating both parameters. With this technique, periodic NIR illumination patterns at alternately low and high spatial frequencies, at six discrete wavelengths between 690 to 970 nm, were sequentially projected upon the medium while a CCD camera collects the diffusely reflected light. Data analysis based assumptions is then performed off-line to recover the medium's optical properties. We conducted a series of experiments demonstrating the changes in absorption and reduced scattering coefficients of commercially available fresh milk and chicken breast tissue under different interference conditions. In addition, information on the refractive index was study under increased pressure. This work demonstrates the utility of NIR spatial light modulation to detect varying sources of interference upon the optical properties of biological samples.

Approximate Bayesian Computation in the estimation of the parameters of the Forbush decrease model

NASA Astrophysics Data System (ADS)

Wawrzynczak, A.; Kopka, P.

2017-12-01

Realistic modeling of the complicated phenomena as Forbush decrease of the galactic cosmic ray intensity is a quite challenging task. One aspect is a numerical solution of the Fokker-Planck equation in five-dimensional space (three spatial variables, the time and particles energy). The second difficulty arises from a lack of detailed knowledge about the spatial and time profiles of the parameters responsible for the creation of the Forbush decrease. Among these parameters, the central role plays a diffusion coefficient. Assessment of the correctness of the proposed model can be done only by comparison of the model output with the experimental observations of the galactic cosmic ray intensity. We apply the Approximate Bayesian Computation (ABC) methodology to match the Forbush decrease model to experimental data. The ABC method is becoming increasing exploited for dynamic complex problems in which the likelihood function is costly to compute. The main idea of all ABC methods is to accept samples as an approximate posterior draw if its associated modeled data are close enough to the observed one. In this paper, we present application of the Sequential Monte Carlo Approximate Bayesian Computation algorithm scanning the space of the diffusion coefficient parameters. The proposed algorithm is adopted to create the model of the Forbush decrease observed by the neutron monitors at the Earth in March 2002. The model of the Forbush decrease is based on the stochastic approach to the solution of the Fokker-Planck equation.

Diffusion of cations in chromia layers grown on iron-base alloys

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

Lobnig, R.E.; Hennesen, K.; Grabke, H.J.

Diffusion of the cations Cr, Fe, Mn, and Ni in Cr{sub 2}O{sub 3} has been investigated at 1,173 K. The diffusion measurements were performed on chromia layers grown on the model alloys Fe-20Cr and Fe-20Cr-12Ni in order to consider effects of small amounts of dissolved alien cations in Cr{sub 2}O{sub 3}. The samples were diffusion annealed in H{sub 2}-H{sub 2}O at an oxygen partial pressure close to the Cr{sub 2}O{sub 3}/Cr equilibrium. For all tracers the lattice-diffusion coefficients are 3-5 orders of magnitude smaller than the grain-boundary diffusion coefficients. The lattice diffusivity of Mn is about two orders of magnitudemore » greater than the other lattice-diffusion coefficients, especially in Cr{sub 2}O{sub 3} grown on Fe-20Cr-12Ni. The values of the diffusion coefficients for Cr, Fe, and Ni are in the same range. Diffusion of the tracers in Cr{sub 2}O{sub 3} grown on different alloys did not show significant differences with the exception of Mn.« less

Many-body Effects in a Laterally Inhomogeneous Semiconductor Quantum Well

NASA Technical Reports Server (NTRS)

Ning, Cun-Zheng; Li, Jian-Zhong; Biegel, Bryan A. (Technical Monitor)

2002-01-01

Many body effects on conduction and diffusion of electrons and holes in a semiconductor quantum well are studied using a microscopic theory. The roles played by the screened Hartree-Fock (SHE) terms and the scattering terms are examined. It is found that the electron and hole conductivities depend only on the scattering terms, while the two-component electron-hole diffusion coefficients depend on both the SHE part and the scattering part. We show that, in the limit of the ambipolax diffusion approximation, however, the diffusion coefficients for carrier density and temperature are independent of electron-hole scattering. In particular, we found that the SHE terms lead to a reduction of density-diffusion coefficients and an increase in temperature-diffusion coefficients. Such a reduction or increase is explained in terms of a density-and temperature dependent energy landscape created by the bandgap renormalization.

Determination of the zincate diffusion coefficient and its application to alkaline battery problems

NASA Technical Reports Server (NTRS)

May, C. E.; Kautz, Harold E.

1978-01-01

The diffusion coefficient for the zincate ion at 24 C was found to be 9.9 X 10 to the minus 7th power squared cm per sec + or - 30 percent in 45 percent potassium hydroxide and 1.4 x 10 to the minus 7 squared cm per sec + or - 25 percent in 40 percent sodium hydroxide. Comparison of these values with literature values at different potassium hydroxide concentrations show that the Stokes-Einstein equation is obeyed. The diffusion coefficient is characteristic of the zincate ion (not the cation) and independent of its concentration. Calculations with the measured value of the diffusion coefficient show that the zinc concentration in an alkaline zincate half cell becomes uniform throughout in tens of hours by diffusion alone. Diffusion equations are derived which are applicable to finite size chambers. Details and discussion of the experimental method are also given.

Coiled to diffuse: Brownian motion of a helical bacterium.

PubMed

Butenko, Alexander V; Mogilko, Emma; Amitai, Lee; Pokroy, Boaz; Sloutskin, Eli

2012-09-11

We employ real-time three-dimensional confocal microscopy to follow the Brownian motion of a fixed helically shaped Leptospira interrogans (LI) bacterium. We extract from our measurements the translational and the rotational diffusion coefficients of this bacterium. A simple theoretical model is suggested, perfectly reproducing the experimental diffusion coefficients, with no tunable parameters. An older theoretical model, where edge effects are neglected, dramatically underestimates the observed rates of translation. Interestingly, the coiling of LI increases its rotational diffusion coefficient by a factor of 5, compared to a (hypothetical) rectified bacterium of the same contour length. Moreover, the translational diffusion coefficients would have decreased by a factor of ~1.5, if LI were rectified. This suggests that the spiral shape of the spirochaete bacteria, in addition to being employed for their active twisting motion, may also increase the ability of these bacteria to explore the surrounding fluid by passive Brownian diffusion.

Determination of the zincate diffusion coefficient and its application to alkaline battery problems

NASA Technical Reports Server (NTRS)

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

1978-01-01

The diffusion coefficient for the zincate ion at 24 C was found to be 9.9 x 10 to the -7th power sq cm/sec + or - 30% in 45% potassium hydroxide and 1.4 x 10 to the -7th power sq cm/sec + or - 25% in 40% sodium hydroxide. Comparison of these values with literature values at different potassium hydroxide concentrations show that the Stokes-Einstein equation is obeyed. The diffusion coefficient is characteristic of the zincate ion (not the cation) and independent of its concentration. Calculations with the measured value of the diffusion coefficient show that the zinc concentration in an alkaline zincate half-cell becomes uniform throughout in tens of hours by diffusion alone. Diffusion equations are derived which are applicable to finite-size chambers. Details and discussion of the experimental method are also given.

Towards real-time diffuse optical tomography for imaging brain functions cooperated with Kalman estimator

NASA Astrophysics Data System (ADS)

Wang, Bingyuan; Zhang, Yao; Liu, Dongyuan; Ding, Xuemei; Dan, Mai; Pan, Tiantian; Wang, Yihan; Li, Jiao; Zhou, Zhongxing; Zhang, Limin; Zhao, Huijuan; Gao, Feng

2018-02-01

Functional near-infrared spectroscopy (fNIRS) is a non-invasive neuroimaging method to monitor the cerebral hemodynamic through the optical changes measured at the scalp surface. It has played a more and more important role in psychology and medical imaging communities. Real-time imaging of brain function using NIRS makes it possible to explore some sophisticated human brain functions unexplored before. Kalman estimator has been frequently used in combination with modified Beer-Lamber Law (MBLL) based optical topology (OT), for real-time brain function imaging. However, the spatial resolution of the OT is low, hampering the application of OT in exploring some complicated brain functions. In this paper, we develop a real-time imaging method combining diffuse optical tomography (DOT) and Kalman estimator, much improving the spatial resolution. Instead of only presenting one spatially distributed image indicating the changes of the absorption coefficients at each time point during the recording process, one real-time updated image using the Kalman estimator is provided. Its each voxel represents the amplitude of the hemodynamic response function (HRF) associated with this voxel. We evaluate this method using some simulation experiments, demonstrating that this method can obtain more reliable spatial resolution images. Furthermore, a statistical analysis is also conducted to help to decide whether a voxel in the field of view is activated or not.

Anomalous Diffusion Measured by a Twice-Refocused Spin Echo Pulse Sequence: Analysis Using Fractional Order Calculus

PubMed Central

2011-01-01

Purpose To theoretically develop and experimentally validate a formulism based on a fractional order calculus (FC) diffusion model to characterize anomalous diffusion in brain tissues measured with a twice-refocused spin-echo (TRSE) pulse sequence. Materials and Methods The FC diffusion model is the fractional order generalization of the Bloch-Torrey equation. Using this model, an analytical expression was derived to describe the diffusion-induced signal attenuation in a TRSE pulse sequence. To experimentally validate this expression, a set of diffusion-weighted (DW) images was acquired at 3 Tesla from healthy human brains using a TRSE sequence with twelve b-values ranging from 0 to 2,600 s/mm2. For comparison, DW images were also acquired using a Stejskal-Tanner diffusion gradient in a single-shot spin-echo echo planar sequence. For both datasets, a Levenberg-Marquardt fitting algorithm was used to extract three parameters: diffusion coefficient D, fractional order derivative in space β, and a spatial parameter μ (in units of μm). Using adjusted R-squared values and standard deviations, D, β and μ values and the goodness-of-fit in three specific regions of interest (ROI) in white matter, gray matter, and cerebrospinal fluid were evaluated for each of the two datasets. In addition, spatially resolved parametric maps were assessed qualitatively. Results The analytical expression for the TRSE sequence, derived from the FC diffusion model, accurately characterized the diffusion-induced signal loss in brain tissues at high b-values. In the selected ROIs, the goodness-of-fit and standard deviations for the TRSE dataset were comparable with the results obtained from the Stejskal-Tanner dataset, demonstrating the robustness of the FC model across multiple data acquisition strategies. Qualitatively, the D, β, and μ maps from the TRSE dataset exhibited fewer artifacts, reflecting the improved immunity to eddy currents. Conclusion The diffusion-induced signal attenuation in a TRSE pulse sequence can be described by an FC diffusion model at high b-values. This model performs equally well for data acquired from the human brain tissues with a TRSE pulse sequence or a conventional Stejskal-Tanner sequence. PMID:21509877

Anomalous diffusion measured by a twice-refocused spin echo pulse sequence: analysis using fractional order calculus.

PubMed

Gao, Qing; Srinivasan, Girish; Magin, Richard L; Zhou, Xiaohong Joe

2011-05-01

To theoretically develop and experimentally validate a formulism based on a fractional order calculus (FC) diffusion model to characterize anomalous diffusion in brain tissues measured with a twice-refocused spin-echo (TRSE) pulse sequence. The FC diffusion model is the fractional order generalization of the Bloch-Torrey equation. Using this model, an analytical expression was derived to describe the diffusion-induced signal attenuation in a TRSE pulse sequence. To experimentally validate this expression, a set of diffusion-weighted (DW) images was acquired at 3 Tesla from healthy human brains using a TRSE sequence with twelve b-values ranging from 0 to 2600 s/mm(2). For comparison, DW images were also acquired using a Stejskal-Tanner diffusion gradient in a single-shot spin-echo echo planar sequence. For both datasets, a Levenberg-Marquardt fitting algorithm was used to extract three parameters: diffusion coefficient D, fractional order derivative in space β, and a spatial parameter μ (in units of μm). Using adjusted R-squared values and standard deviations, D, β, and μ values and the goodness-of-fit in three specific regions of interest (ROIs) in white matter, gray matter, and cerebrospinal fluid, respectively, were evaluated for each of the two datasets. In addition, spatially resolved parametric maps were assessed qualitatively. The analytical expression for the TRSE sequence, derived from the FC diffusion model, accurately characterized the diffusion-induced signal loss in brain tissues at high b-values. In the selected ROIs, the goodness-of-fit and standard deviations for the TRSE dataset were comparable with the results obtained from the Stejskal-Tanner dataset, demonstrating the robustness of the FC model across multiple data acquisition strategies. Qualitatively, the D, β, and μ maps from the TRSE dataset exhibited fewer artifacts, reflecting the improved immunity to eddy currents. The diffusion-induced signal attenuation in a TRSE pulse sequence can be described by an FC diffusion model at high b-values. This model performs equally well for data acquired from the human brain tissues with a TRSE pulse sequence or a conventional Stejskal-Tanner sequence. Copyright © 2011 Wiley-Liss, Inc.

Feasibility of high-resolution one-dimensional relaxation imaging at low magnetic field using a single-sided NMR scanner applied to articular cartilage

NASA Astrophysics Data System (ADS)

Rössler, Erik; Mattea, Carlos; Stapf, Siegfried

2015-02-01

Low field Nuclear Magnetic Resonance increases the contrast of the longitudinal relaxation rate in many biological tissues; one prominent example is hyaline articular cartilage. In order to take advantage of this increased contrast and to profile the depth-dependent variations, high resolution parameter measurements are carried out which can be of critical importance in an early diagnosis of cartilage diseases such as osteoarthritis. However, the maximum achievable spatial resolution of parameter profiles is limited by factors such as sensor geometry, sample curvature, and diffusion limitation. In this work, we report on high-resolution single-sided NMR scanner measurements with a commercial device, and quantify these limitations. The highest achievable spatial resolution on the used profiler, and the lateral dimension of the sensitive volume were determined. Since articular cartilage samples are usually bent, we also focus on averaging effects inside the horizontally aligned sensitive volume and their impact on the relaxation profiles. Taking these critical parameters into consideration, depth-dependent relaxation time profiles with the maximum achievable vertical resolution of 20 μm are discussed, and are correlated with diffusion coefficient profiles in hyaline articular cartilage in order to reconstruct T2 maps from the diffusion-weighted CPMG decays of apparent relaxation rates.

Confinement and diffusion modulate bistability and stochastic switching in a reaction network with positive feedback

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

Mlynarczyk, Paul J.; Pullen, Robert H.; Abel, Steven M., E-mail: abel@utk.edu

2016-01-07

Positive feedback is a common feature in signal transduction networks and can lead to phenomena such as bistability and signal propagation by domain growth. Physical features of the cellular environment, such as spatial confinement and the mobility of proteins, play important but inadequately understood roles in shaping the behavior of signaling networks. Here, we use stochastic, spatially resolved kinetic Monte Carlo simulations to explore a positive feedback network as a function of system size, system shape, and mobility of molecules. We show that these physical properties can markedly alter characteristics of bistability and stochastic switching when compared with well-mixed simulations.more » Notably, systems of equal volume but different shapes can exhibit qualitatively different behaviors under otherwise identical conditions. We show that stochastic switching to a state maintained by positive feedback occurs by cluster formation and growth. Additionally, the frequency at which switching occurs depends nontrivially on the diffusion coefficient, which can promote or suppress switching relative to the well-mixed limit. Taken together, the results provide a framework for understanding how confinement and protein mobility influence emergent features of the positive feedback network by modulating molecular concentrations, diffusion-influenced rate parameters, and spatiotemporal correlations between molecules.« less

Variable order fractional Fokker-Planck equations derived from Continuous Time Random Walks

NASA Astrophysics Data System (ADS)

Straka, Peter

2018-08-01

Continuous Time Random Walk models (CTRW) of anomalous diffusion are studied, where the anomalous exponent β(x) ∈(0 , 1) varies in space. This type of situation occurs e.g. in biophysics, where the density of the intracellular matrix varies throughout a cell. Scaling limits of CTRWs are known to have probability distributions which solve fractional Fokker-Planck type equations (FFPE). This correspondence between stochastic processes and FFPE solutions has many useful extensions e.g. to nonlinear particle interactions and reactions, but has not yet been sufficiently developed for FFPEs of the "variable order" type with non-constant β(x) . In this article, variable order FFPEs (VOFFPE) are derived from scaling limits of CTRWs. The key mathematical tool is the 1-1 correspondence of a CTRW scaling limit to a bivariate Langevin process, which tracks the cumulative sum of jumps in one component and the cumulative sum of waiting times in the other. The spatially varying anomalous exponent is modelled by spatially varying β(x) -stable Lévy noise in the waiting time component. The VOFFPE displays a spatially heterogeneous temporal scaling behaviour, with generalized diffusivity and drift coefficients whose units are length2/timeβ(x) resp. length/timeβ(x). A global change of the time scale results in a spatially varying change in diffusivity and drift. A consequence of the mathematical derivation of a VOFFPE from CTRW limits in this article is that a solution of a VOFFPE can be approximated via Monte Carlo simulations. Based on such simulations, we are able to confirm that the VOFFPE is consistent under a change of the global time scale.

The effect of recombination and attachment on meteor radar diffusion coefficient profiles

NASA Astrophysics Data System (ADS)

Lee, C. S.; Younger, J. P.; Reid, I. M.; Kim, Y. H.; Kim, J.-H.

2013-04-01

Estimates of the ambipolar diffusion coefficient producedusing meteor radar echo decay times display an increasing trend below 80-85 km, which is inconsistent with a diffusion-only theory of the evolution of meteor trails. Data from the 33 MHz meteor radar at King Sejong Station, Antarctica, have been compared with observations from the Aura Earth Observing System Microwave Limb Sounder satellite instrument. It has been found that the height at which the diffusion coefficient gradient reverses follows the height of a constant neutral atmospheric density surface. Numerical simulations of meteor trail diffusion including dissociative recombination with atmospheric ions and three-body attachment of free electrons to neutral molecules indicate that three-body attachment is responsible for the distortion of meteor radar diffusion coefficient profiles at heights below 90 km, including the gradient reversal below 80-85 km. Further investigation has revealed that meteor trails with low initial electron line density produce decay times more consistent with a diffusion-only model of meteor trail evolution.

Rumor Diffusion in an Interests-Based Dynamic Social Network

PubMed Central

Mao, Xinjun; Guessoum, Zahia; Zhou, Huiping

2013-01-01

To research rumor diffusion in social friend network, based on interests, a dynamic friend network is proposed, which has the characteristics of clustering and community, and a diffusion model is also proposed. With this friend network and rumor diffusion model, based on the zombie-city model, some simulation experiments to analyze the characteristics of rumor diffusion in social friend networks have been conducted. The results show some interesting observations: (1) positive information may evolve to become a rumor through the diffusion process that people may modify the information by word of mouth; (2) with the same average degree, a random social network has a smaller clustering coefficient and is more beneficial for rumor diffusion than the dynamic friend network; (3) a rumor is spread more widely in a social network with a smaller global clustering coefficient than in a social network with a larger global clustering coefficient; and (4) a network with a smaller clustering coefficient has a larger efficiency. PMID:24453911

Rumor diffusion in an interests-based dynamic social network.

PubMed

Tang, Mingsheng; Mao, Xinjun; Guessoum, Zahia; Zhou, Huiping

2013-01-01

To research rumor diffusion in social friend network, based on interests, a dynamic friend network is proposed, which has the characteristics of clustering and community, and a diffusion model is also proposed. With this friend network and rumor diffusion model, based on the zombie-city model, some simulation experiments to analyze the characteristics of rumor diffusion in social friend networks have been conducted. The results show some interesting observations: (1) positive information may evolve to become a rumor through the diffusion process that people may modify the information by word of mouth; (2) with the same average degree, a random social network has a smaller clustering coefficient and is more beneficial for rumor diffusion than the dynamic friend network; (3) a rumor is spread more widely in a social network with a smaller global clustering coefficient than in a social network with a larger global clustering coefficient; and (4) a network with a smaller clustering coefficient has a larger efficiency.

Venus' superrotation, mixing length theory and eddy diffusion - A parametric study

NASA Technical Reports Server (NTRS)

Mayr, H. G.; Harris, I.; Schatten, K. H.; Stevens-Rayburn, D. R.; Chan, K. L.

1988-01-01

The concept of the Hadley mechanism is adopted to describe the axisymmetric circulation of the Venus atmosphere. It is shown that, for the atmosphere of a slowly rotating planet such as Venus, a form of the nonliner 'closure' (self-consistent solution) of the fluid dynamics system which constrains the magnitude of the eddy diffusion coefficients can be postulated. A nonlinear one-layer spectral model of the zonally symmetric circulation was then used to establish the relationship between the heat source, the meridional circulation, and the eddy diffusion coefficients, yielding large zonal velocities. Computer experiments indicated that proportional changes in the heat source and eddy diffusion coefficients do not significantly change the zonal velocities. It was also found that, for large eddy diffusion coefficients, the meridional velocity is virtually constant; below a threshold in the diffusion rate, the meridional velocity decreases; and, for large eddy diffusion and small heating rates, the zonal velocities decrease with decreasing planetary rotation rates.

Arbitrary-order corrections for finite-time drift and diffusion coefficients

NASA Astrophysics Data System (ADS)

Anteneodo, C.; Riera, R.

2009-09-01

We address a standard class of diffusion processes with linear drift and quadratic diffusion coefficients. These contributions to dynamic equations can be directly drawn from data time series. However, real data are constrained to finite sampling rates and therefore it is crucial to establish a suitable mathematical description of the required finite-time corrections. Based on Itô-Taylor expansions, we present the exact corrections to the finite-time drift and diffusion coefficients. These results allow to reconstruct the real hidden coefficients from the empirical estimates. We also derive higher-order finite-time expressions for the third and fourth conditional moments that furnish extra theoretical checks for this class of diffusion models. The analytical predictions are compared with the numerical outcomes of representative artificial time series.

Diffusion coefficient and shear viscosity of rigid water models.

PubMed

Tazi, Sami; Boţan, Alexandru; Salanne, Mathieu; Marry, Virginie; Turq, Pierre; Rotenberg, Benjamin

2012-07-18

We report the diffusion coefficient and viscosity of popular rigid water models: two non-polarizable ones (SPC/E with three sites, and TIP4P/2005 with four sites) and a polarizable one (Dang-Chang, four sites). We exploit the dependence of the diffusion coefficient on the system size (Yeh and Hummer 2004 J. Phys. Chem. B 108 15873) to obtain the size-independent value. This also provides an estimate of the viscosity of all water models, which we compare to the Green-Kubo result. In all cases, a good agreement is found. The TIP4P/2005 model is in better agreement with the experimental data for both diffusion and viscosity. The SPC/E and Dang-Chang models overestimate the diffusion coefficient and underestimate the viscosity.

Effective diffusion coefficients of DNAPL waste components in saturated low permeability soil materials.

PubMed

Ayral-Cinar, Derya; Demond, Avery H

2017-12-01

Diffusion is regarded as the dominant transport mechanism into and out of low permeable subsurface lenses and layers in the subsurface. But, some reports of mass storage in such zones are higher than what might be attributable to diffusion, based on estimated diffusion coefficients. Despite the importance of diffusion to efforts to estimate the quantity of residual contamination in the subsurface, relatively few studies present measured diffusion coefficients of organic solutes in saturated low permeability soils. This study reports the diffusion coefficients of a trichloroethylene (TCE), and an anionic surfactant, Aerosol OT (AOT), in water-saturated silt and a silt-montmorillonite (25:75) mixture, obtained using steady-state experiments. The relative diffusivity ranged from 0.11 to 0.17 for all three compounds for the silt and the silt-clay mixture that was allowed to expand. In the case in which the swelling was constrained, the relative diffusivity was about 0.07. In addition, the relative diffusivity of 13 C-labeled TCE through a water saturated silt-clay mixture that had contacted a field dense non-aqueous phase liquid (DNAPL) for 18months was measured and equaled 0.001. These experimental results were compared with the estimates generated using common correlations, and it was found that, in all cases, the measured diffusion coefficients were significantly lower than the estimated. Thus, the discrepancy between mass accumulations observed in the field and the mass storage that can attributable to diffusion may be greater than previously believed. Copyright © 2017. Published by Elsevier B.V.

Fractional order analysis of Sephadex gel structures: NMR measurements reflecting anomalous diffusion

NASA Astrophysics Data System (ADS)

Magin, Richard L.; Akpa, Belinda S.; Neuberger, Thomas; Webb, Andrew G.

2011-12-01

We report the appearance of anomalous water diffusion in hydrophilic Sephadex gels observed using pulse field gradient (PFG) nuclear magnetic resonance (NMR). The NMR diffusion data was collected using a Varian 14.1 Tesla imaging system with a home-built RF saddle coil. A fractional order analysis of the data was used to characterize heterogeneity in the gels for the dynamics of water diffusion in this restricted environment. Several recent studies of anomalous diffusion have used the stretched exponential function to model the decay of the NMR signal, i.e., exp[-( bD) α], where D is the apparent diffusion constant, b is determined the experimental conditions (gradient pulse separation, durations and strength), and α is a measure of structural complexity. In this work, we consider a different case where the spatial Laplacian in the Bloch-Torrey equation is generalized to a fractional order model of diffusivity via a complexity parameter, β, a space constant, μ, and a diffusion coefficient, D. This treatment reverts to the classical result for the integer order case. The fractional order decay model was fit to the diffusion-weighted signal attenuation for a range of b-values (0 < b < 4000 s mm -2). Throughout this range of b values, the parameters β, μ and D, were found to correlate with the porosity and tortuosity of the gel structure.

Measurement of gas diffusion coefficient in liquid-saturated porous media using magnetic resonance imaging

NASA Astrophysics Data System (ADS)

Song, Yongchen; Hao, Min; Zhao, Yuechao; Zhang, Liang

2014-12-01

In this study, the dual-chamber pressure decay method and magnetic resonance imaging (MRI) were used to dynamically visualize the gas diffusion process in liquid-saturated porous media, and the relationship of concentration-distance for gas diffusing into liquid-saturated porous media at different times were obtained by MR images quantitative analysis. A non-iterative finite volume method was successfully applied to calculate the local gas diffusion coefficient in liquid-saturated porous media. The results agreed very well with the conventional pressure decay method, thus it demonstrates that the method was feasible of determining the local diffusion coefficient of gas in liquid-saturated porous media at different times during diffusion process.

Spectral Properties of Limit-Periodic Schrödinger Operators (PhD Thesis)

NASA Astrophysics Data System (ADS)

Gideonse, Hendrik David, XIX

The Acoustic Ramp is a wedge-shaped, number-theoretical quadratic-residue-type acoustic diffuser. Since the late 1970's, several methodologies for the testing and analysis of diffusers have been developed including, the ISO Scattering Coefficient and the AES Diffusion Coefficient. These coefficients are the source of some controversy today and this paper makes the attempt to investigate the benefits and weaknesses of these tools by using them to research and test the Acoustic Ramp. Several issues are exposed in using the coefficients, the most important of which being the validity of the comparison of the diffuser's behavior to that of a like sized flat panel. Further issues comprise of an intuitive disconnect between the perceived merits of polar plots and the numerical value of coefficients derived from the plots.

Measurement of diffusion coefficients important in modeling the absorption rate of carbon dioxide into aqueous N-methyldiethanolamine

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

Rowley, R.L.; Adams, M.E.; Marshall, T.L.

1997-03-01

Natural gas processors use amine treating processes to remove the acid gases H{sub 2}S and CO{sub 2} from gas streams. Absorption rates of gaseous CO{sub 2} into aqueous N-methyldiethanolamine (MDEA) solutions were measured in a quiescent, inverted-tube diffusiometer by monitoring the rate of pressure drop. The absorption rate was found to be insensitive to the diffusion coefficient of CO{sub 2} in solution but very sensitive to the diffusion rate of bicarbonate and protonated MDEA ions. Evidence also suggested that chemical reaction equilibrium is rapid relative to diffusion. A numerical model was developed on the basis of these observations. The modelmore » was used to regress diffusion coefficients of bicarbonate and protonated amine, which must be equivalent by electroneutrality arguments, from measured absorption rates. Complete modeling of the absorption process also required data for the diffusion coefficient of MDEA in water. These were measured using a Taylor dispersion apparatus. CO{sub 2} absorption rates and diffusion coefficients of bicarbonate and protonated MDEA were obtained at 298.2 K and 318.2 K in solutions containing 20, 35, and 50 mass % MDEA in water.« less

Short-scan-time multi-slice diffusion MRI of the mouse cervical spinal cord using echo planar imaging.

PubMed

Callot, Virginie; Duhamel, Guillaume; Cozzone, Patrick J; Kober, Frank

2008-10-01

Mouse spinal cord (SC) diffusion-weighted imaging (DWI) provides important information on tissue morphology and structural changes that may occur during pathologies such as multiple sclerosis or SC injury. The acquisition scheme of the commonly used DWI techniques is based on conventional spin-echo encoding, which is time-consuming. The purpose of this work was to investigate whether the use of echo planar imaging (EPI) would provide good-quality diffusion MR images of mouse SC, as well as accurate measurements of diffusion-derived metrics, and thus enable diffusion tensor imaging (DTI) and highly resolved DWI within reasonable scan times. A four-shot diffusion-weighted spin-echo EPI (SE-EPI) sequence was evaluated at 11.75 T on a group of healthy mice (n = 10). SE-EPI-derived apparent diffusion coefficients of gray and white matter were compared with those obtained using a conventional spin-echo sequence (c-SE) to validate the accuracy of the method. To take advantage of the reduction in acquisition time offered by the EPI sequence, multi-slice DTI acquisitions were performed covering the cervical segments (six slices, six diffusion-encoding directions, three b values) within 30 min (vs 2 h for c-SE). From these measurements, fractional anisotropy and mean diffusivities were calculated, and fiber tracking along the C1 to C6 cervical segments was performed. In addition, high-resolution images (74 x 94 microm(2)) were acquired within 5 min per direction. Clear delineation of gray and white matter and identical apparent diffusion coefficient values were obtained, with a threefold reduction in acquisition time compared with c-SE. While overcoming the difficulties associated with high spatially and temporally resolved DTI measurements, the present SE-EPI approach permitted identification of reliable quantitative parameters with a reproducibility compatible with the detection of pathologies. The SE-EPI method may be particularly valuable when multiple sets of images from the SC are needed, in cases of rapidly evolving conditions, to decrease the duration of anesthesia or to improve MR exploration by including additional MR measurements. Copyright (c) 2008 John Wiley & Sons, Ltd.

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.

Experimental investigation of turbulent diffusion of slightly buoyant droplets in locally isotropic turbulence

NASA Astrophysics Data System (ADS)

Gopalan, Balaji; Malkiel, Edwin; Katz, Joseph

2008-09-01

High-speed inline digital holographic cinematography is used for studying turbulent diffusion of slightly buoyant 0.5-1.2 mm diameter diesel droplets and 50 μm diameter neutral density particles. Experiments are performed in a 50×50×70 mm3 sample volume in a controlled, nearly isotropic turbulence facility, which is characterized by two dimensional particle image velocimetry. An automated tracking program has been used for measuring velocity time history of more than 17 000 droplets and 15 000 particles. For most of the present conditions, rms values of horizontal droplet velocity exceed those of the fluid. The rms values of droplet vertical velocity are higher than those of the fluid only for the highest turbulence level. The turbulent diffusion coefficient is calculated by integration of the ensemble-averaged Lagrangian velocity autocovariance. Trends of the asymptotic droplet diffusion coefficient are examined by noting that it can be viewed as a product of a mean square velocity and a diffusion time scale. To compare the effects of turbulence and buoyancy, the turbulence intensity (ui') is scaled by the droplet quiescent rise velocity (Uq). The droplet diffusion coefficients in horizontal and vertical directions are lower than those of the fluid at low normalized turbulence intensity, but exceed it with increasing normalized turbulence intensity. For most of the present conditions the droplet horizontal diffusion coefficient is higher than the vertical diffusion coefficient, consistent with trends of the droplet velocity fluctuations and in contrast to the trends of the diffusion timescales. The droplet diffusion coefficients scaled by the product of turbulence intensity and an integral length scale are a monotonically increasing function of ui'/Uq.

Electronic transport characterization of silicon wafers by spatially resolved steady-state photocarrier radiometric imaging

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

Wang, Qian; University of the Chinese Academy of Sciences, Beijing 100039; Li, Bincheng, E-mail: bcli@ioe.ac.cn

2015-09-28

Spatially resolved steady-state photocarrier radiometric (PCR) imaging technique is developed to characterize the electronic transport properties of silicon wafers. Based on a nonlinear PCR theory, simulations are performed to investigate the effects of electronic transport parameters (the carrier lifetime, the carrier diffusion coefficient, and the front surface recombination velocity) on the steady-state PCR intensity profiles. The electronic transport parameters of an n-type silicon wafer are simultaneously determined by fitting the measured steady-state PCR intensity profiles to the three-dimensional nonlinear PCR model. The determined transport parameters are in good agreement with the results obtained by the conventional modulated PCR technique withmore » multiple pump beam radii.« less

Gene interference regulates aquaporin-4 expression in swollen tissue of rats with cerebral ischemic edema

PubMed Central

Hu, Hui; Lu, Hong; He, Zhanping; Han, Xiangjun; Chen, Jing; Tu, Rong

2012-01-01

To investigate the effects of mRNA interference on aquaporin-4 expression in swollen tissue of rats with ischemic cerebral edema, and diagnose the significance of diffusion-weighted MRI, we injected 5 μL shRNA- aquaporin-4 (control group) or siRNA- aquaporin-4 solution (1:800) (RNA interference group) into the rat right basal ganglia immediately before occlusion of the middle cerebral artery. At 0.25 hours after occlusion of the middle cerebral artery, diffusion-weighted MRI displayed a high signal; within 2 hours, the relative apparent diffusion coefficient decreased markedly, aquaporin-4 expression increased rapidly, and intracellular edema was obviously aggravated; at 4 and 6 hours, the relative apparent diffusion coefficient slowly returned to control levels, aquaporin-4 expression slightly increased, and angioedema was observed. In the RNA interference group, during 0.25–6 hours after injection of siRNA- aquaporin-4 solution, the relative apparent diffusion coefficient slightly fluctuated and aquaporin-4 expression was upregulated; during 0.5–4 hours, the relative apparent diffusion coefficient was significantly higher, while aquaporin-4 expression was significantly lower when compared with the control group, and intracellular edema was markedly reduced; at 0.25 and 6 hours, the relative apparent diffusion coefficient and aquaporin-4 expression were similar when compared with the control group; obvious angioedema remained at 6 hours. Pearson's correlation test results showed that aquaporin-4 expression was negatively correlated with the apparent diffusion coefficient (r = −0.806, P < 0.01). These findings suggest that upregulated aquaporin-4 expression is likely to be the main molecular mechanism of intracellular edema and may be the molecular basis for decreased relative apparent diffusion coefficient. Aquaporin-4 gene interference can effectively inhibit the upregulation of aquaporin-4 expression during the stage of intracellular edema with time-effectiveness. Moreover, diffusion-weighted MRI can accurately detect intracellular edema. PMID:25657707

Perpendicular Diffusion Coefficient of Comic Rays: The Presence of Weak Adiabatic Focusing

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

Wang, J. F.; Ma, Q. M.; Song, T.

The influence of adiabatic focusing on particle diffusion is an important topic in astrophysics and plasma physics. In the past, several authors have explored the influence of along-field adiabatic focusing on the parallel diffusion of charged energetic particles. In this paper, using the unified nonlinear transport theory developed by Shalchi and the method of He and Schlickeiser, we derive a new nonlinear perpendicular diffusion coefficient for a non-uniform background magnetic field. This formula demonstrates that the particle perpendicular diffusion coefficient is modified by along-field adiabatic focusing. For isotropic pitch-angle scattering and the weak adiabatic focusing limit, the derived perpendicular diffusionmore » coefficient is independent of the sign of adiabatic focusing characteristic length. For the two-component model, we simplify the perpendicular diffusion coefficient up to the second order of the power series of the adiabatic focusing characteristic quantity. We find that the first-order modifying factor is equal to zero and that the sign of the second order is determined by the energy of the particles.« less

Coupled Protein Diffusion and Folding in the Cell

PubMed Central

Guo, Minghao; Gelman, Hannah; Gruebele, Martin

2014-01-01

When a protein unfolds in the cell, its diffusion coefficient is affected by its increased hydrodynamic radius and by interactions of exposed hydrophobic residues with the cytoplasmic matrix, including chaperones. We characterize protein diffusion by photobleaching whole cells at a single point, and imaging the concentration change of fluorescent-labeled protein throughout the cell as a function of time. As a folded reference protein we use green fluorescent protein. The resulting region-dependent anomalous diffusion is well characterized by 2-D or 3-D diffusion equations coupled to a clustering algorithm that accounts for position-dependent diffusion. Then we study diffusion of a destabilized mutant of the enzyme phosphoglycerate kinase (PGK) and of its stable control inside the cell. Unlike the green fluorescent protein control's diffusion coefficient, PGK's diffusion coefficient is a non-monotonic function of temperature, signaling ‘sticking’ of the protein in the cytosol as it begins to unfold. The temperature-dependent increase and subsequent decrease of the PGK diffusion coefficient in the cytosol is greater than a simple size-scaling model suggests. Chaperone binding of the unfolding protein inside the cell is one plausible candidate for even slower diffusion of PGK, and we test the plausibility of this hypothesis experimentally, although we do not rule out other candidates. PMID:25436502

Coupled protein diffusion and folding in the cell.

PubMed

Guo, Minghao; Gelman, Hannah; Gruebele, Martin

2014-01-01

When a protein unfolds in the cell, its diffusion coefficient is affected by its increased hydrodynamic radius and by interactions of exposed hydrophobic residues with the cytoplasmic matrix, including chaperones. We characterize protein diffusion by photobleaching whole cells at a single point, and imaging the concentration change of fluorescent-labeled protein throughout the cell as a function of time. As a folded reference protein we use green fluorescent protein. The resulting region-dependent anomalous diffusion is well characterized by 2-D or 3-D diffusion equations coupled to a clustering algorithm that accounts for position-dependent diffusion. Then we study diffusion of a destabilized mutant of the enzyme phosphoglycerate kinase (PGK) and of its stable control inside the cell. Unlike the green fluorescent protein control's diffusion coefficient, PGK's diffusion coefficient is a non-monotonic function of temperature, signaling 'sticking' of the protein in the cytosol as it begins to unfold. The temperature-dependent increase and subsequent decrease of the PGK diffusion coefficient in the cytosol is greater than a simple size-scaling model suggests. Chaperone binding of the unfolding protein inside the cell is one plausible candidate for even slower diffusion of PGK, and we test the plausibility of this hypothesis experimentally, although we do not rule out other candidates.

Determination of the diffusion coefficient and phase-transfer rate parameter in LaNi{sub 5} and MmNi{sub 3.6}Co{sub 0.8}Mn{sub 0.4}Al{sub 0.3} using microelectrodes

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

Lundqvist, A.; Lindbergh, G.

1998-11-01

A potential-step method for determining the diffusion coefficient and phase-transfer parameter in metal hydrides by using microelectrodes was investigated. It was shown that a large potential step is not enough to ensure a completely diffusion-limited mass transfer if a surface-phase transfer reaction takes place at a finite rate. It was shown, using a kinetic expression for the surface phase-transfer reaction, that the slope of the logarithm of the current vs. time curve will be constant both in the case of the mass-transfer limited by diffusion or by diffusion and a surface-phase transfer. The diffusion coefficient and phase-transfer rate parameter weremore » accurately determined for MmNi{sub 3.6}Co{sub 0.8}Mn{sub 0.4}Al{sub 0.3} using a fit to the whole transient. The diffusion coefficient was found to be (1.3 {+-} 0.3) {times} 10{sup {minus}13} m{sup 2}/s. The fit was good and showed that a pure diffusion model was not enough to explain the observed transient. The diffusion coefficient and phase-transfer rate parameter were also estimated for pure LaNi{sub 5}. A fit of the whole curve showed that neither a pure diffusion model nor a model including phase transfer could explain the whole transient.« less

Determination of diffusion coefficients of carbon dioxide in water between 268 and 473 K in a high-pressure capillary optical cell with in situ Raman spectroscopic measurements

USGS Publications Warehouse

Lu, Wanjun; Guo, Huirong; Chou, I.-Ming; Burruss, R.C.; Li, Lanlan

2013-01-01

Accurate values of diffusion coefficients for carbon dioxide in water and brine at reservoir conditions are essential to our understanding of transport behavior of carbon dioxide in subsurface pore space. However, the experimental data are limited to conditions at low temperatures and pressures. In this study, diffusive transfer of carbon dioxide in water at pressures up to 45 MPa and temperatures from 268 to 473 K was observed within an optical capillary cell via time-dependent Raman spectroscopy. Diffusion coefficients were estimated by the least-squares method for the measured variations in carbon dioxide concentration in the cell at various sample positions and time. At the constant pressure of 20 MPa, the measured diffusion coefficients of carbon dioxide in water increase with increasing temperature from 268 to 473 K. The relationship between diffusion coefficient of carbon dioxide in water [D(CO2) in m2/s] and temperature (T in K) was derived with Speedy–Angell power-law approach as: D(CO2)=D0[T/Ts-1]m where D0 = 13.942 × 10−9 m2/s, Ts = 227.0 K, and m = 1.7094. At constant temperature, diffusion coefficients of carbon dioxide in water decrease with pressure increase. However, this pressure effect is rather small (within a few percent).

Entropy-scaling laws for diffusion coefficients in liquid metals under high pressures

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

Cao, Qi-Long, E-mail: qlcao@mail.ustc.edu.cn; Shao, Ju-Xiang; Wang, Fan-Hou, E-mail: eatonch@gmail.com

2015-04-07

Molecular dynamic simulations on the liquid copper and tungsten are used to investigate the empirical entropy-scaling laws D{sup *}=A exp(BS{sub ex}), proposed independently by Rosenfeld and Dzugutov for diffusion coefficient, under high pressure conditions. We show that the scaling laws hold rather well for them under high pressure conditions. Furthermore, both the original diffusion coefficients and the reduced diffusion coefficients exhibit an Arrhenius relationship D{sub M}=D{sub M}{sup 0} exp(−E{sub M}/K{sub B}T), (M=un,R,D) and the activation energy E{sub M} increases with increasing pressure, the diffusion pre-exponential factors (D{sub R}{sup 0} and D{sub D}{sup 0}) are nearly independent of the pressure and element. Themore » pair correlation entropy, S{sub 2}, depends linearly on the reciprocal temperature S{sub 2}=−E{sub S}/T, and the activation energy, E{sub S}, increases with increasing pressure. In particular, the ratios of the activation energies (E{sub un}, E{sub R}, and E{sub D}) obtained from diffusion coefficients to the activation energy, E{sub S}, obtained from the entropy keep constants in the whole pressure range. Therefore, the entropy-scaling laws for the diffusion coefficients and the Arrhenius law are linked via the temperature dependence of entropy.« less

Solute diffusion in liquid metals

NASA Technical Reports Server (NTRS)

Bhat, B. N.

1973-01-01

A gas model of diffusion in liquid metals is presented. In this model, ions of liquid metals are assumed to behave like the molecules in a dense gas. Diffusion coefficient of solute is discussed with reference to its mass, ionic size, and pair potential. The model is applied to the case of solute diffusion in liquid silver. An attempt was made to predict diffusion coefficients of solutes with reasonable accuracy.

Dynamic characterization of external and internal mass transport in heterotrophic biofilms from microsensors measurements.

PubMed

Guimerà, Xavier; Dorado, Antonio David; Bonsfills, Anna; Gabriel, Gemma; Gabriel, David; Gamisans, Xavier

2016-10-01

Knowledge of mass transport mechanisms in biofilm-based technologies such as biofilters is essential to improve bioreactors performance by preventing mass transport limitation. External and internal mass transport in biofilms was characterized in heterotrophic biofilms grown on a flat plate bioreactor. Mass transport resistance through the liquid-biofilm interphase and diffusion within biofilms were quantified by in situ measurements using microsensors with a high spatial resolution (<50 μm). Experimental conditions were selected using a mathematical procedure based on the Fisher Information Matrix to increase the reliability of experimental data and minimize confidence intervals of estimated mass transport coefficients. The sensitivity of external and internal mass transport resistances to flow conditions within the range of typical fluid velocities over biofilms (Reynolds numbers between 0.5 and 7) was assessed. Estimated external mass transfer coefficients at different liquid phase flow velocities showed discrepancies with studies considering laminar conditions in the diffusive boundary layer near the liquid-biofilm interphase. The correlation of effective diffusivity with flow velocities showed that the heterogeneous structure of biofilms defines the transport mechanisms inside biofilms. Internal mass transport was driven by diffusion through cell clusters and aggregates at Re below 2.8. Conversely, mass transport was driven by advection within pores, voids and water channels at Re above 5.6. Between both flow velocities, mass transport occurred by a combination of advection and diffusion. Effective diffusivities estimated at different biofilm densities showed a linear increase of mass transport resistance due to a porosity decrease up to biofilm densities of 50 g VSS·L(-1). Mass transport was strongly limited at higher biofilm densities. Internal mass transport results were used to propose an empirical correlation to assess the effective diffusivity within biofilms considering the influence of hydrodynamics and biofilm density. Copyright © 2016 Elsevier Ltd. All rights reserved.

Role of Heterogeneous Macromolecular Crowding and Geometrical Irregularity at Central Excitatory Synapses in Shaping Synaptic Transmission

PubMed Central

Gupta, Rahul; Reneaux, Melissa; Karmeshu

2016-01-01

Besides the geometrical tortousity due to the extrasynaptic structures, macromolecular crowding and geometrical irregularities constituting the cleft composition at central excitatory synapses has a major and direct role in retarding the glutamate diffusion within the cleft space. However, the cleft composition may not only coarsely reduce the overall diffusivity of the glutamate but may also lead to substantial spatial variation in the diffusivity across the cleft space. Decrease in the overall diffusivity of the glutamate may have straightforward consequences to the glutamate transients in the cleft. However, how spatial variation in the diffusivity may further affect glutamate transients is an intriguing aspect. Therefore, to understand the role of cleft heterogeneity, the present study adopts a novel approach of glutamate diffusion which considers a gamma statistical distribution of the diffusion coefficient of glutamate (Dglut) across the cleft space, such that its moments discernibly capture the dual impacts of the cleft composition, and further applies the framework of superstatistics. The findings reveal a power law behavior in the glutamate transients, akin to the long-range anomalous subdiffusion, which leads to slower decay profile of cleft glutamate at higher intensity of cleft heterogeneity. Moreover, increase in the cleft heterogeneity is seen to eventually cause slower-rising excitatory postsynaptic currents with higher amplitudes, lesser noise, and prolonged duration of charge transfer across the postsynaptic membrane. Further, with regard to the conventional standard diffusion approach, the study suggests that the effective Dglut essentially derives from the median of the Dglut distribution and does not necessarily need to be the mean Dglut. Together, the findings indicate a strong implication of cleft heterogeneity to the metabolically cost-effective tuning of synaptic response during the phenomenon of plasticity at individual synapses and also provide an additional factor of variability in transmission across identical synapses. PMID:27907112

Matrix diffusion coefficients in volcanic rocks at the Nevada test site: influence of matrix porosity, matrix permeability, and fracture coating minerals.

PubMed

Reimus, Paul W; Callahan, Timothy J; Ware, S Doug; Haga, Marc J; Counce, Dale A

2007-08-15

Diffusion cell experiments were conducted to measure nonsorbing solute matrix diffusion coefficients in forty-seven different volcanic rock matrix samples from eight different locations (with multiple depth intervals represented at several locations) at the Nevada Test Site. The solutes used in the experiments included bromide, iodide, pentafluorobenzoate (PFBA), and tritiated water ((3)HHO). The porosity and saturated permeability of most of the diffusion cell samples were measured to evaluate the correlation of these two variables with tracer matrix diffusion coefficients divided by the free-water diffusion coefficient (D(m)/D*). To investigate the influence of fracture coating minerals on matrix diffusion, ten of the diffusion cells represented paired samples from the same depth interval in which one sample contained a fracture surface with mineral coatings and the other sample consisted of only pure matrix. The log of (D(m)/D*) was found to be positively correlated with both the matrix porosity and the log of matrix permeability. A multiple linear regression analysis indicated that both parameters contributed significantly to the regression at the 95% confidence level. However, the log of the matrix diffusion coefficient was more highly-correlated with the log of matrix permeability than with matrix porosity, which suggests that matrix diffusion coefficients, like matrix permeabilities, have a greater dependence on the interconnectedness of matrix porosity than on the matrix porosity itself. The regression equation for the volcanic rocks was found to provide satisfactory predictions of log(D(m)/D*) for other types of rocks with similar ranges of matrix porosity and permeability as the volcanic rocks, but it did a poorer job predicting log(D(m)/D*) for rocks with lower porosities and/or permeabilities. The presence of mineral coatings on fracture walls did not appear to have a significant effect on matrix diffusion in the ten paired diffusion cell experiments.

Matrix diffusion coefficients in volcanic rocks at the Nevada test site: Influence of matrix porosity, matrix permeability, and fracture coating minerals

NASA Astrophysics Data System (ADS)

Reimus, Paul W.; Callahan, Timothy J.; Ware, S. Doug; Haga, Marc J.; Counce, Dale A.

2007-08-01

Diffusion cell experiments were conducted to measure nonsorbing solute matrix diffusion coefficients in forty-seven different volcanic rock matrix samples from eight different locations (with multiple depth intervals represented at several locations) at the Nevada Test Site. The solutes used in the experiments included bromide, iodide, pentafluorobenzoate (PFBA), and tritiated water ( 3HHO). The porosity and saturated permeability of most of the diffusion cell samples were measured to evaluate the correlation of these two variables with tracer matrix diffusion coefficients divided by the free-water diffusion coefficient ( Dm/ D*). To investigate the influence of fracture coating minerals on matrix diffusion, ten of the diffusion cells represented paired samples from the same depth interval in which one sample contained a fracture surface with mineral coatings and the other sample consisted of only pure matrix. The log of ( Dm/ D*) was found to be positively correlated with both the matrix porosity and the log of matrix permeability. A multiple linear regression analysis indicated that both parameters contributed significantly to the regression at the 95% confidence level. However, the log of the matrix diffusion coefficient was more highly-correlated with the log of matrix permeability than with matrix porosity, which suggests that matrix diffusion coefficients, like matrix permeabilities, have a greater dependence on the interconnectedness of matrix porosity than on the matrix porosity itself. The regression equation for the volcanic rocks was found to provide satisfactory predictions of log( Dm/ D*) for other types of rocks with similar ranges of matrix porosity and permeability as the volcanic rocks, but it did a poorer job predicting log( Dm/ D*) for rocks with lower porosities and/or permeabilities. The presence of mineral coatings on fracture walls did not appear to have a significant effect on matrix diffusion in the ten paired diffusion cell experiments.

Photon diffusion coefficient in scattering and absorbing media.

PubMed

Pierrat, Romain; Greffet, Jean-Jacques; Carminati, Rémi

2006-05-01

We present a unified derivation of the photon diffusion coefficient for both steady-state and time-dependent transport in disordered absorbing media. The derivation is based on a modal analysis of the time-dependent radiative transfer equation. This approach confirms that the dynamic diffusion coefficient is given by the random-walk result D = cl(*)/3, where l(*) is the transport mean free path and c is the energy velocity, independent of the level of absorption. It also shows that the diffusion coefficient for steady-state transport, often used in biomedical optics, depends on absorption, in agreement with recent theoretical and experimental works. These two results resolve a recurrent controversy in light propagation and imaging in scattering media.

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).

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

Sarman, Sten, E-mail: sarman@ownit.nu; Wang, Yong-Lei; Laaksonen, Aatto

The self-diffusion coefficients of nematic phases of various model systems consisting of regular convex calamitic and discotic ellipsoids and non-convex bodies such as bent-core molecules and soft ellipsoid strings have been obtained as functions of the shear rate in a shear flow. Then the self-diffusion coefficient is a second rank tensor with three different diagonal components and two off-diagonal components. These coefficients were found to be determined by a combination of two mechanisms, which previously have been found to govern the self-diffusion of shearing isotropic liquids, namely, (i) shear alignment enhancing the diffusion in the direction parallel to the streamlinesmore » and hindering the diffusion in the perpendicular directions and (ii) the distortion of the shell structure in the liquid whereby a molecule more readily can escape from a surrounding shell of nearest neighbors, so that the mobility increases in every direction. Thus, the diffusion parallel to the streamlines always increases with the shear rate since these mechanisms cooperate in this direction. In the perpendicular directions, these mechanisms counteract each other so that the behaviour becomes less regular. In the case of the nematic phases of the calamitic and discotic ellipsoids and of the bent core molecules, mechanism (ii) prevails so that the diffusion coefficients increase. However, the diffusion coefficients of the soft ellipsoid strings decrease in the direction of the velocity gradient because the broadsides of these molecules are oriented perpendicularly to this direction due the shear alignment (i). The cross coupling coefficient relating a gradient of tracer particles in the direction of the velocity gradient and their flow in the direction of the streamlines is negative and rather large, whereas the other coupling coefficient relating a gradient in the direction of the streamlines and a flow in the direction of the velocity gradient is very small.« less

[Lateral diffusion of saturated phosphatidylcholines in cholesterol-containing bilayers].

PubMed

Filippov, A V; Rudakova, M A; Oradd, G; Lindblom, J

2007-01-01

Lateral diffusion in oriented bilayers of saturated cholesterol-containing phosphatidylcholines, dipalmitoylphosphatidylcholine and dimyrilstoylphosphatidylcholine upon their limiting hydration has been studied by NMR with impulse gradient of magnetic field. For both systems, similar dependences of the coefficient of lateral diffusion on temperature and cholesterol concentration were observed, which agree with the phase diagram showing the presence of regions of ordered and unordered liquid-crystalline phases and a two-phase region. Under similar conditions, the coefficient of lateral diffusion for dipalmytoylphosphatidylcholine has lower values, which is in qualitative agreement with its greater molecular mass. A comparison of data for dipalmytoylphosphatidylcholine with the results obtained earlier for dipalmytoylsphyngomyelin/cholesterol under the same conditions shows, despite a similarity in phase diagrams, greater (two- to threefold) differences in the values of the coefficient of lateral diffusion and a different mode of dependence of the coefficient on cholesterol concentration. A comparison of data for dimyrilstoylphosphatidylcholine with the results obtained previously shows that the values of the coefficient of lateral diffusion and the mode of its dependence on cholesterol concentration coincide in the region of higher concentrations (more than 15 mole %) and differ in the region of lower concentrations (below 15 mole %). The discrepancies may be explained by different contents of water in the systems during the measurements. At a limiting hydration (more than 35%) of water, the coefficient of lateral diffusion decreases with increasing cholesterol concentration. If the content of water is about 25% (as a result of equilibrium hydration from vapors), the coefficient of lateral diffusion of phosphatidylcholine is probably independent of cholesterol concentration. This results from a denser packing of molecules in the bilayer at a lower water concentration, an effect that competes with the ordering effect of cholesterol.

Molecular dynamic simulation of dicationic ionic liquids: effects of anions and alkyl chain length on liquid structure and diffusion.

PubMed

Yeganegi, Saeid; Soltanabadi, Azim; Farmanzadeh, Davood

2012-09-20

Structures and dynamics of nine geminal dicationic ionic liquids (DILs) Cn(mim)2X2, where n = 3, 6, and 9 and X = PF6(-), BF4(-), and Br(-), were studied by molecular dynamic simulations (J. Phys. Chem.B2004, 108, 2038-2047). A force field with a minor modification for C3(mim)2 × 2 was adopted for the simulations. Densities, detailed microscopic structures, mean-square displacements (MSD), and self-diffusivities for various ion pairs from MD simulations have been presented. The calculated densities for C9(mim)2X2 (X = Br(-) and BF4(-)) agreed well with the experimental values. The calculated RDFs show that anions are well organized around the imidazolium rings. The calculated RDFs indicate that, unlike the mono cationic ILs, the anions and cations in DILs distribute homogeneously. Enthalpies of vaporization were calculated and correlated with the structural features of DILs. The local structure of C9(mim)2X2 (X = Br, PF6) was examined by the spatial distribution function (SDF). The calculated SDFs show that similar trends were found by other groups for mono cationic ionic liquids (ILs). The highest probability densities are located around the imidazolium ring hydrogens. The calculated diffusion coefficients show that the ion diffusivities are 1 order of magnitude smaller than that of the mono cationic ionic liquids. The effects of alkyl chain length and anion type on the diffusion coefficient were also studied. The dynamics of the imidazolium rings and the alkyl chain in different time scales have also discussed. The calculated transference numbers show that the anions have the major role in carrying the electric current in a DIL.

A novel multiple headspace extraction gas chromatographic method for measuring the diffusion coefficient of methanol in water and in olive oil.

PubMed

Zhang, Chun-Yun; Chai, Xin-Sheng

2015-03-13

A novel method for the determination of the diffusion coefficient (D) of methanol in water and olive oil has been developed. Based on multiple headspace extraction gas chromatography (MHE-GC), the methanol released from the liquid sample of interest in a closed sample vial was determined in a stepwise fashion. A theoretical model was derived to establish the relationship between the diffusion coefficient and the GC signals from MHE-GC measurements. The results showed that the present method has an excellent precision (RSD<1%) in the linear fitting procedure and good accuracy for the diffusion coefficients of methanol in both water and olive oil, when compared with data reported in the literature. The present method is simple and practical and can be a valuable tool for the determination of the diffusion coefficient of volatile analyte(s) into food simulants from food and beverage packaging material, both in research studies and in actual applications. Copyright © 2015 Elsevier B.V. All rights reserved.

Prediction of stream volatilization coefficients

USGS Publications Warehouse

Rathbun, Ronald E.

1990-01-01

Equations are developed for predicting the liquid-film and gas-film reference-substance parameters for quantifying volatilization of organic solutes from streams. Molecular weight and molecular-diffusion coefficients of the solute are used as correlating parameters. Equations for predicting molecular-diffusion coefficients of organic solutes in water and air are developed, with molecular weight and molal volume as parameters. Mean absolute errors of prediction for diffusion coefficients in water are 9.97% for the molecular-weight equation, 6.45% for the molal-volume equation. The mean absolute error for the diffusion coefficient in air is 5.79% for the molal-volume equation. Molecular weight is not a satisfactory correlating parameter for diffusion in air because two equations are necessary to describe the values in the data set. The best predictive equation for the liquid-film reference-substance parameter has a mean absolute error of 5.74%, with molal volume as the correlating parameter. The best equation for the gas-film parameter has a mean absolute error of 7.80%, with molecular weight as the correlating parameter.

Optimization and Clinical Feasibility of Free-breathing Diffusion-weighted Imaging of the Liver: Comparison with Respiratory-Triggered Diffusion-weighted Imaging.

PubMed

Takayama, Yukihisa; Nishie, Akihiro; Asayama, Yoshiki; Ishigami, Kousei; Kakihara, Daisuke; Ushijima, Yasuhiro; Fujita, Nobuhiro; Yoshiura, Takashi; Takemura, Atsushi; Obara, Makoto; Takahara, Taro; Honda, Hiroshi

2015-01-01

We compared the image quality of free-breathing diffusion-weighted imaging (FB-DWI) to that of respiratory-triggered DWI (RT-DWI) after proper optimization. Three healthy subjects were scanned to optimize magnetic resonance (MR) parameters of FB-DWI to improve image quality, including spatial resolution, image noise, and chemical shift artifacts. After this optimization, we scanned 32 patients with liver disease to assess the clinical feasibility of the optimized FB-DWI. Of the 32 patients, 14 had a total of 28 hepatocellular carcinomas (HCCs), four had a total of 15 metastatic liver tumors, and the other 14 had no tumor. Qualitatively, we compared the image quality scores of FB-DWI with those of RT-DWI with the Wilcoxon signed-rank test. Quantitatively, we compared the signal-to-noise ratios (SNRs) of the liver parenchyma, lesion-to-nonlesion contrast-to-noise ratios (CNRs) and apparent diffusion coefficient (ADC) values of the liver parenchyma and liver tumor by the paired t-test. The average scores of image quality for sharpness of liver contour, image noise, and chemical shift artifacts were significantly higher for FB-DWI than RT-DWI (P < 0.05). SNRs, CNRs, and ADC values of the liver parenchyma and tumors did not differ significantly between the 2 DWI methods. Compared with RT-DWI, the optimized FB-DWI provided better spatial resolution, fewer artifacts, and comparable SNRs, lesion-to-nonlesion CNRs, and ADC values.

Spatial glass transition temperature variations in polymer glass: application to a maltodextrin-water system.

PubMed

van Sleeuwen, Rutger M T; Zhang, Suying; Normand, Valéry

2012-03-12

A model was developed to predict spatial glass transition temperature (T(g)) distributions in glassy maltodextrin particles during transient moisture sorption. The simulation employed a numerical mass transfer model with a concentration dependent apparent diffusion coefficient (D(app)) measured using Dynamic Vapor Sorption. The mass average moisture content increase and the associated decrease in T(g) were successfully modeled over time. Large spatial T(g) variations were predicted in the particle, resulting in a temporary broadening of the T(g) region. Temperature modulated differential scanning calorimetry confirmed that the variation in T(g) in nonequilibrated samples was larger than in equilibrated samples. This experimental broadening was characterized by an almost doubling of the T(g) breadth compared to the start of the experiment. Upon reaching equilibrium, both the experimental and predicted T(g) breadth contracted back to their initial value.

Dissipative particle dynamics study of velocity autocorrelation function and self-diffusion coefficient in terms of interaction potential strength

NASA Astrophysics Data System (ADS)

Zohravi, Elnaz; Shirani, Ebrahim; Pishevar, Ahmadreza; Karimpour, Hossein

2018-07-01

This research focuses on numerically investigating the self-diffusion coefficient and velocity autocorrelation function (VACF) of a dissipative particle dynamics (DPD) fluid as a function of the conservative interaction strength. Analytic solutions to VACF and self-diffusion coefficients in DPD were obtained by many researchers in some restricted cases including ideal gases, without the account of conservative force. As departure from the ideal gas conditions are accentuated with increasing the relative proportion of conservative force, it is anticipated that the VACF should gradually deviate from its normally expected exponentially decay. This trend is confirmed through numerical simulations and an expression in terms of the conservative force parameter, density and temperature is proposed for the self-diffusion coefficient. As it concerned the VACF, the equivalent Langevin equation describing Brownian motion of particles with a harmonic potential is adapted to the problem and reveals an exponentially decaying oscillatory pattern influenced by the conservative force parameter, dissipative parameter and temperature. Although the proposed model for obtaining the self-diffusion coefficient with consideration of the conservative force could not be verified due to computational complexities, nonetheless the Arrhenius dependency of the self-diffusion coefficient to temperature and pressure permits to certify our model over a definite range of DPD parameters.

Interdiffusion and stress development in single-crystalline Pd/Ag bilayers

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

Noah, Martin A., E-mail: m.noah@is.mpg.de; Flötotto, David; Wang, Zumin

Interdiffusion and stress evolution in single-crystalline Pd/single-crystalline Ag thin films were investigated by Auger electron spectroscopy sputter-depth profiling and in-situ X-ray diffraction, respectively. The concentration-dependent chemical diffusion coefficient, as well as the impurity diffusion coefficient of Ag in Pd could be determined in the low temperature range of 356 °C–455 °C. As a consequence of the similarity of the strong concentration-dependences of the intrinsic diffusion coefficients, the chemical diffusion coefficient varies only over three orders of magnitude over the whole composition range, despite the large difference of six orders of magnitude of the self-diffusion coefficients of Ag in Ag and Pd inmore » Pd. It is shown that the Darken-Manning treatment should be adopted for interpretation of the experimental data; the Nernst-Planck treatment yielded physically unreasonable results. Apart from the development of compressive thermal stress, the development of stress in both sublayers separately could be ascribed to compositional stress (tensile in the Ag sublayer and compressive in the Pd sublayer) and dominant relaxation processes, especially in the Ag sublayer. The effect of these internal stresses on the values determined for the diffusion coefficients is shown to be negligible.« less

Advective and diapycnal diffusive oceanic flux in Tenerife - La Gomera Channel

NASA Astrophysics Data System (ADS)

Marrero-Díaz, A.; Rodriguez-Santana, A.; Hernández-Arencibia, M.; Machín, F.; García-Weil, L.

2012-04-01

During the year 2008, using the commercial passenger ship Volcán de Tauce of the Naviera Armas company several months, it was possible to obtain vertical profiles of temperature from expandable bathythermograph probes in eight stations across the Tenerife - La Gomera channel. With these data of temperature we have been estimated vertical sections of potential density and geostrophic transport with high spatial and temporal resolution (5 nm between stations, and one- two months between cruises). The seasonal variability obtained for the geostrophic transport in this channel shows important differences with others Canary Islands channels. From potential density and geostrophic velocity data we estimated the vertical diffusion coefficients and diapycnal diffusive fluxes, using a parameterization that depends of Richardson gradient number. In the center of the channel and close to La Gomera Island, we found higher values for these diffusive fluxes. Convergence and divergence of these fluxes requires further study so that we can draw conclusions about its impact on the distribution of nutrients in the study area and its impact in marine ecosystems. This work is being used in research projects TRAMIC and PROMECA.

The Role of Collateral Paths in Long-Range Diffusion of 3He in Lungs

PubMed Central

Conradi, Mark S.; Yablonskiy, Dmitriy A.; Woods, Jason C.; Gierada, David S.; Bartel, Seth-Emil T.; Haywood, Susan E.; Menard, Christopher

2008-01-01

Rationale and Objectives The hyperpolarized 3He long-range diffusion coefficient (LRDC) in lungs is sensitive to changes in lung structure due to emphysema, reflecting the increase in collateral paths resulting from tissue destruction. However, no clear understanding of LRDC in healthy lungs has emerged. Here we compare LRDC measured in healthy lungs with computer simulations of diffusion along the airway tree with no collateral connections. Materials and Methods Computer simulations of diffusion of spatially modulated spin magnetization were performed in computer generated, symmetric-branching models of lungs and compared with existing LRDC measurements in canine and human lungs. Results The simulations predict LRDC values of order 0.001 cm2/s, approximately 20 times smaller than the measured LRDC. We consider and rule out possible mechanisms for LRDC not included in the simulations: incomplete breath hold, cardiac motion, and passage of dissolved 3He through airway walls. However, a very low density of small (micron) holes in the airways is shown to account for the observed LRDC. Conclusion It is proposed that LRDC in healthy lungs is determined by small collateral pathways. PMID:18486004

A symmetrical image encryption scheme in wavelet and time domain

NASA Astrophysics Data System (ADS)

Luo, Yuling; Du, Minghui; Liu, Junxiu

2015-02-01

There has been an increasing concern for effective storages and secure transactions of multimedia information over the Internet. Then a great variety of encryption schemes have been proposed to ensure the information security while transmitting, but most of current approaches are designed to diffuse the data only in spatial domain which result in reducing storage efficiency. A lightweight image encryption strategy based on chaos is proposed in this paper. The encryption process is designed in transform domain. The original image is decomposed into approximation and detail components using integer wavelet transform (IWT); then as the more important component of the image, the approximation coefficients are diffused by secret keys generated from a spatiotemporal chaotic system followed by inverse IWT to construct the diffused image; finally a plain permutation is performed for diffusion image by the Logistic mapping in order to reduce the correlation between adjacent pixels further. Experimental results and performance analysis demonstrate the proposed scheme is an efficient, secure and robust encryption mechanism and it realizes effective coding compression to satisfy desirable storage.

Diffusion heterogeneity tensor MRI (?-Dti): mathematics and initial applications in spinal cord regeneration after trauma - biomed 2009.

PubMed

Ellington, Benjamin M; Schmit, Brian D; Gourab, Krishnaj; Sieber-Blum, Maya; Hu, Yao F; Schmainda, Kathleen M

2009-01-01

Diffusion weighted magnetic resonance imaging (DWI) is a powerful tool for evaluation of microstructural anomalies in numerous central nervous system pathologies. Diffusion tensor imaging (DTI) allows for the magnitude and direction of water self diffusion to be estimated by sampling the apparent diffusion coefficient (ADC) in various directions. Clinical DWI and DTI performed at a single level of diffusion weighting, however, does not allow for multiple diffusion compartments to be elicited. Furthermore, assumptions made regarding the precise number of diffusion compartments intrinsic to the tissue of interest have resulted in a lack of consensus between investigations. To overcome these challenges, a stretched-exponential model of diffusion was applied to examine the diffusion coefficient and "heterogeneity index" within highly compartmentalized brain tumors. The purpose of the current study is to expand on the stretched-exponential model of diffusion to include directionality of both diffusion heterogeneity and apparent diffusion coefficient. This study develops the mathematics of this new technique along with an initial application in quantifying spinal cord regeneration following acute injection of epidermal neural crest stem cell (EPI-NCSC) grafts.

Determination of diffusion coefficients and diffusion characteristics for chlorferon and diethylthiophosphate in Ca-alginate gel beads.

PubMed

Ha, Jiyeon; Engler, Cady R; Lee, Seung Jae

2008-07-01

Diffusion characteristics of chlorferon and diethylthiophosphate (DETP) in Ca-alginate gel beads were studied to assist in designing and operating bioreactor systems. Diffusion coefficients for chlorferon and DETP in Ca-alginate gel beads determined at conditions suitable for biodegradation studies were 2.70 x 10(-11) m(2)/s and 4.28 x 10(-11) m(2)/s, respectively. Diffusivities of chlorferon and DETP were influenced by several factors, including viscosity of the bulk solution, agitation speed, and the concentrations of diffusing substrate and immobilized cells. Diffusion coefficients increased with increasing agitation speed, probably due to poor mixing at low speed and some attrition of beads at high speeds. Diffusion coefficients also increased with decreasing substrate concentration. Increased cell concentration in the gel beads caused lower diffusivity. Theoretical models to predict diffusivities as a function of cell weight fraction overestimated the effective diffusivities for both chlorferon and DETP, but linear relations between effective diffusivity and cell weight fraction were derived from experimental data. Calcium-alginate gel beads with radii of 1.65-1.70 mm used in this study were not subject to diffusional limitations: external mass transfer resistances were negligible based on Biot number calculations and effectiveness factors indicated that internal mass transfer resistance was negligible. Therefore, the degradation rates of chlorferon and DETP inside Ca-alginate gel beads were reaction-limited. (c) 2007 Wiley Periodicals, Inc.

Microphone array measurement system for analysis of directional and spatial variations of sound fields.

PubMed

Gover, Bradford N; Ryan, James G; Stinson, Michael R

2002-11-01

A measurement system has been developed that is capable of analyzing the directional and spatial variations in a reverberant sound field. A spherical, 32-element array of microphones is used to generate a narrow beam that is steered in 60 directions. Using an omnidirectional loudspeaker as excitation, the sound pressure arriving from each steering direction is measured as a function of time, in the form of pressure impulse responses. By subsequent analysis of these responses, the variation of arriving energy with direction is studied. The directional diffusion and directivity index of the arriving sound can be computed, as can the energy decay rate in each direction. An analysis of the 32 microphone responses themselves allows computation of the point-to-point variation of reverberation time and of sound pressure level, as well as the spatial cross-correlation coefficient, over the extent of the array. The system has been validated in simple sound fields in an anechoic chamber and in a reverberation chamber. The system characterizes these sound fields as expected, both quantitatively from the measures and qualitatively from plots of the arriving energy versus direction. It is anticipated that the system will be of value in evaluating the directional distribution of arriving energy and the degree and diffuseness of sound fields in rooms.

Diffusion coefficients of water in biobased hydrogel polymer matrices by nuclear magnetic resonance imaging

USDA-ARS?s Scientific Manuscript database

The diffusion coefficient of water in biobased hydrogels were measured utilizing a simple NMR method. This method tracks the migration of deuterium oxide through imaging data that is fit to a diffusion equation. The results show that a 5 wt% soybean oil based hydrogel gives aqueous diffusion of 1.37...

Portable vapor diffusion coefficient meter

DOEpatents

Ho, Clifford K [Albuquerque, NM

2007-06-12

An apparatus for measuring the effective vapor diffusion coefficient of a test vapor diffusing through a sample of porous media contained within a test chamber. A chemical sensor measures the time-varying concentration of vapor that has diffused a known distance through the porous media. A data processor contained within the apparatus compares the measured sensor data with analytical predictions of the response curve based on the transient diffusion equation using Fick's Law, iterating on the choice of an effective vapor diffusion coefficient until the difference between the predicted and measured curves is minimized. Optionally, a purge fluid can forced through the porous media, permitting the apparatus to also measure a gas-phase permeability. The apparatus can be made lightweight, self-powered, and portable for use in the field.

Communication: Coordinate-dependent diffusivity from single molecule trajectories

NASA Astrophysics Data System (ADS)

Berezhkovskii, Alexander M.; Makarov, Dmitrii E.

2017-11-01

Single-molecule observations of biomolecular folding are commonly interpreted using the model of one-dimensional diffusion along a reaction coordinate, with a coordinate-independent diffusion coefficient. Recent analysis, however, suggests that more general models are required to account for single-molecule measurements performed with high temporal resolution. Here, we consider one such generalization: a model where the diffusion coefficient can be an arbitrary function of the reaction coordinate. Assuming Brownian dynamics along this coordinate, we derive an exact expression for the coordinate-dependent diffusivity in terms of the splitting probability within an arbitrarily chosen interval and the mean transition path time between the interval boundaries. This formula can be used to estimate the effective diffusion coefficient along a reaction coordinate directly from single-molecule trajectories.

Application of ToFSIMS to Studying Surface Diffusion: Do cocaine and heroin form a two-dimensional gas on surfaces?

NASA Astrophysics Data System (ADS)

Avci, Recep; Maccagnano, Sara; Bohannan, Gary; Gresham, Gary; Groenewold, Gary

2001-03-01

Imaging time-of-flight secondary ion mass spectroscopy ( ToFSIMS) is a practical tool for studying the movement of molecules on material surfaces as a function of time. The high detection sensitivity, rapid data acquisition and reasonable spatial resolution present ideal conditions for such studies. An application of ToFSIMS is presented characterizing the diffusion of large molecules on gold-coated Si wafers. Polydimethylsiloxane (PDMS) was selected for study because it contaminates material surfaces and can be detected easily. Also, the temperature dependent diffusion properties of hydrochlorinated heroin and cocaine are presented as part of a forensic application. While the PDMS diffusion could be explained by a two-dimensional ( 2-D) Brownian motion with a Gaussian probability distribution function (pdf) with a diffusion coefficient of 1.6 μ m^2/sec, the cocaine and to a lesser extent heroin were observed to move nearly freely on the surfaces as though they were part of a 2-D gas evaporating in 2-D from a condensed phase. The results could be described reasonably well using an extreme Lévi pdf with an index of stability α<= 0.01.

Diffusion of organic pollutants within a biofilm in porous media

NASA Astrophysics Data System (ADS)

Fan, Chihhao; Kao, Chen-Fei; Liu, You-Hsi

2017-04-01

The occurrence of aquatic pollution is an inevitable environmental impact resulting from human civilization and societal advancement. Either from the natural or anthropogenic sources, the aqueous contaminants enter the natural environment and aggravate its quality. To assure the aquatic environment quality, the attached-growth biological degradation is often applied to removing organic contaminants by introducing contaminated water into a porous media which is covered by microorganism. Additionally, many natural aquatic systems also form such similar mechanism to increase their self-purification capability. To better understand this transport phenomenon and degradation mechanism in the biofilm for future application, the mathematic characterization of organic contaminant diffusion within the biofilm requires further exploration. The present study aimed to formulate a mathematic representation to quantify the diffusion of the organic contaminant in the biofilm. The BOD was selected as the target contaminant. A series of experiments were conducted to quantify the BOD diffusion in the biofilm under the conditions of influent BOD variation from 50 to 300 mg/L, COD:N:P ratios of 100:5:1 and 100:15:3, with or without auxiliary aeration. For diffusion coefficient calculation, the boundary condition of zero diffusion at the interface between microbial phase and contact media was assumed. With the principle of conservation of mass, the removed contaminants equal those that diffuse into the biofilm, and eq 1 results, and the diffusion coefficient (i.e., eq 2) can be solved through calculus with equations from table of integral. ∂2Sf- Df ∂z2 = Rf (1) --(QSin--QSout)2Y--- Df = 2μmaxxf(Sb + Ks ln-Ks-) Sb+Ks (2) Using the obtained experimental data, the diffusion coefficient was calculated to be 2.02*10-6 m2/d with influent COD of 50 mg/L at COD:N:P ratio of 100:5:1 with aeration, and this coefficient increased to 6.02*10-6 m2/d as the influent concentration increased to 300 mg/L. Meanwhile, the diffusion coefficient decreased to 2.61*10-7 m2/d as the retention time increased to 3 hours. Generally, the variation in diffusion coefficients between different COD:N:P ratios exhibits similar pattern with a slight decrease for the ratio of 100:15:3. The difference in diffusion coefficients between 1 and 2 hours was apparently greater than that between 2 and 3 hours, implying the diffusion was a critical factor for contaminant removal for the treatment condition with retention time of 1 hour or less, because higher retention time leads to better microbial degradation due to sufficient contact time for biological reactions. For 1 hour retention time, the increase in diffusion coefficient becomes limited as the influent COD concentration was equal to or above 150 mg/L. These obtained diffusion coefficients were applied to estimating the treatment efficiency for real domestic sewage. The result was found that the estimated effluent BOD concentrations were quite comparable to that obtained through experimental measurements.

NMR investigation of water diffusion in different biofilm structures.

PubMed

Herrling, Maria P; Weisbrodt, Jessica; Kirkland, Catherine M; Williamson, Nathan H; Lackner, Susanne; Codd, Sarah L; Seymour, Joseph D; Guthausen, Gisela; Horn, Harald

2017-12-01

Mass transfer in biofilms is determined by diffusion. Different mostly invasive approaches have been used to measure diffusion coefficients in biofilms, however, data on heterogeneous biomass under realistic conditions is still missing. To non-invasively elucidate fluid-structure interactions in complex multispecies biofilms pulsed field gradient-nuclear magnetic resonance (PFG-NMR) was applied to measure the water diffusion in five different types of biomass aggregates: one type of sludge flocs, two types of biofilm, and two types of granules. Data analysis is an important issue when measuring heterogeneous systems and is shown to significantly influence the interpretation and understanding of water diffusion. With respect to numerical reproducibility and physico-chemical interpretation, different data processing methods were explored: (bi)-exponential data analysis and the Γ distribution model. Furthermore, the diffusion coefficient distribution in relation to relaxation was studied by D-T 2 maps obtained by 2D inverse Laplace transform (2D ILT). The results show that the effective diffusion coefficients for all biofilm samples ranged from 0.36 to 0.96 relative to that of water. NMR diffusion was linked to biofilm structure (e.g., biomass density, organic and inorganic matter) as observed by magnetic resonance imaging and to traditional biofilm parameters: diffusion was most restricted in granules with compact structures, and fast diffusion was found in heterotrophic biofilms with fluffy structures. The effective diffusion coefficients in the biomass were found to be broadly distributed because of internal biomass heterogeneities, such as gas bubbles, precipitates, and locally changing biofilm densities. Thus, estimations based on biofilm bulk properties in multispecies systems can be overestimated and mean diffusion coefficients might not be sufficiently informative to describe mass transport in biofilms and the near bulk. © 2017 Wiley Periodicals, Inc.

Diffusion of neutral and ionic species in charged membranes: boric acid, arsenite, and water.

PubMed

Goli, Esmaiel; Hiemstra, Tjisse; Van Riemsdijk, Willem H; Rahnemaie, Rasoul; Malakouti, Mohammad Jafar

2010-10-15

Dynamic ion speciation using DMT (Donnan membrane technique) requires insight into the physicochemical characteristics of diffusion in charged membranes (tortuosity, local diffusion coefficients) as well as ion accumulation. The latter can be precluded by studying the diffusion of neutral species, such as boric acid, B(OH)₃⁰(aq), arsenite, As(OH)₃⁰(aq), or water. In this study, the diffusion rate of B(OH)₃⁰ has been evaluated as a function of the concentration, pH, and ionic strength. The rate is linearly dependent on the concentration of solely the neutral species, without a significant contribution of negatively charged species such as B(OH)₄⁻, present at high pH. A striking finding is the very strong effect (factor of ~10) of the type of cation (K(+), Na(+), Ca(2+), Mg(2+), Al(3+), and H(+)) on the diffusion coefficient of B(OH)₃⁰ and also As(OH)₃⁰. The decrease of the diffusion coefficient can be rationalized as an enhancement of the mean viscosity of the confined solution in the membrane. The diffusion coefficients can be described by a semiempirical relationship, linking the mean viscosity of the confined solute of the membrane to the viscosity of the free solution. In proton-saturated membranes, as used in fuel cells, viscosity is relatively more enhanced; i.e., a stronger water network is formed. Extraordinarily, our B(OH)₃-calibrated model (in HNO₃) correctly predicts the reported diffusion coefficient of water (D(H₂O)), measured with ¹H NMR and quasi-elastic neutron scattering in H(+)-Nafion membranes. Upon drying these membranes, the local hydronium, H(H₂O)(n)(+), concentration and corresponding viscosity increase, resulting in a severe reduction of the diffusion coefficient (D(H₂O) ≈ 5-50 times), in agreement with the model. The present study has a second goal, i.e., development of the methodology for measuring the free concentration of neutral species in solution. Our data suggest that the free concentration can be measured with DMT in natural systems if one accounts for the variation in the cation composition of the membrane and corresponding viscosity/diffusion coefficient.

A method for operative quantitative interpretation of multispectral images of biological tissues

NASA Astrophysics Data System (ADS)

Lisenko, S. A.; Kugeiko, M. M.

2013-10-01

A method for operative retrieval of spatial distributions of biophysical parameters of a biological tissue by using a multispectral image of it has been developed. The method is based on multiple regressions between linearly independent components of the diffuse reflection spectrum of the tissue and unknown parameters. Possibilities of the method are illustrated by an example of determining biophysical parameters of the skin (concentrations of melanin, hemoglobin and bilirubin, blood oxygenation, and scattering coefficient of the tissue). Examples of quantitative interpretation of the experimental data are presented.

Interaction of ring current and radiation belt protons with ducted plasmaspheric hiss. 1: Diffusion coefficients and timescales

NASA Technical Reports Server (NTRS)

Kozyra, J. U.; Rasmussen, C. E.; Miller, R. H.; Lyons, L. R.

1994-01-01

Protons that are convected into the inner magnetosphere in response to enhanced magnetic activity can resonate with ducted plasmaspheric hiss in the outer plasmasphere via an anomalous Doppler-shifted cyclotron resonance. Plasmaspheric hiss is a right-hand-polarized electromagnetic emission that is observed to fill the plasmasphere on a routine basis. When plasmaspheric hiss is confined within field-aligned ducts or guided along density gradients, wave normal angles remain largely below 45 deg. This allows resonant interactions with ions at typical ring current and radiation belt energies to take place. Such field-aligned ducts have been observed both within the plasmasphere and in regions outside of the plasmasphere. Wave intensities are estimated using statistical information from studies of detached plasma regions. Diffusion coefficients are presented for a range of L shells and proton energies for a fixed wave distribution. Harmonic resonances in the range N = +/-100 are considered in order to include interactions between hiss at 100 Hz to 2 kHz frequencies, and protons in the energy range between approximately 10 keV and 1000 keV. Diffusion timescales are estimated to be of the order of tens of days and comparable to or shorter than lifetimes for Coulomb decay and charge exchange losses over most of the energy and spatial ranges of interest.

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.

Breast Cancer: Diffusion Kurtosis MR Imaging-Diagnostic Accuracy and Correlation with Clinical-Pathologic Factors.

PubMed

Sun, Kun; Chen, Xiaosong; Chai, Weimin; Fei, Xiaochun; Fu, Caixia; Yan, Xu; Zhan, Ying; Chen, Kemin; Shen, Kunwei; Yan, Fuhua

2015-10-01

To assess diagnostic accuracy with diffusion kurtosis imaging (DKI) in patients with breast lesions and to evaluate the potential association between DKI-derived parameters and breast cancer clinical-pathologic factors. Institutional review board approval and written informed consent were obtained. Data from 97 patients (mean age ± standard deviation, 45.7 years ± 13.1; range, 19-70 years) with 98 lesions (57 malignant and 41 benign) who were treated between January 2014 and April 2014 were retrospectively analyzed. DKI (with b values of 0-2800 sec/mm(2)) and conventional diffusion-weighted imaging data were acquired. Kurtosis and diffusion coefficients from DKI and apparent diffusion coefficients from diffusion-weighted imaging were measured by two radiologists. Student t test, Wilcoxon signed-rank test, Jonckheere-Terpstra test, receiver operating characteristic curves, and Spearman correlation were used for statistical analysis. Kurtosis coefficients were significantly higher in the malignant lesions than in the benign lesions (1.05 ± 0.22 vs 0.65 ± 0.11, respectively; P < .0001). Diffusivity and apparent diffusion coefficients in the malignant lesions were significantly lower than those in the benign lesions (1.13 ± 0.27 vs 1.97 ± 0.33 and 1.02 ± 0.18 vs 1.48 ± 0.33, respectively; P < .0001). Significantly higher specificity for differentiation of malignant from benign lesions was shown with the use of kurtosis and diffusivity coefficients than with the use of apparent diffusion coefficients (83% [34 of 41] and 83% [34 of 41] vs 76% [31 of 41], respectively; P < .0001) with equal sensitivity (95% [54 of 57]). In patients with invasive breast cancer, kurtosis was positively correlated with tumor histologic grade (r = 0.75) and expression of the Ki-67 protein (r = 0.55). Diffusivity was negatively correlated with tumor histologic grades (r = -0.44) and Ki-67 expression (r = -0.46). DKI showed higher specificity than did conventional diffusion-weighted imaging for assessment of benign and malignant breast lesions. Patients with grade 3 breast cancer or tumors with high expression of Ki-67 were associated with higher kurtosis and lower diffusivity coefficients; however, this association must be confirmed in prospective studies. (©) RSNA, 2015 Online supplemental material is available for this article.

Research and Development of Methods for Estimating Physicochemical Properties of Organic Compounds of Environmental Concern

DTIC Science & Technology

1979-02-01

coefficient (at equilibrium) when hysteresis is apparent. 6. Coefficient n in Freundlich equation for 1/n soil or sediment adsorption isotherms ýX - KC . 7...Biodegradation Chemical structures cal clasaes (e.g., Diffusion Correlations phenols). General Diffusion coefficients Equations terms for organic...OF THE FATE AND TRANSPORT OF ORGANIC CHEMICALS Adsorption coefficients: K, n* from Freundlich equation + Desorption coefficients: K’*, n’* from

Self-diffusion in the non-Newtonian regime of shearing liquid crystal model systems based on the Gay-Berne potential

NASA Astrophysics Data System (ADS)

Sarman, Sten; Wang, Yong-Lei; Laaksonen, Aatto

2016-02-01

The self-diffusion coefficients of nematic phases of various model systems consisting of regular convex calamitic and discotic ellipsoids and non-convex bodies such as bent-core molecules and soft ellipsoid strings have been obtained as functions of the shear rate in a shear flow. Then the self-diffusion coefficient is a second rank tensor with three different diagonal components and two off-diagonal components. These coefficients were found to be determined by a combination of two mechanisms, which previously have been found to govern the self-diffusion of shearing isotropic liquids, namely, (i) shear alignment enhancing the diffusion in the direction parallel to the streamlines and hindering the diffusion in the perpendicular directions and (ii) the distortion of the shell structure in the liquid whereby a molecule more readily can escape from a surrounding shell of nearest neighbors, so that the mobility increases in every direction. Thus, the diffusion parallel to the streamlines always increases with the shear rate since these mechanisms cooperate in this direction. In the perpendicular directions, these mechanisms counteract each other so that the behaviour becomes less regular. In the case of the nematic phases of the calamitic and discotic ellipsoids and of the bent core molecules, mechanism (ii) prevails so that the diffusion coefficients increase. However, the diffusion coefficients of the soft ellipsoid strings decrease in the direction of the velocity gradient because the broadsides of these molecules are oriented perpendicularly to this direction due the shear alignment (i). The cross coupling coefficient relating a gradient of tracer particles in the direction of the velocity gradient and their flow in the direction of the streamlines is negative and rather large, whereas the other coupling coefficient relating a gradient in the direction of the streamlines and a flow in the direction of the velocity gradient is very small.

Vertical variation of mixing within porous sediment beds below turbulent flows

PubMed Central

Chandler, I. D.; Pearson, J. M.; van Egmond, R.

2016-01-01

Abstract River ecosystems are influenced by contaminants in the water column, in the pore water and adsorbed to sediment particles. When exchange across the sediment‐water interface (hyporheic exchange) is included in modeling, the mixing coefficient is often assumed to be constant with depth below the interface. Novel fiber‐optic fluorometers have been developed and combined with a modified EROSIMESS system to quantify the vertical variation in mixing coefficient with depth below the sediment‐water interface. The study considered a range of particle diameters and bed shear velocities, with the permeability Péclet number, PeK between 1000 and 77,000 and the shear Reynolds number, Re*, between 5 and 600. Different parameterization of both an interface exchange coefficient and a spatially variable in‐sediment mixing coefficient are explored. The variation of in‐sediment mixing is described by an exponential function applicable over the full range of parameter combinations tested. The empirical relationship enables estimates of the depth to which concentrations of pollutants will penetrate into the bed sediment, allowing the region where exchange will occur faster than molecular diffusion to be determined. PMID:27635104

Experimental Determination of Impurity and Interdiffusion Coefficients in Seven Ti and Zr Binary Systems Using Diffusion Multiples

NASA Astrophysics Data System (ADS)

Chen, Zhangqi; Liu, Zi-Kui; Zhao, Ji-Cheng

2018-05-01

Diffusion coefficients of seven binary systems (Ti-Mo, Ti-Nb, Ti-Ta, Ti-Zr, Zr-Mo, Zr-Nb, and Zr-Ta) at 1200 °C, 1000 °C, and 800 °C were experimentally determined using three Ti-Mo-Nb-Ta-Zr diffusion multiples. Electron probe microanalysis (EPMA) was performed to collect concentration profiles at the binary diffusion regions. Forward simulation analysis (FSA) was then applied to extract both impurity and interdiffusion coefficients in Ti-rich and Zr-rich part of the bcc phase. Excellent agreements between our results and most of the literature data validate the high-throughput approach combining FSA with diffusion multiples to obtain a large amount of systematic diffusion data, which will help establish the diffusion (mobility) databases for the design and development of biomedical and structural Ti alloys.

Diffusion modulation of DNA by toehold exchange

NASA Astrophysics Data System (ADS)

Rodjanapanyakul, Thanapop; Takabatake, Fumi; Abe, Keita; Kawamata, Ibuki; Nomura, Shinichiro M.; Murata, Satoshi

2018-05-01

We propose a method to control the diffusion speed of DNA molecules with a target sequence in a polymer solution. The interaction between solute DNA and diffusion-suppressing DNA that has been anchored to a polymer matrix is modulated by the concentration of the third DNA molecule called the competitor by a mechanism called toehold exchange. Experimental results show that the sequence-specific modulation of the diffusion coefficient is successfully achieved. The diffusion coefficient can be modulated up to sixfold by changing the concentration of the competitor. The specificity of the modulation is also verified under the coexistence of a set of DNA with noninteracting base sequences. With this mechanism, we are able to control the diffusion coefficient of individual DNA species by the concentration of another DNA species. This methodology introduces a programmability to a DNA-based reaction-diffusion system.

Experimental Determination of Impurity and Interdiffusion Coefficients in Seven Ti and Zr Binary Systems Using Diffusion Multiples

NASA Astrophysics Data System (ADS)

Chen, Zhangqi; Liu, Zi-Kui; Zhao, Ji-Cheng

2018-07-01

Diffusion coefficients of seven binary systems (Ti-Mo, Ti-Nb, Ti-Ta, Ti-Zr, Zr-Mo, Zr-Nb, and Zr-Ta) at 1200 °C, 1000 °C, and 800 °C were experimentally determined using three Ti-Mo-Nb-Ta-Zr diffusion multiples. Electron probe microanalysis (EPMA) was performed to collect concentration profiles at the binary diffusion regions. Forward simulation analysis (FSA) was then applied to extract both impurity and interdiffusion coefficients in Ti-rich and Zr-rich part of the bcc phase. Excellent agreements between our results and most of the literature data validate the high-throughput approach combining FSA with diffusion multiples to obtain a large amount of systematic diffusion data, which will help establish the diffusion (mobility) databases for the design and development of biomedical and structural Ti alloys.

Stefan-Maxwell Relations and Heat Flux with Anisotropic Transport Coefficients for Ionized Gases in a Magnetic Field with Application to the Problem of Ambipolar Diffusion

NASA Astrophysics Data System (ADS)

Kolesnichenko, A. V.; Marov, M. Ya.

2018-01-01

The defining relations for the thermodynamic diffusion and heat fluxes in a multicomponent, partially ionized gas mixture in an external electromagnetic field have been obtained by the methods of the kinetic theory. Generalized Stefan-Maxwell relations and algebraic equations for anisotropic transport coefficients (the multicomponent diffusion, thermal diffusion, electric and thermoelectric conductivity coefficients as well as the thermal diffusion ratios) associated with diffusion-thermal processes have been derived. The defining second-order equations are derived by the Chapman-Enskog procedure using Sonine polynomial expansions. The modified Stefan-Maxwell relations are used for the description of ambipolar diffusion in the Earth's ionospheric plasma (in the F region) composed of electrons, ions of many species, and neutral particles in a strong electromagnetic field.

Determination of diffusion coefficients of hydrogen and deuterium in Zr-2.5%Nb pressure tube material using hot vacuum extraction-quadrupole mass spectrometry

NASA Astrophysics Data System (ADS)

Shrivastava, Komal Chandra; Kulkarni, A. S.; Ramanjaneyulu, P. S.; Sunil, Saurav; Saxena, M. K.; Singh, R. N.; Tomar, B. S.; Ramakumar, K. L.

2015-06-01

The diffusion coefficients of hydrogen and deuterium in Zr-2.5%Nb alloy were measured in the temperature range 523 to 673 K, employing hot vacuum extraction-quadrupole mass spectrometry (HVE-QMS). One end of the Zr-2.5%Nb alloy specimens was charged electrolytically with the desired hydrogen isotope. After annealing at different temperatures for a predetermined time, the specimens were cut into thin slices, which were analyzed for their H2/D2 content using the HVE-QMS technique. The depth profile data were fitted into the equation representing the solution of Fick's second law of diffusion. The activation energy of hydrogen/deuterium diffusion was obtained from the Arrhenius relation between the diffusion coefficient and temperature. The temperature dependent diffusion coefficient can be represented as DH = 1.41 × 10-7 exp(-36,000/RT) and DD = 6.16 × 10-8 exp(-35,262/RT) for hydrogen and deuterium, respectively.

Dynamics of the DNA repair proteins WRN and BLM in the nucleoplasm and nucleoli.

PubMed

Bendtsen, Kristian Moss; Jensen, Martin Borch; May, Alfred; Rasmussen, Lene Juel; Trusina, Ala; Bohr, Vilhelm A; Jensen, Mogens H

2014-11-01

We have investigated the mobility of two EGFP-tagged DNA repair proteins, WRN and BLM. In particular, we focused on the dynamics in two locations, the nucleoli and the nucleoplasm. We found that both WRN and BLM use a "DNA-scanning" mechanism, with rapid binding-unbinding to DNA resulting in effective diffusion. In the nucleoplasm WRN and BLM have effective diffusion coefficients of 1.62 and 1.34 μm(2)/s, respectively. Likewise, the dynamics in the nucleoli are also best described by effective diffusion, but with diffusion coefficients a factor of ten lower than in the nucleoplasm. From this large reduction in diffusion coefficient we were able to classify WRN and BLM as DNA damage scanners. In addition to WRN and BLM we also classified other DNA damage proteins and found they all fall into one of two categories. Either they are scanners, similar to WRN and BLM, with very low diffusion coefficients, suggesting a scanning mechanism, or they are almost freely diffusing, suggesting that they interact with DNA only after initiation of a DNA damage response.

Connecting the molecular scale to the continuum scale for diffusion processes in smectite-rich porous media.

PubMed

Bourg, Ian C; Sposito, Garrison

2010-03-15

In this paper, we address the manner in which the continuum-scale diffusive properties of smectite-rich porous media arise from their molecular- and pore-scale features. Our starting point is a successful model of the continuum-scale apparent diffusion coefficient for water tracers and cations, which decomposes it as a sum of pore-scale terms describing diffusion in macropore and interlayer "compartments." We then apply molecular dynamics (MD) simulations to determine molecular-scale diffusion coefficients D(interlayer) of water tracers and representative cations (Na(+), Cs(+), Sr(2+)) in Na-smectite interlayers. We find that a remarkably simple expression relates D(interlayer) to the pore-scale parameter δ(nanopore) ≤ 1, a constrictivity factor that accounts for the lower mobility in interlayers as compared to macropores: δ(nanopore) = D(interlayer)/D(0), where D(0) is the diffusion coefficient in bulk liquid water. Using this scaling expression, we can accurately predict the apparent diffusion coefficients of tracers H(2)0, Na(+), Sr(2+), and Cs(+) in compacted Na-smectite-rich materials.

New method and installation for rapid determination of radon diffusion coefficient in various materials.

PubMed

Tsapalov, Andrey; Gulabyants, Loren; Livshits, Mihail; Kovler, Konstantin

2014-04-01

The mathematical apparatus and the experimental installation for the rapid determination of radon diffusion coefficient in various materials are developed. The single test lasts not longer than 18 h and allows testing numerous materials, such as gaseous and liquid media, as well as soil, concrete and radon-proof membranes, in which diffusion coefficient of radon may vary in an extremely wide range, from 1·10(-12) to 5·10(-5) m(2)/s. The uncertainty of radon diffusion coefficient estimation depends on the permeability of the sample and varies from about 5% (for the most permeable materials) to 40% (for less permeable materials, such as radon-proof membranes). Copyright © 2014. Published by Elsevier Ltd.

Prediction and validation of diffusion coefficients in a model drug delivery system using microsecond atomistic molecular dynamics simulation and vapour sorption analysis.

PubMed

Forrey, Christopher; Saylor, David M; Silverstein, Joshua S; Douglas, Jack F; Davis, Eric M; Elabd, Yossef A

2014-10-14

Diffusion of small to medium sized molecules in polymeric medical device materials underlies a broad range of public health concerns related to unintended leaching from or uptake into implantable medical devices. However, obtaining accurate diffusion coefficients for such systems at physiological temperature represents a formidable challenge, both experimentally and computationally. While molecular dynamics simulation has been used to accurately predict the diffusion coefficients, D, of a handful of gases in various polymers, this success has not been extended to molecules larger than gases, e.g., condensable vapours, liquids, and drugs. We present atomistic molecular dynamics simulation predictions of diffusion in a model drug eluting system that represent a dramatic improvement in accuracy compared to previous simulation predictions for comparable systems. We find that, for simulations of insufficient duration, sub-diffusive dynamics can lead to dramatic over-prediction of D. We present useful metrics for monitoring the extent of sub-diffusive dynamics and explore how these metrics correlate to error in D. We also identify a relationship between diffusion and fast dynamics in our system, which may serve as a means to more rapidly predict diffusion in slowly diffusing systems. Our work provides important precedent and essential insights for utilizing atomistic molecular dynamics simulations to predict diffusion coefficients of small to medium sized molecules in condensed soft matter systems.

Measurement of the Diffusion Coefficient of Water in RP-3 and RP-5 Jet Fuels Using Digital Holography Interferometry

NASA Astrophysics Data System (ADS)

Li, Chaoyue; Feng, Shiyu; Shao, Lei; Pan, Jun; Liu, Weihua

2018-04-01

The diffusion coefficient of water in jet fuel was measured employing double-exposure digital holographic interferometry to clarify the diffusion process and make the aircraft fuel system safe. The experimental method and apparatus are introduced in detail, and the digital image processing program is coded in MATLAB according to the theory of the Fourier transform. At temperatures ranging from 278.15 K to 333.15 K in intervals of 5 K, the diffusion coefficient of water in RP-3 and RP-5 jet fuels ranges from 2.6967 × 10 -10 m2·s-1 to 8.7332 × 10 -10 m2·s-1 and from 2.3517 × 10 -10 m2·s-1 to 8.0099 × 10-10 m2·s-1, respectively. The relationship between the measured diffusion coefficient and temperature can be well fitted by the Arrhenius law. The diffusion coefficient of water in RP-3 jet fuel is higher than that of water in RP-5 jet fuel at the same temperature. Furthermore, the viscosities of the two jet fuels were measured and found to be expressible in the form of the Arrhenius equation. The relationship among the diffusion coefficient, viscosity and temperature is analyzed according to the classic prediction model, namely the Stokes-Einstein correlation, and this correlation is further revised via experimental data to obtain a more accurate predication result.

Effect of the computational domain size and shape on the self-diffusion coefficient in a Lennard-Jones liquid.

PubMed

Kikugawa, Gota; Ando, Shotaro; Suzuki, Jo; Naruke, Yoichi; Nakano, Takeo; Ohara, Taku

2015-01-14

In the present study, molecular dynamics (MD) simulations on the monatomic Lennard-Jones liquid in a periodic boundary system were performed in order to elucidate the effect of the computational domain size and shape on the self-diffusion coefficient measured by the system. So far, the system size dependence in cubic computational domains has been intensively investigated and these studies showed that the diffusion coefficient depends linearly on the inverse of the system size, which is theoretically predicted based on the hydrodynamic interaction. We examined the system size effect not only in the cubic cell systems but also in rectangular cell systems which were created by changing one side length of the cubic cell with the system density kept constant. As a result, the diffusion coefficient in the direction perpendicular to the long side of the rectangular cell significantly increases more or less linearly with the side length. On the other hand, the diffusion coefficient in the direction along the long side is almost constant or slightly decreases. Consequently, anisotropy of the diffusion coefficient emerges in a rectangular cell with periodic boundary conditions even in a bulk liquid simulation. This unexpected result is of critical importance because rectangular fluid systems confined in nanospace, which are present in realistic nanoscale technologies, have been widely studied in recent MD simulations. In order to elucidate the underlying mechanism for this serious system shape effect on the diffusion property, the correlation structures of particle velocities were examined.

Molecular-dynamics simulation of mutual diffusion in nonideal liquid mixtures

NASA Astrophysics Data System (ADS)

Rowley, R. L.; Stoker, J. M.; Giles, N. F.

1991-05-01

The mutual-diffusion coefficients, D 12, of n-hexane, n-heptane, and n-octane in chloroform were modeled using equilibrium molecular-dynamics (MD) simulations of simple Lennard-Jones (LJ) fluids. Pure-component LJ parameters were obtained by comparison of simulations to experimental self-diffusion coefficients. While values of “effective” LJ parameters are not expected to simulate accurately diverse thermophysical properties over a wide range of conditions, it was recently shown that effective parameters obtained from pure self-diffusion coefficients can accurately model mutual diffusion in ideal, liquid mixtures. In this work, similar simulations are used to model diffusion in nonideal mixtures. The same combining rules used in the previous study for the cross-interaction parameters were found to be adequate to represent the composition dependence of D 12. The effect of alkane chain length on D 12 is also correctly predicted by the simulations. A commonly used assumption in empirical correlations of D 12, that its kinetic portion is a simple, compositional average of the intradiffusion coefficients, is inconsistent with the simulation results. In fact, the value of the kinetic portion of D 12 was often outside the range of values bracketed by the two intradiffusion coefficients for the nonideal system modeled here.

Communication: A method to compute the transport coefficient of pure fluids diffusing through planar interfaces from equilibrium molecular dynamics simulations.

PubMed

Vermorel, Romain; Oulebsir, Fouad; Galliero, Guillaume

2017-09-14

The computation of diffusion coefficients in molecular systems ranks among the most useful applications of equilibrium molecular dynamics simulations. However, when dealing with the problem of fluid diffusion through vanishingly thin interfaces, classical techniques are not applicable. This is because the volume of space in which molecules diffuse is ill-defined. In such conditions, non-equilibrium techniques allow for the computation of transport coefficients per unit interface width, but their weak point lies in their inability to isolate the contribution of the different physical mechanisms prone to impact the flux of permeating molecules. In this work, we propose a simple and accurate method to compute the diffusional transport coefficient of a pure fluid through a planar interface from equilibrium molecular dynamics simulations, in the form of a diffusion coefficient per unit interface width. In order to demonstrate its validity and accuracy, we apply our method to the case study of a dilute gas diffusing through a smoothly repulsive single-layer porous solid. We believe this complementary technique can benefit to the interpretation of the results obtained on single-layer membranes by means of complex non-equilibrium methods.

Fluorescence correlation spectroscopy experiments to quantify free diffusion coefficients in reaction-diffusion systems: The case of Ca2 + and its dyes

NASA Astrophysics Data System (ADS)

Sigaut, Lorena; Villarruel, Cecilia; Ponce, María Laura; Ponce Dawson, Silvina

2017-06-01

Many cell signaling pathways involve the diffusion of messengers that bind and unbind to and from intracellular components. Quantifying their net transport rate under different conditions then requires having separate estimates of their free diffusion coefficient and binding or unbinding rates. In this paper, we show how performing sets of fluorescence correlation spectroscopy (FCS) experiments under different conditions, it is possible to quantify free diffusion coefficients and on and off rates of reaction-diffusion systems. We develop the theory and present a practical implementation for the case of the universal second messenger, calcium (Ca2 +) and single-wavelength dyes that increase their fluorescence upon Ca2 + binding. We validate the approach with experiments performed in aqueous solutions containing Ca2 + and Fluo4 dextran (both in its high and low affinity versions). Performing FCS experiments with tetramethylrhodamine-dextran in Xenopus laevis oocytes, we infer the corresponding free diffusion coefficients in the cytosol of these cells. Our approach can be extended to other physiologically relevant reaction-diffusion systems to quantify biophysical parameters that determine the dynamics of various variables of interest.

Transport diffusion in deformed carbon nanotubes

NASA Astrophysics Data System (ADS)

Feng, Jiamei; Chen, Peirong; Zheng, Dongqin; Zhong, Weirong

2018-03-01

Using non-equilibrium molecular dynamics and Monte Carlo methods, we have studied the transport diffusion of gas in deformed carbon nanotubes. Perfect carbon nanotube and various deformed carbon nanotubes are modeled as transport channels. It is found that the transport diffusion coefficient of gas does not change in twisted carbon nanotubes, but changes in XY-distortion, Z-distortion and local defect carbon nanotubes comparing with that of the perfect carbon nanotube. Furthermore, the change of transport diffusion coefficient is found to be associated with the deformation factor. The relationship between transport diffusion coefficient and temperature is also discussed in this paper. Our results may contribute to understanding the mechanism of molecular transport in nano-channel.

Diffusion-plus-drift models for the mass leakage from centrifugal magnetospheres of magnetic hot-stars

NASA Astrophysics Data System (ADS)

Owocki, Stanley P.; Cranmer, Steven R.

2018-03-01

In the subset of luminous, early-type stars with strong, large-scale magnetic fields and moderate to rapid rotation, material from the star's radiatively driven stellar wind outflow becomes trapped by closed magnetic loops, forming a centrifugally supported, corotating magnetosphere. We present here a semi-analytic analysis of how this quasi-steady accumulation of wind mass can be balanced by losses associated with a combination of an outward, centrifugally driven drift in the region beyond the Kepler co-rotation radius, and an inward/outward diffusion near this radius. We thereby derive scaling relations for the equilibrium spatial distribution of mass, and the associated emission measure for observational diagnostics like Balmer line emission. We discuss the potential application of these relations for interpreting surveys of the emission line diagnostics for OB stars with centrifugally supported magnetospheres. For a specific model of turbulent field-line-wandering rooted in surface motions associated with the iron opacity bump, we estimate values for the associated diffusion and drift coefficients.

The surface diffusion coefficient for an arbitrarily curved fluid-fluid interface. (I). General expression

NASA Astrophysics Data System (ADS)

M. C. Sagis, Leonard

2001-03-01

In this paper, we develop a theory for the calculation of the surface diffusion coefficient for an arbitrarily curved fluid-fluid interface. The theory is valid for systems in hydrodynamic equilibrium, with zero mass-averaged velocities in the bulk and interfacial regions. We restrict our attention to systems with isotropic bulk phases, and an interfacial region that is isotropic in the plane parallel to the dividing surface. The dividing surface is assumed to be a simple interface, without memory effects or yield stresses. We derive an expression for the surface diffusion coefficient in terms of two parameters of the interfacial region: the coefficient for plane-parallel diffusion D (AB)aa(ξ) , and the driving force d(B)I||(ξ) . This driving force is the parallel component of the driving force for diffusion in the interfacial region. We derive an expression for this driving force using the entropy balance.

Correlation Between the Field Line and Particle Diffusion Coefficients in the Stochastic Fields of a Tokamak

NASA Astrophysics Data System (ADS)

Calvin, Mark; Punjabi, Alkesh

1996-11-01

We use the method of quasi-magnetic surfaces to calculate the correlation between the field line and particle diffusion coefficients. The magnetic topology of a tokamak is perturbed by a spectrum of neighboring resonant resistive modes. The Hamiltonian equations of motion for the field line are integrated numerically. Poincare plots of the quasi-magnetic surfaces are generated initially and after the field line has traversed a considerable distance. From the areas of the quasi-magnetic surfaces and the field line distance, we estimate the field line diffusion coefficient. We start plasma particles on the initial quasi-surface, and calculate the particle diffusion coefficient from our Monte Carlo method (Punjabi A., Boozer A., Lam M., Kim H. and Burke K., J. Plasma Phys.), 44, 405 (1990). We then estimate the correlation between the particle and field diffusion as the strength of the resistive modes is varied.

Computation of thermodynamic and transport properties to predict thermophoretic effects in an argon-krypton mixture

NASA Astrophysics Data System (ADS)

Miller, Nicholas A. T.; Daivis, Peter J.; Snook, Ian K.; Todd, B. D.

2013-10-01

Thermophoresis is the movement of molecules caused by a temperature gradient. Here we report the results of a study of thermophoresis using non-equilibrium molecular dynamics simulations of a confined argon-krypton fluid subject to two different temperatures at thermostated walls. The resulting temperature profile between the walls is used along with the Soret coefficient to predict the concentration profile that develops across the channel. We obtain the Soret coefficient by calculating the mutual diffusion and thermal diffusion coefficients. We report an appropriate method for calculating the transport coefficients for binary systems, using the Green-Kubo integrals and radial distribution functions obtained from equilibrium molecular dynamics simulations of the bulk fluid. Our method has the unique advantage of separating the mutual diffusion and thermal diffusion coefficients, and calculating the sign and magnitude of their individual contributions to thermophoresis in binary mixtures.

Molecular Diffusion Coefficients: Experimental Determination and Demonstration.

ERIC Educational Resources Information Center

Fate, Gwendolyn; Lynn, David G.

1990-01-01

Presented are laboratory methods which allow the demonstration and determination of the diffusion coefficients of compounds ranging in size from water to small proteins. Included are the procedures involving the use of a spectrometer, UV cell, triterated agar, and oxygen diffusion. Results including quantification are described. (CW)

Free-breathing 3D diffusion MRI for high-resolution hepatic metastasis characterization in small animals.

PubMed

Ribot, Emeline J; Trotier, Aurélien J; Castets, Charles R; Dallaudière, Benjamin; Thiaudière, Eric; Franconi, Jean-Michel; Miraux, Sylvain

2016-02-01

The goal of this study was to develop a 3D diffusion weighted sequence for free breathing liver imaging in small animals at high magnetic field. Hepatic metastases were detected and the apparent diffusion coefficients (ADC) were measured. A 3D SE-EPI sequence was developed by (i) inserting a water-selective excitation radiofrequency pulse to suppress adipose tissue signal and (ii) bipolar diffusion gradients to decrease the sensitivity to respiration motion. Mice with hepatic metastases were imaged at 7T by applying b values from 200 to 1100 s/mm(2). 3D images with high spatial resolution (182 × 156 × 125 µm) were obtained in only 8 min 32 s. The modified DW-SE-EPI sequence allowed to obtain 3D abdominal images of healthy mice with fat SNR 2.5 times lower than without any fat suppression method and sharpness 2.8 times higher than on respiration-triggered images. Due to the high spatial resolution, the core and the periphery of disseminated hepatic metastases were differentiated at high b-values only, demonstrating the presence of edema and proliferating cells (with ADC of 2.65 × 10(-3) and 1.55 × 10(-3) mm(2)/s, respectively). Furthermore, these metastases were accurately distinguished from proliferating ones within the same animal at high b-values (mean ADC of 0.38 × 10(-3) mm(2)/s). Metastases of less than 1.7 mm(3) diameter were detected. The new 3D SE-EPI sequence enabled to obtain diffusion information within liver metastases. In addition of intra-metastasis heterogeneity, differences in diffusion were measured between metastases within an animal. This sequence could be used to obtain diffusion information at high magnetic field.

A quantitative property-property relationship for the internal diffusion coefficients of organic compounds in solid materials.

PubMed

Huang, L; Fantke, P; Ernstoff, A; Jolliet, O

2017-11-01

Indoor releases of organic chemicals encapsulated in solid materials are major contributors to human exposures and are directly related to the internal diffusion coefficient in solid materials. Existing correlations to estimate the diffusion coefficient are only valid for a limited number of chemical-material combinations. This paper develops and evaluates a quantitative property-property relationship (QPPR) to predict diffusion coefficients for a wide range of organic chemicals and materials. We first compiled a training dataset of 1103 measured diffusion coefficients for 158 chemicals in 32 consolidated material types. Following a detailed analysis of the temperature influence, we developed a multiple linear regression model to predict diffusion coefficients as a function of chemical molecular weight (MW), temperature, and material type (adjusted R 2 of .93). The internal validations showed the model to be robust, stable and not a result of chance correlation. The external validation against two separate prediction datasets demonstrated the model has good predicting ability within its applicability domain (Rext2>.8), namely MW between 30 and 1178 g/mol and temperature between 4 and 180°C. By covering a much wider range of organic chemicals and materials, this QPPR facilitates high-throughput estimates of human exposures for chemicals encapsulated in solid materials. © 2017 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Interpretation of diffusion coefficients in nanostructured materials from random walk numerical simulation.

PubMed

Anta, Juan A; Mora-Seró, Iván; Dittrich, Thomas; Bisquert, Juan

2008-08-14

We make use of the numerical simulation random walk (RWNS) method to compute the "jump" diffusion coefficient of electrons in nanostructured materials via mean-square displacement. First, a summary of analytical results is given that relates the diffusion coefficient obtained from RWNS to those in the multiple-trapping (MT) and hopping models. Simulations are performed in a three-dimensional lattice of trap sites with energies distributed according to an exponential distribution and with a step-function distribution centered at the Fermi level. It is observed that once the stationary state is reached, the ensemble of particles follow Fermi-Dirac statistics with a well-defined Fermi level. In this stationary situation the diffusion coefficient obeys the theoretical predictions so that RWNS effectively reproduces the MT model. Mobilities can be also computed when an electrical bias is applied and they are observed to comply with the Einstein relation when compared with steady-state diffusion coefficients. The evolution of the system towards the stationary situation is also studied. When the diffusion coefficients are monitored along simulation time a transition from anomalous to trap-limited transport is observed. The nature of this transition is discussed in terms of the evolution of electron distribution and the Fermi level. All these results will facilitate the use of RW simulation and related methods to interpret steady-state as well as transient experimental techniques.

Estimation of underwater visibility in coastal and inland waters using remote sensing data.

PubMed

Kulshreshtha, Anuj; Shanmugam, Palanisamy

2017-04-01

An optical method is developed to estimate water transparency (or underwater visibility) in terms of Secchi depth (Z sd ), which follows the remote sensing and contrast transmittance theory. The major factors governing the variation in Z sd , namely, turbidity and length attenuation coefficient (1/(c + K d ), c = beam attenuation coefficient; K d  = diffuse attenuation coefficient at 531 nm), are obtained based on band rationing techniques. It was found that the band ratio of remote sensing reflectance (expressed as (R rs (443) + R rs (490))/(R rs (555) + R rs (670)) contains essential information about the water column optical properties and thereby positively correlates to turbidity. The beam attenuation coefficient (c) at 531 nm is obtained by a linear relationship with turbidity. To derive the vertical diffuse attenuation coefficient (K d ) at 531 nm, K d (490) is estimated as a function of reflectance ratio (R rs (670)/R rs (490)), which provides the bio-optical link between chlorophyll concentration and K d (531). The present algorithm was applied to MODIS-Aqua images, and the results were evaluated by matchup comparisons between the remotely estimated Z sd and in situ Z sd in coastal waters off Point Calimere and its adjoining regions on the southeast coast of India. The results showed the pattern of increasing Z sd from shallow turbid waters to deep clear waters. The statistical evaluation of the results showed that the percent mean relative error between the MODIS-Aqua-derived Z sd and in situ Z sd values was within ±25%. A close agreement achieved in spatial contours of MODIS-Aqua-derived Z sd and in situ Z sd for the month of January 2014 and August 2013 promises the model capability to yield accurate estimates of Z sd in coastal, estuarine, and inland waters. The spatial contours have been included to provide the best data visualization of the measured, modeled (in situ), and satellite-derived Z sd products. The modeled and satellite-derived Z sd values were compared with measurement data which yielded RMSE = 0.079, MRE = -0.016, and R 2  = 0.95 for the modeled Z sd and RMSE = 0.075, MRE = 0.020, and R 2  = 0.95 for the satellite-derived Z sd products.

Computer Aided Design of Integrated Circuit Fabrication Processes for VLSI Devices

DTIC Science & Technology

1980-01-01

diffusion coefficient and surface conc,,tration of the chlorine as well as any field present; X is related to the ratio ol the diffusion coefficient to...with polysilicon gat(. .ed contacts, the interaction of oxidation, segregation and diffusion in all regions of the simulation space is a critical

Super-nodal methods for space-time kinetics

NASA Astrophysics Data System (ADS)

Mertyurek, Ugur

The purpose of this research has been to develop an advanced Super-Nodal method to reduce the run time of 3-D core neutronics models, such as in the NESTLE reactor core simulator and FORMOSA nuclear fuel management optimization codes. Computational performance of the neutronics model is increased by reducing the number of spatial nodes used in the core modeling. However, as the number of spatial nodes decreases, the error in the solution increases. The Super-Nodal method reduces the error associated with the use of coarse nodes in the analyses by providing a new set of cross sections and ADFs (Assembly Discontinuity Factors) for the new nodalization. These so called homogenization parameters are obtained by employing consistent collapsing technique. During this research a new type of singularity, namely "fundamental mode singularity", is addressed in the ANM (Analytical Nodal Method) solution. The "Coordinate Shifting" approach is developed as a method to address this singularity. Also, the "Buckling Shifting" approach is developed as an alternative and more accurate method to address the zero buckling singularity, which is a more common and well known singularity problem in the ANM solution. In the course of addressing the treatment of these singularities, an effort was made to provide better and more robust results from the Super-Nodal method by developing several new methods for determining the transverse leakage and collapsed diffusion coefficient, which generally are the two main approximations in the ANM methodology. Unfortunately, the proposed new transverse leakage and diffusion coefficient approximations failed to provide a consistent improvement to the current methodology. However, improvement in the Super-Nodal solution is achieved by updating the homogenization parameters at several time points during a transient. The update is achieved by employing a refinement technique similar to pin-power reconstruction. A simple error analysis based on the relative residual in the 3-D few group diffusion equation at the fine mesh level is also introduced in this work.

Excess Diffuse Light Absorption in Upper Mesophyll Limits CO2 Drawdown and Depresses Photosynthesis1[OPEN

PubMed Central

Gilbert, Matthew E.; McElrone, Andrew J.

2017-01-01

In agricultural and natural systems, diffuse light can enhance plant primary productivity due to deeper penetration into and greater irradiance of the entire canopy. However, for individual sun-grown leaves from three species, photosynthesis is actually less efficient under diffuse compared with direct light. Despite its potential impact on canopy-level productivity, the mechanism for this leaf-level diffuse light photosynthetic depression effect is unknown. Here, we investigate if the spatial distribution of light absorption relative to electron transport capacity in sun- and shade-grown sunflower (Helianthus annuus) leaves underlies its previously observed diffuse light photosynthetic depression. Using a new one-dimensional porous medium finite element gas-exchange model parameterized with light absorption profiles, we found that weaker penetration of diffuse versus direct light into the mesophyll of sun-grown sunflower leaves led to a more heterogenous saturation of electron transport capacity and lowered its CO2 concentration drawdown capacity in the intercellular airspace and chloroplast stroma. This decoupling of light availability from photosynthetic capacity under diffuse light is sufficient to generate an 11% decline in photosynthesis in sun-grown but not shade-grown leaves, primarily because thin shade-grown leaves similarly distribute diffuse and direct light throughout the mesophyll. Finally, we illustrate how diffuse light photosynthetic depression could overcome enhancement in canopies with low light extinction coefficients and/or leaf area, pointing toward a novel direction for future research. PMID:28432257

Excess Diffuse Light Absorption in Upper Mesophyll Limits CO2 Drawdown and Depresses Photosynthesis.

PubMed

Earles, J Mason; Théroux-Rancourt, Guillaume; Gilbert, Matthew E; McElrone, Andrew J; Brodersen, Craig R

2017-06-01

In agricultural and natural systems, diffuse light can enhance plant primary productivity due to deeper penetration into and greater irradiance of the entire canopy. However, for individual sun-grown leaves from three species, photosynthesis is actually less efficient under diffuse compared with direct light. Despite its potential impact on canopy-level productivity, the mechanism for this leaf-level diffuse light photosynthetic depression effect is unknown. Here, we investigate if the spatial distribution of light absorption relative to electron transport capacity in sun- and shade-grown sunflower ( Helianthus annuus ) leaves underlies its previously observed diffuse light photosynthetic depression. Using a new one-dimensional porous medium finite element gas-exchange model parameterized with light absorption profiles, we found that weaker penetration of diffuse versus direct light into the mesophyll of sun-grown sunflower leaves led to a more heterogenous saturation of electron transport capacity and lowered its CO 2 concentration drawdown capacity in the intercellular airspace and chloroplast stroma. This decoupling of light availability from photosynthetic capacity under diffuse light is sufficient to generate an 11% decline in photosynthesis in sun-grown but not shade-grown leaves, primarily because thin shade-grown leaves similarly distribute diffuse and direct light throughout the mesophyll. Finally, we illustrate how diffuse light photosynthetic depression could overcome enhancement in canopies with low light extinction coefficients and/or leaf area, pointing toward a novel direction for future research. © 2017 American Society of Plant Biologists. All Rights Reserved.

Molecular Diffusion in Plasma Membranes of Primary Lymphocytes Measured by Fluorescence Correlation Spectroscopy.

PubMed

Staaf, Elina; Bagawath-Singh, Sunitha; Johansson, Sofia

2017-02-01

Fluorescence correlation spectroscopy (FCS) is a powerful technique for studying the diffusion of molecules within biological membranes with high spatial and temporal resolution. FCS can quantify the molecular concentration and diffusion coefficient of fluorescently labeled molecules in the cell membrane. This technique has the ability to explore the molecular diffusion characteristics of molecules in the plasma membrane of immune cells in steady state (i.e., without processes affecting the result during the actual measurement time). FCS is suitable for studying the diffusion of proteins that are expressed at levels typical for most endogenous proteins. Here, a straightforward and robust method to determine the diffusion rate of cell membrane proteins on primary lymphocytes is demonstrated. An effective way to perform measurements on antibody-stained live cells and commonly occurring observations after acquisition are described. The recent advancements in the development of photo-stable fluorescent dyes can be utilized by conjugating the antibodies of interest to appropriate dyes that do not bleach extensively during the measurements. Additionally, this allows for the detection of slowly diffusing entities, which is a common feature of proteins expressed in cell membranes. The analysis procedure to extract molecular concentration and diffusion parameters from the generated autocorrelation curves is highlighted. In summary, a basic protocol for FCS measurements is provided; it can be followed by immunologists with an understanding of confocal microscopy but with no other previous experience of techniques for measuring dynamic parameters, such as molecular diffusion rates.

Permeation across hydrated DPPC lipid bilayers: simulation of the titrable amphiphilic drug valproic acid.

PubMed

Ulander, Johan; Haymet, A D J

2003-12-01

Valproic acid is a short branched fatty acid used as an anticonvulsant drug whose therapeutic action has been proposed to arise from membrane-disordering properties. Static and kinetic properties of valproic acid interacting with fully hydrated dipalmitoyl phosphatidylcholine lipid bilayers are studied using molecular-dynamics simulations. We calculate spatially resolved free energy profiles and local diffusion coefficients using the distance between the bilayer and valproic acid respective centers-of-mass along the bilayer normal as reaction coordinate. To investigate the pH dependence, we calculate profiles for the neutral valproic acid as well as its water-soluble anionic conjugate base valproate. The local diffusion constants for valproate/valproic acid along the bilayer normal are found to be approximately 10(-6) to 10(-5) cm2 s(-1). Assuming protonation of valproic acid upon association with--or insertion into--the lipid bilayer, we calculate the permeation coefficient to be approximately 2.0 10(-3) cm s(-1), consistent with recent experimental estimates of fast fatty acid transport. The ability of the lipid bilayer to sustain local defects such as water intrusions stresses the importance of going beyond mean field and taking into account correlation effects in theoretical descriptions of bilayer translocation processes.

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.

Secondary Ion Mass Spectrometry for Mg Tracer Diffusion: Issues and Solutions

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

Tuggle, Jay; Giordani, Andrew; Kulkarni, Nagraj S

2014-01-01

A Secondary Ion Mass Spectrometry (SIMS) method has been developed to measure stable Mg isotope tracer diffusion. This SIMS method was then used to calculate Mg self- diffusivities and the data was verified against historical data measured using radio tracers. The SIMS method has been validated as a reliable alternative to the radio-tracer technique for the measurement of Mg self-diffusion coefficients and can be used as a routine method for determining diffusion coefficients.

Test-retest reliability of high angular resolution diffusion imaging acquisition within medial temporal lobe connections assessed via tract based spatial statistics, probabilistic tractography and a novel graph theory metric.

PubMed

Kuhn, T; Gullett, J M; Nguyen, P; Boutzoukas, A E; Ford, A; Colon-Perez, L M; Triplett, W; Carney, P R; Mareci, T H; Price, C C; Bauer, R M

2016-06-01

This study examined the reliability of high angular resolution diffusion tensor imaging (HARDI) data collected on a single individual across several sessions using the same scanner. HARDI data was acquired for one healthy adult male at the same time of day on ten separate days across a one-month period. Environmental factors (e.g. temperature) were controlled across scanning sessions. Tract Based Spatial Statistics (TBSS) was used to assess session-to-session variability in measures of diffusion, fractional anisotropy (FA) and mean diffusivity (MD). To address reliability within specific structures of the medial temporal lobe (MTL; the focus of an ongoing investigation), probabilistic tractography segmented the Entorhinal cortex (ERc) based on connections with Hippocampus (HC), Perirhinal (PRc) and Parahippocampal (PHc) cortices. Streamline tractography generated edge weight (EW) metrics for the aforementioned ERc connections and, as comparison regions, connections between left and right rostral and caudal anterior cingulate cortex (ACC). Coefficients of variation (CoV) were derived for the surface area and volumes of these ERc connectivity-defined regions (CDR) and for EW across all ten scans, expecting that scan-to-scan reliability would yield low CoVs. TBSS revealed no significant variation in FA or MD across scanning sessions. Probabilistic tractography successfully reproduced histologically-verified adjacent medial temporal lobe circuits. Tractography-derived metrics displayed larger ranges of scanner-to-scanner variability. Connections involving HC displayed greater variability than metrics of connection between other investigated regions. By confirming the test retest reliability of HARDI data acquisition, support for the validity of significant results derived from diffusion data can be obtained.

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

Tipireddy, R.; Stinis, P.; Tartakovsky, A. M.

In this paper, we present a novel approach for solving steady-state stochastic partial differential equations (PDEs) with high-dimensional random parameter space. The proposed approach combines spatial domain decomposition with basis adaptation for each subdomain. The basis adaptation is used to address the curse of dimensionality by constructing an accurate low-dimensional representation of the stochastic PDE solution (probability density function and/or its leading statistical moments) in each subdomain. Restricting the basis adaptation to a specific subdomain affords finding a locally accurate solution. Then, the solutions from all of the subdomains are stitched together to provide a global solution. We support ourmore » construction with numerical experiments for a steady-state diffusion equation with a random spatially dependent coefficient. Lastly, our results show that highly accurate global solutions can be obtained with significantly reduced computational costs.« less

Diffuse reflectance relations based on diffusion dipole theory for large absorption and reduced scattering

NASA Astrophysics Data System (ADS)

Bremmer, Rolf H.; van Gemert, Martin J. C.; Faber, Dirk J.; van Leeuwen, Ton G.; Aalders, Maurice C. G.

2013-08-01

Diffuse reflectance spectra are used to determine the optical properties of biological samples. In medicine and forensic science, the turbid objects under study often possess large absorption and/or scattering properties. However, data analysis is frequently based on the diffusion approximation to the radiative transfer equation, implying that it is limited to tissues where the reduced scattering coefficient dominates over the absorption coefficient. Nevertheless, up to absorption coefficients of 20 m at reduced scattering coefficients of 1 and 11.5 mm-1, we observed excellent agreement (r2=0.994) between reflectance measurements of phantoms and the diffuse reflectance equation proposed by Zonios et al. [Appl. Opt. 38, 6628-6637 (1999)], derived as an approximation to one of the diffusion dipole equations of Farrell et al. [Med. Phys. 19, 879-888 (1992)]. However, two parameters were fitted to all phantom experiments, including strongly absorbing samples, implying that the reflectance equation differs from diffusion theory. Yet, the exact diffusion dipole approximation at high reduced scattering and absorption also showed agreement with the phantom measurements. The mathematical structure of the diffuse reflectance relation used, derived by Zonios et al. [Appl. Opt. 38, 6628-6637 (1999)], explains this observation. In conclusion, diffuse reflectance relations derived as an approximation to the diffusion dipole theory of Farrell et al. can analyze reflectance ratios accurately, even for much larger absorption than reduced scattering coefficients. This allows calibration of fiber-probe set-ups so that the object's diffuse reflectance can be related to its absorption even when large. These findings will greatly expand the application of diffuse reflection spectroscopy. In medicine, it may allow the use of blue/green wavelengths and measurements on whole blood, and in forensic science, it may allow inclusion of objects such as blood stains and cloth at crime scenes.

Investigating Whistler Mode Wave Diffusion Coefficients at Mars

NASA Astrophysics Data System (ADS)

Shane, A. D.; Liemohn, M. W.; Xu, S.; Florie, C.

2017-12-01

Observations of electron pitch angle distributions have suggested collisions are not the only pitch angle scattering process occurring in the Martian ionosphere. This unknown scattering process is causing high energy electrons (>100 eV) to become isotropized. Whistler mode waves are one pitch angle scattering mechanism known to preferentially scatter high energy electrons in certain plasma regimes. The distribution of whistler mode wave diffusion coefficients are dependent on the background magnetic field strength and thermal electron density, as well as the frequency and wave normal angle of the wave. We have solved for the whistler mode wave diffusion coefficients using the quasi-linear diffusion equations and have integrated them into a superthermal electron transport (STET) model. Preliminary runs have produced results that qualitatively match the observed electron pitch angle distributions at Mars. We performed parametric sweeps over magnetic field, thermal electron density, wave frequency, and wave normal angle to understand the relationship between the plasma parameters and the diffusion coefficient distributions, but also to investigate what regimes whistler mode waves scatter only high energy electrons. Increasing the magnetic field strength and lowering the thermal electron density shifts the distribution of diffusion coefficients toward higher energies and lower pitch angles. We have created an algorithm to identify Mars Atmosphere Volatile and EvolutioN (MAVEN) observations of high energy isotropic pitch angle distributions in the Martian ionosphere. We are able to map these distributions at Mars, and compare the conditions under which these are observed at Mars with the results of our parametric sweeps. Lastly, we will also look at each term in the kinetic diffusion equation to determine if the energy and mixed diffusion coefficients are important enough to incorporate into STET as well.

Toward Precision and Reproducibility of Diffusion Tensor Imaging: A Multicenter Diffusion Phantom and Traveling Volunteer Study.

PubMed

Palacios, E M; Martin, A J; Boss, M A; Ezekiel, F; Chang, Y S; Yuh, E L; Vassar, M J; Schnyer, D M; MacDonald, C L; Crawford, K L; Irimia, A; Toga, A W; Mukherjee, P

2017-03-01

Precision medicine is an approach to disease diagnosis, treatment, and prevention that relies on quantitative biomarkers that minimize the variability of individual patient measurements. The aim of this study was to assess the intersite variability after harmonization of a high-angular-resolution 3T diffusion tensor imaging protocol across 13 scanners at the 11 academic medical centers participating in the Transforming Research and Clinical Knowledge in Traumatic Brain Injury multisite study. Diffusion MR imaging was acquired from a novel isotropic diffusion phantom developed at the National Institute of Standards and Technology and from the brain of a traveling volunteer on thirteen 3T MR imaging scanners representing 3 major vendors (GE Healthcare, Philips Healthcare, and Siemens). Means of the DTI parameters and their coefficients of variation across scanners were calculated for each DTI metric and white matter tract. For the National Institute of Standards and Technology diffusion phantom, the coefficients of variation of the apparent diffusion coefficient across the 13 scanners was <3.8% for a range of diffusivities from 0.4 to 1.1 × 10 -6 mm 2 /s. For the volunteer, the coefficients of variations across scanners of the 4 primary DTI metrics, each averaged over the entire white matter skeleton, were all <5%. In individual white matter tracts, large central pathways showed good reproducibility with the coefficients of variation consistently below 5%. However, smaller tracts showed more variability, with the coefficients of variation of some DTI metrics reaching 10%. The results suggest the feasibility of standardizing DTI across 3T scanners from different MR imaging vendors in a large-scale neuroimaging research study. © 2017 by American Journal of Neuroradiology.

Effects of soft interactions and bound mobility on diffusion in crowded environments: a model of sticky and slippery obstacles

NASA Astrophysics Data System (ADS)

Stefferson, Michael W.; Norris, Samantha L.; Vernerey, Franck J.; Betterton, Meredith D.; E Hough, Loren

2017-08-01

Crowded environments modify the diffusion of macromolecules, generally slowing their movement and inducing transient anomalous subdiffusion. The presence of obstacles also modifies the kinetics and equilibrium behavior of tracers. While previous theoretical studies of particle diffusion have typically assumed either impenetrable obstacles or binding interactions that immobilize the particle, in many cellular contexts bound particles remain mobile. Examples include membrane proteins or lipids with some entry and diffusion within lipid domains and proteins that can enter into membraneless organelles or compartments such as the nucleolus. Using a lattice model, we studied the diffusive movement of tracer particles which bind to soft obstacles, allowing tracers and obstacles to occupy the same lattice site. For sticky obstacles, bound tracer particles are immobile, while for slippery obstacles, bound tracers can hop without penalty to adjacent obstacles. In both models, binding significantly alters tracer motion. The type and degree of motion while bound is a key determinant of the tracer mobility: slippery obstacles can allow nearly unhindered diffusion, even at high obstacle filling fraction. To mimic compartmentalization in a cell, we examined how obstacle size and a range of bound diffusion coefficients affect tracer dynamics. The behavior of the model is similar in two and three spatial dimensions. Our work has implications for protein movement and interactions within cells.

Diffuse nutrient losses and the impact factors determining their regional differences in four catchments from North to South China

NASA Astrophysics Data System (ADS)

Zhang, Yongyong; Zhou, Yujian; Shao, Quanxi; Liu, Hongbin; Lei, Qiuliang; Zhai, Xiaoyan; Wang, Xuelei

2016-12-01

Diffuse nutrient loss mechanism is complicated and shows remarkably regional differences due to spatial heterogeneities of underlying surface conditions, climate and agricultural practices. Moreover, current available observations are still hard to support the identification of impact factors due to different time or space steps. In this study, an integrated water system model (HEQM) was adopted to obtain the simulated loads of diffuse components (carriers: runoff and sediment; nutrient: total nitrogen (TN) and total phosphorous (TP)) with synchronous scales. Multivariable statistical analysis approaches (Analysis of Similarity and redundancy analysis) were used to assess the regional differences, and to identify impact factors as well as their contributions. Four catchments were selected as our study areas, i.e., Xiahui and Zhangjiafen Catchments of Miyun Basin in North China, Yuliang and Tunxi Catchments of Xin'anjiang Basin in South China. Results showed that the model performances of monthly processes were very good for runoff and good for sediment, TN and TP. The annual average coefficients of all the diffuse components in Xin'anjiang Basin were much greater than those in Miyun Basin, and showed significantly regional differences. All the selected impact factors interpreted 72.87-82.16% of the regional differences of carriers, and 62.72-71.62% of those of nutrient coefficients, respectively. For individual impact factor categories, the critical category was geography, followed by land-use/cover, carriers, climate, as well as soil and agricultural practices in Miyun Basin, or agricultural practices and soil in Xin'anjiang Basin. For individual factors, the critical factors were locations for the carrier regional differences, and carriers or chemical fertilizer for the nutrient regional differences. This study is expected to promote further applications of integrated water system model and multivariable statistical analysis in the diffuse nutrient studies, and provide a scientific support for the diffuse pollution control and management in China.

Modified free volume theory of self-diffusion and molecular theory of shear viscosity of liquid carbon dioxide.

PubMed

Nasrabad, Afshin Eskandari; Laghaei, Rozita; Eu, Byung Chan

2005-04-28

In previous work on the density fluctuation theory of transport coefficients of liquids, it was necessary to use empirical self-diffusion coefficients to calculate the transport coefficients (e.g., shear viscosity of carbon dioxide). In this work, the necessity of empirical input of the self-diffusion coefficients in the calculation of shear viscosity is removed, and the theory is thus made a self-contained molecular theory of transport coefficients of liquids, albeit it contains an empirical parameter in the subcritical regime. The required self-diffusion coefficients of liquid carbon dioxide are calculated by using the modified free volume theory for which the generic van der Waals equation of state and Monte Carlo simulations are combined to accurately compute the mean free volume by means of statistical mechanics. They have been computed as a function of density along four different isotherms and isobars. A Lennard-Jones site-site interaction potential was used to model the molecular carbon dioxide interaction. The density and temperature dependence of the theoretical self-diffusion coefficients are shown to be in excellent agreement with experimental data when the minimum critical free volume is identified with the molecular volume. The self-diffusion coefficients thus computed are then used to compute the density and temperature dependence of the shear viscosity of liquid carbon dioxide by employing the density fluctuation theory formula for shear viscosity as reported in an earlier paper (J. Chem. Phys. 2000, 112, 7118). The theoretical shear viscosity is shown to be robust and yields excellent density and temperature dependence for carbon dioxide. The pair correlation function appearing in the theory has been computed by Monte Carlo simulations.

Anomalous diffusion and dynamics of fluorescence recovery after photobleaching in the random-comb model

NASA Astrophysics Data System (ADS)

Yuste, S. B.; Abad, E.; Baumgaertner, A.

2016-07-01

We address the problem of diffusion on a comb whose teeth display varying lengths. Specifically, the length ℓ of each tooth is drawn from a probability distribution displaying power law behavior at large ℓ ,P (ℓ ) ˜ℓ-(1 +α ) (α >0 ). To start with, we focus on the computation of the anomalous diffusion coefficient for the subdiffusive motion along the backbone. This quantity is subsequently used as an input to compute concentration recovery curves mimicking fluorescence recovery after photobleaching experiments in comblike geometries such as spiny dendrites. Our method is based on the mean-field description provided by the well-tested continuous time random-walk approach for the random-comb model, and the obtained analytical result for the diffusion coefficient is confirmed by numerical simulations of a random walk with finite steps in time and space along the backbone and the teeth. We subsequently incorporate retardation effects arising from binding-unbinding kinetics into our model and obtain a scaling law characterizing the corresponding change in the diffusion coefficient. Finally, we show that recovery curves obtained with the help of the analytical expression for the anomalous diffusion coefficient cannot be fitted perfectly by a model based on scaled Brownian motion, i.e., a standard diffusion equation with a time-dependent diffusion coefficient. However, differences between the exact curves and such fits are small, thereby providing justification for the practical use of models relying on scaled Brownian motion as a fitting procedure for recovery curves arising from particle diffusion in comblike systems.

Fractal Theory and Field Cover Experiments: Implications for the Fractal Characteristics and Radon Diffusion Behavior of Soils and Rocks.

PubMed

Tan, Wanyu; Li, Yongmei; Tan, Kaixuan; Duan, Xianzhe; Liu, Dong; Liu, Zehua

2016-12-01

Radon diffusion and transport through different media is a complex process affected by many factors. In this study, the fractal theories and field covering experiments were used to study the fractal characteristics of particle size distribution (PSD) of six kinds of geotechnical materials (e.g., waste rock, sand, laterite, kaolin, mixture of sand and laterite, and mixture of waste rock and laterite) and their effects on radon diffusion. In addition, the radon diffusion coefficient and diffusion length were calculated. Moreover, new formulas for estimating diffusion coefficient and diffusion length functional of fractal dimension d of PSD were proposed. These results demonstrate the following points: (1) the fractal dimension d of the PSD can be used to characterize the property of soils and rocks in the studies of radon diffusion behavior; (2) the diffusion coefficient and diffusion length decrease with increasing fractal dimension of PSD; and (3) the effectiveness of final covers in reducing radon exhalation of uranium tailings impoundments can be evaluated on the basis of the fractal dimension of PSD of materials.

Measurement of diffusion coefficients of VOCs for building materials: review and development of a calculation procedure.

PubMed

Haghighat, F; Lee, C S; Ghaly, W S

2002-06-01

The measurement and prediction of building material emission rates have been the subject of intensive research over the past decade, resulting in the development of advanced sensory and chemical analysis measurement techniques as well as the development of analytical and numerical models. One of the important input parameters for these models is the diffusion coefficient. Several experimental techniques have been applied to estimate the diffusion coefficient. An extensive literature review of the techniques used to measure this coefficient was carried out, for building materials exposed to volatile organic compounds (VOC). This paper reviews these techniques; it also analyses the results and discusses the possible causes of difference in the reported data. It was noted that the discrepancy between the different results was mainly because of the assumptions made in and the techniques used to analyze the data. For a given technique, the results show that there can be a difference of up to 700% in the reported data. Moreover, the paper proposes what is referred to as the mass exchanger method, to calculate diffusion coefficients considering both diffusion and convection. The results obtained by this mass exchanger method were compared with those obtained by the existing method considering only diffusion. It was demonstrated that, for porous materials, the convection resistance could not be ignored when compared with the diffusion resistance.

Apparent Diffusion Coefficient and Dynamic Contrast-Enhanced Magnetic Resonance Imaging in Pancreatic Cancer: Characteristics and Correlation With Histopathologic Parameters.

PubMed

Ma, Wanling; Li, Na; Zhao, Weiwei; Ren, Jing; Wei, Mengqi; Yang, Yong; Wang, Yingmei; Fu, Xin; Zhang, Zhuoli; Larson, Andrew C; Huan, Yi

2016-01-01

To clarify diffusion and perfusion abnormalities and evaluate correlation between apparent diffusion coefficient (ADC), MR perfusion and histopathologic parameters of pancreatic cancer (PC). Eighteen patients with PC underwent diffusion-weighted imaging and dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI). Parameters of DCE-MRI and ADC of cancer and non-cancerous tissue were compared. Correlation between the rate constant that represents transfer of contrast agent from the arterial blood into the extravascular extracellular space (K, volume of the extravascular extracellular space per unit volume of tissue (Ve), and ADC of PC and histopathologic parameters were analyzed. The rate constant that represents transfer of contrast agent from the extravascular extracellular space into blood plasma, K, tissue volume fraction occupied by vascular space, and ADC of PC were significantly lower than nontumoral pancreases. Ve of PC was significantly higher than that of nontumoral pancreas. Apparent diffusion coefficient and K values of PC were negatively correlated to fibrosis content and fibroblast activation protein staining score. Fibrosis content was positively correlated to Ve. Apparent diffusion coefficient values and parameters of DCE-MRI can differentiate PC from nontumoral pancreases. There are correlations between ADC, K, Ve, and fibrosis content of PC. Fibroblast activation protein staining score of PC is negatively correlated to ADC and K. Apparent diffusion coefficient, K, and Ve may be feasible to predict prognosis of PC.

An improved strip FRAP method for estimating diffusion coefficients: correcting for the degree of photobleaching.

PubMed

Yang, J; Köhler, K; Davis, D M; Burroughs, N J

2010-06-01

Fluorescence recovery after photobleaching is a widely established method for the estimation of diffusion coefficients, strip bleaching with an associated recovery curve analysis being one of the simplest techniques. However, its implementation requires near 100% bleaching in the region of interest with negligible fluorescence loss outside, both constraints being hard to achieve concomitantly for fast diffusing molecules. We demonstrate that when these requirements are not met there is an error in the estimation of the diffusion coefficient D, either an under- or overestimation depending on which assumption is violated the most. We propose a simple modification to the recovery curve analysis incorporating the concept of the relative bleached mass m giving a revised recovery time parametrization tau=m(2)w(2)/4piD for a strip of width w. This modified model removes the requirement of 100% bleaching in the region of interest and allows for limited diffusion of the fluorophore during bleaching. We validate our method by estimating the (volume) diffusion coefficient of FITC-labelled IgG in 60% glycerol solution, D= 4.09 +/- 0.21 microm(2) s(-1), and the (surface) diffusion coefficient of a green-fluorescent protein-tagged class I MHC protein expressed at the surface of a human B cell line, D= 0.32 +/- 0.03 microm(2) s(-1) for a population of cells.

Approximation of effective moisture-diffusion coefficient to characterize performance of a barrier coating

NASA Astrophysics Data System (ADS)

Nagai, Shingo

2013-11-01

We report estimation of the effective diffusion coefficient of moisture through a barrier coating to develop an encapsulation technology for the thin-film electronics industry. This investigation targeted a silicon oxide (SiOx) film that was deposited on a plastic substrate by a large-process-area web coater. Using the finite difference method based on diffusion theory, our estimation of the effective diffusion coefficient of a SiOx film corresponded to that of bulk glass that was previously reported. This result suggested that the low diffusivities of barrier films can be obtained on a mass-production level in the factory. In this investigation, experimental observations and mathematical confirmation revealed the limit of the water vapor transmission rate on the single barrier coating.

Calculation of the fractional interstitial component of boron diffusion and segregation coefficient of boron in Si0.8Ge0.2

NASA Astrophysics Data System (ADS)

Fang, Tilden T.; Fang, Wingra T. C.; Griffin, Peter B.; Plummer, James D.

1996-02-01

Investigation of boron diffusion in strained silicon germanium buried layers reveals a fractional interstitial component of boron diffusion (fBI) in Se0.8Ge0.2 approximately equal to the fBI value in silicon. In conjunction with computer-simulated boron profiles, the results yield an absolute lower-bound of fBI in Si0.8Ge0.2 of ˜0.8. In addition, the experimental methodology provides a unique vehicle for measuring the segregation coefficient; oxidation-enhanced diffusion is used instead of an extended, inert anneal to rapidly diffuse the dopant to equilibrium levels across the interface, allowing the segregation coefficient to be measured more quickly.

Feasibility of high-resolution one-dimensional relaxation imaging at low magnetic field using a single-sided NMR scanner applied to articular cartilage.

PubMed

Rössler, Erik; Mattea, Carlos; Stapf, Siegfried

2015-02-01

Low field Nuclear Magnetic Resonance increases the contrast of the longitudinal relaxation rate in many biological tissues; one prominent example is hyaline articular cartilage. In order to take advantage of this increased contrast and to profile the depth-dependent variations, high resolution parameter measurements are carried out which can be of critical importance in an early diagnosis of cartilage diseases such as osteoarthritis. However, the maximum achievable spatial resolution of parameter profiles is limited by factors such as sensor geometry, sample curvature, and diffusion limitation. In this work, we report on high-resolution single-sided NMR scanner measurements with a commercial device, and quantify these limitations. The highest achievable spatial resolution on the used profiler, and the lateral dimension of the sensitive volume were determined. Since articular cartilage samples are usually bent, we also focus on averaging effects inside the horizontally aligned sensitive volume and their impact on the relaxation profiles. Taking these critical parameters into consideration, depth-dependent relaxation time profiles with the maximum achievable vertical resolution of 20 μm are discussed, and are correlated with diffusion coefficient profiles in hyaline articular cartilage in order to reconstruct T(2) maps from the diffusion-weighted CPMG decays of apparent relaxation rates. Copyright © 2014 Elsevier Inc. All rights reserved.

Chemical release from single-PMMA microparticles monitored by CARS microscopy

NASA Astrophysics Data System (ADS)

Enejder, Annika; Svedberg, Fredrik; Nordstierna, Lars; Nydén, Magnus

2011-03-01

Microparticles loaded with antigens, proteins, DNA, fungicides, and other functional agents emerge as ideal vehicles for vaccine, drug delivery, genetic therapy, surface- and crop protection. The microscopic size of the particles and their collective large specific surface area enables highly active and localized release of the functional substance. In order to develop designs with release profiles optimized for the specific application, it is desirable to map the distribution of the active substance within the particle and how parameters such as size, material and morphology affect release rates at single particle level. Current imaging techniques are limited in resolution, sensitivity, image acquisition time, or sample treatment, excluding dynamic studies of active agents in microparticles. Here, we demonstrate that the combination of CARS and THG microscopy can successfully be used, by mapping the spatial distribution and release rates of the fungicide and food preservative IPBC from different designs of PMMA microparticles at single-particle level. By fitting a radial diffusion model to the experimental data, single particle diffusion coefficients can be determined. We show that release rates are highly dependent on the size and morphology of the particles. Hence, CARS and THG microscopy provides adequate sensitivity and spatial resolution for quantitative studies on how singleparticle properties affect the diffusion of active agents at microscopic level. This will aid the design of innovative microencapsulating systems for controlled release.

Note on coefficient matrices from stochastic Galerkin methods for random diffusion equations

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

Zhou Tao, E-mail: tzhou@lsec.cc.ac.c; Tang Tao, E-mail: ttang@hkbu.edu.h

2010-11-01

In a recent work by Xiu and Shen [D. Xiu, J. Shen, Efficient stochastic Galerkin methods for random diffusion equations, J. Comput. Phys. 228 (2009) 266-281], the Galerkin methods are used to solve stochastic diffusion equations in random media, where some properties for the coefficient matrix of the resulting system are provided. They also posed an open question on the properties of the coefficient matrix. In this work, we will provide some results related to the open question.

Separation of Electric Fields Into Potential and Inductive Parts, and Implications for Radial Diffusion

NASA Astrophysics Data System (ADS)

Chan, A. A.; Ilie, R.; Elkington, S. R.; Albert, J.; Huie, W.

2017-12-01

It has been traditional to separate radiation belt radial-diffusion coefficients into two contributions: an "electrostatic" diffusion coefficient, which is assumed to be due to a potential (non-inductive) electric field, and an "electromagnetic" diffusion coefficient , which is assumed to be due to the combined effect of an inductive electric field and the corresponding time-dependent magnetic field. One difficulty in implementing this separation when using magnetospheric fields obtained from measurements, or from MHD simulations, is that only the total electric field is given; the separation of the electric field into potential and inductive parts is not readily available. In this work we separate the electric field using a numerical method based on the Helmholtz decomposition of the total motional electric field calculated by the BATS-R-US MHD code. The inner boundary for the electric potential is based on the Ridley Ionospheric Model solution and we assume floating boundary conditions in the solar wind. Using different idealized solar wind drivers, including a solar wind density that is oscillating at a single frequency or with a broad spectrum of frequencies, we calculate potential and inductive electric fields, electric and magnetic power spectral densities, and corresponding radial diffusion coefficients. Simulations driven by idealized solar wind conditions show a clear separation of the potential and inductive contributions to the power spectral densities and diffusion coefficients. Simulations with more realistic solar wind drivers are underway to better assess the use of electrostatic and electromagnetic diffusion coefficients in understanding ULF wave-particle interactions in Earth's radiation belts.

The Effect of a Fluorophore Photo-Physics on the Lipid Vesicle Diffusion Coefficient Studied by Fluorescence Correlation Spectroscopy.

PubMed

Drabik, Dominik; Przybyło, Magda; Sikorski, Aleksander; Langner, Marek

2016-03-01

Fluorescence Correlation Spectroscopy (FCS) is a technique, which allows determination of the diffusion coefficient and concentration of fluorescent objects suspended in the solution. The measured parameter is the fluctuation of the fluorescence signal emitted by diffusing molecules. When 100 nm DOPC vesicles labeled with various fluorescent dyes (Fluorescein-PE, NBD-PE, Atto488 DOPE or βBodipy FL) were measured, different values of diffusion coefficients have been obtained. These diffusion coefficients were different from the expected values measured using the dynamic light scattering method (DLS). The FCS was initially developed for solutions containing small fluorescent molecules therefore the observed inconsistency may result from the nature of vesicle suspension itself. The duration of the fluorescence signal may depend on the following factors: the exposure time of the labeled object to the excitation beam, the photo-physical properties (e.g., stability) of a fluorophore, the theoretical model used for the calculations of the diffusion coefficient and optical properties of the vesicle suspension. The diffusion coefficients determined for differently labeled liposomes show that its dependence on vesicle size and quantity of fluorescent probed used for labeling was significant demonstrating that the fluorescence properties of the fluorophore itself (bleaching and/or blinking) were critical factors for a correct outcome of FCS experiment. The new, based on combined FCS and DLS measurements, method for the determination of the focal volume prove itself to be useful for the evaluation of a fluorescence dye with respect to its applicability for FCS experiment.

Effects of molecular size and structure on self-diffusion coefficient and viscosity for saturated hydrocarbons having six carbon atoms.

PubMed

Iwahashi, Makio; Kasahara, Yasutoshi

2007-01-01

Self-diffusion coefficients and viscosities for the saturated hydrocarbons having six carbon atoms such as hexane, 2-methylpentane (2MP), 3-methylpentane (3MP), 2,2-dimethylbutane (22DMB), 2,3-dimethylbutane (23DMB), methylcyclopentane (McP) and cyclohexane (cH) were measured at various constant temperatures; obtained results were discussed in connection with their molar volumes, molecular structures and thermodynamic properties. The values of self-diffusion coefficients as the microscopic property were inversely proportional to those of viscosities as the macroscopic property. The order of their viscosities was almost same to those of their melting temperatures and enthalpies of fusion, which reflect the attractive interactions among their molecules. On the other hand, the order of the self-diffusion coefficients inversely related to the order of the melting temperatures and the enthalpies of the fusion. Namely, the compound having the larger attractive interaction mostly shows the less mobility in its liquid state, e.g., cyclohexane (cH), having the largest attractive interaction and the smallest molar volume exhibits an extremely large viscosity and small self-diffusion coefficient comparing with other hydrocarbons. However, a significant exception was 22DMB, being most close to a sphere: In spite of the smallest attractive interaction and the largest molar volume of 22DMB in the all samples, it has the thirdly larger viscosity and the thirdly smaller self-diffusion coefficient. Consequently, the dynamical properties such as self-diffusion and viscosity for the saturated hydrocarbons are determined not only by their attractive interactions but also by their molecular structures.

Relativistic collective diffusion in one-dimensional systems

NASA Astrophysics Data System (ADS)

Lin, Gui-Wu; Lam, Yu-Yiu; Zheng, Dong-Qin; Zhong, Wei-Rong

2018-05-01

The relativistic collective diffusion in one-dimensional molecular system is investigated through nonequilibrium molecular dynamics with Monte Carlo methods. We have proposed the relationship among the speed, the temperature, the density distribution and the collective diffusion coefficient of particles in a relativistic moving system. It is found that the relativistic speed of the system has no effect on the temperature, but the collective diffusion coefficient decreases to zero as the velocity of the system approaches to the speed of light. The collective diffusion coefficient is modified as D‧ = D(1 ‑w2 c2 )3 2 for satisfying the relativistic circumstances. The present results may contribute to the understanding of the behavior of the particles transport diffusion in a high speed system, as well as enlighten the study of biological metabolism at relativistic high speed situation.

Coupled low-energy - ring current plasma diffusion in the Jovian magnetosphere

NASA Technical Reports Server (NTRS)

Summers, D.; Siscoe, G. L.

1985-01-01

The outwardly diffusing Iogenic plasma and the simultaneously inwardly diffusing ring current plasma in the Jovian magnetosphere are described using a coupled diffusion model which incorporates the effects of the pressure gradient of the ring current into the cross-L diffusion coefficient. The coupled diffusion coefficient is derived by calculating the total energy available to drive the diffusion process. The condition is imposed that the diffusion coefficient takes on a local minimum value at some point in the region L = 7-8, at which point the gradient of the Io plasma density is specified as ramp value given by Siscoe et al. (1981). The hypothesis that the pressure gradient of the ring current causes the diminution of radial plasma transport is tested, and solution profiles for the Iogenic and ring current plasma densities are obtained which imply that the Io plasma ramp is caused by a high-density, low-energy component of the ring current hitherto unobserved directly.

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.

Diffusion Coefficients from Molecular Dynamics Simulations in Binary and Ternary Mixtures

NASA Astrophysics Data System (ADS)

Liu, Xin; Schnell, Sondre K.; Simon, Jean-Marc; Krüger, Peter; Bedeaux, Dick; Kjelstrup, Signe; Bardow, André; Vlugt, Thijs J. H.

2013-07-01

Multicomponent diffusion in liquids is ubiquitous in (bio)chemical processes. It has gained considerable and increasing interest as it is often the rate limiting step in a process. In this paper, we review methods for calculating diffusion coefficients from molecular simulation and predictive engineering models. The main achievements of our research during the past years can be summarized as follows: (1) we introduced a consistent method for computing Fick diffusion coefficients using equilibrium molecular dynamics simulations; (2) we developed a multicomponent Darken equation for the description of the concentration dependence of Maxwell-Stefan diffusivities. In the case of infinite dilution, the multicomponent Darken equation provides an expression for [InlineEquation not available: see fulltext.] which can be used to parametrize the generalized Vignes equation; and (3) a predictive model for self-diffusivities was proposed for the parametrization of the multicomponent Darken equation. This equation accurately describes the concentration dependence of self-diffusivities in weakly associating systems. With these methods, a sound framework for the prediction of mutual diffusion in liquids is achieved.

Partitioning and diffusion of PBDEs through an HDPE geomembrane.

PubMed

Rowe, R Kerry; Saheli, Pooneh T; Rutter, Allison

2016-09-01

Polybrominated diphenyl ether (PBDE) has been measured in MSW landfill leachate and its migration through a modern landfill liner has not been investigated previously. To assure environmental protection, it is important to evaluate the efficacy of landfill liners for controlling the release of PBDE to the environment to a negligible level. The partitioning and diffusion of a commercial mixture of PBDEs (DE-71: predominantly containing six congeners) with respect to a high-density polyethylene (HDPE) geomembrane is examined. The results show that the partitioning coefficients of the six congeners in this mixture range from 700,000 to 7,500,000 and the diffusion coefficients range from 1.3 to 6.0×10(-15)m(2)/s depending on the congener. This combination of very high partitioning coefficients and very low diffusion coefficients suggest that a well constructed HDPE geomembrane liner will be an extremely effective barrier for PBDEs with respect to diffusion from a municipal solid waste landfill, as illustrated by an example. The results for pure diffusion scenario showed that the congeners investigated meet the guidelines by at least a factor of three for an effective geomembrane liner where diffusion is the controlling transport mechanism. Copyright © 2016 Elsevier Ltd. All rights reserved.

DIFF--A 7090 Fortran Program to Determine Neutron Diffusion Constants Relating to a Six-Group Calculation; DIFF--UN PROGRAMME FOR TRAN 7090 POUR DETERMINER LES CONSTANTES DE DIFFUSION NEUTRONIQUE RELATIVES A UN CALCUL A SIX GROUPES

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

Plelnevaux, C.

The computer program DIFF, in Fortran for the IBM 7090, for calculating the neutron diffusion coefficients and attenuation areas (L/sup 2/) necessary for multigroup diffusion calculations for reactor shielding is described. Diffusion coefficients and values of the inverse attenuation length are given for a six group calculation for several interesting shielding materials. (D.C.W.)

Thermal diffusion behavior of nonionic surfactants in water.

PubMed

Ning, Hui; Kita, Rio; Kriegs, Hartmut; Luettmer-Strathmann, Jutta; Wiegand, Simone

2006-06-08

We studied the thermal diffusion behavior of hexaethylene glycol monododecyl ether (C12E6) in water by means of thermal diffusion forced Rayleigh scattering (TDFRS) and determined Soret coefficients, thermal diffusion coefficients, and diffusion constants at different temperatures and concentrations. At low surfactant concentrations, the measured Soret coefficient is positive, which implies that surfactant micelles move toward the cold region in a temperature gradient. For C12E6/water at a high surfactant concentration of w1 = 90 wt % and a temperature of T = 25 degrees C, however, a negative Soret coefficient S(T) was observed. Because the concentration part of the TDFRS diffraction signal for binary systems is expected to consist of a single mode, we were surprised to find a second, slow mode for C12E6/water system in a certain temperature and concentration range. To clarify the origin of this second mode, we investigated also, tetraethylene glycol monohexyl ether (C6E4), tetraethylene glycol monooctyl ether (C8E4), pentaethylene glycol monododecyl ether (C12E5), and octaethylene glycol monohexadecyl ether (C16E8) and compared the results with the previous results for octaethylene glycol monodecyl ether (C10E8). Except for C6E4 and C10E8, a second slow mode was observed in all systems usually for state points close to the phase boundary. The diffusion coefficient and Soret coefficient derived from the fast mode can be identified as the typical mutual diffusion and Soret coefficients of the micellar solutions and compare well with the independently determined diffusion coefficients in a dynamic light scattering experiment. Experiments with added salt show that the slow mode is suppressed by the addition of w(NaCl) = 0.02 mol/L sodium chloride. This suggests that the slow mode is related to the small amount of absorbing ionic dye, less than 10(-5) by weight, which is added in TDFRS experiments to create a temperature grating. The origin of the slow mode of the TDFRS signal will be tentatively interpreted in terms of a ternary mixture of neutral micelles, dye-charged micelles, and water.

Short-time self-diffusion coefficient of a particle in a colloidal suspension bounded by a microchannel: Virial expansions and simulation

NASA Astrophysics Data System (ADS)

Kȩdzierski, Marcin; Wajnryb, Eligiusz

2011-10-01

Self-diffusion of colloidal particles confined to a cylindrical microchannel is considered theoretically and numerically. Virial expansion of the self-diffusion coefficient is performed. Two-body and three-body hydrodynamic interactions are evaluated with high precision using the multipole method. The multipole expansion algorithm is also used to perform numerical simulations of the self-diffusion coefficient, valid for all possible particle packing fractions. Comparison with earlier results shows that the widely used method of reflections is insufficient for calculations of hydrodynamic interactions even for small packing fractions and small particles radii, contrary to the prevalent opinion.

Oxygen chemical diffusion in hypo-stoichiometric MOX

NASA Astrophysics Data System (ADS)

Kato, Masato; Morimoto, Kyoichi; Tamura, Tetsuya; Sunaoshi, Takeo; Konashi, Kenji; Aono, Shigenori; Kashimura, Motoaki

2009-06-01

Kinetics of the oxygen-to-metal ratio change in (U 0.8Pu 0.2)O 2-x and (U 0.7Pu 0.3)O 2-x was evaluated in the temperature range of 1523-1623 K using a thermo-gravimetric technique. The oxygen chemical diffusion coefficients were decided as a function of temperature from the kinetics of the reduction process under a hypo-stoichiometric composition. The diffusion coefficient of (U 0.7Pu 0.3)O 2-x was smaller than that of (U 0.8Pu 0.2)O 2-x. No strong dependence was observed for the diffusion coefficient on the O/M variation of samples.

Diffusion relaxation times of nonequilibrium isolated small bodies and their solid phase ensembles to equilibrium states

NASA Astrophysics Data System (ADS)

Tovbin, Yu. K.

2017-08-01

The possibility of obtaining analytical estimates in a diffusion approximation of the times needed by nonequilibrium small bodies to relax to their equilibrium states based on knowledge of the mass transfer coefficient is considered. This coefficient is expressed as the product of the self-diffusion coefficient and the thermodynamic factor. A set of equations for the diffusion transport of mixture components is formulated, characteristic scales of the size of microheterogeneous phases are identified, and effective mass transfer coefficients are constructed for them. Allowing for the developed interface of coexisting and immiscible phases along with the porosity of solid phases is discussed. This approach can be applied to the diffusion equalization of concentrations of solid mixture components in many physicochemical systems: the mutual diffusion of components in multicomponent systems (alloys, semiconductors, solid mixtures of inert gases) and the mass transfer of an absorbed mobile component in the voids of a matrix consisting of slow components or a mixed composition of mobile and slow components (e.g., hydrogen in metals, oxygen in oxides, and the transfer of molecules through membranes of different natures, including polymeric).

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

Measurement of CO2 diffusivity for carbon sequestration: a microfluidic approach for reservoir-specific analysis.

PubMed

Sell, Andrew; Fadaei, Hossein; Kim, Myeongsub; Sinton, David

2013-01-02

Predicting carbon dioxide (CO(2)) security and capacity in sequestration requires knowledge of CO(2) diffusion into reservoir fluids. In this paper we demonstrate a microfluidic based approach to measuring the mutual diffusion coefficient of carbon dioxide in water and brine. The approach enables formation of fresh CO(2)-liquid interfaces; the resulting diffusion is quantified by imaging fluorescence quenching of a pH-dependent dye, and subsequent analyses. This method was applied to study the effects of site-specific variables--CO(2) pressure and salinity levels--on the diffusion coefficient. In contrast to established, macro-scale pressure-volume-temperature cell methods that require large sample volumes and testing periods of hours/days, this approach requires only microliters of sample, provides results within minutes, and isolates diffusive mass transport from convective effects. The measured diffusion coefficient of CO(2) in water was constant (1.86 [± 0.26] × 10(-9) m(2)/s) over the range of pressures (5-50 bar) tested at 26 °C, in agreement with existing models. The effects of salinity were measured with solutions of 0-5 M NaCl, where the diffusion coefficient varied up to 3 times. These experimental data support existing theory and demonstrate the applicability of this method for reservoir-specific testing.

Statistical theory of diffusion in concentrated bcc and fcc alloys and concentration dependencies of diffusion coefficients in bcc alloys FeCu, FeMn, FeNi, and FeCr

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

Vaks, V. G.; Khromov, K. Yu., E-mail: khromov-ky@nrcki.ru; Pankratov, I. R.

2016-07-15

The statistical theory of diffusion in concentrated bcc and fcc alloys with arbitrary pairwise interatomic interactions based on the master equation approach is developed. Vacancy–atom correlations are described using both the second-shell-jump and the nearest-neighbor-jump approximations which are shown to be usually sufficiently accurate. General expressions for Onsager coefficients in terms of microscopic interatomic interactions and some statistical averages are given. Both the analytical kinetic mean-field and the Monte Carlo methods for finding these averages are described. The theory developed is used to describe sharp concentration dependencies of diffusion coefficients in several iron-based alloy systems. For the bcc alloys FeCu,more » FeMn, and FeNi, we predict the notable increase of the iron self-diffusion coefficient with solute concentration c, up to several times, even though values of c possible for these alloys do not exceed some percent. For the bcc alloys FeCr at high temperatures T ≳ 1400 K, we show that the very strong and peculiar concentration dependencies of both tracer and chemical diffusion coefficients observed in these alloys can be naturally explained by the theory, without invoking exotic models discussed earlier.« less

Ion conduction mechanisms and thermal properties of hydrated and anhydrous phosphoric acids studied with 1H, 2H, and 31P NMR.

PubMed

Aihara, Yuichi; Sonai, Atsuo; Hattori, Mineyuki; Hayamizu, Kikuko

2006-12-14

To understand the behaviors of phosphoric acids in fuel cells, the ion conduction mechanisms of phosphoric acids in condensed states without free water and in a monomer state with water were studied by measuring the ionic conductivity (sigma) using AC impedance, thermal properties, and self-diffusion coefficients (D) and spin-lattice relaxation times (T1) with multinuclear NMR. The self-diffusion coefficient of the protons (H+ or H3O+), H2O, and H located around the phosphate were always larger than the diffusion coefficients of the phosphates and the disparity increased with increasing phosphate concentration. The diffusion coefficients of the samples containing D2O paralleled those in the protonated samples. Since the 1H NMR T1 values exhibited a minimum with temperature, it was possible to determine the correlation times and they were found to be of nanosecond order for a distance of nanometer order for a flip. The agreement of the ionic conductivities measured directly and those calculated from the diffusion coefficients indicates that the ion conduction obeys the Nernst-Einstein equation in the condensed phosphoric acids. The proton diffusion plays a dominant role in the ion conduction, especially in the condensed phosphoric acids.

Distortion-free diffusion MRI using an MRI-guided Tri-Cobalt 60 radiotherapy system: Sequence verification and preliminary clinical experience.

PubMed

Gao, Yu; Han, Fei; Zhou, Ziwu; Cao, Minsong; Kaprealian, Tania; Kamrava, Mitchell; Wang, Chenyang; Neylon, John; Low, Daniel A; Yang, Yingli; Hu, Peng

2017-10-01

Monitoring tumor response during the course of treatment and adaptively modifying treatment plan based on tumor biological feedback may represent a new paradigm for radiotherapy. Diffusion MRI has shown great promises in assessing and predicting tumor response to radiotherapy. However, the conventional diffusion-weighted single-shot echo-planar-imaging (DW-ssEPI) technique suffers from limited resolution, severe distortion, and possibly inaccurate ADC at low field strength. The purpose of this work was to develop a reliable, accurate and distortion-free diffusion MRI technique that is practicable for longitudinal tumor response evaluation and adaptive radiotherapy on a 0.35 T MRI-guided radiotherapy system. A diffusion-prepared turbo spin echo readout (DP-TSE) sequence was developed and compared with the conventional diffusion-weighted single-shot echo-planar-imaging sequence on a 0.35 T MRI-guided radiotherapy system (ViewRay). A spatial integrity phantom was used to quantitate and compare the geometric accuracy of the two diffusion sequences for three orthogonal orientations. The apparent diffusion coefficient (ADC) accuracy was evaluated on a diffusion phantom under both 0 °C and room temperature to cover a diffusivity range between 0.40 × 10 -3 and 2.10 × 10 -3 mm 2 /s. Ten room temperature measurements repeated on five different days were conducted to assess the ADC reproducibility of DP-TSE. Two glioblastoma (GBM) and six sarcoma patients were included to examine the in vivo feasibility. The target registration error (TRE) was calculated to quantitate the geometric accuracy where structural CT or MR images were co-registered to the diffusion images as references. ADC maps from DP-TSE and DW-ssEPI were calculated and compared. A tube phantom was placed next to patients not treated on ViewRay, and ADCs of this reference tube were also compared. The proposed DP-TSE passed the spatial integrity test (< 1 mm within 100 mm radius and < 2 mm within 175 mm radius) under the three orthogonal orientations. The detected errors were 0.474 ± 0.355 mm, 0.475 ± 0.287 mm, and 0.546 ± 0.336 mm in the axial, coronal, and sagittal plane. DW-ssEPI, however, failed the tests due to severe distortion and low signal intensity. Noise correction must be performed for the DW-ssEPI to avoid ADC quantitation errors, whereas it is optional for DP-TSE. At 0 °C, the two sequences provided accurate quantitation with < 3% variation with the reference. In the room temperature study, discrepancies between ADCs from DP-TSE and the reference were within 4%, but could be as high as 8% for DW-ssEPI after the noise correction. Excellent ADC reproducibility with a coefficient of variation < 5% was observed among the 10 measurements of DP-TSE, indicating desirable robustness for ADC-based tumor response assessment. In vivo TRE in DP-TSE was less than 1.6 mm overall, whereas it could be greater than 12 mm in DW-ssEPI. For GBM patients, the CSF and brain tissue ADCs from DP-TSE were within the ranges found in literature. ADC differences between the two techniques were within 8% among the six sarcoma patients. For the reference tube that had a relatively low diffusivity, the two diffusion sequences provided matched measurements. A diffusion technique with excellent geometric fidelity, accurate, and reproducible ADC measurement was demonstrated for longitudinal tumor response assessment using a low-field MRI-guided radiotherapy system. © 2017 American Association of Physicists in Medicine.

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.

Interdiffusion and Intrinsic Diffusion in the Mg-Al System

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

Brennan, Sarah; Bermudez, Katrina; Sohn, Yong Ho

2012-01-01

Solid-to-solid diffusion couples were assembled and annealed to examine the diffusion between pure Mg (99.96%) and Al (99.999%). Diffusion anneals were carried out at 300 , 350 , and 400 C for 720, 360, and 240 hours, respectively. Optical and scanning electron microscopes were utilized to identify the formation of the intermetallic phases, -Al12Mg17 and -Al3Mg2 and absence of the -phase in the diffusion couples. Thicknesses of the -Al12Mg17 and -Al3Mg2 phases were measured and the parabolic growth constants were calculated to determine the activation energies for the growth, 165 and 86 KJ/mole, respectively. Concentration profiles were determined with electronmore » microprobe analysis using pure elemental standards. Composition-dependent interdiffusion coefficients in Mg-solid solution, -Al12Mg17 and - Al3Mg2 and Al-solid solutions were calculated based on the Boltzmann-Matano analysis. Average effective interdiffusion coefficients for each phase were also calculated, and the magnitude was the highest for the -Al3Mg2 phase, followed by -Al12Mg17, Al-solid solution and Mg-solid solution. Intrinsic diffusion coefficients based on Huemann s analysis (e.g., marker plane) were determined for the ~38 at.% Mg in the -Al3Mg2 phase. Activation energies and the pre-exponential factors for the inter- and intrinsic diffusion coefficients were calculated for the temperature range examined. The -Al3Mg2 phase was found to have the lowest activation energies for growth and interdiffusion among all four phases studied. At the marker location in the -Al3Mg2 phase, the intrinsic diffusion of Al was found to be faster than that of Mg. Extrapolations of the impurity diffusion coefficients in the terminal solid solutions were made and compared to the available self- and impurity diffusion data from literature. Thermodynamic factor, tracer diffusion coefficients and atomic mobilities at the marker plane composition were approximated using available literature values of Mg activity in the -Al3Mg2 phase.« less

Image correlation microscopy for uniform illumination.

PubMed

Gaborski, T R; Sealander, M N; Ehrenberg, M; Waugh, R E; McGrath, J L

2010-01-01

Image cross-correlation microscopy is a technique that quantifies the motion of fluorescent features in an image by measuring the temporal autocorrelation function decay in a time-lapse image sequence. Image cross-correlation microscopy has traditionally employed laser-scanning microscopes because the technique emerged as an extension of laser-based fluorescence correlation spectroscopy. In this work, we show that image correlation can also be used to measure fluorescence dynamics in uniform illumination or wide-field imaging systems and we call our new approach uniform illumination image correlation microscopy. Wide-field microscopy is not only a simpler, less expensive imaging modality, but it offers the capability of greater temporal resolution over laser-scanning systems. In traditional laser-scanning image cross-correlation microscopy, lateral mobility is calculated from the temporal de-correlation of an image, where the characteristic length is the illuminating laser beam width. In wide-field microscopy, the diffusion length is defined by the feature size using the spatial autocorrelation function. Correlation function decay in time occurs as an object diffuses from its original position. We show that theoretical and simulated comparisons between Gaussian and uniform features indicate the temporal autocorrelation function depends strongly on particle size and not particle shape. In this report, we establish the relationships between the spatial autocorrelation function feature size, temporal autocorrelation function characteristic time and the diffusion coefficient for uniform illumination image correlation microscopy using analytical, Monte Carlo and experimental validation with particle tracking algorithms. Additionally, we demonstrate uniform illumination image correlation microscopy analysis of adhesion molecule domain aggregation and diffusion on the surface of human neutrophils.

Temporal and spatial profile of brain diffusion-weighted MRI after cardiac arrest

PubMed Central

Mlynash, M.; Campbell, D.M.; Leproust, E.M.; Fischbein, N.J.; Bammer, R.; Eyngorn, I.; Hsia, A.W.; Moseley, M.; Wijman, C.A.C.

2010-01-01

Background and Purpose Diffusion-weighted MRI (DWI) of the brain is a promising technique to help predict functional outcome in comatose survivors of cardiac arrest. We aimed to evaluate prospectively the temporal-spatial profile of brain apparent diffusion coefficient (ADC) changes in comatose survivors during the first 8 days after cardiac arrest. Methods ADC values were measured by two independent and blinded investigators in predefined brain regions in 18 good and 15 poor outcome patients with 38 brain MRIs, and compared with 14 normal controls. The same brain regions were also assessed qualitatively by two other independent and blinded investigators. Results In poor outcome patients, cortical structures, in particular the occipital and temporal lobes, and the putamen exhibited the most profound ADC reductions, which were noted as early as 1.5 days and reached nadir between 3 to 5 days after the arrest. Conversely, when compared to normal controls, good outcome patients exhibited increased diffusivity, in particular in the hippocampus, temporal and occipital lobes, and corona radiata. By the qualitative MRI readings, one or more cortical gray matter structures were read as moderately-to-severely abnormal in all poor outcome patients imaged beyond 54 hours after the arrest, but not in the three patients imaged earlier. Conclusions Brain DWI changes in comatose post-cardiac arrest survivors in the first week after the arrest are region- and time-dependent and differ between good and poor outcome patients. With the increasing use of MRI in this context, it is important to be aware of these relationships. PMID:20595666

Sucrose diffusion in aqueous solution

PubMed Central

Murray, Benjamin J.

2016-01-01

The diffusion of sugar in aqueous solution is important both in nature and in technological applications, yet measurements of diffusion coefficients at low water content are scarce. We report directly measured sucrose diffusion coefficients in aqueous solution. Our technique utilises a Raman isotope tracer method to monitor the diffusion of non-deuterated and deuterated sucrose across a boundary between the two aqueous solutions. At a water activity of 0.4 (equivalent to 90 wt% sucrose) at room temperature, the diffusion coefficient of sucrose was determined to be approximately four orders of magnitude smaller than that of water in the same material. Using literature viscosity data, we show that, although inappropriate for the prediction of water diffusion, the Stokes–Einstein equation works well for predicting sucrose diffusion under the conditions studied. As well as providing information of importance to the fundamental understanding of diffusion in binary solutions, these data have technological, pharmaceutical and medical implications, for example in cryopreservation. Moreover, in the atmosphere, slow organic diffusion may have important implications for aerosol growth, chemistry and evaporation, where processes may be limited by the inability of a molecule to diffuse between the bulk and the surface of a particle. PMID:27364512

High-grade glioma diffusive modeling using statistical tissue information and diffusion tensors extracted from atlases.

PubMed

Roniotis, Alexandros; Manikis, Georgios C; Sakkalis, Vangelis; Zervakis, Michalis E; Karatzanis, Ioannis; Marias, Kostas

2012-03-01

Glioma, especially glioblastoma, is a leading cause of brain cancer fatality involving highly invasive and neoplastic growth. Diffusive models of glioma growth use variations of the diffusion-reaction equation in order to simulate the invasive patterns of glioma cells by approximating the spatiotemporal change of glioma cell concentration. The most advanced diffusive models take into consideration the heterogeneous velocity of glioma in gray and white matter, by using two different discrete diffusion coefficients in these areas. Moreover, by using diffusion tensor imaging (DTI), they simulate the anisotropic migration of glioma cells, which is facilitated along white fibers, assuming diffusion tensors with different diffusion coefficients along each candidate direction of growth. Our study extends this concept by fully exploiting the proportions of white and gray matter extracted by normal brain atlases, rather than discretizing diffusion coefficients. Moreover, the proportions of white and gray matter, as well as the diffusion tensors, are extracted by the respective atlases; thus, no DTI processing is needed. Finally, we applied this novel glioma growth model on real data and the results indicate that prognostication rates can be improved. © 2012 IEEE

Diffusion coefficients of rare earth elements in fcc Fe: A first-principles study

NASA Astrophysics Data System (ADS)

Wang, Haiyan; Gao, Xueyun; Ren, Huiping; Chen, Shuming; Yao, Zhaofeng

2018-01-01

The diffusion data and corresponding detailed insights are particularly important for the understanding of the related kinetic processes in Fe based alloys, e.g. solute strengthening, phase transition, solution treatment etc. We present a density function theory study of the diffusivity of self and solutes (La, Ce, Y and Nb) in fcc Fe. The five-frequency model was employed to calculate the microscopic parameters in the correlation factors of the solute diffusion. The interactions of the solutes with the first nearest-neighbor vacancy (1nn) are all attractive, and can be well understood on the basis of the combination of the strain-relief effects and the electronic effects. It is found that among the investigated species, Ce is the fastest diffusing solute in fcc Fe matrix followed by Nb, and the diffusion coefficients of these two solutes are about an order of magnitude higher than that of Fe self-diffusion. And the results show that the diffusion coefficient of La is slightly higher than that of Y, and both species are comparable to that of Fe self-diffusion.

Analysis of diffusion and binding in cells using the RICS approach.

PubMed

Digman, Michelle A; Gratton, Enrico

2009-04-01

The movement of macromolecules in cells is assumed to occur either through active transport or by diffusion. However, the determination of the diffusion coefficients in cells using fluctuation methods or FRAP frequently give diffusion coefficient that are orders of magnitude smaller than the diffusion coefficients measured for the same macromolecule in solution. It is assumed that the cell internal viscosity is partially responsible for this decrease in the apparent diffusion. When the apparent diffusion is too slow to be due to cytoplasm viscosity, it is assumed that weak binding of the macromolecules to immobile or quasi immobile structures is taking place. In this article, we derive equations for fitting of the RICS (Raster-scan Image Correlations Spectroscopy) data in cells to a model that includes transient binding to immobile structures, and we show that under some conditions, the spatio-temporal correlation provided by the RICS approach can distinguish the process of diffusion and weak binding. We apply the method to determine the diffusion in the cytoplasm and binding of Focal Adhesion Kinase-EGFP to adhesions in MEF cells.

Backstepping-based boundary control design for a fractional reaction diffusion system with a space-dependent diffusion coefficient.

PubMed

Chen, Juan; Cui, Baotong; Chen, YangQuan

2018-06-11

This paper presents a boundary feedback control design for a fractional reaction diffusion (FRD) system with a space-dependent (non-constant) diffusion coefficient via the backstepping method. The contribution of this paper is to generalize the results of backstepping-based boundary feedback control for a FRD system with a space-independent (constant) diffusion coefficient to the case of space-dependent diffusivity. For the boundary stabilization problem of this case, a designed integral transformation treats it as a problem of solving a hyperbolic partial differential equation (PDE) of transformation's kernel, then the well posedness of the kernel PDE is solved for the plant with non-constant diffusivity. Furthermore, by the fractional Lyapunov stability (Mittag-Leffler stability) theory and the backstepping-based boundary feedback controller, the Mittag-Leffler stability of the closed-loop FRD system with non-constant diffusivity is proved. Finally, an extensive numerical example for this closed-loop FRD system with non-constant diffusivity is presented to verify the effectiveness of our proposed controller. Copyright © 2018 ISA. Published by Elsevier Ltd. All rights reserved.

Neutral solute transport across osteochondral interface: A finite element approach.

PubMed

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

2016-12-08

Investigation of the solute transfer across articular cartilage and subchondral bone plate could nurture the understanding of the mechanisms of osteoarthritis (OA) progression. In the current study, we approached the transport of neutral solutes in human (slight OA) and equine (healthy) samples using both computed tomography and biphasic-solute finite element modeling. We developed a multi-zone biphasic-solute finite element model (FEM) accounting for the inhomogeneity of articular cartilage (superficial, middle and deep zones) and subchondral bone plate. Fitting the FEM model to the concentration-time curves of the cartilage and the equilibrium concentration of the subchondral plate/calcified cartilage enabled determination of the diffusion coefficients in the superficial, middle and deep zones of cartilage and subchondral plate. We found slightly higher diffusion coefficients for all zones in the human samples as compared to the equine samples. Generally the diffusion coefficient in the superficial zone of human samples was about 3-fold higher than the middle zone, the diffusion coefficient of the middle zone was 1.5-fold higher than that of the deep zone, and the diffusion coefficient of the deep zone was 1.5-fold higher than that of the subchondral plate/calcified cartilage. Those ratios for equine samples were 9, 2 and 1.5, respectively. Regardless of the species considered, there is a gradual decrease of the diffusion coefficient as one approaches the subchondral plate, whereas the rate of decrease is dependent on the type of species. Copyright © 2016 Elsevier Ltd. All rights reserved.

Mutual diffusion coefficients of heptane isomers in nitrogen: A molecular dynamics study

NASA Astrophysics Data System (ADS)

Chae, Kyungchan; Violi, Angela

2011-01-01

The accurate knowledge of transport properties of pure and mixture fluids is essential for the design of various chemical and mechanical systems that include fluxes of mass, momentum, and energy. In this study we determine the mutual diffusion coefficients of mixtures composed of heptane isomers and nitrogen using molecular dynamics (MD) simulations with fully atomistic intermolecular potential parameters, in conjunction with the Green-Kubo formula. The computed results were compared with the values obtained using the Chapman-Enskog (C-E) equation with Lennard-Jones (LJ) potential parameters derived from the correlations of state values: MD simulations predict a maximum difference of 6% among isomers while the C-E equation presents that of 3% in the mutual diffusion coefficients in the temperature range 500-1000 K. The comparison of two approaches implies that the corresponding state principle can be applied to the models, which are only weakly affected by the anisotropy of the interaction potentials and the large uncertainty will be included in its application for complex polyatomic molecules. The MD simulations successfully address the pure effects of molecular structure among isomers on mutual diffusion coefficients by revealing that the differences of the total mutual diffusion coefficients for the six mixtures are caused mainly by heptane isomers. The cross interaction potential parameters, collision diameter σ _{12}, and potential energy well depth \\varepsilon _{12} of heptane isomers and nitrogen mixtures were also computed from the mutual diffusion coefficients.

Determination of diffusion coefficient in disordered organic semiconductors

NASA Astrophysics Data System (ADS)

Rani, Varsha; Sharma, Akanksha; Ghosh, Subhasis

2016-05-01

Charge carrier transport in organic semiconductors is dominated by positional and energetic disorder in Gaussian density of states (GDOS) and is characterized by hopping through localized states. Due to the immobilization of charge carriers in these localized states, significant non-uniform carrier distribution exists, resulting diffusive transport. A simple, nevertheless powerful technique to determine diffusion coefficient D in disordered organic semiconductors has been presented. Diffusion coefficients of charge carriers in two technologically important organic molecular semiconductors, Pentacene and copper phthalocyanine (CuPc) have been measured from current-voltage (J-V) characteristics of Al/Pentacene/Au and Al/CuPc/Au based Schottky diodes. Ideality factor g and carrier mobility μ have been calculated from the exponential and space charge limited region respectively of J-V characteristics. Classical Einstein relation is not valid in organic semiconductors due to energetic disorders in DOS. Using generalized Einstein relation, diffusion coefficients have been obtained to be 1.31×10-6 and 1.73×10-7 cm2/s for Pentacene and CuPc respectively.

Transport coefficients in high-temperature ionized air flows with electronic excitation

NASA Astrophysics Data System (ADS)

Istomin, V. A.; Oblapenko, G. P.

2018-01-01

Transport coefficients are studied in high-temperature ionized air mixtures using the modified Chapman-Enskog method. The 11-component mixture N2/N2+/N /N+/O2/O2+/O /O+/N O /N O+/e- , taking into account the rotational and vibrational degrees of freedom of molecules and electronic degrees of freedom of both atomic and molecular species, is considered. Using the PAINeT software package, developed by the authors of the paper, in wide temperature range calculations of the thermal conductivity, thermal diffusion, diffusion, and shear viscosity coefficients for an equilibrium ionized air mixture and non-equilibrium flow conditions for mixture compositions, characteristic of those in shock tube experiments and re-entry conditions, are performed. For the equilibrium air case, the computed transport coefficients are compared to those obtained using simplified kinetic theory algorithms. It is shown that neglecting electronic excitation leads to a significant underestimation of the thermal conductivity coefficient at temperatures higher than 25 000 K. For non-equilibrium test cases, it is shown that the thermal diffusion coefficients of neutral species and the self-diffusion coefficients of all species are strongly affected by the mixture composition, while the thermal conductivity coefficient is most strongly influenced by the degree of ionization of the flow. Neglecting electronic excitation causes noticeable underestimation of the thermal conductivity coefficient at temperatures higher than 20 000 K.

Interaction dynamics of two diffusing particles: contact times and influence of nearby surfaces.

PubMed

Tränkle, B; Ruh, D; Rohrbach, A

2016-03-14

Interactions of diffusing particles are governed by hydrodynamics on different length and timescales. The local hydrodynamics can be influenced substantially by simple interfaces. Here, we investigate the interaction dynamics of two micron-sized spheres close to plane interfaces to mimic more complex biological systems or microfluidic environments. Using scanned line optical tweezers and fast 3D interferometric particle tracking, we are able to track the motion of each bead with precisions of a few nanometers and at a rate of 10 kilohertz. From the recorded trajectories, all spatial and temporal information is accessible. This way, we measure diffusion coefficients for two coupling particles at varying distances h to one or two glass interfaces. We analyze their coupling strength and length by cross-correlation analysis relative to h and find a significant decrease in the coupling length when a second particle diffuses nearby. By analysing the times the particles are in close contact, we find that the influence of nearby surfaces and interaction potentials reduce the diffusivity strongly, although we found that the diffusivity hardly affects the contact times and the binding probability between the particles. All experimental results are compared to a theoretical model, which is based on the number of possible diffusion paths following the Catalan numbers and a diffusion probability, which is biased by the spheres' surface potential. The theoretical and experimental results agree very well and therefore enable a better understanding of hydrodynamically coupled interaction processes.

METAL DIFFUSION IN SMOOTHED PARTICLE HYDRODYNAMICS SIMULATIONS OF DWARF GALAXIES

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

Williamson, David; Martel, Hugo; Kawata, Daisuke, E-mail: david-john.williamson.1@ulaval.ca

2016-05-10

We perform a series of smoothed particle hydrodynamics simulations of isolated dwarf galaxies to compare different metal mixing models. In particular, we examine the role of diffusion in the production of enriched outflows and in determining the metallicity distributions of gas and stars. We investigate different diffusion strengths by changing the pre-factor of the diffusion coefficient, by varying how the diffusion coefficient is calculated from the local velocity distribution, and by varying whether the speed of sound is included as a velocity term. Stronger diffusion produces a tighter [O/Fe]–[Fe/H] distribution in the gas and cuts off the gas metallicity distributionmore » function at lower metallicities. Diffusion suppresses the formation of low-metallicity stars, even with weak diffusion, and also strips metals from enriched outflows. This produces a remarkably tight correlation between “metal mass-loading” (mean metal outflow rate divided by mean metal production rate) and the strength of diffusion, even when the diffusion coefficient is calculated in different ways. The effectiveness of outflows at removing metals from dwarf galaxies and the metal distribution of the gas is thus dependent on the strength of diffusion. By contrast, we show that the metallicities of stars are not strongly dependent on the strength of diffusion, provided that some diffusion is present.« less

Comparisons among MRI signs, apparent diffusion coefficient, and fractional anisotropy in dogs with a solitary intracranial meningioma or histiocytic sarcoma.

PubMed

Wada, Masae; Hasegawa, Daisuke; Hamamoto, Yuji; Yu, Yoshihiko; Fujiwara-Igarashi, Aki; Fujita, Michio

2017-07-01

Although MRI has become widely used in small animal practice, little is known about the validity of advanced MRI techniques such as diffusion-weighted imaging and diffusion tensor imaging. The aim of this retrospective analytical observational study was to investigate the characteristics of diffusion parameters, that is the apparent diffusion coefficient and fractional anisotropy, in dogs with a solitary intracranial meningioma or histiocytic sarcoma. Dogs were included based on the performance of diffusion MRI and histological confirmation. Statistical analyses were performed to compare apparent diffusion coefficient and fractional anisotropy for the two types of tumor in the intra- and peritumoral regions. Eleven cases with meningioma and six with histiocytic sarcoma satisfied the inclusion criteria. Significant differences in apparent diffusion coefficient value (× 10 -3 mm 2 /s) between meningioma vs. histiocytic sarcoma were recognized in intratumoral small (1.07 vs. 0.76) and large (1.04 vs. 0.77) regions of interest, in the peritumoral margin (0.93 vs. 1.08), and in the T2 high region (1.21 vs. 1.41). Significant differences in fractional anisotropy values were found in the peritumoral margin (0.29 vs. 0.24) and the T2 high region (0.24 vs. 0.17). The current study identified differences in measurements of apparent diffusion coefficient and fractional anisotropy for meningioma and histiocytic sarcoma in a small sample of dogs. In addition, we observed that all cases of intracranial histiocytic sarcoma showed leptomeningeal enhancement and/or mass formation invading into the sulci in the contrast study. Future studies are needed to determine the sensitivity of these imaging characteristics for differentiating between these tumor types. © 2017 American College of Veterinary Radiology.

An improved procedure for determining grain boundary diffusion coefficients from averaged concentration profiles

NASA Astrophysics Data System (ADS)

Gryaznov, D.; Fleig, J.; Maier, J.

2008-03-01

Whipple's solution of the problem of grain boundary diffusion and Le Claire's relation, which is often used to determine grain boundary diffusion coefficients, are examined for a broad range of ratios of grain boundary to bulk diffusivities Δ and diffusion times t. Different reasons leading to errors in determining the grain boundary diffusivity (DGB) when using Le Claire's relation are discussed. It is shown that nonlinearities of the diffusion profiles in lnCav-y6/5 plots and deviations from "Le Claire's constant" (-0.78) are the major error sources (Cav=averaged concentration, y =coordinate in diffusion direction). An improved relation (replacing Le Claire's constant) is suggested for analyzing diffusion profiles particularly suited for small diffusion lengths (short times) as often required in diffusion experiments on nanocrystalline materials.

Diffusion kinetics of the glucose/glucose oxidase system in swift heavy ion track-based biosensors

NASA Astrophysics Data System (ADS)

Fink, Dietmar; Vacik, Jiri; Hnatowicz, V.; Muñoz Hernandez, G.; Garcia Arrelano, H.; Alfonta, Lital; Kiv, Arik

2017-05-01

For understanding of the diffusion kinetics and their optimization in swift heavy ion track-based biosensors, recently a diffusion simulation was performed. This simulation aimed at yielding the degree of enrichment of the enzymatic reaction products in the highly confined space of the etched ion tracks. A bunch of curves was obtained for the description of such sensors that depend only on the ratio of the diffusion coefficient of the products to that of the analyte within the tracks. As hitherto none of these two diffusion coefficients is accurately known, the present work was undertaken. The results of this paper allow one to quantify the previous simulation and hence yield realistic predictions of glucose-based biosensors. At this occasion, also the influence of the etched track radius on the diffusion coefficients was measured and compared with earlier prediction.

Comparison of nanoparticle diffusion using fluorescence correlation spectroscopy and differential dynamic microscopy within concentrated polymer solutions

NASA Astrophysics Data System (ADS)

Shokeen, Namita; Issa, Christopher; Mukhopadhyay, Ashis

2017-12-01

We studied the diffusion of nanoparticles (NPs) within aqueous entangled solutions of polyethylene oxide (PEO) by using two different optical techniques. Fluorescence correlation spectroscopy, a method widely used to investigate nanoparticle dynamics in polymer solution, was used to measure the long-time diffusion coefficient (D) of 25 nm radius particles within high molecular weight, Mw = 600 kg/mol PEO in water solutions. Differential dynamic microscopy (DDM) was used to determine the wave-vector dependent dynamics of NPs within the same polymer solutions. Our results showed good agreement between the two methods, including demonstration of normal diffusion and almost identical diffusion coefficients obtained by both techniques. The research extends the scope of DDM to study the dynamics and rheological properties of soft matter at a nanoscale. The measured diffusion coefficients followed a scaling theory, which can be explained by the coupling between polymer dynamics and NP motion.

The Steady-State Transport of Oxygen through Hemoglobin Solutions

PubMed Central

Keller, K. H.; Friedlander, S. K.

1966-01-01

The steady-state transport of oxygen through hemoglobin solutions was studied to identify the mechanism of the diffusion augmentation observed at low oxygen tensions. A novel technique employing a platinum-silver oxygen electrode was developed to measure the effective diffusion coefficient of oxygen in steady-state transport. The measurements were made over a wider range of hemoglobin and oxygen concentrations than previously reported. Values of the Brownian motion diffusion coefficient of oxygen in hemoglobin solution were obtained as well as measurements of facilitated transport at low oxygen tensions. Transport rates up to ten times greater than ordinary diffusion rates were found. Predictions of oxygen flux were made assuming that the oxyhemoglobin transport coefficient was equal to the Brownian motion diffusivity which was measured in a separate set of experiments. The close correlation between prediction and experiment indicates that the diffusion of oxyhemoglobin is the mechanism by which steady-state oxygen transport is facilitated. PMID:5943608

Lateral diffusion of proteins in the periplasm of Escherichia coli.

PubMed Central

Brass, J M; Higgins, C F; Foley, M; Rugman, P A; Birmingham, J; Garland, P B

1986-01-01

We have introduced biologically active, fluorescently labeled maltose-binding protein into the periplasmic space of Escherichia coli and measured its lateral diffusion coefficient by the fluorescence photobleaching recovery method. Diffusion of this protein in the periplasm was found to be surprisingly low (lateral diffusion coefficient, 0.9 X 10(-10) cm2 s-1), about 1,000-fold lower than would be expected for diffusion in aqueous medium and almost 100-fold lower than for an equivalent-size protein in the cytoplasm. Galactose-binding protein, myoglobin, and cytochrome c were also introduced into the periplasm and had diffusion coefficients identical to that determined for the maltose-binding protein. For all proteins nearly 100% recovery of fluorescence was obtained after photobleaching, indicating that the periplasm is a single contiguous compartment surrounding the cell. These data have considerable implications for periplasmic structure and for the role of periplasmic proteins in transport and chemotaxis. Images PMID:3005237

Complex Analysis of Diffusion Transport and Microstructure of an Intervertebral Disk.

PubMed

Byvaltsev, V A; Kolesnikov, S I; Belykh, E G; Stepanov, I A; Kalinin, A A; Bardonova, L A; Sudakov, N P; Klimenkov, I V; Nikiforov, S B; Semenov, A V; Perfil'ev, D V; Bespyatykh, I V; Antipina, S L; Giers, M; Prul, M

2017-12-01

We studied the relationship between diffusion transport and morphological and microstructural organization of extracellular matrix of human intervertebral disk. Specimens of the lumbar intervertebral disks without abnormalities were studied ex vivo by diffusion-weighed magnetic resonance imaging, histological and immunohistochemical methods, and electron microscopy. Distribution of the diffusion coefficient in various compartments of the intervertebral disk was studied. Significant correlations between diffusion coefficient and cell density in the nucleus pulposus, posterior aspects of annulus fibrosus, and endplate at the level of the posterior annulus fibrosus were detected for each disk. In disks with nucleus pulposus diffusion coefficient below 15×10 -4 mm 2 /sec, collagens X and XI were detected apart from aggrecan and collagens I and II. The results supplement the concept on the relationship between the microstructure and cell composition of various compartments of the intervertebral disk and parameters of nutrient transport.

Nature of self-diffusion in two-dimensional fluids

NASA Astrophysics Data System (ADS)

Choi, Bongsik; Han, Kyeong Hwan; Kim, Changho; Talkner, Peter; Kidera, Akinori; Lee, Eok Kyun

2017-12-01

Self-diffusion in a two-dimensional simple fluid is investigated by both analytical and numerical means. We investigate the anomalous aspects of self-diffusion in two-dimensional fluids with regards to the mean square displacement, the time-dependent diffusion coefficient, and the velocity autocorrelation function (VACF) using a consistency equation relating these quantities. We numerically confirm the consistency equation by extensive molecular dynamics simulations for finite systems, corroborate earlier results indicating that the kinematic viscosity approaches a finite, non-vanishing value in the thermodynamic limit, and establish the finite size behavior of the diffusion coefficient. We obtain the exact solution of the consistency equation in the thermodynamic limit and use this solution to determine the large time asymptotics of the mean square displacement, the diffusion coefficient, and the VACF. An asymptotic decay law of the VACF resembles the previously known self-consistent form, 1/(t\\sqrt{{ln}t}), however with a rescaled time.

An inverse moisture diffusion algorithm for the determination of diffusion coefficient

Treesearch

Jen Y. Liu; William T. Simpson; Steve P. Verrill

2000-01-01

The finite difference approximation is applied to estimate the moisture-dependent diffusion coefficient by utilizing test data of isothermal moisture desorption in northern red oak (Quercus rubra). The test data contain moisture distributions at discrete locations across the thickness of specimens, which coincides with the radial direction of northern red oak, and at...

An inverse moisture diffusion algorithm for the determination of diffusion coefficient

Treesearch

Jen Y. Liu; William T. Simpson; Steve P. Verrill

2001-01-01

The finite difference approximation is applied to estimate the moisture-dependent diffusion coefficient by utilizing test data of isothermal moisture desorption in northern red oak (Quercus rubra). The test data contain moisture distributions at discrete locations across the thickness of specimens, which coincides with the radial direction of northern red oak, and at...

Correlation Between Minimum Apparent Diffusion Coefficient (ADCmin) and Tumor Cellularity: A Meta-analysis.

PubMed

Surov, Alexey; Meyer, Hans Jonas; Wienke, Andreas

2017-07-01

Diffusion-weighted imaging (DWI) is a magnetic resonance imaging (MRI) technique based on measure of water diffusion that can provide information about tissue microstructure, especially about cell count. Increase of cell density induces restriction of water diffusion and decreases apparent diffusion coefficient (ADC). ADC can be divided into three sub-parameters: ADC minimum or ADC min , mean ADC or ADC mean and ADC maximum or ADC max Some studies have suggested that ADC min shows stronger correlations with cell count in comparison to other ADC fractions and may be used as a parameter for estimation of tumor cellularity. The aim of the present meta-analysis was to summarize correlation coefficients between ADC min and cellularity in different tumors based on large patient data. For this analysis, MEDLINE database was screened for associations between ADC and cell count in different tumors up to September 2016. For this work, only data regarding ADC min were included. Overall, 12 publications with 317 patients were identified. Spearman's correlation coefficient was used to analyze associations between ADC min and cellularity. The reported Pearson correlation coefficients in some publications were converted into Spearman correlation coefficients. The pooled correlation coefficient for all included studies was ρ=-0.59 (95% confidence interval (CI)=-0.72 to -0.45), heterogeneity Tau 2 =0.04 (p<0.0001), I 2 =73%, test for overall effect Z=8.67 (p<0.00001). ADC min correlated moderately with tumor cellularity. The calculated correlation coefficient is not stronger in comparison to the reported coefficient for ADC mean and, therefore, ADC min does not represent a better means to reflect cellularity. Copyright© 2017, International Institute of Anticancer Research (Dr. George J. Delinasios), All rights reserved.

Dispersal and spatial heterogeneity: Single species

USGS Publications Warehouse

DeAngelis, Donald L.; Ni, Wei-Ming; Zhang, Bo

2016-01-01

A recent result for a reaction-diffusion equation is that a population diffusing at any rate in an environment in which resources vary spatially will reach a higher total equilibrium biomass than the population in an environment in which the same total resources are distributed homogeneously. This has so far been proven by Lou for the case in which the reaction term has only one parameter, m(x)">m(x)m(x), varying with spatial location x">xx, which serves as both the intrinsic growth rate coefficient and carrying capacity of the population. However, this striking result seems rather limited when applies to real populations. In order to make the model more relevant for ecologists, we consider a logistic reaction term, with two parameters, r(x)">r(x)r(x) for intrinsic growth rate, and K(x)">K(x)K(x) for carrying capacity. When r(x)">r(x)r(x) and K(x)">K(x)K(x) are proportional, the logistic equation takes a particularly simple form, and the earlier result still holds. In this paper we have established the result for the more general case of a positive correlation between r(x)">r(x)r(x) and K(x)">K(x)K(x) when dispersal rate is small. We review natural and laboratory systems to which these results are relevant and discuss the implications of the results to population theory and conservation ecology.

NMR 1D-imaging of water infiltration into mesoporous matrices.

PubMed

Le Feunteun, Steven; Diat, Olivier; Guillermo, Armel; Poulesquen, Arnaud; Podor, Renaud

2011-04-01

It is shown that coupling nuclear magnetic resonance (NMR) 1D-imaging with the measure of NMR relaxation times and self-diffusion coefficients can be a very powerful approach to investigate fluid infiltration into porous media. Such an experimental design was used to study the very slow seeping of pure water into hydrophobic materials. We consider here three model samples of nuclear waste conditioning matrices which consist in a dispersion of NaNO(3) (highly soluble) and/or BaSO(4) (poorly soluble) salt grains embedded in a bitumen matrix. Beyond studying the moisture progression according to the sample depth, we analyze the water NMR relaxation times and self-diffusion coefficients along its 1D-concentration profile to obtain spatially resolved information on the solution properties and on the porous structure at different scales. It is also shown that, when the relaxation or self-diffusion properties are multimodal, the 1D-profile of each water population is recovered. Three main levels of information were disclosed along the depth-profiles. They concern (i) the water uptake kinetics, (ii) the salinity and the molecular dynamics of the infiltrated solutions and (iii) the microstructure of the water-filled porosities: open networks coexisting with closed pores. All these findings were fully validated and enriched by NMR cryoporometry experiments and by performing environmental scanning electronic microscopy observations. Surprisingly, results clearly show that insoluble salts enhance the water progression and thereby increase the capability of the material to uptake water. Copyright © 2011 Elsevier Inc. All rights reserved.

Time-resolved mapping of water diffusion coefficients in a working soft actuator device.

PubMed

Naji, Leila; Chudek, John A; Baker, Richard T

2008-08-14

Diffusion-weighted imaging was employed to spatially map the distribution of the diffusion coefficient of water, D, in bare, water-soaked, Li(+)-exchanged, cast Nafion and in an ionic polymer-metal composite (IPMC) soft actuator element, prepared from this bare Nafion by impregnation with Pt electrodes. D was evaluated in two orthogonal directions: along one of the long dimensions of the sample (Dx) and through its thickness (Dz). D-maps of the IPMC element were obtained both in the absence of an applied potential and in situ during the application of a 3 V dc potential across the thickness of the sample. In the bare Nafion, D-maps showed uniform values of both Dx and Dz of about 6 x 10 (-10) m(2) s(-1). In the IPMC two effects were observed: (i) D at the electroded surfaces of the IPMC was higher than at the center of the sample; (ii) this difference was much greater in Dz than in Dx . Both effects were explained by the influence of the impregnated Pt electrodes on polymer structure. The D-maps in the electrochemical measurements showed high values of D (up to 8 x 10(-10) m(2) s(-1)) at the cathode and low values (from 1 x 10(-10) m(2) s(-1)) at the anode. This was explained in terms of the effect on the Nafion nanostructure of the forced electro-migration of Li(H2O)x(+) species toward the cathode.

Spatio-temporal imaging of the hemoglobin in the compressed breast with diffuse optical tomography

NASA Astrophysics Data System (ADS)

Boverman, Gregory; Fang, Qianqian; Carp, Stefan A.; Miller, Eric L.; Brooks, Dana H.; Selb, Juliette; Moore, Richard H.; Kopans, Daniel B.; Boas, David A.

2007-07-01

We develop algorithms for imaging the time-varying optical absorption within the breast given diffuse optical tomographic data collected over a time span that is long compared to the dynamics of the medium. Multispectral measurements allow for the determination of the time-varying total hemoglobin concentration and of oxygen saturation. To facilitate the image reconstruction, we decompose the hemodynamics in time into a linear combination of spatio-temporal basis functions, the coefficients of which are estimated using all of the data simultaneously, making use of a Newton-based nonlinear optimization algorithm. The solution of the extremely large least-squares problem which arises in computing the Newton update is obtained iteratively using the LSQR algorithm. A Laplacian spatial regularization operator is applied, and, in addition, we make use of temporal regularization which tends to encourage similarity between the images of the spatio-temporal coefficients. Results are shown for an extensive simulation, in which we are able to image and quantify localized changes in both total hemoglobin concentration and oxygen saturation. Finally, a breast compression study has been performed for a normal breast cancer screening subject, using an instrument which allows for highly accurate co-registration of multispectral diffuse optical measurements with an x-ray tomosynthesis image of the breast. We are able to quantify the global return of blood to the breast following compression, and, in addition, localized changes are observed which correspond to the glandular region of the breast.

Molecular dynamics simulation of imidazolium-based ionic liquids. I. Dynamics and diffusion coefficient.

PubMed

Kowsari, M H; Alavi, Saman; Ashrafizaadeh, Mahmud; Najafi, Bijan

2008-12-14

Molecular dynamics simulations are used to study the dynamics and transport properties of 12 room-temperature ionic liquids of the 1-alkyl-3-methylimidazolium [amim](+) (alkyl = methyl, ethyl, propyl, and butyl) family with PF(6)(-), NO(3)(-), and Cl(-) counterions. The explicit atom transferable force field of Canongia Lopes et al. [J. Phys. Chem. B 108, 2038 (2004)] is used in the simulations. In this first part, the dynamics of the ionic liquids are characterized by studying the mean-square displacement (MSD) and the velocity autocorrelation function (VACF) for the centers of mass of the ions at 400 K. Trajectory averaging was employed to evaluate the diffusion coefficients at two temperatures from the linear slope of MSD(t) functions in the range of 150-300 ps and from the integration of the VACF(t) functions at 400 K. Detailed comparisons are made between the diffusion results from the MSD and VACF methods. The diffusion coefficients from the integration of the VACFs are closer to experimental values than the diffusion coefficients calculated from the slope of MSDs. Both methods can show good agreement with experiment in predicting relative trends in the diffusion coefficients and determining the role of the cation and anion structures on the dynamical behavior of this family of ionic liquids. The MSD and self-diffusion of relatively heavier imidazolium cations are larger than those of the lighter anions from the Einstein results, except for the case of [bmim][Cl]. The cationic transference number generally decreases with temperature, in good agreement with experiments. For the same anion, the cationic transference numbers decrease with increasing length of the alkyl chain, and for the same cation, the trends in the cationic transference numbers are [NO(3)](-) < [Cl](-) < [PF(6)](-). The trends in the diffusion coefficient in the series of cations with identical anions are [emim](+) > [pmim](+) > [bmim](+) and those for anions with identical cations are [NO(3)](-) > [PF(6)](-) > [Cl](-). The [dmim](+) has a relatively low diffusion coefficient due to its symmetric structure and good packing in the liquid phase. The major factor for determining the magnitude of the self-diffusion is the geometric shape of the anion of the ionic liquid. Other important factors are the ion size and the charge delocalization in the anion.

A New Methodology of Spatial Cross-Correlation Analysis

PubMed Central

Chen, Yanguang

2015-01-01

Spatial correlation modeling comprises both spatial autocorrelation and spatial cross-correlation processes. The spatial autocorrelation theory has been well-developed. It is necessary to advance the method of spatial cross-correlation analysis to supplement the autocorrelation analysis. This paper presents a set of models and analytical procedures for spatial cross-correlation analysis. By analogy with Moran’s index newly expressed in a spatial quadratic form, a theoretical framework is derived for geographical cross-correlation modeling. First, two sets of spatial cross-correlation coefficients are defined, including a global spatial cross-correlation coefficient and local spatial cross-correlation coefficients. Second, a pair of scatterplots of spatial cross-correlation is proposed, and the plots can be used to visually reveal the causality behind spatial systems. Based on the global cross-correlation coefficient, Pearson’s correlation coefficient can be decomposed into two parts: direct correlation (partial correlation) and indirect correlation (spatial cross-correlation). As an example, the methodology is applied to the relationships between China’s urbanization and economic development to illustrate how to model spatial cross-correlation phenomena. This study is an introduction to developing the theory of spatial cross-correlation, and future geographical spatial analysis might benefit from these models and indexes. PMID:25993120

A new methodology of spatial cross-correlation analysis.

PubMed

Chen, Yanguang

2015-01-01

Spatial correlation modeling comprises both spatial autocorrelation and spatial cross-correlation processes. The spatial autocorrelation theory has been well-developed. It is necessary to advance the method of spatial cross-correlation analysis to supplement the autocorrelation analysis. This paper presents a set of models and analytical procedures for spatial cross-correlation analysis. By analogy with Moran's index newly expressed in a spatial quadratic form, a theoretical framework is derived for geographical cross-correlation modeling. First, two sets of spatial cross-correlation coefficients are defined, including a global spatial cross-correlation coefficient and local spatial cross-correlation coefficients. Second, a pair of scatterplots of spatial cross-correlation is proposed, and the plots can be used to visually reveal the causality behind spatial systems. Based on the global cross-correlation coefficient, Pearson's correlation coefficient can be decomposed into two parts: direct correlation (partial correlation) and indirect correlation (spatial cross-correlation). As an example, the methodology is applied to the relationships between China's urbanization and economic development to illustrate how to model spatial cross-correlation phenomena. This study is an introduction to developing the theory of spatial cross-correlation, and future geographical spatial analysis might benefit from these models and indexes.

Mass diffusion coefficient measurement for vitreous humor using FEM and MRI

NASA Astrophysics Data System (ADS)

Rattanakijsuntorn, Komsan; Penkova, Anita; Sadha, Satwindar S.

2018-01-01

In early studies, the ‘contour method’ for determining the diffusion coefficient of the vitreous humor was developed. This technique relied on careful injection of an MRI contrast agent (surrogate drug) into the vitreous humor of fresh bovine eyes, and tracking the contours of the contrast agent in time. In addition, an analytical solution was developed for the theoretical contours built on point source model for the injected surrogate drug. The match between theoretical and experimental contours as a least square fit, while floating the diffusion coefficient, led to the value of the diffusion coefficient. This method had its limitation that the initial injection of the surrogate had to be spherical or ellipsoidal because of the analytical result based on the point-source model. With a new finite element model for the analysis in this study, the technique is much less restrictive and handles irregular shapes of the initial bolus. The fresh bovine eyes were used for drug diffusion study in the vitreous and three contrast agents of different molecular masses: gadolinium-diethylenetriaminepentaacetic acid (Gd-DTPA, 938 Da), non-ionic gadoteridol (Prohance, 559 Da), and bovine albumin conjugated with gadolinium (Galbumin, 74 kDa) were used as drug surrogates to visualize the diffusion process by MRI. The 3D finite element model was developed to determine the diffusion coefficients of these surrogates with the images from MRI. This method can be used for other types of bioporous media provided the concentration profile can be visualized (by methods such as MRI or fluorescence).

New sensitive micro-measurements of dynamic surface tension and diffusion coefficients: Validated and tested for the adsorption of 1-Octanol at a microscopic air-water interface and its dissolution into water.

PubMed

Kinoshita, Koji; Parra, Elisa; Needham, David

2017-02-15

Currently available dynamic surface tension (DST) measurement methods, such as Wilhelmy plate, droplet- or bubble-based methods, still have various experimental limitations such as the large size of the interface, convection in the solution, or a certain "dead time" at initial measurement. These limitations create inconsistencies for the kinetic analysis of surfactant adsorption/desorption, especially significant for ionic surfactants. Here, the "micropipette interfacial area-expansion method" was introduced and validated as a new DST measurement having a high enough sensitivity to detect diffusion controlled molecular adsorption at the air-water interfaces. To validate the new technique, the diffusion coefficient of 1-Octanol in water was investigated with existing models: the Ward Tordai model for the long time adsorption regime (1-100s), and the Langmuir and Frumkin adsorption isotherm models for surface excess concentration. We found that the measured diffusion coefficient of 1-Octanol, 7.2±0.8×10 -6 cm 2 /s, showed excellent agreement with the result from an alternative method, "single microdroplet catching method", to measure the diffusion coefficient from diffusion-controlled microdroplet dissolution, 7.3±0.1×10 -6 cm 2 /s. These new techniques for determining adsorption and diffusion coefficients can apply for a range of surface active molecules, especially the less-characterized ionic surfactants, and biological compounds such as lipids, peptides, and proteins. Copyright © 2016 Elsevier Inc. All rights reserved.

A model of partial differential equations for HIV propagation in lymph nodes

NASA Astrophysics Data System (ADS)

Marinho, E. B. S.; Bacelar, F. S.; Andrade, R. F. S.

2012-01-01

A system of partial differential equations is used to model the dissemination of the Human Immunodeficiency Virus (HIV) in CD4+T cells within lymph nodes. Besides diffusion terms, the model also includes a time-delay dependence to describe the time lag required by the immunologic system to provide defenses to new virus strains. The resulting dynamics strongly depends on the properties of the invariant sets of the model, consisting of three fixed points related to the time independent and spatial homogeneous tissue configurations in healthy and infected states. A region in the parameter space is considered, for which the time dependence of the space averaged model variables follows the clinical pattern reported for infected patients: a short scale primary infection, followed by a long latency period of almost complete recovery and third phase characterized by damped oscillations around a value with large HIV counting. Depending on the value of the diffusion coefficient, the latency time increases with respect to that one obtained for the space homogeneous version of the model. It is found that same initial conditions lead to quite different spatial patterns, which depend strongly on the latency interval.

Scalable domain decomposition solvers for stochastic PDEs in high performance computing

DOE PAGES

Desai, Ajit; Khalil, Mohammad; Pettit, Chris; ...

2017-09-21

Stochastic spectral finite element models of practical engineering systems may involve solutions of linear systems or linearized systems for non-linear problems with billions of unknowns. For stochastic modeling, it is therefore essential to design robust, parallel and scalable algorithms that can efficiently utilize high-performance computing to tackle such large-scale systems. Domain decomposition based iterative solvers can handle such systems. And though these algorithms exhibit excellent scalabilities, significant algorithmic and implementational challenges exist to extend them to solve extreme-scale stochastic systems using emerging computing platforms. Intrusive polynomial chaos expansion based domain decomposition algorithms are extended here to concurrently handle high resolutionmore » in both spatial and stochastic domains using an in-house implementation. Sparse iterative solvers with efficient preconditioners are employed to solve the resulting global and subdomain level local systems through multi-level iterative solvers. We also use parallel sparse matrix–vector operations to reduce the floating-point operations and memory requirements. Numerical and parallel scalabilities of these algorithms are presented for the diffusion equation having spatially varying diffusion coefficient modeled by a non-Gaussian stochastic process. Scalability of the solvers with respect to the number of random variables is also investigated.« less

Scalable domain decomposition solvers for stochastic PDEs in high performance computing

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

Desai, Ajit; Khalil, Mohammad; Pettit, Chris

Stochastic spectral finite element models of practical engineering systems may involve solutions of linear systems or linearized systems for non-linear problems with billions of unknowns. For stochastic modeling, it is therefore essential to design robust, parallel and scalable algorithms that can efficiently utilize high-performance computing to tackle such large-scale systems. Domain decomposition based iterative solvers can handle such systems. And though these algorithms exhibit excellent scalabilities, significant algorithmic and implementational challenges exist to extend them to solve extreme-scale stochastic systems using emerging computing platforms. Intrusive polynomial chaos expansion based domain decomposition algorithms are extended here to concurrently handle high resolutionmore » in both spatial and stochastic domains using an in-house implementation. Sparse iterative solvers with efficient preconditioners are employed to solve the resulting global and subdomain level local systems through multi-level iterative solvers. We also use parallel sparse matrix–vector operations to reduce the floating-point operations and memory requirements. Numerical and parallel scalabilities of these algorithms are presented for the diffusion equation having spatially varying diffusion coefficient modeled by a non-Gaussian stochastic process. Scalability of the solvers with respect to the number of random variables is also investigated.« less

Anomalous diffusion and scaling in coupled stochastic processes

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

Bel, Golan; Nemenman, Ilya

2009-01-01

Inspired by problems in biochemical kinetics, we study statistical properties of an overdamped Langevin processes with the friction coefficient depending on the state of a similar, unobserved, process. Integrating out the latter, we derive the Pocker-Planck the friction coefficient of the first depends on the state of the second. Integrating out the latter, we derive the Focker-Planck equation for the probability distribution of the former. This has the fonn of diffusion equation with time-dependent diffusion coefficient, resulting in an anomalous diffusion. The diffusion exponent can not be predicted using a simple scaling argument, and anomalous scaling appears as well. Themore » diffusion exponent of the Weiss-Havlin comb model is derived as a special case, and the same exponent holds even for weakly coupled processes. We compare our theoretical predictions with numerical simulations and find an excellent agreement. The findings caution against treating biochemical systems with unobserved dynamical degrees of freedom by means of standandard, diffusive Langevin descritpion.« less

Influence of structure properties on protein-protein interactions-QSAR modeling of changes in diffusion coefficients.

PubMed

Bauer, Katharina Christin; Hämmerling, Frank; Kittelmann, Jörg; Dürr, Cathrin; Görlich, Fabian; Hubbuch, Jürgen

2017-04-01

Information about protein-protein interactions provides valuable knowledge about the phase behavior of protein solutions during the biopharmaceutical production process. Up to date it is possible to capture their overall impact by an experimentally determined potential of mean force. For the description of this potential, the second virial coefficient B22, the diffusion interaction parameter kD, the storage modulus G', or the diffusion coefficient D is applied. In silico methods do not only have the potential to predict these parameters, but also to provide deeper understanding of the molecular origin of the protein-protein interactions by correlating the data to the protein's three-dimensional structure. This methodology furthermore allows a lower sample consumption and less experimental effort. Of all in silico methods, QSAR modeling, which correlates the properties of the molecule's structure with the experimental behavior, seems to be particularly suitable for this purpose. To verify this, the study reported here dealt with the determination of a QSAR model for the diffusion coefficient of proteins. This model consisted of diffusion coefficients for six different model proteins at various pH values and NaCl concentrations. The generated QSAR model showed a good correlation between experimental and predicted data with a coefficient of determination R2 = 0.9 and a good predictability for an external test set with R2 = 0.91. The information about the properties affecting protein-protein interactions present in solution was in agreement with experiment and theory. Furthermore, the model was able to give a more detailed picture of the protein properties influencing the diffusion coefficient and the acting protein-protein interactions. Biotechnol. Bioeng. 2017;114: 821-831. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Multiple-scattering coefficients and absorption controlled diffusive processes

NASA Astrophysics Data System (ADS)

Godoy, Salvador; García-Colín, L. S.; Micenmacher, Victor

1999-11-01

Multiple-scattering transmission and reflection coefficients (T,R) are introduced in addition to the diffusion coefficient D for the description of ballistic diffusion in the presence of absorption. For 1D (one-dimensional) systems, the measurement of only one between T and D imposes restrictions on the possible values of the other. If D is measured, then T is bounded between the Landauer and Lambert-Beer equations. Measurements of both (T,D) imply the theoretical knowledge of the microscopic absorption Σa and scattering rΣs cross sections.